ergo
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Representation of a molecule as a set of nuclei and total charge. More...
#include <molecule.h>
Public Member Functions | |
Molecule () | |
void | addAtom (ergo_real c, ergo_real x, ergo_real y, ergo_real z) |
void | getExtremeInternuclearDistances (ergo_real &minDist, ergo_real &maxDist) const |
Compute smallest and largest internuclear distances. | |
ergo_real | getNuclearRepulsionEnergy () const |
Compute nuclear repulsion energy. | |
ergo_real | getNuclearElectricFieldEnergy (const Vector3D &electricField) const |
Compute nuclear energy in given electric field. | |
int | getNumberOfElectrons () const |
Compute total number of electrons. | |
int | setFromMoleculeFile (const char *fileName, int netCharge, char **basissetFile) |
Loads molecule from a given file name, assuming given net charge. |
Public Attributes | |
Atom | atoms [MAX_NO_OF_ATOMS] |
ergo_real | netCharge |
int | noOfAtoms |
Static Public Attributes | |
static const int | MAX_NO_OF_ATOMS = 200000 |
Representation of a molecule as a set of nuclei and total charge.
It provides I/O methods and basic manipulation routines.
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inline |
References atoms, Atom::charge, Atom::coords, MAX_NO_OF_ATOMS, and noOfAtoms.
Referenced by main(), and test_small().
Compute smallest and largest internuclear distances.
References A, atoms, B, get_distance_between_atoms(), and noOfAtoms.
Referenced by SCF_general::SCF_general().
Compute nuclear energy in given electric field.
References A, atoms, Atom::charge, Atom::coords, do_output(), LOG_AREA_MAIN, LOG_CAT_INFO, noOfAtoms, and Vector3D::v.
Referenced by SCF_general::do_SCF_iterations().
ergo_real Molecule::getNuclearRepulsionEnergy | ( | ) | const |
Compute nuclear repulsion energy.
References A, atoms, B, Atom::charge, do_output(), get_distance_between_atoms(), LOG_AREA_MAIN, LOG_CAT_INFO, and noOfAtoms.
Referenced by SCF_general::do_SCF_iterations().
int Molecule::getNumberOfElectrons | ( | ) | const |
Compute total number of electrons.
The result is sum of atomic charges plus netCharge.
References atoms, charge, netCharge, and noOfAtoms.
Referenced by calculation_shared(), dft_get_uxc_mt(), dft_get_xc(), dft_get_xc_mt(), dft_lin_resp_mt(), dft_lin_respao(), es_get_polarisability(), es_getexc(), es_run(), SCF_general::SCF_general(), and test_mol().
int Molecule::setFromMoleculeFile | ( | const char * | fileName, |
int | netCharge, | ||
char ** | basissetFile | ||
) |
Loads molecule from a given file name, assuming given net charge.
basissetFile will be set if the file contains basis set and basissetFile is NULL.
References readMoleculeFileInMolFormat(), and readMoleculeFileInXyzFormat().
Referenced by es_mol_read_molecule(), main(), mol_calculation(), and test_mol().
Atom Molecule::atoms[MAX_NO_OF_ATOMS] |
Referenced by addAtom(), compute_dipole_moment_onecoord(), compute_h_core_matrix_simple_dense(), compute_h_core_matrix_sparse(), compute_V_linear(), compute_V_sparse(), SCF_restricted::create_gabedit_file(), do_mulliken_atomic_charges(), SCF_unrestricted::do_spin_flip(), do_tdhf_dynamics(), es_add_atom(), es_run(), get_mulliken_charges(), ErgoMolInfo::getAtom(), ErgoMolInfo::getExps(), getExtremeInternuclearDistances(), getNuclearElectricFieldEnergy(), getNuclearRepulsionEnergy(), getNumberOfElectrons(), getSafeMaxDistance(), main(), SCF_unrestricted::output_density_images(), readMoleculeFileInMolFormat(), readMoleculeFileInXyzFormat(), savePotential(), setup_shells_multi_basis(), and setup_shells_multi_basis_getcount().
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static |
Referenced by addAtom(), es_add_atom(), readMoleculeFileInMolFormat(), and readMoleculeFileInXyzFormat().
ergo_real Molecule::netCharge |
Referenced by es_run(), getNumberOfElectrons(), readMoleculeFileInMolFormat(), and readMoleculeFileInXyzFormat().
int Molecule::noOfAtoms |
Referenced by addAtom(), compute_dipole_moment_onecoord(), compute_h_core_matrix_simple_dense(), compute_h_core_matrix_sparse(), compute_V_linear(), compute_V_sparse(), SCF_restricted::create_gabedit_file(), do_mulliken_atomic_charges(), do_mulliken_spin_densities(), SCF_unrestricted::do_spin_flip(), do_tdhf_dynamics(), es_add_atom(), es_mol_begin(), es_mol_commit(), es_run(), get_mulliken_charges(), ErgoMolInfo::getExps(), getExtremeInternuclearDistances(), getNuclearElectricFieldEnergy(), getNuclearRepulsionEnergy(), getNumberOfElectrons(), getSafeMaxDistance(), main(), SCF_unrestricted::output_density_images(), readMoleculeFileInMolFormat(), readMoleculeFileInXyzFormat(), savePotential(), SCF_general::SCF_general(), setup_shells_multi_basis(), and setup_shells_multi_basis_getcount().