PARADISCYL:Test-Run: Difference between revisions
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Manual 02 for ParaDiS Cylinder Codes
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F10 : output postscript |
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== Tcl script to generate data file == |
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In ParaDiS/tools directory, there is a tcl script '''create_loop_data.tcl''' that will generate a data file. |
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Revision as of 21:07, 2 October 2008
Manual 02 for ParaDiS Cylinder Codes
How to run test simulations
Keonwook Kang and Wei Cai
Run command
The ParaDis Cylinder command line format is exactly same with that of the original ParaDiS codes. Refer the ParaDiS manual for detail. The 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
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
Visualization Window 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 that will generate a data file.
Problems and solutions
./bin/paradiscyl: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory
Fatal: ReadControlFile: Error 2 opening file XXXX
gsl: bessel_In.c:202: ERROR: overflow Default GSL error handler invoked. Aborted