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)
	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)
	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, calc_apply_roto_translation() will be called too.
void	calc_apply_roto_translation ()
	(Re)calculate the optimal roto-translation
void	center_ref_pos ()
	Save center of geometry fo ref positions, then subtract it.
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 () const
	Return the center of geometry of the positions, assuming that coordinates are already pbc-wrapped.
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	calc_fit_gradients ()
	Calculate the derivatives of the fitting transformation.
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
	When updating atomic coordinates, translate them to align with the center of mass of the reference coordinates.
bool	b_rotate
	When updating atom coordinates (and after centering them if b_center is set), rotate the group to align with the reference coordinates.
cvm::rotation	rot
	The rotation calculated automatically if b_rotate is defined.
bool	b_user_defined_fit
	Indicates that the user has explicitly set centerReference or rotateReference, and the corresponding reference: cvc's (eg rmsd, eigenvector) will not override the user's choice.
bool	b_fit_gradients
	Whether or not the derivatives of the roto-translation should be included when calculating the colvar's gradients (default: no).
std::vector< cvm::atom_pos >	ref_pos
	use reference coordinates for b_center or b_rotate
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
	If b_center or b_rotate is true, use this group to define the transformation (default: this 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
	Atom positions at the previous step.
std::vector< cvm::atom_pos >	fit_gradients
	Derivatives of the fitting transformation.

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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 119 of file colvaratoms.h.

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Constructor & Destructor Documentation

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

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 14 of file colvaratoms.C. References colvarmodule::log(), and parse(). : b_center (false), b_rotate (false), b_user_defined_fit (false), ref_pos_group (NULL), b_fit_gradients (false), noforce (false) { cvm::log ("Defining atom group \""+ std::string (key)+"\".\n"); // real work is done by parse parse (conf, key); }

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

Initialize the group after a temporary vector of atoms. Definition at line 28 of file colvaratoms.C. References total_mass. : b_dummy (false), b_center (false), b_rotate (false), ref_pos_group (NULL), b_fit_gradients (false), 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 45 of file colvaratoms.C. References total_mass. Referenced by parse(). : b_dummy (false), b_center (false), b_rotate (false), ref_pos_group (NULL), b_fit_gradients (false), noforce (false) { total_mass = 0.0; }

cvm::atom_group::~atom_group (   )

Destructor. Definition at line 54 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 63 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 rotated to the original frame. Definition at line 719 of file colvaratoms.C. References b_center, colvarmodule::fatal_error(), fit_gradients, colvarmodule::rotation::inverse(), j, ref_pos_group, 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::rmsd::apply_force(), colvar::inertia_z::apply_force(), colvar::inertia::apply_force(), colvar::gyration::apply_force(), colvar::distance_inv::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 " "\"enableForces\" set to off.\n"); if (b_rotate) { // rotate forces back to the original frame cvm::rotation const rot_inv = rot.inverse(); for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) { ai->apply_force (rot_inv.rotate (force * ai->grad)); } } else { for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) { ai->apply_force (force * ai->grad); } } if ((b_center || b_rotate) && b_fit_gradients) { atom_group *group_for_fit = ref_pos_group ? ref_pos_group : this; // add the contribution from the roto-translational fit to the gradients if (b_rotate) { // rotate forces back to the original frame cvm::rotation const rot_inv = rot.inverse(); for (size_t j = 0; j < group_for_fit->size(); j++) { (*group_for_fit)[j].apply_force (rot_inv.rotate (force * group_for_fit->fit_gradients[j])); } } else { for (size_t j = 0; j < group_for_fit->size(); j++) { (*group_for_fit)[j].apply_force (force * group_for_fit->fit_gradients[j]); } } } }

void cvm::atom_group::apply_force (  cvm::rvector const &  force  )

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 766 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 793 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 499 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 489 of file colvaratoms.C. { if (b_dummy) return; for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) { ai->pos += t; } }

void cvm::atom_group::calc_apply_roto_translation (   )

(Re)calculate the optimal roto-translation Definition at line 456 of file colvaratoms.C. References colvarmodule::atom_pos, colvarmodule::rotation::calc_optimal_rotation(), center_of_geometry(), positions(), ref_pos_group, rot, and colvarmodule::rotation::rotate(). Referenced by colvar::calc(), and colvar::cvc::debug_gradients(). { atom_group *fit_group = ref_pos_group ? ref_pos_group : this; if (b_center) { // center on the origin first cvm::atom_pos const cog = fit_group->center_of_geometry(); for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) { ai->pos -= cog; } } if (b_rotate) { // rotate the group (around the center of geometry if b_center is // true, around the origin otherwise) rot.calc_optimal_rotation (fit_group->positions(), ref_pos); for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) { ai->pos = rot.rotate (ai->pos); } } if (b_center) { // align with the center of geometry of ref_pos for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) { ai->pos += ref_pos_cog; } } }

void cvm::atom_group::calc_fit_gradients (   )

Calculate the derivatives of the fitting transformation. Definition at line 592 of file colvaratoms.C. References colvarmodule::atom_pos, b_center, b_rotate, center_of_geometry(), colvarmodule::debug(), colvarmodule::rotation::dQ0_1, fit_gradients, colvarmodule::rotation::inverse(), j, colvarmodule::log(), colvarmodule::quaternion::position_derivative_inner(), colvarmodule::rotation::q, colvarmodule::real, ref_pos_group, rot, and colvarmodule::rotation::rotate(). Referenced by colvar::cvc::debug_gradients(). { if (b_dummy) return; if ((!b_center) && (!b_rotate)) return; // no fit if (cvm::debug()) cvm::log ("Calculating fit gradients.\n"); atom_group *group_for_fit = ref_pos_group ? ref_pos_group : this; group_for_fit->fit_gradients.assign (group_for_fit->size(), cvm::rvector (0.0, 0.0, 0.0)); if (b_center) { // add the center of geometry contribution to the gradients for (size_t i = 0; i < this->size(); i++) { // need to bring the gradients in original frame first cvm::rvector const atom_grad = b_rotate ? (rot.inverse()).rotate ((*this)[i].grad) : (*this)[i].grad; for (size_t j = 0; j < group_for_fit->size(); j++) { group_for_fit->fit_gradients[j] += (-1.0)/(cvm::real (group_for_fit->size())) * atom_grad; } } } if (b_rotate) { // add the rotation matrix contribution to the gradients cvm::rotation const rot_inv = rot.inverse(); cvm::atom_pos const cog = this->center_of_geometry(); for (size_t i = 0; i < this->size(); i++) { cvm::atom_pos const pos_orig = rot_inv.rotate ((b_center ? ((*this)[i].pos - cog) : ((*this)[i].pos))); for (size_t j = 0; j < group_for_fit->size(); j++) { // calculate \partial(R(q) \vec{x}_i)/\partial q) \cdot \partial\xi/\partial\vec{x}_i cvm::quaternion const dxdq = rot.q.position_derivative_inner (pos_orig, (*this)[i].grad); // multiply by \cdot {\partial q}/\partial\vec{x}_j and add it to the fit gradients for (size_t iq = 0; iq < 4; iq++) { group_for_fit->fit_gradients[j] += dxdq[iq] * rot.dQ0_1[j][iq]; } } } } if (cvm::debug()) cvm::log ("Done calculating fit gradients.\n"); }

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 552 of file colvaratoms.C. References colvarmodule::atom_pos. Referenced by calc_apply_roto_translation(), calc_fit_gradients(), colvar::spin_angle::calc_value(), colvar::tilt::calc_value(), colvar::orientation_angle::calc_value(), and colvar::orientation::calc_value(). { if (b_dummy) return dummy_atom_pos; cvm::atom_pos cog (0.0, 0.0, 0.0); for (cvm::atom_const_iter ai = this->begin(); ai != this->end(); ai++) { cog += ai->pos; } cog /= this->size(); return cog; }

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

Return the center of mass of the positions, assuming that coordinates are already pbc-wrapped. Definition at line 566 of file colvaratoms.C. References colvarmodule::atom_pos. Referenced by colvar::distance_xy::calc_gradients(), colvar::distance_z::calc_gradients(), colvar::coordnum::calc_gradients(), 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) 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::center_ref_pos (   )

Save center of geometry fo ref positions, then subtract it. Definition at line 424 of file colvaratoms.C. References colvarmodule::atom_pos, ref_pos, and ref_pos_cog. Referenced by colvar::eigenvector::eigenvector(), parse(), and colvar::rmsd::rmsd(). { // save the center of geometry of ref_pos and then subtract it from // them; in this way it will be possible to use ref_pos also for // the rotational fit // This is called either by atom_group::parse or by CVCs that set // reference positions (eg. RMSD, eigenvector) ref_pos_cog = cvm::atom_pos (0.0, 0.0, 0.0); std::vector<cvm::atom_pos>::iterator pi = 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; } }

void cvm::atom_group::create_sorted_ids (  void   )

Allocates and populates the sorted list of atom ids. Definition at line 402 of file colvaratoms.C. References colvarmodule::fatal_error(), sorted_ids, and colvarmodule::to_str(). Referenced by colvar::eigenvector::eigenvector(), colvar::orientation::orientation(), parse(), and colvar::rmsd::rmsd(). { // 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 )

Initialize the group by looking up its configuration string in conf and parsing it. Definition at line 74 of file colvaratoms.C. References atom_group(), colvarmodule::atom_pos, b_center, b_dummy, b_fit_gradients, b_rotate, b_user_defined_fit, center_ref_pos(), colvarparse::check_keywords(), create_sorted_ids(), colvarmodule::debug(), colvarmodule::decrease_depth(), dummy_atom_pos, colvarmodule::fatal_error(), fit_gradients, colvarmodule::increase_depth(), colvarparse::key_lookup(), colvarmodule::load_atoms(), colvarmodule::load_coords(), colvarmodule::log(), colvarmodule::atom::mass, noforce, ref_pos, ref_pos_group, colvarmodule::rotation::request_group1_gradients(), rot, 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; // } colvarparse::Parse_Mode mode = parse_normal; { // std::vector<int> atom_indexes; std::string numbers_conf = ""; size_t pos = 0; std::vector<int> atom_indexes; while (key_lookup (group_conf, "atomNumbers", numbers_conf, pos)) { if (numbers_conf.size()) { std::istringstream is (numbers_conf); int ia; while (is >> ia) { atom_indexes.push_back (ia); } } if (atom_indexes.size()) { this->reserve (this->size()+atom_indexes.size()); for (size_t i = 0; i < atom_indexes.size(); i++) { this->push_back (cvm::atom (atom_indexes[i])); } } else cvm::fatal_error ("Error: no numbers provided for \"" "atomNumbers\".\n"); atom_indexes.clear(); } } { 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)) { range_count++; if (range_count > psf_segids.size()) { 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; } } if (!b_dummy) { bool enable_forces = true; // disableForces is deprecated if (get_keyval (group_conf, "enableForces", enable_forces, true, mode)) { noforce = !enable_forces; } else { get_keyval (group_conf, "disableForces", noforce, false, mode); } } // FITTING OPTIONS bool b_defined_center = get_keyval (group_conf, "centerReference", b_center, false, mode); bool b_defined_rotate = get_keyval (group_conf, "rotateReference", b_rotate, false, mode); // is the user setting explicit options? b_user_defined_fit = b_defined_center || b_defined_rotate; get_keyval (group_conf, "enableFitGradients", b_fit_gradients, true, mode); if (b_center || b_rotate) { if (b_dummy) cvm::fatal_error ("Error: centerReference or rotateReference " "cannot be defined for a dummy atom.\n"); if (key_lookup (group_conf, "refPositionsGroup")) { // instead of this group, define another group to compute the fit if (ref_pos_group) { cvm::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 *group_for_fit = ref_pos_group ? ref_pos_group : this; get_keyval (group_conf, "refPositions", ref_pos, ref_pos, mode); std::string ref_pos_file; if (get_keyval (group_conf, "refPositionsFile", ref_pos_file, std::string (""), mode)) { if (ref_pos.size()) { cvm::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 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::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 (group_for_fit->size())+ "): to perform a rotational fit, "+ "these numbers should be equal.\n"); } // save the center of geometry of ref_pos and subtract it center_ref_pos(); } else { #if (! defined (COLVARS_STANDALONE)) cvm::fatal_error ("Error: no reference positions provided.\n"); #endif } if (b_fit_gradients) { group_for_fit->fit_gradients.assign (group_for_fit->size(), cvm::atom_pos (0.0, 0.0, 0.0)); rot.request_group1_gradients (group_for_fit->size()); } if (b_rotate && !noforce) { cvm::log ("Warning: atom group \""+std::string (key)+ "\" will be aligned to a fixed orientation given by the reference positions provided. " "If the internal structure of the group changes too much (i.e. its RMSD is comparable " "to its radius of gyration), the optimal rotation and its gradients may become discontinuous. " "If that happens, use refPositionsGroup (or a different definition for it if already defined) " "to align the coordinates.\n"); // initialize rot member data rot.request_group1_gradients (this->size()); } } if (cvm::debug()) cvm::log ("Done initializing atom group with name \""+ std::string (key)+"\".\n"); this->check_keywords (group_conf, key); cvm::log ("Atom group \""+std::string (key)+"\" defined, "+ cvm::to_str (this->size())+" atoms initialized: total mass = "+ cvm::to_str (this->total_mass)+".\n"); cvm::decrease_depth(); }

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

Return a copy of the current atom positions. Definition at line 645 of file colvaratoms.C. References colvarmodule::fatal_error(). Referenced by calc_apply_roto_translation(). { 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 660 of file colvaratoms.C. References colvarmodule::fatal_error(). Referenced by colvar::spin_angle::calc_value(), colvar::tilt::calc_value(), colvar::orientation_angle::calc_value(), and colvar::orientation::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, calc_apply_roto_translation() will be called too. Definition at line 443 of file colvaratoms.C. References ref_pos_group. Referenced by colvar::calc(), colvar::selfcoordnum::calc_value(), colvar::coordnum::calc_value(), colvar::dihedral::calc_value(), colvar::angle::calc_value(), and colvar::cvc::debug_gradients(). { if (b_dummy) return; for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) { ai->read_position(); } if (ref_pos_group) ref_pos_group->read_positions(); }

void cvm::atom_group::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 531 of file colvaratoms.C. References rot, and colvarmodule::rotation::rotate(). Referenced by colvar::calc(), colvar::eigenvector::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 510 of file colvaratoms.C. References rot, and colvarmodule::rotation::rotate(). Referenced by colvar::calc(). { 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 240 of file colvaratoms.h. References ref_pos_group. Referenced by colvar::calc(), colvar::selfcoordnum::calc_value(), and colvar::coordnum::calc_value(). { for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) ai->reset_data(); if (ref_pos_group) ref_pos_group->reset_atoms_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 581 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 705 of file colvaratoms.C. References colvarmodule::fatal_error(). Referenced by colvar::eigenvector::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 690 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 675 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

When updating atomic coordinates, translate them to align with the center of mass of the reference coordinates. Definition at line 145 of file colvaratoms.h. Referenced by apply_colvar_force(), colvar::calc(), calc_fit_gradients(), colvar::cvc::debug_gradients(), colvar::eigenvector::eigenvector(), colvar::gyration::gyration(), parse(), and colvar::rmsd::rmsd().

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 131 of file colvaratoms.h. Referenced by parse(), and colvar::rmsd::rmsd().

bool colvarmodule::atom_group::b_fit_gradients

Whether or not the derivatives of the roto-translation should be included when calculating the colvar's gradients (default: no). Definition at line 165 of file colvaratoms.h. Referenced by colvar::cvc::debug_gradients(), and parse().

bool colvarmodule::atom_group::b_rotate

When updating atom coordinates (and after centering them if b_center is set), rotate the group to align with the reference coordinates. 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 154 of file colvaratoms.h. Referenced by colvar::calc(), calc_fit_gradients(), colvar::rmsd::calc_Jacobian_derivative(), colvar::cvc::debug_gradients(), colvar::eigenvector::eigenvector(), parse(), and colvar::rmsd::rmsd().

bool colvarmodule::atom_group::b_user_defined_fit

Indicates that the user has explicitly set centerReference or rotateReference, and the corresponding reference: cvc's (eg rmsd, eigenvector) will not override the user's choice. Definition at line 161 of file colvaratoms.h. Referenced by colvar::eigenvector::eigenvector(), colvar::gyration::gyration(), parse(), and colvar::rmsd::rmsd().

cvm::atom_pos colvarmodule::atom_group::dummy_atom_pos

dummy atom position Definition at line 133 of file colvaratoms.h. Referenced by parse().

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

Derivatives of the fitting transformation. Definition at line 285 of file colvaratoms.h. Referenced by apply_colvar_force(), calc_fit_gradients(), colvar::cvc::debug_gradients(), 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 184 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::rmsd::apply_force(), colvar::inertia_z::apply_force(), colvar::inertia::apply_force(), colvar::gyration::apply_force(), colvar::distance_inv::apply_force(), colvar::distance_dir::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

Atom positions at the previous step. Definition at line 263 of file colvaratoms.h.

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

use reference coordinates for b_center or b_rotate Definition at line 168 of file colvaratoms.h. Referenced by center_ref_pos(), colvar::eigenvector::eigenvector(), colvar::gyration::gyration(), parse(), and colvar::rmsd::rmsd().

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 173 of file colvaratoms.h. Referenced by center_ref_pos().

atom_group* colvarmodule::atom_group::ref_pos_group

If b_center or b_rotate is true, use this group to define the transformation (default: this group itself). Definition at line 177 of file colvaratoms.h. Referenced by apply_colvar_force(), calc_apply_roto_translation(), calc_fit_gradients(), colvar::cvc::debug_gradients(), parse(), read_positions(), reset_atoms_data(), colvar::rmsd::rmsd(), and ~atom_group().

cvm::rotation colvarmodule::atom_group::rot

The rotation calculated automatically if b_rotate is defined. Definition at line 156 of file colvaratoms.h. Referenced by apply_colvar_force(), apply_force(), apply_forces(), calc_apply_roto_translation(), calc_fit_gradients(), colvar::eigenvector::calc_Jacobian_derivative(), colvar::rmsd::calc_Jacobian_derivative(), colvar::cvc::debug_gradients(), colvar::eigenvector::eigenvector(), parse(), read_system_forces(), read_velocities(), and colvar::rmsd::rmsd().

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 137 of file colvaratoms.h. Referenced by create_sorted_ids(), colvar::eigenvector::eigenvector(), colvar::orientation::orientation(), parse(), and colvar::rmsd::rmsd().

cvm::real colvarmodule::atom_group::total_mass

Total mass of the atom group. Definition at line 180 of file colvaratoms.h. Referenced by add_atom(), atom_group(), colvar::dihedral::calc_gradients(), colvar::angle::calc_gradients(), 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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