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lammps/lib/colvars/colvaratoms.cpp
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colvaratoms.cpp
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/// -*- c++ -*-
#include "colvarmodule.h"
#include "colvarparse.h"
#include "colvaratoms.h"
// member functions of the "atom" class depend tightly on the MD interface, and are
// thus defined in colvarproxy_xxx.cpp
// in this file only atom_group functions are defined
// Note: "conf" is the configuration of the cvc who is using this atom group;
// "key" is the name of the atom group (e.g. "atoms", "group1", "group2", ...)
cvm::atom_group::atom_group(std::string const &conf,
char const *key)
: b_center(false), b_rotate(false), b_user_defined_fit(false),
b_fit_gradients(false),
ref_pos_group(NULL),
noforce(false)
{
cvm::log("Defining atom group \""+
std::string(key)+"\".\n");
// real work is done by parse
parse(conf, key);
}
cvm::atom_group::atom_group(std::vector<cvm::atom> const &atoms)
: b_dummy(false), b_center(false), b_rotate(false),
b_fit_gradients(false), ref_pos_group(NULL),
noforce(false)
{
this->reserve(atoms.size());
for (size_t i = 0; i < atoms.size(); i++) {
this->push_back(atoms[i]);
}
total_mass = 0.0;
for (cvm::atom_iter ai = this->begin();
ai != this->end(); ai++) {
total_mass += ai->mass;
}
}
cvm::atom_group::atom_group()
: b_dummy(false), b_center(false), b_rotate(false),
b_user_defined_fit(false), b_fit_gradients(false),
ref_pos_group(NULL), noforce(false)
{
total_mass = 0.0;
}
cvm::atom_group::~atom_group()
{
if (ref_pos_group) {
delete ref_pos_group;
ref_pos_group = NULL;
}
}
void cvm::atom_group::add_atom(cvm::atom const &a)
{
if (b_dummy) {
cvm::error("Error: cannot add atoms to a dummy group.\n", INPUT_ERROR);
} else {
this->push_back(a);
total_mass += a.mass;
}
}
void cvm::atom_group::reset_mass(std::string &name, int i, int j)
{
total_mass = 0.0;
for (cvm::atom_iter ai = this->begin();
ai != this->end(); ai++) {
total_mass += ai->mass;
}
cvm::log("Re-initialized atom group "+name+":"+cvm::to_str(i)+"/"+
cvm::to_str(j)+". "+ cvm::to_str(this->size())+
" atoms: total mass = "+cvm::to_str(this->total_mass)+".\n");
}
int cvm::atom_group::parse(std::string const &conf,
char const *key)
{
std::string group_conf;
// save_delimiters is set to false for this call, because "conf" is
// not the config string of this group, but of its parent object
// (which has already taken care of the delimiters)
save_delimiters = false;
key_lookup(conf, key, group_conf, dummy_pos);
// restoring the normal value, because we do want keywords checked
// inside "group_conf"
save_delimiters = true;
if (group_conf.size() == 0) {
cvm::error("Error: atom group \""+std::string(key)+
"\" is set, but has no definition.\n",
INPUT_ERROR);
return COLVARS_ERROR;
}
cvm::increase_depth();
cvm::log("Initializing atom group \""+std::string(key)+"\".\n");
// whether or not to include messages in the log
// colvarparse::Parse_Mode mode = parse_silent;
// {
// bool b_verbose;
// get_keyval (group_conf, "verboseOutput", b_verbose, false, parse_silent);
// if (b_verbose) mode = parse_normal;
// }
colvarparse::Parse_Mode mode = parse_normal;
{
// std::vector<int> atom_indexes;
std::string numbers_conf = "";
size_t pos = 0;
std::vector<int> atom_indexes;
while (key_lookup(group_conf, "atomNumbers", numbers_conf, pos)) {
if (numbers_conf.size()) {
std::istringstream is(numbers_conf);
int ia;
while (is >> ia) {
atom_indexes.push_back(ia);
}
}
if (atom_indexes.size()) {
this->reserve(this->size()+atom_indexes.size());
for (size_t i = 0; i < atom_indexes.size(); i++) {
this->push_back(cvm::atom(atom_indexes[i]));
}
if (cvm::get_error()) return COLVARS_ERROR;
} else {
cvm::error("Error: no numbers provided for \""
"atomNumbers\".\n", INPUT_ERROR);
return COLVARS_ERROR;
}
atom_indexes.clear();
}
std::string index_group_name;
if (get_keyval(group_conf, "indexGroup", index_group_name)) {
// use an index group from the index file read globally
std::list<std::string>::iterator names_i = cvm::index_group_names.begin();
std::list<std::vector<int> >::iterator index_groups_i = cvm::index_groups.begin();
for ( ; names_i != cvm::index_group_names.end() ; ++names_i, ++index_groups_i) {
if (*names_i == index_group_name)
break;
}
if (names_i == cvm::index_group_names.end()) {
cvm::error("Error: could not find index group "+
index_group_name+" among those provided by the index file.\n",
INPUT_ERROR);
return COLVARS_ERROR;
}
this->reserve(index_groups_i->size());
for (size_t i = 0; i < index_groups_i->size(); i++) {
this->push_back(cvm::atom((*index_groups_i)[i]));
}
if (cvm::get_error()) return COLVARS_ERROR;
}
}
{
std::string range_conf = "";
size_t pos = 0;
while (key_lookup(group_conf, "atomNumbersRange",
range_conf, pos)) {
if (range_conf.size()) {
std::istringstream is(range_conf);
int initial, final;
char dash;
if ( (is >> initial) && (initial > 0) &&
(is >> dash) && (dash == '-') &&
(is >> final) && (final > 0) ) {
for (int anum = initial; anum <= final; anum++) {
this->push_back(cvm::atom(anum));
}
if (cvm::get_error()) return COLVARS_ERROR;
range_conf = "";
continue;
}
}
cvm::error("Error: no valid definition for \"atomNumbersRange\", \""+
range_conf+"\".\n", INPUT_ERROR);
}
}
std::vector<std::string> psf_segids;
get_keyval(group_conf, "psfSegID", psf_segids, std::vector<std::string> (), mode);
for (std::vector<std::string>::iterator psii = psf_segids.begin();
psii < psf_segids.end(); ++psii) {
if ( (psii->size() == 0) || (psii->size() > 4) ) {
cvm::error("Error: invalid segmend identifier provided, \""+
(*psii)+"\".\n", INPUT_ERROR);
}
}
{
std::string range_conf = "";
size_t pos = 0;
size_t range_count = 0;
std::vector<std::string>::iterator psii = psf_segids.begin();
while (key_lookup(group_conf, "atomNameResidueRange",
range_conf, pos)) {
range_count++;
if (range_count > psf_segids.size()) {
cvm::error("Error: more instances of \"atomNameResidueRange\" than "
"values of \"psfSegID\".\n", INPUT_ERROR);
}
std::string const &psf_segid = psf_segids.size() ? *psii : std::string("");
if (range_conf.size()) {
std::istringstream is(range_conf);
std::string atom_name;
int initial, final;
char dash;
if ( (is >> atom_name) && (atom_name.size()) &&
(is >> initial) && (initial > 0) &&
(is >> dash) && (dash == '-') &&
(is >> final) && (final > 0) ) {
for (int resid = initial; resid <= final; resid++) {
this->push_back(cvm::atom(resid, atom_name, psf_segid));
}
if (cvm::get_error()) return COLVARS_ERROR;
range_conf = "";
} else {
cvm::error("Error: cannot parse definition for \""
"atomNameResidueRange\", \""+
range_conf+"\".\n");
}
} else {
cvm::error("Error: atomNameResidueRange with empty definition.\n");
}
if (psf_segid.size())
++psii;
}
}
{
// read the atoms from a file
std::string atoms_file_name;
if (get_keyval(group_conf, "atomsFile", atoms_file_name, std::string(""), mode)) {
std::string atoms_col;
if (!get_keyval(group_conf, "atomsCol", atoms_col, std::string(""), mode)) {
cvm::error("Error: parameter atomsCol is required if atomsFile is set.\n",
INPUT_ERROR);
}
double atoms_col_value;
bool const atoms_col_value_defined = get_keyval(group_conf, "atomsColValue", atoms_col_value, 0.0, mode);
if (atoms_col_value_defined && (!atoms_col_value)) {
cvm::error("Error: atomsColValue, if provided, must be non-zero.\n", INPUT_ERROR);
}
cvm::load_atoms(atoms_file_name.c_str(), *this, atoms_col, atoms_col_value);
}
}
// Catch any errors from all the initialization steps above
if (cvm::get_error()) return COLVARS_ERROR;
for (std::vector<cvm::atom>::iterator a1 = this->begin();
a1 != this->end(); ++a1) {
std::vector<cvm::atom>::iterator a2 = a1;
++a2;
for ( ; a2 != this->end(); ++a2) {
if (a1->id == a2->id) {
if (cvm::debug())
cvm::log("Discarding doubly counted atom with number "+
cvm::to_str(a1->id+1)+".\n");
a2 = this->erase(a2);
if (a2 == this->end())
break;
}
}
}
if (get_keyval(group_conf, "dummyAtom", dummy_atom_pos, cvm::atom_pos(), mode)) {
b_dummy = true;
this->total_mass = 1.0;
} else
b_dummy = false;
if (b_dummy && (this->size())) {
cvm::error("Error: cannot set up group \""+
std::string(key)+"\" as a dummy atom "
"and provide it with atom definitions.\n", INPUT_ERROR);
}
#if(! defined(COLVARS_STANDALONE))
if ( (!b_dummy) && (!cvm::b_analysis) && (!(this->size())) ) {
cvm::error("Error: no atoms defined for atom group \""+
std::string(key)+"\".\n");
}
#endif
if (!b_dummy) {
// calculate total mass (TODO: this is the step that most needs deferred re-initialization)
this->total_mass = 0.0;
for (cvm::atom_iter ai = this->begin();
ai != this->end(); ai++) {
this->total_mass += ai->mass;
}
// whether these atoms will ever receive forces or not
bool enable_forces = true;
// disableForces is deprecated
if (get_keyval(group_conf, "enableForces", enable_forces, true, mode)) {
noforce = !enable_forces;
} else {
get_keyval(group_conf, "disableForces", noforce, false, colvarparse::parse_silent);
}
}
// FITTING OPTIONS
bool b_defined_center = get_keyval(group_conf, "centerReference", b_center, false, mode);
bool b_defined_rotate = get_keyval(group_conf, "rotateReference", b_rotate, false, mode);
// is the user setting explicit options?
b_user_defined_fit = b_defined_center || b_defined_rotate;
get_keyval(group_conf, "enableFitGradients", b_fit_gradients, true, mode);
if (b_center || b_rotate) {
if (b_dummy)
cvm::error("Error: centerReference or rotateReference "
"cannot be defined for a dummy atom.\n");
if (key_lookup(group_conf, "refPositionsGroup")) {
// instead of this group, define another group to compute the fit
if (ref_pos_group) {
cvm::error("Error: the atom group \""+
std::string(key)+"\" has already a reference group "
"for the rototranslational fit, which was communicated by the "
"colvar component. You should not use refPositionsGroup "
"in this case.\n");
}
cvm::log("Within atom group \""+std::string(key)+"\":\n");
ref_pos_group = new atom_group(group_conf, "refPositionsGroup");
// regardless of the configuration, fit gradients must be calculated by refPositionsGroup
ref_pos_group->b_fit_gradients = this->b_fit_gradients;
this->b_fit_gradients = false;
}
atom_group *group_for_fit = ref_pos_group ? ref_pos_group : this;
get_keyval(group_conf, "refPositions", ref_pos, ref_pos, mode);
std::string ref_pos_file;
if (get_keyval(group_conf, "refPositionsFile", ref_pos_file, std::string(""), mode)) {
if (ref_pos.size()) {
cvm::error("Error: cannot specify \"refPositionsFile\" and "
"\"refPositions\" at the same time.\n");
}
std::string ref_pos_col;
double ref_pos_col_value=0.0;
if (get_keyval(group_conf, "refPositionsCol", ref_pos_col, std::string(""), mode)) {
// if provided, use PDB column to select coordinates
bool found = get_keyval(group_conf, "refPositionsColValue", ref_pos_col_value, 0.0, mode);
if (found && ref_pos_col_value == 0.0)
cvm::error("Error: refPositionsColValue, "
"if provided, must be non-zero.\n");
} else {
// if not, rely on existing atom indices for the group
group_for_fit->create_sorted_ids();
ref_pos.resize(group_for_fit->size());
}
cvm::load_coords(ref_pos_file.c_str(), ref_pos, group_for_fit->sorted_ids,
ref_pos_col, ref_pos_col_value);
}
if (ref_pos.size()) {
if (b_rotate) {
if (ref_pos.size() != group_for_fit->size())
cvm::error("Error: the number of reference positions provided("+
cvm::to_str(ref_pos.size())+
") does not match the number of atoms within \""+
std::string(key)+
"\" ("+cvm::to_str(group_for_fit->size())+
"): to perform a rotational fit, "+
"these numbers should be equal.\n", INPUT_ERROR);
}
// save the center of geometry of ref_pos and subtract it
center_ref_pos();
} else {
#if(! defined(COLVARS_STANDALONE))
cvm::error("Error: no reference positions provided.\n");
#endif
}
if (b_fit_gradients) {
group_for_fit->fit_gradients.assign(group_for_fit->size(), cvm::atom_pos(0.0, 0.0, 0.0));
rot.request_group1_gradients(group_for_fit->size());
}
if (b_rotate && !noforce) {
cvm::log("Warning: atom group \""+std::string(key)+
"\" will be aligned to a fixed orientation given by the reference positions provided. "
"If the internal structure of the group changes too much (i.e. its RMSD is comparable "
"to its radius of gyration), the optimal rotation and its gradients may become discontinuous. "
"If that happens, use refPositionsGroup (or a different definition for it if already defined) "
"to align the coordinates.\n");
// initialize rot member data
rot.request_group1_gradients(this->size());
}
}
if (cvm::debug())
cvm::log("Done initializing atom group with name \""+
std::string(key)+"\".\n");
this->check_keywords(group_conf, key);
if (cvm::get_error()) {
cvm::error("Error setting up atom group \""+std::string(key)+"\".");
return COLVARS_ERROR;
}
cvm::log("Atom group \""+std::string(key)+"\" defined, "+
cvm::to_str(this->size())+" atoms initialized: total mass = "+
cvm::to_str(this->total_mass)+".\n");
cvm::decrease_depth();
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}
int cvm::atom_group::create_sorted_ids(void)
{
// Only do the work if the vector is not yet populated
if (sorted_ids.size())
return COLVARS_OK;
std::list<int> temp_id_list;
cvm::atom_iter ai;
for (ai = this->begin(); ai != this->end(); ai++) {
temp_id_list.push_back(ai->id);
}
temp_id_list.sort();
temp_id_list.unique();
if (temp_id_list.size() != this->size()) {
cvm::error("Error: duplicate atom IDs in atom group? (found " +
cvm::to_str(temp_id_list.size()) +
" unique atom IDs instead of" +
cvm::to_str(this->size()) + ").\n");
return COLVARS_ERROR;
}
sorted_ids = std::vector<int> (temp_id_list.size());
unsigned int id_i = 0;
std::list<int>::iterator li;
for (li = temp_id_list.begin(); li != temp_id_list.end(); ++li) {
sorted_ids[id_i] = *li;
id_i++;
}
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}
void cvm::atom_group::center_ref_pos()
{
// save the center of geometry of ref_pos and then subtract it from
// them; in this way it will be possible to use ref_pos also for
// the rotational fit
// This is called either by atom_group::parse or by CVCs that set
// reference positions (eg. RMSD, eigenvector)
ref_pos_cog = cvm::atom_pos(0.0, 0.0, 0.0);
std::vector<cvm::atom_pos>::iterator pi;
for (pi = ref_pos.begin(); pi != ref_pos.end(); ++pi) {
ref_pos_cog += *pi;
}
ref_pos_cog /= (cvm::real) ref_pos.size();
for (pi = ref_pos.begin(); pi != ref_pos.end(); ++pi) {
(*pi) -= ref_pos_cog;
}
}
void cvm::atom_group::read_positions()
{
if (b_dummy) return;
for (cvm::atom_iter ai = this->begin();
ai != this->end(); ai++) {
ai->read_position();
}
if (ref_pos_group)
ref_pos_group->read_positions();
}
void cvm::atom_group::calc_apply_roto_translation()
{
atom_group *fit_group = ref_pos_group ? ref_pos_group : this;
if (b_center) {
// center on the origin first
cvm::atom_pos const cog = fit_group->center_of_geometry();
for (cvm::atom_iter ai = this->begin();
ai != this->end(); ai++) {
ai->pos -= cog;
}
}
if (b_rotate) {
// rotate the group (around the center of geometry if b_center is
// true, around the origin otherwise)
rot.calc_optimal_rotation(fit_group->positions(), ref_pos);
for (cvm::atom_iter ai = this->begin();
ai != this->end(); ai++) {
ai->pos = rot.rotate(ai->pos);
}
}
if (b_center) {
// align with the center of geometry of ref_pos
for (cvm::atom_iter ai = this->begin();
ai != this->end(); ai++) {
ai->pos += ref_pos_cog;
}
}
}
void cvm::atom_group::apply_translation(cvm::rvector const &t)
{
if (b_dummy) return;
for (cvm::atom_iter ai = this->begin();
ai != this->end(); ai++) {
ai->pos += t;
}
}
void cvm::atom_group::apply_rotation(cvm::rotation const &rot)
{
if (b_dummy) return;
for (cvm::atom_iter ai = this->begin();
ai != this->end(); ai++) {
ai->pos = rot.rotate(ai->pos);
}
}
void cvm::atom_group::read_velocities()
{
if (b_dummy) return;
if (b_rotate) {
for (cvm::atom_iter ai = this->begin();
ai != this->end(); ai++) {
ai->read_velocity();
ai->vel = rot.rotate(ai->vel);
}
} else {
for (cvm::atom_iter ai = this->begin();
ai != this->end(); ai++) {
ai->read_velocity();
}
}
}
void cvm::atom_group::read_system_forces()
{
if (b_dummy) return;
if (b_rotate) {
for (cvm::atom_iter ai = this->begin();
ai != this->end(); ai++) {
ai->read_system_force();
ai->system_force = rot.rotate(ai->system_force);
}
} else {
for (cvm::atom_iter ai = this->begin();
ai != this->end(); ai++) {
ai->read_system_force();
}
}
}
cvm::atom_pos cvm::atom_group::center_of_geometry() const
{
if (b_dummy)
return dummy_atom_pos;
cvm::atom_pos cog(0.0, 0.0, 0.0);
for (cvm::atom_const_iter ai = this->begin();
ai != this->end(); ai++) {
cog += ai->pos;
}
cog /= this->size();
return cog;
}
cvm::atom_pos cvm::atom_group::center_of_mass() const
{
if (b_dummy)
return dummy_atom_pos;
cvm::atom_pos com(0.0, 0.0, 0.0);
for (cvm::atom_const_iter ai = this->begin();
ai != this->end(); ai++) {
com += ai->mass * ai->pos;
}
com /= this->total_mass;
return com;
}
void cvm::atom_group::set_weighted_gradient(cvm::rvector const &grad)
{
if (b_dummy) return;
for (cvm::atom_iter ai = this->begin();
ai != this->end(); ai++) {
ai->grad = (ai->mass/this->total_mass) * grad;
}
}
void cvm::atom_group::calc_fit_gradients()
{
if (b_dummy) return;
if ((!b_center) && (!b_rotate)) return; // no fit
if (cvm::debug())
cvm::log("Calculating fit gradients.\n");
atom_group *group_for_fit = ref_pos_group ? ref_pos_group : this;
group_for_fit->fit_gradients.assign(group_for_fit->size(), cvm::rvector(0.0, 0.0, 0.0));
if (b_center) {
// add the center of geometry contribution to the gradients
for (size_t i = 0; i < this->size(); i++) {
// need to bring the gradients in original frame first
cvm::rvector const atom_grad = b_rotate ?
(rot.inverse()).rotate((*this)[i].grad) :
(*this)[i].grad;
for (size_t j = 0; j < group_for_fit->size(); j++) {
group_for_fit->fit_gradients[j] +=
(-1.0)/(cvm::real(group_for_fit->size())) *
atom_grad;
}
}
}
if (b_rotate) {
// add the rotation matrix contribution to the gradients
cvm::rotation const rot_inv = rot.inverse();
cvm::atom_pos const cog = this->center_of_geometry();
for (size_t i = 0; i < this->size(); i++) {
cvm::atom_pos const pos_orig = rot_inv.rotate((b_center ? ((*this)[i].pos - cog) : ((*this)[i].pos)));
for (size_t j = 0; j < group_for_fit->size(); j++) {
// calculate \partial(R(q) \vec{x}_i)/\partial q) \cdot \partial\xi/\partial\vec{x}_i
cvm::quaternion const dxdq =
rot.q.position_derivative_inner(pos_orig, (*this)[i].grad);
// multiply by \cdot {\partial q}/\partial\vec{x}_j and add it to the fit gradients
for (size_t iq = 0; iq < 4; iq++) {
group_for_fit->fit_gradients[j] += dxdq[iq] * rot.dQ0_1[j][iq];
}
}
}
}
if (cvm::debug())
cvm::log("Done calculating fit gradients.\n");
}
std::vector<cvm::atom_pos> cvm::atom_group::positions() const
{
if (b_dummy) {
cvm::error("Error: positions are not available "
"from a dummy atom group.\n");
}
std::vector<cvm::atom_pos> x(this->size(), 0.0);
cvm::atom_const_iter ai = this->begin();
std::vector<cvm::atom_pos>::iterator xi = x.begin();
for ( ; ai != this->end(); ++xi, ++ai) {
*xi = ai->pos;
}
return x;
}
std::vector<cvm::atom_pos> cvm::atom_group::positions_shifted(cvm::rvector const &shift) const
{
if (b_dummy) {
cvm::error("Error: positions are not available "
"from a dummy atom group.\n");
}
std::vector<cvm::atom_pos> x(this->size(), 0.0);
cvm::atom_const_iter ai = this->begin();
std::vector<cvm::atom_pos>::iterator xi = x.begin();
for ( ; ai != this->end(); ++xi, ++ai) {
*xi = (ai->pos + shift);
}
return x;
}
std::vector<cvm::rvector> cvm::atom_group::velocities() const
{
if (b_dummy) {
cvm::error("Error: velocities are not available "
"from a dummy atom group.\n");
}
std::vector<cvm::rvector> v(this->size(), 0.0);
cvm::atom_const_iter ai = this->begin();
std::vector<cvm::atom_pos>::iterator vi = v.begin();
for ( ; ai != this->end(); vi++, ai++) {
*vi = ai->vel;
}
return v;
}
std::vector<cvm::rvector> cvm::atom_group::system_forces() const
{
if (b_dummy) {
cvm::error("Error: system forces are not available "
"from a dummy atom group.\n");
}
std::vector<cvm::rvector> f(this->size(), 0.0);
cvm::atom_const_iter ai = this->begin();
std::vector<cvm::atom_pos>::iterator fi = f.begin();
for ( ; ai != this->end(); ++fi, ++ai) {
*fi = ai->system_force;
}
return f;
}
cvm::rvector cvm::atom_group::system_force() const
{
if (b_dummy) {
cvm::error("Error: system forces are not available "
"from a dummy atom group.\n");
}
cvm::rvector f(0.0);
for (cvm::atom_const_iter ai = this->begin(); ai != this->end(); ai++) {
f += ai->system_force;
}
return f;
}
void cvm::atom_group::apply_colvar_force(cvm::real const &force)
{
if (b_dummy)
return;
if (noforce) {
cvm::error("Error: sending a force to a group that has "
"\"enableForces\" set to off.\n");
return;
}
if (b_rotate) {
// rotate forces back to the original frame
cvm::rotation const rot_inv = rot.inverse();
for (cvm::atom_iter ai = this->begin();
ai != this->end(); ai++) {
ai->apply_force(rot_inv.rotate(force * ai->grad));
}
} else {
for (cvm::atom_iter ai = this->begin();
ai != this->end(); ai++) {
ai->apply_force(force * ai->grad);
}
}
if ((b_center || b_rotate) && b_fit_gradients) {
atom_group *group_for_fit = ref_pos_group ? ref_pos_group : this;
// add the contribution from the roto-translational fit to the gradients
if (b_rotate) {
// rotate forces back to the original frame
cvm::rotation const rot_inv = rot.inverse();
for (size_t j = 0; j < group_for_fit->size(); j++) {
(*group_for_fit)[j].apply_force(rot_inv.rotate(force * group_for_fit->fit_gradients[j]));
}
} else {
for (size_t j = 0; j < group_for_fit->size(); j++) {
(*group_for_fit)[j].apply_force(force * group_for_fit->fit_gradients[j]);
}
}
}
}
void cvm::atom_group::apply_force(cvm::rvector const &force)
{
if (b_dummy)
return;
if (noforce) {
cvm::error("Error: sending a force to a group that has "
"\"disableForces\" defined.\n");
return;
}
if (b_rotate) {
cvm::rotation const rot_inv = rot.inverse();
for (cvm::atom_iter ai = this->begin();
ai != this->end(); ai++) {
ai->apply_force(rot_inv.rotate((ai->mass/this->total_mass) * force));
}
} else {
for (cvm::atom_iter ai = this->begin();
ai != this->end(); ai++) {
ai->apply_force((ai->mass/this->total_mass) * force);
}
}
}
void cvm::atom_group::apply_forces(std::vector<cvm::rvector> const &forces)
{
if (b_dummy)
return;
if (noforce)
cvm::error("Error: sending a force to a group that has "
"\"disableForces\" defined.\n");
if (forces.size() != this->size()) {
cvm::error("Error: trying to apply an array of forces to an atom "
"group which does not have the same length.\n");
}
if (b_rotate) {
cvm::rotation const rot_inv = rot.inverse();
cvm::atom_iter ai = this->begin();
std::vector<cvm::rvector>::const_iterator fi = forces.begin();
for ( ; ai != this->end(); ++fi, ++ai) {
ai->apply_force(rot_inv.rotate(*fi));
}
} else {
cvm::atom_iter ai = this->begin();
std::vector<cvm::rvector>::const_iterator fi = forces.begin();
for ( ; ai != this->end(); ++fi, ++ai) {
ai->apply_force(*fi);
}
}
}
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