aiida_aimall.controllers

Subclasses of FromGroupSubmissionController designed to prevent too many running processes

The entire aiida_aimall.workchains.subparam.SubstituentParameterWorkChain() can be replicated by linking these together.

Provides controllers for the AimReorWorkChain, AimqbCalculations, GaussianCalculation and SmilesToGaussianWorkChain.

Module Contents

Classes

SmilesToGaussianController	A controller for submitting aiida_aimall.workchains.param_parts.SmilesToGaussianWorkChain()
AimReorSubmissionController	A controller for submitting aiida_aimall.workchains.param_parts.AIMAllReorWorkChain().
AimAllSubmissionController	A controller for submitting aiida_aimall.calculations.AimqbCalculation().
GaussianSubmissionController	A controller for submitting GaussianCalculation.

class aiida_aimall.controllers.SmilesToGaussianController(code_label: str, gauss_opt_params: dict, wfxgroup: str, nprocs: int, mem_mb: int, time_s: int, *args, **kwargs)

Bases: aiida_submission_controller.FromGroupSubmissionController

A controller for submitting aiida_aimall.workchains.param_parts.SmilesToGaussianWorkChain()

Parameters:

• parent_group_label (str) – group label which contains various SMILES as orm.Str nodes

• group_label (str) – group in which to put the GaussianCalculations

• wfxgroup (str) – group in which to store the resulting wfx files

• max_concurrent (int) – maximum number of concurrent processes

• code_label (str) – label of Gaussian code, e.g. gaussian@cedar

• gauss_opt_params (Dict) – Dict of Gaussian parameters to use

• nprocs (int) – number of processors for gaussian calculation

• mem_mb (int) – amount of memory in MB for Gaussian calculation

• time_s (int) – wallclock time in seconds for Gaussian calculation

Returns:

Controller object, periodically use run_in_batches to submit new results

Example

In a typical use case of controllers, it is beneficial to check for new jobs periodically to submit.

Either there may be new members of the parent_group to run, or some of the currently running jobs have run. So once a controller is defined, we can run it in a loop.

controller = SmilesToGaussianController(
    code_label='gaussian@localhost',
    parent_group_label = 'input_smiles', # Add structures to run to input_smiles group
    group_label = 'gaussianopt', # Resulting nodes will be in the gaussianopt group
    max_concurrent = 1,
    wfxgroup = "opt_wfx",
    gauss_opt_params = Dict(dict={
        'link0_parameters': {
            '%chk':'aiida.chk',
            "%mem": "4000MB",
            "%nprocshared": 4,
        },
        'functional':'wb97xd',
        'basis_set':'aug-cc-pvtz',
        'route_parameters': { 'opt':None, 'freq':None},
        }),
    nprocs = 4,
    mem_mb = 6400,
    time_s = 24*3600*7
    )

while True:
    #submit Gaussian batches every hour
    controller.submit_new_batch()
    time.sleep(3600)

parent_group_label: str

group_label: str

code_label: str

max_concurrent: int

gauss_opt_params: dict

wfxgroup: str

nprocs: int

mem_mb: int

time_s: int

WORKFLOW_ENTRY_POINT: str = 'aimall.smitogauss'

get_extra_unique_keys()

Returns a tuple of extras keys in the order needed

get_inputs_and_processclass_from_extras(extras_values)

Constructs input for a GaussianCalculation from extra_values

class aiida_aimall.controllers.AimReorSubmissionController(code_label: str, reor_group: str, aimparameters, *args, **kwargs)

Bases: aiida_submission_controller.FromGroupSubmissionController

A controller for submitting aiida_aimall.workchains.param_parts.AIMAllReorWorkChain().

Parameters:

• parent_group_label – the string of a group label which contains various structures as orm.Str nodes

• group_label – the string of the group to put the GaussianCalculations in

• max_concurrent – maximum number of concurrent processes.

• code_label – label of code, e.g. gaussian@cedar

• reor_group – group in which to place the reoriented structures.

• aimparameters – dict of parameters for running AimQB, to be converted to AimqbParameters by the controller

Returns:

Controller object, periodically use run_in_batches to submit new results

Note

A typical use case is using this as a controller on wfx files created by GaussianCalculation. In that case,

match the parent_group_label here to the wfxgroup provided to the GaussianCalculation. In GaussianOptWorkchain, this is opt_wfx by default

Example

In a typical use case of controllers, it is beneficial to check for new jobs periodically to submit.

Either there may be new members of the parent_group to run, or some of the currently running jobs have run. So once a controller is defined, we can run it in a loop.

controller = AimReorSubmissionController(
    code_label='aimall@localhost',
    parent_group_label = 'wfx', # Add wfx files to run to group wfx
    group_label = 'aim',
    max_concurrent = 1,
    reor_group = "reor_str"
    aimparameters = {"naat": 2, "nproc": 2, "atlaprhocps": True}
)

while True:
    #submit AIM batches every 5 minutes
    i = i+1
    controller.submit_new_batch()
    time.sleep(300)

parent_group_label: str

group_label: str

max_concurrent: int

code_label: str

reor_group: str

aimparameters: dict

WORKFLOW_ENTRY_POINT: str = 'aimall.aimreor'

get_extra_unique_keys()

Returns a tuple of extras keys in the order needed

get_inputs_and_processclass_from_extras(extras_values)

Constructs input for a aiida_aimall.workchains.param_parts.AIMAllReorWorkChain() from extra_values

class aiida_aimall.controllers.AimAllSubmissionController(code_label: str, aim_parser: str, aimparameters: dict, *args, **kwargs)

Bases: aiida_submission_controller.FromGroupSubmissionController

A controller for submitting aiida_aimall.calculations.AimqbCalculation().

Parameters:

• parent_group_label – the string of a group label which contains various structures as orm.Str nodes

• group_label – the string of the group to put the GaussianCalculations in

• max_concurrent – maximum number of concurrent processes. Expected behaviour is to set to a large number since we will be submitting to Cedar which will manage

• code_label – label of code, e.g. gaussian@cedar

• aimparameters – dict of parameters for running AimQB, to be converted to aiida_aimall.data.AimqbParameters() by the controller

• aimparser – str of which AIM parser to use: aimall.base for AimqbBaseParser or aimall.group for AimqbGroupParser

Returns:

Controller object, periodically use run_in_batches to submit new results

Note

A typical use case is using this as a controller on wfx files created by GaussianCalculation. In that case,

match the parent_group_label here to the wfxgroup provided to the GaussianCalculation. In GaussianSubmissionController, this is reor_wfx

Example

In a typical use case of controllers, it is beneficial to check for new jobs periodically to submit.

Either there may be new members of the parent_group to run, or some of the currently running jobs have run. So once a controller is defined, we can run it in a loop.

controller = AimAllSubmissionController(
    code_label='aimall@localhost',
    parent_group_label = 'wfx', # Add wfx files to run to group wfx
    group_label = 'aim_reor',
    max_concurrent = 1,
    aim_parser = 'aimqb.group'
    aimparameters = {"naat": 2, "nproc": 2, "atlaprhocps": True}
)

while True:
    #submit AIM batches every 5 minutes
    i = i+1
    controller.submit_new_batch()
    time.sleep(300)

parent_group_label: str

group_label: str

max_concurrent: int

code_label: str

aim_parser: str

aimparameters: dict

CALCULATION_ENTRY_POINT: str = 'aimall.aimqb'

get_extra_unique_keys()

Returns a tuple of extras keys in the order needed

get_inputs_and_processclass_from_extras(extras_values)

Constructs input for a AimQBCalculation from extra_values

class aiida_aimall.controllers.GaussianSubmissionController(code_label: str, gauss_sp_params: dict, wfxname: str, *args, **kwargs)

Bases: aiida_submission_controller.FromGroupSubmissionController

A controller for submitting GaussianCalculation.

Parameters:

• parent_group_label – the string of a group label which contains various structures as orm.Str nodes

• group_label – the string of the group to put the GaussianCalculations in

• max_concurrent – maximum number of concurrent processes. Expected behaviour is to set to a large number since we will be submitting to Cedar which will manage

• code_label – label of code, e.g. gaussian@cedar

• gauss_sp_params – dictionary of parameters to use in gaussian calculation

• wfxname – Name of the wfx file

Returns:

Controller object, periodically use run_in_batches to submit new results

Note

A typical use case is using this as a controller on Str structures generated by AIMAllReor workchain. These are by

default assigned to the reor_structs group, so have parent_group_label match that

Note

In overall workchain(fragment->optimize->aim+rotate->single point->aim), this is the single point step. Process continues and finishes in AimAllSubmissionController

Example

In a typical use case of controllers, it is beneficial to check for new jobs periodically to submit.

Either there may be new members of the parent_group to run, or some of the currently running jobs have run. So once a controller is defined, we can run it in a loop.

controller = GaussianSubmissionController(
    code_label='gaussian@localhost',
    parent_group_label = 'struct', # Add structures to run to struct group
    group_label = 'gaussiansp', # Resulting nodes will be in the gaussiansp group
    max_concurrent = 1,
    wfxname='output.wfx'
    gauss_sp_params = Dict(dict={
        'link0_parameters': {
            '%chk':'aiida.chk',
            "%mem": "4000MB",
            "%nprocshared": 4,
        },
        'functional':'wb97xd',
        'basis_set':'aug-cc-pvtz',
        'charge': 0,
        'multiplicity': 1,
        'route_parameters': {'nosymmetry':None, 'Output':'WFX'},
        "input_parameters": {"output.wfx": None},
        })
)

while True:
    #submit Gaussian batches every hour
    controller.submit_new_batch()
    time.sleep(3600)

parent_group_label: str

group_label: str

max_concurrent: int

code_label: str

gauss_sp_params: dict

wfxname: str

CALCULATION_ENTRY_POINT: str = 'gaussian'

get_extra_unique_keys()

Returns a tuple of extras keys in the order needed

get_inputs_and_processclass_from_extras(extras_values)

Constructs input for a GaussianWFXCalculation from extra_values

Note: adjust the metadata options later for 6400MB and 7days runtime