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Merge branch 'development' of git.damask.mpie.de:damask/DAMASK into typehints_orientation_rotation

This commit is contained in:
Daniel Otto de Mentock 2022-02-03 11:19:15 +01:00
parent fc8cd6322c 2cb3b2cc45
commit df54bf724c
21 changed files with 180 additions and 270 deletions
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2
PRIVATE

@ -1 +1 @@
Subproject commit 5598ec4892b0921fccf63e8570f9fcd8e0365716 Subproject commit ebb7f0ce78d11275020af0ba60f929f95b446932

178
processing/legacy/geom_grainGrowth.py vendored
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@ -1,178 +0,0 @@
#!/usr/bin/env python3
import os
import sys
from io import StringIO
from optparse import OptionParser
import numpy as np
from scipy import ndimage
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
getInterfaceEnergy = lambda A,B: np.float32((A != B)*1.0) # 1.0 if A & B are distinct, 0.0 otherwise
struc = ndimage.generate_binary_structure(3,1) # 3D von Neumann neighborhood
#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog option(s) [geomfile(s)]', description = """
Smoothen interface roughness by simulated curvature flow.
This is achieved by the diffusion of each initially sharply bounded grain volume within the periodic domain
up to a given distance 'd' voxels.
The final geometry is assembled by selecting at each voxel that grain index for which the concentration remains largest.
References 10.1073/pnas.1111557108 (10.1006/jcph.1994.1105)
""", version = scriptID)
parser.add_option('-d', '--distance',
dest = 'd',
type = 'float', metavar = 'float',
help = 'diffusion distance in voxels [%default]')
parser.add_option('-N', '--iterations',
dest = 'N',
type = 'int', metavar = 'int',
help = 'curvature flow iterations [%default]')
parser.add_option('-i', '--immutable',
action = 'extend', dest = 'immutable', metavar = '<int LIST>',
help = 'list of immutable material indices')
parser.add_option('--ndimage',
dest = 'ndimage', action='store_true',
help = 'use ndimage.gaussian_filter in lieu of explicit FFT')
parser.set_defaults(d = 1,
N = 1,
immutable = [],
ndimage = False,
)
(options, filenames) = parser.parse_args()
options.immutable = list(map(int,options.immutable))
if filenames == []: filenames = [None]
for name in filenames:
damask.util.report(scriptName,name)
geom = damask.Grid.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
grid_original = geom.cells
damask.util.croak(geom)
material = np.tile(geom.material,np.where(grid_original == 1, 2,1)) # make one copy along dimensions with grid == 1
grid = np.array(material.shape)
# --- initialize support data ---------------------------------------------------------------------
# store a copy of the initial material indices to find locations of immutable indices
material_original = np.copy(material)
if not options.ndimage:
X,Y,Z = np.mgrid[0:grid[0],0:grid[1],0:grid[2]]
# Calculates gaussian weights for simulating 3d diffusion
gauss = np.exp(-(X*X + Y*Y + Z*Z)/(2.0*options.d*options.d),dtype=np.float32) \
/np.power(2.0*np.pi*options.d*options.d,(3.0 - np.count_nonzero(grid_original == 1))/2.,dtype=np.float32)
gauss[:,:,:grid[2]//2:-1] = gauss[:,:,1:(grid[2]+1)//2] # trying to cope with uneven (odd) grid size
gauss[:,:grid[1]//2:-1,:] = gauss[:,1:(grid[1]+1)//2,:]
gauss[:grid[0]//2:-1,:,:] = gauss[1:(grid[0]+1)//2,:,:]
gauss = np.fft.rfftn(gauss).astype(np.complex64)
for smoothIter in range(options.N):
interfaceEnergy = np.zeros(material.shape,dtype=np.float32)
for i in (-1,0,1):
for j in (-1,0,1):
for k in (-1,0,1):
# assign interfacial energy to all voxels that have a differing neighbor (in Moore neighborhood)
interfaceEnergy = np.maximum(interfaceEnergy,
getInterfaceEnergy(material,np.roll(np.roll(np.roll(
material,i,axis=0), j,axis=1), k,axis=2)))
# periodically extend interfacial energy array by half a grid size in positive and negative directions
periodic_interfaceEnergy = np.tile(interfaceEnergy,(3,3,3))[grid[0]//2:-grid[0]//2,
grid[1]//2:-grid[1]//2,
grid[2]//2:-grid[2]//2]
# transform bulk volume (i.e. where interfacial energy remained zero), store index of closest boundary voxel
index = ndimage.morphology.distance_transform_edt(periodic_interfaceEnergy == 0.,
return_distances = False,
return_indices = True)
# want array index of nearest voxel on periodically extended boundary
periodic_bulkEnergy = periodic_interfaceEnergy[index[0],
index[1],
index[2]].reshape(2*grid) # fill bulk with energy of nearest interface
if options.ndimage:
periodic_diffusedEnergy = ndimage.gaussian_filter(
np.where(ndimage.morphology.binary_dilation(periodic_interfaceEnergy > 0.,
structure = struc,
iterations = int(round(options.d*2.))-1, # fat boundary
),
periodic_bulkEnergy, # ...and zero everywhere else
0.),
sigma = options.d)
else:
diffusedEnergy = np.fft.irfftn(np.fft.rfftn(
np.where(
ndimage.morphology.binary_dilation(interfaceEnergy > 0.,
structure = struc,
iterations = int(round(options.d*2.))-1),# fat boundary
periodic_bulkEnergy[grid[0]//2:-grid[0]//2, # retain filled energy on fat boundary...
grid[1]//2:-grid[1]//2,
grid[2]//2:-grid[2]//2], # ...and zero everywhere else
0.)).astype(np.complex64) *
gauss).astype(np.float32)
periodic_diffusedEnergy = np.tile(diffusedEnergy,(3,3,3))[grid[0]//2:-grid[0]//2,
grid[1]//2:-grid[1]//2,
grid[2]//2:-grid[2]//2] # periodically extend the smoothed bulk energy
# transform voxels close to interface region
index = ndimage.morphology.distance_transform_edt(periodic_diffusedEnergy >= 0.95*np.amax(periodic_diffusedEnergy),
return_distances = False,
return_indices = True) # want index of closest bulk grain
periodic_material = np.tile(material,(3,3,3))[grid[0]//2:-grid[0]//2,
grid[1]//2:-grid[1]//2,
grid[2]//2:-grid[2]//2] # periodically extend the geometry
material = periodic_material[index[0],
index[1],
index[2]].reshape(2*grid)[grid[0]//2:-grid[0]//2,
grid[1]//2:-grid[1]//2,
grid[2]//2:-grid[2]//2] # extent grains into interface region
# replace immutable materials with closest mutable ones
index = ndimage.morphology.distance_transform_edt(np.in1d(material,options.immutable).reshape(grid),
return_distances = False,
return_indices = True)
material = material[index[0],
index[1],
index[2]]
immutable = np.zeros(material.shape, dtype=np.bool)
# find locations where immutable materials have been in original structure
for micro in options.immutable:
immutable += material_original == micro
# undo any changes involving immutable materials
material = np.where(immutable, material_original,material)
damask.Grid(material = material[0:grid_original[0],0:grid_original[1],0:grid_original[2]],
size = geom.size,
origin = geom.origin,
comments = geom.comments + [scriptID + ' ' + ' '.join(sys.argv[1:])],
)\
.save(sys.stdout if name is None else name)

2
python/damask/VERSION
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@ -1 +1 @@
v3.0.0-alpha5-545-gad74f5dbe v3.0.0-alpha5-556-g97f849c09

2
python/damask/_result.py
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@ -5,7 +5,7 @@ import os
import copy import copy
import datetime import datetime
import warnings import warnings
import xml.etree.ElementTree as ET import xml.etree.ElementTree as ET # noqa
import xml.dom.minidom import xml.dom.minidom
from pathlib import Path from pathlib import Path
from functools import partial from functools import partial

3
python/damask/_typehints.py
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@ -9,3 +9,6 @@ import numpy as np
FloatSequence = Union[np.ndarray,Sequence[float]] FloatSequence = Union[np.ndarray,Sequence[float]]
IntSequence = Union[np.ndarray,Sequence[int]] IntSequence = Union[np.ndarray,Sequence[int]]
FileHandle = Union[TextIO, str, Path] FileHandle = Union[TextIO, str, Path]
NumpyRngSeed = Union[int, IntSequence, np.random.SeedSequence, np.random.Generator]
# BitGenerator does not exists in older numpy versions
#NumpyRngSeed = Union[int, IntSequence, np.random.SeedSequence, np.random.BitGenerator, np.random.Generator]

7
python/damask/seeds.py
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@ -1,3 +1,4 @@
"""Functionality for generation of seed points for Voronoi or Laguerre tessellation.""" """Functionality for generation of seed points for Voronoi or Laguerre tessellation."""
from typing import Tuple as _Tuple from typing import Tuple as _Tuple
@ -5,7 +6,7 @@ from typing import Tuple as _Tuple
from scipy import spatial as _spatial from scipy import spatial as _spatial
import numpy as _np import numpy as _np
from ._typehints import FloatSequence as _FloatSequence, IntSequence as _IntSequence from ._typehints import FloatSequence as _FloatSequence, IntSequence as _IntSequence, NumpyRngSeed as _NumpyRngSeed
from . import util as _util from . import util as _util
from . import grid_filters as _grid_filters from . import grid_filters as _grid_filters
@ -13,7 +14,7 @@ from . import grid_filters as _grid_filters
def from_random(size: _FloatSequence, def from_random(size: _FloatSequence,
N_seeds: int, N_seeds: int,
cells: _IntSequence = None, cells: _IntSequence = None,
rng_seed=None) -> _np.ndarray: rng_seed: _NumpyRngSeed = None) -> _np.ndarray:
""" """
Place seeds randomly in space. Place seeds randomly in space.
@ -53,7 +54,7 @@ def from_Poisson_disc(size: _FloatSequence,
N_candidates: int, N_candidates: int,
distance: float, distance: float,
periodic: bool = True, periodic: bool = True,
rng_seed=None) -> _np.ndarray: rng_seed: _NumpyRngSeed = None) -> _np.ndarray:
""" """
Place seeds according to a Poisson disc distribution. Place seeds according to a Poisson disc distribution.

4
python/damask/util.py
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@ -16,7 +16,7 @@ import numpy as np
import h5py import h5py
from . import version from . import version
from ._typehints import IntSequence, FloatSequence from ._typehints import FloatSequence, NumpyRngSeed
# limit visibility # limit visibility
__all__=[ __all__=[
@ -396,7 +396,7 @@ def execution_stamp(class_name: str,
def hybrid_IA(dist: np.ndarray, def hybrid_IA(dist: np.ndarray,
N: int, N: int,
rng_seed: Union[int, IntSequence] = None) -> np.ndarray: rng_seed: NumpyRngSeed = None) -> np.ndarray:
""" """
Hybrid integer approximation. Hybrid integer approximation.

24
python/tests/test_grid_filters.py
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@ -8,19 +8,19 @@ from damask import seeds
class TestGridFilters: class TestGridFilters:
def test_coordinates0_point(self): def test_coordinates0_point(self):
size = np.random.random(3) size = np.random.random(3) # noqa
cells = np.random.randint(8,32,(3)) cells = np.random.randint(8,32,(3))
coord = grid_filters.coordinates0_point(cells,size) coord = grid_filters.coordinates0_point(cells,size)
assert np.allclose(coord[0,0,0],size/cells*.5) and coord.shape == tuple(cells) + (3,) assert np.allclose(coord[0,0,0],size/cells*.5) and coord.shape == tuple(cells) + (3,)
def test_coordinates0_node(self): def test_coordinates0_node(self):
size = np.random.random(3) size = np.random.random(3) # noqa
cells = np.random.randint(8,32,(3)) cells = np.random.randint(8,32,(3))
coord = grid_filters.coordinates0_node(cells,size) coord = grid_filters.coordinates0_node(cells,size)
assert np.allclose(coord[-1,-1,-1],size) and coord.shape == tuple(cells+1) + (3,) assert np.allclose(coord[-1,-1,-1],size) and coord.shape == tuple(cells+1) + (3,)
def test_coord0(self): def test_coord0(self):
size = np.random.random(3) size = np.random.random(3) # noqa
cells = np.random.randint(8,32,(3)) cells = np.random.randint(8,32,(3))
c = grid_filters.coordinates0_point(cells+1,size+size/cells) c = grid_filters.coordinates0_point(cells+1,size+size/cells)
n = grid_filters.coordinates0_node(cells,size) + size/cells*.5 n = grid_filters.coordinates0_node(cells,size) + size/cells*.5
@ -28,7 +28,7 @@ class TestGridFilters:
@pytest.mark.parametrize('mode',['point','node']) @pytest.mark.parametrize('mode',['point','node'])
def test_grid_DNA(self,mode): def test_grid_DNA(self,mode):
"""Ensure that cellsSizeOrigin_coordinates0_xx is the inverse of coordinates0_xx.""" """Ensure that cellsSizeOrigin_coordinates0_xx is the inverse of coordinates0_xx.""" # noqa
cells = np.random.randint(8,32,(3)) cells = np.random.randint(8,32,(3))
size = np.random.random(3) size = np.random.random(3)
origin = np.random.random(3) origin = np.random.random(3)
@ -37,7 +37,7 @@ class TestGridFilters:
assert np.allclose(cells,_cells) and np.allclose(size,_size) and np.allclose(origin,_origin) assert np.allclose(cells,_cells) and np.allclose(size,_size) and np.allclose(origin,_origin)
def test_displacement_fluct_equivalence(self): def test_displacement_fluct_equivalence(self):
"""Ensure that fluctuations are periodic.""" """Ensure that fluctuations are periodic.""" # noqa
size = np.random.random(3) size = np.random.random(3)
cells = np.random.randint(8,32,(3)) cells = np.random.randint(8,32,(3))
F = np.random.random(tuple(cells)+(3,3)) F = np.random.random(tuple(cells)+(3,3))
@ -45,14 +45,14 @@ class TestGridFilters:
grid_filters.point_to_node(grid_filters.displacement_fluct_point(size,F))) grid_filters.point_to_node(grid_filters.displacement_fluct_point(size,F)))
def test_interpolation_to_node(self): def test_interpolation_to_node(self):
size = np.random.random(3) size = np.random.random(3) # noqa
cells = np.random.randint(8,32,(3)) cells = np.random.randint(8,32,(3))
F = np.random.random(tuple(cells)+(3,3)) F = np.random.random(tuple(cells)+(3,3))
assert np.allclose(grid_filters.coordinates_node(size,F) [1:-1,1:-1,1:-1], assert np.allclose(grid_filters.coordinates_node(size,F) [1:-1,1:-1,1:-1],
grid_filters.point_to_node(grid_filters.coordinates_point(size,F))[1:-1,1:-1,1:-1]) grid_filters.point_to_node(grid_filters.coordinates_point(size,F))[1:-1,1:-1,1:-1])
def test_interpolation_to_cell(self): def test_interpolation_to_cell(self):
cells = np.random.randint(1,30,(3)) cells = np.random.randint(1,30,(3)) # noqa
coordinates_node_x = np.linspace(0,np.pi*2,num=cells[0]+1) coordinates_node_x = np.linspace(0,np.pi*2,num=cells[0]+1)
node_field_x = np.cos(coordinates_node_x) node_field_x = np.cos(coordinates_node_x)
@ -66,7 +66,7 @@ class TestGridFilters:
@pytest.mark.parametrize('mode',['point','node']) @pytest.mark.parametrize('mode',['point','node'])
def test_coordinates0_origin(self,mode): def test_coordinates0_origin(self,mode):
origin= np.random.random(3) origin= np.random.random(3) # noqa
size = np.random.random(3) # noqa size = np.random.random(3) # noqa
cells = np.random.randint(8,32,(3)) cells = np.random.randint(8,32,(3))
shifted = eval(f'grid_filters.coordinates0_{mode}(cells,size,origin)') shifted = eval(f'grid_filters.coordinates0_{mode}(cells,size,origin)')
@ -79,7 +79,7 @@ class TestGridFilters:
@pytest.mark.parametrize('function',[grid_filters.displacement_avg_point, @pytest.mark.parametrize('function',[grid_filters.displacement_avg_point,
grid_filters.displacement_avg_node]) grid_filters.displacement_avg_node])
def test_displacement_avg_vanishes(self,function): def test_displacement_avg_vanishes(self,function):
"""Ensure that random fluctuations in F do not result in average displacement.""" """Ensure that random fluctuations in F do not result in average displacement.""" # noqa
size = np.random.random(3) size = np.random.random(3)
cells = np.random.randint(8,32,(3)) cells = np.random.randint(8,32,(3))
F = np.random.random(tuple(cells)+(3,3)) F = np.random.random(tuple(cells)+(3,3))
@ -89,7 +89,7 @@ class TestGridFilters:
@pytest.mark.parametrize('function',[grid_filters.displacement_fluct_point, @pytest.mark.parametrize('function',[grid_filters.displacement_fluct_point,
grid_filters.displacement_fluct_node]) grid_filters.displacement_fluct_node])
def test_displacement_fluct_vanishes(self,function): def test_displacement_fluct_vanishes(self,function):
"""Ensure that constant F does not result in fluctuating displacement.""" """Ensure that constant F does not result in fluctuating displacement.""" # noqa
size = np.random.random(3) size = np.random.random(3)
cells = np.random.randint(8,32,(3)) cells = np.random.randint(8,32,(3))
F = np.broadcast_to(np.random.random((3,3)), tuple(cells)+(3,3)) F = np.broadcast_to(np.random.random((3,3)), tuple(cells)+(3,3))
@ -142,13 +142,13 @@ class TestGridFilters:
function(unordered,mode) function(unordered,mode)
def test_regrid_identity(self): def test_regrid_identity(self):
size = np.random.random(3) size = np.random.random(3) # noqa
cells = np.random.randint(8,32,(3)) cells = np.random.randint(8,32,(3))
F = np.broadcast_to(np.eye(3), tuple(cells)+(3,3)) F = np.broadcast_to(np.eye(3), tuple(cells)+(3,3))
assert all(grid_filters.regrid(size,F,cells) == np.arange(cells.prod())) assert all(grid_filters.regrid(size,F,cells) == np.arange(cells.prod()))
def test_regrid_double_cells(self): def test_regrid_double_cells(self):
size = np.random.random(3) size = np.random.random(3) # noqa
cells = np.random.randint(8,32,(3)) cells = np.random.randint(8,32,(3))
g = Grid.from_Voronoi_tessellation(cells,size,seeds.from_random(size,10)) g = Grid.from_Voronoi_tessellation(cells,size,seeds.from_random(size,10))
F = np.broadcast_to(np.eye(3), tuple(cells)+(3,3)) F = np.broadcast_to(np.eye(3), tuple(cells)+(3,3))

7
src/grid/DAMASK_grid.f90
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@ -466,7 +466,14 @@ program DAMASK_grid
call MPI_Allreduce(interface_SIGUSR2,signal,1_MPI_INTEGER_KIND,MPI_LOGICAL,MPI_LOR,MPI_COMM_WORLD,err_MPI) call MPI_Allreduce(interface_SIGUSR2,signal,1_MPI_INTEGER_KIND,MPI_LOGICAL,MPI_LOR,MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error' if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
if (mod(inc,loadCases(l)%f_restart) == 0 .or. signal) then if (mod(inc,loadCases(l)%f_restart) == 0 .or. signal) then
do field = 1, nActiveFields
select case (ID(field))
case(FIELD_MECH_ID)
call mechanical_restartWrite call mechanical_restartWrite
case(FIELD_THERMAL_ID)
call grid_thermal_spectral_restartWrite
end select
end do
call CPFEM_restartWrite call CPFEM_restartWrite
endif endif
if (signal) call interface_setSIGUSR2(.false.) if (signal) call interface_setSIGUSR2(.false.)

63
src/grid/grid_thermal_spectral.f90
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@ -16,6 +16,9 @@ module grid_thermal_spectral
use prec use prec
use parallelization use parallelization
use IO use IO
use DAMASK_interface
use HDF5_utilities
use HDF5
use spectral_utilities use spectral_utilities
use discretization_grid use discretization_grid
use homogenization use homogenization
@ -54,13 +57,13 @@ module grid_thermal_spectral
public :: & public :: &
grid_thermal_spectral_init, & grid_thermal_spectral_init, &
grid_thermal_spectral_solution, & grid_thermal_spectral_solution, &
grid_thermal_spectral_restartWrite, &
grid_thermal_spectral_forward grid_thermal_spectral_forward
contains contains
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
!> @brief allocates all neccessary fields and fills them with data !> @brief allocates all neccessary fields and fills them with data
! ToDo: Restart not implemented
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
subroutine grid_thermal_spectral_init(T_0) subroutine grid_thermal_spectral_init(T_0)
@ -72,6 +75,7 @@ subroutine grid_thermal_spectral_init(T_0)
PetscScalar, dimension(:,:,:), pointer :: T_PETSc PetscScalar, dimension(:,:,:), pointer :: T_PETSc
integer(MPI_INTEGER_KIND) :: err_MPI integer(MPI_INTEGER_KIND) :: err_MPI
PetscErrorCode :: err_PETSc PetscErrorCode :: err_PETSc
integer(HID_T) :: fileHandle, groupHandle
class(tNode), pointer :: & class(tNode), pointer :: &
num_grid num_grid
@ -105,12 +109,6 @@ subroutine grid_thermal_spectral_init(T_0)
allocate(T_lastInc(grid(1),grid(2),grid3), source=T_0) allocate(T_lastInc(grid(1),grid(2),grid3), source=T_0)
allocate(T_stagInc(grid(1),grid(2),grid3), source=T_0) allocate(T_stagInc(grid(1),grid(2),grid3), source=T_0)
ce = 0
do k = 1, grid3; do j = 1, grid(2); do i = 1,grid(1)
ce = ce + 1
call homogenization_thermal_setField(T_0,0.0_pReal,ce)
end do; end do; end do
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! initialize solver specific parts of PETSc ! initialize solver specific parts of PETSc
call SNESCreate(PETSC_COMM_WORLD,SNES_thermal,err_PETSc) call SNESCreate(PETSC_COMM_WORLD,SNES_thermal,err_PETSc)
@ -142,13 +140,31 @@ subroutine grid_thermal_spectral_init(T_0)
CHKERRQ(err_PETSc) CHKERRQ(err_PETSc)
call SNESSetFromOptions(SNES_thermal,err_PETSc) ! pull it all together with additional CLI arguments call SNESSetFromOptions(SNES_thermal,err_PETSc) ! pull it all together with additional CLI arguments
CHKERRQ(err_PETSc) CHKERRQ(err_PETSc)
restartRead: if (interface_restartInc > 0) then
print'(/,1x,a,i0,a)', 'reading restart data of increment ', interface_restartInc, ' from file'
fileHandle = HDF5_openFile(getSolverJobName()//'_restart.hdf5','r')
groupHandle = HDF5_openGroup(fileHandle,'solver')
call HDF5_read(T_current,groupHandle,'T',.false.)
call HDF5_read(T_lastInc,groupHandle,'T_lastInc',.false.)
end if restartRead
ce = 0
do k = 1, grid3; do j = 1, grid(2); do i = 1, grid(1)
ce = ce + 1
call homogenization_thermal_setField(T_current(i,j,k),0.0_pReal,ce)
end do; end do; end do
call DMDAVecGetArrayF90(thermal_grid,solution_vec,T_PETSc,err_PETSc) call DMDAVecGetArrayF90(thermal_grid,solution_vec,T_PETSc,err_PETSc)
CHKERRQ(err_PETSc) CHKERRQ(err_PETSc)
T_PETSc = T_current T_PETSc = T_current
call DMDAVecRestoreArrayF90(thermal_grid,solution_vec,T_PETSc,err_PETSc) call DMDAVecRestoreArrayF90(thermal_grid,solution_vec,T_PETSc,err_PETSc)
CHKERRQ(err_PETSc) CHKERRQ(err_PETSc)
call updateReference() call updateReference
end subroutine grid_thermal_spectral_init end subroutine grid_thermal_spectral_init
@ -253,6 +269,37 @@ subroutine grid_thermal_spectral_forward(cutBack)
end subroutine grid_thermal_spectral_forward end subroutine grid_thermal_spectral_forward
!--------------------------------------------------------------------------------------------------
!> @brief Write current solver and constitutive data for restart to file
!--------------------------------------------------------------------------------------------------
subroutine grid_thermal_spectral_restartWrite
PetscErrorCode :: err_PETSc
DM :: dm_local
integer(HID_T) :: fileHandle, groupHandle
PetscScalar, dimension(:,:,:), pointer :: T
call SNESGetDM(SNES_thermal,dm_local,err_PETSc);
CHKERRQ(err_PETSc)
call DMDAVecGetArrayF90(dm_local,solution_vec,T,err_PETSc);
CHKERRQ(err_PETSc)
print'(1x,a)', 'writing thermal solver data required for restart to file'; flush(IO_STDOUT)
fileHandle = HDF5_openFile(getSolverJobName()//'_restart.hdf5','a')
groupHandle = HDF5_openGroup(fileHandle,'solver')
call HDF5_write(T,groupHandle,'T')
call HDF5_write(T_lastInc,groupHandle,'T_lastInc')
call HDF5_closeGroup(groupHandle)
call HDF5_closeFile(fileHandle)
call DMDAVecRestoreArrayF90(dm_local,solution_vec,T,err_PETSc);
CHKERRQ(err_PETSc)
end subroutine grid_thermal_spectral_restartWrite
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
!> @brief forms the spectral thermal residual vector !> @brief forms the spectral thermal residual vector
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------

4
src/homogenization.f90
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@ -414,7 +414,7 @@ subroutine homogenization_restartWrite(fileHandle)
groupHandle(2) = HDF5_addGroup(groupHandle(1),material_name_homogenization(ho)) groupHandle(2) = HDF5_addGroup(groupHandle(1),material_name_homogenization(ho))
call HDF5_write(homogState(ho)%state,groupHandle(2),'omega') ! ToDo: should be done by mech call HDF5_write(homogState(ho)%state,groupHandle(2),'omega_mechanical') ! ToDo: should be done by mech
call HDF5_closeGroup(groupHandle(2)) call HDF5_closeGroup(groupHandle(2))
@ -441,7 +441,7 @@ subroutine homogenization_restartRead(fileHandle)
groupHandle(2) = HDF5_openGroup(groupHandle(1),material_name_homogenization(ho)) groupHandle(2) = HDF5_openGroup(groupHandle(1),material_name_homogenization(ho))
call HDF5_read(homogState(ho)%state0,groupHandle(2),'omega') ! ToDo: should be done by mech call HDF5_read(homogState(ho)%state0,groupHandle(2),'omega_mechanical') ! ToDo: should be done by mech
call HDF5_closeGroup(groupHandle(2)) call HDF5_closeGroup(groupHandle(2))

11
src/phase.f90
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@ -124,11 +124,20 @@ module phase
integer, intent(in) :: ph integer, intent(in) :: ph
end subroutine mechanical_restartWrite end subroutine mechanical_restartWrite
module subroutine thermal_restartWrite(groupHandle,ph)
integer(HID_T), intent(in) :: groupHandle
integer, intent(in) :: ph
end subroutine thermal_restartWrite
module subroutine mechanical_restartRead(groupHandle,ph) module subroutine mechanical_restartRead(groupHandle,ph)
integer(HID_T), intent(in) :: groupHandle integer(HID_T), intent(in) :: groupHandle
integer, intent(in) :: ph integer, intent(in) :: ph
end subroutine mechanical_restartRead end subroutine mechanical_restartRead
module subroutine thermal_restartRead(groupHandle,ph)
integer(HID_T), intent(in) :: groupHandle
integer, intent(in) :: ph
end subroutine thermal_restartRead
module function mechanical_S(ph,en) result(S) module function mechanical_S(ph,en) result(S)
integer, intent(in) :: ph,en integer, intent(in) :: ph,en
@ -641,6 +650,7 @@ subroutine phase_restartWrite(fileHandle)
groupHandle(2) = HDF5_addGroup(groupHandle(1),material_name_phase(ph)) groupHandle(2) = HDF5_addGroup(groupHandle(1),material_name_phase(ph))
call mechanical_restartWrite(groupHandle(2),ph) call mechanical_restartWrite(groupHandle(2),ph)
call thermal_restartWrite(groupHandle(2),ph)
call HDF5_closeGroup(groupHandle(2)) call HDF5_closeGroup(groupHandle(2))
@ -669,6 +679,7 @@ subroutine phase_restartRead(fileHandle)
groupHandle(2) = HDF5_openGroup(groupHandle(1),material_name_phase(ph)) groupHandle(2) = HDF5_openGroup(groupHandle(1),material_name_phase(ph))
call mechanical_restartRead(groupHandle(2),ph) call mechanical_restartRead(groupHandle(2),ph)
call thermal_restartRead(groupHandle(2),ph)
call HDF5_closeGroup(groupHandle(2)) call HDF5_closeGroup(groupHandle(2))

4
src/phase_mechanical.f90
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@ -1248,7 +1248,7 @@ module subroutine mechanical_restartWrite(groupHandle,ph)
integer, intent(in) :: ph integer, intent(in) :: ph
call HDF5_write(plasticState(ph)%state,groupHandle,'omega') call HDF5_write(plasticState(ph)%state,groupHandle,'omega_plastic')
call HDF5_write(phase_mechanical_Fi(ph)%data,groupHandle,'F_i') call HDF5_write(phase_mechanical_Fi(ph)%data,groupHandle,'F_i')
call HDF5_write(phase_mechanical_Li(ph)%data,groupHandle,'L_i') call HDF5_write(phase_mechanical_Li(ph)%data,groupHandle,'L_i')
call HDF5_write(phase_mechanical_Lp(ph)%data,groupHandle,'L_p') call HDF5_write(phase_mechanical_Lp(ph)%data,groupHandle,'L_p')
@ -1265,7 +1265,7 @@ module subroutine mechanical_restartRead(groupHandle,ph)
integer, intent(in) :: ph integer, intent(in) :: ph
call HDF5_read(plasticState(ph)%state0,groupHandle,'omega') call HDF5_read(plasticState(ph)%state0,groupHandle,'omega_plastic')
call HDF5_read(phase_mechanical_Fi0(ph)%data,groupHandle,'F_i') call HDF5_read(phase_mechanical_Fi0(ph)%data,groupHandle,'F_i')
call HDF5_read(phase_mechanical_Li0(ph)%data,groupHandle,'L_i') call HDF5_read(phase_mechanical_Li0(ph)%data,groupHandle,'L_i')
call HDF5_read(phase_mechanical_Lp0(ph)%data,groupHandle,'L_p') call HDF5_read(phase_mechanical_Lp0(ph)%data,groupHandle,'L_p')

45
src/phase_mechanical_eigen_thermalexpansion.f90
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@ -8,10 +8,9 @@ submodule(phase:eigen) thermalexpansion
integer, dimension(:), allocatable :: kinematics_thermal_expansion_instance integer, dimension(:), allocatable :: kinematics_thermal_expansion_instance
type :: tParameters type :: tParameters
real(pReal) :: & type(tPolynomial) :: &
T_ref A_11, &
real(pReal), dimension(3,3,3) :: & A_33
A = 0.0_pReal
end type tParameters end type tParameters
type(tParameters), dimension(:), allocatable :: param type(tParameters), dimension(:), allocatable :: param
@ -34,7 +33,7 @@ module function thermalexpansion_init(kinematics_length) result(myKinematics)
phase, & phase, &
mech, & mech, &
kinematics, & kinematics, &
kinematic_type myConfig
print'(/,1x,a)', '<<<+- phase:mechanical:eigen:thermalexpansion init -+>>>' print'(/,1x,a)', '<<<+- phase:mechanical:eigen:thermalexpansion init -+>>>'
@ -56,21 +55,13 @@ module function thermalexpansion_init(kinematics_length) result(myKinematics)
do k = 1, kinematics%length do k = 1, kinematics%length
if (myKinematics(k,p)) then if (myKinematics(k,p)) then
associate(prm => param(kinematics_thermal_expansion_instance(p))) associate(prm => param(kinematics_thermal_expansion_instance(p)))
kinematic_type => kinematics%get(k)
prm%T_ref = kinematic_type%get_asFloat('T_ref', defaultVal=T_ROOM) myConfig => kinematics%get(k)
prm%A_11 = polynomial(myConfig%asDict(),'A_11','T')
if (any(phase_lattice(p) == ['hP','tI'])) &
prm%A_33 = polynomial(myConfig%asDict(),'A_33','T')
prm%A(1,1,1) = kinematic_type%get_asFloat('A_11')
prm%A(1,1,2) = kinematic_type%get_asFloat('A_11,T', defaultVal=0.0_pReal)
prm%A(1,1,3) = kinematic_type%get_asFloat('A_11,T^2',defaultVal=0.0_pReal)
if (any(phase_lattice(p) == ['hP','tI'])) then
prm%A(3,3,1) = kinematic_type%get_asFloat('A_33')
prm%A(3,3,2) = kinematic_type%get_asFloat('A_33,T', defaultVal=0.0_pReal)
prm%A(3,3,3) = kinematic_type%get_asFloat('A_33,T^2',defaultVal=0.0_pReal)
end if
do i=1, size(prm%A,3)
prm%A(1:3,1:3,i) = lattice_symmetrize_33(prm%A(1:3,1:3,i),phase_lattice(p))
end do
end associate end associate
end if end if
end do end do
@ -91,22 +82,20 @@ module subroutine thermalexpansion_LiAndItsTangent(Li, dLi_dTstar, ph,me)
dLi_dTstar !< derivative of Li with respect to Tstar (4th-order tensor defined to be zero) dLi_dTstar !< derivative of Li with respect to Tstar (4th-order tensor defined to be zero)
real(pReal) :: T, dot_T real(pReal) :: T, dot_T
real(pReal), dimension(3,3) :: A
T = thermal_T(ph,me) T = thermal_T(ph,me)
dot_T = thermal_dot_T(ph,me) dot_T = thermal_dot_T(ph,me)
associate(prm => param(kinematics_thermal_expansion_instance(ph))) associate(prm => param(kinematics_thermal_expansion_instance(ph)))
Li = dot_T * ( &
prm%A(1:3,1:3,1) & ! constant coefficient A = 0.0_pReal
+ prm%A(1:3,1:3,2)*(T - prm%T_ref) & ! linear coefficient A(1,1) = prm%A_11%at(T)
+ prm%A(1:3,1:3,3)*(T - prm%T_ref)**2 & ! quadratic coefficient if (any(phase_lattice(ph) == ['hP','tI'])) A(3,3) = prm%A_33%at(T)
) / & A = lattice_symmetrize_33(A,phase_lattice(ph))
(1.0_pReal & Li = dot_T * A
+ prm%A(1:3,1:3,1)*(T - prm%T_ref) / 1.0_pReal &
+ prm%A(1:3,1:3,2)*(T - prm%T_ref)**2 / 2.0_pReal &
+ prm%A(1:3,1:3,3)*(T - prm%T_ref)**3 / 3.0_pReal &
)
end associate end associate
dLi_dTstar = 0.0_pReal dLi_dTstar = 0.0_pReal

30
src/phase_thermal.f90
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@ -254,6 +254,36 @@ function integrateThermalState(Delta_t, ph,en) result(broken)
end function integrateThermalState end function integrateThermalState
module subroutine thermal_restartWrite(groupHandle,ph)
integer(HID_T), intent(in) :: groupHandle
integer, intent(in) :: ph
integer :: so
do so = 1,thermal_Nsources(ph)
call HDF5_write(thermalState(ph)%p(so)%state,groupHandle,'omega_thermal')
enddo
end subroutine thermal_restartWrite
module subroutine thermal_restartRead(groupHandle,ph)
integer(HID_T), intent(in) :: groupHandle
integer, intent(in) :: ph
integer :: so
do so = 1,thermal_Nsources(ph)
call HDF5_read(thermalState(ph)%p(so)%state0,groupHandle,'omega_thermal')
enddo
end subroutine thermal_restartRead
module subroutine thermal_forward() module subroutine thermal_forward()
integer :: ph, so integer :: ph, so

2
src/polynomials.f90
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@ -163,7 +163,7 @@ subroutine selfTest
'T_ref: '//trim(adjustl(x_ref_s))//IO_EOL 'T_ref: '//trim(adjustl(x_ref_s))//IO_EOL
Dict => YAML_parse_str(trim(YAML_s)) Dict => YAML_parse_str(trim(YAML_s))
p2 = polynomial(dict%asDict(),'C','T') p2 = polynomial(dict%asDict(),'C','T')
if (dNeq(p1%at(x),p2%at(x),1.0e-12_pReal)) error stop 'polynomials: init' if (dNeq(p1%at(x),p2%at(x),1.0e-10_pReal)) error stop 'polynomials: init'
p1 = polynomial(coef*[0.0_pReal,1.0_pReal,0.0_pReal],x_ref) p1 = polynomial(coef*[0.0_pReal,1.0_pReal,0.0_pReal],x_ref)
if (dNeq(p1%at(x_ref+x),-p1%at(x_ref-x),1.0e-10_pReal)) error stop 'polynomials: eval(odd)' if (dNeq(p1%at(x_ref+x),-p1%at(x_ref-x),1.0e-10_pReal)) error stop 'polynomials: eval(odd)'