# -*- coding: utf-8 -*-
"""
Plugin to create a YPP input file and run a calculation with the ypp executable.
"""
from __future__ import absolute_import
import os
from tokenize import Single
import six
from aiida.engine import CalcJob
from aiida_quantumespresso.calculations import _lowercase_dict, _uppercase_dict
from aiida.common.datastructures import CalcInfo
from aiida.common.datastructures import CalcJobState
from aiida.common.exceptions import UniquenessError, InputValidationError, ValidationError
from aiida.common.utils import classproperty
from aiida.orm import Code
from aiida.orm.nodes import Dict
from aiida.orm.nodes import RemoteData, BandsData, ArrayData, FolderData
from aiida.plugins import DataFactory, CalculationFactory
from aiida.common import AIIDA_LOGGER
from aiida.common import LinkType
from aiida_yambo.utils.common_helpers import *
from yambopy.io.inputfile import YamboIn
[docs]PwCalculation = CalculationFactory('quantumespresso.pw')
[docs]YamboCalculation = CalculationFactory('yambo.yambo')
[docs]SingleFileData = DataFactory('core.singlefile')
[docs]__authors__ = " Miki Bonacci (miki.bonacci@unimore.it)," \
" Nicola Spallanzani" \
[docs]class YppCalculation(CalcJob):
"""
AiiDA plugin for the Ypp code.
For more information, refer to http://www.yambo-code.org/
https://github.com/yambo-code/yambo-aiida and http://aiida-yambo.readthedocs.io/en/latest/
"""
# Default input and output files
[docs] _DEFAULT_OUTPUT_FILE = 'aiida.out'
@classmethod
[docs] def define(cls,spec):
super(YppCalculation, cls).define(spec)
spec.input('metadata.options.input_filename', valid_type=six.string_types, default=cls._DEFAULT_INPUT_FILE)
spec.input('metadata.options.output_filename', valid_type=six.string_types, default=cls._DEFAULT_OUTPUT_FILE)
# Default output parser provided by AiiDA
spec.input('metadata.options.parser_name', valid_type=six.string_types, default='yambo.ypp')
# self._SCRATCH_FOLDER = 'SAVE'
spec.input('metadata.options.scratch_folder', valid_type=six.string_types, default='SAVE')
spec.input('metadata.options.logostring', valid_type=six.string_types, default="""
#
# Y88b / e e e 888~~\ ,88~-_
# Y88b / d8b d8b d8b 888 | d888 \
# Y88b/ /Y88b d888bdY88b 888 _/ 88888 |
# Y8Y / Y88b / Y88Y Y888b 888 \ 88888 |
# Y /____Y88b / YY Y888b 888 | Y888 /
# / / Y88b / Y888b 888__/ `88_-~
#
# AIIDA input plugin. YAMBO >4.0 compatible
# http://www.yambo-code.org
#
"""
)
spec.input('settings',valid_type=Dict,
default=Dict(dict={'COPY_DBS':True}),
help='Use an additional node for special settings')
spec.input('parameters',valid_type=Dict,
help='Use a node that specifies the input parameters')
spec.input('parent_folder',valid_type=RemoteData,required=False,
help='Use a remote folder as parent folder (for "restarts and similar"')
spec.input('code',valid_type=Code,
help='Use a main code for ypp calculation')
spec.input(
'nnkp_file',
valid_type=SingleFileData,
required=False,
help=
'The nnkp file'
)
spec.input(
'QP_DB',
valid_type=SingleFileData,
required=False,
help=
'The QP_DB file'
)
spec.input(
'QP_calculations',
valid_type=List,
required=False,
help='List of QP pk/uuid calculations that you want to merge.')
spec.input(
'QP_DB_List',
valid_type=List,
required=False,
help='List of QP pk/uuid SingleFileData that you want to merge.')
spec.exit_code(500, 'ERROR_NO_RETRIEVED_FOLDER',
message='The retrieved folder data node could not be accessed.')
spec.exit_code(501, 'WALLTIME_ERROR',
message='time exceeded the max walltime')
spec.exit_code(502, 'NO_SUCCESS',
message='failed calculation for unknown reason')
spec.exit_code(503, 'PARSER_ANOMALY',
message='Unexpected behavior of YamboFolder')
spec.exit_code(504, 'NNKP_NOT_PRESENT',
message='nnkp file not present')
spec.exit_code(505, 'QP_LIST_NOT_PRESENT',
message='QP list not present')
spec.exit_code(506, 'MERGE_NOT_COMPLETE',
message='QP merging is not completed.')
spec.exit_code(507, 'PARENT_NOT_VALID',
message='parent folder not valid. It has not a QP_DB node as output..')
#outputs definition:
spec.output('output_parameters', valid_type=Dict,
required=True, help='returns the output parameters')
spec.output('array_interpolated_bands', valid_type=ArrayData,
required=False, help='returns the interpolated bands array')
spec.output(
'unsorted_eig_file',
valid_type=SingleFileData,
required=False,
help='The ``.unsorted.eig`` file.'
)
spec.output('QP_DB', valid_type=SingleFileData,
required=False, help='returns the singlefiledata for ndbQP')
[docs] def prepare_for_submission(self, tempfolder):
local_copy_list = []
remote_copy_list = []
remote_symlink_list = []
# Settings can be undefined, and defaults to an empty dictionary.
# They will be used for any input that doen't fit elsewhere.
settings = self.inputs.settings.get_dict()
copy_save = settings.pop('COPY_SAVE', None)
if copy_save is not None:
if not isinstance(copy_save, bool):
raise InputValidationError("COPY_SAVE must be " " a boolean")
copy_dbs = settings.pop('COPY_DBS', None)
if copy_dbs is not None:
if not isinstance(copy_dbs, bool):
raise InputValidationError("COPY_DBS must be " " a boolean")
link_dbs = settings.pop('LINK_DBS', None)
if link_dbs is not None:
if not isinstance(link_dbs, bool):
raise InputValidationError("LINK_DBS must be " " a boolean")
verbose_timing = settings.pop('T_VERBOSE', None)
if verbose_timing is not None:
if not isinstance(verbose_timing, bool):
raise InputValidationError("T_VERBOSE must be " " a boolean")
parameters = self.inputs.parameters
if not isinstance(parameters, Dict):
raise InputValidationError("parameters is not of type Dict")
parent_calc_folder = self.inputs.parent_folder
main_code = self.inputs.code
try:
parent_calc = take_calc_from_remote(parent_calc_folder,level=-1)
except:
parent_calc = take_calc_from_remote(parent_calc_folder,level=0)
yambo_parent = False
ypp_parent=True
if parent_calc.process_type=='aiida.calculations:yambo.yambo':
yambo_parent=True
elif parent_calc.process_type=='aiida.workflows:yambo.yambo.yamborestart':
yambo_parent=True
elif parent_calc.process_type=='aiida.workflows:yambo.yambo.yambowf':
yambo_parent=True
elif parent_calc.process_type=='aiida.workflows:yambo.yambo.yamboconvergence':
yambo_parent=True
elif parent_calc.process_type=='aiida.calculations:yambo.ypp':
ypp_parent=True
elif parent_calc.process_type=='aiida.workflows:yambo.ypp.ypprestart':
ypp_parent=True
else:
raise InputValidationError("YppCalculation parent MUST be a YamboCalculation, not {}".format(parent_calc.process_type))
# TODO: check that remote data must be on the same computer
##############################
# END OF INITIAL INPUT CHECK #
##############################
###################################################
# Prepare ypp input file
###################################################
params_dict = parameters.get_dict()
if 'wannier' in params_dict['arguments']:
#copy_dbs = True
copy_save = True
if not hasattr(self.inputs,'nnkp_file'):
self.report('WARNING: aiida.nnkp file not present in inputs, Needed.')
return self.exit_codes.NNKP_NOT_PRESENT
else:
local_copy_list.append((self.inputs.nnkp_file.uuid, self.inputs.nnkp_file.filename, 'aiida.nnkp'))
if hasattr(self.inputs,'QP_DB'):
local_copy_list.append((self.inputs.QP_DB.uuid, self.inputs.QP_DB.filename, 'ndb.QP')) #in this way also "ndb.QP_merged_ppa" should be copied ok.
if not hasattr(self.inputs,'QP_DB') and hasattr(self.inputs,'parent_folder'):
try:
local_copy_list.append((take_calc_from_remote(self.inputs.parent_folder).outputs.QP_DB.uuid, self.inputs.QP_DB.filename, 'ndb.QP'))
except:
return self.exit_codes.PARENT_NOT_VALID
params_dict['variables']['Seed'] = 'aiida' #self.metadata.options.input_filename.replace('.in','') # depends on the QE seedname, I guess
if 'QPDB_merge' in params_dict['arguments']:
copy_save = True
if not hasattr(self.inputs,'QP_calculations') and not ypp_parent:
self.report('WARNING: QP_calculations list or folders not present in inputs, Needed.')
return self.exit_codes.QP_LIST_NOT_PRESENT
j=0
list_of_dbs = []
if hasattr(self.inputs,'QP_calculations'):
for calc in self.inputs.QP_calculations.get_list():
j+=1
qp = load_node(calc).outputs.QP_db
local_copy_list.append((qp.uuid, qp.filename, 'ndb.QP_'+str(j)))
list_of_dbs.append(['"E"','"+"','"1"','"'+'ndb.QP_'+str(j)+'"'])
elif hasattr(self.inputs,'QP_DB_List'):
for calc in self.inputs.QP_DB_List.get_list():
j+=1
qp = load_node(calc)
local_copy_list.append((qp.uuid, qp.filename, 'ndb.QP_'+str(j)))
list_of_dbs.append(['"E"','"+"','"1"','"'+'ndb.QP_'+str(j)+'"'])
elif not hasattr(self.inputs,'QP_calculations') and ypp_parent:
ypp_parent_calc = take_calc_from_remote(self.inputs.parent_folder)
for file in ypp_parent_calc.outputs.retrieved.base.repository.list_object_names():
if 'ndb.QP' in file:
#qp = load_node(calc).outputs.QP_db
#local_copy_list.append((qp.uuid, qp.filename, 'ndb.QP_'+str(j)))
list_of_dbs.append(['"E"','"+"','"1"','"'+file+'"'])
params_dict['variables']['Actions_and_names'] = [list_of_dbs,'']
y = YamboIn().from_dictionary(params_dict)
input_filename = tempfolder.get_abs_path(self.metadata.options.input_filename)
y.write(input_filename, prefix=self.metadata.options.logostring)
############################################
# set copy of the parent calculation
############################################
try:
parent_calc = parent_calc_folder.get_incoming().all_nodes()[-1] #to load the node from a workchain...
except:
parent_calc = parent_calc_folder.get_incoming().get_node_by_label('remote_folder')
if copy_save:
remote_copy_list.append((parent_calc_folder.computer.uuid,parent_calc_folder.get_remote_path()+"/SAVE/",'./SAVE/'))
else:
try:
remote_symlink_list.append((parent_calc_folder.computer.uuid,parent_calc_folder.get_remote_path()+"/SAVE/",'./SAVE/'))
except:
remote_symlink_list.append((parent_calc_folder.computer.uuid,parent_calc_folder.get_remote_path()+"out/aiida.save/SAVE/",'./SAVE/'))
if copy_dbs:
remote_copy_list.append((parent_calc_folder.computer.uuid,parent_calc_folder.get_remote_path()+"/aiida.out/",'./aiida.out/'))
if link_dbs:
remote_symlink_list.append((parent_calc_folder.computer.uuid,parent_calc_folder.get_remote_path()+"/aiida.out/",'./aiida.out/'))
############################################
# set Calcinfo
############################################
calcinfo = CalcInfo()
calcinfo.uuid = self.uuid
calcinfo.local_copy_list = local_copy_list #here I need to append the nnkp_file...
calcinfo.remote_copy_list = remote_copy_list
calcinfo.remote_symlink_list = remote_symlink_list
# Retrieve by default the output file and the xml file
calcinfo.retrieve_list = []
calcinfo.retrieve_list.append('r*')
calcinfo.retrieve_list.append('l*')
calcinfo.retrieve_list.append('o*')
calcinfo.retrieve_list.append('LOG/l*_CPU_1')
#calcinfo.retrieve_list.append('LOG/l*_CPU_2')
calcinfo.retrieve_list.append('*stderr*') #standard errors
extra_retrieved = []
if 'wannier' in params_dict['arguments']:
calcinfo.retrieve_list.append('*eig')
calcinfo.retrieve_list.append('*nnkp')
if 'QPDB_merge' in params_dict['arguments']:
calcinfo.retrieve_list.append('SAVE/ndb.QP_merged*')
calcinfo.retrieve_list.append('aiida.out/ndb.QP_merged*')
additional = settings.pop('ADDITIONAL_RETRIEVE_LIST',[])
if additional:
extra_retrieved.append(additional)
from aiida.common.datastructures import CodeRunMode, CodeInfo
# c = ypp calculation
c = CodeInfo()
c.withmpi = True
#c.withmpi = self.get_withmpi()
# Here we need something more flexible, because it is not always like that.
# Like something automatic, where you specify 'interpolate bands' or 'excitonic wavefunctions...'
c.cmdline_params = [
"-F", self.metadata.options.input_filename, \
'-J', self.metadata.options.output_filename, \
]
c.code_uuid = main_code.uuid
#logic of the execution
calcinfo.codes_info = [c]
calcinfo.codes_run_mode = CodeRunMode.SERIAL
for extra in extra_retrieved:
calcinfo.retrieve_list.append(extra)
return calcinfo
