colvarmodule::atom_group Class Reference

Group of objects, mostly used by a . More...

#include <colvaratoms.h>

Inheritance diagram for colvarmodule::atom_group:

List of all members.

Public Member Functions
void	create_sorted_ids (void)
	Allocates and populates the sorted list of atom ids.
	atom_group (std::string const &conf, char const *key, atom_group *ref_pos_group=NULL)
	Initialize the group by looking up its configuration string in conf and parsing it; this is actually done by parse(), which is a member function so that a group can be initialized also after construction.
void	parse (std::string const &conf, char const *key, atom_group *ref_pos_group=NULL)
	Initialize the group by looking up its configuration string in conf and parsing it.
	atom_group (std::vector< cvm::atom > const &atoms)
	Initialize the group after a temporary vector of atoms.
void	add_atom (cvm::atom const &a)
	Add an atom to this group.
	atom_group ()
	Default constructor.
	~atom_group ()
	Destructor.
void	read_positions ()
	Get the current positions; if b_center or b_rotate are true, center and/or rotate the coordinates right after reading them.
void	apply_translation (cvm::rvector const &t)
	Move all positions.
void	apply_rotation (cvm::rotation const &q)
	Rotate all positions.
void	read_velocities ()
	Get the current velocities; this must be called always after* read_positions(); if b_rotate is defined, the same rotation applied to the coordinates will be used.
void	read_system_forces ()
	Get the current system_forces; this must be called always after* read_positions(); if b_rotate is defined, the same rotation applied to the coordinates will be used.
void	reset_atoms_data ()
	Call reset_data() for each atom.
std::vector< cvm::atom_pos >	positions () const
	Return a copy of the current atom positions.
std::vector< cvm::atom_pos >	positions_shifted (cvm::rvector const &shift) const
	Return a copy of the current atom positions, shifted by a constant vector.
cvm::atom_pos	center_of_geometry (cvm::atom_pos const &ref_pos)
	Return the center of geometry of the positions.
cvm::atom_pos	center_of_geometry () const
	Return the center of geometry of the positions, assuming that coordinates are already pbc-wrapped.
cvm::atom_pos	center_of_mass (cvm::atom_pos const &ref_pos)
	Return the center of mass of the positions.
cvm::atom_pos	center_of_mass () const
	Return the center of mass of the positions, assuming that coordinates are already pbc-wrapped.
std::vector< cvm::rvector >	velocities () const
	Return a copy of the current atom velocities.
std::vector< cvm::rvector >	system_forces () const
	Return a copy of the system forces.
cvm::rvector	system_force () const
	Return a copy of the aggregated total force on the group.
void	set_weighted_gradient (cvm::rvector const &grad)
	Shorthand: save the specified gradient on each atom, weighting with the atom mass (mostly used in combination with ).
void	apply_colvar_force (cvm::real const &force)
	Used by a (scalar) colvar to apply its force on its members.
void	apply_force (cvm::rvector const &force)
	Apply a force "to the center of mass", i.e. the force is distributed on each atom according to its mass.
void	apply_forces (std::vector< cvm::rvector > const &forces)
	Apply an array of forces directly on the individual atoms; the length of the specified vector must be the same of this .
Public Attributes
bool	b_dummy
	If this option is on, this group merely acts as a wrapper for a fixed position; any calls to atoms within or to functions that return disaggregated data will fail.
cvm::atom_pos	dummy_atom_pos
	dummy atom position
std::vector< int >	sorted_ids
bool	b_center
	Before calculating colvars, move the group to overlap the center of mass of reference coordinates.
bool	b_rotate
	Right after updating atom coordinates (and after centering coordinates, if b_center is true), rotate the group to overlap the reference coordinates. You should not manipulate atoms individually if you turn on this flag.
cvm::rotation	rot
	Rotation between the group and its reference coordinates.
std::vector< cvm::atom_pos >	ref_pos
	In case b_center or b_rotate is true, use these reference coordinates.
cvm::atom_pos	ref_pos_cog
	Center of geometry of the reference coordinates; regardless of whether b_center is true, ref_pos is centered to zero at initialization, and ref_pos_cog serves to center the positions.
atom_group *	ref_pos_group
	In case b_center or b_rotate is true, fit this group to the reference positions (default: the parent group itself).
cvm::real	total_mass
	Total mass of the atom group.
bool	noforce
	Don't apply any force on this group (use its coordinates only to calculate a colvar).
std::vector< cvm::atom_pos >	old_pos
	Store atom positions from the previous step.

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Detailed Description

Group of objects, mostly used by a .

This class inherits from and from std::vector<colvarmodule::atom>, and hence all functions and operators (including the bracket operator, group[i]) can be used on an object. It can be initialized as a vector, or by parsing a keyword in the configuration.

Definition at line 117 of file colvaratoms.h.

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Constructor & Destructor Documentation

cvm::atom_group::atom_group (  std::string const &  conf, char const *  key, atom_group *  ref_pos_group = NULL )

Initialize the group by looking up its configuration string in conf and parsing it; this is actually done by parse(), which is a member function so that a group can be initialized also after construction. Definition at line 12 of file colvaratoms.C. References colvarmodule::log(), and parse(). : 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); }

cvm::atom_group::atom_group (  std::vector< cvm::atom > const &  atoms  )

Initialize the group after a temporary vector of atoms. Definition at line 339 of file colvaratoms.C. References total_mass. : 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 (   )

Default constructor. Definition at line 355 of file colvaratoms.C. References total_mass. Referenced by parse(). : b_dummy (false), b_center (false), b_rotate (false), ref_pos_group (NULL), noforce (false) { total_mass = 0.0; }

cvm::atom_group::~atom_group (   )

Destructor. Definition at line 363 of file colvaratoms.C. References ref_pos_group. { if (ref_pos_group) { delete ref_pos_group; ref_pos_group = NULL; } }

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Member Function Documentation

void cvm::atom_group::add_atom (  cvm::atom const &  a  )

Add an atom to this group. Definition at line 372 of file colvaratoms.C. References colvarmodule::fatal_error(), colvarmodule::atom::mass, and total_mass. { 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::apply_colvar_force (  cvm::real const &  force  )

Used by a (scalar) colvar to apply its force on its members. The (scalar) force is multiplied by the colvar gradient for each atom; this should be used when a colvar with scalar type is used (this is the most frequent case: for colvars with a non-scalar type, the most convenient solution is to sum together the Cartesian forces from all the colvar components, and use apply_force() or apply_forces()). If the group is being rotated to a reference frame (e.g. to express the colvar independently from the solute rotation), the gradients are temporarily to the original frame. Definition at line 671 of file colvaratoms.C. References colvarmodule::fatal_error(), colvarmodule::rotation::inverse(), rot, and colvarmodule::rotation::rotate(). Referenced by colvar::spin_angle::apply_force(), colvar::tilt::apply_force(), colvar::orientation_angle::apply_force(), colvar::eigenvector::apply_force(), colvar::logmsd::apply_force(), colvar::rmsd::apply_force(), colvar::gyration::apply_force(), colvar::min_distance::apply_force(), colvar::distance_xy::apply_force(), colvar::distance_z::apply_force(), colvar::distance::apply_force(), colvar::selfcoordnum::apply_force(), colvar::coordnum::apply_force(), colvar::dihedral::apply_force(), and colvar::angle::apply_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  )

Apply a force "to the center of mass", i.e. the force is distributed on each atom according to its mass. If the group is being rotated to a reference frame (e.g. to express the colvar independently from the solute rotation), the force is rotated back to the original frame. Colvar gradients are not used, either because they were not defined (e.g because the colvar has not a scalar value) or the biases require to micromanage the force. Definition at line 701 of file colvaratoms.C. References colvarmodule::fatal_error(), colvarmodule::rotation::inverse(), rot, and colvarmodule::rotation::rotate(). Referenced by colvar::orientation::apply_force(), colvar::distance_dir::apply_force(), and colvar::distance_vec::apply_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  )

Apply an array of forces directly on the individual atoms; the length of the specified vector must be the same of this . If the group is being rotated to a reference frame (e.g. to express the colvar independently from the solute rotation), the forces are rotated back to the original frame. Colvar gradients are not used, either because they were not defined (e.g because the colvar has not a scalar value) or the biases require to micromanage the forces. Definition at line 728 of file colvaratoms.C. References colvarmodule::fatal_error(), colvarmodule::rotation::inverse(), rot, and colvarmodule::rotation::rotate(). { 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); } } }

void cvm::atom_group::apply_rotation (  cvm::rotation const &  q  )

Rotate all positions. Definition at line 470 of file colvaratoms.C. References colvarmodule::rotation::rotate(). { 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::apply_translation (  cvm::rvector const &  t  )

Move all positions. Definition at line 459 of file colvaratoms.C. Referenced by colvar::gyration::calc_value(). { if (b_dummy) return; for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) { ai->pos += t; } }

cvm::atom_pos cvm::atom_group::center_of_geometry (   )  const

Return the center of geometry of the positions, assuming that coordinates are already pbc-wrapped. Definition at line 540 of file colvaratoms.C. References colvarmodule::atom_pos. { 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_geometry (  cvm::atom_pos const &  ref_pos  )

Return the center of geometry of the positions. Parameters: ref_pos  Use the closest periodic images to this position Definition at line 523 of file colvaratoms.C. References colvarmodule::atom_pos, dummy_atom_pos, and colvarmodule::select_closest_image(). Referenced by colvar::spin_angle::calc_value(), colvar::tilt::calc_value(), colvar::orientation_angle::calc_value(), colvar::orientation::calc_value(), colvar::logmsd::calc_value(), colvar::rmsd::calc_value(), colvar::gyration::calc_value(), and read_positions(). { 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_mass (   )  const

Return the center of mass of the positions, assuming that coordinates are already pbc-wrapped. Definition at line 571 of file colvaratoms.C. References colvarmodule::atom_pos. { 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; }

cvm::atom_pos cvm::atom_group::center_of_mass (  cvm::atom_pos const &  ref_pos  )

Return the center of mass of the positions. Parameters: ref_pos  Use the closest periodic images to this position Definition at line 554 of file colvaratoms.C. References colvarmodule::atom_pos, dummy_atom_pos, and colvarmodule::select_closest_image(). Referenced by colvar::distance_xy::calc_gradients(), colvar::distance_z::calc_gradients(), colvar::coordnum::calc_gradients(), colvar::logmsd::calc_value(), colvar::distance_dir::calc_value(), colvar::distance_xy::calc_value(), colvar::distance_z::calc_value(), colvar::distance_vec::calc_value(), colvar::distance::calc_value(), colvar::coordnum::calc_value(), colvar::dihedral::calc_value(), and colvar::angle::calc_value(). { 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; }

void cvm::atom_group::create_sorted_ids (  void   )

Allocates and populates the sorted list of atom ids. Definition at line 383 of file colvaratoms.C. References colvarmodule::fatal_error(), sorted_ids, and colvarmodule::to_str(). Referenced by colvar::eigenvector::eigenvector(), colvar::orientation::orientation(), and parse(). { // 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::parse (  std::string const &  conf, char const *  key, atom_group *  ref_pos_group = NULL )

Initialize the group by looking up its configuration string in conf and parsing it. Definition at line 26 of file colvaratoms.C. References atom_group(), colvarmodule::atom_pos, b_center, b_dummy, b_rotate, colvarparse::check_keywords(), create_sorted_ids(), colvarmodule::debug(), colvarmodule::decrease_depth(), dummy_atom_pos, colvarmodule::fatal_error(), colvarmodule::increase_depth(), colvarparse::key_lookup(), colvarmodule::load_atoms(), colvarmodule::load_coords(), colvarmodule::log(), noforce, ref_pos, ref_pos_cog, ref_pos_group, sorted_ids, colvarmodule::to_str(), and total_mass. Referenced by atom_group(), and colvar::cvc::parse_group(). { 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(); }

std::vector< cvm::atom_pos > cvm::atom_group::positions (   )  const

Return a copy of the current atom positions. Definition at line 597 of file colvaratoms.C. References colvarmodule::fatal_error(). Referenced by colvar::cvc::fdiff_change(), and read_positions(). { 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

Return a copy of the current atom positions, shifted by a constant vector. Definition at line 612 of file colvaratoms.C. References colvarmodule::fatal_error(). Referenced by colvar::spin_angle::calc_gradients(), colvar::tilt::calc_gradients(), colvar::spin_angle::calc_value(), colvar::tilt::calc_value(), colvar::orientation_angle::calc_value(), colvar::orientation::calc_value(), colvar::logmsd::calc_value(), and colvar::rmsd::calc_value(). { 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; }

void cvm::atom_group::read_positions (   )

Get the current positions; if b_center or b_rotate are true, center and/or rotate the coordinates right after reading them. Definition at line 406 of file colvaratoms.C. References colvarmodule::atom_pos, colvarmodule::rotation::calc_optimal_rotation(), center_of_geometry(), colvarmodule::fatal_error(), positions(), colvarmodule::atom::read_position(), ref_pos_group, rot, and colvarmodule::rotation::rotate(). Referenced by colvar::spin_angle::calc_value(), colvar::tilt::calc_value(), colvar::orientation_angle::calc_value(), colvar::orientation::calc_value(), colvar::eigenvector::calc_value(), colvar::logmsd::calc_value(), colvar::rmsd::calc_value(), colvar::gyration::calc_value(), colvar::distance_dir::calc_value(), colvar::min_distance::calc_value(), colvar::distance_xy::calc_value(), colvar::distance_z::calc_value(), colvar::distance_vec::calc_value(), colvar::distance::calc_value(), colvar::selfcoordnum::calc_value(), colvar::coordnum::calc_value(), colvar::dihedral::calc_value(), and colvar::angle::calc_value(). { 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::read_system_forces (   )

Get the current system_forces; this must be called always after* read_positions(); if b_rotate is defined, the same rotation applied to the coordinates will be used. Definition at line 502 of file colvaratoms.C. References rot, and colvarmodule::rotation::rotate(). Referenced by colvar::eigenvector::calc_force_invgrads(), colvar::logmsd::calc_force_invgrads(), colvar::rmsd::calc_force_invgrads(), colvar::gyration::calc_force_invgrads(), colvar::distance_xy::calc_force_invgrads(), colvar::distance_z::calc_force_invgrads(), colvar::distance::calc_force_invgrads(), colvar::dihedral::calc_force_invgrads(), and colvar::angle::calc_force_invgrads(). { 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(); } } }

void cvm::atom_group::read_velocities (   )

Get the current velocities; this must be called always after* read_positions(); if b_rotate is defined, the same rotation applied to the coordinates will be used. Definition at line 481 of file colvaratoms.C. References rot, and colvarmodule::rotation::rotate(). { 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 colvarmodule::atom_group::reset_atoms_data (   )  [inline]

Call reset_data() for each atom. Definition at line 226 of file colvaratoms.h. Referenced by colvar::spin_angle::calc_value(), colvar::tilt::calc_value(), colvar::orientation_angle::calc_value(), colvar::orientation::calc_value(), colvar::eigenvector::calc_value(), colvar::logmsd::calc_value(), colvar::rmsd::calc_value(), colvar::gyration::calc_value(), colvar::distance_dir::calc_value(), colvar::min_distance::calc_value(), colvar::distance_xy::calc_value(), colvar::distance_z::calc_value(), colvar::distance_vec::calc_value(), colvar::distance::calc_value(), colvar::selfcoordnum::calc_value(), and colvar::coordnum::calc_value(). { for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) ai->reset_data(); }

void cvm::atom_group::set_weighted_gradient (  cvm::rvector const &  grad  )

Shorthand: save the specified gradient on each atom, weighting with the atom mass (mostly used in combination with ). Definition at line 586 of file colvaratoms.C. Referenced by colvar::distance_xy::calc_gradients(), colvar::distance_z::calc_gradients(), colvar::distance::calc_gradients(), and colvar::coordnum::calc_gradients(). { if (b_dummy) return; for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) { ai->grad = (ai->mass/this->total_mass) * grad; } }

cvm::rvector cvm::atom_group::system_force (   )  const

Return a copy of the aggregated total force on the group. Definition at line 657 of file colvaratoms.C. References colvarmodule::fatal_error(). Referenced by colvar::eigenvector::calc_force_invgrads(), colvar::logmsd::calc_force_invgrads(), colvar::rmsd::calc_force_invgrads(), colvar::distance_xy::calc_force_invgrads(), colvar::distance_z::calc_force_invgrads(), colvar::distance::calc_force_invgrads(), colvar::dihedral::calc_force_invgrads(), and colvar::angle::calc_force_invgrads(). { 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; }

std::vector< cvm::rvector > cvm::atom_group::system_forces (   )  const

Return a copy of the system forces. Definition at line 642 of file colvaratoms.C. References colvarmodule::fatal_error(). { 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; }

std::vector< cvm::rvector > cvm::atom_group::velocities (   )  const

Return a copy of the current atom velocities. Definition at line 627 of file colvaratoms.C. References colvarmodule::fatal_error(). { 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; }

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Member Data Documentation

bool colvarmodule::atom_group::b_center

Before calculating colvars, move the group to overlap the center of mass of reference coordinates. Definition at line 143 of file colvaratoms.h. Referenced by colvar::eigenvector::eigenvector(), and parse().

bool colvarmodule::atom_group::b_dummy

If this option is on, this group merely acts as a wrapper for a fixed position; any calls to atoms within or to functions that return disaggregated data will fail. Definition at line 129 of file colvaratoms.h. Referenced by parse().

bool colvarmodule::atom_group::b_rotate

Right after updating atom coordinates (and after centering coordinates, if b_center is true), rotate the group to overlap the reference coordinates. You should not manipulate atoms individually if you turn on this flag. Note: gradients will be calculated in the rotated frame: when forces will be applied, they will rotated back to the original frame Definition at line 153 of file colvaratoms.h. Referenced by colvar::eigenvector::eigenvector(), and parse().

cvm::atom_pos colvarmodule::atom_group::dummy_atom_pos

dummy atom position Definition at line 131 of file colvaratoms.h. Referenced by center_of_geometry(), center_of_mass(), and parse().

bool colvarmodule::atom_group::noforce

Don't apply any force on this group (use its coordinates only to calculate a colvar). Definition at line 174 of file colvaratoms.h. Referenced by colvar::spin_angle::apply_force(), colvar::tilt::apply_force(), colvar::orientation_angle::apply_force(), colvar::orientation::apply_force(), colvar::eigenvector::apply_force(), colvar::logmsd::apply_force(), colvar::rmsd::apply_force(), colvar::gyration::apply_force(), colvar::distance_dir::apply_force(), colvar::min_distance::apply_force(), colvar::distance_xy::apply_force(), colvar::distance_z::apply_force(), colvar::distance_vec::apply_force(), colvar::distance::apply_force(), colvar::selfcoordnum::apply_force(), colvar::coordnum::apply_force(), colvar::dihedral::apply_force(), colvar::angle::apply_force(), colvar::orientation::orientation(), and parse().

std::vector<cvm::atom_pos> colvarmodule::atom_group::old_pos

Store atom positions from the previous step. Definition at line 253 of file colvaratoms.h. Referenced by colvar::cvc::fdiff_change().

std::vector<cvm::atom_pos> colvarmodule::atom_group::ref_pos

In case b_center or b_rotate is true, use these reference coordinates. Definition at line 159 of file colvaratoms.h. Referenced by colvar::eigenvector::eigenvector(), and parse().

cvm::atom_pos colvarmodule::atom_group::ref_pos_cog

Center of geometry of the reference coordinates; regardless of whether b_center is true, ref_pos is centered to zero at initialization, and ref_pos_cog serves to center the positions. Definition at line 163 of file colvaratoms.h. Referenced by parse().

atom_group* colvarmodule::atom_group::ref_pos_group

In case b_center or b_rotate is true, fit this group to the reference positions (default: the parent group itself). Definition at line 166 of file colvaratoms.h. Referenced by parse(), read_positions(), and ~atom_group().

cvm::rotation colvarmodule::atom_group::rot

Rotation between the group and its reference coordinates. Definition at line 155 of file colvaratoms.h. Referenced by apply_colvar_force(), apply_force(), apply_forces(), colvar::eigenvector::calc_Jacobian_derivative(), colvar::eigenvector::eigenvector(), read_positions(), read_system_forces(), and read_velocities().

std::vector<int> colvarmodule::atom_group::sorted_ids

Sorted list of zero-based (internal) atom ids (populated on-demand by create_sorted_ids) Definition at line 135 of file colvaratoms.h. Referenced by create_sorted_ids(), colvar::eigenvector::eigenvector(), colvar::orientation::orientation(), and parse().

cvm::real colvarmodule::atom_group::total_mass

Total mass of the atom group. Definition at line 170 of file colvaratoms.h. Referenced by add_atom(), atom_group(), colvar::dihedral::calc_gradients(), colvar::angle::calc_gradients(), colvar::gyration::calc_value(), and parse().

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The documentation for this class was generated from the following files:

• colvaratoms.h
• colvaratoms.C

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