PARADISCYL:Test-Run
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Manual 02 for ParaDiS Cylinder Codes
How to run test simulations
This document describes the extension of the ParaDiS program that implements the cylindrical free surface boundary condition. This extension is based on Weinberger and Cai, J. Mech. Phys. Solids, 55, 2027 (2007)(PDF). The code is written by Chris Weinberger. It is owned by Chris and is not included in the standard distribution of ParaDiS. Keonwook Kang wrote the first draft of this document, which was later revised by Chris Weinberger and Wei Cai. Please read the manual of ParaDiS before reading this document.
Run command
The command line to run the ParaDiS Cylinder code is the same as that of the original ParaDiS code. See ParaDiS manual for details. The command line format is:
paradiscyl [-r <numCycles>] [-d dataFile] <controlFile>
where:
| <ctrlFile> | Specifies the name of the ParaDiS control parameter file | ||
| -d <dataFile> | Specifies the base name of the file(s) containing the nodal data for the run. If this file name is not supplied, the code looks for a data file named the same as the control file with the file name suffix (if any) replaced with ".data" | ||
| -r <numCycles> | Causes the code to execute a series of <numCycles> cycles during which no force calculations or dislocation movement will occur. These cycles will be used strictly for load-balancing purposes and will be done before the normal cycles. This can be useful when a simulation is started with a uniform domain decomposition and needs time to converge on an optimal decomposition as would occur when restarting a simulation on a different number of cpus |
Examples
Run the following control file, which simulates a dislocation loop inside a cylinder. You will need two input files: one is control file (concentric_loop_test.ctrl) and the other is data file (concentric_loop_test.data). Both files are shown below. See here for details about input files.
$ bin/paradiscyl runs/concentric_loop_test.ctrl
If you see a new pop-up window shown in Fig.1, you are ready to exploit this tool.
Fig.1 ParaDiS Cylinder Codes Test Run. A dislocation loop in a cylinder
concentric_loop_test.ctrl
### DD3d configuration file (use -*-shell-script-*- format) # # input file to be used in conjunction with # the concentric_loop_test.data file. # #Directory to write output files dirname = "outputs/concentric_loop_test" #Input files for PBC image stresses Rijmfile = "inputs/Rijm.cube.out" RijmPBCfile = "inputs/RijmPBC.cube.out" #Total simulation steps maxstep = 100 #The total number of CPUs should be numXdoms * numYdoms * numZdoms numXdoms = 1 numYdoms = 1 numZdoms = 1 #Cells for dislocation grouping (cannot be less than 3) numXcells = 3 numYcells = 3 numZcells = 3 #Fast multipole method specs. fmEnabled = 0 #disable fast multipole fmMPOrder = 2 fmTaylorOrder = 4 fmCorrectionTbl = "inputs/fm-ctab.m2.t4.dat" timestepIntegrator = "backward-euler" # This is necessary! not really repeated from data file! xBoundMin = -3.0e0 xBoundMax = 3.0e0 yBoundMin = -3.0e0 yBoundMax = 3.0e0 zBoundMin = -3.0e0 zBoundMax = 3.0e0 #Boundary Conditions xBoundType = 1 #Free yBoundType = 1 #Free zBoundType = 1 #Free #fundamental length unit #burgMag = 2.725e-10 #(in m) burgMag = 1.0e0 #Elastic constants shearModulus = 1.0e+0 pois = 3.050000e-01 #Mobility Law Function mobilityLaw = "BCC_0a" MobScrew = 1e0 MobEdge = 1e1 MobClimb = 1e-8 CheckScrew = 0.95 #Remesh Rule remeshRule = 2 #Discretization minSeg = 3.000000e-03 maxSeg = 1.000000e-01 maxDT = 1.000000e+02 #Maximum nodal displacement at each time step rmax = 1e0 #Core cut-off radius rc = 1.0e-3 #Core energy Ecore = 0.0e+0 #Turn on elastic interaction elasticinteraction = 1 #Applied stress in Pa (xx,yy,zz,yz,zx,xy) #appliedStress = [ 0. 0. -9e+0 0. 0. 0. ] #appliedStress = [ 0 0 0 0 -3e0 0 ] appliedStress = [ 0 0 0 0 0 0 ] loadType = 0 indxErate = 2 edotdir = [ 0 0 1 ] eRate = 150 #Output specs. savecn = 1 savecnfreq = 10 savecndt = -1.000000e+00 savecntime = 0.000000e+00 savecncounter = 0 saveprop = 1 savepropfreq = 10 savepropdetail = 100 savepropdt = -1.000000e+00 saveproptime = 0.000000e+00 armfile = 1 armfiledt = 1e-3 #Binary restart files binrestart = 0 #write text instead of binary restart file binfile = ""
concentric_loop_test.data
#
# ParaDiS nodal data file (by create_loop_data.tcl)
#
#
# File version number
#
2
#
# Number of data file segments
#
1
#
# Minimum coordinate values (x, y, z)
#
-3 -3 -3
#
# Maximum coordinate values (x, y, z)
#
3 3 3
#
# Node count
#
50
#
# Domain geometry (x, y, z)
#
1 1 1
#
# Domain boundaries (x, y, z)
#
-3
-3
-3
3
3
3
#
# Primary lines: node_tag, x, y, z, num_arms, constraint
# Secondary lines: arm_tag, burgx, burgy, burgz, nx, ny, nz
#
# length in unit of burgMag
10,0 7.9369176105158235e-01 1.0026658685144341e-01 0 2 0
10,1 1 0 0
0 0 1
10,49 -1 0 0
0 0 1
10,1 7.7486652890290486e-01 1.9895190973188384e-01 0 2 0
10,2 1 0 0
0 0 1
10,0 -1 0 0
0 0 1
10,2 7.4382118871060121e-01 2.9449964214774232e-01 0 2 0
10,3 1 0 0
0 0 1
10,1 -1 0 0
0 0 1
10,3 7.0104534403509089e-01 3.8540293928137226e-01 0 2 0
10,4 1 0 0
0 0 1
10,2 -1 0 0
0 0 1
10,4 6.4721359549995805e-01 4.7022820183397851e-01 0 2 0
10,5 1 0 0
0 0 1
10,3 -1 0 0
0 0 1
10,5 5.8317490193712929e-01 5.4763768474295094e-01 0 2 0
10,6 1 0 0
0 0 1
10,4 -1 0 0
0 0 1
10,6 5.0993919179895186e-01 6.1641059422063149e-01 0 2 0
10,7 1 0 0
0 0 1
10,5 -1 0 0
0 0 1
10,7 4.2866143598319728e-01 6.7546234040161213e-01 0 2 0
10,8 1 0 0
0 0 1
10,6 -1 0 0
0 0 1
10,8 3.4062343325205813e-01 7.2386164197281566e-01 0 2 0
10,9 1 0 0
0 0 1
10,7 -1 0 0
0 0 1
10,9 2.4721359549995797e-01 7.6084521303612285e-01 0 2 0
10,10 1 0 0
0 0 1
10,8 -1 0 0
0 0 1
10,10 1.4990505166857981e-01 7.8582980058295093e-01 0 2 0
10,11 1 0 0
0 0 1
10,9 -1 0 0
0 0 1
10,11 5.0232415623450821e-02 7.9842138274261731e-01 0 2 0
10,12 1 0 0
0 0 1
10,10 -1 0 0
0 0 1
10,12 -5.0232415623450724e-02 7.9842138274261731e-01 0 2 0
10,13 1 0 0
0 0 1
10,11 -1 0 0
0 0 1
10,13 -1.4990505166857970e-01 7.8582980058295104e-01 0 2 0
10,14 1 0 0
0 0 1
10,12 -1 0 0
0 0 1
10,14 -2.4721359549995769e-01 7.6084521303612296e-01 0 2 0
10,15 1 0 0
0 0 1
10,13 -1 0 0
0 0 1
10,15 -3.4062343325205818e-01 7.2386164197281566e-01 0 2 0
10,16 1 0 0
0 0 1
10,14 -1 0 0
0 0 1
10,16 -4.2866143598319750e-01 6.7546234040161202e-01 0 2 0
10,17 1 0 0
0 0 1
10,15 -1 0 0
0 0 1
10,17 -5.0993919179895186e-01 6.1641059422063149e-01 0 2 0
10,18 1 0 0
0 0 1
10,16 -1 0 0
0 0 1
10,18 -5.8317490193712906e-01 5.4763768474295105e-01 0 2 0
10,19 1 0 0
0 0 1
10,17 -1 0 0
0 0 1
10,19 -6.4721359549995794e-01 4.7022820183397862e-01 0 2 0
10,20 1 0 0
0 0 1
10,18 -1 0 0
0 0 1
10,20 -7.0104534403509089e-01 3.8540293928137220e-01 0 2 0
10,21 1 0 0
0 0 1
10,19 -1 0 0
0 0 1
10,21 -7.4382118871060110e-01 2.9449964214774255e-01 0 2 0
10,22 1 0 0
0 0 1
10,20 -1 0 0
0 0 1
10,22 -7.7486652890290486e-01 1.9895190973188420e-01 0 2 0
10,23 1 0 0
0 0 1
10,21 -1 0 0
0 0 1
10,23 -7.9369176105158223e-01 1.0026658685144363e-01 0 2 0
10,24 1 0 0
0 0 1
10,22 -1 0 0
0 0 1
10,24 -8.0000000000000004e-01 9.7968508305790183e-17 0 2 0
10,25 1 0 0
0 0 1
10,23 -1 0 0
0 0 1
10,25 -7.9369176105158235e-01 -1.0026658685144343e-01 0 2 0
10,26 1 0 0
0 0 1
10,24 -1 0 0
0 0 1
10,26 -7.7486652890290497e-01 -1.9895190973188367e-01 0 2 0
10,27 1 0 0
0 0 1
10,25 -1 0 0
0 0 1
10,27 -7.4382118871060121e-01 -2.9449964214774232e-01 0 2 0
10,28 1 0 0
0 0 1
10,26 -1 0 0
0 0 1
10,28 -7.0104534403509078e-01 -3.8540293928137231e-01 0 2 0
10,29 1 0 0
0 0 1
10,27 -1 0 0
0 0 1
10,29 -6.4721359549995827e-01 -4.7022820183397818e-01 0 2 0
10,30 1 0 0
0 0 1
10,28 -1 0 0
0 0 1
10,30 -5.8317490193712940e-01 -5.4763768474295071e-01 0 2 0
10,31 1 0 0
0 0 1
10,29 -1 0 0
0 0 1
10,31 -5.0993919179895164e-01 -6.1641059422063149e-01 0 2 0
10,32 1 0 0
0 0 1
10,30 -1 0 0
0 0 1
10,32 -4.2866143598319706e-01 -6.7546234040161224e-01 0 2 0
10,33 1 0 0
0 0 1
10,31 -1 0 0
0 0 1
10,33 -3.4062343325205774e-01 -7.2386164197281588e-01 0 2 0
10,34 1 0 0
0 0 1
10,32 -1 0 0
0 0 1
10,34 -2.4721359549995806e-01 -7.6084521303612285e-01 0 2 0
10,35 1 0 0
0 0 1
10,33 -1 0 0
0 0 1
10,35 -1.4990505166857970e-01 -7.8582980058295104e-01 0 2 0
10,36 1 0 0
0 0 1
10,34 -1 0 0
0 0 1
10,36 -5.0232415623450571e-02 -7.9842138274261731e-01 0 2 0
10,37 1 0 0
0 0 1
10,35 -1 0 0
0 0 1
10,37 5.0232415623450266e-02 -7.9842138274261731e-01 0 2 0
10,38 1 0 0
0 0 1
10,36 -1 0 0
0 0 1
10,38 1.4990505166857943e-01 -7.8582980058295104e-01 0 2 0
10,39 1 0 0
0 0 1
10,37 -1 0 0
0 0 1
10,39 2.4721359549995781e-01 -7.6084521303612296e-01 0 2 0
10,40 1 0 0
0 0 1
10,38 -1 0 0
0 0 1
10,40 3.4062343325205746e-01 -7.2386164197281599e-01 0 2 0
10,41 1 0 0
0 0 1
10,39 -1 0 0
0 0 1
10,41 4.2866143598319745e-01 -6.7546234040161202e-01 0 2 0
10,42 1 0 0
0 0 1
10,40 -1 0 0
0 0 1
10,42 5.0993919179895142e-01 -6.1641059422063171e-01 0 2 0
10,43 1 0 0
0 0 1
10,41 -1 0 0
0 0 1
10,43 5.8317490193712895e-01 -5.4763768474295116e-01 0 2 0
10,44 1 0 0
0 0 1
10,42 -1 0 0
0 0 1
10,44 6.4721359549995794e-01 -4.7022820183397873e-01 0 2 0
10,45 1 0 0
0 0 1
10,43 -1 0 0
0 0 1
10,45 7.0104534403509056e-01 -3.8540293928137292e-01 0 2 0
10,46 1 0 0
0 0 1
10,44 -1 0 0
0 0 1
10,46 7.4382118871060121e-01 -2.9449964214774232e-01 0 2 0
10,47 1 0 0
0 0 1
10,45 -1 0 0
0 0 1
10,47 7.7486652890290486e-01 -1.9895190973188429e-01 0 2 0
10,48 1 0 0
0 0 1
10,46 -1 0 0
0 0 1
10,48 7.9369176105158223e-01 -1.0026658685144373e-01 0 2 0
10,49 1 0 0
0 0 1
10,47 -1 0 0
0 0 1
10,49 8.0000000000000004e-01 -1.9593701661158037e-16 0 2 0
10,0 1 0 0
0 0 1
10,48 -1 0 0
0 0 1
X Window
X Window control parameters
Default set of X window control parameters is given in the file, inputs/paradis.xdefaults. You can change window size, line width, rotation of angles, etc by modifying this file.
View control
Hot keys to manipulate the object displayed in the X window in Fig.1. For example, press r and then use arrow keys to rotate the object.
YWindow: yview: Mouse drag to rotate Hot Keys: F1 : display this message Up : rotate up Down : rotate down Left : rotate left Right : rotate right PgUp : rotate counterclockwise PgDn : rotate clockwise Home : back to initial viewpoint Space : stop rotate p : toggle pause t : translation s : scaling d : move projection infinity point r : rotation f : toggle pbc enableness m : toggle drawframe g : pbc glide x : pbc shift in x y : pbc shift in y z : pbc shift in z w : print window specification F9 : output gif F10 : output postscript
Tcl script to generate data file
In ParaDiS/tools directory, there is a tcl script create_loop_data.tcl. By typing the following commnad,
$ tools/create_loop_data.tcl
you will get the data file concentric_loop_test.data automatically. By manipulating this tcl script, you can easily create a data file for your own ParaDiS simulation.
create_loop_data.tcl
#!/usr/bin/tclsh
#Read status variable from the first argument (if any)
if { $argc == 0 } {
set status 0
} elseif { $argc > 0 } {
set status [lindex $argv 0]
}
puts "status = $status"
set datafile "runs/concentric_loop_test.data"
set version_number 2
set filesegments_number 1
set L 6
set cylinder_radius [expr $L/6]
set loop_rel_radius 0.8
set loop_radius [expr $cylinder_radius * $loop_rel_radius]
set xBoundMin [expr -$L/2]
set yBoundMin [expr -$L/2]
set zBoundMin [expr -$L/2]
set xBoundMax [expr $L/2]
set yBoundMax [expr $L/2]
set zBoundMax [expr $L/2]
set nodes_number 50
set burg_x 1
set burg_y 0
set burg_z 0
set normal_x 0
set normal_y 0
set normal_z 1
set domainID 10
set fileID [open $datafile w]
puts $fileID "#"
puts $fileID "# ParaDiS nodal data file (by create_loop_data.tcl) "
puts $fileID "#"
puts $fileID " "
puts $fileID "#"
puts $fileID "# File version number"
puts $fileID "#"
puts $fileID " "
puts $fileID "$version_number"
puts $fileID " "
puts $fileID "#"
puts $fileID "# Number of data file segments"
puts $fileID "#"
puts $fileID " "
puts $fileID "$filesegments_number"
puts $fileID " "
puts $fileID "#"
puts $fileID "# Minimum coordinate values (x, y, z)"
puts $fileID "#"
puts $fileID ""
puts $fileID "$xBoundMin $yBoundMin $zBoundMin "
puts $fileID " "
puts $fileID "#"
puts $fileID "# Maximum coordinate values (x, y, z)"
puts $fileID "#"
puts $fileID " "
puts $fileID "$xBoundMax $yBoundMax $zBoundMax "
puts $fileID " "
puts $fileID "#"
puts $fileID "# Node count"
puts $fileID "#"
puts $fileID " "
puts $fileID "$nodes_number "
puts $fileID " "
puts $fileID "#"
puts $fileID "# Domain geometry (x, y, z)"
puts $fileID "#"
puts $fileID " "
puts $fileID "1 1 1 "
puts $fileID " "
puts $fileID "#"
puts $fileID "# Domain boundaries (x, y, z)"
puts $fileID "#"
puts $fileID " "
puts $fileID " $xBoundMin"
puts $fileID " $yBoundMin"
puts $fileID " $zBoundMin"
puts $fileID " $zBoundMax"
puts $fileID " $yBoundMax"
puts $fileID " $xBoundMax"
puts $fileID "#"
puts $fileID "# Primary lines: node_tag, x, y, z, num_arms, constraint"
puts $fileID "# Secondary lines: arm_tag, burgx, burgy, burgz, nx, ny, nz"
puts $fileID "#"
puts $fileID "# length in unit of burgMag"
puts $fileID " "
set minus_burg_x [expr -$burg_x]
set minus_burg_y [expr -$burg_y]
set minus_burg_z [expr -$burg_z]
set Pi 3.1415926535897931
for {set n 0} {$n < $nodes_number} {incr n 1} {
set x [format %22.16e [expr $loop_radius*cos(2*$Pi*($n+1.0)/$nodes_number)]]
set y [format %22.16e [expr $loop_radius*sin(2*$Pi*($n+1.0)/$nodes_number)]]
set z 0
set arms_number 2
set flag 0
set n1 [expr $n+1]
set n2 [expr $n-1]
if { $n1 == $nodes_number } { set n1 0 }
if { $n2 == -1 } { set n2 [expr $nodes_number - 1 ] }
puts $fileID " $domainID,$n $x $y $z $arms_number $flag"
puts $fileID " $domainID,$n1 $burg_x $burg_y $burg_z "
puts $fileID " $normal_x $normal_y $normal_z"
puts $fileID " $domainID,$n2 $minus_burg_x $minus_burg_y $minus_burg_z "
puts $fileID " $normal_x $normal_y $normal_z"
}
close $fileID
puts "$datafile created."
puts "bye."
Problems and solutions
If you see the error message below while trying to run ParaDiS cylinder codes,
./bin/paradiscyl: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory
you have to specify the path to the GSL libraries. For example, let's say GSL libraries are in /usr/local/lib directory. Then, you add the following line in ~/.bash_profile
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib/
and then type
source ~/.bash_profile
Error in opening input file
When ParaDiS can not locate input files, it shows the following error message.
Fatal: ReadControlFile: Error 2 opening file XXXX
You check whether you gave the correct directory or name of input files.
Overflow error
Currently, if you declare DEFS += -D_CYLMETHOD1 in makefile, ParaDiS issues the following error message.
gsl: bessel_In.c:202: ERROR: overflow Default GSL error handler invoked. Aborted
THIS ISSUE IS RESOLVED.
Underflow error
You seem to have old version of codes. You download the latest version or suppres the error message by inserting the following line into cylinder/gridstress.c
gsl_set_error_handler_off();
You need to include the header file at the beginning of gridstress.c.
#include <gsl/gsl_errno.h>