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/* Ergo, version 3.8.2, a program for linear scaling electronic structure
* calculations.
* Copyright (C) 2023 Elias Rudberg, Emanuel H. Rubensson, Pawel Salek,
* and Anastasia Kruchinina.
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*
* Primary academic reference:
* Ergo: An open-source program for linear-scaling electronic structure
* calculations,
* Elias Rudberg, Emanuel H. Rubensson, Pawel Salek, and Anastasia
* Kruchinina,
* SoftwareX 7, 107 (2018),
* <http://dx.doi.org/10.1016/j.softx.2018.03.005>
*
* For further information about Ergo, see <http://www.ergoscf.org>.
*/
/** @file molecule.h
@brief Class representing a molecule as a set of atoms with
assiciated coordinates and charges of the atomic nuclei.
@author: Elias Rudberg <em>responsible</em>
*/
#ifndef MOLECULE_HEADER
#define MOLECULE_HEADER
#include <cmath>
#include <vector>
#include <cassert>
#include "realtype.h"
#include "mat_gblas.h"
/** Simple atom representation by its charge and cartesian coordinates.
*
*/
struct Atom {
ergo_real charge;
ergo_real coords[3];
};
/**
* A representation of Vector or point in cartesian space. It provides
* means to compute distance between two pointsi space.
*/
struct Vector3D {
ergo_real v[3];
Vector3D() {}
Vector3D(ergo_real x, ergo_real y, ergo_real z) {
v[0] = x; v[1] = y; v[2] = z;
}
ergo_real& operator[](unsigned i) { return v[i]; }
ergo_real operator[](unsigned i) const { return v[i]; }
/** compute square of distance between two points. */
ergo_real dist2(const ergo_real b[]) const {
ergo_real d, r;
d = v[0]-b[0]; r = d*d;
d = v[1]-b[1]; r += d*d;
d = v[2]-b[2]; r += d*d;
return r;
}
/** compute distance between two points. */
ergo_real dist(const Vector3D& b) const
{ return template_blas_sqrt(dist2(b.v)); }
ergo_real dist(const ergo_real b[]) const
{ return template_blas_sqrt(dist2(b)); }
};
/**
* Representation of a molecule as a set of nuclei and total
* charge. It provides I/O methods and basic manipulation routines.
*/
class Molecule {
private:
std::vector<Atom> atoms;
ergo_real netCharge;
int noOfAtoms;
public:
Molecule() : atoms(10), netCharge(0), noOfAtoms(0) {}
void addAtom(ergo_real c, ergo_real x, ergo_real y, ergo_real z) {
int currListSize = atoms.size();
if(noOfAtoms >= currListSize)
atoms.resize(currListSize*2);
atoms[noOfAtoms].charge = c;
atoms[noOfAtoms].coords[0] = x;
atoms[noOfAtoms].coords[1] = y;
atoms[noOfAtoms].coords[2] = z;
noOfAtoms++;
}
void clear() { noOfAtoms = 0; netCharge = 0; }
void setNetCharge(ergo_real netCharge_) { netCharge = netCharge_; }
void replaceAtom(int i, const Atom & atom) { assert(i >= 0 && i < noOfAtoms); atoms[i] = atom; }
void setAtomList(const std::vector<Atom> atomList) { atoms = atomList; noOfAtoms = atomList.size(); }
const Atom* getAtomListPtr() const { return &atoms[0]; }
const Atom & getAtom(int i) const { return atoms[i]; }
int getNoOfAtoms() const { return noOfAtoms; }
ergo_real getNetCharge() const { return netCharge; }
/** Compute smallest and largest internuclear distances. */
void getExtremeInternuclearDistancesQuadratic(ergo_real & minDist, ergo_real & maxDist) const;
/** Compute nuclear repulsion energy. */
ergo_real getNuclearRepulsionEnergyQuadratic() const;
/** Compute nuclear energy in given electric field. */
ergo_real getNuclearElectricFieldEnergy(const Vector3D& electricField) const;
/** Compute total number of electrons. The result is sum of atomic
charges plus netCharge. */
int getNumberOfElectrons() const;
/** Compute gradient of nuclear repulsion energy w.r.t. changes in nuclear coordinates. Result is added to resultGradient vector. */
void getNuclearRepulsionEnergyGradientContribQuadratic(ergo_real* resultGradient) const;
/** 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. */
int setFromMoleculeFile(const char* fileName,
int netCharge,
char **basissetFile);
};
#endif /* MOLECULE_HEADER */
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