lammps_step

• lammps_step package
  • Submodules
  • lammps_step.custom module
    • Custom
      • Custom.description_text()
      • Custom.get_input()
      • Custom.git_revision
      • Custom.header
      • Custom.version
  • lammps_step.custom_parameters module
    • CustomParameters
      • CustomParameters.parameters
  • lammps_step.custom_step module
    • CustomStep
      • CustomStep.create_node()
      • CustomStep.create_tk_node()
      • CustomStep.description()
      • CustomStep.my_description
  • lammps_step.energy module
    • Energy
      • Energy.analyze()
      • Energy.calculate_enthalpy_of_formation()
      • Energy.description_text()
      • Energy.get_input()
      • Energy.git_revision
      • Energy.header
      • Energy.model
      • Energy.results
      • Energy.task
      • Energy.version
    • subscript()
  • lammps_step.energy_parameters module
    • EnergyParameters
      • EnergyParameters.applies()
      • EnergyParameters.not_applicable_reason()
      • EnergyParameters.not_implemented
      • EnergyParameters.parameters
      • EnergyParameters.pressure_keys
  • lammps_step.energy_step module
    • EnergyStep
      • EnergyStep.create_node()
      • EnergyStep.create_tk_node()
      • EnergyStep.description()
      • EnergyStep.my_description
  • lammps_step.extras module
    • ALLOWED_COMMANDS
    • DISPLAY_UNITS
    • ExtrasError
    • PREFACTORS
    • RESERVED_IDS
    • RESULT_UNITS
    • TREATMENTS
    • VARIABLE_PREFIX
    • autocorrelation()
    • check()
    • check_properties()
    • cleanup_lines()
    • column_metadata()
    • extra_input()
    • green_kubo()
    • h5md_unit()
    • logical_lines()
    • parse_commands()
    • prefactor_value()
    • result_units()
    • unit_kind()
  • lammps_step.gpu_memory_parser module
    • parse_gpu_memory_log()
    • print_gpu_summary()
    • print_multi_gpu_summary()
  • lammps_step.heat_flux module
    • HeatFlux
      • HeatFlux.parser
      • HeatFlux.options
      • HeatFlux.subflowchart
      • HeatFlux.parameters
      • HeatFlux.check_flowchart()
      • HeatFlux.description_text()
      • HeatFlux.extra_definitions()
      • HeatFlux.get_input()
      • HeatFlux.git_revision
      • HeatFlux.header
      • HeatFlux.md_provides()
      • HeatFlux.version
  • lammps_step.heat_flux_parameters module
    • HeatFluxParameters
      • HeatFluxParameters.parameters
  • lammps_step.heat_flux_step module
    • HeatFluxStep
      • HeatFluxStep.create_node()
      • HeatFluxStep.create_tk_node()
      • HeatFluxStep.description()
      • HeatFluxStep.my_description
  • lammps_step.initialization module
    • Initialization
      • Initialization.MDI_QM_input()
      • Initialization.OpenKIM_energy_expression()
      • Initialization.OpenKIM_input()
      • Initialization.PyTorch_energy_expression()
      • Initialization.PyTorch_input()
      • Initialization.description_text()
      • Initialization.get_input()
      • Initialization.git_revision
      • Initialization.header
      • Initialization.kspace_methods
      • Initialization.scale_ion_charges()
      • Initialization.version
    • explicit_kspace()
  • lammps_step.initialization_parameters module
    • InitializationParameters
      • InitializationParameters.obsolete
      • InitializationParameters.parameters
      • InitializationParameters.update()
  • lammps_step.initialization_step module
    • InitializationStep
      • InitializationStep.create_node()
      • InitializationStep.create_tk_node()
      • InitializationStep.description()
      • InitializationStep.my_description
  • lammps_step.installer module
    • Installer
      • Installer.exe_version()
  • lammps_step.lammps module
    • GPU_CLAIM_DIR
    • LAMMPS
      • LAMMPS.FORCEFIELD_TYPES
      • LAMMPS.analyze()
      • LAMMPS.analyze_trajectory()
      • LAMMPS.angle_table()
      • LAMMPS.box_to_cell()
      • LAMMPS.cell_to_box()
      • LAMMPS.check_barostats()
      • LAMMPS.check_following_analyses()
      • LAMMPS.check_for_lammps_error()
      • LAMMPS.create_parser()
      • LAMMPS.description_text()
      • LAMMPS.display_title
      • LAMMPS.display_units
      • LAMMPS.eex
      • LAMMPS.ff_form()
      • LAMMPS.following_nodes()
      • LAMMPS.force_triclinic
      • LAMMPS.forcefield()
      • LAMMPS.forcefield_model_chemistry()
      • LAMMPS.get_dump()
      • LAMMPS.git_revision
      • LAMMPS.have_dreiding_hbonds
      • LAMMPS.mlff_model_chemistry()
      • LAMMPS.model_chemistry()
      • LAMMPS.pytorch_model()
      • LAMMPS.read_dump()
      • LAMMPS.record_timing()
      • LAMMPS.results
      • LAMMPS.run()
      • LAMMPS.set_id()
      • LAMMPS.shake_fix()
      • LAMMPS.structure_data()
      • LAMMPS.version
    • MLFF_PAIR
    • MLFF_TCP_DRIVER
    • NODELAY_SOURCE
    • TIMING_SPEC
    • allocation_note()
    • lammps_error()
    • lammps_error_message()
    • logging_disabled()
    • pline()
    • pvalue()
    • timing_descriptors()
    • unfinished_run_message()
  • lammps_step.lammps_step module
    • LAMMPSStep
      • LAMMPSStep.create_node()
      • LAMMPSStep.create_tk_node()
      • LAMMPSStep.description()
      • LAMMPSStep.my_description
  • lammps_step.lammps_units module
    • from_lammps_units()
    • get_lammps_unit_system()
    • lammps_units()
    • set_lammps_unit_system()
    • to_lammps_units()
  • lammps_step.md_h5md module
    • MDH5MDConverter
      • MDH5MDConverter.ensemble
      • MDH5MDConverter.path
      • MDH5MDConverter.record()
      • MDH5MDConverter.write()
    • h5md_units()
    • periodic_only
    • state_observables
    • write_md_h5md()
  • lammps_step.md_provides module
    • md_provides()
    • request_sampling()
    • sampling_edits()
    • sampling_parameters
    • state_observables
    • static_value()
  • lammps_step.metadata module
    • metadata
  • lammps_step.minimization module
    • Minimization
      • Minimization.analyze()
      • Minimization.description_text()
      • Minimization.get_input()
      • Minimization.get_pressure_text()
      • Minimization.shear_allowed()
      • Minimization.task
  • lammps_step.minimization_parameters module
    • MinimizationParameters
      • MinimizationParameters.parameters
      • MinimizationParameters.pressure_keys
  • lammps_step.minimization_step module
    • MinimizationStep
      • MinimizationStep.create_node()
      • MinimizationStep.create_tk_node()
      • MinimizationStep.description()
      • MinimizationStep.my_description
  • lammps_step.npt module
    • NPT
      • NPT.describe()
      • NPT.description_text()
      • NPT.get_input()
      • NPT.get_pressure_text()
      • NPT.methods
      • NPT.nose_hoover_barostat_options()
      • NPT.shear_allowed()
  • lammps_step.npt_parameters module
    • NPT_Parameters
      • NPT_Parameters.parameters
      • NPT_Parameters.pressure_keys
  • lammps_step.npt_step module
    • NPTStep
      • NPTStep.create_node()
      • NPTStep.create_tk_node()
      • NPTStep.description()
      • NPTStep.my_description
  • lammps_step.nve module
    • MAX_FLUX_SPECIES
    • NVE
      • NVE.analyze()
      • NVE.check_flowchart()
      • NVE.description_text()
      • NVE.extra_definitions()
      • NVE.extra_input()
      • NVE.get_input()
      • NVE.heat_flux_cleanup()
      • NVE.heat_flux_input()
      • NVE.md_provides()
      • NVE.molecular_species()
      • NVE.request_sampling()
      • NVE.sampling_edits()
      • NVE.species_flux_cleanup()
      • NVE.species_flux_input()
      • NVE.task
      • NVE.timestep()
      • NVE.trajectory_input()
    • SAMPLED_FILES
    • TIMESTEP_CHOICES
    • timestep_text()
  • lammps_step.nve_parameters module
    • NVE_Parameters
      • NVE_Parameters.extras
      • NVE_Parameters.not_implemented
      • NVE_Parameters.parameters
      • NVE_Parameters.renamed
      • NVE_Parameters.trajectories
  • lammps_step.nve_step module
    • NVEStep
      • NVEStep.create_node()
      • NVEStep.create_tk_node()
      • NVEStep.description()
      • NVEStep.my_description
  • lammps_step.nvt module
    • NVT
      • NVT.describe()
      • NVT.description_text()
      • NVT.get_input()
  • lammps_step.nvt_parameters module
    • NVT_Parameters
      • NVT_Parameters.parameters
  • lammps_step.nvt_step module
    • NVTStep
      • NVTStep.create_node()
      • NVTStep.create_tk_node()
      • NVTStep.description()
      • NVTStep.my_description
  • lammps_step.tk_custom module
    • TkCustom
      • TkCustom.create_dialog()
      • TkCustom.handle_dialog()
      • TkCustom.right_click()
  • lammps_step.tk_energy module
    • TkEnergy
      • TkEnergy.create_dialog()
      • TkEnergy.right_click()
    • stress_headers()
    • widget_values()
  • lammps_step.tk_heat_flux module
    • TkHeatFlux
      • TkHeatFlux.tk_flowchart
      • TkHeatFlux.node
      • TkHeatFlux.canvas
      • TkHeatFlux.dialog
      • TkHeatFlux.x
      • TkHeatFlux.y
      • TkHeatFlux.w
      • TkHeatFlux.h
      • TkHeatFlux.self
      • TkHeatFlux.create_dialog()
      • TkHeatFlux.reset_dialog()
      • TkHeatFlux.right_click()
      • TkHeatFlux.trajectory_skip
  • lammps_step.tk_initialization module
    • TkInitialization
      • TkInitialization.create_dialog()
      • TkInitialization.general_cb()
      • TkInitialization.kspace_method_cb()
      • TkInitialization.reset_dialog()
      • TkInitialization.right_click()
  • lammps_step.tk_lammps module
    • TkLAMMPS
      • TkLAMMPS.create_dialog()
      • TkLAMMPS.from_flowchart()
      • TkLAMMPS.node_class
      • TkLAMMPS.right_click()
      • TkLAMMPS.update_flowchart()
  • lammps_step.tk_minimization module
    • TkMinimization
      • TkMinimization.create_dialog()
      • TkMinimization.pressure_frame_keys
      • TkMinimization.reset_dialog()
      • TkMinimization.reset_optimization()
      • TkMinimization.reset_pressure_frame()
      • TkMinimization.reset_stress_frame()
      • TkMinimization.stress_keys
  • lammps_step.tk_npt module
    • TkNPT
      • TkNPT.create_dialog()
      • TkNPT.handle_dialog()
      • TkNPT.reset_dialog()
      • TkNPT.reset_pressure_frame()
      • TkNPT.reset_stress_frame()
      • TkNPT.stress_components
  • lammps_step.tk_nve module
    • TkNVE
      • TkNVE.create_dialog()
      • TkNVE.handle_dialog()
      • TkNVE.reset_control_frame()
      • TkNVE.reset_dialog()
      • TkNVE.reset_trajectory_frame()
      • TkNVE.trajectory_layout
      • TkNVE.trajectory_skip
  • lammps_step.tk_nvt module
    • TkNVT
      • TkNVT.create_dialog()
      • TkNVT.reset_dialog()
      • TkNVT.reset_temperature_frame()
  • lammps_step.tk_velocities module
    • TkVelocities
      • TkVelocities.create_dialog()
      • TkVelocities.reset_dialog()
      • TkVelocities.right_click()
  • lammps_step.velocities module
    • Velocities
      • Velocities.description_text()
      • Velocities.get_input()
      • Velocities.git_revision
      • Velocities.header
      • Velocities.version
  • lammps_step.velocities_parameters module
    • VelocitiesParameters
      • VelocitiesParameters.parameters
  • lammps_step.velocities_step module
    • VelocitiesStep
      • VelocitiesStep.create_node()
      • VelocitiesStep.create_tk_node()
      • VelocitiesStep.description()
      • VelocitiesStep.my_description
  • Module contents