/*! \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;
}
/*! \brief Retrieve constant iterator from map given object identifier
* \param[in] objID the object's identification string
*/
CallbackConstIter retrieve(const std::string & objID) const {
if (objID.empty())
PCMSOLVER_ERROR("No object identification string provided to the Factory.");
CallbackConstIter i = callbacks_.find(objID);
if (i == callbacks_.end())
PCMSOLVER_ERROR("The unknown object ID " + objID +
" occurred in the Factory.");
return i;
}
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 tangent_and_bitangent(const Eigen::Vector3d & n_,
Eigen::Vector3d & t_, Eigen::Vector3d & b_)
{
double rmin = 0.99;
double n0 = n_(0), n1 = n_(1), n2 = n_(2);
if (std::abs(n0) <= rmin) {
rmin = std::abs(n0);
t_(0) = 0.0;
t_(1) = - n2 / std::sqrt(1.0 - std::pow(n0, 2));
t_(2) = n1 / std::sqrt(1.0 - std::pow(n0, 2));
}
if (std::abs(n1) <= rmin) {
rmin = std::abs(n1);
t_(0) = n2 / std::sqrt(1.0 - std::pow(n1, 2));
t_(1) = 0.0;
t_(2) = - n0 / std::sqrt(1.0 - std::pow(n1, 2));
}
if (std::abs(n2) <= rmin) {
rmin = std::abs(n2);
t_(0) = n1 / std::sqrt(1.0 - std::pow(n2, 2));
t_(1) = -n0 / std::sqrt(1.0 - std::pow(n2, 2));
t_(2) = 0.0;
}
b_ = n_.cross(t_);
// Check that the calculated Frenet-Serret frame is left-handed (levogiro)
// by checking that the determinant of the matrix whose columns are the normal,
// tangent and bitangent vectors has determinant 1 (the system is orthonormal!)
Eigen::Matrix3d M;
M.col(0) = n_;
M.col(1) = t_;
M.col(2) = b_;
if (boost::math::sign(M.determinant()) != 1) {
PCMSOLVER_ERROR("Frenet-Serret local frame is not left-handed!", BOOST_CURRENT_FUNCTION);
}
}
/*! \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 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();
}
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;
}
/*! Constructor
* \param[in] name name for the log file
* The build parameters are logged first
*/
logger(const std::string & name, printLevel print = coarse)
: globalPrintLevel_(print), policy_(new logPolicy)
{
if(!policy_) {
PCMSOLVER_ERROR("LOGGER: Unable to create the logger instance");
}
policy_->open_ostream(name);
// Write the logfile header
logStream_ << "\t\tPCMSolver execution log\n"
<< buildInfo() << "\n\t\tLog started : " << getTime() << std::endl;
}
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;
}
void CPCMSolver::buildSystemMatrix_impl(const ICavity & cavity,
const IGreensFunction & gf_i,
const IGreensFunction & gf_o,
const IBoundaryIntegralOperator & op) {
if (!isotropic_)
PCMSOLVER_ERROR("C-PCM is defined only for isotropic environments!");
TIMER_ON("Computing S");
double epsilon = gf_o.permittivity();
S_ = op.computeS(cavity, gf_i);
S_ /= (epsilon - 1.0) / (epsilon + correction_);
// Get in Hermitian form
if (hermitivitize_)
utils::hermitivitize(S_);
TIMER_OFF("Computing S");
// Symmetry-pack
// 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();
utils::symmetryPacking(blockS_, S_, dimBlock, nrBlocks);
built_ = true;
}
void Input::reader(const std::string & filename) {
Getkw input_ = Getkw(filename, false, true);
units_ = input_.getStr("UNITS");
CODATAyear_ = input_.getInt("CODATA");
initBohrToAngstrom(bohrToAngstrom, CODATAyear_);
const Section & mol = input_.getSect("MOLECULE");
MEPfromMolecule_ = true;
if (mol.isDefined()) {
geometry_ = mol.getDblVec("GEOMETRY");
MEPfromMolecule_ = mol.getBool("MEP");
}
const Section & cavity = input_.getSect("CAVITY");
cavityType_ = cavity.getStr("TYPE");
area_ = cavity.getDbl("AREA");
if (cavityType_ == "RESTART") {
cavFilename_ = cavity.getStr("NPZFILE");
}
scaling_ = cavity.getBool("SCALING");
radiiSet_ = detail::uppercase(cavity.getStr("RADIISET"));
minimalRadius_ = cavity.getDbl("MINRADIUS");
mode_ = detail::uppercase(cavity.getStr("MODE"));
if (mode_ == "EXPLICIT") {
std::vector<double> spheresInput = cavity.getDblVec("SPHERES");
int j = 0;
int nAtoms = int(spheresInput.size() / 4);
for (int i = 0; i < nAtoms; ++i) {
Eigen::Vector3d center;
center = (Eigen::Vector3d() << spheresInput[j],
spheresInput[j + 1],
spheresInput[j + 2])
.finished();
Sphere sph(center, spheresInput[j + 3]);
spheres_.push_back(sph);
j += 4;
}
// Initialize molecule from spheres only when molecule section is absent
if (!mol.isDefined())
molecule_ = Molecule(spheres_);
} else if (mode_ == "ATOMS") {
atoms_ = cavity.getIntVec("ATOMS");
radii_ = cavity.getDblVec("RADII");
}
// Get the contents of the Medium section
const Section & medium = input_.getSect("MEDIUM");
// Get the name of the solvent
std::string name = medium.getStr("SOLVENT");
if (name == "EXPLICIT") {
hasSolvent_ = false;
// Get the probe radius
probeRadius_ = medium.getDbl("PROBERADIUS");
// Get the contents of the Green<inside> section...
const Section & inside = medium.getSect("GREEN<INSIDE>");
// ...and initialize the data members
greenInsideType_ = inside.getStr("TYPE") + "_" + inside.getStr("DER");
epsilonInside_ = inside.getDbl("EPS");
// Get the contents of the Green<outside> section...
const Section & outside = medium.getSect("GREEN<OUTSIDE>");
// ...and initialize the data members
greenOutsideType_ = outside.getStr("TYPE") + "_" + outside.getStr("DER");
epsilonStaticOutside_ = outside.getDbl("EPS");
epsilonDynamicOutside_ = outside.getDbl("EPSDYN");
epsilonStatic1_ = outside.getDbl("EPS1");
epsilonDynamic1_ = outside.getDbl("EPSDYN1");
epsilonStatic2_ = outside.getDbl("EPS2");
epsilonDynamic2_ = outside.getDbl("EPSDYN2");
center_ = outside.getDbl("CENTER");
width_ = outside.getDbl("WIDTH");
origin_ = outside.getDblVec("INTERFACEORIGIN");
if (outside.getStr("TYPE") == "SPHERICALDIFFUSE") {
greenOutsideType_ += "_" + outside.getStr("PROFILE");
}
maxL_ = outside.getInt("MAXL");
} else { // This part must be reviewed!! Some data members are not initialized...
// Just initialize the solvent object in this class
hasSolvent_ = true;
if (solvents().find(name) == solvents().end()) {
PCMSOLVER_ERROR("Solvent " + name + " NOT found!");
} else {
solvent_ = solvents()[name];
}
probeRadius_ = solvent_.probeRadius * angstromToBohr();
// Specification of the solvent by name means isotropic PCM
// We have to initialize the Green's functions data here, Solvent class
// is an helper class and should not be used in the core classes.
greenInsideType_ = "VACUUM_DERIVATIVE";
epsilonInside_ = 1.0;
greenOutsideType_ = "UNIFORMDIELECTRIC_DERIVATIVE";
epsilonStaticOutside_ = solvent_.epsStatic;
epsilonDynamicOutside_ = solvent_.epsDynamic;
}
integratorType_ = medium.getStr("DIAGONALINTEGRATOR");
integratorScaling_ = medium.getDbl("DIAGONALSCALING");
solverType_ = medium.getStr("SOLVERTYPE");
correction_ = medium.getDbl("CORRECTION");
hermitivitize_ = medium.getBool("MATRIXSYMM");
isDynamic_ = medium.getBool("NONEQUILIBRIUM");
const Section & chgdist = input_.getSect("CHARGEDISTRIBUTION");
if (chgdist.isDefined()) {
// Set monopoles
if (chgdist.getKey<std::vector<double> >("MONOPOLES").isDefined()) {
std::vector<double> mono = chgdist.getDblVec("MONOPOLES");
int j = 0;
int n = int(mono.size() / 4);
multipoles_.monopoles = Eigen::VectorXd::Zero(n);
multipoles_.monopolesSites = Eigen::Matrix3Xd::Zero(3, n);
for (int i = 0; i < n; ++i) {
multipoles_.monopolesSites.col(i) =
(Eigen::Vector3d() << mono[j], mono[j + 1], mono[j + 2]).finished();
multipoles_.monopoles(i) = mono[j + 3];
j += 4;
}
}
// Set dipoles
if (chgdist.getKey<std::vector<double> >("DIPOLES").isDefined()) {
std::vector<double> dipo = chgdist.getDblVec("DIPOLES");
int j = 0;
int n = int(dipo.size() / 6);
multipoles_.dipoles = Eigen::Matrix3Xd::Zero(3, n);
multipoles_.dipolesSites = Eigen::Matrix3Xd::Zero(3, n);
for (int i = 0; i < n; ++i) {
multipoles_.dipolesSites.col(i) =
(Eigen::Vector3d() << dipo[j], dipo[j + 1], dipo[j + 2]).finished();
multipoles_.dipoles.col(i) =
(Eigen::Vector3d() << dipo[j + 3], dipo[j + 4], dipo[j + 5]).finished();
j += 6;
}
}
}
providedBy_ = std::string("API-side");
}
void Input::initMolecule() {
// Gather information necessary to build molecule_
// 1. number of atomic centers
int nuclei = int(geometry_.size() / 4);
// 2. position and charges of atomic centers
Eigen::Matrix3Xd centers = Eigen::Matrix3Xd::Zero(3, nuclei);
Eigen::VectorXd charges = Eigen::VectorXd::Zero(nuclei);
int j = 0;
for (int i = 0; i < nuclei; ++i) {
centers.col(i) =
(Eigen::Vector3d() << geometry_[j], geometry_[j + 1], geometry_[j + 2])
.finished();
charges(i) = geometry_[j + 3];
j += 4;
}
// 3. list of atoms and list of spheres
std::vector<Atom> radiiSet;
std::vector<Atom> atoms;
atoms.reserve(nuclei);
// FIXME Code duplication in function initMolecule in interface/Meddle.cpp
tie(radiiSetName_, radiiSet) = utils::bootstrapRadiiSet().create(radiiSet_);
for (int i = 0; i < charges.size(); ++i) {
int index = int(charges(i)) - 1;
atoms.push_back(radiiSet[index]);
if (scaling_)
atoms[i].radiusScaling = 1.2;
}
// Based on the creation mode (Implicit or Atoms)
// the spheres list might need postprocessing
if (mode_ == "IMPLICIT" || mode_ == "ATOMS") {
for (int i = 0; i < charges.size(); ++i) {
// Convert to Bohr and multiply by scaling factor (alpha)
double radius = atoms[i].radius * angstromToBohr() * atoms[i].radiusScaling;
spheres_.push_back(Sphere(centers.col(i), radius));
}
if (mode_ == "ATOMS") {
// Loop over the atomsInput array to get which atoms will have a user-given
// radius
for (size_t i = 0; i < atoms_.size(); ++i) {
int index =
atoms_[i] - 1; // -1 to go from human readable to machine readable
// Put the new Sphere in place of the implicit-generated one
spheres_[index] = Sphere(centers.col(index), radii_[i]);
}
}
}
// 4. masses
Eigen::VectorXd masses = Eigen::VectorXd::Zero(nuclei);
for (int i = 0; i < masses.size(); ++i) {
masses(i) = atoms[i].mass;
}
// 5. molecular point group
// FIXME currently hardcoded to C1
// OK, now get molecule_
molecule_ = Molecule(nuclei, charges, masses, centers, atoms, spheres_);
// Check that all atoms have a radius attached
std::vector<Atom>::const_iterator res =
std::find_if(atoms.begin(), atoms.end(), invalid);
if (res != atoms.end()) {
std::cout << molecule_ << std::endl;
PCMSOLVER_ERROR("Some atoms do not have a radius attached. Please specify a "
"radius for all atoms (see "
"http://pcmsolver.readthedocs.org/en/latest/users/input.html)!");
}
}
Eigen::MatrixXd doubleLayer(const AnisotropicLiquid<DerivativeTraits, PurisimaIntegrator> & /* gf */, const std::vector<Element> & e) const {
PCMSOLVER_ERROR("PurisimaIntegrator::doubleLayer not implemented yet for AnisotropicLiquid", BOOST_CURRENT_FUNCTION);
return Eigen::MatrixXd::Zero(e.size(), e.size());
}
/*! \brief Subscribes object with objID to factory
* \param[in] objID the object's identification string
* \param[in] functor the creation function related to the object type given
*/
void subscribe(const std::string & objID, const CreateObject & functor) {
bool done = this->registerObject(objID, functor);
if (!done)
PCMSOLVER_ERROR("Subscription of object ID " + objID + " to factory failed!");
}
/*! \brief Unsubscribes object with objID from factory
* \param objID the object's identification string
*/
void unsubscribe(const std::string & objID) {
bool done = this->unRegisterObject(objID);
if (!done)
PCMSOLVER_ERROR("Unsubscription of object ID " + objID +
" from factory failed!");
}