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fragment_manager.cc
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/**
* @file fragment_manager.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Thu Jan 23 2014
* @date last modification: Tue Aug 19 2014
*
* @brief Group manager to handle fragments
*
* @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/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "fragment_manager.hh"
#include "material_cohesive.hh"
#include <numeric>
#include <algorithm>
#include <functional>
__BEGIN_AKANTU__
/* -------------------------------------------------------------------------- */
FragmentManager::FragmentManager(SolidMechanicsModelCohesive & model,
bool dump_data,
const ID & id,
const MemoryID & memory_id) :
GroupManager(model.getMesh(), id, memory_id),
model(model),
mass_center(0, model.getSpatialDimension(), "mass_center"),
mass(0, model.getSpatialDimension(), "mass"),
velocity(0, model.getSpatialDimension(), "velocity"),
inertia_moments(0, model.getSpatialDimension(), "inertia_moments"),
principal_directions(0, model.getSpatialDimension() * model.getSpatialDimension(),
"principal_directions"),
quad_coordinates("quad_coordinates", id),
mass_density("mass_density", id),
nb_elements_per_fragment(0, 1, "nb_elements_per_fragment"),
dump_data(dump_data) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
/// compute quadrature points' coordinates
mesh.initElementTypeMapArray(quad_coordinates,
spatial_dimension,
spatial_dimension,
_not_ghost);
model.getFEEngine().interpolateOnIntegrationPoints(model.getMesh().getNodes(),
quad_coordinates);
/// store mass density per quadrature point
mesh.initElementTypeMapArray(mass_density,
1,
spatial_dimension,
_not_ghost);
storeMassDensityPerIntegrationPoint();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
class CohesiveElementFilter : public GroupManager::ClusteringFilter {
public:
CohesiveElementFilter(const SolidMechanicsModelCohesive & model,
const Real max_damage = 1.) :
model(model), is_unbroken(max_damage) {}
bool operator() (const Element & el) const {
if (el.kind == _ek_regular)
return true;
const Array<UInt> & mat_indexes = model.getMaterialByElement(el.type,
el.ghost_type);
const Array<UInt> & mat_loc_num = model.getMaterialLocalNumbering(el.type,
el.ghost_type);
const MaterialCohesive & mat
= static_cast<const MaterialCohesive &>
(model.getMaterial(mat_indexes(el.element)));
UInt el_index = mat_loc_num(el.element);
UInt nb_quad_per_element
= model.getFEEngine("CohesiveFEEngine").getNbIntegrationPoints(el.type, el.ghost_type);
const Array<Real> & damage_array = mat.getDamage(el.type, el.ghost_type);
AKANTU_DEBUG_ASSERT(nb_quad_per_element * el_index < damage_array.getSize(),
"This quadrature point is out of range");
const Real * element_damage
= damage_array.storage() + nb_quad_per_element * el_index;
UInt unbroken_quads = std::count_if(element_damage,
element_damage + nb_quad_per_element,
is_unbroken);
if (unbroken_quads > 0)
return true;
return false;
}
private:
struct IsUnbrokenFunctor {
IsUnbrokenFunctor(const Real & max_damage) : max_damage(max_damage) {}
bool operator() (const Real & x) {return x < max_damage;}
const Real max_damage;
};
const SolidMechanicsModelCohesive & model;
const IsUnbrokenFunctor is_unbroken;
};
/* -------------------------------------------------------------------------- */
void FragmentManager::buildFragments(Real damage_limit) {
AKANTU_DEBUG_IN();
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
DistributedSynchronizer * cohesive_synchronizer
= const_cast<DistributedSynchronizer *>(model.getCohesiveSynchronizer());
if (cohesive_synchronizer) {
cohesive_synchronizer->computeBufferSize(model, _gst_smmc_damage);
cohesive_synchronizer->asynchronousSynchronize(model, _gst_smmc_damage);
cohesive_synchronizer->waitEndSynchronize(model, _gst_smmc_damage);
}
#endif
DistributedSynchronizer & synchronizer
= const_cast<DistributedSynchronizer &>(model.getSynchronizer());
Mesh & mesh_facets = const_cast<Mesh &>(mesh.getMeshFacets());
UInt spatial_dimension = model.getSpatialDimension();
std::string fragment_prefix("fragment");
/// generate fragments
global_nb_fragment = createClusters(spatial_dimension,
fragment_prefix,
CohesiveElementFilter(model,
damage_limit),
&synchronizer,
&mesh_facets);
nb_fragment = getNbElementGroups(spatial_dimension);
fragment_index.resize(nb_fragment);
UInt * fragment_index_it = fragment_index.storage();
/// loop over fragments
for(const_element_group_iterator it(element_group_begin());
it != element_group_end(); ++it, ++fragment_index_it) {
/// get fragment index
std::string fragment_index_string
= it->first.substr(fragment_prefix.size() + 1);
std::stringstream sstr(fragment_index_string.c_str());
sstr >> *fragment_index_it;
AKANTU_DEBUG_ASSERT(!sstr.fail(), "fragment_index is not an integer");
}
/// compute fragments' mass
computeMass();
if (dump_data) {
createDumpDataArray(fragment_index, "fragments", true);
createDumpDataArray(mass, "fragments mass");
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void FragmentManager::computeMass() {
AKANTU_DEBUG_IN();
UInt spatial_dimension = model.getSpatialDimension();
/// create a unit field per quadrature point, since to compute mass
/// it's neccessary to integrate only density
ElementTypeMapArray<Real> unit_field("unit_field", id);
mesh.initElementTypeMapArray(unit_field,
spatial_dimension,
spatial_dimension,
_not_ghost);
ElementTypeMapArray<Real>::type_iterator it = unit_field.firstType(spatial_dimension,
_not_ghost,
_ek_regular);
ElementTypeMapArray<Real>::type_iterator end = unit_field.lastType(spatial_dimension,
_not_ghost,
_ek_regular);
for (; it != end; ++it) {
ElementType type = *it;
Array<Real> & field_array = unit_field(type);
UInt nb_element = mesh.getNbElement(type);
UInt nb_quad_per_element = model.getFEEngine().getNbIntegrationPoints(type);
field_array.resize(nb_element * nb_quad_per_element);
field_array.set(1.);
}
integrateFieldOnFragments(unit_field, mass);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void FragmentManager::computeCenterOfMass() {
AKANTU_DEBUG_IN();
/// integrate position multiplied by density
integrateFieldOnFragments(quad_coordinates, mass_center);
/// divide it by the fragments' mass
Real * mass_storage = mass.storage();
Real * mass_center_storage = mass_center.storage();
UInt total_components = mass_center.getSize() * mass_center.getNbComponent();
for (UInt i = 0; i < total_components; ++i)
mass_center_storage[i] /= mass_storage[i];
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void FragmentManager::computeVelocity() {
AKANTU_DEBUG_IN();
UInt spatial_dimension = model.getSpatialDimension();
/// compute velocity per quadrature point
ElementTypeMapArray<Real> velocity_field("velocity_field", id);
mesh.initElementTypeMapArray(velocity_field,
spatial_dimension,
spatial_dimension,
_not_ghost);
model.getFEEngine().interpolateOnIntegrationPoints(model.getVelocity(),
velocity_field);
/// integrate on fragments
integrateFieldOnFragments(velocity_field, velocity);
/// divide it by the fragments' mass
Real * mass_storage = mass.storage();
Real * velocity_storage = velocity.storage();
UInt total_components = velocity.getSize() * velocity.getNbComponent();
for (UInt i = 0; i < total_components; ++i)
velocity_storage[i] /= mass_storage[i];
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Given the distance @f$ \mathbf{r} @f$ between a quadrature point
* and its center of mass, the moment of inertia is computed as \f[
* I_\mathrm{CM} = \mathrm{tr}(\mathbf{r}\mathbf{r}^\mathrm{T})
* \mathbf{I} - \mathbf{r}\mathbf{r}^\mathrm{T} \f] for more
* information check Wikipedia
* (http://en.wikipedia.org/wiki/Moment_of_inertia#Identities_for_a_skew-symmetric_matrix)
*
*/
void FragmentManager::computeInertiaMoments() {
AKANTU_DEBUG_IN();
UInt spatial_dimension = model.getSpatialDimension();
computeCenterOfMass();
/// compute local coordinates products with respect to the center of match
ElementTypeMapArray<Real> moments_coords("moments_coords", id);
mesh.initElementTypeMapArray(moments_coords,
spatial_dimension * spatial_dimension,
spatial_dimension,
_not_ghost);
/// resize the by element type
ElementTypeMapArray<Real>::type_iterator it = moments_coords.firstType(spatial_dimension,
_not_ghost,
_ek_regular);
ElementTypeMapArray<Real>::type_iterator end = moments_coords.lastType(spatial_dimension,
_not_ghost,
_ek_regular);
for (; it != end; ++it) {
ElementType type = *it;
Array<Real> & field_array = moments_coords(type);
UInt nb_element = mesh.getNbElement(type);
UInt nb_quad_per_element = model.getFEEngine().getNbIntegrationPoints(type);
field_array.resize(nb_element * nb_quad_per_element);
}
/// compute coordinates
Array<Real>::const_vector_iterator mass_center_it
= mass_center.begin(spatial_dimension);
/// loop over fragments
for(const_element_group_iterator it(element_group_begin());
it != element_group_end(); ++it, ++mass_center_it) {
const ElementTypeMapArray<UInt> & el_list = it->second->getElements();
ElementTypeMapArray<UInt>::type_iterator type_it = el_list.firstType(spatial_dimension,
_not_ghost,
_ek_regular);
ElementTypeMapArray<UInt>::type_iterator type_end = el_list.lastType(spatial_dimension,
_not_ghost,
_ek_regular);
/// loop over elements of the fragment
for (; type_it != type_end; ++type_it) {
ElementType type = *type_it;
UInt nb_quad_per_element = model.getFEEngine().getNbIntegrationPoints(type);
Array<Real> & moments_coords_array = moments_coords(type);
const Array<Real> & quad_coordinates_array = quad_coordinates(type);
const Array<UInt> & el_list_array = el_list(type);
Array<Real>::matrix_iterator moments_begin
= moments_coords_array.begin(spatial_dimension, spatial_dimension);
Array<Real>::const_vector_iterator quad_coordinates_begin
= quad_coordinates_array.begin(spatial_dimension);
Vector<Real> relative_coords(spatial_dimension);
for (UInt el = 0; el < el_list_array.getSize(); ++el) {
UInt global_el = el_list_array(el);
/// loop over quadrature points
for (UInt q = 0; q < nb_quad_per_element; ++q) {
UInt global_q = global_el * nb_quad_per_element + q;
Matrix<Real> moments_matrix = moments_begin[global_q];
const Vector<Real> & quad_coord_vector = quad_coordinates_begin[global_q];
/// to understand this read the documentation written just
/// before this function
relative_coords = quad_coord_vector;
relative_coords -= *mass_center_it;
moments_matrix.outerProduct(relative_coords, relative_coords);
Real trace = moments_matrix.trace();
moments_matrix *= -1.;
moments_matrix += Matrix<Real>::eye(spatial_dimension, trace);
}
}
}
}
/// integrate moments
Array<Real> integrated_moments(global_nb_fragment,
spatial_dimension * spatial_dimension);
integrateFieldOnFragments(moments_coords, integrated_moments);
/// compute and store principal moments
inertia_moments.resize(global_nb_fragment);
principal_directions.resize(global_nb_fragment);
Array<Real>::matrix_iterator integrated_moments_it
= integrated_moments.begin(spatial_dimension, spatial_dimension);
Array<Real>::vector_iterator inertia_moments_it
= inertia_moments.begin(spatial_dimension);
Array<Real>::matrix_iterator principal_directions_it
= principal_directions.begin(spatial_dimension, spatial_dimension);
for (UInt frag = 0; frag < global_nb_fragment; ++frag, ++integrated_moments_it,
++inertia_moments_it, ++principal_directions_it) {
integrated_moments_it->eig(*inertia_moments_it, *principal_directions_it);
}
if (dump_data)
createDumpDataArray(inertia_moments, "moments of inertia");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void FragmentManager::computeAllData() {
AKANTU_DEBUG_IN();
buildFragments();
computeVelocity();
computeInertiaMoments();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void FragmentManager::storeMassDensityPerIntegrationPoint() {
AKANTU_DEBUG_IN();
UInt spatial_dimension = model.getSpatialDimension();
Mesh::type_iterator it = mesh.firstType(spatial_dimension);
Mesh::type_iterator end = mesh.lastType(spatial_dimension);
for (; it != end; ++it) {
ElementType type = *it;
Array<Real> & mass_density_array = mass_density(type);
UInt nb_element = mesh.getNbElement(type);
UInt nb_quad_per_element = model.getFEEngine().getNbIntegrationPoints(type);
mass_density_array.resize(nb_element * nb_quad_per_element);
const Array<UInt> & mat_indexes = model.getMaterialByElement(type);
Real * mass_density_it = mass_density_array.storage();
/// store mass_density for each element and quadrature point
for (UInt el = 0; el < nb_element; ++el) {
Material & mat = model.getMaterial(mat_indexes(el));
for (UInt q = 0; q < nb_quad_per_element; ++q, ++mass_density_it)
*mass_density_it = mat.getRho();
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void FragmentManager::integrateFieldOnFragments(ElementTypeMapArray<Real> & field,
Array<Real> & output) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = model.getSpatialDimension();
UInt nb_component = output.getNbComponent();
/// integration part
output.resize(global_nb_fragment);
output.clear();
UInt * fragment_index_it = fragment_index.storage();
Array<Real>::vector_iterator output_begin = output.begin(nb_component);
/// loop over fragments
for(const_element_group_iterator it(element_group_begin());
it != element_group_end(); ++it, ++fragment_index_it) {
const ElementTypeMapArray<UInt> & el_list = it->second->getElements();
ElementTypeMapArray<UInt>::type_iterator type_it = el_list.firstType(spatial_dimension,
_not_ghost,
_ek_regular);
ElementTypeMapArray<UInt>::type_iterator type_end = el_list.lastType(spatial_dimension,
_not_ghost,
_ek_regular);
/// loop over elements of the fragment
for (; type_it != type_end; ++type_it) {
ElementType type = *type_it;
UInt nb_quad_per_element = model.getFEEngine().getNbIntegrationPoints(type);
const Array<Real> & density_array = mass_density(type);
Array<Real> & field_array = field(type);
const Array<UInt> & elements = el_list(type);
UInt nb_element = elements.getSize();
/// generate array to be integrated by filtering fragment's elements
Array<Real> integration_array(elements.getSize() * nb_quad_per_element,
nb_component);
Array<Real>::matrix_iterator int_array_it
= integration_array.begin_reinterpret(nb_quad_per_element,
nb_component, nb_element);
Array<Real>::matrix_iterator int_array_end
= integration_array.end_reinterpret(nb_quad_per_element,
nb_component, nb_element);
Array<Real>::matrix_iterator field_array_begin
= field_array.begin_reinterpret(nb_quad_per_element,
nb_component,
field_array.getSize() / nb_quad_per_element);
Array<Real>::const_vector_iterator density_array_begin
= density_array.begin_reinterpret(nb_quad_per_element,
density_array.getSize() / nb_quad_per_element);
for (UInt el = 0; int_array_it != int_array_end; ++int_array_it, ++el) {
UInt global_el = elements(el);
*int_array_it = field_array_begin[global_el];
/// multiply field by density
const Vector<Real> & density_vector = density_array_begin[global_el];
for (UInt i = 0; i < nb_quad_per_element; ++i) {
for (UInt j = 0; j < nb_component; ++j) {
(*int_array_it)(i, j) *= density_vector(i);
}
}
}
/// integrate the field over the fragment
Array<Real> integrated_array(elements.getSize(), nb_component);
model.getFEEngine().integrate(integration_array,
integrated_array,
nb_component,
type,
_not_ghost,
elements);
/// sum over all elements and store the result
Vector<Real> output_tmp(output_begin[*fragment_index_it]);
output_tmp += std::accumulate(integrated_array.begin(nb_component),
integrated_array.end(nb_component),
Vector<Real>(nb_component));
}
}
/// sum output over all processors
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
comm.allReduce(output.storage(), global_nb_fragment * nb_component, _so_sum);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void FragmentManager::computeNbElementsPerFragment() {
AKANTU_DEBUG_IN();
UInt spatial_dimension = model.getSpatialDimension();
nb_elements_per_fragment.resize(global_nb_fragment);
nb_elements_per_fragment.clear();
UInt * fragment_index_it = fragment_index.storage();
/// loop over fragments
for(const_element_group_iterator it(element_group_begin());
it != element_group_end(); ++it, ++fragment_index_it) {
const ElementTypeMapArray<UInt> & el_list = it->second->getElements();
ElementTypeMapArray<UInt>::type_iterator type_it = el_list.firstType(spatial_dimension,
_not_ghost,
_ek_regular);
ElementTypeMapArray<UInt>::type_iterator type_end = el_list.lastType(spatial_dimension,
_not_ghost,
_ek_regular);
/// loop over elements of the fragment
for (; type_it != type_end; ++type_it) {
ElementType type = *type_it;
UInt nb_element = el_list(type).getSize();
nb_elements_per_fragment(*fragment_index_it) += nb_element;
}
}
/// sum values over all processors
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
comm.allReduce(nb_elements_per_fragment.storage(), global_nb_fragment, _so_sum);
if (dump_data)
createDumpDataArray(nb_elements_per_fragment, "elements per fragment");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <typename T>
void FragmentManager::createDumpDataArray(Array<T> & data,
std::string name,
bool fragment_index_output) {
AKANTU_DEBUG_IN();
if (data.getSize() == 0) return;
typedef typename Array<T>::vector_iterator data_iterator;
Mesh & mesh_not_const = const_cast<Mesh &>(mesh);
UInt spatial_dimension = mesh.getSpatialDimension();
UInt nb_component = data.getNbComponent();
UInt * fragment_index_it = fragment_index.storage();
data_iterator data_begin = data.begin(nb_component);
/// loop over fragments
for(const_element_group_iterator it(element_group_begin());
it != element_group_end(); ++it, ++fragment_index_it) {
const ElementGroup & fragment = *(it->second);
/// loop over cluster types
ElementGroup::type_iterator type_it = fragment.firstType(spatial_dimension);
ElementGroup::type_iterator type_end = fragment.lastType(spatial_dimension);
for(; type_it != type_end; ++type_it) {
ElementType type = *type_it;
/// init mesh data
Array<T> * mesh_data
= mesh_not_const.getDataPointer<T>(name, type, _not_ghost, nb_component);
data_iterator mesh_data_begin = mesh_data->begin(nb_component);
ElementGroup::const_element_iterator el_it = fragment.element_begin(type);
ElementGroup::const_element_iterator el_end = fragment.element_end(type);
/// fill mesh data
if (fragment_index_output) {
for (; el_it != el_end; ++el_it) {
Vector<T> md_tmp(mesh_data_begin[*el_it]);
md_tmp(0) = *fragment_index_it;
}
} else {
for (; el_it != el_end; ++el_it) {
Vector<T> md_tmp(mesh_data_begin[*el_it]);
md_tmp = data_begin[*fragment_index_it];
}
}
}
}
AKANTU_DEBUG_OUT();
}
__END_AKANTU__
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