IMP Reference Guide
develop.7cb8855c60,2024/10/08
The Integrative Modeling Platform
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The base class for simulators. More...
#include <IMP/atom/Simulator.h>
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 |
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) |
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 |
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 |
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 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 () |
Time steps | |
The simulator has a maximum allowed time step. It can take shorter ones if needed due to stability concerns. As with all times in | |
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 |
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. | |
list | particles |
A Python list of Particles More... | |
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) |
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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overrideprotectedvirtual |
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, IMP::atom::BrownianDynamics, and IMP::spb::MolecularDynamicsWithWte.
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 126 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, IMP::spb::MolecularDynamicsWithWte, and IMP::isd::MolecularDynamics.
double IMP::atom::Simulator::get_last_time_step | ( | ) | const |
Get the time of the last simulated time step (or the maximal time step if the simulation has not started), in units of fs
Definition at line 107 of file Simulator.h.
double IMP::atom::Simulator::get_maximum_time_step | ( | ) | const |
Get the maximum allowed time step in fs.
Definition at line 103 of file Simulator.h.
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.
double IMP::atom::Simulator::get_temperature | ( | ) | const |
Return the simulator temperature in kelvin.
Definition at line 79 of file Simulator.h.
void IMP::atom::Simulator::set_current_time | ( | double | ct | ) |
Sets the current simulation time in femtoseconds to ct.
Definition at line 129 of file Simulator.h.
void IMP::atom::Simulator::set_temperature | ( | double | d | ) |
Set the temperature of the simulator to d in kelvin units.
Sets the temperature of the simulator. Note that some simulators (e.g. BrownianDynamics) may rely on other temperature-dependent constants (e.g. diffusion coefficients via Diffusion decorator) that will need to be updated independently to reflect the new temperature.
d | temperature in K |
Definition at line 91 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, IMP::atom::BrownianDynamics, and IMP::spb::MolecularDynamicsWithWte.
Definition at line 178 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 |
list IMP::atom::Simulator::particles |
A Python list of Particles
Definition at line 166 of file Simulator.h.