Communication between colvars and NAMD (implementation of colvarproxy) More...

#include <colvarproxy_namd.h>

Inheritance diagram for colvarproxy_namd:

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Collaboration diagram for colvarproxy_namd:

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Public Member Functions
void	init_tcl_pointers () override
	Set Tcl pointers. More...

int	setup () override
	(Re)initialize required member data (called after the module) More...

int	reset () override
	Reset proxy state, e.g. requested atoms. More...

int	update_target_temperature ()
	Get the target temperature from the NAMD thermostats supported so far.

void	init_atoms_map ()
	Allocate an atoms map with the same size as the NAMD topology.

int	update_atoms_map (AtomIDList::const_iterator begin, AtomIDList::const_iterator end)

void	calculate ()

void	log (std::string const &message) override
	Print a message to the main log. More...

void	error (std::string const &message) override
	Print a message to the main log and/or let the host code know about it. More...

int	set_unit_system (std::string const &units_in, bool check_only) override
	Request to set the units used internally by Colvars. More...

void	add_energy (cvm::real energy) override
	Pass restraint energy value for current timestep to MD engine. More...

void	request_total_force (bool yesno) override
	Tell the proxy whether total forces are needed (they may not always be available) More...

bool	total_forces_enabled () const override
	Are total forces being used? More...

int	run_force_callback () override
	Run a user-defined colvar forces script. More...

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

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

cvm::real	rand_gaussian () override
	Pseudo-random number with Gaussian distribution. More...

cvm::real	get_accelMD_factor () const override
	Get weight factor from accelMD. More...

bool	accelMD_enabled () const override

int	check_replicas_enabled () override
	Indicate if multi-replica support is available and active. More...

int	replica_index () override
	Index of this replica. More...

int	num_replicas () override
	Total number of replicas. More...

void	replica_comm_barrier () override
	Synchronize replica with others. More...

int	replica_comm_recv (char *msg_data, int buf_len, int src_rep) override
	Receive data from other replica. More...

int	replica_comm_send (char *msg_data, int msg_len, int dest_rep) override
	Send data to other replica. More...

int	check_atom_name_selections_available () override
	Check whether it is possible to select atoms by residue number name. More...

int	init_atom (int atom_number) override

int	check_atom_id (int atom_number) override

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

int	check_atom_id (cvm::residue_id const &residue, std::string const &atom_name, std::string const &segment_id) override
	Check that this atom is valid, but do not initialize it yet. More...

void	clear_atom (int index) override
	Used by the atom class destructor: rather than deleting the array slot (costly) set the corresponding atoms_refcount to zero. More...

void	update_atom_properties (int index)

cvm::rvector	position_distance (cvm::atom_pos const &pos1, cvm::atom_pos const &pos2) const
	Get the PBC-aware distance vector between two positions. More...

int	load_atoms_pdb (char const *filename, cvm::atom_group &atoms, std::string const &pdb_field, double const pdb_field_value) override
	Read a selection of atom IDs from a PDB coordinate file. More...

int	load_coords_pdb (char const *filename, std::vector< cvm::atom_pos > &pos, const std::vector< int > &indices, std::string const &pdb_field, double const pdb_field_value) override
	Load a set of coordinates from a PDB file. More...

int	scalable_group_coms () override
	Whether this proxy implementation has capability for scalable groups. More...

int	init_atom_group (std::vector< int > const &atoms_ids) override
	Prepare this group for collective variables calculation, selecting atoms by internal ids (0-based) More...

void	clear_atom_group (int index) override
	Used by the atom_group class destructor. More...

int	update_group_properties (int index)

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

int	init_volmap_by_id (int volmap_id) override

int	init_volmap_by_name (const char *volmap_name) override

int	check_volmap_by_id (int volmap_id) override

int	check_volmap_by_name (char const *volmap_name) override

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

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

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) override

template<class T >
void	getGridForceGridValue (int flags, T const grid, cvm::atom_iter atom_begin, cvm::atom_iter atom_end, cvm::real value, cvm::real *atom_field)
	Abstraction of the two types of NAMD volumetric maps.

template<class T , int flags>
void	GridForceGridLoop (T const g, cvm::atom_iter atom_begin, cvm::atom_iter atom_end, cvm::real value, cvm::real *atom_field)
	Implementation of inner loop; allows for atom list computation and use.

std::ostream &	output_stream (std::string const &output_name, std::string const description) override

int	flush_output_stream (std::string const &output_name) override
	Flushes the given output file/channel. More...

int	flush_output_streams () override
	Flushes all output files/channels. More...

int	close_output_stream (std::string const &output_name) override
	Closes the given output file/channel. More...

int	close_output_streams () override
	Close all open files/channels to prevent data loss. More...

int	backup_file (char const *filename) override
	Rename the given file, before overwriting it. More...

Public Member Functions inherited from colvarproxy
	colvarproxy ()
	Constructor.

	~colvarproxy () override
	Destructor.

std::string const &	engine_name () const

bool	io_available () override
	Ensure that we're on the main thread (derived class will do actual check) More...

virtual int	request_deletion ()
	Request deallocation of the module (currently only implemented by VMD) More...

bool	delete_requested () const
	Whether deallocation was requested.

virtual int	reset ()
	Reset proxy state, e.g. requested atoms. More...

virtual int	parse_module_config ()
	(Re)initialize the module

virtual int	load_atoms_pdb (char const *filename, cvm::atom_group &atoms, std::string const &pdb_field, double pdb_field_value)
	Read a selection of atom IDs from a PDB coordinate file. More...

virtual int	load_coords_pdb (char const *filename, std::vector< cvm::atom_pos > &pos, std::vector< int > const &sorted_ids, std::string const &pdb_field, double pdb_field_value)
	Load a set of coordinates from a PDB file. More...

virtual int	setup ()
	(Re)initialize required member data (called after the module) More...

bool	engine_ready () const
	Whether the engine allows to fully initialize Colvars immediately.

void	add_config (std::string const &cmd, std::string const &conf)
	Enqueue new configuration text, to be parsed as soon as possible.

virtual int	update_input ()

virtual int	update_output ()
	Update data based on the results of a Colvars call (e.g. send forces)

int	end_of_step ()
	Carry out operations needed before next simulation step is run.

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...

void	add_error_msg (std::string const &message)
	Record error message (used by VMD to collect them after a script call)

std::string const &	get_error_msgs ()
	Retrieve accumulated error messages.

void	clear_error_msgs ()
	As the name says.

bool	simulation_running () const
	Whether a simulation is running (warn against irrecovarable errors)

bool	simulation_continuing () const

int	post_run ()
	Called at the end of a simulation segment (i.e. "run" command)

void	print_input_atomic_data ()
	Print a full list of all input atomic arrays for debug purposes.

void	print_output_atomic_data ()
	Print a full list of all applied forces for debug purposes.

int	get_version_from_string (char const *version_string)
	Convert a version string "YYYY-MM-DD" into an integer.

int	version_number () const
	Get the version number (higher = more recent)

Public Member Functions inherited from colvarproxy_system
	colvarproxy_system ()
	Constructor.

virtual	~colvarproxy_system ()
	Destructor.

virtual int	set_unit_system (std::string const &units, bool check_only)
	Request to set the units used internally by Colvars. More...

cvm::real	angstrom_to_internal (cvm::real l) const
	Convert a length from Angstrom to internal.

cvm::real	internal_to_angstrom (cvm::real l) const
	Convert a length from internal to Angstrom.

cvm::real	boltzmann () const
	Boltzmann constant, with unit the same as energy / K.

cvm::real	target_temperature () const
	Current target temperature of the simulation (K units)

virtual int	set_target_temperature (cvm::real T)
	Set the current target temperature of the simulation (K units)

double	dt () const
	Time step of the simulation (fs units)

virtual int	set_integration_timestep (cvm::real dt)
	Set the current integration timestep of the simulation (fs units)

virtual cvm::real	rand_gaussian (void)
	Pseudo-random number with Gaussian distribution. More...

virtual void	add_energy (cvm::real energy)
	Pass restraint energy value for current timestep to MD engine. More...

virtual cvm::rvector	position_distance (cvm::atom_pos const &pos1, cvm::atom_pos const &pos2) const
	Get the PBC-aware distance vector between two positions. More...

void	update_pbc_lattice ()
	Recompute PBC reciprocal lattice (assumes XYZ periodicity)

void	reset_pbc_lattice ()
	Set the lattice vectors to zero.

virtual void	request_total_force (bool yesno)
	Tell the proxy whether total forces are needed (they may not always be available) More...

virtual bool	total_forces_enabled () const
	Are total forces being used? More...

virtual bool	total_forces_same_step () const
	Are total forces from the current step available? More...

virtual int	get_molid (int &molid)

virtual int	get_alch_lambda (cvm::real *lambda)
	Get value of alchemical lambda parameter from back-end (if available) More...

void	set_alch_lambda (cvm::real lambda)
	Set value of alchemical lambda parameter to be sent to back-end at end of timestep.

virtual int	send_alch_lambda ()
	Send cached value of alchemical lambda parameter to back-end (if available) More...

virtual int	get_dE_dlambda (cvm::real *dE_dlambda)
	Get energy derivative with respect to lambda (if available) More...

virtual int	apply_force_dE_dlambda (cvm::real *force)
	Apply a scalar force on dE_dlambda (back-end distributes it onto atoms)

virtual int	get_d2E_dlambda2 (cvm::real *d2E_dlambda2)
	Get energy second derivative with respect to lambda (if available)

virtual cvm::real	get_accelMD_factor () const
	Get weight factor from accelMD. More...

virtual bool	accelMD_enabled () const

Public Member Functions inherited from colvarproxy_atoms
	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. More...

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. More...

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. More...

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.

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.

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.

Public Member Functions inherited from colvarproxy_atom_groups
	colvarproxy_atom_groups ()
	Constructor.

virtual	~colvarproxy_atom_groups ()
	Destructor.

int	reset ()
	Clear atom group data.

virtual int	scalable_group_coms ()
	Whether this proxy implementation has capability for scalable groups. More...

virtual int	init_atom_group (std::vector< int > const &atoms_ids)
	Prepare this group for collective variables calculation, selecting atoms by internal ids (0-based) More...

virtual void	clear_atom_group (int index)
	Used by the atom_group class destructor. More...

int	get_atom_group_id (int index) const
	Get the numeric ID of the given atom group (for the MD program)

cvm::real	get_atom_group_mass (int index) const
	Get the mass of the given atom group.

cvm::real	get_atom_group_charge (int index) const
	Get the charge of the given atom group.

cvm::rvector	get_atom_group_com (int index) const
	Read the current position of the center of mass given atom group.

cvm::rvector	get_atom_group_total_force (int index) const
	Read the current total force of the given atom group.

void	apply_atom_group_force (int index, cvm::rvector const &new_force)
	Request that this force is applied to the given atom group.

cvm::rvector	get_atom_group_velocity (int)
	Read the current velocity of the given atom group.

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

size_t	get_num_active_atom_groups () const
	Return number of atom groups with positive reference count.

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

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

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

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

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

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

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

cvm::real	rms_atom_groups_applied_force () const
	Get the root-mean-square of the applied forces.

cvm::real	max_atom_groups_applied_force () const
	Get the maximum norm among all applied forces.

Public Member Functions inherited from colvarproxy_volmaps
	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.

Public Member Functions inherited from colvarproxy_smp
	colvarproxy_smp ()
	Constructor.

virtual	~colvarproxy_smp ()
	Destructor.

virtual int	check_smp_enabled ()
	Whether threaded parallelization is available (TODO: make this a cvm::deps feature)

virtual int	smp_colvars_loop ()
	Distribute calculation of colvars (and their components) across threads.

virtual int	smp_biases_loop ()
	Distribute calculation of biases across threads.

virtual int	smp_biases_script_loop ()
	Distribute calculation of biases across threads 2nd through last, with all scripted biased on 1st thread.

virtual int	smp_thread_id ()
	Index of this thread.

virtual int	smp_num_threads ()
	Number of threads sharing this address space.

virtual int	smp_lock ()
	Lock the proxy's shared data for access by a thread, if threads are implemented; if not implemented, does nothing.

virtual int	smp_trylock ()
	Attempt to lock the proxy's shared data.

virtual int	smp_unlock ()
	Release the lock.

Public Member Functions inherited from colvarproxy_replicas
	colvarproxy_replicas ()
	Constructor.

virtual	~colvarproxy_replicas ()
	Destructor.

virtual void	set_replicas_mpi_communicator (replicas_mpi_comm_t comm)
	Set the multiple replicas communicator.

virtual int	check_replicas_enabled ()
	Indicate if multi-replica support is available and active. More...

virtual int	replica_index ()
	Index of this replica. More...

virtual int	num_replicas ()
	Total number of replicas. More...

virtual void	replica_comm_barrier ()
	Synchronize replica with others. More...

virtual int	replica_comm_recv (char *msg_data, int buf_len, int src_rep)
	Receive data from other replica. More...

virtual int	replica_comm_send (char *msg_data, int msg_len, int dest_rep)
	Send data to other replica. More...

Public Member Functions inherited from colvarproxy_script
	colvarproxy_script ()
	Constructor.

virtual	~colvarproxy_script ()
	Destructor.

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 &cvcs, std::vector< cvm::matrix2d< cvm::real > > &gradient)

Public Member Functions inherited from colvarproxy_tcl
	colvarproxy_tcl ()
	Constructor.

virtual	~colvarproxy_tcl ()
	Destructor.

bool	tcl_available ()
	Is Tcl available? (trigger initialization if needed)

char const *	tcl_get_str (void *obj)
	Get a string representation of the Tcl object pointed to by obj.

int	tcl_run_script (std::string const &script)

int	tcl_run_file (std::string const &fileName)

int	tcl_run_force_callback ()
	Tcl implementation of run_force_callback()

int	tcl_run_colvar_callback (std::string const &name, std::vector< const colvarvalue * > const &cvcs, colvarvalue &value)
	Tcl implementation of run_colvar_callback()

int	tcl_run_colvar_gradient_callback (std::string const &name, std::vector< const colvarvalue * > const &cvcs, std::vector< cvm::matrix2d< cvm::real > > &gradient)
	Tcl implementation of run_colvar_gradient_callback()

Tcl_Interp *	get_tcl_interp ()
	Get a pointer to the Tcl interpreter.

void	set_tcl_interp (Tcl_Interp *interp)
	Set the pointer to the Tcl interpreter.

virtual void	init_tcl_pointers ()
	Set Tcl pointers. More...

Public Member Functions inherited from colvarproxy_io
	colvarproxy_io ()
	Constructor.

virtual	~colvarproxy_io ()
	Destructor.

virtual bool	io_available ()
	Ensure that we're on the main thread (derived class will do actual check) More...

virtual int	get_frame (long int &)
	Save the current frame number in the argument given. More...

virtual int	set_frame (long int)
	Set the current frame number (as well as colvarmodule::it) More...

std::string	get_current_work_dir () const
	Get the current working directory of this process.

std::string	join_paths (std::string const &path1, std::string const &path2) const
	Join two paths using the operating system's path separation.

virtual int	backup_file (char const *filename)
	Rename the given file, before overwriting it. More...

int	backup_file (std::string const &filename)
	Rename the given file, before overwriting it.

virtual int	remove_file (char const *filename)
	Remove the given file (on Windows only, rename to filename.old)

int	remove_file (std::string const &filename)
	Remove the given file (on Windows only, rename to filename.old)

virtual int	rename_file (char const filename, char const newfilename)
	Rename the given file.

int	rename_file (std::string const &filename, std::string const &newfilename)
	Rename the given file.

std::string const &	input_prefix () const
	Prefix of the input state file to be read next.

virtual int	set_input_prefix (std::string const &prefix)
	Initialize input_prefix (NOTE: it will be erased after state file is read)

std::string const &	output_prefix () const
	Default prefix to be used for all output files (final configuration)

virtual int	set_output_prefix (std::string const &prefix)
	Set default output prefix.

std::string const &	restart_output_prefix () const
	Prefix of the restart (checkpoint) file to be written next.

virtual int	set_restart_output_prefix (std::string const &prefix)
	Set default restart state file prefix.

int	default_restart_frequency () const
	Default restart frequency (as set by the simulation engine)

virtual int	set_default_restart_frequency (int freq)
	Communicate/set the restart frequency of the simulation engine.

std::istream &	input_stream (std::string const &input_name, std::string const description="file/channel", bool error_on_fail=true)

std::istream &	input_stream_from_string (std::string const &input_name, std::string const &content, std::string const description="string")

bool	input_stream_exists (std::string const &input_name)
	Check if the file/channel is open (without opening it if not)

int	close_input_stream (std::string const &input_name)
	Closes the given input stream.

int	close_input_streams ()
	Closes all input streams.

int	delete_input_stream (std::string const &input_name)
	Same as close_input_stream(), but also removes the corresponding entry from memory.

std::list< std::string >	list_input_stream_names () const
	List all input streams that were opened at some point.

virtual std::ostream &	output_stream (std::string const &output_name, std::string const description)

virtual bool	output_stream_exists (std::string const &output_name)
	Check if the file/channel is open (without opening it if not)

virtual int	flush_output_stream (std::string const &output_name)
	Flushes the given output file/channel. More...

virtual int	flush_output_streams ()
	Flushes all output files/channels. More...

virtual int	close_output_stream (std::string const &output_name)
	Closes the given output file/channel. More...

virtual int	close_output_streams ()
	Close all open files/channels to prevent data loss. More...

Protected Member Functions
void	update_accelMD_info ()

Protected Member Functions inherited from colvarproxy_atoms
int	add_atom_slot (int atom_id)

Protected Member Functions inherited from colvarproxy_atom_groups
int	add_atom_group_slot (int atom_group_id)
	Used by all init_atom_group() functions: create a slot for an atom group not requested yet.

Protected Attributes
std::vector< int >	atoms_map
	Array of atom indices (relative to the colvarproxy arrays), usedfor faster copy of atomic data.

SimParameters *	simparams
	Pointer to the NAMD simulation input object.

Random	random
	NAMD-style PRNG object.

bool	first_timestep

cvm::step_number	previous_NAMD_step

SubmitReduction *	reduction
	Used to submit restraint energy as MISC.

bool	accelMDOn
	Accelerated MD reweighting factor.

cvm::real	amd_weight_factor

Protected Attributes inherited from colvarproxy
bool	engine_ready_
	Whether the engine allows to fully initialize Colvars immediately.

std::string	error_output
	Collected error messages.

bool	b_simulation_running
	Whether a simulation is running (warn against irrecovarable errors)

bool	b_simulation_continuing

bool	b_delete_requested
	Whether the entire module should be deallocated by the host engine.

int	version_int
	Integer representing the version string (allows comparisons)

size_t	features_hash
	Track which features have been acknowledged during the last run.

std::string	engine_name_ = "standalone"
	Name of the simulation engine that the derived proxy object supports.

void *	config_queue_
	Queue of config strings or files to be fed to the module.

Protected Attributes inherited from colvarproxy_system
cvm::real	cached_alch_lambda
	Next value of lambda to be sent to back-end.

bool	cached_alch_lambda_changed
	Whether lambda has been set and needs to be updated in backend.

cvm::real	boltzmann_
	Boltzmann constant in internal Colvars units.

cvm::real	target_temperature_
	Most up to date target temperature (K units); default to 0.0 if undefined.

double	timestep_
	Current integration timestep (engine units); default to 1.0 if undefined.

cvm::real	angstrom_value_
	Value of 1 Angstrom in the internal (front-end) Colvars unit for atomic coordinates. More...

cvm::real	kcal_mol_value_
	Value of 1 kcal/mol in the internal Colvars unit for energy.

bool	total_force_requested
	Whether the total forces have been requested.

Boundaries_type	boundaries_type
	Type of boundary conditions.

cvm::rvector	unit_cell_x
	Bravais lattice vectors.

cvm::rvector	unit_cell_y

cvm::rvector	unit_cell_z

cvm::rvector	reciprocal_cell_x
	Reciprocal lattice vectors.

cvm::rvector	reciprocal_cell_y

cvm::rvector	reciprocal_cell_z

Protected Attributes inherited from colvarproxy_atoms
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 >	atoms_masses
	Masses of the atoms (allow redefinition during a run, as done e.g. in LAMMPS)

std::vector< cvm::real >	atoms_charges
	Charges of the atoms (allow redefinition during a run, as done e.g. in LAMMPS)

std::vector< cvm::rvector >	atoms_positions
	Current three-dimensional positions of the atoms.

std::vector< cvm::rvector >	atoms_total_forces
	Most recent total forces on each atom.

std::vector< 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_

Protected Attributes inherited from colvarproxy_atom_groups
std::vector< int >	atom_groups_ids
	Array of 0-based integers used to uniquely associate atom groups within the host program.

std::vector< size_t >	atom_groups_refcount
	Keep track of how many times each group is used by a separate cvc.

std::vector< cvm::real >	atom_groups_masses
	Total masses of the atom groups.

std::vector< cvm::real >	atom_groups_charges
	Total charges of the atom groups (allow redefinition during a run, as done e.g. in LAMMPS)

std::vector< cvm::rvector >	atom_groups_coms
	Current centers of mass of the atom groups.

std::vector< cvm::rvector >	atom_groups_total_forces
	Most recently updated total forces on the com of each group.

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

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

cvm::real	atom_groups_max_applied_force_
	Maximum norm among all applied group forces.

Protected Attributes inherited from colvarproxy_volmaps
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.

Protected Attributes inherited from colvarproxy_smp
omp_lock_t *	omp_lock_state
	Lock state for OpenMP.

Protected Attributes inherited from colvarproxy_replicas
replicas_mpi_comm_t	replicas_mpi_comm
	MPI communicator containint 1 root proc from each world.

int	replicas_mpi_rank = 0
	Index (rank) of this replica in the MPI implementation.

int	replicas_mpi_num = 1
	Number of replicas in the MPI implementation.

Protected Attributes inherited from colvarproxy_tcl
Tcl_Interp *	tcl_interp_
	Pointer to Tcl interpreter object.

Protected Attributes inherited from colvarproxy_io
std::string	input_prefix_str
	Prefix of the input state file to be read next.

std::string	output_prefix_str
	Default prefix to be used for all output files (final configuration)

std::string	restart_output_prefix_str
	Prefix of the restart (checkpoint) file to be written next.

int	restart_frequency_engine
	How often the simulation engine will write its own restart.

std::map< std::string, std::istream * >	input_streams_
	Container of input files/channels indexed by path name.

std::istream *	input_stream_error_
	Object whose reference is returned when read errors occur.

std::map< std::string, std::ostream * >	output_streams_
	Currently open output files/channels.

std::ostream *	output_stream_error_
	Object whose reference is returned when write errors occur.

Friends
class	cvm::atom

Additional Inherited Members
Public Types inherited from colvarproxy_volmaps
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 Attributes inherited from colvarproxy
colvarmodule *	colvars
	Pointer to the main object.

Public Attributes inherited from colvarproxy_system
std::string	units
	Name of the unit system used internally by Colvars (by default, that of the back-end). Supported depending on the back-end: real (A, kcal/mol), metal (A, eV), electron (Bohr, Hartree), gromacs (nm, kJ/mol) Note: calls to back-end PBC functions assume back-end length unit We use different unit from back-end in VMD bc using PBC functions from colvarproxy base class Colvars internal units are user specified, because the module exchanges info in unknown composite dimensions with user input, while it only exchanges quantities of known dimension with the back-end (length and forces)

cvm::real	indirect_lambda_biasing_force
	Force to be applied onto alch. lambda, propagated from biasing forces on dE_dlambda.

Public Attributes inherited from colvarproxy_smp
bool	b_smp_active

Public Attributes inherited from colvarproxy_script
colvarscript *	script

bool	have_scripts
	Do we have a scripting interface?

Protected Types inherited from colvarproxy_system
enum	Boundaries_type { boundaries_non_periodic , boundaries_pbc_ortho , boundaries_pbc_triclinic , boundaries_unsupported }
	Type of boundary conditions. More...

Detailed Description

Communication between colvars and NAMD (implementation of colvarproxy)

Member Function Documentation

◆ accelMD_enabled()

bool colvarproxy_namd::accelMD_enabled ( ) const

inlineoverridevirtual

Reimplemented from colvarproxy_system.

◆ add_energy()

void colvarproxy_namd::add_energy ( cvm::real energy )

overridevirtual

Pass restraint energy value for current timestep to MD engine.

Reimplemented from colvarproxy_system.

◆ backup_file()

int colvarproxy_namd::backup_file ( char const * filename )

overridevirtual

Rename the given file, before overwriting it.

Reimplemented from colvarproxy_io.

◆ check_atom_id() [1/2]

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

overridevirtual

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

Reimplemented from colvarproxy_atoms.

◆ check_atom_id() [2/2]

int colvarproxy_namd::check_atom_id ( int atom_number )

overridevirtual

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

Reimplemented from colvarproxy_atoms.

◆ check_atom_name_selections_available()

int colvarproxy_namd::check_atom_name_selections_available ( )

overridevirtual

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

Reimplemented from colvarproxy_atoms.

◆ check_replicas_enabled()

int colvarproxy_namd::check_replicas_enabled ( )

overridevirtual

Indicate if multi-replica support is available and active.

Reimplemented from colvarproxy_replicas.

◆ check_volmap_by_id()

int colvarproxy_namd::check_volmap_by_id ( int volmap_id )

overridevirtual

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.

◆ check_volmap_by_name()

int colvarproxy_namd::check_volmap_by_name ( char const * volmap_name )

overridevirtual

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 from colvarproxy_volmaps.

◆ check_volmaps_available()

int colvarproxy_namd::check_volmaps_available ( )

overridevirtual

Test whether this implementation can use volumetric maps as CVs.

Reimplemented from colvarproxy_volmaps.

◆ clear_atom()

void colvarproxy_namd::clear_atom ( int index )

overridevirtual

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

Reimplemented from colvarproxy_atoms.

◆ clear_atom_group()

void colvarproxy_namd::clear_atom_group ( int index )

overridevirtual

Used by the atom_group class destructor.

Reimplemented from colvarproxy_atom_groups.

◆ clear_volmap()

void colvarproxy_namd::clear_volmap ( int index )

overridevirtual

Used by the CVC destructors.

Reimplemented from colvarproxy_volmaps.

◆ close_output_stream()

int colvarproxy_namd::close_output_stream ( std::string const & output_name )

overridevirtual

Closes the given output file/channel.

Reimplemented from colvarproxy_io.

◆ close_output_streams()

int colvarproxy_namd::close_output_streams ( )

overridevirtual

Close all open files/channels to prevent data loss.

Reimplemented from colvarproxy_io.

◆ compute_volmap()

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

overridevirtual

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.

◆ error()

void colvarproxy_namd::error ( std::string const & message )

overridevirtual

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

Reimplemented from colvarproxy.

◆ flush_output_stream()

int colvarproxy_namd::flush_output_stream ( std::string const & output_name )

overridevirtual

Flushes the given output file/channel.

Reimplemented from colvarproxy_io.

◆ flush_output_streams()

int colvarproxy_namd::flush_output_streams ( )

overridevirtual

Flushes all output files/channels.

Reimplemented from colvarproxy_io.

◆ get_accelMD_factor()

cvm::real colvarproxy_namd::get_accelMD_factor ( ) const

inlineoverridevirtual

Get weight factor from accelMD.

Reimplemented from colvarproxy_system.

◆ get_volmap_id_from_name()

int colvarproxy_namd::get_volmap_id_from_name ( char const * volmap_name )

overridevirtual

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

Reimplemented from colvarproxy_volmaps.

◆ init_atom() [1/2]

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

overridevirtual

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.

◆ init_atom() [2/2]

int colvarproxy_namd::init_atom ( int atom_number )

overridevirtual

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

Reimplemented from colvarproxy_atoms.

◆ init_atom_group()

int colvarproxy_namd::init_atom_group ( std::vector< int > const & atoms_ids )

overridevirtual

Prepare this group for collective variables calculation, selecting atoms by internal ids (0-based)

Reimplemented from colvarproxy_atom_groups.

◆ init_tcl_pointers()

void colvarproxy_namd::init_tcl_pointers ( )

overridevirtual

Set Tcl pointers.

Reimplemented from colvarproxy_tcl.

◆ init_volmap_by_id()

int colvarproxy_namd::init_volmap_by_id ( int volmap_id )

overridevirtual

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.

◆ init_volmap_by_name()

int colvarproxy_namd::init_volmap_by_name ( const char * volmap_name )

overridevirtual

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 from colvarproxy_volmaps.

◆ load_atoms_pdb()

int colvarproxy_namd::load_atoms_pdb	(	char const *	filename,
		cvm::atom_group &	atoms,
		std::string const &	pdb_field,
		double const	pdb_field_value
	)

overridevirtual

Read a selection of atom IDs from a PDB coordinate file.

Parameters

[in]	filename	name of the file
[in,out]	atoms	array into which atoms will be read from "filename"
[in]	pdb_field	if the file is a PDB and this string is non-empty, select atoms for which this field is non-zero
[in]	pdb_field_value	if non-zero, select only atoms whose pdb_field equals this

Reimplemented from colvarproxy.

◆ load_coords_pdb()

int colvarproxy_namd::load_coords_pdb	(	char const *	filename,
		std::vector< cvm::atom_pos > &	pos,
		const std::vector< int > &	sorted_ids,
		std::string const &	pdb_field,
		double const	pdb_field_value
	)

overridevirtual

Load a set of coordinates from a PDB file.

Parameters

[in]	filename	name of the file
[in,out]	pos	array of coordinates to fill; if not empty, the number of its elements must match the number of entries in "filename"
[in]	sorted_ids	array of sorted internal IDs, used to loop through the file only once
[in]	pdb_field	if non-empty, only atoms for which this field is non-zero will be processed
[in]	pdb_field_value	if non-zero, process only atoms whose pdb_field equals this

Reimplemented from colvarproxy.

◆ log()

void colvarproxy_namd::log ( std::string const & message )

overridevirtual

Print a message to the main log.

Reimplemented from colvarproxy.

◆ num_replicas()

int colvarproxy_namd::num_replicas ( )

overridevirtual

Total number of replicas.

Reimplemented from colvarproxy_replicas.

◆ output_stream()

std::ostream & colvarproxy_namd::output_stream	(	std::string const &	output_name,
		std::string const	description
	)

overridevirtual

Returns a reference to the named output file/channel (open it if needed)

Parameters

output_name	File name or identifier
description	Purpose of the file

Reimplemented from colvarproxy_io.

◆ position_distance()

cvm::rvector colvarproxy_namd::position_distance	(	cvm::atom_pos const &	pos1,
		cvm::atom_pos const &	pos2
	)		const

virtual

Get the PBC-aware distance vector between two positions.

Reimplemented from colvarproxy_system.

◆ rand_gaussian()

cvm::real colvarproxy_namd::rand_gaussian ( void )

inlineoverridevirtual

Pseudo-random number with Gaussian distribution.

Reimplemented from colvarproxy_system.

◆ replica_comm_barrier()

void colvarproxy_namd::replica_comm_barrier ( )

overridevirtual

Synchronize replica with others.

Reimplemented from colvarproxy_replicas.

◆ replica_comm_recv()

int colvarproxy_namd::replica_comm_recv	(	char *	msg_data,
		int	buf_len,
		int	src_rep
	)

overridevirtual

Receive data from other replica.

Reimplemented from colvarproxy_replicas.

◆ replica_comm_send()

int colvarproxy_namd::replica_comm_send	(	char *	msg_data,
		int	msg_len,
		int	dest_rep
	)

overridevirtual

Send data to other replica.

Reimplemented from colvarproxy_replicas.

◆ replica_index()

int colvarproxy_namd::replica_index ( )

overridevirtual

Index of this replica.

Reimplemented from colvarproxy_replicas.

◆ request_total_force()

void colvarproxy_namd::request_total_force ( bool yesno )

overridevirtual

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

Reimplemented from colvarproxy_system.

◆ reset()

int colvarproxy_namd::reset ( )

overridevirtual

Reset proxy state, e.g. requested atoms.

Reimplemented from colvarproxy.

◆ run_colvar_callback()

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

overridevirtual

Reimplemented from colvarproxy_script.

◆ run_colvar_gradient_callback()

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

overridevirtual

Reimplemented from colvarproxy_script.

◆ run_force_callback()

int colvarproxy_namd::run_force_callback ( )

overridevirtual

Run a user-defined colvar forces script.

Reimplemented from colvarproxy_script.

◆ scalable_group_coms()

int colvarproxy_namd::scalable_group_coms ( )

inlineoverridevirtual

Whether this proxy implementation has capability for scalable groups.

Reimplemented from colvarproxy_atom_groups.

◆ set_unit_system()

int colvarproxy_namd::set_unit_system	(	std::string const &	units,
		bool	check_only
	)

overridevirtual

Request to set the units used internally by Colvars.

Reimplemented from colvarproxy_system.

◆ setup()

int colvarproxy_namd::setup ( )

overridevirtual

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

Reimplemented from colvarproxy.

◆ total_forces_enabled()

bool colvarproxy_namd::total_forces_enabled ( ) const

inlineoverridevirtual

Are total forces being used?

Reimplemented from colvarproxy_system.

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

colvarproxy_namd.h

Public Member Functions

Protected Member Functions

Protected Attributes

Friends

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ accelMD_enabled()

◆ add_energy()

◆ backup_file()

◆ check_atom_id() [1/2]

◆ check_atom_id() [2/2]

◆ check_atom_name_selections_available()

◆ check_replicas_enabled()

◆ check_volmap_by_id()

◆ check_volmap_by_name()

◆ check_volmaps_available()

◆ clear_atom()

◆ clear_atom_group()

◆ clear_volmap()

◆ close_output_stream()

◆ close_output_streams()

◆ compute_volmap()

◆ error()

◆ flush_output_stream()

◆ flush_output_streams()

◆ get_accelMD_factor()

◆ get_volmap_id_from_name()

◆ init_atom() [1/2]

◆ init_atom() [2/2]

◆ init_atom_group()

◆ init_tcl_pointers()

◆ init_volmap_by_id()

◆ init_volmap_by_name()

◆ load_atoms_pdb()

◆ load_coords_pdb()

◆ log()

◆ num_replicas()

◆ output_stream()

◆ position_distance()

◆ rand_gaussian()

◆ replica_comm_barrier()

◆ replica_comm_recv()

◆ replica_comm_send()

◆ replica_index()

◆ request_total_force()

◆ reset()

◆ run_colvar_callback()

◆ run_colvar_gradient_callback()

◆ run_force_callback()

◆ scalable_group_coms()

◆ set_unit_system()

◆ setup()

◆ total_forces_enabled()