diff --git a/packages/core.cmake b/packages/core.cmake
index e362dc234..0261b1224 100644
--- a/packages/core.cmake
+++ b/packages/core.cmake
@@ -1,584 +1,585 @@
#===============================================================================
# @file core.cmake
#
# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Mon Nov 21 2011
# @date last modification: Mon Jan 18 2016
#
# @brief package description for core
#
# @section LICENSE
#
# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
# Solides)
#
# Akantu is free software: you can redistribute it and/or modify it under the
# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
#
# Akantu 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 Lesser General Public License for more
# details.
#
# You should have received a copy of the GNU Lesser General Public License
# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
package_declare(core NOT_OPTIONAL
DESCRIPTION "core package for Akantu"
FEATURES_PUBLIC cxx_strong_enums cxx_defaulted_functions cxx_deleted_functions
cxx_auto_type cxx_decltype_auto
FEATURES_PRIVATE cxx_lambdas cxx_nullptr cxx_delegated_constructors
cxx_range_for )
package_declare_sources(core
common/aka_array.cc
common/aka_array.hh
common/aka_array_tmpl.hh
common/aka_blas_lapack.hh
common/aka_circular_array.hh
common/aka_circular_array_inline_impl.cc
common/aka_common.cc
common/aka_common.hh
common/aka_common_inline_impl.cc
common/aka_csr.hh
common/aka_element_classes_info_inline_impl.cc
common/aka_error.cc
common/aka_error.hh
common/aka_event_handler_manager.hh
common/aka_extern.cc
common/aka_factory.hh
common/aka_fwd.hh
common/aka_grid_dynamic.hh
common/aka_math.cc
common/aka_math.hh
common/aka_math_tmpl.hh
common/aka_memory.cc
common/aka_memory.hh
common/aka_memory_inline_impl.cc
common/aka_named_argument.hh
common/aka_random_generator.hh
common/aka_safe_enum.hh
common/aka_static_memory.cc
common/aka_static_memory.hh
common/aka_static_memory_inline_impl.cc
common/aka_static_memory_tmpl.hh
common/aka_typelist.hh
common/aka_types.hh
common/aka_visitor.hh
common/aka_voigthelper.hh
common/aka_voigthelper_tmpl.hh
common/aka_voigthelper.cc
common/aka_warning.hh
common/aka_warning_restore.hh
common/aka_zip.hh
fe_engine/element_class.cc
fe_engine/element_class.hh
fe_engine/element_class_tmpl.hh
fe_engine/element_classes/element_class_hexahedron_8_inline_impl.cc
fe_engine/element_classes/element_class_hexahedron_20_inline_impl.cc
fe_engine/element_classes/element_class_pentahedron_6_inline_impl.cc
fe_engine/element_classes/element_class_pentahedron_15_inline_impl.cc
fe_engine/element_classes/element_class_point_1_inline_impl.cc
fe_engine/element_classes/element_class_quadrangle_4_inline_impl.cc
fe_engine/element_classes/element_class_quadrangle_8_inline_impl.cc
fe_engine/element_classes/element_class_segment_2_inline_impl.cc
fe_engine/element_classes/element_class_segment_3_inline_impl.cc
fe_engine/element_classes/element_class_tetrahedron_10_inline_impl.cc
fe_engine/element_classes/element_class_tetrahedron_4_inline_impl.cc
fe_engine/element_classes/element_class_triangle_3_inline_impl.cc
fe_engine/element_classes/element_class_triangle_6_inline_impl.cc
fe_engine/fe_engine.cc
fe_engine/fe_engine.hh
fe_engine/fe_engine_inline_impl.cc
fe_engine/fe_engine_template.hh
fe_engine/fe_engine_template_tmpl.hh
fe_engine/geometrical_element.cc
fe_engine/gauss_integration.cc
fe_engine/gauss_integration_tmpl.hh
fe_engine/integrator.hh
fe_engine/integrator_gauss.hh
fe_engine/integrator_gauss_inline_impl.cc
fe_engine/interpolation_element.cc
fe_engine/interpolation_element_tmpl.hh
fe_engine/integration_point.hh
fe_engine/shape_functions.hh
fe_engine/shape_functions_inline_impl.cc
fe_engine/shape_lagrange.cc
fe_engine/shape_lagrange.hh
fe_engine/shape_lagrange_inline_impl.cc
fe_engine/shape_linked.cc
fe_engine/shape_linked.hh
fe_engine/shape_linked_inline_impl.cc
fe_engine/element.hh
io/dumper/dumpable.hh
io/dumper/dumpable.cc
io/dumper/dumpable_dummy.hh
io/dumper/dumpable_inline_impl.hh
io/dumper/dumper_field.hh
io/dumper/dumper_material_padders.hh
io/dumper/dumper_filtered_connectivity.hh
io/dumper/dumper_element_partition.hh
io/mesh_io.cc
io/mesh_io.hh
io/mesh_io/mesh_io_abaqus.cc
io/mesh_io/mesh_io_abaqus.hh
io/mesh_io/mesh_io_diana.cc
io/mesh_io/mesh_io_diana.hh
io/mesh_io/mesh_io_msh.cc
io/mesh_io/mesh_io_msh.hh
io/model_io.cc
io/model_io.hh
io/parser/algebraic_parser.hh
io/parser/input_file_parser.hh
io/parser/parsable.cc
io/parser/parsable.hh
io/parser/parsable_tmpl.hh
io/parser/parser.cc
io/parser/parser_real.cc
io/parser/parser_random.cc
io/parser/parser_types.cc
io/parser/parser_input_files.cc
io/parser/parser.hh
io/parser/parser_tmpl.hh
io/parser/parser_grammar_tmpl.hh
io/parser/cppargparse/cppargparse.hh
io/parser/cppargparse/cppargparse.cc
io/parser/cppargparse/cppargparse_tmpl.hh
io/parser/parameter_registry.cc
io/parser/parameter_registry.hh
io/parser/parameter_registry_tmpl.hh
mesh/element_group.cc
mesh/element_group.hh
mesh/element_group_inline_impl.cc
mesh/element_type_map.cc
mesh/element_type_map.hh
mesh/element_type_map_tmpl.hh
mesh/element_type_map_filter.hh
mesh/group_manager.cc
mesh/group_manager.hh
mesh/group_manager_inline_impl.cc
mesh/mesh.cc
mesh/mesh.hh
mesh/mesh_accessor.hh
mesh/mesh_accessor.cc
mesh/mesh_events.hh
mesh/mesh_filter.hh
mesh/mesh_data.cc
mesh/mesh_data.hh
mesh/mesh_data_tmpl.hh
mesh/mesh_inline_impl.cc
mesh/node_group.cc
mesh/node_group.hh
mesh/node_group_inline_impl.cc
+ mesh/mesh_iterators.hh
mesh_utils/mesh_partition.cc
mesh_utils/mesh_partition.hh
mesh_utils/mesh_partition/mesh_partition_mesh_data.cc
mesh_utils/mesh_partition/mesh_partition_mesh_data.hh
mesh_utils/mesh_partition/mesh_partition_scotch.hh
mesh_utils/mesh_utils_pbc.cc
mesh_utils/mesh_utils.cc
mesh_utils/mesh_utils.hh
mesh_utils/mesh_utils_distribution.cc
mesh_utils/mesh_utils_distribution.hh
mesh_utils/mesh_utils.hh
mesh_utils/mesh_utils_inline_impl.cc
mesh_utils/global_ids_updater.hh
mesh_utils/global_ids_updater.cc
mesh_utils/global_ids_updater_inline_impl.cc
model/boundary_condition.hh
model/boundary_condition_functor.hh
model/boundary_condition_functor_inline_impl.cc
model/boundary_condition_tmpl.hh
model/common/neighborhood_base.hh
model/common/neighborhood_base.cc
model/common/neighborhood_base_inline_impl.cc
model/common/neighborhoods_criterion_evaluation/neighborhood_max_criterion.hh
model/common/neighborhoods_criterion_evaluation/neighborhood_max_criterion.cc
model/common/neighborhoods_criterion_evaluation/neighborhood_max_criterion_inline_impl.cc
model/common/non_local_toolbox/non_local_manager.hh
model/common/non_local_toolbox/non_local_manager.cc
model/common/non_local_toolbox/non_local_manager_inline_impl.cc
model/common/non_local_toolbox/non_local_neighborhood_base.hh
model/common/non_local_toolbox/non_local_neighborhood_base.cc
model/common/non_local_toolbox/non_local_neighborhood.hh
model/common/non_local_toolbox/non_local_neighborhood_tmpl.hh
model/common/non_local_toolbox/non_local_neighborhood_inline_impl.cc
model/dof_manager.cc
model/dof_manager.hh
model/dof_manager_default.cc
model/dof_manager_default.hh
model/dof_manager_default_inline_impl.cc
model/dof_manager_inline_impl.cc
model/model_solver.cc
model/model_solver.hh
model/model_solver_tmpl.hh
model/non_linear_solver.cc
model/non_linear_solver.hh
model/non_linear_solver_default.hh
model/non_linear_solver_lumped.cc
model/non_linear_solver_lumped.hh
model/solver_callback.hh
model/solver_callback.cc
model/time_step_solver.hh
model/time_step_solvers/time_step_solver.cc
model/time_step_solvers/time_step_solver_default.cc
model/time_step_solvers/time_step_solver_default.hh
model/time_step_solvers/time_step_solver_default_explicit.hh
model/non_linear_solver_callback.hh
model/time_step_solvers/time_step_solver_default_solver_callback.hh
model/integration_scheme/generalized_trapezoidal.cc
model/integration_scheme/generalized_trapezoidal.hh
model/integration_scheme/integration_scheme.cc
model/integration_scheme/integration_scheme.hh
model/integration_scheme/integration_scheme_1st_order.cc
model/integration_scheme/integration_scheme_1st_order.hh
model/integration_scheme/integration_scheme_2nd_order.cc
model/integration_scheme/integration_scheme_2nd_order.hh
model/integration_scheme/newmark-beta.cc
model/integration_scheme/newmark-beta.hh
model/integration_scheme/pseudo_time.cc
model/integration_scheme/pseudo_time.hh
model/model.cc
model/model.hh
model/model_inline_impl.cc
model/solid_mechanics/material.cc
model/solid_mechanics/material.hh
model/solid_mechanics/material_inline_impl.cc
model/solid_mechanics/material_selector.hh
model/solid_mechanics/material_selector_tmpl.hh
model/solid_mechanics/materials/internal_field.hh
model/solid_mechanics/materials/internal_field_tmpl.hh
model/solid_mechanics/materials/random_internal_field.hh
model/solid_mechanics/materials/random_internal_field_tmpl.hh
model/solid_mechanics/solid_mechanics_model.cc
model/solid_mechanics/solid_mechanics_model.hh
model/solid_mechanics/solid_mechanics_model_inline_impl.cc
model/solid_mechanics/solid_mechanics_model_io.cc
model/solid_mechanics/solid_mechanics_model_mass.cc
model/solid_mechanics/solid_mechanics_model_material.cc
model/solid_mechanics/solid_mechanics_model_tmpl.hh
model/solid_mechanics/solid_mechanics_model_event_handler.hh
model/solid_mechanics/materials/plane_stress_toolbox.hh
model/solid_mechanics/materials/plane_stress_toolbox_tmpl.hh
model/solid_mechanics/materials/material_core_includes.hh
model/solid_mechanics/materials/material_elastic.cc
model/solid_mechanics/materials/material_elastic.hh
model/solid_mechanics/materials/material_elastic_inline_impl.cc
model/solid_mechanics/materials/material_thermal.cc
model/solid_mechanics/materials/material_thermal.hh
model/solid_mechanics/materials/material_elastic_linear_anisotropic.cc
model/solid_mechanics/materials/material_elastic_linear_anisotropic.hh
model/solid_mechanics/materials/material_elastic_orthotropic.cc
model/solid_mechanics/materials/material_elastic_orthotropic.hh
model/solid_mechanics/materials/material_damage/material_damage.hh
model/solid_mechanics/materials/material_damage/material_damage_tmpl.hh
model/solid_mechanics/materials/material_damage/material_marigo.cc
model/solid_mechanics/materials/material_damage/material_marigo.hh
model/solid_mechanics/materials/material_damage/material_marigo_inline_impl.cc
model/solid_mechanics/materials/material_damage/material_mazars.cc
model/solid_mechanics/materials/material_damage/material_mazars.hh
model/solid_mechanics/materials/material_damage/material_mazars_inline_impl.cc
model/solid_mechanics/materials/material_finite_deformation/material_neohookean.cc
model/solid_mechanics/materials/material_finite_deformation/material_neohookean.hh
model/solid_mechanics/materials/material_finite_deformation/material_neohookean_inline_impl.cc
model/solid_mechanics/materials/material_plastic/material_plastic.cc
model/solid_mechanics/materials/material_plastic/material_plastic.hh
model/solid_mechanics/materials/material_plastic/material_plastic_inline_impl.cc
model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening.cc
model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening.hh
model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening_inline_impl.cc
model/solid_mechanics/materials/material_viscoelastic/material_standard_linear_solid_deviatoric.cc
model/solid_mechanics/materials/material_viscoelastic/material_standard_linear_solid_deviatoric.hh
model/solid_mechanics/materials/material_non_local.hh
model/solid_mechanics/materials/material_non_local_tmpl.hh
model/solid_mechanics/materials/material_non_local_includes.hh
model/solid_mechanics/materials/material_non_local_inline_impl.cc
solver/sparse_solver.cc
solver/sparse_solver.hh
solver/sparse_solver_inline_impl.cc
solver/sparse_matrix.cc
solver/sparse_matrix.hh
solver/sparse_matrix_inline_impl.cc
solver/sparse_matrix_aij.cc
solver/sparse_matrix_aij.hh
solver/sparse_matrix_aij_inline_impl.cc
solver/terms_to_assemble.hh
synchronizer/communication_descriptor_tmpl.hh
synchronizer/communications_tmpl.hh
synchronizer/communication_buffer.hh
synchronizer/communication_buffer_inline_impl.cc
synchronizer/communication_descriptor.hh
synchronizer/communication_tag.hh
synchronizer/communications.hh
synchronizer/data_accessor.cc
synchronizer/data_accessor.hh
synchronizer/element_synchronizer.cc
synchronizer/element_synchronizer.hh
synchronizer/node_synchronizer.cc
synchronizer/node_synchronizer.hh
synchronizer/dof_synchronizer.cc
synchronizer/dof_synchronizer.hh
synchronizer/dof_synchronizer_inline_impl.cc
synchronizer/element_info_per_processor.cc
synchronizer/element_info_per_processor.hh
synchronizer/element_info_per_processor_tmpl.hh
synchronizer/filtered_synchronizer.cc
synchronizer/filtered_synchronizer.hh
synchronizer/grid_synchronizer.cc
synchronizer/grid_synchronizer.hh
synchronizer/grid_synchronizer_tmpl.hh
synchronizer/master_element_info_per_processor.cc
synchronizer/node_info_per_processor.cc
synchronizer/node_info_per_processor.hh
synchronizer/real_static_communicator.hh
synchronizer/slave_element_info_per_processor.cc
synchronizer/static_communicator.cc
synchronizer/static_communicator.hh
synchronizer/static_communicator_dummy.hh
synchronizer/static_communicator_inline_impl.hh
synchronizer/synchronizer.cc
synchronizer/synchronizer.hh
synchronizer/synchronizer_impl.hh
synchronizer/synchronizer_impl_tmpl.hh
synchronizer/synchronizer_registry.cc
synchronizer/synchronizer_registry.hh
synchronizer/synchronizer_tmpl.hh
)
package_declare_elements(core
ELEMENT_TYPES
_point_1
_segment_2
_segment_3
_triangle_3
_triangle_6
_quadrangle_4
_quadrangle_8
_tetrahedron_4
_tetrahedron_10
_pentahedron_6
_pentahedron_15
_hexahedron_8
_hexahedron_20
KIND regular
GEOMETRICAL_TYPES
_gt_point
_gt_segment_2
_gt_segment_3
_gt_triangle_3
_gt_triangle_6
_gt_quadrangle_4
_gt_quadrangle_8
_gt_tetrahedron_4
_gt_tetrahedron_10
_gt_hexahedron_8
_gt_hexahedron_20
_gt_pentahedron_6
_gt_pentahedron_15
INTERPOLATION_TYPES
_itp_lagrange_point_1
_itp_lagrange_segment_2
_itp_lagrange_segment_3
_itp_lagrange_triangle_3
_itp_lagrange_triangle_6
_itp_lagrange_quadrangle_4
_itp_serendip_quadrangle_8
_itp_lagrange_tetrahedron_4
_itp_lagrange_tetrahedron_10
_itp_lagrange_hexahedron_8
_itp_serendip_hexahedron_20
_itp_lagrange_pentahedron_6
_itp_lagrange_pentahedron_15
GEOMETRICAL_SHAPES
_gst_point
_gst_triangle
_gst_square
_gst_prism
GAUSS_INTEGRATION_TYPES
_git_point
_git_segment
_git_triangle
_git_tetrahedron
_git_pentahedron
INTERPOLATION_KIND _itk_lagrangian
FE_ENGINE_LISTS
gradient_on_integration_points
interpolate_on_integration_points
interpolate
compute_normals_on_integration_points
inverse_map
contains
compute_shapes
compute_shapes_derivatives
get_shapes_derivatives
)
package_declare_material_infos(core
LIST AKANTU_CORE_MATERIAL_LIST
INCLUDE material_core_includes.hh
)
package_declare_documentation_files(core
manual.sty
manual.cls
manual.tex
manual-macros.sty
manual-titlepages.tex
manual-authors.tex
manual-introduction.tex
manual-gettingstarted.tex
manual-io.tex
manual-feengine.tex
manual-solidmechanicsmodel.tex
manual-constitutive-laws.tex
manual-lumping.tex
manual-elements.tex
manual-appendix-elements.tex
manual-appendix-materials.tex
manual-appendix-packages.tex
manual-backmatter.tex
manual-bibliography.bib
manual-bibliographystyle.bst
figures/bc_and_ic_example.pdf
figures/boundary.pdf
figures/boundary.svg
figures/dirichlet.pdf
figures/dirichlet.svg
figures/doc_wheel.pdf
figures/doc_wheel.svg
figures/dynamic_analysis.png
figures/explicit_dynamic.pdf
figures/explicit_dynamic.svg
figures/static.pdf
figures/static.svg
figures/hooke_law.pdf
figures/hot-point-1.png
figures/hot-point-2.png
figures/implicit_dynamic.pdf
figures/implicit_dynamic.svg
figures/insertion.pdf
figures/interpolate.pdf
figures/interpolate.svg
figures/problemDomain.pdf_tex
figures/problemDomain.pdf
figures/static_analysis.png
figures/stress_strain_el.pdf
figures/tangent.pdf
figures/tangent.svg
figures/vectors.pdf
figures/vectors.svg
figures/stress_strain_neo.pdf
figures/visco_elastic_law.pdf
figures/isotropic_hardening_plasticity.pdf
figures/stress_strain_visco.pdf
figures/elements/hexahedron_8.pdf
figures/elements/hexahedron_8.svg
figures/elements/quadrangle_4.pdf
figures/elements/quadrangle_4.svg
figures/elements/quadrangle_8.pdf
figures/elements/quadrangle_8.svg
figures/elements/segment_2.pdf
figures/elements/segment_2.svg
figures/elements/segment_3.pdf
figures/elements/segment_3.svg
figures/elements/tetrahedron_10.pdf
figures/elements/tetrahedron_10.svg
figures/elements/tetrahedron_4.pdf
figures/elements/tetrahedron_4.svg
figures/elements/triangle_3.pdf
figures/elements/triangle_3.svg
figures/elements/triangle_6.pdf
figures/elements/triangle_6.svg
figures/elements/xtemp.pdf
)
package_declare_documentation(core
"This package is the core engine of \\akantu. It depends on:"
"\\begin{itemize}"
"\\item A C++ compiler (\\href{http://gcc.gnu.org/}{GCC} >= 4, or \\href{https://software.intel.com/en-us/intel-compilers}{Intel})."
"\\item The cross-platform, open-source \\href{http://www.cmake.org/}{CMake} build system."
"\\item The \\href{http://www.boost.org/}{Boost} C++ portable libraries."
"\\item The \\href{http://www.zlib.net/}{zlib} compression library."
"\\end{itemize}"
""
"Under Ubuntu (14.04 LTS) the installation can be performed using the commands:"
"\\begin{command}"
" > sudo apt-get install cmake libboost-dev zlib1g-dev g++"
"\\end{command}"
""
"Under Mac OS X the installation requires the following steps:"
"\\begin{itemize}"
"\\item Install Xcode"
"\\item Install the command line tools."
"\\item Install the MacPorts project which allows to automatically"
"download and install opensource packages."
"\\end{itemize}"
"Then the following commands should be typed in a terminal:"
"\\begin{command}"
" > sudo port install cmake gcc48 boost"
"\\end{command}"
)
find_program(READLINK_COMMAND readlink)
find_program(ADDR2LINE_COMMAND addr2line)
find_program(PATCH_COMMAND patch)
mark_as_advanced(READLINK_COMMAND)
mark_as_advanced(ADDR2LINE_COMMAND)
package_declare_extra_files_to_package(core
SOURCES
common/aka_element_classes_info.hh.in
common/aka_config.hh.in
model/solid_mechanics/material_list.hh.in
)
if(CMAKE_CXX_COMPILER_ID STREQUAL "Clang" AND (NOT CMAKE_CXX_COMPILER_VERSION VERSION_LESS 3.9))
package_set_compile_flags(core CXX "-Wno-undefined-var-template")
endif()
if(DEFINED AKANTU_CXX11_FLAGS)
package_declare(core_cxx11 NOT_OPTIONAL
DESCRIPTION "C++ 11 additions for Akantu core"
COMPILE_FLAGS CXX "${AKANTU_CXX11_FLAGS}")
if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS "4.6")
set(AKANTU_CORE_CXX11 OFF CACHE BOOL "C++ 11 additions for Akantu core - not supported by the selected compiler" FORCE)
endif()
endif()
package_declare_documentation(core_cxx11
"This option activates some features of the C++11 standard. This is usable with GCC>=4.7 or Intel>=13.")
else()
if(CMAKE_VERSION VERSION_LESS 3.1)
message(FATAL_ERROR "Since version 3.0 Akantu requires at least c++11 capable compiler")
endif()
endif()
diff --git a/src/common/aka_grid_dynamic.hh b/src/common/aka_grid_dynamic.hh
index 8de0a6a78..ccc2bf128 100644
--- a/src/common/aka_grid_dynamic.hh
+++ b/src/common/aka_grid_dynamic.hh
@@ -1,494 +1,472 @@
/**
* @file aka_grid_dynamic.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Feb 21 2013
* @date last modification: Sat Sep 26 2015
*
* @brief Grid that is auto balanced
*
* @section LICENSE
*
* Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_array.hh"
#include "aka_types.hh"
#include <iostream>
/* -------------------------------------------------------------------------- */
#include <map>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_AKA_GRID_DYNAMIC_HH__
#define __AKANTU_AKA_GRID_DYNAMIC_HH__
namespace akantu {
class Mesh;
template<typename T>
class SpatialGrid {
public:
SpatialGrid(UInt dimension) : dimension(dimension),
spacing(dimension),
center(dimension),
lower(dimension),
upper(dimension),
empty_cell() {}
SpatialGrid(UInt dimension,
const Vector<Real> & spacing,
const Vector<Real> & center) : dimension(dimension),
spacing(spacing),
center(center),
lower(dimension),
upper(dimension),
empty_cell() {
for (UInt i = 0; i < dimension; ++i) {
lower(i) = std::numeric_limits<Real>::max();
upper(i) = - std::numeric_limits<Real>::max();
}
}
virtual ~SpatialGrid() {};
class neighbor_cells_iterator;
class cells_iterator;
class CellID {
public:
CellID() : ids() {}
CellID(UInt dimention) : ids(dimention) {}
void setID(UInt dir, Int id) { ids(dir) = id; }
Int getID(UInt dir) const { return ids(dir); }
bool operator<(const CellID & id) const {
return std::lexicographical_compare(ids.storage(), ids.storage() + ids.size(),
id.ids.storage(), id.ids.storage() + id.ids.size());
}
bool operator==(const CellID & id) const {
return std::equal(ids.storage(), ids.storage() + ids.size(),
id.ids.storage());
}
bool operator!=(const CellID & id) const {
return !(operator==(id));
}
private:
friend class neighbor_cells_iterator;
friend class cells_iterator;
Vector<Int> ids;
};
/* -------------------------------------------------------------------------- */
class Cell {
public:
typedef typename std::vector<T>::iterator iterator;
typedef typename std::vector<T>::const_iterator const_iterator;
Cell() : id(), data() { }
Cell(const CellID &cell_id) : id(cell_id), data() { }
bool operator==(const Cell & cell) const { return id == cell.id; }
bool operator!=(const Cell & cell) const { return id != cell.id; }
Cell & add(const T & d) { data.push_back(d); return *this; }
iterator begin() { return data.begin(); }
const_iterator begin() const { return data.begin(); }
iterator end() { return data.end(); }
const_iterator end() const { return data.end(); }
private:
CellID id;
std::vector<T> data;
};
private:
typedef std::map<CellID, Cell> cells_container;
public:
const Cell & getCell(const CellID & cell_id) const {
typename cells_container::const_iterator it = cells.find(cell_id);
if(it != cells.end()) return it->second;
else return empty_cell;
}
typename Cell::iterator beginCell(const CellID & cell_id) {
typename cells_container::iterator it = cells.find(cell_id);
if(it != cells.end()) return it->second.begin();
else return empty_cell.begin();
}
typename Cell::iterator endCell(const CellID & cell_id) {
typename cells_container::iterator it = cells.find(cell_id);
if(it != cells.end()) return it->second.end();
else return empty_cell.end();
}
typename Cell::const_iterator beginCell(const CellID & cell_id) const {
typename cells_container::const_iterator it = cells.find(cell_id);
if(it != cells.end()) return it->second.begin();
else return empty_cell.begin();
}
typename Cell::const_iterator endCell(const CellID & cell_id) const {
typename cells_container::const_iterator it = cells.find(cell_id);
if(it != cells.end()) return it->second.end();
else return empty_cell.end();
}
class neighbor_cells_iterator : private std::iterator<std::forward_iterator_tag, UInt> {
public:
neighbor_cells_iterator(const CellID & cell_id, bool end) :
cell_id(cell_id),
position(cell_id.ids.size(), end ? 1 : -1) {
this->updateIt();
if(end) this->it++;
}
neighbor_cells_iterator& operator++() {
UInt i = 0;
for (; i < position.size() && position(i) == 1; ++i);
if(i == position.size()) ++it;
else {
for (UInt j = 0; j < i; ++j) position(j) = -1;
position(i)++;
updateIt();
}
return *this;
}
neighbor_cells_iterator operator++(int) { neighbor_cells_iterator tmp(*this); operator++(); return tmp; };
bool operator==(const neighbor_cells_iterator& rhs) const { return cell_id == rhs.cell_id && it == rhs.it; };
bool operator!=(const neighbor_cells_iterator& rhs) const { return ! operator==(rhs); };
CellID operator*() const {
CellID cur_cell_id(cell_id);
cur_cell_id.ids += position;
return cur_cell_id;
};
private:
void updateIt() {
it = 0;
for (UInt i = 0; i < position.size(); ++i) it = it * 3 + (position(i) + 1);
}
private:
/// central cell id
const CellID & cell_id;
// number representing the current neighbor in base 3;
UInt it;
Vector<Int> position;
};
class cells_iterator : private std::iterator<std::forward_iterator_tag, CellID> {
public:
cells_iterator(typename std::map<CellID, Cell>::const_iterator it) :
it(it) { }
cells_iterator & operator++() {
this->it++;
return *this;
}
cells_iterator operator++(int) {cells_iterator tmp(*this); operator++(); return tmp; };
bool operator==(const cells_iterator& rhs) const { return it == rhs.it; };
bool operator!=(const cells_iterator& rhs) const { return ! operator==(rhs); };
CellID operator*() const {
CellID cur_cell_id(this->it->first);
return cur_cell_id;
};
private:
/// map iterator
typename std::map<CellID, Cell>::const_iterator it;
};
public:
template<class vector_type>
Cell & insert(const T & d, const vector_type & position) {
CellID cell_id = getCellID(position);
typename cells_container::iterator it = cells.find(cell_id);
if(it == cells.end()) {
Cell cell(cell_id);
// #if defined(AKANTU_NDEBUG)
Cell & tmp = (cells[cell_id] = cell).add(d);
// #else
// Cell & tmp = (cells[cell_id] = cell).add(d, position);
// #endif
for (UInt i = 0; i < dimension; ++i) {
Real posl = center(i) + cell_id.getID(i) * spacing(i);
Real posu = posl + spacing(i);
if(posl < lower(i)) lower(i) = posl;
if(posu > upper(i)) upper(i) = posu;
}
return tmp;
} else {
// #if defined(AKANTU_NDEBUG)
return it->second.add(d);
// #else
// return it->second.add(d, position);
// #endif
}
}
inline neighbor_cells_iterator beginNeighborCells(const CellID & cell_id) const {
return neighbor_cells_iterator(cell_id, false);
}
inline neighbor_cells_iterator endNeighborCells(const CellID & cell_id) const {
return neighbor_cells_iterator(cell_id, true);
}
inline cells_iterator beginCells() const {
typename std::map<CellID, Cell>::const_iterator begin = this->cells.begin();
return cells_iterator(begin);
}
inline cells_iterator endCells() const {
typename std::map<CellID, Cell>::const_iterator end = this->cells.end();
return cells_iterator(end);
}
template<class vector_type>
CellID getCellID(const vector_type & position) const {
CellID cell_id(dimension);
for (UInt i = 0; i < dimension; ++i) {
cell_id.setID(i, getCellID(position(i), i));
}
return cell_id;
}
void printself(std::ostream & stream, int indent = 0) const {
std::string space;
for(Int i = 0; i < indent; i++, space += AKANTU_INDENT);
std::streamsize prec = stream.precision();
std::ios_base::fmtflags ff = stream.flags();
stream.setf (std::ios_base::showbase);
stream.precision(5);
stream << space << "SpatialGrid<" << debug::demangle(typeid(T).name()) << "> [" << std::endl;
stream << space << " + dimension : " << this->dimension << std::endl;
stream << space << " + lower bounds : {";
for (UInt i = 0; i < lower.size(); ++i) { if(i != 0) stream << ", "; stream << lower(i); };
stream << "}" << std::endl;
stream << space << " + upper bounds : {";
for (UInt i = 0; i < upper.size(); ++i) { if(i != 0) stream << ", "; stream << upper(i); };
stream << "}" << std::endl;
stream << space << " + spacing : {";
for (UInt i = 0; i < spacing.size(); ++i) { if(i != 0) stream << ", "; stream << spacing(i); };
stream << "}" << std::endl;
stream << space << " + center : {";
for (UInt i = 0; i < center.size(); ++i) { if(i != 0) stream << ", "; stream << center(i); };
stream << "}" << std::endl;
stream << space << " + nb_cells : " << this->cells.size() << "/";
Vector<Real> dist(this->dimension);
dist = upper;
dist -= lower;
for (UInt i = 0; i < this->dimension; ++i) {
dist(i) /= spacing(i);
}
UInt nb_cells = std::ceil(dist(0));
for (UInt i = 1; i < this->dimension; ++i) {
nb_cells *= std::ceil(dist(i));
}
stream << nb_cells << std::endl;
stream << space << "]" << std::endl;
stream.precision(prec);
stream.flags(ff);
}
void saveAsMesh(Mesh & mesh) const;
private:
/* -------------------------------------------------------------------------- */
inline UInt getCellID(Real position, UInt direction) const {
AKANTU_DEBUG_ASSERT(direction < center.size(), "The direction asked ("
<< direction << ") is out of range " << center.size());
Real dist_center = position - center(direction);
Int id = std::floor(dist_center / spacing(direction));
//if(dist_center < 0) id--;
return id;
}
friend class GridSynchronizer;
public:
AKANTU_GET_MACRO(LowerBounds, lower, const Vector<Real> &);
AKANTU_GET_MACRO(UpperBounds, upper, const Vector<Real> &);
AKANTU_GET_MACRO(Spacing, spacing, const Vector<Real> &);
protected:
UInt dimension;
cells_container cells;
Vector<Real> spacing;
Vector<Real> center;
Vector<Real> lower;
Vector<Real> upper;
Cell empty_cell;
};
/// standard output stream operator
template<typename T>
inline std::ostream & operator <<(std::ostream & stream, const SpatialGrid<T> & _this)
{
_this.printself(stream);
return stream;
}
} // akantu
#include "mesh.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template<typename T>
void SpatialGrid<T>::saveAsMesh(Mesh & mesh) const {
Array<Real> & nodes = const_cast<Array<Real> &>(mesh.getNodes());
ElementType type;
switch(dimension) {
case 1: type = _segment_2; break;
case 2: type = _quadrangle_4; break;
case 3: type = _hexahedron_8; break;
}
mesh.addConnectivityType(type);
- Array<UInt> & connectivity = const_cast<Array<UInt> &>(mesh.getConnectivity(type));
- Array<UInt> & uint_data = *mesh.getDataPointer<UInt>("tag_1", type);
-
- typename cells_container::const_iterator it = cells.begin();
- typename cells_container::const_iterator end = cells.end();
+ auto & connectivity = const_cast<Array<UInt> &>(mesh.getConnectivity(type));
+ auto & uint_data = mesh.getDataPointer<UInt>("tag_1", type);
Vector<Real> pos(dimension);
UInt global_id = 0;
- for (;it != end; ++it, ++global_id) {
+ for (auto & cell_pair : cells) {
UInt cur_node = nodes.getSize();
UInt cur_elem = connectivity.getSize();
- const CellID & cell_id = it->first;
+ const CellID & cell_id = cell_pair.first;
for (UInt i = 0; i < dimension; ++i) pos(i) = center(i) + cell_id.getID(i) * spacing(i);
nodes.push_back(pos);
for (UInt i = 0; i < dimension; ++i) pos(i) += spacing(i);
nodes.push_back(pos);
connectivity.push_back(cur_node);
switch(dimension) {
case 1:
connectivity(cur_elem, 1) = cur_node + 1;
break;
case 2:
pos(0) -= spacing(0); nodes.push_back(pos);
pos(0) += spacing(0); pos(1) -= spacing(1); nodes.push_back(pos);
connectivity(cur_elem, 1) = cur_node + 3;
connectivity(cur_elem, 2) = cur_node + 1;
connectivity(cur_elem, 3) = cur_node + 2;
break;
case 3:
pos(1) -= spacing(1); pos(2) -= spacing(2); nodes.push_back(pos);
pos(1) += spacing(1); nodes.push_back(pos);
pos(0) -= spacing(0); nodes.push_back(pos);
pos(1) -= spacing(1); pos(2) += spacing(2); nodes.push_back(pos);
pos(0) += spacing(0); nodes.push_back(pos);
pos(0) -= spacing(0); pos(1) += spacing(1); nodes.push_back(pos);
connectivity(cur_elem, 1) = cur_node + 2;
connectivity(cur_elem, 2) = cur_node + 3;
connectivity(cur_elem, 3) = cur_node + 4;
connectivity(cur_elem, 4) = cur_node + 5;
connectivity(cur_elem, 5) = cur_node + 6;
connectivity(cur_elem, 6) = cur_node + 1;
connectivity(cur_elem, 7) = cur_node + 7;
break;
}
uint_data.push_back(global_id);
- }
-// #if not defined(AKANTU_NDEBUG)
-// mesh.addConnectivityType(_point_1);
-// Array<UInt> & connectivity_pos = const_cast<Array<UInt> &>(mesh.getConnectivity(_point_1));
-// Array<UInt> & uint_data_pos = *mesh.getDataPointer<UInt>( "tag_1", _point_1);
-// Array<UInt> & uint_data_pos_ghost = *mesh.getDataPointer<UInt>("tag_0", _point_1);
-
-// it = cells.begin();
-// global_id = 0;
-// for (;it != end; ++it, ++global_id) {
-// typename Cell::position_iterator cell_it = it->second.begin_pos();
-// typename Cell::const_iterator cell_it_cont = it->second.begin();
-// typename Cell::position_iterator cell_end = it->second.end_pos();
-// for (;cell_it != cell_end; ++cell_it, ++cell_it_cont) {
-// nodes.push_back(*cell_it);
-// connectivity_pos.push_back(nodes.getSize()-1);
-// uint_data_pos.push_back(global_id);
-// uint_data_pos_ghost.push_back(cell_it_cont->ghost_type==_ghost);
-// }
-// }
-// #endif
+ ++global_id;
+ }
}
} // akantu
#endif /* __AKANTU_AKA_GRID_DYNAMIC_HH__ */
diff --git a/src/fe_engine/element.hh b/src/fe_engine/element.hh
index 3541a12e7..4ec8329b0 100644
--- a/src/fe_engine/element.hh
+++ b/src/fe_engine/element.hh
@@ -1,127 +1,117 @@
/**
* @file element.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 02 2014
* @date last modification: Sat Jul 11 2015
*
* @brief Element helper class
*
* @section LICENSE
*
* Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+/* -------------------------------------------------------------------------- */
+#include "aka_common.hh"
+/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_ELEMENT_HH__
#define __AKANTU_ELEMENT_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Element */
/* -------------------------------------------------------------------------- */
class Element;
extern const Element ElementNull;
class Element {
-
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
-
public:
explicit Element(ElementType type = _not_defined, UInt element = 0,
GhostType ghost_type = _not_ghost, ElementKind kind = _ek_regular) :
type(type), element(element),
ghost_type(ghost_type), kind(kind) {};
Element(const Element & element) {
this->type = element.type;
this->element = element.element;
this->ghost_type = element.ghost_type;
this->kind = element.kind;
}
- virtual ~Element() {};
+ virtual ~Element() = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
-
public:
-
inline bool operator==(const Element & elem) const {
return ((element == elem.element)
&& (type == elem.type)
&& (ghost_type == elem.ghost_type)
&& (kind == elem.kind));
}
inline bool operator!=(const Element & elem) const {
return ((element != elem.element)
|| (type != elem.type)
|| (ghost_type != elem.ghost_type)
|| (kind != elem.kind));
}
- bool operator<(const Element& rhs) const {
+ bool operator<(const Element & rhs) const {
bool res = (rhs == ElementNull) || ((this->kind < rhs.kind) ||
((this->kind == rhs.kind) &&
((this->ghost_type < rhs.ghost_type) ||
((this->ghost_type == rhs.ghost_type) &&
((this->type < rhs.type) ||
((this->type == rhs.type) &&
(this->element < rhs.element)))))));
return res;
}
/// function to print the containt of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
-
public:
-
const ElementType & getType(){return type;}
const UInt & getIndex(){return element;};
const GhostType & getGhostType(){return ghost_type;}
const ElementKind & getElementKind(){return kind;}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
-
public:
ElementType type;
UInt element;
GhostType ghost_type;
ElementKind kind;
};
-struct CompElementLess {
- bool operator() (const Element& lhs, const Element& rhs) const {
- return lhs < rhs;
- }
-};
-
} // akantu
#endif /* __AKANTU_ELEMENT_HH__ */
diff --git a/src/io/mesh_io.cc b/src/io/mesh_io.cc
index e4ed84cca..d2aee2f94 100644
--- a/src/io/mesh_io.cc
+++ b/src/io/mesh_io.cc
@@ -1,156 +1,148 @@
/**
* @file mesh_io.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Mon Jun 01 2015
*
* @brief common part for all mesh io classes
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
* Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
* Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#include "aka_common.hh"
#include "mesh_io.hh"
-
+#include "aka_common.hh"
+#include "aka_zip.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
MeshIO::MeshIO() {
canReadSurface = false;
canReadExtendedData = false;
}
/* -------------------------------------------------------------------------- */
MeshIO::~MeshIO() {}
/* -------------------------------------------------------------------------- */
-MeshIO * MeshIO::getMeshIO(const std::string & filename,
- const MeshIOType & type) {
+std::unique_ptr<MeshIO> MeshIO::getMeshIO(const std::string & filename,
+ const MeshIOType & type) {
MeshIOType t = type;
if (type == _miot_auto) {
std::string::size_type idx = filename.rfind('.');
std::string ext;
if (idx != std::string::npos) {
ext = filename.substr(idx + 1);
}
if (ext == "msh") {
t = _miot_gmsh;
} else if (ext == "diana") {
t = _miot_diana;
} else if (ext == "inp") {
t = _miot_abaqus;
} else
AKANTU_EXCEPTION("Cannot guess the type of file of "
<< filename << " (ext " << ext << "). "
<< "Please provide the MeshIOType to the read function");
}
switch (t) {
case _miot_gmsh:
- return new MeshIOMSH();
+ return std::make_unique<MeshIOMSH>();
#if defined(AKANTU_STRUCTURAL_MECHANICS)
case _miot_gmsh_struct:
- return new MeshIOMSHStruct();
+ return std::make_unique<MeshIOMSHStruct>();
#endif
case _miot_diana:
- return new MeshIODiana();
+ return std::make_unique<MeshIODiana>();
case _miot_abaqus:
- return new MeshIOAbaqus();
+ return std::make_unique<MeshIOAbaqus>();
default:
- return NULL;
+ return nullptr;
}
}
/* -------------------------------------------------------------------------- */
void MeshIO::read(const std::string & filename, Mesh & mesh,
const MeshIOType & type) {
- MeshIO * mesh_io = getMeshIO(filename, type);
+ std::unique_ptr<MeshIO> mesh_io = getMeshIO(filename, type);
mesh_io->read(filename, mesh);
- delete mesh_io;
}
/* -------------------------------------------------------------------------- */
void MeshIO::write(const std::string & filename, Mesh & mesh,
const MeshIOType & type) {
- MeshIO * mesh_io = getMeshIO(filename, type);
+ std::unique_ptr<MeshIO> mesh_io = getMeshIO(filename, type);
mesh_io->write(filename, mesh);
- delete mesh_io;
}
/* -------------------------------------------------------------------------- */
void MeshIO::constructPhysicalNames(const std::string & tag_name, Mesh & mesh) {
-
if (!phys_name_map.empty()) {
for (Mesh::type_iterator type_it = mesh.firstType();
type_it != mesh.lastType(); ++type_it) {
- Array<std::string> * name_vec =
+ auto & name_vec =
mesh.getDataPointer<std::string>("physical_names", *type_it);
- const Array<UInt> & tags_vec = mesh.getData<UInt>(tag_name, *type_it);
+ const auto & tags_vec = mesh.getData<UInt>(tag_name, *type_it);
- for (UInt i(0); i < tags_vec.getSize(); i++) {
- std::map<UInt, std::string>::const_iterator map_it =
- phys_name_map.find(tags_vec(i));
+ for (auto pair : zip(tags_vec, name_vec)) {
+ auto tag = std::get<0>(pair);
+ auto & name = std::get<1>(pair);
+ auto map_it = phys_name_map.find(tag);
if (map_it == phys_name_map.end()) {
std::stringstream sstm;
- sstm << tags_vec(i);
- name_vec->operator()(i) = sstm.str();
+ sstm << tag;
+
+ name = sstm.str();
} else {
- name_vec->operator()(i) = map_it->second;
+ name = map_it->second;
}
}
}
}
}
/* -------------------------------------------------------------------------- */
-
void MeshIO::printself(std::ostream & stream, int indent) const {
-
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
if (phys_name_map.size()) {
-
stream << space << "Physical map:" << std::endl;
-
- std::map<UInt, std::string>::const_iterator it = phys_name_map.begin();
- std::map<UInt, std::string>::const_iterator end = phys_name_map.end();
-
- for (; it != end; ++it) {
- stream << space << it->first << ": " << it->second << std::endl;
+ for (auto & pair : phys_name_map) {
+ stream << space << pair.first << ": " << pair.second << std::endl;
}
}
}
/* -------------------------------------------------------------------------- */
-} // akantu
+} // namespace akantu
diff --git a/src/io/mesh_io.hh b/src/io/mesh_io.hh
index 680d7d418..5e4860613 100644
--- a/src/io/mesh_io.hh
+++ b/src/io/mesh_io.hh
@@ -1,118 +1,118 @@
/**
* @file mesh_io.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Mon Jun 01 2015
*
* @brief interface of a mesh io class, reader and writer
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
* Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
* Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MESH_IO_HH__
#define __AKANTU_MESH_IO_HH__
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh.hh"
#include "mesh_accessor.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class MeshIO {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MeshIO();
virtual ~MeshIO();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void read(const std::string & filename, Mesh & mesh, const MeshIOType & type);
void write(const std::string & filename, Mesh & mesh,
const MeshIOType & type);
/// read a mesh from the file
virtual void read(__attribute__((unused)) const std::string & filename,
__attribute__((unused)) Mesh & mesh) {}
/// write a mesh to a file
virtual void write(__attribute__((unused)) const std::string & filename,
__attribute__((unused)) const Mesh & mesh) {}
/// function to request the manual construction of the physical names maps
virtual void constructPhysicalNames(const std::string & tag_name,
Mesh & mesh);
/// method to permit to be printed to a generic stream
virtual void printself(std::ostream & stream, int indent = 0) const;
/// static contruction of a meshio object
- static MeshIO * getMeshIO(const std::string & filename,
- const MeshIOType & type);
+ static std::unique_ptr<MeshIO> getMeshIO(const std::string & filename,
+ const MeshIOType & type);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
std::map<UInt, std::string> & getPhysicalNameMap() { return phys_name_map; }
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
bool canReadSurface;
bool canReadExtendedData;
/// correspondance between a tag and physical names (if applicable)
std::map<UInt, std::string> phys_name_map;
};
/* -------------------------------------------------------------------------- */
inline std::ostream & operator<<(std::ostream & stream, const MeshIO & _this) {
_this.printself(stream);
return stream;
}
/* -------------------------------------------------------------------------- */
-} // akantu
+} // namespace akantu
-#include "mesh_io_msh.hh"
-#include "mesh_io_diana.hh"
#include "mesh_io_abaqus.hh"
+#include "mesh_io_diana.hh"
+#include "mesh_io_msh.hh"
#if defined(AKANTU_STRUCTURAL_MECHANICS)
#include "mesh_io_msh_struct.hh"
#endif
#endif /* __AKANTU_MESH_IO_HH__ */
diff --git a/src/io/mesh_io/mesh_io_abaqus.cc b/src/io/mesh_io/mesh_io_abaqus.cc
index 2caf717c8..7c3461a79 100644
--- a/src/io/mesh_io/mesh_io_abaqus.cc
+++ b/src/io/mesh_io/mesh_io_abaqus.cc
@@ -1,483 +1,475 @@
/**
* @file mesh_io_abaqus.cc
*
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jan 04 2013
* @date last modification: Fri Dec 11 2015
*
* @brief read a mesh from an abaqus input file
*
* @section LICENSE
*
* Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
// std library header files
#include <fstream>
// akantu header files
#include "mesh_io_abaqus.hh"
#include "mesh.hh"
#include "mesh_utils.hh"
#include "element_group.hh"
#include "node_group.hh"
#if defined(__INTEL_COMPILER)
//#pragma warning ( disable : 383 )
#elif defined (__clang__) // test clang to be sure that when we test for gnu it is only gnu
#elif (defined(__GNUC__) || defined(__GNUG__))
# define GCC_VERSION (__GNUC__ * 10000 + __GNUC_MINOR__ * 100 + __GNUC_PATCHLEVEL__)
# if GCC_VERSION > 40600
# pragma GCC diagnostic push
# endif
# pragma GCC diagnostic ignored "-Wunused-local-typedefs"
#endif
/* -------------------------------------------------------------------------- */
#include <boost/config/warning_disable.hpp>
#include <boost/spirit/include/qi.hpp>
#include <boost/spirit/include/phoenix.hpp>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
MeshIOAbaqus::MeshIOAbaqus() {}
/* -------------------------------------------------------------------------- */
MeshIOAbaqus::~MeshIOAbaqus() {}
/* -------------------------------------------------------------------------- */
namespace spirit = boost::spirit;
namespace qi = boost::spirit::qi;
namespace ascii = boost::spirit::ascii;
namespace lbs = boost::spirit::qi::labels;
namespace phx = boost::phoenix;
/* -------------------------------------------------------------------------- */
void element_read(Mesh & mesh, const ElementType & type, UInt id, const std::vector<Int> & conn,
const std::map<UInt, UInt> & nodes_mapping,
std::map<UInt, Element> & elements_mapping) {
Vector<UInt> tmp_conn(Mesh::getNbNodesPerElement(type));
AKANTU_DEBUG_ASSERT(conn.size() == tmp_conn.size(),
"The nodes in the Abaqus file have too many coordinates"
<< " for the mesh you try to fill.");
mesh.addConnectivityType(type);
Array<UInt> & connectivity = mesh.getConnectivity(type);
UInt i = 0;
for (std::vector<Int>::const_iterator it = conn.begin(); it != conn.end(); ++it) {
std::map<UInt, UInt>::const_iterator nit = nodes_mapping.find(*it);
AKANTU_DEBUG_ASSERT(nit != nodes_mapping.end(),
"There is an unknown node in the connectivity.");
tmp_conn[i++] = nit->second;
}
Element el(type, connectivity.getSize());
elements_mapping[id] = el;
connectivity.push_back(tmp_conn);
}
void node_read(Mesh & mesh, UInt id, const std::vector<Real> & pos,
std::map<UInt, UInt> & nodes_mapping) {
Vector<Real> tmp_pos(mesh.getSpatialDimension());
UInt i = 0;
for (std::vector<Real>::const_iterator it = pos.begin();
it != pos.end() || i < mesh.getSpatialDimension(); ++it)
tmp_pos[i++] = *it;
nodes_mapping[id] = mesh.getNbNodes();
mesh.getNodes().push_back(tmp_pos);
}
/* ------------------------------------------------------------------------ */
void add_element_to_group(ElementGroup * el_grp, UInt element,
const std::map<UInt, Element> & elements_mapping) {
std::map<UInt, Element>::const_iterator eit = elements_mapping.find(element);
AKANTU_DEBUG_ASSERT(eit != elements_mapping.end(),
"There is an unknown element ("
<< element << ") in the in the ELSET "
<< el_grp->getName() << ".");
el_grp->add(eit->second, true, false);
}
ElementGroup * element_group_create(Mesh & mesh, const ID & name) {
Mesh::element_group_iterator eg_it = mesh.element_group_find(name);
if (eg_it != mesh.element_group_end()) {
return eg_it->second;
} else {
return &mesh.createElementGroup(name, _all_dimensions);
}
}
NodeGroup * node_group_create(Mesh & mesh, const ID & name) {
Mesh::node_group_iterator ng_it = mesh.node_group_find(name);
if (ng_it != mesh.node_group_end()) {
return ng_it->second;
} else {
return &mesh.createNodeGroup(name, mesh.getSpatialDimension());
}
}
void add_node_to_group(NodeGroup * node_grp, UInt node,
const std::map<UInt, UInt> & nodes_mapping) {
std::map<UInt, UInt>::const_iterator nit = nodes_mapping.find(node);
AKANTU_DEBUG_ASSERT(nit != nodes_mapping.end(),
"There is an unknown node in the in the NSET "
<< node_grp->getName() << ".");
node_grp->add(nit->second, false);
}
void optimize_group(NodeGroup * grp) { grp->optimize(); }
void optimize_element_group(ElementGroup * grp) { grp->optimize(); }
/* -------------------------------------------------------------------------- */
template <class Iterator> struct AbaqusSkipper : qi::grammar<Iterator> {
AbaqusSkipper() : AbaqusSkipper::base_type(skip, "abaqus_skipper") {
/* clang-format off */
skip
= (ascii::space - spirit::eol)
| "**" >> *(qi::char_ - spirit::eol) >> spirit::eol
;
/* clang-format on */
}
qi::rule<Iterator> skip;
};
/* -------------------------------------------------------------------------- */
template <class Iterator, typename Skipper = AbaqusSkipper<Iterator> >
struct AbaqusMeshGrammar : qi::grammar<Iterator, void(), Skipper> {
public:
AbaqusMeshGrammar(Mesh & mesh)
: AbaqusMeshGrammar::base_type(start, "abaqus_mesh_reader"), mesh(mesh) {
/* clang-format off */
start
= *(
(qi::char_('*')
> ( (qi::no_case[ qi::lit("node output") ] > any_section)
| (qi::no_case[ qi::lit("element output") ] > any_section)
| (qi::no_case[ qi::lit("node") ] > nodes)
| (qi::no_case[ qi::lit("element") ] > elements)
| (qi::no_case[ qi::lit("heading") ] > header)
| (qi::no_case[ qi::lit("elset") ] > elements_set)
| (qi::no_case[ qi::lit("nset") ] > nodes_set)
| (qi::no_case[ qi::lit("material") ] > material)
| (keyword > any_section)
)
)
| spirit::eol
)
;
header
= spirit::eol
> *any_line
;
nodes
= *(qi::char_(',') >> option)
>> spirit::eol
>> *( (qi::int_
> node_position) [ phx::bind(&node_read,
phx::ref(mesh),
lbs::_1,
lbs::_2,
phx::ref(abaqus_nodes_to_akantu)) ]
>> spirit::eol
)
;
elements
= (
( qi::char_(',') >> qi::no_case[qi::lit("type")] >> '='
>> abaqus_element_type [ lbs::_a = lbs::_1 ]
)
^ *(qi::char_(',') >> option)
)
>> spirit::eol
>> *( (qi::int_
> connectivity) [ phx::bind(&element_read,
phx::ref(mesh),
lbs::_a,
lbs::_1,
lbs::_2,
phx::cref(abaqus_nodes_to_akantu),
phx::ref(abaqus_elements_to_akantu)) ]
>> spirit::eol
)
;
elements_set
= (
(
( qi::char_(',') >> qi::no_case[ qi::lit("elset") ] >> '='
>> value [ lbs::_a = phx::bind<ElementGroup *>(&element_group_create,
phx::ref(mesh),
lbs::_1) ]
)
^ *(qi::char_(',') >> option)
)
>> spirit::eol
>> qi::skip
(qi::char_(',') | qi::space)
[ +(qi::int_ [ phx::bind(&add_element_to_group,
lbs::_a,
lbs::_1,
phx::cref(abaqus_elements_to_akantu)
)
]
)
]
) [ phx::bind(&optimize_element_group, lbs::_a) ]
;
nodes_set
= (
(
( qi::char_(',')
>> qi::no_case[ qi::lit("nset") ] >> '='
>> value [ lbs::_a = phx::bind<NodeGroup *>(&node_group_create, phx::ref(mesh), lbs::_1) ]
)
^ *(qi::char_(',') >> option)
)
>> spirit::eol
>> qi::skip
(qi::char_(',') | qi::space)
[ +(qi::int_ [ phx::bind(&add_node_to_group,
lbs::_a,
lbs::_1,
phx::cref(abaqus_nodes_to_akantu)
)
]
)
]
) [ phx::bind(&optimize_group, lbs::_a) ]
;
material
= (
( qi::char_(',') >> qi::no_case[ qi::lit("name") ] >> '='
>> value [ phx::push_back(phx::ref(material_names), lbs::_1) ]
)
^ *(qi::char_(',') >> option)
) >> spirit::eol;
;
node_position
= +(qi::char_(',') > real [ phx::push_back(lbs::_val, lbs::_1) ])
;
connectivity
= +(qi::char_(',') > qi::int_ [ phx::push_back(lbs::_val, lbs::_1) ])
;
any_section
= *(qi::char_(',') >> option) > spirit::eol
> *any_line
;
any_line
= *(qi::char_ - spirit::eol - qi::char_('*')) >> spirit::eol
;
keyword
= qi::lexeme[ +(qi::char_ - (qi::char_('*') | spirit::eol)) ]
;
option
= key > -( '=' >> value );
key
= qi::char_("a-zA-Z_") >> *(qi::char_("a-zA-Z_0-9") | qi::char_('-'))
;
value
= key.alias()
;
BOOST_SPIRIT_DEBUG_NODE(start);
abaqus_element_type.add
#if defined(AKANTU_STRUCTURAL_MECHANICS)
("BE21" , _bernoulli_beam_2)
("BE31" , _bernoulli_beam_3)
#endif
("T3D2" , _segment_2) // Gmsh generates this elements
("T3D3" , _segment_3) // Gmsh generates this elements
("CPE3" , _triangle_3)
("CPS3" , _triangle_3)
("DC2D3" , _triangle_3)
("CPE6" , _triangle_6)
("CPS6" , _triangle_6)
("DC2D6" , _triangle_6)
("CPE4" , _quadrangle_4)
("CPS4" , _quadrangle_4)
("DC2D4" , _quadrangle_4)
("CPE8" , _quadrangle_8)
("CPS8" , _quadrangle_8)
("DC2D8" , _quadrangle_8)
("C3D4" , _tetrahedron_4)
("DC3D4" , _tetrahedron_4)
("C3D8" , _hexahedron_8)
("C3D8R" , _hexahedron_8)
("DC3D8" , _hexahedron_8)
("C3D10" , _tetrahedron_10)
("DC3D10", _tetrahedron_10);
#if !defined(AKANTU_NDEBUG) && defined(AKANTU_CORE_CXX_11)
qi::on_error<qi::fail>(start, error_handler(lbs::_4, lbs::_3, lbs::_2));
#endif
start .name("abaqus-start-rule");
connectivity .name("abaqus-connectivity");
node_position .name("abaqus-nodes-position");
nodes .name("abaqus-nodes");
any_section .name("abaqus-any_section");
header .name("abaqus-header");
material .name("abaqus-material");
elements .name("abaqus-elements");
elements_set .name("abaqus-elements-set");
nodes_set .name("abaqus-nodes-set");
key .name("abaqus-key");
value .name("abaqus-value");
option .name("abaqus-option");
keyword .name("abaqus-keyword");
any_line .name("abaqus-any-line");
abaqus_element_type.name("abaqus-element-type");
/* clang-format on */
}
public:
AKANTU_GET_MACRO(MaterialNames, material_names,
const std::vector<std::string> &);
/* ------------------------------------------------------------------------ */
/* Rules */
/* ------------------------------------------------------------------------ */
private:
qi::rule<Iterator, void(), Skipper> start;
qi::rule<Iterator, std::vector<int>(), Skipper> connectivity;
qi::rule<Iterator, std::vector<Real>(), Skipper> node_position;
qi::rule<Iterator, void(), Skipper> nodes, any_section, header, material;
qi::rule<Iterator, void(), qi::locals<ElementType>, Skipper> elements;
qi::rule<Iterator, void(), qi::locals<ElementGroup *>, Skipper> elements_set;
qi::rule<Iterator, void(), qi::locals<NodeGroup *>, Skipper> nodes_set;
qi::rule<Iterator, std::string(), Skipper> key, value, option, keyword,
any_line;
qi::real_parser<Real, qi::real_policies<Real> > real;
qi::symbols<char, ElementType> abaqus_element_type;
/* ------------------------------------------------------------------------ */
/* Mambers */
/* ------------------------------------------------------------------------ */
private:
/// reference to the mesh to read
Mesh & mesh;
/// correspondance between the numbering of nodes in the abaqus file and in
/// the akantu mesh
std::map<UInt, UInt> abaqus_nodes_to_akantu;
/// correspondance between the element number in the abaqus file and the
/// Element in the akantu mesh
std::map<UInt, Element> abaqus_elements_to_akantu;
/// list of the material names
std::vector<std::string> material_names;
};
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
void MeshIOAbaqus::read(const std::string & filename, Mesh & mesh) {
namespace spirit = boost::spirit;
namespace qi = boost::spirit::qi;
namespace lbs = boost::spirit::qi::labels;
namespace ascii = boost::spirit::ascii;
namespace phx = boost::phoenix;
std::ifstream infile;
infile.open(filename.c_str());
if (!infile.good()) {
AKANTU_DEBUG_ERROR("Cannot open file " << filename);
}
std::string storage; // We will read the contents here.
infile.unsetf(std::ios::skipws); // No white space skipping!
std::copy(std::istream_iterator<char>(infile), std::istream_iterator<char>(),
std::back_inserter(storage));
typedef std::string::const_iterator iterator_t;
typedef AbaqusSkipper<iterator_t> skipper;
typedef AbaqusMeshGrammar<iterator_t, skipper> grammar;
grammar g(mesh);
skipper ws;
iterator_t iter = storage.begin();
iterator_t end = storage.end();
qi::phrase_parse(iter, end, g, ws);
- std::vector<std::string>::const_iterator mnit = g.getMaterialNames().begin();
- std::vector<std::string>::const_iterator mnend = g.getMaterialNames().end();
-
MeshAccessor mesh_accessor(mesh);
- for (; mnit != mnend; ++mnit) {
- Mesh::element_group_iterator eg_it = mesh.element_group_find(*mnit);
- ElementGroup & eg = *eg_it->second;
+ for (auto & mat_name : g.getMaterialNames()) {
+ auto eg_it = mesh.element_group_find(mat_name);
+ auto & eg = *eg_it->second;
if (eg_it != mesh.element_group_end()) {
- ElementGroup::type_iterator tit = eg.firstType();
- ElementGroup::type_iterator tend = eg.lastType();
-
- for (; tit != tend; ++tit) {
+ for (auto & type : eg.elementTypes()) {
Array<std::string> & abaqus_material =
- mesh_accessor.getData<std::string>("abaqus_material", *tit);
+ mesh_accessor.getData<std::string>("abaqus_material", type);
- ElementGroup::const_element_iterator eit = eg.element_begin(*tit);
- ElementGroup::const_element_iterator eend = eg.element_end(*tit);
- for (; eit != eend; ++eit) {
- abaqus_material(*eit) = *mnit;
+ for (auto elem : eg.getElements(type)) {
+ abaqus_material(elem) = mat_name;
}
}
}
}
mesh_accessor.setNbGlobalNodes(mesh.getNodes().getSize());
MeshUtils::fillElementToSubElementsData(mesh);
}
} // akantu
diff --git a/src/io/mesh_io/mesh_io_diana.cc b/src/io/mesh_io/mesh_io_diana.cc
index 2014b6b92..b75e511fd 100644
--- a/src/io/mesh_io/mesh_io_diana.cc
+++ b/src/io/mesh_io/mesh_io_diana.cc
@@ -1,587 +1,604 @@
/**
* @file mesh_io_diana.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Alodie Schneuwly <alodie.schneuwly@epfl.ch>
*
* @date creation: Sat Mar 26 2011
* @date last modification: Thu Jan 21 2016
*
* @brief handles diana meshes
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
* Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
* Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <iostream>
/* -------------------------------------------------------------------------- */
+#include "element_group.hh"
#include "mesh_io_diana.hh"
#include "mesh_utils.hh"
-#include "element_group.hh"
/* -------------------------------------------------------------------------- */
#include <string.h>
/* -------------------------------------------------------------------------- */
#include <stdio.h>
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Methods Implentations */
/* -------------------------------------------------------------------------- */
MeshIODiana::MeshIODiana() {
canReadSurface = true;
canReadExtendedData = true;
_diana_to_akantu_element_types["T9TM"] = _triangle_3;
_diana_to_akantu_element_types["CT6CM"] = _triangle_6;
_diana_to_akantu_element_types["Q12TM"] = _quadrangle_4;
_diana_to_akantu_element_types["CQ8CM"] = _quadrangle_8;
_diana_to_akantu_element_types["TP18L"] = _pentahedron_6;
_diana_to_akantu_element_types["CTP45"] = _pentahedron_15;
_diana_to_akantu_element_types["TE12L"] = _tetrahedron_4;
_diana_to_akantu_element_types["HX24L"] = _hexahedron_8;
_diana_to_akantu_element_types["CHX60"] = _hexahedron_20;
_diana_to_akantu_mat_prop["YOUNG"] = "E";
_diana_to_akantu_mat_prop["DENSIT"] = "rho";
_diana_to_akantu_mat_prop["POISON"] = "nu";
std::map<std::string, ElementType>::iterator it;
for (it = _diana_to_akantu_element_types.begin();
it != _diana_to_akantu_element_types.end(); ++it) {
UInt nb_nodes = Mesh::getNbNodesPerElement(it->second);
UInt * tmp = new UInt[nb_nodes];
for (UInt i = 0; i < nb_nodes; ++i) {
tmp[i] = i;
}
switch (it->second) {
case _tetrahedron_10:
tmp[8] = 9;
tmp[9] = 8;
break;
case _pentahedron_15:
tmp[0] = 2;
tmp[1] = 8;
tmp[2] = 0;
tmp[3] = 6;
tmp[4] = 1;
tmp[5] = 7;
tmp[6] = 11;
tmp[7] = 9;
tmp[8] = 10;
tmp[9] = 5;
tmp[10] = 14;
tmp[11] = 3;
tmp[12] = 12;
tmp[13] = 4;
tmp[14] = 13;
break;
case _hexahedron_20:
tmp[0] = 5;
tmp[1] = 16;
tmp[2] = 4;
tmp[3] = 19;
tmp[4] = 7;
tmp[5] = 18;
tmp[6] = 6;
tmp[7] = 17;
tmp[8] = 13;
tmp[9] = 12;
tmp[10] = 15;
tmp[11] = 14;
tmp[12] = 1;
tmp[13] = 8;
tmp[14] = 0;
tmp[15] = 11;
tmp[16] = 3;
tmp[17] = 10;
tmp[18] = 2;
tmp[19] = 9;
break;
default:
// nothing to change
break;
}
_read_order[it->second] = tmp;
}
}
/* -------------------------------------------------------------------------- */
MeshIODiana::~MeshIODiana() {}
/* -------------------------------------------------------------------------- */
inline void my_getline(std::ifstream & infile, std::string & line) {
std::getline(infile, line); // read the line
size_t pos = line.find("\r"); /// remove the extra \r if needed
line = line.substr(0, pos);
}
/* -------------------------------------------------------------------------- */
void MeshIODiana::read(const std::string & filename, Mesh & mesh) {
AKANTU_DEBUG_IN();
MeshAccessor mesh_accessor(mesh);
std::ifstream infile;
infile.open(filename.c_str());
std::string line;
UInt first_node_number = std::numeric_limits<UInt>::max();
diana_element_number_to_elements.clear();
- if (!infile.good()) { AKANTU_DEBUG_ERROR("Cannot open file " << filename); }
+ if (!infile.good()) {
+ AKANTU_DEBUG_ERROR("Cannot open file " << filename);
+ }
while (infile.good()) {
my_getline(infile, line);
/// read all nodes
if (line == "'COORDINATES'") {
line = readCoordinates(infile, mesh, first_node_number);
}
/// read all elements
if (line == "'ELEMENTS'") {
line = readElements(infile, mesh, first_node_number);
}
/// read the material properties and write a .dat file
- if (line == "'MATERIALS'") { line = readMaterial(infile, filename); }
+ if (line == "'MATERIALS'") {
+ line = readMaterial(infile, filename);
+ }
/// read the material properties and write a .dat file
if (line == "'GROUPS'") {
line = readGroups(infile, mesh, first_node_number);
}
}
infile.close();
mesh_accessor.setNbGlobalNodes(mesh.getNbNodes());
MeshUtils::fillElementToSubElementsData(mesh);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshIODiana::write(__attribute__((unused)) const std::string & filename,
__attribute__((unused)) const Mesh & mesh) {
AKANTU_DEBUG_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
std::string MeshIODiana::readCoordinates(std::ifstream & infile, Mesh & mesh,
UInt & first_node_number) {
AKANTU_DEBUG_IN();
MeshAccessor mesh_accessor(mesh);
Array<Real> & nodes = mesh_accessor.getNodes();
std::string line;
UInt index;
Vector<Real> coord(3);
do {
my_getline(infile, line);
- if ("'ELEMENTS'" == line) break;
+ if ("'ELEMENTS'" == line)
+ break;
std::stringstream sstr_node(line);
sstr_node >> index >> coord(0) >> coord(1) >> coord(2);
first_node_number = first_node_number < index ? first_node_number : index;
nodes.push_back(coord);
} while (true);
AKANTU_DEBUG_OUT();
return line;
}
/* -------------------------------------------------------------------------- */
UInt MeshIODiana::readInterval(std::stringstream & line,
std::set<UInt> & interval) {
UInt first;
line >> first;
- if (line.fail()) { return 0; }
+ if (line.fail()) {
+ return 0;
+ }
interval.insert(first);
UInt second;
int dash;
dash = line.get();
if (dash == '-') {
line >> second;
interval.insert(second);
return 2;
}
if (line.fail())
line.clear(std::ios::eofbit); // in case of get at end of the line
else
line.unget();
return 1;
}
/* -------------------------------------------------------------------------- */
std::string MeshIODiana::readGroups(std::ifstream & infile, Mesh & mesh,
UInt first_node_number) {
AKANTU_DEBUG_IN();
std::string line;
my_getline(infile, line);
bool reading_nodes_group = false;
while (line != "'SUPPORTS'") {
if (line == "NODES") {
reading_nodes_group = true;
my_getline(infile, line);
}
if (line == "ELEMEN") {
reading_nodes_group = false;
my_getline(infile, line);
}
std::stringstream * str = new std::stringstream(line);
UInt id;
std::string name;
char c;
*str >> id >> name >> c;
Array<UInt> * list_ids = new Array<UInt>(0, 1, name);
UInt s = 1;
bool end = false;
while (!end) {
while (!str->eof() && s != 0) {
std::set<UInt> interval;
s = readInterval(*str, interval);
std::set<UInt>::iterator it = interval.begin();
- if (s == 1) list_ids->push_back(*it);
+ if (s == 1)
+ list_ids->push_back(*it);
if (s == 2) {
UInt first = *it;
++it;
UInt second = *it;
for (UInt i = first; i <= second; ++i) {
list_ids->push_back(i);
}
}
}
if (str->fail())
end = true;
else {
my_getline(infile, line);
delete str;
str = new std::stringstream(line);
}
}
delete str;
if (reading_nodes_group) {
NodeGroup & ng = mesh.createNodeGroup(name);
for (UInt i = 0; i < list_ids->getSize(); ++i) {
- UInt node = (*list_ids)(i) - first_node_number;
+ UInt node = (*list_ids)(i)-first_node_number;
ng.add(node, false);
}
delete list_ids;
} else {
ElementGroup & eg = mesh.createElementGroup(name);
for (UInt i = 0; i < list_ids->getSize(); ++i) {
- Element & elem = diana_element_number_to_elements[ (*list_ids)(i)];
- if (elem.type != _not_defined) eg.add(elem, false, false);
+ Element & elem = diana_element_number_to_elements[(*list_ids)(i)];
+ if (elem.type != _not_defined)
+ eg.add(elem, false, false);
}
eg.optimize();
delete list_ids;
}
my_getline(infile, line);
}
AKANTU_DEBUG_OUT();
return line;
}
/* -------------------------------------------------------------------------- */
std::string MeshIODiana::readElements(std::ifstream & infile, Mesh & mesh,
UInt first_node_number) {
AKANTU_DEBUG_IN();
std::string line;
my_getline(infile, line);
if ("CONNECTIVITY" == line) {
line = readConnectivity(infile, mesh, first_node_number);
}
/// read the line corresponding to the materials
- if ("MATERIALS" == line) { line = readMaterialElement(infile, mesh); }
+ if ("MATERIALS" == line) {
+ line = readMaterialElement(infile, mesh);
+ }
AKANTU_DEBUG_OUT();
return line;
}
/* -------------------------------------------------------------------------- */
std::string MeshIODiana::readConnectivity(std::ifstream & infile, Mesh & mesh,
UInt first_node_number) {
AKANTU_DEBUG_IN();
MeshAccessor mesh_accessor(mesh);
Int index;
std::string lline;
std::string diana_type;
ElementType akantu_type, akantu_type_old = _not_defined;
Array<UInt> * connectivity = NULL;
UInt node_per_element = 0;
Element elem;
UInt * read_order = NULL;
while (1) {
my_getline(infile, lline);
// std::cerr << lline << std::endl;
std::stringstream sstr_elem(lline);
- if (lline == "MATERIALS") break;
+ if (lline == "MATERIALS")
+ break;
/// traiter les coordonnees
sstr_elem >> index;
sstr_elem >> diana_type;
akantu_type = _diana_to_akantu_element_types[diana_type];
- if (akantu_type == _not_defined) continue;
+ if (akantu_type == _not_defined)
+ continue;
if (akantu_type != akantu_type_old) {
connectivity = &(mesh_accessor.getConnectivity(akantu_type));
node_per_element = connectivity->getNbComponent();
akantu_type_old = akantu_type;
read_order = _read_order[akantu_type];
}
Vector<UInt> local_connect(node_per_element);
// used if element is written on two lines
UInt j_last = 0;
for (UInt j = 0; j < node_per_element; ++j) {
UInt node_index;
sstr_elem >> node_index;
// check s'il y a pas plus rien après un certain point
if (sstr_elem.fail()) {
sstr_elem.clear();
sstr_elem.ignore();
break;
}
node_index -= first_node_number;
local_connect(read_order[j]) = node_index;
j_last = j;
}
// check if element is written in two lines
if (j_last != (node_per_element - 1)) {
// if this is the case, read on more line
my_getline(infile, lline);
std::stringstream sstr_elem(lline);
for (UInt j = (j_last + 1); j < node_per_element; ++j) {
UInt node_index;
sstr_elem >> node_index;
node_index -= first_node_number;
local_connect(read_order[j]) = node_index;
}
}
connectivity->push_back(local_connect);
elem.type = akantu_type;
elem.element = connectivity->getSize() - 1;
diana_element_number_to_elements[index] = elem;
akantu_number_to_diana_number[elem] = index;
}
AKANTU_DEBUG_OUT();
return lline;
}
/* -------------------------------------------------------------------------- */
std::string MeshIODiana::readMaterialElement(std::ifstream & infile,
Mesh & mesh) {
AKANTU_DEBUG_IN();
std::string line;
std::stringstream sstr_tag_name;
sstr_tag_name << "tag_" << 0;
Mesh::type_iterator it = mesh.firstType();
Mesh::type_iterator end = mesh.lastType();
for (; it != end; ++it) {
UInt nb_element = mesh.getNbElement(*it);
mesh.getDataPointer<UInt>("material", *it, _not_ghost, 1)
- ->resize(nb_element);
+ .resize(nb_element);
}
my_getline(infile, line);
while (line != "'MATERIALS'") {
line =
line.substr(line.find('/') + 1,
std::string::npos); // erase the first slash / of the line
char tutu[250];
strcpy(tutu, line.c_str());
AKANTU_DEBUG_WARNING("reading line " << line);
Array<UInt> temp_id(0, 2);
UInt mat;
while (true) {
std::stringstream sstr_intervals_elements(line);
Vector<UInt> id(2);
char temp;
while (sstr_intervals_elements.good()) {
sstr_intervals_elements >> id(0) >> temp >> id(1); // >> "/" >> mat;
- if (!sstr_intervals_elements.fail()) temp_id.push_back(id);
+ if (!sstr_intervals_elements.fail())
+ temp_id.push_back(id);
}
if (sstr_intervals_elements.fail()) {
sstr_intervals_elements.clear();
sstr_intervals_elements.ignore();
sstr_intervals_elements >> mat;
break;
}
my_getline(infile, line);
}
// loop over elements
// UInt * temp_id_val = temp_id.storage();
for (UInt i = 0; i < temp_id.getSize(); ++i)
for (UInt j = temp_id(i, 0); j <= temp_id(i, 1); ++j) {
Element & element = diana_element_number_to_elements[j];
- if (element.type == _not_defined) continue;
+ if (element.type == _not_defined)
+ continue;
UInt elem = element.element;
ElementType type = element.type;
Array<UInt> & data =
- *(mesh.getDataPointer<UInt>("material", type, _not_ghost));
+ mesh.getDataPointer<UInt>("material", type, _not_ghost);
data(elem) = mat;
}
my_getline(infile, line);
}
AKANTU_DEBUG_OUT();
return line;
}
/* -------------------------------------------------------------------------- */
std::string MeshIODiana::readMaterial(std::ifstream & infile,
const std::string & filename) {
AKANTU_DEBUG_IN();
std::stringstream mat_file_name;
mat_file_name << "material_" << filename;
std::ofstream material_file;
material_file.open(mat_file_name.str().c_str()); // mat_file_name.str());
UInt mat_index;
std::string line;
bool first_mat = true;
bool end = false;
UInt mat_id = 0;
typedef std::map<std::string, Real> MatProp;
MatProp mat_prop;
do {
my_getline(infile, line);
std::stringstream sstr_material(line);
if (("'GROUPS'" == line) || ("'END'" == line)) {
if (!mat_prop.empty()) {
material_file << "material elastic [" << std::endl;
material_file << "\tname = material" << ++mat_id << std::endl;
for (MatProp::iterator it = mat_prop.begin(); it != mat_prop.end();
++it)
material_file << "\t" << it->first << " = " << it->second
<< std::endl;
material_file << "]" << std::endl;
mat_prop.clear();
}
end = true;
} else {
/// traiter les caractéristiques des matériaux
sstr_material >> mat_index;
if (!sstr_material.fail()) {
if (!first_mat) {
if (!mat_prop.empty()) {
material_file << "material elastic [" << std::endl;
material_file << "\tname = material" << ++mat_id << std::endl;
for (MatProp::iterator it = mat_prop.begin(); it != mat_prop.end();
++it)
material_file << "\t" << it->first << " = " << it->second
<< std::endl;
material_file << "]" << std::endl;
mat_prop.clear();
}
}
first_mat = false;
- } else { sstr_material.clear(); }
+ } else {
+ sstr_material.clear();
+ }
std::string prop_name;
sstr_material >> prop_name;
std::map<std::string, std::string>::iterator it;
it = _diana_to_akantu_mat_prop.find(prop_name);
if (it != _diana_to_akantu_mat_prop.end()) {
Real value;
sstr_material >> value;
mat_prop[it->second] = value;
} else {
AKANTU_DEBUG_INFO("In material reader, property " << prop_name
<< "not recognized");
}
}
} while (!end);
AKANTU_DEBUG_OUT();
return line;
}
/* -------------------------------------------------------------------------- */
-} // akantu
+} // namespace akantu
diff --git a/src/io/mesh_io/mesh_io_msh.cc b/src/io/mesh_io/mesh_io_msh.cc
index 44990b5b2..a2efe333e 100644
--- a/src/io/mesh_io/mesh_io_msh.cc
+++ b/src/io/mesh_io/mesh_io_msh.cc
@@ -1,981 +1,981 @@
/**
* @file mesh_io_msh.cc
*
* @author Dana Christen <dana.christen@gmail.com>
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Thu Jan 21 2016
*
* @brief Read/Write for MSH files generated by gmsh
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
* Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
* Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -----------------------------------------------------------------------------
Version (Legacy) 1.0
$NOD
number-of-nodes
node-number x-coord y-coord z-coord
...
$ENDNOD
$ELM
number-of-elements
elm-number elm-type reg-phys reg-elem number-of-nodes node-number-list
...
$ENDELM
-----------------------------------------------------------------------------
Version 2.1
$MeshFormat
version-number file-type data-size
$EndMeshFormat
$Nodes
number-of-nodes
node-number x-coord y-coord z-coord
...
$EndNodes
$Elements
number-of-elements
elm-number elm-type number-of-tags < tag > ... node-number-list
...
$EndElements
$PhysicalNames
number-of-names
physical-dimension physical-number "physical-name"
...
$EndPhysicalNames
$NodeData
number-of-string-tags
< "string-tag" >
...
number-of-real-tags
< real-tag >
...
number-of-integer-tags
< integer-tag >
...
node-number value ...
...
$EndNodeData
$ElementData
number-of-string-tags
< "string-tag" >
...
number-of-real-tags
< real-tag >
...
number-of-integer-tags
< integer-tag >
...
elm-number value ...
...
$EndElementData
$ElementNodeData
number-of-string-tags
< "string-tag" >
...
number-of-real-tags
< real-tag >
...
number-of-integer-tags
< integer-tag >
...
elm-number number-of-nodes-per-element value ...
...
$ElementEndNodeData
-----------------------------------------------------------------------------
elem-type
1: 2-node line.
2: 3-node triangle.
3: 4-node quadrangle.
4: 4-node tetrahedron.
5: 8-node hexahedron.
6: 6-node prism.
7: 5-node pyramid.
8: 3-node second order line
9: 6-node second order triangle
10: 9-node second order quadrangle
11: 10-node second order tetrahedron
12: 27-node second order hexahedron
13: 18-node second order prism
14: 14-node second order pyramid
15: 1-node point.
16: 8-node second order quadrangle
17: 20-node second order hexahedron
18: 15-node second order prism
19: 13-node second order pyramid
20: 9-node third order incomplete triangle
21: 10-node third order triangle
22: 12-node fourth order incomplete triangle
23: 15-node fourth order triangle
24: 15-node fifth order incomplete triangle
25: 21-node fifth order complete triangle
26: 4-node third order edge
27: 5-node fourth order edge
28: 6-node fifth order edge
29: 20-node third order tetrahedron
30: 35-node fourth order tetrahedron
31: 56-node fifth order tetrahedron
-------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include <fstream>
/* -------------------------------------------------------------------------- */
#include "mesh_io.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
// The boost spirit is a work on the way it does not compile so I kept the
// current code. The current code does not handle files generated on Windows
// <CRLF>
// #include <boost/config/warning_disable.hpp>
// #include <boost/spirit/include/qi.hpp>
// #include <boost/spirit/include/phoenix_core.hpp>
// #include <boost/spirit/include/phoenix_fusion.hpp>
// #include <boost/spirit/include/phoenix_object.hpp>
// #include <boost/spirit/include/phoenix_container.hpp>
// #include <boost/spirit/include/phoenix_operator.hpp>
// #include <boost/spirit/include/phoenix_bind.hpp>
// #include <boost/spirit/include/phoenix_stl.hpp>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Methods Implentations */
/* -------------------------------------------------------------------------- */
MeshIOMSH::MeshIOMSH() {
canReadSurface = true;
canReadExtendedData = true;
_msh_nodes_per_elem[_msh_not_defined] = 0;
_msh_nodes_per_elem[_msh_segment_2] = 2;
_msh_nodes_per_elem[_msh_triangle_3] = 3;
_msh_nodes_per_elem[_msh_quadrangle_4] = 4;
_msh_nodes_per_elem[_msh_tetrahedron_4] = 4;
_msh_nodes_per_elem[_msh_hexahedron_8] = 8;
_msh_nodes_per_elem[_msh_prism_1] = 6;
_msh_nodes_per_elem[_msh_pyramid_1] = 1;
_msh_nodes_per_elem[_msh_segment_3] = 3;
_msh_nodes_per_elem[_msh_triangle_6] = 6;
_msh_nodes_per_elem[_msh_quadrangle_9] = 9;
_msh_nodes_per_elem[_msh_tetrahedron_10] = 10;
_msh_nodes_per_elem[_msh_hexahedron_27] = 27;
_msh_nodes_per_elem[_msh_hexahedron_20] = 20;
_msh_nodes_per_elem[_msh_prism_18] = 18;
_msh_nodes_per_elem[_msh_prism_15] = 15;
_msh_nodes_per_elem[_msh_pyramid_14] = 14;
_msh_nodes_per_elem[_msh_point] = 1;
_msh_nodes_per_elem[_msh_quadrangle_8] = 8;
_msh_to_akantu_element_types[_msh_not_defined] = _not_defined;
_msh_to_akantu_element_types[_msh_segment_2] = _segment_2;
_msh_to_akantu_element_types[_msh_triangle_3] = _triangle_3;
_msh_to_akantu_element_types[_msh_quadrangle_4] = _quadrangle_4;
_msh_to_akantu_element_types[_msh_tetrahedron_4] = _tetrahedron_4;
_msh_to_akantu_element_types[_msh_hexahedron_8] = _hexahedron_8;
_msh_to_akantu_element_types[_msh_prism_1] = _pentahedron_6;
_msh_to_akantu_element_types[_msh_pyramid_1] = _not_defined;
_msh_to_akantu_element_types[_msh_segment_3] = _segment_3;
_msh_to_akantu_element_types[_msh_triangle_6] = _triangle_6;
_msh_to_akantu_element_types[_msh_quadrangle_9] = _not_defined;
_msh_to_akantu_element_types[_msh_tetrahedron_10] = _tetrahedron_10;
_msh_to_akantu_element_types[_msh_hexahedron_27] = _not_defined;
_msh_to_akantu_element_types[_msh_hexahedron_20] = _hexahedron_20;
_msh_to_akantu_element_types[_msh_prism_18] = _not_defined;
_msh_to_akantu_element_types[_msh_prism_15] = _pentahedron_15;
_msh_to_akantu_element_types[_msh_pyramid_14] = _not_defined;
_msh_to_akantu_element_types[_msh_point] = _point_1;
_msh_to_akantu_element_types[_msh_quadrangle_8] = _quadrangle_8;
_akantu_to_msh_element_types[_not_defined] = _msh_not_defined;
_akantu_to_msh_element_types[_segment_2] = _msh_segment_2;
_akantu_to_msh_element_types[_segment_3] = _msh_segment_3;
_akantu_to_msh_element_types[_triangle_3] = _msh_triangle_3;
_akantu_to_msh_element_types[_triangle_6] = _msh_triangle_6;
_akantu_to_msh_element_types[_tetrahedron_4] = _msh_tetrahedron_4;
_akantu_to_msh_element_types[_tetrahedron_10] = _msh_tetrahedron_10;
_akantu_to_msh_element_types[_quadrangle_4] = _msh_quadrangle_4;
_akantu_to_msh_element_types[_quadrangle_8] = _msh_quadrangle_8;
_akantu_to_msh_element_types[_hexahedron_8] = _msh_hexahedron_8;
_akantu_to_msh_element_types[_hexahedron_20] = _msh_hexahedron_20;
_akantu_to_msh_element_types[_pentahedron_6] = _msh_prism_1;
_akantu_to_msh_element_types[_pentahedron_15] = _msh_prism_15;
_akantu_to_msh_element_types[_point_1] = _msh_point;
#if defined(AKANTU_STRUCTURAL_MECHANICS)
_akantu_to_msh_element_types[_bernoulli_beam_2] = _msh_segment_2;
_akantu_to_msh_element_types[_bernoulli_beam_3] = _msh_segment_2;
_akantu_to_msh_element_types[_kirchhoff_shell] = _msh_triangle_3;
#endif
std::map<ElementType, MSHElementType>::iterator it;
for (it = _akantu_to_msh_element_types.begin();
it != _akantu_to_msh_element_types.end(); ++it) {
UInt nb_nodes = _msh_nodes_per_elem[it->second];
std::vector<UInt> tmp(nb_nodes);
for (UInt i = 0; i < nb_nodes; ++i) {
tmp[i] = i;
}
switch (it->first) {
case _tetrahedron_10:
tmp[8] = 9;
tmp[9] = 8;
break;
case _pentahedron_6:
tmp[0] = 2;
tmp[1] = 0;
tmp[2] = 1;
tmp[3] = 5;
tmp[4] = 3;
tmp[5] = 4;
break;
case _pentahedron_15:
tmp[0] = 2;
tmp[1] = 0;
tmp[2] = 1;
tmp[3] = 5;
tmp[4] = 3;
tmp[5] = 4;
tmp[6] = 8;
tmp[8] = 11;
tmp[9] = 6;
tmp[10] = 9;
tmp[11] = 10;
tmp[12] = 14;
tmp[14] = 12;
break;
case _hexahedron_20:
tmp[9] = 11;
tmp[10] = 12;
tmp[11] = 9;
tmp[12] = 13;
tmp[13] = 10;
tmp[17] = 19;
tmp[18] = 17;
tmp[19] = 18;
break;
default:
// nothing to change
break;
}
_read_order[it->first] = tmp;
}
}
/* -------------------------------------------------------------------------- */
MeshIOMSH::~MeshIOMSH() {}
/* -------------------------------------------------------------------------- */
/* Spirit stuff */
/* -------------------------------------------------------------------------- */
// namespace _parser {
// namespace spirit = ::boost::spirit;
// namespace qi = ::boost::spirit::qi;
// namespace ascii = ::boost::spirit::ascii;
// namespace lbs = ::boost::spirit::qi::labels;
// namespace phx = ::boost::phoenix;
// /* ------------------------------------------------------------------------
// */
// /* Lazy functors */
// /* ------------------------------------------------------------------------
// */
// struct _Element {
// int index;
// std::vector<int> tags;
// std::vector<int> connectivity;
// ElementType type;
// };
// /* ------------------------------------------------------------------------
// */
// struct lazy_get_nb_nodes_ {
// template <class elem_type> struct result { typedef int type; };
// template <class elem_type> bool operator()(elem_type et) {
// return MeshIOMSH::_msh_nodes_per_elem[et];
// }
// };
// /* ------------------------------------------------------------------------
// */
// struct lazy_element_ {
// template <class id_t, class tags_t, class elem_type, class conn_t>
// struct result {
// typedef _Element type;
// };
// template <class id_t, class tags_t, class elem_type, class conn_t>
// _Element operator()(id_t id, const elem_type & et, const tags_t & t,
// const conn_t & c) {
// _Element tmp_el;
// tmp_el.index = id;
// tmp_el.tags = t;
// tmp_el.connectivity = c;
// tmp_el.type = et;
// return tmp_el;
// }
// };
// /* ------------------------------------------------------------------------
// */
// struct lazy_check_value_ {
// template <class T> struct result { typedef void type; };
// template <class T> void operator()(T v1, T v2) {
// if (v1 != v2) {
// AKANTU_EXCEPTION("The msh parser expected a "
// << v2 << " in the header bug got a " << v1);
// }
// }
// };
// /* ------------------------------------------------------------------------
// */
// struct lazy_node_read_ {
// template <class Mesh, class ID, class V, class size, class Map>
// struct result {
// typedef bool type;
// };
// template <class Mesh, class ID, class V, class size, class Map>
// bool operator()(Mesh & mesh, const ID & id, const V & pos, size max,
// Map & nodes_mapping) const {
// Vector<Real> tmp_pos(mesh.getSpatialDimension());
// UInt i = 0;
// for (typename V::const_iterator it = pos.begin();
// it != pos.end() || i < mesh.getSpatialDimension(); ++it)
// tmp_pos[i++] = *it;
// nodes_mapping[id] = mesh.getNbNodes();
// mesh.getNodes().push_back(tmp_pos);
// return (mesh.getNbNodes() < UInt(max));
// }
// };
// /* ------------------------------------------------------------------------
// */
// struct lazy_element_read_ {
// template <class Mesh, class EL, class size, class NodeMap, class ElemMap>
// struct result {
// typedef bool type;
// };
// template <class Mesh, class EL, class size, class NodeMap, class ElemMap>
// bool operator()(Mesh & mesh, const EL & element, size max,
// const NodeMap & nodes_mapping,
// ElemMap & elements_mapping) const {
// Vector<UInt> tmp_conn(Mesh::getNbNodesPerElement(element.type));
// AKANTU_DEBUG_ASSERT(element.connectivity.size() == tmp_conn.size(),
// "The element "
// << element.index
// << "in the MSH file has too many nodes.");
// mesh.addConnectivityType(element.type);
// Array<UInt> & connectivity = mesh.getConnectivity(element.type);
// UInt i = 0;
// for (std::vector<int>::const_iterator it =
// element.connectivity.begin();
// it != element.connectivity.end(); ++it) {
// typename NodeMap::const_iterator nit = nodes_mapping.find(*it);
// AKANTU_DEBUG_ASSERT(nit != nodes_mapping.end(),
// "There is an unknown node in the connectivity.");
// tmp_conn[i++] = nit->second;
// }
// ::akantu::Element el(element.type, connectivity.getSize());
// elements_mapping[element.index] = el;
// connectivity.push_back(tmp_conn);
// for (UInt i = 0; i < element.tags.size(); ++i) {
// std::stringstream tag_sstr;
// tag_sstr << "tag_" << i;
// Array<UInt> * data =
// mesh.template getDataPointer<UInt>(tag_sstr.str(), element.type,
// _not_ghost);
// data->push_back(element.tags[i]);
// }
// return (mesh.getNbElement() < UInt(max));
// }
// };
// /* ------------------------------------------------------------------------
// */
// template <class Iterator, typename Skipper = ascii::space_type>
// struct MshMeshGrammar : qi::grammar<Iterator, void(), Skipper> {
// public:
// MshMeshGrammar(Mesh & mesh)
// : MshMeshGrammar::base_type(start, "msh_mesh_reader"), mesh(mesh) {
// phx::function<lazy_element_> lazy_element;
// phx::function<lazy_get_nb_nodes_> lazy_get_nb_nodes;
// phx::function<lazy_check_value_> lazy_check_value;
// phx::function<lazy_node_read_> lazy_node_read;
// phx::function<lazy_element_read_> lazy_element_read;
// clang-format off
// start
// = *( known_section | unknown_section
// )
// ;
// known_section
// = qi::char_("$")
// >> sections [ lbs::_a = lbs::_1 ]
// >> qi::lazy(*lbs::_a)
// >> qi::lit("$End")
// //>> qi::lit(phx::ref(lbs::_a))
// ;
// unknown_section
// = qi::char_("$")
// >> qi::char_("") [ lbs::_a = lbs::_1 ]
// >> ignore_section
// >> qi::lit("$End")
// >> qi::lit(phx::val(lbs::_a))
// ;
// mesh_format // version followed by 0 or 1 for ascii or binary
// = version >> (
// ( qi::char_("0")
// >> qi::int_ [ lazy_check_value(lbs::_1, 8) ]
// )
// | ( qi::char_("1")
// >> qi::int_ [ lazy_check_value(lbs::_1, 8) ]
// >> qi::dword [ lazy_check_value(lbs::_1, 1) ]
// )
// )
// ;
// nodes
// = nodes_
// ;
// nodes_
// = qi::int_ [ lbs::_a = lbs::_1 ]
// > *(
// ( qi::int_ >> position ) [ lazy_node_read(phx::ref(mesh),
// lbs::_1,
// phx::cref(lbs::_2),
// lbs::_a,
// phx::ref(this->msh_nodes_to_akantu)) ]
// )
// ;
// element
// = elements_
// ;
// elements_
// = qi::int_ [ lbs::_a = lbs::_1 ]
// > qi::repeat(phx::ref(lbs::_a))[ element [ lazy_element_read(phx::ref(mesh),
// lbs::_1,
// phx::cref(lbs::_a),
// phx::cref(this->msh_nodes_to_akantu),
// phx::ref(this->msh_elemt_to_akantu)) ]]
// ;
// ignore_section
// = *(qi::char_ - qi::char_('$'))
// ;
// interpolation_scheme = ignore_section;
// element_data = ignore_section;
// node_data = ignore_section;
// version
// = qi::int_ [ phx::push_back(lbs::_val, lbs::_1) ]
// >> *( qi::char_(".") >> qi::int_ [ phx::push_back(lbs::_val, lbs::_1) ] )
// ;
// position
// = real [ phx::push_back(lbs::_val, lbs::_1) ]
// > real [ phx::push_back(lbs::_val, lbs::_1) ]
// > real [ phx::push_back(lbs::_val, lbs::_1) ]
// ;
// tags
// = qi::int_ [ lbs::_a = lbs::_1 ]
// > qi::repeat(phx::val(lbs::_a))[ qi::int_ [ phx::push_back(lbs::_val,
// lbs::_1) ] ]
// ;
// element
// = ( qi::int_ [ lbs::_a = lbs::_1 ]
// > msh_element_type [ lbs::_b = lazy_get_nb_nodes(lbs::_1) ]
// > tags [ lbs::_c = lbs::_1 ]
// > connectivity(lbs::_a) [ lbs::_d = lbs::_1 ]
// ) [ lbs::_val = lazy_element(lbs::_a,
// phx::cref(lbs::_b),
// phx::cref(lbs::_c),
// phx::cref(lbs::_d)) ]
// ;
// connectivity
// = qi::repeat(lbs::_r1)[ qi::int_ [ phx::push_back(lbs::_val,
// lbs::_1) ] ]
// ;
// sections.add
// ("MeshFormat", &mesh_format)
// ("Nodes", &nodes)
// ("Elements", &elements)
// ("PhysicalNames", &physical_names)
// ("InterpolationScheme", &interpolation_scheme)
// ("ElementData", &element_data)
// ("NodeData", &node_data);
// msh_element_type.add
// ("0" , _not_defined )
// ("1" , _segment_2 )
// ("2" , _triangle_3 )
// ("3" , _quadrangle_4 )
// ("4" , _tetrahedron_4 )
// ("5" , _hexahedron_8 )
// ("6" , _pentahedron_6 )
// ("7" , _not_defined )
// ("8" , _segment_3 )
// ("9" , _triangle_6 )
// ("10", _not_defined )
// ("11", _tetrahedron_10)
// ("12", _not_defined )
// ("13", _not_defined )
// ("14", _hexahedron_20 )
// ("15", _pentahedron_15)
// ("16", _not_defined )
// ("17", _point_1 )
// ("18", _quadrangle_8 );
// mesh_format .name("MeshFormat" );
// nodes .name("Nodes" );
// elements .name("Elements" );
// physical_names .name("PhysicalNames" );
// interpolation_scheme.name("InterpolationScheme");
// element_data .name("ElementData" );
// node_data .name("NodeData" );
// clang-format on
// }
// /* ----------------------------------------------------------------------
// */
// /* Rules */
// /* ----------------------------------------------------------------------
// */
// private:
// qi::symbols<char, ElementType> msh_element_type;
// qi::symbols<char, qi::rule<Iterator, void(), Skipper> *> sections;
// qi::rule<Iterator, void(), Skipper> start;
// qi::rule<Iterator, void(), Skipper, qi::locals<std::string> >
// unknown_section;
// qi::rule<Iterator, void(), Skipper, qi::locals<qi::rule<Iterator,
// Skipper> *> > known_section;
// qi::rule<Iterator, void(), Skipper> mesh_format, nodes, elements,
// physical_names, ignore_section,
// interpolation_scheme, element_data, node_data, any_line;
// qi::rule<Iterator, void(), Skipper, qi::locals<int> > nodes_;
// qi::rule<Iterator, void(), Skipper, qi::locals< int, int, vector<int>,
// vector<int> > > elements_;
// qi::rule<Iterator, std::vector<int>(), Skipper> version;
// qi::rule<Iterator, _Element(), Skipper, qi::locals<ElementType> >
// element;
// qi::rule<Iterator, std::vector<int>(), Skipper, qi::locals<int> > tags;
// qi::rule<Iterator, std::vector<int>(int), Skipper> connectivity;
// qi::rule<Iterator, std::vector<Real>(), Skipper> position;
// qi::real_parser<Real, qi::real_policies<Real> > real;
// /* ----------------------------------------------------------------------
// */
// /* Members */
// /* ----------------------------------------------------------------------
// */
// private:
// /// reference to the mesh to read
// Mesh & mesh;
// /// correspondance between the numbering of nodes in the abaqus file and
// in
// /// the akantu mesh
// std::map<UInt, UInt> msh_nodes_to_akantu;
// /// correspondance between the element number in the abaqus file and the
// /// Element in the akantu mesh
// std::map<UInt, Element> msh_elemt_to_akantu;
// };
// }
// /* --------------------------------------------------------------------------
// */
// void MeshIOAbaqus::read(const std::string& filename, Mesh& mesh) {
// namespace qi = boost::spirit::qi;
// namespace ascii = boost::spirit::ascii;
// std::ifstream infile;
// infile.open(filename.c_str());
// if(!infile.good()) {
// AKANTU_DEBUG_ERROR("Cannot open file " << filename);
// }
// std::string storage; // We will read the contents here.
// infile.unsetf(std::ios::skipws); // No white space skipping!
// std::copy(std::istream_iterator<char>(infile),
// std::istream_iterator<char>(),
// std::back_inserter(storage));
// typedef std::string::const_iterator iterator_t;
// typedef ascii::space_type skipper;
// typedef _parser::MshMeshGrammar<iterator_t, skipper> grammar;
// grammar g(mesh);
// skipper ws;
// iterator_t iter = storage.begin();
// iterator_t end = storage.end();
// qi::phrase_parse(iter, end, g, ws);
// this->setNbGlobalNodes(mesh, mesh.getNodes().getSize());
// MeshUtils::fillElementToSubElementsData(mesh);
// }
static void my_getline(std::ifstream & infile, std::string & str) {
std::string tmp_str;
std::getline(infile, tmp_str);
str = trim(tmp_str);
}
/* -------------------------------------------------------------------------- */
void MeshIOMSH::read(const std::string & filename, Mesh & mesh) {
MeshAccessor mesh_accessor(mesh);
std::ifstream infile;
infile.open(filename.c_str());
std::string line;
UInt first_node_number = std::numeric_limits<UInt>::max(),
last_node_number = 0, file_format = 1, current_line = 0;
bool has_physical_names = false;
if (!infile.good()) {
AKANTU_DEBUG_ERROR("Cannot open file " << filename);
}
while (infile.good()) {
my_getline(infile, line);
current_line++;
/// read the header
if (line == "$MeshFormat") {
my_getline(infile, line); /// the format line
std::stringstream sstr(line);
std::string version;
sstr >> version;
Int format;
sstr >> format;
if (format != 0)
AKANTU_DEBUG_ERROR("This reader can only read ASCII files.");
my_getline(infile, line); /// the end of block line
current_line += 2;
file_format = 2;
}
/// read the physical names
if (line == "$PhysicalNames") {
has_physical_names = true;
my_getline(infile, line); /// the format line
std::stringstream sstr(line);
UInt num_of_phys_names;
sstr >> num_of_phys_names;
for (UInt k(0); k < num_of_phys_names; k++) {
my_getline(infile, line);
std::stringstream sstr_phys_name(line);
UInt phys_name_id;
UInt phys_dim;
sstr_phys_name >> phys_dim >> phys_name_id;
std::size_t b = line.find("\"");
std::size_t e = line.rfind("\"");
std::string phys_name = line.substr(b + 1, e - b - 1);
phys_name_map[phys_name_id] = phys_name;
}
}
/// read all nodes
if (line == "$Nodes" || line == "$NOD") {
UInt nb_nodes;
my_getline(infile, line);
std::stringstream sstr(line);
sstr >> nb_nodes;
current_line++;
Array<Real> & nodes = mesh_accessor.getNodes();
nodes.resize(nb_nodes);
mesh_accessor.setNbGlobalNodes(nb_nodes);
UInt index;
Real coord[3];
UInt spatial_dimension = nodes.getNbComponent();
/// for each node, read the coordinates
for (UInt i = 0; i < nb_nodes; ++i) {
UInt offset = i * spatial_dimension;
my_getline(infile, line);
std::stringstream sstr_node(line);
sstr_node >> index >> coord[0] >> coord[1] >> coord[2];
current_line++;
first_node_number = std::min(first_node_number, index);
last_node_number = std::max(last_node_number, index);
/// read the coordinates
for (UInt j = 0; j < spatial_dimension; ++j)
nodes.storage()[offset + j] = coord[j];
}
my_getline(infile, line); /// the end of block line
}
/// read all elements
if (line == "$Elements" || line == "$ELM") {
UInt nb_elements;
std::vector<UInt> read_order;
my_getline(infile, line);
std::stringstream sstr(line);
sstr >> nb_elements;
current_line++;
Int index;
UInt msh_type;
ElementType akantu_type, akantu_type_old = _not_defined;
Array<UInt> * connectivity = NULL;
UInt node_per_element = 0;
for (UInt i = 0; i < nb_elements; ++i) {
my_getline(infile, line);
std::stringstream sstr_elem(line);
current_line++;
sstr_elem >> index;
sstr_elem >> msh_type;
/// get the connectivity vector depending on the element type
akantu_type = this->_msh_to_akantu_element_types[(MSHElementType)msh_type];
if (akantu_type == _not_defined) {
AKANTU_DEBUG_WARNING("Unsuported element kind "
<< msh_type << " at line " << current_line);
continue;
}
if (akantu_type != akantu_type_old) {
connectivity = &mesh_accessor.getConnectivity(akantu_type);
// connectivity->resize(0);
node_per_element = connectivity->getNbComponent();
akantu_type_old = akantu_type;
read_order = this->_read_order[akantu_type];
}
/// read tags informations
if (file_format == 2) {
UInt nb_tags;
sstr_elem >> nb_tags;
for (UInt j = 0; j < nb_tags; ++j) {
Int tag;
sstr_elem >> tag;
std::stringstream sstr_tag_name;
sstr_tag_name << "tag_" << j;
- Array<UInt> * data = mesh.getDataPointer<UInt>(
+ Array<UInt> & data = mesh.getDataPointer<UInt>(
sstr_tag_name.str(), akantu_type, _not_ghost);
- data->push_back(tag);
+ data.push_back(tag);
}
} else if (file_format == 1) {
Int tag;
sstr_elem >> tag; // reg-phys
std::string tag_name = "tag_0";
Array<UInt> * data =
- mesh.getDataPointer<UInt>(tag_name, akantu_type, _not_ghost);
+ &mesh.getDataPointer<UInt>(tag_name, akantu_type, _not_ghost);
data->push_back(tag);
sstr_elem >> tag; // reg-elem
tag_name = "tag_1";
- data = mesh.getDataPointer<UInt>(tag_name, akantu_type, _not_ghost);
+ data = &mesh.getDataPointer<UInt>(tag_name, akantu_type, _not_ghost);
data->push_back(tag);
sstr_elem >> tag; // number-of-nodes
}
Vector<UInt> local_connect(node_per_element);
for (UInt j = 0; j < node_per_element; ++j) {
UInt node_index;
sstr_elem >> node_index;
AKANTU_DEBUG_ASSERT(node_index <= last_node_number,
"Node number not in range : line "
<< current_line);
node_index -= first_node_number;
local_connect(read_order[j]) = node_index;
}
connectivity->push_back(local_connect);
}
my_getline(infile, line); /// the end of block line
}
if ((line[0] == '$') && (line.find("End") == std::string::npos)) {
AKANTU_DEBUG_WARNING("Unsuported block_kind " << line << " at line "
<< current_line);
}
}
- mesh.updateTypesOffsets(_not_ghost);
+ //mesh.updateTypesOffsets(_not_ghost);
infile.close();
this->constructPhysicalNames("tag_0", mesh);
if (has_physical_names)
mesh.createGroupsFromMeshData<std::string>("physical_names");
MeshUtils::fillElementToSubElementsData(mesh);
}
/* -------------------------------------------------------------------------- */
void MeshIOMSH::write(const std::string & filename, const Mesh & mesh) {
std::ofstream outfile;
const Array<Real> & nodes = mesh.getNodes();
outfile.open(filename.c_str());
outfile << "$MeshFormat" << std::endl;
outfile << "2.1 0 8" << std::endl;
outfile << "$EndMeshFormat" << std::endl;
outfile << std::setprecision(std::numeric_limits<Real>::digits10);
outfile << "$Nodes" << std::endl;
outfile << nodes.getSize() << std::endl;
outfile << std::uppercase;
for (UInt i = 0; i < nodes.getSize(); ++i) {
Int offset = i * nodes.getNbComponent();
outfile << i + 1;
for (UInt j = 0; j < nodes.getNbComponent(); ++j) {
outfile << " " << nodes.storage()[offset + j];
}
for (UInt p = nodes.getNbComponent(); p < 3; ++p)
outfile << " " << 0.;
outfile << std::endl;
;
}
outfile << std::nouppercase;
outfile << "$EndNodes" << std::endl;
;
outfile << "$Elements" << std::endl;
;
Mesh::type_iterator it =
mesh.firstType(_all_dimensions, _not_ghost, _ek_not_defined);
Mesh::type_iterator end =
mesh.lastType(_all_dimensions, _not_ghost, _ek_not_defined);
Int nb_elements = 0;
for (; it != end; ++it) {
const Array<UInt> & connectivity = mesh.getConnectivity(*it, _not_ghost);
nb_elements += connectivity.getSize();
}
outfile << nb_elements << std::endl;
UInt element_idx = 1;
for (it = mesh.firstType(_all_dimensions, _not_ghost, _ek_not_defined);
it != end; ++it) {
ElementType type = *it;
const Array<UInt> & connectivity = mesh.getConnectivity(type, _not_ghost);
UInt * tag[2] = {NULL, NULL};
try {
const Array<UInt> & data_tag_0 =
mesh.getData<UInt>("tag_0", type, _not_ghost);
tag[0] = data_tag_0.storage();
} catch (...) {
tag[0] = NULL;
}
try {
const Array<UInt> & data_tag_1 =
mesh.getData<UInt>("tag_1", type, _not_ghost);
tag[1] = data_tag_1.storage();
} catch (...) {
tag[1] = NULL;
}
for (UInt i = 0; i < connectivity.getSize(); ++i) {
UInt offset = i * connectivity.getNbComponent();
outfile << element_idx << " " << _akantu_to_msh_element_types[type]
<< " 2";
/// \todo write the real data in the file
for (UInt t = 0; t < 2; ++t)
if (tag[t])
outfile << " " << tag[t][i];
else
outfile << " 0";
for (UInt j = 0; j < connectivity.getNbComponent(); ++j) {
outfile << " " << connectivity.storage()[offset + j] + 1;
}
outfile << std::endl;
element_idx++;
}
}
outfile << "$EndElements" << std::endl;
;
outfile.close();
}
/* -------------------------------------------------------------------------- */
} // akantu
diff --git a/src/mesh/element_group.hh b/src/mesh/element_group.hh
index be5a6ab5c..181d9c3d6 100644
--- a/src/mesh/element_group.hh
+++ b/src/mesh/element_group.hh
@@ -1,188 +1,187 @@
/**
* @file element_group.hh
*
* @author Dana Christen <dana.christen@gmail.com>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri May 03 2013
* @date last modification: Tue Aug 18 2015
*
* @brief Stores information relevent to the notion of domain boundary and
* surfaces.
*
* @section LICENSE
*
* Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_memory.hh"
#include "dumpable.hh"
#include "element_type_map.hh"
#include "node_group.hh"
/* -------------------------------------------------------------------------- */
#include <set>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_ELEMENT_GROUP_HH__
#define __AKANTU_ELEMENT_GROUP_HH__
namespace akantu {
class Mesh;
class Element;
-} // akantu
+} // namespace akantu
namespace akantu {
/* -------------------------------------------------------------------------- */
class ElementGroup : private Memory, public Dumpable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ElementGroup(const std::string & name, const Mesh & mesh,
NodeGroup & node_group, UInt dimension = _all_dimensions,
const std::string & id = "element_group",
const MemoryID & memory_id = 0);
/* ------------------------------------------------------------------------ */
/* Type definitions */
/* ------------------------------------------------------------------------ */
public:
- typedef ElementTypeMapArray<UInt> ElementList;
- typedef Array<UInt> NodeList;
-
- /* ------------------------------------------------------------------------ */
- /* Node iterator */
- /* ------------------------------------------------------------------------ */
- typedef NodeGroup::const_node_iterator const_node_iterator;
- inline const_node_iterator node_begin() const;
- inline const_node_iterator node_end() const;
+ using ElementList = ElementTypeMapArray<UInt>;
+ using NodeList = Array<UInt>;
/* ------------------------------------------------------------------------ */
/* Element iterator */
/* ------------------------------------------------------------------------ */
- typedef ElementList::type_iterator type_iterator;
+ using type_iterator = ElementList::type_iterator;
inline type_iterator firstType(UInt dim = _all_dimensions,
const GhostType & ghost_type = _not_ghost,
const ElementKind & kind = _ek_regular) const;
inline type_iterator lastType(UInt dim = _all_dimensions,
const GhostType & ghost_type = _not_ghost,
const ElementKind & kind = _ek_regular) const;
- typedef Array<UInt>::const_iterator<UInt> const_element_iterator;
+ inline auto elementTypes(UInt dim = _all_dimensions,
+ const GhostType & ghost_type = _not_ghost,
+ const ElementKind & kind = _ek_regular) const {
+ return elements.elementTypes(dim, ghost_type, kind);
+ }
+
+ using const_element_iterator = Array<UInt>::const_iterator<UInt>;
inline const_element_iterator
- element_begin(const ElementType & type,
- const GhostType & ghost_type = _not_ghost) const;
+ begin(const ElementType & type,
+ const GhostType & ghost_type = _not_ghost) const;
inline const_element_iterator
- element_end(const ElementType & type,
- const GhostType & ghost_type = _not_ghost) const;
+ end(const ElementType & type,
+ const GhostType & ghost_type = _not_ghost) const;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// empty the element group
void empty();
/// append another group to this group
/// BE CAREFUL: it doesn't conserve the element order
void append(const ElementGroup & other_group);
/// add an element to the group. By default the it does not add the nodes to
/// the group
inline void add(const Element & el, bool add_nodes = false,
bool check_for_duplicate = true);
/// \todo fix the default for add_nodes : make it coherent with the other
/// method
inline void add(const ElementType & type, UInt element,
const GhostType & ghost_type = _not_ghost,
bool add_nodes = true, bool check_for_duplicate = true);
inline void addNode(UInt node_id, bool check_for_duplicate = true);
inline void removeNode(UInt node_id);
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
/// fill the elements based on the underlying node group.
virtual void fillFromNodeGroup();
// sort and remove duplicated values
void optimize();
private:
inline void addElement(const ElementType & elem_type, UInt elem_id,
const GhostType & ghost_type);
friend class GroupManager;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Elements, elements, UInt);
AKANTU_GET_MACRO(Elements, elements, const ElementTypeMapArray<UInt> &);
AKANTU_GET_MACRO(Nodes, node_group.getNodes(), const Array<UInt> &);
AKANTU_GET_MACRO(NodeGroup, node_group, const NodeGroup &);
AKANTU_GET_MACRO_NOT_CONST(NodeGroup, node_group, NodeGroup &);
AKANTU_GET_MACRO(Dimension, dimension, UInt);
AKANTU_GET_MACRO(Name, name, std::string);
inline UInt getNbNodes() const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// Mesh to which this group belongs
const Mesh & mesh;
/// name of the group
std::string name;
/// list of elements composing the group
ElementList elements;
/// sub list of nodes which are composing the elements
NodeGroup & node_group;
/// group dimension
UInt dimension;
/// empty arry for the iterator to work when an element type not present
Array<UInt> empty_elements;
};
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const ElementGroup & _this) {
_this.printself(stream);
return stream;
}
-} // akantu
+} // namespace akantu
#include "element.hh"
#include "element_group_inline_impl.cc"
#endif /* __AKANTU_ELEMENT_GROUP_HH__ */
diff --git a/src/mesh/element_group_inline_impl.cc b/src/mesh/element_group_inline_impl.cc
index ba16ea036..7ff809849 100644
--- a/src/mesh/element_group_inline_impl.cc
+++ b/src/mesh/element_group_inline_impl.cc
@@ -1,137 +1,135 @@
/**
* @file element_group_inline_impl.cc
*
* @author Dana Christen <dana.christen@gmail.com>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
* @date last modification: Tue Aug 18 2015
*
* @brief Stores information relevent to the notion of domain boundary and
* surfaces.
*
* @section LICENSE
*
* Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "mesh.hh"
+#include "element_group.hh"
+
/* -------------------------------------------------------------------------- */
+#ifndef __AKANTU_ELEMENT_GROUP_INLINE_IMPL_CC__
+#define __AKANTU_ELEMENT_GROUP_INLINE_IMPL_CC__
namespace akantu {
/* -------------------------------------------------------------------------- */
-inline void ElementGroup::add(const Element & el, bool add_nodes,
- bool check_for_duplicate) {
- this->add(el.type,el.element,el.ghost_type,add_nodes,check_for_duplicate);
+inline void ElementGroup::add(const Element & el, bool add_nodes,
+ bool check_for_duplicate) {
+ this->add(el.type, el.element, el.ghost_type, add_nodes, check_for_duplicate);
}
-
/* -------------------------------------------------------------------------- */
-inline void ElementGroup::add(const ElementType & type, UInt element,
- const GhostType & ghost_type,bool add_nodes,
- bool check_for_duplicate) {
+inline void ElementGroup::add(const ElementType & type, UInt element,
+ const GhostType & ghost_type, bool add_nodes,
+ bool check_for_duplicate) {
addElement(type, element, ghost_type);
- if(add_nodes) {
+ if (add_nodes) {
Array<UInt>::const_vector_iterator it =
- mesh.getConnectivity(type, ghost_type).begin(mesh.getNbNodesPerElement(type)) + element;
+ mesh.getConnectivity(type, ghost_type)
+ .begin(mesh.getNbNodesPerElement(type)) +
+ element;
const Vector<UInt> & conn = *it;
- for (UInt i = 0; i < conn.size(); ++i) addNode(conn[i], check_for_duplicate);
+ for (UInt i = 0; i < conn.size(); ++i)
+ addNode(conn[i], check_for_duplicate);
}
}
/* -------------------------------------------------------------------------- */
inline void ElementGroup::addNode(UInt node_id, bool check_for_duplicate) {
node_group.add(node_id, check_for_duplicate);
}
/* -------------------------------------------------------------------------- */
inline void ElementGroup::removeNode(UInt node_id) {
node_group.remove(node_id);
}
/* -------------------------------------------------------------------------- */
inline void ElementGroup::addElement(const ElementType & elem_type,
- UInt elem_id,
- const GhostType & ghost_type) {
- if(!(elements.exists(elem_type, ghost_type))) {
+ UInt elem_id,
+ const GhostType & ghost_type) {
+ if (!(elements.exists(elem_type, ghost_type))) {
elements.alloc(0, 1, elem_type, ghost_type);
}
elements(elem_type, ghost_type).push_back(elem_id);
- this->dimension = UInt(std::max(Int(this->dimension), Int(mesh.getSpatialDimension(elem_type))));
-}
-
-/* -------------------------------------------------------------------------- */
-inline UInt ElementGroup::getNbNodes() const {
- return node_group.getSize();
+ this->dimension = UInt(
+ std::max(Int(this->dimension), Int(mesh.getSpatialDimension(elem_type))));
}
/* -------------------------------------------------------------------------- */
-inline ElementGroup::const_node_iterator ElementGroup::node_begin() const {
- return node_group.begin();
-}
+inline UInt ElementGroup::getNbNodes() const { return node_group.getSize(); }
/* -------------------------------------------------------------------------- */
-inline ElementGroup::const_node_iterator ElementGroup::node_end() const {
- return node_group.end();
-}
-
-/* -------------------------------------------------------------------------- */
-inline ElementGroup::type_iterator ElementGroup::firstType(UInt dim,
- const GhostType & ghost_type,
- const ElementKind & kind) const {
+inline ElementGroup::type_iterator
+ElementGroup::firstType(UInt dim, const GhostType & ghost_type,
+ const ElementKind & kind) const {
return elements.firstType(dim, ghost_type, kind);
}
/* -------------------------------------------------------------------------- */
-inline ElementGroup::type_iterator ElementGroup::lastType(UInt dim,
- const GhostType & ghost_type,
- const ElementKind & kind) const {
+inline ElementGroup::type_iterator
+ElementGroup::lastType(UInt dim, const GhostType & ghost_type,
+ const ElementKind & kind) const {
return elements.lastType(dim, ghost_type, kind);
}
/* -------------------------------------------------------------------------- */
-inline ElementGroup::const_element_iterator ElementGroup::element_begin(const ElementType & type,
- const GhostType & ghost_type) const {
- if(elements.exists(type, ghost_type)) {
+inline ElementGroup::const_element_iterator
+ElementGroup::begin(const ElementType & type,
+ const GhostType & ghost_type) const {
+ if (elements.exists(type, ghost_type)) {
return elements(type, ghost_type).begin();
} else {
return empty_elements.begin();
}
}
/* -------------------------------------------------------------------------- */
-inline ElementGroup::const_element_iterator ElementGroup::element_end(const ElementType & type,
- const GhostType & ghost_type) const {
- if(elements.exists(type, ghost_type)) {
+inline ElementGroup::const_element_iterator
+ElementGroup::end(const ElementType & type,
+ const GhostType & ghost_type) const {
+ if (elements.exists(type, ghost_type)) {
return elements(type, ghost_type).end();
} else {
return empty_elements.end();
}
-
}
/* -------------------------------------------------------------------------- */
-} // akantu
+} // namespace akantu
+
+#endif /* __AKANTU_ELEMENT_GROUP_INLINE_IMPL_CC__ */
diff --git a/src/mesh/element_type_map.cc b/src/mesh/element_type_map.cc
index 3aad70e2e..10ed4c342 100644
--- a/src/mesh/element_type_map.cc
+++ b/src/mesh/element_type_map.cc
@@ -1,50 +1,59 @@
/**
* @file element_type_map.cc
*
* @author Nicolas Richart
*
* @date creation Tue Jun 27 2017
*
* @brief A Documented file.
*
* @section LICENSE
*
* Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#include "mesh.hh"
#include "fe_engine.hh"
+#include "mesh.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
FEEngineElementTypeMapArrayInializer::FEEngineElementTypeMapArrayInializer(
- const FEEngine & fe_engine, UInt spatial_dimension,
- UInt nb_component, const GhostType & ghost_type,
- const ElementKind & element_kind)
- : MeshElementTypeMapArrayInializer(fe_engine.getMesh(), spatial_dimension,
- nb_component, ghost_type, element_kind,
- true, false),
- fe_engine(fe_engine) {}
+ const FEEngine & fe_engine, UInt nb_component, UInt spatial_dimension,
+ const GhostType & ghost_type, const ElementKind & element_kind)
+ : MeshElementTypeMapArrayInializer(
+ fe_engine.getMesh(),
+ nb_component,
+ spatial_dimension == UInt(-2)
+ ? fe_engine.getMesh().getSpatialDimension()
+ : spatial_dimension,
+ ghost_type, element_kind, true, false),
+ fe_engine(fe_engine) {}
-UInt FEEngineElementTypeMapArrayInializer::size(const ElementType & type) const {
+UInt FEEngineElementTypeMapArrayInializer::size(
+ const ElementType & type) const {
return MeshElementTypeMapArrayInializer::size(type) *
- fe_engine.getNbIntegrationPoints(type, this->ghost_type);
+ fe_engine.getNbIntegrationPoints(type, this->ghost_type);
}
-} // akantu
+FEEngineElementTypeMapArrayInializer::ElementTypesIteratorHelper
+FEEngineElementTypeMapArrayInializer::elementTypes() const {
+ return this->fe_engine.elementTypes(spatial_dimension, ghost_type,
+ element_kind);
+}
+} // namespace akantu
diff --git a/src/mesh/element_type_map.hh b/src/mesh/element_type_map.hh
index 141edba25..438683f5c 100644
--- a/src/mesh/element_type_map.hh
+++ b/src/mesh/element_type_map.hh
@@ -1,394 +1,391 @@
/**
* @file element_type_map.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Aug 31 2011
* @date last modification: Fri Oct 02 2015
*
* @brief storage class by element type
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
* Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
* Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_memory.hh"
#include "aka_named_argument.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_ELEMENT_TYPE_MAP_HH__
#define __AKANTU_ELEMENT_TYPE_MAP_HH__
namespace akantu {
class FEEngine;
} // namespace akantu
namespace akantu {
template <class Stored, typename SupportType = ElementType>
class ElementTypeMap;
/* -------------------------------------------------------------------------- */
/* ElementTypeMapBase */
/* -------------------------------------------------------------------------- */
/// Common non templated base class for the ElementTypeMap class
class ElementTypeMapBase {
public:
virtual ~ElementTypeMapBase(){};
};
/* -------------------------------------------------------------------------- */
/* ElementTypeMap */
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
class ElementTypeMap : public ElementTypeMapBase {
public:
ElementTypeMap();
~ElementTypeMap();
inline static std::string printType(const SupportType & type,
const GhostType & ghost_type);
/*! Tests whether a type is present in the object
* @param type the type to check for
* @param ghost_type optional: by default, the data map for non-ghost
* elements is searched
* @return true if the type is present. */
inline bool exists(const SupportType & type,
const GhostType & ghost_type = _not_ghost) const;
/*! get the stored data corresponding to a type
* @param type the type to check for
* @param ghost_type optional: by default, the data map for non-ghost
* elements is searched
* @return stored data corresponding to type. */
inline const Stored &
operator()(const SupportType & type,
const GhostType & ghost_type = _not_ghost) const;
/*! get the stored data corresponding to a type
* @param type the type to check for
* @param ghost_type optional: by default, the data map for non-ghost
* elements is searched
* @return stored data corresponding to type. */
inline Stored & operator()(const SupportType & type,
const GhostType & ghost_type = _not_ghost);
/*! insert data of a new type (not yet present) into the map. THIS METHOD IS
* NOT ARRAY SAFE, when using ElementTypeMapArray, use setArray instead
* @param data to insert
* @param type type of data (if this type is already present in the map,
* an exception is thrown).
* @param ghost_type optional: by default, the data map for non-ghost
* elements is searched
* @return stored data corresponding to type. */
inline Stored & operator()(const Stored & insert, const SupportType & type,
const GhostType & ghost_type = _not_ghost);
/// print helper
virtual void printself(std::ostream & stream, int indent = 0) const;
/* ------------------------------------------------------------------------ */
/* Element type Iterator */
/* ------------------------------------------------------------------------ */
/*! iterator allows to iterate over type-data pairs of the map. The interface
* expects the SupportType to be ElementType. */
typedef std::map<SupportType, Stored> DataMap;
class type_iterator
: private std::iterator<std::forward_iterator_tag, const SupportType> {
public:
typedef const SupportType value_type;
typedef const SupportType * pointer;
typedef const SupportType & reference;
protected:
typedef typename ElementTypeMap<Stored>::DataMap::const_iterator
DataMapIterator;
public:
type_iterator(DataMapIterator & list_begin, DataMapIterator & list_end,
UInt dim, ElementKind ek);
type_iterator(const type_iterator & it);
type_iterator() {}
inline reference operator*();
inline reference operator*() const;
inline type_iterator & operator++();
type_iterator operator++(int);
inline bool operator==(const type_iterator & other) const;
inline bool operator!=(const type_iterator & other) const;
type_iterator & operator=(const type_iterator & other);
private:
DataMapIterator list_begin;
DataMapIterator list_end;
UInt dim;
ElementKind kind;
};
/// helper class to use in range for constructions
class ElementTypesIteratorHelper {
public:
using Container = ElementTypeMap<Stored, SupportType>;
using iterator = typename Container::type_iterator;
ElementTypesIteratorHelper(const Container & container,
UInt dim = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_regular)
: container(std::cref(container)), dim(dim), ghost_type(ghost_type),
kind(kind) {}
ElementTypesIteratorHelper(const ElementTypesIteratorHelper &) = default;
ElementTypesIteratorHelper &
operator=(const ElementTypesIteratorHelper &) = default;
ElementTypesIteratorHelper &
operator=(ElementTypesIteratorHelper &&) = default;
iterator begin() {
return container.get().firstType(dim, ghost_type, kind);
}
iterator end() { return container.get().lastType(dim, ghost_type, kind); }
private:
std::reference_wrapper<const Container> container;
UInt dim;
GhostType ghost_type;
ElementKind kind;
};
/// method to create the helper class to use in range for constructs
ElementTypesIteratorHelper elementTypes(UInt dim = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_regular) const;
/*! Get an iterator to the beginning of a subset datamap. This method expects
* the SupportType to be ElementType.
* @param dim optional: iterate over data of dimension dim (e.g. when
* iterating over (surface) facets of a 3D mesh, dim would be 2).
* by default, all dimensions are considered.
* @param ghost_type optional: by default, the data map for non-ghost
* elements is iterated over.
* @param kind optional: the kind of element to search for (see
* aka_common.hh), by default all kinds are considered
* @return an iterator to the first stored data matching the filters
* or an iterator to the end of the map if none match*/
inline type_iterator firstType(UInt dim = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_not_defined) const;
/*! Get an iterator to the end of a subset datamap. This method expects
* the SupportType to be ElementType.
* @param dim optional: iterate over data of dimension dim (e.g. when
* iterating over (surface) facets of a 3D mesh, dim would be 2).
* by default, all dimensions are considered.
* @param ghost_type optional: by default, the data map for non-ghost
* elements is iterated over.
* @param kind optional: the kind of element to search for (see
* aka_common.hh), by default all kinds are considered
* @return an iterator to the last stored data matching the filters
* or an iterator to the end of the map if none match */
inline type_iterator lastType(UInt dim = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_not_defined) const;
protected:
/*! Direct access to the underlying data map. for internal use by daughter
* classes only
* @param ghost_type whether to return the data map or the ghost_data map
* @return the raw map */
inline DataMap & getData(GhostType ghost_type);
/*! Direct access to the underlying data map. for internal use by daughter
* classes only
* @param ghost_type whether to return the data map or the ghost_data map
* @return the raw map */
inline const DataMap & getData(GhostType ghost_type) const;
/* ------------------------------------------------------------------------ */
protected:
DataMap data;
DataMap ghost_data;
};
/* -------------------------------------------------------------------------- */
/* Some typedefs */
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
class ElementTypeMapArray : public ElementTypeMap<Array<T> *, SupportType>,
public Memory {
public:
typedef T type;
typedef Array<T> array_type;
protected:
typedef ElementTypeMap<Array<T> *, SupportType> parent;
typedef typename parent::DataMap DataMap;
private:
private:
/// standard assigment (copy) operator
void operator=(const ElementTypeMap<T, SupportType> &){};
public:
- typedef typename parent::type_iterator type_iterator;
+ using type_iterator = typename parent::type_iterator;
/*! Constructor
* @param id optional: identifier (string)
* @param parent_id optional: parent identifier. for organizational purposes
* only
* @param memory_id optional: choose a specific memory, defaults to memory 0
*/
ElementTypeMapArray(const ID & id = "by_element_type_array",
const ID & parent_id = "no_parent",
const MemoryID & memory_id = 0)
: parent(), Memory(parent_id + ":" + id, memory_id), name(id){};
/*! allocate memory for a new array
* @param size number of tuples of the new array
* @param nb_component tuple size
* @param type the type under which the array is indexed in the map
* @param ghost_type whether to add the field to the data map or the
* ghost_data map
* @return a reference to the allocated array */
inline Array<T> & alloc(UInt size, UInt nb_component,
const SupportType & type,
const GhostType & ghost_type,
const T & default_value = T());
/*! allocate memory for a new array in both the data and the ghost_data map
* @param size number of tuples of the new array
* @param nb_component tuple size
* @param type the type under which the array is indexed in the map*/
inline void alloc(UInt size, UInt nb_component, const SupportType & type,
const T & default_value = T());
/* get a reference to the array of certain type
* @param type data filed under type is returned
* @param ghost_type optional: by default the non-ghost map is searched
* @return a reference to the array */
inline const Array<T> &
operator()(const SupportType & type,
const GhostType & ghost_type = _not_ghost) const;
/* get a reference to the array of certain type
* @param type data filed under type is returned
* @param ghost_type optional: by default the non-ghost map is searched
* @return a const reference to the array */
inline Array<T> & operator()(const SupportType & type,
const GhostType & ghost_type = _not_ghost);
/*! insert data of a new type (not yet present) into the map.
* @param type type of data (if this type is already present in the map,
* an exception is thrown).
* @param ghost_type optional: by default, the data map for non-ghost
* elements is searched
* @param vect the vector to include into the map
* @return stored data corresponding to type. */
inline void setArray(const SupportType & type, const GhostType & ghost_type,
const Array<T> & vect);
/*! frees all memory related to the data*/
inline void free();
/*! set all values in the ElementTypeMap to zero*/
inline void clear();
/*! deletes and reorders entries in the stored arrays
* @param new_numbering a ElementTypeMapArray of new indices. UInt(-1)
* indicates
* deleted entries. */
inline void
onElementsRemoved(const ElementTypeMapArray<UInt> & new_numbering);
/// text output helper
virtual void printself(std::ostream & stream, int indent = 0) const;
/*! set the id
* @param id the new name
*/
inline void setID(const ID & id) { this->id = id; }
ElementTypeMap<UInt>
getNbComponents(UInt dim = _all_dimensions, GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_not_defined) const {
ElementTypeMap<UInt> nb_components;
- type_iterator tit = this->firstType(dim, ghost_type, kind);
- type_iterator end = this->lastType(dim, ghost_type, kind);
-
- while (tit != end) {
- UInt nb_comp = (*this)(*tit, ghost_type).getNbComponent();
- nb_components(*tit, ghost_type) = nb_comp;
- ++tit;
+ for (auto & type : this->elementTypes(dim, ghost_type, kind)) {
+ UInt nb_comp = (*this)(type, ghost_type).getNbComponent();
+ nb_components(type, ghost_type) = nb_comp;
}
+
return nb_components;
}
/* ------------------------------------------------------------------------ */
/* more evolved allocators */
/* ------------------------------------------------------------------------ */
public:
/// initialize the arrays in accordance to a functor
template <class Func>
void initialize(const Func & f, const T & default_value = T());
/// initialize with sizes and number of components in accordance of a mesh
/// content
template <typename... pack>
void initialize(const Mesh & mesh, pack &&... _pack);
/// initialize with sizes and number of components in accordance of a fe
/// engine content (aka integration points)
template <typename... pack>
void initialize(const FEEngine & fe_engine, pack &&... _pack);
/* ------------------------------------------------------------------------ */
/* Accesssors */
/* ------------------------------------------------------------------------ */
public:
/// get the name of the internal field
AKANTU_GET_MACRO(Name, name, ID);
private:
ElementTypeMapArray operator=(__attribute__((unused))
const ElementTypeMapArray & other){};
/// name of the elment type map: e.g. connectivity, grad_u
ID name;
};
/// to store data Array<Real> by element type
typedef ElementTypeMapArray<Real> ElementTypeMapReal;
/// to store data Array<Int> by element type
typedef ElementTypeMapArray<Int> ElementTypeMapInt;
/// to store data Array<UInt> by element type
typedef ElementTypeMapArray<UInt, ElementType> ElementTypeMapUInt;
/// Map of data of type UInt stored in a mesh
typedef std::map<std::string, Array<UInt> *> UIntDataMap;
typedef ElementTypeMap<UIntDataMap, ElementType> ElementTypeMapUIntDataMap;
} // namespace akantu
#endif /* __AKANTU_ELEMENT_TYPE_MAP_HH__ */
diff --git a/src/mesh/element_type_map_tmpl.hh b/src/mesh/element_type_map_tmpl.hh
index 6a6e038e3..91735c2a0 100644
--- a/src/mesh/element_type_map_tmpl.hh
+++ b/src/mesh/element_type_map_tmpl.hh
@@ -1,623 +1,621 @@
/**
* @file element_type_map_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Aug 31 2011
* @date last modification: Fri Oct 02 2015
*
* @brief implementation of template functions of the ElementTypeMap and
* ElementTypeMapArray classes
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
* Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
* Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_type_map.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
+#include "element_type_conversion.hh"
+/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_ELEMENT_TYPE_MAP_TMPL_HH__
#define __AKANTU_ELEMENT_TYPE_MAP_TMPL_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
-/* ElementTypeMap */
+/* ElementTypeMap */
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline std::string
ElementTypeMap<Stored, SupportType>::printType(const SupportType & type,
const GhostType & ghost_type) {
std::stringstream sstr;
sstr << "(" << ghost_type << ":" << type << ")";
return sstr.str();
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline bool ElementTypeMap<Stored, SupportType>::exists(
const SupportType & type, const GhostType & ghost_type) const {
return this->getData(ghost_type).find(type) !=
this->getData(ghost_type).end();
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline const Stored & ElementTypeMap<Stored, SupportType>::
operator()(const SupportType & type, const GhostType & ghost_type) const {
typename DataMap::const_iterator it = this->getData(ghost_type).find(type);
if (it == this->getData(ghost_type).end())
AKANTU_SILENT_EXCEPTION("No element of type "
<< ElementTypeMap::printType(type, ghost_type)
<< " in this ElementTypeMap<"
<< debug::demangle(typeid(Stored).name())
<< "> class");
return it->second;
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline Stored & ElementTypeMap<Stored, SupportType>::
operator()(const SupportType & type, const GhostType & ghost_type) {
return this->getData(ghost_type)[type];
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline Stored & ElementTypeMap<Stored, SupportType>::
operator()(const Stored & insert, const SupportType & type,
const GhostType & ghost_type) {
typename DataMap::iterator it = this->getData(ghost_type).find(type);
if (it != this->getData(ghost_type).end()) {
AKANTU_SILENT_EXCEPTION("Element of type "
<< ElementTypeMap::printType(type, ghost_type)
<< " already in this ElementTypeMap<"
<< debug::demangle(typeid(Stored).name())
<< "> class");
} else {
DataMap & data = this->getData(ghost_type);
const std::pair<typename DataMap::iterator, bool> & res =
data.insert(std::pair<ElementType, Stored>(type, insert));
it = res.first;
}
return it->second;
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline typename ElementTypeMap<Stored, SupportType>::DataMap &
ElementTypeMap<Stored, SupportType>::getData(GhostType ghost_type) {
if (ghost_type == _not_ghost)
return data;
else
return ghost_data;
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline const typename ElementTypeMap<Stored, SupportType>::DataMap &
ElementTypeMap<Stored, SupportType>::getData(GhostType ghost_type) const {
if (ghost_type == _not_ghost)
return data;
else
return ghost_data;
}
/* -------------------------------------------------------------------------- */
/// Works only if stored is a pointer to a class with a printself method
template <class Stored, typename SupportType>
void ElementTypeMap<Stored, SupportType>::printself(std::ostream & stream,
int indent) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "ElementTypeMap<" << debug::demangle(typeid(Stored).name())
<< "> [" << std::endl;
- for (UInt g = _not_ghost; g <= _ghost; ++g) {
- GhostType gt = (GhostType)g;
-
+ for (auto gt : ghost_types) {
const DataMap & data = getData(gt);
- typename DataMap::const_iterator it;
- for (it = data.begin(); it != data.end(); ++it) {
- stream << space << space << ElementTypeMap::printType(it->first, gt)
+ for (auto & pair : data) {
+ stream << space << space << ElementTypeMap::printType(pair.first, gt)
<< std::endl;
}
}
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
ElementTypeMap<Stored, SupportType>::ElementTypeMap() {
AKANTU_DEBUG_IN();
// std::stringstream sstr;
// if(parent_id != "") sstr << parent_id << ":";
// sstr << id;
// this->id = sstr.str();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
ElementTypeMap<Stored, SupportType>::~ElementTypeMap() {}
/* -------------------------------------------------------------------------- */
/* ElementTypeMapArray */
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
inline Array<T> & ElementTypeMapArray<T, SupportType>::alloc(
UInt size, UInt nb_component, const SupportType & type,
const GhostType & ghost_type, const T & default_value) {
std::string ghost_id = "";
if (ghost_type == _ghost)
ghost_id = ":ghost";
Array<T> * tmp;
typename ElementTypeMapArray<T, SupportType>::DataMap::iterator it =
this->getData(ghost_type).find(type);
if (it == this->getData(ghost_type).end()) {
std::stringstream sstr;
sstr << this->id << ":" << type << ghost_id;
tmp = &(Memory::alloc<T>(sstr.str(), size, nb_component, default_value));
std::stringstream sstrg;
sstrg << ghost_type;
// tmp->setTag(sstrg.str());
this->getData(ghost_type)[type] = tmp;
} else {
AKANTU_DEBUG_INFO(
"The vector "
<< this->id << this->printType(type, ghost_type)
<< " already exists, it is resized instead of allocated.");
tmp = it->second;
it->second->resize(size);
}
return *tmp;
}
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
inline void
ElementTypeMapArray<T, SupportType>::alloc(UInt size, UInt nb_component,
const SupportType & type,
const T & default_value) {
this->alloc(size, nb_component, type, _not_ghost, default_value);
this->alloc(size, nb_component, type, _ghost, default_value);
}
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
inline void ElementTypeMapArray<T, SupportType>::free() {
AKANTU_DEBUG_IN();
- for (UInt g = _not_ghost; g <= _ghost; ++g) {
- GhostType gt = (GhostType)g;
-
+ for (auto gt : ghost_types) {
DataMap & data = this->getData(gt);
- typename DataMap::const_iterator it;
- for (it = data.begin(); it != data.end(); ++it) {
- dealloc(it->second->getID());
+ for (auto & pair : data) {
+ dealloc(pair.second->getID());
}
data.clear();
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
inline void ElementTypeMapArray<T, SupportType>::clear() {
- for (UInt g = _not_ghost; g <= _ghost; ++g) {
- GhostType gt = (GhostType)g;
-
+ for (auto gt : ghost_types) {
DataMap & data = this->getData(gt);
- typename DataMap::const_iterator it;
- for (it = data.begin(); it != data.end(); ++it) {
- it->second->clear();
+ for (auto & vect : data) {
+ vect.second->clear();
}
}
}
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
inline const Array<T> & ElementTypeMapArray<T, SupportType>::
operator()(const SupportType & type, const GhostType & ghost_type) const {
typename ElementTypeMapArray<T, SupportType>::DataMap::const_iterator it =
this->getData(ghost_type).find(type);
if (it == this->getData(ghost_type).end())
AKANTU_SILENT_EXCEPTION("No element of type "
<< ElementTypeMapArray::printType(type, ghost_type)
<< " in this const ElementTypeMapArray<"
<< debug::demangle(typeid(T).name()) << "> class(\""
<< this->id << "\")");
return *(it->second);
}
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
inline Array<T> & ElementTypeMapArray<T, SupportType>::
operator()(const SupportType & type, const GhostType & ghost_type) {
typename ElementTypeMapArray<T, SupportType>::DataMap::iterator it =
this->getData(ghost_type).find(type);
if (it == this->getData(ghost_type).end())
AKANTU_SILENT_EXCEPTION("No element of type "
<< ElementTypeMapArray::printType(type, ghost_type)
<< " in this ElementTypeMapArray<"
<< debug::demangle(typeid(T).name())
<< "> class (\"" << this->id << "\")");
return *(it->second);
}
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
inline void
ElementTypeMapArray<T, SupportType>::setArray(const SupportType & type,
const GhostType & ghost_type,
const Array<T> & vect) {
typename ElementTypeMapArray<T, SupportType>::DataMap::iterator it =
this->getData(ghost_type).find(type);
if (AKANTU_DEBUG_TEST(dblWarning) && it != this->getData(ghost_type).end() &&
it->second != &vect) {
AKANTU_DEBUG_WARNING(
"The Array "
<< this->printType(type, ghost_type)
<< " is already registred, this call can lead to a memory leak.");
}
this->getData(ghost_type)[type] = &(const_cast<Array<T> &>(vect));
}
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
inline void ElementTypeMapArray<T, SupportType>::onElementsRemoved(
const ElementTypeMapArray<UInt> & new_numbering) {
- for (UInt g = _not_ghost; g <= _ghost; ++g) {
- GhostType gt = (GhostType)g;
- ElementTypeMapArray<UInt>::type_iterator it =
- new_numbering.firstType(_all_dimensions, gt, _ek_not_defined);
- ElementTypeMapArray<UInt>::type_iterator end =
- new_numbering.lastType(_all_dimensions, gt, _ek_not_defined);
- for (; it != end; ++it) {
- SupportType type = *it;
- if (this->exists(type, gt)) {
- const Array<UInt> & renumbering = new_numbering(type, gt);
+ for (auto gt : ghost_types) {
+ for (auto & type :
+ new_numbering.elementTypes(_all_dimensions, gt, _ek_not_defined)) {
+ SupportType support_type = convertType<ElementType, SupportType>(type);
+ if (this->exists(support_type, gt)) {
+ const auto & renumbering = new_numbering(type, gt);
if (renumbering.getSize() == 0)
continue;
- Array<T> & vect = this->operator()(type, gt);
- UInt nb_component = vect.getNbComponent();
+
+ auto & vect = this->operator()(support_type, gt);
+ auto nb_component = vect.getNbComponent();
Array<T> tmp(renumbering.getSize(), nb_component);
UInt new_size = 0;
+
for (UInt i = 0; i < vect.getSize(); ++i) {
UInt new_i = renumbering(i);
if (new_i != UInt(-1)) {
memcpy(tmp.storage() + new_i * nb_component,
vect.storage() + i * nb_component, nb_component * sizeof(T));
++new_size;
}
}
tmp.resize(new_size);
vect.copy(tmp);
}
}
}
}
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
void ElementTypeMapArray<T, SupportType>::printself(std::ostream & stream,
int indent) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "ElementTypeMapArray<" << debug::demangle(typeid(T).name())
<< "> [" << std::endl;
for (UInt g = _not_ghost; g <= _ghost; ++g) {
GhostType gt = (GhostType)g;
const DataMap & data = this->getData(gt);
typename DataMap::const_iterator it;
for (it = data.begin(); it != data.end(); ++it) {
stream << space << space << ElementTypeMapArray::printType(it->first, gt)
<< " [" << std::endl;
it->second->printself(stream, indent + 3);
stream << space << space << " ]" << std::endl;
}
}
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
/* SupportType Iterator */
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
ElementTypeMap<Stored, SupportType>::type_iterator::type_iterator(
DataMapIterator & list_begin, DataMapIterator & list_end, UInt dim,
ElementKind ek)
: list_begin(list_begin), list_end(list_end), dim(dim), kind(ek) {}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
ElementTypeMap<Stored, SupportType>::type_iterator::type_iterator(
const type_iterator & it)
: list_begin(it.list_begin), list_end(it.list_end), dim(it.dim),
kind(it.kind) {}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
typename ElementTypeMap<Stored, SupportType>::type_iterator &
ElementTypeMap<Stored, SupportType>::type_iterator::
operator=(const type_iterator & it) {
if (this != &it) {
list_begin = it.list_begin;
list_end = it.list_end;
dim = it.dim;
kind = it.kind;
}
return *this;
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline typename ElementTypeMap<Stored, SupportType>::type_iterator::reference
ElementTypeMap<Stored, SupportType>::type_iterator::operator*() {
return list_begin->first;
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline typename ElementTypeMap<Stored, SupportType>::type_iterator::reference
ElementTypeMap<Stored, SupportType>::type_iterator::operator*() const {
return list_begin->first;
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline typename ElementTypeMap<Stored, SupportType>::type_iterator &
ElementTypeMap<Stored, SupportType>::type_iterator::operator++() {
++list_begin;
while ((list_begin != list_end) &&
(((dim != _all_dimensions) &&
(dim != Mesh::getSpatialDimension(list_begin->first))) ||
((kind != _ek_not_defined) &&
(kind != Mesh::getKind(list_begin->first)))))
++list_begin;
return *this;
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
typename ElementTypeMap<Stored, SupportType>::type_iterator
ElementTypeMap<Stored, SupportType>::type_iterator::operator++(int) {
type_iterator tmp(*this);
operator++();
return tmp;
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline bool ElementTypeMap<Stored, SupportType>::type_iterator::
operator==(const type_iterator & other) const {
return this->list_begin == other.list_begin;
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline bool ElementTypeMap<Stored, SupportType>::type_iterator::
operator!=(const type_iterator & other) const {
return this->list_begin != other.list_begin;
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
typename ElementTypeMap<Stored, SupportType>::ElementTypesIteratorHelper
ElementTypeMap<Stored, SupportType>::elementTypes(UInt dim,
GhostType ghost_type,
ElementKind kind) const {
return ElementTypesIteratorHelper(*this, dim, ghost_type, kind);
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline typename ElementTypeMap<Stored, SupportType>::type_iterator
ElementTypeMap<Stored, SupportType>::firstType(UInt dim, GhostType ghost_type,
ElementKind kind) const {
typename DataMap::const_iterator b, e;
b = getData(ghost_type).begin();
e = getData(ghost_type).end();
// loop until the first valid type
while ((b != e) &&
(((dim != _all_dimensions) &&
(dim != Mesh::getSpatialDimension(b->first))) ||
((kind != _ek_not_defined) && (kind != Mesh::getKind(b->first)))))
++b;
return typename ElementTypeMap<Stored, SupportType>::type_iterator(b, e, dim,
kind);
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline typename ElementTypeMap<Stored, SupportType>::type_iterator
ElementTypeMap<Stored, SupportType>::lastType(UInt dim, GhostType ghost_type,
ElementKind kind) const {
typename DataMap::const_iterator e;
e = getData(ghost_type).end();
return typename ElementTypeMap<Stored, SupportType>::type_iterator(e, e, dim,
kind);
}
/* -------------------------------------------------------------------------- */
/// standard output stream operator
template <class Stored, typename SupportType>
inline std::ostream &
operator<<(std::ostream & stream,
const ElementTypeMap<Stored, SupportType> & _this) {
_this.printself(stream);
return stream;
}
/* -------------------------------------------------------------------------- */
class ElementTypeMapArrayInializer {
public:
ElementTypeMapArrayInializer(UInt spatial_dimension = _all_dimensions,
UInt nb_component = 1,
const GhostType & ghost_type = _not_ghost,
const ElementKind & element_kind = _ek_regular)
: spatial_dimension(spatial_dimension), nb_component(nb_component),
ghost_type(ghost_type), element_kind(element_kind) {}
const GhostType & ghostType() const { return ghost_type; }
protected:
UInt spatial_dimension;
UInt nb_component;
GhostType ghost_type;
ElementKind element_kind;
};
/* -------------------------------------------------------------------------- */
class MeshElementTypeMapArrayInializer : public ElementTypeMapArrayInializer {
public:
MeshElementTypeMapArrayInializer(
- const Mesh & mesh, UInt spatial_dimension = _all_dimensions,
- UInt nb_component = 1, const GhostType & ghost_type = _not_ghost,
+ const Mesh & mesh, UInt nb_component = 1,
+ UInt spatial_dimension = _all_dimensions,
+ const GhostType & ghost_type = _not_ghost,
const ElementKind & element_kind = _ek_regular,
bool with_nb_element = false, bool with_nb_nodes_per_element = false)
: ElementTypeMapArrayInializer(spatial_dimension, nb_component,
ghost_type, element_kind),
mesh(mesh), with_nb_element(with_nb_element),
with_nb_nodes_per_element(with_nb_nodes_per_element) {}
decltype(auto) elementTypes() const {
return mesh.elementTypes(this->spatial_dimension, this->ghost_type,
this->element_kind);
}
virtual UInt size(const ElementType & type) const {
if (with_nb_element)
return mesh.getNbElement(type, this->ghost_type);
return 0;
}
UInt nbComponent(const ElementType & type) const {
if (with_nb_nodes_per_element)
return (this->nb_component * mesh.getNbNodesPerElement(type));
return this->nb_component;
}
protected:
const Mesh & mesh;
bool with_nb_element;
bool with_nb_nodes_per_element;
};
/* -------------------------------------------------------------------------- */
class FEEngineElementTypeMapArrayInializer
: public MeshElementTypeMapArrayInializer {
public:
FEEngineElementTypeMapArrayInializer(
- const FEEngine & fe_engine, UInt spatial_dimension = _all_dimensions,
- UInt nb_component = 1, const GhostType & ghost_type = _not_ghost,
+ const FEEngine & fe_engine, UInt nb_component = 1,
+ UInt spatial_dimension = _all_dimensions,
+ const GhostType & ghost_type = _not_ghost,
const ElementKind & element_kind = _ek_regular);
UInt size(const ElementType & type) const override;
+ using ElementTypesIteratorHelper =
+ ElementTypeMapArray<Real, ElementType>::ElementTypesIteratorHelper;
+
+ ElementTypesIteratorHelper elementTypes() const;
+
protected:
const FEEngine & fe_engine;
};
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
template <class Func>
void ElementTypeMapArray<T, SupportType>::initialize(const Func & f,
const T & default_value) {
for (auto & type : f.elementTypes()) {
if (not this->exists(type, f.ghostType()))
this->alloc(f.size(type), f.nbComponent(type), type, f.ghostType(),
default_value);
}
}
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
template <typename... pack>
void ElementTypeMapArray<T, SupportType>::initialize(const Mesh & mesh,
pack &&... _pack) {
GhostType requested_ghost_type = OPTIONAL_NAMED_ARG(ghost_type, _casper);
bool all_ghost_types = requested_ghost_type == _casper;
for (auto ghost_type : ghost_types) {
if ((not(ghost_type == requested_ghost_type)) and (not all_ghost_types))
continue;
this->initialize(
MeshElementTypeMapArrayInializer(
mesh, OPTIONAL_NAMED_ARG(nb_component, 1),
OPTIONAL_NAMED_ARG(spatial_dimension, mesh.getSpatialDimension()),
ghost_type, OPTIONAL_NAMED_ARG(element_kind, _ek_regular),
OPTIONAL_NAMED_ARG(with_nb_element, false),
OPTIONAL_NAMED_ARG(with_nb_nodes_per_element, false)),
OPTIONAL_NAMED_ARG(default_value, T()));
}
}
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
template <typename... pack>
void ElementTypeMapArray<T, SupportType>::initialize(const FEEngine & fe_engine,
pack &&... _pack) {
bool all_ghost_types = OPTIONAL_NAMED_ARG(all_ghost_types, true);
GhostType requested_ghost_type = OPTIONAL_NAMED_ARG(ghost_type, _not_ghost);
for (auto ghost_type : ghost_types) {
if ((not(ghost_type == requested_ghost_type)) and (not all_ghost_types))
continue;
this->initialize(FEEngineElementTypeMapArrayInializer(
- fe_engine,
- OPTIONAL_NAMED_ARG(spatial_dimension, _all_dimensions),
- OPTIONAL_NAMED_ARG(nb_component, 1), ghost_type,
+ fe_engine, OPTIONAL_NAMED_ARG(nb_component, 1),
+ OPTIONAL_NAMED_ARG(spatial_dimension, UInt(-2)),
+ ghost_type,
OPTIONAL_NAMED_ARG(element_kind, _ek_regular)),
OPTIONAL_NAMED_ARG(default_value, T()));
}
}
} // namespace akantu
#endif /* __AKANTU_ELEMENT_TYPE_MAP_TMPL_HH__ */
diff --git a/src/mesh/group_manager.cc b/src/mesh/group_manager.cc
index 18afdb476..f9517336a 100644
--- a/src/mesh/group_manager.cc
+++ b/src/mesh/group_manager.cc
@@ -1,1030 +1,1041 @@
/**
* @file group_manager.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@gmail.com>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Nov 13 2013
* @date last modification: Mon Aug 17 2015
*
* @brief Stores information about ElementGroup and NodeGroup
*
* @section LICENSE
*
* Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "group_manager.hh"
#include "aka_csr.hh"
#include "data_accessor.hh"
#include "element_group.hh"
#include "element_synchronizer.hh"
#include "mesh.hh"
+#include "mesh_accessor.hh"
#include "mesh_utils.hh"
#include "node_group.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <iterator>
#include <list>
#include <numeric>
#include <queue>
#include <sstream>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
GroupManager::GroupManager(const Mesh & mesh, const ID & id,
const MemoryID & mem_id)
: id(id), memory_id(mem_id), mesh(mesh) {
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
GroupManager::~GroupManager() {
auto eit = element_groups.begin();
auto eend = element_groups.end();
for (; eit != eend; ++eit)
delete (eit->second);
auto nit = node_groups.begin();
auto nend = node_groups.end();
for (; nit != nend; ++nit)
delete (nit->second);
}
/* -------------------------------------------------------------------------- */
NodeGroup & GroupManager::createNodeGroup(const std::string & group_name,
bool replace_group) {
AKANTU_DEBUG_IN();
auto it = node_groups.find(group_name);
if (it != node_groups.end()) {
if (replace_group) {
it->second->empty();
AKANTU_DEBUG_OUT();
return *(it->second);
} else
AKANTU_EXCEPTION(
"Trying to create a node group that already exists:" << group_name);
}
std::stringstream sstr;
sstr << this->id << ":" << group_name << "_node_group";
NodeGroup * node_group =
new NodeGroup(group_name, mesh, sstr.str(), memory_id);
node_groups[group_name] = node_group;
AKANTU_DEBUG_OUT();
return *node_group;
}
/* -------------------------------------------------------------------------- */
template <typename T>
NodeGroup &
GroupManager::createFilteredNodeGroup(const std::string & group_name,
const NodeGroup & source_node_group,
T & filter) {
AKANTU_DEBUG_IN();
NodeGroup & node_group = this->createNodeGroup(group_name);
node_group.append(source_node_group);
if (T::type == FilterFunctor::_node_filter_functor) {
node_group.applyNodeFilter(filter);
} else {
AKANTU_DEBUG_ERROR("ElementFilter cannot be applied to NodeGroup yet."
<< " Needs to be implemented.");
}
AKANTU_DEBUG_OUT();
return node_group;
}
/* -------------------------------------------------------------------------- */
void GroupManager::destroyNodeGroup(const std::string & group_name) {
AKANTU_DEBUG_IN();
NodeGroups::iterator nit = node_groups.find(group_name);
NodeGroups::iterator nend = node_groups.end();
if (nit != nend) {
delete (nit->second);
node_groups.erase(nit);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
ElementGroup & GroupManager::createElementGroup(const std::string & group_name,
UInt dimension,
bool replace_group) {
AKANTU_DEBUG_IN();
NodeGroup & new_node_group =
createNodeGroup(group_name + "_nodes", replace_group);
auto it = element_groups.find(group_name);
if (it != element_groups.end()) {
if (replace_group) {
it->second->empty();
AKANTU_DEBUG_OUT();
return *(it->second);
} else
AKANTU_EXCEPTION("Trying to create a element group that already exists:"
<< group_name);
}
std::stringstream sstr;
sstr << this->id << ":" << group_name << "_element_group";
ElementGroup * element_group = new ElementGroup(
group_name, mesh, new_node_group, dimension, sstr.str(), memory_id);
std::stringstream sstr_nodes;
sstr_nodes << group_name << "_nodes";
node_groups[sstr_nodes.str()] = &new_node_group;
element_groups[group_name] = element_group;
AKANTU_DEBUG_OUT();
return *element_group;
}
/* -------------------------------------------------------------------------- */
void GroupManager::destroyElementGroup(const std::string & group_name,
bool destroy_node_group) {
AKANTU_DEBUG_IN();
auto eit = element_groups.find(group_name);
auto eend = element_groups.end();
if (eit != eend) {
if (destroy_node_group)
destroyNodeGroup(eit->second->getNodeGroup().getName());
delete (eit->second);
element_groups.erase(eit);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void GroupManager::destroyAllElementGroups(bool destroy_node_groups) {
AKANTU_DEBUG_IN();
auto eit = element_groups.begin();
auto eend = element_groups.end();
for (; eit != eend; ++eit) {
if (destroy_node_groups)
destroyNodeGroup(eit->second->getNodeGroup().getName());
delete (eit->second);
}
element_groups.clear();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
ElementGroup & GroupManager::createElementGroup(const std::string & group_name,
UInt dimension,
NodeGroup & node_group) {
AKANTU_DEBUG_IN();
if (element_groups.find(group_name) != element_groups.end())
AKANTU_EXCEPTION(
"Trying to create a element group that already exists:" << group_name);
ElementGroup * element_group =
new ElementGroup(group_name, mesh, node_group, dimension,
id + ":" + group_name + "_element_group", memory_id);
element_groups[group_name] = element_group;
AKANTU_DEBUG_OUT();
return *element_group;
}
/* -------------------------------------------------------------------------- */
template <typename T>
ElementGroup & GroupManager::createFilteredElementGroup(
const std::string & group_name, UInt dimension,
const NodeGroup & node_group, T & filter) {
AKANTU_DEBUG_IN();
ElementGroup * element_group = NULL;
if (T::type == FilterFunctor::_node_filter_functor) {
NodeGroup & filtered_node_group = this->createFilteredNodeGroup(
group_name + "_nodes", node_group, filter);
element_group =
&(this->createElementGroup(group_name, dimension, filtered_node_group));
} else if (T::type == FilterFunctor::_element_filter_functor) {
AKANTU_DEBUG_ERROR(
"Cannot handle an ElementFilter yet. Needs to be implemented.");
}
AKANTU_DEBUG_OUT();
return *element_group;
}
/* -------------------------------------------------------------------------- */
class ClusterSynchronizer : public DataAccessor<Element> {
using DistantIDs = std::set<std::pair<UInt, UInt>>;
public:
ClusterSynchronizer(GroupManager & group_manager, UInt element_dimension,
std::string cluster_name_prefix,
ElementTypeMapArray<UInt> & element_to_fragment,
const ElementSynchronizer & element_synchronizer,
UInt nb_cluster)
: group_manager(group_manager), element_dimension(element_dimension),
cluster_name_prefix(cluster_name_prefix),
element_to_fragment(element_to_fragment),
element_synchronizer(element_synchronizer), nb_cluster(nb_cluster) {}
UInt synchronize() {
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
UInt rank = comm.whoAmI();
UInt nb_proc = comm.getNbProc();
/// find starting index to renumber local clusters
Array<UInt> nb_cluster_per_proc(nb_proc);
nb_cluster_per_proc(rank) = nb_cluster;
comm.allGather(nb_cluster_per_proc);
starting_index = std::accumulate(nb_cluster_per_proc.begin(),
nb_cluster_per_proc.begin() + rank, 0);
UInt global_nb_fragment =
std::accumulate(nb_cluster_per_proc.begin() + rank,
nb_cluster_per_proc.end(), starting_index);
/// create the local to distant cluster pairs with neighbors
element_synchronizer.synchronizeOnce(*this, _gst_gm_clusters);
/// count total number of pairs
Array<int> nb_pairs(nb_proc); // This is potentially a bug for more than
// 2**31 pairs, but due to a all gatherv after
// it must be int to match MPI interfaces
nb_pairs(rank) = distant_ids.size();
comm.allGather(nb_pairs);
UInt total_nb_pairs = std::accumulate(nb_pairs.begin(), nb_pairs.end(), 0);
/// generate pairs global array
UInt local_pair_index =
std::accumulate(nb_pairs.storage(), nb_pairs.storage() + rank, 0);
Array<UInt> total_pairs(total_nb_pairs, 2);
for (auto & ids : distant_ids) {
total_pairs(local_pair_index, 0) = ids.first;
total_pairs(local_pair_index, 1) = ids.second;
++local_pair_index;
}
/// communicate pairs to all processors
nb_pairs *= 2;
comm.allGatherV(total_pairs, nb_pairs);
/// renumber clusters
/// generate fragment list
std::vector<std::set<UInt>> global_clusters;
UInt total_nb_cluster = 0;
Array<bool> is_fragment_in_cluster(global_nb_fragment, 1, false);
std::queue<UInt> fragment_check_list;
while (total_pairs.getSize() != 0) {
/// create a new cluster
++total_nb_cluster;
global_clusters.resize(total_nb_cluster);
std::set<UInt> & current_cluster = global_clusters[total_nb_cluster - 1];
UInt first_fragment = total_pairs(0, 0);
UInt second_fragment = total_pairs(0, 1);
total_pairs.erase(0);
fragment_check_list.push(first_fragment);
fragment_check_list.push(second_fragment);
while (!fragment_check_list.empty()) {
UInt current_fragment = fragment_check_list.front();
UInt * total_pairs_end =
total_pairs.storage() + total_pairs.getSize() * 2;
UInt * fragment_found =
std::find(total_pairs.storage(), total_pairs_end, current_fragment);
if (fragment_found != total_pairs_end) {
UInt position = fragment_found - total_pairs.storage();
UInt pair = position / 2;
UInt other_index = (position + 1) % 2;
fragment_check_list.push(total_pairs(pair, other_index));
total_pairs.erase(pair);
} else {
fragment_check_list.pop();
current_cluster.insert(current_fragment);
is_fragment_in_cluster(current_fragment) = true;
}
}
}
/// add to FragmentToCluster all local fragments
for (UInt c = 0; c < global_nb_fragment; ++c) {
if (!is_fragment_in_cluster(c)) {
++total_nb_cluster;
global_clusters.resize(total_nb_cluster);
std::set<UInt> & current_cluster =
global_clusters[total_nb_cluster - 1];
current_cluster.insert(c);
}
}
/// reorganize element groups to match global clusters
for (UInt c = 0; c < global_clusters.size(); ++c) {
/// create new element group corresponding to current cluster
std::stringstream sstr;
sstr << cluster_name_prefix << "_" << c;
ElementGroup & cluster =
group_manager.createElementGroup(sstr.str(), element_dimension, true);
std::set<UInt>::iterator it = global_clusters[c].begin();
std::set<UInt>::iterator end = global_clusters[c].end();
/// append to current element group all fragments that belong to
/// the same cluster if they exist
for (; it != end; ++it) {
Int local_index = *it - starting_index;
if (local_index < 0 || local_index >= Int(nb_cluster))
continue;
std::stringstream tmp_sstr;
tmp_sstr << "tmp_" << cluster_name_prefix << "_" << local_index;
auto eg_it = group_manager.element_group_find(tmp_sstr.str());
AKANTU_DEBUG_ASSERT(eg_it != group_manager.element_group_end(),
"Temporary fragment \"" << tmp_sstr.str()
<< "\" not found");
cluster.append(*(eg_it->second));
group_manager.destroyElementGroup(tmp_sstr.str(), true);
}
}
return total_nb_cluster;
}
private:
/// functions for parallel communications
inline UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const {
if (tag == _gst_gm_clusters)
return elements.getSize() * sizeof(UInt);
return 0;
}
inline void packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const {
if (tag != _gst_gm_clusters)
return;
Array<Element>::const_iterator<> el_it = elements.begin();
Array<Element>::const_iterator<> el_end = elements.end();
for (; el_it != el_end; ++el_it) {
const Element & el = *el_it;
/// for each element pack its global cluster index
buffer << element_to_fragment(el.type, el.ghost_type)(el.element) +
starting_index;
}
}
inline void unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) {
if (tag != _gst_gm_clusters)
return;
Array<Element>::const_iterator<> el_it = elements.begin();
Array<Element>::const_iterator<> el_end = elements.end();
for (; el_it != el_end; ++el_it) {
UInt distant_cluster;
buffer >> distant_cluster;
const Element & el = *el_it;
UInt local_cluster =
element_to_fragment(el.type, el.ghost_type)(el.element) +
starting_index;
distant_ids.insert(std::make_pair(local_cluster, distant_cluster));
}
}
private:
GroupManager & group_manager;
UInt element_dimension;
std::string cluster_name_prefix;
ElementTypeMapArray<UInt> & element_to_fragment;
const ElementSynchronizer & element_synchronizer;
UInt nb_cluster;
DistantIDs distant_ids;
UInt starting_index;
};
/* -------------------------------------------------------------------------- */
/// \todo this function doesn't work in 1D
UInt GroupManager::createBoundaryGroupFromGeometry() {
UInt spatial_dimension = mesh.getSpatialDimension();
return createClusters(spatial_dimension - 1, "boundary");
}
+/* -------------------------------------------------------------------------- */
+UInt GroupManager::createClusters(
+ UInt element_dimension, Mesh & mesh_facets, std::string cluster_name_prefix,
+ const GroupManager::ClusteringFilter & filter) {
+ return createClusters(element_dimension, cluster_name_prefix, filter, mesh_facets);
+}
+
+/* -------------------------------------------------------------------------- */
+UInt GroupManager::createClusters(
+ UInt element_dimension, std::string cluster_name_prefix,
+ const GroupManager::ClusteringFilter & filter) {
+ std::unique_ptr<Mesh> mesh_facets;
+ if (!mesh_facets && element_dimension > 0) {
+ MeshAccessor mesh_accessor(const_cast<Mesh &>(mesh));
+ mesh_facets = std::make_unique<Mesh>(mesh.getSpatialDimension(),
+ mesh_accessor.getNodesSharedPtr(),
+ "mesh_facets_for_clusters");
+
+ mesh_facets->defineMeshParent(mesh);
+
+ MeshUtils::buildAllFacets(mesh, *mesh_facets, element_dimension,
+ element_dimension - 1);
+ }
+
+ return createClusters(element_dimension, cluster_name_prefix, filter, *mesh_facets);
+}
+
/* -------------------------------------------------------------------------- */
//// \todo if needed element list construction can be optimized by
//// templating the filter class
UInt GroupManager::createClusters(UInt element_dimension,
std::string cluster_name_prefix,
const GroupManager::ClusteringFilter & filter,
- Mesh * mesh_facets) {
+ Mesh & mesh_facets) {
AKANTU_DEBUG_IN();
UInt nb_proc = StaticCommunicator::getStaticCommunicator().getNbProc();
std::string tmp_cluster_name_prefix = cluster_name_prefix;
ElementTypeMapArray<UInt> * element_to_fragment = nullptr;
if (nb_proc > 1 && mesh.isDistributed()) {
element_to_fragment =
new ElementTypeMapArray<UInt>("element_to_fragment", id, memory_id);
- element_to_fragment->initialize(mesh, _nb_component = 1,
- _spatial_dimension = element_dimension,
- _element_kind = _ek_not_defined,
- _with_nb_element = true);
+ element_to_fragment->initialize(
+ mesh, _nb_component = 1, _spatial_dimension = element_dimension,
+ _element_kind = _ek_not_defined, _with_nb_element = true);
// mesh.initElementTypeMapArray(*element_to_fragment, 1, element_dimension,
// false, _ek_not_defined, true);
tmp_cluster_name_prefix = "tmp_" + tmp_cluster_name_prefix;
}
- /// Get facets
- bool mesh_facets_created = false;
-
- if (!mesh_facets && element_dimension > 0) {
- mesh_facets = new Mesh(mesh.getSpatialDimension(), mesh.getNodes().getID(),
- "mesh_facets_for_clusters");
-
- mesh_facets->defineMeshParent(mesh);
-
- MeshUtils::buildAllFacets(mesh, *mesh_facets, element_dimension,
- element_dimension - 1);
- }
-
ElementTypeMapArray<bool> seen_elements("seen_elements", id, memory_id);
seen_elements.initialize(mesh, _spatial_dimension = element_dimension,
- _element_kind = _ek_not_defined,
- _with_nb_element = true);
+ _element_kind = _ek_not_defined,
+ _with_nb_element = true);
// mesh.initElementTypeMapArray(seen_elements, 1, element_dimension, false,
// _ek_not_defined, true);
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType ghost_type = *gt;
Element el;
el.ghost_type = ghost_type;
Mesh::type_iterator type_it =
mesh.firstType(element_dimension, ghost_type, _ek_not_defined);
Mesh::type_iterator type_end =
mesh.lastType(element_dimension, ghost_type, _ek_not_defined);
for (; type_it != type_end; ++type_it) {
el.type = *type_it;
el.kind = Mesh::getKind(*type_it);
UInt nb_element = mesh.getNbElement(*type_it, ghost_type);
Array<bool> & seen_elements_array = seen_elements(el.type, ghost_type);
for (UInt e = 0; e < nb_element; ++e) {
el.element = e;
if (!filter(el))
seen_elements_array(e) = true;
}
}
}
Array<bool> checked_node(mesh.getNbNodes(), 1, false);
UInt nb_cluster = 0;
/// keep looping until all elements are seen
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType ghost_type = *gt;
Element uns_el;
uns_el.ghost_type = ghost_type;
Mesh::type_iterator type_it =
mesh.firstType(element_dimension, ghost_type, _ek_not_defined);
Mesh::type_iterator type_end =
mesh.lastType(element_dimension, ghost_type, _ek_not_defined);
for (; type_it != type_end; ++type_it) {
uns_el.type = *type_it;
Array<bool> & seen_elements_vec =
seen_elements(uns_el.type, uns_el.ghost_type);
for (UInt e = 0; e < seen_elements_vec.getSize(); ++e) {
// skip elements that have been already seen
if (seen_elements_vec(e) == true)
continue;
// set current element
uns_el.element = e;
seen_elements_vec(e) = true;
/// create a new cluster
std::stringstream sstr;
sstr << tmp_cluster_name_prefix << "_" << nb_cluster;
ElementGroup & cluster =
createElementGroup(sstr.str(), element_dimension, true);
++nb_cluster;
// point element are cluster by themself
if (element_dimension == 0) {
cluster.add(uns_el);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(uns_el.type);
Vector<UInt> connect =
mesh.getConnectivity(uns_el.type, uns_el.ghost_type)
.begin(nb_nodes_per_element)[uns_el.element];
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
/// add element's nodes to the cluster
UInt node = connect[n];
if (!checked_node(node)) {
cluster.addNode(node);
checked_node(node) = true;
}
}
continue;
}
std::queue<Element> element_to_add;
element_to_add.push(uns_el);
/// keep looping until current cluster is complete (no more
/// connected elements)
while (!element_to_add.empty()) {
/// take first element and erase it in the queue
Element el = element_to_add.front();
element_to_add.pop();
/// if parallel, store cluster index per element
if (nb_proc > 1 && mesh.isDistributed())
(*element_to_fragment)(el.type, el.ghost_type)(el.element) =
nb_cluster - 1;
/// add current element to the cluster
cluster.add(el);
const Array<Element> & element_to_facet =
- mesh_facets->getSubelementToElement(el.type, el.ghost_type);
+ mesh_facets.getSubelementToElement(el.type, el.ghost_type);
UInt nb_facet_per_element = element_to_facet.getNbComponent();
for (UInt f = 0; f < nb_facet_per_element; ++f) {
const Element & facet = element_to_facet(el.element, f);
if (facet == ElementNull)
continue;
const std::vector<Element> & connected_elements =
- mesh_facets->getElementToSubelement(
+ mesh_facets.getElementToSubelement(
facet.type, facet.ghost_type)(facet.element);
for (UInt elem = 0; elem < connected_elements.size(); ++elem) {
const Element & check_el = connected_elements[elem];
// check if this element has to be skipped
if (check_el == ElementNull || check_el == el)
continue;
Array<bool> & seen_elements_vec_current =
seen_elements(check_el.type, check_el.ghost_type);
if (seen_elements_vec_current(check_el.element) == false) {
seen_elements_vec_current(check_el.element) = true;
element_to_add.push(check_el);
}
}
}
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(el.type);
Vector<UInt> connect = mesh.getConnectivity(el.type, el.ghost_type)
.begin(nb_nodes_per_element)[el.element];
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
/// add element's nodes to the cluster
UInt node = connect[n];
if (!checked_node(node)) {
cluster.addNode(node, false);
checked_node(node) = true;
}
}
}
}
}
}
if (nb_proc > 1 && mesh.isDistributed()) {
ClusterSynchronizer cluster_synchronizer(
*this, element_dimension, cluster_name_prefix, *element_to_fragment,
this->mesh.getElementSynchronizer(), nb_cluster);
nb_cluster = cluster_synchronizer.synchronize();
delete element_to_fragment;
}
- if (mesh_facets_created)
- delete mesh_facets;
-
if (mesh.isDistributed())
this->synchronizeGroupNames();
AKANTU_DEBUG_OUT();
return nb_cluster;
}
/* -------------------------------------------------------------------------- */
template <typename T>
void GroupManager::createGroupsFromMeshData(const std::string & dataset_name) {
std::set<std::string> group_names;
const ElementTypeMapArray<T> & datas = mesh.getData<T>(dataset_name);
typedef typename ElementTypeMapArray<T>::type_iterator type_iterator;
std::map<std::string, UInt> group_dim;
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
type_iterator type_it = datas.firstType(_all_dimensions, *gt);
type_iterator type_end = datas.lastType(_all_dimensions, *gt);
for (; type_it != type_end; ++type_it) {
const Array<T> & dataset = datas(*type_it, *gt);
UInt nb_element = mesh.getNbElement(*type_it, *gt);
AKANTU_DEBUG_ASSERT(dataset.getSize() == nb_element,
"Not the same number of elements ("
<< *type_it << ":" << *gt
<< ") in the map from MeshData ("
<< dataset.getSize() << ") " << dataset_name
<< " and in the mesh (" << nb_element << ")!");
for (UInt e(0); e < nb_element; ++e) {
std::stringstream sstr;
sstr << dataset(e);
std::string gname = sstr.str();
group_names.insert(gname);
std::map<std::string, UInt>::iterator it = group_dim.find(gname);
if (it == group_dim.end()) {
group_dim[gname] = mesh.getSpatialDimension(*type_it);
} else {
it->second = std::max(it->second, mesh.getSpatialDimension(*type_it));
}
}
}
}
std::set<std::string>::iterator git = group_names.begin();
std::set<std::string>::iterator gend = group_names.end();
for (; git != gend; ++git)
createElementGroup(*git, group_dim[*git]);
if (mesh.isDistributed())
this->synchronizeGroupNames();
Element el;
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
el.ghost_type = *gt;
type_iterator type_it = datas.firstType(_all_dimensions, *gt);
type_iterator type_end = datas.lastType(_all_dimensions, *gt);
for (; type_it != type_end; ++type_it) {
el.type = *type_it;
const Array<T> & dataset = datas(*type_it, *gt);
UInt nb_element = mesh.getNbElement(*type_it, *gt);
AKANTU_DEBUG_ASSERT(dataset.getSize() == nb_element,
"Not the same number of elements in the map from "
"MeshData and in the mesh!");
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(el.type);
Array<UInt>::const_iterator<Vector<UInt>> cit =
mesh.getConnectivity(*type_it, *gt).begin(nb_nodes_per_element);
for (UInt e(0); e < nb_element; ++e, ++cit) {
el.element = e;
std::stringstream sstr;
sstr << dataset(e);
ElementGroup & group = getElementGroup(sstr.str());
group.add(el, false, false);
const Vector<UInt> & connect = *cit;
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
UInt node = connect[n];
group.addNode(node, false);
}
}
}
}
git = group_names.begin();
for (; git != gend; ++git) {
getElementGroup(*git).optimize();
}
}
template void GroupManager::createGroupsFromMeshData<std::string>(
const std::string & dataset_name);
template void
GroupManager::createGroupsFromMeshData<UInt>(const std::string & dataset_name);
/* -------------------------------------------------------------------------- */
void GroupManager::createElementGroupFromNodeGroup(
const std::string & name, const std::string & node_group_name,
UInt dimension) {
NodeGroup & node_group = getNodeGroup(node_group_name);
ElementGroup & group = createElementGroup(name, dimension, node_group);
group.fillFromNodeGroup();
}
/* -------------------------------------------------------------------------- */
void GroupManager::printself(std::ostream & stream, int indent) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "GroupManager [" << std::endl;
std::set<std::string> node_group_seen;
for (const_element_group_iterator it(element_group_begin());
it != element_group_end(); ++it) {
it->second->printself(stream, indent + 1);
node_group_seen.insert(it->second->getNodeGroup().getName());
}
for (const_node_group_iterator it(node_group_begin()); it != node_group_end();
++it) {
if (node_group_seen.find(it->second->getName()) == node_group_seen.end())
it->second->printself(stream, indent + 1);
}
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
UInt GroupManager::getNbElementGroups(UInt dimension) const {
if (dimension == _all_dimensions)
return element_groups.size();
ElementGroups::const_iterator it = element_groups.begin();
ElementGroups::const_iterator end = element_groups.end();
UInt count = 0;
for (; it != end; ++it)
count += (it->second->getDimension() == dimension);
return count;
}
/* -------------------------------------------------------------------------- */
void GroupManager::checkAndAddGroups(CommunicationBuffer & buffer) {
AKANTU_DEBUG_IN();
UInt nb_node_group;
buffer >> nb_node_group;
AKANTU_DEBUG_INFO("Received " << nb_node_group << " node group names");
for (UInt ng = 0; ng < nb_node_group; ++ng) {
std::string node_group_name;
buffer >> node_group_name;
if (node_groups.find(node_group_name) == node_groups.end()) {
this->createNodeGroup(node_group_name);
}
AKANTU_DEBUG_INFO("Received node goup name: " << node_group_name);
}
UInt nb_element_group;
buffer >> nb_element_group;
AKANTU_DEBUG_INFO("Received " << nb_element_group << " element group names");
for (UInt eg = 0; eg < nb_element_group; ++eg) {
std::string element_group_name;
buffer >> element_group_name;
std::string node_group_name;
buffer >> node_group_name;
UInt dim;
buffer >> dim;
AKANTU_DEBUG_INFO("Received element group name: "
<< element_group_name << " corresponding to a "
<< Int(dim) << "D group with node group "
<< node_group_name);
NodeGroup & node_group = *node_groups[node_group_name];
if (element_groups.find(element_group_name) == element_groups.end()) {
this->createElementGroup(element_group_name, dim, node_group);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void GroupManager::fillBufferWithGroupNames(
DynamicCommunicationBuffer & comm_buffer) const {
AKANTU_DEBUG_IN();
// packing node group names;
UInt nb_groups = this->node_groups.size();
comm_buffer << nb_groups;
AKANTU_DEBUG_INFO("Sending " << nb_groups << " node group names");
NodeGroups::const_iterator nnames_it = node_groups.begin();
NodeGroups::const_iterator nnames_end = node_groups.end();
for (; nnames_it != nnames_end; ++nnames_it) {
std::string node_group_name = nnames_it->first;
comm_buffer << node_group_name;
AKANTU_DEBUG_INFO("Sending node goupe name: " << node_group_name);
}
// packing element group names with there associated node group name
nb_groups = this->element_groups.size();
comm_buffer << nb_groups;
AKANTU_DEBUG_INFO("Sending " << nb_groups << " element group names");
ElementGroups::const_iterator gnames_it = this->element_groups.begin();
ElementGroups::const_iterator gnames_end = this->element_groups.end();
for (; gnames_it != gnames_end; ++gnames_it) {
ElementGroup & element_group = *(gnames_it->second);
std::string element_group_name = gnames_it->first;
std::string node_group_name = element_group.getNodeGroup().getName();
UInt dim = element_group.getDimension();
comm_buffer << element_group_name;
comm_buffer << node_group_name;
comm_buffer << dim;
AKANTU_DEBUG_INFO("Sending element group name: "
<< element_group_name << " corresponding to a "
<< Int(dim) << "D group with the node group "
<< node_group_name);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void GroupManager::synchronizeGroupNames() {
AKANTU_DEBUG_IN();
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
Int nb_proc = comm.getNbProc();
Int my_rank = comm.whoAmI();
if (nb_proc == 1)
return;
if (my_rank == 0) {
for (Int p = 1; p < nb_proc; ++p) {
CommunicationStatus status;
comm.probe<char>(p, p, status);
AKANTU_DEBUG_INFO("Got " << printMemorySize<char>(status.getSize())
<< " from proc " << p);
CommunicationBuffer recv_buffer(status.getSize());
comm.receive(recv_buffer, p, p);
this->checkAndAddGroups(recv_buffer);
}
DynamicCommunicationBuffer comm_buffer;
this->fillBufferWithGroupNames(comm_buffer);
UInt buffer_size = comm_buffer.getSize();
comm.broadcast(buffer_size, 0);
AKANTU_DEBUG_INFO("Initiating broadcast with "
<< printMemorySize<char>(comm_buffer.getSize()));
comm.broadcast(comm_buffer, 0);
} else {
DynamicCommunicationBuffer comm_buffer;
this->fillBufferWithGroupNames(comm_buffer);
AKANTU_DEBUG_INFO("Sending " << printMemorySize<char>(comm_buffer.getSize())
<< " to proc " << 0);
comm.send(comm_buffer, 0, my_rank);
UInt buffer_size = 0;
comm.broadcast(buffer_size, 0);
AKANTU_DEBUG_INFO("Receiving broadcast with "
<< printMemorySize<char>(comm_buffer.getSize()));
CommunicationBuffer recv_buffer(buffer_size);
comm.broadcast(recv_buffer, 0);
this->checkAndAddGroups(recv_buffer);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
const ElementGroup &
GroupManager::getElementGroup(const std::string & name) const {
const_element_group_iterator it = element_group_find(name);
if (it == element_group_end()) {
AKANTU_EXCEPTION("There are no element groups named "
<< name << " associated to the group manager: " << id);
}
return *(it->second);
}
/* -------------------------------------------------------------------------- */
ElementGroup & GroupManager::getElementGroup(const std::string & name) {
element_group_iterator it = element_group_find(name);
if (it == element_group_end()) {
AKANTU_EXCEPTION("There are no element groups named "
<< name << " associated to the group manager: " << id);
}
return *(it->second);
}
/* -------------------------------------------------------------------------- */
const NodeGroup & GroupManager::getNodeGroup(const std::string & name) const {
const_node_group_iterator it = node_group_find(name);
if (it == node_group_end()) {
AKANTU_EXCEPTION("There are no node groups named "
<< name << " associated to the group manager: " << id);
}
return *(it->second);
}
/* -------------------------------------------------------------------------- */
NodeGroup & GroupManager::getNodeGroup(const std::string & name) {
node_group_iterator it = node_group_find(name);
if (it == node_group_end()) {
AKANTU_EXCEPTION("There are no node groups named "
<< name << " associated to the group manager: " << id);
}
return *(it->second);
}
} // namespace akantu
diff --git a/src/mesh/group_manager.hh b/src/mesh/group_manager.hh
index d4b7dc1a3..731f71f2c 100644
--- a/src/mesh/group_manager.hh
+++ b/src/mesh/group_manager.hh
@@ -1,294 +1,304 @@
/**
* @file group_manager.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@gmail.com>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Nov 13 2013
* @date last modification: Mon Nov 16 2015
*
* @brief Stores information relevent to the notion of element and nodes
*groups.
*
* @section LICENSE
*
* Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_GROUP_MANAGER_HH__
#define __AKANTU_GROUP_MANAGER_HH__
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "element_type_map.hh"
/* -------------------------------------------------------------------------- */
#include <set>
/* -------------------------------------------------------------------------- */
namespace akantu {
class ElementGroup;
class NodeGroup;
class Mesh;
class Element;
class ElementSynchronizer;
template <bool> class CommunicationBufferTemplated;
namespace dumper {
class Field;
}
} // namespace akantu
namespace akantu {
/* -------------------------------------------------------------------------- */
class GroupManager {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
private:
using ElementGroups = std::map<std::string, ElementGroup *>;
using NodeGroups = std::map<std::string, NodeGroup *>;
public:
typedef std::set<ElementType> GroupManagerTypeSet;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
GroupManager(const Mesh & mesh, const ID & id = "group_manager",
const MemoryID & memory_id = 0);
virtual ~GroupManager();
/* ------------------------------------------------------------------------ */
/* Groups iterators */
/* ------------------------------------------------------------------------ */
public:
typedef NodeGroups::iterator node_group_iterator;
typedef ElementGroups::iterator element_group_iterator;
typedef NodeGroups::const_iterator const_node_group_iterator;
typedef ElementGroups::const_iterator const_element_group_iterator;
#ifndef SWIG
#define AKANTU_GROUP_MANAGER_DEFINE_ITERATOR_FUNCTION(group_type, function, \
param_in, param_out) \
inline BOOST_PP_CAT(BOOST_PP_CAT(const_, group_type), _iterator) \
BOOST_PP_CAT(BOOST_PP_CAT(group_type, _), function)(param_in) const { \
return BOOST_PP_CAT(group_type, s).function(param_out); \
}; \
\
inline BOOST_PP_CAT(group_type, _iterator) \
BOOST_PP_CAT(BOOST_PP_CAT(group_type, _), function)(param_in) { \
return BOOST_PP_CAT(group_type, s).function(param_out); \
}
#define AKANTU_GROUP_MANAGER_DEFINE_ITERATOR_FUNCTION_NP(group_type, function) \
AKANTU_GROUP_MANAGER_DEFINE_ITERATOR_FUNCTION( \
group_type, function, BOOST_PP_EMPTY(), BOOST_PP_EMPTY())
AKANTU_GROUP_MANAGER_DEFINE_ITERATOR_FUNCTION_NP(node_group, begin);
AKANTU_GROUP_MANAGER_DEFINE_ITERATOR_FUNCTION_NP(node_group, end);
AKANTU_GROUP_MANAGER_DEFINE_ITERATOR_FUNCTION_NP(element_group, begin);
AKANTU_GROUP_MANAGER_DEFINE_ITERATOR_FUNCTION_NP(element_group, end);
AKANTU_GROUP_MANAGER_DEFINE_ITERATOR_FUNCTION(element_group, find,
const std::string & name, name);
AKANTU_GROUP_MANAGER_DEFINE_ITERATOR_FUNCTION(node_group, find,
const std::string & name, name);
#endif
/* ------------------------------------------------------------------------ */
/* Clustering filter */
/* ------------------------------------------------------------------------ */
public:
class ClusteringFilter {
public:
virtual bool operator()(const Element &) const { return true; }
};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// create an empty node group
NodeGroup & createNodeGroup(const std::string & group_name,
bool replace_group = false);
/// create a node group from another node group but filtered
template <typename T>
NodeGroup & createFilteredNodeGroup(const std::string & group_name,
const NodeGroup & node_group, T & filter);
/// destroy a node group
void destroyNodeGroup(const std::string & group_name);
/// create an element group and the associated node group
ElementGroup & createElementGroup(const std::string & group_name,
UInt dimension = _all_dimensions,
bool replace_group = false);
/// create an element group from another element group but filtered
template <typename T>
ElementGroup &
createFilteredElementGroup(const std::string & group_name, UInt dimension,
const NodeGroup & node_group, T & filter);
/// destroy an element group and the associated node group
void destroyElementGroup(const std::string & group_name,
bool destroy_node_group = false);
/// destroy all element groups and the associated node groups
void destroyAllElementGroups(bool destroy_node_groups = false);
/// create a element group using an existing node group
ElementGroup & createElementGroup(const std::string & group_name,
UInt dimension, NodeGroup & node_group);
/// create groups based on values stored in a given mesh data
template <typename T>
void createGroupsFromMeshData(const std::string & dataset_name);
/// create boundaries group by a clustering algorithm \todo extend to parallel
UInt createBoundaryGroupFromGeometry();
+ /// create element clusters for a given dimension
+ UInt createClusters(UInt element_dimension, Mesh & mesh_facets,
+ std::string cluster_name_prefix = "cluster",
+ const ClusteringFilter & filter = ClusteringFilter());
+
/// create element clusters for a given dimension
UInt createClusters(UInt element_dimension,
std::string cluster_name_prefix = "cluster",
- const ClusteringFilter & filter = ClusteringFilter(),
- Mesh * mesh_facets = nullptr);
+ const ClusteringFilter & filter = ClusteringFilter());
+private:
+ /// create element clusters for a given dimension
+ UInt createClusters(UInt element_dimension, std::string cluster_name_prefix,
+ const ClusteringFilter & filter, Mesh & mesh_facets);
+
+public:
/// Create an ElementGroup based on a NodeGroup
void createElementGroupFromNodeGroup(const std::string & name,
const std::string & node_group,
UInt dimension = _all_dimensions);
virtual void printself(std::ostream & stream, int indent = 0) const;
/// this function insure that the group names are present on all processors
/// /!\ it is a SMP call
void synchronizeGroupNames();
/// register an elemental field to the given group name (overloading for
/// ElementalPartionField)
#ifndef SWIG
template <typename T, template <bool> class dump_type>
dumper::Field * createElementalField(
const ElementTypeMapArray<T> & field, const std::string & group_name,
UInt spatial_dimension, const ElementKind & kind,
ElementTypeMap<UInt> nb_data_per_elem = ElementTypeMap<UInt>());
/// register an elemental field to the given group name (overloading for
/// ElementalField)
template <typename T, template <class> class ret_type,
template <class, template <class> class, bool> class dump_type>
dumper::Field * createElementalField(
const ElementTypeMapArray<T> & field, const std::string & group_name,
UInt spatial_dimension, const ElementKind & kind,
ElementTypeMap<UInt> nb_data_per_elem = ElementTypeMap<UInt>());
/// register an elemental field to the given group name (overloading for
/// MaterialInternalField)
template <typename T,
/// type of InternalMaterialField
template <typename, bool filtered> class dump_type>
dumper::Field * createElementalField(const ElementTypeMapArray<T> & field,
const std::string & group_name,
UInt spatial_dimension,
const ElementKind & kind,
ElementTypeMap<UInt> nb_data_per_elem);
template <typename type, bool flag, template <class, bool> class ftype>
dumper::Field * createNodalField(const ftype<type, flag> * field,
const std::string & group_name,
UInt padding_size = 0);
template <typename type, bool flag, template <class, bool> class ftype>
dumper::Field * createStridedNodalField(const ftype<type, flag> * field,
const std::string & group_name,
UInt size, UInt stride,
UInt padding_size);
protected:
/// fill a buffer with all the group names
void fillBufferWithGroupNames(
CommunicationBufferTemplated<false> & comm_buffer) const;
/// take a buffer and create the missing groups localy
void checkAndAddGroups(CommunicationBufferTemplated<true> & buffer);
/// register an elemental field to the given group name
template <class dump_type, typename field_type>
inline dumper::Field *
createElementalField(const field_type & field, const std::string & group_name,
UInt spatial_dimension, const ElementKind & kind,
ElementTypeMap<UInt> nb_data_per_elem);
/// register an elemental field to the given group name
template <class dump_type, typename field_type>
inline dumper::Field *
createElementalFilteredField(const field_type & field,
const std::string & group_name,
UInt spatial_dimension, const ElementKind & kind,
ElementTypeMap<UInt> nb_data_per_elem);
#endif
/* ------------------------------------------------------------------------ */
/* Accessor */
/* ------------------------------------------------------------------------ */
public:
const ElementGroup & getElementGroup(const std::string & name) const;
const NodeGroup & getNodeGroup(const std::string & name) const;
ElementGroup & getElementGroup(const std::string & name);
NodeGroup & getNodeGroup(const std::string & name);
UInt getNbElementGroups(UInt dimension = _all_dimensions) const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// id to create element and node groups
ID id;
/// memory_id to create element and node groups
MemoryID memory_id;
/// list of the node groups managed
NodeGroups node_groups;
/// list of the element groups managed
ElementGroups element_groups;
/// Mesh to which the element belongs
const Mesh & mesh;
};
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const GroupManager & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#endif /* __AKANTU_GROUP_MANAGER_HH__ */
diff --git a/src/mesh/mesh.cc b/src/mesh/mesh.cc
index 795934832..c06e28f3d 100644
--- a/src/mesh/mesh.cc
+++ b/src/mesh/mesh.cc
@@ -1,523 +1,429 @@
/**
* @file mesh.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Fri Jan 22 2016
*
* @brief class handling meshes
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
* Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
* Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <sstream>
#include "aka_config.hh"
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
#include "group_manager_inline_impl.cc"
#include "mesh.hh"
#include "mesh_io.hh"
/* -------------------------------------------------------------------------- */
#include "element_synchronizer.hh"
#include "mesh_utils_distribution.hh"
#include "node_synchronizer.hh"
#include "static_communicator.hh"
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_IOHELPER
#include "dumper_field.hh"
#include "dumper_internal_material_field.hh"
#endif
/* -------------------------------------------------------------------------- */
namespace akantu {
const Element ElementNull(_not_defined, 0);
/* -------------------------------------------------------------------------- */
void Element::printself(std::ostream & stream, int indent) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "Element [" << type << ", " << element << ", "
<< ghost_type << "]";
}
/* -------------------------------------------------------------------------- */
Mesh::Mesh(UInt spatial_dimension, const ID & id, const MemoryID & memory_id,
StaticCommunicator & communicator)
: Memory(id, memory_id),
- GroupManager(*this, id + ":group_manager", memory_id), nodes(NULL),
- nodes_global_ids(nullptr), nodes_type(0, 1, id + ":nodes_type"),
- nb_global_nodes(0), created_nodes(true),
+ GroupManager(*this, id + ":group_manager", memory_id),
+ nodes_type(0, 1, id + ":nodes_type"),
connectivities("connectivities", id, memory_id),
normals("normals", id, memory_id), spatial_dimension(spatial_dimension),
- types_offsets(Array<UInt>((UInt)_max_element_type + 1, 1)),
- ghost_types_offsets(Array<UInt>((UInt)_max_element_type + 1, 1)),
lower_bounds(spatial_dimension, 0.), upper_bounds(spatial_dimension, 0.),
size(spatial_dimension, 0.), local_lower_bounds(spatial_dimension, 0.),
local_upper_bounds(spatial_dimension, 0.),
- mesh_data("mesh_data", id, memory_id), mesh_facets(nullptr),
- mesh_parent(nullptr), is_mesh_facets(false), is_distributed(false),
- communicator(&communicator), element_synchronizer(nullptr),
- node_synchronizer(nullptr) {
+ mesh_data("mesh_data", id, memory_id), communicator(&communicator) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Mesh::Mesh(UInt spatial_dimension, StaticCommunicator & communicator,
const ID & id, const MemoryID & memory_id)
: Mesh(spatial_dimension, id, memory_id, communicator) {
AKANTU_DEBUG_IN();
+
this->nodes =
- &(alloc<Real>(id + ":coordinates", memory_id, spatial_dimension));
+ std::make_shared<Array<Real>>(0, spatial_dimension, id + ":coordinates");
+
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Mesh::Mesh(UInt spatial_dimension, const ID & id, const MemoryID & memory_id)
: Mesh(spatial_dimension, StaticCommunicator::getStaticCommunicator(), id,
memory_id) {}
-/* -------------------------------------------------------------------------- */
-Mesh::Mesh(UInt spatial_dimension, const ID & nodes_id, const ID & id,
- const MemoryID & memory_id)
- : Mesh(spatial_dimension, id, memory_id,
- StaticCommunicator::getStaticCommunicator()) {
- this->nodes = &(this->getArray<Real>(nodes_id));
- this->nb_global_nodes = this->nodes->getSize();
- this->computeBoundingBox();
-}
+// /* --------------------------------------------------------------------------
+// */ Mesh::Mesh(UInt spatial_dimension, const ID & nodes_id, const ID & id,
+// const MemoryID & memory_id)
+// : Mesh(spatial_dimension, id, memory_id,
+// StaticCommunicator::getStaticCommunicator()) {
+// this->nodes = &(this->getArray<Real>(nodes_id));
+// this->nb_global_nodes = this->nodes->getSize();
+// this->computeBoundingBox();
+// }
/* -------------------------------------------------------------------------- */
-Mesh::Mesh(UInt spatial_dimension, Array<Real> & nodes, const ID & id,
- const MemoryID & memory_id)
+Mesh::Mesh(UInt spatial_dimension, std::shared_ptr<Array<Real>> nodes,
+ const ID & id, const MemoryID & memory_id)
: Mesh(spatial_dimension, id, memory_id,
StaticCommunicator::getStaticCommunicator()) {
- this->nodes = &nodes;
+ this->nodes = nodes;
this->nb_global_nodes = this->nodes->getSize();
this->computeBoundingBox();
}
/* -------------------------------------------------------------------------- */
Mesh & Mesh::initMeshFacets(const ID & id) {
AKANTU_DEBUG_IN();
if (!mesh_facets) {
- mesh_facets = new Mesh(spatial_dimension, *(this->nodes),
- getID() + ":" + id, getMemoryID());
+ mesh_facets = std::make_unique<Mesh>(spatial_dimension, this->nodes,
+ getID() + ":" + id, getMemoryID());
mesh_facets->mesh_parent = this;
mesh_facets->is_mesh_facets = true;
}
AKANTU_DEBUG_OUT();
return *mesh_facets;
}
/* -------------------------------------------------------------------------- */
void Mesh::defineMeshParent(const Mesh & mesh) {
AKANTU_DEBUG_IN();
this->mesh_parent = &mesh;
this->is_mesh_facets = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
-Mesh::~Mesh() {
- AKANTU_DEBUG_IN();
-
- delete mesh_facets;
-
- delete element_synchronizer;
- delete node_synchronizer;
-
- AKANTU_DEBUG_OUT();
-}
+Mesh::~Mesh() = default;
/* -------------------------------------------------------------------------- */
void Mesh::read(const std::string & filename, const MeshIOType & mesh_io_type) {
MeshIO mesh_io;
mesh_io.read(filename, *this, mesh_io_type);
type_iterator it =
this->firstType(spatial_dimension, _not_ghost, _ek_not_defined);
type_iterator last =
this->lastType(spatial_dimension, _not_ghost, _ek_not_defined);
if (it == last)
AKANTU_EXCEPTION(
"The mesh contained in the file "
<< filename << " does not seem to be of the good dimension."
<< " No element of dimension " << spatial_dimension << " where read.");
+
+ this->computeBoundingBox();
}
/* -------------------------------------------------------------------------- */
void Mesh::write(const std::string & filename,
const MeshIOType & mesh_io_type) {
MeshIO mesh_io;
mesh_io.write(filename, *this, mesh_io_type);
}
/* -------------------------------------------------------------------------- */
void Mesh::printself(std::ostream & stream, int indent) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "Mesh [" << std::endl;
stream << space << " + id : " << getID() << std::endl;
stream << space << " + spatial dimension : " << this->spatial_dimension
<< std::endl;
stream << space << " + nodes [" << std::endl;
nodes->printself(stream, indent + 2);
stream << space << " + connectivities [" << std::endl;
connectivities.printself(stream, indent + 2);
stream << space << " ]" << std::endl;
GroupManager::printself(stream, indent + 1);
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
void Mesh::computeBoundingBox() {
AKANTU_DEBUG_IN();
for (UInt k = 0; k < spatial_dimension; ++k) {
local_lower_bounds(k) = std::numeric_limits<double>::max();
local_upper_bounds(k) = -std::numeric_limits<double>::max();
}
for (UInt i = 0; i < nodes->getSize(); ++i) {
// if(!isPureGhostNode(i))
for (UInt k = 0; k < spatial_dimension; ++k) {
local_lower_bounds(k) = std::min(local_lower_bounds[k], (*nodes)(i, k));
local_upper_bounds(k) = std::max(local_upper_bounds[k], (*nodes)(i, k));
}
}
if (this->is_distributed) {
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
Matrix<Real> reduce_bounds(spatial_dimension, 2);
for (UInt k = 0; k < spatial_dimension; ++k) {
reduce_bounds(k, 0) = local_lower_bounds(k);
reduce_bounds(k, 1) = -local_upper_bounds(k);
}
comm.allReduce(reduce_bounds, _so_min);
for (UInt k = 0; k < spatial_dimension; ++k) {
lower_bounds(k) = reduce_bounds(k, 0);
upper_bounds(k) = -reduce_bounds(k, 1);
}
} else {
this->lower_bounds = this->local_lower_bounds;
this->upper_bounds = this->local_upper_bounds;
}
size = upper_bounds - lower_bounds;
AKANTU_DEBUG_OUT();
}
-// /* --------------------------------------------------------------------------
-// */ template <typename T> void
-// Mesh::initElementTypeMapArray(ElementTypeMapArray<T> & vect,
-// UInt nb_component, UInt dim, GhostType gt,
-// const T & default_value,
-// const bool &
-// flag_nb_node_per_elem_multiply,
-// ElementKind element_kind,
-// bool size_to_nb_element) const {
-// AKANTU_DEBUG_IN();
-
-// for (auto type : elementTypes(dim, gt, element_kind)) {
-// // determines the number of component
-// UInt nb_comp = nb_component;
-// if (flag_nb_node_per_elem_multiply)
-// nb_comp *= Mesh::getNbNodesPerElement(type);
-
-// // determines the size
-// UInt size = 0;
-// if (size_to_nb_element)
-// size = this->getNbElement(type, gt);
-
-// // allocate
-// if (not vect.exists(type, gt))
-// vect.alloc(size, nb_comp, type, gt, default_value);
-// }
-// AKANTU_DEBUG_OUT();
-// }
-
-// /* --------------------------------------------------------------------------
-// */ template <typename T> void
-// Mesh::initElementTypeMapArray(ElementTypeMapArray<T> & vect,
-// UInt nb_component, UInt dim,
-// const bool &
-// flag_nb_node_per_elem_multiply,
-// ElementKind element_kind,
-// bool size_to_nb_element) const {
-// AKANTU_DEBUG_IN();
-
-// for (auto ghost_type : ghost_types) {
-// this->initElementTypeMapArray(vect, nb_component, dim, ghost_types,
-// flag_nb_node_per_elem_multiply,
-// element_kind, size_to_nb_element);
-// }
-
-// AKANTU_DEBUG_OUT();
-// }
-
-// /* --------------------------------------------------------------------------
-// */ template <typename T> void
-// Mesh::initElementTypeMapArray(ElementTypeMapArray<T> & vect,
-// UInt nb_component, UInt dim, GhostType gt,
-// const bool &
-// flag_nb_node_per_elem_multiply,
-// ElementKind element_kind,
-// bool size_to_nb_element) const {
-// AKANTU_DEBUG_IN();
-
-// this->initElementTypeMapArray(vect, nb_component, dim, gt, T(),
-// flag_nb_node_per_elem_multiply, element_kind,
-// size_to_nb_element);
-
-// AKANTU_DEBUG_OUT();
-// }
-
-// /* --------------------------------------------------------------------------
-// */ template <typename T> void
-// Mesh::initElementTypeMapArray(ElementTypeMapArray<T> & vect,
-// UInt nb_component, UInt dim, GhostType gt,
-// const T & default_value,
-// const bool &
-// flag_nb_node_per_elem_multiply,
-// ElementKind element_kind,
-// bool size_to_nb_element) const {
-// AKANTU_DEBUG_IN();
-
-// for (auto type : elementTypes(dim, gt, element_kind)) {
-// // determines the number of component
-// UInt nb_comp = nb_component;
-// if (flag_nb_node_per_elem_multiply)
-// nb_comp *= Mesh::getNbNodesPerElement(type);
-
-// // determines the size
-// UInt size = 0;
-// if (size_to_nb_element)
-// size = this->getNbElement(type, gt);
-
-// // allocate
-// if (not vect.exists(type, gt))
-// vect.alloc(size, nb_comp, type, gt, default_value);
-// }
-// AKANTU_DEBUG_OUT();
-// }
-
-// /* --------------------------------------------------------------------------
-// */
-/*
-#define AKANTU_INSTANTIATE_INIT(type) \
- template void Mesh::initElementTypeMapArray<type>( \
- ElementTypeMapArray<type> & vect, UInt nb_component, UInt dim, \
- const bool & flag_nb_elem_multiply, ElementKind element_kind, \
- bool size_to_nb_element) const; \
- template void Mesh::initElementTypeMapArray<type>( \
- ElementTypeMapArray<type> & vect, UInt nb_component, UInt dim, \
- GhostType gt, const bool & flag_nb_elem_multiply, \
- ElementKind element_kind, bool size_to_nb_element) const; \
- template void Mesh::initElementTypeMapArray<type>( \
- ElementTypeMapArray<type> & vect, UInt nb_component, UInt dim, \
- GhostType gt, const type & default_value, \
- const bool & flag_nb_elem_multiply, ElementKind element_kind, \ bool
-size_to_nb_element) const
-*/
-// AKANTU_INSTANTIATE_INIT(Real);
-// AKANTU_INSTANTIATE_INIT(UInt);
-// AKANTU_INSTANTIATE_INIT(Int);
-// AKANTU_INSTANTIATE_INIT(bool);
-
/* -------------------------------------------------------------------------- */
void Mesh::initNormals() {
normals.initialize(*this, _nb_component = spatial_dimension,
_spatial_dimension = spatial_dimension,
_element_kind = _ek_not_defined);
- // this->initElementTypeMapArray(normals, spatial_dimension,
- // spatial_dimension,
- // false, _ek_not_defined);
}
/* -------------------------------------------------------------------------- */
void Mesh::getGlobalConnectivity(
ElementTypeMapArray<UInt> & global_connectivity, UInt dimension,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
for (auto type : elementTypes(dimension, ghost_type)) {
- Array<UInt> & local_conn = connectivities(type, ghost_type);
- Array<UInt> & g_connectivity = global_connectivity(type, ghost_type);
-
- if (!nodes_global_ids)
- nodes_global_ids = mesh_parent->nodes_global_ids;
-
- UInt * local_c = local_conn.storage();
- UInt * global_c = g_connectivity.storage();
-
- UInt nb_terms = local_conn.getSize() * local_conn.getNbComponent();
-
- for (UInt i = 0; i < nb_terms; ++i, ++local_c, ++global_c)
- *global_c = (*nodes_global_ids)(*local_c);
+ auto & local_conn = connectivities(type, ghost_type);
+ auto & g_connectivity = global_connectivity(type, ghost_type);
+
+ UInt nb_nodes = local_conn.getSize() * local_conn.getNbComponent();
+
+ if (!nodes_global_ids && is_mesh_facets) {
+ std::transform(
+ local_conn.begin_reinterpret(nb_nodes),
+ local_conn.end_reinterpret(nb_nodes),
+ g_connectivity.begin_reinterpret(nb_nodes),
+ [& node_ids = *mesh_parent->nodes_global_ids](UInt l)->UInt {
+ return node_ids(l);
+ });
+ } else {
+ std::transform(local_conn.begin_reinterpret(nb_nodes),
+ local_conn.end_reinterpret(nb_nodes),
+ g_connectivity.begin_reinterpret(nb_nodes),
+ [& node_ids = *nodes_global_ids](UInt l)->UInt {
+ return node_ids(l);
+ });
+ }
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
-
DumperIOHelper & Mesh::getGroupDumper(const std::string & dumper_name,
const std::string & group_name) {
-
if (group_name == "all")
return this->getDumper(dumper_name);
else
return element_groups[group_name]->getDumper(dumper_name);
}
/* -------------------------------------------------------------------------- */
template <typename T>
ElementTypeMap<UInt> Mesh::getNbDataPerElem(ElementTypeMapArray<T> & arrays,
const ElementKind & element_kind) {
-
ElementTypeMap<UInt> nb_data_per_elem;
for (auto type : elementTypes(spatial_dimension, _not_ghost, element_kind)) {
UInt nb_elements = this->getNbElement(type);
auto & array = arrays(type);
nb_data_per_elem(type) = array.getNbComponent() * array.getSize();
nb_data_per_elem(type) /= nb_elements;
}
return nb_data_per_elem;
}
/* -------------------------------------------------------------------------- */
-
template ElementTypeMap<UInt>
Mesh::getNbDataPerElem(ElementTypeMapArray<Real> & array,
const ElementKind & element_kind);
template ElementTypeMap<UInt>
Mesh::getNbDataPerElem(ElementTypeMapArray<UInt> & array,
const ElementKind & element_kind);
/* -------------------------------------------------------------------------- */
-
#ifdef AKANTU_USE_IOHELPER
-
template <typename T>
dumper::Field *
Mesh::createFieldFromAttachedData(const std::string & field_id,
const std::string & group_name,
const ElementKind & element_kind) {
dumper::Field * field = nullptr;
ElementTypeMapArray<T> * internal = nullptr;
try {
internal = &(this->getData<T>(field_id));
} catch (...) {
return nullptr;
}
ElementTypeMap<UInt> nb_data_per_elem =
this->getNbDataPerElem(*internal, element_kind);
field = this->createElementalField<T, dumper::InternalMaterialField>(
*internal, group_name, this->spatial_dimension, element_kind,
nb_data_per_elem);
return field;
}
template dumper::Field *
Mesh::createFieldFromAttachedData<Real>(const std::string & field_id,
const std::string & group_name,
const ElementKind & element_kind);
template dumper::Field *
Mesh::createFieldFromAttachedData<UInt>(const std::string & field_id,
const std::string & group_name,
const ElementKind & element_kind);
-
#endif
/* -------------------------------------------------------------------------- */
void Mesh::distribute() {
this->distribute(StaticCommunicator::getStaticCommunicator());
}
/* -------------------------------------------------------------------------- */
void Mesh::distribute(StaticCommunicator & communicator) {
AKANTU_DEBUG_ASSERT(is_distributed == false,
"This mesh is already distribute");
this->communicator = &communicator;
- this->element_synchronizer =
- new ElementSynchronizer(*this, this->getID() + ":element_synchronizer",
- this->getMemoryID(), true);
+ this->element_synchronizer = std::make_unique<ElementSynchronizer>(
+ *this, this->getID() + ":element_synchronizer", this->getMemoryID(),
+ true);
- this->node_synchronizer = new NodeSynchronizer(
+ this->node_synchronizer = std::make_unique<NodeSynchronizer>(
*this, this->getID() + ":node_synchronizer", this->getMemoryID(), true);
Int psize = this->communicator->getNbProc();
#ifdef AKANTU_USE_SCOTCH
Int prank = this->communicator->whoAmI();
if (prank == 0) {
MeshPartitionScotch partition(*this, spatial_dimension);
partition.partitionate(psize);
MeshUtilsDistribution::distributeMeshCentralized(*this, 0, partition);
} else {
MeshUtilsDistribution::distributeMeshCentralized(*this, 0);
}
#else
if (!(psize == 1)) {
AKANTU_DEBUG_ERROR("Cannot distribute a mesh without a partitioning tool");
}
#endif
this->is_distributed = true;
this->element_synchronizer->buildPrankToElement();
this->computeBoundingBox();
}
/* -------------------------------------------------------------------------- */
+void Mesh::getAssociatedElements(const Array<UInt> & node_list,
+ Array<Element> & elements) {
+ for(const auto & node : node_list)
+ for(const auto & element : *nodes_to_elements[node])
+ elements.push_back(element);
+}
+
+/* -------------------------------------------------------------------------- */
+void Mesh::fillNodesToElements() {
+ Element e;
+
+ UInt nb_nodes = nodes->getSize();
+ for (UInt n = 0; n < nb_nodes; ++n) {
+ this->nodes_to_elements[n]->clear();
+ }
+
+ for (auto ghost_type : ghost_types) {
+ e.ghost_type = ghost_type;
+ for (const auto & type :
+ elementTypes(spatial_dimension, ghost_type, _ek_not_defined)) {
+ e.type = type;
+ e.kind = getKind(type);
+
+ UInt nb_element = this->getNbElement(type, ghost_type);
+ Array<UInt>::const_iterator<Vector<UInt>> conn_it =
+ connectivities(type, ghost_type).begin(Mesh::getNbNodesPerElement(type));
+
+ for (UInt el = 0; el < nb_element; ++el, ++conn_it) {
+ e.element = el;
+ const Vector<UInt> & conn = *conn_it;
+ for (UInt n = 0; n < conn.size(); ++n)
+ nodes_to_elements[conn(n)]->insert(e);
+ }
+ }
+ }
+}
} // namespace akantu
diff --git a/src/mesh/mesh.hh b/src/mesh/mesh.hh
index 16aac2d0f..312202a7b 100644
--- a/src/mesh/mesh.hh
+++ b/src/mesh/mesh.hh
@@ -1,613 +1,595 @@
/**
* @file mesh.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Thu Jan 14 2016
*
* @brief the class representing the meshes
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
* Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
* Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MESH_HH__
#define __AKANTU_MESH_HH__
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_event_handler_manager.hh"
#include "aka_memory.hh"
#include "dumpable.hh"
#include "element.hh"
#include "element_class.hh"
#include "element_type_map.hh"
#include "group_manager.hh"
#include "mesh_data.hh"
#include "mesh_events.hh"
/* -------------------------------------------------------------------------- */
#include <set>
/* -------------------------------------------------------------------------- */
namespace akantu {
class StaticCommunicator;
class ElementSynchronizer;
class NodeSynchronizer;
-} // akantu
+} // namespace akantu
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Mesh */
/* -------------------------------------------------------------------------- */
/**
* @class Mesh this contain the coordinates of the nodes in the Mesh.nodes
* Array, and the connectivity. The connectivity are stored in by element
* types.
*
* In order to loop on all element you have to loop on all types like this :
* @code{.cpp}
Mesh::type_iterator it = mesh.firstType(dim, ghost_type);
Mesh::type_iterator end = mesh.lastType(dim, ghost_type);
for(; it != end; ++it) {
UInt nb_element = mesh.getNbElement(*it);
const Array<UInt> & conn = mesh.getConnectivity(*it);
for(UInt e = 0; e < nb_element; ++e) {
...
}
}
@endcode
*/
class Mesh : protected Memory,
public EventHandlerManager<MeshEventHandler>,
public GroupManager,
public Dumpable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
private:
/// default constructor used for chaining, the last parameter is just to
/// differentiate constructors
Mesh(UInt spatial_dimension, const ID & id, const MemoryID & memory_id,
StaticCommunicator & communicator);
public:
/// constructor that create nodes coordinates array
Mesh(UInt spatial_dimension, const ID & id = "mesh",
const MemoryID & memory_id = 0);
/// mesh not distributed and not using the default communicator
Mesh(UInt spatial_dimension, StaticCommunicator & communicator,
const ID & id = "mesh", const MemoryID & memory_id = 0);
/// constructor that use an existing nodes coordinates array, by knowing its
/// ID
- Mesh(UInt spatial_dimension, const ID & nodes_id, const ID & id,
- const MemoryID & memory_id = 0);
+ // Mesh(UInt spatial_dimension, const ID & nodes_id, const ID & id,
+ // const MemoryID & memory_id = 0);
/**
* constructor that use an existing nodes coordinates
* array, by getting the vector of coordinates
*/
- Mesh(UInt spatial_dimension, Array<Real> & nodes, const ID & id = "mesh",
+ Mesh(UInt spatial_dimension, std::shared_ptr<Array<Real>> nodes, const ID & id = "mesh",
const MemoryID & memory_id = 0);
virtual ~Mesh();
/// @typedef ConnectivityTypeList list of the types present in a Mesh
typedef std::set<ElementType> ConnectivityTypeList;
/// read the mesh from a file
void read(const std::string & filename,
const MeshIOType & mesh_io_type = _miot_auto);
/// write the mesh to a file
void write(const std::string & filename,
const MeshIOType & mesh_io_type = _miot_auto);
private:
/// initialize the connectivity to NULL and other stuff
void init();
+ /// function that computes the bounding box (fills xmin, xmax)
+ void computeBoundingBox();
+
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// patitionate the mesh among the processors involved in their computation
virtual void distribute(StaticCommunicator & communicator);
virtual void distribute();
/// function to print the containt of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
- /// function that computes the bounding box (fills xmin, xmax)
- void computeBoundingBox();
-
- // /// init a by-element-type real vector with provided ids
- // template <typename T>
- // void
- // initElementTypeMapArray(ElementTypeMapArray<T> & v, UInt nb_component,
- // UInt spatial_dimension,
- // const bool & flag_nb_node_per_elem_multiply = false,
- // ElementKind element_kind = _ek_regular,
- // bool size_to_nb_element = false)
- // const; /// @todo: think about nicer way to do it
- // template <typename T>
- // void
- // initElementTypeMapArray(ElementTypeMapArray<T> & v, UInt nb_component,
- // UInt spatial_dimension, GhostType ghost_type,
- // const bool & flag_nb_node_per_elem_multiply = false,
- // ElementKind element_kind = _ek_regular,
- // bool size_to_nb_element = false)
- // const; /// @todo: think about nicer way to do it
-
- // template <typename T>
- // void
- // initElementTypeMapArray(ElementTypeMapArray<T> & v, UInt nb_component,
- // UInt spatial_dimension, GhostType ghost_type,
- // const T & default_value,
- // const bool & flag_nb_node_per_elem_multiply = false,
- // ElementKind element_kind = _ek_regular,
- // bool size_to_nb_element = false)
- // const; /// @todo: think about nicer way to do it
-
/// extract coordinates of nodes from an element
template <typename T>
inline void extractNodalValuesFromElement(const Array<T> & nodal_values,
T * elemental_values,
UInt * connectivity, UInt n_nodes,
UInt nb_degree_of_freedom) const;
// /// extract coordinates of nodes from a reversed element
// inline void extractNodalCoordinatesFromPBCElement(Real * local_coords,
// UInt * connectivity,
// UInt n_nodes);
/// convert a element to a linearized element
inline UInt elementToLinearized(const Element & elem) const;
/// convert a linearized element to an element
inline Element linearizedToElement(UInt linearized_element) const;
/// update the types offsets array for the conversions
- inline void updateTypesOffsets(const GhostType & ghost_type);
+ //inline void updateTypesOffsets(const GhostType & ghost_type);
/// add a Array of connectivity for the type <type>.
inline void addConnectivityType(const ElementType & type,
const GhostType & ghost_type = _not_ghost);
/* ------------------------------------------------------------------------ */
template <class Event> inline void sendEvent(Event & event) {
// if(event.getList().getSize() != 0)
EventHandlerManager<MeshEventHandler>::sendEvent<Event>(event);
}
/* ------------------------------------------------------------------------ */
template <typename T>
inline void removeNodesFromArray(Array<T> & vect,
const Array<UInt> & new_numbering);
/// initialize normals
void initNormals();
/// init facets' mesh
Mesh & initMeshFacets(const ID & id = "mesh_facets");
/// define parent mesh
void defineMeshParent(const Mesh & mesh);
/// get global connectivity array
void getGlobalConnectivity(ElementTypeMapArray<UInt> & global_connectivity,
UInt dimension, GhostType ghost_type);
+public:
+ void getAssociatedElements(const Array<UInt> & node_list,
+ Array<Element> & elements);
+
+private:
+ /// fills the nodes_to_elements structure
+ void fillNodesToElements();
+
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get the id of the mesh
AKANTU_GET_MACRO(ID, Memory::id, const ID &);
/// get the id of the mesh
AKANTU_GET_MACRO(MemoryID, Memory::memory_id, const MemoryID &);
/// get the spatial dimension of the mesh = number of component of the
/// coordinates
AKANTU_GET_MACRO(SpatialDimension, spatial_dimension, UInt);
/// get the nodes Array aka coordinates
AKANTU_GET_MACRO(Nodes, *nodes, const Array<Real> &);
AKANTU_GET_MACRO_NOT_CONST(Nodes, *nodes, Array<Real> &);
/// get the normals for the elements
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(Normals, normals, Real);
/// get the number of nodes
AKANTU_GET_MACRO(NbNodes, nodes->getSize(), UInt);
/// get the Array of global ids of the nodes (only used in parallel)
AKANTU_GET_MACRO(GlobalNodesIds, *nodes_global_ids, const Array<UInt> &);
AKANTU_GET_MACRO_NOT_CONST(GlobalNodesIds, *nodes_global_ids, Array<UInt> &);
/// get the global id of a node
inline UInt getNodeGlobalId(UInt local_id) const;
/// get the global id of a node
inline UInt getNodeLocalId(UInt global_id) const;
/// get the global number of nodes
inline UInt getNbGlobalNodes() const;
/// get the nodes type Array
AKANTU_GET_MACRO(NodesType, nodes_type, const Array<NodeType> &);
protected:
AKANTU_GET_MACRO_NOT_CONST(NodesType, nodes_type, Array<NodeType> &);
public:
inline NodeType getNodeType(UInt local_id) const;
/// say if a node is a pure ghost node
inline bool isPureGhostNode(UInt n) const;
/// say if a node is pur local or master node
inline bool isLocalOrMasterNode(UInt n) const;
inline bool isLocalNode(UInt n) const;
inline bool isMasterNode(UInt n) const;
inline bool isSlaveNode(UInt n) const;
AKANTU_GET_MACRO(LowerBounds, lower_bounds, const Vector<Real> &);
AKANTU_GET_MACRO(UpperBounds, upper_bounds, const Vector<Real> &);
AKANTU_GET_MACRO(LocalLowerBounds, local_lower_bounds, const Vector<Real> &);
AKANTU_GET_MACRO(LocalUpperBounds, local_upper_bounds, const Vector<Real> &);
/// get the connectivity Array for a given type
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Connectivity, connectivities, UInt);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(Connectivity, connectivities, UInt);
AKANTU_GET_MACRO(Connectivities, connectivities,
const ElementTypeMapArray<UInt> &);
/// get the number of element of a type in the mesh
inline UInt getNbElement(const ElementType & type,
const GhostType & ghost_type = _not_ghost) const;
/// get the number of element for a given ghost_type and a given dimension
inline UInt getNbElement(const UInt spatial_dimension = _all_dimensions,
const GhostType & ghost_type = _not_ghost,
const ElementKind & kind = _ek_not_defined) const;
- /// get the connectivity list either for the elements or the ghost elements
- inline const ConnectivityTypeList &
- getConnectivityTypeList(const GhostType & ghost_type = _not_ghost) const;
+ // /// get the connectivity list either for the elements or the ghost elements
+ // inline const ConnectivityTypeList &
+ // getConnectivityTypeList(const GhostType & ghost_type = _not_ghost) const;
/// compute the barycenter of a given element
inline void getBarycenter(UInt element, const ElementType & type,
Real * barycenter,
GhostType ghost_type = _not_ghost) const;
inline void getBarycenter(const Element & element,
Vector<Real> & barycenter) const;
/// get the element connected to a subelement
const Array<std::vector<Element>> &
getElementToSubelement(const ElementType & el_type,
const GhostType & ghost_type = _not_ghost) const;
/// get the element connected to a subelement
Array<std::vector<Element>> &
getElementToSubelement(const ElementType & el_type,
const GhostType & ghost_type = _not_ghost);
/// get the subelement connected to an element
const Array<Element> &
getSubelementToElement(const ElementType & el_type,
const GhostType & ghost_type = _not_ghost) const;
/// get the subelement connected to an element
Array<Element> &
getSubelementToElement(const ElementType & el_type,
const GhostType & ghost_type = _not_ghost);
/// get a name field associated to the mesh
template <typename T>
inline const Array<T> &
getData(const std::string & data_name, const ElementType & el_type,
const GhostType & ghost_type = _not_ghost) const;
/// get a name field associated to the mesh
template <typename T>
inline Array<T> & getData(const std::string & data_name,
const ElementType & el_type,
const GhostType & ghost_type = _not_ghost);
/// register a new ElementalTypeMap in the MeshData
template <typename T>
inline ElementTypeMapArray<T> & registerData(const std::string & data_name);
/// get a name field associated to the mesh
template <typename T>
inline const ElementTypeMapArray<T> &
getData(const std::string & data_name) const;
/// get a name field associated to the mesh
template <typename T>
inline ElementTypeMapArray<T> & getData(const std::string & data_name);
template <typename T>
ElementTypeMap<UInt> getNbDataPerElem(ElementTypeMapArray<T> & array,
const ElementKind & element_kind);
template <typename T>
dumper::Field * createFieldFromAttachedData(const std::string & field_id,
const std::string & group_name,
const ElementKind & element_kind);
/// templated getter returning the pointer to data in MeshData (modifiable)
template <typename T>
- inline Array<T> *
+ inline Array<T> &
getDataPointer(const std::string & data_name, const ElementType & el_type,
const GhostType & ghost_type = _not_ghost,
UInt nb_component = 1, bool size_to_nb_element = true,
bool resize_with_parent = false);
/// Facets mesh accessor
inline const Mesh & getMeshFacets() const;
inline Mesh & getMeshFacets();
/// Parent mesh accessor
inline const Mesh & getMeshParent() const;
inline bool isMeshFacets() const { return this->is_mesh_facets; }
/// defines is the mesh is distributed or not
inline bool isDistributed() const { return this->is_distributed; }
#ifndef SWIG
/// return the dumper from a group and and a dumper name
DumperIOHelper & getGroupDumper(const std::string & dumper_name,
const std::string & group_name);
#endif
/* ------------------------------------------------------------------------ */
/* Wrappers on ElementClass functions */
/* ------------------------------------------------------------------------ */
public:
/// get the number of nodes per element for a given element type
static inline UInt getNbNodesPerElement(const ElementType & type);
/// get the number of nodes per element for a given element type considered as
/// a first order element
static inline ElementType getP1ElementType(const ElementType & type);
/// get the kind of the element type
static inline ElementKind getKind(const ElementType & type);
/// get spatial dimension of a type of element
static inline UInt getSpatialDimension(const ElementType & type);
/// get number of facets of a given element type
static inline UInt getNbFacetsPerElement(const ElementType & type);
/// get number of facets of a given element type
static inline UInt getNbFacetsPerElement(const ElementType & type, UInt t);
/// get local connectivity of a facet for a given facet type
static inline MatrixProxy<UInt>
getFacetLocalConnectivity(const ElementType & type, UInt t = 0);
/// get connectivity of facets for a given element
inline Matrix<UInt> getFacetConnectivity(const Element & element,
UInt t = 0) const;
/// get the number of type of the surface element associated to a given
/// element type
static inline UInt getNbFacetTypes(const ElementType & type, UInt t = 0);
/// get the type of the surface element associated to a given element
static inline ElementType getFacetType(const ElementType & type, UInt t = 0);
/// get all the type of the surface element associated to a given element
static inline VectorProxy<ElementType>
getAllFacetTypes(const ElementType & type);
/// get the number of nodes in the given element list
static inline UInt getNbNodesPerElementList(const Array<Element> & elements);
/* ------------------------------------------------------------------------ */
/* Element type Iterator */
/* ------------------------------------------------------------------------ */
- typedef ElementTypeMapArray<UInt, ElementType>::type_iterator type_iterator;
- typedef ElementTypeMapArray<UInt, ElementType>::ElementTypesIteratorHelper
- ElementTypesIteratorHelper;
+ using type_iterator = ElementTypeMapArray<UInt, ElementType>::type_iterator;
+ using ElementTypesIteratorHelper =
+ ElementTypeMapArray<UInt, ElementType>::ElementTypesIteratorHelper;
inline ElementTypesIteratorHelper
elementTypes(UInt dim = _all_dimensions, GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_regular) const {
return connectivities.elementTypes(dim, ghost_type, kind);
}
inline type_iterator firstType(UInt dim = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_regular) const {
return connectivities.firstType(dim, ghost_type, kind);
}
inline type_iterator lastType(UInt dim = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_regular) const {
return connectivities.lastType(dim, ghost_type, kind);
}
AKANTU_GET_MACRO(ElementSynchronizer, *element_synchronizer,
const ElementSynchronizer &);
AKANTU_GET_MACRO_NOT_CONST(ElementSynchronizer, *element_synchronizer,
ElementSynchronizer &);
AKANTU_GET_MACRO(NodeSynchronizer, *node_synchronizer,
const NodeSynchronizer &);
AKANTU_GET_MACRO_NOT_CONST(NodeSynchronizer, *node_synchronizer,
NodeSynchronizer &);
// AKANTU_GET_MACRO_NOT_CONST(Communicator, *communicator, StaticCommunicator
// &);
AKANTU_GET_MACRO(Communicator, *communicator, const StaticCommunicator &);
/* ------------------------------------------------------------------------ */
/* Private methods for friends */
/* ------------------------------------------------------------------------ */
private:
friend class MeshAccessor;
//#if defined(AKANTU_COHESIVE_ELEMENT)
// friend class CohesiveElementInserter;
//#endif
//#if defined(AKANTU_IGFEM)
// template <UInt dim> friend class MeshIgfemSphericalGrowingGel;
//#endif
- AKANTU_GET_MACRO(NodesPointer, nodes, Array<Real> *);
+ AKANTU_GET_MACRO(NodesPointer, *nodes, Array<Real> &);
/// get a pointer to the nodes_global_ids Array<UInt> and create it if
/// necessary
- inline Array<UInt> * getNodesGlobalIdsPointer();
+ inline Array<UInt> & getNodesGlobalIdsPointer();
/// get a pointer to the nodes_type Array<Int> and create it if necessary
- inline Array<NodeType> * getNodesTypePointer();
+ inline Array<NodeType> & getNodesTypePointer();
/// get a pointer to the connectivity Array for the given type and create it
/// if necessary
- inline Array<UInt> *
+ inline Array<UInt> &
getConnectivityPointer(const ElementType & type,
const GhostType & ghost_type = _not_ghost);
/// get a pointer to the element_to_subelement Array for the given type and
/// create it if necessary
- inline Array<std::vector<Element>> *
+ inline Array<std::vector<Element>> &
getElementToSubelementPointer(const ElementType & type,
const GhostType & ghost_type = _not_ghost);
/// get a pointer to the subelement_to_element Array for the given type and
/// create it if necessary
- inline Array<Element> *
+ inline Array<Element> &
getSubelementToElementPointer(const ElementType & type,
const GhostType & ghost_type = _not_ghost);
AKANTU_GET_MACRO_NOT_CONST(MeshData, mesh_data, MeshData &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// array of the nodes coordinates
- Array<Real> * nodes;
+ std::shared_ptr<Array<Real>> nodes;
/// global node ids
- Array<UInt> * nodes_global_ids;
+ std::unique_ptr<Array<UInt>> nodes_global_ids;
/// node type, -3 pure ghost, -2 master for the node, -1 normal node, i in
/// [0-N] slave node and master is proc i
Array<NodeType> nodes_type;
/// global number of nodes;
- UInt nb_global_nodes;
-
- /// boolean to know if the nodes have to be deleted with the mesh or not
- bool created_nodes;
+ UInt nb_global_nodes{0};
/// all class of elements present in this mesh (for heterogenous meshes)
ElementTypeMapArray<UInt> connectivities;
/// map to normals for all class of elements present in this mesh
ElementTypeMapArray<Real> normals;
/// list of all existing types in the mesh
- ConnectivityTypeList type_set;
+ // ConnectivityTypeList type_set;
/// the spatial dimension of this mesh
- UInt spatial_dimension;
+ UInt spatial_dimension{0};
/// types offsets
- Array<UInt> types_offsets;
+ // Array<UInt> types_offsets;
- /// list of all existing types in the mesh
- ConnectivityTypeList ghost_type_set;
- /// ghost types offsets
- Array<UInt> ghost_types_offsets;
+ // /// list of all existing types in the mesh
+ // ConnectivityTypeList ghost_type_set;
+ // /// ghost types offsets
+ // Array<UInt> ghost_types_offsets;
/// min of coordinates
Vector<Real> lower_bounds;
/// max of coordinates
Vector<Real> upper_bounds;
/// size covered by the mesh on each direction
Vector<Real> size;
/// local min of coordinates
Vector<Real> local_lower_bounds;
/// local max of coordinates
Vector<Real> local_upper_bounds;
/// Extra data loaded from the mesh file
MeshData mesh_data;
/// facets' mesh
- Mesh * mesh_facets;
+ std::unique_ptr<Mesh> mesh_facets;
/// parent mesh (this is set for mesh_facets meshes)
- const Mesh * mesh_parent;
+ const Mesh * mesh_parent{nullptr};
/// defines if current mesh is mesh_facets or not
- bool is_mesh_facets;
+ bool is_mesh_facets{false};
/// defines if the mesh is centralized or distributed
- bool is_distributed;
+ bool is_distributed{false};
/// Communicator on which mesh is distributed
- StaticCommunicator * communicator;
+ const StaticCommunicator * communicator;
/// Element synchronizer
- ElementSynchronizer * element_synchronizer;
+ std::unique_ptr<ElementSynchronizer> element_synchronizer;
/// Node synchronizer
- NodeSynchronizer * node_synchronizer;
+ std::unique_ptr<NodeSynchronizer> node_synchronizer;
+
+ using NodesToElements = std::vector<std::unique_ptr<std::set<Element>>>;
+
+ /// This info is stored to simplify the dynamic changes
+ NodesToElements nodes_to_elements;
};
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream, const Element & _this) {
_this.printself(stream);
return stream;
}
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream, const Mesh & _this) {
_this.printself(stream);
return stream;
}
-} // akantu
+} // namespace akantu
/* -------------------------------------------------------------------------- */
/* Inline functions */
/* -------------------------------------------------------------------------- */
#include "element_type_map_tmpl.hh"
#include "mesh_inline_impl.cc"
#endif /* __AKANTU_MESH_HH__ */
diff --git a/src/mesh/mesh_accessor.hh b/src/mesh/mesh_accessor.hh
index abf01fe45..061f20a3b 100644
--- a/src/mesh/mesh_accessor.hh
+++ b/src/mesh/mesh_accessor.hh
@@ -1,129 +1,132 @@
/**
* @file mesh_accessor.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Jun 30 2015
*
* @brief this class allow to access some private member of mesh it is used for
* IO for examples
*
* @section LICENSE
*
* Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
* (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MESH_ACCESSOR_HH__
#define __AKANTU_MESH_ACCESSOR_HH__
namespace akantu {
class NodeSynchronizer;
class ElementSynchronizer;
-} // akantu
+} // namespace akantu
namespace akantu {
class MeshAccessor {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
- MeshAccessor(Mesh & mesh) : _mesh(mesh){};
- virtual ~MeshAccessor(){};
+ explicit MeshAccessor(Mesh & mesh) : _mesh(mesh){};
+ virtual ~MeshAccessor() = default;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get the global number of nodes
inline UInt getNbGlobalNodes() const { return this->_mesh.nb_global_nodes; };
/// set the global number of nodes
inline void setNbGlobalNodes(UInt nb_global_nodes) {
this->_mesh.nb_global_nodes = nb_global_nodes;
};
/// set the mesh as being distributed
inline void setDistributed() { this->_mesh.is_distributed = true; }
/// get a pointer to the nodes_global_ids Array<UInt> and create it if
/// necessary
inline Array<UInt> & getNodesGlobalIds() {
- return *(this->_mesh.getNodesGlobalIdsPointer());
+ return this->_mesh.getNodesGlobalIdsPointer();
}
/// get a pointer to the nodes_type Array<Int> and create it if necessary
inline Array<NodeType> & getNodesType() {
- return *(this->_mesh.getNodesTypePointer());
+ return this->_mesh.getNodesTypePointer();
}
/// get a pointer to the coordinates Array
- inline Array<Real> & getNodes() { return *(this->_mesh.getNodesPointer()); }
+ inline Array<Real> & getNodes() { return this->_mesh.getNodesPointer(); }
+
+ /// get a pointer to the coordinates Array
+ inline std::shared_ptr<Array<Real>> getNodesSharedPtr() { return this->_mesh.nodes; }
/// get a pointer to the connectivity Array for the given type and create it
/// if necessary
inline Array<UInt> &
getConnectivity(const ElementType & type,
const GhostType & ghost_type = _not_ghost) {
- return *(this->_mesh.getConnectivityPointer(type, ghost_type));
+ return this->_mesh.getConnectivityPointer(type, ghost_type);
}
/// get a pointer to the element_to_subelement Array for the given type and
/// create it if necessary
- inline Array<std::vector<Element> > &
+ inline Array<std::vector<Element>> &
getElementToSubelement(const ElementType & type,
const GhostType & ghost_type = _not_ghost) {
- return *(this->_mesh.getElementToSubelementPointer(type, ghost_type));
+ return this->_mesh.getElementToSubelementPointer(type, ghost_type);
}
/// get a pointer to the subelement_to_element Array for the given type and
/// create it if necessary
inline Array<Element> &
getSubelementToElement(const ElementType & type,
const GhostType & ghost_type = _not_ghost) {
- return *(this->_mesh.getSubelementToElementPointer(type, ghost_type));
+ return this->_mesh.getSubelementToElementPointer(type, ghost_type);
}
template <typename T>
inline Array<T> &
getData(const std::string & data_name, const ElementType & el_type,
const GhostType & ghost_type = _not_ghost, UInt nb_component = 1,
bool size_to_nb_element = true, bool resize_with_parent = false) {
- return *(this->_mesh.getDataPointer<T>(data_name, el_type, ghost_type,
- nb_component, size_to_nb_element,
- resize_with_parent));
+ return this->_mesh.getDataPointer<T>(data_name, el_type, ghost_type,
+ nb_component, size_to_nb_element,
+ resize_with_parent);
}
MeshData & getMeshData() { return this->_mesh.getMeshData(); }
/// get the node synchonizer
NodeSynchronizer & getNodeSynchronizer();
/// get the element synchonizer
ElementSynchronizer & getElementSynchronizer();
private:
Mesh & _mesh;
};
-} // akantu
+} // namespace akantu
#endif /* __AKANTU_MESH_ACCESSOR_HH__ */
diff --git a/src/mesh/mesh_inline_impl.cc b/src/mesh/mesh_inline_impl.cc
index 3e74a8532..612d3fe5c 100644
--- a/src/mesh/mesh_inline_impl.cc
+++ b/src/mesh/mesh_inline_impl.cc
@@ -1,630 +1,681 @@
/**
* @file mesh_inline_impl.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Thu Jul 15 2010
* @date last modification: Thu Jan 21 2016
*
* @brief Implementation of the inline functions of the mesh class
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
* Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
* Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_COHESIVE_ELEMENT)
#include "cohesive_element.hh"
#endif
#ifndef __AKANTU_MESH_INLINE_IMPL_CC__
#define __AKANTU_MESH_INLINE_IMPL_CC__
namespace akantu {
/* -------------------------------------------------------------------------- */
inline RemovedNodesEvent::RemovedNodesEvent(const Mesh & mesh)
: new_numbering(mesh.getNbNodes(), 1, "new_numbering") {}
/* -------------------------------------------------------------------------- */
inline RemovedElementsEvent::RemovedElementsEvent(const Mesh & mesh,
ID new_numbering_id)
: new_numbering(new_numbering_id, mesh.getID(), mesh.getMemoryID()) {}
+/* -------------------------------------------------------------------------- */
+template <>
+inline void Mesh::sendEvent<NewElementsEvent>(NewElementsEvent & event) {
+ this->nodes_to_elements.resize(nodes->getSize());
+ for (const auto & elem : event.getList()) {
+ const Array<UInt> & conn = connectivities(elem.type, elem.ghost_type);
+
+ UInt nb_nodes_per_elem = this->getNbNodesPerElement(elem.type);
+
+ for (UInt n = 0; n < nb_nodes_per_elem; ++n) {
+ UInt node = conn(elem.element, n);
+ if (not nodes_to_elements[node])
+ nodes_to_elements[node] = std::make_unique<std::set<Element>>();
+ nodes_to_elements[node]->insert(elem);
+ }
+ }
+
+ EventHandlerManager<MeshEventHandler>::sendEvent(event);
+}
+
+/* -------------------------------------------------------------------------- */
+template <> inline void Mesh::sendEvent<NewNodesEvent>(NewNodesEvent & event) {
+ this->computeBoundingBox();
+
+ EventHandlerManager<MeshEventHandler>::sendEvent(event);
+}
+
/* -------------------------------------------------------------------------- */
template <>
inline void
Mesh::sendEvent<RemovedElementsEvent>(RemovedElementsEvent & event) {
this->connectivities.onElementsRemoved(event.getNewNumbering());
+ this->fillNodesToElements();
+ this->computeBoundingBox();
+
EventHandlerManager<MeshEventHandler>::sendEvent(event);
}
/* -------------------------------------------------------------------------- */
template <>
inline void Mesh::sendEvent<RemovedNodesEvent>(RemovedNodesEvent & event) {
- if (created_nodes)
- this->removeNodesFromArray(*nodes, event.getNewNumbering());
+ const auto & new_numbering = event.getNewNumbering();
+ this->removeNodesFromArray(*nodes, new_numbering);
if (nodes_global_ids)
- this->removeNodesFromArray(*nodes_global_ids, event.getNewNumbering());
+ this->removeNodesFromArray(*nodes_global_ids, new_numbering);
if (nodes_type.getSize() != 0)
- this->removeNodesFromArray(nodes_type, event.getNewNumbering());
+ this->removeNodesFromArray(nodes_type, new_numbering);
+
+ std::vector<std::unique_ptr<std::set<Element>>> tmp(nodes_to_elements.size());
+ auto it = nodes_to_elements.begin();
+
+ UInt new_nb_nodes = 0;
+ for (auto new_i : new_numbering) {
+ if (new_i != UInt(-1)) {
+ tmp[new_i] = std::move(*it);
+ ++new_nb_nodes;
+ }
+ ++it;
+ }
+
+ tmp.resize(new_nb_nodes);
+ std::move(tmp.begin(), tmp.end(), nodes_to_elements.begin());
+
+ computeBoundingBox();
EventHandlerManager<MeshEventHandler>::sendEvent(event);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void Mesh::removeNodesFromArray(Array<T> & vect,
const Array<UInt> & new_numbering) {
Array<T> tmp(vect.getSize(), vect.getNbComponent());
UInt nb_component = vect.getNbComponent();
UInt new_nb_nodes = 0;
for (UInt i = 0; i < new_numbering.getSize(); ++i) {
UInt new_i = new_numbering(i);
if (new_i != UInt(-1)) {
T * to_copy = vect.storage() + i * nb_component;
std::uninitialized_copy(to_copy, to_copy + nb_component,
tmp.storage() + new_i * nb_component);
++new_nb_nodes;
}
}
tmp.resize(new_nb_nodes);
vect.copy(tmp);
}
/* -------------------------------------------------------------------------- */
-inline UInt Mesh::elementToLinearized(const Element & elem) const {
- AKANTU_DEBUG_ASSERT(elem.type < _max_element_type &&
- elem.element < types_offsets.storage()[elem.type + 1],
- "The element " << elem << "does not exists in the mesh "
- << getID());
-
- return types_offsets.storage()[elem.type] + elem.element;
-}
-
-/* -------------------------------------------------------------------------- */
-inline Element Mesh::linearizedToElement(UInt linearized_element) const {
-
- UInt t;
-
- for (t = _not_defined;
- t != _max_element_type && linearized_element >= types_offsets(t); ++t)
- ;
-
- AKANTU_DEBUG_ASSERT(linearized_element < types_offsets(t),
- "The linearized element "
- << linearized_element
- << "does not exists in the mesh " << getID());
-
- --t;
- ElementType type = ElementType(t);
- return Element(type, linearized_element - types_offsets.storage()[t],
- _not_ghost, getKind(type));
-}
-
-/* -------------------------------------------------------------------------- */
-inline void Mesh::updateTypesOffsets(const GhostType & ghost_type) {
- Array<UInt> * types_offsets_ptr = &this->types_offsets;
- if (ghost_type == _ghost)
- types_offsets_ptr = &this->ghost_types_offsets;
- Array<UInt> & types_offsets = *types_offsets_ptr;
-
- types_offsets.clear();
- for (auto type : elementTypes(_all_dimensions, ghost_type, _ek_not_defined))
- types_offsets(type) = connectivities(type, ghost_type).getSize();
-
- for (UInt t = _not_defined + 1; t < _max_element_type; ++t)
- types_offsets(t) += types_offsets(t - 1);
- for (UInt t = _max_element_type; t > _not_defined; --t)
- types_offsets(t) = types_offsets(t - 1);
- types_offsets(0) = 0;
-}
-
-/* -------------------------------------------------------------------------- */
-inline const Mesh::ConnectivityTypeList &
-Mesh::getConnectivityTypeList(const GhostType & ghost_type) const {
- if (ghost_type == _not_ghost)
- return type_set;
- else
- return ghost_type_set;
-}
-
-/* -------------------------------------------------------------------------- */
-inline Array<UInt> * Mesh::getNodesGlobalIdsPointer() {
+// inline UInt Mesh::elementToLinearized(const Element & elem) const {
+// AKANTU_DEBUG_ASSERT(elem.type < _max_element_type &&
+// elem.element < types_offsets.storage()[elem.type +
+// 1],
+// "The element " << elem << "does not exists in the mesh
+// "
+// << getID());
+
+// return types_offsets.storage()[elem.type] + elem.element;
+// }
+
+// /* --------------------------------------------------------------------------
+// */ inline Element Mesh::linearizedToElement(UInt linearized_element) const {
+
+// UInt t;
+
+// for (t = _not_defined;
+// t != _max_element_type && linearized_element >= types_offsets(t); ++t)
+// ;
+
+// AKANTU_DEBUG_ASSERT(linearized_element < types_offsets(t),
+// "The linearized element "
+// << linearized_element
+// << "does not exists in the mesh " << getID());
+
+// --t;
+// ElementType type = ElementType(t);
+// return Element(type, linearized_element - types_offsets.storage()[t],
+// _not_ghost, getKind(type));
+// }
+
+// /* --------------------------------------------------------------------------
+// */ inline void Mesh::updateTypesOffsets(const GhostType & ghost_type) {
+// Array<UInt> * types_offsets_ptr = &this->types_offsets;
+// if (ghost_type == _ghost)
+// types_offsets_ptr = &this->ghost_types_offsets;
+// Array<UInt> & types_offsets = *types_offsets_ptr;
+
+// types_offsets.clear();
+// for (auto type : elementTypes(_all_dimensions, ghost_type,
+// _ek_not_defined))
+// types_offsets(type) = connectivities(type, ghost_type).getSize();
+
+// for (UInt t = _not_defined + 1; t < _max_element_type; ++t)
+// types_offsets(t) += types_offsets(t - 1);
+// for (UInt t = _max_element_type; t > _not_defined; --t)
+// types_offsets(t) = types_offsets(t - 1);
+// types_offsets(0) = 0;
+// }
+
+// /* --------------------------------------------------------------------------
+// */ inline const Mesh::ConnectivityTypeList &
+// Mesh::getConnectivityTypeList(const GhostType & ghost_type) const {
+// if (ghost_type == _not_ghost)
+// return type_set;
+// else
+// return ghost_type_set;
+// }
+
+/* -------------------------------------------------------------------------- */
+inline Array<UInt> & Mesh::getNodesGlobalIdsPointer() {
AKANTU_DEBUG_IN();
- if (nodes_global_ids == NULL) {
- std::stringstream sstr;
- sstr << getID() << ":nodes_global_ids";
- nodes_global_ids = &(alloc<UInt>(sstr.str(), nodes->getSize(), 1));
- for (UInt i = 0; i < nodes->getSize(); ++i) {
- (*nodes_global_ids)(i) = i;
+ if (not nodes_global_ids) {
+ auto nb_nodes = nodes->getSize();
+ nodes_global_ids = std::make_unique<Array<UInt>>(
+ nb_nodes, 1, getID() + ":nodes_global_ids");
+
+ UInt i = 0;
+ for (auto & global_id : *nodes_global_ids) {
+ global_id = ++i;
}
}
+
AKANTU_DEBUG_OUT();
- return nodes_global_ids;
+ return *nodes_global_ids;
}
/* -------------------------------------------------------------------------- */
-inline Array<NodeType> * Mesh::getNodesTypePointer() {
+inline Array<NodeType> & Mesh::getNodesTypePointer() {
AKANTU_DEBUG_IN();
if (nodes_type.getSize() == 0) {
nodes_type.resize(nodes->getSize());
nodes_type.set(_nt_normal);
}
+
AKANTU_DEBUG_OUT();
- return &nodes_type;
+ return nodes_type;
}
/* -------------------------------------------------------------------------- */
-inline Array<UInt> *
+inline Array<UInt> &
Mesh::getConnectivityPointer(const ElementType & type,
const GhostType & ghost_type) {
AKANTU_DEBUG_IN();
Array<UInt> * tmp;
if (!connectivities.exists(type, ghost_type)) {
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
tmp = &(connectivities.alloc(0, nb_nodes_per_element, type, ghost_type));
AKANTU_DEBUG_INFO("The connectivity vector for the type " << type
<< " created");
+ // if (ghost_type == _not_ghost)
+ // type_set.insert(type);
+ // else
+ // ghost_type_set.insert(type);
- if (ghost_type == _not_ghost)
- type_set.insert(type);
- else
- ghost_type_set.insert(type);
-
- updateTypesOffsets(ghost_type);
+ // updateTypesOffsets(ghost_type);
} else {
tmp = &connectivities(type, ghost_type);
}
AKANTU_DEBUG_OUT();
- return tmp;
+ return *tmp;
}
/* -------------------------------------------------------------------------- */
-inline Array<std::vector<Element>> *
+inline Array<std::vector<Element>> &
Mesh::getElementToSubelementPointer(const ElementType & type,
const GhostType & ghost_type) {
- Array<std::vector<Element>> * tmp = getDataPointer<std::vector<Element>>(
- "element_to_subelement", type, ghost_type, 1, true);
- return tmp;
+ return getDataPointer<std::vector<Element>>("element_to_subelement", type,
+ ghost_type, 1, true);
}
/* -------------------------------------------------------------------------- */
-inline Array<Element> *
+inline Array<Element> &
Mesh::getSubelementToElementPointer(const ElementType & type,
const GhostType & ghost_type) {
- Array<Element> * tmp = getDataPointer<Element>(
- "subelement_to_element", type, ghost_type, getNbFacetsPerElement(type),
- true, is_mesh_facets);
- return tmp;
+ return getDataPointer<Element>("subelement_to_element", type, ghost_type,
+ getNbFacetsPerElement(type), true,
+ is_mesh_facets);
}
/* -------------------------------------------------------------------------- */
inline const Array<std::vector<Element>> &
Mesh::getElementToSubelement(const ElementType & type,
const GhostType & ghost_type) const {
return getData<std::vector<Element>>("element_to_subelement", type,
ghost_type);
}
/* -------------------------------------------------------------------------- */
inline Array<std::vector<Element>> &
Mesh::getElementToSubelement(const ElementType & type,
const GhostType & ghost_type) {
return getData<std::vector<Element>>("element_to_subelement", type,
ghost_type);
}
/* -------------------------------------------------------------------------- */
inline const Array<Element> &
Mesh::getSubelementToElement(const ElementType & type,
const GhostType & ghost_type) const {
return getData<Element>("subelement_to_element", type, ghost_type);
}
/* -------------------------------------------------------------------------- */
inline Array<Element> &
Mesh::getSubelementToElement(const ElementType & type,
const GhostType & ghost_type) {
return getData<Element>("subelement_to_element", type, ghost_type);
}
/* -------------------------------------------------------------------------- */
template <typename T>
-inline Array<T> *
+inline Array<T> &
Mesh::getDataPointer(const std::string & data_name, const ElementType & el_type,
const GhostType & ghost_type, UInt nb_component,
bool size_to_nb_element, bool resize_with_parent) {
Array<T> & tmp = mesh_data.getElementalDataArrayAlloc<T>(
data_name, el_type, ghost_type, nb_component);
if (size_to_nb_element) {
if (resize_with_parent)
tmp.resize(mesh_parent->getNbElement(el_type, ghost_type));
else
tmp.resize(this->getNbElement(el_type, ghost_type));
} else {
tmp.resize(0);
}
- return &tmp;
+ return tmp;
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline const Array<T> & Mesh::getData(const std::string & data_name,
const ElementType & el_type,
const GhostType & ghost_type) const {
return mesh_data.getElementalDataArray<T>(data_name, el_type, ghost_type);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline Array<T> & Mesh::getData(const std::string & data_name,
const ElementType & el_type,
const GhostType & ghost_type) {
return mesh_data.getElementalDataArray<T>(data_name, el_type, ghost_type);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline const ElementTypeMapArray<T> &
Mesh::getData(const std::string & data_name) const {
return mesh_data.getElementalData<T>(data_name);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline ElementTypeMapArray<T> & Mesh::getData(const std::string & data_name) {
return mesh_data.getElementalData<T>(data_name);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline ElementTypeMapArray<T> &
Mesh::registerData(const std::string & data_name) {
this->mesh_data.registerElementalData<T>(data_name);
return this->getData<T>(data_name);
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNbElement(const ElementType & type,
const GhostType & ghost_type) const {
try {
const Array<UInt> & conn = connectivities(type, ghost_type);
return conn.getSize();
} catch (...) {
return 0;
}
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNbElement(const UInt spatial_dimension,
const GhostType & ghost_type,
const ElementKind & kind) const {
AKANTU_DEBUG_ASSERT(spatial_dimension <= 3 || spatial_dimension == UInt(-1),
"spatial_dimension is " << spatial_dimension
<< " and is greater than 3 !");
UInt nb_element = 0;
for (auto type : elementTypes(spatial_dimension, ghost_type, kind))
nb_element += getNbElement(type, ghost_type);
return nb_element;
}
/* -------------------------------------------------------------------------- */
inline void Mesh::getBarycenter(UInt element, const ElementType & type,
Real * barycenter, GhostType ghost_type) const {
UInt * conn_val = getConnectivity(type, ghost_type).storage();
UInt nb_nodes_per_element = getNbNodesPerElement(type);
Real * local_coord = new Real[spatial_dimension * nb_nodes_per_element];
UInt offset = element * nb_nodes_per_element;
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
memcpy(local_coord + n * spatial_dimension,
nodes->storage() + conn_val[offset + n] * spatial_dimension,
spatial_dimension * sizeof(Real));
}
Math::barycenter(local_coord, nb_nodes_per_element, spatial_dimension,
barycenter);
delete[] local_coord;
}
/* -------------------------------------------------------------------------- */
inline void Mesh::getBarycenter(const Element & element,
Vector<Real> & barycenter) const {
getBarycenter(element.element, element.type, barycenter.storage(),
element.ghost_type);
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNbNodesPerElement(const ElementType & type) {
UInt nb_nodes_per_element = 0;
#define GET_NB_NODES_PER_ELEMENT(type) \
nb_nodes_per_element = ElementClass<type>::getNbNodesPerElement()
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_NB_NODES_PER_ELEMENT);
#undef GET_NB_NODES_PER_ELEMENT
return nb_nodes_per_element;
}
/* -------------------------------------------------------------------------- */
inline ElementType Mesh::getP1ElementType(const ElementType & type) {
ElementType p1_type = _not_defined;
#define GET_P1_TYPE(type) p1_type = ElementClass<type>::getP1ElementType()
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_P1_TYPE);
#undef GET_P1_TYPE
return p1_type;
}
/* -------------------------------------------------------------------------- */
inline ElementKind Mesh::getKind(const ElementType & type) {
ElementKind kind = _ek_not_defined;
#define GET_KIND(type) kind = ElementClass<type>::getKind()
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_KIND);
#undef GET_KIND
return kind;
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getSpatialDimension(const ElementType & type) {
UInt spatial_dimension = 0;
#define GET_SPATIAL_DIMENSION(type) \
spatial_dimension = ElementClass<type>::getSpatialDimension()
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_SPATIAL_DIMENSION);
#undef GET_SPATIAL_DIMENSION
return spatial_dimension;
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNbFacetTypes(const ElementType & type,
__attribute__((unused)) UInt t) {
UInt nb = 0;
#define GET_NB_FACET_TYPE(type) nb = ElementClass<type>::getNbFacetTypes()
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_NB_FACET_TYPE);
#undef GET_NB_FACET_TYPE
return nb;
}
/* -------------------------------------------------------------------------- */
inline ElementType Mesh::getFacetType(const ElementType & type, UInt t) {
ElementType surface_type = _not_defined;
#define GET_FACET_TYPE(type) surface_type = ElementClass<type>::getFacetType(t)
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_FACET_TYPE);
#undef GET_FACET_TYPE
return surface_type;
}
/* -------------------------------------------------------------------------- */
inline VectorProxy<ElementType>
Mesh::getAllFacetTypes(const ElementType & type) {
#define GET_FACET_TYPE(type) \
UInt nb = ElementClass<type>::getNbFacetTypes(); \
ElementType * elt_ptr = \
const_cast<ElementType *>(ElementClass<type>::getFacetTypeInternal()); \
return VectorProxy<ElementType>(elt_ptr, nb);
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_FACET_TYPE);
#undef GET_FACET_TYPE
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNbFacetsPerElement(const ElementType & type) {
AKANTU_DEBUG_IN();
UInt n_facet = 0;
#define GET_NB_FACET(type) n_facet = ElementClass<type>::getNbFacetsPerElement()
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_NB_FACET);
#undef GET_NB_FACET
AKANTU_DEBUG_OUT();
return n_facet;
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNbFacetsPerElement(const ElementType & type, UInt t) {
AKANTU_DEBUG_IN();
UInt n_facet = 0;
#define GET_NB_FACET(type) \
n_facet = ElementClass<type>::getNbFacetsPerElement(t)
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_NB_FACET);
#undef GET_NB_FACET
AKANTU_DEBUG_OUT();
return n_facet;
}
/* -------------------------------------------------------------------------- */
inline MatrixProxy<UInt>
Mesh::getFacetLocalConnectivity(const ElementType & type, UInt t) {
AKANTU_DEBUG_IN();
#define GET_FACET_CON(type) \
AKANTU_DEBUG_OUT(); \
return ElementClass<type>::getFacetLocalConnectivityPerElement(t)
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_FACET_CON);
#undef GET_FACET_CON
AKANTU_DEBUG_OUT();
return MatrixProxy<UInt>(
nullptr, 0, 0); // This avoid a compilation warning but will certainly
// also cause a segfault if reached
}
/* -------------------------------------------------------------------------- */
inline Matrix<UInt> Mesh::getFacetConnectivity(const Element & element,
UInt t) const {
AKANTU_DEBUG_IN();
Matrix<UInt> local_facets(getFacetLocalConnectivity(element.type, t), false);
Matrix<UInt> facets(local_facets.rows(), local_facets.cols());
const Array<UInt> & conn = connectivities(element.type, element.ghost_type);
for (UInt f = 0; f < facets.rows(); ++f) {
for (UInt n = 0; n < facets.cols(); ++n) {
facets(f, n) = conn(element.element, local_facets(f, n));
}
}
AKANTU_DEBUG_OUT();
return facets;
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void Mesh::extractNodalValuesFromElement(
const Array<T> & nodal_values, T * local_coord, UInt * connectivity,
UInt n_nodes, UInt nb_degree_of_freedom) const {
for (UInt n = 0; n < n_nodes; ++n) {
memcpy(local_coord + n * nb_degree_of_freedom,
nodal_values.storage() + connectivity[n] * nb_degree_of_freedom,
nb_degree_of_freedom * sizeof(T));
}
}
/* -------------------------------------------------------------------------- */
inline void Mesh::addConnectivityType(const ElementType & type,
const GhostType & ghost_type) {
getConnectivityPointer(type, ghost_type);
}
/* -------------------------------------------------------------------------- */
inline bool Mesh::isPureGhostNode(UInt n) const {
return nodes_type.getSize() ? (nodes_type(n) == _nt_pure_gost) : false;
}
/* -------------------------------------------------------------------------- */
inline bool Mesh::isLocalOrMasterNode(UInt n) const {
return nodes_type.getSize()
? (nodes_type(n) == _nt_master) || (nodes_type(n) == _nt_normal)
: true;
}
/* -------------------------------------------------------------------------- */
inline bool Mesh::isLocalNode(UInt n) const {
return nodes_type.getSize() ? nodes_type(n) == _nt_normal : true;
}
/* -------------------------------------------------------------------------- */
inline bool Mesh::isMasterNode(UInt n) const {
return nodes_type.getSize() ? nodes_type(n) == _nt_master : false;
}
/* -------------------------------------------------------------------------- */
inline bool Mesh::isSlaveNode(UInt n) const {
return nodes_type.getSize() ? nodes_type(n) >= 0 : false;
}
/* -------------------------------------------------------------------------- */
inline NodeType Mesh::getNodeType(UInt local_id) const {
return nodes_type.getSize() ? nodes_type(local_id) : _nt_normal;
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNodeGlobalId(UInt local_id) const {
return nodes_global_ids ? (*nodes_global_ids)(local_id) : local_id;
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNodeLocalId(UInt global_id) const {
AKANTU_DEBUG_ASSERT(nodes_global_ids != NULL, "The global ids are note set.");
return nodes_global_ids->find(global_id);
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNbGlobalNodes() const {
return nodes_global_ids ? nb_global_nodes : nodes->getSize();
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNbNodesPerElementList(const Array<Element> & elements) {
UInt nb_nodes_per_element = 0;
UInt nb_nodes = 0;
ElementType current_element_type = _not_defined;
Array<Element>::const_iterator<Element> el_it = elements.begin();
Array<Element>::const_iterator<Element> el_end = elements.end();
for (; el_it != el_end; ++el_it) {
const Element & el = *el_it;
if (el.type != current_element_type) {
current_element_type = el.type;
nb_nodes_per_element = Mesh::getNbNodesPerElement(current_element_type);
}
nb_nodes += nb_nodes_per_element;
}
return nb_nodes;
}
/* -------------------------------------------------------------------------- */
inline Mesh & Mesh::getMeshFacets() {
if (!this->mesh_facets)
AKANTU_EXCEPTION(
"No facet mesh is defined yet! check the buildFacets functions");
return *this->mesh_facets;
}
/* -------------------------------------------------------------------------- */
inline const Mesh & Mesh::getMeshFacets() const {
if (!this->mesh_facets)
AKANTU_EXCEPTION(
"No facet mesh is defined yet! check the buildFacets functions");
return *this->mesh_facets;
}
/* -------------------------------------------------------------------------- */
inline const Mesh & Mesh::getMeshParent() const {
if (!this->mesh_parent)
AKANTU_EXCEPTION(
"No parent mesh is defined! This is only valid in a mesh_facets");
return *this->mesh_parent;
}
/* -------------------------------------------------------------------------- */
-} // akantu
+} // namespace akantu
#endif /* __AKANTU_MESH_INLINE_IMPL_CC__ */
diff --git a/src/mesh/node_group.hh b/src/mesh/node_group.hh
index a1602815a..40af0023e 100644
--- a/src/mesh/node_group.hh
+++ b/src/mesh/node_group.hh
@@ -1,137 +1,141 @@
/**
* @file node_group.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Dec 08 2015
*
* @brief Node group definition
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
* Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
* Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_array.hh"
#include "aka_memory.hh"
#include "mesh_filter.hh"
#include "dumpable.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_NODE_GROUP_HH__
#define __AKANTU_NODE_GROUP_HH__
namespace akantu {
class NodeGroup : public Memory, public Dumpable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NodeGroup(const std::string & name,
const Mesh & mesh,
const std::string & id = "node_group",
const MemoryID & memory_id = 0);
virtual ~NodeGroup();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
typedef Array<UInt>::const_iterator<UInt> const_node_iterator;
/// empty the node group
void empty();
/// iterator to the beginning of the node group
inline const_node_iterator begin() const;
/// iterator to the end of the node group
inline const_node_iterator end() const;
/// add a node and give the local position through an iterator
inline const_node_iterator add(UInt node, bool check_for_duplicate = true);
/// remove a node
inline void remove(UInt node);
+ inline decltype(auto) find(UInt node) const {
+ return node_group.find(node);
+ }
+
/// remove duplicated nodes
void optimize();
/// append a group to current one
void append(const NodeGroup & other_group);
/// apply a filter on current node group
template <typename T>
void applyNodeFilter(T & filter);
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO_NOT_CONST(Nodes, node_group, Array<UInt> &);
AKANTU_GET_MACRO(Nodes, node_group, const Array<UInt> &);
AKANTU_GET_MACRO(Name, name, const std::string &);
/// give the number of nodes in the current group
inline UInt getSize() const;
UInt * storage(){return node_group.storage();};
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// name of the group
std::string name;
/// list of nodes in the group
Array<UInt> & node_group;
/// reference to the mesh in question
//const Mesh & mesh;
};
/// standard output stream operator
inline std::ostream & operator <<(std::ostream & stream, const NodeGroup & _this)
{
_this.printself(stream);
return stream;
}
} // akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "node_group_inline_impl.cc"
#endif /* __AKANTU_NODE_GROUP_HH__ */
diff --git a/src/mesh_utils/cohesive_element_inserter.cc b/src/mesh_utils/cohesive_element_inserter.cc
index 1e282c93f..587afc25c 100644
--- a/src/mesh_utils/cohesive_element_inserter.cc
+++ b/src/mesh_utils/cohesive_element_inserter.cc
@@ -1,451 +1,458 @@
/**
* @file cohesive_element_inserter.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Dec 04 2013
* @date last modification: Sun Oct 04 2015
*
* @brief Cohesive element inserter functions
*
* @section LICENSE
*
* Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "cohesive_element_inserter.hh"
#include "element_group.hh"
#include <algorithm>
#include <limits>
/* -------------------------------------------------------------------------- */
namespace akantu {
CohesiveElementInserter::CohesiveElementInserter(Mesh & mesh, bool is_extrinsic,
const ID & id)
: id(id), mesh(mesh), mesh_facets(mesh.initMeshFacets()),
insertion_facets("insertion_facets", id),
insertion_limits(mesh.getSpatialDimension(), 2),
check_facets("check_facets", id) {
MeshUtils::buildAllFacets(mesh, mesh_facets, 0);
init(is_extrinsic);
}
/* -------------------------------------------------------------------------- */
CohesiveElementInserter::~CohesiveElementInserter() {
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
delete global_ids_updater;
#endif
}
/* -------------------------------------------------------------------------- */
void CohesiveElementInserter::init(bool is_extrinsic) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
MeshUtils::resetFacetToDouble(mesh_facets);
/// initialize facet insertion array
insertion_facets.initialize(mesh_facets,
_spatial_dimension = (spatial_dimension - 1),
_with_nb_element = true);
// mesh_facets.initElementTypeMapArray(
// insertion_facets, 1, spatial_dimension - 1, false, _ek_regular, true);
/// init insertion limits
for (UInt dim = 0; dim < spatial_dimension; ++dim) {
insertion_limits(dim, 0) = std::numeric_limits<Real>::max() * (-1.);
insertion_limits(dim, 1) = std::numeric_limits<Real>::max();
}
if (is_extrinsic) {
check_facets.initialize(mesh_facets,
_spatial_dimension = spatial_dimension - 1);
// mesh_facets.initElementTypeMapArray(check_facets, 1, spatial_dimension -
// 1);
initFacetsCheck();
}
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
facet_synchronizer = NULL;
global_ids_updater = NULL;
#endif
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void CohesiveElementInserter::initFacetsCheck() {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType facet_gt = *gt;
Mesh::type_iterator it =
mesh_facets.firstType(spatial_dimension - 1, facet_gt);
Mesh::type_iterator last =
mesh_facets.lastType(spatial_dimension - 1, facet_gt);
for (; it != last; ++it) {
ElementType facet_type = *it;
Array<bool> & f_check = check_facets(facet_type, facet_gt);
const Array<std::vector<Element>> & element_to_facet =
mesh_facets.getElementToSubelement(facet_type, facet_gt);
UInt nb_facet = element_to_facet.getSize();
f_check.resize(nb_facet);
for (UInt f = 0; f < nb_facet; ++f) {
if (element_to_facet(f)[1] == ElementNull ||
(element_to_facet(f)[0].ghost_type == _ghost &&
element_to_facet(f)[1].ghost_type == _ghost)) {
f_check(f) = false;
} else
f_check(f) = true;
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void CohesiveElementInserter::limitCheckFacets() {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
Vector<Real> bary_facet(spatial_dimension);
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType ghost_type = *gt;
Mesh::type_iterator it =
mesh_facets.firstType(spatial_dimension - 1, ghost_type);
Mesh::type_iterator end =
mesh_facets.lastType(spatial_dimension - 1, ghost_type);
for (; it != end; ++it) {
ElementType type = *it;
Array<bool> & f_check = check_facets(type, ghost_type);
UInt nb_facet = mesh_facets.getNbElement(type, ghost_type);
for (UInt f = 0; f < nb_facet; ++f) {
if (f_check(f)) {
mesh_facets.getBarycenter(f, type, bary_facet.storage(), ghost_type);
UInt coord_in_limit = 0;
while (coord_in_limit < spatial_dimension &&
bary_facet(coord_in_limit) >
insertion_limits(coord_in_limit, 0) &&
bary_facet(coord_in_limit) <
insertion_limits(coord_in_limit, 1))
++coord_in_limit;
if (coord_in_limit != spatial_dimension)
f_check(f) = false;
}
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void CohesiveElementInserter::setLimit(SpacialDirection axis, Real first_limit,
Real second_limit) {
AKANTU_DEBUG_ASSERT(
axis < mesh.getSpatialDimension(),
"You are trying to limit insertion in a direction that doesn't exist");
insertion_limits(axis, 0) = std::min(first_limit, second_limit);
insertion_limits(axis, 1) = std::max(first_limit, second_limit);
}
/* -------------------------------------------------------------------------- */
UInt CohesiveElementInserter::insertIntrinsicElements() {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
Vector<Real> bary_facet(spatial_dimension);
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType ghost_type = *gt;
Mesh::type_iterator it =
mesh_facets.firstType(spatial_dimension - 1, ghost_type);
Mesh::type_iterator end =
mesh_facets.lastType(spatial_dimension - 1, ghost_type);
for (; it != end; ++it) {
const ElementType type_facet = *it;
Array<bool> & f_insertion = insertion_facets(type_facet, ghost_type);
Array<std::vector<Element>> & element_to_facet =
mesh_facets.getElementToSubelement(type_facet, ghost_type);
UInt nb_facet = mesh_facets.getNbElement(type_facet, ghost_type);
for (UInt f = 0; f < nb_facet; ++f) {
if (element_to_facet(f)[1] == ElementNull)
continue;
mesh_facets.getBarycenter(f, type_facet, bary_facet.storage(),
ghost_type);
UInt coord_in_limit = 0;
while (coord_in_limit < spatial_dimension &&
bary_facet(coord_in_limit) >
insertion_limits(coord_in_limit, 0) &&
bary_facet(coord_in_limit) < insertion_limits(coord_in_limit, 1))
++coord_in_limit;
if (coord_in_limit == spatial_dimension)
f_insertion(f) = true;
}
}
}
AKANTU_DEBUG_OUT();
return insertElements();
}
/* -------------------------------------------------------------------------- */
void CohesiveElementInserter::insertIntrinsicElements(std::string physname,
UInt material_index) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
ElementTypeMapArray<UInt> * phys_data;
try {
phys_data = &(mesh_facets.getData<UInt>("physical_names"));
} catch (...) {
phys_data = &(mesh_facets.registerData<UInt>("physical_names"));
phys_data->initialize(mesh_facets,
_spatial_dimension = spatial_dimension - 1,
_with_nb_element = true);
// mesh_facets.initElementTypeMapArray(*phys_data, 1, spatial_dimension - 1,
// false, _ek_regular, true);
}
Vector<Real> bary_facet(spatial_dimension);
mesh_facets.createElementGroup(physname);
GhostType ghost_type = _not_ghost;
Mesh::type_iterator it =
mesh_facets.firstType(spatial_dimension - 1, ghost_type);
Mesh::type_iterator end =
mesh_facets.lastType(spatial_dimension - 1, ghost_type);
for (; it != end; ++it) {
const ElementType type_facet = *it;
Array<bool> & f_insertion = insertion_facets(type_facet, ghost_type);
Array<std::vector<Element>> & element_to_facet =
mesh_facets.getElementToSubelement(type_facet, ghost_type);
UInt nb_facet = mesh_facets.getNbElement(type_facet, ghost_type);
UInt coord_in_limit = 0;
ElementGroup & group = mesh.getElementGroup(physname);
ElementGroup & group_facet = mesh_facets.getElementGroup(physname);
Vector<Real> bary_physgroup(spatial_dimension);
Real norm_bary;
for (ElementGroup::const_element_iterator el_it(
- group.element_begin(type_facet, ghost_type));
- el_it != group.element_end(type_facet, ghost_type); ++el_it) {
+ group.begin(type_facet, ghost_type));
+ el_it != group.end(type_facet, ghost_type); ++el_it) {
UInt e = *el_it;
mesh.getBarycenter(e, type_facet, bary_physgroup.storage(), ghost_type);
#ifndef AKANTU_NDEBUG
bool find_a_partner = false;
#endif
norm_bary = bary_physgroup.norm();
Array<UInt> & material_id = (*phys_data)(type_facet, ghost_type);
for (UInt f = 0; f < nb_facet; ++f) {
if (element_to_facet(f)[1] == ElementNull)
continue;
mesh_facets.getBarycenter(f, type_facet, bary_facet.storage(),
ghost_type);
coord_in_limit = 0;
while (coord_in_limit < spatial_dimension &&
(std::abs(bary_facet(coord_in_limit) -
bary_physgroup(coord_in_limit)) /
norm_bary <
Math::getTolerance()))
++coord_in_limit;
if (coord_in_limit == spatial_dimension) {
f_insertion(f) = true;
#ifndef AKANTU_NDEBUG
find_a_partner = true;
#endif
group_facet.add(type_facet, f, ghost_type, false);
material_id(f) = material_index;
break;
}
}
AKANTU_DEBUG_ASSERT(find_a_partner,
"The element nO "
<< e << " of physical group " << physname
<< " did not find its associated facet!"
<< " Try to decrease math tolerance. "
<< std::endl);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
UInt CohesiveElementInserter::insertElements(bool only_double_facets) {
- NewNodesEvent node_event;
- node_event.getList().extendComponentsInterlaced(2, 1);
+ CohesiveNewNodesEvent node_event;
NewElementsEvent element_event;
+ Array<UInt> new_pairs(0, 2);
+
UInt nb_new_elements = MeshUtils::insertCohesiveElements(
- mesh, mesh_facets, insertion_facets, node_event.getList(),
+ mesh, mesh_facets, insertion_facets, new_pairs,
element_event.getList(), only_double_facets);
- UInt nb_new_nodes = node_event.getList().getSize();
+ UInt nb_new_nodes = new_pairs.getSize();
+ node_event.getList().reserve(nb_new_nodes);
+ node_event.getOldNodesList().reserve(nb_new_nodes);
+ for(UInt n = 0; n < nb_new_nodes; ++n) {
+ node_event.getList().push_back(new_pairs(n, 1));
+ node_event.getOldNodesList().push_back(new_pairs(n, 0));
+ }
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
if (mesh.getNodesType().getSize()) {
/// update nodes type
updateNodesType(mesh, node_event);
updateNodesType(mesh_facets, node_event);
/// update global ids
nb_new_nodes = this->updateGlobalIDs(node_event);
/// compute total number of new elements
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
comm.allReduce(&nb_new_elements, 1, _so_sum);
}
#endif
if (nb_new_nodes > 0)
mesh.sendEvent(node_event);
if (nb_new_elements > 0) {
updateInsertionFacets();
- mesh.updateTypesOffsets(_not_ghost);
+ //mesh.updateTypesOffsets(_not_ghost);
mesh.sendEvent(element_event);
MeshUtils::resetFacetToDouble(mesh_facets);
}
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
if (mesh.getNodesType().getSize()) {
/// update global ids
this->synchronizeGlobalIDs(node_event);
}
#endif
return nb_new_elements;
}
/* -------------------------------------------------------------------------- */
void CohesiveElementInserter::updateInsertionFacets() {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType facet_gt = *gt;
Mesh::type_iterator it =
mesh_facets.firstType(spatial_dimension - 1, facet_gt);
Mesh::type_iterator last =
mesh_facets.lastType(spatial_dimension - 1, facet_gt);
for (; it != last; ++it) {
ElementType facet_type = *it;
Array<bool> & ins_facets = insertion_facets(facet_type, facet_gt);
// this is the extrinsic case
if (check_facets.exists(facet_type, facet_gt)) {
Array<bool> & f_check = check_facets(facet_type, facet_gt);
UInt nb_facets = f_check.getSize();
for (UInt f = 0; f < ins_facets.getSize(); ++f) {
if (ins_facets(f)) {
++nb_facets;
ins_facets(f) = false;
f_check(f) = false;
}
}
f_check.resize(nb_facets);
}
// and this the intrinsic one
else {
ins_facets.resize(mesh_facets.getNbElement(facet_type, facet_gt));
ins_facets.set(false);
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void CohesiveElementInserter::printself(std::ostream & stream,
int indent) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "CohesiveElementInserter [" << std::endl;
stream << space << " + mesh [" << std::endl;
mesh.printself(stream, indent + 2);
stream << space << AKANTU_INDENT << "]" << std::endl;
stream << space << " + mesh_facets [" << std::endl;
mesh_facets.printself(stream, indent + 2);
stream << space << AKANTU_INDENT << "]" << std::endl;
stream << space << "]" << std::endl;
}
} // namespace akantu
diff --git a/src/mesh_utils/cohesive_element_inserter.hh b/src/mesh_utils/cohesive_element_inserter.hh
index 14620c62a..0377b3191 100644
--- a/src/mesh_utils/cohesive_element_inserter.hh
+++ b/src/mesh_utils/cohesive_element_inserter.hh
@@ -1,211 +1,223 @@
/**
* @file cohesive_element_inserter.hh
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Dec 04 2013
* @date last modification: Fri Oct 02 2015
*
* @brief Cohesive element inserter
*
* @section LICENSE
*
* Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_COHESIVE_ELEMENT_INSERTER_HH__
#define __AKANTU_COHESIVE_ELEMENT_INSERTER_HH__
/* -------------------------------------------------------------------------- */
#include "data_accessor.hh"
#include "mesh_utils.hh"
#include <numeric>
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
#include "facet_synchronizer.hh"
#include "global_ids_updater.hh"
#endif
/* -------------------------------------------------------------------------- */
namespace akantu {
class CohesiveElementInserter : public DataAccessor<Element> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
CohesiveElementInserter(Mesh & mesh, bool is_extrinsic = false,
const ID & id = "cohesive_element_inserter");
virtual ~CohesiveElementInserter();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// init function
void init(bool is_extrinsic);
/// set range limitation for intrinsic cohesive element insertion
void setLimit(SpacialDirection axis, Real first_limit, Real second_limit);
/// insert intrinsic cohesive elements in a predefined range
UInt insertIntrinsicElements();
/// preset insertion of intrinsic cohesive elements along
/// a predefined group of facet and assign them a defined material index.
/// insertElement() method has to be called to finalize insertion.
void insertIntrinsicElements(std::string physname, UInt material_index);
/// insert extrinsic cohesive elements (returns the number of new
/// cohesive elements)
UInt insertElements(bool only_double_facets = false);
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
/// limit check facets to match given insertion limits
void limitCheckFacets();
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
/// init parallel variables
void initParallel(FacetSynchronizer * facet_synchronizer,
ElementSynchronizer * element_synchronizer);
#endif
protected:
/// init facets check
void initFacetsCheck();
/// update facet insertion arrays after facets doubling
void updateInsertionFacets();
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
/// update nodes type and global ids for parallel simulations
/// (locally, within each processor)
UInt updateGlobalIDs(NewNodesEvent & node_event);
/// synchronize the global ids among the processors in parallel simulations
void synchronizeGlobalIDs(NewNodesEvent & node_event);
/// update nodes type
void updateNodesType(Mesh & mesh, NewNodesEvent & node_event);
/// functions for parallel communications
inline UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) override;
template <bool pack_mode>
inline void
packUnpackGlobalConnectivity(CommunicationBuffer & buffer,
const Array<Element> & elements) const;
template <bool pack_mode>
inline void
packUnpackGroupedInsertionData(CommunicationBuffer & buffer,
const Array<Element> & elements) const;
#else
/// functions for parallel communications
inline UInt getNbData(const Array<Element> &,
const SynchronizationTag &) const override {
return 0;
}
inline void packData(CommunicationBuffer &, const Array<Element> &,
const SynchronizationTag &) const override {}
inline void unpackData(CommunicationBuffer &, const Array<Element> &,
const SynchronizationTag &) override {}
#endif
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO_NOT_CONST(InsertionFacetsByElement, insertion_facets,
ElementTypeMapArray<bool> &);
AKANTU_GET_MACRO(InsertionFacetsByElement, insertion_facets,
const ElementTypeMapArray<bool> &);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(InsertionFacets, insertion_facets, bool);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(CheckFacets, check_facets, bool);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(CheckFacets, check_facets, bool);
AKANTU_GET_MACRO(MeshFacets, mesh_facets, const Mesh &);
AKANTU_GET_MACRO_NOT_CONST(MeshFacets, mesh_facets, Mesh &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// object id
ID id;
/// main mesh where to insert cohesive elements
Mesh & mesh;
/// mesh containing facets
Mesh & mesh_facets;
/// list of facets where to insert elements
ElementTypeMapArray<bool> insertion_facets;
/// limits for element insertion
Array<Real> insertion_limits;
/// vector containing facets in which extrinsic cohesive elements can be
/// inserted
ElementTypeMapArray<bool> check_facets;
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
/// facet synchronizer
FacetSynchronizer * facet_synchronizer;
/// global connectivity ids updater
GlobalIdsUpdater * global_ids_updater;
#endif
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
#include "cohesive_element_inserter_inline_impl.cc"
#endif
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const CohesiveElementInserter & _this) {
_this.printself(stream);
return stream;
}
+class CohesiveNewNodesEvent : public NewNodesEvent{
+public:
+ CohesiveNewNodesEvent() = default;
+ virtual ~CohesiveNewNodesEvent() = default;
+
+ AKANTU_GET_MACRO_NOT_CONST(OldNodesList, old_nodes, Array<UInt> &);
+ AKANTU_GET_MACRO(OldNodesList, old_nodes, const Array<UInt> &);
+private:
+ Array<UInt> old_nodes;
+};
+
+
} // akantu
#endif /* __AKANTU_COHESIVE_ELEMENT_INSERTER_HH__ */
diff --git a/src/mesh_utils/mesh_partition.cc b/src/mesh_utils/mesh_partition.cc
index 648214182..01ee4574f 100644
--- a/src/mesh_utils/mesh_partition.cc
+++ b/src/mesh_utils/mesh_partition.cc
@@ -1,441 +1,410 @@
/**
* @file mesh_partition.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Aug 17 2010
* @date last modification: Fri Jan 22 2016
*
* @brief implementation of common part of all partitioner
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
* Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
* Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "mesh_partition.hh"
-#include "mesh_utils.hh"
#include "aka_types.hh"
+#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
#include <unordered_map>
/* -------------------------------------------------------------------------- */
-
namespace akantu {
/* -------------------------------------------------------------------------- */
MeshPartition::MeshPartition(const Mesh & mesh, UInt spatial_dimension,
const ID & id, const MemoryID & memory_id)
: Memory(id, memory_id), mesh(mesh), spatial_dimension(spatial_dimension),
partitions("partition", id, memory_id),
ghost_partitions("ghost_partition", id, memory_id),
ghost_partitions_offset("ghost_partition_offset", id, memory_id),
saved_connectivity("saved_connectivity", id, memory_id) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
MeshPartition::~MeshPartition() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* TODO this function should most probably be rewritten in a more modern way
* conversion in c++ of the GENDUALMETIS (mesh.c) function wrote by George in
* Metis (University of Minnesota)
*/
void MeshPartition::buildDualGraph(Array<Int> & dxadj, Array<Int> & dadjncy,
Array<Int> & edge_loads,
const EdgeLoadFunctor & edge_load_func) {
AKANTU_DEBUG_IN();
// tweak mesh;
- const Mesh::ConnectivityTypeList & type_list = mesh.getConnectivityTypeList();
- UInt nb_types = type_list.size();
UInt nb_good_types = 0;
- Vector<UInt> nb_nodes_per_element_p1(nb_types);
-
- Vector<UInt> magic_number(nb_types);
-
- // UInt * conn_val[nb_types];
- Vector<UInt> nb_element(nb_types);
-
- Array<UInt> ** conn = new Array<UInt> *[nb_types];
-
- Array<Element> lin_to_element;
+ std::vector<UInt> nb_nodes_per_element_p1;
+ std::vector<UInt> magic_number;
+ std::vector<UInt> nb_element;
+ std::vector<Array<UInt> *> conn;
Element elem;
elem.ghost_type = _not_ghost;
- const_cast<Mesh &>(mesh).updateTypesOffsets(_not_ghost);
- const_cast<Mesh &>(mesh).updateTypesOffsets(_ghost);
+ UInt spatial_dimension = mesh.getSpatialDimension();
- Mesh::ConnectivityTypeList::const_iterator it;
- for (it = type_list.begin(); it != type_list.end(); ++it) {
- ElementType type = *it;
- if (Mesh::getSpatialDimension(type) != mesh.getSpatialDimension())
- continue;
+ for (auto & type :
+ mesh.elementTypes(spatial_dimension, _not_ghost, _ek_not_defined)) {
elem.type = type;
ElementType type_p1 = Mesh::getP1ElementType(type);
- nb_nodes_per_element_p1[nb_good_types] =
- Mesh::getNbNodesPerElement(type_p1);
- nb_element[nb_good_types] =
- mesh.getConnectivity(type, _not_ghost).getSize();
- magic_number[nb_good_types] =
- Mesh::getNbNodesPerElement(Mesh::getFacetType(type_p1));
-
- conn[nb_good_types] =
- &const_cast<Array<UInt> &>(mesh.getConnectivity(type, _not_ghost));
+ conn.push_back(
+ &const_cast<Array<UInt> &>(mesh.getConnectivity(type, _not_ghost)));
+ nb_nodes_per_element_p1.push_back(Mesh::getNbNodesPerElement(type_p1));
+ nb_element.push_back(conn.back()->getSize());
+ magic_number.push_back(
+ Mesh::getNbNodesPerElement(Mesh::getFacetType(type_p1)));
- for (UInt i = 0; i < nb_element[nb_good_types]; ++i) {
+ for (UInt i = 0; i < nb_element.back(); ++i) {
elem.element = i;
lin_to_element.push_back(elem);
}
- nb_good_types++;
+ ++nb_good_types;
}
- CSR<UInt> node_to_elem;
+ CSR<Element> node_to_elem;
MeshUtils::buildNode2Elements(mesh, node_to_elem);
UInt nb_total_element = 0;
UInt nb_total_node_element = 0;
for (UInt t = 0; t < nb_good_types; ++t) {
nb_total_element += nb_element[t];
nb_total_node_element += nb_element[t] * nb_nodes_per_element_p1[t];
}
dxadj.resize(nb_total_element + 1);
/// initialize the dxadj array
for (UInt t = 0, linerized_el = 0; t < nb_good_types; ++t)
for (UInt el = 0; el < nb_element[t]; ++el, ++linerized_el)
dxadj(linerized_el) = nb_nodes_per_element_p1[t];
/// convert the dxadj_val array in a csr one
for (UInt i = 1; i < nb_total_element; ++i)
dxadj(i) += dxadj(i - 1);
for (UInt i = nb_total_element; i > 0; --i)
dxadj(i) = dxadj(i - 1);
dxadj(0) = 0;
dadjncy.resize(2 * dxadj(nb_total_element));
edge_loads.resize(2 * dxadj(nb_total_element));
/// weight map to determine adjacency
std::unordered_map<UInt, UInt> weight_map;
for (UInt t = 0, linerized_el = 0; t < nb_good_types; ++t) {
for (UInt el = 0; el < nb_element[t]; ++el, ++linerized_el) {
/// fill the weight map
for (UInt n = 0; n < nb_nodes_per_element_p1[t]; ++n) {
UInt node = (*conn[t])(el, n);
- CSR<UInt>::iterator k;
+ CSR<Element>::iterator k;
for (k = node_to_elem.rbegin(node); k != node_to_elem.rend(node); --k) {
- UInt current_el = *k;
+ Element current_element = *k;
+ UInt current_el = lin_to_element.find(current_element);
+
if (current_el <= linerized_el)
break;
auto it_w = weight_map.find(current_el);
if (it_w == weight_map.end()) {
weight_map[current_el] = 1;
} else {
it_w->second++;
}
}
}
/// each element with a weight of the size of a facet are adjacent
for (auto it_w = weight_map.begin(); it_w != weight_map.end(); ++it_w) {
if (it_w->second == magic_number[t]) {
UInt adjacent_el = it_w->first;
#if defined(AKANTU_COHESIVE_ELEMENT)
/// Patch in order to prevent neighboring cohesive elements
/// from detecting each other
- ElementKind linearized_el_kind =
- mesh.linearizedToElement(linerized_el).kind;
- ElementKind adjacent_el_kind =
- mesh.linearizedToElement(adjacent_el).kind;
+ ElementKind linearized_el_kind = lin_to_element(linerized_el).kind;
+ ElementKind adjacent_el_kind = lin_to_element(adjacent_el).kind;
if (linearized_el_kind == adjacent_el_kind &&
linearized_el_kind == _ek_cohesive)
continue;
#endif
UInt index_adj = dxadj(adjacent_el)++;
UInt index_lin = dxadj(linerized_el)++;
dadjncy(index_lin) = adjacent_el;
dadjncy(index_adj) = linerized_el;
}
}
weight_map.clear();
}
}
Int k_start = 0;
for (UInt t = 0, linerized_el = 0, j = 0; t < nb_good_types; ++t)
for (UInt el = 0; el < nb_element[t]; ++el, ++linerized_el) {
for (Int k = k_start; k < dxadj(linerized_el); ++k, ++j)
dadjncy(j) = dadjncy(k);
dxadj(linerized_el) = j;
k_start += nb_nodes_per_element_p1[t];
}
for (UInt i = nb_total_element; i > 0; --i)
dxadj(i) = dxadj(i - 1);
dxadj(0) = 0;
UInt adj = 0;
for (UInt i = 0; i < nb_total_element; ++i) {
UInt nb_adj = dxadj(i + 1) - dxadj(i);
for (UInt j = 0; j < nb_adj; ++j, ++adj) {
Int el_adj_id = dadjncy(dxadj(i) + j);
Element el = lin_to_element(i);
Element el_adj = lin_to_element(el_adj_id);
Int load = edge_load_func(el, el_adj);
edge_loads(adj) = load;
}
}
- delete [] conn;
-
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshPartition::fillPartitionInformation(
const Mesh & mesh, const Int * linearized_partitions) {
AKANTU_DEBUG_IN();
- CSR<UInt> node_to_elem;
+ CSR<Element> node_to_elem;
MeshUtils::buildNode2Elements(mesh, node_to_elem);
- Mesh::type_iterator it =
- mesh.firstType(spatial_dimension, _not_ghost, _ek_not_defined);
- Mesh::type_iterator end =
- mesh.lastType(spatial_dimension, _not_ghost, _ek_not_defined);
-
UInt linearized_el = 0;
- for (; it != end; ++it) {
- ElementType type = *it;
-
+ for (auto & type : mesh.elementTypes(spatial_dimension, _not_ghost, _ek_not_defined)) {
UInt nb_element = mesh.getNbElement(type);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
partitions.alloc(nb_element, 1, type, _not_ghost);
- CSR<UInt> & ghost_part_csr = ghost_partitions_csr(type, _not_ghost);
+ auto & ghost_part_csr = ghost_partitions_csr(type, _not_ghost);
ghost_part_csr.resizeRows(nb_element);
ghost_partitions_offset.alloc(nb_element + 1, 1, type, _ghost);
ghost_partitions.alloc(0, 1, type, _ghost);
const Array<UInt> & connectivity = mesh.getConnectivity(type, _not_ghost);
for (UInt el = 0; el < nb_element; ++el, ++linearized_el) {
UInt part = linearized_partitions[linearized_el];
partitions(type, _not_ghost)(el) = part;
std::list<UInt> list_adj_part;
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
UInt node = connectivity.storage()[el * nb_nodes_per_element + n];
- CSR<UInt>::iterator ne;
+ CSR<Element>::iterator ne;
for (ne = node_to_elem.begin(node); ne != node_to_elem.end(node);
++ne) {
- UInt adj_el = *ne;
+ const Element & adj_element = *ne;
+ UInt adj_el = lin_to_element.find(adj_element);
UInt adj_part = linearized_partitions[adj_el];
if (part != adj_part) {
list_adj_part.push_back(adj_part);
}
}
}
list_adj_part.sort();
list_adj_part.unique();
- for (std::list<UInt>::iterator adj_it = list_adj_part.begin();
- adj_it != list_adj_part.end(); ++adj_it) {
- ghost_part_csr.getRows().push_back(*adj_it);
+ for (auto & adj_part : list_adj_part) {
+ ghost_part_csr.getRows().push_back(adj_part);
ghost_part_csr.rowOffset(el)++;
- ghost_partitions(type, _ghost).push_back(*adj_it);
+ ghost_partitions(type, _ghost).push_back(adj_part);
ghost_partitions_offset(type, _ghost)(el)++;
}
}
ghost_part_csr.countToCSR();
/// convert the ghost_partitions_offset array in an offset array
Array<UInt> & ghost_partitions_offset_ptr =
ghost_partitions_offset(type, _ghost);
for (UInt i = 1; i < nb_element; ++i)
ghost_partitions_offset_ptr(i) += ghost_partitions_offset_ptr(i - 1);
for (UInt i = nb_element; i > 0; --i)
ghost_partitions_offset_ptr(i) = ghost_partitions_offset_ptr(i - 1);
ghost_partitions_offset_ptr(0) = 0;
}
// All Facets
for (Int sp = spatial_dimension - 1; sp >= 0; --sp) {
- Mesh::type_iterator fit = mesh.firstType(sp, _not_ghost, _ek_not_defined);
- Mesh::type_iterator fend = mesh.lastType(sp, _not_ghost, _ek_not_defined);
-
- for (; fit != fend; ++fit) {
- ElementType type = *fit;
-
+ for (auto & type : mesh.elementTypes(sp, _not_ghost, _ek_not_defined)) {
UInt nb_element = mesh.getNbElement(type);
partitions.alloc(nb_element, 1, type, _not_ghost);
AKANTU_DEBUG_INFO("Allocating partitions for " << type);
- CSR<UInt> & ghost_part_csr = ghost_partitions_csr(type, _not_ghost);
+ auto & ghost_part_csr = ghost_partitions_csr(type, _not_ghost);
ghost_part_csr.resizeRows(nb_element);
ghost_partitions_offset.alloc(nb_element + 1, 1, type, _ghost);
ghost_partitions.alloc(0, 1, type, _ghost);
AKANTU_DEBUG_INFO("Allocating ghost_partitions for " << type);
- const Array<std::vector<Element> > & elem_to_subelem =
+ const Array<std::vector<Element>> & elem_to_subelem =
mesh.getElementToSubelement(type, _not_ghost);
for (UInt i(0); i < mesh.getNbElement(type, _not_ghost);
++i) { // Facet loop
const std::vector<Element> & adjacent_elems = elem_to_subelem(i);
if (!adjacent_elems.empty()) {
Element min_elem;
UInt min_part(std::numeric_limits<UInt>::max());
std::set<UInt> adjacent_parts;
for (UInt j(0); j < adjacent_elems.size(); ++j) {
UInt adjacent_elem_id = adjacent_elems[j].element;
UInt adjacent_elem_part =
partitions(adjacent_elems[j].type,
adjacent_elems[j].ghost_type)(adjacent_elem_id);
if (adjacent_elem_part < min_part) {
min_part = adjacent_elem_part;
min_elem = adjacent_elems[j];
}
adjacent_parts.insert(adjacent_elem_part);
}
partitions(type, _not_ghost)(i) = min_part;
- CSR<UInt>::iterator git =
+ auto git =
ghost_partitions_csr(min_elem.type, _not_ghost)
.begin(min_elem.element);
- CSR<UInt>::iterator gend =
+ auto gend =
ghost_partitions_csr(min_elem.type, _not_ghost)
.end(min_elem.element);
for (; git != gend; ++git) {
- adjacent_parts.insert(*git);
+
+ adjacent_parts.insert(min_part);
}
adjacent_parts.erase(min_part);
- std::set<UInt>::const_iterator pit = adjacent_parts.begin();
- std::set<UInt>::const_iterator pend = adjacent_parts.end();
- for (; pit != pend; ++pit) {
- ghost_part_csr.getRows().push_back(*pit);
+ for (auto & part : adjacent_parts) {
+ ghost_part_csr.getRows().push_back(part);
ghost_part_csr.rowOffset(i)++;
- ghost_partitions(type, _ghost).push_back(*pit);
+ ghost_partitions(type, _ghost).push_back(part);
}
ghost_partitions_offset(type, _ghost)(i + 1) =
ghost_partitions_offset(type, _ghost)(i + 1) +
adjacent_elems.size();
} else {
partitions(type, _not_ghost)(i) = 0;
}
}
ghost_part_csr.countToCSR();
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshPartition::tweakConnectivity(const Array<UInt> & pairs) {
AKANTU_DEBUG_IN();
if (pairs.getSize() == 0)
return;
Mesh::type_iterator it =
mesh.firstType(spatial_dimension, _not_ghost, _ek_not_defined);
Mesh::type_iterator end =
mesh.lastType(spatial_dimension, _not_ghost, _ek_not_defined);
for (; it != end; ++it) {
ElementType type = *it;
Array<UInt> & conn =
const_cast<Array<UInt> &>(mesh.getConnectivity(type, _not_ghost));
UInt nb_nodes_per_element = conn.getNbComponent();
UInt nb_element = conn.getSize();
Array<UInt> & saved_conn = saved_connectivity.alloc(
nb_element, nb_nodes_per_element, type, _not_ghost);
saved_conn.copy(conn);
for (UInt i = 0; i < pairs.getSize(); ++i) {
for (UInt el = 0; el < nb_element; ++el) {
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
if (pairs(i, 1) == conn(el, n))
conn(el, n) = pairs(i, 0);
}
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshPartition::restoreConnectivity() {
AKANTU_DEBUG_IN();
ElementTypeMapArray<UInt>::type_iterator it = saved_connectivity.firstType(
spatial_dimension, _not_ghost, _ek_not_defined);
ElementTypeMapArray<UInt>::type_iterator end = saved_connectivity.lastType(
spatial_dimension, _not_ghost, _ek_not_defined);
for (; it != end; ++it) {
ElementType type = *it;
Array<UInt> & conn =
const_cast<Array<UInt> &>(mesh.getConnectivity(type, _not_ghost));
Array<UInt> & saved_conn = saved_connectivity(type, _not_ghost);
conn.copy(saved_conn);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
-} // akantu
+} // namespace akantu
diff --git a/src/mesh_utils/mesh_partition.hh b/src/mesh_utils/mesh_partition.hh
index 849530369..0d3ad6346 100644
--- a/src/mesh_utils/mesh_partition.hh
+++ b/src/mesh_utils/mesh_partition.hh
@@ -1,150 +1,152 @@
/**
* @file mesh_partition.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Sep 01 2015
*
* @brief tools to partitionate a mesh
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
* Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
* Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MESH_PARTITION_HH__
#define __AKANTU_MESH_PARTITION_HH__
/* -------------------------------------------------------------------------- */
-#include "aka_memory.hh"
#include "aka_csr.hh"
+#include "aka_memory.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class MeshPartition : protected Memory {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
-
MeshPartition(const Mesh & mesh, UInt spatial_dimension,
const ID & id = "MeshPartitioner",
- const MemoryID & memory_id = 0);
+ const MemoryID & memory_id = 0);
virtual ~MeshPartition();
class EdgeLoadFunctor {
public:
virtual Int operator()(__attribute__((unused)) const Element & el1,
- __attribute__((unused)) const Element & el2) const = 0;
+ __attribute__((unused))
+ const Element & el2) const = 0;
};
class ConstEdgeLoadFunctor : public EdgeLoadFunctor {
public:
virtual inline Int operator()(__attribute__((unused)) const Element & el1,
- __attribute__((unused)) const Element & el2) const {
+ __attribute__((unused))
+ const Element & el2) const {
return 1;
}
};
-
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// define a partition of the mesh
- virtual void partitionate(UInt nb_part,
- const EdgeLoadFunctor & edge_load_func = ConstEdgeLoadFunctor(),
- const Array<UInt> & pairs = Array<UInt>()) = 0;
+ virtual void
+ partitionate(UInt nb_part,
+ const EdgeLoadFunctor & edge_load_func = ConstEdgeLoadFunctor(),
+ const Array<UInt> & pairs = Array<UInt>()) = 0;
/// reorder the nodes to reduce the filling during the factorization of a
/// matrix that has a profil based on the connectivity of the mesh
virtual void reorder() = 0;
/// fill the partitions array with a given linearized partition information
- void fillPartitionInformation(const Mesh & mesh, const Int * linearized_partitions);
+ void fillPartitionInformation(const Mesh & mesh,
+ const Int * linearized_partitions);
protected:
-
/// build the dual graph of the mesh, for all element of spatial_dimension
void buildDualGraph(Array<Int> & dxadj, Array<Int> & dadjncy,
- Array<Int> & edge_loads,
- const EdgeLoadFunctor & edge_load_func);
+ Array<Int> & edge_loads,
+ const EdgeLoadFunctor & edge_load_func);
/// tweak the mesh to handle the PBC pairs
void tweakConnectivity(const Array<UInt> & pairs);
/// restore the mesh that has been tweaked
void restoreConnectivity();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
-
AKANTU_GET_MACRO(Partitions, partitions, const ElementTypeMapArray<UInt> &);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Partition, partitions, UInt);
- AKANTU_GET_MACRO(GhostPartitionCSR, ghost_partitions_csr, const ElementTypeMap< CSR<UInt> > &);
+ AKANTU_GET_MACRO(GhostPartitionCSR, ghost_partitions_csr,
+ const ElementTypeMap<CSR<UInt>> &);
AKANTU_GET_MACRO(NbPartition, nb_partitions, UInt);
AKANTU_SET_MACRO(NbPartition, nb_partitions, UInt);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// id
std::string id;
/// the mesh to partition
const Mesh & mesh;
/// dimension of the elements to consider in the mesh
UInt spatial_dimension;
/// number of partitions
UInt nb_partitions;
/// partition numbers
ElementTypeMapArray<UInt> partitions;
- ElementTypeMap< CSR<UInt> > ghost_partitions_csr;
+ ElementTypeMap<CSR<UInt>> ghost_partitions_csr;
ElementTypeMapArray<UInt> ghost_partitions;
ElementTypeMapArray<UInt> ghost_partitions_offset;
Array<UInt> * permutation;
ElementTypeMapArray<UInt> saved_connectivity;
+ Array<Element> lin_to_element;
};
-} // akantu
+} // namespace akantu
#ifdef AKANTU_USE_SCOTCH
#include "mesh_partition_scotch.hh"
#endif
#endif /* __AKANTU_MESH_PARTITION_HH__ */
diff --git a/src/mesh_utils/mesh_utils.cc b/src/mesh_utils/mesh_utils.cc
index 61ee0a24a..e0e53ad49 100644
--- a/src/mesh_utils/mesh_utils.cc
+++ b/src/mesh_utils/mesh_utils.cc
@@ -1,2342 +1,2342 @@
/**
* @file mesh_utils.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Leonardo Snozzi <leonardo.snozzi@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Aug 20 2010
* @date last modification: Fri Jan 22 2016
*
* @brief All mesh utils necessary for various tasks
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
* Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
* Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "mesh_utils.hh"
#include "element_synchronizer.hh"
#include "fe_engine.hh"
#include "mesh_accessor.hh"
/* -------------------------------------------------------------------------- */
#include <limits>
#include <numeric>
#include <queue>
#include <set>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
void MeshUtils::buildNode2Elements(const Mesh & mesh,
CSR<Element> & node_to_elem,
UInt spatial_dimension) {
AKANTU_DEBUG_IN();
if (spatial_dimension == _all_dimensions)
spatial_dimension = mesh.getSpatialDimension();
/// count number of occurrence of each node
UInt nb_nodes = mesh.getNbNodes();
/// array for the node-element list
node_to_elem.resizeRows(nb_nodes);
node_to_elem.clearRows();
AKANTU_DEBUG_ASSERT(
mesh.firstType(spatial_dimension) != mesh.lastType(spatial_dimension),
"Some elements must be found in right dimension to compute facets!");
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
Mesh::type_iterator first =
mesh.firstType(spatial_dimension, *gt, _ek_not_defined);
Mesh::type_iterator last =
mesh.lastType(spatial_dimension, *gt, _ek_not_defined);
for (; first != last; ++first) {
ElementType type = *first;
UInt nb_element = mesh.getNbElement(type, *gt);
Array<UInt>::const_iterator<Vector<UInt>> conn_it =
mesh.getConnectivity(type, *gt).begin(
Mesh::getNbNodesPerElement(type));
for (UInt el = 0; el < nb_element; ++el, ++conn_it)
for (UInt n = 0; n < conn_it->size(); ++n)
++node_to_elem.rowOffset((*conn_it)(n));
}
}
node_to_elem.countToCSR();
node_to_elem.resizeCols();
/// rearrange element to get the node-element list
Element e;
node_to_elem.beginInsertions();
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
Mesh::type_iterator first =
mesh.firstType(spatial_dimension, *gt, _ek_not_defined);
Mesh::type_iterator last =
mesh.lastType(spatial_dimension, *gt, _ek_not_defined);
e.ghost_type = *gt;
for (; first != last; ++first) {
ElementType type = *first;
e.type = type;
e.kind = Mesh::getKind(type);
UInt nb_element = mesh.getNbElement(type, *gt);
Array<UInt>::const_iterator<Vector<UInt>> conn_it =
mesh.getConnectivity(type, *gt).begin(
Mesh::getNbNodesPerElement(type));
for (UInt el = 0; el < nb_element; ++el, ++conn_it) {
e.element = el;
for (UInt n = 0; n < conn_it->size(); ++n)
node_to_elem.insertInRow((*conn_it)(n), e);
}
}
}
node_to_elem.endInsertions();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* This function should disappear in the future (used in mesh partitioning)
*/
-void MeshUtils::buildNode2Elements(const Mesh & mesh, CSR<UInt> & node_to_elem,
- UInt spatial_dimension) {
- AKANTU_DEBUG_IN();
- if (spatial_dimension == _all_dimensions)
- spatial_dimension = mesh.getSpatialDimension();
- UInt nb_nodes = mesh.getNbNodes();
-
- const Mesh::ConnectivityTypeList & type_list = mesh.getConnectivityTypeList();
- Mesh::ConnectivityTypeList::const_iterator it;
-
- UInt nb_types = type_list.size();
- UInt nb_good_types = 0;
-
- Vector<UInt> nb_nodes_per_element(nb_types);
- UInt ** conn_val = new UInt *[nb_types];
- Vector<UInt> nb_element(nb_types);
-
- for (it = type_list.begin(); it != type_list.end(); ++it) {
- ElementType type = *it;
- if (Mesh::getSpatialDimension(type) != spatial_dimension)
- continue;
-
- nb_nodes_per_element[nb_good_types] = Mesh::getNbNodesPerElement(type);
- conn_val[nb_good_types] = mesh.getConnectivity(type, _not_ghost).storage();
- nb_element[nb_good_types] =
- mesh.getConnectivity(type, _not_ghost).getSize();
- nb_good_types++;
- }
-
- AKANTU_DEBUG_ASSERT(
- nb_good_types != 0,
- "Some elements must be found in right dimension to compute facets!");
-
- /// array for the node-element list
- node_to_elem.resizeRows(nb_nodes);
- node_to_elem.clearRows();
-
- /// count number of occurrence of each node
- for (UInt t = 0; t < nb_good_types; ++t) {
- for (UInt el = 0; el < nb_element[t]; ++el) {
- UInt el_offset = el * nb_nodes_per_element[t];
- for (UInt n = 0; n < nb_nodes_per_element[t]; ++n) {
- ++node_to_elem.rowOffset(conn_val[t][el_offset + n]);
- }
- }
- }
-
- node_to_elem.countToCSR();
- node_to_elem.resizeCols();
- node_to_elem.beginInsertions();
-
- /// rearrange element to get the node-element list
- for (UInt t = 0, linearized_el = 0; t < nb_good_types; ++t)
- for (UInt el = 0; el < nb_element[t]; ++el, ++linearized_el) {
- UInt el_offset = el * nb_nodes_per_element[t];
- for (UInt n = 0; n < nb_nodes_per_element[t]; ++n)
- node_to_elem.insertInRow(conn_val[t][el_offset + n], linearized_el);
- }
-
- node_to_elem.endInsertions();
- delete[] conn_val;
- AKANTU_DEBUG_OUT();
-}
+// void MeshUtils::buildNode2Elements(const Mesh & mesh, CSR<UInt> & node_to_elem,
+// UInt spatial_dimension) {
+// AKANTU_DEBUG_IN();
+// if (spatial_dimension == _all_dimensions)
+// spatial_dimension = mesh.getSpatialDimension();
+// UInt nb_nodes = mesh.getNbNodes();
+
+// const Mesh::ConnectivityTypeList & type_list = mesh.getConnectivityTypeList();
+// Mesh::ConnectivityTypeList::const_iterator it;
+
+// UInt nb_types = type_list.size();
+// UInt nb_good_types = 0;
+
+// Vector<UInt> nb_nodes_per_element(nb_types);
+// UInt ** conn_val = new UInt *[nb_types];
+// Vector<UInt> nb_element(nb_types);
+
+// for (it = type_list.begin(); it != type_list.end(); ++it) {
+// ElementType type = *it;
+// if (Mesh::getSpatialDimension(type) != spatial_dimension)
+// continue;
+
+// nb_nodes_per_element[nb_good_types] = Mesh::getNbNodesPerElement(type);
+// conn_val[nb_good_types] = mesh.getConnectivity(type, _not_ghost).storage();
+// nb_element[nb_good_types] =
+// mesh.getConnectivity(type, _not_ghost).getSize();
+// nb_good_types++;
+// }
+
+// AKANTU_DEBUG_ASSERT(
+// nb_good_types != 0,
+// "Some elements must be found in right dimension to compute facets!");
+
+// /// array for the node-element list
+// node_to_elem.resizeRows(nb_nodes);
+// node_to_elem.clearRows();
+
+// /// count number of occurrence of each node
+// for (UInt t = 0; t < nb_good_types; ++t) {
+// for (UInt el = 0; el < nb_element[t]; ++el) {
+// UInt el_offset = el * nb_nodes_per_element[t];
+// for (UInt n = 0; n < nb_nodes_per_element[t]; ++n) {
+// ++node_to_elem.rowOffset(conn_val[t][el_offset + n]);
+// }
+// }
+// }
+
+// node_to_elem.countToCSR();
+// node_to_elem.resizeCols();
+// node_to_elem.beginInsertions();
+
+// /// rearrange element to get the node-element list
+// for (UInt t = 0, linearized_el = 0; t < nb_good_types; ++t)
+// for (UInt el = 0; el < nb_element[t]; ++el, ++linearized_el) {
+// UInt el_offset = el * nb_nodes_per_element[t];
+// for (UInt n = 0; n < nb_nodes_per_element[t]; ++n)
+// node_to_elem.insertInRow(conn_val[t][el_offset + n], linearized_el);
+// }
+
+// node_to_elem.endInsertions();
+// delete[] conn_val;
+// AKANTU_DEBUG_OUT();
+// }
/* -------------------------------------------------------------------------- */
void MeshUtils::buildNode2ElementsElementTypeMap(const Mesh & mesh,
CSR<UInt> & node_to_elem,
const ElementType & type,
const GhostType & ghost_type) {
AKANTU_DEBUG_IN();
UInt nb_nodes = mesh.getNbNodes();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_elements = mesh.getConnectivity(type, ghost_type).getSize();
UInt * conn_val = mesh.getConnectivity(type, ghost_type).storage();
/// array for the node-element list
node_to_elem.resizeRows(nb_nodes);
node_to_elem.clearRows();
/// count number of occurrence of each node
for (UInt el = 0; el < nb_elements; ++el) {
UInt el_offset = el * nb_nodes_per_element;
for (UInt n = 0; n < nb_nodes_per_element; ++n)
++node_to_elem.rowOffset(conn_val[el_offset + n]);
}
/// convert the occurrence array in a csr one
node_to_elem.countToCSR();
node_to_elem.resizeCols();
node_to_elem.beginInsertions();
/// save the element index in the node-element list
for (UInt el = 0; el < nb_elements; ++el) {
UInt el_offset = el * nb_nodes_per_element;
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
node_to_elem.insertInRow(conn_val[el_offset + n], el);
}
}
node_to_elem.endInsertions();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::buildFacets(Mesh & mesh) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType gt_facet = *gt;
Mesh::type_iterator it = mesh.firstType(spatial_dimension - 1, gt_facet);
Mesh::type_iterator end = mesh.lastType(spatial_dimension - 1, gt_facet);
for (; it != end; ++it) {
mesh.getConnectivity(*it, *gt).resize(0);
// \todo inform the mesh event handler
}
}
buildFacetsDimension(mesh, mesh, true, spatial_dimension);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::buildAllFacets(const Mesh & mesh, Mesh & mesh_facets,
UInt to_dimension) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
buildAllFacets(mesh, mesh_facets, spatial_dimension, to_dimension);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::buildAllFacets(const Mesh & mesh, Mesh & mesh_facets,
UInt from_dimension, UInt to_dimension) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(
mesh_facets.isMeshFacets(),
"The mesh_facets should be initialized with initMeshFacets");
const ElementTypeMapArray<UInt> * prank_to_element = nullptr;
if (mesh.isDistributed()) {
prank_to_element = &(mesh.getElementSynchronizer().getPrankToElement());
}
/// generate facets
buildFacetsDimension(mesh, mesh_facets, false, from_dimension,
prank_to_element);
/// copy nodes type
MeshAccessor mesh_accessor_facets(mesh_facets);
mesh_accessor_facets.getNodesType().copy(mesh.getNodesType());
/// sort facets and generate sub-facets
for (UInt i = from_dimension - 1; i > to_dimension; --i) {
buildFacetsDimension(mesh_facets, mesh_facets, false, i, prank_to_element);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::buildFacetsDimension(
const Mesh & mesh, Mesh & mesh_facets, bool boundary_only, UInt dimension,
const ElementTypeMapArray<UInt> * prank_to_element) {
AKANTU_DEBUG_IN();
// save the current parent of mesh_facets and set it temporarly to mesh since
// mesh is the one containing the elements for which mesh_facets has the
// sub-elements
// example: if the function is called with mesh = mesh_facets
const Mesh * mesh_facets_parent = nullptr;
try {
mesh_facets_parent = &mesh_facets.getMeshParent();
} catch (...) {
}
mesh_facets.defineMeshParent(mesh);
MeshAccessor mesh_accessor(mesh_facets);
UInt spatial_dimension = mesh.getSpatialDimension();
const Array<Real> & mesh_facets_nodes = mesh_facets.getNodes();
const Array<Real>::const_vector_iterator mesh_facets_nodes_it =
mesh_facets_nodes.begin(spatial_dimension);
CSR<Element> node_to_elem;
buildNode2Elements(mesh, node_to_elem, dimension);
Array<UInt> counter;
std::vector<Element> connected_elements;
// init the SubelementToElement data to improve performance
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType ghost_type = *gt;
Mesh::type_iterator first = mesh.firstType(dimension, ghost_type);
Mesh::type_iterator last = mesh.lastType(dimension, ghost_type);
for (; first != last; ++first) {
ElementType type = *first;
mesh_accessor.getSubelementToElement(type, ghost_type);
Vector<ElementType> facet_types = mesh.getAllFacetTypes(type);
for (UInt ft = 0; ft < facet_types.size(); ++ft) {
ElementType facet_type = facet_types(ft);
mesh_accessor.getElementToSubelement(facet_type, ghost_type);
mesh_accessor.getConnectivity(facet_type, ghost_type);
}
}
}
Element current_element;
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType ghost_type = *gt;
GhostType facet_ghost_type = ghost_type;
current_element.ghost_type = ghost_type;
Mesh::type_iterator first = mesh.firstType(dimension, ghost_type);
Mesh::type_iterator last = mesh.lastType(dimension, ghost_type);
for (; first != last; ++first) {
ElementType type = *first;
Vector<ElementType> facet_types = mesh.getAllFacetTypes(type);
current_element.type = type;
for (UInt ft = 0; ft < facet_types.size(); ++ft) {
ElementType facet_type = facet_types(ft);
UInt nb_element = mesh.getNbElement(type, ghost_type);
Array<std::vector<Element>> * element_to_subelement =
&mesh_facets.getElementToSubelement(facet_type, ghost_type);
Array<UInt> * connectivity_facets =
&mesh_facets.getConnectivity(facet_type, ghost_type);
UInt nb_facet_per_element = mesh.getNbFacetsPerElement(type, ft);
const Array<UInt> & element_connectivity =
mesh.getConnectivity(type, ghost_type);
const Matrix<UInt> facet_local_connectivity =
mesh.getFacetLocalConnectivity(type, ft);
UInt nb_nodes_per_facet = connectivity_facets->getNbComponent();
Vector<UInt> facet(nb_nodes_per_facet);
for (UInt el = 0; el < nb_element; ++el) {
current_element.element = el;
for (UInt f = 0; f < nb_facet_per_element; ++f) {
for (UInt n = 0; n < nb_nodes_per_facet; ++n)
facet(n) =
element_connectivity(el, facet_local_connectivity(f, n));
UInt first_node_nb_elements = node_to_elem.getNbCols(facet(0));
counter.resize(first_node_nb_elements);
counter.clear();
// loop over the other nodes to search intersecting elements,
// which are the elements that share another node with the
// starting element after first_node
CSR<Element>::iterator first_node_elements =
node_to_elem.begin(facet(0));
CSR<Element>::iterator first_node_elements_end =
node_to_elem.end(facet(0));
UInt local_el = 0;
for (; first_node_elements != first_node_elements_end;
++first_node_elements, ++local_el) {
for (UInt n = 1; n < nb_nodes_per_facet; ++n) {
CSR<Element>::iterator node_elements_begin =
node_to_elem.begin(facet(n));
CSR<Element>::iterator node_elements_end =
node_to_elem.end(facet(n));
counter(local_el) +=
std::count(node_elements_begin, node_elements_end,
*first_node_elements);
}
}
// counting the number of elements connected to the facets and
// taking the minimum element number, because the facet should
// be inserted just once
UInt nb_element_connected_to_facet = 0;
Element minimum_el = ElementNull;
connected_elements.clear();
for (UInt el_f = 0; el_f < first_node_nb_elements; el_f++) {
Element real_el = node_to_elem(facet(0), el_f);
if (counter(el_f) == nb_nodes_per_facet - 1) {
++nb_element_connected_to_facet;
minimum_el = std::min(minimum_el, real_el);
connected_elements.push_back(real_el);
}
}
if (minimum_el == current_element) {
bool full_ghost_facet = false;
UInt n = 0;
while (n < nb_nodes_per_facet && mesh.isPureGhostNode(facet(n)))
++n;
if (n == nb_nodes_per_facet)
full_ghost_facet = true;
if (!full_ghost_facet) {
if (!boundary_only ||
(boundary_only && nb_element_connected_to_facet == 1)) {
std::vector<Element> elements;
// build elements_on_facets: linearized_el must come first
// in order to store the facet in the correct direction
// and avoid to invert the sign in the normal computation
elements.push_back(current_element);
/// boundary facet
if (nb_element_connected_to_facet == 1)
elements.push_back(ElementNull);
/// internal facet
else if (nb_element_connected_to_facet == 2) {
elements.push_back(connected_elements[1]);
/// check if facet is in between ghost and normal
/// elements: if it's the case, the facet is either
/// ghost or not ghost. The criterion to decide this
/// is arbitrary. It was chosen to check the processor
/// id (prank) of the two neighboring elements. If
/// prank of the ghost element is lower than prank of
/// the normal one, the facet is not ghost, otherwise
/// it's ghost
GhostType gt[2] = {_not_ghost, _not_ghost};
for (UInt el = 0; el < connected_elements.size(); ++el)
gt[el] = connected_elements[el].ghost_type;
if (gt[0] + gt[1] == 1) {
if (prank_to_element) {
UInt prank[2];
for (UInt el = 0; el < 2; ++el) {
UInt current_el = connected_elements[el].element;
ElementType current_type =
connected_elements[el].type;
GhostType current_gt =
connected_elements[el].ghost_type;
const Array<UInt> & prank_to_el =
(*prank_to_element)(current_type, current_gt);
prank[el] = prank_to_el(current_el);
}
bool ghost_one = (gt[0] != _ghost);
if (prank[ghost_one] > prank[!ghost_one])
facet_ghost_type = _not_ghost;
else
facet_ghost_type = _ghost;
connectivity_facets = &mesh_facets.getConnectivity(
facet_type, facet_ghost_type);
element_to_subelement =
&mesh_facets.getElementToSubelement(
facet_type, facet_ghost_type);
}
}
}
/// facet of facet
else {
for (UInt i = 1; i < nb_element_connected_to_facet; ++i) {
elements.push_back(connected_elements[i]);
}
}
element_to_subelement->push_back(elements);
connectivity_facets->push_back(facet);
/// current facet index
UInt current_facet = connectivity_facets->getSize() - 1;
/// loop on every element connected to current facet and
/// insert current facet in the first free spot of the
/// subelement_to_element vector
for (UInt elem = 0; elem < elements.size(); ++elem) {
Element loc_el = elements[elem];
if (loc_el.type != _not_defined) {
Array<Element> & subelement_to_element =
mesh_facets.getSubelementToElement(loc_el.type,
loc_el.ghost_type);
UInt nb_facet_per_loc_element =
subelement_to_element.getNbComponent();
for (UInt f_in = 0; f_in < nb_facet_per_loc_element;
++f_in) {
if (subelement_to_element(loc_el.element, f_in).type ==
_not_defined) {
subelement_to_element(loc_el.element, f_in).type =
facet_type;
subelement_to_element(loc_el.element, f_in).element =
current_facet;
subelement_to_element(loc_el.element, f_in)
.ghost_type = facet_ghost_type;
break;
}
}
}
}
/// reset connectivity in case a facet was found in
/// between ghost and normal elements
if (facet_ghost_type != ghost_type) {
facet_ghost_type = ghost_type;
connectivity_facets = &mesh_accessor.getConnectivity(
facet_type, facet_ghost_type);
element_to_subelement =
&mesh_accessor.getElementToSubelement(facet_type,
facet_ghost_type);
}
}
}
}
}
}
}
}
}
// restore the parent of mesh_facet
if (mesh_facets_parent)
mesh_facets.defineMeshParent(*mesh_facets_parent);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::renumberMeshNodes(Mesh & mesh,
Array<UInt> & local_connectivities,
UInt nb_local_element, UInt nb_ghost_element,
ElementType type,
Array<UInt> & old_nodes_numbers) {
AKANTU_DEBUG_IN();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
std::map<UInt, UInt> renumbering_map;
for (UInt i = 0; i < old_nodes_numbers.getSize(); ++i) {
renumbering_map[old_nodes_numbers(i)] = i;
}
/// renumber the nodes
renumberNodesInConnectivity(local_connectivities,
(nb_local_element + nb_ghost_element) *
nb_nodes_per_element,
renumbering_map);
std::map<UInt, UInt>::iterator it = renumbering_map.begin();
std::map<UInt, UInt>::iterator end = renumbering_map.end();
old_nodes_numbers.resize(renumbering_map.size());
for (; it != end; ++it) {
old_nodes_numbers(it->second) = it->first;
}
renumbering_map.clear();
MeshAccessor mesh_accessor(mesh);
/// copy the renumbered connectivity to the right place
Array<UInt> & local_conn = mesh_accessor.getConnectivity(type);
local_conn.resize(nb_local_element);
memcpy(local_conn.storage(), local_connectivities.storage(),
nb_local_element * nb_nodes_per_element * sizeof(UInt));
Array<UInt> & ghost_conn = mesh_accessor.getConnectivity(type, _ghost);
ghost_conn.resize(nb_ghost_element);
memcpy(ghost_conn.storage(),
local_connectivities.storage() +
nb_local_element * nb_nodes_per_element,
nb_ghost_element * nb_nodes_per_element * sizeof(UInt));
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::renumberNodesInConnectivity(
Array<UInt> & list_nodes, UInt nb_nodes,
std::map<UInt, UInt> & renumbering_map) {
AKANTU_DEBUG_IN();
UInt * connectivity = list_nodes.storage();
UInt new_node_num = renumbering_map.size();
for (UInt n = 0; n < nb_nodes; ++n, ++connectivity) {
UInt & node = *connectivity;
std::map<UInt, UInt>::iterator it = renumbering_map.find(node);
if (it == renumbering_map.end()) {
UInt old_node = node;
renumbering_map[old_node] = new_node_num;
node = new_node_num;
++new_node_num;
} else {
node = it->second;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::purifyMesh(Mesh & mesh) {
AKANTU_DEBUG_IN();
std::map<UInt, UInt> renumbering_map;
RemovedNodesEvent remove_nodes(mesh);
Array<UInt> & nodes_removed = remove_nodes.getList();
for (UInt gt = _not_ghost; gt <= _ghost; ++gt) {
GhostType ghost_type = (GhostType)gt;
Mesh::type_iterator it =
mesh.firstType(_all_dimensions, ghost_type, _ek_not_defined);
Mesh::type_iterator end =
mesh.lastType(_all_dimensions, ghost_type, _ek_not_defined);
for (; it != end; ++it) {
ElementType type(*it);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
Array<UInt> & connectivity = mesh.getConnectivity(type, ghost_type);
UInt nb_element(connectivity.getSize());
renumberNodesInConnectivity(
connectivity, nb_element * nb_nodes_per_element, renumbering_map);
}
}
Array<UInt> & new_numbering = remove_nodes.getNewNumbering();
std::fill(new_numbering.begin(), new_numbering.end(), UInt(-1));
std::map<UInt, UInt>::iterator it = renumbering_map.begin();
std::map<UInt, UInt>::iterator end = renumbering_map.end();
for (; it != end; ++it) {
new_numbering(it->first) = it->second;
}
for (UInt i = 0; i < new_numbering.getSize(); ++i) {
if (new_numbering(i) == UInt(-1))
nodes_removed.push_back(i);
}
mesh.sendEvent(remove_nodes);
AKANTU_DEBUG_OUT();
}
#if defined(AKANTU_COHESIVE_ELEMENT)
/* -------------------------------------------------------------------------- */
UInt MeshUtils::insertCohesiveElements(
Mesh & mesh, Mesh & mesh_facets,
const ElementTypeMapArray<bool> & facet_insertion,
Array<UInt> & doubled_nodes, Array<Element> & new_elements,
bool only_double_facets) {
UInt spatial_dimension = mesh.getSpatialDimension();
UInt elements_to_insert = updateFacetToDouble(mesh_facets, facet_insertion);
if (elements_to_insert > 0) {
if (spatial_dimension == 1) {
doublePointFacet(mesh, mesh_facets, doubled_nodes);
} else {
doubleFacet(mesh, mesh_facets, spatial_dimension - 1, doubled_nodes,
true);
findSubfacetToDouble<false>(mesh, mesh_facets);
if (spatial_dimension == 2) {
doubleSubfacet<2>(mesh, mesh_facets, doubled_nodes);
} else if (spatial_dimension == 3) {
doubleFacet(mesh, mesh_facets, 1, doubled_nodes, false);
findSubfacetToDouble<true>(mesh, mesh_facets);
doubleSubfacet<3>(mesh, mesh_facets, doubled_nodes);
}
}
if (!only_double_facets)
updateCohesiveData(mesh, mesh_facets, new_elements);
}
return elements_to_insert;
}
#endif
/* -------------------------------------------------------------------------- */
void MeshUtils::doubleNodes(Mesh & mesh, const std::vector<UInt> & old_nodes,
Array<UInt> & doubled_nodes) {
AKANTU_DEBUG_IN();
Array<Real> & position = mesh.getNodes();
UInt spatial_dimension = mesh.getSpatialDimension();
UInt old_nb_nodes = position.getSize();
UInt new_nb_nodes = old_nb_nodes + old_nodes.size();
UInt old_nb_doubled_nodes = doubled_nodes.getSize();
UInt new_nb_doubled_nodes = old_nb_doubled_nodes + old_nodes.size();
position.resize(new_nb_nodes);
doubled_nodes.resize(new_nb_doubled_nodes);
Array<Real>::iterator<Vector<Real>> position_begin =
position.begin(spatial_dimension);
for (UInt n = 0; n < old_nodes.size(); ++n) {
UInt new_node = old_nb_nodes + n;
/// store doubled nodes
doubled_nodes(old_nb_doubled_nodes + n, 0) = old_nodes[n];
doubled_nodes(old_nb_doubled_nodes + n, 1) = new_node;
/// update position
std::copy(position_begin + old_nodes[n], position_begin + old_nodes[n] + 1,
position_begin + new_node);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::doubleFacet(Mesh & mesh, Mesh & mesh_facets,
UInt facet_dimension, Array<UInt> & doubled_nodes,
bool facet_mode) {
AKANTU_DEBUG_IN();
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType gt_facet = *gt;
Mesh::type_iterator it = mesh_facets.firstType(facet_dimension, gt_facet);
Mesh::type_iterator end = mesh_facets.lastType(facet_dimension, gt_facet);
for (; it != end; ++it) {
ElementType type_facet = *it;
Array<UInt> & f_to_double =
mesh_facets.getData<UInt>("facet_to_double", type_facet, gt_facet);
UInt nb_facet_to_double = f_to_double.getSize();
if (nb_facet_to_double == 0)
continue;
ElementType type_subfacet = Mesh::getFacetType(type_facet);
const UInt nb_subfacet_per_facet =
Mesh::getNbFacetsPerElement(type_facet);
GhostType gt_subfacet = _casper;
Array<std::vector<Element>> * f_to_subfacet = NULL;
Array<Element> & subfacet_to_facet =
mesh_facets.getSubelementToElement(type_facet, gt_facet);
Array<UInt> & conn_facet =
mesh_facets.getConnectivity(type_facet, gt_facet);
UInt nb_nodes_per_facet = conn_facet.getNbComponent();
UInt old_nb_facet = conn_facet.getSize();
UInt new_nb_facet = old_nb_facet + nb_facet_to_double;
conn_facet.resize(new_nb_facet);
subfacet_to_facet.resize(new_nb_facet);
UInt new_facet = old_nb_facet - 1;
Element new_facet_el(type_facet, 0, gt_facet);
Array<Element>::iterator<Vector<Element>> subfacet_to_facet_begin =
subfacet_to_facet.begin(nb_subfacet_per_facet);
Array<UInt>::iterator<Vector<UInt>> conn_facet_begin =
conn_facet.begin(nb_nodes_per_facet);
for (UInt facet = 0; facet < nb_facet_to_double; ++facet) {
UInt old_facet = f_to_double(facet);
++new_facet;
/// adding a new facet by copying original one
/// copy connectivity in new facet
std::copy(conn_facet_begin + old_facet,
conn_facet_begin + old_facet + 1,
conn_facet_begin + new_facet);
/// update subfacet_to_facet
std::copy(subfacet_to_facet_begin + old_facet,
subfacet_to_facet_begin + old_facet + 1,
subfacet_to_facet_begin + new_facet);
new_facet_el.element = new_facet;
/// loop on every subfacet
for (UInt sf = 0; sf < nb_subfacet_per_facet; ++sf) {
Element & subfacet = subfacet_to_facet(old_facet, sf);
if (subfacet == ElementNull)
continue;
if (gt_subfacet != subfacet.ghost_type) {
gt_subfacet = subfacet.ghost_type;
f_to_subfacet = &mesh_facets.getElementToSubelement(
type_subfacet, subfacet.ghost_type);
}
/// update facet_to_subfacet array
(*f_to_subfacet)(subfacet.element).push_back(new_facet_el);
}
}
/// update facet_to_subfacet and _segment_3 facets if any
if (!facet_mode) {
updateSubfacetToFacet(mesh_facets, type_facet, gt_facet, true);
updateFacetToSubfacet(mesh_facets, type_facet, gt_facet, true);
updateQuadraticSegments<true>(mesh, mesh_facets, type_facet, gt_facet,
doubled_nodes);
} else
updateQuadraticSegments<false>(mesh, mesh_facets, type_facet, gt_facet,
doubled_nodes);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
UInt MeshUtils::updateFacetToDouble(
Mesh & mesh_facets, const ElementTypeMapArray<bool> & facet_insertion) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh_facets.getSpatialDimension();
UInt nb_facets_to_double = 0.;
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType gt_facet = *gt;
Mesh::type_iterator it =
mesh_facets.firstType(spatial_dimension - 1, gt_facet);
Mesh::type_iterator end =
mesh_facets.lastType(spatial_dimension - 1, gt_facet);
for (; it != end; ++it) {
ElementType type_facet = *it;
const Array<bool> & f_insertion = facet_insertion(type_facet, gt_facet);
Array<UInt> & f_to_double =
mesh_facets.getData<UInt>("facet_to_double", type_facet, gt_facet);
Array<std::vector<Element>> & element_to_facet =
mesh_facets.getElementToSubelement(type_facet, gt_facet);
ElementType el_type = _not_defined;
GhostType el_gt = _casper;
UInt nb_facet_per_element = 0;
Element old_facet_el(type_facet, 0, gt_facet);
Array<Element> * facet_to_element = NULL;
for (UInt f = 0; f < f_insertion.getSize(); ++f) {
if (f_insertion(f) == false)
continue;
++nb_facets_to_double;
if (element_to_facet(f)[1].type == _not_defined
#if defined(AKANTU_COHESIVE_ELEMENT)
|| element_to_facet(f)[1].kind == _ek_cohesive
#endif
) {
AKANTU_DEBUG_WARNING("attempt to double a facet on the boundary");
continue;
}
f_to_double.push_back(f);
UInt new_facet = mesh_facets.getNbElement(type_facet, gt_facet) +
f_to_double.getSize() - 1;
old_facet_el.element = f;
/// update facet_to_element vector
Element & elem_to_update = element_to_facet(f)[1];
UInt el = elem_to_update.element;
if (elem_to_update.ghost_type != el_gt ||
elem_to_update.type != el_type) {
el_type = elem_to_update.type;
el_gt = elem_to_update.ghost_type;
facet_to_element =
&mesh_facets.getSubelementToElement(el_type, el_gt);
nb_facet_per_element = facet_to_element->getNbComponent();
}
Element * f_update =
std::find(facet_to_element->storage() + el * nb_facet_per_element,
facet_to_element->storage() + el * nb_facet_per_element +
nb_facet_per_element,
old_facet_el);
AKANTU_DEBUG_ASSERT(
facet_to_element->storage() + el * nb_facet_per_element !=
facet_to_element->storage() + el * nb_facet_per_element +
nb_facet_per_element,
"Facet not found");
f_update->element = new_facet;
/// update elements connected to facet
std::vector<Element> first_facet_list = element_to_facet(f);
element_to_facet.push_back(first_facet_list);
/// set new and original facets as boundary facets
element_to_facet(new_facet)[0] = element_to_facet(new_facet)[1];
element_to_facet(f)[1] = ElementNull;
element_to_facet(new_facet)[1] = ElementNull;
}
}
}
AKANTU_DEBUG_OUT();
return nb_facets_to_double;
}
/* -------------------------------------------------------------------------- */
void MeshUtils::resetFacetToDouble(Mesh & mesh_facets) {
AKANTU_DEBUG_IN();
for (UInt g = _not_ghost; g <= _ghost; ++g) {
GhostType gt = (GhostType)g;
Mesh::type_iterator it = mesh_facets.firstType(_all_dimensions, gt);
Mesh::type_iterator end = mesh_facets.lastType(_all_dimensions, gt);
for (; it != end; ++it) {
ElementType type = *it;
mesh_facets.getDataPointer<UInt>("facet_to_double", type, gt, 1, false);
mesh_facets.getDataPointer<std::vector<Element>>(
"facets_to_subfacet_double", type, gt, 1, false);
mesh_facets.getDataPointer<std::vector<Element>>(
"elements_to_subfacet_double", type, gt, 1, false);
mesh_facets.getDataPointer<std::vector<Element>>(
"subfacets_to_subsubfacet_double", type, gt, 1, false);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <bool subsubfacet_mode>
void MeshUtils::findSubfacetToDouble(Mesh & mesh, Mesh & mesh_facets) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh_facets.getSpatialDimension();
if (spatial_dimension == 1)
return;
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType gt_facet = *gt;
Mesh::type_iterator it =
mesh_facets.firstType(spatial_dimension - 1, gt_facet);
Mesh::type_iterator end =
mesh_facets.lastType(spatial_dimension - 1, gt_facet);
for (; it != end; ++it) {
ElementType type_facet = *it;
Array<UInt> & f_to_double =
mesh_facets.getData<UInt>("facet_to_double", type_facet, gt_facet);
UInt nb_facet_to_double = f_to_double.getSize();
if (nb_facet_to_double == 0)
continue;
ElementType type_subfacet = Mesh::getFacetType(type_facet);
GhostType gt_subfacet = _casper;
ElementType type_subsubfacet = Mesh::getFacetType(type_subfacet);
GhostType gt_subsubfacet = _casper;
Array<UInt> * conn_subfacet = NULL;
Array<UInt> * sf_to_double = NULL;
Array<std::vector<Element>> * sf_to_subfacet_double = NULL;
Array<std::vector<Element>> * f_to_subfacet_double = NULL;
Array<std::vector<Element>> * el_to_subfacet_double = NULL;
UInt nb_subfacet = Mesh::getNbFacetsPerElement(type_facet);
UInt nb_subsubfacet;
UInt nb_nodes_per_sf_el;
if (subsubfacet_mode) {
nb_nodes_per_sf_el = Mesh::getNbNodesPerElement(type_subsubfacet);
nb_subsubfacet = Mesh::getNbFacetsPerElement(type_subfacet);
} else
nb_nodes_per_sf_el = Mesh::getNbNodesPerElement(type_subfacet);
Array<Element> & subfacet_to_facet =
mesh_facets.getSubelementToElement(type_facet, gt_facet);
Array<std::vector<Element>> & element_to_facet =
mesh_facets.getElementToSubelement(type_facet, gt_facet);
Array<Element> * subsubfacet_to_subfacet = NULL;
UInt old_nb_facet = subfacet_to_facet.getSize() - nb_facet_to_double;
Element current_facet(type_facet, 0, gt_facet);
std::vector<Element> element_list;
std::vector<Element> facet_list;
std::vector<Element> * subfacet_list;
if (subsubfacet_mode)
subfacet_list = new std::vector<Element>;
/// map to filter subfacets
Array<std::vector<Element>> * facet_to_subfacet = NULL;
/// this is used to make sure that both new and old facets are
/// checked
UInt facets[2];
/// loop on every facet
for (UInt f_index = 0; f_index < 2; ++f_index) {
for (UInt facet = 0; facet < nb_facet_to_double; ++facet) {
facets[bool(f_index)] = f_to_double(facet);
facets[!bool(f_index)] = old_nb_facet + facet;
UInt old_facet = facets[0];
UInt new_facet = facets[1];
Element & starting_element = element_to_facet(new_facet)[0];
current_facet.element = old_facet;
/// loop on every subfacet
for (UInt sf = 0; sf < nb_subfacet; ++sf) {
Element & subfacet = subfacet_to_facet(old_facet, sf);
if (subfacet == ElementNull)
continue;
if (gt_subfacet != subfacet.ghost_type) {
gt_subfacet = subfacet.ghost_type;
if (subsubfacet_mode) {
subsubfacet_to_subfacet = &mesh_facets.getSubelementToElement(
type_subfacet, gt_subfacet);
} else {
conn_subfacet =
&mesh_facets.getConnectivity(type_subfacet, gt_subfacet);
sf_to_double = &mesh_facets.getData<UInt>(
"facet_to_double", type_subfacet, gt_subfacet);
f_to_subfacet_double =
&mesh_facets.getData<std::vector<Element>>(
"facets_to_subfacet_double", type_subfacet,
gt_subfacet);
el_to_subfacet_double =
&mesh_facets.getData<std::vector<Element>>(
"elements_to_subfacet_double", type_subfacet,
gt_subfacet);
facet_to_subfacet = &mesh_facets.getElementToSubelement(
type_subfacet, gt_subfacet);
}
}
if (subsubfacet_mode) {
/// loop on every subsubfacet
for (UInt ssf = 0; ssf < nb_subsubfacet; ++ssf) {
Element & subsubfacet =
(*subsubfacet_to_subfacet)(subfacet.element, ssf);
if (subsubfacet == ElementNull)
continue;
if (gt_subsubfacet != subsubfacet.ghost_type) {
gt_subsubfacet = subsubfacet.ghost_type;
conn_subfacet = &mesh_facets.getConnectivity(type_subsubfacet,
gt_subsubfacet);
sf_to_double = &mesh_facets.getData<UInt>(
"facet_to_double", type_subsubfacet, gt_subsubfacet);
sf_to_subfacet_double =
&mesh_facets.getData<std::vector<Element>>(
"subfacets_to_subsubfacet_double", type_subsubfacet,
gt_subsubfacet);
f_to_subfacet_double =
&mesh_facets.getData<std::vector<Element>>(
"facets_to_subfacet_double", type_subsubfacet,
gt_subsubfacet);
el_to_subfacet_double =
&mesh_facets.getData<std::vector<Element>>(
"elements_to_subfacet_double", type_subsubfacet,
gt_subsubfacet);
facet_to_subfacet = &mesh_facets.getElementToSubelement(
type_subsubfacet, gt_subsubfacet);
}
UInt global_ssf = subsubfacet.element;
Vector<UInt> subsubfacet_connectivity(
conn_subfacet->storage() + global_ssf * nb_nodes_per_sf_el,
nb_nodes_per_sf_el);
/// check if subsubfacet is to be doubled
if (findElementsAroundSubfacet<true>(
mesh, mesh_facets, starting_element, current_facet,
subsubfacet_connectivity, element_list, facet_list,
subfacet_list) == false &&
removeElementsInVector(*subfacet_list,
(*facet_to_subfacet)(global_ssf)) ==
false) {
sf_to_double->push_back(global_ssf);
sf_to_subfacet_double->push_back(*subfacet_list);
f_to_subfacet_double->push_back(facet_list);
el_to_subfacet_double->push_back(element_list);
}
}
} else {
const UInt global_sf = subfacet.element;
Vector<UInt> subfacet_connectivity(
conn_subfacet->storage() + global_sf * nb_nodes_per_sf_el,
nb_nodes_per_sf_el);
/// check if subfacet is to be doubled
if (findElementsAroundSubfacet<false>(
mesh, mesh_facets, starting_element, current_facet,
subfacet_connectivity, element_list,
facet_list) == false &&
removeElementsInVector(
facet_list, (*facet_to_subfacet)(global_sf)) == false) {
sf_to_double->push_back(global_sf);
f_to_subfacet_double->push_back(facet_list);
el_to_subfacet_double->push_back(element_list);
}
}
}
}
}
if (subsubfacet_mode)
delete subfacet_list;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_COHESIVE_ELEMENT)
void MeshUtils::updateCohesiveData(Mesh & mesh, Mesh & mesh_facets,
Array<Element> & new_elements) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
bool third_dimension = spatial_dimension == 3;
MeshAccessor mesh_facets_accessor(mesh_facets);
for (auto gt_facet : ghost_types) {
for (auto type_facet :
mesh_facets.elementTypes(spatial_dimension - 1, gt_facet)) {
Array<UInt> & f_to_double =
mesh_facets.getData<UInt>("facet_to_double", type_facet, gt_facet);
UInt nb_facet_to_double = f_to_double.getSize();
if (nb_facet_to_double == 0)
continue;
ElementType type_cohesive = FEEngine::getCohesiveElementType(type_facet);
auto & facet_to_coh_element =
mesh_facets_accessor.getSubelementToElement(type_cohesive, gt_facet);
auto & conn_facet = mesh_facets.getConnectivity(type_facet, gt_facet);
auto & conn_cohesive = mesh.getConnectivity(type_cohesive, gt_facet);
UInt nb_nodes_per_facet = Mesh::getNbNodesPerElement(type_facet);
Array<std::vector<Element>> & element_to_facet =
mesh_facets.getElementToSubelement(type_facet, gt_facet);
UInt old_nb_cohesive_elements = conn_cohesive.getSize();
UInt new_nb_cohesive_elements =
conn_cohesive.getSize() + nb_facet_to_double;
UInt old_nb_facet = element_to_facet.getSize() - nb_facet_to_double;
facet_to_coh_element.resize(new_nb_cohesive_elements);
conn_cohesive.resize(new_nb_cohesive_elements);
UInt new_elements_old_size = new_elements.getSize();
new_elements.resize(new_elements_old_size + nb_facet_to_double);
Element c_element(type_cohesive, 0, gt_facet, _ek_cohesive);
Element f_element(type_facet, 0, gt_facet);
UInt facets[2];
for (UInt facet = 0; facet < nb_facet_to_double; ++facet) {
/// (in 3D cohesive elements connectivity is inverted)
facets[third_dimension] = f_to_double(facet);
facets[!third_dimension] = old_nb_facet + facet;
UInt cohesive_element = old_nb_cohesive_elements + facet;
/// store doubled facets
f_element.element = facets[0];
facet_to_coh_element(cohesive_element, 0) = f_element;
f_element.element = facets[1];
facet_to_coh_element(cohesive_element, 1) = f_element;
/// modify cohesive elements' connectivity
for (UInt n = 0; n < nb_nodes_per_facet; ++n) {
conn_cohesive(cohesive_element, n) = conn_facet(facets[0], n);
conn_cohesive(cohesive_element, n + nb_nodes_per_facet) =
conn_facet(facets[1], n);
}
/// update element_to_facet vectors
c_element.element = cohesive_element;
element_to_facet(facets[0])[1] = c_element;
element_to_facet(facets[1])[1] = c_element;
/// add cohesive element to the element event list
new_elements(new_elements_old_size + facet) = c_element;
}
}
}
AKANTU_DEBUG_OUT();
}
#endif
/* -------------------------------------------------------------------------- */
void MeshUtils::doublePointFacet(Mesh & mesh, Mesh & mesh_facets,
Array<UInt> & doubled_nodes) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
if (spatial_dimension != 1)
return;
Array<Real> & position = mesh.getNodes();
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType gt_facet = *gt;
Mesh::type_iterator it =
mesh_facets.firstType(spatial_dimension - 1, gt_facet);
Mesh::type_iterator end =
mesh_facets.lastType(spatial_dimension - 1, gt_facet);
for (; it != end; ++it) {
ElementType type_facet = *it;
Array<UInt> & conn_facet =
mesh_facets.getConnectivity(type_facet, gt_facet);
Array<std::vector<Element>> & element_to_facet =
mesh_facets.getElementToSubelement(type_facet, gt_facet);
const Array<UInt> & f_to_double =
mesh_facets.getData<UInt>("facet_to_double", type_facet, gt_facet);
UInt nb_facet_to_double = f_to_double.getSize();
UInt old_nb_facet = element_to_facet.getSize() - nb_facet_to_double;
UInt new_nb_facet = element_to_facet.getSize();
UInt old_nb_nodes = position.getSize();
UInt new_nb_nodes = old_nb_nodes + nb_facet_to_double;
position.resize(new_nb_nodes);
conn_facet.resize(new_nb_facet);
UInt old_nb_doubled_nodes = doubled_nodes.getSize();
doubled_nodes.resize(old_nb_doubled_nodes + nb_facet_to_double);
for (UInt facet = 0; facet < nb_facet_to_double; ++facet) {
UInt old_facet = f_to_double(facet);
UInt new_facet = old_nb_facet + facet;
ElementType type = element_to_facet(new_facet)[0].type;
UInt el = element_to_facet(new_facet)[0].element;
GhostType gt = element_to_facet(new_facet)[0].ghost_type;
UInt old_node = conn_facet(old_facet);
UInt new_node = old_nb_nodes + facet;
/// update position
position(new_node) = position(old_node);
conn_facet(new_facet) = new_node;
Array<UInt> & conn_segment = mesh.getConnectivity(type, gt);
UInt nb_nodes_per_segment = conn_segment.getNbComponent();
/// update facet connectivity
UInt i;
for (i = 0;
conn_segment(el, i) != old_node && i <= nb_nodes_per_segment; ++i)
;
conn_segment(el, i) = new_node;
doubled_nodes(old_nb_doubled_nodes + facet, 0) = old_node;
doubled_nodes(old_nb_doubled_nodes + facet, 1) = new_node;
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <bool third_dim_segments>
void MeshUtils::updateQuadraticSegments(Mesh & mesh, Mesh & mesh_facets,
ElementType type_facet,
GhostType gt_facet,
Array<UInt> & doubled_nodes) {
AKANTU_DEBUG_IN();
if (type_facet != _segment_3)
return;
Array<UInt> & f_to_double =
mesh_facets.getData<UInt>("facet_to_double", type_facet, gt_facet);
UInt nb_facet_to_double = f_to_double.getSize();
UInt old_nb_facet =
mesh_facets.getNbElement(type_facet, gt_facet) - nb_facet_to_double;
Array<UInt> & conn_facet = mesh_facets.getConnectivity(type_facet, gt_facet);
Array<std::vector<Element>> & element_to_facet =
mesh_facets.getElementToSubelement(type_facet, gt_facet);
/// this ones matter only for segments in 3D
Array<std::vector<Element>> * el_to_subfacet_double = NULL;
Array<std::vector<Element>> * f_to_subfacet_double = NULL;
if (third_dim_segments) {
el_to_subfacet_double = &mesh_facets.getData<std::vector<Element>>(
"elements_to_subfacet_double", type_facet, gt_facet);
f_to_subfacet_double = &mesh_facets.getData<std::vector<Element>>(
"facets_to_subfacet_double", type_facet, gt_facet);
}
std::vector<UInt> middle_nodes;
for (UInt facet = 0; facet < nb_facet_to_double; ++facet) {
UInt old_facet = f_to_double(facet);
UInt node = conn_facet(old_facet, 2);
if (!mesh.isPureGhostNode(node))
middle_nodes.push_back(node);
}
UInt n = doubled_nodes.getSize();
doubleNodes(mesh, middle_nodes, doubled_nodes);
for (UInt facet = 0; facet < nb_facet_to_double; ++facet) {
UInt old_facet = f_to_double(facet);
UInt old_node = conn_facet(old_facet, 2);
if (mesh.isPureGhostNode(old_node))
continue;
UInt new_node = doubled_nodes(n, 1);
UInt new_facet = old_nb_facet + facet;
conn_facet(new_facet, 2) = new_node;
if (third_dim_segments) {
updateElementalConnectivity(mesh_facets, old_node, new_node,
element_to_facet(new_facet));
updateElementalConnectivity(mesh, old_node, new_node,
(*el_to_subfacet_double)(facet),
&(*f_to_subfacet_double)(facet));
} else {
updateElementalConnectivity(mesh, old_node, new_node,
element_to_facet(new_facet));
}
++n;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::updateSubfacetToFacet(Mesh & mesh_facets,
ElementType type_subfacet,
GhostType gt_subfacet, bool facet_mode) {
AKANTU_DEBUG_IN();
Array<UInt> & sf_to_double =
mesh_facets.getData<UInt>("facet_to_double", type_subfacet, gt_subfacet);
UInt nb_subfacet_to_double = sf_to_double.getSize();
/// update subfacet_to_facet vector
ElementType type_facet = _not_defined;
GhostType gt_facet = _casper;
Array<Element> * subfacet_to_facet = NULL;
UInt nb_subfacet_per_facet = 0;
UInt old_nb_subfacet = mesh_facets.getNbElement(type_subfacet, gt_subfacet) -
nb_subfacet_to_double;
Array<std::vector<Element>> * facet_list = NULL;
if (facet_mode)
facet_list = &mesh_facets.getData<std::vector<Element>>(
"facets_to_subfacet_double", type_subfacet, gt_subfacet);
else
facet_list = &mesh_facets.getData<std::vector<Element>>(
"subfacets_to_subsubfacet_double", type_subfacet, gt_subfacet);
Element old_subfacet_el(type_subfacet, 0, gt_subfacet);
Element new_subfacet_el(type_subfacet, 0, gt_subfacet);
for (UInt sf = 0; sf < nb_subfacet_to_double; ++sf) {
old_subfacet_el.element = sf_to_double(sf);
new_subfacet_el.element = old_nb_subfacet + sf;
for (UInt f = 0; f < (*facet_list)(sf).size(); ++f) {
Element & facet = (*facet_list)(sf)[f];
if (facet.type != type_facet || facet.ghost_type != gt_facet) {
type_facet = facet.type;
gt_facet = facet.ghost_type;
subfacet_to_facet =
&mesh_facets.getSubelementToElement(type_facet, gt_facet);
nb_subfacet_per_facet = subfacet_to_facet->getNbComponent();
}
Element * sf_update = std::find(
subfacet_to_facet->storage() + facet.element * nb_subfacet_per_facet,
subfacet_to_facet->storage() + facet.element * nb_subfacet_per_facet +
nb_subfacet_per_facet,
old_subfacet_el);
AKANTU_DEBUG_ASSERT(subfacet_to_facet->storage() +
facet.element * nb_subfacet_per_facet !=
subfacet_to_facet->storage() +
facet.element * nb_subfacet_per_facet +
nb_subfacet_per_facet,
"Subfacet not found");
*sf_update = new_subfacet_el;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::updateFacetToSubfacet(Mesh & mesh_facets,
ElementType type_subfacet,
GhostType gt_subfacet, bool facet_mode) {
AKANTU_DEBUG_IN();
Array<UInt> & sf_to_double =
mesh_facets.getData<UInt>("facet_to_double", type_subfacet, gt_subfacet);
UInt nb_subfacet_to_double = sf_to_double.getSize();
Array<std::vector<Element>> & facet_to_subfacet =
mesh_facets.getElementToSubelement(type_subfacet, gt_subfacet);
Array<std::vector<Element>> * facet_to_subfacet_double = NULL;
if (facet_mode) {
facet_to_subfacet_double = &mesh_facets.getData<std::vector<Element>>(
"facets_to_subfacet_double", type_subfacet, gt_subfacet);
} else {
facet_to_subfacet_double = &mesh_facets.getData<std::vector<Element>>(
"subfacets_to_subsubfacet_double", type_subfacet, gt_subfacet);
}
UInt old_nb_subfacet = facet_to_subfacet.getSize();
facet_to_subfacet.resize(old_nb_subfacet + nb_subfacet_to_double);
for (UInt sf = 0; sf < nb_subfacet_to_double; ++sf)
facet_to_subfacet(old_nb_subfacet + sf) = (*facet_to_subfacet_double)(sf);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MeshUtils::doubleSubfacet(Mesh & mesh, Mesh & mesh_facets,
Array<UInt> & doubled_nodes) {
AKANTU_DEBUG_IN();
if (spatial_dimension == 1)
return;
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType gt_subfacet = *gt;
Mesh::type_iterator it = mesh_facets.firstType(0, gt_subfacet);
Mesh::type_iterator end = mesh_facets.lastType(0, gt_subfacet);
for (; it != end; ++it) {
ElementType type_subfacet = *it;
Array<UInt> & sf_to_double = mesh_facets.getData<UInt>(
"facet_to_double", type_subfacet, gt_subfacet);
UInt nb_subfacet_to_double = sf_to_double.getSize();
if (nb_subfacet_to_double == 0)
continue;
AKANTU_DEBUG_ASSERT(
type_subfacet == _point_1,
"Only _point_1 subfacet doubling is supported at the moment");
Array<UInt> & conn_subfacet =
mesh_facets.getConnectivity(type_subfacet, gt_subfacet);
UInt old_nb_subfacet = conn_subfacet.getSize();
UInt new_nb_subfacet = old_nb_subfacet + nb_subfacet_to_double;
conn_subfacet.resize(new_nb_subfacet);
std::vector<UInt> nodes_to_double;
UInt old_nb_doubled_nodes = doubled_nodes.getSize();
/// double nodes
for (UInt sf = 0; sf < nb_subfacet_to_double; ++sf) {
UInt old_subfacet = sf_to_double(sf);
nodes_to_double.push_back(conn_subfacet(old_subfacet));
}
doubleNodes(mesh, nodes_to_double, doubled_nodes);
/// add new nodes in connectivity
for (UInt sf = 0; sf < nb_subfacet_to_double; ++sf) {
UInt new_subfacet = old_nb_subfacet + sf;
UInt new_node = doubled_nodes(old_nb_doubled_nodes + sf, 1);
conn_subfacet(new_subfacet) = new_node;
}
/// update facet and element connectivity
Array<std::vector<Element>> & f_to_subfacet_double =
mesh_facets.getData<std::vector<Element>>("facets_to_subfacet_double",
type_subfacet, gt_subfacet);
Array<std::vector<Element>> & el_to_subfacet_double =
mesh_facets.getData<std::vector<Element>>(
"elements_to_subfacet_double", type_subfacet, gt_subfacet);
Array<std::vector<Element>> * sf_to_subfacet_double = NULL;
if (spatial_dimension == 3)
sf_to_subfacet_double = &mesh_facets.getData<std::vector<Element>>(
"subfacets_to_subsubfacet_double", type_subfacet, gt_subfacet);
for (UInt sf = 0; sf < nb_subfacet_to_double; ++sf) {
UInt old_node = doubled_nodes(old_nb_doubled_nodes + sf, 0);
UInt new_node = doubled_nodes(old_nb_doubled_nodes + sf, 1);
updateElementalConnectivity(mesh, old_node, new_node,
el_to_subfacet_double(sf),
&f_to_subfacet_double(sf));
updateElementalConnectivity(mesh_facets, old_node, new_node,
f_to_subfacet_double(sf));
if (spatial_dimension == 3)
updateElementalConnectivity(mesh_facets, old_node, new_node,
(*sf_to_subfacet_double)(sf));
}
if (spatial_dimension == 2) {
updateSubfacetToFacet(mesh_facets, type_subfacet, gt_subfacet, true);
updateFacetToSubfacet(mesh_facets, type_subfacet, gt_subfacet, true);
} else if (spatial_dimension == 3) {
updateSubfacetToFacet(mesh_facets, type_subfacet, gt_subfacet, false);
updateFacetToSubfacet(mesh_facets, type_subfacet, gt_subfacet, false);
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::flipFacets(
Mesh & mesh_facets, const ElementTypeMapArray<UInt> & global_connectivity,
GhostType gt_facet) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh_facets.getSpatialDimension();
/// get global connectivity for local mesh
ElementTypeMapArray<UInt> global_connectivity_tmp("global_connectivity_tmp",
mesh_facets.getID(),
mesh_facets.getMemoryID());
global_connectivity_tmp.initialize(
mesh_facets, _spatial_dimension = spatial_dimension - 1,
_with_nb_nodes_per_element = true, _with_nb_element = true);
// mesh_facets.initElementTypeMapArray(global_connectivity_tmp, 1,
// spatial_dimension - 1, gt_facet,
// true, _ek_regular, true);
mesh_facets.getGlobalConnectivity(global_connectivity_tmp,
spatial_dimension - 1, gt_facet);
/// loop on every facet
for (auto type_facet :
mesh_facets.elementTypes(spatial_dimension - 1, gt_facet)) {
auto & connectivity = mesh_facets.getConnectivity(type_facet, gt_facet);
const auto & g_connectivity = global_connectivity(type_facet, gt_facet);
auto & el_to_f = mesh_facets.getElementToSubelement(type_facet, gt_facet);
auto & subfacet_to_facet =
mesh_facets.getSubelementToElement(type_facet, gt_facet);
UInt nb_subfacet_per_facet = subfacet_to_facet.getNbComponent();
UInt nb_nodes_per_facet = connectivity.getNbComponent();
UInt nb_facet = connectivity.getSize();
UInt nb_nodes_per_P1_facet =
Mesh::getNbNodesPerElement(Mesh::getP1ElementType(type_facet));
auto & global_conn_tmp = global_connectivity_tmp(type_facet, gt_facet);
auto conn_it = connectivity.begin(nb_nodes_per_facet);
auto gconn_tmp_it = global_conn_tmp.begin(nb_nodes_per_facet);
auto conn_glob_it = g_connectivity.begin(nb_nodes_per_facet);
auto subf_to_f = subfacet_to_facet.begin(nb_subfacet_per_facet);
UInt * conn_tmp_pointer = new UInt[nb_nodes_per_facet];
Vector<UInt> conn_tmp(conn_tmp_pointer, nb_nodes_per_facet);
Element el_tmp;
Element * subf_tmp_pointer = new Element[nb_subfacet_per_facet];
Vector<Element> subf_tmp(subf_tmp_pointer, nb_subfacet_per_facet);
for (UInt f = 0; f < nb_facet;
++f, ++conn_it, ++gconn_tmp_it, ++subf_to_f, ++conn_glob_it) {
Vector<UInt> & gconn_tmp = *gconn_tmp_it;
const Vector<UInt> & conn_glob = *conn_glob_it;
Vector<UInt> & conn_local = *conn_it;
/// skip facet if connectivities are the same
if (gconn_tmp == conn_glob)
continue;
/// re-arrange connectivity
conn_tmp = conn_local;
UInt * begin = conn_glob.storage();
UInt * end = conn_glob.storage() + nb_nodes_per_facet;
for (UInt n = 0; n < nb_nodes_per_facet; ++n) {
UInt * new_node = std::find(begin, end, gconn_tmp(n));
AKANTU_DEBUG_ASSERT(new_node != end, "Node not found");
UInt new_position = new_node - begin;
conn_local(new_position) = conn_tmp(n);
}
/// if 3D, check if facets are just rotated
if (spatial_dimension == 3) {
/// find first node
UInt * new_node = std::find(begin, end, gconn_tmp(0));
AKANTU_DEBUG_ASSERT(new_node != end, "Node not found");
UInt new_position = new_node - begin;
UInt n = 1;
/// count how many nodes in the received connectivity follow
/// the same order of those in the local connectivity
for (; n < nb_nodes_per_P1_facet &&
gconn_tmp(n) ==
conn_glob((new_position + n) % nb_nodes_per_P1_facet);
++n)
;
/// skip the facet inversion if facet is just rotated
if (n == nb_nodes_per_P1_facet)
continue;
}
/// update data to invert facet
el_tmp = el_to_f(f)[0];
el_to_f(f)[0] = el_to_f(f)[1];
el_to_f(f)[1] = el_tmp;
subf_tmp = (*subf_to_f);
(*subf_to_f)(0) = subf_tmp(1);
(*subf_to_f)(1) = subf_tmp(0);
}
delete[] subf_tmp_pointer;
delete[] conn_tmp_pointer;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::fillElementToSubElementsData(Mesh & mesh) {
AKANTU_DEBUG_IN();
if (mesh.getNbElement(mesh.getSpatialDimension() - 1) == 0) {
AKANTU_DEBUG_INFO("There are not facets, add them in the mesh file or call "
"the buildFacet method.");
return;
}
UInt spatial_dimension = mesh.getSpatialDimension();
ElementTypeMapArray<Real> barycenters("barycenter_tmp", mesh.getID(),
mesh.getMemoryID());
barycenters.initialize(mesh, _nb_component = spatial_dimension,
_spatial_dimension = _all_dimensions);
// mesh.initElementTypeMapArray(barycenters, spatial_dimension,
// _all_dimensions);
Element element;
for (auto ghost_type : ghost_types) {
element.ghost_type = ghost_type;
for (auto & type : mesh.elementTypes(_all_dimensions, ghost_type)) {
element.type = type;
UInt nb_element = mesh.getNbElement(type, ghost_type);
Array<Real> & barycenters_arr = barycenters(type, ghost_type);
barycenters_arr.resize(nb_element);
auto bary = barycenters_arr.begin(spatial_dimension);
auto bary_end = barycenters_arr.end(spatial_dimension);
for (UInt el = 0; bary != bary_end; ++bary, ++el) {
element.element = el;
mesh.getBarycenter(element, *bary);
}
}
}
MeshAccessor mesh_accessor(mesh);
for (Int sp(spatial_dimension); sp >= 1; --sp) {
if (mesh.getNbElement(sp) == 0)
continue;
for (auto ghost_type : ghost_types) {
for (auto & type : mesh.elementTypes(sp, ghost_type)) {
mesh_accessor.getSubelementToElement(type, ghost_type)
.resize(mesh.getNbElement(type, ghost_type));
mesh_accessor.getSubelementToElement(type, ghost_type).clear();
}
for (auto & type : mesh.elementTypes(sp - 1, ghost_type)) {
mesh_accessor.getElementToSubelement(type, ghost_type)
.resize(mesh.getNbElement(type, ghost_type));
mesh.getElementToSubelement(type, ghost_type).clear();
}
}
CSR<Element> nodes_to_elements;
buildNode2Elements(mesh, nodes_to_elements, sp);
Element facet_element;
for (auto ghost_type : ghost_types) {
facet_element.ghost_type = ghost_type;
for (auto & type : mesh.elementTypes(sp - 1, ghost_type)) {
facet_element.type = type;
auto & element_to_subelement =
mesh.getElementToSubelement(type, ghost_type);
const auto & connectivity = mesh.getConnectivity(type, ghost_type);
auto fit = connectivity.begin(mesh.getNbNodesPerElement(type));
auto fend = connectivity.end(mesh.getNbNodesPerElement(type));
UInt fid = 0;
for (; fit != fend; ++fit, ++fid) {
const Vector<UInt> & facet = *fit;
facet_element.element = fid;
std::map<Element, UInt> element_seen_counter;
UInt nb_nodes_per_facet =
mesh.getNbNodesPerElement(Mesh::getP1ElementType(type));
for (UInt n(0); n < nb_nodes_per_facet; ++n) {
auto eit = nodes_to_elements.begin(facet(n));
auto eend = nodes_to_elements.end(facet(n));
for (; eit != eend; ++eit) {
auto & elem = *eit;
auto cit = element_seen_counter.find(elem);
if (cit != element_seen_counter.end()) {
cit->second++;
} else {
element_seen_counter[elem] = 1;
}
}
}
std::vector<Element> connected_elements;
auto cit = element_seen_counter.begin();
auto cend = element_seen_counter.end();
for (; cit != cend; ++cit) {
if (cit->second == nb_nodes_per_facet)
connected_elements.push_back(cit->first);
}
auto ceit = connected_elements.begin();
auto ceend = connected_elements.end();
for (; ceit != ceend; ++ceit)
element_to_subelement(fid).push_back(*ceit);
for (UInt ce = 0; ce < connected_elements.size(); ++ce) {
Element & elem = connected_elements[ce];
Array<Element> & subelement_to_element =
mesh_accessor.getSubelementToElement(elem.type,
elem.ghost_type);
UInt f(0);
for (; f < mesh.getNbFacetsPerElement(elem.type) &&
subelement_to_element(elem.element, f) != ElementNull;
++f)
;
AKANTU_DEBUG_ASSERT(
f < mesh.getNbFacetsPerElement(elem.type),
"The element " << elem << " seems to have too many facets!! ("
<< f << " < "
<< mesh.getNbFacetsPerElement(elem.type) << ")");
subelement_to_element(elem.element, f) = facet_element;
}
}
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <bool third_dim_points>
bool MeshUtils::findElementsAroundSubfacet(
const Mesh & mesh, const Mesh & mesh_facets,
const Element & starting_element, const Element & end_facet,
const Vector<UInt> & subfacet_connectivity,
std::vector<Element> & elem_list, std::vector<Element> & facet_list,
std::vector<Element> * subfacet_list) {
AKANTU_DEBUG_IN();
/// preallocated stuff before starting
bool facet_matched = false;
elem_list.clear();
facet_list.clear();
if (third_dim_points)
subfacet_list->clear();
elem_list.push_back(starting_element);
const Array<UInt> * facet_connectivity = NULL;
const Array<UInt> * sf_connectivity = NULL;
const Array<Element> * facet_to_element = NULL;
const Array<Element> * subfacet_to_facet = NULL;
ElementType current_type = _not_defined;
GhostType current_ghost_type = _casper;
ElementType current_facet_type = _not_defined;
GhostType current_facet_ghost_type = _casper;
ElementType current_subfacet_type = _not_defined;
GhostType current_subfacet_ghost_type = _casper;
const Array<std::vector<Element>> * element_to_facet = NULL;
const Element * opposing_el = NULL;
std::queue<Element> elements_to_check;
elements_to_check.push(starting_element);
/// keep going until there are elements to check
while (!elements_to_check.empty()) {
/// check current element
Element & current_el = elements_to_check.front();
if (current_el.type != current_type ||
current_el.ghost_type != current_ghost_type) {
current_type = current_el.type;
current_ghost_type = current_el.ghost_type;
facet_to_element =
&mesh_facets.getSubelementToElement(current_type, current_ghost_type);
}
/// loop over each facet of the element
for (UInt f = 0; f < facet_to_element->getNbComponent(); ++f) {
const Element & current_facet =
(*facet_to_element)(current_el.element, f);
if (current_facet == ElementNull)
continue;
if (current_facet_type != current_facet.type ||
current_facet_ghost_type != current_facet.ghost_type) {
current_facet_type = current_facet.type;
current_facet_ghost_type = current_facet.ghost_type;
element_to_facet = &mesh_facets.getElementToSubelement(
current_facet_type, current_facet_ghost_type);
facet_connectivity = &mesh_facets.getConnectivity(
current_facet_type, current_facet_ghost_type);
if (third_dim_points)
subfacet_to_facet = &mesh_facets.getSubelementToElement(
current_facet_type, current_facet_ghost_type);
}
/// check if end facet is reached
if (current_facet == end_facet)
facet_matched = true;
/// add this facet if not already passed
if (std::find(facet_list.begin(), facet_list.end(), current_facet) ==
facet_list.end() &&
hasElement(*facet_connectivity, current_facet,
subfacet_connectivity)) {
facet_list.push_back(current_facet);
if (third_dim_points) {
/// check subfacets
for (UInt sf = 0; sf < subfacet_to_facet->getNbComponent(); ++sf) {
const Element & current_subfacet =
(*subfacet_to_facet)(current_facet.element, sf);
if (current_subfacet == ElementNull)
continue;
if (current_subfacet_type != current_subfacet.type ||
current_subfacet_ghost_type != current_subfacet.ghost_type) {
current_subfacet_type = current_subfacet.type;
current_subfacet_ghost_type = current_subfacet.ghost_type;
sf_connectivity = &mesh_facets.getConnectivity(
current_subfacet_type, current_subfacet_ghost_type);
}
if (std::find(subfacet_list->begin(), subfacet_list->end(),
current_subfacet) == subfacet_list->end() &&
hasElement(*sf_connectivity, current_subfacet,
subfacet_connectivity))
subfacet_list->push_back(current_subfacet);
}
}
} else
continue;
/// consider opposing element
if ((*element_to_facet)(current_facet.element)[0] == current_el)
opposing_el = &(*element_to_facet)(current_facet.element)[1];
else
opposing_el = &(*element_to_facet)(current_facet.element)[0];
/// skip null elements since they are on a boundary
if (*opposing_el == ElementNull)
continue;
/// skip this element if already added
if (std::find(elem_list.begin(), elem_list.end(), *opposing_el) !=
elem_list.end())
continue;
/// only regular elements have to be checked
if (opposing_el->kind == _ek_regular)
elements_to_check.push(*opposing_el);
elem_list.push_back(*opposing_el);
#ifndef AKANTU_NDEBUG
const Array<UInt> & conn_elem =
mesh.getConnectivity(opposing_el->type, opposing_el->ghost_type);
AKANTU_DEBUG_ASSERT(
hasElement(conn_elem, *opposing_el, subfacet_connectivity),
"Subfacet doesn't belong to this element");
#endif
}
/// erased checked element from the list
elements_to_check.pop();
}
AKANTU_DEBUG_OUT();
return facet_matched;
}
/* -------------------------------------------------------------------------- */
-void MeshUtils::buildSegmentToNodeType(const Mesh & mesh, Mesh & mesh_facets) {
- buildAllFacets(mesh, mesh_facets, 1);
-
- UInt spatial_dimension = mesh.getSpatialDimension();
-
- const ElementTypeMapArray<UInt> & element_to_rank =
- mesh.getElementSynchronizer().getPrankToElement();
- Int local_rank = StaticCommunicator::getStaticCommunicator().whoAmI();
-
- for (ghost_type_t::iterator gt = ghost_type_t::begin();
- gt != ghost_type_t::end(); ++gt) {
- GhostType ghost_type = *gt;
- Mesh::type_iterator it = mesh_facets.firstType(1, ghost_type);
- Mesh::type_iterator end = mesh_facets.lastType(1, ghost_type);
- for (; it != end; ++it) {
- ElementType type = *it;
- UInt nb_segments = mesh_facets.getNbElement(type, ghost_type);
-
- // allocate the data
- Array<Int> & segment_to_nodetype = *(mesh_facets.getDataPointer<Int>(
- "segment_to_nodetype", type, ghost_type));
-
- std::set<Element> connected_elements;
- const Array<std::vector<Element>> & segment_to_2Delement =
- mesh_facets.getElementToSubelement(type, ghost_type);
-
- // loop over segments
- for (UInt s = 0; s < nb_segments; ++s) {
-
- // determine the elements connected to the segment
- connected_elements.clear();
- const std::vector<Element> & twoD_elements = segment_to_2Delement(s);
-
- if (spatial_dimension == 2) {
- // if 2D just take the elements connected to the segments
- connected_elements.insert(twoD_elements.begin(), twoD_elements.end());
- } else if (spatial_dimension == 3) {
- // if 3D a second loop is needed to get to the 3D elements
- std::vector<Element>::const_iterator facet = twoD_elements.begin();
-
- for (; facet != twoD_elements.end(); ++facet) {
- const std::vector<Element> & threeD_elements =
- mesh_facets.getElementToSubelement(
- facet->type, facet->ghost_type)(facet->element);
- connected_elements.insert(threeD_elements.begin(),
- threeD_elements.end());
- }
- }
-
- // get the minimum processor rank associated to the connected
- // elements and verify if ghost and not ghost elements are
- // found
- Int minimum_rank = std::numeric_limits<Int>::max();
-
- // two booleans saying if not ghost and ghost elements are found in the
- // loop
- bool ghost_found[2];
- ghost_found[0] = false;
- ghost_found[1] = false;
-
- std::set<Element>::iterator connected_elements_it =
- connected_elements.begin();
-
- for (; connected_elements_it != connected_elements.end();
- ++connected_elements_it) {
- if (*connected_elements_it == ElementNull)
- continue;
- ghost_found[connected_elements_it->ghost_type] = true;
- const Array<UInt> & el_to_rank_array = element_to_rank(
- connected_elements_it->type, connected_elements_it->ghost_type);
- minimum_rank =
- std::min(minimum_rank,
- Int(el_to_rank_array(connected_elements_it->element)));
- }
-
- // if no ghost elements are found the segment is local
- if (!ghost_found[1])
- segment_to_nodetype(s) = -1;
- // if no not ghost elements are found the segment is pure ghost
- else if (!ghost_found[0])
- segment_to_nodetype(s) = -3;
- // if the minimum rank is equal to the local rank, the segment is master
- else if (local_rank == minimum_rank)
- segment_to_nodetype(s) = -2;
- // if the minimum rank is less than the local rank, the segment is slave
- else if (local_rank > minimum_rank)
- segment_to_nodetype(s) = minimum_rank;
- else
- AKANTU_DEBUG_ERROR("The local rank cannot be smaller than the "
- "minimum rank if both ghost and not ghost "
- "elements are found");
- }
- }
- }
-}
+// void MeshUtils::buildSegmentToNodeType(const Mesh & mesh, Mesh & mesh_facets) {
+// buildAllFacets(mesh, mesh_facets, 1);
+
+// UInt spatial_dimension = mesh.getSpatialDimension();
+
+// const ElementTypeMapArray<UInt> & element_to_rank =
+// mesh.getElementSynchronizer().getPrankToElement();
+// Int local_rank = StaticCommunicator::getStaticCommunicator().whoAmI();
+
+// for (ghost_type_t::iterator gt = ghost_type_t::begin();
+// gt != ghost_type_t::end(); ++gt) {
+// GhostType ghost_type = *gt;
+// Mesh::type_iterator it = mesh_facets.firstType(1, ghost_type);
+// Mesh::type_iterator end = mesh_facets.lastType(1, ghost_type);
+// for (; it != end; ++it) {
+// ElementType type = *it;
+// UInt nb_segments = mesh_facets.getNbElement(type, ghost_type);
+
+// // allocate the data
+// Array<Int> & segment_to_nodetype = *(mesh_facets.getDataPointer<Int>(
+// "segment_to_nodetype", type, ghost_type));
+
+// std::set<Element> connected_elements;
+// const Array<std::vector<Element>> & segment_to_2Delement =
+// mesh_facets.getElementToSubelement(type, ghost_type);
+
+// // loop over segments
+// for (UInt s = 0; s < nb_segments; ++s) {
+
+// // determine the elements connected to the segment
+// connected_elements.clear();
+// const std::vector<Element> & twoD_elements = segment_to_2Delement(s);
+
+// if (spatial_dimension == 2) {
+// // if 2D just take the elements connected to the segments
+// connected_elements.insert(twoD_elements.begin(), twoD_elements.end());
+// } else if (spatial_dimension == 3) {
+// // if 3D a second loop is needed to get to the 3D elements
+// std::vector<Element>::const_iterator facet = twoD_elements.begin();
+
+// for (; facet != twoD_elements.end(); ++facet) {
+// const std::vector<Element> & threeD_elements =
+// mesh_facets.getElementToSubelement(
+// facet->type, facet->ghost_type)(facet->element);
+// connected_elements.insert(threeD_elements.begin(),
+// threeD_elements.end());
+// }
+// }
+
+// // get the minimum processor rank associated to the connected
+// // elements and verify if ghost and not ghost elements are
+// // found
+// Int minimum_rank = std::numeric_limits<Int>::max();
+
+// // two booleans saying if not ghost and ghost elements are found in the
+// // loop
+// bool ghost_found[2];
+// ghost_found[0] = false;
+// ghost_found[1] = false;
+
+// std::set<Element>::iterator connected_elements_it =
+// connected_elements.begin();
+
+// for (; connected_elements_it != connected_elements.end();
+// ++connected_elements_it) {
+// if (*connected_elements_it == ElementNull)
+// continue;
+// ghost_found[connected_elements_it->ghost_type] = true;
+// const Array<UInt> & el_to_rank_array = element_to_rank(
+// connected_elements_it->type, connected_elements_it->ghost_type);
+// minimum_rank =
+// std::min(minimum_rank,
+// Int(el_to_rank_array(connected_elements_it->element)));
+// }
+
+// // if no ghost elements are found the segment is local
+// if (!ghost_found[1])
+// segment_to_nodetype(s) = -1;
+// // if no not ghost elements are found the segment is pure ghost
+// else if (!ghost_found[0])
+// segment_to_nodetype(s) = -3;
+// // if the minimum rank is equal to the local rank, the segment is master
+// else if (local_rank == minimum_rank)
+// segment_to_nodetype(s) = -2;
+// // if the minimum rank is less than the local rank, the segment is slave
+// else if (local_rank > minimum_rank)
+// segment_to_nodetype(s) = minimum_rank;
+// else
+// AKANTU_DEBUG_ERROR("The local rank cannot be smaller than the "
+// "minimum rank if both ghost and not ghost "
+// "elements are found");
+// }
+// }
+// }
+// }
/* -------------------------------------------------------------------------- */
UInt MeshUtils::updateLocalMasterGlobalConnectivity(Mesh & mesh,
UInt local_nb_new_nodes) {
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
Int rank = comm.whoAmI();
Int nb_proc = comm.getNbProc();
if (nb_proc == 1)
return local_nb_new_nodes;
/// resize global ids array
Array<UInt> & nodes_global_ids = mesh.getGlobalNodesIds();
UInt old_nb_nodes = mesh.getNbNodes() - local_nb_new_nodes;
nodes_global_ids.resize(mesh.getNbNodes());
/// compute the number of global nodes based on the number of old nodes
Vector<UInt> old_local_master_nodes(nb_proc);
for (UInt n = 0; n < old_nb_nodes; ++n)
if (mesh.isLocalOrMasterNode(n))
++old_local_master_nodes(rank);
comm.allGather(old_local_master_nodes);
UInt old_global_nodes =
std::accumulate(old_local_master_nodes.storage(),
old_local_master_nodes.storage() + nb_proc, 0);
/// compute amount of local or master doubled nodes
Vector<UInt> local_master_nodes(nb_proc);
for (UInt n = old_nb_nodes; n < mesh.getNbNodes(); ++n)
if (mesh.isLocalOrMasterNode(n))
++local_master_nodes(rank);
comm.allGather(local_master_nodes);
/// update global number of nodes
UInt total_nb_new_nodes = std::accumulate(
local_master_nodes.storage(), local_master_nodes.storage() + nb_proc, 0);
if (total_nb_new_nodes == 0)
return 0;
/// set global ids of local and master nodes
UInt starting_index =
std::accumulate(local_master_nodes.storage(),
local_master_nodes.storage() + rank, old_global_nodes);
for (UInt n = old_nb_nodes; n < mesh.getNbNodes(); ++n) {
if (mesh.isLocalOrMasterNode(n)) {
nodes_global_ids(n) = starting_index;
++starting_index;
}
}
MeshAccessor mesh_accessor(mesh);
mesh_accessor.setNbGlobalNodes(old_global_nodes + total_nb_new_nodes);
return total_nb_new_nodes;
}
/* -------------------------------------------------------------------------- */
// Deactivating -Wunused-parameter
#if defined(__INTEL_COMPILER)
//#pragma warning ( disable : 383 )
#elif defined(__clang__) // test clang to be sure that when we test for gnu it
// is only gnu
#elif (defined(__GNUC__) || defined(__GNUG__))
#define GCC_VERSION \
(__GNUC__ * 10000 + __GNUC_MINOR__ * 100 + __GNUC_PATCHLEVEL__)
#if GCC_VERSION > 40600
#pragma GCC diagnostic push
#endif
#pragma GCC diagnostic ignored "-Wunused-parameter"
#endif
/* -------------------------------------------------------------------------- */
void MeshUtils::updateElementalConnectivity(
Mesh & mesh, UInt old_node, UInt new_node,
const std::vector<Element> & element_list,
__attribute__((unused)) const std::vector<Element> * facet_list) {
AKANTU_DEBUG_IN();
ElementType el_type = _not_defined;
GhostType gt_type = _casper;
Array<UInt> * conn_elem = NULL;
#if defined(AKANTU_COHESIVE_ELEMENT)
const Array<Element> * cohesive_facets = NULL;
#endif
UInt nb_nodes_per_element = 0;
UInt * n_update = NULL;
for (UInt el = 0; el < element_list.size(); ++el) {
const Element & elem = element_list[el];
if (elem.type == _not_defined)
continue;
if (elem.type != el_type || elem.ghost_type != gt_type) {
el_type = elem.type;
gt_type = elem.ghost_type;
conn_elem = &mesh.getConnectivity(el_type, gt_type);
nb_nodes_per_element = conn_elem->getNbComponent();
#if defined(AKANTU_COHESIVE_ELEMENT)
if (elem.kind == _ek_cohesive)
cohesive_facets =
&mesh.getMeshFacets().getSubelementToElement(el_type, gt_type);
#endif
}
#if defined(AKANTU_COHESIVE_ELEMENT)
if (elem.kind == _ek_cohesive) {
AKANTU_DEBUG_ASSERT(
facet_list != NULL,
"Provide a facet list in order to update cohesive elements");
/// loop over cohesive element's facets
for (UInt f = 0, n = 0; f < 2; ++f, n += nb_nodes_per_element / 2) {
const Element & facet = (*cohesive_facets)(elem.element, f);
/// skip facets if not present in the list
if (std::find(facet_list->begin(), facet_list->end(), facet) ==
facet_list->end())
continue;
n_update = std::find(
conn_elem->storage() + elem.element * nb_nodes_per_element + n,
conn_elem->storage() + elem.element * nb_nodes_per_element + n +
nb_nodes_per_element / 2,
old_node);
AKANTU_DEBUG_ASSERT(n_update !=
conn_elem->storage() +
elem.element * nb_nodes_per_element + n +
nb_nodes_per_element / 2,
"Node not found in current element");
/// update connectivity
*n_update = new_node;
}
} else {
#endif
n_update =
std::find(conn_elem->storage() + elem.element * nb_nodes_per_element,
conn_elem->storage() + elem.element * nb_nodes_per_element +
nb_nodes_per_element,
old_node);
AKANTU_DEBUG_ASSERT(n_update != conn_elem->storage() +
elem.element * nb_nodes_per_element +
nb_nodes_per_element,
"Node not found in current element");
/// update connectivity
*n_update = new_node;
#if defined(AKANTU_COHESIVE_ELEMENT)
}
#endif
}
AKANTU_DEBUG_OUT();
}
// Reactivating -Wunused-parameter
#if defined(__INTEL_COMPILER)
//#pragma warning ( disable : 383 )
#elif defined(__clang__) // test clang to be sure that when we test for gnu it
// is only gnu
#elif defined(__GNUG__)
#if GCC_VERSION > 40600
#pragma GCC diagnostic pop
#else
#pragma GCC diagnostic warning "-Wunused-parameter"
#endif
#endif
/* -------------------------------------------------------------------------- */
} // namespace akantu
// LocalWords: ElementType
diff --git a/src/mesh_utils/mesh_utils.hh b/src/mesh_utils/mesh_utils.hh
index 2c79aaa1a..a63d000a4 100644
--- a/src/mesh_utils/mesh_utils.hh
+++ b/src/mesh_utils/mesh_utils.hh
@@ -1,244 +1,245 @@
/**
* @file mesh_utils.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Leonardo Snozzi <leonardo.snozzi@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Fri Oct 02 2015
*
* @brief All mesh utils necessary for various tasks
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
* Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
* Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh.hh"
#include "aka_csr.hh"
/* -------------------------------------------------------------------------- */
#include <vector>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MESH_UTILS_HH__
#define __AKANTU_MESH_UTILS_HH__
/* -------------------------------------------------------------------------- */
namespace akantu {
class MeshUtils {
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// build a CSR<UInt> that contains for each node the linearized number of
/// the connected elements of a given spatial dimension
- static void buildNode2Elements(const Mesh & mesh, CSR<UInt> & node_to_elem,
- UInt spatial_dimension = _all_dimensions);
+ // static void buildNode2Elements(const Mesh & mesh, CSR<UInt> & node_to_elem,
+ // UInt spatial_dimension = _all_dimensions);
+
/// build a CSR<Element> that contains for each node the list of connected
/// elements of a given spatial dimension
static void buildNode2Elements(const Mesh & mesh, CSR<Element> & node_to_elem,
UInt spatial_dimension = _all_dimensions);
/// build a CSR<UInt> that contains for each node the number of
/// the connected elements of a given ElementType
static void
buildNode2ElementsElementTypeMap(const Mesh & mesh, CSR<UInt> & node_to_elem,
const ElementType & type,
const GhostType & ghost_type = _not_ghost);
/// build the facets elements on the boundaries of a mesh
static void buildFacets(Mesh & mesh);
/// build all the facets elements: boundary and internals and store them in
/// the mesh_facets for element of dimension from_dimension to to_dimension
static void buildAllFacets(const Mesh & mesh, Mesh & mesh_facets,
UInt from_dimension, UInt to_dimension);
/// build all the facets elements: boundary and internals and store them in
/// the mesh_facets
static void buildAllFacets(const Mesh & mesh, Mesh & mesh_facets,
UInt to_dimension = 0);
/// build facets for a given spatial dimension
static void buildFacetsDimension(
const Mesh & mesh, Mesh & mesh_facets, bool boundary_only, UInt dimension,
const ElementTypeMapArray<UInt> * prank_to_element = nullptr);
/// take the local_connectivity array as the array of local and ghost
/// connectivity, renumber the nodes and set the connectivity of the mesh
static void renumberMeshNodes(Mesh & mesh, Array<UInt> & local_connectivities,
UInt nb_local_element, UInt nb_ghost_element,
ElementType type, Array<UInt> & old_nodes);
/// compute pbc pair for a given direction
static void computePBCMap(const Mesh & mymesh, const UInt dir,
std::map<UInt, UInt> & pbc_pair);
/// compute pbc pair for a surface pair
static void computePBCMap(const Mesh & mymesh,
const std::pair<Surface, Surface> & surface_pair,
std::map<UInt, UInt> & pbc_pair);
/// remove not connected nodes /!\ this functions renumbers the nodes.
static void purifyMesh(Mesh & mesh);
#if defined(AKANTU_COHESIVE_ELEMENT)
/// function to insert cohesive elements on the selected facets
/// @return number of facets that have been doubled
static UInt
insertCohesiveElements(Mesh & mesh, Mesh & mesh_facets,
const ElementTypeMapArray<bool> & facet_insertion,
Array<UInt> & doubled_nodes,
Array<Element> & new_elements,
bool only_double_facets);
#endif
/// fill the subelement to element and the elements to subelements data
static void fillElementToSubElementsData(Mesh & mesh);
/// flip facets based on global connectivity
static void flipFacets(Mesh & mesh_facets,
const ElementTypeMapArray<UInt> & global_connectivity,
GhostType gt_facet);
/// provide list of elements around a node and check if a given
/// facet is reached
template <bool third_dim_points>
static bool findElementsAroundSubfacet(
const Mesh & mesh, const Mesh & mesh_facets,
const Element & starting_element, const Element & end_facet,
const Vector<UInt> & subfacet_connectivity,
std::vector<Element> & elem_list, std::vector<Element> & facet_list,
std::vector<Element> * subfacet_list = nullptr);
/// function to check if a node belongs to a given element
static inline bool hasElement(const Array<UInt> & connectivity,
const Element & el, const Vector<UInt> & nodes);
/// reset facet_to_double arrays in the Mesh
static void resetFacetToDouble(Mesh & mesh_facets);
/// associate a node type to each segment in the mesh
- static void buildSegmentToNodeType(const Mesh & mesh, Mesh & mesh_facets);
+ // static void buildSegmentToNodeType(const Mesh & mesh, Mesh & mesh_facets);
/// update local and master global connectivity when new nodes are added
static UInt updateLocalMasterGlobalConnectivity(Mesh & mesh,
UInt old_nb_nodes);
private:
/// match pairs that are on the associated pbc's
static void matchPBCPairs(const Mesh & mymesh, const UInt dir,
Array<UInt> & selected_left,
Array<UInt> & selected_right,
std::map<UInt, UInt> & pbc_pair);
/// function used by all the renumbering functions
static void
renumberNodesInConnectivity(Array<UInt> & list_nodes, UInt nb_nodes,
std::map<UInt, UInt> & renumbering_map);
/// update facet_to_subfacet
static void updateFacetToSubfacet(Mesh & mesh_facets,
ElementType type_subfacet,
GhostType gt_subfacet, bool facet_mode);
/// update subfacet_to_facet
static void updateSubfacetToFacet(Mesh & mesh_facets,
ElementType type_subfacet,
GhostType gt_subfacet, bool facet_mode);
/// function to double a given facet and update the list of doubled
/// nodes
static void doubleFacet(Mesh & mesh, Mesh & mesh_facets, UInt facet_dimension,
Array<UInt> & doubled_nodes, bool facet_mode);
/// function to double a subfacet given start and end index for
/// local facet_to_subfacet vector, and update the list of doubled
/// nodes
template <UInt spatial_dimension>
static void doubleSubfacet(Mesh & mesh, Mesh & mesh_facets,
Array<UInt> & doubled_nodes);
/// double a node
static void doubleNodes(Mesh & mesh, const std::vector<UInt> & old_nodes,
Array<UInt> & doubled_nodes);
/// fill facet_to_double array in the mesh
/// returns the number of facets to be doubled
static UInt
updateFacetToDouble(Mesh & mesh_facets,
const ElementTypeMapArray<bool> & facet_insertion);
/// find subfacets to be doubled
template <bool subsubfacet_mode>
static void findSubfacetToDouble(Mesh & mesh, Mesh & mesh_facets);
/// double facets (points) in 1D
static void doublePointFacet(Mesh & mesh, Mesh & mesh_facets,
Array<UInt> & doubled_nodes);
#if defined(AKANTU_COHESIVE_ELEMENT)
/// update cohesive element data
static void updateCohesiveData(Mesh & mesh, Mesh & mesh_facets,
Array<Element> & new_elements);
#endif
/// update elemental connectivity after doubling a node
inline static void
updateElementalConnectivity(Mesh & mesh, UInt old_node, UInt new_node,
const std::vector<Element> & element_list,
const std::vector<Element> * facet_list = NULL);
/// double middle nodes if facets are _segment_3
template <bool third_dim_segments>
static void updateQuadraticSegments(Mesh & mesh, Mesh & mesh_facets,
ElementType type_facet,
GhostType gt_facet,
Array<UInt> & doubled_nodes);
/// remove elements on a vector
inline static bool
removeElementsInVector(const std::vector<Element> & elem_to_remove,
std::vector<Element> & elem_list);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "mesh_utils_inline_impl.cc"
} // akantu
#endif /* __AKANTU_MESH_UTILS_HH__ */
diff --git a/src/synchronizer/master_element_info_per_processor.cc b/src/synchronizer/master_element_info_per_processor.cc
index 44560563c..7699f00d5 100644
--- a/src/synchronizer/master_element_info_per_processor.cc
+++ b/src/synchronizer/master_element_info_per_processor.cc
@@ -1,490 +1,485 @@
/**
* @file master_element_info_per_processor.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Fri Mar 11 14:57:13 2016
*
* @brief
*
* @section LICENSE
*
* Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
+#include "aka_zip.hh"
#include "element_group.hh"
#include "element_info_per_processor.hh"
#include "element_synchronizer.hh"
#include "mesh_utils.hh"
#include "static_communicator.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <iostream>
#include <map>
+#include <tuple>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
MasterElementInfoPerProc::MasterElementInfoPerProc(
ElementSynchronizer & synchronizer, UInt message_cnt, UInt root,
ElementType type, const MeshPartition & partition)
: ElementInfoPerProc(synchronizer, message_cnt, root, type),
partition(partition), all_nb_local_element(nb_proc, 0),
all_nb_ghost_element(nb_proc, 0), all_nb_element_to_send(nb_proc, 0) {
Vector<UInt> size(5);
size(0) = (UInt)type;
if (type != _not_defined) {
nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
nb_element = mesh.getNbElement(type);
const Array<UInt> & partition_num =
this->partition.getPartition(this->type, _not_ghost);
const CSR<UInt> & ghost_partition =
this->partition.getGhostPartitionCSR()(this->type, _not_ghost);
for (UInt el = 0; el < nb_element; ++el) {
this->all_nb_local_element[partition_num(el)]++;
for (CSR<UInt>::const_iterator part = ghost_partition.begin(el);
part != ghost_partition.end(el); ++part) {
this->all_nb_ghost_element[*part]++;
}
this->all_nb_element_to_send[partition_num(el)] +=
ghost_partition.getNbCols(el) + 1;
}
/// tag info
std::vector<std::string> tag_names;
this->getMeshData().getTagNames(tag_names, type);
this->nb_tags = tag_names.size();
size(4) = nb_tags;
for (UInt p = 0; p < nb_proc; ++p) {
if (p != root) {
size(1) = this->all_nb_local_element[p];
size(2) = this->all_nb_ghost_element[p];
size(3) = this->all_nb_element_to_send[p];
AKANTU_DEBUG_INFO(
"Sending connectivities informations to proc "
<< p << " TAG("
<< Tag::genTag(this->rank, this->message_count, Tag::_SIZES)
<< ")");
comm.send(size, p,
Tag::genTag(this->rank, this->message_count, Tag::_SIZES));
} else {
this->nb_local_element = this->all_nb_local_element[p];
this->nb_ghost_element = this->all_nb_ghost_element[p];
}
}
} else {
for (UInt p = 0; p < this->nb_proc; ++p) {
if (p != this->root) {
AKANTU_DEBUG_INFO(
"Sending empty connectivities informations to proc "
<< p << " TAG("
<< Tag::genTag(this->rank, this->message_count, Tag::_SIZES)
<< ")");
comm.send(size, p,
Tag::genTag(this->rank, this->message_count, Tag::_SIZES));
}
}
}
}
/* ------------------------------------------------------------------------ */
void MasterElementInfoPerProc::synchronizeConnectivities() {
const Array<UInt> & partition_num =
this->partition.getPartition(this->type, _not_ghost);
const CSR<UInt> & ghost_partition =
this->partition.getGhostPartitionCSR()(this->type, _not_ghost);
std::vector<Array<UInt>> buffers(this->nb_proc);
auto conn_it = this->mesh.getConnectivity(this->type, _not_ghost)
.begin(this->nb_nodes_per_element);
auto conn_end = this->mesh.getConnectivity(this->type, _not_ghost)
.end(this->nb_nodes_per_element);
/// copying the local connectivity
auto part_it = partition_num.begin();
for (; conn_it != conn_end; ++conn_it, ++part_it) {
const auto & conn = *conn_it;
for (UInt i = 0; i < conn.size(); ++i) {
buffers[*part_it].push_back(conn[i]);
}
}
/// copying the connectivity of ghost element
conn_it = this->mesh.getConnectivity(this->type, _not_ghost)
.begin(this->nb_nodes_per_element);
for (UInt el = 0; conn_it != conn_end; ++el, ++conn_it) {
for (auto part = ghost_partition.begin(el); part != ghost_partition.end(el);
++part) {
UInt proc = *part;
const Vector<UInt> & conn = *conn_it;
for (UInt i = 0; i < conn.size(); ++i) {
buffers[proc].push_back(conn[i]);
}
}
}
#ifndef AKANTU_NDEBUG
for (UInt p = 0; p < this->nb_proc; ++p) {
UInt size = this->nb_nodes_per_element *
(this->all_nb_local_element[p] + this->all_nb_ghost_element[p]);
AKANTU_DEBUG_ASSERT(
buffers[p].getSize() == size,
"The connectivity data packed in the buffer are not correct");
}
#endif
/// send all connectivity and ghost information to all processors
std::vector<CommunicationRequest> requests;
for (UInt p = 0; p < this->nb_proc; ++p) {
if (p != this->root) {
AKANTU_DEBUG_INFO(
"Sending connectivities to proc "
<< p << " TAG("
<< Tag::genTag(this->rank, this->message_count, Tag::_CONNECTIVITY)
<< ")");
requests.push_back(comm.asyncSend(
buffers[p], p,
Tag::genTag(this->rank, this->message_count, Tag::_CONNECTIVITY)));
}
}
Array<UInt> & old_nodes = this->getNodesGlobalIds();
/// create the renumbered connectivity
AKANTU_DEBUG_INFO("Renumbering local connectivities");
MeshUtils::renumberMeshNodes(mesh, buffers[root], all_nb_local_element[root],
all_nb_ghost_element[root], type, old_nodes);
comm.waitAll(requests);
comm.freeCommunicationRequest(requests);
}
/* ------------------------------------------------------------------------ */
void MasterElementInfoPerProc::synchronizePartitions() {
const Array<UInt> & partition_num =
this->partition.getPartition(this->type, _not_ghost);
const CSR<UInt> & ghost_partition =
this->partition.getGhostPartitionCSR()(this->type, _not_ghost);
std::vector<Array<UInt>> buffers(this->partition.getNbPartition());
/// splitting the partition information to send them to processors
Vector<UInt> count_by_proc(nb_proc, 0);
for (UInt el = 0; el < nb_element; ++el) {
UInt proc = partition_num(el);
buffers[proc].push_back(ghost_partition.getNbCols(el));
UInt i(0);
for (CSR<UInt>::const_iterator part = ghost_partition.begin(el);
part != ghost_partition.end(el); ++part, ++i) {
buffers[proc].push_back(*part);
}
}
for (UInt el = 0; el < nb_element; ++el) {
UInt i(0);
for (CSR<UInt>::const_iterator part = ghost_partition.begin(el);
part != ghost_partition.end(el); ++part, ++i) {
buffers[*part].push_back(partition_num(el));
}
}
#ifndef AKANTU_NDEBUG
for (UInt p = 0; p < this->nb_proc; ++p) {
AKANTU_DEBUG_ASSERT(
buffers[p].getSize() ==
(this->all_nb_ghost_element[p] + this->all_nb_element_to_send[p]),
"Data stored in the buffer are most probably wrong");
}
#endif
std::vector<CommunicationRequest> requests;
/// last data to compute the communication scheme
for (UInt p = 0; p < this->nb_proc; ++p) {
if (p != this->root) {
AKANTU_DEBUG_INFO(
"Sending partition informations to proc "
<< p << " TAG("
<< Tag::genTag(this->rank, this->message_count, Tag::_PARTITIONS)
<< ")");
requests.push_back(comm.asyncSend(
buffers[p], p,
Tag::genTag(this->rank, this->message_count, Tag::_PARTITIONS)));
}
}
if (Mesh::getSpatialDimension(this->type) ==
this->mesh.getSpatialDimension()) {
AKANTU_DEBUG_INFO("Creating communications scheme");
this->fillCommunicationScheme(buffers[this->rank]);
}
comm.waitAll(requests);
comm.freeCommunicationRequest(requests);
}
/* -------------------------------------------------------------------------- */
void MasterElementInfoPerProc::synchronizeTags() {
AKANTU_DEBUG_IN();
if (this->nb_tags == 0) {
AKANTU_DEBUG_OUT();
return;
}
UInt mesh_data_sizes_buffer_length;
MeshData & mesh_data = this->getMeshData();
/// tag info
std::vector<std::string> tag_names;
mesh_data.getTagNames(tag_names, type);
// Make sure the tags are sorted (or at least not in random order),
// because they come from a map !!
std::sort(tag_names.begin(), tag_names.end());
// Sending information about the tags in mesh_data: name, data type and
// number of components of the underlying array associated to the current
// type
DynamicCommunicationBuffer mesh_data_sizes_buffer;
std::vector<std::string>::const_iterator names_it = tag_names.begin();
std::vector<std::string>::const_iterator names_end = tag_names.end();
for (; names_it != names_end; ++names_it) {
mesh_data_sizes_buffer << *names_it;
mesh_data_sizes_buffer << mesh_data.getTypeCode(*names_it);
mesh_data_sizes_buffer << mesh_data.getNbComponent(*names_it, type);
}
mesh_data_sizes_buffer_length = mesh_data_sizes_buffer.getSize();
AKANTU_DEBUG_INFO(
"Broadcasting the size of the information about the mesh data tags: ("
<< mesh_data_sizes_buffer_length << ").");
comm.broadcast(mesh_data_sizes_buffer_length, root);
AKANTU_DEBUG_INFO(
"Broadcasting the information about the mesh data tags, addr "
<< (void *)mesh_data_sizes_buffer.storage());
if (mesh_data_sizes_buffer_length != 0)
comm.broadcast(mesh_data_sizes_buffer, root);
if (mesh_data_sizes_buffer_length != 0) {
// Sending the actual data to each processor
DynamicCommunicationBuffer * buffers =
new DynamicCommunicationBuffer[nb_proc];
std::vector<std::string>::const_iterator names_it = tag_names.begin();
std::vector<std::string>::const_iterator names_end = tag_names.end();
// Loop over each tag for the current type
for (; names_it != names_end; ++names_it) {
// Type code of the current tag (i.e. the tag named *names_it)
this->fillTagBuffer(buffers, *names_it);
}
std::vector<CommunicationRequest> requests;
for (UInt p = 0; p < nb_proc; ++p) {
if (p != root) {
AKANTU_DEBUG_INFO("Sending "
<< buffers[p].getSize()
<< " bytes of mesh data to proc " << p << " TAG("
<< Tag::genTag(this->rank, this->message_count,
Tag::_MESH_DATA)
<< ")");
requests.push_back(comm.asyncSend(
buffers[p], p,
Tag::genTag(this->rank, this->message_count, Tag::_MESH_DATA)));
}
}
names_it = tag_names.begin();
// Loop over each tag for the current type
for (; names_it != names_end; ++names_it) {
// Reinitializing the mesh data on the master
this->fillMeshData(buffers[root], *names_it,
mesh_data.getTypeCode(*names_it),
mesh_data.getNbComponent(*names_it, type));
}
comm.waitAll(requests);
comm.freeCommunicationRequest(requests);
requests.clear();
delete[] buffers;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <typename T>
void MasterElementInfoPerProc::fillTagBufferTemplated(
DynamicCommunicationBuffer * buffers, const std::string & tag_name) {
MeshData & mesh_data = this->getMeshData();
const Array<T> & data = mesh_data.getElementalDataArray<T>(tag_name, type);
const Array<UInt> & partition_num =
this->partition.getPartition(this->type, _not_ghost);
const CSR<UInt> & ghost_partition =
this->partition.getGhostPartitionCSR()(this->type, _not_ghost);
// Not possible to use the iterator because it potentially triggers the
// creation of complex
// type templates (such as akantu::Vector< std::vector<Element> > which don't
// implement the right interface
// (e.g. operator<< in that case).
// typename Array<T>::template const_iterator< Vector<T> > data_it =
// data.begin(data.getNbComponent());
// typename Array<T>::template const_iterator< Vector<T> > data_end =
// data.end(data.getNbComponent());
const T * data_it = data.storage();
const T * data_end = data.storage() + data.getSize() * data.getNbComponent();
const UInt * part = partition_num.storage();
/// copying the data, element by element
for (; data_it != data_end; ++part) {
for (UInt j(0); j < data.getNbComponent(); ++j, ++data_it) {
buffers[*part] << *data_it;
}
}
data_it = data.storage();
/// copying the data for the ghost element
for (UInt el(0); data_it != data_end;
data_it += data.getNbComponent(), ++el) {
CSR<UInt>::const_iterator it = ghost_partition.begin(el);
CSR<UInt>::const_iterator end = ghost_partition.end(el);
for (; it != end; ++it) {
UInt proc = *it;
for (UInt j(0); j < data.getNbComponent(); ++j) {
buffers[proc] << data_it[j];
}
}
}
}
/* -------------------------------------------------------------------------- */
void MasterElementInfoPerProc::fillTagBuffer(
DynamicCommunicationBuffer * buffers, const std::string & tag_name) {
MeshData & mesh_data = this->getMeshData();
#define AKANTU_DISTRIBUTED_SYNHRONIZER_TAG_DATA(r, extra_param, elem) \
case BOOST_PP_TUPLE_ELEM(2, 0, elem): { \
this->fillTagBufferTemplated<BOOST_PP_TUPLE_ELEM(2, 1, elem)>(buffers, \
tag_name); \
break; \
}
MeshDataTypeCode data_type_code = mesh_data.getTypeCode(tag_name);
switch (data_type_code) {
BOOST_PP_SEQ_FOR_EACH(AKANTU_DISTRIBUTED_SYNHRONIZER_TAG_DATA, ,
AKANTU_MESH_DATA_TYPES)
default:
AKANTU_DEBUG_ERROR("Could not obtain the type of tag" << tag_name << "!");
break;
}
#undef AKANTU_DISTRIBUTED_SYNHRONIZER_TAG_DATA
}
/* -------------------------------------------------------------------------- */
void MasterElementInfoPerProc::synchronizeGroups() {
AKANTU_DEBUG_IN();
DynamicCommunicationBuffer * buffers =
new DynamicCommunicationBuffer[nb_proc];
- typedef std::vector<std::vector<std::string>> ElementToGroup;
+ using ElementToGroup = std::vector<std::vector<std::string>>;
ElementToGroup element_to_group;
element_to_group.resize(nb_element);
- GroupManager::const_element_group_iterator egi = mesh.element_group_begin();
- GroupManager::const_element_group_iterator ege = mesh.element_group_end();
+ auto egi = mesh.element_group_begin();
+ auto ege = mesh.element_group_end();
for (; egi != ege; ++egi) {
ElementGroup & eg = *(egi->second);
std::string name = egi->first;
- ElementGroup::const_element_iterator eit =
- eg.element_begin(type, _not_ghost);
- ElementGroup::const_element_iterator eend =
- eg.element_end(type, _not_ghost);
- for (; eit != eend; ++eit) {
- element_to_group[*eit].push_back(name);
+ for (const auto & element : eg.getElements(type, _not_ghost)) {
+ element_to_group[element].push_back(name);
}
- eit = eg.element_begin(type, _not_ghost);
- if (eit != eend)
+ auto eit = eg.begin(type, _not_ghost);
+ if (eit != eg.end(type, _not_ghost))
const_cast<Array<UInt> &>(eg.getElements(type)).empty();
}
- const Array<UInt> & partition_num =
+ const auto & partition_num =
this->partition.getPartition(this->type, _not_ghost);
- const CSR<UInt> & ghost_partition =
+ const auto & ghost_partition =
this->partition.getGhostPartitionCSR()(this->type, _not_ghost);
- /// preparing the buffers
- const UInt * part = partition_num.storage();
-
/// copying the data, element by element
ElementToGroup::const_iterator data_it = element_to_group.begin();
ElementToGroup::const_iterator data_end = element_to_group.end();
- for (; data_it != data_end; ++part, ++data_it) {
- buffers[*part] << *data_it;
+ for (auto pair : zip(partition_num, element_to_group)) {
+ buffers[std::get<0>(pair)] << std::get<1>(pair);
}
data_it = element_to_group.begin();
/// copying the data for the ghost element
for (UInt el(0); data_it != data_end; ++data_it, ++el) {
CSR<UInt>::const_iterator it = ghost_partition.begin(el);
CSR<UInt>::const_iterator end = ghost_partition.end(el);
for (; it != end; ++it) {
UInt proc = *it;
buffers[proc] << *data_it;
}
}
std::vector<CommunicationRequest> requests;
for (UInt p = 0; p < this->nb_proc; ++p) {
if (p == this->rank)
continue;
AKANTU_DEBUG_INFO("Sending element groups to proc "
<< p << " TAG("
<< Tag::genTag(this->rank, p, Tag::_ELEMENT_GROUP)
<< ")");
requests.push_back(comm.asyncSend(
buffers[p], p, Tag::genTag(this->rank, p, Tag::_ELEMENT_GROUP)));
}
this->fillElementGroupsFromBuffer(buffers[this->rank]);
comm.waitAll(requests);
comm.freeCommunicationRequest(requests);
requests.clear();
delete[] buffers;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
-} // akantu
+} // namespace akantu
diff --git a/test/test_common/test_grid.cc b/test/test_common/test_grid.cc
index 3edc9d699..6dff392f9 100644
--- a/test/test_common/test_grid.cc
+++ b/test/test_common/test_grid.cc
@@ -1,108 +1,107 @@
/**
* @file test_grid.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Jul 15 2010
* @date last modification: Thu Aug 06 2015
*
* @brief Test the grid object
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
* Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
* Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <iostream>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_grid_dynamic.hh"
#include "mesh.hh"
#include "mesh_io.hh"
using namespace akantu;
int main(int argc, char *argv[]) {
const UInt spatial_dimension = 2;
akantu::initialize(argc, argv);
Mesh circle(spatial_dimension);
circle.read("circle.msh");
- circle.computeBoundingBox();
const Vector<Real> & l = circle.getLocalLowerBounds();
const Vector<Real> & u = circle.getLocalUpperBounds();
Real spacing[spatial_dimension] = {0.2, 0.2};
Vector<Real> s(spacing, spatial_dimension);
Vector<Real> c = u;
c += l;
c /= 2.;
SpatialGrid<Element> grid(spatial_dimension, s, c);
Vector<Real> bary(spatial_dimension);
Element el;
el.ghost_type = _not_ghost;
Mesh::type_iterator it = circle.firstType(spatial_dimension);
Mesh::type_iterator last_type = circle.lastType (spatial_dimension);
for(; it != last_type; ++it) {
UInt nb_element = circle.getNbElement(*it);
el.type = *it;
for (UInt e = 0; e < nb_element; ++e) {
circle.getBarycenter(e, el.type, bary.storage());
el.element = e;
grid.insert(el, bary);
}
}
std::cout << grid << std::endl;
Mesh mesh(spatial_dimension, "save");
grid.saveAsMesh(mesh);
mesh.write("grid.msh");
Vector<Real> pos(spatial_dimension);
// const SpatialGrid<Element>::CellID & id = grid.getCellID(pos);
// #if !defined AKANTU_NDEBUG
// SpatialGrid<Element>::neighbor_cells_iterator nit = grid.beginNeighborCells(id);
// SpatialGrid<Element>::neighbor_cells_iterator nend = grid.endNeighborCells(id);
// for(;nit != nend; ++nit) {
// std::cout << std::endl;
// const SpatialGrid<Element>::Cell & cell = grid.getCell(*nit);
// SpatialGrid<Element>::Cell::const_iterator cit = cell.begin();
// SpatialGrid<Element>::Cell::position_iterator pit = cell.begin_pos();
// SpatialGrid<Element>::Cell::const_iterator cend = cell.end();
// for (; cit != cend; ++cit, ++pit) {
// std::cout << *cit << " " << *pit << std::endl;
// }
// }
// #endif
akantu::finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_fe_engine/test_fe_engine_gauss_integration.cc b/test/test_fe_engine/test_fe_engine_gauss_integration.cc
index 225b15096..815cc9ae8 100644
--- a/test/test_fe_engine/test_fe_engine_gauss_integration.cc
+++ b/test/test_fe_engine/test_fe_engine_gauss_integration.cc
@@ -1,204 +1,203 @@
/**
* @file test_fe_engine_precomputation.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Jun 14 2010
* @date last modification: Mon Jul 13 2015
*
* @brief test integration on elements, this test consider that mesh is a cube
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
* Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
* Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "fe_engine.hh"
#include "shape_lagrange.hh"
#include "integrator_gauss.hh"
/* -------------------------------------------------------------------------- */
#include <iostream>
/* -------------------------------------------------------------------------- */
using namespace akantu;
typedef FEEngineTemplate<IntegratorGauss, ShapeLagrange> FEM;
const ElementType type = TYPE;
// cst x x^2 x^3
// x^4 x^5
Real alpha[3][6] = {{0.40062394, 0.13703225, 0.51731446, 0.87830084, 0.5410543,
0.71842292}, // x
{0.41861835, 0.11080576, 0.49874043, 0.49077504, 0.85073835,
0.66259755}, // y
{0.92620845, 0.7503478, 0.62962232, 0.31662719, 0.64069644,
0.30878135}}; // z
static Vector<Real> eval_poly(UInt degree, const Vector<Real> & x) {
Vector<Real> res(x.size());
for (UInt i = 0; i < degree + 1; ++i) {
for (UInt d = 0; d < x.size(); ++d) {
res(d) += std::pow(x(d), i) * alpha[d][i];
}
}
return res;
}
static Vector<Real> eval_int(UInt degree, const Vector<Real> & a,
const Vector<Real> & b) {
Vector<Real> res(a.size());
for (UInt i = 0; i < degree + 1; ++i) {
for (UInt d = 0; d < a.size(); ++d) {
res(d) += (std::pow(b(d), i + 1) - std::pow(a(d), i + 1)) * alpha[d][i] / Real(i + 1);
}
}
if (a.size() == 3) {
res(_x) *= std::abs(b(_y) - a(_y)) * std::abs(b(_z) - a(_z));
res(_y) *= std::abs(b(_x) - a(_x)) * std::abs(b(_z) - a(_z));
res(_z) *= std::abs(b(_y) - a(_y)) * std::abs(b(_x) - a(_x));
} else if (a.size() == 2) {
res(_x) *= std::abs(b(_y) - a(_y));
res(_y) *= std::abs(b(_x) - a(_x));
}
return res;
}
template <UInt degree>
static Vector<Real> integrate_poly(UInt poly_degree, FEM & fem) {
Mesh & mesh = fem.getMesh();
UInt dim = mesh.getSpatialDimension();
Matrix<Real> integration_points =
fem.getIntegrator().getIntegrationPoints<type, degree>();
// Vector<Real> integration_weights =
// fem.getIntegrator().getIntegrationWeights<type, degree>();
// for (UInt i = 0; i < integration_points.cols(); ++i) {
// std::cout << "q(" << i << ") = " << Vector<Real>(integration_points(i))
// << " - w(" << i << ") = "<< integration_weights[i] << std::endl;
// }
UInt nb_integration_points = integration_points.cols();
UInt nb_element = mesh.getNbElement(type);
UInt shapes_size = ElementClass<type>::getShapeSize();
Array<Real> shapes(0, shapes_size);
fem.getShapeFunctions().computeShapesOnIntegrationPoints<type>(
mesh.getNodes(), integration_points, shapes, _not_ghost);
UInt vect_size = nb_integration_points * nb_element;
Array<Real> integration_points_pos(vect_size, dim);
fem.getShapeFunctions().interpolateOnIntegrationPoints<type>(
mesh.getNodes(), integration_points_pos, dim, shapes);
Array<Real> polynomial(vect_size, dim);
Array<Real>::vector_iterator P_it = polynomial.begin(dim);
Array<Real>::vector_iterator P_end = polynomial.end(dim);
Array<Real>::const_vector_iterator x_it = integration_points_pos.begin(dim);
for (; P_it != P_end; ++P_it, ++x_it) {
*P_it = eval_poly(poly_degree, *x_it);
// std::cout << "Q = " << *x_it << std::endl;
// std::cout << "P(Q) = " << *P_it << std::endl;
}
Vector<Real> res(dim);
Array<Real> polynomial_1d(vect_size, 1);
for (UInt d = 0; d < dim; ++d) {
Array<Real>::const_vector_iterator P_it = polynomial.begin(dim);
Array<Real>::const_vector_iterator P_end = polynomial.end(dim);
Array<Real>::scalar_iterator P1_it = polynomial_1d.begin();
for (; P_it != P_end; ++P_it, ++P1_it) {
*P1_it = (*P_it)(d);
// std::cout << "P(Q, d) = " << *P1_it << std::endl;
}
res(d) = fem.getIntegrator().integrate<type, degree>(polynomial_1d);
}
return res;
}
int main(int argc, char * argv[]) {
akantu::initialize(argc, argv);
const UInt dim = ElementClass<type>::getSpatialDimension();
Mesh mesh(dim);
std::stringstream meshfilename;
meshfilename << type << ".msh";
mesh.read(meshfilename.str());
FEM fem(mesh, dim, "my_fem");
- mesh.computeBoundingBox();
const Vector<Real> & lower = mesh.getLowerBounds();
const Vector<Real> & upper = mesh.getUpperBounds();
bool ok = true;
for (UInt d = 0; d < 6; ++d) {
Vector<Real> res(dim);
switch (d) {
case 0:
res = integrate_poly<1>(d, fem);
break;
case 1:
res = integrate_poly<1>(d, fem);
break;
case 2:
res = integrate_poly<2>(d, fem);
break;
case 3:
res = integrate_poly<3>(d, fem);
break;
case 4:
res = integrate_poly<4>(d, fem);
break;
case 5:
res = integrate_poly<5>(d, fem);
break;
}
Vector<Real> exact(dim);
exact = eval_int(d, lower, upper);
Vector<Real> error(dim);
error = exact - res;
Real error_n = error.norm<L_inf>();
if (error_n > 5e-14) {
std::cout << d << " -> Resultat " << res << " - ";
std::cout << "Exact" << exact << " -- ";
std::cout << error << " {" << error_n << "}" << std::endl;
ok = false;
}
}
finalize();
if (ok)
return 0;
else
return 1;
}
diff --git a/test/test_fe_engine/test_inverse_map.cc b/test/test_fe_engine/test_inverse_map.cc
index 5aef24bce..9ecdcb234 100644
--- a/test/test_fe_engine/test_inverse_map.cc
+++ b/test/test_fe_engine/test_inverse_map.cc
@@ -1,106 +1,106 @@
/**
* @file test_inverse_map.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
*
* @date creation: Fri Sep 03 2010
* @date last modification: Thu Oct 15 2015
*
* @brief test of the fem class
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
* Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
* Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "fe_engine.hh"
-#include "shape_lagrange.hh"
#include "integrator_gauss.hh"
+#include "shape_lagrange.hh"
/* -------------------------------------------------------------------------- */
#include <cstdlib>
#include <iostream>
/* -------------------------------------------------------------------------- */
using namespace akantu;
-int main(int argc, char *argv[]) {
+int main(int argc, char * argv[]) {
akantu::initialize(argc, argv);
debug::setDebugLevel(dblTest);
const ElementType type = TYPE;
UInt dim = ElementClass<type>::getSpatialDimension();
Mesh my_mesh(dim);
- my_mesh.computeBoundingBox();
const Vector<Real> & lower = my_mesh.getLowerBounds();
const Vector<Real> & upper = my_mesh.getUpperBounds();
- std::stringstream meshfilename; meshfilename << type << ".msh";
+ std::stringstream meshfilename;
+ meshfilename << type << ".msh";
my_mesh.read(meshfilename.str());
UInt nb_elements = my_mesh.getNbElement(type);
///
- FEEngineTemplate<IntegratorGauss,ShapeLagrange> *fem =
- new FEEngineTemplate<IntegratorGauss,ShapeLagrange>(my_mesh, dim, "my_fem");
+ FEEngineTemplate<IntegratorGauss, ShapeLagrange> * fem =
+ new FEEngineTemplate<IntegratorGauss, ShapeLagrange>(my_mesh, dim,
+ "my_fem");
fem->initShapeFunctions();
UInt nb_quad_points = fem->getNbIntegrationPoints(type);
/// get the quadrature points coordinates
- Array<Real> coord_on_quad(nb_quad_points*nb_elements,
- my_mesh.getSpatialDimension(),
- "coord_on_quad");
-
- fem->interpolateOnIntegrationPoints(my_mesh.getNodes(),
- coord_on_quad,
- my_mesh.getSpatialDimension(),
- type);
+ Array<Real> coord_on_quad(nb_quad_points * nb_elements,
+ my_mesh.getSpatialDimension(), "coord_on_quad");
+ fem->interpolateOnIntegrationPoints(my_mesh.getNodes(), coord_on_quad,
+ my_mesh.getSpatialDimension(), type);
/// loop over the quadrature points
- Array<Real>::iterator< Vector<Real> > it = coord_on_quad.begin(dim);
+ Array<Real>::iterator<Vector<Real>> it = coord_on_quad.begin(dim);
Vector<Real> natural_coords(dim);
Matrix<Real> quad = GaussIntegrationElement<type>::getQuadraturePoints();
- for(UInt el = 0 ; el < nb_elements ; ++el){
- for(UInt q = 0 ; q < nb_quad_points ; ++q){
+ for (UInt el = 0; el < nb_elements; ++el) {
+ for (UInt q = 0; q < nb_quad_points; ++q) {
fem->inverseMap(*it, el, type, natural_coords);
for (UInt i = 0; i < dim; ++i) {
- __attribute__ ((unused)) const Real eps = 1e-13;
- AKANTU_DEBUG_ASSERT(std::abs((natural_coords(i) - quad(i,q))/(upper(i)-lower(i))) < eps,
- "real coordinates inversion test failed:"
- << natural_coords(i) << " - " << quad(i, q)
- << " = " << (natural_coords(i) - quad(i, q))/(upper(i)-lower(i)));
+ __attribute__((unused)) const Real eps = 1e-13;
+ AKANTU_DEBUG_ASSERT(
+ std::abs((natural_coords(i) - quad(i, q)) / (upper(i) - lower(i))) <
+ eps,
+ "real coordinates inversion test failed:"
+ << natural_coords(i) << " - " << quad(i, q) << " = "
+ << (natural_coords(i) - quad(i, q)) / (upper(i) - lower(i)));
}
++it;
}
}
- std::cout << "inverse completed over " << nb_elements << " elements" << std::endl;
+ std::cout << "inverse completed over " << nb_elements << " elements"
+ << std::endl;
delete fem;
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_mesh_utils/CMakeLists.txt b/test/test_mesh_utils/CMakeLists.txt
index 70f83bed2..f96c07092 100644
--- a/test/test_mesh_utils/CMakeLists.txt
+++ b/test/test_mesh_utils/CMakeLists.txt
@@ -1,50 +1,55 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Fri Oct 22 2010
# @date last modification: Fri Sep 18 2015
#
# @brief configuration for MeshUtils tests
#
# @section LICENSE
#
# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
# Solides)
#
# Akantu is free software: you can redistribute it and/or modify it under the
# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
#
# Akantu 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 Lesser General Public License for more
# details.
#
# You should have received a copy of the GNU Lesser General Public License
# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
#===============================================================================
# List of tests
#===============================================================================
add_akantu_test(test_mesh_io "Test mesh io object")
add_akantu_test(test_pbc_tweak "Test pbc facilities")
add_akantu_test(test_buildfacets "Tests for the generation of facets")
add_akantu_test(test_segment_nodetype "segment_nodetype")
register_test(test_purify_mesh
SOURCES test_purify_mesh.cc
FILES_TO_COPY purify_mesh.msh
PACKAGE core
)
-add_akantu_test(test_mesh_partitionate "Test mesh partition creation")
-
+add_mesh(test_mesh_iterators_mesh iterators_mesh.geo 3 1 OUTPUT iterators_mesh.msh)
+register_test(test_mesh_iterators
+ SOURCES test_mesh_iterators.cc
+ PACKAGE core
+ DEPENDS test_mesh_iterators_mesh
+ )
+add_akantu_test(test_mesh_partitionate "Test mesh partition creation")
diff --git a/test/test_mesh_utils/test_buildfacets/test_buildfacets_hexahedron_20.cc b/test/test_mesh_utils/test_buildfacets/test_buildfacets_hexahedron_20.cc
index 9f814dc7b..2934e326c 100644
--- a/test/test_mesh_utils/test_buildfacets/test_buildfacets_hexahedron_20.cc
+++ b/test/test_mesh_utils/test_buildfacets/test_buildfacets_hexahedron_20.cc
@@ -1,143 +1,143 @@
/**
* @file test_buildfacets_hexahedron_20.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue May 08 2012
* @date last modification: Sat Sep 19 2015
*
* @brief Test to check the building of the facets. Mesh with hexahedrons
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
* Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
* Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <iostream>
#include <limits>
#include <fstream>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char *argv[]) {
initialize(argc, argv);
const UInt spatial_dimension = 3;
const ElementType type = _hexahedron_20;
Mesh mesh(spatial_dimension);
mesh.read("hexahedron_20.msh");
- Mesh mesh_facets(mesh.initMeshFacets("mesh_facets"));
+ Mesh & mesh_facets = mesh.initMeshFacets("mesh_facets");
MeshUtils::buildAllFacets(mesh, mesh_facets);
// debug::setDebugLevel(dblDump);
// std::cout << mesh << std::endl;
// std::cout << mesh_facets << std::endl;
const ElementType type_facet = mesh.getFacetType(type);
const ElementType type_subfacet = mesh.getFacetType(type_facet);
const ElementType type_subsubfacet = mesh.getFacetType(type_subfacet);
/* ------------------------------------------------------------------------ */
/* Element to Subelement testing */
/* ------------------------------------------------------------------------ */
const Array< std::vector<Element> > & el_to_subel3 = mesh_facets.getElementToSubelement(type_facet);
const Array< std::vector<Element> > & el_to_subel2 = mesh_facets.getElementToSubelement(type_subfacet);
const Array< std::vector<Element> > & el_to_subel1 = mesh_facets.getElementToSubelement(type_subsubfacet);
std::cout << "ElementToSubelement3" << std::endl;
for (UInt i = 0; i < el_to_subel3.getSize(); ++i) {
std::cout << type_facet << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j){
std::cout << el_to_subel3(i)[j].type << " " << el_to_subel3(i)[j].element << ", ";
}
std::cout << " " << std::endl;
}
std::cout << "ElementToSubelement2" << std::endl;
for (UInt i = 0; i < el_to_subel2.getSize(); ++i) {
std::cout << type_subfacet << " " << i << " connected to ";
for (UInt j = 0; j < el_to_subel2(i).size(); ++j){
std::cout << el_to_subel2(i)[j].type << " " << el_to_subel2(i)[j].element << ", ";
}
std::cout << " " << std::endl;
}
std::cout << "ElementToSubelement1" << std::endl;
for (UInt i = 0; i < el_to_subel1.getSize(); ++i) {
std::cout << type_subsubfacet << " " << i << " connected to ";
for (UInt j = 0; j < el_to_subel1(i).size(); ++j){
std::cout << el_to_subel1(i)[j].type << " " << el_to_subel1(i)[j].element << ", ";
}
std::cout << " " << std::endl;
}
/* ------------------------------------------------------------------------ */
/* Subelement to Element testing */
/* ------------------------------------------------------------------------ */
const Array<Element> & subel_to_el3 = mesh_facets.getSubelementToElement(type);
const Array<Element> & subel_to_el2 = mesh_facets.getSubelementToElement(type_facet);
const Array<Element> & subel_to_el1 = mesh_facets.getSubelementToElement(type_subfacet);
std::cout << " " << std::endl;
std::cout << "SubelementToElement3" << std::endl;
for (UInt i = 0; i < subel_to_el3.getSize(); ++i) {
std::cout << type << " " << i << " connected to ";
for (UInt j = 0; j < 6; ++j){
std::cout << subel_to_el3(i, j).type << " " << subel_to_el3(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
std::cout << "SubelementToElement2" << std::endl;
for (UInt i = 0; i < subel_to_el2.getSize(); ++i) {
std::cout << type_facet << " " << i << " connected to ";
for (UInt j = 0; j < 4; ++j){
std::cout << subel_to_el2(i, j).type << " " << subel_to_el2(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
std::cout << "SubelementToElement1" << std::endl;
for (UInt i = 0; i < subel_to_el1.getSize(); ++i) {
std::cout << type_subfacet << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j){
std::cout << subel_to_el1(i, j).type << " " << subel_to_el1(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_mesh_utils/test_buildfacets/test_buildfacets_hexahedron_8.cc b/test/test_mesh_utils/test_buildfacets/test_buildfacets_hexahedron_8.cc
index 1ea23ee9c..21f6a9261 100644
--- a/test/test_mesh_utils/test_buildfacets/test_buildfacets_hexahedron_8.cc
+++ b/test/test_mesh_utils/test_buildfacets/test_buildfacets_hexahedron_8.cc
@@ -1,144 +1,144 @@
/**
* @file test_buildfacets_hexahedron_8.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue May 08 2012
* @date last modification: Sat Sep 19 2015
*
* @brief Test to check the building of the facets. Mesh with hexahedrons
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
* Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
* Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <iostream>
#include <limits>
#include <fstream>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char *argv[]) {
initialize(argc, argv);
const UInt spatial_dimension = 3;
const ElementType type = _hexahedron_8;
Mesh mesh(spatial_dimension);
mesh.read("hexahedron_8.msh");
- Mesh mesh_facets(mesh.initMeshFacets("mesh_facets"));
+ Mesh & mesh_facets = mesh.initMeshFacets("mesh_facets");
MeshUtils::buildAllFacets(mesh, mesh_facets);
// debug::setDebugLevel(dblDump);
// std::cout << mesh << std::endl;
// std::cout << mesh_facets << std::endl;
const ElementType type_facet = mesh.getFacetType(type);
const ElementType type_subfacet = mesh.getFacetType(type_facet);
const ElementType type_subsubfacet = mesh.getFacetType(type_subfacet);
/* ------------------------------------------------------------------------ */
/* Element to Subelement testing */
/* ------------------------------------------------------------------------ */
const Array< std::vector<Element> > & el_to_subel3 = mesh_facets.getElementToSubelement(type_facet);
const Array< std::vector<Element> > & el_to_subel2 = mesh_facets.getElementToSubelement(type_subfacet);
const Array< std::vector<Element> > & el_to_subel1 = mesh_facets.getElementToSubelement(type_subsubfacet);
std::cout << "ElementToSubelement3" << std::endl;
for (UInt i = 0; i < el_to_subel3.getSize(); ++i) {
std::cout << type_facet << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j){
std::cout << el_to_subel3(i)[j].type << " " << el_to_subel3(i)[j].element << ", ";
}
std::cout << " " << std::endl;
}
std::cout << "ElementToSubelement2" << std::endl;
for (UInt i = 0; i < el_to_subel2.getSize(); ++i) {
std::cout << type_subfacet << " " << i << " connected to ";
for (UInt j = 0; j < el_to_subel2(i).size(); ++j){
std::cout << el_to_subel2(i)[j].type << " " << el_to_subel2(i)[j].element << ", ";
}
std::cout << " " << std::endl;
}
std::cout << "ElementToSubelement1" << std::endl;
for (UInt i = 0; i < el_to_subel1.getSize(); ++i) {
std::cout << type_subsubfacet << " " << i << " connected to ";
for (UInt j = 0; j < el_to_subel1(i).size(); ++j){
std::cout << el_to_subel1(i)[j].type << " " << el_to_subel1(i)[j].element << ", ";
}
std::cout << " " << std::endl;
}
/* ------------------------------------------------------------------------ */
/* Subelement to Element testing */
/* ------------------------------------------------------------------------ */
const Array<Element> & subel_to_el3 = mesh_facets.getSubelementToElement(type);
const Array<Element> & subel_to_el2 = mesh_facets.getSubelementToElement(type_facet);
const Array<Element> & subel_to_el1 = mesh_facets.getSubelementToElement(type_subfacet);
std::cout << " " << std::endl;
std::cout << "SubelementToElement3" << std::endl;
for (UInt i = 0; i < subel_to_el3.getSize(); ++i) {
std::cout << type << " " << i << " connected to ";
for (UInt j = 0; j < 6; ++j){
std::cout << subel_to_el3(i, j).type << " " << subel_to_el3(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
std::cout << "SubelementToElement2" << std::endl;
for (UInt i = 0; i < subel_to_el2.getSize(); ++i) {
std::cout << type_facet << " " << i << " connected to ";
for (UInt j = 0; j < 4; ++j){
std::cout << subel_to_el2(i, j).type << " " << subel_to_el2(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
std::cout << "SubelementToElement1" << std::endl;
for (UInt i = 0; i < subel_to_el1.getSize(); ++i) {
std::cout << type_subfacet << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j){
std::cout << subel_to_el1(i, j).type << " " << subel_to_el1(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_mesh_utils/test_buildfacets/test_buildfacets_mixed2d_linear.cc b/test/test_mesh_utils/test_buildfacets/test_buildfacets_mixed2d_linear.cc
index 05aa17362..e9d6975a8 100644
--- a/test/test_mesh_utils/test_buildfacets/test_buildfacets_mixed2d_linear.cc
+++ b/test/test_mesh_utils/test_buildfacets/test_buildfacets_mixed2d_linear.cc
@@ -1,128 +1,128 @@
/**
* @file test_buildfacets_mixed2d_linear.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
*
* @date creation: Fri Sep 18 2015
* @date last modification: Sat Sep 19 2015
*
* @brief Test to check the building of the facets. Mesh with quadrangles
* and triangles
*
* @section LICENSE
*
* Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
* (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <iostream>
#include <limits>
#include <fstream>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char *argv[]) {
initialize(argc, argv);
const UInt spatial_dimension = 2;
const ElementType type1 = _quadrangle_4;
const ElementType type2 = _triangle_3;
Mesh mesh(spatial_dimension);
mesh.read("mixed2d_linear.msh");
- Mesh mesh_facets(mesh.initMeshFacets("mesh_facets"));
+ Mesh & mesh_facets = mesh.initMeshFacets("mesh_facets");
MeshUtils::buildAllFacets(mesh, mesh_facets);
const ElementType type_facet = mesh.getFacetType(type1);
const ElementType type_subfacet = mesh.getFacetType(type_facet);
/* ------------------------------------------------------------------------ */
/* Element to Subelement testing */
/* ------------------------------------------------------------------------ */
const Array< std::vector<Element> > & el_to_subel2 = mesh_facets.getElementToSubelement(type_facet);
const Array< std::vector<Element> > & el_to_subel1 = mesh_facets.getElementToSubelement(type_subfacet);
std::cout << "ElementToSubelement2" << std::endl;
for (UInt i = 0; i < el_to_subel2.getSize(); ++i) {
std::cout << type_facet << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j){
std::cout << el_to_subel2(i)[j].type << " " << el_to_subel2(i)[j].element << ", ";
}
std::cout << " " << std::endl;
}
std::cout << "ElementToSubelement1" << std::endl;
for (UInt i = 0; i < el_to_subel1.getSize(); ++i) {
std::cout << type_subfacet << " " << i << " connected to ";
for (UInt j = 0; j < el_to_subel1(i).size(); ++j){
std::cout << el_to_subel1(i)[j].type << " " << el_to_subel1(i)[j].element << ", ";
}
std::cout << " " << std::endl;
}
/* ------------------------------------------------------------------------ */
/* Subelement to Element testing */
/* ------------------------------------------------------------------------ */
const Array<Element> & subel_to_el2_1 = mesh_facets.getSubelementToElement(type1);
const Array<Element> & subel_to_el2_2 = mesh_facets.getSubelementToElement(type2);
const Array<Element> & subel_to_el1 = mesh_facets.getSubelementToElement(type_facet);
std::cout << " " << std::endl;
std::cout << "SubelementToElement2" << std::endl;
for (UInt i = 0; i < subel_to_el2_1.getSize(); ++i) {
std::cout << type1 << " " << i << " connected to ";
for (UInt j = 0; j < 4; ++j){
std::cout << subel_to_el2_1(i, j).type << " " << subel_to_el2_1(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
for (UInt i = 0; i < subel_to_el2_2.getSize(); ++i) {
std::cout << type2 << " " << i << " connected to ";
for (UInt j = 0; j < 3; ++j){
std::cout << subel_to_el2_2(i, j).type << " " << subel_to_el2_2(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
std::cout << "SubelementToElement1" << std::endl;
for (UInt i = 0; i < subel_to_el1.getSize(); ++i) {
std::cout << type_facet << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j){
std::cout << subel_to_el1(i, j).type << " " << subel_to_el1(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_mesh_utils/test_buildfacets/test_buildfacets_mixed2d_quadratic.cc b/test/test_mesh_utils/test_buildfacets/test_buildfacets_mixed2d_quadratic.cc
index 96bbd9bda..e13f63e65 100644
--- a/test/test_mesh_utils/test_buildfacets/test_buildfacets_mixed2d_quadratic.cc
+++ b/test/test_mesh_utils/test_buildfacets/test_buildfacets_mixed2d_quadratic.cc
@@ -1,128 +1,128 @@
/**
* @file test_buildfacets_mixed2d_quadratic.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
*
* @date creation: Fri Sep 18 2015
* @date last modification: Sat Sep 19 2015
*
* @brief Test to check the building of the facets. Mesh with quadrangles
* and triangles
*
* @section LICENSE
*
* Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
* (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <iostream>
#include <limits>
#include <fstream>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char *argv[]) {
initialize(argc, argv);
const UInt spatial_dimension = 2;
const ElementType type1 = _quadrangle_8;
const ElementType type2 = _triangle_6;
Mesh mesh(spatial_dimension);
mesh.read("mixed2d_quadratic.msh");
- Mesh mesh_facets(mesh.initMeshFacets("mesh_facets"));
+ Mesh & mesh_facets = mesh.initMeshFacets("mesh_facets");
MeshUtils::buildAllFacets(mesh, mesh_facets);
const ElementType type_facet = mesh.getFacetType(type1);
const ElementType type_subfacet = mesh.getFacetType(type_facet);
/* ------------------------------------------------------------------------ */
/* Element to Subelement testing */
/* ------------------------------------------------------------------------ */
const Array< std::vector<Element> > & el_to_subel2 = mesh_facets.getElementToSubelement(type_facet);
const Array< std::vector<Element> > & el_to_subel1 = mesh_facets.getElementToSubelement(type_subfacet);
std::cout << "ElementToSubelement2" << std::endl;
for (UInt i = 0; i < el_to_subel2.getSize(); ++i) {
std::cout << type_facet << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j){
std::cout << el_to_subel2(i)[j].type << " " << el_to_subel2(i)[j].element << ", ";
}
std::cout << " " << std::endl;
}
std::cout << "ElementToSubelement1" << std::endl;
for (UInt i = 0; i < el_to_subel1.getSize(); ++i) {
std::cout << type_subfacet << " " << i << " connected to ";
for (UInt j = 0; j < el_to_subel1(i).size(); ++j){
std::cout << el_to_subel1(i)[j].type << " " << el_to_subel1(i)[j].element << ", ";
}
std::cout << " " << std::endl;
}
/* ------------------------------------------------------------------------ */
/* Subelement to Element testing */
/* ------------------------------------------------------------------------ */
const Array<Element> & subel_to_el2_1 = mesh_facets.getSubelementToElement(type1);
const Array<Element> & subel_to_el2_2 = mesh_facets.getSubelementToElement(type2);
const Array<Element> & subel_to_el1 = mesh_facets.getSubelementToElement(type_facet);
std::cout << " " << std::endl;
std::cout << "SubelementToElement2" << std::endl;
for (UInt i = 0; i < subel_to_el2_1.getSize(); ++i) {
std::cout << type1 << " " << i << " connected to ";
for (UInt j = 0; j < 4; ++j){
std::cout << subel_to_el2_1(i, j).type << " " << subel_to_el2_1(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
for (UInt i = 0; i < subel_to_el2_2.getSize(); ++i) {
std::cout << type2 << " " << i << " connected to ";
for (UInt j = 0; j < 3; ++j){
std::cout << subel_to_el2_2(i, j).type << " " << subel_to_el2_2(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
std::cout << "SubelementToElement1" << std::endl;
for (UInt i = 0; i < subel_to_el1.getSize(); ++i) {
std::cout << type_facet << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j){
std::cout << subel_to_el1(i, j).type << " " << subel_to_el1(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_mesh_utils/test_buildfacets/test_buildfacets_mixed3d_linear.cc b/test/test_mesh_utils/test_buildfacets/test_buildfacets_mixed3d_linear.cc
index 13fd0dd0e..452d24767 100644
--- a/test/test_mesh_utils/test_buildfacets/test_buildfacets_mixed3d_linear.cc
+++ b/test/test_mesh_utils/test_buildfacets/test_buildfacets_mixed3d_linear.cc
@@ -1,167 +1,167 @@
/**
* @file test_buildfacets_mixed3d_linear.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
*
* @date creation: Tue May 08 2012
* @date last modification: Sat Sep 19 2015
*
* @brief Test to check the building of the facets. Mesh with hexahedrons
* and pentahedrons
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
* Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
* Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <iostream>
#include <limits>
#include <fstream>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char *argv[]) {
initialize(argc, argv);
const UInt spatial_dimension = 3;
const ElementType type1 = _hexahedron_8;
const ElementType type2 = _pentahedron_6;
Mesh mesh(spatial_dimension);
mesh.read("mixed3d_linear.msh");
- Mesh mesh_facets(mesh.initMeshFacets("mesh_facets"));
+ Mesh & mesh_facets = mesh.initMeshFacets("mesh_facets");
MeshUtils::buildAllFacets(mesh, mesh_facets);
const ElementType type_facet1 = mesh.getFacetType(type1);
const ElementType type_facet2 = mesh.getFacetType(type2);
const ElementType type_subfacet = mesh.getFacetType(type_facet1);
const ElementType type_subsubfacet = mesh.getFacetType(type_subfacet);
/* ------------------------------------------------------------------------ */
/* Element to Subelement testing */
/* ------------------------------------------------------------------------ */
const Array< std::vector<Element> > & el_to_subel3_1 = mesh_facets.getElementToSubelement(type_facet1);
const Array< std::vector<Element> > & el_to_subel3_2 = mesh_facets.getElementToSubelement(type_facet2);
const Array< std::vector<Element> > & el_to_subel2 = mesh_facets.getElementToSubelement(type_subfacet);
const Array< std::vector<Element> > & el_to_subel1 = mesh_facets.getElementToSubelement(type_subsubfacet);
std::cout << "ElementToSubelement3" << std::endl;
for (UInt i = 0; i < el_to_subel3_1.getSize(); ++i) {
std::cout << type_facet1 << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j){
std::cout << el_to_subel3_1(i)[j].type << " " << el_to_subel3_1(i)[j].element << ", ";
}
std::cout << " " << std::endl;
}
for (UInt i = 0; i < el_to_subel3_2.getSize(); ++i) {
std::cout << type_facet2 << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j){
std::cout << el_to_subel3_2(i)[j].type << " " << el_to_subel3_2(i)[j].element << ", ";
}
std::cout << " " << std::endl;
}
std::cout << "ElementToSubelement2" << std::endl;
for (UInt i = 0; i < el_to_subel2.getSize(); ++i) {
std::cout << type_subfacet << " " << i << " connected to ";
for (UInt j = 0; j < el_to_subel2(i).size(); ++j){
std::cout << el_to_subel2(i)[j].type << " " << el_to_subel2(i)[j].element << ", ";
}
std::cout << " " << std::endl;
}
std::cout << "ElementToSubelement1" << std::endl;
for (UInt i = 0; i < el_to_subel1.getSize(); ++i) {
std::cout << type_subsubfacet << " " << i << " connected to ";
for (UInt j = 0; j < el_to_subel1(i).size(); ++j){
std::cout << el_to_subel1(i)[j].type << " " << el_to_subel1(i)[j].element << ", ";
}
std::cout << " " << std::endl;
}
/* ------------------------------------------------------------------------ */
/* Subelement to Element testing */
/* ------------------------------------------------------------------------ */
const Array<Element> & subel_to_el3_1 = mesh_facets.getSubelementToElement(type1);
const Array<Element> & subel_to_el3_2 = mesh_facets.getSubelementToElement(type2);
const Array<Element> & subel_to_el2_1 = mesh_facets.getSubelementToElement(type_facet1);
const Array<Element> & subel_to_el2_2 = mesh_facets.getSubelementToElement(type_facet2);
const Array<Element> & subel_to_el1 = mesh_facets.getSubelementToElement(type_subfacet);
std::cout << " " << std::endl;
std::cout << "SubelementToElement3" << std::endl;
for (UInt i = 0; i < subel_to_el3_1.getSize(); ++i) {
std::cout << type1 << " " << i << " connected to ";
for (UInt j = 0; j < 6; ++j){
std::cout << subel_to_el3_1(i, j).type << " " << subel_to_el3_1(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
for (UInt i = 0; i < subel_to_el3_2.getSize(); ++i) {
std::cout << type2 << " " << i << " connected to ";
for (UInt j = 0; j < 5; ++j){
std::cout << subel_to_el3_2(i, j).type << " " << subel_to_el3_2(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
std::cout << "SubelementToElement2" << std::endl;
for (UInt i = 0; i < subel_to_el2_1.getSize(); ++i) {
std::cout << type_facet1 << " " << i << " connected to ";
for (UInt j = 0; j < 4; ++j){
std::cout << subel_to_el2_1(i, j).type << " " << subel_to_el2_1(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
for (UInt i = 0; i < subel_to_el2_2.getSize(); ++i) {
std::cout << type_facet2 << " " << i << " connected to ";
for (UInt j = 0; j < 3; ++j){
std::cout << subel_to_el2_2(i, j).type << " " << subel_to_el2_2(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
std::cout << "SubelementToElement1" << std::endl;
for (UInt i = 0; i < subel_to_el1.getSize(); ++i) {
std::cout << type_subfacet << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j){
std::cout << subel_to_el1(i, j).type << " " << subel_to_el1(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_mesh_utils/test_buildfacets/test_buildfacets_mixed3d_quadratic.cc b/test/test_mesh_utils/test_buildfacets/test_buildfacets_mixed3d_quadratic.cc
index 4ebdd56d5..ab397a3d0 100644
--- a/test/test_mesh_utils/test_buildfacets/test_buildfacets_mixed3d_quadratic.cc
+++ b/test/test_mesh_utils/test_buildfacets/test_buildfacets_mixed3d_quadratic.cc
@@ -1,169 +1,169 @@
/**
* @file test_buildfacets_mixed3d_quadratic.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
*
* @date creation: Tue May 08 2012
* @date last modification: Sat Sep 19 2015
*
* @brief Test to check the building of the facets. Mesh with hexahedrons
* and pentahedrons
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
* Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
* Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <iostream>
#include <limits>
#include <fstream>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char *argv[]) {
initialize(argc, argv);
const UInt spatial_dimension = 3;
const ElementType type1 = _hexahedron_20;
const ElementType type2 = _pentahedron_15;
Mesh mesh(spatial_dimension);
mesh.read("mixed3d_quadratic.msh");
- Mesh mesh_facets(mesh.initMeshFacets("mesh_facets"));
+ Mesh & mesh_facets = mesh.initMeshFacets("mesh_facets");
MeshUtils::buildAllFacets(mesh, mesh_facets);
const ElementType type_facet1 = mesh.getFacetType(type1);
const ElementType type_facet2 = mesh.getFacetType(type2);
const ElementType type_subfacet = mesh.getFacetType(type_facet1);
const ElementType type_subsubfacet = mesh.getFacetType(type_subfacet);
/* ------------------------------------------------------------------------ */
/* Element to Subelement testing */
/* ------------------------------------------------------------------------ */
const Array< std::vector<Element> > & el_to_subel3_1 = mesh_facets.getElementToSubelement(type_facet1);
const Array< std::vector<Element> > & el_to_subel3_2 = mesh_facets.getElementToSubelement(type_facet2);
const Array< std::vector<Element> > & el_to_subel2 = mesh_facets.getElementToSubelement(type_subfacet);
const Array< std::vector<Element> > & el_to_subel1 = mesh_facets.getElementToSubelement(type_subsubfacet);
std::cout << "ElementToSubelement3" << std::endl;
for (UInt i = 0; i < el_to_subel3_1.getSize(); ++i) {
std::cout << type_facet1 << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j){
std::cout << el_to_subel3_1(i)[j].type << " " << el_to_subel3_1(i)[j].element << ", ";
}
std::cout << " " << std::endl;
}
for (UInt i = 0; i < el_to_subel3_2.getSize(); ++i) {
std::cout << type_facet2 << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j){
std::cout << el_to_subel3_2(i)[j].type << " " << el_to_subel3_2(i)[j].element << ", ";
}
std::cout << " " << std::endl;
}
std::cout << "ElementToSubelement2" << std::endl;
for (UInt i = 0; i < el_to_subel2.getSize(); ++i) {
std::cout << type_subfacet << " " << i << " connected to ";
for (UInt j = 0; j < el_to_subel2(i).size(); ++j){
std::cout << el_to_subel2(i)[j].type << " " << el_to_subel2(i)[j].element << ", ";
}
std::cout << " " << std::endl;
}
std::cout << "ElementToSubelement1" << std::endl;
for (UInt i = 0; i < el_to_subel1.getSize(); ++i) {
std::cout << type_subsubfacet << " " << i << " connected to ";
for (UInt j = 0; j < el_to_subel1(i).size(); ++j){
std::cout << el_to_subel1(i)[j].type << " " << el_to_subel1(i)[j].element << ", ";
}
std::cout << " " << std::endl;
}
/* ------------------------------------------------------------------------ */
/* Subelement to Element testing */
/* ------------------------------------------------------------------------ */
const Array<Element> & subel_to_el3_1 = mesh_facets.getSubelementToElement(type1);
const Array<Element> & subel_to_el3_2 = mesh_facets.getSubelementToElement(type2);
const Array<Element> & subel_to_el2_1 = mesh_facets.getSubelementToElement(type_facet1);
const Array<Element> & subel_to_el2_2 = mesh_facets.getSubelementToElement(type_facet2);
const Array<Element> & subel_to_el1 = mesh_facets.getSubelementToElement(type_subfacet);
std::cout << " " << std::endl;
std::cout << "SubelementToElement3" << std::endl;
for (UInt i = 0; i < subel_to_el3_1.getSize(); ++i) {
std::cout << type1 << " " << i << " connected to ";
for (UInt j = 0; j < 6; ++j){
std::cout << subel_to_el3_1(i, j).type << " " << subel_to_el3_1(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
for (UInt i = 0; i < subel_to_el3_2.getSize(); ++i) {
std::cout << type2 << " " << i << " connected to ";
for (UInt j = 0; j < 5; ++j){
std::cout << subel_to_el3_2(i, j).type << " " << subel_to_el3_2(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
std::cout << "SubelementToElement2" << std::endl;
for (UInt i = 0; i < subel_to_el2_1.getSize(); ++i) {
std::cout << type_facet1 << " " << i << " connected to ";
for (UInt j = 0; j < 4; ++j){
std::cout << subel_to_el2_1(i, j).type << " " << subel_to_el2_1(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
std::cout << "SubelementToElement2" << std::endl;
for (UInt i = 0; i < subel_to_el2_2.getSize(); ++i) {
std::cout << type_facet2 << " " << i << " connected to ";
for (UInt j = 0; j < 3; ++j){
std::cout << subel_to_el2_2(i, j).type << " " << subel_to_el2_2(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
std::cout << "SubelementToElement1" << std::endl;
for (UInt i = 0; i < subel_to_el1.getSize(); ++i) {
std::cout << type_subfacet << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j){
std::cout << subel_to_el1(i, j).type << " " << subel_to_el1(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_mesh_utils/test_buildfacets/test_buildfacets_pentahedron_15.cc b/test/test_mesh_utils/test_buildfacets/test_buildfacets_pentahedron_15.cc
index 208ed4af1..1b63049d6 100644
--- a/test/test_mesh_utils/test_buildfacets/test_buildfacets_pentahedron_15.cc
+++ b/test/test_mesh_utils/test_buildfacets/test_buildfacets_pentahedron_15.cc
@@ -1,148 +1,148 @@
/**
* @file test_buildfacets_pentahedron_15.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
*
* @date creation: Tue May 08 2012
* @date last modification: Mon Sep 28 2015
*
* @brief Test for cohesive elements
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
* Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
* Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <iostream>
#include <limits>
#include <fstream>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char *argv[]) {
initialize(argc, argv);
const UInt spatial_dimension = 3;
const ElementType type = _pentahedron_15;
Mesh mesh(spatial_dimension);
mesh.read("pentahedron_15.msh");
- Mesh mesh_facets(mesh.initMeshFacets("mesh_facets"));
+ Mesh & mesh_facets = mesh.initMeshFacets("mesh_facets");
MeshUtils::buildAllFacets(mesh, mesh_facets);
Vector<ElementType> types_facet = mesh.getAllFacetTypes(type);
const ElementType type_subfacet = mesh.getFacetType(types_facet(0));
const ElementType type_subsubfacet = mesh.getFacetType(type_subfacet);
/* ------------------------------------------------------------------------ */
/* Element to Subelement testing */
/* ------------------------------------------------------------------------ */
for (UInt ft = 0; ft < types_facet.size(); ++ft) {
ElementType type_facet = types_facet(ft);
Array< std::vector<Element> > & el_to_subel3 = mesh_facets.getElementToSubelement(type_facet);
std::cout << "ElementToSubelement3" << std::endl;
for (UInt i = 0; i < el_to_subel3.getSize(); ++i) {
std::cout << type_facet << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j){
std::cout << el_to_subel3(i)[j].type << " " << el_to_subel3(i)[j].element << ", ";
}
std::cout << " " << std::endl;
}
}
const Array< std::vector<Element> > & el_to_subel2 = mesh_facets.getElementToSubelement(type_subfacet);
const Array< std::vector<Element> > & el_to_subel1 = mesh_facets.getElementToSubelement(type_subsubfacet);
std::cout << "ElementToSubelement2" << std::endl;
for (UInt i = 0; i < el_to_subel2.getSize(); ++i) {
std::cout << type_subfacet << " " << i << " connected to ";
for (UInt j = 0; j < el_to_subel2(i).size(); ++j){
std::cout << el_to_subel2(i)[j].type << " " << el_to_subel2(i)[j].element << ", ";
}
std::cout << " " << std::endl;
}
std::cout << "ElementToSubelement1" << std::endl;
for (UInt i = 0; i < el_to_subel1.getSize(); ++i) {
std::cout << type_subsubfacet << " " << i << " connected to ";
for (UInt j = 0; j < el_to_subel1(i).size(); ++j){
std::cout << el_to_subel1(i)[j].type << " " << el_to_subel1(i)[j].element << ", ";
}
std::cout << " " << std::endl;
}
/* ------------------------------------------------------------------------ */
/* Subelement to Element testing */
/* ------------------------------------------------------------------------ */
const Array<Element> & subel_to_el3 = mesh_facets.getSubelementToElement(type);
std::cout << " " << std::endl;
std::cout << "SubelementToElement3" << std::endl;
for (UInt i = 0; i < subel_to_el3.getSize(); ++i) {
std::cout << type << " " << i << " connected to ";
for (UInt j = 0; j < subel_to_el3.getNbComponent(); ++j){
std::cout << subel_to_el3(i, j).type << " " << subel_to_el3(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
for (UInt ft = 0; ft < types_facet.size(); ++ft) {
ElementType type_facet = types_facet(ft);
Array<Element> & subel_to_el2 = mesh_facets.getSubelementToElement(type_facet);
std::cout << "SubelementToElement2" << std::endl;
for (UInt i = 0; i < subel_to_el2.getSize(); ++i) {
std::cout << type_facet << " " << i << " connected to ";
for (UInt j = 0; j < subel_to_el2.getNbComponent(); ++j){
std::cout << subel_to_el2(i, j).type << " " << subel_to_el2(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
}
const Array<Element> & subel_to_el1 = mesh_facets.getSubelementToElement(type_subfacet);
std::cout << "SubelementToElement1" << std::endl;
for (UInt i = 0; i < subel_to_el1.getSize(); ++i) {
std::cout << type_subfacet << " " << i << " connected to ";
for (UInt j = 0; j < subel_to_el1.getNbComponent(); ++j){
std::cout << subel_to_el1(i, j).type << " " << subel_to_el1(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_mesh_utils/test_buildfacets/test_buildfacets_pentahedron_6.cc b/test/test_mesh_utils/test_buildfacets/test_buildfacets_pentahedron_6.cc
index b11759516..36b8b0033 100644
--- a/test/test_mesh_utils/test_buildfacets/test_buildfacets_pentahedron_6.cc
+++ b/test/test_mesh_utils/test_buildfacets/test_buildfacets_pentahedron_6.cc
@@ -1,148 +1,148 @@
/**
* @file test_buildfacets_pentahedron_6.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
*
* @date creation: Tue May 08 2012
* @date last modification: Mon Sep 28 2015
*
* @brief Test for cohesive elements
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
* Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
* Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <iostream>
#include <limits>
#include <fstream>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char *argv[]) {
initialize(argc, argv);
const UInt spatial_dimension = 3;
const ElementType type = _pentahedron_6;
Mesh mesh(spatial_dimension);
mesh.read("pentahedron_6.msh");
- Mesh mesh_facets(mesh.initMeshFacets("mesh_facets"));
+ Mesh & mesh_facets = mesh.initMeshFacets("mesh_facets");
MeshUtils::buildAllFacets(mesh, mesh_facets);
Vector<ElementType> types_facet = mesh.getAllFacetTypes(type);
const ElementType type_subfacet = mesh.getFacetType(types_facet(0));
const ElementType type_subsubfacet = mesh.getFacetType(type_subfacet);
/* ------------------------------------------------------------------------ */
/* Element to Subelement testing */
/* ------------------------------------------------------------------------ */
for (UInt ft = 0; ft < types_facet.size(); ++ft) {
ElementType type_facet = types_facet(ft);
Array< std::vector<Element> > & el_to_subel3 = mesh_facets.getElementToSubelement(type_facet);
std::cout << "ElementToSubelement3" << std::endl;
for (UInt i = 0; i < el_to_subel3.getSize(); ++i) {
std::cout << type_facet << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j){
std::cout << el_to_subel3(i)[j].type << " " << el_to_subel3(i)[j].element << ", ";
}
std::cout << " " << std::endl;
}
}
const Array< std::vector<Element> > & el_to_subel2 = mesh_facets.getElementToSubelement(type_subfacet);
const Array< std::vector<Element> > & el_to_subel1 = mesh_facets.getElementToSubelement(type_subsubfacet);
std::cout << "ElementToSubelement2" << std::endl;
for (UInt i = 0; i < el_to_subel2.getSize(); ++i) {
std::cout << type_subfacet << " " << i << " connected to ";
for (UInt j = 0; j < el_to_subel2(i).size(); ++j){
std::cout << el_to_subel2(i)[j].type << " " << el_to_subel2(i)[j].element << ", ";
}
std::cout << " " << std::endl;
}
std::cout << "ElementToSubelement1" << std::endl;
for (UInt i = 0; i < el_to_subel1.getSize(); ++i) {
std::cout << type_subsubfacet << " " << i << " connected to ";
for (UInt j = 0; j < el_to_subel1(i).size(); ++j){
std::cout << el_to_subel1(i)[j].type << " " << el_to_subel1(i)[j].element << ", ";
}
std::cout << " " << std::endl;
}
/* ------------------------------------------------------------------------ */
/* Subelement to Element testing */
/* ------------------------------------------------------------------------ */
const Array<Element> & subel_to_el3 = mesh_facets.getSubelementToElement(type);
std::cout << " " << std::endl;
std::cout << "SubelementToElement3" << std::endl;
for (UInt i = 0; i < subel_to_el3.getSize(); ++i) {
std::cout << type << " " << i << " connected to ";
for (UInt j = 0; j < subel_to_el3.getNbComponent(); ++j){
std::cout << subel_to_el3(i, j).type << " " << subel_to_el3(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
for (UInt ft = 0; ft < types_facet.size(); ++ft) {
ElementType type_facet = types_facet(ft);
Array<Element> & subel_to_el2 = mesh_facets.getSubelementToElement(type_facet);
std::cout << "SubelementToElement2" << std::endl;
for (UInt i = 0; i < subel_to_el2.getSize(); ++i) {
std::cout << type_facet << " " << i << " connected to ";
for (UInt j = 0; j < subel_to_el2.getNbComponent(); ++j){
std::cout << subel_to_el2(i, j).type << " " << subel_to_el2(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
}
const Array<Element> & subel_to_el1 = mesh_facets.getSubelementToElement(type_subfacet);
std::cout << "SubelementToElement1" << std::endl;
for (UInt i = 0; i < subel_to_el1.getSize(); ++i) {
std::cout << type_subfacet << " " << i << " connected to ";
for (UInt j = 0; j < subel_to_el1.getNbComponent(); ++j){
std::cout << subel_to_el1(i, j).type << " " << subel_to_el1(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_mesh_utils/test_buildfacets/test_buildfacets_quadrangle_4.cc b/test/test_mesh_utils/test_buildfacets/test_buildfacets_quadrangle_4.cc
index 52d73dd7b..c8c002fe8 100644
--- a/test/test_mesh_utils/test_buildfacets/test_buildfacets_quadrangle_4.cc
+++ b/test/test_mesh_utils/test_buildfacets/test_buildfacets_quadrangle_4.cc
@@ -1,116 +1,116 @@
/**
* @file test_buildfacets_quadrangle_4.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
*
* @date creation: Fri Sep 18 2015
* @date last modification: Sat Sep 19 2015
*
* @brief Test to check the building of the facets. Mesh with quadrangles
*
* @section LICENSE
*
* Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
* (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <iostream>
#include <limits>
#include <fstream>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char *argv[]) {
initialize(argc, argv);
const UInt spatial_dimension = 2;
const ElementType type = _quadrangle_4;
Mesh mesh(spatial_dimension);
mesh.read("quadrangle_4.msh");
- Mesh mesh_facets(mesh.initMeshFacets("mesh_facets"));
+ Mesh & mesh_facets = mesh.initMeshFacets("mesh_facets");
MeshUtils::buildAllFacets(mesh, mesh_facets);
const ElementType type_facet = mesh.getFacetType(type);
const ElementType type_subfacet = mesh.getFacetType(type_facet);
/* ------------------------------------------------------------------------ */
/* Element to Subelement testing */
/* ------------------------------------------------------------------------ */
const Array< std::vector<Element> > & el_to_subel2 = mesh_facets.getElementToSubelement(type_facet);
const Array< std::vector<Element> > & el_to_subel1 = mesh_facets.getElementToSubelement(type_subfacet);
std::cout << "ElementToSubelement2" << std::endl;
for (UInt i = 0; i < el_to_subel2.getSize(); ++i) {
std::cout << type_facet << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j){
std::cout << el_to_subel2(i)[j].type << " " << el_to_subel2(i)[j].element << ", ";
}
std::cout << " " << std::endl;
}
std::cout << "ElementToSubelement1" << std::endl;
for (UInt i = 0; i < el_to_subel1.getSize(); ++i) {
std::cout << type_subfacet << " " << i << " connected to ";
for (UInt j = 0; j < el_to_subel1(i).size(); ++j){
std::cout << el_to_subel1(i)[j].type << " " << el_to_subel1(i)[j].element << ", ";
}
std::cout << " " << std::endl;
}
/* ------------------------------------------------------------------------ */
/* Subelement to Element testing */
/* ------------------------------------------------------------------------ */
const Array<Element> & subel_to_el2 = mesh_facets.getSubelementToElement(type);
const Array<Element> & subel_to_el1 = mesh_facets.getSubelementToElement(type_facet);
std::cout << " " << std::endl;
std::cout << "SubelementToElement2" << std::endl;
for (UInt i = 0; i < subel_to_el2.getSize(); ++i) {
std::cout << type << " " << i << " connected to ";
for (UInt j = 0; j < 4; ++j){
std::cout << subel_to_el2(i, j).type << " " << subel_to_el2(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
std::cout << "SubelementToElement1" << std::endl;
for (UInt i = 0; i < subel_to_el1.getSize(); ++i) {
std::cout << type_facet << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j){
std::cout << subel_to_el1(i, j).type << " " << subel_to_el1(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_mesh_utils/test_buildfacets/test_buildfacets_quadrangle_8.cc b/test/test_mesh_utils/test_buildfacets/test_buildfacets_quadrangle_8.cc
index 0072e9aa5..513ac474d 100644
--- a/test/test_mesh_utils/test_buildfacets/test_buildfacets_quadrangle_8.cc
+++ b/test/test_mesh_utils/test_buildfacets/test_buildfacets_quadrangle_8.cc
@@ -1,116 +1,116 @@
/**
* @file test_buildfacets_quadrangle_8.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
*
* @date creation: Fri Sep 18 2015
* @date last modification: Sat Sep 19 2015
*
* @brief Test to check the building of the facets. Mesh with quadrangles
*
* @section LICENSE
*
* Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
* (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <iostream>
#include <limits>
#include <fstream>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char *argv[]) {
initialize(argc, argv);
const UInt spatial_dimension = 2;
const ElementType type = _quadrangle_8;
Mesh mesh(spatial_dimension);
mesh.read("quadrangle_8.msh");
- Mesh mesh_facets(mesh.initMeshFacets("mesh_facets"));
+ Mesh & mesh_facets = mesh.initMeshFacets("mesh_facets");
MeshUtils::buildAllFacets(mesh, mesh_facets);
const ElementType type_facet = mesh.getFacetType(type);
const ElementType type_subfacet = mesh.getFacetType(type_facet);
/* ------------------------------------------------------------------------ */
/* Element to Subelement testing */
/* ------------------------------------------------------------------------ */
const Array< std::vector<Element> > & el_to_subel2 = mesh_facets.getElementToSubelement(type_facet);
const Array< std::vector<Element> > & el_to_subel1 = mesh_facets.getElementToSubelement(type_subfacet);
std::cout << "ElementToSubelement2" << std::endl;
for (UInt i = 0; i < el_to_subel2.getSize(); ++i) {
std::cout << type_facet << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j){
std::cout << el_to_subel2(i)[j].type << " " << el_to_subel2(i)[j].element << ", ";
}
std::cout << " " << std::endl;
}
std::cout << "ElementToSubelement1" << std::endl;
for (UInt i = 0; i < el_to_subel1.getSize(); ++i) {
std::cout << type_subfacet << " " << i << " connected to ";
for (UInt j = 0; j < el_to_subel1(i).size(); ++j){
std::cout << el_to_subel1(i)[j].type << " " << el_to_subel1(i)[j].element << ", ";
}
std::cout << " " << std::endl;
}
/* ------------------------------------------------------------------------ */
/* Subelement to Element testing */
/* ------------------------------------------------------------------------ */
const Array<Element> & subel_to_el2 = mesh_facets.getSubelementToElement(type);
const Array<Element> & subel_to_el1 = mesh_facets.getSubelementToElement(type_facet);
std::cout << " " << std::endl;
std::cout << "SubelementToElement2" << std::endl;
for (UInt i = 0; i < subel_to_el2.getSize(); ++i) {
std::cout << type << " " << i << " connected to ";
for (UInt j = 0; j < 4; ++j){
std::cout << subel_to_el2(i, j).type << " " << subel_to_el2(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
std::cout << "SubelementToElement1" << std::endl;
for (UInt i = 0; i < subel_to_el1.getSize(); ++i) {
std::cout << type_facet << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j){
std::cout << subel_to_el1(i, j).type << " " << subel_to_el1(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_mesh_utils/test_buildfacets/test_buildfacets_tetrahedron_10.cc b/test/test_mesh_utils/test_buildfacets/test_buildfacets_tetrahedron_10.cc
index 70495db8b..8b9767f68 100644
--- a/test/test_mesh_utils/test_buildfacets/test_buildfacets_tetrahedron_10.cc
+++ b/test/test_mesh_utils/test_buildfacets/test_buildfacets_tetrahedron_10.cc
@@ -1,143 +1,143 @@
/**
* @file test_buildfacets_tetrahedron_10.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue May 08 2012
* @date last modification: Sat Sep 19 2015
*
* @brief Test for cohesive elements
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
* Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
* Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <iostream>
#include <limits>
#include <fstream>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char *argv[]) {
initialize(argc, argv);
const UInt spatial_dimension = 3;
const ElementType type = _tetrahedron_10;
Mesh mesh(spatial_dimension);
mesh.read("tetrahedron_10.msh");
- Mesh mesh_facets(mesh.initMeshFacets("mesh_facets"));
+ Mesh & mesh_facets = mesh.initMeshFacets("mesh_facets");
MeshUtils::buildAllFacets(mesh, mesh_facets);
// debug::setDebugLevel(dblDump);
// std::cout << mesh << std::endl;
// std::cout << mesh_facets << std::endl;
const ElementType type_facet = mesh.getFacetType(type);
const ElementType type_subfacet = mesh.getFacetType(type_facet);
const ElementType type_subsubfacet = mesh.getFacetType(type_subfacet);
/* ------------------------------------------------------------------------ */
/* Element to Subelement testing */
/* ------------------------------------------------------------------------ */
const Array< std::vector<Element> > & el_to_subel3 = mesh_facets.getElementToSubelement(type_facet);
const Array< std::vector<Element> > & el_to_subel2 = mesh_facets.getElementToSubelement(type_subfacet);
const Array< std::vector<Element> > & el_to_subel1 = mesh_facets.getElementToSubelement(type_subsubfacet);
std::cout << "ElementToSubelement3" << std::endl;
for (UInt i = 0; i < el_to_subel3.getSize(); ++i) {
std::cout << type_facet << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j){
std::cout << el_to_subel3(i)[j].type << " " << el_to_subel3(i)[j].element << ", ";
}
std::cout << " " << std::endl;
}
std::cout << "ElementToSubelement2" << std::endl;
for (UInt i = 0; i < el_to_subel2.getSize(); ++i) {
std::cout << type_subfacet << " " << i << " connected to ";
for (UInt j = 0; j < el_to_subel2(i).size(); ++j){
std::cout << el_to_subel2(i)[j].type << " " << el_to_subel2(i)[j].element << ", ";
}
std::cout << " " << std::endl;
}
std::cout << "ElementToSubelement1" << std::endl;
for (UInt i = 0; i < el_to_subel1.getSize(); ++i) {
std::cout << type_subsubfacet << " " << i << " connected to ";
for (UInt j = 0; j < el_to_subel1(i).size(); ++j){
std::cout << el_to_subel1(i)[j].type << " " << el_to_subel1(i)[j].element << ", ";
}
std::cout << " " << std::endl;
}
/* ------------------------------------------------------------------------ */
/* Subelement to Element testing */
/* ------------------------------------------------------------------------ */
const Array<Element> & subel_to_el3 = mesh_facets.getSubelementToElement(type);
const Array<Element> & subel_to_el2 = mesh_facets.getSubelementToElement(type_facet);
const Array<Element> & subel_to_el1 = mesh_facets.getSubelementToElement(type_subfacet);
std::cout << " " << std::endl;
std::cout << "SubelementToElement3" << std::endl;
for (UInt i = 0; i < subel_to_el3.getSize(); ++i) {
std::cout << type << " " << i << " connected to ";
for (UInt j = 0; j < 4; ++j){
std::cout << subel_to_el3(i, j).type << " " << subel_to_el3(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
std::cout << "SubelementToElement2" << std::endl;
for (UInt i = 0; i < subel_to_el2.getSize(); ++i) {
std::cout << type_facet << " " << i << " connected to ";
for (UInt j = 0; j < 3; ++j){
std::cout << subel_to_el2(i, j).type << " " << subel_to_el2(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
std::cout << "SubelementToElement1" << std::endl;
for (UInt i = 0; i < subel_to_el1.getSize(); ++i) {
std::cout << type_subfacet << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j){
std::cout << subel_to_el1(i, j).type << " " << subel_to_el1(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_mesh_utils/test_buildfacets/test_buildfacets_triangle_3.cc b/test/test_mesh_utils/test_buildfacets/test_buildfacets_triangle_3.cc
index 383648403..604241e37 100644
--- a/test/test_mesh_utils/test_buildfacets/test_buildfacets_triangle_3.cc
+++ b/test/test_mesh_utils/test_buildfacets/test_buildfacets_triangle_3.cc
@@ -1,116 +1,116 @@
/**
* @file test_buildfacets_triangle_3.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
*
* @date creation: Fri Sep 18 2015
* @date last modification: Sat Sep 19 2015
*
* @brief Test to check the building of the facets. Mesh with triangles
*
* @section LICENSE
*
* Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
* (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <iostream>
#include <limits>
#include <fstream>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char *argv[]) {
initialize(argc, argv);
const UInt spatial_dimension = 2;
const ElementType type = _triangle_3;
Mesh mesh(spatial_dimension);
mesh.read("triangle_3.msh");
- Mesh mesh_facets(mesh.initMeshFacets("mesh_facets"));
+ Mesh & mesh_facets = mesh.initMeshFacets("mesh_facets");
MeshUtils::buildAllFacets(mesh, mesh_facets);
const ElementType type_facet = mesh.getFacetType(type);
const ElementType type_subfacet = mesh.getFacetType(type_facet);
/* ------------------------------------------------------------------------ */
/* Element to Subelement testing */
/* ------------------------------------------------------------------------ */
const Array< std::vector<Element> > & el_to_subel2 = mesh_facets.getElementToSubelement(type_facet);
const Array< std::vector<Element> > & el_to_subel1 = mesh_facets.getElementToSubelement(type_subfacet);
std::cout << "ElementToSubelement2" << std::endl;
for (UInt i = 0; i < el_to_subel2.getSize(); ++i) {
std::cout << type_facet << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j){
std::cout << el_to_subel2(i)[j].type << " " << el_to_subel2(i)[j].element << ", ";
}
std::cout << " " << std::endl;
}
std::cout << "ElementToSubelement1" << std::endl;
for (UInt i = 0; i < el_to_subel1.getSize(); ++i) {
std::cout << type_subfacet << " " << i << " connected to ";
for (UInt j = 0; j < el_to_subel1(i).size(); ++j){
std::cout << el_to_subel1(i)[j].type << " " << el_to_subel1(i)[j].element << ", ";
}
std::cout << " " << std::endl;
}
/* ------------------------------------------------------------------------ */
/* Subelement to Element testing */
/* ------------------------------------------------------------------------ */
const Array<Element> & subel_to_el2 = mesh_facets.getSubelementToElement(type);
const Array<Element> & subel_to_el1 = mesh_facets.getSubelementToElement(type_facet);
std::cout << " " << std::endl;
std::cout << "SubelementToElement2" << std::endl;
for (UInt i = 0; i < subel_to_el2.getSize(); ++i) {
std::cout << type << " " << i << " connected to ";
for (UInt j = 0; j < 3; ++j){
std::cout << subel_to_el2(i, j).type << " " << subel_to_el2(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
std::cout << "SubelementToElement1" << std::endl;
for (UInt i = 0; i < subel_to_el1.getSize(); ++i) {
std::cout << type_facet << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j){
std::cout << subel_to_el1(i, j).type << " " << subel_to_el1(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_mesh_utils/test_buildfacets/test_buildfacets_triangle_6.cc b/test/test_mesh_utils/test_buildfacets/test_buildfacets_triangle_6.cc
index 5e0a5f12d..b28d0c719 100644
--- a/test/test_mesh_utils/test_buildfacets/test_buildfacets_triangle_6.cc
+++ b/test/test_mesh_utils/test_buildfacets/test_buildfacets_triangle_6.cc
@@ -1,116 +1,116 @@
/**
* @file test_buildfacets_triangle_6.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
*
* @date creation: Fri Sep 18 2015
* @date last modification: Sat Sep 19 2015
*
* @brief Test to check the building of the facets. Mesh with triangles
*
* @section LICENSE
*
* Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
* (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <iostream>
#include <limits>
#include <fstream>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char *argv[]) {
initialize(argc, argv);
const UInt spatial_dimension = 2;
const ElementType type = _triangle_6;
Mesh mesh(spatial_dimension);
mesh.read("triangle_6.msh");
- Mesh mesh_facets(mesh.initMeshFacets("mesh_facets"));
+ Mesh & mesh_facets = mesh.initMeshFacets("mesh_facets");
MeshUtils::buildAllFacets(mesh, mesh_facets);
const ElementType type_facet = mesh.getFacetType(type);
const ElementType type_subfacet = mesh.getFacetType(type_facet);
/* ------------------------------------------------------------------------ */
/* Element to Subelement testing */
/* ------------------------------------------------------------------------ */
const Array< std::vector<Element> > & el_to_subel2 = mesh_facets.getElementToSubelement(type_facet);
const Array< std::vector<Element> > & el_to_subel1 = mesh_facets.getElementToSubelement(type_subfacet);
std::cout << "ElementToSubelement2" << std::endl;
for (UInt i = 0; i < el_to_subel2.getSize(); ++i) {
std::cout << type_facet << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j){
std::cout << el_to_subel2(i)[j].type << " " << el_to_subel2(i)[j].element << ", ";
}
std::cout << " " << std::endl;
}
std::cout << "ElementToSubelement1" << std::endl;
for (UInt i = 0; i < el_to_subel1.getSize(); ++i) {
std::cout << type_subfacet << " " << i << " connected to ";
for (UInt j = 0; j < el_to_subel1(i).size(); ++j){
std::cout << el_to_subel1(i)[j].type << " " << el_to_subel1(i)[j].element << ", ";
}
std::cout << " " << std::endl;
}
/* ------------------------------------------------------------------------ */
/* Subelement to Element testing */
/* ------------------------------------------------------------------------ */
const Array<Element> & subel_to_el2 = mesh_facets.getSubelementToElement(type);
const Array<Element> & subel_to_el1 = mesh_facets.getSubelementToElement(type_facet);
std::cout << " " << std::endl;
std::cout << "SubelementToElement2" << std::endl;
for (UInt i = 0; i < subel_to_el2.getSize(); ++i) {
std::cout << type << " " << i << " connected to ";
for (UInt j = 0; j < 3; ++j){
std::cout << subel_to_el2(i, j).type << " " << subel_to_el2(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
std::cout << "SubelementToElement1" << std::endl;
for (UInt i = 0; i < subel_to_el1.getSize(); ++i) {
std::cout << type_facet << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j){
std::cout << subel_to_el1(i, j).type << " " << subel_to_el1(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_mesh_utils/test_segment_nodetype/CMakeLists.txt b/test/test_mesh_utils/test_segment_nodetype/CMakeLists.txt
index aea1a0789..01a5ad4b6 100644
--- a/test/test_mesh_utils/test_segment_nodetype/CMakeLists.txt
+++ b/test/test_mesh_utils/test_segment_nodetype/CMakeLists.txt
@@ -1,34 +1,34 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Marco Vocialta <marco.vocialta@epfl.ch>
#
# @date creation: Fri Sep 18 2015
#
# @brief CMakeLists for segment nodetype tests
#
# @section LICENSE
#
# Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
# (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# Akantu is free software: you can redistribute it and/or modify it under the
# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
#
# Akantu 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 Lesser General Public License for more
# details.
#
# You should have received a copy of the GNU Lesser General Public License
# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
-register_test(test_segment_nodetype
- SOURCES test_segment_nodetype.cc
- FILES_TO_COPY mesh.msh
- PACKAGE parallel
- )
+# register_test(test_segment_nodetype
+# SOURCES test_segment_nodetype.cc
+# FILES_TO_COPY mesh.msh
+# PACKAGE parallel
+# )
diff --git a/test/test_mesh_utils/test_segment_nodetype/test_segment_nodetype.cc b/test/test_mesh_utils/test_segment_nodetype/test_segment_nodetype.cc
index 07cff2289..a3d7bb111 100644
--- a/test/test_mesh_utils/test_segment_nodetype/test_segment_nodetype.cc
+++ b/test/test_mesh_utils/test_segment_nodetype/test_segment_nodetype.cc
@@ -1,97 +1,97 @@
/**
* @file test_segment_nodetype.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Sep 18 2015
*
* @brief Test to verify that the node type is correctly associated to
* the segments in parallel
*
* @section LICENSE
*
* Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
* (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_synchronizer.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
initialize(argc, argv);
UInt spatial_dimension = 3;
Mesh mesh(spatial_dimension);
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
// partition the mesh
if (prank == 0) {
mesh.read("mesh.msh");
}
mesh.distribute();
// compute the node types for each segment
- Mesh mesh_facets(mesh.initMeshFacets());
+ Mesh & mesh_facets = mesh.initMeshFacets();
MeshUtils::buildSegmentToNodeType(mesh, mesh_facets);
// verify that the number of segments per node type makes sense
std::map<Int, UInt> nb_facets_per_nodetype;
UInt nb_segments = 0;
for (auto ghost_type : ghost_types) {
const Array<Int> & segment_to_nodetype =
mesh_facets.getData<Int>("segment_to_nodetype", _segment_2, ghost_type);
// count the number of segments per node type
for (auto & stn : segment_to_nodetype) {
if (nb_facets_per_nodetype.find(stn) == nb_facets_per_nodetype.end())
nb_facets_per_nodetype[stn] = 1;
else
++nb_facets_per_nodetype[stn];
}
nb_segments += segment_to_nodetype.getSize();
}
// checking the solution
if (nb_segments != 24)
AKANTU_DEBUG_ERROR("The number of segments is wrong");
if (prank == 0) {
if (nb_facets_per_nodetype[-1] != 3 || nb_facets_per_nodetype[-2] != 9 ||
nb_facets_per_nodetype[-3] != 12)
AKANTU_DEBUG_ERROR(
"The segments of processor 0 have the wrong node type");
if (nb_facets_per_nodetype.size() > 3)
AKANTU_DEBUG_ERROR("Processor 0 cannot have any slave segment");
}
if (prank == psize - 1 &&
nb_facets_per_nodetype.find(-2) != nb_facets_per_nodetype.end())
AKANTU_DEBUG_ERROR("The last processor must not have any master facets");
finalize();
return 0;
}
diff --git a/test/test_model/test_solid_mechanics_model/patch_tests/explicit/patch_test_explicit.cc b/test/test_model/test_solid_mechanics_model/patch_tests/explicit/patch_test_explicit.cc
index 1e199d191..8641b1041 100644
--- a/test/test_model/test_solid_mechanics_model/patch_tests/explicit/patch_test_explicit.cc
+++ b/test/test_model/test_solid_mechanics_model/patch_tests/explicit/patch_test_explicit.cc
@@ -1,313 +1,312 @@
/**
* @file patch_test_explicit.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Cyprien Wolff <cyprien.wolff@epfl.ch>
*
* @date creation: Sat Apr 16 2011
* @date last modification: Thu Oct 15 2015
*
* @brief patch test for elastic material in solid mechanics model
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
* Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
* Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
#include <fstream>
/* -------------------------------------------------------------------------- */
using namespace akantu;
Real alpha[3][4] = {{0.01, 0.02, 0.03, 0.04},
{0.05, 0.06, 0.07, 0.08},
{0.09, 0.10, 0.11, 0.12}};
/* -------------------------------------------------------------------------- */
template <ElementType type, bool plane_strain>
static Matrix<Real> prescribed_strain() {
UInt spatial_dimension = ElementClass<type>::getSpatialDimension();
Matrix<Real> strain(spatial_dimension, spatial_dimension);
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = 0; j < spatial_dimension; ++j) {
strain(i, j) = alpha[i][j + 1];
}
}
return strain;
}
template <ElementType type, bool is_plane_strain>
static Matrix<Real> prescribed_stress() {
UInt spatial_dimension = ElementClass<type>::getSpatialDimension();
Matrix<Real> stress(spatial_dimension, spatial_dimension);
// plane strain in 2d
Matrix<Real> strain(spatial_dimension, spatial_dimension);
Matrix<Real> pstrain;
pstrain = prescribed_strain<type, is_plane_strain>();
Real nu = 0.3;
Real E = 2.1e11;
Real trace = 0;
/// symetric part of the strain tensor
for (UInt i = 0; i < spatial_dimension; ++i)
for (UInt j = 0; j < spatial_dimension; ++j)
strain(i, j) = 0.5 * (pstrain(i, j) + pstrain(j, i));
for (UInt i = 0; i < spatial_dimension; ++i)
trace += strain(i, i);
if (spatial_dimension == 1) {
stress(0, 0) = E * strain(0, 0);
} else {
if (is_plane_strain) {
Real Ep = E / (1 + nu);
for (UInt i = 0; i < spatial_dimension; ++i)
for (UInt j = 0; j < spatial_dimension; ++j) {
stress(i, j) = Ep * strain(i, j);
if (i == j)
stress(i, j) += Ep * (nu / (1 - 2 * nu)) * trace;
}
} else {
Real Ep = E / (1 + nu);
for (UInt i = 0; i < spatial_dimension; ++i)
for (UInt j = 0; j < spatial_dimension; ++j) {
stress(i, j) = Ep * strain(i, j);
if (i == j)
stress(i, j) += (nu * E) / (1 - (nu * nu)) * trace;
}
}
}
return stress;
}
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
std::string input_file;
if (PLANE_STRAIN)
input_file = "material_check_stress_plane_strain.dat";
else
input_file = "material_check_stress_plane_stress.dat";
initialize(input_file, argc, argv);
debug::setDebugLevel(dblWarning);
UInt dim = ElementClass<TYPE>::getSpatialDimension();
const ElementType element_type = TYPE;
UInt damping_steps = 600000;
UInt damping_interval = 50;
Real damping_ratio = 0.99;
UInt additional_steps = 20000;
UInt max_steps = damping_steps + additional_steps;
/// load mesh
Mesh my_mesh(dim);
std::stringstream filename;
filename << TYPE << ".msh";
my_mesh.read(filename.str());
UInt nb_nodes = my_mesh.getNbNodes();
/// declaration of model
SolidMechanicsModel my_model(my_mesh);
/// model initialization
my_model.initFull();
std::cout << my_model.getMaterial(0) << std::endl;
Real time_step = my_model.getStableTimeStep() / 100.;
my_model.setTimeStep(time_step);
my_model.assembleMassLumped();
std::cout << "The number of time steps is: " << max_steps << " (" << time_step
<< "s)" << std::endl;
// boundary conditions
const Array<Real> & coordinates = my_mesh.getNodes();
Array<Real> & displacement = my_model.getDisplacement();
Array<bool> & boundary = my_model.getBlockedDOFs();
MeshUtils::buildFacets(my_mesh);
my_mesh.createBoundaryGroupFromGeometry();
// Loop over (Sub)Boundar(ies) to block the nodes
for (GroupManager::const_element_group_iterator it(
my_mesh.element_group_begin());
it != my_mesh.element_group_end(); ++it)
- for (ElementGroup::const_node_iterator nodes_it(it->second->node_begin());
- nodes_it != it->second->node_end(); ++nodes_it)
+ for (const auto & node : it->second->getNodeGroup())
for (UInt i = 0; i < dim; ++i)
- boundary(*nodes_it, i) = true;
+ boundary(node, i) = true;
// set the position of all nodes to the static solution
for (UInt n = 0; n < nb_nodes; ++n) {
for (UInt i = 0; i < dim; ++i) {
displacement(n, i) = alpha[i][0];
for (UInt j = 0; j < dim; ++j) {
displacement(n, i) += alpha[i][j + 1] * coordinates(n, j);
}
}
}
Array<Real> & velocity = my_model.getVelocity();
std::ofstream energy;
std::stringstream energy_filename;
energy_filename << "energy_" << TYPE << ".csv";
energy.open(energy_filename.str().c_str());
energy << "id,time,ekin" << std::endl;
Real ekin_mean = 0.;
//#define DEBUG_TEST
#ifdef DEBUG_TEST
my_model.solveStep();
my_model.addDumpField("strain");
my_model.addDumpField("stress");
my_model.addDumpField("external_force");
my_model.addDumpField("internal_force");
my_model.addDumpField("velocity");
my_model.addDumpField("acceleration");
my_model.addDumpField("displacement");
my_model.dump();
#endif
/* ------------------------------------------------------------------------ */
/* Main loop */
/* ------------------------------------------------------------------------ */
UInt s;
for (s = 1; s <= max_steps; ++s) {
if (s % 10000 == 0)
std::cout << "passing step " << s << "/" << max_steps << " ("
<< s * time_step << "s)" << std::endl;
// damp velocity in order to find equilibrium
if ((s < damping_steps) && (s % damping_interval == 0)) {
velocity *= damping_ratio;
}
if (s % 1000 == 0) {
ekin_mean = ekin_mean / 1000.;
std::cout << "Ekin mean = " << ekin_mean << std::endl;
if (ekin_mean < 1e-10)
break;
ekin_mean = 0.;
}
my_model.solveStep();
akantu::Real ekin = my_model.getEnergy("kinetic");
ekin_mean += ekin;
if (s % 1000 == 0)
energy << s << "," << s * time_step << "," << ekin << std::endl;
}
energy.close();
UInt nb_quadrature_points =
my_model.getFEEngine().getNbIntegrationPoints(TYPE);
Array<Real> & stress_vect = const_cast<Array<Real> &>(
my_model.getMaterial(0).getStress(element_type));
Array<Real> & strain_vect =
const_cast<Array<Real> &>(my_model.getMaterial(0).getGradU(element_type));
Array<Real>::matrix_iterator stress_it = stress_vect.begin(dim, dim);
Array<Real>::matrix_iterator strain_it = strain_vect.begin(dim, dim);
Matrix<Real> presc_stress;
presc_stress = prescribed_stress<TYPE, PLANE_STRAIN>();
Matrix<Real> presc_strain;
presc_strain = prescribed_strain<TYPE, PLANE_STRAIN>();
UInt nb_element = my_mesh.getNbElement(TYPE);
Real strain_tolerance = 1e-13;
Real stress_tolerance = 1e-13;
for (UInt el = 0; el < nb_element; ++el) {
for (UInt q = 0; q < nb_quadrature_points; ++q) {
Matrix<Real> & stress = *stress_it;
Matrix<Real> & strain = *strain_it;
Matrix<Real> diff(dim, dim);
diff = strain;
diff -= presc_strain;
Real strain_error = diff.norm<L_inf>() / strain.norm<L_inf>();
if (strain_error > strain_tolerance) {
std::cerr << "strain error: " << strain_error << " > "
<< strain_tolerance << std::endl;
std::cerr << "strain: " << strain << std::endl
<< "prescribed strain: " << presc_strain << std::endl;
return EXIT_FAILURE;
} else {
std::cerr << "strain error: " << strain_error << " < "
<< strain_tolerance << std::endl;
}
diff = stress;
diff -= presc_stress;
Real stress_error = diff.norm<L_inf>() / stress.norm<L_inf>();
if (stress_error > stress_tolerance) {
std::cerr << "stress error: " << stress_error << " > "
<< stress_tolerance << std::endl;
std::cerr << "stress: " << stress << std::endl
<< "prescribed stress: " << presc_stress << std::endl;
return EXIT_FAILURE;
} else {
std::cerr << "stress error: " << stress_error << " < "
<< stress_tolerance << std::endl;
}
++stress_it;
++strain_it;
}
}
for (UInt n = 0; n < nb_nodes; ++n) {
for (UInt i = 0; i < dim; ++i) {
Real disp = alpha[i][0];
for (UInt j = 0; j < dim; ++j) {
disp += alpha[i][j + 1] * coordinates(n, j);
}
if (!(std::abs(displacement(n, i) - disp) < 1e-7)) {
std::cerr << "displacement(" << n << ", " << i
<< ")=" << displacement(n, i) << " should be equal to "
<< disp << "(" << displacement(n, i) - disp << ")"
<< std::endl;
return EXIT_FAILURE;
}
}
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_solid_mechanics_model/patch_tests/explicit/patch_test_explicit_anisotropic.cc b/test/test_model/test_solid_mechanics_model/patch_tests/explicit/patch_test_explicit_anisotropic.cc
index fde87d4e0..e3d06c526 100644
--- a/test/test_model/test_solid_mechanics_model/patch_tests/explicit/patch_test_explicit_anisotropic.cc
+++ b/test/test_model/test_solid_mechanics_model/patch_tests/explicit/patch_test_explicit_anisotropic.cc
@@ -1,314 +1,312 @@
/**
* @file patch_test_explicit_anisotropic.cc
*
* @author Till Junge <till.junge@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Cyprien Wolff <cyprien.wolff@epfl.ch>
*
* @date creation: Sat Apr 16 2011
* @date last modification: Thu Oct 15 2015
*
* @brief patch test for elastic material in solid mechanics model
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
* Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
* Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
#include <fstream>
/* -------------------------------------------------------------------------- */
using namespace akantu;
Real alpha[3][4] = {{0.01, 0.02, 0.03, 0.04},
{0.05, 0.06, 0.07, 0.08},
{0.09, 0.10, 0.11, 0.12}};
// Stiffness tensor, rotated by hand
Real C[3][3][3][3] = {
{{{112.93753505, 1.85842452538e-10, -4.47654358027e-10},
{1.85847317471e-10, 54.2334345331, -3.69840984824},
{-4.4764768395e-10, -3.69840984824, 56.848605217}},
{{1.85847781609e-10, 25.429294233, -3.69840984816},
{25.429294233, 3.31613847493e-10, -8.38797920011e-11},
{-3.69840984816, -8.38804581349e-11, -1.97875715813e-10}},
{{-4.47654358027e-10, -3.69840984816, 28.044464917},
{-3.69840984816, 2.09374961813e-10, 9.4857455224e-12},
{28.044464917, 9.48308098714e-12, -2.1367885239e-10}}},
{{{1.85847781609e-10, 25.429294233, -3.69840984816},
{25.429294233, 3.31613847493e-10, -8.38793479119e-11},
{-3.69840984816, -8.38795699565e-11, -1.97876381947e-10}},
{{54.2334345331, 3.31617400207e-10, 2.09372075233e-10},
{3.3161562385e-10, 115.552705733, -3.15093728886e-10},
{2.09372075233e-10, -3.15090176173e-10, 54.2334345333}},
{{-3.69840984824, -8.38795699565e-11, 9.48219280872e-12},
{-8.38795699565e-11, -3.1509195253e-10, 25.4292942335},
{9.48441325477e-12, 25.4292942335, 3.69840984851}}},
{{{-4.47653469848e-10, -3.69840984816, 28.044464917},
{-3.69840984816, 2.09374073634e-10, 9.48752187924e-12},
{28.044464917, 9.48552347779e-12, -2.1367885239e-10}},
{{-3.69840984824, -8.3884899027e-11, 9.48219280872e-12},
{-8.3884899027e-11, -3.150972816e-10, 25.4292942335},
{9.48041645188e-12, 25.4292942335, 3.69840984851}},
{{56.848605217, -1.97875493768e-10, -2.13681516925e-10},
{-1.97877270125e-10, 54.2334345333, 3.69840984851},
{-2.13683293282e-10, 3.69840984851, 112.93753505}}}};
/* -------------------------------------------------------------------------- */
template <ElementType type> static Matrix<Real> prescribed_grad_u() {
UInt spatial_dimension = ElementClass<type>::getSpatialDimension();
Matrix<Real> grad_u(spatial_dimension, spatial_dimension);
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = 0; j < spatial_dimension; ++j) {
grad_u(i, j) = alpha[i][j + 1];
}
}
return grad_u;
}
template <ElementType type> static Matrix<Real> prescribed_stress() {
UInt spatial_dimension = ElementClass<type>::getSpatialDimension();
Matrix<Real> stress(spatial_dimension, spatial_dimension);
// plane strain in 2d
Matrix<Real> strain(spatial_dimension, spatial_dimension);
Matrix<Real> pstrain;
pstrain = prescribed_grad_u<type>();
Real trace = 0;
/// symetric part of the strain tensor
for (UInt i = 0; i < spatial_dimension; ++i)
for (UInt j = 0; j < spatial_dimension; ++j)
strain(i, j) = 0.5 * (pstrain(i, j) + pstrain(j, i));
for (UInt i = 0; i < spatial_dimension; ++i)
trace += strain(i, i);
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = 0; j < spatial_dimension; ++j) {
stress(i, j) = 0;
for (UInt k = 0; k < spatial_dimension; ++k) {
for (UInt l = 0; l < spatial_dimension; ++l) {
stress(i, j) += C[i][j][k][l] * strain(k, l);
}
}
}
}
return stress;
}
#define TYPE _tetrahedron_4
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
initialize("material_anisotropic.dat", argc, argv);
UInt dim = ElementClass<TYPE>::getSpatialDimension();
const ElementType element_type = TYPE;
UInt damping_steps = 600000;
UInt damping_interval = 50;
Real damping_ratio = 0.99;
UInt additional_steps = 20000;
UInt max_steps = damping_steps + additional_steps;
/// load mesh
Mesh my_mesh(dim);
std::stringstream filename;
filename << TYPE << ".msh";
my_mesh.read(filename.str());
UInt nb_nodes = my_mesh.getNbNodes();
/// declaration of model
SolidMechanicsModel model(my_mesh);
/// model initialization
model.initFull();
std::cout << model.getMaterial(0) << std::endl;
Real time_step = model.getStableTimeStep() / 5.;
model.setTimeStep(time_step);
std::cout << "The number of time steps is: " << max_steps << " (" << time_step
<< "s)" << std::endl;
// boundary conditions
const Array<Real> & coordinates = my_mesh.getNodes();
Array<Real> & displacement = model.getDisplacement();
Array<bool> & boundary = model.getBlockedDOFs();
MeshUtils::buildFacets(my_mesh);
my_mesh.createBoundaryGroupFromGeometry();
// Loop over (Sub)Boundar(ies)
// Loop over (Sub)Boundar(ies)
for (GroupManager::const_element_group_iterator it(
my_mesh.element_group_begin());
it != my_mesh.element_group_end(); ++it) {
- for (ElementGroup::const_node_iterator nodes_it(it->second->node_begin());
- nodes_it != it->second->node_end(); ++nodes_it) {
- UInt n(*nodes_it);
- std::cout << "Node " << *nodes_it << std::endl;
+ for (const auto & n : it->second->getNodeGroup()) {
+ std::cout << "Node " << n << std::endl;
for (UInt i = 0; i < dim; ++i) {
displacement(n, i) = alpha[i][0];
for (UInt j = 0; j < dim; ++j) {
displacement(n, i) += alpha[i][j + 1] * coordinates(n, j);
}
boundary(n, i) = true;
}
}
}
// Actually, loop over all nodes, since I wanna test a static solution
for (UInt n = 0; n < nb_nodes; ++n) {
for (UInt i = 0; i < dim; ++i) {
displacement(n, i) = alpha[i][0];
for (UInt j = 0; j < dim; ++j) {
displacement(n, i) += alpha[i][j + 1] * coordinates(n, j);
}
}
}
Array<Real> & velocity = model.getVelocity();
std::ofstream energy;
std::stringstream energy_filename;
energy_filename << "energy_" << TYPE << ".csv";
energy.open(energy_filename.str().c_str());
energy << "id,time,ekin" << std::endl;
Real ekin_mean = 0.;
/* ------------------------------------------------------------------------ */
/* Main loop */
/* ------------------------------------------------------------------------ */
UInt s;
for (s = 1; s <= max_steps; ++s) {
if (s % 10000 == 0)
std::cout << "passing step " << s << "/" << max_steps << " ("
<< s * time_step << "s)" << std::endl;
// damp velocity in order to find equilibrium
if ((s < damping_steps) && (s % damping_interval == 0)) {
velocity *= damping_ratio;
}
if (s % 1000 == 0) {
ekin_mean = ekin_mean / 1000.;
std::cout << "Ekin mean = " << ekin_mean << std::endl;
if (ekin_mean < 1e-10)
break;
ekin_mean = 0.;
}
model.solveStep();
Real ekin = model.getEnergy("kinetic");
ekin_mean += ekin;
if (s % 1000 == 0)
energy << s << "," << s * time_step << "," << ekin << std::endl;
}
energy.close();
UInt nb_quadrature_points = model.getFEEngine().getNbIntegrationPoints(TYPE);
Array<Real> & stress_vect =
const_cast<Array<Real> &>(model.getMaterial(0).getStress(element_type));
Array<Real> & gradu_vect =
const_cast<Array<Real> &>(model.getMaterial(0).getGradU(element_type));
Array<Real>::iterator<Matrix<Real>> stress_it = stress_vect.begin(dim, dim);
Array<Real>::iterator<Matrix<Real>> gradu_it = gradu_vect.begin(dim, dim);
Matrix<Real> presc_stress;
presc_stress = prescribed_stress<TYPE>();
Matrix<Real> presc_gradu;
presc_gradu = prescribed_grad_u<TYPE>();
UInt nb_element = my_mesh.getNbElement(TYPE);
Real gradu_tolerance = 1e-9;
Real stress_tolerance = 1e-2;
if (s > max_steps) {
stress_tolerance = 1e-4;
gradu_tolerance = 1e-7;
}
for (UInt el = 0; el < nb_element; ++el) {
for (UInt q = 0; q < nb_quadrature_points; ++q) {
Matrix<Real> & stress = *stress_it;
Matrix<Real> & gradu = *gradu_it;
for (UInt i = 0; i < dim; ++i) {
for (UInt j = 0; j < dim; ++j) {
if (!(std::abs(gradu(i, j) - presc_gradu(i, j)) < gradu_tolerance)) {
std::cerr << "gradu[" << i << "," << j << "] = " << gradu(i, j)
<< " but should be = " << presc_gradu(i, j) << " (-"
<< std::abs(gradu(i, j) - presc_gradu(i, j))
<< ") [el : " << el << " - q : " << q << "]" << std::endl;
std::cerr << gradu << presc_gradu << std::endl;
return EXIT_FAILURE;
}
if (!(std::abs(stress(i, j) - presc_stress(i, j)) <
stress_tolerance)) {
std::cerr << "stress[" << i << "," << j << "] = " << stress(i, j)
<< " but should be = " << presc_stress(i, j) << " (-"
<< std::abs(stress(i, j) - presc_stress(i, j))
<< ") [el : " << el << " - q : " << q << "]" << std::endl;
std::cerr << stress << presc_stress << std::endl;
return EXIT_FAILURE;
}
}
}
++stress_it;
++gradu_it;
}
}
for (UInt n = 0; n < nb_nodes; ++n) {
for (UInt i = 0; i < dim; ++i) {
Real disp = alpha[i][0];
for (UInt j = 0; j < dim; ++j) {
disp += alpha[i][j + 1] * coordinates(n, j);
}
if (!(std::abs(displacement(n, i) - disp) < 1e-7)) {
std::cerr << "displacement(" << n << ", " << i
<< ")=" << displacement(n, i) << " should be equal to "
<< disp << "(" << displacement(n, i) - disp << ")"
<< std::endl;
return EXIT_FAILURE;
}
}
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_solid_mechanics_model/patch_tests/implicit/patch_test_implicit.cc b/test/test_model/test_solid_mechanics_model/patch_tests/implicit/patch_test_implicit.cc
index 173cf03b1..499f183db 100644
--- a/test/test_model/test_solid_mechanics_model/patch_tests/implicit/patch_test_implicit.cc
+++ b/test/test_model/test_solid_mechanics_model/patch_tests/implicit/patch_test_implicit.cc
@@ -1,249 +1,247 @@
/**
* @file patch_test_implicit.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sat Apr 16 2011
* @date last modification: Thu Oct 15 2015
*
* @brief patch test for elastic material in solid mechanics model
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
* Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
* Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "non_linear_solver.hh"
#include "solid_mechanics_model.hh"
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
Real alpha[3][4] = {{0.01, 0.02, 0.03, 0.04},
{0.05, 0.06, 0.07, 0.08},
{0.09, 0.10, 0.11, 0.12}};
/* -------------------------------------------------------------------------- */
template <ElementType type, bool is_plane_strain>
static Matrix<Real> prescribed_strain() {
UInt spatial_dimension = ElementClass<type>::getSpatialDimension();
Matrix<Real> strain(spatial_dimension, spatial_dimension);
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = 0; j < spatial_dimension; ++j) {
strain(i, j) = alpha[i][j + 1];
}
}
return strain;
}
template <ElementType type, bool is_plane_strain>
static Matrix<Real> prescribed_stress() {
UInt spatial_dimension = ElementClass<type>::getSpatialDimension();
Matrix<Real> stress(spatial_dimension, spatial_dimension);
// plane strain in 2d
Matrix<Real> strain(spatial_dimension, spatial_dimension);
Matrix<Real> pstrain;
pstrain = prescribed_strain<type, is_plane_strain>();
Real nu = 0.3;
Real E = 2.1e11;
Real trace = 0;
/// symetric part of the strain tensor
for (UInt i = 0; i < spatial_dimension; ++i)
for (UInt j = 0; j < spatial_dimension; ++j)
strain(i, j) = 0.5 * (pstrain(i, j) + pstrain(j, i));
for (UInt i = 0; i < spatial_dimension; ++i)
trace += strain(i, i);
Real lambda = nu * E / ((1 + nu) * (1 - 2 * nu));
Real mu = E / (2 * (1 + nu));
if (!is_plane_strain) {
std::cout << "toto" << std::endl;
lambda = nu * E / (1 - nu * nu);
}
if (spatial_dimension == 1) {
stress(0, 0) = E * strain(0, 0);
} else {
for (UInt i = 0; i < spatial_dimension; ++i)
for (UInt j = 0; j < spatial_dimension; ++j) {
stress(i, j) = (i == j) * lambda * trace + 2 * mu * strain(i, j);
}
}
return stress;
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
std::string input_file;
if (PLANE_STRAIN)
input_file = "material_check_stress_plane_strain.dat";
else
input_file = "material_check_stress_plane_stress.dat";
initialize(input_file, argc, argv);
UInt dim = ElementClass<TYPE>::getSpatialDimension();
const ElementType element_type = TYPE;
/// load mesh
Mesh mesh(dim);
std::stringstream filename;
filename << TYPE << ".msh";
mesh.read(filename.str());
UInt nb_nodes = mesh.getNbNodes();
/// declaration of model
SolidMechanicsModel model(mesh);
/// model initialization
model.initFull(_analysis_method = _static);
const Array<Real> & coordinates = mesh.getNodes();
Array<Real> & displacement = model.getDisplacement();
Array<bool> & boundary = model.getBlockedDOFs();
MeshUtils::buildFacets(mesh);
mesh.createBoundaryGroupFromGeometry();
// Loop over (Sub)Boundar(ies)
for (GroupManager::const_element_group_iterator it(
mesh.element_group_begin());
it != mesh.element_group_end(); ++it) {
- for (ElementGroup::const_node_iterator nodes_it(it->second->node_begin());
- nodes_it != it->second->node_end(); ++nodes_it) {
- UInt n(*nodes_it);
- std::cout << "Node " << *nodes_it << std::endl;
+ for (const auto & n : it->second->getNodeGroup()) {
+ std::cout << "Node " << n << std::endl;
for (UInt i = 0; i < dim; ++i) {
displacement(n, i) = alpha[i][0];
for (UInt j = 0; j < dim; ++j) {
displacement(n, i) += alpha[i][j + 1] * coordinates(n, j);
}
boundary(n, i) = true;
}
}
}
/* ------------------------------------------------------------------------ */
/* Static solve */
/* ------------------------------------------------------------------------ */
auto & solver = model.getNonLinearSolver();
solver.set("max_iterations", 2);
solver.set("threshold", 2e-4);
solver.set("convergence_type", _scc_residual);
model.solveStep();
model.getDOFManager().getMatrix("K").saveMatrix("clown_matrix.mtx");
/* ------------------------------------------------------------------------ */
/* Checks */
/* ------------------------------------------------------------------------ */
UInt nb_quadrature_points =
model.getFEEngine().getNbIntegrationPoints(element_type);
Array<Real> & stress_vect =
const_cast<Array<Real> &>(model.getMaterial(0).getStress(element_type));
Array<Real> & strain_vect =
const_cast<Array<Real> &>(model.getMaterial(0).getGradU(element_type));
Array<Real>::matrix_iterator stress_it = stress_vect.begin(dim, dim);
Array<Real>::matrix_iterator strain_it = strain_vect.begin(dim, dim);
Matrix<Real> presc_stress;
presc_stress = prescribed_stress<TYPE, PLANE_STRAIN>();
Matrix<Real> presc_strain;
presc_strain = prescribed_strain<TYPE, PLANE_STRAIN>();
UInt nb_element = mesh.getNbElement(TYPE);
Real strain_tolerance = 1e-13;
Real stress_tolerance = 1e-13;
for (UInt el = 0; el < nb_element; ++el) {
for (UInt q = 0; q < nb_quadrature_points; ++q) {
Matrix<Real> & stress = *stress_it;
Matrix<Real> & strain = *strain_it;
Matrix<Real> diff(dim, dim);
diff = strain;
diff -= presc_strain;
Real strain_error = diff.norm<L_inf>() / strain.norm<L_inf>();
if (strain_error > strain_tolerance) {
std::cerr << "strain error: " << strain_error << " > "
<< strain_tolerance << std::endl;
std::cerr << "strain: " << strain << std::endl
<< "prescribed strain: " << presc_strain << std::endl;
return EXIT_FAILURE;
} else {
std::cerr << "strain error: " << strain_error << " < "
<< strain_tolerance << std::endl;
}
diff = stress;
diff -= presc_stress;
Real stress_error = diff.norm<L_inf>() / stress.norm<L_inf>();
if (stress_error > stress_tolerance) {
std::cerr << "stress error: " << stress_error << " > "
<< stress_tolerance << std::endl;
std::cerr << "stress: " << stress << std::endl
<< "prescribed stress: " << presc_stress << std::endl;
return EXIT_FAILURE;
} else {
std::cerr << "stress error: " << stress_error << " < "
<< stress_tolerance << std::endl;
}
++stress_it;
++strain_it;
}
}
for (UInt n = 0; n < nb_nodes; ++n) {
for (UInt i = 0; i < dim; ++i) {
Real disp = alpha[i][0];
for (UInt j = 0; j < dim; ++j) {
disp += alpha[i][j + 1] * coordinates(n, j);
}
if (!(std::abs(displacement(n, i) - disp) < 2e-15)) {
std::cerr << "displacement(" << n << ", " << i
<< ")=" << displacement(n, i) << " should be equal to "
<< disp << std::endl;
return EXIT_FAILURE;
}
}
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_1d_element/test_cohesive_1d_element.cc b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_1d_element/test_cohesive_1d_element.cc
index 345c7de54..f8755cf90 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_1d_element/test_cohesive_1d_element.cc
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_1d_element/test_cohesive_1d_element.cc
@@ -1,122 +1,121 @@
/**
* @file test_cohesive_1d_element.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 14 2013
* @date last modification: Sun Oct 19 2014
*
* @brief Test for 1D cohesive elements
*
* @section LICENSE
*
* Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
initialize("material.dat", argc, argv);
const UInt max_steps = 2000;
const Real strain_rate = 4;
UInt spatial_dimension = 1;
Mesh mesh(spatial_dimension, "mesh");
mesh.read("bar.msh");
SolidMechanicsModelCohesive model(mesh);
model.initFull(
SolidMechanicsModelCohesiveOptions(_explicit_lumped_mass, true));
Real time_step = model.getStableTimeStep() * 0.01;
model.setTimeStep(time_step);
std::cout << "Time step: " << time_step << std::endl;
model.assembleMassLumped();
- mesh.computeBoundingBox();
Real posx_max = mesh.getUpperBounds()(0);
Real posx_min = mesh.getLowerBounds()(0);
/// initial conditions
Array<Real> & velocity = model.getVelocity();
const Array<Real> & position = mesh.getNodes();
UInt nb_nodes = mesh.getNbNodes();
for (UInt n = 0; n < nb_nodes; ++n)
velocity(n) = strain_rate * (position(n) - (posx_max + posx_min) / 2.);
/// boundary conditions
Array<bool> & boundary = model.getBlockedDOFs();
Array<Real> & displacement = model.getDisplacement();
Real disp_increment = strain_rate * (posx_max - posx_min) / 2. * time_step;
for (UInt node = 0; node < mesh.getNbNodes(); ++node) {
if (Math::are_float_equal(position(node), posx_min)) { // left side
boundary(node) = true;
}
if (Math::are_float_equal(position(node), posx_max)) { // right side
boundary(node) = true;
}
}
model.synchronizeBoundaries();
model.assembleInternalForces();
for (UInt s = 1; s <= max_steps; ++s) {
model.checkCohesiveStress();
model.solveStep();
UInt nb_cohesive_elements = mesh.getNbElement(_cohesive_1d_2);
if (s % 10 == 0) {
std::cout << "passing step " << s << "/" << max_steps
<< ", number of cohesive elemets:" << nb_cohesive_elements
<< std::endl;
}
/// update external work and boundary conditions
for (UInt n = 0; n < mesh.getNbNodes(); ++n) {
if (Math::are_float_equal(position(n), posx_min)) // left side
displacement(n) -= disp_increment;
if (Math::are_float_equal(position(n), posx_max)) // right side
displacement(n) += disp_increment;
}
}
Real Ed = model.getEnergy("dissipated");
Real Edt = 100 * 3;
std::cout << Ed << std::endl;
if (Ed < Edt * 0.999 || Ed > Edt * 1.001 || std::isnan(Ed)) {
std::cout << "The dissipated energy is incorrect" << std::endl;
finalize();
return EXIT_FAILURE;
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_materials/test_interpolate_stress.cc b/test/test_model/test_solid_mechanics_model/test_materials/test_interpolate_stress.cc
index 9fab6b8ca..952d1bb85 100644
--- a/test/test_model/test_solid_mechanics_model/test_materials/test_interpolate_stress.cc
+++ b/test/test_model/test_solid_mechanics_model/test_materials/test_interpolate_stress.cc
@@ -1,181 +1,181 @@
/**
* @file test_interpolate_stress.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Thu Jun 07 2012
* @date last modification: Thu Oct 15 2015
*
* @brief Test for the stress interpolation function
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
* Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
* Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <iostream>
#include <limits>
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
Real function(Real x, Real y, Real z) { return 100. + 2. * x + 3. * y + 4 * z; }
int main(int argc, char * argv[]) {
initialize("../material.dat", argc, argv);
debug::setDebugLevel(dblWarning);
const UInt spatial_dimension = 3;
const ElementType type = _tetrahedron_10;
Mesh mesh(spatial_dimension);
mesh.read("interpolation.msh");
const ElementType type_facet = mesh.getFacetType(type);
- Mesh mesh_facets(mesh.initMeshFacets("mesh_facets"));
+ Mesh & mesh_facets = mesh.initMeshFacets("mesh_facets");
MeshUtils::buildAllFacets(mesh, mesh_facets);
SolidMechanicsModel model(mesh);
/// model initialization
model.initFull();
Array<Real> & position = mesh.getNodes();
UInt nb_facet = mesh_facets.getNbElement(type_facet);
UInt nb_element = mesh.getNbElement(type);
/// compute quadrature points positions on facets
typedef FEEngineTemplate<IntegratorGauss, ShapeLagrange> MyFEEngineType;
model.registerFEEngineObject<MyFEEngineType>("FacetsFEEngine", mesh_facets,
spatial_dimension - 1);
model.getFEEngine("FacetsFEEngine").initShapeFunctions();
UInt nb_quad_per_facet =
model.getFEEngine("FacetsFEEngine").getNbIntegrationPoints(type_facet);
UInt nb_tot_quad = nb_quad_per_facet * nb_facet;
Array<Real> quad_facets(nb_tot_quad, spatial_dimension);
model.getFEEngine("FacetsFEEngine")
.interpolateOnIntegrationPoints(position, quad_facets, spatial_dimension,
type_facet);
Array<Element> & facet_to_element = mesh_facets.getSubelementToElement(type);
UInt nb_facet_per_elem = facet_to_element.getNbComponent();
ElementTypeMapArray<Real> element_quad_facet;
element_quad_facet.alloc(nb_element * nb_facet_per_elem * nb_quad_per_facet,
spatial_dimension, type);
ElementTypeMapArray<Real> interpolated_stress("interpolated_stress", "");
interpolated_stress.initialize(
mesh, _nb_component = spatial_dimension * spatial_dimension,
_spatial_dimension = spatial_dimension);
Array<Real> & interp_stress = interpolated_stress(type);
interp_stress.resize(nb_element * nb_facet_per_elem * nb_quad_per_facet);
Array<Real> & el_q_facet = element_quad_facet(type);
for (UInt el = 0; el < nb_element; ++el) {
for (UInt f = 0; f < nb_facet_per_elem; ++f) {
UInt global_facet = facet_to_element(el, f).element;
for (UInt q = 0; q < nb_quad_per_facet; ++q) {
for (UInt s = 0; s < spatial_dimension; ++s) {
el_q_facet(el * nb_facet_per_elem * nb_quad_per_facet +
f * nb_quad_per_facet + q,
s) = quad_facets(global_facet * nb_quad_per_facet + q, s);
}
}
}
}
/// compute quadrature points position of the elements
UInt nb_quad_per_element = model.getFEEngine().getNbIntegrationPoints(type);
UInt nb_tot_quad_el = nb_quad_per_element * nb_element;
Array<Real> quad_elements(nb_tot_quad_el, spatial_dimension);
model.getFEEngine().interpolateOnIntegrationPoints(position, quad_elements,
spatial_dimension, type);
/// assign some values to stresses
Array<Real> & stress =
const_cast<Array<Real> &>(model.getMaterial(0).getStress(type));
for (UInt q = 0; q < nb_tot_quad_el; ++q) {
for (UInt s = 0; s < spatial_dimension * spatial_dimension; ++s) {
stress(q, s) = s * function(quad_elements(q, 0), quad_elements(q, 1),
quad_elements(q, 2));
}
}
/// interpolate stresses on facets' quadrature points
model.getMaterial(0).initElementalFieldInterpolation(element_quad_facet);
model.getMaterial(0).interpolateStress(interpolated_stress);
Real tolerance = 1.e-10;
/// check results
for (UInt el = 0; el < nb_element; ++el) {
for (UInt f = 0; f < nb_facet_per_elem; ++f) {
for (UInt q = 0; q < nb_quad_per_facet; ++q) {
for (UInt s = 0; s < spatial_dimension * spatial_dimension; ++s) {
Real x = el_q_facet(el * nb_facet_per_elem * nb_quad_per_facet +
f * nb_quad_per_facet + q,
0);
Real y = el_q_facet(el * nb_facet_per_elem * nb_quad_per_facet +
f * nb_quad_per_facet + q,
1);
Real z = el_q_facet(el * nb_facet_per_elem * nb_quad_per_facet +
f * nb_quad_per_facet + q,
2);
Real theoretical = s * function(x, y, z);
Real numerical =
interp_stress(el * nb_facet_per_elem * nb_quad_per_facet +
f * nb_quad_per_facet + q,
s);
if (std::abs(theoretical - numerical) > tolerance) {
std::cout << "Theoretical and numerical values aren't coincident!"
<< std::endl;
return EXIT_FAILURE;
}
}
}
}
}
std::cout << "OK: Stress interpolation test passed." << std::endl;
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_materials/test_material_thermal.cc b/test/test_model/test_solid_mechanics_model/test_materials/test_material_thermal.cc
index 325e3881e..9eeeaa40c 100644
--- a/test/test_model/test_solid_mechanics_model/test_materials/test_material_thermal.cc
+++ b/test/test_model/test_solid_mechanics_model/test_materials/test_material_thermal.cc
@@ -1,101 +1,100 @@
/**
* @file test_material_thermal.cc
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Wed Aug 04 2010
* @date last modification: Sun Oct 19 2014
*
* @brief test of the class akantu::MaterialThermal
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
* Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
* Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <iostream>
/* -------------------------------------------------------------------------- */
#include "non_linear_solver.hh"
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
debug::setDebugLevel(dblWarning);
initialize("material_thermal.dat", argc, argv);
Math::setTolerance(1.e-13);
Mesh mesh(2);
mesh.read("square.msh");
SolidMechanicsModel model(mesh);
model.initFull(_analysis_method = _static);
- mesh.computeBoundingBox();
const Vector<Real> & min = mesh.getLowerBounds();
const Vector<Real> & max = mesh.getUpperBounds();
Array<Real> & pos = mesh.getNodes();
Array<bool> & boundary = model.getBlockedDOFs();
Array<Real> & disp = model.getDisplacement();
for (UInt i = 0; i < mesh.getNbNodes(); ++i) {
if (Math::are_float_equal(pos(i, 0), min(0))) {
boundary(i, 0) = true;
}
if (Math::are_float_equal(pos(i, 1), min(1))) {
boundary(i, 1) = true;
}
}
model.setBaseName("test_material_thermal");
model.addDumpField("displacement");
model.addDumpField("strain");
model.addDumpField("stress");
model.addDumpField("delta_T");
auto & solver = model.getNonLinearSolver("static");
solver.set("max_iterations", 2);
solver.set("threshold", 1e-10);
model.solveStep();
for (UInt i = 0; i < mesh.getNbNodes(); ++i) {
if (Math::are_float_equal(pos(i, 0), max(0)) &&
Math::are_float_equal(pos(i, 1), max(1))) {
if (!Math::are_float_equal(disp(i, 0), 1.0) ||
!Math::are_float_equal(disp(i, 1), 1.0)) {
AKANTU_DEBUG_ERROR("Test not passed");
return EXIT_FAILURE;
}
}
}
model.dump();
finalize();
std::cout << "Test passed" << std::endl;
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_materials/test_multi_material_elastic.cc b/test/test_model/test_solid_mechanics_model/test_materials/test_multi_material_elastic.cc
index a354718ad..b087bfb75 100644
--- a/test/test_model/test_solid_mechanics_model/test_materials/test_multi_material_elastic.cc
+++ b/test/test_model/test_solid_mechanics_model/test_materials/test_multi_material_elastic.cc
@@ -1,92 +1,92 @@
#include <solid_mechanics_model.hh>
#include "non_linear_solver.hh"
using namespace akantu;
int main(int argc, char *argv[]) {
initialize("test_multi_material_elastic.dat", argc, argv);
UInt spatial_dimension = 2;
Mesh mesh(spatial_dimension);
mesh.read("test_multi_material_elastic.msh");
- mesh.createGroupsFromMeshData<std::string>("physical_names");
SolidMechanicsModel model(mesh);
MeshDataMaterialSelector<std::string> mat_sel("physical_names", model);
model.setMaterialSelector(mat_sel);
model.initFull(_analysis_method = _static);
model.applyBC(BC::Dirichlet::FlagOnly(_y), "ground");
model.applyBC(BC::Dirichlet::FlagOnly(_x), "corner");
Vector<Real> trac(spatial_dimension, 0.);
trac(_y) = 1.;
model.applyBC(BC::Neumann::FromTraction(trac), "air");
- model.addDumpField("force");
- model.addDumpField("residual");
+ model.addDumpField("external_force");
+ model.addDumpField("internal_force");
model.addDumpField("blocked_dofs");
model.addDumpField("displacement");
model.addDumpField("stress");
model.addDumpField("grad_u");
//model.dump();
auto & solver = model.getNonLinearSolver("static");
solver.set("max_iterations", 1);
solver.set("threshold", 1e-8);
solver.set("convergence_type", _scc_residual);
+ model.solveStep();
//model.dump();
std::map<std::string, Matrix<Real>> ref_strain;
ref_strain["strong"] = Matrix<Real>(spatial_dimension, spatial_dimension, 0.);
ref_strain["strong"](_y, _y) = .5;
ref_strain["weak"] = Matrix<Real>(spatial_dimension, spatial_dimension, 0.);
ref_strain["weak"](_y, _y) = 1;
Matrix<Real> ref_stress(spatial_dimension, spatial_dimension, 0.);
ref_stress(_y, _y) = 1.;
std::vector<std::string> mats = {"strong", "weak"};
typedef Array<Real>::const_matrix_iterator mat_it;
auto check = [](mat_it it, mat_it end, const Matrix<Real> & ref) -> bool {
for(;it != end; ++it) {
Real dist = (*it - ref).norm<L_2>();
//std::cout << *it << " " << dist << " " << (dist < 1e-10 ? "OK" : "Not OK") << std::endl;
if (dist > 1e-10) return false;
}
return true;
};
auto tit = mesh.firstType(spatial_dimension);
auto tend = mesh.lastType(spatial_dimension);
for (; tit != tend; ++tit) {
auto & type = *tit;
for(auto mat_id : mats) {
auto & stress = model.getMaterial(mat_id).getStress(type);
auto & grad_u = model.getMaterial(mat_id).getGradU(type);
auto sit = stress.begin(spatial_dimension, spatial_dimension);
auto send = stress.end(spatial_dimension, spatial_dimension);
auto git = grad_u.begin(spatial_dimension, spatial_dimension);
auto gend = grad_u.end(spatial_dimension, spatial_dimension);
if(!check(sit, send, ref_stress)) AKANTU_DEBUG_ERROR("The stresses are not correct");
if(!check(git, gend, ref_strain[mat_id])) AKANTU_DEBUG_ERROR("The grad_u are not correct");
}
}
finalize();
return 0;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_solid_mechanics_model_material_eigenstrain.cc b/test/test_model/test_solid_mechanics_model/test_solid_mechanics_model_material_eigenstrain.cc
index 5b363ef62..2b1fafe0d 100644
--- a/test/test_model/test_solid_mechanics_model/test_solid_mechanics_model_material_eigenstrain.cc
+++ b/test/test_model/test_solid_mechanics_model/test_solid_mechanics_model_material_eigenstrain.cc
@@ -1,203 +1,201 @@
/**
* @file test_solid_mechanics_model_material_eigenstrain.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sat Apr 16 2011
* @date last modification: Wed Aug 12 2015
*
* @brief test the internal field prestrain
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
* Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
* Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model.hh"
#include "non_linear_solver.hh"
using namespace akantu;
Real alpha [3][4] = { { 0.01, 0.02, 0.03, 0.04 },
{ 0.05, 0.06, 0.07, 0.08 },
{ 0.09, 0.10, 0.11, 0.12 } };
/* -------------------------------------------------------------------------- */
template<ElementType type>
static Matrix<Real> prescribed_strain() {
UInt spatial_dimension = ElementClass<type>::getSpatialDimension();
Matrix<Real> strain(spatial_dimension, spatial_dimension);
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = 0; j < spatial_dimension; ++j) {
strain(i, j) = alpha[i][j + 1];
}
}
return strain;
}
template<ElementType type>
static Matrix<Real> prescribed_stress(Matrix<Real> prescribed_eigengradu) {
UInt spatial_dimension = ElementClass<type>::getSpatialDimension();
Matrix<Real> stress(spatial_dimension, spatial_dimension);
//plane strain in 2d
Matrix<Real> strain(spatial_dimension, spatial_dimension);
Matrix<Real> pstrain;
pstrain = prescribed_strain<type>();
Real nu = 0.3;
Real E = 2.1e11;
Real trace = 0;
/// symetric part of the strain tensor
for (UInt i = 0; i < spatial_dimension; ++i)
for (UInt j = 0; j < spatial_dimension; ++j)
strain(i,j) = 0.5 * (pstrain(i, j) + pstrain(j, i));
// elastic strain is equal to elastic strain minus the eigenstrain
strain -= prescribed_eigengradu;
for (UInt i = 0; i < spatial_dimension; ++i) trace += strain(i,i);
Real lambda = nu * E / ((1 + nu) * (1 - 2*nu));
Real mu = E / (2 * (1 + nu));
if(spatial_dimension == 1) {
stress(0, 0) = E * strain(0, 0);
} else {
for (UInt i = 0; i < spatial_dimension; ++i)
for (UInt j = 0; j < spatial_dimension; ++j) {
stress(i, j) = (i == j)*lambda*trace + 2*mu*strain(i, j);
}
}
return stress;
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
int main(int argc, char *argv[]) {
initialize("material_elastic_plane_strain.dat", argc, argv);
UInt dim = 3;
const ElementType element_type = _tetrahedron_4;
Matrix<Real> prescribed_eigengradu(dim, dim);
prescribed_eigengradu.set(0.1);
/// load mesh
Mesh mesh(dim);
mesh.read("cube_3d_tet_4.msh");
/// declaration of model
SolidMechanicsModel model(mesh);
/// model initialization
model.initFull(_analysis_method = _static);
//model.getNewSolver("static", _tsst_static, _nls_newton_raphson_modified);
auto & solver = model.getNonLinearSolver("static");
solver.set("threshold", 2e-4);
solver.set("max_iterations", 2);
solver.set("convergence_type", _scc_residual);
const Array<Real> & coordinates = mesh.getNodes();
Array<Real> & displacement = model.getDisplacement();
Array<bool> & boundary = model.getBlockedDOFs();
MeshUtils::buildFacets(mesh);
mesh.createBoundaryGroupFromGeometry();
// Loop over (Sub)Boundar(ies)
for(GroupManager::const_element_group_iterator it(mesh.element_group_begin());
it != mesh.element_group_end(); ++it) {
- for(ElementGroup::const_node_iterator nodes_it(it->second->node_begin());
- nodes_it!= it->second->node_end(); ++nodes_it) {
- UInt n(*nodes_it);
- std::cout << "Node " << *nodes_it << std::endl;
+ for(const auto & n : it->second->getNodeGroup()) {
+ std::cout << "Node " << n << std::endl;
for (UInt i = 0; i < dim; ++i) {
displacement(n, i) = alpha[i][0];
for (UInt j = 0; j < dim; ++j) {
displacement(n, i) += alpha[i][j + 1] * coordinates(n, j);
}
boundary(n, i) = true;
}
}
}
/* ------------------------------------------------------------------------ */
/* Apply eigenstrain in each element */
/* ------------------------------------------------------------------------ */
Array<Real> & eigengradu_vect =
model.getMaterial(0).getInternal<Real>("eigen_grad_u")(element_type);
auto eigengradu_it = eigengradu_vect.begin(dim, dim);
auto eigengradu_end = eigengradu_vect.end(dim, dim);
for (; eigengradu_it != eigengradu_end; ++eigengradu_it) {
*eigengradu_it = prescribed_eigengradu;
}
/* ------------------------------------------------------------------------ */
/* Static solve */
/* ------------------------------------------------------------------------ */
model.solveStep();
std::cout << "Converged in " << Int(solver.get("nb_iterations"))
<< " (" << Real(solver.get("error")) << ")" << std::endl;
/* ------------------------------------------------------------------------ */
/* Checks */
/* ------------------------------------------------------------------------ */
const Array<Real> & stress_vect = model.getMaterial(0).getStress(element_type);
auto stress_it = stress_vect.begin(dim, dim);
auto stress_end = stress_vect.end(dim, dim);
Matrix<Real> presc_stress;
presc_stress = prescribed_stress<element_type>(prescribed_eigengradu);
Real stress_tolerance = 1e-13;
for (; stress_it != stress_end; ++stress_it) {
const auto & stress = *stress_it;
Matrix<Real> diff(dim, dim);
diff = stress;
diff -= presc_stress;
Real stress_error = diff.norm<L_inf>() / stress.norm<L_inf>();
if(stress_error > stress_tolerance) {
std::cerr << "stress error: " << stress_error
<< " > " << stress_tolerance << std::endl;
std::cerr << "stress: " << stress << std::endl
<< "prescribed stress: " << presc_stress << std::endl;
return EXIT_FAILURE;
} // else {
// std::cerr << "stress error: " << stress_error
// << " < " << stress_tolerance << std::endl;
// }
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_synchronizer/test_data_distribution.cc b/test/test_synchronizer/test_data_distribution.cc
index d3c8db9c9..2efd1498e 100644
--- a/test/test_synchronizer/test_data_distribution.cc
+++ b/test/test_synchronizer/test_data_distribution.cc
@@ -1,197 +1,197 @@
/**
* @file test_data_distribution.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Sep 05 2014
* @date last modification: Sun Oct 19 2014
*
* @brief Test the mesh distribution on creation of a distributed synchonizer
*
* @section LICENSE
*
* Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "element_group.hh"
#include "element_synchronizer.hh"
#include "mesh_partition_mesh_data.hh"
#include "aka_random_generator.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
initialize(argc, argv);
const UInt spatial_dimension = 3;
Mesh mesh_group_after(spatial_dimension, "after");
Mesh mesh_group_before(spatial_dimension, "before");
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
if (prank == 0) {
mesh_group_before.read("data_split.msh");
mesh_group_after.read("data_split.msh");
mesh_group_before.registerData<UInt>("global_id");
mesh_group_after.registerData<UInt>("global_id");
for (Mesh::type_iterator tit = mesh_group_after.firstType(_all_dimensions);
tit != mesh_group_after.lastType(_all_dimensions); ++tit) {
Array<UInt> & gidb =
- *(mesh_group_before.getDataPointer<UInt>("global_id", *tit));
+ mesh_group_before.getDataPointer<UInt>("global_id", *tit);
Array<UInt> & gida =
- *(mesh_group_after.getDataPointer<UInt>("global_id", *tit));
+ mesh_group_after.getDataPointer<UInt>("global_id", *tit);
Array<UInt>::scalar_iterator ait = gida.begin();
Array<UInt>::scalar_iterator bit = gidb.begin();
Array<UInt>::scalar_iterator end = gida.end();
for (UInt i = 0; ait != end; ++ait, ++i, ++bit) {
*bit = i;
*ait = i;
}
}
}
RandomGenerator<UInt>::seed(1);
mesh_group_before.distribute();
RandomGenerator<UInt>::seed(1);
mesh_group_after.distribute();
if (prank == 0)
std::cout << mesh_group_after;
GroupManager::element_group_iterator grp_ait =
mesh_group_after.element_group_begin();
GroupManager::element_group_iterator grp_end =
mesh_group_after.element_group_end();
for (; grp_ait != grp_end; ++grp_ait) {
std::string grp = grp_ait->first;
const ElementGroup & bgrp = mesh_group_before.getElementGroup(grp);
const ElementGroup & agrp = *grp_ait->second;
for (ghost_type_t::iterator git = ghost_type_t::begin();
git != ghost_type_t::end(); ++git) {
GhostType ghost_type = *git;
for (Mesh::type_iterator tit =
bgrp.firstType(_all_dimensions, ghost_type);
tit != bgrp.lastType(_all_dimensions, ghost_type); ++tit) {
- Array<UInt> & gidb = *(mesh_group_before.getDataPointer<UInt>(
- "global_id", *tit, ghost_type));
- Array<UInt> & gida = *(mesh_group_after.getDataPointer<UInt>(
- "global_id", *tit, ghost_type));
+ Array<UInt> & gidb = mesh_group_before.getDataPointer<UInt>(
+ "global_id", *tit, ghost_type);
+ Array<UInt> & gida = mesh_group_after.getDataPointer<UInt>(
+ "global_id", *tit, ghost_type);
Array<UInt> bgelem(bgrp.getElements(*tit, ghost_type));
Array<UInt> agelem(agrp.getElements(*tit, ghost_type));
Array<UInt>::scalar_iterator ait = agelem.begin();
Array<UInt>::scalar_iterator bit = bgelem.begin();
Array<UInt>::scalar_iterator end = agelem.end();
for (; ait != end; ++ait, ++bit) {
*bit = gidb(*bit);
*ait = gida(*ait);
}
std::sort(bgelem.begin(), bgelem.end());
std::sort(agelem.begin(), agelem.end());
if (!std::equal(bgelem.begin(), bgelem.end(), agelem.begin())) {
std::cerr << "The filters array for the group " << grp
<< " and for the element type " << *tit << ", "
<< ghost_type << " do not match" << std::endl;
debug::setDebugLevel(dblTest);
std::cerr << bgelem << std::endl;
std::cerr << agelem << std::endl;
debug::debugger.exit(EXIT_FAILURE);
}
}
}
}
GroupManager::node_group_iterator ngrp_ait =
mesh_group_after.node_group_begin();
GroupManager::node_group_iterator ngrp_end =
mesh_group_after.node_group_end();
for (; ngrp_ait != ngrp_end; ++ngrp_ait) {
std::string grp = ngrp_ait->first;
const NodeGroup & bgrp = mesh_group_before.getNodeGroup(grp);
const NodeGroup & agrp = *ngrp_ait->second;
const Array<UInt> & gidb = mesh_group_before.getGlobalNodesIds();
const Array<UInt> & gida = mesh_group_after.getGlobalNodesIds();
Array<UInt> bgnode(0, 1);
Array<UInt> agnode(0, 1);
Array<UInt>::const_scalar_iterator ait = agrp.begin();
Array<UInt>::const_scalar_iterator bit = bgrp.begin();
Array<UInt>::const_scalar_iterator end = agrp.end();
for (; ait != end; ++ait, ++bit) {
if (psize > 1) {
if (mesh_group_before.isLocalOrMasterNode(*bit))
bgnode.push_back(gidb(*bit));
if (mesh_group_after.isLocalOrMasterNode(*ait))
agnode.push_back(gida(*ait));
}
}
std::sort(bgnode.begin(), bgnode.end());
std::sort(agnode.begin(), agnode.end());
if (!std::equal(bgnode.begin(), bgnode.end(), agnode.begin())) {
std::cerr << "The filters array for the group " << grp << " do not match"
<< std::endl;
debug::setDebugLevel(dblTest);
std::cerr << bgnode << std::endl;
std::cerr << agnode << std::endl;
debug::debugger.exit(EXIT_FAILURE);
}
}
mesh_group_after.getElementGroup("inside").setBaseName("after_inside");
mesh_group_after.getElementGroup("inside").dump();
mesh_group_after.getElementGroup("outside").setBaseName("after_outside");
mesh_group_after.getElementGroup("outside").dump();
mesh_group_after.getElementGroup("volume").setBaseName("after_volume");
mesh_group_after.getElementGroup("volume").dump();
mesh_group_before.getElementGroup("inside").setBaseName("before_inside");
mesh_group_before.getElementGroup("inside").dump();
mesh_group_before.getElementGroup("outside").setBaseName("before_outside");
mesh_group_before.getElementGroup("outside").dump();
mesh_group_before.getElementGroup("volume").setBaseName("before_volume");
mesh_group_before.getElementGroup("volume").dump();
finalize();
return EXIT_SUCCESS;
}