nanover.ase package

Interface between NanoVer and ASE.

Submodules

• nanover.ase.converter module
  • add_ase_box_vectors_to_frame_data()
  • add_ase_forces_to_frame_data()
  • add_ase_positions_to_frame_data()
  • add_ase_state_to_frame_data()
  • add_ase_topology_to_frame_data()
  • add_ase_velocities_to_frame_data()
  • add_frame_data_positions_to_ase()
  • add_frame_data_topology_to_ase()
  • ase_atoms_to_frame_data()
  • ase_to_frame_data()
  • frame_data_to_ase()
  • generate_bonds_from_ase()
  • get_radius_of_element()
• nanover.ase.imd_calculator module
  • ImdCalculator
    • ImdCalculator.add_to_frame_data()
    • ImdCalculator.calculate()
    • ImdCalculator.calculator
    • ImdCalculator.interactions
    • ImdCalculator.reset_temperature
    • ImdCalculator.temperature
    • ImdCalculator.update_interactions()
  • ImdForceManager
    • ImdForceManager.add_to_frame_data()
    • ImdForceManager.update_interactions()
  • get_periodic_box_lengths()
• nanover.ase.null_calculator module
  • NullCalculator
    • NullCalculator.calculate()
• nanover.ase.omm_calculator module
  • OpenMMCalculator
    • OpenMMCalculator.calculate()
    • OpenMMCalculator.from_xml()
    • OpenMMCalculator.generate_atoms()
    • OpenMMCalculator.implemented_properties
    • OpenMMCalculator.make_frame_converter()
    • OpenMMCalculator.set_periodic_bounds()
    • OpenMMCalculator.simulation
    • OpenMMCalculator.topology
• nanover.ase.simulation module
  • ASEAtomsToFrameData
  • ASESimulation
    • ASESimulation.advance_by_one_step()
    • ASESimulation.advance_by_seconds()
    • ASESimulation.advance_to_next_report()
    • ASESimulation.atoms
    • ASESimulation.from_ase_dynamics()
    • ASESimulation.from_openmm_simulation()
    • ASESimulation.load()
    • ASESimulation.make_regular_frame()
    • ASESimulation.make_topology_frame()
    • ASESimulation.reset()
  • InitialState
    • InitialState.cell
    • InitialState.positions
    • InitialState.velocities
• nanover.ase.thermo module
  • compute_dof()
  • compute_instantaneous_temperature()
• nanover.ase.trajectory_logger module
  • TrajectoryLogger
    • TrajectoryLogger.atoms
    • TrajectoryLogger.base_path
    • TrajectoryLogger.close()
    • TrajectoryLogger.format
    • TrajectoryLogger.frame_index
    • TrajectoryLogger.parallel
    • TrajectoryLogger.reset()
    • TrajectoryLogger.timestamping
    • TrajectoryLogger.write()
  • UnsupportedFormatError
  • validate_ase_can_append_filename()
  • validate_ase_can_append_format()
• nanover.ase.wall_constraint module
  • VelocityWallConstraint
    • VelocityWallConstraint.adjust_forces()
    • VelocityWallConstraint.adjust_momenta()
    • VelocityWallConstraint.adjust_positions()