Merge branch 'development' into 'empty-table-init'
# Conflicts: # python/damask/_table.py
This commit is contained in:
Philip Eisenlohr
commit
4746ac890b
2
PRIVATE
2
PRIVATE
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|
@ -1 +1 @@
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Subproject commit 1766c855e54668d6225c9b22db536be7052605bc
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Subproject commit 0e82975b23a1bd4310c523388f1cadf1b8e03dd0
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@ -482,7 +482,7 @@ class ConfigMaterial(Config):
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"""
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N,n,shaped = 1,1,{}
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map_dim = {'O':-1,'F_i':-2}
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map_dim = {'O':-1,'V_e':-2}
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for k,v in kwargs.items():
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shaped[k] = np.array(v)
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s = shaped[k].shape[:map_dim.get(k,None)]
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@ -494,12 +494,12 @@ class ConfigMaterial(Config):
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if 'v' not in kwargs:
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shaped['v'] = np.broadcast_to(1/n,(N,n))
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map_shape = {'O':(N,n,4),'F_i':(N,n,3,3)}
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map_shape = {'O':(N,n,4),'V_e':(N,n,3,3)}
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for k,v in shaped.items():
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target = map_shape.get(k,(N,n))
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obj = np.broadcast_to(v.reshape(util.shapeshifter(v.shape, target, mode = 'right')), target)
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for i in range(N):
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if k in ['phase','O','v','F_i']:
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if k in ['phase','O','v','V_e']:
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for j in range(n):
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mat[i]['constituents'][j][k] = obj[i,j].item() if isinstance(obj[i,j],np.generic) else obj[i,j]
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else:
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@ -50,15 +50,16 @@ class Grid:
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Coordinates of grid origin in meter. Defaults to [0.0,0.0,0.0].
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initial_conditions : dictionary, optional
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Labels and values of the inital conditions at each material point.
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comments : (list of) str, optional
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Comments, e.g. history of operations.
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comments : str or iterable of str, optional
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Additional, human-readable information, e.g. history of operations.
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"""
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self.material = material
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self.size = size # type: ignore
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self.origin = origin # type: ignore
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self.initial_conditions = {} if initial_conditions is None else initial_conditions
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self.comments = [] if comments is None else comments # type: ignore
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comments_ = [comments] if isinstance(comments,str) else comments
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self.comments = [] if comments_ is None else [str(c) for c in comments_]
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def __repr__(self) -> str:
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"""Give short human-readable summary."""
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@ -1,4 +1,5 @@
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import multiprocessing as mp
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from multiprocessing.synchronize import Lock
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import re
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import fnmatch
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import os
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@ -10,6 +11,7 @@ from pathlib import Path
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from functools import partial
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from collections import defaultdict
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from collections.abc import Iterable
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from typing import Union, Callable, Any, Sequence, Literal, Dict, List, Tuple
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import h5py
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import numpy as np
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@ -22,19 +24,21 @@ from . import grid_filters
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from . import mechanics
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from . import tensor
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from . import util
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from ._typehints import FloatSequence, IntSequence
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h5py3 = h5py.__version__[0] == '3'
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chunk_size = 1024**2//8 # for compression in HDF5
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prefix_inc = 'increment_'
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def _read(dataset):
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def _read(dataset: h5py._hl.dataset.Dataset) -> np.ndarray:
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"""Read a dataset and its metadata into a numpy.ndarray."""
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metadata = {k:(v.decode() if not h5py3 and type(v) is bytes else v) for k,v in dataset.attrs.items()}
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dtype = np.dtype(dataset.dtype,metadata=metadata)
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dtype = np.dtype(dataset.dtype,metadata=metadata) # type: ignore
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return np.array(dataset,dtype=dtype)
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def _match(requested,existing):
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def _match(requested,
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existing: h5py._hl.base.KeysViewHDF5) -> List[Any]:
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"""Find matches among two sets of labels."""
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def flatten_list(list_of_lists):
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return [e for e_ in list_of_lists for e in e_]
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@ -50,7 +54,10 @@ def _match(requested,existing):
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return sorted(set(flatten_list([fnmatch.filter(existing,r) for r in requested_])),
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key=util.natural_sort)
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def _empty_like(dataset,N_materialpoints,fill_float,fill_int):
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def _empty_like(dataset: np.ma.core.MaskedArray,
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N_materialpoints: int,
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fill_float: float,
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fill_int: int) -> np.ma.core.MaskedArray:
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"""Create empty numpy.ma.MaskedArray."""
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return ma.array(np.empty((N_materialpoints,)+dataset.shape[1:],dataset.dtype),
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fill_value = fill_float if dataset.dtype in np.sctypes['float'] else fill_int,
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@ -84,7 +91,7 @@ class Result:
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"""
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def __init__(self,fname):
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def __init__(self, fname: Union[str, Path]):
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"""
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New result view bound to a HDF5 file.
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@ -102,7 +109,7 @@ class Result:
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if self.version_major != 0 or not 12 <= self.version_minor <= 14:
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raise TypeError(f'unsupported DADF5 version "{self.version_major}.{self.version_minor}"')
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if self.version_major == 0 and self.version_minor < 14:
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self.export_setup = None
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self.export_setup = None # type: ignore
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self.structured = 'cells' in f['geometry'].attrs.keys()
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@ -111,7 +118,7 @@ class Result:
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self.size = f['geometry'].attrs['size']
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self.origin = f['geometry'].attrs['origin']
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else:
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self.add_curl = self.add_divergence = self.add_gradient = None
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self.add_curl = self.add_divergence = self.add_gradient = None # type: ignore
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r = re.compile(rf'{prefix_inc}([0-9]+)')
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self.increments = sorted([i for i in f.keys() if r.match(i)],key=util.natural_sort)
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@ -126,7 +133,7 @@ class Result:
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self.phase = f['cell_to/phase']['label'].astype('str')
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self.phases = sorted(np.unique(self.phase),key=util.natural_sort)
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self.fields = []
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self.fields: List[str] = []
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for c in self.phases:
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self.fields += f['/'.join([self.increments[0],'phase',c])].keys()
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for m in self.homogenizations:
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@ -144,14 +151,14 @@ class Result:
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self._protected = True
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def __copy__(self):
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def __copy__(self) -> "Result":
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"""Create deep copy."""
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return copy.deepcopy(self)
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copy = __copy__
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def __repr__(self):
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def __repr__(self) -> str:
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"""Give short human-readable summary."""
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with h5py.File(self.fname,'r') as f:
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header = [f'Created by {f.attrs["creator"]}',
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@ -171,12 +178,12 @@ class Result:
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def _manage_view(self,
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action,
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increments=None,
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times=None,
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phases=None,
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homogenizations=None,
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fields=None):
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action: Literal['set', 'add', 'del'],
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increments: Union[int, Sequence[int], str, Sequence[str], bool] = None,
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times: Union[float, Sequence[float], str, Sequence[str], bool] = None,
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phases: Union[str, Sequence[str], bool] = None,
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homogenizations: Union[str, Sequence[str], bool] = None,
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fields: Union[str, Sequence[str], bool] = None) -> "Result":
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"""
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Manages the visibility of the groups.
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@ -204,8 +211,7 @@ class Result:
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datasets = '*'
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elif datasets is False:
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datasets = []
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choice = list(datasets).copy() if hasattr(datasets,'__iter__') and not isinstance(datasets,str) else \
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[datasets]
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choice = [datasets] if not hasattr(datasets,'__iter__') or isinstance(datasets,str) else list(datasets) # type: ignore
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if what == 'increments':
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choice = [c if isinstance(c,str) and c.startswith(prefix_inc) else
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@ -216,7 +222,7 @@ class Result:
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if choice == ['*']:
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choice = self.increments
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else:
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iterator = map(float,choice)
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iterator = map(float,choice) # type: ignore
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choice = []
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for c in iterator:
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idx = np.searchsorted(self.times,c)
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@ -224,7 +230,7 @@ class Result:
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if np.isclose(c,self.times[idx]):
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choice.append(self.increments[idx])
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elif np.isclose(c,self.times[idx+1]):
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choice.append(self.increments[idx+1])
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choice.append(self.increments[idx+1]) # type: ignore
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valid = _match(choice,getattr(self,what))
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existing = set(self.visible[what])
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@ -241,7 +247,9 @@ class Result:
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return dup
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def increments_in_range(self,start=None,end=None):
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def increments_in_range(self,
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start: Union[str, int] = None,
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end: Union[str, int] = None) -> Sequence[int]:
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"""
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Get all increments within a given range.
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@ -263,7 +271,9 @@ class Result:
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self.incs[-1] if end is None else end))
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return [i for i in self.incs if s <= i <= e]
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def times_in_range(self,start=None,end=None):
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def times_in_range(self,
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start: float = None,
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end: float = None) -> Sequence[int]:
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"""
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Get all increments within a given time range.
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@ -286,12 +296,12 @@ class Result:
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def view(self,*,
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increments=None,
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times=None,
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phases=None,
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homogenizations=None,
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fields=None,
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protected=None):
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increments: Union[int, Sequence[int], str, Sequence[str], bool] = None,
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times: Union[float, Sequence[float], str, Sequence[str], bool] = None,
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phases: Union[str, Sequence[str], bool] = None,
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homogenizations: Union[str, Sequence[str], bool] = None,
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fields: Union[str, Sequence[str], bool] = None,
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protected: bool = None) -> "Result":
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"""
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Set view.
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@ -343,11 +353,11 @@ class Result:
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def view_more(self,*,
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increments=None,
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times=None,
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phases=None,
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homogenizations=None,
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fields=None):
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increments: Union[int, Sequence[int], str, Sequence[str], bool] = None,
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times: Union[float, Sequence[float], str, Sequence[str], bool] = None,
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phases: Union[str, Sequence[str], bool] = None,
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homogenizations: Union[str, Sequence[str], bool] = None,
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fields: Union[str, Sequence[str], bool] = None) -> "Result":
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"""
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Add to view.
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|
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@ -386,11 +396,11 @@ class Result:
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|||
|
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def view_less(self,*,
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increments=None,
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times=None,
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phases=None,
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homogenizations=None,
|
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fields=None):
|
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increments: Union[int, Sequence[int], str, Sequence[str], bool] = None,
|
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times: Union[float, Sequence[float], str, Sequence[str], bool] = None,
|
||||
phases: Union[str, Sequence[str], bool] = None,
|
||||
homogenizations: Union[str, Sequence[str], bool] = None,
|
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fields: Union[str, Sequence[str], bool] = None) -> "Result":
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"""
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Remove from view.
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|
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@ -427,7 +437,9 @@ class Result:
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return self._manage_view('del',increments,times,phases,homogenizations,fields)
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|
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|
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def rename(self,name_src,name_dst):
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def rename(self,
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name_src: str,
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name_dst: str):
|
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"""
|
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Rename/move datasets (within the same group/folder).
|
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|
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|
|
@ -468,7 +480,7 @@ class Result:
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del f[path_src]
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|
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|
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def remove(self,name):
|
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def remove(self, name: str):
|
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"""
|
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Remove/delete datasets.
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|
||||
|
|
@ -502,7 +514,7 @@ class Result:
|
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if path in f.keys(): del f[path]
|
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|
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|
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def list_data(self):
|
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def list_data(self) -> List[str]:
|
||||
"""
|
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Collect information on all active datasets in the file.
|
||||
|
||||
|
|
@ -533,7 +545,8 @@ class Result:
|
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return msg
|
||||
|
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|
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def enable_user_function(self,func):
|
||||
def enable_user_function(self,
|
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func: Callable):
|
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globals()[func.__name__]=func
|
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print(f'Function {func.__name__} enabled in add_calculation.')
|
||||
|
||||
|
|
@ -544,7 +557,7 @@ class Result:
|
|||
|
||||
|
||||
@property
|
||||
def coordinates0_point(self):
|
||||
def coordinates0_point(self) -> np.ndarray:
|
||||
"""Initial/undeformed cell center coordinates."""
|
||||
if self.structured:
|
||||
return grid_filters.coordinates0_point(self.cells,self.size,self.origin).reshape(-1,3,order='F')
|
||||
|
|
@ -553,7 +566,7 @@ class Result:
|
|||
return f['geometry/x_p'][()]
|
||||
|
||||
@property
|
||||
def coordinates0_node(self):
|
||||
def coordinates0_node(self) -> np.ndarray:
|
||||
"""Initial/undeformed nodal coordinates."""
|
||||
if self.structured:
|
||||
return grid_filters.coordinates0_node(self.cells,self.size,self.origin).reshape(-1,3,order='F')
|
||||
|
|
@ -562,7 +575,7 @@ class Result:
|
|||
return f['geometry/x_n'][()]
|
||||
|
||||
@property
|
||||
def geometry0(self):
|
||||
def geometry0(self) -> VTK:
|
||||
"""Initial/undeformed geometry."""
|
||||
if self.structured:
|
||||
return VTK.from_image_data(self.cells,self.size,self.origin)
|
||||
|
|
@ -575,7 +588,7 @@ class Result:
|
|||
|
||||
|
||||
@staticmethod
|
||||
def _add_absolute(x):
|
||||
def _add_absolute(x: Dict[str, Any]) -> Dict[str, Any]:
|
||||
return {
|
||||
'data': np.abs(x['data']),
|
||||
'label': f'|{x["label"]}|',
|
||||
|
|
@ -585,7 +598,7 @@ class Result:
|
|||
'creator': 'add_absolute'
|
||||
}
|
||||
}
|
||||
def add_absolute(self,x):
|
||||
def add_absolute(self, x: str):
|
||||
"""
|
||||
Add absolute value.
|
||||
|
||||
|
|
@ -599,7 +612,7 @@ class Result:
|
|||
|
||||
|
||||
@staticmethod
|
||||
def _add_calculation(**kwargs):
|
||||
def _add_calculation(**kwargs) -> Dict[str, Any]:
|
||||
formula = kwargs['formula']
|
||||
for d in re.findall(r'#(.*?)#',formula):
|
||||
formula = formula.replace(f'#{d}#',f"kwargs['{d}']['data']")
|
||||
|
|
@ -617,7 +630,11 @@ class Result:
|
|||
'creator': 'add_calculation'
|
||||
}
|
||||
}
|
||||
def add_calculation(self,formula,name,unit='n/a',description=None):
|
||||
def add_calculation(self,
|
||||
formula: str,
|
||||
name: str,
|
||||
unit: str = 'n/a',
|
||||
description: str = None):
|
||||
"""
|
||||
Add result of a general formula.
|
||||
|
||||
|
|
@ -667,7 +684,7 @@ class Result:
|
|||
|
||||
|
||||
@staticmethod
|
||||
def _add_stress_Cauchy(P,F):
|
||||
def _add_stress_Cauchy(P: Dict[str, Any], F: Dict[str, Any]) -> Dict[str, Any]:
|
||||
return {
|
||||
'data': mechanics.stress_Cauchy(P['data'],F['data']),
|
||||
'label': 'sigma',
|
||||
|
|
@ -679,7 +696,9 @@ class Result:
|
|||
'creator': 'add_stress_Cauchy'
|
||||
}
|
||||
}
|
||||
def add_stress_Cauchy(self,P='P',F='F'):
|
||||
def add_stress_Cauchy(self,
|
||||
P: str = 'P',
|
||||
F: str = 'F'):
|
||||
"""
|
||||
Add Cauchy stress calculated from first Piola-Kirchhoff stress and deformation gradient.
|
||||
|
||||
|
|
@ -695,7 +714,7 @@ class Result:
|
|||
|
||||
|
||||
@staticmethod
|
||||
def _add_determinant(T):
|
||||
def _add_determinant(T: Dict[str, Any]) -> Dict[str, Any]:
|
||||
return {
|
||||
'data': np.linalg.det(T['data']),
|
||||
'label': f"det({T['label']})",
|
||||
|
|
@ -705,7 +724,7 @@ class Result:
|
|||
'creator': 'add_determinant'
|
||||
}
|
||||
}
|
||||
def add_determinant(self,T):
|
||||
def add_determinant(self, T: str):
|
||||
"""
|
||||
Add the determinant of a tensor.
|
||||
|
||||
|
|
@ -727,7 +746,7 @@ class Result:
|
|||
|
||||
|
||||
@staticmethod
|
||||
def _add_deviator(T):
|
||||
def _add_deviator(T: Dict[str, Any]) -> Dict[str, Any]:
|
||||
return {
|
||||
'data': tensor.deviatoric(T['data']),
|
||||
'label': f"s_{T['label']}",
|
||||
|
|
@ -737,7 +756,7 @@ class Result:
|
|||
'creator': 'add_deviator'
|
||||
}
|
||||
}
|
||||
def add_deviator(self,T):
|
||||
def add_deviator(self, T: str):
|
||||
"""
|
||||
Add the deviatoric part of a tensor.
|
||||
|
||||
|
|
@ -759,13 +778,15 @@ class Result:
|
|||
|
||||
|
||||
@staticmethod
|
||||
def _add_eigenvalue(T_sym,eigenvalue):
|
||||
def _add_eigenvalue(T_sym: Dict[str, Any], eigenvalue: Literal['max, mid, min']) -> Dict[str, Any]:
|
||||
if eigenvalue == 'max':
|
||||
label,p = 'maximum',2
|
||||
elif eigenvalue == 'mid':
|
||||
label,p = 'intermediate',1
|
||||
elif eigenvalue == 'min':
|
||||
label,p = 'minimum',0
|
||||
else:
|
||||
raise ValueError(f'invalid eigenvalue: {eigenvalue}')
|
||||
|
||||
return {
|
||||
'data': tensor.eigenvalues(T_sym['data'])[:,p],
|
||||
|
|
@ -776,7 +797,9 @@ class Result:
|
|||
'creator': 'add_eigenvalue'
|
||||
}
|
||||
}
|
||||
def add_eigenvalue(self,T_sym,eigenvalue='max'):
|
||||
def add_eigenvalue(self,
|
||||
T_sym: str,
|
||||
eigenvalue: Literal['max', 'mid', 'min'] = 'max'):
|
||||
"""
|
||||
Add eigenvalues of symmetric tensor.
|
||||
|
||||
|
|
@ -800,13 +823,16 @@ class Result:
|
|||
|
||||
|
||||
@staticmethod
|
||||
def _add_eigenvector(T_sym,eigenvalue):
|
||||
def _add_eigenvector(T_sym: Dict[str, Any], eigenvalue: Literal['max', 'mid', 'min']) -> Dict[str, Any]:
|
||||
if eigenvalue == 'max':
|
||||
label,p = 'maximum',2
|
||||
elif eigenvalue == 'mid':
|
||||
label,p = 'intermediate',1
|
||||
elif eigenvalue == 'min':
|
||||
label,p = 'minimum',0
|
||||
else:
|
||||
raise ValueError(f'invalid eigenvalue: {eigenvalue}')
|
||||
|
||||
return {
|
||||
'data': tensor.eigenvectors(T_sym['data'])[:,p],
|
||||
'label': f"v_{eigenvalue}({T_sym['label']})",
|
||||
|
|
@ -817,7 +843,9 @@ class Result:
|
|||
'creator': 'add_eigenvector'
|
||||
}
|
||||
}
|
||||
def add_eigenvector(self,T_sym,eigenvalue='max'):
|
||||
def add_eigenvector(self,
|
||||
T_sym: str,
|
||||
eigenvalue: Literal['max', 'mid', 'min'] = 'max'):
|
||||
"""
|
||||
Add eigenvector of symmetric tensor.
|
||||
|
||||
|
|
@ -834,7 +862,7 @@ class Result:
|
|||
|
||||
|
||||
@staticmethod
|
||||
def _add_IPF_color(l,q):
|
||||
def _add_IPF_color(l: FloatSequence, q: Dict[str, Any]) -> Dict[str, Any]:
|
||||
m = util.scale_to_coprime(np.array(l))
|
||||
lattice = q['meta']['lattice']
|
||||
o = Orientation(rotation = q['data'],lattice=lattice)
|
||||
|
|
@ -849,7 +877,9 @@ class Result:
|
|||
'creator': 'add_IPF_color'
|
||||
}
|
||||
}
|
||||
def add_IPF_color(self,l,q='O'):
|
||||
def add_IPF_color(self,
|
||||
l: FloatSequence,
|
||||
q: str = 'O'):
|
||||
"""
|
||||
Add RGB color tuple of inverse pole figure (IPF) color.
|
||||
|
||||
|
|
@ -874,7 +904,7 @@ class Result:
|
|||
|
||||
|
||||
@staticmethod
|
||||
def _add_maximum_shear(T_sym):
|
||||
def _add_maximum_shear(T_sym: Dict[str, Any]) -> Dict[str, Any]:
|
||||
return {
|
||||
'data': mechanics.maximum_shear(T_sym['data']),
|
||||
'label': f"max_shear({T_sym['label']})",
|
||||
|
|
@ -884,7 +914,7 @@ class Result:
|
|||
'creator': 'add_maximum_shear'
|
||||
}
|
||||
}
|
||||
def add_maximum_shear(self,T_sym):
|
||||
def add_maximum_shear(self, T_sym: str):
|
||||
"""
|
||||
Add maximum shear components of symmetric tensor.
|
||||
|
||||
|
|
@ -898,7 +928,7 @@ class Result:
|
|||
|
||||
|
||||
@staticmethod
|
||||
def _add_equivalent_Mises(T_sym,kind):
|
||||
def _add_equivalent_Mises(T_sym: Dict[str, Any], kind: str) -> Dict[str, Any]:
|
||||
k = kind
|
||||
if k is None:
|
||||
if T_sym['meta']['unit'] == '1':
|
||||
|
|
@ -918,7 +948,9 @@ class Result:
|
|||
'creator': 'add_Mises'
|
||||
}
|
||||
}
|
||||
def add_equivalent_Mises(self,T_sym,kind=None):
|
||||
def add_equivalent_Mises(self,
|
||||
T_sym: str,
|
||||
kind: str = None):
|
||||
"""
|
||||
Add the equivalent Mises stress or strain of a symmetric tensor.
|
||||
|
||||
|
|
@ -949,10 +981,10 @@ class Result:
|
|||
|
||||
|
||||
@staticmethod
|
||||
def _add_norm(x,ord):
|
||||
def _add_norm(x: Dict[str, Any], ord: Union[int, float, Literal['fro', 'nuc']]) -> Dict[str, Any]:
|
||||
o = ord
|
||||
if len(x['data'].shape) == 2:
|
||||
axis = 1
|
||||
axis: Union[int, Tuple[int, int]] = 1
|
||||
t = 'vector'
|
||||
if o is None: o = 2
|
||||
elif len(x['data'].shape) == 3:
|
||||
|
|
@ -971,7 +1003,9 @@ class Result:
|
|||
'creator': 'add_norm'
|
||||
}
|
||||
}
|
||||
def add_norm(self,x,ord=None):
|
||||
def add_norm(self,
|
||||
x: str,
|
||||
ord: Union[int, float, Literal['fro', 'nuc']] = None):
|
||||
"""
|
||||
Add the norm of vector or tensor.
|
||||
|
||||
|
|
@ -987,7 +1021,7 @@ class Result:
|
|||
|
||||
|
||||
@staticmethod
|
||||
def _add_stress_second_Piola_Kirchhoff(P,F):
|
||||
def _add_stress_second_Piola_Kirchhoff(P: Dict[str, Any], F: Dict[str, Any]) -> Dict[str, Any]:
|
||||
return {
|
||||
'data': mechanics.stress_second_Piola_Kirchhoff(P['data'],F['data']),
|
||||
'label': 'S',
|
||||
|
|
@ -999,7 +1033,9 @@ class Result:
|
|||
'creator': 'add_stress_second_Piola_Kirchhoff'
|
||||
}
|
||||
}
|
||||
def add_stress_second_Piola_Kirchhoff(self,P='P',F='F'):
|
||||
def add_stress_second_Piola_Kirchhoff(self,
|
||||
P: str = 'P',
|
||||
F: str = 'F'):
|
||||
"""
|
||||
Add second Piola-Kirchhoff stress calculated from first Piola-Kirchhoff stress and deformation gradient.
|
||||
|
||||
|
|
@ -1023,7 +1059,11 @@ class Result:
|
|||
|
||||
|
||||
@staticmethod
|
||||
def _add_pole(q,uvw,hkl,with_symmetry,normalize):
|
||||
def _add_pole(q: Dict[str, Any],
|
||||
uvw: FloatSequence,
|
||||
hkl: FloatSequence,
|
||||
with_symmetry: bool,
|
||||
normalize: bool) -> Dict[str, Any]:
|
||||
c = q['meta']['c/a'] if 'c/a' in q['meta'] else 1
|
||||
brackets = ['[]','()','⟨⟩','{}'][(uvw is None)*1+with_symmetry*2]
|
||||
label = 'p^' + '{}{} {} {}{}'.format(brackets[0],
|
||||
|
|
@ -1042,7 +1082,13 @@ class Result:
|
|||
'creator': 'add_pole'
|
||||
}
|
||||
}
|
||||
def add_pole(self,q='O',*,uvw=None,hkl=None,with_symmetry=False,normalize=True):
|
||||
def add_pole(self,
|
||||
q: str = 'O',
|
||||
*,
|
||||
uvw: FloatSequence = None,
|
||||
hkl: FloatSequence = None,
|
||||
with_symmetry: bool = False,
|
||||
normalize: bool = True):
|
||||
"""
|
||||
Add lab frame vector along lattice direction [uvw] or plane normal (hkl).
|
||||
|
||||
|
|
@ -1067,7 +1113,7 @@ class Result:
|
|||
|
||||
|
||||
@staticmethod
|
||||
def _add_rotation(F):
|
||||
def _add_rotation(F: Dict[str, Any]) -> Dict[str, Any]:
|
||||
return {
|
||||
'data': mechanics.rotation(F['data']).as_matrix(),
|
||||
'label': f"R({F['label']})",
|
||||
|
|
@ -1077,7 +1123,7 @@ class Result:
|
|||
'creator': 'add_rotation'
|
||||
}
|
||||
}
|
||||
def add_rotation(self,F):
|
||||
def add_rotation(self, F: str):
|
||||
"""
|
||||
Add rotational part of a deformation gradient.
|
||||
|
||||
|
|
@ -1099,7 +1145,7 @@ class Result:
|
|||
|
||||
|
||||
@staticmethod
|
||||
def _add_spherical(T):
|
||||
def _add_spherical(T: Dict[str, Any]) -> Dict[str, Any]:
|
||||
return {
|
||||
'data': tensor.spherical(T['data'],False),
|
||||
'label': f"p_{T['label']}",
|
||||
|
|
@ -1109,7 +1155,7 @@ class Result:
|
|||
'creator': 'add_spherical'
|
||||
}
|
||||
}
|
||||
def add_spherical(self,T):
|
||||
def add_spherical(self, T: str):
|
||||
"""
|
||||
Add the spherical (hydrostatic) part of a tensor.
|
||||
|
||||
|
|
@ -1131,7 +1177,7 @@ class Result:
|
|||
|
||||
|
||||
@staticmethod
|
||||
def _add_strain(F,t,m):
|
||||
def _add_strain(F: Dict[str, Any], t: Literal['V', 'U'], m: float) -> Dict[str, Any]:
|
||||
return {
|
||||
'data': mechanics.strain(F['data'],t,m),
|
||||
'label': f"epsilon_{t}^{m}({F['label']})",
|
||||
|
|
@ -1141,7 +1187,10 @@ class Result:
|
|||
'creator': 'add_strain'
|
||||
}
|
||||
}
|
||||
def add_strain(self,F='F',t='V',m=0.0):
|
||||
def add_strain(self,
|
||||
F: str = 'F',
|
||||
t: Literal['V', 'U'] = 'V',
|
||||
m: float = 0.0):
|
||||
"""
|
||||
Add strain tensor of a deformation gradient.
|
||||
|
||||
|
|
@ -1177,7 +1226,7 @@ class Result:
|
|||
|
||||
|
||||
@staticmethod
|
||||
def _add_stretch_tensor(F,t):
|
||||
def _add_stretch_tensor(F: Dict[str, Any], t: str) -> Dict[str, Any]:
|
||||
return {
|
||||
'data': (mechanics.stretch_left if t.upper() == 'V' else mechanics.stretch_right)(F['data']),
|
||||
'label': f"{t}({F['label']})",
|
||||
|
|
@ -1188,7 +1237,9 @@ class Result:
|
|||
'creator': 'add_stretch_tensor'
|
||||
}
|
||||
}
|
||||
def add_stretch_tensor(self,F='F',t='V'):
|
||||
def add_stretch_tensor(self,
|
||||
F: str = 'F',
|
||||
t: Literal['V', 'U'] = 'V'):
|
||||
"""
|
||||
Add stretch tensor of a deformation gradient.
|
||||
|
||||
|
|
@ -1205,7 +1256,7 @@ class Result:
|
|||
|
||||
|
||||
@staticmethod
|
||||
def _add_curl(f,size):
|
||||
def _add_curl(f: Dict[str, Any], size: np.ndarray) -> Dict[str, Any]:
|
||||
return {
|
||||
'data': grid_filters.curl(size,f['data']),
|
||||
'label': f"curl({f['label']})",
|
||||
|
|
@ -1215,7 +1266,7 @@ class Result:
|
|||
'creator': 'add_curl'
|
||||
}
|
||||
}
|
||||
def add_curl(self,f):
|
||||
def add_curl(self, f: str):
|
||||
"""
|
||||
Add curl of a field.
|
||||
|
||||
|
|
@ -1234,7 +1285,7 @@ class Result:
|
|||
|
||||
|
||||
@staticmethod
|
||||
def _add_divergence(f,size):
|
||||
def _add_divergence(f: Dict[str, Any], size: np.ndarray) -> Dict[str, Any]:
|
||||
return {
|
||||
'data': grid_filters.divergence(size,f['data']),
|
||||
'label': f"divergence({f['label']})",
|
||||
|
|
@ -1244,7 +1295,7 @@ class Result:
|
|||
'creator': 'add_divergence'
|
||||
}
|
||||
}
|
||||
def add_divergence(self,f):
|
||||
def add_divergence(self, f: str):
|
||||
"""
|
||||
Add divergence of a field.
|
||||
|
||||
|
|
@ -1263,7 +1314,7 @@ class Result:
|
|||
|
||||
|
||||
@staticmethod
|
||||
def _add_gradient(f,size):
|
||||
def _add_gradient(f: Dict[str, Any], size: np.ndarray) -> Dict[str, Any]:
|
||||
return {
|
||||
'data': grid_filters.gradient(size,f['data'] if len(f['data'].shape) == 4 else \
|
||||
f['data'].reshape(f['data'].shape+(1,))),
|
||||
|
|
@ -1274,7 +1325,7 @@ class Result:
|
|||
'creator': 'add_gradient'
|
||||
}
|
||||
}
|
||||
def add_gradient(self,f):
|
||||
def add_gradient(self, f: str):
|
||||
"""
|
||||
Add gradient of a field.
|
||||
|
||||
|
|
@ -1292,7 +1343,11 @@ class Result:
|
|||
self._add_generic_grid(self._add_gradient,{'f':f},{'size':self.size})
|
||||
|
||||
|
||||
def _add_generic_grid(self,func,datasets,args={},constituents=None):
|
||||
def _add_generic_grid(self,
|
||||
func: Callable,
|
||||
datasets: Dict[str, str],
|
||||
args: Dict[str, str] = {},
|
||||
constituents = None):
|
||||
"""
|
||||
General function to add data on a regular grid.
|
||||
|
||||
|
|
@ -1313,11 +1368,13 @@ class Result:
|
|||
|
||||
at_cell_ph,in_data_ph,at_cell_ho,in_data_ho = self._mappings()
|
||||
|
||||
increments = self.place(list(datasets.values()),False)
|
||||
if not increments: raise RuntimeError("received invalid dataset")
|
||||
with h5py.File(self.fname, 'a') as f:
|
||||
for increment in self.place(datasets.values(),False).items():
|
||||
for increment in increments.items():
|
||||
for ty in increment[1].items():
|
||||
for field in ty[1].items():
|
||||
d = list(field[1].values())[0]
|
||||
d: np.ma.MaskedArray = list(field[1].values())[0]
|
||||
if np.any(d.mask): continue
|
||||
dataset = {'f':{'data':np.reshape(d.data,tuple(self.cells)+d.data.shape[1:]),
|
||||
'label':list(datasets.values())[0],
|
||||
|
|
@ -1331,21 +1388,26 @@ class Result:
|
|||
result1 = result[at_cell_ho[x]]
|
||||
|
||||
path = '/'.join(['/',increment[0],ty[0],x,field[0]])
|
||||
dataset = f[path].create_dataset(r['label'],data=result1)
|
||||
h5_dataset = f[path].create_dataset(r['label'],data=result1)
|
||||
|
||||
now = datetime.datetime.now().astimezone()
|
||||
dataset.attrs['created'] = now.strftime('%Y-%m-%d %H:%M:%S%z') if h5py3 else \
|
||||
h5_dataset.attrs['created'] = now.strftime('%Y-%m-%d %H:%M:%S%z') if h5py3 else \
|
||||
now.strftime('%Y-%m-%d %H:%M:%S%z').encode()
|
||||
|
||||
for l,v in r['meta'].items():
|
||||
dataset.attrs[l.lower()]=v if h5py3 else v.encode()
|
||||
creator = dataset.attrs['creator'] if h5py3 else \
|
||||
dataset.attrs['creator'].decode()
|
||||
dataset.attrs['creator'] = f'damask.Result.{creator} v{damask.version}' if h5py3 else \
|
||||
h5_dataset.attrs[l.lower()]=v if h5py3 else v.encode()
|
||||
creator = h5_dataset.attrs['creator'] if h5py3 else \
|
||||
h5_dataset.attrs['creator'].decode()
|
||||
h5_dataset.attrs['creator'] = f'damask.Result.{creator} v{damask.version}' if h5py3 else \
|
||||
f'damask.Result.{creator} v{damask.version}'.encode()
|
||||
|
||||
|
||||
def _job_pointwise(self,group,func,datasets,args,lock):
|
||||
def _job_pointwise(self,
|
||||
group: str,
|
||||
callback: Callable,
|
||||
datasets: Dict[str, str],
|
||||
args: Dict[str, str],
|
||||
lock: Lock) -> List[Union[None, Any]]:
|
||||
"""Execute job for _add_generic_pointwise."""
|
||||
try:
|
||||
datasets_in = {}
|
||||
|
|
@ -1358,19 +1420,23 @@ class Result:
|
|||
'meta': {k:(v.decode() if not h5py3 and type(v) is bytes else v) \
|
||||
for k,v in loc.attrs.items()}}
|
||||
lock.release()
|
||||
r = func(**datasets_in,**args)
|
||||
r = callback(**datasets_in,**args)
|
||||
return [group,r]
|
||||
except Exception as err:
|
||||
print(f'Error during calculation: {err}.')
|
||||
return [None,None]
|
||||
|
||||
def _add_generic_pointwise(self,func,datasets,args={}):
|
||||
|
||||
def _add_generic_pointwise(self,
|
||||
func: Callable,
|
||||
datasets: Dict[str, Any],
|
||||
args: Dict[str, Any] = {}):
|
||||
"""
|
||||
General function to add pointwise data.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
func : function
|
||||
callback : function
|
||||
Callback function that calculates a new dataset from one or
|
||||
more datasets per HDF5 group.
|
||||
datasets : dictionary
|
||||
|
|
@ -1396,9 +1462,9 @@ class Result:
|
|||
print('No matching dataset found, no data was added.')
|
||||
return
|
||||
|
||||
default_arg = partial(self._job_pointwise,func=func,datasets=datasets,args=args,lock=lock)
|
||||
default_arg = partial(self._job_pointwise,callback=func,datasets=datasets,args=args,lock=lock)
|
||||
|
||||
for group,result in util.show_progress(pool.imap_unordered(default_arg,groups),len(groups)):
|
||||
for group,result in util.show_progress(pool.imap_unordered(default_arg,groups),len(groups)):# type: ignore
|
||||
if not result:
|
||||
continue
|
||||
lock.acquire()
|
||||
|
|
@ -1410,15 +1476,14 @@ class Result:
|
|||
dataset.attrs['overwritten'] = True
|
||||
else:
|
||||
shape = result['data'].shape
|
||||
if result['data'].size >= chunk_size*2:
|
||||
if compress := (result['data'].size >= chunk_size*2):
|
||||
chunks = (chunk_size//np.prod(shape[1:]),)+shape[1:]
|
||||
compression = ('gzip',6)
|
||||
else:
|
||||
chunks = shape
|
||||
compression = (None,None)
|
||||
dataset = f[group].create_dataset(result['label'],data=result['data'],
|
||||
maxshape=shape, chunks=chunks,
|
||||
compression=compression[0], compression_opts=compression[1],
|
||||
compression = 'gzip' if compress else None,
|
||||
compression_opts = 6 if compress else None,
|
||||
shuffle=True,fletcher32=True)
|
||||
|
||||
now = datetime.datetime.now().astimezone()
|
||||
|
|
@ -1440,7 +1505,8 @@ class Result:
|
|||
pool.join()
|
||||
|
||||
|
||||
def export_XDMF(self,output='*'):
|
||||
def export_XDMF(self,
|
||||
output: Union[str, List[str]] = '*'):
|
||||
"""
|
||||
Write XDMF file to directly visualize data from DADF5 file.
|
||||
|
||||
|
|
@ -1574,7 +1640,13 @@ class Result:
|
|||
return at_cell_ph,in_data_ph,at_cell_ho,in_data_ho
|
||||
|
||||
|
||||
def export_VTK(self,output='*',mode='cell',constituents=None,fill_float=np.nan,fill_int=0,parallel=True):
|
||||
def export_VTK(self,
|
||||
output: Union[str,list] = '*',
|
||||
mode: str = 'cell',
|
||||
constituents: IntSequence = None,
|
||||
fill_float: float = np.nan,
|
||||
fill_int: int = 0,
|
||||
parallel: bool = True):
|
||||
"""
|
||||
Export to VTK cell/point data.
|
||||
|
||||
|
|
@ -1612,12 +1684,12 @@ class Result:
|
|||
else:
|
||||
raise ValueError(f'invalid mode "{mode}"')
|
||||
|
||||
v.comments = util.execution_stamp('Result','export_VTK')
|
||||
v.comments = [util.execution_stamp('Result','export_VTK')]
|
||||
|
||||
N_digits = int(np.floor(np.log10(max(1,self.incs[-1]))))+1
|
||||
|
||||
constituents_ = constituents if isinstance(constituents,Iterable) else \
|
||||
(range(self.N_constituents) if constituents is None else [constituents])
|
||||
(range(self.N_constituents) if constituents is None else [constituents]) # type: ignore
|
||||
|
||||
suffixes = [''] if self.N_constituents == 1 or isinstance(constituents,int) else \
|
||||
[f'#{c}' for c in constituents_]
|
||||
|
|
@ -1637,7 +1709,7 @@ class Result:
|
|||
|
||||
for ty in ['phase','homogenization']:
|
||||
for field in self.visible['fields']:
|
||||
outs = {}
|
||||
outs: Dict[str, np.ma.core.MaskedArray] = {}
|
||||
for label in self.visible[ty+'s']:
|
||||
if field not in f['/'.join([inc,ty,label])].keys(): continue
|
||||
|
||||
|
|
@ -1665,7 +1737,10 @@ class Result:
|
|||
v.save(f'{self.fname.stem}_inc{inc[10:].zfill(N_digits)}',parallel=parallel)
|
||||
|
||||
|
||||
def get(self,output='*',flatten=True,prune=True):
|
||||
def get(self,
|
||||
output: Union[str, List[str]] = '*',
|
||||
flatten: bool = True,
|
||||
prune: bool = True):
|
||||
"""
|
||||
Collect data per phase/homogenization reflecting the group/folder structure in the DADF5 file.
|
||||
|
||||
|
|
@ -1687,7 +1762,7 @@ class Result:
|
|||
Datasets structured by phase/homogenization and according to selected view.
|
||||
|
||||
"""
|
||||
r = {}
|
||||
r = {} # type: ignore
|
||||
|
||||
with h5py.File(self.fname,'r') as f:
|
||||
for inc in util.show_progress(self.visible['increments']):
|
||||
|
|
@ -1710,7 +1785,13 @@ class Result:
|
|||
return None if (type(r) == dict and r == {}) else r
|
||||
|
||||
|
||||
def place(self,output='*',flatten=True,prune=True,constituents=None,fill_float=np.nan,fill_int=0):
|
||||
def place(self,
|
||||
output: Union[str, List[str]] = '*',
|
||||
flatten: bool = True,
|
||||
prune: bool = True,
|
||||
constituents: IntSequence = None,
|
||||
fill_float: float = np.nan,
|
||||
fill_int: int = 0):
|
||||
"""
|
||||
Merge data into spatial order that is compatible with the damask.VTK geometry representation.
|
||||
|
||||
|
|
@ -1748,10 +1829,10 @@ class Result:
|
|||
Datasets structured by spatial position and according to selected view.
|
||||
|
||||
"""
|
||||
r = {}
|
||||
r = {} # type: ignore
|
||||
|
||||
constituents_ = constituents if isinstance(constituents,Iterable) else \
|
||||
(range(self.N_constituents) if constituents is None else [constituents])
|
||||
constituents_ = list(map(int,constituents)) if isinstance(constituents,Iterable) else \
|
||||
(range(self.N_constituents) if constituents is None else [constituents]) # type: ignore
|
||||
|
||||
suffixes = [''] if self.N_constituents == 1 or isinstance(constituents,int) else \
|
||||
[f'#{c}' for c in constituents_]
|
||||
|
|
@ -1797,7 +1878,9 @@ class Result:
|
|||
return None if (type(r) == dict and r == {}) else r
|
||||
|
||||
|
||||
def export_setup(self,output='*',overwrite=False):
|
||||
def export_setup(self,
|
||||
output: Union[str, List[str]] = '*',
|
||||
overwrite: bool = False):
|
||||
"""
|
||||
Export configuration files.
|
||||
|
||||
|
|
@ -1811,7 +1894,7 @@ class Result:
|
|||
Defaults to False.
|
||||
|
||||
"""
|
||||
def export(name,obj,output,overwrite):
|
||||
def export(name: str, obj: Union[h5py.Dataset,h5py.Group], output: Union[str,List[str]], overwrite: bool):
|
||||
if type(obj) == h5py.Dataset and _match(output,[name]):
|
||||
d = obj.attrs['description'] if h5py3 else obj.attrs['description'].decode()
|
||||
if not Path(name).exists() or overwrite:
|
||||
|
|
|
|||
|
|
@ -1,6 +1,6 @@
|
|||
import re
|
||||
import copy
|
||||
from typing import Union, Tuple, List
|
||||
from typing import Union, Tuple, List, Iterable
|
||||
|
||||
import pandas as pd
|
||||
import numpy as np
|
||||
|
|
@ -12,9 +12,9 @@ class Table:
|
|||
"""Manipulate multi-dimensional spreadsheet-like data."""
|
||||
|
||||
def __init__(self,
|
||||
shapes: dict = {},
|
||||
data: np.ndarray = None,
|
||||
comments: Union[str, list] = None):
|
||||
shapes: dict,
|
||||
data: np.ndarray,
|
||||
comments: Union[str, Iterable[str]] = None):
|
||||
"""
|
||||
New spreadsheet.
|
||||
|
||||
|
|
@ -30,7 +30,7 @@ class Table:
|
|||
|
||||
"""
|
||||
comments_ = [comments] if isinstance(comments,str) else comments
|
||||
self.comments = [] if comments_ is None else [c for c in comments_]
|
||||
self.comments = [] if comments_ is None else [str(c) for c in comments_]
|
||||
self.shapes = { k:(v,) if isinstance(v,(np.int64,np.int32,int)) else v for k,v in shapes.items() }
|
||||
self.data = pd.DataFrame(data=data)
|
||||
self._relabel('uniform')
|
||||
|
|
@ -434,8 +434,8 @@ class Table:
|
|||
|
||||
|
||||
def rename(self,
|
||||
old: Union[str, List[str]],
|
||||
new: Union[str, List[str]],
|
||||
old: Union[str, Iterable[str]],
|
||||
new: Union[str, Iterable[str]],
|
||||
info: str = None) -> 'Table':
|
||||
"""
|
||||
Rename column data.
|
||||
|
|
|
|||
|
|
@ -103,7 +103,7 @@ class VTK:
|
|||
|
||||
Parameters
|
||||
----------
|
||||
comments : str or list of str
|
||||
comments : str or sequence of str
|
||||
Comments.
|
||||
|
||||
"""
|
||||
|
|
@ -153,11 +153,11 @@ class VTK:
|
|||
|
||||
Parameters
|
||||
----------
|
||||
cells : iterable of int, len (3)
|
||||
cells : sequence of int, len (3)
|
||||
Number of cells along each dimension.
|
||||
size : iterable of float, len (3)
|
||||
size : sequence of float, len (3)
|
||||
Physical length along each dimension.
|
||||
origin : iterable of float, len (3), optional
|
||||
origin : sequence of float, len (3), optional
|
||||
Coordinates of grid origin.
|
||||
|
||||
Returns
|
||||
|
|
@ -257,7 +257,7 @@ class VTK:
|
|||
|
||||
Parameters
|
||||
----------
|
||||
grid : iterables of floats, len (3)
|
||||
grid : sequence of sequences of floats, len (3)
|
||||
Grid coordinates along x, y, and z directions.
|
||||
|
||||
Returns
|
||||
|
|
|
|||
|
|
@ -113,15 +113,15 @@ class TestConfigMaterial:
|
|||
@pytest.mark.parametrize('N,n,kw',[
|
||||
(1,1,{'phase':'Gold',
|
||||
'O':[1,0,0,0],
|
||||
'F_i':np.eye(3),
|
||||
'V_e':np.eye(3),
|
||||
'homogenization':'SX'}),
|
||||
(3,1,{'phase':'Gold',
|
||||
'O':Rotation.from_random(3),
|
||||
'F_i':np.broadcast_to(np.eye(3),(3,3,3)),
|
||||
'V_e':np.broadcast_to(np.eye(3),(3,3,3)),
|
||||
'homogenization':'SX'}),
|
||||
(2,3,{'phase':np.broadcast_to(['a','b','c'],(2,3)),
|
||||
'O':Rotation.from_random((2,3)),
|
||||
'F_i':np.broadcast_to(np.eye(3),(2,3,3,3)),
|
||||
'V_e':np.broadcast_to(np.eye(3),(2,3,3,3)),
|
||||
'homogenization':['SX','PX']}),
|
||||
])
|
||||
def test_material_add(self,kw,N,n):
|
||||
|
|
|
|||
|
|
@ -48,7 +48,7 @@ module HDF5_utilities
|
|||
!> @details for parallel IO, all dimension except for the last need to match
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
interface HDF5_write
|
||||
#if defined(__GFORTRAN__) && __GNUC__<11
|
||||
#if defined(__GFORTRAN__)
|
||||
module procedure HDF5_write_real1
|
||||
module procedure HDF5_write_real2
|
||||
module procedure HDF5_write_real3
|
||||
|
|
@ -1214,7 +1214,7 @@ subroutine HDF5_read_int7(dataset,loc_id,datasetName,parallel)
|
|||
|
||||
end subroutine HDF5_read_int7
|
||||
|
||||
#if defined(__GFORTRAN__) && __GNUC__<11
|
||||
#if defined(__GFORTRAN__)
|
||||
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
!> @brief write dataset of type real with 1 dimension
|
||||
|
|
@ -1631,7 +1631,7 @@ subroutine HDF5_write_str(dataset,loc_id,datasetName)
|
|||
|
||||
end subroutine HDF5_write_str
|
||||
|
||||
#if defined(__GFORTRAN__) && __GNUC__<11
|
||||
#if defined(__GFORTRAN__)
|
||||
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
!> @brief write dataset of type integer with 1 dimension
|
||||
|
|
|
|||
|
|
@ -428,6 +428,8 @@ subroutine IO_error(error_ID,el,ip,g,instance,ext_msg)
|
|||
msg = 'too many systems requested'
|
||||
case (146)
|
||||
msg = 'number of values does not match'
|
||||
case (147)
|
||||
msg = 'V_e needs to be symmetric'
|
||||
case (148)
|
||||
msg = 'Nconstituents mismatch between homogenization and material'
|
||||
|
||||
|
|
|
|||
|
|
@ -27,7 +27,7 @@ module material
|
|||
|
||||
|
||||
type(tRotationContainer), dimension(:), allocatable, public, protected :: material_O_0
|
||||
type(tTensorContainer), dimension(:), allocatable, public, protected :: material_F_i_0
|
||||
type(tTensorContainer), dimension(:), allocatable, public, protected :: material_V_e_0
|
||||
|
||||
integer, dimension(:), allocatable, public, protected :: &
|
||||
homogenization_Nconstituents !< number of grains in each homogenization
|
||||
|
|
@ -133,7 +133,7 @@ subroutine parse()
|
|||
allocate(material_v(homogenization_maxNconstituents,discretization_Ncells),source=0.0_pReal)
|
||||
|
||||
allocate(material_O_0(materials%length))
|
||||
allocate(material_F_i_0(materials%length))
|
||||
allocate(material_V_e_0(materials%length))
|
||||
|
||||
allocate(ho_of(materials%length))
|
||||
allocate(ph_of(materials%length,homogenization_maxNconstituents),source=-1)
|
||||
|
|
@ -154,7 +154,7 @@ subroutine parse()
|
|||
if (constituents%length /= homogenization%get_asInt('N_constituents')) call IO_error(148)
|
||||
|
||||
allocate(material_O_0(ma)%data(constituents%length))
|
||||
allocate(material_F_i_0(ma)%data(1:3,1:3,constituents%length))
|
||||
allocate(material_V_e_0(ma)%data(1:3,1:3,constituents%length))
|
||||
|
||||
do co = 1, constituents%length
|
||||
constituent => constituents%get(co)
|
||||
|
|
@ -162,7 +162,9 @@ subroutine parse()
|
|||
ph_of(ma,co) = phases%getIndex(constituent%get_asString('phase'))
|
||||
|
||||
call material_O_0(ma)%data(co)%fromQuaternion(constituent%get_as1dFloat('O',requiredSize=4))
|
||||
material_F_i_0(ma)%data(1:3,1:3,co) = constituent%get_as2dFloat('F_i',defaultVal=math_I3,requiredShape=[3,3])
|
||||
material_V_e_0(ma)%data(1:3,1:3,co) = constituent%get_as2dFloat('V_e',defaultVal=math_I3,requiredShape=[3,3])
|
||||
if (any(dNeq(material_V_e_0(ma)%data(1:3,1:3,co),transpose(material_V_e_0(ma)%data(1:3,1:3,co))))) &
|
||||
call IO_error(147)
|
||||
|
||||
end do
|
||||
if (dNeq(sum(v_of(ma,:)),1.0_pReal,1.e-9_pReal)) call IO_error(153,ext_msg='constituent')
|
||||
|
|
|
|||
|
|
@ -210,7 +210,6 @@ module subroutine mechanical_init(phases)
|
|||
Nmembers
|
||||
class(tNode), pointer :: &
|
||||
num_crystallite, &
|
||||
|
||||
phase, &
|
||||
mech
|
||||
|
||||
|
|
@ -239,11 +238,8 @@ module subroutine mechanical_init(phases)
|
|||
|
||||
allocate(phase_mechanical_Fe(ph)%data(3,3,Nmembers))
|
||||
allocate(phase_mechanical_Fi(ph)%data(3,3,Nmembers))
|
||||
allocate(phase_mechanical_Fi0(ph)%data(3,3,Nmembers))
|
||||
allocate(phase_mechanical_Fp(ph)%data(3,3,Nmembers))
|
||||
allocate(phase_mechanical_Fp0(ph)%data(3,3,Nmembers))
|
||||
allocate(phase_mechanical_F(ph)%data(3,3,Nmembers))
|
||||
allocate(phase_mechanical_F0(ph)%data(3,3,Nmembers))
|
||||
allocate(phase_mechanical_Li(ph)%data(3,3,Nmembers),source=0.0_pReal)
|
||||
allocate(phase_mechanical_Li0(ph)%data(3,3,Nmembers),source=0.0_pReal)
|
||||
allocate(phase_mechanical_Lp(ph)%data(3,3,Nmembers),source=0.0_pReal)
|
||||
|
|
@ -265,23 +261,19 @@ module subroutine mechanical_init(phases)
|
|||
ma = discretization_materialAt((ce-1)/discretization_nIPs+1)
|
||||
do co = 1,homogenization_Nconstituents(material_homogenizationID(ce))
|
||||
ph = material_phaseID(co,ce)
|
||||
phase_mechanical_Fi0(ph)%data(1:3,1:3,material_phaseEntry(co,ce)) = material_F_i_0(ma)%data(1:3,1:3,co)
|
||||
en = material_phaseEntry(co,ce)
|
||||
phase_mechanical_F(ph)%data(1:3,1:3,en) = math_I3
|
||||
phase_mechanical_Fp(ph)%data(1:3,1:3,en) = material_O_0(ma)%data(co)%asMatrix() ! Fp reflects initial orientation (see 10.1016/j.actamat.2006.01.005)
|
||||
phase_mechanical_Fe(ph)%data(1:3,1:3,en) = matmul(material_V_e_0(ma)%data(1:3,1:3,co), &
|
||||
transpose(phase_mechanical_Fp(ph)%data(1:3,1:3,en)))
|
||||
phase_mechanical_Fi(ph)%data(1:3,1:3,en) = material_O_0(ma)%data(co)%rotate(math_inv33(material_V_e_0(ma)%data(1:3,1:3,co)))
|
||||
enddo
|
||||
enddo
|
||||
|
||||
do ph = 1, phases%length
|
||||
do en = 1, count(material_phaseID == ph)
|
||||
|
||||
phase_mechanical_Fp0(ph)%data(1:3,1:3,en) = phase_O_0(ph)%data(en)%asMatrix() ! Fp reflects initial orientation (see 10.1016/j.actamat.2006.01.005)
|
||||
phase_mechanical_Fp0(ph)%data(1:3,1:3,en) = phase_mechanical_Fp0(ph)%data(1:3,1:3,en) &
|
||||
/ math_det33(phase_mechanical_Fp0(ph)%data(1:3,1:3,en))**(1.0_pReal/3.0_pReal)
|
||||
phase_mechanical_F0(ph)%data(1:3,1:3,en) = math_I3
|
||||
phase_mechanical_Fe(ph)%data(1:3,1:3,en) = math_inv33(matmul(phase_mechanical_Fi0(ph)%data(1:3,1:3,en), &
|
||||
phase_mechanical_Fp0(ph)%data(1:3,1:3,en))) ! assuming that euler angles are given in internal strain free configuration
|
||||
enddo
|
||||
phase_mechanical_Fp(ph)%data = phase_mechanical_Fp0(ph)%data
|
||||
phase_mechanical_Fi(ph)%data = phase_mechanical_Fi0(ph)%data
|
||||
phase_mechanical_F(ph)%data = phase_mechanical_F0(ph)%data
|
||||
phase_mechanical_F0(ph)%data = phase_mechanical_F(ph)%data
|
||||
phase_mechanical_Fp0(ph)%data = phase_mechanical_Fp(ph)%data
|
||||
phase_mechanical_Fi0(ph)%data = phase_mechanical_Fi(ph)%data
|
||||
enddo
|
||||
|
||||
|
||||
|
|
@ -318,7 +310,6 @@ module subroutine mechanical_init(phases)
|
|||
|
||||
end select
|
||||
|
||||
|
||||
call eigen_init(phases)
|
||||
|
||||
|
||||
|
|
@ -1244,6 +1235,9 @@ module function phase_mechanical_dPdF(Delta_t,co,ce) result(dPdF)
|
|||
end function phase_mechanical_dPdF
|
||||
|
||||
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
!< @brief Write restart information to file.
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
module subroutine mechanical_restartWrite(groupHandle,ph)
|
||||
|
||||
integer(HID_T), intent(in) :: groupHandle
|
||||
|
|
@ -1251,36 +1245,41 @@ module subroutine mechanical_restartWrite(groupHandle,ph)
|
|||
|
||||
|
||||
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')
|
||||
call HDF5_write(phase_mechanical_Fp(ph)%data,groupHandle,'F_p')
|
||||
call HDF5_write(phase_mechanical_S(ph)%data,groupHandle,'S')
|
||||
call HDF5_write(phase_mechanical_F(ph)%data,groupHandle,'F')
|
||||
call HDF5_write(phase_mechanical_Fp(ph)%data,groupHandle,'F_p')
|
||||
call HDF5_write(phase_mechanical_Fi(ph)%data,groupHandle,'F_i')
|
||||
call HDF5_write(phase_mechanical_Lp(ph)%data,groupHandle,'L_p')
|
||||
call HDF5_write(phase_mechanical_Li(ph)%data,groupHandle,'L_i')
|
||||
|
||||
end subroutine mechanical_restartWrite
|
||||
|
||||
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
!< @brief Read restart information from file.
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
module subroutine mechanical_restartRead(groupHandle,ph)
|
||||
|
||||
integer(HID_T), intent(in) :: groupHandle
|
||||
integer, intent(in) :: ph
|
||||
|
||||
integer :: en
|
||||
|
||||
|
||||
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')
|
||||
call HDF5_read(phase_mechanical_Fp0(ph)%data,groupHandle,'F_p')
|
||||
call HDF5_read(phase_mechanical_S0(ph)%data,groupHandle,'S')
|
||||
call HDF5_read(phase_mechanical_F0(ph)%data,groupHandle,'F')
|
||||
call HDF5_read(phase_mechanical_Fp0(ph)%data,groupHandle,'F_p')
|
||||
call HDF5_read(phase_mechanical_Fi0(ph)%data,groupHandle,'F_i')
|
||||
call HDF5_read(phase_mechanical_Lp0(ph)%data,groupHandle,'L_p')
|
||||
call HDF5_read(phase_mechanical_Li0(ph)%data,groupHandle,'L_i')
|
||||
|
||||
end subroutine mechanical_restartRead
|
||||
|
||||
|
||||
!----------------------------------------------------------------------------------------------
|
||||
!< @brief Get first Piola-Kichhoff stress (for use by non-mech physics)
|
||||
!----------------------------------------------------------------------------------------------
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
!< @brief Get first Piola-Kichhoff stress (for use by non-mech physics).
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
module function mechanical_S(ph,en) result(S)
|
||||
|
||||
integer, intent(in) :: ph,en
|
||||
|
|
@ -1292,9 +1291,9 @@ module function mechanical_S(ph,en) result(S)
|
|||
end function mechanical_S
|
||||
|
||||
|
||||
!----------------------------------------------------------------------------------------------
|
||||
!< @brief Get plastic velocity gradient (for use by non-mech physics)
|
||||
!----------------------------------------------------------------------------------------------
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
!< @brief Get plastic velocity gradient (for use by non-mech physics).
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
module function mechanical_L_p(ph,en) result(L_p)
|
||||
|
||||
integer, intent(in) :: ph,en
|
||||
|
|
@ -1306,9 +1305,9 @@ module function mechanical_L_p(ph,en) result(L_p)
|
|||
end function mechanical_L_p
|
||||
|
||||
|
||||
!----------------------------------------------------------------------------------------------
|
||||
!< @brief Get elastic deformation gradient (for use by non-mech physics)
|
||||
!----------------------------------------------------------------------------------------------
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
!< @brief Get elastic deformation gradient (for use by non-mech physics).
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
module function mechanical_F_e(ph,en) result(F_e)
|
||||
|
||||
integer, intent(in) :: ph,en
|
||||
|
|
@ -1320,9 +1319,9 @@ module function mechanical_F_e(ph,en) result(F_e)
|
|||
end function mechanical_F_e
|
||||
|
||||
|
||||
!----------------------------------------------------------------------------------------------
|
||||
!< @brief Get second Piola-Kichhoff stress (for use by homogenization)
|
||||
!----------------------------------------------------------------------------------------------
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
!< @brief Get second Piola-Kichhoff stress (for use by homogenization).
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
module function phase_P(co,ce) result(P)
|
||||
|
||||
integer, intent(in) :: co, ce
|
||||
|
|
@ -1334,9 +1333,9 @@ module function phase_P(co,ce) result(P)
|
|||
end function phase_P
|
||||
|
||||
|
||||
!----------------------------------------------------------------------------------------------
|
||||
!< @brief Get deformation gradient (for use by homogenization)
|
||||
!----------------------------------------------------------------------------------------------
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
!< @brief Get deformation gradient (for use by homogenization).
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
module function phase_F(co,ce) result(F)
|
||||
|
||||
integer, intent(in) :: co, ce
|
||||
|
|
@ -1348,9 +1347,9 @@ module function phase_F(co,ce) result(F)
|
|||
end function phase_F
|
||||
|
||||
|
||||
!----------------------------------------------------------------------------------------------
|
||||
!< @brief Set deformation gradient (for use by homogenization)
|
||||
!----------------------------------------------------------------------------------------------
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
!< @brief Set deformation gradient (for use by homogenization).
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
module subroutine phase_set_F(F,co,ce)
|
||||
|
||||
real(pReal), dimension(3,3), intent(in) :: F
|
||||
|
|
|
|||
|
|
@ -323,17 +323,16 @@ pure function rotTensor2(self,T,active) result(tRot)
|
|||
|
||||
logical :: passive
|
||||
|
||||
|
||||
if (present(active)) then
|
||||
passive = .not. active
|
||||
else
|
||||
passive = .true.
|
||||
endif
|
||||
|
||||
if (passive) then
|
||||
tRot = matmul(matmul(self%asMatrix(),T),transpose(self%asMatrix()))
|
||||
else
|
||||
tRot = matmul(matmul(transpose(self%asMatrix()),T),self%asMatrix())
|
||||
endif
|
||||
tRot = merge(matmul(matmul(self%asMatrix(),T),transpose(self%asMatrix())), &
|
||||
matmul(matmul(transpose(self%asMatrix()),T),self%asMatrix()), &
|
||||
passive)
|
||||
|
||||
end function rotTensor2
|
||||
|
||||
|
|
@ -450,6 +449,7 @@ pure function qu2om(qu) result(om)
|
|||
om(1,3) = 2.0_pReal*(qu(2)*qu(4)+qu(1)*qu(3))
|
||||
|
||||
if (sign(1.0_pReal,P) < 0.0_pReal) om = transpose(om)
|
||||
om = om/math_det33(om)**(1.0_pReal/3.0_pReal)
|
||||
|
||||
end function qu2om
|
||||
|
||||
|
|
@ -575,7 +575,7 @@ end function qu2cu
|
|||
|
||||
!---------------------------------------------------------------------------------------------------
|
||||
!> @author Martin Diehl, Max-Planck-Institut für Eisenforschung GmbH
|
||||
!> @brief convert rotation matrix to cubochoric
|
||||
!> @brief convert rotation matrix to unit quaternion
|
||||
!> @details the original formulation (direct conversion) had (numerical?) issues
|
||||
!---------------------------------------------------------------------------------------------------
|
||||
pure function om2qu(om) result(qu)
|
||||
|
|
@ -602,14 +602,15 @@ pure function om2qu(om) result(qu)
|
|||
endif
|
||||
endif
|
||||
if(sign(1.0_pReal,qu(1))<0.0_pReal) qu =-1.0_pReal * qu
|
||||
qu = qu*[1.0_pReal,P,P,P]
|
||||
qu(2:4) = merge(qu(2:4),qu(2:4)*P,dEq0(qu(2:4)))
|
||||
qu = qu/norm2(qu)
|
||||
|
||||
end function om2qu
|
||||
|
||||
|
||||
!---------------------------------------------------------------------------------------------------
|
||||
!> @author Marc De Graef, Carnegie Mellon University
|
||||
!> @brief orientation matrix to Euler angles
|
||||
!> @brief convert orientation matrix to Euler angles
|
||||
!> @details Two step check for special cases to avoid invalid operations (not needed for python)
|
||||
!---------------------------------------------------------------------------------------------------
|
||||
pure function om2eu(om) result(eu)
|
||||
|
|
@ -1334,8 +1335,8 @@ pure function cu2ho(cu) result(ho)
|
|||
! transform to sphere grid (inverse Lambert)
|
||||
! [note that there is no need to worry about dividing by zero, since XYZ(3) can not become zero]
|
||||
c = sum(T**2)
|
||||
s = PI * c/(24.0*XYZ(3)**2)
|
||||
c = sqrt(PI) * c / sqrt(24.0_pReal) / XYZ(3)
|
||||
s = c * PI/(24.0*XYZ(3)**2)
|
||||
c = c * sqrt(PI/24.0_pReal) / XYZ(3)
|
||||
q = sqrt( 1.0 - s )
|
||||
LamXYZ = [ T(order(2)) * q, T(order(1)) * q, PREF * XYZ(3) - c ]
|
||||
end if special
|
||||
|
|
|
|||
Loading…
Reference in New Issue