int tclcommand_analyze_set_parse_trapmol(Tcl_Interp *interp, int argc, char **argv)
{
#ifdef MOLFORCES
#ifdef EXTERNAL_FORCES
int trap_flag = 0;
int noforce_flag =0;
int i;
#endif
#endif
int mol_num;
double spring_constant;
double drag_constant;
int isrelative;
DoubleList trap_center;
IntList trap_coords;
IntList noforce_coords;
char usage[] = "trapmol usage: <mol_id> { <xpos> <ypos> <zpos> } <isrelative> <spring_constant> <drag_constant> coords { <trapped_coord> <trapped_coord> <trapped_coord> } noforce_coords {<noforce_coord> <noforce_coord> <noforce_coord>}";
init_doublelist(&trap_center);
init_intlist(&trap_coords);
alloc_intlist(&trap_coords,3);
init_intlist(&noforce_coords);
alloc_intlist(&noforce_coords,3);
/* Unless coords are specified the default is just to trap it completely */
trap_coords.e[0] = 1;
trap_coords.e[1] = 1;
trap_coords.e[2] = 1;
Tcl_ResetResult(interp);
/* The first argument should be a molecule number */
if (!ARG0_IS_I(mol_num)) {
Tcl_AppendResult(interp, "first argument should be a molecule id", (char *)NULL);
Tcl_AppendResult(interp, usage, (char *)NULL);
return TCL_ERROR;
} else {
/* Sanity checks */
if (mol_num > n_molecules) {
Tcl_AppendResult(interp, "trapmol: cannot trap mol %d because it does not exist",mol_num , (char *)NULL);
return TCL_ERROR;
}
argc--;
argv++;
}
/* The next argument should be a double list specifying the trap center */
if (!ARG0_IS_DOUBLELIST(trap_center)) {
Tcl_AppendResult(interp, "second argument should be a double list", (char *)NULL);
Tcl_AppendResult(interp, usage , (char *)NULL);
return TCL_ERROR;
} else {
argc -= 1;
argv += 1;
}
/* The next argument should be an integer specifying whether the trap is relative (fraction of box_l) or absolute */
if (!ARG0_IS_I(isrelative)) {
Tcl_AppendResult(interp, "third argument should be an integer", (char *)NULL);
Tcl_AppendResult(interp, usage, (char *)NULL);
return TCL_ERROR;
} else {
argc -= 1;
argv += 1;
}
/* The next argument should be the spring constant for the trap */
if (!ARG0_IS_D(spring_constant)) {
Tcl_AppendResult(interp, "fourth argument should be a double", (char *)NULL);
Tcl_AppendResult(interp, usage, (char *)NULL);
return TCL_ERROR;
} else {
argc -= 1;
argv += 1;
}
/* The next argument should be the drag constant for the trap */
if (!ARG0_IS_D(drag_constant)) {
Tcl_AppendResult(interp, "fifth argument should be a double", (char *)NULL);
Tcl_AppendResult(interp, usage, (char *)NULL);
return TCL_ERROR;
} else {
argc -= 1;
argv += 1;
}
/* Process optional arguments */
while ( argc > 0 ) {
if ( ARG0_IS_S("coords") ) {
if ( !ARG_IS_INTLIST(1,trap_coords) ) {
Tcl_AppendResult(interp, "an intlist is required to specify coords", (char *)NULL);
Tcl_AppendResult(interp, usage, (char *)NULL);
return TCL_ERROR;
}
argc -= 2;
argv += 2;
} else if ( ARG0_IS_S("noforce_coords")) {
if ( !ARG_IS_INTLIST(1,noforce_coords) ) {
Tcl_AppendResult(interp, "an intlist is required to specify coords", (char *)NULL);
Tcl_AppendResult(interp, usage, (char *)NULL);
return TCL_ERROR;
}
argc -= 2;
argv += 2;
} else {
Tcl_AppendResult(interp, "an option is not recognised", (char *)NULL);
Tcl_AppendResult(interp, usage, (char *)NULL);
return TCL_ERROR;
}
}
#ifdef MOLFORCES
#ifdef EXTERNAL_FORCES
for (i = 0; i < 3; i++) {
if (trap_coords.e[i])
trap_flag |= COORD_FIXED(i);
if (noforce_coords.e[i])
noforce_flag |= COORD_FIXED(i);
}
if (set_molecule_trap(mol_num, trap_flag,&trap_center,spring_constant, drag_constant, noforce_flag, isrelative) == TCL_ERROR) {
Tcl_AppendResult(interp, "set topology first", (char *)NULL);
return TCL_ERROR;
}
#else
Tcl_AppendResult(interp, "Error: EXTERNAL_FORCES not defined ", (char *)NULL);
return TCL_ERROR;
#endif
#endif
realloc_doublelist(&trap_center,0);
realloc_intlist(&trap_coords,0);
realloc_intlist(&noforce_coords,0);
return tclcommand_analyze_set_parse_topo_part_sync(interp);
}
int tabulated_set_params(int part_type_a, int part_type_b, char* filename)
{
IA_parameters *data;
FILE* fp;
int npoints;
double minval, maxval;
int i, newsize;
int token;
double dummr;
token = 0;
data = get_ia_param_safe(part_type_a, part_type_b);
if (!data)
return 1;
if (strlen(filename) > MAXLENGTH_TABFILE_NAME-1 )
return 2;
/* Open the file containing force and energy tables */
fp = fopen( filename , "r");
if ( !fp )
return 3;
/* Look for a line starting with # */
while ( token != EOF) {
token = fgetc(fp);
if ( token == '#' ) { break; }
}
if ( token == EOF ) {
fclose(fp);
return 4;
}
/* First read two important parameters we read in the data later*/
if (fscanf( fp , "%d %lf %lf", &npoints, &minval, &maxval) != 3) return 5;
// Set the newsize to the same as old size : only changed if a new force table is being added.
newsize = tabulated_forces.max;
if ( data->TAB_npoints == 0){
// A new potential will be added so set the number of points, the startindex and newsize
data->TAB_npoints = npoints;
data->TAB_startindex = tabulated_forces.max;
newsize += npoints;
} else {
// We have existing data for this pair of monomer types check array sizing
if ( data->TAB_npoints != npoints ) {
fclose(fp);
return 6;
}
}
/* Update parameters symmetrically */
data->TAB_maxval = maxval;
data->TAB_minval = minval;
strcpy(data->TAB_filename,filename);
/* Calculate dependent parameters */
data->TAB_stepsize = (maxval-minval)/(double)(data->TAB_npoints - 1);
/* Allocate space for new data */
realloc_doublelist(&tabulated_forces,newsize);
realloc_doublelist(&tabulated_energies,newsize);
/* Read in the new force and energy table data */
for (i =0 ; i < npoints ; i++)
{
if (fscanf(fp,"%lf %lf %lf",&dummr,
&(tabulated_forces.e[i+data->TAB_startindex]),
&(tabulated_energies.e[i+data->TAB_startindex])) != 3) return 5;
}
fclose(fp);
/* broadcast interaction parameters including force and energy tables*/
mpi_bcast_ia_params(part_type_a, part_type_b);
mpi_cap_forces(force_cap);
return 0;
}
