Simple molecular dynamics optimizer.
The particles to be optimized must have optimizable x,y,z attributes and a non-optimizable mass attribute; this optimizer assumes the score to be energy in kcal/mol, the xyz coordinates to be in angstroms, and the mass to be in AMU (g/mol).
Particles without optimized x,y,z and nonoptimized mass are skipped.
- See Also
- VelocityScalingOptimizerState
-
LangevinThermostatOptimizerState
-
BerendsenThermostatOptimizerState
-
RemoveRigidMotionOptimizerState
Definition at line 33 of file MolecularDynamicsWithWte.h.
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| MolecularDynamicsWithWte (Model *m, double emin, double emax, double sigma, double gamma, double w0) |
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virtual void | assign_velocities (Float temperature) |
| Assign velocities representative of the given temperature. More...
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virtual double | do_step (const ParticleIndexes &sc, double dt) override |
| Perform a single time step. More...
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double | get_bias (double score) const |
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Floats | get_bias_buffer () const |
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virtual bool | get_is_simulation_particle (ParticleIndex p) const override |
| Return true if the passed particle is appropriate for the simulation. More...
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virtual Float | get_kinetic_energy () const |
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Float | get_kinetic_temperature (Float ekinetic) const |
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int | get_nbin () const |
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void | rescale_velocities (Float rescale) |
| Rescale velocities. More...
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void | set_bias (const Floats &bias) |
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void | set_velocity_cap (Float velocity_cap) |
| Set maximum velocity in A/fs. More...
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void | set_w0 (double w0) |
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virtual void | setup (const ParticleIndexes &ps) override |
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| Simulator (Model *m, std::string name="Simulator %1%", double wave_factor=1.0) |
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double | get_current_time () const |
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double | get_kt () const |
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ParticleIndexes | get_simulation_particle_indexes () const |
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ParticlesTemp | get_simulation_particles () const |
| Returns the set of particles used in the simulation. More...
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double | get_temperature () const |
| Return the simulator temperature in kelvin. More...
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void | set_current_time (double ct) |
| Sets the current simulation time in femtoseconds to ct. More...
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void | set_temperature (double d) |
| Set the temperature of the simulator to d in kelvin units. More...
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double | simulate (double time_in_fs) |
| Simulate for a given time in fs. More...
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double | simulate_wave (double time_in_fs, double max_time_step_factor=10.0, double base=1.5) |
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void | set_maximum_time_step (double ts) |
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double | get_maximum_time_step () const |
| Get the maximum allowed time step in fs. More...
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double | get_last_time_step () const |
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void | remove_particle (Particle *d) |
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void | remove_particles (const Particles &d) |
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void | set_particles (const Particles &ps) |
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void | set_particles_order (const Particles &objs) |
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unsigned int | add_particle (Particle *obj) |
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void | add_particles (const Particles &objs) |
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void | clear_particles () |
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unsigned int | get_number_of_particles () const |
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bool | get_has_particles () |
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Particle * | get_particle (unsigned int i) const |
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Particles | get_particles () const |
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void | erase_particle (unsigned int i) |
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void | reserve_particles (unsigned int sz) |
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| Optimizer (Model *m, std::string name="Optimizer %1%") |
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double | get_last_score () const |
| Return the score found in the last evaluate. More...
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ScoringFunction * | get_scoring_function () const |
| Return the scoring function that is being used. More...
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bool | get_stop_on_good_score () const |
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double | optimize (unsigned int max_steps) |
| Optimize the model for up to max_steps iterations. More...
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virtual void | set_scoring_function (ScoringFunctionAdaptor sf) |
| Set the scoring function to use. More...
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void | set_stop_on_good_score (bool tf) |
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void | remove_optimizer_state (OptimizerState *d) |
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void | remove_optimizer_states (const OptimizerStates &d) |
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void | set_optimizer_states (const OptimizerStates &ps) |
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void | set_optimizer_states_order (const OptimizerStates &objs) |
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unsigned int | add_optimizer_state (OptimizerState *obj) |
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void | add_optimizer_states (const OptimizerStates &objs) |
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void | clear_optimizer_states () |
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unsigned int | get_number_of_optimizer_states () const |
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bool | get_has_optimizer_states () |
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OptimizerState * | get_optimizer_state (unsigned int i) const |
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OptimizerStates | get_optimizer_states () const |
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void | erase_optimizer_state (unsigned int i) |
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void | reserve_optimizer_states (unsigned int sz) |
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| ModelObject (Model *m, std::string name) |
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bool | get_has_dependencies () const |
| Return whether this object has dependencies computed. More...
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bool | get_has_required_score_states () const |
| Return whether score states are computed. More...
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ModelObjectsTemp | get_inputs () const |
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ModelObjectsTemps | get_interactions () const |
| Get the interacting sets induced by this ModelObject. More...
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Model * | get_model () const |
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ModelObjectsTemp | get_outputs () const |
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const ScoreStatesTemp & | get_required_score_states () const |
| Get the score states that are ancestors of this in the dependency graph. More...
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void | set_has_dependencies (bool tf) |
| Either invalidate the dependencies or ensure they are correct. More...
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void | set_has_required_score_states (bool tf) |
| Compute the required score states. More...
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virtual void | clear_caches () |
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CheckLevel | get_check_level () const |
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LogLevel | get_log_level () const |
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virtual VersionInfo | get_version_info () const |
| Get information about the module and version of the object. More...
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void | set_check_level (CheckLevel l) |
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void | set_log_level (LogLevel l) |
| Set the logging level used in this object. More...
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void | set_was_used (bool tf) const |
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void | show (std::ostream &out=std::cout) const |
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const std::string & | get_name () const |
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void | set_name (std::string name) |
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virtual std::string | get_type_name () const |
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