treeset: use eigen instead of sparse13 #2643
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src/nrniv/matrixmap.cpp
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| @@ -54,7 +55,11 @@ void MatrixMap::alloc(int start, int nnode, Node** nodes, int* layer) { | |||
| } else { | |||
| jt = start + j - nnode; | |||
| } | |||
| ptree_[plen_] = spGetElement(_nt->_sp13mat, it, jt); | |||
| if (it == 0 || jt == 0) { | |||
| ptree_[plen_] = &place_holder; | |||
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This is a joke of sparse13 I can explain that (this is funny)
| spPrint(_nt->_sp13mat, 1, 0, 1); | ||
| std::cout << &_nt->_sparseMat << std::endl; | ||
| } else { | ||
| int i, n = spGetSize(_nt->_sp13mat, 0); | ||
| spPrint(_nt->_sp13mat, 1, 1, 1); | ||
| for (i = 1; i <= n; ++i) { | ||
| std::cout << &_nt->_sparseMat << std::endl; | ||
| int n = _nt->_sparseMat->cols(); | ||
| for (int i = 1; i <= n; ++i) { |
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What should we do about that? I'm for removing...
| namespace Eigen { | ||
| template <typename _Scalar, int _Options, typename _StorageIndex> | ||
| class SparseMatrix; | ||
| } |
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This file is installed and use, so if we include <Eigen> we need to install Eigen header too...
| void* _vcv; /* replaces old cvode_instance and nrn_cvode_ */ | ||
| double* _sparse_rhs; /* rhs matrix for sparse13 solver. updates to and from this vector | ||
| need to be transfered to actual_rhs */ | ||
| Eigen::SparseMatrix<double, 1, int>* _sparseMat{}; /* handle to general sparse matrix */ |
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We give number otherwise we have to declare the enum behind the option and I have no idea how to do that without conflict at resolution...
| spSolve(_nt->_sp13mat, _nt->_sp13_rhs, _nt->_sp13_rhs); | ||
| _nt->_sparseMat->makeCompressed(); | ||
| Eigen::SparseLU<Eigen::SparseMatrix<double, Eigen::RowMajor>> lu(*_nt->_sparseMat); | ||
| Eigen::Map<Eigen::VectorXd> rhs(_nt->_sparse_rhs + 1, _nt->_sparseMat->cols()); |
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other joke of sparse13 the matrix is 1-indexed so we use the vector off by one.
| Eigen::SparseMatrix<double, Eigen::RowMajor>& m_ = *_nt->_sparseMat; | ||
| for (int k = 0; k < m_.outerSize(); ++k) { | ||
| for (Eigen::SparseMatrix<double, Eigen::RowMajor>::InnerIterator it(m_, k); it; ++it) { | ||
| it.valueRef() = 0.; | ||
| } | ||
| } |
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An other funny joke of sparse13 the function spClear just reset all pre-declared number to 0 instead of removing them (it should be like that because this is a sparse matrix...).
src/nrnoc/treeset.cpp
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| const Node* nd = nt->_v_node[in]; | ||
| const Extnode* nde = nd->extnode; | ||
| const Node* pnd = nt->_v_parent[in]; | ||
| int i = nd->eqn_index_; | ||
| nt->_sparseMat->coeffRef(i - 1, i - 1) = 0.; | ||
| if (nde) { | ||
| for (int ie = 0; ie < nlayer; ++ie) { | ||
| int k = i + ie + 1; | ||
| nt->_sparseMat->coeffRef(k - 1, k - 1) = 0.; | ||
| nt->_sparseMat->coeffRef(k - 1, k - 2) = 0; | ||
| nt->_sparseMat->coeffRef(k - 2, k - 1) = 0; | ||
| } | ||
| } | ||
| if (pnd) { | ||
| int j = pnd->eqn_index_; | ||
| nt->_sparseMat->coeffRef(j - 1, i - 1); | ||
| nt->_sparseMat->coeffRef(i - 1, j - 1); | ||
| if (nde && pnd->extnode) | ||
| for (int ie = 0; ie < nlayer; ++ie) { | ||
| int kp = j + ie + 1; | ||
| int k = i + ie + 1; | ||
| nt->_sparseMat->coeffRef(kp - 1, k - 1) = 0; | ||
| nt->_sparseMat->coeffRef(k - 1, kp - 1) = 0; | ||
| } | ||
| } | ||
| } | ||
| // nt->_sparseMat->makeCompressed(); | ||
| for (in = 0; in < nt->end; ++in) { |
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This is a copy of the code below for allocating values.
sparse13 is more or less a linked list of single value so when we get pointer afterward they are stable.
Eigen is a kind of vector of values. So can be reallocate. So we reserve all the values rights now and get the pointer afterward.
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Please retry analysis of this Pull-Request directly on SonarCloud |
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Superseeded by #3142 |
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