IMP::isd::MolecularDynamics Class Reference
Molecular dynamics optimizer on 1-D and 3-D particles. More...
#include <IMP/isd/MolecularDynamics.h>
Inheritance diagram for IMP::isd::MolecularDynamics:Public Member Functions | |
| MolecularDynamics (Model *m=nullptr) | |
| void | assign_velocities (Float temperature) |
| Assign velocities representative of the given temperature. | |
| Float | get_kinetic_energy () const |
| Public Member Functions inherited from IMP::atom::MolecularDynamics | |
| MolecularDynamics (Model *m=nullptr) | |
| Float | get_kinetic_temperature (Float ekinetic) const |
| void | set_velocity_cap (Float velocity_cap) |
| Set maximum velocity in A/fs. More... | |
| 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) |
Protected Member Functions | |
| bool | get_is_simulation_particle (ParticleIndex pi) const |
| void | propagate_coordinates (const ParticleIndexes &ps, double step_size) |
| First part of velocity Verlet (update coordinates and half-step velocity) | |
| void | propagate_velocities (const ParticleIndexes &ps, double step_size) |
| Second part of velocity Verlet (update velocity) | |
| void | setup_degrees_of_freedom (const ParticleIndexes &ps) |
| Protected Member Functions inherited from IMP::atom::MolecularDynamics | |
| void | cap_velocity_component (Float &vel) |
| Cap a velocity component to the maximum value. | |
| void | initialize () |
Protected Attributes | |
| FloatKey | vnuis_ |
| Keys of the xyz velocities. | |
| Protected Attributes inherited from IMP::atom::MolecularDynamics | |
| int | degrees_of_freedom_ |
| Number of degrees of freedom in the system. | |
| Float | velocity_cap_ |
| Maximum absolute value of a single velocity component. | |
| FloatKey | vs_ [3] |
| Keys of the xyz velocities. | |
Additional Inherited Members | |
| 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 be XYZs or Nuisances, and should have a non-optimizable mass.
- See Also
- MolecularDynamics in the atom module for more details
Definition at line 25 of file isd/MolecularDynamics.h.
Constructor & Destructor Documentation
Score based on the provided model
Member Function Documentation
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protectedvirtual |
Return true if the passed particle is appropriate for the simulation.
Reimplemented from IMP::atom::MolecularDynamics.
|
virtual |
- Returns
- the current kinetic energy of the system, in kcal/mol
Reimplemented from IMP::atom::MolecularDynamics.
The documentation for this class was generated from the following file: