| abort_by_energy_enabled_ (defined in MolecularDynamics) | MolecularDynamics | [protected] |
| abort_energy_ (defined in MolecularDynamics) | MolecularDynamics | [protected] |
| atom_vector_ (defined in MolecularDynamics) | MolecularDynamics | [protected] |
| calculateFactors() (defined in MicroCanonicalMD) | MicroCanonicalMD | [protected] |
| current_temperature_ (defined in MolecularDynamics) | MolecularDynamics | [protected] |
| current_time_ (defined in MolecularDynamics) | MolecularDynamics | [protected] |
| enableEnergyAbortCondition(bool state) | MolecularDynamics | |
| energy_output_frequency_ (defined in MolecularDynamics) | MolecularDynamics | [protected] |
| energyAbortConditionEnabled() const | MolecularDynamics | |
| force_field_ptr_ (defined in MolecularDynamics) | MolecularDynamics | [protected] |
| getEnergyOutputFrequency() const | MolecularDynamics | |
| getEnergyToAbort() const | MolecularDynamics | |
| getForceField() const | MolecularDynamics | |
| getKineticEnergy() const | MolecularDynamics | |
| getMaximalNumberOfIterations() const | MolecularDynamics | |
| getMaximalSimulationTime() const | MolecularDynamics | |
| getNumberOfIterations() const | MolecularDynamics | |
| getPotentialEnergy() const | MolecularDynamics | |
| getSnapShotFrequency() const | MolecularDynamics | |
| getTemperature() const | MolecularDynamics | |
| getTime() const | MolecularDynamics | |
| getTimeStep() const | MolecularDynamics | |
| getTotalEnergy() const | MolecularDynamics | |
| isValid() const | MolecularDynamics | |
| kinetic_energy_ (defined in MolecularDynamics) | MolecularDynamics | [protected] |
| mass_factor_ (defined in MicroCanonicalMD) | MicroCanonicalMD | [protected] |
| maximal_number_of_iterations_ (defined in MolecularDynamics) | MolecularDynamics | [protected] |
| MicroCanonicalMD() | MicroCanonicalMD | |
| MicroCanonicalMD(ForceField &myforcefield) | MicroCanonicalMD | |
| MicroCanonicalMD(ForceField &myforcefield, SnapShotManager *ssm) | MicroCanonicalMD | |
| MicroCanonicalMD(ForceField &myforcefield, SnapShotManager *ssm, const Options &myoptions) | MicroCanonicalMD | |
| MicroCanonicalMD(const MicroCanonicalMD &rhs) | MicroCanonicalMD | |
| MolecularDynamics() | MolecularDynamics | |
| MolecularDynamics(ForceField &force_field) | MolecularDynamics | |
| MolecularDynamics(const MolecularDynamics &rhs) | MolecularDynamics | |
| number_of_iteration_ (defined in MolecularDynamics) | MolecularDynamics | [protected] |
| operator=(const MicroCanonicalMD &rhs) | MicroCanonicalMD | |
| MolecularDynamics::operator=(const MolecularDynamics &rhs) | MolecularDynamics | |
| options | MolecularDynamics | |
| reference_temperature_ (defined in MolecularDynamics) | MolecularDynamics | [protected] |
| set(const MolecularDynamics &rhs) | MolecularDynamics | |
| setCurrentTime(double time) | MolecularDynamics | |
| setEnergyOutputFrequency(Size number) | MolecularDynamics | |
| setEnergyToAbort(float value) | MolecularDynamics | |
| setMaximalNumberOfIterations(Size number) | MolecularDynamics | |
| setMaximalSimulationTime(double time) | MolecularDynamics | |
| setNumberOfIteration(Size number) | MolecularDynamics | |
| setReferenceTemperature(double temperature) | MolecularDynamics | |
| setSnapShotFrequency(Size number) | MolecularDynamics | |
| setTimeStep(double step) | MicroCanonicalMD | [virtual] |
| setup(ForceField &myforcefield, SnapShotManager *ssm) | MicroCanonicalMD | [virtual] |
| setup(ForceField &myforcefield, SnapShotManager *ssm, const Options &myoptions) | MicroCanonicalMD | [virtual] |
| simulate(bool restart=false) | MolecularDynamics | |
| simulateIterations(Size number, bool restart=false) | MicroCanonicalMD | [virtual] |
| simulateTime(double simulation_time, bool restart=false) | MolecularDynamics | |
| snapshot_frequency_ (defined in MolecularDynamics) | MolecularDynamics | [protected] |
| snapshot_manager_ptr_ (defined in MolecularDynamics) | MolecularDynamics | [protected] |
| specificSetup() | MicroCanonicalMD | [virtual] |
| system_ptr_ (defined in MolecularDynamics) | MolecularDynamics | [protected] |
| time_step_ (defined in MolecularDynamics) | MolecularDynamics | [protected] |
| total_energy_ (defined in MolecularDynamics) | MolecularDynamics | [protected] |
| updateInstantaneousTemperature() (defined in MolecularDynamics) | MolecularDynamics | [protected] |
| valid_ (defined in MolecularDynamics) | MolecularDynamics | [protected] |
| ~MicroCanonicalMD() | MicroCanonicalMD | [virtual] |
| ~MolecularDynamics() | MolecularDynamics | [virtual] |