diff --git a/.github/workflows/Python.yml b/.github/workflows/Python.yml
index 4c199b81c..b3d714f92 100644
--- a/.github/workflows/Python.yml
+++ b/.github/workflows/Python.yml
@@ -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:
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 6da114938..f3e74e030 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -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"
@@ -79,63 +79,63 @@ 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_grid_GNU-64bit:
+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
-test_mesh_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
-test_grid_IntelLLVM:
+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
-test_mesh_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 $MSC
@@ -158,7 +158,7 @@ setup_mesh:
- cmake -DDAMASK_SOLVER=MESH -DCMAKE_INSTALL_PREFIX=${TESTROOT} ${CI_PROJECT_DIR}
- make -j2 all install
-compile_Marc:
+setup_Marc:
stage: compile
script:
- module load $IntelMarc $HDF5Marc $MSC
diff --git a/COPYING b/COPYING
index bc08fe2e4..bbba84b05 100644
--- a/COPYING
+++ b/COPYING
@@ -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.
+ Copyright (C) 2007 Free Software Foundation, Inc.
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.
diff --git a/LICENSE b/LICENSE
index 0aaac06e9..8f9664407 100644
--- a/LICENSE
+++ b/LICENSE
@@ -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 .
+You should have received a copy of the GNU Affero General Public License
+along with this program. If not, see .
diff --git a/PRIVATE b/PRIVATE
index b898a8b55..5598ec489 160000
--- a/PRIVATE
+++ b/PRIVATE
@@ -1 +1 @@
-Subproject commit b898a8b5552bd9d1c555edc3d8134564dd32fe53
+Subproject commit 5598ec4892b0921fccf63e8570f9fcd8e0365716
diff --git a/examples/config/phase/mechanical/plastic/phenopowerlaw_Mg.yaml b/examples/config/phase/mechanical/plastic/phenopowerlaw_Mg.yaml
index 0ae04928d..8a3147604 100644
--- a/examples/config/phase/mechanical/plastic/phenopowerlaw_Mg.yaml
+++ b/examples/config/phase/mechanical/plastic/phenopowerlaw_Mg.yaml
@@ -6,7 +6,7 @@ references:
output: [xi_sl, xi_tw]
-N_sl: [3, 3, 6, 0, 6] # basal, prism, -, 1. pyr, -, 2. pyr
+N_sl: [3, 3, 6, 0, 6] # basal, prism, 1. pyr, -, 2. pyr
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,
diff --git a/examples/config/phase/mechanical/plastic/phenopowerlaw_Ti.yaml b/examples/config/phase/mechanical/plastic/phenopowerlaw_Ti.yaml
index 1db6adc6b..890f580cc 100644
--- a/examples/config/phase/mechanical/plastic/phenopowerlaw_Ti.yaml
+++ b/examples/config/phase/mechanical/plastic/phenopowerlaw_Ti.yaml
@@ -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
+N_sl: [3, 3, 0, 12] # basal, prism, -, 1. pyr
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
diff --git a/img/COPYING b/img/COPYING
index 55872ace2..2aef54637 100644
--- a/img/COPYING
+++ b/img/COPYING
@@ -1,94 +1,312 @@
-Creative Commons Attribution-NoDerivatives 4.0 International Public License
+Creative Commons Attribution-NoDerivatives 4.0 International Public
+License
-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
+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.
-Section 1 – Definitions.
- Adapted Material means material subject to Copyright and Similar Rights that is derived from or based upon the Licensed Material and in which the Licensed Material is translated, altered, arranged, transformed, or otherwise modified in a manner requiring permission under the Copyright and Similar Rights held by the Licensor. For purposes of this Public License, where the Licensed Material is a musical work, performance, or sound recording, Adapted Material is always produced where the Licensed Material is synched in timed relation with a moving image.
- Copyright and Similar Rights means copyright and/or similar rights closely related to copyright including, without limitation, performance, broadcast, sound recording, and Sui Generis Database Rights, without regard to how the rights are labeled or categorized. For purposes of this Public License, the rights specified in Section 2(b)(1)-(2) are not Copyright and Similar Rights.
- Effective Technological Measures means those measures that, in the absence of proper authority, may not be circumvented under laws fulfilling obligations under Article 11 of the WIPO Copyright Treaty adopted on December 20, 1996, and/or similar international agreements.
- Exceptions and Limitations means fair use, fair dealing, and/or any other exception or limitation to Copyright and Similar Rights that applies to Your use of the Licensed Material.
- Licensed Material means the artistic or literary work, database, or other material to which the Licensor applied this Public License.
- Licensed Rights means the rights granted to You subject to the terms and conditions of this Public License, which are limited to all Copyright and Similar Rights that apply to Your use of the Licensed Material and that the Licensor has authority to license.
- Licensor means the individual(s) or entity(ies) granting rights under this Public License.
- Share means to provide material to the public by any means or process that requires permission under the Licensed Rights, such as reproduction, public display, public performance, distribution, dissemination, communication, or importation, and to make material available to the public including in ways that members of the public may access the material from a place and at a time individually chosen by them.
- Sui Generis Database Rights means rights other than copyright resulting from Directive 96/9/EC of the European Parliament and of the Council of 11 March 1996 on the legal protection of databases, as amended and/or succeeded, as well as other essentially equivalent rights anywhere in the world.
- You means the individual or entity exercising the Licensed Rights under this Public License. Your has a corresponding meaning.
+Section 1 -- Definitions.
-Section 2 – Scope.
+ a. Adapted Material means material subject to Copyright and Similar
+ Rights that is derived from or based upon the Licensed Material
+ and in which the Licensed Material is translated, altered,
+ arranged, transformed, or otherwise modified in a manner requiring
+ permission under the Copyright and Similar Rights held by the
+ Licensor. For purposes of this Public License, where the Licensed
+ Material is a musical work, performance, or sound recording,
+ Adapted Material is always produced where the Licensed Material is
+ synched in timed relation with a moving image.
- License grant.
- Subject to the terms and conditions of this Public License, the Licensor hereby grants You a worldwide, royalty-free, non-sublicensable, non-exclusive, irrevocable license to exercise the Licensed Rights in the Licensed Material to:
- reproduce and Share the Licensed Material, in whole or in part; and
- produce and reproduce, but not Share, Adapted Material.
- Exceptions and Limitations. For the avoidance of doubt, where Exceptions and Limitations apply to Your use, this Public License does not apply, and You do not need to comply with its terms and conditions.
- Term. The term of this Public License is specified in Section 6(a).
- Media and formats; technical modifications allowed. The Licensor authorizes You to exercise the Licensed Rights in all media and formats whether now known or hereafter created, and to make technical modifications necessary to do so. The Licensor waives and/or agrees not to assert any right or authority to forbid You from making technical modifications necessary to exercise the Licensed Rights, including technical modifications necessary to circumvent Effective Technological Measures. For purposes of this Public License, simply making modifications authorized by this Section 2(a)(4) never produces Adapted Material.
- Downstream recipients.
- Offer from the Licensor – Licensed Material. Every recipient of the Licensed Material automatically receives an offer from the Licensor to exercise the Licensed Rights under the terms and conditions of this Public License.
- No downstream restrictions. You may not offer or impose any additional or different terms or conditions on, or apply any Effective Technological Measures to, the Licensed Material if doing so restricts exercise of the Licensed Rights by any recipient of the Licensed Material.
- No endorsement. Nothing in this Public License constitutes or may be construed as permission to assert or imply that You are, or that Your use of the Licensed Material is, connected with, or sponsored, endorsed, or granted official status by, the Licensor or others designated to receive attribution as provided in Section 3(a)(1)(A)(i).
+ b. Copyright and Similar Rights means copyright and/or similar rights
+ closely related to copyright including, without limitation,
+ performance, broadcast, sound recording, and Sui Generis Database
+ Rights, without regard to how the rights are labeled or
+ categorized. For purposes of this Public License, the rights
+ specified in Section 2(b)(1)-(2) are not Copyright and Similar
+ Rights.
- Other rights.
- Moral rights, such as the right of integrity, are not licensed under this Public License, nor are publicity, privacy, and/or other similar personality rights; however, to the extent possible, the Licensor waives and/or agrees not to assert any such rights held by the Licensor to the limited extent necessary to allow You to exercise the Licensed Rights, but not otherwise.
- Patent and trademark rights are not licensed under this Public License.
- To the extent possible, the Licensor waives any right to collect royalties from You for the exercise of the Licensed Rights, whether directly or through a collecting society under any voluntary or waivable statutory or compulsory licensing scheme. In all other cases the Licensor expressly reserves any right to collect such royalties.
+ c. Effective Technological Measures means those measures that, in the
+ absence of proper authority, may not be circumvented under laws
+ fulfilling obligations under Article 11 of the WIPO Copyright
+ Treaty adopted on December 20, 1996, and/or similar international
+ agreements.
-Section 3 – License Conditions.
+ d. Exceptions and Limitations means fair use, fair dealing, and/or
+ any other exception or limitation to Copyright and Similar Rights
+ that applies to Your use of the Licensed Material.
-Your exercise of the Licensed Rights is expressly made subject to the following conditions.
+ e. Licensed Material means the artistic or literary work, database,
+ or other material to which the Licensor applied this Public
+ License.
- Attribution.
+ f. Licensed Rights means the rights granted to You subject to the
+ terms and conditions of this Public License, which are limited to
+ all Copyright and Similar Rights that apply to Your use of the
+ Licensed Material and that the Licensor has authority to license.
- If You Share the Licensed Material, You must:
- retain the following if it is supplied by the Licensor with the Licensed Material:
- identification of the creator(s) of the Licensed Material and any others designated to receive attribution, in any reasonable manner requested by the Licensor (including by pseudonym if designated);
- a copyright notice;
- a notice that refers to this Public License;
- a notice that refers to the disclaimer of warranties;
- a URI or hyperlink to the Licensed Material to the extent reasonably practicable;
- indicate if You modified the Licensed Material and retain an indication of any previous modifications; and
- indicate the Licensed Material is licensed under this Public License, and include the text of, or the URI or hyperlink to, this Public License.
- For the avoidance of doubt, You do not have permission under this Public License to Share Adapted Material.
- You may satisfy the conditions in Section 3(a)(1) in any reasonable manner based on the medium, means, and context in which You Share the Licensed Material. For example, it may be reasonable to satisfy the conditions by providing a URI or hyperlink to a resource that includes the required information.
- If requested by the Licensor, You must remove any of the information required by Section 3(a)(1)(A) to the extent reasonably practicable.
+ g. Licensor means the individual(s) or entity(ies) granting rights
+ under this Public License.
-Section 4 – Sui Generis Database Rights.
+ h. Share means to provide material to the public by any means or
+ process that requires permission under the Licensed Rights, such
+ as reproduction, public display, public performance, distribution,
+ dissemination, communication, or importation, and to make material
+ available to the public including in ways that members of the
+ public may access the material from a place and at a time
+ individually chosen by them.
-Where the Licensed Rights include Sui Generis Database Rights that apply to Your use of the Licensed Material:
+ i. Sui Generis Database Rights means rights other than copyright
+ resulting from Directive 96/9/EC of the European Parliament and of
+ the Council of 11 March 1996 on the legal protection of databases,
+ as amended and/or succeeded, as well as other essentially
+ equivalent rights anywhere in the world.
- for the avoidance of doubt, Section 2(a)(1) grants You the right to extract, reuse, reproduce, and Share all or a substantial portion of the contents of the database, provided You do not Share Adapted Material;
- if You include all or a substantial portion of the database contents in a database in which You have Sui Generis Database Rights, then the database in which You have Sui Generis Database Rights (but not its individual contents) is Adapted Material; and
- You must comply with the conditions in Section 3(a) if You Share all or a substantial portion of the contents of the database.
+ j. You means the individual or entity exercising the Licensed Rights
+ under this Public License. Your has a corresponding meaning.
-For the avoidance of doubt, this Section 4 supplements and does not replace Your obligations under this Public License where the Licensed Rights include other Copyright and Similar Rights.
-Section 5 – Disclaimer of Warranties and Limitation of Liability.
+Section 2 -- Scope.
- Unless otherwise separately undertaken by the Licensor, to the extent possible, the Licensor offers the Licensed Material as-is and as-available, and makes no representations or warranties of any kind concerning the Licensed Material, whether express, implied, statutory, or other. This includes, without limitation, warranties of title, merchantability, fitness for a particular purpose, non-infringement, absence of latent or other defects, accuracy, or the presence or absence of errors, whether or not known or discoverable. Where disclaimers of warranties are not allowed in full or in part, this disclaimer may not apply to You.
- To the extent possible, in no event will the Licensor be liable to You on any legal theory (including, without limitation, negligence) or otherwise for any direct, special, indirect, incidental, consequential, punitive, exemplary, or other losses, costs, expenses, or damages arising out of this Public License or use of the Licensed Material, even if the Licensor has been advised of the possibility of such losses, costs, expenses, or damages. Where a limitation of liability is not allowed in full or in part, this limitation may not apply to You.
+ a. License grant.
- The disclaimer of warranties and limitation of liability provided above shall be interpreted in a manner that, to the extent possible, most closely approximates an absolute disclaimer and waiver of all liability.
+ 1. Subject to the terms and conditions of this Public License,
+ the Licensor hereby grants You a worldwide, royalty-free,
+ non-sublicensable, non-exclusive, irrevocable license to
+ exercise the Licensed Rights in the Licensed Material to:
-Section 6 – Term and Termination.
+ a. reproduce and Share the Licensed Material, in whole or
+ in part; and
- This Public License applies for the term of the Copyright and Similar Rights licensed here. However, if You fail to comply with this Public License, then Your rights under this Public License terminate automatically.
+ b. produce and reproduce, but not Share, Adapted Material.
- Where Your right to use the Licensed Material has terminated under Section 6(a), it reinstates:
- automatically as of the date the violation is cured, provided it is cured within 30 days of Your discovery of the violation; or
- upon express reinstatement by the Licensor.
- For the avoidance of doubt, this Section 6(b) does not affect any right the Licensor may have to seek remedies for Your violations of this Public License.
- For the avoidance of doubt, the Licensor may also offer the Licensed Material under separate terms or conditions or stop distributing the Licensed Material at any time; however, doing so will not terminate this Public License.
- Sections 1, 5, 6, 7, and 8 survive termination of this Public License.
+ 2. Exceptions and Limitations. For the avoidance of doubt, where
+ Exceptions and Limitations apply to Your use, this Public
+ License does not apply, and You do not need to comply with
+ its terms and conditions.
-Section 7 – Other Terms and Conditions.
+ 3. Term. The term of this Public License is specified in Section
+ 6(a).
- The Licensor shall not be bound by any additional or different terms or conditions communicated by You unless expressly agreed.
- Any arrangements, understandings, or agreements regarding the Licensed Material not stated herein are separate from and independent of the terms and conditions of this Public License.
+ 4. Media and formats; technical modifications allowed. The
+ Licensor authorizes You to exercise the Licensed Rights in
+ all media and formats whether now known or hereafter created,
+ and to make technical modifications necessary to do so. The
+ Licensor waives and/or agrees not to assert any right or
+ authority to forbid You from making technical modifications
+ necessary to exercise the Licensed Rights, including
+ technical modifications necessary to circumvent Effective
+ Technological Measures. For purposes of this Public License,
+ simply making modifications authorized by this Section 2(a)
+ (4) never produces Adapted Material.
-Section 8 – Interpretation.
+ 5. Downstream recipients.
- For the avoidance of doubt, this Public License does not, and shall not be interpreted to, reduce, limit, restrict, or impose conditions on any use of the Licensed Material that could lawfully be made without permission under this Public License.
- To the extent possible, if any provision of this Public License is deemed unenforceable, it shall be automatically reformed to the minimum extent necessary to make it enforceable. If the provision cannot be reformed, it shall be severed from this Public License without affecting the enforceability of the remaining terms and conditions.
- No term or condition of this Public License will be waived and no failure to comply consented to unless expressly agreed to by the Licensor.
- Nothing in this Public License constitutes or may be interpreted as a limitation upon, or waiver of, any privileges and immunities that apply to the Licensor or You, including from the legal processes of any jurisdiction or authority.
+ a. Offer from the Licensor -- Licensed Material. Every
+ recipient of the Licensed Material automatically
+ receives an offer from the Licensor to exercise the
+ Licensed Rights under the terms and conditions of this
+ Public License.
+
+ b. No downstream restrictions. You may not offer or impose
+ any additional or different terms or conditions on, or
+ apply any Effective Technological Measures to, the
+ Licensed Material if doing so restricts exercise of the
+ Licensed Rights by any recipient of the Licensed
+ Material.
+
+ 6. No endorsement. Nothing in this Public License constitutes or
+ may be construed as permission to assert or imply that You
+ are, or that Your use of the Licensed Material is, connected
+ with, or sponsored, endorsed, or granted official status by,
+ the Licensor or others designated to receive attribution as
+ provided in Section 3(a)(1)(A)(i).
+
+ b. Other rights.
+
+ 1. Moral rights, such as the right of integrity, are not
+ licensed under this Public License, nor are publicity,
+ privacy, and/or other similar personality rights; however, to
+ the extent possible, the Licensor waives and/or agrees not to
+ assert any such rights held by the Licensor to the limited
+ extent necessary to allow You to exercise the Licensed
+ Rights, but not otherwise.
+
+ 2. Patent and trademark rights are not licensed under this
+ Public License.
+
+ 3. To the extent possible, the Licensor waives any right to
+ collect royalties from You for the exercise of the Licensed
+ Rights, whether directly or through a collecting society
+ under any voluntary or waivable statutory or compulsory
+ licensing scheme. In all other cases the Licensor expressly
+ reserves any right to collect such royalties.
+
+
+Section 3 -- License Conditions.
+
+Your exercise of the Licensed Rights is expressly made subject to the
+following conditions.
+
+ a. Attribution.
+
+ 1. If You Share the Licensed Material, You must:
+
+ a. retain the following if it is supplied by the Licensor
+ with the Licensed Material:
+
+ i. identification of the creator(s) of the Licensed
+ Material and any others designated to receive
+ attribution, in any reasonable manner requested by
+ the Licensor (including by pseudonym if
+ designated);
+
+ ii. a copyright notice;
+
+ iii. a notice that refers to this Public License;
+
+ iv. a notice that refers to the disclaimer of
+ warranties;
+
+ v. a URI or hyperlink to the Licensed Material to the
+ extent reasonably practicable;
+
+ b. indicate if You modified the Licensed Material and
+ retain an indication of any previous modifications; and
+
+ c. indicate the Licensed Material is licensed under this
+ Public License, and include the text of, or the URI or
+ hyperlink to, this Public License.
+
+ For the avoidance of doubt, You do not have permission under
+ this Public License to Share Adapted Material.
+
+ 2. You may satisfy the conditions in Section 3(a)(1) in any
+ reasonable manner based on the medium, means, and context in
+ which You Share the Licensed Material. For example, it may be
+ reasonable to satisfy the conditions by providing a URI or
+ hyperlink to a resource that includes the required
+ information.
+
+ 3. If requested by the Licensor, You must remove any of the
+ information required by Section 3(a)(1)(A) to the extent
+ reasonably practicable.
+
+
+Section 4 -- Sui Generis Database Rights.
+
+Where the Licensed Rights include Sui Generis Database Rights that
+apply to Your use of the Licensed Material:
+
+ a. for the avoidance of doubt, Section 2(a)(1) grants You the right
+ to extract, reuse, reproduce, and Share all or a substantial
+ portion of the contents of the database, provided You do not Share
+ Adapted Material;
+ b. if You include all or a substantial portion of the database
+ contents in a database in which You have Sui Generis Database
+ Rights, then the database in which You have Sui Generis Database
+ Rights (but not its individual contents) is Adapted Material; and
+ 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.
+
+For the avoidance of doubt, this Section 4 supplements and does not
+replace Your obligations under this Public License where the Licensed
+Rights include other Copyright and Similar Rights.
+
+
+Section 5 -- Disclaimer of Warranties and Limitation of Liability.
+
+ a. UNLESS OTHERWISE SEPARATELY UNDERTAKEN BY THE LICENSOR, TO THE
+ EXTENT POSSIBLE, THE LICENSOR OFFERS THE LICENSED MATERIAL AS-IS
+ AND AS-AVAILABLE, AND MAKES NO REPRESENTATIONS OR WARRANTIES OF
+ ANY KIND CONCERNING THE LICENSED MATERIAL, WHETHER EXPRESS,
+ IMPLIED, STATUTORY, OR OTHER. THIS INCLUDES, WITHOUT LIMITATION,
+ WARRANTIES OF TITLE, MERCHANTABILITY, FITNESS FOR A PARTICULAR
+ PURPOSE, NON-INFRINGEMENT, ABSENCE OF LATENT OR OTHER DEFECTS,
+ ACCURACY, OR THE PRESENCE OR ABSENCE OF ERRORS, WHETHER OR NOT
+ KNOWN OR DISCOVERABLE. WHERE DISCLAIMERS OF WARRANTIES ARE NOT
+ ALLOWED IN FULL OR IN PART, THIS DISCLAIMER MAY NOT APPLY TO YOU.
+
+ b. TO THE EXTENT POSSIBLE, IN NO EVENT WILL THE LICENSOR BE LIABLE
+ TO YOU ON ANY LEGAL THEORY (INCLUDING, WITHOUT LIMITATION,
+ NEGLIGENCE) OR OTHERWISE FOR ANY DIRECT, SPECIAL, INDIRECT,
+ INCIDENTAL, CONSEQUENTIAL, PUNITIVE, EXEMPLARY, OR OTHER LOSSES,
+ COSTS, EXPENSES, OR DAMAGES ARISING OUT OF THIS PUBLIC LICENSE OR
+ USE OF THE LICENSED MATERIAL, EVEN IF THE LICENSOR HAS BEEN
+ ADVISED OF THE POSSIBILITY OF SUCH LOSSES, COSTS, EXPENSES, OR
+ DAMAGES. WHERE A LIMITATION OF LIABILITY IS NOT ALLOWED IN FULL OR
+ IN PART, THIS LIMITATION MAY NOT APPLY TO YOU.
+
+ c. The disclaimer of warranties and limitation of liability provided
+ above shall be interpreted in a manner that, to the extent
+ possible, most closely approximates an absolute disclaimer and
+ waiver of all liability.
+
+
+Section 6 -- Term and Termination.
+
+ a. This Public License applies for the term of the Copyright and
+ Similar Rights licensed here. However, if You fail to comply with
+ this Public License, then Your rights under this Public License
+ terminate automatically.
+
+ b. Where Your right to use the Licensed Material has terminated under
+ Section 6(a), it reinstates:
+
+ 1. automatically as of the date the violation is cured, provided
+ it is cured within 30 days of Your discovery of the
+ violation; or
+
+ 2. upon express reinstatement by the Licensor.
+
+ For the avoidance of doubt, this Section 6(b) does not affect any
+ right the Licensor may have to seek remedies for Your violations
+ of this Public License.
+
+ c. For the avoidance of doubt, the Licensor may also offer the
+ Licensed Material under separate terms or conditions or stop
+ distributing the Licensed Material at any time; however, doing so
+ will not terminate this Public License.
+
+ d. Sections 1, 5, 6, 7, and 8 survive termination of this Public
+ License.
+
+
+Section 7 -- Other Terms and Conditions.
+
+ a. The Licensor shall not be bound by any additional or different
+ terms or conditions communicated by You unless expressly agreed.
+
+ b. Any arrangements, understandings, or agreements regarding the
+ Licensed Material not stated herein are separate from and
+ independent of the terms and conditions of this Public License.
+
+
+Section 8 -- Interpretation.
+
+ a. For the avoidance of doubt, this Public License does not, and
+ shall not be interpreted to, reduce, limit, restrict, or impose
+ conditions on any use of the Licensed Material that could lawfully
+ be made without permission under this Public License.
+
+ b. To the extent possible, if any provision of this Public License is
+ deemed unenforceable, it shall be automatically reformed to the
+ minimum extent necessary to make it enforceable. If the provision
+ cannot be reformed, it shall be severed from this Public License
+ without affecting the enforceability of the remaining terms and
+ conditions.
+
+ c. No term or condition of this Public License will be waived and no
+ failure to comply consented to unless expressly agreed to by the
+ Licensor.
+
+ d. Nothing in this Public License constitutes or may be interpreted
+ as a limitation upon, or waiver of, any privileges and immunities
+ that apply to the Licensor or You, including from the legal
+ processes of any jurisdiction or authority.
diff --git a/python/damask/VERSION b/python/damask/VERSION
index 11b9d06bd..750043c40 100644
--- a/python/damask/VERSION
+++ b/python/damask/VERSION
@@ -1 +1 @@
-v3.0.0-alpha5-389-ga000e477c
+v3.0.0-alpha5-518-g4fa97b9a3
diff --git a/python/damask/__init__.py b/python/damask/__init__.py
index 584a97e87..aa3c36b07 100644
--- a/python/damask/__init__.py
+++ b/python/damask/__init__.py
@@ -21,8 +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
diff --git a/python/damask/_colormap.py b/python/damask/_colormap.py
index 2c7f01d94..93bd83cdc 100644
--- a/python/damask/_colormap.py
+++ b/python/damask/_colormap.py
@@ -63,6 +63,14 @@ class Colormap(mpl.colors.ListedColormap):
"""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()
@@ -250,7 +258,7 @@ class Colormap(mpl.colors.ListedColormap):
np.logical_or (np.isnan(field), field == gap)) # mask NaN (and gap if present)
l,r = (field[mask].min(),field[mask].max()) if bounds is None else \
- np.array(bounds,float)[:2]
+ (bounds[0],bounds[1])
delta,avg = r-l,0.5*abs(r+l)
diff --git a/python/damask/_grid.py b/python/damask/_grid.py
index 5006e1b40..94f7eefd0 100644
--- a/python/damask/_grid.py
+++ b/python/damask/_grid.py
@@ -4,7 +4,7 @@ import warnings
import multiprocessing as mp
from functools import partial
import typing
-from typing import Union, Optional, TextIO, List, Sequence
+from typing import Union, Optional, TextIO, List, Sequence, Literal
from pathlib import Path
import numpy as np
@@ -70,7 +70,7 @@ class Grid:
])
- def __copy__(self) -> "Grid":
+ def __copy__(self) -> 'Grid':
"""Create deep copy."""
return copy.deepcopy(self)
@@ -161,7 +161,7 @@ class Grid:
@staticmethod
- def load(fname: Union[str, Path]) -> "Grid":
+ def load(fname: Union[str, Path]) -> 'Grid':
"""
Load from VTK image data file.
@@ -190,7 +190,7 @@ class Grid:
@typing. no_type_check
@staticmethod
- def load_ASCII(fname)-> "Grid":
+ def load_ASCII(fname)-> 'Grid':
"""
Load from geom file.
@@ -264,7 +264,7 @@ class Grid:
@staticmethod
- def load_Neper(fname: Union[str, Path]) -> "Grid":
+ def load_Neper(fname: Union[str, Path]) -> 'Grid':
"""
Load from Neper VTK file.
@@ -279,7 +279,7 @@ class Grid:
Grid-based geometry from file.
"""
- v = VTK.load(fname,'vtkImageData')
+ v = VTK.load(fname,'ImageData')
cells = np.array(v.vtk_data.GetDimensions())-1
bbox = np.array(v.vtk_data.GetBounds()).reshape(3,2).T
@@ -292,7 +292,7 @@ class Grid:
def load_DREAM3D(fname: Union[str, Path],
feature_IDs: str = None, cell_data: str = None,
phases: str = 'Phases', Euler_angles: str = 'EulerAngles',
- base_group: str = None) -> "Grid":
+ base_group: str = None) -> 'Grid':
"""
Load DREAM.3D (HDF5) file.
@@ -354,7 +354,7 @@ class Grid:
@staticmethod
def from_table(table: Table,
coordinates: str,
- labels: Union[str, Sequence[str]]) -> "Grid":
+ labels: Union[str, Sequence[str]]) -> 'Grid':
"""
Create grid from ASCII table.
@@ -422,13 +422,14 @@ class Grid:
Grid-based geometry from tessellation.
"""
+ weights_p: FloatSequence
if periodic:
weights_p = np.tile(weights,27) # Laguerre weights (1,2,3,1,2,3,...,1,2,3)
seeds_p = np.vstack((seeds -np.array([size[0],0.,0.]),seeds, seeds +np.array([size[0],0.,0.])))
seeds_p = np.vstack((seeds_p-np.array([0.,size[1],0.]),seeds_p,seeds_p+np.array([0.,size[1],0.])))
seeds_p = np.vstack((seeds_p-np.array([0.,0.,size[2]]),seeds_p,seeds_p+np.array([0.,0.,size[2]])))
else:
- weights_p = weights
+ weights_p = np.array(weights,float)
seeds_p = seeds
coords = grid_filters.coordinates0_point(cells,size).reshape(-1,3)
@@ -452,7 +453,7 @@ class Grid:
size: FloatSequence,
seeds: np.ndarray,
material: IntSequence = None,
- periodic: bool = True) -> "Grid":
+ periodic: bool = True) -> 'Grid':
"""
Create grid from Voronoi tessellation.
@@ -538,7 +539,7 @@ class Grid:
surface: str,
threshold: float = 0.0,
periods: int = 1,
- materials: IntSequence = (0,1)) -> "Grid":
+ materials: IntSequence = (0,1)) -> 'Grid':
"""
Create grid from definition of triply periodic minimal surface.
@@ -674,7 +675,7 @@ class Grid:
def show(self) -> None:
"""Show on screen."""
- VTK.from_rectilinear_grid(self.cells,self.size,self.origin).show()
+ VTK.from_image_data(self.cells,self.size,self.origin).show()
def add_primitive(self,
@@ -684,7 +685,7 @@ class Grid:
fill: int = None,
R: Rotation = Rotation(),
inverse: bool = False,
- periodic: bool = True) -> "Grid":
+ periodic: bool = True) -> 'Grid':
"""
Insert a primitive geometric object at a given position.
@@ -769,7 +770,7 @@ class Grid:
)
- def mirror(self, directions: Sequence[str], reflect: bool = False) -> "Grid":
+ def mirror(self, directions: Sequence[str], reflect: bool = False) -> 'Grid':
"""
Mirror grid along given directions.
@@ -821,7 +822,7 @@ class Grid:
)
- def flip(self, directions: Sequence[str]) -> "Grid":
+ def flip(self, directions: Union[Literal['x', 'y', 'z'], Sequence[Literal['x', 'y', 'z']]]) -> 'Grid':
"""
Flip grid along given directions.
@@ -841,7 +842,8 @@ class Grid:
if not set(directions).issubset(valid):
raise ValueError(f'invalid direction {set(directions).difference(valid)} specified')
- mat = np.flip(self.material, (valid.index(d) for d in directions if d in valid))
+
+ mat = np.flip(self.material, [valid.index(d) for d in directions if d in valid])
return Grid(material = mat,
size = self.size,
@@ -850,7 +852,7 @@ class Grid:
)
- def scale(self, cells: IntSequence, periodic: bool = True) -> "Grid":
+ def scale(self, cells: IntSequence, periodic: bool = True) -> 'Grid':
"""
Scale grid to new cells.
@@ -897,7 +899,7 @@ class Grid:
def clean(self,
stencil: int = 3,
selection: IntSequence = None,
- periodic: bool = True) -> "Grid":
+ periodic: bool = True) -> 'Grid':
"""
Smooth grid by selecting most frequent material index within given stencil at each location.
@@ -937,7 +939,7 @@ class Grid:
)
- def renumber(self) -> "Grid":
+ def renumber(self) -> 'Grid':
"""
Renumber sorted material indices as 0,...,N-1.
@@ -956,7 +958,7 @@ class Grid:
)
- def rotate(self, R: Rotation, fill: int = None) -> "Grid":
+ def rotate(self, R: Rotation, fill: int = None) -> 'Grid':
"""
Rotate grid (pad if required).
@@ -973,14 +975,13 @@ class Grid:
Updated grid-based geometry.
"""
- if fill is None: fill = np.nanmax(self.material) + 1
- dtype = float if isinstance(fill,float) or self.material.dtype in np.sctypes['float'] else int
-
material = self.material
# These rotations are always applied in the reference coordinate system, i.e. (z,x,z) not (z,x',z'')
# see https://www.cs.utexas.edu/~theshark/courses/cs354/lectures/cs354-14.pdf
for angle,axes in zip(R.as_Euler_angles(degrees=True)[::-1], [(0,1),(1,2),(0,1)]):
- material_temp = ndimage.rotate(material,angle,axes,order=0,prefilter=False,output=dtype,cval=fill)
+ material_temp = ndimage.rotate(material,angle,axes,order=0,prefilter=False,
+ output=self.material.dtype,
+ cval=np.nanmax(self.material) + 1 if fill is None else fill)
# avoid scipy interpolation errors for rotations close to multiples of 90°
material = material_temp if np.prod(material_temp.shape) != np.prod(material.shape) else \
np.rot90(material,k=np.rint(angle/90.).astype(int),axes=axes)
@@ -997,7 +998,7 @@ class Grid:
def canvas(self,
cells: IntSequence = None,
offset: IntSequence = None,
- fill: int = None) -> "Grid":
+ fill: int = None) -> 'Grid':
"""
Crop or enlarge/pad grid.
@@ -1031,10 +1032,8 @@ class Grid:
"""
offset_ = np.array(offset,int) if offset is not None else np.zeros(3,int)
cells_ = np.array(cells,int) if cells is not None else self.cells
- if fill is None: fill = np.nanmax(self.material) + 1
- dtype = float if int(fill) != fill or self.material.dtype in np.sctypes['float'] else int
- canvas = np.full(cells_,fill,dtype)
+ canvas = np.full(cells_,np.nanmax(self.material) + 1 if fill is None else fill,self.material.dtype)
LL = np.clip( offset_, 0,np.minimum(self.cells, cells_+offset_))
UR = np.clip( offset_+cells_, 0,np.minimum(self.cells, cells_+offset_))
@@ -1050,7 +1049,7 @@ class Grid:
)
- def substitute(self, from_material: IntSequence, to_material: IntSequence) -> "Grid":
+ def substitute(self, from_material: IntSequence, to_material: IntSequence) -> 'Grid':
"""
Substitute material indices.
@@ -1067,20 +1066,18 @@ class Grid:
Updated grid-based geometry.
"""
- def mp(entry, mapper):
- return mapper[entry] if entry in mapper else entry
+ material = self.material.copy()
+ for f,t in zip(from_material,to_material): # ToDo Python 3.10 has strict mode for zip
+ material[self.material==f] = t
- mp = np.vectorize(mp)
- mapper = dict(zip(from_material,to_material))
-
- return Grid(material = mp(self.material,mapper).reshape(self.cells),
+ return Grid(material = material,
size = self.size,
origin = self.origin,
comments = self.comments+[util.execution_stamp('Grid','substitute')],
)
- def sort(self) -> "Grid":
+ def sort(self) -> 'Grid':
"""
Sort material indices such that min(material) is located at (0,0,0).
@@ -1106,7 +1103,7 @@ class Grid:
vicinity: int = 1,
offset: int = None,
trigger: IntSequence = [],
- periodic: bool = True) -> "Grid":
+ periodic: bool = True) -> 'Grid':
"""
Offset material index of points in the vicinity of xxx.
diff --git a/python/damask/_result.py b/python/damask/_result.py
index c87b51a89..02d4174c9 100644
--- a/python/damask/_result.py
+++ b/python/damask/_result.py
@@ -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),
diff --git a/python/damask/_table.py b/python/damask/_table.py
index a65971f39..fed309439 100644
--- a/python/damask/_table.py
+++ b/python/damask/_table.py
@@ -1,15 +1,18 @@
import re
import copy
+from pathlib import Path
+from typing import Union, Optional, 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: Optional[Union[str, list]] = None):
"""
New spreadsheet.
@@ -30,7 +33,7 @@ class Table:
self._relabel('uniform')
- def __repr__(self):
+ def __repr__(self) -> str:
"""Brief overview."""
self._relabel('shapes')
data_repr = self.data.__repr__()
@@ -38,7 +41,7 @@ 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 +88,19 @@ 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 +108,7 @@ 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 +131,34 @@ 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: Optional[str]):
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 +186,11 @@ 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 +219,7 @@ class Table:
@staticmethod
- def load(fname):
+ def load(fname: FileHandle) -> 'Table':
"""
Load from ASCII table file.
@@ -229,11 +240,8 @@ 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 +269,7 @@ class Table:
@staticmethod
- def load_ang(fname):
+ def load_ang(fname: FileHandle) -> 'Table':
"""
Load from ang file.
@@ -286,11 +294,8 @@ 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()
@@ -312,11 +317,11 @@ class Table:
@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 +341,7 @@ 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.
@@ -356,7 +361,7 @@ class Table:
"""
dup = self.copy()
- dup._add_comment(label,data.shape[1:],info)
+ dup._add_comment(label, data.shape[1:], info)
m = re.match(r'(.*)\[((\d+,)*(\d+))\]',label)
if m:
key = m.group(1)
@@ -369,7 +374,7 @@ 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 +406,7 @@ class Table:
return dup
- def delete(self,label):
+ def delete(self, label: str) -> 'Table':
"""
Delete column data.
@@ -422,7 +427,7 @@ 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 +453,7 @@ 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.
@@ -481,7 +486,7 @@ class Table:
return dup
- def append(self,other):
+ def append(self, other: 'Table') -> 'Table':
"""
Append other table vertically (similar to numpy.vstack).
@@ -506,7 +511,7 @@ class Table:
return dup
- def join(self,other):
+ def join(self, other: 'Table') -> 'Table':
"""
Append other table horizontally (similar to numpy.hstack).
@@ -533,7 +538,7 @@ class Table:
return dup
- def save(self,fname):
+ def save(self, fname: FileHandle):
"""
Save as plain text file.
@@ -543,9 +548,8 @@ 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 +559,7 @@ 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)
diff --git a/python/damask/_vtk.py b/python/damask/_vtk.py
index dbbfb1b10..4e3f27e0e 100644
--- a/python/damask/_vtk.py
+++ b/python/damask/_vtk.py
@@ -2,6 +2,7 @@ import os
import warnings
import multiprocessing as mp
from pathlib import Path
+from typing import Union, Literal, List
import numpy as np
import vtk
@@ -9,6 +10,7 @@ from vtk.util.numpy_support import numpy_to_vtk as np_to_vtk
from vtk.util.numpy_support import numpy_to_vtkIdTypeArray as np_to_vtkIdTypeArray
from vtk.util.numpy_support import vtk_to_numpy as vtk_to_np
+from ._typehints import FloatSequence, IntSequence
from . import util
from . import Table
@@ -20,7 +22,7 @@ class VTK:
High-level interface to VTK.
"""
- def __init__(self,vtk_data):
+ def __init__(self, vtk_data: vtk.vtkDataSet):
"""
New spatial visualization.
@@ -36,7 +38,7 @@ class VTK:
@staticmethod
- def from_image_data(cells,size,origin=np.zeros(3)):
+ def from_image_data(cells: IntSequence, size: FloatSequence, origin: FloatSequence = np.zeros(3)) -> 'VTK':
"""
Create VTK of type vtk.vtkImageData.
@@ -60,13 +62,13 @@ class VTK:
vtk_data = vtk.vtkImageData()
vtk_data.SetDimensions(*(np.array(cells)+1))
vtk_data.SetOrigin(*(np.array(origin)))
- vtk_data.SetSpacing(*(size/cells))
+ vtk_data.SetSpacing(*(np.array(size)/np.array(cells)))
return VTK(vtk_data)
@staticmethod
- def from_rectilinear_grid(grid,size,origin=np.zeros(3)):
+ def from_rectilinear_grid(grid: np.ndarray, size: FloatSequence, origin: FloatSequence = np.zeros(3)) -> 'VTK':
"""
Create VTK of type vtk.vtkRectilinearGrid.
@@ -98,7 +100,7 @@ class VTK:
@staticmethod
- def from_unstructured_grid(nodes,connectivity,cell_type):
+ def from_unstructured_grid(nodes: np.ndarray, connectivity: np.ndarray, cell_type: str) -> 'VTK':
"""
Create VTK of type vtk.vtkUnstructuredGrid.
@@ -138,7 +140,7 @@ class VTK:
@staticmethod
- def from_poly_data(points):
+ def from_poly_data(points: np.ndarray) -> 'VTK':
"""
Create VTK of type vtk.polyData.
@@ -172,15 +174,17 @@ class VTK:
@staticmethod
- def load(fname,dataset_type=None):
+ def load(fname: Union[str, Path],
+ dataset_type: Literal['ImageData', 'UnstructuredGrid', 'PolyData'] = None) -> 'VTK':
"""
Load from VTK file.
Parameters
----------
fname : str or pathlib.Path
- Filename for reading. Valid extensions are .vti, .vtr, .vtu, .vtp, and .vtk.
- dataset_type : {'vtkImageData', ''vtkRectilinearGrid', 'vtkUnstructuredGrid', 'vtkPolyData'}, optional
+ Filename for reading.
+ Valid extensions are .vti, .vtr, .vtu, .vtp, and .vtk.
+ dataset_type : {'ImageData', 'UnstructuredGrid', 'PolyData'}, optional
Name of the vtk.vtkDataSet subclass when opening a .vtk file.
Returns
@@ -234,7 +238,7 @@ class VTK:
def _write(writer):
"""Wrapper for parallel writing."""
writer.Write()
- def save(self,fname,parallel=True,compress=True):
+ def save(self, fname: Union[str, Path], parallel: bool = True, compress: bool = True):
"""
Save as VTK file.
@@ -280,7 +284,7 @@ class VTK:
# Check https://blog.kitware.com/ghost-and-blanking-visibility-changes/ for missing data
# Needs support for damask.Table
- def add(self,data,label=None):
+ def add(self, data: Union[np.ndarray, np.ma.MaskedArray], label: str = None):
"""
Add data to either cells or points.
@@ -327,7 +331,7 @@ class VTK:
raise TypeError
- def get(self,label):
+ def get(self, label: str) -> np.ndarray:
"""
Get either cell or point data.
@@ -369,7 +373,7 @@ class VTK:
raise ValueError(f'Array "{label}" not found.')
- def get_comments(self):
+ def get_comments(self) -> List[str]:
"""Return the comments."""
fielddata = self.vtk_data.GetFieldData()
for a in range(fielddata.GetNumberOfArrays()):
@@ -379,7 +383,7 @@ class VTK:
return []
- def set_comments(self,comments):
+ def set_comments(self, comments: Union[str, List[str]]):
"""
Set comments.
@@ -396,7 +400,7 @@ class VTK:
self.vtk_data.GetFieldData().AddArray(s)
- def add_comments(self,comments):
+ def add_comments(self, comments: Union[str, List[str]]):
"""
Add comments.
@@ -409,7 +413,7 @@ class VTK:
self.set_comments(self.get_comments() + ([comments] if isinstance(comments,str) else comments))
- def __repr__(self):
+ def __repr__(self) -> str:
"""ASCII representation of the VTK data."""
writer = vtk.vtkDataSetWriter()
writer.SetHeader(f'# {util.execution_stamp("VTK")}')
@@ -419,7 +423,7 @@ class VTK:
return writer.GetOutputString()
- def show(self) -> None:
+ def show(self):
"""
Render.
@@ -442,22 +446,24 @@ class VTK:
mapper = vtk.vtkDataSetMapper()
mapper.SetInputData(self.vtk_data)
+
actor = vtk.vtkActor()
actor.SetMapper(mapper)
+ actor.GetProperty().SetColor(230/255,150/255,68/255)
ren = vtk.vtkRenderer()
+ ren.AddActor(actor)
+ ren.SetBackground(67/255,128/255,208/255)
window = vtk.vtkRenderWindow()
window.AddRenderer(ren)
-
- ren.AddActor(actor)
- ren.SetBackground(0.2,0.2,0.2)
-
window.SetSize(width,height)
+ window.SetWindowName(util.execution_stamp('VTK','show'))
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(window)
-
- iren.Initialize()
- window.Render()
- iren.Start()
+ if os.name == 'posix' and 'DISPLAY' not in os.environ:
+ print('Found no rendering device')
+ else:
+ window.Render()
+ iren.Start()
diff --git a/python/damask/seeds.py b/python/damask/seeds.py
index 6ff150df3..e6d1f9613 100644
--- a/python/damask/seeds.py
+++ b/python/damask/seeds.py
@@ -79,7 +79,7 @@ def from_Poisson_disc(size: _FloatSequence, N_seeds: int, N_candidates: int, dis
s = 1
i = 0
- progress = _util._ProgressBar(N_seeds+1,'',50)
+ progress = _util.ProgressBar(N_seeds+1,'',50)
while s < N_seeds:
i += 1
candidates = rng.random((N_candidates,3))*_np.broadcast_to(size,(N_candidates,3))
diff --git a/python/damask/util.py b/python/damask/util.py
index 0581302db..2872762b9 100644
--- a/python/damask/util.py
+++ b/python/damask/util.py
@@ -7,12 +7,16 @@ import subprocess
import shlex
import re
import fractions
+import collections.abc as abc
from functools import reduce
+from typing import Union, Tuple, Iterable, Callable, Dict, List, Any, Literal, Optional
+from pathlib import Path
import numpy as np
import h5py
from . import version
+from ._typehints import FloatSequence
# limit visibility
__all__=[
@@ -50,16 +54,16 @@ _colors = {
####################################################################################################
# Functions
####################################################################################################
-def srepr(arg,glue = '\n'):
+def srepr(msg, glue: str = '\n') -> str:
r"""
Join items with glue string.
Parameters
----------
- arg : iterable
+ msg : object with __repr__ or sequence of objects with __repr__
Items to join.
glue : str, optional
- Glue used for joining operation. Defaults to \n.
+ Glue used for joining operation. Defaults to '\n'.
Returns
-------
@@ -67,21 +71,21 @@ def srepr(arg,glue = '\n'):
String representation of the joined items.
"""
- if (not hasattr(arg, 'strip') and
- (hasattr(arg, '__getitem__') or
- hasattr(arg, '__iter__'))):
- return glue.join(str(x) for x in arg)
+ if (not hasattr(msg, 'strip') and
+ (hasattr(msg, '__getitem__') or
+ hasattr(msg, '__iter__'))):
+ return glue.join(str(x) for x in msg)
else:
- return arg if isinstance(arg,str) else repr(arg)
+ return msg if isinstance(msg,str) else repr(msg)
-def emph(what):
+def emph(msg) -> str:
"""
Format with emphasis.
Parameters
----------
- what : object with __repr__ or iterable of objects with __repr__.
+ msg : object with __repr__ or sequence of objects with __repr__
Message to format.
Returns
@@ -90,15 +94,15 @@ def emph(what):
Formatted string representation of the joined items.
"""
- return _colors['bold']+srepr(what)+_colors['end_color']
+ return _colors['bold']+srepr(msg)+_colors['end_color']
-def deemph(what):
+def deemph(msg) -> str:
"""
Format with deemphasis.
Parameters
----------
- what : object with __repr__ or iterable of objects with __repr__.
+ msg : object with __repr__ or sequence of objects with __repr__
Message to format.
Returns
@@ -107,15 +111,15 @@ def deemph(what):
Formatted string representation of the joined items.
"""
- return _colors['dim']+srepr(what)+_colors['end_color']
+ return _colors['dim']+srepr(msg)+_colors['end_color']
-def warn(what):
+def warn(msg) -> str:
"""
Format for warning.
Parameters
----------
- what : object with __repr__ or iterable of objects with __repr__.
+ msg : object with __repr__ or sequence of objects with __repr__
Message to format.
Returns
@@ -124,15 +128,15 @@ def warn(what):
Formatted string representation of the joined items.
"""
- return _colors['warning']+emph(what)+_colors['end_color']
+ return _colors['warning']+emph(msg)+_colors['end_color']
-def strikeout(what):
+def strikeout(msg) -> str:
"""
Format as strikeout.
Parameters
----------
- what : object with __repr__ or iterable of objects with __repr__.
+ msg : object with __repr__ or iterable of objects with __repr__
Message to format.
Returns
@@ -141,10 +145,10 @@ def strikeout(what):
Formatted string representation of the joined items.
"""
- return _colors['crossout']+srepr(what)+_colors['end_color']
+ return _colors['crossout']+srepr(msg)+_colors['end_color']
-def run(cmd,wd='./',env=None,timeout=None):
+def run(cmd: str, wd: str = './', env: Dict[str, str] = None, timeout: int = None) -> Tuple[str, str]:
"""
Run a command.
@@ -153,7 +157,7 @@ def run(cmd,wd='./',env=None,timeout=None):
cmd : str
Command to be executed.
wd : str, optional
- Working directory of process. Defaults to ./ .
+ Working directory of process. Defaults to './'.
env : dict, optional
Environment for execution.
timeout : integer, optional
@@ -185,7 +189,7 @@ def run(cmd,wd='./',env=None,timeout=None):
execute = run
-def natural_sort(key):
+def natural_sort(key: str) -> List[Union[int, str]]:
"""
Natural sort.
@@ -200,7 +204,10 @@ def natural_sort(key):
return [ convert(c) for c in re.split('([0-9]+)', key) ]
-def show_progress(iterable,N_iter=None,prefix='',bar_length=50):
+def show_progress(iterable: Iterable,
+ N_iter: int = None,
+ prefix: str = '',
+ bar_length: int = 50) -> Any:
"""
Decorate a loop with a progress bar.
@@ -208,39 +215,49 @@ def show_progress(iterable,N_iter=None,prefix='',bar_length=50):
Parameters
----------
- iterable : iterable or function with yield statement
- Iterable (or function with yield statement) to be decorated.
+ iterable : iterable
+ Iterable to be decorated.
N_iter : int, optional
- Total number of iterations. Required unless obtainable as len(iterable).
+ Total number of iterations. Required if iterable is not a sequence.
prefix : str, optional
Prefix string.
bar_length : int, optional
Length of progress bar in characters. Defaults to 50.
"""
- if N_iter in [0,1] or (hasattr(iterable,'__len__') and len(iterable) <= 1):
+ if isinstance(iterable,abc.Sequence):
+ if N_iter is None:
+ N = len(iterable)
+ else:
+ raise ValueError('N_iter given for sequence')
+ else:
+ if N_iter is None:
+ raise ValueError('N_iter not given')
+ else:
+ N = N_iter
+
+ if N <= 1:
for item in iterable:
yield item
else:
- status = _ProgressBar(N_iter if N_iter is not None else len(iterable),prefix,bar_length)
-
+ status = ProgressBar(N,prefix,bar_length)
for i,item in enumerate(iterable):
yield item
status.update(i)
-def scale_to_coprime(v):
+def scale_to_coprime(v: FloatSequence) -> np.ndarray:
"""
Scale vector to co-prime (relatively prime) integers.
Parameters
----------
- v : numpy.ndarray of shape (:)
+ v : sequence of float, len (:)
Vector to scale.
Returns
-------
- m : numpy.ndarray of shape (:)
+ m : numpy.ndarray, shape (:)
Vector scaled to co-prime numbers.
"""
@@ -257,17 +274,21 @@ def scale_to_coprime(v):
except AttributeError:
return a * b // np.gcd(a, b)
- m = (np.array(v) * reduce(lcm, map(lambda x: int(get_square_denominator(x)),v)) ** 0.5).astype(int)
+ v_ = np.array(v)
+ m = (v_ * reduce(lcm, map(lambda x: int(get_square_denominator(x)),v_))**0.5).astype(int)
m = m//reduce(np.gcd,m)
with np.errstate(invalid='ignore'):
- if not np.allclose(np.ma.masked_invalid(v/m),v[np.argmax(abs(v))]/m[np.argmax(abs(v))]):
- raise ValueError(f'Invalid result {m} for input {v}. Insufficient precision?')
+ if not np.allclose(np.ma.masked_invalid(v_/m),v_[np.argmax(abs(v_))]/m[np.argmax(abs(v_))]):
+ raise ValueError(f'Invalid result {m} for input {v_}. Insufficient precision?')
return m
-def project_equal_angle(vector,direction='z',normalize=True,keepdims=False):
+def project_equal_angle(vector: np.ndarray,
+ direction: Literal['x', 'y', 'z'] = 'z',
+ normalize: bool = True,
+ keepdims: bool = False) -> np.ndarray:
"""
Apply equal-angle projection to vector.
@@ -275,9 +296,8 @@ def project_equal_angle(vector,direction='z',normalize=True,keepdims=False):
----------
vector : numpy.ndarray, shape (...,3)
Vector coordinates to be projected.
- direction : str
- Projection direction 'x', 'y', or 'z'.
- Defaults to 'z'.
+ direction : {'x', 'y', 'z'}
+ Projection direction. Defaults to 'z'.
normalize : bool
Ensure unit length of input vector. Defaults to True.
keepdims : bool
@@ -309,7 +329,10 @@ def project_equal_angle(vector,direction='z',normalize=True,keepdims=False):
return np.roll(np.block([v[...,:2]/(1.0+np.abs(v[...,2:3])),np.zeros_like(v[...,2:3])]),
-shift if keepdims else 0,axis=-1)[...,:3 if keepdims else 2]
-def project_equal_area(vector,direction='z',normalize=True,keepdims=False):
+def project_equal_area(vector: np.ndarray,
+ direction: Literal['x', 'y', 'z'] = 'z',
+ normalize: bool = True,
+ keepdims: bool = False) -> np.ndarray:
"""
Apply equal-area projection to vector.
@@ -317,9 +340,8 @@ def project_equal_area(vector,direction='z',normalize=True,keepdims=False):
----------
vector : numpy.ndarray, shape (...,3)
Vector coordinates to be projected.
- direction : str
- Projection direction 'x', 'y', or 'z'.
- Defaults to 'z'.
+ direction : {'x', 'y', 'z'}
+ Projection direction. Defaults to 'z'.
normalize : bool
Ensure unit length of input vector. Defaults to True.
keepdims : bool
@@ -351,15 +373,14 @@ def project_equal_area(vector,direction='z',normalize=True,keepdims=False):
return np.roll(np.block([v[...,:2]/np.sqrt(1.0+np.abs(v[...,2:3])),np.zeros_like(v[...,2:3])]),
-shift if keepdims else 0,axis=-1)[...,:3 if keepdims else 2]
-
-def execution_stamp(class_name,function_name=None):
+def execution_stamp(class_name: str, function_name: str = None) -> str:
"""Timestamp the execution of a (function within a) class."""
now = datetime.datetime.now().astimezone().strftime('%Y-%m-%d %H:%M:%S%z')
_function_name = '' if function_name is None else f'.{function_name}'
return f'damask.{class_name}{_function_name} v{version} ({now})'
-def hybrid_IA(dist,N,rng_seed=None):
+def hybrid_IA(dist: np.ndarray, N: int, rng_seed = None) -> np.ndarray:
"""
Hybrid integer approximation.
@@ -387,7 +408,10 @@ def hybrid_IA(dist,N,rng_seed=None):
return np.repeat(np.arange(len(dist)),repeats)[np.random.default_rng(rng_seed).permutation(N_inv_samples)[:N]]
-def shapeshifter(fro,to,mode='left',keep_ones=False):
+def shapeshifter(fro: Tuple[int, ...],
+ to: Tuple[int, ...],
+ mode: Literal['left','right'] = 'left',
+ keep_ones: bool = False) -> Tuple[Optional[int], ...]:
"""
Return dimensions that reshape 'fro' to become broadcastable to 'to'.
@@ -398,9 +422,9 @@ def shapeshifter(fro,to,mode='left',keep_ones=False):
to : tuple
Target shape of array after broadcasting.
len(to) cannot be less than len(fro).
- mode : str, optional
+ mode : {'left', 'right'}, optional
Indicates whether new axes are preferably added to
- either 'left' or 'right' of the original shape.
+ either left or right of the original shape.
Defaults to 'left'.
keep_ones : bool, optional
Treat '1' in fro as literal value instead of dimensional placeholder.
@@ -434,21 +458,22 @@ def shapeshifter(fro,to,mode='left',keep_ones=False):
fro = (1,) if not len(fro) else fro
to = (1,) if not len(to) else to
try:
- grp = re.match(beg[mode]
+ match = re.match(beg[mode]
+f',{sep[mode]}'.join(map(lambda x: f'{x}'
if x>1 or (keep_ones and len(fro)>1) else
'\\d+',fro))
- +f',{end[mode]}',
- ','.join(map(str,to))+',').groups()
- except AttributeError:
+ +f',{end[mode]}',','.join(map(str,to))+',')
+ assert match
+ grp = match.groups()
+ except AssertionError:
raise ValueError(f'Shapes can not be shifted {fro} --> {to}')
- fill = ()
+ fill: Tuple[Optional[int], ...] = ()
for g,d in zip(grp,fro+(None,)):
fill += (1,)*g.count(',')+(d,)
return fill[:-1]
-def shapeblender(a,b):
+def shapeblender(a: Tuple[int, ...], b: Tuple[int, ...]) -> Tuple[int, ...]:
"""
Return a shape that overlaps the rightmost entries of 'a' with the leftmost of 'b'.
@@ -476,7 +501,7 @@ def shapeblender(a,b):
return a + b[i:]
-def extend_docstring(extra_docstring):
+def extend_docstring(extra_docstring: str) -> Callable:
"""
Decorator: Append to function's docstring.
@@ -492,7 +517,7 @@ def extend_docstring(extra_docstring):
return _decorator
-def extended_docstring(f,extra_docstring):
+def extended_docstring(f: Callable, extra_docstring: str) -> Callable:
"""
Decorator: Combine another function's docstring with a given docstring.
@@ -510,7 +535,7 @@ def extended_docstring(f,extra_docstring):
return _decorator
-def DREAM3D_base_group(fname):
+def DREAM3D_base_group(fname: Union[str, Path]) -> str:
"""
Determine the base group of a DREAM.3D file.
@@ -536,7 +561,7 @@ def DREAM3D_base_group(fname):
return base_group
-def DREAM3D_cell_data_group(fname):
+def DREAM3D_cell_data_group(fname: Union[str, Path]) -> str:
"""
Determine the cell data group of a DREAM.3D file.
@@ -568,18 +593,18 @@ def DREAM3D_cell_data_group(fname):
return cell_data_group
-def Bravais_to_Miller(*,uvtw=None,hkil=None):
+def Bravais_to_Miller(*, uvtw: np.ndarray = None, hkil: np.ndarray = None) -> np.ndarray:
"""
Transform 4 Miller–Bravais indices to 3 Miller indices of crystal direction [uvw] or plane normal (hkl).
Parameters
----------
- uvtw|hkil : numpy.ndarray of shape (...,4)
+ uvtw|hkil : numpy.ndarray, shape (...,4)
Miller–Bravais indices of crystallographic direction [uvtw] or plane normal (hkil).
Returns
-------
- uvw|hkl : numpy.ndarray of shape (...,3)
+ uvw|hkl : numpy.ndarray, shape (...,3)
Miller indices of [uvw] direction or (hkl) plane normal.
"""
@@ -595,18 +620,18 @@ def Bravais_to_Miller(*,uvtw=None,hkil=None):
return np.einsum('il,...l',basis,axis)
-def Miller_to_Bravais(*,uvw=None,hkl=None):
+def Miller_to_Bravais(*, uvw: np.ndarray = None, hkl: np.ndarray = None) -> np.ndarray:
"""
Transform 3 Miller indices to 4 Miller–Bravais indices of crystal direction [uvtw] or plane normal (hkil).
Parameters
----------
- uvw|hkl : numpy.ndarray of shape (...,3)
+ uvw|hkl : numpy.ndarray, shape (...,3)
Miller indices of crystallographic direction [uvw] or plane normal (hkl).
Returns
-------
- uvtw|hkil : numpy.ndarray of shape (...,4)
+ uvtw|hkil : numpy.ndarray, shape (...,4)
Miller–Bravais indices of [uvtw] direction or (hkil) plane normal.
"""
@@ -624,7 +649,7 @@ def Miller_to_Bravais(*,uvw=None,hkl=None):
return np.einsum('il,...l',basis,axis)
-def dict_prune(d):
+def dict_prune(d: Dict) -> Dict:
"""
Recursively remove empty dictionaries.
@@ -650,7 +675,7 @@ def dict_prune(d):
return new
-def dict_flatten(d):
+def dict_flatten(d: Dict) -> Dict:
"""
Recursively remove keys of single-entry dictionaries.
@@ -678,14 +703,14 @@ def dict_flatten(d):
####################################################################################################
# Classes
####################################################################################################
-class _ProgressBar:
+class ProgressBar:
"""
Report progress of an interation as a status bar.
Works for 0-based loops, ETA is estimated by linear extrapolation.
"""
- def __init__(self,total,prefix,bar_length):
+ def __init__(self, total: int, prefix: str, bar_length: int):
"""
Set current time as basis for ETA estimation.
@@ -708,7 +733,7 @@ class _ProgressBar:
sys.stderr.write(f"{self.prefix} {'░'*self.bar_length} 0% ETA n/a")
sys.stderr.flush()
- def update(self,iteration):
+ def update(self, iteration: int) -> None:
fraction = (iteration+1) / self.total
filled_length = int(self.bar_length * fraction)
diff --git a/python/setup.py b/python/setup.py
index 1740b54a5..abb8053a9 100644
--- a/python/setup.py
+++ b/python/setup.py
@@ -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',
],
)
diff --git a/python/tests/test_Colormap.py b/python/tests/test_Colormap.py
index 156907670..12a26e550 100644
--- a/python/tests/test_Colormap.py
+++ b/python/tests/test_Colormap.py
@@ -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]),
diff --git a/python/tests/test_Crystal.py b/python/tests/test_Crystal.py
index 9c6de965d..235ed554a 100644
--- a/python/tests/test_Crystal.py
+++ b/python/tests/test_Crystal.py
@@ -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([
diff --git a/python/tests/test_Grid.py b/python/tests/test_Grid.py
index 2b9ca22f4..6dd94f4bb 100644
--- a/python/tests/test_Grid.py
+++ b/python/tests/test_Grid.py
@@ -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)
diff --git a/python/tests/test_Orientation.py b/python/tests/test_Orientation.py
index 9f623fc6c..2a32adea4 100644
--- a/python/tests/test_Orientation.py
+++ b/python/tests/test_Orientation.py
@@ -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)
diff --git a/python/tests/test_Result.py b/python/tests/test_Result.py
index 4fea08eb3..1da56dedf 100644
--- a/python/tests/test_Result.py
+++ b/python/tests/test_Result.py
@@ -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'))
diff --git a/python/tests/test_Rotation.py b/python/tests/test_Rotation.py
index 2d623adf5..a431bc64b 100644
--- a/python/tests/test_Rotation.py
+++ b/python/tests/test_Rotation.py
@@ -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)
diff --git a/python/tests/test_VTK.py b/python/tests/test_VTK.py
index 68224ff33..e59409a20 100644
--- a/python/tests/test_VTK.py
+++ b/python/tests/test_VTK.py
@@ -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
diff --git a/src/YAML_types.f90 b/src/YAML_types.f90
index 5884c2850..c57f602cf 100644
--- a/src/YAML_types.f90
+++ b/src/YAML_types.f90
@@ -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
diff --git a/src/grid/discretization_grid.f90 b/src/grid/discretization_grid.f90
index 738206f9a..8de2de6ef 100644
--- a/src/grid/discretization_grid.f90
+++ b/src/grid/discretization_grid.f90
@@ -27,14 +27,14 @@ module discretization_grid
private
integer, dimension(3), public, protected :: &
- grid !< (global) grid
+ grid !< (global) grid
integer, public, protected :: &
- grid3, & !< (local) grid in 3rd direction
+ grid3, & !< (local) grid in 3rd direction
grid3Offset !< (local) grid offset in 3rd direction
real(pReal), dimension(3), public, protected :: &
- geomSize !< (global) physical size
+ geomSize !< (global) physical size
real(pReal), public, protected :: &
- size3, & !< (local) size in 3rd direction
+ size3, & !< (local) size in 3rd direction
size3offset !< (local) size offset in 3rd direction
public :: &
diff --git a/src/grid/grid_damage_spectral.f90 b/src/grid/grid_damage_spectral.f90
index 8955f9d66..96b72dbcc 100644
--- a/src/grid/grid_damage_spectral.f90
+++ b/src/grid/grid_damage_spectral.f90
@@ -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
@@ -105,10 +104,18 @@ subroutine grid_damage_spectral_init()
call PetscOptionsInsertString(PETSC_NULL_OPTIONS,num_grid%get_asString('petsc_options',defaultVal=''),err_PETSc)
CHKERRQ(err_PETSc)
+!--------------------------------------------------------------------------------------------------
+! init fields
+ 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)
+
!--------------------------------------------------------------------------------------------------
! initialize solver specific parts of PETSc
- call SNESCreate(PETSC_COMM_WORLD,damage_snes,err_PETSc); CHKERRQ(err_PETSc)
- call SNESSetOptionsPrefix(damage_snes,'damage_',err_PETSc);CHKERRQ(err_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)
@@ -122,39 +129,41 @@ subroutine grid_damage_spectral_init()
[int(grid(1),pPetscInt)],[int(grid(2),pPetscInt)],localK, & ! local grid
damage_grid,err_PETSc) ! handle, error
CHKERRQ(err_PETSc)
- call SNESSetDM(damage_snes,damage_grid,err_PETSc); CHKERRQ(err_PETSc) ! connect snes to da
- 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); CHKERRQ(err_PETSc) ! global solution vector (grid x 1, i.e. every def grad tensor)
+ 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 SNESSetFromOptions(damage_snes,err_PETSc); CHKERRQ(err_PETSc) ! pull it all together with additional CLI arguments
- call SNESGetType(damage_snes,snes_type,err_PETSc); 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(damage_snes,lBound,uBound,err_PETSc) ! variable bounds for variational inequalities like contact mechanics, damage etc.
- call DMRestoreGlobalVector(damage_grid,lBound,err_PETSc); CHKERRQ(err_PETSc)
- call DMRestoreGlobalVector(damage_grid,uBound,err_PETSc); CHKERRQ(err_PETSc)
+ 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
-
-!--------------------------------------------------------------------------------------------------
-! init fields
- call DMDAGetCorners(damage_grid,xstart,ystart,zstart,xend,yend,zend,err_PETSc)
+ call VecSet(solution_vec,1.0_pReal,err_PETSc)
CHKERRQ(err_PETSc)
- 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,err_PETSc); CHKERRQ(err_PETSc)
-
- call updateReference
+ call updateReference()
end subroutine grid_damage_spectral_init
@@ -181,9 +190,9 @@ 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,err_PETSc)
+ call SNESSolve(SNES_damage,PETSC_NULL_VEC,solution_vec,err_PETSc)
CHKERRQ(err_PETSc)
- call SNESGetConvergedReason(damage_snes,reason,err_PETSc)
+ call SNESGetConvergedReason(SNES_damage,reason,err_PETSc)
CHKERRQ(err_PETSc)
if (reason < 1) then
@@ -209,8 +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,err_PETSc); CHKERRQ(err_PETSc)
- call VecMax(solution_vec,devNull,phi_max,err_PETSc); CHKERRQ(err_PETSc)
+ 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
@@ -228,7 +239,7 @@ subroutine grid_damage_spectral_forward(cutBack)
logical, intent(in) :: cutBack
integer :: i, j, k, ce
DM :: dm_local
- PetscScalar, dimension(:,:,:), pointer :: x_scal
+ PetscScalar, dimension(:,:,:), pointer :: phi_PETSc
PetscErrorCode :: err_PETSc
if (cutBack) then
@@ -236,11 +247,12 @@ subroutine grid_damage_spectral_forward(cutBack)
phi_stagInc = phi_lastInc
!--------------------------------------------------------------------------------------------------
! reverting damage field state
- call SNESGetDM(damage_snes,dm_local,err_PETSc); CHKERRQ(err_PETSc)
- call DMDAVecGetArrayF90(dm_local,solution_vec,x_scal,err_PETSc) !< get the data out of PETSc to work with
+ call SNESGetDM(SNES_damage,dm_local,err_PETSc)
CHKERRQ(err_PETSc)
- x_scal(xstart:xend,ystart:yend,zstart:zend) = phi_current
- call DMDAVecRestoreArrayF90(dm_local,solution_vec,x_scal,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)
@@ -258,7 +270,7 @@ end subroutine grid_damage_spectral_forward
!--------------------------------------------------------------------------------------------------
!> @brief forms the spectral damage residual vector
!--------------------------------------------------------------------------------------------------
-subroutine formResidual(in,x_scal,f_scal,dummy,dummy_err)
+subroutine formResidual(in,x_scal,r,dummy,err_PETSc)
DMDALocalInfo, dimension(DMDA_LOCAL_INFO_SIZE) :: &
in
@@ -267,9 +279,9 @@ subroutine formResidual(in,x_scal,f_scal,dummy,dummy_err)
x_scal
PetscScalar, dimension( &
X_RANGE,Y_RANGE,Z_RANGE), intent(out) :: &
- f_scal
+ r
PetscObject :: dummy
- PetscErrorCode :: dummy_err
+ PetscErrorCode :: err_PETSc
integer :: i, j, k, ce
@@ -310,7 +322,8 @@ subroutine formResidual(in,x_scal,f_scal,dummy,dummy_err)
!--------------------------------------------------------------------------------------------------
! 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
diff --git a/src/grid/grid_mech_FEM.f90 b/src/grid/grid_mech_FEM.f90
index 010f11cea..6a3f1323d 100644
--- a/src/grid/grid_mech_FEM.f90
+++ b/src/grid/grid_mech_FEM.f90
@@ -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.
@@ -146,7 +145,7 @@ 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_mg_levels_ksp_type chebyshev', &
+ &-mechanical_ksp_max_it 25', &
err_PETSc)
CHKERRQ(err_PETSc)
call PetscOptionsInsertString(PETSC_NULL_OPTIONS,num_grid%get_asString('petsc_options',defaultVal=''),err_PETSc)
@@ -160,9 +159,9 @@ subroutine grid_mechanical_FEM_init
!--------------------------------------------------------------------------------------------------
! initialize solver specific parts of PETSc
- call SNESCreate(PETSC_COMM_WORLD,mechanical_snes,err_PETSc)
+ call SNESCreate(PETSC_COMM_WORLD,SNES_mechanical,err_PETSc)
CHKERRQ(err_PETSc)
- call SNESSetOptionsPrefix(mechanical_snes,'mechanical_',err_PETSc)
+ call SNESSetOptionsPrefix(SNES_mechanical,'mechanical_',err_PETSc)
CHKERRQ(err_PETSc)
localK = 0_pPetscInt
localK(worldrank) = int(grid3,pPetscInt)
@@ -177,8 +176,6 @@ subroutine grid_mechanical_FEM_init
[int(grid(1),pPetscInt)],[int(grid(2),pPetscInt)],localK, & ! local grid
mechanical_grid,err_PETSc)
CHKERRQ(err_PETSc)
- call SNESSetDM(mechanical_snes,mechanical_grid,err_PETSc)
- CHKERRQ(err_PETSc)
call DMsetFromOptions(mechanical_grid,err_PETSc)
CHKERRQ(err_PETSc)
call DMsetUp(mechanical_grid,err_PETSc)
@@ -195,28 +192,28 @@ subroutine grid_mechanical_FEM_init
CHKERRQ(err_PETSc)
call DMSNESSetJacobianLocal(mechanical_grid,formJacobian,PETSC_NULL_SNES,err_PETSc)
CHKERRQ(err_PETSc)
- call SNESSetConvergenceTest(mechanical_snes,converged,PETSC_NULL_SNES,PETSC_NULL_FUNCTION,err_PETSc) ! specify custom convergence check function "_converged"
+ call SNESSetConvergenceTest(SNES_mechanical,converged,PETSC_NULL_SNES,PETSC_NULL_FUNCTION,err_PETSc) ! specify custom convergence check function "_converged"
CHKERRQ(err_PETSc)
- call SNESSetMaxLinearSolveFailures(mechanical_snes, huge(1_pPetscInt), err_PETSc) ! ignore linear solve failures
+ call SNESSetMaxLinearSolveFailures(SNES_mechanical, huge(1_pPetscInt), err_PETSc) ! ignore linear solve failures
CHKERRQ(err_PETSc)
- call SNESSetFromOptions(mechanical_snes,err_PETSc) ! pull it all together with additional cli arguments
+ 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,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 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,err_PETSc) ! local grid extent
- CHKERRQ(err_PETSc)
- xend = xstart+xend-1
- yend = ystart+yend-1
- zend = zstart+zend-1
delta = geomSize/real(grid,pReal) ! grid spacing
detJ = product(delta) ! cell volume
@@ -311,14 +308,9 @@ 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,err_PETSc)
+ call SNESsolve(SNES_mechanical,PETSC_NULL_VEC,solution_current,err_PETSc)
CHKERRQ(err_PETSc)
-
-!--------------------------------------------------------------------------------------------------
-! check convergence
- call SNESGetConvergedReason(mechanical_snes,reason,err_PETSc)
+ call SNESGetConvergedReason(SNES_mechanical,reason,err_PETSc)
CHKERRQ(err_PETSc)
solution%converged = reason > 0
@@ -386,9 +378,11 @@ subroutine grid_mechanical_FEM_forward(cutBack,guess,Delta_t,Delta_t_old,t_remai
call VecScale(solution_rate,1.0_pReal/Delta_t_old,err_PETSc)
CHKERRQ(err_PETSc)
else
- call VecSet(solution_rate,0.0_pReal,err_PETSc); CHKERRQ(err_PETSc)
+ call VecSet(solution_rate,0.0_pReal,err_PETSc)
+ CHKERRQ(err_PETSc)
endif
- call VecCopy(solution_current,solution_lastInc,err_PETSc); CHKERRQ(err_PETSc)
+ call VecCopy(solution_current,solution_lastInc,err_PETSc)
+ CHKERRQ(err_PETSc)
F_lastInc = F
@@ -515,6 +509,7 @@ subroutine converged(snes_local,PETScIter,devNull1,devNull2,fnorm,reason,dummy,e
err_BC/BCTol, ' (',err_BC, ' Pa, tol = ',BCTol,')'
print'(/,1x,a)', '==========================================================================='
flush(IO_STDOUT)
+ err_PETSc = 0
end subroutine converged
@@ -527,7 +522,7 @@ subroutine formResidual(da_local,x_local, &
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 :: &
@@ -538,9 +533,9 @@ subroutine formResidual(da_local,x_local, &
integer(MPI_INTEGER_KIND) :: err_MPI
real(pReal), dimension(3,3,3,3) :: devNull
- call SNESGetNumberFunctionEvals(mechanical_snes,nfuncs,err_PETSc)
+ call SNESGetNumberFunctionEvals(SNES_mechanical,nfuncs,err_PETSc)
CHKERRQ(err_PETSc)
- call SNESGetIterationNumber(mechanical_snes,PETScIter,err_PETSc)
+ call SNESGetIterationNumber(SNES_mechanical,PETScIter,err_PETSc)
CHKERRQ(err_PETSc)
if (nfuncs == 0 .and. PETScIter == 0) totalIter = -1 ! new increment
@@ -559,17 +554,18 @@ subroutine formResidual(da_local,x_local, &
!--------------------------------------------------------------------------------------------------
! get deformation gradient
- call DMDAVecGetArrayF90(da_local,x_local,x_scal,err_PETSc);CHKERRQ(err_PETSc)
- 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,err_PETSc);CHKERRQ(err_PETSc)
+ call DMDAVecRestoreArrayF90(da_local,x_local,x_scal,err_PETSc)
+ CHKERRQ(err_PETSc)
!--------------------------------------------------------------------------------------------------
! evaluate constitutive response
@@ -586,47 +582,53 @@ subroutine formResidual(da_local,x_local, &
!--------------------------------------------------------------------------------------------------
! constructing residual
- call VecSet(f_local,0.0_pReal,err_PETSc);CHKERRQ(err_PETSc)
- call DMDAVecGetArrayF90(da_local,f_local,f_scal,err_PETSc);CHKERRQ(err_PETSc)
- call DMDAVecGetArrayF90(da_local,x_local,x_scal,err_PETSc);CHKERRQ(err_PETSc)
+ 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,err_PETSc);CHKERRQ(err_PETSc)
- call DMDAVecRestoreArrayF90(da_local,f_local,f_scal,err_PETSc);CHKERRQ(err_PETSc)
+ 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,err_PETSc);CHKERRQ(err_PETSc)
- 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,err_PETSc);CHKERRQ(err_PETSc)
+ 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
@@ -643,7 +645,7 @@ subroutine formJacobian(da_local,x_local,Jac_pre,Jac,dummy,err_PETSc)
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
@@ -658,11 +660,12 @@ subroutine formJacobian(da_local,x_local,Jac_pre,Jac,dummy,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)
- ele = 0
- do k = zstart, zend; do j = ystart, yend; do i = xstart, xend
+ 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
@@ -678,49 +681,52 @@ subroutine formJacobian(da_local,x_local,Jac_pre,Jac,dummy,err_PETSc)
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_pPETScInt,row,24_pPetscInt,col,K_ele,ADD_VALUES,err_PETSc)
CHKERRQ(err_PETSc)
enddo; enddo; enddo
- 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 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
+ 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)
- 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)
+ 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,err_PETSc)
- CHKERRQ(err_PETSc) ! initialize to undeformed coordinates (ToDo: use ip coordinates)
+ 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
+ CHKERRQ(err_PETSc) ! get rigid body deformation modes
call DMRestoreGlobalVector(da_local,coordinates,err_PETSc)
CHKERRQ(err_PETSc)
call MatSetNullSpace(Jac,matnull,err_PETSc)
diff --git a/src/grid/grid_mech_spectral_basic.f90 b/src/grid/grid_mech_spectral_basic.f90
index 74400f160..c60c542d0 100644
--- a/src/grid/grid_mech_spectral_basic.f90
+++ b/src/grid/grid_mech_spectral_basic.f90
@@ -50,7 +50,7 @@ module grid_mechanical_spectral_basic
!--------------------------------------------------------------------------------------------------
! PETSc data
DM :: da
- SNES :: snes
+ SNES :: SNES_mechanical
Vec :: solution_vec
!--------------------------------------------------------------------------------------------------
@@ -158,8 +158,10 @@ subroutine grid_mechanical_spectral_basic_init
!--------------------------------------------------------------------------------------------------
! initialize solver specific parts of PETSc
- call SNESCreate(PETSC_COMM_WORLD,snes,err_PETSc); CHKERRQ(err_PETSc)
- call SNESSetOptionsPrefix(snes,'mechanical_',err_PETSc);CHKERRQ(err_PETSc)
+ 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)
@@ -173,19 +175,25 @@ subroutine grid_mechanical_spectral_basic_init
[int(grid(1),pPetscInt)],[int(grid(2),pPetscInt)],localK, & ! local grid
da,err_PETSc) ! handle, error
CHKERRQ(err_PETSc)
- call SNESSetDM(snes,da,err_PETSc); CHKERRQ(err_PETSc) ! connect snes to da
- call DMsetFromOptions(da,err_PETSc); CHKERRQ(err_PETSc)
- call DMsetUp(da,err_PETSc); CHKERRQ(err_PETSc)
- call DMcreateGlobalVector(da,solution_vec,err_PETSc); CHKERRQ(err_PETSc) ! global solution vector (grid x 9, i.e. every def grad tensor)
+ 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,converged,PETSC_NULL_SNES,PETSC_NULL_FUNCTION,err_PETSc) ! specify custom convergence check function "converged"
+ 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)
- call SNESsetFromOptions(snes,err_PETSc); CHKERRQ(err_PETSc) ! pull it all together with additional CLI arguments
!--------------------------------------------------------------------------------------------------
! init fields
- call DMDAVecGetArrayF90(da,solution_vec,F,err_PETSc); CHKERRQ(err_PETSc) ! 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'
@@ -218,7 +226,8 @@ 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,err_PETSc); CHKERRQ(err_PETSc) ! 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'
@@ -270,13 +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,err_PETSc); CHKERRQ(err_PETSc)
-
-!--------------------------------------------------------------------------------------------------
-! check convergence
- call SNESGetConvergedReason(snes,reason,err_PETSc); CHKERRQ(err_PETSc)
+ 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
@@ -310,7 +316,8 @@ subroutine grid_mechanical_spectral_basic_forward(cutBack,guess,Delta_t,Delta_t_
PetscScalar, pointer, dimension(:,:,:,:) :: F
- call DMDAVecGetArrayF90(da,solution_vec,F,err_PETSc); CHKERRQ(err_PETSc)
+ call DMDAVecGetArrayF90(da,solution_vec,F,err_PETSc)
+ CHKERRQ(err_PETSc)
if (cutBack) then
C_volAvg = C_volAvgLastInc
@@ -353,7 +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,err_PETSc); CHKERRQ(err_PETSc)
+ call DMDAVecRestoreArrayF90(da,solution_vec,F,err_PETSc)
+ CHKERRQ(err_PETSc)
!--------------------------------------------------------------------------------------------------
! set module wide available data
@@ -372,9 +380,11 @@ subroutine grid_mechanical_spectral_basic_updateCoords
PetscErrorCode :: err_PETSc
PetscScalar, dimension(:,:,:,:), pointer :: F
- call DMDAVecGetArrayF90(da,solution_vec,F,err_PETSc); CHKERRQ(err_PETSc)
+ call DMDAVecGetArrayF90(da,solution_vec,F,err_PETSc)
+ CHKERRQ(err_PETSc)
call utilities_updateCoords(F)
- call DMDAVecRestoreArrayF90(da,solution_vec,F,err_PETSc); CHKERRQ(err_PETSc)
+ call DMDAVecRestoreArrayF90(da,solution_vec,F,err_PETSc)
+ CHKERRQ(err_PETSc)
end subroutine grid_mechanical_spectral_basic_updateCoords
@@ -388,7 +398,8 @@ subroutine grid_mechanical_spectral_basic_restartWrite
integer(HID_T) :: fileHandle, groupHandle
PetscScalar, dimension(:,:,:,:), pointer :: F
- call DMDAVecGetArrayF90(da,solution_vec,F,err_PETSc); CHKERRQ(err_PETSc)
+ 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)
@@ -415,7 +426,8 @@ subroutine grid_mechanical_spectral_basic_restartWrite
if (num%update_gamma) call utilities_saveReferenceStiffness
- call DMDAVecRestoreArrayF90(da,solution_vec,F,err_PETSc); CHKERRQ(err_PETSc)
+ call DMDAVecRestoreArrayF90(da,solution_vec,F,err_PETSc)
+ CHKERRQ(err_PETSc)
end subroutine grid_mechanical_spectral_basic_restartWrite
@@ -457,6 +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
@@ -465,13 +478,13 @@ end subroutine converged
!> @brief forms the residual vector
!--------------------------------------------------------------------------------------------------
subroutine formResidual(in, F, &
- residuum, dummy, err_PETSc)
+ 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 :: &
@@ -481,8 +494,10 @@ subroutine formResidual(in, F, &
PetscErrorCode :: err_PETSc
integer(MPI_INTEGER_KIND) :: err_MPI
- call SNESGetNumberFunctionEvals(snes,nfuncs,err_PETSc); CHKERRQ(err_PETSc)
- call SNESGetIterationNumber(snes,PETScIter,err_PETSc); CHKERRQ(err_PETSc)
+ 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
@@ -500,7 +515,7 @@ 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_INTEGER_KIND,MPI_LOGICAL,MPI_LOR,MPI_COMM_WORLD,err_MPI)
@@ -515,7 +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
@@ -523,7 +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
diff --git a/src/grid/grid_mech_spectral_polarisation.f90 b/src/grid/grid_mech_spectral_polarisation.f90
index 765a1a5a7..810047403 100644
--- a/src/grid/grid_mech_spectral_polarisation.f90
+++ b/src/grid/grid_mech_spectral_polarisation.f90
@@ -55,7 +55,7 @@ module grid_mechanical_spectral_polarisation
!--------------------------------------------------------------------------------------------------
! PETSc data
DM :: da
- SNES :: snes
+ SNES :: SNES_mechanical
Vec :: solution_vec
!--------------------------------------------------------------------------------------------------
@@ -178,8 +178,10 @@ subroutine grid_mechanical_spectral_polarisation_init
!--------------------------------------------------------------------------------------------------
! initialize solver specific parts of PETSc
- call SNESCreate(PETSC_COMM_WORLD,snes,err_PETSc); CHKERRQ(err_PETSc)
- call SNESSetOptionsPrefix(snes,'mechanical_',err_PETSc);CHKERRQ(err_PETSc)
+ 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)
@@ -193,19 +195,25 @@ subroutine grid_mechanical_spectral_polarisation_init
[int(grid(1),pPetscInt)],[int(grid(2),pPetscInt)],localK, & ! local grid
da,err_PETSc) ! handle, error
CHKERRQ(err_PETSc)
- call SNESSetDM(snes,da,err_PETSc); CHKERRQ(err_PETSc) ! connect snes to da
- call DMsetFromOptions(da,err_PETSc); CHKERRQ(err_PETSc)
- call DMsetUp(da,err_PETSc); CHKERRQ(err_PETSc)
- call DMcreateGlobalVector(da,solution_vec,err_PETSc); CHKERRQ(err_PETSc) ! global solution vector (grid x 18, i.e. every def grad tensor)
+ 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,converged,PETSC_NULL_SNES,PETSC_NULL_FUNCTION,err_PETSc) ! specify custom convergence check function "converged"
+ 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)
- call SNESsetFromOptions(snes,err_PETSc); CHKERRQ(err_PETSc) ! pull it all together with additional CLI arguments
!--------------------------------------------------------------------------------------------------
! init fields
- call DMDAVecGetArrayF90(da,solution_vec,FandF_tau,err_PETSc); CHKERRQ(err_PETSc) ! 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,:,:,:)
@@ -285,7 +293,7 @@ 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
@@ -303,13 +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,err_PETSc); CHKERRQ(err_PETSc)
-
-!--------------------------------------------------------------------------------------------------
-! check convergence
- call SNESGetConvergedReason(snes,reason,err_PETSc); CHKERRQ(err_PETSc)
+ 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
@@ -345,7 +350,8 @@ subroutine grid_mechanical_spectral_polarisation_forward(cutBack,guess,Delta_t,D
real(pReal), dimension(3,3) :: F_lambda33
- call DMDAVecGetArrayF90(da,solution_vec,FandF_tau,err_PETSc); CHKERRQ(err_PETSc)
+ call DMDAVecGetArrayF90(da,solution_vec,FandF_tau,err_PETSc)
+ CHKERRQ(err_PETSc)
F => FandF_tau(0: 8,:,:,:)
F_tau => FandF_tau(9:17,:,:,:)
@@ -446,7 +452,8 @@ subroutine grid_mechanical_spectral_polarisation_restartWrite
integer(HID_T) :: fileHandle, groupHandle
PetscScalar, dimension(:,:,:,:), pointer :: FandF_tau, F, F_tau
- call DMDAVecGetArrayF90(da,solution_vec,FandF_tau,err_PETSc); CHKERRQ(err_PETSc)
+ call DMDAVecGetArrayF90(da,solution_vec,FandF_tau,err_PETSc)
+ CHKERRQ(err_PETSc)
F => FandF_tau(0: 8,:,:,:)
F_tau => FandF_tau(9:17,:,:,:)
@@ -523,6 +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
@@ -531,18 +539,18 @@ end subroutine converged
!> @brief forms the residual vector
!--------------------------------------------------------------------------------------------------
subroutine formResidual(in, FandF_tau, &
- residuum, dummy,err_PETSc)
+ 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
@@ -554,21 +562,23 @@ subroutine formResidual(in, FandF_tau, &
!---------------------------------------------------------------------------------------------------
- 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_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,err_PETSc); CHKERRQ(err_PETSc)
- call SNESGetIterationNumber(snes,PETScIter,err_PETSc); CHKERRQ(err_PETSc)
+ 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
@@ -602,13 +612,13 @@ 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)
+ 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)
!--------------------------------------------------------------------------------------------------
@@ -619,7 +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
@@ -628,11 +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
!--------------------------------------------------------------------------------------------------
diff --git a/src/grid/grid_thermal_spectral.f90 b/src/grid/grid_thermal_spectral.f90
index 8862df725..f102cf2c1 100644
--- a/src/grid/grid_thermal_spectral.f90
+++ b/src/grid/grid_thermal_spectral.f90
@@ -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
@@ -100,10 +99,24 @@ subroutine grid_thermal_spectral_init(T_0)
call PetscOptionsInsertString(PETSC_NULL_OPTIONS,num_grid%get_asString('petsc_options',defaultVal=''),err_PETSc)
CHKERRQ(err_PETSc)
+!--------------------------------------------------------------------------------------------------
+! init fields
+ 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
+ call homogenization_thermal_setField(T_0,0.0_pReal,ce)
+ end do; end do; end do
+
!--------------------------------------------------------------------------------------------------
! initialize solver specific parts of PETSc
- call SNESCreate(PETSC_COMM_WORLD,thermal_snes,err_PETSc); CHKERRQ(err_PETSc)
- call SNESSetOptionsPrefix(thermal_snes,'thermal_',err_PETSc);CHKERRQ(err_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)
@@ -117,42 +130,25 @@ subroutine grid_thermal_spectral_init(T_0)
[int(grid(1),pPetscInt)],[int(grid(2),pPetscInt)],localK, & ! local grid
thermal_grid,err_PETSc) ! handle, error
CHKERRQ(err_PETSc)
- call SNESSetDM(thermal_snes,thermal_grid,err_PETSc); CHKERRQ(err_PETSc) ! connect snes to da
- call DMsetFromOptions(thermal_grid,err_PETSc); CHKERRQ(err_PETSc)
- call DMsetUp(thermal_grid,err_PETSc); 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 SNESSetFromOptions(thermal_snes,err_PETSc); CHKERRQ(err_PETSc) ! pull it all together with additional CLI arguments
-
-!--------------------------------------------------------------------------------------------------
-! init fields
- call DMDAGetCorners(thermal_grid,xstart,ystart,zstart,xend,yend,zend,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)
- 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)
-
- 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,err_PETSc)
CHKERRQ(err_PETSc)
- T_PETSc(xstart:xend,ystart:yend,zstart:zend) = T_current
+ 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
@@ -179,9 +175,9 @@ 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,err_PETSc)
+ call SNESSolve(SNES_thermal,PETSC_NULL_VEC,solution_vec,err_PETSc)
CHKERRQ(err_PETSc)
- call SNESGetConvergedReason(thermal_snes,reason,err_PETSc)
+ call SNESGetConvergedReason(SNES_thermal,reason,err_PETSc)
CHKERRQ(err_PETSc)
if (reason < 1) then
@@ -207,8 +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,err_PETSc); CHKERRQ(err_PETSc)
- call VecMax(solution_vec,devNull,T_max,err_PETSc); CHKERRQ(err_PETSc)
+ 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
@@ -226,7 +224,7 @@ subroutine grid_thermal_spectral_forward(cutBack)
logical, intent(in) :: cutBack
integer :: i, j, k, ce
DM :: dm_local
- PetscScalar, dimension(:,:,:), pointer :: x_scal
+ PetscScalar, dimension(:,:,:), pointer :: T_PETSc
PetscErrorCode :: err_PETSc
if (cutBack) then
@@ -235,12 +233,12 @@ subroutine grid_thermal_spectral_forward(cutBack)
!--------------------------------------------------------------------------------------------------
! reverting thermal field state
- call SNESGetDM(thermal_snes,dm_local,err_PETSc)
+ call SNESGetDM(SNES_thermal,dm_local,err_PETSc)
CHKERRQ(err_PETSc)
- call DMDAVecGetArrayF90(dm_local,solution_vec,x_scal,err_PETSc) !< get the data out of PETSc to work with
+ call DMDAVecGetArrayF90(dm_local,solution_vec,T_PETSc,err_PETSc) !< get the data out of PETSc to work with
CHKERRQ(err_PETSc)
- x_scal(xstart:xend,ystart:yend,zstart:zend) = T_current
- call DMDAVecRestoreArrayF90(dm_local,solution_vec,x_scal,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)
@@ -258,7 +256,7 @@ end subroutine grid_thermal_spectral_forward
!--------------------------------------------------------------------------------------------------
!> @brief forms the spectral thermal residual vector
!--------------------------------------------------------------------------------------------------
-subroutine formResidual(in,x_scal,f_scal,dummy,dummy_err)
+subroutine formResidual(in,x_scal,r,dummy,err_PETSc)
DMDALocalInfo, dimension(DMDA_LOCAL_INFO_SIZE) :: &
in
@@ -267,9 +265,9 @@ subroutine formResidual(in,x_scal,f_scal,dummy,dummy_err)
x_scal
PetscScalar, dimension( &
X_RANGE,Y_RANGE,Z_RANGE), intent(out) :: &
- f_scal
+ r
PetscObject :: dummy
- PetscErrorCode :: dummy_err
+ PetscErrorCode :: err_PETSc
integer :: i, j, k, ce
T_current = x_scal
@@ -304,7 +302,8 @@ subroutine formResidual(in,x_scal,f_scal,dummy,dummy_err)
!--------------------------------------------------------------------------------------------------
! 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
diff --git a/src/grid/spectral_utilities.f90 b/src/grid/spectral_utilities.f90
index 80cde388f..ee5fd4c82 100644
--- a/src/grid/spectral_utilities.f90
+++ b/src/grid/spectral_utilities.f90
@@ -156,7 +156,7 @@ subroutine spectral_utilities_init
integer(C_INTPTR_T) :: alloc_local, local_K, local_K_offset
integer(C_INTPTR_T), parameter :: &
scalarSize = 1_C_INTPTR_T, &
- vecSize = 3_C_INTPTR_T, &
+ vectorSize = 3_C_INTPTR_T, &
tensorSize = 9_C_INTPTR_T
character(len=*), parameter :: &
PETSCDEBUG = ' -snes_view -snes_monitor '
@@ -274,7 +274,7 @@ subroutine spectral_utilities_init
call c_f_pointer(tensorField, tensorField_fourier, [3_C_INTPTR_T,3_C_INTPTR_T, &
gridFFTW(1)/2_C_INTPTR_T + 1_C_INTPTR_T , gridFFTW(2),local_K]) ! place a pointer for a fourier tensor representation
- vectorField = fftw_alloc_complex(vecSize*alloc_local)
+ vectorField = fftw_alloc_complex(vectorSize*alloc_local)
call c_f_pointer(vectorField, vectorField_real, [3_C_INTPTR_T,&
2_C_INTPTR_T*(gridFFTW(1)/2_C_INTPTR_T + 1_C_INTPTR_T),gridFFTW(2),local_K]) ! place a pointer for a real vector representation
call c_f_pointer(vectorField, vectorField_fourier,[3_C_INTPTR_T,&
@@ -288,42 +288,42 @@ subroutine spectral_utilities_init
!--------------------------------------------------------------------------------------------------
! tensor MPI fftw plans
- planTensorForth = fftw_mpi_plan_many_dft_r2c(3, [gridFFTW(3),gridFFTW(2),gridFFTW(1)], & ! dimension, logical length in each dimension in reversed order
- tensorSize, FFTW_MPI_DEFAULT_BLOCK, FFTW_MPI_DEFAULT_BLOCK, &! no. of transforms, default iblock and oblock
- tensorField_real, tensorField_fourier, & ! input data, output data
- PETSC_COMM_WORLD, FFTW_planner_flag) ! use all processors, planer precision
+ planTensorForth = fftw_mpi_plan_many_dft_r2c(3,gridFFTW(3:1:-1),tensorSize, &
+ FFTW_MPI_DEFAULT_BLOCK,FFTW_MPI_DEFAULT_BLOCK, &
+ tensorField_real,tensorField_fourier, &
+ PETSC_COMM_WORLD,FFTW_planner_flag)
if (.not. c_associated(planTensorForth)) error stop 'FFTW error'
- planTensorBack = fftw_mpi_plan_many_dft_c2r(3, [gridFFTW(3),gridFFTW(2),gridFFTW(1)], & ! dimension, logical length in each dimension in reversed order
- tensorSize, FFTW_MPI_DEFAULT_BLOCK, FFTW_MPI_DEFAULT_BLOCK, &! no. of transforms, default iblock and oblock
- tensorField_fourier,tensorField_real, & ! input data, output data
- PETSC_COMM_WORLD, FFTW_planner_flag) ! all processors, planer precision
+ planTensorBack = fftw_mpi_plan_many_dft_c2r(3,gridFFTW(3:1:-1),tensorSize, &
+ FFTW_MPI_DEFAULT_BLOCK, FFTW_MPI_DEFAULT_BLOCK, &
+ tensorField_fourier,tensorField_real, &
+ PETSC_COMM_WORLD, FFTW_planner_flag)
if (.not. c_associated(planTensorBack)) error stop 'FFTW error'
!--------------------------------------------------------------------------------------------------
! vector MPI fftw plans
- planVectorForth = fftw_mpi_plan_many_dft_r2c(3, [gridFFTW(3),gridFFTW(2),gridFFTW(1)], & ! dimension, logical length in each dimension in reversed order
- vecSize, FFTW_MPI_DEFAULT_BLOCK, FFTW_MPI_DEFAULT_BLOCK,&! no. of transforms, default iblock and oblock
- vectorField_real, vectorField_fourier, & ! input data, output data
- PETSC_COMM_WORLD, FFTW_planner_flag) ! use all processors, planer precision
- if (.not. C_ASSOCIATED(planVectorForth)) error stop 'FFTW error'
- planVectorBack = fftw_mpi_plan_many_dft_c2r(3, [gridFFTW(3),gridFFTW(2),gridFFTW(1)], & ! dimension, logical length in each dimension in reversed order
- vecSize, FFTW_MPI_DEFAULT_BLOCK, FFTW_MPI_DEFAULT_BLOCK, & ! no. of transforms, default iblock and oblock
- vectorField_fourier,vectorField_real, & ! input data, output data
- PETSC_COMM_WORLD, FFTW_planner_flag) ! all processors, planer precision
- if (.not. C_ASSOCIATED(planVectorBack)) error stop 'FFTW error'
+ planVectorForth = fftw_mpi_plan_many_dft_r2c(3,gridFFTW(3:1:-1),vectorSize, &
+ FFTW_MPI_DEFAULT_BLOCK,FFTW_MPI_DEFAULT_BLOCK, &
+ vectorField_real,vectorField_fourier, &
+ PETSC_COMM_WORLD,FFTW_planner_flag)
+ if (.not. c_associated(planVectorForth)) error stop 'FFTW error'
+ planVectorBack = fftw_mpi_plan_many_dft_c2r(3,gridFFTW(3:1:-1),vectorSize, &
+ FFTW_MPI_DEFAULT_BLOCK, FFTW_MPI_DEFAULT_BLOCK, &
+ vectorField_fourier,vectorField_real, &
+ PETSC_COMM_WORLD, FFTW_planner_flag)
+ if (.not. c_associated(planVectorBack)) error stop 'FFTW error'
!--------------------------------------------------------------------------------------------------
! scalar MPI fftw plans
- planScalarForth = fftw_mpi_plan_many_dft_r2c(3, [gridFFTW(3),gridFFTW(2),gridFFTW(1)], & ! dimension, logical length in each dimension in reversed order
- scalarSize, FFTW_MPI_DEFAULT_BLOCK, FFTW_MPI_DEFAULT_BLOCK, &! no. of transforms, default iblock and oblock
- scalarField_real, scalarField_fourier, & ! input data, output data
- PETSC_COMM_WORLD, FFTW_planner_flag) ! use all processors, planer precision
- if (.not. C_ASSOCIATED(planScalarForth)) error stop 'FFTW error'
- planScalarBack = fftw_mpi_plan_many_dft_c2r(3, [gridFFTW(3),gridFFTW(2),gridFFTW(1)], & ! dimension, logical length in each dimension in reversed order, no. of transforms
- scalarSize, FFTW_MPI_DEFAULT_BLOCK, FFTW_MPI_DEFAULT_BLOCK, &! no. of transforms, default iblock and oblock
- scalarField_fourier,scalarField_real, & ! input data, output data
- PETSC_COMM_WORLD, FFTW_planner_flag) ! use all processors, planer precision
- if (.not. C_ASSOCIATED(planScalarBack)) error stop 'FFTW error'
+ planScalarForth = fftw_mpi_plan_many_dft_r2c(3,gridFFTW(3:1:-1),scalarSize, &
+ FFTW_MPI_DEFAULT_BLOCK,FFTW_MPI_DEFAULT_BLOCK, &
+ scalarField_real,scalarField_fourier, &
+ PETSC_COMM_WORLD,FFTW_planner_flag)
+ if (.not. c_associated(planScalarForth)) error stop 'FFTW error'
+ planScalarBack = fftw_mpi_plan_many_dft_c2r(3,gridFFTW(3:1:-1),scalarSize, &
+ FFTW_MPI_DEFAULT_BLOCK, FFTW_MPI_DEFAULT_BLOCK, &
+ scalarField_fourier,scalarField_real, &
+ PETSC_COMM_WORLD, FFTW_planner_flag)
+ if (.not. c_associated(planScalarBack)) error stop 'FFTW error'
!--------------------------------------------------------------------------------------------------
! calculation of discrete angular frequencies, ordered as in FFTW (wrap around)
diff --git a/src/lattice.f90 b/src/lattice.f90
index 3089aa30b..e18c71edf 100644
--- a/src/lattice.f90
+++ b/src/lattice.f90
@@ -587,8 +587,8 @@ function lattice_C66_trans(Ntrans,C_parent66,lattice_target, &
!--------------------------------------------------------------------------------------------------
!> @brief Non-schmid projections for bcc with up to 6 coefficients
-! Koester et al. 2012, Acta Materialia 60 (2012) 3894–3901, eq. (17)
-! Gröger et al. 2008, Acta Materialia 56 (2008) 5412–5425, table 1
+! https://doi.org/10.1016/j.actamat.2012.03.053, eq. (17)
+! https://doi.org/10.1016/j.actamat.2008.07.037, table 1
!--------------------------------------------------------------------------------------------------
function lattice_nonSchmidMatrix(Nslip,nonSchmidCoefficients,sense) result(nonSchmidMatrix)
@@ -602,6 +602,7 @@ function lattice_nonSchmidMatrix(Nslip,nonSchmidCoefficients,sense) result(nonSc
type(rotation) :: R
integer :: i
+
if (abs(sense) /= 1) error stop 'Sense in lattice_nonSchmidMatrix'
coordinateSystem = buildCoordinateSystem(Nslip,BCC_NSLIPSYSTEM,BCC_SYSTEMSLIP,'cI',0.0_pReal)
@@ -634,7 +635,9 @@ end function lattice_nonSchmidMatrix
!--------------------------------------------------------------------------------------------------
!> @brief Slip-slip interaction matrix
-!> details only active slip systems are considered
+!> @details only active slip systems are considered
+!> @details https://doi.org/10.1016/j.actamat.2016.12.040 (fcc: Tab S4-1, bcc: Tab S5-1)
+!> @details https://doi.org/10.1016/j.ijplas.2014.06.010 (hex: Tab 3b)
!--------------------------------------------------------------------------------------------------
function lattice_interaction_SlipBySlip(Nslip,interactionValues,lattice) result(interactionMatrix)
@@ -646,6 +649,7 @@ function lattice_interaction_SlipBySlip(Nslip,interactionValues,lattice) result(
integer, dimension(:), allocatable :: NslipMax
integer, dimension(:,:), allocatable :: interactionTypes
+
integer, dimension(FCC_NSLIP,FCC_NSLIP), parameter :: &
FCC_INTERACTIONSLIPSLIP = reshape( [&
1, 2, 2, 4, 7, 5, 3, 5, 5, 4, 6, 7, 10,11,10,11,12,13, & ! -----> acting (forest)
@@ -750,41 +754,113 @@ function lattice_interaction_SlipBySlip(Nslip,interactionValues,lattice) result(
integer, dimension(HEX_NSLIP,HEX_NSLIP), parameter :: &
HEX_INTERACTIONSLIPSLIP = reshape( [&
! basal prism 1. pyr 1. pyr 2. pyr
- 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
- 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
+ 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
- 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
+ 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
- 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
+ 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 non-collinear
+ !< 10 & - & basal/pyramidal collinear
+ !< 11 & - & prismatic/pyramidal non-collinear
+ !< 12 & - & prismatic/pyramidal collinear
+ !< 13 & - & pyramidal self-interaction
+ !< 14 & - & pyramidal non-collinear
+ !< 15 & - & pyramidal collinear
+ !< 16 & - & pyramidal /prismatic non-collinear
+ !< 17 & - & pyramidal /prismatic collinear
+ !< 18 & - & pyramidal /basal non-collinear
+ !< 19 & - & pyramidal /basal collinear
+ !< 20 & - & basal/1. order pyramidal semi-collinear
+ !< 21 & - & basal/1. order pyramidal
+ !< 22 & - & basal/1. order pyramidal
+ !< 23 & - & prismatic/1. order pyramidal semi-collinear
+ !< 24 & - & prismatic/1. order pyramidal
+ !< 25 & - & prismatic/1. order pyramidal semi-coplanar?
+ !< 26 & - & pyramidal /1. order pyramidal coplanar
+ !< 27 & - & pyramidal /1. order pyramidal
+ !< 28 & - & pyramidal /1. order pyramidal semi-collinear
+ !< 29 & - & pyramidal /1. order pyramidal semi-coplanar
+ !< 30 & - & 1. order pyramidal self-interaction
+ !< 31 & - & 1. order pyramidal coplanar
+ !< 32 & - & 1. order pyramidal
+ !< 33 & - & 1. order pyramidal
+ !< 34 & - & 1. order pyramidal semi-coplanar
+ !< 35 & - & 1. order pyramidal semi-coplanar
+ !< 36 & - & 1. order pyramidal collinear
+ !< 37 & - & 1. order pyramidal /pyramidal coplanar
+ !< 38 & - & 1. order pyramidal /pyramidal semi-collinear
+ !< 39 & - & 1. order pyramidal /pyramidal
+ !< 40 & - & 1. order pyramidal /pyramidal semi-coplanar
+ !< 41 & - & 1. order pyramidal /prismatic semi-collinear
+ !< 42 & - & 1. order pyramidal /prismatic semi-coplanar
+ !< 43 & - & 1. order pyramidal /prismatic
+ !< 44 & - & 1. order pyramidal /basal semi-collinear
+ !< 45 & - & 1. order pyramidal /basal
+ !< 46 & - & 1. order pyramidal /basal
+ !< 47 & 8 & basal/2. order pyramidal non-collinear
+ !< 48 & 7 & basal/2. order pyramidal semi-collinear
+ !< 49 & 10 & prismatic/2. order pyramidal
+ !< 50 & 9 & prismatic/2. order pyramidal semi-collinear
+ !< 51 & - & pyramidal /2. order pyramidal
+ !< 52 & - & pyramidal /2. order pyramidal semi collinear
+ !< 53 & - & 1. order pyramidal /2. order pyramidal
+ !< 54 & - & 1. order pyramidal /2. order pyramidal
+ !< 55 & - & 1. order pyramidal /2. order pyramidal
+ !< 56 & - & 1. order pyramidal /2. order pyramidal collinear
+ !< 57 & S3 & 2. order pyramidal self-interaction
+ !< 58 & 16 & 2. order pyramidal non-collinear
+ !< 59 & 15 & 2. order pyramidal semi-collinear
+ !< 60 & - & 2. order pyramidal /1. order pyramidal
+ !< 61 & - & 2. order pyramidal /1. order pyramidal collinear
+ !< 62 & - & 2. order pyramidal /1. order pyramidal
+ !< 63 & - & 2. order pyramidal /1. order pyramidal
+ !< 64 & - & 2. order pyramidal /pyramidal non-collinear
+ !< 65 & - & 2. order pyramidal /pyramidal semi-collinear
+ !< 66 & 14 & 2. order pyramidal /prismatic non-collinear
+ !< 67 & 13 & 2. order pyramidal /prismatic semi-collinear
+ !< 68 & 12 & 2. order pyramidal /basal non-collinear
+ !< 69 & 11 & 2. order pyramidal /basal semi-collinear
integer, dimension(BCT_NSLIP,BCT_NSLIP), parameter :: &
BCT_INTERACTIONSLIPSLIP = reshape( [&
diff --git a/src/material.f90 b/src/material.f90
index 52940ee4a..1e3a4b4ec 100644
--- a/src/material.f90
+++ b/src/material.f90
@@ -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
diff --git a/src/math.f90 b/src/math.f90
index 3ea4d6a08..db0666ab0 100644
--- a/src/math.f90
+++ b/src/math.f90
@@ -84,38 +84,34 @@ contains
subroutine math_init
real(pReal), dimension(4) :: randTest
- integer :: &
- randSize, &
- randomSeed !< fixed seeding for pseudo-random number generator, Default 0: use random seed
- integer, dimension(:), allocatable :: randInit
+ integer :: randSize
+ integer, dimension(:), allocatable :: seed
class(tNode), pointer :: &
num_generic
+
print'(/,1x,a)', '<<<+- math init -+>>>'; flush(IO_STDOUT)
num_generic => config_numerics%get('generic',defaultVal=emptyDict)
- randomSeed = num_generic%get_asInt('random_seed', defaultVal = 0)
call random_seed(size=randSize)
- allocate(randInit(randSize))
- if (randomSeed > 0) then
- randInit = randomSeed
+ allocate(seed(randSize))
+
+ if (num_generic%contains('random_seed')) then
+ seed = num_generic%get_as1dInt('random_seed',requiredSize=randSize)
else
call random_seed()
- call random_seed(get = randInit)
- randInit(2:randSize) = randInit(1)
- 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
diff --git a/src/parallelization.f90 b/src/parallelization.f90
index d9ca15981..29deaf724 100644
--- a/src/parallelization.f90
+++ b/src/parallelization.f90
@@ -53,6 +53,7 @@ contains
subroutine parallelization_init
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
@@ -112,6 +113,7 @@ subroutine parallelization_init
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
diff --git a/src/phase_mechanical_eigen_thermalexpansion.f90 b/src/phase_mechanical_eigen_thermalexpansion.f90
index 087cf7d3d..70bf84cd8 100644
--- a/src/phase_mechanical_eigen_thermalexpansion.f90
+++ b/src/phase_mechanical_eigen_thermalexpansion.f90
@@ -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 &
)
diff --git a/src/phase_mechanical_elastic.f90 b/src/phase_mechanical_elastic.f90
index bb530747b..8972367d5 100644
--- a/src/phase_mechanical_elastic.f90
+++ b/src/phase_mechanical_elastic.f90
@@ -101,32 +101,32 @@ pure module function elastic_C66(ph,en) result(C66)
T = thermal_T(ph,en)
C66(1,1) = prm%C_11(1) &
- + prm%C_11(2)*(T - prm%T_ref)**1 &
+ + prm%C_11(2)*(T - prm%T_ref) &
+ 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(2)*(T - prm%T_ref) &
+ 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(2)*(T - prm%T_ref) &
+ prm%C_44(3)*(T - prm%T_ref)**2
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(2)*(T - prm%T_ref) &
+ 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(2)*(T - prm%T_ref) &
+ prm%C_33(3)*(T - prm%T_ref)**2
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(2)*(T - prm%T_ref) &
+ prm%C_66(3)*(T - prm%T_ref)**2
end if
diff --git a/src/rotations.f90 b/src/rotations.f90
index b4728e38b..b73fbe8da 100644
--- a/src/rotations.f90
+++ b/src/rotations.f90
@@ -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