ichor.cli.main_menu_submenus.molecular_dynamics_menu.molecular_dynamics_submenus package

Submodules

ichor.cli.main_menu_submenus.molecular_dynamics_menu.molecular_dynamics_submenus.amber_submenu module

class AmberMenuFunctions

Bases: object

static select_dt()

Select the delta t for the timestep of AMBER.

static select_ln_gamma()

Select the ln_gamma of AMBER. Check the manual for description.

static select_number_of_timesteps()

Selects the number of timesteps in AMBER simulation.

static select_temperature()

Select temperature of AMBER simulation.

static select_write_every_nth_timestep()

Select how often to write xyz coordinates from AMBER simulation.

static submit_amber_to_compute()

Asks for user input and submits AMBER job to compute node.

static xyz_from_mdcrd()

class AmberMenuOptions(selected_temperature: int, selected_number_of_timesteps: int, selected_write_coordinates_every_nth_timestep: int, selected_dt: float, selected_ln_gamma: float)

Bases: MenuOptions

selected_dt: float

selected_ln_gamma: float

selected_number_of_timesteps: int

selected_temperature: int

selected_write_coordinates_every_nth_timestep: int

ask_user_for_mdcrd_paths()

ichor.cli.main_menu_submenus.molecular_dynamics_menu.molecular_dynamics_submenus.cp2k_submenu module

class CP2KMenuFunctions

Bases: object

static select_basis_set()

Select basis set used by CP2K.

static select_method()

Select the method used by CP2K.

static select_molecular_charge()

Select molecular charge of CP2K.

static select_number_of_timesteps()

Selects the number of timesteps in CP2K simulation.

static select_numer_of_cores()

Select the number of cores to use for CP2K.

static select_spin_multiplicity()

Select the spin multiplicty used by CP2K.

static select_temperature()

Select temperature of CP2K simulation.

static submit_cp2k_to_compute()

Submits CP2K job to compute node with the given settings.

class CP2KMenuOptions(selected_method: str, selected_basis_set: str, selected_temperature: int, selected_number_of_timesteps: int, selected_molecular_charge: int, selected_spin_multiplicity: int, selected_number_of_cores: int)

Bases: MenuOptions

selected_basis_set: str

selected_method: str

selected_molecular_charge: int

selected_number_of_cores: int

selected_number_of_timesteps: int

selected_spin_multiplicity: int

selected_temperature: int

Module contents