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lammps/lib/colvars/colvaratoms.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 "colvarmodule.h"
#include "colvarparse.h"
#include "colvaratoms.h"
cvm::atom::atom()
{
index = -1;
id = -1;
reset_data();
}
cvm::atom::atom(int atom_number)
{
colvarproxy *p = cvm::proxy;
index = p->init_atom(atom_number);
if (cvm::debug()) {
cvm::log("The index of this atom in the colvarproxy arrays is "+
cvm::to_str(index)+".\n");
}
id = p->get_atom_id(index);
update_mass();
reset_data();
}
cvm::atom::atom(cvm::residue_id const &residue,
std::string const &atom_name,
std::string const &segment_id)
{
colvarproxy *p = cvm::proxy;
index = p->init_atom(residue, atom_name, segment_id);
if (cvm::debug()) {
cvm::log("The index of this atom in the colvarproxy_namd arrays is "+
cvm::to_str(index)+".\n");
}
id = p->get_atom_id(index);
update_mass();
reset_data();
}
cvm::atom::atom(atom const &a)
: index(a.index)
{
id = (cvm::proxy)->get_atom_id(index);
update_mass();
reset_data();
}
cvm::atom::~atom()
{
if (index >= 0) {
(cvm::proxy)->clear_atom(index);
}
}
// TODO change this arrangement
// 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_in)
{
key = key_in;
cvm::log("Defining atom group \"" + key + "\".\n");
init();
// real work is done by parse
parse(conf);
setup();
}
cvm::atom_group::atom_group(std::vector<cvm::atom> const &atoms_in)
{
init();
atoms = atoms_in;
setup();
}
cvm::atom_group::atom_group()
{
init();
}
cvm::atom_group::~atom_group()
{
if (is_enabled(f_ag_scalable)) {
(cvm::proxy)->clear_atom_group(index);
index = -1;
}
if (fitting_group) {
delete fitting_group;
fitting_group = NULL;
}
}
int cvm::atom_group::add_atom(cvm::atom const &a)
{
if (a.id < 0) {
return COLVARS_ERROR;
}
for (size_t i = 0; i < atoms_ids.size(); i++) {
if (atoms_ids[i] == a.id) {
if (cvm::debug())
cvm::log("Discarding doubly counted atom with number "+
cvm::to_str(a.id+1)+".\n");
return COLVARS_OK;
}
}
// for consistency with add_atom_id(), we update the list as well
atoms_ids.push_back(a.id);
atoms.push_back(a);
total_mass += a.mass;
total_charge += a.charge;
return COLVARS_OK;
}
int cvm::atom_group::add_atom_id(int aid)
{
if (aid < 0) {
return COLVARS_ERROR;
}
for (size_t i = 0; i < atoms_ids.size(); i++) {
if (atoms_ids[i] == aid) {
if (cvm::debug())
cvm::log("Discarding doubly counted atom with number "+
cvm::to_str(aid+1)+".\n");
return COLVARS_OK;
}
}
atoms_ids.push_back(aid);
return COLVARS_OK;
}
int cvm::atom_group::remove_atom(cvm::atom_iter ai)
{
if (is_enabled(f_ag_scalable)) {
cvm::error("Error: cannot remove atoms from a scalable group.\n", INPUT_ERROR);
return COLVARS_ERROR;
}
if (!this->size()) {
cvm::error("Error: trying to remove an atom from an empty group.\n", INPUT_ERROR);
return COLVARS_ERROR;
} else {
total_mass -= ai->mass;
total_charge -= ai->charge;
atoms_ids.erase(atoms_ids.begin() + (ai - atoms.begin()));
atoms.erase(ai);
}
return COLVARS_OK;
}
int cvm::atom_group::init()
{
if (!key.size()) key = "unnamed";
description = "atom group " + key;
// These will be overwritten by parse(), if initializing from a config string
atoms.clear();
// TODO: check with proxy whether atom forces etc are available
init_ag_requires();
index = -1;
b_dummy = false;
b_center = false;
b_rotate = false;
b_user_defined_fit = false;
b_fit_gradients = false;
fitting_group = NULL;
noforce = false;
total_mass = 0.0;
total_charge = 0.0;
cog.reset();
com.reset();
return COLVARS_OK;
}
int cvm::atom_group::setup()
{
for (cvm::atom_iter ai = atoms.begin(); ai != atoms.end(); ai++) {
ai->update_mass();
ai->update_charge();
}
update_total_mass();
update_total_charge();
return COLVARS_OK;
}
void cvm::atom_group::update_total_mass()
{
if (b_dummy) {
total_mass = 1.0;
return;
}
if (is_enabled(f_ag_scalable)) {
total_mass = (cvm::proxy)->get_atom_group_mass(index);
} else {
total_mass = 0.0;
for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) {
total_mass += ai->mass;
}
}
}
void cvm::atom_group::reset_mass(std::string &name, int i, int j)
{
update_total_mass();
cvm::log("Re-initialized atom group "+name+":"+cvm::to_str(i)+"/"+
cvm::to_str(j)+". "+ cvm::to_str(atoms_ids.size())+
" atoms: total mass = "+cvm::to_str(total_mass)+".\n");
}
void cvm::atom_group::update_total_charge()
{
if (b_dummy) {
total_charge = 0.0;
return;
}
if (is_enabled(f_ag_scalable)) {
total_charge = (cvm::proxy)->get_atom_group_charge(index);
} else {
total_charge = 0.0;
for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) {
total_charge += ai->charge;
}
}
}
int cvm::atom_group::parse(std::string const &conf)
{
std::string group_conf;
// TODO move this to the cvc class constructor/init
// 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.c_str(), 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 \""+key+
"\" is set, but has no definition.\n",
INPUT_ERROR);
return COLVARS_ERROR;
}
cvm::increase_depth();
cvm::log("Initializing atom group \""+key+"\".\n");
description = "atom group " + key;
// 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;
int parse_error = COLVARS_OK;
{
std::string numbers_conf = "";
size_t pos = 0;
while (key_lookup(group_conf, "atomNumbers", numbers_conf, pos)) {
parse_error |= add_atom_numbers(numbers_conf);
numbers_conf = "";
}
}
{
std::string index_group_name;
if (get_keyval(group_conf, "indexGroup", index_group_name)) {
// use an index group from the index file read globally
parse_error |= add_index_group(index_group_name);
}
}
{
std::string range_conf = "";
size_t pos = 0;
while (key_lookup(group_conf, "atomNumbersRange",
range_conf, pos)) {
parse_error |= add_atom_numbers_range(range_conf);
range_conf = "";
}
}
{
std::vector<std::string> psf_segids;
get_keyval(group_conf, "psfSegID", psf_segids, std::vector<std::string>());
std::vector<std::string>::iterator psii;
for (psii = psf_segids.begin(); psii < psf_segids.end(); ++psii) {
if ( (psii->size() == 0) || (psii->size() > 4) ) {
cvm::error("Error: invalid PSF segment identifier provided, \""+
(*psii)+"\".\n", INPUT_ERROR);
}
}
std::string range_conf = "";
size_t pos = 0;
size_t range_count = 0;
psii = psf_segids.begin();
while (key_lookup(group_conf, "atomNameResidueRange",
range_conf, pos)) {
range_count++;
if (psf_segids.size() && (range_count > psf_segids.size())) {
cvm::error("Error: more instances of \"atomNameResidueRange\" than "
"values of \"psfSegID\".\n", INPUT_ERROR);
} else {
parse_error |= add_atom_name_residue_range(psf_segids.size() ?
*psii : std::string(""), range_conf);
if (psf_segids.size()) psii++;
}
range_conf = "";
}
}
{
// read the atoms from a file
std::string atoms_file_name;
if (get_keyval(group_conf, "atomsFile", atoms_file_name, std::string(""))) {
std::string atoms_col;
if (!get_keyval(group_conf, "atomsCol", atoms_col, std::string(""))) {
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);
if (atoms_col_value_defined && (!atoms_col_value)) {
cvm::error("Error: atomsColValue, if provided, must be non-zero.\n", INPUT_ERROR);
}
// NOTE: calls to add_atom() and/or add_atom_id() are in the proxy-implemented function
cvm::load_atoms(atoms_file_name.c_str(), *this, atoms_col, atoms_col_value);
}
}
// Catch any errors from all the initialization steps above
if (parse_error || cvm::get_error()) return (parse_error || cvm::get_error());
// checks of doubly-counted atoms have been handled by add_atom() already
if (get_keyval(group_conf, "dummyAtom", dummy_atom_pos, cvm::atom_pos())) {
b_dummy = true;
// note: atoms_ids.size() is used here in lieu of atoms.size(),
// which can be empty for scalable groups
if (atoms_ids.size()) {
cvm::error("Error: cannot set up group \""+
key+"\" as a dummy atom "
"and provide it with atom definitions.\n", INPUT_ERROR);
}
} else {
b_dummy = false;
if (!(atoms_ids.size())) {
cvm::error("Error: no atoms defined for atom group \""+
key+"\".\n", INPUT_ERROR);
}
// 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)) {
noforce = !enable_forces;
} else {
get_keyval(group_conf, "disableForces", noforce, false, colvarparse::parse_silent);
}
}
// We need to know the fitting options to decide whether the group is scalable
parse_error |= parse_fitting_options(group_conf);
if (is_available(f_ag_scalable_com) && !b_rotate) {
enable(f_ag_scalable_com);
enable(f_ag_scalable);
}
if (is_enabled(f_ag_scalable) && !b_dummy) {
cvm::log("Enabling scalable calculation for group \""+this->key+"\".\n");
index = (cvm::proxy)->init_atom_group(atoms_ids);
}
bool b_print_atom_ids = false;
get_keyval(group_conf, "printAtomIDs", b_print_atom_ids, false, colvarparse::parse_silent);
// TODO move this to colvarparse object
check_keywords(group_conf, key.c_str());
if (cvm::get_error()) {
cvm::error("Error setting up atom group \""+key+"\".");
return COLVARS_ERROR;
}
// Calculate all required properties (such as total mass)
setup();
if (cvm::debug())
cvm::log("Done initializing atom group \""+key+"\".\n");
cvm::log("Atom group \""+key+"\" defined, "+
cvm::to_str(atoms_ids.size())+" atoms initialized: total mass = "+
cvm::to_str(total_mass)+", total charge = "+
cvm::to_str(total_charge)+".\n");
if (b_print_atom_ids) {
cvm::log("Internal definition of the atom group:\n");
cvm::log(print_atom_ids());
}
cvm::decrease_depth();
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}
int cvm::atom_group::add_atom_numbers(std::string const &numbers_conf)
{
std::vector<int> atom_indexes;
if (numbers_conf.size()) {
std::istringstream is(numbers_conf);
int ia;
while (is >> ia) {
atom_indexes.push_back(ia);
}
}
if (atom_indexes.size()) {
atoms_ids.reserve(atoms_ids.size()+atom_indexes.size());
if (is_enabled(f_ag_scalable)) {
for (size_t i = 0; i < atom_indexes.size(); i++) {
add_atom_id((cvm::proxy)->check_atom_id(atom_indexes[i]));
}
} else {
// if we are handling the group on rank 0, better allocate the vector in one shot
atoms.reserve(atoms.size()+atom_indexes.size());
for (size_t i = 0; i < atom_indexes.size(); i++) {
add_atom(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;
}
return COLVARS_OK;
}
int cvm::atom_group::add_index_group(std::string const &index_group_name)
{
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;
}
atoms_ids.reserve(atoms_ids.size()+index_groups_i->size());
if (is_enabled(f_ag_scalable)) {
for (size_t i = 0; i < index_groups_i->size(); i++) {
add_atom_id((cvm::proxy)->check_atom_id((*index_groups_i)[i]));
}
} else {
atoms.reserve(atoms.size()+index_groups_i->size());
for (size_t i = 0; i < index_groups_i->size(); i++) {
add_atom(cvm::atom((*index_groups_i)[i]));
}
}
if (cvm::get_error())
return COLVARS_ERROR;
return COLVARS_OK;
}
int cvm::atom_group::add_atom_numbers_range(std::string const &range_conf)
{
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) ) {
atoms_ids.reserve(atoms_ids.size() + (final - initial + 1));
if (is_enabled(f_ag_scalable)) {
for (int anum = initial; anum <= final; anum++) {
add_atom_id((cvm::proxy)->check_atom_id(anum));
}
} else {
atoms.reserve(atoms.size() + (final - initial + 1));
for (int anum = initial; anum <= final; anum++) {
add_atom(cvm::atom(anum));
}
}
}
if (cvm::get_error()) return COLVARS_ERROR;
} else {
cvm::error("Error: no valid definition for \"atomNumbersRange\", \""+
range_conf+"\".\n", INPUT_ERROR);
return COLVARS_ERROR;
}
return COLVARS_OK;
}
int cvm::atom_group::add_atom_name_residue_range(std::string const &psf_segid,
std::string const &range_conf)
{
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) ) {
atoms_ids.reserve(atoms_ids.size() + (final - initial + 1));
if (is_enabled(f_ag_scalable)) {
for (int resid = initial; resid <= final; resid++) {
add_atom_id((cvm::proxy)->check_atom_id(resid, atom_name, psf_segid));
}
} else {
atoms.reserve(atoms.size() + (final - initial + 1));
for (int resid = initial; resid <= final; resid++) {
add_atom(cvm::atom(resid, atom_name, psf_segid));
}
}
if (cvm::get_error()) return COLVARS_ERROR;
} else {
cvm::error("Error: cannot parse definition for \""
"atomNameResidueRange\", \""+
range_conf+"\".\n");
return COLVARS_ERROR;
}
} else {
cvm::error("Error: atomNameResidueRange with empty definition.\n");
return COLVARS_ERROR;
}
return COLVARS_OK;
}
std::string const cvm::atom_group::print_atom_ids() const
{
size_t line_count = 0;
std::ostringstream os("");
for (size_t i = 0; i < atoms_ids.size(); i++) {
os << " " << std::setw(9) << atoms_ids[i];
if (++line_count == 7) {
os << "\n";
line_count = 0;
}
}
return os.str();
}
int cvm::atom_group::parse_fitting_options(std::string const &group_conf)
{
bool b_defined_center = get_keyval(group_conf, "centerReference", b_center, false);
bool b_defined_rotate = get_keyval(group_conf, "rotateReference", b_rotate, false);
// 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);
if (b_center || b_rotate) {
if (b_dummy)
cvm::error("Error: centerReference or rotateReference "
"cannot be defined for a dummy atom.\n");
bool b_ref_pos_group = false;
if (key_lookup(group_conf, "refPositionsGroup")) {
b_ref_pos_group = true;
cvm::log("Warning: keyword \"refPositionsGroup\" is deprecated: please use \"fittingGroup\" instead.\n");
}
if (b_ref_pos_group || key_lookup(group_conf, "fittingGroup")) {
// instead of this group, define another group to compute the fit
if (fitting_group) {
cvm::error("Error: the atom group \""+
key+"\" has already a reference group "
"for the rototranslational fit, which was communicated by the "
"colvar component. You should not use fittingGroup "
"in this case.\n");
}
cvm::log("Within atom group \""+key+"\":\n");
fitting_group = b_ref_pos_group ?
new atom_group(group_conf, "refPositionsGroup") :
new atom_group(group_conf, "fittingGroup");
// regardless of the configuration, fit gradients must be calculated by fittingGroup
fitting_group->b_fit_gradients = this->b_fit_gradients;
}
atom_group *group_for_fit = fitting_group ? fitting_group : this;
get_keyval(group_conf, "refPositions", ref_pos, ref_pos);
std::string ref_pos_file;
if (get_keyval(group_conf, "refPositionsFile", ref_pos_file, std::string(""))) {
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(""))) {
// if provided, use PDB column to select coordinates
bool found = get_keyval(group_conf, "refPositionsColValue", ref_pos_col_value, 0.0);
if (found && ref_pos_col_value == 0.0) {
cvm::error("Error: refPositionsColValue, "
"if provided, must be non-zero.\n", INPUT_ERROR);
return COLVARS_ERROR;
}
} 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 \""+
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 {
cvm::error("Error: no reference positions provided.\n", INPUT_ERROR);
return COLVARS_ERROR;
}
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 \""+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 fittingGroup (or a different definition for it if already defined) "
"to align the coordinates.\n");
// initialize rot member data
rot.request_group1_gradients(group_for_fit->size());
}
}
return 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;
for (cvm::atom_iter 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()
{
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 (fitting_group)
fitting_group->read_positions();
}
int cvm::atom_group::calc_required_properties()
{
// TODO check if the com is needed?
calc_center_of_mass();
calc_center_of_geometry();
if (!is_enabled(f_ag_scalable)) {
if (b_center || b_rotate) {
if (fitting_group) {
fitting_group->calc_center_of_geometry();
}
calc_apply_roto_translation();
// update COM and COG after fitting
calc_center_of_geometry();
calc_center_of_mass();
if (fitting_group) {
fitting_group->calc_center_of_geometry();
}
}
}
// TODO calculate elements of scalable cvc's here before reduction
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}
void cvm::atom_group::calc_apply_roto_translation()
{
// store the laborarory-frame COGs for when they are needed later
cog_orig = this->center_of_geometry();
if (fitting_group) {
fitting_group->cog_orig = fitting_group->center_of_geometry();
}
if (b_center) {
// center on the origin first
cvm::atom_pos const rpg_cog = fitting_group ?
fitting_group->center_of_geometry() : this->center_of_geometry();
apply_translation(-1.0 * rpg_cog);
if (fitting_group) {
fitting_group->apply_translation(-1.0 * rpg_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(fitting_group ?
fitting_group->positions() :
this->positions(),
ref_pos);
cvm::atom_iter ai;
for (ai = this->begin(); ai != this->end(); ai++) {
ai->pos = rot.rotate(ai->pos);
}
if (fitting_group) {
for (ai = fitting_group->begin(); ai != fitting_group->end(); ai++) {
ai->pos = rot.rotate(ai->pos);
}
}
}
if (b_center) {
// align with the center of geometry of ref_pos
apply_translation(ref_pos_cog);
if (fitting_group) {
fitting_group->apply_translation(ref_pos_cog);
}
}
// update of COM and COG is done from the calling routine
}
void cvm::atom_group::apply_translation(cvm::rvector const &t)
{
if (b_dummy) {
cvm::error("Error: cannot translate the coordinates of a dummy atom group.\n", INPUT_ERROR);
return;
}
if (is_enabled(f_ag_scalable)) {
cvm::error("Error: cannot translate the coordinates of a scalable atom group.\n", INPUT_ERROR);
return;
}
for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) {
ai->pos += t;
}
}
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();
}
}
}
// TODO make this a calc function
void cvm::atom_group::read_total_forces()
{
if (b_dummy) return;
if (b_rotate) {
for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) {
ai->read_total_force();
ai->total_force = rot.rotate(ai->total_force);
}
} else {
for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) {
ai->read_total_force();
}
}
}
int cvm::atom_group::calc_center_of_geometry()
{
if (b_dummy) {
cog = dummy_atom_pos;
} else {
cog.reset();
for (cvm::atom_const_iter ai = this->begin(); ai != this->end(); ai++) {
cog += ai->pos;
}
cog /= this->size();
}
return COLVARS_OK;
}
int cvm::atom_group::calc_center_of_mass()
{
if (b_dummy) {
com = dummy_atom_pos;
if (cvm::debug()) {
cvm::log("Dummy atom center of mass = "+cvm::to_str(com)+"\n");
}
} else if (is_enabled(f_ag_scalable)) {
com = (cvm::proxy)->get_atom_group_com(index);
} else {
com.reset();
for (cvm::atom_const_iter ai = this->begin(); ai != this->end(); ai++) {
com += ai->mass * ai->pos;
}
com /= total_mass;
}
return COLVARS_OK;
}
int cvm::atom_group::calc_dipole(cvm::atom_pos const &com)
{
if (b_dummy) {
cvm::error("Error: trying to compute the dipole of an empty group.\n", INPUT_ERROR);
return COLVARS_ERROR;
}
dip.reset();
for (cvm::atom_const_iter ai = this->begin(); ai != this->end(); ai++) {
dip += ai->charge * (ai->pos - com);
}
return COLVARS_OK;
}
void cvm::atom_group::set_weighted_gradient(cvm::rvector const &grad)
{
if (b_dummy) return;
if (is_enabled(f_ag_scalable)) {
scalar_com_gradient = grad;
return;
}
for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) {
ai->grad = (ai->mass/total_mass) * grad;
}
}
void cvm::atom_group::calc_fit_gradients()
{
if (b_dummy) return;
if (cvm::debug())
cvm::log("Calculating fit gradients.\n");
atom_group *group_for_fit = fitting_group ? fitting_group : this;
if (b_center) {
// add the center of geometry contribution to the gradients
cvm::rvector atom_grad;
for (size_t i = 0; i < this->size(); i++) {
atom_grad += atoms[i].grad;
}
if (b_rotate) atom_grad = (rot.inverse()).rotate(atom_grad);
atom_grad *= (-1.0)/(cvm::real(group_for_fit->size()));
for (size_t j = 0; j < group_for_fit->size(); j++) {
group_for_fit->fit_gradients[j] = atom_grad;
}
}
if (b_rotate) {
// add the rotation matrix contribution to the gradients
cvm::rotation const rot_inv = rot.inverse();
for (size_t i = 0; i < this->size(); i++) {
// compute centered, unrotated position
cvm::atom_pos const pos_orig =
rot_inv.rotate((b_center ? (atoms[i].pos - ref_pos_cog) : (atoms[i].pos)));
// 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, atoms[i].grad);
for (size_t j = 0; j < group_for_fit->size(); j++) {
// multiply by {\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", INPUT_ERROR);
}
if (is_enabled(f_ag_scalable)) {
cvm::error("Error: atomic positions are not available "
"from a scalable atom group.\n", INPUT_ERROR);
}
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", INPUT_ERROR);
}
if (is_enabled(f_ag_scalable)) {
cvm::error("Error: atomic positions are not available "
"from a scalable atom group.\n", INPUT_ERROR);
}
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", INPUT_ERROR);
}
if (is_enabled(f_ag_scalable)) {
cvm::error("Error: atomic velocities are not available "
"from a scalable atom group.\n", INPUT_ERROR);
}
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::total_forces() const
{
if (b_dummy) {
cvm::error("Error: total forces are not available "
"from a dummy atom group.\n", INPUT_ERROR);
}
if (is_enabled(f_ag_scalable)) {
cvm::error("Error: atomic total forces are not available "
"from a scalable atom group.\n", INPUT_ERROR);
}
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->total_force;
}
return f;
}
// TODO make this an accessor
cvm::rvector cvm::atom_group::total_force() const
{
if (b_dummy) {
cvm::error("Error: total total forces are not available "
"from a dummy atom group.\n", INPUT_ERROR);
}
if (is_enabled(f_ag_scalable)) {
return (cvm::proxy)->get_atom_group_total_force(index);
}
cvm::rvector f(0.0);
for (cvm::atom_const_iter ai = this->begin(); ai != this->end(); ai++) {
f += ai->total_force;
}
return f;
}
void cvm::atom_group::apply_colvar_force(cvm::real const &force)
{
if (cvm::debug()) {
log("Communicating a colvar force from atom group to the MD engine.\n");
}
if (b_dummy) return;
if (noforce) {
cvm::error("Error: sending a force to a group that has "
"\"enableForces\" set to off.\n");
return;
}
if (is_enabled(f_ag_scalable)) {
(cvm::proxy)->apply_atom_group_force(index, force * scalar_com_gradient);
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 = fitting_group ? fitting_group : this;
// Fit gradients are already calculated in "laboratory" frame
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 (cvm::debug()) {
log("Communicating a colvar force from atom group to the MD engine.\n");
}
if (b_dummy) return;
if (noforce) {
cvm::error("Error: sending a force to a group that has "
"\"enableForces\" set to off.\n");
return;
}
if (is_enabled(f_ag_scalable)) {
(cvm::proxy)->apply_atom_group_force(index, force);
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/total_mass) * force));
}
} else {
for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) {
ai->apply_force((ai->mass/total_mass) * force);
}
}
}
// Static members
std::vector<colvardeps::feature *> cvm::atom_group::ag_features;
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