void ComputeGridForce::doForce(FullAtom* p, Results* r)
{
SimParameters *simParams = Node::Object()->simParameters;
Molecule *mol = Node::Object()->molecule;
Force *forces = r->f[Results::normal];
BigReal energy = 0;
Force extForce = 0.;
Tensor extVirial;
int numAtoms = homePatch->getNumAtoms();
if ( mol->numGridforceGrids < 1 ) NAMD_bug("No grids loaded in ComputeGridForce::doForce()");
for (int gridnum = 0; gridnum < mol->numGridforceGrids; gridnum++) {
GridforceGrid *grid = mol->get_gridfrc_grid(gridnum);
if (homePatch->flags.step % GF_OVERLAPCHECK_FREQ == 0) {
// only check on node 0 and every GF_OVERLAPCHECK_FREQ steps
if (simParams->langevinPistonOn || simParams->berendsenPressureOn) {
// check for grid overlap if pressure control is on
// not needed without pressure control, since the check is also performed on startup
if (!grid->fits_lattice(homePatch->lattice)) {
char errmsg[512];
if (simParams->gridforcechecksize) {
sprintf(errmsg, "Warning: Periodic cell basis too small for Gridforce grid %d. Set gridforcechecksize off in configuration file to ignore.\n", gridnum);
NAMD_die(errmsg);
}
}
}
}
Position center = grid->get_center();
if (homePatch->flags.step % 100 == 1) {
DebugM(3, "center = " << center << "\n" << endi);
DebugM(3, "e = " << grid->get_e() << "\n" << endi);
}
if (grid->get_grid_type() == GridforceGrid::GridforceGridTypeFull) {
GridforceFullMainGrid *g = (GridforceFullMainGrid *)grid;
do_calc(g, gridnum, p, numAtoms, mol, forces, energy, extForce, extVirial);
} else if (grid->get_grid_type() == GridforceGrid::GridforceGridTypeLite) {
GridforceLiteGrid *g = (GridforceLiteGrid *)grid;
do_calc(g, gridnum, p, numAtoms, mol, forces, energy, extForce, extVirial);
}
}
reduction->item(REDUCTION_MISC_ENERGY) += energy;
ADD_VECTOR_OBJECT(reduction,REDUCTION_EXT_FORCE_NORMAL,extForce);
ADD_TENSOR_OBJECT(reduction,REDUCTION_VIRIAL_NORMAL,extVirial);
reduction->submit();
}
void ComputeGlobal::recvResults(ComputeGlobalResultsMsg *msg) {
DebugM(3,"Receiving results (" << msg->aid.size() << " forces, "
<< msg->newgdef.size() << " new group atoms) on client\n");
// set the forces only if we aren't going to resend the data
int setForces = !msg->resendCoordinates;
if(setForces) { // we are requested to
// Store forces to patches
PatchMap *patchMap = PatchMap::Object();
int numPatches = patchMap->numPatches();
AtomMap *atomMap = AtomMap::Object();
const Lattice & lattice = patchList[0].p->lattice;
ResizeArrayIter<PatchElem> ap(patchList);
Force **f = new Force*[numPatches];
FullAtom **t = new FullAtom*[numPatches];
for ( int i = 0; i < numPatches; ++i ) { f[i] = 0; t[i] = 0; }
Force extForce = 0.;
Tensor extVirial;
for (ap = ap.begin(); ap != ap.end(); ap++) {
(*ap).r = (*ap).forceBox->open();
f[(*ap).patchID] = (*ap).r->f[Results::normal];
t[(*ap).patchID] = (*ap).p->getAtomList().begin();
}
AtomIDList::iterator a = msg->aid.begin();
AtomIDList::iterator a_e = msg->aid.end();
ForceList::iterator f2 = msg->f.begin();
for ( ; a != a_e; ++a, ++f2 ) {
DebugM(1,"processing atom "<<(*a)<<", F="<<(*f2)<<"...\n");
/* XXX if (*a) is out of bounds here we get a segfault */
LocalID localID = atomMap->localID(*a);
if ( localID.pid == notUsed || ! f[localID.pid] ) continue;
Force f_atom = (*f2);
f[localID.pid][localID.index] += f_atom;
Position x_orig = t[localID.pid][localID.index].position;
Transform trans = t[localID.pid][localID.index].transform;
Position x_atom = lattice.reverse_transform(x_orig,trans);
extForce += f_atom;
extVirial += outer(f_atom,x_atom);
}
DebugM(1,"done with the loop\n");
// calculate forces for atoms in groups
Molecule *mol = Node::Object()->molecule;
AtomIDList::iterator g_i, g_e;
g_i = gdef.begin(); g_e = gdef.end();
ResizeArray<BigReal>::iterator gm_i = gmass.begin();
ForceList::iterator gf_i = msg->gforce.begin();
//iout << iDEBUG << "recvResults\n" << endi;
for ( ; g_i != g_e; ++g_i, ++gm_i, ++gf_i ) {
//iout << iDEBUG << *gf_i << '\n' << endi;
Vector accel = (*gf_i) / (*gm_i);
for ( ; *g_i != -1; ++g_i ) {
//iout << iDEBUG << *g_i << '\n' << endi;
LocalID localID = atomMap->localID(*g_i);
if ( localID.pid == notUsed || ! f[localID.pid] ) continue;
Force f_atom = accel * mol->atommass(*g_i);
f[localID.pid][localID.index] += f_atom;
Position x_orig = t[localID.pid][localID.index].position;
Transform trans = t[localID.pid][localID.index].transform;
Position x_atom = lattice.reverse_transform(x_orig,trans);
extForce += f_atom;
extVirial += outer(f_atom,x_atom);
}
}
DebugM(1,"done with the groups\n");
for (ap = ap.begin(); ap != ap.end(); ap++) {
(*ap).forceBox->close(&((*ap).r));
}
delete [] f;
delete [] t;
ADD_VECTOR_OBJECT(reduction,REDUCTION_EXT_FORCE_NORMAL,extForce);
ADD_TENSOR_OBJECT(reduction,REDUCTION_VIRIAL_NORMAL,extVirial);
reduction->submit();
}
// done setting the forces
// Get reconfiguration if present
if ( msg->reconfig ) configure(msg->newaid, msg->newgdef);
// send another round of data if requested
if(msg->resendCoordinates) {
DebugM(3,"Sending requested data right away\n");
sendData();
}
delete msg;
DebugM(3,"Done processing results\n");
}