int GlobalMasterFreeEnergy::getPosition(int atomid, Position &position)
{
AtomIDList::const_iterator a_i = getAtomIdBegin();
AtomIDList::const_iterator a_e = getAtomIdEnd();
PositionList::const_iterator p_i = getAtomPositionBegin();
for ( ; a_i != a_e; ++a_i, ++p_i ) {
if ( *a_i == atomid ) {
position = *p_i;
return 0; // success
}
}
return -1; // failure
}
void colvarproxy_namd::calculate()
{
if (first_timestep) {
this->setup();
colvars->setup();
colvars->setup_input();
colvars->setup_output();
first_timestep = false;
} else {
// Use the time step number inherited from GlobalMaster
if ( step - previous_NAMD_step == 1 ) {
colvars->it++;
}
// Other cases could mean:
// - run 0
// - beginning of a new run statement
// then the internal counter should not be incremented
}
previous_NAMD_step = step;
{
Vector const a = lattice->a();
Vector const b = lattice->b();
Vector const c = lattice->c();
unit_cell_x.set(a.x, a.y, a.z);
unit_cell_y.set(b.x, b.y, c.z);
unit_cell_z.set(c.x, c.y, c.z);
}
if (!lattice->a_p() && !lattice->b_p() && !lattice->c_p()) {
boundaries_type = boundaries_non_periodic;
reset_pbc_lattice();
} else if (lattice->a_p() && lattice->b_p() && lattice->c_p()) {
if (lattice->orthogonal()) {
boundaries_type = boundaries_pbc_ortho;
} else {
boundaries_type = boundaries_pbc_triclinic;
}
colvarproxy_system::update_pbc_lattice();
} else {
boundaries_type = boundaries_unsupported;
}
if (cvm::debug()) {
log(std::string(cvm::line_marker)+
"colvarproxy_namd, step no. "+cvm::to_str(colvars->it)+"\n"+
"Updating atomic data arrays.\n");
}
// must delete the forces applied at the previous step: we can do
// that because they have already been used and copied to other
// memory locations
modifyForcedAtoms().clear();
modifyAppliedForces().clear();
// prepare local arrays
for (size_t i = 0; i < atoms_ids.size(); i++) {
atoms_positions[i] = cvm::rvector(0.0, 0.0, 0.0);
atoms_total_forces[i] = cvm::rvector(0.0, 0.0, 0.0);
atoms_new_colvar_forces[i] = cvm::rvector(0.0, 0.0, 0.0);
}
for (size_t i = 0; i < atom_groups_ids.size(); i++) {
atom_groups_total_forces[i] = cvm::rvector(0.0, 0.0, 0.0);
atom_groups_new_colvar_forces[i] = cvm::rvector(0.0, 0.0, 0.0);
}
// create the atom map if needed
size_t const n_all_atoms = Node::Object()->molecule->numAtoms;
if (atoms_map.size() != n_all_atoms) {
atoms_map.resize(n_all_atoms);
atoms_map.assign(n_all_atoms, -1);
update_atoms_map(getAtomIdBegin(), getAtomIdEnd());
}
// if new atomic positions or forces have been communicated by other GlobalMasters, add them to the atom map
if ((int(atoms_ids.size()) < (getAtomIdEnd() - getAtomIdBegin())) ||
(int(atoms_ids.size()) < (getForceIdEnd() - getForceIdBegin()))) {
update_atoms_map(getAtomIdBegin(), getAtomIdEnd());
update_atoms_map(getForceIdBegin(), getForceIdEnd());
}
{
if (cvm::debug()) {
log("Updating positions arrays.\n");
}
size_t n_positions = 0;
AtomIDList::const_iterator a_i = getAtomIdBegin();
AtomIDList::const_iterator a_e = getAtomIdEnd();
PositionList::const_iterator p_i = getAtomPositionBegin();
for ( ; a_i != a_e; ++a_i, ++p_i ) {
atoms_positions[atoms_map[*a_i]] = cvm::rvector((*p_i).x, (*p_i).y, (*p_i).z);
n_positions++;
}
// The following had to be relaxed because some atoms may be forced without their position being requested
// if (n_positions < atoms_ids.size()) {
// cvm::error("Error: did not receive the positions of all atoms.\n", BUG_ERROR);
// }
}
if (total_force_requested && cvm::step_relative() > 0) {
// sort the force arrays the previous step
// (but only do so if there *is* a previous step!)
{
if (cvm::debug()) {
log("Updating total forces arrays.\n");
}
size_t n_total_forces = 0;
AtomIDList::const_iterator a_i = getForceIdBegin();
AtomIDList::const_iterator a_e = getForceIdEnd();
ForceList::const_iterator f_i = getTotalForce();
for ( ; a_i != a_e; ++a_i, ++f_i ) {
atoms_total_forces[atoms_map[*a_i]] = cvm::rvector((*f_i).x, (*f_i).y, (*f_i).z);
n_total_forces++;
}
if (n_total_forces < atoms_ids.size()) {
cvm::error("Error: total forces were requested, but total forces "
"were not received for all atoms.\n"
"The most probable cause is combination of energy "
"minimization with a biasing method that requires MD (e.g. ABF).\n"
"Always run minimization and ABF separately.", INPUT_ERROR);
}
}
{
if (cvm::debug()) {
log("Updating group total forces arrays.\n");
}
ForceList::const_iterator f_i = getGroupTotalForceBegin();
ForceList::const_iterator f_e = getGroupTotalForceEnd();
size_t i = 0;
if ((f_e - f_i) != ((int) atom_groups_ids.size())) {
cvm::error("Error: total forces were requested for scalable groups, "
"but they are not in the same number from the number of groups.\n"
"The most probable cause is combination of energy "
"minimization with a biasing method that requires MD (e.g. ABF).\n"
"Always run minimization and ABF separately.", INPUT_ERROR);
}
for ( ; f_i != f_e; f_i++, i++) {
atom_groups_total_forces[i] = cvm::rvector((*f_i).x, (*f_i).y, (*f_i).z);
}
}
}
{
if (cvm::debug()) {
log("Updating group positions arrays.\n");
}
// update group data (only coms available so far)
size_t ig;
// note: getGroupMassBegin() could be used here, but masses and charges
// have already been calculated from the last call to setup()
PositionList::const_iterator gp_i = getGroupPositionBegin();
for (ig = 0; gp_i != getGroupPositionEnd(); gp_i++, ig++) {
atom_groups_coms[ig] = cvm::rvector(gp_i->x, gp_i->y, gp_i->z);
}
}
if (cvm::debug()) {
log("atoms_ids = "+cvm::to_str(atoms_ids)+"\n");
log("atoms_ncopies = "+cvm::to_str(atoms_ncopies)+"\n");
log("atoms_masses = "+cvm::to_str(atoms_masses)+"\n");
log("atoms_charges = "+cvm::to_str(atoms_charges)+"\n");
log("atoms_positions = "+cvm::to_str(atoms_positions)+"\n");
log("atoms_total_forces = "+cvm::to_str(atoms_total_forces)+"\n");
log(cvm::line_marker);
log("atom_groups_ids = "+cvm::to_str(atom_groups_ids)+"\n");
log("atom_groups_ncopies = "+cvm::to_str(atom_groups_ncopies)+"\n");
log("atom_groups_masses = "+cvm::to_str(atom_groups_masses)+"\n");
log("atom_groups_charges = "+cvm::to_str(atom_groups_charges)+"\n");
log("atom_groups_coms = "+cvm::to_str(atom_groups_coms)+"\n");
log("atom_groups_total_forces = "+cvm::to_str(atom_groups_total_forces)+"\n");
log(cvm::line_marker);
}
// call the collective variable module
if (colvars->calc() != COLVARS_OK) {
cvm::error("Error in the collective variables module.\n", COLVARS_ERROR);
}
if (cvm::debug()) {
log(cvm::line_marker);
log("atoms_new_colvar_forces = "+cvm::to_str(atoms_new_colvar_forces)+"\n");
log(cvm::line_marker);
log("atom_groups_new_colvar_forces = "+cvm::to_str(atom_groups_new_colvar_forces)+"\n");
log(cvm::line_marker);
}
// communicate all forces to the MD integrator
for (size_t i = 0; i < atoms_ids.size(); i++) {
cvm::rvector const &f = atoms_new_colvar_forces[i];
modifyForcedAtoms().add(atoms_ids[i]);
modifyAppliedForces().add(Vector(f.x, f.y, f.z));
}
{
// zero out the applied forces on each group
modifyGroupForces().resize(modifyRequestedGroups().size());
ForceList::iterator gf_i = modifyGroupForces().begin();
for (int ig = 0; gf_i != modifyGroupForces().end(); gf_i++, ig++) {
cvm::rvector const &f = atom_groups_new_colvar_forces[ig];
*gf_i = Vector(f.x, f.y, f.z);
}
}
// send MISC energy
reduction->submit();
// NAMD does not destruct GlobalMaster objects, so we must remember
// to write all output files at the end of a run
if (step == simparams->N) {
colvars->write_restart_file(cvm::output_prefix()+".colvars.state");
colvars->write_output_files();
}
}