/* new version for new topology structure */
int analyze_fold_molecules(float *coord, double shift[3])
{
int m,p,i, tmp;
int mol_size, ind;
double cm_tmp, com[3];
#ifdef LEES_EDWARDS
if(lees_edwards_offset != 0.0 ){
fprintf(stderr, "Error: Folding molecules not supported under Lees-Edwards.\n");
exit(8);
}
#endif
/* check molecule information */
if ( n_molecules < 0 ) return ES_ERROR;
if (!sortPartCfg()) {
ostringstream msg;
msg <<"analyze_fold_molecules: could not sort particle config, particle ids not consecutive?";
runtimeError(msg);
return ES_ERROR;
}
/* loop molecules */
for(m=0; m<n_molecules; m++) {
mol_size = topology[m].part.n;
if(mol_size > 0) {
/* calc center of mass */
calc_mol_center_of_mass(topology[m],com);
/* fold coordinates */
for(i=0; i<3; i++) {
if ( PERIODIC(i) ) {
tmp = (int)floor((com[i]+shift[i])*box_l_i[i]);
cm_tmp =0.0;
for(p=0; p<mol_size; p++) {
ind = 3*topology[m].part.e[p] + i;
coord[ind] -= tmp*box_l[i];
coord[ind] += shift[i];
cm_tmp += coord[ind];
}
cm_tmp /= (double)mol_size;
if(cm_tmp < -10e-6 || cm_tmp > box_l[i]+10e-6) {
ostringstream msg;
msg <<"analyze_fold_molecules: chain center of mass is out of range (coord " << i << ": " << cm_tmp << " not in box_l " << box_l[i] << ")";
runtimeError(msg);
return ES_ERROR;
}
}
}
}
}
return ES_OK;
}
/**Incorporates mass of each particle*/
double calc_mol_gyr_radius2(Molecule mol)
{
int i, id;
double rg=0.0, M=0.0, com[3], diff_vec[3];
calc_mol_center_of_mass(mol, com);
for(i=0; i<mol.part.n; i++) {
id = mol.part.e[i];
vecsub(partCfg[id].r.p, com, diff_vec);
rg += sqrlen(diff_vec);
M += PMASS(partCfg[id]);
}
return (rg/M);
}
/* new version for new topology structure */
int analyze_fold_molecules(float *coord, double shift[3])
{
int m,p,i, tmp;
int mol_size, ind;
double cm_tmp, com[3];
/* check molecule information */
if ( n_molecules < 0 ) return (TCL_ERROR);
if (!sortPartCfg()) {
char *errtxt = runtime_error(128);
ERROR_SPRINTF(errtxt, "{059 analyze_fold_molecules: could not sort particle config, particle ids not consecutive?} ");
return TCL_ERROR;
}
/* loop molecules */
for(m=0; m<n_molecules; m++) {
mol_size = topology[m].part.n;
if(mol_size > 0) {
/* calc center of mass */
calc_mol_center_of_mass(topology[m],com);
/* fold coordinates */
for(i=0; i<3; i++) {
if ( PERIODIC(i) ) {
tmp = (int)floor((com[i]+shift[i])*box_l_i[i]);
cm_tmp =0.0;
for(p=0; p<mol_size; p++) {
ind = 3*topology[m].part.e[p] + i;
coord[ind] -= tmp*box_l[i];
coord[ind] += shift[i];
cm_tmp += coord[ind];
}
cm_tmp /= (double)mol_size;
if(cm_tmp < -10e-6 || cm_tmp > box_l[i]+10e-6) {
char *errtxt = runtime_error(128 + TCL_INTEGER_SPACE + 2*TCL_DOUBLE_SPACE);
ERROR_SPRINTF(errtxt,"{060 analyze_fold_molecules: chain center of mass is out of range (coord %d: %.14f not in box_l %.14f)} ",
i,cm_tmp,box_l[i]);
return (TCL_ERROR);
}
}
}
}
}
return (TCL_OK);
}
