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; }