forked from lijiext/lammps
502 lines
15 KiB
C++
502 lines
15 KiB
C++
// -*- c++ -*-
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// This file is part of the Collective Variables module (Colvars).
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// The original version of Colvars and its updates are located at:
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// https://github.com/colvars/colvars
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// Please update all Colvars source files before making any changes.
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// If you wish to distribute your changes, please submit them to the
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// Colvars repository at GitHub.
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#include "colvarmodule.h"
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#include "colvarvalue.h"
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#include "colvarparse.h"
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#include "colvar.h"
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#include "colvarcomp.h"
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//////////////////////////////////////////////////////////////////////
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// alpha component
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//////////////////////////////////////////////////////////////////////
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colvar::alpha_angles::alpha_angles(std::string const &conf)
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: cvc(conf)
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{
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if (cvm::debug())
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cvm::log("Initializing alpha_angles object.\n");
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function_type = "alpha_angles";
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enable(f_cvc_explicit_gradient);
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x.type(colvarvalue::type_scalar);
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std::string segment_id;
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get_keyval(conf, "psfSegID", segment_id, std::string("MAIN"));
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std::vector<int> residues;
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{
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std::string residues_conf = "";
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key_lookup(conf, "residueRange", &residues_conf);
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if (residues_conf.size()) {
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std::istringstream is(residues_conf);
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int initial, final;
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char dash;
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if ( (is >> initial) && (initial > 0) &&
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(is >> dash) && (dash == '-') &&
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(is >> final) && (final > 0) ) {
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for (int rnum = initial; rnum <= final; rnum++) {
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residues.push_back(rnum);
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}
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}
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} else {
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cvm::error("Error: no residues defined in \"residueRange\".\n");
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return;
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}
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}
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if (residues.size() < 5) {
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cvm::error("Error: not enough residues defined in \"residueRange\".\n");
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return;
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}
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std::string const &sid = segment_id;
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std::vector<int> const &r = residues;
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get_keyval(conf, "hBondCoeff", hb_coeff, 0.5);
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if ( (hb_coeff < 0.0) || (hb_coeff > 1.0) ) {
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cvm::error("Error: hBondCoeff must be defined between 0 and 1.\n");
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return;
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}
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get_keyval(conf, "angleRef", theta_ref, 88.0);
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get_keyval(conf, "angleTol", theta_tol, 15.0);
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if (hb_coeff < 1.0) {
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for (size_t i = 0; i < residues.size()-2; i++) {
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theta.push_back(new colvar::angle(cvm::atom(r[i ], "CA", sid),
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cvm::atom(r[i+1], "CA", sid),
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cvm::atom(r[i+2], "CA", sid)));
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register_atom_group(theta.back()->atom_groups[0]);
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register_atom_group(theta.back()->atom_groups[1]);
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register_atom_group(theta.back()->atom_groups[2]);
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}
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} else {
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cvm::log("The hBondCoeff specified will disable the Calpha-Calpha-Calpha angle terms.\n");
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}
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{
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cvm::real r0;
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size_t en, ed;
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get_keyval(conf, "hBondCutoff", r0, (3.3 * cvm::unit_angstrom()));
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get_keyval(conf, "hBondExpNumer", en, 6);
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get_keyval(conf, "hBondExpDenom", ed, 8);
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if (hb_coeff > 0.0) {
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for (size_t i = 0; i < residues.size()-4; i++) {
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hb.push_back(new colvar::h_bond(cvm::atom(r[i ], "O", sid),
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cvm::atom(r[i+4], "N", sid),
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r0, en, ed));
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register_atom_group(hb.back()->atom_groups[0]);
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}
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} else {
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cvm::log("The hBondCoeff specified will disable the hydrogen bond terms.\n");
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}
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}
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if (cvm::debug())
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cvm::log("Done initializing alpha_angles object.\n");
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}
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colvar::alpha_angles::alpha_angles()
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: cvc()
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{
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function_type = "alpha_angles";
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enable(f_cvc_explicit_gradient);
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x.type(colvarvalue::type_scalar);
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}
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colvar::alpha_angles::~alpha_angles()
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{
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while (theta.size() != 0) {
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delete theta.back();
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theta.pop_back();
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}
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while (hb.size() != 0) {
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delete hb.back();
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hb.pop_back();
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}
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// Our references to atom groups have become invalid now that children cvcs are deleted
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atom_groups.clear();
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}
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void colvar::alpha_angles::calc_value()
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{
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x.real_value = 0.0;
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if (theta.size()) {
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cvm::real const theta_norm =
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(1.0-hb_coeff) / cvm::real(theta.size());
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for (size_t i = 0; i < theta.size(); i++) {
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(theta[i])->calc_value();
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cvm::real const t = ((theta[i])->value().real_value-theta_ref)/theta_tol;
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cvm::real const f = ( (1.0 - (t*t)) /
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(1.0 - (t*t*t*t)) );
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x.real_value += theta_norm * f;
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if (cvm::debug())
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cvm::log("Calpha-Calpha angle no. "+cvm::to_str(i+1)+" in \""+
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this->name+"\" has a value of "+
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(cvm::to_str((theta[i])->value().real_value))+
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" degrees, f = "+cvm::to_str(f)+".\n");
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}
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}
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if (hb.size()) {
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cvm::real const hb_norm =
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hb_coeff / cvm::real(hb.size());
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for (size_t i = 0; i < hb.size(); i++) {
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(hb[i])->calc_value();
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x.real_value += hb_norm * (hb[i])->value().real_value;
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if (cvm::debug())
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cvm::log("Hydrogen bond no. "+cvm::to_str(i+1)+" in \""+
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this->name+"\" has a value of "+
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(cvm::to_str((hb[i])->value().real_value))+".\n");
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}
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}
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}
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void colvar::alpha_angles::calc_gradients()
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{
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size_t i;
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for (i = 0; i < theta.size(); i++)
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(theta[i])->calc_gradients();
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for (i = 0; i < hb.size(); i++)
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(hb[i])->calc_gradients();
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}
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void colvar::alpha_angles::collect_gradients(std::vector<int> const &atom_ids, std::vector<cvm::rvector> &atomic_gradients)
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{
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cvm::real cvc_coeff = sup_coeff * cvm::real(sup_np) * cvm::integer_power(value().real_value, sup_np-1);
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if (theta.size()) {
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cvm::real const theta_norm = (1.0-hb_coeff) / cvm::real(theta.size());
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for (size_t i = 0; i < theta.size(); i++) {
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cvm::real const t = ((theta[i])->value().real_value-theta_ref)/theta_tol;
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cvm::real const f = ( (1.0 - (t*t)) /
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(1.0 - (t*t*t*t)) );
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cvm::real const dfdt =
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1.0/(1.0 - (t*t*t*t)) *
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( (-2.0 * t) + (-1.0*f)*(-4.0 * (t*t*t)) );
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// Coeficient of this CVC's gradient in the colvar gradient, times coefficient of this
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// angle's gradient in the CVC's gradient
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cvm::real const coeff = cvc_coeff * theta_norm * dfdt * (1.0/theta_tol);
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for (size_t j = 0; j < theta[i]->atom_groups.size(); j++) {
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cvm::atom_group &ag = *(theta[i]->atom_groups[j]);
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for (size_t k = 0; k < ag.size(); k++) {
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size_t a = std::lower_bound(atom_ids.begin(), atom_ids.end(),
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ag[k].id) - atom_ids.begin();
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atomic_gradients[a] += coeff * ag[k].grad;
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}
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}
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}
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}
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if (hb.size()) {
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cvm::real const hb_norm = hb_coeff / cvm::real(hb.size());
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for (size_t i = 0; i < hb.size(); i++) {
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// Coeficient of this CVC's gradient in the colvar gradient, times coefficient of this
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// hbond's gradient in the CVC's gradient
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cvm::real const coeff = cvc_coeff * 0.5 * hb_norm;
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for (size_t j = 0; j < hb[i]->atom_groups.size(); j++) {
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cvm::atom_group &ag = *(hb[i]->atom_groups[j]);
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for (size_t k = 0; k < ag.size(); k++) {
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size_t a = std::lower_bound(atom_ids.begin(), atom_ids.end(),
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ag[k].id) - atom_ids.begin();
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atomic_gradients[a] += coeff * ag[k].grad;
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}
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}
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}
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}
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}
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void colvar::alpha_angles::apply_force(colvarvalue const &force)
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{
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if (theta.size()) {
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cvm::real const theta_norm =
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(1.0-hb_coeff) / cvm::real(theta.size());
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for (size_t i = 0; i < theta.size(); i++) {
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cvm::real const t = ((theta[i])->value().real_value-theta_ref)/theta_tol;
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cvm::real const f = ( (1.0 - (t*t)) /
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(1.0 - (t*t*t*t)) );
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cvm::real const dfdt =
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1.0/(1.0 - (t*t*t*t)) *
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( (-2.0 * t) + (-1.0*f)*(-4.0 * (t*t*t)) );
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(theta[i])->apply_force(theta_norm *
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dfdt * (1.0/theta_tol) *
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force.real_value );
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}
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}
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if (hb.size()) {
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cvm::real const hb_norm =
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hb_coeff / cvm::real(hb.size());
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for (size_t i = 0; i < hb.size(); i++) {
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(hb[i])->apply_force(0.5 * hb_norm * force.real_value);
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}
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}
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}
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simple_scalar_dist_functions(alpha_angles)
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//////////////////////////////////////////////////////////////////////
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// dihedral principal component
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//////////////////////////////////////////////////////////////////////
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colvar::dihedPC::dihedPC(std::string const &conf)
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: cvc(conf)
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{
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if (cvm::debug())
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cvm::log("Initializing dihedral PC object.\n");
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function_type = "dihedPC";
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// Supported through references to atom groups of children cvcs
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enable(f_cvc_explicit_gradient);
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x.type(colvarvalue::type_scalar);
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std::string segment_id;
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get_keyval(conf, "psfSegID", segment_id, std::string("MAIN"));
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std::vector<int> residues;
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{
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std::string residues_conf = "";
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key_lookup(conf, "residueRange", &residues_conf);
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if (residues_conf.size()) {
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std::istringstream is(residues_conf);
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int initial, final;
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char dash;
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if ( (is >> initial) && (initial > 0) &&
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(is >> dash) && (dash == '-') &&
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(is >> final) && (final > 0) ) {
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for (int rnum = initial; rnum <= final; rnum++) {
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residues.push_back(rnum);
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}
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}
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} else {
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cvm::error("Error: no residues defined in \"residueRange\".\n");
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return;
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}
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}
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if (residues.size() < 2) {
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cvm::error("Error: dihedralPC requires at least two residues.\n");
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return;
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}
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std::string const &sid = segment_id;
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std::vector<int> const &r = residues;
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std::string vecFileName;
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int vecNumber;
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if (get_keyval(conf, "vectorFile", vecFileName, vecFileName)) {
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get_keyval(conf, "vectorNumber", vecNumber, 0);
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if (vecNumber < 1) {
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cvm::error("A positive value of vectorNumber is required.");
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return;
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}
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std::ifstream vecFile;
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vecFile.open(vecFileName.c_str());
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if (!vecFile.good()) {
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cvm::error("Error opening dihedral PCA vector file " + vecFileName + " for reading");
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}
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// TODO: adapt to different formats by setting this flag
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bool eigenvectors_as_columns = true;
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if (eigenvectors_as_columns) {
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// Carma-style dPCA file
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std::string line;
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cvm::real c;
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while (vecFile.good()) {
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getline(vecFile, line);
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if (line.length() < 2) break;
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std::istringstream ls(line);
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for (int i=0; i<vecNumber; i++) ls >> c;
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coeffs.push_back(c);
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}
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}
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/* TODO Uncomment this when different formats are recognized
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else {
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// Eigenvectors as lines
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// Skip to the right line
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for (int i = 1; i<vecNumber; i++)
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vecFile.ignore(999999, '\n');
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if (!vecFile.good()) {
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cvm::error("Error reading dihedral PCA vector file " + vecFileName);
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}
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std::string line;
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getline(vecFile, line);
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std::istringstream ls(line);
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cvm::real c;
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while (ls.good()) {
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ls >> c;
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coeffs.push_back(c);
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}
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}
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*/
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vecFile.close();
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} else {
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get_keyval(conf, "vector", coeffs, coeffs);
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}
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if ( coeffs.size() != 4 * (residues.size() - 1)) {
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cvm::error("Error: wrong number of coefficients: " +
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cvm::to_str(coeffs.size()) + ". Expected " +
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cvm::to_str(4 * (residues.size() - 1)) +
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" (4 coeffs per residue, minus one residue).\n");
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return;
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}
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for (size_t i = 0; i < residues.size()-1; i++) {
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// Psi
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theta.push_back(new colvar::dihedral(cvm::atom(r[i ], "N", sid),
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cvm::atom(r[i ], "CA", sid),
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cvm::atom(r[i ], "C", sid),
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cvm::atom(r[i+1], "N", sid)));
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register_atom_group(theta.back()->atom_groups[0]);
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register_atom_group(theta.back()->atom_groups[1]);
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register_atom_group(theta.back()->atom_groups[2]);
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register_atom_group(theta.back()->atom_groups[3]);
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// Phi (next res)
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theta.push_back(new colvar::dihedral(cvm::atom(r[i ], "C", sid),
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cvm::atom(r[i+1], "N", sid),
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cvm::atom(r[i+1], "CA", sid),
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cvm::atom(r[i+1], "C", sid)));
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register_atom_group(theta.back()->atom_groups[0]);
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register_atom_group(theta.back()->atom_groups[1]);
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register_atom_group(theta.back()->atom_groups[2]);
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register_atom_group(theta.back()->atom_groups[3]);
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}
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if (cvm::debug())
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cvm::log("Done initializing dihedPC object.\n");
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}
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colvar::dihedPC::dihedPC()
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: cvc()
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{
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function_type = "dihedPC";
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// Supported through references to atom groups of children cvcs
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enable(f_cvc_explicit_gradient);
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x.type(colvarvalue::type_scalar);
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}
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colvar::dihedPC::~dihedPC()
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{
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while (theta.size() != 0) {
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delete theta.back();
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theta.pop_back();
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}
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// Our references to atom groups have become invalid now that children cvcs are deleted
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atom_groups.clear();
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}
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void colvar::dihedPC::calc_value()
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{
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x.real_value = 0.0;
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for (size_t i = 0; i < theta.size(); i++) {
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theta[i]->calc_value();
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cvm::real const t = (PI / 180.) * theta[i]->value().real_value;
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x.real_value += coeffs[2*i ] * cvm::cos(t)
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+ coeffs[2*i+1] * cvm::sin(t);
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}
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}
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void colvar::dihedPC::calc_gradients()
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{
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for (size_t i = 0; i < theta.size(); i++) {
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theta[i]->calc_gradients();
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}
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}
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void colvar::dihedPC::collect_gradients(std::vector<int> const &atom_ids, std::vector<cvm::rvector> &atomic_gradients)
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{
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cvm::real cvc_coeff = sup_coeff * cvm::real(sup_np) * cvm::integer_power(value().real_value, sup_np-1);
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for (size_t i = 0; i < theta.size(); i++) {
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cvm::real const t = (PI / 180.) * theta[i]->value().real_value;
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cvm::real const dcosdt = - (PI / 180.) * cvm::sin(t);
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cvm::real const dsindt = (PI / 180.) * cvm::cos(t);
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// Coeficient of this dihedPC's gradient in the colvar gradient, times coefficient of this
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// dihedral's gradient in the dihedPC's gradient
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cvm::real const coeff = cvc_coeff * (coeffs[2*i] * dcosdt + coeffs[2*i+1] * dsindt);
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for (size_t j = 0; j < theta[i]->atom_groups.size(); j++) {
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cvm::atom_group &ag = *(theta[i]->atom_groups[j]);
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for (size_t k = 0; k < ag.size(); k++) {
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size_t a = std::lower_bound(atom_ids.begin(), atom_ids.end(),
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ag[k].id) - atom_ids.begin();
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atomic_gradients[a] += coeff * ag[k].grad;
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}
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}
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}
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}
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void colvar::dihedPC::apply_force(colvarvalue const &force)
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{
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for (size_t i = 0; i < theta.size(); i++) {
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cvm::real const t = (PI / 180.) * theta[i]->value().real_value;
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cvm::real const dcosdt = - (PI / 180.) * cvm::sin(t);
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cvm::real const dsindt = (PI / 180.) * cvm::cos(t);
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theta[i]->apply_force((coeffs[2*i ] * dcosdt +
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coeffs[2*i+1] * dsindt) * force);
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}
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}
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simple_scalar_dist_functions(dihedPC)
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