http://micro.stanford.edu/mediawiki/api.php?action=feedcontributions&feedformat=atom&user=JieyinMicro and Nano Mechanics Group - User contributions [en]2026-07-05T19:02:05ZUser contributionsMediaWiki 1.39.7http://micro.stanford.edu/mediawiki/index.php?title=M02_Making_a_Perfect_Crystal&diff=5055M02 Making a Perfect Crystal2011-01-14T22:49:57Z<p>Jieyin: /* Body-centered-cubic crystal */</p>
<hr />
<div><H1 ALIGN="CENTER"><FONT SIZE="-1">Manual 02 for MD++ </FONT> <br />
<BR><br />
Making a Perfect Crystal</H1><br />
<DIV><br />
<br />
<P ALIGN="CENTER"><STRONG>Keonwook Kang and Wei Cai</STRONG></P><br />
</DIV><br />
<P ALIGN="CENTER">[[ Nov 25 ]], [[2007]]</P><br />
<P><br />
<BR><HR><br />
<!--Table of Child-Links--><br />
<br />
Many solid materials have a periodic crystal structure.<ref>Glass is a counter-example, which is noncrystalline. We call it an amorphous material. Sometimes people consider it as supercooled liquid instead of a true solid, because, like a liquid, glass can flow under shear stress, although at very slow rate.</ref> <br />
For example, copper and aluminum have the face-centered-cubic (FCC) structure, while molybdenum and tungsten have the body-centered-cubic (BCC) structure under ambient conditions. The periodic arrangement of atoms simplifies the process of setting up<br />
an atomistic simulation, because we can use a periodic array of atoms as the<br />
initial condition. Thus, building up a crystal structure is often the first step in<br />
the atomistic simulation of solids. In this manual, we will learn how to build several<br />
crystal structures in MD++ with the example scripts.<br />
<BR><HR><br />
<br />
== Face-centered-cubic crystal ==<br />
First, let's make a perfect FCC aluminum crystal. The script file '''al.script''',<br />
together with other script files discussed in this manual, can be found in the<br />
directory '''MD++/scripts/ME346'''. To run this script file, type<br />
<br />
$ cd ~/Codes/MD++<br />
$ bin/md_gpp scripts/ME346/al.script<br />
<br />
The executable file, '''md_gpp''' does not contain any potential model, but can be<br />
used to visualize the atomic structure, as mentioned in the [[M01 Introduction to MD++|Manual 01]].<ref>You can compile the executable '''alglue_gpp''', which is a glue potential model for<br />
aluminum by typing <br />
$ make alglue build=R.</ref> <br />
Here is the content of the '''al.script''' file.<br />
<br />
<pre><br />
# -*-shell-script-*-<br />
setnolog<br />
setoverwrite<br />
dirname = runs/al-example # To specify run directory<br />
<br />
#--------------------------------------------<br />
# Create Perfect Lattice Configuration<br />
crystalstructure = face-centered-cubic<br />
latticeconst = 4.05 # lattice constant for Al (unit: Angstrom)<br />
latticesize = [ 1 0 0 1 # c1 = 1*[1 0 0] periodicity vec. in x<br />
0 1 0 1 # c2 = 1*[0 1 0] periodicity vec. in y<br />
0 0 1 1] # c3 = 1*[0 0 1] periodicity vec. in z<br />
makecrystal<br />
<br />
#-------------------------------------------------------------<br />
# Plot Configuration<br />
atomradius = 1.0 bondradius = 0.3 bondlength = 0<br />
atomcolor = blue highlightcolor = purple backgroundcolor = gray<br />
bondcolor = red fixatomcolor = yellow<br />
plotfreq = 10 win_width = 600 win_height = 600<br />
rotateangles = [ 0 0 0 1.0 ]<br />
openwin alloccolors rotate saverot eval plot<br />
sleep quit<br />
</pre><br />
<br />
<gallery caption="Fig.1 Visualization of FCC structure" widths="200px" heights="200px" perrow="3"><br />
Image:fcc.jpg|(a) Conventional image of FCC unit cell<br />
Image:al1X1X1.jpg|(b) FCC unit cell in MD++. One corner atom and three face-centered atoms per cell<br />
Image:al3X3X3.jpg|(c) FCC of 3X3X3 cells<br />
</gallery><br />
<br />
FCC, as well as HCP (Hexagonal Close Packed), is a close-packed crystal structure. In Fig.1(a), you can see the conventional image of FCC unit cell structure, where there is an atom at every corner and every face center of the cube. Since each corner atom is shared by 8 adjacent cubes and each face-centered atom is shared by 2 cubes, the total number of atoms per unit cell will be <math>8 \times 1/8 + 6 \times 1/2 = 4</math>. In MD++, four atoms will be plotted per unti cell as shown in Fig.1(b), which is exactly what you see when you run '''al.script'''. Now imagine that the unit cell is replicated periodically in all 3 directions to fill the entire space. This would create an infinitely large crystal. We can create a larger crystal by modifying the '''latticesize''' variable, ''e.g.''<br />
<br />
latticesize = [ 1 0 0 3<br />
0 1 0 3<br />
0 0 1 3]<br />
<br />
This creates a crystal with <math>3 \times 3 \times 3 = 27</math> unit cells as shown in the Fig.1(c). The '''plot''' section of this script file will be explained in Manual 06.<br />
<br />
''Ex. 1'' Make a perfect crystal of copper (Cu) of 4 X 4 X 4 unit<br />
cells. Cu has an FCC crystal structure and its equilibrium lattice constant<br />
is <math>a = </math>3.6030 &Aring;. You can use '''md_gpp''' as the executable file<ref>For MD simulations of Cu or Al, the fourth column of latticesize should not be smaller than 4 due to the relatively large cut-off radius in their potential models ('''eam''' or '''alglue''').</ref> if you only want to visualize the structure. Use '''eam_gpp''' if you would like to do some computation using the potential model. (For example, the '''eval''' command computes the total potential energy of the structure.) For the latter case, you need to insert the following two lines into your script file after '''dirname'''.<br />
<br />
potfile = ~/Codes/MD++/potentials/EAMDATA/eamdata.Cu<br />
eamgrid = 5000 readeam<br />
<br />
This reads the data needed by the EAM potential model of Cu.<br />
<br />
''Ex. 2'' Make a perfect crystal of argon (Ar) of 4 X 4 X 4 unit cells.<br />
Ar is inert gas at room temperature but its solid state is face-centered-cubic crystal below its melting temperature <math>T_m = </math>83.81K. Ar can be simulated<br />
by the Leonard-Jones potential model or the executable '''lj_gpp'''. Modify '''scripts/ME346/ar.script''' and run it by typing<br />
<br />
$ bin/lj_gpp scripts/ME346/ar.script<br />
<br />
----<br />
<br />
== Body-centered-cubic crystal ==<br />
The BCC structure has an atom at every corner and body-center of each cube<br />
(unit cell), as shown in Fig.2(a). Molybdenum (Mo) is one example of BCC materials.<br />
Run '''mo.script''' file by typing<br />
<br />
$ bin/fs_gpp scripts/ME346/mo.script<br />
<br />
Here is the content of the '''mo.script''' file.<br />
<pre><br />
# -*-shell-script-*-<br />
setnolog<br />
setoverwrite<br />
dirname = runs/mo-example<br />
<br />
#--------------------------------------------<br />
# Read the potential file<br />
potfile = ~/Codes/MD++/potentials/mo_pot readpot<br />
<br />
#--------------------------------------------<br />
# Create Perfect Lattice Configuration<br />
crystalstructure = body-centered-cubic<br />
latticeconst = 3.1472 # in Angstrom for Mo<br />
latticesize = [ 1 0 0 3<br />
0 1 0 3<br />
0 0 1 3 ]<br />
makecrystal finalcnfile = perf.cn writecn<br />
<br />
#---------------------------------------------<br />
# Plot Configuration<br />
atomradius = 1.0 bondradius = 0.3 bondlength = 0<br />
atomcolor = orange highlightcolor = purple backgroundcolor = gray<br />
bondcolor = red fixatomcolor = yellow<br />
plotfreq = 10 win_width = 600 win_height = 600<br />
rotateangles = [ 0 0 0 1 ]<br />
openwin alloccolors rotate saverot eval plot<br />
sleep quit<br />
</pre><br />
<br />
<gallery caption="Fig.2 Visualization of BCC structure" widths="200px" heights="200px" perrow="3"><br />
Image:Bcc.jpg|(a) Conventional image of BCC unit cell<br />
Image:mo1X1X1.jpg|(b) BCC unit cell in MD++. One corner atom and one body-centered atom per cell<br />
Image:mo3X3X3.jpg|(c) BCC of 3X3X3 cells<br />
</gallery><br />
<br />
In the Fig.2(c), the simulation box (''i.e.'' supercell) is defined by three periodicity<br />
vectors, <math>\mathbf{c}_1</math>, <math>\mathbf{c}_2</math> and <math>\mathbf{c}_3</math>:<br />
<math>\mathbf{c}_1 = 3[100], \mathbf{c}_2 = 3[010], \mathbf{c}_3 = 3[001]. </math><br />
The command '''makecrystal''' generates the perfect crystal of molybdenum based<br />
on the given variables, '''crystalstructure'''<ref>Other possible values for crystalstructure are “simple-cubic”, “face-centered-cubic”,“L1_2”, “L1_0”, “diamond-cubic”, “zinc-blende”, etc. For a complete list, please read<br />
'''src/lattice.h'''.</ref> , '''latticeconst''', and '''latticesize'''. <br />
The configuration will be saved as '''perf.cn''' in the directory of '''runs/mo-example''' by the command '''writecn'''. The configuration file contains the number of atoms and the position of all the atoms in terms of scaled coordinates followed by a 3 X 3 matrix, <math>\mathbf{H}</math>, whose columns are the three periodicity vectors, <math>\mathbf{c}_1</math>, <math>\mathbf{c}_2</math> and <math>\mathbf{c}_3</math>. The real coordinates of an atom, <math>\mathbf{r} = (x, y, z)^T</math> is related to the scaled coordinates <math>\mathbf{s} = (s_x, s_y, s_z)^T</math> through matrix multiplication<br />
<br />
{|border="0" align="center"<br />
|<math> \mathbf{r} = a\mathbf{H}\cdot \mathbf{s} </math>.<br />
|}<br />
<br />
where <math>a</math> is the lattice constant.<br />
<br />
''Ex. 3'' Make a perfect crystal of tantalum (Ta) with repeat vectors <math>\mathbf{c}_1 = 3[1 1 0], \mathbf{c}_2 = 3[1 \bar{1} 0], \mathbf{c}_3 = 4[0 0 1]</math>. <br />
Ta has a BCC lattice structure with an equilibrium lattice constant <math>a =</math> 3.3058 &Aring;. <br />
Read the FS potential file for Ta by inserting the following line in the script.<br />
<br />
potfile = ~/Codes/MD++/potentials/ta_pot readpot<br />
<BR><HR><br />
<br />
== Diamond-cubic crystal ==<br />
Silicon (Si) has diamond-cubic structure, which can be regarded as two FCC structures offset by [1 1 1]/4. You can run the example script '''si.script''' by typing<br />
<br />
$ bin/sw_gpp scripts/ME346/si.script<br />
<br />
where the executable '''sw_gpp''' contains the SW potential model for Si. The<br />
visualization window will look like Fig.3(b). Here is the content of the '''si.script''' file.<br />
<pre><br />
# -*-shell-script-*-<br />
setnolog<br />
setoverwrite<br />
dirname = runs/si-example<br />
<br />
#------------------------------------------------------------<br />
#Create Perfect Lattice Configuration<br />
#<br />
crystalstructure = diamond-cubic<br />
latticeconst = 5.43095 # (in Angstrom) for Si<br />
latticesize = [ 1 0 0 2<br />
0 1 0 2<br />
0 0 1 2 ]<br />
makecrystal writecn<br />
<br />
#------------------------------------------------------------<br />
#Plot Configuration<br />
#<br />
atomradius = 0.67 bondradius = 0.3 bondlength = 2.8285 <br />
atomcolor = orange highlightcolor = purple<br />
bondcolor = red backgroundcolor = gray70<br />
plotfreq = 10 rotateangles = [ 0 0 0 1.25 ]<br />
openwin alloccolors rotate saverot eval plot<br />
sleep quit<br />
</pre><br />
<br />
<gallery caption="Fig.3 Visualization of DC structure" widths="200px" heights="200px" perrow="2"><br />
Image:Dc_unitcell.jpg|(a) DC unit cell in MD++. 8 atoms per cell<br />
Image:Dc_2x2x2cell.jpg|(c) DC of 2X2X2 cells<br />
</gallery><br />
<br />
== Zinc Sulphide (ZnS) ==<br />
ZnS is a two component material and has two lattice structures (zinc-blende and Wurtzite). Through the following example script, we will learn how to use MD++ to generate multi-component material in zinc-blende strucutre or Wurtzite structure.<br />
<br />
$ bin/md_gpp scripts/Examples/example06a-ZnS.script<br />
<br />
Here is the content of the '''example06a-ZnS.script''' file, which will creat a Zinc-blende structure of ZnS.<br />
<pre><br />
# -*-shell-script-*-<br />
# Zincblende structure of ZnS<br />
setnolog<br />
setoverwrite<br />
dirname = runs/ZnS-example<br />
#------------------------------------------------------------<br />
#Create Perfect Lattice Configuration<br />
#<br />
latticestructure = zinc-blende<br />
element0 = Zn element1 = S atommass = [65.409 32.065] # g/mol<br />
latticeconst = 5.42 #(A) <br />
latticesize = [ 1 0 0 2 #(x)<br />
0 1 0 2 #(y)<br />
0 0 1 2 ] #(z)<br />
makecrystal finalcnfile = perf.cn writecn<br />
#------------------------------------------------------------<br />
#Plot Configuration<br />
#<br />
atomradius = [1.3 1] #bondradius = 0.3 bondlength = 2.8285<br />
atomcolor0 = "light grey" atomcolor1 = yellow<br />
highlightcolor = purple bondcolor = red backgroundcolor = gray<br />
fixatomcolor = yellow<br />
plot_atom_info = 1<br />
plotfreq = 10<br />
rotateangles = [ 0 0 0 1.2 ]<br />
openwin alloccolors rotate saverot refreshnnlist eval plot<br />
sleep quit<br />
</pre><br />
Similarly, you can create a Wurtzite structure by the following script, '''example06b-ZnS.script'''.<br />
<pre><br />
# -*-shell-script-*-<br />
# Wurtzite structure of ZnS<br />
# (screw dislocation motion under fixed boundary)<br />
setnolog<br />
setoverwrite<br />
dirname = runs/ZnS-example<br />
#------------------------------------------------------------<br />
#Create Perfect Lattice Configuration<br />
#<br />
latticestructure = wurtzite<br />
element0 = Zn element1 = S atommass = [65.409 32.065] # g/mol<br />
latticeconst = [3.82 0 6.24] #(in Angstrom)<br />
latticesize = [ 1 0 0 2 #(x)<br />
0 1 0 2 #(y)<br />
0 0 1 2 ] #(z)<br />
makecrystal finalcnfile = perf.cn writecn<br />
#------------------------------------------------------------<br />
#Plot Configuration<br />
#<br />
atomradius = [0.8 1] bondradius = 0.3 bondlength = 3.25<br />
atomcolor0 = "light grey" atomcolor1 = yellow<br />
highlightcolor = purple bondcolor = red backgroundcolor = gray<br />
fixatomcolor = yellow<br />
plot_atom_info = 1<br />
plotfreq = 10<br />
rotateangles = [ 0 0 0 1.2 ]<br />
openwin alloccolors rotate saverot refreshnnlist eval plot<br />
sleep quit<br />
</pre><br />
<gallery caption="Fig.4 ZnS structure" widths="200px" heights="200px" perrow="2"><br />
Image:ZnS_zincblende.gif|(a) Zinc-blende structure of ZnS<br />
Image:ZnS_wurtzite.gif|(c) Wurtzite structure of ZnS<br />
</gallery><br />
<br />
== Notes ==<br />
<br />
<references/></div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5046ParaDiS Manual Updated2011-01-13T02:16:10Z<p>Jieyin: /* How to set up data-file */</p>
<hr />
<div>Written by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. <br />
<br />
While reading this document, don't forget to check out [[paradis.stanford.edu]] for a complete and searchable table of parameters in ParaDiS code (some parameter names are not up-to-date). Detailed descriptions can be found in the official documentation ParaDiSInfo.txt.<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following structures exist<br />
<pre><br />
dataFileVersion = 4<br />
numFileSegments = 1<br />
minCoordinates = [<br />
-4.000000e+003<br />
-4.000000e+003<br />
-4.000000e+003<br />
]<br />
maxCoordinates = [<br />
4.000000e+003<br />
4.000000e+003<br />
4.000000e+003<br />
]<br />
nodeCount = 192<br />
dataDecompType = 1<br />
dataDecompGeometry = [<br />
1<br />
1<br />
1<br />
]<br />
domainDecomposition =<br />
-4.000000e+003<br />
-4.000000e+003<br />
-4.000000e+003<br />
4.000000e+003<br />
4.000000e+003<br />
4.000000e+003<br />
<br />
#<br />
# Primary lines: node_tag, x, y, z, num_arms, constraint<br />
# Secondary lines: arm_tag, burgx, burgy, burgz, nx, ny, nz<br />
#<br />
# length in unit of burgMag<br />
<br />
nodalData =<br />
0,0 3.52197261266669e+003 -2.10366848600532e+003 8.35974608889734e+002 2 7<br />
0,1 -0.707107 0.707107 0 1 1 1<br />
0,15 0.707107 -0.707107 0 -0.408248 -0.408248 0.816497<br />
...<br />
</pre><br />
<br />
You need to set your own data file parameters, usually including minCoordinates, maxCoordinates, nodeCount, domainDecomposition and nodalData. The nodalData is a long array of data. You may want to create it from '''Matlab''' if there exists too many nodes in your simulation box.<br />
<br />
===How to set up ctrl-file===<br />
<br />
The structure of the ctrl file is explained by parts. <br />
<br />
1 First is the basic setup information for the simulation,<br />
<br />
<pre><br />
#Directory to write output files<br />
dirname = "outputs/filename"<br />
<br />
#Input files for PBC image stresses<br />
Rijmfile = "inputs/Rijm.cube.out"<br />
RijmPBCfile = "inputs/RijmPBC.cube.out"<br />
<br />
#Total simulation steps<br />
maxstep = 100<br />
<br />
#The total number of CPUs should be numXdoms * numYdoms * numZdoms<br />
numXdoms = 1<br />
numYdoms = 1<br />
numZdoms = 1<br />
<br />
#Cells for dislocation grouping (cannot be less than 3)<br />
numXcells = 3<br />
numYcells = 3<br />
numZcells = 3<br />
<br />
#Fast multipole method specs.<br />
fmEnabled = 0 #disable fast multipole<br />
fmMPOrder = 2<br />
fmTaylorOrder = 4<br />
fmCorrectionTbl = "Inputs/fm-ctab.m2.t4.dat"<br />
</pre><br />
<br />
You can set the directory name where you want to store the output. You can also set the total number of simulation steps <tt>maxstep</tt>. As for numXdoms, numYdoms and numZdoms, note that the product should be the total number of CPUs. This setting is crucial for parallel jobs. When all of them as set as 2, the total number of CUPs is 8. This should be consistant with the pbs file setting, which will be discussed in the end of this manual. If you want to enable fast multipole method (FMM), you need to set <tt>fmEnabled = 1</tt> and assign the path for the corresponding table.<br />
<br />
2 Next is some settings on geometry, material parameters etc<br />
<br />
<pre><br />
<br />
timestepIntegrator = "trapezoid"<br />
<br />
#Boundary conditions<br />
xBoundType = 0<br />
yBoundType = 0<br />
zBoundType = 0<br />
<br />
#Fundamental length unit<br />
burgMag = 2.556120e-010<br />
<br />
#Elastic constants<br />
shearModulus = 40000000000.000000<br />
pois = 0.369000<br />
<br />
#Mobility law function<br />
mobilityLaw = "FCC_0"<br />
enforceGlidePlanes = 1<br />
enableCrossSlip = -1<br />
MobScrew = 1.000000e+005<br />
MobEdge = 1.000000e+005<br />
MobClimb = 1.000000e-002<br />
<br />
#Discretization<br />
maxSeg = 200.000000<br />
minSeg = 10.000000<br />
<br />
#Maximum nodal displacement at each time step<br />
rmax = 100<br />
<br />
#Error tolerance in determining time step<br />
rTol = 0.721688<br />
<br />
#Maximum time step<br />
maxDT = 1<br />
<br />
#Core cut-off radius<br />
rc = 2.886751<br />
<br />
#Core energy<br />
Ecore = 0.000000e+000<br />
<br />
#Turn on elastic interaction<br />
elasticinteraction = 1<br />
</pre><br />
<br />
Variable <tt>xBoundType</tt> defines the type of problem space boundaries in the X dimension. Valid values are 0, 1 and 2 respectively for periodic, free surface, and reflecting.<br />
<br />
The value of <tt>burgMag</tt> is the unit of length for all length variables in ParaDiS simulation, such as nodal positions and Burgers vectors (in data file, those data should be expressed in terms of the same <tt>burgMag</tt>)<br />
<br />
The setting for mobility law is important, which should be consistent with the system you simulate. Cross-slip is enabled only when <tt>enableCrossSlip = 1</tt>. You need to adjust some of the geometric parameters to fit your problem.<br />
<br />
3 Third is the loading conditions<br />
<br />
<pre><br />
#Applied stress in Pa (xx,yy,zz,yz,zx,xy)<br />
appliedStress = [ 0 0 0 0 0 0 ]<br />
<br />
#Constant Strain rate<br />
loadType = 1<br />
edotdir = [ 0.0 0.0 1.0 ]<br />
eRate = 100.0<br />
</pre><br />
<br />
<tt>loadType</tt> defines the type of load on the system. Usually we set it as 0 (creep, i.e. constant external stress) or 1 (constant strain rate). For detailed explanations for value 2, 3 and 4, please refer to the variable table. When <tt>loadType = 0</tt>, you need to set <tt>appliedStress</tt>(zero vector for relaxation). When <tt>loadType = 1</tt>, you need to define strain rate direction <tt>edotdir</tt> and strain rate <tt>eRate</tt>.<br />
<br />
4 And the last part is settings on saving,<br />
<br />
<pre><br />
#Save files<br />
savecn = 1<br />
savecnfreq = 100<br />
<br />
#Save Properties<br />
saveprop = 1<br />
savepropfreq = 1<br />
#winDefaultsFile = "inputs/paradis.xdefaults"<br />
</pre><br />
<br />
By setting <tt>savencn = 1</tt>, saving is enabled at a frequency of <tt>savecnfreq</tt>. Lines relevant to saving properties and visulization are discussed in later part of this manual.<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
Gnuplot is a useful plotting software. You can plot the obtained properties data with gnupot, for example, stress vs strain curve. Before using gnuplot, make sure it is installed on your cluster. You also need to enable X server (test by typing <tt>xclock</tt>). By typing <tt>gnuplot</tt>, you can start using following command lines. For a given (X,Y) data pair, the gnuplot command is<br />
<pre><br />
gnuplot> plot "filename" using 1:2 with lines<br />
</pre><br />
where "using 1:2" means plotting using the 1st and 2nd column from the given data file. "with lines" is a style option, you can change to "with points", "with steps", "with dots" or "with impulses". Click [http://t16web.lanl.gov/Kawano/gnuplot/intro/style-e.html] for a detailed description of the styles.<br />
To draw multiple lines, you can type<br />
<pre><br />
gnuplot> plot "A" using 1:2 title "data A" with lines, \<br />
"B" u 1:2 t "data B" with p, \<br />
"C" u 2:3 t "data C" w d<br />
</pre><br />
You can use \ to separate continuous lines. <tt>title</tt> is used to label different lines. You can abbreviate some of the commands, for example, u for using, t for title, w for with, l for lines, p for points and d for dots.<br />
<br />
To change the labels of X and Y axes, you can use<br />
<pre><br />
gnuplot> set xlabel "x-axis"<br />
gnuplot> set ylabel "y-xais"<br />
gnuplot> set title "y vs x"<br />
gnuplot> replot<br />
</pre><br />
<br />
You can also change the ranges of X and Y axes,<br />
<pre><br />
gnuplot> set xrange [0:2]<br />
gnuplot> set yrange [0:1]<br />
gnuplot> replot<br />
</pre><br />
<br />
To assign the color of the line(line type), you need to add corresponding number after "l". For example, black solid(-1), black dot(0), red(1), green (2), blue(3), margenta(4), cyan(5) and yellow(6). To modify the width of the line at the same time, you can use option "w l lt 2 lw 4", for instance, where lt means linetype and lw means linewidth.<br />
<br />
==How to visualize the results==<br />
To visualize the simulation results, here are two methods. One is to run simulation interactively one one CPU and perform observation. The other is to record the configuration at certain simulation steps and make movies from them.<br />
===xwindow===<br />
Make sure x11 server is enabled for the session(test by "xclock"; using <tt>ssh -X username@domain</tt> when you log into clusters) and the ParaDiS code is compiled for single CPU("MODE = SERIAL, XLIB_MODE = ON" in makefile.setup). Check the following setting in <tt>/inputs/paradis.xdefaults</tt> if you set it as "winDefaultsFile" in your ctrl file.<br />
<pre><br />
enable_window = 1 <br />
</pre><br />
By executing<br />
<pre><br />
bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl<br />
</pre><br />
You should be able to see the xwindow. By setting "maxstep = 0" in the ctrl file, you can obtain the configuration (snapshot) for any given simulation step. When the simulation step is large, you might want to consider the other method.<br />
<br />
===Atomeye===<br />
Atomeye is a powerful visualization tool. To enable Atomeye, you need to add following lines in the ctrl file<br />
<pre><br />
atomeye = 1<br />
atomeyefreq = 1<br />
atomeyesegradius = 5<br />
</pre><br />
To view atomeye files, you can use command<br />
<pre><br />
$ tools/atomeye/A.i686 outputs/filename/atomeye/paradis0001.cfg<br />
</pre><br />
To create jpg files press y to convert all cfg files in the same directory. <br />
<br />
To convert these jpg files to a movie, the command is<br />
<pre><br />
$ convert -delay 4 -quality 95 *.jpg mymovie.mpg<br />
</pre><br />
where -delay and -quality flags are optional; if -delay > 4, extra frames are added to make the movie run more slowly; default quality is 75 and the maximum is 100. Note that encode packages need to be preinstalled for the machine or cluster.<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
In a typical pbs file, we have following lines as header:<br />
<br />
<pre><br />
#!/bin/bash<br />
#PBS -N jobname<br />
#PBS -j oe<br />
#PBS -l nodes=8:ppn=8,walltime=24:00:00<br />
#PBS -V<br />
<br />
### ---------------------------------------<br />
### BEGINNING OF EXECUTION<br />
### ---------------------------------------<br />
<br />
echo The master node of this job is `hostname`<br />
echo The working directory is `echo $PBS_O_WORKDIR`<br />
echo This job runs on the following nodes:<br />
echo `cat $PBS_NODEFILE`<br />
<br />
ncpu=`cat $PBS_NODEFILE | wc -w`<br />
echo "Number of processors = $ncpu "<br />
### end of information preamble<br />
<br />
cd $PBS_O_WORKDIR<br />
<br />
echo $PWD<br />
<br />
#cmd="mpiexec -np $ncpu bin/meam-lammps_mpich scripts/work/si_ge/si-meam-lammps.tcl"<br />
#time $cmd<br />
</pre><br />
<br />
You need to set the job name, wait time, number of nodes and ppn (number of processors per node, for example, ppn = 8 for wcr clusters)<br />
<br />
To submit jobs using a single processor, you need to add the following line<br />
<pre><br />
#bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl &> serial.out<br />
</pre><br />
where log file is <tt>serial.out</tt>.<br />
<br />
For parallel jobs, add<br />
<pre><br />
#mpiexec -np $ncpu bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl &> parallel.out<br />
</pre><br />
where log file is <tt>parallel.out</tt>.<br />
<br />
===What if the job is stopped===<br />
You can continue from the stored files under directory <tt>outputs/filename/restart</tt> by<br />
<pre><br />
$bin/paradis outputs/filename/restart/restart.cn<br />
</pre></div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5045ParaDiS Manual Updated2011-01-13T02:15:50Z<p>Jieyin: </p>
<hr />
<div>Written by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. <br />
<br />
While reading this document, don't forget to check out [[paradis.stanford.edu]] for a complete and searchable table of parameters in ParaDiS code (some parameter names are not up-to-date). Detailed descriptions can be found in the official documentation ParaDiSInfo.txt.<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following structures exist<br />
<pre><br />
dataFileVersion = 4<br />
numFileSegments = 1<br />
minCoordinates = [<br />
-4.000000e+003<br />
-4.000000e+003<br />
-4.000000e+003<br />
]<br />
maxCoordinates = [<br />
4.000000e+003<br />
4.000000e+003<br />
4.000000e+003<br />
]<br />
nodeCount = 192<br />
dataDecompType = 1<br />
dataDecompGeometry = [<br />
1<br />
1<br />
1<br />
]<br />
domainDecomposition =<br />
-4.000000e+003<br />
-4.000000e+003<br />
-4.000000e+003<br />
4.000000e+003<br />
4.000000e+003<br />
4.000000e+003<br />
<br />
#<br />
# Primary lines: node_tag, x, y, z, num_arms, constraint<br />
# Secondary lines: arm_tag, burgx, burgy, burgz, nx, ny, nz<br />
#<br />
# length in unit of burgMag<br />
<br />
nodalData =<br />
0,0 3.52197261266669e+003 -2.10366848600532e+003 8.35974608889734e+002 2 7<br />
0,1 -0.707107 0.707107 0 1 1 1<br />
0,15 0.707107 -0.707107 0 -0.408248 -0.408248 0.816497<br />
...<br />
</pre><br />
<br />
You need to set your own data file parameters, usually including minCoordinates, maxCoordinates, nodeCount, domainDecomposition and nodalData. The nodalData is a long array of data. You may want to create it from Matlab if there exists too many nodes in your simulation box.<br />
<br />
===How to set up ctrl-file===<br />
<br />
The structure of the ctrl file is explained by parts. <br />
<br />
1 First is the basic setup information for the simulation,<br />
<br />
<pre><br />
#Directory to write output files<br />
dirname = "outputs/filename"<br />
<br />
#Input files for PBC image stresses<br />
Rijmfile = "inputs/Rijm.cube.out"<br />
RijmPBCfile = "inputs/RijmPBC.cube.out"<br />
<br />
#Total simulation steps<br />
maxstep = 100<br />
<br />
#The total number of CPUs should be numXdoms * numYdoms * numZdoms<br />
numXdoms = 1<br />
numYdoms = 1<br />
numZdoms = 1<br />
<br />
#Cells for dislocation grouping (cannot be less than 3)<br />
numXcells = 3<br />
numYcells = 3<br />
numZcells = 3<br />
<br />
#Fast multipole method specs.<br />
fmEnabled = 0 #disable fast multipole<br />
fmMPOrder = 2<br />
fmTaylorOrder = 4<br />
fmCorrectionTbl = "Inputs/fm-ctab.m2.t4.dat"<br />
</pre><br />
<br />
You can set the directory name where you want to store the output. You can also set the total number of simulation steps <tt>maxstep</tt>. As for numXdoms, numYdoms and numZdoms, note that the product should be the total number of CPUs. This setting is crucial for parallel jobs. When all of them as set as 2, the total number of CUPs is 8. This should be consistant with the pbs file setting, which will be discussed in the end of this manual. If you want to enable fast multipole method (FMM), you need to set <tt>fmEnabled = 1</tt> and assign the path for the corresponding table.<br />
<br />
2 Next is some settings on geometry, material parameters etc<br />
<br />
<pre><br />
<br />
timestepIntegrator = "trapezoid"<br />
<br />
#Boundary conditions<br />
xBoundType = 0<br />
yBoundType = 0<br />
zBoundType = 0<br />
<br />
#Fundamental length unit<br />
burgMag = 2.556120e-010<br />
<br />
#Elastic constants<br />
shearModulus = 40000000000.000000<br />
pois = 0.369000<br />
<br />
#Mobility law function<br />
mobilityLaw = "FCC_0"<br />
enforceGlidePlanes = 1<br />
enableCrossSlip = -1<br />
MobScrew = 1.000000e+005<br />
MobEdge = 1.000000e+005<br />
MobClimb = 1.000000e-002<br />
<br />
#Discretization<br />
maxSeg = 200.000000<br />
minSeg = 10.000000<br />
<br />
#Maximum nodal displacement at each time step<br />
rmax = 100<br />
<br />
#Error tolerance in determining time step<br />
rTol = 0.721688<br />
<br />
#Maximum time step<br />
maxDT = 1<br />
<br />
#Core cut-off radius<br />
rc = 2.886751<br />
<br />
#Core energy<br />
Ecore = 0.000000e+000<br />
<br />
#Turn on elastic interaction<br />
elasticinteraction = 1<br />
</pre><br />
<br />
Variable <tt>xBoundType</tt> defines the type of problem space boundaries in the X dimension. Valid values are 0, 1 and 2 respectively for periodic, free surface, and reflecting.<br />
<br />
The value of <tt>burgMag</tt> is the unit of length for all length variables in ParaDiS simulation, such as nodal positions and Burgers vectors (in data file, those data should be expressed in terms of the same <tt>burgMag</tt>)<br />
<br />
The setting for mobility law is important, which should be consistent with the system you simulate. Cross-slip is enabled only when <tt>enableCrossSlip = 1</tt>. You need to adjust some of the geometric parameters to fit your problem.<br />
<br />
3 Third is the loading conditions<br />
<br />
<pre><br />
#Applied stress in Pa (xx,yy,zz,yz,zx,xy)<br />
appliedStress = [ 0 0 0 0 0 0 ]<br />
<br />
#Constant Strain rate<br />
loadType = 1<br />
edotdir = [ 0.0 0.0 1.0 ]<br />
eRate = 100.0<br />
</pre><br />
<br />
<tt>loadType</tt> defines the type of load on the system. Usually we set it as 0 (creep, i.e. constant external stress) or 1 (constant strain rate). For detailed explanations for value 2, 3 and 4, please refer to the variable table. When <tt>loadType = 0</tt>, you need to set <tt>appliedStress</tt>(zero vector for relaxation). When <tt>loadType = 1</tt>, you need to define strain rate direction <tt>edotdir</tt> and strain rate <tt>eRate</tt>.<br />
<br />
4 And the last part is settings on saving,<br />
<br />
<pre><br />
#Save files<br />
savecn = 1<br />
savecnfreq = 100<br />
<br />
#Save Properties<br />
saveprop = 1<br />
savepropfreq = 1<br />
#winDefaultsFile = "inputs/paradis.xdefaults"<br />
</pre><br />
<br />
By setting <tt>savencn = 1</tt>, saving is enabled at a frequency of <tt>savecnfreq</tt>. Lines relevant to saving properties and visulization are discussed in later part of this manual.<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
Gnuplot is a useful plotting software. You can plot the obtained properties data with gnupot, for example, stress vs strain curve. Before using gnuplot, make sure it is installed on your cluster. You also need to enable X server (test by typing <tt>xclock</tt>). By typing <tt>gnuplot</tt>, you can start using following command lines. For a given (X,Y) data pair, the gnuplot command is<br />
<pre><br />
gnuplot> plot "filename" using 1:2 with lines<br />
</pre><br />
where "using 1:2" means plotting using the 1st and 2nd column from the given data file. "with lines" is a style option, you can change to "with points", "with steps", "with dots" or "with impulses". Click [http://t16web.lanl.gov/Kawano/gnuplot/intro/style-e.html] for a detailed description of the styles.<br />
To draw multiple lines, you can type<br />
<pre><br />
gnuplot> plot "A" using 1:2 title "data A" with lines, \<br />
"B" u 1:2 t "data B" with p, \<br />
"C" u 2:3 t "data C" w d<br />
</pre><br />
You can use \ to separate continuous lines. <tt>title</tt> is used to label different lines. You can abbreviate some of the commands, for example, u for using, t for title, w for with, l for lines, p for points and d for dots.<br />
<br />
To change the labels of X and Y axes, you can use<br />
<pre><br />
gnuplot> set xlabel "x-axis"<br />
gnuplot> set ylabel "y-xais"<br />
gnuplot> set title "y vs x"<br />
gnuplot> replot<br />
</pre><br />
<br />
You can also change the ranges of X and Y axes,<br />
<pre><br />
gnuplot> set xrange [0:2]<br />
gnuplot> set yrange [0:1]<br />
gnuplot> replot<br />
</pre><br />
<br />
To assign the color of the line(line type), you need to add corresponding number after "l". For example, black solid(-1), black dot(0), red(1), green (2), blue(3), margenta(4), cyan(5) and yellow(6). To modify the width of the line at the same time, you can use option "w l lt 2 lw 4", for instance, where lt means linetype and lw means linewidth.<br />
<br />
==How to visualize the results==<br />
To visualize the simulation results, here are two methods. One is to run simulation interactively one one CPU and perform observation. The other is to record the configuration at certain simulation steps and make movies from them.<br />
===xwindow===<br />
Make sure x11 server is enabled for the session(test by "xclock"; using <tt>ssh -X username@domain</tt> when you log into clusters) and the ParaDiS code is compiled for single CPU("MODE = SERIAL, XLIB_MODE = ON" in makefile.setup). Check the following setting in <tt>/inputs/paradis.xdefaults</tt> if you set it as "winDefaultsFile" in your ctrl file.<br />
<pre><br />
enable_window = 1 <br />
</pre><br />
By executing<br />
<pre><br />
bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl<br />
</pre><br />
You should be able to see the xwindow. By setting "maxstep = 0" in the ctrl file, you can obtain the configuration (snapshot) for any given simulation step. When the simulation step is large, you might want to consider the other method.<br />
<br />
===Atomeye===<br />
Atomeye is a powerful visualization tool. To enable Atomeye, you need to add following lines in the ctrl file<br />
<pre><br />
atomeye = 1<br />
atomeyefreq = 1<br />
atomeyesegradius = 5<br />
</pre><br />
To view atomeye files, you can use command<br />
<pre><br />
$ tools/atomeye/A.i686 outputs/filename/atomeye/paradis0001.cfg<br />
</pre><br />
To create jpg files press y to convert all cfg files in the same directory. <br />
<br />
To convert these jpg files to a movie, the command is<br />
<pre><br />
$ convert -delay 4 -quality 95 *.jpg mymovie.mpg<br />
</pre><br />
where -delay and -quality flags are optional; if -delay > 4, extra frames are added to make the movie run more slowly; default quality is 75 and the maximum is 100. Note that encode packages need to be preinstalled for the machine or cluster.<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
In a typical pbs file, we have following lines as header:<br />
<br />
<pre><br />
#!/bin/bash<br />
#PBS -N jobname<br />
#PBS -j oe<br />
#PBS -l nodes=8:ppn=8,walltime=24:00:00<br />
#PBS -V<br />
<br />
### ---------------------------------------<br />
### BEGINNING OF EXECUTION<br />
### ---------------------------------------<br />
<br />
echo The master node of this job is `hostname`<br />
echo The working directory is `echo $PBS_O_WORKDIR`<br />
echo This job runs on the following nodes:<br />
echo `cat $PBS_NODEFILE`<br />
<br />
ncpu=`cat $PBS_NODEFILE | wc -w`<br />
echo "Number of processors = $ncpu "<br />
### end of information preamble<br />
<br />
cd $PBS_O_WORKDIR<br />
<br />
echo $PWD<br />
<br />
#cmd="mpiexec -np $ncpu bin/meam-lammps_mpich scripts/work/si_ge/si-meam-lammps.tcl"<br />
#time $cmd<br />
</pre><br />
<br />
You need to set the job name, wait time, number of nodes and ppn (number of processors per node, for example, ppn = 8 for wcr clusters)<br />
<br />
To submit jobs using a single processor, you need to add the following line<br />
<pre><br />
#bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl &> serial.out<br />
</pre><br />
where log file is <tt>serial.out</tt>.<br />
<br />
For parallel jobs, add<br />
<pre><br />
#mpiexec -np $ncpu bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl &> parallel.out<br />
</pre><br />
where log file is <tt>parallel.out</tt>.<br />
<br />
===What if the job is stopped===<br />
You can continue from the stored files under directory <tt>outputs/filename/restart</tt> by<br />
<pre><br />
$bin/paradis outputs/filename/restart/restart.cn<br />
</pre></div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5044ParaDiS Manual Updated2011-01-13T02:14:18Z<p>Jieyin: /* How to set up ctrl-file */</p>
<hr />
<div>Written by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. <br />
<br />
While reading this document, don't forget to check out [[paradis.stanford.edu]] for a complete and searchable table of parameters in ParaDiS code (some parameter names are not up-to-date). Detailed descriptions can be found in the official documentation ParaDiSInfo.txt.<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following structures exist<br />
<pre><br />
dataFileVersion = 4<br />
numFileSegments = 1<br />
minCoordinates = [<br />
-4.000000e+003<br />
-4.000000e+003<br />
-4.000000e+003<br />
]<br />
maxCoordinates = [<br />
4.000000e+003<br />
4.000000e+003<br />
4.000000e+003<br />
]<br />
nodeCount = 192<br />
dataDecompType = 1<br />
dataDecompGeometry = [<br />
1<br />
1<br />
1<br />
]<br />
domainDecomposition =<br />
-4.000000e+003<br />
-4.000000e+003<br />
-4.000000e+003<br />
4.000000e+003<br />
4.000000e+003<br />
4.000000e+003<br />
<br />
#<br />
# Primary lines: node_tag, x, y, z, num_arms, constraint<br />
# Secondary lines: arm_tag, burgx, burgy, burgz, nx, ny, nz<br />
#<br />
# length in unit of burgMag<br />
<br />
nodalData =<br />
0,0 3.52197261266669e+003 -2.10366848600532e+003 8.35974608889734e+002 2 7<br />
0,1 -0.707107 0.707107 0 1 1 1<br />
0,15 0.707107 -0.707107 0 -0.408248 -0.408248 0.816497<br />
...<br />
</pre><br />
<br />
You need to set your own data file parameters, usually including minCoordinates, maxCoordinates, nodeCount, domainDecomposition and nodalData. The nodalData is a long array of data. You may want to create it from Matlab if there exists too many nodes in your simulation box.<br />
<br />
===How to set up ctrl-file===<br />
<br />
The structure of the ctrl file is explained by parts. <br />
<br />
1 First is the basic setup information for the simulation,<br />
<br />
<pre><br />
#Directory to write output files<br />
dirname = "outputs/filename"<br />
<br />
#Input files for PBC image stresses<br />
Rijmfile = "inputs/Rijm.cube.out"<br />
RijmPBCfile = "inputs/RijmPBC.cube.out"<br />
<br />
#Total simulation steps<br />
maxstep = 100<br />
<br />
#The total number of CPUs should be numXdoms * numYdoms * numZdoms<br />
numXdoms = 1<br />
numYdoms = 1<br />
numZdoms = 1<br />
<br />
#Cells for dislocation grouping (cannot be less than 3)<br />
numXcells = 3<br />
numYcells = 3<br />
numZcells = 3<br />
<br />
#Fast multipole method specs.<br />
fmEnabled = 0 #disable fast multipole<br />
fmMPOrder = 2<br />
fmTaylorOrder = 4<br />
fmCorrectionTbl = "Inputs/fm-ctab.m2.t4.dat"<br />
</pre><br />
<br />
You can set the directory name where you want to store the output. You can also set the total number of simulation steps <tt>maxstep</tt>. As for numXdoms, numYdoms and numZdoms, note that the product should be the total number of CPUs. This setting is crucial for parallel jobs. When all of them as set as 2, the total number of CUPs is 8. This should be consistant with the pbs file setting, which will be discussed in the end of this manual. If you want to enable fast multipole method (FMM), you need to set <tt>fmEnabled = 1</tt> and assign the path for the corresponding table.<br />
<br />
2 Next is some settings on geometry, material parameters etc<br />
<br />
<pre><br />
<br />
timestepIntegrator = "trapezoid"<br />
<br />
#Boundary conditions<br />
xBoundType = 0<br />
yBoundType = 0<br />
zBoundType = 0<br />
<br />
#Fundamental length unit<br />
burgMag = 2.556120e-010<br />
<br />
#Elastic constants<br />
shearModulus = 40000000000.000000<br />
pois = 0.369000<br />
<br />
#Mobility law function<br />
mobilityLaw = "FCC_0"<br />
enforceGlidePlanes = 1<br />
enableCrossSlip = -1<br />
MobScrew = 1.000000e+005<br />
MobEdge = 1.000000e+005<br />
MobClimb = 1.000000e-002<br />
<br />
#Discretization<br />
maxSeg = 200.000000<br />
minSeg = 10.000000<br />
<br />
#Maximum nodal displacement at each time step<br />
rmax = 100<br />
<br />
#Error tolerance in determining time step<br />
rTol = 0.721688<br />
<br />
#Maximum time step<br />
maxDT = 1<br />
<br />
#Core cut-off radius<br />
rc = 2.886751<br />
<br />
#Core energy<br />
Ecore = 0.000000e+000<br />
<br />
#Turn on elastic interaction<br />
elasticinteraction = 1<br />
</pre><br />
<br />
Variable <tt>xBoundType</tt> defines the type of problem space boundaries in the X dimension. Valid values are 0, 1 and 2 respectively for periodic, free surface, and reflecting.<br />
<br />
The value of <tt>burgMag</tt> is the unit of length for all length variables in ParaDiS simulation, such as nodal positions and Burgers vectors (in data file, those data should be expressed in terms of the same <tt>burgMag</tt>)<br />
<br />
The setting for mobility law is important, which should be consistent with the system you simulate. Cross-slip is enabled only when <tt>enableCrossSlip = 1</tt>. You need to adjust some of the geometric parameters to fit your problem.<br />
<br />
3 Third is the loading conditions<br />
<br />
<pre><br />
#Applied stress in Pa (xx,yy,zz,yz,zx,xy)<br />
appliedStress = [ 0 0 0 0 0 0 ]<br />
<br />
#Constant Strain rate<br />
loadType = 1<br />
edotdir = [ 0.0 0.0 1.0 ]<br />
eRate = 100.0<br />
</pre><br />
<br />
<tt>loadType</tt> defines the type of load on the system. Usually we set it as 0 (creep, i.e. constant external stress) or 1 (constant strain rate). For detailed explanations for value 2, 3 and 4, please refer to the variable table. When <tt>loadType = 0</tt>, you need to set <tt>appliedStress</tt>(zero vector for relaxation). When <tt>loadType = 1</tt>, you need to define strain rate direction <tt>edotdir</tt> and strain rate <tt>eRate</tt>.<br />
<br />
4 And the last part is settings on saving,<br />
<br />
<pre><br />
#Save files<br />
savecn = 1<br />
savecnfreq = 100<br />
<br />
#Save Properties<br />
saveprop = 1<br />
savepropfreq = 1<br />
#winDefaultsFile = "inputs/paradis.xdefaults"<br />
</pre><br />
<br />
By setting <tt>savencn = 1</tt>, saving is enabled at a frequency of <tt>savecnfreq</tt>. Lines relevant to saving properties and visulization are discussed in later part of this manual.<br />
<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
Gnuplot is a useful plotting software. You can plot the obtained properties data with gnupot, for example, stress vs strain curve. Before using gnuplot, make sure it is installed on your cluster. You also need to enable X server (test by typing <tt>xclock</tt>). By typing <tt>gnuplot</tt>, you can start using following command lines. For a given (X,Y) data pair, the gnuplot command is<br />
<pre><br />
gnuplot> plot "filename" using 1:2 with lines<br />
</pre><br />
where "using 1:2" means plotting using the 1st and 2nd column from the given data file. "with lines" is a style option, you can change to "with points", "with steps", "with dots" or "with impulses". Click [http://t16web.lanl.gov/Kawano/gnuplot/intro/style-e.html] for a detailed description of the styles.<br />
To draw multiple lines, you can type<br />
<pre><br />
gnuplot> plot "A" using 1:2 title "data A" with lines, \<br />
"B" u 1:2 t "data B" with p, \<br />
"C" u 2:3 t "data C" w d<br />
</pre><br />
You can use \ to separate continuous lines. <tt>title</tt> is used to label different lines. You can abbreviate some of the commands, for example, u for using, t for title, w for with, l for lines, p for points and d for dots.<br />
<br />
To change the labels of X and Y axes, you can use<br />
<pre><br />
gnuplot> set xlabel "x-axis"<br />
gnuplot> set ylabel "y-xais"<br />
gnuplot> set title "y vs x"<br />
gnuplot> replot<br />
</pre><br />
<br />
You can also change the ranges of X and Y axes,<br />
<pre><br />
gnuplot> set xrange [0:2]<br />
gnuplot> set yrange [0:1]<br />
gnuplot> replot<br />
</pre><br />
<br />
To assign the color of the line(line type), you need to add corresponding number after "l". For example, black solid(-1), black dot(0), red(1), green (2), blue(3), margenta(4), cyan(5) and yellow(6). To modify the width of the line at the same time, you can use option "w l lt 2 lw 4", for instance, where lt means linetype and lw means linewidth.<br />
<br />
==How to visualize the results==<br />
To visualize the simulation results, here are two methods. One is to run simulation interactively one one CPU and perform observation. The other is to record the configuration at certain simulation steps and make movies from them.<br />
===xwindow===<br />
Make sure x11 server is enabled for the session(test by "xclock"; using <tt>ssh -X username@domain</tt> when you log into clusters) and the ParaDiS code is compiled for single CPU("MODE = SERIAL, XLIB_MODE = ON" in makefile.setup). Check the following setting in <tt>/inputs/paradis.xdefaults</tt> if you set it as "winDefaultsFile" in your ctrl file.<br />
<pre><br />
enable_window = 1 <br />
</pre><br />
By executing<br />
<pre><br />
bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl<br />
</pre><br />
You should be able to see the xwindow. By setting "maxstep = 0" in the ctrl file, you can obtain the configuration (snapshot) for any given simulation step. When the simulation step is large, you might want to consider the other method.<br />
<br />
===Atomeye===<br />
Atomeye is a powerful visualization tool. To enable Atomeye, you need to add following lines in the ctrl file<br />
<pre><br />
atomeye = 1<br />
atomeyefreq = 1<br />
atomeyesegradius = 5<br />
</pre><br />
To view atomeye files, you can use command<br />
<pre><br />
$ tools/atomeye/A.i686 outputs/filename/atomeye/paradis0001.cfg<br />
</pre><br />
To create jpg files press y to convert all cfg files in the same directory. <br />
<br />
To convert these jpg files to a movie, the command is<br />
<pre><br />
$ convert -delay 4 -quality 95 *.jpg mymovie.mpg<br />
</pre><br />
where -delay and -quality flags are optional; if -delay > 4, extra frames are added to make the movie run more slowly; default quality is 75 and the maximum is 100. Note that encode packages need to be preinstalled for the machine or cluster.<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
In a typical pbs file, we have following lines as header:<br />
<br />
<pre><br />
#!/bin/bash<br />
#PBS -N jobname<br />
#PBS -j oe<br />
#PBS -l nodes=8:ppn=8,walltime=24:00:00<br />
#PBS -V<br />
<br />
### ---------------------------------------<br />
### BEGINNING OF EXECUTION<br />
### ---------------------------------------<br />
<br />
echo The master node of this job is `hostname`<br />
echo The working directory is `echo $PBS_O_WORKDIR`<br />
echo This job runs on the following nodes:<br />
echo `cat $PBS_NODEFILE`<br />
<br />
ncpu=`cat $PBS_NODEFILE | wc -w`<br />
echo "Number of processors = $ncpu "<br />
### end of information preamble<br />
<br />
cd $PBS_O_WORKDIR<br />
<br />
echo $PWD<br />
<br />
#cmd="mpiexec -np $ncpu bin/meam-lammps_mpich scripts/work/si_ge/si-meam-lammps.tcl"<br />
#time $cmd<br />
</pre><br />
<br />
You need to set the job name, wait time, number of nodes and ppn (number of processors per node, for example, ppn = 8 for wcr clusters)<br />
<br />
To submit jobs using a single processor, you need to add the following line<br />
<pre><br />
#bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl &> serial.out<br />
</pre><br />
where log file is <tt>serial.out</tt>.<br />
<br />
For parallel jobs, add<br />
<pre><br />
#mpiexec -np $ncpu bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl &> parallel.out<br />
</pre><br />
where log file is <tt>parallel.out</tt>.<br />
<br />
===What if the job is stopped===<br />
You can continue from the stored files under directory <tt>outputs/filename/restart</tt> by<br />
<pre><br />
$bin/paradis outputs/filename/restart/restart.cn<br />
</pre></div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5043ParaDiS Manual Updated2011-01-13T02:12:54Z<p>Jieyin: /* How to set up ctrl-file */</p>
<hr />
<div>Written by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. <br />
<br />
While reading this document, don't forget to check out [[paradis.stanford.edu]] for a complete and searchable table of parameters in ParaDiS code (some parameter names are not up-to-date). Detailed descriptions can be found in the official documentation ParaDiSInfo.txt.<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following structures exist<br />
<pre><br />
dataFileVersion = 4<br />
numFileSegments = 1<br />
minCoordinates = [<br />
-4.000000e+003<br />
-4.000000e+003<br />
-4.000000e+003<br />
]<br />
maxCoordinates = [<br />
4.000000e+003<br />
4.000000e+003<br />
4.000000e+003<br />
]<br />
nodeCount = 192<br />
dataDecompType = 1<br />
dataDecompGeometry = [<br />
1<br />
1<br />
1<br />
]<br />
domainDecomposition =<br />
-4.000000e+003<br />
-4.000000e+003<br />
-4.000000e+003<br />
4.000000e+003<br />
4.000000e+003<br />
4.000000e+003<br />
<br />
#<br />
# Primary lines: node_tag, x, y, z, num_arms, constraint<br />
# Secondary lines: arm_tag, burgx, burgy, burgz, nx, ny, nz<br />
#<br />
# length in unit of burgMag<br />
<br />
nodalData =<br />
0,0 3.52197261266669e+003 -2.10366848600532e+003 8.35974608889734e+002 2 7<br />
0,1 -0.707107 0.707107 0 1 1 1<br />
0,15 0.707107 -0.707107 0 -0.408248 -0.408248 0.816497<br />
...<br />
</pre><br />
<br />
You need to set your own data file parameters, usually including minCoordinates, maxCoordinates, nodeCount, domainDecomposition and nodalData. The nodalData is a long array of data. You may want to create it from Matlab if there exists too many nodes in your simulation box.<br />
<br />
===How to set up ctrl-file===<br />
<br />
The structure of the ctrl file is explained by parts. <br />
<br />
1 First is the basic setup information for the simulation,<br />
<br />
<pre><br />
#Directory to write output files<br />
dirname = "outputs/filename"<br />
<br />
#Input files for PBC image stresses<br />
Rijmfile = "inputs/Rijm.cube.out"<br />
RijmPBCfile = "inputs/RijmPBC.cube.out"<br />
<br />
#Total simulation steps<br />
maxstep = 100<br />
<br />
#The total number of CPUs should be numXdoms * numYdoms * numZdoms<br />
numXdoms = 1<br />
numYdoms = 1<br />
numZdoms = 1<br />
<br />
#Cells for dislocation grouping (cannot be less than 3)<br />
numXcells = 3<br />
numYcells = 3<br />
numZcells = 3<br />
<br />
#Fast multipole method specs.<br />
fmEnabled = 0 #disable fast multipole<br />
fmMPOrder = 2<br />
fmTaylorOrder = 4<br />
fmCorrectionTbl = "Inputs/fm-ctab.m2.t4.dat"<br />
</pre><br />
<br />
You can set the directory name where you want to store the output. You can also set the total number of simulation steps <tt>maxstep</tt>. As for numXdoms, numYdoms and numZdoms, note that the product should be the total number of CPUs. This setting is crucial for parallel jobs. When all of them as set as 2, the total number of CUPs is 8. This should be consistant with the pbs file setting, which will be discussed in the end of this manual. If you want to enable fast multipole method (FMM), you need to set <tt>fmEnabled = 1</tt> and assign the path for the corresponding table.<br />
<br />
2 Next is some settings on geometry, material parameters etc<br />
<br />
<pre><br />
<br />
timestepIntegrator = "trapezoid"<br />
<br />
#Boundary conditions<br />
xBoundType = 0<br />
yBoundType = 0<br />
zBoundType = 0<br />
<br />
#Fundamental length unit<br />
burgMag = 2.556120e-010<br />
<br />
#Elastic constants<br />
shearModulus = 40000000000.000000<br />
pois = 0.369000<br />
<br />
#Mobility law function<br />
mobilityLaw = "FCC_0"<br />
enforceGlidePlanes = 1<br />
enableCrossSlip = -1<br />
MobScrew = 1.000000e+005<br />
MobEdge = 1.000000e+005<br />
MobClimb = 1.000000e-002<br />
<br />
#Discretization<br />
maxSeg = 200.000000<br />
minSeg = 10.000000<br />
<br />
#Maximum nodal displacement at each time step<br />
rmax = 100<br />
<br />
#Error tolerance in determining time step<br />
rTol = 0.721688<br />
<br />
#Maximum time step<br />
maxDT = 1<br />
<br />
#Core cut-off radius<br />
rc = 2.886751<br />
<br />
#Core energy<br />
Ecore = 0.000000e+000<br />
<br />
#Turn on elastic interaction<br />
elasticinteraction = 1<br />
</pre><br />
<br />
Variable <tt>xBoundType</tt> defines the type of problem space boundaries in the X dimension. Valid values are 0, 1 and 2 respectively for periodic, free surface, and reflecting.<br />
<br />
The value of <tt>burgMag</tt> is the unit of length for all length variables in ParaDiS simulation, such as nodal positions and Burgers vectors (in data file, those data should be expressed in terms of the same <tt>burgMag</tt>)<br />
<br />
The setting for mobility law is important, which should be consistent with the system you simulate. Cross-slip is enabled only when <tt>enableCrossSlip = 1</tt>. You need to adjust some of the geometric parameters to fit your problem.<br />
<br />
3 Third is the loading conditions<br />
<br />
<pre><br />
#Applied stress in Pa (xx,yy,zz,yz,zx,xy)<br />
appliedStress = [ 0 0 0 0 0 0 ]<br />
<br />
#Constant Strain rate<br />
loadType = 1<br />
edotdir = [ 0.0 0.0 1.0 ]<br />
eRate = 100.0<br />
</pre><br />
<br />
<tt>loadType</tt> defines the type of load on the system. Usually we set it as 0 (creep, i.e. constant external stress) or 1 (constant strain rate). For detailed explanations for value 2, 3 and 4, please refer to the variable table. When <tt>loadType = 0</tt>, you need to set <tt>appliedStress</tt>(zero vector for relaxation). When <tt>loadType = 1</tt>, you need to define strain rate direction <tt>edotdir</tt> and strain rate <tt>eRate</tt>.<br />
<br />
4 And the last part is settings on saving,<br />
<br />
<pre><br />
#Save files<br />
savecn = 1<br />
savecnfreq = 100<br />
<br />
#Save Properties<br />
saveprop = 1<br />
savepropfreq = 1<br />
#winDefaultsFile = "inputs/paradis.xdefaults"<br />
</pre><br />
<br />
Lines relevant to saving properties and visulization are discussed in later part of this manual.<br />
<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
Gnuplot is a useful plotting software. You can plot the obtained properties data with gnupot, for example, stress vs strain curve. Before using gnuplot, make sure it is installed on your cluster. You also need to enable X server (test by typing <tt>xclock</tt>). By typing <tt>gnuplot</tt>, you can start using following command lines. For a given (X,Y) data pair, the gnuplot command is<br />
<pre><br />
gnuplot> plot "filename" using 1:2 with lines<br />
</pre><br />
where "using 1:2" means plotting using the 1st and 2nd column from the given data file. "with lines" is a style option, you can change to "with points", "with steps", "with dots" or "with impulses". Click [http://t16web.lanl.gov/Kawano/gnuplot/intro/style-e.html] for a detailed description of the styles.<br />
To draw multiple lines, you can type<br />
<pre><br />
gnuplot> plot "A" using 1:2 title "data A" with lines, \<br />
"B" u 1:2 t "data B" with p, \<br />
"C" u 2:3 t "data C" w d<br />
</pre><br />
You can use \ to separate continuous lines. <tt>title</tt> is used to label different lines. You can abbreviate some of the commands, for example, u for using, t for title, w for with, l for lines, p for points and d for dots.<br />
<br />
To change the labels of X and Y axes, you can use<br />
<pre><br />
gnuplot> set xlabel "x-axis"<br />
gnuplot> set ylabel "y-xais"<br />
gnuplot> set title "y vs x"<br />
gnuplot> replot<br />
</pre><br />
<br />
You can also change the ranges of X and Y axes,<br />
<pre><br />
gnuplot> set xrange [0:2]<br />
gnuplot> set yrange [0:1]<br />
gnuplot> replot<br />
</pre><br />
<br />
To assign the color of the line(line type), you need to add corresponding number after "l". For example, black solid(-1), black dot(0), red(1), green (2), blue(3), margenta(4), cyan(5) and yellow(6). To modify the width of the line at the same time, you can use option "w l lt 2 lw 4", for instance, where lt means linetype and lw means linewidth.<br />
<br />
==How to visualize the results==<br />
To visualize the simulation results, here are two methods. One is to run simulation interactively one one CPU and perform observation. The other is to record the configuration at certain simulation steps and make movies from them.<br />
===xwindow===<br />
Make sure x11 server is enabled for the session(test by "xclock"; using <tt>ssh -X username@domain</tt> when you log into clusters) and the ParaDiS code is compiled for single CPU("MODE = SERIAL, XLIB_MODE = ON" in makefile.setup). Check the following setting in <tt>/inputs/paradis.xdefaults</tt> if you set it as "winDefaultsFile" in your ctrl file.<br />
<pre><br />
enable_window = 1 <br />
</pre><br />
By executing<br />
<pre><br />
bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl<br />
</pre><br />
You should be able to see the xwindow. By setting "maxstep = 0" in the ctrl file, you can obtain the configuration (snapshot) for any given simulation step. When the simulation step is large, you might want to consider the other method.<br />
<br />
===Atomeye===<br />
Atomeye is a powerful visualization tool. To enable Atomeye, you need to add following lines in the ctrl file<br />
<pre><br />
atomeye = 1<br />
atomeyefreq = 1<br />
atomeyesegradius = 5<br />
</pre><br />
To view atomeye files, you can use command<br />
<pre><br />
$ tools/atomeye/A.i686 outputs/filename/atomeye/paradis0001.cfg<br />
</pre><br />
To create jpg files press y to convert all cfg files in the same directory. <br />
<br />
To convert these jpg files to a movie, the command is<br />
<pre><br />
$ convert -delay 4 -quality 95 *.jpg mymovie.mpg<br />
</pre><br />
where -delay and -quality flags are optional; if -delay > 4, extra frames are added to make the movie run more slowly; default quality is 75 and the maximum is 100. Note that encode packages need to be preinstalled for the machine or cluster.<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
In a typical pbs file, we have following lines as header:<br />
<br />
<pre><br />
#!/bin/bash<br />
#PBS -N jobname<br />
#PBS -j oe<br />
#PBS -l nodes=8:ppn=8,walltime=24:00:00<br />
#PBS -V<br />
<br />
### ---------------------------------------<br />
### BEGINNING OF EXECUTION<br />
### ---------------------------------------<br />
<br />
echo The master node of this job is `hostname`<br />
echo The working directory is `echo $PBS_O_WORKDIR`<br />
echo This job runs on the following nodes:<br />
echo `cat $PBS_NODEFILE`<br />
<br />
ncpu=`cat $PBS_NODEFILE | wc -w`<br />
echo "Number of processors = $ncpu "<br />
### end of information preamble<br />
<br />
cd $PBS_O_WORKDIR<br />
<br />
echo $PWD<br />
<br />
#cmd="mpiexec -np $ncpu bin/meam-lammps_mpich scripts/work/si_ge/si-meam-lammps.tcl"<br />
#time $cmd<br />
</pre><br />
<br />
You need to set the job name, wait time, number of nodes and ppn (number of processors per node, for example, ppn = 8 for wcr clusters)<br />
<br />
To submit jobs using a single processor, you need to add the following line<br />
<pre><br />
#bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl &> serial.out<br />
</pre><br />
where log file is <tt>serial.out</tt>.<br />
<br />
For parallel jobs, add<br />
<pre><br />
#mpiexec -np $ncpu bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl &> parallel.out<br />
</pre><br />
where log file is <tt>parallel.out</tt>.<br />
<br />
===What if the job is stopped===<br />
You can continue from the stored files under directory <tt>outputs/filename/restart</tt> by<br />
<pre><br />
$bin/paradis outputs/filename/restart/restart.cn<br />
</pre></div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5042ParaDiS Manual Updated2011-01-13T02:00:34Z<p>Jieyin: /* How to set up ctrl-file */</p>
<hr />
<div>Written by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. <br />
<br />
While reading this document, don't forget to check out [[paradis.stanford.edu]] for a complete and searchable table of parameters in ParaDiS code (some parameter names are not up-to-date). Detailed descriptions can be found in the official documentation ParaDiSInfo.txt.<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following structures exist<br />
<pre><br />
dataFileVersion = 4<br />
numFileSegments = 1<br />
minCoordinates = [<br />
-4.000000e+003<br />
-4.000000e+003<br />
-4.000000e+003<br />
]<br />
maxCoordinates = [<br />
4.000000e+003<br />
4.000000e+003<br />
4.000000e+003<br />
]<br />
nodeCount = 192<br />
dataDecompType = 1<br />
dataDecompGeometry = [<br />
1<br />
1<br />
1<br />
]<br />
domainDecomposition =<br />
-4.000000e+003<br />
-4.000000e+003<br />
-4.000000e+003<br />
4.000000e+003<br />
4.000000e+003<br />
4.000000e+003<br />
<br />
#<br />
# Primary lines: node_tag, x, y, z, num_arms, constraint<br />
# Secondary lines: arm_tag, burgx, burgy, burgz, nx, ny, nz<br />
#<br />
# length in unit of burgMag<br />
<br />
nodalData =<br />
0,0 3.52197261266669e+003 -2.10366848600532e+003 8.35974608889734e+002 2 7<br />
0,1 -0.707107 0.707107 0 1 1 1<br />
0,15 0.707107 -0.707107 0 -0.408248 -0.408248 0.816497<br />
...<br />
</pre><br />
<br />
You need to set your own data file parameters, usually including minCoordinates, maxCoordinates, nodeCount, domainDecomposition and nodalData. The nodalData is a long array of data. You may want to create it from Matlab if there exists too many nodes in your simulation box.<br />
<br />
===How to set up ctrl-file===<br />
<br />
The structure of the ctrl file is explained by parts. <br />
<br />
1 First is the basic setup information for the simulation,<br />
<br />
<pre><br />
#Directory to write output files<br />
dirname = "outputs/filename"<br />
<br />
#Input files for PBC image stresses<br />
Rijmfile = "inputs/Rijm.cube.out"<br />
RijmPBCfile = "inputs/RijmPBC.cube.out"<br />
<br />
#Total simulation steps<br />
maxstep = 100<br />
<br />
#The total number of CPUs should be numXdoms * numYdoms * numZdoms<br />
numXdoms = 1<br />
numYdoms = 1<br />
numZdoms = 1<br />
<br />
#Cells for dislocation grouping (cannot be less than 3)<br />
numXcells = 3<br />
numYcells = 3<br />
numZcells = 3<br />
<br />
#Fast multipole method specs.<br />
fmEnabled = 0 #disable fast multipole<br />
fmMPOrder = 2<br />
fmTaylorOrder = 4<br />
fmCorrectionTbl = "Inputs/fm-ctab.m2.t4.dat"<br />
</pre><br />
<br />
You can set the directory name where you want to store the output. You can also set the total number of simulation steps <tt>maxstep</tt>. As for numXdoms, numYdoms and numZdoms, note that the product should be the total number of CPUs. This setting is crucial for parallel jobs. When all of them as set as 2, the total number of CUPs is 8. This should be consistant with the pbs file setting, which will be discussed in the end of this manual. If you want to enable fast multipole method (FMM), you need to set <tt>fmEnabled = 1</tt> and assign the path for the corresponding table.<br />
<br />
2 Next is some settings on geometry, material parameters etc<br />
<br />
<pre><br />
<br />
timestepIntegrator = "trapezoid"<br />
<br />
#Boundary conditions<br />
xBoundType = 0<br />
yBoundType = 0<br />
zBoundType = 0<br />
<br />
#Fundamental length unit<br />
burgMag = 2.556120e-010<br />
<br />
#Elastic constants<br />
shearModulus = 40000000000.000000<br />
pois = 0.369000<br />
<br />
#Mobility law function<br />
mobilityLaw = "FCC_0"<br />
enforceGlidePlanes = 1<br />
enableCrossSlip = -1<br />
MobScrew = 1.000000e+005<br />
MobEdge = 1.000000e+005<br />
MobClimb = 1.000000e-002<br />
<br />
#Discretization<br />
maxSeg = 200.000000<br />
minSeg = 10.000000<br />
<br />
#Maximum nodal displacement at each time step<br />
rmax = 100<br />
<br />
#Error tolerance in determining time step<br />
rTol = 0.721688<br />
<br />
#Maximum time step<br />
maxDT = 1<br />
<br />
#Core cut-off radius<br />
rc = 2.886751<br />
<br />
#Core energy<br />
Ecore = 0.000000e+000<br />
<br />
#Turn on elastic interaction<br />
elasticinteraction = 1<br />
</pre><br />
<br />
Variable <tt>xBoundType</tt> defines the type of problem space boundaries in the X dimension. Valid values are 0, 1 and 2 respectively for periodic, free surface, and reflecting.<br />
<br />
The value of <tt>burgMag</tt> is the unit of length for all length variables in ParaDiS simulation, such as nodal positions and Burgers vectors (in data file, those data should be expressed in terms of the same <tt>burgMag</tt>)<br />
<br />
<br />
3 Third is the loading conditions<br />
<br />
<pre><br />
#Applied stress in Pa (xx,yy,zz,yz,zx,xy)<br />
appliedStress = [ 0 0 0 0 0 0 ]<br />
<br />
#Constant Strain rate<br />
loadType = 1<br />
edotdir = [ 0.0 0.0 1.0 ]<br />
eRate = 100000.0<br />
</pre><br />
<br />
4 And the last part is settings on saving,<br />
<br />
<pre><br />
#Save files<br />
savecn = 1<br />
savecnfreq = 100<br />
<br />
#Save Properties<br />
saveprop = 1<br />
savepropfreq = 1<br />
#winDefaultsFile = "inputs/paradis.xdefaults2"<br />
</pre><br />
<br />
Some visualization options<br />
<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
Gnuplot is a useful plotting software. You can plot the obtained properties data with gnupot, for example, stress vs strain curve. Before using gnuplot, make sure it is installed on your cluster. You also need to enable X server (test by typing <tt>xclock</tt>). By typing <tt>gnuplot</tt>, you can start using following command lines. For a given (X,Y) data pair, the gnuplot command is<br />
<pre><br />
gnuplot> plot "filename" using 1:2 with lines<br />
</pre><br />
where "using 1:2" means plotting using the 1st and 2nd column from the given data file. "with lines" is a style option, you can change to "with points", "with steps", "with dots" or "with impulses". Click [http://t16web.lanl.gov/Kawano/gnuplot/intro/style-e.html] for a detailed description of the styles.<br />
To draw multiple lines, you can type<br />
<pre><br />
gnuplot> plot "A" using 1:2 title "data A" with lines, \<br />
"B" u 1:2 t "data B" with p, \<br />
"C" u 2:3 t "data C" w d<br />
</pre><br />
You can use \ to separate continuous lines. <tt>title</tt> is used to label different lines. You can abbreviate some of the commands, for example, u for using, t for title, w for with, l for lines, p for points and d for dots.<br />
<br />
To change the labels of X and Y axes, you can use<br />
<pre><br />
gnuplot> set xlabel "x-axis"<br />
gnuplot> set ylabel "y-xais"<br />
gnuplot> set title "y vs x"<br />
gnuplot> replot<br />
</pre><br />
<br />
You can also change the ranges of X and Y axes,<br />
<pre><br />
gnuplot> set xrange [0:2]<br />
gnuplot> set yrange [0:1]<br />
gnuplot> replot<br />
</pre><br />
<br />
To assign the color of the line(line type), you need to add corresponding number after "l". For example, black solid(-1), black dot(0), red(1), green (2), blue(3), margenta(4), cyan(5) and yellow(6). To modify the width of the line at the same time, you can use option "w l lt 2 lw 4", for instance, where lt means linetype and lw means linewidth.<br />
<br />
==How to visualize the results==<br />
To visualize the simulation results, here are two methods. One is to run simulation interactively one one CPU and perform observation. The other is to record the configuration at certain simulation steps and make movies from them.<br />
===xwindow===<br />
Make sure x11 server is enabled for the session(test by "xclock"; using <tt>ssh -X username@domain</tt> when you log into clusters) and the ParaDiS code is compiled for single CPU("MODE = SERIAL, XLIB_MODE = ON" in makefile.setup). Check the following setting in <tt>/inputs/paradis.xdefaults</tt> if you set it as "winDefaultsFile" in your ctrl file.<br />
<pre><br />
enable_window = 1 <br />
</pre><br />
By executing<br />
<pre><br />
bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl<br />
</pre><br />
You should be able to see the xwindow. By setting "maxstep = 0" in the ctrl file, you can obtain the configuration (snapshot) for any given simulation step. When the simulation step is large, you might want to consider the other method.<br />
<br />
===Atomeye===<br />
Atomeye is a powerful visualization tool. To enable Atomeye, you need to add following lines in the ctrl file<br />
<pre><br />
atomeye = 1<br />
atomeyefreq = 1<br />
atomeyesegradius = 5<br />
</pre><br />
To view atomeye files, you can use command<br />
<pre><br />
$ tools/atomeye/A.i686 outputs/filename/atomeye/paradis0001.cfg<br />
</pre><br />
To create jpg files press y to convert all cfg files in the same directory. <br />
<br />
To convert these jpg files to a movie, the command is<br />
<pre><br />
$ convert -delay 4 -quality 95 *.jpg mymovie.mpg<br />
</pre><br />
where -delay and -quality flags are optional; if -delay > 4, extra frames are added to make the movie run more slowly; default quality is 75 and the maximum is 100. Note that encode packages need to be preinstalled for the machine or cluster.<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
In a typical pbs file, we have following lines as header:<br />
<br />
<pre><br />
#!/bin/bash<br />
#PBS -N jobname<br />
#PBS -j oe<br />
#PBS -l nodes=8:ppn=8,walltime=24:00:00<br />
#PBS -V<br />
<br />
### ---------------------------------------<br />
### BEGINNING OF EXECUTION<br />
### ---------------------------------------<br />
<br />
echo The master node of this job is `hostname`<br />
echo The working directory is `echo $PBS_O_WORKDIR`<br />
echo This job runs on the following nodes:<br />
echo `cat $PBS_NODEFILE`<br />
<br />
ncpu=`cat $PBS_NODEFILE | wc -w`<br />
echo "Number of processors = $ncpu "<br />
### end of information preamble<br />
<br />
cd $PBS_O_WORKDIR<br />
<br />
echo $PWD<br />
<br />
#cmd="mpiexec -np $ncpu bin/meam-lammps_mpich scripts/work/si_ge/si-meam-lammps.tcl"<br />
#time $cmd<br />
</pre><br />
<br />
You need to set the job name, wait time, number of nodes and ppn (number of processors per node, for example, ppn = 8 for wcr clusters)<br />
<br />
To submit jobs using a single processor, you need to add the following line<br />
<pre><br />
#bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl &> serial.out<br />
</pre><br />
where log file is <tt>serial.out</tt>.<br />
<br />
For parallel jobs, add<br />
<pre><br />
#mpiexec -np $ncpu bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl &> parallel.out<br />
</pre><br />
where log file is <tt>parallel.out</tt>.<br />
<br />
===What if the job is stopped===<br />
You can continue from the stored files under directory <tt>outputs/filename/restart</tt> by<br />
<pre><br />
$bin/paradis outputs/filename/restart/restart.cn<br />
</pre></div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5041ParaDiS Manual Updated2011-01-13T01:56:29Z<p>Jieyin: /* How to set up ctrl-file */</p>
<hr />
<div>Written by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. <br />
<br />
While reading this document, don't forget to check out [[paradis.stanford.edu]] for a complete and searchable table of parameters in ParaDiS code (some parameter names are not up-to-date). Detailed descriptions can be found in the official documentation ParaDiSInfo.txt.<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following structures exist<br />
<pre><br />
dataFileVersion = 4<br />
numFileSegments = 1<br />
minCoordinates = [<br />
-4.000000e+003<br />
-4.000000e+003<br />
-4.000000e+003<br />
]<br />
maxCoordinates = [<br />
4.000000e+003<br />
4.000000e+003<br />
4.000000e+003<br />
]<br />
nodeCount = 192<br />
dataDecompType = 1<br />
dataDecompGeometry = [<br />
1<br />
1<br />
1<br />
]<br />
domainDecomposition =<br />
-4.000000e+003<br />
-4.000000e+003<br />
-4.000000e+003<br />
4.000000e+003<br />
4.000000e+003<br />
4.000000e+003<br />
<br />
#<br />
# Primary lines: node_tag, x, y, z, num_arms, constraint<br />
# Secondary lines: arm_tag, burgx, burgy, burgz, nx, ny, nz<br />
#<br />
# length in unit of burgMag<br />
<br />
nodalData =<br />
0,0 3.52197261266669e+003 -2.10366848600532e+003 8.35974608889734e+002 2 7<br />
0,1 -0.707107 0.707107 0 1 1 1<br />
0,15 0.707107 -0.707107 0 -0.408248 -0.408248 0.816497<br />
...<br />
</pre><br />
<br />
You need to set your own data file parameters, usually including minCoordinates, maxCoordinates, nodeCount, domainDecomposition and nodalData. The nodalData is a long array of data. You may want to create it from Matlab if there exists too many nodes in your simulation box.<br />
<br />
===How to set up ctrl-file===<br />
<br />
The structure of the ctrl file is explained by parts. <br />
<br />
1 First is the basic setup information for the simulation,<br />
<br />
<pre><br />
#Directory to write output files<br />
dirname = "outputs/filename"<br />
<br />
#Input files for PBC image stresses<br />
Rijmfile = "inputs/Rijm.cube.out"<br />
RijmPBCfile = "inputs/RijmPBC.cube.out"<br />
<br />
#Total simulation steps<br />
maxstep = 100<br />
<br />
#The total number of CPUs should be numXdoms * numYdoms * numZdoms<br />
numXdoms = 1<br />
numYdoms = 1<br />
numZdoms = 1<br />
<br />
#Cells for dislocation grouping (cannot be less than 3)<br />
numXcells = 3<br />
numYcells = 3<br />
numZcells = 3<br />
<br />
#Fast multipole method specs.<br />
fmEnabled = 0 #disable fast multipole<br />
fmMPOrder = 2<br />
fmTaylorOrder = 4<br />
fmCorrectionTbl = "Inputs/fm-ctab.m2.t4.dat"<br />
</pre><br />
<br />
You can set the directory name where you want to store the output. You can also set the total number of simulation steps <tt>maxstep</tt>. As for numXdoms, numYdoms and numZdoms, note that the product should be the total number of CPUs. This setting is crucial for parallel jobs. When all of them as set as 2, the total number of CUPs is 8. This should be consistant with the pbs file setting, which will be discussed in the end of this manual. If you want to enable fast multipole method (FMM), you need to set <tt>fmEnabled = 1</tt> and assign the path for the corresponding table.<br />
<br />
2 Next is some settings on geometry, material parameters etc<br />
<br />
<pre><br />
<br />
timestepIntegrator = "trapezoid"<br />
<br />
#Boundary conditions<br />
xBoundType = 0<br />
yBoundType = 0<br />
zBoundType = 0<br />
<br />
#Fundamental length unit<br />
burgMag = 2.556120e-010<br />
<br />
#Elastic constants<br />
shearModulus = 40000000000.000000<br />
pois = 0.369000<br />
<br />
#Mobility law function<br />
mobilityLaw = "FCC_0"<br />
enforceGlidePlanes = 1<br />
enableCrossSlip = -1<br />
MobScrew = 1.000000e+005<br />
MobEdge = 1.000000e+005<br />
MobClimb = 1.000000e-002<br />
<br />
#Discretization<br />
maxSeg = 200.000000<br />
minSeg = 10.000000<br />
<br />
#Maximum nodal displacement at each time step<br />
rmax = 100<br />
<br />
#Error tolerance in determining time step<br />
rTol = 0.721688<br />
<br />
#Maximum time step<br />
maxDT = 1<br />
<br />
#Core cut-off radius<br />
rc = 2.886751<br />
<br />
#Core energy<br />
Ecore = 0.000000e+000<br />
<br />
#Turn on elastic interaction<br />
elasticinteraction = 1<br />
</pre><br />
<br />
3 Third is the loading conditions<br />
<br />
<pre><br />
#Applied stress in Pa (xx,yy,zz,yz,zx,xy)<br />
appliedStress = [ 0 0 0 0 0 0 ]<br />
<br />
#Constant Strain rate<br />
loadType = 1<br />
edotdir = [ 0.0 0.0 1.0 ]<br />
eRate = 100000.0<br />
</pre><br />
<br />
4 And the last part is settings on saving,<br />
<br />
<pre><br />
#Save files<br />
savecn = 1<br />
savecnfreq = 100<br />
<br />
#Save Properties<br />
saveprop = 1<br />
savepropfreq = 1<br />
#winDefaultsFile = "inputs/paradis.xdefaults2"<br />
</pre><br />
<br />
Some visualization options<br />
<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
Gnuplot is a useful plotting software. You can plot the obtained properties data with gnupot, for example, stress vs strain curve. Before using gnuplot, make sure it is installed on your cluster. You also need to enable X server (test by typing <tt>xclock</tt>). By typing <tt>gnuplot</tt>, you can start using following command lines. For a given (X,Y) data pair, the gnuplot command is<br />
<pre><br />
gnuplot> plot "filename" using 1:2 with lines<br />
</pre><br />
where "using 1:2" means plotting using the 1st and 2nd column from the given data file. "with lines" is a style option, you can change to "with points", "with steps", "with dots" or "with impulses". Click [http://t16web.lanl.gov/Kawano/gnuplot/intro/style-e.html] for a detailed description of the styles.<br />
To draw multiple lines, you can type<br />
<pre><br />
gnuplot> plot "A" using 1:2 title "data A" with lines, \<br />
"B" u 1:2 t "data B" with p, \<br />
"C" u 2:3 t "data C" w d<br />
</pre><br />
You can use \ to separate continuous lines. <tt>title</tt> is used to label different lines. You can abbreviate some of the commands, for example, u for using, t for title, w for with, l for lines, p for points and d for dots.<br />
<br />
To change the labels of X and Y axes, you can use<br />
<pre><br />
gnuplot> set xlabel "x-axis"<br />
gnuplot> set ylabel "y-xais"<br />
gnuplot> set title "y vs x"<br />
gnuplot> replot<br />
</pre><br />
<br />
You can also change the ranges of X and Y axes,<br />
<pre><br />
gnuplot> set xrange [0:2]<br />
gnuplot> set yrange [0:1]<br />
gnuplot> replot<br />
</pre><br />
<br />
To assign the color of the line(line type), you need to add corresponding number after "l". For example, black solid(-1), black dot(0), red(1), green (2), blue(3), margenta(4), cyan(5) and yellow(6). To modify the width of the line at the same time, you can use option "w l lt 2 lw 4", for instance, where lt means linetype and lw means linewidth.<br />
<br />
==How to visualize the results==<br />
To visualize the simulation results, here are two methods. One is to run simulation interactively one one CPU and perform observation. The other is to record the configuration at certain simulation steps and make movies from them.<br />
===xwindow===<br />
Make sure x11 server is enabled for the session(test by "xclock"; using <tt>ssh -X username@domain</tt> when you log into clusters) and the ParaDiS code is compiled for single CPU("MODE = SERIAL, XLIB_MODE = ON" in makefile.setup). Check the following setting in <tt>/inputs/paradis.xdefaults</tt> if you set it as "winDefaultsFile" in your ctrl file.<br />
<pre><br />
enable_window = 1 <br />
</pre><br />
By executing<br />
<pre><br />
bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl<br />
</pre><br />
You should be able to see the xwindow. By setting "maxstep = 0" in the ctrl file, you can obtain the configuration (snapshot) for any given simulation step. When the simulation step is large, you might want to consider the other method.<br />
<br />
===Atomeye===<br />
Atomeye is a powerful visualization tool. To enable Atomeye, you need to add following lines in the ctrl file<br />
<pre><br />
atomeye = 1<br />
atomeyefreq = 1<br />
atomeyesegradius = 5<br />
</pre><br />
To view atomeye files, you can use command<br />
<pre><br />
$ tools/atomeye/A.i686 outputs/filename/atomeye/paradis0001.cfg<br />
</pre><br />
To create jpg files press y to convert all cfg files in the same directory. <br />
<br />
To convert these jpg files to a movie, the command is<br />
<pre><br />
$ convert -delay 4 -quality 95 *.jpg mymovie.mpg<br />
</pre><br />
where -delay and -quality flags are optional; if -delay > 4, extra frames are added to make the movie run more slowly; default quality is 75 and the maximum is 100. Note that encode packages need to be preinstalled for the machine or cluster.<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
In a typical pbs file, we have following lines as header:<br />
<br />
<pre><br />
#!/bin/bash<br />
#PBS -N jobname<br />
#PBS -j oe<br />
#PBS -l nodes=8:ppn=8,walltime=24:00:00<br />
#PBS -V<br />
<br />
### ---------------------------------------<br />
### BEGINNING OF EXECUTION<br />
### ---------------------------------------<br />
<br />
echo The master node of this job is `hostname`<br />
echo The working directory is `echo $PBS_O_WORKDIR`<br />
echo This job runs on the following nodes:<br />
echo `cat $PBS_NODEFILE`<br />
<br />
ncpu=`cat $PBS_NODEFILE | wc -w`<br />
echo "Number of processors = $ncpu "<br />
### end of information preamble<br />
<br />
cd $PBS_O_WORKDIR<br />
<br />
echo $PWD<br />
<br />
#cmd="mpiexec -np $ncpu bin/meam-lammps_mpich scripts/work/si_ge/si-meam-lammps.tcl"<br />
#time $cmd<br />
</pre><br />
<br />
You need to set the job name, wait time, number of nodes and ppn (number of processors per node, for example, ppn = 8 for wcr clusters)<br />
<br />
To submit jobs using a single processor, you need to add the following line<br />
<pre><br />
#bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl &> serial.out<br />
</pre><br />
where log file is <tt>serial.out</tt>.<br />
<br />
For parallel jobs, add<br />
<pre><br />
#mpiexec -np $ncpu bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl &> parallel.out<br />
</pre><br />
where log file is <tt>parallel.out</tt>.<br />
<br />
===What if the job is stopped===<br />
You can continue from the stored files under directory <tt>outputs/filename/restart</tt> by<br />
<pre><br />
$bin/paradis outputs/filename/restart/restart.cn<br />
</pre></div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5040ParaDiS Manual Updated2011-01-13T01:55:51Z<p>Jieyin: /* How to set up ctrl-file */</p>
<hr />
<div>Written by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. <br />
<br />
While reading this document, don't forget to check out [[paradis.stanford.edu]] for a complete and searchable table of parameters in ParaDiS code (some parameter names are not up-to-date). Detailed descriptions can be found in the official documentation ParaDiSInfo.txt.<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following structures exist<br />
<pre><br />
dataFileVersion = 4<br />
numFileSegments = 1<br />
minCoordinates = [<br />
-4.000000e+003<br />
-4.000000e+003<br />
-4.000000e+003<br />
]<br />
maxCoordinates = [<br />
4.000000e+003<br />
4.000000e+003<br />
4.000000e+003<br />
]<br />
nodeCount = 192<br />
dataDecompType = 1<br />
dataDecompGeometry = [<br />
1<br />
1<br />
1<br />
]<br />
domainDecomposition =<br />
-4.000000e+003<br />
-4.000000e+003<br />
-4.000000e+003<br />
4.000000e+003<br />
4.000000e+003<br />
4.000000e+003<br />
<br />
#<br />
# Primary lines: node_tag, x, y, z, num_arms, constraint<br />
# Secondary lines: arm_tag, burgx, burgy, burgz, nx, ny, nz<br />
#<br />
# length in unit of burgMag<br />
<br />
nodalData =<br />
0,0 3.52197261266669e+003 -2.10366848600532e+003 8.35974608889734e+002 2 7<br />
0,1 -0.707107 0.707107 0 1 1 1<br />
0,15 0.707107 -0.707107 0 -0.408248 -0.408248 0.816497<br />
...<br />
</pre><br />
<br />
You need to set your own data file parameters, usually including minCoordinates, maxCoordinates, nodeCount, domainDecomposition and nodalData. The nodalData is a long array of data. You may want to create it from Matlab if there exists too many nodes in your simulation box.<br />
<br />
===How to set up ctrl-file===<br />
<br />
The structure of the ctrl file is explained by parts. <br />
<br />
1 First is the basic setup information for the simulation,<br />
<br />
<pre><br />
#Directory to write output files<br />
dirname = "outputs/filename"<br />
<br />
#Input files for PBC image stresses<br />
Rijmfile = "inputs/Rijm.cube.out"<br />
RijmPBCfile = "inputs/RijmPBC.cube.out"<br />
<br />
#Total simulation steps<br />
maxstep = 100<br />
<br />
#The total number of CPUs should be numXdoms * numYdoms * numZdoms<br />
numXdoms = 1<br />
numYdoms = 1<br />
numZdoms = 1<br />
<br />
#Cells for dislocation grouping (cannot be less than 3)<br />
numXcells = 3<br />
numYcells = 3<br />
numZcells = 3<br />
<br />
#Fast multipole method specs.<br />
fmEnabled = 0 #disable fast multipole<br />
fmMPOrder = 2<br />
fmTaylorOrder = 4<br />
fmCorrectionTbl = "Inputs/fm-ctab.m2.t4.dat"<br />
</pre><br />
<br />
You can set the directory name where you want to store the output. You can also set the total number of simulation steps <tt>maxstep</tt>. As for numXdoms, numYdoms and numZdoms, note that the product should be the total number of CPUs. This setting is crucial for parallel jobs. When all of them as set as 2, the total number of CUPs is 8. This should be consistant with the pbs file setting, which will be discussed in the end of this manual. If you want to enable fast multipole method (FMM), you need to set <tt>fmEnabled = 1</tt> and assign the path for the corresponding table.<br />
<br />
2 Next is some settings on geometry, material parameters etc<br />
<br />
<pre><br />
<br />
timestepIntegrator = "trapezoid"<br />
<br />
#Boundary conditions<br />
xBoundType = 0<br />
yBoundType = 0<br />
zBoundType = 0<br />
<br />
<br />
#Fundamental length unit<br />
burgMag = 2.556120e-010<br />
<br />
#Elastic constants<br />
shearModulus = 40000000000.000000<br />
pois = 0.369000<br />
<br />
#Mobility law function<br />
mobilityLaw = "FCC_0"<br />
enforceGlidePlanes = 1<br />
enableCrossSlip = -1<br />
MobScrew = 1.000000e+005<br />
MobEdge = 1.000000e+005<br />
MobClimb = 1.000000e-002<br />
<br />
#Discretization<br />
maxSeg = 200.000000<br />
minSeg = 10.000000<br />
<br />
#Maximum nodal displacement at each time step<br />
rmax = 100<br />
<br />
#Error tolerance in determining time step<br />
rTol = 0.721688<br />
<br />
#Maximum time step<br />
maxDT = 1<br />
<br />
#Core cut-off radius<br />
rc = 2.886751<br />
<br />
<br />
#Core energy<br />
Ecore = 0.000000e+000<br />
<br />
#Turn on elastic interaction<br />
elasticinteraction = 1<br />
<br />
</pre><br />
<br />
3 Third is the loading conditions<br />
<br />
<pre><br />
#Applied stress in Pa (xx,yy,zz,yz,zx,xy)<br />
appliedStress = [ 0 0 0 0 0 0 ]<br />
<br />
#Constant Strain rate<br />
loadType = 1<br />
edotdir = [ 0.0 0.0 1.0 ]<br />
eRate = 100000.0<br />
<br />
</pre><br />
<br />
4 And the last part is settings on saving,<br />
<br />
<pre><br />
#Save files<br />
savecn = 1<br />
savecnfreq = 100<br />
<br />
#Save Properties<br />
saveprop = 1<br />
savepropfreq = 1<br />
#winDefaultsFile = "inputs/paradis.xdefaults2"<br />
</pre><br />
<br />
Some visualization options<br />
<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
Gnuplot is a useful plotting software. You can plot the obtained properties data with gnupot, for example, stress vs strain curve. Before using gnuplot, make sure it is installed on your cluster. You also need to enable X server (test by typing <tt>xclock</tt>). By typing <tt>gnuplot</tt>, you can start using following command lines. For a given (X,Y) data pair, the gnuplot command is<br />
<pre><br />
gnuplot> plot "filename" using 1:2 with lines<br />
</pre><br />
where "using 1:2" means plotting using the 1st and 2nd column from the given data file. "with lines" is a style option, you can change to "with points", "with steps", "with dots" or "with impulses". Click [http://t16web.lanl.gov/Kawano/gnuplot/intro/style-e.html] for a detailed description of the styles.<br />
To draw multiple lines, you can type<br />
<pre><br />
gnuplot> plot "A" using 1:2 title "data A" with lines, \<br />
"B" u 1:2 t "data B" with p, \<br />
"C" u 2:3 t "data C" w d<br />
</pre><br />
You can use \ to separate continuous lines. <tt>title</tt> is used to label different lines. You can abbreviate some of the commands, for example, u for using, t for title, w for with, l for lines, p for points and d for dots.<br />
<br />
To change the labels of X and Y axes, you can use<br />
<pre><br />
gnuplot> set xlabel "x-axis"<br />
gnuplot> set ylabel "y-xais"<br />
gnuplot> set title "y vs x"<br />
gnuplot> replot<br />
</pre><br />
<br />
You can also change the ranges of X and Y axes,<br />
<pre><br />
gnuplot> set xrange [0:2]<br />
gnuplot> set yrange [0:1]<br />
gnuplot> replot<br />
</pre><br />
<br />
To assign the color of the line(line type), you need to add corresponding number after "l". For example, black solid(-1), black dot(0), red(1), green (2), blue(3), margenta(4), cyan(5) and yellow(6). To modify the width of the line at the same time, you can use option "w l lt 2 lw 4", for instance, where lt means linetype and lw means linewidth.<br />
<br />
==How to visualize the results==<br />
To visualize the simulation results, here are two methods. One is to run simulation interactively one one CPU and perform observation. The other is to record the configuration at certain simulation steps and make movies from them.<br />
===xwindow===<br />
Make sure x11 server is enabled for the session(test by "xclock"; using <tt>ssh -X username@domain</tt> when you log into clusters) and the ParaDiS code is compiled for single CPU("MODE = SERIAL, XLIB_MODE = ON" in makefile.setup). Check the following setting in <tt>/inputs/paradis.xdefaults</tt> if you set it as "winDefaultsFile" in your ctrl file.<br />
<pre><br />
enable_window = 1 <br />
</pre><br />
By executing<br />
<pre><br />
bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl<br />
</pre><br />
You should be able to see the xwindow. By setting "maxstep = 0" in the ctrl file, you can obtain the configuration (snapshot) for any given simulation step. When the simulation step is large, you might want to consider the other method.<br />
<br />
===Atomeye===<br />
Atomeye is a powerful visualization tool. To enable Atomeye, you need to add following lines in the ctrl file<br />
<pre><br />
atomeye = 1<br />
atomeyefreq = 1<br />
atomeyesegradius = 5<br />
</pre><br />
To view atomeye files, you can use command<br />
<pre><br />
$ tools/atomeye/A.i686 outputs/filename/atomeye/paradis0001.cfg<br />
</pre><br />
To create jpg files press y to convert all cfg files in the same directory. <br />
<br />
To convert these jpg files to a movie, the command is<br />
<pre><br />
$ convert -delay 4 -quality 95 *.jpg mymovie.mpg<br />
</pre><br />
where -delay and -quality flags are optional; if -delay > 4, extra frames are added to make the movie run more slowly; default quality is 75 and the maximum is 100. Note that encode packages need to be preinstalled for the machine or cluster.<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
In a typical pbs file, we have following lines as header:<br />
<br />
<pre><br />
#!/bin/bash<br />
#PBS -N jobname<br />
#PBS -j oe<br />
#PBS -l nodes=8:ppn=8,walltime=24:00:00<br />
#PBS -V<br />
<br />
### ---------------------------------------<br />
### BEGINNING OF EXECUTION<br />
### ---------------------------------------<br />
<br />
echo The master node of this job is `hostname`<br />
echo The working directory is `echo $PBS_O_WORKDIR`<br />
echo This job runs on the following nodes:<br />
echo `cat $PBS_NODEFILE`<br />
<br />
ncpu=`cat $PBS_NODEFILE | wc -w`<br />
echo "Number of processors = $ncpu "<br />
### end of information preamble<br />
<br />
cd $PBS_O_WORKDIR<br />
<br />
echo $PWD<br />
<br />
#cmd="mpiexec -np $ncpu bin/meam-lammps_mpich scripts/work/si_ge/si-meam-lammps.tcl"<br />
#time $cmd<br />
</pre><br />
<br />
You need to set the job name, wait time, number of nodes and ppn (number of processors per node, for example, ppn = 8 for wcr clusters)<br />
<br />
To submit jobs using a single processor, you need to add the following line<br />
<pre><br />
#bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl &> serial.out<br />
</pre><br />
where log file is <tt>serial.out</tt>.<br />
<br />
For parallel jobs, add<br />
<pre><br />
#mpiexec -np $ncpu bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl &> parallel.out<br />
</pre><br />
where log file is <tt>parallel.out</tt>.<br />
<br />
===What if the job is stopped===<br />
You can continue from the stored files under directory <tt>outputs/filename/restart</tt> by<br />
<pre><br />
$bin/paradis outputs/filename/restart/restart.cn<br />
</pre></div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5039ParaDiS Manual Updated2011-01-13T01:42:12Z<p>Jieyin: </p>
<hr />
<div>Written by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. <br />
<br />
While reading this document, don't forget to check out [[paradis.stanford.edu]] for a complete and searchable table of parameters in ParaDiS code (some parameter names are not up-to-date). Detailed descriptions can be found in the official documentation ParaDiSInfo.txt.<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following structures exist<br />
<pre><br />
dataFileVersion = 4<br />
numFileSegments = 1<br />
minCoordinates = [<br />
-4.000000e+003<br />
-4.000000e+003<br />
-4.000000e+003<br />
]<br />
maxCoordinates = [<br />
4.000000e+003<br />
4.000000e+003<br />
4.000000e+003<br />
]<br />
nodeCount = 192<br />
dataDecompType = 1<br />
dataDecompGeometry = [<br />
1<br />
1<br />
1<br />
]<br />
domainDecomposition =<br />
-4.000000e+003<br />
-4.000000e+003<br />
-4.000000e+003<br />
4.000000e+003<br />
4.000000e+003<br />
4.000000e+003<br />
<br />
#<br />
# Primary lines: node_tag, x, y, z, num_arms, constraint<br />
# Secondary lines: arm_tag, burgx, burgy, burgz, nx, ny, nz<br />
#<br />
# length in unit of burgMag<br />
<br />
nodalData =<br />
0,0 3.52197261266669e+003 -2.10366848600532e+003 8.35974608889734e+002 2 7<br />
0,1 -0.707107 0.707107 0 1 1 1<br />
0,15 0.707107 -0.707107 0 -0.408248 -0.408248 0.816497<br />
...<br />
</pre><br />
<br />
You need to set your own data file parameters, usually including minCoordinates, maxCoordinates, nodeCount, domainDecomposition and nodalData. The nodalData is a long array of data. You may want to create it from Matlab if there exists too many nodes in your simulation box.<br />
<br />
===How to set up ctrl-file===<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
Gnuplot is a useful plotting software. You can plot the obtained properties data with gnupot, for example, stress vs strain curve. Before using gnuplot, make sure it is installed on your cluster. You also need to enable X server (test by typing <tt>xclock</tt>). By typing <tt>gnuplot</tt>, you can start using following command lines. For a given (X,Y) data pair, the gnuplot command is<br />
<pre><br />
gnuplot> plot "filename" using 1:2 with lines<br />
</pre><br />
where "using 1:2" means plotting using the 1st and 2nd column from the given data file. "with lines" is a style option, you can change to "with points", "with steps", "with dots" or "with impulses". Click [http://t16web.lanl.gov/Kawano/gnuplot/intro/style-e.html] for a detailed description of the styles.<br />
To draw multiple lines, you can type<br />
<pre><br />
gnuplot> plot "A" using 1:2 title "data A" with lines, \<br />
"B" u 1:2 t "data B" with p, \<br />
"C" u 2:3 t "data C" w d<br />
</pre><br />
You can use \ to separate continuous lines. <tt>title</tt> is used to label different lines. You can abbreviate some of the commands, for example, u for using, t for title, w for with, l for lines, p for points and d for dots.<br />
<br />
To change the labels of X and Y axes, you can use<br />
<pre><br />
gnuplot> set xlabel "x-axis"<br />
gnuplot> set ylabel "y-xais"<br />
gnuplot> set title "y vs x"<br />
gnuplot> replot<br />
</pre><br />
<br />
You can also change the ranges of X and Y axes,<br />
<pre><br />
gnuplot> set xrange [0:2]<br />
gnuplot> set yrange [0:1]<br />
gnuplot> replot<br />
</pre><br />
<br />
To assign the color of the line(line type), you need to add corresponding number after "l". For example, black solid(-1), black dot(0), red(1), green (2), blue(3), margenta(4), cyan(5) and yellow(6). To modify the width of the line at the same time, you can use option "w l lt 2 lw 4", for instance, where lt means linetype and lw means linewidth.<br />
<br />
==How to visualize the results==<br />
To visualize the simulation results, here are two methods. One is to run simulation interactively one one CPU and perform observation. The other is to record the configuration at certain simulation steps and make movies from them.<br />
===xwindow===<br />
Make sure x11 server is enabled for the session(test by "xclock"; using <tt>ssh -X username@domain</tt> when you log into clusters) and the ParaDiS code is compiled for single CPU("MODE = SERIAL, XLIB_MODE = ON" in makefile.setup). Check the following setting in <tt>/inputs/paradis.xdefaults</tt> if you set it as "winDefaultsFile" in your ctrl file.<br />
<pre><br />
enable_window = 1 <br />
</pre><br />
By executing<br />
<pre><br />
bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl<br />
</pre><br />
You should be able to see the xwindow. By setting "maxstep = 0" in the ctrl file, you can obtain the configuration (snapshot) for any given simulation step. When the simulation step is large, you might want to consider the other method.<br />
<br />
===Atomeye===<br />
Atomeye is a powerful visualization tool. To enable Atomeye, you need to add following lines in the ctrl file<br />
<pre><br />
atomeye = 1<br />
atomeyefreq = 1<br />
atomeyesegradius = 5<br />
</pre><br />
To view atomeye files, you can use command<br />
<pre><br />
$ tools/atomeye/A.i686 outputs/filename/atomeye/paradis0001.cfg<br />
</pre><br />
To create jpg files press y to convert all cfg files in the same directory. <br />
<br />
To convert these jpg files to a movie, the command is<br />
<pre><br />
$ convert -delay 4 -quality 95 *.jpg mymovie.mpg<br />
</pre><br />
where -delay and -quality flags are optional; if -delay > 4, extra frames are added to make the movie run more slowly; default quality is 75 and the maximum is 100. Note that encode packages need to be preinstalled for the machine or cluster.<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
In a typical pbs file, we have following lines as header:<br />
<br />
<pre><br />
#!/bin/bash<br />
#PBS -N jobname<br />
#PBS -j oe<br />
#PBS -l nodes=8:ppn=8,walltime=24:00:00<br />
#PBS -V<br />
<br />
### ---------------------------------------<br />
### BEGINNING OF EXECUTION<br />
### ---------------------------------------<br />
<br />
echo The master node of this job is `hostname`<br />
echo The working directory is `echo $PBS_O_WORKDIR`<br />
echo This job runs on the following nodes:<br />
echo `cat $PBS_NODEFILE`<br />
<br />
ncpu=`cat $PBS_NODEFILE | wc -w`<br />
echo "Number of processors = $ncpu "<br />
### end of information preamble<br />
<br />
cd $PBS_O_WORKDIR<br />
<br />
echo $PWD<br />
<br />
#cmd="mpiexec -np $ncpu bin/meam-lammps_mpich scripts/work/si_ge/si-meam-lammps.tcl"<br />
#time $cmd<br />
</pre><br />
<br />
You need to set the job name, wait time, number of nodes and ppn (number of processors per node, for example, ppn = 8 for wcr clusters)<br />
<br />
To submit jobs using a single processor, you need to add the following line<br />
<pre><br />
#bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl &> serial.out<br />
</pre><br />
where log file is <tt>serial.out</tt>.<br />
<br />
For parallel jobs, add<br />
<pre><br />
#mpiexec -np $ncpu bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl &> parallel.out<br />
</pre><br />
where log file is <tt>parallel.out</tt>.<br />
<br />
===What if the job is stopped===<br />
You can continue from the stored files under directory <tt>outputs/filename/restart</tt> by<br />
<pre><br />
$bin/paradis outputs/filename/restart/restart.cn<br />
</pre></div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5038ParaDiS Manual Updated2011-01-13T01:40:47Z<p>Jieyin: /* How to obtain the latest ParaDiS codes */</p>
<hr />
<div>Under construction by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. This guide includes following how-tos:<br />
<br />
While reading this document, don't forget to check out paradis.stanford.edu for a complete and searchable table of parameters in ParaDiS code (some parameter names are not up-to-date). Detailed descriptions can be found in the official documentation ParaDiSInfo.txt.<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following structures exist<br />
<pre><br />
dataFileVersion = 4<br />
numFileSegments = 1<br />
minCoordinates = [<br />
-4.000000e+003<br />
-4.000000e+003<br />
-4.000000e+003<br />
]<br />
maxCoordinates = [<br />
4.000000e+003<br />
4.000000e+003<br />
4.000000e+003<br />
]<br />
nodeCount = 192<br />
dataDecompType = 1<br />
dataDecompGeometry = [<br />
1<br />
1<br />
1<br />
]<br />
domainDecomposition =<br />
-4.000000e+003<br />
-4.000000e+003<br />
-4.000000e+003<br />
4.000000e+003<br />
4.000000e+003<br />
4.000000e+003<br />
<br />
#<br />
# Primary lines: node_tag, x, y, z, num_arms, constraint<br />
# Secondary lines: arm_tag, burgx, burgy, burgz, nx, ny, nz<br />
#<br />
# length in unit of burgMag<br />
<br />
nodalData =<br />
0,0 3.52197261266669e+003 -2.10366848600532e+003 8.35974608889734e+002 2 7<br />
0,1 -0.707107 0.707107 0 1 1 1<br />
0,15 0.707107 -0.707107 0 -0.408248 -0.408248 0.816497<br />
...<br />
</pre><br />
<br />
You need to set your own data file parameters, usually including minCoordinates, maxCoordinates, nodeCount, domainDecomposition and nodalData. The nodalData is a long array of data. You may want to create it from Matlab if there exists too many nodes in your simulation box.<br />
<br />
===How to set up ctrl-file===<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
Gnuplot is a useful plotting software. You can plot the obtained properties data with gnupot, for example, stress vs strain curve. Before using gnuplot, make sure it is installed on your cluster. You also need to enable X server (test by typing <tt>xclock</tt>). By typing <tt>gnuplot</tt>, you can start using following command lines. For a given (X,Y) data pair, the gnuplot command is<br />
<pre><br />
gnuplot> plot "filename" using 1:2 with lines<br />
</pre><br />
where "using 1:2" means plotting using the 1st and 2nd column from the given data file. "with lines" is a style option, you can change to "with points", "with steps", "with dots" or "with impulses". Click [http://t16web.lanl.gov/Kawano/gnuplot/intro/style-e.html] for a detailed description of the styles.<br />
To draw multiple lines, you can type<br />
<pre><br />
gnuplot> plot "A" using 1:2 title "data A" with lines, \<br />
"B" u 1:2 t "data B" with p, \<br />
"C" u 2:3 t "data C" w d<br />
</pre><br />
You can use \ to separate continuous lines. <tt>title</tt> is used to label different lines. You can abbreviate some of the commands, for example, u for using, t for title, w for with, l for lines, p for points and d for dots.<br />
<br />
To change the labels of X and Y axes, you can use<br />
<pre><br />
gnuplot> set xlabel "x-axis"<br />
gnuplot> set ylabel "y-xais"<br />
gnuplot> set title "y vs x"<br />
gnuplot> replot<br />
</pre><br />
<br />
You can also change the ranges of X and Y axes,<br />
<pre><br />
gnuplot> set xrange [0:2]<br />
gnuplot> set yrange [0:1]<br />
gnuplot> replot<br />
</pre><br />
<br />
To assign the color of the line(line type), you need to add corresponding number after "l". For example, black solid(-1), black dot(0), red(1), green (2), blue(3), margenta(4), cyan(5) and yellow(6). To modify the width of the line at the same time, you can use option "w l lt 2 lw 4", for instance, where lt means linetype and lw means linewidth.<br />
<br />
==How to visualize the results==<br />
To visualize the simulation results, here are two methods. One is to run simulation interactively one one CPU and perform observation. The other is to record the configuration at certain simulation steps and make movies from them.<br />
===xwindow===<br />
Make sure x11 server is enabled for the session(test by "xclock"; using <tt>ssh -X username@domain</tt> when you log into clusters) and the ParaDiS code is compiled for single CPU("MODE = SERIAL, XLIB_MODE = ON" in makefile.setup). Check the following setting in <tt>/inputs/paradis.xdefaults</tt> if you set it as "winDefaultsFile" in your ctrl file.<br />
<pre><br />
enable_window = 1 <br />
</pre><br />
By executing<br />
<pre><br />
bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl<br />
</pre><br />
You should be able to see the xwindow. By setting "maxstep = 0" in the ctrl file, you can obtain the configuration (snapshot) for any given simulation step. When the simulation step is large, you might want to consider the other method.<br />
<br />
===Atomeye===<br />
Atomeye is a powerful visualization tool. To enable Atomeye, you need to add following lines in the ctrl file<br />
<pre><br />
atomeye = 1<br />
atomeyefreq = 1<br />
atomeyesegradius = 5<br />
</pre><br />
To view atomeye files, you can use command<br />
<pre><br />
$ tools/atomeye/A.i686 outputs/filename/atomeye/paradis0001.cfg<br />
</pre><br />
To create jpg files press y to convert all cfg files in the same directory. <br />
<br />
To convert these jpg files to a movie, the command is<br />
<pre><br />
$ convert -delay 4 -quality 95 *.jpg mymovie.mpg<br />
</pre><br />
where -delay and -quality flags are optional; if -delay > 4, extra frames are added to make the movie run more slowly; default quality is 75 and the maximum is 100. Note that encode packages need to be preinstalled for the machine or cluster.<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
In a typical pbs file, we have following lines as header:<br />
<br />
<pre><br />
#!/bin/bash<br />
#PBS -N jobname<br />
#PBS -j oe<br />
#PBS -l nodes=8:ppn=8,walltime=24:00:00<br />
#PBS -V<br />
<br />
### ---------------------------------------<br />
### BEGINNING OF EXECUTION<br />
### ---------------------------------------<br />
<br />
echo The master node of this job is `hostname`<br />
echo The working directory is `echo $PBS_O_WORKDIR`<br />
echo This job runs on the following nodes:<br />
echo `cat $PBS_NODEFILE`<br />
<br />
ncpu=`cat $PBS_NODEFILE | wc -w`<br />
echo "Number of processors = $ncpu "<br />
### end of information preamble<br />
<br />
cd $PBS_O_WORKDIR<br />
<br />
echo $PWD<br />
<br />
#cmd="mpiexec -np $ncpu bin/meam-lammps_mpich scripts/work/si_ge/si-meam-lammps.tcl"<br />
#time $cmd<br />
</pre><br />
<br />
You need to set the job name, wait time, number of nodes and ppn (number of processors per node, for example, ppn = 8 for wcr clusters)<br />
<br />
To submit jobs using a single processor, you need to add the following line<br />
<pre><br />
#bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl &> serial.out<br />
</pre><br />
where log file is <tt>serial.out</tt>.<br />
<br />
For parallel jobs, add<br />
<pre><br />
#mpiexec -np $ncpu bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl &> parallel.out<br />
</pre><br />
where log file is <tt>parallel.out</tt>.<br />
<br />
===What if the job is stopped===<br />
You can continue from the stored files under directory <tt>outputs/filename/restart</tt> by<br />
<pre><br />
$bin/paradis outputs/filename/restart/restart.cn<br />
</pre></div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5037ParaDiS Manual Updated2011-01-13T01:38:19Z<p>Jieyin: /* How to set up data-file */</p>
<hr />
<div>Under construction by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. This guide includes following how-tos:<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following structures exist<br />
<pre><br />
dataFileVersion = 4<br />
numFileSegments = 1<br />
minCoordinates = [<br />
-4.000000e+003<br />
-4.000000e+003<br />
-4.000000e+003<br />
]<br />
maxCoordinates = [<br />
4.000000e+003<br />
4.000000e+003<br />
4.000000e+003<br />
]<br />
nodeCount = 192<br />
dataDecompType = 1<br />
dataDecompGeometry = [<br />
1<br />
1<br />
1<br />
]<br />
domainDecomposition =<br />
-4.000000e+003<br />
-4.000000e+003<br />
-4.000000e+003<br />
4.000000e+003<br />
4.000000e+003<br />
4.000000e+003<br />
<br />
#<br />
# Primary lines: node_tag, x, y, z, num_arms, constraint<br />
# Secondary lines: arm_tag, burgx, burgy, burgz, nx, ny, nz<br />
#<br />
# length in unit of burgMag<br />
<br />
nodalData =<br />
0,0 3.52197261266669e+003 -2.10366848600532e+003 8.35974608889734e+002 2 7<br />
0,1 -0.707107 0.707107 0 1 1 1<br />
0,15 0.707107 -0.707107 0 -0.408248 -0.408248 0.816497<br />
...<br />
</pre><br />
<br />
You need to set your own data file parameters, usually including minCoordinates, maxCoordinates, nodeCount, domainDecomposition and nodalData. The nodalData is a long array of data. You may want to create it from Matlab if there exists too many nodes in your simulation box.<br />
<br />
===How to set up ctrl-file===<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
Gnuplot is a useful plotting software. You can plot the obtained properties data with gnupot, for example, stress vs strain curve. Before using gnuplot, make sure it is installed on your cluster. You also need to enable X server (test by typing <tt>xclock</tt>). By typing <tt>gnuplot</tt>, you can start using following command lines. For a given (X,Y) data pair, the gnuplot command is<br />
<pre><br />
gnuplot> plot "filename" using 1:2 with lines<br />
</pre><br />
where "using 1:2" means plotting using the 1st and 2nd column from the given data file. "with lines" is a style option, you can change to "with points", "with steps", "with dots" or "with impulses". Click [http://t16web.lanl.gov/Kawano/gnuplot/intro/style-e.html] for a detailed description of the styles.<br />
To draw multiple lines, you can type<br />
<pre><br />
gnuplot> plot "A" using 1:2 title "data A" with lines, \<br />
"B" u 1:2 t "data B" with p, \<br />
"C" u 2:3 t "data C" w d<br />
</pre><br />
You can use \ to separate continuous lines. <tt>title</tt> is used to label different lines. You can abbreviate some of the commands, for example, u for using, t for title, w for with, l for lines, p for points and d for dots.<br />
<br />
To change the labels of X and Y axes, you can use<br />
<pre><br />
gnuplot> set xlabel "x-axis"<br />
gnuplot> set ylabel "y-xais"<br />
gnuplot> set title "y vs x"<br />
gnuplot> replot<br />
</pre><br />
<br />
You can also change the ranges of X and Y axes,<br />
<pre><br />
gnuplot> set xrange [0:2]<br />
gnuplot> set yrange [0:1]<br />
gnuplot> replot<br />
</pre><br />
<br />
To assign the color of the line(line type), you need to add corresponding number after "l". For example, black solid(-1), black dot(0), red(1), green (2), blue(3), margenta(4), cyan(5) and yellow(6). To modify the width of the line at the same time, you can use option "w l lt 2 lw 4", for instance, where lt means linetype and lw means linewidth.<br />
<br />
==How to visualize the results==<br />
To visualize the simulation results, here are two methods. One is to run simulation interactively one one CPU and perform observation. The other is to record the configuration at certain simulation steps and make movies from them.<br />
===xwindow===<br />
Make sure x11 server is enabled for the session(test by "xclock"; using <tt>ssh -X username@domain</tt> when you log into clusters) and the ParaDiS code is compiled for single CPU("MODE = SERIAL, XLIB_MODE = ON" in makefile.setup). Check the following setting in <tt>/inputs/paradis.xdefaults</tt> if you set it as "winDefaultsFile" in your ctrl file.<br />
<pre><br />
enable_window = 1 <br />
</pre><br />
By executing<br />
<pre><br />
bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl<br />
</pre><br />
You should be able to see the xwindow. By setting "maxstep = 0" in the ctrl file, you can obtain the configuration (snapshot) for any given simulation step. When the simulation step is large, you might want to consider the other method.<br />
<br />
===Atomeye===<br />
Atomeye is a powerful visualization tool. To enable Atomeye, you need to add following lines in the ctrl file<br />
<pre><br />
atomeye = 1<br />
atomeyefreq = 1<br />
atomeyesegradius = 5<br />
</pre><br />
To view atomeye files, you can use command<br />
<pre><br />
$ tools/atomeye/A.i686 outputs/filename/atomeye/paradis0001.cfg<br />
</pre><br />
To create jpg files press y to convert all cfg files in the same directory. <br />
<br />
To convert these jpg files to a movie, the command is<br />
<pre><br />
$ convert -delay 4 -quality 95 *.jpg mymovie.mpg<br />
</pre><br />
where -delay and -quality flags are optional; if -delay > 4, extra frames are added to make the movie run more slowly; default quality is 75 and the maximum is 100. Note that encode packages need to be preinstalled for the machine or cluster.<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
In a typical pbs file, we have following lines as header:<br />
<br />
<pre><br />
#!/bin/bash<br />
#PBS -N jobname<br />
#PBS -j oe<br />
#PBS -l nodes=8:ppn=8,walltime=24:00:00<br />
#PBS -V<br />
<br />
### ---------------------------------------<br />
### BEGINNING OF EXECUTION<br />
### ---------------------------------------<br />
<br />
echo The master node of this job is `hostname`<br />
echo The working directory is `echo $PBS_O_WORKDIR`<br />
echo This job runs on the following nodes:<br />
echo `cat $PBS_NODEFILE`<br />
<br />
ncpu=`cat $PBS_NODEFILE | wc -w`<br />
echo "Number of processors = $ncpu "<br />
### end of information preamble<br />
<br />
cd $PBS_O_WORKDIR<br />
<br />
echo $PWD<br />
<br />
#cmd="mpiexec -np $ncpu bin/meam-lammps_mpich scripts/work/si_ge/si-meam-lammps.tcl"<br />
#time $cmd<br />
</pre><br />
<br />
You need to set the job name, wait time, number of nodes and ppn (number of processors per node, for example, ppn = 8 for wcr clusters)<br />
<br />
To submit jobs using a single processor, you need to add the following line<br />
<pre><br />
#bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl &> serial.out<br />
</pre><br />
where log file is <tt>serial.out</tt>.<br />
<br />
For parallel jobs, add<br />
<pre><br />
#mpiexec -np $ncpu bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl &> parallel.out<br />
</pre><br />
where log file is <tt>parallel.out</tt>.<br />
<br />
===What if the job is stopped===<br />
You can continue from the stored files under directory <tt>outputs/filename/restart</tt> by<br />
<pre><br />
$bin/paradis outputs/filename/restart/restart.cn<br />
</pre></div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5036ParaDiS Manual Updated2011-01-13T01:37:12Z<p>Jieyin: /* How to set up data-file */</p>
<hr />
<div>Under construction by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. This guide includes following how-tos:<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following structures exist<br />
<pre><br />
dataFileVersion = 4<br />
numFileSegments = 1<br />
minCoordinates = [<br />
-4.000000e+003<br />
-4.000000e+003<br />
-4.000000e+003<br />
]<br />
maxCoordinates = [<br />
4.000000e+003<br />
4.000000e+003<br />
4.000000e+003<br />
]<br />
nodeCount = 192<br />
dataDecompType = 1<br />
dataDecompGeometry = [<br />
1<br />
1<br />
1<br />
]<br />
domainDecomposition =<br />
-4.000000e+003<br />
-4.000000e+003<br />
-4.000000e+003<br />
4.000000e+003<br />
4.000000e+003<br />
4.000000e+003<br />
<br />
#<br />
# Primary lines: node_tag, x, y, z, num_arms, constraint<br />
# Secondary lines: arm_tag, burgx, burgy, burgz, nx, ny, nz<br />
#<br />
# length in unit of burgMag<br />
<br />
nodalData =<br />
0,0 3.52197261266669e+003 -2.10366848600532e+003 8.35974608889734e+002 2 7<br />
0,1 -0.707107 0.707107 0<br />
1 1 1<br />
0,15 0.707107 -0.707107 0<br />
-0.408248 -0.408248 0.816497<br />
</pre><br />
<br />
You need to set your own data file parameters, usually including minCoordinates, maxCoordinates, nodeCount, domainDecomposition and nodalData. The nodalData is a long array of data. You may want to create it from Matlab if there exists too many nodes in your simulation box.<br />
<br />
===How to set up ctrl-file===<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
Gnuplot is a useful plotting software. You can plot the obtained properties data with gnupot, for example, stress vs strain curve. Before using gnuplot, make sure it is installed on your cluster. You also need to enable X server (test by typing <tt>xclock</tt>). By typing <tt>gnuplot</tt>, you can start using following command lines. For a given (X,Y) data pair, the gnuplot command is<br />
<pre><br />
gnuplot> plot "filename" using 1:2 with lines<br />
</pre><br />
where "using 1:2" means plotting using the 1st and 2nd column from the given data file. "with lines" is a style option, you can change to "with points", "with steps", "with dots" or "with impulses". Click [http://t16web.lanl.gov/Kawano/gnuplot/intro/style-e.html] for a detailed description of the styles.<br />
To draw multiple lines, you can type<br />
<pre><br />
gnuplot> plot "A" using 1:2 title "data A" with lines, \<br />
"B" u 1:2 t "data B" with p, \<br />
"C" u 2:3 t "data C" w d<br />
</pre><br />
You can use \ to separate continuous lines. <tt>title</tt> is used to label different lines. You can abbreviate some of the commands, for example, u for using, t for title, w for with, l for lines, p for points and d for dots.<br />
<br />
To change the labels of X and Y axes, you can use<br />
<pre><br />
gnuplot> set xlabel "x-axis"<br />
gnuplot> set ylabel "y-xais"<br />
gnuplot> set title "y vs x"<br />
gnuplot> replot<br />
</pre><br />
<br />
You can also change the ranges of X and Y axes,<br />
<pre><br />
gnuplot> set xrange [0:2]<br />
gnuplot> set yrange [0:1]<br />
gnuplot> replot<br />
</pre><br />
<br />
To assign the color of the line(line type), you need to add corresponding number after "l". For example, black solid(-1), black dot(0), red(1), green (2), blue(3), margenta(4), cyan(5) and yellow(6). To modify the width of the line at the same time, you can use option "w l lt 2 lw 4", for instance, where lt means linetype and lw means linewidth.<br />
<br />
==How to visualize the results==<br />
To visualize the simulation results, here are two methods. One is to run simulation interactively one one CPU and perform observation. The other is to record the configuration at certain simulation steps and make movies from them.<br />
===xwindow===<br />
Make sure x11 server is enabled for the session(test by "xclock"; using <tt>ssh -X username@domain</tt> when you log into clusters) and the ParaDiS code is compiled for single CPU("MODE = SERIAL, XLIB_MODE = ON" in makefile.setup). Check the following setting in <tt>/inputs/paradis.xdefaults</tt> if you set it as "winDefaultsFile" in your ctrl file.<br />
<pre><br />
enable_window = 1 <br />
</pre><br />
By executing<br />
<pre><br />
bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl<br />
</pre><br />
You should be able to see the xwindow. By setting "maxstep = 0" in the ctrl file, you can obtain the configuration (snapshot) for any given simulation step. When the simulation step is large, you might want to consider the other method.<br />
<br />
===Atomeye===<br />
Atomeye is a powerful visualization tool. To enable Atomeye, you need to add following lines in the ctrl file<br />
<pre><br />
atomeye = 1<br />
atomeyefreq = 1<br />
atomeyesegradius = 5<br />
</pre><br />
To view atomeye files, you can use command<br />
<pre><br />
$ tools/atomeye/A.i686 outputs/filename/atomeye/paradis0001.cfg<br />
</pre><br />
To create jpg files press y to convert all cfg files in the same directory. <br />
<br />
To convert these jpg files to a movie, the command is<br />
<pre><br />
$ convert -delay 4 -quality 95 *.jpg mymovie.mpg<br />
</pre><br />
where -delay and -quality flags are optional; if -delay > 4, extra frames are added to make the movie run more slowly; default quality is 75 and the maximum is 100. Note that encode packages need to be preinstalled for the machine or cluster.<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
In a typical pbs file, we have following lines as header:<br />
<br />
<pre><br />
#!/bin/bash<br />
#PBS -N jobname<br />
#PBS -j oe<br />
#PBS -l nodes=8:ppn=8,walltime=24:00:00<br />
#PBS -V<br />
<br />
### ---------------------------------------<br />
### BEGINNING OF EXECUTION<br />
### ---------------------------------------<br />
<br />
echo The master node of this job is `hostname`<br />
echo The working directory is `echo $PBS_O_WORKDIR`<br />
echo This job runs on the following nodes:<br />
echo `cat $PBS_NODEFILE`<br />
<br />
ncpu=`cat $PBS_NODEFILE | wc -w`<br />
echo "Number of processors = $ncpu "<br />
### end of information preamble<br />
<br />
cd $PBS_O_WORKDIR<br />
<br />
echo $PWD<br />
<br />
#cmd="mpiexec -np $ncpu bin/meam-lammps_mpich scripts/work/si_ge/si-meam-lammps.tcl"<br />
#time $cmd<br />
</pre><br />
<br />
You need to set the job name, wait time, number of nodes and ppn (number of processors per node, for example, ppn = 8 for wcr clusters)<br />
<br />
To submit jobs using a single processor, you need to add the following line<br />
<pre><br />
#bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl &> serial.out<br />
</pre><br />
where log file is <tt>serial.out</tt>.<br />
<br />
For parallel jobs, add<br />
<pre><br />
#mpiexec -np $ncpu bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl &> parallel.out<br />
</pre><br />
where log file is <tt>parallel.out</tt>.<br />
<br />
===What if the job is stopped===<br />
You can continue from the stored files under directory <tt>outputs/filename/restart</tt> by<br />
<pre><br />
$bin/paradis outputs/filename/restart/restart.cn<br />
</pre></div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5035ParaDiS Manual Updated2011-01-13T01:30:29Z<p>Jieyin: /* xwindow */</p>
<hr />
<div>Under construction by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. This guide includes following how-tos:<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following lines exist<br />
<br />
===How to set up ctrl-file===<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
Gnuplot is a useful plotting software. You can plot the obtained properties data with gnupot, for example, stress vs strain curve. Before using gnuplot, make sure it is installed on your cluster. You also need to enable X server (test by typing <tt>xclock</tt>). By typing <tt>gnuplot</tt>, you can start using following command lines. For a given (X,Y) data pair, the gnuplot command is<br />
<pre><br />
gnuplot> plot "filename" using 1:2 with lines<br />
</pre><br />
where "using 1:2" means plotting using the 1st and 2nd column from the given data file. "with lines" is a style option, you can change to "with points", "with steps", "with dots" or "with impulses". Click [http://t16web.lanl.gov/Kawano/gnuplot/intro/style-e.html] for a detailed description of the styles.<br />
To draw multiple lines, you can type<br />
<pre><br />
gnuplot> plot "A" using 1:2 title "data A" with lines, \<br />
"B" u 1:2 t "data B" with p, \<br />
"C" u 2:3 t "data C" w d<br />
</pre><br />
You can use \ to separate continuous lines. <tt>title</tt> is used to label different lines. You can abbreviate some of the commands, for example, u for using, t for title, w for with, l for lines, p for points and d for dots.<br />
<br />
To change the labels of X and Y axes, you can use<br />
<pre><br />
gnuplot> set xlabel "x-axis"<br />
gnuplot> set ylabel "y-xais"<br />
gnuplot> set title "y vs x"<br />
gnuplot> replot<br />
</pre><br />
<br />
You can also change the ranges of X and Y axes,<br />
<pre><br />
gnuplot> set xrange [0:2]<br />
gnuplot> set yrange [0:1]<br />
gnuplot> replot<br />
</pre><br />
<br />
To assign the color of the line(line type), you need to add corresponding number after "l". For example, black solid(-1), black dot(0), red(1), green (2), blue(3), margenta(4), cyan(5) and yellow(6). To modify the width of the line at the same time, you can use option "w l lt 2 lw 4", for instance, where lt means linetype and lw means linewidth.<br />
<br />
==How to visualize the results==<br />
To visualize the simulation results, here are two methods. One is to run simulation interactively one one CPU and perform observation. The other is to record the configuration at certain simulation steps and make movies from them.<br />
===xwindow===<br />
Make sure x11 server is enabled for the session(test by "xclock"; using <tt>ssh -X username@domain</tt> when you log into clusters) and the ParaDiS code is compiled for single CPU("MODE = SERIAL, XLIB_MODE = ON" in makefile.setup). Check the following setting in <tt>/inputs/paradis.xdefaults</tt> if you set it as "winDefaultsFile" in your ctrl file.<br />
<pre><br />
enable_window = 1 <br />
</pre><br />
By executing<br />
<pre><br />
bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl<br />
</pre><br />
You should be able to see the xwindow. By setting "maxstep = 0" in the ctrl file, you can obtain the configuration (snapshot) for any given simulation step. When the simulation step is large, you might want to consider the other method.<br />
<br />
===Atomeye===<br />
Atomeye is a powerful visualization tool. To enable Atomeye, you need to add following lines in the ctrl file<br />
<pre><br />
atomeye = 1<br />
atomeyefreq = 1<br />
atomeyesegradius = 5<br />
</pre><br />
To view atomeye files, you can use command<br />
<pre><br />
$ tools/atomeye/A.i686 outputs/filename/atomeye/paradis0001.cfg<br />
</pre><br />
To create jpg files press y to convert all cfg files in the same directory. <br />
<br />
To convert these jpg files to a movie, the command is<br />
<pre><br />
$ convert -delay 4 -quality 95 *.jpg mymovie.mpg<br />
</pre><br />
where -delay and -quality flags are optional; if -delay > 4, extra frames are added to make the movie run more slowly; default quality is 75 and the maximum is 100. Note that encode packages need to be preinstalled for the machine or cluster.<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
In a typical pbs file, we have following lines as header:<br />
<br />
<pre><br />
#!/bin/bash<br />
#PBS -N jobname<br />
#PBS -j oe<br />
#PBS -l nodes=8:ppn=8,walltime=24:00:00<br />
#PBS -V<br />
<br />
### ---------------------------------------<br />
### BEGINNING OF EXECUTION<br />
### ---------------------------------------<br />
<br />
echo The master node of this job is `hostname`<br />
echo The working directory is `echo $PBS_O_WORKDIR`<br />
echo This job runs on the following nodes:<br />
echo `cat $PBS_NODEFILE`<br />
<br />
ncpu=`cat $PBS_NODEFILE | wc -w`<br />
echo "Number of processors = $ncpu "<br />
### end of information preamble<br />
<br />
cd $PBS_O_WORKDIR<br />
<br />
echo $PWD<br />
<br />
#cmd="mpiexec -np $ncpu bin/meam-lammps_mpich scripts/work/si_ge/si-meam-lammps.tcl"<br />
#time $cmd<br />
</pre><br />
<br />
You need to set the job name, wait time, number of nodes and ppn (number of processors per node, for example, ppn = 8 for wcr clusters)<br />
<br />
To submit jobs using a single processor, you need to add the following line<br />
<pre><br />
#bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl &> serial.out<br />
</pre><br />
where log file is <tt>serial.out</tt>.<br />
<br />
For parallel jobs, add<br />
<pre><br />
#mpiexec -np $ncpu bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl &> parallel.out<br />
</pre><br />
where log file is <tt>parallel.out</tt>.<br />
<br />
===What if the job is stopped===<br />
You can continue from the stored files under directory <tt>outputs/filename/restart</tt> by<br />
<pre><br />
$bin/paradis outputs/filename/restart/restart.cn<br />
</pre></div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5034ParaDiS Manual Updated2011-01-13T01:25:38Z<p>Jieyin: /* pbs file */</p>
<hr />
<div>Under construction by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. This guide includes following how-tos:<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following lines exist<br />
<br />
===How to set up ctrl-file===<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
Gnuplot is a useful plotting software. You can plot the obtained properties data with gnupot, for example, stress vs strain curve. Before using gnuplot, make sure it is installed on your cluster. You also need to enable X server (test by typing <tt>xclock</tt>). By typing <tt>gnuplot</tt>, you can start using following command lines. For a given (X,Y) data pair, the gnuplot command is<br />
<pre><br />
gnuplot> plot "filename" using 1:2 with lines<br />
</pre><br />
where "using 1:2" means plotting using the 1st and 2nd column from the given data file. "with lines" is a style option, you can change to "with points", "with steps", "with dots" or "with impulses". Click [http://t16web.lanl.gov/Kawano/gnuplot/intro/style-e.html] for a detailed description of the styles.<br />
To draw multiple lines, you can type<br />
<pre><br />
gnuplot> plot "A" using 1:2 title "data A" with lines, \<br />
"B" u 1:2 t "data B" with p, \<br />
"C" u 2:3 t "data C" w d<br />
</pre><br />
You can use \ to separate continuous lines. <tt>title</tt> is used to label different lines. You can abbreviate some of the commands, for example, u for using, t for title, w for with, l for lines, p for points and d for dots.<br />
<br />
To change the labels of X and Y axes, you can use<br />
<pre><br />
gnuplot> set xlabel "x-axis"<br />
gnuplot> set ylabel "y-xais"<br />
gnuplot> set title "y vs x"<br />
gnuplot> replot<br />
</pre><br />
<br />
You can also change the ranges of X and Y axes,<br />
<pre><br />
gnuplot> set xrange [0:2]<br />
gnuplot> set yrange [0:1]<br />
gnuplot> replot<br />
</pre><br />
<br />
To assign the color of the line(line type), you need to add corresponding number after "l". For example, black solid(-1), black dot(0), red(1), green (2), blue(3), margenta(4), cyan(5) and yellow(6). To modify the width of the line at the same time, you can use option "w l lt 2 lw 4", for instance, where lt means linetype and lw means linewidth.<br />
<br />
==How to visualize the results==<br />
To visualize the simulation results, here are two methods. One is to run simulation interactively one one CPU and perform observation. The other is to record the configuration at certain simulation steps and make movies from them.<br />
===xwindow===<br />
Make sure x11 server is enabled for the session(test by "xclock") and the ParaDiS code is compiled for single CPU("MODE = SERIAL, XLIB_MODE = ON" in makefile.setup). By executing<br />
<pre><br />
bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl<br />
</pre><br />
You should be able to see the xwindow. By setting "maxstep = 0" in the ctrl file, you can obtain the configuration (snapshot) for any given simulation step. When the simulation step is large, you might want to consider the other method.<br />
<br />
===Atomeye===<br />
Atomeye is a powerful visualization tool. To enable Atomeye, you need to add following lines in the ctrl file<br />
<pre><br />
atomeye = 1<br />
atomeyefreq = 1<br />
atomeyesegradius = 5<br />
</pre><br />
To view atomeye files, you can use command<br />
<pre><br />
$ tools/atomeye/A.i686 outputs/filename/atomeye/paradis0001.cfg<br />
</pre><br />
To create jpg files press y to convert all cfg files in the same directory. <br />
<br />
To convert these jpg files to a movie, the command is<br />
<pre><br />
$ convert -delay 4 -quality 95 *.jpg mymovie.mpg<br />
</pre><br />
where -delay and -quality flags are optional; if -delay > 4, extra frames are added to make the movie run more slowly; default quality is 75 and the maximum is 100. Note that encode packages need to be preinstalled for the machine or cluster.<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
In a typical pbs file, we have following lines as header:<br />
<br />
<pre><br />
#!/bin/bash<br />
#PBS -N jobname<br />
#PBS -j oe<br />
#PBS -l nodes=8:ppn=8,walltime=24:00:00<br />
#PBS -V<br />
<br />
### ---------------------------------------<br />
### BEGINNING OF EXECUTION<br />
### ---------------------------------------<br />
<br />
echo The master node of this job is `hostname`<br />
echo The working directory is `echo $PBS_O_WORKDIR`<br />
echo This job runs on the following nodes:<br />
echo `cat $PBS_NODEFILE`<br />
<br />
ncpu=`cat $PBS_NODEFILE | wc -w`<br />
echo "Number of processors = $ncpu "<br />
### end of information preamble<br />
<br />
cd $PBS_O_WORKDIR<br />
<br />
echo $PWD<br />
<br />
#cmd="mpiexec -np $ncpu bin/meam-lammps_mpich scripts/work/si_ge/si-meam-lammps.tcl"<br />
#time $cmd<br />
</pre><br />
<br />
You need to set the job name, wait time, number of nodes and ppn (number of processors per node, for example, ppn = 8 for wcr clusters)<br />
<br />
To submit jobs using a single processor, you need to add the following line<br />
<pre><br />
#bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl &> serial.out<br />
</pre><br />
where log file is <tt>serial.out</tt>.<br />
<br />
For parallel jobs, add<br />
<pre><br />
#mpiexec -np $ncpu bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl &> parallel.out<br />
</pre><br />
where log file is <tt>parallel.out</tt>.<br />
<br />
===What if the job is stopped===<br />
You can continue from the stored files under directory <tt>outputs/filename/restart</tt> by<br />
<pre><br />
$bin/paradis outputs/filename/restart/restart.cn<br />
</pre></div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5033ParaDiS Manual Updated2011-01-13T01:24:26Z<p>Jieyin: /* What if the job is stopped */</p>
<hr />
<div>Under construction by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. This guide includes following how-tos:<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following lines exist<br />
<br />
===How to set up ctrl-file===<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
Gnuplot is a useful plotting software. You can plot the obtained properties data with gnupot, for example, stress vs strain curve. Before using gnuplot, make sure it is installed on your cluster. You also need to enable X server (test by typing <tt>xclock</tt>). By typing <tt>gnuplot</tt>, you can start using following command lines. For a given (X,Y) data pair, the gnuplot command is<br />
<pre><br />
gnuplot> plot "filename" using 1:2 with lines<br />
</pre><br />
where "using 1:2" means plotting using the 1st and 2nd column from the given data file. "with lines" is a style option, you can change to "with points", "with steps", "with dots" or "with impulses". Click [http://t16web.lanl.gov/Kawano/gnuplot/intro/style-e.html] for a detailed description of the styles.<br />
To draw multiple lines, you can type<br />
<pre><br />
gnuplot> plot "A" using 1:2 title "data A" with lines, \<br />
"B" u 1:2 t "data B" with p, \<br />
"C" u 2:3 t "data C" w d<br />
</pre><br />
You can use \ to separate continuous lines. <tt>title</tt> is used to label different lines. You can abbreviate some of the commands, for example, u for using, t for title, w for with, l for lines, p for points and d for dots.<br />
<br />
To change the labels of X and Y axes, you can use<br />
<pre><br />
gnuplot> set xlabel "x-axis"<br />
gnuplot> set ylabel "y-xais"<br />
gnuplot> set title "y vs x"<br />
gnuplot> replot<br />
</pre><br />
<br />
You can also change the ranges of X and Y axes,<br />
<pre><br />
gnuplot> set xrange [0:2]<br />
gnuplot> set yrange [0:1]<br />
gnuplot> replot<br />
</pre><br />
<br />
To assign the color of the line(line type), you need to add corresponding number after "l". For example, black solid(-1), black dot(0), red(1), green (2), blue(3), margenta(4), cyan(5) and yellow(6). To modify the width of the line at the same time, you can use option "w l lt 2 lw 4", for instance, where lt means linetype and lw means linewidth.<br />
<br />
==How to visualize the results==<br />
To visualize the simulation results, here are two methods. One is to run simulation interactively one one CPU and perform observation. The other is to record the configuration at certain simulation steps and make movies from them.<br />
===xwindow===<br />
Make sure x11 server is enabled for the session(test by "xclock") and the ParaDiS code is compiled for single CPU("MODE = SERIAL, XLIB_MODE = ON" in makefile.setup). By executing<br />
<pre><br />
bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl<br />
</pre><br />
You should be able to see the xwindow. By setting "maxstep = 0" in the ctrl file, you can obtain the configuration (snapshot) for any given simulation step. When the simulation step is large, you might want to consider the other method.<br />
<br />
===Atomeye===<br />
Atomeye is a powerful visualization tool. To enable Atomeye, you need to add following lines in the ctrl file<br />
<pre><br />
atomeye = 1<br />
atomeyefreq = 1<br />
atomeyesegradius = 5<br />
</pre><br />
To view atomeye files, you can use command<br />
<pre><br />
$ tools/atomeye/A.i686 outputs/filename/atomeye/paradis0001.cfg<br />
</pre><br />
To create jpg files press y to convert all cfg files in the same directory. <br />
<br />
To convert these jpg files to a movie, the command is<br />
<pre><br />
$ convert -delay 4 -quality 95 *.jpg mymovie.mpg<br />
</pre><br />
where -delay and -quality flags are optional; if -delay > 4, extra frames are added to make the movie run more slowly; default quality is 75 and the maximum is 100. Note that encode packages need to be preinstalled for the machine or cluster.<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
In a typical pbs file, we have following lines as header:<br />
<br />
<pre><br />
#!/bin/bash<br />
#PBS -N jobname<br />
#PBS -j oe<br />
#PBS -l nodes=8:ppn=8,walltime=24:00:00<br />
#PBS -V<br />
<br />
### ---------------------------------------<br />
### BEGINNING OF EXECUTION<br />
### ---------------------------------------<br />
<br />
echo The master node of this job is `hostname`<br />
echo The working directory is `echo $PBS_O_WORKDIR`<br />
echo This job runs on the following nodes:<br />
echo `cat $PBS_NODEFILE`<br />
<br />
ncpu=`cat $PBS_NODEFILE | wc -w`<br />
echo "Number of processors = $ncpu "<br />
### end of information preamble<br />
<br />
cd $PBS_O_WORKDIR<br />
<br />
echo $PWD<br />
<br />
#cmd="mpiexec -np $ncpu bin/meam-lammps_mpich scripts/work/si_ge/si-meam-lammps.tcl"<br />
#time $cmd<br />
</pre><br />
<br />
You need to set the job name, wait time, number of nodes and ppn (number of processors per node, for example, ppn = 8 for wcr clusters)<br />
<br />
To submit jobs using a single processor, <br />
<pre><br />
#bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl &> serial.out<br />
</pre><br />
<br />
or parallel jobs,<br />
<pre><br />
#mpiexec -np $ncpu bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl &> parallel.out<br />
</pre><br />
<br />
===What if the job is stopped===<br />
You can continue from the stored files under directory <tt>outputs/filename/restart</tt> by<br />
<pre><br />
$bin/paradis outputs/filename/restart/restart.cn<br />
</pre></div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5032ParaDiS Manual Updated2011-01-13T01:20:06Z<p>Jieyin: /* What if the job is stopped */</p>
<hr />
<div>Under construction by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. This guide includes following how-tos:<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following lines exist<br />
<br />
===How to set up ctrl-file===<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
Gnuplot is a useful plotting software. You can plot the obtained properties data with gnupot, for example, stress vs strain curve. Before using gnuplot, make sure it is installed on your cluster. You also need to enable X server (test by typing <tt>xclock</tt>). By typing <tt>gnuplot</tt>, you can start using following command lines. For a given (X,Y) data pair, the gnuplot command is<br />
<pre><br />
gnuplot> plot "filename" using 1:2 with lines<br />
</pre><br />
where "using 1:2" means plotting using the 1st and 2nd column from the given data file. "with lines" is a style option, you can change to "with points", "with steps", "with dots" or "with impulses". Click [http://t16web.lanl.gov/Kawano/gnuplot/intro/style-e.html] for a detailed description of the styles.<br />
To draw multiple lines, you can type<br />
<pre><br />
gnuplot> plot "A" using 1:2 title "data A" with lines, \<br />
"B" u 1:2 t "data B" with p, \<br />
"C" u 2:3 t "data C" w d<br />
</pre><br />
You can use \ to separate continuous lines. <tt>title</tt> is used to label different lines. You can abbreviate some of the commands, for example, u for using, t for title, w for with, l for lines, p for points and d for dots.<br />
<br />
To change the labels of X and Y axes, you can use<br />
<pre><br />
gnuplot> set xlabel "x-axis"<br />
gnuplot> set ylabel "y-xais"<br />
gnuplot> set title "y vs x"<br />
gnuplot> replot<br />
</pre><br />
<br />
You can also change the ranges of X and Y axes,<br />
<pre><br />
gnuplot> set xrange [0:2]<br />
gnuplot> set yrange [0:1]<br />
gnuplot> replot<br />
</pre><br />
<br />
To assign the color of the line(line type), you need to add corresponding number after "l". For example, black solid(-1), black dot(0), red(1), green (2), blue(3), margenta(4), cyan(5) and yellow(6). To modify the width of the line at the same time, you can use option "w l lt 2 lw 4", for instance, where lt means linetype and lw means linewidth.<br />
<br />
==How to visualize the results==<br />
To visualize the simulation results, here are two methods. One is to run simulation interactively one one CPU and perform observation. The other is to record the configuration at certain simulation steps and make movies from them.<br />
===xwindow===<br />
Make sure x11 server is enabled for the session(test by "xclock") and the ParaDiS code is compiled for single CPU("MODE = SERIAL, XLIB_MODE = ON" in makefile.setup). By executing<br />
<pre><br />
bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl<br />
</pre><br />
You should be able to see the xwindow. By setting "maxstep = 0" in the ctrl file, you can obtain the configuration (snapshot) for any given simulation step. When the simulation step is large, you might want to consider the other method.<br />
<br />
===Atomeye===<br />
Atomeye is a powerful visualization tool. To enable Atomeye, you need to add following lines in the ctrl file<br />
<pre><br />
atomeye = 1<br />
atomeyefreq = 1<br />
atomeyesegradius = 5<br />
</pre><br />
To view atomeye files, you can use command<br />
<pre><br />
$ tools/atomeye/A.i686 outputs/filename/atomeye/paradis0001.cfg<br />
</pre><br />
To create jpg files press y to convert all cfg files in the same directory. <br />
<br />
To convert these jpg files to a movie, the command is<br />
<pre><br />
$ convert -delay 4 -quality 95 *.jpg mymovie.mpg<br />
</pre><br />
where -delay and -quality flags are optional; if -delay > 4, extra frames are added to make the movie run more slowly; default quality is 75 and the maximum is 100. Note that encode packages need to be preinstalled for the machine or cluster.<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
In a typical pbs file, we have following lines as header:<br />
<br />
<pre><br />
#!/bin/bash<br />
#PBS -N jobname<br />
#PBS -j oe<br />
#PBS -l nodes=8:ppn=8,walltime=24:00:00<br />
#PBS -V<br />
<br />
### ---------------------------------------<br />
### BEGINNING OF EXECUTION<br />
### ---------------------------------------<br />
<br />
echo The master node of this job is `hostname`<br />
echo The working directory is `echo $PBS_O_WORKDIR`<br />
echo This job runs on the following nodes:<br />
echo `cat $PBS_NODEFILE`<br />
<br />
ncpu=`cat $PBS_NODEFILE | wc -w`<br />
echo "Number of processors = $ncpu "<br />
### end of information preamble<br />
<br />
cd $PBS_O_WORKDIR<br />
<br />
echo $PWD<br />
<br />
#cmd="mpiexec -np $ncpu bin/meam-lammps_mpich scripts/work/si_ge/si-meam-lammps.tcl"<br />
#time $cmd<br />
</pre><br />
<br />
You need to set the job name, wait time, number of nodes and ppn (number of processors per node, for example, ppn = 8 for wcr clusters)<br />
<br />
To submit jobs using a single processor, <br />
<pre><br />
#bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl &> serial.out<br />
</pre><br />
<br />
or parallel jobs,<br />
<pre><br />
#mpiexec -np $ncpu bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl &> parallel.out<br />
</pre><br />
<br />
===What if the job is stopped===<br />
You can continue from the stored restart.data file under directory</div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5031ParaDiS Manual Updated2011-01-13T01:17:01Z<p>Jieyin: /* pbs file */</p>
<hr />
<div>Under construction by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. This guide includes following how-tos:<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following lines exist<br />
<br />
===How to set up ctrl-file===<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
Gnuplot is a useful plotting software. You can plot the obtained properties data with gnupot, for example, stress vs strain curve. Before using gnuplot, make sure it is installed on your cluster. You also need to enable X server (test by typing <tt>xclock</tt>). By typing <tt>gnuplot</tt>, you can start using following command lines. For a given (X,Y) data pair, the gnuplot command is<br />
<pre><br />
gnuplot> plot "filename" using 1:2 with lines<br />
</pre><br />
where "using 1:2" means plotting using the 1st and 2nd column from the given data file. "with lines" is a style option, you can change to "with points", "with steps", "with dots" or "with impulses". Click [http://t16web.lanl.gov/Kawano/gnuplot/intro/style-e.html] for a detailed description of the styles.<br />
To draw multiple lines, you can type<br />
<pre><br />
gnuplot> plot "A" using 1:2 title "data A" with lines, \<br />
"B" u 1:2 t "data B" with p, \<br />
"C" u 2:3 t "data C" w d<br />
</pre><br />
You can use \ to separate continuous lines. <tt>title</tt> is used to label different lines. You can abbreviate some of the commands, for example, u for using, t for title, w for with, l for lines, p for points and d for dots.<br />
<br />
To change the labels of X and Y axes, you can use<br />
<pre><br />
gnuplot> set xlabel "x-axis"<br />
gnuplot> set ylabel "y-xais"<br />
gnuplot> set title "y vs x"<br />
gnuplot> replot<br />
</pre><br />
<br />
You can also change the ranges of X and Y axes,<br />
<pre><br />
gnuplot> set xrange [0:2]<br />
gnuplot> set yrange [0:1]<br />
gnuplot> replot<br />
</pre><br />
<br />
To assign the color of the line(line type), you need to add corresponding number after "l". For example, black solid(-1), black dot(0), red(1), green (2), blue(3), margenta(4), cyan(5) and yellow(6). To modify the width of the line at the same time, you can use option "w l lt 2 lw 4", for instance, where lt means linetype and lw means linewidth.<br />
<br />
==How to visualize the results==<br />
To visualize the simulation results, here are two methods. One is to run simulation interactively one one CPU and perform observation. The other is to record the configuration at certain simulation steps and make movies from them.<br />
===xwindow===<br />
Make sure x11 server is enabled for the session(test by "xclock") and the ParaDiS code is compiled for single CPU("MODE = SERIAL, XLIB_MODE = ON" in makefile.setup). By executing<br />
<pre><br />
bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl<br />
</pre><br />
You should be able to see the xwindow. By setting "maxstep = 0" in the ctrl file, you can obtain the configuration (snapshot) for any given simulation step. When the simulation step is large, you might want to consider the other method.<br />
<br />
===Atomeye===<br />
Atomeye is a powerful visualization tool. To enable Atomeye, you need to add following lines in the ctrl file<br />
<pre><br />
atomeye = 1<br />
atomeyefreq = 1<br />
atomeyesegradius = 5<br />
</pre><br />
To view atomeye files, you can use command<br />
<pre><br />
$ tools/atomeye/A.i686 outputs/filename/atomeye/paradis0001.cfg<br />
</pre><br />
To create jpg files press y to convert all cfg files in the same directory. <br />
<br />
To convert these jpg files to a movie, the command is<br />
<pre><br />
$ convert -delay 4 -quality 95 *.jpg mymovie.mpg<br />
</pre><br />
where -delay and -quality flags are optional; if -delay > 4, extra frames are added to make the movie run more slowly; default quality is 75 and the maximum is 100. Note that encode packages need to be preinstalled for the machine or cluster.<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
In a typical pbs file, we have following lines as header:<br />
<br />
<pre><br />
#!/bin/bash<br />
#PBS -N jobname<br />
#PBS -j oe<br />
#PBS -l nodes=8:ppn=8,walltime=24:00:00<br />
#PBS -V<br />
<br />
### ---------------------------------------<br />
### BEGINNING OF EXECUTION<br />
### ---------------------------------------<br />
<br />
echo The master node of this job is `hostname`<br />
echo The working directory is `echo $PBS_O_WORKDIR`<br />
echo This job runs on the following nodes:<br />
echo `cat $PBS_NODEFILE`<br />
<br />
ncpu=`cat $PBS_NODEFILE | wc -w`<br />
echo "Number of processors = $ncpu "<br />
### end of information preamble<br />
<br />
cd $PBS_O_WORKDIR<br />
<br />
echo $PWD<br />
<br />
#cmd="mpiexec -np $ncpu bin/meam-lammps_mpich scripts/work/si_ge/si-meam-lammps.tcl"<br />
#time $cmd<br />
</pre><br />
<br />
You need to set the job name, wait time, number of nodes and ppn (number of processors per node, for example, ppn = 8 for wcr clusters)<br />
<br />
To submit jobs using a single processor, <br />
<pre><br />
#bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl &> serial.out<br />
</pre><br />
<br />
or parallel jobs,<br />
<pre><br />
#mpiexec -np $ncpu bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl &> parallel.out<br />
</pre><br />
<br />
===What if the job is stopped===</div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5030ParaDiS Manual Updated2011-01-13T01:14:30Z<p>Jieyin: /* pbs file */</p>
<hr />
<div>Under construction by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. This guide includes following how-tos:<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following lines exist<br />
<br />
===How to set up ctrl-file===<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
Gnuplot is a useful plotting software. You can plot the obtained properties data with gnupot, for example, stress vs strain curve. Before using gnuplot, make sure it is installed on your cluster. You also need to enable X server (test by typing <tt>xclock</tt>). By typing <tt>gnuplot</tt>, you can start using following command lines. For a given (X,Y) data pair, the gnuplot command is<br />
<pre><br />
gnuplot> plot "filename" using 1:2 with lines<br />
</pre><br />
where "using 1:2" means plotting using the 1st and 2nd column from the given data file. "with lines" is a style option, you can change to "with points", "with steps", "with dots" or "with impulses". Click [http://t16web.lanl.gov/Kawano/gnuplot/intro/style-e.html] for a detailed description of the styles.<br />
To draw multiple lines, you can type<br />
<pre><br />
gnuplot> plot "A" using 1:2 title "data A" with lines, \<br />
"B" u 1:2 t "data B" with p, \<br />
"C" u 2:3 t "data C" w d<br />
</pre><br />
You can use \ to separate continuous lines. <tt>title</tt> is used to label different lines. You can abbreviate some of the commands, for example, u for using, t for title, w for with, l for lines, p for points and d for dots.<br />
<br />
To change the labels of X and Y axes, you can use<br />
<pre><br />
gnuplot> set xlabel "x-axis"<br />
gnuplot> set ylabel "y-xais"<br />
gnuplot> set title "y vs x"<br />
gnuplot> replot<br />
</pre><br />
<br />
You can also change the ranges of X and Y axes,<br />
<pre><br />
gnuplot> set xrange [0:2]<br />
gnuplot> set yrange [0:1]<br />
gnuplot> replot<br />
</pre><br />
<br />
To assign the color of the line(line type), you need to add corresponding number after "l". For example, black solid(-1), black dot(0), red(1), green (2), blue(3), margenta(4), cyan(5) and yellow(6). To modify the width of the line at the same time, you can use option "w l lt 2 lw 4", for instance, where lt means linetype and lw means linewidth.<br />
<br />
==How to visualize the results==<br />
To visualize the simulation results, here are two methods. One is to run simulation interactively one one CPU and perform observation. The other is to record the configuration at certain simulation steps and make movies from them.<br />
===xwindow===<br />
Make sure x11 server is enabled for the session(test by "xclock") and the ParaDiS code is compiled for single CPU("MODE = SERIAL, XLIB_MODE = ON" in makefile.setup). By executing<br />
<pre><br />
bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl<br />
</pre><br />
You should be able to see the xwindow. By setting "maxstep = 0" in the ctrl file, you can obtain the configuration (snapshot) for any given simulation step. When the simulation step is large, you might want to consider the other method.<br />
<br />
===Atomeye===<br />
Atomeye is a powerful visualization tool. To enable Atomeye, you need to add following lines in the ctrl file<br />
<pre><br />
atomeye = 1<br />
atomeyefreq = 1<br />
atomeyesegradius = 5<br />
</pre><br />
To view atomeye files, you can use command<br />
<pre><br />
$ tools/atomeye/A.i686 outputs/filename/atomeye/paradis0001.cfg<br />
</pre><br />
To create jpg files press y to convert all cfg files in the same directory. <br />
<br />
To convert these jpg files to a movie, the command is<br />
<pre><br />
$ convert -delay 4 -quality 95 *.jpg mymovie.mpg<br />
</pre><br />
where -delay and -quality flags are optional; if -delay > 4, extra frames are added to make the movie run more slowly; default quality is 75 and the maximum is 100. Note that encode packages need to be preinstalled for the machine or cluster.<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
In a typical pbs file, we have following lines as header:<br />
<br />
<pre><br />
#!/bin/bash<br />
#PBS -N jobname<br />
#PBS -j oe<br />
#PBS -l nodes=8:ppn=8,walltime=24:00:00<br />
#PBS -V<br />
<br />
### ---------------------------------------<br />
### BEGINNING OF EXECUTION<br />
### ---------------------------------------<br />
<br />
echo The master node of this job is `hostname`<br />
echo The working directory is `echo $PBS_O_WORKDIR`<br />
echo This job runs on the following nodes:<br />
echo `cat $PBS_NODEFILE`<br />
<br />
ncpu=`cat $PBS_NODEFILE | wc -w`<br />
echo "Number of processors = $ncpu "<br />
### end of information preamble<br />
<br />
cd $PBS_O_WORKDIR<br />
<br />
echo $PWD<br />
<br />
#cmd="mpiexec -np $ncpu bin/meam-lammps_mpich scripts/work/si_ge/si-meam-lammps.tcl"<br />
#time $cmd<br />
</pre><br />
<br />
You need to set the job name, wait time, number of nodes and ppn (number of processors per node, for example, ppn = 8 for wcr clusters)<br />
<br />
===What if the job is stopped===</div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5029ParaDiS Manual Updated2011-01-13T01:14:12Z<p>Jieyin: /* pbs file */</p>
<hr />
<div>Under construction by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. This guide includes following how-tos:<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following lines exist<br />
<br />
===How to set up ctrl-file===<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
Gnuplot is a useful plotting software. You can plot the obtained properties data with gnupot, for example, stress vs strain curve. Before using gnuplot, make sure it is installed on your cluster. You also need to enable X server (test by typing <tt>xclock</tt>). By typing <tt>gnuplot</tt>, you can start using following command lines. For a given (X,Y) data pair, the gnuplot command is<br />
<pre><br />
gnuplot> plot "filename" using 1:2 with lines<br />
</pre><br />
where "using 1:2" means plotting using the 1st and 2nd column from the given data file. "with lines" is a style option, you can change to "with points", "with steps", "with dots" or "with impulses". Click [http://t16web.lanl.gov/Kawano/gnuplot/intro/style-e.html] for a detailed description of the styles.<br />
To draw multiple lines, you can type<br />
<pre><br />
gnuplot> plot "A" using 1:2 title "data A" with lines, \<br />
"B" u 1:2 t "data B" with p, \<br />
"C" u 2:3 t "data C" w d<br />
</pre><br />
You can use \ to separate continuous lines. <tt>title</tt> is used to label different lines. You can abbreviate some of the commands, for example, u for using, t for title, w for with, l for lines, p for points and d for dots.<br />
<br />
To change the labels of X and Y axes, you can use<br />
<pre><br />
gnuplot> set xlabel "x-axis"<br />
gnuplot> set ylabel "y-xais"<br />
gnuplot> set title "y vs x"<br />
gnuplot> replot<br />
</pre><br />
<br />
You can also change the ranges of X and Y axes,<br />
<pre><br />
gnuplot> set xrange [0:2]<br />
gnuplot> set yrange [0:1]<br />
gnuplot> replot<br />
</pre><br />
<br />
To assign the color of the line(line type), you need to add corresponding number after "l". For example, black solid(-1), black dot(0), red(1), green (2), blue(3), margenta(4), cyan(5) and yellow(6). To modify the width of the line at the same time, you can use option "w l lt 2 lw 4", for instance, where lt means linetype and lw means linewidth.<br />
<br />
==How to visualize the results==<br />
To visualize the simulation results, here are two methods. One is to run simulation interactively one one CPU and perform observation. The other is to record the configuration at certain simulation steps and make movies from them.<br />
===xwindow===<br />
Make sure x11 server is enabled for the session(test by "xclock") and the ParaDiS code is compiled for single CPU("MODE = SERIAL, XLIB_MODE = ON" in makefile.setup). By executing<br />
<pre><br />
bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl<br />
</pre><br />
You should be able to see the xwindow. By setting "maxstep = 0" in the ctrl file, you can obtain the configuration (snapshot) for any given simulation step. When the simulation step is large, you might want to consider the other method.<br />
<br />
===Atomeye===<br />
Atomeye is a powerful visualization tool. To enable Atomeye, you need to add following lines in the ctrl file<br />
<pre><br />
atomeye = 1<br />
atomeyefreq = 1<br />
atomeyesegradius = 5<br />
</pre><br />
To view atomeye files, you can use command<br />
<pre><br />
$ tools/atomeye/A.i686 outputs/filename/atomeye/paradis0001.cfg<br />
</pre><br />
To create jpg files press y to convert all cfg files in the same directory. <br />
<br />
To convert these jpg files to a movie, the command is<br />
<pre><br />
$ convert -delay 4 -quality 95 *.jpg mymovie.mpg<br />
</pre><br />
where -delay and -quality flags are optional; if -delay > 4, extra frames are added to make the movie run more slowly; default quality is 75 and the maximum is 100. Note that encode packages need to be preinstalled for the machine or cluster.<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
In a typical pbs file, we have following lines as header:<br />
<br />
<pre><br />
#!/bin/bash<br />
#PBS -N jobname<br />
#PBS -j oe<br />
#PBS -l nodes=8:ppn=8,walltime=24:00:00<br />
#PBS -V<br />
<br />
### ---------------------------------------<br />
### BEGINNING OF EXECUTION<br />
### ---------------------------------------<br />
<br />
echo The master node of this job is `hostname`<br />
echo The working directory is `echo $PBS_O_WORKDIR`<br />
echo This job runs on the following nodes:<br />
echo `cat $PBS_NODEFILE`<br />
<br />
ncpu=`cat $PBS_NODEFILE | wc -w`<br />
echo "Number of processors = $ncpu "<br />
### end of information preamble<br />
<br />
cd $PBS_O_WORKDIR<br />
<br />
echo $PWD<br />
<br />
#cmd="mpiexec -np $ncpu bin/meam-lammps_mpich scripts/work/si_ge/si-meam-lammps.tcl"<br />
#time $cmd<br />
</pre><br />
<br />
You need to set the job name, number of nodes and ppn (number of processors per node, for example, ppn = 8 for wcr clusters)<br />
<br />
===What if the job is stopped===</div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5028ParaDiS Manual Updated2011-01-12T23:31:42Z<p>Jieyin: /* Atomeye */</p>
<hr />
<div>Under construction by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. This guide includes following how-tos:<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following lines exist<br />
<br />
===How to set up ctrl-file===<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
Gnuplot is a useful plotting software. You can plot the obtained properties data with gnupot, for example, stress vs strain curve. Before using gnuplot, make sure it is installed on your cluster. You also need to enable X server (test by typing <tt>xclock</tt>). By typing <tt>gnuplot</tt>, you can start using following command lines. For a given (X,Y) data pair, the gnuplot command is<br />
<pre><br />
gnuplot> plot "filename" using 1:2 with lines<br />
</pre><br />
where "using 1:2" means plotting using the 1st and 2nd column from the given data file. "with lines" is a style option, you can change to "with points", "with steps", "with dots" or "with impulses". Click [http://t16web.lanl.gov/Kawano/gnuplot/intro/style-e.html] for a detailed description of the styles.<br />
To draw multiple lines, you can type<br />
<pre><br />
gnuplot> plot "A" using 1:2 title "data A" with lines, \<br />
"B" u 1:2 t "data B" with p, \<br />
"C" u 2:3 t "data C" w d<br />
</pre><br />
You can use \ to separate continuous lines. <tt>title</tt> is used to label different lines. You can abbreviate some of the commands, for example, u for using, t for title, w for with, l for lines, p for points and d for dots.<br />
<br />
To change the labels of X and Y axes, you can use<br />
<pre><br />
gnuplot> set xlabel "x-axis"<br />
gnuplot> set ylabel "y-xais"<br />
gnuplot> set title "y vs x"<br />
gnuplot> replot<br />
</pre><br />
<br />
You can also change the ranges of X and Y axes,<br />
<pre><br />
gnuplot> set xrange [0:2]<br />
gnuplot> set yrange [0:1]<br />
gnuplot> replot<br />
</pre><br />
<br />
To assign the color of the line(line type), you need to add corresponding number after "l". For example, black solid(-1), black dot(0), red(1), green (2), blue(3), margenta(4), cyan(5) and yellow(6). To modify the width of the line at the same time, you can use option "w l lt 2 lw 4", for instance, where lt means linetype and lw means linewidth.<br />
<br />
==How to visualize the results==<br />
To visualize the simulation results, here are two methods. One is to run simulation interactively one one CPU and perform observation. The other is to record the configuration at certain simulation steps and make movies from them.<br />
===xwindow===<br />
Make sure x11 server is enabled for the session(test by "xclock") and the ParaDiS code is compiled for single CPU("MODE = SERIAL, XLIB_MODE = ON" in makefile.setup). By executing<br />
<pre><br />
bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl<br />
</pre><br />
You should be able to see the xwindow. By setting "maxstep = 0" in the ctrl file, you can obtain the configuration (snapshot) for any given simulation step. When the simulation step is large, you might want to consider the other method.<br />
<br />
===Atomeye===<br />
Atomeye is a powerful visualization tool. To enable Atomeye, you need to add following lines in the ctrl file<br />
<pre><br />
atomeye = 1<br />
atomeyefreq = 1<br />
atomeyesegradius = 5<br />
</pre><br />
To view atomeye files, you can use command<br />
<pre><br />
$ tools/atomeye/A.i686 outputs/filename/atomeye/paradis0001.cfg<br />
</pre><br />
To create jpg files press y to convert all cfg files in the same directory. <br />
<br />
To convert these jpg files to a movie, the command is<br />
<pre><br />
$ convert -delay 4 -quality 95 *.jpg mymovie.mpg<br />
</pre><br />
where -delay and -quality flags are optional; if -delay > 4, extra frames are added to make the movie run more slowly; default quality is 75 and the maximum is 100. Note that encode packages need to be preinstalled for the machine or cluster.<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
===What if the job is stopped===</div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5027ParaDiS Manual Updated2011-01-12T23:31:11Z<p>Jieyin: /* Atomeye */</p>
<hr />
<div>Under construction by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. This guide includes following how-tos:<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following lines exist<br />
<br />
===How to set up ctrl-file===<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
Gnuplot is a useful plotting software. You can plot the obtained properties data with gnupot, for example, stress vs strain curve. Before using gnuplot, make sure it is installed on your cluster. You also need to enable X server (test by typing <tt>xclock</tt>). By typing <tt>gnuplot</tt>, you can start using following command lines. For a given (X,Y) data pair, the gnuplot command is<br />
<pre><br />
gnuplot> plot "filename" using 1:2 with lines<br />
</pre><br />
where "using 1:2" means plotting using the 1st and 2nd column from the given data file. "with lines" is a style option, you can change to "with points", "with steps", "with dots" or "with impulses". Click [http://t16web.lanl.gov/Kawano/gnuplot/intro/style-e.html] for a detailed description of the styles.<br />
To draw multiple lines, you can type<br />
<pre><br />
gnuplot> plot "A" using 1:2 title "data A" with lines, \<br />
"B" u 1:2 t "data B" with p, \<br />
"C" u 2:3 t "data C" w d<br />
</pre><br />
You can use \ to separate continuous lines. <tt>title</tt> is used to label different lines. You can abbreviate some of the commands, for example, u for using, t for title, w for with, l for lines, p for points and d for dots.<br />
<br />
To change the labels of X and Y axes, you can use<br />
<pre><br />
gnuplot> set xlabel "x-axis"<br />
gnuplot> set ylabel "y-xais"<br />
gnuplot> set title "y vs x"<br />
gnuplot> replot<br />
</pre><br />
<br />
You can also change the ranges of X and Y axes,<br />
<pre><br />
gnuplot> set xrange [0:2]<br />
gnuplot> set yrange [0:1]<br />
gnuplot> replot<br />
</pre><br />
<br />
To assign the color of the line(line type), you need to add corresponding number after "l". For example, black solid(-1), black dot(0), red(1), green (2), blue(3), margenta(4), cyan(5) and yellow(6). To modify the width of the line at the same time, you can use option "w l lt 2 lw 4", for instance, where lt means linetype and lw means linewidth.<br />
<br />
==How to visualize the results==<br />
To visualize the simulation results, here are two methods. One is to run simulation interactively one one CPU and perform observation. The other is to record the configuration at certain simulation steps and make movies from them.<br />
===xwindow===<br />
Make sure x11 server is enabled for the session(test by "xclock") and the ParaDiS code is compiled for single CPU("MODE = SERIAL, XLIB_MODE = ON" in makefile.setup). By executing<br />
<pre><br />
bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl<br />
</pre><br />
You should be able to see the xwindow. By setting "maxstep = 0" in the ctrl file, you can obtain the configuration (snapshot) for any given simulation step. When the simulation step is large, you might want to consider the other method.<br />
<br />
===Atomeye===<br />
Atomeye is a powerful visualization tool. To enable Atomeye, you need to add following lines in the ctrl file<br />
<pre><br />
atomeye = 1<br />
atomeyefreq = 1<br />
atomeyesegradius = 5<br />
</pre><br />
To view atomeye files, you can use command<br />
<pre><br />
$ tools/atomeye/A.i686 runs/filename/atomeye/paradis0001.cfg<br />
</pre><br />
To create jpg files press y to convert all cfg files in the same directory. <br />
<br />
To convert these jpg files to a movie, the command is<br />
<pre><br />
$ convert -delay 4 -quality 95 *.jpg mymovie.mpg<br />
</pre><br />
where -delay and -quality flags are optional; if -delay > 4, extra frames are added to make the movie run more slowly; default quality is 75 and the maximum is 100. Note that encode packages need to be preinstalled for the machine or cluster.<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
===What if the job is stopped===</div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5026ParaDiS Manual Updated2011-01-12T23:29:43Z<p>Jieyin: /* Atomeye */</p>
<hr />
<div>Under construction by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. This guide includes following how-tos:<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following lines exist<br />
<br />
===How to set up ctrl-file===<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
Gnuplot is a useful plotting software. You can plot the obtained properties data with gnupot, for example, stress vs strain curve. Before using gnuplot, make sure it is installed on your cluster. You also need to enable X server (test by typing <tt>xclock</tt>). By typing <tt>gnuplot</tt>, you can start using following command lines. For a given (X,Y) data pair, the gnuplot command is<br />
<pre><br />
gnuplot> plot "filename" using 1:2 with lines<br />
</pre><br />
where "using 1:2" means plotting using the 1st and 2nd column from the given data file. "with lines" is a style option, you can change to "with points", "with steps", "with dots" or "with impulses". Click [http://t16web.lanl.gov/Kawano/gnuplot/intro/style-e.html] for a detailed description of the styles.<br />
To draw multiple lines, you can type<br />
<pre><br />
gnuplot> plot "A" using 1:2 title "data A" with lines, \<br />
"B" u 1:2 t "data B" with p, \<br />
"C" u 2:3 t "data C" w d<br />
</pre><br />
You can use \ to separate continuous lines. <tt>title</tt> is used to label different lines. You can abbreviate some of the commands, for example, u for using, t for title, w for with, l for lines, p for points and d for dots.<br />
<br />
To change the labels of X and Y axes, you can use<br />
<pre><br />
gnuplot> set xlabel "x-axis"<br />
gnuplot> set ylabel "y-xais"<br />
gnuplot> set title "y vs x"<br />
gnuplot> replot<br />
</pre><br />
<br />
You can also change the ranges of X and Y axes,<br />
<pre><br />
gnuplot> set xrange [0:2]<br />
gnuplot> set yrange [0:1]<br />
gnuplot> replot<br />
</pre><br />
<br />
To assign the color of the line(line type), you need to add corresponding number after "l". For example, black solid(-1), black dot(0), red(1), green (2), blue(3), margenta(4), cyan(5) and yellow(6). To modify the width of the line at the same time, you can use option "w l lt 2 lw 4", for instance, where lt means linetype and lw means linewidth.<br />
<br />
==How to visualize the results==<br />
To visualize the simulation results, here are two methods. One is to run simulation interactively one one CPU and perform observation. The other is to record the configuration at certain simulation steps and make movies from them.<br />
===xwindow===<br />
Make sure x11 server is enabled for the session(test by "xclock") and the ParaDiS code is compiled for single CPU("MODE = SERIAL, XLIB_MODE = ON" in makefile.setup). By executing<br />
<pre><br />
bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl<br />
</pre><br />
You should be able to see the xwindow. By setting "maxstep = 0" in the ctrl file, you can obtain the configuration (snapshot) for any given simulation step. When the simulation step is large, you might want to consider the other method.<br />
<br />
===Atomeye===<br />
Atomeye is a powerful visualization tool. To enable Atomeye, you need to add following lines in the ctrl file<br />
<pre><br />
atomeye = 1<br />
atomeyefreq = 1<br />
atomeyesegradius = 5<br />
</pre><br />
To view atomeye files, you can use command<br />
$ tools/atomeye/A.i686 PartialsTests/partial3/atomeye/paradis0001.cfg<br />
To create jpg files press y to convert all cfg files in the same directory. To convert jpg files to movie, the command is<br />
$ convert -delay 4 -quality 95 *.jpg myfirstmovie.mpg<br />
where -delay and -quality flags are optional; if -delay > 4, extra frames are added to make the movie run more slowly; default quality is 75 and the maximum is 100. Note that encode packages need to be preinstalled for the machine or cluster.<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
===What if the job is stopped===</div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5025ParaDiS Manual Updated2011-01-12T23:27:42Z<p>Jieyin: /* xwindow */</p>
<hr />
<div>Under construction by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. This guide includes following how-tos:<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following lines exist<br />
<br />
===How to set up ctrl-file===<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
Gnuplot is a useful plotting software. You can plot the obtained properties data with gnupot, for example, stress vs strain curve. Before using gnuplot, make sure it is installed on your cluster. You also need to enable X server (test by typing <tt>xclock</tt>). By typing <tt>gnuplot</tt>, you can start using following command lines. For a given (X,Y) data pair, the gnuplot command is<br />
<pre><br />
gnuplot> plot "filename" using 1:2 with lines<br />
</pre><br />
where "using 1:2" means plotting using the 1st and 2nd column from the given data file. "with lines" is a style option, you can change to "with points", "with steps", "with dots" or "with impulses". Click [http://t16web.lanl.gov/Kawano/gnuplot/intro/style-e.html] for a detailed description of the styles.<br />
To draw multiple lines, you can type<br />
<pre><br />
gnuplot> plot "A" using 1:2 title "data A" with lines, \<br />
"B" u 1:2 t "data B" with p, \<br />
"C" u 2:3 t "data C" w d<br />
</pre><br />
You can use \ to separate continuous lines. <tt>title</tt> is used to label different lines. You can abbreviate some of the commands, for example, u for using, t for title, w for with, l for lines, p for points and d for dots.<br />
<br />
To change the labels of X and Y axes, you can use<br />
<pre><br />
gnuplot> set xlabel "x-axis"<br />
gnuplot> set ylabel "y-xais"<br />
gnuplot> set title "y vs x"<br />
gnuplot> replot<br />
</pre><br />
<br />
You can also change the ranges of X and Y axes,<br />
<pre><br />
gnuplot> set xrange [0:2]<br />
gnuplot> set yrange [0:1]<br />
gnuplot> replot<br />
</pre><br />
<br />
To assign the color of the line(line type), you need to add corresponding number after "l". For example, black solid(-1), black dot(0), red(1), green (2), blue(3), margenta(4), cyan(5) and yellow(6). To modify the width of the line at the same time, you can use option "w l lt 2 lw 4", for instance, where lt means linetype and lw means linewidth.<br />
<br />
==How to visualize the results==<br />
To visualize the simulation results, here are two methods. One is to run simulation interactively one one CPU and perform observation. The other is to record the configuration at certain simulation steps and make movies from them.<br />
===xwindow===<br />
Make sure x11 server is enabled for the session(test by "xclock") and the ParaDiS code is compiled for single CPU("MODE = SERIAL, XLIB_MODE = ON" in makefile.setup). By executing<br />
<pre><br />
bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl<br />
</pre><br />
You should be able to see the xwindow. By setting "maxstep = 0" in the ctrl file, you can obtain the configuration (snapshot) for any given simulation step. When the simulation step is large, you might want to consider the other method.<br />
<br />
===Atomeye===<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
===What if the job is stopped===</div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5024ParaDiS Manual Updated2011-01-12T23:25:46Z<p>Jieyin: /* How to visualize the results */</p>
<hr />
<div>Under construction by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. This guide includes following how-tos:<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following lines exist<br />
<br />
===How to set up ctrl-file===<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
Gnuplot is a useful plotting software. You can plot the obtained properties data with gnupot, for example, stress vs strain curve. Before using gnuplot, make sure it is installed on your cluster. You also need to enable X server (test by typing <tt>xclock</tt>). By typing <tt>gnuplot</tt>, you can start using following command lines. For a given (X,Y) data pair, the gnuplot command is<br />
<pre><br />
gnuplot> plot "filename" using 1:2 with lines<br />
</pre><br />
where "using 1:2" means plotting using the 1st and 2nd column from the given data file. "with lines" is a style option, you can change to "with points", "with steps", "with dots" or "with impulses". Click [http://t16web.lanl.gov/Kawano/gnuplot/intro/style-e.html] for a detailed description of the styles.<br />
To draw multiple lines, you can type<br />
<pre><br />
gnuplot> plot "A" using 1:2 title "data A" with lines, \<br />
"B" u 1:2 t "data B" with p, \<br />
"C" u 2:3 t "data C" w d<br />
</pre><br />
You can use \ to separate continuous lines. <tt>title</tt> is used to label different lines. You can abbreviate some of the commands, for example, u for using, t for title, w for with, l for lines, p for points and d for dots.<br />
<br />
To change the labels of X and Y axes, you can use<br />
<pre><br />
gnuplot> set xlabel "x-axis"<br />
gnuplot> set ylabel "y-xais"<br />
gnuplot> set title "y vs x"<br />
gnuplot> replot<br />
</pre><br />
<br />
You can also change the ranges of X and Y axes,<br />
<pre><br />
gnuplot> set xrange [0:2]<br />
gnuplot> set yrange [0:1]<br />
gnuplot> replot<br />
</pre><br />
<br />
To assign the color of the line(line type), you need to add corresponding number after "l". For example, black solid(-1), black dot(0), red(1), green (2), blue(3), margenta(4), cyan(5) and yellow(6). To modify the width of the line at the same time, you can use option "w l lt 2 lw 4", for instance, where lt means linetype and lw means linewidth.<br />
<br />
==How to visualize the results==<br />
To visualize the simulation results, here are two methods. One is to run simulation interactively one one CPU and perform observation. The other is to record the configuration at certain simulation steps and make movies from them.<br />
===xwindow===<br />
Make sure x11 server is enabled (test by "xclock") and the ParaDiS code is compiled for single CPU(MODE = SERIAL in makefile.setup). By executing<br />
<pre><br />
bin/paradis -d runs/datafile.data runs/ctrlfile.ctrl<br />
</pre><br />
You should be able to see the xwindow. By setting "maxstep = 0" in the ctrl file, you can obtain the configuration (snapshot) for any given simulation step. When the simulation step is large, you might want to consider the other method.<br />
===Atomeye===<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
===What if the job is stopped===</div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5023ParaDiS Manual Updated2011-01-12T23:16:55Z<p>Jieyin: /* How to visualize the results */</p>
<hr />
<div>Under construction by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. This guide includes following how-tos:<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following lines exist<br />
<br />
===How to set up ctrl-file===<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
Gnuplot is a useful plotting software. You can plot the obtained properties data with gnupot, for example, stress vs strain curve. Before using gnuplot, make sure it is installed on your cluster. You also need to enable X server (test by typing <tt>xclock</tt>). By typing <tt>gnuplot</tt>, you can start using following command lines. For a given (X,Y) data pair, the gnuplot command is<br />
<pre><br />
gnuplot> plot "filename" using 1:2 with lines<br />
</pre><br />
where "using 1:2" means plotting using the 1st and 2nd column from the given data file. "with lines" is a style option, you can change to "with points", "with steps", "with dots" or "with impulses". Click [http://t16web.lanl.gov/Kawano/gnuplot/intro/style-e.html] for a detailed description of the styles.<br />
To draw multiple lines, you can type<br />
<pre><br />
gnuplot> plot "A" using 1:2 title "data A" with lines, \<br />
"B" u 1:2 t "data B" with p, \<br />
"C" u 2:3 t "data C" w d<br />
</pre><br />
You can use \ to separate continuous lines. <tt>title</tt> is used to label different lines. You can abbreviate some of the commands, for example, u for using, t for title, w for with, l for lines, p for points and d for dots.<br />
<br />
To change the labels of X and Y axes, you can use<br />
<pre><br />
gnuplot> set xlabel "x-axis"<br />
gnuplot> set ylabel "y-xais"<br />
gnuplot> set title "y vs x"<br />
gnuplot> replot<br />
</pre><br />
<br />
You can also change the ranges of X and Y axes,<br />
<pre><br />
gnuplot> set xrange [0:2]<br />
gnuplot> set yrange [0:1]<br />
gnuplot> replot<br />
</pre><br />
<br />
To assign the color of the line(line type), you need to add corresponding number after "l". For example, black solid(-1), black dot(0), red(1), green (2), blue(3), margenta(4), cyan(5) and yellow(6). To modify the width of the line at the same time, you can use option "w l lt 2 lw 4", for instance, where lt means linetype and lw means linewidth.<br />
<br />
==How to visualize the results==<br />
To visualize the simulation results, here are two methods. One is to run simulation interactively one one CPU and perform observation. The other is to record the configuration at certain simulation steps and make movies from them.<br />
===xwindow===<br />
Make sure x11 server is enabled (test by "xclock") and the ParaDiS code is compiled for single CPU(MODE = SERIAL in makefile.setup).<br />
===Atomeye===<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
===What if the job is stopped===</div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5022ParaDiS Manual Updated2011-01-12T23:11:40Z<p>Jieyin: /* Gnuplot */</p>
<hr />
<div>Under construction by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. This guide includes following how-tos:<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following lines exist<br />
<br />
===How to set up ctrl-file===<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
Gnuplot is a useful plotting software. You can plot the obtained properties data with gnupot, for example, stress vs strain curve. Before using gnuplot, make sure it is installed on your cluster. You also need to enable X server (test by typing <tt>xclock</tt>). By typing <tt>gnuplot</tt>, you can start using following command lines. For a given (X,Y) data pair, the gnuplot command is<br />
<pre><br />
gnuplot> plot "filename" using 1:2 with lines<br />
</pre><br />
where "using 1:2" means plotting using the 1st and 2nd column from the given data file. "with lines" is a style option, you can change to "with points", "with steps", "with dots" or "with impulses". Click [http://t16web.lanl.gov/Kawano/gnuplot/intro/style-e.html] for a detailed description of the styles.<br />
To draw multiple lines, you can type<br />
<pre><br />
gnuplot> plot "A" using 1:2 title "data A" with lines, \<br />
"B" u 1:2 t "data B" with p, \<br />
"C" u 2:3 t "data C" w d<br />
</pre><br />
You can use \ to separate continuous lines. <tt>title</tt> is used to label different lines. You can abbreviate some of the commands, for example, u for using, t for title, w for with, l for lines, p for points and d for dots.<br />
<br />
To change the labels of X and Y axes, you can use<br />
<pre><br />
gnuplot> set xlabel "x-axis"<br />
gnuplot> set ylabel "y-xais"<br />
gnuplot> set title "y vs x"<br />
gnuplot> replot<br />
</pre><br />
<br />
You can also change the ranges of X and Y axes,<br />
<pre><br />
gnuplot> set xrange [0:2]<br />
gnuplot> set yrange [0:1]<br />
gnuplot> replot<br />
</pre><br />
<br />
To assign the color of the line(line type), you need to add corresponding number after "l". For example, black solid(-1), black dot(0), red(1), green (2), blue(3), margenta(4), cyan(5) and yellow(6). To modify the width of the line at the same time, you can use option "w l lt 2 lw 4", for instance, where lt means linetype and lw means linewidth.<br />
<br />
==How to visualize the results==<br />
===xwindow===<br />
===Atomeye===<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
===What if the job is stopped===</div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5021ParaDiS Manual Updated2011-01-12T23:00:55Z<p>Jieyin: /* Gnuplot */</p>
<hr />
<div>Under construction by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. This guide includes following how-tos:<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following lines exist<br />
<br />
===How to set up ctrl-file===<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
Gnuplot is a useful plotting software. You can plot the obtained properties data with gnupot, for example, stress vs strain curve. Before using gnuplot, make sure it is installed on your cluster. You also need to enable X server (test by typing <tt>xclock</tt>). By typing <tt>gnuplot</tt>, you can start using following command lines. For a given (X,Y) data pair, the gnuplot command is<br />
<pre><br />
gnuplot> plot "filename" using 1:2 with lines<br />
</pre><br />
where "using 1:2" means plotting using the 1st and 2nd column from the given data file. "with lines" is a style option, you can change to "with points", "with steps", "with dots" or "with impulses". Click [http://t16web.lanl.gov/Kawano/gnuplot/intro/style-e.html] for a detailed description of the styles.<br />
To draw multiple lines, you can type<br />
<pre><br />
gnuplot> plot "A" using 1:2 title "data A" with lines, \<br />
"B" u 1:2 t "data B" with p, \<br />
"C" u 2:3 t "data C" w d<br />
</pre><br />
You can use \ to separate continuous lines. <tt>title</tt> is used to label different lines. You can abbreviate some of the commands, for example, u for using, t for title, w for with, l for lines, p for points and d for dots.<br />
<br />
To change the labels of X and Y axes, you can use<br />
<pre><br />
gnuplot> set xlabel "x-axis"<br />
gnuplot> set ylabel "y-xais"<br />
gnuplot> set title "y vs x"<br />
gnuplot> replot<br />
</pre><br />
<br />
You can also change the ranges of X and Y axes,<br />
<pre><br />
gnuplot> set xrange [0:2]<br />
gnuplot> set yrange [0:1]<br />
gnuplot> replot<br />
</pre><br />
<br />
To assign the color of the line(line type), you need to add corresponding number after "l". For example, black solid(-1), black dot(0), red(1), green (2), blue(3), margenta(4), cyan(5) and yellow(6). To modify the width of the line, you can use option "w l lw 4", for instance.<br />
<br />
==How to visualize the results==<br />
===xwindow===<br />
===Atomeye===<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
===What if the job is stopped===</div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5020ParaDiS Manual Updated2011-01-12T22:59:43Z<p>Jieyin: /* Gnuplot */</p>
<hr />
<div>Under construction by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. This guide includes following how-tos:<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following lines exist<br />
<br />
===How to set up ctrl-file===<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
Before using gnuplot, make sure it is installed on your cluster. You also need to enable X server (test by typing <tt>xclock</tt>). By typing <tt>gnuplot</tt>, you can start using following command lines. For a given (X,Y) data pair, the gnuplot command is<br />
<pre><br />
gnuplot> plot "filename" using 1:2 with lines<br />
</pre><br />
where "using 1:2" means plotting using the 1st and 2nd column from the given data file. "with lines" is a style option, you can change to "with points", "with steps", "with dots" or "with impulses". Click [http://t16web.lanl.gov/Kawano/gnuplot/intro/style-e.html] for a detailed description of the styles.<br />
To draw multiple lines, you can type<br />
<pre><br />
gnuplot> plot "A" using 1:2 title "data A" with lines, \<br />
"B" u 1:2 t "data B" with p, \<br />
"C" u 2:3 t "data C" w d<br />
</pre><br />
You can use \ to separate continuous lines. <tt>title</tt> is used to label different lines. You can abbreviate some of the commands, for example, u for using, t for title, w for with, l for lines, p for points and d for dots.<br />
<br />
To change the labels of X and Y axes, you can use<br />
<pre><br />
gnuplot> set xlabel "x-axis"<br />
gnuplot> set ylabel "y-xais"<br />
gnuplot> set title "y vs x"<br />
gnuplot> replot<br />
</pre><br />
<br />
You can also change the ranges of X and Y axes,<br />
<pre><br />
gnuplot> set xrange [0:2]<br />
gnuplot> set yrange [0:1]<br />
gnuplot> replot<br />
</pre><br />
<br />
To assign the color of the line(line type), you need to add corresponding number after "l". For example, black solid(-1), black dot(0), red(1), green (2), blue(3), margenta(4), cyan(5) and yellow(6). To modify the width of the line, you can use option "w l lw 4", for instance.<br />
<br />
==How to visualize the results==<br />
===xwindow===<br />
===Atomeye===<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
===What if the job is stopped===</div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5019ParaDiS Manual Updated2011-01-12T22:56:04Z<p>Jieyin: /* Gnuplot */</p>
<hr />
<div>Under construction by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. This guide includes following how-tos:<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following lines exist<br />
<br />
===How to set up ctrl-file===<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
Before using gnuplot, make sure it is installed on your cluster. You also need to enable X server (test by typing <tt>xclock</tt>). By typing <tt>gnuplot</tt>, you can start using following command lines. For a given (X,Y) data pair, the gnuplot command is<br />
<pre><br />
gnuplot> plot "filename" using 1:2 with lines<br />
</pre><br />
where "using 1:2" means plotting using the 1st and 2nd column from the given data file. "with lines" is a style option, you can change to "with points", "with steps", "with dots" or "with impulses". Click [http://t16web.lanl.gov/Kawano/gnuplot/intro/style-e.html] for a detailed description of the styles.<br />
To draw multiple lines, you can type<br />
<pre><br />
gnuplot> plot "A" using 1:2 title "data A" with lines, \<br />
"B" u 1:2 t "data B" with p, \<br />
"C" u 2:3 t "data C" w d<br />
</pre><br />
You can use \ to separate continuous lines. <tt>title</tt> is used to label different lines. You can abbreviate some of the commands, for example, u for using, t for title, w for with, l for lines, p for points and d for dots.<br />
<br />
To change the labels of X and Y axes, you can use<br />
<pre><br />
gnuplot> set xlabel "x-axis"<br />
gnuplot> set ylabel "y-xais"<br />
gnuplot> set title "y vs x"<br />
gnuplot> replot<br />
</pre><br />
<br />
You can also change the ranges of X and Y axes,<br />
<pre><br />
gnuplot> set xrange [0:2]<br />
gnuplot> set yrange [0:1]<br />
gnuplot> replot<br />
</pre><br />
<br />
To assign the color of the line(line type), you need to add corresponding number after "l". For example, black solid(-1), black dot(0), red(1), green (2), blue(3), margenta(4), cyan(5) and yellow(6).<br />
<br />
==How to visualize the results==<br />
===xwindow===<br />
===Atomeye===<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
===What if the job is stopped===</div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5018ParaDiS Manual Updated2011-01-12T22:50:18Z<p>Jieyin: /* Gnuplot */</p>
<hr />
<div>Under construction by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. This guide includes following how-tos:<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following lines exist<br />
<br />
===How to set up ctrl-file===<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
Before using gnuplot, make sure it is installed on your cluster. You also need to enable X server (test by typing <tt>xclock</tt>). By typing <tt>gnuplot</tt>, you can start using following command lines. For a given (X,Y) data pair, the gnuplot command is<br />
<pre><br />
gnuplot> plot "filename" using 1:2 with lines<br />
</pre><br />
where "using 1:2" means plotting using the 1st and 2nd column from the given data file. "with lines" is a style option, you can change to "with points", "with steps", "with dots" or "with impulses". Click [http://t16web.lanl.gov/Kawano/gnuplot/intro/style-e.html] for a detailed description of the styles.<br />
To draw multiple lines, you can type<br />
<pre><br />
gnuplot> plot "A" using 1:2 title "data A" with lines, \<br />
"B" u 1:2 t "data B" with p, \<br />
"C" u 2:3 t "data C" w d<br />
</pre><br />
You can use \ to separate continuous lines. <tt>title</tt> is used to label different lines. You can abbreviate some of the commands, for example, u for using, t for title, w for with, l for lines, p for points and d for dots.<br />
<br />
To change the labels of X and Y axes, you can use<br />
<pre><br />
gnuplot> set xlabel "x-axis"<br />
gnuplot> set ylabel "y-xais"<br />
gnuplot> set title "y vs x"<br />
gnuplot> replot<br />
</pre><br />
<br />
You can also change the ranges of X and Y axes,<br />
<pre><br />
gnuplot> set xrange [0:2]<br />
gnuplot> set yrange [0:1]<br />
gnuplot> replot<br />
</pre><br />
<br />
To assign the color of the line, you need to add corresponding number after "l". For example, black solid(-1), black dot(0), red(1), green (2), blue(3), margenta(4), cyan(5) and yellow(6).<br />
<br />
==How to visualize the results==<br />
===xwindow===<br />
===Atomeye===<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
===What if the job is stopped===</div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5017ParaDiS Manual Updated2011-01-12T22:50:06Z<p>Jieyin: /* Gnuplot */</p>
<hr />
<div>Under construction by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. This guide includes following how-tos:<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following lines exist<br />
<br />
===How to set up ctrl-file===<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
Before using gnuplot, make sure it is installed on your cluster. You also need to enable X server (test by typing <tt>xclock</tt>). By typing <tt>gnuplot</tt>, you can start using following command lines. For a given (X,Y) data pair, the gnuplot command is<br />
<pre><br />
gnuplot> plot "filename" using 1:2 with lines<br />
</pre><br />
where "using 1:2" means plotting using the 1st and 2nd column from the given data file. "with lines" is a style option, you can change to "with points", "with steps", "with dots" or "with impulses". Click ["here",http://t16web.lanl.gov/Kawano/gnuplot/intro/style-e.html] for a detailed description of the styles.<br />
To draw multiple lines, you can type<br />
<pre><br />
gnuplot> plot "A" using 1:2 title "data A" with lines, \<br />
"B" u 1:2 t "data B" with p, \<br />
"C" u 2:3 t "data C" w d<br />
</pre><br />
You can use \ to separate continuous lines. <tt>title</tt> is used to label different lines. You can abbreviate some of the commands, for example, u for using, t for title, w for with, l for lines, p for points and d for dots.<br />
<br />
To change the labels of X and Y axes, you can use<br />
<pre><br />
gnuplot> set xlabel "x-axis"<br />
gnuplot> set ylabel "y-xais"<br />
gnuplot> set title "y vs x"<br />
gnuplot> replot<br />
</pre><br />
<br />
You can also change the ranges of X and Y axes,<br />
<pre><br />
gnuplot> set xrange [0:2]<br />
gnuplot> set yrange [0:1]<br />
gnuplot> replot<br />
</pre><br />
<br />
To assign the color of the line, you need to add corresponding number after "l". For example, black solid(-1), black dot(0), red(1), green (2), blue(3), margenta(4), cyan(5) and yellow(6).<br />
<br />
==How to visualize the results==<br />
===xwindow===<br />
===Atomeye===<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
===What if the job is stopped===</div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5016ParaDiS Manual Updated2011-01-12T22:49:40Z<p>Jieyin: /* Gnuplot */</p>
<hr />
<div>Under construction by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. This guide includes following how-tos:<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following lines exist<br />
<br />
===How to set up ctrl-file===<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
Before using gnuplot, make sure it is installed on your cluster. You also need to enable X server (test by typing <tt>xclock</tt>). By typing <tt>gnuplot</tt>, you can start using following command lines. For a given (X,Y) data pair, the gnuplot command is<br />
<pre><br />
gnuplot> plot "filename" using 1:2 with lines<br />
</pre><br />
where "using 1:2" means plotting using the 1st and 2nd column from the given data file. "with lines" is a style option, you can change to "with points", "with steps", "with dots" or "with impulses". Click [http://t16web.lanl.gov/Kawano/gnuplot/intro/style-e.html] for a detailed description of the styles.<br />
To draw multiple lines, you can type<br />
<pre><br />
gnuplot> plot "A" using 1:2 title "data A" with lines, \<br />
"B" u 1:2 t "data B" with p, \<br />
"C" u 2:3 t "data C" w d<br />
</pre><br />
You can use \ to separate continuous lines. <tt>title</tt> is used to label different lines. You can abbreviate some of the commands, for example, u for using, t for title, w for with, l for lines, p for points and d for dots.<br />
<br />
To change the labels of X and Y axes, you can use<br />
<pre><br />
gnuplot> set xlabel "x-axis"<br />
gnuplot> set ylabel "y-xais"<br />
gnuplot> set title "y vs x"<br />
gnuplot> replot<br />
</pre><br />
<br />
You can also change the ranges of X and Y axes,<br />
<pre><br />
gnuplot> set xrange [0:2]<br />
gnuplot> set yrange [0:1]<br />
gnuplot> replot<br />
</pre><br />
<br />
To assign the color of the line, you need to add corresponding number after "l". For example, black solid(-1), black dot(0), red(1), green (2), blue(3), margenta(4), cyan(5) and yellow(6).<br />
<br />
==How to visualize the results==<br />
===xwindow===<br />
===Atomeye===<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
===What if the job is stopped===</div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5015ParaDiS Manual Updated2011-01-12T22:43:23Z<p>Jieyin: /* Gnuplot */</p>
<hr />
<div>Under construction by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. This guide includes following how-tos:<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following lines exist<br />
<br />
===How to set up ctrl-file===<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
Before using gnuplot, make sure it is installed on your cluster. You also need to enable X server (test by typing <tt>xclock</tt>). By typing <tt>gnuplot</tt>, you can start using following command lines. For a given (X,Y) data pair, the gnuplot command is<br />
<pre><br />
gnuplot> plot "filename" using 1:2 with lines<br />
</pre><br />
where "using 1:2" means plotting using the 1st and 2nd column from the given data file. "with lines" is a style option, you can change to "with points", "with steps", "with dots" or "with impulses". Click [http://t16web.lanl.gov/Kawano/gnuplot/intro/style-e.html] for a detailed description of the styles.<br />
To draw multiple lines, you can type<br />
<pre><br />
gnuplot> plot "A" using 1:2 title "data A" with lines, \<br />
"B" u 1:2 t "data B" with p, \<br />
"C" u 2:3 t "data C" w d<br />
</pre><br />
You can use \ to separate continuous lines. <tt>title</tt> is used to label different lines. You can abbreviate some of the commands, for example, u for using, t for title, w for with, l for lines, p for points and d for dots.<br />
<br />
To change the labels of X and Y axes, you can use<br />
<pre><br />
gnuplot> set xlabel "x-axis"<br />
gnuplot> set ylabel "y-xais"<br />
gnuplot> set title "y vs x"<br />
gnuplot> replot<br />
</pre><br />
You can also change the ranges of X and Y axes,<br />
<pre><br />
gnuplot> set xrange [0:2]<br />
gnuplot> set yrange [0:1]<br />
gnuplot> replot<br />
</pre><br />
<br />
==How to visualize the results==<br />
===xwindow===<br />
===Atomeye===<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
===What if the job is stopped===</div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5014ParaDiS Manual Updated2011-01-12T22:42:57Z<p>Jieyin: /* Gnuplot */</p>
<hr />
<div>Under construction by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. This guide includes following how-tos:<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following lines exist<br />
<br />
===How to set up ctrl-file===<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
Before using gnuplot, make sure it is installed on your cluster. You also need to enable X server (test by typing <tt>xclock</tt>). By typing <tt>gnuplot</tt>, you can start using following command lines. For a given (X,Y) data pair, the gnuplot command is<br />
<pre><br />
gnuplot> plot "filename" using 1:2 with lines<br />
</pre><br />
where "using 1:2" means plotting using the 1st and 2nd column from the given data file. "with lines" is a style option, you can change to "with points", "with steps", "with dots" or "with impulses". Click [http://t16web.lanl.gov/Kawano/gnuplot/intro/style-e.html] for a detailed description of the styles.<br />
To draw multiple lines, you can type<br />
<pre><br />
gnuplot> plot "A" using 1:2 title "data A" with lines, \<br />
"B" u 1:2 t "data B" with p, \<br />
"C" u 2:3 t "data C" w l<br />
</pre><br />
You can use \ to separate continuous lines. <tt>title</tt> is used to label different lines. You can abbreviate some of the commands, for example, u for using, t for title, w for with, l for lines and p for points.<br />
To change the labels of X and Y axes, you can use<br />
<pre><br />
gnuplot> set xlabel "x-axis"<br />
gnuplot> set ylabel "y-xais"<br />
gnuplot> set title "y vs x"<br />
gnuplot> replot<br />
</pre><br />
You can also change the ranges of X and Y axes,<br />
<pre><br />
gnuplot> set xrange [0:2]<br />
gnuplot> set yrange [0:1]<br />
gnuplot> replot<br />
</pre><br />
<br />
==How to visualize the results==<br />
===xwindow===<br />
===Atomeye===<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
===What if the job is stopped===</div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5013ParaDiS Manual Updated2011-01-12T22:42:24Z<p>Jieyin: /* Gnuplot */</p>
<hr />
<div>Under construction by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. This guide includes following how-tos:<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following lines exist<br />
<br />
===How to set up ctrl-file===<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
Before using gnuplot, make sure it is installed on your cluster. You also need to enable X server (test by typing <tt>xclock</tt>). By typing <tt>gnuplot</tt>, you can start using following command lines. For a given (X,Y) data pair, the gnuplot command is<br />
<pre><br />
gnuplot> plot "filename" using 1:2 with lines<br />
</pre><br />
where "using 1:2" means plotting using the 1st and 2nd column from the given data file. "with lines" is a style option, you can change to "with points", "with steps", "with dots" or "with impulses". Click [here|http://t16web.lanl.gov/Kawano/gnuplot/intro/style-e.html] for a detailed description of the styles.<br />
To draw multiple lines, you can type<br />
<pre><br />
gnuplot> plot "A" using 1:2 title "data A" with lines, \<br />
"B" u 1:2 t "data B" with p, \<br />
"C" u 2:3 t "data C" w l<br />
</pre><br />
You can use \ to separate continuous lines. <tt>title</tt> is used to label different lines. You can abbreviate some of the commands, for example, u for using, t for title, w for with, l for lines and p for points.<br />
To change the labels of X and Y axes, you can use<br />
<pre><br />
gnuplot> set xlabel "x-axis"<br />
gnuplot> set ylabel "y-xais"<br />
gnuplot> set title "y vs x"<br />
gnuplot> replot<br />
</pre><br />
You can also change the ranges of X and Y axes,<br />
<pre><br />
gnuplot> set xrange [0:2]<br />
gnuplot> set yrange [0:1]<br />
gnuplot> replot<br />
</pre><br />
<br />
==How to visualize the results==<br />
===xwindow===<br />
===Atomeye===<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
===What if the job is stopped===</div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5012ParaDiS Manual Updated2011-01-12T22:42:07Z<p>Jieyin: /* Gnuplot */</p>
<hr />
<div>Under construction by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. This guide includes following how-tos:<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following lines exist<br />
<br />
===How to set up ctrl-file===<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
Before using gnuplot, make sure it is installed on your cluster. You also need to enable X server (test by typing <tt>xclock</tt>). By typing <tt>gnuplot</tt>, you can start using following command lines. For a given (X,Y) data pair, the gnuplot command is<br />
<pre><br />
gnuplot> plot "filename" using 1:2 with lines<br />
</pre><br />
where "using 1:2" means plotting using the 1st and 2nd column from the given data file. "with lines" is a style option, you can change to "with points", "with steps", "with dots" or "with impulses". Click [here,http://t16web.lanl.gov/Kawano/gnuplot/intro/style-e.html] for a detailed description of the styles.<br />
To draw multiple lines, you can type<br />
<pre><br />
gnuplot> plot "A" using 1:2 title "data A" with lines, \<br />
"B" u 1:2 t "data B" with p, \<br />
"C" u 2:3 t "data C" w l<br />
</pre><br />
You can use \ to separate continuous lines. <tt>title</tt> is used to label different lines. You can abbreviate some of the commands, for example, u for using, t for title, w for with, l for lines and p for points.<br />
To change the labels of X and Y axes, you can use<br />
<pre><br />
gnuplot> set xlabel "x-axis"<br />
gnuplot> set ylabel "y-xais"<br />
gnuplot> set title "y vs x"<br />
gnuplot> replot<br />
</pre><br />
You can also change the ranges of X and Y axes,<br />
<pre><br />
gnuplot> set xrange [0:2]<br />
gnuplot> set yrange [0:1]<br />
gnuplot> replot<br />
</pre><br />
<br />
==How to visualize the results==<br />
===xwindow===<br />
===Atomeye===<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
===What if the job is stopped===</div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5011ParaDiS Manual Updated2011-01-12T22:41:00Z<p>Jieyin: /* Gnuplot */</p>
<hr />
<div>Under construction by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. This guide includes following how-tos:<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following lines exist<br />
<br />
===How to set up ctrl-file===<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
Before using gnuplot, make sure it is installed on your cluster. You also need to enable X server (test by typing <tt>xclock</tt>). By typing <tt>gnuplot</tt>, you can start using following command lines. For a given (X,Y) data pair, the gnuplot command is<br />
<pre><br />
gnuplot> plot "filename" using 1:2 with lines<br />
</pre><br />
where "using 1:2" means plotting using the 1st and 2nd column from the given data file. "with lines" is a style option, you can change to "with points", "with steps", "with dots" or "with impulses". Click here[http://t16web.lanl.gov/Kawano/gnuplot/intro/style-e.html] for a detailed description of the styles.<br />
To draw multiple lines, you can type<br />
<pre><br />
gnuplot> plot "A" using 1:2 title "data A" with lines, \<br />
"B" u 1:2 t "data B" with p, \<br />
"C" u 2:3 t "data C" w l<br />
</pre><br />
You can use \ to separate continuous lines. <tt>title</tt> is used to label different lines. You can abbreviate some of the commands, for example, u for using, t for title, w for with, l for lines and p for points.<br />
To change the labels of X and Y axes, you can use<br />
<pre><br />
gnuplot> set xlabel "x-axis"<br />
gnuplot> set ylabel "y-xais"<br />
gnuplot> set title "y vs x"<br />
gnuplot> replot<br />
</pre><br />
You can also change the ranges of X and Y axes,<br />
<pre><br />
gnuplot> set xrange [0:2]<br />
gnuplot> set yrange [0:1]<br />
gnuplot> replot<br />
</pre><br />
<br />
==How to visualize the results==<br />
===xwindow===<br />
===Atomeye===<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
===What if the job is stopped===</div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5010ParaDiS Manual Updated2011-01-12T22:39:01Z<p>Jieyin: /* Gnuplot */</p>
<hr />
<div>Under construction by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. This guide includes following how-tos:<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following lines exist<br />
<br />
===How to set up ctrl-file===<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
Before using gnuplot, make sure it is installed on your cluster. You also need to enable X server (test by typing <tt>xclock</tt>). By typing <tt>gnuplot</tt>, you can start using following command lines. For a given (X,Y) data pair, the gnuplot command is<br />
<pre><br />
gnuplot> plot "filename" using 1:2 with lines<br />
</pre><br />
where "using 1:2" means plotting using the 1st and 2nd column from the given data file. "with lines" is a style option, you can change to "with points", "with steps", "with dots" or "with impulses". Click [here http://t16web.lanl.gov/Kawano/gnuplot/intro/style-e.html] for a detailed description of the styles.<br />
To draw multiple lines, you can type<br />
<pre><br />
gnuplot> plot "A" using 1:2 title "data A" with lines, \<br />
"B" u 1:2 t "data B" with p, \<br />
"C" u 2:3 t "data C" w l<br />
</pre><br />
You can use \ to separate continuous lines. <tt>title</tt> is used to label different lines. You can abbreviate some of the commands, for example, u for using, t for title, w for with, l for lines and p for points.<br />
To change the labels of X and Y axes, you can use<br />
<pre><br />
gnuplot> set xlabel "x-axis"<br />
gnuplot> set ylabel "y-xais"<br />
gnuplot> set title "y vs x"<br />
gnuplot> replot<br />
</pre><br />
You can also change the ranges of X and Y axes,<br />
<pre><br />
gnuplot> set xrange [0:2]<br />
gnuplot> set yrange [0:1]<br />
gnuplot> replot<br />
</pre><br />
<br />
==How to visualize the results==<br />
===xwindow===<br />
===Atomeye===<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
===What if the job is stopped===</div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5009ParaDiS Manual Updated2011-01-12T22:38:48Z<p>Jieyin: /* Gnuplot */</p>
<hr />
<div>Under construction by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. This guide includes following how-tos:<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following lines exist<br />
<br />
===How to set up ctrl-file===<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
Before using gnuplot, make sure it is installed on your cluster. You also need to enable X server (test by typing <tt>xclock</tt>). By typing <tt>gnuplot</tt>, you can start using following command lines. For a given (X,Y) data pair, the gnuplot command is<br />
<pre><br />
gnuplot> plot "filename" using 1:2 with lines<br />
</pre><br />
where "using 1:2" means plotting using the 1st and 2nd column from the given data file. "with lines" is a style option, you can change to "with points", "with steps", "with dots" or "with impulses". Click [http://t16web.lanl.gov/Kawano/gnuplot/intro/style-e.html] for a detailed description of the styles.<br />
To draw multiple lines, you can type<br />
<pre><br />
gnuplot> plot "A" using 1:2 title "data A" with lines, \<br />
"B" u 1:2 t "data B" with p, \<br />
"C" u 2:3 t "data C" w l<br />
</pre><br />
You can use \ to separate continuous lines. <tt>title</tt> is used to label different lines. You can abbreviate some of the commands, for example, u for using, t for title, w for with, l for lines and p for points.<br />
To change the labels of X and Y axes, you can use<br />
<pre><br />
gnuplot> set xlabel "x-axis"<br />
gnuplot> set ylabel "y-xais"<br />
gnuplot> set title "y vs x"<br />
gnuplot> replot<br />
</pre><br />
You can also change the ranges of X and Y axes,<br />
<pre><br />
gnuplot> set xrange [0:2]<br />
gnuplot> set yrange [0:1]<br />
gnuplot> replot<br />
</pre><br />
<br />
==How to visualize the results==<br />
===xwindow===<br />
===Atomeye===<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
===What if the job is stopped===</div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5008ParaDiS Manual Updated2011-01-12T22:38:22Z<p>Jieyin: /* Gnuplot */</p>
<hr />
<div>Under construction by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. This guide includes following how-tos:<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following lines exist<br />
<br />
===How to set up ctrl-file===<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
Before using gnuplot, make sure it is installed on your cluster. You also need to enable X server (test by typing <tt>xclock</tt>). By typing <tt>gnuplot</tt>, you can start using following command lines. For a given (X,Y) data pair, the gnuplot command is<br />
<pre><br />
gnuplot> plot "filename" using 1:2 with lines<br />
</pre><br />
where "using 1:2" means plotting using the 1st and 2nd column from the given data file. "with lines" is a style option, you can change to "with points", "with steps", "with dots" or "with impulses". Click [here]http://t16web.lanl.gov/Kawano/gnuplot/intro/style-e.html for a detailed description of the styles.<br />
To draw multiple lines, you can type<br />
<pre><br />
gnuplot> plot "A" using 1:2 title "data A" with lines, \<br />
"B" u 1:2 t "data B" with p, \<br />
"C" u 2:3 t "data C" w l<br />
</pre><br />
You can use \ to separate continuous lines. <tt>title</tt> is used to label different lines. You can abbreviate some of the commands, for example, u for using, t for title, w for with, l for lines and p for points.<br />
To change the labels of X and Y axes, you can use<br />
<pre><br />
gnuplot> set xlabel "x-axis"<br />
gnuplot> set ylabel "y-xais"<br />
gnuplot> set title "y vs x"<br />
gnuplot> replot<br />
</pre><br />
You can also change the ranges of X and Y axes,<br />
<pre><br />
gnuplot> set xrange [0:2]<br />
gnuplot> set yrange [0:1]<br />
gnuplot> replot<br />
</pre><br />
<br />
==How to visualize the results==<br />
===xwindow===<br />
===Atomeye===<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
===What if the job is stopped===</div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5007ParaDiS Manual Updated2011-01-12T22:36:25Z<p>Jieyin: /* Gnuplot */</p>
<hr />
<div>Under construction by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. This guide includes following how-tos:<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following lines exist<br />
<br />
===How to set up ctrl-file===<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
Before using gnuplot, make sure it is installed on your cluster. You also need to enable X server (test by typing <tt>xclock</tt>). By typing <tt>gnuplot</tt>, you can start using following command lines. For a given (X,Y) data pair, the gnuplot command is<br />
<pre><br />
gnuplot> plot "filename" using 1:2 with lines<br />
</pre><br />
where "using 1:2" means plotting using the 1st and 2nd column from the given data file. "with lines" is a style option, you can change to "with points", "with steps" or "with impulses".<br />
To draw multiple lines, you can type<br />
<pre><br />
gnuplot> plot "A" using 1:2 title "data A" with lines, \<br />
"B" u 1:2 t "data B" with p, \<br />
"C" u 2:3 t "data C" w l<br />
</pre><br />
You can use \ to separate continuous lines. <tt>title</tt> is used to label different lines. You can abbreviate some of the commands, for example, u for using, t for title, w for with, l for lines and p for points.<br />
To change the labels of X and Y axes, you can use<br />
<pre><br />
gnuplot> set xlabel "x-axis"<br />
gnuplot> set ylabel "y-xais"<br />
gnuplot> set title "y vs x"<br />
gnuplot> replot<br />
</pre><br />
You can also change the ranges of X and Y axes,<br />
<pre><br />
gnuplot> set xrange [0:2]<br />
gnuplot> set yrange [0:1]<br />
gnuplot> replot<br />
</pre><br />
<br />
==How to visualize the results==<br />
===xwindow===<br />
===Atomeye===<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
===What if the job is stopped===</div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5006ParaDiS Manual Updated2011-01-12T22:35:22Z<p>Jieyin: /* Gnuplot */</p>
<hr />
<div>Under construction by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. This guide includes following how-tos:<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following lines exist<br />
<br />
===How to set up ctrl-file===<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
Before using gnuplot, make sure it is installed on your cluster. You also need to enable X server (test by typing <tt>xclock</tt>). By typing <tt>gnuplot</tt>, you can start using following command lines. For a given (X,Y) data pair, the gnuplot command is<br />
<pre><br />
gnuplot> plot "filename" using 1:2 with lines<br />
</pre><br />
where "using 1:2" means plotting using the 1st and 2nd column from the given data file. "with lines" is a style option, you can change to "with points", "with steps" or "with impulses".<br />
To draw multiple lines, you can type<br />
<pre><br />
gnuplot> plot "A" using 1:2 title "data A" with lines, \<br />
"B" u 1:2 t "data B" with p, \<br />
"C" u 2:3 t "data C" w l<br />
</pre><br />
You can use \ to separate continuous lines. <tt>title</tt> is used to label different lines. You can abbreviate some of the commands, for example, u for using, t for title, w for with, l for lines and p for points.<br />
To change the labels of X and Y axes, you can use<br />
<pre><br />
gnuplot> set xlabel "x-axis"<br />
gnuplot> set ylabel "y-xais"<br />
gnuplot> set title "y vs x"<br />
gnuplot> replot<br />
</pre><br />
<br />
==How to visualize the results==<br />
===xwindow===<br />
===Atomeye===<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
===What if the job is stopped===</div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5005ParaDiS Manual Updated2011-01-12T22:35:03Z<p>Jieyin: /* Gnuplot */</p>
<hr />
<div>Under construction by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. This guide includes following how-tos:<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following lines exist<br />
<br />
===How to set up ctrl-file===<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
Before using gnuplot, make sure it is installed on your cluster. You also need to enable X server (test by typing <tt>xclock</tt>). By typing <tt>gnuplot</tt>, you can start using following command lines. For a given (X,Y) data pair, the gnuplot command is<br />
<pre><br />
gnuplot> plot "filename" using 1:2 with lines<br />
</pre><br />
where "using 1:2" means plotting using the 1st and 2nd column from the given data file. "with lines" is a style option, you can change to "with points", "with steps" or "with impulses".<br />
To draw multiple lines, you can type<br />
<pre><br />
gnuplot> plot "A" using 1:2 title "data A" with lines, \<br />
"B" u 1:2 t "data B" with p, \<br />
"C" u 2:3 t "data C" w l<br />
</pre><br />
You can use \ to separate continuous lines. <tt>title</tt> is used to label different lines. You can abbreviate some of the commands, for example, u for using, t for title, w for with, l for lines and p for points.<br />
To change the labels of X and Y axes, you can use<br />
<pre><br />
gnuplot> set xlabel "x-axis"<br />
gnuplot> set ylabel "y-xais"<br />
gnuplot> set title "y vs x"<br />
replot<br />
</pre><br />
<br />
==How to visualize the results==<br />
===xwindow===<br />
===Atomeye===<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
===What if the job is stopped===</div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5004ParaDiS Manual Updated2011-01-12T22:30:36Z<p>Jieyin: /* Gnuplot */</p>
<hr />
<div>Under construction by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. This guide includes following how-tos:<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following lines exist<br />
<br />
===How to set up ctrl-file===<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
Before using gnuplot, make sure it is installed on your cluster. You also need to enable X server (test by typing <tt>xclock</tt>). For a given (X,Y) data pair, the gnuplot command is<br />
<pre><br />
plot "filename" using 1:2 with lines<br />
</pre><br />
where "using 1:2" means plotting using the 1st and 2nd column from the given data file. "with lines" is a style option, you can change to "with points", "with steps" or "with impulses".<br />
To draw multiple lines, you can type<br />
<pre><br />
plot "A" using 1:2 title "data A" with lines, \<br />
"B" u 1:2 t "data B" with p, \<br />
"C" u 2:3 t "data C" w l<br />
</pre><br />
You can use \ to separate continuous lines. <tt>title</tt> is used to label different lines. You can abbreviate some of the commands, for example, u for using, t for title, w for with, l for lines and p for points.<br />
<br />
==How to visualize the results==<br />
===xwindow===<br />
===Atomeye===<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
===What if the job is stopped===</div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5003ParaDiS Manual Updated2011-01-12T22:23:00Z<p>Jieyin: /* Gnuplot */</p>
<hr />
<div>Under construction by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. This guide includes following how-tos:<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following lines exist<br />
<br />
===How to set up ctrl-file===<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
Before using gnuplot, make sure it is installed on your cluster. You also need to enable X server (test by typing <tt>xclock</tt>). For a given (X,Y) data pair, the gnuplot command is<br />
<pre><br />
plot "filename" using 1:2 with lines<br />
</pre><br />
where "using 1:2" means plotting using the 1st and 2nd column from the given data file. "with lines" is a style option, you can change to "with points", "with steps" or "with impulses".<br />
<br />
==How to visualize the results==<br />
===xwindow===<br />
===Atomeye===<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
===What if the job is stopped===</div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5002ParaDiS Manual Updated2011-01-12T22:14:32Z<p>Jieyin: /* Description of recorded properties */</p>
<hr />
<div>Under construction by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. This guide includes following how-tos:<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following lines exist<br />
<br />
===How to set up ctrl-file===<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
<br />
==How to visualize the results==<br />
===xwindow===<br />
===Atomeye===<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
===What if the job is stopped===</div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5001ParaDiS Manual Updated2011-01-12T22:14:13Z<p>Jieyin: /* Description of recorded properties */</p>
<hr />
<div>Under construction by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. This guide includes following how-tos:<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following lines exist<br />
<br />
===How to set up ctrl-file===<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/$m^2$)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
<br />
==How to visualize the results==<br />
===xwindow===<br />
===Atomeye===<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
===What if the job is stopped===</div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=5000ParaDiS Manual Updated2011-01-12T22:13:49Z<p>Jieyin: /* Where to find the recorded properties */</p>
<hr />
<div>Under construction by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. This guide includes following how-tos:<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following lines exist<br />
<br />
===How to set up ctrl-file===<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Description of recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
<br />
==How to visualize the results==<br />
===xwindow===<br />
===Atomeye===<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
===What if the job is stopped===</div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=4999ParaDiS Manual Updated2011-01-12T22:13:30Z<p>Jieyin: /* Where to find the recorded properties */</p>
<hr />
<div>Under construction by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. This guide includes following how-tos:<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following lines exist<br />
<br />
===How to set up ctrl-file===<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Where to find the recorded properties===<br />
By default, properties are saved to the following path<br />
<pre><br />
~/Codes/ParaDiS/outputs/ctrl_file_name/properties<br />
</pre><br />
<br />
Usually there are six files. <br />
<br />
1 <tt>time_Plastic_strain</tt> contains two columns of data:<br />
1: elapsed simulation time<br />
2: plastic strain<br />
2 <tt>stress_Plastic_strain</tt> is generated only if loadType = 1 (constant strain rate) or 4 (cyclic loading). The first two columns of this file are plastic strain and stress respectively.<br />
3 <tt>stress_Total_strain </tt> is generated only if loadType = 1. The first two columns of this file are total strain and stress. Notice that total strain is the sum of plastic strain and elastic strain. <br />
4 <tt>density</tt> The first three columns of this file are<br />
1: plastic strain<br />
2: total strain<br />
3: dislocation density (/m^2)<br />
5 <tt>alleps</tt> contrains 9 columns of data:<br />
1: smulation timestep number<br />
2: elapsed simulation time<br />
3-8: plastic strain component<br />
9: dislocation density<br />
6 <tt>epsdot</tt> contains 2 columns of data<br />
1: elapsed simulation time<br />
2: plastic strain rate<br />
<br />
For detailed descriptions of the recorded data, please refer to the official ParaDiS manual.<br />
<br />
===Gnuplot===<br />
<br />
==How to visualize the results==<br />
===xwindow===<br />
===Atomeye===<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
===What if the job is stopped===</div>Jieyinhttp://micro.stanford.edu/mediawiki/index.php?title=ParaDiS_Manual_Updated&diff=4998ParaDiS Manual Updated2011-01-12T21:37:37Z<p>Jieyin: /* Settings in the ctrl file */</p>
<hr />
<div>Under construction by Jie Yin<br />
<br />
Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. This guide includes following how-tos:<br />
<br />
==How to obtain the latest ParaDiS codes==<br />
<br />
It is highly recommended to create directory <tt>Codes</tt> under your home directory. Currently ParaDiS codes are maintained through Subversion. For current group members or collaborators, you can '''obtain''' the latest version of ParaDiS by typing the following,<br />
<br />
<pre><br />
cd ~/Codes<br />
svn co https://micro.stanford.edu/svn/ParaDiS [./dirname]<br />
</pre><br />
<br />
Directory <tt>~/Codes/ParaDiS</tt> (or <tt>~/Codes/dirname</tt>) will be created with latest checked out revision. It is your svn local repository. You can '''update''' your local ParaDiS codes by simply typing<br />
<br />
<pre><br />
cd ~/Codes/ParaDiS<br />
svn update<br />
</pre><br />
<br />
If you create a new file called <tt>newfile.c</tt>, you can '''add''' it to your local repository <tt> ~/Codes/ParaDiS </tt><br />
<br />
<pre><br />
$ svn add newfile.c<br />
</pre><br />
<br />
or '''commit''' the change to ParaDiS codes after some modifications<br />
<br />
<pre><br />
$ svn commit newfile.c<br />
</pre><br />
<br />
==How to compile ParaDiS==<br />
<br />
'''Before compilation''', you need to modify the '''settings''' in <tt>makefile.setup</tt>, which is under directory <tt>~/Codes/ParaDiS</tt>. Currently many system types are supported. In the first few lines, you can see following lines<br />
<br />
<pre><br />
SYS = wcr<br />
<br />
MODE = SERIAL<br />
#MODE = PARALLEL<br />
<br />
#XLIB_MODE = OFF<br />
XLIB = MODE = ON<br />
</pre><br />
<br />
<tt>SYS</tt> defines the system type. Detailed descriptions can be found in file <tt>makefile.sys</tt>. You can also change to <tt>linux</tt> if it best described your system type. <br />
<br />
<tt>MODE</tt> is the execution mode. <tt>PARALLEL</tt> is to enable compile-time support for MPI and multi-CPU support and <tt>SERIAL</tt> is for single-CPU compilation. Usually <tt>SERIAL</tt> is used for debugging and visulization purpose. For computation intensive jobs, you should choose <tt>PARALLEL</tt> mode.<br />
<br />
<tt>XLIB_MODE = ON</tt> is only valid when you want to enable xwindow plotting capability (at the same time <tt>MODE = SERIAL</tt> ). Otherwise you should set it <tt>OFF</tt>.<br />
<br />
'''After saving your settings''', you can start compilation by simply typing the following,<br />
<br />
<pre><br />
$ make<br />
</pre><br />
<br />
If you want to compile faster on a multi-CPU machine, you can use command<br />
<br />
<pre><br />
$ make -j8<br />
</pre><br />
<br />
where 8 means the number of processors used for compilation.<br />
<br />
If you want to re-compile ParaDiS, e.g. after some modification to source files or system settings, you need to "make clean" before "make"<br />
<br />
<pre><br />
$ make clean<br />
</pre><br />
<br />
==How to run a test case==<br />
<br />
To run a DD simulation, you need to prepare <tt>.ctrl</tt> file and <tt>.data</tt> file. <tt>.ctrl</tt> file includes controlling parameters needed for the simulation while <tt>.data</tt> file usually describe the geometric parameters of the simulation system, e.g. cell size, nodal coordinates. To run a test case, the basic command is shown as following<br />
<br />
<pre><br />
bin/paradis -d runs/testfile.data runs/testfile.ctrl<br />
</pre><br />
<br />
The executable is <tt>paradis</tt>. When <tt>-d</tt> is used, your <tt>.data</tt> file does not have to be in the same directory or of the same name as your <tt>.ctrl</tt> file. In most cases, people create the two files with same names and put them under the same directory, then you can use<br />
<br />
<pre><br />
bin/paradis runs/testfile.ctrl<br />
</pre><br />
<br />
===How to set up data-file===<br />
In most <tt>.data</tt> files, following lines exist<br />
<br />
===How to set up ctrl-file===<br />
===How to create input files with Matlab===<br />
<br />
==How to record properties==<br />
===Settings in the ctrl file===<br />
At the bottom of <tt>.ctrl</tt> file, following lines are needed,<br />
<pre><br />
#Save Properties<br />
saveprop = 1 <br />
savepropfreq = 1<br />
</pre><br />
which indicate saving properties is enabled and the saving frequency is once per simulation step.<br />
<br />
===Where to find the recorded properties===<br />
===Gnuplot===<br />
<br />
==How to visualize the results==<br />
===xwindow===<br />
===Atomeye===<br />
<br />
==How to submit parallel jobs==<br />
===pbs file===<br />
===What if the job is stopped===</div>Jieyin