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lammps/lib/colvars/colvarcomp_distances.cpp
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colvarcomp_distances.cpp
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#include <cmath>
#include "colvarmodule.h"
#include "colvarvalue.h"
#include "colvarparse.h"
#include "colvar.h"
#include "colvarcomp.h"
// "twogroup" flag defaults to true; set to false by selfCoordNum
// (only distance-derived component based on only one group)
colvar::distance::distance (std::string const &conf, bool twogroups)
: cvc (conf)
{
function_type = "distance";
b_inverse_gradients = true;
b_Jacobian_derivative = true;
if (get_keyval (conf, "forceNoPBC", b_no_PBC, false)) {
cvm::log ("Computing distance using absolute positions (not minimal-image)");
}
if (twogroups && get_keyval (conf, "oneSiteSystemForce", b_1site_force, false)) {
cvm::log ("Computing system force on group 1 only");
}
parse_group (conf, "group1", group1);
atom_groups.push_back (&group1);
if (twogroups) {
parse_group (conf, "group2", group2);
atom_groups.push_back (&group2);
}
x.type (colvarvalue::type_scalar);
}
colvar::distance::distance()
: cvc ()
{
function_type = "distance";
b_inverse_gradients = true;
b_Jacobian_derivative = true;
b_1site_force = false;
x.type (colvarvalue::type_scalar);
}
void colvar::distance::calc_value()
{
if (b_no_PBC) {
dist_v = group2.center_of_mass() - group1.center_of_mass();
} else {
dist_v = cvm::position_distance (group1.center_of_mass(),
group2.center_of_mass());
}
x.real_value = dist_v.norm();
}
void colvar::distance::calc_gradients()
{
cvm::rvector const u = dist_v.unit();
group1.set_weighted_gradient (-1.0 * u);
group2.set_weighted_gradient ( u);
}
void colvar::distance::calc_force_invgrads()
{
group1.read_system_forces();
if ( b_1site_force ) {
ft.real_value = -1.0 * (group1.system_force() * dist_v.unit());
} else {
group2.read_system_forces();
ft.real_value = 0.5 * ((group2.system_force() - group1.system_force()) * dist_v.unit());
}
}
void colvar::distance::calc_Jacobian_derivative()
{
jd.real_value = x.real_value ? (2.0 / x.real_value) : 0.0;
}
void colvar::distance::apply_force (colvarvalue const &force)
{
if (!group1.noforce)
group1.apply_colvar_force (force.real_value);
if (!group2.noforce)
group2.apply_colvar_force (force.real_value);
}
colvar::distance_vec::distance_vec (std::string const &conf)
: distance (conf)
{
function_type = "distance_vec";
x.type (colvarvalue::type_vector);
}
colvar::distance_vec::distance_vec()
: distance()
{
function_type = "distance_vec";
x.type (colvarvalue::type_vector);
}
void colvar::distance_vec::calc_value()
{
if (b_no_PBC) {
x.rvector_value = group2.center_of_mass() - group1.center_of_mass();
} else {
x.rvector_value = cvm::position_distance (group1.center_of_mass(),
group2.center_of_mass());
}
}
void colvar::distance_vec::calc_gradients()
{
// gradients are not stored: a 3x3 matrix for each atom would be
// needed to store just the identity matrix
}
void colvar::distance_vec::apply_force (colvarvalue const &force)
{
if (!group1.noforce)
group1.apply_force (-1.0 * force.rvector_value);
if (!group2.noforce)
group2.apply_force ( force.rvector_value);
}
colvar::distance_z::distance_z (std::string const &conf)
: cvc (conf)
{
function_type = "distance_z";
b_inverse_gradients = true;
b_Jacobian_derivative = true;
x.type (colvarvalue::type_scalar);
// TODO detect PBC from MD engine (in simple cases)
// and then update period in real time
if (period != 0.0)
b_periodic = true;
if ((wrap_center != 0.0) && (period == 0.0)) {
cvm::fatal_error ("Error: wrapAround was defined in a distanceZ component,"
" but its period has not been set.\n");
}
parse_group (conf, "main", main);
parse_group (conf, "ref", ref1);
atom_groups.push_back (&main);
atom_groups.push_back (&ref1);
// this group is optional
parse_group (conf, "ref2", ref2, true);
if (ref2.size()) {
atom_groups.push_back (&ref2);
cvm::log ("Using axis joining the centers of mass of groups \"ref\" and \"ref2\"");
fixed_axis = false;
if (key_lookup (conf, "axis"))
cvm::log ("Warning: explicit axis definition will be ignored!");
} else {
if (get_keyval (conf, "axis", axis, cvm::rvector (0.0, 0.0, 1.0))) {
if (axis.norm2() == 0.0)
cvm::fatal_error ("Axis vector is zero!");
if (axis.norm2() != 1.0) {
axis = axis.unit();
cvm::log ("The normalized axis is: "+cvm::to_str (axis)+".\n");
}
}
fixed_axis = true;
}
if (get_keyval (conf, "forceNoPBC", b_no_PBC, false)) {
cvm::log ("Computing distance using absolute positions (not minimal-image)");
}
if (get_keyval (conf, "oneSiteSystemForce", b_1site_force, false)) {
cvm::log ("Computing system force on group \"main\" only");
}
}
colvar::distance_z::distance_z()
{
function_type = "distance_z";
b_inverse_gradients = true;
b_Jacobian_derivative = true;
x.type (colvarvalue::type_scalar);
}
void colvar::distance_z::calc_value()
{
if (fixed_axis) {
if (b_no_PBC) {
dist_v = main.center_of_mass() - ref1.center_of_mass();
} else {
dist_v = cvm::position_distance (ref1.center_of_mass(),
main.center_of_mass());
}
} else {
if (b_no_PBC) {
dist_v = main.center_of_mass() -
(0.5 * (ref1.center_of_mass() + ref2.center_of_mass()));
axis = ref2.center_of_mass() - ref1.center_of_mass();
} else {
dist_v = cvm::position_distance (0.5 * (ref1.center_of_mass() +
ref2.center_of_mass()), main.center_of_mass());
axis = cvm::position_distance (ref1.center_of_mass(), ref2.center_of_mass());
}
axis_norm = axis.norm();
axis = axis.unit();
}
x.real_value = axis * dist_v;
this->wrap (x);
}
void colvar::distance_z::calc_gradients()
{
main.set_weighted_gradient ( axis );
if (fixed_axis) {
ref1.set_weighted_gradient (-1.0 * axis);
} else {
if (b_no_PBC) {
ref1.set_weighted_gradient ( 1.0 / axis_norm * (main.center_of_mass() - ref2.center_of_mass() -
x.real_value * axis ));
ref2.set_weighted_gradient ( 1.0 / axis_norm * (ref1.center_of_mass() - main.center_of_mass() +
x.real_value * axis ));
} else {
ref1.set_weighted_gradient ( 1.0 / axis_norm * (
cvm::position_distance (ref2.center_of_mass(), main.center_of_mass()) - x.real_value * axis ));
ref2.set_weighted_gradient ( 1.0 / axis_norm * (
cvm::position_distance (main.center_of_mass(), ref1.center_of_mass()) + x.real_value * axis ));
}
}
}
void colvar::distance_z::calc_force_invgrads()
{
main.read_system_forces();
if (fixed_axis && !b_1site_force) {
ref1.read_system_forces();
ft.real_value = 0.5 * ((main.system_force() - ref1.system_force()) * axis);
} else {
ft.real_value = main.system_force() * axis;
}
}
void colvar::distance_z::calc_Jacobian_derivative()
{
jd.real_value = 0.0;
}
void colvar::distance_z::apply_force (colvarvalue const &force)
{
if (!ref1.noforce)
ref1.apply_colvar_force (force.real_value);
if (ref2.size() && !ref2.noforce)
ref2.apply_colvar_force (force.real_value);
if (!main.noforce)
main.apply_colvar_force (force.real_value);
}
colvar::distance_xy::distance_xy (std::string const &conf)
: distance_z (conf)
{
function_type = "distance_xy";
b_inverse_gradients = true;
b_Jacobian_derivative = true;
x.type (colvarvalue::type_scalar);
}
colvar::distance_xy::distance_xy()
: distance_z()
{
function_type = "distance_xy";
b_inverse_gradients = true;
b_Jacobian_derivative = true;
x.type (colvarvalue::type_scalar);
}
void colvar::distance_xy::calc_value()
{
if (b_no_PBC) {
dist_v = main.center_of_mass() - ref1.center_of_mass();
} else {
dist_v = cvm::position_distance (ref1.center_of_mass(),
main.center_of_mass());
}
if (!fixed_axis) {
if (b_no_PBC) {
v12 = ref2.center_of_mass() - ref1.center_of_mass();
} else {
v12 = cvm::position_distance (ref1.center_of_mass(), ref2.center_of_mass());
}
axis_norm = v12.norm();
axis = v12.unit();
}
dist_v_ortho = dist_v - (dist_v * axis) * axis;
x.real_value = dist_v_ortho.norm();
}
void colvar::distance_xy::calc_gradients()
{
// Intermediate quantity (r_P3 / r_12 where P is the projection
// of 3 (main) on the plane orthogonal to 12, containing 1 (ref1))
cvm::real A;
cvm::real x_inv;
if (x.real_value == 0.0) return;
x_inv = 1.0 / x.real_value;
if (fixed_axis) {
ref1.set_weighted_gradient (-1.0 * x_inv * dist_v_ortho);
main.set_weighted_gradient ( x_inv * dist_v_ortho);
} else {
if (b_no_PBC) {
v13 = main.center_of_mass() - ref1.center_of_mass();
} else {
v13 = cvm::position_distance (ref1.center_of_mass(), main.center_of_mass());
}
A = (dist_v * axis) / axis_norm;
ref1.set_weighted_gradient ( (A - 1.0) * x_inv * dist_v_ortho);
ref2.set_weighted_gradient ( -A * x_inv * dist_v_ortho);
main.set_weighted_gradient ( 1.0 * x_inv * dist_v_ortho);
}
}
void colvar::distance_xy::calc_force_invgrads()
{
main.read_system_forces();
if (fixed_axis && !b_1site_force) {
ref1.read_system_forces();
ft.real_value = 0.5 / x.real_value * ((main.system_force() - ref1.system_force()) * dist_v_ortho);
} else {
ft.real_value = 1.0 / x.real_value * main.system_force() * dist_v_ortho;
}
}
void colvar::distance_xy::calc_Jacobian_derivative()
{
jd.real_value = x.real_value ? (1.0 / x.real_value) : 0.0;
}
void colvar::distance_xy::apply_force (colvarvalue const &force)
{
if (!ref1.noforce)
ref1.apply_colvar_force (force.real_value);
if (ref2.size() && !ref2.noforce)
ref2.apply_colvar_force (force.real_value);
if (!main.noforce)
main.apply_colvar_force (force.real_value);
}
colvar::distance_dir::distance_dir (std::string const &conf)
: distance (conf)
{
function_type = "distance_dir";
x.type (colvarvalue::type_unitvector);
}
colvar::distance_dir::distance_dir()
: distance()
{
function_type = "distance_dir";
x.type (colvarvalue::type_unitvector);
}
void colvar::distance_dir::calc_value()
{
if (b_no_PBC) {
dist_v = group2.center_of_mass() - group1.center_of_mass();
} else {
dist_v = cvm::position_distance (group1.center_of_mass(),
group2.center_of_mass());
}
x.rvector_value = dist_v.unit();
}
void colvar::distance_dir::calc_gradients()
{
// gradients are computed on the fly within apply_force()
// Note: could be a problem if a future bias relies on gradient
// calculations...
}
void colvar::distance_dir::apply_force (colvarvalue const &force)
{
// remove the radial force component
cvm::real const iprod = force.rvector_value * x.rvector_value;
cvm::rvector const force_tang = force.rvector_value - iprod * x.rvector_value;
if (!group1.noforce)
group1.apply_force (-1.0 * force_tang);
if (!group2.noforce)
group2.apply_force ( force_tang);
}
colvar::distance_inv::distance_inv (std::string const &conf)
: distance (conf)
{
function_type = "distance_inv";
get_keyval (conf, "exponent", exponent, 6);
if (exponent%2) {
cvm::fatal_error ("Error: odd exponent provided, can only use even ones.\n");
}
if (exponent <= 0) {
cvm::fatal_error ("Error: negative or zero exponent provided.\n");
}
for (cvm::atom_iter ai1 = group1.begin(); ai1 != group1.end(); ai1++) {
for (cvm::atom_iter ai2 = group2.begin(); ai2 != group2.end(); ai2++) {
if (ai1->id == ai2->id)
cvm::fatal_error ("Error: group1 and group1 have some atoms in common: this is not allowed for distanceInv.\n");
}
}
b_inverse_gradients = false;
b_Jacobian_derivative = false;
x.type (colvarvalue::type_scalar);
}
colvar::distance_inv::distance_inv()
{
function_type = "distance_inv";
exponent = 6;
b_inverse_gradients = false;
b_Jacobian_derivative = false;
b_1site_force = false;
x.type (colvarvalue::type_scalar);
}
void colvar::distance_inv::calc_value()
{
x.real_value = 0.0;
if (b_no_PBC) {
for (cvm::atom_iter ai1 = group1.begin(); ai1 != group1.end(); ai1++) {
for (cvm::atom_iter ai2 = group2.begin(); ai2 != group2.end(); ai2++) {
cvm::rvector const dv = ai2->pos - ai1->pos;
cvm::real const d2 = dv.norm2();
cvm::real dinv = 1.0;
for (int ne = 0; ne < exponent/2; ne++)
dinv *= 1.0/d2;
x.real_value += dinv;
cvm::rvector const dsumddv = -(cvm::real (exponent)) * dinv/d2 * dv;
ai1->grad += -1.0 * dsumddv;
ai2->grad += dsumddv;
}
}
} else {
for (cvm::atom_iter ai1 = group1.begin(); ai1 != group1.end(); ai1++) {
for (cvm::atom_iter ai2 = group2.begin(); ai2 != group2.end(); ai2++) {
cvm::rvector const dv = cvm::position_distance (ai1->pos, ai2->pos);
cvm::real const d2 = dv.norm2();
cvm::real dinv = 1.0;
for (int ne = 0; ne < exponent/2; ne++)
dinv *= 1.0/d2;
x.real_value += dinv;
cvm::rvector const dsumddv = -(cvm::real (exponent)) * dinv/d2 * dv;
ai1->grad += -1.0 * dsumddv;
ai2->grad += dsumddv;
}
}
}
x.real_value *= 1.0 / cvm::real (group1.size() * group2.size());
x.real_value = std::pow (x.real_value, -1.0/(cvm::real (exponent)));
}
void colvar::distance_inv::calc_gradients()
{
cvm::real const dxdsum = (-1.0/(cvm::real (exponent))) * std::pow (x.real_value, exponent+1) / cvm::real (group1.size() * group2.size());
for (cvm::atom_iter ai1 = group1.begin(); ai1 != group1.end(); ai1++) {
ai1->grad *= dxdsum;
}
for (cvm::atom_iter ai2 = group2.begin(); ai2 != group2.end(); ai2++) {
ai2->grad *= dxdsum;
}
}
void colvar::distance_inv::apply_force (colvarvalue const &force)
{
if (!group1.noforce)
group1.apply_colvar_force (force.real_value);
if (!group2.noforce)
group2.apply_colvar_force (force.real_value);
}
colvar::gyration::gyration (std::string const &conf)
: cvc (conf)
{
function_type = "gyration";
b_inverse_gradients = true;
b_Jacobian_derivative = true;
parse_group (conf, "atoms", atoms);
atom_groups.push_back (&atoms);
if (atoms.b_user_defined_fit) {
cvm::log ("WARNING: explicit fitting parameters were provided for atom group \"atoms\".");
} else {
atoms.b_center = true;
atoms.ref_pos.assign (1, cvm::rvector (0.0, 0.0, 0.0));
}
x.type (colvarvalue::type_scalar);
}
colvar::gyration::gyration()
{
function_type = "gyration";
b_inverse_gradients = true;
b_Jacobian_derivative = true;
x.type (colvarvalue::type_scalar);
}
void colvar::gyration::calc_value()
{
x.real_value = 0.0;
for (cvm::atom_iter ai = atoms.begin(); ai != atoms.end(); ai++) {
x.real_value += (ai->pos).norm2();
}
x.real_value = std::sqrt (x.real_value / cvm::real (atoms.size()));
}
void colvar::gyration::calc_gradients()
{
cvm::real const drdx = 1.0/(cvm::real (atoms.size()) * x.real_value);
for (cvm::atom_iter ai = atoms.begin(); ai != atoms.end(); ai++) {
ai->grad = drdx * ai->pos;
}
if (b_debug_gradients) {
cvm::log ("Debugging gradients:\n");
debug_gradients (atoms);
}
}
void colvar::gyration::calc_force_invgrads()
{
atoms.read_system_forces();
cvm::real const dxdr = 1.0/x.real_value;
ft.real_value = 0.0;
for (cvm::atom_iter ai = atoms.begin(); ai != atoms.end(); ai++) {
ft.real_value += dxdr * ai->pos * ai->system_force;
}
}
void colvar::gyration::calc_Jacobian_derivative()
{
jd = x.real_value ? (3.0 * cvm::real (atoms.size()) - 4.0) / x.real_value : 0.0;
}
void colvar::gyration::apply_force (colvarvalue const &force)
{
if (!atoms.noforce)
atoms.apply_colvar_force (force.real_value);
}
colvar::inertia::inertia (std::string const &conf)
: gyration (conf)
{
function_type = "inertia";
b_inverse_gradients = false;
b_Jacobian_derivative = false;
x.type (colvarvalue::type_scalar);
}
colvar::inertia::inertia()
{
function_type = "inertia";
x.type (colvarvalue::type_scalar);
}
void colvar::inertia::calc_value()
{
x.real_value = 0.0;
for (cvm::atom_iter ai = atoms.begin(); ai != atoms.end(); ai++) {
x.real_value += (ai->pos).norm2();
}
}
void colvar::inertia::calc_gradients()
{
for (cvm::atom_iter ai = atoms.begin(); ai != atoms.end(); ai++) {
ai->grad = 2.0 * ai->pos;
}
if (b_debug_gradients) {
cvm::log ("Debugging gradients:\n");
debug_gradients (atoms);
}
}
void colvar::inertia::apply_force (colvarvalue const &force)
{
if (!atoms.noforce)
atoms.apply_colvar_force (force.real_value);
}
colvar::inertia_z::inertia_z (std::string const &conf)
: inertia (conf)
{
function_type = "inertia_z";
if (get_keyval (conf, "axis", axis, cvm::rvector (0.0, 0.0, 1.0))) {
if (axis.norm2() == 0.0)
cvm::fatal_error ("Axis vector is zero!");
if (axis.norm2() != 1.0) {
axis = axis.unit();
cvm::log ("The normalized axis is: "+cvm::to_str (axis)+".\n");
}
}
x.type (colvarvalue::type_scalar);
}
colvar::inertia_z::inertia_z()
{
function_type = "inertia_z";
x.type (colvarvalue::type_scalar);
}
void colvar::inertia_z::calc_value()
{
x.real_value = 0.0;
for (cvm::atom_iter ai = atoms.begin(); ai != atoms.end(); ai++) {
cvm::real const iprod = ai->pos * axis;
x.real_value += iprod * iprod;
}
}
void colvar::inertia_z::calc_gradients()
{
for (cvm::atom_iter ai = atoms.begin(); ai != atoms.end(); ai++) {
ai->grad = 2.0 * (ai->pos * axis) * axis;
}
if (b_debug_gradients) {
cvm::log ("Debugging gradients:\n");
debug_gradients (atoms);
}
}
void colvar::inertia_z::apply_force (colvarvalue const &force)
{
if (!atoms.noforce)
atoms.apply_colvar_force (force.real_value);
}
colvar::rmsd::rmsd (std::string const &conf)
: cvc (conf)
{
b_inverse_gradients = true;
b_Jacobian_derivative = true;
function_type = "rmsd";
x.type (colvarvalue::type_scalar);
parse_group (conf, "atoms", atoms);
atom_groups.push_back (&atoms);
if (atoms.b_dummy)
cvm::fatal_error ("Error: \"atoms\" cannot be a dummy atom.");
if (atoms.ref_pos_group != NULL) {
cvm::log ("The option \"refPositionsGroup\" (alternative group for fitting) was enabled: "
"Jacobian derivatives of the RMSD will not be calculated.\n");
b_Jacobian_derivative = false;
}
// the following is a simplified version of the corresponding atom group options;
// we need this because the reference coordinates defined inside the atom group
// may be used only for fitting, and even more so if ref_pos_group is used
if (get_keyval (conf, "refPositions", ref_pos, ref_pos)) {
cvm::log ("Using reference positions from configuration file to calculate the variable.\n");
if (ref_pos.size() != atoms.size()) {
cvm::fatal_error ("Error: the number of reference positions provided ("+
cvm::to_str (ref_pos.size())+
") does not match the number of atoms of group \"atoms\" ("+
cvm::to_str (atoms.size())+").\n");
}
}
{
std::string ref_pos_file;
if (get_keyval (conf, "refPositionsFile", ref_pos_file, std::string (""))) {
if (ref_pos.size()) {
cvm::fatal_error ("Error: cannot specify \"refPositionsFile\" and "
"\"refPositions\" at the same time.\n");
}
std::string ref_pos_col;
double ref_pos_col_value;
if (get_keyval (conf, "refPositionsCol", ref_pos_col, std::string (""))) {
// if provided, use PDB column to select coordinates
bool found = get_keyval (conf, "refPositionsColValue", ref_pos_col_value, 0.0);
if (found && !ref_pos_col_value)
cvm::fatal_error ("Error: refPositionsColValue, "
"if provided, must be non-zero.\n");
} else {
// if not, rely on existing atom indices for the group
atoms.create_sorted_ids();
}
ref_pos.resize (atoms.size());
cvm::load_coords (ref_pos_file.c_str(), ref_pos, atoms.sorted_ids,
ref_pos_col, ref_pos_col_value);
}
}
if (atoms.b_user_defined_fit) {
cvm::log ("WARNING: explicit fitting parameters were provided for atom group \"atoms\".");
} else {
// Default: fit everything
cvm::log ("Enabling \"centerReference\" and \"rotateReference\", to minimize RMSD before calculating it as a variable: "
"if this is not the desired behavior, disable them explicitly within the \"atoms\" block.\n");
atoms.b_center = true;
atoms.b_rotate = true;
// default case: reference positions for calculating the rmsd are also those used
// for fitting
atoms.ref_pos = ref_pos;
atoms.center_ref_pos();
// request the calculation of the derivatives of the rotation defined by the atom group
atoms.rot.request_group1_gradients (atoms.size());
// request derivatives of optimal rotation wrt reference coordinates for Jacobian:
// this is only required for ABF, but we do both groups here for better caching
atoms.rot.request_group2_gradients (atoms.size());
}
}
void colvar::rmsd::calc_value()
{
// rotational-translational fit is handled by the atom group
x.real_value = 0.0;
for (size_t ia = 0; ia < atoms.size(); ia++) {
x.real_value += (atoms[ia].pos - ref_pos[ia]).norm2();
}
x.real_value /= cvm::real (atoms.size()); // MSD
x.real_value = std::sqrt (x.real_value);
}
void colvar::rmsd::calc_gradients()
{
cvm::real const drmsddx2 = (x.real_value > 0.0) ?
0.5 / (x.real_value * cvm::real (atoms.size())) :
0.0;
for (size_t ia = 0; ia < atoms.size(); ia++) {
atoms[ia].grad = (drmsddx2 * 2.0 * (atoms[ia].pos - ref_pos[ia]));
}
if (b_debug_gradients) {
cvm::log ("Debugging gradients:\n");
debug_gradients (atoms);
}
}
void colvar::rmsd::apply_force (colvarvalue const &force)
{
if (!atoms.noforce)
atoms.apply_colvar_force (force.real_value);
}
void colvar::rmsd::calc_force_invgrads()
{
atoms.read_system_forces();
ft.real_value = 0.0;
// Note: gradient square norm is 1/N_atoms
for (size_t ia = 0; ia < atoms.size(); ia++) {
ft.real_value += atoms[ia].grad * atoms[ia].system_force;
}
ft.real_value *= atoms.size();
}
void colvar::rmsd::calc_Jacobian_derivative()
{
// divergence of the rotated coordinates (including only derivatives of the rotation matrix)
cvm::real divergence = 0.0;
if (atoms.b_rotate) {
// gradient of the rotation matrix
cvm::matrix2d <cvm::rvector, 3, 3> grad_rot_mat;
// gradients of products of 2 quaternion components
cvm::rvector g11, g22, g33, g01, g02, g03, g12, g13, g23;
for (size_t ia = 0; ia < atoms.size(); ia++) {
// Gradient of optimal quaternion wrt current Cartesian position
cvm::vector1d< cvm::rvector, 4 > &dq = atoms.rot.dQ0_1[ia];
g11 = 2.0 * (atoms.rot.q)[1]*dq[1];
g22 = 2.0 * (atoms.rot.q)[2]*dq[2];
g33 = 2.0 * (atoms.rot.q)[3]*dq[3];
g01 = (atoms.rot.q)[0]*dq[1] + (atoms.rot.q)[1]*dq[0];
g02 = (atoms.rot.q)[0]*dq[2] + (atoms.rot.q)[2]*dq[0];
g03 = (atoms.rot.q)[0]*dq[3] + (atoms.rot.q)[3]*dq[0];
g12 = (atoms.rot.q)[1]*dq[2] + (atoms.rot.q)[2]*dq[1];
g13 = (atoms.rot.q)[1]*dq[3] + (atoms.rot.q)[3]*dq[1];
g23 = (atoms.rot.q)[2]*dq[3] + (atoms.rot.q)[3]*dq[2];
// Gradient of the rotation matrix wrt current Cartesian position
grad_rot_mat[0][0] = -2.0 * (g22 + g33);
grad_rot_mat[1][0] = 2.0 * (g12 + g03);
grad_rot_mat[2][0] = 2.0 * (g13 - g02);
grad_rot_mat[0][1] = 2.0 * (g12 - g03);
grad_rot_mat[1][1] = -2.0 * (g11 + g33);
grad_rot_mat[2][1] = 2.0 * (g01 + g23);
grad_rot_mat[0][2] = 2.0 * (g02 + g13);
grad_rot_mat[1][2] = 2.0 * (g23 - g01);
grad_rot_mat[2][2] = -2.0 * (g11 + g22);
cvm::atom_pos &y = ref_pos[ia];
for (size_t alpha = 0; alpha < 3; alpha++) {
for (size_t beta = 0; beta < 3; beta++) {
divergence += grad_rot_mat[beta][alpha][alpha] * y[beta];
// Note: equation was derived for inverse rotation (see colvars paper)
// so here the matrix is transposed
// (eq would give divergence += grad_rot_mat[alpha][beta][alpha] * y[beta];)
}
}
}
}
jd.real_value = x.real_value > 0.0 ? (3.0 * atoms.size() - 4.0 - divergence) / x.real_value : 0.0;
}
colvar::eigenvector::eigenvector (std::string const &conf)
: cvc (conf)
{
b_inverse_gradients = true;
b_Jacobian_derivative = true;
function_type = "eigenvector";
x.type (colvarvalue::type_scalar);
parse_group (conf, "atoms", atoms);
atom_groups.push_back (&atoms);
{
bool const b_inline = get_keyval (conf, "refPositions", ref_pos, ref_pos);
if (b_inline) {
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)) {
if (b_inline)
cvm::fatal_error ("Error: refPositions and refPositionsFile cannot be specified at the same time.\n");
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);
}
}
// save for later the geometric center of the provided positions (may not be the origin)
cvm::rvector ref_pos_center (0.0, 0.0, 0.0);
for (size_t i = 0; i < atoms.size(); i++) {
ref_pos_center += ref_pos[i];
}
ref_pos_center *= 1.0 / atoms.size();
if (atoms.b_user_defined_fit) {
cvm::log ("WARNING: explicit fitting parameters were provided for atom group \"atoms\".\n");
} else {
// default: fit everything
cvm::log ("Enabling \"centerReference\" and \"rotateReference\", to minimize RMSD before calculating the vector projection: "
"if this is not the desired behavior, disable them explicitly within the \"atoms\" block.\n");
atoms.b_center = true;
atoms.b_rotate = true;
atoms.ref_pos = ref_pos;
atoms.center_ref_pos();
// request the calculation of the derivatives of the rotation defined by the atom group
atoms.rot.request_group1_gradients (atoms.size());
// request derivatives of optimal rotation wrt reference coordinates for Jacobian:
// this is only required for ABF, but we do both groups here for better caching
atoms.rot.request_group2_gradients (atoms.size());
}
{
bool const b_inline = get_keyval (conf, "vector", eigenvec, eigenvec);
// now load the eigenvector
if (b_inline) {
cvm::log ("Using vector components from input file.\n");
if (eigenvec.size() != atoms.size()) {
cvm::fatal_error ("Error: vector components do not "
"match the number of requested atoms.\n");
}
}
std::string file_name;
if (get_keyval (conf, "vectorFile", file_name)) {
if (b_inline)
cvm::fatal_error ("Error: vector and vectorFile cannot be specified at the same time.\n");
std::string file_col;
double file_col_value;
if (get_keyval (conf, "vectorCol", file_col, std::string (""))) {
// use PDB flags if column is provided
bool found = get_keyval (conf, "vectorColValue", file_col_value, 0.0);
if (found && !file_col_value)
cvm::fatal_error ("Error: vectorColValue, "
"if provided, must be non-zero.\n");
} else {
// if not, use atom indices
atoms.create_sorted_ids();
}
eigenvec.resize (atoms.size());
cvm::load_coords (file_name.c_str(), eigenvec, atoms.sorted_ids, file_col, file_col_value);
}
}
if (!ref_pos.size() || !eigenvec.size()) {
cvm::fatal_error ("Error: both reference coordinates"
"and eigenvector must be defined.\n");
}
cvm::rvector eig_center (0.0, 0.0, 0.0);
for (size_t i = 0; i < atoms.size(); i++) {
eig_center += eigenvec[i];
}
eig_center *= 1.0 / atoms.size();
cvm::log ("Geometric center of the provided vector: "+cvm::to_str (eig_center)+"\n");
bool b_difference_vector = false;
get_keyval (conf, "differenceVector", b_difference_vector, false);
if (b_difference_vector) {
if (atoms.b_center) {
// both sets should be centered on the origin for fitting
for (size_t i = 0; i < atoms.size(); i++) {
eigenvec[i] -= eig_center;
ref_pos[i] -= ref_pos_center;
}
}
if (atoms.b_rotate) {
atoms.rot.calc_optimal_rotation (eigenvec, ref_pos);
for (size_t i = 0; i < atoms.size(); i++) {
eigenvec[i] = atoms.rot.rotate (eigenvec[i]);
}
}
cvm::log ("\"differenceVector\" is on: subtracting the reference positions from the provided vector: v = v - x0.\n");
for (size_t i = 0; i < atoms.size(); i++) {
eigenvec[i] -= ref_pos[i];
}
if (atoms.b_center) {
// bring back the ref positions to where they were
for (size_t i = 0; i < atoms.size(); i++) {
ref_pos[i] += ref_pos_center;
}
}
} else {
cvm::log ("Centering the provided vector to zero.\n");
for (size_t i = 0; i < atoms.size(); i++) {
eigenvec[i] -= eig_center;
}
}
// cvm::log ("The first three components (v1x, v1y, v1z) of the resulting vector are: "+cvm::to_str (eigenvec[0])+".\n");
// for inverse gradients
eigenvec_invnorm2 = 0.0;
for (size_t i = 0; i < atoms.size(); i++) {
eigenvec_invnorm2 += eigenvec[i].norm2();
}
eigenvec_invnorm2 = 1.0 / eigenvec_invnorm2;
if (b_difference_vector) {
cvm::log ("\"differenceVector\" is on: normalizing the vector.\n");
for (size_t i = 0; i < atoms.size(); i++) {
eigenvec[i] *= eigenvec_invnorm2;
}
} else {
cvm::log ("The norm of the vector is |v| = "+cvm::to_str (eigenvec_invnorm2)+".\n");
}
}
void colvar::eigenvector::calc_value()
{
x.real_value = 0.0;
for (size_t i = 0; i < atoms.size(); i++) {
x.real_value += (atoms[i].pos - ref_pos[i]) * eigenvec[i];
}
}
void colvar::eigenvector::calc_gradients()
{
for (size_t ia = 0; ia < atoms.size(); ia++) {
atoms[ia].grad = eigenvec[ia];
}
if (b_debug_gradients) {
cvm::log ("Debugging gradients:\n");
debug_gradients (atoms);
}
}
void colvar::eigenvector::apply_force (colvarvalue const &force)
{
if (!atoms.noforce)
atoms.apply_colvar_force (force.real_value);
}
void colvar::eigenvector::calc_force_invgrads()
{
atoms.read_system_forces();
ft.real_value = 0.0;
for (size_t ia = 0; ia < atoms.size(); ia++) {
ft.real_value += eigenvec_invnorm2 * atoms[ia].grad *
atoms[ia].system_force;
}
}
void colvar::eigenvector::calc_Jacobian_derivative()
{
// gradient of the rotation matrix
cvm::matrix2d <cvm::rvector, 3, 3> grad_rot_mat;
cvm::quaternion &quat0 = atoms.rot.q;
// gradients of products of 2 quaternion components
cvm::rvector g11, g22, g33, g01, g02, g03, g12, g13, g23;
cvm::atom_pos x_relative;
cvm::real sum = 0.0;
for (size_t ia = 0; ia < atoms.size(); ia++) {
// Gradient of optimal quaternion wrt current Cartesian position
// trick: d(R^-1)/dx = d(R^t)/dx = (dR/dx)^t
// we can just transpose the derivatives of the direct matrix
cvm::vector1d< cvm::rvector, 4 > &dq_1 = atoms.rot.dQ0_1[ia];
g11 = 2.0 * quat0[1]*dq_1[1];
g22 = 2.0 * quat0[2]*dq_1[2];
g33 = 2.0 * quat0[3]*dq_1[3];
g01 = quat0[0]*dq_1[1] + quat0[1]*dq_1[0];
g02 = quat0[0]*dq_1[2] + quat0[2]*dq_1[0];
g03 = quat0[0]*dq_1[3] + quat0[3]*dq_1[0];
g12 = quat0[1]*dq_1[2] + quat0[2]*dq_1[1];
g13 = quat0[1]*dq_1[3] + quat0[3]*dq_1[1];
g23 = quat0[2]*dq_1[3] + quat0[3]*dq_1[2];
// Gradient of the inverse rotation matrix wrt current Cartesian position
// (transpose of the gradient of the direct rotation)
grad_rot_mat[0][0] = -2.0 * (g22 + g33);
grad_rot_mat[0][1] = 2.0 * (g12 + g03);
grad_rot_mat[0][2] = 2.0 * (g13 - g02);
grad_rot_mat[1][0] = 2.0 * (g12 - g03);
grad_rot_mat[1][1] = -2.0 * (g11 + g33);
grad_rot_mat[1][2] = 2.0 * (g01 + g23);
grad_rot_mat[2][0] = 2.0 * (g02 + g13);
grad_rot_mat[2][1] = 2.0 * (g23 - g01);
grad_rot_mat[2][2] = -2.0 * (g11 + g22);
for (size_t i = 0; i < 3; i++) {
for (size_t j = 0; j < 3; j++) {
sum += grad_rot_mat[i][j][i] * eigenvec[ia][j];
}
}
}
jd.real_value = sum * std::sqrt (eigenvec_invnorm2);
}
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