QMD_Trajectories module

QMDTrajTask

class esteem.tasks.qmd_trajectories.QMDTrajTask(**kwargs)

run()

Sets up and runs an ab initio molecular dynamics run on a given molecule (whose name is provided by args.seed) in the ground or excited state (specified by args.target).

Results, including a trajectory file with the stored snapshots, are saved to files appending args.suffix to the seed and state, for use in future runs.

The run is divided into equilibration (args.nequil runs of args.qmd_steps MD steps each, with timestep args.qmd_timestep), then snapshot generation (args.nsnap runs of args.qmd_steps MD steps each, with timestep args.qmd_timestep).

A thermostat (wrapper-dependent) at temperature args.temp means we stay in the NVT ensemble.

Constraints can be applied using args.constraints - the meaning depends on the underlying wrapper.

Optionally can be used to recalculate singlepoint energies for the steps of a pre-existing trajectory.

args: namespace or class

Full set of arguments to the QMD_Trajectories task - see below for a listing.

Key arguments include basis, func, qmd_timestep, qmd_steps, nsnap, nequil, temp, constraints

Generate with a call to qmd_trajectories.make_parser()

wrapper: namespace or class

List of functions for running components of the job, with members including:

singlepoint, geom_opt and qmd.

Task Arguments

usage: __main__.py [-h] [--seed SEED] [--traj_suffix TRAJ_SUFFIX]
                   [--geom_prefix GEOM_PREFIX] [--basis BASIS] [--func FUNC]
                   [--disp DISP] [--target TARGET] [--charges [CHARGES]]
                   [--restart RESTART] [--md_timestep MD_TIMESTEP]
                   [--md_steps MD_STEPS] [--temp TEMP] [--ntraj NTRAJ]
                   [--nsnap NSNAP] [--solvent SOLVENT]
                   [--solvent_settings SOLVENT_SETTINGS]
                   [--input_suffix INPUT_SUFFIX]
                   [--input_traj_range INPUT_TRAJ_RANGE] [--nequil NEQUIL]
                   [--which-trajs WHICH_TRAJS] [--constraints CONSTRAINTS]
                   [--dynamics DYNAMICS]

Named Arguments

--seed, -s
--traj_suffix, -S
	String to append to names of trajectories Default: “training”
--geom_prefix, -G
	String to append to filenames for initial geometries Default: “”
--basis, -b	Basis set definition (or other run parameter) Default: “6-311++G**”
--func, -f	Exchange-Correlation functional (or other run parameter) Default: “PBE0”
--disp, -d	Apply Grimme-D3 Dispersion Default: True
--target, -t	Excited state index (None for ground state)
--charges, -C	Charges on molecular species. Not for command-line use Default: {}
--restart, -r	If the trajectory has been run for one excited state already, setting this to true attempts to make the calculator restart at each geometry Default: False
--md_timestep, -q
	Molecular dynamics timestep (wrapper-dependent units, fs for NWChem) Default: 0.5
--md_steps, -Q	Number of timesteps in each molecular dynamics run Default: 100
--temp, -T	Thermostat temperature (NVT ensemble) Default: 300.0
--ntraj, -n	Total number of named (A_Z,a-z) trajectories Default: 1
--nsnap, -N	Number of snapshot runs Default: 100
--solvent, -i	Solvent for implicit solvent runs.
--solvent_settings
	Solvent settings for implicit solvent runs.
--input_suffix, -I
	Appended string to identify input trajectory: if present, the run will resample an existing trajectory
--input_traj_range, -R
	Range of snapshots to use from input trajectory
--nequil, -e	Number of equilibration runs. Default: 5
--which-trajs, -w
	Which trajectories should be generated, named with letters A-Z, a-z
--constraints, -c
	Constraints (wrapper-dependent)
--dynamics, -X	Dynamics (ASE Dynamics class)

Standalone module routines