Detailed Description

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

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

See Also: atom::MolecularDynamics for more details

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

Public Member Functions
	MolecularDynamics (Model *m=nullptr)

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

Float	get_kinetic_energy () const override
	Return the current kinetic energy of the system, in kcal/mol. More...

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

virtual double	do_step (const ParticleIndexes &sc, double dt) override
	Perform a single time step. More...

Float	get_kinetic_temperature (Float ekinetic) const
	Return the current kinetic temperature of the system. More...

virtual std::string	get_type_name () const override

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

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

virtual void	setup (const ParticleIndexes &ps) override

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

double	get_current_time () const

double	get_kt () const

ParticleIndexes	get_simulation_particle_indexes () const

ParticlesTemp	get_simulation_particles () const
	Returns the set of particles used in the simulation. More...

double	get_temperature () const
	Return the simulator temperature in kelvin. More...

void	set_current_time (double ct)
	Sets the current simulation time in femtoseconds to ct. More...

void	set_temperature (double d)
	Set the temperature of the simulator to d in kelvin units. More...

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
	Get the maximum allowed time step in fs. More...

double	get_last_time_step () const

void	remove_particle (Particle *d)

void	remove_particles (const Particles &d)

void	set_particles (const Particles &ps)

void	set_particles_order (const Particles &objs)

unsigned int	add_particle (Particle *obj)

void	add_particles (const Particles &objs)

void	clear_particles ()

unsigned int	get_number_of_particles () const

bool	get_has_particles ()

Particle *	get_particle (unsigned int i) const

Particles	get_particles () const

void	erase_particle (unsigned int i)

void	reserve_particles (unsigned int sz)

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

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

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

bool	get_stop_on_good_score () const

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

virtual void	set_scoring_function (ScoringFunctionAdaptor sf)
	Set the scoring function to use. More...

void	set_stop_on_good_score (bool tf)

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	erase_optimizer_state (unsigned int i)

void	reserve_optimizer_states (unsigned int sz)

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

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

bool	get_has_required_score_states () const
	Return whether score states are computed. More...

ModelObjectsTemp	get_inputs () const

ModelObjectsTemps	get_interactions () const
	Get the interacting sets induced by this ModelObject. More...

Model *	get_model () const

ModelObjectsTemp	get_outputs () const

const ScoreStatesTemp &	get_required_score_states () const
	Get the score states that are ancestors of this in the dependency graph. More...

void	set_has_dependencies (bool tf)
	Either invalidate the dependencies or ensure they are correct. More...

void	set_has_required_score_states (bool tf)
	Compute the required score states. More...

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

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 (ParticleIndex pi) const override
	Return true if the passed particle is appropriate for the simulation. More...

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

void	propagate_velocities (const ParticleIndexes &ps, double step_size) override
	Second part of velocity Verlet (update velocity) More...

void	setup_degrees_of_freedom (const ParticleIndexes &ps) override

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

void	initialize ()

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

virtual double	do_simulate (double time)

virtual double	do_simulate_wave (double time_in_fs, double max_time_step_factor=10.0, double base=1.5)

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

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

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::ModelObject
virtual ModelObjectsTemps	do_get_interactions () const

virtual void	handle_set_has_required_score_states (bool)

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

virtual void	do_destroy ()

Protected Attributes
FloatKey	vnuis_
	Keys of the xyz velocities. More...

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

Float	velocity_cap_
	Maximum absolute value of a single velocity component. More...