from aiida.common import datastructures
from aiida.engine import CalcJob
from aiida.orm import SinglefileData, Int, Float, Str, Bool, List, Dict, ArrayData, XyData, SinglefileData, FolderData, RemoteData
from os import listdir
from os.path import isfile, join
import os
[docs]class UppASD(CalcJob):
"""
| AiiDA calculation plugin wrapping the SD executable (from UppASD packages).
:param CalcJob: father class
:type CalcJob: aiida.engine.CalcJob class
"""
[docs] @classmethod
def define(cls, 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.
"""
super(UppASD, cls).define(spec)
# input file sections :
spec.input('prepared_file_folder', valid_type=Str, required=False,
help='path to prepared_file_folder')
spec.input('except_filenames', valid_type=List, required=False,
help='list of excepted filenames')
spec.input('inpsd_dict', valid_type=Dict,
help='the dict of inpsd.dat', required=False) # default=lambda: Dict(dict={})
spec.input('exchange', valid_type=Dict,
help='the dict of exchange.dat', required=False)
spec.input('retrieve_list_name', valid_type=List,
help='list of output file name')
# output sections:
spec.output('totenergy', valid_type=ArrayData, required=False,
help='all data that stored in totenergy.out')
spec.output('coord', valid_type=ArrayData, required=False,
help='all data that stored in coord.out')
spec.output('qpoints', valid_type=ArrayData, required=False,
help='all data that stored in qpoints.out')
spec.output('averages', valid_type=ArrayData, required=False,
help='all data that stored in averages.out')
spec.output('qm_sweep', valid_type=ArrayData, required=False,
help='all data that stored in qm_sweep.out')
spec.output('qm_minima', valid_type=ArrayData, required=False,
help='all data that stored in qm_minima.out')
spec.output('mom_states_traj', valid_type=ArrayData, required=False,
help='all data that stored in moment.out')
spec.output('dmdata_out', valid_type=ArrayData, required=False,
help='all data that stored in dmdata_xx.out')
spec.output('struct_out', valid_type=ArrayData, required=False,
help='all data that stored in dmdata_xx.out')
spec.exit_code(100, 'ERROR_MISSING_OUTPUT_FILES',
message='Calculation did not produce all expected output files.')
[docs] def find_out_files(self,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"
:param filepath: path of input folder.
:type filepath: str
:param except_files: 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 []
:type except_files: list, optional
:return: a list of file names for input and generate tags.
"""
if ".DS_Store" not in except_files:
except_files.append(".DS_Store")
filenames = [f for f in listdir(filepath) if (
isfile(join(filepath, f)) and f not in except_files)]
return filenames
[docs] def prepare_for_submission(self, 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'
:param folder: an `aiida.common.folders.Folder` where the plugin should temporarily place all files needed by the calculation.
:type folder: aiida.common.folders.Folder
:return: calcinfo
"""
calcinfo = datastructures.CalcInfo()
local_list = []
user_define_dict_name_list = []
auto_name = globals()
input_filenames = self.find_out_files(
self.inputs.prepared_file_folder.value, self.inputs.except_filenames.get_list())
for name in input_filenames:
auto_name[name] = SinglefileData(
file=os.path.join(self.inputs.prepared_file_folder.value, name)).store()
#J_ij exchange parameters
if 'exchange' not in input_filenames: # nothing in inpsd dict
#note that we take the inpsd.dat first, that means if we have both inpsd dict and inpsd.dat file we only use inpsd.dat file
# Create input file: inpsd.dat
with folder.open('exchange', 'a+') as f: #here input_filename is an input option not a list
for flag in self.inputs.exchange.attributes_keys():
f.write(f'{self.inputs.exchange[flag]}\n')
user_define_dict_name_list.append('exchange') #for activation of 'exchange' flag
if 'inpsd' not in input_filenames: # nothing in inpsd dict
#note that we take the inpsd.dat first, that means if we have both inpsd dict and inpsd.dat file we only use inpsd.dat file
# Create input file: inpsd.dat
with folder.open(self.options.input_filename, 'a+') as f: #here input_filename is an input option not a list
for flag in self.inputs.inpsd_dict.attributes_keys():
f.write(f'{flag}'+f' {self.inputs.inpsd_dict[flag]}\n')
for name in input_filenames:
f.write(f'{name} ./{name}\n')
for name_ud in user_define_dict_name_list:
f.write(f'{name_ud} ./{name_ud}\n')
for name in input_filenames:
if str(name) != 'inpsd':
#I believe all our user are kind people, they will not do evail things with eval() function :-) , ToDo: replace eval() here to make sure the safity
local_list.append((eval(name).uuid, eval(
name).filename, eval(name).filename))
else:
local_list.append(
(eval(name).uuid, eval(name).filename, 'inpsd.dat'))
calcinfo.local_copy_list = local_list
input_retrieve_list_name = self.inputs.retrieve_list_name
codeinfo = datastructures.CodeInfo()
# note that nothing need here for UppASD,(at least now :-) )
codeinfo.cmdline_params = []
codeinfo.code_uuid = self.inputs.code.uuid
calcinfo.codes_info = [codeinfo]
calcinfo.retrieve_list = input_retrieve_list_name.get_list()
return calcinfo