colvaratoms.cpp
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Created: Wed, Aug 28, 12:37

colvaratoms.cpp
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	#include "colvarmodule.h"
	#include "colvarparse.h"
	#include "colvaratoms.h"


	// atom member functions depend tightly on the MD interface, and are
	// thus defined in colvarproxy_xxx.cpp


	// atom_group member functions

	cvm::atom_group::atom_group (std::string const &conf,
	char const *key,
	atom_group *ref_pos_group_in)
	: b_center (false), b_rotate (false),
	ref_pos_group (NULL), // this is always set within parse(),
	// regardless of ref_pos_group_in
	noforce (false)
	{
	cvm::log ("Defining atom group \""+
	std::string (key)+"\".\n");
	parse (conf, key, ref_pos_group_in);
	}


	void cvm::atom_group::parse (std::string const &conf,
	char const *key,
	atom_group *ref_pos_group_in)
	{
	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::fatal_error ("Error: atom group \""+
	std::string (key)+"\" is set, but "
	"has no definition.\n");
	}

	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;
	}

	{
	// get the atoms by numbers
	std::vector<int> atom_indexes;
	if (get_keyval (group_conf, "atomNumbers", atom_indexes, atom_indexes, mode)) {
	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]));
	}
	} else
	cvm::fatal_error ("Error: no numbers provided for \""
	"atomNumbers\".\n");
	}
	}

	{
	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));
	}
	range_conf = "";
	continue;
	}
	}

	cvm::fatal_error ("Error: no valid definition for \""
	"atomNumbersRange\", \""+
	range_conf+"\".\n");
	}
	}

	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::fatal_error ("Error: invalid segmend identifier provided, \""+
	(*psii)+"\".\n");
	}
	}

	{
	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)) {

	if (psii > psf_segids.end()) {
	cvm::fatal_error ("Error: more instances of \"atomNameResidueRange\" than "
	"values of \"psfSegID\".\n");
	}

	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));
	}
	range_conf = "";
	} else {
	cvm::fatal_error ("Error: cannot parse definition for \""
	"atomNameResidueRange\", \""+
	range_conf+"\".\n");
	}

	} else {
	cvm::fatal_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::fatal_error ("Error: parameter atomsCol is required if atomsFile is set.\n");
	}

	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::fatal_error ("Error: atomsColValue, "
	"if provided, must be non-zero.\n");

	cvm::load_atoms (atoms_file_name.c_str(), *this, atoms_col, atoms_col_value);
	}
	}

	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::fatal_error ("Error: cannot set up group \""+
	std::string (key)+"\" as a dummy atom "
	"and provide it with atom definitions.\n");

	#if (! defined (COLVARS_STANDALONE))
	if ( (!b_dummy) && (!cvm::b_analysis) && (!(this->size())) ) {
	cvm::fatal_error ("Error: no atoms defined for atom group \""+
	std::string (key)+"\".\n");
	}
	#endif

	if (!b_dummy) {
	this->total_mass = 0.0;
	for (cvm::atom_iter ai = this->begin();
	ai != this->end(); ai++) {
	this->total_mass += ai->mass;
	}
	}

	get_keyval (group_conf, "disableForces", noforce, false, mode);

	get_keyval (group_conf, "centerReference", b_center, false, mode);
	get_keyval (group_conf, "rotateReference", b_rotate, false, mode);

	if (b_center \|\| b_rotate) {

	if (b_dummy)
	cvm::fatal_error ("Error: cannot set \"centerReference\" or "
	"\"rotateReference\" with \"dummyAtom\".\n");

	// use refPositionsGroup instead of this group as the one which is
	// used to fit the coordinates
	if (key_lookup (group_conf, "refPositionsGroup")) {
	if (ref_pos_group) {
	cvm::fatal_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");
	}

	atom_group *ag = ref_pos_group ? ref_pos_group : this;

	if (get_keyval (group_conf, "refPositions", ref_pos, ref_pos, mode)) {
	cvm::log ("Using reference positions from input file.\n");
	if (ref_pos.size() != ag->size()) {
	cvm::fatal_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 (ag->size())+").\n");
	}
	}

	std::string ref_pos_file;
	if (get_keyval (group_conf, "refPositionsFile", ref_pos_file, std::string (""), mode)) {

	if (ref_pos.size()) {
	cvm::fatal_error ("Error: cannot specify \"refPositionsFile\" and "
	"\"refPositions\" at the same time.\n");
	}

	std::string ref_pos_col;
	double ref_pos_col_value;

	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)
	cvm::fatal_error ("Error: refPositionsColValue, "
	"if provided, must be non-zero.\n");
	} else {
	// if not, rely on existing atom indices for the group
	ag->create_sorted_ids();
	}
	cvm::load_coords (ref_pos_file.c_str(), ref_pos, ag->sorted_ids,
	ref_pos_col, ref_pos_col_value);
	}

	if (ref_pos.size()) {

	if (b_rotate) {
	if (ref_pos.size() != ag->size())
	cvm::fatal_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 (ag->size())+").\n");
	}

	// save the center of mass of ref_pos and then subtract it from
	// them; in this way it is possible to use the coordinates for
	// the rotational fit, if needed
	ref_pos_cog = cvm::atom_pos (0.0, 0.0, 0.0);
	std::vector<cvm::atom_pos>::iterator pi = ref_pos.begin();
	for ( ; pi != ref_pos.end(); pi++) {
	ref_pos_cog += *pi;
	}
	ref_pos_cog /= (cvm::real) ref_pos.size();

	for (std::vector<cvm::atom_pos>::iterator pi = ref_pos.begin();
	pi != ref_pos.end(); pi++) {
	(*pi) -= ref_pos_cog;
	}
	} else {
	#if (! defined (COLVARS_STANDALONE))
	if (!cvm::b_analysis)
	cvm::fatal_error ("Error: no reference positions provided.\n");
	#endif
	}

	if (b_rotate && !noforce) {
	cvm::log ("Warning: atom group \""+std::string (key)+
	"\" is set to be rotated to a reference orientation: "
	"a torque different than zero on this group "
	"could make the simulation unstable. "
	"If this happens, set \"disableForces\" to yes "
	"for this group.\n");
	}

	}


	if (cvm::debug())
	cvm::log ("Done initializing atom group with name \""+
	std::string (key)+"\".\n");

	this->check_keywords (group_conf, key);

	cvm::log ("Atom group \""+std::string (key)+"\" defined, "+
	cvm::to_str (this->size())+" initialized: total mass = "+
	cvm::to_str (this->total_mass)+".\n");

	cvm::decrease_depth();
	}


	cvm::atom_group::atom_group (std::vector<cvm::atom> const &atoms)
	: b_dummy (false), b_center (false), b_rotate (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),
	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::fatal_error ("Error: cannot add atoms to a dummy group.\n");
	} else {
	this->push_back (a);
	total_mass += a.mass;
	}
	}


	void cvm::atom_group::create_sorted_ids (void)
	{
	// Only do the work if the vector is not yet populated
	if (sorted_ids.size())
	return;

	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::fatal_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");
	}
	sorted_ids = std::vector<int> (temp_id_list.begin(), temp_id_list.end());
	return;
	}


	void cvm::atom_group::read_positions()
	{
	if (b_dummy) return;

	#if (! defined (COLVARS_STANDALONE))
	if (!this->size())
	cvm::fatal_error ("Error: no atoms defined in the requested group.\n");
	#endif

	for (cvm::atom_iter ai = this->begin();
	ai != this->end(); ai++) {
	ai->read_position();
	}

	if (ref_pos_group)
	ref_pos_group->read_positions();

	atom_group *fit_group = ref_pos_group ? ref_pos_group : this;

	if (b_center) {
	// store aside the current center of geometry (all positions will be
	// set to the closest images to the first one) and then center on
	// the origin
	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); store the rotation, in
	// order to bring back the forces to the original frame before
	// applying them
	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) {
	// use 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 (cvm::atom_pos const &ref_pos)
	{
	if (b_dummy) {
	cvm::select_closest_image (dummy_atom_pos, ref_pos);
	return dummy_atom_pos;
	}

	cvm::atom_pos cog (0.0, 0.0, 0.0);
	for (cvm::atom_iter ai = this->begin();
	ai != this->end(); ai++) {
	cvm::select_closest_image (ai->pos, ref_pos);
	cog += ai->pos;
	}
	cog /= this->size();
	return cog;
	}

	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 (cvm::atom_pos const &ref_pos)
	{
	if (b_dummy) {
	cvm::select_closest_image (dummy_atom_pos, ref_pos);
	return dummy_atom_pos;
	}

	cvm::atom_pos com (0.0, 0.0, 0.0);
	for (cvm::atom_iter ai = this->begin();
	ai != this->end(); ai++) {
	cvm::select_closest_image (ai->pos, ref_pos);
	com += ai->mass * ai->pos;
	}
	com /= this->total_mass;
	return com;
	}

	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;
	}
	}


	std::vector<cvm::atom_pos> cvm::atom_group::positions() const
	{
	if (b_dummy)
	cvm::fatal_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::fatal_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::fatal_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::fatal_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::fatal_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::fatal_error ("Error: sending a force to a group that has "
	"\"disableForces\" defined.\n");

	if (b_rotate) {

	// get the forces back from the rotated 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 {

	// no need to manipulate gradients, they are still in the original
	// frame
	for (cvm::atom_iter ai = this->begin();
	ai != this->end(); ai++) {
	ai->apply_force (force * ai->grad);
	}
	}
	}


	void cvm::atom_group::apply_force (cvm::rvector const &force)
	{
	if (b_dummy)
	return;

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

	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::fatal_error ("Error: sending a force to a group that has "
	"\"disableForces\" defined.\n");

	if (forces.size() != this->size()) {
	cvm::fatal_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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