505 lines
15 KiB
C++
505 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 "colvar.h"
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#include "colvarcomp.h"
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#include "colvar_rotation_derivative.h"
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struct colvar::orientation::rotation_derivative_impl_: public rotation_derivative<cvm::atom_pos, cvm::atom_pos> {
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public:
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rotation_derivative_impl_(colvar::orientation* orientation_cvc):
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rotation_derivative<cvm::atom_pos, cvm::atom_pos>(
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orientation_cvc->rot, orientation_cvc->ref_pos, orientation_cvc->shifted_pos) {}
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};
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colvar::orientation::orientation()
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{
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set_function_type("orientation");
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rot_deriv_impl = std::unique_ptr<rotation_derivative_impl_>(new rotation_derivative_impl_(this));
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disable(f_cvc_explicit_gradient);
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x.type(colvarvalue::type_quaternion);
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}
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colvar::orientation::~orientation() {}
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int colvar::orientation::init(std::string const &conf)
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{
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int error_code = cvc::init(conf);
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atoms = parse_group(conf, "atoms");
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if (!atoms || atoms->size() == 0) {
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return error_code | COLVARS_INPUT_ERROR;
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}
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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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return cvm::error("Error: reference positions do not "
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"match the number of requested atoms.\n", COLVARS_INPUT_ERROR);
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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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return cvm::error("Error: refPositionsColValue, "
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"if provided, must be non-zero.\n", COLVARS_INPUT_ERROR);
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}
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}
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ref_pos.resize(atoms->size());
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error_code |= cvm::load_coords(file_name.c_str(), &ref_pos, atoms,
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file_col, file_col_value);
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}
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}
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if (error_code != COLVARS_OK) return error_code;
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if (!ref_pos.size()) {
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return cvm::error("Error: must define a set of "
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"reference coordinates.\n", COLVARS_INPUT_ERROR);
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}
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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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cvm::log("Centering the reference coordinates on the origin by subtracting "
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"the center of geometry at "+
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cvm::to_str(-1.0 * ref_cog)+"; 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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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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// If the debug gradients feature is active, debug the rotation gradients
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// (note that this won't be active for the orientation CVC itself, because
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// colvardeps prevents the flag's activation)
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rot.b_debug_gradients = is_enabled(f_cvc_debug_gradient);
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return error_code;
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}
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void colvar::orientation::calc_value()
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{
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atoms_cog = atoms->center_of_geometry();
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shifted_pos = atoms->positions_shifted(-1.0 * atoms_cog);
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rot.calc_optimal_rotation(ref_pos, shifted_pos);
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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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rot_deriv_impl->prepare_derivative(rotation_derivative_dldq::use_dq);
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cvm::vector1d<cvm::rvector> dq0_2;
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for (size_t ia = 0; ia < atoms->size(); ia++) {
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rot_deriv_impl->calc_derivative_wrt_group2(ia, nullptr, &dq0_2);
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for (size_t i = 0; i < 4; i++) {
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(*atoms)[ia].apply_force(FQ[i] * dq0_2[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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void colvar::orientation::wrap(colvarvalue & /* x_unwrapped */) const {}
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colvar::orientation_angle::orientation_angle()
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{
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set_function_type("orientationAngle");
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init_as_angle();
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enable(f_cvc_explicit_gradient);
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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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shifted_pos = atoms->positions_shifted(-1.0 * atoms_cog);
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rot.calc_optimal_rotation(ref_pos, shifted_pos);
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if ((rot.q).q0 >= 0.0) {
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x.real_value = (180.0/PI) * 2.0 * cvm::acos((rot.q).q0);
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} else {
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x.real_value = (180.0/PI) * 2.0 * cvm::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) / cvm::sqrt(1.0 - ((rot.q).q0 * (rot.q).q0))) :
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0.0 );
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rot_deriv_impl->prepare_derivative(rotation_derivative_dldq::use_dq);
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cvm::vector1d<cvm::rvector> dq0_2;
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for (size_t ia = 0; ia < atoms->size(); ia++) {
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rot_deriv_impl->calc_derivative_wrt_group2(ia, nullptr, &dq0_2);
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(*atoms)[ia].grad = (dxdq0 * dq0_2[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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cvc::apply_force(force);
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}
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cvm::real colvar::orientation_angle::dist2(colvarvalue const &x1, colvarvalue const &x2) const
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{
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return cvc::dist2(x1, x2);
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}
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colvarvalue colvar::orientation_angle::dist2_lgrad(colvarvalue const &x1,
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colvarvalue const &x2) const
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{
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return cvc::dist2_lgrad(x1, x2);
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}
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colvarvalue colvar::orientation_angle::dist2_rgrad(colvarvalue const &x1,
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colvarvalue const &x2) const
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{
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return cvc::dist2_rgrad(x1, x2);
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}
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void colvar::orientation_angle::wrap(colvarvalue & /* x_unwrapped */) const {}
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colvar::orientation_proj::orientation_proj()
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{
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set_function_type("orientationProj");
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enable(f_cvc_explicit_gradient);
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x.type(colvarvalue::type_scalar);
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init_scalar_boundaries(0.0, 1.0);
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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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shifted_pos = atoms->positions_shifted(-1.0 * atoms_cog);
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rot.calc_optimal_rotation(ref_pos, shifted_pos);
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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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rot_deriv_impl->prepare_derivative(rotation_derivative_dldq::use_dq);
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cvm::vector1d<cvm::rvector> dq0_2;
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for (size_t ia = 0; ia < atoms->size(); ia++) {
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rot_deriv_impl->calc_derivative_wrt_group2(ia, nullptr, &dq0_2);
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(*atoms)[ia].grad = (dxdq0 * dq0_2[0]);
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}
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}
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colvar::tilt::tilt()
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{
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set_function_type("tilt");
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x.type(colvarvalue::type_scalar);
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enable(f_cvc_explicit_gradient);
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init_scalar_boundaries(-1.0, 1.0);
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}
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int colvar::tilt::init(std::string const &conf)
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{
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int error_code = orientation_proj::init(conf);
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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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return error_code;
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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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shifted_pos = atoms->positions_shifted(-1.0 * atoms_cog);
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rot.calc_optimal_rotation(ref_pos, shifted_pos);
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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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rot_deriv_impl->prepare_derivative(rotation_derivative_dldq::use_dq);
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cvm::vector1d<cvm::rvector> dq0_2;
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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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rot_deriv_impl->calc_derivative_wrt_group2(ia, nullptr, &dq0_2);
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for (size_t iq = 0; iq < 4; iq++) {
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(*atoms)[ia].grad += (dxdq[iq] * dq0_2[iq]);
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}
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}
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}
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colvar::spin_angle::spin_angle()
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{
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set_function_type("spinAngle");
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init_as_periodic_angle();
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enable(f_cvc_explicit_gradient);
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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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shifted_pos = atoms->positions_shifted(-1.0 * atoms_cog);
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rot.calc_optimal_rotation(ref_pos, shifted_pos);
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x.real_value = rot.spin_angle(axis);
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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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rot_deriv_impl->prepare_derivative(rotation_derivative_dldq::use_dq);
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cvm::vector1d<cvm::rvector> dq0_2;
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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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rot_deriv_impl->calc_derivative_wrt_group2(ia, nullptr, &dq0_2);
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for (size_t iq = 0; iq < 4; iq++) {
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(*atoms)[ia].grad += (dxdq[iq] * dq0_2[iq]);
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}
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}
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}
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colvar::euler_phi::euler_phi()
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{
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set_function_type("eulerPhi");
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init_as_periodic_angle();
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enable(f_cvc_explicit_gradient);
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}
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void colvar::euler_phi::calc_value()
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{
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atoms_cog = atoms->center_of_geometry();
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shifted_pos = atoms->positions_shifted(-1.0 * atoms_cog);
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rot.calc_optimal_rotation(ref_pos, shifted_pos);
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const cvm::real& q0 = rot.q.q0;
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const cvm::real& q1 = rot.q.q1;
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const cvm::real& q2 = rot.q.q2;
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const cvm::real& q3 = rot.q.q3;
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const cvm::real tmp_y = 2 * (q0 * q1 + q2 * q3);
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const cvm::real tmp_x = 1 - 2 * (q1 * q1 + q2 * q2);
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x.real_value = cvm::atan2(tmp_y, tmp_x) * (180.0/PI);
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}
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void colvar::euler_phi::calc_gradients()
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{
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const cvm::real& q0 = rot.q.q0;
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const cvm::real& q1 = rot.q.q1;
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const cvm::real& q2 = rot.q.q2;
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const cvm::real& q3 = rot.q.q3;
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const cvm::real denominator = (2 * q0 * q1 + 2 * q2 * q3) * (2 * q0 * q1 + 2 * q2 * q3) + (-2 * q1 * q1 - 2 * q2 * q2 + 1) * (-2 * q1 * q1 - 2 * q2 * q2 + 1);
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const cvm::real dxdq0 = (180.0/PI) * 2 * q1 * (-2 * q1 * q1 - 2 * q2 * q2 + 1) / denominator;
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const cvm::real dxdq1 = (180.0/PI) * (2 * q0 * (-2 * q1 * q1 - 2 * q2 * q2 + 1) - 4 * q1 * (-2 * q0 * q1 - 2 * q2 * q3)) / denominator;
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const cvm::real dxdq2 = (180.0/PI) * (-4 * q2 * (-2 * q0 * q1 - 2 * q2 * q3) + 2 * q3 * (-2 * q1 * q1 - 2 * q2 * q2 + 1)) / denominator;
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const cvm::real dxdq3 = (180.0/PI) * 2 * q2 * (-2 * q1 * q1 - 2 * q2 * q2 + 1) / denominator;
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rot_deriv_impl->prepare_derivative(rotation_derivative_dldq::use_dq);
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cvm::vector1d<cvm::rvector> dq0_2;
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for (size_t ia = 0; ia < atoms->size(); ia++) {
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rot_deriv_impl->calc_derivative_wrt_group2(ia, nullptr, &dq0_2);
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(*atoms)[ia].grad = (dxdq0 * dq0_2[0]) +
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(dxdq1 * dq0_2[1]) +
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(dxdq2 * dq0_2[2]) +
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(dxdq3 * dq0_2[3]);
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}
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}
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colvar::euler_psi::euler_psi()
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{
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set_function_type("eulerPsi");
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init_as_periodic_angle();
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enable(f_cvc_explicit_gradient);
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}
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void colvar::euler_psi::calc_value()
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{
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atoms_cog = atoms->center_of_geometry();
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shifted_pos = atoms->positions_shifted(-1.0 * atoms_cog);
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rot.calc_optimal_rotation(ref_pos, shifted_pos);
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const cvm::real& q0 = rot.q.q0;
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const cvm::real& q1 = rot.q.q1;
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const cvm::real& q2 = rot.q.q2;
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const cvm::real& q3 = rot.q.q3;
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const cvm::real tmp_y = 2 * (q0 * q3 + q1 * q2);
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const cvm::real tmp_x = 1 - 2 * (q2 * q2 + q3 * q3);
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x.real_value = cvm::atan2(tmp_y, tmp_x) * (180.0/PI);
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}
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void colvar::euler_psi::calc_gradients()
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{
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const cvm::real& q0 = rot.q.q0;
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const cvm::real& q1 = rot.q.q1;
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const cvm::real& q2 = rot.q.q2;
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const cvm::real& q3 = rot.q.q3;
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const cvm::real denominator = (2 * q0 * q3 + 2 * q1 * q2) * (2 * q0 * q3 + 2 * q1 * q2) + (-2 * q2 * q2 - 2 * q3 * q3 + 1) * (-2 * q2 * q2 - 2 * q3 * q3 + 1);
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const cvm::real dxdq0 = (180.0/PI) * 2 * q3 * (-2 * q2 * q2 - 2 * q3 * q3 + 1) / denominator;
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const cvm::real dxdq1 = (180.0/PI) * 2 * q2 * (-2 * q2 * q2 - 2 * q3 * q3 + 1) / denominator;
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const cvm::real dxdq2 = (180.0/PI) * (2 * q1 * (-2 * q2 * q2 - 2 * q3 * q3 + 1) - 4 * q2 * (-2 * q0 * q3 - 2 * q1 * q2)) / denominator;
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const cvm::real dxdq3 = (180.0/PI) * (2 * q0 * (-2 * q2 * q2 - 2 * q3 * q3 + 1) - 4 * q3 * (-2 * q0 * q3 - 2 * q1 * q2)) / denominator;
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rot_deriv_impl->prepare_derivative(rotation_derivative_dldq::use_dq);
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cvm::vector1d<cvm::rvector> dq0_2;
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for (size_t ia = 0; ia < atoms->size(); ia++) {
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rot_deriv_impl->calc_derivative_wrt_group2(ia, nullptr, &dq0_2);
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(*atoms)[ia].grad = (dxdq0 * dq0_2[0]) +
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(dxdq1 * dq0_2[1]) +
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(dxdq2 * dq0_2[2]) +
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(dxdq3 * dq0_2[3]);
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}
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}
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colvar::euler_theta::euler_theta()
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{
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set_function_type("eulerTheta");
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init_as_angle();
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enable(f_cvc_explicit_gradient);
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}
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void colvar::euler_theta::calc_value()
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{
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atoms_cog = atoms->center_of_geometry();
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|
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shifted_pos = atoms->positions_shifted(-1.0 * atoms_cog);
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rot.calc_optimal_rotation(ref_pos, shifted_pos);
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|
|
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const cvm::real& q0 = rot.q.q0;
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const cvm::real& q1 = rot.q.q1;
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const cvm::real& q2 = rot.q.q2;
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const cvm::real& q3 = rot.q.q3;
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x.real_value = cvm::asin(2 * (q0 * q2 - q3 * q1)) * (180.0/PI);
|
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}
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|
|
|
|
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void colvar::euler_theta::calc_gradients()
|
|
{
|
|
const cvm::real& q0 = rot.q.q0;
|
|
const cvm::real& q1 = rot.q.q1;
|
|
const cvm::real& q2 = rot.q.q2;
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|
const cvm::real& q3 = rot.q.q3;
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const cvm::real denominator = cvm::sqrt(1 - (2 * q0 * q2 - 2 * q1 * q3) * (2 * q0 * q2 - 2 * q1 * q3));
|
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const cvm::real dxdq0 = (180.0/PI) * 2 * q2 / denominator;
|
|
const cvm::real dxdq1 = (180.0/PI) * -2 * q3 / denominator;
|
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const cvm::real dxdq2 = (180.0/PI) * 2 * q0 / denominator;
|
|
const cvm::real dxdq3 = (180.0/PI) * -2 * q1 / denominator;
|
|
rot_deriv_impl->prepare_derivative(rotation_derivative_dldq::use_dq);
|
|
cvm::vector1d<cvm::rvector> dq0_2;
|
|
for (size_t ia = 0; ia < atoms->size(); ia++) {
|
|
rot_deriv_impl->calc_derivative_wrt_group2(ia, nullptr, &dq0_2);
|
|
(*atoms)[ia].grad = (dxdq0 * dq0_2[0]) +
|
|
(dxdq1 * dq0_2[1]) +
|
|
(dxdq2 * dq0_2[2]) +
|
|
(dxdq3 * dq0_2[3]);
|
|
}
|
|
}
|