void ComputeGlobal::configure(AtomIDList &newaid, AtomIDList &newgdef) {
DebugM(4,"Receiving configuration (" << newaid.size() <<
" atoms and " << newgdef.size() << " atoms/groups) on client\n");
AtomIDList::iterator a, a_e;
for (a=aid.begin(),a_e=aid.end(); a!=a_e; ++a)
isRequested[*a] = 0;
// store data
aid.swap(newaid);
gdef.swap(newgdef);
for (a=aid.begin(),a_e=aid.end(); a!=a_e; ++a)
isRequested[*a] = 1;
// calculate group masses
Molecule *mol = Node::Object()->molecule;
gmass.resize(0);
AtomIDList::iterator g_i, g_e;
g_i = gdef.begin(); g_e = gdef.end();
for ( ; g_i != g_e; ++g_i ) {
BigReal mass = 0;
for ( ; *g_i != -1; ++g_i ) {
mass += mol->atommass(*g_i);
}
gmass.add(mass);
}
}
void colvarproxy_namd::update_atom_properties(int index)
{
Molecule *mol = Node::Object()->molecule;
// update mass
double const mass = mol->atommass(atoms_ids[index]);
if (mass <= 0.001) {
this->log("Warning: near-zero mass for atom "+
cvm::to_str(atoms_ids[index]+1)+
"; expect unstable dynamics if you apply forces to it.\n");
}
atoms_masses[index] = mass;
// update charge
atoms_charges[index] = mol->atomcharge(atoms_ids[index]);
}
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");
}
void ComputeGlobal::sendData()
{
DebugM(2,"sendData\n");
// Get positions from patches
PatchMap *patchMap = PatchMap::Object();
int numPatches = patchMap->numPatches();
AtomMap *atomMap = AtomMap::Object();
const Lattice & lattice = patchList[0].p->lattice;
ResizeArrayIter<PatchElem> ap(patchList);
CompAtom **x = new CompAtom*[numPatches];
FullAtom **t = new FullAtom*[numPatches];
for ( int i = 0; i < numPatches; ++i ) { x[i] = 0; t[i] = 0; }
int step = -1;
for (ap = ap.begin(); ap != ap.end(); ap++) {
x[(*ap).patchID] = (*ap).positionBox->open();
t[(*ap).patchID] = (*ap).p->getAtomList().begin();
step = (*ap).p->flags.step;
}
ComputeGlobalDataMsg *msg = new ComputeGlobalDataMsg;
msg->step = step;
AtomIDList::iterator a = aid.begin();
AtomIDList::iterator a_e = aid.end();
for ( ; a != a_e; ++a ) {
LocalID localID = atomMap->localID(*a);
if ( localID.pid == notUsed || ! x[localID.pid] ) continue;
msg->aid.add(*a);
Position x_orig = x[localID.pid][localID.index].position;
Transform trans = t[localID.pid][localID.index].transform;
msg->p.add(lattice.reverse_transform(x_orig,trans));
}
// calculate group centers of mass
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();
for ( ; g_i != g_e; ++g_i, ++gm_i ) {
Vector com(0,0,0);
for ( ; *g_i != -1; ++g_i ) {
LocalID localID = atomMap->localID(*g_i);
if ( localID.pid == notUsed || ! x[localID.pid] ) continue;
Position x_orig = x[localID.pid][localID.index].position;
Transform trans = t[localID.pid][localID.index].transform;
com += lattice.reverse_transform(x_orig,trans) * mol->atommass(*g_i);
}
com /= *gm_i;
DebugM(1,"Adding center of mass "<<com<<"\n");
msg->gcom.add(com);
}
for (ap = ap.begin(); ap != ap.end(); ap++) {
(*ap).positionBox->close(&(x[(*ap).patchID]));
}
msg->fid.swap(fid);
msg->tf.swap(totalForce);
fid.resize(0);
totalForce.resize(0);
delete [] x;
delete [] t;
DebugM(3,"Sending data (" << msg->aid.size() << " positions) on client\n");
comm->sendComputeGlobalData(msg);
}
