tutorials/bicrystal/generateInputFiles.py

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"""Generate bicrystal_48 with a prismatic-loop density in both grains."""
import argparse
import os
from pathlib import Path
import sys
 
repository = Path(__file__).resolve().parents[2]
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument("--output-dir", type=Path, default=Path(__file__).resolve().parent,
                    help="Simulation folder (defaults to this tutorial folder).")
args = parser.parse_args()
args.output_dir.mkdir(parents=True, exist_ok=True)
os.chdir(args.output_dir.resolve())
sys.path.insert(0, str(repository / "python"))
from modlibUtils import *
 
 
# Create folder structure
folders=['config','F','inputFiles']
for x in folders:
    if not os.path.exists(x):
        os.makedirs(x)
 
# Make a local copy of DefectiveCrystal parameters file and modify that copy if necessary
DCfile='DefectiveCrystal.txt'
DCfileTemplate=str(repository)+'/Library/DefectiveCrystal/'+DCfile
print("\033[1;32mCreating  DDfile\033[0m")
shutil.copy2(DCfileTemplate,'inputFiles/'+DCfile)
setInputVariable('inputFiles/'+DCfile,'physics','DislocationDynamics ElasticDeformation')
setInputVariable('inputFiles/'+DCfile,'useFEM','0')
setInputVariable('inputFiles/'+DCfile,'Nsteps','10000')  # number of simulation steps
setInputVariable('inputFiles/'+DCfile,'maxResolveSteps','0')  # number of simulation steps
setInputVariable('inputFiles/'+DCfile,'dtMax','1e25')
setInputVariable('inputFiles/'+DCfile,'outputFrequency','1')  # output frequency
 
# Replace the template's restart setting and its misleading legacy comment.
dcPath=Path('inputFiles')/DCfile
dcLines=dcPath.read_text().splitlines(keepends=True)
for index, line in enumerate(dcLines):
    if line.split('=',1)[0].strip()=='startAtTimeStep':
        dcLines[index]='startAtTimeStep=-1; # Restart step: -1 selects the last recorded step in F/F_0.txt; 0 starts at frame 0; a positive value selects that frame.\n'
dcPath.write_text(''.join(dcLines))
 
# Make a local copy of DD parameters file and modify that copy if necessary
DDfile='DD.txt'
DDfileTemplate=str(repository)+'/Library/DislocationDynamics/'+DDfile
print("\033[1;32mCreating  DDfile\033[0m")
shutil.copy2(DDfileTemplate,'inputFiles/'+DDfile)
setInputVariable('inputFiles/'+DDfile,'timeSteppingMethod','adaptive') # adaptive or fixed
setInputVariable('inputFiles/'+DDfile,'dxMax','10') # max nodal displacement for when timeSteppingMethod=adaptive
setInputVariable('inputFiles/'+DDfile,'use_velocityFilter','1') # don't filter velocity if noise is enabled
setInputVariable('inputFiles/'+DDfile,'alphaLineTension','1.0') # dimensionless scale factor in for line tension forces
setInputVariable('inputFiles/'+DDfile,'Lmin','25')  # min segment length (in Burgers vector units)
setInputVariable('inputFiles/'+DDfile,'Lmax','150')  # max segment length (in Burgers vector units)
setInputVariable('inputFiles/'+DDfile,'outputQuadraturePoints','0')  # output quadrature data
setInputVariable('inputFiles/'+DDfile,'glideSolverType','Galerkin')  # type of glide solver, or none
setInputVariable('inputFiles/'+DDfile,'climbSolverType','none')  # type of clim solver, or none
setInputVariable('inputFiles/'+DDfile,'crossSlipModel','0')  # crossSlipModel
 
# Make a local copy of material file, and modify that copy if necessary
materialFile='W.txt';
materialFileTemplate=str(repository)+'/Library/Materials/'+materialFile;
print("\033[1;32mCreating  materialFile\033[0m")
shutil.copy2(materialFileTemplate,'inputFiles/'+materialFile)
#setInputVariable('inputFiles/'+materialFile,'enabledSlipSystems','full<111>{110}')
b_SI=getValueInFile('inputFiles/'+materialFile,'b_SI')
 
# Make a local copy of ElasticDeformation file, and modify that copy if necessary
elasticDeformatinoFile='ElasticDeformation.txt';
elasticDeformatinoFileTemplate=str(repository)+'/Library/ElasticDeformation/'+elasticDeformatinoFile;
print("\033[1;32mCreating  elasticDeformatinoFile\033[0m")
shutil.copy2(elasticDeformatinoFileTemplate,'inputFiles/'+elasticDeformatinoFile)
setInputVector('inputFiles/'+elasticDeformatinoFile,'ExternalStress0',np.zeros(6),'applied stress')
# Voigt order: 11, 22, 33, 12, 23, 13. Strain rate is per simulation time b/cs.
strainRate33 = 1e-8
setInputVector('inputFiles/'+elasticDeformatinoFile, 'ExternalStrainRate',
               np.array([0.0, 0.0, strainRate33, 0.0, 0.0, 0.0]), 'applied strain rate in the global 33 direction')
setInputVector('inputFiles/'+elasticDeformatinoFile, 'stiffnessRatio',
               np.array([0.0, 0.0, 1e20, 0.0, 0.0, 0.0]), 'strain control in 33; zero-stress control in the other components')
 
# Create polycrystal.txt using local material file
meshFile='bicrystal_48.msh';
meshFileTemplate=str(repository)+'/Library/Meshes/'+meshFile;
print("\033[1;32mCreating  polycrystalFile\033[0m")
shutil.copy2(meshFileTemplate,'inputFiles/'+meshFile)
pf=PolyCrystalFile(materialFile);
pf.absoluteTemperature=300;
pf.meshFile=meshFile
# Grain 1: crystal and global coordinates aligned.
pf.grain1globalX1 = np.array([1.0, 0.0, 0.0])
pf.grain1globalX3 = np.array([0.0, 0.0, 1.0])
pf.boxScaling=np.array([1e-6,1e-6,1e-6])/b_SI # scale of each mesh coordinate in Burgers vector units
pf.X0=np.array([0,0,0]) # Mesh nodes X are mapped to x=F*(X-X0)
pf.periodicFaceIDs=np.array([-1])
# Grain 2's rational rotation (cos=4/5, sin=3/5) requires the
# axial BCC repeat counts to be multiples of five for commensurate periods.
# Preserve the intended approximately 1-micrometer scale in both grains.
pf.compute()
repeatCounts = 5 * np.maximum(1, np.round(pf.boxScaling / (5 * pf.boxEdgesLatticeLengths)))
pf.boxScaling = repeatCounts * pf.boxEdgesLatticeLengths
pf.write('inputFiles')
# The mesh contains grains 1 and 2. Grain 2 is rotated 36.87 degrees about Y.
with open('inputFiles/polycrystal.txt', 'a') as polycrystalFile:
    polycrystalFile.write('C2G2=0.8 0 0.6\n     0 1 0\n     -0.6 0 0.8; # grain 2 crystal-to-global rotation\n')
 
# Random prismatic loops throughout both grains. Density is total dislocation
# line length per unit volume; radii are in meters.
microstructureName = 'prismaticLoopsDensity.txt'
microstructureFile = 'inputFiles/' + microstructureName
shutil.copy2(repository / 'Library/Microstructures/prismaticLoopsDensity.txt',
             microstructureFile)
setInputVariable(microstructureFile, 'targetDensity_SI', '1e13')  # m^-2
setInputVariable(microstructureFile, 'radiusDistributionMean_SI', '1e-7')  # 100 nm
setInputVariable(microstructureFile, 'radiusDistributionStd_SI', '0')  # fixed radius
setInputVector(microstructureFile, 'allowedGrainIDs', np.array([1, 2]), 'allow placement in both grains')
setInputVariable(microstructureFile, 'allowedSlipSystemIDs', '-1')  # all slip systems
with open('inputFiles/initialMicrostructure.txt', 'w') as initialMicrostructureFile:
    initialMicrostructureFile.write('microstructureFile=' + microstructureName + ';\n')
 
# Generate the populated frame 0 with microstructureGenerator before running DDomp.
print('Inputs ready: ' + str(Path.cwd()))
print('Run microstructureGenerator, then DDomp, using this simulation folder.')