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IMP Reference Guide
2.6.1
The Integrative Modeling Platform
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The base class for simulators. More...
#include <IMP/atom/Simulator.h>
Inheritance diagram for IMP::atom::Simulator:The base class for simulators.
A simulator is an optimizer with dynamic tracking of time, such that each frame is associated with a (possibly variable size) time step.
The simulation can be invoked directly by calling simulate(fs) for a given time in femtoseconds, or by calling Optimizer::optimize(nf) for a given number of frames.
Definition at line 34 of file Simulator.h.
Public Member Functions | |
| 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 |
| void | set_current_time (double ct) |
| Sets the current simulation time in femtoseconds to ct. More... | |
| 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) |
| 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 | 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 |
| virtual VersionInfo | get_version_info () const |
| Get information about the module and version of the object. More... | |
| 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) |
| virtual std::string | get_type_name () const |
Protected Member Functions | |
| 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) |
| virtual double | do_step (const ParticleIndexes &sc, double dt)=0 |
| Perform a single time step. More... | |
| virtual bool | get_is_simulation_particle (ParticleIndex p) const =0 |
| Return true if the passed particle is appropriate for the simulation. More... | |
| virtual void | setup (const ParticleIndexes &) |
| 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 () |
Explicitly accessing the particles list | |
One can explicitly specify which particles should be used for the simulation, or retrieve information about the list of particles. Each particle must be a Mass and core::XYZ particle. If none are specified, the model is searched for appropriate particles, based on the get_simulation_particles() method, which can be overridden by child classes. | |
| 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) |
| IMP::atom::Simulator::Simulator | ( | Model * | m, |
| std::string | name = "Simulator %1%", |
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| double | wave_factor = 1.0 |
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| ) |
| m | model associated with simulator |
| name | simulator name where %1% is a joker |
| wave_factor | if >=1.001, use wave time step size with larger maximal time step, using simulate_wave() when calling optimize() |
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protectedvirtual |
override this function to do actual optimization
Implements IMP::Optimizer.
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protectedvirtual |
called by simulate() - calls setup() and then calls do_step() iteratively till given simulation time is completed
| time | time to simulate |
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protectedvirtual |
Calls the protected method setup() and then calls method do_step() iteratively, and using a self adjusting time step that can grow up to max_time_step_factor times than the default time step returned by get_maximum_time_step()
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protectedpure virtual |
Perform a single time step.
| [in] | sc | the particles that should be moved |
| [in] | dt | maximum time step value |
Implemented in IMP::atom::MolecularDynamics, and IMP::atom::BrownianDynamics.
| double IMP::atom::Simulator::get_current_time | ( | ) | const |
returns the simulation time in femtoseconds that was performed by this simulator since it was constructed
Definition at line 107 of file Simulator.h.
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protectedpure virtual |
Return true if the passed particle is appropriate for the simulation.
Implemented in IMP::atom::MolecularDynamics, IMP::atom::BrownianDynamics, and IMP::isd::MolecularDynamics.
| ParticleIndexes IMP::atom::Simulator::get_simulation_particle_indexes | ( | ) | const |
Same as get_simulation_particles(), but returns particle model indexes.
| ParticlesTemp IMP::atom::Simulator::get_simulation_particles | ( | ) | const |
Returns the set of particles used in the simulation.
If a non-empty set of particles was provided explicitly by earlier calls to the particles list accessor methods, eg, add_particles(), this set it returned. Otherwise, the associated Model object is searched for appropriate particles that have a mass and XYZ decorators.
| void IMP::atom::Simulator::set_current_time | ( | double | ct | ) |
Sets the current simulation time in femtoseconds to ct.
Definition at line 110 of file Simulator.h.
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protectedvirtual |
Perform any setup operations needed before running a series of simulation steps
Reimplemented in IMP::atom::MolecularDynamics, and IMP::atom::BrownianDynamics.
Definition at line 159 of file Simulator.h.
| double IMP::atom::Simulator::simulate | ( | double | time_in_fs | ) |
Simulate for a given time in fs.
simulate for at least the passed time, by calling do_simulate() with optimizing states turned on
| time_in_fs | time in femtoseconds |
| double IMP::atom::Simulator::simulate_wave | ( | double | time_in_fs, |
| double | max_time_step_factor = 10.0, |
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| double | base = 1.5 |
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| ) |
Simulate for a given time in fs using a wave step function with maximal time step increased by up to max_time_step_factor simulate for at least the passed time, by calling do_simulate_wave() with optimizing states turned on
| time_in_fs | time_in_fs in femtoseconds |
| max_time_step_factor | the maximal factor by which the maximum time step is exceeded |
| base | base by which time step increases or decreases during the wave |
