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/* Ergo, version 3.8, a program for linear scaling electronic structure
* calculations.
* Copyright (C) 2019 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.cc
@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>
*/
#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"
static ergo_real
get_distance_between_atoms(const Atom& atomA, const Atom& atomB)
{
int i;
ergo_real sum = 0;
for(i = 0; i < 3; i++)
{
ergo_real dx = atomB.coords[i] - atomA.coords[i];
sum += dx*dx;
}
return template_blas_sqrt(sum);
}
void
Molecule::getExtremeInternuclearDistancesQuadratic(ergo_real & minDist, ergo_real & maxDist) const
{
minDist = maxDist = 0; // This matters if there is only one atom.
bool firstTime = true;
for(int A = 0; A < noOfAtoms; A++)
for(int B = A+1; B < noOfAtoms; B++) {
const Atom& atomA = atoms[A];
const Atom& atomB = atoms[B];
ergo_real RAB = get_distance_between_atoms(atomA, atomB);
if(firstTime) {
minDist = maxDist = RAB;
firstTime = false;
}
else {
minDist = RAB < minDist ? RAB : minDist;
maxDist = RAB > maxDist ? RAB : maxDist;
}
}
}
ergo_real
Molecule::getNuclearRepulsionEnergyQuadratic() const
{
int A, B;
ergo_real sum;
int N = noOfAtoms;
do_output(LOG_CAT_INFO, LOG_AREA_MAIN,
"get_nuclear_repulsion_energy, N = %i", N);
sum = 0;
for(A = 0; A < N; A++)
for(B = A+1; B < N; B++)
{
const Atom& atomA = atoms[A];
const Atom& atomB = atoms[B];
ergo_real ZA = atomA.charge;
ergo_real ZB = atomB.charge;
ergo_real RAB = get_distance_between_atoms(atomA, atomB);
sum += ZA * ZB / RAB;
}
do_output(LOG_CAT_INFO, LOG_AREA_MAIN,
"get_nuclear_repulsion_energy returning energy %33.22f", (double)sum);
return sum;
}
void
Molecule::getNuclearRepulsionEnergyGradientContribQuadratic(ergo_real* resultGradient) const
{
int N = noOfAtoms;
int A, B;
for(A = 0; A < N; A++)
for(B = A+1; B < N; B++) {
const Atom& atomA = atoms[A];
const Atom& atomB = atoms[B];
ergo_real ZA = atomA.charge;
ergo_real ZB = atomB.charge;
ergo_real dx = atomB.coords[0] - atomA.coords[0];
ergo_real dy = atomB.coords[1] - atomA.coords[1];
ergo_real dz = atomB.coords[2] - atomA.coords[2];
ergo_real r = template_blas_sqrt(dx*dx + dy*dy + dz*dz);
ergo_real derivative_x = ZA * ZB * (-0.5) * 2.0 * dx / (r*r*r);
ergo_real derivative_y = ZA * ZB * (-0.5) * 2.0 * dy / (r*r*r);
ergo_real derivative_z = ZA * ZB * (-0.5) * 2.0 * dz / (r*r*r);
resultGradient[A*3+0] += -1 * derivative_x;
resultGradient[A*3+1] += -1 * derivative_y;
resultGradient[A*3+2] += -1 * derivative_z;
resultGradient[B*3+0] += 1 * derivative_x;
resultGradient[B*3+1] += 1 * derivative_y;
resultGradient[B*3+2] += 1 * derivative_z;
}
}
ergo_real
Molecule::getNuclearElectricFieldEnergy(const Vector3D& electricField) const
{
int N = noOfAtoms;
do_output(LOG_CAT_INFO, LOG_AREA_MAIN,
"get_nuclear_electric_field_energy, N = %i", N);
ergo_real sum = 0;
int A;
for(A = 0; A < N; A++)
{
const Atom* atom = &atoms[A];
sum += atom->charge * atom->coords[0] * electricField.v[0];
sum += atom->charge * atom->coords[1] * electricField.v[1];
sum += atom->charge * atom->coords[2] * electricField.v[2];
} // END FOR A
do_output(LOG_CAT_INFO, LOG_AREA_MAIN,
"get_nuclear_electric_field_energy returning energy %33.22f", (double)sum);
return sum;
}
int
Molecule::getNumberOfElectrons() const
{
int i;
ergo_real noOfElectrons;
ergo_real sum = 0;
for(i = 0; i < noOfAtoms; i++)
sum += atoms[i].charge;
noOfElectrons = sum - netCharge;
return (int)noOfElectrons;
}
static int
readMoleculeFileInMolFormat(Molecule* result, const char* fileName,
int netCharge, char **basisfilename)
{
int nAtoms, nAtomsCurrType;
int i, j, ii, lineLen, noOfAtomTypes, atomTypeNo, can_read_basset;
char* p;
ergo_real unitFactor, atomCharge;
long int fileSize = get_file_size(fileName);
if(fileSize < 0) {
do_output(LOG_CAT_ERROR, LOG_AREA_MAIN, "error getting file size for file '%s'", fileName);
return -1;
}
FILE* f = fopen(fileName, "rt");
if(f == NULL)
{
do_output(LOG_CAT_ERROR, LOG_AREA_MAIN, "error opening file '%s'", fileName);
return -1;
}
size_t bufSize = fileSize + 10000;
std::vector<char> buf(bufSize);
memset(&buf[0], 0, bufSize);
int nBytes = (int)fread(&buf[0], sizeof(char), bufSize, f);
fclose(f);
if(nBytes <= 0) {
do_output(LOG_CAT_ERROR, LOG_AREA_MAIN, "error reading file '%s'", fileName);
return -1;
}
do_output(LOG_CAT_INFO, LOG_AREA_MAIN, "File '%s' read OK, nBytes = %i", fileName, nBytes);
nAtoms = 0;
p = &buf[0];
// skip 3 or 4 lines
if(strncmp(p, "BASIS", 5) == 0) { i = 3; can_read_basset = 1; }
else if(strncmp(p, "ATOMDF", 6) == 0 ||
strncmp(p, "ATOMBASIS", 9) == 0) { i = 2; can_read_basset = 0; }
else
{
do_output(LOG_CAT_ERROR, LOG_AREA_MAIN, "Unsupported molecule input file type");
return -1;
}
while((*p != '\n') && (*p != '\0')) p++; /* skip first line */
p++;
// if basisfilename is NULL we skip getting basis set string.
if(basisfilename)
{
if(can_read_basset && !*basisfilename) {
char *eol = strchr(p, '\n');
if(eol) {
while (--eol>p && *eol == ' ')
;
if (eol>p) {
size_t len = eol-p+1;
*basisfilename = (char*)ergo_malloc(len+1);
strncpy(*basisfilename, p, len);
(*basisfilename)[len] = '\0';
}
}
}
}
while(i--) {
while((*p != '\n') && (*p != '\0')) p++;
p++;
}
if(*p == '\0') return -2;
// the molecule input can follow in a fixed or a free format.
unitFactor = 1.0;
if( sscanf(p, "%d", &noOfAtomTypes) == 1)
{
// check if Angstrom flag is set
lineLen = 0;
for(ii = 0; ii <= 19; ii++)
{
if((p[ii] == '\n') || (p[ii] == '\0'))
break;
lineLen++;
}
if(lineLen > 19)
{
if(p[19] != ' ')
unitFactor = UNIT_one_Angstrom;
}
// skip till end of line
while(*p && *p != '\n') p++;
}
else
{ /* "free" format */
do {
if(strncasecmp(p, "Atomtypes=", 10) == 0)
sscanf(p+10, "%d", &noOfAtomTypes);
else if(strncmp(p, "Angstrom", 8) == 0)
unitFactor = UNIT_one_Angstrom;
while(*p && *p != '\n' && *p != ' ') p++;
if(*p != ' ') break;
p++;
} while(1);
}
if(*p == '\n') p++;
do_output(LOG_CAT_INFO, LOG_AREA_MAIN,
"noOfAtomTypes = %i dist. unit=%f au", noOfAtomTypes, unitFactor);
if(noOfAtomTypes <= 0)
{
do_output(LOG_CAT_ERROR, LOG_AREA_MAIN, "Error: (noOfAtomTypes <= 0)");
return -3;
}
for(atomTypeNo = 0; atomTypeNo < noOfAtomTypes; atomTypeNo++)
{
// now p should point to beginning of new atom type
float charge;
if(*p == '\0')
{
do_output(LOG_CAT_ERROR, LOG_AREA_MAIN, "error in readMoleculeFile for atom type %i",
atomTypeNo+1);
return -4;
}
do_output(LOG_CAT_INFO, LOG_AREA_MAIN, "atomTypeNo = %i", atomTypeNo);
// skip blanks
while(*p == ' ') p++;
if(*p == '\0') return -5;
// if the first character on the line is a digit, we assume fixed format
if(*p >= '0' && *p <= '9')
{
charge = (float)atof(p);
while(*p != ' ' && *p != '\n' && *p != '\0') p++;
// skip blanks
while(*p == ' ') p++;
// now we expect another digit
if(*p < '0' || *p > '9')
return -6;
nAtomsCurrType = atoi(p);
while(*p != ' ' && *p != '\n' && *p != '\0') p++;
// skip blanks
while(*p == ' ') p++;
// now we expect end of line
if(*p != '\n')
return -7;
p++;
}
else
{ /* "free" format */
charge = -1;
nAtomsCurrType = -1;
do {
if(strncmp(p, "Charge=", 7) == 0)
sscanf(p+7, "%f", &charge);
else if(strncmp(p, "Atoms=", 6) == 0)
sscanf(p+6, "%d", &nAtomsCurrType);
while(*p && *p != '\n' && *p != ' ') p++;
if(*p != ' ') break;
p++;
} while(1);
if(charge < 0) {
do_output(LOG_CAT_ERROR, LOG_AREA_MAIN,
"Invalid charge = %5.2f", (double)charge);
return -8;
}
if(nAtomsCurrType < 0) {
do_output(LOG_CAT_ERROR, LOG_AREA_MAIN,
"Invalid number of atoms = %i", nAtomsCurrType);
return -8;
}
}
do_output(LOG_CAT_INFO, LOG_AREA_MAIN,
"charge = %5.2f, nAtomsCurrType = %i", (double)charge, nAtomsCurrType);
atomCharge = charge;
if(atomCharge <= 0)
return -9;
for(i = 0; i < nAtomsCurrType; i++)
{
// skip atom label
while(*p == ' ') p++;
while((*p != ' ') && (*p != '\0')) p++;
if(*p == '\0') return -10;
while(*p == ' ') p++;
// read coordinates
ergo_real coords[3];
for(j = 0; j < 3; j++)
{
// skip blanks
while(*p == ' ') p++;
if(*p == '\0') return -11;
coords[j] = atof(p) * unitFactor;
while((*p != ' ') && (*p != '\n') && (*p != '\0')) p++;
if(*p == '\0') return -12;
}
// skip rest of line
while((*p != '\n') && (*p != '\0'))
p++;
p++;
result->addAtom(atomCharge, coords[0], coords[1], coords[2]);
nAtoms++;
} // END FOR i
} // END FOR atomTypeNo
// done. now there should be nothing more in the file.
while(*p != '\0')
{
if(*p != ' ' && *p != '\n')
{
do_output(LOG_CAT_ERROR, LOG_AREA_MAIN, "error in readMoleculeFile: "
"non-blank character found after last atom.");
return -14;
}
p++;
}
#if 0
for(i = 0; i < nAtoms; i++)
{
printf("%5.2f %22.11f %22.11f %22.11f\n",
result->atoms[i].charge,
result->atoms[i].coords[0],
result->atoms[i].coords[1],
result->atoms[i].coords[2]);
}
#endif
assert(result->getNoOfAtoms() == nAtoms);
result->setNetCharge(netCharge);
return 0;
}
int
Molecule::setFromMoleculeFile(const char* fileName,
int netCharge, char **basisfilename)
{
// Check filename extension
int len = strlen(fileName);
if(len < 5)
{
// Too short to have a 3-letter extension after dot.
// Assume mol format.
return readMoleculeFileInMolFormat(this, fileName, netCharge,
basisfilename);
}
const char* extensionPtr = &fileName[len-4];
if(strcasecmp(extensionPtr, ".xyz") == 0)
return readMoleculeFileInXyzFormat(*this, fileName, netCharge, false);
// Not xyz, assume mol format.
return readMoleculeFileInMolFormat(this, fileName, netCharge,
basisfilename);
}
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