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lammps/lib/colvars/colvarcomp_coordnums.cpp
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colvarcomp_coordnums.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 "colvarparse.h"
#include "colvaratoms.h"
#include "colvarvalue.h"
#include "colvar.h"
#include "colvarcomp.h"
template<bool calculate_gradients>
cvm::real colvar::coordnum::switching_function(cvm::real const &r0,
int const &en,
int const &ed,
cvm::atom &A1,
cvm::atom &A2)
{
cvm::rvector const diff = cvm::position_distance(A1.pos, A2.pos);
cvm::real const l2 = diff.norm2()/(r0*r0);
// Assume en and ed are even integers, and avoid sqrt in the following
int const en2 = en/2;
int const ed2 = ed/2;
cvm::real const xn = std::pow(l2, en2);
cvm::real const xd = std::pow(l2, ed2);
cvm::real const func = (1.0-xn)/(1.0-xd);
if (calculate_gradients) {
cvm::real const dFdl2 = (1.0/(1.0-xd))*(en2*(xn/l2) - func*ed2*(xd/l2))*(-1.0);
cvm::rvector const dl2dx = (2.0/(r0*r0))*diff;
A1.grad += (-1.0)*dFdl2*dl2dx;
A2.grad += dFdl2*dl2dx;
}
return func;
}
template<bool calculate_gradients>
cvm::real colvar::coordnum::switching_function(cvm::rvector const &r0_vec,
int const &en,
int const &ed,
cvm::atom &A1,
cvm::atom &A2)
{
cvm::rvector const diff = cvm::position_distance(A1.pos, A2.pos);
cvm::rvector const scal_diff(diff.x/r0_vec.x, diff.y/r0_vec.y, diff.z/r0_vec.z);
cvm::real const l2 = scal_diff.norm2();
// Assume en and ed are even integers, and avoid sqrt in the following
int const en2 = en/2;
int const ed2 = ed/2;
cvm::real const xn = std::pow(l2, en2);
cvm::real const xd = std::pow(l2, ed2);
cvm::real const func = (1.0-xn)/(1.0-xd);
if (calculate_gradients) {
cvm::real const dFdl2 = (1.0/(1.0-xd))*(en2*(xn/l2) - func*ed2*(xd/l2))*(-1.0);
cvm::rvector const dl2dx((2.0/(r0_vec.x*r0_vec.x))*diff.x,
(2.0/(r0_vec.y*r0_vec.y))*diff.y,
(2.0/(r0_vec.z*r0_vec.z))*diff.z);
A1.grad += (-1.0)*dFdl2*dl2dx;
A2.grad += dFdl2*dl2dx;
}
return func;
}
colvar::coordnum::coordnum(std::string const &conf)
: cvc(conf), b_anisotropic(false), b_group2_center_only(false)
{
function_type = "coordnum";
x.type(colvarvalue::type_scalar);
group1 = parse_group(conf, "group1");
group2 = parse_group(conf, "group2");
if (group1->b_dummy) {
cvm::error("Error: only group2 is allowed to be a dummy atom\n");
return;
}
bool const b_isotropic = get_keyval(conf, "cutoff", r0,
cvm::real(4.0 * cvm::unit_angstrom()));
if (get_keyval(conf, "cutoff3", r0_vec, cvm::rvector(4.0 * cvm::unit_angstrom(),
4.0 * cvm::unit_angstrom(),
4.0 * cvm::unit_angstrom()))) {
if (b_isotropic) {
cvm::error("Error: cannot specify \"cutoff\" and \"cutoff3\" at the same time.\n",
INPUT_ERROR);
return;
}
b_anisotropic = true;
// remove meaningless negative signs
if (r0_vec.x < 0.0) r0_vec.x *= -1.0;
if (r0_vec.y < 0.0) r0_vec.y *= -1.0;
if (r0_vec.z < 0.0) r0_vec.z *= -1.0;
}
get_keyval(conf, "expNumer", en, int(6) );
get_keyval(conf, "expDenom", ed, int(12));
if ( (en%2) || (ed%2) ) {
cvm::error("Error: odd exponents provided, can only use even ones.\n", INPUT_ERROR);
}
if (!is_enabled(f_cvc_pbc_minimum_image)) {
cvm::log("Warning: only minimum-image distances are used by this variable.\n");
}
get_keyval(conf, "group2CenterOnly", b_group2_center_only, group2->b_dummy);
}
colvar::coordnum::coordnum()
: b_anisotropic(false), b_group2_center_only(false)
{
function_type = "coordnum";
x.type(colvarvalue::type_scalar);
}
void colvar::coordnum::calc_value()
{
x.real_value = 0.0;
if (b_group2_center_only) {
// create a fake atom to hold the group2 com coordinates
cvm::atom group2_com_atom;
group2_com_atom.pos = group2->center_of_mass();
if (b_anisotropic) {
for (cvm::atom_iter ai1 = group1->begin(); ai1 != group1->end(); ai1++)
x.real_value += switching_function<false>(r0_vec, en, ed, *ai1, group2_com_atom);
} else {
for (cvm::atom_iter ai1 = group1->begin(); ai1 != group1->end(); ai1++)
x.real_value += switching_function<false>(r0, en, ed, *ai1, group2_com_atom);
}
} else {
if (b_anisotropic) {
for (cvm::atom_iter ai1 = group1->begin(); ai1 != group1->end(); ai1++)
for (cvm::atom_iter ai2 = group2->begin(); ai2 != group2->end(); ai2++) {
x.real_value += switching_function<false>(r0_vec, en, ed, *ai1, *ai2);
}
} else {
for (cvm::atom_iter ai1 = group1->begin(); ai1 != group1->end(); ai1++)
for (cvm::atom_iter ai2 = group2->begin(); ai2 != group2->end(); ai2++) {
x.real_value += switching_function<false>(r0, en, ed, *ai1, *ai2);
}
}
}
}
void colvar::coordnum::calc_gradients()
{
if (b_group2_center_only) {
// create a fake atom to hold the group2 com coordinates
cvm::atom group2_com_atom;
group2_com_atom.pos = group2->center_of_mass();
if (b_anisotropic) {
for (cvm::atom_iter ai1 = group1->begin(); ai1 != group1->end(); ai1++)
switching_function<true>(r0_vec, en, ed, *ai1, group2_com_atom);
} else {
for (cvm::atom_iter ai1 = group1->begin(); ai1 != group1->end(); ai1++)
switching_function<true>(r0, en, ed, *ai1, group2_com_atom);
}
group2->set_weighted_gradient(group2_com_atom.grad);
} else {
if (b_anisotropic) {
for (cvm::atom_iter ai1 = group1->begin(); ai1 != group1->end(); ai1++)
for (cvm::atom_iter ai2 = group2->begin(); ai2 != group2->end(); ai2++) {
switching_function<true>(r0_vec, en, ed, *ai1, *ai2);
}
} else {
for (cvm::atom_iter ai1 = group1->begin(); ai1 != group1->end(); ai1++)
for (cvm::atom_iter ai2 = group2->begin(); ai2 != group2->end(); ai2++) {
switching_function<true>(r0, en, ed, *ai1, *ai2);
}
}
}
}
void colvar::coordnum::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);
}
simple_scalar_dist_functions(coordnum)
// h_bond member functions
colvar::h_bond::h_bond(std::string const &conf)
: cvc(conf)
{
if (cvm::debug())
cvm::log("Initializing h_bond object.\n");
function_type = "h_bond";
x.type(colvarvalue::type_scalar);
int a_num, d_num;
get_keyval(conf, "acceptor", a_num, -1);
get_keyval(conf, "donor", d_num, -1);
if ( (a_num == -1) || (d_num == -1) ) {
cvm::error("Error: either acceptor or donor undefined.\n");
return;
}
cvm::atom acceptor = cvm::atom(a_num);
cvm::atom donor = cvm::atom(d_num);
register_atom_group(new cvm::atom_group);
atom_groups[0]->add_atom(acceptor);
atom_groups[0]->add_atom(donor);
get_keyval(conf, "cutoff", r0, (3.3 * cvm::unit_angstrom()));
get_keyval(conf, "expNumer", en, 6);
get_keyval(conf, "expDenom", ed, 8);
if ( (en%2) || (ed%2) ) {
cvm::error("Error: odd exponents provided, can only use even ones.\n");
return;
}
if (cvm::debug())
cvm::log("Done initializing h_bond object.\n");
}
colvar::h_bond::h_bond(cvm::atom const &acceptor,
cvm::atom const &donor,
cvm::real r0_i, int en_i, int ed_i)
: r0(r0_i), en(en_i), ed(ed_i)
{
function_type = "h_bond";
x.type(colvarvalue::type_scalar);
register_atom_group(new cvm::atom_group);
atom_groups[0]->add_atom(acceptor);
atom_groups[0]->add_atom(donor);
}
colvar::h_bond::h_bond()
: cvc()
{
function_type = "h_bond";
x.type(colvarvalue::type_scalar);
}
colvar::h_bond::~h_bond()
{
delete atom_groups[0];
}
void colvar::h_bond::calc_value()
{
x.real_value = colvar::coordnum::switching_function<false>(r0, en, ed, (*atom_groups[0])[0], (*atom_groups[0])[1]);
}
void colvar::h_bond::calc_gradients()
{
colvar::coordnum::switching_function<true>(r0, en, ed, (*atom_groups[0])[0], (*atom_groups[0])[1]);
}
void colvar::h_bond::apply_force(colvarvalue const &force)
{
(atom_groups[0])->apply_colvar_force(force);
}
simple_scalar_dist_functions(h_bond)
colvar::selfcoordnum::selfcoordnum(std::string const &conf)
: cvc(conf)
{
function_type = "selfcoordnum";
x.type(colvarvalue::type_scalar);
group1 = parse_group(conf, "group1");
get_keyval(conf, "cutoff", r0, cvm::real(4.0 * cvm::unit_angstrom()));
get_keyval(conf, "expNumer", en, int(6) );
get_keyval(conf, "expDenom", ed, int(12));
if ( (en%2) || (ed%2) ) {
cvm::error("Error: odd exponents provided, can only use even ones.\n");
return;
}
if (!is_enabled(f_cvc_pbc_minimum_image)) {
cvm::log("Warning: only minimum-image distances are used by this variable.\n");
}
}
colvar::selfcoordnum::selfcoordnum()
{
function_type = "selfcoordnum";
x.type(colvarvalue::type_scalar);
}
void colvar::selfcoordnum::calc_value()
{
x.real_value = 0.0;
for (size_t i = 0; i < group1->size() - 1; i++) {
for (size_t j = i + 1; j < group1->size(); j++) {
x.real_value += colvar::coordnum::switching_function<false>(r0, en, ed, (*group1)[i], (*group1)[j]);
}
}
}
void colvar::selfcoordnum::calc_gradients()
{
for (size_t i = 0; i < group1->size() - 1; i++) {
for (size_t j = i + 1; j < group1->size(); j++) {
colvar::coordnum::switching_function<true>(r0, en, ed, (*group1)[i], (*group1)[j]);
}
}
}
void colvar::selfcoordnum::apply_force(colvarvalue const &force)
{
if (!group1->noforce) {
group1->apply_colvar_force(force.real_value);
}
}
simple_scalar_dist_functions(selfcoordnum)
// groupcoordnum member functions
colvar::groupcoordnum::groupcoordnum(std::string const &conf)
: distance(conf), b_anisotropic(false)
{
function_type = "groupcoordnum";
x.type(colvarvalue::type_scalar);
// group1 and group2 are already initialized by distance()
if (group1->b_dummy || group2->b_dummy) {
cvm::error("Error: neither group can be a dummy atom\n");
return;
}
bool const b_scale = get_keyval(conf, "cutoff", r0,
cvm::real(4.0 * cvm::unit_angstrom()));
if (get_keyval(conf, "cutoff3", r0_vec,
cvm::rvector(4.0, 4.0, 4.0), parse_silent)) {
if (b_scale) {
cvm::error("Error: cannot specify \"scale\" and "
"\"scale3\" at the same time.\n");
return;
}
b_anisotropic = true;
// remove meaningless negative signs
if (r0_vec.x < 0.0) r0_vec.x *= -1.0;
if (r0_vec.y < 0.0) r0_vec.y *= -1.0;
if (r0_vec.z < 0.0) r0_vec.z *= -1.0;
}
get_keyval(conf, "expNumer", en, int(6) );
get_keyval(conf, "expDenom", ed, int(12));
if ( (en%2) || (ed%2) ) {
cvm::error("Error: odd exponents provided, can only use even ones.\n");
return;
}
if (!is_enabled(f_cvc_pbc_minimum_image)) {
cvm::log("Warning: only minimum-image distances are used by this variable.\n");
}
}
colvar::groupcoordnum::groupcoordnum()
: b_anisotropic(false)
{
function_type = "groupcoordnum";
x.type(colvarvalue::type_scalar);
}
template<bool calculate_gradients>
cvm::real colvar::groupcoordnum::switching_function(cvm::real const &r0,
int const &en,
int const &ed,
cvm::atom &A1,
cvm::atom &A2)
{
cvm::rvector const diff = cvm::position_distance(A1.pos, A2.pos);
cvm::real const l2 = diff.norm2()/(r0*r0);
// Assume en and ed are even integers, and avoid sqrt in the following
int const en2 = en/2;
int const ed2 = ed/2;
cvm::real const xn = std::pow(l2, en2);
cvm::real const xd = std::pow(l2, ed2);
cvm::real const func = (1.0-xn)/(1.0-xd);
if (calculate_gradients) {
cvm::real const dFdl2 = (1.0/(1.0-xd))*(en2*(xn/l2) - func*ed2*(xd/l2))*(-1.0);
cvm::rvector const dl2dx = (2.0/(r0*r0))*diff;
A1.grad += (-1.0)*dFdl2*dl2dx;
A2.grad += dFdl2*dl2dx;
}
return func;
}
#if 0 // AMG: I don't think there's any reason to support anisotropic,
// and I don't have those flags below in calc_value, but
// if I need them, I'll also need to uncomment this method
template<bool calculate_gradients>
cvm::real colvar::groupcoordnum::switching_function(cvm::rvector const &r0_vec,
int const &en,
int const &ed,
cvm::atom &A1,
cvm::atom &A2)
{
cvm::rvector const diff = cvm::position_distance(A1.pos, A2.pos);
cvm::rvector const scal_diff(diff.x/r0_vec.x, diff.y/r0_vec.y, diff.z/r0_vec.z);
cvm::real const l2 = scal_diff.norm2();
// Assume en and ed are even integers, and avoid sqrt in the following
int const en2 = en/2;
int const ed2 = ed/2;
cvm::real const xn = std::pow(l2, en2);
cvm::real const xd = std::pow(l2, ed2);
cvm::real const func = (1.0-xn)/(1.0-xd);
if (calculate_gradients) {
cvm::real const dFdl2 = (1.0/(1.0-xd))*(en2*(xn/l2) - func*ed2*(xd/l2))*(-1.0);
cvm::rvector const dl2dx((2.0/(r0_vec.x*r0_vec.x))*diff.x,
(2.0/(r0_vec.y*r0_vec.y))*diff.y,
(2.0/(r0_vec.z*r0_vec.z))*diff.z);
A1.grad += (-1.0)*dFdl2*dl2dx;
A2.grad += dFdl2*dl2dx;
}
return func;
}
#endif
void colvar::groupcoordnum::calc_value()
{
// create fake atoms to hold the com coordinates
cvm::atom group1_com_atom;
cvm::atom group2_com_atom;
group1_com_atom.pos = group1->center_of_mass();
group2_com_atom.pos = group2->center_of_mass();
x.real_value = coordnum::switching_function<false>(r0, en, ed,
group1_com_atom, group2_com_atom);
}
void colvar::groupcoordnum::calc_gradients()
{
cvm::atom group1_com_atom;
cvm::atom group2_com_atom;
group1_com_atom.pos = group1->center_of_mass();
group2_com_atom.pos = group2->center_of_mass();
coordnum::switching_function<true>(r0, en, ed, group1_com_atom, group2_com_atom);
group1->set_weighted_gradient(group1_com_atom.grad);
group2->set_weighted_gradient(group2_com_atom.grad);
}
void colvar::groupcoordnum::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);
}
simple_scalar_dist_functions(groupcoordnum)
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