Merge commit 'v2.0.3-2793-g6c260945'

This commit is contained in:
Test User 2020-07-03 03:10:54 +02:00
commit b0ced02e15
16 changed files with 154 additions and 118 deletions

View File

@ -1,4 +1,4 @@
import multiprocessing
import multiprocessing as mp
import re
import inspect
import glob
@ -413,17 +413,18 @@ class Result:
for i in self.iterate('increments'):
message += f'\n{i} ({self.times[self.increments.index(i)]}s)\n'
for o,p in zip(['constituents','materialpoints'],['con_physics','mat_physics']):
message += f' {o[:-1]}\n'
for oo in self.iterate(o):
message += f' {oo}\n'
message += f' {oo}\n'
for pp in self.iterate(p):
message += f' {pp}\n'
message += f' {pp}\n'
group = '/'.join([i,o[:-1],oo,pp]) # o[:-1]: plural/singular issue
for d in f[group].keys():
try:
dataset = f['/'.join([group,d])]
unit = f" / {dataset.attrs['Unit'].decode()}" if 'Unit' in dataset.attrs else ''
description = dataset.attrs['Description'].decode()
message += f' {d}{unit}: {description}\n'
message += f' {d}{unit}: {description}\n'
except KeyError:
pass
return message
@ -703,7 +704,6 @@ class Result:
label,p = 'intermediate',1
elif eigenvalue == 'min':
label,p = 'minimum',0
print('p',eigenvalue)
return {
'data': mechanics.eigenvectors(T_sym['data'])[:,p],
'label': f"v_{eigenvalue}({T_sym['label']})",
@ -1066,8 +1066,8 @@ class Result:
"""
num_threads = Environment().options['DAMASK_NUM_THREADS']
pool = multiprocessing.Pool(int(num_threads) if num_threads is not None else None)
lock = multiprocessing.Manager().Lock()
pool = mp.Pool(int(num_threads) if num_threads is not None else None)
lock = mp.Manager().Lock()
groups = self.groups_with_datasets(datasets.values())
default_arg = partial(self._job,func=func,datasets=datasets,args=args,lock=lock)
@ -1222,7 +1222,7 @@ class Result:
elif mode.lower()=='point':
v = VTK.from_polyData(self.cell_coordinates())
N_digits = int(np.floor(np.log10(int(self.increments[-1][3:]))))+1
N_digits = int(np.floor(np.log10(max(1,int(self.increments[-1][3:])))))+1
for inc in util.show_progress(self.iterate('increments'),len(self.selection['increments'])):

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@ -155,7 +155,7 @@ class Rotation:
def broadcast_to(self,shape):
if isinstance(shape,int): shape = (shape,)
if isinstance(shape,(int,np.integer)): shape = (shape,)
if self.shape == ():
q = np.broadcast_to(self.quaternion,shape+(4,))
else:

View File

@ -1,3 +1,4 @@
import multiprocessing as mp
from pathlib import Path
import pandas as pd
@ -159,8 +160,11 @@ class VTK:
return VTK(geom)
def write(self,fname):
@staticmethod
def _write(writer):
"""Wrapper for parallel writing."""
writer.Write()
def write(self,fname,parallel=True):
"""
Write to file.
@ -168,6 +172,8 @@ class VTK:
----------
fname : str or pathlib.Path
Filename for writing.
parallel : boolean, optional
Write data in parallel background process. Defaults to True.
"""
if isinstance(self.geom,vtk.vtkRectilinearGrid):
@ -185,8 +191,11 @@ class VTK:
writer.SetCompressorTypeToZLib()
writer.SetDataModeToBinary()
writer.SetInputData(self.geom)
writer.Write()
if parallel:
mp_writer = mp.Process(target=self._write,args=(writer,))
mp_writer.start()
else:
writer.Write()
# Check https://blog.kitware.com/ghost-and-blanking-visibility-changes/ for missing data
@ -197,14 +206,21 @@ class VTK:
N_cells = self.geom.GetNumberOfCells()
if isinstance(data,np.ndarray):
d = np_to_vtk(num_array=data.reshape(data.shape[0],-1),deep=True)
if label is None:
raise ValueError('No label defined for numpy.ndarray')
if data.dtype in [np.float64, np.float128]: # avoid large files
d = np_to_vtk(num_array=data.astype(np.float32).reshape(data.shape[0],-1),deep=True)
else:
d = np_to_vtk(num_array=data.reshape(data.shape[0],-1),deep=True)
d.SetName(label)
if data.shape[0] == N_cells:
self.geom.GetCellData().AddArray(d)
elif data.shape[0] == N_points:
self.geom.GetPointData().AddArray(d)
else:
raise ValueError(f'Invalid shape {data.shape[0]}')
elif isinstance(data,pd.DataFrame):
raise NotImplementedError('pd.DataFrame')
elif isinstance(data,Table):

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@ -3,11 +3,11 @@
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<Piece NumberOfPoints="10" NumberOfVerts="0" NumberOfLines="0" NumberOfStrips="0" NumberOfPolys="0">
<PointData>
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<Value index="0">
0.7453559925
0.74535601471
</Value>
<Value index="1">
2.4494897428

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@ -3,27 +3,27 @@
<RectilinearGrid WholeExtent="0 5 0 6 0 7">
<Piece Extent="0 5 0 6 0 7">
<PointData>
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@ -1,3 +1,7 @@
import os
import filecmp
import time
import pytest
import numpy as np
@ -17,7 +21,7 @@ class TestVTK:
origin = np.random.random(3)
v = VTK.from_rectilinearGrid(grid,size,origin)
string = v.__repr__()
v.write(tmp_path/'rectilinearGrid')
v.write(tmp_path/'rectilinearGrid',False)
vtr = VTK.from_file(tmp_path/'rectilinearGrid.vtr')
with open(tmp_path/'rectilinearGrid.vtk','w') as f:
f.write(string)
@ -25,10 +29,10 @@ class TestVTK:
assert(string == vtr.__repr__() == vtk.__repr__())
def test_polyData(self,tmp_path):
points = np.random.rand(3,100)
points = np.random.rand(100,3)
v = VTK.from_polyData(points)
string = v.__repr__()
v.write(tmp_path/'polyData')
v.write(tmp_path/'polyData',False)
vtp = VTK.from_file(tmp_path/'polyData.vtp')
with open(tmp_path/'polyData.vtk','w') as f:
f.write(string)
@ -47,14 +51,30 @@ class TestVTK:
connectivity = np.random.choice(np.arange(n),n,False).reshape(-1,n)
v = VTK.from_unstructuredGrid(nodes,connectivity,cell_type)
string = v.__repr__()
v.write(tmp_path/'unstructuredGrid')
v.write(tmp_path/'unstructuredGrid',False)
vtu = VTK.from_file(tmp_path/'unstructuredGrid.vtu')
with open(tmp_path/'unstructuredGrid.vtk','w') as f:
f.write(string)
vtk = VTK.from_file(tmp_path/'unstructuredGrid.vtk','unstructuredgrid')
assert(string == vtu.__repr__() == vtk.__repr__())
@pytest.mark.parametrize('name,dataset_type',[('this_file_does_not_exist.vtk',None),
def test_parallel_out(self,tmp_path):
points = np.random.rand(102,3)
v = VTK.from_polyData(points)
fname_s = tmp_path/'single.vtp'
fname_p = tmp_path/'parallel.vtp'
v.write(fname_s,False)
v.write(fname_p,True)
for i in range(10):
if os.path.isfile(fname_p) and filecmp.cmp(fname_s,fname_p):
assert(True)
return
time.sleep(.5)
assert(False)
@pytest.mark.parametrize('name,dataset_type',[('this_file_does_not_exist.vtk', None),
('this_file_does_not_exist.vtk','vtk'),
('this_file_does_not_exist.vtx', None)])
def test_invalid_dataset_type(self,dataset_type,name):

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@ -6,7 +6,7 @@
!> @brief Interfacing between the PETSc-based solvers and the material subroutines provided
!! by DAMASK
!> @details Interfacing between the PETSc-based solvers and the material subroutines provided
!> by DAMASK. Interpretating the command line arguments to get load case, geometry file,
!> by DAMASK. Interpreting the command line arguments to get load case, geometry file,
!> and working directory.
!--------------------------------------------------------------------------------------------------
#define PETSC_MAJOR 3
@ -340,7 +340,7 @@ end function getGeometryFile
!--------------------------------------------------------------------------------------------------
!> @brief relative path of loadcase from command line arguments
!> @brief relative path of load case from command line arguments
!--------------------------------------------------------------------------------------------------
function getLoadCaseFile(loadCaseParameter)

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@ -375,7 +375,7 @@ subroutine constitutive_init
constitutive_source_maxSizeDotState = 0
PhaseLoop2:do ph = 1,material_Nphase
!--------------------------------------------------------------------------------------------------
! partition and inititalize state
! partition and initialize state
plasticState(ph)%partionedState0 = plasticState(ph)%state0
plasticState(ph)%state = plasticState(ph)%partionedState0
forall(s = 1:phase_Nsources(ph))
@ -450,7 +450,7 @@ end subroutine constitutive_dependentState
!--------------------------------------------------------------------------------------------------
!> @brief contains the constitutive equation for calculating the velocity gradient
! ToDo: Discuss wheter it makes sense if crystallite handles the configuration conversion, i.e.
! ToDo: Discuss whether it makes sense if crystallite handles the configuration conversion, i.e.
! Mp in, dLp_dMp out
!--------------------------------------------------------------------------------------------------
subroutine constitutive_LpAndItsTangents(Lp, dLp_dS, dLp_dFi, &
@ -660,7 +660,7 @@ end subroutine constitutive_SandItsTangents
!--------------------------------------------------------------------------------------------------
!> @brief returns the 2nd Piola-Kirchhoff stress tensor and its tangent with respect to
!> the elastic and intermeidate deformation gradients using Hookes law
!> the elastic and intermediate deformation gradients using Hooke's law
!--------------------------------------------------------------------------------------------------
subroutine constitutive_hooke_SandItsTangents(S, dS_dFe, dS_dFi, &
Fe, Fi, ipc, ip, el)

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@ -37,7 +37,7 @@ submodule(constitutive) plastic_nonlocal
! BEGIN DEPRECATED
integer, dimension(:,:,:), allocatable :: &
iRhoU, & !< state indices for unblocked density
iV, & !< state indices for dislcation velocities
iV, & !< state indices for dislocation velocities
iD !< state indices for stable dipole height
!END DEPRECATED

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@ -9,7 +9,7 @@ submodule(homogenization) homogenization_mech_none
contains
!--------------------------------------------------------------------------------------------------
!> @brief allocates all neccessary fields, reads information from material configuration file
!> @brief allocates all necessary fields, reads information from material configuration file
!--------------------------------------------------------------------------------------------------
module subroutine mech_none_init

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@ -102,7 +102,7 @@ end function kinematics_thermal_expansion_initialStrain
!--------------------------------------------------------------------------------------------------
!> @brief contains the constitutive equation for calculating the velocity gradient
!> @brief constitutive equation for calculating the velocity gradient
!--------------------------------------------------------------------------------------------------
subroutine kinematics_thermal_expansion_LiAndItsTangent(Li, dLi_dTstar, ipc, ip, el)

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@ -1,6 +1,6 @@
!-------------------------------------------------------------------------------------------------
!> @author Martin Diehl, Max-Planck-Institut für Eisenforschung GmbH
!> @brief linked list
!> @brief Linked list
!--------------------------------------------------------------------------------------------------
module list
use prec

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@ -1,7 +1,7 @@
!--------------------------------------------------------------------------------------------------
!> @author Pratheek Shanthraj, Max-Planck-Institut für Eisenforschung GmbH
!> @author Luv Sharma, Max-Planck-Institut für Eisenforschung GmbH
!> @brief material subroutine incoprorating isotropic ductile damage source mechanism
!> @brief material subroutine incorporating isotropic ductile damage source mechanism
!> @details to be done
!--------------------------------------------------------------------------------------------------
module source_damage_isoDuctile

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@ -1,6 +1,6 @@
!--------------------------------------------------------------------------------------------------
!> @author Martin Diehl, Max-Planck-Institut für Eisenforschung GmbH
!> @brief provides wrappers to C routines
!> @author Martin Diehl, Max-Planck-Institut für Eisenforschung GmbH
!> @brief Wrappers to C routines for system operations
!--------------------------------------------------------------------------------------------------
module system_routines
use, intrinsic :: ISO_C_Binding

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@ -73,7 +73,7 @@ end subroutine thermal_conduction_init
!--------------------------------------------------------------------------------------------------
!> @brief returns heat generation rate
!> @brief return heat generation rate
!--------------------------------------------------------------------------------------------------
subroutine thermal_conduction_getSourceAndItsTangent(Tdot, dTdot_dT, T, ip, el)
@ -132,7 +132,7 @@ end subroutine thermal_conduction_getSourceAndItsTangent
!--------------------------------------------------------------------------------------------------
!> @brief returns homogenized thermal conductivity in reference configuration
!> @brief return homogenized thermal conductivity in reference configuration
!--------------------------------------------------------------------------------------------------
function thermal_conduction_getConductivity(ip,el)

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@ -12,7 +12,7 @@ module thermal_isothermal
contains
!--------------------------------------------------------------------------------------------------
!> @brief allocates all neccessary fields, reads information from material configuration file
!> @brief allocates fields, reads information from material configuration file
!--------------------------------------------------------------------------------------------------
subroutine thermal_isothermal_init