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Merge remote-tracking branch 'origin/development' into remove-grain-growth

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Martin Diehl 2022-02-02 09:00:52 +01:00
parent 29cbf1304b dc5ab9aee9
commit 63465f4d27
73 changed files with 3122 additions and 2132 deletions
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2
.github/workflows/Python.yml vendored
View File

@ -9,7 +9,7 @@ jobs:
strategy:
matrix:
python-version: ['3.7', '3.8', '3.9'] #, '3.10']
python-version: ['3.8', '3.9'] #, '3.10']
os: [ubuntu-latest, macos-latest]
steps:

63
.gitlab-ci.yml
View File

@ -46,7 +46,7 @@ variables:
# ++++++++++++ PETSc ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
PETSC_GNU: "Libraries/PETSc/3.16.1/GNU-10-OpenMPI-4.1.1"
PETSC_INTELLLVM: "Libraries/PETSc/3.16.3/oneAPI-2022.0.1-IntelMPI-2021.5.0"
PETSC_INTEL: "Libraries/PETSc/3.16.2/Intel-2022.0.1-IntelMPI-2021.5.0"
PETSC_INTEL: "Libraries/PETSc/3.16.3/Intel-2022.0.1-IntelMPI-2021.5.0"
# ++++++++++++ MSC Marc +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
MSC: "FEM/MSC/2021.3.1"
IntelMarc: "Compiler/Intel/19.1.2 Libraries/IMKL/2020"
@ -79,49 +79,69 @@ mypy:
###################################################################################################
test_grid_GNU:
grid_GNU:
stage: compile
script:
- module load ${COMPILER_GNU} ${MPI_GNU} ${PETSC_GNU}
- cd PRIVATE/testing/pytest
- pytest -k 'compile and grid' --basetemp ${TESTROOT}/compile_grid_GNU
test_mesh_GNU:
mesh_GNU:
stage: compile
script:
- module load ${COMPILER_GNU} ${MPI_GNU} ${PETSC_GNU}
- cd PRIVATE/testing/pytest
- pytest -k 'compile and mesh' --basetemp ${TESTROOT}/compile_mesh_GNU
test_mesh_IntelLLVM:
grid_GNU-64bit:
stage: compile
script:
- module load Compiler/GNU/10 Libraries/PETSc/3.16.2/64bit
- cd PRIVATE/testing/pytest
- pytest -k 'compile and grid' --basetemp ${TESTROOT}/compile_grid_GNU-64bit
mesh_GNU-64bit:
stage: compile
script:
- module load Compiler/GNU/10 Libraries/PETSc/3.16.2/64bit
- cd PRIVATE/testing/pytest
- pytest -k 'compile and mesh' --basetemp ${TESTROOT}/compile_mesh_GNU-64bit
grid_IntelLLVM:
stage: compile
script:
- module load ${COMPILER_INTELLLVM} ${MPI_INTELLLVM} ${PETSC_INTELLLVM}
- cd PRIVATE/testing/pytest
- pytest -k 'compile and grid' --basetemp ${TESTROOT}/compile_grid_IntelLLVM
mesh_IntelLLVM:
stage: compile
script:
- module load ${COMPILER_INTELLLVM} ${MPI_INTELLLVM} ${PETSC_INTELLLVM}
- cd PRIVATE/testing/pytest
- pytest -k 'compile and mesh' --basetemp ${TESTROOT}/compile_mesh_IntelLLVM
test_grid_Intel:
grid_Intel:
stage: compile
script:
- module load ${COMPILER_INTEL} ${MPI_INTEL} ${PETSC_INTEL}
- cd PRIVATE/testing/pytest
- pytest -k 'compile and grid' --basetemp ${TESTROOT}/compile_grid_Intel
test_mesh_Intel:
mesh_Intel:
stage: compile
script:
- module load ${COMPILER_INTEL} ${MPI_INTEL} ${PETSC_INTEL}
- cd PRIVATE/testing/pytest
- pytest -k 'compile and mesh' --basetemp ${TESTROOT}/compile_mesh_Intel
test_Marc:
Marc_Intel:
stage: compile
script:
- module load $IntelMarc $HDF5Marc $MSC
- cd PRIVATE/testing/pytest
- pytest -k 'compile and Marc' --basetemp ${TESTROOT}/compile_Marc
setup_grid:
stage: compile
script:
@ -138,7 +158,7 @@ setup_mesh:
- cmake -DDAMASK_SOLVER=MESH -DCMAKE_INSTALL_PREFIX=${TESTROOT} ${CI_PROJECT_DIR}
- make -j2 all install
compile_Marc:
setup_Marc:
stage: compile
script:
- module load $IntelMarc $HDF5Marc $MSC
@ -172,6 +192,10 @@ Marc:
###################################################################################################
grid_runtime:
stage: performance
before_script:
- ${LOCAL_HOME}/bin/queue ${CI_JOB_ID} --blocking
- source env/DAMASK.sh
- echo Job start:" $(date)"
script:
- module load ${COMPILER_INTEL} ${MPI_INTEL} ${PETSC_INTEL}
- cd $(mktemp -d)
@ -186,10 +210,6 @@ grid_runtime:
--output_dir ./
--tag ${CI_COMMIT_SHA}
- if [ ${CI_COMMIT_BRANCH} == development ]; then git commit -am ${CI_PIPELINE_ID}_${CI_COMMIT_SHA}; git push; fi
before_script:
- ${LOCAL_HOME}/bin/queue ${CI_JOB_ID} --blocking
- source env/DAMASK.sh
- echo Job start:" $(date)"
###################################################################################################
@ -209,19 +229,10 @@ update_revision:
script:
- cd $(mktemp -d)
- git clone -q git@git.damask.mpie.de:damask/DAMASK.git .
- git checkout ${CI_COMMIT_SHA}
- export VERSION=$(git describe)
- git pull
- export VERSION=$(git describe ${CI_COMMIT_SHA})
- echo ${VERSION} > python/damask/VERSION
- git add python/damask/VERSION
- git commit -m "[skip ci] updated version information after successful test of $VERSION"
- export UPDATEDREV=$(git describe) # tested state + 1 commit
- git checkout master
- git pull
- git merge $UPDATEDREV -s recursive -X ours # conflicts occur only for inconsistent state
- git push
- git checkout development
- git pull
- git merge master -s recursive -X ours -m "[skip ci] Merge branch 'master' into development" # only possible conflict is in VERSION file
- git push origin development # development is unchanged (as master is based on it) but has updated VERSION file
- git commit python/damask/VERSION -m "[skip ci] updated version information after successful test of $VERSION"
- if [ ${CI_COMMIT_SHA} == $(git rev-parse HEAD^) ]; then git push origin HEAD:master HEAD:development; fi
only:
- development

110
COPYING
View File

@ -1,23 +1,21 @@
GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
GNU AFFERO GENERAL PUBLIC LICENSE
Version 3, 19 November 2007
Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
Preamble
The GNU General Public License is a free, copyleft license for
software and other kinds of works.
The GNU Affero General Public License is a free, copyleft license for
software and other kinds of works, specifically designed to ensure
cooperation with the community in the case of network server software.
The licenses for most software and other practical works are designed
to take away your freedom to share and change the works. By contrast,
the GNU General Public License is intended to guarantee your freedom to
our General Public Licenses are intended to guarantee your freedom to
share and change all versions of a program--to make sure it remains free
software for all its users. We, the Free Software Foundation, use the
GNU General Public License for most of our software; it applies also to
any other work released this way by its authors. You can apply it to
your programs, too.
software for all its users.
When we speak of free software, we are referring to freedom, not
price. Our General Public Licenses are designed to make sure that you
@ -26,44 +24,34 @@ them if you wish), that you receive source code or can get it if you
want it, that you can change the software or use pieces of it in new
free programs, and that you know you can do these things.
To protect your rights, we need to prevent others from denying you
these rights or asking you to surrender the rights. Therefore, you have
certain responsibilities if you distribute copies of the software, or if
you modify it: responsibilities to respect the freedom of others.
Developers that use our General Public Licenses protect your rights
with two steps: (1) assert copyright on the software, and (2) offer
you this License which gives you legal permission to copy, distribute
and/or modify the software.
For example, if you distribute copies of such a program, whether
gratis or for a fee, you must pass on to the recipients the same
freedoms that you received. You must make sure that they, too, receive
or can get the source code. And you must show them these terms so they
know their rights.
A secondary benefit of defending all users' freedom is that
improvements made in alternate versions of the program, if they
receive widespread use, become available for other developers to
incorporate. Many developers of free software are heartened and
encouraged by the resulting cooperation. However, in the case of
software used on network servers, this result may fail to come about.
The GNU General Public License permits making a modified version and
letting the public access it on a server without ever releasing its
source code to the public.
Developers that use the GNU GPL protect your rights with two steps:
(1) assert copyright on the software, and (2) offer you this License
giving you legal permission to copy, distribute and/or modify it.
The GNU Affero General Public License is designed specifically to
ensure that, in such cases, the modified source code becomes available
to the community. It requires the operator of a network server to
provide the source code of the modified version running there to the
users of that server. Therefore, public use of a modified version, on
a publicly accessible server, gives the public access to the source
code of the modified version.
For the developers' and authors' protection, the GPL clearly explains
that there is no warranty for this free software. For both users' and
authors' sake, the GPL requires that modified versions be marked as
changed, so that their problems will not be attributed erroneously to
authors of previous versions.
Some devices are designed to deny users access to install or run
modified versions of the software inside them, although the manufacturer
can do so. This is fundamentally incompatible with the aim of
protecting users' freedom to change the software. The systematic
pattern of such abuse occurs in the area of products for individuals to
use, which is precisely where it is most unacceptable. Therefore, we
have designed this version of the GPL to prohibit the practice for those
products. If such problems arise substantially in other domains, we
stand ready to extend this provision to those domains in future versions
of the GPL, as needed to protect the freedom of users.
Finally, every program is threatened constantly by software patents.
States should not allow patents to restrict development and use of
software on general-purpose computers, but in those that do, we wish to
avoid the special danger that patents applied to a free program could
make it effectively proprietary. To prevent this, the GPL assures that
patents cannot be used to render the program non-free.
An older license, called the Affero General Public License and
published by Affero, was designed to accomplish similar goals. This is
a different license, not a version of the Affero GPL, but Affero has
released a new version of the Affero GPL which permits relicensing under
this license.
The precise terms and conditions for copying, distribution and
modification follow.
@ -72,7 +60,7 @@ modification follow.
0. Definitions.
"This License" refers to version 3 of the GNU General Public License.
"This License" refers to version 3 of the GNU Affero General Public License.
"Copyright" also means copyright-like laws that apply to other kinds of
works, such as semiconductor masks.
@ -549,35 +537,45 @@ to collect a royalty for further conveying from those to whom you convey
the Program, the only way you could satisfy both those terms and this
License would be to refrain entirely from conveying the Program.
13. Use with the GNU Affero General Public License.
13. Remote Network Interaction; Use with the GNU General Public License.
Notwithstanding any other provision of this License, if you modify the
Program, your modified version must prominently offer all users
interacting with it remotely through a computer network (if your version
supports such interaction) an opportunity to receive the Corresponding
Source of your version by providing access to the Corresponding Source
from a network server at no charge, through some standard or customary
means of facilitating copying of software. This Corresponding Source
shall include the Corresponding Source for any work covered by version 3
of the GNU General Public License that is incorporated pursuant to the
following paragraph.
Notwithstanding any other provision of this License, you have
permission to link or combine any covered work with a work licensed
under version 3 of the GNU Affero General Public License into a single
under version 3 of the GNU General Public License into a single
combined work, and to convey the resulting work. The terms of this
License will continue to apply to the part which is the covered work,
but the special requirements of the GNU Affero General Public License,
section 13, concerning interaction through a network will apply to the
combination as such.
but the work with which it is combined will remain governed by version
3 of the GNU General Public License.
14. Revised Versions of this License.
The Free Software Foundation may publish revised and/or new versions of
the GNU General Public License from time to time. Such new versions will
be similar in spirit to the present version, but may differ in detail to
the GNU Affero General Public License from time to time. Such new versions
will be similar in spirit to the present version, but may differ in detail to
address new problems or concerns.
Each version is given a distinguishing version number. If the
Program specifies that a certain numbered version of the GNU General
Program specifies that a certain numbered version of the GNU Affero General
Public License "or any later version" applies to it, you have the
option of following the terms and conditions either of that numbered
version or of any later version published by the Free Software
Foundation. If the Program does not specify a version number of the
GNU General Public License, you may choose any version ever published
GNU Affero General Public License, you may choose any version ever published
by the Free Software Foundation.
If the Program specifies that a proxy can decide which future
versions of the GNU General Public License can be used, that proxy's
versions of the GNU Affero General Public License can be used, that proxy's
public statement of acceptance of a version permanently authorizes you
to choose that version for the Program.

12
LICENSE
View File

@ -1,14 +1,14 @@
Copyright 2011-2021 Max-Planck-Institut für Eisenforschung GmbH
Copyright 2011-2022 Max-Planck-Institut für Eisenforschung GmbH
DAMASK is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Affero General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
You should have received a copy of the GNU Affero General Public License
along with this program. If not, see <https://www.gnu.org/licenses/>.

2
PRIVATE

@ -1 +1 @@
Subproject commit b898a8b5552bd9d1c555edc3d8134564dd32fe53
Subproject commit 5598ec4892b0921fccf63e8570f9fcd8e0365716

12
examples/config/phase/mechanical/plastic/phenopowerlaw_Mg.yaml
View File

@ -6,7 +6,7 @@ references:
output: [xi_sl, xi_tw]
N_sl: [3, 3, 6, 0, 6] # basal, prism, -, 1. pyr<a>, -, 2. pyr<c+a>
N_sl: [3, 3, 6, 0, 6] # basal, prism, 1. pyr<a>, -, 2. pyr<c+a>
N_tw: [6, 0, 6] # tension, -, compression
xi_0_sl: [10.e+6, 55.e+6, 60.e+6, 0., 60.e+6]
@ -23,9 +23,13 @@ f_sat_sl-tw: 10.0
h_0_sl-sl: 500.0e+6
h_0_tw-tw: 50.0e+6
h_0_tw-sl: 150.0e+6
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] # 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, 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
h_tw-tw: [+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_tw-sl: [1.0, -1.0, 1.0, -1.0, 1.0, -1.0, 1.0, -1.0, 1.0, -1.0,

9
examples/config/phase/mechanical/plastic/phenopowerlaw_Ti.yaml
View File

@ -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>
N_sl: [3, 3, 0, 12] # basal, prism, -, 1. pyr<c+a>
n_sl: 20
a_sl: 2.0
dot_gamma_0_sl: 0.001
@ -20,5 +20,8 @@ xi_inf_sl: [568.e+6, 150.e+7, 0.0, 3420.e+6]
# L. Wang et al. :
# xi_0_sl: [127.e+6, 96.e+6, 0.0, 240.e+6]
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

358
img/COPYING
View File

@ -1,94 +1,312 @@
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Creative Commons Attribution-NoDerivatives 4.0 International Public
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By exercising the Licensed Rights (defined below), You accept and agree to be bound by the terms and conditions of this Creative Commons Attribution-NoDerivatives 4.0 International Public License ("Public License"). To the extent this Public License may be interpreted as a contract, You are granted the Licensed Rights in consideration of Your acceptance of these terms and conditions, and the Licensor grants You such rights in consideration of benefits the Licensor receives from making the Licensed Material available under these terms and conditions.
By exercising the Licensed Rights (defined below), You accept and agree
to be bound by the terms and conditions of this Creative Commons
Attribution-NoDerivatives 4.0 International Public License ("Public
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contract, You are granted the Licensed Rights in consideration of Your
acceptance of these terms and conditions, and the Licensor grants You
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Adapted Material;
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c. You must comply with the conditions in Section 3(a) if You Share
all or a substantial portion of the contents of the database.
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terminate automatically.
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6
install/MarcMentat/2020/Marc_tools/include_linux64.patch vendored
View File

@ -12,17 +12,15 @@
# AEM
if test "$MARCDLLOUTDIR" = ""; then
@@ -390,8 +395,8 @@
@@ -390,7 +395,7 @@
I8DEFINES=
I8CDEFINES=
else
- I8FFLAGS="-i8"
- I8DEFINES="-DI64"
+ I8FFLAGS="-i8 -integer-size 64"
+ I8DEFINES="-DI64 -DINT=8"
I8DEFINES="-DI64"
I8CDEFINES="-U_DOUBLE -D_SINGLE"
fi
@@ -498,7 +503,7 @@
PROFILE=" $PROFILE -pg"
fi

6
install/MarcMentat/2021.2/Marc_tools/include_linux64.patch vendored
View File

@ -12,17 +12,15 @@
# AEM
if test "$MARCDLLOUTDIR" = ""; then
@@ -439,8 +444,8 @@
@@ -439,7 +444,7 @@
I8DEFINES=
I8CDEFINES=
else
- I8FFLAGS="-i8"
- I8DEFINES="-DI64"
+ I8FFLAGS="-i8 -integer-size 64"
+ I8DEFINES="-DI64 -DINT=8"
I8DEFINES="-DI64"
I8CDEFINES="-U_DOUBLE -D_SINGLE"
fi
@@ -556,7 +561,7 @@
PROFILE=" $PROFILE -pg"
fi

6
install/MarcMentat/2021.3.1/Marc_tools/include_linux64.patch vendored
View File

@ -12,17 +12,15 @@
# AEM
if test "$MARCDLLOUTDIR" = ""; then
DLLOUTDIR="$MARC_LIB"
@@ -439,8 +444,8 @@ if test "$MARC_INTEGER_SIZE" = "i4" ; then
@@ -439,7 +444,7 @@ if test "$MARC_INTEGER_SIZE" = "i4" ; then
I8DEFINES=
I8CDEFINES=
else
- I8FFLAGS="-i8"
- I8DEFINES="-DI64"
+ I8FFLAGS="-i8 -integer-size 64"
+ I8DEFINES="-DI64 -DINT=8"
I8DEFINES="-DI64"
I8CDEFINES="-U_DOUBLE -D_SINGLE"
fi
@@ -556,7 +561,7 @@ then
PROFILE=" $PROFILE -pg"
fi

2
python/damask/VERSION
View File

@ -1 +1 @@
v3.0.0-alpha5-375-g76fe2d2b3
v3.0.0-alpha5-545-gad74f5dbe

3
python/damask/__init__.py
View File

@ -8,6 +8,7 @@ with open(_Path(__file__).parent/_Path('VERSION')) as _f:
version = _re.sub(r'^v','',_f.readline().strip())
__version__ = version
from . import _typehints # noqa
from . import util # noqa
from . import seeds # noqa
from . import tensor # noqa
@ -20,8 +21,8 @@ from ._rotation import Rotation # noqa
from ._crystal import Crystal # noqa
from ._orientation import Orientation # noqa
from ._table import Table # noqa
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

87
python/damask/_colormap.py
View File

@ -3,13 +3,9 @@ import json
import functools
import colorsys
from pathlib import Path
from typing import Sequence, Union, TextIO
from typing import Union, TextIO
import numpy as np
try:
from numpy.typing import ArrayLike
except ImportError:
ArrayLike = Union[np.ndarray,Sequence[float]] # type: ignore
import scipy.interpolate as interp
import matplotlib as mpl
if os.name == 'posix' and 'DISPLAY' not in os.environ:
@ -18,6 +14,7 @@ import matplotlib.pyplot as plt
from matplotlib import cm
from PIL import Image
from ._typehints import FloatSequence, FileHandle
from . import util
from . import Table
@ -50,22 +47,35 @@ class Colormap(mpl.colors.ListedColormap):
"""
def __eq__(self, other: object) -> bool:
def __eq__(self,
other: object) -> bool:
"""Test equality of colormaps."""
if not isinstance(other, Colormap):
return NotImplemented
return len(self.colors) == len(other.colors) \
and bool(np.all(self.colors == other.colors))
def __add__(self, other: 'Colormap') -> 'Colormap':
def __add__(self,
other: 'Colormap') -> 'Colormap':
"""Concatenate."""
return Colormap(np.vstack((self.colors,other.colors)),
f'{self.name}+{other.name}')
def __iadd__(self, other: 'Colormap') -> 'Colormap':
def __iadd__(self,
other: 'Colormap') -> 'Colormap':
"""Concatenate (in-place)."""
return self.__add__(other)
def __mul__(self,
factor: int) -> 'Colormap':
"""Repeat."""
return Colormap(np.vstack([self.colors]*factor),f'{self.name}*{factor}')
def __imul__(self,
factor: int) -> 'Colormap':
"""Repeat (in-place)."""
return self.__mul__(factor)
def __invert__(self) -> 'Colormap':
"""Reverse."""
return self.reversed()
@ -82,8 +92,8 @@ class Colormap(mpl.colors.ListedColormap):
@staticmethod
def from_range(low: ArrayLike,
high: ArrayLike,
def from_range(low: FloatSequence,
high: FloatSequence,
name: str = 'DAMASK colormap',
N: int = 256,
model: str = 'rgb') -> 'Colormap':
@ -156,7 +166,8 @@ class Colormap(mpl.colors.ListedColormap):
@staticmethod
def from_predefined(name: str, N: int = 256) -> 'Colormap':
def from_predefined(name: str,
N: int = 256) -> 'Colormap':
"""
Select from a set of predefined colormaps.
@ -197,7 +208,7 @@ class Colormap(mpl.colors.ListedColormap):
def at(self,
fraction : Union[float,Sequence[float]]) -> np.ndarray:
fraction : Union[float,FloatSequence]) -> np.ndarray:
"""
Interpolate color at fraction.
@ -208,7 +219,7 @@ class Colormap(mpl.colors.ListedColormap):
Returns
-------
color : np.ndarray, shape(...,4)
color : numpy.ndarray, shape(...,4)
RGBA values of interpolated color(s).
Examples
@ -229,7 +240,7 @@ class Colormap(mpl.colors.ListedColormap):
def shade(self,
field: np.ndarray,
bounds: ArrayLike = None,
bounds: FloatSequence = None,
gap: float = None) -> Image:
"""
Generate PIL image of 2D field using colormap.
@ -253,12 +264,10 @@ 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]
(bounds[0],bounds[1])
delta,avg = r-l,0.5*abs(r+l)
if abs(delta) * 1e8 <= avg: # delta is similar to numerical noise
l,r = l-0.5*avg*np.sign(delta),r+0.5*avg*np.sign(delta), # extend range to have actual data centered within
if abs(delta := r-l) * 1e8 <= (avg := 0.5*abs(r+l)): # delta is similar to numerical noise
l,r = (l-0.5*avg*np.sign(delta),r+0.5*avg*np.sign(delta)) # extend range to have actual data centered within
return Image.fromarray(
(np.dstack((
@ -270,7 +279,8 @@ class Colormap(mpl.colors.ListedColormap):
mode='RGBA')
def reversed(self, name: str = None) -> 'Colormap':
def reversed(self,
name: str = None) -> 'Colormap':
"""
Reverse.
@ -291,12 +301,12 @@ class Colormap(mpl.colors.ListedColormap):
>>> damask.Colormap.from_predefined('stress').reversed()
"""
rev = super(Colormap,self).reversed(name)
rev = super().reversed(name)
return Colormap(np.array(rev.colors),rev.name[:-4] if rev.name.endswith('_r_r') else rev.name)
def _get_file_handle(self,
fname: Union[TextIO, str, Path, None],
fname: Union[FileHandle, None],
suffix: str = '') -> TextIO:
"""
Provide file handle.
@ -323,7 +333,8 @@ class Colormap(mpl.colors.ListedColormap):
return fname
def save_paraview(self, fname: Union[TextIO, str, Path] = None):
def save_paraview(self,
fname: FileHandle = None):
"""
Save as JSON file for use in Paraview.
@ -350,7 +361,8 @@ class Colormap(mpl.colors.ListedColormap):
fhandle.write('\n')
def save_ASCII(self, fname: Union[TextIO, str, Path] = None):
def save_ASCII(self,
fname: FileHandle = None):
"""
Save as ASCII file.
@ -365,7 +377,7 @@ class Colormap(mpl.colors.ListedColormap):
t.save(self._get_file_handle(fname,'.txt'))
def save_GOM(self, fname: Union[TextIO, str, Path] = None):
def save_GOM(self, fname: FileHandle = None):
"""
Save as ASCII file for use in GOM Aramis.
@ -385,7 +397,8 @@ class Colormap(mpl.colors.ListedColormap):
self._get_file_handle(fname,'.legend').write(GOM_str)
def save_gmsh(self, fname: Union[TextIO, str, Path] = None):
def save_gmsh(self,
fname: FileHandle = None):
"""
Save as ASCII file for use in gmsh.
@ -423,11 +436,11 @@ class Colormap(mpl.colors.ListedColormap):
def adjust_hue(msh_sat, msh_unsat):
"""If saturation of one of the two colors is much less than the other, hue of the less."""
if msh_sat[0] >= msh_unsat[0]:
return msh_sat[2]
else:
hSpin = msh_sat[1]/np.sin(msh_sat[1])*np.sqrt(msh_unsat[0]**2.0-msh_sat[0]**2)/msh_sat[0]
if msh_sat[2] < - np.pi/3.0: hSpin *= -1.0
return msh_sat[2] + hSpin
return msh_sat[2]
hSpin = msh_sat[1]/np.sin(msh_sat[1])*np.sqrt(msh_unsat[0]**2.0-msh_sat[0]**2)/msh_sat[0]
if msh_sat[2] < - np.pi/3.0: hSpin *= -1.0
return msh_sat[2] + hSpin
lo = np.array(low)
hi = np.array(high)
@ -440,9 +453,9 @@ class Colormap(mpl.colors.ListedColormap):
else:
lo = np.array([M_mid,0.0,0.0])
frac = 2.0*frac - 1.0
if lo[1] < 0.05 and hi[1] > 0.05:
if lo[1] < 0.05 < hi[1]:
lo[2] = adjust_hue(hi,lo)
elif lo[1] > 0.05 and hi[1] < 0.05:
elif hi[1] < 0.05 < lo[1]:
hi[2] = adjust_hue(lo,hi)
return (1.0 - frac) * lo + frac * hi
@ -471,7 +484,7 @@ class Colormap(mpl.colors.ListedColormap):
'gnuplot', 'gnuplot2', 'CMRmap', 'cubehelix', 'brg',
'gist_rainbow', 'rainbow', 'jet', 'nipy_spectral', 'gist_ncar']}
_predefined_DAMASK = {'orientation': {'low': [0.933334,0.878432,0.878431],
_predefined_DAMASK = {'orientation': {'low': [0.933334,0.878432,0.878431], # noqa
'high': [0.250980,0.007843,0.000000]},
'strain': {'low': [0.941177,0.941177,0.870588],
'high': [0.266667,0.266667,0.000000]},
@ -616,7 +629,8 @@ class Colormap(mpl.colors.ListedColormap):
@staticmethod
def _lab2xyz(lab: np.ndarray, ref_white: np.ndarray = _REF_WHITE) -> np.ndarray:
def _lab2xyz(lab: np.ndarray,
ref_white: np.ndarray = _REF_WHITE) -> np.ndarray:
"""
CIE Lab to CIE Xyz.
@ -647,7 +661,8 @@ class Colormap(mpl.colors.ListedColormap):
])*ref_white
@staticmethod
def _xyz2lab(xyz: np.ndarray, ref_white: np.ndarray = _REF_WHITE) -> np.ndarray:
def _xyz2lab(xyz: np.ndarray,
ref_white: np.ndarray = _REF_WHITE) -> np.ndarray:
"""
CIE Xyz to CIE Lab.

55
python/damask/_config.py
View File

@ -2,25 +2,34 @@ import copy
from io import StringIO
from collections.abc import Iterable
import abc
from pathlib import Path
from typing import Union, Dict, Any, Type, TypeVar
import numpy as np
import yaml
from ._typehints import FileHandle
from . import Rotation
MyType = TypeVar('MyType', bound='Config')
class NiceDumper(yaml.SafeDumper):
"""Make YAML readable for humans."""
def write_line_break(self, data=None):
def write_line_break(self,
data: str = None):
super().write_line_break(data)
if len(self.indents) == 1:
super().write_line_break()
def increase_indent(self, flow=False, indentless=False):
def increase_indent(self,
flow: bool = False,
indentless: bool = False):
return super().increase_indent(flow, False)
def represent_data(self, data):
def represent_data(self,
data: Any):
"""Cast Config objects and its subclasses to dict."""
if isinstance(data, dict) and type(data) != dict:
return self.represent_data(dict(data))
@ -31,14 +40,17 @@ class NiceDumper(yaml.SafeDumper):
else:
return super().represent_data(data)
def ignore_aliases(self, data):
def ignore_aliases(self,
data: Any) -> bool:
"""Do not use references to existing objects."""
return True
class Config(dict):
"""YAML-based configuration."""
def __init__(self,yml=None,**kwargs):
def __init__(self,
yml: Union[str, Dict[str, Any]] = None,
**kwargs):
"""Initialize from YAML, dict, or key=value pairs."""
if isinstance(yml,str):
kwargs.update(yaml.safe_load(yml))
@ -47,7 +59,7 @@ class Config(dict):
super().__init__(**kwargs)
def __repr__(self):
def __repr__(self) -> str:
"""Show as in file."""
output = StringIO()
self.save(output)
@ -55,14 +67,15 @@ class Config(dict):
return ''.join(output.readlines())
def __copy__(self):
def __copy__(self: MyType) -> MyType:
"""Create deep copy."""
return copy.deepcopy(self)
copy = __copy__
def __or__(self,other):
def __or__(self: MyType,
other) -> MyType:
"""
Update configuration with contents of other.
@ -76,18 +89,24 @@ class Config(dict):
updated : damask.Config
Updated configuration.
Note
----
This functionality is a backport for Python 3.8
"""
duplicate = self.copy()
duplicate.update(other)
return duplicate
def __ior__(self,other):
def __ior__(self: MyType,
other) -> MyType:
"""Update configuration with contents of other."""
return self.__or__(other)
def delete(self,keys):
def delete(self: MyType,
keys: Union[Iterable, str]) -> MyType:
"""
Remove configuration keys.
@ -109,7 +128,8 @@ class Config(dict):
@classmethod
def load(cls,fname):
def load(cls: Type[MyType],
fname: FileHandle) -> MyType:
"""
Load from yaml file.
@ -124,14 +144,15 @@ class Config(dict):
Configuration from file.
"""
try:
if isinstance(fname, (str, Path)):
fhandle = open(fname)
except TypeError:
else:
fhandle = fname
return cls(yaml.safe_load(fhandle))
def save(self,fname,**kwargs):
def save(self,
fname: FileHandle,
**kwargs):
"""
Save to yaml file.
@ -143,9 +164,9 @@ class Config(dict):
Keyword arguments parsed to yaml.dump.
"""
try:
if isinstance(fname, (str, Path)):
fhandle = open(fname,'w',newline='\n')
except TypeError:
else:
fhandle = fname
if 'width' not in kwargs:

54
python/damask/_configmaterial.py
View File

@ -1,10 +1,14 @@
import numpy as np
import h5py
from typing import Sequence, Dict, Any, Collection
from ._typehints import FileHandle
from . import Config
from . import Rotation
from . import Orientation
from . import util
from . import Table
class ConfigMaterial(Config):
"""
@ -17,7 +21,9 @@ class ConfigMaterial(Config):
"""
def __init__(self,d=None,**kwargs):
def __init__(self,
d: Dict[str, Any] = None,
**kwargs):
"""
New material configuration.
@ -30,14 +36,17 @@ class ConfigMaterial(Config):
Initial content specified as pairs of key=value.
"""
default: Collection
if d is None:
for section,default in {'material':[],'homogenization':{},'phase':{}}.items():
for section, default in {'material':[],'homogenization':{},'phase':{}}.items():
if section not in kwargs: kwargs.update({section:default})
super().__init__(d,**kwargs)
def save(self,fname='material.yaml',**kwargs):
def save(self,
fname: FileHandle = 'material.yaml',
**kwargs):
"""
Save to yaml file.
@ -53,7 +62,8 @@ class ConfigMaterial(Config):
@classmethod
def load(cls,fname='material.yaml'):
def load(cls,
fname: FileHandle = 'material.yaml') -> 'ConfigMaterial':
"""
Load from yaml file.
@ -72,10 +82,14 @@ class ConfigMaterial(Config):
@staticmethod
def load_DREAM3D(fname,
grain_data=None,cell_data=None,cell_ensemble_data='CellEnsembleData',
phases='Phases',Euler_angles='EulerAngles',phase_names='PhaseName',
base_group=None):
def load_DREAM3D(fname: str,
grain_data: str = None,
cell_data: str = None,
cell_ensemble_data: str = 'CellEnsembleData',
phases: str = 'Phases',
Euler_angles: str = 'EulerAngles',
phase_names: str = 'PhaseName',
base_group: str = None) -> 'ConfigMaterial':
"""
Load DREAM.3D (HDF5) file.
@ -154,7 +168,8 @@ class ConfigMaterial(Config):
@staticmethod
def from_table(table,**kwargs):
def from_table(table: Table,
**kwargs) -> 'ConfigMaterial':
"""
Generate from an ASCII table.
@ -207,7 +222,7 @@ class ConfigMaterial(Config):
@property
def is_complete(self):
def is_complete(self) -> bool:
"""
Check for completeness.
@ -267,12 +282,11 @@ class ConfigMaterial(Config):
if homogenization - set(self['homogenization']):
print(f'Homogenization(s) {homogenization-set(self["homogenization"])} missing')
ok = False
return ok
@property
def is_valid(self):
def is_valid(self) -> bool:
"""
Check for valid content.
@ -316,7 +330,10 @@ class ConfigMaterial(Config):
return ok
def material_rename_phase(self,mapping,ID=None,constituent=None):
def material_rename_phase(self,
mapping: Dict[str, str],
ID: Sequence[int] = None,
constituent: Sequence[int] = None) -> 'ConfigMaterial':
"""
Change phase name in material.
@ -347,7 +364,9 @@ class ConfigMaterial(Config):
return dup
def material_rename_homogenization(self,mapping,ID=None):
def material_rename_homogenization(self,
mapping: Dict[str, str],
ID: Sequence[int] = None) -> 'ConfigMaterial':
"""
Change homogenization name in material.
@ -374,7 +393,8 @@ class ConfigMaterial(Config):
return dup
def material_add(self,**kwargs):
def material_add(self,
**kwargs: Any) -> 'ConfigMaterial':
"""
Add material entries.
@ -453,7 +473,7 @@ class ConfigMaterial(Config):
N = max(N,s[0]) if len(s)>0 else N
n = max(n,s[1]) if len(s)>1 else n
mat = [{'constituents':[{} for _ in range(n)]} for _ in range(N)]
mat: Sequence[dict] = [{'constituents':[{} for _ in range(n)]} for _ in range(N)]
if 'v' not in kwargs:
shaped['v'] = np.broadcast_to(1/n,(N,n))
@ -461,7 +481,7 @@ class ConfigMaterial(Config):
map_shape = {'O':(N,n,4),'F_i':(N,n,3,3)}
for k,v in shaped.items():
target = map_shape.get(k,(N,n))
obj = np.broadcast_to(v.reshape(util.shapeshifter(v.shape,target,mode='right')),target)
obj = np.broadcast_to(v.reshape(util.shapeshifter(v.shape, target, mode = 'right')), target)
for i in range(N):
if k in ['phase','O','v','F_i']:
for j in range(n):

35
python/damask/_crystal.py
View File

@ -33,9 +33,9 @@ class Crystal():
def __init__(self,*,
family = None,
lattice = None,
a = None,b = None,c = None,
alpha = None,beta = None,gamma = None,
degrees = False):
a: float = None, b: float = None, c: float = None,
alpha: float = None, beta: float = None, gamma: float = None,
degrees: bool = False):
"""
Representation of crystal in terms of crystal family or Bravais lattice.
@ -62,7 +62,7 @@ class Crystal():
Angles are given in degrees. Defaults to False.
"""
if family not in [None] + list(lattice_symmetries.values()):
if family is not None and family not in list(lattice_symmetries.values()):
raise KeyError(f'invalid crystal family "{family}"')
if lattice is not None and family is not None and family != lattice_symmetries[lattice]:
raise KeyError(f'incompatible family "{family}" for lattice "{lattice}"')
@ -107,9 +107,6 @@ class Crystal():
if np.any([np.roll([self.alpha,self.beta,self.gamma],r)[0]
>= np.sum(np.roll([self.alpha,self.beta,self.gamma],r)[1:]) for r in range(3)]):
raise ValueError ('each lattice angle must be less than sum of others')
else:
self.a = self.b = self.c = None
self.alpha = self.beta = self.gamma = None
def __repr__(self):
@ -122,7 +119,8 @@ class Crystal():
'α={:.5g}°, β={:.5g}°, γ={:.5g}°'.format(*np.degrees(self.parameters[3:]))])
def __eq__(self,other):
def __eq__(self,
other: object) -> bool:
"""
Equal to other.
@ -132,6 +130,8 @@ class Crystal():
Crystal to check for equality.
"""
if not isinstance(other, Crystal):
return NotImplemented
return self.lattice == other.lattice and \
self.parameters == other.parameters and \
self.family == other.family
@ -139,8 +139,7 @@ class Crystal():
@property
def parameters(self):
"""Return lattice parameters a, b, c, alpha, beta, gamma."""
return (self.a,self.b,self.c,self.alpha,self.beta,self.gamma)
if hasattr(self,'a'): return (self.a,self.b,self.c,self.alpha,self.beta,self.gamma)
@property
def immutable(self):
@ -269,7 +268,7 @@ class Crystal():
https://doi.org/10.1063/1.1661333
"""
if None in self.parameters:
if self.parameters is None:
raise KeyError('missing crystal lattice parameters')
return np.array([
[1,0,0],
@ -315,7 +314,9 @@ class Crystal():
+ _lattice_points.get(self.lattice if self.lattice == 'hP' else \
self.lattice[-1],None),dtype=float)
def to_lattice(self, *, direction: np.ndarray = None, plane: np.ndarray = None) -> np.ndarray:
def to_lattice(self, *,
direction: np.ndarray = None,
plane: np.ndarray = None) -> np.ndarray:
"""
Calculate lattice vector corresponding to crystal frame direction or plane normal.
@ -339,7 +340,9 @@ class Crystal():
return np.einsum('il,...l',basis,axis)
def to_frame(self, *, uvw: np.ndarray = None, hkl: np.ndarray = None) -> np.ndarray:
def to_frame(self, *,
uvw: np.ndarray = None,
hkl: np.ndarray = None) -> np.ndarray:
"""
Calculate crystal frame vector along lattice direction [uvw] or plane normal (hkl).
@ -362,7 +365,8 @@ class Crystal():
return np.einsum('il,...l',basis,axis)
def kinematics(self, mode: str) -> Dict[str, List[np.ndarray]]:
def kinematics(self,
mode: str) -> Dict[str, List[np.ndarray]]:
"""
Return crystal kinematics systems.
@ -621,7 +625,8 @@ class Crystal():
'plane': [m[:,3:6] for m in master]}
def relation_operations(self, model: str) -> Tuple[str, Rotation]:
def relation_operations(self,
model: str) -> Tuple[str, Rotation]:
"""
Crystallographic orientation relationships for phase transformations.

436
python/damask/_grid.py
View File

@ -3,6 +3,9 @@ import copy
import warnings
import multiprocessing as mp
from functools import partial
import typing
from typing import Union, Optional, TextIO, List, Sequence
from pathlib import Path
import numpy as np
import pandas as pd
@ -13,7 +16,8 @@ from . import VTK
from . import util
from . import grid_filters
from . import Rotation
from . import Table
from ._typehints import FloatSequence, IntSequence
class Grid:
"""
@ -25,30 +29,34 @@ class Grid:
the physical size.
"""
def __init__(self,material,size,origin=[0.0,0.0,0.0],comments=[]):
def __init__(self,
material: np.ndarray,
size: FloatSequence,
origin: FloatSequence = np.zeros(3),
comments: Union[str, Sequence[str]] = None):
"""
New geometry definition for grid solvers.
Parameters
----------
material : numpy.ndarray of shape (:,:,:)
material : numpy.ndarray, shape (:,:,:)
Material indices. The shape of the material array defines
the number of cells.
size : list or numpy.ndarray of shape (3)
size : sequence of float, len (3)
Physical size of grid in meter.
origin : list or numpy.ndarray of shape (3), optional
Coordinates of grid origin in meter.
comments : list of str, optional
origin : sequence of float, len (3), optional
Coordinates of grid origin in meter. Defaults to [0.0,0.0,0.0].
comments : (list of) str, optional
Comments, e.g. history of operations.
"""
self.material = material
self.size = size
self.origin = origin
self.comments = comments
self.size = size # type: ignore
self.origin = origin # type: ignore
self.comments = [] if comments is None else comments # type: ignore
def __repr__(self):
def __repr__(self) -> str:
"""Basic information on grid definition."""
mat_min = np.nanmin(self.material)
mat_max = np.nanmax(self.material)
@ -62,14 +70,15 @@ class Grid:
])
def __copy__(self):
def __copy__(self) -> 'Grid':
"""Create deep copy."""
return copy.deepcopy(self)
copy = __copy__
def __eq__(self,other):
def __eq__(self,
other: object) -> bool:
"""
Test equality of other.
@ -79,85 +88,91 @@ class Grid:
Grid to compare self against.
"""
return (np.allclose(other.size,self.size)
if not isinstance(other, Grid):
return NotImplemented
return bool(np.allclose(other.size,self.size)
and np.allclose(other.origin,self.origin)
and np.all(other.cells == self.cells)
and np.all(other.material == self.material))
@property
def material(self):
def material(self) -> np.ndarray:
"""Material indices."""
return self._material
@material.setter
def material(self,material):
def material(self,
material: np.ndarray):
if len(material.shape) != 3:
raise ValueError(f'invalid material shape {material.shape}')
elif material.dtype not in np.sctypes['float'] + np.sctypes['int']:
if material.dtype not in np.sctypes['float'] and material.dtype not in np.sctypes['int']:
raise TypeError(f'invalid material data type {material.dtype}')
else:
self._material = np.copy(material)
if self.material.dtype in np.sctypes['float'] and \
np.all(self.material == self.material.astype(int).astype(float)):
self._material = self.material.astype(int)
self._material = np.copy(material)
if self.material.dtype in np.sctypes['float'] and \
np.all(self.material == self.material.astype(int).astype(float)):
self._material = self.material.astype(int)
@property
def size(self):
def size(self) -> np.ndarray:
"""Physical size of grid in meter."""
return self._size
@size.setter
def size(self,size):
def size(self,
size: FloatSequence):
if len(size) != 3 or any(np.array(size) < 0):
raise ValueError(f'invalid size {size}')
else:
self._size = np.array(size)
self._size = np.array(size)
@property
def origin(self):
def origin(self) -> np.ndarray:
"""Coordinates of grid origin in meter."""
return self._origin
@origin.setter
def origin(self,origin):
def origin(self,
origin: FloatSequence):
if len(origin) != 3:
raise ValueError(f'invalid origin {origin}')
else:
self._origin = np.array(origin)
self._origin = np.array(origin)
@property
def comments(self):
def comments(self) -> List[str]:
"""Comments, e.g. history of operations."""
return self._comments
@comments.setter
def comments(self,comments):
def comments(self,
comments: Union[str, Sequence[str]]):
self._comments = [str(c) for c in comments] if isinstance(comments,list) else [str(comments)]
@property
def cells(self):
def cells(self) -> np.ndarray:
"""Number of cells in x,y,z direction."""
return np.asarray(self.material.shape)
@property
def N_materials(self):
def N_materials(self) -> int:
"""Number of (unique) material indices within grid."""
return np.unique(self.material).size
@staticmethod
def load(fname):
def load(fname: Union[str, Path]) -> 'Grid':
"""
Load from VTK image data file.
Parameters
----------
fname : str or or pathlib.Path
fname : str or pathlib.Path
Grid file to read. Valid extension is .vti, which will be appended
if not given.
@ -178,8 +193,9 @@ class Grid:
comments=comments)
@typing. no_type_check
@staticmethod
def load_ASCII(fname):
def load_ASCII(fname)-> 'Grid':
"""
Load from geom file.
@ -198,15 +214,17 @@ class Grid:
"""
warnings.warn('Support for ASCII-based geom format will be removed in DAMASK 3.0.0', DeprecationWarning,2)
try:
if isinstance(fname, (str, Path)):
f = open(fname)
except TypeError:
elif isinstance(fname, TextIO):
f = fname
else:
raise TypeError
f.seek(0)
try:
header_length,keyword = f.readline().split()[:2]
header_length = int(header_length)
header_length_,keyword = f.readline().split()[:2]
header_length = int(header_length_)
except ValueError:
header_length,keyword = (-1, 'invalid')
if not keyword.startswith('head') or header_length < 3:
@ -216,8 +234,7 @@ class Grid:
content = f.readlines()
for i,line in enumerate(content[:header_length]):
items = line.split('#')[0].lower().strip().split()
key = items[0] if items else ''
if key == 'grid':
if (key := items[0] if items else '') == 'grid':
cells = np.array([ int(dict(zip(items[1::2],items[2::2]))[i]) for i in ['a','b','c']])
elif key == 'size':
size = np.array([float(dict(zip(items[1::2],items[2::2]))[i]) for i in ['x','y','z']])
@ -226,19 +243,18 @@ class Grid:
else:
comments.append(line.strip())
material = np.empty(cells.prod()) # initialize as flat array
material = np.empty(int(cells.prod())) # initialize as flat array
i = 0
for line in content[header_length:]:
items = line.split('#')[0].split()
if len(items) == 3:
if items[1].lower() == 'of':
items = np.ones(int(items[0]))*float(items[2])
if len(items := line.split('#')[0].split()) == 3:
if items[1].lower() == 'of':
material_entry = np.ones(int(items[0]))*float(items[2])
elif items[1].lower() == 'to':
items = np.linspace(int(items[0]),int(items[2]),
material_entry = np.linspace(int(items[0]),int(items[2]),
abs(int(items[2])-int(items[0]))+1,dtype=float)
else: items = list(map(float,items))
else: items = list(map(float,items))
material[i:i+len(items)] = items
else: material_entry = list(map(float, items))
else: material_entry = list(map(float, items))
material[i:i+len(material_entry)] = material_entry
i += len(items)
if i != cells.prod():
@ -251,13 +267,13 @@ class Grid:
@staticmethod
def load_Neper(fname):
def load_Neper(fname: Union[str, Path]) -> 'Grid':
"""
Load from Neper VTK file.
Parameters
----------
fname : str, pathlib.Path, or file handle
fname : str or pathlib.Path
Geometry file to read.
Returns
@ -266,7 +282,7 @@ 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
@ -276,10 +292,10 @@ class Grid:
@staticmethod
def load_DREAM3D(fname,
feature_IDs=None,cell_data=None,
phases='Phases',Euler_angles='EulerAngles',
base_group=None):
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':
"""
Load DREAM.3D (HDF5) file.
@ -290,24 +306,24 @@ class Grid:
Parameters
----------
fname : str
fname : str or or pathlib.Path
Filename of the DREAM.3D (HDF5) file.
feature_IDs : str
feature_IDs : str, optional
Name of the dataset containing the mapping between cells and
grain-wise data. Defaults to 'None', in which case cell-wise
data is used.
cell_data : str
cell_data : str, optional
Name of the group (folder) containing cell-wise data. Defaults to
None in wich case it is automatically detected.
phases : str
phases : str, optional
Name of the dataset containing the phase ID. It is not used for
grain-wise data, i.e. when feature_IDs is not None.
Defaults to 'Phases'.
Euler_angles : str
Euler_angles : str, optional
Name of the dataset containing the crystallographic orientation as
Euler angles in radians It is not used for grain-wise data, i.e.
when feature_IDs is not None. Defaults to 'EulerAngles'.
base_group : str
base_group : str, optional
Path to the group (folder) that contains geometry (_SIMPL_GEOMETRY),
and grain- or cell-wise data. Defaults to None, in which case
it is set as the path that contains _SIMPL_GEOMETRY/SPACING.
@ -339,7 +355,9 @@ class Grid:
@staticmethod
def from_table(table,coordinates,labels):
def from_table(table: Table,
coordinates: str,
labels: Union[str, Sequence[str]]) -> 'Grid':
"""
Create grid from ASCII table.
@ -350,7 +368,7 @@ class Grid:
coordinates : str
Label of the vector column containing the spatial coordinates.
Need to be ordered (1./x fast, 3./z slow).
labels : str or list of str
labels : (list of) str
Label(s) of the columns containing the material definition.
Each unique combination of values results in one material ID.
@ -372,28 +390,35 @@ class Grid:
@staticmethod
def _find_closest_seed(seeds, weights, point):
def _find_closest_seed(seeds: np.ndarray,
weights: np.ndarray,
point: np.ndarray) -> np.integer:
return np.argmin(np.sum((np.broadcast_to(point,(len(seeds),3))-seeds)**2,axis=1) - weights)
@staticmethod
def from_Laguerre_tessellation(cells,size,seeds,weights,material=None,periodic=True):
def from_Laguerre_tessellation(cells: IntSequence,
size: FloatSequence,
seeds: np.ndarray,
weights: FloatSequence,
material: IntSequence = None,
periodic: bool = True):
"""
Create grid from Laguerre tessellation.
Parameters
----------
cells : int numpy.ndarray of shape (3)
cells : sequence of int, len (3)
Number of cells in x,y,z direction.
size : list or numpy.ndarray of shape (3)
size : sequence of float, len (3)
Physical size of the grid in meter.
seeds : numpy.ndarray of shape (:,3)
seeds : numpy.ndarray, shape (:,3)
Position of the seed points in meter. All points need to lay within the box.
weights : numpy.ndarray of shape (seeds.shape[0])
weights : sequence of float, len (seeds.shape[0])
Weights of the seeds. Setting all weights to 1.0 gives a standard Voronoi tessellation.
material : numpy.ndarray of shape (seeds.shape[0]), optional
material : sequence of int, len (seeds.shape[0]), optional
Material ID of the seeds.
Defaults to None, in which case materials are consecutively numbered.
periodic : Boolean, optional
periodic : bool, optional
Assume grid to be periodic. Defaults to True.
Returns
@ -402,13 +427,14 @@ 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)
@ -421,29 +447,33 @@ class Grid:
if periodic: material_ %= len(weights)
return Grid(material = material_ if material is None else material[material_],
return Grid(material = material_ if material is None else np.array(material)[material_],
size = size,
comments = util.execution_stamp('Grid','from_Laguerre_tessellation'),
)
@staticmethod
def from_Voronoi_tessellation(cells,size,seeds,material=None,periodic=True):
def from_Voronoi_tessellation(cells: IntSequence,
size: FloatSequence,
seeds: np.ndarray,
material: IntSequence = None,
periodic: bool = True) -> 'Grid':
"""
Create grid from Voronoi tessellation.
Parameters
----------
cells : int numpy.ndarray of shape (3)
cells : sequence of int, len (3)
Number of cells in x,y,z direction.
size : list or numpy.ndarray of shape (3)
size : sequence of float, len (3)
Physical size of the grid in meter.
seeds : numpy.ndarray of shape (:,3)
seeds : numpy.ndarray, shape (:,3)
Position of the seed points in meter. All points need to lay within the box.
material : numpy.ndarray of shape (seeds.shape[0]), optional
material : sequence of int, len (seeds.shape[0]), optional
Material ID of the seeds.
Defaults to None, in which case materials are consecutively numbered.
periodic : Boolean, optional
periodic : bool, optional
Assume grid to be periodic. Defaults to True.
Returns
@ -460,7 +490,7 @@ class Grid:
except TypeError:
material_ = tree.query(coords, n_jobs = int(os.environ.get('OMP_NUM_THREADS',4)))[1] # scipy <1.6
return Grid(material = (material_ if material is None else material[material_]).reshape(cells),
return Grid(material = (material_ if material is None else np.array(material)[material_]).reshape(cells),
size = size,
comments = util.execution_stamp('Grid','from_Voronoi_tessellation'),
)
@ -509,15 +539,20 @@ class Grid:
@staticmethod
def from_minimal_surface(cells,size,surface,threshold=0.0,periods=1,materials=(0,1)):
def from_minimal_surface(cells: IntSequence,
size: FloatSequence,
surface: str,
threshold: float = 0.0,
periods: int = 1,
materials: IntSequence = (0,1)) -> 'Grid':
"""
Create grid from definition of triply periodic minimal surface.
Parameters
----------
cells : int numpy.ndarray of shape (3)
cells : sequence of int, len (3)
Number of cells in x,y,z direction.
size : list or numpy.ndarray of shape (3)
size : sequence of float, len (3)
Physical size of the grid in meter.
surface : str
Type of the minimal surface. See notes for details.
@ -525,7 +560,7 @@ class Grid:
Threshold of the minimal surface. Defaults to 0.0.
periods : integer, optional.
Number of periods per unit cell. Defaults to 1.
materials : (int, int), optional
materials : sequence of int, len (2)
Material IDs. Defaults to (0,1).
Returns
@ -566,22 +601,21 @@ class Grid:
>>> import numpy as np
>>> import damask
>>> damask.Grid.from_minimal_surface(np.array([64]*3,int),np.ones(3),
... 'Gyroid')
cells a b c: 64 x 64 x 64
size x y z: 1.0 x 1.0 x 1.0
origin x y z: 0.0 0.0 0.0
>>> damask.Grid.from_minimal_surface([64]*3,np.ones(3)*1.e-4,'Gyroid')
cells : 64 x 64 x 64
size : 0.0001 x 0.0001 x 0.0001 / m³
origin: 0.0 0.0 0.0 / m
# materials: 2
Minimal surface of 'Neovius' type. non-default material IDs.
>>> import numpy as np
>>> import damask
>>> damask.Grid.from_minimal_surface(np.array([80]*3,int),np.ones(3),
>>> damask.Grid.from_minimal_surface([80]*3,np.ones(3)*5.e-4,
... 'Neovius',materials=(1,5))
cells a b c: 80 x 80 x 80
size x y z: 1.0 x 1.0 x 1.0
origin x y z: 0.0 0.0 0.0
cells : 80 x 80 x 80
size : 0.0005 x 0.0005 x 0.0005 / m³
origin: 0.0 0.0 0.0 / m
# materials: 2 (min: 1, max: 5)
"""
@ -595,7 +629,9 @@ class Grid:
)
def save(self,fname,compress=True):
def save(self,
fname: Union[str, Path],
compress: bool = True):
"""
Save as VTK image data file.
@ -611,10 +647,11 @@ class Grid:
v.add(self.material.flatten(order='F'),'material')
v.add_comments(self.comments)
v.save(fname if str(fname).endswith('.vti') else str(fname)+'.vti',parallel=False,compress=compress)
v.save(fname,parallel=False,compress=compress)
def save_ASCII(self,fname):
def save_ASCII(self,
fname: Union[str, TextIO]):
"""
Save as geom file.
@ -644,26 +681,33 @@ class Grid:
header='\n'.join(header), fmt=format_string, comments='')
def show(self):
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,dimension,center,exponent,
fill=None,R=Rotation(),inverse=False,periodic=True):
def add_primitive(self,
dimension: Union[FloatSequence, IntSequence],
center: Union[FloatSequence, IntSequence],
exponent: Union[FloatSequence, float],
fill: int = None,
R: Rotation = Rotation(),
inverse: bool = False,
periodic: bool = True) -> 'Grid':
"""
Insert a primitive geometric object at a given position.
Parameters
----------
dimension : int or float numpy.ndarray of shape (3)
Dimension (diameter/side length) of the primitive. If given as
integers, cell centers are addressed.
If given as floats, coordinates are addressed.
center : int or float numpy.ndarray of shape (3)
Center of the primitive. If given as integers, cell centers are addressed.
If given as floats, coordinates in space are addressed.
exponent : numpy.ndarray of shape (3) or float
dimension : sequence of int or float, len (3)
Dimension (diameter/side length) of the primitive.
If given as integers, cell centers are addressed.
If given as floats, physical coordinates are addressed.
center : sequence of int or float, len (3)
Center of the primitive.
If given as integers, cell centers are addressed.
If given as floats, physical coordinates are addressed.
exponent : float or sequence of float, len (3)
Exponents for the three axes.
0 gives octahedron (ǀxǀ^(2^0) + ǀyǀ^(2^0) + ǀzǀ^(2^0) < 1)
1 gives sphere (ǀxǀ^(2^1) + ǀyǀ^(2^1) + ǀzǀ^(2^1) < 1)
@ -671,10 +715,10 @@ class Grid:
Fill value for primitive. Defaults to material.max()+1.
R : damask.Rotation, optional
Rotation of primitive. Defaults to no rotation.
inverse : Boolean, optional
inverse : bool, optional
Retain original materials within primitive and fill outside.
Defaults to False.
periodic : Boolean, optional
periodic : bool, optional
Assume grid to be periodic. Defaults to True.
Returns
@ -690,9 +734,9 @@ class Grid:
>>> import damask
>>> g = damask.Grid(np.zeros([64]*3,int), np.ones(3)*1e-4)
>>> g.add_primitive(np.ones(3)*5e-5,np.ones(3)*5e-5,1)
cells a b c: 64 x 64 x 64
size x y z: 0.0001 x 0.0001 x 0.0001
origin x y z: 0.0 0.0 0.0
cells : 64 x 64 x 64
size : 0.0001 x 0.0001 x 0.0001 / m³
origin: 0.0 0.0 0.0 / m
# materials: 2
Add a cube at the origin.
@ -701,9 +745,9 @@ class Grid:
>>> import damask
>>> g = damask.Grid(np.zeros([64]*3,int), np.ones(3)*1e-4)
>>> g.add_primitive(np.ones(3,int)*32,np.zeros(3),np.inf)
cells a b c: 64 x 64 x 64
size x y z: 0.0001 x 0.0001 x 0.0001
origin x y z: 0.0 0.0 0.0
cells : 64 x 64 x 64
size : 0.0001 x 0.0001 x 0.0001 / m³
origin: 0.0 0.0 0.0 / m
# materials: 2
"""
@ -734,15 +778,16 @@ class Grid:
)
def mirror(self,directions,reflect=False):
def mirror(self,
directions: Sequence[str],
reflect: bool = False) -> 'Grid':
"""
Mirror grid along given directions.
Parameters
----------
directions : iterable containing str
directions : (sequence of) {'x', 'y', 'z'}
Direction(s) along which the grid is mirrored.
Valid entries are 'x', 'y', 'z'.
reflect : bool, optional
Reflect (include) outermost layers. Defaults to False.
@ -759,17 +804,16 @@ class Grid:
>>> import damask
>>> g = damask.Grid(np.zeros([32]*3,int), np.ones(3)*1e-4)
>>> g.mirror('xy',True)
cells a b c: 64 x 64 x 32
size x y z: 0.0002 x 0.0002 x 0.0001
origin x y z: 0.0 0.0 0.0
cells : 64 x 64 x 32
size : 0.0002 x 0.0002 x 0.0001 / m³
origin: 0.0 0.0 0.0 / m
# materials: 1
"""
valid = ['x','y','z']
if not set(directions).issubset(valid):
if not set(directions).issubset(valid := ['x', 'y', 'z']):
raise ValueError(f'invalid direction {set(directions).difference(valid)} specified')
limits = [None,None] if reflect else [-2,0]
limits: Sequence[Optional[int]] = [None,None] if reflect else [-2,0]
mat = self.material.copy()
if 'x' in directions:
@ -786,15 +830,15 @@ class Grid:
)
def flip(self,directions):
def flip(self,
directions: Sequence[str]) -> 'Grid':
"""
Flip grid along given directions.
Parameters
----------
directions : iterable containing str
directions : (sequence of) {'x', 'y', 'z'}
Direction(s) along which the grid is flipped.
Valid entries are 'x', 'y', 'z'.
Returns
-------
@ -802,11 +846,11 @@ class Grid:
Updated grid-based geometry.
"""
valid = ['x','y','z']
if not set(directions).issubset(valid):
if not set(directions).issubset(valid := ['x', 'y', 'z']):
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,
@ -815,15 +859,17 @@ class Grid:
)
def scale(self,cells,periodic=True):
def scale(self,
cells: IntSequence,
periodic: bool = True) -> 'Grid':
"""
Scale grid to new cells.
Parameters
----------
cells : numpy.ndarray of shape (3)
cells : sequence of int, len (3)
Number of cells in x,y,z direction.
periodic : Boolean, optional
periodic : bool, optional
Assume grid to be periodic. Defaults to True.
Returns
@ -839,9 +885,9 @@ class Grid:
>>> import damask
>>> g = damask.Grid(np.zeros([32]*3,int),np.ones(3)*1e-4)
>>> g.scale(g.cells*2)
cells a b c: 64 x 64 x 64
size x y z: 0.0001 x 0.0001 x 0.0001
origin x y z: 0.0 0.0 0.0
cells : 64 x 64 x 64
size : 0.0001 x 0.0001 x 0.0001 / m³
origin: 0.0 0.0 0.0 / m
# materials: 1
"""
@ -859,7 +905,10 @@ class Grid:
)
def clean(self,stencil=3,selection=None,periodic=True):
def clean(self,
stencil: int = 3,
selection: IntSequence = None,
periodic: bool = True) -> 'Grid':
"""
Smooth grid by selecting most frequent material index within given stencil at each location.
@ -867,9 +916,9 @@ class Grid:
----------
stencil : int, optional
Size of smoothing stencil.
selection : list, optional
selection : sequence of int, optional
Field values that can be altered. Defaults to all.
periodic : Boolean, optional
periodic : bool, optional
Assume grid to be periodic. Defaults to True.
Returns
@ -878,7 +927,7 @@ class Grid:
Updated grid-based geometry.
"""
def mostFrequent(arr,selection=None):
def mostFrequent(arr: np.ndarray, selection = None):
me = arr[arr.size//2]
if selection is None or me in selection:
unique, inverse = np.unique(arr, return_inverse=True)
@ -899,7 +948,7 @@ class Grid:
)
def renumber(self):
def renumber(self) -> 'Grid':
"""
Renumber sorted material indices as 0,...,N-1.
@ -918,7 +967,9 @@ class Grid:
)
def rotate(self,R,fill=None):
def rotate(self,
R: Rotation,
fill: int = None) -> 'Grid':
"""
Rotate grid (pad if required).
@ -926,7 +977,7 @@ class Grid:
----------
R : damask.Rotation
Rotation to apply to the grid.
fill : int or float, optional
fill : int, optional
Material index to fill the corners. Defaults to material.max() + 1.
Returns
@ -935,14 +986,13 @@ 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)
@ -956,17 +1006,20 @@ class Grid:
)
def canvas(self,cells=None,offset=None,fill=None):
def canvas(self,
cells: IntSequence = None,
offset: IntSequence = None,
fill: int = None) -> 'Grid':
"""
Crop or enlarge/pad grid.
Parameters
----------
cells : numpy.ndarray of shape (3)
cells : sequence of int, len (3), optional
Number of cells x,y,z direction.
offset : numpy.ndarray of shape (3)
offset : sequence of int, len (3), optional
Offset (measured in cells) from old to new grid [0,0,0].
fill : int or float, optional
fill : int, optional
Material index to fill the background. Defaults to material.max() + 1.
Returns
@ -981,42 +1034,43 @@ class Grid:
>>> import numpy as np
>>> import damask
>>> g = damask.Grid(np.zeros([32]*3,int),np.ones(3)*1e-4)
>>> g.canvas(np.array([32,32,16],int))
cells a b c: 33 x 32 x 16
size x y z: 0.0001 x 0.0001 x 5e-05
origin x y z: 0.0 0.0 0.0
>>> g.canvas([32,32,16])
cells : 33 x 32 x 16
size : 0.0001 x 0.0001 x 5e-05 / m³
origin: 0.0 0.0 0.0 / m
# materials: 1
"""
if offset is None: offset = 0
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
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
canvas = np.full(self.cells if cells is None else 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))
ll = np.clip(-offset, 0,np.minimum( cells,self.cells-offset))
ur = np.clip(-offset+self.cells,0,np.minimum( cells,self.cells-offset))
LL = np.clip( offset_, 0,np.minimum(self.cells, cells_+offset_))
UR = np.clip( offset_+cells_, 0,np.minimum(self.cells, cells_+offset_))
ll = np.clip(-offset_, 0,np.minimum( cells_,self.cells-offset_))
ur = np.clip(-offset_+self.cells,0,np.minimum( cells_,self.cells-offset_))
canvas[ll[0]:ur[0],ll[1]:ur[1],ll[2]:ur[2]] = self.material[LL[0]:UR[0],LL[1]:UR[1],LL[2]:UR[2]]
return Grid(material = canvas,
size = self.size/self.cells*np.asarray(canvas.shape),
origin = self.origin+offset*self.size/self.cells,
origin = self.origin+offset_*self.size/self.cells,
comments = self.comments+[util.execution_stamp('Grid','canvas')],
)
def substitute(self,from_material,to_material):
def substitute(self,
from_material: IntSequence,
to_material: IntSequence) -> 'Grid':
"""
Substitute material indices.
Parameters
----------
from_material : iterable of ints
from_material : sequence of int
Material indices to be substituted.
to_material : iterable of ints
to_material : sequence of int
New material indices.
Returns
@ -1025,20 +1079,18 @@ 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):
def sort(self) -> 'Grid':
"""
Sort material indices such that min(material) is located at (0,0,0).
@ -1060,7 +1112,11 @@ class Grid:
)
def vicinity_offset(self,vicinity=1,offset=None,trigger=[],periodic=True):
def vicinity_offset(self,
vicinity: int = 1,
offset: int = None,
trigger: IntSequence = [],
periodic: bool = True) -> 'Grid':
"""
Offset material index of points in the vicinity of xxx.
@ -1076,10 +1132,10 @@ class Grid:
offset : int, optional
Offset (positive or negative) to tag material indices,
defaults to material.max()+1.
trigger : list of ints, optional
trigger : sequence of int, optional
List of material indices that trigger a change.
Defaults to [], meaning that any different neighbor triggers a change.
periodic : Boolean, optional
periodic : bool, optional
Assume grid to be periodic. Defaults to True.
Returns
@ -1088,8 +1144,7 @@ class Grid:
Updated grid-based geometry.
"""
def tainted_neighborhood(stencil,trigger):
def tainted_neighborhood(stencil: np.ndarray, trigger):
me = stencil[stencil.shape[0]//2]
return np.any(stencil != me if len(trigger) == 0 else
np.in1d(stencil,np.array(list(set(trigger) - {me}))))
@ -1108,17 +1163,19 @@ class Grid:
)
def get_grain_boundaries(self,periodic=True,directions='xyz'):
def get_grain_boundaries(self,
periodic: bool = True,
directions: Sequence[str] = 'xyz') -> VTK:
"""
Create VTK unstructured grid containing grain boundaries.
Parameters
----------
periodic : Boolean, optional
periodic : bool, optional
Assume grid to be periodic. Defaults to True.
directions : iterable containing str, optional
directions : (sequence of) {'x', 'y', 'z'}, optional
Direction(s) along which the boundaries are determined.
Valid entries are 'x', 'y', 'z'. Defaults to 'xyz'.
Defaults to 'xyz'.
Returns
-------
@ -1126,8 +1183,7 @@ class Grid:
VTK-based geometry of grain boundary network.
"""
valid = ['x','y','z']
if not set(directions).issubset(valid):
if not set(directions).issubset(valid := ['x', 'y', 'z']):
raise ValueError(f'invalid direction {set(directions).difference(valid)} specified')
o = [[0, self.cells[0]+1, np.prod(self.cells[:2]+1)+self.cells[0]+1, np.prod(self.cells[:2]+1)],

12
python/damask/_orientation.py
View File

@ -393,8 +393,8 @@ class Orientation(Rotation,Crystal):
Returns
-------
in : numpy.ndarray of quaternion.shape
Boolean array indicating whether Rodrigues-Frank vector falls into fundamental zone.
in : numpy.ndarray of bool, quaternion.shape
Whether Rodrigues-Frank vector falls into fundamental zone.
Notes
-----
@ -437,8 +437,8 @@ class Orientation(Rotation,Crystal):
Returns
-------
in : numpy.ndarray of quaternion.shape
Boolean array indicating whether Rodrigues-Frank vector falls into disorientation FZ.
in : numpy.ndarray of bool, quaternion.shape
Whether Rodrigues-Frank vector falls into disorientation FZ.
References
----------
@ -651,8 +651,8 @@ class Orientation(Rotation,Crystal):
Returns
-------
in : numpy.ndarray of shape (...)
Boolean array indicating whether vector falls into SST.
in : numpy.ndarray, shape (...)
Whether vector falls into SST.
"""
if not isinstance(vector,np.ndarray) or vector.shape[-1] != 3:

4
python/damask/_result.py
View File

@ -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),
@ -1817,7 +1817,7 @@ class Result:
output : (list of) str, optional
Names of the datasets to export to the file.
Defaults to '*', in which case all datasets are exported.
overwrite : boolean, optional
overwrite : bool, optional
Overwrite existing configuration files.
Defaults to False.

28
python/damask/_rotation.py
View File

@ -671,7 +671,7 @@ class Rotation:
----------
q : numpy.ndarray of shape (...,4)
Unit quaternion (q_0, q_1, q_2, q_3) in positive real hemisphere, i.e. ǀqǀ = 1, q_0 ≥ 0.
accept_homomorph : boolean, optional
accept_homomorph : bool, optional
Allow homomorphic variants, i.e. q_0 < 0 (negative real hemisphere).
Defaults to False.
P : int ∈ {-1,1}, optional
@ -706,7 +706,7 @@ class Rotation:
phi : numpy.ndarray of shape (...,3)
Euler angles (φ_1 ∈ [0,2π], ϕ ∈ [0,π], φ_2 ∈ [0,2π])
or (φ_1 ∈ [0,360], ϕ ∈ [0,180], φ_2 ∈ [0,360]) if degrees == True.
degrees : boolean, optional
degrees : bool, optional
Euler angles are given in degrees. Defaults to False.
Notes
@ -737,9 +737,9 @@ class Rotation:
axis_angle : numpy.ndarray of shape (...,4)
Axis and angle (n_1, n_2, n_3, ω) with ǀnǀ = 1 and ω ∈ [0,π]
or ω ∈ [0,180] if degrees == True.
degrees : boolean, optional
degrees : bool, optional
Angle ω is given in degrees. Defaults to False.
normalize: boolean, optional
normalize: bool, optional
Allow ǀnǀ ≠ 1. Defaults to False.
P : int ∈ {-1,1}, optional
Sign convention. Defaults to -1.
@ -773,9 +773,9 @@ class Rotation:
----------
basis : numpy.ndarray of shape (...,3,3)
Three three-dimensional lattice basis vectors.
orthonormal : boolean, optional
orthonormal : bool, optional
Basis is strictly orthonormal, i.e. is free of stretch components. Defaults to True.
reciprocal : boolean, optional
reciprocal : bool, optional
Basis vectors are given in reciprocal (instead of real) space. Defaults to False.
"""
@ -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.
@ -851,7 +850,7 @@ class Rotation:
----------
rho : numpy.ndarray of shape (...,4)
Rodrigues–Frank vector (n_1, n_2, n_3, tan(ω/2)) with ǀnǀ = 1 and ω ∈ [0,π].
normalize : boolean, optional
normalize : bool, optional
Allow ǀnǀ ≠ 1. Defaults to False.
P : int ∈ {-1,1}, optional
Sign convention. Defaults to -1.
@ -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).
@ -977,9 +975,9 @@ class Rotation:
N : integer, optional
Number of discrete orientations to be sampled from the given ODF.
Defaults to 500.
degrees : boolean, optional
degrees : bool, optional
Euler space grid coordinates are in degrees. Defaults to True.
fractions : boolean, optional
fractions : bool, optional
ODF values correspond to volume fractions, not probability densities.
Defaults to True.
rng_seed: {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional
@ -1033,7 +1031,7 @@ class Rotation:
Standard deviation of (Gaussian) misorientation distribution.
N : int, optional
Number of samples. Defaults to 500.
degrees : boolean, optional
degrees : bool, optional
sigma is given in degrees. Defaults to True.
rng_seed : {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional
A seed to initialize the BitGenerator.
@ -1072,7 +1070,7 @@ class Rotation:
Defaults to 0.
N : int, optional
Number of samples. Defaults to 500.
degrees : boolean, optional
degrees : bool, optional
sigma, alpha, and beta are given in degrees.
rng_seed : {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional
A seed to initialize the BitGenerator.

144
python/damask/_table.py
View File

@ -1,15 +1,21 @@
import re
import copy
from pathlib import Path
from typing import Union, Tuple, List
import pandas as pd
import numpy as np
from ._typehints import FileHandle
from . import util
class Table:
"""Manipulate multi-dimensional spreadsheet-like data."""
def __init__(self,data,shapes,comments=None):
def __init__(self,
data: np.ndarray,
shapes: dict,
comments: Union[str, list] = None):
"""
New spreadsheet.
@ -30,7 +36,7 @@ class Table:
self._relabel('uniform')
def __repr__(self):
def __repr__(self) -> str:
"""Brief overview."""
self._relabel('shapes')
data_repr = self.data.__repr__()
@ -38,7 +44,8 @@ class Table:
return '\n'.join(['# '+c for c in self.comments])+'\n'+data_repr
def __getitem__(self,item):
def __getitem__(self,
item: Union[slice, Tuple[slice, ...]]) -> 'Table':
"""
Slice the Table according to item.
@ -85,19 +92,21 @@ class Table:
comments=self.comments)
def __len__(self):
def __len__(self) -> int:
"""Number of rows."""
return len(self.data)
def __copy__(self):
def __copy__(self) -> 'Table':
"""Create deep copy."""
return copy.deepcopy(self)
copy = __copy__
def _label(self,what,how):
def _label(self,
what: Union[str, List[str]],
how: str) -> List[str]:
"""
Expand labels according to data shape.
@ -105,7 +114,7 @@ class Table:
----------
what : str or list
Labels to expand.
how : str
how : {'uniform, 'shapes', 'linear'}
Mode of labeling.
'uniform' ==> v v v
'shapes' ==> 3:v v v
@ -128,30 +137,38 @@ class Table:
return labels
def _relabel(self,how):
def _relabel(self,
how: str):
"""
Modify labeling of data in-place.
Parameters
----------
how : str
how : {'uniform, 'shapes', 'linear'}
Mode of labeling.
'uniform' ==> v v v
'shapes' ==> 3:v v v
'linear' ==> 1_v 2_v 3_v
"""
self.data.columns = self._label(self.shapes,how)
self.data.columns = self._label(self.shapes,how) #type: ignore
def _add_comment(self,label,shape,info):
def _add_comment(self,
label: str,
shape: Tuple[int, ...],
info: str = None):
if info is not None:
specific = f'{label}{" "+str(shape) if np.prod(shape,dtype=int) > 1 else ""}: {info}'
general = util.execution_stamp('Table')
self.comments.append(f'{specific} / {general}')
def isclose(self,other,rtol=1e-5,atol=1e-8,equal_nan=True):
def isclose(self,
other: 'Table',
rtol: float = 1e-5,
atol: float = 1e-8,
equal_nan: bool = True) -> np.ndarray:
"""
Report where values are approximately equal to corresponding ones of other Table.
@ -179,7 +196,11 @@ class Table:
equal_nan=equal_nan)
def allclose(self,other,rtol=1e-5,atol=1e-8,equal_nan=True):
def allclose(self,
other: 'Table',
rtol: float = 1e-5,
atol: float = 1e-8,
equal_nan: bool = True) -> bool:
"""
Test whether all values are approximately equal to corresponding ones of other Table.
@ -208,7 +229,7 @@ class Table:
@staticmethod
def load(fname):
def load(fname: FileHandle) -> 'Table':
"""
Load from ASCII table file.
@ -229,11 +250,8 @@ class Table:
Table data from file.
"""
try:
f = open(fname)
except TypeError:
f = fname
f.seek(0)
f = open(fname) if isinstance(fname, (str, Path)) else fname
f.seek(0)
comments = []
line = f.readline().strip()
@ -261,7 +279,7 @@ class Table:
@staticmethod
def load_ang(fname):
def load_ang(fname: FileHandle) -> 'Table':
"""
Load from ang file.
@ -286,11 +304,8 @@ class Table:
Table data from file.
"""
try:
f = open(fname)
except TypeError:
f = fname
f.seek(0)
f = open(fname) if isinstance(fname, (str, Path)) else fname
f.seek(0)
content = f.readlines()
@ -304,19 +319,19 @@ class Table:
data = np.loadtxt(content)
shapes = {'eu':3, 'pos':2, 'IQ':1, 'CI':1, 'ID':1, 'intensity':1, 'fit':1}
remainder = data.shape[1]-sum(shapes.values())
if remainder > 0: # 3.8 can do: if (remainder := data.shape[1]-sum(shapes.values())) > 0
if (remainder := data.shape[1]-sum(shapes.values())) > 0:
shapes['unknown'] = remainder
return Table(data,shapes,comments)
@property
def labels(self):
def labels(self) -> List[Tuple[int, ...]]:
return list(self.shapes)
def get(self,label):
def get(self,
label: str) -> np.ndarray:
"""
Get column data.
@ -336,7 +351,10 @@ class Table:
return data.astype(type(data.flatten()[0]))
def set(self,label,data,info=None):
def set(self,
label: str,
data: np.ndarray,
info: str = None) -> 'Table':
"""
Set column data.
@ -356,9 +374,8 @@ class Table:
"""
dup = self.copy()
dup._add_comment(label,data.shape[1:],info)
m = re.match(r'(.*)\[((\d+,)*(\d+))\]',label)
if m:
dup._add_comment(label, data.shape[1:], info)
if m := re.match(r'(.*)\[((\d+,)*(\d+))\]',label):
key = m.group(1)
idx = np.ravel_multi_index(tuple(map(int,m.group(2).split(","))),
self.shapes[key])
@ -369,7 +386,10 @@ class Table:
return dup
def add(self,label,data,info=None):
def add(self,
label: str,
data: np.ndarray,
info: str = None) -> 'Table':
"""
Add column data.
@ -401,7 +421,8 @@ class Table:
return dup
def delete(self,label):
def delete(self,
label: str) -> 'Table':
"""
Delete column data.
@ -422,7 +443,10 @@ class Table:
return dup
def rename(self,old,new,info=None):
def rename(self,
old: Union[str, List[str]],
new: Union[str, List[str]],
info: str = None) -> 'Table':
"""
Rename column data.
@ -448,7 +472,9 @@ class Table:
return dup
def sort_by(self,labels,ascending=True):
def sort_by(self,
labels: Union[str, List[str]],
ascending: Union[bool, List[bool]] = True) -> 'Table':
"""
Sort table by values of given labels.
@ -467,8 +493,7 @@ class Table:
"""
labels_ = [labels] if isinstance(labels,str) else labels.copy()
for i,l in enumerate(labels_):
m = re.match(r'(.*)\[((\d+,)*(\d+))\]',l)
if m:
if m := re.match(r'(.*)\[((\d+,)*(\d+))\]',l):
idx = np.ravel_multi_index(tuple(map(int,m.group(2).split(','))),
self.shapes[m.group(1)])
labels_[i] = f'{1+idx}_{m.group(1)}'
@ -481,7 +506,8 @@ class Table:
return dup
def append(self,other):
def append(self,
other: 'Table') -> 'Table':
"""
Append other table vertically (similar to numpy.vstack).
@ -500,13 +526,14 @@ class Table:
"""
if self.shapes != other.shapes or not self.data.columns.equals(other.data.columns):
raise KeyError('Labels or shapes or order do not match')
else:
dup = self.copy()
dup.data = dup.data.append(other.data,ignore_index=True)
return dup
dup = self.copy()
dup.data = dup.data.append(other.data,ignore_index=True)
return dup
def join(self,other):
def join(self,
other: 'Table') -> 'Table':
"""
Append other table horizontally (similar to numpy.hstack).
@ -525,15 +552,16 @@ class Table:
"""
if set(self.shapes) & set(other.shapes) or self.data.shape[0] != other.data.shape[0]:
raise KeyError('Duplicated keys or row count mismatch')
else:
dup = self.copy()
dup.data = dup.data.join(other.data)
for key in other.shapes:
dup.shapes[key] = other.shapes[key]
return dup
dup = self.copy()
dup.data = dup.data.join(other.data)
for key in other.shapes:
dup.shapes[key] = other.shapes[key]
return dup
def save(self,fname):
def save(self,
fname: FileHandle):
"""
Save as plain text file.
@ -543,9 +571,8 @@ class Table:
Filename or file for writing.
"""
seen = set()
labels = []
for l in [x for x in self.data.columns if not (x in seen or seen.add(x))]:
for l in list(dict.fromkeys(self.data.columns)):
if self.shapes[l] == (1,):
labels.append(f'{l}')
elif len(self.shapes[l]) == 1:
@ -555,10 +582,7 @@ class Table:
labels += [f'{util.srepr(self.shapes[l],"x")}:{i+1}_{l}' \
for i in range(np.prod(self.shapes[l]))]
try:
fhandle = open(fname,'w',newline='\n')
except TypeError:
fhandle = fname
f = open(fname,'w',newline='\n') if isinstance(fname, (str, Path)) else fname
fhandle.write('\n'.join([f'# {c}' for c in self.comments] + [' '.join(labels)])+'\n')
self.data.to_csv(fhandle,sep=' ',na_rep='nan',index=False,header=False)
f.write('\n'.join([f'# {c}' for c in self.comments] + [' '.join(labels)])+'\n')
self.data.to_csv(f,sep=' ',na_rep='nan',index=False,header=False)

11
python/damask/_typehints.py Normal file
View File

@ -0,0 +1,11 @@
"""Functionality for typehints."""
from typing import Sequence, Union, TextIO
from pathlib import Path
import numpy as np
FloatSequence = Union[np.ndarray,Sequence[float]]
IntSequence = Union[np.ndarray,Sequence[int]]
FileHandle = Union[TextIO, str, Path]

81
python/damask/_vtk.py
View File

@ -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 +22,8 @@ class VTK:
High-level interface to VTK.
"""
def __init__(self,vtk_data):
def __init__(self,
vtk_data: vtk.vtkDataSet):
"""
New spatial visualization.
@ -28,15 +31,17 @@ class VTK:
----------
vtk_data : subclass of vtk.vtkDataSet
Description of geometry and topology, optionally with attached data.
Valid types are vtk.vtkRectilinearGrid, vtk.vtkUnstructuredGrid,
or vtk.vtkPolyData.
Valid types are vtk.vtkImageData, vtk.vtkUnstructuredGrid,
vtk.vtkPolyData, and vtk.vtkRectilinearGrid.
"""
self.vtk_data = vtk_data
@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 +65,15 @@ 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 +105,9 @@ 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 +147,7 @@ class VTK:
@staticmethod
def from_poly_data(points):
def from_poly_data(points: np.ndarray) -> 'VTK':
"""
Create VTK of type vtk.polyData.
@ -172,15 +181,17 @@ 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
@ -191,8 +202,7 @@ class VTK:
"""
if not os.path.isfile(fname): # vtk has a strange error handling
raise FileNotFoundError(f'No such file: {fname}')
ext = Path(fname).suffix
if ext == '.vtk' or dataset_type is not None:
if (ext := Path(fname).suffix) == '.vtk' or dataset_type is not None:
reader = vtk.vtkGenericDataObjectReader()
reader.SetFileName(str(fname))
if dataset_type is None:
@ -234,7 +244,11 @@ 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.
@ -242,7 +256,7 @@ class VTK:
----------
fname : str or pathlib.Path
Filename for writing.
parallel : boolean, optional
parallel : bool, optional
Write data in parallel background process. Defaults to True.
compress : bool, optional
Compress with zlib algorithm. Defaults to True.
@ -280,7 +294,9 @@ 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 +343,8 @@ class VTK:
raise TypeError
def get(self,label):
def get(self,
label: str) -> np.ndarray:
"""
Get either cell or point data.
@ -369,7 +386,7 @@ 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 +396,8 @@ class VTK:
return []
def set_comments(self,comments):
def set_comments(self,
comments: Union[str, List[str]]):
"""
Set comments.
@ -396,7 +414,8 @@ 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 +428,7 @@ 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")}')
@ -436,28 +455,30 @@ class VTK:
width = tk.winfo_screenwidth()
height = tk.winfo_screenheight()
tk.destroy()
except Exception as e:
except Exception:
width = 1024
height = 768
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()
window.Render()
iren.Start()
if os.name == 'posix' and 'DISPLAY' not in os.environ:
print('Found no rendering device')
else:
window.Render()
iren.Start()

188
python/damask/grid_filters.py
View File

@ -12,21 +12,25 @@ the following operations are required for tensorial data:
"""
from typing import Sequence, Tuple, Union
from typing import Tuple as _Tuple
from scipy import spatial as _spatial
import numpy as _np
from ._typehints import FloatSequence as _FloatSequence, IntSequence as _IntSequence
def _ks(size: _np.ndarray, cells: Union[_np.ndarray,Sequence[int]], first_order: bool = False) -> _np.ndarray:
def _ks(size: _FloatSequence,
cells: _IntSequence,
first_order: bool = False) -> _np.ndarray:
"""
Get wave numbers operator.
Parameters
----------
size : numpy.ndarray of shape (3)
size : sequence of float, len (3)
Physical size of the periodic field.
cells : numpy.ndarray of shape (3)
cells : sequence of int, len (3)
Number of cells.
first_order : bool, optional
Correction for first order derivatives, defaults to False.
@ -45,20 +49,21 @@ def _ks(size: _np.ndarray, cells: Union[_np.ndarray,Sequence[int]], first_order:
return _np.stack(_np.meshgrid(k_sk,k_sj,k_si,indexing = 'ij'), axis=-1)
def curl(size: _np.ndarray, f: _np.ndarray) -> _np.ndarray:
def curl(size: _FloatSequence,
f: _np.ndarray) -> _np.ndarray:
u"""
Calculate curl of a vector or tensor field in Fourier space.
Parameters
----------
size : numpy.ndarray of shape (3)
size : sequence of float, len (3)
Physical size of the periodic field.
f : numpy.ndarray of shape (:,:,:,3) or (:,:,:,3,3)
f : numpy.ndarray, shape (:,:,:,3) or (:,:,:,3,3)
Periodic field of which the curl is calculated.
Returns
-------
∇ × f : numpy.ndarray
∇ × f : numpy.ndarray, shape (:,:,:,3) or (:,:,:,3,3)
Curl of f.
"""
@ -76,20 +81,21 @@ def curl(size: _np.ndarray, f: _np.ndarray) -> _np.ndarray:
return _np.fft.irfftn(curl_,axes=(0,1,2),s=f.shape[:3])
def divergence(size: _np.ndarray, f: _np.ndarray) -> _np.ndarray:
def divergence(size: _FloatSequence,
f: _np.ndarray) -> _np.ndarray:
u"""
Calculate divergence of a vector or tensor field in Fourier space.
Parameters
----------
size : numpy.ndarray of shape (3)
size : sequence of float, len (3)
Physical size of the periodic field.
f : numpy.ndarray of shape (:,:,:,3) or (:,:,:,3,3)
f : numpy.ndarray, shape (:,:,:,3) or (:,:,:,3,3)
Periodic field of which the divergence is calculated.
Returns
-------
∇ · f : numpy.ndarray
∇ · f : numpy.ndarray, shape (:,:,:,1) or (:,:,:,3)
Divergence of f.
"""
@ -103,20 +109,21 @@ def divergence(size: _np.ndarray, f: _np.ndarray) -> _np.ndarray:
return _np.fft.irfftn(div_,axes=(0,1,2),s=f.shape[:3])
def gradient(size: _np.ndarray, f: _np.ndarray) -> _np.ndarray:
def gradient(size: _FloatSequence,
f: _np.ndarray) -> _np.ndarray:
u"""
Calculate gradient of a scalar or vector fieldin Fourier space.
Calculate gradient of a scalar or vector field in Fourier space.
Parameters
----------
size : numpy.ndarray of shape (3)
size : sequence of float, len (3)
Physical size of the periodic field.
f : numpy.ndarray of shape (:,:,:,1) or (:,:,:,3)
f : numpy.ndarray, shape (:,:,:,1) or (:,:,:,3)
Periodic field of which the gradient is calculated.
Returns
-------
∇ f : numpy.ndarray
∇ f : numpy.ndarray, shape (:,:,:,3) or (:,:,:,3,3)
Divergence of f.
"""
@ -130,29 +137,30 @@ def gradient(size: _np.ndarray, f: _np.ndarray) -> _np.ndarray:
return _np.fft.irfftn(grad_,axes=(0,1,2),s=f.shape[:3])
def coordinates0_point(cells: Union[ _np.ndarray,Sequence[int]],
size: _np.ndarray,
origin: _np.ndarray = _np.zeros(3)) -> _np.ndarray:
def coordinates0_point(cells: _IntSequence,
size: _FloatSequence,
origin: _FloatSequence = _np.zeros(3)) -> _np.ndarray:
"""
Cell center positions (undeformed).
Parameters
----------
cells : numpy.ndarray of shape (3)
cells : sequence of int, len (3)
Number of cells.
size : numpy.ndarray of shape (3)
size : sequence of float, len (3)
Physical size of the periodic field.
origin : numpy.ndarray, optional
origin : sequence of float, len(3), optional
Physical origin of the periodic field. Defaults to [0.0,0.0,0.0].
Returns
-------
x_p_0 : numpy.ndarray
x_p_0 : numpy.ndarray, shape (:,:,:,3)
Undeformed cell center coordinates.
"""
start = origin + size/_np.array(cells)*.5
end = origin + size - size/_np.array(cells)*.5
size_ = _np.array(size,float)
start = origin + size_/_np.array(cells,int)*.5
end = origin + size_ - size_/_np.array(cells,int)*.5
return _np.stack(_np.meshgrid(_np.linspace(start[0],end[0],cells[0]),
_np.linspace(start[1],end[1],cells[1]),
@ -160,24 +168,25 @@ def coordinates0_point(cells: Union[ _np.ndarray,Sequence[int]],
axis = -1)
def displacement_fluct_point(size: _np.ndarray, F: _np.ndarray) -> _np.ndarray:
def displacement_fluct_point(size: _FloatSequence,
F: _np.ndarray) -> _np.ndarray:
"""
Cell center displacement field from fluctuation part of the deformation gradient field.
Parameters
----------
size : numpy.ndarray of shape (3)
size : sequence of float, len (3)
Physical size of the periodic field.
F : numpy.ndarray
F : numpy.ndarray, shape (:,:,:,3,3)
Deformation gradient field.
Returns
-------
u_p_fluct : numpy.ndarray
u_p_fluct : numpy.ndarray, shape (:,:,:,3)
Fluctuating part of the cell center displacements.
"""
integrator = 0.5j*size/_np.pi
integrator = 0.5j*_np.array(size,float)/_np.pi
k_s = _ks(size,F.shape[:3],False)
k_s_squared = _np.einsum('...l,...l',k_s,k_s)
@ -192,20 +201,21 @@ def displacement_fluct_point(size: _np.ndarray, F: _np.ndarray) -> _np.ndarray:
return _np.fft.irfftn(displacement,axes=(0,1,2),s=F.shape[:3])
def displacement_avg_point(size: _np.ndarray, F: _np.ndarray) -> _np.ndarray:
def displacement_avg_point(size: _FloatSequence,
F: _np.ndarray) -> _np.ndarray:
"""
Cell center displacement field from average part of the deformation gradient field.
Parameters
----------
size : numpy.ndarray of shape (3)
size : sequence of float, len (3)
Physical size of the periodic field.
F : numpy.ndarray
F : numpy.ndarray, shape (:,:,:,3,3)
Deformation gradient field.
Returns
-------
u_p_avg : numpy.ndarray
u_p_avg : numpy.ndarray, shape (:,:,:,3)
Average part of the cell center displacements.
"""
@ -213,42 +223,45 @@ def displacement_avg_point(size: _np.ndarray, F: _np.ndarray) -> _np.ndarray:
return _np.einsum('ml,ijkl->ijkm',F_avg - _np.eye(3),coordinates0_point(F.shape[:3],size))
def displacement_point(size: _np.ndarray, F: _np.ndarray) -> _np.ndarray:
def displacement_point(size: _FloatSequence,
F: _np.ndarray) -> _np.ndarray:
"""
Cell center displacement field from deformation gradient field.
Parameters
----------
size : numpy.ndarray of shape (3)
size : sequence of float, len (3)
Physical size of the periodic field.
F : numpy.ndarray
F : numpy.ndarray, shape (:,:,:,3,3)
Deformation gradient field.
Returns
-------
u_p : numpy.ndarray
u_p : numpy.ndarray, shape (:,:,:,3)
Cell center displacements.
"""
return displacement_avg_point(size,F) + displacement_fluct_point(size,F)
def coordinates_point(size: _np.ndarray, F: _np.ndarray, origin: _np.ndarray = _np.zeros(3)) -> _np.ndarray:
def coordinates_point(size: _FloatSequence,
F: _np.ndarray,
origin: _FloatSequence = _np.zeros(3)) -> _np.ndarray:
"""
Cell center positions.
Parameters
----------
size : numpy.ndarray of shape (3)
size : sequence of float, len (3)
Physical size of the periodic field.
F : numpy.ndarray
F : numpy.ndarray, shape (:,:,:,3,3)
Deformation gradient field.
origin : numpy.ndarray of shape (3), optional
origin : sequence of float, len(3), optional
Physical origin of the periodic field. Defaults to [0.0,0.0,0.0].
Returns
-------
x_p : numpy.ndarray
x_p : numpy.ndarray, shape (:,:,:,3)
Cell center coordinates.
"""
@ -256,14 +269,14 @@ def coordinates_point(size: _np.ndarray, F: _np.ndarray, origin: _np.ndarray = _
def cellsSizeOrigin_coordinates0_point(coordinates0: _np.ndarray,
ordered: bool = True) -> Tuple[_np.ndarray,_np.ndarray,_np.ndarray]:
ordered: bool = True) -> _Tuple[_np.ndarray,_np.ndarray,_np.ndarray]:
"""
Return grid 'DNA', i.e. cells, size, and origin from 1D array of point positions.
Parameters
----------
coordinates0 : numpy.ndarray of shape (:,3)
Undeformed cell coordinates.
coordinates0 : numpy.ndarray, shape (:,3)
Undeformed cell center coordinates.
ordered : bool, optional
Expect coordinates0 data to be ordered (x fast, z slow).
Defaults to True.
@ -277,7 +290,7 @@ def cellsSizeOrigin_coordinates0_point(coordinates0: _np.ndarray,
coords = [_np.unique(coordinates0[:,i]) for i in range(3)]
mincorner = _np.array(list(map(min,coords)))
maxcorner = _np.array(list(map(max,coords)))
cells = _np.array(list(map(len,coords)),'i')
cells = _np.array(list(map(len,coords)),int)
size = cells/_np.maximum(cells-1,1) * (maxcorner-mincorner)
delta = size/cells
origin = mincorner - delta*.5
@ -305,24 +318,24 @@ def cellsSizeOrigin_coordinates0_point(coordinates0: _np.ndarray,
return (cells,size,origin)
def coordinates0_node(cells: Union[_np.ndarray,Sequence[int]],
size: _np.ndarray,
origin: _np.ndarray = _np.zeros(3)) -> _np.ndarray:
def coordinates0_node(cells: _IntSequence,
size: _FloatSequence,
origin: _FloatSequence = _np.zeros(3)) -> _np.ndarray:
"""
Nodal positions (undeformed).
Parameters
----------
cells : numpy.ndarray of shape (3)
cells : sequence of int, len (3)
Number of cells.
size : numpy.ndarray of shape (3)
size : sequence of float, len (3)
Physical size of the periodic field.
origin : numpy.ndarray of shape (3), optional
origin : sequence of float, len(3), optional
Physical origin of the periodic field. Defaults to [0.0,0.0,0.0].
Returns
-------
x_n_0 : numpy.ndarray
x_n_0 : numpy.ndarray, shape (:,:,:,3)
Undeformed nodal coordinates.
"""
@ -332,40 +345,42 @@ def coordinates0_node(cells: Union[_np.ndarray,Sequence[int]],
axis = -1)
def displacement_fluct_node(size: _np.ndarray, F: _np.ndarray) -> _np.ndarray:
def displacement_fluct_node(size: _FloatSequence,
F: _np.ndarray) -> _np.ndarray:
"""
Nodal displacement field from fluctuation part of the deformation gradient field.
Parameters
----------
size : numpy.ndarray of shape (3)
size : sequence of float, len (3)
Physical size of the periodic field.
F : numpy.ndarray
F : numpy.ndarray, shape (:,:,:,3,3)
Deformation gradient field.
Returns
-------
u_n_fluct : numpy.ndarray
u_n_fluct : numpy.ndarray, shape (:,:,:,3)
Fluctuating part of the nodal displacements.
"""
return point_to_node(displacement_fluct_point(size,F))
def displacement_avg_node(size: _np.ndarray, F: _np.ndarray) -> _np.ndarray:
def displacement_avg_node(size: _FloatSequence,
F: _np.ndarray) -> _np.ndarray:
"""
Nodal displacement field from average part of the deformation gradient field.
Parameters
----------
size : numpy.ndarray of shape (3)
size : sequence of float, len (3)
Physical size of the periodic field.
F : numpy.ndarray
F : numpy.ndarray, shape (:,:,:,3,3)
Deformation gradient field.
Returns
-------
u_n_avg : numpy.ndarray
u_n_avg : numpy.ndarray, shape (:,:,:,3)
Average part of the nodal displacements.
"""
@ -373,42 +388,45 @@ def displacement_avg_node(size: _np.ndarray, F: _np.ndarray) -> _np.ndarray:
return _np.einsum('ml,ijkl->ijkm',F_avg - _np.eye(3),coordinates0_node(F.shape[:3],size))
def displacement_node(size: _np.ndarray, F: _np.ndarray) -> _np.ndarray:
def displacement_node(size: _FloatSequence,
F: _np.ndarray) -> _np.ndarray:
"""
Nodal displacement field from deformation gradient field.
Parameters
----------
size : numpy.ndarray of shape (3)
size : sequence of float, len (3)
Physical size of the periodic field.
F : numpy.ndarray
F : numpy.ndarray, shape (:,:,:,3,3)
Deformation gradient field.
Returns
-------
u_p : numpy.ndarray
u_p : numpy.ndarray, shape (:,:,:,3)
Nodal displacements.
"""
return displacement_avg_node(size,F) + displacement_fluct_node(size,F)
def coordinates_node(size: _np.ndarray, F: _np.ndarray, origin: _np.ndarray = _np.zeros(3)) -> _np.ndarray:
def coordinates_node(size: _FloatSequence,
F: _np.ndarray,
origin: _FloatSequence = _np.zeros(3)) -> _np.ndarray:
"""
Nodal positions.
Parameters
----------
size : numpy.ndarray of shape (3)
size : sequence of float, len (3)
Physical size of the periodic field.
F : numpy.ndarray
F : numpy.ndarray, shape (:,:,:,3,3)
Deformation gradient field.
origin : numpy.ndarray of shape (3), optional
origin : sequence of float, len(3), optional
Physical origin of the periodic field. Defaults to [0.0,0.0,0.0].
Returns
-------
x_n : numpy.ndarray
x_n : numpy.ndarray, shape (:,:,:,3)
Nodal coordinates.
"""
@ -416,13 +434,13 @@ def coordinates_node(size: _np.ndarray, F: _np.ndarray, origin: _np.ndarray = _n
def cellsSizeOrigin_coordinates0_node(coordinates0: _np.ndarray,
ordered: bool = True) -> Tuple[_np.ndarray,_np.ndarray,_np.ndarray]:
ordered: bool = True) -> _Tuple[_np.ndarray,_np.ndarray,_np.ndarray]:
"""
Return grid 'DNA', i.e. cells, size, and origin from 1D array of nodal positions.
Parameters
----------
coordinates0 : numpy.ndarray of shape (:,3)
coordinates0 : numpy.ndarray, shape (:,3)
Undeformed nodal coordinates.
ordered : bool, optional
Expect coordinates0 data to be ordered (x fast, z slow).
@ -437,7 +455,7 @@ def cellsSizeOrigin_coordinates0_node(coordinates0: _np.ndarray,
coords = [_np.unique(coordinates0[:,i]) for i in range(3)]
mincorner = _np.array(list(map(min,coords)))
maxcorner = _np.array(list(map(max,coords)))
cells = _np.array(list(map(len,coords)),'i') - 1
cells = _np.array(list(map(len,coords)),int) - 1
size = maxcorner-mincorner
origin = mincorner
@ -463,12 +481,12 @@ def point_to_node(cell_data: _np.ndarray) -> _np.ndarray:
Parameters
----------
cell_data : numpy.ndarray of shape (:,:,:,...)
cell_data : numpy.ndarray, shape (:,:,:,...)
Data defined on the cell centers of a periodic grid.
Returns
-------
node_data : numpy.ndarray of shape (:,:,:,...)
node_data : numpy.ndarray, shape (:,:,:,...)
Data defined on the nodes of a periodic grid.
"""
@ -485,12 +503,12 @@ def node_to_point(node_data: _np.ndarray) -> _np.ndarray:
Parameters
----------
node_data : numpy.ndarray of shape (:,:,:,...)
node_data : numpy.ndarray, shape (:,:,:,...)
Data defined on the nodes of a periodic grid.
Returns
-------
cell_data : numpy.ndarray of shape (:,:,:,...)
cell_data : numpy.ndarray, shape (:,:,:,...)
Data defined on the cell centers of a periodic grid.
"""
@ -507,7 +525,7 @@ def coordinates0_valid(coordinates0: _np.ndarray) -> bool:
Parameters
----------
coordinates0 : numpy.ndarray
coordinates0 : numpy.ndarray, shape (:,3)
Array of undeformed cell coordinates.
Returns
@ -523,17 +541,19 @@ def coordinates0_valid(coordinates0: _np.ndarray) -> bool:
return False
def regrid(size: _np.ndarray, F: _np.ndarray, cells: Union[_np.ndarray,Sequence[int]]) -> _np.ndarray:
def regrid(size: _FloatSequence,
F: _np.ndarray,
cells: _IntSequence) -> _np.ndarray:
"""
Return mapping from coordinates in deformed configuration to a regular grid.
Parameters
----------
size : numpy.ndarray of shape (3)
size : sequence of float, len (3)
Physical size.
F : numpy.ndarray of shape (:,:,:,3,3)
F : numpy.ndarray, shape (:,:,:,3,3), shape (:,:,:,3,3)
Deformation gradient field.
cells : numpy.ndarray of shape (3)
cells : sequence of int, len (3)
Cell count along x,y,z of remapping grid.
"""

20
python/damask/mechanics.py
View File

@ -5,7 +5,7 @@ All routines operate on numpy.ndarrays of shape (...,3,3).
"""
from typing import Sequence
from typing import Sequence as _Sequence
import numpy as _np
@ -122,7 +122,9 @@ def rotation(T: _np.ndarray) -> _rotation.Rotation:
return _rotation.Rotation.from_matrix(_polar_decomposition(T,'R')[0])
def strain(F: _np.ndarray, t: str, m: float) -> _np.ndarray:
def strain(F: _np.ndarray,
t: str,
m: float) -> _np.ndarray:
"""
Calculate strain tensor (Seth–Hill family).
@ -162,7 +164,8 @@ def strain(F: _np.ndarray, t: str, m: float) -> _np.ndarray:
return eps
def stress_Cauchy(P: _np.ndarray, F: _np.ndarray) -> _np.ndarray:
def stress_Cauchy(P: _np.ndarray,
F: _np.ndarray) -> _np.ndarray:
"""
Calculate the Cauchy stress (true stress).
@ -184,7 +187,8 @@ def stress_Cauchy(P: _np.ndarray, F: _np.ndarray) -> _np.ndarray:
return _tensor.symmetric(_np.einsum('...,...ij,...kj',1.0/_np.linalg.det(F),P,F))
def stress_second_Piola_Kirchhoff(P: _np.ndarray, F: _np.ndarray) -> _np.ndarray:
def stress_second_Piola_Kirchhoff(P: _np.ndarray,
F: _np.ndarray) -> _np.ndarray:
"""
Calculate the second Piola-Kirchhoff stress.
@ -243,7 +247,8 @@ def stretch_right(T: _np.ndarray) -> _np.ndarray:
return _polar_decomposition(T,'U')[0]
def _polar_decomposition(T: _np.ndarray, requested: Sequence[str]) -> tuple:
def _polar_decomposition(T: _np.ndarray,
requested: _Sequence[str]) -> tuple:
"""
Perform singular value decomposition.
@ -251,7 +256,7 @@ def _polar_decomposition(T: _np.ndarray, requested: Sequence[str]) -> tuple:
----------
T : numpy.ndarray, shape (...,3,3)
Tensor of which the singular values are computed.
requested : iterable of str
requested : sequence of {'R', 'U', 'V'}
Requested outputs: ‘R’ for the rotation tensor,
‘V’ for left stretch tensor and ‘U’ for right stretch tensor.
@ -273,7 +278,8 @@ def _polar_decomposition(T: _np.ndarray, requested: Sequence[str]) -> tuple:
return tuple(output)
def _equivalent_Mises(T_sym: _np.ndarray, s: float) -> _np.ndarray:
def _equivalent_Mises(T_sym: _np.ndarray,
s: float) -> _np.ndarray:
"""
Base equation for Mises equivalent of a stress or strain tensor.

61
python/damask/seeds.py
View File

@ -1,25 +1,29 @@
"""Functionality for generation of seed points for Voronoi or Laguerre tessellation."""
from typing import Sequence,Tuple
from typing import Tuple as _Tuple
from scipy import spatial as _spatial
import numpy as _np
from ._typehints import FloatSequence as _FloatSequence, IntSequence as _IntSequence
from . import util as _util
from . import grid_filters as _grid_filters
def from_random(size: _np.ndarray, N_seeds: int, cells: _np.ndarray = None, rng_seed=None) -> _np.ndarray:
def from_random(size: _FloatSequence,
N_seeds: int,
cells: _IntSequence = None,
rng_seed=None) -> _np.ndarray:
"""
Place seeds randomly in space.
Parameters
----------
size : numpy.ndarray of shape (3)
size : sequence of float, len (3)
Physical size of the seeding domain.
N_seeds : int
Number of seeds.
cells : numpy.ndarray of shape (3), optional.
cells : sequence of int, len (3), optional.
If given, ensures that each seed results in a grain when a standard Voronoi
tessellation is performed using the given grid resolution (i.e. size/cells).
rng_seed : {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional
@ -28,29 +32,34 @@ def from_random(size: _np.ndarray, N_seeds: int, cells: _np.ndarray = None, rng_
Returns
-------
coords : numpy.ndarray of shape (N_seeds,3)
coords : numpy.ndarray, shape (N_seeds,3)
Seed coordinates in 3D space.
"""
size_ = _np.array(size,float)
rng = _np.random.default_rng(rng_seed)
if cells is None:
coords = rng.random((N_seeds,3)) * size
coords = rng.random((N_seeds,3)) * size_
else:
grid_coords = _grid_filters.coordinates0_point(cells,size).reshape(-1,3,order='F')
coords = grid_coords[rng.choice(_np.prod(cells),N_seeds, replace=False)] \
+ _np.broadcast_to(size/cells,(N_seeds,3))*(rng.random((N_seeds,3))*.5-.25) # wobble without leaving cells
+ _np.broadcast_to(size_/_np.array(cells,int),(N_seeds,3))*(rng.random((N_seeds,3))*.5-.25) # wobble w/o leaving grid
return coords
def from_Poisson_disc(size: _np.ndarray, N_seeds: int, N_candidates: int, distance: float,
periodic: bool = True, rng_seed=None) -> _np.ndarray:
def from_Poisson_disc(size: _FloatSequence,
N_seeds: int,
N_candidates: int,
distance: float,
periodic: bool = True,
rng_seed=None) -> _np.ndarray:
"""
Place seeds according to a Poisson disc distribution.
Parameters
----------
size : numpy.ndarray of shape (3)
size : sequence of float, len (3)
Physical size of the seeding domain.
N_seeds : int
Number of seeds.
@ -58,7 +67,7 @@ def from_Poisson_disc(size: _np.ndarray, N_seeds: int, N_candidates: int, distan
Number of candidates to consider for finding best candidate.
distance : float
Minimum acceptable distance to other seeds.
periodic : boolean, optional
periodic : bool, optional
Calculate minimum distance for periodically repeated grid.
rng_seed : {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional
A seed to initialize the BitGenerator. Defaults to None.
@ -66,27 +75,26 @@ def from_Poisson_disc(size: _np.ndarray, N_seeds: int, N_candidates: int, distan
Returns
-------
coords : numpy.ndarray of shape (N_seeds,3)
coords : numpy.ndarray, shape (N_seeds,3)
Seed coordinates in 3D space.
"""
rng = _np.random.default_rng(rng_seed)
coords = _np.empty((N_seeds,3))
coords[0] = rng.random(3) * size
coords[0] = rng.random(3) * _np.array(size,float)
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))
tree = _spatial.cKDTree(coords[:s],boxsize=size) if periodic else \
_spatial.cKDTree(coords[:s])
distances = tree.query(candidates)[0]
best = distances.argmax()
if distances[best] > distance: # require minimum separation
if distances.max() > distance: # require minimum separation
i = 0
coords[s] = candidates[best] # maximum separation to existing point cloud
coords[s] = candidates[distances.argmax()] # maximum separation to existing point cloud
s += 1
progress.update(s)
@ -96,8 +104,11 @@ def from_Poisson_disc(size: _np.ndarray, N_seeds: int, N_candidates: int, distan
return coords
def from_grid(grid, selection: Sequence[int] = None,
invert: bool = False, average: bool = False, periodic: bool = True) -> Tuple[_np.ndarray, _np.ndarray]:
def from_grid(grid,
selection: _IntSequence = None,
invert_selection: bool = False,
average: bool = False,
periodic: bool = True) -> _Tuple[_np.ndarray, _np.ndarray]:
"""
Create seeds from grid description.
@ -105,24 +116,24 @@ def from_grid(grid, selection: Sequence[int] = None,
----------
grid : damask.Grid
Grid from which the material IDs are used as seeds.
selection : iterable of integers, optional
selection : sequence of int, optional
Material IDs to consider.
invert : boolean, false
invert_selection : bool, optional
Consider all material IDs except those in selection. Defaults to False.
average : boolean, optional
average : bool, optional
Seed corresponds to center of gravity of material ID cloud.
periodic : boolean, optional
periodic : bool, optional
Center of gravity accounts for periodic boundaries.
Returns
-------
coords, materials : numpy.ndarray of shape (:,3), numpy.ndarray of shape (:)
coords, materials : numpy.ndarray, shape (:,3); numpy.ndarray, shape (:)
Seed coordinates in 3D space, material IDs.
"""
material = grid.material.reshape((-1,1),order='F')
mask = _np.full(grid.cells.prod(),True,dtype=bool) if selection is None else \
_np.isin(material,selection,invert=invert).flatten()
_np.isin(material,selection,invert=invert_selection).flatten()
coords = _grid_filters.coordinates0_point(grid.cells,grid.size).reshape(-1,3,order='F')
if not average:

11
python/damask/tensor.py
View File

@ -45,7 +45,8 @@ def eigenvalues(T_sym: _np.ndarray) -> _np.ndarray:
return _np.linalg.eigvalsh(symmetric(T_sym))
def eigenvectors(T_sym: _np.ndarray, RHS: bool = False) -> _np.ndarray:
def eigenvectors(T_sym: _np.ndarray,
RHS: bool = False) -> _np.ndarray:
"""
Eigenvectors of a symmetric tensor.
@ -63,14 +64,14 @@ def eigenvectors(T_sym: _np.ndarray, RHS: bool = False) -> _np.ndarray:
associated eigenvalues.
"""
(u,v) = _np.linalg.eigh(symmetric(T_sym))
_,v = _np.linalg.eigh(symmetric(T_sym))
if RHS:
v[_np.linalg.det(v) < 0.0,:,2] *= -1.0
if RHS: v[_np.linalg.det(v) < 0.0,:,2] *= -1.0
return v
def spherical(T: _np.ndarray, tensor: bool = True) -> _np.ndarray:
def spherical(T: _np.ndarray,
tensor: bool = True) -> _np.ndarray:
"""
Calculate spherical part of a tensor.

218
python/damask/util.py
View File

@ -7,12 +7,16 @@ import subprocess
import shlex
import re
import fractions
from collections import abc
from functools import reduce
from typing import Union, Tuple, Iterable, Callable, Dict, List, Any, Literal, SupportsIndex, Sequence
from pathlib import Path
import numpy as np
import h5py
from . import version
from ._typehints import IntSequence, FloatSequence
# limit visibility
__all__=[
@ -50,16 +54,17 @@ _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 +72,21 @@ 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 +95,15 @@ 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 +112,15 @@ 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 +129,15 @@ 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 +146,13 @@ 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 +161,7 @@ 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 +193,7 @@ 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 +208,10 @@ 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 +219,49 @@ 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')
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 +278,21 @@ 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.
@ -275,22 +300,25 @@ 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
Maintain three-dimensional output coordinates. Defaults to False.
Two-dimensional output uses right-handed frame spanned by
the next and next-next axis relative to the projection direction,
e.g. x-y when projecting along z and z-x when projecting along y.
Maintain three-dimensional output coordinates.
Defaults to False.
Returns
-------
coordinates : numpy.ndarray, shape (...,2 | 3)
Projected coordinates.
Notes
-----
Two-dimensional output uses right-handed frame spanned by
the next and next-next axis relative to the projection direction,
e.g. x-y when projecting along z and z-x when projecting along y.
Examples
--------
>>> import damask
@ -309,7 +337,10 @@ 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.
@ -317,22 +348,26 @@ 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
Maintain three-dimensional output coordinates. Defaults to False.
Two-dimensional output uses right-handed frame spanned by
the next and next-next axis relative to the projection direction,
e.g. x-y when projecting along z and z-x when projecting along y.
Maintain three-dimensional output coordinates.
Defaults to False.
Returns
-------
coordinates : numpy.ndarray, shape (...,2 | 3)
Projected coordinates.
Notes
-----
Two-dimensional output uses right-handed frame spanned by
the next and next-next axis relative to the projection direction,
e.g. x-y when projecting along z and z-x when projecting along y.
Examples
--------
>>> import damask
@ -351,15 +386,17 @@ 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: Union[int, IntSequence] = None) -> np.ndarray:
"""
Hybrid integer approximation.
@ -387,7 +424,10 @@ 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) -> Sequence[SupportsIndex]:
"""
Return dimensions that reshape 'fro' to become broadcastable to 'to'.
@ -398,9 +438,9 @@ 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.
@ -423,7 +463,7 @@ def shapeshifter(fro,to,mode='left',keep_ones=False):
"""
if not len(fro) and not len(to): return ()
if len(fro) == 0 and len(to) == 0: return ()
beg = dict(left ='(^.*\\b)',
right='(^.*?\\b)')
@ -431,24 +471,26 @@ def shapeshifter(fro,to,mode='left',keep_ones=False):
right='(.*?\\b)')
end = dict(left ='(.*?$)',
right='(.*$)')
fro = (1,) if not len(fro) else fro
to = (1,) if not len(to) else to
fro = (1,) if len(fro) == 0 else fro
to = (1,) if len(to) == 0 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: Any = ()
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, ...]) -> Sequence[SupportsIndex]:
"""
Return a shape that overlaps the rightmost entries of 'a' with the leftmost of 'b'.
@ -476,7 +518,7 @@ 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 +534,8 @@ 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 +553,7 @@ 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 +579,7 @@ 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 +611,20 @@ 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 +640,20 @@ 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 +671,7 @@ 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 +697,7 @@ 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 +725,17 @@ 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.
@ -708,12 +758,12 @@ 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)
if filled_length > int(self.bar_length * self.fraction_last) or \
if filled_length := int(self.bar_length * fraction) > int(self.bar_length * self.fraction_last) or \
datetime.datetime.now() - self.time_last_update > datetime.timedelta(seconds=10):
self.time_last_update = datetime.datetime.now()
bar = '█' * filled_length + '░' * (self.bar_length - filled_length)

2
python/mypy.ini
View File

@ -1,3 +1,5 @@
[mypy]
warn_redundant_casts = True
[mypy-scipy.*]
ignore_missing_imports = True
[mypy-h5py.*]

4
python/setup.py
View File

@ -16,7 +16,7 @@ setuptools.setup(
url='https://damask.mpie.de',
packages=setuptools.find_packages(),
include_package_data=True,
python_requires = '>=3.7',
python_requires = '>=3.8',
install_requires = [
'pandas>=0.24', # requires numpy
'numpy>=1.17', # needed for default_rng
@ -30,7 +30,7 @@ setuptools.setup(
'Intended Audience :: Science/Research',
'Topic :: Scientific/Engineering',
'Programming Language :: Python :: 3',
'License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)',
'License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+)',
'Operating System :: OS Independent',
],
)

6
python/tests/test_Colormap.py
View File

@ -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])])
@ -139,6 +140,11 @@ class TestColormap:
c += c
assert (np.allclose(c.colors[:len(c.colors)//2],c.colors[len(c.colors)//2:]))
def test_mul(self):
c = o = Colormap.from_predefined('jet')
o *= 2
assert c+c == o
@pytest.mark.parametrize('N,cmap,at,result',[
(8,'gray',0.5,[0.5,0.5,0.5]),
(17,'gray',0.5,[0.5,0.5,0.5]),

3
python/tests/test_Crystal.py
View File

@ -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([

22
python/tests/test_Grid.py
View File

@ -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)
@ -237,12 +238,27 @@ class TestGrid:
modified)
def test_canvas(self,default):
def test_canvas_extend(self,default):
cells = default.cells
grid_add = np.random.randint(0,30,(3))
modified = default.canvas(cells + grid_add)
cells_add = np.random.randint(0,30,(3))
modified = default.canvas(cells + cells_add)
assert np.all(modified.material[:cells[0],:cells[1],:cells[2]] == default.material)
@pytest.mark.parametrize('sign',[+1,-1])
@pytest.mark.parametrize('extra_offset',[0,-1])
def test_canvas_move_out(self,sign,extra_offset):
g = Grid(np.zeros(np.random.randint(3,30,(3)),int),np.ones(3))
o = sign*np.ones(3)*g.cells.min() +extra_offset*sign
if extra_offset == 0:
assert np.all(g.canvas(offset=o).material == 1)
else:
assert np.all(np.unique(g.canvas(offset=o).material) == (0,1))
def test_canvas_cells(self,default):
g = Grid(np.zeros(np.random.randint(3,30,(3)),int),np.ones(3))
cells = np.random.randint(1,30,(3))
offset = np.random.randint(-30,30,(3))
assert np.all(g.canvas(cells,offset).cells == cells)
@pytest.mark.parametrize('center1,center2',[(np.random.random(3)*.5,np.random.random()*8),
(np.random.randint(4,8,(3)),np.random.randint(9,12,(3)))])

9
python/tests/test_Orientation.py
View File

@ -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)

3
python/tests/test_Result.py
View File

@ -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'))

9
python/tests/test_Rotation.py
View File

@ -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)

4
python/tests/test_VTK.py
View File

@ -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

2
python/tests/test_seeds.py
View File

@ -67,5 +67,5 @@ class TestSeeds:
coords = seeds.from_random(size,N_seeds,cells)
grid = Grid.from_Voronoi_tessellation(cells,size,coords)
selection=np.random.randint(N_seeds)+1
coords,material = seeds.from_grid(grid,average=average,periodic=periodic,invert=invert,selection=[selection])
coords,material = seeds.from_grid(grid,average=average,periodic=periodic,invert_selection=invert,selection=[selection])
assert selection not in material if invert else (selection==material).all()

36
src/CPFEM.f90
View File

@ -14,6 +14,7 @@ module CPFEM
use config
use math
use rotations
use polynomials
use lattice
use material
use phase
@ -32,18 +33,18 @@ module CPFEM
real(pReal), dimension (:,:,:,:), allocatable, private :: &
CPFEM_dcsdE_knownGood !< known good tangent
integer(pInt), public :: &
cycleCounter = 0_pInt !< needs description
integer, public :: &
cycleCounter = 0 !< needs description
integer(pInt), parameter, public :: &
CPFEM_CALCRESULTS = 2_pInt**0_pInt, &
CPFEM_AGERESULTS = 2_pInt**1_pInt, &
CPFEM_BACKUPJACOBIAN = 2_pInt**2_pInt, &
CPFEM_RESTOREJACOBIAN = 2_pInt**3_pInt
integer, parameter, public :: &
CPFEM_CALCRESULTS = 2**0, &
CPFEM_AGERESULTS = 2**1, &
CPFEM_BACKUPJACOBIAN = 2**2, &
CPFEM_RESTOREJACOBIAN = 2**3
type, private :: tNumerics
integer :: &
iJacoStiffness !< frequency of stiffness update
iJacoStiffness !< frequency of stiffness update
end type tNumerics
type(tNumerics), private :: num
@ -83,6 +84,7 @@ subroutine CPFEM_initAll
call config_init
call math_init
call rotations_init
call polynomials_init
call lattice_init
call discretization_marc_init
call material_init(.false.)
@ -134,12 +136,12 @@ end subroutine CPFEM_init
!--------------------------------------------------------------------------------------------------
subroutine CPFEM_general(mode, ffn, ffn1, temperature_inp, dt, elFE, ip, cauchyStress, jacobian)
integer(pInt), intent(in) :: elFE, & !< FE element number
integer, intent(in) :: elFE, & !< FE element number
ip !< integration point number
real(pReal), intent(in) :: dt !< time increment
real(pReal), dimension (3,3), intent(in) :: ffn, & !< deformation gradient for t=t0
ffn1 !< deformation gradient for t=t1
integer(pInt), intent(in) :: mode !< computation mode 1: regular computation plus aging of results
integer, intent(in) :: mode !< computation mode 1: regular computation plus aging of results
real(pReal), intent(in) :: temperature_inp !< temperature
real(pReal), dimension(6), intent(out) :: cauchyStress !< stress as 6 vector
real(pReal), dimension(6,6), intent(out) :: jacobian !< jacobian as 66 tensor (Consistent tangent dcs/dE)
@ -150,7 +152,7 @@ subroutine CPFEM_general(mode, ffn, ffn1, temperature_inp, dt, elFE, ip, cauchyS
real(pReal), dimension (3,3,3,3) :: H_sym, &
H
integer(pInt) elCP, & ! crystal plasticity element number
integer elCP, & ! crystal plasticity element number
i, j, k, l, m, n, ph, homog, mySource,ce
real(pReal), parameter :: ODD_STRESS = 1e15_pReal, & !< return value for stress if terminallyIll
@ -171,17 +173,17 @@ subroutine CPFEM_general(mode, ffn, ffn1, temperature_inp, dt, elFE, ip, cauchyS
print'(a,/)', '#############################################'; flush (6)
endif
if (iand(mode, CPFEM_BACKUPJACOBIAN) /= 0_pInt) &
if (iand(mode, CPFEM_BACKUPJACOBIAN) /= 0) &
CPFEM_dcsde_knownGood = CPFEM_dcsde
if (iand(mode, CPFEM_RESTOREJACOBIAN) /= 0_pInt) &
if (iand(mode, CPFEM_RESTOREJACOBIAN) /= 0) &
CPFEM_dcsde = CPFEM_dcsde_knownGood
if (iand(mode, CPFEM_AGERESULTS) /= 0_pInt) call CPFEM_forward
if (iand(mode, CPFEM_AGERESULTS) /= 0) call CPFEM_forward
homogenization_F0(1:3,1:3,ce) = ffn
homogenization_F(1:3,1:3,ce) = ffn1
if (iand(mode, CPFEM_CALCRESULTS) /= 0_pInt) then
if (iand(mode, CPFEM_CALCRESULTS) /= 0) then
validCalculation: if (terminallyIll) then
call random_number(rnd)
@ -264,8 +266,8 @@ end subroutine CPFEM_forward
!--------------------------------------------------------------------------------------------------
subroutine CPFEM_results(inc,time)
integer(pInt), intent(in) :: inc
real(pReal), intent(in) :: time
integer, intent(in) :: inc
real(pReal), intent(in) :: time
call results_openJobFile
call results_addIncrement(inc,time)

2
src/CPFEM2.f90
View File

@ -16,6 +16,7 @@ module CPFEM2
use config
use math
use rotations
use polynomials
use lattice
use material
use phase
@ -57,6 +58,7 @@ subroutine CPFEM_initAll
call config_init
call math_init
call rotations_init
call polynomials_init
call lattice_init
#if defined(MESH)
call discretization_mesh_init(restart=interface_restartInc>0)

6
src/DAMASK_Marc.f90
View File

@ -223,9 +223,9 @@ subroutine hypela2(d,g,e,de,s,t,dt,ngens,m,nn,kcus,matus,ndi,nshear,disp, &
integer :: computationMode, i, node, CPnodeID
integer(pI32) :: defaultNumThreadsInt !< default value set by Marc
integer(pInt), save :: &
theInc = -1_pInt, & !< needs description
lastLovl = 0_pInt !< lovl in previous call to marc hypela2
integer, save :: &
theInc = -1, & !< needs description
lastLovl = 0 !< lovl in previous call to marc hypela2
real(pReal), save :: &
theTime = 0.0_pReal, & !< needs description
theDelta = 0.0_pReal

15
src/HDF5_utilities.f90
View File

@ -1857,13 +1857,13 @@ subroutine initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_
localShape
integer(HSIZE_T), intent(out), dimension(size(localShape,1)):: &
myStart, &
globalShape !< shape of the dataset (all processes)
globalShape !< shape of the dataset (all processes)
integer(HID_T), intent(out) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer, dimension(worldsize) :: &
readSize !< contribution of all processes
integer :: ierr
integer :: hdferr
integer(MPI_INTEGER_KIND) :: err_MPI
!-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties (is collective for MPI)
@ -1877,8 +1877,8 @@ subroutine initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_
if (parallel) then
call H5Pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
if (ierr /= 0) error stop 'MPI error'
call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_INTEGER,MPI_SUM,PETSC_COMM_WORLD,err_MPI) ! get total output size over each process
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
end if
#endif
myStart = int(0,HSIZE_T)
@ -1956,7 +1956,8 @@ subroutine initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
integer, dimension(worldsize) :: writeSize !< contribution of all processes
integer(HID_T) :: dcpl
integer :: ierr, hdferr
integer :: hdferr
integer(MPI_INTEGER_KIND) :: err_MPI
integer(HSIZE_T), parameter :: chunkSize = 1024_HSIZE_T**2/8_HSIZE_T
@ -1977,8 +1978,8 @@ subroutine initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
writeSize(worldrank+1) = int(myShape(ubound(myShape,1)))
#ifdef PETSC
if (parallel) then
call MPI_allreduce(MPI_IN_PLACE,writeSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
if (ierr /= 0) error stop 'MPI error'
call MPI_allreduce(MPI_IN_PLACE,writeSize,worldsize,MPI_INTEGER,MPI_SUM,PETSC_COMM_WORLD,err_MPI) ! get total output size over each process
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
end if
#endif
myStart = int(0,HSIZE_T)

6
src/YAML_parse.f90
View File

@ -191,8 +191,10 @@ logical function isScalar(line)
character(len=*), intent(in) :: line
isScalar = (.not.isKeyValue(line) .and. .not.isKey(line) .and. .not.isListItem(line) &
.and. .not.isFlow(line))
isScalar = (.not. isKeyValue(line) .and. &
.not. isKey(line) .and. &
.not. isListItem(line) .and. &
.not. isFlow(line))
end function isScalar

286
src/YAML_types.f90
View File

@ -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
@ -221,22 +223,22 @@ subroutine selfTest
select type(s1)
class is(tScalar)
s1 = '2'
endselect
end select
select type(s2)
class is(tScalar)
s2 = '3'
endselect
end select
select type(s3)
class is(tScalar)
s3 = '4'
endselect
end select
select type(s4)
class is(tScalar)
s4 = '5'
endselect
end select
allocate(tList::l1)
@ -249,14 +251,14 @@ subroutine selfTest
if (any(dNeq(l1%as1dFloat(),[2.0_pReal,3.0_pReal]))) error stop 'tList_as1dFloat'
if (n%get_asInt(1) /= 2) error stop 'byIndex_asInt'
if (dNeq(n%get_asFloat(2),3.0_pReal)) error stop 'byIndex_asFloat'
endselect
end select
allocate(tList::l3)
select type(l3)
class is(tList)
call l3%append(s3)
call l3%append(s4)
endselect
end select
allocate(tList::l2)
select type(l2)
@ -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
@ -385,12 +396,13 @@ function tNode_get_byIndex(self,i) result(node)
class(tItem), pointer :: item
integer :: j
select type(self)
class is(tList)
self_ => self%asList()
class default
call IO_error(706,ext_msg='Expected list')
endselect
end select
item => self_%first
@ -409,15 +421,14 @@ end function tNode_get_byIndex
!--------------------------------------------------------------------------------------------------
function tNode_get_byIndex_asFloat(self,i) result(nodeAsFloat)
class(tNode), intent(in), target :: self
integer, intent(in) :: i
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
integer, intent(in) :: i
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()
@ -457,21 +468,20 @@ end function tNode_get_byIndex_asInt
!--------------------------------------------------------------------------------------------------
function tNode_get_byIndex_asBool(self,i) result(nodeAsBool)
class(tNode), intent(in), target :: self
integer, intent(in) :: i
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()
class default
call IO_error(706,ext_msg='Expected scalar Boolean')
endselect
end select
end function tNode_get_byIndex_asBool
@ -481,21 +491,20 @@ end function tNode_get_byIndex_asBool
!--------------------------------------------------------------------------------------------------
function tNode_get_byIndex_asString(self,i) result(nodeAsString)
class(tNode), intent(in), target :: self
integer, intent(in) :: i
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()
class default
call IO_error(706,ext_msg='Expected scalar string')
endselect
end select
end function tNode_get_byIndex_asString
@ -505,21 +514,20 @@ end function tNode_get_byIndex_asString
!--------------------------------------------------------------------------------------------------
function tNode_get_byIndex_as1dFloat(self,i) result(nodeAs1dFloat)
class(tNode), intent(in), target :: self
integer, intent(in) :: i
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()
class default
call IO_error(706,ext_msg='Expected list of floats')
endselect
end select
end function tNode_get_byIndex_as1dFloat
@ -529,21 +537,20 @@ end function tNode_get_byIndex_as1dFloat
!--------------------------------------------------------------------------------------------------
function tNode_get_byIndex_as1dInt(self,i) result(nodeAs1dInt)
class(tNode), intent(in), target :: self
integer, intent(in) :: i
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()
class default
call IO_error(706,ext_msg='Expected list of integers')
endselect
end select
end function tNode_get_byIndex_as1dInt
@ -553,21 +560,20 @@ end function tNode_get_byIndex_as1dInt
!--------------------------------------------------------------------------------------------------
function tNode_get_byIndex_as1dBool(self,i) result(nodeAs1dBool)
class(tNode), intent(in), target :: self
integer, intent(in) :: i
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()
class default
call IO_error(706,ext_msg='Expected list of Booleans')
endselect
end select
end function tNode_get_byIndex_as1dBool
@ -577,21 +583,20 @@ end function tNode_get_byIndex_as1dBool
!--------------------------------------------------------------------------------------------------
function tNode_get_byIndex_as1dString(self,i) result(nodeAs1dString)
class(tNode), intent(in), target :: self
integer, intent(in) :: i
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()
class default
call IO_error(706,ext_msg='Expected list of strings')
endselect
end select
end function tNode_get_byIndex_as1dString
@ -609,22 +614,50 @@ 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()
item => dict%first
do j = 1, min(i,dict%length)-1
item => item%next
enddo
end do
class default
call IO_error(706,ext_msg='Expected dict')
endselect
end select
key = item%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
!-------------------------------------------------------------------------------------------------
@ -658,7 +691,7 @@ function tNode_contains(self,k) result(exists)
enddo
class default
call IO_error(706,ext_msg='Expected list or dict')
endselect
end select
end function tNode_contains
@ -686,7 +719,7 @@ function tNode_get_byKey(self,k,defaultVal) result(node)
self_ => self%asDict()
class default
call IO_error(706,ext_msg='Expected dict for key '//k)
endselect
end select
j = 1
item => self_%first
@ -713,23 +746,22 @@ end function tNode_get_byKey
!--------------------------------------------------------------------------------------------------
function tNode_get_byKey_asFloat(self,k,defaultVal) result(nodeAsFloat)
class(tNode), intent(in), target :: self
character(len=*), intent(in) :: k
real(pReal), intent(in),optional :: defaultVal
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()
class default
call IO_error(706,ext_msg='Expected scalar float for key '//k)
endselect
end select
elseif (present(defaultVal)) then
nodeAsFloat = defaultVal
else
@ -744,23 +776,22 @@ end function tNode_get_byKey_asFloat
!--------------------------------------------------------------------------------------------------
function tNode_get_byKey_asInt(self,k,defaultVal) result(nodeAsInt)
class(tNode), intent(in), target :: self
character(len=*), intent(in) :: k
integer, intent(in),optional :: defaultVal
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()
class default
call IO_error(706,ext_msg='Expected scalar integer for key '//k)
endselect
end select
elseif (present(defaultVal)) then
nodeAsInt = defaultVal
else
@ -775,23 +806,22 @@ end function tNode_get_byKey_asInt
!--------------------------------------------------------------------------------------------------
function tNode_get_byKey_asBool(self,k,defaultVal) result(nodeAsBool)
class(tNode), intent(in), target :: self
character(len=*), intent(in) :: k
logical, intent(in),optional :: defaultVal
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()
class default
call IO_error(706,ext_msg='Expected scalar Boolean for key '//k)
endselect
end select
elseif (present(defaultVal)) then
nodeAsBool = defaultVal
else
@ -806,23 +836,22 @@ end function tNode_get_byKey_asBool
!--------------------------------------------------------------------------------------------------
function tNode_get_byKey_asString(self,k,defaultVal) result(nodeAsString)
class(tNode), intent(in), target :: self
character(len=*), intent(in) :: k
character(len=*), intent(in),optional :: defaultVal
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()
class default
call IO_error(706,ext_msg='Expected scalar string for key '//k)
endselect
end select
elseif (present(defaultVal)) then
nodeAsString = defaultVal
else
@ -837,25 +866,24 @@ end function tNode_get_byKey_asString
!--------------------------------------------------------------------------------------------------
function tNode_get_byKey_as1dFloat(self,k,defaultVal,requiredSize) result(nodeAs1dFloat)
class(tNode), intent(in), target :: self
character(len=*), intent(in) :: k
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()
class default
call IO_error(706,ext_msg='Expected 1D float array for key '//k)
endselect
end select
elseif (present(defaultVal)) then
nodeAs1dFloat = defaultVal
else
@ -874,25 +902,24 @@ end function tNode_get_byKey_as1dFloat
!--------------------------------------------------------------------------------------------------
function tNode_get_byKey_as2dFloat(self,k,defaultVal,requiredShape) result(nodeAs2dFloat)
class(tNode), intent(in), target :: self
character(len=*), intent(in) :: k
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()
class default
call IO_error(706,ext_msg='Expected 2D float array for key '//k)
endselect
end select
elseif(present(defaultVal)) then
nodeAs2dFloat = defaultVal
else
@ -911,24 +938,22 @@ end function tNode_get_byKey_as2dFloat
!--------------------------------------------------------------------------------------------------
function tNode_get_byKey_as1dInt(self,k,defaultVal,requiredSize) result(nodeAs1dInt)
class(tNode), intent(in), target :: self
character(len=*), intent(in) :: k
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()
class default
call IO_error(706,ext_msg='Expected 1D integer array for key '//k)
endselect
end select
elseif (present(defaultVal)) then
nodeAs1dInt = defaultVal
else
@ -947,23 +972,22 @@ end function tNode_get_byKey_as1dInt
!--------------------------------------------------------------------------------------------------
function tNode_get_byKey_as1dBool(self,k,defaultVal) result(nodeAs1dBool)
class(tNode), intent(in), target :: self
character(len=*), intent(in) :: k
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()
class default
call IO_error(706,ext_msg='Expected 1D Boolean array for key '//k)
endselect
end select
elseif (present(defaultVal)) then
nodeAs1dBool = defaultVal
else
@ -978,23 +1002,22 @@ end function tNode_get_byKey_as1dBool
!--------------------------------------------------------------------------------------------------
function tNode_get_byKey_as1dString(self,k,defaultVal) result(nodeAs1dString)
class(tNode), intent(in), target :: self
character(len=*), intent(in) :: k
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()
class default
call IO_error(706,ext_msg='Expected 1D string array for key '//k)
endselect
end select
elseif (present(defaultVal)) then
nodeAs1dString = defaultVal
else
@ -1015,11 +1038,11 @@ function output_as1dString(self) result(output) !ToDo: SR: Re
class(tNode), pointer :: output_list
integer :: o
output_list => self%get('output',defaultVal=emptyList)
output_list => self%get('output',defaultVal=emptyList)
allocate(output(output_list%length))
do o = 1, output_list%length
output(o) = output_list%get_asString(o)
enddo
end do
end function output_as1dString
@ -1042,7 +1065,7 @@ function tNode_get_byKey_asIndex(self,key) result(keyIndex)
do while (associated(item%next) .and. item%key /= key)
item => item%next
keyIndex = keyIndex+1
enddo
end do
if (item%key /= key) call IO_error(140,ext_msg=key)
@ -1087,7 +1110,7 @@ recursive function tList_asFormattedString(self,indent) result(str)
if (i /= 1) str = str//repeat(' ',indent_)
str = str//'- '//item%node%asFormattedString(indent_+2)
item => item%next
enddo
end do
end function tList_asFormattedString
@ -1119,9 +1142,9 @@ recursive function tDict_asFormattedString(self,indent) result(str)
str = str//trim(item%key)//': '//item%node%asFormattedString(indent_+len_trim(item%key)+2)
class default
str = str//trim(item%key)//':'//IO_EOL//repeat(' ',indent_+2)//item%node%asFormattedString(indent_+2)
endselect
end select
item => item%next
enddo
end do
end function tDict_asFormattedString
@ -1190,13 +1213,14 @@ 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
scalar => item%node%asScalar()
tList_as1dFloat(i) = scalar%asFloat()
item => item%next
enddo
end do
end function tList_as1dFloat
@ -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))
@ -1220,9 +1245,9 @@ function tList_as2dFloat(self)
do i=1,self%length
row => self%get(i)
row_data => row%asList()
if(row_data%length /= size(tList_as2dFloat,2)) call IO_error(709,ext_msg='Varying number of columns')
if (row_data%length /= size(tList_as2dFloat,2)) call IO_error(709,ext_msg='Varying number of columns')
tList_as2dFloat(i,:) = self%get_as1dFloat(i)
enddo
end do
end function tList_as2dFloat
@ -1239,13 +1264,14 @@ 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
scalar => item%node%asScalar()
tList_as1dInt(i) = scalar%asInt()
item => item%next
enddo
end do
end function tList_as1dInt
@ -1262,13 +1288,14 @@ 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
scalar => item%node%asScalar()
tList_as1dBool(i) = scalar%asBool()
item => item%next
enddo
end do
end function tList_as1dBool
@ -1285,13 +1312,14 @@ function tList_as1dString(self)
type(tItem), pointer :: item
type(tScalar), pointer :: scalar
len_max = 0
item => self%first
do i = 1, self%length
scalar => item%node%asScalar()
len_max = max(len_max, len_trim(scalar%asString()))
item => item%next
enddo
end do
allocate(character(len=len_max) :: tList_as1dString(self%length))
item => self%first

2
src/base64.f90
View File

@ -151,7 +151,7 @@ pure logical function validBase64(base64_str)
l = len(base64_str,pI64)
validBase64 = .true.
if(mod(l,4_pI64)/=0_pI64 .or. l < 4_pInt) validBase64 = .false.
if(mod(l,4_pI64)/=0_pI64 .or. l < 4_pI64) validBase64 = .false.
if(verify(base64_str(:l-2_pI64),base64_encoding, kind=pI64) /= 0_pI64) validBase64 = .false.
if(verify(base64_str(l-1_pI64:),base64_encoding//'=',kind=pI64) /= 0_pI64) validBase64 = .false.

1
src/commercialFEM_fileList.f90
View File

@ -14,6 +14,7 @@
#include "LAPACK_interface.f90"
#include "math.f90"
#include "rotations.f90"
#include "polynomials.f90"
#include "lattice.f90"
#include "element.f90"
#include "geometry_plastic_nonlocal.f90"

14
src/grid/DAMASK_grid.f90
View File

@ -75,7 +75,6 @@ program DAMASK_grid
integer :: &
i, j, m, field, &
errorID = 0, &
ierr,&
cutBackLevel = 0, & !< cut back level \f$ t = \frac{t_{inc}}{2^l} \f$
stepFraction = 0, & !< fraction of current time interval
l = 0, & !< current load case
@ -86,6 +85,7 @@ program DAMASK_grid
nActiveFields = 0, &
maxCutBack, & !< max number of cut backs
stagItMax !< max number of field level staggered iterations
integer(MPI_INTEGER_KIND) :: err_MPI
character(len=pStringLen) :: &
incInfo
@ -455,23 +455,23 @@ program DAMASK_grid
print'(/,1x,a,i0,a)', 'increment ', totalIncsCounter, ' NOT converged'
endif; flush(IO_STDOUT)
call MPI_Allreduce(interface_SIGUSR1,signal,1,MPI_LOGICAL,MPI_LOR,MPI_COMM_WORLD,ierr)
if (ierr /= 0) error stop 'MPI error'
call MPI_Allreduce(interface_SIGUSR1,signal,1_MPI_INTEGER_KIND,MPI_LOGICAL,MPI_LOR,MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
if (mod(inc,loadCases(l)%f_out) == 0 .or. signal) then
print'(/,1x,a)', '... writing results to file ...............................................'
flush(IO_STDOUT)
call CPFEM_results(totalIncsCounter,t)
endif
if (signal) call interface_setSIGUSR1(.false.)
call MPI_Allreduce(interface_SIGUSR2,signal,1,MPI_LOGICAL,MPI_LOR,MPI_COMM_WORLD,ierr)
if (ierr /= 0) error stop 'MPI error'
call MPI_Allreduce(interface_SIGUSR2,signal,1_MPI_INTEGER_KIND,MPI_LOGICAL,MPI_LOR,MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
if (mod(inc,loadCases(l)%f_restart) == 0 .or. signal) then
call mechanical_restartWrite
call CPFEM_restartWrite
endif
if (signal) call interface_setSIGUSR2(.false.)
call MPI_Allreduce(interface_SIGTERM,signal,1,MPI_LOGICAL,MPI_LOR,MPI_COMM_WORLD,ierr)
if (ierr /= 0) error stop 'MPI error'
call MPI_Allreduce(interface_SIGTERM,signal,1_MPI_INTEGER_KIND,MPI_LOGICAL,MPI_LOR,MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
if (signal) exit loadCaseLooping
endif skipping

35
src/grid/discretization_grid.f90
View File

@ -62,8 +62,8 @@ subroutine discretization_grid_init(restart)
integer :: &
j, &
debug_element, debug_ip, &
ierr
debug_element, debug_ip
integer(MPI_INTEGER_KIND) :: err_MPI
integer(C_INTPTR_T) :: &
devNull, z, z_offset
integer, dimension(worldsize) :: &
@ -88,13 +88,13 @@ subroutine discretization_grid_init(restart)
end if
call MPI_Bcast(grid,3,MPI_INTEGER,0,MPI_COMM_WORLD, ierr)
if (ierr /= 0) error stop 'MPI error'
call MPI_Bcast(grid,3_MPI_INTEGER_KIND,MPI_INTEGER,0_MPI_INTEGER_KIND,MPI_COMM_WORLD, err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
if (grid(1) < 2) call IO_error(844, ext_msg='cells(1) must be larger than 1')
call MPI_Bcast(geomSize,3,MPI_DOUBLE,0,MPI_COMM_WORLD, ierr)
if (ierr /= 0) error stop 'MPI error'
call MPI_Bcast(origin,3,MPI_DOUBLE,0,MPI_COMM_WORLD, ierr)
if (ierr /= 0) error stop 'MPI error'
call MPI_Bcast(geomSize,3_MPI_INTEGER_KIND,MPI_DOUBLE,0_MPI_INTEGER_KIND,MPI_COMM_WORLD, err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
call MPI_Bcast(origin,3_MPI_INTEGER_KIND,MPI_DOUBLE,0_MPI_INTEGER_KIND,MPI_COMM_WORLD, err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
print'(/,1x,a,3(i12,1x))', 'cells a b c: ', grid
print '(1x,a,3(es12.5,1x))', 'size x y z: ', geomSize
@ -118,14 +118,17 @@ subroutine discretization_grid_init(restart)
myGrid = [grid(1:2),grid3]
mySize = [geomSize(1:2),size3]
call MPI_Gather(product(grid(1:2))*grid3Offset,1,MPI_INTEGER,displs, 1,MPI_INTEGER,0,MPI_COMM_WORLD,ierr)
if (ierr /= 0) error stop 'MPI error'
call MPI_Gather(product(myGrid), 1,MPI_INTEGER,sendcounts,1,MPI_INTEGER,0,MPI_COMM_WORLD,ierr)
if (ierr /= 0) error stop 'MPI error'
call MPI_Gather(product(grid(1:2))*grid3Offset, 1_MPI_INTEGER_KIND,MPI_INTEGER,displs,&
1_MPI_INTEGER_KIND,MPI_INTEGER,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
call MPI_Gather(product(myGrid), 1_MPI_INTEGER_KIND,MPI_INTEGER,sendcounts,&
1_MPI_INTEGER_KIND,MPI_INTEGER,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
allocate(materialAt(product(myGrid)))
call MPI_Scatterv(materialAt_global,sendcounts,displs,MPI_INTEGER,materialAt,size(materialAt),MPI_INTEGER,0,MPI_COMM_WORLD,ierr)
if (ierr /= 0) error stop 'MPI error'
call MPI_Scatterv(materialAt_global,sendcounts,displs,MPI_INTEGER,materialAt,size(materialAt),&
MPI_INTEGER,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
call discretization_init(materialAt, &
IPcoordinates0(myGrid,mySize,grid3Offset), &
@ -307,7 +310,7 @@ subroutine readVTI(grid,geomSize,origin,material, &
case('Float64')
as_Int = int(prec_bytesToC_DOUBLE (asBytes(base64_str,headerType,compressed)))
case default
call IO_error(844_pInt,ext_msg='unknown data type: '//trim(dataType))
call IO_error(844,ext_msg='unknown data type: '//trim(dataType))
end select
end function as_Int
@ -335,7 +338,7 @@ subroutine readVTI(grid,geomSize,origin,material, &
case('Float64')
as_pReal = real(prec_bytesToC_DOUBLE (asBytes(base64_str,headerType,compressed)),pReal)
case default
call IO_error(844_pInt,ext_msg='unknown data type: '//trim(dataType))
call IO_error(844,ext_msg='unknown data type: '//trim(dataType))
end select
end function as_pReal

163
src/grid/grid_damage_spectral.f90
View File

@ -39,9 +39,8 @@ module grid_damage_spectral
type(tSolutionParams) :: params
!--------------------------------------------------------------------------------------------------
! PETSc data
SNES :: damage_snes
SNES :: SNES_damage
Vec :: solution_vec
PetscInt :: xstart, xend, ystart, yend, zstart, zend
real(pReal), dimension(:,:,:), allocatable :: &
phi_current, & !< field of current damage
phi_lastInc, & !< field of previous damage
@ -69,7 +68,8 @@ subroutine grid_damage_spectral_init()
PetscInt, dimension(0:worldsize-1) :: localK
DM :: damage_grid
Vec :: uBound, lBound
PetscErrorCode :: ierr
integer(MPI_INTEGER_KIND) :: err_MPI
PetscErrorCode :: err_PETSc
class(tNode), pointer :: &
num_grid, &
num_generic
@ -99,60 +99,71 @@ subroutine grid_damage_spectral_init()
!--------------------------------------------------------------------------------------------------
! set default and user defined options for PETSc
call PetscOptionsInsertString(PETSC_NULL_OPTIONS,'-damage_snes_type newtonls -damage_snes_mf &
&-damage_snes_ksp_ew -damage_ksp_type fgmres',ierr)
CHKERRQ(ierr)
call PetscOptionsInsertString(PETSC_NULL_OPTIONS,num_grid%get_asString('petsc_options',defaultVal=''),ierr)
CHKERRQ(ierr)
!--------------------------------------------------------------------------------------------------
! initialize solver specific parts of PETSc
call SNESCreate(PETSC_COMM_WORLD,damage_snes,ierr); CHKERRQ(ierr)
call SNESSetOptionsPrefix(damage_snes,'damage_',ierr);CHKERRQ(ierr)
localK = 0
localK(worldrank) = grid3
call MPI_Allreduce(MPI_IN_PLACE,localK,worldsize,MPI_INTEGER,MPI_SUM,MPI_COMM_WORLD,ierr)
call DMDACreate3D(PETSC_COMM_WORLD, &
DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, & ! cut off stencil at boundary
DMDA_STENCIL_BOX, & ! Moore (26) neighborhood around central point
grid(1),grid(2),grid(3), & ! global grid
1, 1, worldsize, &
1, 0, & ! #dof (damage phase field), ghost boundary width (domain overlap)
[grid(1)],[grid(2)],localK, & ! local grid
damage_grid,ierr) ! handle, error
CHKERRQ(ierr)
call SNESSetDM(damage_snes,damage_grid,ierr); CHKERRQ(ierr) ! connect snes to da
call DMsetFromOptions(damage_grid,ierr); CHKERRQ(ierr)
call DMsetUp(damage_grid,ierr); CHKERRQ(ierr)
call DMCreateGlobalVector(damage_grid,solution_vec,ierr); CHKERRQ(ierr) ! global solution vector (grid x 1, i.e. every def grad tensor)
call DMDASNESSetFunctionLocal(damage_grid,INSERT_VALUES,formResidual,PETSC_NULL_SNES,ierr) ! residual vector of same shape as solution vector
CHKERRQ(ierr)
call SNESSetFromOptions(damage_snes,ierr); CHKERRQ(ierr) ! pull it all together with additional CLI arguments
call SNESGetType(damage_snes,snes_type,ierr); CHKERRQ(ierr)
if (trim(snes_type) == 'vinewtonrsls' .or. &
trim(snes_type) == 'vinewtonssls') then
call DMGetGlobalVector(damage_grid,lBound,ierr); CHKERRQ(ierr)
call DMGetGlobalVector(damage_grid,uBound,ierr); CHKERRQ(ierr)
call VecSet(lBound,0.0_pReal,ierr); CHKERRQ(ierr)
call VecSet(uBound,1.0_pReal,ierr); CHKERRQ(ierr)
call SNESVISetVariableBounds(damage_snes,lBound,uBound,ierr) ! variable bounds for variational inequalities like contact mechanics, damage etc.
call DMRestoreGlobalVector(damage_grid,lBound,ierr); CHKERRQ(ierr)
call DMRestoreGlobalVector(damage_grid,uBound,ierr); CHKERRQ(ierr)
end if
&-damage_snes_ksp_ew -damage_ksp_type fgmres',err_PETSc)
CHKERRQ(err_PETSc)
call PetscOptionsInsertString(PETSC_NULL_OPTIONS,num_grid%get_asString('petsc_options',defaultVal=''),err_PETSc)
CHKERRQ(err_PETSc)
!--------------------------------------------------------------------------------------------------
! init fields
call DMDAGetCorners(damage_grid,xstart,ystart,zstart,xend,yend,zend,ierr)
CHKERRQ(ierr)
xend = xstart + xend - 1
yend = ystart + yend - 1
zend = zstart + zend - 1
allocate(phi_current(grid(1),grid(2),grid3), source=1.0_pReal)
allocate(phi_lastInc(grid(1),grid(2),grid3), source=1.0_pReal)
allocate(phi_stagInc(grid(1),grid(2),grid3), source=1.0_pReal)
call VecSet(solution_vec,1.0_pReal,ierr); CHKERRQ(ierr)
!--------------------------------------------------------------------------------------------------
! initialize solver specific parts of PETSc
call SNESCreate(PETSC_COMM_WORLD,SNES_damage,err_PETSc)
CHKERRQ(err_PETSc)
call SNESSetOptionsPrefix(SNES_damage,'damage_',err_PETSc)
CHKERRQ(err_PETSc)
localK = 0_pPetscInt
localK(worldrank) = int(grid3,pPetscInt)
call MPI_Allreduce(MPI_IN_PLACE,localK,worldsize,MPI_INTEGER,MPI_SUM,MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
call DMDACreate3D(PETSC_COMM_WORLD, &
DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, & ! cut off stencil at boundary
DMDA_STENCIL_BOX, & ! Moore (26) neighborhood around central point
int(grid(1),pPetscInt),int(grid(2),pPetscInt),int(grid(3),pPetscInt), & ! global grid
1_pPetscInt, 1_pPetscInt, int(worldsize,pPetscInt), &
1_pPetscInt, 0_pPetscInt, & ! #dof (phi, scalar), ghost boundary width (domain overlap)
[int(grid(1),pPetscInt)],[int(grid(2),pPetscInt)],localK, & ! local grid
damage_grid,err_PETSc) ! handle, error
CHKERRQ(err_PETSc)
call DMsetFromOptions(damage_grid,err_PETSc)
CHKERRQ(err_PETSc)
call DMsetUp(damage_grid,err_PETSc)
CHKERRQ(err_PETSc)
call DMCreateGlobalVector(damage_grid,solution_vec,err_PETSc) ! global solution vector (grid x 1, i.e. every def grad tensor)
CHKERRQ(err_PETSc)
call DMDASNESSetFunctionLocal(damage_grid,INSERT_VALUES,formResidual,PETSC_NULL_SNES,err_PETSc) ! residual vector of same shape as solution vector
CHKERRQ(err_PETSc)
call SNESSetDM(SNES_damage,damage_grid,err_PETSc)
CHKERRQ(err_PETSc)
call SNESSetFromOptions(SNES_damage,err_PETSc) ! pull it all together with additional CLI arguments
CHKERRQ(err_PETSc)
call SNESGetType(SNES_damage,snes_type,err_PETSc)
CHKERRQ(err_PETSc)
if (trim(snes_type) == 'vinewtonrsls' .or. &
trim(snes_type) == 'vinewtonssls') then
call DMGetGlobalVector(damage_grid,lBound,err_PETSc)
CHKERRQ(err_PETSc)
call DMGetGlobalVector(damage_grid,uBound,err_PETSc)
CHKERRQ(err_PETSc)
call VecSet(lBound,0.0_pReal,err_PETSc)
CHKERRQ(err_PETSc)
call VecSet(uBound,1.0_pReal,err_PETSc)
CHKERRQ(err_PETSc)
call SNESVISetVariableBounds(SNES_damage,lBound,uBound,err_PETSc) ! variable bounds for variational inequalities
CHKERRQ(err_PETSc)
call DMRestoreGlobalVector(damage_grid,lBound,err_PETSc)
CHKERRQ(err_PETSc)
call DMRestoreGlobalVector(damage_grid,uBound,err_PETSc)
CHKERRQ(err_PETSc)
end if
call VecSet(solution_vec,1.0_pReal,err_PETSc)
CHKERRQ(err_PETSc)
call updateReference
call updateReference()
end subroutine grid_damage_spectral_init
@ -169,7 +180,8 @@ function grid_damage_spectral_solution(Delta_t) result(solution)
PetscInt :: devNull
PetscReal :: phi_min, phi_max, stagNorm
PetscErrorCode :: ierr
integer(MPI_INTEGER_KIND) :: err_MPI
PetscErrorCode :: err_PETSc
SNESConvergedReason :: reason
solution%converged =.false.
@ -178,8 +190,10 @@ function grid_damage_spectral_solution(Delta_t) result(solution)
! set module wide availabe data
params%Delta_t = Delta_t
call SNESSolve(damage_snes,PETSC_NULL_VEC,solution_vec,ierr); CHKERRQ(ierr)
call SNESGetConvergedReason(damage_snes,reason,ierr); CHKERRQ(ierr)
call SNESSolve(SNES_damage,PETSC_NULL_VEC,solution_vec,err_PETSc)
CHKERRQ(err_PETSc)
call SNESGetConvergedReason(SNES_damage,reason,err_PETSc)
CHKERRQ(err_PETSc)
if (reason < 1) then
solution%converged = .false.
@ -189,9 +203,11 @@ function grid_damage_spectral_solution(Delta_t) result(solution)
solution%iterationsNeeded = totalIter
end if
stagNorm = maxval(abs(phi_current - phi_stagInc))
call MPI_Allreduce(MPI_IN_PLACE,stagNorm,1,MPI_DOUBLE,MPI_MAX,MPI_COMM_WORLD,ierr)
call MPI_Allreduce(MPI_IN_PLACE,stagNorm,1_MPI_INTEGER_KIND,MPI_DOUBLE,MPI_MAX,MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
solution%stagConverged = stagNorm < max(num%eps_damage_atol, num%eps_damage_rtol*maxval(phi_current))
call MPI_Allreduce(MPI_IN_PLACE,solution%stagConverged,1,MPI_LOGICAL,MPI_LAND,MPI_COMM_WORLD,ierr)
call MPI_Allreduce(MPI_IN_PLACE,solution%stagConverged,1_MPI_INTEGER_KIND,MPI_LOGICAL,MPI_LAND,MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
phi_stagInc = phi_current
!--------------------------------------------------------------------------------------------------
@ -202,8 +218,10 @@ function grid_damage_spectral_solution(Delta_t) result(solution)
call homogenization_set_phi(phi_current(i,j,k),ce)
end do; end do; end do
call VecMin(solution_vec,devNull,phi_min,ierr); CHKERRQ(ierr)
call VecMax(solution_vec,devNull,phi_max,ierr); CHKERRQ(ierr)
call VecMin(solution_vec,devNull,phi_min,err_PETSc)
CHKERRQ(err_PETSc)
call VecMax(solution_vec,devNull,phi_max,err_PETSc)
CHKERRQ(err_PETSc)
if (solution%converged) &
print'(/,1x,a)', '... nonlocal damage converged .....................................'
print'(/,1x,a,f8.6,2x,f8.6,2x,e11.4)', 'Minimum|Maximum|Delta Damage = ', phi_min, phi_max, stagNorm
@ -221,18 +239,21 @@ subroutine grid_damage_spectral_forward(cutBack)
logical, intent(in) :: cutBack
integer :: i, j, k, ce
DM :: dm_local
PetscScalar, dimension(:,:,:), pointer :: x_scal
PetscErrorCode :: ierr
PetscScalar, dimension(:,:,:), pointer :: phi_PETSc
PetscErrorCode :: err_PETSc
if (cutBack) then
phi_current = phi_lastInc
phi_stagInc = phi_lastInc
!--------------------------------------------------------------------------------------------------
! reverting damage field state
call SNESGetDM(damage_snes,dm_local,ierr); CHKERRQ(ierr)
call DMDAVecGetArrayF90(dm_local,solution_vec,x_scal,ierr); CHKERRQ(ierr) !< get the data out of PETSc to work with
x_scal(xstart:xend,ystart:yend,zstart:zend) = phi_current
call DMDAVecRestoreArrayF90(dm_local,solution_vec,x_scal,ierr); CHKERRQ(ierr)
call SNESGetDM(SNES_damage,dm_local,err_PETSc)
CHKERRQ(err_PETSc)
call DMDAVecGetArrayF90(dm_local,solution_vec,phi_PETSc,err_PETSc) !< get the data out of PETSc to work with
CHKERRQ(err_PETSc)
phi_PETSc = phi_current
call DMDAVecRestoreArrayF90(dm_local,solution_vec,phi_PETSc,err_PETSc)
CHKERRQ(err_PETSc)
ce = 0
do k = 1, grid3; do j = 1, grid(2); do i = 1,grid(1)
ce = ce + 1
@ -249,7 +270,7 @@ end subroutine grid_damage_spectral_forward
!--------------------------------------------------------------------------------------------------
!> @brief forms the spectral damage residual vector
!--------------------------------------------------------------------------------------------------
subroutine formResidual(in,x_scal,f_scal,dummy,ierr)
subroutine formResidual(in,x_scal,r,dummy,err_PETSc)
DMDALocalInfo, dimension(DMDA_LOCAL_INFO_SIZE) :: &
in
@ -258,9 +279,9 @@ subroutine formResidual(in,x_scal,f_scal,dummy,ierr)
x_scal
PetscScalar, dimension( &
X_RANGE,Y_RANGE,Z_RANGE), intent(out) :: &
f_scal
r
PetscObject :: dummy
PetscErrorCode :: ierr
PetscErrorCode :: err_PETSc
integer :: i, j, k, ce
@ -301,7 +322,8 @@ subroutine formResidual(in,x_scal,f_scal,dummy,ierr)
!--------------------------------------------------------------------------------------------------
! constructing residual
f_scal = scalarField_real(1:grid(1),1:grid(2),1:grid3) - phi_current
r = scalarField_real(1:grid(1),1:grid(2),1:grid3) - phi_current
err_PETSc = 0
end subroutine formResidual
@ -311,7 +333,8 @@ end subroutine formResidual
!--------------------------------------------------------------------------------------------------
subroutine updateReference()
integer :: ce,ierr
integer :: ce
integer(MPI_INTEGER_KIND) :: err_MPI
K_ref = 0.0_pReal
@ -322,9 +345,11 @@ subroutine updateReference()
end do
K_ref = K_ref*wgt
call MPI_Allreduce(MPI_IN_PLACE,K_ref,9,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,ierr)
call MPI_Allreduce(MPI_IN_PLACE,K_ref,9_MPI_INTEGER_KIND,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
mu_ref = mu_ref*wgt
call MPI_Allreduce(MPI_IN_PLACE,mu_ref,1,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,ierr)
call MPI_Allreduce(MPI_IN_PLACE,mu_ref,1_MPI_INTEGER_KIND,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
end subroutine updateReference

408
src/grid/grid_mech_FEM.f90
View File

@ -50,7 +50,7 @@ module grid_mechanical_FEM
!--------------------------------------------------------------------------------------------------
! PETSc data
DM :: mechanical_grid
SNES :: mechanical_snes
SNES :: SNES_mechanical
Vec :: solution_current, solution_lastInc, solution_rate
!--------------------------------------------------------------------------------------------------
@ -60,7 +60,6 @@ module grid_mechanical_FEM
real(pReal), dimension(3) :: delta
real(pReal), dimension(3,8) :: BMat
real(pReal), dimension(8,8) :: HGMat
PetscInt :: xstart,ystart,zstart,xend,yend,zend
!--------------------------------------------------------------------------------------------------
! stress, stiffness and compliance average etc.
@ -107,7 +106,8 @@ subroutine grid_mechanical_FEM_init
1.0_pReal,-1.0_pReal,-1.0_pReal,-1.0_pReal, &
1.0_pReal, 1.0_pReal, 1.0_pReal, 1.0_pReal], [4,8])
real(pReal), dimension(3,3,3,3) :: devNull
PetscErrorCode :: ierr
PetscErrorCode :: err_PETSc
integer(MPI_INTEGER_KIND) :: err_MPI
PetscScalar, pointer, dimension(:,:,:,:) :: &
u_current,u_lastInc
PetscInt, dimension(0:worldsize-1) :: localK
@ -145,12 +145,11 @@ subroutine grid_mechanical_FEM_init
! set default and user defined options for PETSc
call PetscOptionsInsertString(PETSC_NULL_OPTIONS, &
'-mechanical_snes_type newtonls -mechanical_ksp_type fgmres &
&-mechanical_ksp_max_it 25 -mechanical_pc_type ml &
&-mechanical_mg_levels_ksp_type chebyshev', &
ierr)
CHKERRQ(ierr)
call PetscOptionsInsertString(PETSC_NULL_OPTIONS,num_grid%get_asString('petsc_options',defaultVal=''),ierr)
CHKERRQ(ierr)
&-mechanical_ksp_max_it 25', &
err_PETSc)
CHKERRQ(err_PETSc)
call PetscOptionsInsertString(PETSC_NULL_OPTIONS,num_grid%get_asString('petsc_options',defaultVal=''),err_PETSc)
CHKERRQ(err_PETSc)
!--------------------------------------------------------------------------------------------------
! allocate global fields
@ -160,62 +159,61 @@ subroutine grid_mechanical_FEM_init
!--------------------------------------------------------------------------------------------------
! initialize solver specific parts of PETSc
call SNESCreate(PETSC_COMM_WORLD,mechanical_snes,ierr)
CHKERRQ(ierr)
call SNESSetOptionsPrefix(mechanical_snes,'mechanical_',ierr)
CHKERRQ(ierr)
localK = 0
localK(worldrank) = grid3
call MPI_Allreduce(MPI_IN_PLACE,localK,worldsize,MPI_INTEGER,MPI_SUM,MPI_COMM_WORLD,ierr)
call SNESCreate(PETSC_COMM_WORLD,SNES_mechanical,err_PETSc)
CHKERRQ(err_PETSc)
call SNESSetOptionsPrefix(SNES_mechanical,'mechanical_',err_PETSc)
CHKERRQ(err_PETSc)
localK = 0_pPetscInt
localK(worldrank) = int(grid3,pPetscInt)
call MPI_Allreduce(MPI_IN_PLACE,localK,worldsize,MPI_INTEGER,MPI_SUM,MPI_COMM_WORLD,err_MPI)
if(err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
call DMDACreate3d(PETSC_COMM_WORLD, &
DM_BOUNDARY_PERIODIC, DM_BOUNDARY_PERIODIC, DM_BOUNDARY_PERIODIC, &
DMDA_STENCIL_BOX, &
grid(1),grid(2),grid(3), &
1, 1, worldsize, &
3, 1, &
[grid(1)],[grid(2)],localK, &
mechanical_grid,ierr)
CHKERRQ(ierr)
call SNESSetDM(mechanical_snes,mechanical_grid,ierr)
CHKERRQ(ierr)
call DMsetFromOptions(mechanical_grid,ierr)
CHKERRQ(ierr)
call DMsetUp(mechanical_grid,ierr)
CHKERRQ(ierr)
call DMDASetUniformCoordinates(mechanical_grid,0.0_pReal,geomSize(1),0.0_pReal,geomSize(2),0.0_pReal,geomSize(3),ierr)
CHKERRQ(ierr)
call DMCreateGlobalVector(mechanical_grid,solution_current,ierr)
CHKERRQ(ierr)
call DMCreateGlobalVector(mechanical_grid,solution_lastInc,ierr)
CHKERRQ(ierr)
call DMCreateGlobalVector(mechanical_grid,solution_rate ,ierr)
CHKERRQ(ierr)
call DMSNESSetFunctionLocal(mechanical_grid,formResidual,PETSC_NULL_SNES,ierr)
CHKERRQ(ierr)
call DMSNESSetJacobianLocal(mechanical_grid,formJacobian,PETSC_NULL_SNES,ierr)
CHKERRQ(ierr)
call SNESSetConvergenceTest(mechanical_snes,converged,PETSC_NULL_SNES,PETSC_NULL_FUNCTION,ierr) ! specify custom convergence check function "_converged"
CHKERRQ(ierr)
call SNESSetMaxLinearSolveFailures(mechanical_snes, huge(1), ierr) ! ignore linear solve failures
CHKERRQ(ierr)
call SNESSetFromOptions(mechanical_snes,ierr) ! pull it all together with additional cli arguments
CHKERRQ(ierr)
int(grid(1),pPetscInt),int(grid(2),pPetscInt),int(grid(3),pPetscInt), & ! global grid
1_pPetscInt, 1_pPetscInt, int(worldsize,pPetscInt), &
3_pPetscInt, 1_pPetscInt, & ! #dof (u, vector), ghost boundary width (domain overlap)
[int(grid(1),pPetscInt)],[int(grid(2),pPetscInt)],localK, & ! local grid
mechanical_grid,err_PETSc)
CHKERRQ(err_PETSc)
call DMsetFromOptions(mechanical_grid,err_PETSc)
CHKERRQ(err_PETSc)
call DMsetUp(mechanical_grid,err_PETSc)
CHKERRQ(err_PETSc)
call DMDASetUniformCoordinates(mechanical_grid,0.0_pReal,geomSize(1),0.0_pReal,geomSize(2),0.0_pReal,geomSize(3),err_PETSc)
CHKERRQ(err_PETSc)
call DMCreateGlobalVector(mechanical_grid,solution_current,err_PETSc)
CHKERRQ(err_PETSc)
call DMCreateGlobalVector(mechanical_grid,solution_lastInc,err_PETSc)
CHKERRQ(err_PETSc)
call DMCreateGlobalVector(mechanical_grid,solution_rate ,err_PETSc)
CHKERRQ(err_PETSc)
call DMSNESSetFunctionLocal(mechanical_grid,formResidual,PETSC_NULL_SNES,err_PETSc)
CHKERRQ(err_PETSc)
call DMSNESSetJacobianLocal(mechanical_grid,formJacobian,PETSC_NULL_SNES,err_PETSc)
CHKERRQ(err_PETSc)
call SNESSetConvergenceTest(SNES_mechanical,converged,PETSC_NULL_SNES,PETSC_NULL_FUNCTION,err_PETSc) ! specify custom convergence check function "_converged"
CHKERRQ(err_PETSc)
call SNESSetMaxLinearSolveFailures(SNES_mechanical, huge(1_pPetscInt), err_PETSc) ! ignore linear solve failures
CHKERRQ(err_PETSc)
call SNESSetDM(SNES_mechanical,mechanical_grid,err_PETSc)
CHKERRQ(err_PETSc)
call SNESSetFromOptions(SNES_mechanical,err_PETSc) ! pull it all together with additional cli arguments
CHKERRQ(err_PETSc)
!--------------------------------------------------------------------------------------------------
! init fields
call VecSet(solution_current,0.0_pReal,ierr);CHKERRQ(ierr)
call VecSet(solution_lastInc,0.0_pReal,ierr);CHKERRQ(ierr)
call VecSet(solution_rate ,0.0_pReal,ierr);CHKERRQ(ierr)
call DMDAVecGetArrayF90(mechanical_grid,solution_current,u_current,ierr)
CHKERRQ(ierr)
call DMDAVecGetArrayF90(mechanical_grid,solution_lastInc,u_lastInc,ierr)
CHKERRQ(ierr)
call VecSet(solution_current,0.0_pReal,err_PETSc)
CHKERRQ(err_PETSc)
call VecSet(solution_lastInc,0.0_pReal,err_PETSc)
CHKERRQ(err_PETSc)
call VecSet(solution_rate ,0.0_pReal,err_PETSc)
CHKERRQ(err_PETSc)
call DMDAVecGetArrayF90(mechanical_grid,solution_current,u_current,err_PETSc)
CHKERRQ(err_PETSc)
call DMDAVecGetArrayF90(mechanical_grid,solution_lastInc,u_lastInc,err_PETSc)
CHKERRQ(err_PETSc)
call DMDAGetCorners(mechanical_grid,xstart,ystart,zstart,xend,yend,zend,ierr) ! local grid extent
CHKERRQ(ierr)
xend = xstart+xend-1
yend = ystart+yend-1
zend = zstart+zend-1
delta = geomSize/real(grid,pReal) ! grid spacing
detJ = product(delta) ! cell volume
@ -240,17 +238,17 @@ subroutine grid_mechanical_FEM_init
groupHandle = HDF5_openGroup(fileHandle,'solver')
call HDF5_read(P_aim,groupHandle,'P_aim',.false.)
call MPI_Bcast(P_aim,9,MPI_DOUBLE,0,MPI_COMM_WORLD,ierr)
if(ierr /=0) error stop 'MPI error'
call MPI_Bcast(P_aim,9_MPI_INTEGER_KIND,MPI_DOUBLE,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
if(err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
call HDF5_read(F_aim,groupHandle,'F_aim',.false.)
call MPI_Bcast(F_aim,9,MPI_DOUBLE,0,MPI_COMM_WORLD,ierr)
if(ierr /=0) error stop 'MPI error'
call MPI_Bcast(F_aim,9_MPI_INTEGER_KIND,MPI_DOUBLE,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
if(err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
call HDF5_read(F_aim_lastInc,groupHandle,'F_aim_lastInc',.false.)
call MPI_Bcast(F_aim_lastInc,9,MPI_DOUBLE,0,MPI_COMM_WORLD,ierr)
if(ierr /=0) error stop 'MPI error'
call MPI_Bcast(F_aim_lastInc,9_MPI_INTEGER_KIND,MPI_DOUBLE,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
if(err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
call HDF5_read(F_aimDot,groupHandle,'F_aimDot',.false.)
call MPI_Bcast(F_aimDot,9,MPI_DOUBLE,0,MPI_COMM_WORLD,ierr)
if(ierr /=0) error stop 'MPI error'
call MPI_Bcast(F_aimDot,9_MPI_INTEGER_KIND,MPI_DOUBLE,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
if(err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
call HDF5_read(F,groupHandle,'F')
call HDF5_read(F_lastInc,groupHandle,'F_lastInc')
call HDF5_read(u_current,groupHandle,'u')
@ -266,19 +264,19 @@ subroutine grid_mechanical_FEM_init
call utilities_constitutiveResponse(P_current,P_av,C_volAvg,devNull, & ! stress field, stress avg, global average of stiffness and (min+max)/2
F, & ! target F
0.0_pReal) ! time increment
call DMDAVecRestoreArrayF90(mechanical_grid,solution_current,u_current,ierr)
CHKERRQ(ierr)
call DMDAVecRestoreArrayF90(mechanical_grid,solution_lastInc,u_lastInc,ierr)
CHKERRQ(ierr)
call DMDAVecRestoreArrayF90(mechanical_grid,solution_current,u_current,err_PETSc)
CHKERRQ(err_PETSc)
call DMDAVecRestoreArrayF90(mechanical_grid,solution_lastInc,u_lastInc,err_PETSc)
CHKERRQ(err_PETSc)
restartRead2: if (interface_restartInc > 0) then
print'(1x,a,i0,a)', 'reading more restart data of increment ', interface_restartInc, ' from file'
call HDF5_read(C_volAvg,groupHandle,'C_volAvg',.false.)
call MPI_Bcast(C_volAvg,81,MPI_DOUBLE,0,MPI_COMM_WORLD,ierr)
if(ierr /=0) error stop 'MPI error'
call MPI_Bcast(C_volAvg,81_MPI_INTEGER_KIND,MPI_DOUBLE,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
if(err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
call HDF5_read(C_volAvgLastInc,groupHandle,'C_volAvgLastInc',.false.)
call MPI_Bcast(C_volAvgLastInc,81,MPI_DOUBLE,0,MPI_COMM_WORLD,ierr)
if(ierr /=0) error stop 'MPI error'
call MPI_Bcast(C_volAvgLastInc,81_MPI_INTEGER_KIND,MPI_DOUBLE,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
if(err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
call HDF5_closeGroup(groupHandle)
call HDF5_closeFile(fileHandle)
@ -301,7 +299,7 @@ function grid_mechanical_FEM_solution(incInfoIn) result(solution)
solution
!--------------------------------------------------------------------------------------------------
! PETSc Data
PetscErrorCode :: ierr
PetscErrorCode :: err_PETSc
SNESConvergedReason :: reason
incInfo = incInfoIn
@ -310,15 +308,10 @@ function grid_mechanical_FEM_solution(incInfoIn) result(solution)
! update stiffness (and gamma operator)
S = utilities_maskedCompliance(params%rotation_BC,params%stress_mask,C_volAvg)
!--------------------------------------------------------------------------------------------------
! solve BVP
call SNESsolve(mechanical_snes,PETSC_NULL_VEC,solution_current,ierr)
CHKERRQ(ierr)
!--------------------------------------------------------------------------------------------------
! check convergence
call SNESGetConvergedReason(mechanical_snes,reason,ierr)
CHKERRQ(ierr)
call SNESsolve(SNES_mechanical,PETSC_NULL_VEC,solution_current,err_PETSc)
CHKERRQ(err_PETSc)
call SNESGetConvergedReason(SNES_mechanical,reason,err_PETSc)
CHKERRQ(err_PETSc)
solution%converged = reason > 0
solution%iterationsNeeded = totalIter
@ -348,22 +341,22 @@ subroutine grid_mechanical_FEM_forward(cutBack,guess,Delta_t,Delta_t_old,t_remai
deformation_BC
type(rotation), intent(in) :: &
rotation_BC
PetscErrorCode :: ierr
PetscErrorCode :: err_PETSc
PetscScalar, pointer, dimension(:,:,:,:) :: &
u_current,u_lastInc
call DMDAVecGetArrayF90(mechanical_grid,solution_current,u_current,ierr)
CHKERRQ(ierr)
call DMDAVecGetArrayF90(mechanical_grid,solution_lastInc,u_lastInc,ierr)
CHKERRQ(ierr)
call DMDAVecGetArrayF90(mechanical_grid,solution_current,u_current,err_PETSc)
CHKERRQ(err_PETSc)
call DMDAVecGetArrayF90(mechanical_grid,solution_lastInc,u_lastInc,err_PETSc)
CHKERRQ(err_PETSc)
if (cutBack) then
C_volAvg = C_volAvgLastInc
else
C_volAvgLastInc = C_volAvg
F_aimDot = merge(merge(.0_pReal,(F_aim-F_aim_lastInc)/Delta_t_old,stress_BC%mask),.0_pReal,guess) ! estimate deformation rate for prescribed stress components
F_aimDot = merge(merge(.0_pReal,(F_aim-F_aim_lastInc)/Delta_t_old,stress_BC%mask),.0_pReal,guess) ! estimate deformation rate for prescribed stress components
F_aim_lastInc = F_aim
!-----------------------------------------------------------------------------------------------
@ -380,13 +373,16 @@ subroutine grid_mechanical_FEM_forward(cutBack,guess,Delta_t,Delta_t_old,t_remai
endif
if (guess) then
call VecWAXPY(solution_rate,-1.0_pReal,solution_lastInc,solution_current,ierr)
CHKERRQ(ierr)
call VecScale(solution_rate,1.0_pReal/Delta_t_old,ierr); CHKERRQ(ierr)
call VecWAXPY(solution_rate,-1.0_pReal,solution_lastInc,solution_current,err_PETSc)
CHKERRQ(err_PETSc)
call VecScale(solution_rate,1.0_pReal/Delta_t_old,err_PETSc)
CHKERRQ(err_PETSc)
else
call VecSet(solution_rate,0.0_pReal,ierr); CHKERRQ(ierr)
call VecSet(solution_rate,0.0_pReal,err_PETSc)
CHKERRQ(err_PETSc)
endif
call VecCopy(solution_current,solution_lastInc,ierr); CHKERRQ(ierr)
call VecCopy(solution_current,solution_lastInc,err_PETSc)
CHKERRQ(err_PETSc)
F_lastInc = F
@ -401,12 +397,12 @@ subroutine grid_mechanical_FEM_forward(cutBack,guess,Delta_t,Delta_t_old,t_remai
if (stress_BC%myType=='dot_P') P_aim = P_aim &
+ merge(.0_pReal,stress_BC%values,stress_BC%mask)*Delta_t
call VecAXPY(solution_current,Delta_t,solution_rate,ierr); CHKERRQ(ierr)
call DMDAVecRestoreArrayF90(mechanical_grid,solution_current,u_current,ierr)
CHKERRQ(ierr)
call DMDAVecRestoreArrayF90(mechanical_grid,solution_lastInc,u_lastInc,ierr)
CHKERRQ(ierr)
call VecAXPY(solution_current,Delta_t,solution_rate,err_PETSc)
CHKERRQ(err_PETSc)
call DMDAVecRestoreArrayF90(mechanical_grid,solution_current,u_current,err_PETSc)
CHKERRQ(err_PETSc)
call DMDAVecRestoreArrayF90(mechanical_grid,solution_lastInc,u_lastInc,err_PETSc)
CHKERRQ(err_PETSc)
!--------------------------------------------------------------------------------------------------
! set module wide available data
@ -432,15 +428,15 @@ end subroutine grid_mechanical_FEM_updateCoords
!--------------------------------------------------------------------------------------------------
subroutine grid_mechanical_FEM_restartWrite
PetscErrorCode :: ierr
PetscErrorCode :: err_PETSc
integer(HID_T) :: fileHandle, groupHandle
PetscScalar, dimension(:,:,:,:), pointer :: u_current,u_lastInc
call DMDAVecGetArrayF90(mechanical_grid,solution_current,u_current,ierr)
CHKERRQ(ierr)
call DMDAVecGetArrayF90(mechanical_grid,solution_lastInc,u_lastInc,ierr)
CHKERRQ(ierr)
call DMDAVecGetArrayF90(mechanical_grid,solution_current,u_current,err_PETSc)
CHKERRQ(err_PETSc)
call DMDAVecGetArrayF90(mechanical_grid,solution_lastInc,u_lastInc,err_PETSc)
CHKERRQ(err_PETSc)
print'(1x,a)', 'writing solver data required for restart to file'; flush(IO_STDOUT)
@ -466,10 +462,10 @@ subroutine grid_mechanical_FEM_restartWrite
call HDF5_closeFile(fileHandle)
endif
call DMDAVecRestoreArrayF90(mechanical_grid,solution_current,u_current,ierr)
CHKERRQ(ierr)
call DMDAVecRestoreArrayF90(mechanical_grid,solution_lastInc,u_lastInc,ierr)
CHKERRQ(ierr)
call DMDAVecRestoreArrayF90(mechanical_grid,solution_current,u_current,err_PETSc)
CHKERRQ(err_PETSc)
call DMDAVecRestoreArrayF90(mechanical_grid,solution_lastInc,u_lastInc,err_PETSc)
CHKERRQ(err_PETSc)
end subroutine grid_mechanical_FEM_restartWrite
@ -477,7 +473,7 @@ end subroutine grid_mechanical_FEM_restartWrite
!--------------------------------------------------------------------------------------------------
!> @brief convergence check
!--------------------------------------------------------------------------------------------------
subroutine converged(snes_local,PETScIter,devNull1,devNull2,fnorm,reason,dummy,ierr)
subroutine converged(snes_local,PETScIter,devNull1,devNull2,fnorm,reason,dummy,err_PETSc)
SNES :: snes_local
PetscInt, intent(in) :: PETScIter
@ -487,7 +483,7 @@ subroutine converged(snes_local,PETScIter,devNull1,devNull2,fnorm,reason,dummy,i
fnorm
SNESConvergedReason :: reason
PetscObject :: dummy
PetscErrorCode :: ierr
PetscErrorCode :: err_PETSc
real(pReal) :: &
err_div, &
divTol, &
@ -513,6 +509,7 @@ subroutine converged(snes_local,PETScIter,devNull1,devNull2,fnorm,reason,dummy,i
err_BC/BCTol, ' (',err_BC, ' Pa, tol = ',BCTol,')'
print'(/,1x,a)', '==========================================================================='
flush(IO_STDOUT)
err_PETSc = 0
end subroutine converged
@ -521,24 +518,25 @@ end subroutine converged
!> @brief forms the residual vector
!--------------------------------------------------------------------------------------------------
subroutine formResidual(da_local,x_local, &
f_local,dummy,ierr)
f_local,dummy,err_PETSc)
DM :: da_local
Vec :: x_local, f_local
PetscScalar, pointer,dimension(:,:,:,:) :: x_scal, f_scal
PetscScalar, pointer,dimension(:,:,:,:) :: x_scal, r
PetscScalar, dimension(8,3) :: x_elem, f_elem
PetscInt :: i, ii, j, jj, k, kk, ctr, ele
PetscInt :: &
PETScIter, &
nfuncs
PetscObject :: dummy
PetscErrorCode :: ierr
PetscErrorCode :: err_PETSc
integer(MPI_INTEGER_KIND) :: err_MPI
real(pReal), dimension(3,3,3,3) :: devNull
call SNESGetNumberFunctionEvals(mechanical_snes,nfuncs,ierr)
CHKERRQ(ierr)
call SNESGetIterationNumber(mechanical_snes,PETScIter,ierr)
CHKERRQ(ierr)
call SNESGetNumberFunctionEvals(SNES_mechanical,nfuncs,err_PETSc)
CHKERRQ(err_PETSc)
call SNESGetIterationNumber(SNES_mechanical,PETScIter,err_PETSc)
CHKERRQ(err_PETSc)
if (nfuncs == 0 .and. PETScIter == 0) totalIter = -1 ! new increment
@ -556,24 +554,26 @@ subroutine formResidual(da_local,x_local, &
!--------------------------------------------------------------------------------------------------
! get deformation gradient
call DMDAVecGetArrayF90(da_local,x_local,x_scal,ierr);CHKERRQ(ierr)
do k = zstart, zend; do j = ystart, yend; do i = xstart, xend
call DMDAVecGetArrayF90(da_local,x_local,x_scal,err_PETSc)
CHKERRQ(err_PETSc)
do k = grid3offset+1, grid3offset+grid3; do j = 1, grid(2); do i = 1, grid(1)
ctr = 0
do kk = 0, 1; do jj = 0, 1; do ii = 0, 1
do kk = -1, 0; do jj = -1, 0; do ii = -1, 0
ctr = ctr + 1
x_elem(ctr,1:3) = x_scal(0:2,i+ii,j+jj,k+kk)
enddo; enddo; enddo
ii = i-xstart+1; jj = j-ystart+1; kk = k-zstart+1
F(1:3,1:3,ii,jj,kk) = params%rotation_BC%rotate(F_aim,active=.true.) + transpose(matmul(BMat,x_elem))
F(1:3,1:3,i,j,k-grid3offset) = params%rotation_BC%rotate(F_aim,active=.true.) + transpose(matmul(BMat,x_elem))
enddo; enddo; enddo
call DMDAVecRestoreArrayF90(da_local,x_local,x_scal,ierr);CHKERRQ(ierr)
call DMDAVecRestoreArrayF90(da_local,x_local,x_scal,err_PETSc)
CHKERRQ(err_PETSc)
!--------------------------------------------------------------------------------------------------
! evaluate constitutive response
call utilities_constitutiveResponse(P_current,&
P_av,C_volAvg,devNull, &
F,params%Delta_t,params%rotation_BC)
call MPI_Allreduce(MPI_IN_PLACE,terminallyIll,1,MPI_LOGICAL,MPI_LOR,MPI_COMM_WORLD,ierr)
call MPI_Allreduce(MPI_IN_PLACE,terminallyIll,1_MPI_INTEGER_KIND,MPI_LOGICAL,MPI_LOR,MPI_COMM_WORLD,err_MPI)
if(err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
!--------------------------------------------------------------------------------------------------
! stress BC handling
@ -582,47 +582,53 @@ subroutine formResidual(da_local,x_local, &
!--------------------------------------------------------------------------------------------------
! constructing residual
call VecSet(f_local,0.0_pReal,ierr);CHKERRQ(ierr)
call DMDAVecGetArrayF90(da_local,f_local,f_scal,ierr);CHKERRQ(ierr)
call DMDAVecGetArrayF90(da_local,x_local,x_scal,ierr);CHKERRQ(ierr)
call VecSet(f_local,0.0_pReal,err_PETSc)
CHKERRQ(err_PETSc)
call DMDAVecGetArrayF90(da_local,f_local,r,err_PETSc)
CHKERRQ(err_PETSc)
call DMDAVecGetArrayF90(da_local,x_local,x_scal,err_PETSc)
CHKERRQ(err_PETSc)
ele = 0
do k = zstart, zend; do j = ystart, yend; do i = xstart, xend
do k = grid3offset+1, grid3offset+grid3; do j = 1, grid(2); do i = 1, grid(1)
ctr = 0
do kk = 0, 1; do jj = 0, 1; do ii = 0, 1
do kk = -1, 0; do jj = -1, 0; do ii = -1, 0
ctr = ctr + 1
x_elem(ctr,1:3) = x_scal(0:2,i+ii,j+jj,k+kk)
enddo; enddo; enddo
ii = i-xstart+1; jj = j-ystart+1; kk = k-zstart+1
ele = ele + 1
f_elem = matmul(transpose(BMat),transpose(P_current(1:3,1:3,ii,jj,kk)))*detJ + &
f_elem = matmul(transpose(BMat),transpose(P_current(1:3,1:3,i,j,k-grid3offset)))*detJ + &
matmul(HGMat,x_elem)*(homogenization_dPdF(1,1,1,1,ele) + &
homogenization_dPdF(2,2,2,2,ele) + &
homogenization_dPdF(3,3,3,3,ele))/3.0_pReal
ctr = 0
do kk = 0, 1; do jj = 0, 1; do ii = 0, 1
do kk = -1, 0; do jj = -1, 0; do ii = -1, 0
ctr = ctr + 1
f_scal(0:2,i+ii,j+jj,k+kk) = f_scal(0:2,i+ii,j+jj,k+kk) + f_elem(ctr,1:3)
r(0:2,i+ii,j+jj,k+kk) = r(0:2,i+ii,j+jj,k+kk) + f_elem(ctr,1:3)
enddo; enddo; enddo
enddo; enddo; enddo
call DMDAVecRestoreArrayF90(da_local,x_local,x_scal,ierr);CHKERRQ(ierr)
call DMDAVecRestoreArrayF90(da_local,f_local,f_scal,ierr);CHKERRQ(ierr)
call DMDAVecRestoreArrayF90(da_local,x_local,x_scal,err_PETSc)
CHKERRQ(err_PETSc)
call DMDAVecRestoreArrayF90(da_local,f_local,r,err_PETSc)
CHKERRQ(err_PETSc)
!--------------------------------------------------------------------------------------------------
! applying boundary conditions
call DMDAVecGetArrayF90(da_local,f_local,f_scal,ierr);CHKERRQ(ierr)
if (zstart == 0) then
f_scal(0:2,xstart,ystart,zstart) = 0.0
f_scal(0:2,xend+1,ystart,zstart) = 0.0
f_scal(0:2,xstart,yend+1,zstart) = 0.0
f_scal(0:2,xend+1,yend+1,zstart) = 0.0
endif
if (zend + 1 == grid(3)) then
f_scal(0:2,xstart,ystart,zend+1) = 0.0
f_scal(0:2,xend+1,ystart,zend+1) = 0.0
f_scal(0:2,xstart,yend+1,zend+1) = 0.0
f_scal(0:2,xend+1,yend+1,zend+1) = 0.0
endif
call DMDAVecRestoreArrayF90(da_local,f_local,f_scal,ierr);CHKERRQ(ierr)
call DMDAVecGetArrayF90(da_local,f_local,r,err_PETSc)
CHKERRQ(err_PETSc)
if (grid3offset == 0) then
r(0:2,0, 0, 0) = 0.0_pReal
r(0:2,grid(1),0, 0) = 0.0_pReal
r(0:2,0, grid(2),0) = 0.0_pReal
r(0:2,grid(1),grid(2),0) = 0.0_pReal
end if
if (grid3+grid3offset == grid(3)) then
r(0:2,0, 0, grid(3)) = 0.0_pReal
r(0:2,grid(1),0, grid(3)) = 0.0_pReal
r(0:2,0, grid(2),grid(3)) = 0.0_pReal
r(0:2,grid(1),grid(2),grid(3)) = 0.0_pReal
end if
call DMDAVecRestoreArrayF90(da_local,f_local,r,err_PETSc)
CHKERRQ(err_PETSc)
end subroutine formResidual
@ -630,7 +636,7 @@ end subroutine formResidual
!--------------------------------------------------------------------------------------------------
!> @brief forms the FEM stiffness matrix
!--------------------------------------------------------------------------------------------------
subroutine formJacobian(da_local,x_local,Jac_pre,Jac,dummy,ierr)
subroutine formJacobian(da_local,x_local,Jac_pre,Jac,dummy,err_PETSc)
DM :: da_local
Vec :: x_local, coordinates
@ -639,24 +645,27 @@ subroutine formJacobian(da_local,x_local,Jac_pre,Jac,dummy,ierr)
PetscScalar,pointer,dimension(:,:,:,:) :: x_scal
PetscScalar,dimension(24,24) :: K_ele
PetscScalar,dimension(9,24) :: BMatFull
PetscInt :: i, ii, j, jj, k, kk, ctr, ele
PetscInt :: i, ii, j, jj, k, kk, ctr, ce
PetscInt,dimension(3),parameter :: rows = [0, 1, 2]
PetscScalar :: diag
PetscObject :: dummy
MatNullSpace :: matnull
PetscErrorCode :: ierr
PetscErrorCode :: err_PETSc
BMatFull = 0.0
BMatFull(1:3,1 :8 ) = BMat
BMatFull(4:6,9 :16) = BMat
BMatFull(7:9,17:24) = BMat
call MatSetOption(Jac,MAT_KEEP_NONZERO_PATTERN,PETSC_TRUE,ierr); CHKERRQ(ierr)
call MatSetOption(Jac,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE,ierr); CHKERRQ(ierr)
call MatZeroEntries(Jac,ierr); CHKERRQ(ierr)
ele = 0
do k = zstart, zend; do j = ystart, yend; do i = xstart, xend
call MatSetOption(Jac,MAT_KEEP_NONZERO_PATTERN,PETSC_TRUE,err_PETSc)
CHKERRQ(err_PETSc)
call MatSetOption(Jac,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE,err_PETSc)
CHKERRQ(err_PETSc)
call MatZeroEntries(Jac,err_PETSc)
CHKERRQ(err_PETSc)
ce = 0
do k = grid3offset+1, grid3offset+grid3; do j = 1, grid(2); do i = 1, grid(1)
ctr = 0
do kk = 0, 1; do jj = 0, 1; do ii = 0, 1
do kk = -1, 0; do jj = -1, 0; do ii = -1, 0
ctr = ctr + 1
col(MatStencil_i,ctr ) = i+ii
col(MatStencil_j,ctr ) = j+jj
@ -672,49 +681,60 @@ subroutine formJacobian(da_local,x_local,Jac_pre,Jac,dummy,ierr)
col(MatStencil_c,ctr+16) = 2
enddo; enddo; enddo
row = col
ele = ele + 1
ce = ce + 1
K_ele = 0.0
K_ele(1 :8 ,1 :8 ) = HGMat*(homogenization_dPdF(1,1,1,1,ele) + &
homogenization_dPdF(2,2,2,2,ele) + &
homogenization_dPdF(3,3,3,3,ele))/3.0_pReal
K_ele(9 :16,9 :16) = HGMat*(homogenization_dPdF(1,1,1,1,ele) + &
homogenization_dPdF(2,2,2,2,ele) + &
homogenization_dPdF(3,3,3,3,ele))/3.0_pReal
K_ele(17:24,17:24) = HGMat*(homogenization_dPdF(1,1,1,1,ele) + &
homogenization_dPdF(2,2,2,2,ele) + &
homogenization_dPdF(3,3,3,3,ele))/3.0_pReal
K_ele(1 :8 ,1 :8 ) = HGMat*(homogenization_dPdF(1,1,1,1,ce) + &
homogenization_dPdF(2,2,2,2,ce) + &
homogenization_dPdF(3,3,3,3,ce))/3.0_pReal
K_ele(9 :16,9 :16) = HGMat*(homogenization_dPdF(1,1,1,1,ce) + &
homogenization_dPdF(2,2,2,2,ce) + &
homogenization_dPdF(3,3,3,3,ce))/3.0_pReal
K_ele(17:24,17:24) = HGMat*(homogenization_dPdF(1,1,1,1,ce) + &
homogenization_dPdF(2,2,2,2,ce) + &
homogenization_dPdF(3,3,3,3,ce))/3.0_pReal
K_ele = K_ele + &
matmul(transpose(BMatFull), &
matmul(reshape(reshape(homogenization_dPdF(1:3,1:3,1:3,1:3,ele), &
matmul(reshape(reshape(homogenization_dPdF(1:3,1:3,1:3,1:3,ce), &
shape=[3,3,3,3], order=[2,1,4,3]),shape=[9,9]),BMatFull))*detJ
call MatSetValuesStencil(Jac,24,row,24,col,K_ele,ADD_VALUES,ierr)
CHKERRQ(ierr)
call MatSetValuesStencil(Jac,24_pPETScInt,row,24_pPetscInt,col,K_ele,ADD_VALUES,err_PETSc)
CHKERRQ(err_PETSc)
enddo; enddo; enddo
call MatAssemblyBegin(Jac,MAT_FINAL_ASSEMBLY,ierr); CHKERRQ(ierr)
call MatAssemblyEnd(Jac,MAT_FINAL_ASSEMBLY,ierr); CHKERRQ(ierr)
call MatAssemblyBegin(Jac_pre,MAT_FINAL_ASSEMBLY,ierr); CHKERRQ(ierr)
call MatAssemblyEnd(Jac_pre,MAT_FINAL_ASSEMBLY,ierr); CHKERRQ(ierr)
call MatAssemblyBegin(Jac,MAT_FINAL_ASSEMBLY,err_PETSc)
CHKERRQ(err_PETSc)
call MatAssemblyEnd(Jac,MAT_FINAL_ASSEMBLY,err_PETSc)
CHKERRQ(err_PETSc)
call MatAssemblyBegin(Jac_pre,MAT_FINAL_ASSEMBLY,err_PETSc)
CHKERRQ(err_PETSc)
call MatAssemblyEnd(Jac_pre,MAT_FINAL_ASSEMBLY,err_PETSc)
CHKERRQ(err_PETSc)
!--------------------------------------------------------------------------------------------------
! applying boundary conditions
diag = (C_volAvg(1,1,1,1)/delta(1)**2 + &
C_volAvg(2,2,2,2)/delta(2)**2 + &
C_volAvg(3,3,3,3)/delta(3)**2)*detJ
call MatZeroRowsColumns(Jac,size(rows),rows,diag,PETSC_NULL_VEC,PETSC_NULL_VEC,ierr)
CHKERRQ(ierr)
call DMGetGlobalVector(da_local,coordinates,ierr); CHKERRQ(ierr)
call DMDAVecGetArrayF90(da_local,coordinates,x_scal,ierr); CHKERRQ(ierr)
ele = 0
do k = zstart, zend; do j = ystart, yend; do i = xstart, xend
ele = ele + 1
x_scal(0:2,i,j,k) = discretization_IPcoords(1:3,ele)
diag = (C_volAvg(1,1,1,1)/delta(1)**2 + C_volAvg(2,2,2,2)/delta(2)**2 + C_volAvg(3,3,3,3)/delta(3)**2) &
* detJ
call MatZeroRowsColumns(Jac,size(rows,kind=pPetscInt),rows,diag,PETSC_NULL_VEC,PETSC_NULL_VEC,err_PETSc)
CHKERRQ(err_PETSc)
call DMGetGlobalVector(da_local,coordinates,err_PETSc)
CHKERRQ(err_PETSc)
call DMDAVecGetArrayF90(da_local,coordinates,x_scal,err_PETSc)
CHKERRQ(err_PETSc)
ce = 0
do k = grid3offset+1, grid3offset+grid3; do j = 1, grid(2); do i = 1, grid(1)
ce = ce + 1
x_scal(0:2,i-1,j-1,k-1) = discretization_IPcoords(1:3,ce)
enddo; enddo; enddo
call DMDAVecRestoreArrayF90(da_local,coordinates,x_scal,ierr); CHKERRQ(ierr) ! initialize to undeformed coordinates (ToDo: use ip coordinates)
call MatNullSpaceCreateRigidBody(coordinates,matnull,ierr); CHKERRQ(ierr) ! get rigid body deformation modes
call DMRestoreGlobalVector(da_local,coordinates,ierr); CHKERRQ(ierr)
call MatSetNullSpace(Jac,matnull,ierr); CHKERRQ(ierr)
call MatSetNearNullSpace(Jac,matnull,ierr); CHKERRQ(ierr)
call MatNullSpaceDestroy(matnull,ierr); CHKERRQ(ierr)
call DMDAVecRestoreArrayF90(da_local,coordinates,x_scal,err_PETSc)
CHKERRQ(err_PETSc) ! initialize to undeformed coordinates (ToDo: use ip coordinates)
call MatNullSpaceCreateRigidBody(coordinates,matnull,err_PETSc)
CHKERRQ(err_PETSc) ! get rigid body deformation modes
call DMRestoreGlobalVector(da_local,coordinates,err_PETSc)
CHKERRQ(err_PETSc)
call MatSetNullSpace(Jac,matnull,err_PETSc)
CHKERRQ(err_PETSc)
call MatSetNearNullSpace(Jac,matnull,err_PETSc)
CHKERRQ(err_PETSc)
call MatNullSpaceDestroy(matnull,err_PETSc)
CHKERRQ(err_PETSc)
end subroutine formJacobian

166
src/grid/grid_mech_spectral_basic.f90
View File

@ -50,7 +50,7 @@ module grid_mechanical_spectral_basic
!--------------------------------------------------------------------------------------------------
! PETSc data
DM :: da
SNES :: snes
SNES :: SNES_mechanical
Vec :: solution_vec
!--------------------------------------------------------------------------------------------------
@ -97,7 +97,8 @@ contains
subroutine grid_mechanical_spectral_basic_init
real(pReal), dimension(3,3,grid(1),grid(2),grid3) :: P
PetscErrorCode :: ierr
PetscErrorCode :: err_PETSc
integer(MPI_INTEGER_KIND) :: err_MPI
PetscScalar, pointer, dimension(:,:,:,:) :: &
F ! pointer to solution data
PetscInt, dimension(0:worldsize-1) :: localK
@ -145,10 +146,10 @@ subroutine grid_mechanical_spectral_basic_init
!--------------------------------------------------------------------------------------------------
! set default and user defined options for PETSc
call PetscOptionsInsertString(PETSC_NULL_OPTIONS,'-mechanical_snes_type ngmres',ierr)
CHKERRQ(ierr)
call PetscOptionsInsertString(PETSC_NULL_OPTIONS,num_grid%get_asString('petsc_options',defaultVal=''),ierr)
CHKERRQ(ierr)
call PetscOptionsInsertString(PETSC_NULL_OPTIONS,'-mechanical_snes_type ngmres',err_PETSc)
CHKERRQ(err_PETSc)
call PetscOptionsInsertString(PETSC_NULL_OPTIONS,num_grid%get_asString('petsc_options',defaultVal=''),err_PETSc)
CHKERRQ(err_PETSc)
!--------------------------------------------------------------------------------------------------
! allocate global fields
@ -157,33 +158,42 @@ subroutine grid_mechanical_spectral_basic_init
!--------------------------------------------------------------------------------------------------
! initialize solver specific parts of PETSc
call SNESCreate(PETSC_COMM_WORLD,snes,ierr); CHKERRQ(ierr)
call SNESSetOptionsPrefix(snes,'mechanical_',ierr);CHKERRQ(ierr)
localK = 0
localK(worldrank) = grid3
call MPI_Allreduce(MPI_IN_PLACE,localK,worldsize,MPI_INTEGER,MPI_SUM,MPI_COMM_WORLD,ierr)
call SNESCreate(PETSC_COMM_WORLD,SNES_mechanical,err_PETSc)
CHKERRQ(err_PETSc)
call SNESSetOptionsPrefix(SNES_mechanical,'mechanical_',err_PETSc)
CHKERRQ(err_PETSc)
localK = 0_pPetscInt
localK(worldrank) = int(grid3,pPetscInt)
call MPI_Allreduce(MPI_IN_PLACE,localK,worldsize,MPI_INTEGER,MPI_SUM,MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
call DMDACreate3d(PETSC_COMM_WORLD, &
DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, & ! cut off stencil at boundary
DMDA_STENCIL_BOX, & ! Moore (26) neighborhood around central point
grid(1),grid(2),grid(3), & ! global grid
1 , 1, worldsize, &
9, 0, & ! #dof (F tensor), ghost boundary width (domain overlap)
[grid(1)],[grid(2)],localK, & ! local grid
da,ierr) ! handle, error
CHKERRQ(ierr)
call SNESSetDM(snes,da,ierr); CHKERRQ(ierr) ! connect snes to da
call DMsetFromOptions(da,ierr); CHKERRQ(ierr)
call DMsetUp(da,ierr); CHKERRQ(ierr)
call DMcreateGlobalVector(da,solution_vec,ierr); CHKERRQ(ierr) ! global solution vector (grid x 9, i.e. every def grad tensor)
call DMDASNESsetFunctionLocal(da,INSERT_VALUES,formResidual,PETSC_NULL_SNES,ierr) ! residual vector of same shape as solution vector
CHKERRQ(ierr)
call SNESsetConvergenceTest(snes,converged,PETSC_NULL_SNES,PETSC_NULL_FUNCTION,ierr) ! specify custom convergence check function "converged"
CHKERRQ(ierr)
call SNESsetFromOptions(snes,ierr); CHKERRQ(ierr) ! pull it all together with additional CLI arguments
int(grid(1),pPetscInt),int(grid(2),pPetscInt),int(grid(3),pPetscInt), & ! global grid
1_pPetscInt, 1_pPetscInt, int(worldsize,pPetscInt), &
9_pPetscInt, 0_pPetscInt, & ! #dof (F, tensor), ghost boundary width (domain overlap)
[int(grid(1),pPetscInt)],[int(grid(2),pPetscInt)],localK, & ! local grid
da,err_PETSc) ! handle, error
CHKERRQ(err_PETSc)
call DMsetFromOptions(da,err_PETSc)
CHKERRQ(err_PETSc)
call DMsetUp(da,err_PETSc)
CHKERRQ(err_PETSc)
call DMcreateGlobalVector(da,solution_vec,err_PETSc) ! global solution vector (grid x 9, i.e. every def grad tensor)
CHKERRQ(err_PETSc)
call DMDASNESsetFunctionLocal(da,INSERT_VALUES,formResidual,PETSC_NULL_SNES,err_PETSc) ! residual vector of same shape as solution vector
CHKERRQ(err_PETSc)
call SNESsetConvergenceTest(SNES_mechanical,converged,PETSC_NULL_SNES,PETSC_NULL_FUNCTION,err_PETSc) ! specify custom convergence check function "converged"
CHKERRQ(err_PETSc)
call SNESSetDM(SNES_mechanical,da,err_PETSc)
CHKERRQ(err_PETSc)
call SNESsetFromOptions(SNES_mechanical,err_PETSc) ! pull it all together with additional CLI arguments
CHKERRQ(err_PETSc)
!--------------------------------------------------------------------------------------------------
! init fields
call DMDAVecGetArrayF90(da,solution_vec,F,ierr); CHKERRQ(ierr) ! places pointer on PETSc data
call DMDAVecGetArrayF90(da,solution_vec,F,err_PETSc) ! places pointer on PETSc data
CHKERRQ(err_PETSc)
restartRead: if (interface_restartInc > 0) then
print'(/,1x,a,i0,a)', 'reading restart data of increment ', interface_restartInc, ' from file'
@ -192,17 +202,17 @@ subroutine grid_mechanical_spectral_basic_init
groupHandle = HDF5_openGroup(fileHandle,'solver')
call HDF5_read(P_aim,groupHandle,'P_aim',.false.)
call MPI_Bcast(P_aim,9,MPI_DOUBLE,0,MPI_COMM_WORLD,ierr)
if (ierr /=0) error stop 'MPI error'
call MPI_Bcast(P_aim,9_MPI_INTEGER_KIND,MPI_DOUBLE,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
call HDF5_read(F_aim,groupHandle,'F_aim',.false.)
call MPI_Bcast(F_aim,9,MPI_DOUBLE,0,MPI_COMM_WORLD,ierr)
if (ierr /=0) error stop 'MPI error'
call MPI_Bcast(F_aim,9_MPI_INTEGER_KIND,MPI_DOUBLE,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
call HDF5_read(F_aim_lastInc,groupHandle,'F_aim_lastInc',.false.)
call MPI_Bcast(F_aim_lastInc,9,MPI_DOUBLE,0,MPI_COMM_WORLD,ierr)
if (ierr /=0) error stop 'MPI error'
call MPI_Bcast(F_aim_lastInc,9_MPI_INTEGER_KIND,MPI_DOUBLE,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
call HDF5_read(F_aimDot,groupHandle,'F_aimDot',.false.)
call MPI_Bcast(F_aimDot,9,MPI_DOUBLE,0,MPI_COMM_WORLD,ierr)
if (ierr /=0) error stop 'MPI error'
call MPI_Bcast(F_aimDot,9_MPI_INTEGER_KIND,MPI_DOUBLE,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
call HDF5_read(F,groupHandle,'F')
call HDF5_read(F_lastInc,groupHandle,'F_lastInc')
@ -216,24 +226,28 @@ subroutine grid_mechanical_spectral_basic_init
call utilities_constitutiveResponse(P,P_av,C_volAvg,C_minMaxAvg, & ! stress field, stress avg, global average of stiffness and (min+max)/2
reshape(F,shape(F_lastInc)), & ! target F
0.0_pReal) ! time increment
call DMDAVecRestoreArrayF90(da,solution_vec,F,ierr); CHKERRQ(ierr) ! deassociate pointer
call DMDAVecRestoreArrayF90(da,solution_vec,F,err_PETSc) ! deassociate pointer
CHKERRQ(err_PETSc)
restartRead2: if (interface_restartInc > 0) then
print'(1x,a,i0,a)', 'reading more restart data of increment ', interface_restartInc, ' from file'
call HDF5_read(C_volAvg,groupHandle,'C_volAvg',.false.)
call MPI_Bcast(C_volAvg,81,MPI_DOUBLE,0,MPI_COMM_WORLD,ierr)
if (ierr /=0) error stop 'MPI error'
call MPI_Bcast(C_volAvg,81_MPI_INTEGER_KIND,MPI_DOUBLE,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
call HDF5_read(C_volAvgLastInc,groupHandle,'C_volAvgLastInc',.false.)
call MPI_Bcast(C_volAvgLastInc,81,MPI_DOUBLE,0,MPI_COMM_WORLD,ierr)
if (ierr /=0) error stop 'MPI error'
call MPI_Bcast(C_volAvgLastInc,81_MPI_INTEGER_KIND,MPI_DOUBLE,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
call HDF5_closeGroup(groupHandle)
call HDF5_closeFile(fileHandle)
call MPI_File_open(MPI_COMM_WORLD, trim(getSolverJobName())//'.C_ref', &
MPI_MODE_RDONLY,MPI_INFO_NULL,fileUnit,ierr)
call MPI_File_read(fileUnit,C_minMaxAvg,81,MPI_DOUBLE,MPI_STATUS_IGNORE,ierr)
call MPI_File_close(fileUnit,ierr)
MPI_MODE_RDONLY,MPI_INFO_NULL,fileUnit,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
call MPI_File_read(fileUnit,C_minMaxAvg,81_MPI_INTEGER_KIND,MPI_DOUBLE,MPI_STATUS_IGNORE,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
call MPI_File_close(fileUnit,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
end if restartRead2
call utilities_updateGamma(C_minMaxAvg)
@ -255,7 +269,7 @@ function grid_mechanical_spectral_basic_solution(incInfoIn) result(solution)
solution
!--------------------------------------------------------------------------------------------------
! PETSc Data
PetscErrorCode :: ierr
PetscErrorCode :: err_PETSc
SNESConvergedReason :: reason
incInfo = incInfoIn
@ -265,13 +279,10 @@ function grid_mechanical_spectral_basic_solution(incInfoIn) result(solution)
S = utilities_maskedCompliance(params%rotation_BC,params%stress_mask,C_volAvg)
if (num%update_gamma) call utilities_updateGamma(C_minMaxAvg)
!--------------------------------------------------------------------------------------------------
! solve BVP
call SNESsolve(snes,PETSC_NULL_VEC,solution_vec,ierr); CHKERRQ(ierr)
!--------------------------------------------------------------------------------------------------
! check convergence
call SNESGetConvergedReason(snes,reason,ierr); CHKERRQ(ierr)
call SNESsolve(SNES_mechanical,PETSC_NULL_VEC,solution_vec,err_PETSc)
CHKERRQ(err_PETSc)
call SNESGetConvergedReason(SNES_mechanical,reason,err_PETSc)
CHKERRQ(err_PETSc)
solution%converged = reason > 0
solution%iterationsNeeded = totalIter
@ -301,11 +312,12 @@ subroutine grid_mechanical_spectral_basic_forward(cutBack,guess,Delta_t,Delta_t_
deformation_BC
type(rotation), intent(in) :: &
rotation_BC
PetscErrorCode :: ierr
PetscErrorCode :: err_PETSc
PetscScalar, pointer, dimension(:,:,:,:) :: F
call DMDAVecGetArrayF90(da,solution_vec,F,ierr); CHKERRQ(ierr)
call DMDAVecGetArrayF90(da,solution_vec,F,err_PETSc)
CHKERRQ(err_PETSc)
if (cutBack) then
C_volAvg = C_volAvgLastInc
@ -314,7 +326,7 @@ subroutine grid_mechanical_spectral_basic_forward(cutBack,guess,Delta_t,Delta_t_
C_volAvgLastInc = C_volAvg
C_minMaxAvgLastInc = C_minMaxAvg
F_aimDot = merge(merge(.0_pReal,(F_aim-F_aim_lastInc)/Delta_t_old,stress_BC%mask),.0_pReal,guess) ! estimate deformation rate for prescribed stress components
F_aimDot = merge(merge(.0_pReal,(F_aim-F_aim_lastInc)/Delta_t_old,stress_BC%mask),.0_pReal,guess) ! estimate deformation rate for prescribed stress components
F_aim_lastInc = F_aim
!-----------------------------------------------------------------------------------------------
@ -348,7 +360,8 @@ subroutine grid_mechanical_spectral_basic_forward(cutBack,guess,Delta_t,Delta_t_
F = reshape(utilities_forwardField(Delta_t,F_lastInc,Fdot, & ! estimate of F at end of time+Delta_t that matches rotated F_aim on average
rotation_BC%rotate(F_aim,active=.true.)),[9,grid(1),grid(2),grid3])
call DMDAVecRestoreArrayF90(da,solution_vec,F,ierr); CHKERRQ(ierr)
call DMDAVecRestoreArrayF90(da,solution_vec,F,err_PETSc)
CHKERRQ(err_PETSc)
!--------------------------------------------------------------------------------------------------
! set module wide available data
@ -364,12 +377,14 @@ end subroutine grid_mechanical_spectral_basic_forward
!--------------------------------------------------------------------------------------------------
subroutine grid_mechanical_spectral_basic_updateCoords
PetscErrorCode :: ierr
PetscErrorCode :: err_PETSc
PetscScalar, dimension(:,:,:,:), pointer :: F
call DMDAVecGetArrayF90(da,solution_vec,F,ierr); CHKERRQ(ierr)
call DMDAVecGetArrayF90(da,solution_vec,F,err_PETSc)
CHKERRQ(err_PETSc)
call utilities_updateCoords(F)
call DMDAVecRestoreArrayF90(da,solution_vec,F,ierr); CHKERRQ(ierr)
call DMDAVecRestoreArrayF90(da,solution_vec,F,err_PETSc)
CHKERRQ(err_PETSc)
end subroutine grid_mechanical_spectral_basic_updateCoords
@ -379,11 +394,12 @@ end subroutine grid_mechanical_spectral_basic_updateCoords
!--------------------------------------------------------------------------------------------------
subroutine grid_mechanical_spectral_basic_restartWrite
PetscErrorCode :: ierr
PetscErrorCode :: err_PETSc
integer(HID_T) :: fileHandle, groupHandle
PetscScalar, dimension(:,:,:,:), pointer :: F
call DMDAVecGetArrayF90(da,solution_vec,F,ierr); CHKERRQ(ierr)
call DMDAVecGetArrayF90(da,solution_vec,F,err_PETSc)
CHKERRQ(err_PETSc)
print'(1x,a)', 'writing solver data required for restart to file'; flush(IO_STDOUT)
@ -410,7 +426,8 @@ subroutine grid_mechanical_spectral_basic_restartWrite
if (num%update_gamma) call utilities_saveReferenceStiffness
call DMDAVecRestoreArrayF90(da,solution_vec,F,ierr); CHKERRQ(ierr)
call DMDAVecRestoreArrayF90(da,solution_vec,F,err_PETSc)
CHKERRQ(err_PETSc)
end subroutine grid_mechanical_spectral_basic_restartWrite
@ -418,7 +435,7 @@ end subroutine grid_mechanical_spectral_basic_restartWrite
!--------------------------------------------------------------------------------------------------
!> @brief convergence check
!--------------------------------------------------------------------------------------------------
subroutine converged(snes_local,PETScIter,devNull1,devNull2,devNull3,reason,dummy,ierr)
subroutine converged(snes_local,PETScIter,devNull1,devNull2,devNull3,reason,dummy,err_PETSc)
SNES :: snes_local
PetscInt, intent(in) :: PETScIter
@ -428,7 +445,7 @@ subroutine converged(snes_local,PETScIter,devNull1,devNull2,devNull3,reason,dumm
devNull3
SNESConvergedReason :: reason
PetscObject :: dummy
PetscErrorCode :: ierr
PetscErrorCode :: err_PETSc
real(pReal) :: &
divTol, &
BCTol
@ -452,6 +469,7 @@ subroutine converged(snes_local,PETScIter,devNull1,devNull2,devNull3,reason,dumm
err_BC/BCTol, ' (',err_BC, ' Pa, tol = ',BCTol,')'
print'(/,1x,a)', '==========================================================================='
flush(IO_STDOUT)
err_PETSc = 0
end subroutine converged
@ -460,23 +478,26 @@ end subroutine converged
!> @brief forms the residual vector
!--------------------------------------------------------------------------------------------------
subroutine formResidual(in, F, &
residuum, dummy, ierr)
r, dummy, err_PETSc)
DMDALocalInfo, dimension(DMDA_LOCAL_INFO_SIZE) :: in !< DMDA info (needs to be named "in" for macros like XRANGE to work)
PetscScalar, dimension(3,3,XG_RANGE,YG_RANGE,ZG_RANGE), &
intent(in) :: F !< deformation gradient field
PetscScalar, dimension(3,3,X_RANGE,Y_RANGE,Z_RANGE), &
intent(out) :: residuum !< residuum field
intent(out) :: r !< residuum field
real(pReal), dimension(3,3) :: &
deltaF_aim
PetscInt :: &
PETScIter, &
nfuncs
PetscObject :: dummy
PetscErrorCode :: ierr
PetscErrorCode :: err_PETSc
integer(MPI_INTEGER_KIND) :: err_MPI
call SNESGetNumberFunctionEvals(snes,nfuncs,ierr); CHKERRQ(ierr)
call SNESGetIterationNumber(snes,PETScIter,ierr); CHKERRQ(ierr)
call SNESGetNumberFunctionEvals(SNES_mechanical,nfuncs,err_PETSc)
CHKERRQ(err_PETSc)
call SNESGetIterationNumber(SNES_mechanical,PETScIter,err_PETSc)
CHKERRQ(err_PETSc)
if (nfuncs == 0 .and. PETScIter == 0) totalIter = -1 ! new increment
@ -494,10 +515,11 @@ subroutine formResidual(in, F, &
!--------------------------------------------------------------------------------------------------
! evaluate constitutive response
call utilities_constitutiveResponse(residuum, & ! "residuum" gets field of first PK stress (to save memory)
call utilities_constitutiveResponse(r, & ! residuum gets field of first PK stress (to save memory)
P_av,C_volAvg,C_minMaxAvg, &
F,params%Delta_t,params%rotation_BC)
call MPI_Allreduce(MPI_IN_PLACE,terminallyIll,1,MPI_LOGICAL,MPI_LOR,MPI_COMM_WORLD,ierr)
call MPI_Allreduce(MPI_IN_PLACE,terminallyIll,1_MPI_INTEGER_KIND,MPI_LOGICAL,MPI_LOR,MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
!--------------------------------------------------------------------------------------------------
! stress BC handling
@ -508,7 +530,7 @@ subroutine formResidual(in, F, &
!--------------------------------------------------------------------------------------------------
! updated deformation gradient using fix point algorithm of basic scheme
tensorField_real = 0.0_pReal
tensorField_real(1:3,1:3,1:grid(1),1:grid(2),1:grid3) = residuum ! store fPK field for subsequent FFT forward transform
tensorField_real(1:3,1:3,1:grid(1),1:grid(2),1:grid3) = r ! store fPK field for subsequent FFT forward transform
call utilities_FFTtensorForward ! FFT forward of global "tensorField_real"
err_div = utilities_divergenceRMS() ! divRMS of tensorField_fourier for later use
call utilities_fourierGammaConvolution(params%rotation_BC%rotate(deltaF_aim,active=.true.)) ! convolution of Gamma and tensorField_fourier
@ -516,7 +538,7 @@ subroutine formResidual(in, F, &
!--------------------------------------------------------------------------------------------------
! constructing residual
residuum = tensorField_real(1:3,1:3,1:grid(1),1:grid(2),1:grid3) ! Gamma*P gives correction towards div(P) = 0, so needs to be zero, too
r = tensorField_real(1:3,1:3,1:grid(1),1:grid(2),1:grid3) ! Gamma*P gives correction towards div(P) = 0, so needs to be zero, too
end subroutine formResidual

198
src/grid/grid_mech_spectral_polarisation.f90
View File

@ -55,7 +55,7 @@ module grid_mechanical_spectral_polarisation
!--------------------------------------------------------------------------------------------------
! PETSc data
DM :: da
SNES :: snes
SNES :: SNES_mechanical
Vec :: solution_vec
!--------------------------------------------------------------------------------------------------
@ -108,7 +108,8 @@ contains
subroutine grid_mechanical_spectral_polarisation_init
real(pReal), dimension(3,3,grid(1),grid(2),grid3) :: P
PetscErrorCode :: ierr
PetscErrorCode :: err_PETSc
integer(MPI_INTEGER_KIND) :: err_MPI
PetscScalar, pointer, dimension(:,:,:,:) :: &
FandF_tau, & ! overall pointer to solution data
F, & ! specific (sub)pointer
@ -163,10 +164,10 @@ subroutine grid_mechanical_spectral_polarisation_init
!--------------------------------------------------------------------------------------------------
! set default and user defined options for PETSc
call PetscOptionsInsertString(PETSC_NULL_OPTIONS,'-mechanical_snes_type ngmres',ierr)
CHKERRQ(ierr)
call PetscOptionsInsertString(PETSC_NULL_OPTIONS,num_grid%get_asString('petsc_options',defaultVal=''),ierr)
CHKERRQ(ierr)
call PetscOptionsInsertString(PETSC_NULL_OPTIONS,'-mechanical_snes_type ngmres',err_PETSc)
CHKERRQ(err_PETSc)
call PetscOptionsInsertString(PETSC_NULL_OPTIONS,num_grid%get_asString('petsc_options',defaultVal=''),err_PETSc)
CHKERRQ(err_PETSc)
!--------------------------------------------------------------------------------------------------
! allocate global fields
@ -177,33 +178,42 @@ subroutine grid_mechanical_spectral_polarisation_init
!--------------------------------------------------------------------------------------------------
! initialize solver specific parts of PETSc
call SNESCreate(PETSC_COMM_WORLD,snes,ierr); CHKERRQ(ierr)
call SNESSetOptionsPrefix(snes,'mechanical_',ierr);CHKERRQ(ierr)
localK = 0
localK(worldrank) = grid3
call MPI_Allreduce(MPI_IN_PLACE,localK,worldsize,MPI_INTEGER,MPI_SUM,MPI_COMM_WORLD,ierr)
call SNESCreate(PETSC_COMM_WORLD,SNES_mechanical,err_PETSc)
CHKERRQ(err_PETSc)
call SNESSetOptionsPrefix(SNES_mechanical,'mechanical_',err_PETSc)
CHKERRQ(err_PETSc)
localK = 0_pPetscInt
localK(worldrank) = int(grid3,pPetscInt)
call MPI_Allreduce(MPI_IN_PLACE,localK,worldsize,MPI_INTEGER,MPI_SUM,MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
call DMDACreate3d(PETSC_COMM_WORLD, &
DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, & ! cut off stencil at boundary
DMDA_STENCIL_BOX, & ! Moore (26) neighborhood around central point
grid(1),grid(2),grid(3), & ! global grid
1 , 1, worldsize, &
18, 0, & ! #dof (F tensor), ghost boundary width (domain overlap)
[grid(1)],[grid(2)],localK, & ! local grid
da,ierr) ! handle, error
CHKERRQ(ierr)
call SNESSetDM(snes,da,ierr); CHKERRQ(ierr) ! connect snes to da
call DMsetFromOptions(da,ierr); CHKERRQ(ierr)
call DMsetUp(da,ierr); CHKERRQ(ierr)
call DMcreateGlobalVector(da,solution_vec,ierr); CHKERRQ(ierr) ! global solution vector (grid x 18, i.e. every def grad tensor)
call DMDASNESsetFunctionLocal(da,INSERT_VALUES,formResidual,PETSC_NULL_SNES,ierr) ! residual vector of same shape as solution vector
CHKERRQ(ierr)
call SNESsetConvergenceTest(snes,converged,PETSC_NULL_SNES,PETSC_NULL_FUNCTION,ierr) ! specify custom convergence check function "converged"
CHKERRQ(ierr)
call SNESsetFromOptions(snes,ierr); CHKERRQ(ierr) ! pull it all together with additional CLI arguments
int(grid(1),pPetscInt),int(grid(2),pPetscInt),int(grid(3),pPetscInt), & ! global grid
1_pPetscInt, 1_pPetscInt, int(worldsize,pPetscInt), &
18_pPetscInt, 0_pPetscInt, & ! #dof (2xtensor), ghost boundary width (domain overlap)
[int(grid(1),pPetscInt)],[int(grid(2),pPetscInt)],localK, & ! local grid
da,err_PETSc) ! handle, error
CHKERRQ(err_PETSc)
call DMsetFromOptions(da,err_PETSc)
CHKERRQ(err_PETSc)
call DMsetUp(da,err_PETSc)
CHKERRQ(err_PETSc)
call DMcreateGlobalVector(da,solution_vec,err_PETSc) ! global solution vector (grid x 18, i.e. every def grad tensor)
CHKERRQ(err_PETSc)
call DMDASNESsetFunctionLocal(da,INSERT_VALUES,formResidual,PETSC_NULL_SNES,err_PETSc) ! residual vector of same shape as solution vector
CHKERRQ(err_PETSc)
call SNESsetConvergenceTest(SNES_mechanical,converged,PETSC_NULL_SNES,PETSC_NULL_FUNCTION,err_PETSc) ! specify custom convergence check function "converged"
CHKERRQ(err_PETSc)
call SNESSetDM(SNES_mechanical,da,err_PETSc)
CHKERRQ(err_PETSc)
call SNESsetFromOptions(SNES_mechanical,err_PETSc) ! pull it all together with additional CLI arguments
CHKERRQ(err_PETSc)
!--------------------------------------------------------------------------------------------------
! init fields
call DMDAVecGetArrayF90(da,solution_vec,FandF_tau,ierr); CHKERRQ(ierr) ! places pointer on PETSc data
call DMDAVecGetArrayF90(da,solution_vec,FandF_tau,err_PETSc) ! places pointer on PETSc data
CHKERRQ(err_PETSc)
F => FandF_tau(0: 8,:,:,:)
F_tau => FandF_tau(9:17,:,:,:)
@ -214,17 +224,17 @@ subroutine grid_mechanical_spectral_polarisation_init
groupHandle = HDF5_openGroup(fileHandle,'solver')
call HDF5_read(P_aim,groupHandle,'P_aim',.false.)
call MPI_Bcast(P_aim,9,MPI_DOUBLE,0,MPI_COMM_WORLD,ierr)
if (ierr /=0) error stop 'MPI error'
call MPI_Bcast(P_aim,9_MPI_INTEGER_KIND,MPI_DOUBLE,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
call HDF5_read(F_aim,groupHandle,'F_aim',.false.)
call MPI_Bcast(F_aim,9,MPI_DOUBLE,0,MPI_COMM_WORLD,ierr)
if (ierr /=0) error stop 'MPI error'
call MPI_Bcast(F_aim,9_MPI_INTEGER_KIND,MPI_DOUBLE,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
call HDF5_read(F_aim_lastInc,groupHandle,'F_aim_lastInc',.false.)
call MPI_Bcast(F_aim_lastInc,9,MPI_DOUBLE,0,MPI_COMM_WORLD,ierr)
if (ierr /=0) error stop 'MPI error'
call MPI_Bcast(F_aim_lastInc,9_MPI_INTEGER_KIND,MPI_DOUBLE,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
call HDF5_read(F_aimDot,groupHandle,'F_aimDot',.false.)
call MPI_Bcast(F_aimDot,9,MPI_DOUBLE,0,MPI_COMM_WORLD,ierr)
if (ierr /=0) error stop 'MPI error'
call MPI_Bcast(F_aimDot,9_MPI_INTEGER_KIND,MPI_DOUBLE,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
call HDF5_read(F,groupHandle,'F')
call HDF5_read(F_lastInc,groupHandle,'F_lastInc')
call HDF5_read(F_tau,groupHandle,'F_tau')
@ -242,24 +252,28 @@ subroutine grid_mechanical_spectral_polarisation_init
call utilities_constitutiveResponse(P,P_av,C_volAvg,C_minMaxAvg, & ! stress field, stress avg, global average of stiffness and (min+max)/2
reshape(F,shape(F_lastInc)), & ! target F
0.0_pReal) ! time increment
call DMDAVecRestoreArrayF90(da,solution_vec,FandF_tau,ierr); CHKERRQ(ierr) ! deassociate pointer
call DMDAVecRestoreArrayF90(da,solution_vec,FandF_tau,err_PETSc) ! deassociate pointer
CHKERRQ(err_PETSc)
restartRead2: if (interface_restartInc > 0) then
print'(1x,a,i0,a)', 'reading more restart data of increment ', interface_restartInc, ' from file'
call HDF5_read(C_volAvg,groupHandle,'C_volAvg',.false.)
call MPI_Bcast(C_volAvg,81,MPI_DOUBLE,0,MPI_COMM_WORLD,ierr)
if (ierr /=0) error stop 'MPI error'
call MPI_Bcast(C_volAvg,81_MPI_INTEGER_KIND,MPI_DOUBLE,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
call HDF5_read(C_volAvgLastInc,groupHandle,'C_volAvgLastInc',.false.)
call MPI_Bcast(C_volAvgLastInc,81,MPI_DOUBLE,0,MPI_COMM_WORLD,ierr)
if (ierr /=0) error stop 'MPI error'
call MPI_Bcast(C_volAvgLastInc,81_MPI_INTEGER_KIND,MPI_DOUBLE,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
call HDF5_closeGroup(groupHandle)
call HDF5_closeFile(fileHandle)
call MPI_File_open(MPI_COMM_WORLD, trim(getSolverJobName())//'.C_ref', &
MPI_MODE_RDONLY,MPI_INFO_NULL,fileUnit,ierr)
call MPI_File_read(fileUnit,C_minMaxAvg,81,MPI_DOUBLE,MPI_STATUS_IGNORE,ierr)
call MPI_File_close(fileUnit,ierr)
MPI_MODE_RDONLY,MPI_INFO_NULL,fileUnit,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
call MPI_File_read(fileUnit,C_minMaxAvg,81_MPI_INTEGER_KIND,MPI_DOUBLE,MPI_STATUS_IGNORE,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
call MPI_File_close(fileUnit,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
end if restartRead2
call utilities_updateGamma(C_minMaxAvg)
@ -279,11 +293,11 @@ function grid_mechanical_spectral_polarisation_solution(incInfoIn) result(soluti
! input data for solution
character(len=*), intent(in) :: &
incInfoIn
type(tSolutionState) :: &
type(tSolutionState) :: &
solution
!--------------------------------------------------------------------------------------------------
! PETSc Data
PetscErrorCode :: ierr
PetscErrorCode :: err_PETSc
SNESConvergedReason :: reason
incInfo = incInfoIn
@ -297,13 +311,10 @@ function grid_mechanical_spectral_polarisation_solution(incInfoIn) result(soluti
S_scale = math_invSym3333(C_minMaxAvg)
end if
!--------------------------------------------------------------------------------------------------
! solve BVP
call SNESsolve(snes,PETSC_NULL_VEC,solution_vec,ierr); CHKERRQ(ierr)
!--------------------------------------------------------------------------------------------------
! check convergence
call SNESGetConvergedReason(snes,reason,ierr); CHKERRQ(ierr)
call SNESSolve(SNES_mechanical,PETSC_NULL_VEC,solution_vec,err_PETSc)
CHKERRQ(err_PETSc)
call SNESGetConvergedReason(SNES_mechanical,reason,err_PETSc)
CHKERRQ(err_PETSc)
solution%converged = reason > 0
solution%iterationsNeeded = totalIter
@ -333,13 +344,14 @@ subroutine grid_mechanical_spectral_polarisation_forward(cutBack,guess,Delta_t,D
deformation_BC
type(rotation), intent(in) :: &
rotation_BC
PetscErrorCode :: ierr
PetscErrorCode :: err_PETSc
PetscScalar, pointer, dimension(:,:,:,:) :: FandF_tau, F, F_tau
integer :: i, j, k
real(pReal), dimension(3,3) :: F_lambda33
call DMDAVecGetArrayF90(da,solution_vec,FandF_tau,ierr); CHKERRQ(ierr)
call DMDAVecGetArrayF90(da,solution_vec,FandF_tau,err_PETSc)
CHKERRQ(err_PETSc)
F => FandF_tau(0: 8,:,:,:)
F_tau => FandF_tau(9:17,:,:,:)
@ -402,7 +414,8 @@ subroutine grid_mechanical_spectral_polarisation_forward(cutBack,guess,Delta_t,D
end do; end do; end do
end if
call DMDAVecRestoreArrayF90(da,solution_vec,FandF_tau,ierr); CHKERRQ(ierr)
call DMDAVecRestoreArrayF90(da,solution_vec,FandF_tau,err_PETSc)
CHKERRQ(err_PETSc)
!--------------------------------------------------------------------------------------------------
! set module wide available data
@ -418,12 +431,14 @@ end subroutine grid_mechanical_spectral_polarisation_forward
!--------------------------------------------------------------------------------------------------
subroutine grid_mechanical_spectral_polarisation_updateCoords
PetscErrorCode :: ierr
PetscErrorCode :: err_PETSc
PetscScalar, dimension(:,:,:,:), pointer :: FandF_tau
call DMDAVecGetArrayF90(da,solution_vec,FandF_tau,ierr); CHKERRQ(ierr)
call DMDAVecGetArrayF90(da,solution_vec,FandF_tau,err_PETSc)
CHKERRQ(err_PETSc)
call utilities_updateCoords(FandF_tau(0:8,:,:,:))
call DMDAVecRestoreArrayF90(da,solution_vec,FandF_tau,ierr); CHKERRQ(ierr)
call DMDAVecRestoreArrayF90(da,solution_vec,FandF_tau,err_PETSc)
CHKERRQ(err_PETSc)
end subroutine grid_mechanical_spectral_polarisation_updateCoords
@ -433,11 +448,12 @@ end subroutine grid_mechanical_spectral_polarisation_updateCoords
!--------------------------------------------------------------------------------------------------
subroutine grid_mechanical_spectral_polarisation_restartWrite
PetscErrorCode :: ierr
PetscErrorCode :: err_PETSc
integer(HID_T) :: fileHandle, groupHandle
PetscScalar, dimension(:,:,:,:), pointer :: FandF_tau, F, F_tau
call DMDAVecGetArrayF90(da,solution_vec,FandF_tau,ierr); CHKERRQ(ierr)
call DMDAVecGetArrayF90(da,solution_vec,FandF_tau,err_PETSc)
CHKERRQ(err_PETSc)
F => FandF_tau(0: 8,:,:,:)
F_tau => FandF_tau(9:17,:,:,:)
@ -467,7 +483,8 @@ subroutine grid_mechanical_spectral_polarisation_restartWrite
if (num%update_gamma) call utilities_saveReferenceStiffness
call DMDAVecRestoreArrayF90(da,solution_vec,FandF_tau,ierr); CHKERRQ(ierr)
call DMDAVecRestoreArrayF90(da,solution_vec,FandF_tau,err_PETSc)
CHKERRQ(err_PETSc)
end subroutine grid_mechanical_spectral_polarisation_restartWrite
@ -475,7 +492,7 @@ end subroutine grid_mechanical_spectral_polarisation_restartWrite
!--------------------------------------------------------------------------------------------------
!> @brief convergence check
!--------------------------------------------------------------------------------------------------
subroutine converged(snes_local,PETScIter,devNull1,devNull2,devNull3,reason,dummy,ierr)
subroutine converged(snes_local,PETScIter,devNull1,devNull2,devNull3,reason,dummy,err_PETSc)
SNES :: snes_local
PetscInt, intent(in) :: PETScIter
@ -485,7 +502,7 @@ subroutine converged(snes_local,PETScIter,devNull1,devNull2,devNull3,reason,dumm
devNull3
SNESConvergedReason :: reason
PetscObject :: dummy
PetscErrorCode :: ierr
PetscErrorCode :: err_PETSc
real(pReal) :: &
curlTol, &
divTol, &
@ -513,6 +530,7 @@ subroutine converged(snes_local,PETScIter,devNull1,devNull2,devNull3,reason,dumm
err_BC/BCTol, ' (',err_BC, ' Pa, tol = ',BCTol,')'
print'(/,1x,a)', '==========================================================================='
flush(IO_STDOUT)
err_PETSc = 0
end subroutine converged
@ -521,42 +539,46 @@ end subroutine converged
!> @brief forms the residual vector
!--------------------------------------------------------------------------------------------------
subroutine formResidual(in, FandF_tau, &
residuum, dummy,ierr)
r, dummy,err_PETSc)
DMDALocalInfo, dimension(DMDA_LOCAL_INFO_SIZE) :: in !< DMDA info (needs to be named "in" for macros like XRANGE to work)
PetscScalar, dimension(3,3,2,XG_RANGE,YG_RANGE,ZG_RANGE), &
target, intent(in) :: FandF_tau
PetscScalar, dimension(3,3,2,X_RANGE,Y_RANGE,Z_RANGE),&
target, intent(out) :: residuum !< residuum field
target, intent(out) :: r !< residuum field
PetscScalar, pointer, dimension(:,:,:,:,:) :: &
F, &
F_tau, &
residual_F, &
residual_F_tau
r_F, &
r_F_tau
PetscInt :: &
PETScIter, &
nfuncs
PetscObject :: dummy
PetscErrorCode :: ierr
integer :: &
PetscErrorCode :: err_PETSc
integer(MPI_INTEGER_KIND) :: err_MPI
integer :: &
i, j, k, e
!---------------------------------------------------------------------------------------------------
F => FandF_tau(1:3,1:3,1,&
XG_RANGE,YG_RANGE,ZG_RANGE)
F_tau => FandF_tau(1:3,1:3,2,&
XG_RANGE,YG_RANGE,ZG_RANGE)
residual_F => residuum(1:3,1:3,1,&
X_RANGE, Y_RANGE, Z_RANGE)
residual_F_tau => residuum(1:3,1:3,2,&
X_RANGE, Y_RANGE, Z_RANGE)
F => FandF_tau(1:3,1:3,1,&
XG_RANGE,YG_RANGE,ZG_RANGE)
F_tau => FandF_tau(1:3,1:3,2,&
XG_RANGE,YG_RANGE,ZG_RANGE)
r_F => r(1:3,1:3,1,&
X_RANGE, Y_RANGE, Z_RANGE)
r_F_tau => r(1:3,1:3,2,&
X_RANGE, Y_RANGE, Z_RANGE)
F_av = sum(sum(sum(F,dim=5),dim=4),dim=3) * wgt
call MPI_Allreduce(MPI_IN_PLACE,F_av,9,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,ierr)
call MPI_Allreduce(MPI_IN_PLACE,F_av,9_MPI_INTEGER_KIND,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
call SNESGetNumberFunctionEvals(snes,nfuncs,ierr); CHKERRQ(ierr)
call SNESGetIterationNumber(snes,PETScIter,ierr); CHKERRQ(ierr)
call SNESGetNumberFunctionEvals(SNES_mechanical,nfuncs,err_PETSc)
CHKERRQ(err_PETSc)
call SNESGetIterationNumber(SNES_mechanical,PETScIter,err_PETSc)
CHKERRQ(err_PETSc)
if (nfuncs == 0 .and. PETScIter == 0) totalIter = -1 ! new increment
@ -590,14 +612,14 @@ subroutine formResidual(in, FandF_tau, &
!--------------------------------------------------------------------------------------------------
! constructing residual
residual_F_tau = num%beta*F - tensorField_real(1:3,1:3,1:grid(1),1:grid(2),1:grid3)
r_F_tau = num%beta*F - tensorField_real(1:3,1:3,1:grid(1),1:grid(2),1:grid3)
!--------------------------------------------------------------------------------------------------
! evaluate constitutive response
call utilities_constitutiveResponse(residual_F, & ! "residuum" gets field of first PK stress (to save memory)
call utilities_constitutiveResponse(r_F, & ! "residuum" gets field of first PK stress (to save memory)
P_av,C_volAvg,C_minMaxAvg, &
F - residual_F_tau/num%beta,params%Delta_t,params%rotation_BC)
call MPI_Allreduce(MPI_IN_PLACE,terminallyIll,1,MPI_LOGICAL,MPI_LOR,MPI_COMM_WORLD,ierr)
F - r_F_tau/num%beta,params%Delta_t,params%rotation_BC)
call MPI_Allreduce(MPI_IN_PLACE,terminallyIll,1_MPI_INTEGER_KIND,MPI_LOGICAL,MPI_LOR,MPI_COMM_WORLD,err_MPI)
!--------------------------------------------------------------------------------------------------
! stress BC handling
@ -607,7 +629,7 @@ subroutine formResidual(in, FandF_tau, &
params%stress_mask)))
! calculate divergence
tensorField_real = 0.0_pReal
tensorField_real(1:3,1:3,1:grid(1),1:grid(2),1:grid3) = residual_F !< stress field in disguise
tensorField_real(1:3,1:3,1:grid(1),1:grid(2),1:grid3) = r_F !< stress field in disguise
call utilities_FFTtensorForward
err_div = utilities_divergenceRMS() !< root mean squared error in divergence of stress
@ -616,11 +638,11 @@ subroutine formResidual(in, FandF_tau, &
e = 0
do k = 1, grid3; do j = 1, grid(2); do i = 1, grid(1)
e = e + 1
residual_F(1:3,1:3,i,j,k) = &
r_F(1:3,1:3,i,j,k) = &
math_mul3333xx33(math_invSym3333(homogenization_dPdF(1:3,1:3,1:3,1:3,e) + C_scale), &
residual_F(1:3,1:3,i,j,k) - matmul(F(1:3,1:3,i,j,k), &
r_F(1:3,1:3,i,j,k) - matmul(F(1:3,1:3,i,j,k), &
math_mul3333xx33(C_scale,F_tau(1:3,1:3,i,j,k) - F(1:3,1:3,i,j,k) - math_I3))) &
+ residual_F_tau(1:3,1:3,i,j,k)
+ r_F_tau(1:3,1:3,i,j,k)
end do; end do; end do
!--------------------------------------------------------------------------------------------------

149
src/grid/grid_thermal_spectral.f90
View File

@ -38,9 +38,8 @@ module grid_thermal_spectral
type(tSolutionParams) :: params
!--------------------------------------------------------------------------------------------------
! PETSc data
SNES :: thermal_snes
Vec :: solution_vec
PetscInt :: xstart, xend, ystart, yend, zstart, zend
SNES :: SNES_thermal
Vec :: solution_vec
real(pReal), dimension(:,:,:), allocatable :: &
T_current, & !< field of current temperature
T_lastInc, & !< field of previous temperature
@ -71,7 +70,8 @@ subroutine grid_thermal_spectral_init(T_0)
integer :: i, j, k, ce
DM :: thermal_grid
PetscScalar, dimension(:,:,:), pointer :: T_PETSc
PetscErrorCode :: ierr
integer(MPI_INTEGER_KIND) :: err_MPI
PetscErrorCode :: err_PETSc
class(tNode), pointer :: &
num_grid
@ -94,60 +94,61 @@ subroutine grid_thermal_spectral_init(T_0)
!--------------------------------------------------------------------------------------------------
! set default and user defined options for PETSc
call PetscOptionsInsertString(PETSC_NULL_OPTIONS,'-thermal_snes_type newtonls -thermal_snes_mf &
&-thermal_snes_ksp_ew -thermal_ksp_type fgmres',ierr)
CHKERRQ(ierr)
call PetscOptionsInsertString(PETSC_NULL_OPTIONS,num_grid%get_asString('petsc_options',defaultVal=''),ierr)
CHKERRQ(ierr)
!--------------------------------------------------------------------------------------------------
! initialize solver specific parts of PETSc
call SNESCreate(PETSC_COMM_WORLD,thermal_snes,ierr); CHKERRQ(ierr)
call SNESSetOptionsPrefix(thermal_snes,'thermal_',ierr);CHKERRQ(ierr)
localK = 0
localK(worldrank) = grid3
call MPI_Allreduce(MPI_IN_PLACE,localK,worldsize,MPI_INTEGER,MPI_SUM,MPI_COMM_WORLD,ierr)
call DMDACreate3D(PETSC_COMM_WORLD, &
DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, & ! cut off stencil at boundary
DMDA_STENCIL_BOX, & ! Moore (26) neighborhood around central point
grid(1),grid(2),grid(3), & ! global grid
1, 1, worldsize, &
1, 0, & ! #dof (T field), ghost boundary width (domain overlap)
[grid(1)],[grid(2)],localK, & ! local grid
thermal_grid,ierr) ! handle, error
CHKERRQ(ierr)
call SNESSetDM(thermal_snes,thermal_grid,ierr); CHKERRQ(ierr) ! connect snes to da
call DMsetFromOptions(thermal_grid,ierr); CHKERRQ(ierr)
call DMsetUp(thermal_grid,ierr); CHKERRQ(ierr)
call DMCreateGlobalVector(thermal_grid,solution_vec,ierr); CHKERRQ(ierr) ! global solution vector (grid x 1, i.e. every def grad tensor)
call DMDASNESSetFunctionLocal(thermal_grid,INSERT_VALUES,formResidual,PETSC_NULL_SNES,ierr) ! residual vector of same shape as solution vector
CHKERRQ(ierr)
call SNESSetFromOptions(thermal_snes,ierr); CHKERRQ(ierr) ! pull it all together with additional CLI arguments
&-thermal_snes_ksp_ew -thermal_ksp_type fgmres',err_PETSc)
CHKERRQ(err_PETSc)
call PetscOptionsInsertString(PETSC_NULL_OPTIONS,num_grid%get_asString('petsc_options',defaultVal=''),err_PETSc)
CHKERRQ(err_PETSc)
!--------------------------------------------------------------------------------------------------
! init fields
call DMDAGetCorners(thermal_grid,xstart,ystart,zstart,xend,yend,zend,ierr)
CHKERRQ(ierr)
xend = xstart + xend - 1
yend = ystart + yend - 1
zend = zstart + zend - 1
allocate(T_current(grid(1),grid(2),grid3), source=0.0_pReal)
allocate(T_lastInc(grid(1),grid(2),grid3), source=0.0_pReal)
allocate(T_stagInc(grid(1),grid(2),grid3), source=0.0_pReal)
allocate(T_current(grid(1),grid(2),grid3), source=T_0)
allocate(T_lastInc(grid(1),grid(2),grid3), source=T_0)
allocate(T_stagInc(grid(1),grid(2),grid3), source=T_0)
ce = 0
do k = 1, grid3; do j = 1, grid(2); do i = 1,grid(1)
ce = ce + 1
T_current(i,j,k) = T_0
T_lastInc(i,j,k) = T_current(i,j,k)
T_stagInc(i,j,k) = T_current(i,j,k)
call homogenization_thermal_setField(T_0,0.0_pReal,ce)
end do; end do; end do
call DMDAVecGetArrayF90(thermal_grid,solution_vec,T_PETSc,ierr); CHKERRQ(ierr)
T_PETSc(xstart:xend,ystart:yend,zstart:zend) = T_current
call DMDAVecRestoreArrayF90(thermal_grid,solution_vec,T_PETSc,ierr); CHKERRQ(ierr)
!--------------------------------------------------------------------------------------------------
! initialize solver specific parts of PETSc
call SNESCreate(PETSC_COMM_WORLD,SNES_thermal,err_PETSc)
CHKERRQ(err_PETSc)
call SNESSetOptionsPrefix(SNES_thermal,'thermal_',err_PETSc)
CHKERRQ(err_PETSc)
localK = 0_pPetscInt
localK(worldrank) = int(grid3,pPetscInt)
call MPI_Allreduce(MPI_IN_PLACE,localK,worldsize,MPI_INTEGER,MPI_SUM,MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
call DMDACreate3D(PETSC_COMM_WORLD, &
DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, & ! cut off stencil at boundary
DMDA_STENCIL_BOX, & ! Moore (26) neighborhood around central point
int(grid(1),pPetscInt),int(grid(2),pPetscInt),int(grid(3),pPetscInt), & ! global grid
1_pPetscInt, 1_pPetscInt, int(worldsize,pPetscInt), &
1_pPetscInt, 0_pPetscInt, & ! #dof (T, scalar), ghost boundary width (domain overlap)
[int(grid(1),pPetscInt)],[int(grid(2),pPetscInt)],localK, & ! local grid
thermal_grid,err_PETSc) ! handle, error
CHKERRQ(err_PETSc)
call DMsetFromOptions(thermal_grid,err_PETSc)
CHKERRQ(err_PETSc)
call DMsetUp(thermal_grid,err_PETSc)
CHKERRQ(err_PETSc)
call DMCreateGlobalVector(thermal_grid,solution_vec,err_PETSc) ! global solution vector (grid x 1, i.e. every def grad tensor)
CHKERRQ(err_PETSc)
call DMDASNESSetFunctionLocal(thermal_grid,INSERT_VALUES,formResidual,PETSC_NULL_SNES,err_PETSc) ! residual vector of same shape as solution vector
CHKERRQ(err_PETSc)
call SNESSetDM(SNES_thermal,thermal_grid,err_PETSc)
CHKERRQ(err_PETSc)
call SNESSetFromOptions(SNES_thermal,err_PETSc) ! pull it all together with additional CLI arguments
CHKERRQ(err_PETSc)
call DMDAVecGetArrayF90(thermal_grid,solution_vec,T_PETSc,err_PETSc)
CHKERRQ(err_PETSc)
T_PETSc = T_current
call DMDAVecRestoreArrayF90(thermal_grid,solution_vec,T_PETSc,err_PETSc)
CHKERRQ(err_PETSc)
call updateReference
call updateReference()
end subroutine grid_thermal_spectral_init
@ -164,7 +165,8 @@ function grid_thermal_spectral_solution(Delta_t) result(solution)
PetscInt :: devNull
PetscReal :: T_min, T_max, stagNorm
PetscErrorCode :: ierr
integer(MPI_INTEGER_KIND) :: err_MPI
PetscErrorCode :: err_PETSc
SNESConvergedReason :: reason
solution%converged =.false.
@ -173,8 +175,10 @@ function grid_thermal_spectral_solution(Delta_t) result(solution)
! set module wide availabe data
params%Delta_t = Delta_t
call SNESSolve(thermal_snes,PETSC_NULL_VEC,solution_vec,ierr); CHKERRQ(ierr)
call SNESGetConvergedReason(thermal_snes,reason,ierr); CHKERRQ(ierr)
call SNESSolve(SNES_thermal,PETSC_NULL_VEC,solution_vec,err_PETSc)
CHKERRQ(err_PETSc)
call SNESGetConvergedReason(SNES_thermal,reason,err_PETSc)
CHKERRQ(err_PETSc)
if (reason < 1) then
solution%converged = .false.
@ -184,9 +188,11 @@ function grid_thermal_spectral_solution(Delta_t) result(solution)
solution%iterationsNeeded = totalIter
end if
stagNorm = maxval(abs(T_current - T_stagInc))
call MPI_Allreduce(MPI_IN_PLACE,stagNorm,1,MPI_DOUBLE,MPI_MAX,MPI_COMM_WORLD,ierr)
call MPI_Allreduce(MPI_IN_PLACE,stagNorm,1_MPI_INTEGER_KIND,MPI_DOUBLE,MPI_MAX,MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
solution%stagConverged = stagNorm < max(num%eps_thermal_atol, num%eps_thermal_rtol*maxval(T_current))
call MPI_Allreduce(MPI_IN_PLACE,solution%stagConverged,1,MPI_LOGICAL,MPI_LAND,MPI_COMM_WORLD,ierr)
call MPI_Allreduce(MPI_IN_PLACE,solution%stagConverged,1_MPI_INTEGER_KIND,MPI_LOGICAL,MPI_LAND,MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
T_stagInc = T_current
!--------------------------------------------------------------------------------------------------
@ -197,8 +203,10 @@ function grid_thermal_spectral_solution(Delta_t) result(solution)
call homogenization_thermal_setField(T_current(i,j,k),(T_current(i,j,k)-T_lastInc(i,j,k))/params%Delta_t,ce)
end do; end do; end do
call VecMin(solution_vec,devNull,T_min,ierr); CHKERRQ(ierr)
call VecMax(solution_vec,devNull,T_max,ierr); CHKERRQ(ierr)
call VecMin(solution_vec,devNull,T_min,err_PETSc)
CHKERRQ(err_PETSc)
call VecMax(solution_vec,devNull,T_max,err_PETSc)
CHKERRQ(err_PETSc)
if (solution%converged) &
print'(/,1x,a)', '... thermal conduction converged ..................................'
print'(/,1x,a,f8.4,2x,f8.4,2x,f8.4)', 'Minimum|Maximum|Delta Temperature / K = ', T_min, T_max, stagNorm
@ -216,8 +224,8 @@ subroutine grid_thermal_spectral_forward(cutBack)
logical, intent(in) :: cutBack
integer :: i, j, k, ce
DM :: dm_local
PetscScalar, dimension(:,:,:), pointer :: x_scal
PetscErrorCode :: ierr
PetscScalar, dimension(:,:,:), pointer :: T_PETSc
PetscErrorCode :: err_PETSc
if (cutBack) then
T_current = T_lastInc
@ -225,10 +233,13 @@ subroutine grid_thermal_spectral_forward(cutBack)
!--------------------------------------------------------------------------------------------------
! reverting thermal field state
call SNESGetDM(thermal_snes,dm_local,ierr); CHKERRQ(ierr)
call DMDAVecGetArrayF90(dm_local,solution_vec,x_scal,ierr); CHKERRQ(ierr) !< get the data out of PETSc to work with
x_scal(xstart:xend,ystart:yend,zstart:zend) = T_current
call DMDAVecRestoreArrayF90(dm_local,solution_vec,x_scal,ierr); CHKERRQ(ierr)
call SNESGetDM(SNES_thermal,dm_local,err_PETSc)
CHKERRQ(err_PETSc)
call DMDAVecGetArrayF90(dm_local,solution_vec,T_PETSc,err_PETSc) !< get the data out of PETSc to work with
CHKERRQ(err_PETSc)
T_PETSc = T_current
call DMDAVecRestoreArrayF90(dm_local,solution_vec,T_PETSc,err_PETSc)
CHKERRQ(err_PETSc)
ce = 0
do k = 1, grid3; do j = 1, grid(2); do i = 1,grid(1)
ce = ce + 1
@ -245,7 +256,7 @@ end subroutine grid_thermal_spectral_forward
!--------------------------------------------------------------------------------------------------
!> @brief forms the spectral thermal residual vector
!--------------------------------------------------------------------------------------------------
subroutine formResidual(in,x_scal,f_scal,dummy,ierr)
subroutine formResidual(in,x_scal,r,dummy,err_PETSc)
DMDALocalInfo, dimension(DMDA_LOCAL_INFO_SIZE) :: &
in
@ -254,9 +265,9 @@ subroutine formResidual(in,x_scal,f_scal,dummy,ierr)
x_scal
PetscScalar, dimension( &
X_RANGE,Y_RANGE,Z_RANGE), intent(out) :: &
f_scal
r
PetscObject :: dummy
PetscErrorCode :: ierr
PetscErrorCode :: err_PETSc
integer :: i, j, k, ce
T_current = x_scal
@ -291,7 +302,8 @@ subroutine formResidual(in,x_scal,f_scal,dummy,ierr)
!--------------------------------------------------------------------------------------------------
! constructing residual
f_scal = T_current - scalarField_real(1:grid(1),1:grid(2),1:grid3)
r = T_current - scalarField_real(1:grid(1),1:grid(2),1:grid3)
err_PETSc = 0
end subroutine formResidual
@ -301,7 +313,8 @@ end subroutine formResidual
!--------------------------------------------------------------------------------------------------
subroutine updateReference()
integer :: ce,ierr
integer :: ce
integer(MPI_INTEGER_KIND) :: err_MPI
K_ref = 0.0_pReal
@ -312,9 +325,11 @@ subroutine updateReference()
end do
K_ref = K_ref*wgt
call MPI_Allreduce(MPI_IN_PLACE,K_ref,9,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,ierr)
call MPI_Allreduce(MPI_IN_PLACE,K_ref,9_MPI_INTEGER_KIND,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
mu_ref = mu_ref*wgt
call MPI_Allreduce(MPI_IN_PLACE,mu_ref,1,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,ierr)
call MPI_Allreduce(MPI_IN_PLACE,mu_ref,1_MPI_INTEGER_KIND,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
end subroutine updateReference

161
src/grid/spectral_utilities.f90
View File

@ -144,7 +144,7 @@ contains
!--------------------------------------------------------------------------------------------------
subroutine spectral_utilities_init
PetscErrorCode :: ierr
PetscErrorCode :: err_PETSc
integer :: i, j, k, &
FFTW_planner_flag
integer, dimension(3) :: k_s
@ -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 '
@ -193,13 +193,13 @@ subroutine spectral_utilities_init
'add more using the "PETSc_options" keyword in numerics.yaml'
flush(IO_STDOUT)
call PetscOptionsClear(PETSC_NULL_OPTIONS,ierr)
CHKERRQ(ierr)
if (debugPETSc) call PetscOptionsInsertString(PETSC_NULL_OPTIONS,trim(PETSCDEBUG),ierr)
CHKERRQ(ierr)
call PetscOptionsClear(PETSC_NULL_OPTIONS,err_PETSc)
CHKERRQ(err_PETSc)
if (debugPETSc) call PetscOptionsInsertString(PETSC_NULL_OPTIONS,trim(PETSCDEBUG),err_PETSc)
CHKERRQ(err_PETSc)
call PetscOptionsInsertString(PETSC_NULL_OPTIONS,&
num_grid%get_asString('PETSc_options',defaultVal=''),ierr)
CHKERRQ(ierr)
num_grid%get_asString('PETSc_options',defaultVal=''),err_PETSc)
CHKERRQ(err_PETSc)
grid1Red = grid(1)/2 + 1
wgt = 1.0/real(product(grid),pReal)
@ -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
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
if (.not. C_ASSOCIATED(planTensorBack)) error stop 'FFTW error'
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(3:1:-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)
@ -559,8 +559,9 @@ end subroutine utilities_fourierGreenConvolution
!--------------------------------------------------------------------------------------------------
real(pReal) function utilities_divergenceRMS()
integer :: i, j, k, ierr
complex(pReal), dimension(3) :: rescaledGeom
integer :: i, j, k
integer(MPI_INTEGER_KIND) :: err_MPI
complex(pReal), dimension(3) :: rescaledGeom
print'(/,1x,a)', '... calculating divergence ................................................'
flush(IO_STDOUT)
@ -589,8 +590,8 @@ real(pReal) function utilities_divergenceRMS()
conjg(-xi1st(1:3,grid1Red,j,k))*rescaledGeom))**2)
enddo; enddo
if (grid(1) == 1) utilities_divergenceRMS = utilities_divergenceRMS * 0.5_pReal ! counted twice in case of grid(1) == 1
call MPI_Allreduce(MPI_IN_PLACE,utilities_divergenceRMS,1,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,ierr)
if (ierr /=0) error stop 'MPI error'
call MPI_Allreduce(MPI_IN_PLACE,utilities_divergenceRMS,1_MPI_INTEGER_KIND,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
utilities_divergenceRMS = sqrt(utilities_divergenceRMS) * wgt ! RMS in real space calculated with Parsevals theorem from Fourier space
end function utilities_divergenceRMS
@ -601,7 +602,8 @@ end function utilities_divergenceRMS
!--------------------------------------------------------------------------------------------------
real(pReal) function utilities_curlRMS()
integer :: i, j, k, l, ierr
integer :: i, j, k, l
integer(MPI_INTEGER_KIND) :: err_MPI
complex(pReal), dimension(3,3) :: curl_fourier
complex(pReal), dimension(3) :: rescaledGeom
@ -649,8 +651,8 @@ real(pReal) function utilities_curlRMS()
+ sum(curl_fourier%re**2 + curl_fourier%im**2) ! this layer (Nyquist) does not have a conjugate complex counterpart (if grid(1) /= 1)
enddo; enddo
call MPI_Allreduce(MPI_IN_PLACE,utilities_curlRMS,1,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,ierr)
if (ierr /=0) error stop 'MPI error'
call MPI_Allreduce(MPI_IN_PLACE,utilities_curlRMS,1_MPI_INTEGER_KIND,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
utilities_curlRMS = sqrt(utilities_curlRMS) * wgt
if (grid(1) == 1) utilities_curlRMS = utilities_curlRMS * 0.5_pReal ! counted twice in case of grid(1) == 1
@ -799,8 +801,8 @@ subroutine utilities_constitutiveResponse(P,P_av,C_volAvg,C_minmaxAvg,&
type(rotation), intent(in), optional :: rotation_BC !< rotation of load frame
integer :: &
i,ierr
integer :: i
integer(MPI_INTEGER_KIND) :: err_MPI
real(pReal), dimension(3,3,3,3) :: dPdF_max, dPdF_min
real(pReal) :: dPdF_norm_max, dPdF_norm_min
real(pReal), dimension(2) :: valueAndRank !< pair of min/max norm of dPdF to synchronize min/max of dPdF
@ -818,7 +820,8 @@ subroutine utilities_constitutiveResponse(P,P_av,C_volAvg,C_minmaxAvg,&
P = reshape(homogenization_P, [3,3,grid(1),grid(2),grid3])
P_av = sum(sum(sum(P,dim=5),dim=4),dim=3) * wgt
call MPI_Allreduce(MPI_IN_PLACE,P_av,9,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,ierr)
call MPI_Allreduce(MPI_IN_PLACE,P_av,9_MPI_INTEGER_KIND,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
if (debugRotation) print'(/,1x,a,/,2(3(2x,f12.4,1x)/),3(2x,f12.4,1x))', &
'Piola--Kirchhoff stress (lab) / MPa =', transpose(P_av)*1.e-6_pReal
if (present(rotation_BC)) P_av = rotation_BC%rotate(P_av)
@ -842,22 +845,22 @@ subroutine utilities_constitutiveResponse(P,P_av,C_volAvg,C_minmaxAvg,&
enddo
valueAndRank = [dPdF_norm_max,real(worldrank,pReal)]
call MPI_Allreduce(MPI_IN_PLACE,valueAndRank,1, MPI_2DOUBLE_PRECISION, MPI_MAXLOC, MPI_COMM_WORLD, ierr)
if (ierr /= 0) error stop 'MPI error'
call MPI_Bcast(dPdF_max,81,MPI_DOUBLE,int(valueAndRank(2)),MPI_COMM_WORLD, ierr)
if (ierr /= 0) error stop 'MPI error'
call MPI_Allreduce(MPI_IN_PLACE,valueAndRank,1_MPI_INTEGER_KIND,MPI_2DOUBLE_PRECISION,MPI_MAXLOC,MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
call MPI_Bcast(dPdF_max,81_MPI_INTEGER_KIND,MPI_DOUBLE,int(valueAndRank(2),MPI_INTEGER_KIND),MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
valueAndRank = [dPdF_norm_min,real(worldrank,pReal)]
call MPI_Allreduce(MPI_IN_PLACE,valueAndRank,1, MPI_2DOUBLE_PRECISION, MPI_MINLOC, MPI_COMM_WORLD, ierr)
if (ierr /= 0) error stop 'MPI error'
call MPI_Bcast(dPdF_min,81,MPI_DOUBLE,int(valueAndRank(2)),MPI_COMM_WORLD, ierr)
if (ierr /= 0) error stop 'MPI error'
call MPI_Allreduce(MPI_IN_PLACE,valueAndRank,1_MPI_INTEGER_KIND,MPI_2DOUBLE_PRECISION,MPI_MINLOC,MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
call MPI_Bcast(dPdF_min,81_MPI_INTEGER_KIND,MPI_DOUBLE,int(valueAndRank(2),MPI_INTEGER_KIND),MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
C_minmaxAvg = 0.5_pReal*(dPdF_max + dPdF_min)
C_volAvg = sum(homogenization_dPdF,dim=5)
call MPI_Allreduce(MPI_IN_PLACE,C_volAvg,81,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,ierr)
if (ierr /= 0) error stop 'MPI error'
call MPI_Allreduce(MPI_IN_PLACE,C_volAvg,81_MPI_INTEGER_KIND,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
C_volAvg = C_volAvg * wgt
@ -906,12 +909,13 @@ function utilities_forwardField(Delta_t,field_lastInc,rate,aim)
real(pReal), dimension(3,3,grid(1),grid(2),grid3) :: &
utilities_forwardField
real(pReal), dimension(3,3) :: fieldDiff !< <a + adot*t> - aim
PetscErrorCode :: ierr
integer(MPI_INTEGER_KIND) :: err_MPI
utilities_forwardField = field_lastInc + rate*Delta_t
if (present(aim)) then !< correct to match average
fieldDiff = sum(sum(sum(utilities_forwardField,dim=5),dim=4),dim=3)*wgt
call MPI_Allreduce(MPI_IN_PLACE,fieldDiff,9,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,ierr)
call MPI_Allreduce(MPI_IN_PLACE,fieldDiff,9_MPI_INTEGER_KIND,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
fieldDiff = fieldDiff - aim
utilities_forwardField = utilities_forwardField - &
spread(spread(spread(fieldDiff,3,grid(1)),4,grid(2)),5,grid3)
@ -981,9 +985,10 @@ subroutine utilities_updateCoords(F)
real(pReal), dimension(3, grid(1)+1,grid(2)+1,grid3+1) :: nodeCoords
integer :: &
i,j,k,n, &
rank_t, rank_b, &
c, &
ierr
c
integer(MPI_INTEGER_KIND) :: &
rank_t, rank_b
integer(MPI_INTEGER_KIND) :: err_MPI
#if (PETSC_VERSION_MAJOR==3 && PETSC_VERSION_MINOR>14) && !defined(PETSC_HAVE_MPI_F90MODULE_VISIBILITY)
type(MPI_Request), dimension(4) :: request
type(MPI_Status), dimension(4) :: status
@ -1025,30 +1030,30 @@ subroutine utilities_updateCoords(F)
!--------------------------------------------------------------------------------------------------
! average F
if (grid3Offset == 0) Favg = real(tensorField_fourier(1:3,1:3,1,1,1),pReal)*wgt
call MPI_Bcast(Favg,9,MPI_DOUBLE,0,MPI_COMM_WORLD,ierr)
if (ierr /=0) error stop 'MPI error'
call MPI_Bcast(Favg,9_MPI_INTEGER_KIND,MPI_DOUBLE,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
!--------------------------------------------------------------------------------------------------
! pad cell center fluctuations along z-direction (needed when running MPI simulation)
IPfluct_padded(1:3,1:grid(1),1:grid(2),2:grid3+1) = vectorField_real(1:3,1:grid(1),1:grid(2),1:grid3)
c = product(shape(IPfluct_padded(:,:,:,1))) !< amount of data to transfer
rank_t = modulo(worldrank+1,worldsize)
rank_b = modulo(worldrank-1,worldsize)
rank_t = modulo(worldrank+1_MPI_INTEGER_KIND,worldsize)
rank_b = modulo(worldrank-1_MPI_INTEGER_KIND,worldsize)
! send bottom layer to process below
call MPI_Isend(IPfluct_padded(:,:,:,2), c,MPI_DOUBLE,rank_b,0,MPI_COMM_WORLD,request(1),ierr)
if (ierr /=0) error stop 'MPI error'
call MPI_Irecv(IPfluct_padded(:,:,:,grid3+2),c,MPI_DOUBLE,rank_t,0,MPI_COMM_WORLD,request(2),ierr)
if (ierr /=0) error stop 'MPI error'
call MPI_Isend(IPfluct_padded(:,:,:,2), c,MPI_DOUBLE,rank_b,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,request(1),err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
call MPI_Irecv(IPfluct_padded(:,:,:,grid3+2),c,MPI_DOUBLE,rank_t,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,request(2),err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
! send top layer to process above
call MPI_Isend(IPfluct_padded(:,:,:,grid3+1),c,MPI_DOUBLE,rank_t,1,MPI_COMM_WORLD,request(3),ierr)
if (ierr /=0) error stop 'MPI error'
call MPI_Irecv(IPfluct_padded(:,:,:,1), c,MPI_DOUBLE,rank_b,1,MPI_COMM_WORLD,request(4),ierr)
if (ierr /=0) error stop 'MPI error'
call MPI_Isend(IPfluct_padded(:,:,:,grid3+1),c,MPI_DOUBLE,rank_t,1_MPI_INTEGER_KIND,MPI_COMM_WORLD,request(3),err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
call MPI_Irecv(IPfluct_padded(:,:,:,1), c,MPI_DOUBLE,rank_b,1_MPI_INTEGER_KIND,MPI_COMM_WORLD,request(4),err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
call MPI_Waitall(4,request,status,ierr)
if (ierr /=0) error stop 'MPI error'
call MPI_Waitall(4,request,status,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
#if (PETSC_VERSION_MAJOR==3 && PETSC_VERSION_MINOR>14) && !defined(PETSC_HAVE_MPI_F90MODULE_VISIBILITY)
! ToDo
#else

142
src/lattice.f90
View File

@ -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( [&

13
src/material.f90
View File

@ -66,7 +66,7 @@ subroutine material_init(restart)
print'(/,1x,a)', '<<<+- material init -+>>>'; flush(IO_STDOUT)
call parse
call parse()
print'(/,1x,a)', 'parsed material.yaml'
@ -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

32
src/math.f90
View File

@ -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)
endif
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'(/,a,i2)', ' size of random seed: ', randSize
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

6
src/mesh/DAMASK_mesh.f90
View File

@ -78,7 +78,7 @@ program DAMASK_mesh
type(tLoadCase), allocatable, dimension(:) :: loadCases !< array of all load cases
type(tSolutionState), allocatable, dimension(:) :: solres
PetscInt :: faceSet, currentFaceSet, dimPlex
PetscErrorCode :: ierr
PetscErrorCode :: err_PETSc
integer(kind(COMPONENT_UNDEFINED_ID)) :: ID
external :: &
quit
@ -98,8 +98,8 @@ program DAMASK_mesh
if (maxCutBack < 0) call IO_error(301,ext_msg='maxCutBack')
! reading basic information from load case file and allocate data structure containing load cases
call DMGetDimension(geomMesh,dimPlex,ierr) !< dimension of mesh (2D or 3D)
CHKERRA(ierr)
call DMGetDimension(geomMesh,dimPlex,err_PETSc) !< dimension of mesh (2D or 3D)
CHKERRA(err_PETSc)
allocate(solres(1))
!--------------------------------------------------------------------------------------------------

64
src/mesh/FEM_utilities.f90
View File

@ -50,7 +50,7 @@ module FEM_utilities
type, public :: tSolutionState !< return type of solution from FEM solver variants
logical :: converged = .true.
logical :: stagConverged = .true.
integer :: iterationsNeeded = 0
PetscInt :: iterationsNeeded = 0_pPETSCINT
end type tSolutionState
type, public :: tComponentBC
@ -92,7 +92,7 @@ subroutine FEM_utilities_init
p_i !< integration order (quadrature rule)
character(len=*), parameter :: &
PETSCDEBUG = ' -snes_view -snes_monitor '
PetscErrorCode :: ierr
PetscErrorCode :: err_PETSc
logical :: debugPETSc !< use some in debug defined options for more verbose PETSc solution
@ -103,9 +103,9 @@ subroutine FEM_utilities_init
p_s = num_mesh%get_asInt('p_s',defaultVal = 2)
p_i = num_mesh%get_asInt('p_i',defaultVal = p_s)
if (p_s < 1_pInt .or. p_s > size(FEM_nQuadrature,2)) &
if (p_s < 1 .or. p_s > size(FEM_nQuadrature,2)) &
call IO_error(821,ext_msg='shape function order (p_s) out of bounds')
if (p_i < max(1_pInt,p_s-1_pInt) .or. p_i > p_s) &
if (p_i < max(1,p_s-1) .or. p_i > p_s) &
call IO_error(821,ext_msg='integration order (p_i) out of bounds')
debug_mesh => config_debug%get('mesh',defaultVal=emptyList)
@ -116,20 +116,20 @@ subroutine FEM_utilities_init
trim(PETScDebug), &
'add more using the "PETSc_options" keyword in numerics.yaml'
flush(IO_STDOUT)
call PetscOptionsClear(PETSC_NULL_OPTIONS,ierr)
CHKERRQ(ierr)
if(debugPETSc) call PetscOptionsInsertString(PETSC_NULL_OPTIONS,trim(PETSCDEBUG),ierr)
CHKERRQ(ierr)
call PetscOptionsClear(PETSC_NULL_OPTIONS,err_PETSc)
CHKERRQ(err_PETSc)
if(debugPETSc) call PetscOptionsInsertString(PETSC_NULL_OPTIONS,trim(PETSCDEBUG),err_PETSc)
CHKERRQ(err_PETSc)
call PetscOptionsInsertString(PETSC_NULL_OPTIONS,'-mechanical_snes_type newtonls &
&-mechanical_snes_linesearch_type cp -mechanical_snes_ksp_ew &
&-mechanical_snes_ksp_ew_rtol0 0.01 -mechanical_snes_ksp_ew_rtolmax 0.01 &
&-mechanical_ksp_type fgmres -mechanical_ksp_max_it 25', ierr)
CHKERRQ(ierr)
call PetscOptionsInsertString(PETSC_NULL_OPTIONS,num_mesh%get_asString('PETSc_options',defaultVal=''),ierr)
CHKERRQ(ierr)
&-mechanical_ksp_type fgmres -mechanical_ksp_max_it 25', err_PETSc)
CHKERRQ(err_PETSc)
call PetscOptionsInsertString(PETSC_NULL_OPTIONS,num_mesh%get_asString('PETSc_options',defaultVal=''),err_PETSc)
CHKERRQ(err_PETSc)
write(petsc_optionsOrder,'(a,i0)') '-mechFE_petscspace_degree ', p_s
call PetscOptionsInsertString(PETSC_NULL_OPTIONS,trim(petsc_optionsOrder),ierr)
CHKERRQ(ierr)
call PetscOptionsInsertString(PETSC_NULL_OPTIONS,trim(petsc_optionsOrder),err_PETSc)
CHKERRQ(err_PETSc)
wgt = 1.0/real(mesh_maxNips*mesh_NcpElemsGlobal,pReal)
@ -144,10 +144,9 @@ subroutine utilities_constitutiveResponse(timeinc,P_av,forwardData)
real(pReal), intent(in) :: timeinc !< loading time
logical, intent(in) :: forwardData !< age results
real(pReal),intent(out), dimension(3,3) :: P_av !< average PK stress
PetscErrorCode :: ierr
integer(MPI_INTEGER_KIND) :: err_MPI
print'(/,1x,a)', '... evaluating constitutive response ......................................'
@ -157,7 +156,9 @@ subroutine utilities_constitutiveResponse(timeinc,P_av,forwardData)
cutBack = .false.
P_av = sum(homogenization_P,dim=3) * wgt
call MPI_Allreduce(MPI_IN_PLACE,P_av,9,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,ierr)
call MPI_Allreduce(MPI_IN_PLACE,P_av,9_MPI_INTEGER_KIND,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
end subroutine utilities_constitutiveResponse
@ -174,26 +175,29 @@ subroutine utilities_projectBCValues(localVec,section,field,comp,bcPointsIS,BCVa
PetscInt, pointer :: bcPoints(:)
PetscScalar, pointer :: localArray(:)
PetscScalar :: BCValue,BCDotValue,timeinc
PetscErrorCode :: ierr
PetscErrorCode :: err_PETSc
call PetscSectionGetFieldComponents(section,field,numComp,ierr); CHKERRQ(ierr)
call ISGetSize(bcPointsIS,nBcPoints,ierr); CHKERRQ(ierr)
if (nBcPoints > 0) call ISGetIndicesF90(bcPointsIS,bcPoints,ierr)
call VecGetArrayF90(localVec,localArray,ierr); CHKERRQ(ierr)
call PetscSectionGetFieldComponents(section,field,numComp,err_PETSc)
CHKERRQ(err_PETSc)
call ISGetSize(bcPointsIS,nBcPoints,err_PETSc)
CHKERRQ(err_PETSc)
if (nBcPoints > 0) call ISGetIndicesF90(bcPointsIS,bcPoints,err_PETSc)
call VecGetArrayF90(localVec,localArray,err_PETSc); CHKERRQ(err_PETSc)
do point = 1, nBcPoints
call PetscSectionGetFieldDof(section,bcPoints(point),field,numDof,ierr)
CHKERRQ(ierr)
call PetscSectionGetFieldOffset(section,bcPoints(point),field,offset,ierr)
CHKERRQ(ierr)
call PetscSectionGetFieldDof(section,bcPoints(point),field,numDof,err_PETSc)
CHKERRQ(err_PETSc)
call PetscSectionGetFieldOffset(section,bcPoints(point),field,offset,err_PETSc)
CHKERRQ(err_PETSc)
do dof = offset+comp+1, offset+numDof, numComp
localArray(dof) = localArray(dof) + BCValue + BCDotValue*timeinc
end do
end do
call VecRestoreArrayF90(localVec,localArray,ierr); CHKERRQ(ierr)
call VecAssemblyBegin(localVec, ierr); CHKERRQ(ierr)
call VecAssemblyEnd (localVec, ierr); CHKERRQ(ierr)
if (nBcPoints > 0) call ISRestoreIndicesF90(bcPointsIS,bcPoints,ierr)
call VecRestoreArrayF90(localVec,localArray,err_PETSc); CHKERRQ(err_PETSc)
call VecAssemblyBegin(localVec, err_PETSc); CHKERRQ(err_PETSc)
call VecAssemblyEnd (localVec, err_PETSc); CHKERRQ(err_PETSc)
if (nBcPoints > 0) call ISRestoreIndicesF90(bcPointsIS,bcPoints,err_PETSc)
CHKERRQ(err_PETSc)
end subroutine utilities_projectBCValues

117
src/mesh/discretization_mesh.f90
View File

@ -71,21 +71,22 @@ subroutine discretization_mesh_init(restart)
logical, intent(in) :: restart
integer :: dimPlex, &
PetscInt :: dimPlex, &
mesh_Nnodes, & !< total number of nodes in mesh
j, &
debug_element, debug_ip
PetscSF :: sf
DM :: globalMesh
PetscInt :: nFaceSets
PetscInt :: nFaceSets, Nboundaries, NelemsGlobal, Nelems
PetscInt, pointer, dimension(:) :: pFaceSets
IS :: faceSetIS
PetscErrorCode :: ierr
integer, dimension(:), allocatable :: &
PetscErrorCode :: err_PETSc
integer(MPI_INTEGER_KIND) :: err_MPI
PetscInt, dimension(:), allocatable :: &
materialAt
class(tNode), pointer :: &
num_mesh
integer :: p_i !< integration order (quadrature rule)
integer :: p_i, dim !< integration order (quadrature rule)
type(tvec) :: coords_node0
print'(/,1x,a)', '<<<+- discretization_mesh init -+>>>'
@ -100,56 +101,64 @@ subroutine discretization_mesh_init(restart)
debug_element = config_debug%get_asInt('element',defaultVal=1)
debug_ip = config_debug%get_asInt('integrationpoint',defaultVal=1)
call DMPlexCreateFromFile(PETSC_COMM_WORLD,interface_geomFile,PETSC_TRUE,globalMesh,ierr)
CHKERRQ(ierr)
call DMGetDimension(globalMesh,dimPlex,ierr)
CHKERRQ(ierr)
call DMGetStratumSize(globalMesh,'depth',dimPlex,mesh_NcpElemsGlobal,ierr)
CHKERRQ(ierr)
print'()'
call DMView(globalMesh, PETSC_VIEWER_STDOUT_WORLD,ierr)
CHKERRQ(ierr)
call DMPlexCreateFromFile(PETSC_COMM_WORLD,interface_geomFile,PETSC_TRUE,globalMesh,err_PETSc)
CHKERRQ(err_PETSc)
call DMGetDimension(globalMesh,dimPlex,err_PETSc)
CHKERRQ(err_PETSc)
call DMGetStratumSize(globalMesh,'depth',dimPlex,NelemsGlobal,err_PETSc)
CHKERRQ(err_PETSc)
mesh_NcpElemsGlobal = int(NelemsGlobal)
call DMView(globalMesh, PETSC_VIEWER_STDOUT_WORLD,err_PETSc)
CHKERRQ(err_PETSc)
! get number of IDs in face sets (for boundary conditions?)
call DMGetLabelSize(globalMesh,'Face Sets',mesh_Nboundaries,ierr)
CHKERRQ(ierr)
call MPI_Bcast(mesh_Nboundaries,1,MPI_INTEGER,0,MPI_COMM_WORLD,ierr)
call MPI_Bcast(mesh_NcpElemsGlobal,1,MPI_INTEGER,0,MPI_COMM_WORLD,ierr)
call MPI_Bcast(dimPlex,1,MPI_INTEGER,0,MPI_COMM_WORLD,ierr)
call DMGetLabelSize(globalMesh,'Face Sets',Nboundaries,err_PETSc)
CHKERRQ(err_PETSc)
mesh_Nboundaries = int(Nboundaries)
call MPI_Bcast(mesh_Nboundaries,1_MPI_INTEGER_KIND,MPI_INTEGER,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
call MPI_Bcast(mesh_NcpElemsGlobal,1_MPI_INTEGER_KIND,MPI_INTEGER,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
dim = int(dimPlex)
call MPI_Bcast(dim,1_MPI_INTEGER_KIND,MPI_INTEGER,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
dimPlex = int(dim,pPETSCINT)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
if (worldrank == 0) then
call DMClone(globalMesh,geomMesh,ierr)
call DMClone(globalMesh,geomMesh,err_PETSc)
else
call DMPlexDistribute(globalMesh,0,sf,geomMesh,ierr)
call DMPlexDistribute(globalMesh,0_pPETSCINT,sf,geomMesh,err_PETSc)
endif
CHKERRQ(ierr)
CHKERRQ(err_PETSc)
allocate(mesh_boundaries(mesh_Nboundaries), source = 0)
call DMGetLabelSize(globalMesh,'Face Sets',nFaceSets,ierr)
CHKERRQ(ierr)
call DMGetLabelIdIS(globalMesh,'Face Sets',faceSetIS,ierr)
CHKERRQ(ierr)
allocate(mesh_boundaries(mesh_Nboundaries), source = 0_pPETSCINT)
call DMGetLabelSize(globalMesh,'Face Sets',nFaceSets,err_PETSc)
CHKERRQ(err_PETSc)
call DMGetLabelIdIS(globalMesh,'Face Sets',faceSetIS,err_PETSc)
CHKERRQ(err_PETSc)
if (nFaceSets > 0) then
call ISGetIndicesF90(faceSetIS,pFaceSets,ierr)
CHKERRQ(ierr)
call ISGetIndicesF90(faceSetIS,pFaceSets,err_PETSc)
CHKERRQ(err_PETSc)
mesh_boundaries(1:nFaceSets) = pFaceSets
CHKERRQ(ierr)
call ISRestoreIndicesF90(faceSetIS,pFaceSets,ierr)
CHKERRQ(err_PETSc)
call ISRestoreIndicesF90(faceSetIS,pFaceSets,err_PETSc)
endif
call MPI_Bcast(mesh_boundaries,mesh_Nboundaries,MPI_INTEGER,0,MPI_COMM_WORLD,ierr)
call MPI_Bcast(mesh_boundaries,mesh_Nboundaries,MPI_INTEGER,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
call DMDestroy(globalMesh,ierr); CHKERRQ(ierr)
call DMDestroy(globalMesh,err_PETSc); CHKERRQ(err_PETSc)
call DMGetStratumSize(geomMesh,'depth',dimPlex,mesh_NcpElems,ierr)
CHKERRQ(ierr)
call DMGetStratumSize(geomMesh,'depth',0,mesh_Nnodes,ierr)
CHKERRQ(ierr)
call DMGetStratumSize(geomMesh,'depth',dimPlex,Nelems,err_PETSc)
CHKERRQ(err_PETSc)
mesh_NcpElems = int(Nelems)
call DMGetStratumSize(geomMesh,'depth',0_pPETSCINT,mesh_Nnodes,err_PETSc)
CHKERRQ(err_PETSc)
! Get initial nodal coordinates
call DMGetCoordinates(geomMesh,coords_node0,ierr)
CHKERRQ(ierr)
call VecGetArrayF90(coords_node0, mesh_node0_temp,ierr)
CHKERRQ(ierr)
call DMGetCoordinates(geomMesh,coords_node0,err_PETSc)
CHKERRQ(err_PETSc)
call VecGetArrayF90(coords_node0, mesh_node0_temp,err_PETSc)
CHKERRQ(err_PETSc)
mesh_maxNips = FEM_nQuadrature(dimPlex,p_i)
@ -158,10 +167,10 @@ subroutine discretization_mesh_init(restart)
allocate(materialAt(mesh_NcpElems))
do j = 1, mesh_NcpElems
call DMGetLabelValue(geomMesh,'Cell Sets',j-1,materialAt(j),ierr)
CHKERRQ(ierr)
call DMGetLabelValue(geomMesh,'Cell Sets',j-1,materialAt(j),err_PETSc)
CHKERRQ(err_PETSc)
enddo
materialAt = materialAt + 1
materialAt = materialAt + 1_pPETSCINT
if (debug_element < 1 .or. debug_element > mesh_NcpElems) call IO_error(602,ext_msg='element')
if (debug_ip < 1 .or. debug_ip > mesh_maxNips) call IO_error(602,ext_msg='IP')
@ -170,7 +179,7 @@ subroutine discretization_mesh_init(restart)
mesh_node0(1:dimPlex,:) = reshape(mesh_node0_temp,[dimPlex,mesh_Nnodes])
call discretization_init(materialAt,&
call discretization_init(int(materialAt),&
reshape(mesh_ipCoordinates,[3,mesh_maxNips*mesh_NcpElems]), &
mesh_node0)
@ -188,16 +197,17 @@ subroutine mesh_FEM_build_ipVolumes(dimPlex)
PetscReal :: vol
PetscReal, pointer,dimension(:) :: pCent, pNorm
PetscInt :: cellStart, cellEnd, cell
PetscErrorCode :: ierr
PetscErrorCode :: err_PETSc
allocate(mesh_ipVolume(mesh_maxNips,mesh_NcpElems),source=0.0_pReal)
call DMPlexGetHeightStratum(geomMesh,0,cellStart,cellEnd,ierr); CHKERRQ(ierr)
call DMPlexGetHeightStratum(geomMesh,0_pPETSCINT,cellStart,cellEnd,err_PETSc)
CHKERRQ(err_PETSc)
allocate(pCent(dimPlex))
allocate(pNorm(dimPlex))
do cell = cellStart, cellEnd-1
call DMPlexComputeCellGeometryFVM(geomMesh,cell,vol,pCent,pNorm,ierr)
CHKERRQ(ierr)
call DMPlexComputeCellGeometryFVM(geomMesh,cell,vol,pCent,pNorm,err_PETSc)
CHKERRQ(err_PETSc)
mesh_ipVolume(:,cell+1) = vol/real(mesh_maxNips,pReal)
enddo
@ -215,7 +225,7 @@ subroutine mesh_FEM_build_ipCoordinates(dimPlex,qPoints)
PetscReal, pointer,dimension(:) :: pV0, pCellJ, pInvcellJ
PetscReal :: detJ
PetscInt :: cellStart, cellEnd, cell, qPt, dirI, dirJ, qOffset
PetscErrorCode :: ierr
PetscErrorCode :: err_PETSc
allocate(mesh_ipCoordinates(3,mesh_maxNips,mesh_NcpElems),source=0.0_pReal)
@ -223,10 +233,11 @@ subroutine mesh_FEM_build_ipCoordinates(dimPlex,qPoints)
allocate(pV0(dimPlex))
allocatE(pCellJ(dimPlex**2))
allocatE(pinvCellJ(dimPlex**2))
call DMPlexGetHeightStratum(geomMesh,0,cellStart,cellEnd,ierr); CHKERRQ(ierr)
call DMPlexGetHeightStratum(geomMesh,0_pPETSCINT,cellStart,cellEnd,err_PETSc)
CHKERRQ(err_PETSc)
do cell = cellStart, cellEnd-1 !< loop over all elements
call DMPlexComputeCellGeometryAffineFEM(geomMesh,cell,pV0,pCellJ,pInvcellJ,detJ,ierr)
CHKERRQ(ierr)
call DMPlexComputeCellGeometryAffineFEM(geomMesh,cell,pV0,pCellJ,pInvcellJ,detJ,err_PETSc)
CHKERRQ(err_PETSc)
qOffset = 0
do qPt = 1, mesh_maxNips
do dirI = 1, dimPlex

434
src/mesh/mesh_mech_FEM.f90
View File

@ -40,7 +40,7 @@ module mesh_mechanical_FEM
type(tSolutionParams) :: params
type, private :: tNumerics
integer :: &
PetscInt :: &
p_i, & !< integration order (quadrature rule)
itmax
logical :: &
@ -55,7 +55,8 @@ module mesh_mechanical_FEM
! PETSc data
SNES :: mechanical_snes
Vec :: solution, solution_rate, solution_local
PetscInt :: dimPlex, cellDof, nQuadrature, nBasis
PetscInt :: dimPlex, cellDof, nBasis
integer :: nQuadrature
PetscReal, allocatable, target :: qPoints(:), qWeights(:)
MatNullSpace :: matnull
@ -104,11 +105,11 @@ subroutine FEM_mechanical_init(fieldBC)
PetscReal :: detJ
PetscReal, allocatable, target :: cellJMat(:,:)
PetscScalar, pointer :: px_scal(:)
PetscScalar, allocatable, target :: x_scal(:)
PetscScalar, pointer, dimension(:) :: px_scal
PetscScalar, allocatable, target, dimension(:) :: x_scal
character(len=*), parameter :: prefix = 'mechFE_'
PetscErrorCode :: ierr
PetscErrorCode :: err_PETSc
real(pReal), dimension(3,3) :: devNull
class(tNode), pointer :: &
num_mesh
@ -118,8 +119,8 @@ subroutine FEM_mechanical_init(fieldBC)
!-----------------------------------------------------------------------------
! read numerical parametes and do sanity checks
num_mesh => config_numerics%get('mesh',defaultVal=emptyDict)
num%p_i = num_mesh%get_asInt('p_i',defaultVal = 2)
num%itmax = num_mesh%get_asInt('itmax',defaultVal=250)
num%p_i = int(num_mesh%get_asInt('p_i',defaultVal = 2),pPETSCINT)
num%itmax = int(num_mesh%get_asInt('itmax',defaultVal=250),pPETSCINT)
num%BBarStabilisation = num_mesh%get_asBool('bbarstabilisation',defaultVal = .false.)
num%eps_struct_atol = num_mesh%get_asFloat('eps_struct_atol', defaultVal = 1.0e-10_pReal)
num%eps_struct_rtol = num_mesh%get_asFloat('eps_struct_rtol', defaultVal = 1.0e-4_pReal)
@ -130,8 +131,8 @@ subroutine FEM_mechanical_init(fieldBC)
!--------------------------------------------------------------------------------------------------
! Setup FEM mech mesh
call DMClone(geomMesh,mechanical_mesh,ierr); CHKERRQ(ierr)
call DMGetDimension(mechanical_mesh,dimPlex,ierr); CHKERRQ(ierr)
call DMClone(geomMesh,mechanical_mesh,err_PETSc); CHKERRQ(err_PETSc)
call DMGetDimension(mechanical_mesh,dimPlex,err_PETSc); CHKERRQ(err_PETSc)
!--------------------------------------------------------------------------------------------------
! Setup FEM mech discretization
@ -140,96 +141,104 @@ subroutine FEM_mechanical_init(fieldBC)
nQuadrature = FEM_nQuadrature( dimPlex,num%p_i)
qPointsP => qPoints
qWeightsP => qWeights
call PetscQuadratureCreate(PETSC_COMM_SELF,mechQuad,ierr); CHKERRQ(ierr)
CHKERRQ(ierr)
call PetscQuadratureCreate(PETSC_COMM_SELF,mechQuad,err_PETSc)
CHKERRQ(err_PETSc)
nc = dimPlex
call PetscQuadratureSetData(mechQuad,dimPlex,nc,nQuadrature,qPointsP,qWeightsP,ierr)
CHKERRQ(ierr)
call PetscQuadratureSetData(mechQuad,dimPlex,nc,int(nQuadrature,pPETSCINT),qPointsP,qWeightsP,err_PETSc)
CHKERRQ(err_PETSc)
call PetscFECreateDefault(PETSC_COMM_SELF,dimPlex,nc,PETSC_TRUE,prefix, &
num%p_i,mechFE,ierr); CHKERRQ(ierr)
call PetscFESetQuadrature(mechFE,mechQuad,ierr); CHKERRQ(ierr)
call PetscFEGetDimension(mechFE,nBasis,ierr); CHKERRQ(ierr)
num%p_i,mechFE,err_PETSc); CHKERRQ(err_PETSc)
call PetscFESetQuadrature(mechFE,mechQuad,err_PETSc); CHKERRQ(err_PETSc)
call PetscFEGetDimension(mechFE,nBasis,err_PETSc); CHKERRQ(err_PETSc)
nBasis = nBasis/nc
call DMAddField(mechanical_mesh,PETSC_NULL_DMLABEL,mechFE,ierr); CHKERRQ(ierr)
call DMCreateDS(mechanical_mesh,ierr); CHKERRQ(ierr)
call DMGetDS(mechanical_mesh,mechDS,ierr); CHKERRQ(ierr)
call PetscDSGetTotalDimension(mechDS,cellDof,ierr); CHKERRQ(ierr)
call PetscFEDestroy(mechFE,ierr); CHKERRQ(ierr)
call PetscQuadratureDestroy(mechQuad,ierr); CHKERRQ(ierr)
call DMAddField(mechanical_mesh,PETSC_NULL_DMLABEL,mechFE,err_PETSc)
CHKERRQ(err_PETSc)
call DMCreateDS(mechanical_mesh,err_PETSc); CHKERRQ(err_PETSc)
call DMGetDS(mechanical_mesh,mechDS,err_PETSc); CHKERRQ(err_PETSc)
call PetscDSGetTotalDimension(mechDS,cellDof,err_PETSc); CHKERRQ(err_PETSc)
call PetscFEDestroy(mechFE,err_PETSc); CHKERRQ(err_PETSc)
call PetscQuadratureDestroy(mechQuad,err_PETSc); CHKERRQ(err_PETSc)
!--------------------------------------------------------------------------------------------------
! Setup FEM mech boundary conditions
call DMGetLabel(mechanical_mesh,'Face Sets',BCLabel,ierr); CHKERRQ(ierr)
call DMPlexLabelComplete(mechanical_mesh,BCLabel,ierr); CHKERRQ(ierr)
call DMGetLocalSection(mechanical_mesh,section,ierr); CHKERRQ(ierr)
call DMGetLabel(mechanical_mesh,'Face Sets',BCLabel,err_PETSc)
CHKERRQ(err_PETSc)
call DMPlexLabelComplete(mechanical_mesh,BCLabel,err_PETSc); CHKERRQ(err_PETSc)
call DMGetLocalSection(mechanical_mesh,section,err_PETSc); CHKERRQ(err_PETSc)
allocate(pnumComp(1), source=dimPlex)
allocate(pnumDof(0:dimPlex), source = 0)
allocate(pnumDof(0:dimPlex), source = 0_pPETSCINT)
do topologDim = 0, dimPlex
call DMPlexGetDepthStratum(mechanical_mesh,topologDim,cellStart,cellEnd,ierr)
CHKERRQ(ierr)
call PetscSectionGetDof(section,cellStart,pnumDof(topologDim),ierr)
CHKERRQ(ierr)
call DMPlexGetDepthStratum(mechanical_mesh,topologDim,cellStart,cellEnd,err_PETSc)
CHKERRQ(err_PETSc)
call PetscSectionGetDof(section,cellStart,pnumDof(topologDim),err_PETSc)
CHKERRQ(err_PETSc)
enddo
numBC = 0
do field = 1, dimPlex; do faceSet = 1, mesh_Nboundaries
if (fieldBC%componentBC(field)%Mask(faceSet)) numBC = numBC + 1
enddo; enddo
allocate(pbcField(numBC), source=0)
allocate(pbcField(numBC), source=0_pPETSCINT)
allocate(pbcComps(numBC))
allocate(pbcPoints(numBC))
numBC = 0
do field = 1, dimPlex; do faceSet = 1, mesh_Nboundaries
if (fieldBC%componentBC(field)%Mask(faceSet)) then
numBC = numBC + 1
call ISCreateGeneral(PETSC_COMM_WORLD,1,[field-1],PETSC_COPY_VALUES,pbcComps(numBC),ierr)
CHKERRQ(ierr)
call DMGetStratumSize(mechanical_mesh,'Face Sets',mesh_boundaries(faceSet),bcSize,ierr)
CHKERRQ(ierr)
call ISCreateGeneral(PETSC_COMM_WORLD,1_pPETSCINT,[field-1],PETSC_COPY_VALUES,pbcComps(numBC),err_PETSc)
CHKERRQ(err_PETSc)
call DMGetStratumSize(mechanical_mesh,'Face Sets',mesh_boundaries(faceSet),bcSize,err_PETSc)
CHKERRQ(err_PETSc)
if (bcSize > 0) then
call DMGetStratumIS(mechanical_mesh,'Face Sets',mesh_boundaries(faceSet),bcPoint,ierr)
CHKERRQ(ierr)
call ISGetIndicesF90(bcPoint,pBcPoint,ierr); CHKERRQ(ierr)
call ISCreateGeneral(PETSC_COMM_WORLD,bcSize,pBcPoint,PETSC_COPY_VALUES,pbcPoints(numBC),ierr)
CHKERRQ(ierr)
call ISRestoreIndicesF90(bcPoint,pBcPoint,ierr); CHKERRQ(ierr)
call ISDestroy(bcPoint,ierr); CHKERRQ(ierr)
call DMGetStratumIS(mechanical_mesh,'Face Sets',mesh_boundaries(faceSet),bcPoint,err_PETSc)
CHKERRQ(err_PETSc)
call ISGetIndicesF90(bcPoint,pBcPoint,err_PETSc); CHKERRQ(err_PETSc)
call ISCreateGeneral(PETSC_COMM_WORLD,bcSize,pBcPoint,PETSC_COPY_VALUES,pbcPoints(numBC),err_PETSc)
CHKERRQ(err_PETSc)
call ISRestoreIndicesF90(bcPoint,pBcPoint,err_PETSc); CHKERRQ(err_PETSc)
call ISDestroy(bcPoint,err_PETSc); CHKERRQ(err_PETSc)
else
call ISCreateGeneral(PETSC_COMM_WORLD,0,[0],PETSC_COPY_VALUES,pbcPoints(numBC),ierr)
CHKERRQ(ierr)
call ISCreateGeneral(PETSC_COMM_WORLD,0_pPETSCINT,[0_pPETSCINT],PETSC_COPY_VALUES,pbcPoints(numBC),err_PETSc)
CHKERRQ(err_PETSc)
endif
endif
enddo; enddo
call DMPlexCreateSection(mechanical_mesh,nolabel,pNumComp,pNumDof, &
numBC,pBcField,pBcComps,pBcPoints,PETSC_NULL_IS,section,ierr)
CHKERRQ(ierr)
call DMSetSection(mechanical_mesh,section,ierr); CHKERRQ(ierr)
numBC,pBcField,pBcComps,pBcPoints,PETSC_NULL_IS,section,err_PETSc)
CHKERRQ(err_PETSc)
call DMSetSection(mechanical_mesh,section,err_PETSc); CHKERRQ(err_PETSc)
do faceSet = 1, numBC
call ISDestroy(pbcPoints(faceSet),ierr); CHKERRQ(ierr)
call ISDestroy(pbcPoints(faceSet),err_PETSc); CHKERRQ(err_PETSc)
enddo
!--------------------------------------------------------------------------------------------------
! initialize solver specific parts of PETSc
call SNESCreate(PETSC_COMM_WORLD,mechanical_snes,ierr);CHKERRQ(ierr)
call SNESSetOptionsPrefix(mechanical_snes,'mechanical_',ierr);CHKERRQ(ierr)
call SNESSetDM(mechanical_snes,mechanical_mesh,ierr); CHKERRQ(ierr) !< set the mesh for non-linear solver
call DMCreateGlobalVector(mechanical_mesh,solution ,ierr); CHKERRQ(ierr) !< locally owned displacement Dofs
call DMCreateGlobalVector(mechanical_mesh,solution_rate ,ierr); CHKERRQ(ierr) !< locally owned velocity Dofs to guess solution at next load step
call DMCreateLocalVector (mechanical_mesh,solution_local ,ierr); CHKERRQ(ierr) !< locally owned velocity Dofs to guess solution at next load step
call DMSNESSetFunctionLocal(mechanical_mesh,FEM_mechanical_formResidual,PETSC_NULL_VEC,ierr) !< function to evaluate residual forces
CHKERRQ(ierr)
call DMSNESSetJacobianLocal(mechanical_mesh,FEM_mechanical_formJacobian,PETSC_NULL_VEC,ierr) !< function to evaluate stiffness matrix
CHKERRQ(ierr)
call SNESSetMaxLinearSolveFailures(mechanical_snes, huge(1), ierr); CHKERRQ(ierr) !< ignore linear solve failures
call SNESSetConvergenceTest(mechanical_snes,FEM_mechanical_converged,PETSC_NULL_VEC,PETSC_NULL_FUNCTION,ierr)
CHKERRQ(ierr)
call SNESSetTolerances(mechanical_snes,1.0,0.0,0.0,num%itmax,num%itmax,ierr)
CHKERRQ(ierr)
call SNESSetFromOptions(mechanical_snes,ierr); CHKERRQ(ierr)
call SNESCreate(PETSC_COMM_WORLD,mechanical_snes,err_PETSc);CHKERRQ(err_PETSc)
call SNESSetOptionsPrefix(mechanical_snes,'mechanical_',err_PETSc)
CHKERRQ(err_PETSc)
call SNESSetDM(mechanical_snes,mechanical_mesh,err_PETSc) ! set the mesh for non-linear solver
CHKERRQ(err_PETSc)
call DMCreateGlobalVector(mechanical_mesh,solution, err_PETSc) ! locally owned displacement Dofs
CHKERRQ(err_PETSc)
call DMCreateGlobalVector(mechanical_mesh,solution_rate, err_PETSc) ! locally owned velocity Dofs to guess solution at next load step
CHKERRQ(err_PETSc)
call DMCreateLocalVector (mechanical_mesh,solution_local,err_PETSc) ! locally owned velocity Dofs to guess solution at next load step
CHKERRQ(err_PETSc)
call DMSNESSetFunctionLocal(mechanical_mesh,FEM_mechanical_formResidual,PETSC_NULL_VEC,err_PETSc) ! function to evaluate residual forces
CHKERRQ(err_PETSc)
call DMSNESSetJacobianLocal(mechanical_mesh,FEM_mechanical_formJacobian,PETSC_NULL_VEC,err_PETSc) ! function to evaluate stiffness matrix
CHKERRQ(err_PETSc)
call SNESSetMaxLinearSolveFailures(mechanical_snes, huge(1_pPETSCINT), err_PETSc) ! ignore linear solve failures
CHKERRQ(err_PETSc)
call SNESSetConvergenceTest(mechanical_snes,FEM_mechanical_converged,PETSC_NULL_VEC,PETSC_NULL_FUNCTION,err_PETSc)
CHKERRQ(err_PETSc)
call SNESSetTolerances(mechanical_snes,1.0,0.0,0.0,num%itmax,num%itmax,err_PETSc)
CHKERRQ(err_PETSc)
call SNESSetFromOptions(mechanical_snes,err_PETSc); CHKERRQ(err_PETSc)
!--------------------------------------------------------------------------------------------------
! init fields
call VecSet(solution ,0.0,ierr); CHKERRQ(ierr)
call VecSet(solution_rate ,0.0,ierr); CHKERRQ(ierr)
call VecSet(solution ,0.0,err_PETSc); CHKERRQ(err_PETSc)
call VecSet(solution_rate ,0.0,err_PETSc); CHKERRQ(err_PETSc)
allocate(x_scal(cellDof))
allocate(nodalWeightsP(1))
allocate(nodalPointsP(dimPlex))
@ -237,26 +246,26 @@ subroutine FEM_mechanical_init(fieldBC)
allocate(pcellJ(dimPlex**2))
allocate(pinvcellJ(dimPlex**2))
allocate(cellJMat(dimPlex,dimPlex))
call PetscDSGetDiscretization(mechDS,0,mechFE,ierr)
CHKERRQ(ierr)
call PetscFEGetDualSpace(mechFE,mechDualSpace,ierr); CHKERRQ(ierr)
call DMPlexGetHeightStratum(mechanical_mesh,0,cellStart,cellEnd,ierr)
CHKERRQ(ierr)
call PetscDSGetDiscretization(mechDS,0_pPETSCINT,mechFE,err_PETSc)
CHKERRQ(err_PETSc)
call PetscFEGetDualSpace(mechFE,mechDualSpace,err_PETSc); CHKERRQ(err_PETSc)
call DMPlexGetHeightStratum(mechanical_mesh,0_pPETSCINT,cellStart,cellEnd,err_PETSc)
CHKERRQ(err_PETSc)
do cell = cellStart, cellEnd-1 !< loop over all elements
x_scal = 0.0_pReal
call DMPlexComputeCellGeometryAffineFEM(mechanical_mesh,cell,pV0,pCellJ,pInvcellJ,detJ,ierr)
CHKERRQ(ierr)
call DMPlexComputeCellGeometryAffineFEM(mechanical_mesh,cell,pV0,pCellJ,pInvcellJ,detJ,err_PETSc)
CHKERRQ(err_PETSc)
cellJMat = reshape(pCellJ,shape=[dimPlex,dimPlex])
do basis = 0, nBasis*dimPlex-1, dimPlex
call PetscDualSpaceGetFunctional(mechDualSpace,basis,functional,ierr)
CHKERRQ(ierr)
call PetscQuadratureGetData(functional,dimPlex,nc,nNodalPoints,nodalPointsP,nodalWeightsP,ierr)
CHKERRQ(ierr)
call PetscDualSpaceGetFunctional(mechDualSpace,basis,functional,err_PETSc)
CHKERRQ(err_PETSc)
call PetscQuadratureGetData(functional,dimPlex,nc,nNodalPoints,nodalPointsP,nodalWeightsP,err_PETSc)
CHKERRQ(err_PETSc)
x_scal(basis+1:basis+dimPlex) = pV0 + matmul(transpose(cellJMat),nodalPointsP + 1.0_pReal)
enddo
px_scal => x_scal
call DMPlexVecSetClosure(mechanical_mesh,section,solution_local,cell,px_scal,5,ierr)
CHKERRQ(ierr)
call DMPlexVecSetClosure(mechanical_mesh,section,solution_local,cell,px_scal,5,err_PETSc)
CHKERRQ(err_PETSc)
enddo
call utilities_constitutiveResponse(0.0_pReal,devNull,.true.)
@ -279,7 +288,7 @@ type(tSolutionState) function FEM_mechanical_solution( &
character(len=*), intent(in) :: &
incInfoIn
PetscErrorCode :: ierr
PetscErrorCode :: err_PETSc
SNESConvergedReason :: reason
incInfo = incInfoIn
@ -289,8 +298,10 @@ type(tSolutionState) function FEM_mechanical_solution( &
params%timeinc = timeinc
params%fieldBC = fieldBC
call SNESSolve(mechanical_snes,PETSC_NULL_VEC,solution,ierr); CHKERRQ(ierr) ! solve mechanical_snes based on solution guess (result in solution)
call SNESGetConvergedReason(mechanical_snes,reason,ierr); CHKERRQ(ierr) ! solution converged?
call SNESSolve(mechanical_snes,PETSC_NULL_VEC,solution,err_PETSc) ! solve mechanical_snes based on solution guess (result in solution)
CHKERRQ(err_PETSc)
call SNESGetConvergedReason(mechanical_snes,reason,err_PETSc) ! solution converged?
CHKERRQ(err_PETSc)
terminallyIll = .false.
if (reason < 1) then ! 0: still iterating (will not occur), negative -> convergence error
@ -298,8 +309,8 @@ type(tSolutionState) function FEM_mechanical_solution( &
FEM_mechanical_solution%iterationsNeeded = num%itmax
else ! >= 1 proper convergence (or terminally ill)
FEM_mechanical_solution%converged = .true.
call SNESGetIterationNumber(mechanical_snes,FEM_mechanical_solution%iterationsNeeded,ierr)
CHKERRQ(ierr)
call SNESGetIterationNumber(mechanical_snes,FEM_mechanical_solution%iterationsNeeded,err_PETSc)
CHKERRQ(err_PETSc)
endif
print'(/,1x,a)', '==========================================================================='
@ -311,11 +322,12 @@ end function FEM_mechanical_solution
!--------------------------------------------------------------------------------------------------
!> @brief forms the FEM residual vector
!--------------------------------------------------------------------------------------------------
subroutine FEM_mechanical_formResidual(dm_local,xx_local,f_local,dummy,ierr)
subroutine FEM_mechanical_formResidual(dm_local,xx_local,f_local,dummy,err_PETSc)
DM :: dm_local
PetscObject,intent(in) :: dummy
PetscErrorCode :: ierr
PetscErrorCode :: err_PETSc
integer(MPI_INTEGER_KIND) :: err_MPI
PetscDS :: prob
Vec :: x_local, f_local, xx_local
@ -339,22 +351,25 @@ subroutine FEM_mechanical_formResidual(dm_local,xx_local,f_local,dummy,ierr)
allocate(pinvcellJ(dimPlex**2))
allocate(x_scal(cellDof))
call DMGetLocalSection(dm_local,section,ierr); CHKERRQ(ierr)
call DMGetDS(dm_local,prob,ierr); CHKERRQ(ierr)
call PetscDSGetTabulation(prob,0,basisField,basisFieldDer,ierr)
CHKERRQ(ierr)
call DMPlexGetHeightStratum(dm_local,0,cellStart,cellEnd,ierr); CHKERRQ(ierr)
call DMGetLocalVector(dm_local,x_local,ierr); CHKERRQ(ierr)
call VecWAXPY(x_local,1.0,xx_local,solution_local,ierr); CHKERRQ(ierr)
call DMGetLocalSection(dm_local,section,err_PETSc); CHKERRQ(err_PETSc)
call DMGetDS(dm_local,prob,err_PETSc); CHKERRQ(err_PETSc)
call PetscDSGetTabulation(prob,0_pPETSCINT,basisField,basisFieldDer,err_PETSc)
CHKERRQ(err_PETSc)
call DMPlexGetHeightStratum(dm_local,0_pPETSCINT,cellStart,cellEnd,err_PETSc)
CHKERRQ(err_PETSc)
call DMGetLocalVector(dm_local,x_local,err_PETSc)
CHKERRQ(err_PETSc)
call VecWAXPY(x_local,1.0,xx_local,solution_local,err_PETSc)
CHKERRQ(err_PETSc)
do field = 1, dimPlex; do face = 1, mesh_Nboundaries
if (params%fieldBC%componentBC(field)%Mask(face)) then
call DMGetStratumSize(dm_local,'Face Sets',mesh_boundaries(face),bcSize,ierr)
call DMGetStratumSize(dm_local,'Face Sets',mesh_boundaries(face),bcSize,err_PETSc)
if (bcSize > 0) then
call DMGetStratumIS(dm_local,'Face Sets',mesh_boundaries(face),bcPoints,ierr)
CHKERRQ(ierr)
call utilities_projectBCValues(x_local,section,0,field-1,bcPoints, &
call DMGetStratumIS(dm_local,'Face Sets',mesh_boundaries(face),bcPoints,err_PETSc)
CHKERRQ(err_PETSc)
call utilities_projectBCValues(x_local,section,0_pPETSCINT,field-1,bcPoints, &
0.0_pReal,params%fieldBC%componentBC(field)%Value(face),params%timeinc)
call ISDestroy(bcPoints,ierr); CHKERRQ(ierr)
call ISDestroy(bcPoints,err_PETSc); CHKERRQ(err_PETSc)
endif
endif
enddo; enddo
@ -363,12 +378,12 @@ subroutine FEM_mechanical_formResidual(dm_local,xx_local,f_local,dummy,ierr)
! evaluate field derivatives
do cell = cellStart, cellEnd-1 !< loop over all elements
call PetscSectionGetNumFields(section,numFields,ierr)
CHKERRQ(ierr)
call DMPlexVecGetClosure(dm_local,section,x_local,cell,x_scal,ierr) !< get Dofs belonging to element
CHKERRQ(ierr)
call DMPlexComputeCellGeometryAffineFEM(dm_local,cell,pV0,pCellJ,pInvcellJ,detJ,ierr)
CHKERRQ(ierr)
call PetscSectionGetNumFields(section,numFields,err_PETSc)
CHKERRQ(err_PETSc)
call DMPlexVecGetClosure(dm_local,section,x_local,cell,x_scal,err_PETSc) !< get Dofs belonging to element
CHKERRQ(err_PETSc)
call DMPlexComputeCellGeometryAffineFEM(dm_local,cell,pV0,pCellJ,pInvcellJ,detJ,err_PETSc)
CHKERRQ(err_PETSc)
IcellJMat = reshape(pInvcellJ,shape=[dimPlex,dimPlex])
do qPt = 0, nQuadrature-1
m = cell*nQuadrature + qPt+1
@ -392,23 +407,24 @@ subroutine FEM_mechanical_formResidual(dm_local,xx_local,f_local,dummy,ierr)
enddo
endif
call DMPlexVecRestoreClosure(dm_local,section,x_local,cell,x_scal,ierr)
CHKERRQ(ierr)
call DMPlexVecRestoreClosure(dm_local,section,x_local,cell,x_scal,err_PETSc)
CHKERRQ(err_PETSc)
enddo
!--------------------------------------------------------------------------------------------------
! evaluate constitutive response
call utilities_constitutiveResponse(params%timeinc,P_av,ForwardData)
call MPI_Allreduce(MPI_IN_PLACE,terminallyIll,1,MPI_LOGICAL,MPI_LOR,MPI_COMM_WORLD,ierr)
call MPI_Allreduce(MPI_IN_PLACE,terminallyIll,1_MPI_INTEGER_KIND,MPI_LOGICAL,MPI_LOR,MPI_COMM_WORLD,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
ForwardData = .false.
!--------------------------------------------------------------------------------------------------
! integrating residual
do cell = cellStart, cellEnd-1 !< loop over all elements
call DMPlexVecGetClosure(dm_local,section,x_local,cell,x_scal,ierr) !< get Dofs belonging to element
CHKERRQ(ierr)
call DMPlexComputeCellGeometryAffineFEM(dm_local,cell,pV0,pCellJ,pInvcellJ,detJ,ierr)
CHKERRQ(ierr)
call DMPlexVecGetClosure(dm_local,section,x_local,cell,x_scal,err_PETSc) !< get Dofs belonging to element
CHKERRQ(err_PETSc)
call DMPlexComputeCellGeometryAffineFEM(dm_local,cell,pV0,pCellJ,pInvcellJ,detJ,err_PETSc)
CHKERRQ(err_PETSc)
IcellJMat = reshape(pInvcellJ,shape=[dimPlex,dimPlex])
f_scal = 0.0
do qPt = 0, nQuadrature-1
@ -429,12 +445,12 @@ subroutine FEM_mechanical_formResidual(dm_local,xx_local,f_local,dummy,ierr)
enddo
f_scal = f_scal*abs(detJ)
pf_scal => f_scal
call DMPlexVecSetClosure(dm_local,section,f_local,cell,pf_scal,ADD_VALUES,ierr)
CHKERRQ(ierr)
call DMPlexVecRestoreClosure(dm_local,section,x_local,cell,x_scal,ierr)
CHKERRQ(ierr)
call DMPlexVecSetClosure(dm_local,section,f_local,cell,pf_scal,ADD_VALUES,err_PETSc)
CHKERRQ(err_PETSc)
call DMPlexVecRestoreClosure(dm_local,section,x_local,cell,x_scal,err_PETSc)
CHKERRQ(err_PETSc)
enddo
call DMRestoreLocalVector(dm_local,x_local,ierr); CHKERRQ(ierr)
call DMRestoreLocalVector(dm_local,x_local,err_PETSc); CHKERRQ(err_PETSc)
end subroutine FEM_mechanical_formResidual
@ -442,13 +458,13 @@ end subroutine FEM_mechanical_formResidual
!--------------------------------------------------------------------------------------------------
!> @brief forms the FEM stiffness matrix
!--------------------------------------------------------------------------------------------------
subroutine FEM_mechanical_formJacobian(dm_local,xx_local,Jac_pre,Jac,dummy,ierr)
subroutine FEM_mechanical_formJacobian(dm_local,xx_local,Jac_pre,Jac,dummy,err_PETSc)
DM :: dm_local
Mat :: Jac_pre, Jac
PetscObject, intent(in) :: dummy
PetscErrorCode :: ierr
PetscErrorCode :: err_PETSc
PetscDS :: prob
Vec :: x_local, xx_local
@ -478,34 +494,43 @@ subroutine FEM_mechanical_formJacobian(dm_local,xx_local,Jac_pre,Jac,dummy,ierr)
allocate(pcellJ(dimPlex**2))
allocate(pinvcellJ(dimPlex**2))
call MatSetOption(Jac,MAT_KEEP_NONZERO_PATTERN,PETSC_TRUE,ierr); CHKERRQ(ierr)
call MatSetOption(Jac,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE,ierr); CHKERRQ(ierr)
call MatZeroEntries(Jac,ierr); CHKERRQ(ierr)
call DMGetDS(dm_local,prob,ierr); CHKERRQ(ierr)
call PetscDSGetTabulation(prob,0,basisField,basisFieldDer,ierr)
call DMGetLocalSection(dm_local,section,ierr); CHKERRQ(ierr)
call DMGetGlobalSection(dm_local,gSection,ierr); CHKERRQ(ierr)
call MatSetOption(Jac,MAT_KEEP_NONZERO_PATTERN,PETSC_TRUE,err_PETSc)
CHKERRQ(err_PETSc)
call MatSetOption(Jac,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE,err_PETSc)
CHKERRQ(err_PETSc)
call MatZeroEntries(Jac,err_PETSc)
CHKERRQ(err_PETSc)
call DMGetDS(dm_local,prob,err_PETSc)
CHKERRQ(err_PETSc)
call PetscDSGetTabulation(prob,0_pPETSCINT,basisField,basisFieldDer,err_PETSc)
call DMGetLocalSection(dm_local,section,err_PETSc)
CHKERRQ(err_PETSc)
call DMGetGlobalSection(dm_local,gSection,err_PETSc)
CHKERRQ(err_PETSc)
call DMGetLocalVector(dm_local,x_local,ierr); CHKERRQ(ierr)
call VecWAXPY(x_local,1.0_pReal,xx_local,solution_local,ierr); CHKERRQ(ierr)
call DMGetLocalVector(dm_local,x_local,err_PETSc)
CHKERRQ(err_PETSc)
call VecWAXPY(x_local,1.0_pReal,xx_local,solution_local,err_PETSc)
CHKERRQ(err_PETSc)
do field = 1, dimPlex; do face = 1, mesh_Nboundaries
if (params%fieldBC%componentBC(field)%Mask(face)) then
call DMGetStratumSize(dm_local,'Face Sets',mesh_boundaries(face),bcSize,ierr)
call DMGetStratumSize(dm_local,'Face Sets',mesh_boundaries(face),bcSize,err_PETSc)
if (bcSize > 0) then
call DMGetStratumIS(dm_local,'Face Sets',mesh_boundaries(face),bcPoints,ierr)
CHKERRQ(ierr)
call utilities_projectBCValues(x_local,section,0,field-1,bcPoints, &
call DMGetStratumIS(dm_local,'Face Sets',mesh_boundaries(face),bcPoints,err_PETSc)
CHKERRQ(err_PETSc)
call utilities_projectBCValues(x_local,section,0_pPETSCINT,field-1,bcPoints, &
0.0_pReal,params%fieldBC%componentBC(field)%Value(face),params%timeinc)
call ISDestroy(bcPoints,ierr); CHKERRQ(ierr)
call ISDestroy(bcPoints,err_PETSc); CHKERRQ(err_PETSc)
endif
endif
enddo; enddo
call DMPlexGetHeightStratum(dm_local,0,cellStart,cellEnd,ierr); CHKERRQ(ierr)
call DMPlexGetHeightStratum(dm_local,0_pPETSCINT,cellStart,cellEnd,err_PETSc)
CHKERRQ(err_PETSc)
do cell = cellStart, cellEnd-1 !< loop over all elements
call DMPlexVecGetClosure(dm_local,section,x_local,cell,x_scal,ierr) !< get Dofs belonging to element
CHKERRQ(ierr)
call DMPlexComputeCellGeometryAffineFEM(dm_local,cell,pV0,pCellJ,pInvcellJ,detJ,ierr)
CHKERRQ(ierr)
call DMPlexVecGetClosure(dm_local,section,x_local,cell,x_scal,err_PETSc) !< get Dofs belonging to element
CHKERRQ(err_PETSc)
call DMPlexComputeCellGeometryAffineFEM(dm_local,cell,pV0,pCellJ,pInvcellJ,detJ,err_PETSc)
CHKERRQ(err_PETSc)
K_eA = 0.0
K_eB = 0.0
MatB = 0.0
@ -531,11 +556,11 @@ subroutine FEM_mechanical_formJacobian(dm_local,xx_local,Jac_pre,Jac,dummy,ierr)
FInv = math_inv33(F)
K_eA = K_eA + matmul(transpose(BMat),MatA)*math_det33(FInv)**(1.0/real(dimPlex))
K_eB = K_eB - &
matmul(transpose(matmul(reshape(homogenization_F(1:dimPlex,1:dimPlex,m),shape=[dimPlex*dimPlex,1]), &
matmul(transpose(matmul(reshape(homogenization_F(1:dimPlex,1:dimPlex,m),shape=[dimPlex**2,1_pPETSCINT]), &
matmul(reshape(FInv(1:dimPlex,1:dimPlex), &
shape=[1,dimPlex*dimPlex],order=[2,1]),BMat))),MatA)
shape=[1_pPETSCINT,dimPlex**2],order=[2,1]),BMat))),MatA)
MatB = MatB &
+ matmul(reshape(homogenization_F(1:dimPlex,1:dimPlex,m),shape=[1,dimPlex*dimPlex]),MatA)
+ matmul(reshape(homogenization_F(1:dimPlex,1:dimPlex,m),shape=[1_pPETSCINT,dimPlex**2]),MatA)
FAvg = FAvg + F
BMatAvg = BMatAvg + BMat
else
@ -546,39 +571,40 @@ subroutine FEM_mechanical_formJacobian(dm_local,xx_local,Jac_pre,Jac,dummy,ierr)
FInv = math_inv33(FAvg)
K_e = K_eA*math_det33(FAvg/real(nQuadrature))**(1.0/real(dimPlex)) + &
(matmul(matmul(transpose(BMatAvg), &
reshape(FInv(1:dimPlex,1:dimPlex),shape=[dimPlex*dimPlex,1],order=[2,1])),MatB) + &
reshape(FInv(1:dimPlex,1:dimPlex),shape=[dimPlex**2,1_pPETSCINT],order=[2,1])),MatB) + &
K_eB)/real(dimPlex)
else
K_e = K_eA
endif
K_e = (K_e + eps*math_eye(cellDof)) * abs(detJ)
K_e = (K_e + eps*math_eye(int(cellDof))) * abs(detJ)
#ifndef __INTEL_COMPILER
pK_e(1:cellDOF**2) => K_e
#else
! https://software.intel.com/en-us/forums/intel-fortran-compiler/topic/782230 (bug)
allocate(pK_e(cellDOF**2),source = reshape(K_e,[cellDOF**2]))
#endif
call DMPlexMatSetClosure(dm_local,section,gSection,Jac,cell,pK_e,ADD_VALUES,ierr)
CHKERRQ(ierr)
call DMPlexVecRestoreClosure(dm_local,section,x_local,cell,x_scal,ierr)
CHKERRQ(ierr)
call DMPlexMatSetClosure(dm_local,section,gSection,Jac,cell,pK_e,ADD_VALUES,err_PETSc)
CHKERRQ(err_PETSc)
call DMPlexVecRestoreClosure(dm_local,section,x_local,cell,x_scal,err_PETSc)
CHKERRQ(err_PETSc)
enddo
call MatAssemblyBegin(Jac,MAT_FINAL_ASSEMBLY,ierr); CHKERRQ(ierr)
call MatAssemblyEnd(Jac,MAT_FINAL_ASSEMBLY,ierr); CHKERRQ(ierr)
call MatAssemblyBegin(Jac_pre,MAT_FINAL_ASSEMBLY,ierr); CHKERRQ(ierr)
call MatAssemblyEnd(Jac_pre,MAT_FINAL_ASSEMBLY,ierr); CHKERRQ(ierr)
call DMRestoreLocalVector(dm_local,x_local,ierr); CHKERRQ(ierr)
call MatAssemblyBegin(Jac,MAT_FINAL_ASSEMBLY,err_PETSc); CHKERRQ(err_PETSc)
call MatAssemblyEnd(Jac,MAT_FINAL_ASSEMBLY,err_PETSc); CHKERRQ(err_PETSc)
call MatAssemblyBegin(Jac_pre,MAT_FINAL_ASSEMBLY,err_PETSc); CHKERRQ(err_PETSc)
call MatAssemblyEnd(Jac_pre,MAT_FINAL_ASSEMBLY,err_PETSc); CHKERRQ(err_PETSc)
call DMRestoreLocalVector(dm_local,x_local,err_PETSc); CHKERRQ(err_PETSc)
!--------------------------------------------------------------------------------------------------
! apply boundary conditions
#if (PETSC_VERSION_MINOR < 14)
call DMPlexCreateRigidBody(dm_local,matnull,ierr); CHKERRQ(ierr)
call DMPlexCreateRigidBody(dm_local,matnull,err_PETSc); CHKERRQ(err_PETSc)
#else
call DMPlexCreateRigidBody(dm_local,0,matnull,ierr); CHKERRQ(ierr)
call DMPlexCreateRigidBody(dm_local,0_pPETSCINT,matnull,err_PETSc)
CHKERRQ(err_PETSc)
#endif
call MatSetNullSpace(Jac,matnull,ierr); CHKERRQ(ierr)
call MatSetNearNullSpace(Jac,matnull,ierr); CHKERRQ(ierr)
call MatNullSpaceDestroy(matnull,ierr); CHKERRQ(ierr)
call MatSetNullSpace(Jac,matnull,err_PETSc); CHKERRQ(err_PETSc)
call MatSetNearNullSpace(Jac,matnull,err_PETSc); CHKERRQ(err_PETSc)
call MatNullSpaceDestroy(matnull,err_PETSc); CHKERRQ(err_PETSc)
end subroutine FEM_mechanical_formJacobian
@ -601,43 +627,43 @@ subroutine FEM_mechanical_forward(guess,timeinc,timeinc_old,fieldBC)
Vec :: x_local
PetscSection :: section
IS :: bcPoints
PetscErrorCode :: ierr
PetscErrorCode :: err_PETSc
!--------------------------------------------------------------------------------------------------
! forward last inc
if (guess .and. .not. cutBack) then
ForwardData = .True.
homogenization_F0 = homogenization_F
call SNESGetDM(mechanical_snes,dm_local,ierr); CHKERRQ(ierr) !< retrieve mesh info from mechanical_snes into dm_local
call DMGetSection(dm_local,section,ierr); CHKERRQ(ierr)
call DMGetLocalVector(dm_local,x_local,ierr); CHKERRQ(ierr)
call VecSet(x_local,0.0_pReal,ierr); CHKERRQ(ierr)
call DMGlobalToLocalBegin(dm_local,solution,INSERT_VALUES,x_local,ierr) !< retrieve my partition of global solution vector
CHKERRQ(ierr)
call DMGlobalToLocalEnd(dm_local,solution,INSERT_VALUES,x_local,ierr)
CHKERRQ(ierr)
call VecAXPY(solution_local,1.0,x_local,ierr); CHKERRQ(ierr)
call SNESGetDM(mechanical_snes,dm_local,err_PETSc); CHKERRQ(err_PETSc) !< retrieve mesh info from mechanical_snes into dm_local
call DMGetSection(dm_local,section,err_PETSc); CHKERRQ(err_PETSc)
call DMGetLocalVector(dm_local,x_local,err_PETSc); CHKERRQ(err_PETSc)
call VecSet(x_local,0.0_pReal,err_PETSc); CHKERRQ(err_PETSc)
call DMGlobalToLocalBegin(dm_local,solution,INSERT_VALUES,x_local,err_PETSc) !< retrieve my partition of global solution vector
CHKERRQ(err_PETSc)
call DMGlobalToLocalEnd(dm_local,solution,INSERT_VALUES,x_local,err_PETSc)
CHKERRQ(err_PETSc)
call VecAXPY(solution_local,1.0,x_local,err_PETSc); CHKERRQ(err_PETSc)
do field = 1, dimPlex; do face = 1, mesh_Nboundaries
if (fieldBC%componentBC(field)%Mask(face)) then
call DMGetStratumSize(dm_local,'Face Sets',mesh_boundaries(face),bcSize,ierr)
call DMGetStratumSize(dm_local,'Face Sets',mesh_boundaries(face),bcSize,err_PETSc)
if (bcSize > 0) then
call DMGetStratumIS(dm_local,'Face Sets',mesh_boundaries(face),bcPoints,ierr)
CHKERRQ(ierr)
call utilities_projectBCValues(solution_local,section,0,field-1,bcPoints, &
call DMGetStratumIS(dm_local,'Face Sets',mesh_boundaries(face),bcPoints,err_PETSc)
CHKERRQ(err_PETSc)
call utilities_projectBCValues(solution_local,section,0_pPETSCINT,field-1,bcPoints, &
0.0_pReal,fieldBC%componentBC(field)%Value(face),timeinc_old)
call ISDestroy(bcPoints,ierr); CHKERRQ(ierr)
call ISDestroy(bcPoints,err_PETSc); CHKERRQ(err_PETSc)
endif
endif
enddo; enddo
call DMRestoreLocalVector(dm_local,x_local,ierr); CHKERRQ(ierr)
call DMRestoreLocalVector(dm_local,x_local,err_PETSc); CHKERRQ(err_PETSc)
!--------------------------------------------------------------------------------------------------
! update rate and forward last inc
call VecCopy(solution,solution_rate,ierr); CHKERRQ(ierr)
call VecScale(solution_rate,1.0/timeinc_old,ierr); CHKERRQ(ierr)
call VecCopy(solution,solution_rate,err_PETSc); CHKERRQ(err_PETSc)
call VecScale(solution_rate,1.0/timeinc_old,err_PETSc); CHKERRQ(err_PETSc)
endif
call VecCopy(solution_rate,solution,ierr); CHKERRQ(ierr)
call VecScale(solution,timeinc,ierr); CHKERRQ(ierr)
call VecCopy(solution_rate,solution,err_PETSc); CHKERRQ(err_PETSc)
call VecScale(solution,timeinc,err_PETSc); CHKERRQ(err_PETSc)
end subroutine FEM_mechanical_forward
@ -645,24 +671,24 @@ end subroutine FEM_mechanical_forward
!--------------------------------------------------------------------------------------------------
!> @brief reporting
!--------------------------------------------------------------------------------------------------
subroutine FEM_mechanical_converged(snes_local,PETScIter,xnorm,snorm,fnorm,reason,dummy,ierr)
subroutine FEM_mechanical_converged(snes_local,PETScIter,xnorm,snorm,fnorm,reason,dummy,err_PETSc)
SNES :: snes_local
PetscInt :: PETScIter
PetscReal :: xnorm,snorm,fnorm,divTol
SNESConvergedReason :: reason
PetscObject :: dummy
PetscErrorCode :: ierr
PetscErrorCode :: err_PETSc
!--------------------------------------------------------------------------------------------------
! report
divTol = max(maxval(abs(P_av(1:dimPlex,1:dimPlex)))*num%eps_struct_rtol,num%eps_struct_atol)
call SNESConvergedDefault(snes_local,PETScIter,xnorm,snorm,fnorm/divTol,reason,dummy,ierr)
CHKERRQ(ierr)
call SNESConvergedDefault(snes_local,PETScIter,xnorm,snorm,fnorm/divTol,reason,dummy,err_PETSc)
CHKERRQ(err_PETSc)
if (terminallyIll) reason = SNES_DIVERGED_FUNCTION_DOMAIN
print'(/,1x,a,a,i0,a,i0,f0.3)', trim(incInfo), &
' @ Iteration ',PETScIter,' mechanical residual norm = ', &
int(fnorm/divTol),fnorm/divTol-int(fnorm/divTol)
int(fnorm/divTol),fnorm/divTol-int(fnorm/divTol) ! ToDo: int casting?
print'(/,1x,a,/,2(3(2x,f12.4,1x)/),3(2x,f12.4,1x))', &
'Piola--Kirchhoff stress / MPa =',transpose(P_av)*1.e-6_pReal
flush(IO_STDOUT)
@ -675,9 +701,7 @@ end subroutine FEM_mechanical_converged
!--------------------------------------------------------------------------------------------------
subroutine FEM_mechanical_updateCoords()
real(pReal), pointer, dimension(:) :: &
nodeCoords_linear !< nodal coordinates (dimPlex*Nnodes)
real(pReal), pointer, dimension(:,:) :: &
PetscReal, pointer, dimension(:,:) :: &
nodeCoords !< nodal coordinates (3,Nnodes)
real(pReal), pointer, dimension(:,:,:) :: &
ipCoords !< ip coordinates (3,nQuadrature,mesh_NcpElems)
@ -690,42 +714,47 @@ subroutine FEM_mechanical_updateCoords()
DM :: dm_local
Vec :: x_local
PetscErrorCode :: ierr
PetscErrorCode :: err_PETSc
PetscInt :: pStart, pEnd, p, s, e, q, &
cellStart, cellEnd, c, n
PetscSection :: section
PetscQuadrature :: mechQuad
PetscReal, dimension(:), pointer :: basisField, basisFieldDer
PetscScalar, dimension(:), pointer :: x_scal
PetscReal, dimension(:), pointer :: basisField, basisFieldDer, &
nodeCoords_linear !< nodal coordinates (dimPlex*Nnodes)
PetscScalar, dimension(:), pointer :: x_scal
call SNESGetDM(mechanical_snes,dm_local,ierr); CHKERRQ(ierr)
call DMGetDS(dm_local,mechQuad,ierr); CHKERRQ(ierr)
call DMGetLocalSection(dm_local,section,ierr); CHKERRQ(ierr)
call DMGetLocalVector(dm_local,x_local,ierr); CHKERRQ(ierr)
call DMGetDimension(dm_local,dimPlex,ierr); CHKERRQ(ierr)
call SNESGetDM(mechanical_snes,dm_local,err_PETSc); CHKERRQ(err_PETSc)
call DMGetDS(dm_local,mechQuad,err_PETSc); CHKERRQ(err_PETSc)
call DMGetLocalSection(dm_local,section,err_PETSc); CHKERRQ(err_PETSc)
call DMGetLocalVector(dm_local,x_local,err_PETSc); CHKERRQ(err_PETSc)
call DMGetDimension(dm_local,dimPlex,err_PETSc); CHKERRQ(err_PETSc)
! write cell vertex displacements
call DMPlexGetDepthStratum(dm_local,0,pStart,pEnd,ierr); CHKERRQ(ierr)
call DMPlexGetDepthStratum(dm_local,0_pPETSCINT,pStart,pEnd,err_PETSc)
CHKERRQ(err_PETSc)
allocate(nodeCoords(3,pStart:pEnd-1),source=0.0_pReal)
call VecGetArrayF90(x_local,nodeCoords_linear,ierr); CHKERRQ(ierr)
call VecGetArrayF90(x_local,nodeCoords_linear,err_PETSc); CHKERRQ(err_PETSc)
do p=pStart, pEnd-1
call DMPlexGetPointLocal(dm_local, p, s, e, ierr); CHKERRQ(ierr)
call DMPlexGetPointLocal(dm_local, p, s, e, err_PETSc); CHKERRQ(err_PETSc)
nodeCoords(1:dimPlex,p)=nodeCoords_linear(s+1:e)
enddo
call discretization_setNodeCoords(nodeCoords)
call VecRestoreArrayF90(x_local,nodeCoords_linear,ierr); CHKERRQ(ierr)
call VecRestoreArrayF90(x_local,nodeCoords_linear,err_PETSc); CHKERRQ(err_PETSc)
! write ip displacements
call DMPlexGetHeightStratum(dm_local,0,cellStart,cellEnd,ierr); CHKERRQ(ierr)
call PetscDSGetTabulation(mechQuad,0,basisField,basisFieldDer,ierr); CHKERRQ(ierr)
call DMPlexGetHeightStratum(dm_local,0_pPETSCINT,cellStart,cellEnd,err_PETSc)
CHKERRQ(err_PETSc)
call PetscDSGetTabulation(mechQuad,0_pPETSCINT,basisField,basisFieldDer,err_PETSc)
CHKERRQ(err_PETSc)
allocate(ipCoords(3,nQuadrature,mesh_NcpElems),source=0.0_pReal)
do c=cellStart,cellEnd-1
qOffset=0
call DMPlexVecGetClosure(dm_local,section,x_local,c,x_scal,ierr); CHKERRQ(ierr) !< get nodal coordinates of each element
call DMPlexVecGetClosure(dm_local,section,x_local,c,x_scal,err_PETSc) !< get nodal coordinates of each element
CHKERRQ(err_PETSc)
do qPt=0,nQuadrature-1
qOffset= qPt * (size(basisField)/nQuadrature)
do comp=0,dimPlex-1 !< loop over components
do comp=0,dimPlex-1 !< loop over components
nOffset=0
q = comp
do n=0,nBasis-1
@ -737,10 +766,11 @@ subroutine FEM_mechanical_updateCoords()
enddo
enddo
enddo
call DMPlexVecRestoreClosure(dm_local,section,x_local,c,x_scal,ierr); CHKERRQ(ierr)
call DMPlexVecRestoreClosure(dm_local,section,x_local,c,x_scal,err_PETSc)
CHKERRQ(err_PETSc)
end do
call discretization_setIPcoords(reshape(ipCoords,[3,mesh_NcpElems*nQuadrature]))
call DMRestoreLocalVector(dm_local,x_local,ierr); CHKERRQ(ierr)
call DMRestoreLocalVector(dm_local,x_local,err_PETSc); CHKERRQ(err_PETSc)
end subroutine FEM_mechanical_updateCoords

76
src/parallelization.f90
View File

@ -20,9 +20,17 @@ module parallelization
implicit none
private
integer, protected, public :: &
worldrank = 0, & !< MPI worldrank (/=0 for MPI simulations only)
worldsize = 1 !< MPI worldsize (/=1 for MPI simulations only)
#ifndef PETSC
integer, parameter, public :: &
MPI_INTEGER_KIND = pI64
integer(MPI_INTEGER_KIND), parameter, public :: &
worldrank = 0_MPI_INTEGER_KIND, & !< MPI dummy worldrank
worldsize = 1_MPI_INTEGER_KIND !< MPI dummy worldsize
#else
integer(MPI_INTEGER_KIND), protected, public :: &
worldrank = 0_MPI_INTEGER_KIND, & !< MPI worldrank (/=0 for MPI simulations only)
worldsize = 1_MPI_INTEGER_KIND !< MPI worldsize (/=1 for MPI simulations only)
#endif
#ifndef PETSC
public :: parallelization_bcast_str
@ -44,54 +52,68 @@ contains
!--------------------------------------------------------------------------------------------------
subroutine parallelization_init
integer :: err, typeSize
integer(MPI_INTEGER_KIND) :: err_MPI, typeSize
character(len=4) :: rank_str
!$ integer :: got_env, threadLevel
!$ integer(pI32) :: OMP_NUM_THREADS
!$ character(len=6) NumThreadsString
PetscErrorCode :: petsc_err
PetscErrorCode :: err_PETSc
#ifdef _OPENMP
! If openMP is enabled, check if the MPI libary supports it and initialize accordingly.
! Otherwise, the first call to PETSc will do the initialization.
call MPI_Init_Thread(MPI_THREAD_FUNNELED,threadLevel,err)
if (err /= 0) error stop 'MPI init failed'
call MPI_Init_Thread(MPI_THREAD_FUNNELED,threadLevel,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI init failed'
if (threadLevel<MPI_THREAD_FUNNELED) error stop 'MPI library does not support OpenMP'
#endif
#if defined(DEBUG)
call PetscInitialize(PETSC_NULL_CHARACTER,petsc_err)
call PetscInitialize(PETSC_NULL_CHARACTER,err_PETSc)
#else
call PetscInitializeNoArguments(petsc_err)
call PetscInitializeNoArguments(err_PETSc)
#endif
CHKERRQ(petsc_err)
CHKERRQ(err_PETSc)
#if defined(DEBUG) && defined(__INTEL_COMPILER)
call PetscSetFPTrap(PETSC_FP_TRAP_ON,petsc_err)
call PetscSetFPTrap(PETSC_FP_TRAP_ON,err_PETSc)
#else
call PetscSetFPTrap(PETSC_FP_TRAP_OFF,petsc_err)
call PetscSetFPTrap(PETSC_FP_TRAP_OFF,err_PETSc)
#endif
CHKERRQ(petsc_err)
CHKERRQ(err_PETSc)
call MPI_Comm_rank(MPI_COMM_WORLD,worldrank,err)
if (err /= 0) error stop 'Could not determine worldrank'
call MPI_Comm_rank(MPI_COMM_WORLD,worldrank,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) &
error stop 'Could not determine worldrank'
if (worldrank == 0) print'(/,1x,a)', '<<<+- parallelization init -+>>>'
call MPI_Comm_size(MPI_COMM_WORLD,worldsize,err)
if (err /= 0) error stop 'Could not determine worldsize'
call MPI_Comm_size(MPI_COMM_WORLD,worldsize,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) &
error stop 'Could not determine worldsize'
if (worldrank == 0) print'(/,1x,a,i3)', 'MPI processes: ',worldsize
call MPI_Type_size(MPI_INTEGER,typeSize,err)
if (err /= 0) error stop 'Could not determine MPI integer size'
if (typeSize*8 /= bit_size(0)) error stop 'Mismatch between MPI and DAMASK integer'
call MPI_Type_size(MPI_INTEGER,typeSize,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) &
error stop 'Could not determine size of MPI_INTEGER'
if (typeSize*8_MPI_INTEGER_KIND /= int(bit_size(0),MPI_INTEGER_KIND)) &
error stop 'Mismatch between MPI_INTEGER and DAMASK default integer'
call MPI_Type_size(MPI_DOUBLE,typeSize,err)
if (err /= 0) error stop 'Could not determine MPI real size'
if (typeSize*8 /= storage_size(0.0_pReal)) error stop 'Mismatch between MPI and DAMASK real'
call MPI_Type_size(MPI_INTEGER8,typeSize,err_MPI)
if (err_MPI /= 0) &
error stop 'Could not determine size of MPI_INTEGER8'
if (typeSize*8_MPI_INTEGER_KIND /= int(bit_size(0_pI64),MPI_INTEGER_KIND)) &
error stop 'Mismatch between MPI_INTEGER8 and DAMASK pI64'
call MPI_Type_size(MPI_DOUBLE,typeSize,err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) &
error stop 'Could not determine size of MPI_DOUBLE'
if (typeSize*8_MPI_INTEGER_KIND /= int(storage_size(0.0_pReal),MPI_INTEGER_KIND)) &
error stop 'Mismatch between MPI_DOUBLE and DAMASK pReal'
if (worldrank /= 0) then
close(OUTPUT_UNIT) ! disable output
write(rank_str,'(i4.4)') worldrank ! use for MPI debug filenames
open(OUTPUT_UNIT,file='/dev/null',status='replace') ! close() alone will leave some temp files in cwd
endif
@ -119,14 +141,14 @@ subroutine parallelization_bcast_str(string)
character(len=:), allocatable, intent(inout) :: string
integer :: strlen, ierr ! pI64 for strlen not supported by MPI
integer(MPI_INTEGER_KIND) :: strlen, err_MPI
if (worldrank == 0) strlen = len(string)
call MPI_Bcast(strlen,1,MPI_INTEGER,0,MPI_COMM_WORLD, ierr)
if (worldrank == 0) strlen = len(string,MPI_INTEGER_KIND)
call MPI_Bcast(strlen,1_MPI_INTEGER_KIND,MPI_INTEGER,0_MPI_INTEGER_KIND,MPI_COMM_WORLD, err_MPI)
if (worldrank /= 0) allocate(character(len=strlen)::string)
call MPI_Bcast(string,strlen,MPI_CHARACTER,0,MPI_COMM_WORLD, ierr)
call MPI_Bcast(string,strlen,MPI_CHARACTER,0_MPI_INTEGER_KIND,MPI_COMM_WORLD, err_MPI)
end subroutine parallelization_bcast_str

1
src/phase.f90
View File

@ -8,6 +8,7 @@ module phase
use constants
use math
use rotations
use polynomials
use IO
use config
use material

4
src/phase_mechanical_eigen_thermalexpansion.f90
View File

@ -99,11 +99,11 @@ module subroutine thermalexpansion_LiAndItsTangent(Li, dLi_dTstar, ph,me)
associate(prm => param(kinematics_thermal_expansion_instance(ph)))
Li = dot_T * ( &
prm%A(1:3,1:3,1) & ! constant coefficient
+ prm%A(1:3,1:3,2)*(T - prm%T_ref)**1 & ! linear coefficient
+ prm%A(1:3,1:3,2)*(T - prm%T_ref) & ! linear coefficient
+ prm%A(1:3,1:3,3)*(T - prm%T_ref)**2 & ! quadratic coefficient
) / &
(1.0_pReal &
+ prm%A(1:3,1:3,1)*(T - prm%T_ref)**1 / 1.0_pReal &
+ prm%A(1:3,1:3,1)*(T - prm%T_ref) / 1.0_pReal &
+ prm%A(1:3,1:3,2)*(T - prm%T_ref)**2 / 2.0_pReal &
+ prm%A(1:3,1:3,3)*(T - prm%T_ref)**3 / 3.0_pReal &
)

80
src/phase_mechanical_elastic.f90
View File

@ -1,15 +1,13 @@
submodule(phase:mechanical) elastic
type :: tParameters
real(pReal),dimension(3) :: &
C_11 = 0.0_pReal, &
C_12 = 0.0_pReal, &
C_13 = 0.0_pReal, &
C_33 = 0.0_pReal, &
C_44 = 0.0_pReal, &
C_66 = 0.0_pReal
real(pReal) :: &
T_ref
type(tPolynomial) :: &
C_11, &
C_12, &
C_13, &
C_33, &
C_44, &
C_66
end type tParameters
type(tParameters), allocatable, dimension(:) :: param
@ -47,35 +45,17 @@ module subroutine elastic_init(phases)
associate(prm => param(ph))
prm%T_ref = elastic%get_asFloat('T_ref', defaultVal=T_ROOM)
prm%C_11(1) = elastic%get_asFloat('C_11')
prm%C_11(2) = elastic%get_asFloat('C_11,T', defaultVal=0.0_pReal)
prm%C_11(3) = elastic%get_asFloat('C_11,T^2',defaultVal=0.0_pReal)
prm%C_12(1) = elastic%get_asFloat('C_12')
prm%C_12(2) = elastic%get_asFloat('C_12,T', defaultVal=0.0_pReal)
prm%C_12(3) = elastic%get_asFloat('C_12,T^2',defaultVal=0.0_pReal)
prm%C_44(1) = elastic%get_asFloat('C_44')
prm%C_44(2) = elastic%get_asFloat('C_44,T', defaultVal=0.0_pReal)
prm%C_44(3) = elastic%get_asFloat('C_44,T^2',defaultVal=0.0_pReal)
prm%C_11 = polynomial(elastic%asDict(),'C_11','T')
prm%C_12 = polynomial(elastic%asDict(),'C_12','T')
prm%C_44 = polynomial(elastic%asDict(),'C_44','T')
if (any(phase_lattice(ph) == ['hP','tI'])) then
prm%C_13(1) = elastic%get_asFloat('C_13')
prm%C_13(2) = elastic%get_asFloat('C_13,T', defaultVal=0.0_pReal)
prm%C_13(3) = elastic%get_asFloat('C_13,T^2',defaultVal=0.0_pReal)
prm%C_33(1) = elastic%get_asFloat('C_33')
prm%C_33(2) = elastic%get_asFloat('C_33,T', defaultVal=0.0_pReal)
prm%C_33(3) = elastic%get_asFloat('C_33,T^2',defaultVal=0.0_pReal)
prm%C_13 = polynomial(elastic%asDict(),'C_13','T')
prm%C_33 = polynomial(elastic%asDict(),'C_33','T')
end if
if (phase_lattice(ph) == 'tI') then
prm%C_66(1) = elastic%get_asFloat('C_66')
prm%C_66(2) = elastic%get_asFloat('C_66,T', defaultVal=0.0_pReal)
prm%C_66(3) = elastic%get_asFloat('C_66,T^2',defaultVal=0.0_pReal)
end if
if (phase_lattice(ph) == 'tI') &
prm%C_66 = polynomial(elastic%asDict(),'C_66','T')
end associate
end do
@ -97,38 +77,20 @@ pure module function elastic_C66(ph,en) result(C66)
associate(prm => param(ph))
C66 = 0.0_pReal
T = thermal_T(ph,en)
C66(1,1) = prm%C_11(1) &
+ prm%C_11(2)*(T - prm%T_ref)**1 &
+ prm%C_11(3)*(T - prm%T_ref)**2
C66(1,2) = prm%C_12(1) &
+ prm%C_12(2)*(T - prm%T_ref)**1 &
+ prm%C_12(3)*(T - prm%T_ref)**2
C66(4,4) = prm%C_44(1) &
+ prm%C_44(2)*(T - prm%T_ref)**1 &
+ prm%C_44(3)*(T - prm%T_ref)**2
C66(1,1) = prm%C_11%at(T)
C66(1,2) = prm%C_12%at(T)
C66(4,4) = prm%C_44%at(T)
if (any(phase_lattice(ph) == ['hP','tI'])) then
C66(1,3) = prm%C_13(1) &
+ prm%C_13(2)*(T - prm%T_ref)**1 &
+ prm%C_13(3)*(T - prm%T_ref)**2
C66(3,3) = prm%C_33(1) &
+ prm%C_33(2)*(T - prm%T_ref)**1 &
+ prm%C_33(3)*(T - prm%T_ref)**2
C66(1,3) = prm%C_13%at(T)
C66(3,3) = prm%C_33%at(T)
end if
if (phase_lattice(ph) == 'tI') then
C66(6,6) = prm%C_66(1) &
+ prm%C_66(2)*(T - prm%T_ref)**1 &
+ prm%C_66(3)*(T - prm%T_ref)**2
end if
if (phase_lattice(ph) == 'tI') C66(6,6) = prm%C_66%at(T)
C66 = lattice_symmetrize_C66(C66,phase_lattice(ph))

221
src/phase_mechanical_plastic_dislotwin.f90
View File

@ -17,17 +17,17 @@ submodule(phase:plastic) dislotwin
p_sb = 1.0_pReal, & !< p-exponent in shear band velocity
q_sb = 1.0_pReal, & !< q-exponent in shear band velocity
i_tw = 1.0_pReal, & !< adjustment parameter to calculate MFP for twinning
L_tw = 1.0_pReal, & !< Length of twin nuclei in Burgers vectors
L_tr = 1.0_pReal, & !< Length of trans nuclei in Burgers vectors
L_tw = 1.0_pReal, & !< length of twin nuclei in Burgers vectors: TODO unit should be meters
L_tr = 1.0_pReal, & !< length of trans nuclei in Burgers vectors: TODO unit should be meters
x_c_tw = 1.0_pReal, & !< critical distance for formation of twin nucleus
x_c_tr = 1.0_pReal, & !< critical distance for formation of trans nucleus
V_cs = 1.0_pReal, & !< cross slip volume
xi_sb = 1.0_pReal, & !< value for shearband resistance
v_sb = 1.0_pReal, & !< value for shearband velocity_0
E_sb = 1.0_pReal, & !< activation energy for shear bands
delta_G = 1.0_pReal, & !< Free energy difference between austensite and martensite
delta_G = 1.0_pReal, & !< free energy difference between austensite and martensite
i_tr = 1.0_pReal, & !< adjustment parameter to calculate MFP for transformation
h = 1.0_pReal, & !< Stack height of hex nucleus
h = 1.0_pReal, & !< stack height of hex nucleus
T_ref = T_ROOM, &
a_cI = 1.0_pReal, &
a_cF = 1.0_pReal
@ -40,14 +40,13 @@ submodule(phase:plastic) dislotwin
Q_sl,& !< activation energy for glide [J] for each slip system
v_0, & !< dislocation velocity prefactor [m/s] for each slip system
dot_N_0_tw, & !< twin nucleation rate [1/m³s] for each twin system
dot_N_0_tr, & !< trans nucleation rate [1/m³s] for each trans system
t_tw, & !< twin thickness [m] for each twin system
i_sl, & !< Adj. parameter for distance between 2 forest dislocations for each slip system
t_tr, & !< martensite lamellar thickness [m] for each trans system
p, & !< p-exponent in glide velocity
q, & !< q-exponent in glide velocity
r, & !< r-exponent in twin nucleation rate
s, & !< s-exponent in trans nucleation rate
r, & !< exponent in twin nucleation rate
s, & !< exponent in trans nucleation rate
tau_0, & !< strength due to elements in solid solution
gamma_char, & !< characteristic shear for twins
B, & !< drag coefficient
@ -102,11 +101,7 @@ submodule(phase:plastic) dislotwin
Lambda_tr, & !< mean free path between 2 obstacles seen by a growing martensite
tau_pass, & !< threshold stress for slip
tau_hat_tw, & !< threshold stress for twinning
tau_hat_tr, & !< threshold stress for transformation
V_tw, & !< volume of a new twin
V_tr, & !< volume of a new martensite disc
tau_r_tw, & !< stress to bring partials close together (twin)
tau_r_tr !< stress to bring partials close together (trans)
tau_hat_tr !< threshold stress for transformation
end type tDislotwinDependentState
!--------------------------------------------------------------------------------------------------
@ -153,10 +148,10 @@ module function plastic_dislotwin_init() result(myPlasticity)
print'(/,a,i0)', ' # phases: ',count(myPlasticity); flush(IO_STDOUT)
print'(/,1x,a)', 'A. Ma and F. Roters, Acta Materialia 52(12):3603–3612, 2004'
print'( 1x,a)', 'https://doi.org/10.1016/j.actamat.2004.04.012'//IO_EOL
print'( 1x,a)', 'https://doi.org/10.1016/j.actamat.2004.04.012'
print'(/,1x,a)', 'F. Roters et al., Computational Materials Science 39:91–95, 2007'
print'( 1x,a)', 'https://doi.org/10.1016/j.commatsci.2006.04.014'//IO_EOL
print'( 1x,a)', 'https://doi.org/10.1016/j.commatsci.2006.04.014'
print'(/,1x,a)', 'S.L. Wong et al., Acta Materialia 118:140–151, 2016'
print'( 1x,a)', 'https://doi.org/10.1016/j.actamat.2016.07.032'
@ -306,10 +301,10 @@ module function plastic_dislotwin_init() result(myPlasticity)
prm%b_tr = pl%get_as1dFloat('b_tr')
prm%b_tr = math_expand(prm%b_tr,prm%N_tr)
prm%h = pl%get_asFloat('h', defaultVal=0.0_pReal) ! ToDo: How to handle that???
prm%i_tr = pl%get_asFloat('i_tr', defaultVal=0.0_pReal) ! ToDo: How to handle that???
prm%h = pl%get_asFloat('h', defaultVal=0.0_pReal) ! ToDo: This is not optional!
prm%i_tr = pl%get_asFloat('i_tr', defaultVal=0.0_pReal) ! ToDo: This is not optional!
prm%delta_G = pl%get_asFloat('delta_G')
prm%x_c_tr = pl%get_asFloat('x_c_tr', defaultVal=0.0_pReal) ! ToDo: How to handle that???
prm%x_c_tr = pl%get_asFloat('x_c_tr', defaultVal=0.0_pReal) ! ToDo: This is not optional!
prm%L_tr = pl%get_asFloat('L_tr')
prm%a_cI = pl%get_asFloat('a_cI', defaultVal=0.0_pReal)
prm%a_cF = pl%get_asFloat('a_cF', defaultVal=0.0_pReal)
@ -324,10 +319,6 @@ module function plastic_dislotwin_init() result(myPlasticity)
prm%a_cI, &
prm%a_cF)
if (phase_lattice(ph) /= 'cF') then
prm%dot_N_0_tr = pl%get_as1dFloat('dot_N_0_tr')
prm%dot_N_0_tr = math_expand(prm%dot_N_0_tr,prm%N_tr)
endif
prm%t_tr = pl%get_as1dFloat('t_tr')
prm%t_tr = math_expand(prm%t_tr,prm%N_tr)
prm%s = pl%get_as1dFloat('p_tr',defaultVal=[0.0_pReal])
@ -339,11 +330,8 @@ module function plastic_dislotwin_init() result(myPlasticity)
if ( prm%i_tr < 0.0_pReal) extmsg = trim(extmsg)//' i_tr'
if (any(prm%t_tr < 0.0_pReal)) extmsg = trim(extmsg)//' t_tr'
if (any(prm%s < 0.0_pReal)) extmsg = trim(extmsg)//' p_tr'
if (phase_lattice(ph) /= 'cF') then
if (any(prm%dot_N_0_tr < 0.0_pReal)) extmsg = trim(extmsg)//' dot_N_0_tr'
end if
else transActive
allocate(prm%s,prm%b_tr,prm%t_tr,prm%dot_N_0_tr,source=emptyRealArray)
allocate(prm%s,prm%b_tr,prm%t_tr,source=emptyRealArray)
allocate(prm%h_tr_tr(0,0))
end if transActive
@ -443,13 +431,9 @@ module function plastic_dislotwin_init() result(myPlasticity)
allocate(dst%Lambda_tw (prm%sum_N_tw,Nmembers),source=0.0_pReal)
allocate(dst%tau_hat_tw (prm%sum_N_tw,Nmembers),source=0.0_pReal)
allocate(dst%tau_r_tw (prm%sum_N_tw,Nmembers),source=0.0_pReal)
allocate(dst%V_tw (prm%sum_N_tw,Nmembers),source=0.0_pReal)
allocate(dst%Lambda_tr (prm%sum_N_tr,Nmembers),source=0.0_pReal)
allocate(dst%tau_hat_tr (prm%sum_N_tr,Nmembers),source=0.0_pReal)
allocate(dst%tau_r_tr (prm%sum_N_tr,Nmembers),source=0.0_pReal)
allocate(dst%V_tr (prm%sum_N_tr,Nmembers),source=0.0_pReal)
end associate
@ -656,12 +640,14 @@ module subroutine dislotwin_dotState(Mp,T,ph,en)
dot_gamma_tr
real(pReal) :: &
mu, &
nu
nu, &
Gamma
associate(prm => param(ph), stt => state(ph), dot => dotState(ph), dst => dependentState(ph))
mu = elastic_mu(ph,en)
nu = elastic_nu(ph,en)
Gamma = prm%Gamma_sf(1) + prm%Gamma_sf(2) * (T-prm%T_ref)
f_matrix = 1.0_pReal &
- sum(stt%f_tw(1:prm%sum_N_tw,en)) &
@ -689,8 +675,7 @@ module subroutine dislotwin_dotState(Mp,T,ph,en)
else
! Argon & Moffat, Acta Metallurgica, Vol. 29, pg 293 to 299, 1981
sigma_cl = dot_product(prm%n0_sl(1:3,i),matmul(Mp,prm%n0_sl(1:3,i)))
b_d = merge(24.0_pReal*PI*(1.0_pReal - nu)/(2.0_pReal + nu) &
* (prm%Gamma_sf(1) + prm%Gamma_sf(2) * T) / (mu*prm%b_sl(i)), &
b_d = merge(24.0_pReal*PI*(1.0_pReal - nu)/(2.0_pReal + nu) * Gamma / (mu*prm%b_sl(i)), &
1.0_pReal, &
prm%ExtendedDislocations)
v_cl = 2.0_pReal*prm%omega*b_d**2*exp(-prm%Q_cl/(K_B*T)) &
@ -742,8 +727,6 @@ module subroutine dislotwin_dependentState(T,ph,en)
real(pReal), dimension(param(ph)%sum_N_tr) :: &
inv_lambda_tr_tr, & !< 1/mean free distance between 2 martensite stacks from different systems seen by a growing martensite
f_over_t_tr
real(pReal), dimension(:), allocatable :: &
x0
real(pReal) :: &
mu, &
nu
@ -756,7 +739,7 @@ module subroutine dislotwin_dependentState(T,ph,en)
sumf_tw = sum(stt%f_tw(1:prm%sum_N_tw,en))
sumf_tr = sum(stt%f_tr(1:prm%sum_N_tr,en))
Gamma = prm%Gamma_sf(1) + prm%Gamma_sf(2) * T
Gamma = prm%Gamma_sf(1) + prm%Gamma_sf(2) * (T-prm%T_ref)
!* rescaled volume fraction for topology
f_over_t_tw = stt%f_tw(1:prm%sum_N_tw,en)/prm%t_tw ! this is per system ...
@ -786,16 +769,6 @@ module subroutine dislotwin_dependentState(T,ph,en)
+ 3.0_pReal*prm%b_tr*mu/(prm%L_tr*prm%b_tr) &
+ prm%h*prm%delta_G/(3.0_pReal*prm%b_tr)
dst%V_tw(:,en) = (PI/4.0_pReal)*prm%t_tw*dst%Lambda_tw(:,en)**2
dst%V_tr(:,en) = (PI/4.0_pReal)*prm%t_tr*dst%Lambda_tr(:,en)**2
x0 = mu*prm%b_tw**2/(Gamma*8.0_pReal*PI)*(2.0_pReal+nu)/(1.0_pReal-nu) ! ToDo: In the paper, this is the Burgers vector for slip
dst%tau_r_tw(:,en) = mu*prm%b_tw/(2.0_pReal*PI)*(1.0_pReal/(x0+prm%x_c_tw)+cos(pi/3.0_pReal)/x0)
x0 = mu*prm%b_tr**2/(Gamma*8.0_pReal*PI)*(2.0_pReal+nu)/(1.0_pReal-nu) ! ToDo: In the paper, this is the Burgers vector for slip
dst%tau_r_tr(:,en) = mu*prm%b_tr/(2.0_pReal*PI)*(1.0_pReal/(x0+prm%x_c_tr)+cos(pi/3.0_pReal)/x0)
end associate
end subroutine dislotwin_dependentState
@ -959,48 +932,68 @@ pure subroutine kinetics_tw(Mp,T,dot_gamma_sl,ph,en,&
real(pReal), dimension(param(ph)%sum_N_tw), optional, intent(out) :: &
ddot_gamma_dtau_tw
real, dimension(param(ph)%sum_N_tw) :: &
tau, &
Ndot0, &
stressRatio_r, &
ddot_gamma_dtau
integer :: i,s1,s2
real :: &
tau, tau_r, &
dot_N_0, &
x0, V, &
Gamma, &
mu, nu, &
P_ncs, dP_ncs_dtau, &
P, dP_dtau
integer, dimension(2) :: &
s
integer :: i
associate(prm => param(ph), stt => state(ph), dst => dependentState(ph))
do i = 1, prm%sum_N_tw
tau(i) = math_tensordot(Mp,prm%P_tw(1:3,1:3,i))
isFCC: if (prm%fccTwinTransNucleation) then
s1=prm%fcc_twinNucleationSlipPair(1,i)
s2=prm%fcc_twinNucleationSlipPair(2,i)
if (tau(i) < dst%tau_r_tw(i,en)) then ! ToDo: correct?
Ndot0=(abs(dot_gamma_sl(s1))*(stt%rho_mob(s2,en)+stt%rho_dip(s2,en))+&
abs(dot_gamma_sl(s2))*(stt%rho_mob(s1,en)+stt%rho_dip(s1,en)))/&
(prm%L_tw*prm%b_sl(i))*&
(1.0_pReal-exp(-prm%V_cs/(K_B*T)*(dst%tau_r_tw(i,en)-tau(i))))
else
Ndot0=0.0_pReal
end if
else isFCC
Ndot0=prm%dot_N_0_tw(i)
end if isFCC
end do
isFCC: if (prm%fccTwinTransNucleation) then
mu = elastic_mu(ph,en)
nu = elastic_nu(ph,en)
Gamma = prm%Gamma_sf(1) + prm%Gamma_sf(2) * (T-prm%T_ref)
significantStress: where(tau > tol_math_check)
StressRatio_r = (dst%tau_hat_tw(:,en)/tau)**prm%r
dot_gamma_tw = prm%gamma_char * dst%V_tw(:,en) * Ndot0*exp(-StressRatio_r)
ddot_gamma_dtau = (dot_gamma_tw*prm%r/tau)*StressRatio_r
else where significantStress
dot_gamma_tw = 0.0_pReal
ddot_gamma_dtau = 0.0_pReal
end where significantStress
do i = 1, prm%sum_N_tw
tau = math_tensordot(Mp,prm%P_tw(1:3,1:3,i))
x0 = mu*prm%b_tw(i)**2*(2.0_pReal+nu)/(Gamma*8.0_pReal*PI*(1.0_pReal-nu)) ! ToDo: In the paper, the Burgers vector for slip is used
tau_r = mu*prm%b_tw(i)/(2.0_pReal*PI)*(1.0_pReal/(x0+prm%x_c_tw)+cos(PI/3.0_pReal)/x0) ! ToDo: In the paper, the Burgers vector for slip is used
if (tau > tol_math_check .and. tau < tau_r) then
P = exp(-(dst%tau_hat_tw(i,en)/tau)**prm%r(i))
dP_dTau = prm%r(i) * (dst%tau_hat_tw(i,en)/tau)**prm%r(i)/tau * P
s = prm%fcc_twinNucleationSlipPair(1:2,i)
dot_N_0 = sum(abs(dot_gamma_sl(s(2:1:-1)))*(stt%rho_mob(s,en)+stt%rho_dip(s,en))) &
/ (prm%L_tw*prm%b_sl(i))
P_ncs = 1.0_pReal-exp(-prm%V_cs/(K_B*T)*(tau_r-tau))
dP_ncs_dtau = prm%V_cs / (K_B * T) * (P_ncs - 1.0_pReal)
V = PI/4.0_pReal*dst%Lambda_tw(i,en)**2*prm%t_tw(i)
dot_gamma_tw(i) = V*dot_N_0*P_ncs*P
if (present(ddot_gamma_dtau_tw)) &
ddot_gamma_dtau_tw(i) = V*dot_N_0*(P*dP_ncs_dtau + P_ncs*dP_dtau)
else
dot_gamma_tw(i) = 0.0_pReal
if (present(ddot_gamma_dtau_tw)) ddot_gamma_dtau_tw(i) = 0.0_pReal
end if
end do
else isFCC
do i = 1, prm%sum_N_tw
error stop 'not implemented'
tau = math_tensordot(Mp,prm%P_tw(1:3,1:3,i))
if (tau > tol_math_check) then
dot_gamma_tw(i) = 0.0_pReal
if (present(ddot_gamma_dtau_tw)) ddot_gamma_dtau_tw(i) = 0.0_pReal
else
dot_gamma_tw(i) = 0.0_pReal
if (present(ddot_gamma_dtau_tw)) ddot_gamma_dtau_tw(i) = 0.0_pReal
end if
end do
end if isFCC
end associate
if (present(ddot_gamma_dtau_tw)) ddot_gamma_dtau_tw = ddot_gamma_dtau
end subroutine kinetics_tw
@ -1029,47 +1022,53 @@ pure subroutine kinetics_tr(Mp,T,dot_gamma_sl,ph,en,&
real(pReal), dimension(param(ph)%sum_N_tr), optional, intent(out) :: &
ddot_gamma_dtau_tr
real, dimension(param(ph)%sum_N_tr) :: &
tau, &
Ndot0, &
stressRatio_s, &
ddot_gamma_dtau
integer :: i,s1,s2
real :: &
tau, tau_r, &
dot_N_0, &
x0, V, &
Gamma, &
mu, nu, &
P_ncs, dP_ncs_dtau, &
P, dP_dtau
integer, dimension(2) :: &
s
integer :: i
associate(prm => param(ph), stt => state(ph), dst => dependentState(ph))
mu = elastic_mu(ph,en)
nu = elastic_nu(ph,en)
Gamma = prm%Gamma_sf(1) + prm%Gamma_sf(2) * (T-prm%T_ref)
do i = 1, prm%sum_N_tr
tau(i) = math_tensordot(Mp,prm%P_tr(1:3,1:3,i))
isFCC: if (prm%fccTwinTransNucleation) then
s1=prm%fcc_twinNucleationSlipPair(1,i)
s2=prm%fcc_twinNucleationSlipPair(2,i)
if (tau(i) < dst%tau_r_tr(i,en)) then ! ToDo: correct?
Ndot0=(abs(dot_gamma_sl(s1))*(stt%rho_mob(s2,en)+stt%rho_dip(s2,en))+&
abs(dot_gamma_sl(s2))*(stt%rho_mob(s1,en)+stt%rho_dip(s1,en)))/&
(prm%L_tr*prm%b_sl(i))*&
(1.0_pReal-exp(-prm%V_cs/(K_B*T)*(dst%tau_r_tr(i,en)-tau(i))))
else
Ndot0=0.0_pReal
end if
else isFCC
Ndot0=prm%dot_N_0_tr(i)
end if isFCC
tau = math_tensordot(Mp,prm%P_tr(1:3,1:3,i))
x0 = mu*prm%b_tr(i)**2*(2.0_pReal+nu)/(Gamma*8.0_pReal*PI*(1.0_pReal-nu)) ! ToDo: In the paper, the Burgers vector for slip is used
tau_r = mu*prm%b_tr(i)/(2.0_pReal*PI)*(1.0_pReal/(x0+prm%x_c_tr)+cos(PI/3.0_pReal)/x0) ! ToDo: In the paper, the Burgers vector for slip is used
if (tau > tol_math_check .and. tau < tau_r) then
P = exp(-(dst%tau_hat_tr(i,en)/tau)**prm%s(i))
dP_dTau = prm%s(i) * (dst%tau_hat_tr(i,en)/tau)**prm%s(i)/tau * P
s = prm%fcc_twinNucleationSlipPair(1:2,i)
dot_N_0 = sum(abs(dot_gamma_sl(s(2:1:-1)))*(stt%rho_mob(s,en)+stt%rho_dip(s,en))) &
/ (prm%L_tr*prm%b_sl(i))
P_ncs = 1.0_pReal-exp(-prm%V_cs/(K_B*T)*(tau_r-tau))
dP_ncs_dtau = prm%V_cs / (K_B * T) * (P_ncs - 1.0_pReal)
V = PI/4.0_pReal*dst%Lambda_tr(i,en)**2*prm%t_tr(i)
dot_gamma_tr(i) = V*dot_N_0*P_ncs*P
if (present(ddot_gamma_dtau_tr)) &
ddot_gamma_dtau_tr(i) = V*dot_N_0*(P*dP_ncs_dtau + P_ncs*dP_dtau)
else
dot_gamma_tr(i) = 0.0_pReal
if (present(ddot_gamma_dtau_tr)) ddot_gamma_dtau_tr(i) = 0.0_pReal
end if
end do
significantStress: where(tau > tol_math_check)
StressRatio_s = (dst%tau_hat_tr(:,en)/tau)**prm%s
dot_gamma_tr = dst%V_tr(:,en) * Ndot0*exp(-StressRatio_s)
ddot_gamma_dtau = (dot_gamma_tr*prm%s/tau)*StressRatio_s
else where significantStress
dot_gamma_tr = 0.0_pReal
ddot_gamma_dtau = 0.0_pReal
end where significantStress
end associate
if (present(ddot_gamma_dtau_tr)) ddot_gamma_dtau_tr = ddot_gamma_dtau
end subroutine kinetics_tr
end submodule dislotwin

3
src/phase_mechanical_plastic_nonlocal.f90
View File

@ -203,7 +203,7 @@ module function plastic_nonlocal_init() result(myPlasticity)
print'(/,a,i0)', ' # phases: ',Ninstances; flush(IO_STDOUT)
print'(/,1x,a)', 'C. Reuber et al., Acta Materialia 71:333–348, 2014'
print'( 1x,a)', 'https://doi.org/10.1016/j.actamat.2014.03.012'//IO_EOL
print'( 1x,a)', 'https://doi.org/10.1016/j.actamat.2014.03.012'
print'(/,1x,a)', 'C. Kords, Dissertation RWTH Aachen, 2014'
print'( 1x,a)', 'http://publications.rwth-aachen.de/record/229993'
@ -1570,7 +1570,6 @@ subroutine stateInit(ini,phase,Nentries)
upto, &
s
real(pReal), dimension(2) :: &
noise, &
rnd
real(pReal) :: &
meanDensity, &

179
src/polynomials.f90 Normal file
View File

@ -0,0 +1,179 @@
!--------------------------------------------------------------------------------------------------
!> @author Martin Diehl, KU Leuven
!> @brief Polynomial representation for variable data
!--------------------------------------------------------------------------------------------------
module polynomials
use prec
use IO
use YAML_parse
use YAML_types
implicit none
private
type, public :: tPolynomial
real(pReal), dimension(:), allocatable :: coef
real(pReal) :: x_ref
contains
procedure, public :: at => eval
procedure, public :: der1_at => eval_der1
end type tPolynomial
interface polynomial
module procedure polynomial_from_dict
module procedure polynomial_from_coef
end interface polynomial
public :: &
polynomial, &
polynomials_init
contains
!--------------------------------------------------------------------------------------------------
!> @brief Run self-test.
!--------------------------------------------------------------------------------------------------
subroutine polynomials_init()
print'(/,1x,a)', '<<<+- polynomials init -+>>>'; flush(IO_STDOUT)
call selfTest()
end subroutine polynomials_init
!--------------------------------------------------------------------------------------------------
!> @brief Initialize a Polynomial from Coefficients.
!--------------------------------------------------------------------------------------------------
function polynomial_from_coef(coef,x_ref) result(p)
real(pReal), dimension(:), intent(in) :: coef
real(pReal), intent(in) :: x_ref
type(tPolynomial) :: p
allocate(p%coef(0:size(coef)-1),source=coef) ! should be zero based
p%x_ref = x_ref
end function polynomial_from_coef
!--------------------------------------------------------------------------------------------------
!> @brief Initialize a Polynomial from a Dictionary with Coefficients.
!--------------------------------------------------------------------------------------------------
function polynomial_from_dict(dict,y,x) result(p)
type(tDict), intent(in) :: dict
character(len=*), intent(in) :: y, x
type(tPolynomial) :: p
real(pReal), dimension(:), allocatable :: coef
real(pReal) :: x_ref
allocate(coef(1),source=dict%get_asFloat(y))
if (dict%contains(y//','//x)) then
x_ref = dict%get_asFloat(x//'_ref')
coef = [coef,dict%get_asFloat(y//','//x)]
if (dict%contains(y//','//x//'^2')) then
coef = [coef,dict%get_asFloat(y//','//x//'^2')]
end if
else
x_ref = huge(0.0_pReal) ! Simplify debugging
end if
p = Polynomial(coef,x_ref)
end function polynomial_from_dict
!--------------------------------------------------------------------------------------------------
!> @brief Evaluate a Polynomial.
!--------------------------------------------------------------------------------------------------
pure function eval(self,x) result(y)
class(tPolynomial), intent(in) :: self
real(pReal), intent(in) :: x
real(pReal) :: y
integer :: i
y = self%coef(0)
do i = 1, ubound(self%coef,1)
y = y + self%coef(i) * (x-self%x_ref)**i
enddo
end function eval
!--------------------------------------------------------------------------------------------------
!> @brief Evaluate a first derivative of Polynomial.
!--------------------------------------------------------------------------------------------------
pure function eval_der1(self,x) result(y)
class(tPolynomial), intent(in) :: self
real(pReal), intent(in) :: x
real(pReal) :: y
integer :: i
y = 0.0_pReal
do i = 1, ubound(self%coef,1)
y = y + real(i,pReal)*self%coef(i) * (x-self%x_ref)**(i-1)
enddo
end function eval_der1
!--------------------------------------------------------------------------------------------------
!> @brief Check correctness of polynomical functionality.
!--------------------------------------------------------------------------------------------------
subroutine selfTest
type(tPolynomial) :: p1, p2
real(pReal), dimension(3) :: coef
real(pReal) :: x_ref, x
class(tNode), pointer :: dict
character(len=pStringLen), dimension(3) :: coef_s
character(len=pStringLen) :: x_ref_s, x_s, YAML_s
call random_number(coef)
call random_number(x_ref)
call random_number(x)
coef = coef*10_pReal -0.5_pReal
x_ref = x_ref*10_pReal -0.5_pReal
x = x*10_pReal -0.5_pReal
p1 = polynomial(coef,x_ref)
if (dNeq(p1%at(x_ref),coef(1))) error stop 'polynomial: @ref'
write(coef_s(1),*) coef(1)
write(coef_s(2),*) coef(2)
write(coef_s(3),*) coef(3)
write(x_ref_s,*) x_ref
write(x_s,*) x
YAML_s = 'C: '//trim(adjustl(coef_s(1)))//IO_EOL//&
'C,T: '//trim(adjustl(coef_s(2)))//IO_EOL//&
'C,T^2: '//trim(adjustl(coef_s(3)))//IO_EOL//&
'T_ref: '//trim(adjustl(x_ref_s))//IO_EOL
Dict => YAML_parse_str(trim(YAML_s))
p2 = polynomial(dict%asDict(),'C','T')
if (dNeq(p1%at(x),p2%at(x),1.0e-12_pReal)) error stop 'polynomials: init'
p1 = polynomial(coef*[0.0_pReal,1.0_pReal,0.0_pReal],x_ref)
if (dNeq(p1%at(x_ref+x),-p1%at(x_ref-x),1.0e-10_pReal)) error stop 'polynomials: eval(odd)'
if (dNeq(p1%der1_at(x),p1%der1_at(5.0_pReal*x),1.0e-10_pReal)) error stop 'polynomials: eval_der(odd)'
p1 = polynomial(coef*[0.0_pReal,0.0_pReal,1.0_pReal],x_ref)
if (dNeq(p1%at(x_ref+x),p1%at(x_ref-x),1e-10_pReal)) error stop 'polynomials: eval(even)'
if (dNeq(p1%der1_at(x_ref+x),-p1%der1_at(x_ref-x),1e-10_pReal)) error stop 'polynomials: eval_der(even)'
end subroutine selfTest
end module polynomials

26
src/prec.f90
View File

@ -10,6 +10,11 @@ module prec
use, intrinsic :: IEEE_arithmetic
use, intrinsic :: ISO_C_binding
#ifdef PETSC
#include <petsc/finclude/petscsys.h>
use PETScSys
#endif
implicit none
public
@ -17,13 +22,12 @@ module prec
integer, parameter :: pReal = IEEE_selected_real_kind(15,307) !< number with 15 significant digits, up to 1e+-307 (typically 64 bit)
integer, parameter :: pI32 = selected_int_kind(9) !< number with at least up to +-1e9 (typically 32 bit)
integer, parameter :: pI64 = selected_int_kind(18) !< number with at least up to +-1e18 (typically 64 bit)
#if(INT==8)
integer, parameter :: pInt = pI64
#else
integer, parameter :: pInt = pI32
#ifdef PETSC
PetscInt, private :: dummy
integer, parameter :: pPETSCINT = kind(dummy)
#endif
integer, parameter :: pStringLen = 256 !< default string length
integer, parameter :: pPathLen = 4096 !< maximum length of a path name on linux
integer, parameter :: pSTRINGLEN = 256 !< default string length
integer, parameter :: pPATHLEN = 4096 !< maximum length of a path name on linux
real(pReal), parameter :: tol_math_check = 1.0e-8_pReal !< tolerance for internal math self-checks (rotation)
@ -268,7 +272,7 @@ subroutine selfTest
integer, allocatable, dimension(:) :: realloc_lhs_test
real(pReal), dimension(1) :: f
integer(pInt), dimension(1) :: i
integer(pI64), dimension(1) :: i
real(pReal), dimension(2) :: r
@ -289,11 +293,11 @@ subroutine selfTest
f = real(prec_bytesToC_DOUBLE(int([0,0,0,-32,+119,+65,+115,65],C_SIGNED_CHAR)),pReal)
if (dNeq(f(1),20191102.0_pReal,0.0_pReal)) error stop 'prec_bytesToC_DOUBLE'
i = int(prec_bytesToC_INT32_T(int([+126,+23,+52,+1],C_SIGNED_CHAR)),pInt)
if (i(1) /= 20191102_pInt) error stop 'prec_bytesToC_INT32_T'
i = int(prec_bytesToC_INT32_T(int([+126,+23,+52,+1],C_SIGNED_CHAR)),pI64)
if (i(1) /= 20191102_pI64) error stop 'prec_bytesToC_INT32_T'
i = int(prec_bytesToC_INT64_T(int([+126,+23,+52,+1,0,0,0,0],C_SIGNED_CHAR)),pInt)
if (i(1) /= 20191102_pInt) error stop 'prec_bytesToC_INT64_T'
i = int(prec_bytesToC_INT64_T(int([+126,+23,+52,+1,0,0,0,0],C_SIGNED_CHAR)),pI64)
if (i(1) /= 20191102_pI64) error stop 'prec_bytesToC_INT64_T'
end subroutine selfTest

28
src/quit.f90
View File

@ -15,20 +15,23 @@ subroutine quit(stop_id)
implicit none
integer, intent(in) :: stop_id
integer, dimension(8) :: dateAndTime
integer :: error
PetscErrorCode :: ierr = 0
integer :: err_HDF5
integer(MPI_INTEGER_KIND) :: err_MPI
PetscErrorCode :: err_PETSc
call h5open_f(error)
if (error /= 0) write(6,'(a,i5)') ' Error in h5open_f ',error ! prevents error if not opened yet
call h5close_f(error)
if (error /= 0) write(6,'(a,i5)') ' Error in h5close_f ',error
call h5open_f(err_HDF5)
if (err_HDF5 /= 0_MPI_INTEGER_KIND) write(6,'(a,i5)') ' Error in h5open_f ',err_HDF5 ! prevents error if not opened yet
call h5close_f(err_HDF5)
if (err_HDF5 /= 0_MPI_INTEGER_KIND) write(6,'(a,i5)') ' Error in h5close_f ',err_HDF5
call PetscFinalize(ierr)
CHKERRQ(ierr)
call PetscFinalize(err_PETSc)
CHKERRQ(err_PETSc)
#ifdef _OPENMP
call MPI_finalize(error)
if (error /= 0) write(6,'(a,i5)') ' Error in MPI_finalize',error
call MPI_finalize(err_MPI)
if (err_MPI /= 0_MPI_INTEGER_KIND) write(6,'(a,i5)') ' Error in MPI_finalize',err_MPI
#else
err_MPI = 0_MPI_INTEGER_KIND
#endif
call date_and_time(values = dateAndTime)
@ -40,7 +43,10 @@ subroutine quit(stop_id)
dateAndTime(6),':',&
dateAndTime(7)
if (stop_id == 0 .and. ierr == 0 .and. error == 0) stop 0 ! normal termination
if (stop_id == 0 .and. &
err_HDF5 == 0 .and. &
err_MPI == 0_MPI_INTEGER_KIND .and. &
err_PETSC == 0) stop 0 ! normal termination
stop 1 ! error (message from IO_error)
end subroutine quit

66
src/results.f90
View File

@ -497,16 +497,17 @@ subroutine results_mapping_phase(ID,entry,label)
integer, dimension(:,:), intent(in) :: entry !< phase entry at (co,ce)
character(len=*), dimension(:), intent(in) :: label !< label of each phase section
integer, dimension(size(entry,1),size(entry,2)) :: &
integer(pI64), dimension(size(entry,1),size(entry,2)) :: &
entryGlobal
integer, dimension(size(label),0:worldsize-1) :: entryOffset !< offset in entry counting per process
integer, dimension(0:worldsize-1) :: writeSize !< amount of data written per process
integer(pI64), dimension(size(label),0:worldsize-1) :: entryOffset !< offset in entry counting per process
integer, dimension(0:worldsize-1) :: writeSize !< amount of data written per process
integer(HSIZE_T), dimension(2) :: &
myShape, & !< shape of the dataset (this process)
myOffset, &
totalShape !< shape of the dataset (all processes)
integer(HID_T) :: &
pI64_t, & !< HDF5 type for pI64 (8 bit integer)
loc_id, & !< identifier of group in file
dtype_id, & !< identifier of compound data type
label_id, & !< identifier of label (string) in compound data type
@ -518,7 +519,8 @@ subroutine results_mapping_phase(ID,entry,label)
dt_id
integer(SIZE_T) :: type_size_string, type_size_int
integer :: hdferr, ierr, ce, co
integer :: hdferr, ce, co
integer(MPI_INTEGER_KIND) :: err_MPI
writeSize = 0
@ -528,28 +530,28 @@ subroutine results_mapping_phase(ID,entry,label)
if(hdferr < 0) error stop 'HDF5 error'
#ifndef PETSC
entryGlobal = entry -1 ! 0-based
entryGlobal = int(entry -1,pI64) ! 0-based
#else
!--------------------------------------------------------------------------------------------------
! MPI settings and communication
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call MPI_Allreduce(MPI_IN_PLACE,writeSize,worldsize,MPI_INT,MPI_SUM,MPI_COMM_WORLD,ierr) ! get output at each process
if(ierr /= 0) error stop 'MPI error'
call MPI_Allreduce(MPI_IN_PLACE,writeSize,worldsize,MPI_INTEGER,MPI_SUM,MPI_COMM_WORLD,err_MPI) ! get output at each process
if(err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
entryOffset = 0
entryOffset = 0_pI64
do co = 1, size(ID,1)
do ce = 1, size(ID,2)
entryOffset(ID(co,ce),worldrank) = entryOffset(ID(co,ce),worldrank) +1
entryOffset(ID(co,ce),worldrank) = entryOffset(ID(co,ce),worldrank) +1_pI64
end do
end do
call MPI_Allreduce(MPI_IN_PLACE,entryOffset,size(entryOffset),MPI_INT,MPI_SUM,MPI_COMM_WORLD,ierr)! get offset at each process
if(ierr /= 0) error stop 'MPI error'
call MPI_Allreduce(MPI_IN_PLACE,entryOffset,size(entryOffset),MPI_INTEGER8,MPI_SUM,MPI_COMM_WORLD,err_MPI)! get offset at each process
if(err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
entryOffset(:,worldrank) = sum(entryOffset(:,0:worldrank-1),2)
do co = 1, size(ID,1)
do ce = 1, size(ID,2)
entryGlobal(co,ce) = entry(co,ce) -1 + entryOffset(ID(co,ce),worldrank)
entryGlobal(co,ce) = int(entry(co,ce),pI64) -1_pI64 + entryOffset(ID(co,ce),worldrank)
end do
end do
#endif
@ -567,14 +569,15 @@ subroutine results_mapping_phase(ID,entry,label)
call h5tget_size_f(dt_id, type_size_string, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5tget_size_f(H5T_NATIVE_INTEGER, type_size_int, hdferr)
pI64_t = h5kind_to_type(kind(entryGlobal),H5_INTEGER_KIND)
call h5tget_size_f(pI64_t, type_size_int, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5tcreate_f(H5T_COMPOUND_F, type_size_string + type_size_int, dtype_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5tinsert_f(dtype_id, 'label', 0_SIZE_T, dt_id,hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5tinsert_f(dtype_id, 'entry', type_size_string, H5T_NATIVE_INTEGER, hdferr)
call h5tinsert_f(dtype_id, 'entry', type_size_string, pI64_t, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
!--------------------------------------------------------------------------------------------------
@ -586,7 +589,7 @@ subroutine results_mapping_phase(ID,entry,label)
call h5tcreate_f(H5T_COMPOUND_F, type_size_int, entry_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5tinsert_f(entry_id, 'entry', 0_SIZE_T, H5T_NATIVE_INTEGER, hdferr)
call h5tinsert_f(entry_id, 'entry', 0_SIZE_T, pI64_t, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5tclose_f(dt_id, hdferr)
@ -650,16 +653,17 @@ subroutine results_mapping_homogenization(ID,entry,label)
integer, dimension(:), intent(in) :: entry !< homogenization entry at (ce)
character(len=*), dimension(:), intent(in) :: label !< label of each homogenization section
integer, dimension(size(entry,1)) :: &
integer(pI64), dimension(size(entry,1)) :: &
entryGlobal
integer, dimension(size(label),0:worldsize-1) :: entryOffset !< offset in entry counting per process
integer, dimension(0:worldsize-1) :: writeSize !< amount of data written per process
integer(pI64), dimension(size(label),0:worldsize-1) :: entryOffset !< offset in entry counting per process
integer, dimension(0:worldsize-1) :: writeSize !< amount of data written per process
integer(HSIZE_T), dimension(1) :: &
myShape, & !< shape of the dataset (this process)
myOffset, &
totalShape !< shape of the dataset (all processes)
integer(HID_T) :: &
pI64_t, & !< HDF5 type for pI64 (8 bit integer)
loc_id, & !< identifier of group in file
dtype_id, & !< identifier of compound data type
label_id, & !< identifier of label (string) in compound data type
@ -671,7 +675,8 @@ subroutine results_mapping_homogenization(ID,entry,label)
dt_id
integer(SIZE_T) :: type_size_string, type_size_int
integer :: hdferr, ierr, ce
integer :: hdferr, ce
integer(MPI_INTEGER_KIND) :: err_MPI
writeSize = 0
@ -681,25 +686,25 @@ subroutine results_mapping_homogenization(ID,entry,label)
if(hdferr < 0) error stop 'HDF5 error'
#ifndef PETSC
entryGlobal = entry -1 ! 0-based
entryGlobal = int(entry -1,pI64) ! 0-based
#else
!--------------------------------------------------------------------------------------------------
! MPI settings and communication
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call MPI_Allreduce(MPI_IN_PLACE,writeSize,worldsize,MPI_INT,MPI_SUM,MPI_COMM_WORLD,ierr) ! get output at each process
if(ierr /= 0) error stop 'MPI error'
call MPI_Allreduce(MPI_IN_PLACE,writeSize,worldsize,MPI_INTEGER,MPI_SUM,MPI_COMM_WORLD,err_MPI) ! get output at each process
if(err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
entryOffset = 0
entryOffset = 0_pI64
do ce = 1, size(ID,1)
entryOffset(ID(ce),worldrank) = entryOffset(ID(ce),worldrank) +1
entryOffset(ID(ce),worldrank) = entryOffset(ID(ce),worldrank) +1_pI64
end do
call MPI_Allreduce(MPI_IN_PLACE,entryOffset,size(entryOffset),MPI_INT,MPI_SUM,MPI_COMM_WORLD,ierr)! get offset at each process
if(ierr /= 0) error stop 'MPI error'
call MPI_Allreduce(MPI_IN_PLACE,entryOffset,size(entryOffset),MPI_INTEGER8,MPI_SUM,MPI_COMM_WORLD,err_MPI)! get offset at each process
if(err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
entryOffset(:,worldrank) = sum(entryOffset(:,0:worldrank-1),2)
do ce = 1, size(ID,1)
entryGlobal(ce) = entry(ce) -1 + entryOffset(ID(ce),worldrank)
entryGlobal(ce) = int(entry(ce),pI64) -1_pI64 + entryOffset(ID(ce),worldrank)
end do
#endif
@ -716,14 +721,15 @@ subroutine results_mapping_homogenization(ID,entry,label)
call h5tget_size_f(dt_id, type_size_string, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5tget_size_f(H5T_NATIVE_INTEGER, type_size_int, hdferr)
pI64_t = h5kind_to_type(kind(entryGlobal),H5_INTEGER_KIND)
call h5tget_size_f(pI64_t, type_size_int, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5tcreate_f(H5T_COMPOUND_F, type_size_string + type_size_int, dtype_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5tinsert_f(dtype_id, 'label', 0_SIZE_T, dt_id,hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5tinsert_f(dtype_id, 'entry', type_size_string, H5T_NATIVE_INTEGER, hdferr)
call h5tinsert_f(dtype_id, 'entry', type_size_string, pI64_t, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
!--------------------------------------------------------------------------------------------------
@ -735,7 +741,7 @@ subroutine results_mapping_homogenization(ID,entry,label)
call h5tcreate_f(H5T_COMPOUND_F, type_size_int, entry_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5tinsert_f(entry_id, 'entry', 0_SIZE_T, H5T_NATIVE_INTEGER, hdferr)
call h5tinsert_f(entry_id, 'entry', 0_SIZE_T, pI64_t, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5tclose_f(dt_id, hdferr)

14
src/rotations.f90
View File

@ -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