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Merge pull request #396 from alxbilger/bindingslinearsystem
Introduce bindings to linear system
2 parents 3df782d + 2b27939 commit 67ff25b

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+358
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‎bindings/Modules/CMakeLists.txt

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project(Bindings.Modules)
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set(MODULEBINDINGS_MODULE_LIST SofaBaseTopology SofaDeformable SofaLinearSolver SofaConstraintSolver)
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set(MODULEBINDINGS_MODULE_LIST
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SofaBaseTopology
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SofaDeformable
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SofaLinearSolver
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SofaLinearSystem
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SofaConstraintSolver
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)
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sofa_find_package(Sofa.GL QUIET)
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if(Sofa.GL_FOUND)

‎bindings/Modules/src/SofaPython3/SofaLinearSystem/Binding_LinearSystem.cpp

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/******************************************************************************
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* SOFA, Simulation Open-Framework Architecture *
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* (c) 2021 INRIA, USTL, UJF, CNRS, MGH *
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* *
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* This program is free software; you can redistribute it and/or modify it *
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* under the terms of the GNU Lesser General Public License as published by *
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* the Free Software Foundation; either version 2.1 of the License, or (at *
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* your option) any later version. *
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* *
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* This program is distributed in the hope that it will be useful, but WITHOUT *
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* ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or *
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* FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License *
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* for more details. *
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* *
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* You should have received a copy of the GNU Lesser General Public License *
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* along with this program. If not, see <http://www.gnu.org/licenses/>. *
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*******************************************************************************
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* Contact information: [email protected] *
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******************************************************************************/
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#include <SofaPython3/SofaLinearSystem/Binding_LinearSystem.h>
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#include <SofaPython3/SofaLinearSystem/Binding_LinearSystem_doc.h>
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#include <pybind11/pybind11.h>
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#include <SofaPython3/Sofa/Core/Binding_Base.h>
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#include <SofaPython3/PythonFactory.h>
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#include <sofa/component/linearsystem/TypedMatrixLinearSystem.h>
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#include <pybind11/eigen.h>
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#include <sofa/linearalgebra/CompressedRowSparseMatrix.h>
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namespace py { using namespace pybind11; }
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namespace sofapython3 {
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template<class Real>
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using EigenSparseMatrix = Eigen::SparseMatrix<Real, Eigen::RowMajor>;
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template<class Real>
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using EigenMatrixMap = Eigen::Map<Eigen::SparseMatrix<Real, Eigen::RowMajor> >;
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template<class Real>
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using Vector = Eigen::Matrix<Real,Eigen::Dynamic, 1>;
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template<class Real>
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using EigenVectorMap = Eigen::Map<Vector<Real>>;
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template<class TBlock>
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EigenSparseMatrix<typename sofa::linearalgebra::CompressedRowSparseMatrix<TBlock>::Real>
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toEigen(sofa::linearalgebra::CompressedRowSparseMatrix<TBlock>& matrix)
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{
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using Real = typename sofa::linearalgebra::CompressedRowSparseMatrix<TBlock>::Real;
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if constexpr (std::is_same_v<TBlock, Real>)
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{
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matrix.compress();
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return EigenMatrixMap<Real>(matrix.rows(), matrix.cols(), matrix.getColsValue().size(),
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(typename EigenMatrixMap<Real>::StorageIndex*)matrix.rowBegin.data(),
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(typename EigenMatrixMap<Real>::StorageIndex*)matrix.colsIndex.data(),
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matrix.colsValue.data());
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}
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else
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{
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sofa::linearalgebra::CompressedRowSparseMatrix<typename TBlock::Real> filtered;
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filtered.copyNonZeros(matrix);
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filtered.compress();
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return EigenMatrixMap<Real>(filtered.rows(), filtered.cols(), filtered.getColsValue().size(),
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(typename EigenMatrixMap<Real>::StorageIndex*)filtered.rowBegin.data(),
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(typename EigenMatrixMap<Real>::StorageIndex*)filtered.colsIndex.data(),
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filtered.colsValue.data());
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}
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}
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template<class TBlock>
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void bindLinearSystems(py::module &m)
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{
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using CRS = sofa::linearalgebra::CompressedRowSparseMatrix<TBlock>;
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using Real = typename CRS::Real;
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using CRSLinearSystem = sofa::component::linearsystem::TypedMatrixLinearSystem<CRS, sofa::linearalgebra::FullVector<Real> >;
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const std::string typeName = CRSLinearSystem::GetClass()->className + CRSLinearSystem::GetCustomTemplateName();
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py::class_<CRSLinearSystem,
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sofa::core::objectmodel::BaseObject,
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sofapython3::py_shared_ptr<CRSLinearSystem> > c(m, typeName.c_str(), sofapython3::doc::linearsystem::linearSystemClass);
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c.def("A", [](CRSLinearSystem& self) -> EigenSparseMatrix<Real>
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{
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if (CRS* matrix = self.getSystemMatrix())
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{
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if (matrix->colsValue.empty()) //null matrix: contains no entries
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{
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return EigenSparseMatrix<Real>{matrix->rows(), matrix->cols()};
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}
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return toEigen(*matrix);
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}
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return {};
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}, sofapython3::doc::linearsystem::linearSystem_A);
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c.def("b", [](CRSLinearSystem& self) -> Vector<Real>
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{
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if (auto* vector = self.getRHSVector())
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{
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return EigenVectorMap<Real>(vector->ptr(), vector->size());
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}
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return {};
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}, sofapython3::doc::linearsystem::linearSystem_b);
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c.def("x", [](CRSLinearSystem& self) -> Vector<Real>
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{
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if (auto* vector = self.getSolutionVector())
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{
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return EigenVectorMap<Real>(vector->ptr(), vector->size());
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}
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return {};
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}, sofapython3::doc::linearsystem::linearSystem_x);
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/// register the binding in the downcasting subsystem
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PythonFactory::registerType<CRSLinearSystem>([](sofa::core::objectmodel::Base* object)
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{
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return py::cast(dynamic_cast<CRSLinearSystem*>(object));
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});
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}
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void moduleAddLinearSystem(py::module &m)
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{
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bindLinearSystems<SReal>(m);
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bindLinearSystems<sofa::type::Mat<3, 3, SReal> >(m);
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}
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}

‎bindings/Modules/src/SofaPython3/SofaLinearSystem/Binding_LinearSystem.h

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/******************************************************************************
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* SOFA, Simulation Open-Framework Architecture *
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* (c) 2021 INRIA, USTL, UJF, CNRS, MGH *
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* *
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* This program is free software; you can redistribute it and/or modify it *
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* under the terms of the GNU Lesser General Public License as published by *
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* the Free Software Foundation; either version 2.1 of the License, or (at *
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* your option) any later version. *
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* *
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* This program is distributed in the hope that it will be useful, but WITHOUT *
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* ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or *
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* FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License *
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* for more details. *
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* *
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* You should have received a copy of the GNU Lesser General Public License *
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* along with this program. If not, see <http://www.gnu.org/licenses/>. *
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*******************************************************************************
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* Contact information: [email protected] *
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******************************************************************************/
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#pragma once
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#include <pybind11/pybind11.h>
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namespace sofapython3
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{
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void moduleAddLinearSystem(pybind11::module &m);
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} /// namespace sofapython3
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‎bindings/Modules/src/SofaPython3/SofaLinearSystem/Binding_LinearSystem_doc.h

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/******************************************************************************
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* SOFA, Simulation Open-Framework Architecture *
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* (c) 2021 INRIA, USTL, UJF, CNRS, MGH *
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* *
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* This program is free software; you can redistribute it and/or modify it *
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* under the terms of the GNU Lesser General Public License as published by *
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* the Free Software Foundation; either version 2.1 of the License, or (at *
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* your option) any later version. *
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* *
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* This program is distributed in the hope that it will be useful, but WITHOUT *
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* ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or *
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* FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License *
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* for more details. *
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* *
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* You should have received a copy of the GNU Lesser General Public License *
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* along with this program. If not, see <http://www.gnu.org/licenses/>. *
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*******************************************************************************
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* Contact information: [email protected] *
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******************************************************************************/
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#pragma once
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namespace sofapython3::doc::linearsystem {
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static auto linearSystemClass =
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R"(
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Linear system. Supports only CompressedRowSparseMatrix.
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example:
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------------
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linear_system = root.addObject('MatrixLinearSystem', template='CompressedRowSparseMatrixd')
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)";
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static auto linearSystem_A =
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R"(
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Returns the global system matrix as a scipy sparse matrix
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example:
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------------
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linear_system = root.addObject('MatrixLinearSystem', template='CompressedRowSparseMatrixd')
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matrix = linear_system.A()
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)";
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static auto linearSystem_b =
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R"(
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Returns the global system right hand side as a numpy array
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example:
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------------
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linear_system = root.addObject('MatrixLinearSystem', template='CompressedRowSparseMatrixd')
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matrix = linear_system.b()
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)";
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static auto linearSystem_x =
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R"(
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Returns the global system solution vector as a numpy array
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example:
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------------
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linear_system = root.addObject('MatrixLinearSystem', template='CompressedRowSparseMatrixd')
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matrix = linear_system.x()
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)";
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} // namespace sofapython3::doc::baseCamera

‎bindings/Modules/src/SofaPython3/SofaLinearSystem/CMakeLists.txt

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project(Bindings.Modules.SofaLinearSystem)
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set(HEADER_FILES
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${CMAKE_CURRENT_SOURCE_DIR}/Binding_LinearSystem.h
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${CMAKE_CURRENT_SOURCE_DIR}/Binding_LinearSystem_doc.h
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)
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set(SOURCE_FILES
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${CMAKE_CURRENT_SOURCE_DIR}/Binding_LinearSystem.cpp
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${CMAKE_CURRENT_SOURCE_DIR}/Module_SofaLinearSystem.cpp
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)
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if (NOT TARGET SofaPython3::Plugin)
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find_package(SofaPython3 REQUIRED COMPONENTS Plugin Bindings.Sofa)
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endif()
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sofa_find_package(Sofa.Component.LinearSystem REQUIRED)
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SP3_add_python_module(
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TARGET ${PROJECT_NAME}
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PACKAGE Bindings.Modules
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MODULE SofaLinearSystem
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DESTINATION Sofa
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SOURCES ${SOURCE_FILES}
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HEADERS ${HEADER_FILES}
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DEPENDS Sofa.Component.LinearSystem SofaPython3::Plugin SofaPython3::Bindings.Sofa.Core
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)

‎bindings/Modules/src/SofaPython3/SofaLinearSystem/Module_SofaLinearSystem.cpp

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/******************************************************************************
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* SofaPython3 plugin *
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* (c) 2021 CNRS, University of Lille, INRIA *
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* *
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* This program is free software; you can redistribute it and/or modify it *
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* under the terms of the GNU Lesser General Public License as published by *
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* the Free Software Foundation; either version 2.1 of the License, or (at *
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* your option) any later version. *
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* *
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* This program is distributed in the hope that it will be useful, but WITHOUT *
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* ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or *
12+
* FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License *
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* for more details. *
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* *
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* You should have received a copy of the GNU Lesser General Public License *
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* along with this program. If not, see <http://www.gnu.org/licenses/>. *
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*******************************************************************************
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* Contact information: [email protected] *
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******************************************************************************/
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#include <pybind11/pybind11.h>
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#include <SofaPython3/SofaLinearSystem/Binding_LinearSystem.h>
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namespace sofapython3
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{
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PYBIND11_MODULE(SofaLinearSystem, m)
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{
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moduleAddLinearSystem(m);
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}
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} // namespace sofapython3
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