Molecule H2()
{
int nAtoms = 2;
Eigen::Vector3d H1( 0.735000, 0.000000, 0.000000);
Eigen::Vector3d H2(-0.735000, 0.000000, 0.000000);
Eigen::MatrixXd geom(3, nAtoms);
geom.col(0) = H1.transpose();
geom.col(1) = H2.transpose();
Eigen::Vector2d charges, masses;
charges << 1.0, 1.0;
masses << 1.0078250, 1.0078250;
std::vector<Atom> atoms;
double radiusH = 1.20;
atoms.push_back( Atom("Hydrogen", "H", charges(0), masses(0), radiusH, H1, 1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(1), masses(1), radiusH, H2, 1.0) );
std::vector<Sphere> spheres;
Sphere sph2(H1, radiusH);
Sphere sph3(H2, radiusH);
spheres.push_back(sph2);
spheres.push_back(sph3);
Symmetry pGroup = buildGroup(0, 0, 0, 0);
return Molecule(nAtoms, charges, masses, geom, atoms, spheres, pGroup);
};
void OneCLJGenerator::addParticle(int id, double x, double y, double z, ParticleContainer* particleContainer,
Domain* domain, DomainDecompBase* domainDecomp) {
vector<Component>& dcomponents = domain->getComponents();
vector<double> v_;
v_.resize(3);
// Velocity
for (int dim = 0; dim < 3; dim++) {
v_[dim] = randdouble(-0.5, 0.5);
}
double dotprod_v = 0;
for (unsigned int i = 0; i < v_.size(); i++) {
dotprod_v += v_[i] * v_[i];
}
// Velocity Correction
double vCorr = sqrt(3.0 * _temperature / dotprod_v);
for (unsigned int i = 0; i < v_.size(); i++) {
v_[i] *= vCorr;
}
Molecule m1 = Molecule(id, 0, x, y, z, v_[0], v_[1], v_[2], 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, &dcomponents);
particleContainer->addParticle(m1);
//dcomponents[0].incrnumMolecules();
//domain->setglobalRotDOF(dcomponents[0].rot_dof()+domain->getglobalRotDOF());
}
Molecule C2H4()
{
int nAtoms = 6;
Eigen::Vector3d C1(0.0000000000, 0.0000000000, 1.2578920000);
Eigen::Vector3d H1(0.0000000000, 1.7454620000, 2.3427160000);
Eigen::Vector3d H2(0.0000000000, -1.7454620000, 2.3427160000);
Eigen::Vector3d C2(0.0000000000, 0.0000000000, -1.2578920000);
Eigen::Vector3d H3(0.0000000000, 1.7454620000, -2.3427160000);
Eigen::Vector3d H4(0.0000000000, -1.7454620000, -2.3427160000);
Eigen::MatrixXd geom(3, nAtoms);
geom.col(0) = C1.transpose();
geom.col(1) = H1.transpose();
geom.col(2) = H2.transpose();
geom.col(3) = C2.transpose();
geom.col(4) = H3.transpose();
geom.col(5) = H4.transpose();
Eigen::VectorXd charges(6), masses(6);
charges << 6.0, 1.0, 1.0, 6.0, 1.0, 1.0;
masses << 12.00, 1.0078250, 1.0078250, 12.0, 1.0078250, 1.0078250;
double radiusC = (1.70 * 1.20) / convertBohrToAngstrom;
double radiusH = (1.20 * 1.20) / convertBohrToAngstrom;
std::vector<Atom> atoms;
atoms.push_back( Atom("Carbon", "C", charges(0), masses(0), radiusC, C1, 1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(1), masses(1), radiusH, H1, 1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(2), masses(2), radiusH, H2, 1.0) );
atoms.push_back( Atom("Carbon", "C", charges(3), masses(3), radiusC, C2, 1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(4), masses(4), radiusH, H3, 1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(5), masses(5), radiusH, H4, 1.0) );
std::vector<Sphere> spheres;
Sphere sph1(C1, radiusC);
Sphere sph2(H1, radiusH);
Sphere sph3(H2, radiusH);
Sphere sph4(C2, radiusC);
Sphere sph5(H3, radiusH);
Sphere sph6(H4, radiusH);
spheres.push_back(sph1);
spheres.push_back(sph2);
spheres.push_back(sph3);
spheres.push_back(sph4);
spheres.push_back(sph5);
spheres.push_back(sph6);
// D2h as generated by Oxy, Oxz, Oyz
Symmetry pGroup = buildGroup(3, 4, 2, 1);
return Molecule(nAtoms, charges, masses, geom, atoms, spheres, pGroup);
};
Box::Box()
{
changedMol = Molecule();
environment = NULL;
atoms = NULL;
molecules = NULL;
bonds = NULL;
angles = NULL;
dihedrals = NULL;
hops = NULL;
atomCount = 0;
moleculeCount = 0;
}
Molecule H3()
{
int nAtoms = 3;
Eigen::Vector3d H1( 0.735000, 0.000000, -1.333333);
Eigen::Vector3d H2(-0.735000, 0.000000, -1.333333);
Eigen::Vector3d H3( 0.000000, 0.000000, 2.666667);
Eigen::MatrixXd geom(3, nAtoms);
geom.col(0) = H1.transpose();
geom.col(1) = H2.transpose();
geom.col(2) = H3.transpose();
Eigen::Vector3d charges, masses;
charges << 1.0, 1.0, 1.0;
masses << 1.0078250, 1.0078250, 1.0078250;
std::vector<Atom> atoms;
double radiusH = (1.20 * 1.20) / convertBohrToAngstrom;
atoms.push_back( Atom("Hydrogen", "H", charges(0), masses(0), radiusH, H1, 1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(1), masses(1), radiusH, H2, 1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(2), masses(2), radiusH, H3, 1.0) );
std::vector<Sphere> spheres;
Sphere sph2(H1, radiusH);
Sphere sph3(H2, radiusH);
Sphere sph4(H3, radiusH);
spheres.push_back(sph2);
spheres.push_back(sph3);
spheres.push_back(sph4);
enum pointGroup { pgC1, pgC2, pgCs, pgCi, pgD2, pgC2v, pgC2h, pgD2h };
Symmetry pGroup;
switch(group) {
case(pgC1):
pGroup = buildGroup(0, 0, 0, 0);
break;
case(pgC2v):
// C2v as generated by Oyz and Oxz
pGroup = buildGroup(2, 1, 2, 0);
break;
default:
pGroup = buildGroup(0, 0, 0, 0);
break;
}
return Molecule(nAtoms, charges, masses, geom, atoms, spheres, pGroup);
};
Molecule NH3()
{
int nAtoms = 4;
Eigen::Vector3d N( -0.000000000, -0.104038047, 0.000000000);
Eigen::Vector3d H1(-0.901584415, 0.481847022, -1.561590016);
Eigen::Vector3d H2(-0.901584415, 0.481847022, 1.561590016);
Eigen::Vector3d H3( 1.803168833, 0.481847022, 0.000000000);
Eigen::MatrixXd geom(3, nAtoms);
geom.col(0) = N.transpose();
geom.col(1) = H1.transpose();
geom.col(2) = H2.transpose();
geom.col(3) = H3.transpose();
Eigen::Vector4d charges, masses;
charges << 7.0, 1.0, 1.0, 1.0;
masses << 14.0030740, 1.0078250, 1.0078250, 1.0078250;
std::vector<Atom> atoms;
atoms.push_back( Atom("Nitrogen", "N", charges(0), masses(0), 2.929075493, N,
1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(1), masses(1), 2.267671349, H1,
1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(2), masses(2), 2.267671349, H2,
1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(3), masses(3), 2.267671349, H3,
1.0) );
std::vector<Sphere> spheres;
Sphere sph1(N, 2.929075493);
Sphere sph2(H1, 2.267671349);
Sphere sph3(H2, 2.267671349);
Sphere sph4(H3, 2.267671349);
spheres.push_back(sph1);
spheres.push_back(sph2);
spheres.push_back(sph3);
spheres.push_back(sph4);
// C1
Symmetry pGroup = buildGroup(0, 0, 0, 0);
return Molecule(nAtoms, charges, masses, geom, atoms, spheres, pGroup);
};
Molecule CH3()
{
int nAtoms = 4;
Eigen::Vector3d C1( 0.0006122714, 0.0000000000, 0.0000000000);
Eigen::Vector3d H1( 1.5162556382, -1.3708721537, 0.0000000000);
Eigen::Vector3d H2(-0.7584339548, 0.6854360769, 1.7695110698);
Eigen::Vector3d H3(-0.7584339548, 0.6854360769, -1.7695110698);
Eigen::MatrixXd geom(3, nAtoms);
geom.col(0) = C1.transpose();
geom.col(1) = H1.transpose();
geom.col(2) = H2.transpose();
geom.col(3) = H3.transpose();
Eigen::Vector4d charges, masses;
charges << 6.0, 1.0, 1.0, 1.0;
masses << 12.00, 1.0078250, 1.0078250, 1.0078250;
double radiusC = (1.70 * 1.20) / convertBohrToAngstrom;
double radiusH = (1.20 * 1.20) / convertBohrToAngstrom;
std::vector<Atom> atoms;
atoms.push_back( Atom("Carbon", "C", charges(0), masses(0), radiusC, C1, 1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(1), masses(1), radiusH, H1, 1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(2), masses(2), radiusH, H2, 1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(3), masses(3), radiusH, H3, 1.0) );
std::vector<Sphere> spheres;
Sphere sph1(C1, radiusC);
Sphere sph2(H1, radiusH);
Sphere sph3(H2, radiusH);
Sphere sph4(H3, radiusH);
spheres.push_back(sph1);
spheres.push_back(sph2);
spheres.push_back(sph3);
spheres.push_back(sph4);
// Cs as generated by Oxy
Symmetry pGroup = buildGroup(1, 4, 0, 0);
return Molecule(nAtoms, charges, masses, geom, atoms, spheres, pGroup);
};
Molecule kmeans(ABCbls const &clusterables, int64_t nclusters) {
if (clusterables.size() < std::size_t(nclusters)) {
nclusters = clusterables.size();
}
auto objective_min = std::numeric_limits<double>::max();
int64_t init_seed = 1000;
int64_t best_seed = 1000;
for (auto i = 0; i < 50; ++i) {
math::clustering::Kmeans kmeans(init_seed);
auto clusters = kmeans.cluster<AtomBasedCluster>(clusterables, nclusters);
auto value = math::clustering::kmeans_objective(clusters);
if (value < objective_min) {
best_seed = init_seed;
objective_min = value;
}
init_seed += 1000;
}
return Molecule(convert_to_clusterable(
math::clustering::Kmeans(best_seed).cluster<AtomBasedCluster>(clusterables,
nclusters)));
}
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)!");
}
}
Molecule C6H6()
{
int nAtoms = 12;
// These are in Angstrom
Eigen::Vector3d C1(5.274, 1.999, -8.568);
Eigen::Vector3d C2(6.627, 2.018, -8.209);
Eigen::Vector3d C3(7.366, 0.829, -8.202);
Eigen::Vector3d C4(6.752, -0.379, -8.554);
Eigen::Vector3d C5(5.399, -0.398, -8.912);
Eigen::Vector3d C6(4.660, 0.791, -8.919);
Eigen::Vector3d H1(4.704, 2.916, -8.573);
Eigen::Vector3d H2(7.101, 2.950, -7.938);
Eigen::Vector3d H3(8.410, 0.844, -7.926);
Eigen::Vector3d H4(7.322, -1.296, -8.548);
Eigen::Vector3d H5(4.925, -1.330, -9.183);
Eigen::Vector3d H6(3.616, 0.776, -9.196);
// Scale
C1 /= convertBohrToAngstrom;
C2 /= convertBohrToAngstrom;
C3 /= convertBohrToAngstrom;
C4 /= convertBohrToAngstrom;
C5 /= convertBohrToAngstrom;
C6 /= convertBohrToAngstrom;
H1 /= convertBohrToAngstrom;
H2 /= convertBohrToAngstrom;
H3 /= convertBohrToAngstrom;
H4 /= convertBohrToAngstrom;
H5 /= convertBohrToAngstrom;
H6 /= convertBohrToAngstrom;
Eigen::MatrixXd geom(3, nAtoms);
geom.col(0) = C1.transpose();
geom.col(1) = C2.transpose();
geom.col(2) = C3.transpose();
geom.col(3) = C4.transpose();
geom.col(4) = C5.transpose();
geom.col(5) = C6.transpose();
geom.col(6) = H1.transpose();
geom.col(7) = H2.transpose();
geom.col(8) = H3.transpose();
geom.col(9) = H4.transpose();
geom.col(10) = H5.transpose();
geom.col(11) = H6.transpose();
Eigen::VectorXd charges(12), masses(12);
charges << 6.0, 6.0, 6.0, 6.0, 6.0, 6.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0;
masses << 12.00, 12.0, 12.0, 12.0, 12.0, 12.0, 1.0078250, 1.0078250, 1.0078250,
1.0078250, 1.0078250, 1.0078250;
double radiusC = 1.70 / convertBohrToAngstrom;
double radiusH = 1.20 / convertBohrToAngstrom;
std::vector<Atom> atoms;
atoms.push_back( Atom("Carbon", "C", charges(0), masses(0), radiusC, C1, 1.0) );
atoms.push_back( Atom("Carbon", "C", charges(1), masses(1), radiusC, C2, 1.0) );
atoms.push_back( Atom("Carbon", "C", charges(2), masses(2), radiusC, C3, 1.0) );
atoms.push_back( Atom("Carbon", "C", charges(3), masses(3), radiusC, C4, 1.0) );
atoms.push_back( Atom("Carbon", "C", charges(4), masses(4), radiusC, C5, 1.0) );
atoms.push_back( Atom("Carbon", "C", charges(5), masses(5), radiusC, C6, 1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(6), masses(6), radiusH, H1, 1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(7), masses(7), radiusH, H2, 1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(8), masses(8), radiusH, H3, 1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(9), masses(9), radiusH, H4, 1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(10), masses(10), radiusH, H5, 1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(11), masses(11), radiusH, H6, 1.0) );
std::vector<Sphere> spheres;
Sphere sph1(C1, radiusC);
Sphere sph2(C2, radiusC);
Sphere sph3(C3, radiusC);
Sphere sph4(C4, radiusC);
Sphere sph5(C5, radiusC);
Sphere sph6(C6, radiusC);
Sphere sph7(H1, radiusH);
Sphere sph8(H2, radiusH);
Sphere sph9(H3, radiusH);
Sphere sph10(H4, radiusH);
Sphere sph11(H5, radiusH);
Sphere sph12(H6, radiusH);
spheres.push_back(sph1);
spheres.push_back(sph2);
spheres.push_back(sph3);
spheres.push_back(sph4);
spheres.push_back(sph5);
spheres.push_back(sph6);
spheres.push_back(sph7);
spheres.push_back(sph8);
spheres.push_back(sph9);
spheres.push_back(sph10);
spheres.push_back(sph11);
spheres.push_back(sph12);
// D2h as generated by Oxy, Oxz, Oyz
Symmetry pGroup = buildGroup(0, 0, 0, 0);
return Molecule(nAtoms, charges, masses, geom, atoms, spheres, pGroup);
};
Molecule CO2()
{
int nAtoms = 3;
Eigen::Vector3d C1( 0.0000000000, 0.0000000000, 0.0000000000);
Eigen::Vector3d O1( 2.1316110791, 0.0000000000, 0.0000000000);
Eigen::Vector3d O2(-2.1316110791, 0.0000000000, 0.0000000000);
Eigen::MatrixXd geom(3, nAtoms);
geom.col(0) = C1.transpose();
geom.col(1) = O1.transpose();
geom.col(2) = O2.transpose();
Eigen::Vector3d charges, masses;
charges << 6.0, 8.0, 8.0;
masses << 12.00, 15.9949150, 15.9949150;
std::vector<Atom> atoms;
double radiusC = (1.70 * 1.20) / convertBohrToAngstrom;
double radiusO = (1.52 * 1.20) / convertBohrToAngstrom;
atoms.push_back( Atom("Carbon", "C", charges(0), masses(0), radiusC, C1, 1.0) );
atoms.push_back( Atom("Oxygen", "O", charges(1), masses(1), radiusO, O1, 1.0) );
atoms.push_back( Atom("Oxygen", "O", charges(2), masses(2), radiusO, O2, 1.0) );
std::vector<Sphere> spheres;
Sphere sph1(C1, radiusC);
Sphere sph2(O1, radiusO);
Sphere sph3(O2, radiusO);
spheres.push_back(sph1);
spheres.push_back(sph2);
spheres.push_back(sph3);
enum pointGroup { pgC1, pgC2, pgCs, pgCi, pgD2, pgC2v, pgC2h, pgD2h };
Symmetry pGroup;
switch(group) {
case(pgC1):
pGroup = buildGroup(0, 0, 0, 0);
break;
case(pgC2):
// C2 as generated by C2z
pGroup = buildGroup(1, 3, 0, 0);
break;
case(pgCs):
// Cs as generated by Oyz
pGroup = buildGroup(1, 1, 0, 0);
break;
case(pgCi):
// Ci as generated by i
pGroup = buildGroup(1, 7, 0, 0);
break;
case(pgD2):
// D2 as generated by C2z and C2x
pGroup = buildGroup(2, 3, 6, 0);
break;
case(pgC2v):
// C2v as generated by Oyz and Oxz
pGroup = buildGroup(2, 1, 2, 0);
break;
case(pgC2h):
// C2h as generated by Oxy and i
pGroup = buildGroup(2, 4, 7, 0);
break;
case(pgD2h):
// D2h as generated by Oxy, Oxz and Oyz
pGroup = buildGroup(3, 4, 2, 1);
break;
default:
pGroup = buildGroup(0, 0, 0, 0);
break;
}
return Molecule(nAtoms, charges, masses, geom, atoms, spheres, pGroup);
};
