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ReadCarFile.c
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Fri, Jul 26, 11:25

ReadCarFile.c
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/*
* This function opens the .car file and extracts coordinate information
* into the atoms Atom structure
*/
#include "msi2lmp.h"
#include <stdlib.h>
#include <string.h>
#include <math.h>
/* ----------------------------------------------------------------------
set global box params
assumes boxlo/hi and triclinic tilts are already set
------------------------------------------------------------------------- */
void set_box(double box[3][3], double *h, double *h_inv)
{
h[0] = box[1][0] - box[0][0];
h[1] = box[1][1] - box[0][1];
h[2] = box[1][2] - box[0][2];
h_inv[0] = 1.0/h[0];
h_inv[1] = 1.0/h[1];
h_inv[2] = 1.0/h[2];
h[3] = box[2][2];
h[4] = box[2][1];
h[5] = box[2][0];
h_inv[3] = -h[3] / (h[1]*h[2]);
h_inv[4] = (h[3]*h[5] - h[1]*h[4]) / (h[0]*h[1]*h[2]);
h_inv[5] = -h[5] / (h[0]*h[1]);
}
/* ----------------------------------------------------------------------
convert triclinic 0-1 lamda coords to box coords for one atom
x = H lamda + x0;
lamda and x can point to same 3-vector
------------------------------------------------------------------------- */
void lamda2x(double *lamda, double *x, double *h, double *boxlo)
{
x[0] = h[0]*lamda[0] + h[5]*lamda[1] + h[4]*lamda[2] + boxlo[0];
x[1] = h[1]*lamda[1] + h[3]*lamda[2] + boxlo[1];
x[2] = h[2]*lamda[2] + boxlo[2];
}
/* ----------------------------------------------------------------------
convert box coords to triclinic 0-1 lamda coords for one atom
lamda = H^-1 (x - x0)
x and lamda can point to same 3-vector
------------------------------------------------------------------------- */
void x2lamda(double *x, double *lamda, double *h_inv, double *boxlo)
{
double delta[3];
delta[0] = x[0] - boxlo[0];
delta[1] = x[1] - boxlo[1];
delta[2] = x[2] - boxlo[2];
lamda[0] = h_inv[0]*delta[0] + h_inv[5]*delta[1] + h_inv[4]*delta[2];
lamda[1] = h_inv[1]*delta[1] + h_inv[3]*delta[2];
lamda[2] = h_inv[2]*delta[2];
}
void ReadCarFile(void)
{
char line[MAX_LINE_LENGTH]; /* Stores lines as they are read in */
int k,m,n; /* counters */
int skip; /* lines to skip at beginning of file */
double lowest, highest; /* temp coordinate finding variables */
double total_q;
double sq_c;
double cos_alpha; /* Added by SLTM Sept 13, 2010 */
double cos_gamma;
double sin_gamma;
double cos_beta;
double sin_beta;
double A, B, C;
double center[3];
double hmat[6];
double hinv[6];
double lamda[3];
/* Open .car file for reading */
sprintf(line,"%s.car",rootname);
if (pflag > 0) printf(" Reading car file: %s\n",line);
if( (CarF = fopen(line,"r")) == NULL ) {
printf("Cannot open %s\n",line);
exit(33);
}
/* Determine Number of molecules & atoms */
rewind(CarF);
no_molecules = -1; /* Set to -1 because counter will be incremented an
extra time at the end of the file */
fgets(line,MAX_LINE_LENGTH,CarF); /* Read header line */
/* Check for periodicity, if present, read cell constants */
if( strncmp(fgets(line,MAX_LINE_LENGTH,CarF),"PBC=ON",6) == 0) {
periodic = 1;
skip = 5; /* Data starts 5 lines from beginning of file */
fgets(line,MAX_LINE_LENGTH,CarF); /* Comment line */
fgets(line,MAX_LINE_LENGTH,CarF); /* Date stamp */
fscanf(CarF,"%*s %lf %lf %lf %lf %lf %lf %*s",
&pbc[0],&pbc[1],&pbc[2],&pbc[3],&pbc[4],&pbc[5]);
/* Added triclinic flag for non-orthogonal boxes Oct 5, 2010 SLTM */
if(pbc[3] != 90.0 || pbc[4] != 90.0 || pbc[5] != 90.0) {
TriclinicFlag = 1;
} else TriclinicFlag = 0;
} else {
periodic = 0;
skip = 4;
if (pflag > 1) {
printf(" %s is not a periodic system\n", rootname);
printf(" Assigning cell parameters based on coordinates\n");
}
fgets(line,MAX_LINE_LENGTH, CarF); /* Comment line */
fgets(line,MAX_LINE_LENGTH, CarF); /* Date Stamp */
}
/* First pass through file -- Count molecules */
while(fgets(line,MAX_LINE_LENGTH,CarF) != NULL )
if( strncmp(line,"end",3) == 0 )
no_molecules++;
/* Allocate space to keep track of the number of atoms within a molecule */
no_atoms = (int *) calloc(no_molecules,sizeof(int));
if ( no_atoms == NULL ) {
printf("Could not allocate memory for no_atoms\n");
exit(32);
}
/* Second pass through file -- Count atoms */
rewind(CarF);
for(n=0; n < skip; n++) /* Skip beginning lines */
fgets(line,MAX_LINE_LENGTH,CarF);
for(n=0; n < no_molecules; n++)
while( strncmp(fgets(line,MAX_LINE_LENGTH,CarF),"end",3) )
no_atoms[n]++;
for( total_no_atoms=0, n=0; n < no_molecules; n++ )
total_no_atoms += no_atoms[n];
molecule = (struct MoleculeList *) calloc(no_molecules,
sizeof(struct MoleculeList));
if (molecule == NULL) {
printf("Unable to allocate memory for molecule structure\n");
exit(32);
}
molecule[0].start = 0;
molecule[0].end = no_atoms[0];
for (n=1; n < no_molecules; n++) {
molecule[n].start = molecule[n-1].end;
molecule[n].end = molecule[n].start + no_atoms[n];
}
/* Allocate space for atoms Atom structures */
atoms = (struct Atom *) calloc(total_no_atoms,sizeof(struct Atom));
if( atoms == NULL ) {
printf("Could not allocate memory for AtomList\n");
exit(32);
}
/* Third pass through file -- Read+Parse Car File */
center[0] = center[1] = center[2] = 0.0;
rewind(CarF);
for(n=0; n < skip; n++)
fgets(line,MAX_LINE_LENGTH,CarF);
for(m=0; m < no_molecules; m++) {
for(k=molecule[m].start; k <
molecule[m].end; k++) {
atoms[k].molecule = m;
atoms[k].no = k;
fscanf(CarF,"%s %lf %lf %lf %*s %d %s %s %lf",
atoms[k].name,
&(atoms[k].x[0]),
&(atoms[k].x[1]),
&(atoms[k].x[2]),
&(atoms[k].molecule),
atoms[k].potential,
atoms[k].element,
&(atoms[k].q));
atoms[k].x[0] += shift[0];
atoms[k].x[1] += shift[1];
atoms[k].x[2] += shift[2];
if (centerflag) {
center[0] += atoms[k].x[0];
center[1] += atoms[k].x[1];
center[2] += atoms[k].x[2];
}
}
fgets(line,MAX_LINE_LENGTH,CarF);
fgets(line,MAX_LINE_LENGTH,CarF);
} /* End m (molecule) loop */
center[0] /= (double) total_no_atoms;
center[1] /= (double) total_no_atoms;
center[2] /= (double) total_no_atoms;
for (total_q=0.0,k=0; k < total_no_atoms; k++)
total_q += atoms[k].q;
if (pflag > 1) {
printf(" There are %d atoms in %d molecules in this file\n",
total_no_atoms,no_molecules);
printf(" The total charge in the system is %7.3f.\n",total_q);
}
/* Search coordinates to find lowest and highest for x, y, and z */
if (periodic == 0) {
/* Added if/else statment STLM Oct 5 2010 */
if (TriclinicFlag == 0) {
/* no need to re-center the box, if we use min/max values */
center[0] = center[1] = center[2] = 0.0;
for ( k = 0; k < 3; k++) {
lowest = atoms[0].x[k];
highest = atoms[0].x[k];
for ( m = 1; m < total_no_atoms; m++) {
if (atoms[m].x[k] < lowest) lowest = atoms[m].x[k];
if (atoms[m].x[k] > highest) highest = atoms[m].x[k];
}
box[0][k] = lowest - 0.5;
box[1][k] = highest + 0.5;
box[2][k] = 0.0;
}
} else {
printf("This tool only works for periodic systems with triclinic boxes");
exit(32);
}
} else {
if (pflag > 2)
printf(" pbc[0] %f pbc[1] %f pbc[2] %f\n", pbc[0] ,pbc[1] ,pbc[2]);
if (TriclinicFlag == 0) {
for (k=0; k < 3; k++) {
box[0][k] = -0.5*pbc[k] + center[k] + shift[k];
box[1][k] = 0.5*pbc[k] + center[k] + shift[k];
box[2][k] = 0.0;
}
} else {
sq_c = pbc[2]*pbc[2];
cos_alpha = cos(pbc[3]*PI_180);
cos_gamma = cos(pbc[5]*PI_180);
sin_gamma = sin(pbc[5]*PI_180);
cos_beta = cos(pbc[4]*PI_180);
sin_beta = sin(pbc[4]*PI_180);
if (pflag > 2) {
printf(" pbc[3] %f pbc[4] %f pbc[5] %f\n", pbc[3] ,pbc[4] ,pbc[5]);
printf(" cos_alpha %f cos_beta %f cos_gamma %f\n", cos_alpha ,cos_beta ,cos_gamma);
}
A = pbc[0];
B = pbc[1];
C = pbc[2];
box[0][0] = -0.5*A + center[0] + shift[0];
box[1][0] = 0.5*A + center[0] + shift[0];
box[0][1] = -0.5*B*sin_gamma + center[1] + shift[1];
box[1][1] = 0.5*B*sin_gamma + center[1] + shift[1];
box[0][2] = -0.5*sqrt(sq_c * sin_beta*sin_beta - C*(cos_alpha-cos_gamma*cos_beta)/sin_gamma) + center[2] + shift[2];
box[1][2] = 0.5*sqrt(sq_c * sin_beta*sin_beta - C*(cos_alpha-cos_gamma*cos_beta)/sin_gamma) + center[2] + shift[2];
box[2][0] = B * cos_gamma; /* This is xy SLTM */
box[2][1] = C * cos_beta; /* This is xz SLTM */
box[2][2] = C*(cos_alpha-cos_gamma*cos_beta)/sin_gamma; /* This is yz SLTM */
}
}
/* compute image flags */
set_box(box,hmat,hinv);
n = 0;
for (m = 0; m < total_no_atoms; m++) {
double tmp;
int w=0;
x2lamda(atoms[m].x,lamda,hinv,box[0]);
for (k = 0; k < 3; ++k) {
tmp = floor(lamda[k]);
atoms[m].image[k] = tmp;
lamda[k] -= tmp;
if (tmp != 0.0) ++w;
}
lamda2x(lamda, atoms[m].x,hmat,box[0]);
if (w > 0) ++n;
}
/* warn if atoms are outside the box */
if (n > 0) {
if (periodic) {
if (pflag > 1)
printf(" %d of %d atoms with nonzero image flags\n\n",n,total_no_atoms);
} else {
if (iflag == 0 || (pflag > 1))
printf(" %d of %d atoms outside the box\n\n",n,total_no_atoms);
condexit(32);
}
}
/* Close .car file */
if (fclose(CarF) !=0) {
printf("Error closing %s.car\n", rootname);
exit(31);
}
}
/* End ReadCarFile() */

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