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
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
|
/* 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 fermi_contact.cc implements "Fermi contact" integrals. The
formulas are give in the hyperfine project.
@author: Pawel Salek <em>responsible</em>
*/
#include <memory>
static const double GE = 2.0023193044;
#include "memorymanag.h"
#include "basisinfo.h"
#include "aos.h"
#include "density_description_file.h"
#include "Matrix.h"
#include "MatrixSymmetric.h"
struct FCAccumulator {
const ergo_real *basisFuncValues; /**< vector of basis function values at
* given point in space. */
explicit FCAccumulator(const ergo_real *bfs) : basisFuncValues(bfs) {}
ergo_real accumulate(const ergo_real& dij, int i, int j) const
{
return dij*basisFuncValues[i]*basisFuncValues[j];
}
};
template<class Accumulator>
ergo_real
accumulate(int n, const ergo_real *spinMat, const Accumulator& ac)
{
ergo_real res = 0;
for(int col=0; col<n; col++)
for(int row=0; row<n; row++) {
ergo_real c = ac.accumulate(spinMat[row + col*n], row, col);
res += c;
}
return res;
}
/** computeFermiContact computes the Fermi contact interaction for
given molecule and specified spin density.
@param bis basis set specification.
@param spinDensity spin density defined as D_alpha-D_beta.
@param R the cartesian coordinates to which we compute interaction
to.
@param result will contain the interaction if the function succeeds.
@return 0 on success, -1 on failure.
*/
int
computeFermiContact(const BasisInfoStruct& bis,
const ergo_real* spinDensity,
const Vector3D& R, ergo_real& result)
{
ergo_real *bfs = new ergo_real[bis.noOfBasisFuncs];
memset(bfs, 0, sizeof(bfs[0])*bis.noOfBasisFuncs);
int bfBlock[2] = { 0, bis.noOfShells };
dft_get_orbs(1, bfs, &R.v, 1, &bfBlock, 0, bis);
result = accumulate(bis.noOfBasisFuncs, spinDensity, FCAccumulator(bfs));
delete []bfs;
return 0;
}
#if 0
static void
printmat(const char*label, int n, const ergo_real *m)
{
for(int row=0; row<n; row++) {
for(int col=0; col<n; col++)
printf("%14f ", (double)m[row + col*n]);
puts("");
}
}
#endif
int main(int argc, char *argv[])
{
static char usage[] =
"fermi_contact SPIN_DENSITY_FILE [MOLECULE]\n"
"\tComputes Fermi contact term for given unrestricted density file.\n"
"\tThe first file is assumed to contain the alpha and beta densities.\n"
"\tThe optional second file contains molecular geometry.\n"
"\n"
"Spin couplings to all basis function centers are computed\n"
"if only one file is specified. If the molecule file is specified\n"
"as well, the labels from there are used to tag the atoms.\n";
if(argc <= 1) {
fputs(usage, stderr);
return 1;
}
IntegralInfo integralInfo(true);
ergo_real *densMatrix[2] = { NULL, NULL };
BasisInfoStruct *basisRead = NULL;
if (ddf_load_density(argv[1], 2, integralInfo,
&basisRead, densMatrix)) {
fprintf(stderr, "Loading unrestricted densities from '%s' failed. "
"Calculation aborted.\n", argv[1]);
return 1;
}
#if 0
printmat("ALPHA", basisRead->noOfBasisFuncs, densMatrix[0]);
printmat("BETA", basisRead->noOfBasisFuncs, densMatrix[1]);
#endif
/* Create spin density */
int nElements = basisRead->noOfBasisFuncs*basisRead->noOfBasisFuncs;
for(int i=0; i<nElements; i++)
densMatrix[0][i] -= densMatrix[1][i];
if (argc>=3) {
Molecule molecule;
printf("Loading molecule from %s\n", argv[2]);
int res = molecule.setFromMoleculeFile
(argv[2], 0, /* we are guessing the net charge here */
NULL);
if(res) {
fprintf(stderr,
"Molecule file '%s' specified but could not be loaded.\n",
argv[2]);
return 1;
}
printf("%-6s %6s %12s %12s : %5s\n", "Charge",
"X", "Y", "Z", "FC Coupling");
for(int iAtom=0; iAtom<molecule.getNoOfAtoms(); iAtom++) {
const Atom &atom = molecule.getAtom(iAtom);
ergo_real fc;
Vector3D pos(atom.coords[0], atom.coords[1], atom.coords[2]);
if (computeFermiContact(*basisRead, densMatrix[0], pos, fc) ) {
fprintf(stderr, "Calculation of FC SS failed for atom %d\n",
iAtom+1);
break;
} else {
printf("%-6.1f %12.6f %12.6f %12.6f : %17.10g\n", (double)atom.charge,
(double)pos[0], (double)pos[1], (double)pos[2],
(double)(4*M_PI*GE*fc/3.0));
}
}
} else { /* No molecule file specified - use basis function centers */
printf("FC Couplings\n"
"%6s %12s %12s : %s\n",
"X", "Y", "Z", "FC Coupling");
Vector3D lastPos(-12345e6, -12345e6, -12345e6);
for(int iShell=0; iShell<basisRead->noOfShells; iShell++) {
const ShellSpecStruct &shell = basisRead->shellList[iShell];
ergo_real fc;
Vector3D pos(shell.centerCoords[0], shell.centerCoords[1],
shell.centerCoords[2]);
if(pos.dist(lastPos) >0.1) {
if (computeFermiContact(*basisRead, densMatrix[0], pos, fc) ) {
fprintf(stderr, "Calculation of FC SS failed for shell %d\n",
iShell+1);
break;
} else {
printf("%12.6f %12.6f %12.6f : %17.10g\n",
(double)pos[0], (double)pos[1], (double)pos[2],
(double)(4*M_PI*GE*fc/3.0));
}
}
lastPos = pos;
}
}
ergo_free(densMatrix[0]);
ergo_free(densMatrix[1]);
delete basisRead;
return 0;
}
|
