1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
|
/* Ergo, version 3.5, a program for linear scaling electronic structure
* calculations.
* Copyright (C) 2016 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:
* KohnâSham Density Functional Theory Electronic Structure Calculations
* with Linearly Scaling Computational Time and Memory Usage,
* Elias Rudberg, Emanuel H. Rubensson, and Pawel Salek,
* J. Chem. Theory Comput. 7, 340 (2011),
* <http://dx.doi.org/10.1021/ct100611z>
*
* For further information about Ergo, see <http://www.ergoscf.org>.
*/
#ifndef MOLECULE_HEADER
#define MOLECULE_HEADER
#include <cmath>
#include <vector>
#include <cassert>
#include "realtype.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 std::sqrt(dist2(b.v)); }
ergo_real dist(const ergo_real b[]) const
{ return std::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 getExtremeInternuclearDistances(ergo_real & minDist, ergo_real & maxDist) const;
/** Compute nuclear repulsion energy. */
ergo_real getNuclearRepulsionEnergy() 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 getNuclearRepulsionEnergyGradientContrib(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 */
|
