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.
More...

virtual int

init_volmap_by_name (char const *volmap_name)

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.
More...

virtual int

check_volmap_by_id (int volmap_id)

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.
More...

virtual int

check_volmap_by_name (char const *volmap_name)

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.
More...

int

init_volmap_by_name (std::string const &volmap_name)

Request and prepare this volumetric map for use by Colvars. More...

int

check_volmap_by_name (std::string const &volmap_name)

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

virtual void

clear_volmap (int index)

\brief 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). More...

cvm::real

get_volmap_value (int index) const

Read the current value of the volumetric map. More...

void

apply_volmap_force (int index, cvm::real const &new_force)

Request that this force is applied to the given volumetric map. More...

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)

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).

More...

void

compute_rms_volmaps_applied_force ()

Compute the root-mean-square of the applied forces. More...

void

compute_max_volmaps_applied_force ()

Compute the maximum norm among all applied forces. More...

Protected Attributes

std::vector< int >

volmaps_ids

\brief Array of numeric IDs of volumetric maps. More...

std::vector< size_t >

volmaps_refcount

\brief Keep track of how many times each vol map is used by a separate colvar object. More...

std::vector< cvm::real >

volmaps_values

\brief Current values of the vol maps. More...

std::vector< cvm::real >

volmaps_new_colvar_forces

\brief Forces applied from colvars, to be communicated to the MD integrator. More...

cvm::real

volmaps_rms_applied_force_

Root-mean-square of the the applied forces. More...

cvm::real

volmaps_max_applied_force_

Maximum norm among all applied forces. More...

Detailed Description

\brief Container of grid-based objects.

Definition at line 8 of file colvarproxy_volmaps.h.

Member Enumeration Documentation

anonymous enum

Flags controlling what computation is done on the map.

Enumeration values:

volmap_flag_null

volmap_flag_gradients

volmap_flag_use_atom_field

Definition at line 92 of file colvarproxy_volmaps.h.

Constructor & Destructor Documentation

colvarproxy_volmaps::colvarproxy_volmaps ( )

Contructor.

Definition at line 15 of file colvarproxy_volmaps.C.
References volmaps_max_applied_force_, and volmaps_rms_applied_force_.

colvarproxy_volmaps::~colvarproxy_volmaps ( ) [virtual]

Destructor.

Definition at line 21 of file colvarproxy_volmaps.C.

Member Function Documentation

int colvarproxy_volmaps::add_volmap_slot ( int volmap_id )

Create a slot for a volumetric map not requested yet.

Definition at line 43 of file colvarproxy_volmaps.C.
References volmaps_ids, volmaps_new_colvar_forces, volmaps_refcount, and volmaps_values.
Referenced by colvarproxy_vmd::init_volmap_by_id.

void colvarproxy_volmaps::apply_volmap_force ( int index,

cvm::real const & new_force

) [inline]

Request that this force is applied to the given volumetric map.

Definition at line 72 of file colvarproxy_volmaps.h.
References volmaps_new_colvar_forces.
Referenced by colvar::map_total::apply_force.

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.
Definition at line 53 of file colvarproxy_volmaps.C.
References COLVARS_NOT_IMPLEMENTED, and colvarmodule::error.
Referenced by colvar::map_total::init.

int colvarproxy_volmaps::check_volmap_by_name ( std::string const & volmap_name )

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

Definition at line 85 of file colvarproxy_volmaps.C.
References check_volmap_by_name.

virtual 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.

Referenced by check_volmap_by_name, get_volmap_id_from_name, and colvar::map_total::init.

void colvarproxy_volmaps::clear_volmap ( int index ) [virtual]

\brief Used by the CVC destructors.

Reimplemented in colvarproxy_vmd.
Definition at line 91 of file colvarproxy_volmaps.C.
References COLVARS_INPUT_ERROR, colvarmodule::error, volmaps_ids, and volmaps_refcount.
Referenced by colvarproxy_vmd::clear_volmap, and reset.

void colvarproxy_volmaps::compute_max_volmaps_applied_force ( )

Compute the maximum norm among all applied forces.

Definition at line 130 of file colvarproxy_volmaps.C.
References volmaps_max_applied_force_.
Referenced by colvarproxy::end_of_step.

void colvarproxy_volmaps::compute_rms_volmaps_applied_force ( )

Compute the root-mean-square of the applied forces.

Definition at line 123 of file colvarproxy_volmaps.C.
References volmaps_rms_applied_force_.
Referenced by colvarproxy::end_of_step.

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.
Definition at line 112 of file colvarproxy_volmaps.C.
References COLVARS_NOT_IMPLEMENTED.
Referenced by colvar::map_total::calc_value.

int colvarproxy_volmaps::get_volmap_id ( int index ) const [inline]

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

Definition at line 60 of file colvarproxy_volmaps.h.
References volmaps_ids.

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).

Definition at line 104 of file colvarproxy_volmaps.C.
References check_volmap_by_name.
Referenced by colvar::map_total::init.

cvm::real colvarproxy_volmaps::get_volmap_value ( int index ) const [inline]

Read the current value of the volumetric map.

Definition at line 66 of file colvarproxy_volmaps.h.
References volmaps_values.
Referenced by colvar::map_total::calc_value.

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.
Definition at line 73 of file colvarproxy_volmaps.C.
Referenced by colvar::map_total::init.

int colvarproxy_volmaps::init_volmap_by_name ( std::string const & volmap_name )

Request and prepare this volumetric map for use by Colvars.

Definition at line 79 of file colvarproxy_volmaps.C.
References 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.

Definition at line 67 of file colvarproxy_volmaps.C.
Referenced by colvar::map_total::init, and init_volmap_by_name.

int colvarproxy_volmaps::reset ( )

Clear volumetric map data.

Reimplemented in colvarproxy.
Definition at line 30 of file colvarproxy_volmaps.C.
References clear_volmap, volmaps_ids, volmaps_new_colvar_forces, volmaps_refcount, and volmaps_values.

int colvarproxy_volmaps::volmaps_available ( ) [virtual]

\brief Whether this implementation has capability to use volumetric maps.

Definition at line 24 of file colvarproxy_volmaps.C.
References COLVARS_NOT_IMPLEMENTED.

Member Data Documentation

std::vector<int> colvarproxy_volmaps::volmaps_ids [protected]

\brief Array of numeric IDs of volumetric maps.

Definition at line 107 of file colvarproxy_volmaps.h.
Referenced by add_volmap_slot, clear_volmap, get_volmap_id, colvarproxy_vmd::init_volmap_by_id, colvarproxy::print_input_atomic_data, and reset.

cvm::real colvarproxy_volmaps::volmaps_max_applied_force_ [protected]

Maximum norm among all applied forces.

Definition at line 124 of file colvarproxy_volmaps.h.
Referenced by colvarproxy_volmaps, and compute_max_volmaps_applied_force.

std::vector<cvm::real> colvarproxy_volmaps::volmaps_new_colvar_forces [protected]

\brief Forces applied from colvars, to be communicated to the MD integrator.

Definition at line 118 of file colvarproxy_volmaps.h.
Referenced by add_volmap_slot, apply_volmap_force, colvarproxy::print_output_atomic_data, and reset.

std::vector<size_t> colvarproxy_volmaps::volmaps_refcount [protected]

\brief Keep track of how many times each vol map is used by a separate colvar object.

Definition at line 111 of file colvarproxy_volmaps.h.
Referenced by add_volmap_slot, clear_volmap, colvarproxy_vmd::init_volmap_by_id, and reset.

cvm::real colvarproxy_volmaps::volmaps_rms_applied_force_ [protected]

Root-mean-square of the the applied forces.

Definition at line 121 of file colvarproxy_volmaps.h.
Referenced by colvarproxy_volmaps, and compute_rms_volmaps_applied_force.

std::vector<cvm::real> colvarproxy_volmaps::volmaps_values [protected]

\brief Current values of the vol maps.

Definition at line 114 of file colvarproxy_volmaps.h.
Referenced by add_volmap_slot, get_volmap_value, colvarproxy::print_input_atomic_data, and reset.

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

Generated on Sun Sep 15 02:46:30 2024 for VMD (current) by