Molecular dynamics optimizer on 1-D and 3-D particles. More...

#include <IMP/isd/MolecularDynamics.h>

Inheritance diagram for IMP::isd::MolecularDynamics:

Public Member Functions
	MolecularDynamics (kernel::Model *m=nullptr)

void	assign_velocities (Float temperature)
	Assign velocities representative of the given temperature.

Float	get_kinetic_energy () const

Public Member Functions inherited from IMP::atom::MolecularDynamics
	MolecularDynamics (kernel::Model *m)

virtual double	do_step (const kernel::ParticleIndexes &sc, double dt)

Float	get_kinetic_temperature (Float ekinetic) const

virtual std::string	get_type_name () const

virtual ::IMP::base::VersionInfo	get_version_info () const
	Get information about the module and version of the object.

void	set_velocity_cap (Float velocity_cap)
	Set maximum velocity in A/fs. More...

virtual void	setup (const kernel::ParticleIndexes &ps)

Public Member Functions inherited from IMP::atom::Simulator
	Simulator (kernel::Model *m, std::string name="Simulator %1%", double wave_factor=1.0)

double	get_current_time () const

double	get_kt () const

kernel::ParticleIndexes	get_simulation_particle_indexes () const

kernel::ParticlesTemp	get_simulation_particles () const

double	get_temperature () const

void	set_current_time (double ct)

void	set_temperature (double d)

double	simulate (double time_in_fs)
	Simulate for a given time in fs. More...

double	simulate_wave (double time_in_fs, double max_time_step_factor=10.0, double base=1.5)

void	set_maximum_time_step (double ts)

double	get_maximum_time_step () const

double	get_last_time_step () const

void	remove_particle (kernel::Particle *d)

void	remove_particles (const kernel::Particles &d)

void	set_particles (const kernel::Particles &ps)

void	set_particles_order (const kernel::Particles &objs)

unsigned int	add_particle (kernel::Particle *obj)

void	add_particles (const kernel::Particles &objs)

void	clear_particles ()

unsigned int	get_number_of_particles () const

bool	get_has_particles ()

kernel::Particle *	get_particle (unsigned int i) const

kernel::Particles	get_particles () const

void	reserve_particles (unsigned int sz)

Public Member Functions inherited from IMP::kernel::Optimizer
	Optimizer (kernel::Model *m, std::string name="Optimizer %1%")

	Optimizer ()

void	clear_range_cache ()

Float	get_derivative (FloatIndex fi) const

double	get_last_score () const
	Return the score found in the last evaluate.

FloatIndexes	get_optimized_attributes () const

Restraints	get_restraints () const

double	get_scaled_derivative (FloatIndex fi) const

double	get_scaled_value (FloatIndex fi) const

double	get_score_threshold () const

ScoringFunction *	get_scoring_function () const
	Return the scoring function that is being used.

bool	get_stop_on_good_score () const

Float	get_value (FloatIndex fi) const

double	get_width (FloatKey k) const

double	optimize (unsigned int max_steps)
	Optimize the model for up to max_steps iterations. More...

void	set_restraints (const RestraintsTemp &rs)

void	set_scaled_value (FloatIndex fi, Float v) const

void	set_score_threshold (double s)

virtual void	set_scoring_function (ScoringFunctionAdaptor sf)

void	set_stop_on_good_score (bool tf)

void	set_value (FloatIndex fi, double v) const

double	width (FloatKey k) const

void	remove_optimizer_state (OptimizerState *d)

void	remove_optimizer_states (const OptimizerStates &d)

void	set_optimizer_states (const OptimizerStates &ps)

void	set_optimizer_states_order (const OptimizerStates &objs)

unsigned int	add_optimizer_state (OptimizerState *obj)

void	add_optimizer_states (const OptimizerStates &objs)

void	clear_optimizer_states ()

unsigned int	get_number_of_optimizer_states () const

bool	get_has_optimizer_states ()

OptimizerState *	get_optimizer_state (unsigned int i) const

OptimizerStates	get_optimizer_states () const

void	reserve_optimizer_states (unsigned int sz)

Public Member Functions inherited from IMP::kernel::ModelObject
	ModelObject (kernel::Model *m, std::string name)

	ModelObject (std::string name)

bool	get_has_dependencies () const
	Return whether this object has dependencies computed.

bool	get_has_required_score_states () const

ModelObjectsTemp	get_inputs () const

ModelObjectsTemps	get_interactions () const

bool	get_is_part_of_model () const

Model *	get_model () const

ModelObjectsTemp	get_outputs () const

const ScoreStatesTemp &	get_required_score_states () const

void	set_has_dependencies (bool tf)

void	set_has_required_score_states (bool tf)

virtual void	set_model (kernel::Model *m)

Public Member Functions inherited from IMP::base::Object
virtual void	clear_caches ()

virtual void	do_destroy ()

CheckLevel	get_check_level () const

LogLevel	get_log_level () const

void	set_check_level (CheckLevel l)

void	set_log_level (LogLevel l)
	Set the logging level used in this object. More...

void	set_was_used (bool tf) const

void	show (std::ostream &out=std::cout) const

const std::string &	get_name () const

void	set_name (std::string name)

Protected Member Functions
bool	get_is_simulation_particle (kernel::ParticleIndex pi) const

void	propagate_coordinates (const kernel::ParticleIndexes &ps, double step_size)
	First part of velocity Verlet (update coordinates and half-step velocity)

void	propagate_velocities (const kernel::ParticleIndexes &ps, double step_size)
	Second part of velocity Verlet (update velocity)

void	setup_degrees_of_freedom (const kernel::ParticleIndexes &ps)

Protected Member Functions inherited from IMP::atom::MolecularDynamics
void	cap_velocity_component (Float &vel)
	Cap a velocity component to the maximum value.

void	initialize ()

Protected Member Functions inherited from IMP::atom::Simulator
virtual Float	do_optimize (unsigned int max_steps)
	override this function to do actual optimization

Protected Member Functions inherited from IMP::kernel::Optimizer
virtual ModelObjectsTemp	do_get_inputs () const

virtual ModelObjectsTemp	do_get_outputs () const
	don't return anything here to avoid pointless dependencies

ModelObjectsTemp	get_optimizer_state_inputs () const

void	update_states () const
	Update optimizer states, should be called at each successful step. More...

Protected Member Functions inherited from IMP::kernel::ModelObject
virtual ModelObjectsTemps	do_get_interactions () const

virtual void	handle_set_has_required_score_states (bool)

Protected Member Functions inherited from IMP::base::Object
	Object (std::string name)
	Construct an object with the given name. More...

	Object ()

Protected Attributes
FloatKey	vnuis_
	Keys of the xyz velocities.

Protected Attributes inherited from IMP::atom::MolecularDynamics
int	degrees_of_freedom_
	Number of degrees of freedom in the system.

Float	velocity_cap_
	Maximum absolute value of a single velocity component.

FloatKey	vs_ [3]
	Keys of the xyz velocities.

Detailed Description

The particles to be optimized must be XYZs or Nuisances, and should have a non-optimizable mass.

See Also: MolecularDynamics in the atom module for more details

Definition at line 25 of file isd/MolecularDynamics.h.

Constructor & Destructor Documentation

IMP::isd::MolecularDynamics::MolecularDynamics ( kernel::Model * m = nullptr )

Score based on the provided model

Member Function Documentation

bool IMP::isd::MolecularDynamics::get_is_simulation_particle ( kernel::ParticleIndex p ) const

protectedvirtual

Return true if the passed particle is appropriate for the simulation.

Reimplemented from IMP::atom::MolecularDynamics.

Float IMP::isd::MolecularDynamics::get_kinetic_energy ( ) const

virtual

Returns: the current kinetic energy of the system, in kcal/mol

Reimplemented from IMP::atom::MolecularDynamics.

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

isd/MolecularDynamics.h

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation