aiida_aimall.workchains.subparam

WorkChain for calculating substituent parameters developed by authors

Module Contents

Classes

SubstituentParameterWorkChain

A workchain to calculate properties of substituents, R, in R-H molecules.

class aiida_aimall.workchains.subparam.SubstituentParameterWorkChain(inputs: dict | None = None, logger: logging.Logger | None = None, runner: aiida.engine.runners.Runner | None = None, enable_persistence: bool = True)

Bases: aiida_aimall.workchains.input.BaseInputWorkChain

A workchain to calculate properties of substituents, R, in R-H molecules.

This is a multistep calculation, consisting of a Gaussian calculation, an AIMQB calculation, Python reorientation to the defined coordinate system, a Gaussian single point calculation, and a final AIMQB calculation on the single point wfx calculation. Substituent Properties are then extracted using the AimqbGroupParser.

gauss_opt_params

Parameters for the Gaussian optimization calculations

Type:

aiida.orm.Dict

gauss_sp_params

Parameters for the Gaussian single point calculations

Type:

aiida.orm.Dict

aim_params

Command line parameters for AIMQB

Type:

AimqbParameters

gauss_code

Code for Gaussian software

Type:

aiida.orm.Code

frag_label

Optional fragment label for the calculation

Type:

aiida.orm.Str

opt_wfx_group

Optional group to put optimization wavefunctions in

Type:

aiida.orm.Str

sp_wfx_group

Optional group to put single point wavefunctions in

Type:

aiida.orm.Str

gaussian_opt_group

Optional group to put optimization GaussianCalculations in

Type:

aiida.orm.Str

gaussian_sp_group

Optional group to put single point GaussianCalculations in

Type:

aiida.orm.Str

wfx_filename

Optional wfx file name

Type:

aiida.orm.Str

aim_code

Code for AIMQB software

Type:

aiida.orm.Code

dry_run

Whether or not this is a dry run of the WorkChain

Type:

aiida.orm.Bool

Note

Here, the group for a substiuent is defined in an R-H molecule. Atom 1 is the atom in the group R that is attached to the hydrogen, and the hydrogen should be atom 2. These align with the default settings of an AimqbCalculation using an AimqbGroupParser.

Example

from aiida.plugins import WorkflowFactory, DataFactory
from aiida.orm import Dict, StructureData, load_code
from aiida.engine import submit
from aiida import load_profile
import io
import ase.io

load_profile()

SubstituentParameterWorkchain = WorkflowFactory('aimall.subparam')
AimqbParameters = DataFactory('aimall.aimqb')
aim_input = AimqbParameters({'nproc':2,'naat':2,'atlaprhocps':True})
gaussian_opt = Dict(
            {
                "link0_parameters": {
                    "%chk": "aiida.chk",
                    "%mem": "3200MB",  # Currently set to use 8000 MB in .sh files
                    "%nprocshared": 4,
                },
                "functional": "wb97xd",
                "basis_set": "aug-cc-pvtz",
                "charge": 0,
                "multiplicity": 1,
                "route_parameters": {"opt": None, "Output": "WFX"},
                "input_parameters": {"output.wfx": None},
            }
)
gaussian_sp = Dict(
            {
                "link0_parameters": {
                    "%chk": "aiida.chk",
                    "%mem": "3200MB",  # Currently set to use 8000 MB in .sh files
                    "%nprocshared": 4,
                },
                "functional": "wb97xd",
                "basis_set": "aug-cc-pvtz",
                "charge": 0,
                "multiplicity": 1,
                "route_parameters": {"nosymmetry": None, "Output": "WFX"},
                "input_parameters": {"output.wfx": None},
            }
)
f = io.StringIO(
                "5\n\n C -0.1 2.0 -0.02\nH 0.3 1.0 -0.02\nH 0.3 2.5 0.8\nH 0.3 2.5 -0.9\nH -1.2 2.0 -0.02"
            )
struct_data = StructureData(ase=ase.io.read(f, format="xyz"))
f.close()
builder = SubstituentParameterWorkchain.get_builder()
builder.g16_code = load_code('gaussian@localhost')
builder.aim_code = load_code('aimall@localhost')
builder.g16_opt_params = gaussian_opt
builder.g16_sp_params = gaussian_sp
builder.structure = struct_data
builder.aim_params = aim_input
submit(builder)

classmethod define(spec)

Define workchain steps

get_substituent_inputs_step()

Get a dictionary of the substituent input for a given SMILES

gauss_opt()

Submit the Gaussian optimization

classify_opt_wfx()

Add the wavefunction file from the previous step to the correct group and set the extras

aim_reor()

Submit the Aimqb calculation and reorientation

gauss_sp()

Run Gaussian Single Point calculation

classify_sp_wfx()

Add the wavefunction file from the previous step to the correct group and set the extras

aim()

Run Final AIM Calculation

result()

Put results in output node