pcmsolver/src/interface/Meddle.cpp at master · PCMSolver/pcmsolver · GitHub

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* PCMSolver, an API for the Polarizable Continuum Model

* This file is part of PCMSolver.

* PCMSolver 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.

* PCMSolver 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 PCMSolver. If not, see <http://www.gnu.org/licenses/>.

* For information on the complete list of contributors to the

* PCMSolver API, see: <http://pcmsolver.readthedocs.io/>

#include "Meddle.hpp"

#include "PCMInput.h"

#include "pcmsolver.h"

#include <string>

#include <vector>

#include "Config.hpp"

#include <Eigen/Core>

#include "bi_operators/BIOperatorData.hpp"

#include "bi_operators/BoundaryIntegralOperator.hpp"

#include "cavity/Cavity.hpp"

#include "cavity/CavityData.hpp"

#include "green/Green.hpp"

#include "green/GreenData.hpp"

#include "mmfq/FQOhno.hpp"

#include "solver/Solver.hpp"

#include "solver/SolverData.hpp"

#include "Citation.hpp"

#include "VersionInfo.hpp"

#include "utils/Atom.hpp"

#include "utils/Factory.hpp"

#include "utils/Solvent.hpp"

#include "utils/Sphere.hpp"

#include "utils/cnpy.hpp"

#ifndef AS_TYPE

#define AS_TYPE(Type, Obj) reinterpret_cast<Type *>(Obj)

#endif

#ifndef AS_CTYPE

#define AS_CTYPE(Type, Obj) reinterpret_cast<const Type *>(Obj)

#endif

pcmsolver_context_t * pcmsolver_new(pcmsolver_reader_t input_reading,

int nr_nuclei,

double charges[],

double coordinates[],

int symmetry_info[],

PCMInput * host_input,

HostWriter writer) {

return pcmsolver_new_v1112(input_reading,

nr_nuclei,

charges,

coordinates,

symmetry_info,

"@pcmsolver.inp",

host_input,

writer);

}

pcmsolver_context_t * pcmsolver_new_v1112(pcmsolver_reader_t input_reading,

int nr_nuclei,

double charges[],

double coordinates[],

int symmetry_info[],

const char * parsed_fname,

PCMInput * host_input,

HostWriter writer) {

if (input_reading) {

// Use host_input data structured as passed from host

return AS_TYPE(

pcmsolver_context_t,

new pcm::Meddle(

nr_nuclei, charges, coordinates, symmetry_info, *host_input, writer));

} else {

// Use the parsed PCMSolver input file parsed_fname, as found on disk

return AS_TYPE(

pcmsolver_context_t,

new pcm::Meddle(

nr_nuclei, charges, coordinates, symmetry_info, writer, parsed_fname));

}

pcmsolver_context_t * pcmsolver_new_read_host(int nr_nuclei,

double charges[],

double coordinates[],

int symmetry_info[],

HostWriter writer) {

return AS_TYPE(

pcmsolver_context_t,

new pcm::Meddle(nr_nuclei, charges, coordinates, symmetry_info, writer));

}

PCMInput pcmsolver_default_input() {

PCMInput host_input;

// These parameters would be set by the host input reading

// Length and area parameters are all assumed to be in Angstrom,

// the module will convert to Bohr internally

strcpy(host_input.cavity_type, "gepol");

host_input.patch_level = 2;

host_input.coarsity = 0.5;

host_input.area = 0.2;

host_input.min_distance = 0.1;

host_input.der_order = 4;

host_input.scaling = true;

strcpy(host_input.radii_set, "bondi");

strcpy(host_input.restart_name, "cavity.npz");

host_input.min_radius = 100.0;

strcpy(host_input.solver_type, "iefpcm");

strcpy(host_input.solvent, "water");

strcpy(host_input.equation_type, "secondkind");

host_input.correction = 0.0;

host_input.probe_radius = 1.0;

strcpy(host_input.inside_type, "vacuum");

host_input.outside_epsilon = 1.0;

strcpy(host_input.outside_type, "uniformdielectric");

return host_input;

}

namespace pcm {

void Meddle::CTORBody() {

// Write PCMSolver output header

infoStream_ << "~~~~~~~~~~ PCMSolver ~~~~~~~~~~\n";

infoStream_ << "Using CODATA " << input_.CODATAyear() << " set of constants."

<< std::endl;

infoStream_ << "Input parsing done " << input_.providedBy() << std::endl;

if (input_.isFQ()) { /* MMFQ calculation */

hasFQ_ = true;

TIMER_ON("Meddle::initMMFQ");

initMMFQ();

TIMER_OFF("Meddle::initMMFQ");

} else { /* Pure PCM calculation */

TIMER_ON("Meddle::initCavity");

initCavity();

TIMER_OFF("Meddle::initCavity");

TIMER_ON("Meddle::initStaticSolver");

initStaticSolver();

TIMER_OFF("Meddle::initStaticSolver");

if (input_.isDynamic()) {

TIMER_ON("Meddle::initDynamicSolver");

initDynamicSolver();

TIMER_OFF("Meddle::initDynamicSolver");

}

Meddle::Meddle(const Input & input, const HostWriter & write)

: hostWriter_(write),

input_(input),

host_input_(pcmsolver_default_input()),

cavity_(nullptr),

K_0_(nullptr),

K_d_(nullptr),

FQ_(nullptr),

hasDynamic_(false),

hasFQ_(false) {

input_.initMolecule();

CTORBody();

}

Meddle::Meddle(const std::string & inputFileName, const HostWriter & write)

: hostWriter_(write),

input_(Input(inputFileName)),

host_input_(pcmsolver_default_input()),

cavity_(nullptr),

K_0_(nullptr),

K_d_(nullptr),

FQ_(nullptr),

hasDynamic_(false),

hasFQ_(false) {

input_.initMolecule();

CTORBody();

}

Meddle::Meddle(int nr_nuclei,

double charges[],

double coordinates[],

int symmetry_info[],

const HostWriter & write,

const std::string & inputFileName)

: hostWriter_(write),

input_(Input(inputFileName.empty() ? "@pcmsolver.inp" : inputFileName)),

host_input_(pcmsolver_default_input()),

cavity_(nullptr),

K_0_(nullptr),

K_d_(nullptr),

FQ_(nullptr),

hasDynamic_(false),

hasFQ_(false) {

TIMER_ON("Meddle::initInput");

initInput(nr_nuclei, charges, coordinates, symmetry_info);

TIMER_OFF("Meddle::initInput");

CTORBody();

}

Meddle::Meddle(int nr_nuclei,

double charges[],

double coordinates[],

int symmetry_info[],

const PCMInput & host_input,

const HostWriter & write)

: hostWriter_(write),

input_(Input(host_input)),

host_input_(host_input),

cavity_(nullptr),

K_0_(nullptr),

K_d_(nullptr),

FQ_(nullptr),

hasDynamic_(false),

hasFQ_(false) {

TIMER_ON("Meddle::initInput");

initInput(nr_nuclei, charges, coordinates, symmetry_info);

TIMER_OFF("Meddle::initInput");

CTORBody();

}

Meddle::Meddle(int nr_nuclei,

double charges[],

double coordinates[],

int symmetry_info[],

const HostWriter & write)

: hostWriter_(write),

input_(Input(pcmsolver_default_input())),

host_input_(pcmsolver_default_input()),

cavity_(nullptr),

K_0_(nullptr),

K_d_(nullptr),

FQ_(nullptr),

hasDynamic_(false),

hasFQ_(false) {

// This one does a deferred initialization:

// The CTORBody function is not called at this point, but during refresh

TIMER_ON("Meddle::initInput");

initInput(nr_nuclei, charges, coordinates, symmetry_info, true);

TIMER_OFF("Meddle::initInput");

}

} // namespace pcm

void pcmsolver_delete(pcmsolver_context_t * context) {

if (!context)

return;

delete AS_TYPE(pcm::Meddle, context);

}

pcm::Meddle::~Meddle() {

if (hasFQ_) { /* MMFQ calculation */

delete FQ_;

} else { /* Pure PCM calculation */

delete cavity_;

delete K_0_;

if (hasDynamic_)

delete K_d_;

}

PCMSolverIndex pcmsolver_get_cavity_size(pcmsolver_context_t * context) {

return (AS_CTYPE(pcm::Meddle, context)->getCavitySize());

}

PCMSolverIndex pcm::Meddle::getCavitySize() const { return std::get<0>(size_); }

PCMSolverIndex pcmsolver_get_irreducible_cavity_size(pcmsolver_context_t * context) {

return (AS_CTYPE(pcm::Meddle, context)->getIrreducibleCavitySize());

}

PCMSolverIndex pcm::Meddle::getIrreducibleCavitySize() const {

return std::get<1>(size_);

}

void pcmsolver_get_centers(pcmsolver_context_t * context, double centers[]) {

TIMER_ON("pcmsolver_get_centers");

AS_CTYPE(pcm::Meddle, context)->getCenters(centers);

TIMER_OFF("pcmsolver_get_centers");

}

void pcm::Meddle::getCenters(double centers[]) const {

TIMER_ON("Meddle::getCenters");

if (hasFQ_) { /* MMFQ calculation */

PCMSolverIndex size = input_.fragments().sites.cols();

Eigen::Map<Eigen::Matrix3Xd>(centers, 3, size) = input_.fragments().sites;

} else { /* Pure PCM calculation */

Eigen::Map<Eigen::Matrix3Xd>(centers, 3, cavity_->size()) =

cavity_->elementCenter();

}

TIMER_OFF("Meddle::getCenters");

}

void pcmsolver_get_center(pcmsolver_context_t * context, int its, double center[]) {

AS_CTYPE(pcm::Meddle, context)->getCenter(its, center);

}

void pcm::Meddle::getCenter(int its, double center[]) const {

if (hasFQ_) { /* MMFQ calculation */

Eigen::Map<Eigen::Matrix3Xd>(center, 3, 1) =

input_.fragments().sites.col(its - 1);

} else { /* Pure PCM calculation */

Eigen::Map<Eigen::Vector3d>(center, 3, 1) = cavity_->elementCenter(its - 1);

}

void pcmsolver_get_areas(pcmsolver_context_t * context, double areas[]) {

AS_CTYPE(pcm::Meddle, context)->getAreas(areas);

}

void pcm::Meddle::getAreas(double areas[]) const {

Eigen::Map<Eigen::VectorXd>(areas, cavity_->size(), 1) = cavity_->elementArea();

}

double pcmsolver_compute_polarization_energy(pcmsolver_context_t * context,

const char * mep_name,

const char * asc_name) {

return (

AS_CTYPE(pcm::Meddle, context)

->computePolarizationEnergy(std::string(mep_name), std::string(asc_name)));

}

double pcm::Meddle::computePolarizationEnergy(const std::string & mep_name,

const std::string & asc_name) const {

double energy = 0.0;

if (hasFQ_) { /* MMFQ calculation */

// Dot product of MEP + Electronegativities times Fluctuating charges

energy = (functions_.at(mep_name) + input_.fragments().chi)

.dot(functions_.at(asc_name));

if (input_.isNonPolarizable()) { /* HACK Nonpolarizable doesn't need 1/2 */

energy *= 2.0;

}

} else { /* Pure PCM calculation */

// Dot product of MEP and ASC surface function

energy = functions_.at(mep_name).dot(functions_.at(asc_name));

}

return (energy / 2.0);

}

double pcmsolver_get_asc_dipole(pcmsolver_context_t * context,

const char * asc_name,

double dipole[]) {

return (

AS_CTYPE(pcm::Meddle, context)->getASCDipole(std::string(asc_name), dipole));

}

double pcm::Meddle::getASCDipole(const std::string & asc_name,

double dipole[]) const {

Eigen::Vector3d asc_dipole = cavity_->elementCenter() * functions_.at(asc_name);

// Bind to host-allocated array

Eigen::Map<Eigen::Vector3d>(dipole, 3, 1) = asc_dipole;

return asc_dipole.norm();

}

void pcmsolver_compute_asc(pcmsolver_context_t * context,

const char * mep_name,

const char * asc_name,

int irrep) {

TIMER_ON("pcmsolver_compute_asc");

AS_TYPE(pcm::Meddle, context)

->computeASC(std::string(mep_name), std::string(asc_name), irrep);

TIMER_OFF("pcmsolver_compute_asc");

}

void pcm::Meddle::computeASC(const std::string & mep_name,

const std::string & asc_name,

int irrep) {

// Get the proper iterators

SurfaceFunctionMapConstIter iter_pot = functions_.find(mep_name);

Eigen::VectorXd asc = Eigen::VectorXd::Zero(iter_pot->second.size());

if (hasFQ_) { /* MMFQ calculation */

if (input_.isNonPolarizable()) { /* HACK We store point charges in the eta vector

asc = input_.fragments().eta;

} else {

asc = FQ_->computeCharge(iter_pot->second);

}

} else { /* Pure PCM calculation */

asc = K_0_->computeCharge(iter_pot->second, irrep);

// Renormalize

asc /= double(cavity_->pointGroup().nrIrrep());

}

// Insert it into the map

if (functions_.count(asc_name) == 1) { // Key in map already

functions_[asc_name] = asc;

} else { // Create key-value pair

functions_.insert(std::make_pair(asc_name, asc));

}

void pcmsolver_compute_response_asc(pcmsolver_context_t * context,

const char * mep_name,

const char * asc_name,

int irrep) {

TIMER_ON("pcmsolver_compute_response_asc");

AS_TYPE(pcm::Meddle, context)

->computeResponseASC(std::string(mep_name), std::string(asc_name), irrep);

TIMER_OFF("pcmsolver_compute_response_asc");

}

void pcm::Meddle::computeResponseASC(const std::string & mep_name,

const std::string & asc_name,

int irrep) {

// Get the proper iterators

SurfaceFunctionMapConstIter iter_pot = functions_.find(mep_name);

Eigen::VectorXd asc = Eigen::VectorXd::Zero(iter_pot->second.size());

if (hasFQ_) { /* MMFQ calculation */

if (!input_.isNonPolarizable()) { /* HACK Can we do it more cleanly/clearly? */

// Do NOT add classical (electronegativities) contributions to RHS

asc = FQ_->computeCharge(iter_pot->second, false);

}

} else { /* Pure PCM calculation */

if (hasDynamic_) {

asc = K_d_->computeCharge(iter_pot->second, irrep);

} else {

asc = K_0_->computeCharge(iter_pot->second, irrep);

}

// Renormalize

asc /= double(cavity_->pointGroup().nrIrrep());

}

if (functions_.count(asc_name) == 1) { // Key in map already

functions_[asc_name] = asc;

} else { // Create key-value pair

functions_.insert(std::make_pair(asc_name, asc));

}

void pcmsolver_get_surface_function(pcmsolver_context_t * context,

PCMSolverIndex size,

double values[],

const char * name) {

TIMER_ON("pcmsolver_get_surface_function");

AS_CTYPE(pcm::Meddle, context)

->getSurfaceFunction(size, values, std::string(name));

TIMER_OFF("pcmsolver_get_surface_function");

}

void pcm::Meddle::getSurfaceFunction(PCMSolverIndex size,

double values[],

const std::string & name) const {

if (std::get<0>(size_) != size)

PCMSOLVER_ERROR("The " + name + " SurfaceFunction is bigger than the cavity!");

SurfaceFunctionMapConstIter iter = functions_.find(name);

if (iter == functions_.end())

PCMSOLVER_ERROR("The " + name + " SurfaceFunction does not exist.");

Eigen::Map<Eigen::VectorXd>(values, size, 1) = iter->second;

}

void pcmsolver_set_surface_function(pcmsolver_context_t * context,

PCMSolverIndex size,

double values[],

const char * name) {

TIMER_ON("pcmsolver_set_surface_function");

AS_TYPE(pcm::Meddle, context)->setSurfaceFunction(size, values, std::string(name));

TIMER_OFF("pcmsolver_set_surface_function");

}

void pcm::Meddle::setSurfaceFunction(PCMSolverIndex size,

double values[],

const std::string & name) {

if (std::get<0>(size_) != size)

PCMSOLVER_ERROR("The " + name + " SurfaceFunction is bigger than the cavity!");

Eigen::VectorXd func = Eigen::Map<Eigen::VectorXd>(values, size, 1);

if (functions_.count(name) == 1) { // Key in map already

functions_[name] = func;

} else {

functions_.insert(std::make_pair(name, func));

}

void pcmsolver_print_surface_function(pcmsolver_context_t * context,

const char * name) {

AS_CTYPE(pcm::Meddle, context)->printSurfaceFunction(std::string(name));

}

void pcm::Meddle::printSurfaceFunction(const std::string & name) const {

if (functions_.count(name) == 1) { // Key in map already

std::ostringstream print_sf;

Eigen::IOFormat fmt(Eigen::FullPrecision);

print_sf << functions_.at(name).format(fmt) << std::endl;

hostWriter_(print_sf);

} else {

PCMSOLVER_ERROR("You are trying to print a nonexistent SurfaceFunction!");

}

void pcmsolver_save_surface_functions(pcmsolver_context_t * context) {

AS_CTYPE(pcm::Meddle, context)->saveSurfaceFunctions();

}

void pcm::Meddle::saveSurfaceFunctions() const {

hostWriter_("\nDumping surface functions to .npy files");

for (auto sf_pair : functions_) {

cnpy::custom::npy_save(sf_pair.first + ".npy", sf_pair.second);

}

void pcmsolver_save_surface_function(pcmsolver_context_t * context,

const char * name) {

AS_CTYPE(pcm::Meddle, context)->saveSurfaceFunction(std::string(name));

}

void pcm::Meddle::saveSurfaceFunction(const std::string & name) const {

SurfaceFunctionMapConstIter it = functions_.find(name);

cnpy::custom::npy_save(name + ".npy", it->second);

}

void pcmsolver_load_surface_function(pcmsolver_context_t * context,

const char * name) {

AS_TYPE(pcm::Meddle, context)->loadSurfaceFunction(std::string(name));

}

void pcm::Meddle::loadSurfaceFunction(const std::string & name) {

hostWriter_("\nLoading surface function " + name + " from .npy file");

Eigen::VectorXd values = cnpy::custom::npy_load<double>(name + ".npy");

if (values.size() != std::get<0>(size_))

PCMSOLVER_ERROR("The loaded " + name +

" surface function is bigger than the cavity!");

// Append to global map

if (functions_.count(name) == 1) { // Key in map already

functions_[name] = values;

} else {

functions_.insert(std::make_pair(name, values));

}

void pcmsolver_write_timings(pcmsolver_context_t * context) {

AS_CTYPE(pcm::Meddle, context)->writeTimings();

}

void pcm::Meddle::writeTimings() const { TIMER_DONE("pcmsolver.timer.dat"); }

void pcmsolver_refresh(pcmsolver_context_t * context) {

AS_TYPE(pcm::Meddle, context)->refresh();

}

void pcm::Meddle::refresh() {

// Gather info to refresh Molecule

// FIXME I need to refresh it because scaling of radii is done there -.-

Symmetry pg = molecule().pointGroup();

size_t nuclei = molecule().nAtoms();

Eigen::VectorXd chgs = molecule().charges();

Eigen::MatrixXd cnts = molecule().geometry();

// Refresh input_

input_ = Input(host_input_);

// Refresh Molecule

input_.molecule(detail::initMolecule(input_, pg, nuclei, chgs, cnts, false));

CTORBody();

}

void pcmsolver_set_bool_option(pcmsolver_context_t * context,

const char * parameter,

bool value) {

AS_TYPE(pcm::Meddle, context)->setInputOption(std::string(parameter), value);

}

void pcm::Meddle::setInputOption(std::string parameter, bool value) {

detail::PCMInputFields p = detail::string_to_enum(parameter);

switch (p) {

case detail::PCMInputFields::scaling:

host_input_.scaling = value;

break;

default:

std::ostringstream errmsg;

errmsg << "Unknown parameter " << parameter << std::endl;

errmsg << " See http://pcmsolver.readthedocs.org/en/latest/users/input.html"

<< std::endl;

PCMSOLVER_ERROR(errmsg.str());

}

void pcmsolver_set_int_option(pcmsolver_context_t * context,

const char * parameter,

int value) {

AS_TYPE(pcm::Meddle, context)->setInputOption(std::string(parameter), value);

}

void pcm::Meddle::setInputOption(std::string parameter, int value) {

detail::PCMInputFields p = detail::string_to_enum(parameter);

switch (p) {

case detail::PCMInputFields::patch_level:

host_input_.patch_level = value;

break;

case detail::PCMInputFields::der_order:

host_input_.der_order = value;

break;

default:

std::ostringstream errmsg;

errmsg << "Unknown parameter " << parameter << std::endl;

errmsg << " See http://pcmsolver.readthedocs.org/en/latest/users/input.html"

<< std::endl;

PCMSOLVER_ERROR(errmsg.str());

}

void pcmsolver_set_double_option(pcmsolver_context_t * context,

const char * parameter,

double value) {

AS_TYPE(pcm::Meddle, context)->setInputOption(std::string(parameter), value);

}

void pcm::Meddle::setInputOption(std::string parameter, double value) {

detail::PCMInputFields p = detail::string_to_enum(parameter);

switch (p) {

case detail::PCMInputFields::coarsity:

host_input_.coarsity = value;

break;

case detail::PCMInputFields::area:

host_input_.area = value;

break;

case detail::PCMInputFields::min_distance:

host_input_.min_distance = value;

break;

case detail::PCMInputFields::min_radius:

host_input_.min_radius = value;

break;

case detail::PCMInputFields::correction:

host_input_.correction = value;

break;

case detail::PCMInputFields::probe_radius:

host_input_.probe_radius = value;

break;

case detail::PCMInputFields::outside_epsilon:

host_input_.outside_epsilon = value;

break;

default:

std::ostringstream errmsg;

errmsg << "Unknown parameter " << parameter << std::endl;

errmsg << " See http://pcmsolver.readthedocs.org/en/latest/users/input.html"

<< std::endl;

PCMSOLVER_ERROR(errmsg.str());

}

void pcmsolver_set_string_option(pcmsolver_context_t * context,

const char * parameter,

const char * value) {

AS_TYPE(pcm::Meddle, context)

->setInputOption(std::string(parameter), std::string(value));

}

void pcm::Meddle::setInputOption(std::string parameter, std::string value) {

detail::PCMInputFields p = detail::string_to_enum(parameter);

switch (p) {

case detail::PCMInputFields::cavity_type:

strcpy(host_input_.cavity_type, value.c_str());

break;

case detail::PCMInputFields::radii_set:

strcpy(host_input_.radii_set, value.c_str());

break;

case detail::PCMInputFields::restart_name:

strcpy(host_input_.restart_name, value.c_str());

break;

case detail::PCMInputFields::solver_type:

strcpy(host_input_.solver_type, value.c_str());

break;

case detail::PCMInputFields::solvent:

strcpy(host_input_.solvent, value.c_str());

break;

case detail::PCMInputFields::equation_type:

strcpy(host_input_.equation_type, value.c_str());

break;

case detail::PCMInputFields::inside_type:

strcpy(host_input_.inside_type, value.c_str());

break;

case detail::PCMInputFields::outside_type:

strcpy(host_input_.outside_type, value.c_str());

break;

default:

std::ostringstream errmsg;

errmsg << "Unknown parameter " << parameter << std::endl;

errmsg << " See http://pcmsolver.readthedocs.org/en/latest/users/input.html"

<< std::endl;

PCMSOLVER_ERROR(errmsg.str());

}

void pcmsolver_print(pcmsolver_context_t * context) {

AS_CTYPE(pcm::Meddle, context)->printInfo();

}

void pcm::Meddle::printInfo() const { hostWriter_(infoStream_); }

void pcmsolver_citation(HostWriter writer) { writer(citation_message().c_str()); }

std::string pcm::Meddle::printCitation() const { return citation_message(); }

bool pcmsolver_is_compatible_library(void) {

unsigned int major = (pcm::pcmsolver_get_version() >> 16);

return (major == PROJECT_VERSION_MAJOR);

}

unsigned int pcm::pcmsolver_get_version(void) { return PCMSOLVER_VERSION; }

namespace pcm {

Molecule Meddle::molecule() const { return input_.molecule(); }

Eigen::Matrix3Xd Meddle::getCenters() const { return cavity_->elementCenter(); }

void Meddle::initInput(int nr_nuclei,

double charges[],

double coordinates[],

int symmetry_info[],

bool deferred_init) {

// Position and charges of atomic centers

Eigen::VectorXd chg = Eigen::Map<Eigen::VectorXd>(charges, nr_nuclei, 1);

Eigen::Matrix3Xd centers = Eigen::Map<Eigen::Matrix3Xd>(coordinates, 3, nr_nuclei);

if (input_.mode() != "EXPLICIT") {

auto pg = Symmetry(

symmetry_info[0], symmetry_info[1], symmetry_info[2], symmetry_info[3]);

input_.molecule(

detail::initMolecule(input_, pg, nr_nuclei, chg, centers, deferred_init));

}

void Meddle::initCavity() {

cavity_ = cavity::bootstrapFactory().create(input_.cavityParams().cavityType,

input_.cavityParams());

size_ = std::make_tuple(cavity_->size(), cavity_->irreducible_size());

cavity_->saveCavity();

infoStream_ << "========== Cavity " << std::endl;

infoStream_ << "Atomic radii set: " << input_.radiiSetName() << std::endl;

infoStream_ << *cavity_;

}

void Meddle::initStaticSolver() {

IGreensFunction * gf_i = green::bootstrapFactory().create(

input_.insideGreenParams().greensFunctionType, input_.insideGreenParams());

IGreensFunction * gf_o = green::bootstrapFactory().create(

input_.outsideStaticGreenParams().greensFunctionType,

input_.outsideStaticGreenParams());

K_0_ = solver::bootstrapFactory().create(input_.solverParams().solverType,

input_.solverParams());

IBoundaryIntegralOperator * biop = bi_operators::bootstrapFactory().create(

input_.integratorParams().integratorType, input_.integratorParams());

K_0_->buildSystemMatrix(*cavity_, *gf_i, *gf_o, *biop);

delete biop;

// Perform Gauss' theorem check for nuclear charges

if (!hasFQ_)

GaussCheck();

infoStream_ << "========== Static solver " << std::endl;

infoStream_ << *K_0_ << std::endl;

mediumInfo(gf_i, gf_o);

delete gf_o;

delete gf_i;

}

void Meddle::initDynamicSolver() {

IGreensFunction * gf_i = green::bootstrapFactory().create(

input_.insideGreenParams().greensFunctionType, input_.insideGreenParams());

IGreensFunction * gf_o = green::bootstrapFactory().create(

input_.outsideDynamicGreenParams().greensFunctionType,

input_.outsideDynamicGreenParams());

K_d_ = solver::bootstrapFactory().create(input_.solverParams().solverType,

input_.solverParams());

IBoundaryIntegralOperator * biop = bi_operators::bootstrapFactory().create(

input_.integratorParams().integratorType, input_.integratorParams());

K_d_->buildSystemMatrix(*cavity_, *gf_i, *gf_o, *biop);

hasDynamic_ = true;

delete biop;

infoStream_ << "========== Dynamic solver " << std::endl;

infoStream_ << *K_d_ << std::endl;

mediumInfo(gf_i, gf_o);

delete gf_o;

delete gf_i;

}

void Meddle::initMMFQ() {

FQ_ = new mmfq::FQOhno(input_.fragments(), input_.isNonPolarizable());

size_ = std::make_tuple(input_.fragments().sites.cols(),

input_.fragments().sites.cols());

hasFQ_ = true;

infoStream_ << "========== MMFQ solver " << std::endl;

infoStream_ << *FQ_ << std::endl;

}

void Meddle::mediumInfo(IGreensFunction * gf_i, IGreensFunction * gf_o) {

using utils::Solvent;

infoStream_ << "============ Medium " << std::endl;

if (input_.fromSolvent()) {

infoStream_ << "Medium initialized from solvent built-in data." << std::endl;

Solvent solvent = input_.solvent();

infoStream_ << solvent << std::endl;

}

std::stringstream tmp;

tmp << ".... Inside " << std::endl;

tmp << *gf_i << std::endl;

tmp << ".... Outside " << std::endl;

tmp << *gf_o;

infoStream_ << tmp.str() << std::endl;

}

void Meddle::GaussCheck() const {

Eigen::VectorXd nuclear_mep = computeMEP(input_.molecule(), cavity_->elements());

Eigen::VectorXd nuclear_asc = K_0_->computeCharge(nuclear_mep);

double total_nuclear_asc = nuclear_asc.sum() * cavity_->pointGroup().nrIrrep();

double gauss_nuclear_asc = GaussEstimate(input_.molecule().charges(),

input_.outsideStaticGreenParams().epsilon,

input_.correction());

double abs_rel_diff =

std::abs((total_nuclear_asc - gauss_nuclear_asc) / gauss_nuclear_asc);

std::stringstream tmp;

if (!utils::isZero(abs_rel_diff, 1.0e-2)) {

std::ostringstream errmsg;

errmsg

<< "Absolute value of the relative difference between the Gauss' theorem ("

<< gauss_nuclear_asc << ") ";

errmsg << "and computed (" << total_nuclear_asc << ") values ";

errmsg << "of the total nuclear ASC higher than threshold (" << abs_rel_diff

<< ")." << std::endl;

errmsg << "Consider changing the average area of the cavity finite elements."

<< std::endl;

errmsg

<< "Please report this issue: https://github.com/PCMSolver/pcmsolver/issues"

<< std::endl;

PCMSOLVER_ERROR(errmsg.str());

}

namespace detail {

Molecule initMolecule(const Input & inp,

const Symmetry & pg,

int nuclei,

const Eigen::VectorXd & charges,

const Eigen::Matrix3Xd & centers,

bool deferred_init) {

bool scaling = inp.scaling();

std::string set = inp.radiiSet();

std::vector<Atom> radiiSet;

std::vector<Atom> atoms;

// FIXME Code duplication in function initMolecule in interface/Input.cpp

tie(ignore, radiiSet) = utils::bootstrapRadiiSet().create(set);

std::vector<Sphere> spheres;

atoms.reserve(nuclei);

spheres.reserve(nuclei);

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;

// 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));

}

Eigen::VectorXd masses = Eigen::VectorXd::Zero(nuclei);

for (int i = 0; i < masses.size(); ++i) {

masses(i) = atoms[i].mass;

}

// Based on the creation mode (Implicit or Atoms)

// the spheres list might need postprocessing

if (inp.mode() == "ATOMS") {

initSpheresAtoms(inp, centers, spheres);

}

// OK, now get molecule

Molecule molecule(nuclei, charges, masses, centers, atoms, spheres, pg);

// 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() && !deferred_init) {

std::ostringstream errmsg;

errmsg << "In the molecule:\n" << molecule << std::endl;

errmsg << "Some atoms do not have a radius attached." << std::endl;

errmsg << "Please specify a radius for all atoms!" << std::endl;

errmsg << " See http://pcmsolver.readthedocs.org/en/latest/users/input.html"

<< std::endl;

PCMSOLVER_ERROR(errmsg.str());

}

return molecule;

}

void initSpheresAtoms(const Input & inp,

const Eigen::Matrix3Xd & sphereCenter_,

std::vector<Sphere> & spheres_) {

// Loop over the atomsInput array to get which atoms will have a user-given radius

for (size_t i = 0; i < inp.atoms().size(); ++i) {

size_t index =

inp.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(sphereCenter_.col(index), inp.radii(i));

}

void print(const PCMInput & inp) {

std::cout << "cavity type " << std::string(inp.cavity_type) << std::endl;

std::cout << "patch level " << inp.patch_level << std::endl;

std::cout << "coarsity " << inp.coarsity << std::endl;

std::cout << "area " << inp.area << std::endl;

std::cout << "min distance " << inp.min_distance << std::endl;

std::cout << "der order " << inp.der_order << std::endl;

std::cout << "scaling " << inp.scaling << std::endl;

std::cout << "radii set " << std::string(inp.radii_set) << std::endl;

std::cout << "restart name " << std::string(inp.restart_name) << std::endl;

std::cout << "min radius " << inp.min_radius << std::endl;

std::cout << "solver type " << std::string(inp.solver_type) << std::endl;

std::cout << "solvent " << std::string(inp.solvent) << std::endl;

std::cout << "equation type " << std::string(inp.equation_type) << std::endl;

std::cout << "correction " << inp.correction << std::endl;

std::cout << "probe_radius " << inp.probe_radius << std::endl;

std::cout << "inside type " << std::string(inp.inside_type) << std::endl;

std::cout << "outside type " << std::string(inp.outside_type) << std::endl;

std::cout << "epsilon outside " << inp.outside_epsilon << std::endl;

}

} // namespace detail

} // namespace pcm

pcmsolver/src/interface/Meddle.cpp at master · PCMSolver/pcmsolver · GitHub

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