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lammps/tools/lmp2arc/src/unwrap_molecules.c
e7e5ba4e4688lammps-icms

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unwrap_molecules.c
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#include "lmp2.h"
void unwrap_molecules(struct NewAtomCoordinates *coord,struct Sys *sysinfo)
{
int iflag[5],nflag[5],icase;
register int i,iax,imol;
int min_true,max_true;
if (trueflag) {
/* Use trueflags to "unwrap" molecules */
for (imol=0; imol < sysinfo->no_molecules; imol++) {
for (iax=0; iax < 3; iax++) {
min_true = 1000;
max_true = -1000;
for (i=sysinfo->molinfo[imol].start; i < sysinfo->molinfo[imol].end;
i++) {
if (coord[i].truef[iax] < min_true) min_true = coord[i].truef[iax];
if (coord[i].truef[iax] > max_true) max_true = coord[i].truef[iax];
}
if ((min_true > 0) || (max_true < 0)) {
for (i=sysinfo->molinfo[imol].start; i < sysinfo->molinfo[imol].end;
i++) coord[i].truef[iax] -= min_true;
}
} /* end loop over iax */
} /* end loop over imol */
}
else {
/* Use coordinates to "unwrap" molecules */
for (imol=0; imol < sysinfo->no_molecules; imol++) {
for (iax=0; iax < 3; iax++) {
for (i=0; i<5; i++) { iflag[i] = 0; nflag[i] = 0;}
for (i=sysinfo->molinfo[imol].start; i < sysinfo->molinfo[imol].end;
i++) {
if (coord[i].fract[iax] <= 0.20)
nflag[0]++;
else if ((coord[i].fract[iax] > 0.20) && (coord[i].fract[iax] <= 0.40))
nflag[1]++;
else if ((coord[i].fract[iax] > 0.40) && (coord[i].fract[iax] <= 0.60))
nflag[2]++;
else if ((coord[i].fract[iax] > 0.60) && (coord[i].fract[iax] <= 0.80))
nflag[3]++;
else if ((coord[i].fract[iax] > 0.80) && (coord[i].fract[iax] <= 1.00))
nflag[4]++;
}
for (i=0; i<5; i++) { if (nflag[i] > 0) iflag[i] = 1; }
icase = 10000*iflag[0] + 1000*iflag[1] + 100*iflag[2] + 10*iflag[3] + iflag[4];
switch (icase) {
case 10001:
if (nflag[0] > nflag[4]) {
for (i=sysinfo->molinfo[imol].start; i < sysinfo->molinfo[imol].end;
i++) if (coord[i].fract[iax] > 0.80) coord[i].fract[iax] -= 1.0;
}
else {
for (i=sysinfo->molinfo[imol].start; i < sysinfo->molinfo[imol].end;
i++) if (coord[i].fract[iax] <= 0.20) coord[i].fract[iax] += 1.0;
}
break;
case 11001:
for (i=sysinfo->molinfo[imol].start; i < sysinfo->molinfo[imol].end;
i++) if (coord[i].fract[iax] > 0.80) coord[i].fract[iax] -= 1.0;
break;
case 10011:
for (i=sysinfo->molinfo[imol].start; i < sysinfo->molinfo[imol].end;
i++) if (coord[i].fract[iax] < 0.20) coord[i].fract[iax] += 1.0;
break;
case 11101:
for (i=sysinfo->molinfo[imol].start; i < sysinfo->molinfo[imol].end;
i++) if (coord[i].fract[iax] > 0.80) coord[i].fract[iax] -= 1.0;
break;
case 10111:
for (i=sysinfo->molinfo[imol].start; i < sysinfo->molinfo[imol].end;
i++) if (coord[i].fract[iax] < 0.20) coord[i].fract[iax] += 1.0;
break;
case 11011:
if ((nflag[0]+nflag[1]) > (nflag[3]+nflag[4])) {
for (i=sysinfo->molinfo[imol].start; i < sysinfo->molinfo[imol].end;
i++) if (coord[i].fract[iax] > 0.60) coord[i].fract[iax] -= 1.0;
}
else {
for (i=sysinfo->molinfo[imol].start; i < sysinfo->molinfo[imol].end;
i++) if (coord[i].fract[iax] <= 0.40) coord[i].fract[iax] += 1.0;
}
break;
default:
break;
} /* end switch */
} /* end loop over imol*/
} /* end loop over iax */
} /* end if on trueflag */
}
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