#include "TestingMolecules.hpp"
#include "UniformDielectric.hpp"
#include "IEFSolver.hpp"
#include "Symmetry.hpp"
/*! \class IEFSolver
* \test \b NH3GePol tests IEFSolver using ammonia and a GePol cavity
*/
TEST_CASE("Test solver for the IEFPCM with NH3 molecule and a GePol cavity", "[solver][iefpcm][iefpcm_gepol-NH3]")
{
Molecule molec = NH3();
double area = 0.4;
double probeRadius = 0.0;
double minRadius = 100.0;
GePolCavity cavity = GePolCavity(molec, area, probeRadius, minRadius);
cavity.saveCavity("nh3.npz");
double permittivity = 78.39;
Vacuum<AD_directional, CollocationIntegrator> gfInside = Vacuum<AD_directional, CollocationIntegrator>();
UniformDielectric<AD_directional, CollocationIntegrator> gfOutside =
UniformDielectric<AD_directional, CollocationIntegrator>(permittivity);
bool symm = true;
IEFSolver solver(symm);
solver.buildSystemMatrix(cavity, gfInside, gfOutside);
double Ncharge = 7.0;
double Hcharge = 1.0;
size_t size = cavity.size();
Eigen::VectorXd fake_mep = computeMEP(molec, cavity.elements());
// The total ASC for a dielectric is -Q*(epsilon-1)/epsilon
double totalASC = -charge * (permittivity - 1) / permittivity;
/*! \class IEFSolver
* \test \b pointChargeGePolC1 tests IEFSolver using a point charge with a GePol
* cavity in C1 symmetry
* We are forcing the usage of the buildAnisotropicMatrix method.
* The results are compared with Gauss' theorem and the results from the
* buildIsotropicMatrix method
* The point charge is at the origin.
*/
WHEN("the point group is C1") {
Molecule point = dummy<0>(2.929075493);
double area = 0.4;
double probeRadius = 0.0;
double minRadius = 100.0;
GePolCavity cavity(point, area, probeRadius, minRadius, "C1");
IEFSolver aniso_solver(symm);
aniso_solver.buildAnisotropicMatrix(cavity, gf_i, gf_o, op);
IEFSolver iso_solver(symm);
iso_solver.buildIsotropicMatrix(cavity, gf_i, gf_o, op);
int size = cavity.size();
Eigen::VectorXd fake_mep = computeMEP(cavity.elements(), charge);
THEN("the total apparent surface charge is") {
Eigen::VectorXd aniso_fake_asc = aniso_solver.computeCharge(fake_mep);
Eigen::VectorXd iso_fake_asc = iso_solver.computeCharge(fake_mep);
int nr_irrep = cavity.pointGroup().nrIrrep();
#include <Eigen/Core>
#include "GePolCavity.hpp"
#include "Molecule.hpp"
#include "PhysicalConstants.hpp"
#include "Symmetry.hpp"
#include "TestingMolecules.hpp"
TEST_CASE("GePol cavity for the benzene molecule", "[gepol][gepol_C6H6]")
{
double area = 0.3 / convertBohr2ToAngstrom2;
double probeRadius = 1.385 / convertBohrToAngstrom;
// Addition of spheres is enabled, but will not happen in this particular case
double minRadius = 10.0 / convertBohrToAngstrom;
Molecule molec = C6H6();
GePolCavity cavity = GePolCavity(molec, area, probeRadius, minRadius, "c6h6");
cavity.saveCavity("c6h6.npz");
/*! \class GePolCavity
* \test \b GePolCavityC6H6AddTest_size tests GePol cavity size for C6H6 in C1 symmetry with added spheres
*/
SECTION("Test size")
{
int size = 644;
size_t actualSize = cavity.size();
REQUIRE(size == actualSize);
}
/*! \class GePolCavity
* \test \b GePolCavityC6H6AddTest_area tests GePol cavity surface area for C6H6 in C1 symmetry with added spheres
*/
Vacuum<AD_directional, CollocationIntegrator>();
bool symm = true;
double charge = 8.0;
double totalASC = - charge * (eps1 - 1) / eps1;
/*! \class IEFSolver
* \test \b pointChargeDiffuseGePol tests IEFSolver using a point charge with a GePol cavity and a spherical diffuse interface
* The spherical diffuse interface is centered at the origin, while the point charge is away from the origin.
*/
WHEN("the spherical diffuse layer is centered at the origin and the charge is away from the origin")
{
Molecule point = dummy<0>(2.929075493, origin);
double area = 1.0;
double probeRadius = 0.0;
double minRadius = 100.0;
GePolCavity cavity = GePolCavity(point, area, probeRadius, minRadius);
SphericalDiffuse<CollocationIntegrator, OneLayerTanh> gfOutside =
SphericalDiffuse<CollocationIntegrator, OneLayerTanh>(eps1, eps2, width, center, Eigen::Vector3d::Zero(), 3);
IEFSolver solver(symm);
solver.buildSystemMatrix(cavity, gfInside, gfOutside);
size_t size = cavity.size();
Eigen::VectorXd fake_mep = computeMEP(cavity.elements(), charge, origin);
for (size_t i = 0; i < size; ++i) {
INFO("fake_mep(" << i << ") = " << fake_mep(i));
}
THEN("the apparent surface charge is")
{
Eigen::VectorXd fake_asc = Eigen::VectorXd::Zero(size);
fake_asc = solver.computeCharge(fake_mep);
double totalFakeASC = fake_asc.sum();
#include "Molecule.hpp"
#include "Vacuum.hpp"
#include "UniformDielectric.hpp"
#include "CPCMSolver.hpp"
#include "TestingMolecules.hpp"
/*! \class CPCMSolver
* \test \b C2H4GePolD2h tests CPCMSolver using C2H4 with a GePol cavity in D2h symmetry
*/
TEST_CASE("Test solver for the CPCM and the C2H4 molecule in D2h symmetry", "[cpcm][cpcm_symmetry][cpcm_gepol-C2H4_D2h]")
{
Molecule molec = C2H4();
double area = 0.2 / convertBohr2ToAngstrom2;
double probeRadius = 1.385 / convertBohrToAngstrom;
double minRadius = 100.0 / convertBohrToAngstrom;
GePolCavity cavity = GePolCavity(molec, area, probeRadius, minRadius, "cpcm_d2h_noadd");
double permittivity = 78.39;
Vacuum<AD_directional, CollocationIntegrator> gfInside = Vacuum<AD_directional, CollocationIntegrator>();
UniformDielectric<AD_directional, CollocationIntegrator> gfOutside =
UniformDielectric<AD_directional, CollocationIntegrator>(permittivity);
bool symm = true;
double correction = 0.0;
CPCMSolver solver(symm, correction);
solver.buildSystemMatrix(cavity, gfInside, gfOutside);
double Ccharge = 6.0;
double Hcharge = 1.0;
size_t size = cavity.size();
Eigen::VectorXd fake_mep = computeMEP(molec, cavity.elements());
using dielectric_profile::OneLayerErf;
using dielectric_profile::OneLayerTanh;
using green::SphericalDiffuse;
using green::SphericalSharp;
using green::UniformDielectric;
using green::Vacuum;
SCENARIO("A collocation integrator with approximate diagonal elements",
"[bi_operators][bi_operators_collocation]") {
GIVEN("A GePol cavity for a single sphere in the origin") {
double radius = 1.44;
Eigen::Vector3d offset;
offset << 1.0, 2.0, 3.0;
Molecule molec = dummy<0>(1.44 / bohrToAngstrom(), offset);
double area = 10.0;
GePolCavity cavity = GePolCavity(molec, area, 0.0, 100.0);
Eigen::MatrixXd results = Eigen::MatrixXd::Zero(cavity.size(), cavity.size());
Eigen::MatrixXd reference = Eigen::MatrixXd::Zero(cavity.size(), cavity.size());
Collocation op;
/*! \class Collocation
* \test \b CollocationTest_vacuum tests the evaluation by collocation
* of the vacuum matrix representations of S and D
*/
WHEN("the vacuum Green's function is used") {
Vacuum<> gf;
THEN("the matrix elements of S are") {
results = op.computeS(cavity, gf);
reference = cnpy::custom::npy_load<double>("vacuum_S_collocation.npy");
for (int i = 0; i < cavity.size(); ++i) {
for (int j = 0; j < cavity.size(); ++j) {
