diff --git a/SConstruct b/SConstruct
index fb2efbe..a0dc6b9 100644
--- a/SConstruct
+++ b/SConstruct
@@ -1,473 +1,473 @@
# -*- mode:python; coding: utf-8 -*-
# vim: set ft=python:
# @file
-# @section LICENSE
+# LICENSE
#
# Copyright (©) 2016-2021 EPFL (École Polytechnique Fédérale de Lausanne),
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# This program is free software: you can redistribute it and/or modify
# 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 Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see .
# ------------------------------------------------------------------------------
# Imports
# ------------------------------------------------------------------------------
from __future__ import print_function
import sys
import os
from subprocess import check_output
# Import below not strictly necessary, but good for pep8
from SCons.Script import (
EnsurePythonVersion,
EnsureSConsVersion,
Help,
Environment,
Variables,
EnumVariable,
PathVariable,
BoolVariable,
ListVariable,
Split,
Export,
Dir,
)
from SCons.Errors import StopError
from SCons import __version__ as scons_version
from version import get_git_subst
from detect import (
FindFFTW,
FindBoost,
FindThrust,
FindCuda,
FindExpolit,
FindPybind11
)
from INFOS import TAMAAS_INFOS
# ------------------------------------------------------------------------------
EnsurePythonVersion(2, 7)
EnsureSConsVersion(2, 4)
# ------------------------------------------------------------------------------
def detect_dependencies(env):
"Detect all dependencies"
fftw_comp = {
'omp': ['omp'],
'threads': ['threads'],
'none': [],
}
fftw_components = fftw_comp[env['fftw_threads']]
if main_env['use_mpi']:
fftw_components.append('mpi')
FindFFTW(env, fftw_components, precision=env['real_type'])
FindBoost(env, ['boost/preprocessor/seq.hpp'])
FindExpolit(env)
thrust_var = 'THRUST_ROOT'
# Take cuda version of thrust if available
if 'CUDA_ROOT' in env['ENV']:
thrust_var = 'CUDA_ROOT'
FindThrust(env, env['backend'], thrust_var)
# Activate cuda if needed
if env['backend'] == 'cuda':
FindCuda(env)
if env['build_python']:
FindPybind11(env)
def subdir(env, dir):
"Building a sub-directory"
return env.SConscript(env.File('SConscript', dir),
variant_dir=env.Dir(dir, env['build_dir']),
duplicate=True)
# ------------------------------------------------------------------------------
# Main compilation
# ------------------------------------------------------------------------------
# Compilation colors
colors = {
'cyan': '\033[96m',
'purple': '\033[95m',
'blue': '\033[94m',
'green': '\033[92m',
'yellow': '\033[93m',
'gray': '\033[38;5;8m',
'orange': '\033[38;5;208m',
'red': '\033[91m',
'end': '\033[0m'
}
# Inherit all environment variables (for CXX detection, etc.)
main_env = Environment(
ENV=os.environ,
)
# Set tamaas information
for k, v in TAMAAS_INFOS.items():
main_env[k] = v
main_env['COLOR_DICT'] = colors
main_env.AddMethod(subdir, 'SubDirectory')
# Build variables
vars = Variables('build-setup.conf')
vars.AddVariables(
EnumVariable('build_type', 'Build type', 'release',
allowed_values=('release', 'profiling', 'debug'),
ignorecase=2),
EnumVariable('backend', 'Thrust backend', 'omp',
allowed_values=('cpp', 'omp', 'tbb'),
ignorecase=2),
EnumVariable('fftw_threads', 'Threads FFTW library preference', 'omp',
allowed_values=('omp', 'threads', 'none'),
ignorecase=2),
EnumVariable('sanitizer', 'Sanitizer type', 'none',
allowed_values=('none', 'memory', 'leaks', 'address'),
ignorecase=2),
PathVariable('prefix',
'Prefix where to install', '/usr/local'),
# Dependencies paths
PathVariable('FFTW_ROOT',
'FFTW custom path', os.getenv('FFTW_ROOT', ''),
PathVariable.PathAccept),
PathVariable('THRUST_ROOT',
'Thrust custom path', os.getenv('THRUST_ROOT', ''),
PathVariable.PathAccept),
PathVariable('BOOST_ROOT',
'Boost custom path', os.getenv('BOOST_ROOT', ''),
PathVariable.PathAccept),
PathVariable('CUDA_ROOT',
'Cuda custom path', os.getenv('CUDA_ROOT', ''),
PathVariable.PathAccept),
# Dependencies provided as submodule get different default
PathVariable('GTEST_ROOT',
'Googletest custom path',
os.getenv('GTEST_ROOT', '#third-party/googletest/googletest'),
PathVariable.PathAccept),
PathVariable('PYBIND11_ROOT',
'Pybind11 custom path',
os.getenv('PYBIND11_ROOT', '#third-party/pybind11/include'),
PathVariable.PathAccept),
PathVariable('EXPOLIT_ROOT',
'Expolit custom path',
os.getenv('EXPOLIT_ROOT', '#third-party/expolit/include'),
PathVariable.PathAccept),
# Executables
('CXX', 'Compiler', os.getenv('CXX', 'g++')),
('MPICXX', 'MPI Compiler wrapper', os.getenv('MPICXX', 'mpicxx')),
('py_exec', 'Python executable', 'python3'),
# Compiler flags
('CXXFLAGS', 'C++ compiler flags', os.getenv('CXXFLAGS', "")),
# Cosmetic
BoolVariable('verbose', 'Activate verbosity', False),
BoolVariable('color', 'Color the non-verbose compilation output', False),
# Tamaas components
BoolVariable('build_doc', 'Build documentation', False),
BoolVariable('build_tests', 'Build test suite', False),
BoolVariable('build_python', 'Build python wrapper', True),
# Documentation
ListVariable('doc_builders', 'Generated documentation formats',
default='html', names=Split("html man")), # TODO include latex
# Dependencies
BoolVariable('use_googletest', 'Build tests using GTest', False),
BoolVariable('use_mpi', 'Builds multi-process parallelism', False),
# Distribution options
BoolVariable('strip_info', 'Strip binary of added information', False),
BoolVariable('build_static_lib', "Build a static libTamaas", False),
# Type variables
EnumVariable('real_type', 'Type for real precision variables', 'double',
allowed_values=('double', 'long double')),
EnumVariable('integer_type', 'Type for integer variables', 'int',
allowed_values=('int', 'long')),
)
# Set variables of environment
vars.Update(main_env)
help_text = vars.GenerateHelpText(main_env)
help_text += """
Commands:
scons [build] [options]... Compile Tamaas (and additional modules/tests)
scons install [prefix=/your/prefix] [options]... Install Tamaas to prefix
scons dev Install symlink to Tamaas python module (useful to development purposes)
scons test Run tests with pytest
scons doc Compile documentation with Doxygen and Sphinx+Breathe
scons archive Create a gzipped archive from source
""" # noqa
Help(help_text)
# Save all options, not just those that differ from default
with open('build-setup.conf', 'w') as setup:
for option in vars.options:
setup.write("# " + option.help.replace('\n', '\n# ') + "\n")
setup.write("{} = '{}'\n".format(option.key, main_env[option.key]))
main_env['should_configure'] = \
not main_env.GetOption('clean') and not main_env.GetOption('help')
build_type = main_env['build_type']
build_dir = 'build-${build_type}'
main_env['build_dir'] = main_env.Dir(build_dir)
# Printing some build infos
if main_env['should_configure']:
print('-- SCons {} (Python {}.{})'.format(scons_version,
sys.version_info.major,
sys.version_info.minor))
print(main_env.subst("-- Build type: ${build_type}\n"
"-- Thrust backend: ${backend}\n"
"-- FFTW threads: ${fftw_threads}\n"
"-- MPI: ${use_mpi}\n"
"-- Build directory: ${build_dir}"))
# Setting up the python name with version
if main_env['build_python']:
args = (main_env.subst("${py_exec} -c").split()
+ ["from distutils.sysconfig import get_python_version;"
"print(get_python_version())"])
main_env['py_version'] = bytes(check_output(args)).decode()
print(main_env.subst('-- Python version (bindings): $py_version'))
verbose = main_env['verbose']
# Remove colors if not set
if not main_env['color']:
for key in colors:
colors[key] = ''
if not verbose:
main_env['CXXCOMSTR'] = main_env['SHCXXCOMSTR'] = \
u'{0}[Compiling ($SHCXX)] {1}$SOURCE'.format(colors['green'],
colors['end'])
main_env['LINKCOMSTR'] = main_env['SHLINKCOMSTR'] = \
u'{0}[Linking] {1}$TARGET'.format(colors['purple'],
colors['end'])
main_env['ARCOMSTR'] = u'{}[Ar]{} $TARGET'.format(colors['purple'],
colors['end'])
main_env['RANLIBCOMSTR'] = \
u'{}[Randlib]{} $TARGET'.format(colors['purple'],
colors['end'])
main_env['PRINT_CMD_LINE_FUNC'] = pretty_cmd_print
# Include paths
main_env.AppendUnique(CPPPATH=['#/src',
'#/src/core',
'#/src/mpi',
'#/src/bem',
'#/src/surface',
'#/src/python',
'#/src/percolation',
'#/src/model',
'#/src/model/elasto_plastic',
'#/src/solvers',
'#/src/gpu',
'#/python'])
# Changing the shared object extension
main_env['SHOBJSUFFIX'] = '.o'
# Back to gcc if cuda is activated
if main_env['backend'] == "cuda" and "g++" not in main_env['CXX']:
raise StopError('GCC should be used when compiling with CUDA')
# OpenMP flags - compiler dependent
omp_flags = {
"g++": ["-fopenmp"],
"clang++": ["-fopenmp"],
"icpc": ["-qopenmp"]
}
def cxx_alias(cxx):
for k in omp_flags.keys():
if k in cxx:
return k
raise StopError('Unsupported compiler: ' + cxx)
cxx = cxx_alias(main_env['CXX'])
# Setting main compilation flags
main_env['CXXFLAGS'] = Split(main_env['CXXFLAGS'])
main_env['LINKFLAGS'] = main_env['CXXFLAGS']
main_env.AppendUnique(
CXXFLAGS=Split('-std=c++14 -Wall -Wextra -pedantic'),
CPPDEFINES={
'TAMAAS_LOOP_BACKEND': 'TAMAAS_LOOP_BACKEND_${backend.upper()}',
'TAMAAS_FFTW_BACKEND': 'TAMAAS_FFTW_BACKEND_${fftw_threads.upper()}'
},
)
# Adding OpenMP flags
if main_env['backend'] == 'omp':
main_env.AppendUnique(CXXFLAGS=omp_flags[cxx])
main_env.AppendUnique(LINKFLAGS=omp_flags[cxx])
else:
main_env.AppendUnique(CXXFLAGS=['-Wno-unknown-pragmas'])
# Correct bug in clang?
if main_env['backend'] == 'omp' and cxx == "clang++":
main_env.AppendUnique(LIBS=["atomic"])
elif main_env['backend'] == 'tbb':
main_env.AppendUnique(LIBS=['tbb'])
# Manage MPI compiler
if main_env['use_mpi']:
main_env['CXX'] = '$MPICXX'
main_env.AppendUnique(CPPDEFINES=['TAMAAS_USE_MPI'])
main_env.AppendUnique(CXXFLAGS=['-Wno-cast-function-type'])
# Flags and options
if main_env['build_type'] == 'debug':
main_env.AppendUnique(CPPDEFINES=['TAMAAS_DEBUG'])
# Define the scalar types
main_env.AppendUnique(CPPDEFINES={'TAMAAS_REAL_TYPE': '${real_type}',
'TAMAAS_INT_TYPE': '${integer_type}'})
# Compilation flags
cxxflags_dict = {
"debug": Split("-g -O0"),
"profiling": Split("-g -O3 -fno-omit-frame-pointer"),
"release": Split("-O3")
}
if main_env['sanitizer'] != 'none':
if main_env['backend'] == 'cuda':
raise StopError(
"Sanitizers with cuda are not yet supported!")
cxxflags_dict[build_type].append('-fsanitize=${sanitizer}')
main_env.AppendUnique(CXXFLAGS=cxxflags_dict[build_type])
main_env.AppendUnique(SHLINKFLAGS=cxxflags_dict[build_type])
main_env.AppendUnique(LINKFLAGS=cxxflags_dict[build_type])
if main_env['should_configure']:
basic_checks(main_env)
detect_dependencies(main_env)
# Writing information file
main_env.Tool('textfile')
main_env['SUBST_DICT'] = get_git_subst()
# Empty values if requested
if main_env['strip_info']:
for k in main_env['SUBST_DICT']:
main_env['SUBST_DICT'][k] = ""
# Substitution of environment file
main_env['SUBST_DICT'].update({
'@build_type@': '$build_type',
'@build_dir@': '${build_dir.abspath}',
'@build_version@': '$version',
})
# Environment file content
env_content = """export PYTHONPATH=@build_dir@/python:$$PYTHONPATH
export LD_LIBRARY_PATH=@build_dir@/src:$$LD_LIBRARY_PATH
"""
# Writing environment file
env_file = main_env.Textfile(
main_env.File('tamaas_environment.sh', main_env['build_dir']),
env_content)
# Default targets
build_targets = ['build-cpp', env_file]
install_targets = ['install-lib']
if main_env._get_major_minor_revision(scons_version)[0] >= 4:
main_env.Tool('compilation_db')
main_env.CompilationDatabase(PRINT_CMD_LINE_FUNC=pretty_cmd_print)
# Building Tamaas library
Export('main_env')
main_env.SubDirectory('src')
# Building Tamaas extra components
for dir in ['python', 'tests']:
if main_env['build_{}'.format(dir)] and not main_env.GetOption('help'):
main_env.SubDirectory(dir)
build_targets.append('build-{}'.format(dir))
# Building API + Sphinx documentation if requested
if main_env['build_doc']:
main_env.SubDirectory('doc')
main_env.Alias('doc', 'build-doc')
install_targets.append('install-doc')
else:
dummy_command(main_env, 'doc', 'Command "doc" does not do anything'
' without documentation activated ("build_doc=True")')
# Define dummy dev command when python is deactivated
if not main_env['build_python']:
dummy_command(main_env, 'dev', 'Command "dev" does not do anything'
+ ' without python activated ("build_python=True")')
else:
install_targets.append('install-python')
# Define dummy test command when tests are deactivated
if not main_env['build_tests']:
dummy_command(main_env, 'test', 'Command "test" does not do anything'
+ ' without tests activated ("build_tests=True")')
# Definition of target aliases, a.k.a. sub-commands
main_env.Alias('build', build_targets)
# Define proper install targets
main_env.Alias('install', install_targets)
# Default target is to build stuff
main_env.Default('build')
# Building a tar archive
archive = main_env.Command(
'tamaas-${version}.tar.gz',
'',
('tar --exclude-vcs --exclude-vcs-ignores '
'--exclude=third-party/googletest '
'--exclude=third-party/pybind11 '
'--exclude=joss '
'--exclude=".*" '
'-czf $TARGET {}'.format(Dir('.').name)),
chdir='..',
)
main_env.Alias('archive', archive)
diff --git a/doc/SConscript b/doc/SConscript
index ba7eb35..c8b3aec 100644
--- a/doc/SConscript
+++ b/doc/SConscript
@@ -1,94 +1,94 @@
# -*- mode:python; coding: utf-8 -*-
# vim: set ft=python:
# @file
-# @section LICENSE
+# LICENSE
#
# Copyright (©) 2016-2021 EPFL (École Polytechnique Fédérale de Lausanne),
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as published
# by the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see .
from __future__ import print_function
from SCons.Script import Import, Glob, Dir, File
def add_sources(source_list, dirname, fnames):
source_list += Dir(dirname).glob('*.hh')
source_list += Dir(dirname).glob('*.cpp')
Import('main_env')
Import('libTamaas')
doc_env = main_env.Clone()
# Generating Doxyfile
doxygen_verbose = {True: "NO", False: "YES"}
doxyfile_target = doc_env.Substfile('doxygen/Doxyfile', 'doxygen/Doxyfile.in',
SUBST_DICT={
'@version@': '$version',
'@build_dir@': Dir('doxygen').path,
'@logo@': File('icon.svg').path,
'@src_dir@': Dir('#src').abspath,
'@verbose@':
doxygen_verbose[doc_env["verbose"]],
})
# Generate Doxygen API documentation
doc_env.Tool('doxygen')
doxygen_target = doc_env.Doxygen('doxygen/xml/index.xml',
[doxyfile_target, 'icon.svg'])
# Adding all source files as dependencies
sources = []
Dir('#src').walk(add_sources, sources)
doc_env.Depends(doxygen_target, sources)
# Generate Sphinx User documentation
sphinx_targets_map = {
"html": "sphinx/html/index.html",
"man": "sphinx/tamaas.1",
"latex": "sphinx/latex/Tamaas.tex"
}
doc_env.Tool('sphinx')
doc_env['IMPLICIT_COMMAND_DEPENDENCIES'] = 0
sphinx_sources = [Glob('sphinx/source/*'), Glob('sphinx/source/figures/*')]
sphinx_targets = {
builder: doc_env.Sphinx(sphinx_targets_map[builder], sphinx_sources)
for builder in doc_env['doc_builders']
}
doc_env.Depends(sphinx_targets.values(), doxygen_target)
# Alias for both docs
doc_targets = [doxygen_target] + sphinx_targets.values()
main_env.Alias('build-doc', doc_targets)
# Install target for documentation
share = Dir('share', doc_env['prefix'])
doc_install = []
sphinx_prefix_map = {}
if "html" in doc_env['doc_builders']:
doc_install.append(doc_env.Install(target=share.Dir('doc').Dir('tamaas'),
source=sphinx_targets['html'][0].dir))
if "man" in doc_env['doc_builders']:
doc_install.append(doc_env.Install(target=share.Dir('man').Dir('man1'),
source=sphinx_targets['man']))
main_env.Alias('install-doc', doc_install)
diff --git a/doc/sphinx/source/conf.py b/doc/sphinx/source/conf.py
index 24eeb1b..df5fbc7 100644
--- a/doc/sphinx/source/conf.py
+++ b/doc/sphinx/source/conf.py
@@ -1,241 +1,243 @@
# -*- coding: utf-8 -*-
#
# Configuration file for the Sphinx documentation builder.
#
# This file does only contain a selection of the most common options. For a
# full list see the documentation:
# http://www.sphinx-doc.org/en/master/config
# -- Path setup --------------------------------------------------------------
# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
#
import os
import sys
import subprocess
+import warnings
+warnings.filterwarnings("ignore")
# -- Project information -----------------------------------------------------
project = 'Tamaas'
copyright = "2019-2021, EPFL (École Polytechnique Fédérale de Lausanne)," \
+ " Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)"
author = 'Lucas Frérot'
# Looking for SConstruct file
def find_root(limit):
path = '..'
for i in range(limit):
dir_entries = os.listdir(path)
if 'INFOS.py' in dir_entries:
return path
else:
path = os.path.join('..', path)
raise RuntimeError('Could not find INFOS.py '
'in the {} parent directories'.format(limit))
root = find_root(4)
sys.path.insert(0, os.path.abspath(root))
from INFOS import TAMAAS_INFOS # noqa
# The short X.Y version
version = '.'.join(TAMAAS_INFOS['version'].split('.')[:2])
# The full version, including alpha/beta/rc tags
release = TAMAAS_INFOS['version']
# -- General configuration ---------------------------------------------------
# If your documentation needs a minimal Sphinx version, state it here.
#
# needs_sphinx = '1.0'
# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = [
'sphinx.ext.autodoc',
'sphinx.ext.mathjax',
'sphinx.ext.viewcode',
'sphinx.ext.intersphinx',
'sphinx.ext.imgconverter',
'breathe',
]
# Add any paths that contain templates here, relative to this directory.
templates_path = ['.templates']
# The suffix(es) of source filenames.
# You can specify multiple suffix as a list of string:
#
# source_suffix = ['.rst', '.md']
source_suffix = '.rst'
# The master toctree document.
master_doc = 'index'
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#
# This is also used if you do content translation via gettext catalogs.
# Usually you set "language" from the command line for these cases.
language = None
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This pattern also affects html_static_path and html_extra_path.
exclude_patterns = []
# The name of the Pygments (syntax highlighting) style to use.
pygments_style = None
# -- Options for HTML output -------------------------------------------------
# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
#
html_theme = 'sphinx_rtd_theme'
# Theme options are theme-specific and customize the look and feel of a theme
# further. For a list of options available for each theme, see the
# documentation.
#
# html_theme_options = {}
html_logo = '../../icon.svg'
# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
html_static_path = []
# Custom sidebar templates, must be a dictionary that maps document names
# to template names.
#
# The default sidebars (for documents that don't match any pattern) are
# defined by theme itself. Builtin themes are using these templates by
# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
# 'searchbox.html']``.
#
# html_sidebars = {}
# -- Options for HTMLHelp output ---------------------------------------------
# Output file base name for HTML help builder.
htmlhelp_basename = 'Tamaasdoc'
# -- Options for LaTeX output ------------------------------------------------
latex_engine = 'lualatex'
latex_elements = {
# The paper size ('letterpaper' or 'a4paper').
#
# 'papersize': 'letterpaper',
# The font size ('10pt', '11pt' or '12pt').
#
# 'pointsize': '10pt',
# Additional stuff for the LaTeX preamble.
#
# 'preamble': '',
# Latex figure (float) alignment
#
# 'figure_align': 'htbp',
}
# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title,
# author, documentclass [howto, manual, or own class]).
latex_documents = [
(master_doc, 'Tamaas.tex', 'Tamaas Documentation',
author, 'manual'),
]
# -- Options for manual page output ------------------------------------------
# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
(master_doc, 'tamaas', 'a library for fast periodic rough contact',
[author], 1)
]
# -- Options for Texinfo output ----------------------------------------------
# Grouping the document tree into Texinfo files. List of tuples
# (source start file, target name, title, author,
# dir menu entry, description, category)
texinfo_documents = [
(master_doc, 'Tamaas', 'Tamaas Documentation',
author, 'Tamaas', 'One line description of project.',
'Miscellaneous'),
]
# -- Options for Epub output -------------------------------------------------
# Bibliographic Dublin Core info.
epub_title = project
# The unique identifier of the text. This can be a ISBN number
# or the project homepage.
#
# epub_identifier = ''
# A unique identification for the text.
#
# epub_uid = ''
# A list of files that should not be packed into the epub file.
epub_exclude_files = ['search.html']
# -- Extension configuration -------------------------------------------------
# If on RTD build, run doxygen
on_read_the_docs = os.environ.get('READTHEDOCS') == 'True'
if on_read_the_docs:
SUBST_DICT = {
'@version@': TAMAAS_INFOS['version'],
'@build_dir@': 'doxygen',
'@logo@': 'icon.svg',
'@src_dir@': '../src/',
'@verbose@': "YES",
}
current_dir = os.getcwd()
os.chdir('../..')
with open('doxygen/Doxyfile.in', 'r') as doxyfile:
contents = doxyfile.read()
for k, v in SUBST_DICT.items():
contents = contents.replace(k, v)
with open('doxygen/Doxyfile', 'w') as doxyfile:
doxyfile.write(contents)
subprocess.call('doxygen doxygen/Doxyfile', shell=True)
os.chdir(current_dir)
breathe_projects = {
'tamaas': '../../doxygen/xml'
}
breathe_default_project = 'tamaas'
intersphinx_mapping = {
'numpy': ('https://numpy.org/doc/stable/', None),
'scipy': ('https://docs.scipy.org/doc/scipy/reference', None),
}
diff --git a/examples/adhesion.py b/examples/adhesion.py
index 6c44bb1..84bcad8 100644
--- a/examples/adhesion.py
+++ b/examples/adhesion.py
@@ -1,122 +1,122 @@
#!/usr/bin/env python3
# @file
-# @section LICENSE
+# LICENSE
#
# Copyright (©) 2016-2021 EPFL (École Polytechnique Fédérale de Lausanne),
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# This program is free software: you can redistribute it and/or modify
# 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 Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see .
import tamaas as tm
import matplotlib.pyplot as plt
import numpy as np
import argparse
from matplotlib.colors import ListedColormap
class AdhesionPython(tm.Functional):
"""
Functional class that extends a C++ class and implements the virtual
methods
"""
def __init__(self, rho, gamma):
tm.Functional.__init__(self)
self.rho = rho
self.gamma = gamma
def computeF(self, gap, pressure):
return -self.gamma * np.sum(np.exp(-gap / self.rho))
def computeGradF(self, gap, gradient):
gradient += self.gamma * np.exp(-gap / self.rho) / self.rho
parser = argparse.ArgumentParser()
parser.add_argument('--local-functional', dest="py_adh", action="store_true",
help="use the adhesion functional written in python")
args = parser.parse_args()
# Surface size
n = 1024
# Surface generator
sg = tm.SurfaceGeneratorFilter2D([n, n])
sg.random_seed = 0
# Spectrum
sg.spectrum = tm.Isopowerlaw2D()
# Parameters
sg.spectrum.q0 = 16
sg.spectrum.q1 = 16
sg.spectrum.q2 = 64
sg.spectrum.hurst = 0.8
# Generating surface
surface = sg.buildSurface()
surface /= n
plt.imshow(surface)
plt.title('Rough surface')
# Creating model
model = tm.ModelFactory.createModel(tm.model_type.basic_2d, [1., 1.], [n, n])
# Solver
solver = tm.PolonskyKeerRey(model, surface, 1e-12,
tm.PolonskyKeerRey.gap,
tm.PolonskyKeerRey.gap)
adhesion_params = {
"rho": 2e-3,
"surface_energy": 2e-5
}
# Use the python derived from C++ functional class
if args.py_adh:
adhesion = AdhesionPython(adhesion_params["rho"],
adhesion_params["surface_energy"])
# Use the C++ class
else:
adhesion = tm.ExponentialAdhesionFunctional(surface)
adhesion.parameters = adhesion_params
solver.addFunctionalTerm(adhesion)
# Solve for target pressure
g_target = 5e-2
solver.solve(g_target)
tractions = model.traction
plt.figure()
plt.imshow(tractions)
plt.colorbar()
plt.title('Contact tractions')
plt.figure()
zones = np.zeros_like(tractions)
tol = 1e-6
zones[tractions > tol] = 1
zones[tractions < -tol] = -1
plt.imshow(zones, cmap=ListedColormap(['white', 'gray', 'black']))
plt.colorbar(ticks=[-2/3, 0, 2/3]).set_ticklabels([
'Adhesion', 'No Contact', 'Contact'
])
plt.title('Contact and Adhesion Zones')
plt.show()
diff --git a/examples/plasticity.py b/examples/plasticity.py
index 139973e..2683e1f 100644
--- a/examples/plasticity.py
+++ b/examples/plasticity.py
@@ -1,85 +1,85 @@
#!/usr/bin/env python3
# @file
-# @section LICENSE
+# LICENSE
#
# Copyright (©) 2016-2021 EPFL (École Polytechnique Fédérale de Lausanne),
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# This program is free software: you can redistribute it and/or modify
# 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 Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see .
import numpy as np
import tamaas as tm
from tamaas.dumpers import H5Dumper as Dumper
from tamaas.nonlinear_solvers import DFSANECXXSolver as Solver, ToleranceManager
# Definition of modeled domain
model_type = tm.model_type.volume_2d
discretization = [32, 51, 51]
flat_domain = [1, 1]
system_size = [0.5] + flat_domain
# Creation of model
model = tm.ModelFactory.createModel(model_type,
system_size,
discretization)
model.E = 1.
model.nu = 0.3
# Setup for plasticity
residual = tm.ModelFactory.createResidual(model,
sigma_y=0.1 * model.E,
hardening=0.01 * model.E)
# Possibly change integration method
# residual.setIntegrationMethod(tm.integration_method.cutoff, 1e-12)
# Setup non-linear solver with variable tolerance
epsolver = ToleranceManager(1e-5, 1e-9, 1/4)(Solver)(residual)
# Setup for contact
x = np.linspace(0, system_size[1], discretization[1],
endpoint=False, dtype=tm.dtype)
y = np.linspace(0, system_size[2], discretization[2],
endpoint=False, dtype=tm.dtype)
xx, yy = np.meshgrid(x, y, indexing='ij')
R = 0.2
surface = -((xx - flat_domain[0] / 2)**2 +
(yy - flat_domain[1] / 2)**2) / (2 * R)
# Extract local part of the global surface
local_shape = tm.mpi.local_shape(surface.shape)
offset = tm.mpi.local_offset(surface.shape)
local_surface = surface[offset:offset+local_shape[0], :].copy()
csolver = tm.PolonskyKeerRey(model, local_surface, 1e-12,
tm.PolonskyKeerRey.pressure,
tm.PolonskyKeerRey.pressure)
# EPIC setup
epic = tm.EPICSolver(csolver, epsolver, 1e-7)
# Dumper
dumper_helper = Dumper('hertz', 'displacement', 'stress', 'plastic_strain')
model.addDumper(dumper_helper)
loads = np.linspace(0.001, 0.005, 3)
for i, load in enumerate(loads):
epic.acceleratedSolve(load)
model.dump()
tm.Logger().get(tm.LogLevel.info) \
<< "---> Solved load step {}/{}".format(i+1, len(loads))
diff --git a/examples/rough_contact.py b/examples/rough_contact.py
index aa53e80..4502767 100644
--- a/examples/rough_contact.py
+++ b/examples/rough_contact.py
@@ -1,64 +1,64 @@
#!/usr/bin/env python3
# @file
-# @section LICENSE
+# LICENSE
#
# Copyright (©) 2016-2021 EPFL (École Polytechnique Fédérale de Lausanne),
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# This program is free software: you can redistribute it and/or modify
# 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 Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see .
import tamaas as tm
import matplotlib.pyplot as plt
# Initialize threads and fftw
tm.set_log_level(tm.LogLevel.info) # Show progression of solver
# Surface size
n = 512
# Surface generator
sg = tm.SurfaceGeneratorFilter2D([n, n])
sg.random_seed = 0
# Spectrum
sg.spectrum = tm.Isopowerlaw2D()
# Parameters
sg.spectrum.q0 = 16
sg.spectrum.q1 = 16
sg.spectrum.q2 = 64
sg.spectrum.hurst = 0.8
# Generating surface
surface = sg.buildSurface()
surface /= tm.Statistics2D.computeSpectralRMSSlope(surface)
plt.imshow(surface)
# Creating model
model = tm.ModelFactory.createModel(tm.model_type.basic_2d, [1., 1.], [n, n])
# Solver
solver = tm.PolonskyKeerRey(model, surface, 1e-12)
# Solve for target pressure
p_target = 0.1
solver.solve(p_target)
plt.figure()
plt.imshow(model.traction)
plt.title('Contact tractions')
print(model.traction.mean())
plt.show()
diff --git a/examples/saturated.py b/examples/saturated.py
index dfad863..b9f772a 100644
--- a/examples/saturated.py
+++ b/examples/saturated.py
@@ -1,66 +1,66 @@
# -*- coding: utf-8 -*-
# @file
-# @section LICENSE
+# LICENSE
#
# Copyright (©) 2016-2021 EPFL (École Polytechnique Fédérale de Lausanne),
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# This program is free software: you can redistribute it and/or modify
# 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 Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see .
import tamaas as tm
import numpy as np
import matplotlib.pyplot as plt
grid_size = 256
load = 1.6
p_sat = 100
iso = tm.Isopowerlaw2D()
iso.q0 = 4
iso.q1 = 4
iso.q2 = 16
iso.hurst = 0.8
sg = tm.SurfaceGeneratorFilter2D([grid_size, grid_size])
sg.random_seed = 2
sg.spectrum = iso
surface = sg.buildSurface()
surface -= np.max(surface)
model = tm.ModelFactory.createModel(tm.model_type.basic_2d,
[1., 1.], [grid_size, grid_size])
model.E = 1.
model.nu = 0
esolver = tm.PolonskyKeerRey(model, surface, 1e-12,
tm.PolonskyKeerRey.pressure,
tm.PolonskyKeerRey.pressure)
esolver.solve(load)
elastic_tractions = model.traction.copy()
plt.imshow(elastic_tractions)
plt.title('Elastic contact tractions')
plt.colorbar()
model.traction[:] = 0.
solver = tm.KatoSaturated(model, surface, 1e-12, p_sat)
solver.dump_freq = 1
solver.max_iter = 200
solver.solve(load)
plt.figure()
plt.imshow(model.traction)
plt.title('Saturated contact tractions')
plt.colorbar()
plt.show()
diff --git a/examples/statistics.py b/examples/statistics.py
index f47b220..142404a 100644
--- a/examples/statistics.py
+++ b/examples/statistics.py
@@ -1,83 +1,83 @@
#!/usr/bin/env python3
# @file
-# @section LICENSE
+# LICENSE
#
# Copyright (©) 2016-2021 EPFL (École Polytechnique Fédérale de Lausanne),
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# This program is free software: you can redistribute it and/or modify
# 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 Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see .
import os
import numpy as np
import matplotlib.pyplot as plt
import tamaas as tm
from matplotlib.colors import LogNorm
tm.set_log_level(tm.LogLevel.info) # Show progression of solver
# Surface size
n = 512
# Surface generator
sg = tm.SurfaceGeneratorFilter2D([n, n])
sg.random_seed = 0
# Spectrum
sg.spectrum = tm.Isopowerlaw2D()
# Parameters
sg.spectrum.q0 = 16
sg.spectrum.q1 = 16
sg.spectrum.q2 = 64
sg.spectrum.hurst = 0.8
# Generating surface
surface = sg.buildSurface()
# Computing PSD and shifting for plot
psd = tm.Statistics2D.computePowerSpectrum(surface)
psd = np.fft.fftshift(psd, axes=0)
plt.imshow(psd.real, norm=LogNorm())
plt.gca().set_title('Power Spectrum Density')
plt.gcf().tight_layout()
# Computing autocorrelation and shifting for plot
acf = tm.Statistics2D.computeAutocorrelation(surface)
acf = np.fft.fftshift(acf)
plt.figure()
plt.imshow(acf)
plt.gca().set_title('Autocorrelation')
plt.gcf().tight_layout()
plt.show()
# Write the rough surface in paraview's VTK format
try:
import uvw
try:
os.mkdir('paraview')
except FileExistsError:
pass
x = np.linspace(0, 1, n, endpoint=True)
y = x.copy()
with uvw.RectilinearGrid(os.path.join('paraview', 'surface.vtr'),
(x, y)) as grid:
grid.addPointData(uvw.DataArray(surface, range(2), 'surface'))
except ImportError:
print("uvw not installed, will not write VTK file")
pass
diff --git a/examples/stresses.py b/examples/stresses.py
index 9fbf92e..d5ff938 100644
--- a/examples/stresses.py
+++ b/examples/stresses.py
@@ -1,122 +1,122 @@
#!/usr/bin/env python3
# @file
-# @section LICENSE
+# LICENSE
#
# Copyright (©) 2016-2021 EPFL (École Polytechnique Fédérale de Lausanne),
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# This program is free software: you can redistribute it and/or modify
# 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 Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see .
import argparse
import os
import numpy as np
import tamaas as tm
from tamaas.dumpers import H5Dumper as Dumper
from tamaas.dumpers._helper import hdf5toVTK
parser = argparse.ArgumentParser(
description="Hertzian tractios applied on elastic half-space")
parser.add_argument("radius", type=float, help="Radius of sphere")
parser.add_argument("load", type=float, help="Applied normal force")
parser.add_argument("name", help="Output file name")
parser.add_argument("--plots", help='Show surface normal stress',
action="store_true")
args = parser.parse_args()
# Definition of modeled domain
model_type = tm.model_type.volume_2d
discretization = [32, 127, 127]
system_size = [0.25, 1., 1.]
# Material contants
E = 1. # Young's modulus
nu = 0.3 # Poisson's ratio
E_star = E/(1-nu**2) # Hertz modulus
# Creation of model
model = tm.ModelFactory.createModel(model_type,
system_size,
discretization)
model.E = E
model.nu = nu
# Setup for integral operators
residual = tm.ModelFactory.createResidual(model, 0, 0)
# Coordinates
x = np.linspace(0, system_size[1], discretization[1], endpoint=False)
y = np.linspace(0, system_size[2], discretization[2], endpoint=False)
x, y = np.meshgrid(x, y, indexing='ij')
center = [0.5, 0.5]
r = np.sqrt((x-center[0])**2 + (y-center[1])**2)
# Span of local data
local_size = model.boundary_shape
local_offset = tm.mpi.local_offset(r.shape)
local_slice = np.s_[local_offset:local_offset+local_size[0], :]
# Sphere
R = args.radius
P = args.load
# Contact area
a = (3*P*R/(4*E_star))**(1/3)
p_0 = 3 * P / (2 * np.pi * a**2)
# Pressure definition
traction = model.traction
hertz_traction = np.zeros(discretization[1:])
hertz_traction[r < a] = p_0 * np.sqrt(1 - (r[r < a] / a)**2)
traction[..., 2] = hertz_traction[local_slice]
# Array references
displacement = model.displacement
stress = model['stress']
gradient = np.zeros_like(stress)
# Getting integral operators
boussinesq = model.operators["boussinesq"]
boussinesq_gradient = model.operators["boussinesq_gradient"]
# Applying operators
boussinesq(traction, displacement)
boussinesq_gradient(traction, gradient)
model.operators["hooke"](gradient, stress)
# Dumper
dumper_helper = Dumper(args.name, 'stress')
model.addDumper(dumper_helper)
model.dump()
# Converting HDF dump to VTK
with tm.mpi.sequential():
if tm.mpi.rank() == 0:
hdf5toVTK(os.path.join('hdf5', 'stress_0000.h5'), args.name)
if args.plots:
import matplotlib.pyplot as plt # noqa
fig, ax = plt.subplots(1, 2)
fig.suptitle("Rank {}".format(tm.mpi.rank()))
ax[0].set_title("Traction")
ax[1].set_title("Normal Stress")
ax[0].imshow(traction[..., 2])
ax[1].imshow(stress[0, ..., 2])
fig.tight_layout()
plt.show()
diff --git a/python/SConscript b/python/SConscript
index 1ba61c3..727cd67 100644
--- a/python/SConscript
+++ b/python/SConscript
@@ -1,159 +1,159 @@
# -*- mode:python; coding: utf-8 -*-
# vim: set ft=python:
# @file
-# @section LICENSE
+# LICENSE
#
# Copyright (©) 2016-2021 EPFL (École Polytechnique Fédérale de Lausanne),
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# This program is free software: you can redistribute it and/or modify
# 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 Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see .
from __future__ import print_function
from SCons.Script import Import, Split, Copy, Dir
Import('main_env')
# Pybind11 wrapper
env_pybind = main_env.Clone(SHLIBPREFIX='')
# Remove pedantic warnings
cxx_flags = env_pybind['CXXFLAGS']
try:
del cxx_flags[cxx_flags.index('-pedantic')]
except ValueError:
pass
env_pybind.Tool(pybind11)
pybind_sources = Split("""
tamaas_module.cpp
wrap/core.cpp
wrap/percolation.cpp
wrap/surface.cpp
wrap/model.cpp
wrap/solvers.cpp
wrap/compute.cpp
wrap/mpi.cpp
wrap/test_features.cpp
""")
# Setting paths to find libTamaas
env_pybind.AppendUnique(LIBPATH=['../src'])
# Link against a static libTamaas
if env_pybind['build_static_lib']:
env_pybind.PrependUnique(LIBS=['Tamaas']) # keep other libs for link
env_pybind['RPATH'] = "" # no need for rpath w/ static lib
# Link against a dynamic libTamaas
else:
env_pybind.AppendUnique(RPATH=[
"'$$$$ORIGIN/../../src'", # path to lib in build_dir
"'$$$$ORIGIN/../../..'", # path to lib in install prefix
])
env_pybind['LIBS'] = ['Tamaas'] # discard other libs for link
# Building the pybind library
tamaas_wrap = env_pybind.Pybind11Module(
target='tamaas/_tamaas',
source=pybind_sources,
)
# For some reason link happens too early
Import('libTamaas')
env_pybind.Depends(tamaas_wrap, libTamaas)
# Copying the __init__.py file with extra python classes
copy_env = env_pybind.Clone()
# Copying additional python files
python_files = """
compute.py
dumpers/__init__.py
dumpers/_helper.py
nonlinear_solvers/__init__.py
""".split()
targets = [tamaas_wrap]
targets += [
copy_env.Command(copy_env.File(f, 'tamaas'),
copy_env.File(f, '#python/tamaas'),
Copy("$TARGET", "$SOURCE"))
for f in python_files
]
targets.append(copy_env.Command('MANIFEST.in', '#python/MANIFEST.in',
Copy("$TARGET", "$SOURCE")))
subst_env = env_pybind.Clone(
SUBST_DICT={
'@version@': '$version',
'@authors@': str(copy_env['authors']),
'@email@': '$email',
# TODO change when issue with unicode fixed
# '@copyright@': '$copyright',
# '@maintainer@': '$maintainer',
}
)
subst_env.Tool('textfile')
targets.append(subst_env.Substfile('setup.py.in'))
targets.append(subst_env.Substfile('tamaas/__init__.py.in'))
# Defining alias for python builds
main_env.Alias('build-python', targets)
# Checking if we can use pip to install (more convenient for end-user)
install_env = main_env.Clone()
conf = Configure(install_env,
custom_tests={'CheckPythonModule': CheckPythonModule})
has_pip = conf.CheckPythonModule('pip')
install_env = conf.Finish()
# Current build directory
install_env['PYDIR'] = Dir('.')
# Setting command line for installation
if has_pip:
install_env['PYINSTALLCOM'] = '${py_exec} -m pip install -U $PYOPTIONS .'
install_env['PYDEVELOPCOM'] = \
'${py_exec} -m pip install $PYOPTIONS -e .[all]'
else:
install_env['PYINSTALLCOM'] = '${py_exec} setup.py install $PYOPTIONS'
install_env['PYDEVELOPCOM'] = '${py_exec} setup.py develop $PYOPTIONS'
install_env['py_version'] = get_python_version(install_env)
install_env.PrependENVPath(
'PYTHONPATH',
install_env.subst('${prefix}/lib/python${py_version}/site-packages'))
# Specify install target
python_install = install_env.Command(
'.python_install_phony',
targets, install_env['PYINSTALLCOM'], PYOPTIONS='--prefix ${prefix}',
chdir=install_env['PYDIR'])
python_install_dev = install_env.Command(
'.python_install_local_phony',
targets, install_env['PYDEVELOPCOM'], PYOPTIONS='--user',
chdir=install_env['PYDIR'])
# Defining aliases
main_env.Alias('install-python', python_install)
main_env.Alias('dev', python_install_dev)
diff --git a/python/cast.hh b/python/cast.hh
index 803e119..485ad7f 100644
--- a/python/cast.hh
+++ b/python/cast.hh
@@ -1,182 +1,182 @@
/**
* @file
- * @section LICENSE
+ * LICENSE
*
* Copyright (©) 2016-2021 EPFL (École Polytechnique Fédérale de Lausanne),
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* This program is free software: you can redistribute it and/or modify
* 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 Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see .
*
*/
/* -------------------------------------------------------------------------- */
#ifndef CAST_HH
#define CAST_HH
/* -------------------------------------------------------------------------- */
#include "grid_base.hh"
#include "grid.hh"
#include "numpy.hh"
/* -------------------------------------------------------------------------- */
#include
#include
/* -------------------------------------------------------------------------- */
namespace pybind11 {
// Format descriptor necessary for correct wrap of tamaas complex type
template
struct format_descriptor<
tamaas::complex, detail::enable_if_t::value>> {
static constexpr const char c = format_descriptor::c;
static constexpr const char value[3] = {'Z', c, '\0'};
static std::string format() { return std::string(value); }
};
#ifndef PYBIND11_CPP17
template
constexpr const char format_descriptor<
tamaas::complex,
detail::enable_if_t::value>>::value[3];
#endif
namespace detail {
// declare tamaas complex as a complex type for pybind11
template
struct is_complex> : std::true_type {};
template
struct is_fmt_numeric,
detail::enable_if_t::value>>
: std::true_type {
static constexpr int index = is_fmt_numeric::index + 3;
};
static inline handle policy_switch(return_value_policy policy, handle parent) {
switch (policy) {
case return_value_policy::copy:
case return_value_policy::move:
return handle();
case return_value_policy::automatic_reference: // happens in python-derived
// classes
case return_value_policy::reference:
return none();
case return_value_policy::reference_internal:
return parent;
default:
TAMAAS_EXCEPTION("Policy is not handled");
}
}
template
handle grid_to_python(const tamaas::Grid& grid,
return_value_policy policy, handle parent) {
parent = policy_switch(policy, parent); // reusing variable
std::vector sizes(dim);
std::copy(grid.sizes().begin(), grid.sizes().end(), sizes.begin());
if (grid.getNbComponents() != 1)
sizes.push_back(grid.getNbComponents());
return array(sizes, grid.getInternalData(), parent).release();
}
/**
* Type caster for grid classes
* inspired by https://tinyurl.com/y8m47qh3 from T. De Geus
* and pybind11/eigen.h
*/
template class G, typename T,
tamaas::UInt dim>
struct type_caster> {
using type = G;
using array_type =
array_t;
public:
PYBIND11_TYPE_CASTER(type, _("GridWrap"));
/**
* Conversion part 1 (Python->C++): convert a PyObject into a grid
* instance or return false upon failure. The second argument
* indicates whether implicit conversions should be applied.
*/
bool load(handle src, bool convert) {
if (!array_type::check_(src) or !convert)
return false;
auto buf = array_type::ensure(src);
if (!buf) return false;
value.move(tamaas::wrap::GridNumpy>(buf));
return true;
}
/**
* Conversion part 2 (C++ -> Python): convert a grid instance into
* a Python object. The second and third arguments are used to
* indicate the return value policy and parent object (for
* ``return_value_policy::reference_internal``) and are generally
* ignored by implicit casters.
*/
static handle cast(const type& src, return_value_policy policy,
handle parent) {
return grid_to_python(src, policy, parent);
}
};
/**
* Type caster for GridBase classes
*/
template
struct type_caster> {
using type = tamaas::GridBase;
using array_type =
array_t;
public:
PYBIND11_TYPE_CASTER(type, _("GridBaseWrap"));
bool load(handle src, bool convert) {
if (!array_type::check_(src) or !convert)
return false;
auto buf = array_type::ensure(src);
if (!buf) return false;
value.move(tamaas::wrap::GridBaseNumpy(buf));
return true;
}
static handle cast(const type& src, return_value_policy policy,
handle parent) {
#define GRID_BASE_CASE(unused1, unused2, dim) \
case dim: { \
const auto& conv = dynamic_cast&>(src); \
return grid_to_python(conv, policy, parent); \
}
switch (src.getDimension()) {
BOOST_PP_SEQ_FOR_EACH(GRID_BASE_CASE, ~, (1)(2)(3));
default:
return nullptr;
}
#undef GRID_BASE_CASE
}
};
} // namespace detail
} // namespace pybind11
#endif // CAST_HH
diff --git a/python/numpy.hh b/python/numpy.hh
index 4ae8e31..70329b3 100644
--- a/python/numpy.hh
+++ b/python/numpy.hh
@@ -1,93 +1,93 @@
/**
* @file
- * @section LICENSE
+ * LICENSE
*
* Copyright (©) 2016-2021 EPFL (École Polytechnique Fédérale de Lausanne),
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* This program is free software: you can redistribute it and/or modify
* 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 Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see .
*
*/
/* -------------------------------------------------------------------------- */
#ifndef NUMPY_HH
#define NUMPY_HH
/* -------------------------------------------------------------------------- */
#include "grid_base.hh"
#include "tamaas.hh"
/* -------------------------------------------------------------------------- */
#include
#include
namespace tamaas {
namespace wrap {
namespace py = pybind11;
/// Type alias for usual numpy array type
template
using numpy = py::array_t;
/// GridBase helper class wrapping numpy array
template
class GridBaseNumpy : public GridBase {
public:
GridBaseNumpy(numpy& buffer) : GridBase() {
this->nb_components = 1;
this->data.wrapMemory(buffer.mutable_data(), buffer.size());
}
};
/// Grid helper class wrapping numpy array
template
class GridNumpy : public Parent {
public:
GridNumpy(numpy& buffer) : Parent() {
auto* array_shape = buffer.shape();
const UInt ndim = buffer.ndim();
if (ndim > Parent::dimension + 1 || ndim < Parent::dimension)
TAMAAS_EXCEPTION(
"Numpy array dimension do not match expected grid dimensions");
if (ndim == Parent::dimension + 1)
this->nb_components = array_shape[ndim - 1];
std::copy_n(array_shape, Parent::dimension, this->n.begin());
this->computeStrides();
this->data.wrapMemory(buffer.mutable_data(), this->computeSize());
}
};
/// Surface helper class wrapping numpy array
template
class SurfaceNumpy : public Parent {
public:
SurfaceNumpy(numpy& buffer) : Parent() {
auto* array_shape = buffer.shape();
if (buffer.ndim() != 2)
TAMAAS_EXCEPTION(
"Numpy array dimension do not match expected surface dimensions");
std::copy_n(array_shape, Parent::dimension, this->n.begin());
this->computeStrides();
this->data.wrapMemory(buffer.mutable_data(), this->computeSize());
}
};
} // namespace wrap
} // namespace tamaas
#endif // NUMPY_HH
diff --git a/python/tamaas/__init__.py.in b/python/tamaas/__init__.py.in
index ee05ad3..c4f8179 100644
--- a/python/tamaas/__init__.py.in
+++ b/python/tamaas/__init__.py.in
@@ -1,59 +1,59 @@
# -*- mode:python; coding: utf-8 -*-
# @file
-# @section LICENSE
+# LICENSE
#
# Copyright (©) 2016-2021 EPFL (École Polytechnique Fédérale de Lausanne),
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# This program is free software: you can redistribute it and/or modify
# 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 Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see .
"""
Tamaas is a library dedicated to the fast treatment of rough contact problems.
See https://tamaas.readthedocs.io for documentation on how to use Tamaas.
See __author__, __license__, __copyright__ for extra information about Tamaas.
"""
__version__ = "@version@"
__author__ = @authors@
# TODO Change copyright when is issue with unicode is found
__copyright__ = u"Copyright (©) 2016-2021 EPFL " \
+ u"(École Polytechnique Fédérale de Lausanne), " \
+ u"Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)"
__license__ = "AGPLv3"
__maintainer__ = "Lucas Frérot"
__email__ = "@email@"
try:
from ._tamaas import model_type
from ._tamaas import _type_traits as __tt
type_traits = {
model_type.basic_1d: __tt.basic_1d,
model_type.basic_2d: __tt.basic_2d,
model_type.surface_1d: __tt.surface_1d,
model_type.surface_2d: __tt.surface_2d,
model_type.volume_1d: __tt.volume_1d,
model_type.volume_2d: __tt.volume_2d,
}
del __tt
from ._tamaas import * # noqa
except ImportError as e:
print("Error trying to import _tamaas:\n{}".format(e))
raise e
diff --git a/python/tamaas/compute.py b/python/tamaas/compute.py
index b300a90..d220349 100644
--- a/python/tamaas/compute.py
+++ b/python/tamaas/compute.py
@@ -1,22 +1,22 @@
# -*- coding: utf-8 -*-
# @file
-# @section LICENSE
+# LICENSE
#
# Copyright (©) 2016-2021 EPFL (École Polytechnique Fédérale de Lausanne),
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# This program is free software: you can redistribute it and/or modify
# 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 Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see .
from ._tamaas.compute import * # noqa
diff --git a/python/tamaas/dumpers/__init__.py b/python/tamaas/dumpers/__init__.py
index 93fdb73..8e7aafe 100644
--- a/python/tamaas/dumpers/__init__.py
+++ b/python/tamaas/dumpers/__init__.py
@@ -1,343 +1,343 @@
# -*- mode:python; coding: utf-8 -*-
# @file
-# @section LICENSE
+# LICENSE
#
# Copyright (©) 2016-2021 EPFL (École Polytechnique Fédérale de Lausanne),
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# This program is free software: you can redistribute it and/or modify
# 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 Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see .
"""
Dumpers for the class tamaas.Model
"""
from __future__ import print_function
from sys import stderr
from os import makedirs
import os.path
import numpy as np
from .. import ModelDumper, model_type, mpi, type_traits
from ._helper import step_dump, directory_dump, local_slice, _is_surface_field
def _get_attributes(model):
"Get model attributes"
return {
'model_type': str(model.type),
'system_size': model.system_size,
'discretization': model.global_shape,
}
class FieldDumper(ModelDumper):
"""Abstract dumper for python classes using fields"""
postfix = ''
extension = ''
name_format = "{basename}{postfix}.{extension}"
def __init__(self, basename, *fields, **kwargs):
"""Construct with desired fields"""
super(FieldDumper, self).__init__()
self.basename = basename
self.fields = list(fields)
self.all_fields = kwargs.get('all_fields', False)
def add_field(self, field):
"""Add another field to the dump"""
if field not in self.fields:
self.fields.append(field)
def dump_to_file(self, file_descriptor, model):
"""Dump to a file (name or handle)"""
def get_fields(self, model):
"""Get the desired fields"""
if not self.all_fields:
requested_fields = self.fields
else:
requested_fields = list(model)
return {field: model[field] for field in requested_fields}
def dump(self, model):
"Dump model"
self.dump_to_file(self.file_path, model)
@property
def file_path(self):
"""Get the default filename"""
return self.name_format.format(basename=self.basename,
postfix=self.postfix,
extension=self.extension)
@directory_dump('numpys')
@step_dump
class NumpyDumper(FieldDumper):
"""Dumper to compressed numpy files"""
extension = 'npz'
def dump_to_file(self, file_descriptor, model):
"""Saving to compressed multi-field Numpy format"""
if mpi.size() > 1:
raise RuntimeError("NumpyDumper does not function "
"at all in parallel")
np.savez_compressed(file_descriptor, attrs=_get_attributes(model),
**self.get_fields(model))
try:
import h5py
@directory_dump('hdf5')
@step_dump
class H5Dumper(FieldDumper):
"""Dumper to HDF5 file format"""
extension = 'h5'
def dump_to_file(self, file_descriptor, model):
"""Saving to HDF5 with metadata about the model"""
# Setup for MPI
if not h5py.get_config().mpi and mpi.size() > 1:
raise RuntimeError("HDF5 does not have MPI support")
if mpi.size() > 1:
from mpi4py import MPI # noqa
mpi_args = dict(driver='mpio', comm=MPI.COMM_WORLD)
comp_args = {} # compression does not work in parallel
else:
mpi_args = {}
comp_args = dict(compression='gzip', compression_opts=7)
with h5py.File(file_descriptor, 'w', **mpi_args) as handle:
# Writing data
for name, field in self.get_fields(model).items():
shape = list(field.shape)
if mpi.size() > 1:
xdim = 0 if _is_surface_field(field, model) else 1
shape[xdim] = MPI.COMM_WORLD.allreduce(shape[xdim])
dset = handle.create_dataset(name, shape, field.dtype,
**comp_args)
dset[local_slice(field, model)] = field
# Writing metadata
for name, attr in _get_attributes(model).items():
handle.attrs[name] = attr
except ImportError:
pass
try:
import uvw # noqa
@directory_dump('paraview')
@step_dump
class UVWDumper(FieldDumper):
"""Dumper to VTK files for elasto-plastic calculations"""
extension = 'vtr'
forbidden_fields = ['traction', 'gap']
def dump_to_file(self, file_descriptor, model):
"""Dump displacements, plastic deformations and stresses"""
if mpi.size() > 1:
raise RuntimeError("UVWDumper does not function "
"properly in parallel")
bdim = len(model.boundary_shape)
# Local MPI size
lsize = model.shape
gsize = mpi.global_shape(model.boundary_shape)
gshape = gsize
if len(lsize) > bdim:
gshape = [model.shape[0]] + gshape
# Space coordinates
coordinates = [np.linspace(0, L, N, endpoint=False)
for L, N in zip(model.system_size, gshape)]
# If model has subsurfce domain, z-coordinate is always first
dimension_indices = np.arange(bdim)
if len(lsize) > bdim:
dimension_indices += 1
dimension_indices = np.concatenate((dimension_indices, [0]))
coordinates[0] = \
np.linspace(0, model.system_size[0], gshape[0])
offset = np.zeros_like(dimension_indices)
offset[0] = mpi.local_offset(gsize)
rectgrid = uvw.RectilinearGrid if mpi.size() == 1 \
else uvw.parallel.PRectilinearGrid
# Creating rectilinear grid with correct order for components
coordlist = [coordinates[i][o:o+lsize[i]]
for i, o in zip(dimension_indices, offset)]
grid = rectgrid(
file_descriptor, coordlist,
compression=True,
offsets=offset,
)
# Iterator over fields we want to dump
fields_it = filter(lambda t: t[0] not in self.forbidden_fields,
self.get_fields(model).items())
# We make fields periodic for visualization
for name, field in fields_it:
array = uvw.DataArray(field, dimension_indices, name)
grid.addPointData(array)
grid.write()
@directory_dump('paraview')
class UVWGroupDumper(FieldDumper):
"Dumper to ParaViewData files"
extension = 'pvd'
def __init__(self, basename, *fields, **kwargs):
"""Construct with desired fields"""
super(UVWGroupDumper, self).__init__(basename, *fields, **kwargs)
subdir = os.path.join('paraview', basename + '-VTR')
if not os.path.exists(subdir):
makedirs(subdir)
self.uvw_dumper = UVWDumper(
os.path.join(basename + '-VTR', basename), *fields, **kwargs
)
self.group = uvw.ParaViewData(self.file_path, compression=True)
def dump_to_file(self, file_descriptor, model):
self.group.addFile(
self.uvw_dumper.file_path.replace('paraview/', ''),
timestep=self.uvw_dumper.count
)
self.group.write()
self.uvw_dumper.dump(model)
except ImportError as error:
print(error, file=stderr)
try:
from netCDF4 import Dataset
@directory_dump('netcdf')
class NetCDFDumper(FieldDumper):
"""Dumper to netCDF4 files"""
extension = "nc"
boundary_fields = ['traction', 'gap']
def _file_setup(self, grp, model):
grp.createDimension('frame', None)
# Local dimensions
model_dim = len(model.shape)
voigt_dim = type_traits[model.type].voigt
self._vec = grp.createDimension('spatial', model_dim)
self._tens = grp.createDimension('Voigt', voigt_dim)
self.model_info = model.global_shape, model.type
global_boundary_shape = mpi.global_shape(model.boundary_shape)
# Create boundary dimensions
for label, size, length in zip(
"xy",
global_boundary_shape,
model.boundary_system_size
):
grp.createDimension(label, size)
coord = grp.createVariable(label, 'f8', (label,))
coord[:] = np.linspace(0, length, size, endpoint=False)
self._create_variables(
grp, model,
lambda f: _is_surface_field(f[1], model),
global_boundary_shape, "xy"
)
# Create volume dimension
if model.type in {model_type.volume_1d, model_type.volume_2d}:
size = model.shape[0]
grp.createDimension("z", size)
coord = grp.createVariable("z", 'f8', ("z",))
coord[:] = np.linspace(0, model.system_size[0], size)
self._create_variables(
grp, model,
lambda f: not _is_surface_field(f[1], model),
model.global_shape, "zxy"
)
self.has_setup = True
def dump_to_file(self, file_descriptor, model):
if mpi.size() > 1:
raise RuntimeError("NetCDFDumper does not function "
"properly in parallel")
mode = 'a' if os.path.isfile(file_descriptor) \
and getattr(self, 'has_setup', False) else 'w'
with Dataset(file_descriptor, mode,
format='NETCDF4_CLASSIC',
parallel=mpi.size() > 1) as rootgrp:
if rootgrp.dimensions == {}:
self._file_setup(rootgrp, model)
if self.model_info != (model.global_shape, model.type):
raise Exception("Unexpected model {}".format(model))
self._dump_generic(rootgrp, model)
def _create_variables(self, grp, model, predicate,
shape, dimensions):
field_dim = len(shape)
fields = list(filter(predicate, self.get_fields(model).items()))
dim_labels = list(dimensions[:field_dim])
for label, data in fields:
local_dim = []
# If we have an extra component
if data.ndim > field_dim:
if data.shape[-1] == self._tens.size:
local_dim = [self._tens.name]
elif data.shape[-1] == self._vec.size:
local_dim = [self._vec.name]
grp.createVariable(label, 'f8',
['frame'] + dim_labels + local_dim,
zlib=True)
def _dump_generic(self, grp, model):
fields = self.get_fields(model).items()
new_frame = grp.dimensions['frame'].size
for label, data in fields:
var = grp[label]
slice_in_global = (new_frame,) + local_slice(data, model)
var[slice_in_global] = np.array(data, dtype=np.double)
except ImportError:
pass
diff --git a/python/tamaas/dumpers/_helper.py b/python/tamaas/dumpers/_helper.py
index 60e3e0f..8e90a52 100644
--- a/python/tamaas/dumpers/_helper.py
+++ b/python/tamaas/dumpers/_helper.py
@@ -1,141 +1,141 @@
# -*- mode:python; coding: utf-8 -*-
# @file
-# @section LICENSE
+# LICENSE
#
# Copyright (©) 2016-2021 EPFL (École Polytechnique Fédérale de Lausanne),
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# This program is free software: you can redistribute it and/or modify
# 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 Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see .
"""
Helper functions for dumpers
"""
from functools import wraps
from collections import defaultdict
import os
import numpy as np
from .. import model_type, type_traits, mpi
__all__ = ["step_dump", "directory_dump"]
def _is_surface_field(field, model):
bn = model.boundary_shape
return list(field.shape[:len(bn)]) == bn
def local_slice(field, model):
n = model.shape
bn = model.boundary_shape
gshape = mpi.global_shape(bn)
offsets = np.zeros_like(gshape)
offsets[0] = mpi.local_offset(gshape)
if not _is_surface_field(field, model) and len(n) > len(bn):
gshape = [n[0]] + gshape
offsets = np.concatenate(([0], offsets))
return tuple((slice(offset, offset+size, None)
for offset, size in zip(offsets, field.shape)))
def step_dump(cls):
"""
Decorator for dumper with counter for steps
"""
orig_init = cls.__init__
orig_dump = cls.dump
@wraps(cls.__init__)
def __init__(obj, *args, **kwargs):
orig_init(obj, *args, **kwargs)
obj.count = 0
def postfix(obj):
return "_{:04d}".format(obj.count)
@wraps(cls.dump)
def dump(obj, *args, **kwargs):
orig_dump(obj, *args, **kwargs)
obj.count += 1
cls.__init__ = __init__
cls.dump = dump
cls.postfix = property(postfix)
return cls
def directory_dump(directory=""):
"Decorator for dumper in a directory"
def actual_decorator(cls):
orig_dump = cls.dump
orig_filepath = cls.file_path.fget
@wraps(cls.dump)
def dump(obj, *args, **kwargs):
if not os.path.exists(directory) and mpi.rank() == 0:
os.mkdir(directory)
if not os.path.isdir(directory) and mpi.rank() == 0:
raise Exception('{} is not a directory'.format(directory))
orig_dump(obj, *args, **kwargs)
@wraps(cls.file_path.fget)
def file_path(obj):
return os.path.join(directory, orig_filepath(obj))
cls.dump = dump
cls.file_path = property(file_path)
return cls
return actual_decorator
def hdf5toVTK(inpath, outname):
"Convert HDF5 dump of a model to VTK"
import h5py as h5 # noqa
from .. import ModelFactory # noqa
from . import UVWDumper # noqa
type_translate = {
'model_type.basic_1d': model_type.basic_1d,
'model_type.basic_2d': model_type.basic_2d,
'model_type.surface_1d': model_type.surface_1d,
'model_type.surface_2d': model_type.surface_2d,
'model_type.volume_1d': model_type.volume_1d,
'model_type.volume_2d': model_type.volume_2d,
}
with h5.File(inpath, 'r') as h5file:
model_t = h5file.attrs['model_type']
system_size = list(h5file.attrs['system_size'])
n = list(h5file.attrs['discretization'])
model = ModelFactory.createModel(type_translate[model_t],
system_size, n)
fields = []
for field in h5file:
model.registerField(field, h5file[field][:])
fields.append(field)
uvw_dumper = UVWDumper(outname, *fields)
uvw_dumper << model
diff --git a/python/tamaas/nonlinear_solvers/__init__.py b/python/tamaas/nonlinear_solvers/__init__.py
index e4e6368..67a9ca3 100644
--- a/python/tamaas/nonlinear_solvers/__init__.py
+++ b/python/tamaas/nonlinear_solvers/__init__.py
@@ -1,168 +1,168 @@
# -*- mode:python; coding: utf-8 -*-
# @file
-# @section LICENSE
+# LICENSE
#
# Copyright (©) 2016-2021 EPFL (École Polytechnique Fédérale de Lausanne),
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# This program is free software: you can redistribute it and/or modify
# 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 Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see .
"""
Pulling solvers to nonlinear_solvers module
"""
from functools import wraps
import numpy as np
from scipy.sparse.linalg import LinearOperator, lgmres
from scipy.linalg import norm
from scipy.optimize import newton_krylov, root
from scipy.optimize.nonlin import NoConvergence
from .. import EPSolver, Logger, LogLevel, mpi
from .._tamaas import _tolerance_manager
from .._tamaas import _DFSANESolver as DFSANECXXSolver
__all__ = ['NLNoConvergence',
'DFSANESolver',
'DFSANECXXSolver',
'NewtonKrylovSolver',
'ToleranceManager']
class NLNoConvergence(Exception):
"""Convergence not reached exception"""
class ScipySolver(EPSolver):
"""
Base class for solvers wrapping SciPy routines
"""
def __init__(self, residual, _, callback=None):
super(ScipySolver, self).__init__(residual)
if mpi.size() > 1:
raise RuntimeError("Scipy solvers cannot be used with MPI; "
"DFSANECXXSolver can be used instead")
self.callback = callback
self._x = self.getStrainIncrement()
self._residual = self.getResidual()
self.options = {'ftol': 0, 'fatol': 1e-9}
def solve(self):
"""
Solve the nonlinear plasticity equation using the scipy_solve routine
"""
# For initial guess, compute the strain due to boundary tractions
# self._residual.computeResidual(self._x)
# self._x[...] = self._residual.getVector()
EPSolver.beforeSolve(self)
# Scipy root callback
def compute_residual(vec):
self._residual.computeResidual(vec)
return self._residual.getVector().copy()
# Solve
self._x[...] = self.scipy_solve(compute_residual)
# Computing displacements
self._residual.computeResidualDisplacement(self._x)
def reset(self):
"Set solution vector to zero"
self._x[...] = 0
class NewtonKrylovSolver(ScipySolver):
"""
Solve using a finite-difference Newton-Krylov method
"""
def __init__(self, residual, model=None, callback=None):
ScipySolver.__init__(self, residual, model,
callback=callback)
def scipy_solve(self, compute_residual):
"Solve R(delta epsilon) = 0 using a newton-krylov method"
try:
return newton_krylov(compute_residual, self._x,
f_tol=self.tolerance,
verbose=True, callback=self.callback)
except NoConvergence:
raise NLNoConvergence("Newton-Krylov did not converge")
class DFSANESolver(ScipySolver):
"""
Solve using a spectral residual jacobianless method
"""
def __init__(self, residual, model=None, callback=None):
ScipySolver.__init__(self, residual, model,
callback=callback)
def scipy_solve(self, compute_residual):
"Solve R(delta epsilon) = 0 using a df-sane method"
solution = root(compute_residual,
self._x,
method='df-sane',
options={'ftol': 0, 'fatol': self.tolerance},
callback=self.callback)
Logger().get(LogLevel.info) << \
"DF-SANE/Scipy: {} ({} iterations, {})".format(
solution.message,
solution.nit,
self.tolerance)
if not solution.success:
raise NLNoConvergence("DF-SANE/Scipy did not converge")
return solution.x.copy()
def ToleranceManager(start, end, rate):
"Decorator to manage tolerance of non-linear solver"
# start /= rate # just anticipating first multiplication
def actual_decorator(cls):
orig_init = cls.__init__
orig_solve = cls.solve
orig_update_state = cls.updateState
@wraps(cls.__init__)
def __init__(obj, *args, **kwargs):
orig_init(obj, *args, **kwargs)
obj.setToleranceManager(_tolerance_manager(start, end, rate))
@wraps(cls.solve)
def new_solve(obj, *args, **kwargs):
ftol = obj.tolerance
ftol *= rate
obj.tolerance = max(ftol, end)
return orig_solve(obj, *args, **kwargs)
@wraps(cls.updateState)
def updateState(obj, *args, **kwargs):
obj.tolerance = start
return orig_update_state(obj, *args, **kwargs)
cls.__init__ = __init__
# cls.solve = new_solve
# cls.updateState = updateState
return cls
return actual_decorator
diff --git a/python/tamaas_module.cpp b/python/tamaas_module.cpp
index eebb496..60dafa9 100644
--- a/python/tamaas_module.cpp
+++ b/python/tamaas_module.cpp
@@ -1,80 +1,80 @@
/**
* @file
- * @section LICENSE
+ * LICENSE
*
* Copyright (©) 2016-2021 EPFL (École Polytechnique Fédérale de Lausanne),
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* This program is free software: you can redistribute it and/or modify
* 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 Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see .
*
*/
/* -------------------------------------------------------------------------- */
#include "tamaas.hh"
#include "tamaas_info.hh"
#include "wrap.hh"
/* -------------------------------------------------------------------------- */
#include
/* -------------------------------------------------------------------------- */
namespace tamaas {
namespace py = pybind11;
namespace detail {
template
struct dtype_helper {
static const py::dtype dtype;
};
template <>
const py::dtype dtype_helper::dtype("=f8");
template <>
const py::dtype dtype_helper::dtype("=f16");
} // namespace detail
/// Creating the tamaas python module
PYBIND11_MODULE(_tamaas, mod) {
mod.doc() = "Tamaas module for python";
// Wrapping the base methods
mod.def("initialize", &initialize, py::arg("num_threads") = 0,
"Initialize tamaas with desired number of threads");
mod.def("finalize", &finalize, "Final cleanup");
// Default dtype of numpy arrays
mod.attr("dtype") = detail::dtype_helper::dtype;
// Wrapping release information
auto info = py::class_(mod, "TamaasInfo");
info.attr("version") = TamaasInfo::version;
info.attr("build_type") = TamaasInfo::build_type;
info.attr("branch") = TamaasInfo::branch;
info.attr("commit") = TamaasInfo::commit;
info.attr("diff") = TamaasInfo::diff;
info.attr("remotes") = TamaasInfo::remotes;
info.attr("has_mpi") = TamaasInfo::has_mpi;
// Wrapping tamaas components
wrap::wrapCore(mod);
wrap::wrapPercolation(mod);
wrap::wrapSurface(mod);
wrap::wrapModel(mod);
wrap::wrapSolvers(mod);
wrap::wrapCompute(mod);
wrap::wrapMPI(mod);
/// Wrapping test features
wrap::wrapTestFeatures(mod);
}
} // namespace tamaas
diff --git a/python/wrap.hh b/python/wrap.hh
index 9d182a2..f497c0c 100644
--- a/python/wrap.hh
+++ b/python/wrap.hh
@@ -1,77 +1,77 @@
/**
* @file
- * @section LICENSE
+ * LICENSE
*
* Copyright (©) 2016-2021 EPFL (École Polytechnique Fédérale de Lausanne),
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* This program is free software: you can redistribute it and/or modify
* 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 Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see .
*
*/
/* -------------------------------------------------------------------------- */
#ifndef WRAP_HH
#define WRAP_HH
/* -------------------------------------------------------------------------- */
#include "cast.hh"
#include "numpy.hh"
#include "tamaas.hh"
/* -------------------------------------------------------------------------- */
#include
/* -------------------------------------------------------------------------- */
namespace tamaas {
namespace wrap {
namespace py = pybind11;
/// For naming classes templated with dimension
inline std::string makeDimensionName(const std::string& name, UInt dim) {
std::stringstream str;
str << name << dim << "D";
return str.str();
}
/* -------------------------------------------------------------------------- */
/* Prototypes for wrapping of tamaas components */
/* -------------------------------------------------------------------------- */
void wrapCore(py::module& mod);
void wrapPercolation(py::module& mod);
void wrapSurface(py::module& mod);
void wrapModel(py::module& mod);
void wrapSolvers(py::module& mod);
void wrapTestFeatures(py::module& mod);
void wrapCompute(py::module& mod);
void wrapMPI(py::module& mod);
/* -------------------------------------------------------------------------- */
/* Deprecation macro */
/* -------------------------------------------------------------------------- */
#define TAMAAS_DEPRECATE(olds, news) \
do { \
PyErr_WarnEx(PyExc_DeprecationWarning, \
olds " is deprecated, use " news " instead.", 1); \
} while (0)
#define TAMAAS_DEPRECATE_ACCESSOR(acc, type, property) \
#acc, [](const type& m) -> decltype(m.acc()) { \
TAMAAS_DEPRECATE(#acc "()", "the " property " property"); \
return m.acc(); \
}
} // namespace wrap
} // namespace tamaas
#endif // WRAP_HH
diff --git a/python/wrap/compute.cpp b/python/wrap/compute.cpp
index 126fd69..a1c232e 100644
--- a/python/wrap/compute.cpp
+++ b/python/wrap/compute.cpp
@@ -1,67 +1,67 @@
/**
* @file
- * @section LICENSE
+ * LICENSE
*
* Copyright (©) 2016-2021 EPFL (École Polytechnique Fédérale de Lausanne),
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* This program is free software: you can redistribute it and/or modify
* 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 Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see .
*
*/
/* -------------------------------------------------------------------------- */
#include "computes.hh"
#include "wrap.hh"
/* -------------------------------------------------------------------------- */
namespace tamaas {
namespace wrap {
using namespace py::literals;
void wrapCompute(py::module& mod) {
auto compute_mod = mod.def_submodule("compute");
compute_mod.def(
"eigenvalues",
[](model_type type, Grid& eigs, const Grid& field) {
eigenvalues(type, eigs, field);
},
"model_type"_a, "eigenvalues_out"_a, "field"_a);
compute_mod.def("von_mises",
[](model_type type, Grid& vm,
const Grid& field) { vonMises(type, vm, field); },
"model_type"_a, "von_mises"_a, "field"_a);
compute_mod.def(
"deviatoric",
[](model_type type, Grid& dev, const Grid& field) {
deviatoric(type, dev, field);
},
"model_type"_a, "deviatoric"_a, "field"_a);
compute_mod.def("to_voigt",
[](const Grid& field) {
if (field.getNbComponents() == 9) {
Grid voigt(field.sizes(), 6);
Loop::loop([](auto in, auto out) { out.symmetrize(in); },
range>(field),
range>(voigt));
return voigt;
} else
TAMAAS_EXCEPTION(
"Wrong number of components to symmetrize");
},
"Convert a 3D tensor field to voigt notation",
py::return_value_policy::copy);
}
} // namespace wrap
} // namespace tamaas
diff --git a/python/wrap/core.cpp b/python/wrap/core.cpp
index 775e840..e290dc7 100644
--- a/python/wrap/core.cpp
+++ b/python/wrap/core.cpp
@@ -1,105 +1,105 @@
/**
* @file
- * @section LICENSE
+ * LICENSE
*
* Copyright (©) 2016-2021 EPFL (École Polytechnique Fédérale de Lausanne),
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* This program is free software: you can redistribute it and/or modify
* 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 Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see .
*
*/
/* -------------------------------------------------------------------------- */
#include "logger.hh"
#include "statistics.hh"
#include "wrap.hh"
#include
/* -------------------------------------------------------------------------- */
namespace tamaas {
/* -------------------------------------------------------------------------- */
namespace wrap {
using namespace py::literals;
/* -------------------------------------------------------------------------- */
template
void wrapStatistics(py::module& mod) {
auto name = makeDimensionName("Statistics", dim);
py::class_>(mod, name.c_str())
.def_static("computePowerSpectrum",
&Statistics::computePowerSpectrum,
py::return_value_policy::move)
.def_static("computeAutocorrelation",
&Statistics::computeAutocorrelation,
py::return_value_policy::move)
.def_static("computeMoments", &Statistics::computeMoments)
.def_static("computeSpectralRMSSlope",
&Statistics::computeSpectralRMSSlope)
.def_static("computeRMSHeights", &Statistics::computeRMSHeights)
.def_static("contact", &Statistics::contact, "tractions"_a,
"perimeter"_a = 0,
"Compute the (corrected) contact area. Permieter is the "
"total contact perimeter in number of segments.");
}
/* -------------------------------------------------------------------------- */
void wrapCore(py::module& mod) {
// Exposing logging facility
py::enum_(mod, "LogLevel")
.value("debug", LogLevel::debug)
.value("info", LogLevel::info)
.value("warning", LogLevel::warning)
.value("error", LogLevel::error);
mod.def("set_log_level", [](LogLevel level) { Logger::setLevel(level); });
py::class_(mod, "Logger")
.def(py::init<>())
.def("get",
[](Logger& logger, LogLevel level) -> Logger& {
logger.get(level);
return logger;
})
.def("__lshift__", [](Logger& logger, std::string msg) -> Logger& {
auto level = logger.getWishLevel();
if (level >= Logger::getCurrentLevel() and
not(mpi::rank() != 0 and level == LogLevel::info)) {
py::print(msg, "file"_a = py::module::import("sys").attr("stderr"));
}
return logger;
});
wrapStatistics<1>(mod);
wrapStatistics<2>(mod);
mod.def("to_voigt",
[](const Grid& field) {
Logger().get(LogLevel::warning)
<< "tamaas.to_voigt deprecated. Use tamaas.compute.to_voigt\n";
if (field.getNbComponents() == 9) {
Grid voigt(field.sizes(), 6);
Loop::loop([](auto in, auto out) { out.symmetrize(in); },
range>(field),
range>(voigt));
return voigt;
} else
TAMAAS_EXCEPTION("Wrong number of components to symmetrize");
},
"Convert a 3D tensor field to voigt notation",
py::return_value_policy::copy);
}
} // namespace wrap
/* -------------------------------------------------------------------------- */
} // namespace tamaas
diff --git a/python/wrap/model.cpp b/python/wrap/model.cpp
index 0ae985c..87fb854 100644
--- a/python/wrap/model.cpp
+++ b/python/wrap/model.cpp
@@ -1,431 +1,431 @@
/**
* @file
- * @section LICENSE
+ * LICENSE
*
* Copyright (©) 2016-2021 EPFL (École Polytechnique Fédérale de Lausanne),
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* This program is free software: you can redistribute it and/or modify
* 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 Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see .
*
*/
/* -------------------------------------------------------------------------- */
#include "model.hh"
#include "adhesion_functional.hh"
#include "functional.hh"
#include "integral_operator.hh"
#include "model_dumper.hh"
#include "model_extensions.hh"
#include "model_factory.hh"
#include "numpy.hh"
#include "residual.hh"
#include "wrap.hh"
#include
/* -------------------------------------------------------------------------- */
namespace tamaas {
namespace wrap {
using namespace py::literals;
struct model_operator_accessor {
Model& m;
decltype(auto) get(std::string name) {
return m.getIntegralOperator(std::move(name));
}
};
/// Wrap functional classes
void wrapFunctionals(py::module& mod) {
py::class_,
functional::wrap::PyFunctional>
func(mod, "Functional");
func.def(py::init<>())
.def("computeF", &functional::Functional::computeF)
.def("computeGradF", &functional::Functional::computeGradF);
py::class_ adh(mod, "AdhesionFunctional",
func);
adh.def_property("parameters", &functional::AdhesionFunctional::getParameters,
&functional::AdhesionFunctional::setParameters)
.def("setParameters",
[](functional::AdhesionFunctional& f,
const std::map& m) {
TAMAAS_DEPRECATE("setParameters()", "the parameters property");
f.setParameters(m);
});
py::class_(
mod, "ExponentialAdhesionFunctional", adh)
.def(py::init&>(), "surface"_a);
py::class_(
mod, "MaugisAdhesionFunctional", adh)
.def(py::init&>(), "surface"_a);
py::class_(
mod, "SquaredExponentialAdhesionFunctional", adh)
.def(py::init&>(), "surface"_a);
}
template
std::unique_ptr> instanciateFromNumpy(numpy& num) {
std::unique_ptr> result = nullptr;
switch (num.ndim()) {
case 2:
result = std::make_unique>>(num);
return result;
case 3:
result = std::make_unique>>(num);
return result;
case 4:
result = std::make_unique>>(num);
return result;
default:
TAMAAS_EXCEPTION("instanciateFromNumpy expects the last dimension of numpy "
"array to be the number of components");
}
}
/// Wrap IntegralOperator
void wrapIntegralOperator(py::module& mod) {
py::class_(mod, "IntegralOperator")
.def("apply",
[](IntegralOperator& op, numpy input, numpy output) {
TAMAAS_DEPRECATE("apply()", "the () operator");
auto in = instanciateFromNumpy(input);
auto out = instanciateFromNumpy(output);
op.apply(*in, *out);
})
.def(TAMAAS_DEPRECATE_ACCESSOR(getModel, IntegralOperator, "model"),
py::return_value_policy::reference)
.def(TAMAAS_DEPRECATE_ACCESSOR(getKind, IntegralOperator, "kind"))
.def(TAMAAS_DEPRECATE_ACCESSOR(getType, IntegralOperator, "type"))
.def("__call__",
[](IntegralOperator& op, numpy input, numpy output) {
auto in = instanciateFromNumpy(input);
auto out = instanciateFromNumpy(output);
op.apply(*in, *out);
})
.def("updateFromModel", &IntegralOperator::updateFromModel)
.def_property_readonly("kind", &IntegralOperator::getKind)
.def_property_readonly("model", &IntegralOperator::getModel)
.def_property_readonly("type", &IntegralOperator::getType);
py::enum_(mod, "integration_method")
.value("linear", integration_method::linear)
.value("cutoff", integration_method::cutoff);
}
/// Wrap BEEngine classes
void wrapBEEngine(py::module& mod) {
py::class_(mod, "BEEngine")
.def("solveNeumann", &BEEngine::solveNeumann)
.def("solveDirichlet", &BEEngine::solveDirichlet)
.def("registerNeumann", &BEEngine::registerNeumann)
.def("registerDirichlet", &BEEngine::registerDirichlet)
.def(TAMAAS_DEPRECATE_ACCESSOR(getModel, BEEngine, "model"),
py::return_value_policy::reference)
.def_property_readonly("model", &BEEngine::getModel);
}
template
void wrapModelTypeTrait(py::module& mod) {
using trait = model_type_traits;
py::class_(mod, trait::repr)
.def_property_readonly_static("dimension",
[](py::object) { return trait::dimension; })
.def_property_readonly_static(
"components", [](py::object) { return trait::components; })
.def_property_readonly_static(
"boundary_dimension",
[](py::object) { return trait::boundary_dimension; })
.def_property_readonly_static("voigt",
[](py::object) { return trait::voigt; })
.def_property_readonly_static("indices",
[](py::object) { return trait::indices; });
}
/// Wrap Models
void wrapModelClass(py::module& mod) {
py::enum_(mod, "model_type")
.value("basic_1d", model_type::basic_1d)
.value("basic_2d", model_type::basic_2d)
.value("surface_1d", model_type::surface_1d)
.value("surface_2d", model_type::surface_2d)
.value("volume_1d", model_type::volume_1d)
.value("volume_2d", model_type::volume_2d);
auto trait_mod = mod.def_submodule("_type_traits");
wrapModelTypeTrait(trait_mod);
wrapModelTypeTrait(trait_mod);
wrapModelTypeTrait(trait_mod);
wrapModelTypeTrait(trait_mod);
wrapModelTypeTrait(trait_mod);
wrapModelTypeTrait(trait_mod);
py::class_(mod, "_model_operator_acessor")
.def(py::init())
.def("__getitem__",
[](model_operator_accessor& acc, std::string name) {
try {
return acc.get(name);
} catch (std::out_of_range&) {
throw py::key_error(name);
}
},
py::return_value_policy::reference_internal)
.def("__contains__",
[](model_operator_accessor& acc, std::string key) {
const auto ops = acc.m.getIntegralOperators();
return std::find(ops.begin(), ops.end(), key) != ops.end();
})
.def("__iter__",
[](const model_operator_accessor& acc) {
const auto& ops = acc.m.getIntegralOperatorsMap();
return py::make_key_iterator(ops.cbegin(), ops.cend());
},
py::keep_alive<0, 1>());
py::class_(mod, "Model")
.def_property_readonly("type", &Model::getType)
.def_property("E", &Model::getYoungModulus, &Model::setYoungModulus,
"Young's modulus")
.def_property("nu", &Model::getPoissonRatio, &Model::setPoissonRatio,
"Poisson's ratio")
.def_property_readonly("mu", &Model::getShearModulus, "Shear modulus")
.def_property_readonly("E_star", &Model::getHertzModulus,
"Contact (Hertz) modulus")
.def_property_readonly("be_engine", &Model::getBEEngine)
.def("setElasticity",
[](Model& m, Real E, Real nu) {
TAMAAS_DEPRECATE("setElasticity()", "the E and nu properties");
m.setElasticity(E, nu);
},
"E"_a, "nu"_a)
.def(TAMAAS_DEPRECATE_ACCESSOR(getHertzModulus, Model, "E_star"))
.def(TAMAAS_DEPRECATE_ACCESSOR(getYoungModulus, Model, "E"))
.def(TAMAAS_DEPRECATE_ACCESSOR(getShearModulus, Model, "mu"))
.def(TAMAAS_DEPRECATE_ACCESSOR(getPoissonRatio, Model, "nu"))
.def(TAMAAS_DEPRECATE_ACCESSOR(getTraction, Model, "traction"),
py::return_value_policy::reference_internal)
.def(TAMAAS_DEPRECATE_ACCESSOR(getDisplacement, Model, "displacement"),
py::return_value_policy::reference_internal)
.def(TAMAAS_DEPRECATE_ACCESSOR(getSystemSize, Model, "system_size"))
.def(TAMAAS_DEPRECATE_ACCESSOR(getDiscretization, Model, "shape"))
.def(TAMAAS_DEPRECATE_ACCESSOR(getBoundarySystemSize, Model,
"boundary_system_size"))
.def(TAMAAS_DEPRECATE_ACCESSOR(getBoundaryDiscretization, Model,
"boundary_shape"))
.def("solveNeumann", &Model::solveNeumann)
.def("solveDirichlet", &Model::solveDirichlet)
.def("dump", &Model::dump)
.def("addDumper", &Model::addDumper, "dumper"_a, py::keep_alive<1, 2>())
.def("getBEEngine",
[](Model& m) -> decltype(m.getBEEngine()) {
TAMAAS_DEPRECATE("getBEEngine()", "the be_engine property");
return m.getBEEngine();
},
py::return_value_policy::reference_internal)
.def("getIntegralOperator",
[](const Model& m, std::string name) {
TAMAAS_DEPRECATE("getIntegralOperator()",
"the operators property");
return m.getIntegralOperator(std::move(name));
},
"operator_name"_a, py::return_value_policy::reference_internal)
.def("registerField",
[](Model& m, std::string name, numpy field) {
TAMAAS_DEPRECATE("registerField()", "the [] operator");
auto f = instanciateFromNumpy(field);
m.registerField(name, std::move(f));
},
"field_name"_a, "field"_a, py::keep_alive<1, 3>())
.def("getField",
[](const Model& m, std::string name) -> decltype(m.getField(name)) {
TAMAAS_DEPRECATE("getField()", "the [] operator");
return m.getField(std::move(name));
},
"field_name"_a, py::return_value_policy::reference_internal)
.def("getFields",
[](const Model& m) {
TAMAAS_DEPRECATE("getFields()", "list(model)");
return m.getFields();
},
"Return fields list")
.def("applyElasticity",
[](Model& model, numpy stress, numpy strain) {
auto out = instanciateFromNumpy(stress);
auto in = instanciateFromNumpy(strain);
model.applyElasticity(*out, *in);
},
"Apply Hooke's law")
// Python magic functions
.def("__repr__",
[](const Model& m) {
std::stringstream ss;
ss << m;
return ss.str();
})
.def("__getitem__",
[](const Model& m, std::string key) -> decltype(m[key]) {
try {
return m[key];
} catch (std::out_of_range&) {
throw py::key_error(key);
}
},
py::return_value_policy::reference_internal, "Get field")
.def("__setitem__",
[](Model& m, std::string name, numpy field) {
auto f = instanciateFromNumpy(field);
m.registerField(name, std::move(f));
},
py::keep_alive<1, 3>(), "Register new field")
.def("__contains__",
[](const Model& m, std::string key) {
const auto fields = m.getFields();
return std::find(fields.begin(), fields.end(), std::move(key)) !=
fields.end();
},
py::keep_alive<0, 1>(), "Test field existence")
.def("__iter__",
[](const Model& m) {
const auto& fields = m.getFieldsMap();
return py::make_key_iterator(fields.cbegin(), fields.cend());
},
py::keep_alive<0, 1>(), "Iterator on fields")
.def_property_readonly(
"operators", [](Model& m) { return model_operator_accessor{m}; },
"Returns a dict-like object allowing access to the model's "
"integral "
"operators")
// More python-like access to model properties
.def_property_readonly("shape", &Model::getDiscretization,
"Discretization (local in MPI environment)")
.def_property_readonly("global_shape", &Model::getGlobalDiscretization,
"Global discretization (in MPI environement)")
.def_property_readonly("boundary_shape",
&Model::getBoundaryDiscretization,
"Number of points on boundary")
.def_property_readonly("system_size", &Model::getSystemSize,
"Size of physical domain")
.def_property_readonly("boundary_system_size",
&Model::getBoundarySystemSize,
"Physical size of surface")
.def_property_readonly("traction",
(const GridBase& (Model::*)() const) &
Model::getTraction,
"Surface traction field")
.def_property_readonly("displacement",
(const GridBase& (Model::*)() const) &
Model::getDisplacement,
"Displacement field");
py::class_>(
mod, "ModelDumper")
.def(py::init<>())
.def("dump", &ModelDumper::dump, "model"_a, "Dump model")
.def("__lshift__",
[](ModelDumper& dumper, Model& model) { dumper << model; },
"Dump model");
}
/// Wrap factory for models
void wrapModelFactory(py::module& mod) {
py::class_(mod, "ModelFactory")
.def_static("createModel", &ModelFactory::createModel, "model_type"_a,
"system_size"_a, "global_discretization"_a,
"Create a new model of a given type, physical size and "
"*global* discretization")
.def_static("createResidual", &ModelFactory::createResidual, "model"_a,
"sigma_y"_a, "hardening"_a = 0.,
"Create an isotropic linear hardening residual")
.def_static("registerVolumeOperators",
&ModelFactory::registerVolumeOperators, "model"_a,
"Register Boussinesq and Mindlin operators to model");
}
/// Wrap residual class
void wrapResidual(py::module& mod) {
// TODO adapt to n-dim
py::class_(mod, "Residual")
.def(py::init())
.def("computeResidual",
[](Residual& res, numpy& x) {
auto in = instanciateFromNumpy(x);
res.computeResidual(*in);
})
.def("computeStress",
[](Residual& res, numpy& x) {
auto in = instanciateFromNumpy(x);
res.computeStress(*in);
})
.def("updateState",
[](Residual& res, numpy& x) {
auto in = instanciateFromNumpy(x);
res.updateState(*in);
})
.def("computeResidualDisplacement",
[](Residual& res, numpy& x) {
auto in = instanciateFromNumpy(x);
res.computeResidualDisplacement(*in);
})
.def("applyTangent",
[](Residual& res, numpy& output, numpy& input,
numpy& current_strain_inc) {
auto out = instanciateFromNumpy(output);
auto in = instanciateFromNumpy(input);
auto inc = instanciateFromNumpy(current_strain_inc);
res.applyTangent(*out, *in, *inc);
},
"output"_a, "input"_a, "current_strain_increment"_a)
.def("getVector", &Residual::getVector,
py::return_value_policy::reference_internal)
.def("getPlasticStrain", &Residual::getPlasticStrain,
py::return_value_policy::reference_internal)
.def("getStress", &Residual::getStress,
py::return_value_policy::reference_internal)
.def("setIntegrationMethod", &Residual::setIntegrationMethod, "method"_a,
"cutoff"_a = 1e-12)
.def_property("yield_stress", &Residual::getYieldStress,
&Residual::setYieldStress)
.def_property("hardening_modulus", &Residual::getHardeningModulus,
&Residual::setHardeningModulus)
.def_property_readonly("model", &Residual::getModel);
}
void wrapModel(py::module& mod) {
wrapBEEngine(mod);
wrapModelClass(mod);
wrapModelFactory(mod);
wrapFunctionals(mod);
wrapResidual(mod);
wrapIntegralOperator(mod);
}
} // namespace wrap
} // namespace tamaas
diff --git a/python/wrap/model_extensions.hh b/python/wrap/model_extensions.hh
index 7da97c6..a21d6bc 100644
--- a/python/wrap/model_extensions.hh
+++ b/python/wrap/model_extensions.hh
@@ -1,132 +1,132 @@
/**
* @file
- * @section LICENSE
+ * LICENSE
*
* Copyright (©) 2016-2021 EPFL (École Polytechnique Fédérale de Lausanne),
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* This program is free software: you can redistribute it and/or modify
* 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 Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see .
*
*/
/* -------------------------------------------------------------------------- */
#include "functional.hh"
#include "model.hh"
#include "model_dumper.hh"
#include "residual.hh"
#include "wrap.hh"
#include
/* -------------------------------------------------------------------------- */
namespace tamaas {
/* -------------------------------------------------------------------------- */
namespace functional {
namespace wrap {
/// Class for extension of Functional in python
class PyFunctional : public Functional {
public:
using Functional::Functional;
// Overriding pure virtual functions
Real computeF(GridBase& variable, GridBase& dual) const override {
PYBIND11_OVERLOAD_PURE(Real, Functional, computeF, variable, dual);
}
void computeGradF(GridBase& variable,
GridBase& gradient) const override {
PYBIND11_OVERLOAD_PURE(void, Functional, computeGradF, variable, gradient);
}
};
} // namespace wrap
} // namespace functional
/* -------------------------------------------------------------------------- */
namespace wrap {
/* -------------------------------------------------------------------------- */
class PyModelDumper : public ModelDumper {
public:
using ModelDumper::ModelDumper;
void dump(const Model& model) override {
PYBIND11_OVERLOAD_PURE(void, ModelDumper, dump, model);
}
};
/* -------------------------------------------------------------------------- */
class PyResidual : public Residual {
public:
using Residual::Residual;
void computeResidual(GridBase& strain_increment) override {
PYBIND11_OVERLOAD_PURE(void, Residual, computeResidual, strain_increment);
}
void applyTangent(GridBase& output, GridBase& input,
GridBase& current_strain_increment) override {
PYBIND11_OVERLOAD_PURE(void, Residual, applyTangent, output, input,
current_strain_increment);
}
void computeStress(GridBase& strain_increment) override {
PYBIND11_OVERLOAD_PURE(void, Residual, computeStress, strain_increment);
}
void updateState(GridBase& converged_strain_increment) override {
PYBIND11_OVERLOAD_PURE(void, Residual, updateState,
converged_strain_increment);
}
const GridBase& getVector() const override {
PYBIND11_OVERLOAD_PURE(const GridBase&, Residual, getVector);
}
const GridBase& getPlasticStrain() const override {
PYBIND11_OVERLOAD_PURE(const GridBase&, Residual, getPlasticStrain);
}
const GridBase& getStress() const override {
PYBIND11_OVERLOAD_PURE(const GridBase&, Residual, getStress);
}
void computeResidualDisplacement(GridBase& strain_increment) override {
PYBIND11_OVERLOAD_PURE(void, Residual, computeResidualDisplacement,
strain_increment);
}
void setIntegrationMethod(integration_method method, Real cutoff) override {
PYBIND11_OVERLOAD_PURE(void, Residual, setIntegrationMethod, method,
cutoff);
}
Real getYieldStress() const override {
PYBIND11_OVERLOAD_PURE(Real, Residual, getYieldStress);
}
Real getHardeningModulus() const override {
PYBIND11_OVERLOAD_PURE(Real, Residual, getHardeningModulus);
}
void setYieldStress(Real val) override {
PYBIND11_OVERLOAD_PURE(void, Residual, setYieldStress, val);
}
void setHardeningModulus(Real val) override {
PYBIND11_OVERLOAD_PURE(void, Residual, setHardeningModulus, val);
}
};
/* -------------------------------------------------------------------------- */
} // namespace wrap
/* -------------------------------------------------------------------------- */
} // namespace tamaas
diff --git a/python/wrap/mpi.cpp b/python/wrap/mpi.cpp
index 96c1262..2fdfb3f 100644
--- a/python/wrap/mpi.cpp
+++ b/python/wrap/mpi.cpp
@@ -1,89 +1,89 @@
/**
* @file
- * @section LICENSE
+ * LICENSE
*
* Copyright (©) 2016-2021 EPFL (École Polytechnique Fédérale de Lausanne),
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* This program is free software: you can redistribute it and/or modify
* 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 Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see .
*
*/
/* -------------------------------------------------------------------------- */
#include "mpi_interface.hh"
#include "partitioner.hh"
#include "wrap.hh"
#include
/* -------------------------------------------------------------------------- */
namespace tamaas {
/* -------------------------------------------------------------------------- */
namespace wrap {
using namespace py::literals;
/* -------------------------------------------------------------------------- */
void wrapMPI(py::module& mod) {
auto mpi_mod = mod.def_submodule("mpi");
py::class_(mpi_mod, "sequential")
.def(py::init<>())
.def("__enter__", [](mpi::sequential& obj) { obj.enter(); })
.def("__exit__", [](mpi::sequential& obj, py::object, py::object,
py::object) { obj.exit(); });
mpi_mod.def("local_shape",
[](std::vector global) {
switch (global.size()) {
case 1:
return Partitioner<1>::local_size(global);
case 2:
return Partitioner<2>::local_size(global);
default:
TAMAAS_EXCEPTION("Please provide a 1D/2D shape");
}
},
"global_shape"_a, "Gives the local size of a 1D/2D global shape");
mpi_mod.def("global_shape",
[](std::vector local) {
switch (local.size()) {
case 1:
return Partitioner<1>::global_size(local);
case 2:
return Partitioner<2>::global_size(local);
default:
TAMAAS_EXCEPTION("Please provide a 1D/2D shape");
}
},
"local_shape"_a, "Gives the global shape of a 1D/2D local shape");
mpi_mod.def("local_offset",
[](std::vector global) {
switch (global.size()) {
case 1:
return Partitioner<1>::local_offset(global);
case 2:
return Partitioner<2>::local_offset(global);
default:
TAMAAS_EXCEPTION("Please provide a 1D/2D shape");
}
},
"global_shape"_a,
"Gives the local offset of a 1D/2D global shape");
mpi_mod.def("size", []() { return mpi::size(); });
mpi_mod.def("rank", []() { return mpi::rank(); });
}
} // namespace wrap
/* -------------------------------------------------------------------------- */
} // namespace tamaas
diff --git a/python/wrap/percolation.cpp b/python/wrap/percolation.cpp
index 25924a4..60b6d31 100644
--- a/python/wrap/percolation.cpp
+++ b/python/wrap/percolation.cpp
@@ -1,93 +1,93 @@
/**
* @file
- * @section LICENSE
+ * LICENSE
*
* Copyright (©) 2016-2021 EPFL (École Polytechnique Fédérale de Lausanne),
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* This program is free software: you can redistribute it and/or modify
* 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 Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see .
*
*/
/* -------------------------------------------------------------------------- */
#include "flood_fill.hh"
#include "wrap.hh"
/* -------------------------------------------------------------------------- */
#include
/* -------------------------------------------------------------------------- */
namespace tamaas {
namespace wrap {
/* -------------------------------------------------------------------------- */
using namespace py::literals;
/* -------------------------------------------------------------------------- */
template
void wrapCluster(py::module& mod) {
auto name = makeDimensionName("Cluster", dim);
py::class_>(mod, name.c_str())
.def(py::init<>())
.def_property_readonly("area", &Cluster::getArea, "Area of cluster")
.def_property_readonly("points", &Cluster::getPoints,
"Get list of points of cluster")
.def_property_readonly("perimeter", &Cluster::getPerimeter,
"Get perimeter of cluster")
.def_property_readonly("bounding_box", &Cluster::boundingBox,
"Compute the bounding box of a cluster")
.def(TAMAAS_DEPRECATE_ACCESSOR(getArea, Cluster, "area"))
.def(TAMAAS_DEPRECATE_ACCESSOR(getPoints, Cluster, "points"))
.def(TAMAAS_DEPRECATE_ACCESSOR(getPerimeter, Cluster, "perimeter"))
.def("__str__", [](const Cluster& cluster) {
std::stringstream sstr;
sstr << '{';
auto&& points = cluster.getPoints();
auto print_point = [&sstr](const auto& point) {
sstr << '(';
for (UInt i = 0; i < point.size() - 1; ++i)
sstr << point[i] << ", ";
sstr << point.back() << ')';
};
auto point_it = points.begin();
for (UInt p = 0; p < points.size() - 1; ++p) {
print_point(*(point_it++));
sstr << ", ";
}
print_point(points.back());
sstr << "}";
return sstr.str();
});
}
void wrapPercolation(py::module& mod) {
wrapCluster<1>(mod);
wrapCluster<2>(mod);
wrapCluster<3>(mod);
py::class_(mod, "FloodFill")
.def_static("getSegments", &FloodFill::getSegments,
"Return a list of segments from boolean map", "contact"_a)
.def_static("getClusters", &FloodFill::getClusters,
"Return a list of clusters from boolean map", "contact"_a,
"diagonal"_a)
.def_static("getVolumes", &FloodFill::getVolumes,
"Return a list of volume clusters", "map"_a, "diagonal"_a);
}
} // namespace wrap
} // namespace tamaas
diff --git a/python/wrap/solvers.cpp b/python/wrap/solvers.cpp
index c7a9187..42ca273 100644
--- a/python/wrap/solvers.cpp
+++ b/python/wrap/solvers.cpp
@@ -1,188 +1,188 @@
/**
* @file
- * @section LICENSE
+ * LICENSE
*
* Copyright (©) 2016-2021 EPFL (École Polytechnique Fédérale de Lausanne),
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* This program is free software: you can redistribute it and/or modify
* 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 Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see .
*
*/
/* -------------------------------------------------------------------------- */
#include "beck_teboulle.hh"
#include "condat.hh"
#include "contact_solver.hh"
#include "dfsane_solver.hh"
#include "ep_solver.hh"
#include "epic.hh"
#include "kato.hh"
#include "kato_saturated.hh"
#include "polonsky_keer_rey.hh"
#include "polonsky_keer_tan.hh"
#include "wrap.hh"
#include
/* -------------------------------------------------------------------------- */
namespace tamaas {
namespace wrap {
/* -------------------------------------------------------------------------- */
using namespace py::literals;
class PyEPSolver : public EPSolver {
public:
using EPSolver::EPSolver;
void solve() override { PYBIND11_OVERLOAD_PURE(void, EPSolver, solve); }
void updateState() override {
PYBIND11_OVERLOAD(void, EPSolver, updateState);
}
};
/* -------------------------------------------------------------------------- */
void wrapSolvers(py::module& mod) {
py::class_(mod, "ContactSolver")
.def("setMaxIterations",
[](ContactSolver& m, UInt iter) {
TAMAAS_DEPRECATE("setMaxIterations()", "the max_iter property");
m.setMaxIterations(iter);
},
"max_iter"_a)
.def("setDumpFrequency",
[](ContactSolver& m, UInt freq) {
TAMAAS_DEPRECATE("setDumpFrequency()", "the dump_freq property");
m.setDumpFrequency(freq);
},
"dump_freq"_a)
.def_property("max_iter", &ContactSolver::getMaxIterations,
&ContactSolver::setMaxIterations,
"Maximum number of iterations")
.def_property("dump_freq", &ContactSolver::getDumpFrequency,
&ContactSolver::setDumpFrequency,
"Frequency of displaying solver info")
.def_property_readonly("model", &ContactSolver::getModel)
.def_property_readonly("surface", &ContactSolver::getSurface)
.def("addFunctionalTerm", &ContactSolver::addFunctionalTerm)
.def("solve", py::overload_cast>(&ContactSolver::solve),
"target_force"_a,
py::call_guard())
.def("solve", py::overload_cast(&ContactSolver::solve),
"target_normal_pressure"_a,
py::call_guard());
py::class_ pkr(mod, "PolonskyKeerRey");
// Need to export enum values before defining PKR constructor
py::enum_(pkr, "type")
.value("gap", PolonskyKeerRey::gap)
.value("pressure", PolonskyKeerRey::pressure)
.export_values();
pkr.def(py::init&, Real, PolonskyKeerRey::type,
PolonskyKeerRey::type>(),
"model"_a, "surface"_a, "tolerance"_a,
"primal_type"_a = PolonskyKeerRey::type::pressure,
"constraint_type"_a = PolonskyKeerRey::type::pressure,
py::keep_alive<1, 2>(), py::keep_alive<1, 3>())
.def("computeError", &PolonskyKeerRey::computeError);
py::class_(mod, "KatoSaturated")
.def(py::init&, Real, Real>(), "model"_a,
"surface"_a, "tolerance"_a, "pmax"_a, py::keep_alive<1, 2>(),
py::keep_alive<1, 3>())
.def_property("pmax", &KatoSaturated::getPMax, &KatoSaturated::setPMax);
py::class_ kato(mod, "Kato");
kato.def(py::init&, Real, Real>(), "model"_a,
"surface"_a, "tolerance"_a, "mu"_a, py::keep_alive<1, 2>(),
py::keep_alive<1, 3>())
.def("solve", &Kato::solve, "p0"_a, "proj_iter"_a = 50)
.def("solveRelaxed", &Kato::solveRelaxed, "g0"_a)
.def("solveRegularized", &Kato::solveRegularized, "p0"_a, "r"_a = 0.01)
.def("computeCost", &Kato::computeCost, "use_tresca"_a = false);
py::class_ bt(mod, "BeckTeboulle");
bt.def(py::init&, Real, Real>(), "model"_a,
"surface"_a, "tolerance"_a, "mu"_a, py::keep_alive<1, 2>(),
py::keep_alive<1, 3>())
.def("solve", &BeckTeboulle::solve, "p0"_a)
.def("computeCost", &BeckTeboulle::computeCost);
py::class_ cd(mod, "Condat");
cd.def(py::init&, Real, Real>(), "model"_a,
"surface"_a, "tolerance"_a, "mu"_a, py::keep_alive<1, 2>(),
py::keep_alive<1, 3>())
.def("solve", &Condat::solve, "p0"_a, "grad_step"_a = 0.9)
.def("computeCost", &Condat::computeCost);
py::class_ pkt(mod, "PolonskyKeerTan");
pkt.def(py::init&, Real, Real>(), "model"_a,
"surface"_a, "tolerance"_a, "mu"_a, py::keep_alive<1, 2>(),
py::keep_alive<1, 3>())
.def("solve", &PolonskyKeerTan::solve, "p0"_a)
.def("solveTresca", &PolonskyKeerTan::solveTresca, "p0"_a)
.def("computeCost", &PolonskyKeerTan::computeCost,
"use_tresca"_a = false);
py::class_(mod, "_tolerance_manager")
.def(py::init());
py::class_(mod, "EPSolver")
.def(py::init(), "residual"_a, py::keep_alive<1, 2>())
.def("solve", &EPSolver::solve)
.def("getStrainIncrement", &EPSolver::getStrainIncrement,
py::return_value_policy::reference_internal)
.def("getResidual", &EPSolver::getResidual,
py::return_value_policy::reference_internal)
.def("updateState", &EPSolver::updateState)
.def_property("tolerance", &EPSolver::getTolerance,
&EPSolver::setTolerance)
.def("setToleranceManager", &EPSolver::setToleranceManager)
.def("beforeSolve", &EPSolver::beforeSolve);
py::class_(mod, "_DFSANESolver")
.def(py::init(), "residual"_a, py::keep_alive<1, 2>())
.def(py::init([](Residual& res, Model&) {
return std::make_unique(res);
}),
"residual"_a, "model"_a, py::keep_alive<1, 2>(),
"Deprecated constructor: only here for compatibility reasons");
py::class_(mod, "EPICSolver")
.def(py::init(),
"contact_solver"_a, "elasto_plastic_solver"_a, "tolerance"_a = 1e-10,
"relaxation"_a = 0.3, py::keep_alive<1, 2>(), py::keep_alive<1, 3>())
.def("solve",
[](EPICSolver& solver, Real pressure) {
return solver.solve(std::vector{pressure});
},
"normal_pressure"_a,
py::call_guard())
.def("acceleratedSolve",
[](EPICSolver& solver, Real pressure) {
return solver.acceleratedSolve(std::vector{pressure});
},
"normal_pressure"_a,
py::call_guard());
}
} // namespace wrap
} // namespace tamaas
diff --git a/python/wrap/surface.cpp b/python/wrap/surface.cpp
index 6898229..b87cc11 100644
--- a/python/wrap/surface.cpp
+++ b/python/wrap/surface.cpp
@@ -1,170 +1,170 @@
/**
* @file
- * @section LICENSE
+ * LICENSE
*
* Copyright (©) 2016-2021 EPFL (École Polytechnique Fédérale de Lausanne),
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* This program is free software: you can redistribute it and/or modify
* 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 Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see .
*
*/
/* -------------------------------------------------------------------------- */
#include "isopowerlaw.hh"
#include "regularized_powerlaw.hh"
#include "surface_generator_filter.hh"
#include "surface_generator_random_phase.hh"
#include "wrap.hh"
#include
/* -------------------------------------------------------------------------- */
namespace tamaas {
/* -------------------------------------------------------------------------- */
namespace wrap {
using namespace py::literals;
/* -------------------------------------------------------------------------- */
template
class PyFilter : public Filter {
public:
using Filter::Filter;
// Overriding pure virtual functions
void
computeFilter(GridHermitian& filter_coefficients) const override {
PYBIND11_OVERLOAD_PURE(void, Filter, computeFilter,
filter_coefficients);
}
};
template
void wrapFilter(py::module& mod) {
auto name = makeDimensionName("Filter", dim);
py::class_, std::shared_ptr>, PyFilter>(
mod, name.c_str())
.def(py::init<>())
.def("computeFilter",
(void (Filter::*)(GridHermitian&) const) &
Filter::computeFilter);
}
/* -------------------------------------------------------------------------- */
template
void wrapIsopowerlaw(py::module& mod) {
std::string name = makeDimensionName("Isopowerlaw", dim);
py::class_, Filter, std::shared_ptr>>(
mod, name.c_str())
.def(py::init<>())
.def_property("q0", &Isopowerlaw::getQ0, &Isopowerlaw::setQ0,
"Long wavelength cutoff")
.def_property("q1", &Isopowerlaw::getQ1, &Isopowerlaw::setQ1,
"Rolloff wavelength")
.def_property("q2", &Isopowerlaw::getQ2, &Isopowerlaw::setQ2,
"Short wavelength cutoff")
.def_property("hurst", &Isopowerlaw::getHurst,
&Isopowerlaw::setHurst, "Hurst exponent")
.def("rmsHeights", &Isopowerlaw::rmsHeights,
"Theoretical RMS of heights")
.def("moments", &Isopowerlaw::moments,
"Theoretical first 3 moments of spectrum")
.def("alpha", &Isopowerlaw::alpha, "Nayak's bandwidth parameter")
.def("rmsSlopes", &Isopowerlaw::rmsSlopes,
"Theoretical RMS of slopes");
name = makeDimensionName("RegularizedPowerlaw", dim);
py::class_, Filter,
std::shared_ptr>>(mod, name.c_str())
.def(py::init<>())
.def_property("q1", &RegularizedPowerlaw::getQ1,
&RegularizedPowerlaw::setQ1, "Long wavelength cutoff")
.def_property("q2", &RegularizedPowerlaw::getQ2,
&RegularizedPowerlaw::setQ2, "Short wavelength cutoff")
.def_property("hurst", &RegularizedPowerlaw::getHurst,
&RegularizedPowerlaw::setHurst, "Hurst exponent");
}
/* -------------------------------------------------------------------------- */
template
void wrapSurfaceGenerators(py::module& mod) {
std::string generator_name = makeDimensionName("SurfaceGenerator", dim);
py::class_>(mod, generator_name.c_str())
.def("buildSurface", &SurfaceGenerator::buildSurface,
py::return_value_policy::reference_internal)
.def("setSizes",
[](SurfaceGenerator& m, std::array s) {
TAMAAS_DEPRECATE("setSizes()", "the shape property");
m.setSizes(std::move(s));
})
.def("setRandomSeed",
[](SurfaceGenerator& m, long s) {
TAMAAS_DEPRECATE("setRandomSeed()", "the random_seed property");
m.setRandomSeed(s);
})
.def_property("random_seed", &SurfaceGenerator::getRandomSeed,
&SurfaceGenerator::setRandomSeed,
"Random generator seed")
.def_property("shape", &SurfaceGenerator::getSizes,
py::overload_cast>(
&SurfaceGenerator::setSizes),
"Global shape of surfaces");
std::string filter_name = makeDimensionName("SurfaceGeneratorFilter", dim);
py::class_, SurfaceGenerator>(
mod, filter_name.c_str())
.def(py::init<>(), "Default constructor")
.def(py::init>(),
"Initialize with global surface shape")
.def("setFilter",
[](SurfaceGeneratorFilter& m, std::shared_ptr> s) {
TAMAAS_DEPRECATE("setFilter()", "the spectrum property");
m.setSpectrum(std::move(s));
},
"Set PSD filter", "filter"_a)
.def("setSpectrum",
[](SurfaceGeneratorFilter& m, std::shared_ptr> s) {
TAMAAS_DEPRECATE("setSpectrum()", "the spectrum property");
m.setSpectrum(std::move(s));
},
"Set PSD filter", "filter"_a)
.def_property("spectrum", &SurfaceGeneratorFilter