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Merge branch 'SimplifiedvtkRectilinear' into development

This commit is contained in:
Philip Eisenlohr 2016-04-25 10:23:50 -05:00
parent db7c4bba45 c67fbe7653
commit 36f41341ec
9 changed files with 137 additions and 855 deletions
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4
code/constitutive.f90
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@ -399,8 +399,6 @@ function constitutive_homogenizedC(ipc,ip,el)
plastic_titanmod_homogenizedC
use plastic_dislotwin, only: &
plastic_dislotwin_homogenizedC
use plastic_disloucla, only: &
plastic_disloucla_homogenizedC
use lattice, only: &
lattice_C66
@ -414,8 +412,6 @@ function constitutive_homogenizedC(ipc,ip,el)
plasticityType: select case (phase_plasticity(material_phase(ipc,ip,el)))
case (PLASTICITY_DISLOTWIN_ID) plasticityType
constitutive_homogenizedC = plastic_dislotwin_homogenizedC(ipc,ip,el)
case (PLASTICITY_DISLOUCLA_ID) plasticityType
constitutive_homogenizedC = plastic_disloucla_homogenizedC(ipc,ip,el)
case (PLASTICITY_TITANMOD_ID) plasticityType
constitutive_homogenizedC = plastic_titanmod_homogenizedC (ipc,ip,el)
case default plasticityType

823
code/plastic_disloUCLA.f90
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File diff suppressed because it is too large Load Diff

23
code/plastic_isotropic.f90
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@ -140,9 +140,10 @@ subroutine plastic_isotropic_init(fileUnit)
sizeDeltaState
character(len=65536) :: &
tag = '', &
outputtag = '', &
line = '', &
extmsg = ''
character(len=64) :: &
outputtag = ''
integer(pInt) :: NipcMyPhase
mainProcess: if (worldrank == 0) then
@ -382,8 +383,7 @@ subroutine plastic_isotropic_LpAndItsTangent(Lp,dLp_dTstar99,Tstar_v,ipc,ip,el)
math_mul33xx33, &
math_transpose33
use material, only: &
phaseAt, phasememberAt, &
plasticState, &
phasememberAt, &
material_phase, &
phase_plasticityInstance
@ -413,7 +413,7 @@ subroutine plastic_isotropic_LpAndItsTangent(Lp,dLp_dTstar99,Tstar_v,ipc,ip,el)
k, l, m, n
of = phasememberAt(ipc,ip,el) ! phasememberAt should be tackled by material and be renamed to material_phasemember
instance = phase_plasticityInstance(phaseAt(ipc,ip,el)) ! "phaseAt" equivalent to "material_phase" !!
instance = phase_plasticityInstance(material_phase(ipc,ip,el))
Tstar_dev_33 = math_deviatoric33(math_Mandel6to33(Tstar_v)) ! deviatoric part of 2nd Piola-Kirchhoff stress
squarenorm_Tstar_dev = math_mul33xx33(Tstar_dev_33,Tstar_dev_33)
@ -463,8 +463,7 @@ subroutine plastic_isotropic_LiAndItsTangent(Li,dLi_dTstar_3333,Tstar_v,ipc,ip,e
math_spherical33, &
math_mul33xx33
use material, only: &
phaseAt, phasememberAt, &
plasticState, &
phasememberAt, &
material_phase, &
phase_plasticityInstance
@ -491,7 +490,7 @@ real(pReal) :: &
k, l, m, n
of = phasememberAt(ipc,ip,el) ! phasememberAt should be tackled by material and be renamed to material_phasemember
instance = phase_plasticityInstance(phaseAt(ipc,ip,el)) ! "phaseAt" equivalent to "material_phase" !!
instance = phase_plasticityInstance(material_phase(ipc,ip,el))
Tstar_sph_33 = math_spherical33(math_Mandel6to33(Tstar_v)) ! spherical part of 2nd Piola-Kirchhoff stress
squarenorm_Tstar_sph = math_mul33xx33(Tstar_sph_33,Tstar_sph_33)
@ -529,8 +528,7 @@ subroutine plastic_isotropic_dotState(Tstar_v,ipc,ip,el)
use math, only: &
math_mul6x6
use material, only: &
phaseAt, phasememberAt, &
plasticState, &
phasememberAt, &
material_phase, &
phase_plasticityInstance
@ -553,7 +551,7 @@ subroutine plastic_isotropic_dotState(Tstar_v,ipc,ip,el)
of !< shortcut notation for offset position in state array
of = phasememberAt(ipc,ip,el) ! phasememberAt should be tackled by material and be renamed to material_phasemember
instance = phase_plasticityInstance(phaseAt(ipc,ip,el)) ! "phaseAt" equivalent to "material_phase" !!
instance = phase_plasticityInstance(material_phase(ipc,ip,el))
!--------------------------------------------------------------------------------------------------
! norm of (deviatoric) 2nd Piola-Kirchhoff stress
@ -609,8 +607,7 @@ function plastic_isotropic_postResults(Tstar_v,ipc,ip,el)
math_mul6x6
use material, only: &
material_phase, &
plasticState, &
phaseAt, phasememberAt, &
phasememberAt, &
phase_plasticityInstance
implicit none
@ -634,7 +631,7 @@ function plastic_isotropic_postResults(Tstar_v,ipc,ip,el)
o
of = phasememberAt(ipc,ip,el) ! phasememberAt should be tackled by material and be renamed to material_phasemember
instance = phase_plasticityInstance(phaseAt(ipc,ip,el)) ! "phaseAt" equivalent to "material_phase" !!
instance = phase_plasticityInstance(material_phase(ipc,ip,el))
!--------------------------------------------------------------------------------------------------
! norm of (deviatoric) 2nd Piola-Kirchhoff stress

33
examples/SpectralMethod/example_postprocess.py
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@ -1,33 +0,0 @@
#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os
import glob
from subprocess import call
geom_name = '20grains16x16x16_tensionX'
postResults = 'postResults --cr f,p --split --separation x,y,z '+geom_name+'.spectralOut'
sts = call(postResults, shell=True)
os.chdir('./postProc/')
ascii_files = glob.glob(geom_name+'_inc*.txt')
print ascii_files
showTable = "showTable -a "
addCauchy = 'addCauchy '
addMises = 'addMises -s Cauchy '
addStrainTensors = "addStrainTensors -0 -v "
visualize3D = "3Dvisualize -s 'Mises(Cauchy)',1_p Cauchy "
postProc = [addCauchy, addMises, addStrainTensors, visualize3D]
for f in ascii_files:
print f
for p in postProc:
p = p+f
print p
sts = call(p,shell=True)

17
examples/SpectralMethod/example_run.py
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@ -1,17 +0,0 @@
#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import sys
resolutions = [16,32,64]
resolution = resolutions[0]
try:
resolution = int(sys.argv[1])
except:
pass
if resolution not in resolutions:
resolution = resolutions[0]
from subprocess import call
call('make run%s'%('x'.join([str(resolution)]*3)), shell=True)

12
processing/post/addDisplacement.py
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@ -141,13 +141,13 @@ for name in filenames:
if table.label_dimension(options.defgrad) != 9:
errors.append('deformation gradient "{}" is not a 3x3 tensor.'.format(options.defgrad))
coordDim = table.label_dimension(options.pos)
coordDim = table.label_dimension(options.coords)
if not 3 >= coordDim >= 1:
errors.append('coordinates "{}" need to have one, two, or three dimensions.'.format(options.pos))
errors.append('coordinates "{}" need to have one, two, or three dimensions.'.format(options.coords))
elif coordDim < 3:
remarks.append('appending {} dimension{} to coordinates "{}"...'.format(3-coordDim,
's' if coordDim < 2 else '',
options.pos))
options.coords))
if remarks != []: damask.util.croak(remarks)
if errors != []:
@ -157,7 +157,7 @@ for name in filenames:
# --------------- figure out size and grid ---------------------------------------------------------
table.data_readArray([options.defgrad,options.pos])
table.data_readArray([options.defgrad,options.coords])
table.data_rewind()
if len(table.data.shape) < 2: table.data.shape += (1,) # expand to 2D shape
@ -196,8 +196,8 @@ for name in filenames:
table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
table.labels_append((['{}_pos' .format(i+1) for i in xrange(3)] if options.nodal else []) +
['{}_avg({}).{}' .format(i+1,options.defgrad,options.pos) for i in xrange(3)] +
['{}_fluct({}).{}'.format(i+1,options.defgrad,options.pos) for i in xrange(3)] )
['{}_avg({}).{}' .format(i+1,options.defgrad,options.coords) for i in xrange(3)] +
['{}_fluct({}).{}'.format(i+1,options.defgrad,options.coords) for i in xrange(3)] )
table.head_write()
# ------------------------------------------ output data -------------------------------------------

14
processing/post/vtk_pointcloud.py
View File

@ -49,7 +49,9 @@ for name in filenames:
remarks = []
coordDim = table.label_dimension(options.pos)
if not 3 >= coordDim >= 1: errors.append('coordinates "{}" need to have one, two, or three dimensions.'.format(options.pos))
elif coordDim < 3: remarks.append('appending {} dimensions to coordinates "{}"...'.format(3-coordDim,options.pos))
elif coordDim < 3: remarks.append('appending {} dimension{} to coordinates "{}"...'.format(3-coordDim,
's' if coordDim < 2 else '',
options.pos))
if remarks != []: damask.util.croak(remarks)
if errors != []:
@ -82,16 +84,16 @@ for name in filenames:
# ------------------------------------------ output result ---------------------------------------
writer = vtk.vtkXMLPolyDataWriter()
writer.SetCompressorTypeToZLib()
if name:
writer = vtk.vtkXMLPolyDataWriter()
writer.SetCompressorTypeToZLib()
writer.SetDataModeToBinary()
writer.SetFileName(os.path.join(os.path.split(name)[0],
os.path.splitext(os.path.split(name)[1])[0] +
'.' + writer.GetDefaultFileExtension()))
else:
writer.SetDataModeToAscii()
writer = vtk.vtkDataSetWriter()
writer.SetHeader('# powered by '+scriptID)
writer.WriteToOutputStringOn()
if vtk.VTK_MAJOR_VERSION <= 5: writer.SetInput(Polydata)
@ -99,6 +101,6 @@ for name in filenames:
writer.Write()
if name is None: sys.stdout.write(writer.GetOutputString())
if name is None: sys.stdout.write(writer.GetOutputString()[:writer.GetOutputStringLength()]) # limiting of outputString is fix for vtk <7.0
table.close()

57
processing/post/vtk_rectilinearGrid.py
View File

@ -6,7 +6,6 @@ import numpy as np
import damask
from optparse import OptionParser
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
@ -15,7 +14,7 @@ scriptID = ' '.join([scriptName,damask.version])
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
Create regular voxel grid from points in an ASCIItable (or geom file).
Create regular voxel grid from points in an ASCIItable.
""", version = scriptID)
@ -29,15 +28,9 @@ parser.add_option('-p',
dest = 'pos',
type = 'string', metavar = 'string',
help = 'label of coordinates [%default]')
parser.add_option('-g',
'--geom',
dest = 'geom',
action = 'store_true',
help = 'geom input format')
parser.set_defaults(mode = 'cell',
pos = 'pos',
geom = False,
)
(options, filenames) = parser.parse_args()
@ -47,10 +40,9 @@ parser.set_defaults(mode = 'cell',
if filenames == []: filenames = [None]
for name in filenames:
isGeom = options.geom or (name is not None and name.endswith('.geom'))
try: table = damask.ASCIItable(name = name,
buffered = False,
labeled = not isGeom,
labeled = True,
readonly = True,
)
except: continue
@ -62,9 +54,11 @@ for name in filenames:
remarks = []
errors = []
coordDim = 3 if isGeom else table.label_dimension(options.pos)
coordDim = table.label_dimension(options.pos)
if not 3 >= coordDim >= 1: errors.append('coordinates "{}" need to have one, two, or three dimensions.'.format(options.pos))
elif coordDim < 3: remarks.append('appending {} dimensions to coordinates "{}"...'.format(3-coordDim,options.pos))
elif coordDim < 3: remarks.append('appending {} dimension{} to coordinates "{}"...'.format(3-coordDim,
's' if coordDim < 2 else '',
options.pos))
if remarks != []: damask.util.croak(remarks)
if errors != []:
@ -74,32 +68,24 @@ for name in filenames:
# --------------- figure out size and grid ---------------------------------------------------------
if isGeom:
info,extra_header = table.head_getGeom()
coords = [np.linspace(info['origin'][i],
info['origin'][i]+info['size'][i],
num = info['grid'][i]+1,
endpoint = True,
) for i in xrange(3)]
else:
table.data_readArray(options.pos)
if len(table.data.shape) < 2: table.data.shape += (1,) # expand to 2D shape
if table.data.shape[1] < 3:
table.data = np.hstack((table.data,
np.zeros((table.data.shape[0],
3-table.data.shape[1]),dtype='f'))) # fill coords up to 3D with zeros
table.data_readArray(options.pos)
if len(table.data.shape) < 2: table.data.shape += (1,) # expand to 2D shape
if table.data.shape[1] < 3:
table.data = np.hstack((table.data,
np.zeros((table.data.shape[0],
3-table.data.shape[1]),dtype='f'))) # fill coords up to 3D with zeros
coords = [np.unique(table.data[:,i]) for i in xrange(3)]
coords = [np.unique(table.data[:,i]) for i in xrange(3)]
if options.mode == 'cell':
coords = [0.5 * np.array([3.0 * coords[i][0] - coords[i][0 + len(coords[i]) > 1]] + \
[coords[i][j-1] + coords[i][j] for j in xrange(1,len(coords[i]))] + \
[3.0 * coords[i][-1] - coords[i][-1 - (len(coords[i]) > 1)]]) for i in xrange(3)]
if options.mode == 'cell':
coords = [0.5 * np.array([3.0 * coords[i][0] - coords[i][0 + len(coords[i]) > 1]] + \
[coords[i][j-1] + coords[i][j] for j in xrange(1,len(coords[i]))] + \
[3.0 * coords[i][-1] - coords[i][-1 - (len(coords[i]) > 1)]]) for i in xrange(3)]
grid = np.array(map(len,coords),'i')
N = grid.prod() if options.mode == 'point' or isGeom else (grid-1).prod()
N = grid.prod() if options.mode == 'point' else (grid-1).prod()
if not isGeom and N != len(table.data):
if N != len(table.data):
errors.append('data count {} does not match grid {}x{}x{}.'.format(N,*(grid - (options.mode == 'cell')) ))
if errors != []:
damask.util.croak(errors)
@ -132,7 +118,7 @@ for name in filenames:
writer.SetDataModeToBinary()
writer.SetFileName(os.path.join(os.path.split(name)[0],
os.path.splitext(os.path.split(name)[1])[0] +
('' if isGeom else '_{}({})'.format(options.pos, options.mode)) +
'_{}({})'.format(options.pos, options.mode) +
'.' + writer.GetDefaultFileExtension()))
else:
writer = vtk.vtkDataSetWriter()
@ -144,7 +130,6 @@ for name in filenames:
writer.Write()
if name is None: sys.stdout.write(writer.GetOutputString() if name else
writer.GetOutputString()[0:writer.GetOutputStringLength()])
if name is None: sys.stdout.write(writer.GetOutputString()[:writer.GetOutputStringLength()]) # limiting of outputString is fix for vtk <7.0
table.close()

9
processing/pre/geom_check.sh
View File

@ -2,8 +2,10 @@
for geom in "$@"
do
vtk_rectilinearGrid \
--geom $geom
geom_toTable \
< $geom \
| \
vtk_rectilinearGrid > ${geom%.*}.vtk
geom_toTable \
< $geom \
@ -11,5 +13,6 @@ do
vtk_addRectilinearGridData \
--scalar microstructure \
--inplace \
--vtk ${geom%.*}.vtr
--vtk ${geom%.*}.vtk
rm ${geom%.*}.vtk
done