void ComputeExtMgr::recvCoord(ExtCoordMsg *msg) {
if ( ! numSources ) {
numSources = (PatchMap::Object())->numNodesWithPatches();
coordMsgs = new ExtCoordMsg*[numSources];
for ( int i=0; i<numSources; ++i ) { coordMsgs[i] = 0; }
numArrived = 0;
numAtoms = Node::Object()->molecule->numAtoms;
coord = new ComputeExtAtom[numAtoms];
force = new ExtForce[numAtoms];
}
int i;
for ( i=0; i < msg->numAtoms; ++i ) {
coord[msg->coord[i].id] = msg->coord[i];
}
coordMsgs[numArrived] = msg;
++numArrived;
if ( numArrived < numSources ) return;
numArrived = 0;
// ALL DATA ARRIVED --- CALCULATE FORCES
Lattice lattice = msg->lattice;
SimParameters *simParams = Node::Object()->simParameters;
FILE *file;
int iret;
// write coordinates to file
//iout << "writing to file " << simParams->extCoordFilename << "\n" << endi;
file = fopen(simParams->extCoordFilename,"w");
if ( ! file ) { NAMD_die(strerror(errno)); }
for ( i=0; i<numAtoms; ++i ) {
int id = coord[i].id + 1;
double charge = coord[i].charge;
double x = coord[i].position.x;
double y = coord[i].position.y;
double z = coord[i].position.z;
iret = fprintf(file,"%d %f %f %f %f\n",id,charge,x,y,z);
if ( iret < 0 ) { NAMD_die(strerror(errno)); }
}
// write periodic cell lattice (0 0 0 if non-periodic)
Vector a = lattice.a(); if ( ! lattice.a_p() ) a = Vector(0,0,0);
Vector b = lattice.b(); if ( ! lattice.b_p() ) b = Vector(0,0,0);
Vector c = lattice.c(); if ( ! lattice.c_p() ) c = Vector(0,0,0);
iret = fprintf(file,"%f %f %f\n%f %f %f\n%f %f %f\n",
a.x, a.y, a.z, b.x, b.y, b.z, c.x, c.y, c.z);
if ( iret < 0 ) { NAMD_die(strerror(errno)); }
fclose(file);
// run user-specified command
//iout << "running command " << simParams->extForcesCommand << "\n" << endi;
iret = system(simParams->extForcesCommand);
if ( iret == -1 ) { NAMD_die(strerror(errno)); }
if ( iret ) { NAMD_die("Error running command for external forces."); }
// remove coordinate file
iret = remove(simParams->extCoordFilename);
if ( iret ) { NAMD_die(strerror(errno)); }
// read forces from file (overwrite positions)
//iout << "reading from file " << simParams->extForceFilename << "\n" << endi;
file = fopen(simParams->extForceFilename,"r");
if ( ! file ) { NAMD_die(strerror(errno)); }
for ( i=0; i<numAtoms; ++i ) {
int id, replace;
double x, y, z;
iret = fscanf(file,"%d %d %lf %lf %lf\n", &id, &replace, &x, &y, &z);
if ( iret != 5 ) { NAMD_die("Error reading external forces file."); }
if ( id != i + 1 ) { NAMD_die("Atom ID error in external forces file."); }
force[i].force.x = x; force[i].force.y = y; force[i].force.z = z;
force[i].replace = replace;
}
// read energy and virial if they are present
// virial used by NAMD is -'ve of normal convention, so reverse it!
// virial[i][j] in file should be sum of -1 * f_i * r_j
double energy;
double virial[3][3];
iret = fscanf(file,"%lf\n", &energy);
if ( iret != 1 ) {
energy = 0;
for ( int k=0; k<3; ++k ) for ( int l=0; l<3; ++l ) virial[k][l] = 0;
} else {
iret = fscanf(file,"%lf %lf %lf\n%lf %lf %lf\n%lf %lf %lf\n",
&virial[0][0], &virial[0][1], &virial[0][2],
&virial[1][0], &virial[1][1], &virial[1][2],
&virial[2][0], &virial[2][1], &virial[2][2]);
if ( iret != 9 ) {
for ( int k=0; k<3; ++k ) for ( int l=0; l<3; ++l ) virial[k][l] = 0;
} else {
// virial used by NAMD is -'ve of normal convention, so reverse it!
for ( int k=0; k<3; ++k ) for ( int l=0; l<3; ++l ) virial[k][l] *= -1.0;
}
}
fclose(file);
// remove force file
iret = remove(simParams->extForceFilename);
if ( iret ) { NAMD_die(strerror(errno)); }
// distribute forces
for ( int j=0; j < numSources; ++j ) {
ExtCoordMsg *cmsg = coordMsgs[j];
coordMsgs[j] = 0;
ExtForceMsg *fmsg = new (cmsg->numAtoms, 0) ExtForceMsg;
for ( int i=0; i < cmsg->numAtoms; ++i ) {
fmsg->force[i] = force[cmsg->coord[i].id];
}
if ( ! j ) {
fmsg->energy = energy;
for ( int k=0; k<3; ++k ) for ( int l=0; l<3; ++l )
fmsg->virial[k][l] = virial[k][l];
} else {
fmsg->energy = 0;
for ( int k=0; k<3; ++k ) for ( int l=0; l<3; ++l )
fmsg->virial[k][l] = 0;
}
extProxy[cmsg->sourceNode].recvForce(fmsg);
delete cmsg;
}
}
void ComputeMsmSerialMgr::recvCoord(MsmSerialCoordMsg *msg) {
if ( ! numSources ) {
numSources = (PatchMap::Object())->numNodesWithPatches();
coordMsgs = new MsmSerialCoordMsg*[numSources];
for ( int i=0; i<numSources; ++i ) { coordMsgs[i] = 0; }
numArrived = 0;
numAtoms = Node::Object()->molecule->numAtoms;
coord = new ComputeMsmSerialAtom[numAtoms];
force = new MsmSerialForce[numAtoms];
}
int i;
for ( i=0; i < msg->numAtoms; ++i ) {
coord[msg->coord[i].id] = msg->coord[i];
}
coordMsgs[numArrived] = msg;
++numArrived;
if ( numArrived < numSources ) return;
numArrived = 0;
// ALL DATA ARRIVED --- CALCULATE FORCES
Lattice lattice = msg->lattice;
SimParameters *simParams = Node::Object()->simParameters;
double energy = 0;
double virial[3][3];
int rc = 0; // return code
if ( ! msmsolver ) {
//
// setup MSM solver
//
msmsolver = NL_msm_create();
if ( ! msmsolver ) NAMD_die("unable to create MSM solver");
double dielectric = simParams->dielectric;
double cutoff = simParams->cutoff;
double gridspacing = simParams->MSMGridSpacing;
double padding = simParams->MSMPadding;
int approx = simParams->MSMApprox;
int split = simParams->MSMSplit;
int nlevels = simParams->MSMLevels;
int msmflags = 0;
msmflags |= (lattice.a_p() ? NL_MSM_PERIODIC_VEC1 : 0);
msmflags |= (lattice.b_p() ? NL_MSM_PERIODIC_VEC2 : 0);
msmflags |= (lattice.c_p() ? NL_MSM_PERIODIC_VEC3 : 0);
msmflags |= NL_MSM_COMPUTE_LONG_RANGE; // compute only long-range part
//msmflags |= NL_MSM_COMPUTE_ALL;
//printf("msmflags = %x\n", msmflags);
rc = NL_msm_configure(msmsolver, gridspacing, approx, split, nlevels);
if (rc) NAMD_die("unable to configure MSM solver");
Vector u=lattice.a(), v=lattice.b(), w=lattice.c(), c=lattice.origin();
Vector ru=lattice.a_r(), rv=lattice.b_r(), rw=lattice.c_r();
if ((msmflags & NL_MSM_PERIODIC_ALL) != NL_MSM_PERIODIC_ALL) {
// called only if there is some non-periodic boundary
int isperiodic = (msmflags & NL_MSM_PERIODIC_ALL);
//printf("calling rescale\n");
rescale_nonperiodic_cell(u, v, w, c, ru, rv, rw,
isperiodic, numAtoms, coord, padding, gridspacing);
}
double vec1[3], vec2[3], vec3[3], center[3];
vec1[0] = u.x;
vec1[1] = u.y;
vec1[2] = u.z;
vec2[0] = v.x;
vec2[1] = v.y;
vec2[2] = v.z;
vec3[0] = w.x;
vec3[1] = w.y;
vec3[2] = w.z;
center[0] = c.x;
center[1] = c.y;
center[2] = c.z;
#if 0
printf("dielectric = %g\n", dielectric);
printf("vec1 = %g %g %g\n", vec1[0], vec1[1], vec1[2]);
printf("vec2 = %g %g %g\n", vec2[0], vec2[1], vec2[2]);
printf("vec3 = %g %g %g\n", vec3[0], vec3[1], vec3[2]);
printf("center = %g %g %g\n", center[0], center[1], center[2]);
printf("cutoff = %g\n", cutoff);
printf("numatoms = %d\n", numAtoms);
#endif
rc = NL_msm_setup(msmsolver, cutoff, vec1, vec2, vec3, center, msmflags);
if (rc) NAMD_die("unable to set up MSM solver");
msmcoord = new double[4*numAtoms];
msmforce = new double[3*numAtoms];
if (msmcoord==0 || msmforce==0) NAMD_die("can't allocate MSM atom buffers");
// scale charges - these won't change
double celec = sqrt(COULOMB / simParams->dielectric);
for (i = 0; i < numAtoms; i++) {
msmcoord[4*i+3] = celec * coord[i].charge;
}
}
// evaluate long-range MSM forces
for (i = 0; i < numAtoms; i++) {
msmcoord[4*i ] = coord[i].position.x;
msmcoord[4*i+1] = coord[i].position.y;
msmcoord[4*i+2] = coord[i].position.z;
}
for (i = 0; i < numAtoms; i++) {
msmforce[3*i ] = 0;
msmforce[3*i+1] = 0;
msmforce[3*i+2] = 0;
}
rc = NL_msm_compute_force(msmsolver, msmforce, &energy, msmcoord, numAtoms);
if (rc) NAMD_die("error evaluating MSM forces");
for (i = 0; i < numAtoms; i++) {
force[i].x = msmforce[3*i ];
force[i].y = msmforce[3*i+1];
force[i].z = msmforce[3*i+2];
}
// MSM does not yet calculate virial
for (int k=0; k < 3; k++) {
for (int l=0; l < 3; l++) {
virial[k][l] = 0;
}
}
// distribute forces
for (int j=0; j < numSources; j++) {
MsmSerialCoordMsg *cmsg = coordMsgs[j];
coordMsgs[j] = 0;
MsmSerialForceMsg *fmsg = new (cmsg->numAtoms, 0) MsmSerialForceMsg;
for (int i=0; i < cmsg->numAtoms; i++) {
fmsg->force[i] = force[cmsg->coord[i].id];
}
if ( ! j ) { // set virial and energy only for first message
fmsg->energy = energy;
for (int k=0; k < 3; k++) {
for (int l=0; l < 3; l++) {
fmsg->virial[k][l] = virial[k][l];
}
}
}
else { // set other messages to zero, add into reduction only once
fmsg->energy = 0;
for (int k=0; k < 3; k++) {
for (int l=0; l < 3; l++) {
fmsg->virial[k][l] = 0;
}
}
}
msmProxy[cmsg->sourceNode].recvForce(fmsg);
delete cmsg;
}
}
int ScriptTcl::Tcl_coorfile(ClientData clientData,
Tcl_Interp *interp, int argc, char *argv[]) {
ScriptTcl *script = (ScriptTcl *)clientData;
script->initcheck();
if (argc == 4 && !strcmp(argv[1], "open")) {
if (strcmp(argv[2], "dcd")) {
NAMD_die("Sorry, coorfile presently supports only DCD files");
}
filehandle = dcdplugin->open_file_read(argv[3], "dcd", &numatoms);
if (!filehandle) {
Tcl_AppendResult(interp, "coorfile: Error opening file ", argv[3], NULL);
return TCL_ERROR;
}
if (numatoms != Node::Object()->pdb->num_atoms()) {
Tcl_AppendResult(interp, "Coordinate file ", argv[3],
"\ncontains the wrong number of atoms.", NULL);
return TCL_ERROR;
}
coords = new float[3*numatoms];
vcoords = new Vector[3*numatoms];
iout << iINFO << "Coordinate file " << argv[3] << " opened for reading.\n"
<< endi;
} else if (argc == 2 && !strcmp(argv[1], "read")) {
if (filehandle == NULL) {
Tcl_AppendResult(interp, "coorfile read: Error, no file open for reading",
NULL);
return TCL_ERROR;
}
molfile_timestep_t ts;
ts.coords = coords;
int rc = dcdplugin->read_next_timestep(filehandle, numatoms, &ts);
if (rc) { // EOF
Tcl_SetObjResult(interp, Tcl_NewIntObj(-1));
return TCL_OK;
}
iout << iINFO << "Reading timestep from file.\n" << endi;
Lattice lattice;
if (get_lattice_from_ts(&lattice, &ts)) {
iout << iINFO << "Updating unit cell from timestep.\n" << endi;
if ( lattice.a_p() && ! script->state->lattice.a_p() ||
lattice.b_p() && ! script->state->lattice.b_p() ||
lattice.c_p() && ! script->state->lattice.c_p() ) {
iout << iWARN << "Cell basis vectors should be specified before reading trajectory.\n" << endi;
}
// update Controller's lattice, but don't change the origin!
Vector a(0.); if ( script->state->lattice.a_p() ) a = lattice.a();
Vector b(0.); if ( script->state->lattice.b_p() ) b = lattice.b();
Vector c(0.); if ( script->state->lattice.c_p() ) c = lattice.c();
script->state->lattice.set(a,b,c);
SetLatticeMsg *msg = new SetLatticeMsg;
msg->lattice = script->state->lattice;
(CProxy_PatchMgr(CkpvAccess(BOCclass_group).patchMgr)).setLattice(msg);
script->barrier();
}
for (int i=0; i<numatoms; i++) {
vcoords[i].x = coords[3*i+0];
vcoords[i].y = coords[3*i+1];
vcoords[i].z = coords[3*i+2];
}
Node::Object()->pdb->set_all_positions(vcoords);
script->reinitAtoms();
Tcl_SetObjResult(interp, Tcl_NewIntObj(0));
} else if (argc == 2 && !strcmp(argv[1], "close")) {
if (!filehandle) {
Tcl_AppendResult(interp, "coorfile close: No file opened for reading!",
NULL);
return TCL_OK;
}
iout << iINFO << "Closing coordinate file.\n" << endi;
dcdplugin->close_file_read(filehandle);
filehandle = NULL;
delete [] coords;
delete [] vcoords;
} else if (argc ==2 && !strcmp(argv[1], "skip")) {
if (filehandle == NULL) {
Tcl_AppendResult(interp, "coorfile skip: Error, no file open for reading",
NULL);
return TCL_ERROR;
}
int rc = dcdplugin->read_next_timestep(filehandle, numatoms, NULL);
if (rc) { // EOF
Tcl_SetObjResult(interp, Tcl_NewIntObj(-1));
return TCL_OK;
}
Tcl_SetObjResult(interp, Tcl_NewIntObj(0));
} else {
NAMD_die("Unknown option passed to coorfile");
}
return TCL_OK;
}