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py_mesh.cc
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/**
* @file py_mesh.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Philip Mueller <philip.paul.mueller@bluemail.ch>
* @author Mohit Pundir <mohit.pundir@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sun Jun 16 2019
* @date last modification: Mon Mar 15 2021
*
* @brief pybind11 interface to Mesh
*
*
* @section LICENSE
*
* Copyright (©) 2018-2021 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_config.hh"
/* -------------------------------------------------------------------------- */
#include "py_aka_array.hh"
/* -------------------------------------------------------------------------- */
#include <mesh.hh>
#include <mesh_accessor.hh>
#include <mesh_utils.hh>
/* -------------------------------------------------------------------------- */
#include <pybind11/pybind11.h>
#include <pybind11/stl.h>
/* -------------------------------------------------------------------------- */
namespace py = pybind11;
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace {
/* ------------------------------------------------------------------------ */
template <typename T>
auto register_element_type_map_array(py::module & mod,
const std::string & name) {
auto element_type_map_class =
py::class_<ElementTypeMapArray<T>,
std::shared_ptr<ElementTypeMapArray<T>>>(
mod, ("ElementTypeMapArray" + name).c_str())
.def(py::init<const ID &, const ID &>(),
py::arg("id") = "by_element_type_array",
py::arg("parent_id") = "no_parent")
.def(
"__call__",
[](ElementTypeMapArray<T> & self, ElementType type,
GhostType ghost_type) -> decltype(auto) {
return self(type, ghost_type);
},
py::arg("type"), py::arg("ghost_type") = _not_ghost,
py::return_value_policy::reference, py::keep_alive<0, 1>())
.def(
"elementTypes",
[](ElementTypeMapArray<T> & self, UInt _dim,
GhostType _ghost_type,
ElementKind _kind) -> std::vector<ElementType> {
auto types = self.elementTypes(_dim, _ghost_type, _kind);
std::vector<ElementType> _types;
for (auto && t : types) {
_types.push_back(t);
}
return _types;
},
py::arg("dim") = _all_dimensions,
py::arg("ghost_type") = _not_ghost,
py::arg("kind") = _ek_regular)
.def(
"initialize",
[](ElementTypeMapArray<T> & self, const Mesh & mesh,
GhostType ghost_type, Int nb_component,
Int spatial_dimension, ElementKind element_kind,
bool with_nb_element, bool with_nb_nodes_per_element,
T default_value, bool do_not_default) {
self.initialize(
mesh, _ghost_type = ghost_type,
_nb_component = nb_component,
_spatial_dimension =
(spatial_dimension == -2 ? mesh.getSpatialDimension()
: spatial_dimension),
_element_kind = element_kind,
_with_nb_element = with_nb_element,
_with_nb_nodes_per_element = with_nb_nodes_per_element,
_default_value = default_value,
_do_not_default = do_not_default);
},
py::arg("mesh"), py::arg("ghost_type") = _casper,
py::arg("nb_component") = 1, py::arg("spatial_dimension") = -2,
py::arg("element_kind") = _ek_not_defined,
py::arg("with_nb_element") = false,
py::arg("with_nb_nodes_per_element") = false,
py::arg("default_value") = T{},
py::arg("do_not_default") = false);
return element_type_map_class;
}
} // namespace
/* -------------------------------------------------------------------------- */
void register_mesh(py::module & mod) {
py::class_<Mesh::PeriodicSlaves>(mod, "PeriodicSlaves")
.def(
"__iter__",
[](Mesh::PeriodicSlaves & _this) {
return py::make_iterator(_this.begin(), _this.end());
},
py::keep_alive<0, 1>());
py::class_<MeshData>(mod, "MeshData")
.def(
"getElementalDataUInt",
[](MeshData & _this, const ID & name) -> decltype(auto) {
return _this.getElementalData<UInt>(name);
},
py::return_value_policy::reference)
.def(
"getElementalDataReal",
[](MeshData & _this, const ID & name) -> decltype(auto) {
return _this.getElementalData<Real>(name);
},
py::return_value_policy::reference);
py::class_<Mesh, GroupManager, Dumpable, MeshData>(mod, "Mesh",
py::multiple_inheritance())
.def(py::init<Int, const ID &>(), py::arg("spatial_dimension"),
py::arg("id") = "mesh")
.def("read", &Mesh::read, py::arg("filename"),
py::arg("mesh_io_type") = _miot_auto, "read the mesh from a file")
.def(
"getNodes",
[](Mesh & self) -> decltype(auto) { return self.getNodes(); },
py::return_value_policy::reference)
.def("getNbNodes", &Mesh::getNbNodes)
.def(
"getConnectivity",
[](Mesh & self, ElementType type) -> decltype(auto) {
return self.getConnectivity(type);
},
py::return_value_policy::reference)
.def(
"getConnectivities",
[](Mesh & self) -> decltype(auto) {
return self.getConnectivities();
},
py::return_value_policy::reference)
.def(
"addConnectivityType",
[](Mesh & self, ElementType type, GhostType ghost_type) -> void {
self.addConnectivityType(type, ghost_type);
},
py::arg("type"), py::arg("ghost_type") = _not_ghost)
.def("distribute", [](Mesh & self) { self.distribute(); })
.def("isDistributed",
[](const Mesh & self) { return self.isDistributed(); })
.def("fillNodesToElements", &Mesh::fillNodesToElements,
py::arg("dimension") = _all_dimensions)
.def("getAssociatedElements",
[](Mesh & self, const Idx & node, py::list list) {
Array<Element> elements;
self.getAssociatedElements(node, elements);
for (auto && element : elements) {
list.append(element);
}
})
.def("makePeriodic",
[](Mesh & self, const SpatialDirection & direction) {
self.makePeriodic(direction);
})
.def(
"getNbElement",
[](Mesh & self, const Int spatial_dimension, GhostType ghost_type,
ElementKind kind) {
return self.getNbElement(spatial_dimension, ghost_type, kind);
},
py::arg("spatial_dimension") = _all_dimensions,
py::arg("ghost_type") = _not_ghost, py::arg("kind") = _ek_not_defined)
.def(
"getNbElement",
[](Mesh & self, ElementType type, GhostType ghost_type) {
return self.getNbElement(type, ghost_type);
},
py::arg("type"), py::arg("ghost_type") = _not_ghost)
.def_static(
"getSpatialDimension",
[](ElementType & type) { return Mesh::getSpatialDimension(type); })
.def(
"getDataReal",
[](Mesh & _this, const ID & name, ElementType type,
GhostType ghost_type) -> decltype(auto) {
return _this.getData<Real>(name, type, ghost_type);
},
py::arg("name"), py::arg("type"), py::arg("ghost_type") = _not_ghost,
py::return_value_policy::reference)
.def(
"hasDataReal",
[](Mesh & _this, const ID & name, ElementType type,
GhostType ghost_type) -> bool {
return _this.hasData<Real>(name, type, ghost_type);
},
py::arg("name"), py::arg("type"), py::arg("ghost_type") = _not_ghost)
.def("isPeriodic", [](const Mesh & _this) { return _this.isPeriodic(); })
.def("getPeriodicMaster", &Mesh::getPeriodicMaster)
.def("getPeriodicSlaves", &Mesh::getPeriodicSlaves)
.def("isPeriodicSlave", &Mesh::isPeriodicSlave)
.def("isPeriodicMaster", &Mesh::isPeriodicMaster)
.def(
"getMeshFacets",
[](const Mesh & self) -> const Mesh & {
return self.getMeshFacets();
},
py::return_value_policy::reference)
.def("initMeshFacets", &Mesh::initMeshFacets,
py::arg("id") = "mesh_facets", py::return_value_policy::reference);
/* ------------------------------------------------------------------------ */
py::class_<MeshUtils>(mod, "MeshUtils")
.def_static("buildFacets", &MeshUtils::buildFacets);
py::class_<MeshAccessor>(mod, "MeshAccessor")
.def(py::init<Mesh &>(), py::arg("mesh"))
.def(
"resizeConnectivity",
[](MeshAccessor & self, Int new_size, ElementType type, GhostType gt)
-> void { self.resizeConnectivity(new_size, type, gt); },
py::arg("new_size"), py::arg("type"),
py::arg("ghost_type") = _not_ghost)
.def(
"resizeNodes",
[](MeshAccessor & self, Int new_size) -> void {
self.resizeNodes(new_size);
},
py::arg("new_size"))
.def("makeReady", &MeshAccessor::makeReady);
register_element_type_map_array<Real>(mod, "Real");
register_element_type_map_array<UInt>(mod, "UInt");
register_element_type_map_array<Int>(mod, "Int");
register_element_type_map_array<bool>(mod, "bool");
// register_element_type_map_array<std::string>(mod, "String");
}
} // namespace akantu
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