Merge remote-tracking branch 'origin/development' into typehints_table
This commit is contained in:
Martin Diehl
commit
803c85c2ef
|
|
@ -46,7 +46,7 @@ variables:
|
|||
# ++++++++++++ PETSc ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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||||
PETSC_GNU: "Libraries/PETSc/3.16.1/GNU-10-OpenMPI-4.1.1"
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PETSC_INTELLLVM: "Libraries/PETSc/3.16.3/oneAPI-2022.0.1-IntelMPI-2021.5.0"
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||||
PETSC_INTEL: "Libraries/PETSc/3.16.2/Intel-2022.0.1-IntelMPI-2021.5.0"
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||||
PETSC_INTEL: "Libraries/PETSc/3.16.3/Intel-2022.0.1-IntelMPI-2021.5.0"
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||||
# ++++++++++++ MSC Marc +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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MSC: "FEM/MSC/2021.3.1"
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IntelMarc: "Compiler/Intel/19.1.2 Libraries/IMKL/2020"
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||||
|
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@ -79,63 +79,63 @@ mypy:
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|||
|
||||
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###################################################################################################
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test_grid_GNU:
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grid_GNU:
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stage: compile
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script:
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- module load ${COMPILER_GNU} ${MPI_GNU} ${PETSC_GNU}
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- cd PRIVATE/testing/pytest
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- pytest -k 'compile and grid' --basetemp ${TESTROOT}/compile_grid_GNU
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|
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test_mesh_GNU:
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mesh_GNU:
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stage: compile
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script:
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- module load ${COMPILER_GNU} ${MPI_GNU} ${PETSC_GNU}
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- cd PRIVATE/testing/pytest
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- pytest -k 'compile and mesh' --basetemp ${TESTROOT}/compile_mesh_GNU
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test_grid_GNU-64bit:
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grid_GNU-64bit:
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stage: compile
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script:
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- module load Compiler/GNU/10 Libraries/PETSc/3.16.2/64bit
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- cd PRIVATE/testing/pytest
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- pytest -k 'compile and grid' --basetemp ${TESTROOT}/compile_grid_GNU-64bit
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test_mesh_GNU-64bit:
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mesh_GNU-64bit:
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stage: compile
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script:
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- module load Compiler/GNU/10 Libraries/PETSc/3.16.2/64bit
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- cd PRIVATE/testing/pytest
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- pytest -k 'compile and mesh' --basetemp ${TESTROOT}/compile_mesh_GNU-64bit
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test_grid_IntelLLVM:
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grid_IntelLLVM:
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stage: compile
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script:
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- module load ${COMPILER_INTELLLVM} ${MPI_INTELLLVM} ${PETSC_INTELLLVM}
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- cd PRIVATE/testing/pytest
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- pytest -k 'compile and grid' --basetemp ${TESTROOT}/compile_grid_IntelLLVM
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test_mesh_IntelLLVM:
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mesh_IntelLLVM:
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stage: compile
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script:
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- module load ${COMPILER_INTELLLVM} ${MPI_INTELLLVM} ${PETSC_INTELLLVM}
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- cd PRIVATE/testing/pytest
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- pytest -k 'compile and mesh' --basetemp ${TESTROOT}/compile_mesh_IntelLLVM
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test_grid_Intel:
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grid_Intel:
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stage: compile
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||||
script:
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- module load ${COMPILER_INTEL} ${MPI_INTEL} ${PETSC_INTEL}
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- cd PRIVATE/testing/pytest
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- pytest -k 'compile and grid' --basetemp ${TESTROOT}/compile_grid_Intel
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test_mesh_Intel:
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mesh_Intel:
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||||
stage: compile
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script:
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||||
- module load ${COMPILER_INTEL} ${MPI_INTEL} ${PETSC_INTEL}
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||||
- cd PRIVATE/testing/pytest
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- pytest -k 'compile and mesh' --basetemp ${TESTROOT}/compile_mesh_Intel
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||||
|
||||
test_Marc:
|
||||
Marc_Intel:
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||||
stage: compile
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||||
script:
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- module load $IntelMarc $HDF5Marc $MSC
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|
|
@ -158,7 +158,7 @@ setup_mesh:
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- cmake -DDAMASK_SOLVER=MESH -DCMAKE_INSTALL_PREFIX=${TESTROOT} ${CI_PROJECT_DIR}
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- make -j2 all install
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||||
|
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compile_Marc:
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||||
setup_Marc:
|
||||
stage: compile
|
||||
script:
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||||
- module load $IntelMarc $HDF5Marc $MSC
|
||||
|
|
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|||
2
PRIVATE
2
PRIVATE
|
|
@ -1 +1 @@
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|||
Subproject commit b898a8b5552bd9d1c555edc3d8134564dd32fe53
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Subproject commit d570b4a1fac5b9b99d026d3ff9bf593615e22ce5
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|
|
@ -6,7 +6,7 @@ references:
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|||
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||||
output: [xi_sl, xi_tw]
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N_sl: [3, 3, 6, 0, 6] # basal, prism, -, 1. pyr<a>, -, 2. pyr<c+a>
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N_sl: [3, 3, 6, 0, 6] # basal, prism, 1. pyr<a>, -, 2. pyr<c+a>
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N_tw: [6, 0, 6] # tension, -, compression
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||||
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||||
xi_0_sl: [10.e+6, 55.e+6, 60.e+6, 0., 60.e+6]
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||||
|
|
@ -23,9 +23,13 @@ f_sat_sl-tw: 10.0
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|||
h_0_sl-sl: 500.0e+6
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||||
h_0_tw-tw: 50.0e+6
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||||
h_0_tw-sl: 150.0e+6
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||||
h_sl-sl: [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0,
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||||
1.0, 1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0,
|
||||
1.0, 1.0, 1.0, -1.0, 1.0, 1.0, -1.0, 1.0, +1.0, 1.0] # unused entries are indicated by -1.0
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||||
h_sl-sl: [+1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0,
|
||||
+1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, -1.0,
|
||||
-1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0,
|
||||
-1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0,
|
||||
-1.0, -1.0, -1.0, -1.0, -1.0, -1.0, 1.0, 1.0, 1.0, 1.0,
|
||||
+1.0, 1.0, -1.0, -1.0, -1.0, -1.0, 1.0, 1.0, 1.0, 1.0,
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||||
-1.0, -1.0, -1.0, -1.0, 1.0, 1.0, 1.0, 1.0, 1.0] # unused entries are indicated by -1.0
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||||
h_tw-tw: [+1.0, 1.0, -1.0, -1.0, -1.0, -1.0, 1.0, -1.0, 1.0, 1.0,
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||||
-1.0, 1.0] # unused entries are indicated by -1.0
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h_tw-sl: [1.0, -1.0, 1.0, -1.0, 1.0, -1.0, 1.0, -1.0, 1.0, -1.0,
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||||
|
|
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|||
|
|
@ -8,7 +8,7 @@ references:
|
|||
https://doi.org/10.1016/j.actamat.2017.05.015
|
||||
output: [gamma_sl]
|
||||
|
||||
N_sl: [3, 3, 0, 12] # basal, 1. prism, -, 1. pyr<c+a>
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||||
N_sl: [3, 3, 0, 12] # basal, prism, -, 1. pyr<c+a>
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||||
n_sl: 20
|
||||
a_sl: 2.0
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||||
dot_gamma_0_sl: 0.001
|
||||
|
|
@ -20,5 +20,8 @@ xi_inf_sl: [568.e+6, 150.e+7, 0.0, 3420.e+6]
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|||
# L. Wang et al. :
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||||
# xi_0_sl: [127.e+6, 96.e+6, 0.0, 240.e+6]
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||||
|
||||
h_sl-sl: [+1.0, 1.0, 1.0, 1.0, 1.0, 1.0, -1.0, -1.0, -1.0, -1.0,
|
||||
-1.0, -1.0, +1.0, 1.0, -1.0, 1.0, 1.0, -1.0, 1.0, 1.0] # unused entries are indicated by -1.0
|
||||
h_sl-sl: [+1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, -1.0, -1.0,
|
||||
-1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, 1.0,
|
||||
+1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0,
|
||||
+1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0,
|
||||
+1.0, 1.0, 1.0, 1.0, 1.0, 1.0] # unused entries are indicated by -1.0
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||||
|
|
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|||
|
|
@ -1 +1 @@
|
|||
v3.0.0-alpha5-389-ga000e477c
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v3.0.0-alpha5-475-g160eb1c60
|
||||
|
|
|
|||
|
|
@ -21,8 +21,8 @@ from ._rotation import Rotation # noqa
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from ._crystal import Crystal # noqa
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||||
from ._orientation import Orientation # noqa
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from ._table import Table # noqa
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||||
from ._vtk import VTK # noqa
|
||||
from ._colormap import Colormap # noqa
|
||||
from ._vtk import VTK # noqa
|
||||
from ._config import Config # noqa
|
||||
from ._configmaterial import ConfigMaterial # noqa
|
||||
from ._grid import Grid # noqa
|
||||
|
|
|
|||
|
|
@ -250,7 +250,7 @@ class Colormap(mpl.colors.ListedColormap):
|
|||
np.logical_or (np.isnan(field), field == gap)) # mask NaN (and gap if present)
|
||||
|
||||
l,r = (field[mask].min(),field[mask].max()) if bounds is None else \
|
||||
np.array(bounds,float)[:2]
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||||
(bounds[0],bounds[1])
|
||||
|
||||
delta,avg = r-l,0.5*abs(r+l)
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||||
|
||||
|
|
|
|||
|
|
@ -4,7 +4,7 @@ import warnings
|
|||
import multiprocessing as mp
|
||||
from functools import partial
|
||||
import typing
|
||||
from typing import Union, Optional, TextIO, List, Sequence
|
||||
from typing import Union, Optional, TextIO, List, Sequence, Literal
|
||||
from pathlib import Path
|
||||
|
||||
import numpy as np
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||||
|
|
@ -70,7 +70,7 @@ class Grid:
|
|||
])
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||||
|
||||
|
||||
def __copy__(self) -> "Grid":
|
||||
def __copy__(self) -> 'Grid':
|
||||
"""Create deep copy."""
|
||||
return copy.deepcopy(self)
|
||||
|
||||
|
|
@ -161,7 +161,7 @@ class Grid:
|
|||
|
||||
|
||||
@staticmethod
|
||||
def load(fname: Union[str, Path]) -> "Grid":
|
||||
def load(fname: Union[str, Path]) -> 'Grid':
|
||||
"""
|
||||
Load from VTK image data file.
|
||||
|
||||
|
|
@ -190,7 +190,7 @@ class Grid:
|
|||
|
||||
@typing. no_type_check
|
||||
@staticmethod
|
||||
def load_ASCII(fname)-> "Grid":
|
||||
def load_ASCII(fname)-> 'Grid':
|
||||
"""
|
||||
Load from geom file.
|
||||
|
||||
|
|
@ -264,7 +264,7 @@ class Grid:
|
|||
|
||||
|
||||
@staticmethod
|
||||
def load_Neper(fname: Union[str, Path]) -> "Grid":
|
||||
def load_Neper(fname: Union[str, Path]) -> 'Grid':
|
||||
"""
|
||||
Load from Neper VTK file.
|
||||
|
||||
|
|
@ -279,7 +279,7 @@ class Grid:
|
|||
Grid-based geometry from file.
|
||||
|
||||
"""
|
||||
v = VTK.load(fname,'vtkImageData')
|
||||
v = VTK.load(fname,'ImageData')
|
||||
cells = np.array(v.vtk_data.GetDimensions())-1
|
||||
bbox = np.array(v.vtk_data.GetBounds()).reshape(3,2).T
|
||||
|
||||
|
|
@ -292,7 +292,7 @@ class Grid:
|
|||
def load_DREAM3D(fname: Union[str, Path],
|
||||
feature_IDs: str = None, cell_data: str = None,
|
||||
phases: str = 'Phases', Euler_angles: str = 'EulerAngles',
|
||||
base_group: str = None) -> "Grid":
|
||||
base_group: str = None) -> 'Grid':
|
||||
"""
|
||||
Load DREAM.3D (HDF5) file.
|
||||
|
||||
|
|
@ -354,7 +354,7 @@ class Grid:
|
|||
@staticmethod
|
||||
def from_table(table: Table,
|
||||
coordinates: str,
|
||||
labels: Union[str, Sequence[str]]) -> "Grid":
|
||||
labels: Union[str, Sequence[str]]) -> 'Grid':
|
||||
"""
|
||||
Create grid from ASCII table.
|
||||
|
||||
|
|
@ -422,13 +422,14 @@ class Grid:
|
|||
Grid-based geometry from tessellation.
|
||||
|
||||
"""
|
||||
weights_p: FloatSequence
|
||||
if periodic:
|
||||
weights_p = np.tile(weights,27) # Laguerre weights (1,2,3,1,2,3,...,1,2,3)
|
||||
seeds_p = np.vstack((seeds -np.array([size[0],0.,0.]),seeds, seeds +np.array([size[0],0.,0.])))
|
||||
seeds_p = np.vstack((seeds_p-np.array([0.,size[1],0.]),seeds_p,seeds_p+np.array([0.,size[1],0.])))
|
||||
seeds_p = np.vstack((seeds_p-np.array([0.,0.,size[2]]),seeds_p,seeds_p+np.array([0.,0.,size[2]])))
|
||||
else:
|
||||
weights_p = weights
|
||||
weights_p = np.array(weights,float)
|
||||
seeds_p = seeds
|
||||
|
||||
coords = grid_filters.coordinates0_point(cells,size).reshape(-1,3)
|
||||
|
|
@ -452,7 +453,7 @@ class Grid:
|
|||
size: FloatSequence,
|
||||
seeds: np.ndarray,
|
||||
material: IntSequence = None,
|
||||
periodic: bool = True) -> "Grid":
|
||||
periodic: bool = True) -> 'Grid':
|
||||
"""
|
||||
Create grid from Voronoi tessellation.
|
||||
|
||||
|
|
@ -538,7 +539,7 @@ class Grid:
|
|||
surface: str,
|
||||
threshold: float = 0.0,
|
||||
periods: int = 1,
|
||||
materials: IntSequence = (0,1)) -> "Grid":
|
||||
materials: IntSequence = (0,1)) -> 'Grid':
|
||||
"""
|
||||
Create grid from definition of triply periodic minimal surface.
|
||||
|
||||
|
|
@ -674,7 +675,7 @@ class Grid:
|
|||
|
||||
def show(self) -> None:
|
||||
"""Show on screen."""
|
||||
VTK.from_rectilinear_grid(self.cells,self.size,self.origin).show()
|
||||
VTK.from_image_data(self.cells,self.size,self.origin).show()
|
||||
|
||||
|
||||
def add_primitive(self,
|
||||
|
|
@ -684,7 +685,7 @@ class Grid:
|
|||
fill: int = None,
|
||||
R: Rotation = Rotation(),
|
||||
inverse: bool = False,
|
||||
periodic: bool = True) -> "Grid":
|
||||
periodic: bool = True) -> 'Grid':
|
||||
"""
|
||||
Insert a primitive geometric object at a given position.
|
||||
|
||||
|
|
@ -769,7 +770,7 @@ class Grid:
|
|||
)
|
||||
|
||||
|
||||
def mirror(self, directions: Sequence[str], reflect: bool = False) -> "Grid":
|
||||
def mirror(self, directions: Sequence[str], reflect: bool = False) -> 'Grid':
|
||||
"""
|
||||
Mirror grid along given directions.
|
||||
|
||||
|
|
@ -821,7 +822,7 @@ class Grid:
|
|||
)
|
||||
|
||||
|
||||
def flip(self, directions: Sequence[str]) -> "Grid":
|
||||
def flip(self, directions: Union[Literal['x', 'y', 'z'], Sequence[Literal['x', 'y', 'z']]]) -> 'Grid':
|
||||
"""
|
||||
Flip grid along given directions.
|
||||
|
||||
|
|
@ -841,7 +842,8 @@ class Grid:
|
|||
if not set(directions).issubset(valid):
|
||||
raise ValueError(f'invalid direction {set(directions).difference(valid)} specified')
|
||||
|
||||
mat = np.flip(self.material, (valid.index(d) for d in directions if d in valid))
|
||||
|
||||
mat = np.flip(self.material, [valid.index(d) for d in directions if d in valid])
|
||||
|
||||
return Grid(material = mat,
|
||||
size = self.size,
|
||||
|
|
@ -850,7 +852,7 @@ class Grid:
|
|||
)
|
||||
|
||||
|
||||
def scale(self, cells: IntSequence, periodic: bool = True) -> "Grid":
|
||||
def scale(self, cells: IntSequence, periodic: bool = True) -> 'Grid':
|
||||
"""
|
||||
Scale grid to new cells.
|
||||
|
||||
|
|
@ -897,7 +899,7 @@ class Grid:
|
|||
def clean(self,
|
||||
stencil: int = 3,
|
||||
selection: IntSequence = None,
|
||||
periodic: bool = True) -> "Grid":
|
||||
periodic: bool = True) -> 'Grid':
|
||||
"""
|
||||
Smooth grid by selecting most frequent material index within given stencil at each location.
|
||||
|
||||
|
|
@ -937,7 +939,7 @@ class Grid:
|
|||
)
|
||||
|
||||
|
||||
def renumber(self) -> "Grid":
|
||||
def renumber(self) -> 'Grid':
|
||||
"""
|
||||
Renumber sorted material indices as 0,...,N-1.
|
||||
|
||||
|
|
@ -956,7 +958,7 @@ class Grid:
|
|||
)
|
||||
|
||||
|
||||
def rotate(self, R: Rotation, fill: int = None) -> "Grid":
|
||||
def rotate(self, R: Rotation, fill: int = None) -> 'Grid':
|
||||
"""
|
||||
Rotate grid (pad if required).
|
||||
|
||||
|
|
@ -973,14 +975,13 @@ class Grid:
|
|||
Updated grid-based geometry.
|
||||
|
||||
"""
|
||||
if fill is None: fill = np.nanmax(self.material) + 1
|
||||
dtype = float if isinstance(fill,float) or self.material.dtype in np.sctypes['float'] else int
|
||||
|
||||
material = self.material
|
||||
# These rotations are always applied in the reference coordinate system, i.e. (z,x,z) not (z,x',z'')
|
||||
# see https://www.cs.utexas.edu/~theshark/courses/cs354/lectures/cs354-14.pdf
|
||||
for angle,axes in zip(R.as_Euler_angles(degrees=True)[::-1], [(0,1),(1,2),(0,1)]):
|
||||
material_temp = ndimage.rotate(material,angle,axes,order=0,prefilter=False,output=dtype,cval=fill)
|
||||
material_temp = ndimage.rotate(material,angle,axes,order=0,prefilter=False,
|
||||
output=self.material.dtype,
|
||||
cval=np.nanmax(self.material) + 1 if fill is None else fill)
|
||||
# avoid scipy interpolation errors for rotations close to multiples of 90°
|
||||
material = material_temp if np.prod(material_temp.shape) != np.prod(material.shape) else \
|
||||
np.rot90(material,k=np.rint(angle/90.).astype(int),axes=axes)
|
||||
|
|
@ -997,7 +998,7 @@ class Grid:
|
|||
def canvas(self,
|
||||
cells: IntSequence = None,
|
||||
offset: IntSequence = None,
|
||||
fill: int = None) -> "Grid":
|
||||
fill: int = None) -> 'Grid':
|
||||
"""
|
||||
Crop or enlarge/pad grid.
|
||||
|
||||
|
|
@ -1031,10 +1032,8 @@ class Grid:
|
|||
"""
|
||||
offset_ = np.array(offset,int) if offset is not None else np.zeros(3,int)
|
||||
cells_ = np.array(cells,int) if cells is not None else self.cells
|
||||
if fill is None: fill = np.nanmax(self.material) + 1
|
||||
dtype = float if int(fill) != fill or self.material.dtype in np.sctypes['float'] else int
|
||||
|
||||
canvas = np.full(cells_,fill,dtype)
|
||||
canvas = np.full(cells_,np.nanmax(self.material) + 1 if fill is None else fill,self.material.dtype)
|
||||
|
||||
LL = np.clip( offset_, 0,np.minimum(self.cells, cells_+offset_))
|
||||
UR = np.clip( offset_+cells_, 0,np.minimum(self.cells, cells_+offset_))
|
||||
|
|
@ -1050,7 +1049,7 @@ class Grid:
|
|||
)
|
||||
|
||||
|
||||
def substitute(self, from_material: IntSequence, to_material: IntSequence) -> "Grid":
|
||||
def substitute(self, from_material: IntSequence, to_material: IntSequence) -> 'Grid':
|
||||
"""
|
||||
Substitute material indices.
|
||||
|
||||
|
|
@ -1067,20 +1066,18 @@ class Grid:
|
|||
Updated grid-based geometry.
|
||||
|
||||
"""
|
||||
def mp(entry, mapper):
|
||||
return mapper[entry] if entry in mapper else entry
|
||||
material = self.material.copy()
|
||||
for f,t in zip(from_material,to_material): # ToDo Python 3.10 has strict mode for zip
|
||||
material[self.material==f] = t
|
||||
|
||||
mp = np.vectorize(mp)
|
||||
mapper = dict(zip(from_material,to_material))
|
||||
|
||||
return Grid(material = mp(self.material,mapper).reshape(self.cells),
|
||||
return Grid(material = material,
|
||||
size = self.size,
|
||||
origin = self.origin,
|
||||
comments = self.comments+[util.execution_stamp('Grid','substitute')],
|
||||
)
|
||||
|
||||
|
||||
def sort(self) -> "Grid":
|
||||
def sort(self) -> 'Grid':
|
||||
"""
|
||||
Sort material indices such that min(material) is located at (0,0,0).
|
||||
|
||||
|
|
@ -1106,7 +1103,7 @@ class Grid:
|
|||
vicinity: int = 1,
|
||||
offset: int = None,
|
||||
trigger: IntSequence = [],
|
||||
periodic: bool = True) -> "Grid":
|
||||
periodic: bool = True) -> 'Grid':
|
||||
"""
|
||||
Offset material index of points in the vicinity of xxx.
|
||||
|
||||
|
|
|
|||
|
|
@ -981,7 +981,7 @@ class Result:
|
|||
t = 'tensor'
|
||||
if o is None: o = 'fro'
|
||||
else:
|
||||
raise ValueError(f'invalid norm order {ord}')
|
||||
raise ValueError(f'invalid shape of {x["label"]}')
|
||||
|
||||
return {
|
||||
'data': np.linalg.norm(x['data'],ord=o,axis=axis,keepdims=True),
|
||||
|
|
|
|||
|
|
@ -812,8 +812,7 @@ class Rotation:
|
|||
return Rotation.from_basis(R)
|
||||
|
||||
@staticmethod
|
||||
def from_parallel(a,b,
|
||||
**kwargs):
|
||||
def from_parallel(a,b):
|
||||
"""
|
||||
Initialize from pairs of two orthogonal lattice basis vectors.
|
||||
|
||||
|
|
@ -963,8 +962,7 @@ class Rotation:
|
|||
N = 500,
|
||||
degrees = True,
|
||||
fractions = True,
|
||||
rng_seed = None,
|
||||
**kwargs):
|
||||
rng_seed = None):
|
||||
"""
|
||||
Sample discrete values from a binned orientation distribution function (ODF).
|
||||
|
||||
|
|
|
|||
|
|
@ -2,6 +2,7 @@ import os
|
|||
import warnings
|
||||
import multiprocessing as mp
|
||||
from pathlib import Path
|
||||
from typing import Union, Literal, List
|
||||
|
||||
import numpy as np
|
||||
import vtk
|
||||
|
|
@ -9,6 +10,7 @@ from vtk.util.numpy_support import numpy_to_vtk as np_to_vtk
|
|||
from vtk.util.numpy_support import numpy_to_vtkIdTypeArray as np_to_vtkIdTypeArray
|
||||
from vtk.util.numpy_support import vtk_to_numpy as vtk_to_np
|
||||
|
||||
from ._typehints import FloatSequence, IntSequence
|
||||
from . import util
|
||||
from . import Table
|
||||
|
||||
|
|
@ -20,7 +22,7 @@ class VTK:
|
|||
High-level interface to VTK.
|
||||
"""
|
||||
|
||||
def __init__(self,vtk_data):
|
||||
def __init__(self, vtk_data: vtk.vtkDataSet):
|
||||
"""
|
||||
New spatial visualization.
|
||||
|
||||
|
|
@ -36,7 +38,7 @@ class VTK:
|
|||
|
||||
|
||||
@staticmethod
|
||||
def from_image_data(cells,size,origin=np.zeros(3)):
|
||||
def from_image_data(cells: IntSequence, size: FloatSequence, origin: FloatSequence = np.zeros(3)) -> 'VTK':
|
||||
"""
|
||||
Create VTK of type vtk.vtkImageData.
|
||||
|
||||
|
|
@ -60,13 +62,13 @@ class VTK:
|
|||
vtk_data = vtk.vtkImageData()
|
||||
vtk_data.SetDimensions(*(np.array(cells)+1))
|
||||
vtk_data.SetOrigin(*(np.array(origin)))
|
||||
vtk_data.SetSpacing(*(size/cells))
|
||||
vtk_data.SetSpacing(*(np.array(size)/np.array(cells)))
|
||||
|
||||
return VTK(vtk_data)
|
||||
|
||||
|
||||
@staticmethod
|
||||
def from_rectilinear_grid(grid,size,origin=np.zeros(3)):
|
||||
def from_rectilinear_grid(grid: np.ndarray, size: FloatSequence, origin: FloatSequence = np.zeros(3)) -> 'VTK':
|
||||
"""
|
||||
Create VTK of type vtk.vtkRectilinearGrid.
|
||||
|
||||
|
|
@ -98,7 +100,7 @@ class VTK:
|
|||
|
||||
|
||||
@staticmethod
|
||||
def from_unstructured_grid(nodes,connectivity,cell_type):
|
||||
def from_unstructured_grid(nodes: np.ndarray, connectivity: np.ndarray, cell_type: str) -> 'VTK':
|
||||
"""
|
||||
Create VTK of type vtk.vtkUnstructuredGrid.
|
||||
|
||||
|
|
@ -138,7 +140,7 @@ class VTK:
|
|||
|
||||
|
||||
@staticmethod
|
||||
def from_poly_data(points):
|
||||
def from_poly_data(points: np.ndarray) -> 'VTK':
|
||||
"""
|
||||
Create VTK of type vtk.polyData.
|
||||
|
||||
|
|
@ -172,15 +174,17 @@ class VTK:
|
|||
|
||||
|
||||
@staticmethod
|
||||
def load(fname,dataset_type=None):
|
||||
def load(fname: Union[str, Path],
|
||||
dataset_type: Literal['ImageData', 'UnstructuredGrid', 'PolyData'] = None) -> 'VTK':
|
||||
"""
|
||||
Load from VTK file.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
fname : str or pathlib.Path
|
||||
Filename for reading. Valid extensions are .vti, .vtr, .vtu, .vtp, and .vtk.
|
||||
dataset_type : {'vtkImageData', ''vtkRectilinearGrid', 'vtkUnstructuredGrid', 'vtkPolyData'}, optional
|
||||
Filename for reading.
|
||||
Valid extensions are .vti, .vtr, .vtu, .vtp, and .vtk.
|
||||
dataset_type : {'ImageData', 'UnstructuredGrid', 'PolyData'}, optional
|
||||
Name of the vtk.vtkDataSet subclass when opening a .vtk file.
|
||||
|
||||
Returns
|
||||
|
|
@ -234,7 +238,7 @@ class VTK:
|
|||
def _write(writer):
|
||||
"""Wrapper for parallel writing."""
|
||||
writer.Write()
|
||||
def save(self,fname,parallel=True,compress=True):
|
||||
def save(self, fname: Union[str, Path], parallel: bool = True, compress: bool = True):
|
||||
"""
|
||||
Save as VTK file.
|
||||
|
||||
|
|
@ -280,7 +284,7 @@ class VTK:
|
|||
|
||||
# Check https://blog.kitware.com/ghost-and-blanking-visibility-changes/ for missing data
|
||||
# Needs support for damask.Table
|
||||
def add(self,data,label=None):
|
||||
def add(self, data: Union[np.ndarray, np.ma.MaskedArray], label: str = None):
|
||||
"""
|
||||
Add data to either cells or points.
|
||||
|
||||
|
|
@ -327,7 +331,7 @@ class VTK:
|
|||
raise TypeError
|
||||
|
||||
|
||||
def get(self,label):
|
||||
def get(self, label: str) -> np.ndarray:
|
||||
"""
|
||||
Get either cell or point data.
|
||||
|
||||
|
|
@ -369,7 +373,7 @@ class VTK:
|
|||
raise ValueError(f'Array "{label}" not found.')
|
||||
|
||||
|
||||
def get_comments(self):
|
||||
def get_comments(self) -> List[str]:
|
||||
"""Return the comments."""
|
||||
fielddata = self.vtk_data.GetFieldData()
|
||||
for a in range(fielddata.GetNumberOfArrays()):
|
||||
|
|
@ -379,7 +383,7 @@ class VTK:
|
|||
return []
|
||||
|
||||
|
||||
def set_comments(self,comments):
|
||||
def set_comments(self, comments: Union[str, List[str]]):
|
||||
"""
|
||||
Set comments.
|
||||
|
||||
|
|
@ -396,7 +400,7 @@ class VTK:
|
|||
self.vtk_data.GetFieldData().AddArray(s)
|
||||
|
||||
|
||||
def add_comments(self,comments):
|
||||
def add_comments(self, comments: Union[str, List[str]]):
|
||||
"""
|
||||
Add comments.
|
||||
|
||||
|
|
@ -409,7 +413,7 @@ class VTK:
|
|||
self.set_comments(self.get_comments() + ([comments] if isinstance(comments,str) else comments))
|
||||
|
||||
|
||||
def __repr__(self):
|
||||
def __repr__(self) -> str:
|
||||
"""ASCII representation of the VTK data."""
|
||||
writer = vtk.vtkDataSetWriter()
|
||||
writer.SetHeader(f'# {util.execution_stamp("VTK")}')
|
||||
|
|
@ -419,7 +423,7 @@ class VTK:
|
|||
return writer.GetOutputString()
|
||||
|
||||
|
||||
def show(self) -> None:
|
||||
def show(self):
|
||||
"""
|
||||
Render.
|
||||
|
||||
|
|
@ -442,22 +446,24 @@ class VTK:
|
|||
|
||||
mapper = vtk.vtkDataSetMapper()
|
||||
mapper.SetInputData(self.vtk_data)
|
||||
|
||||
actor = vtk.vtkActor()
|
||||
actor.SetMapper(mapper)
|
||||
actor.GetProperty().SetColor(230/255,150/255,68/255)
|
||||
|
||||
ren = vtk.vtkRenderer()
|
||||
ren.AddActor(actor)
|
||||
ren.SetBackground(67/255,128/255,208/255)
|
||||
|
||||
window = vtk.vtkRenderWindow()
|
||||
window.AddRenderer(ren)
|
||||
|
||||
ren.AddActor(actor)
|
||||
ren.SetBackground(0.2,0.2,0.2)
|
||||
|
||||
window.SetSize(width,height)
|
||||
window.SetWindowName(util.execution_stamp('VTK','show'))
|
||||
|
||||
iren = vtk.vtkRenderWindowInteractor()
|
||||
iren.SetRenderWindow(window)
|
||||
|
||||
iren.Initialize()
|
||||
if os.name == 'posix' and 'DISPLAY' not in os.environ:
|
||||
print('Found no rendering device')
|
||||
else:
|
||||
window.Render()
|
||||
iren.Start()
|
||||
|
|
|
|||
|
|
@ -79,7 +79,7 @@ def from_Poisson_disc(size: _FloatSequence, N_seeds: int, N_candidates: int, dis
|
|||
|
||||
s = 1
|
||||
i = 0
|
||||
progress = _util._ProgressBar(N_seeds+1,'',50)
|
||||
progress = _util.ProgressBar(N_seeds+1,'',50)
|
||||
while s < N_seeds:
|
||||
i += 1
|
||||
candidates = rng.random((N_candidates,3))*_np.broadcast_to(size,(N_candidates,3))
|
||||
|
|
|
|||
|
|
@ -7,12 +7,16 @@ import subprocess
|
|||
import shlex
|
||||
import re
|
||||
import fractions
|
||||
import collections.abc as abc
|
||||
from functools import reduce
|
||||
from typing import Union, Tuple, Iterable, Callable, Dict, List, Any, Literal, Optional
|
||||
from pathlib import Path
|
||||
|
||||
import numpy as np
|
||||
import h5py
|
||||
|
||||
from . import version
|
||||
from ._typehints import FloatSequence
|
||||
|
||||
# limit visibility
|
||||
__all__=[
|
||||
|
|
@ -50,16 +54,16 @@ _colors = {
|
|||
####################################################################################################
|
||||
# Functions
|
||||
####################################################################################################
|
||||
def srepr(arg,glue = '\n'):
|
||||
def srepr(msg, glue: str = '\n') -> str:
|
||||
r"""
|
||||
Join items with glue string.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
arg : iterable
|
||||
msg : object with __repr__ or sequence of objects with __repr__
|
||||
Items to join.
|
||||
glue : str, optional
|
||||
Glue used for joining operation. Defaults to \n.
|
||||
Glue used for joining operation. Defaults to '\n'.
|
||||
|
||||
Returns
|
||||
-------
|
||||
|
|
@ -67,21 +71,21 @@ def srepr(arg,glue = '\n'):
|
|||
String representation of the joined items.
|
||||
|
||||
"""
|
||||
if (not hasattr(arg, 'strip') and
|
||||
(hasattr(arg, '__getitem__') or
|
||||
hasattr(arg, '__iter__'))):
|
||||
return glue.join(str(x) for x in arg)
|
||||
if (not hasattr(msg, 'strip') and
|
||||
(hasattr(msg, '__getitem__') or
|
||||
hasattr(msg, '__iter__'))):
|
||||
return glue.join(str(x) for x in msg)
|
||||
else:
|
||||
return arg if isinstance(arg,str) else repr(arg)
|
||||
return msg if isinstance(msg,str) else repr(msg)
|
||||
|
||||
|
||||
def emph(what):
|
||||
def emph(msg) -> str:
|
||||
"""
|
||||
Format with emphasis.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
what : object with __repr__ or iterable of objects with __repr__.
|
||||
msg : object with __repr__ or sequence of objects with __repr__
|
||||
Message to format.
|
||||
|
||||
Returns
|
||||
|
|
@ -90,15 +94,15 @@ def emph(what):
|
|||
Formatted string representation of the joined items.
|
||||
|
||||
"""
|
||||
return _colors['bold']+srepr(what)+_colors['end_color']
|
||||
return _colors['bold']+srepr(msg)+_colors['end_color']
|
||||
|
||||
def deemph(what):
|
||||
def deemph(msg) -> str:
|
||||
"""
|
||||
Format with deemphasis.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
what : object with __repr__ or iterable of objects with __repr__.
|
||||
msg : object with __repr__ or sequence of objects with __repr__
|
||||
Message to format.
|
||||
|
||||
Returns
|
||||
|
|
@ -107,15 +111,15 @@ def deemph(what):
|
|||
Formatted string representation of the joined items.
|
||||
|
||||
"""
|
||||
return _colors['dim']+srepr(what)+_colors['end_color']
|
||||
return _colors['dim']+srepr(msg)+_colors['end_color']
|
||||
|
||||
def warn(what):
|
||||
def warn(msg) -> str:
|
||||
"""
|
||||
Format for warning.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
what : object with __repr__ or iterable of objects with __repr__.
|
||||
msg : object with __repr__ or sequence of objects with __repr__
|
||||
Message to format.
|
||||
|
||||
Returns
|
||||
|
|
@ -124,15 +128,15 @@ def warn(what):
|
|||
Formatted string representation of the joined items.
|
||||
|
||||
"""
|
||||
return _colors['warning']+emph(what)+_colors['end_color']
|
||||
return _colors['warning']+emph(msg)+_colors['end_color']
|
||||
|
||||
def strikeout(what):
|
||||
def strikeout(msg) -> str:
|
||||
"""
|
||||
Format as strikeout.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
what : object with __repr__ or iterable of objects with __repr__.
|
||||
msg : object with __repr__ or iterable of objects with __repr__
|
||||
Message to format.
|
||||
|
||||
Returns
|
||||
|
|
@ -141,10 +145,10 @@ def strikeout(what):
|
|||
Formatted string representation of the joined items.
|
||||
|
||||
"""
|
||||
return _colors['crossout']+srepr(what)+_colors['end_color']
|
||||
return _colors['crossout']+srepr(msg)+_colors['end_color']
|
||||
|
||||
|
||||
def run(cmd,wd='./',env=None,timeout=None):
|
||||
def run(cmd: str, wd: str = './', env: Dict[str, str] = None, timeout: int = None) -> Tuple[str, str]:
|
||||
"""
|
||||
Run a command.
|
||||
|
||||
|
|
@ -153,7 +157,7 @@ def run(cmd,wd='./',env=None,timeout=None):
|
|||
cmd : str
|
||||
Command to be executed.
|
||||
wd : str, optional
|
||||
Working directory of process. Defaults to ./ .
|
||||
Working directory of process. Defaults to './'.
|
||||
env : dict, optional
|
||||
Environment for execution.
|
||||
timeout : integer, optional
|
||||
|
|
@ -185,7 +189,7 @@ def run(cmd,wd='./',env=None,timeout=None):
|
|||
execute = run
|
||||
|
||||
|
||||
def natural_sort(key):
|
||||
def natural_sort(key: str) -> List[Union[int, str]]:
|
||||
"""
|
||||
Natural sort.
|
||||
|
||||
|
|
@ -200,7 +204,10 @@ def natural_sort(key):
|
|||
return [ convert(c) for c in re.split('([0-9]+)', key) ]
|
||||
|
||||
|
||||
def show_progress(iterable,N_iter=None,prefix='',bar_length=50):
|
||||
def show_progress(iterable: Iterable,
|
||||
N_iter: int = None,
|
||||
prefix: str = '',
|
||||
bar_length: int = 50) -> Any:
|
||||
"""
|
||||
Decorate a loop with a progress bar.
|
||||
|
||||
|
|
@ -208,39 +215,49 @@ def show_progress(iterable,N_iter=None,prefix='',bar_length=50):
|
|||
|
||||
Parameters
|
||||
----------
|
||||
iterable : iterable or function with yield statement
|
||||
Iterable (or function with yield statement) to be decorated.
|
||||
iterable : iterable
|
||||
Iterable to be decorated.
|
||||
N_iter : int, optional
|
||||
Total number of iterations. Required unless obtainable as len(iterable).
|
||||
Total number of iterations. Required if iterable is not a sequence.
|
||||
prefix : str, optional
|
||||
Prefix string.
|
||||
bar_length : int, optional
|
||||
Length of progress bar in characters. Defaults to 50.
|
||||
|
||||
"""
|
||||
if N_iter in [0,1] or (hasattr(iterable,'__len__') and len(iterable) <= 1):
|
||||
if isinstance(iterable,abc.Sequence):
|
||||
if N_iter is None:
|
||||
N = len(iterable)
|
||||
else:
|
||||
raise ValueError('N_iter given for sequence')
|
||||
else:
|
||||
if N_iter is None:
|
||||
raise ValueError('N_iter not given')
|
||||
else:
|
||||
N = N_iter
|
||||
|
||||
if N <= 1:
|
||||
for item in iterable:
|
||||
yield item
|
||||
else:
|
||||
status = _ProgressBar(N_iter if N_iter is not None else len(iterable),prefix,bar_length)
|
||||
|
||||
status = ProgressBar(N,prefix,bar_length)
|
||||
for i,item in enumerate(iterable):
|
||||
yield item
|
||||
status.update(i)
|
||||
|
||||
|
||||
def scale_to_coprime(v):
|
||||
def scale_to_coprime(v: FloatSequence) -> np.ndarray:
|
||||
"""
|
||||
Scale vector to co-prime (relatively prime) integers.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
v : numpy.ndarray of shape (:)
|
||||
v : sequence of float, len (:)
|
||||
Vector to scale.
|
||||
|
||||
Returns
|
||||
-------
|
||||
m : numpy.ndarray of shape (:)
|
||||
m : numpy.ndarray, shape (:)
|
||||
Vector scaled to co-prime numbers.
|
||||
|
||||
"""
|
||||
|
|
@ -257,17 +274,21 @@ def scale_to_coprime(v):
|
|||
except AttributeError:
|
||||
return a * b // np.gcd(a, b)
|
||||
|
||||
m = (np.array(v) * reduce(lcm, map(lambda x: int(get_square_denominator(x)),v)) ** 0.5).astype(int)
|
||||
v_ = np.array(v)
|
||||
m = (v_ * reduce(lcm, map(lambda x: int(get_square_denominator(x)),v_))**0.5).astype(int)
|
||||
m = m//reduce(np.gcd,m)
|
||||
|
||||
with np.errstate(invalid='ignore'):
|
||||
if not np.allclose(np.ma.masked_invalid(v/m),v[np.argmax(abs(v))]/m[np.argmax(abs(v))]):
|
||||
raise ValueError(f'Invalid result {m} for input {v}. Insufficient precision?')
|
||||
if not np.allclose(np.ma.masked_invalid(v_/m),v_[np.argmax(abs(v_))]/m[np.argmax(abs(v_))]):
|
||||
raise ValueError(f'Invalid result {m} for input {v_}. Insufficient precision?')
|
||||
|
||||
return m
|
||||
|
||||
|
||||
def project_equal_angle(vector,direction='z',normalize=True,keepdims=False):
|
||||
def project_equal_angle(vector: np.ndarray,
|
||||
direction: Literal['x', 'y', 'z'] = 'z',
|
||||
normalize: bool = True,
|
||||
keepdims: bool = False) -> np.ndarray:
|
||||
"""
|
||||
Apply equal-angle projection to vector.
|
||||
|
||||
|
|
@ -275,9 +296,8 @@ def project_equal_angle(vector,direction='z',normalize=True,keepdims=False):
|
|||
----------
|
||||
vector : numpy.ndarray, shape (...,3)
|
||||
Vector coordinates to be projected.
|
||||
direction : str
|
||||
Projection direction 'x', 'y', or 'z'.
|
||||
Defaults to 'z'.
|
||||
direction : {'x', 'y', 'z'}
|
||||
Projection direction. Defaults to 'z'.
|
||||
normalize : bool
|
||||
Ensure unit length of input vector. Defaults to True.
|
||||
keepdims : bool
|
||||
|
|
@ -309,7 +329,10 @@ def project_equal_angle(vector,direction='z',normalize=True,keepdims=False):
|
|||
return np.roll(np.block([v[...,:2]/(1.0+np.abs(v[...,2:3])),np.zeros_like(v[...,2:3])]),
|
||||
-shift if keepdims else 0,axis=-1)[...,:3 if keepdims else 2]
|
||||
|
||||
def project_equal_area(vector,direction='z',normalize=True,keepdims=False):
|
||||
def project_equal_area(vector: np.ndarray,
|
||||
direction: Literal['x', 'y', 'z'] = 'z',
|
||||
normalize: bool = True,
|
||||
keepdims: bool = False) -> np.ndarray:
|
||||
"""
|
||||
Apply equal-area projection to vector.
|
||||
|
||||
|
|
@ -317,9 +340,8 @@ def project_equal_area(vector,direction='z',normalize=True,keepdims=False):
|
|||
----------
|
||||
vector : numpy.ndarray, shape (...,3)
|
||||
Vector coordinates to be projected.
|
||||
direction : str
|
||||
Projection direction 'x', 'y', or 'z'.
|
||||
Defaults to 'z'.
|
||||
direction : {'x', 'y', 'z'}
|
||||
Projection direction. Defaults to 'z'.
|
||||
normalize : bool
|
||||
Ensure unit length of input vector. Defaults to True.
|
||||
keepdims : bool
|
||||
|
|
@ -351,15 +373,14 @@ def project_equal_area(vector,direction='z',normalize=True,keepdims=False):
|
|||
return np.roll(np.block([v[...,:2]/np.sqrt(1.0+np.abs(v[...,2:3])),np.zeros_like(v[...,2:3])]),
|
||||
-shift if keepdims else 0,axis=-1)[...,:3 if keepdims else 2]
|
||||
|
||||
|
||||
def execution_stamp(class_name,function_name=None):
|
||||
def execution_stamp(class_name: str, function_name: str = None) -> str:
|
||||
"""Timestamp the execution of a (function within a) class."""
|
||||
now = datetime.datetime.now().astimezone().strftime('%Y-%m-%d %H:%M:%S%z')
|
||||
_function_name = '' if function_name is None else f'.{function_name}'
|
||||
return f'damask.{class_name}{_function_name} v{version} ({now})'
|
||||
|
||||
|
||||
def hybrid_IA(dist,N,rng_seed=None):
|
||||
def hybrid_IA(dist: np.ndarray, N: int, rng_seed = None) -> np.ndarray:
|
||||
"""
|
||||
Hybrid integer approximation.
|
||||
|
||||
|
|
@ -387,7 +408,10 @@ def hybrid_IA(dist,N,rng_seed=None):
|
|||
return np.repeat(np.arange(len(dist)),repeats)[np.random.default_rng(rng_seed).permutation(N_inv_samples)[:N]]
|
||||
|
||||
|
||||
def shapeshifter(fro,to,mode='left',keep_ones=False):
|
||||
def shapeshifter(fro: Tuple[int, ...],
|
||||
to: Tuple[int, ...],
|
||||
mode: Literal['left','right'] = 'left',
|
||||
keep_ones: bool = False) -> Tuple[Optional[int], ...]:
|
||||
"""
|
||||
Return dimensions that reshape 'fro' to become broadcastable to 'to'.
|
||||
|
||||
|
|
@ -398,9 +422,9 @@ def shapeshifter(fro,to,mode='left',keep_ones=False):
|
|||
to : tuple
|
||||
Target shape of array after broadcasting.
|
||||
len(to) cannot be less than len(fro).
|
||||
mode : str, optional
|
||||
mode : {'left', 'right'}, optional
|
||||
Indicates whether new axes are preferably added to
|
||||
either 'left' or 'right' of the original shape.
|
||||
either left or right of the original shape.
|
||||
Defaults to 'left'.
|
||||
keep_ones : bool, optional
|
||||
Treat '1' in fro as literal value instead of dimensional placeholder.
|
||||
|
|
@ -434,21 +458,22 @@ def shapeshifter(fro,to,mode='left',keep_ones=False):
|
|||
fro = (1,) if not len(fro) else fro
|
||||
to = (1,) if not len(to) else to
|
||||
try:
|
||||
grp = re.match(beg[mode]
|
||||
match = re.match(beg[mode]
|
||||
+f',{sep[mode]}'.join(map(lambda x: f'{x}'
|
||||
if x>1 or (keep_ones and len(fro)>1) else
|
||||
'\\d+',fro))
|
||||
+f',{end[mode]}',
|
||||
','.join(map(str,to))+',').groups()
|
||||
except AttributeError:
|
||||
+f',{end[mode]}',','.join(map(str,to))+',')
|
||||
assert match
|
||||
grp = match.groups()
|
||||
except AssertionError:
|
||||
raise ValueError(f'Shapes can not be shifted {fro} --> {to}')
|
||||
fill = ()
|
||||
fill: Tuple[Optional[int], ...] = ()
|
||||
for g,d in zip(grp,fro+(None,)):
|
||||
fill += (1,)*g.count(',')+(d,)
|
||||
return fill[:-1]
|
||||
|
||||
|
||||
def shapeblender(a,b):
|
||||
def shapeblender(a: Tuple[int, ...], b: Tuple[int, ...]) -> Tuple[int, ...]:
|
||||
"""
|
||||
Return a shape that overlaps the rightmost entries of 'a' with the leftmost of 'b'.
|
||||
|
||||
|
|
@ -476,7 +501,7 @@ def shapeblender(a,b):
|
|||
return a + b[i:]
|
||||
|
||||
|
||||
def extend_docstring(extra_docstring):
|
||||
def extend_docstring(extra_docstring: str) -> Callable:
|
||||
"""
|
||||
Decorator: Append to function's docstring.
|
||||
|
||||
|
|
@ -492,7 +517,7 @@ def extend_docstring(extra_docstring):
|
|||
return _decorator
|
||||
|
||||
|
||||
def extended_docstring(f,extra_docstring):
|
||||
def extended_docstring(f: Callable, extra_docstring: str) -> Callable:
|
||||
"""
|
||||
Decorator: Combine another function's docstring with a given docstring.
|
||||
|
||||
|
|
@ -510,7 +535,7 @@ def extended_docstring(f,extra_docstring):
|
|||
return _decorator
|
||||
|
||||
|
||||
def DREAM3D_base_group(fname):
|
||||
def DREAM3D_base_group(fname: Union[str, Path]) -> str:
|
||||
"""
|
||||
Determine the base group of a DREAM.3D file.
|
||||
|
||||
|
|
@ -536,7 +561,7 @@ def DREAM3D_base_group(fname):
|
|||
|
||||
return base_group
|
||||
|
||||
def DREAM3D_cell_data_group(fname):
|
||||
def DREAM3D_cell_data_group(fname: Union[str, Path]) -> str:
|
||||
"""
|
||||
Determine the cell data group of a DREAM.3D file.
|
||||
|
||||
|
|
@ -568,18 +593,18 @@ def DREAM3D_cell_data_group(fname):
|
|||
return cell_data_group
|
||||
|
||||
|
||||
def Bravais_to_Miller(*,uvtw=None,hkil=None):
|
||||
def Bravais_to_Miller(*, uvtw: np.ndarray = None, hkil: np.ndarray = None) -> np.ndarray:
|
||||
"""
|
||||
Transform 4 Miller–Bravais indices to 3 Miller indices of crystal direction [uvw] or plane normal (hkl).
|
||||
|
||||
Parameters
|
||||
----------
|
||||
uvtw|hkil : numpy.ndarray of shape (...,4)
|
||||
uvtw|hkil : numpy.ndarray, shape (...,4)
|
||||
Miller–Bravais indices of crystallographic direction [uvtw] or plane normal (hkil).
|
||||
|
||||
Returns
|
||||
-------
|
||||
uvw|hkl : numpy.ndarray of shape (...,3)
|
||||
uvw|hkl : numpy.ndarray, shape (...,3)
|
||||
Miller indices of [uvw] direction or (hkl) plane normal.
|
||||
|
||||
"""
|
||||
|
|
@ -595,18 +620,18 @@ def Bravais_to_Miller(*,uvtw=None,hkil=None):
|
|||
return np.einsum('il,...l',basis,axis)
|
||||
|
||||
|
||||
def Miller_to_Bravais(*,uvw=None,hkl=None):
|
||||
def Miller_to_Bravais(*, uvw: np.ndarray = None, hkl: np.ndarray = None) -> np.ndarray:
|
||||
"""
|
||||
Transform 3 Miller indices to 4 Miller–Bravais indices of crystal direction [uvtw] or plane normal (hkil).
|
||||
|
||||
Parameters
|
||||
----------
|
||||
uvw|hkl : numpy.ndarray of shape (...,3)
|
||||
uvw|hkl : numpy.ndarray, shape (...,3)
|
||||
Miller indices of crystallographic direction [uvw] or plane normal (hkl).
|
||||
|
||||
Returns
|
||||
-------
|
||||
uvtw|hkil : numpy.ndarray of shape (...,4)
|
||||
uvtw|hkil : numpy.ndarray, shape (...,4)
|
||||
Miller–Bravais indices of [uvtw] direction or (hkil) plane normal.
|
||||
|
||||
"""
|
||||
|
|
@ -624,7 +649,7 @@ def Miller_to_Bravais(*,uvw=None,hkl=None):
|
|||
return np.einsum('il,...l',basis,axis)
|
||||
|
||||
|
||||
def dict_prune(d):
|
||||
def dict_prune(d: Dict) -> Dict:
|
||||
"""
|
||||
Recursively remove empty dictionaries.
|
||||
|
||||
|
|
@ -650,7 +675,7 @@ def dict_prune(d):
|
|||
return new
|
||||
|
||||
|
||||
def dict_flatten(d):
|
||||
def dict_flatten(d: Dict) -> Dict:
|
||||
"""
|
||||
Recursively remove keys of single-entry dictionaries.
|
||||
|
||||
|
|
@ -678,14 +703,14 @@ def dict_flatten(d):
|
|||
####################################################################################################
|
||||
# Classes
|
||||
####################################################################################################
|
||||
class _ProgressBar:
|
||||
class ProgressBar:
|
||||
"""
|
||||
Report progress of an interation as a status bar.
|
||||
|
||||
Works for 0-based loops, ETA is estimated by linear extrapolation.
|
||||
"""
|
||||
|
||||
def __init__(self,total,prefix,bar_length):
|
||||
def __init__(self, total: int, prefix: str, bar_length: int):
|
||||
"""
|
||||
Set current time as basis for ETA estimation.
|
||||
|
||||
|
|
@ -708,7 +733,7 @@ class _ProgressBar:
|
|||
sys.stderr.write(f"{self.prefix} {'░'*self.bar_length} 0% ETA n/a")
|
||||
sys.stderr.flush()
|
||||
|
||||
def update(self,iteration):
|
||||
def update(self, iteration: int) -> None:
|
||||
|
||||
fraction = (iteration+1) / self.total
|
||||
filled_length = int(self.bar_length * fraction)
|
||||
|
|
|
|||
|
|
@ -81,6 +81,7 @@ class TestColormap:
|
|||
assert Colormap.from_predefined('strain') == Colormap.from_predefined('strain')
|
||||
assert Colormap.from_predefined('strain') != Colormap.from_predefined('stress')
|
||||
assert Colormap.from_predefined('strain',N=128) != Colormap.from_predefined('strain',N=64)
|
||||
assert not Colormap.from_predefined('strain',N=128) == 1
|
||||
|
||||
@pytest.mark.parametrize('low,high',[((0,0,0),(1,1,1)),
|
||||
([0,0,0],[1,1,1])])
|
||||
|
|
|
|||
|
|
@ -40,6 +40,9 @@ class TestCrystal:
|
|||
alpha=alpha,beta=beta,gamma=gamma)
|
||||
assert np.allclose(np.eye(3),np.einsum('ik,jk',c.basis_real,c.basis_reciprocal))
|
||||
|
||||
def test_basis_invalid(self):
|
||||
with pytest.raises(KeyError):
|
||||
Crystal(family='cubic').basis_real
|
||||
|
||||
@pytest.mark.parametrize('keyFrame,keyLattice',[('uvw','direction'),('hkl','plane'),])
|
||||
@pytest.mark.parametrize('vector',np.array([
|
||||
|
|
|
|||
|
|
@ -44,6 +44,7 @@ class TestGrid:
|
|||
|
||||
def test_equal(self,default):
|
||||
assert default == default
|
||||
assert not default == 42
|
||||
|
||||
def test_repr(self,default):
|
||||
print(default)
|
||||
|
|
|
|||
|
|
@ -364,6 +364,11 @@ class TestOrientation:
|
|||
table.save(reference)
|
||||
assert np.allclose(P,Table.load(reference).get('Schmid'))
|
||||
|
||||
def test_Schmid_invalid(self):
|
||||
with pytest.raises(KeyError):
|
||||
Orientation(lattice='fcc').Schmid()
|
||||
|
||||
|
||||
### vectorization tests ###
|
||||
|
||||
@pytest.mark.parametrize('lattice',['hP','cI','cF']) # tI not included yet
|
||||
|
|
@ -505,3 +510,7 @@ class TestOrientation:
|
|||
for loc in np.random.randint(0,blend,(10,len(blend))):
|
||||
assert np.allclose(o[tuple(loc[:len(o.shape)])].to_pole(uvw=v[tuple(loc[-len(v.shape[:-1]):])]),
|
||||
o.to_pole(uvw=v)[tuple(loc)])
|
||||
|
||||
def test_mul_invalid(self):
|
||||
with pytest.raises(TypeError):
|
||||
Orientation.from_random(lattice='cF')*np.ones(3)
|
||||
|
|
|
|||
|
|
@ -102,6 +102,9 @@ class TestResult:
|
|||
with pytest.raises(AttributeError):
|
||||
default.view('invalid',True)
|
||||
|
||||
def test_add_invalid(self,default):
|
||||
default.add_absolute('xxxx')
|
||||
|
||||
def test_add_absolute(self,default):
|
||||
default.add_absolute('F_e')
|
||||
in_memory = np.abs(default.place('F_e'))
|
||||
|
|
|
|||
|
|
@ -792,6 +792,11 @@ class TestRotation:
|
|||
R = Rotation.from_random(shape,rng_seed=1)
|
||||
assert R == R if shape is None else (R == R).all()
|
||||
|
||||
@pytest.mark.parametrize('shape',[None,5,(4,6)])
|
||||
def test_allclose(self,shape):
|
||||
R = Rotation.from_random(shape,rng_seed=1)
|
||||
assert R.allclose(R)
|
||||
|
||||
@pytest.mark.parametrize('shape',[None,5,(4,6)])
|
||||
def test_unequal(self,shape):
|
||||
R = Rotation.from_random(shape,rng_seed=1)
|
||||
|
|
@ -1124,3 +1129,7 @@ class TestRotation:
|
|||
weights_r = np.histogramdd(Eulers_r,steps,rng)[0].flatten(order='F')/N * np.sum(weights)
|
||||
|
||||
assert np.sqrt(((weights_r - weights) ** 2).mean()) < 5
|
||||
|
||||
def test_mul_invalid(self):
|
||||
with pytest.raises(TypeError):
|
||||
Rotation.from_random()*np.ones(3)
|
||||
|
|
|
|||
|
|
@ -28,6 +28,10 @@ class TestVTK:
|
|||
def _patch_execution_stamp(self, patch_execution_stamp):
|
||||
print('patched damask.util.execution_stamp')
|
||||
|
||||
def test_show(sef,default,monkeypatch):
|
||||
monkeypatch.delenv('DISPLAY',raising=False)
|
||||
default.show()
|
||||
|
||||
def test_rectilinearGrid(self,tmp_path):
|
||||
cells = np.random.randint(5,10,3)*2
|
||||
size = np.random.random(3) + 1.0
|
||||
|
|
|
|||
|
|
@ -62,6 +62,8 @@ module YAML_types
|
|||
tNode_get_byKey_as1dString => tNode_get_byKey_as1dString
|
||||
procedure :: &
|
||||
getKey => tNode_get_byIndex_asKey
|
||||
procedure :: &
|
||||
Keys => tNode_getKeys
|
||||
procedure :: &
|
||||
getIndex => tNode_get_byKey_asIndex
|
||||
procedure :: &
|
||||
|
|
@ -117,7 +119,7 @@ module YAML_types
|
|||
|
||||
type, extends(tNode), public :: tList
|
||||
|
||||
class(tItem), pointer :: first => null()
|
||||
class(tItem), pointer :: first => NULL()
|
||||
|
||||
contains
|
||||
procedure :: asFormattedString => tList_asFormattedString
|
||||
|
|
@ -144,8 +146,8 @@ module YAML_types
|
|||
|
||||
type :: tItem
|
||||
character(len=:), allocatable :: key
|
||||
class(tNode), pointer :: node => null()
|
||||
class(tItem), pointer :: next => null()
|
||||
class(tNode), pointer :: node => NULL()
|
||||
class(tItem), pointer :: next => NULL()
|
||||
|
||||
contains
|
||||
final :: tItem_finalize
|
||||
|
|
@ -332,9 +334,12 @@ function tNode_asScalar(self) result(scalar)
|
|||
class(tNode), intent(in), target :: self
|
||||
class(tScalar), pointer :: scalar
|
||||
|
||||
|
||||
select type(self)
|
||||
class is(tScalar)
|
||||
scalar => self
|
||||
class default
|
||||
nullify(scalar)
|
||||
end select
|
||||
|
||||
end function tNode_asScalar
|
||||
|
|
@ -348,9 +353,12 @@ function tNode_asList(self) result(list)
|
|||
class(tNode), intent(in), target :: self
|
||||
class(tList), pointer :: list
|
||||
|
||||
|
||||
select type(self)
|
||||
class is(tList)
|
||||
list => self
|
||||
class default
|
||||
nullify(list)
|
||||
end select
|
||||
|
||||
end function tNode_asList
|
||||
|
|
@ -364,9 +372,12 @@ function tNode_asDict(self) result(dict)
|
|||
class(tNode), intent(in), target :: self
|
||||
class(tDict), pointer :: dict
|
||||
|
||||
|
||||
select type(self)
|
||||
class is(tDict)
|
||||
dict => self
|
||||
class default
|
||||
nullify(dict)
|
||||
end select
|
||||
|
||||
end function tNode_asDict
|
||||
|
|
@ -385,6 +396,7 @@ function tNode_get_byIndex(self,i) result(node)
|
|||
class(tItem), pointer :: item
|
||||
integer :: j
|
||||
|
||||
|
||||
select type(self)
|
||||
class is(tList)
|
||||
self_ => self%asList()
|
||||
|
|
@ -409,15 +421,14 @@ end function tNode_get_byIndex
|
|||
!--------------------------------------------------------------------------------------------------
|
||||
function tNode_get_byIndex_asFloat(self,i) result(nodeAsFloat)
|
||||
|
||||
class(tNode), intent(in), target :: self
|
||||
class(tNode), intent(in) :: self
|
||||
integer, intent(in) :: i
|
||||
real(pReal) :: nodeAsFloat
|
||||
|
||||
class(tNode), pointer :: node
|
||||
type(tScalar), pointer :: scalar
|
||||
|
||||
node => self%get(i)
|
||||
select type(node)
|
||||
|
||||
select type(node => self%get(i))
|
||||
class is(tScalar)
|
||||
scalar => node%asScalar()
|
||||
nodeAsFloat = scalar%asFloat()
|
||||
|
|
@ -433,15 +444,15 @@ end function tNode_get_byIndex_asFloat
|
|||
!--------------------------------------------------------------------------------------------------
|
||||
function tNode_get_byIndex_asInt(self,i) result(nodeAsInt)
|
||||
|
||||
class(tNode), intent(in), target :: self
|
||||
class(tNode), intent(in) :: self
|
||||
integer, intent(in) :: i
|
||||
integer :: nodeAsInt
|
||||
|
||||
class(tNode), pointer :: node
|
||||
type(tScalar), pointer :: scalar
|
||||
|
||||
node => self%get(i)
|
||||
select type(node)
|
||||
|
||||
select type(node => self%get(i))
|
||||
class is(tScalar)
|
||||
scalar => node%asScalar()
|
||||
nodeAsInt = scalar%asInt()
|
||||
|
|
@ -457,15 +468,14 @@ end function tNode_get_byIndex_asInt
|
|||
!--------------------------------------------------------------------------------------------------
|
||||
function tNode_get_byIndex_asBool(self,i) result(nodeAsBool)
|
||||
|
||||
class(tNode), intent(in), target :: self
|
||||
class(tNode), intent(in) :: self
|
||||
integer, intent(in) :: i
|
||||
logical :: nodeAsBool
|
||||
|
||||
class(tNode), pointer :: node
|
||||
type(tScalar), pointer :: scalar
|
||||
|
||||
node => self%get(i)
|
||||
select type(node)
|
||||
|
||||
select type(node => self%get(i))
|
||||
class is(tScalar)
|
||||
scalar => node%asScalar()
|
||||
nodeAsBool = scalar%asBool()
|
||||
|
|
@ -481,15 +491,14 @@ end function tNode_get_byIndex_asBool
|
|||
!--------------------------------------------------------------------------------------------------
|
||||
function tNode_get_byIndex_asString(self,i) result(nodeAsString)
|
||||
|
||||
class(tNode), intent(in), target :: self
|
||||
class(tNode), intent(in) :: self
|
||||
integer, intent(in) :: i
|
||||
character(len=:), allocatable :: nodeAsString
|
||||
|
||||
class(tNode), pointer :: node
|
||||
type(tScalar), pointer :: scalar
|
||||
|
||||
node => self%get(i)
|
||||
select type(node)
|
||||
|
||||
select type(node => self%get(i))
|
||||
class is(tScalar)
|
||||
scalar => node%asScalar()
|
||||
nodeAsString = scalar%asString()
|
||||
|
|
@ -505,15 +514,14 @@ end function tNode_get_byIndex_asString
|
|||
!--------------------------------------------------------------------------------------------------
|
||||
function tNode_get_byIndex_as1dFloat(self,i) result(nodeAs1dFloat)
|
||||
|
||||
class(tNode), intent(in), target :: self
|
||||
class(tNode), intent(in) :: self
|
||||
integer, intent(in) :: i
|
||||
real(pReal), dimension(:), allocatable :: nodeAs1dFloat
|
||||
|
||||
class(tNode), pointer :: node
|
||||
class(tList), pointer :: list
|
||||
|
||||
node => self%get(i)
|
||||
select type(node)
|
||||
|
||||
select type(node => self%get(i))
|
||||
class is(tList)
|
||||
list => node%asList()
|
||||
nodeAs1dFloat = list%as1dFloat()
|
||||
|
|
@ -529,15 +537,14 @@ end function tNode_get_byIndex_as1dFloat
|
|||
!--------------------------------------------------------------------------------------------------
|
||||
function tNode_get_byIndex_as1dInt(self,i) result(nodeAs1dInt)
|
||||
|
||||
class(tNode), intent(in), target :: self
|
||||
class(tNode), intent(in) :: self
|
||||
integer, intent(in) :: i
|
||||
integer, dimension(:), allocatable :: nodeAs1dInt
|
||||
|
||||
class(tNode), pointer :: node
|
||||
class(tList), pointer :: list
|
||||
|
||||
node => self%get(i)
|
||||
select type(node)
|
||||
|
||||
select type(node => self%get(i))
|
||||
class is(tList)
|
||||
list => node%asList()
|
||||
nodeAs1dInt = list%as1dInt()
|
||||
|
|
@ -553,15 +560,14 @@ end function tNode_get_byIndex_as1dInt
|
|||
!--------------------------------------------------------------------------------------------------
|
||||
function tNode_get_byIndex_as1dBool(self,i) result(nodeAs1dBool)
|
||||
|
||||
class(tNode), intent(in), target :: self
|
||||
class(tNode), intent(in) :: self
|
||||
integer, intent(in) :: i
|
||||
logical, dimension(:), allocatable :: nodeAs1dBool
|
||||
|
||||
class(tNode), pointer :: node
|
||||
class(tList), pointer :: list
|
||||
|
||||
node => self%get(i)
|
||||
select type(node)
|
||||
|
||||
select type(node => self%get(i))
|
||||
class is(tList)
|
||||
list => node%asList()
|
||||
nodeAs1dBool = list%as1dBool()
|
||||
|
|
@ -577,15 +583,14 @@ end function tNode_get_byIndex_as1dBool
|
|||
!--------------------------------------------------------------------------------------------------
|
||||
function tNode_get_byIndex_as1dString(self,i) result(nodeAs1dString)
|
||||
|
||||
class(tNode), intent(in), target :: self
|
||||
class(tNode), intent(in) :: self
|
||||
integer, intent(in) :: i
|
||||
character(len=:), allocatable, dimension(:) :: nodeAs1dString
|
||||
|
||||
class(tNode), pointer :: node
|
||||
type(tList), pointer :: list
|
||||
|
||||
node => self%get(i)
|
||||
select type(node)
|
||||
|
||||
select type(node => self%get(i))
|
||||
class is(tList)
|
||||
list => node%asList()
|
||||
nodeAs1dString = list%as1dString()
|
||||
|
|
@ -609,6 +614,7 @@ function tNode_get_byIndex_asKey(self,i) result(key)
|
|||
type(tDict), pointer :: dict
|
||||
type(tItem), pointer :: item
|
||||
|
||||
|
||||
select type(self)
|
||||
class is(tDict)
|
||||
dict => self%asDict()
|
||||
|
|
@ -625,6 +631,33 @@ function tNode_get_byIndex_asKey(self,i) result(key)
|
|||
end function tNode_get_byIndex_asKey
|
||||
|
||||
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
!> @brief Get all keys from a dictionary
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
function tNode_getKeys(self) result(keys)
|
||||
|
||||
class(tNode), intent(in) :: self
|
||||
character(len=:), dimension(:), allocatable :: keys
|
||||
|
||||
character(len=pStringLen), dimension(:), allocatable :: temp
|
||||
integer :: j, l
|
||||
|
||||
|
||||
allocate(temp(self%length))
|
||||
l = 0
|
||||
do j = 1, self%length
|
||||
temp(j) = self%getKey(j)
|
||||
l = max(len_trim(temp(j)),l)
|
||||
end do
|
||||
|
||||
allocate(character(l)::keys(self%length))
|
||||
do j = 1, self%length
|
||||
keys(j) = trim(temp(j))
|
||||
end do
|
||||
|
||||
end function tNode_getKeys
|
||||
|
||||
|
||||
!-------------------------------------------------------------------------------------------------
|
||||
!> @brief Checks if a given key/item is present in the dict/list
|
||||
!-------------------------------------------------------------------------------------------------
|
||||
|
|
@ -713,17 +746,16 @@ end function tNode_get_byKey
|
|||
!--------------------------------------------------------------------------------------------------
|
||||
function tNode_get_byKey_asFloat(self,k,defaultVal) result(nodeAsFloat)
|
||||
|
||||
class(tNode), intent(in), target :: self
|
||||
class(tNode), intent(in) :: self
|
||||
character(len=*), intent(in) :: k
|
||||
real(pReal), intent(in), optional :: defaultVal
|
||||
real(pReal) :: nodeAsFloat
|
||||
|
||||
class(tNode), pointer :: node
|
||||
type(tScalar), pointer :: scalar
|
||||
|
||||
|
||||
if (self%contains(k)) then
|
||||
node => self%get(k)
|
||||
select type(node)
|
||||
select type(node => self%get(k))
|
||||
class is(tScalar)
|
||||
scalar => node%asScalar()
|
||||
nodeAsFloat = scalar%asFloat()
|
||||
|
|
@ -744,17 +776,16 @@ end function tNode_get_byKey_asFloat
|
|||
!--------------------------------------------------------------------------------------------------
|
||||
function tNode_get_byKey_asInt(self,k,defaultVal) result(nodeAsInt)
|
||||
|
||||
class(tNode), intent(in), target :: self
|
||||
class(tNode), intent(in) :: self
|
||||
character(len=*), intent(in) :: k
|
||||
integer, intent(in), optional :: defaultVal
|
||||
integer :: nodeAsInt
|
||||
|
||||
class(tNode), pointer :: node
|
||||
type(tScalar), pointer :: scalar
|
||||
|
||||
|
||||
if (self%contains(k)) then
|
||||
node => self%get(k)
|
||||
select type(node)
|
||||
select type(node => self%get(k))
|
||||
class is(tScalar)
|
||||
scalar => node%asScalar()
|
||||
nodeAsInt = scalar%asInt()
|
||||
|
|
@ -775,17 +806,16 @@ end function tNode_get_byKey_asInt
|
|||
!--------------------------------------------------------------------------------------------------
|
||||
function tNode_get_byKey_asBool(self,k,defaultVal) result(nodeAsBool)
|
||||
|
||||
class(tNode), intent(in), target :: self
|
||||
class(tNode), intent(in) :: self
|
||||
character(len=*), intent(in) :: k
|
||||
logical, intent(in), optional :: defaultVal
|
||||
logical :: nodeAsBool
|
||||
|
||||
class(tNode), pointer :: node
|
||||
type(tScalar), pointer :: scalar
|
||||
|
||||
|
||||
if (self%contains(k)) then
|
||||
node => self%get(k)
|
||||
select type(node)
|
||||
select type(node => self%get(k))
|
||||
class is(tScalar)
|
||||
scalar => node%asScalar()
|
||||
nodeAsBool = scalar%asBool()
|
||||
|
|
@ -806,17 +836,16 @@ end function tNode_get_byKey_asBool
|
|||
!--------------------------------------------------------------------------------------------------
|
||||
function tNode_get_byKey_asString(self,k,defaultVal) result(nodeAsString)
|
||||
|
||||
class(tNode), intent(in), target :: self
|
||||
class(tNode), intent(in) :: self
|
||||
character(len=*), intent(in) :: k
|
||||
character(len=*), intent(in), optional :: defaultVal
|
||||
character(len=:), allocatable :: nodeAsString
|
||||
|
||||
class(tNode), pointer :: node
|
||||
type(tScalar), pointer :: scalar
|
||||
|
||||
|
||||
if (self%contains(k)) then
|
||||
node => self%get(k)
|
||||
select type(node)
|
||||
select type(node => self%get(k))
|
||||
class is(tScalar)
|
||||
scalar => node%asScalar()
|
||||
nodeAsString = scalar%asString()
|
||||
|
|
@ -837,19 +866,18 @@ end function tNode_get_byKey_asString
|
|||
!--------------------------------------------------------------------------------------------------
|
||||
function tNode_get_byKey_as1dFloat(self,k,defaultVal,requiredSize) result(nodeAs1dFloat)
|
||||
|
||||
class(tNode), intent(in), target :: self
|
||||
class(tNode), intent(in) :: self
|
||||
character(len=*), intent(in) :: k
|
||||
real(pReal), intent(in), dimension(:), optional :: defaultVal
|
||||
integer, intent(in), optional :: requiredSize
|
||||
|
||||
real(pReal), dimension(:), allocatable :: nodeAs1dFloat
|
||||
|
||||
class(tNode), pointer :: node
|
||||
type(tList), pointer :: list
|
||||
|
||||
|
||||
if (self%contains(k)) then
|
||||
node => self%get(k)
|
||||
select type(node)
|
||||
select type(node => self%get(k))
|
||||
class is(tList)
|
||||
list => node%asList()
|
||||
nodeAs1dFloat = list%as1dFloat()
|
||||
|
|
@ -874,19 +902,18 @@ end function tNode_get_byKey_as1dFloat
|
|||
!--------------------------------------------------------------------------------------------------
|
||||
function tNode_get_byKey_as2dFloat(self,k,defaultVal,requiredShape) result(nodeAs2dFloat)
|
||||
|
||||
class(tNode), intent(in), target :: self
|
||||
class(tNode), intent(in) :: self
|
||||
character(len=*), intent(in) :: k
|
||||
real(pReal), intent(in), dimension(:,:), optional :: defaultVal
|
||||
integer, intent(in), dimension(2), optional :: requiredShape
|
||||
|
||||
real(pReal), dimension(:,:), allocatable :: nodeAs2dFloat
|
||||
|
||||
class(tNode), pointer :: node
|
||||
type(tList), pointer :: rows
|
||||
|
||||
|
||||
if(self%contains(k)) then
|
||||
node => self%get(k)
|
||||
select type(node)
|
||||
select type(node => self%get(k))
|
||||
class is(tList)
|
||||
rows => node%asList()
|
||||
nodeAs2dFloat = rows%as2dFloat()
|
||||
|
|
@ -911,18 +938,16 @@ end function tNode_get_byKey_as2dFloat
|
|||
!--------------------------------------------------------------------------------------------------
|
||||
function tNode_get_byKey_as1dInt(self,k,defaultVal,requiredSize) result(nodeAs1dInt)
|
||||
|
||||
class(tNode), intent(in), target :: self
|
||||
class(tNode), intent(in) :: self
|
||||
character(len=*), intent(in) :: k
|
||||
integer, dimension(:), intent(in), optional :: defaultVal
|
||||
integer, intent(in), optional :: requiredSize
|
||||
integer, dimension(:), allocatable :: nodeAs1dInt
|
||||
|
||||
class(tNode), pointer :: node
|
||||
type(tList), pointer :: list
|
||||
|
||||
if (self%contains(k)) then
|
||||
node => self%get(k)
|
||||
select type(node)
|
||||
select type(node => self%get(k))
|
||||
class is(tList)
|
||||
list => node%asList()
|
||||
nodeAs1dInt = list%as1dInt()
|
||||
|
|
@ -947,17 +972,16 @@ end function tNode_get_byKey_as1dInt
|
|||
!--------------------------------------------------------------------------------------------------
|
||||
function tNode_get_byKey_as1dBool(self,k,defaultVal) result(nodeAs1dBool)
|
||||
|
||||
class(tNode), intent(in), target :: self
|
||||
class(tNode), intent(in) :: self
|
||||
character(len=*), intent(in) :: k
|
||||
logical, dimension(:), intent(in), optional :: defaultVal
|
||||
logical, dimension(:), allocatable :: nodeAs1dBool
|
||||
|
||||
class(tNode), pointer :: node
|
||||
type(tList), pointer :: list
|
||||
|
||||
|
||||
if (self%contains(k)) then
|
||||
node => self%get(k)
|
||||
select type(node)
|
||||
select type(node => self%get(k))
|
||||
class is(tList)
|
||||
list => node%asList()
|
||||
nodeAs1dBool = list%as1dBool()
|
||||
|
|
@ -978,17 +1002,16 @@ end function tNode_get_byKey_as1dBool
|
|||
!--------------------------------------------------------------------------------------------------
|
||||
function tNode_get_byKey_as1dString(self,k,defaultVal) result(nodeAs1dString)
|
||||
|
||||
class(tNode), intent(in), target :: self
|
||||
class(tNode), intent(in) :: self
|
||||
character(len=*), intent(in) :: k
|
||||
character(len=*), intent(in), dimension(:), optional :: defaultVal
|
||||
character(len=:), allocatable, dimension(:) :: nodeAs1dString
|
||||
|
||||
class(tNode), pointer :: node
|
||||
type(tList), pointer :: list
|
||||
|
||||
|
||||
if (self%contains(k)) then
|
||||
node => self%get(k)
|
||||
select type(node)
|
||||
select type(node => self%get(k))
|
||||
class is(tList)
|
||||
list => node%asList()
|
||||
nodeAs1dString = list%as1dString()
|
||||
|
|
@ -1190,6 +1213,7 @@ function tList_as1dFloat(self)
|
|||
type(tItem), pointer :: item
|
||||
type(tScalar), pointer :: scalar
|
||||
|
||||
|
||||
allocate(tList_as1dFloat(self%length))
|
||||
item => self%first
|
||||
do i = 1, self%length
|
||||
|
|
@ -1213,6 +1237,7 @@ function tList_as2dFloat(self)
|
|||
class(tNode), pointer :: row
|
||||
type(tList), pointer :: row_data
|
||||
|
||||
|
||||
row => self%get(1)
|
||||
row_data => row%asList()
|
||||
allocate(tList_as2dFloat(self%length,row_data%length))
|
||||
|
|
@ -1239,6 +1264,7 @@ function tList_as1dInt(self)
|
|||
type(tItem), pointer :: item
|
||||
type(tScalar), pointer :: scalar
|
||||
|
||||
|
||||
allocate(tList_as1dInt(self%length))
|
||||
item => self%first
|
||||
do i = 1, self%length
|
||||
|
|
@ -1262,6 +1288,7 @@ function tList_as1dBool(self)
|
|||
type(tItem), pointer :: item
|
||||
type(tScalar), pointer :: scalar
|
||||
|
||||
|
||||
allocate(tList_as1dBool(self%length))
|
||||
item => self%first
|
||||
do i = 1, self%length
|
||||
|
|
@ -1285,6 +1312,7 @@ function tList_as1dString(self)
|
|||
type(tItem), pointer :: item
|
||||
type(tScalar), pointer :: scalar
|
||||
|
||||
|
||||
len_max = 0
|
||||
item => self%first
|
||||
do i = 1, self%length
|
||||
|
|
|
|||
|
|
@ -156,7 +156,7 @@ subroutine spectral_utilities_init
|
|||
integer(C_INTPTR_T) :: alloc_local, local_K, local_K_offset
|
||||
integer(C_INTPTR_T), parameter :: &
|
||||
scalarSize = 1_C_INTPTR_T, &
|
||||
vecSize = 3_C_INTPTR_T, &
|
||||
vectorSize = 3_C_INTPTR_T, &
|
||||
tensorSize = 9_C_INTPTR_T
|
||||
character(len=*), parameter :: &
|
||||
PETSCDEBUG = ' -snes_view -snes_monitor '
|
||||
|
|
@ -274,7 +274,7 @@ subroutine spectral_utilities_init
|
|||
call c_f_pointer(tensorField, tensorField_fourier, [3_C_INTPTR_T,3_C_INTPTR_T, &
|
||||
gridFFTW(1)/2_C_INTPTR_T + 1_C_INTPTR_T , gridFFTW(2),local_K]) ! place a pointer for a fourier tensor representation
|
||||
|
||||
vectorField = fftw_alloc_complex(vecSize*alloc_local)
|
||||
vectorField = fftw_alloc_complex(vectorSize*alloc_local)
|
||||
call c_f_pointer(vectorField, vectorField_real, [3_C_INTPTR_T,&
|
||||
2_C_INTPTR_T*(gridFFTW(1)/2_C_INTPTR_T + 1_C_INTPTR_T),gridFFTW(2),local_K]) ! place a pointer for a real vector representation
|
||||
call c_f_pointer(vectorField, vectorField_fourier,[3_C_INTPTR_T,&
|
||||
|
|
@ -288,42 +288,42 @@ subroutine spectral_utilities_init
|
|||
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
! tensor MPI fftw plans
|
||||
planTensorForth = fftw_mpi_plan_many_dft_r2c(3, [gridFFTW(3),gridFFTW(2),gridFFTW(1)], & ! dimension, logical length in each dimension in reversed order
|
||||
tensorSize, FFTW_MPI_DEFAULT_BLOCK, FFTW_MPI_DEFAULT_BLOCK, &! no. of transforms, default iblock and oblock
|
||||
tensorField_real, tensorField_fourier, & ! input data, output data
|
||||
PETSC_COMM_WORLD, FFTW_planner_flag) ! use all processors, planer precision
|
||||
planTensorForth = fftw_mpi_plan_many_dft_r2c(3,gridFFTW(3:1:-1),tensorSize, &
|
||||
FFTW_MPI_DEFAULT_BLOCK,FFTW_MPI_DEFAULT_BLOCK, &
|
||||
tensorField_real,tensorField_fourier, &
|
||||
PETSC_COMM_WORLD,FFTW_planner_flag)
|
||||
if (.not. c_associated(planTensorForth)) error stop 'FFTW error'
|
||||
planTensorBack = fftw_mpi_plan_many_dft_c2r(3, [gridFFTW(3),gridFFTW(2),gridFFTW(1)], & ! dimension, logical length in each dimension in reversed order
|
||||
tensorSize, FFTW_MPI_DEFAULT_BLOCK, FFTW_MPI_DEFAULT_BLOCK, &! no. of transforms, default iblock and oblock
|
||||
tensorField_fourier,tensorField_real, & ! input data, output data
|
||||
PETSC_COMM_WORLD, FFTW_planner_flag) ! all processors, planer precision
|
||||
planTensorBack = fftw_mpi_plan_many_dft_c2r(3,gridFFTW(3:1:-1),tensorSize, &
|
||||
FFTW_MPI_DEFAULT_BLOCK, FFTW_MPI_DEFAULT_BLOCK, &
|
||||
tensorField_fourier,tensorField_real, &
|
||||
PETSC_COMM_WORLD, FFTW_planner_flag)
|
||||
if (.not. c_associated(planTensorBack)) error stop 'FFTW error'
|
||||
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
! vector MPI fftw plans
|
||||
planVectorForth = fftw_mpi_plan_many_dft_r2c(3, [gridFFTW(3),gridFFTW(2),gridFFTW(1)], & ! dimension, logical length in each dimension in reversed order
|
||||
vecSize, FFTW_MPI_DEFAULT_BLOCK, FFTW_MPI_DEFAULT_BLOCK,&! no. of transforms, default iblock and oblock
|
||||
vectorField_real, vectorField_fourier, & ! input data, output data
|
||||
PETSC_COMM_WORLD, FFTW_planner_flag) ! use all processors, planer precision
|
||||
if (.not. C_ASSOCIATED(planVectorForth)) error stop 'FFTW error'
|
||||
planVectorBack = fftw_mpi_plan_many_dft_c2r(3, [gridFFTW(3),gridFFTW(2),gridFFTW(1)], & ! dimension, logical length in each dimension in reversed order
|
||||
vecSize, FFTW_MPI_DEFAULT_BLOCK, FFTW_MPI_DEFAULT_BLOCK, & ! no. of transforms, default iblock and oblock
|
||||
vectorField_fourier,vectorField_real, & ! input data, output data
|
||||
PETSC_COMM_WORLD, FFTW_planner_flag) ! all processors, planer precision
|
||||
if (.not. C_ASSOCIATED(planVectorBack)) error stop 'FFTW error'
|
||||
planVectorForth = fftw_mpi_plan_many_dft_r2c(3,gridFFTW(3:1:-1),vectorSize, &
|
||||
FFTW_MPI_DEFAULT_BLOCK,FFTW_MPI_DEFAULT_BLOCK, &
|
||||
vectorField_real,vectorField_fourier, &
|
||||
PETSC_COMM_WORLD,FFTW_planner_flag)
|
||||
if (.not. c_associated(planVectorForth)) error stop 'FFTW error'
|
||||
planVectorBack = fftw_mpi_plan_many_dft_c2r(3,gridFFTW(3:1:-1),vectorSize, &
|
||||
FFTW_MPI_DEFAULT_BLOCK, FFTW_MPI_DEFAULT_BLOCK, &
|
||||
vectorField_fourier,vectorField_real, &
|
||||
PETSC_COMM_WORLD, FFTW_planner_flag)
|
||||
if (.not. c_associated(planVectorBack)) error stop 'FFTW error'
|
||||
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
! scalar MPI fftw plans
|
||||
planScalarForth = fftw_mpi_plan_many_dft_r2c(3, [gridFFTW(3),gridFFTW(2),gridFFTW(1)], & ! dimension, logical length in each dimension in reversed order
|
||||
scalarSize, FFTW_MPI_DEFAULT_BLOCK, FFTW_MPI_DEFAULT_BLOCK, &! no. of transforms, default iblock and oblock
|
||||
scalarField_real, scalarField_fourier, & ! input data, output data
|
||||
PETSC_COMM_WORLD, FFTW_planner_flag) ! use all processors, planer precision
|
||||
if (.not. C_ASSOCIATED(planScalarForth)) error stop 'FFTW error'
|
||||
planScalarBack = fftw_mpi_plan_many_dft_c2r(3, [gridFFTW(3),gridFFTW(2),gridFFTW(1)], & ! dimension, logical length in each dimension in reversed order, no. of transforms
|
||||
scalarSize, FFTW_MPI_DEFAULT_BLOCK, FFTW_MPI_DEFAULT_BLOCK, &! no. of transforms, default iblock and oblock
|
||||
scalarField_fourier,scalarField_real, & ! input data, output data
|
||||
PETSC_COMM_WORLD, FFTW_planner_flag) ! use all processors, planer precision
|
||||
if (.not. C_ASSOCIATED(planScalarBack)) error stop 'FFTW error'
|
||||
planScalarForth = fftw_mpi_plan_many_dft_r2c(3,gridFFTW(3:1:-1),scalarSize, &
|
||||
FFTW_MPI_DEFAULT_BLOCK,FFTW_MPI_DEFAULT_BLOCK, &
|
||||
scalarField_real,scalarField_fourier, &
|
||||
PETSC_COMM_WORLD,FFTW_planner_flag)
|
||||
if (.not. c_associated(planScalarForth)) error stop 'FFTW error'
|
||||
planScalarBack = fftw_mpi_plan_many_dft_c2r(3,gridFFTW(3:1:-1),scalarSize, &
|
||||
FFTW_MPI_DEFAULT_BLOCK, FFTW_MPI_DEFAULT_BLOCK, &
|
||||
scalarField_fourier,scalarField_real, &
|
||||
PETSC_COMM_WORLD, FFTW_planner_flag)
|
||||
if (.not. c_associated(planScalarBack)) error stop 'FFTW error'
|
||||
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
! calculation of discrete angular frequencies, ordered as in FFTW (wrap around)
|
||||
|
|
|
|||
142
src/lattice.f90
142
src/lattice.f90
|
|
@ -587,8 +587,8 @@ function lattice_C66_trans(Ntrans,C_parent66,lattice_target, &
|
|||
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
!> @brief Non-schmid projections for bcc with up to 6 coefficients
|
||||
! Koester et al. 2012, Acta Materialia 60 (2012) 3894–3901, eq. (17)
|
||||
! Gröger et al. 2008, Acta Materialia 56 (2008) 5412–5425, table 1
|
||||
! https://doi.org/10.1016/j.actamat.2012.03.053, eq. (17)
|
||||
! https://doi.org/10.1016/j.actamat.2008.07.037, table 1
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
function lattice_nonSchmidMatrix(Nslip,nonSchmidCoefficients,sense) result(nonSchmidMatrix)
|
||||
|
||||
|
|
@ -602,6 +602,7 @@ function lattice_nonSchmidMatrix(Nslip,nonSchmidCoefficients,sense) result(nonSc
|
|||
type(rotation) :: R
|
||||
integer :: i
|
||||
|
||||
|
||||
if (abs(sense) /= 1) error stop 'Sense in lattice_nonSchmidMatrix'
|
||||
|
||||
coordinateSystem = buildCoordinateSystem(Nslip,BCC_NSLIPSYSTEM,BCC_SYSTEMSLIP,'cI',0.0_pReal)
|
||||
|
|
@ -634,7 +635,9 @@ end function lattice_nonSchmidMatrix
|
|||
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
!> @brief Slip-slip interaction matrix
|
||||
!> details only active slip systems are considered
|
||||
!> @details only active slip systems are considered
|
||||
!> @details https://doi.org/10.1016/j.actamat.2016.12.040 (fcc: Tab S4-1, bcc: Tab S5-1)
|
||||
!> @details https://doi.org/10.1016/j.ijplas.2014.06.010 (hex: Tab 3b)
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
function lattice_interaction_SlipBySlip(Nslip,interactionValues,lattice) result(interactionMatrix)
|
||||
|
||||
|
|
@ -646,6 +649,7 @@ function lattice_interaction_SlipBySlip(Nslip,interactionValues,lattice) result(
|
|||
integer, dimension(:), allocatable :: NslipMax
|
||||
integer, dimension(:,:), allocatable :: interactionTypes
|
||||
|
||||
|
||||
integer, dimension(FCC_NSLIP,FCC_NSLIP), parameter :: &
|
||||
FCC_INTERACTIONSLIPSLIP = reshape( [&
|
||||
1, 2, 2, 4, 7, 5, 3, 5, 5, 4, 6, 7, 10,11,10,11,12,13, & ! -----> acting (forest)
|
||||
|
|
@ -750,41 +754,113 @@ function lattice_interaction_SlipBySlip(Nslip,interactionValues,lattice) result(
|
|||
integer, dimension(HEX_NSLIP,HEX_NSLIP), parameter :: &
|
||||
HEX_INTERACTIONSLIPSLIP = reshape( [&
|
||||
! basal prism 1. pyr<a> 1. pyr<c+a> 2. pyr<c+a>
|
||||
1, 2, 2, 3, 3, 3, 7, 7, 7, 7, 7, 7, 13,13,13,13,13,13,13,13,13,13,13,13, 21,21,21,21,21,21, & ! -----> acting (forest)
|
||||
2, 1, 2, 3, 3, 3, 7, 7, 7, 7, 7, 7, 13,13,13,13,13,13,13,13,13,13,13,13, 21,21,21,21,21,21, & ! | basal
|
||||
2, 2, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 13,13,13,13,13,13,13,13,13,13,13,13, 21,21,21,21,21,21, & ! |
|
||||
1, 2, 2, 3, 4, 4, 9,10, 9, 9,10, 9, 20,21,22,22,21,20,20,21,22,22,21,20, 47,47,48,47,47,48, & ! -----> acting (forest)
|
||||
2, 1, 2, 4, 3, 4, 10, 9, 9,10, 9, 9, 22,22,21,20,20,21,22,22,21,20,20,21, 47,48,47,47,48,47, & ! | basal
|
||||
2, 2, 1, 4, 4, 3, 9, 9,10, 9, 9,10, 21,20,20,21,22,22,21,20,20,21,22,22, 48,47,47,48,47,47, & ! |
|
||||
! v
|
||||
6, 6, 6, 4, 5, 5, 8, 8, 8, 8, 8, 8, 14,14,14,14,14,14,14,14,14,14,14,14, 22,22,22,22,22,22, & ! reacting (primary)
|
||||
6, 6, 6, 5, 4, 5, 8, 8, 8, 8, 8, 8, 14,14,14,14,14,14,14,14,14,14,14,14, 22,22,22,22,22,22, & ! prism
|
||||
6, 6, 6, 5, 5, 4, 8, 8, 8, 8, 8, 8, 14,14,14,14,14,14,14,14,14,14,14,14, 22,22,22,22,22,22, &
|
||||
7, 8, 8, 5, 6, 6, 11,12,11,11,12,11, 23,24,25,25,24,23,23,24,25,25,24,23, 49,49,50,49,49,50, & ! reacting (primary)
|
||||
8, 7, 8, 6, 5, 6, 12,11,11,12,11,11, 25,25,24,23,23,24,25,25,24,23,23,24, 49,50,49,49,50,49, & ! prism
|
||||
8, 8, 7, 6, 6, 5, 11,11,12,11,11,12, 24,23,23,24,25,25,24,23,23,24,25,25, 50,49,49,50,49,49, &
|
||||
|
||||
12,12,12, 11,11,11, 9,10,10,10,10,10, 15,15,15,15,15,15,15,15,15,15,15,15, 23,23,23,23,23,23, &
|
||||
12,12,12, 11,11,11, 10, 9,10,10,10,10, 15,15,15,15,15,15,15,15,15,15,15,15, 23,23,23,23,23,23, &
|
||||
12,12,12, 11,11,11, 10,10, 9,10,10,10, 15,15,15,15,15,15,15,15,15,15,15,15, 23,23,23,23,23,23, &
|
||||
12,12,12, 11,11,11, 10,10,10, 9,10,10, 15,15,15,15,15,15,15,15,15,15,15,15, 23,23,23,23,23,23, & ! 1. pyr<a>
|
||||
12,12,12, 11,11,11, 10,10,10,10, 9,10, 15,15,15,15,15,15,15,15,15,15,15,15, 23,23,23,23,23,23, &
|
||||
12,12,12, 11,11,11, 10,10,10,10,10, 9, 15,15,15,15,15,15,15,15,15,15,15,15, 23,23,23,23,23,23, &
|
||||
18,19,18, 16,17,16, 13,14,14,15,14,14, 26,26,27,28,28,27,29,29,27,28,28,27, 51,52,51,51,52,51, &
|
||||
19,18,18, 17,16,16, 14,13,14,14,15,14, 28,27,26,26,27,28,28,27,29,29,27,28, 51,51,52,51,51,52, &
|
||||
18,18,19, 16,16,17, 14,14,13,14,14,15, 27,28,28,27,26,26,27,28,28,27,29,29, 52,51,51,52,51,51, &
|
||||
18,19,18, 16,17,16, 15,14,14,13,14,14, 29,29,27,28,28,27,26,26,27,28,28,27, 51,52,51,51,52,51, & ! 1. pyr<a>
|
||||
19,18,18, 17,16,16, 14,15,14,14,13,14, 28,27,29,29,27,28,28,27,26,26,27,28, 51,51,52,51,51,52, &
|
||||
18,18,19, 16,16,17, 14,14,15,14,14,13, 27,28,28,27,29,29,27,28,28,27,26,26, 52,51,51,52,51,51, &
|
||||
|
||||
20,20,20, 19,19,19, 18,18,18,18,18,18, 16,17,17,17,17,17,17,17,17,17,17,17, 24,24,24,24,24,24, &
|
||||
20,20,20, 19,19,19, 18,18,18,18,18,18, 17,16,17,17,17,17,17,17,17,17,17,17, 24,24,24,24,24,24, &
|
||||
20,20,20, 19,19,19, 18,18,18,18,18,18, 17,17,16,17,17,17,17,17,17,17,17,17, 24,24,24,24,24,24, &
|
||||
20,20,20, 19,19,19, 18,18,18,18,18,18, 17,17,17,16,17,17,17,17,17,17,17,17, 24,24,24,24,24,24, &
|
||||
20,20,20, 19,19,19, 18,18,18,18,18,18, 17,17,17,17,16,17,17,17,17,17,17,17, 24,24,24,24,24,24, &
|
||||
20,20,20, 19,19,19, 18,18,18,18,18,18, 17,17,17,17,17,16,17,17,17,17,17,17, 24,24,24,24,24,24, &
|
||||
20,20,20, 19,19,19, 18,18,18,18,18,18, 17,17,17,17,17,17,16,17,17,17,17,17, 24,24,24,24,24,24, & ! 1. pyr<c+a>
|
||||
20,20,20, 19,19,19, 18,18,18,18,18,18, 17,17,17,17,17,17,17,16,17,17,17,17, 24,24,24,24,24,24, &
|
||||
20,20,20, 19,19,19, 18,18,18,18,18,18, 17,17,17,17,17,17,17,17,16,17,17,17, 24,24,24,24,24,24, &
|
||||
20,20,20, 19,19,19, 18,18,18,18,18,18, 17,17,17,17,17,17,17,17,17,16,17,17, 24,24,24,24,24,24, &
|
||||
20,20,20, 19,19,19, 18,18,18,18,18,18, 17,17,17,17,17,17,17,17,17,17,16,17, 24,24,24,24,24,24, &
|
||||
20,20,20, 19,19,19, 18,18,18,18,18,18, 17,17,17,17,17,17,17,17,17,17,17,16, 24,24,24,24,24,24, &
|
||||
44,45,46, 41,42,43, 37,38,39,40,38,39, 30,31,32,32,32,33,34,35,32,32,32,36, 53,54,55,53,54,56, &
|
||||
46,45,44, 43,42,41, 37,39,38,40,39,38, 31,30,36,32,32,32,35,34,33,32,32,32, 56,54,53,55,54,53, &
|
||||
45,46,44, 42,43,41, 39,37,38,39,40,38, 32,36,30,31,32,32,32,33,34,35,32,32, 56,53,54,55,53,54, &
|
||||
45,44,46, 42,41,43, 38,37,39,38,40,39, 32,32,31,30,36,32,32,32,35,34,33,32, 53,56,54,53,55,54, &
|
||||
46,44,45, 43,41,42, 38,39,37,38,39,40, 32,32,32,36,30,31,32,32,32,33,34,35, 54,56,53,54,55,53, &
|
||||
44,46,45, 41,43,42, 39,38,37,39,38,40, 33,32,32,32,31,30,36,32,32,32,35,34, 54,53,56,54,53,55, &
|
||||
44,45,46, 41,42,43, 40,38,39,37,38,39, 34,35,32,32,32,36,30,31,32,32,32,33, 53,54,56,53,54,55, & ! 1. pyr<c+a>
|
||||
46,45,44, 43,42,41, 40,39,38,37,39,38, 35,34,33,32,32,32,31,30,36,32,32,32, 55,54,53,56,54,53, &
|
||||
45,46,44, 42,43,41, 39,40,38,39,37,38, 32,33,34,35,32,32,32,36,30,31,32,32, 55,53,54,56,53,54, &
|
||||
45,44,46, 42,41,43, 38,40,39,38,37,39, 32,32,35,34,33,32,32,32,31,30,36,32, 53,55,54,53,56,54, &
|
||||
46,44,45, 43,41,42, 38,39,40,38,39,37, 32,32,32,33,34,35,32,32,32,36,30,31, 54,55,53,54,56,53, &
|
||||
44,46,45, 41,43,42, 39,38,40,39,38,37, 36,32,32,32,35,34,33,32,32,32,31,30, 54,53,55,54,53,56, &
|
||||
|
||||
30,30,30, 29,29,29, 28,28,28,28,28,28, 27,27,27,27,27,27,27,27,27,27,27,27, 25,26,26,26,26,26, &
|
||||
30,30,30, 29,29,29, 28,28,28,28,28,28, 27,27,27,27,27,27,27,27,27,27,27,27, 26,25,26,26,26,26, &
|
||||
30,30,30, 29,29,29, 28,28,28,28,28,28, 27,27,27,27,27,27,27,27,27,27,27,27, 26,26,25,26,26,26, &
|
||||
30,30,30, 29,29,29, 28,28,28,28,28,28, 27,27,27,27,27,27,27,27,27,27,27,27, 26,26,26,25,26,26, & ! 2. pyr<c+a>
|
||||
30,30,30, 29,29,29, 28,28,28,28,28,28, 27,27,27,27,27,27,27,27,27,27,27,27, 26,26,26,26,25,26, &
|
||||
30,30,30, 29,29,29, 28,28,28,28,28,28, 27,27,27,27,27,27,27,27,27,27,27,27, 26,26,26,26,26,25 &
|
||||
68,68,69, 66,66,67, 64,64,65,64,65,65, 60,61,61,60,62,62,60,63,63,60,62,62, 57,58,58,59,58,58, &
|
||||
68,69,68, 66,67,66, 65,64,64,65,64,64, 62,62,60,61,61,60,62,62,60,63,63,60, 58,57,58,58,59,58, &
|
||||
69,68,68, 67,66,66, 64,65,64,64,65,64, 63,60,62,62,60,61,61,60,62,62,60,63, 58,58,57,58,58,59, &
|
||||
68,68,69, 66,66,67, 64,64,65,64,64,65, 60,63,63,60,62,62,60,61,61,60,62,62, 59,58,58,57,58,58, & ! 2. pyr<c+a>
|
||||
68,69,68, 66,67,66, 65,64,64,65,64,64, 62,62,60,63,63,60,62,62,60,61,61,60, 58,59,58,58,57,58, &
|
||||
69,68,68, 67,66,66, 64,65,64,64,65,64, 61,60,62,62,60,63,63,60,62,62,60,61, 58,58,59,58,58,57 &
|
||||
],shape(HEX_INTERACTIONSLIPSLIP)) !< Slip-slip interaction types for hex (onion peel naming scheme)
|
||||
!< 10.1016/j.ijplas.2014.06.010 table 3
|
||||
!< 10.1080/14786435.2012.699689 table 2 and 3
|
||||
!< index & label & description
|
||||
!< 1 & S1 & basal self-interaction
|
||||
!< 2 & 1 & basal/basal coplanar
|
||||
!< 3 & 3 & basal/prismatic collinear
|
||||
!< 4 & 4 & basal/prismatic non-collinear
|
||||
!< 5 & S2 & prismatic self-interaction
|
||||
!< 6 & 2 & prismatic/prismatic
|
||||
!< 7 & 5 & prismatic/basal collinear
|
||||
!< 8 & 6 & prismatic/basal non-collinear
|
||||
!< 9 & - & basal/pyramidal <a> non-collinear
|
||||
!< 10 & - & basal/pyramidal <a> collinear
|
||||
!< 11 & - & prismatic/pyramidal <a> non-collinear
|
||||
!< 12 & - & prismatic/pyramidal <a> collinear
|
||||
!< 13 & - & pyramidal <a> self-interaction
|
||||
!< 14 & - & pyramidal <a> non-collinear
|
||||
!< 15 & - & pyramidal <a> collinear
|
||||
!< 16 & - & pyramidal <a>/prismatic non-collinear
|
||||
!< 17 & - & pyramidal <a>/prismatic collinear
|
||||
!< 18 & - & pyramidal <a>/basal non-collinear
|
||||
!< 19 & - & pyramidal <a>/basal collinear
|
||||
!< 20 & - & basal/1. order pyramidal <c+a> semi-collinear
|
||||
!< 21 & - & basal/1. order pyramidal <c+a>
|
||||
!< 22 & - & basal/1. order pyramidal <c+a>
|
||||
!< 23 & - & prismatic/1. order pyramidal <c+a> semi-collinear
|
||||
!< 24 & - & prismatic/1. order pyramidal <c+a>
|
||||
!< 25 & - & prismatic/1. order pyramidal <c+a> semi-coplanar?
|
||||
!< 26 & - & pyramidal <a>/1. order pyramidal <c+a> coplanar
|
||||
!< 27 & - & pyramidal <a>/1. order pyramidal <c+a>
|
||||
!< 28 & - & pyramidal <a>/1. order pyramidal <c+a> semi-collinear
|
||||
!< 29 & - & pyramidal <a>/1. order pyramidal <c+a> semi-coplanar
|
||||
!< 30 & - & 1. order pyramidal <c+a> self-interaction
|
||||
!< 31 & - & 1. order pyramidal <c+a> coplanar
|
||||
!< 32 & - & 1. order pyramidal <c+a>
|
||||
!< 33 & - & 1. order pyramidal <c+a>
|
||||
!< 34 & - & 1. order pyramidal <c+a> semi-coplanar
|
||||
!< 35 & - & 1. order pyramidal <c+a> semi-coplanar
|
||||
!< 36 & - & 1. order pyramidal <c+a> collinear
|
||||
!< 37 & - & 1. order pyramidal <c+a>/pyramidal <a> coplanar
|
||||
!< 38 & - & 1. order pyramidal <c+a>/pyramidal <a> semi-collinear
|
||||
!< 39 & - & 1. order pyramidal <c+a>/pyramidal <a>
|
||||
!< 40 & - & 1. order pyramidal <c+a>/pyramidal <a> semi-coplanar
|
||||
!< 41 & - & 1. order pyramidal <c+a>/prismatic semi-collinear
|
||||
!< 42 & - & 1. order pyramidal <c+a>/prismatic semi-coplanar
|
||||
!< 43 & - & 1. order pyramidal <c+a>/prismatic
|
||||
!< 44 & - & 1. order pyramidal <c+a>/basal semi-collinear
|
||||
!< 45 & - & 1. order pyramidal <c+a>/basal
|
||||
!< 46 & - & 1. order pyramidal <c+a>/basal
|
||||
!< 47 & 8 & basal/2. order pyramidal <c+a> non-collinear
|
||||
!< 48 & 7 & basal/2. order pyramidal <c+a> semi-collinear
|
||||
!< 49 & 10 & prismatic/2. order pyramidal <c+a>
|
||||
!< 50 & 9 & prismatic/2. order pyramidal <c+a> semi-collinear
|
||||
!< 51 & - & pyramidal <a>/2. order pyramidal <c+a>
|
||||
!< 52 & - & pyramidal <a>/2. order pyramidal <c+a> semi collinear
|
||||
!< 53 & - & 1. order pyramidal <c+a>/2. order pyramidal <c+a>
|
||||
!< 54 & - & 1. order pyramidal <c+a>/2. order pyramidal <c+a>
|
||||
!< 55 & - & 1. order pyramidal <c+a>/2. order pyramidal <c+a>
|
||||
!< 56 & - & 1. order pyramidal <c+a>/2. order pyramidal <c+a> collinear
|
||||
!< 57 & S3 & 2. order pyramidal <c+a> self-interaction
|
||||
!< 58 & 16 & 2. order pyramidal <c+a> non-collinear
|
||||
!< 59 & 15 & 2. order pyramidal <c+a> semi-collinear
|
||||
!< 60 & - & 2. order pyramidal <c+a>/1. order pyramidal <c+a>
|
||||
!< 61 & - & 2. order pyramidal <c+a>/1. order pyramidal <c+a> collinear
|
||||
!< 62 & - & 2. order pyramidal <c+a>/1. order pyramidal <c+a>
|
||||
!< 63 & - & 2. order pyramidal <c+a>/1. order pyramidal <c+a>
|
||||
!< 64 & - & 2. order pyramidal <c+a>/pyramidal <a> non-collinear
|
||||
!< 65 & - & 2. order pyramidal <c+a>/pyramidal <a> semi-collinear
|
||||
!< 66 & 14 & 2. order pyramidal <c+a>/prismatic non-collinear
|
||||
!< 67 & 13 & 2. order pyramidal <c+a>/prismatic semi-collinear
|
||||
!< 68 & 12 & 2. order pyramidal <c+a>/basal non-collinear
|
||||
!< 69 & 11 & 2. order pyramidal <c+a>/basal semi-collinear
|
||||
|
||||
integer, dimension(BCT_NSLIP,BCT_NSLIP), parameter :: &
|
||||
BCT_INTERACTIONSLIPSLIP = reshape( [&
|
||||
|
|
|
|||
|
|
@ -108,8 +108,14 @@ subroutine parse()
|
|||
homogenizations => config_material%get('homogenization')
|
||||
|
||||
call sanityCheck(materials, homogenizations)
|
||||
|
||||
#if defined (__GFORTRAN__)
|
||||
material_name_phase = getKeys(phases)
|
||||
material_name_homogenization = getKeys(homogenizations)
|
||||
#else
|
||||
material_name_phase = phases%Keys()
|
||||
material_name_homogenization = homogenizations%Keys()
|
||||
#endif
|
||||
|
||||
allocate(homogenization_Nconstituents(homogenizations%length))
|
||||
do h=1, homogenizations%length
|
||||
|
|
@ -203,9 +209,9 @@ subroutine sanityCheck(materials,homogenizations)
|
|||
|
||||
end subroutine sanityCheck
|
||||
|
||||
|
||||
#if defined (__GFORTRAN__)
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
!> @brief Get all keys from a dictionary
|
||||
!> @brief %keys() is broken on gfortran
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
function getKeys(dict)
|
||||
|
||||
|
|
@ -228,5 +234,6 @@ function getKeys(dict)
|
|||
end do
|
||||
|
||||
end function getKeys
|
||||
#endif
|
||||
|
||||
end module material
|
||||
|
|
|
|||
28
src/math.f90
28
src/math.f90
|
|
@ -84,38 +84,34 @@ contains
|
|||
subroutine math_init
|
||||
|
||||
real(pReal), dimension(4) :: randTest
|
||||
integer :: &
|
||||
randSize, &
|
||||
randomSeed !< fixed seeding for pseudo-random number generator, Default 0: use random seed
|
||||
integer, dimension(:), allocatable :: randInit
|
||||
integer :: randSize
|
||||
integer, dimension(:), allocatable :: seed
|
||||
class(tNode), pointer :: &
|
||||
num_generic
|
||||
|
||||
|
||||
print'(/,1x,a)', '<<<+- math init -+>>>'; flush(IO_STDOUT)
|
||||
|
||||
num_generic => config_numerics%get('generic',defaultVal=emptyDict)
|
||||
randomSeed = num_generic%get_asInt('random_seed', defaultVal = 0)
|
||||
|
||||
call random_seed(size=randSize)
|
||||
allocate(randInit(randSize))
|
||||
if (randomSeed > 0) then
|
||||
randInit = randomSeed
|
||||
allocate(seed(randSize))
|
||||
|
||||
if (num_generic%contains('random_seed')) then
|
||||
seed = num_generic%get_as1dInt('random_seed',requiredSize=randSize)
|
||||
else
|
||||
call random_seed()
|
||||
call random_seed(get = randInit)
|
||||
randInit(2:randSize) = randInit(1)
|
||||
call random_seed(get = seed)
|
||||
end if
|
||||
|
||||
call random_seed(put = randInit)
|
||||
call random_seed(put = seed)
|
||||
call random_number(randTest)
|
||||
|
||||
print'(/,a,i2)', ' size of random seed: ', randSize
|
||||
print'( a,i0)', ' value of random seed: ', randInit(1)
|
||||
print'( a,4(/,26x,f17.14),/)', ' start of random sequence: ', randTest
|
||||
print*, 'value of random seed: ', seed
|
||||
print'( a,4(/,26x,f17.14))', ' start of random sequence: ', randTest
|
||||
|
||||
call random_seed(put = randInit)
|
||||
|
||||
call selfTest
|
||||
call selfTest()
|
||||
|
||||
end subroutine math_init
|
||||
|
||||
|
|
|
|||
|
|
@ -270,7 +270,7 @@ pure elemental subroutine standardize(self)
|
|||
|
||||
class(rotation), intent(inout) :: self
|
||||
|
||||
if (self%q(1) < 0.0_pReal) self%q = - self%q
|
||||
if (sign(1.0_pReal,self%q(1)) < 0.0_pReal) self%q = - self%q
|
||||
|
||||
end subroutine standardize
|
||||
|
||||
|
|
@ -450,7 +450,7 @@ pure function qu2om(qu) result(om)
|
|||
om(3,2) = 2.0_pReal*(qu(4)*qu(3)+qu(1)*qu(2))
|
||||
om(1,3) = 2.0_pReal*(qu(2)*qu(4)+qu(1)*qu(3))
|
||||
|
||||
if (P < 0.0_pReal) om = transpose(om)
|
||||
if (sign(1.0_pReal,P) < 0.0_pReal) om = transpose(om)
|
||||
|
||||
end function qu2om
|
||||
|
||||
|
|
@ -480,7 +480,7 @@ pure function qu2eu(qu) result(eu)
|
|||
atan2( 2.0_pReal*chi, q03-q12 ), &
|
||||
atan2(( P*qu(1)*qu(3)+qu(2)*qu(4))*chi, (-P*qu(1)*qu(2)+qu(3)*qu(4))*chi )]
|
||||
endif degenerated
|
||||
where(eu<0.0_pReal) eu = mod(eu+2.0_pReal*PI,[2.0_pReal*PI,PI,2.0_pReal*PI])
|
||||
where(sign(1.0_pReal,eu)<0.0_pReal) eu = mod(eu+2.0_pReal*PI,[2.0_pReal*PI,PI,2.0_pReal*PI])
|
||||
|
||||
end function qu2eu
|
||||
|
||||
|
|
@ -602,7 +602,7 @@ pure function om2qu(om) result(qu)
|
|||
qu = [ (om(2,1) - om(1,2)) /s,(om(1,3) + om(3,1)) / s,(om(2,3) + om(3,2)) / s,0.25_pReal * s]
|
||||
endif
|
||||
endif
|
||||
if(qu(1)<0._pReal) qu =-1.0_pReal * qu
|
||||
if(sign(1.0_pReal,qu(1))<0.0_pReal) qu =-1.0_pReal * qu
|
||||
qu = qu*[1.0_pReal,P,P,P]
|
||||
|
||||
end function om2qu
|
||||
|
|
@ -628,7 +628,7 @@ pure function om2eu(om) result(eu)
|
|||
eu = [atan2(om(1,2),om(1,1)), 0.5_pReal*PI*(1.0_pReal-om(3,3)),0.0_pReal ]
|
||||
end if
|
||||
where(abs(eu) < 1.e-8_pReal) eu = 0.0_pReal
|
||||
where(eu<0.0_pReal) eu = mod(eu+2.0_pReal*PI,[2.0_pReal*PI,PI,2.0_pReal*PI])
|
||||
where(sign(1.0_pReal,eu)<0.0_pReal) eu = mod(eu+2.0_pReal*PI,[2.0_pReal*PI,PI,2.0_pReal*PI])
|
||||
|
||||
end function om2eu
|
||||
|
||||
|
|
@ -735,7 +735,7 @@ pure function eu2qu(eu) result(qu)
|
|||
-P*sPhi*cos(ee(1)-ee(3)), &
|
||||
-P*sPhi*sin(ee(1)-ee(3)), &
|
||||
-P*cPhi*sin(ee(1)+ee(3))]
|
||||
if(qu(1) < 0.0_pReal) qu = qu * (-1.0_pReal)
|
||||
if(sign(1.0_pReal,qu(1)) < 0.0_pReal) qu = qu * (-1.0_pReal)
|
||||
|
||||
end function eu2qu
|
||||
|
||||
|
|
@ -792,7 +792,7 @@ pure function eu2ax(eu) result(ax)
|
|||
else
|
||||
ax(1:3) = -P/tau * [ t*cos(delta), t*sin(delta), sin(sigma) ] ! passive axis-angle pair so a minus sign in front
|
||||
ax(4) = alpha
|
||||
if (alpha < 0.0_pReal) ax = -ax ! ensure alpha is positive
|
||||
if (sign(1.0_pReal,alpha) < 0.0_pReal) ax = -ax ! ensure alpha is positive
|
||||
end if
|
||||
|
||||
end function eu2ax
|
||||
|
|
|
|||
Loading…
Reference in New Issue