forked from lijiext/lammps
428 lines
9.8 KiB
C++
428 lines
9.8 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 <cmath>
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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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colvar::orientation::orientation(std::string const &conf)
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: cvc(conf)
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{
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function_type = "orientation";
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atoms = parse_group(conf, "atoms");
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enable(f_cvc_implicit_gradient);
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x.type(colvarvalue::type_quaternion);
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ref_pos.reserve(atoms->size());
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if (get_keyval(conf, "refPositions", ref_pos, ref_pos)) {
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cvm::log("Using reference positions from input file.\n");
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if (ref_pos.size() != atoms->size()) {
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cvm::error("Error: reference positions do not "
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"match the number of requested atoms.\n");
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return;
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}
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}
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{
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std::string file_name;
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if (get_keyval(conf, "refPositionsFile", file_name)) {
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std::string file_col;
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double file_col_value=0.0;
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if (get_keyval(conf, "refPositionsCol", file_col, std::string(""))) {
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// use PDB flags if column is provided
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bool found = get_keyval(conf, "refPositionsColValue", file_col_value, 0.0);
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if (found && file_col_value==0.0) {
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cvm::error("Error: refPositionsColValue, "
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"if provided, must be non-zero.\n");
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return;
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}
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} else {
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// if not, use atom indices
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atoms->create_sorted_ids();
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}
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ref_pos.resize(atoms->size());
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cvm::load_coords(file_name.c_str(), ref_pos, atoms->sorted_ids, file_col, file_col_value);
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}
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}
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if (!ref_pos.size()) {
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cvm::error("Error: must define a set of "
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"reference coordinates.\n");
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return;
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}
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cvm::log("Centering the reference coordinates: it is "
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"assumed that each atom is the closest "
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"periodic image to the center of geometry.\n");
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cvm::rvector ref_cog(0.0, 0.0, 0.0);
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size_t i;
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for (i = 0; i < ref_pos.size(); i++) {
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ref_cog += ref_pos[i];
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}
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ref_cog /= cvm::real(ref_pos.size());
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for (i = 0; i < ref_pos.size(); i++) {
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ref_pos[i] -= ref_cog;
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}
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get_keyval(conf, "closestToQuaternion", ref_quat, cvm::quaternion(1.0, 0.0, 0.0, 0.0));
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// initialize rot member data
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if (!atoms->noforce) {
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rot.request_group2_gradients(atoms->size());
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}
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}
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colvar::orientation::orientation()
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: cvc()
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{
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function_type = "orientation";
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enable(f_cvc_implicit_gradient);
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x.type(colvarvalue::type_quaternion);
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}
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void colvar::orientation::calc_value()
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{
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rot.b_debug_gradients = is_enabled(f_cvc_debug_gradient);
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atoms_cog = atoms->center_of_geometry();
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rot.calc_optimal_rotation(ref_pos, atoms->positions_shifted(-1.0 * atoms_cog));
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if ((rot.q).inner(ref_quat) >= 0.0) {
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x.quaternion_value = rot.q;
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} else {
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x.quaternion_value = -1.0 * rot.q;
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}
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}
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void colvar::orientation::calc_gradients()
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{
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// gradients have already been calculated and stored within the
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// member object "rot"; we're not using the "grad" member of each
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// atom object, because it only can represent the gradient of a
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// scalar colvar
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}
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void colvar::orientation::apply_force(colvarvalue const &force)
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{
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cvm::quaternion const &FQ = force.quaternion_value;
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if (!atoms->noforce) {
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for (size_t ia = 0; ia < atoms->size(); ia++) {
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for (size_t i = 0; i < 4; i++) {
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(*atoms)[ia].apply_force(FQ[i] * rot.dQ0_2[ia][i]);
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}
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}
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}
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}
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cvm::real colvar::orientation::dist2(colvarvalue const &x1,
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colvarvalue const &x2) const
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{
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return x1.quaternion_value.dist2(x2);
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}
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colvarvalue colvar::orientation::dist2_lgrad(colvarvalue const &x1,
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colvarvalue const &x2) const
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{
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return x1.quaternion_value.dist2_grad(x2);
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}
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colvarvalue colvar::orientation::dist2_rgrad(colvarvalue const &x1,
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colvarvalue const &x2) const
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{
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return x2.quaternion_value.dist2_grad(x1);
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}
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colvar::orientation_angle::orientation_angle(std::string const &conf)
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: orientation(conf)
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{
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function_type = "orientation_angle";
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x.type(colvarvalue::type_scalar);
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}
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colvar::orientation_angle::orientation_angle()
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: orientation()
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{
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function_type = "orientation_angle";
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x.type(colvarvalue::type_scalar);
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}
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void colvar::orientation_angle::calc_value()
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{
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atoms_cog = atoms->center_of_geometry();
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rot.calc_optimal_rotation(ref_pos, atoms->positions_shifted(-1.0 * atoms_cog));
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if ((rot.q).q0 >= 0.0) {
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x.real_value = (180.0/PI) * 2.0 * std::acos((rot.q).q0);
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} else {
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x.real_value = (180.0/PI) * 2.0 * std::acos(-1.0 * (rot.q).q0);
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}
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}
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void colvar::orientation_angle::calc_gradients()
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{
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cvm::real const dxdq0 =
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( ((rot.q).q0 * (rot.q).q0 < 1.0) ?
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((180.0 / PI) * (-2.0) / std::sqrt(1.0 - ((rot.q).q0 * (rot.q).q0))) :
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0.0 );
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for (size_t ia = 0; ia < atoms->size(); ia++) {
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(*atoms)[ia].grad = (dxdq0 * (rot.dQ0_2[ia])[0]);
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}
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}
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void colvar::orientation_angle::apply_force(colvarvalue const &force)
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{
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cvm::real const &fw = force.real_value;
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if (!atoms->noforce) {
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atoms->apply_colvar_force(fw);
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}
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}
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simple_scalar_dist_functions(orientation_angle)
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colvar::orientation_proj::orientation_proj(std::string const &conf)
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: orientation(conf)
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{
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function_type = "orientation_proj";
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x.type(colvarvalue::type_scalar);
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}
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colvar::orientation_proj::orientation_proj()
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: orientation()
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{
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function_type = "orientation_proj";
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x.type(colvarvalue::type_scalar);
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}
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void colvar::orientation_proj::calc_value()
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{
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atoms_cog = atoms->center_of_geometry();
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rot.calc_optimal_rotation(ref_pos, atoms->positions_shifted(-1.0 * atoms_cog));
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x.real_value = 2.0 * (rot.q).q0 * (rot.q).q0 - 1.0;
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}
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void colvar::orientation_proj::calc_gradients()
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{
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cvm::real const dxdq0 = 2.0 * 2.0 * (rot.q).q0;
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for (size_t ia = 0; ia < atoms->size(); ia++) {
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(*atoms)[ia].grad = (dxdq0 * (rot.dQ0_2[ia])[0]);
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}
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}
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void colvar::orientation_proj::apply_force(colvarvalue const &force)
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{
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cvm::real const &fw = force.real_value;
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if (!atoms->noforce) {
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atoms->apply_colvar_force(fw);
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}
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}
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simple_scalar_dist_functions(orientation_proj)
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colvar::tilt::tilt(std::string const &conf)
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: orientation(conf)
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{
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function_type = "tilt";
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get_keyval(conf, "axis", axis, cvm::rvector(0.0, 0.0, 1.0));
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if (axis.norm2() != 1.0) {
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axis /= axis.norm();
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cvm::log("Normalizing rotation axis to "+cvm::to_str(axis)+".\n");
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}
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x.type(colvarvalue::type_scalar);
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}
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colvar::tilt::tilt()
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: orientation()
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{
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function_type = "tilt";
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x.type(colvarvalue::type_scalar);
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}
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void colvar::tilt::calc_value()
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{
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atoms_cog = atoms->center_of_geometry();
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rot.calc_optimal_rotation(ref_pos, atoms->positions_shifted(-1.0 * atoms_cog));
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x.real_value = rot.cos_theta(axis);
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}
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void colvar::tilt::calc_gradients()
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{
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cvm::quaternion const dxdq = rot.dcos_theta_dq(axis);
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for (size_t ia = 0; ia < atoms->size(); ia++) {
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(*atoms)[ia].grad = cvm::rvector(0.0, 0.0, 0.0);
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for (size_t iq = 0; iq < 4; iq++) {
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(*atoms)[ia].grad += (dxdq[iq] * (rot.dQ0_2[ia])[iq]);
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}
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}
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}
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void colvar::tilt::apply_force(colvarvalue const &force)
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{
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cvm::real const &fw = force.real_value;
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if (!atoms->noforce) {
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atoms->apply_colvar_force(fw);
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}
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}
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simple_scalar_dist_functions(tilt)
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colvar::spin_angle::spin_angle(std::string const &conf)
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: orientation(conf)
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{
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function_type = "spin_angle";
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get_keyval(conf, "axis", axis, cvm::rvector(0.0, 0.0, 1.0));
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if (axis.norm2() != 1.0) {
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axis /= axis.norm();
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cvm::log("Normalizing rotation axis to "+cvm::to_str(axis)+".\n");
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}
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period = 360.0;
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b_periodic = true;
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x.type(colvarvalue::type_scalar);
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}
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colvar::spin_angle::spin_angle()
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: orientation()
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{
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function_type = "spin_angle";
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period = 360.0;
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b_periodic = true;
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x.type(colvarvalue::type_scalar);
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}
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void colvar::spin_angle::calc_value()
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{
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atoms_cog = atoms->center_of_geometry();
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rot.calc_optimal_rotation(ref_pos, atoms->positions_shifted(-1.0 * atoms_cog));
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x.real_value = rot.spin_angle(axis);
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this->wrap(x);
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}
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void colvar::spin_angle::calc_gradients()
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{
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cvm::quaternion const dxdq = rot.dspin_angle_dq(axis);
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for (size_t ia = 0; ia < atoms->size(); ia++) {
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(*atoms)[ia].grad = cvm::rvector(0.0, 0.0, 0.0);
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for (size_t iq = 0; iq < 4; iq++) {
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(*atoms)[ia].grad += (dxdq[iq] * (rot.dQ0_2[ia])[iq]);
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}
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}
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}
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void colvar::spin_angle::apply_force(colvarvalue const &force)
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{
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cvm::real const &fw = force.real_value;
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if (!atoms->noforce) {
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atoms->apply_colvar_force(fw);
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}
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}
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cvm::real colvar::spin_angle::dist2(colvarvalue const &x1,
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colvarvalue const &x2) const
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{
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cvm::real diff = x1.real_value - x2.real_value;
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diff = (diff < -180.0 ? diff + 360.0 : (diff > 180.0 ? diff - 360.0 : diff));
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return diff * diff;
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}
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colvarvalue colvar::spin_angle::dist2_lgrad(colvarvalue const &x1,
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colvarvalue const &x2) const
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{
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cvm::real diff = x1.real_value - x2.real_value;
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diff = (diff < -180.0 ? diff + 360.0 : (diff > 180.0 ? diff - 360.0 : diff));
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return 2.0 * diff;
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}
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colvarvalue colvar::spin_angle::dist2_rgrad(colvarvalue const &x1,
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colvarvalue const &x2) const
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{
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cvm::real diff = x1.real_value - x2.real_value;
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diff = (diff < -180.0 ? diff + 360.0 : (diff > 180.0 ? diff - 360.0 : diff));
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return (-2.0) * diff;
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}
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void colvar::spin_angle::wrap(colvarvalue &x) const
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{
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if ((x.real_value - wrap_center) >= 180.0) {
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x.real_value -= 360.0;
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return;
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}
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if ((x.real_value - wrap_center) < -180.0) {
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x.real_value += 360.0;
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return;
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}
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return;
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}
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