forked from lijiext/lammps
652 lines
19 KiB
C++
652 lines
19 KiB
C++
// -*- 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 "colvarmodule.h"
|
|
#include "colvarparse.h"
|
|
#include "colvaratoms.h"
|
|
#include "colvarvalue.h"
|
|
#include "colvar.h"
|
|
#include "colvarcomp.h"
|
|
|
|
|
|
|
|
template<int flags>
|
|
cvm::real colvar::coordnum::switching_function(cvm::real const &r0,
|
|
cvm::rvector const &r0_vec,
|
|
int en,
|
|
int ed,
|
|
cvm::atom &A1,
|
|
cvm::atom &A2,
|
|
bool **pairlist_elem,
|
|
cvm::real pairlist_tol)
|
|
{
|
|
if ((flags & ef_use_pairlist) && !(flags & ef_rebuild_pairlist)) {
|
|
bool const within = **pairlist_elem;
|
|
(*pairlist_elem)++;
|
|
if (!within) {
|
|
return 0.0;
|
|
}
|
|
}
|
|
|
|
cvm::rvector const r0sq_vec(r0_vec.x*r0_vec.x,
|
|
r0_vec.y*r0_vec.y,
|
|
r0_vec.z*r0_vec.z);
|
|
|
|
cvm::rvector const diff = cvm::position_distance(A1.pos, A2.pos);
|
|
|
|
cvm::rvector const scal_diff(diff.x/((flags & ef_anisotropic) ?
|
|
r0_vec.x : r0),
|
|
diff.y/((flags & ef_anisotropic) ?
|
|
r0_vec.y : r0),
|
|
diff.z/((flags & ef_anisotropic) ?
|
|
r0_vec.z : r0));
|
|
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 = cvm::integer_power(l2, en2);
|
|
cvm::real const xd = cvm::integer_power(l2, ed2);
|
|
//The subtraction and division stretches the function back to the range of [0,1] from [pairlist_tol,1]
|
|
cvm::real const func = (((1.0-xn)/(1.0-xd)) - pairlist_tol) / (1.0-pairlist_tol);
|
|
|
|
if (flags & ef_rebuild_pairlist) {
|
|
//Particles just outside of the cutoff also are considered if they come near.
|
|
**pairlist_elem = (func > (-pairlist_tol * 0.5)) ? true : false;
|
|
(*pairlist_elem)++;
|
|
}
|
|
//If the value is too small, we need to exclude it, rather than let it contribute to the sum or the gradients.
|
|
if (func < 0)
|
|
return 0;
|
|
|
|
if (flags & ef_gradients) {
|
|
//This is the old, completely correct expression for dFdl2:
|
|
//cvm::real const dFdl2 = (1.0/(1.0-xd))*(en2*(xn/l2) -
|
|
// func*ed2*(xd/l2))*(-1.0);
|
|
//This can become:
|
|
//cvm::real const dFdl2 = (1.0/(1.0-xd))*(en2*(xn/l2)*(1.0-xn)/(1.0-xn) -
|
|
// func*ed2*(xd/l2))*(-1.0);
|
|
//Recognizing that func = (1.0-xn)/(1.0-xd), we can group together the "func" and get a version of dFdl2 that is 0
|
|
//when func=0, which lets us skip this gradient calculation when func=0.
|
|
cvm::real const dFdl2 = func * ((ed2*xd/((1.0-xd)*l2)) - (en2*xn/((1.0-xn)*l2)));
|
|
cvm::rvector const dl2dx((2.0/((flags & ef_anisotropic) ? r0sq_vec.x :
|
|
r0*r0)) * diff.x,
|
|
(2.0/((flags & ef_anisotropic) ? r0sq_vec.y :
|
|
r0*r0)) * diff.y,
|
|
(2.0/((flags & ef_anisotropic) ? r0sq_vec.z :
|
|
r0*r0)) * 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), pairlist(NULL)
|
|
|
|
{
|
|
function_type = "coordnum";
|
|
x.type(colvarvalue::type_scalar);
|
|
|
|
colvarproxy *proxy = cvm::main()->proxy;
|
|
|
|
group1 = parse_group(conf, "group1");
|
|
group2 = parse_group(conf, "group2");
|
|
|
|
if (group1 == NULL || group2 == NULL) {
|
|
cvm::error("Error: failed to initialize atom groups.\n",
|
|
INPUT_ERROR);
|
|
return;
|
|
}
|
|
|
|
if (int atom_number = cvm::atom_group::overlap(*group1, *group2)) {
|
|
cvm::error("Error: group1 and group2 share a common atom (number: " +
|
|
cvm::to_str(atom_number) + ")\n", INPUT_ERROR);
|
|
return;
|
|
}
|
|
|
|
if (group1->b_dummy) {
|
|
cvm::error("Error: only group2 is allowed to be a dummy atom\n",
|
|
INPUT_ERROR);
|
|
return;
|
|
}
|
|
|
|
bool const b_isotropic = get_keyval(conf, "cutoff", r0,
|
|
cvm::real(4.0 * proxy->angstrom_value));
|
|
|
|
if (get_keyval(conf, "cutoff3", r0_vec,
|
|
cvm::rvector(4.0 * proxy->angstrom_value,
|
|
4.0 * proxy->angstrom_value,
|
|
4.0 * proxy->angstrom_value))) {
|
|
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, 6);
|
|
get_keyval(conf, "expDenom", ed, 12);
|
|
|
|
if ( (en%2) || (ed%2) ) {
|
|
cvm::error("Error: odd exponent(s) provided, can only use even ones.\n",
|
|
INPUT_ERROR);
|
|
}
|
|
|
|
if ( (en <= 0) || (ed <= 0) ) {
|
|
cvm::error("Error: negative exponent(s) provided.\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);
|
|
|
|
get_keyval(conf, "tolerance", tolerance, 0.0);
|
|
if (tolerance > 0) {
|
|
get_keyval(conf, "pairListFrequency", pairlist_freq, 100);
|
|
if ( ! (pairlist_freq > 0) ) {
|
|
cvm::error("Error: non-positive pairlistfrequency provided.\n",
|
|
INPUT_ERROR);
|
|
return; // and do not allocate the pairlists below
|
|
}
|
|
if (b_group2_center_only) {
|
|
pairlist = new bool[group1->size()];
|
|
}
|
|
else {
|
|
pairlist = new bool[group1->size() * group2->size()];
|
|
}
|
|
}
|
|
|
|
init_scalar_boundaries(0.0, b_group2_center_only ? group1->size() :
|
|
group1->size() * group2->size());
|
|
}
|
|
|
|
|
|
colvar::coordnum::~coordnum()
|
|
{
|
|
if (pairlist != NULL) {
|
|
delete [] pairlist;
|
|
}
|
|
}
|
|
|
|
|
|
template<int flags> void colvar::coordnum::main_loop(bool **pairlist_elem)
|
|
{
|
|
if (b_group2_center_only) {
|
|
cvm::atom group2_com_atom;
|
|
group2_com_atom.pos = group2->center_of_mass();
|
|
for (cvm::atom_iter ai1 = group1->begin(); ai1 != group1->end(); ai1++) {
|
|
x.real_value += switching_function<flags>(r0, r0_vec, en, ed,
|
|
*ai1, group2_com_atom,
|
|
pairlist_elem,
|
|
tolerance);
|
|
}
|
|
if (b_group2_center_only) {
|
|
group2->set_weighted_gradient(group2_com_atom.grad);
|
|
}
|
|
} 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<flags>(r0, r0_vec, en, ed,
|
|
*ai1, *ai2,
|
|
pairlist_elem,
|
|
tolerance);
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
|
|
template<int compute_flags> int colvar::coordnum::compute_coordnum()
|
|
{
|
|
bool const use_pairlist = (pairlist != NULL);
|
|
bool const rebuild_pairlist = (pairlist != NULL) &&
|
|
(cvm::step_relative() % pairlist_freq == 0);
|
|
|
|
bool *pairlist_elem = use_pairlist ? pairlist : NULL;
|
|
|
|
if (b_anisotropic) {
|
|
|
|
if (use_pairlist) {
|
|
if (rebuild_pairlist) {
|
|
int const flags = compute_flags | ef_anisotropic | ef_use_pairlist |
|
|
ef_rebuild_pairlist;
|
|
main_loop<flags>(&pairlist_elem);
|
|
} else {
|
|
int const flags = compute_flags | ef_anisotropic | ef_use_pairlist;
|
|
main_loop<flags>(&pairlist_elem);
|
|
}
|
|
|
|
} else {
|
|
|
|
int const flags = compute_flags | ef_anisotropic;
|
|
main_loop<flags>(NULL);
|
|
}
|
|
|
|
} else {
|
|
|
|
if (use_pairlist) {
|
|
|
|
if (rebuild_pairlist) {
|
|
int const flags = compute_flags | ef_use_pairlist | ef_rebuild_pairlist;
|
|
main_loop<flags>(&pairlist_elem);
|
|
} else {
|
|
int const flags = compute_flags | ef_use_pairlist;
|
|
main_loop<flags>(&pairlist_elem);
|
|
}
|
|
|
|
} else {
|
|
|
|
int const flags = compute_flags;
|
|
main_loop<flags>(NULL);
|
|
}
|
|
}
|
|
|
|
return COLVARS_OK;
|
|
}
|
|
|
|
|
|
void colvar::coordnum::calc_value()
|
|
{
|
|
x.real_value = 0.0;
|
|
if (is_enabled(f_cvc_gradient)) {
|
|
compute_coordnum<ef_gradients>();
|
|
} else {
|
|
compute_coordnum<ef_null>();
|
|
}
|
|
}
|
|
|
|
|
|
void colvar::coordnum::calc_gradients()
|
|
{
|
|
// Gradients are computed by calc_value() if f_cvc_gradients is enabled
|
|
}
|
|
|
|
|
|
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);
|
|
init_scalar_boundaries(0.0, 1.0);
|
|
|
|
colvarproxy *proxy = cvm::main()->proxy;
|
|
|
|
int a_num = -1, d_num = -1;
|
|
get_keyval(conf, "acceptor", a_num, a_num);
|
|
get_keyval(conf, "donor", d_num, a_num);
|
|
|
|
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 * proxy->angstrom_value));
|
|
get_keyval(conf, "expNumer", en, 6);
|
|
get_keyval(conf, "expDenom", ed, 8);
|
|
|
|
if ( (en%2) || (ed%2) ) {
|
|
cvm::error("Error: odd exponent(s) provided, can only use even ones.\n",
|
|
INPUT_ERROR);
|
|
}
|
|
|
|
if ( (en <= 0) || (ed <= 0) ) {
|
|
cvm::error("Error: negative exponent(s) provided.\n",
|
|
INPUT_ERROR);
|
|
}
|
|
|
|
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);
|
|
init_scalar_boundaries(0.0, 1.0);
|
|
|
|
register_atom_group(new cvm::atom_group);
|
|
atom_groups[0]->add_atom(acceptor);
|
|
atom_groups[0]->add_atom(donor);
|
|
}
|
|
|
|
|
|
void colvar::h_bond::calc_value()
|
|
{
|
|
int const flags = coordnum::ef_null;
|
|
cvm::rvector const r0_vec(0.0); // TODO enable the flag?
|
|
x.real_value =
|
|
coordnum::switching_function<flags>(r0, r0_vec, en, ed,
|
|
(*atom_groups[0])[0],
|
|
(*atom_groups[0])[1],
|
|
NULL, 0.0);
|
|
}
|
|
|
|
|
|
void colvar::h_bond::calc_gradients()
|
|
{
|
|
int const flags = coordnum::ef_gradients;
|
|
cvm::rvector const r0_vec(0.0); // TODO enable the flag?
|
|
coordnum::switching_function<flags>(r0, r0_vec, en, ed,
|
|
(*atom_groups[0])[0],
|
|
(*atom_groups[0])[1],
|
|
NULL, 0.0);
|
|
}
|
|
|
|
|
|
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), pairlist(NULL)
|
|
{
|
|
function_type = "selfcoordnum";
|
|
x.type(colvarvalue::type_scalar);
|
|
|
|
colvarproxy *proxy = cvm::main()->proxy;
|
|
|
|
group1 = parse_group(conf, "group1");
|
|
|
|
get_keyval(conf, "cutoff", r0, cvm::real(4.0 * proxy->angstrom_value));
|
|
get_keyval(conf, "expNumer", en, 6);
|
|
get_keyval(conf, "expDenom", ed, 12);
|
|
|
|
|
|
if ( (en%2) || (ed%2) ) {
|
|
cvm::error("Error: odd exponent(s) provided, can only use even ones.\n",
|
|
INPUT_ERROR);
|
|
}
|
|
|
|
if ( (en <= 0) || (ed <= 0) ) {
|
|
cvm::error("Error: negative exponent(s) provided.\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, "tolerance", tolerance, 0.0);
|
|
if (tolerance > 0) {
|
|
get_keyval(conf, "pairListFrequency", pairlist_freq, 100);
|
|
if ( ! (pairlist_freq > 0) ) {
|
|
cvm::error("Error: non-positive pairlistfrequency provided.\n",
|
|
INPUT_ERROR);
|
|
return;
|
|
}
|
|
pairlist = new bool[(group1->size()-1) * (group1->size()-1)];
|
|
}
|
|
|
|
init_scalar_boundaries(0.0, (group1->size()-1) * (group1->size()-1));
|
|
}
|
|
|
|
|
|
colvar::selfcoordnum::~selfcoordnum()
|
|
{
|
|
if (pairlist != NULL) {
|
|
delete [] pairlist;
|
|
}
|
|
}
|
|
|
|
|
|
template<int compute_flags> int colvar::selfcoordnum::compute_selfcoordnum()
|
|
{
|
|
cvm::rvector const r0_vec(0.0); // TODO enable the flag?
|
|
|
|
bool const use_pairlist = (pairlist != NULL);
|
|
bool const rebuild_pairlist = (pairlist != NULL) &&
|
|
(cvm::step_relative() % pairlist_freq == 0);
|
|
|
|
bool *pairlist_elem = use_pairlist ? pairlist : NULL;
|
|
size_t i = 0, j = 0;
|
|
size_t const n = group1->size();
|
|
|
|
// Always isotropic (TODO: enable the ellipsoid?)
|
|
|
|
if (use_pairlist) {
|
|
|
|
if (rebuild_pairlist) {
|
|
int const flags = compute_flags | coordnum::ef_use_pairlist |
|
|
coordnum::ef_rebuild_pairlist;
|
|
for (i = 0; i < n - 1; i++) {
|
|
for (j = i + 1; j < n; j++) {
|
|
x.real_value +=
|
|
coordnum::switching_function<flags>(r0, r0_vec, en, ed,
|
|
(*group1)[i],
|
|
(*group1)[j],
|
|
&pairlist_elem,
|
|
tolerance);
|
|
}
|
|
}
|
|
} else {
|
|
int const flags = compute_flags | coordnum::ef_use_pairlist;
|
|
for (i = 0; i < n - 1; i++) {
|
|
for (j = i + 1; j < n; j++) {
|
|
x.real_value +=
|
|
coordnum::switching_function<flags>(r0, r0_vec, en, ed,
|
|
(*group1)[i],
|
|
(*group1)[j],
|
|
&pairlist_elem,
|
|
tolerance);
|
|
}
|
|
}
|
|
}
|
|
|
|
} else { // if (use_pairlist) {
|
|
|
|
int const flags = compute_flags | coordnum::ef_null;
|
|
for (i = 0; i < n - 1; i++) {
|
|
for (j = i + 1; j < n; j++) {
|
|
x.real_value +=
|
|
coordnum::switching_function<flags>(r0, r0_vec, en, ed,
|
|
(*group1)[i],
|
|
(*group1)[j],
|
|
&pairlist_elem,
|
|
tolerance);
|
|
}
|
|
}
|
|
}
|
|
|
|
return COLVARS_OK;
|
|
}
|
|
|
|
|
|
void colvar::selfcoordnum::calc_value()
|
|
{
|
|
x.real_value = 0.0;
|
|
if (is_enabled(f_cvc_gradient)) {
|
|
compute_selfcoordnum<coordnum::ef_gradients>();
|
|
} else {
|
|
compute_selfcoordnum<coordnum::ef_null>();
|
|
}
|
|
}
|
|
|
|
|
|
void colvar::selfcoordnum::calc_gradients()
|
|
{
|
|
// Gradients are computed by calc_value() if f_cvc_gradients is enabled
|
|
}
|
|
|
|
|
|
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);
|
|
init_scalar_boundaries(0.0, 1.0);
|
|
|
|
colvarproxy *proxy = cvm::main()->proxy;
|
|
|
|
// 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 * proxy->angstrom_value));
|
|
|
|
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, 6);
|
|
get_keyval(conf, "expDenom", ed, 12);
|
|
|
|
if ( (en%2) || (ed%2) ) {
|
|
cvm::error("Error: odd exponent(s) provided, can only use even ones.\n",
|
|
INPUT_ERROR);
|
|
}
|
|
|
|
if ( (en <= 0) || (ed <= 0) ) {
|
|
cvm::error("Error: negative exponent(s) provided.\n",
|
|
INPUT_ERROR);
|
|
}
|
|
|
|
if (!is_enabled(f_cvc_pbc_minimum_image)) {
|
|
cvm::log("Warning: only minimum-image distances are used by this variable.\n");
|
|
}
|
|
|
|
}
|
|
|
|
|
|
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();
|
|
if (b_anisotropic) {
|
|
int const flags = coordnum::ef_anisotropic;
|
|
x.real_value = coordnum::switching_function<flags>(r0, r0_vec, en, ed,
|
|
group1_com_atom,
|
|
group2_com_atom,
|
|
NULL, 0.0);
|
|
} else {
|
|
int const flags = coordnum::ef_null;
|
|
x.real_value = coordnum::switching_function<flags>(r0, r0_vec, en, ed,
|
|
group1_com_atom,
|
|
group2_com_atom,
|
|
NULL, 0.0);
|
|
}
|
|
}
|
|
|
|
|
|
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();
|
|
|
|
if (b_anisotropic) {
|
|
int const flags = coordnum::ef_gradients | coordnum::ef_anisotropic;
|
|
coordnum::switching_function<flags>(r0, r0_vec, en, ed,
|
|
group1_com_atom,
|
|
group2_com_atom,
|
|
NULL, 0.0);
|
|
} else {
|
|
int const flags = coordnum::ef_gradients;
|
|
coordnum::switching_function<flags>(r0, r0_vec, en, ed,
|
|
group1_com_atom,
|
|
group2_com_atom,
|
|
NULL, 0.0);
|
|
}
|
|
|
|
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)
|