void control_AllegroDogHome::init(int mode)
{
const TCHAR* prop = NULL;
float* val = NULL;
int* ival = NULL;
prop = getProperty(_T("JDOF"));
if (prop)
_jdof = parse_atoi(prop);
_findDevices();
_q.resize(_jdof);
_q.zero();
val = new float[_jdof];
ival = new int[_jdof];
prop = getProperty(_T("dT"));
if (prop)
_dT = parse_atof(prop);
prop = getProperty(_T("speed"));
if (prop)
_home_speed = _ttoi(prop);
else
_home_speed = 200;
prop = getProperty(_T("direction"));
if (prop)
{
for (int i=0; i<_jdof; i++)
ival[i] = 0;
parse_ivector(ival, _jdof, prop);
for (int i=0; i<_jdof; i++)
_home_direction[i] = (ival[i] == 0 ? ival[0] : ival[i]);
}
prop = getProperty(_T("offset"));
if (prop)
{
for (int i=0; i<_jdof; i++)
ival[i] = 0;
parse_ivector(ival, _jdof, prop);
for (int i=0; i<_jdof; i++)
_home_offset[i] = (ival[i] == 0 ? ival[0] : ival[i]);
}
prop = getProperty(_T("offset_tune"));
if (prop)
{
for (int i=0; i<_jdof; i++)
ival[i] = 0;
parse_ivector(ival, _jdof, prop);
for (int i=0; i<_jdof; i++)
_home_offset_tune[i] = (ival[i] == 0 ? ival[0] : ival[i]);
}
delete [] val;
////////////////////////////////////////////////////
_sharedMemory = findDevice(_T("SharedMemory"));
}
static int obj_Cgmap(ClientData /*UNUSED*/, Tcl_Interp *interp, int argc, Tcl_Obj * const objv[])
{
Tcl_Obj *atomselect = NULL;
Tcl_Obj *object = NULL;
Tcl_Obj *bytes = NULL;
Tcl_Obj *bytes_append = NULL;
Tcl_Obj *sel = NULL;
float *coords = NULL;
float *coords_append = NULL;
const char *blockid_field = "user";
const char *order_field = "user2";
const char *weight_field= "user3";
int nframes, natoms, ncoords, result, length;
int first, last, stride;
int molid, append_molid;
natoms = ncoords = result = 0;
molid = append_molid = 0;
first = last = 0;
stride = 1;
nframes = 1;
std::vector<float> weight;
std::vector<int> bead;
std::vector<int> index;
// Parse Arguments
int n = 1;
while (n < argc) {
const char *cmd = Tcl_GetString(objv[n]);
if (!strncmp(cmd, "-molid", 7)) {
if (Tcl_GetIntFromObj(interp,objv[n+1], &molid) != TCL_OK) {return TCL_ERROR;}
n += 2;
} else if (!strncmp(cmd, "-append", 8)) {
if (Tcl_GetIntFromObj(interp,objv[n+1], &append_molid) != TCL_OK) {return TCL_ERROR;}
n += 2;
} else if (!strncmp(cmd, "-sel", 5)) {
sel = objv[n+1];
n += 2;
} else if (!strncmp(cmd, "-first", 5)) {
if (Tcl_GetIntFromObj(interp,objv[n+1], &first) != TCL_OK) {return TCL_ERROR;}
n += 2;
} else if (!strncmp(cmd, "-last", 4)) {
if (Tcl_GetIntFromObj(interp,objv[n+1], &last) != TCL_OK) {return TCL_ERROR;}
n += 2;
} else if (!strncmp(cmd, "-stride", 6)) {
if (Tcl_GetIntFromObj(interp,objv[n+1], &stride) != TCL_OK) {return TCL_ERROR;}
n += 2;
} else if (!strncmp(cmd, "-weight", 7)) {
weight_field = Tcl_GetString(objv[n+1]);
n += 2;
} else if (!strncmp(cmd, "-blockid", 7)) {
blockid_field = Tcl_GetString(objv[n+1]);
n += 2;
} else if (!strncmp(cmd, "-order", 6)) {
order_field = Tcl_GetString(objv[n+1]);
n += 2;
} else {
Tcl_WrongNumArgs(interp,1,objv, (char *)"molid");
return TCL_ERROR;
}
}
// Create an internal selection that we can manipulate if none was defined
// Note that a passed selection overides the passed molid
if (!sel) {
Tcl_Obj *script = Tcl_ObjPrintf("atomselect %i all", molid);
if (Tcl_EvalObjEx(interp, script, TCL_EVAL_DIRECT) != TCL_OK) {
Tcl_SetResult(interp, (char *) "Cgmap: error calling atomselect", TCL_STATIC);
return TCL_ERROR;
}
atomselect = Tcl_GetObjResult(interp);
Tcl_IncrRefCount(atomselect);
} else {
// Create a internal selection that is a COPY of the passed selection
atomselect = Tcl_DuplicateObj(sel);
Tcl_IncrRefCount(atomselect);
// Get the molid
Tcl_Obj *script = Tcl_DuplicateObj(sel);
Tcl_AppendToObj(script, " molid", -1);
if(Tcl_EvalObjEx(interp, script, TCL_EVAL_DIRECT) != TCL_OK) {
Tcl_SetResult(interp, (char *) "Cgmap: error calling atomselect", TCL_STATIC);
return TCL_ERROR;
}
Tcl_Obj *molid_result = Tcl_GetObjResult(interp);
if (Tcl_GetIntFromObj(interp, molid_result, &molid) != TCL_OK) {return TCL_ERROR;}
}
// Get the number of frames
Tcl_Obj *script = Tcl_ObjPrintf("molinfo %i get numframes", molid);
if (Tcl_EvalObjEx(interp, script, TCL_EVAL_DIRECT) != TCL_OK) {
Tcl_SetResult(interp, (char *) "Cgmap: error calling molinfo for nframes", TCL_STATIC);
return TCL_ERROR;
}
object = Tcl_GetObjResult(interp);
if (Tcl_GetIntFromObj(interp, object, &nframes) != TCL_OK) {
Tcl_SetResult(interp, (char *) "Cgmap: error parsing number of frames", TCL_STATIC);
return TCL_ERROR;
}
if ( first < 0 || first >= nframes ) {
Tcl_SetResult(interp, (char *) "Cgmap: illegal value of first_frame", TCL_STATIC);
return TCL_ERROR;
}
if ( last == -1 || last > nframes || last < first ) last = nframes;
// Get the number of atoms from selection
script = Tcl_DuplicateObj(atomselect);
Tcl_AppendToObj(script, " num", -1);
if (Tcl_EvalObjEx(interp, script, TCL_EVAL_DIRECT) != TCL_OK) {
Tcl_SetResult(interp, (char *) "Cgmap: error calling atomselect", TCL_STATIC);
return TCL_ERROR;
}
object = Tcl_GetObjResult(interp);
if (Tcl_GetIntFromObj(interp, object, &natoms) != TCL_OK) {
Tcl_SetResult(interp, (char *) "Cgmap: error parsing number of atoms", TCL_STATIC);
return TCL_ERROR;
}
// Make sure we actually have some atoms
if (natoms == 0) {
Tcl_SetResult(interp, (char *) "Cgmap: Selection or molecule contains no atoms", TCL_STATIC);
return TCL_ERROR;
}
// Get the weights (mass)
script = Tcl_DuplicateObj(atomselect);
Tcl_AppendPrintfToObj (script, " get %s", weight_field);
if (Tcl_EvalObjEx(interp, script, TCL_EVAL_DIRECT) != TCL_OK) {
Tcl_SetResult(interp, (char *) "Cgmap: error calling atomselect for weights", TCL_STATIC);
return TCL_ERROR;
}
ncoords = parse_vector(Tcl_GetObjResult(interp), weight, interp);
if (ncoords == -1) {
Tcl_SetResult(interp, (char *) "Cgmap: error parsing atomselect result", TCL_STATIC);
return TCL_ERROR;
}
// Get the bead IDs
script = Tcl_DuplicateObj(atomselect);
Tcl_AppendPrintfToObj (script, " get %s", blockid_field);
if (Tcl_EvalObjEx(interp, script, TCL_EVAL_DIRECT) != TCL_OK) {
Tcl_SetResult(interp, (char *) "Cgmap: error calling atomselect for blocks", TCL_STATIC);
return TCL_ERROR;
}
ncoords = parse_ivector(Tcl_GetObjResult(interp), bead, interp, true);
if (ncoords == -1) {
Tcl_SetResult(interp, (char *) "Cgmap: error parsing atomselect result", TCL_STATIC);
return TCL_ERROR;
}
// Get the atom IDs, we use these as a map when accessing the coordinate array
// user2 is set via ::CGit::setBeadID
script = Tcl_DuplicateObj(atomselect);
Tcl_AppendPrintfToObj (script, " get %s", order_field);
if (Tcl_EvalObjEx(interp, script, TCL_EVAL_DIRECT) != TCL_OK) {
Tcl_SetResult(interp, (char *) "Cgmap: error calling atomselect for order", TCL_STATIC);
return TCL_ERROR;
}
ncoords = parse_ivector(Tcl_GetObjResult(interp), index, interp, true);
if (ncoords == -1) {
Tcl_SetResult(interp, (char *) "Cgmap: error parsing atomselect result", TCL_STATIC);
return TCL_ERROR;
}
// Get current frame of the target mol
script = Tcl_ObjPrintf("molinfo %d get frame", append_molid);
if (Tcl_EvalObjEx(interp, script, TCL_EVAL_DIRECT) != TCL_OK) {
Tcl_SetResult(interp, (char *) "Cgmap: error getting append mol's current frame", TCL_STATIC);
return TCL_ERROR;
}
int append_frame = 0;
object = Tcl_GetObjResult(interp);
if (Tcl_GetIntFromObj(interp, object, &append_frame) != TCL_OK) {
Tcl_SetResult(interp, (char *) "Cgmap: error parsing append mol's current frame", TCL_STATIC);
return TCL_ERROR;
}
//Get number of atoms in target (append) mol
script = Tcl_ObjPrintf("molinfo %i get numatoms", append_molid);
if (Tcl_EvalObjEx(interp, script, TCL_EVAL_DIRECT) != TCL_OK) {
Tcl_SetResult(interp, (char *) "Cgmap: error getting append mol's number of atoms", TCL_STATIC);
return TCL_ERROR;
}
int append_natoms = 0;
object = Tcl_GetObjResult(interp);
if (Tcl_GetIntFromObj(interp, object, &append_natoms) != TCL_OK) {
Tcl_SetResult(interp, (char *) "Cgmap: error parsing append mol's number of atoms", TCL_STATIC);
return TCL_ERROR;
}
int print = ((last - first) / 10);
if (print < 10) print = 10;
if (print > 100) print = 100;
//Loop over frames, calculate COMS, set coordinates in target mol
for (int frame = first;
frame <= last && frame < nframes;
frame += stride) {
if (frame % print == 0) {
//Tcl_Obj *msg = Tcl_ObjPrintf ("puts \"Mapping frame %i\"", frame);
Tcl_Obj *msg = Tcl_ObjPrintf ("vmdcon -info \"CGit> Mapping frame %i\"", frame);
result = Tcl_EvalObjEx(interp, msg, TCL_EVAL_DIRECT);
if (result != TCL_OK) { return TCL_ERROR; }
}
//Update the frames
Tcl_Obj *mol_chgframe = Tcl_ObjPrintf ("molinfo top set frame %i", frame);
if (Tcl_EvalObjEx(interp, mol_chgframe, TCL_EVAL_DIRECT) != TCL_OK)
return TCL_ERROR;
// Get the coordinates of the molecules in the reference mol
Tcl_Obj *get_ts = Tcl_ObjPrintf("gettimestep %d %i", molid, frame);
if (Tcl_EvalObjEx(interp, get_ts, TCL_EVAL_DIRECT) != TCL_OK) {
Tcl_SetResult(interp, (char *) "Cgmap: error getting coordinates", TCL_STATIC);
return TCL_ERROR;
}
bytes = Tcl_GetObjResult(interp);
Tcl_IncrRefCount(bytes);
Tcl_InvalidateStringRep (bytes);
coords = reinterpret_cast<float *> (Tcl_GetByteArrayFromObj(bytes, &length));
/** Create a new frame for append_mol **/
Tcl_ObjPrintf("animate dup %i", append_molid);
if (Tcl_EvalObjEx(interp, get_ts, TCL_EVAL_DIRECT) != TCL_OK) {
Tcl_SetResult(interp, (char *) "Cgmap: error adding frame to append mol", TCL_STATIC);
return TCL_ERROR;
}
append_frame++;
Tcl_Obj *setframe = Tcl_ObjPrintf("molinfo %i set frame %i; display update", molid, frame);
if (Tcl_EvalObjEx(interp, setframe, TCL_EVAL_DIRECT) != TCL_OK) {
Tcl_SetResult(interp, (char *) "Cgmap: error updating source frame", TCL_STATIC);
return TCL_ERROR;
}
// Copy PBC conditions
Tcl_Obj *setpbc = Tcl_ObjPrintf("molinfo %i set {a b c} [molinfo %i get {a b c}]", append_molid, molid);
if (Tcl_EvalObjEx(interp, setpbc, TCL_EVAL_DIRECT) != TCL_OK) {
Tcl_SetResult(interp, (char *) "Cgmap: error updating PBC", TCL_STATIC);
return TCL_ERROR;
}
// Get the coordinates of the molecules in the target (append) mol
get_ts = Tcl_ObjPrintf("gettimestep %d %i", append_molid, append_frame);
if (Tcl_EvalObjEx(interp, get_ts, TCL_EVAL_DIRECT) != TCL_OK) {
Tcl_SetResult(interp, (char *) "Cgmap: error getting coordinates", TCL_STATIC);
return TCL_ERROR;
}
bytes_append = Tcl_GetObjResult(interp);
Tcl_IncrRefCount(bytes_append);
Tcl_InvalidateStringRep(bytes_append);
coords_append = reinterpret_cast<float *> (Tcl_GetByteArrayFromObj(bytes_append, &length));
//loop over coordinates and beads, calculate COMs
int current_bead, current_atom;
current_bead = current_atom = 0;
// Nested loop to work on each bead at a time
float w,x,y,z;
int j = 0;
for (int start_atom = 0; start_atom < natoms; ) {
current_bead = bead[start_atom];
w = x = y = z = 0;
// Calculate COM for each bead
for ( current_atom = start_atom;
current_atom < natoms && bead[current_atom] == current_bead;
current_atom++) {
//Lookup the atom index from the selection
unsigned int idx = index[current_atom];
float tw = weight[current_atom];
w += tw;
x += tw * coords[3*idx];
y += tw * coords[3*idx+1];
z += tw * coords[3*idx+2];
}
if (w == 0) {
Tcl_SetResult(interp, (char *) "Cgmap: Bad weight can't total zero", TCL_STATIC);
return TCL_ERROR;
}
// Insert calculated COMS into append_mols coordinate array
// Need to figure out some kind of bounds checking here...
coords_append[3 * j ] = x / w;
coords_append[3 * j + 1] = y / w;
coords_append[3 * j + 2] = z / w;
start_atom = current_atom;
j++;
} // bead loop
// call rawtimestep to set byte array for append_mol
Tcl_Obj *set_ts[5];
set_ts[0] = Tcl_NewStringObj("rawtimestep", -1);
set_ts[1] = Tcl_ObjPrintf("%d",append_molid);
set_ts[2] = bytes_append;
set_ts[3] = Tcl_NewStringObj("-frame", -1);
set_ts[4] = Tcl_NewIntObj(append_frame);
if (Tcl_EvalObjv (interp, 5, set_ts, 0) != TCL_OK)
return TCL_ERROR;
//Cleanup
Tcl_DecrRefCount(bytes);
Tcl_DecrRefCount(bytes_append);
} // Frame loop
//Cleanup
Tcl_DecrRefCount(atomselect);
Tcl_SetResult(interp, (char *) "", TCL_STATIC);
return TCL_OK;
}
