colvaratoms.cpp
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Created: Sun, Apr 27, 19:07

colvaratoms.cpp
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	// -- c++ --

	#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 = "atoms";
	atoms.clear();

	// TODO: check with proxy whether atom forces etc are available
	init_ag_requires();

	index = -1;

	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)) {
	cvm::combine_errors(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
	cvm::combine_errors(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)) {
	cvm::combine_errors(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 {
	cvm::combine_errors(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);
	}

	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);
	}
	}

	if (is_enabled(f_ag_scalable) && !b_dummy) {
	index = (cvm::proxy)->init_atom_group(atoms_ids);
	}

	cvm::combine_errors(parse_error, parse_fitting_options(group_conf));

	// 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");

	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;
	}


	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_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();
	}
	}
	}


	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::system_forces() const
	{
	if (b_dummy) {
	cvm::error("Error: system forces are not available "
	"from a dummy atom group.\n", INPUT_ERROR);
	}

	if (is_enabled(f_ag_scalable)) {
	cvm::error("Error: atomic system 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->system_force;
	}
	return f;
	}


	// TODO make this an accessor
	cvm::rvector cvm::atom_group::system_force() const
	{
	if (b_dummy) {
	cvm::error("Error: total system forces are not available "
	"from a dummy atom group.\n", INPUT_ERROR);
	}

	if (is_enabled(f_ag_scalable)) {
	return (cvm::proxy)->get_atom_group_system_force(index);
	}

	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 (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 (b_dummy)
	return;

	if (noforce) {
	cvm::error("Error: sending a force to a group that has "
	"\"disableForces\" defined.\n");
	return;
	}

	if (is_enabled(f_ag_scalable)) {
	(cvm::proxy)->apply_atom_group_force(index, force);
	}

	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<cvm::deps::feature *> cvm::atom_group::ag_features;

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