int main(int argc, char** argv){
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);
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);
double probeRadius = 1.385; // Probe Radius for water
int patchLevel = 2;
double coarsity = 0.5;
WaveletCavity cavity(spheres, probeRadius, patchLevel, coarsity);
cavity.readCavity("molec_dyadic.dat");
double permittivity = 78.39;
Vacuum * gfInside = new Vacuum(2); // Automatic directional derivative
UniformDielectric * gfOutside = new UniformDielectric(2, permittivity);
int firstKind = 0;
PWCSolver solver(gfInside, gfOutside, firstKind);
solver.buildSystemMatrix(cavity);
cavity.uploadPoints(solver.getQuadratureLevel(), solver.getT_(), false);
}
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);
};
Molecule dummy(double radius, const Eigen::Vector3d & center)
{
std::vector<Sphere> spheres;
Sphere sph1(center, radius);
spheres.push_back(sph1);
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;
}
Molecule dummy(spheres);
dummy.pointGroup(pGroup);
return dummy;
};
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 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);
};
