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IMP
2.1.1
The Integrative Modeling Platform
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IMP
2.1.1
The Integrative Modeling Platform
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Maintains temperature during molecular dynamics by velocity scaling. More...
#include <IMP/atom/VelocityScalingOptimizerState.h>
Inheritance diagram for IMP::atom::VelocityScalingOptimizerState:Public Member Functions | |
| VelocityScalingOptimizerState (const kernel::Particles &pis, Float temperature, unsigned skip_steps) | |
| VelocityScalingOptimizerState (kernel::Model *m, kernel::ParticleIndexesAdaptor pis, double temperature) | |
| virtual std::string | get_type_name () const |
| virtual ::IMP::base::VersionInfo | get_version_info () const |
| Get information about the module and version of the object. | |
| void | rescale_velocities () const |
| Rescale the velocities now. | |
| void | set_particles (const kernel::Particles &pis) |
| Set the particles to use. | |
| void | set_temperature (Float temperature) |
| Set the temperature to use. | |
| Public Member Functions inherited from IMP::kernel::OptimizerState | |
| OptimizerState (kernel::Model *m, std::string name) | |
| OptimizerState (std::string name="OptimizerState %1%") | |
| unsigned int | get_number_of_updates () const |
| Return the number of times update has been called. | |
| Optimizer * | get_optimizer () const |
| unsigned int | get_period () const |
| virtual void | reset () |
| virtual void | set_is_optimizing (bool) |
| void | set_number_of_updates (unsigned int n) |
| Set the counter. | |
| void | set_period (unsigned int p) |
| virtual void | update () |
| Called when the Optimizer accepts a new conformation. More... | |
| void | update_always () |
| Public Member Functions inherited from IMP::kernel::ModelObject | |
| ModelObject (kernel::Model *m, std::string name) | |
| ModelObject (std::string name) | |
| virtual void | do_set_model (kernel::Model *) |
| bool | get_has_dependencies () const |
| Return whether this object has dependencies computed. | |
| bool | get_has_required_score_states () const |
| ModelObjectsTemp | get_inputs () const |
| ModelObjectsTemps | get_interactions () const |
| bool | get_is_part_of_model () const |
| Model * | get_model () const |
| ModelObjectsTemp | get_outputs () const |
| const ScoreStatesTemp & | get_required_score_states () const |
| void | set_has_dependencies (bool tf) |
| void | set_has_required_score_states (bool tf) |
| virtual void | set_model (kernel::Model *m) |
| Public Member Functions inherited from IMP::base::Object | |
| virtual void | clear_caches () |
| virtual void | do_destroy () |
| 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_update (unsigned int call) |
| Protected Member Functions inherited from IMP::kernel::OptimizerState | |
| virtual ModelObjectsTemp | do_get_inputs () const |
| virtual ModelObjectsTemp | do_get_outputs () const |
| virtual void | do_set_is_optimizing (bool) |
| Protected Member Functions inherited from IMP::kernel::ModelObject | |
| virtual ModelObjectsTemps | do_get_interactions () const |
| virtual void | handle_set_has_required_score_states (bool) |
| Protected Member Functions inherited from IMP::base::Object | |
| Object (std::string name) | |
| Construct an object with the given name. More... | |
| Object () | |
This OptimizerState, when used with the MolecularDynamics optimizer, implements a simple thermostat by periodically rescaling the velocities. (Note that this results in discontinuous dynamics.)
Definition at line 26 of file VelocityScalingOptimizerState.h.
| IMP::atom::VelocityScalingOptimizerState::VelocityScalingOptimizerState | ( | const kernel::Particles & | pis, |
| Float | temperature, | ||
| unsigned | skip_steps | ||
| ) |
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protectedvirtual |
This method is called every get_period() update calls. The number of times this method has been called since the last reset or start of the optimization run is passed.
Reimplemented from IMP::kernel::OptimizerState.