Gollum Siesta workflow

Description

The GollumSiestaWorkchain workflow produces files with the transmission and the number of open channels from the electronic structure calculated with Siesta.

Important

In order for this workflow to work it is also necessary to install the aiida_siesta plugin (http://aiida-siesta-plugin.readthedocs.io/en/latest/)

The inputs to the Gollum workchain include the Siesta code, the Gollum code, the structures of the leads and the extended molecule, the protocol, the number of kpoints in the leads and the extended molecule and some parameters.

The Gollum package can calculate transport properties such as the transmission and the number of open channels either from tight-binding or ab-initio simulations. In the latter case, it can use the Siesta or QuantumEspresso-Wannier90 codes. This workflow presents an example of transport calculation with the Siesta code. First, it launches a Siesta calculation to simulate the leads, then another Siesta calculation for the extended molecule and finally a Gollum simulation to calculate the transport properties.

Supported Gollum versions

At least 2.0.0 version of the code, which can be downloaded from the Golum webpage (http://www.physics.lancs.ac.uk/gollum/index.php/downloads).

Inputs

• siesta_code

A code associated to the Siesta plugin

• gollum_code

A code associated to the Gollum plugin

• structure_le, class StructureData

A Siesta structure for the leads.

• structure_em, class StructureData

A Siesta structure for the extended molecule.

• protocol, class Str

Either “standard” or “fast”. Each has its own set of associated parameters.

• standard:

  {
     'dm_convergence_threshold': 1.0e-4,
     'min_meshcutoff': 150, # In Rydberg (!)
     'electronic_temperature': "25.0 meV",
     'pseudo_familyname': 'si_ldapsf',
     'atomic_heuristics': {
         'Au': { 'cutoff': 100 }
     },
     'basis': {
         'pao-energy-shift': '100 meV',
         'pao-basis-size': 'DZP'
     }
   }
  

• fast:

  {
     'dm_convergence_threshold': 1.0e-3,
     'min_meshcutoff': 80, # In Rydberg (!)
     'electronic_temperature': "25.0 meV",
     'pseudo_familyname': 'si_ldapsf',
     'atomic_heuristics': {
         'Au': { 'cutoff': 50 }
     },
     'basis': {
         'pao-energy-shift': '100 meV',
         'pao-basis-size': 'SZ'
     }
   }
  

• kpoints_le, class KpointsData

An array with the number of k-points along each direction in the leads

• kpoints_em, class KpointsData

An array with the number of k-points along each direction in the extended molecule

• parameters, class ParameterData

Some parameters for the Gollum simulation (typically the leadp and atom blocks).

Outputs

• open_channels ArrayData

The number of open channels of the first electrode (we assume at the moment that both electrodes are equal). In case of a spin-polarized calculation the output distinguishes between spin-up and down channels.

• transmission ArrayData

The transmission between electrodes. In case of a spin-polarized calculation the output distinguishes between spin-up and down transmissions.