Container of atomic data for processing by Colvars. More...

#include <colvarproxy.h>

Inheritance diagram for colvarproxy_atoms:

[legend]

Public Types
template<typename T>
using	allocator_type = colvars_gpu::CudaHostAllocator<T>
using	atom_buffer_real_t = std::vector<cvm::real, allocator_type<cvm::real>>
using	atom_buffer_rvector_t = std::vector<cvm::rvector, allocator_type<cvm::rvector>>

Public Member Functions
	colvarproxy_atoms ()
	Constructor.
virtual	~colvarproxy_atoms ()
	Destructor.
virtual int	init_atom (int atom_number)
virtual int	check_atom_id (int atom_number)
virtual int	check_atom_name_selections_available ()
	Check whether it is possible to select atoms by residue number name.
virtual int	init_atom (cvm::residue_id const &residue, std::string const &atom_name, std::string const &segment_id)
virtual int	check_atom_id (cvm::residue_id const &residue, std::string const &atom_name, std::string const &segment_id)
	Check that this atom is valid, but do not initialize it yet.
virtual void	clear_atom (int index)
	Used by the atom class destructor: rather than deleting the array slot (costly) set the corresponding atoms_refcount to zero.
int	reset ()
	Clear atomic data.
int	get_atom_id (int index) const
cvm::real	get_atom_mass (int index) const
void	increase_refcount (int index)
cvm::real	get_atom_charge (int index) const
cvm::rvector	get_atom_position (int index) const
cvm::rvector	get_atom_total_force (int index) const
void	apply_atom_force (int index, cvm::rvector const &new_force)
cvm::rvector	get_atom_velocity (int)
	Read the current velocity of the given atom.
std::vector< int > const *	get_atom_ids () const
size_t	get_num_active_atoms () const
	Return number of atoms with positive reference count.
atom_buffer_real_t const *	get_atom_masses () const
atom_buffer_real_t *	modify_atom_masses ()
atom_buffer_real_t const *	get_atom_charges ()
atom_buffer_real_t *	modify_atom_charges ()
atom_buffer_rvector_t const *	get_atom_positions () const
atom_buffer_rvector_t *	modify_atom_positions ()
atom_buffer_rvector_t const *	get_atom_total_forces () const
atom_buffer_rvector_t *	modify_atom_total_forces ()
atom_buffer_rvector_t const *	get_atom_applied_forces () const
atom_buffer_rvector_t *	modify_atom_applied_forces ()
void	compute_rms_atoms_applied_force ()
	Compute the root-mean-square of the applied forces.
void	compute_max_atoms_applied_force ()
	Compute the maximum norm among all applied forces.
cvm::real	rms_atoms_applied_force () const
	Get the root-mean-square of the applied forces.
cvm::real	max_atoms_applied_force () const
	Get the maximum norm among all applied forces.
int	max_atoms_applied_force_id () const
	Get the atom ID with the largest applied force.
bool	modified_atom_list () const
	Whether the atom list has been modified internally.
void	reset_modified_atom_list ()
	Reset the modified atom list flag.
bool	updated_masses () const
	Record whether masses have been updated.
bool	updated_charges () const
	Record whether masses have been updated.

Protected Member Functions
int	add_atom_slot (int atom_id)
int	find_atom_by_id (int atom_id)
	Find the index of an atom by its ID.

Protected Attributes
std::vector< int >	atoms_ids
	Array of 0-based integers used to uniquely associate atoms within the host program.
std::vector< size_t >	atoms_refcount
	Keep track of how many times each atom is used by a separate colvar object.
std::vector< cvm::real, allocator_type< cvm::real > >	atoms_masses
	Masses of the atoms (allow redefinition during a run, as done e.g. in LAMMPS).
std::vector< cvm::real, allocator_type< cvm::real > >	atoms_charges
	Charges of the atoms (allow redefinition during a run, as done e.g. in LAMMPS).
std::vector< cvm::rvector, allocator_type< cvm::rvector > >	atoms_positions
	Current three-dimensional positions of the atoms.
std::vector< cvm::rvector, allocator_type< cvm::rvector > >	atoms_total_forces
	Most recent total forces on each atom.
std::vector< cvm::rvector, allocator_type< cvm::rvector > >	atoms_new_colvar_forces
	Forces applied from colvars, to be communicated to the MD integrator.
cvm::real	atoms_rms_applied_force_
	Root-mean-square of the applied forces.
cvm::real	atoms_max_applied_force_
	Maximum norm among all applied forces.
int	atoms_max_applied_force_id_
	ID of the atom with the maximum norm among all applied forces.
bool	modified_atom_list_
	Whether the atom list has been modified internally.
bool	updated_masses_
	Whether the masses and charges have been updated from the host code.
bool	updated_charges_

Detailed Description

Container of atomic data for processing by Colvars.

Member Function Documentation

◆ add_atom_slot()

int colvarproxy_atoms::add_atom_slot ( int atom_id )

protected

Used by all init_atom() functions: create a slot for an atom not requested yet; returns the index in the arrays

◆ apply_atom_force()

void colvarproxy_atoms::apply_atom_force	(	int	index,
		cvm::rvector const &	new_force )

inline

Request that this force is applied to the given atom

Parameters

index	Internal index in the Colvars arrays
new_force	Force to add

◆ check_atom_id() [1/2]

int colvarproxy_atoms::check_atom_id	(	cvm::residue_id const &	residue,
		std::string const &	atom_name,
		std::string const &	segment_id )

virtual

Check that this atom is valid, but do not initialize it yet.

Reimplemented in colvarproxy_lammps, colvarproxy_namd, and colvarproxy_vmd.

◆ check_atom_id() [2/2]

int colvarproxy_atoms::check_atom_id ( int atom_number )

virtual

Check that this atom number is valid, but do not initialize the corresponding atom yet

Reimplemented in colvarproxy_lammps, colvarproxy_namd, and colvarproxy_vmd.

◆ check_atom_name_selections_available()

int colvarproxy_atoms::check_atom_name_selections_available ( )

virtual

Check whether it is possible to select atoms by residue number name.

Reimplemented in colvarproxy_namd, and colvarproxy_vmd.

◆ clear_atom()

void colvarproxy_atoms::clear_atom ( int index )

virtual

Used by the atom class destructor: rather than deleting the array slot (costly) set the corresponding atoms_refcount to zero.

Reimplemented in colvarproxy_namd.

◆ find_atom_by_id()

int colvarproxy_atoms::find_atom_by_id ( int atom_id )

protected

Find the index of an atom by its ID.

Parameters

atom_id Atom ID to search for

Returns: Index of the atom in the arrays, or -1 if not found

◆ get_atom_charge()

cvm::real colvarproxy_atoms::get_atom_charge ( int index ) const

inline

Get the charge of the given atom

Parameters