Container of grid-based objects. More...

#include <colvarproxy_volmaps.h>

Inheritance diagram for colvarproxy_volmaps:

[legend]

Public Types
enum	{ volmap_flag_null = 0 , volmap_flag_gradients = 1 , volmap_flag_use_atom_field = (1<<8) }
	Flags controlling what computation is done on the map.

Public Member Functions
	colvarproxy_volmaps ()
	Contructor.

virtual	~colvarproxy_volmaps ()
	Destructor.

int	reset ()
	Clear volumetric map data.

virtual int	check_volmaps_available ()
	Test whether this implementation can use volumetric maps as CVs. More...

int	add_volmap_slot (int volmap_id)
	Create a slot for a volumetric map not requested yet.

virtual int	init_volmap_by_id (int volmap_id)

virtual int	init_volmap_by_name (char const *volmap_name)

virtual int	check_volmap_by_id (int volmap_id)

virtual int	check_volmap_by_name (char const *volmap_name)

int	init_volmap_by_name (std::string const &volmap_name)
	Request and prepare this volumetric map for use by Colvars.

int	check_volmap_by_name (std::string const &volmap_name)
	Check that the given volmap name is valid (return COLVARS_OK if it is)

virtual void	clear_volmap (int index)
	Used by the CVC destructors. More...

virtual int	get_volmap_id_from_name (char const *volmap_name)
	Get the numeric ID of the given volumetric map (for the MD program) More...

int	get_volmap_id (int index) const
	Get the numeric ID of the given volumetric map (for the MD program)

cvm::real	get_volmap_value (int index) const
	Read the current value of the volumetric map.

void	apply_volmap_force (int index, cvm::real const &new_force)
	Request that this force is applied to the given volumetric map.

virtual int	compute_volmap (int flags, int volmap_id, cvm::atom_iter atom_begin, cvm::atom_iter atom_end, cvm::real value, cvm::real atom_field)

void	compute_rms_volmaps_applied_force ()
	Compute the root-mean-square of the applied forces.

void	compute_max_volmaps_applied_force ()
	Compute the maximum norm among all applied forces.

Protected Attributes
std::vector< int >	volmaps_ids
	Array of numeric IDs of volumetric maps.

std::vector< size_t >	volmaps_refcount
	Keep track of how many times each vol map is used by a separate colvar object.

std::vector< cvm::real >	volmaps_values
	Current values of the vol maps.

std::vector< cvm::real >	volmaps_new_colvar_forces
	Forces applied from colvars, to be communicated to the MD integrator.

cvm::real	volmaps_rms_applied_force_
	Root-mean-square of the the applied forces.

cvm::real	volmaps_max_applied_force_
	Maximum norm among all applied forces.

Detailed Description

Container of grid-based objects.

Member Function Documentation

◆ check_volmap_by_id()

int colvarproxy_volmaps::check_volmap_by_id ( int volmap_id )

virtual

Check that the given volmap ID is valid (return COLVARS_OK if it is)

Parameters

volmap_id Numeric ID used by the MD engine

Returns: Error code

Reimplemented in colvarproxy_vmd, and colvarproxy_namd.

◆ check_volmap_by_name()

int colvarproxy_volmaps::check_volmap_by_name ( char const * volmap_name )

virtual

Check that the given volmap name is valid (return COLVARS_OK if it is)

Parameters

volmap_name Name used by the MD engine

Returns: Error code

Reimplemented in colvarproxy_namd.

◆ check_volmaps_available()

int colvarproxy_volmaps::check_volmaps_available ( )

virtual

Test whether this implementation can use volumetric maps as CVs.

Reimplemented in colvarproxy_vmd, and colvarproxy_namd.

◆ clear_volmap()

void colvarproxy_volmaps::clear_volmap ( int index )

virtual

Used by the CVC destructors.

Reimplemented in colvarproxy_vmd, and colvarproxy_namd.

◆ compute_volmap()

int colvarproxy_volmaps::compute_volmap	(	int	flags,
		int	volmap_id,
		cvm::atom_iter	atom_begin,
		cvm::atom_iter	atom_end,
		cvm::real *	value,
		cvm::real *	atom_field
	)

virtual

Re-weigh an atomic field (e.g. a colvar) by the value of a volumetric map

Parameters

flags	Combination of flags
volmap_id	Numeric index of the map (no need to request it)
atom_begin	Iterator pointing to first atom
atom_end	Iterator pointing past the last atom
value	Pointer to location of total to increment
atom_field	Array of atomic field values (if NULL, ones are used)

Reimplemented in colvarproxy_vmd, and colvarproxy_namd.

◆ get_volmap_id_from_name()

int colvarproxy_volmaps::get_volmap_id_from_name ( char const * volmap_name )

virtual

Get the numeric ID of the given volumetric map (for the MD program)

Reimplemented in colvarproxy_namd.

◆ init_volmap_by_id()

int colvarproxy_volmaps::init_volmap_by_id ( int volmap_id )

virtual

Request and prepare this volumetric map for use by Colvars

Parameters

volmap_id Numeric ID used by the MD engine

Returns: Index of the map in the colvarproxy arrays

Reimplemented in colvarproxy_vmd, and colvarproxy_namd.

◆ init_volmap_by_name()

int colvarproxy_volmaps::init_volmap_by_name ( char const * volmap_name )

virtual

Request and prepare this volumetric map for use by Colvars

Parameters

volmap_name Name used by the MD engine

Returns: Index of the map in the colvarproxy arrays

Reimplemented in colvarproxy_namd.

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

colvarproxy_volmaps.h
colvarproxy_volmaps.cpp

Public Types

Public Member Functions

Protected Attributes

Detailed Description

Member Function Documentation

◆ check_volmap_by_id()

◆ check_volmap_by_name()

◆ check_volmaps_available()

◆ clear_volmap()

◆ compute_volmap()

◆ get_volmap_id_from_name()

◆ init_volmap_by_id()

◆ init_volmap_by_name()