Simple Brownian dynamics optimizer. More...
#include <IMP/atom/BrownianDynamics.h>
Inheritance diagram for IMP::atom::BrownianDynamics:Public Member Functions | |
| BrownianDynamics (Model *m, std::string name="BrownianDynamics%1%") | |
| Create the optimizer. More... | |
| void | set_maximum_move (double ms) |
| void | set_use_stochastic_runge_kutta (bool tf) |
| Public Member Functions inherited from IMP::atom::Simulator | |
| Simulator (Model *m, std::string name="Simulator %1%") | |
| Create the optimizer. More... | |
| double | get_current_time () const |
| double | get_kt () const |
| ParticleIndexes | get_simulation_particle_indexes () const |
| ParticlesTemp | get_simulation_particles () const |
| double | get_temperature () const |
| IMP_OPTIMIZER (Simulator) | |
| void | set_temperature (double d) |
| double | simulate (double time_in_fs) |
| Simulate until the given time in fs. | |
| void | set_maximum_time_step (double ts) |
| double | get_maximum_time_step () const |
| 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 | reserve_particles (unsigned int sz) |
| Public Member Functions inherited from IMP::kernel::Optimizer | |
| Optimizer (Model *m, std::string name="Optimizer %1%") | |
| double | get_last_score () const |
| Return the score found in the last evaluate. | |
| Model * | get_model () const |
| Get the model being optimized. | |
| ScoringFunction * | get_scoring_function () const |
| Return the scoring function that is being used. | |
| bool | get_stop_on_good_score () const |
| double | optimize (unsigned int max_steps) |
| Optimize the model for up to max_steps iterations. More... | |
| void | set_model (Model *m) |
| Set the model being optimized. More... | |
| virtual void | set_scoring_function (ScoringFunctionAdaptor sf) |
| void | set_stop_on_good_score (bool tf) |
| virtual void | show (std::ostream &out=std::cout) const |
| Print info about the optimizer state. More... | |
| 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::base::Object | |
| virtual void | clear_caches () |
| virtual IMP::base::VersionInfo | get_version_info () const =0 |
| Get information about the module and version of the object. | |
| 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) |
Additional Inherited Members | |
| Protected Member Functions inherited from IMP::kernel::Optimizer | |
| virtual double | do_optimize (unsigned int ns)=0 |
| override this function to do actual optimization | |
| void | update_states () const |
| Update optimizer states, should be called at each successful step. More... | |
| double | width (FloatKey k) const |
| FloatIndexes | get_optimized_attributes () const |
| void | set_value (FloatIndex fi, double v) const |
| Float | get_value (FloatIndex fi) const |
| Float | get_derivative (FloatIndex fi) const |
| void | set_scaled_value (FloatIndex fi, Float v) const |
| double | get_scaled_value (FloatIndex fi) const |
| double | get_scaled_derivative (FloatIndex fi) const |
| void | clear_range_cache () |
| Clear the cache of range information. Do this at the start of optimization. | |
| Related Functions inherited from IMP::atom::Simulator | |
| void | set_current_time (double ct) |
| typedef IMP::base::Vector < IMP::base::WeakPointer < Simulator > > | SimulatorsTemp |
Detailed Description
The particles to be optimized must have optimizable x,y,z attributes and a non-optimizable "Stokes radius"; this optimizer assumes the score to be energy in kcal/mol, the xyz coordinates to be in angstroms and the diffusion coefficent be in cm^2/s
Particles without optimized x,y,z and nonoptimized D are skipped.
Rigid bodies are supported.
BrownianDynamics uses a SimulationParameters particle to store the parameters of the simulation. Such a particle must be passed on creation. The BrownianDynamics object will at least see updates to the SimulationParamters particle which occur before the call to BrownianDynamics::optimize() or BrownianDynamics::simulate(), changing the the parameters during optimization has undefined results.
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.
- See Also
- Diffusion
Definition at line 52 of file BrownianDynamics.h.
Constructor & Destructor Documentation
| IMP::atom::BrownianDynamics::BrownianDynamics | ( | Model * | m, |
| std::string | name = "BrownianDynamics%1%" |
||
| ) |
If sc is not null, that container will be used to find particles to move, otherwise the model will be searched.
The documentation for this class was generated from the following file: