void operator()(GNode item, Galois::UserContext<GNode>& ctx) {
if (!graph->containsNode(item, Galois::ALL))
return;
Cavity* cavp = NULL;
if (Version == detDisjoint) {
bool used;
LocalState* localState = (LocalState*) ctx.getLocalState(used);
if (used) {
localState->cav.update(item, ctx);
return;
} else {
cavp = &localState->cav;
}
}
if (Version == detDisjoint) {
cavp->initialize(item);
cavp->build();
cavp->computePost();
} else {
Cavity cav(graph, ctx.getPerIterAlloc());
cav.initialize(item);
cav.build();
cav.computePost();
if (Version == detPrefix)
return;
cav.update(item, ctx);
}
}
/*! \brief Builds the CPCM matrix
* \param[in] cav the discretized cavity
* \param[in] gf_i Green's function inside the cavity
* \param[in] epsilon permittivity outside the cavity
* \param[in] correction CPCM correction factor
* \return the \f$ \mathbf{K} = f(\varepsilon)\mathbf{S}^{-1} \f$ matrix
*
* This function calculates the PCM matrix.
* The matrix is not symmetrized and is not symmetry packed.
*/
inline Eigen::MatrixXd CPCMMatrix(const Cavity & cav, const IGreensFunction & gf_i, double epsilon, double correction)
{
// The total size of the cavity
size_t cavitySize = cav.size();
// The number of irreps in the group
int nrBlocks = cav.pointGroup().nrIrrep();
// The size of the irreducible portion of the cavity
int dimBlock = cav.irreducible_size();
// Compute SI and DI on the whole cavity, regardless of symmetry
TIMER_ON("Computing SI");
Eigen::MatrixXd SI = gf_i.singleLayer(cav.elements());
TIMER_OFF("Computing SI");
// Perform symmetry blocking
// If the group is C1 avoid symmetry blocking, we will just pack the fullPCMMatrix
// into "block diagonal" when all other manipulations are done.
if (cav.pointGroup().nrGenerators() != 0) {
TIMER_ON("Symmetry blocking");
symmetryBlocking(SI, cavitySize, dimBlock, nrBlocks);
TIMER_OFF("Symmetry blocking");
}
double fact = (epsilon - 1.0)/(epsilon + correction);
// Invert SI using LU decomposition with full pivoting
// This is a rank-revealing LU decomposition, this allows us
// to test if SI is invertible before attempting to invert it.
Eigen::FullPivLU<Eigen::MatrixXd> SI_LU(SI);
if (!(SI_LU.isInvertible()))
PCMSOLVER_ERROR("SI matrix is not invertible!", BOOST_CURRENT_FUNCTION);
return fact * SI_LU.inverse();
}
/*! \brief Builds the **anisotropic** IEFPCM matrix
* \param[in] cav the discretized cavity
* \param[in] gf_i Green's function inside the cavity
* \param[in] gf_o Green's function outside the cavity
* \return the \f$ \mathbf{K} = \mathbf{T}^{-1}\mathbf{R}\mathbf{A} \f$ matrix
*
* This function calculates the PCM matrix. We use the following definitions:
* \f[
* \begin{align}
* \mathbf{T} &=
* \left(2\pi\mathbf{I} - \mathbf{D}_\mathrm{e}\mathbf{A}\right)\mathbf{S}_\mathrm{i}
* +\mathbf{S}_\mathrm{e}\left(2\pi\mathbf{I} +
* \mathbf{A}\mathbf{D}_\mathrm{i}^\dagger\right) \\
* \mathbf{R} &=
* \left(2\pi\mathbf{A}^{-1} - \mathbf{D}_\mathrm{e}\right) -
* \mathbf{S}_\mathrm{e}\mathbf{S}^{-1}_\mathrm{i}\left(2\pi\mathbf{A}^{-1}-\mathbf{D}_\mathrm{i}\right)
* \end{align}
* \f]
* The matrix is not symmetrized and is not symmetry packed.
*/
inline Eigen::MatrixXd anisotropicIEFMatrix(const Cavity & cav, const IGreensFunction & gf_i, const IGreensFunction & gf_o)
{
// The total size of the cavity
size_t cavitySize = cav.size();
// The number of irreps in the group
int nrBlocks = cav.pointGroup().nrIrrep();
// The size of the irreducible portion of the cavity
int dimBlock = cav.irreducible_size();
// Compute SI, DI and SE, DE on the whole cavity, regardless of symmetry
TIMER_ON("Computing SI");
Eigen::MatrixXd SI = gf_i.singleLayer(cav.elements());
TIMER_OFF("Computing SI");
TIMER_ON("Computing DI");
Eigen::MatrixXd DI = gf_i.doubleLayer(cav.elements());
TIMER_OFF("Computing DI");
TIMER_ON("Computing SE");
Eigen::MatrixXd SE = gf_o.singleLayer(cav.elements());
TIMER_OFF("Computing SE");
TIMER_ON("Computing DE");
Eigen::MatrixXd DE = gf_o.doubleLayer(cav.elements());
TIMER_OFF("Computing DE");
// Perform symmetry blocking
// If the group is C1 avoid symmetry blocking, we will just pack the fullPCMMatrix
// into "block diagonal" when all other manipulations are done.
if (cav.pointGroup().nrGenerators() != 0) {
TIMER_ON("Symmetry blocking");
symmetryBlocking(DI, cavitySize, dimBlock, nrBlocks);
symmetryBlocking(SI, cavitySize, dimBlock, nrBlocks);
symmetryBlocking(DE, cavitySize, dimBlock, nrBlocks);
symmetryBlocking(SE, cavitySize, dimBlock, nrBlocks);
TIMER_OFF("Symmetry blocking");
}
Eigen::MatrixXd a = cav.elementArea().asDiagonal();
Eigen::MatrixXd Id = Eigen::MatrixXd::Identity(cavitySize, cavitySize);
// 1. Form T
TIMER_ON("Assemble T matrix");
Eigen::MatrixXd fullPCMMatrix = ((2 * M_PI * Id - DE * a) * SI + SE * (2 * M_PI * Id + a * DI.adjoint().eval()));
TIMER_OFF("Assemble T matrix");
// 2. Invert T using LU decomposition with full pivoting
// This is a rank-revealing LU decomposition, this allows us
// to test if T is invertible before attempting to invert it.
TIMER_ON("Invert T matrix");
Eigen::FullPivLU<Eigen::MatrixXd> T_LU(fullPCMMatrix);
if (!(T_LU.isInvertible())) PCMSOLVER_ERROR("T matrix is not invertible!", BOOST_CURRENT_FUNCTION);
fullPCMMatrix = T_LU.inverse();
TIMER_OFF("Invert T matrix");
Eigen::FullPivLU<Eigen::MatrixXd> SI_LU(SI);
if (!(SI_LU.isInvertible())) PCMSOLVER_ERROR("SI matrix is not invertible!", BOOST_CURRENT_FUNCTION);
TIMER_ON("Assemble T^-1R matrix");
fullPCMMatrix *= ((2 * M_PI * Id - DE * a) - SE * SI_LU.inverse() * (2 * M_PI * Id - DI * a));
TIMER_OFF("Assemble T^-1R matrix");
return fullPCMMatrix;
}
void IEFSolver::buildIsotropicMatrix(const Cavity & cav, const IGreensFunction & gf_i, const IGreensFunction & gf_o)
{
fullPCMMatrix_ = isotropicIEFMatrix(cav, gf_i, profiles::epsilon(gf_o.permittivity()));
// Symmetrize K := (K + K+)/2
if (hermitivitize_) {
hermitivitize(fullPCMMatrix_);
}
// Pack into a block diagonal matrix
// The number of irreps in the group
int nrBlocks = cav.pointGroup().nrIrrep();
// The size of the irreducible portion of the cavity
int dimBlock = cav.irreducible_size();
// For the moment just packs into a std::vector<Eigen::MatrixXd>
symmetryPacking(blockPCMMatrix_, fullPCMMatrix_, dimBlock, nrBlocks);
built_ = true;
}
/*! \brief Builds the **anisotropic** \f$ \mathbf{R}_\infty \f$ matrix
* \param[in] cav the discretized cavity
* \param[in] gf_i Green's function inside the cavity
* \param[in] gf_o Green's function outside the cavity
* \return the \f$ \mathbf{R}_\infty\mathbf{A} \f$ matrix
*
* We use the following definition:
* \f[
* \mathbf{R}_\infty =
* \left(2\pi\mathbf{A}^{-1} - \mathbf{D}_\mathrm{e}\right) -
* \mathbf{S}_\mathrm{e}\mathbf{S}^{-1}_\mathrm{i}\left(2\pi\mathbf{A}^{-1}-\mathbf{D}_\mathrm{i}\right)
* \f]
* The matrix is not symmetrized and is not symmetry packed.
*/
inline Eigen::MatrixXd anisotropicRinfinity(const Cavity & cav, const IGreensFunction & gf_i, const IGreensFunction & gf_o)
{
// The total size of the cavity
size_t cavitySize = cav.size();
// The number of irreps in the group
int nrBlocks = cav.pointGroup().nrIrrep();
// The size of the irreducible portion of the cavity
int dimBlock = cav.irreducible_size();
// Compute SI, DI and SE, DE on the whole cavity, regardless of symmetry
Eigen::MatrixXd SI = gf_i.singleLayer(cav.elements());
Eigen::MatrixXd DI = gf_i.doubleLayer(cav.elements());
Eigen::MatrixXd SE = gf_o.singleLayer(cav.elements());
Eigen::MatrixXd DE = gf_o.doubleLayer(cav.elements());
// Perform symmetry blocking
// If the group is C1 avoid symmetry blocking, we will just pack the matrix
// into "block diagonal" when all other manipulations are done.
if (cav.pointGroup().nrGenerators() != 0) {
symmetryBlocking(DI, cavitySize, dimBlock, nrBlocks);
symmetryBlocking(SI, cavitySize, dimBlock, nrBlocks);
symmetryBlocking(DE, cavitySize, dimBlock, nrBlocks);
symmetryBlocking(SE, cavitySize, dimBlock, nrBlocks);
}
Eigen::MatrixXd a = cav.elementArea().asDiagonal();
Eigen::MatrixXd Id = Eigen::MatrixXd::Identity(cavitySize, cavitySize);
// Form T
Eigen::FullPivLU<Eigen::MatrixXd> SI_LU(SI);
if (!(SI_LU.isInvertible())) PCMSOLVER_ERROR("SI matrix is not invertible!", BOOST_CURRENT_FUNCTION);
return ((2 * M_PI * Id - DE * a) - SE * SI_LU.inverse() * (2 * M_PI * Id - DI * a));
}
/*! \brief Builds the **anisotropic** \f$ \mathbf{T}_\varepsilon \f$ matrix
* \param[in] cav the discretized cavity
* \param[in] gf_i Green's function inside the cavity
* \param[in] gf_o Green's function outside the cavity
* \return the \f$ \mathbf{T}_\varepsilon \f$ matrix
*
* We use the following definition:
* \f[
* \mathbf{T}_\varepsilon =
* \left(2\pi\mathbf{I} - \mathbf{D}_\mathrm{e}\mathbf{A}\right)\mathbf{S}_\mathrm{i}
* +\mathbf{S}_\mathrm{e}\left(2\pi\mathbf{I} +
* \mathbf{A}\mathbf{D}_\mathrm{i}^\dagger\right)
* \f]
* The matrix is not symmetrized and is not symmetry packed.
*/
inline Eigen::MatrixXd anisotropicTEpsilon(const Cavity & cav, const IGreensFunction & gf_i, const IGreensFunction & gf_o)
{
// The total size of the cavity
size_t cavitySize = cav.size();
// The number of irreps in the group
int nrBlocks = cav.pointGroup().nrIrrep();
// The size of the irreducible portion of the cavity
int dimBlock = cav.irreducible_size();
// Compute SI, DI and SE, DE on the whole cavity, regardless of symmetry
Eigen::MatrixXd SI = gf_i.singleLayer(cav.elements());
Eigen::MatrixXd DI = gf_i.doubleLayer(cav.elements());
Eigen::MatrixXd SE = gf_o.singleLayer(cav.elements());
Eigen::MatrixXd DE = gf_o.doubleLayer(cav.elements());
// Perform symmetry blocking
// If the group is C1 avoid symmetry blocking, we will just pack the matrix
// into "block diagonal" when all other manipulations are done.
if (cav.pointGroup().nrGenerators() != 0) {
symmetryBlocking(DI, cavitySize, dimBlock, nrBlocks);
symmetryBlocking(SI, cavitySize, dimBlock, nrBlocks);
symmetryBlocking(DE, cavitySize, dimBlock, nrBlocks);
symmetryBlocking(SE, cavitySize, dimBlock, nrBlocks);
}
Eigen::MatrixXd a = cav.elementArea().asDiagonal();
Eigen::MatrixXd Id = Eigen::MatrixXd::Identity(cavitySize, cavitySize);
// Form T
return ((2 * M_PI * Id - DE * a) * SI + SE * (2 * M_PI * Id + a * DI.adjoint().eval()));
}
void IEFSolver::buildAnisotropicMatrix(const Cavity & cav, const IGreensFunction & gf_i, const IGreensFunction & gf_o)
{
// The total size of the cavity
size_t cavitySize = cav.size();
// The number of irreps in the group
int nrBlocks = cav.pointGroup().nrIrrep();
// The size of the irreducible portion of the cavity
int dimBlock = cav.irreducible_size();
// Compute SI, DI and SE, DE on the whole cavity, regardless of symmetry
Eigen::MatrixXd SI = gf_i.singleLayer(cav.elements());
Eigen::MatrixXd DI = gf_i.doubleLayer(cav.elements());
Eigen::MatrixXd SE = gf_o.singleLayer(cav.elements());
Eigen::MatrixXd DE = gf_o.doubleLayer(cav.elements());
// Perform symmetry blocking
// If the group is C1 avoid symmetry blocking, we will just pack the fullPCMMatrix
// into "block diagonal" when all other manipulations are done.
if (cav.pointGroup().nrGenerators() != 0) {
symmetryBlocking(DI, cavitySize, dimBlock, nrBlocks);
symmetryBlocking(SI, cavitySize, dimBlock, nrBlocks);
symmetryBlocking(DE, cavitySize, dimBlock, nrBlocks);
symmetryBlocking(SE, cavitySize, dimBlock, nrBlocks);
}
Eigen::MatrixXd a = cav.elementArea().asDiagonal();
Eigen::MatrixXd aInv = a.inverse();
// 1. Form T
fullPCMMatrix_ = ((2 * M_PI * aInv - DE) * a * SI + SE * a * (2 * M_PI * aInv + DI.adjoint().eval()));
// 2. Invert T using LU decomposition with full pivoting
// This is a rank-revealing LU decomposition, this allows us
// to test if T is invertible before attempting to invert it.
Eigen::FullPivLU<Eigen::MatrixXd> T_LU(fullPCMMatrix_);
if (!(T_LU.isInvertible())) PCMSOLVER_ERROR("T matrix is not invertible!");
fullPCMMatrix_ = T_LU.inverse();
Eigen::FullPivLU<Eigen::MatrixXd> SI_LU(SI);
if (!(SI_LU.isInvertible())) PCMSOLVER_ERROR("SI matrix is not invertible!");
fullPCMMatrix_ *= ((2 * M_PI * aInv - DE) - SE * SI_LU.inverse() * (2 * M_PI * aInv - DI));
fullPCMMatrix_ *= a;
// 5. Symmetrize K := (K + K+)/2
if (hermitivitize_) {
hermitivitize(fullPCMMatrix_);
}
// Pack into a block diagonal matrix
// For the moment just packs into a std::vector<Eigen::MatrixXd>
symmetryPacking(blockPCMMatrix_, fullPCMMatrix_, dimBlock, nrBlocks);
std::ofstream matrixOut("PCM_matrix");
matrixOut << "fullPCMMatrix" << std::endl;
matrixOut << fullPCMMatrix_ << std::endl;
for (int i = 0; i < nrBlocks; ++i) {
matrixOut << "Block number " << i << std::endl;
matrixOut << blockPCMMatrix_[i] << std::endl;
}
built_ = true;
}
void IEFSolver::buildIsotropicMatrix(const Cavity & cav, const IGreensFunction & gf_i, const IGreensFunction & gf_o)
{
// The total size of the cavity
size_t cavitySize = cav.size();
// The number of irreps in the group
int nrBlocks = cav.pointGroup().nrIrrep();
// The size of the irreducible portion of the cavity
int dimBlock = cav.irreducible_size();
// Compute SI and DI on the whole cavity, regardless of symmetry
Eigen::MatrixXd SI = gf_i.singleLayer(cav.elements());
Eigen::MatrixXd DI = gf_i.doubleLayer(cav.elements());
// Perform symmetry blocking
// If the group is C1 avoid symmetry blocking, we will just pack the fullPCMMatrix
// into "block diagonal" when all other manipulations are done.
if (cav.pointGroup().nrGenerators() != 0) {
symmetryBlocking(DI, cavitySize, dimBlock, nrBlocks);
symmetryBlocking(SI, cavitySize, dimBlock, nrBlocks);
}
Eigen::MatrixXd a = cav.elementArea().asDiagonal();
Eigen::MatrixXd aInv = Eigen::MatrixXd::Zero(cavitySize, cavitySize);
aInv = a.inverse();
// Tq = -Rv -> q = -(T^-1 * R)v = -Kv
// T = (2 * M_PI * fact * aInv - DI) * a * SI; R = (2 * M_PI * aInv - DI)
// fullPCMMatrix_ = K = T^-1 * R * a
// 1. Form T
double epsilon = profiles::epsilon(gf_o.permittivity());
double fact = (epsilon + 1.0)/(epsilon - 1.0);
fullPCMMatrix_ = (2 * M_PI * fact * aInv - DI) * a * SI;
// 2. Invert T using LU decomposition with full pivoting
// This is a rank-revealing LU decomposition, this allows us
// to test if T is invertible before attempting to invert it.
Eigen::FullPivLU<Eigen::MatrixXd> T_LU(fullPCMMatrix_);
if (!(T_LU.isInvertible()))
PCMSOLVER_ERROR("T matrix is not invertible!");
fullPCMMatrix_ = T_LU.inverse();
// 3. Multiply T^-1 and R
fullPCMMatrix_ *= (2 * M_PI * aInv - DI);
// 4. Multiply by a
fullPCMMatrix_ *= a;
// 5. Symmetrize K := (K + K+)/2
if (hermitivitize_) {
hermitivitize(fullPCMMatrix_);
}
// Pack into a block diagonal matrix
// For the moment just packs into a std::vector<Eigen::MatrixXd>
symmetryPacking(blockPCMMatrix_, fullPCMMatrix_, dimBlock, nrBlocks);
std::ofstream matrixOut("PCM_matrix");
matrixOut << "fullPCMMatrix" << std::endl;
matrixOut << fullPCMMatrix_ << std::endl;
for (int i = 0; i < nrBlocks; ++i) {
matrixOut << "Block number " << i << std::endl;
matrixOut << blockPCMMatrix_[i] << std::endl;
}
built_ = true;
}
/*! \brief Builds the **isotropic** IEFPCM matrix
* \param[in] cav the discretized cavity
* \param[in] gf_i Green's function inside the cavity
* \param[in] epsilon permittivity outside the cavity
* \return the \f$ \mathbf{K} = \mathbf{T}^{-1}\mathbf{R}\mathbf{A} \f$ matrix
*
* This function calculates the PCM matrix. We use the following definitions:
* \f[
* \begin{align}
* \mathbf{T} &=
* \left(2\pi\frac{\varepsilon+1}{\varepsilon-1}\mathbf{I} - \mathbf{D}_\mathrm{i}\mathbf{A}\right)\mathbf{S}_\mathrm{i} \\
* \mathbf{R} &=
* \left(2\pi\mathbf{A}^{-1} - \mathbf{D}_\mathrm{i}\right)
* \end{align}
* \f]
* The matrix is not symmetrized and is not symmetry packed.
*/
inline Eigen::MatrixXd isotropicIEFMatrix(const Cavity & cav, const IGreensFunction & gf_i, double epsilon)
{
// The total size of the cavity
size_t cavitySize = cav.size();
// The number of irreps in the group
int nrBlocks = cav.pointGroup().nrIrrep();
// The size of the irreducible portion of the cavity
int dimBlock = cav.irreducible_size();
// Compute SI and DI on the whole cavity, regardless of symmetry
TIMER_ON("Computing SI");
Eigen::MatrixXd SI = gf_i.singleLayer(cav.elements());
TIMER_OFF("Computing SI");
TIMER_ON("Computing DI");
Eigen::MatrixXd DI = gf_i.doubleLayer(cav.elements());
TIMER_OFF("Computing DI");
// Perform symmetry blocking
// If the group is C1 avoid symmetry blocking, we will just pack the fullPCMMatrix
// into "block diagonal" when all other manipulations are done.
if (cav.pointGroup().nrGenerators() != 0) {
TIMER_ON("Symmetry blocking");
symmetryBlocking(DI, cavitySize, dimBlock, nrBlocks);
symmetryBlocking(SI, cavitySize, dimBlock, nrBlocks);
TIMER_OFF("Symmetry blocking");
}
Eigen::MatrixXd a = cav.elementArea().asDiagonal();
Eigen::MatrixXd Id = Eigen::MatrixXd::Identity(cavitySize, cavitySize);
// Tq = -Rv -> q = -(T^-1 * R)v = -Kv
// T = (2 * M_PI * fact * aInv - DI) * a * SI; R = (2 * M_PI * aInv - DI)
// fullPCMMatrix_ = K = T^-1 * R * a
// 1. Form T
double fact = (epsilon + 1.0)/(epsilon - 1.0);
TIMER_ON("Assemble T matrix");
Eigen::MatrixXd fullPCMMatrix = (2 * M_PI * fact * Id - DI * a) * SI;
TIMER_OFF("Assemble T matrix");
// 2. Invert T using LU decomposition with full pivoting
// This is a rank-revealing LU decomposition, this allows us
// to test if T is invertible before attempting to invert it.
TIMER_ON("Invert T matrix");
Eigen::FullPivLU<Eigen::MatrixXd> T_LU(fullPCMMatrix);
if (!(T_LU.isInvertible()))
PCMSOLVER_ERROR("T matrix is not invertible!", BOOST_CURRENT_FUNCTION);
fullPCMMatrix = T_LU.inverse();
TIMER_OFF("Invert T matrix");
// 3. Multiply T^-1 and R
TIMER_ON("Assemble T^-1R matrix");
fullPCMMatrix *= (2 * M_PI * Id - DI * a);
TIMER_OFF("Assemble T^-1R matrix");
return fullPCMMatrix;
}
void CPCMSolver::buildSystemMatrix_impl(const Cavity & cavity, const IGreensFunction & gf_i, const IGreensFunction & gf_o)
{
if (!isotropic_) PCMSOLVER_ERROR("C-PCM is defined only for isotropic environments!");
// The total size of the cavity
size_t cavitySize = cavity.size();
// The number of irreps in the group
int nrBlocks = cavity.pointGroup().nrIrrep();
// The size of the irreducible portion of the cavity
int dimBlock = cavity.irreducible_size();
// Compute SI on the whole cavity, regardless of symmetry
Eigen::MatrixXd SI = gf_i.singleLayer(cavity.elements());
// Perform symmetry blocking only for the SI matrix as the DI matrix is not used.
// If the group is C1 avoid symmetry blocking, we will just pack the fullPCMMatrix
// into "block diagonal" when all other manipulations are done.
if (cavity.pointGroup().nrGenerators() != 0) {
symmetryBlocking(SI, cavitySize, dimBlock, nrBlocks);
}
double epsilon = profiles::epsilon(gf_o.permittivity());
double fact = (epsilon - 1.0)/(epsilon + correction_);
// Invert SI using LU decomposition with full pivoting
// This is a rank-revealing LU decomposition, this allows us
// to test if SI is invertible before attempting to invert it.
Eigen::FullPivLU<Eigen::MatrixXd> SI_LU(SI);
if (!(SI_LU.isInvertible()))
PCMSOLVER_ERROR("SI matrix is not invertible!");
fullPCMMatrix_ = fact * SI_LU.inverse();
// 5. Symmetrize K := (K + K+)/2
if (hermitivitize_) {
hermitivitize(fullPCMMatrix_);
}
symmetryPacking(blockPCMMatrix_, fullPCMMatrix_, dimBlock, nrBlocks);
built_ = true;
}
