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IMP Reference Guide  develop.c9d213c767,2020/05/28
The Integrative Modeling Platform
IMP::gsl::Simplex Class Reference

A simplex optimizer taken from GSL. More...

#include <IMP/gsl/Simplex.h>

+ Inheritance diagram for IMP::gsl::Simplex:

Detailed Description

A simplex optimizer taken from GSL.

Simplex works by modifying a simplex in the space of the optimized attributes. The algorithm may not behave well when using score states, such as those involved in rigid bodies, which significantly change the values of the attributes. Then, again, it may work just fine. But be aware that it is not understood.

The main advantage of Simplex is that it is a local optimizer that does not require derivatives.

Definition at line 27 of file Simplex.h.

Public Member Functions

 Simplex (Model *m)
 
virtual Float do_optimize (unsigned int max_steps)
 override this function to do actual optimization 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...
 
- Public Member Functions inherited from IMP::gsl::GSLOptimizer
 GSLOptimizer (Model *m)
 
void set_stop_score (double d)
 Stop the optimization if the score falls below this value. More...
 
- Public Member Functions inherited from IMP::AttributeOptimizer
 AttributeOptimizer (Model *m, std::string name="Optimizer %1%")
 
- 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)
 

Parameters

The parameters are:

  • minimum_size: the optimization stops when the size of the simplex falls below this. The size is defined as the average distance from the centroid to the simplex vertices. (Default 0.1)
  • initial_length: the length of the initial sizes of the simplex. Make sure that this covers the optimal solution, given the starting configuration. (Default 1)
Note
Both quantities are relative to rescaled attributes and so should be numbers between 0 and 1.
void set_initial_length (double length)
 
void set_minimum_size (double d)
 

Additional Inherited Members

- Protected Member Functions inherited from IMP::AttributeOptimizer
double get_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. More...
 
- 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 ()
 

Member Function Documentation

virtual Float IMP::gsl::Simplex::do_optimize ( unsigned int  ns)
virtual

override this function to do actual optimization

Implements IMP::Optimizer.

virtual ::IMP::VersionInfo IMP::gsl::Simplex::get_version_info ( ) const
virtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 67 of file Simplex.h.


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