ichor.hpc.molecular_dynamics package

Submodules

ichor.hpc.molecular_dynamics.amber module

submit_amber(input_file_path: str | Path, temperature: int, nsteps: int = 1000000, write_coord_every: int = 10, system_name: str | None = None, ncores: int = 2, dt=0.001, ln_gamma=0.7) → JobID

Submits an amber job to compute node.

Parameters:

  • input_file_path – A XYZ, GJF, PointsDirectory (uses 1st point), or PointDirectory Path

  • temperature – The temperature to run the simulation at

  • nsteps – The number of timesteps in the simulation, defaults to 1_000_000

  • write_coord_every – Write out coordinates to mdcrd file every nth timestep, defaults to 10

  • system_name – The name of the system. If left to None, then the name of the file input_file_path is used, defaults to None

  • ncores – The number of cores to use for the job. Note that even though 2 cores are used, AMBER only runs in serial (1 core) for a single moleucle simulation. However, running on 2 cores means that the CSF3 1-core queue is omitted as it can be long. , defaults to 2

  • dt – Timestep time in picoseconds, default is 0.001

  • ln_gamma – The collision frequency in picoseconds, defaults to 0.7

Returns:

A JobID instance containing information about the submitted job.

ichor.hpc.molecular_dynamics.cp2k module

submit_cp2k(input_file: str | Path, system_name: str, temperature: int, nsteps: int, method: str = 'BLYP', basis_set: str = '6-31G*', molecular_charge: int = 0, spin_multiplicity: int = 1, ncores=2) → JobID

Submits a CP2K job to a compute node.

Parameters:

  • input_file – A XYZ (.xyz) or GJF (.gjf) file that contains the starting geometry.

  • system_name – The name of the chemical system

  • temperature – The temperature at which to run the simulation

  • nsteps – The number of timeteps to run the simulation for

  • method – The method which to use for the simulation, defaults to “BLYP”

  • basis_set – The basis set which to use for the simulation, defaults to “6-31G*”

  • molecular_charge – The charge of the system, defaults to 0

  • spin_multiplicity – The spin multiplicity of the system, defaults to 1

  • ncores – The number of cores to use for the simulation, defaults to 2

Raises:

ValueError – If incorrect filetype (not xyz or gjf) is passed in

Returns:

An object containing information for the submitted job

Return type:

ichor.hpc.batch_system.jobs.JobID

Module contents