Merge branch 'development' of git.damask.mpie.de:damask/DAMASK into typehints_orientation_rotation
This commit is contained in:
Daniel Otto de Mentock
commit
df54bf724c
2
PRIVATE
2
PRIVATE
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@ -1 +1 @@
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Subproject commit 5598ec4892b0921fccf63e8570f9fcd8e0365716
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Subproject commit ebb7f0ce78d11275020af0ba60f929f95b446932
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@ -1,178 +0,0 @@
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#!/usr/bin/env python3
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import os
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import sys
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from io import StringIO
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from optparse import OptionParser
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import numpy as np
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from scipy import ndimage
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import damask
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scriptName = os.path.splitext(os.path.basename(__file__))[0]
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scriptID = ' '.join([scriptName,damask.version])
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getInterfaceEnergy = lambda A,B: np.float32((A != B)*1.0) # 1.0 if A & B are distinct, 0.0 otherwise
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struc = ndimage.generate_binary_structure(3,1) # 3D von Neumann neighborhood
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#--------------------------------------------------------------------------------------------------
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# MAIN
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#--------------------------------------------------------------------------------------------------
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog option(s) [geomfile(s)]', description = """
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Smoothen interface roughness by simulated curvature flow.
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This is achieved by the diffusion of each initially sharply bounded grain volume within the periodic domain
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up to a given distance 'd' voxels.
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The final geometry is assembled by selecting at each voxel that grain index for which the concentration remains largest.
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References 10.1073/pnas.1111557108 (10.1006/jcph.1994.1105)
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""", version = scriptID)
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parser.add_option('-d', '--distance',
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dest = 'd',
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type = 'float', metavar = 'float',
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help = 'diffusion distance in voxels [%default]')
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parser.add_option('-N', '--iterations',
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dest = 'N',
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type = 'int', metavar = 'int',
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help = 'curvature flow iterations [%default]')
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parser.add_option('-i', '--immutable',
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action = 'extend', dest = 'immutable', metavar = '<int LIST>',
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help = 'list of immutable material indices')
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parser.add_option('--ndimage',
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dest = 'ndimage', action='store_true',
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help = 'use ndimage.gaussian_filter in lieu of explicit FFT')
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parser.set_defaults(d = 1,
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N = 1,
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immutable = [],
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ndimage = False,
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)
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(options, filenames) = parser.parse_args()
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options.immutable = list(map(int,options.immutable))
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if filenames == []: filenames = [None]
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for name in filenames:
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damask.util.report(scriptName,name)
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geom = damask.Grid.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
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grid_original = geom.cells
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damask.util.croak(geom)
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material = np.tile(geom.material,np.where(grid_original == 1, 2,1)) # make one copy along dimensions with grid == 1
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grid = np.array(material.shape)
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# --- initialize support data ---------------------------------------------------------------------
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# store a copy of the initial material indices to find locations of immutable indices
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material_original = np.copy(material)
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if not options.ndimage:
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X,Y,Z = np.mgrid[0:grid[0],0:grid[1],0:grid[2]]
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# Calculates gaussian weights for simulating 3d diffusion
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gauss = np.exp(-(X*X + Y*Y + Z*Z)/(2.0*options.d*options.d),dtype=np.float32) \
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/np.power(2.0*np.pi*options.d*options.d,(3.0 - np.count_nonzero(grid_original == 1))/2.,dtype=np.float32)
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gauss[:,:,:grid[2]//2:-1] = gauss[:,:,1:(grid[2]+1)//2] # trying to cope with uneven (odd) grid size
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gauss[:,:grid[1]//2:-1,:] = gauss[:,1:(grid[1]+1)//2,:]
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gauss[:grid[0]//2:-1,:,:] = gauss[1:(grid[0]+1)//2,:,:]
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gauss = np.fft.rfftn(gauss).astype(np.complex64)
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for smoothIter in range(options.N):
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interfaceEnergy = np.zeros(material.shape,dtype=np.float32)
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for i in (-1,0,1):
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for j in (-1,0,1):
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for k in (-1,0,1):
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# assign interfacial energy to all voxels that have a differing neighbor (in Moore neighborhood)
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interfaceEnergy = np.maximum(interfaceEnergy,
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getInterfaceEnergy(material,np.roll(np.roll(np.roll(
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material,i,axis=0), j,axis=1), k,axis=2)))
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# periodically extend interfacial energy array by half a grid size in positive and negative directions
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periodic_interfaceEnergy = np.tile(interfaceEnergy,(3,3,3))[grid[0]//2:-grid[0]//2,
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grid[1]//2:-grid[1]//2,
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grid[2]//2:-grid[2]//2]
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# transform bulk volume (i.e. where interfacial energy remained zero), store index of closest boundary voxel
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index = ndimage.morphology.distance_transform_edt(periodic_interfaceEnergy == 0.,
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return_distances = False,
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return_indices = True)
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# want array index of nearest voxel on periodically extended boundary
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periodic_bulkEnergy = periodic_interfaceEnergy[index[0],
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index[1],
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index[2]].reshape(2*grid) # fill bulk with energy of nearest interface
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if options.ndimage:
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periodic_diffusedEnergy = ndimage.gaussian_filter(
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np.where(ndimage.morphology.binary_dilation(periodic_interfaceEnergy > 0.,
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structure = struc,
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iterations = int(round(options.d*2.))-1, # fat boundary
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),
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periodic_bulkEnergy, # ...and zero everywhere else
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0.),
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sigma = options.d)
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else:
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diffusedEnergy = np.fft.irfftn(np.fft.rfftn(
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np.where(
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ndimage.morphology.binary_dilation(interfaceEnergy > 0.,
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structure = struc,
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iterations = int(round(options.d*2.))-1),# fat boundary
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periodic_bulkEnergy[grid[0]//2:-grid[0]//2, # retain filled energy on fat boundary...
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grid[1]//2:-grid[1]//2,
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grid[2]//2:-grid[2]//2], # ...and zero everywhere else
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0.)).astype(np.complex64) *
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gauss).astype(np.float32)
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periodic_diffusedEnergy = np.tile(diffusedEnergy,(3,3,3))[grid[0]//2:-grid[0]//2,
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grid[1]//2:-grid[1]//2,
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grid[2]//2:-grid[2]//2] # periodically extend the smoothed bulk energy
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# transform voxels close to interface region
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index = ndimage.morphology.distance_transform_edt(periodic_diffusedEnergy >= 0.95*np.amax(periodic_diffusedEnergy),
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return_distances = False,
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return_indices = True) # want index of closest bulk grain
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periodic_material = np.tile(material,(3,3,3))[grid[0]//2:-grid[0]//2,
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grid[1]//2:-grid[1]//2,
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grid[2]//2:-grid[2]//2] # periodically extend the geometry
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material = periodic_material[index[0],
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index[1],
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index[2]].reshape(2*grid)[grid[0]//2:-grid[0]//2,
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grid[1]//2:-grid[1]//2,
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grid[2]//2:-grid[2]//2] # extent grains into interface region
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# replace immutable materials with closest mutable ones
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index = ndimage.morphology.distance_transform_edt(np.in1d(material,options.immutable).reshape(grid),
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return_distances = False,
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return_indices = True)
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material = material[index[0],
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index[1],
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index[2]]
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immutable = np.zeros(material.shape, dtype=np.bool)
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# find locations where immutable materials have been in original structure
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for micro in options.immutable:
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immutable += material_original == micro
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# undo any changes involving immutable materials
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material = np.where(immutable, material_original,material)
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damask.Grid(material = material[0:grid_original[0],0:grid_original[1],0:grid_original[2]],
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size = geom.size,
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origin = geom.origin,
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comments = geom.comments + [scriptID + ' ' + ' '.join(sys.argv[1:])],
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)\
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.save(sys.stdout if name is None else name)
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@ -1 +1 @@
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v3.0.0-alpha5-545-gad74f5dbe
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v3.0.0-alpha5-556-g97f849c09
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@ -5,7 +5,7 @@ import os
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import copy
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import datetime
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import warnings
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import xml.etree.ElementTree as ET
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import xml.etree.ElementTree as ET # noqa
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import xml.dom.minidom
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from pathlib import Path
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from functools import partial
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@ -9,3 +9,6 @@ import numpy as np
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FloatSequence = Union[np.ndarray,Sequence[float]]
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IntSequence = Union[np.ndarray,Sequence[int]]
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FileHandle = Union[TextIO, str, Path]
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NumpyRngSeed = Union[int, IntSequence, np.random.SeedSequence, np.random.Generator]
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# BitGenerator does not exists in older numpy versions
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#NumpyRngSeed = Union[int, IntSequence, np.random.SeedSequence, np.random.BitGenerator, np.random.Generator]
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|
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@ -1,3 +1,4 @@
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"""Functionality for generation of seed points for Voronoi or Laguerre tessellation."""
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from typing import Tuple as _Tuple
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@ -5,7 +6,7 @@ from typing import Tuple as _Tuple
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from scipy import spatial as _spatial
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import numpy as _np
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from ._typehints import FloatSequence as _FloatSequence, IntSequence as _IntSequence
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from ._typehints import FloatSequence as _FloatSequence, IntSequence as _IntSequence, NumpyRngSeed as _NumpyRngSeed
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from . import util as _util
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from . import grid_filters as _grid_filters
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@ -13,7 +14,7 @@ from . import grid_filters as _grid_filters
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def from_random(size: _FloatSequence,
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N_seeds: int,
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cells: _IntSequence = None,
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rng_seed=None) -> _np.ndarray:
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rng_seed: _NumpyRngSeed = None) -> _np.ndarray:
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"""
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Place seeds randomly in space.
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@ -53,7 +54,7 @@ def from_Poisson_disc(size: _FloatSequence,
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N_candidates: int,
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distance: float,
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periodic: bool = True,
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rng_seed=None) -> _np.ndarray:
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rng_seed: _NumpyRngSeed = None) -> _np.ndarray:
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"""
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Place seeds according to a Poisson disc distribution.
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|
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@ -16,7 +16,7 @@ import numpy as np
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import h5py
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from . import version
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from ._typehints import IntSequence, FloatSequence
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from ._typehints import FloatSequence, NumpyRngSeed
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# limit visibility
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__all__=[
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@ -396,7 +396,7 @@ def execution_stamp(class_name: str,
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def hybrid_IA(dist: np.ndarray,
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N: int,
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rng_seed: Union[int, IntSequence] = None) -> np.ndarray:
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rng_seed: NumpyRngSeed = None) -> np.ndarray:
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"""
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Hybrid integer approximation.
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|
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@ -287,7 +287,7 @@ class TestOrientation:
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@pytest.mark.parametrize('family',crystal_families)
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@pytest.mark.parametrize('proper',[True,False])
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def test_in_SST(self,family,proper):
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assert Orientation(family=family).in_SST(np.zeros(3),proper)
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assert Orientation(family=family).in_SST(np.zeros(3),proper)
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@pytest.mark.parametrize('function',['in_SST','IPF_color'])
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def test_invalid_argument(self,function):
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@ -367,13 +367,13 @@ class TestResult:
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@pytest.mark.parametrize('mode',['cell','node'])
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def test_coordinates(self,default,mode):
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if mode == 'cell':
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a = grid_filters.coordinates0_point(default.cells,default.size,default.origin)
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b = default.coordinates0_point.reshape(tuple(default.cells)+(3,),order='F')
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elif mode == 'node':
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a = grid_filters.coordinates0_node(default.cells,default.size,default.origin)
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b = default.coordinates0_node.reshape(tuple(default.cells+1)+(3,),order='F')
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assert np.allclose(a,b)
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if mode == 'cell':
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a = grid_filters.coordinates0_point(default.cells,default.size,default.origin)
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b = default.coordinates0_point.reshape(tuple(default.cells)+(3,),order='F')
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elif mode == 'node':
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a = grid_filters.coordinates0_node(default.cells,default.size,default.origin)
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b = default.coordinates0_node.reshape(tuple(default.cells+1)+(3,),order='F')
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assert np.allclose(a,b)
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@pytest.mark.parametrize('output',['F','*',['P'],['P','F']],ids=range(4))
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@pytest.mark.parametrize('fname',['12grains6x7x8_tensionY.hdf5'],ids=range(1))
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@ -421,7 +421,7 @@ class TestResult:
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def test_XDMF_datatypes(self,tmp_path,single_phase,update,ref_path):
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for shape in [('scalar',()),('vector',(3,)),('tensor',(3,3)),('matrix',(12,))]:
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for dtype in ['f4','f8','i1','i2','i4','i8','u1','u2','u4','u8']:
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single_phase.add_calculation(f"np.ones(np.shape(#F#)[0:1]+{shape[1]},'{dtype}')",f'{shape[0]}_{dtype}')
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single_phase.add_calculation(f"np.ones(np.shape(#F#)[0:1]+{shape[1]},'{dtype}')",f'{shape[0]}_{dtype}')
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fname = os.path.splitext(os.path.basename(single_phase.fname))[0]+'.xdmf'
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os.chdir(tmp_path)
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single_phase.export_XDMF()
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|
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@ -1076,19 +1076,19 @@ class TestRotation:
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def test_from_fiber_component(self,N,sigma):
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p = []
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for run in range(5):
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alpha = np.random.random()*2*np.pi,np.arccos(np.random.random())
|
||||
beta = np.random.random()*2*np.pi,np.arccos(np.random.random())
|
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alpha = np.random.random()*2*np.pi,np.arccos(np.random.random())
|
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beta = np.random.random()*2*np.pi,np.arccos(np.random.random())
|
||||
|
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f_in_C = np.array([np.sin(alpha[0])*np.cos(alpha[1]), np.sin(alpha[0])*np.sin(alpha[1]), np.cos(alpha[0])])
|
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f_in_S = np.array([np.sin(beta[0] )*np.cos(beta[1] ), np.sin(beta[0] )*np.sin(beta[1] ), np.cos(beta[0] )])
|
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ax = np.append(np.cross(f_in_C,f_in_S), - np.arccos(np.dot(f_in_C,f_in_S)))
|
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n = Rotation.from_axis_angle(ax if ax[3] > 0.0 else ax*-1.0 ,normalize=True) # rotation to align fiber axis in crystal and sample system
|
||||
f_in_C = np.array([np.sin(alpha[0])*np.cos(alpha[1]), np.sin(alpha[0])*np.sin(alpha[1]), np.cos(alpha[0])])
|
||||
f_in_S = np.array([np.sin(beta[0] )*np.cos(beta[1] ), np.sin(beta[0] )*np.sin(beta[1] ), np.cos(beta[0] )])
|
||||
ax = np.append(np.cross(f_in_C,f_in_S), - np.arccos(np.dot(f_in_C,f_in_S)))
|
||||
n = Rotation.from_axis_angle(ax if ax[3] > 0.0 else ax*-1.0 ,normalize=True) # rotation to align fiber axis in crystal and sample system
|
||||
|
||||
o = Rotation.from_fiber_component(alpha,beta,np.radians(sigma),N,False)
|
||||
angles = np.arccos(np.clip(np.dot(o@np.broadcast_to(f_in_S,(N,3)),n@f_in_S),-1,1))
|
||||
dist = np.array(angles) * (np.random.randint(0,2,N)*2-1)
|
||||
o = Rotation.from_fiber_component(alpha,beta,np.radians(sigma),N,False)
|
||||
angles = np.arccos(np.clip(np.dot(o@np.broadcast_to(f_in_S,(N,3)),n@f_in_S),-1,1))
|
||||
dist = np.array(angles) * (np.random.randint(0,2,N)*2-1)
|
||||
|
||||
p.append(stats.normaltest(dist)[1])
|
||||
p.append(stats.normaltest(dist)[1])
|
||||
|
||||
sigma_out = np.degrees(np.std(dist))
|
||||
p = np.average(p)
|
||||
|
|
|
|||
|
|
@ -173,11 +173,11 @@ class TestVTK:
|
|||
polyData = VTK.from_poly_data(points)
|
||||
polyData.add(points,'coordinates')
|
||||
if update:
|
||||
polyData.save(ref_path/'polyData')
|
||||
polyData.save(ref_path/'polyData')
|
||||
else:
|
||||
reference = VTK.load(ref_path/'polyData.vtp')
|
||||
assert polyData.__repr__() == reference.__repr__() and \
|
||||
np.allclose(polyData.get('coordinates'),points)
|
||||
reference = VTK.load(ref_path/'polyData.vtp')
|
||||
assert polyData.__repr__() == reference.__repr__() and \
|
||||
np.allclose(polyData.get('coordinates'),points)
|
||||
|
||||
@pytest.mark.xfail(int(vtk.vtkVersion.GetVTKVersion().split('.')[0])<8, reason='missing METADATA')
|
||||
def test_compare_reference_rectilinearGrid(self,update,ref_path,tmp_path):
|
||||
|
|
@ -189,8 +189,8 @@ class TestVTK:
|
|||
rectilinearGrid.add(np.ascontiguousarray(c),'cell')
|
||||
rectilinearGrid.add(np.ascontiguousarray(n),'node')
|
||||
if update:
|
||||
rectilinearGrid.save(ref_path/'rectilinearGrid')
|
||||
rectilinearGrid.save(ref_path/'rectilinearGrid')
|
||||
else:
|
||||
reference = VTK.load(ref_path/'rectilinearGrid.vtr')
|
||||
assert rectilinearGrid.__repr__() == reference.__repr__() and \
|
||||
np.allclose(rectilinearGrid.get('cell'),c)
|
||||
reference = VTK.load(ref_path/'rectilinearGrid.vtr')
|
||||
assert rectilinearGrid.__repr__() == reference.__repr__() and \
|
||||
np.allclose(rectilinearGrid.get('cell'),c)
|
||||
|
|
|
|||
|
|
@ -8,19 +8,19 @@ from damask import seeds
|
|||
class TestGridFilters:
|
||||
|
||||
def test_coordinates0_point(self):
|
||||
size = np.random.random(3)
|
||||
size = np.random.random(3) # noqa
|
||||
cells = np.random.randint(8,32,(3))
|
||||
coord = grid_filters.coordinates0_point(cells,size)
|
||||
assert np.allclose(coord[0,0,0],size/cells*.5) and coord.shape == tuple(cells) + (3,)
|
||||
|
||||
def test_coordinates0_node(self):
|
||||
size = np.random.random(3)
|
||||
size = np.random.random(3) # noqa
|
||||
cells = np.random.randint(8,32,(3))
|
||||
coord = grid_filters.coordinates0_node(cells,size)
|
||||
assert np.allclose(coord[-1,-1,-1],size) and coord.shape == tuple(cells+1) + (3,)
|
||||
|
||||
def test_coord0(self):
|
||||
size = np.random.random(3)
|
||||
size = np.random.random(3) # noqa
|
||||
cells = np.random.randint(8,32,(3))
|
||||
c = grid_filters.coordinates0_point(cells+1,size+size/cells)
|
||||
n = grid_filters.coordinates0_node(cells,size) + size/cells*.5
|
||||
|
|
@ -28,16 +28,16 @@ class TestGridFilters:
|
|||
|
||||
@pytest.mark.parametrize('mode',['point','node'])
|
||||
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))
|
||||
size = np.random.random(3)
|
||||
origin = np.random.random(3)
|
||||
coord0 = eval(f'grid_filters.coordinates0_{mode}(cells,size,origin)') # noqa
|
||||
coord0 = eval(f'grid_filters.coordinates0_{mode}(cells,size,origin)') # noqa
|
||||
_cells,_size,_origin = eval(f'grid_filters.cellsSizeOrigin_coordinates0_{mode}(coord0.reshape(-1,3,order="F"))')
|
||||
assert np.allclose(cells,_cells) and np.allclose(size,_size) and np.allclose(origin,_origin)
|
||||
|
||||
def test_displacement_fluct_equivalence(self):
|
||||
"""Ensure that fluctuations are periodic."""
|
||||
"""Ensure that fluctuations are periodic.""" # noqa
|
||||
size = np.random.random(3)
|
||||
cells = np.random.randint(8,32,(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)))
|
||||
|
||||
def test_interpolation_to_node(self):
|
||||
size = np.random.random(3)
|
||||
size = np.random.random(3) # noqa
|
||||
cells = np.random.randint(8,32,(3))
|
||||
F = np.random.random(tuple(cells)+(3,3))
|
||||
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])
|
||||
|
||||
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)
|
||||
node_field_x = np.cos(coordinates_node_x)
|
||||
|
|
@ -66,7 +66,7 @@ class TestGridFilters:
|
|||
|
||||
@pytest.mark.parametrize('mode',['point','node'])
|
||||
def test_coordinates0_origin(self,mode):
|
||||
origin= np.random.random(3)
|
||||
origin= np.random.random(3) # noqa
|
||||
size = np.random.random(3) # noqa
|
||||
cells = np.random.randint(8,32,(3))
|
||||
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,
|
||||
grid_filters.displacement_avg_node])
|
||||
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)
|
||||
cells = np.random.randint(8,32,(3))
|
||||
F = np.random.random(tuple(cells)+(3,3))
|
||||
|
|
@ -89,7 +89,7 @@ class TestGridFilters:
|
|||
@pytest.mark.parametrize('function',[grid_filters.displacement_fluct_point,
|
||||
grid_filters.displacement_fluct_node])
|
||||
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)
|
||||
cells = np.random.randint(8,32,(3))
|
||||
F = np.broadcast_to(np.random.random((3,3)), tuple(cells)+(3,3))
|
||||
|
|
@ -142,13 +142,13 @@ class TestGridFilters:
|
|||
function(unordered,mode)
|
||||
|
||||
def test_regrid_identity(self):
|
||||
size = np.random.random(3)
|
||||
size = np.random.random(3) # noqa
|
||||
cells = np.random.randint(8,32,(3))
|
||||
F = np.broadcast_to(np.eye(3), tuple(cells)+(3,3))
|
||||
assert all(grid_filters.regrid(size,F,cells) == np.arange(cells.prod()))
|
||||
|
||||
def test_regrid_double_cells(self):
|
||||
size = np.random.random(3)
|
||||
size = np.random.random(3) # noqa
|
||||
cells = np.random.randint(8,32,(3))
|
||||
g = Grid.from_Voronoi_tessellation(cells,size,seeds.from_random(size,10))
|
||||
F = np.broadcast_to(np.eye(3), tuple(cells)+(3,3))
|
||||
|
|
|
|||
|
|
@ -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)
|
||||
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
|
||||
if (mod(inc,loadCases(l)%f_restart) == 0 .or. signal) then
|
||||
call mechanical_restartWrite
|
||||
do field = 1, nActiveFields
|
||||
select case (ID(field))
|
||||
case(FIELD_MECH_ID)
|
||||
call mechanical_restartWrite
|
||||
case(FIELD_THERMAL_ID)
|
||||
call grid_thermal_spectral_restartWrite
|
||||
end select
|
||||
end do
|
||||
call CPFEM_restartWrite
|
||||
endif
|
||||
if (signal) call interface_setSIGUSR2(.false.)
|
||||
|
|
|
|||
|
|
@ -16,6 +16,9 @@ module grid_thermal_spectral
|
|||
use prec
|
||||
use parallelization
|
||||
use IO
|
||||
use DAMASK_interface
|
||||
use HDF5_utilities
|
||||
use HDF5
|
||||
use spectral_utilities
|
||||
use discretization_grid
|
||||
use homogenization
|
||||
|
|
@ -54,13 +57,13 @@ module grid_thermal_spectral
|
|||
public :: &
|
||||
grid_thermal_spectral_init, &
|
||||
grid_thermal_spectral_solution, &
|
||||
grid_thermal_spectral_restartWrite, &
|
||||
grid_thermal_spectral_forward
|
||||
|
||||
contains
|
||||
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
!> @brief allocates all neccessary fields and fills them with data
|
||||
! ToDo: Restart not implemented
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
subroutine grid_thermal_spectral_init(T_0)
|
||||
|
||||
|
|
@ -72,6 +75,7 @@ subroutine grid_thermal_spectral_init(T_0)
|
|||
PetscScalar, dimension(:,:,:), pointer :: T_PETSc
|
||||
integer(MPI_INTEGER_KIND) :: err_MPI
|
||||
PetscErrorCode :: err_PETSc
|
||||
integer(HID_T) :: fileHandle, groupHandle
|
||||
class(tNode), pointer :: &
|
||||
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_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
|
||||
call SNESCreate(PETSC_COMM_WORLD,SNES_thermal,err_PETSc)
|
||||
|
|
@ -142,13 +140,31 @@ subroutine grid_thermal_spectral_init(T_0)
|
|||
CHKERRQ(err_PETSc)
|
||||
call SNESSetFromOptions(SNES_thermal,err_PETSc) ! pull it all together with additional CLI arguments
|
||||
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)
|
||||
CHKERRQ(err_PETSc)
|
||||
T_PETSc = T_current
|
||||
call DMDAVecRestoreArrayF90(thermal_grid,solution_vec,T_PETSc,err_PETSc)
|
||||
CHKERRQ(err_PETSc)
|
||||
|
||||
call updateReference()
|
||||
call updateReference
|
||||
|
||||
end subroutine grid_thermal_spectral_init
|
||||
|
||||
|
|
@ -253,6 +269,37 @@ subroutine grid_thermal_spectral_forward(cutBack)
|
|||
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
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
|
|
|
|||
|
|
@ -414,7 +414,7 @@ subroutine homogenization_restartWrite(fileHandle)
|
|||
|
||||
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))
|
||||
|
||||
|
|
@ -441,7 +441,7 @@ subroutine homogenization_restartRead(fileHandle)
|
|||
|
||||
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))
|
||||
|
||||
|
|
|
|||
|
|
@ -124,11 +124,20 @@ module phase
|
|||
integer, intent(in) :: ph
|
||||
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)
|
||||
integer(HID_T), intent(in) :: groupHandle
|
||||
integer, intent(in) :: ph
|
||||
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)
|
||||
integer, intent(in) :: ph,en
|
||||
|
|
@ -641,6 +650,7 @@ subroutine phase_restartWrite(fileHandle)
|
|||
groupHandle(2) = HDF5_addGroup(groupHandle(1),material_name_phase(ph))
|
||||
|
||||
call mechanical_restartWrite(groupHandle(2),ph)
|
||||
call thermal_restartWrite(groupHandle(2),ph)
|
||||
|
||||
call HDF5_closeGroup(groupHandle(2))
|
||||
|
||||
|
|
@ -669,6 +679,7 @@ subroutine phase_restartRead(fileHandle)
|
|||
groupHandle(2) = HDF5_openGroup(groupHandle(1),material_name_phase(ph))
|
||||
|
||||
call mechanical_restartRead(groupHandle(2),ph)
|
||||
call thermal_restartRead(groupHandle(2),ph)
|
||||
|
||||
call HDF5_closeGroup(groupHandle(2))
|
||||
|
||||
|
|
|
|||
|
|
@ -1248,7 +1248,7 @@ module subroutine mechanical_restartWrite(groupHandle,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_Li(ph)%data,groupHandle,'L_i')
|
||||
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
|
||||
|
||||
|
||||
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_Li0(ph)%data,groupHandle,'L_i')
|
||||
call HDF5_read(phase_mechanical_Lp0(ph)%data,groupHandle,'L_p')
|
||||
|
|
|
|||
|
|
@ -8,10 +8,9 @@ submodule(phase:eigen) thermalexpansion
|
|||
integer, dimension(:), allocatable :: kinematics_thermal_expansion_instance
|
||||
|
||||
type :: tParameters
|
||||
real(pReal) :: &
|
||||
T_ref
|
||||
real(pReal), dimension(3,3,3) :: &
|
||||
A = 0.0_pReal
|
||||
type(tPolynomial) :: &
|
||||
A_11, &
|
||||
A_33
|
||||
end type tParameters
|
||||
|
||||
type(tParameters), dimension(:), allocatable :: param
|
||||
|
|
@ -34,7 +33,7 @@ module function thermalexpansion_init(kinematics_length) result(myKinematics)
|
|||
phase, &
|
||||
mech, &
|
||||
kinematics, &
|
||||
kinematic_type
|
||||
myConfig
|
||||
|
||||
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
|
||||
if (myKinematics(k,p)) then
|
||||
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 if
|
||||
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)
|
||||
|
||||
real(pReal) :: T, dot_T
|
||||
real(pReal), dimension(3,3) :: A
|
||||
|
||||
|
||||
T = thermal_T(ph,me)
|
||||
dot_T = thermal_dot_T(ph,me)
|
||||
|
||||
associate(prm => param(kinematics_thermal_expansion_instance(ph)))
|
||||
Li = dot_T * ( &
|
||||
prm%A(1:3,1:3,1) & ! constant coefficient
|
||||
+ prm%A(1:3,1:3,2)*(T - prm%T_ref) & ! linear coefficient
|
||||
+ prm%A(1:3,1:3,3)*(T - prm%T_ref)**2 & ! quadratic coefficient
|
||||
) / &
|
||||
(1.0_pReal &
|
||||
+ 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 &
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+ prm%A(1:3,1:3,3)*(T - prm%T_ref)**3 / 3.0_pReal &
|
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)
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||||
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||||
A = 0.0_pReal
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A(1,1) = prm%A_11%at(T)
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||||
if (any(phase_lattice(ph) == ['hP','tI'])) A(3,3) = prm%A_33%at(T)
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||||
A = lattice_symmetrize_33(A,phase_lattice(ph))
|
||||
Li = dot_T * A
|
||||
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||||
end associate
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||||
dLi_dTstar = 0.0_pReal
|
||||
|
||||
|
|
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|||
|
|
@ -48,7 +48,7 @@ module subroutine elastic_init(phases)
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|||
prm%C_11 = polynomial(elastic%asDict(),'C_11','T')
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||||
prm%C_12 = polynomial(elastic%asDict(),'C_12','T')
|
||||
prm%C_44 = polynomial(elastic%asDict(),'C_44','T')
|
||||
|
||||
|
||||
if (any(phase_lattice(ph) == ['hP','tI'])) then
|
||||
prm%C_13 = polynomial(elastic%asDict(),'C_13','T')
|
||||
prm%C_33 = polynomial(elastic%asDict(),'C_33','T')
|
||||
|
|
@ -77,7 +77,7 @@ pure module function elastic_C66(ph,en) result(C66)
|
|||
|
||||
|
||||
associate(prm => param(ph))
|
||||
|
||||
|
||||
C66 = 0.0_pReal
|
||||
T = thermal_T(ph,en)
|
||||
|
||||
|
|
|
|||
|
|
@ -254,6 +254,36 @@ function integrateThermalState(Delta_t, ph,en) result(broken)
|
|||
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()
|
||||
|
||||
integer :: ph, so
|
||||
|
|
|
|||
|
|
@ -163,7 +163,7 @@ subroutine selfTest
|
|||
'T_ref: '//trim(adjustl(x_ref_s))//IO_EOL
|
||||
Dict => YAML_parse_str(trim(YAML_s))
|
||||
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)
|
||||
if (dNeq(p1%at(x_ref+x),-p1%at(x_ref-x),1.0e-10_pReal)) error stop 'polynomials: eval(odd)'
|
||||
|
|
|
|||
Loading…
Reference in New Issue