aiida_aimall.workchains.qc_programs

Workchains to interface various quantum software with AiiDA

Module Contents

Classes

QMToAIMWorkChain	Workchain to link quantum chemistry jobs without plugins to AIMAll
GaussianToAIMWorkChain	A workchain to submit a Gaussian calculation and automatically setup an AIMAll calculation on the output
GenerateWFXToAIMWorkChain	Workchain to generate a wfx file from computational chemistry output files and submit that to an AIMQB Calculation

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

Bases: aiida.engine.WorkChain

Workchain to link quantum chemistry jobs without plugins to AIMAll

shell_metadata

Metadata for the shell calculation

Type:

aiida.orm.Dict

shell_retrieved

List of files to store in database

Type:

aiida.orm.List

shell_input_file

Input file for the calculation software

Type:

aiida.orm.SinglefileData

shell_cmdline

Command line terminal command

Type:

aiida.orm.Str

wfx_filename

Filename of the wfx file

Type:

aiida.orm.Str

aim_code

Code for AIMQB

Type:

aiida.orm.Code

aim_file_ext

Type:

aiida.orm.Str

aim_parser

Entry point for parser to use.

Type:

aiida.orm.Str

dry_run

Whether or not this is a trial run

Type:

aiida.orm.Bool

Example

# ORCA Example
from aiida_shell import ShellCode
from aiida.orm import load_computer, List, SinglefileData, Str, load_code
QMToAIMWorkchain = WorkflowFactory('aimall.qmtoaim')
# already have an orca code setup,  you can use the codeblock above to do so
code = load_code('orca@cedar')
builder = QMToAIMWorkchain.get_builder()
builder.shell_code = code
pre_str = 'module load StdEnv/2020; module load gcc/10.3.0; module load openmpi/4.1.1; module load orca/5.0.4'
builder.shell_metadata = Dict(
    {
        'options': {
            'withmpi': False,
            # modules for the compute cluster to load
            'prepend_text': pre_str,
            'resources': {
                'num_machines': 1,
                'num_mpiprocs_per_machine': 4,
            },
            'max_memory_kb': int(3200 * 1.25) * 1024,
            'max_wallclock_seconds': 3600
        }
    }
)
# again, for tutorial, using a string parsed as file in place of providing an input file
file_string = '! B3LYP def2-SVP Opt AIM PAL4\n*xyz 0 1\nH 0.0 0.0 0.0\nH 0.0 0.0 1.0\n*'
input_file = SinglefileData(io.BytesIO(file_string.encode()))
builder.shell_input_file = input_file
# get the resulting wfx and opt file, the above command creates a file file.txt
# so we replace the txt with the output extensions we want
shell_list = List([input_file.filename.replace('txt','wfx'),input_file.filename.replace('txt','opt'),])
builder.shell_retrieved = shell_list
builder.shell_cmdline = Str('{file}')
builder.aim_code = load_code('aimall@localhost')
builder.aim_params = AimqbParameters({'nproc':2,'naat':2,'atlaprhocps':True})
submit(builder)

classmethod define(spec)

Define the specification of the process, including its inputs, outputs and known exit codes.

A metadata input namespace is defined, with optional ports that are not stored in the database.

shell_job()

Launch a shell job

aim()

Launch an AIMQB calculation

result()

Put results in output node

class aiida_aimall.workchains.qc_programs.GaussianToAIMWorkChain(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 submit a Gaussian calculation and automatically setup an AIMAll calculation on the output

gauss_params

Parameters for the Gaussian calculation

Type:

aiida.orm.Dict

aim_params

Parameters for the AIMQB calculation

Type:

AimqbParameters

gauss_code

Code for Gaussian software

Type:

aiida.orm.Code

frag_label

Label of the fragment

Type:

aiida.orm.Str

wfx_group

Group to put the wfx file in

Type:

aiida.orm.Str

gaussian_group

Group to put the GaussianCalculation in

Type:

aiida.orm.Str

aim_code

Code for AIMQB software

Type:

aiida.orm.Code

dry_run

Whether the run is a dry run

Type:

aiida.orm.Bool

wfx_filename

Name of the wfx file produced in the calculation

Type:

aiida.orm.Str

Example

from aiida import load_profile
from aiida.plugins import WorkflowFactory, DataFactory
from aiida.orm import Dict, StructureData, load_code
import io
import ase.io
from aiida.engine import submit
load_profile()
GaussianToAIMWorkChain = WorkflowFactory('aimall.gausstoaim')
AimqbParameters = DataFactory('aimall.aimqb')
gaussian_input = 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},
                })
aim_input = AimqbParameters({'nproc':2,'naat':2,'atlaprhocps':True})
# For tutorial purpose, representing a xyz file as a string, and parsing it to get strcutre data
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 = GaussianToAIMWorkChain.get_builder()
builder.g16_params = gaussian_input
builder.aim_params = aim_input
builder.structure = struct_data
builder.gauss_code = load_code('gaussian@localhost')
builder.aim_code = load_code('aimall@localhost')
submit(builder)

classmethod define(spec)

Define workchain steps

gauss()

Run Gaussian calculation

classify_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

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

Bases: aiida.engine.WorkChain

Workchain to generate a wfx file from computational chemistry output files and submit that to an AIMQB Calculation

input_file

File to convert to a wfx file. Should be .cp2k.out or .molden

Type:

aiida.orm.SinglefileData

aim_params

Command line parameters for AIMQB

Type:

AimqbParameters

aim_code

AIMQB code

Type:

aiida.orm.Code

Example

from aiida import load_profile
from aiida.plugins import WorkflowFactory, DataFactory
from aiida.orm import load_node, load_code, SinglefileData
from aiida.engine import submit

load_profile()
GenerateWFXToAIMWorkChain = WorkflowFactory("aimall.wfxtoaim")
AimqbParameters = DataFactory("aimall.aimqb")
# predefined Molden input file in database
single_file = SinglefileData('/absolute/path/to/file')
aim_params = AimqbParameters({"naat": 2, "nproc": 2, "atlaprhocps": True})
aim_code = load_code("aimall@localhost")
builder = GenerateWFXToAIMWorkChain.get_builder()
builder.input_file = single_file
builder.aim_params = aim_params
builder.aim_code = aim_code
submit(builder)

Note

This workchain uses the IOData module of the Ayer’s group Horton to generate the wfx files. Supported file formats include .fchk files, molden files (from Molpro, Orca, PSI4, Turbomole, and Molden), and CP2K atom log files. Further note that .fchk files can simply be provided directly to an AimqbCalculation.

While IOData accepts other file formats, these formats are the ones available that contain the necessary information to generate wfc files

classmethod define(spec)

Define the specification of the process, including its inputs, outputs and known exit codes.

A metadata input namespace is defined, with optional ports that are not stored in the database.

generate_wfx()

Given SinglefileData generates a wfx file if IOData is capable

aim()

Run AIM on the generated wfx file

result()

Put results in output node