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colvarproxy_atoms Class Reference

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

#include <colvarproxy.h>

Inheritance diagram for colvarproxy_atoms:

List of all members.

Public Methods

colvarproxy_atoms ()

Constructor. More...

virtual ~colvarproxy_atoms ()

Destructor. More...

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 void clear_atom (int index)

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

virtual int load_atoms (char const *filename, cvm::atom_group &atoms, std::string const &pdb_field, double 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, std::vector< int > const &sorted_ids, std::string const &pdb_field, double pdb_field_value=0.0)

\brief Load a set of coordinates from a file (usually PDB); if "pos" is already allocated, the number of its elements must match the number of entries in "filename"
Parameters:

filename name of the file

pos array of coordinates

sorted_ids array of sorted internal IDs, used to loop through the file only once

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...

int reset ()

Clear atomic data. More...

int get_atom_id (int index) const

Get the numeric ID of the given atom
Parameters:

index Internal index in the Colvars arrays.

More...

cvm::real get_atom_mass (int index) const

Get the mass of the given atom
Parameters:

index Internal index in the Colvars arrays.

More...

void increase_refcount (int index)

Increase the reference count of the given atom
Parameters:

index Internal index in the Colvars arrays.

More...

cvm::real get_atom_charge (int index) const

Get the charge of the given atom
Parameters:

index Internal index in the Colvars arrays.

More...

cvm::rvector get_atom_position (int index) const

Read the current position of the given atom
Parameters:

index Internal index in the Colvars arrays.

More...

cvm::rvector get_atom_total_force (int index) const

Read the current total force of the given atom
Parameters:

index Internal index in the Colvars arrays.

More...

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

Request that this force is applied to the given atom
Parameters:

index Internal index in the Colvars arrays

new_force Force to add.

More...

cvm::rvector get_atom_velocity (int)

Read the current velocity of the given atom. More...

std::vector< int > const * get_atom_ids () const

size_t get_num_active_atoms () const

Return number of atoms with positive reference count. More...

std::vector< cvm::real > const * get_atom_masses () const

std::vector< cvm::real > * modify_atom_masses ()

std::vector< cvm::real > const * get_atom_charges ()

std::vector< cvm::real > * modify_atom_charges ()

std::vector< cvm::rvector
> const * get_atom_positions () const

std::vector< cvm::rvector > * modify_atom_positions ()

std::vector< cvm::rvector
> const * get_atom_total_forces () const

std::vector< cvm::rvector > * modify_atom_total_forces ()

std::vector< cvm::rvector
> const * get_atom_applied_forces () const

std::vector< cvm::rvector > * modify_atom_applied_forces ()

void compute_rms_atoms_applied_force ()

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

void compute_max_atoms_applied_force ()

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

cvm::real rms_atoms_applied_force () const

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

cvm::real max_atoms_applied_force () const

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

int max_atoms_applied_force_id () const

Get the atom ID with the largest applied force. More...

bool updated_masses () const

Record whether masses have been updated. More...

bool updated_charges () const

Record whether masses have been updated. More...

Protected Methods

int add_atom_slot (int atom_id)

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

Protected Attributes

std::vector< int > atoms_ids

\brief Array of 0-based integers used to uniquely associate atoms within the host program. More...

std::vector< size_t > atoms_refcount

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

std::vector< cvm::real > atoms_masses

\brief Masses of the atoms (allow redefinition during a run, as done e.g. in LAMMPS). More...

std::vector< cvm::real > atoms_charges

\brief Charges of the atoms (allow redefinition during a run, as done e.g. in LAMMPS). More...

std::vector< cvm::rvector > atoms_positions

\brief Current three-dimensional positions of the atoms. More...

std::vector< cvm::rvector > atoms_total_forces

\brief Most recent total forces on each atom. More...

std::vector< cvm::rvector > atoms_new_colvar_forces

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

cvm::real atoms_rms_applied_force_

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

cvm::real atoms_max_applied_force_

Maximum norm among all applied forces. More...

int atoms_max_applied_force_id_

ID of the atom with the maximum norm among all applied forces. More...

bool updated_masses_

Whether the masses and charges have been updated from the host code. More...

bool updated_charges_

Whether the masses and charges have been updated from the host code. More...

Detailed Description

\brief Container of atomic data for processing by Colvars.

Definition at line 41 of file colvarproxy.h.

Constructor & Destructor Documentation

colvarproxy_atoms::colvarproxy_atoms ( )

Constructor.

Definition at line 22 of file colvarproxy.C.

References atoms_max_applied_force_, atoms_max_applied_force_id_, atoms_rms_applied_force_, updated_charges_, and updated_masses_.

colvarproxy_atoms::~colvarproxy_atoms ( ) [virtual]

Destructor.

Definition at line 30 of file colvarproxy.C.

References reset.

Member Function Documentation

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.

Definition at line 49 of file colvarproxy.C.

References atoms_charges, atoms_ids, atoms_masses, atoms_new_colvar_forces, atoms_positions, atoms_refcount, and atoms_total_forces.

Referenced by colvarproxy_vmd::init_atom.

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.

Definition at line 148 of file colvarproxy.h.

References atoms_new_colvar_forces.

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_vmd.

Definition at line 84 of file colvarproxy.C.

References COLVARS_NOT_IMPLEMENTED, and init_atom.

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_vmd.

Definition at line 68 of file colvarproxy.C.

References COLVARS_NOT_IMPLEMENTED.

void colvarproxy_atoms::clear_atom ( int index ) [virtual]

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

Definition at line 93 of file colvarproxy.C.

References atoms_ids, atoms_refcount, COLVARS_INPUT_ERROR, and colvarmodule::error.

void colvarproxy_atoms::compute_max_atoms_applied_force ( )

Compute the maximum norm among all applied forces.

Definition at line 145 of file colvarproxy.C.

References atoms_ids, atoms_max_applied_force_, atoms_max_applied_force_id_, and atoms_new_colvar_forces.

Referenced by colvarproxy::end_of_step.

void colvarproxy_atoms::compute_rms_atoms_applied_force ( )

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

Definition at line 138 of file colvarproxy.C.

References atoms_rms_applied_force_.

Referenced by colvarproxy::end_of_step.

std::vector<cvm::rvector> const* colvarproxy_atoms::get_atom_applied_forces ( ) const [inline]

Definition at line 214 of file colvarproxy.h.

References atoms_new_colvar_forces.

cvm::real colvarproxy_atoms::get_atom_charge ( int index ) const [inline]

Get the charge of the given atom

Parameters:: index Internal index in the Colvars arrays.

Definition at line 126 of file colvarproxy.h.

References atoms_charges.

Referenced by colvarmodule::atom::update_charge.

std::vector<cvm::real> const* colvarproxy_atoms::get_atom_charges ( ) [inline]

Definition at line 182 of file colvarproxy.h.

References atoms_charges.

int colvarproxy_atoms::get_atom_id ( int index ) const [inline]

Get the numeric ID of the given atom

Parameters:: index Internal index in the Colvars arrays.

Definition at line 105 of file colvarproxy.h.

References atoms_ids.

std::vector<int> const* colvarproxy_atoms::get_atom_ids ( ) const [inline]

Definition at line 162 of file colvarproxy.h.

References atoms_ids.

cvm::real colvarproxy_atoms::get_atom_mass ( int index ) const [inline]

Get the mass of the given atom

Parameters:: index Internal index in the Colvars arrays.

Definition at line 112 of file colvarproxy.h.

References atoms_masses.

Referenced by colvarmodule::atom::update_mass.

std::vector<cvm::real> const* colvarproxy_atoms::get_atom_masses ( ) const [inline]

Definition at line 170 of file colvarproxy.h.

References atoms_masses.

cvm::rvector colvarproxy_atoms::get_atom_position ( int index ) const [inline]

Read the current position of the given atom

Parameters:: index Internal index in the Colvars arrays.

Definition at line 133 of file colvarproxy.h.

References atoms_positions.

std::vector<cvm::rvector> const* colvarproxy_atoms::get_atom_positions ( ) const [inline]

Definition at line 194 of file colvarproxy.h.

References atoms_positions.

cvm::rvector colvarproxy_atoms::get_atom_total_force ( int index ) const [inline]

Read the current total force of the given atom

Parameters:: index Internal index in the Colvars arrays.

Definition at line 140 of file colvarproxy.h.

References atoms_total_forces.

std::vector<cvm::rvector> const* colvarproxy_atoms::get_atom_total_forces ( ) const [inline]

Definition at line 204 of file colvarproxy.h.

References atoms_total_forces.

cvm::rvector colvarproxy_atoms::get_atom_velocity ( int ) [inline]

Read the current velocity of the given atom.

Definition at line 154 of file colvarproxy.h.

References COLVARS_NOT_IMPLEMENTED, and colvarmodule::error.

size_t colvarproxy_atoms::get_num_active_atoms ( ) const

Return number of atoms with positive reference count.

Definition at line 105 of file colvarproxy.C.

References atoms_refcount, and result.

void colvarproxy_atoms::increase_refcount ( int index ) [inline]

Increase the reference count of the given atom

Parameters:: index Internal index in the Colvars arrays.

Definition at line 119 of file colvarproxy.h.

References atoms_refcount.

int colvarproxy_atoms::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 in colvarproxy_vmd.

Definition at line 74 of file colvarproxy.C.

References COLVARS_NOT_IMPLEMENTED, and colvarmodule::error.

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

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

Reimplemented in colvarproxy_vmd.

Definition at line 62 of file colvarproxy.C.

References COLVARS_NOT_IMPLEMENTED.

Referenced by check_atom_id.

int colvarproxy_atoms::load_atoms ( char const * filename,

cvm::atom_group & atoms,

std::string const & pdb_field,

double 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 in colvarproxy_vmd.

Definition at line 115 of file colvarproxy.C.

References COLVARS_NOT_IMPLEMENTED, and colvarmodule::error.

int colvarproxy_atoms::load_coords ( char const * filename,

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

std::vector< int > const & sorted_ids,

std::string const & pdb_field,

double pdb_field_value = 0.0

) [virtual]

\brief Load a set of coordinates from a file (usually PDB); if "pos" is already allocated, the number of its elements must match the number of entries in "filename"

Parameters:: filename name of the file

pos array of coordinates

sorted_ids array of sorted internal IDs, used to loop through the file only once

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.

Definition at line 126 of file colvarproxy.C.

References COLVARS_NOT_IMPLEMENTED, and colvarmodule::error.

cvm::real colvarproxy_atoms::max_atoms_applied_force ( ) const [inline]

Get the maximum norm among all applied forces.

Definition at line 237 of file colvarproxy.h.

References atoms_max_applied_force_.

int colvarproxy_atoms::max_atoms_applied_force_id ( ) const [inline]

Get the atom ID with the largest applied force.

Definition at line 243 of file colvarproxy.h.

References atoms_max_applied_force_id_.

std::vector<cvm::rvector>* colvarproxy_atoms::modify_atom_applied_forces ( ) [inline]

Definition at line 219 of file colvarproxy.h.

References atoms_new_colvar_forces.

std::vector<cvm::real>* colvarproxy_atoms::modify_atom_charges ( ) [inline]

Definition at line 187 of file colvarproxy.h.

References atoms_charges, and updated_charges_.

std::vector<cvm::real>* colvarproxy_atoms::modify_atom_masses ( ) [inline]

Definition at line 175 of file colvarproxy.h.

References atoms_masses, and updated_masses_.

std::vector<cvm::rvector>* colvarproxy_atoms::modify_atom_positions ( ) [inline]

Definition at line 199 of file colvarproxy.h.

References atoms_positions.

std::vector<cvm::rvector>* colvarproxy_atoms::modify_atom_total_forces ( ) [inline]

Definition at line 209 of file colvarproxy.h.

References atoms_total_forces.

int colvarproxy_atoms::reset ( )

Clear atomic data.

Reimplemented in colvarproxy.

Definition at line 36 of file colvarproxy.C.

References atoms_charges, atoms_ids, atoms_masses, atoms_new_colvar_forces, atoms_positions, atoms_refcount, and atoms_total_forces.

Referenced by colvarproxy::reset, and ~colvarproxy_atoms.

cvm::real colvarproxy_atoms::rms_atoms_applied_force ( ) const [inline]

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

Definition at line 231 of file colvarproxy.h.

References atoms_rms_applied_force_.

bool colvarproxy_atoms::updated_charges ( ) const [inline]

Record whether masses have been updated.

Definition at line 255 of file colvarproxy.h.

References updated_charges_.

bool colvarproxy_atoms::updated_masses ( ) const [inline]

Record whether masses have been updated.

Definition at line 249 of file colvarproxy.h.

References updated_masses_.

Member Data Documentation

std::vector<cvm::real> colvarproxy_atoms::atoms_charges [protected]

\brief Charges of the atoms (allow redefinition during a run, as done e.g. in LAMMPS).

Definition at line 270 of file colvarproxy.h.

Referenced by add_atom_slot, get_atom_charge, get_atom_charges, colvarproxy_vmd::init_atom, modify_atom_charges, colvarproxy::print_input_atomic_data, reset, and colvarproxy_vmd::update_atomic_properties.

std::vector<int> colvarproxy_atoms::atoms_ids [protected]

\brief Array of 0-based integers used to uniquely associate atoms within the host program.

Definition at line 264 of file colvarproxy.h.

Referenced by add_atom_slot, clear_atom, compute_max_atoms_applied_force, get_atom_id, get_atom_ids, colvarproxy_vmd::init_atom, colvarproxy::print_input_atomic_data, reset, colvarproxy_vmd::update_atomic_properties, and colvarproxy_vmd::update_input.

std::vector<cvm::real> colvarproxy_atoms::atoms_masses [protected]

\brief Masses of the atoms (allow redefinition during a run, as done e.g. in LAMMPS).

Definition at line 268 of file colvarproxy.h.

Referenced by add_atom_slot, get_atom_mass, get_atom_masses, colvarproxy_vmd::init_atom, modify_atom_masses, colvarproxy::print_input_atomic_data, reset, and colvarproxy_vmd::update_atomic_properties.

cvm::real colvarproxy_atoms::atoms_max_applied_force_ [protected]

Maximum norm among all applied forces.

Definition at line 282 of file colvarproxy.h.

Referenced by colvarproxy_atoms, compute_max_atoms_applied_force, and max_atoms_applied_force.

int colvarproxy_atoms::atoms_max_applied_force_id_ [protected]

ID of the atom with the maximum norm among all applied forces.

Definition at line 285 of file colvarproxy.h.

Referenced by colvarproxy_atoms, compute_max_atoms_applied_force, and max_atoms_applied_force_id.

std::vector<cvm::rvector> colvarproxy_atoms::atoms_new_colvar_forces [protected]

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

Definition at line 276 of file colvarproxy.h.

Referenced by add_atom_slot, apply_atom_force, compute_max_atoms_applied_force, get_atom_applied_forces, modify_atom_applied_forces, colvarproxy::print_output_atomic_data, reset, and colvarproxy_vmd::update_input.

std::vector<cvm::rvector> colvarproxy_atoms::atoms_positions [protected]

\brief Current three-dimensional positions of the atoms.

Definition at line 272 of file colvarproxy.h.

Referenced by add_atom_slot, get_atom_position, get_atom_positions, modify_atom_positions, colvarproxy::print_input_atomic_data, reset, and colvarproxy_vmd::update_input.

std::vector<size_t> colvarproxy_atoms::atoms_refcount [protected]

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

Definition at line 266 of file colvarproxy.h.

Referenced by add_atom_slot, clear_atom, get_num_active_atoms, increase_refcount, colvarproxy_vmd::init_atom, colvarproxy::print_input_atomic_data, and reset.

cvm::real colvarproxy_atoms::atoms_rms_applied_force_ [protected]

Root-mean-square of the applied forces.

Definition at line 279 of file colvarproxy.h.

Referenced by colvarproxy_atoms, compute_rms_atoms_applied_force, and rms_atoms_applied_force.

std::vector<cvm::rvector> colvarproxy_atoms::atoms_total_forces [protected]

\brief Most recent total forces on each atom.

Definition at line 274 of file colvarproxy.h.

Referenced by add_atom_slot, get_atom_total_force, get_atom_total_forces, modify_atom_total_forces, colvarproxy::print_input_atomic_data, and reset.

bool colvarproxy_atoms::updated_charges_ [protected]

Whether the masses and charges have been updated from the host code.

Definition at line 288 of file colvarproxy.h.

Referenced by colvarproxy_atoms, colvarproxy_vmd::colvarproxy_vmd, colvarproxy::end_of_step, modify_atom_charges, and updated_charges.

bool colvarproxy_atoms::updated_masses_ [protected]

Whether the masses and charges have been updated from the host code.

Definition at line 288 of file colvarproxy.h.

Referenced by colvarproxy_atoms, colvarproxy_vmd::colvarproxy_vmd, colvarproxy::end_of_step, modify_atom_masses, and updated_masses.

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