colvarmodule::atom Class Reference

Stores numeric id, mass and all mutable data for an atom, mostly used by a . More...

#include <colvaratoms.h>

List of all members.

Public Member Functions
	atom ()
	Default constructor, setting id to a non-valid value.
	atom (int const &atom_number)
	Initialize an atom for collective variable calculation and get its internal identifier.
	atom (cvm::residue_id const &residue, std::string const &atom_name, std::string const &segment_id)
	Initialize an atom for collective variable calculation and get its internal identifier.
	atom (atom const &a)
	Copy constructor.
	~atom ()
	Destructor.
void	reset_data ()
	Set non-constant data (everything except id and mass) to zero.
void	read_position ()
	Get the current position.
void	read_velocity ()
	Get the current velocity.
void	read_system_force ()
	Get the system force.
void	apply_force (cvm::rvector const &new_force)
	Apply a force to the atom.
Public Attributes
int	id
	Internal identifier.
cvm::real	mass
	Mass.
cvm::atom_pos	pos
	Current position (copied from the program, can be manipulated).
cvm::rvector	vel
	Current velocity (copied from the program, can be manipulated).
cvm::rvector	system_force
	System force at the previous step (copied from the program, can be manipulated).
cvm::rvector	grad
	Gradient of a scalar collective variable with respect to this atom.
Protected Attributes
size_t	index
	Index in the list of atoms involved by the colvars (NOT in the global topology!).

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Detailed Description

Stores numeric id, mass and all mutable data for an atom, mostly used by a .

This class may be used (although not necessarily) to keep atomic data (id, mass, position and collective variable derivatives) altogether. There may be multiple instances with identical numeric id, all acting independently: forces communicated through these instances will be summed together.

Read/write operations depend on the underlying code: hence, some member functions are defined in colvarproxy_xxx.h.

Definition at line 18 of file colvaratoms.h.

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Constructor & Destructor Documentation

colvarmodule::atom::atom (   )  [inline]

Default constructor, setting id to a non-valid value. Definition at line 59 of file colvaratoms.h. {}

cvm::atom::atom (  int const &  atom_number  )

Initialize an atom for collective variable calculation and get its internal identifier. Parameters: atom_number  Atom index in the system topology (starting from 1) Definition at line 439 of file colvarproxy_namd.C. References AtomID, Molecule::atommass(), colvarmodule::debug(), colvarmodule::fatal_error(), index, colvarmodule::log(), mass, Node::molecule, Molecule::numAtoms, Node::Object(), and reset_data(). { // NAMD internal numbering starts from zero AtomID const aid (atom_number-1); if (cvm::debug()) cvm::log ("Adding atom "+cvm::to_str (aid+1)+ " for collective variables calculation.\n"); if ( (aid < 0) || (aid >= Node::Object()->molecule->numAtoms) ) cvm::fatal_error ("Error: invalid atom number specified, "+ cvm::to_str (atom_number)+"\n"); this->index = ((colvarproxy_namd *) cvm::proxy)->init_namd_atom (aid); if (cvm::debug()) cvm::log ("The index of this atom in the colvarproxy_namd arrays is "+ cvm::to_str (this->index)+".\n"); this->id = aid; this->mass = Node::Object()->molecule->atommass (aid); this->reset_data(); }

cvm::atom::atom (  cvm::residue_id const &  residue, std::string const &  atom_name, std::string const &  segment_id )

Initialize an atom for collective variable calculation and get its internal identifier. Parameters: residue  Residue number atom_name  Name of the atom in the residue segment_id  For PSF topologies, the segment identifier; for other type of topologies, may not be required Definition at line 464 of file colvarproxy_namd.C. References AtomID, Molecule::atommass(), colvarmodule::debug(), colvarmodule::fatal_error(), Molecule::get_atom_from_name(), index, colvarmodule::log(), mass, Node::molecule, Node::Object(), and reset_data(). { AtomID const aid = Node::Object()->molecule->get_atom_from_name (segment_id.c_str(), residue, atom_name.c_str()); if (cvm::debug()) cvm::log ("Adding atom \""+ atom_name+"\" in residue "+ cvm::to_str (residue)+ " (index "+cvm::to_str (aid)+ ") for collective variables calculation.\n"); if (aid < 0) { // get_atom_from_name() has returned an error value cvm::fatal_error ("Error: could not find atom \""+ atom_name+"\" in residue "+ cvm::to_str (residue)+ ( (segment_id != "MAIN") ? (", segment \""+segment_id+"\"") : ("") )+ "\n"); } this->index = ((colvarproxy_namd *) cvm::proxy)->init_namd_atom (aid); if (cvm::debug()) cvm::log ("The index of this atom in the colvarproxy_namd arrays is "+ cvm::to_str (this->index)+".\n"); this->id = aid; this->mass = Node::Object()->molecule->atommass (aid); this->reset_data(); }

cvm::atom::atom (  atom const &  a  )

Copy constructor. Definition at line 502 of file colvarproxy_namd.C. References colvarproxy_namd::colvars_atoms_ncopies. : index (a.index), id (a.id), mass (a.mass) { // init_namd_atom() has already been called by a's constructor, no // need to call it again // need to increment the counter anyway colvarproxy_namd *gm = (colvarproxy_namd *) cvm::proxy; gm->colvars_atoms_ncopies[this->index] += 1; }

cvm::atom::~atom (   )

Destructor. Definition at line 514 of file colvarproxy_namd.C. References colvarproxy_namd::colvars_atoms_ncopies. { colvarproxy_namd *gm = (colvarproxy_namd *) cvm::proxy; if (gm->colvars_atoms_ncopies[this->index] > 0) gm->colvars_atoms_ncopies[this->index] -= 1; }

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Member Function Documentation

void cvm::atom::apply_force (  cvm::rvector const &  new_force  )

Apply a force to the atom. The force will be used later by the MD integrator, the collective variables module does not integrate equations of motion. Multiple calls to this function by either the same object or different objects with identical , will all add to the existing MD force. Definition at line 543 of file colvarproxy_namd.C. References ResizeArray< Elem >::add(), GlobalMaster::modifyAppliedForces(), GlobalMaster::modifyForcedAtoms(), colvarmodule::rvector::x, colvarmodule::rvector::y, and colvarmodule::rvector::z. Referenced by colvar::h_bond::apply_force(). { colvarproxy_namd *gm = (colvarproxy_namd *) cvm::proxy; gm->modifyForcedAtoms().add (this->id); gm->modifyAppliedForces().add (Vector (new_force.x, new_force.y, new_force.z)); }

void cvm::atom::read_position (   )

Get the current position. Definition at line 522 of file colvarproxy_namd.C. References pos, and colvarproxy_namd::positions. Referenced by colvar::h_bond::calc_value(), and colvarmodule::atom_group::read_positions(). { colvarproxy_namd const * const gm = (colvarproxy_namd *) cvm::proxy; this->pos = gm->positions[this->index]; }

void cvm::atom::read_system_force (   )

Get the system force. Definition at line 536 of file colvarproxy_namd.C. References colvarproxy_namd::applied_forces, system_force, and colvarproxy_namd::total_forces. { colvarproxy_namd const * const gm = (colvarproxy_namd *) cvm::proxy; this->system_force = gm->total_forces[this->index] - gm->applied_forces[this->index]; }

void cvm::atom::read_velocity (   )

Get the current velocity. Definition at line 529 of file colvarproxy_namd.C. References colvarmodule::fatal_error(). { cvm::fatal_error ("Error: NAMD does not have yet a way to communicate " "atom velocities to the colvars.\n"); }

void colvarmodule::atom::reset_data (   )  [inline]

Set non-constant data (everything except id and mass) to zero. Definition at line 82 of file colvaratoms.h. References colvarmodule::atom_pos. Referenced by atom(), and colvar::h_bond::calc_value(). { pos = atom_pos (0.0); vel = grad = system_force = rvector (0.0); }

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Member Data Documentation

cvm::rvector colvarmodule::atom::grad

Gradient of a scalar collective variable with respect to this atom. This can only handle a scalar collective variable (i.e. when the member is used from the class), which is also the most frequent case. For more complex types of objects, atomic gradients should be defined within the specific implementation Definition at line 56 of file colvaratoms.h. Referenced by colvar::h_bond::apply_force(), colvar::coordnum::calc_gradients(), and colvar::coordnum::switching_function().

int colvarmodule::atom::id

Internal identifier. Definition at line 29 of file colvaratoms.h.

size_t colvarmodule::atom::index [protected]

Index in the list of atoms involved by the colvars (NOT in the global topology!). Definition at line 24 of file colvaratoms.h. Referenced by atom().

cvm::real colvarmodule::atom::mass

Mass. Definition at line 32 of file colvaratoms.h. Referenced by colvarmodule::atom_group::add_atom(), and atom().

cvm::atom_pos colvarmodule::atom::pos

Current position (copied from the program, can be manipulated). Definition at line 36 of file colvaratoms.h. Referenced by colvar::coordnum::calc_gradients(), colvar::coordnum::calc_value(), read_position(), and colvar::coordnum::switching_function().

cvm::rvector colvarmodule::atom::system_force

System force at the previous step (copied from the program, can be manipulated). Definition at line 44 of file colvaratoms.h. Referenced by read_system_force().

cvm::rvector colvarmodule::atom::vel

Current velocity (copied from the program, can be manipulated). Definition at line 40 of file colvaratoms.h.

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

• colvaratoms.h
• colvarproxy_namd.C

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