int colvarproxy_namd::load_atoms(char const *pdb_filename,
cvm::atom_group &atoms,
std::string const &pdb_field_str,
double const pdb_field_value)
{
if (pdb_field_str.size() == 0)
cvm::error("Error: must define which PDB field to use "
"in order to define atoms from a PDB file.\n", INPUT_ERROR);
PDB *pdb = new PDB(pdb_filename);
size_t const pdb_natoms = pdb->num_atoms();
e_pdb_field pdb_field_index = pdb_field_str2enum(pdb_field_str);
for (size_t ipdb = 0; ipdb < pdb_natoms; ipdb++) {
double atom_pdb_field_value = 0.0;
switch (pdb_field_index) {
case e_pdb_occ:
atom_pdb_field_value = (pdb->atom(ipdb))->occupancy();
break;
case e_pdb_beta:
atom_pdb_field_value = (pdb->atom(ipdb))->temperaturefactor();
break;
case e_pdb_x:
atom_pdb_field_value = (pdb->atom(ipdb))->xcoor();
break;
case e_pdb_y:
atom_pdb_field_value = (pdb->atom(ipdb))->ycoor();
break;
case e_pdb_z:
atom_pdb_field_value = (pdb->atom(ipdb))->zcoor();
break;
default:
break;
}
if ( (pdb_field_value) &&
(atom_pdb_field_value != pdb_field_value) ) {
continue;
} else if (atom_pdb_field_value == 0.0) {
continue;
}
if (atoms.is_enabled(colvardeps::f_ag_scalable)) {
atoms.add_atom_id(ipdb);
} else {
atoms.add_atom(cvm::atom(ipdb+1));
}
}
delete pdb;
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}
colvarvalue colvar::cvc::fdiff_change (cvm::atom_group &group)
{
colvarvalue change (x.type());
if (group.old_pos.size()) {
for (size_t i = 0; i < group.size(); i++) {
cvm::rvector const &pold = group.old_pos[i];
cvm::rvector const &p = group[i].pos;
change += group[i].grad * (p - pold);
}
}
// save for next step
group.old_pos = group.positions();
return change;
}
void colvar::cvc::parse_group (std::string const &conf,
char const *group_key,
cvm::atom_group &group,
bool optional)
{
if (key_lookup (conf, group_key)) {
group.parse (conf, group_key);
} else {
if (! optional) {
cvm::fatal_error ("Error: definition for atom group \""+
std::string (group_key)+"\" not found.\n");
}
}
}
void colvar::cvc::parse_group (std::string const &conf,
char const *group_key,
cvm::atom_group &group,
bool optional)
{
if (key_lookup (conf, group_key)) {
if (group.parse (conf, group_key) != COLVARS_OK) {
cvm::error ("Error parsing definition for atom group \""+
std::string (group_key)+"\".\n");
return;
}
} else {
if (! optional) {
cvm::error ("Error: definition for atom group \""+
std::string (group_key)+"\" not found.\n");
return;
}
}
}
void colvar::cvc::debug_gradients (cvm::atom_group &group)
{
// this function should work for any scalar variable:
// the only difference will be the name of the atom group (here, "group")
if (group.b_dummy) return;
cvm::rotation const rot_0 = group.rot;
cvm::rotation const rot_inv = group.rot.inverse();
cvm::real const x_0 = x.real_value;
// cvm::log ("gradients = "+cvm::to_str (gradients)+"\n");
// it only makes sense to debug the fit gradients
// when the fitting group is the same as this group
if (group.b_rotate || group.b_center)
if (group.b_fit_gradients && (group.ref_pos_group == NULL)) {
group.calc_fit_gradients();
if (group.b_rotate) {
// fit_gradients are in the original frame, we should print them in the rotated frame
for (size_t j = 0; j < group.fit_gradients.size(); j++) {
group.fit_gradients[j] = rot_0.rotate (group.fit_gradients[j]);
}
}
cvm::log ("fit_gradients = "+cvm::to_str (group.fit_gradients)+"\n");
if (group.b_rotate) {
for (size_t j = 0; j < group.fit_gradients.size(); j++) {
group.fit_gradients[j] = rot_inv.rotate (group.fit_gradients[j]);
}
}
}
for (size_t ia = 0; ia < group.size(); ia++) {
// tests are best conducted in the unrotated (simulation) frame
cvm::rvector const atom_grad = group.b_rotate ?
rot_inv.rotate (group[ia].grad) :
group[ia].grad;
for (size_t id = 0; id < 3; id++) {
// (re)read original positions
group.read_positions();
// change one coordinate
group[ia].pos[id] += cvm::debug_gradients_step_size;
// (re)do the fit (if defined)
if (group.b_center || group.b_rotate) {
group.calc_apply_roto_translation();
}
calc_value();
cvm::real const x_1 = x.real_value;
cvm::log ("Atom "+cvm::to_str (ia)+", component "+cvm::to_str (id)+":\n");
cvm::log ("dx(actual) = "+cvm::to_str (x_1 - x_0,
21, 14)+"\n");
//cvm::real const dx_pred = (group.fit_gradients.size() && (group.ref_pos_group == NULL)) ?
cvm::real const dx_pred = (group.fit_gradients.size()) ?
(cvm::debug_gradients_step_size * (atom_grad[id] + group.fit_gradients[ia][id])) :
(cvm::debug_gradients_step_size * atom_grad[id]);
cvm::log ("dx(interp) = "+cvm::to_str (dx_pred,
21, 14)+"\n");
cvm::log ("|dx(actual) - dx(interp)|/|dx(actual)| = "+
cvm::to_str (std::fabs (x_1 - x_0 - dx_pred) /
std::fabs (x_1 - x_0), 12, 5)+"\n");
}
}
/*
* The code below is WIP
*/
// if (group.ref_pos_group != NULL) {
// cvm::atom_group &ref = *group.ref_pos_group;
// group.calc_fit_gradients();
//
// for (size_t ia = 0; ia < ref.size(); ia++) {
//
// for (size_t id = 0; id < 3; id++) {
// // (re)read original positions
// group.read_positions();
// ref.read_positions();
// // change one coordinate
// ref[ia].pos[id] += cvm::debug_gradients_step_size;
// group.calc_apply_roto_translation();
// calc_value();
// cvm::real const x_1 = x.real_value;
// cvm::log ("refPosGroup atom "+cvm::to_str (ia)+", component "+cvm::to_str (id)+":\n");
// cvm::log ("dx(actual) = "+cvm::to_str (x_1 - x_0,
// 21, 14)+"\n");
// //cvm::real const dx_pred = (group.fit_gradients.size() && (group.ref_pos_group == NULL)) ?
// // cvm::real const dx_pred = (group.fit_gradients.size()) ?
// // (cvm::debug_gradients_step_size * (atom_grad[id] + group.fit_gradients[ia][id])) :
// // (cvm::debug_gradients_step_size * atom_grad[id]);
// cvm::real const dx_pred = cvm::debug_gradients_step_size * ref.fit_gradients[ia][id];
// cvm::log ("dx(interp) = "+cvm::to_str (dx_pred,
// 21, 14)+"\n");
// cvm::log ("|dx(actual) - dx(interp)|/|dx(actual)| = "+
// cvm::to_str (std::fabs (x_1 - x_0 - dx_pred) /
// std::fabs (x_1 - x_0),
// 12, 5)+
// ".\n");
// }
// }
// }
return;
}
