diff --git a/packages/00_core.cmake b/packages/00_core.cmake
index b8e823857..8dc96d9a1 100644
--- a/packages/00_core.cmake
+++ b/packages/00_core.cmake
@@ -1,434 +1,435 @@
#===============================================================================
# @file 00_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: Fri Sep 19 2014
#
# @brief package description for core
#
# @section LICENSE
#
# Copyright (©) 2010-2012, 2014 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/>.
#
#===============================================================================
set(AKANTU_CORE ON CACHE INTERNAL "core package for Akantu" FORCE)
set(AKANTU_CORE_FILES
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_error.cc
common/aka_error.hh
common/aka_event_handler_manager.hh
common/aka_extern.cc
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_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.cc
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_pentahedron_6_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_data_tmpl.hh
fe_engine/geometrical_element.cc
fe_engine/integration_element.cc
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/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_inline_impl.hh
io/dumper/dumper_field.hh
io/dumper/dumper_material_padders.hh
io/dumper/dumper_filtered_connectivity.hh
io/dumper/dumper_element_type.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.hh
io/parser/parser_tmpl.hh
io/parser/cppargparse/cppargparse.hh
io/parser/cppargparse/cppargparse.cc
io/parser/cppargparse/cppargparse_tmpl.hh
mesh/element_group.cc
mesh/element_group.hh
mesh/element_group_inline_impl.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_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_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_pbc.cc
mesh_utils/mesh_utils.cc
mesh_utils/mesh_utils.hh
mesh_utils/mesh_utils_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/integration_scheme/generalized_trapezoidal.hh
model/integration_scheme/generalized_trapezoidal_inline_impl.cc
model/integration_scheme/integration_scheme_1st_order.hh
model/integration_scheme/integration_scheme_2nd_order.hh
model/integration_scheme/newmark-beta.hh
model/integration_scheme/newmark-beta_inline_impl.cc
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_list.hh
model/solid_mechanics/material_random_internal.hh
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_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_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
solver/solver.cc
solver/solver.hh
+ solver/solver_inline_impl.cc
solver/sparse_matrix.cc
solver/sparse_matrix.hh
solver/sparse_matrix_inline_impl.cc
solver/static_solver.hh
solver/static_solver.cc
synchronizer/communication_buffer.hh
synchronizer/communication_buffer_inline_impl.cc
synchronizer/data_accessor.cc
synchronizer/data_accessor.hh
synchronizer/data_accessor_inline_impl.cc
synchronizer/distributed_synchronizer.cc
synchronizer/distributed_synchronizer.hh
synchronizer/distributed_synchronizer_tmpl.hh
synchronizer/dof_synchronizer.cc
synchronizer/dof_synchronizer.hh
synchronizer/dof_synchronizer_inline_impl.cc
synchronizer/filtered_synchronizer.cc
synchronizer/filtered_synchronizer.hh
synchronizer/mpi_type_wrapper.hh
synchronizer/pbc_synchronizer.cc
synchronizer/pbc_synchronizer.hh
synchronizer/real_static_communicator.hh
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_registry.cc
synchronizer/synchronizer_registry.hh
)
set(AKANTU_CORE_DEB_DEPEND
libboost-dev
)
set(AKANTU_CORE_TESTS
test_csr
test_facet_element_mapping
test_facet_extraction_tetrahedron_4
test_facet_extraction_triangle_3
test_grid
test_interpolate_stress
test_local_material
test_material_damage_non_local
test_material_thermal
test_matrix
test_mesh_boundary
test_mesh_data
test_mesh_io_msh
test_mesh_io_msh_physical_names
test_mesh_partitionate_mesh_data
test_parser
test_dumper
test_pbc_tweak
test_purify_mesh
test_solid_mechanics_model_bar_traction2d
test_solid_mechanics_model_bar_traction2d_structured
test_solid_mechanics_model_bar_traction2d_structured_pbc
test_solid_mechanics_model_boundary_condition
test_solid_mechanics_model_circle_2
test_solid_mechanics_model_cube3d
test_solid_mechanics_model_cube3d_pbc
test_solid_mechanics_model_cube3d_tetra10
test_solid_mechanics_model_square
test_solid_mechanics_model_material_eigenstrain
test_static_memory
test_surface_extraction_tetrahedron_4
test_surface_extraction_triangle_3
test_vector
test_vector_iterator
test_weight
test_math
test_material_standard_linear_solid_deviatoric_relaxation
test_material_standard_linear_solid_deviatoric_relaxation_tension
test_material_plasticity
)
set(AKANTU_CORE_MANUAL_FILES
manual.sty
manual.cls
manual.tex
manual-macros.sty
manual-titlepages.tex
manual-introduction.tex
manual-gettingstarted.tex
manual-io.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
)
find_program(READLINK_COMMAND readlink)
find_program(ADDR2LINE_COMMAND addr2line)
mark_as_advanced(READLINK_COMMAND)
mark_as_advanced(ADDR2LINE_COMMAND)
include(CheckFunctionExists)
check_function_exists(clock_gettime _clock_gettime)
if(NOT _clock_gettime)
set(AKANTU_USE_OBSOLETE_GETTIMEOFDAY ON)
else()
set(AKANTU_USE_OBSOLETE_GETTIMEOFDAY OFF)
endif()
set(AKANTU_CORE_DOCUMENTATION
"
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 build-essential cmake-curses-gui libboost-dev zlib1g-dev
\\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}
")
\ No newline at end of file
diff --git a/packages/50_parallel.cmake b/packages/50_parallel.cmake
index 2a91df104..173a943d8 100644
--- a/packages/50_parallel.cmake
+++ b/packages/50_parallel.cmake
@@ -1,48 +1,49 @@
#===============================================================================
# @file 50_parallel.cmake
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Tue Oct 16 2012
# @date last modification: Wed Jun 11 2014
#
# @brief meta package description for parallelization
#
# @section LICENSE
#
# Copyright (©) 2010-2012, 2014 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/>.
#
#===============================================================================
add_meta_package(PARALLEL "Add parallel support in Akantu" OFF MPI SCOTCH)
set(AKANTU_PARALLEL_TESTS
test_solid_mechanics_model_bar_traction2d_parallel
test_solid_mechanics_model_segment_parallel
test_solid_mechanics_model_pbc_parallel
test_synchronizer_communication
test_dof_synchronizer
+ test_dof_synchronizer_communication
test_solid_mechanics_model_reassign_material
)
set(AKANTU_PARALLEL_MANUAL_FILES
manual-parallel.tex
)
set(AKANTU_PARALLEL_DOCUMENTATION "
This option activates the parallel features of AKANTU.
" )
diff --git a/packages/84_petsc.cmake b/packages/84_petsc.cmake
index dceacb9ba..ddbec6201 100644
--- a/packages/84_petsc.cmake
+++ b/packages/84_petsc.cmake
@@ -1,45 +1,48 @@
#===============================================================================
# @file petsc.cmake
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
# @author Alejandro M. Aragón <alejandro.aragon@epfl.ch>
# @author Aurelia Cuba Ramos <aurelia.cubaramos@epfl.ch>
#
# @date Mon Nov 21 18:19:15 2011
#
# @brief package description for PETSc support
#
# @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/>.
#
#===============================================================================
add_optional_external_package(PETSc "Add PETSc support in akantu" OFF ARGS COMPONENT ARGS CXX)
add_internal_package_dependencies(petsc parallel)
set(AKANTU_PETSC_FILES
solver/petsc_matrix.hh
solver/petsc_matrix.cc
solver/petsc_matrix_inline_impl.cc
solver/solver_petsc.hh
solver/solver_petsc.cc
+ solver/petsc_wrapper.hh
)
set(AKANTU_PETSC_TESTS
test_petsc_matrix_profile
+ test_petsc_matrix_apply_boundary
+ test_solver_petsc
)
diff --git a/src/common/aka_common.hh b/src/common/aka_common.hh
index 0f5da70bc..bb4076853 100644
--- a/src/common/aka_common.hh
+++ b/src/common/aka_common.hh
@@ -1,697 +1,699 @@
/**
* @file aka_common.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Jun 14 2010
* @date last modification: Mon Sep 15 2014
*
* @brief common type descriptions for akantu
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 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
*
* All common things to be included in the projects files
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_COMMON_HH__
#define __AKANTU_COMMON_HH__
/* -------------------------------------------------------------------------- */
#include <list>
#include <limits>
#include <boost/preprocessor.hpp>
/* -------------------------------------------------------------------------- */
#define __BEGIN_AKANTU__ namespace akantu {
#define __END_AKANTU__ };
/* -------------------------------------------------------------------------- */
#define __BEGIN_AKANTU_DUMPER__ namespace dumper {
#define __END_AKANTU_DUMPER__ }
/* -------------------------------------------------------------------------- */
#if defined(WIN32)
# define __attribute__(x)
#endif
/* -------------------------------------------------------------------------- */
#include "aka_config.hh"
#include "aka_error.hh"
#include "aka_safe_enum.hh"
/* -------------------------------------------------------------------------- */
__BEGIN_AKANTU__
/* -------------------------------------------------------------------------- */
/* Common types */
/* -------------------------------------------------------------------------- */
typedef double Real;
typedef unsigned int UInt;
typedef unsigned long long UInt64;
typedef signed int Int;
typedef std::string ID;
static const Real UINT_INIT_VALUE = 0;
#ifdef AKANTU_NDEBUG
static const Real REAL_INIT_VALUE = 0;
#else
static const Real REAL_INIT_VALUE = std::numeric_limits<Real>::quiet_NaN();
#endif
/* -------------------------------------------------------------------------- */
/* Memory types */
/* -------------------------------------------------------------------------- */
typedef UInt MemoryID;
/* -------------------------------------------------------------------------- */
/* Mesh/FEM/Model types */
/* -------------------------------------------------------------------------- */
typedef std::string Surface;
typedef std::pair<Surface, Surface> SurfacePair;
typedef std::list< SurfacePair > SurfacePairList;
/* -------------------------------------------------------------------------- */
extern const UInt _all_dimensions;
/// @boost sequence of element to loop on in global tasks
#define AKANTU_ek_regular_ELEMENT_TYPE \
(_point_1) \
(_segment_2) \
(_segment_3) \
(_triangle_3) \
(_triangle_6) \
(_quadrangle_4) \
(_quadrangle_8) \
(_tetrahedron_4) \
(_tetrahedron_10) \
(_pentahedron_6) \
(_hexahedron_8)
#if defined(AKANTU_STRUCTURAL_MECHANICS)
#define AKANTU_ek_structural_ELEMENT_TYPE \
(_bernoulli_beam_2) \
(_bernoulli_beam_3) \
(_kirchhoff_shell)
#else
#define AKANTU_ek_structural_ELEMENT_TYPE
#endif
#if defined(AKANTU_COHESIVE_ELEMENT)
# define AKANTU_ek_cohesive_ELEMENT_TYPE \
(_cohesive_2d_4) \
(_cohesive_2d_6) \
(_cohesive_1d_2) \
(_cohesive_3d_6) \
(_cohesive_3d_12)
#else
# define AKANTU_ek_cohesive_ELEMENT_TYPE
#endif
#if defined(AKANTU_IGFEM)
#define AKANTU_ek_igfem_ELEMENT_TYPE \
(_igfem_triangle_3)
#else
#define AKANTU_ek_igfem_ELEMENT_TYPE
#endif
#define AKANTU_ALL_ELEMENT_TYPE \
AKANTU_ek_regular_ELEMENT_TYPE \
AKANTU_ek_cohesive_ELEMENT_TYPE \
AKANTU_ek_structural_ELEMENT_TYPE \
AKANTU_ek_igfem_ELEMENT_TYPE
#define AKANTU_NOT_STRUCTURAL_ELEMENT_TYPE \
AKANTU_ek_regular_ELEMENT_TYPE \
AKANTU_ek_cohesive_ELEMENT_TYPE \
AKANTU_ek_igfem_ELEMENT_TYPE
/// @enum ElementType type of elements
enum ElementType {
_not_defined,
_point_1,
_segment_2, ///< first order segment
_segment_3, ///< second order segment
_triangle_3, ///< first order triangle
_triangle_6, ///< second order triangle
_tetrahedron_4, ///< first order tetrahedron
_tetrahedron_10, ///< second order tetrahedron
_quadrangle_4, ///< first order quadrangle
_quadrangle_8, ///< second order quadrangle
_hexahedron_8, ///< first order hexahedron
_pentahedron_6, ///< first order pentahedron
#if defined (AKANTU_STRUCTURAL_MECHANICS)
_bernoulli_beam_2, ///< Bernoulli beam 2D
_bernoulli_beam_3, ///< Bernoulli beam 3D
_kirchhoff_shell, ///< Kirchhoff shell
#endif
#if defined(AKANTU_COHESIVE_ELEMENT)
_cohesive_2d_4, ///< first order 2D cohesive
_cohesive_2d_6, ///< second order 2D cohesive
_cohesive_1d_2, ///< first order 1D cohesive
_cohesive_3d_6, ///< first order 3D cohesive
_cohesive_3d_12, ///< second order 3D cohesive
#endif
#if defined(AKANTU_IGFEM)
_igfem_triangle_3, ///< first order triangle for IGFEM
#endif
_max_element_type
};
/// @enum GeometricalType type of element potentially contained in a Mesh
enum GeometricalType {
_gt_point, ///< point @remark only for some algorithm to be generic like mesh partitioning */
_gt_segment_2, ///< 2 nodes segment
_gt_segment_3, ///< 3 nodes segment
_gt_triangle_3, ///< 3 nodes triangle
_gt_triangle_6, ///< 6 nodes triangle
_gt_quadrangle_4, ///< 4 nodes quadrangle
_gt_quadrangle_8, ///< 8 nodes quadrangle
_gt_tetrahedron_4, ///< 4 nodes tetrahedron
_gt_tetrahedron_10, ///< 10 nodes tetrahedron
_gt_hexahedron_8, ///< 8 nodes hexahedron
_gt_pentahedron_6, ///< 6 nodes pentahedron
#if defined(AKANTU_COHESIVE_ELEMENT)
_gt_cohesive_2d_4, ///< 4 nodes 2D cohesive
_gt_cohesive_2d_6, ///< 6 nodes 2D cohesive
_gt_cohesive_1d_2, ///< 2 nodes 1D cohesive
_gt_cohesive_3d_6, ///< 6 nodes 3D cohesive
_gt_cohesive_3d_12, ///< 12 nodes 3D cohesive
#endif
_gt_not_defined
};
/// @enum InterpolationType type of elements
enum InterpolationType {
_itp_lagrange_point_1, ///< zeroth (!) order lagrangian point (for compatibility purposes)
_itp_lagrange_segment_2, ///< first order lagrangian segment
_itp_lagrange_segment_3, ///< second order lagrangian segment
_itp_lagrange_triangle_3, ///< first order lagrangian triangle
_itp_lagrange_triangle_6, ///< second order lagrangian triangle
_itp_lagrange_quadrangle_4, ///< first order lagrangian quadrangle
_itp_serendip_quadrangle_8, /**< second order serendipian quadrangle
@remark used insted of the 9 node
lagrangian element */
_itp_lagrange_tetrahedron_4, ///< first order lagrangian tetrahedron
_itp_lagrange_tetrahedron_10, ///< second order lagrangian tetrahedron
_itp_lagrange_hexahedron_8, ///< first order lagrangian hexahedron
_itp_lagrange_pentahedron_6, ///< first order lagrangian pentahedron
#if defined(AKANTU_STRUCTURAL_MECHANICS)
_itp_bernoulli_beam, ///< Bernoulli beam
_itp_kirchhoff_shell, ///< Kirchhoff shell
#endif
_itp_not_defined
};
//! standard output stream operator for ElementType
inline std::ostream & operator <<(std::ostream & stream, ElementType type);
#define AKANTU_REGULAR_KIND (_ek_regular)
#ifdef AKANTU_COHESIVE_ELEMENT
# define AKANTU_COHESIVE_KIND (_ek_cohesive)
#else
# define AKANTU_COHESIVE_KIND
#endif
#ifdef AKANTU_STRUCTURAL_MECHANICS
# define AKANTU_STRUCTURAL_KIND (_ek_structural)
#else
# define AKANTU_STRUCTURAL_KIND
#endif
#ifdef AKANTU_IGFEM
# define AKANTU_IGFEM_KIND (_ek_igfem)
#else
# define AKANTU_IGFEM_KIND
#endif
#define AKANTU_ELEMENT_KIND \
AKANTU_REGULAR_KIND \
AKANTU_COHESIVE_KIND \
AKANTU_STRUCTURAL_KIND \
AKANTU_IGFEM_KIND
enum ElementKind {
BOOST_PP_SEQ_ENUM(AKANTU_ELEMENT_KIND),
_ek_not_defined
};
/// small help to use names for directions
enum SpacialDirection {
_x = 0,
_y = 1,
_z = 2
};
/// enum MeshIOType type of mesh reader/writer
enum MeshIOType {
_miot_auto, ///< Auto guess of the reader to use based on the extension
_miot_gmsh, ///< Gmsh files
_miot_gmsh_struct, ///< Gsmh reader with reintpretation of elements has structures elements
_miot_diana, ///< TNO Diana mesh format
_miot_abaqus ///< Abaqus mesh format
};
/// enum AnalysisMethod type of solving method used to solve the equation of motion
enum AnalysisMethod {
_static,
_implicit_dynamic,
_explicit_lumped_mass,
_explicit_lumped_capacity,
_explicit_consistent_mass
};
//! enum ContactResolutionMethod types of solving for the contact
enum ContactResolutionMethod {
_penalty,
_lagrangian,
_augmented_lagrangian,
_nitsche,
_mortar
};
//! enum ContactImplementationMethod types for different contact implementations
enum ContactImplementationMethod {
_none,
_uzawa,
_generalized_newton
};
/// enum SolveConvergenceMethod different resolution algorithms
enum SolveConvergenceMethod {
_scm_newton_raphson_tangent, ///< Newton-Raphson with tangent matrix
_scm_newton_raphson_tangent_modified, ///< Newton-Raphson with constant tangent matrix
_scm_newton_raphson_tangent_not_computed ///< Newton-Raphson with constant tangent matrix (user has to assemble it)
};
/// enum SolveConvergenceCriteria different convergence criteria
enum SolveConvergenceCriteria {
_scc_residual, ///< Use residual to test the convergence
_scc_increment, ///< Use increment to test the convergence
_scc_residual_mass_wgh ///< Use residual weighted by inv. nodal mass to testb
};
/// enum CohesiveMethod type of insertion of cohesive elements
enum CohesiveMethod {
_intrinsic,
_extrinsic
};
/// myfunction(double * position, double * stress/force, double * normal, unsigned int material_id)
typedef void (*BoundaryFunction)(double *,double *, double*, unsigned int);
/// @enum BoundaryFunctionType type of function passed for boundary conditions
enum BoundaryFunctionType {
_bft_stress,
_bft_traction,
_bft_traction_local
};
/// @enum SparseMatrixType type of sparse matrix used
enum SparseMatrixType {
_unsymmetric,
_symmetric
};
/* -------------------------------------------------------------------------- */
/* Contact */
/* -------------------------------------------------------------------------- */
typedef ID ContactID;
typedef ID ContactSearchID;
typedef ID ContactNeighborStructureID;
enum ContactType {
_ct_not_defined = 0,
_ct_2d_expli = 1,
_ct_3d_expli = 2,
_ct_rigid = 3
};
enum ContactSearchType {
_cst_not_defined = 0,
_cst_2d_expli = 1,
_cst_expli = 2
};
enum ContactNeighborStructureType {
_cnst_not_defined = 0,
_cnst_regular_grid = 1,
_cnst_2d_grid = 2
};
/* -------------------------------------------------------------------------- */
/* Friction */
/* -------------------------------------------------------------------------- */
typedef ID FrictionID;
/* -------------------------------------------------------------------------- */
/* Ghosts handling */
/* -------------------------------------------------------------------------- */
typedef ID SynchronizerID;
/// @enum CommunicatorType type of communication method to use
enum CommunicatorType {
_communicator_mpi,
_communicator_dummy
};
/// @enum SynchronizationTag type of synchronizations
enum SynchronizationTag {
//--- SolidMechanicsModel tags ---
_gst_smm_mass, //< synchronization of the SolidMechanicsModel.mass
_gst_smm_for_gradu, //< synchronization of the SolidMechanicsModel.displacement
_gst_smm_boundary, //< synchronization of the boundary, forces, velocities and displacement
_gst_smm_uv, //< synchronization of the nodal velocities and displacement
_gst_smm_res, //< synchronization of the nodal residual
_gst_smm_init_mat, //< synchronization of the data to initialize materials
_gst_smm_stress, //< synchronization of the stresses to compute the internal forces
_gst_smmc_facets, //< synchronization of facet data to setup facet synch
_gst_smmc_facets_conn, //< synchronization of facet global connectivity
_gst_smmc_facets_stress, //< synchronization of facets' stress to setup facet synch
_gst_smmc_damage, //< synchronization of damage
//--- CohesiveElementInserter tags ---
_gst_ce_inserter, //< synchronization of global nodes id of newly inserted cohesive elements
//--- GroupManager tags ---
_gst_gm_clusters, //< synchronization of clusters
//--- HeatTransfer tags ---
_gst_htm_capacity, //< synchronization of the nodal heat capacity
_gst_htm_temperature, //< synchronization of the nodal temperature
_gst_htm_gradient_temperature, //< synchronization of the element gradient temperature
//--- LevelSet tags ---
/// synchronization of the nodal level set value phi
_gst_htm_phi,
/// synchronization of the element gradient phi
_gst_htm_gradient_phi,
//--- Material non local ---
_gst_mnl_for_average, //< synchronization of data to average in non local material
_gst_mnl_weight, //< synchronization of data for the weight computations
//--- General tags ---
_gst_test, //< Test tag
_gst_material_id, //< synchronization of the material ids
_gst_for_dump, //< everything that needs to be synch before dump
//--- Contact & Friction ---
_gst_cf_nodal, //< synchronization of disp, velo, and current position
- _gst_cf_incr //< synchronization of increment
+ _gst_cf_incr, //< synchronization of increment
+ ///--- Solver tags ---
+ _gst_solver_solution //< synchronization of the solution obained with the PETSc solver
};
/// standard output stream operator for SynchronizationTag
inline std::ostream & operator <<(std::ostream & stream, SynchronizationTag type);
/// @enum GhostType type of ghost
enum GhostType {
_not_ghost,
_ghost,
_casper // not used but a real cute ghost
};
/* -------------------------------------------------------------------------- */
struct GhostType_def {
typedef GhostType type;
static const type _begin_ = _not_ghost;
static const type _end_ = _casper;
};
typedef safe_enum<GhostType_def> ghost_type_t;
/// standard output stream operator for GhostType
inline std::ostream & operator <<(std::ostream & stream, GhostType type);
/// @enum SynchronizerOperation reduce operation that the synchronizer can perform
enum SynchronizerOperation {
_so_sum,
_so_min,
_so_max,
_so_null
};
/* -------------------------------------------------------------------------- */
/* Global defines */
/* -------------------------------------------------------------------------- */
#define AKANTU_MIN_ALLOCATION 2000
#define AKANTU_INDENT " "
#define AKANTU_INCLUDE_INLINE_IMPL
/* -------------------------------------------------------------------------- */
// int 2 type construct
template <int d>
struct Int2Type {
enum { result = d };
};
// type 2 type construct
template <class T>
class Type2Type {
typedef T OriginalType;
};
/* -------------------------------------------------------------------------- */
template<class T>
struct is_scalar {
enum{ value = false };
};
#define AKANTU_SPECIFY_IS_SCALAR(type) \
template<> \
struct is_scalar<type> { \
enum { value = true }; \
}
AKANTU_SPECIFY_IS_SCALAR(Real);
AKANTU_SPECIFY_IS_SCALAR(UInt);
AKANTU_SPECIFY_IS_SCALAR(Int);
AKANTU_SPECIFY_IS_SCALAR(bool);
template < typename T1, typename T2 >
struct is_same {
enum { value = false }; // is_same represents a bool.
};
template < typename T >
struct is_same<T, T> {
enum { value = true };
};
/* -------------------------------------------------------------------------- */
#define AKANTU_SET_MACRO(name, variable, type) \
inline void set##name (type variable) { \
this->variable = variable; \
}
#define AKANTU_GET_MACRO(name, variable, type) \
inline type get##name () const { \
return variable; \
}
#define AKANTU_GET_MACRO_NOT_CONST(name, variable, type) \
inline type get##name () { \
return variable; \
}
#define AKANTU_GET_MACRO_BY_SUPPORT_TYPE(name, variable, type, \
support, con) \
inline con Array<type> & \
get##name (const support & el_type, \
const GhostType & ghost_type = _not_ghost) con { \
return variable(el_type, ghost_type); \
}
#define AKANTU_GET_MACRO_BY_ELEMENT_TYPE(name, variable, type) \
AKANTU_GET_MACRO_BY_SUPPORT_TYPE(name, variable, type, ElementType,)
#define AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(name, variable, type) \
AKANTU_GET_MACRO_BY_SUPPORT_TYPE(name, variable, type, ElementType, const)
#define AKANTU_GET_MACRO_BY_GEOMETRIE_TYPE(name, variable, type) \
AKANTU_GET_MACRO_BY_SUPPORT_TYPE(name, variable, type, GeometricalType,)
#define AKANTU_GET_MACRO_BY_GEOMETRIE_TYPE_CONST(name, variable, type) \
AKANTU_GET_MACRO_BY_SUPPORT_TYPE(name, variable, type, GeometricalType, const)
/* -------------------------------------------------------------------------- */
/// initialize the static part of akantu
void initialize(int & argc, char ** & argv);
/// initialize the static part of akantu and read the global input_file
void initialize(const std::string & input_file, int & argc, char ** & argv);
/* -------------------------------------------------------------------------- */
/// finilize correctly akantu and clean the memory
void finalize ();
/* -------------------------------------------------------------------------- */
/*
* For intel compiler annoying remark
*/
#if defined(__INTEL_COMPILER)
/// remark #981: operands are evaluated in unspecified order
#pragma warning ( disable : 981 )
/// remark #383: value copied to temporary, reference to temporary used
#pragma warning ( disable : 383 )
#endif //defined(__INTEL_COMPILER)
/* -------------------------------------------------------------------------- */
/* string manipulation */
/* -------------------------------------------------------------------------- */
inline std::string to_lower(const std::string & str);
/* -------------------------------------------------------------------------- */
inline std::string trim(const std::string & to_trim);
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
/// give a string representation of the a human readable size in bit
template<typename T>
std::string printMemorySize(UInt size);
/* -------------------------------------------------------------------------- */
__END_AKANTU__
#include "aka_fwd.hh"
__BEGIN_AKANTU__
/// get access to the internal argument parser
cppargparse::ArgumentParser & getStaticArgumentParser();
/// get access to the internal input file parser
Parser & getStaticParser();
/// get access to the user part of the internal input file parser
const ParserSection & getUserParser();
__END_AKANTU__
/* -------------------------------------------------------------------------- */
// BOOST PART: TOUCH ONLY IF YOU KNOW WHAT YOU ARE DOING
#define AKANTU_BOOST_CASE_MACRO(r,macro,type) \
case type : { macro(type); break; }
#define AKANTU_BOOST_LIST_SWITCH(macro1, list1, var) \
do { \
switch(var) { \
BOOST_PP_SEQ_FOR_EACH(AKANTU_BOOST_CASE_MACRO, macro1, list1) \
default: { \
AKANTU_DEBUG_ERROR("Type (" << var << ") not handled by this function"); \
} \
} \
} while(0)
#define AKANTU_BOOST_ELEMENT_SWITCH(macro1, list1) \
AKANTU_BOOST_LIST_SWITCH(macro1, list1, type)
#define AKANTU_BOOST_ALL_ELEMENT_SWITCH(macro) \
AKANTU_BOOST_ELEMENT_SWITCH(macro, \
AKANTU_ALL_ELEMENT_TYPE)
#define AKANTU_BOOST_REGULAR_ELEMENT_SWITCH(macro) \
AKANTU_BOOST_ELEMENT_SWITCH(macro, \
AKANTU_ek_regular_ELEMENT_TYPE)
#define AKANTU_BOOST_COHESIVE_ELEMENT_SWITCH(macro) \
AKANTU_BOOST_ELEMENT_SWITCH(macro, \
AKANTU_ek_cohesive_ELEMENT_TYPE)
#define AKANTU_BOOST_STRUCTURAL_ELEMENT_SWITCH(macro) \
AKANTU_BOOST_ELEMENT_SWITCH(macro, \
AKANTU_ek_structural_ELEMENT_TYPE)
#define AKANTU_BOOST_IGFEM_ELEMENT_SWITCH(macro) \
AKANTU_BOOST_ELEMENT_SWITCH(macro, \
AKANTU_ek_igfem_ELEMENT_TYPE)
#define AKANTU_BOOST_LIST_MACRO(r, macro, type) \
macro(type)
#define AKANTU_BOOST_APPLY_ON_LIST(macro, list) \
BOOST_PP_SEQ_FOR_EACH(AKANTU_BOOST_LIST_MACRO, macro, list)
#define AKANTU_BOOST_ALL_ELEMENT_LIST(macro) \
AKANTU_BOOST_APPLY_ON_LIST(macro, \
AKANTU_ALL_ELEMENT_TYPE)
#define AKANTU_BOOST_REGULAR_ELEMENT_LIST(macro) \
AKANTU_BOOST_APPLY_ON_LIST(macro, \
AKANTU_ek_regular_ELEMENT_TYPE)
#define AKANTU_BOOST_STRUCTURAL_ELEMENT_LIST(macro) \
AKANTU_BOOST_APPLY_ON_LIST(macro, \
AKANTU_ek_structural_ELEMENT_TYPE)
#define AKANTU_BOOST_COHESIVE_ELEMENT_LIST(macro) \
AKANTU_BOOST_APPLY_ON_LIST(macro, \
AKANTU_ek_cohesive_ELEMENT_TYPE)
#define AKANTU_BOOST_IGFEM_ELEMENT_LIST(macro) \
AKANTU_BOOST_APPLY_ON_LIST(macro, \
AKANTU_ek_igfem_ELEMENT_TYPE)
#define AKANTU_GET_ELEMENT_LIST(kind) \
AKANTU##kind##_ELEMENT_TYPE
#define AKANTU_BOOST_KIND_ELEMENT_SWITCH(macro, kind) \
AKANTU_BOOST_ELEMENT_SWITCH(macro, \
AKANTU_GET_ELEMENT_LIST(kind))
// BOOST_PP_SEQ_TO_LIST does not exists in Boost < 1.49
#define AKANTU_GENERATE_KIND_LIST(seq) \
BOOST_PP_TUPLE_TO_LIST(BOOST_PP_SEQ_SIZE(seq), \
BOOST_PP_SEQ_TO_TUPLE(seq))
#define AKANTU_ELEMENT_KIND_BOOST_LIST AKANTU_GENERATE_KIND_LIST(AKANTU_ELEMENT_KIND)
#define AKANTU_BOOST_ALL_KIND_LIST(macro, list) \
BOOST_PP_LIST_FOR_EACH(AKANTU_BOOST_LIST_MACRO, macro, list)
#define AKANTU_BOOST_ALL_KIND(macro) \
AKANTU_BOOST_ALL_KIND_LIST(macro, AKANTU_ELEMENT_KIND_BOOST_LIST)
#define AKANTU_BOOST_ALL_KIND_SWITCH(macro) \
AKANTU_BOOST_LIST_SWITCH(macro, \
AKANTU_ELEMENT_KIND, \
kind)
/// define kept for compatibility reasons (they are most probably not needed
/// anymore) \todo check if they can be removed
#define AKANTU_REGULAR_ELEMENT_TYPE AKANTU_ek_regular_ELEMENT_TYPE
#define AKANTU_COHESIVE_ELEMENT_TYPE AKANTU_ek_cohesive_ELEMENT_TYPE
#define AKANTU_STRUCTURAL_ELEMENT_TYPE AKANTU_ek_structural_ELEMENT_TYPE
#define AKANTU_IGFEM_ELEMENT_TYPE AKANTU_ek_igfem_ELEMENT_TYPE
#include "aka_common_inline_impl.cc"
#endif /* __AKANTU_COMMON_HH__ */
diff --git a/src/common/aka_common_inline_impl.cc b/src/common/aka_common_inline_impl.cc
index 98f333536..f7da7198f 100644
--- a/src/common/aka_common_inline_impl.cc
+++ b/src/common/aka_common_inline_impl.cc
@@ -1,233 +1,234 @@
/**
* @file aka_common_inline_impl.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Dec 01 2011
* @date last modification: Wed Jul 23 2014
*
* @brief inline implementations of common akantu type descriptions
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 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
*
* All common things to be included in the projects files
*
*/
#include <algorithm>
#include <iomanip>
#include <cctype>
__BEGIN_AKANTU__
/* -------------------------------------------------------------------------- */
//! standard output stream operator for ElementType
inline std::ostream & operator <<(std::ostream & stream, ElementType type)
{
#define STRINGIFY(type) \
stream << BOOST_PP_STRINGIZE(type)
switch(type) {
BOOST_PP_SEQ_FOR_EACH(AKANTU_BOOST_CASE_MACRO, \
STRINGIFY, \
AKANTU_ALL_ELEMENT_TYPE)
case _not_defined: stream << "_not_defined"; break;
case _max_element_type: stream << "_max_element_type"; break;
}
#undef STRINGIFY
return stream;
}
/* -------------------------------------------------------------------------- */
//! standard output stream operator for ElementType
inline std::ostream & operator <<(std::ostream & stream, ElementKind kind )
{
#define STRINGIFY(kind) \
stream << BOOST_PP_STRINGIZE(kind)
AKANTU_BOOST_ALL_KIND_SWITCH(STRINGIFY);
#undef STRINGIFY
return stream;
}
/* -------------------------------------------------------------------------- */
/// standard output stream operator for InterpolationType
inline std::ostream & operator <<(std::ostream & stream, InterpolationType type)
{
switch(type)
{
case _itp_lagrange_point_1 : stream << "_itp_lagrange_point_1" ; break;
case _itp_lagrange_segment_2 : stream << "_itp_lagrange_segment_2" ; break;
case _itp_lagrange_segment_3 : stream << "_itp_lagrange_segment_3" ; break;
case _itp_lagrange_triangle_3 : stream << "_itp_lagrange_triangle_3" ; break;
case _itp_lagrange_triangle_6 : stream << "_itp_lagrange_triangle_6" ; break;
case _itp_lagrange_quadrangle_4 : stream << "_itp_lagrange_quadrangle_4" ; break;
case _itp_serendip_quadrangle_8 : stream << "_itp_serendip_quadrangle_8" ; break;
case _itp_lagrange_tetrahedron_4 : stream << "_itp_lagrange_tetrahedron_4" ; break;
case _itp_lagrange_tetrahedron_10 : stream << "_itp_lagrange_tetrahedron_10"; break;
case _itp_lagrange_hexahedron_8 : stream << "_itp_lagrange_hexahedron_8" ; break;
case _itp_lagrange_pentahedron_6 : stream << "_itp_lagrange_pentahedron_6" ; break;
#if defined(AKANTU_STRUCTURAL_MECHANICS)
case _itp_bernoulli_beam : stream << "_itp_bernoulli_beam" ; break;
case _itp_kirchhoff_shell : stream << "_itp_kirchhoff_shell" ; break;
#endif
case _itp_not_defined : stream << "_itp_not_defined" ; break;
}
return stream;
}
/* -------------------------------------------------------------------------- */
/// standard output stream operator for GhostType
inline std::ostream & operator <<(std::ostream & stream, GhostType type)
{
switch(type)
{
case _not_ghost : stream << "not_ghost"; break;
case _ghost : stream << "ghost" ; break;
case _casper : stream << "Casper the friendly ghost"; break;
}
return stream;
}
/* -------------------------------------------------------------------------- */
/// standard output stream operator for SynchronizationTag
inline std::ostream & operator <<(std::ostream & stream, SynchronizationTag type)
{
switch(type)
{
case _gst_smm_mass : stream << "_gst_smm_mass" ; break;
case _gst_smm_for_gradu : stream << "_gst_smm_for_gradu" ; break;
case _gst_smm_boundary : stream << "_gst_smm_boundary" ; break;
case _gst_smm_uv : stream << "_gst_smm_uv" ; break;
case _gst_smm_res : stream << "_gst_smm_res" ; break;
case _gst_smm_init_mat : stream << "_gst_smm_init_mat" ; break;
case _gst_smm_stress : stream << "_gst_smm_stress" ; break;
case _gst_smmc_facets : stream << "_gst_smmc_facets" ; break;
case _gst_smmc_facets_conn : stream << "_gst_smmc_facets_conn" ; break;
case _gst_smmc_facets_stress : stream << "_gst_smmc_facets_stress" ; break;
case _gst_smmc_damage : stream << "_gst_smmc_damage" ; break;
case _gst_ce_inserter : stream << "_gst_ce_inserter" ; break;
case _gst_gm_clusters : stream << "_gst_gm_clusters" ; break;
case _gst_htm_capacity : stream << "_gst_htm_capacity" ; break;
case _gst_htm_temperature : stream << "_gst_htm_temperature" ; break;
case _gst_htm_gradient_temperature : stream << "_gst_htm_gradient_temperature"; break;
case _gst_htm_phi : stream << "_gst_htm_phi" ; break;
case _gst_htm_gradient_phi : stream << "_gst_htm_gradient_phi" ; break;
case _gst_mnl_for_average : stream << "_gst_mnl_for_average" ; break;
case _gst_mnl_weight : stream << "_gst_mnl_weight" ; break;
case _gst_test : stream << "_gst_test" ; break;
case _gst_material_id : stream << "_gst_material_id" ; break;
case _gst_for_dump : stream << "_gst_for_dump" ; break;
case _gst_cf_nodal : stream << "_gst_cf_nodal" ; break;
case _gst_cf_incr : stream << "_gst_cf_incr" ; break;
+ case _gst_solver_solution : stream << "_gst_solver_solution" ; break;
}
return stream;
}
/* -------------------------------------------------------------------------- */
/// standard output stream operator for SolveConvergenceCriteria
inline std::ostream & operator <<(std::ostream & stream, SolveConvergenceCriteria criteria)
{
switch(criteria) {
case _scc_residual : stream << "_scc_residual" ; break;
case _scc_increment: stream << "_scc_increment"; break;
case _scc_residual_mass_wgh: stream << "_scc_residual_mass_wgh"; break;
}
return stream;
}
/* -------------------------------------------------------------------------- */
inline std::string to_lower(const std::string & str) {
std::string lstr = str;
std::transform(lstr.begin(),
lstr.end(),
lstr.begin(),
(int(*)(int))tolower);
return lstr;
}
/* -------------------------------------------------------------------------- */
inline std::string trim(const std::string & to_trim) {
std::string trimed = to_trim;
//left trim
trimed.erase(trimed.begin(),
std::find_if(trimed.begin(),
trimed.end(),
std::not1(std::ptr_fun<int, int>(isspace))));
// right trim
trimed.erase(std::find_if(trimed.rbegin(),
trimed.rend(),
std::not1(std::ptr_fun<int, int>(isspace))).base(),
trimed.end());
return trimed;
}
__END_AKANTU__
#include <cmath>
__BEGIN_AKANTU__
/* -------------------------------------------------------------------------- */
template<typename T>
std::string printMemorySize(UInt size) {
Real real_size = size * sizeof(T);
UInt mult = (std::log(real_size) / std::log(2)) / 10;
std::stringstream sstr;
real_size /= Real(1 << (10 * mult));
sstr << std::setprecision(2) << std::fixed << real_size;
std::string size_prefix;
switch(mult) {
case 0: sstr << ""; break;
case 1: sstr << "Ki"; break;
case 2: sstr << "Mi"; break;
case 3: sstr << "Gi"; break; // I started on this type of machines
// (32bit computers) (Nicolas)
case 4: sstr << "Ti"; break;
case 5: sstr << "Pi"; break;
case 6: sstr << "Ei"; break; // theoritical limit of RAM of the current
// computers in 2014 (64bit computers) (Nicolas)
case 7: sstr << "Zi"; break;
case 8: sstr << "Yi"; break;
default:
AKANTU_DEBUG_ERROR("The programmer in 2014 didn't thought so far (even wikipedia does not go further)."
<< " You have at least 1024 times more than a yobibit of RAM!!!"
<< " Just add the prefix corresponding in this switch case.");
}
sstr << "Byte";
return sstr.str();
}
__END_AKANTU__
diff --git a/src/model/solid_mechanics/solid_mechanics_model.cc b/src/model/solid_mechanics/solid_mechanics_model.cc
index ce40bc72f..f25f0280f 100644
--- a/src/model/solid_mechanics/solid_mechanics_model.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model.cc
@@ -1,1830 +1,1840 @@
/**
* @file solid_mechanics_model.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Jul 27 2010
* @date last modification: Fri Sep 19 2014
*
* @brief Implementation of the SolidMechanicsModel class
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 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_math.hh"
#include "aka_common.hh"
#include "solid_mechanics_model.hh"
#include "group_manager_inline_impl.cc"
#include "dumpable_inline_impl.hh"
#include "integration_scheme_2nd_order.hh"
#include "element_group.hh"
#include "static_communicator.hh"
#include "dof_synchronizer.hh"
#include "element_group.hh"
#include <cmath>
#ifdef AKANTU_USE_MUMPS
#include "solver_mumps.hh"
#endif
#ifdef AKANTU_USE_IOHELPER
# include "dumper_field.hh"
# include "dumper_paraview.hh"
# include "dumper_homogenizing_field.hh"
# include "dumper_material_internal_field.hh"
# include "dumper_elemental_field.hh"
# include "dumper_material_padders.hh"
# include "dumper_element_partition.hh"
# include "dumper_iohelper.hh"
#endif
/* -------------------------------------------------------------------------- */
__BEGIN_AKANTU__
const SolidMechanicsModelOptions default_solid_mechanics_model_options(_explicit_lumped_mass, false);
/* -------------------------------------------------------------------------- */
/**
* A solid mechanics model need a mesh and a dimension to be created. the model
* by it self can not do a lot, the good init functions should be called in
* order to configure the model depending on what we want to do.
*
* @param mesh mesh representing the model we want to simulate
* @param dim spatial dimension of the problem, if dim = 0 (default value) the
* dimension of the problem is assumed to be the on of the mesh
* @param id an id to identify the model
*/
SolidMechanicsModel::SolidMechanicsModel(Mesh & mesh,
UInt dim,
const ID & id,
const MemoryID & memory_id) :
Model(mesh, dim, id, memory_id),
BoundaryCondition<SolidMechanicsModel>(),
time_step(NAN), f_m2a(1.0),
mass_matrix(NULL),
velocity_damping_matrix(NULL),
stiffness_matrix(NULL),
jacobian_matrix(NULL),
element_index_by_material("element index by material", id),
material_selector(new DefaultMaterialSelector(element_index_by_material)),
is_default_material_selector(true),
integrator(NULL),
increment_flag(false), solver(NULL),
synch_parallel(NULL),
are_materials_instantiated(false) {
AKANTU_DEBUG_IN();
createSynchronizerRegistry(this);
registerFEEngineObject<MyFEEngineType>("SolidMechanicsFEEngine", mesh, spatial_dimension);
this->displacement = NULL;
this->mass = NULL;
this->velocity = NULL;
this->acceleration = NULL;
this->force = NULL;
this->residual = NULL;
this->blocked_dofs = NULL;
this->increment = NULL;
this->increment_acceleration = NULL;
this->dof_synchronizer = NULL;
this->previous_displacement = NULL;
materials.clear();
mesh.registerEventHandler(*this);
#if defined(AKANTU_USE_IOHELPER)
this->mesh.registerDumper<DumperParaview>("paraview_all", id, true);
this->mesh.addDumpMesh(mesh, spatial_dimension, _not_ghost, _ek_regular);
#endif
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
SolidMechanicsModel::~SolidMechanicsModel() {
AKANTU_DEBUG_IN();
std::vector<Material *>::iterator mat_it;
for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
delete *mat_it;
}
materials.clear();
delete integrator;
delete solver;
delete mass_matrix;
delete velocity_damping_matrix;
if(stiffness_matrix && stiffness_matrix != jacobian_matrix)
delete stiffness_matrix;
delete jacobian_matrix;
delete synch_parallel;
if(is_default_material_selector) {
delete material_selector;
material_selector = NULL;
}
AKANTU_DEBUG_OUT();
}
void SolidMechanicsModel::setTimeStep(Real time_step) {
this->time_step = time_step;
#if defined(AKANTU_USE_IOHELPER)
this->mesh.getDumper().setTimeStep(time_step);
#endif
}
/* -------------------------------------------------------------------------- */
/* Initialisation */
/* -------------------------------------------------------------------------- */
/**
* This function groups many of the initialization in on function. For most of
* basics case the function should be enough. The functions initialize the
* model, the internal vectors, set them to 0, and depending on the parameters
* it also initialize the explicit or implicit solver.
*
* @param material_file the file containing the materials to use
* @param method the analysis method wanted. See the akantu::AnalysisMethod for
* the different possibilities
*/
void SolidMechanicsModel::initFull(const ModelOptions & options) {
Model::initFull(options);
const SolidMechanicsModelOptions & smm_options =
dynamic_cast<const SolidMechanicsModelOptions &>(options);
method = smm_options.analysis_method;
// initialize the vectors
initArrays();
// set the initial condition to 0
force->clear();
velocity->clear();
acceleration->clear();
displacement->clear();
// initialize pcb
if(pbc_pair.size()!=0)
initPBC();
// initialize the time integration schemes
switch(method) {
case _explicit_lumped_mass:
initExplicit();
break;
case _explicit_consistent_mass:
initSolver();
initExplicit();
break;
case _implicit_dynamic:
initImplicit(true);
break;
case _static:
initImplicit(false);
break;
default:
AKANTU_EXCEPTION("analysis method not recognised by SolidMechanicsModel");
break;
}
// initialize the materials
if(this->parser->getLastParsedFile() != "") {
instantiateMaterials();
}
if(!smm_options.no_init_materials) {
initMaterials();
}
if(increment_flag)
initBC(*this, *displacement, *increment, *force);
else
initBC(*this, *displacement, *force);
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::initParallel(MeshPartition * partition,
DataAccessor * data_accessor) {
AKANTU_DEBUG_IN();
if (data_accessor == NULL) data_accessor = this;
synch_parallel = &createParallelSynch(partition,data_accessor);
synch_registry->registerSynchronizer(*synch_parallel, _gst_material_id);
synch_registry->registerSynchronizer(*synch_parallel, _gst_smm_mass);
synch_registry->registerSynchronizer(*synch_parallel, _gst_smm_stress);
synch_registry->registerSynchronizer(*synch_parallel, _gst_smm_boundary);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::initFEEngineBoundary() {
FEEngine & fem_boundary = getFEEngineBoundary();
fem_boundary.initShapeFunctions(_not_ghost);
fem_boundary.initShapeFunctions(_ghost);
fem_boundary.computeNormalsOnControlPoints(_not_ghost);
fem_boundary.computeNormalsOnControlPoints(_ghost);
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::initExplicit(AnalysisMethod analysis_method) {
AKANTU_DEBUG_IN();
//in case of switch from implicit to explicit
if(!this->isExplicit())
method = analysis_method;
if (integrator) delete integrator;
integrator = new CentralDifference();
UInt nb_nodes = acceleration->getSize();
UInt nb_degree_of_freedom = acceleration->getNbComponent();
std::stringstream sstr; sstr << id << ":increment_acceleration";
increment_acceleration = &(alloc<Real>(sstr.str(), nb_nodes, nb_degree_of_freedom, Real()));
AKANTU_DEBUG_OUT();
}
void SolidMechanicsModel::initArraysPreviousDisplacment() {
AKANTU_DEBUG_IN();
SolidMechanicsModel::setIncrementFlagOn();
UInt nb_nodes = mesh.getNbNodes();
std::stringstream sstr_disp_t;
sstr_disp_t << id << ":previous_displacement";
previous_displacement = &(alloc<Real > (sstr_disp_t.str(), nb_nodes, spatial_dimension, 0.));
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Allocate all the needed vectors. By default their are not necessarily set to
* 0
*
*/
void SolidMechanicsModel::initArrays() {
AKANTU_DEBUG_IN();
UInt nb_nodes = mesh.getNbNodes();
std::stringstream sstr_disp; sstr_disp << id << ":displacement";
// std::stringstream sstr_mass; sstr_mass << id << ":mass";
std::stringstream sstr_velo; sstr_velo << id << ":velocity";
std::stringstream sstr_acce; sstr_acce << id << ":acceleration";
std::stringstream sstr_forc; sstr_forc << id << ":force";
std::stringstream sstr_resi; sstr_resi << id << ":residual";
std::stringstream sstr_boun; sstr_boun << id << ":blocked_dofs";
displacement = &(alloc<Real>(sstr_disp.str(), nb_nodes, spatial_dimension, REAL_INIT_VALUE));
// mass = &(alloc<Real>(sstr_mass.str(), nb_nodes, spatial_dimension, 0));
velocity = &(alloc<Real>(sstr_velo.str(), nb_nodes, spatial_dimension, REAL_INIT_VALUE));
acceleration = &(alloc<Real>(sstr_acce.str(), nb_nodes, spatial_dimension, REAL_INIT_VALUE));
force = &(alloc<Real>(sstr_forc.str(), nb_nodes, spatial_dimension, REAL_INIT_VALUE));
residual = &(alloc<Real>(sstr_resi.str(), nb_nodes, spatial_dimension, REAL_INIT_VALUE));
blocked_dofs = &(alloc<bool>(sstr_boun.str(), nb_nodes, spatial_dimension, false));
std::stringstream sstr_curp; sstr_curp << id << ":current_position";
current_position = &(alloc<Real>(sstr_curp.str(), 0, spatial_dimension, REAL_INIT_VALUE));
for(UInt g = _not_ghost; g <= _ghost; ++g) {
GhostType gt = (GhostType) g;
Mesh::type_iterator it = mesh.firstType(spatial_dimension, gt, _ek_not_defined);
Mesh::type_iterator end = mesh.lastType(spatial_dimension, gt, _ek_not_defined);
for(; it != end; ++it) {
UInt nb_element = mesh.getNbElement(*it, gt);
element_index_by_material.alloc(nb_element, 2, *it, gt);
}
}
dof_synchronizer = new DOFSynchronizer(mesh, spatial_dimension);
dof_synchronizer->initLocalDOFEquationNumbers();
dof_synchronizer->initGlobalDOFEquationNumbers();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Initialize the model,basically it pre-compute the shapes, shapes derivatives
* and jacobian
*
*/
void SolidMechanicsModel::initModel() {
/// \todo add the current position as a parameter to initShapeFunctions for
/// large deformation
getFEEngine().initShapeFunctions(_not_ghost);
getFEEngine().initShapeFunctions(_ghost);
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::initPBC() {
Model::initPBC();
registerPBCSynchronizer();
// as long as there are ones on the diagonal of the matrix, we can put boudandary true for slaves
std::map<UInt, UInt>::iterator it = pbc_pair.begin();
std::map<UInt, UInt>::iterator end = pbc_pair.end();
UInt dim = mesh.getSpatialDimension();
while(it != end) {
for (UInt i=0; i<dim; ++i)
(*blocked_dofs)((*it).first,i) = true;
++it;
}
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::registerPBCSynchronizer(){
PBCSynchronizer * synch = new PBCSynchronizer(pbc_pair);
synch_registry->registerSynchronizer(*synch, _gst_smm_uv);
synch_registry->registerSynchronizer(*synch, _gst_smm_mass);
synch_registry->registerSynchronizer(*synch, _gst_smm_res);
synch_registry->registerSynchronizer(*synch, _gst_for_dump);
changeLocalEquationNumberForPBC(pbc_pair, mesh.getSpatialDimension());
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::updateCurrentPosition() {
AKANTU_DEBUG_IN();
UInt nb_nodes = mesh.getNbNodes();
current_position->resize(nb_nodes);
Real * current_position_val = current_position->storage();
Real * position_val = mesh.getNodes().storage();
Real * displacement_val = displacement->storage();
/// compute current_position = initial_position + displacement
memcpy(current_position_val, position_val, nb_nodes*spatial_dimension*sizeof(Real));
for (UInt n = 0; n < nb_nodes*spatial_dimension; ++n) {
*current_position_val++ += *displacement_val++;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::initializeUpdateResidualData() {
AKANTU_DEBUG_IN();
UInt nb_nodes = mesh.getNbNodes();
residual->resize(nb_nodes);
/// copy the forces in residual for boundary conditions
memcpy(residual->storage(), force->storage(), nb_nodes*spatial_dimension*sizeof(Real));
// start synchronization
synch_registry->asynchronousSynchronize(_gst_smm_uv);
synch_registry->waitEndSynchronize(_gst_smm_uv);
updateCurrentPosition();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/* Explicit scheme */
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
/**
* This function compute the second member of the motion equation. That is to
* say the sum of forces @f$ r = F_{ext} - F_{int} @f$. @f$ F_{ext} @f$ is given
* by the user in the force vector, and @f$ F_{int} @f$ is computed as @f$
* F_{int} = \int_{\Omega} N \sigma d\Omega@f$
*
*/
void SolidMechanicsModel::updateResidual(bool need_initialize) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_INFO("Assemble the internal forces");
// f = f_ext - f_int
// f = f_ext
if(need_initialize) initializeUpdateResidualData();
AKANTU_DEBUG_INFO("Compute local stresses");
std::vector<Material *>::iterator mat_it;
for (mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
Material & mat = **mat_it;
mat.computeAllStresses(_not_ghost);
}
#ifdef AKANTU_DAMAGE_NON_LOCAL
/* ------------------------------------------------------------------------ */
/* Computation of the non local part */
synch_registry->asynchronousSynchronize(_gst_mnl_for_average);
AKANTU_DEBUG_INFO("Compute non local stresses for local elements");
for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
Material & mat = **mat_it;
mat.computeAllNonLocalStresses(_not_ghost);
}
AKANTU_DEBUG_INFO("Wait distant non local stresses");
synch_registry->waitEndSynchronize(_gst_mnl_for_average);
AKANTU_DEBUG_INFO("Compute non local stresses for ghosts elements");
for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
Material & mat = **mat_it;
mat.computeAllNonLocalStresses(_ghost);
}
#endif
/* ------------------------------------------------------------------------ */
/* assembling the forces internal */
// communicate the stress
AKANTU_DEBUG_INFO("Send data for residual assembly");
synch_registry->asynchronousSynchronize(_gst_smm_stress);
AKANTU_DEBUG_INFO("Assemble residual for local elements");
for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
Material & mat = **mat_it;
mat.assembleResidual(_not_ghost);
}
AKANTU_DEBUG_INFO("Wait distant stresses");
// finalize communications
synch_registry->waitEndSynchronize(_gst_smm_stress);
AKANTU_DEBUG_INFO("Assemble residual for ghost elements");
for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
Material & mat = **mat_it;
mat.assembleResidual(_ghost);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::computeStresses() {
if (isExplicit()) {
// start synchronization
synch_registry->asynchronousSynchronize(_gst_smm_uv);
synch_registry->waitEndSynchronize(_gst_smm_uv);
// compute stresses on all local elements for each materials
std::vector<Material *>::iterator mat_it;
for (mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
Material & mat = **mat_it;
mat.computeAllStresses(_not_ghost);
}
/* ------------------------------------------------------------------------ */
#ifdef AKANTU_DAMAGE_NON_LOCAL
/* Computation of the non local part */
synch_registry->asynchronousSynchronize(_gst_mnl_for_average);
for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
Material & mat = **mat_it;
mat.computeAllNonLocalStresses(_not_ghost);
}
synch_registry->waitEndSynchronize(_gst_mnl_for_average);
for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
Material & mat = **mat_it;
mat.computeAllNonLocalStresses(_ghost);
}
#endif
} else {
std::vector<Material *>::iterator mat_it;
for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
Material & mat = **mat_it;
mat.computeAllStressesFromTangentModuli(_not_ghost);
}
}
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::updateResidualInternal() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_INFO("Update the residual");
// f = f_ext - f_int - Ma - Cv = r - Ma - Cv;
if(method != _static) {
// f -= Ma
if(mass_matrix) {
// if full mass_matrix
Array<Real> * Ma = new Array<Real>(*acceleration, true, "Ma");
*Ma *= *mass_matrix;
/// \todo check unit conversion for implicit dynamics
// *Ma /= f_m2a
*residual -= *Ma;
delete Ma;
} else if (mass) {
// else lumped mass
UInt nb_nodes = acceleration->getSize();
UInt nb_degree_of_freedom = acceleration->getNbComponent();
Real * mass_val = mass->storage();
Real * accel_val = acceleration->storage();
Real * res_val = residual->storage();
bool * blocked_dofs_val = blocked_dofs->storage();
for (UInt n = 0; n < nb_nodes * nb_degree_of_freedom; ++n) {
if(!(*blocked_dofs_val)) {
*res_val -= *accel_val * *mass_val /f_m2a;
}
blocked_dofs_val++;
res_val++;
mass_val++;
accel_val++;
}
} else {
AKANTU_DEBUG_ERROR("No function called to assemble the mass matrix.");
}
// f -= Cv
if(velocity_damping_matrix) {
Array<Real> * Cv = new Array<Real>(*velocity);
*Cv *= *velocity_damping_matrix;
*residual -= *Cv;
delete Cv;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::updateAcceleration() {
AKANTU_DEBUG_IN();
updateResidualInternal();
if(method == _explicit_lumped_mass) {
/* residual = residual_{n+1} - M * acceleration_n therefore
solution = increment acceleration not acceleration */
solveLumped(*increment_acceleration,
*mass,
*residual,
*blocked_dofs,
f_m2a);
} else if (method == _explicit_consistent_mass) {
solve<NewmarkBeta::_acceleration_corrector>(*increment_acceleration);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::solveLumped(Array<Real> & x,
const Array<Real> & A,
const Array<Real> & b,
const Array<bool> & blocked_dofs,
Real alpha) {
Real * A_val = A.storage();
Real * b_val = b.storage();
Real * x_val = x.storage();
bool * blocked_dofs_val = blocked_dofs.storage();
UInt nb_degrees_of_freedom = x.getSize() * x.getNbComponent();
for (UInt n = 0; n < nb_degrees_of_freedom; ++n) {
if(!(*blocked_dofs_val)) {
*x_val = alpha * (*b_val / *A_val);
}
x_val++;
A_val++;
b_val++;
blocked_dofs_val++;
}
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::explicitPred() {
AKANTU_DEBUG_IN();
if(increment_flag) {
if(previous_displacement) increment->copy(*previous_displacement);
else increment->copy(*displacement);
}
AKANTU_DEBUG_ASSERT(integrator,"itegrator should have been allocated: "
<< "have called initExplicit ? "
<< "or initImplicit ?");
integrator->integrationSchemePred(time_step,
*displacement,
*velocity,
*acceleration,
*blocked_dofs);
if(increment_flag) {
Real * inc_val = increment->storage();
Real * dis_val = displacement->storage();
UInt nb_degree_of_freedom = displacement->getSize() * displacement->getNbComponent();
for (UInt n = 0; n < nb_degree_of_freedom; ++n) {
*inc_val = *dis_val - *inc_val;
inc_val++;
dis_val++;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::explicitCorr() {
AKANTU_DEBUG_IN();
integrator->integrationSchemeCorrAccel(time_step,
*displacement,
*velocity,
*acceleration,
*blocked_dofs,
*increment_acceleration);
if(previous_displacement) previous_displacement->copy(*displacement);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::solveStep() {
AKANTU_DEBUG_IN();
EventManager::sendEvent(SolidMechanicsModelEvent::BeforeSolveStepEvent(method));
this->explicitPred();
this->updateResidual();
this->updateAcceleration();
this->explicitCorr();
EventManager::sendEvent(SolidMechanicsModelEvent::AfterSolveStepEvent(method));
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/* Implicit scheme */
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
/**
* Initialize the solver and create the sparse matrices needed.
*
*/
void SolidMechanicsModel::initSolver(__attribute__((unused)) SolverOptions & options) {
-#if !defined(AKANTU_USE_MUMPS) // or other solver in the future \todo add AKANTU_HAS_SOLVER in CMake
+#if !defined(AKANTU_USE_MUMPS) && !defined(AKANTU_USE_PETSC)// or other solver in the future \todo add AKANTU_HAS_SOLVER in CMake
AKANTU_DEBUG_ERROR("You should at least activate one solver.");
#else
UInt nb_global_nodes = mesh.getNbGlobalNodes();
delete jacobian_matrix;
std::stringstream sstr; sstr << id << ":jacobian_matrix";
- jacobian_matrix = new SparseMatrix(nb_global_nodes * spatial_dimension, _symmetric, sstr.str(), memory_id);
+#ifdef AKANTU_USE_PETSC
+ jacobian_matrix = new SparseMatrix(nb_global_nodes * spatial_dimension, _symmetric, sstr.str(), memory_id);
+#else
+ jacobian_matrix = new PETScMatrix(nb_global_nodes * spatial_dimension, _symmetric, sstr.str(), memory_id);
+#endif //AKANTU_USE PETSC
jacobian_matrix->buildProfile(mesh, *dof_synchronizer, spatial_dimension);
if (!isExplicit()) {
delete stiffness_matrix;
std::stringstream sstr_sti; sstr_sti << id << ":stiffness_matrix";
+#ifdef AKANTU_USE_PETSC
stiffness_matrix = new SparseMatrix(*jacobian_matrix, sstr_sti.str(), memory_id);
+#else
+ stiffness_matrix = new SparseMatrix(nb_global_nodes * spatial_dimension, _symmetric, sstr.str(), memory_id);
+ stiffness_matrix->buildProfile();
+#endif //AKANTU_USE_PETSC
}
-#ifdef AKANTU_USE_MUMPS
std::stringstream sstr_solv; sstr_solv << id << ":solver";
+#ifdef AKANTU_USE_MUMPS
solver = new SolverMumps(*jacobian_matrix, sstr_solv.str());
-
dof_synchronizer->initScatterGatherCommunicationScheme();
+#elif defined(AKANTU_USE_PETSC)
+ solver = new SolverPETSc(*jacobian_matrix, sstr_solv.str());
#else
AKANTU_DEBUG_ERROR("You should at least activate one solver.");
#endif //AKANTU_USE_MUMPS
if(solver)
solver->initialize(options);
#endif //AKANTU_HAS_SOLVER
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::initJacobianMatrix() {
#ifdef AKANTU_USE_MUMPS
// @todo make it more flexible: this is an ugly patch to treat the case of non
// fix profile of the K matrix
delete jacobian_matrix;
std::stringstream sstr_sti; sstr_sti << id << ":jacobian_matrix";
jacobian_matrix = new SparseMatrix(*stiffness_matrix, sstr_sti.str(), memory_id);
std::stringstream sstr_solv; sstr_solv << id << ":solver";
delete solver;
solver = new SolverMumps(*jacobian_matrix, sstr_solv.str());
if(solver)
solver->initialize(_solver_no_options);
#else
- AKANTU_DEBUG_ERROR("You should at least activate one solver.");
+ AKANTU_DEBUG_ERROR("You need to activate the solver mumps.");
#endif
}
/* -------------------------------------------------------------------------- */
/**
* Initialize the implicit solver, either for dynamic or static cases,
*
* @param dynamic
*/
void SolidMechanicsModel::initImplicit(bool dynamic, SolverOptions & solver_options) {
AKANTU_DEBUG_IN();
method = dynamic ? _implicit_dynamic : _static;
if (!increment) setIncrementFlagOn();
initSolver(solver_options);
if(method == _implicit_dynamic) {
if(integrator) delete integrator;
integrator = new TrapezoidalRule2();
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::initialAcceleration() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_INFO("Solving Ma = f");
Solver * acc_solver = NULL;
std::stringstream sstr; sstr << id << ":tmp_mass_matrix";
SparseMatrix * tmp_mass = new SparseMatrix(*mass_matrix, sstr.str(), memory_id);
#ifdef AKANTU_USE_MUMPS
std::stringstream sstr_solver; sstr << id << ":solver_mass_matrix";
acc_solver = new SolverMumps(*mass_matrix, sstr_solver.str());
dof_synchronizer->initScatterGatherCommunicationScheme();
#else
AKANTU_DEBUG_ERROR("You should at least activate one solver.");
#endif //AKANTU_USE_MUMPS
acc_solver->initialize();
tmp_mass->applyBoundary(*blocked_dofs);
acc_solver->setRHS(*residual);
acc_solver->solve(*acceleration);
delete acc_solver;
delete tmp_mass;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::assembleStiffnessMatrix() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_INFO("Assemble the new stiffness matrix.");
stiffness_matrix->clear();
// call compute stiffness matrix on each local elements
std::vector<Material *>::iterator mat_it;
for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
(*mat_it)->assembleStiffnessMatrix(_not_ghost);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
SparseMatrix & SolidMechanicsModel::initVelocityDampingMatrix() {
if(!velocity_damping_matrix)
velocity_damping_matrix =
new SparseMatrix(*jacobian_matrix, id + ":velocity_damping_matrix", memory_id);
return *velocity_damping_matrix;
}
/* -------------------------------------------------------------------------- */
template<>
bool SolidMechanicsModel::testConvergence<_scc_increment>(Real tolerance, Real & error){
AKANTU_DEBUG_IN();
UInt nb_nodes = displacement->getSize();
UInt nb_degree_of_freedom = displacement->getNbComponent();
error = 0;
Real norm[2] = {0., 0.};
Real * increment_val = increment->storage();
bool * blocked_dofs_val = blocked_dofs->storage();
Real * displacement_val = displacement->storage();
for (UInt n = 0; n < nb_nodes; ++n) {
bool is_local_node = mesh.isLocalOrMasterNode(n);
for (UInt d = 0; d < nb_degree_of_freedom; ++d) {
if(!(*blocked_dofs_val) && is_local_node) {
norm[0] += *increment_val * *increment_val;
norm[1] += *displacement_val * *displacement_val;
}
blocked_dofs_val++;
increment_val++;
displacement_val++;
}
}
StaticCommunicator::getStaticCommunicator().allReduce(norm, 2, _so_sum);
norm[0] = sqrt(norm[0]);
norm[1] = sqrt(norm[1]);
AKANTU_DEBUG_ASSERT(!Math::isnan(norm[0]), "Something goes wrong in the solve phase");
if (norm[1] < Math::getTolerance()) {
error = norm[0];
AKANTU_DEBUG_OUT();
// cout<<"Error 1: "<<error<<endl;
return error < tolerance;
}
AKANTU_DEBUG_OUT();
if(norm[1] > Math::getTolerance())
error = norm[0] / norm[1];
else
error = norm[0]; //In case the total displacement is zero!
// cout<<"Error 2: "<<error<<endl;
return (error < tolerance);
}
/* -------------------------------------------------------------------------- */
template<>
bool SolidMechanicsModel::testConvergence<_scc_residual>(Real tolerance, Real & norm) {
AKANTU_DEBUG_IN();
UInt nb_nodes = residual->getSize();
norm = 0;
Real * residual_val = residual->storage();
bool * blocked_dofs_val = blocked_dofs->storage();
for (UInt n = 0; n < nb_nodes; ++n) {
bool is_local_node = mesh.isLocalOrMasterNode(n);
if(is_local_node) {
for (UInt d = 0; d < spatial_dimension; ++d) {
if(!(*blocked_dofs_val)) {
norm += *residual_val * *residual_val;
}
blocked_dofs_val++;
residual_val++;
}
} else {
blocked_dofs_val += spatial_dimension;
residual_val += spatial_dimension;
}
}
StaticCommunicator::getStaticCommunicator().allReduce(&norm, 1, _so_sum);
norm = sqrt(norm);
AKANTU_DEBUG_ASSERT(!Math::isnan(norm), "Something goes wrong in the solve phase");
AKANTU_DEBUG_OUT();
return (norm < tolerance);
}
/* -------------------------------------------------------------------------- */
template<>
bool SolidMechanicsModel::testConvergence<_scc_residual_mass_wgh>(Real tolerance,
Real & norm) {
AKANTU_DEBUG_IN();
UInt nb_nodes = residual->getSize();
norm = 0;
Real * residual_val = residual->storage();
Real * mass_val = this->mass->storage();
bool * blocked_dofs_val = blocked_dofs->storage();
for (UInt n = 0; n < nb_nodes; ++n) {
bool is_local_node = mesh.isLocalOrMasterNode(n);
if(is_local_node) {
for (UInt d = 0; d < spatial_dimension; ++d) {
if(!(*blocked_dofs_val)) {
norm += *residual_val * *residual_val/(*mass_val * *mass_val);
}
blocked_dofs_val++;
residual_val++;
mass_val++;
}
} else {
blocked_dofs_val += spatial_dimension;
residual_val += spatial_dimension;
mass_val += spatial_dimension;
}
}
StaticCommunicator::getStaticCommunicator().allReduce(&norm, 1, _so_sum);
norm = sqrt(norm);
AKANTU_DEBUG_ASSERT(!Math::isnan(norm), "Something goes wrong in the solve phase");
AKANTU_DEBUG_OUT();
return (norm < tolerance);
}
/* -------------------------------------------------------------------------- */
bool SolidMechanicsModel::testConvergenceResidual(Real tolerance){
AKANTU_DEBUG_IN();
Real error=0;
bool res = this->testConvergence<_scc_residual>(tolerance, error);
AKANTU_DEBUG_OUT();
return res;
}
/* -------------------------------------------------------------------------- */
bool SolidMechanicsModel::testConvergenceResidual(Real tolerance, Real & error){
AKANTU_DEBUG_IN();
bool res = this->testConvergence<_scc_residual>(tolerance, error);
AKANTU_DEBUG_OUT();
return res;
}
/* -------------------------------------------------------------------------- */
bool SolidMechanicsModel::testConvergenceIncrement(Real tolerance){
AKANTU_DEBUG_IN();
Real error=0;
bool res = this->testConvergence<_scc_increment>(tolerance, error);
AKANTU_DEBUG_OUT();
return res;
}
/* -------------------------------------------------------------------------- */
bool SolidMechanicsModel::testConvergenceIncrement(Real tolerance, Real & error){
AKANTU_DEBUG_IN();
bool res = this->testConvergence<_scc_increment>(tolerance, error);
AKANTU_DEBUG_OUT();
return res;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::implicitPred() {
AKANTU_DEBUG_IN();
if(previous_displacement) previous_displacement->copy(*displacement);
if(method == _implicit_dynamic)
integrator->integrationSchemePred(time_step,
*displacement,
*velocity,
*acceleration,
*blocked_dofs);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::implicitCorr() {
AKANTU_DEBUG_IN();
if(method == _implicit_dynamic) {
integrator->integrationSchemeCorrDispl(time_step,
*displacement,
*velocity,
*acceleration,
*blocked_dofs,
*increment);
} else {
UInt nb_nodes = displacement->getSize();
UInt nb_degree_of_freedom = displacement->getNbComponent() * nb_nodes;
Real * incr_val = increment->storage();
Real * disp_val = displacement->storage();
bool * boun_val = blocked_dofs->storage();
for (UInt j = 0; j < nb_degree_of_freedom; ++j, ++disp_val, ++incr_val, ++boun_val){
*incr_val *= (1. - *boun_val);
*disp_val += *incr_val;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::updateIncrement() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(previous_displacement,"The previous displacement has to be initialized."
<< " Are you working with Finite or Ineslactic deformations?");
UInt nb_nodes = displacement->getSize();
UInt nb_degree_of_freedom = displacement->getNbComponent() * nb_nodes;
Real * incr_val = increment->storage();
Real * disp_val = displacement->storage();
Real * prev_disp_val = previous_displacement->storage();
for (UInt j = 0; j < nb_degree_of_freedom; ++j, ++disp_val, ++incr_val, ++prev_disp_val)
*incr_val = (*disp_val - *prev_disp_val);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::updatePreviousDisplacement() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(previous_displacement,"The previous displacement has to be initialized."
<< " Are you working with Finite or Ineslactic deformations?");
previous_displacement->copy(*displacement);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/* Information */
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::synchronizeBoundaries() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(synch_registry,"Synchronizer registry was not initialized."
<< " Did you call initParallel?");
synch_registry->synchronize(_gst_smm_boundary);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::synchronizeResidual() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(synch_registry,"Synchronizer registry was not initialized."
<< " Did you call initPBC?");
synch_registry->synchronize(_gst_smm_res);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::setIncrementFlagOn() {
AKANTU_DEBUG_IN();
if(!increment) {
UInt nb_nodes = mesh.getNbNodes();
std::stringstream sstr_inc; sstr_inc << id << ":increment";
increment = &(alloc<Real>(sstr_inc.str(), nb_nodes, spatial_dimension, 0.));
}
increment_flag = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Real SolidMechanicsModel::getStableTimeStep() {
AKANTU_DEBUG_IN();
Real min_dt = getStableTimeStep(_not_ghost);
/// reduction min over all processors
StaticCommunicator::getStaticCommunicator().allReduce(&min_dt, 1, _so_min);
AKANTU_DEBUG_OUT();
return min_dt;
}
/* -------------------------------------------------------------------------- */
Real SolidMechanicsModel::getStableTimeStep(const GhostType & ghost_type) {
AKANTU_DEBUG_IN();
Material ** mat_val = &(materials.at(0));
Real min_dt = std::numeric_limits<Real>::max();
updateCurrentPosition();
Element elem;
elem.ghost_type = ghost_type;
elem.kind = _ek_regular;
Mesh::type_iterator it = mesh.firstType(spatial_dimension, ghost_type);
Mesh::type_iterator end = mesh.lastType(spatial_dimension, ghost_type);
for(; it != end; ++it) {
elem.type = *it;
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(*it);
UInt nb_element = mesh.getNbElement(*it);
Array<UInt>::iterator< Vector<UInt> > eibm =
element_index_by_material(*it, ghost_type).begin(2);
Array<Real> X(0, nb_nodes_per_element*spatial_dimension);
FEEngine::extractNodalToElementField(mesh, *current_position,
X, *it, _not_ghost);
Array<Real>::matrix_iterator X_el =
X.begin(spatial_dimension, nb_nodes_per_element);
for (UInt el = 0; el < nb_element; ++el, ++X_el, ++eibm) {
elem.element = (*eibm)(1);
Real el_h = getFEEngine().getElementInradius(*X_el, *it);
Real el_c = mat_val[(*eibm)(0)]->getCelerity(elem);
Real el_dt = el_h / el_c;
min_dt = std::min(min_dt, el_dt);
}
}
AKANTU_DEBUG_OUT();
return min_dt;
}
/* -------------------------------------------------------------------------- */
Real SolidMechanicsModel::getPotentialEnergy() {
AKANTU_DEBUG_IN();
Real energy = 0.;
/// call update residual on each local elements
std::vector<Material *>::iterator mat_it;
for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
energy += (*mat_it)->getPotentialEnergy();
}
/// reduction sum over all processors
StaticCommunicator::getStaticCommunicator().allReduce(&energy, 1, _so_sum);
AKANTU_DEBUG_OUT();
return energy;
}
/* -------------------------------------------------------------------------- */
Real SolidMechanicsModel::getKineticEnergy() {
AKANTU_DEBUG_IN();
if (!mass && !mass_matrix)
AKANTU_DEBUG_ERROR("No function called to assemble the mass matrix.");
Real ekin = 0.;
UInt nb_nodes = mesh.getNbNodes();
Real * vel_val = velocity->storage();
Real * mass_val = mass->storage();
for (UInt n = 0; n < nb_nodes; ++n) {
Real mv2 = 0;
bool is_local_node = mesh.isLocalOrMasterNode(n);
bool is_not_pbc_slave_node = !isPBCSlaveNode(n);
bool count_node = is_local_node && is_not_pbc_slave_node;
for (UInt i = 0; i < spatial_dimension; ++i) {
if (count_node)
mv2 += *vel_val * *vel_val * *mass_val;
vel_val++;
mass_val++;
}
ekin += mv2;
}
StaticCommunicator::getStaticCommunicator().allReduce(&ekin, 1, _so_sum);
AKANTU_DEBUG_OUT();
return ekin * .5;
}
/* -------------------------------------------------------------------------- */
Real SolidMechanicsModel::getKineticEnergy(const ElementType & type, UInt index) {
AKANTU_DEBUG_IN();
UInt nb_quadrature_points = getFEEngine().getNbQuadraturePoints(type);
Array<Real> vel_on_quad(nb_quadrature_points, spatial_dimension);
Array<UInt> filter_element(1, 1, index);
getFEEngine().interpolateOnQuadraturePoints(*velocity, vel_on_quad,
spatial_dimension,
type, _not_ghost,
filter_element);
Array<Real>::vector_iterator vit = vel_on_quad.begin(spatial_dimension);
Array<Real>::vector_iterator vend = vel_on_quad.end(spatial_dimension);
Vector<Real> rho_v2(nb_quadrature_points);
Real rho = materials[element_index_by_material(type)(index, 0)]->getRho();
for (UInt q = 0; vit != vend; ++vit, ++q) {
rho_v2(q) = rho * vit->dot(*vit);
}
AKANTU_DEBUG_OUT();
return .5*getFEEngine().integrate(rho_v2, type, index);
}
/* -------------------------------------------------------------------------- */
Real SolidMechanicsModel::getExternalWork() {
AKANTU_DEBUG_IN();
Real * velo = velocity->storage();
Real * forc = force->storage();
Real * resi = residual->storage();
bool * boun = blocked_dofs->storage();
Real work = 0.;
UInt nb_nodes = mesh.getNbNodes();
for (UInt n = 0; n < nb_nodes; ++n) {
bool is_local_node = mesh.isLocalOrMasterNode(n);
bool is_not_pbc_slave_node = !isPBCSlaveNode(n);
bool count_node = is_local_node && is_not_pbc_slave_node;
for (UInt i = 0; i < spatial_dimension; ++i) {
if (count_node) {
if(*boun)
work -= *resi * *velo * time_step;
else
work += *forc * *velo * time_step;
}
++velo;
++forc;
++resi;
++boun;
}
}
StaticCommunicator::getStaticCommunicator().allReduce(&work, 1, _so_sum);
AKANTU_DEBUG_OUT();
return work;
}
/* -------------------------------------------------------------------------- */
Real SolidMechanicsModel::getEnergy(const std::string & energy_id) {
AKANTU_DEBUG_IN();
if (energy_id == "kinetic") {
return getKineticEnergy();
} else if (energy_id == "external work"){
return getExternalWork();
}
Real energy = 0.;
std::vector<Material *>::iterator mat_it;
for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
energy += (*mat_it)->getEnergy(energy_id);
}
/// reduction sum over all processors
StaticCommunicator::getStaticCommunicator().allReduce(&energy, 1, _so_sum);
AKANTU_DEBUG_OUT();
return energy;
}
/* -------------------------------------------------------------------------- */
Real SolidMechanicsModel::getEnergy(const std::string & energy_id,
const ElementType & type,
UInt index){
AKANTU_DEBUG_IN();
if (energy_id == "kinetic") {
return getKineticEnergy(type, index);
}
std::vector<Material *>::iterator mat_it;
Vector<UInt> mat = element_index_by_material(type, _not_ghost).begin(2)[index];
Real energy = materials[mat(0)]->getEnergy(energy_id, type, mat(1));
AKANTU_DEBUG_OUT();
return energy;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::onNodesAdded(const Array<UInt> & nodes_list,
__attribute__((unused)) const NewNodesEvent & event) {
AKANTU_DEBUG_IN();
UInt nb_nodes = mesh.getNbNodes();
if(displacement) displacement->resize(nb_nodes);
if(mass ) mass ->resize(nb_nodes);
if(velocity ) velocity ->resize(nb_nodes);
if(acceleration) acceleration->resize(nb_nodes);
if(force ) force ->resize(nb_nodes);
if(residual ) residual ->resize(nb_nodes);
if(blocked_dofs) blocked_dofs->resize(nb_nodes);
if(previous_displacement) previous_displacement->resize(nb_nodes);
if(increment_acceleration) increment_acceleration->resize(nb_nodes);
if(increment) increment->resize(nb_nodes);
if(current_position) current_position->resize(nb_nodes);
delete dof_synchronizer;
dof_synchronizer = new DOFSynchronizer(mesh, spatial_dimension);
dof_synchronizer->initLocalDOFEquationNumbers();
dof_synchronizer->initGlobalDOFEquationNumbers();
std::vector<Material *>::iterator mat_it;
for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
(*mat_it)->onNodesAdded(nodes_list, event);
}
if (method != _explicit_lumped_mass) {
delete stiffness_matrix;
delete jacobian_matrix;
delete solver;
SolverOptions solver_options;
initImplicit((method == _implicit_dynamic), solver_options);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::onElementsAdded(const Array<Element> & element_list,
const NewElementsEvent & event) {
AKANTU_DEBUG_IN();
getFEEngine().initShapeFunctions(_not_ghost);
getFEEngine().initShapeFunctions(_ghost);
Array<Element>::const_iterator<Element> it = element_list.begin();
Array<Element>::const_iterator<Element> end = element_list.end();
/// \todo have rules to choose the correct material
UInt mat_id = 0;
UInt * mat_id_vect = NULL;
try {
const NewMaterialElementsEvent & event_mat = dynamic_cast<const NewMaterialElementsEvent &>(event);
mat_id_vect = event_mat.getMaterialList().storage();
} catch(...) { }
for (UInt el = 0; it != end; ++it, ++el) {
const Element & elem = *it;
if(mat_id_vect) mat_id = mat_id_vect[el];
else mat_id = (*material_selector)(elem);
Material & mat = *materials[mat_id];
UInt mat_index = mat.addElement(elem.type, elem.element, elem.ghost_type);
Vector<UInt> id(2);
id[0] = mat_id; id[1] = mat_index;
if(!element_index_by_material.exists(elem.type, elem.ghost_type))
element_index_by_material.alloc(0, 2, elem.type, elem.ghost_type);
element_index_by_material(elem.type, elem.ghost_type).push_back(id);
}
std::vector<Material *>::iterator mat_it;
for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
(*mat_it)->onElementsAdded(element_list, event);
}
if(method != _explicit_lumped_mass) AKANTU_DEBUG_TO_IMPLEMENT();
assembleMassLumped();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::onElementsRemoved(__attribute__((unused)) const Array<Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
const RemovedElementsEvent & event) {
// MeshUtils::purifyMesh(mesh);
getFEEngine().initShapeFunctions(_not_ghost);
getFEEngine().initShapeFunctions(_ghost);
std::vector<Material *>::iterator mat_it;
for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
(*mat_it)->onElementsRemoved(element_list, new_numbering, event);
}
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::onNodesRemoved(__attribute__((unused)) const Array<UInt> & element_list,
const Array<UInt> & new_numbering,
__attribute__((unused)) const RemovedNodesEvent & event) {
if(displacement) mesh.removeNodesFromArray(*displacement, new_numbering);
if(mass ) mesh.removeNodesFromArray(*mass , new_numbering);
if(velocity ) mesh.removeNodesFromArray(*velocity , new_numbering);
if(acceleration) mesh.removeNodesFromArray(*acceleration, new_numbering);
if(force ) mesh.removeNodesFromArray(*force , new_numbering);
if(residual ) mesh.removeNodesFromArray(*residual , new_numbering);
if(blocked_dofs) mesh.removeNodesFromArray(*blocked_dofs, new_numbering);
if(increment_acceleration) mesh.removeNodesFromArray(*increment_acceleration, new_numbering);
if(increment) mesh.removeNodesFromArray(*increment , new_numbering);
delete dof_synchronizer;
dof_synchronizer = new DOFSynchronizer(mesh, spatial_dimension);
dof_synchronizer->initLocalDOFEquationNumbers();
dof_synchronizer->initGlobalDOFEquationNumbers();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::reassignMaterial() {
AKANTU_DEBUG_IN();
std::vector< Array<Element> > element_to_add (materials.size());
std::vector< Array<Element> > element_to_remove(materials.size());
Element element;
for (ghost_type_t::iterator gt = ghost_type_t::begin(); gt != ghost_type_t::end(); ++gt) {
GhostType ghost_type = *gt;
element.ghost_type = ghost_type;
Mesh::type_iterator it = mesh.firstType(spatial_dimension, ghost_type, _ek_regular);
Mesh::type_iterator end = mesh.lastType(spatial_dimension, ghost_type, _ek_regular);
for(; it != end; ++it) {
ElementType type = *it;
element.type = type;
element.kind = Mesh::getKind(type);
UInt nb_element = mesh.getNbElement(type, ghost_type);
Array<UInt> & el_index_by_mat = element_index_by_material(type, ghost_type);
for (UInt el = 0; el < nb_element; ++el) {
element.element = el;
UInt old_material = el_index_by_mat(el, 0);
UInt new_material = (*material_selector)(element);
if(old_material != new_material) {
element_to_add [new_material].push_back(element);
element_to_remove[old_material].push_back(element);
}
}
}
}
std::vector<Material *>::iterator mat_it;
UInt mat_index = 0;
for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it, ++mat_index) {
(*mat_it)->removeElements(element_to_remove[mat_index]);
(*mat_it)->addElements (element_to_add[mat_index]);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
bool SolidMechanicsModel::isInternal(const std::string & field_name,
const ElementKind & element_kind){
bool is_internal = false;
/// check if at least one material contains field_id as an internal
for (UInt m = 0; m < materials.size() && !is_internal; ++m) {
is_internal |= materials[m]->isInternal(field_name, element_kind);
}
return is_internal;
}
/* -------------------------------------------------------------------------- */
ElementTypeMap<UInt> SolidMechanicsModel::getInternalDataPerElem(const std::string & field_name,
const ElementKind & element_kind){
if (!(this->isInternal(field_name,element_kind))) AKANTU_EXCEPTION("unknown internal " << field_name);
for (UInt m = 0; m < materials.size() ; ++m) {
if (materials[m]->isInternal(field_name, element_kind))
return materials[m]->getInternalDataPerElem(field_name,element_kind);
}
return ElementTypeMap<UInt>();
}
/* -------------------------------------------------------------------------- */
ElementTypeMapArray<Real> & SolidMechanicsModel::flattenInternal(const std::string & field_name,
const ElementKind & kind){
std::pair<std::string,ElementKind> key(field_name,kind);
if (this->registered_internals.count(key) == 0){
this->registered_internals[key] =
new ElementTypeMapArray<Real>(field_name,this->id);
}
ElementTypeMapArray<Real> * internal_flat = this->registered_internals[key];
for (UInt m = 0; m < materials.size(); ++m)
materials[m]->flattenInternal(field_name,*internal_flat,_not_ghost,kind);
return *internal_flat;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::flattenAllRegisteredInternals(const ElementKind & kind){
std::map<std::pair<std::string,ElementKind>,ElementTypeMapArray<Real> *> ::iterator it = this->registered_internals.begin();
std::map<std::pair<std::string,ElementKind>,ElementTypeMapArray<Real> *>::iterator end = this->registered_internals.end();
while (it != end){
if (kind == it->first.second)
this->flattenInternal(it->first.first,kind);
++it;
}
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::onDump(){
this->flattenAllRegisteredInternals(_ek_regular);
}
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_IOHELPER
dumper::Field * SolidMechanicsModel
::createElementalField(const std::string & field_name,
const std::string & group_name,
bool padding_flag,
const ElementKind & kind){
dumper::Field * field = NULL;
if(field_name == "partitions")
field = mesh.createElementalField<UInt, dumper::ElementPartitionField>(mesh.getConnectivities(),group_name,this->spatial_dimension,kind);
else if(field_name == "element_index_by_material")
field = mesh.createElementalField<UInt, Vector, dumper::ElementalField >(element_index_by_material,group_name,this->spatial_dimension,kind);
else {
bool is_internal = this->isInternal(field_name,kind);
if (is_internal) {
ElementTypeMap<UInt> nb_data_per_elem = this->getInternalDataPerElem(field_name,kind);
ElementTypeMapArray<Real> & internal_flat = this->flattenInternal(field_name,kind);
field = mesh.createElementalField<Real, dumper::InternalMaterialField>(internal_flat,
group_name,
this->spatial_dimension,kind,nb_data_per_elem);
//treat the paddings
if (padding_flag){
if (field_name == "stress"){
if (this->spatial_dimension == 2) {
dumper::StressPadder<2> * foo = new dumper::StressPadder<2>(*this);
field = dumper::FieldComputeProxy::createFieldCompute(field,*foo);
}
}
// else if (field_name == "strain"){
// if (this->spatial_dimension == 2) {
// dumper::StrainPadder<2> * foo = new dumper::StrainPadder<2>(*this);
// field = dumper::FieldComputeProxy::createFieldCompute(field,*foo);
// }
// }
}
// homogenize the field
dumper::ComputeFunctorInterface * foo =
dumper::HomogenizerProxy::createHomogenizer(*field);
field = dumper::FieldComputeProxy::createFieldCompute(field,*foo);
}
}
return field;
}
/* -------------------------------------------------------------------------- */
dumper::Field * SolidMechanicsModel::createNodalFieldReal(const std::string & field_name,
const std::string & group_name,
bool padding_flag) {
std::map<std::string,Array<Real>* > real_nodal_fields;
real_nodal_fields["displacement" ] = displacement;
real_nodal_fields["mass" ] = mass;
real_nodal_fields["velocity" ] = velocity;
real_nodal_fields["acceleration" ] = acceleration;
real_nodal_fields["force" ] = force;
real_nodal_fields["residual" ] = residual;
real_nodal_fields["increment" ] = increment;
dumper::Field * field = NULL;
if (padding_flag)
field = mesh.createNodalField(real_nodal_fields[field_name],group_name, 3);
else
field = mesh.createNodalField(real_nodal_fields[field_name],group_name);
return field;
}
/* -------------------------------------------------------------------------- */
dumper::Field * SolidMechanicsModel::createNodalFieldBool(const std::string & field_name,
const std::string & group_name,
bool padding_flag) {
std::map<std::string,Array<bool>* > uint_nodal_fields;
uint_nodal_fields["blocked_dofs" ] = blocked_dofs;
dumper::Field * field = NULL;
field = mesh.createNodalField(uint_nodal_fields[field_name],group_name);
return field;
}
/* -------------------------------------------------------------------------- */
#else
/* -------------------------------------------------------------------------- */
dumper::Field * SolidMechanicsModel
::createElementalField(const std::string & field_name,
const std::string & group_name,
bool padding_flag,
const ElementKind & kind){
return NULL;
}
/* -------------------------------------------------------------------------- */
dumper::Field * SolidMechanicsModel::createNodalFieldReal(const std::string & field_name,
const std::string & group_name,
bool padding_flag) {
return NULL;
}
/* -------------------------------------------------------------------------- */
dumper::Field * SolidMechanicsModel::createNodalFieldBool(const std::string & field_name,
const std::string & group_name,
bool padding_flag) {
return NULL;
}
#endif
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::dump(const std::string & dumper_name) {
this->onDump();
EventManager::sendEvent(SolidMechanicsModelEvent::BeforeDumpEvent());
synch_registry->synchronize(_gst_for_dump);
mesh.dump(dumper_name);
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::dump(const std::string & dumper_name, UInt step) {
this->onDump();
EventManager::sendEvent(SolidMechanicsModelEvent::BeforeDumpEvent());
synch_registry->synchronize(_gst_for_dump);
mesh.dump(dumper_name, step);
}
/* ------------------------------------------------------------------------- */
void SolidMechanicsModel::dump(const std::string & dumper_name, Real time, UInt step) {
this->onDump();
EventManager::sendEvent(SolidMechanicsModelEvent::BeforeDumpEvent());
synch_registry->synchronize(_gst_for_dump);
mesh.dump(dumper_name, time, step);
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::dump() {
this->onDump();
EventManager::sendEvent(SolidMechanicsModelEvent::BeforeDumpEvent());
mesh.dump();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::dump(UInt step) {
this->onDump();
EventManager::sendEvent(SolidMechanicsModelEvent::BeforeDumpEvent());
mesh.dump(step);
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::dump(Real time, UInt step) {
this->onDump();
EventManager::sendEvent(SolidMechanicsModelEvent::BeforeDumpEvent());
mesh.dump(time, step);
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::computeCauchyStresses() {
AKANTU_DEBUG_IN();
// call compute stiffness matrix on each local elements
std::vector<Material *>::iterator mat_it;
for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
Material & mat = **mat_it;
if(mat.isFiniteDeformation())
mat.computeAllCauchyStresses(_not_ghost);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::saveStressAndStrainBeforeDamage() {
EventManager::sendEvent(SolidMechanicsModelEvent::BeginningOfDamageIterationEvent());
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::updateEnergiesAfterDamage() {
EventManager::sendEvent(SolidMechanicsModelEvent::AfterDamageEvent());
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::printself(std::ostream & stream, int indent) const {
std::string space;
for(Int i = 0; i < indent; i++, space += AKANTU_INDENT);
stream << space << "Solid Mechanics Model [" << std::endl;
stream << space << " + id : " << id << std::endl;
stream << space << " + spatial dimension : " << spatial_dimension << std::endl;
stream << space << " + fem [" << std::endl;
getFEEngine().printself(stream, indent + 2);
stream << space << AKANTU_INDENT << "]" << std::endl;
stream << space << " + nodals information [" << std::endl;
displacement->printself(stream, indent + 2);
mass ->printself(stream, indent + 2);
velocity ->printself(stream, indent + 2);
acceleration->printself(stream, indent + 2);
force ->printself(stream, indent + 2);
residual ->printself(stream, indent + 2);
blocked_dofs->printself(stream, indent + 2);
stream << space << AKANTU_INDENT << "]" << std::endl;
stream << space << " + connectivity type information [" << std::endl;
element_index_by_material.printself(stream, indent + 2);
stream << space << AKANTU_INDENT << "]" << std::endl;
stream << space << " + materials [" << std::endl;
std::vector<Material *>::const_iterator mat_it;
for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
const Material & mat = *(*mat_it);
mat.printself(stream, indent + 1);
}
stream << space << AKANTU_INDENT << "]" << std::endl;
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
__END_AKANTU__
diff --git a/src/model/solid_mechanics/solid_mechanics_model.hh b/src/model/solid_mechanics/solid_mechanics_model.hh
index 5209ed661..9a6b33463 100644
--- a/src/model/solid_mechanics/solid_mechanics_model.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model.hh
@@ -1,737 +1,736 @@
/**
* @file solid_mechanics_model.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Jul 27 2010
* @date last modification: Tue Sep 16 2014
*
* @brief Model of Solid Mechanics
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 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_SOLID_MECHANICS_MODEL_HH__
#define __AKANTU_SOLID_MECHANICS_MODEL_HH__
/* -------------------------------------------------------------------------- */
#include <fstream>
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_types.hh"
#include "model.hh"
#include "data_accessor.hh"
#include "mesh.hh"
#include "dumpable.hh"
#include "boundary_condition.hh"
#include "integrator_gauss.hh"
#include "shape_lagrange.hh"
#include "integration_scheme_2nd_order.hh"
#include "solver.hh"
#include "material_selector.hh"
#include "solid_mechanics_model_event_handler.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class Material;
class IntegrationScheme2ndOrder;
class SparseMatrix;
class DumperIOHelper;
}
/* -------------------------------------------------------------------------- */
__BEGIN_AKANTU__
struct SolidMechanicsModelOptions : public ModelOptions {
SolidMechanicsModelOptions(AnalysisMethod analysis_method = _explicit_lumped_mass,
bool no_init_materials = false) :
analysis_method(analysis_method),
no_init_materials(no_init_materials) { }
AnalysisMethod analysis_method;
bool no_init_materials;
};
extern const SolidMechanicsModelOptions default_solid_mechanics_model_options;
class SolidMechanicsModel : public Model,
public DataAccessor,
public MeshEventHandler,
public BoundaryCondition<SolidMechanicsModel>,
public EventHandlerManager<SolidMechanicsModelEventHandler> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
class NewMaterialElementsEvent : public NewElementsEvent {
public:
AKANTU_GET_MACRO_NOT_CONST(MaterialList, material, Array <UInt> &);
AKANTU_GET_MACRO(MaterialList, material, const Array <UInt> &);
protected:
Array <UInt> material;
};
typedef FEEngineTemplate <IntegratorGauss, ShapeLagrange> MyFEEngineType;
protected:
typedef EventHandlerManager <SolidMechanicsModelEventHandler> EventManager;
public:
SolidMechanicsModel(Mesh & mesh,
UInt spatial_dimension = _all_dimensions,
const ID & id = "solid_mechanics_model",
const MemoryID & memory_id = 0);
virtual ~SolidMechanicsModel();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize completely the model
virtual void initFull(const ModelOptions & options = default_solid_mechanics_model_options);
/// initialize the fem object needed for boundary conditions
void initFEEngineBoundary();
/// register the tags associated with the parallel synchronizer
void initParallel(MeshPartition *partition, DataAccessor *data_accessor = NULL);
/// allocate all vectors
void initArrays();
/// allocate all vectors
void initArraysPreviousDisplacment();
/// initialize all internal arrays for materials
virtual void initMaterials();
/// initialize the model
virtual void initModel();
/// init PBC synchronizer
void initPBC();
/// function to print the containt of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
/* ------------------------------------------------------------------------ */
/* PBC */
/* ------------------------------------------------------------------------ */
public:
/// change the equation number for proper assembly when using PBC
void changeEquationNumberforPBC(std::map <UInt, UInt> & pbc_pair);
/// synchronize Residual for output
void synchronizeResidual();
protected:
/// register PBC synchronizer
void registerPBCSynchronizer();
/* ------------------------------------------------------------------------ */
/* Explicit */
/* ------------------------------------------------------------------------ */
public:
/// initialize the stuff for the explicit scheme
void initExplicit(AnalysisMethod analysis_method = _explicit_lumped_mass);
bool isExplicit() {
return method == _explicit_lumped_mass || method == _explicit_consistent_mass;
}
/// initialize the array needed by updateResidual (residual, current_position)
void initializeUpdateResidualData();
/// update the current position vector
void updateCurrentPosition();
/// assemble the residual for the explicit scheme
virtual void updateResidual(bool need_initialize = true);
/**
* \brief compute the acceleration from the residual
* this function is the explicit equivalent to solveDynamic in implicit
* In the case of lumped mass just divide the residual by the mass
* In the case of not lumped mass call solveDynamic<_acceleration_corrector>
*/
void updateAcceleration();
void updateIncrement();
void updatePreviousDisplacement();
void saveStressAndStrainBeforeDamage();
void updateEnergiesAfterDamage();
/// Solve the system @f[ A x = \alpha b @f] with A a lumped matrix
void solveLumped(Array <Real> & x,
const Array <Real> & A,
const Array <Real> & b,
const Array <bool> & blocked_dofs,
Real alpha);
/// explicit integration predictor
void explicitPred();
/// explicit integration corrector
void explicitCorr();
public:
void solveStep();
/* ------------------------------------------------------------------------ */
/* Implicit */
/* ------------------------------------------------------------------------ */
public:
/// initialize the solver and the jacobian_matrix (called by initImplicit)
void initSolver(SolverOptions & options = _solver_no_options);
/// initialize the stuff for the implicit solver
void initImplicit(bool dynamic = false,
SolverOptions & solver_options = _solver_no_options);
/// solve Ma = f to get the initial acceleration
void initialAcceleration();
/// assemble the stiffness matrix
void assembleStiffnessMatrix();
public:
/**
* solve a step (predictor + convergence loop + corrector) using the
* the given convergence method (see akantu::SolveConvergenceMethod)
* and the given convergence criteria (see
* akantu::SolveConvergenceCriteria)
**/
template <SolveConvergenceMethod method, SolveConvergenceCriteria criteria>
bool solveStep(Real tolerance, UInt max_iteration = 100);
template <SolveConvergenceMethod method, SolveConvergenceCriteria criteria>
bool solveStep(Real tolerance,
Real & error,
UInt max_iteration = 100,
bool do_not_factorize = false);
public:
/**
* solve Ku = f using the the given convergence method (see
* akantu::SolveConvergenceMethod) and the given convergence
* criteria (see akantu::SolveConvergenceCriteria)
**/
template <SolveConvergenceMethod cmethod, SolveConvergenceCriteria criteria>
bool solveStatic(Real tolerance, UInt max_iteration,
bool do_not_factorize = false);
/// test if the system is converged
template <SolveConvergenceCriteria criteria>
bool testConvergence(Real tolerance, Real & error);
/// test the convergence (norm of increment)
bool testConvergenceIncrement(Real tolerance) __attribute__((deprecated));
bool testConvergenceIncrement(Real tolerance, Real & error) __attribute__((deprecated));
/// test the convergence (norm of residual)
bool testConvergenceResidual(Real tolerance) __attribute__((deprecated));
bool testConvergenceResidual(Real tolerance, Real & error) __attribute__((deprecated));
/// create and return the velocity damping matrix
SparseMatrix & initVelocityDampingMatrix();
/// implicit time integration predictor
void implicitPred();
/// implicit time integration corrector
void implicitCorr();
/// compute the Cauchy stress on user demand.
void computeCauchyStresses();
protected:
/// finish the computation of residual to solve in increment
void updateResidualInternal();
/// compute the support reaction and store it in force
void updateSupportReaction();
public:
//protected: Daniel changed it just for a test
/// compute A and solve @f[ A\delta u = f_ext - f_int @f]
template <NewmarkBeta::IntegrationSchemeCorrectorType type>
void solve(Array<Real> &increment, Real block_val = 1.,
- bool need_factorize = true, bool has_profile_changed = false,
- const Array<Real> &rhs = Array<Real>());
+ bool need_factorize = true, bool has_profile_changed = false);
private:
/// re-initialize the J matrix (to use if the profile of K changed)
void initJacobianMatrix();
/* ------------------------------------------------------------------------ */
/* Explicit/Implicit */
/* ------------------------------------------------------------------------ */
public:
/// Update the stresses for the computation of the residual of the Stiffness
/// matrix in the case of finite deformation
void computeStresses();
/// synchronize the ghost element boundaries values
void synchronizeBoundaries();
/* ------------------------------------------------------------------------ */
/* Materials (solid_mechanics_model_material.cc) */
/* ------------------------------------------------------------------------ */
public:
/// registers all the custom materials of a given type present in the input file
template <typename M>
void registerNewCustomMaterials(const ID & mat_type);
/// register an empty material of a given type
template <typename M>
Material & registerNewEmptyMaterial(const std::string & name);
// /// Use a UIntData in the mesh to specify the material to use per element
// void setMaterialIDsFromIntData(const std::string & data_name);
/// reassigns materials depending on the material selector
virtual void reassignMaterial();
protected:
/// register a material in the dynamic database
template <typename M>
Material & registerNewMaterial(const ParserSection & mat_section);
/// read the material files to instantiate all the materials
void instantiateMaterials();
/* ------------------------------------------------------------------------ */
/* Mass (solid_mechanics_model_mass.cc) */
/* ------------------------------------------------------------------------ */
public:
/// assemble the lumped mass matrix
void assembleMassLumped();
/// assemble the mass matrix for consistent mass resolutions
void assembleMass();
protected:
/// assemble the lumped mass matrix for local and ghost elements
void assembleMassLumped(GhostType ghost_type);
/// assemble the mass matrix for either _ghost or _not_ghost elements
void assembleMass(GhostType ghost_type);
/// fill a vector of rho
void computeRho(Array <Real> & rho,
ElementType type,
GhostType ghost_type);
/* ------------------------------------------------------------------------ */
/* Data Accessor inherited members */
/* ------------------------------------------------------------------------ */
public:
inline virtual UInt getNbDataForElements(const Array <Element> & elements,
- SynchronizationTag tag) const;
+ SynchronizationTag tag) const;
inline virtual void packElementData(CommunicationBuffer & buffer,
const Array <Element> & elements,
SynchronizationTag tag) const;
inline virtual void unpackElementData(CommunicationBuffer & buffer,
const Array <Element> & elements,
SynchronizationTag tag);
inline virtual UInt getNbDataToPack(SynchronizationTag tag) const;
inline virtual UInt getNbDataToUnpack(SynchronizationTag tag) const;
inline virtual void packData(CommunicationBuffer & buffer,
const UInt index,
SynchronizationTag tag) const;
inline virtual void unpackData(CommunicationBuffer & buffer,
const UInt index,
SynchronizationTag tag);
protected:
inline void splitElementByMaterial(const Array <Element> & elements,
Array <Element> * elements_per_mat) const;
/* ------------------------------------------------------------------------ */
/* Mesh Event Handler inherited members */
/* ------------------------------------------------------------------------ */
protected:
virtual void onNodesAdded(const Array <UInt> & nodes_list,
const NewNodesEvent & event);
virtual void onNodesRemoved(const Array <UInt> & element_list,
const Array <UInt> & new_numbering,
const RemovedNodesEvent & event);
virtual void onElementsAdded(const Array <Element> & nodes_list,
const NewElementsEvent & event);
virtual void onElementsRemoved(const Array <Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
const RemovedElementsEvent & event);
/* ------------------------------------------------------------------------ */
/* Dumpable interface (kept for convenience) and dumper relative functions */
/* ------------------------------------------------------------------------ */
public:
virtual void onDump();
//! decide wether a field is a material internal or not
bool isInternal(const std::string & field_name, const ElementKind & element_kind);
//! give the amount of data per element
ElementTypeMap<UInt> getInternalDataPerElem(const std::string & field_name,
const ElementKind & kind);
//! flatten a given material internal field
ElementTypeMapArray<Real> & flattenInternal(const std::string & field_name,
const ElementKind & kind);
//! flatten all the registered material internals
void flattenAllRegisteredInternals(const ElementKind & kind);
virtual dumper::Field * createNodalFieldReal(const std::string & field_name,
const std::string & group_name,
bool padding_flag);
virtual dumper::Field * createNodalFieldBool(const std::string & field_name,
const std::string & group_name,
bool padding_flag);
virtual dumper::Field * createElementalField(const std::string & field_name,
const std::string & group_name,
bool padding_flag,
const ElementKind & kind);
virtual void dump(const std::string & dumper_name);
virtual void dump(const std::string & dumper_name, UInt step);
virtual void dump(const std::string & dumper_name, Real time, UInt step);
virtual void dump();
virtual void dump(UInt step);
virtual void dump(Real time, UInt step);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// return the dimension of the system space
AKANTU_GET_MACRO(SpatialDimension, spatial_dimension, UInt);
/// get the current value of the time step
AKANTU_GET_MACRO(TimeStep, time_step, Real);
/// set the value of the time step
void setTimeStep(Real time_step);
/// get the value of the conversion from forces/ mass to acceleration
AKANTU_GET_MACRO(F_M2A, f_m2a, Real);
/// set the value of the conversion from forces/ mass to acceleration
AKANTU_SET_MACRO(F_M2A, f_m2a, Real);
/// get the SolidMechanicsModel::displacement vector
AKANTU_GET_MACRO(Displacement, *displacement, Array <Real> &);
/// get the SolidMechanicsModel::previous_displacement vector
AKANTU_GET_MACRO(PreviousDisplacement, *previous_displacement, Array <Real> &);
/// get the SolidMechanicsModel::current_position vector \warn only consistent
/// after a call to SolidMechanicsModel::updateCurrentPosition
AKANTU_GET_MACRO(CurrentPosition, *current_position, const Array <Real> &);
/// get the SolidMechanicsModel::increment vector \warn only consistent if
/// SolidMechanicsModel::setIncrementFlagOn has been called before
AKANTU_GET_MACRO(Increment, *increment, Array <Real> &);
/// get the lumped SolidMechanicsModel::mass vector
AKANTU_GET_MACRO(Mass, *mass, Array <Real> &);
/// get the SolidMechanicsModel::velocity vector
AKANTU_GET_MACRO(Velocity, *velocity, Array <Real> &);
/// get the SolidMechanicsModel::acceleration vector, updated by
/// SolidMechanicsModel::updateAcceleration
AKANTU_GET_MACRO(Acceleration, *acceleration, Array <Real> &);
/// get the SolidMechanicsModel::force vector (boundary forces)
AKANTU_GET_MACRO(Force, *force, Array <Real> &);
/// get the SolidMechanicsModel::residual vector, computed by
/// SolidMechanicsModel::updateResidual
AKANTU_GET_MACRO(Residual, *residual, Array <Real> &);
/// get the SolidMechanicsModel::blocked_dofs vector
AKANTU_GET_MACRO(BlockedDOFs, *blocked_dofs, Array <bool> &);
/// get the SolidMechnicsModel::incrementAcceleration vector
AKANTU_GET_MACRO(IncrementAcceleration, *increment_acceleration, Array <Real> &);
/// get the value of the SolidMechanicsModel::increment_flag
AKANTU_GET_MACRO(IncrementFlag, increment_flag, bool);
/// get a particular material (by material index)
inline Material & getMaterial(UInt mat_index);
/// get a particular material (by material index)
inline const Material & getMaterial(UInt mat_index) const;
/// get a particular material (by material name)
inline Material & getMaterial(const std::string & name);
/// get a particular material (by material name)
inline const Material & getMaterial(const std::string & name) const;
/// get a particular material id from is name
inline UInt getMaterialIndex(const std::string & name) const;
/// give the number of materials
inline UInt getNbMaterials() const {
return materials.size();
}
inline void setMaterialSelector(MaterialSelector & selector);
/// give the material internal index from its id
Int getInternalIndexFromID(const ID & id) const;
/// compute the stable time step
Real getStableTimeStep();
/// compute the potential energy
Real getPotentialEnergy();
/// compute the kinetic energy
Real getKineticEnergy();
Real getKineticEnergy(const ElementType & type, UInt index);
/// compute the external work (for impose displacement, the velocity should be given too)
Real getExternalWork();
/// get the energies
Real getEnergy(const std::string & energy_id);
/// compute the energy for energy
Real getEnergy(const std::string & energy_id, const ElementType & type, UInt index);
/**
* @brief set the SolidMechanicsModel::increment_flag to on, the activate the
* update of the SolidMechanicsModel::increment vector
*/
void setIncrementFlagOn();
/// get the stiffness matrix
AKANTU_GET_MACRO(StiffnessMatrix, *stiffness_matrix, SparseMatrix &);
/// get the global jacobian matrix of the system
AKANTU_GET_MACRO(GlobalJacobianMatrix, *jacobian_matrix, const SparseMatrix &);
/// get the mass matrix
AKANTU_GET_MACRO(MassMatrix, *mass_matrix, SparseMatrix &);
/// get the velocity damping matrix
AKANTU_GET_MACRO(VelocityDampingMatrix, *velocity_damping_matrix, SparseMatrix &);
/// get the FEEngine object to integrate or interpolate on the boundary
inline FEEngine & getFEEngineBoundary(const ID & name = "");
/// get integrator
AKANTU_GET_MACRO(Integrator, *integrator, const IntegrationScheme2ndOrder &);
/// get access to the internal solver
AKANTU_GET_MACRO(Solver, *solver, Solver &);
/// get synchronizer
AKANTU_GET_MACRO(Synchronizer, *synch_parallel, const DistributedSynchronizer &);
AKANTU_GET_MACRO(ElementIndexByMaterial, element_index_by_material, const ElementTypeMapArray <UInt> &);
/// vectors containing local material element index for each global element index
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(ElementIndexByMaterial, element_index_by_material, UInt);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(ElementIndexByMaterial, element_index_by_material, UInt);
/// Get the type of analysis method used
AKANTU_GET_MACRO(AnalysisMethod, method, AnalysisMethod);
template <int dim, class model_type>
friend struct ContactData;
template <int Dim, AnalysisMethod s, ContactResolutionMethod r>
friend class ContactResolution;
protected:
friend class Material;
template <UInt DIM, template <UInt> class WeightFunction>
friend class MaterialNonLocal;
protected:
/// compute the stable time step
Real getStableTimeStep(const GhostType & ghost_type);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// time step
Real time_step;
/// conversion coefficient form force/mass to acceleration
Real f_m2a;
/// displacements array
Array <Real> *displacement;
/// displacements array at the previous time step (used in finite deformation)
Array <Real> *previous_displacement;
/// lumped mass array
Array <Real> *mass;
/// velocities array
Array <Real> *velocity;
/// accelerations array
Array <Real> *acceleration;
/// accelerations array
Array <Real> *increment_acceleration;
/// forces array
Array <Real> *force;
/// residuals array
Array <Real> *residual;
/// array specifing if a degree of freedom is blocked or not
Array <bool> *blocked_dofs;
/// array of current position used during update residual
Array <Real> *current_position;
/// mass matrix
SparseMatrix *mass_matrix;
/// velocity damping matrix
SparseMatrix *velocity_damping_matrix;
/// stiffness matrix
SparseMatrix *stiffness_matrix;
/// jacobian matrix @f[A = cM + dD + K@f] with @f[c = \frac{1}{\beta \Delta
/// t^2}, d = \frac{\gamma}{\beta \Delta t} @f]
SparseMatrix *jacobian_matrix;
/// vectors containing local material element index for each global element index
ElementTypeMapArray<UInt> element_index_by_material;
/// list of used materials
std::vector <Material *> materials;
/// mapping between material name and material internal id
std::map <std::string, UInt> materials_names_to_id;
/// class defining of to choose a material
MaterialSelector *material_selector;
/// define if it is the default selector or not
bool is_default_material_selector;
/// integration scheme of second order used
IntegrationScheme2ndOrder *integrator;
/// increment of displacement
Array <Real> *increment;
/// flag defining if the increment must be computed or not
bool increment_flag;
/// solver for implicit
Solver *solver;
/// analysis method check the list in akantu::AnalysisMethod
AnalysisMethod method;
/// internal synchronizer for parallel computations
DistributedSynchronizer *synch_parallel;
/// tells if the material are instantiated
bool are_materials_instantiated;
/// map a registered internals to be flattened for dump purposes
std::map<std::pair<std::string,ElementKind>,ElementTypeMapArray<Real> *> registered_internals;
};
/* -------------------------------------------------------------------------- */
namespace BC {
namespace Neumann {
typedef FromHigherDim FromStress;
typedef FromSameDim FromTraction;
}
}
__END_AKANTU__
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "parser.hh"
#include "material.hh"
__BEGIN_AKANTU__
#include "solid_mechanics_model_tmpl.hh"
#if defined (AKANTU_INCLUDE_INLINE_IMPL)
# include "solid_mechanics_model_inline_impl.cc"
#endif
/// standard output stream operator
inline std::ostream & operator << (std::ostream & stream, const SolidMechanicsModel &_this) {
_this.printself(stream);
return stream;
}
__END_AKANTU__
#include "material_selector_tmpl.hh"
#endif /* __AKANTU_SOLID_MECHANICS_MODEL_HH__ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_inline_impl.cc b/src/model/solid_mechanics/solid_mechanics_model_inline_impl.cc
index d4aece91b..48d6b26f6 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_inline_impl.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_inline_impl.cc
@@ -1,609 +1,608 @@
/**
* @file solid_mechanics_model_inline_impl.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Aug 04 2010
* @date last modification: Mon Sep 15 2014
*
* @brief Implementation of the inline functions of the SolidMechanicsModel class
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 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/>.
*
*/
/* -------------------------------------------------------------------------- */
inline Material & SolidMechanicsModel::getMaterial(UInt mat_index) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(mat_index < materials.size(),
"The model " << id << " has no material no "<< mat_index);
AKANTU_DEBUG_OUT();
return *materials[mat_index];
}
/* -------------------------------------------------------------------------- */
inline const Material & SolidMechanicsModel::getMaterial(UInt mat_index) const {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(mat_index < materials.size(),
"The model " << id << " has no material no "<< mat_index);
AKANTU_DEBUG_OUT();
return *materials[mat_index];
}
/* -------------------------------------------------------------------------- */
inline Material & SolidMechanicsModel::getMaterial(const std::string & name) {
AKANTU_DEBUG_IN();
std::map<std::string, UInt>::const_iterator it = materials_names_to_id.find(name);
AKANTU_DEBUG_ASSERT(it != materials_names_to_id.end(),
"The model " << id << " has no material named "<< name);
AKANTU_DEBUG_OUT();
return *materials[it->second];
}
/* -------------------------------------------------------------------------- */
inline UInt SolidMechanicsModel::getMaterialIndex(const std::string & name) const {
AKANTU_DEBUG_IN();
std::map<std::string, UInt>::const_iterator it = materials_names_to_id.find(name);
AKANTU_DEBUG_ASSERT(it != materials_names_to_id.end(),
"The model " << id << " has no material named "<< name);
AKANTU_DEBUG_OUT();
return it->second;
}
/* -------------------------------------------------------------------------- */
inline const Material & SolidMechanicsModel::getMaterial(const std::string & name) const {
AKANTU_DEBUG_IN();
std::map<std::string, UInt>::const_iterator it = materials_names_to_id.find(name);
AKANTU_DEBUG_ASSERT(it != materials_names_to_id.end(),
"The model " << id << " has no material named "<< name);
AKANTU_DEBUG_OUT();
return *materials[it->second];
}
/* -------------------------------------------------------------------------- */
inline void SolidMechanicsModel::setMaterialSelector(MaterialSelector & selector) {
if(is_default_material_selector) delete material_selector;
material_selector = &selector;
is_default_material_selector = false;
}
/* -------------------------------------------------------------------------- */
inline FEEngine & SolidMechanicsModel::getFEEngineBoundary(const ID & name) {
return dynamic_cast<FEEngine &>(getFEEngineClassBoundary<MyFEEngineType>(name));
}
/* -------------------------------------------------------------------------- */
inline void SolidMechanicsModel::splitElementByMaterial(const Array<Element> & elements,
Array<Element> * elements_per_mat) const {
ElementType current_element_type = _not_defined;
GhostType current_ghost_type = _casper;
const Array<UInt> * elem_mat = NULL;
Array<Element>::const_iterator<Element> it = elements.begin();
Array<Element>::const_iterator<Element> end = elements.end();
for (; it != end; ++it) {
Element el = *it;
if(el.type != current_element_type || el.ghost_type != current_ghost_type) {
current_element_type = el.type;
current_ghost_type = el.ghost_type;
elem_mat = &element_index_by_material(el.type, el.ghost_type);
}
UInt old_id = el.element;
el.element = (*elem_mat)(old_id, 1);
elements_per_mat[(*elem_mat)(old_id, 0)].push_back(el);
}
}
/* -------------------------------------------------------------------------- */
inline UInt SolidMechanicsModel::getNbDataForElements(const Array<Element> & elements,
SynchronizationTag tag) const {
AKANTU_DEBUG_IN();
UInt size = 0;
UInt nb_nodes_per_element = 0;
Array<Element>::const_iterator<Element> it = elements.begin();
Array<Element>::const_iterator<Element> end = elements.end();
for (; it != end; ++it) {
const Element & el = *it;
nb_nodes_per_element += Mesh::getNbNodesPerElement(el.type);
}
switch(tag) {
case _gst_material_id: {
size += elements.getSize() * 2 * sizeof(UInt);
break;
}
case _gst_smm_mass: {
size += nb_nodes_per_element * sizeof(Real) * spatial_dimension; // mass vector
break;
}
case _gst_smm_for_gradu: {
size += nb_nodes_per_element * spatial_dimension * sizeof(Real); // displacement
break;
}
case _gst_smm_boundary: {
// force, displacement, boundary
size += nb_nodes_per_element * spatial_dimension * (2 * sizeof(Real) + sizeof(bool));
break;
}
default: { }
}
if(tag != _gst_material_id) {
Array<Element> * elements_per_mat = new Array<Element>[materials.size()];
this->splitElementByMaterial(elements, elements_per_mat);
for (UInt i = 0; i < materials.size(); ++i) {
size += materials[i]->getNbDataForElements(elements_per_mat[i], tag);
}
delete [] elements_per_mat;
}
AKANTU_DEBUG_OUT();
return size;
}
/* -------------------------------------------------------------------------- */
inline void SolidMechanicsModel::packElementData(CommunicationBuffer & buffer,
const Array<Element> & elements,
SynchronizationTag tag) const {
AKANTU_DEBUG_IN();
switch(tag) {
case _gst_material_id: {
packElementalDataHelper(element_index_by_material, buffer, elements, false, getFEEngine());
break;
}
case _gst_smm_mass: {
packNodalDataHelper(*mass, buffer, elements, mesh);
break;
}
case _gst_smm_for_gradu: {
packNodalDataHelper(*displacement, buffer, elements, mesh);
break;
}
case _gst_smm_boundary: {
packNodalDataHelper(*force, buffer, elements, mesh);
packNodalDataHelper(*velocity, buffer, elements, mesh);
packNodalDataHelper(*blocked_dofs, buffer, elements, mesh);
break;
}
default: {
}
}
if(tag != _gst_material_id) {
Array<Element> * elements_per_mat = new Array<Element>[materials.size()];
splitElementByMaterial(elements, elements_per_mat);
for (UInt i = 0; i < materials.size(); ++i) {
materials[i]->packElementData(buffer, elements_per_mat[i], tag);
}
delete [] elements_per_mat;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
inline void SolidMechanicsModel::unpackElementData(CommunicationBuffer & buffer,
const Array<Element> & elements,
SynchronizationTag tag) {
AKANTU_DEBUG_IN();
switch(tag) {
case _gst_material_id: {
unpackElementalDataHelper(element_index_by_material, buffer, elements,
false, getFEEngine());
break;
}
case _gst_smm_mass: {
unpackNodalDataHelper(*mass, buffer, elements, mesh);
break;
}
case _gst_smm_for_gradu: {
unpackNodalDataHelper(*displacement, buffer, elements, mesh);
break;
}
case _gst_smm_boundary: {
unpackNodalDataHelper(*force, buffer, elements, mesh);
unpackNodalDataHelper(*velocity, buffer, elements, mesh);
unpackNodalDataHelper(*blocked_dofs, buffer, elements, mesh);
break;
}
default: {
}
}
if(tag != _gst_material_id) {
Array<Element> * elements_per_mat = new Array<Element>[materials.size()];
splitElementByMaterial(elements, elements_per_mat);
for (UInt i = 0; i < materials.size(); ++i) {
materials[i]->unpackElementData(buffer, elements_per_mat[i], tag);
}
delete [] elements_per_mat;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
inline UInt SolidMechanicsModel::getNbDataToPack(SynchronizationTag tag) const {
AKANTU_DEBUG_IN();
UInt size = 0;
// UInt nb_nodes = mesh.getNbNodes();
switch(tag) {
case _gst_smm_uv: {
size += sizeof(Real) * spatial_dimension * 2;
break;
}
case _gst_smm_res: {
size += sizeof(Real) * spatial_dimension;
break;
}
case _gst_smm_mass: {
size += sizeof(Real) * spatial_dimension;
break;
}
case _gst_for_dump: {
size += sizeof(Real) * spatial_dimension * 5;
break;
}
default: {
AKANTU_DEBUG_ERROR("Unknown ghost synchronization tag : " << tag);
}
}
AKANTU_DEBUG_OUT();
return size;
}
/* -------------------------------------------------------------------------- */
inline UInt SolidMechanicsModel::getNbDataToUnpack(SynchronizationTag tag) const {
AKANTU_DEBUG_IN();
UInt size = 0;
// UInt nb_nodes = mesh.getNbNodes();
switch(tag) {
case _gst_smm_uv: {
size += sizeof(Real) * spatial_dimension * 2;
break;
}
case _gst_smm_res: {
size += sizeof(Real) * spatial_dimension;
break;
}
case _gst_smm_mass: {
size += sizeof(Real) * spatial_dimension;
break;
}
case _gst_for_dump: {
size += sizeof(Real) * spatial_dimension * 5;
break;
}
default: {
AKANTU_DEBUG_ERROR("Unknown ghost synchronization tag : " << tag);
}
}
AKANTU_DEBUG_OUT();
return size;
}
/* -------------------------------------------------------------------------- */
inline void SolidMechanicsModel::packData(CommunicationBuffer & buffer,
const UInt index,
SynchronizationTag tag) const {
AKANTU_DEBUG_IN();
switch(tag) {
case _gst_smm_uv: {
Array<Real>::const_vector_iterator it_disp = displacement->begin(spatial_dimension);
Array<Real>::const_vector_iterator it_velo = velocity->begin(spatial_dimension);
buffer << it_disp[index];
buffer << it_velo[index];
break;
}
case _gst_smm_res: {
Array<Real>::const_vector_iterator it_res = residual->begin(spatial_dimension);
buffer << it_res[index];
break;
}
case _gst_smm_mass: {
AKANTU_DEBUG_INFO("pack mass of node " << index << " which is " << (*mass)(index,0));
Array<Real>::const_vector_iterator it_mass = mass->begin(spatial_dimension);
buffer << it_mass[index];
break;
}
case _gst_for_dump: {
Array<Real>::const_vector_iterator it_disp = displacement->begin(spatial_dimension);
Array<Real>::const_vector_iterator it_velo = velocity->begin(spatial_dimension);
Array<Real>::const_vector_iterator it_acce = acceleration->begin(spatial_dimension);
Array<Real>::const_vector_iterator it_resi = residual->begin(spatial_dimension);
Array<Real>::const_vector_iterator it_forc = force->begin(spatial_dimension);
buffer << it_disp[index];
buffer << it_velo[index];
buffer << it_acce[index];
buffer << it_resi[index];
buffer << it_forc[index];
break;
}
default: {
AKANTU_DEBUG_ERROR("Unknown ghost synchronization tag : " << tag);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
inline void SolidMechanicsModel::unpackData(CommunicationBuffer & buffer,
const UInt index,
SynchronizationTag tag) {
AKANTU_DEBUG_IN();
switch(tag) {
case _gst_smm_uv: {
Array<Real>::vector_iterator it_disp = displacement->begin(spatial_dimension);
Array<Real>::vector_iterator it_velo = velocity->begin(spatial_dimension);
buffer >> it_disp[index];
buffer >> it_velo[index];
break;
}
case _gst_smm_res: {
Array<Real>::vector_iterator it_res = residual->begin(spatial_dimension);
buffer >> it_res[index];
break;
}
case _gst_smm_mass: {
AKANTU_DEBUG_INFO("mass of node " << index << " was " << (*mass)(index,0));
Array<Real>::vector_iterator it_mass = mass->begin(spatial_dimension);
buffer >> it_mass[index];
AKANTU_DEBUG_INFO("mass of node " << index << " is now " << (*mass)(index,0));
break;
}
case _gst_for_dump: {
Array<Real>::vector_iterator it_disp = displacement->begin(spatial_dimension);
Array<Real>::vector_iterator it_velo = velocity->begin(spatial_dimension);
Array<Real>::vector_iterator it_acce = acceleration->begin(spatial_dimension);
Array<Real>::vector_iterator it_resi = residual->begin(spatial_dimension);
Array<Real>::vector_iterator it_forc = force->begin(spatial_dimension);
buffer >> it_disp[index];
buffer >> it_velo[index];
buffer >> it_acce[index];
buffer >> it_resi[index];
buffer >> it_forc[index];
break;
}
default: {
AKANTU_DEBUG_ERROR("Unknown ghost synchronization tag : " << tag);
}
}
AKANTU_DEBUG_OUT();
}
__END_AKANTU__
#include "sparse_matrix.hh"
#include "solver.hh"
__BEGIN_AKANTU__
/* -------------------------------------------------------------------------- */
template <NewmarkBeta::IntegrationSchemeCorrectorType type>
void SolidMechanicsModel::solve(Array<Real> &increment, Real block_val,
- bool need_factorize, bool has_profile_changed,
- const Array<Real> &rhs) {
+ bool need_factorize, bool has_profile_changed) {
if(has_profile_changed) {
this->initJacobianMatrix();
need_factorize = true;
}
updateResidualInternal(); //doesn't do anything for static
if(need_factorize) {
Real c = 0.,d = 0.,e = 0.;
if(method == _static) {
AKANTU_DEBUG_INFO("Solving K inc = r");
e = 1.;
} else {
AKANTU_DEBUG_INFO("Solving (c M + d C + e K) inc = r");
NewmarkBeta * nmb_int = dynamic_cast<NewmarkBeta *>(integrator);
c = nmb_int->getAccelerationCoefficient<type>(time_step);
d = nmb_int->getVelocityCoefficient<type>(time_step);
e = nmb_int->getDisplacementCoefficient<type>(time_step);
}
jacobian_matrix->clear();
// J = c M + d C + e K
if(stiffness_matrix)
jacobian_matrix->add(*stiffness_matrix, e);
if(mass_matrix)
jacobian_matrix->add(*mass_matrix, c);
#if !defined(AKANTU_NDEBUG)
if(mass_matrix && AKANTU_DEBUG_TEST(dblDump))
mass_matrix->saveMatrix("M.mtx");
#endif
if(velocity_damping_matrix)
jacobian_matrix->add(*velocity_damping_matrix, d);
jacobian_matrix->applyBoundary(*blocked_dofs, block_val);
#if !defined(AKANTU_NDEBUG)
if(AKANTU_DEBUG_TEST(dblDump))
jacobian_matrix->saveMatrix("J.mtx");
#endif
solver->factorize();
}
- if (rhs.getSize() != 0)
- solver->setRHS(rhs);
- else
+ // if (rhs.getSize() != 0)
+ // solver->setRHS(rhs);
+ // else
solver->setRHS(*residual);
// solve @f[ J \delta w = r @f]
solver->solve(increment);
UInt nb_nodes = displacement-> getSize();
UInt nb_degree_of_freedom = displacement->getNbComponent() * nb_nodes;
bool * blocked_dofs_val = blocked_dofs->storage();
Real * increment_val = increment.storage();
for (UInt j = 0; j < nb_degree_of_freedom;
++j,++increment_val, ++blocked_dofs_val) {
if ((*blocked_dofs_val))
*increment_val = 0.0;
}
}
/* -------------------------------------------------------------------------- */
template<SolveConvergenceMethod cmethod, SolveConvergenceCriteria criteria>
bool SolidMechanicsModel::solveStatic(Real tolerance, UInt max_iteration,
bool do_not_factorize) {
AKANTU_DEBUG_INFO("Solving Ku = f");
AKANTU_DEBUG_ASSERT(stiffness_matrix != NULL,
"You should first initialize the implicit solver and assemble the stiffness matrix by calling initImplicit");
AnalysisMethod analysis_method=method;
Real error = 0.;
method=_static;
bool converged = this->template solveStep<cmethod, criteria>(tolerance, error, max_iteration, do_not_factorize);
method=analysis_method;
return converged;
}
/* -------------------------------------------------------------------------- */
template<SolveConvergenceMethod cmethod, SolveConvergenceCriteria criteria>
bool SolidMechanicsModel::solveStep(Real tolerance,
UInt max_iteration) {
Real error = 0.;
return this->template solveStep<cmethod,criteria>(tolerance,
error,
max_iteration);
}
/* -------------------------------------------------------------------------- */
template<SolveConvergenceMethod cmethod, SolveConvergenceCriteria criteria>
bool SolidMechanicsModel::solveStep(Real tolerance, Real & error, UInt max_iteration,
bool do_not_factorize) {
EventManager::sendEvent(SolidMechanicsModelEvent::BeforeSolveStepEvent(method));
this->implicitPred();
this->updateResidual();
AKANTU_DEBUG_ASSERT(stiffness_matrix != NULL,
"You should first initialize the implicit solver and assemble the stiffness matrix");
bool need_factorize = !do_not_factorize;
if (method==_implicit_dynamic) {
AKANTU_DEBUG_ASSERT(mass_matrix != NULL,
"You should first initialize the implicit solver and assemble the mass matrix");
}
switch (cmethod) {
case _scm_newton_raphson_tangent:
case _scm_newton_raphson_tangent_not_computed:
break;
case _scm_newton_raphson_tangent_modified:
this->assembleStiffnessMatrix();
break;
default:
AKANTU_DEBUG_ERROR("The resolution method " << cmethod << " has not been implemented!");
}
UInt iter = 0;
bool converged = false;
error = 0.;
if(criteria == _scc_residual) {
converged = this->testConvergence<criteria> (tolerance, error);
if(converged) return converged;
}
do {
if (cmethod == _scm_newton_raphson_tangent)
this->assembleStiffnessMatrix();
solve<NewmarkBeta::_displacement_corrector> (*increment, 1., need_factorize);
this->implicitCorr();
if(criteria == _scc_residual) this->updateResidual();
converged = this->testConvergence<criteria> (tolerance, error);
if(criteria == _scc_increment && !converged) this->updateResidual();
//this->dump();
iter++;
AKANTU_DEBUG_INFO("[" << criteria << "] Convergence iteration "
<< std::setw(std::log10(max_iteration)) << iter
<< ": error " << error << (converged ? " < " : " > ") << tolerance);
switch (cmethod) {
case _scm_newton_raphson_tangent:
need_factorize = true;
break;
case _scm_newton_raphson_tangent_not_computed:
case _scm_newton_raphson_tangent_modified:
need_factorize = false;
break;
default:
AKANTU_DEBUG_ERROR("The resolution method " << cmethod << " has not been implemented!");
}
} while (!converged && iter < max_iteration);
// this makes sure that you have correct strains and stresses after the solveStep function (e.g., for dumping)
if(criteria == _scc_increment) this->updateResidual();
if (converged) {
EventManager::sendEvent(SolidMechanicsModelEvent::AfterSolveStepEvent(method));
} else if(iter == max_iteration) {
AKANTU_DEBUG_WARNING("[" << criteria << "] Convergence not reached after "
<< std::setw(std::log10(max_iteration)) << iter <<
" iteration" << (iter == 1 ? "" : "s") << "!" << std::endl);
}
return converged;
}
diff --git a/src/solver/petsc_matrix.cc b/src/solver/petsc_matrix.cc
index 793f8a196..e64367c3f 100644
--- a/src/solver/petsc_matrix.cc
+++ b/src/solver/petsc_matrix.cc
@@ -1,534 +1,625 @@
/**
* @file petsc_matrix.cc
* @author Aurelia Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @date Mon Jul 21 17:40:41 2014
*
* @brief Implementation of PETSc matrix class
*
* @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 "petsc_matrix.hh"
#include "static_communicator.hh"
#include "static_communicator_mpi.hh"
#include "mpi_type_wrapper.hh"
#include "dof_synchronizer.hh"
+#include "petsc_wrapper.hh"
/* -------------------------------------------------------------------------- */
#include <cstring>
-#include <mpi.h>
-#include <petscmat.h>
-#include <petscao.h>
-#include <petscis.h>
#include <petscsys.h>
-
__BEGIN_AKANTU__
-struct PETScWrapper {
- Mat mat;
- AO ao;
- ISLocalToGlobalMapping mapping;
- /// pointer to the MPI communicator for PETSc commands
- MPI_Comm communicator;
-};
+// struct PETScWrapper {
+// Mat mat;
+// AO ao;
+// ISLocalToGlobalMapping mapping;
+// /// pointer to the MPI communicator for PETSc commands
+// MPI_Comm communicator;
+// };
/* -------------------------------------------------------------------------- */
PETScMatrix::PETScMatrix(UInt size,
const SparseMatrixType & sparse_matrix_type,
const ID & id,
const MemoryID & memory_id) :
SparseMatrix(size, sparse_matrix_type, id, memory_id),
- petsc_wrapper(new PETScWrapper),
- d_nnz(0,1,"dnnz"),
- o_nnz(0,1,"onnz"),
+ petsc_matrix_wrapper(new PETScMatrixWrapper),
+ d_nnz(0,1,"dnnz"),
+ o_nnz(0,1,"onnz"),
first_global_index(0),
- is_petsc_matrix_initialized(false) {
+ is_petsc_matrix_initialized(false) {
AKANTU_DEBUG_IN();
StaticSolver::getStaticSolver().registerEventHandler(*this);
this->offset = 0;
this->init();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
PETScMatrix::PETScMatrix(const SparseMatrix & matrix,
const ID & id,
const MemoryID & memory_id) :
SparseMatrix(matrix, id, memory_id),
- petsc_wrapper(new PETScWrapper),
+ petsc_matrix_wrapper(new PETScMatrixWrapper),
d_nnz(0,1,"dnnz"),
o_nnz(0,1,"onnz"),
first_global_index(0),
is_petsc_matrix_initialized(false) {
- AKANTU_DEBUG_IN();
- StaticSolver::getStaticSolver().registerEventHandler(*this);
- this->offset = 0;
- this->init();
+ // AKANTU_DEBUG_IN();
+ // StaticSolver::getStaticSolver().registerEventHandler(*this);
+ // this->offset = 0;
+ // this->init();
- AKANTU_DEBUG_OUT();
+ // AKANTU_DEBUG_OUT();
+ AKANTU_DEBUG_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
PETScMatrix::~PETScMatrix() {
AKANTU_DEBUG_IN();
+ /// destroy all the PETSc data structures used for this matrix
this->destroyInternalData();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void PETScMatrix::init() {
AKANTU_DEBUG_IN();
+ /// set the communicator that should be used by PETSc
#if defined(AKANTU_USE_MPI)
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
const StaticCommunicatorMPI & mpi_st_comm =
dynamic_cast<const StaticCommunicatorMPI &>(comm.getRealStaticCommunicator());
- this->petsc_wrapper->communicator = mpi_st_comm.getMPITypeWrapper().getMPICommunicator();
+ this->petsc_matrix_wrapper->communicator = mpi_st_comm.getMPITypeWrapper().getMPICommunicator();
#else
- this->petsc_wrapper->communicator = PETSC_COMM_SELF;
+ this->petsc_matrix_wrapper->communicator = PETSC_COMM_SELF;
#endif
PetscErrorCode ierr;
-
- ierr = MatCreate(this->petsc_wrapper->communicator, &(this->petsc_wrapper->mat)); CHKERRXX(ierr);
- /// set matrix type
- ierr = MatSetType(this->petsc_wrapper->mat, MATAIJ); CHKERRXX(ierr);
+
+ /// create the PETSc matrix object
+ ierr = MatCreate(this->petsc_matrix_wrapper->communicator, &(this->petsc_matrix_wrapper->mat)); CHKERRXX(ierr);
- //if (this->sparse_matrix_type==_symmetric)
- /// set flag for symmetry to enable ICC/Cholesky preconditioner
- // ierr = MatSetOption(this->petsc_wrapper->mat, MAT_SYMMETRIC, PETSC_TRUE); CHKERRXX(ierr);
+ /**
+ * Set the matrix type
+ * @todo PETSc does currently not support a straightforward way to
+ * apply Dirichlet boundary conditions for MPISBAIJ
+ * matrices. Therefore always the entire matrix is allocated. It
+ * would be possible to use MATSBAIJ for sequential matrices in case
+ * memory becomes critical. Also, block matrices would give a much
+ * better performance. Modify this in the future!
+ */
+ ierr = MatSetType(this->petsc_matrix_wrapper->mat, MATAIJ); CHKERRXX(ierr);
+
this->is_petsc_matrix_initialized = true;
-
+
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
-void PETScMatrix::resize(const DOFSynchronizer & dof_synchronizer) {
+/**
+ * With this method each processor computes the dimensions of the
+ * local matrix, i.e. the part of the global matrix it is storing.
+ * @param dof_synchronizer dof synchronizer that maps the local
+ * dofs to the global dofs and the equation numbers, i.e., the
+ * position at which the dof is assembled in the matrix
+ */
+void PETScMatrix::setSize() {
AKANTU_DEBUG_IN();
PetscErrorCode ierr;
- this->dof_synchronizer = &const_cast<DOFSynchronizer &>(dof_synchronizer);
-
/// find the number of dofs corresponding to master or local nodes
- UInt nb_dofs = dof_synchronizer.getNbDOFs();
+ UInt nb_dofs = this->dof_synchronizer->getNbDOFs();
UInt nb_local_master_dofs = 0;
/// create array to store the global equation number of all local and master dofs
Array<Int> local_master_eq_nbs(nb_dofs);
Array<Int>::scalar_iterator it_eq_nb = local_master_eq_nbs.begin();
- /// get the pointer to the gloabl equation number array
- Int * eq_nb_val = dof_synchronizer.getGlobalDOFEquationNumbers().storage();
+ /// get the pointer to the global equation number array
+ Int * eq_nb_val = this->dof_synchronizer->getGlobalDOFEquationNumbers().storage();
for (UInt i = 0; i <nb_dofs; ++i) {
- if (dof_synchronizer.isLocalOrMasterDOF(i) ) {
+ if (this->dof_synchronizer->isLocalOrMasterDOF(i) ) {
*it_eq_nb = eq_nb_val[i];
++it_eq_nb;
++nb_local_master_dofs;
}
}
local_master_eq_nbs.resize(nb_local_master_dofs);
/// set the local size
this->local_size = nb_local_master_dofs;
/// resize PETSc matrix
#if defined(AKANTU_USE_MPI)
- ierr = MatSetSizes(this->petsc_wrapper->mat, this->local_size, this->local_size, this->size, this->size); CHKERRXX(ierr);
+ ierr = MatSetSizes(this->petsc_matrix_wrapper->mat, this->local_size, this->local_size, this->size, this->size); CHKERRXX(ierr);
#else
- ierr = MatSetSizes(this->petsc_wrapper->mat, this->local_size, this->local_size); CHKERRXX(ierr);
+ ierr = MatSetSizes(this->petsc_matrix_wrapper->mat, this->local_size, this->local_size); CHKERRXX(ierr);
#endif
/// create mapping from akantu global numbering to petsc global numbering
this->createGlobalAkantuToPETScMap(local_master_eq_nbs.storage());
+
+
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
+/**
+ * This method generates a mapping from the global Akantu equation
+ * numbering to the global PETSc dof ordering
+ * @param local_master_eq_nbs_ptr Int pointer to the array of equation
+ * numbers of all local or master dofs, i.e. the row indices of the
+ * local matrix
+ */
void PETScMatrix::createGlobalAkantuToPETScMap(Int* local_master_eq_nbs_ptr) {
AKANTU_DEBUG_IN();
PetscErrorCode ierr;
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
UInt rank = comm.whoAmI();
//initialize vector to store the number of local and master nodes that are assigned to each processor
Vector<UInt> master_local_ndofs_per_proc(nb_proc);
/// store the nb of master and local dofs on each processor
master_local_ndofs_per_proc(rank) = this->local_size;
/// exchange the information among all processors
comm.allGather(master_local_ndofs_per_proc.storage(), 1);
/// each processor creates a map for his akantu global dofs to the corresponding petsc global dofs
/// determine the PETSc-index for the first dof on each processor
for (UInt i = 0; i < rank; ++i) {
this->first_global_index += master_local_ndofs_per_proc(i);
}
/// create array for petsc ordering
Array<Int> petsc_dofs(this->local_size);
Array<Int>::scalar_iterator it_petsc_dofs = petsc_dofs.begin();
for (Int i = this->first_global_index; i < this->first_global_index + this->local_size; ++i, ++it_petsc_dofs) {
*it_petsc_dofs = i;
}
- ierr = AOCreateBasic(this->petsc_wrapper->communicator, this->local_size, local_master_eq_nbs_ptr, petsc_dofs.storage(), &(this->petsc_wrapper->ao)); CHKERRXX(ierr);
+ ierr = AOCreateBasic(this->petsc_matrix_wrapper->communicator, this->local_size, local_master_eq_nbs_ptr, petsc_dofs.storage(), &(this->petsc_matrix_wrapper->ao)); CHKERRXX(ierr);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
// void PETScMatrix::createLocalAkantuToPETScMap(const DOFSynchronizer & dof_synchronizer) {
// AKANTU_DEBUG_IN();
-// AKANTU_DEBUG_ASSERT(this->petsc_wrapper->ao != NULL,
+// AKANTU_DEBUG_ASSERT(this->petsc_matrix_wrapper->ao != NULL,
// "You should first create a mapping from the global"
// << " Akantu numbering to the global PETSc numbering");
+// PetscErrorCode ierr;
+
// this->dof_synchronizer = &const_cast<DOFSynchronizer &>(dof_synchronizer);
// /// get the number of dofs
// Int nb_dofs = dof_synchronizer.getNbDOFs();
// /// get the global equation numbers for each node
// Array<Int> global_dof_equation_numbers = dof_synchronizer.getGlobalDOFEquationNumbers();
// /// map the global dof equation numbers to the corresponding PETSc ordering
-// AOApplicationToPETSc(this->petsc_wrapper->ao, nb_dofs,
-// global_dof_equation_numbers.storage());
+// ierr = AOApplicationToPETSc(this->petsc_matrix_wrapper->ao, nb_dofs,
+// global_dof_equation_numbers.storage()); CHKERRXX(ierr);
// /// create the mapping from the local Akantu ordering to the global PETSc ordering
-// ISLocalToGlobalMappingCreate(this->petsc_wrapper->communicator,
+// ierr = ISLocalToGlobalMappingCreate(this->petsc_matrix_wrapper->communicator,
// 1, nb_dofs, global_dof_equation_numbers.storage(),
-// PETSC_COPY_VALUES, mapping);
+// PETSC_COPY_VALUES, &(this->petsc_matrix_wrapper-mapping)); CHKERRXX(ierr);
// AKANTU_DEBUG_OUT();
// }
/* -------------------------------------------------------------------------- */
+/**
+ * This function creates the non-zero pattern of the PETSc matrix. In
+ * PETSc the parallel matrix is partitioned across processors such
+ * that the first m0 rows belong to process 0, the next m1 rows belong
+ * to process 1, the next m2 rows belong to process 2 etc.. where
+ * m0,m1,m2,.. are the input parameter 'm'. i.e each processor stores
+ * values corresponding to [m x N] submatrix
+ * (http://www.mcs.anl.gov/petsc/).
+ * @param mesh mesh discretizing the domain we want to analyze
+ * @param dof_synchronizer dof synchronizer that maps the local
+ * dofs to the global dofs and the equation numbers, i.e., the
+ * position at which the dof is assembled in the matrix
+ */
+
void PETScMatrix::buildProfile(const Mesh & mesh, const DOFSynchronizer & dof_synchronizer, UInt nb_degree_of_freedom) {
AKANTU_DEBUG_IN();
//clearProfile();
-
+ this->dof_synchronizer = &const_cast<DOFSynchronizer &>(dof_synchronizer);
+ this->setSize();
PetscErrorCode ierr;
/// resize arrays to store the number of nonzeros in each row
this->d_nnz.resize(this->local_size);
this->o_nnz.resize(this->local_size);
/// set arrays to zero everywhere
this->d_nnz.set(0);
this->o_nnz.set(0);
- this->dof_synchronizer = &const_cast<DOFSynchronizer &>(dof_synchronizer);
// if(irn_jcn_to_k) delete irn_jcn_to_k;
// irn_jcn_to_k = new std::map<std::pair<UInt, UInt>, UInt>;
coordinate_list_map::iterator irn_jcn_k_it;
Int * eq_nb_val = dof_synchronizer.getGlobalDOFEquationNumbers().storage();
UInt nb_global_dofs = dof_synchronizer.getNbGlobalDOFs();
/// Loop over all the ghost types
for (ghost_type_t::iterator gt = ghost_type_t::begin(); gt != ghost_type_t::end(); ++gt) {
const GhostType & ghost_type = *gt;
Mesh::type_iterator it = mesh.firstType(mesh.getSpatialDimension(), ghost_type, _ek_not_defined);
Mesh::type_iterator end = mesh.lastType (mesh.getSpatialDimension(), ghost_type, _ek_not_defined);
for(; it != end; ++it) {
- UInt nb_element = mesh.getNbElement(*it);
+ UInt nb_element = mesh.getNbElement(*it, ghost_type);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(*it);
UInt size_mat = nb_nodes_per_element * nb_degree_of_freedom;
UInt * conn_val = mesh.getConnectivity(*it, ghost_type).storage();
Int * local_eq_nb_val = new Int[nb_degree_of_freedom * nb_nodes_per_element];
for (UInt e = 0; e < nb_element; ++e) {
Int * tmp_local_eq_nb_val = local_eq_nb_val;
for (UInt i = 0; i < nb_nodes_per_element; ++i) {
UInt n = conn_val[i];
for (UInt d = 0; d < nb_degree_of_freedom; ++d) {
+ /**
+ * !!!!!!Careful!!!!!! This is a ugly fix. @todo this is a
+ * very ugly fix, because the offset for the global
+ * equation number, where the dof will be assembled, is
+ * hardcoded. In the future a class dof manager has to be
+ * added to Akantu to handle the mapping between the dofs
+ * and the equation numbers
+ *
+ */
+
*tmp_local_eq_nb_val++ = eq_nb_val[n * nb_degree_of_freedom + d] - (dof_synchronizer.isPureGhostDOF(n * nb_degree_of_freedom + d) ? nb_global_dofs : 0);
}
- // memcpy(tmp_local_eq_nb_val, eq_nb_val + n * nb_degree_of_freedom, nb_degree_of_freedom * sizeof(Int));
- // tmp_local_eq_nb_val += nb_degree_of_freedom;
}
for (UInt i = 0; i < size_mat; ++i) {
Int c_irn = local_eq_nb_val[i];
- UInt j_start = (sparse_matrix_type == _symmetric) ? i : 0;
+ UInt j_start = 0;
for (UInt j = j_start; j < size_mat; ++j) {
Int c_jcn = local_eq_nb_val[j];
Array<Int> index_pair(2,1);
index_pair(0) = c_irn;
index_pair(1) = c_jcn;
- AOApplicationToPetsc(this->petsc_wrapper->ao, 2, index_pair.storage());
- if(sparse_matrix_type == _symmetric && (index_pair(0) > index_pair(1)))
- std::swap(index_pair(0), index_pair(1));
+ AOApplicationToPetsc(this->petsc_matrix_wrapper->ao, 2, index_pair.storage());
if (index_pair(0) >= first_global_index && index_pair(0) < first_global_index + this->local_size) {
- KeyCOO irn_jcn = key(c_irn, c_jcn);
+ KeyCOO irn_jcn = keyPETSc(c_irn, c_jcn);
irn_jcn_k_it = irn_jcn_k.find(irn_jcn);
if (irn_jcn_k_it == irn_jcn_k.end()) {
irn_jcn_k[irn_jcn] = nb_non_zero;
// check if node is slave node
if (index_pair(1) >= first_global_index && index_pair(1) < first_global_index + this->local_size)
this->d_nnz(index_pair(0) - first_global_index) += 1;
else
this->o_nnz(index_pair(0) - first_global_index) += 1;
nb_non_zero++;
}
}
}
}
conn_val += nb_nodes_per_element;
}
delete [] local_eq_nb_val;
}
}
// /// for pbc @todo correct it for parallel
// if(StaticCommunicator::getStaticCommunicator().getNbProc() == 1) {
// for (UInt i = 0; i < size; ++i) {
// KeyCOO irn_jcn = key(i, i);
// irn_jcn_k_it = irn_jcn_k.find(irn_jcn);
// if(irn_jcn_k_it == irn_jcn_k.end()) {
// irn_jcn_k[irn_jcn] = nb_non_zero;
// irn.push_back(i + 1);
// jcn.push_back(i + 1);
// nb_non_zero++;
// }
// }
// }
// std::string mat_type;
// mat_type.resize(20, 'a');
// std::cout << "MatType: " << mat_type << std::endl;
// const char * mat_type_ptr = mat_type.c_str();
-
MatType type;
- MatGetType(this->petsc_wrapper->mat, &type);
-
- // PetscTypeCompare((PetscObject)(this->petsc_wrapper->mat),MATSEQAIJ,&sametype);
- //ierr = PetscTypeCompare(pet, MATSEQAIJ, &sametype); CHKERRXX(ierr);
-
+ MatGetType(this->petsc_matrix_wrapper->mat, &type);
+ std::cout << "the matrix type is: " << type << std::endl;
+ /**
+ * PETSc will use only one of the following preallocation commands
+ * depending on the matrix type and ignore the rest. Note that for
+ * the block matrix format a block size of 1 is used. This might
+ * result in bad performance. @todo For better results implement
+ * buildProfile() with larger block size.
+ *
+ */
/// build profile:
if (strcmp(type, MATSEQAIJ) == 0) {
- ierr = MatSeqAIJSetPreallocation(this->petsc_wrapper->mat,
- 0, d_nnz.storage()); CHKERRXX(ierr);
+ ierr = MatSeqAIJSetPreallocation(this->petsc_matrix_wrapper->mat,
+ 0, d_nnz.storage()); CHKERRXX(ierr);
} else if ((strcmp(type, MATMPIAIJ) == 0)) {
- ierr = MatMPIAIJSetPreallocation(this->petsc_wrapper->mat,
- 0, d_nnz.storage(), 0,
- o_nnz.storage()); CHKERRXX(ierr);
+ ierr = MatMPIAIJSetPreallocation(this->petsc_matrix_wrapper->mat,
+ 0, d_nnz.storage(), 0,
+ o_nnz.storage()); CHKERRXX(ierr);
} else {
AKANTU_DEBUG_ERROR("The type " << type << " of PETSc matrix is not handled by"
- << " akantu in the preallocation step");
+ << " akantu in the preallocation step");
}
+ //ierr = MatSeqSBAIJSetPreallocation(this->petsc_matrix_wrapper->mat, 1,
+ // 0, d_nnz.storage()); CHKERRXX(ierr);
+
+ if (this->sparse_matrix_type==_symmetric) {
+ /// set flag for symmetry to enable ICC/Cholesky preconditioner
+ ierr = MatSetOption(this->petsc_matrix_wrapper->mat, MAT_SYMMETRIC, PETSC_TRUE); CHKERRXX(ierr);
+ }
+ /// once the profile has been build ignore any new nonzero locations
+ ierr = MatSetOption(this->petsc_matrix_wrapper->mat, MAT_NEW_NONZERO_LOCATIONS, PETSC_TRUE); CHKERRXX(ierr);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
-void PETScMatrix::saveMatrix(const std::string & filename) const {
+/**
+ * Method to save the nonzero pattern and the values stored at each position
+ * @param filename name of the file in which the information will be stored
+ */
+void PETScMatrix::saveMatrix(const std::string & filename) const{
AKANTU_DEBUG_IN();
PetscErrorCode ierr;
-
+
/// create Petsc viewer
PetscViewer viewer;
- ierr = PetscViewerASCIIOpen(this->petsc_wrapper->communicator, filename.c_str(), &viewer); CHKERRXX(ierr);
+ ierr = PetscViewerASCIIOpen(this->petsc_matrix_wrapper->communicator, filename.c_str(), &viewer); CHKERRXX(ierr);
/// set the format
PetscViewerSetFormat(viewer, PETSC_VIEWER_DEFAULT); CHKERRXX(ierr);
/// save the matrix
- ierr = MatView(this->petsc_wrapper->mat, viewer); CHKERRXX(ierr);
+ ierr = MatView(this->petsc_matrix_wrapper->mat, viewer); CHKERRXX(ierr);
/// destroy the viewer
ierr = PetscViewerDestroy(&viewer); CHKERRXX(ierr);
AKANTU_DEBUG_OUT();
}
-// /* -------------------------------------------------------------------------- */
-// Array<Real> & operator*=(Array<Real> & vect, const PETScMatrix & mat) {
-// AKANTU_DEBUG_IN();
-
-// Array<Real> result
-// MatMult(this->mat, vect, )
-
-// // AKANTU_DEBUG_ASSERT((vect.getSize()*vect.getNbComponent() == mat.getSize()) &&
-// // (vect.getNbComponent() == mat.getNbDegreOfFreedom()),
-// // "The size of the matrix and the vector do not match");
-
-// const PETScMatrixType & sparse_matrix_type = mat.getPETScMatrixType();
-// DOFSynchronizer * dof_synchronizer = mat.getDOFSynchronizerPointer();
-
-// UInt nb_non_zero = mat.getNbNonZero();
-// Real * tmp = new Real [vect.getNbComponent() * vect.getSize()];
-// std::fill_n(tmp, vect.getNbComponent() * vect.getSize(), 0);
-
-// Int * i_val = mat.getIRN().storage();
-// Int * j_val = mat.getJCN().storage();
-// Real * a_val = mat.getA().storage();
-
-// Real * vect_val = vect.storage();
-
-// for (UInt k = 0; k < nb_non_zero; ++k) {
-// UInt i = *(i_val++);
-// UInt j = *(j_val++);
-// Real a = *(a_val++);
-
-// UInt local_i = i - 1;
-// UInt local_j = j - 1;
-// if(dof_synchronizer) {
-// local_i = dof_synchronizer->getDOFLocalID(local_i);
-// local_j = dof_synchronizer->getDOFLocalID(local_j);
-// }
-
-// tmp[local_i] += a * vect_val[local_j];
-// if((sparse_matrix_type == _symmetric) && (local_i != local_j))
-// tmp[local_j] += a * vect_val[local_i];
-// }
-
-// memcpy(vect_val, tmp, vect.getNbComponent() * vect.getSize() * sizeof(Real));
-// delete [] tmp;
-
-// if(dof_synchronizer)
-// dof_synchronizer->reduceSynchronize<AddOperation>(vect);
-
-// AKANTU_DEBUG_OUT();
-
-// return vect;
-// }
-
-// /* -------------------------------------------------------------------------- */
-// void PETScMatrix::copyContent(const PETScMatrix & matrix) {
-// AKANTU_DEBUG_IN();
-// AKANTU_DEBUG_ASSERT(nb_non_zero == matrix.getNbNonZero(),
-// "The two matrices don't have the same profiles");
-
-// MatCopy(this->mat, matrix->mat, SAME_NONZERO_PATTERN);
-
-// AKANTU_DEBUG_OUT();
-// }
-
-// ///* -------------------------------------------------------------------------- */
-// //void PETScMatrix::copyProfile(const PETScMatrix & matrix) {
-// // AKANTU_DEBUG_IN();
-// // irn = matrix.irn;
-// // jcn = matrix.jcn;
-// // nb_non_zero = matrix.nb_non_zero;
-// // irn_jcn_k = matrix.irn_jcn_k;
-// // a.resize(nb_non_zero);
-// // AKANTU_DEBUG_OUT();
-// //}
-
/* -------------------------------------------------------------------------- */
+/**
+ * Method to add an Akantu sparse matrix to the PETSc matrix
+ * @param matrix Akantu sparse matrix to be added
+ * @param alpha the factor specifying how many times the matrix should be added
+ */
void PETScMatrix::add(const SparseMatrix & matrix, Real alpha) {
PetscErrorCode ierr;
// AKANTU_DEBUG_ASSERT(nb_non_zero == matrix.getNbNonZero(),
// "The two matrix don't have the same profiles");
for (UInt n = 0; n < matrix.getNbNonZero(); ++n) {
Array<Int> index(2,1);
index(0) = matrix.getIRN()(n)-matrix.getOffset();
index(1) = matrix.getJCN()(n)-matrix.getOffset();
- AOApplicationToPetsc(this->petsc_wrapper->ao, 2, index.storage());
- if (_symmetric && index(0) > index(1))
+ AOApplicationToPetsc(this->petsc_matrix_wrapper->ao, 2, index.storage());
+ if (this->sparse_matrix_type == _symmetric && index(0) > index(1))
std::swap(index(0), index(1));
- ierr = MatSetValue(this->petsc_wrapper->mat, index(0), index(1), matrix.getA()(n) * alpha, ADD_VALUES); CHKERRXX(ierr);
+ /// MatSetValue might be very slow for MATBAIJ, might need to use MatSetValuesBlocked
+ ierr = MatSetValue(this->petsc_matrix_wrapper->mat, index(0), index(1), matrix.getA()(n) * alpha, ADD_VALUES); CHKERRXX(ierr);
+ /// chek if sparse matrix to be added is symmetric. In this case
+ /// the value also needs to be added at the transposed location in
+ /// the matrix because PETSc is using the full profile, also for symmetric matrices
+ if (matrix.getSparseMatrixType() == _symmetric && index(0) != index(1))
+ ierr = MatSetValue(this->petsc_matrix_wrapper->mat, index(1), index(0), matrix.getA()(n) * alpha, ADD_VALUES); CHKERRXX(ierr);
}
+ this->performAssembly();
+}
-
+/* -------------------------------------------------------------------------- */
+/**
+ * Method to add another PETSc matrix to this PETSc matrix
+ * @param matrix PETSc matrix to be added
+ * @param alpha the factor specifying how many times the matrix should be added
+ */
+void PETScMatrix::add(const PETScMatrix & matrix, Real alpha) {
+ PetscErrorCode ierr;
+ ierr = MatAXPY(this->petsc_matrix_wrapper->mat, alpha, matrix.petsc_matrix_wrapper->mat, SAME_NONZERO_PATTERN); CHKERRXX(ierr);
+ this->performAssembly();
}
/* -------------------------------------------------------------------------- */
+/**
+ * MatSetValues() generally caches the values. The matrix is ready to
+ * use only after MatAssemblyBegin() and MatAssemblyEnd() have been
+ * called. (http://www.mcs.anl.gov/petsc/)
+ */
void PETScMatrix::performAssembly() {
PetscErrorCode ierr;
- ierr = MatAssemblyBegin(this->petsc_wrapper->mat, MAT_FINAL_ASSEMBLY); CHKERRXX(ierr);
- ierr = MatAssemblyEnd(this->petsc_wrapper->mat, MAT_FINAL_ASSEMBLY); CHKERRXX(ierr);
+ ierr = MatAssemblyBegin(this->petsc_matrix_wrapper->mat, MAT_FINAL_ASSEMBLY); CHKERRXX(ierr);
+ ierr = MatAssemblyEnd(this->petsc_matrix_wrapper->mat, MAT_FINAL_ASSEMBLY); CHKERRXX(ierr);
}
/* -------------------------------------------------------------------------- */
+/**
+ * Method is called when the static solver is destroyed, just before
+ * PETSc is finalized. So all PETSc objects need to be destroyed at
+ * this point.
+ */
void PETScMatrix::beforeStaticSolverDestroy() {
AKANTU_DEBUG_IN();
try{
this->destroyInternalData();
} catch(...) {}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
+ /// destroy all the PETSc data structures used for this matrix
void PETScMatrix::destroyInternalData() {
AKANTU_DEBUG_IN();
if(this->is_petsc_matrix_initialized) {
PetscErrorCode ierr;
- ierr = MatDestroy(&(this->petsc_wrapper->mat)); CHKERRXX(ierr);
- delete petsc_wrapper;
+ ierr = MatDestroy(&(this->petsc_matrix_wrapper->mat)); CHKERRXX(ierr);
+ delete petsc_matrix_wrapper;
this->is_petsc_matrix_initialized = false;
}
AKANTU_DEBUG_OUT();
}
+
+/* -------------------------------------------------------------------------- */
+/// access K(i, j). Works only for dofs on this processor!!!!
+Real PETScMatrix::operator()(UInt i, UInt j) const{
+ AKANTU_DEBUG_IN();
+
+ AKANTU_DEBUG_ASSERT(this->dof_synchronizer->isLocalOrMasterDOF(i) && this->dof_synchronizer->isLocalOrMasterDOF(j), "Operator works only for dofs on this processor");
+
+ Array<Int> index(2,1);
+ index(0) = this->dof_synchronizer->getDOFGlobalID(i);
+ index(1) = this->dof_synchronizer->getDOFGlobalID(j);
+ AOApplicationToPetsc(this->petsc_matrix_wrapper->ao, 2, index.storage());
+
+ Real value = 0;
+
+ PetscErrorCode ierr;
+ /// @todo MatGetValue might be very slow for MATBAIJ, might need to use MatGetValuesBlocked
+ ierr = MatGetValues(this->petsc_matrix_wrapper->mat, 1, &index(0), 1, &index(1), &value); CHKERRXX(ierr);
+
+
+ AKANTU_DEBUG_OUT();
+
+
+ return value;
+
+}
+
+/* -------------------------------------------------------------------------- */
+/**
+ * Apply Dirichlet boundary conditions by zeroing the rows and columns which correspond to blocked dofs
+ * @param boundary array of booleans which are true if the dof at this position is blocked
+ * @param block_val the value in the diagonal entry of blocked rows
+ */
+void PETScMatrix::applyBoundary(const Array<bool> & boundary, Real block_val) {
+ AKANTU_DEBUG_IN();
+
+ PetscErrorCode ierr;
+
+ /// get the global equation numbers to find the rows that need to be zeroed for the blocked dofs
+ Int * eq_nb_val = dof_synchronizer->getGlobalDOFEquationNumbers().storage();
+
+ /// every processor calls the MatSetZero() only for his local or master dofs. This assures that not two processors or more try to zero the same row
+ Int nb_blocked_local_master_eq_nb = 0;
+ Array<Int> blocked_local_master_eq_nb(this->local_size / boundary.getNbComponent(), boundary.getNbComponent());
+ Int * blocked_lm_eq_nb_ptr = blocked_local_master_eq_nb.storage();
+ for (UInt i = 0; i < boundary.getSize(); ++i) {
+ for (UInt j = 0; j < boundary.getNbComponent(); ++j) {
+ UInt local_dof = i * boundary.getNbComponent() + j;
+ if (boundary(i, j) == true && this->dof_synchronizer->isLocalOrMasterDOF(local_dof)) {
+ Int global_eq_nb = *eq_nb_val;
+ *blocked_lm_eq_nb_ptr = global_eq_nb;
+ ++ nb_blocked_local_master_eq_nb;
+ ++blocked_lm_eq_nb_ptr;
+ ++eq_nb_val;
+ }
+ }
+ }
+ blocked_local_master_eq_nb.resize(nb_blocked_local_master_eq_nb/boundary.getNbComponent());
+
+
+ ierr = AOApplicationToPetsc(this->petsc_matrix_wrapper->ao, nb_blocked_local_master_eq_nb, blocked_local_master_eq_nb.storage() ); CHKERRXX(ierr);
+ ierr = MatZeroRowsColumns(this->petsc_matrix_wrapper->mat, nb_blocked_local_master_eq_nb, blocked_local_master_eq_nb.storage(), block_val, 0, 0); CHKERRXX(ierr);
+
+ this->performAssembly();
+ AKANTU_DEBUG_OUT();
+}
+
+/* -------------------------------------------------------------------------- */
+/// set all entries to zero while keeping the same nonzero pattern
+void PETScMatrix::clear() {
+ MatZeroEntries(this->petsc_matrix_wrapper->mat);
+}
+
__END_AKANTU__
diff --git a/src/solver/petsc_matrix.hh b/src/solver/petsc_matrix.hh
index ea1369539..d09eae806 100644
--- a/src/solver/petsc_matrix.hh
+++ b/src/solver/petsc_matrix.hh
@@ -1,158 +1,146 @@
/**
* @file petsc_matrix.hh
* @author Aurelia Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @date Mon Jul 21 14:49:49 2014
*
* @brief Interface for PETSc matrices
*
* @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/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_PETSC_MATRIX_HH__
#define __AKANTU_PETSC_MATRIX_HH__
/* -------------------------------------------------------------------------- */
#include "sparse_matrix.hh"
#include "static_communicator.hh"
#include "static_solver.hh"
/* -------------------------------------------------------------------------- */
__BEGIN_AKANTU__
-class PETScWrapper;
+class PETScMatrixWrapper;
class PETScMatrix : public SparseMatrix, StaticSolverEventHandler {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
PETScMatrix(UInt size,
const SparseMatrixType & sparse_matrix_type,
const ID & id = "petsc_matrix",
const MemoryID & memory_id = 0);
PETScMatrix(const SparseMatrix & matrix,
const ID & id = "petsc_matrix",
const MemoryID & memory_id = 0);
virtual ~PETScMatrix();
private:
/// init internal PETSc matrix
void init();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
- /// resize PETSc matrix
- void resize(const DOFSynchronizer & dof_synchronizer);
- void createGlobalAkantuToPETScMap(Int* local_master_eq_nbs_ptr);
-
- // /// remove the existing profile
- // inline void clearProfile();
-
- // /// add a non-zero element
- // virtual UInt addToProfile(UInt i, UInt j);
-
- // /// set the matrix to 0
- // inline void clear();
-
- // /// assemble a local matrix in the sparse one
- // inline void addToMatrix(UInt i, UInt j, Real value);
+ /// set the matrix to 0
+ virtual void clear();
/// fill the profil of the matrix
virtual void buildProfile(const Mesh & mesh, const DOFSynchronizer & dof_synchronizer, UInt nb_degree_of_freedom);
- // /// modify the matrix to "remove" the blocked dof
- // virtual void applyBoundary(const Array<bool> & boundary, Real block_val = 1.);
-
- /// perform assembly so that matrix is ready for use
- void performAssembly();
-
- // /// restore the profile that was before removing the boundaries
- // virtual void restoreProfile();
+ /// modify the matrix to "remove" the blocked dof
+ virtual void applyBoundary(const Array<bool> & boundary, Real block_val = 1.);
- // /// save the profil in a file using the MatrixMarket file format
- // virtual void saveProfile(const std::string & filename) const;
-
- /// save the matrix in a file using the MatrixMarket file format
+ /// save the matrix in a ASCII file format
virtual void saveMatrix(const std::string & filename) const;
- // /// copy assuming the profile are the same
- // virtual void copyContent(const SparseMatrix & matrix);
-
- // /// copy profile
- // // void copyProfile(const SparseMatrix & matrix);
-
- /// add matrix assuming the profile are the same
+ /// add a sparse matrix assuming the profile are the same
virtual void add(const SparseMatrix & matrix, Real alpha);
+ /// add a petsc matrix assuming the profile are the same
+ virtual void add(const PETScMatrix & matrix, Real alpha);
- // /// diagonal lumping
- // virtual void lump(Array<Real> & lumped);
-
- // /// function to print the contain of the class
- // //virtual void printself(std::ostream & stream, int indent = 0) const;
virtual void beforeStaticSolverDestroy();
+ Real operator()(UInt i, UInt j) const;
+
+protected:
+ inline KeyCOO keyPETSc(UInt i, UInt j) const {
+ return std::make_pair(i, j);
+ }
+
private:
virtual void destroyInternalData();
+ /// set the size of the PETSc matrix
+ void setSize();
+ void createGlobalAkantuToPETScMap(Int* local_master_eq_nbs_ptr);
+ void createLocalAkantuToPETScMap(const DOFSynchronizer & dof_synchronizer);
+ /// perform assembly so that matrix is ready for use
+ void performAssembly();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
+public:
+
+ AKANTU_GET_MACRO(PETScMatrixWrapper, petsc_matrix_wrapper, PETScMatrixWrapper*);
+ AKANTU_GET_MACRO(LocalSize, local_size, Int);
+ /// AKANTU_GET_MACRO(LocalSize, local_size, Int);
+
+
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// store the PETSc structures
- PETScWrapper * petsc_wrapper;
+ PETScMatrixWrapper * petsc_matrix_wrapper;
/// size of the diagonal part of the matrix partition
Int local_size;
/// number of nonzeros in every row of the diagonal part
Array<Int> d_nnz;
/// number of nonzeros in every row of the off-diagonal part
Array<Int> o_nnz;
/// the global index of the first local row
Int first_global_index;
/// bool to indicate if the matrix data has been initialized by calling MatCreate
bool is_petsc_matrix_initialized;
-
};
__END_AKANTU__
-#endif /* __AKANTU_PETSCI_MATRIX_HH__ */
+#endif /* __AKANTU_PETSC_MATRIX_HH__ */
diff --git a/src/solver/petsc_wrapper.hh b/src/solver/petsc_wrapper.hh
index af1704e44..14bd59b4e 100644
--- a/src/solver/petsc_wrapper.hh
+++ b/src/solver/petsc_wrapper.hh
@@ -1,61 +1,62 @@
/**
* @file petsc_wrapper.hh
* @author Aurelia Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @date Mon Jul 21 17:40:41 2014
*
* @brief Wrapper of PETSc structures
*
* @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/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_PETSC_WRAPPER_HH__
#define __AKANTU_PETSC_WRAPPER_HH__
/* -------------------------------------------------------------------------- */
#include <mpi.h>
#include <petscmat.h>
+#include <petscvec.h>
#include <petscao.h>
#include <petscis.h>
#include <petscksp.h>
__BEGIN_AKANTU__
struct PETScMatrixWrapper {
Mat mat;
AO ao;
ISLocalToGlobalMapping mapping;
/// pointer to the MPI communicator for PETSc commands
MPI_Comm communicator;
};
struct PETScSolverWrapper {
KSP ksp;
Vec solution;
Vec rhs;
/// pointer to the MPI communicator for PETSc commands
MPI_Comm communicator;
};
__END_AKANTU__
#endif /* __AKANTU_PETSC_WRAPPER_HH__ */
diff --git a/src/solver/solver.cc b/src/solver/solver.cc
index ee6706eb4..7d9d4746e 100644
--- a/src/solver/solver.cc
+++ b/src/solver/solver.cc
@@ -1,76 +1,87 @@
/**
* @file solver.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Dec 13 2010
* @date last modification: Wed Nov 13 2013
*
* @brief Solver interface class
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 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 "solver.hh"
+#include "dof_synchronizer.hh"
/* -------------------------------------------------------------------------- */
__BEGIN_AKANTU__
SolverOptions _solver_no_options(true);
/* -------------------------------------------------------------------------- */
Solver::Solver(SparseMatrix & matrix,
const ID & id,
const MemoryID & memory_id) :
Memory(id, memory_id), StaticSolverEventHandler(),
matrix(&matrix),
is_matrix_allocated(false),
mesh(NULL),
- communicator(StaticCommunicator::getStaticCommunicator()){
+ communicator(StaticCommunicator::getStaticCommunicator()),
+ solution(NULL),
+ synch_registry(NULL) {
AKANTU_DEBUG_IN();
StaticSolver::getStaticSolver().registerEventHandler(*this);
+ //createSynchronizerRegistry();
+ this->synch_registry = new SynchronizerRegistry(*this);
+ synch_registry->registerSynchronizer(this->matrix->getDOFSynchronizer(), _gst_solver_solution);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Solver::~Solver() {
AKANTU_DEBUG_IN();
this->destroyInternalData();
-
+ delete synch_registry;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Solver::beforeStaticSolverDestroy() {
AKANTU_DEBUG_IN();
try{
this->destroyInternalData();
} catch(...) {}
AKANTU_DEBUG_OUT();
}
+/* -------------------------------------------------------------------------- */
+void Solver::createSynchronizerRegistry() {
+ //this->synch_registry = new SynchronizerRegistry(this);
+}
+
__END_AKANTU__
diff --git a/src/solver/solver.hh b/src/solver/solver.hh
index 99bb1bd4a..9377bd932 100644
--- a/src/solver/solver.hh
+++ b/src/solver/solver.hh
@@ -1,134 +1,165 @@
/**
* @file solver.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
+ * @author Aurelia Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
* @date creation: Mon Dec 13 2010
* @date last modification: Mon Sep 15 2014
*
* @brief interface for solvers
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 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_SOLVER_HH__
#define __AKANTU_SOLVER_HH__
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_memory.hh"
#include "aka_array.hh"
#include "sparse_matrix.hh"
#include "mesh.hh"
#include "static_communicator.hh"
#include "static_solver.hh"
+#include "data_accessor.hh"
+#include "synchronizer_registry.hh"
/* -------------------------------------------------------------------------- */
__BEGIN_AKANTU__
class SolverOptions {
public:
SolverOptions(bool no_option = false) : no_option(no_option) { }
virtual ~SolverOptions() {}
private:
bool no_option;
};
extern SolverOptions _solver_no_options;
class Solver : protected Memory,
- public StaticSolverEventHandler {
+ public StaticSolverEventHandler,
+ public DataAccessor {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
Solver(SparseMatrix & matrix,
const ID & id = "solver",
const MemoryID & memory_id = 0);
virtual ~Solver();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the solver
virtual void initialize(SolverOptions & options = _solver_no_options) = 0;
virtual void analysis() {};
virtual void factorize() {};
/// solve
virtual void solve(Array<Real> & solution) = 0;
virtual void solve() = 0;
- virtual void setRHS(const Array<Real> & rhs) = 0;
+ virtual void setRHS(Array<Real> & rhs) = 0;
/// function to print the contain of the class
// virtual void printself(std::ostream & stream, int indent = 0) const;
protected:
virtual void destroyInternalData() {};
public:
virtual void beforeStaticSolverDestroy();
+ void createSynchronizerRegistry();
+ /* ------------------------------------------------------------------------ */
+ /* Data Accessor inherited members */
+ /* ------------------------------------------------------------------------ */
+public:
+ inline virtual UInt getNbDataForDOFs(const Array <UInt> & dofs,
+ SynchronizationTag tag) const;
+
+ inline virtual void packDOFData(CommunicationBuffer & buffer,
+ const Array<UInt> & dofs,
+ SynchronizationTag tag) const;
+
+ inline virtual void unpackDOFData(CommunicationBuffer & buffer,
+ const Array<UInt> & dofs,
+ SynchronizationTag tag);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(RHS, *rhs, Array<Real> &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// the matrix
SparseMatrix * matrix;
/// is sparse matrix allocated
bool is_matrix_allocated;
/// the right hand side
Array<Real> * rhs;
/// mesh
const Mesh * mesh;
/// pointer to the communicator
StaticCommunicator & communicator;
+
+ /// the solution obtained from the solve step
+ Array<Real> * solution;
+
+ /// synchronizer registry
+ SynchronizerRegistry * synch_registry;
+
};
+/* -------------------------------------------------------------------------- */
+/* inline functions */
+/* -------------------------------------------------------------------------- */
+
+#include "solver_inline_impl.cc"
__END_AKANTU__
#endif /* __AKANTU_SOLVER_HH__ */
diff --git a/src/solver/solver_mumps.cc b/src/solver/solver_mumps.cc
index 526f034e3..68ba81c0d 100644
--- a/src/solver/solver_mumps.cc
+++ b/src/solver/solver_mumps.cc
@@ -1,374 +1,374 @@
/**
* @file solver_mumps.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Dec 13 2010
* @date last modification: Mon Sep 15 2014
*
* @brief implem of SolverMumps class
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 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
*
* @subsection Ctrl_param Control parameters
*
* ICNTL(1),
* ICNTL(2),
* ICNTL(3) : output streams for error, diagnostics, and global messages
*
* ICNTL(4) : verbose level : 0 no message - 4 all messages
*
* ICNTL(5) : type of matrix, 0 assembled, 1 elementary
*
* ICNTL(6) : control the permutation and scaling(default 7) see mumps doc for
* more information
*
* ICNTL(7) : determine the pivot order (default 7) see mumps doc for more
* information
*
* ICNTL(8) : describe the scaling method used
*
* ICNTL(9) : 1 solve A x = b, 0 solve At x = b
*
* ICNTL(10) : number of iterative refinement when NRHS = 1
*
* ICNTL(11) : > 0 return statistics
*
* ICNTL(12) : only used for SYM = 2, ordering strategy
*
* ICNTL(13) :
*
* ICNTL(14) : percentage of increase of the estimated working space
*
* ICNTL(15-17) : not used
*
* ICNTL(18) : only used if ICNTL(5) = 0, 0 matrix centralized, 1 structure on
* host and mumps give the mapping, 2 structure on host and distributed matrix
* for facto, 3 distributed matrix
*
* ICNTL(19) : > 0, Shur complement returned
*
* ICNTL(20) : 0 rhs dense, 1 rhs sparse
*
* ICNTL(21) : 0 solution in rhs, 1 solution distributed in ISOL_loc and SOL_loc
* allocated by user
*
* ICNTL(22) : 0 in-core, 1 out-of-core
*
* ICNTL(23) : maximum memory allocatable by mumps pre proc
*
* ICNTL(24) : controls the detection of "null pivot rows"
*
* ICNTL(25) :
*
* ICNTL(26) :
*
* ICNTL(27) :
*
* ICNTL(28) : 0 automatic choice, 1 sequential analysis, 2 parallel analysis
*
* ICNTL(29) : 0 automatic choice, 1 PT-Scotch, 2 ParMetis
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#if defined(AKANTU_USE_MPI)
# include "static_communicator_mpi.hh"
# include "mpi_type_wrapper.hh"
#endif
#include "solver_mumps.hh"
#include "dof_synchronizer.hh"
/* -------------------------------------------------------------------------- */
// static std::ostream & operator <<(std::ostream & stream, const DMUMPS_STRUC_C & _this) {
// stream << "DMUMPS Data [" << std::endl;
// stream << " + job : " << _this.job << std::endl;
// stream << " + par : " << _this.par << std::endl;
// stream << " + sym : " << _this.sym << std::endl;
// stream << " + comm_fortran : " << _this.comm_fortran << std::endl;
// stream << " + nz : " << _this.nz << std::endl;
// stream << " + irn : " << _this.irn << std::endl;
// stream << " + jcn : " << _this.jcn << std::endl;
// stream << " + nz_loc : " << _this.nz_loc << std::endl;
// stream << " + irn_loc : " << _this.irn_loc << std::endl;
// stream << " + jcn_loc : " << _this.jcn_loc << std::endl;
// stream << "]";
// return stream;
// }
__BEGIN_AKANTU__
/* -------------------------------------------------------------------------- */
SolverMumps::SolverMumps(SparseMatrix & matrix,
const ID & id,
const MemoryID & memory_id) :
Solver(matrix, id, memory_id), is_mumps_data_initialized(false), rhs_is_local(true) {
AKANTU_DEBUG_IN();
#ifdef AKANTU_USE_MPI
parallel_method = SolverMumpsOptions::_fully_distributed;
#else //AKANTU_USE_MPI
parallel_method = SolverMumpsOptions::_not_parallel;
#endif //AKANTU_USE_MPI
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
SolverMumps::~SolverMumps() { }
/* -------------------------------------------------------------------------- */
void SolverMumps::destroyInternalData() {
AKANTU_DEBUG_IN();
if(this->is_mumps_data_initialized) {
this->mumps_data.job = _smj_destroy; // destroy
dmumps_c(&this->mumps_data);
this->is_mumps_data_initialized = false;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolverMumps::initMumpsData() {
// Default Scaling
icntl(8) = 77;
// Assembled matrix
icntl(5) = 0;
/// Default centralized dense second member
icntl(20) = 0;
icntl(21) = 0;
icntl(28) = 0; //automatic choice for analysis analysis
switch(this->parallel_method) {
case SolverMumpsOptions::_fully_distributed:
icntl(18) = 3; //fully distributed
this->mumps_data.nz_loc = matrix->getNbNonZero();
this->mumps_data.irn_loc = matrix->getIRN().storage();
this->mumps_data.jcn_loc = matrix->getJCN().storage();
break;
case SolverMumpsOptions::_not_parallel:
case SolverMumpsOptions::_master_slave_distributed:
icntl(18) = 0; //centralized
if(prank == 0) {
this->mumps_data.nz = matrix->getNbNonZero();
this->mumps_data.irn = matrix->getIRN().storage();
this->mumps_data.jcn = matrix->getJCN().storage();
} else {
this->mumps_data.nz = 0;
this->mumps_data.irn = NULL;
this->mumps_data.jcn = NULL;
}
break;
default:
AKANTU_DEBUG_ERROR("This case should not happen!!");
}
}
/* -------------------------------------------------------------------------- */
void SolverMumps::initialize(SolverOptions & options) {
AKANTU_DEBUG_IN();
if(SolverMumpsOptions * opt = dynamic_cast<SolverMumpsOptions *>(&options)) {
this->parallel_method = opt->parallel_method;
}
this->mumps_data.par = 1; // The host is part of computations
switch(this->parallel_method) {
case SolverMumpsOptions::_not_parallel: break;
case SolverMumpsOptions::_master_slave_distributed:
this->mumps_data.par = 0; // The host is not part of the computations
case SolverMumpsOptions::_fully_distributed:
#ifdef AKANTU_USE_MPI
const StaticCommunicatorMPI & mpi_st_comm = dynamic_cast<const StaticCommunicatorMPI &>(communicator.getRealStaticCommunicator());
this->mumps_data.comm_fortran = MPI_Comm_c2f(mpi_st_comm.getMPITypeWrapper().getMPICommunicator());
#endif
break;
}
this->mumps_data.sym = 2 * (matrix->getSparseMatrixType() == _symmetric);
this->prank = communicator.whoAmI();
this->mumps_data.job = _smj_initialize; //initialize
dmumps_c(&this->mumps_data);
this->is_mumps_data_initialized = true;
/* ------------------------------------------------------------------------ */
UInt size = matrix->getSize();
if(prank == 0) {
std::stringstream sstr_rhs; sstr_rhs << id << ":rhs";
this->rhs = &(alloc<Real>(sstr_rhs.str(), size, 1, 0.));
} else {
this->rhs = NULL;
}
this->mumps_data.nz_alloc = 0;
this->mumps_data.n = size;
/* ------------------------------------------------------------------------ */
// Output setup
if(AKANTU_DEBUG_TEST(dblTrace)) {
icntl(1) = 6;
icntl(2) = 2;
icntl(3) = 2;
icntl(4) = 4;
} else {
/// No outputs
icntl(1) = 6; // error output
icntl(2) = 0; // dignostics output
icntl(3) = 0; // informations
icntl(4) = 0; // no outputs
}
if(AKANTU_DEBUG_TEST(dblDump)) {
strcpy(this->mumps_data.write_problem, "mumps_matrix.mtx");
}
this->analysis();
// icntl(14) = 80;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
-void SolverMumps::setRHS(const Array<Real> & rhs) {
+void SolverMumps::setRHS(Array<Real> & rhs) {
if(prank == 0) {
- std::copy(rhs.storage(), rhs.storage() + this->rhs->getSize(), this->rhs->storage());
+ //std::copy(rhs.storage(), rhs.storage() + this->rhs->getSize(), this->rhs->storage());
- // DebugLevel dbl = debug::getDebugLevel();
-// debug::setDebugLevel(dblError);
-// matrix->getDOFSynchronizer().gather(rhs, 0, this->rhs);
-// debug::setDebugLevel(dbl);
+ DebugLevel dbl = debug::getDebugLevel();
+ debug::setDebugLevel(dblError);
+ matrix->getDOFSynchronizer().gather(rhs, 0, this->rhs);
+ debug::setDebugLevel(dbl);
} else {
this->matrix->getDOFSynchronizer().gather(rhs, 0);
}
}
/* -------------------------------------------------------------------------- */
void SolverMumps::analysis() {
AKANTU_DEBUG_IN();
initMumpsData();
this->mumps_data.job = _smj_analyze; //analyze
dmumps_c(&this->mumps_data);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolverMumps::factorize() {
AKANTU_DEBUG_IN();
if(parallel_method == SolverMumpsOptions::_fully_distributed)
this->mumps_data.a_loc = this->matrix->getA().storage();
else {
if(prank == 0)
this->mumps_data.a = this->matrix->getA().storage();
}
if(prank == 0) {
this->mumps_data.rhs = this->rhs->storage();
}
this->mumps_data.job = _smj_factorize; // factorize
dmumps_c(&this->mumps_data);
this->printError();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolverMumps::solve() {
AKANTU_DEBUG_IN();
if(prank == 0) {
this->mumps_data.rhs = this->rhs->storage();
}
this->mumps_data.job = _smj_solve; // solve
dmumps_c(&this->mumps_data);
this->printError();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolverMumps::solve(Array<Real> & solution) {
AKANTU_DEBUG_IN();
this->solve();
if(prank == 0) {
-// matrix->getDOFSynchronizer().scatter(solution, 0, this->rhs);
- std::copy(this->rhs->storage(), this->rhs->storage() + this->rhs->getSize(), solution.storage());
+ matrix->getDOFSynchronizer().scatter(solution, 0, this->rhs);
+// std::copy(this->rhs->storage(), this->rhs->storage() + this->rhs->getSize(), solution.storage());
} else {
this->matrix->getDOFSynchronizer().scatter(solution, 0);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolverMumps::printError() {
if(info(1) != 0) {
communicator.allReduce(&info(1), 1, _so_min);
switch(info(1)) {
case -10: AKANTU_DEBUG_ERROR("The matrix is singular"); break;
case -9: {
icntl(14) += 10;
if(icntl(14) != 90) {
//std::cout << "Dynamic memory increase of 10%" << std::endl;
this->analysis();
this->factorize();
this->solve();
} else {
AKANTU_DEBUG_ERROR("The MUMPS workarray is too small INFO(2)=" << info(2) << "No further increase possible"); break;
}
}
default:
AKANTU_DEBUG_ERROR("Error in mumps during solve process, check mumps user guide INFO(1) ="
<< info(1));
}
}
}
__END_AKANTU__
diff --git a/src/solver/solver_mumps.hh b/src/solver/solver_mumps.hh
index 5bff7da6d..c843439d1 100644
--- a/src/solver/solver_mumps.hh
+++ b/src/solver/solver_mumps.hh
@@ -1,154 +1,154 @@
/**
* @file solver_mumps.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Dec 13 2010
* @date last modification: Mon Sep 15 2014
*
* @brief Solver class implementation for the mumps solver
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 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_SOLVER_MUMPS_HH__
#define __AKANTU_SOLVER_MUMPS_HH__
#include <dmumps_c.h>
#include "solver.hh"
#include "static_communicator.hh"
__BEGIN_AKANTU__
class SolverMumpsOptions : public SolverOptions {
public:
enum ParallelMethod {
_not_parallel,
_fully_distributed,
_master_slave_distributed
};
SolverMumpsOptions(ParallelMethod parallel_method = _fully_distributed) :
SolverOptions(),
parallel_method(parallel_method) { }
private:
friend class SolverMumps;
ParallelMethod parallel_method;
};
class SolverMumps : public Solver {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
SolverMumps(SparseMatrix & sparse_matrix,
const ID & id = "solver_mumps",
const MemoryID & memory_id = 0);
virtual ~SolverMumps();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// build the profile and do the analysis part
- void initialize(SolverOptions & options = _solver_no_options);
+ virtual void initialize(SolverOptions & options = _solver_no_options);
void initializeSlave(SolverOptions & options = _solver_no_options);
/// analysis (symbolic facto + permutations)
- void analysis();
+ virtual void analysis();
/// factorize the matrix
- void factorize();
+ virtual void factorize();
/// solve the system
- void solve(Array<Real> & solution);
- void solve();
+ virtual void solve(Array<Real> & solution);
+ virtual void solve();
void solveSlave();
- virtual void setRHS(const Array<Real> & rhs);
+ virtual void setRHS(Array<Real> & rhs);
private:
/// print the error if any happened in mumps
void printError();
/// clean the mumps info
- void destroyInternalData();
+ virtual void destroyInternalData();
/// set internal values;
void initMumpsData();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
private:
/// access the control variable
inline Int & icntl(UInt i) {
return mumps_data.icntl[i - 1];
}
/// access the results info
inline Int & info(UInt i) {
return mumps_data.info[i - 1];
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// mumps data
DMUMPS_STRUC_C mumps_data;
/// specify if the mumps_data are initialized or not
bool is_mumps_data_initialized;
UInt prank;
/* ------------------------------------------------------------------------ */
/* Local types */
/* ------------------------------------------------------------------------ */
private:
SolverMumpsOptions::ParallelMethod parallel_method;
bool rhs_is_local;
enum SolverMumpsJob {
_smj_initialize = -1,
_smj_analyze = 1,
_smj_factorize = 2,
_smj_solve = 3,
_smj_analyze_factorize = 4,
_smj_factorize_solve = 5,
_smj_complete = 6, // analyze, factorize, solve
_smj_destroy = -2
};
};
__END_AKANTU__
#endif /* __AKANTU_SOLVER_MUMPS_HH__ */
diff --git a/src/solver/solver_petsc.cc b/src/solver/solver_petsc.cc
index ce058bc87..09b3c0c74 100644
--- a/src/solver/solver_petsc.cc
+++ b/src/solver/solver_petsc.cc
@@ -1,954 +1,1082 @@
-// /**
-// * @file solver_petsc.cc
-// *
-// * @author Nicolas Richart <nicolas.richart@epfl.ch>
-// # @author Alejandro M. Aragón <alejandro.aragon@epfl.ch>
-// *
-// * @date Mon Dec 13 10:48:06 2010
-// *
-// * @brief Solver class implementation for the petsc solver
-// *
-// * @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/>.
-// *
-// */
-
-// /* -------------------------------------------------------------------------- */
-// #ifdef AKANTU_USE_MPI
-// #include "static_communicator_mpi.hh"
-// #endif
-
-// #include "solver_petsc.hh"
-// #include "dof_synchronizer.hh"
-
-// __BEGIN_AKANTU__
+/**
+ * @file solver_petsc.cc
+ *
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
+ # @author Alejandro M. Aragón <alejandro.aragon@epfl.ch>
+ * @author Aurelia Cuba Ramos <aurelia.cubaramos@epfl.ch>
+ *
+ * @date Mon Dec 13 10:48:06 2010
+ *
+ * @brief Solver class implementation for the petsc solver
+ *
+ * @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 <petscksp.h>
+#include "solver_petsc.hh"
+#include "petsc_wrapper.hh"
+#include "petsc_matrix.hh"
+#include "static_communicator.hh"
+#include "static_communicator_mpi.hh"
+#include "mpi_type_wrapper.hh"
+#include "dof_synchronizer.hh"
+__BEGIN_AKANTU__
+
+/* -------------------------------------------------------------------------- */
+SolverPETSc::SolverPETSc(SparseMatrix & matrix,
+ const ID & id,
+ const MemoryID & memory_id) :
+ Solver(matrix, id, memory_id), is_petsc_data_initialized(false),
+ petsc_solver_wrapper(new PETScSolverWrapper) {
+}
+
+/* -------------------------------------------------------------------------- */
+SolverPETSc::~SolverPETSc() {
+ AKANTU_DEBUG_IN();
+
+ this->destroyInternalData();
+
+ AKANTU_DEBUG_OUT();
+ }
+/* -------------------------------------------------------------------------- */
+void SolverPETSc::destroyInternalData() {
+ AKANTU_DEBUG_IN();
+
+ if(this->is_petsc_data_initialized) {
+ PetscErrorCode ierr;
+ ierr = KSPDestroy(&(this->petsc_solver_wrapper->ksp)); CHKERRXX(ierr);
+ ierr = VecDestroy(&(this->petsc_solver_wrapper->rhs)); CHKERRXX(ierr);
+ ierr = VecDestroy(&(this->petsc_solver_wrapper->solution)); CHKERRXX(ierr);
+ delete petsc_solver_wrapper;
+
+ this->is_petsc_data_initialized = false;
+ }
+
+ AKANTU_DEBUG_OUT();
+}
+
+/* -------------------------------------------------------------------------- */
+void SolverPETSc::initialize(SolverOptions & options) {
+ AKANTU_DEBUG_IN();
+
+#if defined(AKANTU_USE_MPI)
+ StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
+ const StaticCommunicatorMPI & mpi_st_comm =
+ dynamic_cast<const StaticCommunicatorMPI &>(comm.getRealStaticCommunicator());
+ this->petsc_solver_wrapper->communicator = mpi_st_comm.getMPITypeWrapper().getMPICommunicator();
+#else
+ this->petsc_solver_wrapper->communicator = PETSC_COMM_SELF;
+#endif
+
+ PetscErrorCode ierr;
+
+ /// create a solver context
+ ierr = KSPCreate(this->petsc_solver_wrapper->communicator, &(this->petsc_solver_wrapper->ksp)); CHKERRXX(ierr);
+
+ /// set the matrix that defines the linear system and the matrix for preconditioning (here they are the same)
+ PETScMatrix * petsc_matrix = static_cast<PETScMatrix*>(this->matrix);
+
+#if PETSC_VERSION_MAJOR >= 3 && PETSC_VERSION_MINOR >= 5
+ ierr = KSPSetOperators(this->petsc_solver_wrapper->ksp, petsc_matrix->getPETScMatrixWrapper()->mat, petsc_matrix->getPETScMatrixWrapper()->mat); CHKERRXX(ierr);
+#else
+ ierr = KSPSetOperators(this->petsc_solver_wrapper->ksp, petsc_matrix->getPETScMatrixWrapper()->mat, petsc_matrix->getPETScMatrixWrapper()->mat, SAME_NONZERO_PATTERN); CHKERRXX(ierr);
+#endif
+
+ ierr = VecCreate(this->petsc_solver_wrapper->communicator, &(this->petsc_solver_wrapper->rhs)); CHKERRXX(ierr);
+
+ this->is_petsc_data_initialized = true;
+ AKANTU_DEBUG_OUT();
+}
+
+/* -------------------------------------------------------------------------- */
+void SolverPETSc::setRHS(Array<Real> & rhs) {
+ PetscErrorCode ierr;
+ PETScMatrix * petsc_matrix = static_cast<PETScMatrix*>(this->matrix);
+ ierr = VecSetSizes((this->petsc_solver_wrapper->rhs), petsc_matrix->getLocalSize(), petsc_matrix->getSize()); CHKERRXX(ierr);
+ ierr = VecSetFromOptions((this->petsc_solver_wrapper->rhs)); CHKERRXX(ierr);
+
+ for (UInt i = 0; i < rhs.getSize(); ++i) {
+ if (matrix->getDOFSynchronizer().isLocalOrMasterDOF(i)) {
+ Int i_global = matrix->getDOFSynchronizer().getDOFGlobalID(i);
+ AOApplicationToPetsc(petsc_matrix->getPETScMatrixWrapper()->ao, 1, &(i_global) );
+ ierr = VecSetValue((this->petsc_solver_wrapper->rhs), i_global, rhs(i), INSERT_VALUES); CHKERRXX(ierr);
+ }
+ }
+ ierr = VecAssemblyBegin(this->petsc_solver_wrapper->rhs); CHKERRXX(ierr);
+ ierr = VecAssemblyEnd(this->petsc_solver_wrapper->rhs); CHKERRXX(ierr);
+ ierr = VecDuplicate((this->petsc_solver_wrapper->rhs), &(this->petsc_solver_wrapper->solution)); CHKERRXX(ierr);
+
+
+}
+
+/* -------------------------------------------------------------------------- */
+void SolverPETSc::solve() {
+ AKANTU_DEBUG_IN();
+
+ PetscErrorCode ierr;
+ ierr = KSPSolve(this->petsc_solver_wrapper->ksp, this->petsc_solver_wrapper->rhs, this->petsc_solver_wrapper->solution); CHKERRXX(ierr);
+
+ AKANTU_DEBUG_OUT();
+}
+
+/* -------------------------------------------------------------------------- */
+void SolverPETSc::solve(Array<Real> & solution) {
+ AKANTU_DEBUG_IN();
+
+ this->solution = &solution;
+ this->solve();
+
+ PetscErrorCode ierr;
+ PETScMatrix * petsc_matrix = static_cast<PETScMatrix*>(this->matrix);
+
+
+ // ierr = VecGetOwnershipRange(this->petsc_solver_wrapper->solution, solution_begin, solution_end); CHKERRXX(ierr);
+ // ierr = VecGetArray(this->petsc_solver_wrapper->solution, PetscScalar **array); CHKERRXX(ierr);
+
+ for (UInt i = 0; i < solution.getSize(); ++i) {
+ if (this->matrix->getDOFSynchronizer().isLocalOrMasterDOF(i)) {
+ Int i_global = this->matrix->getDOFSynchronizer().getDOFGlobalID(i);
+ ierr = AOApplicationToPetsc(petsc_matrix->getPETScMatrixWrapper()->ao, 1, &(i_global) ); CHKERRXX(ierr);
+ ierr = VecGetValues(this->petsc_solver_wrapper->solution, 1, &i_global, &solution(i)); CHKERRXX(ierr);
+
+ }
+ }
+
+ synch_registry->synchronize(_gst_solver_solution);
+
+ AKANTU_DEBUG_OUT();
+}
+
+/* -------------------------------------------------------------------------- */
// void finalize_petsc() {
// static bool finalized = false;
// if (!finalized) {
// cout<<"*** INFO *** PETSc is finalizing..."<<endl;
// // finalize PETSc
// PetscErrorCode ierr = PetscFinalize();CHKERRCONTINUE(ierr);
// finalized = true;
// }
// }
// SolverPETSc::sparse_vector_type
// SolverPETSc::operator()(const SolverPETSc::sparse_matrix_type& AA,
// const SolverPETSc::sparse_vector_type& bb) {
// #ifdef CPPUTILS_VERBOSE
// // parallel output stream
// Output_stream out;
// // timer
// cpputils::ctimer timer;
// out<<"Inside PETSc solver: "<<timer<<endl;
// #endif
// #ifdef CPPUTILS_VERBOSE
// out<<" Inside operator()(const sparse_matrix_type&, const sparse_vector_type&)... "<<timer<<endl;
// #endif
// assert(AA.rows() == bb.size());
// // KSP ksp; //!< linear solver context
// Vec b; /* RHS */
// PC pc; /* preconditioner context */
// PetscErrorCode ierr;
// PetscInt nlocal;
// PetscInt n = bb.size();
// VecScatter ctx;
// /*
// Create vectors. Note that we form 1 vector from scratch and
// then duplicate as needed. For this simple case let PETSc decide how
// many elements of the vector are stored on each processor. The second
// argument to VecSetSizes() below causes PETSc to decide.
// */
// ierr = VecCreate(PETSC_COMM_WORLD,&b);CHKERRCONTINUE(ierr);
// ierr = VecSetSizes(b,PETSC_DECIDE,n);CHKERRCONTINUE(ierr);
// ierr = VecSetFromOptions(b);CHKERRCONTINUE(ierr);
// if (!allocated_) {
// ierr = VecDuplicate(b,&x_);CHKERRCONTINUE(ierr);
// } else
// VecZeroEntries(x_);
// #ifdef CPPUTILS_VERBOSE
// out<<" Vectors created... "<<timer<<endl;
// #endif
// /* Set hight-hand-side vector */
// for (sparse_vector_type::const_hash_iterator it = bb.map_.begin(); it != bb.map_.end(); ++it) {
// int row = it->first;
// ierr = VecSetValues(b, 1, &row, &it->second, ADD_VALUES);
// }
// #ifdef CPPUTILS_VERBOSE
// out<<" Right hand side set... "<<timer<<endl;
// #endif
// /*
// Assemble vector, using the 2-step process:
// VecAssemblyBegin(), VecAssemblyEnd()
// Computations can be done while messages are in transition
// by placing code between these two statements.
// */
// ierr = VecAssemblyBegin(b);CHKERRCONTINUE(ierr);
// ierr = VecAssemblyEnd(b);CHKERRCONTINUE(ierr);
// #ifdef CPPUTILS_VERBOSE
// out<<" Right-hand-side vector assembled... "<<timer<<endl;
// ierr = VecView(b,PETSC_VIEWER_STDOUT_WORLD);CHKERRCONTINUE(ierr);
// Vec b_all;
// ierr = VecScatterCreateToAll(b, &ctx, &b_all);CHKERRCONTINUE(ierr);
// ierr = VecScatterBegin(ctx,b,b_all,INSERT_VALUES,SCATTER_FORWARD);CHKERRCONTINUE(ierr);
// ierr = VecScatterEnd(ctx,b,b_all,INSERT_VALUES,SCATTER_FORWARD);CHKERRCONTINUE(ierr);
// value_type nrm;
// VecNorm(b_all,NORM_2,&nrm);
// out<<" Norm of right hand side... "<<nrm<<endl;
// #endif
// /* Identify the starting and ending mesh points on each
// processor for the interior part of the mesh. We let PETSc decide
// above. */
// // PetscInt rstart,rend;
// // ierr = VecGetOwnershipRange(x_,&rstart,&rend);CHKERRCONTINUE(ierr);
// ierr = VecGetLocalSize(x_,&nlocal);CHKERRCONTINUE(ierr);
// /*
// Create matrix. When using MatCreate(), the matrix format can
// be specified at runtime.
// Performance tuning note: For problems of substantial size,
// preallocation of matrix memory is crucial for attaining good
// performance. See the matrix chapter of the users manual for details.
// We pass in nlocal as the "local" size of the matrix to force it
// to have the same parallel layout as the vector created above.
// */
// if (!allocated_) {
// ierr = MatCreate(PETSC_COMM_WORLD,&A_);CHKERRCONTINUE(ierr);
// ierr = MatSetSizes(A_,nlocal,nlocal,n,n);CHKERRCONTINUE(ierr);
// ierr = MatSetFromOptions(A_);CHKERRCONTINUE(ierr);
// ierr = MatSetUp(A_);CHKERRCONTINUE(ierr);
// } else {
// // zero-out matrix
// MatZeroEntries(A_);
// }
// /*
// Assemble matrix.
// The linear system is distributed across the processors by
// chunks of contiguous rows, which correspond to contiguous
// sections of the mesh on which the problem is discretized.
// For matrix assembly, each processor contributes entries for
// the part that it owns locally.
// */
// #ifdef CPPUTILS_VERBOSE
// out<<" Zeroed-out sparse matrix entries... "<<timer<<endl;
// #endif
// for (sparse_matrix_type::const_hash_iterator it = AA.map_.begin(); it != AA.map_.end(); ++it) {
// // get subscripts
// std::pair<size_t,size_t> subs = AA.unhash(it->first);
// PetscInt row = subs.first;
// PetscInt col = subs.second;
// ierr = MatSetValues(A_, 1, &row, 1, &col, &it->second, ADD_VALUES);CHKERRCONTINUE(ierr);
// }
// #ifdef CPPUTILS_VERBOSE
// out<<" Filled sparse matrix... "<<timer<<endl;
// #endif
// /* Assemble the matrix */
// ierr = MatAssemblyBegin(A_,MAT_FINAL_ASSEMBLY);CHKERRCONTINUE(ierr);
// ierr = MatAssemblyEnd(A_,MAT_FINAL_ASSEMBLY);CHKERRCONTINUE(ierr);
// if (!allocated_) {
// // set after the first MatAssemblyEnd
// // ierr = MatSetOption(A_, MAT_NEW_NONZERO_LOCATIONS, PETSC_FALSE);CHKERRCONTINUE(ierr);
// ierr = MatSetOption(A_, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE);CHKERRCONTINUE(ierr);
// }
// #ifdef CPPUTILS_VERBOSE
// out<<" Sparse matrix assembled... "<<timer<<endl;
// // view matrix
// MatView(A_, PETSC_VIEWER_STDOUT_WORLD);
// MatNorm(A_,NORM_FROBENIUS,&nrm);
// out<<" Norm of stiffness matrix... "<<nrm<<endl;
// #endif
// /*
// Set operators. Here the matrix that defines the linear system
// also serves as the preconditioning matrix.
// */
// // ierr = KSPSetOperators(ksp,A_,A_,DIFFERENT_NONZERO_PATTERN);CHKERRCONTINUE(ierr);
// ierr = KSPSetOperators(ksp_,A_,A_,SAME_NONZERO_PATTERN);CHKERRCONTINUE(ierr);
// //
// // /*
// // Set runtime options, e.g.,
// // -ksp_type <type> -pc_type <type> -ksp_monitor -ksp_rtol <rtol>
// // These options will override those specified above as long as
// // KSPSetFromOptions() is called _after_ any other customization
// // routines.
// // */
// // ierr = KSPSetFromOptions(ksp);CHKERRCONTINUE(ierr);
// #ifdef CPPUTILS_VERBOSE
// out<<" Solving system... "<<timer<<endl;
// #endif
// /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// Solve the linear system
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
// /*
// Solve linear system
// */
// ierr = KSPSolve(ksp_,b,x_);CHKERRCONTINUE(ierr);
// #ifdef CPPUTILS_VERBOSE
// /*
// View solver info; we could instead use the option -ksp_view to
// print this info to the screen at the conclusion of KSPSolve().
// */
// ierr = KSPView(ksp_,PETSC_VIEWER_STDOUT_WORLD);CHKERRCONTINUE(ierr);
// int iter;
// KSPGetIterationNumber(ksp_, &iter);
// out<<" System solved in "<<iter<<" iterations... "<<timer<<endl;
// KSPConvergedReason reason;
// ierr = KSPGetConvergedReason(ksp_,&reason);CHKERRCONTINUE(ierr);
// if (reason < 0)
// out<<"*** WARNING *** PETSc solver diverged with flag ";
// else
// out<<"*** INFO *** PETSc solver converged with flag ";
// if (reason == KSP_CONVERGED_RTOL)
// out<<"KSP_CONVERGED_RTOL"<<endl;
// else if (reason == KSP_CONVERGED_ATOL)
// out<<"KSP_CONVERGED_ATOL"<<endl;
// else if (reason == KSP_CONVERGED_ITS)
// out<<"KSP_CONVERGED_ITS"<<endl;
// else if (reason == KSP_CONVERGED_CG_NEG_CURVE)
// out<<"KSP_CONVERGED_CG_NEG_CURVE"<<endl;
// else if (reason == KSP_CONVERGED_CG_CONSTRAINED)
// out<<"KSP_CONVERGED_CG_CONSTRAINED"<<endl;
// else if (reason == KSP_CONVERGED_STEP_LENGTH)
// out<<"KSP_CONVERGED_STEP_LENGTH"<<endl;
// else if (reason == KSP_CONVERGED_HAPPY_BREAKDOWN)
// out<<"KSP_CONVERGED_HAPPY_BREAKDOWN"<<endl;
// else if (reason == KSP_DIVERGED_NULL)
// out<<"KSP_DIVERGED_NULL"<<endl;
// else if (reason == KSP_DIVERGED_ITS)
// out<<"KSP_DIVERGED_ITS"<<endl;
// else if (reason == KSP_DIVERGED_DTOL)
// out<<"KSP_DIVERGED_DTOL"<<endl;
// else if (reason == KSP_DIVERGED_BREAKDOWN)
// out<<"KSP_DIVERGED_BREAKDOWN"<<endl;
// else if (reason == KSP_DIVERGED_BREAKDOWN_BICG)
// out<<"KSP_DIVERGED_BREAKDOWN_BICG"<<endl;
// else if (reason == KSP_DIVERGED_NONSYMMETRIC)
// out<<"KSP_DIVERGED_NONSYMMETRIC"<<endl;
// else if (reason == KSP_DIVERGED_INDEFINITE_PC)
// out<<"KSP_DIVERGED_INDEFINITE_PC"<<endl;
// else if (reason == KSP_DIVERGED_NAN)
// out<<"KSP_DIVERGED_NAN"<<endl;
// else if (reason == KSP_DIVERGED_INDEFINITE_MAT)
// out<<"KSP_DIVERGED_INDEFINITE_MAT"<<endl;
// else if (reason == KSP_CONVERGED_ITERATING)
// out<<"KSP_CONVERGED_ITERATING"<<endl;
// PetscReal rnorm;
// ierr = KSPGetResidualNorm(ksp_,&rnorm);CHKERRCONTINUE(ierr);
// out<<"PETSc last residual norm computed: "<<rnorm<<endl;
// ierr = VecView(x_,PETSC_VIEWER_STDOUT_WORLD);CHKERRCONTINUE(ierr);
// VecNorm(x_,NORM_2,&nrm);
// out<<" Norm of solution vector... "<<nrm<<endl;
// #endif
// /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// Check solution and clean up
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
// Vec x_all;
// ierr = VecScatterCreateToAll(x_, &ctx, &x_all);CHKERRCONTINUE(ierr);
// ierr = VecScatterBegin(ctx,x_,x_all,INSERT_VALUES,SCATTER_FORWARD);CHKERRCONTINUE(ierr);
// ierr = VecScatterEnd(ctx,x_,x_all,INSERT_VALUES,SCATTER_FORWARD);CHKERRCONTINUE(ierr);
// #ifdef CPPUTILS_VERBOSE
// out<<" Solution vector scattered... "<<timer<<endl;
// VecNorm(x_all,NORM_2,&nrm);
// out<<" Norm of scattered vector... "<<nrm<<endl;
// // ierr = VecView(x_all,PETSC_VIEWER_STDOUT_WORLD);CHKERRCONTINUE(ierr);
// #endif
// /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// Get values from solution and store them in the object that will be
// returned
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
// sparse_vector_type xx(bb.size());
// /* Set solution vector */
// double zero = 0.;
// double val;
// for (sparse_vector_type::const_hash_iterator it = bb.map_.begin(); it != bb.map_.end(); ++it) {
// int row = it->first;
// ierr = VecGetValues(x_all, 1, &row, &val);
// if (val != zero)
// xx[row] = val;
// }
// #ifdef CPPUTILS_VERBOSE
// out<<" Solution vector copied... "<<timer<<endl;
// // out<<" Norm of copied solution vector... "<<norm(xx, Insert_t)<<endl;
// #endif
// /*
// Free work space. All PETSc objects should be destroyed when they
// are no longer needed.
// */
// ierr = VecDestroy(&b);CHKERRCONTINUE(ierr);
// // ierr = KSPDestroy(&ksp);CHKERRCONTINUE(ierr);
// // set allocated flag
// if (!allocated_) {
// allocated_ = true;
// }
// #ifdef CPPUTILS_VERBOSE
// out<<" Temporary data structures destroyed... "<<timer<<endl;
// #endif
// return xx;
// }
// SolverPETSc::sparse_vector_type SolverPETSc::operator()(const SolverPETSc::sparse_matrix_type& KKpf, const SolverPETSc::sparse_matrix_type& KKpp, const SolverPETSc::sparse_vector_type& UUp) {
// #ifdef CPPUTILS_VERBOSE
// // parallel output stream
// Output_stream out;
// // timer
// cpputils::ctimer timer;
// out<<"Inside SolverPETSc::operator()(const sparse_matrix&, const sparse_matrix&, const sparse_vector&). "<<timer<<endl;
// #endif
// Mat Kpf, Kpp;
// Vec Up, Pf, Pp;
// PetscErrorCode ierr = MatCreate(PETSC_COMM_WORLD,&Kpf);CHKERRCONTINUE(ierr);
// ierr = MatCreate(PETSC_COMM_WORLD,&Kpp);CHKERRCONTINUE(ierr);
// #ifdef CPPUTILS_VERBOSE
// out<<" Allocating memory... "<<timer<<endl;
// #endif
// ierr = MatSetFromOptions(Kpf);CHKERRCONTINUE(ierr);
// ierr = MatSetFromOptions(Kpp);CHKERRCONTINUE(ierr);
// ierr = MatSetSizes(Kpf,PETSC_DECIDE,PETSC_DECIDE, KKpf.rows(), KKpf.columns());CHKERRCONTINUE(ierr);
// ierr = MatSetSizes(Kpp,PETSC_DECIDE,PETSC_DECIDE, KKpp.rows(), KKpp.columns());CHKERRCONTINUE(ierr);
// // get number of non-zeros in both diagonal and non-diagonal portions of the matrix
// std::pair<size_t,size_t> Kpf_nz = KKpf.non_zero_off_diagonal();
// std::pair<size_t,size_t> Kpp_nz = KKpp.non_zero_off_diagonal();
// ierr = MatMPIAIJSetPreallocation(Kpf, Kpf_nz.first, PETSC_NULL, Kpf_nz.second, PETSC_NULL); CHKERRCONTINUE(ierr);
// ierr = MatMPIAIJSetPreallocation(Kpp, Kpp_nz.first, PETSC_NULL, Kpp_nz.second, PETSC_NULL); CHKERRCONTINUE(ierr);
// ierr = MatSeqAIJSetPreallocation(Kpf, Kpf_nz.first, PETSC_NULL); CHKERRCONTINUE(ierr);
// ierr = MatSeqAIJSetPreallocation(Kpp, Kpp_nz.first, PETSC_NULL); CHKERRCONTINUE(ierr);
// for (sparse_matrix_type::const_hash_iterator it = KKpf.map_.begin(); it != KKpf.map_.end(); ++it) {
// // get subscripts
// std::pair<size_t,size_t> subs = KKpf.unhash(it->first);
// int row = subs.first;
// int col = subs.second;
// ierr = MatSetValues(Kpf, 1, &row, 1, &col, &it->second, ADD_VALUES);CHKERRCONTINUE(ierr);
// }
// for (sparse_matrix_type::const_hash_iterator it = KKpp.map_.begin(); it != KKpp.map_.end(); ++it) {
// // get subscripts
// std::pair<size_t,size_t> subs = KKpp.unhash(it->first);
// int row = subs.first;
// int col = subs.second;
// ierr = MatSetValues(Kpf, 1, &row, 1, &col, &it->second, ADD_VALUES);CHKERRCONTINUE(ierr);
// }
// #ifdef CPPUTILS_VERBOSE
// out<<" Filled sparse matrices... "<<timer<<endl;
// #endif
// /*
// Assemble matrix, using the 2-step process:
// MatAssemblyBegin(), MatAssemblyEnd()
// Computations can be done while messages are in transition
// by placing code between these two statements.
// */
// ierr = MatAssemblyBegin(Kpf,MAT_FINAL_ASSEMBLY);CHKERRCONTINUE(ierr);
// ierr = MatAssemblyBegin(Kpp,MAT_FINAL_ASSEMBLY);CHKERRCONTINUE(ierr);
// ierr = MatAssemblyEnd(Kpf,MAT_FINAL_ASSEMBLY);CHKERRCONTINUE(ierr);
// ierr = MatAssemblyEnd(Kpp,MAT_FINAL_ASSEMBLY);CHKERRCONTINUE(ierr);
// #ifdef CPPUTILS_VERBOSE
// out<<" Sparse matrices assembled... "<<timer<<endl;
// #endif
// ierr = VecCreate(PETSC_COMM_WORLD,&Up);CHKERRCONTINUE(ierr);
// ierr = VecSetSizes(Up,PETSC_DECIDE, UUp.size());CHKERRCONTINUE(ierr);
// ierr = VecSetFromOptions(Up);CHKERRCONTINUE(ierr);
// ierr = VecCreate(PETSC_COMM_WORLD,&Pf);CHKERRCONTINUE(ierr);
// ierr = VecSetSizes(Pf,PETSC_DECIDE, KKpf.rows());CHKERRCONTINUE(ierr);
// ierr = VecSetFromOptions(Pf);CHKERRCONTINUE(ierr);
// ierr = VecDuplicate(Pf,&Pp);CHKERRCONTINUE(ierr);
// #ifdef CPPUTILS_VERBOSE
// out<<" Vectors created... "<<timer<<endl;
// #endif
// /* Set hight-hand-side vector */
// for (sparse_vector_type::const_hash_iterator it = UUp.map_.begin(); it != UUp.map_.end(); ++it) {
// int row = it->first;
// ierr = VecSetValues(Up, 1, &row, &it->second, ADD_VALUES);
// }
// /*
// Assemble vector, using the 2-step process:
// VecAssemblyBegin(), VecAssemblyEnd()
// Computations can be done while messages are in transition
// by placing code between these two statements.
// */
// ierr = VecAssemblyBegin(Up);CHKERRCONTINUE(ierr);
// ierr = VecAssemblyEnd(Up);CHKERRCONTINUE(ierr);
// // add Kpf*Uf
// ierr = MatMult(Kpf, x_, Pf);
// // add Kpp*Up
// ierr = MatMultAdd(Kpp, Up, Pf, Pp);
// #ifdef CPPUTILS_VERBOSE
// out<<" Matrices multiplied... "<<timer<<endl;
// #endif
// VecScatter ctx;
// Vec Pp_all;
// ierr = VecScatterCreateToAll(Pp, &ctx, &Pp_all);CHKERRCONTINUE(ierr);
// ierr = VecScatterBegin(ctx,Pp,Pp_all,INSERT_VALUES,SCATTER_FORWARD);CHKERRCONTINUE(ierr);
// ierr = VecScatterEnd(ctx,Pp,Pp_all,INSERT_VALUES,SCATTER_FORWARD);CHKERRCONTINUE(ierr);
// #ifdef CPPUTILS_VERBOSE
// out<<" Vector scattered... "<<timer<<endl;
// #endif
// /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// Get values from solution and store them in the object that will be
// returned
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
// sparse_vector_type pp(KKpf.rows());
// // get reaction vector
// for (int i=0; i<KKpf.rows(); ++i) {
// PetscScalar v;
// ierr = VecGetValues(Pp_all, 1, &i, &v);
// if (v != PetscScalar())
// pp[i] = v;
// }
// #ifdef CPPUTILS_VERBOSE
// out<<" Vector copied... "<<timer<<endl;
// #endif
// ierr = MatDestroy(&Kpf);CHKERRCONTINUE(ierr);
// ierr = MatDestroy(&Kpp);CHKERRCONTINUE(ierr);
// ierr = VecDestroy(&Up);CHKERRCONTINUE(ierr);
// ierr = VecDestroy(&Pf);CHKERRCONTINUE(ierr);
// ierr = VecDestroy(&Pp);CHKERRCONTINUE(ierr);
// ierr = VecDestroy(&Pp_all);CHKERRCONTINUE(ierr);
// #ifdef CPPUTILS_VERBOSE
// out<<" Temporary data structures destroyed... "<<timer<<endl;
// #endif
// return pp;
// }
// SolverPETSc::sparse_vector_type SolverPETSc::operator()(const SolverPETSc::sparse_vector_type& aa, const SolverPETSc::sparse_vector_type& bb) {
// assert(aa.size() == bb.size());
// #ifdef CPPUTILS_VERBOSE
// // parallel output stream
// Output_stream out;
// // timer
// cpputils::ctimer timer;
// out<<"Inside SolverPETSc::operator()(const sparse_vector&, const sparse_vector&). "<<timer<<endl;
// #endif
// Vec r;
// PetscErrorCode ierr = VecCreate(PETSC_COMM_WORLD,&r);CHKERRCONTINUE(ierr);
// ierr = VecSetSizes(r,PETSC_DECIDE, aa.size());CHKERRCONTINUE(ierr);
// ierr = VecSetFromOptions(r);CHKERRCONTINUE(ierr);
// #ifdef CPPUTILS_VERBOSE
// out<<" Vectors created... "<<timer<<endl;
// #endif
// // set values
// for (sparse_vector_type::const_hash_iterator it = aa.map_.begin(); it != aa.map_.end(); ++it) {
// int row = it->first;
// ierr = VecSetValues(r, 1, &row, &it->second, ADD_VALUES);
// }
// for (sparse_vector_type::const_hash_iterator it = bb.map_.begin(); it != bb.map_.end(); ++it) {
// int row = it->first;
// ierr = VecSetValues(r, 1, &row, &it->second, ADD_VALUES);
// }
// /*
// Assemble vector, using the 2-step process:
// VecAssemblyBegin(), VecAssemblyEnd()
// Computations can be done while messages are in transition
// by placing code between these two statements.
// */
// ierr = VecAssemblyBegin(r);CHKERRCONTINUE(ierr);
// ierr = VecAssemblyEnd(r);CHKERRCONTINUE(ierr);
// sparse_vector_type rr(aa.size());
// for (sparse_vector_type::const_hash_iterator it = aa.map_.begin(); it != aa.map_.end(); ++it) {
// int row = it->first;
// ierr = VecGetValues(r, 1, &row, &rr[row]);
// }
// for (sparse_vector_type::const_hash_iterator it = bb.map_.begin(); it != bb.map_.end(); ++it) {
// int row = it->first;
// ierr = VecGetValues(r, 1, &row, &rr[row]);
// }
// #ifdef CPPUTILS_VERBOSE
// out<<" Vector copied... "<<timer<<endl;
// #endif
// ierr = VecDestroy(&r);CHKERRCONTINUE(ierr);
// #ifdef CPPUTILS_VERBOSE
// out<<" Temporary data structures destroyed... "<<timer<<endl;
// #endif
// return rr;
// }
// SolverPETSc::value_type SolverPETSc::norm(const SolverPETSc::sparse_matrix_type& aa, Element_insertion_type flag) {
// #ifdef CPPUTILS_VERBOSE
// // parallel output stream
// Output_stream out;
// // timer
// cpputils::ctimer timer;
// out<<"Inside SolverPETSc::norm(const sparse_matrix&). "<<timer<<endl;
// #endif
// Mat r;
// PetscErrorCode ierr = MatCreate(PETSC_COMM_WORLD,&r);CHKERRCONTINUE(ierr);
// ierr = MatSetSizes(r,PETSC_DECIDE,PETSC_DECIDE, aa.rows(), aa.columns());CHKERRCONTINUE(ierr);
// ierr = MatSetFromOptions(r);CHKERRCONTINUE(ierr);
// #ifdef CPPUTILS_VERBOSE
// out<<" Matrix created... "<<timer<<endl;
// #endif
// // set values
// for (sparse_vector_type::const_hash_iterator it = aa.map_.begin(); it != aa.map_.end(); ++it) {
// // get subscripts
// std::pair<size_t,size_t> subs = aa.unhash(it->first);
// int row = subs.first;
// int col = subs.second;
// if (flag == Add_t)
// ierr = MatSetValues(r, 1, &row, 1, &col, &it->second, ADD_VALUES);
// else if (flag == Insert_t)
// ierr = MatSetValues(r, 1, &row, 1, &col, &it->second, INSERT_VALUES);
// CHKERRCONTINUE(ierr);
// }
// #ifdef CPPUTILS_VERBOSE
// out<<" Matrix filled..."<<timer<<endl;
// #endif
// /*
// Assemble vector, using the 2-step process:
// VecAssemblyBegin(), VecAssemblyEnd()
// Computations can be done while messages are in transition
// by placing code between these two statements.
// */
// ierr = MatAssemblyBegin(r,MAT_FINAL_ASSEMBLY);CHKERRCONTINUE(ierr);
// ierr = MatAssemblyEnd(r,MAT_FINAL_ASSEMBLY);CHKERRCONTINUE(ierr);
// value_type nrm;
// MatNorm(r,NORM_FROBENIUS,&nrm);
// #ifdef CPPUTILS_VERBOSE
// out<<" Norm computed... "<<timer<<endl;
// #endif
// ierr = MatDestroy(&r);CHKERRCONTINUE(ierr);
// #ifdef CPPUTILS_VERBOSE
// out<<" Temporary data structures destroyed... "<<timer<<endl;
// #endif
// return nrm;
// }
// SolverPETSc::value_type SolverPETSc::norm(const SolverPETSc::sparse_vector_type& aa, Element_insertion_type flag) {
// #ifdef CPPUTILS_VERBOSE
// // parallel output stream
// Output_stream out;
// // timer
// cpputils::ctimer timer;
// out<<"Inside SolverPETSc::norm(const sparse_vector&). "<<timer<<endl;
// #endif
// Vec r;
// PetscErrorCode ierr = VecCreate(PETSC_COMM_WORLD,&r);CHKERRCONTINUE(ierr);
// ierr = VecSetSizes(r,PETSC_DECIDE, aa.size());CHKERRCONTINUE(ierr);
// ierr = VecSetFromOptions(r);CHKERRCONTINUE(ierr);
// #ifdef CPPUTILS_VERBOSE
// out<<" Vector created... "<<timer<<endl;
// #endif
// // set values
// for (sparse_vector_type::const_hash_iterator it = aa.map_.begin(); it != aa.map_.end(); ++it) {
// int row = it->first;
// if (flag == Add_t)
// ierr = VecSetValues(r, 1, &row, &it->second, ADD_VALUES);
// else if (flag == Insert_t)
// ierr = VecSetValues(r, 1, &row, &it->second, INSERT_VALUES);
// CHKERRCONTINUE(ierr);
// }
// #ifdef CPPUTILS_VERBOSE
// out<<" Vector filled..."<<timer<<endl;
// #endif
// /*
// Assemble vector, using the 2-step process:
// VecAssemblyBegin(), VecAssemblyEnd()
// Computations can be done while messages are in transition
// by placing code between these two statements.
// */
// ierr = VecAssemblyBegin(r);CHKERRCONTINUE(ierr);
// ierr = VecAssemblyEnd(r);CHKERRCONTINUE(ierr);
// value_type nrm;
// VecNorm(r,NORM_2,&nrm);
// #ifdef CPPUTILS_VERBOSE
// out<<" Norm computed... "<<timer<<endl;
// #endif
// ierr = VecDestroy(&r);CHKERRCONTINUE(ierr);
// #ifdef CPPUTILS_VERBOSE
// out<<" Temporary data structures destroyed... "<<timer<<endl;
// #endif
// return nrm;
// }
// //
// ///* -------------------------------------------------------------------------- */
// //SolverMumps::SolverMumps(SparseMatrix & matrix,
// // const ID & id,
// // const MemoryID & memory_id) :
// //Solver(matrix, id, memory_id), is_mumps_data_initialized(false), rhs_is_local(true) {
// // AKANTU_DEBUG_IN();
// //
// //#ifdef AKANTU_USE_MPI
// // parallel_method = SolverMumpsOptions::_fully_distributed;
// //#else //AKANTU_USE_MPI
// // parallel_method = SolverMumpsOptions::_master_slave_distributed;
// //#endif //AKANTU_USE_MPI
// //
// // CommunicatorEventHandler & comm_event_handler = *this;
// //
// // communicator.registerEventHandler(comm_event_handler);
// //
// // AKANTU_DEBUG_OUT();
// //}
// //
// ///* -------------------------------------------------------------------------- */
// //SolverMumps::~SolverMumps() {
// // AKANTU_DEBUG_IN();
// //
// // AKANTU_DEBUG_OUT();
// //}
// //
// ///* -------------------------------------------------------------------------- */
// //void SolverMumps::destroyMumpsData() {
// // AKANTU_DEBUG_IN();
// //
// // if(is_mumps_data_initialized) {
// // mumps_data.job = _smj_destroy; // destroy
// // dmumps_c(&mumps_data);
// // is_mumps_data_initialized = false;
// // }
// //
// // AKANTU_DEBUG_OUT();
// //}
// //
// ///* -------------------------------------------------------------------------- */
// //void SolverMumps::onCommunicatorFinalize(const StaticCommunicator & comm) {
// // AKANTU_DEBUG_IN();
// //
// // try{
// // const StaticCommunicatorMPI & comm_mpi =
// // dynamic_cast<const StaticCommunicatorMPI &>(comm.getRealStaticCommunicator());
// // if(mumps_data.comm_fortran == MPI_Comm_c2f(comm_mpi.getMPICommunicator()))
// // destroyMumpsData();
// // } catch(...) {}
// //
// // AKANTU_DEBUG_OUT();
// //}
// //
// ///* -------------------------------------------------------------------------- */
// //void SolverMumps::initMumpsData(SolverMumpsOptions::ParallelMethod parallel_method) {
// // switch(parallel_method) {
// // case SolverMumpsOptions::_fully_distributed:
// // icntl(18) = 3; //fully distributed
// // icntl(28) = 0; //automatic choice
// //
// // mumps_data.nz_loc = matrix->getNbNonZero();
// // mumps_data.irn_loc = matrix->getIRN().values;
// // mumps_data.jcn_loc = matrix->getJCN().values;
// // break;
// // case SolverMumpsOptions::_master_slave_distributed:
// // if(prank == 0) {
// // mumps_data.nz = matrix->getNbNonZero();
// // mumps_data.irn = matrix->getIRN().values;
// // mumps_data.jcn = matrix->getJCN().values;
// // } else {
// // mumps_data.nz = 0;
// // mumps_data.irn = NULL;
// // mumps_data.jcn = NULL;
// //
// // icntl(18) = 0; //centralized
// // icntl(28) = 0; //sequential analysis
// // }
// // break;
// // }
// //}
// //
// ///* -------------------------------------------------------------------------- */
// //void SolverMumps::initialize(SolverOptions & options) {
// // AKANTU_DEBUG_IN();
// //
// // mumps_data.par = 1;
// //
// // if(SolverMumpsOptions * opt = dynamic_cast<SolverMumpsOptions *>(&options)) {
// // if(opt->parallel_method == SolverMumpsOptions::_master_slave_distributed) {
// // mumps_data.par = 0;
// // }
// // }
// //
// // mumps_data.sym = 2 * (matrix->getSparseMatrixType() == _symmetric);
// // prank = communicator.whoAmI();
// //#ifdef AKANTU_USE_MPI
// // mumps_data.comm_fortran = MPI_Comm_c2f(dynamic_cast<const StaticCommunicatorMPI &>(communicator.getRealStaticCommunicator()).getMPICommunicator());
// //#endif
// //
// // if(AKANTU_DEBUG_TEST(dblTrace)) {
// // icntl(1) = 2;
// // icntl(2) = 2;
// // icntl(3) = 2;
// // icntl(4) = 4;
// // }
// //
// // mumps_data.job = _smj_initialize; //initialize
// // dmumps_c(&mumps_data);
// // is_mumps_data_initialized = true;
// //
// // /* ------------------------------------------------------------------------ */
// // UInt size = matrix->getSize();
// //
// // if(prank == 0) {
// // std::stringstream sstr_rhs; sstr_rhs << id << ":rhs";
// // rhs = &(alloc<Real>(sstr_rhs.str(), size, 1, REAL_INIT_VALUE));
// // } else {
// // rhs = NULL;
// // }
// //
// // /// No outputs
// // icntl(1) = 0;
// // icntl(2) = 0;
// // icntl(3) = 0;
// // icntl(4) = 0;
// // mumps_data.nz_alloc = 0;
// //
// // if (AKANTU_DEBUG_TEST(dblDump)) icntl(4) = 4;
// //
// // mumps_data.n = size;
// //
// // if(AKANTU_DEBUG_TEST(dblDump)) {
// // strcpy(mumps_data.write_problem, "mumps_matrix.mtx");
// // }
// //
// // /* ------------------------------------------------------------------------ */
// // // Default Scaling
// // icntl(8) = 77;
// //
// // icntl(5) = 0; // Assembled matrix
// //
// // SolverMumpsOptions * opt = dynamic_cast<SolverMumpsOptions *>(&options);
// // if(opt)
// // parallel_method = opt->parallel_method;
// //
// // initMumpsData(parallel_method);
// //
// // mumps_data.job = _smj_analyze; //analyze
// // dmumps_c(&mumps_data);
// //
// // AKANTU_DEBUG_OUT();
// //}
// //
// ///* -------------------------------------------------------------------------- */
// //void SolverMumps::setRHS(Array<Real> & rhs) {
// // if(prank == 0) {
// // matrix->getDOFSynchronizer().gather(rhs, 0, this->rhs);
// // } else {
// // matrix->getDOFSynchronizer().gather(rhs, 0);
// // }
// //}
// //
// ///* -------------------------------------------------------------------------- */
// //void SolverMumps::solve() {
// // AKANTU_DEBUG_IN();
// //
// // if(parallel_method == SolverMumpsOptions::_fully_distributed)
// // mumps_data.a_loc = matrix->getA().values;
// // else
// // if(prank == 0) {
// // mumps_data.a = matrix->getA().values;
// // }
// //
// // if(prank == 0) {
// // mumps_data.rhs = rhs->values;
// // }
// //
// // /// Default centralized dense second member
// // icntl(20) = 0;
// // icntl(21) = 0;
// //
// // mumps_data.job = _smj_factorize_solve; //solve
// // dmumps_c(&mumps_data);
// //
// // AKANTU_DEBUG_ASSERT(info(1) != -10, "Singular matrix");
// // AKANTU_DEBUG_ASSERT(info(1) == 0,
// // "Error in mumps during solve process, check mumps user guide INFO(1) ="
// // << info(1));
// //
// // AKANTU_DEBUG_OUT();
// //}
// //
// ///* -------------------------------------------------------------------------- */
// //void SolverMumps::solve(Array<Real> & solution) {
// // AKANTU_DEBUG_IN();
// //
// // solve();
// //
// // if(prank == 0) {
// // matrix->getDOFSynchronizer().scatter(solution, 0, this->rhs);
// // } else {
// // matrix->getDOFSynchronizer().scatter(solution, 0);
// // }
// //
// // AKANTU_DEBUG_OUT();
// //}
+__END_AKANTU__
-// __END_AKANTU__
diff --git a/src/solver/solver_petsc.hh b/src/solver/solver_petsc.hh
index 352a2db88..40c27c7d5 100644
--- a/src/solver/solver_petsc.hh
+++ b/src/solver/solver_petsc.hh
@@ -1,271 +1,165 @@
/**
* @file solver_petsc.hh
*
# @author Alejandro M. Aragón <alejandro.aragon@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
+ * @author Aurelia Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
* @date Mon Dec 13 10:48:06 2010
*
- * @brief Solver class implementation for the petsc solver
+ * @brief Solver class interface for the petsc solver
*
* @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/>.
*
*/
/* -------------------------------------------------------------------------- */
-// #ifndef __AKANTU_SOLVER_PETSC_HH__
-// #define __AKANTU_SOLVER_PETSC_HH__
+#ifndef __AKANTU_SOLVER_PETSC_HH__
+#define __AKANTU_SOLVER_PETSC_HH__
+/* -------------------------------------------------------------------------- */
+#include "solver.hh"
-// #include <petscksp.h>
+/* -------------------------------------------------------------------------- */
+__BEGIN_AKANTU__
-// #include "solver.hh"
-// #include "static_communicator.hh"
-// #include "sparse_matrix.hh"
+class PETScSolverWrapper;
-// __BEGIN_AKANTU__
+class SolverPETSc : public Solver {
+ /* ------------------------------------------------------------------------ */
+ /* Constructors/Destructors */
+ /* ------------------------------------------------------------------------ */
+public:
+ SolverPETSc(SparseMatrix & sparse_matrix,
+ const ID & id = "solver_petsc",
+ const MemoryID & memory_id = 0);
-// struct SolverPETSc : public Solver, public CommunicatorEventHandler {
-
-// typedef double value_type;
-// typedef sparse_vector<value_type> sparse_vector_type;
-// typedef SparseMatrix sparse_matrix_type;
-
-// Mat A_; //!< linear system matrix
-// Vec x_; //!< Solution vector
-// KSP ksp_; //!< linear solver context
-
-// bool allocated_;
+ virtual ~SolverPETSc();
+
+ /* ------------------------------------------------------------------------ */
+ /* Methods */
+ /* ------------------------------------------------------------------------ */
+public:
+ /// create the solver context and set the matrices
+ virtual void initialize(SolverOptions & options = _solver_no_options);
+ virtual void setRHS(Array<Real> & rhs);
+ virtual void solve();
+ virtual void solve(Array<Real> & solution);
+private:
+ /// clean the petsc data
+ virtual void destroyInternalData();
+
+private:
+
+ /// specify if the petsc_data is initialized or not
+ bool is_petsc_data_initialized;
+
+ /// store the PETSc structures
+ PETScSolverWrapper * petsc_solver_wrapper;
+
+
+
+};
+
// SolverPETSc(int argc, char *argv[]) : allocated_(false) {
-
-// PetscInitialize(&argc, &argv,NULL,NULL);
-// PetscErrorCode ierr;
-
-// // create linear solver context
-// ierr = KSPCreate(PETSC_COMM_WORLD, &ksp_);CHKERRCONTINUE(ierr);
-
-// // initial nonzero guess
-// ierr = KSPSetInitialGuessNonzero(ksp_,PETSC_TRUE); CHKERRCONTINUE(ierr);
-
-// // set runtime options
-// ierr = KSPSetFromOptions(ksp_);CHKERRCONTINUE(ierr);
-
// /*
// Set linear solver defaults for this problem (optional).
// - By extracting the KSP and PC contexts from the KSP context,
// we can then directly call any KSP and PC routines to set
// various options.
// - The following four statements are optional; all of these
// parameters could alternatively be specified at runtime via
// KSPSetFromOptions();
// */
// // ierr = KSPGetPC(ksp_,&pc);CHKERRCONTINUE(ierr);
// // ierr = PCSetType(pc,PCILU);CHKERRCONTINUE(ierr);
// // ierr = PCSetType(pc,PCJACOBI);CHKERRCONTINUE(ierr);
// ierr = KSPSetTolerances(ksp_,1.e-5,PETSC_DEFAULT,PETSC_DEFAULT,PETSC_DEFAULT);CHKERRCONTINUE(ierr);
// }
// //! Overload operator() to solve system of linear equations
// sparse_vector_type operator()(const sparse_matrix_type& AA, const sparse_vector_type& bb);
// //! Overload operator() to obtain reaction vector
// sparse_vector_type operator()(const sparse_matrix_type& Kpf, const sparse_matrix_type& Kpp, const sparse_vector_type& Up);
// //! Overload operator() to obtain the addition two vectors
// sparse_vector_type operator()(const sparse_vector_type& aa, const sparse_vector_type& bb);
// value_type norm(const sparse_matrix_type& aa, Element_insertion_type it = Add_t);
// value_type norm(const sparse_vector_type& aa, Element_insertion_type it = Add_t);
// // NOTE: the destructor will return an error if it is called after MPI_Finalize is
// // called because it uses collect communication to free-up allocated memory.
// ~SolverPETSc() {
// static bool exit = false;
// if (!exit) {
// // add finalize PETSc function at exit
// atexit(finalize);
// exit = true;
// }
// if (allocated_) {
// PetscErrorCode ierr = MatDestroy(&A_);CHKERRCONTINUE(ierr);
// ierr = VecDestroy(&x_);CHKERRCONTINUE(ierr);
// ierr = KSPDestroy(&ksp_);CHKERRCONTINUE(ierr);
// }
// }
// /* from the PETSc library, these are the options that can be passed
// to the command line
// Options Database Keys
// -options_table - Calls PetscOptionsView()
// -options_left - Prints unused options that remain in the database
// -objects_left - Prints list of all objects that have not been freed
// -mpidump - Calls PetscMPIDump()
// -malloc_dump - Calls PetscMallocDump()
// -malloc_info - Prints total memory usage
// -malloc_log - Prints summary of memory usage
// Options Database Keys for Profiling
// -log_summary [filename] - Prints summary of flop and timing information to screen.
// If the filename is specified the summary is written to the file. See PetscLogView().
// -log_summary_python [filename] - Prints data on of flop and timing usage to a file or screen.
// -log_all [filename] - Logs extensive profiling information See PetscLogDump().
// -log [filename] - Logs basic profiline information See PetscLogDump().
// -log_sync - Log the synchronization in scatters, inner products and norms
// -log_mpe [filename] - Creates a logfile viewable by the utility Upshot/Nupshot (in MPICH distribution)
-// */
-// static void finalize() {
-
-// static bool finalized = false;
-// if (!finalized) {
-
-// cout<<"*** INFO *** PETSc is finalizing..."<<endl;
-
-// // finalize PETSc
-// PetscErrorCode ierr = PetscFinalize();CHKERRCONTINUE(ierr);
-// finalized = true;
-
-// cout<<"*** INFO *** Process "<<Parallel_base::rank_<<" is finalizing..."<<endl;
-
-// // finalize MPI
-// MPI_Finalize();
// }
// }
// };
-// class SolverPETSc : public Solver, public CommunicatorEventHandler {
-// /* ------------------------------------------------------------------------ */
-// /* Constructors/Destructors */
-// /* ------------------------------------------------------------------------ */
-// public:
-
-// SolverPETSc(SparseMatrix & sparse_matrix,
-// const ID & id = "solver_petsc",
-// const MemoryID & memory_id = 0);
-
-// virtual SolverPETSc();
-
-// /* ------------------------------------------------------------------------ */
-// /* Methods */
-// /* ------------------------------------------------------------------------ */
-// public:
-
-// /// build the profile and do the analysis part
-// void initialize(SolverOptions & options = _solver_no_options);
-
-// void initializeSlave(SolverOptions & options = _solver_no_options);
-
-
-// /// factorize and solve the system
-// void solve(Array<Real> & solution);
-// void solve();
-
-// void solveSlave();
-
-// virtual void setRHS(Array<Real> & rhs);
-
-// /// function to print the contain of the class
-// // virtual void printself(std::ostream & stream, int indent = 0) const;
-
-// virtual void onCommunicatorFinalize(const StaticCommunicator & communicator);
-
-// private:
-
-// void destroyMumpsData();
-
-// inline Int & icntl(UInt i) {
-// return mumps_data.icntl[i - 1];
-// }
-
-// inline Int & info(UInt i) {
-// return mumps_data.info[i - 1];
-// }
-
-// void initMumpsData(SolverMumpsOptions::ParallelMethod parallel_method);
-
-// /* ------------------------------------------------------------------------ */
-// /* Accessors */
-// /* ------------------------------------------------------------------------ */
-// public:
-
-// /* ------------------------------------------------------------------------ */
-// /* Class Members */
-// /* ------------------------------------------------------------------------ */
-// private:
-
-// /// mumps data
-// DMUMPS_STRUC_C mumps_data;
-
-// /// specify if the mumps_data are initialized or not
-// bool is_mumps_data_initialized;
-
-// UInt prank;
-
-// /* ------------------------------------------------------------------------ */
-// /* Local types */
-// /* ------------------------------------------------------------------------ */
-
-// private:
-// SolverMumpsOptions::ParallelMethod parallel_method;
-
-// bool rhs_is_local;
-
-// enum SolverMumpsJob {
-// _smj_initialize = -1,
-// _smj_analyze = 1,
-// _smj_factorize = 2,
-// _smj_solve = 3,
-// _smj_analyze_factorize = 4,
-// _smj_factorize_solve = 5,
-// _smj_complete = 6, // analyze, factorize, solve
-// _smj_destroy = -2
-// };
-// };
-
-
-// /* -------------------------------------------------------------------------- */
-// /* inline functions */
-// /* -------------------------------------------------------------------------- */
-
-// //#include "solver_mumps_inline_impl.cc"
-
-// /// standard output stream operator
-// // inline std::ostream & operator <<(std::ostream & stream, const SolverMumps & _this)
-// // {
-// // _this.printself(stream);
-// // return stream;
-// // }
-// __END_AKANTU__
+__END_AKANTU__
-// #endif /* __AKANTU_SOLVER_PETSC_HH__ */
+#endif /* __AKANTU_SOLVER_PETSC_HH__ */
diff --git a/src/solver/sparse_matrix.hh b/src/solver/sparse_matrix.hh
index 60a03e966..fad877951 100644
--- a/src/solver/sparse_matrix.hh
+++ b/src/solver/sparse_matrix.hh
@@ -1,251 +1,259 @@
/**
* @file sparse_matrix.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Dec 13 2010
* @date last modification: Mon Sep 15 2014
*
* @brief sparse matrix storage class (distributed assembled matrix)
* This is a COO format (Coordinate List)
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 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_SPARSE_MATRIX_HH__
#define __AKANTU_SPARSE_MATRIX_HH__
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#ifndef __INTEL_COMPILER
namespace std {
namespace tr1 {
template<typename a, typename b>
struct hash< std::pair<a, b> > {
private:
const hash<a> ah;
const hash<b> bh;
public:
hash() : ah(), bh() {}
size_t operator()(const std::pair<a, b> &p) const {
size_t seed = ah(p.first);
return bh(p.second) + 0x9e3779b9 + (seed<<6) + (seed>>2);
}
};
}
} // namespaces
#endif
__BEGIN_AKANTU__
class DOFSynchronizer;
-class SparseMatrix : private Memory {
+class SparseMatrix : protected Memory {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
SparseMatrix(UInt size,
const SparseMatrixType & sparse_matrix_type,
const ID & id = "sparse_matrix",
const MemoryID & memory_id = 0);
SparseMatrix(const SparseMatrix & matrix,
const ID & id = "sparse_matrix",
const MemoryID & memory_id = 0);
virtual ~SparseMatrix();
typedef std::pair<UInt, UInt> KeyCOO;
typedef unordered_map<KeyCOO, UInt>::type coordinate_list_map;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// remove the existing profile
inline void clearProfile();
/// add a non-zero element
virtual UInt addToProfile(UInt i, UInt j);
/// set the matrix to 0
inline void clear();
/// assemble a local matrix in the sparse one
inline void addToMatrix(UInt i, UInt j, Real value);
/// set the size of the matrix
void resize(UInt size)
{ this->size = size; }
virtual void buildProfile(const Mesh & mesh, const DOFSynchronizer & dof_synchronizer, UInt nb_degree_of_freedom);
/// modify the matrix to "remove" the blocked dof
virtual void applyBoundary(const Array<bool> & boundary, Real block_val = 1.);
// /// modify the matrix to "remove" the blocked dof
// void applyBoundaryNormal(Array<bool> & boundary_normal, Array<Real> & EulerAngles, Array<Real> & rhs, const Array<Real> & matrix, Array<Real> & rhs_rotated);
/// save the profil in a file using the MatrixMarket file format
virtual void saveProfile(const std::string & filename) const;
/// save the matrix in a file using the MatrixMarket file format
virtual void saveMatrix(const std::string & filename) const;
/// copy assuming the profile are the same
virtual void copyContent(const SparseMatrix & matrix);
/// copy profile
// void copyProfile(const SparseMatrix & matrix);
/// add matrix assuming the profile are the same
virtual void add(const SparseMatrix & matrix, Real alpha);
/// diagonal lumping
virtual void lump(Array<Real> & lumped);
/// function to print the contain of the class
//virtual void printself(std::ostream & stream, int indent = 0) const;
protected:
inline KeyCOO key(UInt i, UInt j) const {
if(sparse_matrix_type == _symmetric && (i > j))
return std::make_pair(j, i);
return std::make_pair(i, j);
}
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// return the values at potition i, j
inline Real operator()(UInt i, UInt j) const;
inline Real & operator()(UInt i, UInt j);
AKANTU_GET_MACRO(IRN, irn, const Array<Int> &);
AKANTU_GET_MACRO(JCN, jcn, const Array<Int> &);
AKANTU_GET_MACRO(A, a, const Array<Real> &);
AKANTU_GET_MACRO(NbNonZero, nb_non_zero, UInt);
AKANTU_GET_MACRO(Size, size, UInt);
AKANTU_GET_MACRO(SparseMatrixType, sparse_matrix_type, const SparseMatrixType &);
AKANTU_GET_MACRO(Offset, offset, UInt);
const DOFSynchronizer & getDOFSynchronizer() const {
AKANTU_DEBUG_ASSERT(dof_synchronizer != NULL,
"DOFSynchronizer not initialized in the SparseMatrix!");
return *dof_synchronizer;
}
+ DOFSynchronizer & getDOFSynchronizer() {
+ AKANTU_DEBUG_ASSERT(dof_synchronizer != NULL,
+ "DOFSynchronizer not initialized in the SparseMatrix!");
+ return *dof_synchronizer;
+ }
+
private:
AKANTU_GET_MACRO(DOFSynchronizerPointer, dof_synchronizer, DOFSynchronizer *);
friend Array<Real> & operator*=(Array<Real> & vect, const SparseMatrix & mat);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// id of the SparseMatrix
ID id;
/// sparce matrix type
SparseMatrixType sparse_matrix_type;
/// Mesh corresponding to the profile
// const Mesh * mesh;
/// Size of the matrix
UInt size;
/// number of processors
UInt nb_proc;
/// number of non zero element
UInt nb_non_zero;
/// row indexes
Array<Int> irn;
/// column indexes
Array<Int> jcn;
/// values : A[k] = Matrix[irn[k]][jcn[k]]
Array<Real> a;
/// saved row indexes
Array<Int> * irn_save;
/// saved column indexes
Array<Int> * jcn_save;
/// saved size
UInt size_save;
/// information to know where to assemble an element in a global sparse matrix
// ElementTypeMapArray<UInt> element_to_sparse_profile;
/* map for (i,j) -> k correspondence \warning std::map are slow
* \todo improve with hash_map (non standard in stl) or unordered_map (boost or C++0x)
*/
coordinate_list_map irn_jcn_k;
DOFSynchronizer * dof_synchronizer;
// std::map<std::pair<UInt, UInt>, UInt> * irn_jcn_to_k;
/// offset to inidcate whether row and column indices start at 0 (C/C++) or 1 (Fortran)
UInt offset;
+
+
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#if defined (AKANTU_INCLUDE_INLINE_IMPL)
# include "sparse_matrix_inline_impl.cc"
#endif
// /// standard output stream operator
// inline std::ostream & operator <<(std::ostream & stream, const SparseMatrix & _this)
// {
// _this.printself(stream);
// return stream;
// }
Array<Real> & operator*=(Array<Real> & vect, const SparseMatrix & mat);
__END_AKANTU__
#endif /* __AKANTU_SPARSE_MATRIX_HH__ */
diff --git a/src/synchronizer/data_accessor.hh b/src/synchronizer/data_accessor.hh
index 8324bdc8c..9d8001934 100644
--- a/src/synchronizer/data_accessor.hh
+++ b/src/synchronizer/data_accessor.hh
@@ -1,217 +1,268 @@
/**
* @file data_accessor.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Jun 16 2011
* @date last modification: Thu Jun 05 2014
*
* @brief Interface of accessors for pack_unpack system
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 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_DATA_ACCESSOR_HH__
#define __AKANTU_DATA_ACCESSOR_HH__
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh.hh"
#include "fe_engine.hh"
#include "communication_buffer.hh"
/* -------------------------------------------------------------------------- */
__BEGIN_AKANTU__
class DataAccessor {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
DataAccessor();
virtual ~DataAccessor();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/**
* @brief get the number of data to exchange for a given akantu::Element and a
* given akantu::SynchronizationTag
*/
virtual UInt getNbDataForElements(__attribute__((unused)) const Array<Element> & elements,
__attribute__((unused)) SynchronizationTag tag) const {
AKANTU_DEBUG_TO_IMPLEMENT();
}
+ /**
+ * @brief get the number of data to exchange for a given degree of freedom and a
+ * given akantu::SynchronizationTag
+ */
+ virtual UInt getNbDataForDOFs(__attribute__((unused)) const Array<UInt> & dofs,
+ __attribute__((unused)) SynchronizationTag tag) const {
+ AKANTU_DEBUG_TO_IMPLEMENT();
+ }
+
/**
* @brief get the number of data to send for a given
* akantu::SynchronizationTag
*/
virtual UInt getNbDataToPack(__attribute__((unused)) SynchronizationTag tag) const {
AKANTU_DEBUG_TO_IMPLEMENT();
}
/**
* @brief get the number of data to receive for a given
* akantu::SynchronizationTag
*/
virtual UInt getNbDataToUnpack(__attribute__((unused)) SynchronizationTag tag) const {
AKANTU_DEBUG_TO_IMPLEMENT();
}
/**
* @brief pack the data for a given akantu::Element and a given
* akantu::SynchronizationTag
*/
virtual void packElementData(__attribute__((unused)) CommunicationBuffer & buffer,
__attribute__((unused)) const Array<Element> & element,
__attribute__((unused)) SynchronizationTag tag) const {
AKANTU_DEBUG_TO_IMPLEMENT();
}
/**
* @brief pack the data for a given index and a given
* akantu::SynchronizationTag
*/
virtual void packData(__attribute__((unused)) CommunicationBuffer & buffer,
__attribute__((unused)) const UInt index,
__attribute__((unused)) SynchronizationTag tag) const {
AKANTU_DEBUG_TO_IMPLEMENT();
}
+ /**
+ * @brief pack the data for the dofs and a given
+ * akantu::SynchronizationTag
+ */
+ virtual void packDOFData(__attribute__((unused)) CommunicationBuffer & buffer,
+ __attribute__((unused)) const Array<UInt> & dofs,
+ __attribute__((unused)) SynchronizationTag tag) const {
+ AKANTU_DEBUG_TO_IMPLEMENT();
+ }
+
/**
* @brief unpack the data for a given akantu::Element and a given
* akantu::SynchronizationTag
*/
virtual void unpackElementData(__attribute__((unused)) CommunicationBuffer & buffer,
__attribute__((unused)) const Array<Element> & element,
__attribute__((unused)) SynchronizationTag tag) {
AKANTU_DEBUG_TO_IMPLEMENT();
}
/**
* @brief unpack the data for a given index and a given
* akantu::SynchronizationTag
*/
virtual void unpackData(__attribute__((unused)) CommunicationBuffer & buffer,
__attribute__((unused)) const UInt index,
__attribute__((unused)) SynchronizationTag tag) {
AKANTU_DEBUG_TO_IMPLEMENT();
}
+ /**
+ * @brief unpack the data for the dofs and a given
+ * akantu::SynchronizationTag
+ */
+ virtual void unpackDOFData(__attribute__((unused)) CommunicationBuffer & buffer,
+ __attribute__((unused)) const Array<UInt> & dofs,
+ __attribute__((unused)) SynchronizationTag tag) {
+ AKANTU_DEBUG_TO_IMPLEMENT();
+ }
+
public:
template<typename T>
static inline void packNodalDataHelper(const Array<T> & data,
CommunicationBuffer & buffer,
const Array<Element> & elements,
const Mesh & mesh) {
packUnpackNodalDataHelper<T, true>(const_cast<Array<T> &>(data),
buffer,
elements,
mesh);
}
template<typename T>
static inline void unpackNodalDataHelper(Array<T> & data,
CommunicationBuffer & buffer,
const Array<Element> & elements,
const Mesh & mesh) {
packUnpackNodalDataHelper<T, false>(data,
buffer,
elements,
mesh);
}
template<typename T, bool pack_helper>
static inline void packUnpackNodalDataHelper(Array<T> & data,
CommunicationBuffer & buffer,
const Array<Element> & elements,
const Mesh & mesh);
template<typename T, bool pack_helper>
static inline void packUnpackElementalDataHelper(ElementTypeMapArray<T> & data_to_pack,
CommunicationBuffer & buffer,
const Array<Element> & element,
bool per_quadrature_point_data,
const FEEngine & fem);
-
template<typename T>
static inline void packElementalDataHelper(const ElementTypeMapArray<T> & data_to_pack,
CommunicationBuffer & buffer,
const Array<Element> & elements,
bool per_quadrature_point,
const FEEngine & fem) {
packUnpackElementalDataHelper<T, true>(const_cast<ElementTypeMapArray<T> &>(data_to_pack),
buffer,
elements,
per_quadrature_point,
fem);
}
template<typename T>
- inline void unpackElementalDataHelper(ElementTypeMapArray<T> & data_to_unpack,
+ static inline void unpackElementalDataHelper(ElementTypeMapArray<T> & data_to_unpack,
CommunicationBuffer & buffer,
const Array<Element> & elements,
bool per_quadrature_point,
const FEEngine & fem) {
packUnpackElementalDataHelper<T, false>(data_to_unpack,
buffer,
elements,
per_quadrature_point,
fem);
}
+ template<typename T, bool pack_helper>
+ static inline void packUnpackDOFDataHelper(Array<T> & data,
+ CommunicationBuffer & buffer,
+ const Array<UInt> & dofs);
+
+ template<typename T>
+ static inline void packDOFDataHelper(const Array<T> & data_to_pack,
+ CommunicationBuffer & buffer,
+ const Array<UInt> & dofs) {
+ packUnpackDOFDataHelper<T, true>(const_cast<Array<T> &>(data_to_pack),
+ buffer,
+ dofs);
+ }
+
+ template<typename T>
+ static inline void unpackDOFDataHelper(Array<T> & data_to_unpack,
+ CommunicationBuffer & buffer,
+ const Array<UInt> & dofs) {
+ packUnpackDOFDataHelper<T, false>(data_to_unpack,
+ buffer,
+ dofs);
+ }
+
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "data_accessor_inline_impl.cc"
// /// standard output stream operator
// inline std::ostream & operator <<(std::ostream & stream, const DataAccessor & _this)
// {
// _this.printself(stream);
// return stream;
// }
__END_AKANTU__
#endif /* __AKANTU_DATA_ACCESSOR_HH__ */
diff --git a/src/synchronizer/data_accessor_inline_impl.cc b/src/synchronizer/data_accessor_inline_impl.cc
index dc8c0b6dc..8bba84c11 100644
--- a/src/synchronizer/data_accessor_inline_impl.cc
+++ b/src/synchronizer/data_accessor_inline_impl.cc
@@ -1,107 +1,125 @@
/**
* @file data_accessor_inline_impl.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Sep 18 2013
* @date last modification: Thu Jun 05 2014
*
* @brief Implementation of the inline functions of the DataAccessor class
*
* @section LICENSE
*
* Copyright (©) 2014 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/>.
*
*/
/* -------------------------------------------------------------------------- */
template<typename T, bool pack_helper>
inline void DataAccessor::packUnpackNodalDataHelper(Array<T> & data,
CommunicationBuffer & buffer,
const Array<Element> & elements,
const Mesh & mesh) {
UInt nb_component = data.getNbComponent();
UInt nb_nodes_per_element = 0;
ElementType current_element_type = _not_defined;
GhostType current_ghost_type = _casper;
UInt * conn = NULL;
Array<Element>::const_iterator<Element> it = elements.begin();
Array<Element>::const_iterator<Element> end = elements.end();
for (; it != end; ++it) {
const Element & el = *it;
if(el.type != current_element_type || el.ghost_type != current_ghost_type) {
current_element_type = el.type;
current_ghost_type = el.ghost_type;
conn = mesh.getConnectivity(el.type, el.ghost_type).storage();
nb_nodes_per_element = Mesh::getNbNodesPerElement(el.type);
}
UInt el_offset = el.element * nb_nodes_per_element;
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
UInt offset_conn = conn[el_offset + n];
Vector<T> data_vect(data.storage() + offset_conn * nb_component,
nb_component);
if(pack_helper)
buffer << data_vect;
else
buffer >> data_vect;
}
}
}
/* -------------------------------------------------------------------------- */
template<typename T, bool pack_helper>
inline void DataAccessor::packUnpackElementalDataHelper(ElementTypeMapArray<T> & data_to_pack,
CommunicationBuffer & buffer,
const Array<Element> & element,
bool per_quadrature_point_data,
const FEEngine & fem) {
ElementType current_element_type = _not_defined;
GhostType current_ghost_type = _casper;
UInt nb_quad_per_elem = 0;
UInt nb_component = 0;
Array<T> * vect = NULL;
Array<Element>::const_iterator<Element> it = element.begin();
Array<Element>::const_iterator<Element> end = element.end();
for (; it != end; ++it) {
const Element & el = *it;
if(el.type != current_element_type || el.ghost_type != current_ghost_type) {
current_element_type = el.type;
current_ghost_type = el.ghost_type;
vect = &data_to_pack(el.type, el.ghost_type);
if(per_quadrature_point_data)
nb_quad_per_elem = fem.getNbQuadraturePoints(el.type,
el.ghost_type);
else nb_quad_per_elem = 1;
nb_component = vect->getNbComponent();
}
Vector<T> data(vect->storage() + el.element * nb_component * nb_quad_per_elem,
nb_component * nb_quad_per_elem);
if(pack_helper)
buffer << data;
else
buffer >> data;
}
}
+
+/* -------------------------------------------------------------------------- */
+template<typename T, bool pack_helper>
+inline void DataAccessor::packUnpackDOFDataHelper(Array<T> & data,
+ CommunicationBuffer & buffer,
+ const Array<UInt> & dofs) {
+ Array<UInt>::const_scalar_iterator it_dof = dofs.begin();
+ Array<UInt>::const_scalar_iterator end_dof = dofs.end();
+ T * data_ptr = data.storage();
+
+ for (; it_dof != end_dof; ++it_dof) {
+ if(pack_helper)
+ buffer << data_ptr[*it_dof];
+ else
+ buffer >> data_ptr[*it_dof];
+ }
+}
+
diff --git a/src/synchronizer/distributed_synchronizer.cc b/src/synchronizer/distributed_synchronizer.cc
index c497e7069..d698c9fea 100644
--- a/src/synchronizer/distributed_synchronizer.cc
+++ b/src/synchronizer/distributed_synchronizer.cc
@@ -1,1652 +1,1651 @@
/**
* @file distributed_synchronizer.cc
*
* @author Dana Christen <dana.christen@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Jun 16 2011
* @date last modification: Fri Sep 05 2014
*
* @brief implementation of a communicator using a static_communicator for real
* send/receive
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 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 "distributed_synchronizer.hh"
#include "static_communicator.hh"
#include "mesh_utils.hh"
#include "mesh_data.hh"
#include "element_group.hh"
/* -------------------------------------------------------------------------- */
#include <map>
#include <iostream>
#include <algorithm>
#if defined(AKANTU_DEBUG_TOOLS)
# include "aka_debug_tools.hh"
#endif
/* -------------------------------------------------------------------------- */
__BEGIN_AKANTU__
/* -------------------------------------------------------------------------- */
DistributedSynchronizer::DistributedSynchronizer(Mesh & mesh,
SynchronizerID id,
MemoryID memory_id) :
Synchronizer(id, memory_id),
mesh(mesh),
- static_communicator(&StaticCommunicator::getStaticCommunicator()),
prank_to_element("prank_to_element", id)
{
AKANTU_DEBUG_IN();
nb_proc = static_communicator->getNbProc();
rank = static_communicator->whoAmI();
send_element = new Array<Element>[nb_proc];
recv_element = new Array<Element>[nb_proc];
mesh.registerEventHandler(*this);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
DistributedSynchronizer::~DistributedSynchronizer() {
AKANTU_DEBUG_IN();
for (UInt p = 0; p < nb_proc; ++p) {
send_element[p].clear();
recv_element[p].clear();
}
delete [] send_element;
delete [] recv_element;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
DistributedSynchronizer * DistributedSynchronizer::
createDistributedSynchronizerMesh(Mesh & mesh,
const MeshPartition * partition,
UInt root,
SynchronizerID id,
MemoryID memory_id) {
AKANTU_DEBUG_IN();
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
UInt nb_proc = comm.getNbProc();
UInt my_rank = comm.whoAmI();
DistributedSynchronizer & communicator = *(new DistributedSynchronizer(mesh, id, memory_id));
if(nb_proc == 1) return &communicator;
UInt * local_connectivity = NULL;
UInt * local_partitions = NULL;
Array<UInt> * old_nodes = mesh.getNodesGlobalIdsPointer();
old_nodes->resize(0);
Array<Real> * nodes = mesh.getNodesPointer();
UInt spatial_dimension = nodes->getNbComponent();
mesh.synchronizeGroupNames();
/* ------------------------------------------------------------------------ */
/* Local (rank == root) */
/* ------------------------------------------------------------------------ */
if(my_rank == root) {
AKANTU_DEBUG_ASSERT(partition->getNbPartition() == nb_proc,
"The number of partition does not match the number of processors: " <<
partition->getNbPartition() << " != " << nb_proc);
/**
* connectivity and communications scheme construction
*/
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);
UInt count = 0;
/* --- MAIN LOOP ON TYPES --- */
for(; it != end; ++it) {
ElementType type = *it;
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_element = mesh.getNbElement(*it);
UInt nb_local_element[nb_proc];
UInt nb_ghost_element[nb_proc];
UInt nb_element_to_send[nb_proc];
memset(nb_local_element, 0, nb_proc*sizeof(UInt));
memset(nb_ghost_element, 0, nb_proc*sizeof(UInt));
memset(nb_element_to_send, 0, nb_proc*sizeof(UInt));
/// \todo change this ugly way to avoid a problem if an element
/// type is present in the mesh but not in the partitions
const Array<UInt> * tmp_partition_num = NULL;
try {
tmp_partition_num = &partition->getPartition(type, _not_ghost);
} catch(...) {
continue;
}
const Array<UInt> & partition_num = *tmp_partition_num;
const CSR<UInt> & ghost_partition = partition->getGhostPartitionCSR()(type, _not_ghost);
/* -------------------------------------------------------------------- */
/// constructing the reordering structures
for (UInt el = 0; el < nb_element; ++el) {
nb_local_element[partition_num(el)]++;
for (CSR<UInt>::const_iterator part = ghost_partition.begin(el);
part != ghost_partition.end(el);
++part) {
nb_ghost_element[*part]++;
}
nb_element_to_send[partition_num(el)] += ghost_partition.getNbCols(el) + 1;
}
/// allocating buffers
UInt * buffers[nb_proc];
UInt * buffers_tmp[nb_proc];
for (UInt p = 0; p < nb_proc; ++p) {
UInt size = nb_nodes_per_element * (nb_local_element[p] +
nb_ghost_element[p]);
buffers[p] = new UInt[size];
buffers_tmp[p] = buffers[p];
}
/// copying the local connectivity
UInt * conn_val = mesh.getConnectivity(type, _not_ghost).storage();
for (UInt el = 0; el < nb_element; ++el) {
memcpy(buffers_tmp[partition_num(el)],
conn_val + el * nb_nodes_per_element,
nb_nodes_per_element * sizeof(UInt));
buffers_tmp[partition_num(el)] += nb_nodes_per_element;
}
/// copying the connectivity of ghost element
for (UInt el = 0; el < nb_element; ++el) {
for (CSR<UInt>::const_iterator part = ghost_partition.begin(el);
part != ghost_partition.end(el);
++part) {
UInt proc = *part;
memcpy(buffers_tmp[proc],
conn_val + el * nb_nodes_per_element,
nb_nodes_per_element * sizeof(UInt));
buffers_tmp[proc] += nb_nodes_per_element;
}
}
/// tag info
std::vector<std::string> tag_names;
mesh.getMeshData().getTagNames(tag_names, type);
UInt nb_tags = tag_names.size();
/* -------->>>>-SIZE + CONNECTIVITY------------------------------------ */
/// send all connectivity and ghost information to all processors
std::vector<CommunicationRequest *> requests;
for (UInt p = 0; p < nb_proc; ++p) {
if(p != root) {
UInt size[5];
size[0] = (UInt) type;
size[1] = nb_local_element[p];
size[2] = nb_ghost_element[p];
size[3] = nb_element_to_send[p];
size[4] = nb_tags;
AKANTU_DEBUG_INFO("Sending connectivities informations to proc " << p << " TAG("<< Tag::genTag(my_rank, count, TAG_SIZES) <<")");
comm.send(size, 5, p, Tag::genTag(my_rank, count, TAG_SIZES));
AKANTU_DEBUG_INFO("Sending connectivities to proc " << p << " TAG("<< Tag::genTag(my_rank, count, TAG_CONNECTIVITY) <<")");
requests.push_back(comm.asyncSend(buffers[p],
nb_nodes_per_element * (nb_local_element[p] +
nb_ghost_element[p]),
p, Tag::genTag(my_rank, count, TAG_CONNECTIVITY)));
} else {
local_connectivity = buffers[p];
}
}
/// create the renumbered connectivity
AKANTU_DEBUG_INFO("Renumbering local connectivities");
MeshUtils::renumberMeshNodes(mesh,
local_connectivity,
nb_local_element[root],
nb_ghost_element[root],
type,
*old_nodes);
comm.waitAll(requests);
comm.freeCommunicationRequest(requests);
requests.clear();
for (UInt p = 0; p < nb_proc; ++p) {
delete [] buffers[p];
}
/* -------------------------------------------------------------------- */
for (UInt p = 0; p < nb_proc; ++p) {
buffers[p] = new UInt[nb_ghost_element[p] + nb_element_to_send[p]];
buffers_tmp[p] = buffers[p];
}
/// splitting the partition information to send them to processors
UInt count_by_proc[nb_proc];
memset(count_by_proc, 0, nb_proc*sizeof(UInt));
for (UInt el = 0; el < nb_element; ++el) {
*(buffers_tmp[partition_num(el)]++) = 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_tmp[partition_num(el)]++) = *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_tmp[*part]++) = partition_num(el);
}
}
/* -------->>>>-PARTITIONS--------------------------------------------- */
/// last data to compute the communication scheme
for (UInt p = 0; p < nb_proc; ++p) {
if(p != root) {
AKANTU_DEBUG_INFO("Sending partition informations to proc " << p << " TAG("<< Tag::genTag(my_rank, count, TAG_PARTITIONS) <<")");
requests.push_back(comm.asyncSend(buffers[p],
nb_element_to_send[p] + nb_ghost_element[p],
p, Tag::genTag(my_rank, count, TAG_PARTITIONS)));
} else {
local_partitions = buffers[p];
}
}
if(Mesh::getSpatialDimension(type) == mesh.getSpatialDimension()) {
AKANTU_DEBUG_INFO("Creating communications scheme");
communicator.fillCommunicationScheme(local_partitions,
nb_local_element[root],
nb_ghost_element[root],
type);
}
comm.waitAll(requests);
comm.freeCommunicationRequest(requests);
requests.clear();
for (UInt p = 0; p < nb_proc; ++p) {
delete [] buffers[p];
}
/* -------------------------------------------------------------------- */
/// send data assossiated to the mesh
/* -------->>>>-TAGS--------------------------------------------------- */
synchronizeTagsSend(communicator, root, mesh, nb_tags, type,
partition_num,
ghost_partition,
nb_local_element[root],
nb_ghost_element[root]);
/* -------------------------------------------------------------------- */
/// send data assossiated to groups
/* -------->>>>-GROUPS------------------------------------------------- */
synchronizeElementGroups(communicator, root, mesh, type,
partition_num,
ghost_partition,
nb_element);
++count;
}
/* -------->>>>-SIZE----------------------------------------------------- */
for (UInt p = 0; p < nb_proc; ++p) {
if(p != root) {
UInt size[5];
size[0] = (UInt) _not_defined;
size[1] = 0;
size[2] = 0;
size[3] = 0;
size[4] = 0;
AKANTU_DEBUG_INFO("Sending empty connectivities informations to proc " << p << " TAG("<< Tag::genTag(my_rank, count, TAG_SIZES) <<")");
comm.send(size, 5, p, Tag::genTag(my_rank, count, TAG_SIZES));
}
}
/* ---------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
/**
* Nodes coordinate construction and synchronization
*/
std::multimap< UInt, std::pair<UInt, UInt> > nodes_to_proc;
/// get the list of nodes to send and send them
Real * local_nodes = NULL;
UInt nb_nodes_per_proc[nb_proc];
UInt * nodes_per_proc[nb_proc];
comm.broadcast(&(mesh.nb_global_nodes), 1, root);
/* --------<<<<-NB_NODES + NODES----------------------------------------- */
for (UInt p = 0; p < nb_proc; ++p) {
UInt nb_nodes = 0;
// UInt * buffer;
if(p != root) {
AKANTU_DEBUG_INFO("Receiving number of nodes from proc " << p << " TAG("<< Tag::genTag(p, 0, TAG_NB_NODES) <<")");
comm.receive(&nb_nodes, 1, p, Tag::genTag(p, 0, TAG_NB_NODES));
nodes_per_proc[p] = new UInt[nb_nodes];
nb_nodes_per_proc[p] = nb_nodes;
AKANTU_DEBUG_INFO("Receiving list of nodes from proc " << p << " TAG("<< Tag::genTag(p, 0, TAG_NODES) <<")");
comm.receive(nodes_per_proc[p], nb_nodes, p, Tag::genTag(p, 0, TAG_NODES));
} else {
nb_nodes = old_nodes->getSize();
nb_nodes_per_proc[p] = nb_nodes;
nodes_per_proc[p] = old_nodes->storage();
}
/// get the coordinates for the selected nodes
Real * nodes_to_send = new Real[nb_nodes * spatial_dimension];
Real * nodes_to_send_tmp = nodes_to_send;
for (UInt n = 0; n < nb_nodes; ++n) {
memcpy(nodes_to_send_tmp,
nodes->storage() + spatial_dimension * nodes_per_proc[p][n],
spatial_dimension * sizeof(Real));
// nodes_to_proc.insert(std::make_pair(buffer[n], std::make_pair(p, n)));
nodes_to_send_tmp += spatial_dimension;
}
/* -------->>>>-COORDINATES-------------------------------------------- */
if(p != root) { /// send them for distant processors
AKANTU_DEBUG_INFO("Sending coordinates to proc " << p << " TAG("<< Tag::genTag(my_rank, 0, TAG_COORDINATES) <<")");
comm.send(nodes_to_send, nb_nodes * spatial_dimension, p, Tag::genTag(my_rank, 0, TAG_COORDINATES));
delete [] nodes_to_send;
} else { /// save them for local processor
local_nodes = nodes_to_send;
}
}
/// construct the local nodes coordinates
UInt nb_nodes = old_nodes->getSize();
nodes->resize(nb_nodes);
memcpy(nodes->storage(), local_nodes, nb_nodes * spatial_dimension * sizeof(Real));
delete [] local_nodes;
Array<Int> * nodes_type_per_proc[nb_proc];
for (UInt p = 0; p < nb_proc; ++p) {
nodes_type_per_proc[p] = new Array<Int>(nb_nodes_per_proc[p]);
}
communicator.fillNodesType(mesh);
/* --------<<<<-NODES_TYPE-1--------------------------------------------- */
for (UInt p = 0; p < nb_proc; ++p) {
if(p != root) {
AKANTU_DEBUG_INFO("Receiving first nodes types from proc " << p << " TAG("<< Tag::genTag(my_rank, count, TAG_NODES_TYPE) <<")");
comm.receive(nodes_type_per_proc[p]->storage(),
nb_nodes_per_proc[p], p, Tag::genTag(p, 0, TAG_NODES_TYPE));
} else {
nodes_type_per_proc[p]->copy(mesh.getNodesType());
}
for (UInt n = 0; n < nb_nodes_per_proc[p]; ++n) {
if((*nodes_type_per_proc[p])(n) == -2)
nodes_to_proc.insert(std::make_pair(nodes_per_proc[p][n], std::make_pair(p, n)));
}
}
std::multimap< UInt, std::pair<UInt, UInt> >::iterator it_node;
std::pair< std::multimap< UInt, std::pair<UInt, UInt> >::iterator,
std::multimap< UInt, std::pair<UInt, UInt> >::iterator > it_range;
for (UInt i = 0; i < mesh.nb_global_nodes; ++i) {
it_range = nodes_to_proc.equal_range(i);
if(it_range.first == nodes_to_proc.end() || it_range.first->first != i) continue;
UInt node_type = (it_range.first)->second.first;
for (it_node = it_range.first; it_node != it_range.second; ++it_node) {
UInt proc = it_node->second.first;
UInt node = it_node->second.second;
if(proc != node_type)
nodes_type_per_proc[proc]->storage()[node] = node_type;
}
}
/* -------->>>>-NODES_TYPE-2--------------------------------------------- */
std::vector<CommunicationRequest *> requests;
for (UInt p = 0; p < nb_proc; ++p) {
if(p != root) {
AKANTU_DEBUG_INFO("Sending nodes types to proc " << p << " TAG("<< Tag::genTag(my_rank, 0, TAG_NODES_TYPE) <<")");
requests.push_back(comm.asyncSend(nodes_type_per_proc[p]->storage(),
nb_nodes_per_proc[p], p, Tag::genTag(my_rank, 0, TAG_NODES_TYPE)));
} else {
mesh.getNodesTypePointer()->copy(*nodes_type_per_proc[p]);
}
}
comm.waitAll(requests);
comm.freeCommunicationRequest(requests);
requests.clear();
for (UInt p = 0; p < nb_proc; ++p) {
if(p != root) delete [] nodes_per_proc[p];
delete nodes_type_per_proc[p];
}
/* -------->>>>-NODE GROUPS --------------------------------------------- */
synchronizeNodeGroupsMaster(communicator, root, mesh);
/* ---------------------------------------------------------------------- */
/* Distant (rank != root) */
/* ---------------------------------------------------------------------- */
} else {
/**
* connectivity and communications scheme construction on distant processors
*/
ElementType type = _not_defined;
UInt count = 0;
do {
/* --------<<<<-SIZE--------------------------------------------------- */
UInt size[5] = { 0 };
comm.receive(size, 5, root, Tag::genTag(root, count, TAG_SIZES));
type = (ElementType) size[0];
UInt nb_local_element = size[1];
UInt nb_ghost_element = size[2];
UInt nb_element_to_send = size[3];
UInt nb_tags = size[4];
if(type != _not_defined) {
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
/* --------<<<<-CONNECTIVITY----------------------------------------- */
local_connectivity = new UInt[(nb_local_element + nb_ghost_element) *
nb_nodes_per_element];
AKANTU_DEBUG_INFO("Receiving connectivities from proc " << root);
comm.receive(local_connectivity, nb_nodes_per_element * (nb_local_element +
nb_ghost_element),
root, Tag::genTag(root, count, TAG_CONNECTIVITY));
AKANTU_DEBUG_INFO("Renumbering local connectivities");
MeshUtils::renumberMeshNodes(mesh,
local_connectivity,
nb_local_element,
nb_ghost_element,
type,
*old_nodes);
delete [] local_connectivity;
/* --------<<<<-PARTITIONS--------------------------------------------- */
local_partitions = new UInt[nb_element_to_send + nb_ghost_element * 2];
AKANTU_DEBUG_INFO("Receiving partition informations from proc " << root);
comm.receive(local_partitions,
nb_element_to_send + nb_ghost_element * 2,
root, Tag::genTag(root, count, TAG_PARTITIONS));
if(Mesh::getSpatialDimension(type) == mesh.getSpatialDimension()) {
AKANTU_DEBUG_INFO("Creating communications scheme");
communicator.fillCommunicationScheme(local_partitions,
nb_local_element,
nb_ghost_element,
type);
}
delete [] local_partitions;
/* --------<<<<-TAGS------------------------------------------------- */
synchronizeTagsRecv(communicator, root, mesh, nb_tags, type,
nb_local_element,
nb_ghost_element);
/* --------<<<<-GROUPS----------------------------------------------- */
synchronizeElementGroups(communicator, root, mesh, type);
}
++count;
} while(type != _not_defined);
/**
* Nodes coordinate construction and synchronization on distant processors
*/
comm.broadcast(&(mesh.nb_global_nodes), 1, root);
/* -------->>>>-NB_NODES + NODES----------------------------------------- */
AKANTU_DEBUG_INFO("Sending list of nodes to proc " << root);
UInt nb_nodes = old_nodes->getSize();
comm.send(&nb_nodes, 1, root, Tag::genTag(my_rank, 0, TAG_NB_NODES));
comm.send(old_nodes->storage(), nb_nodes, root, Tag::genTag(my_rank, 0, TAG_NODES));
/* --------<<<<-COORDINATES---------------------------------------------- */
nodes->resize(nb_nodes);
AKANTU_DEBUG_INFO("Receiving coordinates from proc " << root);
comm.receive(nodes->storage(), nb_nodes * spatial_dimension, root, Tag::genTag(root, 0, TAG_COORDINATES));
communicator.fillNodesType(mesh);
/* -------->>>>-NODES_TYPE-1--------------------------------------------- */
Int * nodes_types = mesh.getNodesTypePointer()->storage();
AKANTU_DEBUG_INFO("Sending first nodes types to proc " << root);
comm.send(nodes_types, nb_nodes,
root, Tag::genTag(my_rank, 0, TAG_NODES_TYPE));
/* --------<<<<-NODES_TYPE-2--------------------------------------------- */
AKANTU_DEBUG_INFO("Receiving nodes types from proc " << root);
comm.receive(nodes_types, nb_nodes,
root, Tag::genTag(root, 0, TAG_NODES_TYPE));
/* --------<<<<-NODE GROUPS --------------------------------------------- */
synchronizeNodeGroupsSlaves(communicator, root, mesh);
}
MeshUtils::fillElementToSubElementsData(mesh);
mesh.is_distributed = true;
AKANTU_DEBUG_OUT();
return &communicator;
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::fillTagBuffer(const MeshData & mesh_data,
DynamicCommunicationBuffer * buffers,
const std::string & tag_name,
const ElementType & el_type,
const Array<UInt> & partition_num,
const CSR<UInt> & ghost_partition) {
#define AKANTU_DISTRIBUTED_SYNHRONIZER_TAG_DATA(r, extra_param, elem) \
case BOOST_PP_TUPLE_ELEM(2, 0, elem) : { \
fillTagBufferTemplated<BOOST_PP_TUPLE_ELEM(2, 1, elem)>(mesh_data, buffers, tag_name, el_type, partition_num, ghost_partition); \
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 DistributedSynchronizer::fillNodesType(Mesh & mesh) {
AKANTU_DEBUG_IN();
UInt nb_nodes = mesh.getNbNodes();
Int * nodes_type = mesh.getNodesTypePointer()->storage();
UInt * nodes_set = new UInt[nb_nodes];
std::fill_n(nodes_set, nb_nodes, 0);
const UInt NORMAL_SET = 1;
const UInt GHOST_SET = 2;
bool * already_seen = new bool[nb_nodes];
for(UInt g = _not_ghost; g <= _ghost; ++g) {
GhostType gt = (GhostType) g;
UInt set = NORMAL_SET;
if (gt == _ghost) set = GHOST_SET;
std::fill_n(already_seen, nb_nodes, false);
Mesh::type_iterator it = mesh.firstType(_all_dimensions, gt, _ek_not_defined);
Mesh::type_iterator end = mesh.lastType(_all_dimensions, gt, _ek_not_defined);
for(; it != end; ++it) {
ElementType type = *it;
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_element = mesh.getNbElement(type, gt);
Array<UInt>::iterator< Vector<UInt> > conn_it = mesh.getConnectivity(type, gt).begin(nb_nodes_per_element);
for (UInt e = 0; e < nb_element; ++e, ++conn_it) {
Vector<UInt> & conn = *conn_it;
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
AKANTU_DEBUG_ASSERT(conn(n) < nb_nodes, "Node " << conn(n)
<< " bigger than number of nodes " << nb_nodes);
if(!already_seen[conn(n)]) {
nodes_set[conn(n)] += set;
already_seen[conn(n)] = true;
}
}
}
}
}
delete [] already_seen;
for (UInt i = 0; i < nb_nodes; ++i) {
if(nodes_set[i] == NORMAL_SET) nodes_type[i] = -1;
else if(nodes_set[i] == GHOST_SET) nodes_type[i] = -3;
else if(nodes_set[i] == (GHOST_SET + NORMAL_SET)) nodes_type[i] = -2;
}
delete [] nodes_set;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::fillCommunicationScheme(const UInt * partition,
UInt nb_local_element,
UInt nb_ghost_element,
ElementType type) {
AKANTU_DEBUG_IN();
Element element;
element.type = type;
element.kind = Mesh::getKind(type);
const UInt * part = partition;
part = partition;
for (UInt lel = 0; lel < nb_local_element; ++lel) {
UInt nb_send = *part; part++;
element.element = lel;
element.ghost_type = _not_ghost;
for (UInt p = 0; p < nb_send; ++p) {
UInt proc = *part; part++;
AKANTU_DEBUG(dblAccessory, "Must send : " << element << " to proc " << proc);
(send_element[proc]).push_back(element);
}
}
for (UInt gel = 0; gel < nb_ghost_element; ++gel) {
UInt proc = *part; part++;
element.element = gel;
element.ghost_type = _ghost;
AKANTU_DEBUG(dblAccessory, "Must recv : " << element << " from proc " << proc);
recv_element[proc].push_back(element);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::asynchronousSynchronize(DataAccessor & data_accessor,
SynchronizationTag tag) {
AKANTU_DEBUG_IN();
if (communications.find(tag) == communications.end())
computeBufferSize(data_accessor, tag);
Communication & communication = communications[tag];
AKANTU_DEBUG_ASSERT(communication.send_requests.size() == 0,
"There must be some pending sending communications. Tag is " << tag);
std::map<SynchronizationTag, UInt>::iterator t_it = tag_counter.find(tag);
UInt counter = 0;
if(t_it == tag_counter.end()) {
tag_counter[tag] = 0;
} else {
counter = ++(t_it->second);
}
for (UInt p = 0; p < nb_proc; ++p) {
UInt ssize = communication.size_to_send[p];
if(p == rank || ssize == 0) continue;
CommunicationBuffer & buffer = communication.send_buffer[p];
buffer.resize(ssize);
#ifndef AKANTU_NDEBUG
UInt nb_elements = send_element[p].getSize();
AKANTU_DEBUG_INFO("Packing data for proc " << p
<< " (" << ssize << "/" << nb_elements
<<" data to send/elements)");
/// pack barycenters in debug mode
Array<Element>::const_iterator<Element> bit = send_element[p].begin();
Array<Element>::const_iterator<Element> bend = send_element[p].end();
for (; bit != bend; ++bit) {
const Element & element = *bit;
Vector<Real> barycenter(mesh.getSpatialDimension());
mesh.getBarycenter(element.element, element.type, barycenter.storage(), element.ghost_type);
buffer << barycenter;
}
#endif
data_accessor.packElementData(buffer, send_element[p], tag);
AKANTU_DEBUG_ASSERT(buffer.getPackedSize() == ssize,
"a problem have been introduced with "
<< "false sent sizes declaration "
<< buffer.getPackedSize() << " != " << ssize);
AKANTU_DEBUG_INFO("Posting send to proc " << p
<< " (tag: " << tag << " - " << ssize << " data to send)"
<< " [" << Tag::genTag(rank, counter, tag) << "]");
communication.send_requests.push_back(static_communicator->asyncSend(buffer.storage(),
ssize,
p,
Tag::genTag(rank, counter, tag)));
}
AKANTU_DEBUG_ASSERT(communication.recv_requests.size() == 0,
"There must be some pending receive communications");
for (UInt p = 0; p < nb_proc; ++p) {
UInt rsize = communication.size_to_receive[p];
if(p == rank || rsize == 0) continue;
CommunicationBuffer & buffer = communication.recv_buffer[p];
buffer.resize(rsize);
AKANTU_DEBUG_INFO("Posting receive from proc " << p
<< " (tag: " << tag << " - " << rsize << " data to receive) "
<< " [" << Tag::genTag(p, counter, tag) << "]");
communication.recv_requests.push_back(static_communicator->asyncReceive(buffer.storage(),
rsize,
p,
Tag::genTag(p, counter, tag)));
}
#if defined(AKANTU_DEBUG_TOOLS) && defined(AKANTU_CORE_CXX11)
static std::set<SynchronizationTag> tags;
if(tags.find(tag) == tags.end()) {
debug::element_manager.print(debug::_dm_synch,
[&send_element, rank, nb_proc, tag, id](const Element & el)->std::string {
std::stringstream out;
UInt elp = 0;
for (UInt p = 0; p < nb_proc; ++p) {
UInt pos = send_element[p].find(el);
if(pos != UInt(-1)) {
if(elp > 0) out << std::endl;
out << id << " send (" << pos << "/" << send_element[p].getSize() << ") to proc " << p << " tag:" << tag;
++elp;
}
}
return out.str();
});
debug::element_manager.print(debug::_dm_synch,
[&recv_element, rank, nb_proc, tag, id](const Element & el)->std::string {
std::stringstream out;
UInt elp = 0;
for (UInt p = 0; p < nb_proc; ++p) {
if(p == rank) continue;
UInt pos = recv_element[p].find(el);
if(pos != UInt(-1)) {
if(elp > 0) out << std::endl;
out << id << " recv (" << pos << "/" << recv_element[p].getSize() << ") from proc " << p << " tag:" << tag;
++elp;
}
}
return out.str();
});
tags.insert(tag);
}
#endif
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::waitEndSynchronize(DataAccessor & data_accessor,
SynchronizationTag tag) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(communications.find(tag) != communications.end(), "No communication with the tag \""
<< tag <<"\" started");
Communication & communication = communications[tag];
std::vector<CommunicationRequest *> req_not_finished;
std::vector<CommunicationRequest *> * req_not_finished_tmp = &req_not_finished;
std::vector<CommunicationRequest *> * recv_requests_tmp = &(communication.recv_requests);
// static_communicator->waitAll(recv_requests);
while(!recv_requests_tmp->empty()) {
for (std::vector<CommunicationRequest *>::iterator req_it = recv_requests_tmp->begin();
req_it != recv_requests_tmp->end() ; ++req_it) {
CommunicationRequest * req = *req_it;
if(static_communicator->testRequest(req)) {
UInt proc = req->getSource();
AKANTU_DEBUG_INFO("Unpacking data coming from proc " << proc);
CommunicationBuffer & buffer = communication.recv_buffer[proc];
#ifndef AKANTU_NDEBUG
Array<Element>::const_iterator<Element> bit = recv_element[proc].begin();
Array<Element>::const_iterator<Element> bend = recv_element[proc].end();
UInt spatial_dimension = mesh.getSpatialDimension();
for (; bit != bend; ++bit) {
const Element & element = *bit;
Vector<Real> barycenter_loc(spatial_dimension);
mesh.getBarycenter(element.element,
element.type,
barycenter_loc.storage(),
element.ghost_type);
Vector<Real> barycenter(spatial_dimension);
buffer >> barycenter;
Real tolerance = Math::getTolerance();
Real bary_norm = barycenter.norm();
for (UInt i = 0; i < spatial_dimension; ++i) {
if((std::abs((barycenter(i) - barycenter_loc(i))/bary_norm) <= tolerance) ||
- (std::abs(barycenter_loc(i)) <= 0 && std::abs(barycenter(i)) <= tolerance)) continue;
+ (std::abs(barycenter_loc(i)) <= tolerance && std::abs(barycenter(i)) <= tolerance)) continue;
AKANTU_DEBUG_ERROR("Unpacking an unknown value for the element: "
<< element
<< "(barycenter[" << i << "] = " << barycenter_loc(i)
<< " and buffer[" << i << "] = " << barycenter(i) << ") ["
<< std::abs((barycenter(i) - barycenter_loc(i))/barycenter_loc(i))
<< "] - tag: " << tag);
}
}
#endif
data_accessor.unpackElementData(buffer, recv_element[proc], tag);
buffer.resize(0);
AKANTU_DEBUG_ASSERT(buffer.getLeftToUnpack() == 0,
"all data have not been unpacked: "
<< buffer.getLeftToUnpack() << " bytes left");
static_communicator->freeCommunicationRequest(req);
} else {
req_not_finished_tmp->push_back(req);
}
}
std::vector<CommunicationRequest *> * swap = req_not_finished_tmp;
req_not_finished_tmp = recv_requests_tmp;
recv_requests_tmp = swap;
req_not_finished_tmp->clear();
}
AKANTU_DEBUG_INFO("Waiting that every send requests are received");
static_communicator->waitAll(communication.send_requests);
for (std::vector<CommunicationRequest *>::iterator req_it = communication.send_requests.begin();
req_it != communication.send_requests.end() ; ++req_it) {
CommunicationRequest & req = *(*req_it);
if(static_communicator->testRequest(&req)) {
UInt proc = req.getDestination();
CommunicationBuffer & buffer = communication.send_buffer[proc];
buffer.resize(0);
static_communicator->freeCommunicationRequest(&req);
}
}
communication.send_requests.clear();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::computeBufferSize(DataAccessor & data_accessor,
SynchronizationTag tag) {
AKANTU_DEBUG_IN();
communications[tag].resize(nb_proc);
for (UInt p = 0; p < nb_proc; ++p) {
UInt ssend = 0;
UInt sreceive = 0;
if(p != rank) {
if(send_element[p].getSize() != 0) {
#ifndef AKANTU_NDEBUG
ssend += send_element[p].getSize() * mesh.getSpatialDimension() * sizeof(Real);
#endif
ssend += data_accessor.getNbDataForElements(send_element[p], tag);
AKANTU_DEBUG_INFO("I have " << ssend << "(" << ssend / 1024.
<< "kB - "<< send_element[p].getSize() <<" element(s)) data to send to " << p << " for tag "
<< tag);
}
if(recv_element[p].getSize() != 0) {
#ifndef AKANTU_NDEBUG
sreceive += recv_element[p].getSize() * mesh.getSpatialDimension() * sizeof(Real);
#endif
sreceive += data_accessor.getNbDataForElements(recv_element[p], tag);
AKANTU_DEBUG_INFO("I have " << sreceive << "(" << sreceive / 1024.
<< "kB - "<< recv_element[p].getSize() <<" element(s)) data to receive for tag "
<< tag);
}
}
communications[tag].size_to_send [p] = ssend;
communications[tag].size_to_receive[p] = sreceive;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::printself(std::ostream & stream, int indent) const {
std::string space;
for(Int i = 0; i < indent; i++, space += AKANTU_INDENT);
Int prank = StaticCommunicator::getStaticCommunicator().whoAmI();
Int psize = StaticCommunicator::getStaticCommunicator().getNbProc();
stream << "[" << prank << "/" << psize << "]" << space << "DistributedSynchronizer [" << std::endl;
for (UInt p = 0; p < nb_proc; ++p) {
if (p == UInt(prank)) continue;
stream << "[" << prank << "/" << psize << "]" << space
<< " + Communication to proc " << p << " [" << std::endl;
if(AKANTU_DEBUG_TEST(dblDump)) {
stream << "[" << prank << "/" << psize << "]" << space
<< " - Element to send to proc " << p << " [" << std::endl;
Array<Element>::iterator<Element> it_el = send_element[p].begin();
Array<Element>::iterator<Element> end_el = send_element[p].end();
for(;it_el != end_el; ++it_el)
stream << "[" << prank << "/" << psize << "]" << space << " " << *it_el << std::endl;
stream << "[" << prank << "/" << psize << "]" << space << " ]" << std::endl;
stream << "[" << prank << "/" << psize << "]" << space
<< " - Element to recv from proc " << p << " [" << std::endl;
it_el = recv_element[p].begin();
end_el = recv_element[p].end();
for(;it_el != end_el; ++it_el)
stream << "[" << prank << "/" << psize << "]"
<< space << " " << *it_el << std::endl;
stream << "[" << prank << "/" << psize << "]" << space << " ]" << std::endl;
}
std::map< SynchronizationTag, Communication>::const_iterator it = communications.begin();
std::map< SynchronizationTag, Communication>::const_iterator end = communications.end();
for (; it != end; ++it) {
const SynchronizationTag & tag = it->first;
const Communication & communication = it->second;
UInt ssend = communication.size_to_send[p];
UInt sreceive = communication.size_to_receive[p];
stream << "[" << prank << "/" << psize << "]" << space << " - Tag " << tag << " -> " << ssend << "byte(s) -- <- " << sreceive << "byte(s)" << std::endl;
}
}
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::onElementsRemoved(const Array<Element> & element_to_remove,
const ElementTypeMapArray<UInt> & new_numbering,
__attribute__((unused)) const RemovedElementsEvent & event) {
AKANTU_DEBUG_IN();
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
UInt psize = comm.getNbProc();
UInt prank = comm.whoAmI();
std::vector<CommunicationRequest *> isend_requests;
Array<UInt> * list_of_el = new Array<UInt>[nb_proc];
// Handling ghost elements
for (UInt p = 0; p < psize; ++p) {
if (p == prank) continue;
Array<Element> & recv = recv_element[p];
if(recv.getSize() == 0) continue;
Array<Element>::iterator<Element> recv_begin = recv.begin();
Array<Element>::iterator<Element> recv_end = recv.end();
Array<Element>::const_iterator<Element> er_it = element_to_remove.begin();
Array<Element>::const_iterator<Element> er_end = element_to_remove.end();
Array<UInt> & list = list_of_el[p];
for (UInt i = 0; recv_begin != recv_end; ++i, ++recv_begin) {
const Element & el = *recv_begin;
Array<Element>::const_iterator<Element> pos = std::find(er_it, er_end, el);
if(pos == er_end) {
list.push_back(i);
}
}
if(list.getSize() == recv.getSize())
list.push_back(UInt(0));
else list.push_back(UInt(-1));
AKANTU_DEBUG_INFO("Sending a message of size " << list.getSize() << " to proc " << p << " TAG(" << Tag::genTag(prank, 0, 0) << ")");
isend_requests.push_back(comm.asyncSend(list.storage(), list.getSize(),
p, Tag::genTag(prank, 0, 0)));
list.erase(list.getSize() - 1);
if(list.getSize() == recv.getSize()) continue;
Array<Element> new_recv;
for (UInt nr = 0; nr < list.getSize(); ++nr) {
Element & el = recv(list(nr));
el.element = new_numbering(el.type, el.ghost_type)(el.element);
new_recv.push_back(el);
}
AKANTU_DEBUG_INFO("I had " << recv.getSize() << " elements to recv from proc " << p << " and "
<< list.getSize() << " elements to keep. I have "
<< new_recv.getSize() << " elements left.");
recv.copy(new_recv);
}
for (UInt p = 0; p < psize; ++p) {
if (p == prank) continue;
Array<Element> & send = send_element[p];
if(send.getSize() == 0) continue;
CommunicationStatus status;
AKANTU_DEBUG_INFO("Getting number of elements of proc " << p << " not needed anymore TAG("<< Tag::genTag(p, 0, 0) <<")");
comm.probe<UInt>(p, Tag::genTag(p, 0, 0), status);
Array<UInt> list(status.getSize());
AKANTU_DEBUG_INFO("Receiving list of elements (" << status.getSize() - 1
<< " elements) no longer needed by proc " << p
<< " TAG("<< Tag::genTag(p, 0, 0) <<")");
comm.receive(list.storage(), list.getSize(),
p, Tag::genTag(p, 0, 0));
if(list.getSize() == 1 && list(0) == 0) continue;
list.erase(list.getSize() - 1);
Array<Element> new_send;
for (UInt ns = 0; ns < list.getSize(); ++ns) {
new_send.push_back(send(list(ns)));
}
AKANTU_DEBUG_INFO("I had " << send.getSize() << " elements to send to proc " << p << " and "
<< list.getSize() << " elements to keep. I have "
<< new_send.getSize() << " elements left.");
send.copy(new_send);
}
comm.waitAll(isend_requests);
comm.freeCommunicationRequest(isend_requests);
delete [] list_of_el;
AKANTU_DEBUG_OUT();
}
// void DistributedSynchronizer::checkCommunicationScheme() {
// for (UInt p = 0; p < psize; ++p) {
// if (p == prank) continue;
// for(UInt e(0), e < recv_element.getSize())
// }
// }
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::buildPrankToElement() {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
mesh.initElementTypeMapArray(prank_to_element,
1,
spatial_dimension,
false,
_ek_not_defined,
true);
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);
/// assign prank to all not ghost elements
for (; it != end; ++it) {
UInt nb_element = mesh.getNbElement(*it);
Array<UInt> & prank_to_el = prank_to_element(*it);
for (UInt el = 0; el < nb_element; ++el) {
prank_to_el(el) = rank;
}
}
/// assign prank to all ghost elements
for (UInt p = 0; p < nb_proc; ++p) {
UInt nb_ghost_element = recv_element[p].getSize();
for (UInt el = 0; el < nb_ghost_element; ++el) {
UInt element = recv_element[p](el).element;
ElementType type = recv_element[p](el).type;
GhostType ghost_type = recv_element[p](el).ghost_type;
Array<UInt> & prank_to_el = prank_to_element(type, ghost_type);
prank_to_el(element) = p;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::filterElementsByKind(DistributedSynchronizer * new_synchronizer,
ElementKind kind) {
AKANTU_DEBUG_IN();
Array<Element> * newsy_send_element = new_synchronizer->send_element;
Array<Element> * newsy_recv_element = new_synchronizer->recv_element;
Array<Element> * new_send_element = new Array<Element>[nb_proc];
Array<Element> * new_recv_element = new Array<Element>[nb_proc];
for (UInt p = 0; p < nb_proc; ++p) {
/// send element copying part
new_send_element[p].resize(0);
for (UInt el = 0; el < send_element[p].getSize(); ++el) {
Element & element = send_element[p](el);
if (element.kind == kind)
newsy_send_element[p].push_back(element);
else
new_send_element[p].push_back(element);
}
/// recv element copying part
new_recv_element[p].resize(0);
for (UInt el = 0; el < recv_element[p].getSize(); ++el) {
Element & element = recv_element[p](el);
if (element.kind == kind)
newsy_recv_element[p].push_back(element);
else
new_recv_element[p].push_back(element);
}
}
/// deleting and reassigning old pointers
delete [] send_element;
delete [] recv_element;
send_element = new_send_element;
recv_element = new_recv_element;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::reset() {
AKANTU_DEBUG_IN();
for (UInt p = 0; p < nb_proc; ++p) {
send_element[p].resize(0);
recv_element[p].resize(0);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::synchronizeTagsSend(DistributedSynchronizer & communicator,
UInt root,
Mesh & mesh,
UInt nb_tags,
const ElementType & type,
const Array<UInt> & partition_num,
const CSR<UInt> & ghost_partition,
UInt nb_local_element,
UInt nb_ghost_element) {
AKANTU_DEBUG_IN();
static UInt count = 0;
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
UInt nb_proc = comm.getNbProc();
UInt my_rank = comm.whoAmI();
if(nb_tags == 0) {
AKANTU_DEBUG_OUT();
return;
}
UInt mesh_data_sizes_buffer_length;
MeshData & mesh_data = mesh.getMeshData();
/// tag info
std::vector<std::string> tag_names;
mesh.getMeshData().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, 1, 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.storage(), mesh_data_sizes_buffer.getSize(), root);
if(mesh_data_sizes_buffer_length !=0) {
//Sending the actual data to each processor
DynamicCommunicationBuffer buffers[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)
communicator.fillTagBuffer(mesh_data,
buffers,
*names_it,
type,
partition_num,
ghost_partition);
}
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(my_rank, count, TAG_MESH_DATA) <<")");
requests.push_back(comm.asyncSend(buffers[p].storage(),
buffers[p].getSize(), p, Tag::genTag(my_rank, 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
communicator.populateMeshData(mesh_data,
buffers[root],
*names_it,
type,
mesh_data.getTypeCode(*names_it),
mesh_data.getNbComponent(*names_it, type),
nb_local_element,
nb_ghost_element);
}
comm.waitAll(requests);
comm.freeCommunicationRequest(requests);
requests.clear();
}
++count;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::synchronizeTagsRecv(DistributedSynchronizer & communicator,
UInt root,
Mesh & mesh,
UInt nb_tags,
const ElementType & type,
UInt nb_local_element,
UInt nb_ghost_element) {
AKANTU_DEBUG_IN();
static UInt count = 0;
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
if(nb_tags == 0) {
AKANTU_DEBUG_OUT();
return;
}
/* --------<<<<-TAGS------------------------------------------------- */
UInt mesh_data_sizes_buffer_length = 0;
CommunicationBuffer mesh_data_sizes_buffer;
MeshData & mesh_data = mesh.getMeshData();
AKANTU_DEBUG_INFO("Receiving the size of the information about the mesh data tags.");
comm.broadcast(&mesh_data_sizes_buffer_length, 1, root);
if(mesh_data_sizes_buffer_length != 0) {
mesh_data_sizes_buffer.resize(mesh_data_sizes_buffer_length);
AKANTU_DEBUG_INFO("Receiving the information about the mesh data tags, addr " << (void*)mesh_data_sizes_buffer.storage());
comm.broadcast(mesh_data_sizes_buffer.storage(), mesh_data_sizes_buffer_length, root);
AKANTU_DEBUG_INFO("Size of the information about the mesh data: " << mesh_data_sizes_buffer_length);
std::vector<std::string> tag_names;
std::vector<MeshDataTypeCode> tag_type_codes;
std::vector<UInt> tag_nb_component;
tag_names.resize(nb_tags);
tag_type_codes.resize(nb_tags);
tag_nb_component.resize(nb_tags);
CommunicationBuffer mesh_data_buffer;
UInt type_code_int;
for(UInt i(0); i < nb_tags; ++i) {
mesh_data_sizes_buffer >> tag_names[i];
mesh_data_sizes_buffer >> type_code_int;
tag_type_codes[i] = static_cast<MeshDataTypeCode>(type_code_int);
mesh_data_sizes_buffer >> tag_nb_component[i];
}
std::vector<std::string>::const_iterator names_it = tag_names.begin();
std::vector<std::string>::const_iterator names_end = tag_names.end();
CommunicationStatus mesh_data_comm_status;
AKANTU_DEBUG_INFO("Checking size of data to receive for mesh data TAG("
<< Tag::genTag(root, count, TAG_MESH_DATA) << ")");
comm.probe<char>(root, Tag::genTag(root, count, TAG_MESH_DATA), mesh_data_comm_status);
UInt mesh_data_buffer_size(mesh_data_comm_status.getSize());
AKANTU_DEBUG_INFO("Receiving " << mesh_data_buffer_size
<< " bytes of mesh data TAG("
<< Tag::genTag(root, count, TAG_MESH_DATA) << ")");
mesh_data_buffer.resize(mesh_data_buffer_size);
comm.receive(mesh_data_buffer.storage(),
mesh_data_buffer_size,
root,
Tag::genTag(root, count, TAG_MESH_DATA));
// Loop over each tag for the current type
UInt k(0);
for(; names_it != names_end; ++names_it, ++k) {
communicator.populateMeshData(mesh_data, mesh_data_buffer,
*names_it, type,
tag_type_codes[k],
tag_nb_component[k],
nb_local_element, nb_ghost_element);
}
}
++count;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<class CommunicationBuffer>
void DistributedSynchronizer::fillElementGroupsFromBuffer(DistributedSynchronizer & communicator,
Mesh & mesh,
const ElementType & type,
CommunicationBuffer & buffer) {
AKANTU_DEBUG_IN();
Element el;
el.type = type;
for (ghost_type_t::iterator gt = ghost_type_t::begin(); gt != ghost_type_t::end(); ++gt) {
UInt nb_element = mesh.getNbElement(type, *gt);
el.ghost_type = *gt;
for (UInt e = 0; e < nb_element; ++e) {
el.element = e;
std::vector<std::string> element_to_group;
buffer >> element_to_group;
AKANTU_DEBUG_ASSERT(e < mesh.getNbElement(type, *gt), "The mesh does not have the element " << e);
std::vector<std::string>::iterator it = element_to_group.begin();
std::vector<std::string>::iterator end = element_to_group.end();
for (; it != end; ++it) {
mesh.getElementGroup(*it).add(el, false, false);
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::synchronizeElementGroups(DistributedSynchronizer & communicator,
UInt root,
Mesh & mesh,
const ElementType & type,
const Array<UInt> & partition_num,
const CSR<UInt> & ghost_partition,
UInt nb_element) {
AKANTU_DEBUG_IN();
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
UInt nb_proc = comm.getNbProc();
UInt my_rank = comm.whoAmI();
DynamicCommunicationBuffer buffers[nb_proc];
typedef std::vector< std::vector<std::string> > ElementToGroup;
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();
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);
}
eit = eg.element_begin(type, _not_ghost);
if(eit != eend)
const_cast<Array<UInt> &>(eg.getElements(type)).empty();
}
/// 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;
}
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 < nb_proc; ++p) {
if(p == my_rank) continue;
AKANTU_DEBUG_INFO("Sending element groups to proc " << p
<< " TAG("<< Tag::genTag(my_rank, p, TAG_ELEMENT_GROUP) <<")");
requests.push_back(comm.asyncSend(buffers[p].storage(),
buffers[p].getSize(),
p,
Tag::genTag(my_rank, p, TAG_ELEMENT_GROUP)));
}
fillElementGroupsFromBuffer(communicator, mesh, type, buffers[my_rank]);
comm.waitAll(requests);
comm.freeCommunicationRequest(requests);
requests.clear();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::synchronizeElementGroups(DistributedSynchronizer & communicator,
UInt root,
Mesh & mesh,
const ElementType & type) {
AKANTU_DEBUG_IN();
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
UInt my_rank = comm.whoAmI();
AKANTU_DEBUG_INFO("Receiving element groups from proc " << root
<< " TAG("<< Tag::genTag(root, my_rank, TAG_ELEMENT_GROUP) <<")");
CommunicationStatus status;
comm.probe<char>(root, Tag::genTag(root, my_rank, TAG_ELEMENT_GROUP), status);
CommunicationBuffer buffer(status.getSize());
comm.receive(buffer.storage(), buffer.getSize(), root, Tag::genTag(root, my_rank, TAG_ELEMENT_GROUP));
fillElementGroupsFromBuffer(communicator, mesh, type, buffer);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<class CommunicationBuffer>
void DistributedSynchronizer::fillNodeGroupsFromBuffer(DistributedSynchronizer & communicator,
Mesh & mesh,
CommunicationBuffer & buffer) {
AKANTU_DEBUG_IN();
std::vector< std::vector<std::string> > node_to_group;
buffer >> node_to_group;
AKANTU_DEBUG_ASSERT(node_to_group.size() == mesh.getNbGlobalNodes(),
"Not the good amount of nodes where transmitted");
const Array<UInt> & global_nodes = mesh.getGlobalNodesIds();
Array<UInt>::const_scalar_iterator nbegin = global_nodes.begin();
Array<UInt>::const_scalar_iterator nit = global_nodes.begin();
Array<UInt>::const_scalar_iterator nend = global_nodes.end();
for (; nit != nend; ++nit) {
std::vector<std::string>::iterator it = node_to_group[*nit].begin();
std::vector<std::string>::iterator end = node_to_group[*nit].end();
for (; it != end; ++it) {
mesh.getNodeGroup(*it).add(nit - nbegin, false);
}
}
GroupManager::const_node_group_iterator ngi = mesh.node_group_begin();
GroupManager::const_node_group_iterator nge = mesh.node_group_end();
for (; ngi != nge; ++ngi) {
NodeGroup & ng = *(ngi->second);
ng.optimize();
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::synchronizeNodeGroupsMaster(DistributedSynchronizer & communicator,
UInt root,
Mesh & mesh) {
AKANTU_DEBUG_IN();
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
UInt nb_proc = comm.getNbProc();
UInt my_rank = comm.whoAmI();
UInt nb_total_nodes = mesh.getNbGlobalNodes();
DynamicCommunicationBuffer buffer;
typedef std::vector< std::vector<std::string> > NodeToGroup;
NodeToGroup node_to_group;
node_to_group.resize(nb_total_nodes);
GroupManager::const_node_group_iterator ngi = mesh.node_group_begin();
GroupManager::const_node_group_iterator nge = mesh.node_group_end();
for (; ngi != nge; ++ngi) {
NodeGroup & ng = *(ngi->second);
std::string name = ngi->first;
NodeGroup::const_node_iterator nit = ng.begin();
NodeGroup::const_node_iterator nend = ng.end();
for (; nit != nend; ++nit) {
node_to_group[*nit].push_back(name);
}
nit = ng.begin();
if(nit != nend)
ng.empty();
}
buffer << node_to_group;
std::vector<CommunicationRequest *> requests;
for (UInt p = 0; p < nb_proc; ++p) {
if(p == my_rank) continue;
AKANTU_DEBUG_INFO("Sending node groups to proc " << p
<< " TAG("<< Tag::genTag(my_rank, p, TAG_NODE_GROUP) <<")");
requests.push_back(comm.asyncSend(buffer.storage(),
buffer.getSize(),
p,
Tag::genTag(my_rank, p, TAG_NODE_GROUP)));
}
fillNodeGroupsFromBuffer(communicator, mesh, buffer);
comm.waitAll(requests);
comm.freeCommunicationRequest(requests);
requests.clear();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::synchronizeNodeGroupsSlaves(DistributedSynchronizer & communicator,
UInt root,
Mesh & mesh) {
AKANTU_DEBUG_IN();
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
UInt my_rank = comm.whoAmI();
AKANTU_DEBUG_INFO("Receiving node groups from proc " << root
<< " TAG("<< Tag::genTag(root, my_rank, TAG_NODE_GROUP) <<")");
CommunicationStatus status;
comm.probe<char>(root, Tag::genTag(root, my_rank, TAG_NODE_GROUP), status);
CommunicationBuffer buffer(status.getSize());
comm.receive(buffer.storage(), buffer.getSize(), root, Tag::genTag(root, my_rank, TAG_NODE_GROUP));
fillNodeGroupsFromBuffer(communicator, mesh, buffer);
AKANTU_DEBUG_OUT();
}
__END_AKANTU__
diff --git a/src/synchronizer/distributed_synchronizer.hh b/src/synchronizer/distributed_synchronizer.hh
index 64976adad..2edd12ab1 100644
--- a/src/synchronizer/distributed_synchronizer.hh
+++ b/src/synchronizer/distributed_synchronizer.hh
@@ -1,293 +1,268 @@
/**
* @file distributed_synchronizer.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Jun 16 2011
* @date last modification: Fri Sep 05 2014
*
* @brief wrapper to the static communicator
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 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_DISTRIBUTED_SYNCHRONIZER_HH__
#define __AKANTU_DISTRIBUTED_SYNCHRONIZER_HH__
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_array.hh"
-#include "static_communicator.hh"
#include "synchronizer.hh"
#include "mesh.hh"
#include "mesh_partition.hh"
#include "communication_buffer.hh"
/* -------------------------------------------------------------------------- */
__BEGIN_AKANTU__
class DistributedSynchronizer : public Synchronizer, public MeshEventHandler {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
DistributedSynchronizer(Mesh & mesh,
SynchronizerID id = "distributed_synchronizer",
MemoryID memory_id = 0);
public:
virtual ~DistributedSynchronizer();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// get a mesh and a partition and create the local mesh and the associated
/// DistributedSynchronizer
static DistributedSynchronizer *
createDistributedSynchronizerMesh(Mesh & mesh,
const MeshPartition * partition,
UInt root = 0,
SynchronizerID id = "distributed_synchronizer",
MemoryID memory_id = 0);
/* ------------------------------------------------------------------------ */
/* Inherited from Synchronizer */
/* ------------------------------------------------------------------------ */
/// asynchronous synchronization of ghosts
void asynchronousSynchronize(DataAccessor & data_accessor,SynchronizationTag tag);
/// wait end of asynchronous synchronization of ghosts
void waitEndSynchronize(DataAccessor & data_accessor,SynchronizationTag tag);
/// build processor to element corrispondance
void buildPrankToElement();
virtual void printself(std::ostream & stream, int indent = 0) const;
/// mesh event handler onRemovedElement
virtual void onElementsRemoved(const Array<Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
const RemovedElementsEvent & event);
/// filter elements of a certain kind and copy them into a new synchronizer
void filterElementsByKind(DistributedSynchronizer * new_synchronizer,
ElementKind kind);
/// reset send and recv element lists
void reset();
/// compute buffer size for a given tag and data accessor
void computeBufferSize(DataAccessor & data_accessor, SynchronizationTag tag);
protected:
/// fill the nodes type vector
void fillNodesType(Mesh & mesh);
void fillNodesType(const MeshData & mesh_data,
DynamicCommunicationBuffer * buffers,
const std::string & tag_name,
const ElementType & el_type,
const Array<UInt> & partition_num);
template<typename T>
void fillTagBufferTemplated(const MeshData & mesh_data,
DynamicCommunicationBuffer * buffers,
const std::string & tag_name,
const ElementType & el_type,
const Array<UInt> & partition_num,
const CSR<UInt> & ghost_partition);
void fillTagBuffer(const MeshData & mesh_data,
DynamicCommunicationBuffer * buffers,
const std::string & tag_name,
const ElementType & el_type,
const Array<UInt> & partition_num,
const CSR<UInt> & ghost_partition);
template<typename T, typename BufferType>
void populateMeshDataTemplated(MeshData & mesh_data,
BufferType & buffer,
const std::string & tag_name,
const ElementType & el_type,
UInt nb_component,
UInt nb_local_element,
UInt nb_ghost_element);
template <typename BufferType>
void populateMeshData(MeshData & mesh_data,
BufferType & buffer,
const std::string & tag_name,
const ElementType & el_type,
const MeshDataTypeCode & type_code,
UInt nb_component,
UInt nb_local_element,
UInt nb_ghost_element);
/// fill the communications array of a distributedSynchronizer based on a partition array
void fillCommunicationScheme(const UInt * partition,
UInt nb_local_element,
UInt nb_ghost_element,
ElementType type);
/// function that handels the MeshData to be split (root side)
static void synchronizeTagsSend(DistributedSynchronizer & communicator,
UInt root,
Mesh & mesh,
UInt nb_tags,
const ElementType & type,
const Array<UInt> & partition_num,
const CSR<UInt> & ghost_partition,
UInt nb_local_element,
UInt nb_ghost_element);
/// function that handles the MeshData to be split (other nodes)
static void synchronizeTagsRecv(DistributedSynchronizer & communicator,
UInt root,
Mesh & mesh,
UInt nb_tags,
const ElementType & type,
UInt nb_local_element,
UInt nb_ghost_element);
/// function that handles the preexisting groups in the mesh
static void synchronizeElementGroups(DistributedSynchronizer & communicator,
UInt root,
Mesh & mesh,
const ElementType & type,
const Array<UInt> & partition_num,
const CSR<UInt> & ghost_partition,
UInt nb_element);
/// function that handles the preexisting groups in the mesh
static void synchronizeElementGroups(DistributedSynchronizer & communicator,
UInt root,
Mesh & mesh,
const ElementType & type);
template<class CommunicationBuffer>
static void fillElementGroupsFromBuffer(DistributedSynchronizer & communicator,
Mesh & mesh,
const ElementType & type,
CommunicationBuffer & buffer);
/// function that handles the preexisting groups in the mesh
static void synchronizeNodeGroupsMaster(DistributedSynchronizer & communicator,
UInt root,
Mesh & mesh);
/// function that handles the preexisting groups in the mesh
static void synchronizeNodeGroupsSlaves(DistributedSynchronizer & communicator,
UInt root,
Mesh & mesh);
template<class CommunicationBuffer>
static void fillNodeGroupsFromBuffer(DistributedSynchronizer & communicator,
Mesh & mesh,
CommunicationBuffer & buffer);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(PrankToElement, prank_to_element, const ElementTypeMapArray<UInt> &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
enum CommTags {
TAG_SIZES = 0,
TAG_CONNECTIVITY = 1,
TAG_DATA = 2,
TAG_PARTITIONS = 3,
TAG_NB_NODES = 4,
TAG_NODES = 5,
TAG_COORDINATES = 6,
TAG_NODES_TYPE = 7,
TAG_MESH_DATA = 8,
TAG_ELEMENT_GROUP = 9,
TAG_NODE_GROUP = 10,
};
protected:
/// reference to the underlying mesh
Mesh & mesh;
- /// the static memory instance
- StaticCommunicator * static_communicator;
-
- class Communication {
- public:
- void resize(UInt size) {
- send_buffer.resize(size);
- recv_buffer.resize(size);
- size_to_send .resize(size);
- size_to_receive.resize(size);
- }
-
- public:
- /// size of data to send to each processor
- std::vector<UInt> size_to_send;
- /// size of data to recv to each processor
- std::vector<UInt> size_to_receive;
- std::vector< CommunicationBuffer > send_buffer;
- std::vector< CommunicationBuffer > recv_buffer;
-
- std::vector<CommunicationRequest *> send_requests;
- std::vector<CommunicationRequest *> recv_requests;
- };
-
std::map<SynchronizationTag, Communication> communications;
/// list of element to send to proc p
Array<Element> * send_element;
/// list of element to receive from proc p
Array<Element> * recv_element;
UInt nb_proc;
UInt rank;
friend class FilteredSynchronizer;
friend class FacetSynchronizer;
ElementTypeMapArray<UInt> prank_to_element;
};
__END_AKANTU__
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "distributed_synchronizer_tmpl.hh"
#endif /* __AKANTU_DISTRIBUTED_SYNCHRONIZER_HH__ */
diff --git a/src/synchronizer/dof_synchronizer.cc b/src/synchronizer/dof_synchronizer.cc
index d15d02d0a..4b986fe97 100644
--- a/src/synchronizer/dof_synchronizer.cc
+++ b/src/synchronizer/dof_synchronizer.cc
@@ -1,258 +1,501 @@
/**
* @file dof_synchronizer.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
+ * @author Aurelia Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
* @date creation: Fri Jun 17 2011
* @date last modification: Thu Mar 27 2014
*
* @brief DOF synchronizing object implementation
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 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 "dof_synchronizer.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
__BEGIN_AKANTU__
/* -------------------------------------------------------------------------- */
+/**
+ * A DOFSynchronizer needs a mesh and the number of degrees of freedom
+ * per node to be created. In the constructor computes the local and global dof
+ * number for each dof. The member
+ * proc_informations (std vector) is resized with the number of mpi
+ * processes. Each entry in the vector is a PerProcInformations object
+ * that contains the interactions of the current mpi process (prank) with the
+ * mpi process corresponding to the position of that entry. Every
+ * ProcInformations object contains one array with the dofs that have
+ * to be sent to prank and a second one with dofs that willl be received form prank.
+ * This information is needed for the asychronous communications. The
+ * constructor sets up this information.
+ * @param mesh mesh discretizing the domain we want to analyze
+ * @param nb_degree_of_freedom number of degrees of freedom per node
+ */
DOFSynchronizer::DOFSynchronizer(const Mesh & mesh, UInt nb_degree_of_freedom) :
global_dof_equation_numbers(0, 1, "global_equation_number"),
local_dof_equation_numbers(0, 1, "local_equation_number"),
dof_global_ids(0, 1, "global_ids"),
dof_types(0, 1, "types") {
- gather_scatter_scheme_initialized = false;
- communicator = &StaticCommunicator::getStaticCommunicator();
+ gather_scatter_scheme_initialized = false;
- prank = communicator->whoAmI();
- psize = communicator->getNbProc();
+ prank = static_communicator->whoAmI();
+ psize = static_communicator->getNbProc();
proc_informations.resize(psize);
UInt nb_nodes = mesh.getNbNodes();
nb_dofs = nb_nodes * nb_degree_of_freedom;
dof_global_ids.resize(nb_dofs);
dof_types.resize(nb_dofs);
nb_global_dofs = mesh.getNbGlobalNodes() * nb_degree_of_freedom;
+ /// compute the global id for each dof and store the dof type (pure ghost, slave, master or local)
UInt * dof_global_id = dof_global_ids.storage();
Int * dof_type = dof_types.storage();
for(UInt n = 0, ld = 0; n < nb_nodes; ++n) {
UInt node_global_id = mesh.getNodeGlobalId(n);
UInt node_type = mesh.getNodeType(n);
for (UInt d = 0; d < nb_degree_of_freedom; ++d, ++ld) {
*dof_global_id = node_global_id * nb_degree_of_freedom + d;
global_dof_to_local[*dof_global_id] = ld;
*(dof_type++) = node_type;
dof_global_id++;
}
}
if(psize == 1) return;
/// creating communication scheme
dof_global_id = dof_global_ids.storage();
dof_type = dof_types.storage();
for (UInt n = 0; n < nb_dofs; ++n) {
+ /// check if dof is slave. In that case the value stored in
+ /// dof_type corresponds to the process that has the corresponding
+ /// master dof
if(*dof_type >= 0) {
+ /// has to receive n from proc[*dof_type]
proc_informations[*dof_type].master_dofs.push_back(n);
}
dof_type++;
}
+ /// at this point the master nodes in PerProcInfo are known
/// exchanging information
for (UInt p = 1; p < psize; ++p) {
UInt sendto = (psize + prank + p) % psize;
UInt recvfrom = (psize + prank - p) % psize;
+ /// send the master nodes
UInt nb_master_dofs = proc_informations[sendto].master_dofs.getSize();
UInt * master_dofs = proc_informations[sendto].master_dofs.storage();
UInt * send_buffer = new UInt[nb_master_dofs];
for (UInt d = 0; d < nb_master_dofs; ++d) {
send_buffer[d] = dof_global_id[master_dofs[d]];
}
UInt nb_slave_dofs = 0;
UInt * recv_buffer;
std::vector<CommunicationRequest *> requests;
- requests.push_back(communicator->asyncSend(&nb_master_dofs, 1, sendto, 0));
+ requests.push_back(static_communicator->asyncSend(&nb_master_dofs, 1, sendto, 0));
if(nb_master_dofs != 0) {
- AKANTU_DEBUG(dblInfo, "Sending "<< nb_master_dofs << " nodes to " << sendto + 1);
- requests.push_back(communicator->asyncSend(send_buffer, nb_master_dofs, sendto, 1));
+ AKANTU_DEBUG(dblInfo, "Sending "<< nb_master_dofs << " dofs to " << sendto + 1);
+ requests.push_back(static_communicator->asyncSend(send_buffer, nb_master_dofs, sendto, 1));
}
- communicator->receive(&nb_slave_dofs, 1, recvfrom, 0);
+
+ /// Receive the info and store them as slave nodes
+ static_communicator->receive(&nb_slave_dofs, 1, recvfrom, 0);
if(nb_slave_dofs != 0) {
- AKANTU_DEBUG(dblInfo, "Receiving "<< nb_slave_dofs << " nodes from " << recvfrom + 1);
+ AKANTU_DEBUG(dblInfo, "Receiving "<< nb_slave_dofs << " dofs from " << recvfrom + 1);
proc_informations[recvfrom].slave_dofs.resize(nb_slave_dofs);
recv_buffer = proc_informations[recvfrom].slave_dofs.storage();
- communicator->receive(recv_buffer, nb_slave_dofs, recvfrom, 1);
+ static_communicator->receive(recv_buffer, nb_slave_dofs, recvfrom, 1);
}
for (UInt d = 0; d < nb_slave_dofs; ++d) {
recv_buffer[d] = global_dof_to_local[recv_buffer[d]];
}
- communicator->waitAll(requests);
- communicator->freeCommunicationRequest(requests);
+ static_communicator->waitAll(requests);
+ static_communicator->freeCommunicationRequest(requests);
requests.clear();
delete [] send_buffer;
}
}
/* -------------------------------------------------------------------------- */
DOFSynchronizer::~DOFSynchronizer() {
}
/* -------------------------------------------------------------------------- */
void DOFSynchronizer::initLocalDOFEquationNumbers() {
AKANTU_DEBUG_IN();
local_dof_equation_numbers.resize(nb_dofs);
Int * dof_equation_number = local_dof_equation_numbers.storage();
for (UInt d = 0; d < nb_dofs; ++d) {
*(dof_equation_number++) = d;
}
//local_dof_equation_numbers.resize(nb_dofs);
AKANTU_DEBUG_OUT();
}
+/* -------------------------------------------------------------------------- */
+void DOFSynchronizer::asynchronousSynchronize(DataAccessor & data_accessor,
+ SynchronizationTag tag) {
+ AKANTU_DEBUG_IN();
+
+ if (communications.find(tag) == communications.end())
+ computeBufferSize(data_accessor, tag);
+
+ Communication & communication = communications[tag];
+
+ AKANTU_DEBUG_ASSERT(communication.send_requests.size() == 0,
+ "There must be some pending sending communications. Tag is " << tag);
+
+ std::map<SynchronizationTag, UInt>::iterator t_it = tag_counter.find(tag);
+ UInt counter = 0;
+ if(t_it == tag_counter.end()) {
+ tag_counter[tag] = 0;
+ } else {
+ counter = ++(t_it->second);
+ }
+
+ for (UInt p = 0; p < psize; ++p) {
+ UInt ssize = communication.size_to_send[p];
+ if(p == prank || ssize == 0) continue;
+
+ CommunicationBuffer & buffer = communication.send_buffer[p];
+ buffer.resize(ssize);
+#ifndef AKANTU_NDEBUG
+ UInt nb_dofs = proc_informations[p].slave_dofs.getSize();
+ AKANTU_DEBUG_INFO("Packing data for proc " << p
+ << " (" << ssize << "/" << nb_dofs
+ <<" data to send/dofs)");
+
+ /// pack global equation numbers in debug mode
+ Array<UInt>::const_iterator<UInt> bit = proc_informations[p].slave_dofs.begin();
+ Array<UInt>::const_iterator<UInt> bend = proc_informations[p].slave_dofs.end();
+ for (; bit != bend; ++bit) {
+ buffer << global_dof_equation_numbers[*bit];
+ }
+#endif
+
+
+ /// dof synchronizer needs to send the data corresponding to the
+ data_accessor.packDOFData(buffer, proc_informations[p].slave_dofs, tag);
+
+ AKANTU_DEBUG_ASSERT(buffer.getPackedSize() == ssize,
+ "a problem has been introduced with "
+ << "false sent sizes declaration "
+ << buffer.getPackedSize() << " != " << ssize);
+ AKANTU_DEBUG_INFO("Posting send to proc " << p
+ << " (tag: " << tag << " - " << ssize << " data to send)"
+ << " [" << Tag::genTag(prank, counter, tag) << "]");
+ communication.send_requests.push_back(static_communicator->asyncSend(buffer.storage(),
+ ssize,
+ p,
+ Tag::genTag(prank, counter, tag)));
+ }
+
+ AKANTU_DEBUG_ASSERT(communication.recv_requests.size() == 0,
+ "There must be some pending receive communications");
+
+ for (UInt p = 0; p < psize; ++p) {
+ UInt rsize = communication.size_to_receive[p];
+ if(p == prank || rsize == 0) continue;
+ CommunicationBuffer & buffer = communication.recv_buffer[p];
+ buffer.resize(rsize);
+
+ AKANTU_DEBUG_INFO("Posting receive from proc " << p
+ << " (tag: " << tag << " - " << rsize << " data to receive) "
+ << " [" << Tag::genTag(p, counter, tag) << "]");
+ communication.recv_requests.push_back(static_communicator->asyncReceive(buffer.storage(),
+ rsize,
+ p,
+ Tag::genTag(p, counter, tag)));
+ }
+
+ AKANTU_DEBUG_OUT();
+}
+
+/* -------------------------------------------------------------------------- */
+void DOFSynchronizer::waitEndSynchronize(DataAccessor & data_accessor,
+ SynchronizationTag tag) {
+ AKANTU_DEBUG_IN();
+
+ AKANTU_DEBUG_ASSERT(communications.find(tag) != communications.end(), "No communication with the tag \""
+ << tag <<"\" started");
+
+ Communication & communication = communications[tag];
+
+ std::vector<CommunicationRequest *> req_not_finished;
+ std::vector<CommunicationRequest *> * req_not_finished_tmp = &req_not_finished;
+ std::vector<CommunicationRequest *> * recv_requests_tmp = &(communication.recv_requests);
+
+ // static_communicator->waitAll(recv_requests);
+ while(!recv_requests_tmp->empty()) {
+ for (std::vector<CommunicationRequest *>::iterator req_it = recv_requests_tmp->begin();
+ req_it != recv_requests_tmp->end() ; ++req_it) {
+ CommunicationRequest * req = *req_it;
+
+ if(static_communicator->testRequest(req)) {
+ UInt proc = req->getSource();
+ AKANTU_DEBUG_INFO("Unpacking data coming from proc " << proc);
+ CommunicationBuffer & buffer = communication.recv_buffer[proc];
+
+#ifndef AKANTU_NDEBUG
+ Array<UInt>::const_iterator<UInt> bit = proc_informations[proc].master_dofs.begin();
+ Array<UInt>::const_iterator<UInt> bend = proc_informations[proc].master_dofs.end();
+
+ for (; bit != bend; ++bit) {
+ Int global_dof_eq_nb_loc = global_dof_equation_numbers[*bit];
+ Int global_dof_eq_nb = 0;
+ buffer >> global_dof_eq_nb;
+ Real tolerance = Math::getTolerance();
+ if(std::abs(global_dof_eq_nb - global_dof_eq_nb_loc) <= tolerance) continue;
+ AKANTU_DEBUG_ERROR("Unpacking an unknown global dof equation number for dof: "
+ << *bit
+ << "(global dof equation number = " << global_dof_eq_nb
+ << " and buffer = " << global_dof_eq_nb << ") ["
+ << std::abs(global_dof_eq_nb - global_dof_eq_nb_loc)
+ << "] - tag: " << tag);
+ }
+
+#endif
+
+ data_accessor.unpackDOFData(buffer, proc_informations[proc].master_dofs, tag);
+ buffer.resize(0);
+
+ AKANTU_DEBUG_ASSERT(buffer.getLeftToUnpack() == 0,
+ "all data have not been unpacked: "
+ << buffer.getLeftToUnpack() << " bytes left");
+ static_communicator->freeCommunicationRequest(req);
+ } else {
+ req_not_finished_tmp->push_back(req);
+ }
+ }
+
+ std::vector<CommunicationRequest *> * swap = req_not_finished_tmp;
+ req_not_finished_tmp = recv_requests_tmp;
+ recv_requests_tmp = swap;
+
+ req_not_finished_tmp->clear();
+ }
+
+
+ AKANTU_DEBUG_INFO("Waiting that every send requests are received");
+ static_communicator->waitAll(communication.send_requests);
+ for (std::vector<CommunicationRequest *>::iterator req_it = communication.send_requests.begin();
+ req_it != communication.send_requests.end() ; ++req_it) {
+ CommunicationRequest & req = *(*req_it);
+
+ if(static_communicator->testRequest(&req)) {
+ UInt proc = req.getDestination();
+ CommunicationBuffer & buffer = communication.send_buffer[proc];
+ buffer.resize(0);
+ static_communicator->freeCommunicationRequest(&req);
+ }
+ }
+ communication.send_requests.clear();
+
+ AKANTU_DEBUG_OUT();
+
+
+}
+
+/* -------------------------------------------------------------------------- */
+/**
+ * This function computes the buffer size needed for in order to send data or receive data.
+ * @param data_accessor object of a class that needs to use the DOFSynchronizer. This class has to inherit from the * DataAccessor interface.
+ * @param tag synchronization tag: indicates what variable should be sychronized, e.g. mass, nodal residual, etc.
+ * for the SolidMechanicsModel
+ */
+void DOFSynchronizer::computeBufferSize(DataAccessor & data_accessor,
+ SynchronizationTag tag) {
+ AKANTU_DEBUG_IN();
+
+ communications[tag].resize(psize);
+
+ for (UInt p = 0; p < psize; ++p) {
+ /// initialize the size of data that we be sent and received
+ UInt ssend = 0;
+ UInt sreceive = 0;
+ if(p != prank) {
+ /// check if processor prank has to send dof information to p
+ if(proc_informations[p].slave_dofs.getSize() != 0) {
+
+
+#ifndef AKANTU_NDEBUG
+ /// in debug mode increase buffer size to send the positions
+ /// of nodes in the direction that correspond to the dofs
+ ssend += proc_informations[p].slave_dofs.getSize() * sizeof(Int);
+#endif
+ ssend += data_accessor.getNbDataForDOFs(proc_informations[p].slave_dofs, tag);
+ AKANTU_DEBUG_INFO("I have " << ssend << "(" << ssend / 1024.
+ << "kB - "<< proc_informations[p].slave_dofs.getSize() <<" dof(s)) data to send to " << p << " for tag "
+ << tag);
+ }
+
+ /// check if processor prank has to receive dof information from p
+ if(proc_informations[p].master_dofs.getSize() != 0) {
+#ifndef AKANTU_NDEBUG
+ /// in debug mode increase buffer size to receive the
+ /// positions of nodes in the direction that correspond to the
+ /// dofs
+ sreceive += proc_informations[p].master_dofs.getSize() * sizeof(Int);
+#endif
+ sreceive += data_accessor.getNbDataForDOFs(proc_informations[p].master_dofs, tag);
+ AKANTU_DEBUG_INFO("I have " << sreceive << "(" << sreceive / 1024.
+ << "kB - "<< proc_informations[p].master_dofs.getSize() <<" dof(s)) data to receive for tag "
+ << tag);
+ }
+ }
+
+ communications[tag].size_to_send [p] = ssend;
+ communications[tag].size_to_receive[p] = sreceive;
+ }
+
+ AKANTU_DEBUG_OUT();
+}
+
/* -------------------------------------------------------------------------- */
void DOFSynchronizer::initGlobalDOFEquationNumbers() {
AKANTU_DEBUG_IN();
global_dof_equation_numbers.resize(nb_dofs);
Int * dof_type = dof_types.storage();
UInt * dof_global_id = dof_global_ids.storage();
Int * dof_equation_number = global_dof_equation_numbers.storage();
for(UInt d = 0; d < nb_dofs; ++d) {
/// if ghost dof the equation_number is greater than nb_global_dofs
Int global_eq_num = *dof_global_id + (*dof_type > -3 ? 0 : nb_global_dofs);
*(dof_equation_number) = global_eq_num;
global_dof_equation_number_to_local[global_eq_num] = d;
dof_equation_number++;
dof_global_id++;
dof_type++;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DOFSynchronizer::initScatterGatherCommunicationScheme() {
AKANTU_DEBUG_IN();
if(psize == 1 || gather_scatter_scheme_initialized) {
if(psize == 1) gather_scatter_scheme_initialized = true;
AKANTU_DEBUG_OUT();
return;
}
/// creating communication scheme
UInt * dof_global_id = dof_global_ids.storage();
Int * dof_type = dof_types.storage();
Array<UInt> * local_dofs = new Array<UInt>(0,2);
UInt local_dof_val[2];
nb_needed_dofs = 0;
nb_local_dofs = 0;
for (UInt n = 0; n < nb_dofs; ++n) {
if(*dof_type != -3) {
local_dof_val[0] = *dof_global_id;
if(*dof_type == -1 || *dof_type == -2) {
local_dof_val[1] = 0; // master for this node, shared or not
nb_local_dofs++;
} else if (*dof_type >= 0) {
nb_needed_dofs++;
local_dof_val[1] = 1; // slave node
}
local_dofs->push_back(local_dof_val);
}
dof_type++;
dof_global_id++;
}
Int * nb_dof_per_proc = new Int[psize];
nb_dof_per_proc[prank] = local_dofs->getSize();
- communicator->allGather(nb_dof_per_proc, 1);
+ static_communicator->allGather(nb_dof_per_proc, 1);
AKANTU_DEBUG(dblDebug, "I have " << local_dofs->getSize() << " not ghost dofs ("
<< nb_local_dofs << " local and " << nb_needed_dofs << " slave)");
UInt pos = 0;
for (UInt p = 0; p < prank; ++p) pos += nb_dof_per_proc[p];
UInt nb_total_dofs = pos;
for (UInt p = prank; p < psize; ++p) nb_total_dofs += nb_dof_per_proc[p];
Int * nb_values = new Int[psize];
for (UInt p = 0; p < psize; ++p) nb_values[p] = nb_dof_per_proc[p] * 2;
UInt * buffer = new UInt[2*nb_total_dofs];
memcpy(buffer + 2 * pos, local_dofs->storage(), local_dofs->getSize() * 2 * sizeof(UInt));
delete local_dofs;
- communicator->allGatherV(buffer, nb_values);
+ static_communicator->allGatherV(buffer, nb_values);
UInt * tmp_buffer = buffer;
for (UInt p = 0; p < psize; ++p) {
UInt proc_p_nb_dof = nb_dof_per_proc[p];
if (p != prank){
AKANTU_DEBUG(dblDebug, "I get " << proc_p_nb_dof << "(" << nb_values[p] << ") dofs from " << p + 1);
proc_informations[p].dofs.resize(0);
for (UInt dd = 0; dd < proc_p_nb_dof; ++dd) {
UInt dof = tmp_buffer[2*dd];
if(tmp_buffer[2*dd + 1] == 0)
proc_informations[p].dofs.push_back(dof);
else
proc_informations[p].needed_dofs.push_back(dof);
}
AKANTU_DEBUG(dblDebug, "Proc " << p + 1 << " sends me "
<< proc_informations[p].dofs.getSize() << " local dofs, and "
<< proc_informations[p].needed_dofs.getSize() << " slave dofs");
}
tmp_buffer += 2*proc_p_nb_dof;
}
delete [] nb_dof_per_proc;
delete [] buffer;
delete [] nb_values;
gather_scatter_scheme_initialized = true;
AKANTU_DEBUG_OUT();
}
__END_AKANTU__
diff --git a/src/synchronizer/dof_synchronizer.hh b/src/synchronizer/dof_synchronizer.hh
index 731820c60..16f2f9a77 100644
--- a/src/synchronizer/dof_synchronizer.hh
+++ b/src/synchronizer/dof_synchronizer.hh
@@ -1,224 +1,237 @@
/**
* @file dof_synchronizer.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
+ * @author Aurelia Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
* @date creation: Fri Jun 17 2011
* @date last modification: Fri Mar 21 2014
*
* @brief Synchronize Array of DOFs
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 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 "static_communicator.hh"
+#include "synchronizer.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_DOF_SYNCHRONIZER_HH__
#define __AKANTU_DOF_SYNCHRONIZER_HH__
__BEGIN_AKANTU__
class Mesh;
template<typename T>
class AddOperation {
public:
inline T operator()(T & b, T & a) { return a + b; };
};
-class DOFSynchronizer {
+class DOFSynchronizer : public Synchronizer {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
DOFSynchronizer(const Mesh & mesh, UInt nb_degree_of_freedom);
virtual ~DOFSynchronizer();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
+ /// asynchronous synchronization of ghosts
+ virtual void asynchronousSynchronize(DataAccessor & data_accessor,SynchronizationTag tag);
+
+ /// wait end of asynchronous synchronization of ghosts
+ virtual void waitEndSynchronize(DataAccessor & data_accessor,SynchronizationTag tag);
+
+ /// compute buffer size for a given tag and data accessor
+ virtual void computeBufferSize(DataAccessor & data_accessor, SynchronizationTag tag);
+
/// init the scheme for scatter and gather operation, need extra memory
void initScatterGatherCommunicationScheme();
/// initialize the equation number with local ids
void initLocalDOFEquationNumbers();
/// initialize the equation number with local ids
void initGlobalDOFEquationNumbers();
/**
* Gather the DOF value on the root proccessor
*
* @param to_gather data to gather
* @param root processor on which data are gathered
* @param gathered Array containing the gathered data, only valid on root processor
*/
template<typename T>
void gather(const Array<T> & to_gather, UInt root,
Array<T> * gathered = NULL) const;
/**
* Scatter a DOF Array form root to all processors
*
* @param scattered data to scatter, only valid on root processor
* @param root processor scattering data
* @param to_scatter result of scattered data
*/
template<typename T>
void scatter(Array<T> & scattered, UInt root,
const Array<T> * to_scatter = NULL) const;
template<typename T> void synchronize(Array<T> & vector) const ;
template<template <class> class Op, typename T> void reduceSynchronize(Array<T> & vector) const;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get the equation_number Array
AKANTU_GET_MACRO(LocalDOFEquationNumbers, local_dof_equation_numbers, const Array<Int> &);
AKANTU_GET_MACRO(GlobalDOFEquationNumbers, global_dof_equation_numbers, const Array<Int> &);
Array<Int> * getLocalDOFEquationNumbersPointer(){return &local_dof_equation_numbers;};
Array<Int> * getGlobalDOFEquationNumbersPointer(){return &global_dof_equation_numbers;};
typedef unordered_map<Int, UInt>::type GlobalEquationNumberMap;
AKANTU_GET_MACRO(GlobalEquationNumberToLocal, global_dof_equation_number_to_local, const GlobalEquationNumberMap &)
/// get the Array of global ids of the dofs
AKANTU_GET_MACRO(DOFGlobalIDs, dof_global_ids, const Array<UInt> &);
/// get the global id of a dof
inline UInt getDOFGlobalID(UInt local_id) const {
return dof_global_ids(local_id);
}
/// get the local id of a global dof
inline UInt getDOFLocalID(UInt global_id) const {
return global_dof_to_local.find(global_id)->second;
}
/// get the DOF type Array
AKANTU_GET_MACRO(DOFTypes, dof_types, const Array<Int> &);
AKANTU_GET_MACRO(NbDOFs, nb_dofs, UInt);
AKANTU_GET_MACRO(NbGlobalDOFs, nb_global_dofs, UInt);
/// say if a node is a pure ghost node
inline bool isPureGhostDOF(UInt n) const;
/// say if a node is pure local or master node
inline bool isLocalOrMasterDOF(UInt n) const;
inline bool isLocalDOF(UInt n) const;
inline bool isMasterDOF(UInt n) const;
inline bool isSlaveDOF(UInt n) const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// equation number position where a dof is synchronized in the matrix (by default = global id)
Array<Int> global_dof_equation_numbers;
Array<Int> local_dof_equation_numbers;
GlobalEquationNumberMap global_dof_equation_number_to_local;
/// DOF global id
Array<UInt> dof_global_ids;
/*
* DOF type -3 pure ghost, -2 master for the dof, -1 normal dof, i in
* [0-N] slave dof and master is proc i
*/
Array<Int> dof_types;
/// number of dofs
UInt nb_dofs;
UInt nb_global_dofs;
unordered_map<UInt, UInt>::type global_dof_to_local;
UInt prank;
UInt psize;
- StaticCommunicator * communicator;
struct PerProcInformations {
/// dofs to send to the proc
Array<UInt> slave_dofs;
/// dofs to recvs from the proc
Array<UInt> master_dofs;
/* ---------------------------------------------------------------------- */
/* Data for gather/scatter */
/* ---------------------------------------------------------------------- */
/// the dof that the node handle
Array<UInt> dofs;
/// the dof that the proc need
Array<UInt> needed_dofs;
};
std::vector<PerProcInformations> proc_informations;
/// nb dofs with type -1 or -2
UInt nb_local_dofs;
/// nb dof with type >= 0
UInt nb_needed_dofs;
bool gather_scatter_scheme_initialized;
+
+
+ std::map<SynchronizationTag, Communication> communications;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#if defined (AKANTU_INCLUDE_INLINE_IMPL)
# include "dof_synchronizer_inline_impl.cc"
#endif
/// standard output stream operator
// inline std::ostream & operator <<(std::ostream & stream, const DOFSynchronizer & _this)
// {
// _this.printself(stream);
// return stream;
// }
__END_AKANTU__
#endif /* __AKANTU_DOF_SYNCHRONIZER_HH__ */
diff --git a/src/synchronizer/dof_synchronizer_inline_impl.cc b/src/synchronizer/dof_synchronizer_inline_impl.cc
index 399be4abe..ee040e3b4 100644
--- a/src/synchronizer/dof_synchronizer_inline_impl.cc
+++ b/src/synchronizer/dof_synchronizer_inline_impl.cc
@@ -1,315 +1,315 @@
/**
* @file dof_synchronizer_inline_impl.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 17 2011
* @date last modification: Thu Jun 05 2014
*
* @brief DOFSynchronizer inline implementation
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 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/>.
*
*/
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template<typename T> void DOFSynchronizer::gather(const Array<T> & to_gather, UInt root,
Array<T> * gathered) const {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(gather_scatter_scheme_initialized == true, "You should call initScatterGatherCommunicationScheme before trying to gather a Array !!");
if(psize == 1) {
gathered->copy(to_gather, true);
AKANTU_DEBUG_OUT();
return;
}
UInt * dof_global_id = dof_global_ids.storage();
Int * dof_type = dof_types.storage();
T * to_gather_val = to_gather.storage();
T * buffer;
if(prank == root) {
gathered->resize(nb_global_dofs / gathered->getNbComponent());
buffer = gathered->storage();
} else
buffer = new T[nb_local_dofs];
UInt dof = 0;
for (UInt d = 0; d < nb_dofs; ++d) {
if(*dof_type != -3) {
if(*dof_type == -1 || *dof_type == -2) {
if (prank == root) dof = *dof_global_id;
buffer[dof++] = *to_gather_val;
}
}
dof_type++;
dof_global_id++;
to_gather_val++;
}
if (prank == root) {
for (UInt p = 0; p < psize; ++p) {
if(p == root) continue;
UInt nb_dofs = proc_informations[p].dofs.getSize();
AKANTU_DEBUG_INFO("Gather - Receiving " << nb_dofs << " from " << p);
if(nb_dofs) {
buffer = new T[nb_dofs];
- communicator->receive(buffer, nb_dofs, p, 0);
+ static_communicator->receive(buffer, nb_dofs, p, 0);
T * buffer_tmp = buffer;
UInt * remote_dofs = proc_informations[p].dofs.storage();
for (UInt d = 0; d < nb_dofs; ++d) {
gathered->storage()[*remote_dofs++] = *(buffer_tmp++);
}
delete [] buffer;
}
}
} else {
AKANTU_DEBUG_INFO("Gather - Sending " << nb_local_dofs << " to " << root);
if(nb_local_dofs)
- communicator->send(buffer, nb_local_dofs, root, 0);
+ static_communicator->send(buffer, nb_local_dofs, root, 0);
delete [] buffer;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<typename T> void DOFSynchronizer::scatter(Array<T> & scattered, UInt root,
const Array<T> * to_scatter) const {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(gather_scatter_scheme_initialized == true, "You should call initScatterGatherCommunicationScheme before trying to scatter a Array !!");
if(psize == 1) {
scattered.copy(*to_scatter, true);
AKANTU_DEBUG_OUT();
return;
}
scattered.resize(nb_dofs / scattered.getNbComponent());
UInt * dof_global_id = dof_global_ids.storage();
Int * dof_type = dof_types.storage();
if (prank == root) {
for (UInt p = 0; p < psize; ++p) {
if(p == root) continue;
UInt nb_needed_dof = proc_informations[p].needed_dofs.getSize();
UInt nb_local_dof = proc_informations[p].dofs.getSize();
AKANTU_DEBUG_INFO("Scatter - Sending " << nb_local_dof + nb_needed_dof << " to " << p);
if(nb_local_dof + nb_needed_dof) {
T * send_buffer = new T[nb_local_dof + nb_needed_dof];
T * buffer_tmp = send_buffer;
UInt * remote_dofs = proc_informations[p].dofs.storage();
for (UInt d = 0; d < nb_local_dof; ++d) {
*(buffer_tmp++) = to_scatter->storage()[*remote_dofs++];
}
remote_dofs = proc_informations[p].needed_dofs.storage();
for (UInt d = 0; d < nb_needed_dof; ++d) {
*(buffer_tmp++) = to_scatter->storage()[*remote_dofs++];
}
- communicator->send(send_buffer, nb_local_dof + nb_needed_dof, p, 0);
+ static_communicator->send(send_buffer, nb_local_dof + nb_needed_dof, p, 0);
delete [] send_buffer;
}
}
T * scattered_val = scattered.storage();
for (UInt d = 0; d < nb_dofs; ++d) {
if(*dof_type != -3) {
if(*dof_type >= -2)
*scattered_val = to_scatter->storage()[*dof_global_id];
}
scattered_val++;
dof_type++;
dof_global_id++;
}
} else {
T * buffer;
AKANTU_DEBUG_INFO("Scatter - Receiving " << nb_dofs << " from " << root);
if(nb_local_dofs + nb_needed_dofs) {
buffer = new T[nb_local_dofs + nb_needed_dofs];
- communicator->receive(buffer, nb_local_dofs + nb_needed_dofs, root, 0);
+ static_communicator->receive(buffer, nb_local_dofs + nb_needed_dofs, root, 0);
T * scattered_val = scattered.storage();
UInt local_dofs = 0;
UInt needed_dofs = nb_local_dofs;
for (UInt d = 0; d < nb_dofs; ++d) {
if(*dof_type != -3) {
if(*dof_type == -1 || *dof_type == -2)
*scattered_val = buffer[local_dofs++];
else if(*dof_type >= 0)
*scattered_val = buffer[needed_dofs++];
}
scattered_val++;
dof_type++;
}
delete [] buffer;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<typename T> void DOFSynchronizer::synchronize(Array<T> & dof_vector) const {
AKANTU_DEBUG_IN();
if(psize == 1) {
AKANTU_DEBUG_OUT();
return;
}
for (UInt p = 1; p < psize; ++p) {
UInt sendto = (psize + prank + p) % psize;
UInt recvfrom = (psize + prank - p) % psize;
UInt nb_slave_dofs = proc_informations[sendto].slave_dofs.getSize();
UInt * slave_dofs = proc_informations[sendto].slave_dofs.storage();
UInt nb_master_dofs = proc_informations[recvfrom].master_dofs.getSize();
UInt * master_dofs = proc_informations[recvfrom].master_dofs.storage();
T * send_buffer = new T[nb_slave_dofs];
T * recv_buffer = new T[nb_master_dofs];
for (UInt d = 0; d < nb_slave_dofs; ++d) {
AKANTU_DEBUG_ASSERT(dof_types(slave_dofs[d]) == -2,
"Sending node " << slave_dofs[d]
<< "(gid" << dof_global_ids(d) << ") to proc "
<< sendto << " but it is not a master node.");
send_buffer[d] = dof_vector.storage()[slave_dofs[d]];
}
/// ring blocking communications
CommunicationRequest * request = NULL;
- if(nb_slave_dofs != 0) request = communicator->asyncSend(send_buffer, nb_slave_dofs, sendto , 0);
- if(nb_master_dofs != 0) communicator->receive(recv_buffer, nb_master_dofs, recvfrom, 0);
+ if(nb_slave_dofs != 0) request = static_communicator->asyncSend(send_buffer, nb_slave_dofs, sendto , 0);
+ if(nb_master_dofs != 0) static_communicator->receive(recv_buffer, nb_master_dofs, recvfrom, 0);
for (UInt d = 0; d < nb_master_dofs; ++d) {
AKANTU_DEBUG_ASSERT(dof_types(master_dofs[d]) >= 0,
"Received node " << master_dofs[d]
<< "(gid" << dof_global_ids(d) << ") from proc "
<< recvfrom << " but it is not a slave node.");
dof_vector.storage()[master_dofs[d]] = recv_buffer[d];
}
if(nb_slave_dofs != 0) {
- communicator->wait(request);
- communicator->freeCommunicationRequest(request);
+ static_communicator->wait(request);
+ static_communicator->freeCommunicationRequest(request);
}
delete [] send_buffer;
delete [] recv_buffer;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<template <class> class Op, typename T> void DOFSynchronizer::reduceSynchronize(Array<T> & dof_vector) const {
AKANTU_DEBUG_IN();
if(psize == 1) {
AKANTU_DEBUG_OUT();
return;
}
for (UInt p = 1; p < psize; ++p) {
UInt sendto = (psize + prank + p) % psize;
UInt recvfrom = (psize + prank - p) % psize;
UInt nb_slave_dofs = proc_informations[recvfrom].slave_dofs.getSize();
UInt * slave_dofs = proc_informations[recvfrom].slave_dofs.storage();
UInt nb_master_dofs = proc_informations[sendto].master_dofs.getSize();
UInt * master_dofs = proc_informations[sendto].master_dofs.storage();
T * send_buffer = new T[nb_master_dofs];
T * recv_buffer = new T[nb_slave_dofs];
for (UInt d = 0; d < nb_master_dofs; ++d) {
send_buffer[d] = dof_vector.storage()[master_dofs[d]];
}
CommunicationRequest * request = NULL;
- if(nb_master_dofs != 0) request = communicator->asyncSend(send_buffer, nb_master_dofs, sendto , 0);
- if(nb_slave_dofs != 0) communicator->receive(recv_buffer, nb_slave_dofs, recvfrom, 0);
+ if(nb_master_dofs != 0) request = static_communicator->asyncSend(send_buffer, nb_master_dofs, sendto , 0);
+ if(nb_slave_dofs != 0) static_communicator->receive(recv_buffer, nb_slave_dofs, recvfrom, 0);
Op<T> oper;
for (UInt d = 0; d < nb_slave_dofs; ++d) {
dof_vector.storage()[slave_dofs[d]] = oper(dof_vector.storage()[slave_dofs[d]], recv_buffer[d]);
}
if(nb_master_dofs != 0) {
- communicator->wait(request);
- communicator->freeCommunicationRequest(request);
+ static_communicator->wait(request);
+ static_communicator->freeCommunicationRequest(request);
}
delete [] send_buffer;
delete [] recv_buffer;
}
synchronize(dof_vector);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
inline bool DOFSynchronizer::isPureGhostDOF(UInt n) const {
return dof_types.getSize() ? (dof_types(n) == -3) : false;
}
/* -------------------------------------------------------------------------- */
inline bool DOFSynchronizer::isLocalOrMasterDOF(UInt n) const {
return dof_types.getSize() ? (dof_types(n) == -2) || (dof_types(n) == -1) : true;
}
/* -------------------------------------------------------------------------- */
inline bool DOFSynchronizer::isLocalDOF(UInt n) const {
return dof_types.getSize() ? dof_types(n) == -1 : true;
}
/* -------------------------------------------------------------------------- */
inline bool DOFSynchronizer::isMasterDOF(UInt n) const {
return dof_types.getSize() ? dof_types(n) == -2 : false;
}
/* -------------------------------------------------------------------------- */
inline bool DOFSynchronizer::isSlaveDOF(UInt n) const {
return dof_types.getSize() ? dof_types(n) >= 0 : false;
}
diff --git a/src/synchronizer/synchronizer.cc b/src/synchronizer/synchronizer.cc
index beab3974c..bcd018f79 100644
--- a/src/synchronizer/synchronizer.cc
+++ b/src/synchronizer/synchronizer.cc
@@ -1,56 +1,57 @@
/**
* @file synchronizer.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Sep 01 2010
* @date last modification: Wed Nov 13 2013
*
* @brief implementation of the common part
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 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 "synchronizer.hh"
/* -------------------------------------------------------------------------- */
__BEGIN_AKANTU__
/* -------------------------------------------------------------------------- */
Synchronizer::Synchronizer(SynchronizerID id, MemoryID memory_id) :
- Memory(id, memory_id) {
+ Memory(id, memory_id),
+ static_communicator(&StaticCommunicator::getStaticCommunicator()) {
}
/* -------------------------------------------------------------------------- */
void Synchronizer::synchronize(DataAccessor & data_accessor,
SynchronizationTag tag) {
AKANTU_DEBUG_IN();
asynchronousSynchronize(data_accessor,tag);
waitEndSynchronize(data_accessor,tag);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
__END_AKANTU__
diff --git a/src/synchronizer/synchronizer.hh b/src/synchronizer/synchronizer.hh
index a4b4c232f..46c01892b 100644
--- a/src/synchronizer/synchronizer.hh
+++ b/src/synchronizer/synchronizer.hh
@@ -1,133 +1,163 @@
/**
* @file synchronizer.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
+ * @author Aurelia Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
* @date creation: Wed Sep 01 2010
* @date last modification: Tue Apr 30 2013
*
* @brief interface for communicator and pbc synchronizers
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 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_SYNCHRONIZER_HH__
#define __AKANTU_SYNCHRONIZER_HH__
/* -------------------------------------------------------------------------- */
#include "aka_memory.hh"
#include "data_accessor.hh"
+#include "real_static_communicator.hh"
+#include "static_communicator.hh"
+
/* -------------------------------------------------------------------------- */
#include <map>
/* -------------------------------------------------------------------------- */
__BEGIN_AKANTU__
class Synchronizer : protected Memory {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
Synchronizer(SynchronizerID id = "synchronizer", MemoryID memory_id = 0);
virtual ~Synchronizer() { };
virtual void printself(__attribute__((unused)) std::ostream & stream,
__attribute__((unused)) int indent = 0) const {};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// synchronize ghosts
void synchronize(DataAccessor & data_accessor,SynchronizationTag tag);
/// asynchronous synchronization of ghosts
virtual void asynchronousSynchronize(DataAccessor & data_accessor,SynchronizationTag tag) = 0;
/// wait end of asynchronous synchronization of ghosts
virtual void waitEndSynchronize(DataAccessor & data_accessor,SynchronizationTag tag) = 0;
/// compute buffer size for a given tag and data accessor
virtual void computeBufferSize(DataAccessor & data_accessor, SynchronizationTag tag)=0;
/**
* tag = |__________20_________|___8____|_4_|
* | proc | num mes| ct|
*/
class Tag {
public:
operator int() { return int(tag); }
template<typename CommTag>
static inline Tag genTag(int proc, UInt msg_count, CommTag tag) {
Tag t;
t.tag = (((proc & 0xFFFFF) << 12) + ((msg_count & 0xFF) << 4) + ((Int)tag & 0xF));
return t;
}
virtual void printself(std::ostream & stream,
__attribute__((unused)) int indent = 0) const {
stream << (tag >> 12) << ":" << (tag >> 4 & 0xFF) << ":" << (tag & 0xF);
}
private:
UInt tag;
};
protected:
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
+
+ class Communication {
+ public:
+ void resize(UInt size) {
+ send_buffer.resize(size);
+ recv_buffer.resize(size);
+ size_to_send .resize(size);
+ size_to_receive.resize(size);
+ }
+
+ public:
+ /// size of data to send to each processor
+ std::vector<UInt> size_to_send;
+ /// size of data to recv to each processor
+ std::vector<UInt> size_to_receive;
+ std::vector< CommunicationBuffer > send_buffer;
+ std::vector< CommunicationBuffer > recv_buffer;
+
+ std::vector<CommunicationRequest *> send_requests;
+ std::vector<CommunicationRequest *> recv_requests;
+ };
+
/// id of the synchronizer
SynchronizerID id;
/// message counter per tag
std::map<SynchronizationTag, UInt> tag_counter;
+
+
+ /// the static memory instance
+ StaticCommunicator * static_communicator;
};
/// standard output stream operator
inline std::ostream & operator <<(std::ostream & stream, const Synchronizer & _this)
{
_this.printself(stream);
return stream;
}
inline std::ostream & operator <<(std::ostream & stream, const Synchronizer::Tag & _this)
{
_this.printself(stream);
return stream;
}
__END_AKANTU__
#endif /* __AKANTU_SYNCHRONIZER_HH__ */
diff --git a/src/synchronizer/synchronizer_registry.hh b/src/synchronizer/synchronizer_registry.hh
index 7b116afef..5e7e09617 100644
--- a/src/synchronizer/synchronizer_registry.hh
+++ b/src/synchronizer/synchronizer_registry.hh
@@ -1,115 +1,115 @@
/**
* @file synchronizer_registry.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
*
* @date creation: Thu Jun 16 2011
* @date last modification: Tue Nov 06 2012
*
* @brief Registry of synchronizers
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 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_SYNCHRONIZER_REGISTRY_HH__
#define __AKANTU_SYNCHRONIZER_REGISTRY_HH__
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "data_accessor.hh"
#include "synchronizer.hh"
/* -------------------------------------------------------------------------- */
__BEGIN_AKANTU__
class SynchronizerRegistry {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
SynchronizerRegistry(DataAccessor & data_accessor);
virtual ~SynchronizerRegistry();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// synchronize operation
void synchronize(SynchronizationTag tag);
/// asynchronous synchronization
void asynchronousSynchronize(SynchronizationTag tag);
/// wait end of asynchronous synchronization
void waitEndSynchronize(SynchronizationTag tag);
/// register a new synchronization
void registerSynchronizer(Synchronizer & synchronizer,SynchronizationTag tag);
-
+
/// function to print the containt of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
// /// number of tags registered
// UInt nb_synchronization_tags;
typedef std::multimap<SynchronizationTag, Synchronizer *> Tag2Sync;
/// list of registered synchronization
Tag2Sync synchronizers;
/// data accessor that will permit to do the pack/unpack things
DataAccessor & data_accessor;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
// #include "synchronizer_registry_inline_impl.cc"
/// standard output stream operator
inline std::ostream & operator <<(std::ostream & stream, const SynchronizerRegistry & _this)
{
_this.printself(stream);
return stream;
}
__END_AKANTU__
#endif /* __AKANTU_SYNCHRONIZER_REGISTRY_HH__ */
diff --git a/test/test_solver/CMakeLists.txt b/test/test_solver/CMakeLists.txt
index 42f17633c..ee414464d 100644
--- a/test/test_solver/CMakeLists.txt
+++ b/test/test_solver/CMakeLists.txt
@@ -1,54 +1,64 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Mon Dec 13 2010
# @date last modification: Tue Nov 06 2012
#
# @brief configuration for solver tests
#
# @section LICENSE
#
# Copyright (©) 2014 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
#
#===============================================================================
add_mesh(test_solver_mesh triangle.geo 2 1)
register_test(test_sparse_matrix_profile
SOURCES test_sparse_matrix_profile.cc
DEPENDENCIES test_solver_mesh
)
register_test(test_sparse_matrix_assemble
SOURCES test_sparse_matrix_assemble.cc
DEPENDENCIES test_solver_mesh
)
register_test(test_sparse_matrix_product
SOURCES test_sparse_matrix_product.cc
FILES_TO_COPY bar.msh
)
register_test(test_petsc_matrix_profile
SOURCES test_petsc_matrix_profile.cc
DEPENDENCIES test_solver_mesh
+ )
+
+register_test(test_petsc_matrix_apply_boundary
+ SOURCES test_petsc_matrix_apply_boundary.cc
+ DEPENDENCIES test_solver_mesh
+ )
+
+register_test(test_solver_petsc
+ SOURCES test_solver_petsc.cc
+ DEPENDENCIES profile.mtx
)
\ No newline at end of file
diff --git a/test/test_solver/test_petsc_matrix_profile.cc b/test/test_solver/test_petsc_matrix_profile.cc
index 04b32cbfe..1a8f2f4e7 100644
--- a/test/test_solver/test_petsc_matrix_profile.cc
+++ b/test/test_solver/test_petsc_matrix_profile.cc
@@ -1,126 +1,137 @@
/**
* @file test_petsc_matrix_profile.cc
* @author Aurelia Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @date Wed Jul 30 12:34:08 2014
*
* @brief test the profile generation of the PETScMatrix class
*
* @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 <cstdlib>
/* -------------------------------------------------------------------------- */
#include "static_communicator.hh"
#include "aka_common.hh"
#include "aka_csr.hh"
#include "mesh.hh"
#include "mesh_io.hh"
#include "mesh_utils.hh"
#include "distributed_synchronizer.hh"
#include "petsc_matrix.hh"
#include "fe_engine.hh"
#include "dof_synchronizer.hh"
#include "mesh_partition_scotch.hh"
using namespace akantu;
int main(int argc, char *argv[]) {
initialize(argc, argv);
const ElementType element_type = _triangle_3;
const GhostType ghost_type = _not_ghost;
UInt spatial_dimension = 2;
StaticCommunicator & comm = akantu::StaticCommunicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
/// read the mesh and partition it
Mesh mesh(spatial_dimension);
/* ------------------------------------------------------------------------ */
/* Parallel initialization */
/* ------------------------------------------------------------------------ */
DistributedSynchronizer * communicator = NULL;
if(prank == 0) {
/// creation mesh
mesh.read("triangle.msh");
MeshPartitionScotch * partition = new MeshPartitionScotch(mesh, spatial_dimension);
partition->partitionate(psize);
communicator = DistributedSynchronizer::createDistributedSynchronizerMesh(mesh, partition);
delete partition;
} else {
communicator = DistributedSynchronizer::createDistributedSynchronizerMesh(mesh, NULL);
}
FEEngine *fem = new FEEngineTemplate<IntegratorGauss,ShapeLagrange,_ek_regular>(mesh, spatial_dimension, "my_fem");
DOFSynchronizer dof_synchronizer(mesh, spatial_dimension);
UInt nb_global_nodes = mesh.getNbGlobalNodes();
dof_synchronizer.initGlobalDOFEquationNumbers();
// fill the matrix with
UInt nb_element = mesh.getNbElement(element_type);
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(element_type);
UInt nb_dofs_per_element = spatial_dimension * nb_nodes_per_element;
- SparseMatrix K(nb_global_nodes * spatial_dimension, _symmetric);
+ SparseMatrix K(nb_global_nodes * spatial_dimension, _unsymmetric);
K.buildProfile(mesh, dof_synchronizer, spatial_dimension);
Matrix<Real> element_input(nb_dofs_per_element, nb_dofs_per_element, 1);
Array<Real> K_e = Array<Real>(nb_element, nb_dofs_per_element * nb_dofs_per_element, "K_e");
Array<Real>::matrix_iterator K_e_it = K_e.begin(nb_dofs_per_element, nb_dofs_per_element);
Array<Real>::matrix_iterator K_e_end = K_e.end(nb_dofs_per_element, nb_dofs_per_element);
for(; K_e_it != K_e_end; ++K_e_it)
*K_e_it = element_input;
// assemble the test matrix
fem->assembleMatrix(K_e, K, spatial_dimension, element_type, ghost_type);
CSR<Element> node_to_elem;
MeshUtils::buildNode2Elements(mesh, node_to_elem, spatial_dimension);
for (UInt i = 0; i < mesh.getNbNodes(); ++i) {
std::cout << node_to_elem.getNbCols(i) << std::endl;
}
- PETScMatrix petsc_matrix(nb_global_nodes * spatial_dimension, _symmetric);
-
- petsc_matrix.resize(dof_synchronizer);
+ PETScMatrix petsc_matrix(nb_global_nodes * spatial_dimension, _unsymmetric);
+
petsc_matrix.buildProfile(mesh, dof_synchronizer, spatial_dimension);
petsc_matrix.add(K, 1);
- petsc_matrix.performAssembly();
+ // for (UInt i = 0; i < mesh.getNbNodes(); ++i) {
+ // for (UInt j = 0; j < spatial_dimension; ++j) {
+ // UInt dof = i * spatial_dimension + j;
+ // if (dof_synchronizer.isLocalOrMasterDOF(dof)) {
+ // UInt global_dof = dof_synchronizer.getDOFGlobalID(dof);
+ // std::cout << "K(" << global_dof << "," << global_dof << ")=" << petsc_matrix(dof,dof) << std::endl;
+ // std::cout << node_to_elem.getNbCols(i) << std::endl;
+ // }
+ // }
+ // }
+
+
+
- petsc_matrix.saveMatrix("profile.mtx");
+ petsc_matrix.saveMatrix("profile.dat");
delete communicator;
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_synchronizer/CMakeLists.txt b/test/test_synchronizer/CMakeLists.txt
index 52a6c6b31..971dbc550 100644
--- a/test/test_synchronizer/CMakeLists.txt
+++ b/test/test_synchronizer/CMakeLists.txt
@@ -1,62 +1,68 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Sun Sep 12 2010
# @date last modification: Fri Sep 05 2014
#
# @brief configuration for synchronizer tests
#
# @section LICENSE
#
# Copyright (©) 2010-2012, 2014 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
#
#===============================================================================
add_mesh(test_synchronizer_communication_mesh
cube.geo 3 2)
register_test(test_synchronizer_communication
SOURCES test_synchronizer_communication.cc
DEPENDENCIES test_synchronizer_communication_mesh
PACKAGE parallel
)
if(AKANTU_DAMAGE_NON_LOCAL)
add_executable(test_grid_synchronizer_check_neighbors test_grid_synchronizer_check_neighbors.cc)
target_link_libraries(test_grid_synchronizer_check_neighbors akantu)
endif()
register_test(test_grid_synchronizer
SOURCES test_grid_synchronizer.cc test_data_accessor.hh
DEPENDENCIES test_synchronizer_communication_mesh test_grid_synchronizer_check_neighbors
EXTRA_FILES test_grid_synchronizer_check_neighbors.cc test_grid_tools.hh
PACKAGE damage_non_local
)
register_test(test_dof_synchronizer
SOURCES test_dof_synchronizer.cc test_data_accessor.hh
FILES_TO_COPY bar.msh)
+register_test(test_dof_synchronizer_communication
+ SOURCES test_dof_synchronizer_communication.cc test_dof_data_accessor.hh
+ DEPENDENCIES test_synchronizer_communication_mesh
+ PACKAGE parallel
+ )
+
register_test(test_data_distribution
SOURCES test_data_distribution.cc
FILES_TO_COPY data_split.msh
PACKAGE parallel
)