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IMP Reference Guide  develop.716bca0a46,2020/04/04
The Integrative Modeling Platform
IMP::atom::BrownianDynamics Class Reference

Simple Brownian dynamics simulator. More...

#include <IMP/atom/BrownianDynamics.h>

+ Inheritance diagram for IMP::atom::BrownianDynamics:

Detailed Description

Simple Brownian dynamics simulator.

This is an implementation of a Brownian Dynamics simulator.

Input particles and score

Each optimized particle must have x,y,z attributes that are optimizable. In addition, each optimized particle must be decorated with the Diffusion decorator. Optionally, the RigidBodyDiffusion decorator can be used to specify a rotational diffusion coefficient for core::RigidBody particles. The optimizer assumes the scoring function to be energy in kcal/mol, and the xyz coordinates to be in angstroms and the diffusion coefficient of each particle be in \(A^2/fs\) (or \(Radian^2/fs\) for rotational diffusion coefficient). Particles without optimized x,y,z and nonoptimized D are skipped.

The optimizer can either automatically determine which particles to use from the model or be passed a SingletonContainer for the particles. If such a container is passed, particles added to it during optimization state updates are handled properly.

Simulation

At each simulation time step, each particle is translated in the direction of the sum of a random diffusion vector and the gradient of the scoring function (force field) at the particle coordinates. The translation is proportional to the particle diffusion coefficient, the time step size, and the inverse of kT. Note that particle masses are not considered, only their diffusion coefficients.

Similarly, rigid bodies are rotated by the sum of a random torque and a force field torque, proportionally to the rotational diffusion coefficient and the time step size, and inversely proportional to kT.

Time step

The time step is always equal precisely to Simulator::get_maximum_time_step() when using either Simulator::simulate() or Optimizer::optimize()

For more information and a demonstration of using this class, see the Brownian dynamics tutorial.

See Also
Diffusion
RigidBodyDiffusion

Definition at line 80 of file BrownianDynamics.h.

Public Member Functions

 BrownianDynamics (Model *m, std::string name="BrownianDynamics%1%", double wave_factor=1.0, unsigned int random_pool_size=10000)
 Create the optimizer. More...
 
virtual std::string get_type_name () const
 
virtual ::IMP::VersionInfo get_version_info () const
 Get information about the module and version of the object. More...
 
void set_maximum_move (double ms_in_A)
 sets the maximum move in A along either x,y or z axes More...
 
void set_use_stochastic_runge_kutta (bool tf)
 Set whether to use the stochastic Runge Kutta scheme. More...
 
- 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 temeprature 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 ()
 
Particleget_particle (unsigned int i) const
 
Particles get_particles () const
 
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...
 
ScoringFunctionget_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 ()
 
OptimizerStateget_optimizer_state (unsigned int i) const
 
OptimizerStates get_optimizer_states () const
 
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...
 
Modelget_model () const
 
ModelObjectsTemp get_outputs () const
 
const ScoreStatesTempget_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

virtual void do_advance_chunk (double dtfs, double ikt, const ParticleIndexes &ps, unsigned int begin, unsigned int end)
 
virtual double do_step (const ParticleIndexes &sc, double dt_fs)
 
algebra::Vector3D const & get_force (unsigned int i) const
 get the force felt on particle i in kCal/mol/A More...
 
algebra::Vector3Ds const & get_forces () const
 get the force vectors felt on each particle in kCal/mol/A More...
 
virtual bool get_is_simulation_particle (ParticleIndex p) const
 Return true if the passed particle is appropriate for the simulation. More...
 
bool get_is_srk () const
 
double get_max_step () const
 
double get_sample (double sigma)
 
void reset_random_pool ()
 regenerate internal cached pool of random numbers More...
 
void set_force (unsigned int i, algebra::Vector3D const &f)
 set the force felt on particle i to f More...
 
virtual void setup (const ParticleIndexes &ps)
 
- Protected Member Functions inherited from IMP::atom::Simulator
virtual Float do_optimize (unsigned int max_steps)
 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
 
virtual ModelObjectsTemp do_get_outputs () const
 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 ()
 

Constructor & Destructor Documentation

IMP::atom::BrownianDynamics::BrownianDynamics ( Model m,
std::string  name = "BrownianDynamics%1%",
double  wave_factor = 1.0,
unsigned int  random_pool_size = 10000 
)

Create the optimizer.

If sc is not null, that container will be used to find particles to move, otherwise the model will be searched.

Parameters
mmodel associated with bd
namename of bd object
wave_factorfor wave step function, see Simulator object, if >1.001 or so, creates a wave of time steps that are larger by up to wave_factor from formal maximal time step
random_pool_sizenumber of random numbers in internal pool used to accelerate random number generation. Memory requirement scales accordingly.
Note
wave_factor is an advanced feature - if you're not sure, just use its default, see also Simulator::simulate_wave()

Member Function Documentation

virtual void IMP::atom::BrownianDynamics::do_advance_chunk ( double  dtfs,
double  ikt,
const ParticleIndexes ps,
unsigned int  begin,
unsigned int  end 
)
protectedvirtual

advances a chunk of ps from index begin to end

Parameters
dtfstime step in femtoseconds
iktinverse kT for current chunk step
psparticle indexes to advance
beginbeginning index of chunk of ps
endend index of chunk of ps

Reimplemented in IMP::atom::BrownianDynamicsTAMD, and IMP::npctransport::BrownianDynamicsTAMDWithSlabSupport.

virtual double IMP::atom::BrownianDynamics::do_step ( const ParticleIndexes sc,
double  dt_fs 
)
protectedvirtual

Calls do_advance_chunk() to advance ps in chunks

Parameters
scparticles to simulate in this step
dt_fsstep size in femtoseconds
Returns
the time step actually simulated (for this class, it is always equal to the input dt_fs)

Implements IMP::atom::Simulator.

algebra::Vector3D const& IMP::atom::BrownianDynamics::get_force ( unsigned int  i) const
protected

get the force felt on particle i in kCal/mol/A

Definition at line 185 of file BrownianDynamics.h.

algebra::Vector3Ds const& IMP::atom::BrownianDynamics::get_forces ( ) const
protected

get the force vectors felt on each particle in kCal/mol/A

Definition at line 181 of file BrownianDynamics.h.

virtual bool IMP::atom::BrownianDynamics::get_is_simulation_particle ( ParticleIndex  p) const
protectedvirtual

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

Implements IMP::atom::Simulator.

bool IMP::atom::BrownianDynamics::get_is_srk ( ) const
protected

returns true if implementing the Stochastic Runga-Kutta Brownian Dynamics variant

Definition at line 157 of file BrownianDynamics.h.

double IMP::atom::BrownianDynamics::get_max_step ( ) const
protected

returns the maximal step size allowed in this simulation in A along x, y or z axes

Definition at line 153 of file BrownianDynamics.h.

double IMP::atom::BrownianDynamics::get_sample ( double  sigma)
protected

returns a normally distributed sample with mean zero and std-dev sigma

Definition at line 165 of file BrownianDynamics.h.

virtual ::IMP::VersionInfo IMP::atom::BrownianDynamics::get_version_info ( ) const
virtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 116 of file BrownianDynamics.h.

void IMP::atom::BrownianDynamics::reset_random_pool ( )
protected

regenerate internal cached pool of random numbers

void IMP::atom::BrownianDynamics::set_force ( unsigned int  i,
algebra::Vector3D const &  f 
)
protected

set the force felt on particle i to f

Definition at line 176 of file BrownianDynamics.h.

void IMP::atom::BrownianDynamics::set_maximum_move ( double  ms_in_A)

sets the maximum move in A along either x,y or z axes

Definition at line 111 of file BrownianDynamics.h.

void IMP::atom::BrownianDynamics::set_use_stochastic_runge_kutta ( bool  tf)

Set whether to use the stochastic Runge Kutta scheme.

Definition at line 114 of file BrownianDynamics.h.

virtual void IMP::atom::BrownianDynamics::setup ( const ParticleIndexes ps)
protectedvirtual

a set of setup operations before a series of simulation steps

Reimplemented from IMP::atom::Simulator.


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