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colvarcomp_rotations.cpp
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Wed, May 29, 12:53

colvarcomp_rotations.cpp
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// -*- c++ -*-
// This file is part of the Collective Variables module (Colvars).
// The original version of Colvars and its updates are located at:
// https://github.com/colvars/colvars
// Please update all Colvars source files before making any changes.
// If you wish to distribute your changes, please submit them to the
// Colvars repository at GitHub.
#include <cmath>
#include "colvarmodule.h"
#include "colvarvalue.h"
#include "colvarparse.h"
#include "colvar.h"
#include "colvarcomp.h"
colvar::orientation::orientation(std::string const &conf)
: cvc(conf)
{
function_type = "orientation";
atoms = parse_group(conf, "atoms");
enable(f_cvc_implicit_gradient);
x.type(colvarvalue::type_quaternion);
ref_pos.reserve(atoms->size());
if (get_keyval(conf, "refPositions", ref_pos, ref_pos)) {
cvm::log("Using reference positions from input file.\n");
if (ref_pos.size() != atoms->size()) {
cvm::error("Error: reference positions do not "
"match the number of requested atoms.\n");
return;
}
}
{
std::string file_name;
if (get_keyval(conf, "refPositionsFile", file_name)) {
std::string file_col;
double file_col_value=0.0;
if (get_keyval(conf, "refPositionsCol", file_col, std::string(""))) {
// use PDB flags if column is provided
bool found = get_keyval(conf, "refPositionsColValue", file_col_value, 0.0);
if (found && file_col_value==0.0) {
cvm::error("Error: refPositionsColValue, "
"if provided, must be non-zero.\n");
return;
}
} else {
// if not, use atom indices
atoms->create_sorted_ids();
}
ref_pos.resize(atoms->size());
cvm::load_coords(file_name.c_str(), ref_pos, atoms->sorted_ids, file_col, file_col_value);
}
}
if (!ref_pos.size()) {
cvm::error("Error: must define a set of "
"reference coordinates.\n");
return;
}
cvm::log("Centering the reference coordinates: it is "
"assumed that each atom is the closest "
"periodic image to the center of geometry.\n");
cvm::rvector ref_cog(0.0, 0.0, 0.0);
size_t i;
for (i = 0; i < ref_pos.size(); i++) {
ref_cog += ref_pos[i];
}
ref_cog /= cvm::real(ref_pos.size());
for (i = 0; i < ref_pos.size(); i++) {
ref_pos[i] -= ref_cog;
}
get_keyval(conf, "closestToQuaternion", ref_quat, cvm::quaternion(1.0, 0.0, 0.0, 0.0));
// initialize rot member data
if (!atoms->noforce) {
rot.request_group2_gradients(atoms->size());
}
}
colvar::orientation::orientation()
: cvc()
{
function_type = "orientation";
enable(f_cvc_implicit_gradient);
x.type(colvarvalue::type_quaternion);
}
void colvar::orientation::calc_value()
{
rot.b_debug_gradients = is_enabled(f_cvc_debug_gradient);
atoms_cog = atoms->center_of_geometry();
rot.calc_optimal_rotation(ref_pos, atoms->positions_shifted(-1.0 * atoms_cog));
if ((rot.q).inner(ref_quat) >= 0.0) {
x.quaternion_value = rot.q;
} else {
x.quaternion_value = -1.0 * rot.q;
}
}
void colvar::orientation::calc_gradients()
{
// gradients have already been calculated and stored within the
// member object "rot"; we're not using the "grad" member of each
// atom object, because it only can represent the gradient of a
// scalar colvar
}
void colvar::orientation::apply_force(colvarvalue const &force)
{
cvm::quaternion const &FQ = force.quaternion_value;
if (!atoms->noforce) {
for (size_t ia = 0; ia < atoms->size(); ia++) {
for (size_t i = 0; i < 4; i++) {
(*atoms)[ia].apply_force(FQ[i] * rot.dQ0_2[ia][i]);
}
}
}
}
cvm::real colvar::orientation::dist2(colvarvalue const &x1,
colvarvalue const &x2) const
{
return x1.quaternion_value.dist2(x2);
}
colvarvalue colvar::orientation::dist2_lgrad(colvarvalue const &x1,
colvarvalue const &x2) const
{
return x1.quaternion_value.dist2_grad(x2);
}
colvarvalue colvar::orientation::dist2_rgrad(colvarvalue const &x1,
colvarvalue const &x2) const
{
return x2.quaternion_value.dist2_grad(x1);
}
colvar::orientation_angle::orientation_angle(std::string const &conf)
: orientation(conf)
{
function_type = "orientation_angle";
x.type(colvarvalue::type_scalar);
}
colvar::orientation_angle::orientation_angle()
: orientation()
{
function_type = "orientation_angle";
x.type(colvarvalue::type_scalar);
}
void colvar::orientation_angle::calc_value()
{
atoms_cog = atoms->center_of_geometry();
rot.calc_optimal_rotation(ref_pos, atoms->positions_shifted(-1.0 * atoms_cog));
if ((rot.q).q0 >= 0.0) {
x.real_value = (180.0/PI) * 2.0 * std::acos((rot.q).q0);
} else {
x.real_value = (180.0/PI) * 2.0 * std::acos(-1.0 * (rot.q).q0);
}
}
void colvar::orientation_angle::calc_gradients()
{
cvm::real const dxdq0 =
( ((rot.q).q0 * (rot.q).q0 < 1.0) ?
((180.0 / PI) * (-2.0) / std::sqrt(1.0 - ((rot.q).q0 * (rot.q).q0))) :
0.0 );
for (size_t ia = 0; ia < atoms->size(); ia++) {
(*atoms)[ia].grad = (dxdq0 * (rot.dQ0_2[ia])[0]);
}
}
void colvar::orientation_angle::apply_force(colvarvalue const &force)
{
cvm::real const &fw = force.real_value;
if (!atoms->noforce) {
atoms->apply_colvar_force(fw);
}
}
simple_scalar_dist_functions(orientation_angle)
colvar::orientation_proj::orientation_proj(std::string const &conf)
: orientation(conf)
{
function_type = "orientation_proj";
x.type(colvarvalue::type_scalar);
}
colvar::orientation_proj::orientation_proj()
: orientation()
{
function_type = "orientation_proj";
x.type(colvarvalue::type_scalar);
}
void colvar::orientation_proj::calc_value()
{
atoms_cog = atoms->center_of_geometry();
rot.calc_optimal_rotation(ref_pos, atoms->positions_shifted(-1.0 * atoms_cog));
x.real_value = 2.0 * (rot.q).q0 * (rot.q).q0 - 1.0;
}
void colvar::orientation_proj::calc_gradients()
{
cvm::real const dxdq0 = 2.0 * 2.0 * (rot.q).q0;
for (size_t ia = 0; ia < atoms->size(); ia++) {
(*atoms)[ia].grad = (dxdq0 * (rot.dQ0_2[ia])[0]);
}
}
void colvar::orientation_proj::apply_force(colvarvalue const &force)
{
cvm::real const &fw = force.real_value;
if (!atoms->noforce) {
atoms->apply_colvar_force(fw);
}
}
simple_scalar_dist_functions(orientation_proj)
colvar::tilt::tilt(std::string const &conf)
: orientation(conf)
{
function_type = "tilt";
get_keyval(conf, "axis", axis, cvm::rvector(0.0, 0.0, 1.0));
if (axis.norm2() != 1.0) {
axis /= axis.norm();
cvm::log("Normalizing rotation axis to "+cvm::to_str(axis)+".\n");
}
x.type(colvarvalue::type_scalar);
}
colvar::tilt::tilt()
: orientation()
{
function_type = "tilt";
x.type(colvarvalue::type_scalar);
}
void colvar::tilt::calc_value()
{
atoms_cog = atoms->center_of_geometry();
rot.calc_optimal_rotation(ref_pos, atoms->positions_shifted(-1.0 * atoms_cog));
x.real_value = rot.cos_theta(axis);
}
void colvar::tilt::calc_gradients()
{
cvm::quaternion const dxdq = rot.dcos_theta_dq(axis);
for (size_t ia = 0; ia < atoms->size(); ia++) {
(*atoms)[ia].grad = cvm::rvector(0.0, 0.0, 0.0);
for (size_t iq = 0; iq < 4; iq++) {
(*atoms)[ia].grad += (dxdq[iq] * (rot.dQ0_2[ia])[iq]);
}
}
}
void colvar::tilt::apply_force(colvarvalue const &force)
{
cvm::real const &fw = force.real_value;
if (!atoms->noforce) {
atoms->apply_colvar_force(fw);
}
}
simple_scalar_dist_functions(tilt)
colvar::spin_angle::spin_angle(std::string const &conf)
: orientation(conf)
{
function_type = "spin_angle";
get_keyval(conf, "axis", axis, cvm::rvector(0.0, 0.0, 1.0));
if (axis.norm2() != 1.0) {
axis /= axis.norm();
cvm::log("Normalizing rotation axis to "+cvm::to_str(axis)+".\n");
}
period = 360.0;
b_periodic = true;
x.type(colvarvalue::type_scalar);
}
colvar::spin_angle::spin_angle()
: orientation()
{
function_type = "spin_angle";
period = 360.0;
b_periodic = true;
x.type(colvarvalue::type_scalar);
}
void colvar::spin_angle::calc_value()
{
atoms_cog = atoms->center_of_geometry();
rot.calc_optimal_rotation(ref_pos, atoms->positions_shifted(-1.0 * atoms_cog));
x.real_value = rot.spin_angle(axis);
this->wrap(x);
}
void colvar::spin_angle::calc_gradients()
{
cvm::quaternion const dxdq = rot.dspin_angle_dq(axis);
for (size_t ia = 0; ia < atoms->size(); ia++) {
(*atoms)[ia].grad = cvm::rvector(0.0, 0.0, 0.0);
for (size_t iq = 0; iq < 4; iq++) {
(*atoms)[ia].grad += (dxdq[iq] * (rot.dQ0_2[ia])[iq]);
}
}
}
void colvar::spin_angle::apply_force(colvarvalue const &force)
{
cvm::real const &fw = force.real_value;
if (!atoms->noforce) {
atoms->apply_colvar_force(fw);
}
}
cvm::real colvar::spin_angle::dist2(colvarvalue const &x1,
colvarvalue const &x2) const
{
cvm::real diff = x1.real_value - x2.real_value;
diff = (diff < -180.0 ? diff + 360.0 : (diff > 180.0 ? diff - 360.0 : diff));
return diff * diff;
}
colvarvalue colvar::spin_angle::dist2_lgrad(colvarvalue const &x1,
colvarvalue const &x2) const
{
cvm::real diff = x1.real_value - x2.real_value;
diff = (diff < -180.0 ? diff + 360.0 : (diff > 180.0 ? diff - 360.0 : diff));
return 2.0 * diff;
}
colvarvalue colvar::spin_angle::dist2_rgrad(colvarvalue const &x1,
colvarvalue const &x2) const
{
cvm::real diff = x1.real_value - x2.real_value;
diff = (diff < -180.0 ? diff + 360.0 : (diff > 180.0 ? diff - 360.0 : diff));
return (-2.0) * diff;
}
void colvar::spin_angle::wrap(colvarvalue &x) const
{
if ((x.real_value - wrap_center) >= 180.0) {
x.real_value -= 360.0;
return;
}
if ((x.real_value - wrap_center) < -180.0) {
x.real_value += 360.0;
return;
}
return;
}

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