UppASD_AiiDA package

Subpackages

• UppASD_AiiDA.utils package
  • Submodules
  • UppASD_AiiDA.utils.inpsd_parser module
  • Module contents

Submodules

UppASD_AiiDA.core_CLI module

UppASD_AiiDA.core_calcs module

class UppASD_AiiDA.core_calcs.UppASD(*args: Any, **kwargs: Any)

Bases: aiida.engine.processes.calcjobs.calcjob.CalcJob

AiiDA calculation plugin wrapping the SD executable (from UppASD packages).

Parameters

CalcJob (aiida.engine.CalcJob class) – father class

__abstractmethods__ = frozenset({})

__module__ = 'UppASD_AiiDA.core_calcs'

_abc_impl = <_abc_data object>

classmethod define(spec)

Define inputs and outputs of the calculation.

Note that you can add whatever flags here as wanted.

(Recommand add “required=False,”)

Remember that only if you put the output port here, your parser in

core_parser.py will work. otherwise you will go an error report or

could not see your parsed output array in database.

You can also use our example down there to make your output port.

#example:

#spec.output(‘xx_out’, valid_type=ArrayData, required=False,

# help=’’)

ToDo : we need to write all the possible output port here. so our user could

be easier.

find_out_files(filepath, except_files=[])

find out file names in the folder of input path and exclude files in except_files(a list)

Note that we have set the default except file : “.DS_Store”

Parameters

• filepath (str) – path of input folder.

• except_files (list, optional) – list of file name that need to be excluded. Make sure only need file with correct name(same name with flags) could be placed in the input folder., defaults to []

Returns

a list of file names for input and generate tags.

prepare_for_submission(folder)

IMPORTANT! we assumed that you have responsibility to name all

file in the input folder with same name of input flag that need

to generate in inspd.dat file.

And of course you can just put everything into the folder and send

it to aiida like what show in demo1 but remember to name ‘inpsd.dat’

as ‘inpsd’ without the file extension name’.out’

Parameters

folder (aiida.common.folders.Folder) – an aiida.common.folders.Folder where the plugin should temporarily place all files needed by the calculation.

Returns

calcinfo

UppASD_AiiDA.core_parser module

Parser for UppASD

class UppASD_AiiDA.core_parser.SpinDynamic_core_parser(node)

Bases: aiida.parsers.parser.Parser

Note that, all the parser here are just demos,or in other word, basic version(np.array) You can change it as you want and parser it to fit your need.

:param Parser father class aiida.parsers.parser :type Parser aiida.parsers.parser module :return: parsed numpy array

__abstractmethods__ = frozenset({})

__module__ = 'UppASD_AiiDA.core_parser'

_abc_impl = <_abc_data object>

averages_file_paser(file_name_of_averages)

:param file_name_of_averages averages file :type file_name_of_averages opened output file :return: np.array

coord_file_paser(file_name_of_coord)

:param file_name_of_coord coord file :type file_name_of_coord opened output file :return: np array

dm_out_parser(dmdata_out_file)

:param dmdata_out_file dmdata file :type dmdata_out_file opened output file :return: np.array

moment_file_paser(mom_out_file)

:param mom_out_file moment file :type mom_out_file opened output file :return: np.array

parse(**kwargs)

IMPORTANT, All parser should be connect to the output port in core_calcs, since all files have been retrieved into the retrieved folder, we have no need to care about how many output file will UppASD generate, only thing that need to care is when parsering them into the data type you need, all parser should be connect to the output port in core_calcs

qm_minima_file_paser(file_name_of_qm_minima)

:param file_name_of_qm_minima qm minima file :type file_name_of_qm_minima opened output file :return: np.array

qm_sweep_file_paser(file_name_of_qm_sweep)

:param file_name_of_qm_sweep qm sweep file :type file_name_of_qm_sweep opened output file :return: np.array

qpoints_file_paser(file_name_of_qpoints)

:param file_name_of_qpoints points file :type file_name_of_qpoints opened output file :return: np array

struct_out_parser(struct_out_file)

:param dmdata_out_file dmdata file :type dmdata_out_file opened output file :return: np.array

total_energy_file_paser(file_name_of_total_energy)

:param file_name_of_total_energy :type file_name_of_total_energy opened file :return: np array

Module contents

UppASD-AiiDA interface