Clusters module

ClustersTask

class esteem.tasks.clusters.ClustersTask(**kwargs)

run()

Main routine for processing clusters and running them for excitations.

The steps involved are:

1. Load the trajectory file of MD snapshots, which for a given solvent solute pair it expects to find at ‘{solute}_{solvent}_solv.traj’ in the current directory

2. ‘Carve’ spheres out of the trajectory, that is to say:

   1. Delete counterions (checking they are not within the sphere first)

   b. Delete any whole solvent molecules for which no atoms of the solvent molecule are within self.radius of any atom in the solute molecule.

   c. Label solvent molecules with a tag if they are within self.kernel by the criteria above.

   d. Rotate and center the cluster in the simulation cell, using the two most-distant pairs of carbon atoms in the solute to find a common ‘plane’ for the solute snapshots.

3. Calculate electronic excitations for each cluster. This can currently be done with the ONETEP wrapper functions or with NWChem but other wrappers can be added.

Arguments

self: Argument list for the task, with attributes including:

solute, solvent, radius, output, task_id, counterions, charges kernel, basis, func, boxsize, impsolv,``nroots``, cleanup, continuation

wrapper: class

Wrapper to use in the Clusters task

Output:

If self.task_id is None, excited state calculations for the whole trajectory. If has a int value, then an excited state calculation for just that frame in the trajectory.

carve_spheres(soluseed, solvseed, counterions=None, solvent_radius=0.0, kernel_radius=0.0, nmol_solvent_targ=None, boxsize=None, task_id=None)

Carves out spheres from a periodic solvent model, centered on the solute

calc_all_excitations(soluseed, solvseed, traj_carved, excit_func, charge=0, calc_params={}, impsolv=None, nroots=1, writeonly=False, continuation=False, cleanup=False)

Loop over trajectory frames and do an excited states calculation for each one

calc_all_vibrations(soluseed, solvseed, traj_carved, geom_opt_func, freq_func, charge=0, calc_params={}, impsolv=None, nroots=1, writeonly=False, continuation=False, cleanup=False)

Loop over trajectory frames and do a vibrational frequency calculation for each one

Standalone module routines

Performs processing of Molecular Dynamics Trajectories to extract cluster models centered on the solute molecule and including all solvent molecules within a given range

esteem.tasks.clusters.delete_counterions(t, solvent_radius, nat_tot, nat_solute, nat_counterions)

Deletes counterions from an Atoms model. Assumes they appear in the range [nat_solute:nat_solute+nat_counterions]

esteem.tasks.clusters.delete_excess_molecules(t, nat_tot, nat_solvent, nat_solute, nmol_solvent_targ)

Deletes solvent molecules

esteem.tasks.clusters.delete_distant_molecules(t, solvent_radius, nat_tot, nat_solvent, nmol_solvent, nat_solute)

Deletes solvent molecules beyond a certain radius from the solute from an Atoms model Assumes that the first nat_solute atoms are the solute, and after that solvent atoms are arranged in nmol_solvent groups of size nat_solvent

esteem.tasks.clusters.label_nearby_molecules(t, kernel_radius, nat_tot, nat_solvent, nmol_solvent, nat_solute)

Adds a tag to solvent molecules within a certain radius from the solute to an Atoms model Assumes that the first nat_solute atoms are the solute, and after that solvent atoms are arranged in nmol_solvent groups of size nat_solvent

esteem.tasks.clusters.rotate_and_center_solute(t, nat_solute=None, boxsize=None)

Rotates a cluster model so the solute is centered and lies in the xy plane

Command-line usage