void IMD::calculate(){
if(comm.Get_rank()==0 && connected && plumed.getStep()%transferRate==0 && vmdsock_selwrite(clientsock,0)) {
double scale=10.0*plumed.getAtoms().getUnits().getLength();
Vector ref;
for(int i=0;i<natoms;i++){
Vector pos=getPosition(i);
if(wrap) pos=pbcDistance(ref,pos);
coord[3*i+0]=static_cast<float>((pos[0]*scale));
coord[3*i+1]=static_cast<float>((pos[1]*scale));
coord[3*i+2]=static_cast<float>((pos[2]*scale));
}
imd_send_fcoords(clientsock,natoms,&coord[0]);
}
}
int tclcommand_imd_parse_pos(Tcl_Interp *interp, int argc, char **argv)
{
enum flag {NONE, UNFOLDED, FOLD_CHAINS};
double shift[3] = {0.0,0.0,0.0};
//double part_selected=n_total_particles;
float *coord;
int flag = NONE;
int i, j;
// Determine how many arguments we have and set the value of flag
switch (argc)
{
case 2:
flag = NONE;
break;
case 3:
{
if (ARG_IS_S(2,"-unfolded"))
{flag = UNFOLDED;}
else if (ARG_IS_S(2,"-fold_chains"))
{flag = FOLD_CHAINS;}
else{
Tcl_AppendResult(interp, "wrong flag to",argv[0],
" positions: should be \" -fold_chains or -unfolded \"",
(char *) NULL);
return (TCL_ERROR);
}
}
break;
default:
Tcl_AppendResult(interp, "wrong # args: should be \"",
argv[0], " positions [-flag]\"",
(char *) NULL);
return (TCL_ERROR);
}
if (!initsock) {
Tcl_AppendResult(interp, "no connection",
(char *) NULL);
return (TCL_OK);
}
if (!sock) {
if (tclcommand_imd_print_check_connect(interp) == TCL_ERROR)
return (TCL_ERROR);
/* no VMD is ok, but tell the user */
if (!sock) {
Tcl_AppendResult(interp, "no connection",
(char *) NULL);
return (TCL_OK);
}
}
if (tclcommand_imd_print_drain_socket(interp) == TCL_ERROR)
return (TCL_ERROR);
/* we do not consider a non connected VMD as error, but tell the user */
if (!sock) {
Tcl_AppendResult(interp, "no connection",
(char *) NULL);
return (TCL_OK);
}
if (!(vmdsock_selwrite(sock, 60) > 0)) {
Tcl_AppendResult(interp, "could not write to IMD socket.",
(char *) NULL);
return (TCL_ERROR);
}
if (n_part != max_seen_particle + 1) {
Tcl_AppendResult(interp, "for IMD, store particles consecutively starting with 0.",
(char *) NULL);
return (TCL_ERROR);
}
updatePartCfg(WITH_BONDS);
coord = (float*)Utils::malloc(n_part*3*sizeof(float));
/* sort partcles according to identities */
for (i = 0; i < n_part; i++) {
int dummy[3] = {0,0,0};
double tmpCoord[3];
tmpCoord[0] = partCfg[i].r.p[0];
tmpCoord[1] = partCfg[i].r.p[1];
tmpCoord[2] = partCfg[i].r.p[2];
if (flag == NONE) { // perform folding by particle
fold_position(tmpCoord, dummy);
}
j = 3*partCfg[i].p.identity;
coord[j ] = tmpCoord[0];
coord[j + 1] = tmpCoord[1];
coord[j + 2] = tmpCoord[2];
}
// Use information from the analyse set command to fold chain molecules
if ( flag == FOLD_CHAINS ){
if(analyze_fold_molecules(coord, shift ) != TCL_OK){
Tcl_AppendResult(interp, "could not fold chains: \"analyze set chains <chain_start> <n_chains> <chain_length>\" must be used first",
(char *) NULL);
return (TCL_ERROR);
}
}
if (imd_send_fcoords(sock, n_part, coord)) {
Tcl_AppendResult(interp, "could not write to IMD socket.",
(char *) NULL);
return (TCL_ERROR);
}
free(coord);
Tcl_AppendResult(interp, "connected",
(char *) NULL);
return (TCL_OK);
}
