Update data required by Colvars module (e.g. read atom positions) TODO Break up colvarproxy_namd and colvarproxy_lammps function into these. More...

virtual cvm::real

rand_gaussian ()

\brief Pseudo-random number with Gaussian distribution. More...

virtual int

get_molid (int &molid)

Get the molecule ID when called in VMD; raise error otherwise
Parameters:

molid Set this argument equal to the current VMD molid.

More...

virtual int

get_frame (long int &f)

\brief Save the current frame number in the argument given. More...

virtual int

set_frame (long int f)

\brief Set the current frame number (as well as colvarmodule::it). More...

virtual void

init_tcl_pointers ()

Set Tcl pointers. More...

virtual void

add_energy (cvm::real energy)

Pass restraint energy value for current timestep to MD engine. More...

virtual void

request_total_force (bool yesno)

\brief Tell the proxy whether total forces are needed (they may not always be available). More...

virtual void

log (std::string const &message)

Print a message to the main log. More...

virtual void

error (std::string const &message)

Print a message to the main log and/or let the host code know about it. More...

virtual int

set_unit_system (std::string const &units_in, bool check_only)

\brief Request to set the units used internally by Colvars. More...

virtual int

run_force_callback ()

Run a user-defined colvar forces script. More...

virtual int

run_colvar_callback (std::string const &name, std::vector< const colvarvalue * > const &cvcs, colvarvalue &value)

virtual int

run_colvar_gradient_callback (std::string const &name, std::vector< const colvarvalue * > const &cvc_values, std::vector< cvm::matrix2d< cvm::real > > &gradient)

virtual int

load_atoms (char const *filename, cvm::atom_group &atoms, std::string const &pdb_field, double const pdb_field_value=0.0)

\brief Select atom IDs from a file (usually PDB)
Parameters:

filename name of the file

atoms array to which atoms read from "filename" will be appended

pdb_field (optional) if the file is a PDB and this string is non-empty, select atoms for which this field is non-zero

pdb_field_value (optional) if non-zero, select only atoms whose pdb_field equals this.

More...

virtual int

load_coords (char const *filename, std::vector< cvm::atom_pos > &pos, const std::vector< int > &indices, std::string const &pdb_field, double const pdb_field_value=0.0)

virtual int

init_atom (int atom_number)

Prepare this atom for collective variables calculation, selecting it by numeric index (1-based). More...

virtual int

check_atom_id (int atom_number)

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

virtual int

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

Select this atom for collective variables calculation, using name and residue number. Not all programs support this: leave this function as is in those cases. More...

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. More...

virtual int

init_volmap_by_id (int volmap_id)

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

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 void

clear_volmap (int index)

\brief Used by the CVC destructors. 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...

template<int flags> void

compute_voldata (VolumetricData const *voldata, cvm::atom_iter atom_begin, cvm::atom_iter atom_end, cvm::real *value, cvm::real *atom_field)

int

get_alch_lambda (cvm::real *lambda)

Get value of alchemical lambda parameter from back-end (stub). More...

int

send_alch_lambda (void)

Set value of alchemical lambda parameter in back-end (stub). More...

int

get_dE_dlambda (cvm::real *dE_dlambda)

Get energy derivative with respect to lambda (stub). More...

Protected Attributes

VMDApp *

vmd

pointer to the VMD main object. More...

int

vmdmolid

VMD molecule ID being used (must be provided at construction). More...

DrawMolecule *

vmdmol

pointer to VMD molecule (derived from vmdmolid). More...

long int

vmdmol_frame

current frame (returned by vmdmol->frame()). More...

Inform

msgColvars

output object. More...

Detailed Description

\brief Communication between colvars and VMD (implementation of colvarproxy).

Definition at line 32 of file colvarproxy_vmd.h.

Constructor & Destructor Documentation

colvarproxy_vmd::colvarproxy_vmd ( Tcl_Interp * interp,

VMDApp * vmd,

int molid

)

Constructor
Parameters:

interl Pointer to Tcl interpreter

vmd Pointer to VMDApp object

molid Molecule ID (>= 0).

Definition at line 71 of file colvarproxy_vmd.C.
References colvarproxy_system::angstrom_value_, colvarproxy::b_simulation_running, colvarmodule::cite_feature, COLVARPROXY_VERSION, colvarproxy::colvars, colvarmodule::cv_traj_freq, colvarproxy::get_version_from_string, colvarproxy_script::have_scripts, colvarproxy_system::kcal_mol_value_, colvarmodule::log, colvarmodule::restart_out_freq, colvarproxy_tcl::set_tcl_interp, setup, colvarmodule::setup_input, colvarmodule::setup_output, colvarproxy_atoms::updated_charges_, colvarproxy_atoms::updated_masses_, colvarproxy::version_int, vmd_srandom, and VMDCON_INFO.

colvarproxy_vmd::~colvarproxy_vmd ( ) [virtual]

Definition at line 123 of file colvarproxy_vmd.C.

Member Function Documentation

void colvarproxy_vmd::add_energy ( cvm::real energy ) [virtual]

Pass restraint energy value for current timestep to MD engine.

Reimplemented from colvarproxy_system.
Definition at line 261 of file colvarproxy_vmd.C.

int colvarproxy_vmd::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 from colvarproxy_atoms.
Definition at line 684 of file colvarproxy_vmd.C.
References BaseMolecule::atom, BaseMolecule::atomNames, Residue::atoms, COLVARS_INPUT_ERROR, colvarmodule::error, MolAtom::nameindex, BaseMolecule::nResidues, ResizeArray< int >::num, Residue::resid, BaseMolecule::residue, MolAtom::segnameindex, BaseMolecule::segNames, and vmdmol.

int colvarproxy_vmd::check_atom_id ( int atom_number ) [virtual]

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

Reimplemented from colvarproxy_atoms.
Definition at line 634 of file colvarproxy_vmd.C.
References COLVARS_INPUT_ERROR, colvarmodule::debug, colvarmodule::error, colvarmodule::log, BaseMolecule::nAtoms, and vmdmol.
Referenced by init_atom.

int colvarproxy_vmd::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 from colvarproxy_volmaps.
Definition at line 775 of file colvarproxy_vmd.C.
References COLVARS_INPUT_ERROR, colvarmodule::error, BaseMolecule::num_volume_data, and vmdmol.
Referenced by init_volmap_by_id.

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

\brief Used by the CVC destructors.

Reimplemented from colvarproxy_volmaps.
Definition at line 785 of file colvarproxy_vmd.C.
References colvarproxy_volmaps::clear_volmap.

template<int flags>

void colvarproxy_vmd::compute_voldata ( VolumetricData const * voldata,

cvm::atom_iter atom_begin,

cvm::atom_iter atom_end,

cvm::real * value,

cvm::real * atom_field

)

Definition at line 792 of file colvarproxy_vmd.C.
References colvarproxy_system::internal_to_angstrom, colvarproxy_system::position_distance, colvarproxy_volmaps::volmap_flag_gradients, colvarproxy_volmaps::volmap_flag_use_atom_field, VolumetricData::voxel_coord_from_cartesian_coord, VolumetricData::voxel_gradient_interpolate, VolumetricData::voxel_value_interpolate, VolumetricData::xsize, VolumetricData::ysize, and VolumetricData::zsize.

int colvarproxy_vmd::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 from colvarproxy_volmaps.
Definition at line 855 of file colvarproxy_vmd.C.
References BaseMolecule::get_volume_data, NULL, vmdmol, colvarproxy_volmaps::volmap_flag_gradients, colvarproxy_volmaps::volmap_flag_null, and colvarproxy_volmaps::volmap_flag_use_atom_field.

void colvarproxy_vmd::error ( std::string const & message ) [virtual]

Print a message to the main log and/or let the host code know about it.

Reimplemented from colvarproxy.
Definition at line 316 of file colvarproxy_vmd.C.
References colvarproxy::add_error_msg, and log.
Referenced by setup, update_atomic_properties, and update_input.

int colvarproxy_vmd::get_alch_lambda ( cvm::real * lambda ) [inline, virtual]

Get value of alchemical lambda parameter from back-end (stub).

Reimplemented from colvarproxy_system.
Definition at line 127 of file colvarproxy_vmd.h.

int colvarproxy_vmd::get_dE_dlambda ( cvm::real * dE_dlambda ) [inline, virtual]

Get energy derivative with respect to lambda (stub).

Reimplemented from colvarproxy_system.
Definition at line 136 of file colvarproxy_vmd.h.

int colvarproxy_vmd::get_frame ( long int & f ) [virtual]

\brief Save the current frame number in the argument given.

Reimplemented from colvarproxy_io.
Definition at line 330 of file colvarproxy_vmd.C.
References vmdmol_frame.

int colvarproxy_vmd::get_molid ( int & molid ) [virtual]

Get the molecule ID when called in VMD; raise error otherwise
Parameters:

molid Set this argument equal to the current VMD molid.

Reimplemented from colvarproxy_system.
Definition at line 323 of file colvarproxy_vmd.C.
References vmdmolid.

int colvarproxy_vmd::init_atom ( cvm::residue_id const & residue,

std::string const & atom_name,

std::string const & segment_id

) [virtual]

Select this atom for collective variables calculation, using name and residue number. Not all programs support this: leave this function as is in those cases.

Reimplemented from colvarproxy_atoms.
Definition at line 722 of file colvarproxy_vmd.C.
References colvarproxy_atoms::add_atom_slot, colvarproxy_atoms::atoms_charges, colvarproxy_atoms::atoms_ids, colvarproxy_atoms::atoms_masses, colvarproxy_atoms::atoms_refcount, BaseMolecule::charge, check_atom_id, colvarmodule::debug, colvarmodule::log, BaseMolecule::mass, and vmdmol.

int colvarproxy_vmd::init_atom ( int atom_number ) [virtual]

Prepare this atom for collective variables calculation, selecting it by numeric index (1-based).

Reimplemented from colvarproxy_atoms.
Definition at line 653 of file colvarproxy_vmd.C.
References colvarproxy_atoms::add_atom_slot, colvarproxy_atoms::atoms_charges, colvarproxy_atoms::atoms_ids, colvarproxy_atoms::atoms_masses, colvarproxy_atoms::atoms_refcount, BaseMolecule::charge, check_atom_id, COLVARS_INPUT_ERROR, BaseMolecule::mass, and vmdmol.

void colvarproxy_vmd::init_tcl_pointers ( ) [virtual]

Set Tcl pointers.

Reimplemented from colvarproxy_tcl.
Definition at line 353 of file colvarproxy_vmd.C.
References colvarproxy_tcl::init_tcl_pointers.

int colvarproxy_vmd::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 from colvarproxy_volmaps.
Definition at line 754 of file colvarproxy_vmd.C.
References colvarproxy_volmaps::add_volmap_slot, check_volmap_by_id, colvarproxy_volmaps::volmaps_ids, and colvarproxy_volmaps::volmaps_refcount.

int colvarproxy_vmd::load_atoms ( char const * filename,

cvm::atom_group & atoms,

std::string const & pdb_field,

double const pdb_field_value = 0.0

) [virtual]

\brief Select atom IDs from a file (usually PDB)
Parameters:

filename name of the file

atoms array to which atoms read from "filename" will be appended

pdb_field (optional) if the file is a PDB and this string is non-empty, select atoms for which this field is non-zero

pdb_field_value (optional) if non-zero, select only atoms whose pdb_field equals this.

Reimplemented from colvarproxy_atoms.
Definition at line 565 of file colvarproxy_vmd.C.
References atoms, FileSpec::autobonds, BaseMolecule::beta, COLVARS_ERROR, COLVARS_FILE_ERROR, COLVARS_INPUT_ERROR, e_pdb_beta, e_pdb_field, e_pdb_occ, e_pdb_x, e_pdb_y, e_pdb_z, colvarmodule::error, colvarmodule::get_error, DrawMolecule::get_frame, colvarmodule::log, MoleculeList::mol_from_id, VMDApp::molecule_delete, VMDApp::molecule_load, VMDApp::molecule_make_top, VMDApp::moleculeList, BaseMolecule::nAtoms, BaseMolecule::occupancy, pdb_field_str2enum, Timestep::pos, colvarmodule::set_error_bits, vmd, and vmdmolid.

int colvarproxy_vmd::load_coords ( char const * filename,

std::vector< cvm::atom_pos > & pos,

const std::vector< int > & indices,

std::string const & pdb_field,

double const pdb_field_value = 0.0

) [virtual]

Definition at line 439 of file colvarproxy_vmd.C.
References colvarproxy_system::angstrom_to_internal, colvarmodule::atom_pos, FileSpec::autobonds, BaseMolecule::beta, COLVARS_BUG_ERROR, COLVARS_ERROR, COLVARS_FILE_ERROR, COLVARS_INPUT_ERROR, e_pdb_beta, e_pdb_field, e_pdb_none, e_pdb_occ, e_pdb_x, e_pdb_y, e_pdb_z, colvarmodule::error, colvarmodule::get_error, DrawMolecule::get_frame, MoleculeList::mol_from_id, VMDApp::molecule_delete, VMDApp::molecule_load, VMDApp::molecule_make_top, VMDApp::moleculeList, BaseMolecule::nAtoms, BaseMolecule::occupancy, pdb_field_str2enum, Timestep::pos, vmd, and vmdmolid.

void colvarproxy_vmd::log ( std::string const & message ) [virtual]

Print a message to the main log.

Reimplemented from colvarproxy.
Definition at line 306 of file colvarproxy_vmd.C.
References msgColvars.
Referenced by error.

cvm::real colvarproxy_vmd::rand_gaussian ( ) [virtual]

\brief Pseudo-random number with Gaussian distribution.

Reimplemented from colvarproxy_system.
Definition at line 149 of file colvarproxy_vmd.C.
References vmd_random_gaussian.

int colvarproxy_vmd::request_deletion ( ) [virtual]

Request deallocation of the module (currently only implemented by VMD).

Reimplemented from colvarproxy.
Definition at line 127 of file colvarproxy_vmd.C.
References colvarproxy::b_delete_requested.

void colvarproxy_vmd::request_total_force ( bool yesno ) [virtual]

\brief Tell the proxy whether total forces are needed (they may not always be available).

Reimplemented from colvarproxy_system.
Definition at line 295 of file colvarproxy_vmd.C.
References colvarmodule::log, and colvarproxy_system::total_force_requested.

int colvarproxy_vmd::run_colvar_callback ( std::string const & name,

std::vector< const colvarvalue * > const & cvcs,

colvarvalue & value

) [virtual]

Reimplemented from colvarproxy_script.
Definition at line 372 of file colvarproxy_vmd.C.
References colvarproxy_tcl::tcl_run_colvar_callback.

int colvarproxy_vmd::run_colvar_gradient_callback ( std::string const & name,

std::vector< const colvarvalue * > const & cvc_values,

std::vector< cvm::matrix2d< cvm::real > > & gradient

) [virtual]

Reimplemented from colvarproxy_script.
Definition at line 380 of file colvarproxy_vmd.C.
References colvarproxy_tcl::tcl_run_colvar_gradient_callback.

int colvarproxy_vmd::run_force_callback ( ) [virtual]

Run a user-defined colvar forces script.

Reimplemented from colvarproxy_script.
Definition at line 367 of file colvarproxy_vmd.C.
References colvarproxy_tcl::tcl_run_force_callback.

int colvarproxy_vmd::send_alch_lambda ( void ) [inline, virtual]

Set value of alchemical lambda parameter in back-end (stub).

Reimplemented from colvarproxy_system.
Definition at line 133 of file colvarproxy_vmd.h.

int colvarproxy_vmd::set_frame ( long int f ) [virtual]

\brief Set the current frame number (as well as colvarmodule::it).

Reimplemented from colvarproxy_io.
Definition at line 337 of file colvarproxy_vmd.C.
References colvarproxy::colvars, COLVARS_NO_SUCH_FRAME, DrawMolecule::get_frame, colvarmodule::it, NULL, update_input, vmdmol, and vmdmol_frame.
Referenced by setup.

int colvarproxy_vmd::set_unit_system ( std::string const & units_in,

bool check_only

) [virtual]

\brief Request to set the units used internally by Colvars.

Reimplemented from colvarproxy_system.
Definition at line 155 of file colvarproxy_vmd.C.
References colvarproxy_system::angstrom_value_, COLVARS_ERROR, colvarmodule::error, colvarproxy_system::kcal_mol_value_, and colvarproxy_system::units.

int colvarproxy_vmd::setup ( ) [virtual]

(Re)initialize required member data (called after the module).

Reimplemented from colvarproxy.
Definition at line 134 of file colvarproxy_vmd.C.
References colvarproxy::colvars, COLVARS_ERROR, error, DrawMolecule::frame, MoleculeList::mol_from_id, VMDApp::moleculeList, set_frame, colvarproxy::setup, colvarmodule::update_engine_parameters, vmd, vmdmol, and vmdmolid.
Referenced by colvarproxy_vmd.

int colvarproxy_vmd::update_atomic_properties ( )

\brief Update mass, charge, etc.

Definition at line 266 of file colvarproxy_vmd.C.
References colvarproxy_atoms::atoms_charges, colvarproxy_atoms::atoms_ids, colvarproxy_atoms::atoms_masses, BaseMolecule::charge, COLVARS_BUG_ERROR, error, BaseMolecule::mass, NULL, and vmdmol.
Referenced by update_input.

Member Data Documentation

Inform colvarproxy_vmd::msgColvars [protected]

output object.

Definition at line 156 of file colvarproxy_vmd.h.
Referenced by log.

VMDApp* colvarproxy_vmd::vmd [protected]

pointer to the VMD main object.

Definition at line 144 of file colvarproxy_vmd.h.
Referenced by load_atoms, load_coords, setup, and update_input.

DrawMolecule* colvarproxy_vmd::vmdmol [protected]

pointer to VMD molecule (derived from vmdmolid).

Definition at line 150 of file colvarproxy_vmd.h.
Referenced by check_atom_id, check_volmap_by_id, compute_volmap, init_atom, set_frame, setup, update_atomic_properties, and update_input.

long int colvarproxy_vmd::vmdmol_frame [protected]

current frame (returned by vmdmol->frame()).

Definition at line 153 of file colvarproxy_vmd.h.
Referenced by get_frame, set_frame, and update_input.

int colvarproxy_vmd::vmdmolid [protected]

VMD molecule ID being used (must be provided at construction).

Definition at line 147 of file colvarproxy_vmd.h.
Referenced by get_molid, load_atoms, load_coords, setup, and update_input.

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

Generated on Tue Dec 3 02:47:20 2024 for VMD (current) by