molecule.cc File Reference

Class representing a molecule as a set of atoms with assiciated coordinates and charges of the atomic nuclei. More...

#include <stdio.h>
#include <stdlib.h>
#include <memory.h>
#include <math.h>
#include <string.h>
#include <cassert>
#include "molecule.h"
#include "xyz_file_parser.h"
#include "output.h"
#include "memorymanag.h"
#include "units.h"
#include "utilities.h"

Functions
static ergo_real	get_distance_between_atoms (const Atom &atomA, const Atom &atomB)
static int	readMoleculeFileInMolFormat (Molecule *result, const char *fileName, int netCharge, char **basisfilename)

Detailed Description

Class representing a molecule as a set of atoms with assiciated coordinates and charges of the atomic nuclei.

Author

: Elias Rudberg responsible

Function Documentation

static ergo_real get_distance_between_atoms ( const Atom &  atomA, const Atom &  atomB  )

static

References Atom::coords, and template_blas_sqrt().

Referenced by Molecule::getExtremeInternuclearDistancesQuadratic(), and Molecule::getNuclearRepulsionEnergyQuadratic().

static int readMoleculeFileInMolFormat ( Molecule *  result, const char *  fileName, int  netCharge, char **  basisfilename  )

static

References Molecule::addAtom(), Molecule::atoms, charge, do_output(), ergo_malloc(), mat::get_file_size(), Molecule::getNoOfAtoms(), LOG_AREA_MAIN, LOG_CAT_ERROR, LOG_CAT_INFO, Molecule::setNetCharge(), and UNIT_one_Angstrom.

Referenced by Molecule::setFromMoleculeFile().