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colvarcomp_rotations.C
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rLAMMPS lammps
colvarcomp_rotations.C
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#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";
parse_group (conf, "atoms", atoms);
atom_groups.push_back (&atoms);
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::fatal_error ("Error: reference positions do not "
"match the number of requested atoms.\n");
}
}
{
std::string file_name;
if (get_keyval (conf, "refPositionsFile", file_name)) {
std::string file_col;
double file_col_value;
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)
cvm::fatal_error ("Error: refPositionsColValue, "
"if provided, must be non-zero.\n");
} 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::fatal_error ("Error: must define a set of "
"reference coordinates.\n");
}
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 cog (0.0, 0.0, 0.0);
for (size_t i = 0; i < ref_pos.size(); i++) {
cog += ref_pos[i];
}
cog /= cvm::real (ref_pos.size());
for (size_t i = 0; i < ref_pos.size(); i++) {
ref_pos[i] -= 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());
}
rot.b_debug_gradients = this->b_debug_gradients;
}
colvar::orientation::orientation()
: cvc ()
{
function_type = "orientation";
x.type (colvarvalue::type_quaternion);
}
void colvar::orientation::calc_value()
{
atoms.reset_atoms_data();
atoms.read_positions();
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]);
}
}
}
}
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.reset_atoms_data();
atoms.read_positions();
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);
}
}
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.reset_atoms_data();
atoms.read_positions();
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]);
}
}
if (cvm::debug()) {
std::vector<cvm::atom_pos> pos_test (atoms.positions_shifted (-1.0 * atoms_cog));
for (size_t comp = 0; comp < 3; comp++) {
// correct this cartesian component for the "new" center of geometry
for (size_t ia = 0; ia < atoms.size(); ia++) {
pos_test[ia][comp] -=
cvm::debug_gradients_step_size / cvm::real (atoms.size());
}
for (size_t ia = 0; ia < atoms.size(); ia++) {
pos_test[ia][comp] += cvm::debug_gradients_step_size;
rot.calc_optimal_rotation (ref_pos, pos_test);
pos_test[ia][comp] -= cvm::debug_gradients_step_size;
cvm::log ("|dx(real) - dx(pred)|/dx(real) = "+
cvm::to_str (std::fabs (rot.cos_theta (axis) - x.real_value -
cvm::debug_gradients_step_size * atoms[ia].grad[comp]) /
std::fabs (rot.cos_theta (axis) - x.real_value),
cvm::cv_width, cvm::cv_prec)+".\n");
}
for (size_t ia = 0; ia < atoms.size(); ia++) {
pos_test[ia][comp] +=
cvm::debug_gradients_step_size / cvm::real (atoms.size());
}
}
}
}
void colvar::tilt::apply_force (colvarvalue const &force)
{
cvm::real const &fw = force.real_value;
if (!atoms.noforce) {
atoms.apply_colvar_force (fw);
}
}
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.reset_atoms_data();
atoms.read_positions();
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]);
}
}
if (cvm::debug()) {
std::vector<cvm::atom_pos> pos_test (atoms.positions_shifted (-1.0 * atoms_cog));
for (size_t comp = 0; comp < 3; comp++) {
// correct this cartesian component for the "new" center of geometry
for (size_t ia = 0; ia < atoms.size(); ia++) {
pos_test[ia][comp] -=
cvm::debug_gradients_step_size / cvm::real (atoms.size());
}
for (size_t ia = 0; ia < atoms.size(); ia++) {
pos_test[ia][comp] += cvm::debug_gradients_step_size;
rot.calc_optimal_rotation (ref_pos, pos_test);
pos_test[ia][comp] -= cvm::debug_gradients_step_size;
cvm::log ("|dx(real) - dx(pred)|/dx(real) = "+
cvm::to_str (std::fabs (rot.spin_angle (axis) - x.real_value -
cvm::debug_gradients_step_size * atoms[ia].grad[comp]) /
std::fabs (rot.spin_angle (axis) - x.real_value),
cvm::cv_width, cvm::cv_prec)+".\n");
}
for (size_t ia = 0; ia < atoms.size(); ia++) {
pos_test[ia][comp] +=
cvm::debug_gradients_step_size / cvm::real (atoms.size());
}
}
}
}
void colvar::spin_angle::apply_force (colvarvalue const &force)
{
cvm::real const &fw = force.real_value;
if (!atoms.noforce) {
atoms.apply_colvar_force (fw);
}
}
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