int tclcommand_analyze_set_parse_chain_topology(Tcl_Interp *interp, int argc, char **argv)
{
/* parses a chain topology (e.g. in 'analyze ( rg | <rg> ) [chain start n chains chain length]' , or
in 'analyze set chains <chain_start> <n_chains> <chain_length>') */
int m, i, pc;
if (argc < 3) {
Tcl_AppendResult(interp, "chain structure info consists of <start> <n> <length>", (char *)NULL);
return TCL_ERROR;
}
if (! (ARG0_IS_I(chain_start) && ARG1_IS_I(chain_n_chains) && ARG_IS_I(2, chain_length)))
return TCL_ERROR;
realloc_topology(chain_n_chains);
pc = 0;
for (m = 0; m < n_molecules; m++) {
topology[m].type = 0;
realloc_intlist(&topology[m].part, topology[m].part.n = chain_length);
for (i = 0; i < chain_length; i++)
topology[m].part.e[i] = pc++;
}
return TCL_OK;
}
int tclcommand_analyze_parse_cwvac(Tcl_Interp *interp, int argc, char **argv)
{
/* 'analyze { cwvac } <maxtau> <interval> [<chain_start> <n_chains> <chain_length>]' */
/***********************************************************************************************************/
char buffer[4*TCL_DOUBLE_SPACE+7];
int i, maxtau, interval;
double *avac, *evac;
if (argc < 2) {
Tcl_AppendResult(interp, "Wrong # of args! Usage: analyze gkmobility <maxtau> <interval> [<chain_start> <n_chains> <chain_length>]",
(char *)NULL);
return (TCL_ERROR);
} else {
if (!ARG0_IS_I(maxtau))
return (TCL_ERROR);
if (!ARG1_IS_I(interval))
return (TCL_ERROR);
argc-=2; argv+=2;
}
if (tclcommand_analyze_set_parse_chain_topology_check(interp, argc, argv) == TCL_ERROR) return TCL_ERROR;
if ((chain_n_chains == 0) || (chain_length == 0)) {
Tcl_AppendResult(interp, "The chain topology has not been set",(char *)NULL); return TCL_ERROR;
}
if (maxtau <=0) {
Tcl_AppendResult(interp, "Nothing to be done - choose <maxtau> greater zero!",(char *)NULL); return TCL_ERROR;
}
if (interval <= 0) {
Tcl_AppendResult(interp, "<interval> has to be positive", (char *)NULL);
return TCL_ERROR;
}
updatePartCfg(WITHOUT_BONDS);
analyze_cwvac(maxtau, interval, &avac, &evac);
// create return string
sprintf(buffer, "{ ");
Tcl_AppendResult(interp, buffer, (char *)NULL);
for(i=0;i<=maxtau;i++) {
sprintf(buffer,"%e ",avac[i]);
Tcl_AppendResult(interp, buffer, (char *)NULL);
}
sprintf(buffer, "} { ");
Tcl_AppendResult(interp, buffer, (char *)NULL);
for(i=0;i<=maxtau;i++) {
sprintf(buffer,"%e ",evac[i]);
Tcl_AppendResult(interp, buffer, (char *)NULL);
}
sprintf(buffer, "}");
Tcl_AppendResult(interp, buffer, (char *)NULL);
free(avac); free(evac);
return (TCL_OK);
}
int tclcommand_analyze_parse_and_print_pressure_mol(Tcl_Interp *interp,int argc, char **argv)
{
char buffer[TCL_DOUBLE_SPACE];
int type1, type2;
double psum;
#ifdef ELECTROSTATICS
#ifndef INTER_RF
Tcl_ResetResult(interp);
Tcl_AppendResult(interp, "parse_and_print_pressure_mol is only possible with INTER_RF ", (char *)NULL);
return (TCL_ERROR);
#endif
#endif
updatePartCfg(WITHOUT_BONDS);
if (!sortPartCfg()) {
char *errtxt = runtime_error(128);
ERROR_SPRINTF(errtxt, "{059 parse_and_print_pressure_mol: could not sort particle config, particle ids not consecutive?} ");
return TCL_ERROR;
}
if (argc < 2) {
Tcl_ResetResult(interp);
Tcl_AppendResult(interp, "usage: analyze pressure_mol <type1> <type2>", (char *)NULL);
return (TCL_ERROR);
}
if (!ARG0_IS_I(type1)) {
Tcl_ResetResult(interp);
Tcl_AppendResult(interp, "usage: analyze pressure_mol <type1> <type2>", (char *)NULL);
return (TCL_ERROR);
}
if (!ARG1_IS_I(type2)) {
Tcl_ResetResult(interp);
Tcl_AppendResult(interp, "usage: analyze pressure_mol <type1> <type2>", (char *)NULL);
return (TCL_ERROR);
}
argc-=2;
argv+=2;
if (n_molecules==0) {
Tcl_ResetResult(interp);
Tcl_AppendResult(interp, "No molecules defined !", (char *)NULL);
return (TCL_ERROR);
}
psum=calc_pressure_mol(type1,type2);
//sprintf(buffer,"%i",type1);
//Tcl_AppendResult(interp,"{ analyze pressure_mol ",buffer," ",(char *)NULL);
//sprintf(buffer,"%i",type2);
//Tcl_AppendResult(interp,buffer," ",(char *)NULL);
sprintf(buffer,"%e",psum);
Tcl_AppendResult(interp, buffer,(char *)NULL);
return TCL_OK;
}
int tclcommand_analyze_parse_and_print_energy_kinetic_mol(Tcl_Interp *interp,int argc, char **argv)
{
char buffer[TCL_DOUBLE_SPACE];
int type;
double Ekin;
updatePartCfg(WITHOUT_BONDS);
if (!sortPartCfg()) {
char *errtxt = runtime_error(128);
ERROR_SPRINTF(errtxt, "{059 parse_and_print_energy_kinetic_mol: could not sort particle config, particle ids not consecutive?} ");
return TCL_ERROR;
}
if (argc < 1) {
Tcl_ResetResult(interp);
Tcl_AppendResult(interp, "usage: analyze energy_kinetic <type>", (char *)NULL);
return (TCL_ERROR);
}
if (!ARG0_IS_I(type)) {
Tcl_ResetResult(interp);
Tcl_AppendResult(interp, "usage: analyze energy_kinetic <type>", (char *)NULL);
return (TCL_ERROR);
}
argc-=1;
argv+=1;
if (n_molecules==0) {
Tcl_ResetResult(interp);
Tcl_AppendResult(interp, "No molecules defined !", (char *)NULL);
return (TCL_ERROR);
}
Ekin=calc_energy_kinetic_mol(type);
if (Ekin < 0.0) {
Tcl_ResetResult(interp);
sprintf(buffer,"%i",-(int)Ekin);
Tcl_AppendResult(interp,"Could not fetch com in calc_energy_kinetic_mol! From mol_id",buffer, (char *)NULL);
return (TCL_ERROR);
}
//sprintf(buffer,"%i",type);
//Tcl_AppendResult(interp,"{ analyze pressure_mol ",buffer," ",(char *)NULL);
sprintf(buffer,"%e",Ekin);
Tcl_AppendResult(interp, buffer,(char *)NULL);
return TCL_OK;
}
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 tclcommand_analyze_parse_local_stress_tensor(Tcl_Interp *interp, int argc, char **argv)
{
char buffer[TCL_DOUBLE_SPACE];
int periodic[3];
double range_start[3];
double range[3];
int bins[3];
int i,j,k,l;
DoubleList *TensorInBin;
PTENSOR_TRACE(fprintf(stderr,"%d: Running tclcommand_analyze_parse_local_stress_tensor\n",this_node));
/* 'analyze stress profile ' */
if (argc != 12) {
Tcl_ResetResult(interp);
Tcl_AppendResult(interp, "local_stress_tensor requires 12 inputs: x_periodic, y_periodic, z_periodic, x_range_start, y_range_start, z_range_start, x_range, y_range, z_range, x_bins, y_bins, z_bins", (char *)NULL);
return(TCL_ERROR);
}
const char *usage = "usage: analyse local_stress_tensor <x_periodic> <y_periodic> <z_periodic> <x_range_start> <y_range_start> <z_range_start> <x_range> <y_range> <z_range> <x_bins> <y_bins> <z_bins>";
for (i=0;i<3;i++) {
if ( !ARG0_IS_I(periodic[i]) ) {
Tcl_ResetResult(interp);
Tcl_AppendResult(interp,usage, (char *)NULL);
return (TCL_ERROR);
} else {
argc -= 1;
argv += 1;
}
}
for (i=0;i<3;i++) {
if ( !ARG0_IS_D(range_start[i]) ) {
Tcl_ResetResult(interp);
Tcl_AppendResult(interp,usage, (char *)NULL);
return (TCL_ERROR);
} else {
argc -= 1;
argv += 1;
}
}
for (i=0;i<3;i++) {
if ( !ARG0_IS_D(range[i]) ) {
Tcl_ResetResult(interp);
Tcl_AppendResult(interp,usage, (char *)NULL);
return (TCL_ERROR);
} else {
argc -= 1;
argv += 1;
}
}
for (i=0;i<3;i++) {
if ( !ARG0_IS_I(bins[i]) ) {
Tcl_ResetResult(interp);
Tcl_AppendResult(interp,usage, (char *)NULL);
return (TCL_ERROR);
} else {
argc -= 1;
argv += 1;
}
}
/* Allocate a doublelist of bins to keep track of stress profile */
TensorInBin = (DoubleList *)malloc(bins[0]*bins[1]*bins[2]*sizeof(DoubleList));
if ( TensorInBin ) {
/* Initialize the stress profile */
for ( i = 0 ; i < bins[0]*bins[1]*bins[2]; i++ ) {
init_doublelist(&TensorInBin[i]);
alloc_doublelist(&TensorInBin[i],9);
for ( j = 0 ; j < 9 ; j++ ) {
TensorInBin[i].e[j] = 0.0;
}
}
} else {
Tcl_AppendResult(interp,"could not allocate memory for local_stress_tensor", (char *)NULL);
return (TCL_ERROR);
}
mpi_local_stress_tensor(TensorInBin, bins, periodic,range_start, range);
PTENSOR_TRACE(fprintf(stderr,"%d: tclcommand_analyze_parse_local_stress_tensor: finished mpi_local_stress_tensor \n",this_node));
/* Write stress profile to Tcl export */
Tcl_AppendResult(interp, "{ LocalStressTensor } ", (char *)NULL);
for ( i = 0 ; i < bins[0] ; i++) {
for ( j = 0 ; j < bins[1] ; j++) {
for ( k = 0 ; k < bins[2] ; k++) {
Tcl_AppendResult(interp, " { ", (char *)NULL);
sprintf(buffer," { %d %d %d } ",i,j,k);
Tcl_AppendResult(interp,buffer, (char *)NULL);
Tcl_AppendResult(interp, " { ", (char *)NULL);
for ( l = 0 ; l < 9 ; l++) {
Tcl_PrintDouble(interp,TensorInBin[i*bins[1]*bins[2]+j*bins[2]+k].e[l],buffer);
Tcl_AppendResult(interp, buffer, (char *)NULL);
Tcl_AppendResult(interp, " ", (char *)NULL);
}
Tcl_AppendResult(interp, " } ", (char *)NULL);
Tcl_AppendResult(interp, " } ", (char *)NULL);
}
}
}
/* Free memory */
for ( i = 0 ; i < bins[0]*bins[1]*bins[2] ; i++ ) {
realloc_doublelist(&TensorInBin[i],0);
}
free(TensorInBin);
return TCL_OK;
}
int tclcommand_readpdb(ClientData data, Tcl_Interp *interp, int argc, char *argv[]) {
char *pdb_file = NULL;
char *itp_file = NULL;
int first_id = -1;
int first_type = 0;
int type = -1;
bool fit = false;
bool lj_internal = false;
double lj_rel_cutoff = 2.5;
bool lj_diagonal = false;
std::vector<PdbLJInteraction> ljinteractions;
argc--;
argv++;
while(argc > 0) {
if(ARG0_IS_S("pdb_file")) {
argc--;
argv++;
pdb_file = argv[0];
} else if (ARG0_IS_S("itp_file")) {
argc--;
argv++;
itp_file = argv[0];
} else if (ARG0_IS_S("type")) {
argc--;
argv++;
if(!ARG0_IS_I(type)) {
Tcl_AppendResult(interp, "type takes exactly one integer argument.\n", (char *)NULL);
return TCL_ERROR;
}
} else if (ARG0_IS_S("first_id")) {
argc--;
argv++;
if(!ARG0_IS_I(first_id)) {
Tcl_AppendResult(interp, "first_id takes exactly one integer argument.\n", (char *)NULL);
return TCL_ERROR;
}
} else if (ARG0_IS_S("first_type")) {
argc--;
argv++;
if(!ARG0_IS_I(first_type)) {
Tcl_AppendResult(interp, "first_type takes exactly one integer argument.\n", (char *)NULL);
return TCL_ERROR;
}
} else if (ARG0_IS_S("lj_rel_cutoff")) {
argc--;
argv++;
if(!ARG0_IS_D(lj_rel_cutoff)) {
return TCL_ERROR;
}
} else if (ARG0_IS_S("rescale_box")) {
fit = true;
} else if (ARG0_IS_S("lj_internal")) {
lj_internal = true;
lj_diagonal = false;
} else if (ARG0_IS_S("lj_diagonal")) {
lj_internal = true;
lj_diagonal = true;
} else if (ARG0_IS_S("lj_with")) {
argc--;
argv++;
if(argc < 3)
return TCL_ERROR;
struct PdbLJInteraction ljia;
if(!ARG0_IS_I(ljia.other_type)) {
return TCL_ERROR;
}
argc--;
argv++;
if(!ARG0_IS_D(ljia.epsilon)) {
return TCL_ERROR;
}
argc--;
argv++;
if(!ARG0_IS_D(ljia.sigma)) {
return TCL_ERROR;
}
ljinteractions.push_back(ljia);
}
else {
usage(interp);
return TCL_ERROR;
}
argc--;
argv++;
}
if((type < 0) || (first_id < 0) || (pdb_file == NULL)) {
usage(interp);
return TCL_ERROR;
}
const int n_part = pdb_add_particles_from_file(pdb_file, first_id, type, ljinteractions, lj_rel_cutoff, itp_file, first_type, fit, lj_internal, lj_diagonal);
if(!n_part) {
Tcl_AppendResult(interp, "Could not parse pdb file.", (char *)NULL);
return TCL_ERROR;
}
char buffer[32];
snprintf(buffer, sizeof(buffer), "%d", n_part);
Tcl_AppendResult(interp, buffer, (char *)NULL);
return TCL_OK;
}