# -*- coding: utf-8 -*-
###############################################################################
# Copyright (c), Forschungszentrum Jülich GmbH, IAS-1/PGI-1, Germany. #
# All rights reserved. #
# This file is part of the AiiDA-FLEUR package. #
# #
# The code is hosted on GitHub at https://github.com/JuDFTteam/aiida-fleur #
# For further information on the license, see the LICENSE.txt file #
# For further information please visit http://www.flapw.de or #
# http://aiida-fleur.readthedocs.io/en/develop/ #
###############################################################################
"""
In this module is the :class:`~aiida_fleur.data.fleurinp.FleurinpData` class, and methods for FLEUR
input manipulation plus methods for extration of AiiDA data structures.
"""
# TODO: maybe add a modify method which returns a fleurinpmodifier class
# TODO: inpxml to dict: maybe kpts should not be written to the dict? same with symmetry
# TODO: test for large input files, I believe the recursion is still quite slow..
# TODO: 2D cell get kpoints and get structure also be carefull with tria = T!!!
# TODO : maybe save when get_structure or get_kpoints was executed on fleurinp,
# because otherwise return this node instead of creating a new one!
# TODO: get rid of duplicate code for parsing the inp.xml to an etree
from __future__ import absolute_import
from __future__ import print_function
import os
import io
import re
import six
from lxml import etree
from aiida.orm import Data, Node, load_node
from aiida.common.exceptions import InputValidationError, ValidationError
from aiida.engine.processes.functions import calcfunction as cf
from aiida_fleur.tools.xml_util import replace_tag
from aiida_fleur.fleur_schema.schemafile_index import get_internal_search_paths, get_schema_paths
from aiida_fleur.common.constants import bohr_a as BOHR_A
[docs]class FleurinpData(Data):
"""
AiiDA data object representing everything a FLEUR calculation needs.
It is initialized with an absolute path to an ``inp.xml`` file or a
FolderData node containing ``inp.xml``.
Other files can also be added that will be copied to the remote machine, where the
calculation takes place.
It stores the files in the repository and stores the input parameters of the
``inp.xml`` file of FLEUR in the database as a python dictionary (as internal attributes).
When an ``inp.xml`` (name important!) file is added to files, FleurinpData searches
for a corresponding xml schema file in the PYTHONPATH environment variable.
Therefore, it is recommend to have the plug-in source code directory in the python environment.
If no corresponding schema file is found an error is raised.
FleurinpData also provides the user with
methods to extract AiiDA StructureData and
KpointsData nodes.
Remember that most attributes of AiiDA nodes can not be changed after they
have been stored in the database! Therefore, you have to use the FleurinpModifier class and its
methods if you want to change somthing in the ``inp.xml`` file. You will retrieve a new
FleurinpData that way and start a new calculation from it.
"""
# search in current folder and search in aiida source code
# we want to search in the Aiida source directory, get it from python path,
# maybe better from somewhere else.
# TODO: don not walk the whole python path, test if dir below is aiida?
# needs to be improved, schema file is often after new installation not found...
# installation with pip should always lead to a schema file in the python path, or even specific place
[docs] def __init__(self, **kwargs):
"""
Initialize a FleurinpData object set the files given
"""
files = kwargs.pop('files', None)
for filename in files:
if 'inp.xml' in filename:
files.pop(files.index(filename))
files.append(filename)
break
node = kwargs.pop('node', None)
super(FleurinpData, self).__init__(**kwargs)
search_paths = []
ifolders = get_internal_search_paths()
ischemas = get_schema_paths()
for path in ischemas:
search_paths.append(path)
for path in ifolders:
search_paths.append(path)
search_paths.append('./')
# Now add also python path maybe will be decaptivated
# if pythonpath is non existent catch error
try:
pythonpath = os.environ['PYTHONPATH'].split(':')
except KeyError:
pythonpath = []
for path in pythonpath[:]:
search_paths.append(path)
self.set_attribute('_has_schema', False)
self.set_attribute('_schema_file_path', None)
self.set_attribute('_search_paths', search_paths)
if files:
if node:
self.set_files(files, node=node)
else:
self.set_files(files)
# ignore machine dependent attributes in hash
_hash_ignored_attributes = ['_schema_file_path', '_search_paths']
@property
def _has_schema(self):
"""
Boolean property, which stores if a schema file is already known
"""
return self.get_attribute('_has_schema')
@property
def _schema_file_path(self):
"""
A string, which stores the absolute path to the schemafile found
"""
return self.get_attribute('_schema_file_path')
@property
def _search_paths(self):
"""
A string, which stores the paths to search for schemafiles
"""
return self.get_attribute('_search_paths')
@_has_schema.setter
def _has_schema(self, boolean):
"""
Setter for has_schema
"""
self.set_attribute('_has_schema', boolean)
@_schema_file_path.setter
def _schema_file_path(self, schemapath):
"""
Setter for the schema file path
"""
self.set_attribute('_schema_file_path', schemapath)
# files
@property
def files(self):
"""
Returns the list of the names of the files stored
"""
return self.get_attribute('files', [])
@files.setter
def files(self, filelist, node=None):
"""
Add a list of files to FleurinpData.
Alternative use setter method.
:param files: list of filepaths or filenames of node is specified
:param node: a Folder node containing files from the filelist
"""
for file1 in filelist:
self.set_file(file1, node=node)
[docs] def set_files(self, files, node=None):
"""
Add the list of files to the :class:`~aiida_fleur.data.fleurinp.FleurinpData` instance.
Can by used as an alternative to the setter.
:param files: list of abolute filepaths or filenames of node is specified
:param node: a :class:`~aiida.orm.FolderData` node containing files from the filelist
"""
for file1 in files:
self.set_file(file1, node=node)
[docs] def set_file(self, filename, dst_filename=None, node=None):
"""
Add a file to the :class:`~aiida_fleur.data.fleurinp.FleurinpData` instance.
:param filename: absolute path to the file or a filename of node is specified
:param node: a :class:`~aiida.orm.FolderData` node containing the file
"""
self._add_path(filename, dst_filename=dst_filename, node=node)
[docs] def open(self, path='inp.xml', mode='r', key=None):
"""
Returns an open file handle to the content of this data node.
:param key: name of the file to be opened
:param mode: the mode with which to open the file handle
:returns: A file handle in read mode
"""
from aiida.orm.nodes.node import WarnWhenNotEntered # deep import might change
if key is not None:
path = key
return WarnWhenNotEntered(self._repository.open(path, mode=mode), repr(self))
[docs] def get_content(self, filename='inp.xml'):
"""
Returns the content of the single file stored for this data node.
:returns: A string of the file content
"""
with self.open(path=filename, mode='r') as handle:
return handle.read()
[docs] def del_file(self, filename):
"""
Remove a file from FleurinpData instancefind
:param filename: name of the file to be removed from FleurinpData instance
"""
# remove from files attr list
if filename in self.get_attribute('files'):
try:
self.get_attribute('files').remove(filename)
# self._del_attribute(‘filename')
except AttributeError:
# There was no file set
pass
# remove from sandbox folder
if filename in self.list_object_names(): # get_folder_list():
self.delete_object(filename)
[docs] def find_schema(self, inp_version_number):
"""
Method which searches for a schema files (.xsd) which correspond
to the input xml file. (compares the version numbers)
:param inp_version_number: a version of ``inp.xml`` file schema to be found
:return: A two-element tuple:
1. A list of paths where schema files are located
2. A boolen which shows if the required version schema file was found
"""
# user changed version number, or no file yet known.
# TODO test if this still does the right thing if user adds one
# inp.xml and then an inp.xml with different version.
# or after copying and read
schemafile_paths = []
for path in self._search_paths: # paths:
for root, dirs, files in os.walk(path):
for file1 in files:
if file1.endswith('.xsd'):
if ('Fleur' in file1) or ('fleur' in file1):
schemafile_path = os.path.join(root, file1)
schemafile_paths.append(schemafile_path)
i = 0
imin = 0
imax = 0
schemafile = open(schemafile_path, 'r')
for line in schemafile.readlines():
i = i + 1
# This kind of hardcoded
if re.search('name="FleurVersionType"', line):
imax = i + 10 # maybe make larger or different
imin = i
schema_version_numbers = []
if imin < i <= imax:
if re.search('enumeration value', line):
schema_version_number = re.findall(r'\d+.\d+', line)[0]
elif re.search('simpleType>', line):
break
schema_version_numbers.append(schema_version_number)
schemafile.close()
# test if schemafiles works with multiple fleur versions
for version_number in schema_version_numbers:
if version_number == inp_version_number:
# we found the right schemafile for the current inp.xml
self.set_attribute('_schema_file_path', schemafile_path)
self.set_attribute('_has_schema', True)
return schemafile_paths, True
return schemafile_paths, False
def _add_path(self, file1, dst_filename=None, node=None):
"""
Add a single file to the FleurinpData folder.
The destination name can be different. ``inp.xml`` is a special case.
file names are stored in the db, the whole file in the reporsitory.
:param file1: the file to be added, either string, absolute path, or filelike object whose contents to copy
Hint: Pass io.BytesIO(b"my string") to construct the file directly from a string.
:param dst_filename: string, new filename for given file in repo and db
:param node: aiida.orm.Node, usually FolderData if node is given get the 'file1' from the node
:raise: ValueError, InputValidationError
:return: None
"""
# TODO? Maybe only certain files should be allowed to be added
# contra: has to be maintained, also these files can be inputed from byte strings...
#_list_of_allowed_files = ['inp.xml', 'enpara', 'cdn1', 'sym.out', 'kpts']
if node:
if not isinstance(node, Node):
node = load_node(node) # if this fails it will raise
if file1 not in node.list_object_names():
# throw error, you try to add something that is not there
raise ValueError('file1 has to be in the specified node')
is_filelike = True
if dst_filename is None:
final_filename = file1
else:
final_filename = dst_filename
# Override file1 with bytestring of file
# since we have to use 'with', and node has no method to copy files
# we read the whole file and write it again later
# this is not so nice, but we assume that input files are rather small...
with node.open(file1, mode='rb') as file2:
file1 = io.BytesIO(file2.read())
elif isinstance(file1, six.string_types):
is_filelike = False
if not os.path.isabs(file1):
file1 = os.path.abspath(file1)
#raise ValueError("Pass an absolute path for file1: {}".format(file1))
if not os.path.isfile(file1):
raise ValueError('file1 must exist and must be a single file: {}'.format(file1))
if dst_filename is None:
final_filename = os.path.split(file1)[1]
else:
final_filename = dst_filename
else:
is_filelike = True
if dst_filename is None:
try:
final_filename = os.path.basename(file1.name) # Not sure if this still works for aiida>2.0
except AttributeError:
final_filename = 'inp.xml' # fall back to default
else:
final_filename = dst_filename
key = final_filename
old_file_list = self.list_object_names()
old_files_list = self.get_attribute('files', [])
# remove file from folder first if it exists
if final_filename not in old_file_list:
old_files_list.append(final_filename)
else:
try:
old_file_list.remove(final_filename)
except ValueError:
pass
if is_filelike:
self.put_object_from_filelike(file1, key, mode='wb')
else:
self.put_object_from_file(file1, key)
self.set_attribute('files', old_files_list) # We want to keep the other files
### Special case: 'inp.xml' ###
# here this is hardcoded, might want to change? get filename from elsewhere
if final_filename == 'inp.xml':
# get input file version number
inp_version_number = None
lines = self.get_content(filename=final_filename).split('\n')
for line in lines:
if re.search('fleurInputVersion', str(line)):
inp_version_number = re.findall(r'\d+.\d+', str(line))[0]
break
if inp_version_number is None:
raise InputValidationError('No fleurInputVersion number found '
'in given input file: {}. {}'
'Please check if this is a valid fleur input file. '
'It can not be validated and I can not use it. '
''.format(file1, lines))
# search for Schema file with same version number
schemafile_paths, found = self.find_schema(inp_version_number)
if (not self._has_schema) and (self._schema_file_path is None):
err_msg = ('No XML schema file (.xsd) with matching version number {} '
'to the inp.xml file was found. I have looked here: {} '
'and have found only these schema files for Fleur: {}. '
'I need this file to validate your input and to know the structure '
'of the current inp.xml file, sorry.'.format(inp_version_number, self._search_paths,
schemafile_paths))
raise InputValidationError(err_msg)
if self._schema_file_path is None:
schemafile_paths, found = self.find_schema(inp_version_number)
if not found:
err_msg = ('No XML schema file (.xsd) with matching version number {} '
'to the inp.xml file was found. I have looked here: {} '
'and have found only these schema files for Fleur: {}. '
'I need this file to validate your input and to know the structure '
'of the current inp.xml file, sorry.'.format(inp_version_number, self._search_paths,
schemafile_paths))
raise InputValidationError(err_msg)
# finally set inp dict of Fleurinpdata
self._set_inp_dict()
def _set_inp_dict(self):
"""
Sets the inputxml_dict from the ``inp.xml`` file attached to FleurinpData
1. get ``inp.xml`` structure/layout
2. load ``inp.xml`` file
3. call inpxml_to_dict
4. set inputxml_dict
"""
from aiida_fleur.tools.xml_util import get_inpxml_file_structure, inpxml_todict, clear_xml
import tempfile
# get inpxml structure
inpxmlstructure = get_inpxml_file_structure()
# read xmlinp file into an etree with autocomplition from schema
# we do not validate here because we want this to always succeed
xmlschema_doc = etree.parse(self._schema_file_path)
xmlschema = etree.XMLSchema(xmlschema_doc)
parser = etree.XMLParser(attribute_defaults=True, encoding='utf-8')
# dtd_validation=True
with self.open(path='inp.xml', mode='r') as inpxmlfile:
tree_x = etree.parse(inpxmlfile, parser)
# relax.xml should be available to be used in xinclude
# hence copy relax.xml from the retrieved node into the temp file
fo = tempfile.NamedTemporaryFile(mode='w', delete=False)
try:
with self.open(path='relax.xml', mode='r') as relax_file:
relax_content = relax_file.read()
except FileNotFoundError:
relax_content = ''
fo.write(relax_content)
tempfile_name = fo.name
fo.close()
# replace relax.xml by the temp file path
tree_x_string = etree.tostring(tree_x)
tree_x_string = tree_x_string.replace(bytes('relax.xml', 'utf-8'), bytes(tempfile_name, 'utf-8'))
tree_x = etree.fromstring(tree_x_string).getroottree()
# replace XInclude parts to validate against schema
tree_x = clear_xml(tree_x)
os.remove(tempfile_name)
# check if it validates against the schema
if not xmlschema.validate(tree_x):
# get a more information on what does not validate
message = ''
parser_on_fly = etree.XMLParser(attribute_defaults=True, schema=xmlschema, encoding='utf-8')
inpxmlfile = etree.tostring(tree_x)
try:
tree_x = etree.fromstring(inpxmlfile, parser_on_fly)
except etree.XMLSyntaxError as msg:
message = msg
raise InputValidationError('Input file does not validate against the schema: {}'.format(message))
raise InputValidationError('Input file is not validated against the schema.' 'Reason is unknown')
# convert etree into python dictionary
root = tree_x.getroot()
inpxml_dict = inpxml_todict(root, inpxmlstructure)
# set inpxml_dict attribute
self.set_attribute('inp_dict', inpxml_dict)
# dict with inp paramters parsed from inp.xml
@property
def inp_dict(self):
"""
Returns the inp_dict (the representation of the ``inp.xml`` file) as it will
or is stored in the database.
"""
return self.get_attribute('inp_dict', {})
# TODO better validation? other files, if has a schema
def _validate(self):
"""
A validation method. Checks if an ``inp.xml`` file is in the FleurinpData.
"""
#from aiida.common.exceptions import ValidationError
super(FleurinpData, self)._validate()
if 'inp.xml' in self.files:
# has_inpxml = True # does nothing so far
pass
else:
raise ValidationError('inp.xml file not in attribute "files". '
'FleurinpData needs to have and inp.xml file!')
[docs] def get_fleur_modes(self):
'''
Analyses ``inp.xml`` file to set up a calculation mode. 'Modes' are paths a FLEUR
calculation can take, resulting in different output files.
This files can be automatically addded to the retrieve_list of the calculation.
Common modes are: scf, jspin2, dos, band, pot8, lda+U, eels, ...
:return: a dictionary containing all possible modes. A mode is activated assigning a
non-empty string to the corresponding key.
'''
# TODO these should be retrieved by looking at the inpfile structure and
# then setting the paths.
# use methods from fleur parser...
# For now they are hardcoded.
# 'dos': '/fleurInput/output',
# 'band': '/fleurInput/output',
# 'jspins': '/fleurInput/calculationSetup/magnetism',
fleur_modes = {'jspins': '', 'dos': '', 'band': '', 'ldau': '', 'forces': '', 'force_theorem': '', 'gw': ''}
if 'inp.xml' in self.files:
fleur_modes['jspins'] = self.inp_dict['calculationSetup']['magnetism']['jspins']
fleur_modes['dos'] = self.inp_dict['output']['dos'] # 'fleurInput']
fleur_modes['band'] = self.inp_dict['output']['band']
fleur_modes['forces'] = self.inp_dict['calculationSetup']['geometryOptimization']['l_f']
fleur_modes['force_theorem'] = 'forceTheorem' in self.inp_dict
try:
fleur_modes['gw'] = int(self.inp_dict['calculationSetup']['expertModes']['gw']) != 0
except KeyError:
fleur_modes['gw'] = False
ldau = False # TODO test if ldau in inp_dict....
fleur_modes['ldau'] = False
return fleur_modes
[docs] def get_structuredata_ncf(self):
"""
This routine returns an AiiDA Structure Data type produced from the ``inp.xml``
file. not a calcfunction
:param self: a FleurinpData instance to be parsed into a StructureData
:returns: StructureData node, or None
"""
from aiida.orm import StructureData
from aiida_fleur.tools.StructureData_util import rel_to_abs, rel_to_abs_f
# StructureData = DataFactory(‘structure’)
# Disclaimer: this routine needs some xpath expressions. these are hardcoded here,
# therefore maintainance might be needed, if you want to circumvent this, you have
# to get all the paths from somewhere.
#######
# all hardcoded xpaths used and attributes names:
bravaismatrix_bulk_xpath = '/fleurInput/cell/bulkLattice/bravaisMatrix/'
bravaismatrix_film_xpath = '/fleurInput/cell/filmLattice/bravaisMatrix/'
species_xpath = '/fleurInput/atomSpecies/species'
all_atom_groups_xpath = '/fleurInput/atomGroups/atomGroup'
species_attrib_name = 'name'
species_attrib_element = 'element'
row1_tag_name = 'row-1'
row2_tag_name = 'row-2'
row3_tag_name = 'row-3'
atom_group_attrib_species = 'species'
atom_group_tag_abspos = 'absPos'
atom_group_tag_relpos = 'relPos'
atom_group_tag_filmpos = 'filmPos'
########
if 'inp.xml' not in self.files:
print('cannot get a StructureData because fleurinpdata has no inp.xml file yet')
# TODO what to do in this case?
return None
# read in inpxml
if self._schema_file_path: # Schema there, parse with schema
xmlschema_doc = etree.parse(self._schema_file_path)
xmlschema = etree.XMLSchema(xmlschema_doc)
parser = etree.XMLParser(attribute_defaults=True, encoding='utf-8')
with self.open(path='inp.xml', mode='r') as inpxmlfile:
tree = etree.parse(inpxmlfile, parser)
tree.xinclude()
# remove comments from inp.xml
comments = tree.xpath('//comment()')
for c in comments:
p = c.getparent()
p.remove(c)
if not xmlschema.validate(tree):
raise ValueError('Input file is not validated against the schema.')
else: # schema not there, parse without
print('parsing inp.xml without XMLSchema')
with self.open(path='inp.xml', mode='r') as inpxmlfile:
tree = etree.parse(inpxmlfile)
tree.xinclude()
# remove comments from inp.xml
comments = tree.xpath('//comment()')
for c in comments:
p = c.getparent()
p.remove(c)
root = tree.getroot()
# Fleur uses atomic units, convert to Angstrom
# get cell matrix from inp.xml
row1 = root.xpath(bravaismatrix_bulk_xpath + row1_tag_name) # [0].text.split()
cell = None
if row1: # bulk calculation
row1 = row1[0].text.split()
row2 = root.xpath(bravaismatrix_bulk_xpath + row2_tag_name)[0].text.split()
row3 = root.xpath(bravaismatrix_bulk_xpath + row3_tag_name)[0].text.split()
# TODO? allow math?
for i, cor in enumerate(row1):
row1[i] = float(cor) * BOHR_A
for i, cor in enumerate(row2):
row2[i] = float(cor) * BOHR_A
for i, cor in enumerate(row3):
row3[i] = float(cor) * BOHR_A
cell = [row1, row2, row3]
# create new structure Node
struc = StructureData(cell=cell)
struc.pbc = [True, True, True]
elif root.xpath(bravaismatrix_film_xpath + row1_tag_name):
# film calculation
row1 = root.xpath(bravaismatrix_film_xpath + row1_tag_name)[0].text.split()
row2 = root.xpath(bravaismatrix_film_xpath + row2_tag_name)[0].text.split()
row3 = root.xpath(bravaismatrix_film_xpath + row3_tag_name)[0].text.split()
for i, cor in enumerate(row1):
row1[i] = float(cor) * BOHR_A
for i, cor in enumerate(row2):
row2[i] = float(cor) * BOHR_A
for i, cor in enumerate(row3):
row3[i] = float(cor) * BOHR_A
# row3 = [0, 0, 0]#? TODO:what has it to be in this case?
cell = [row1, row2, row3]
struc = StructureData(cell=cell)
struc.pbc = [True, True, False]
if cell is None:
print('Could not extract Bravias matrix out of inp.xml. Is the '
'Bravias matrix explicitly given? i.e Latnam definition '
'not supported.')
return None
# get species for atom kinds
#species = root.xpath(species_xpath)
species_name = root.xpath(species_xpath + '/@' + species_attrib_name)
species_element = root.xpath(species_xpath + '/@' + species_attrib_element)
# alternativ: loop over species and species.get(species_attrib_name)
# save species info in a dict
species_dict = {}
for i, spec in enumerate(species_name):
species_dict[spec] = {species_attrib_element: species_element[i]}
# Now we have to get all atomgroups, look what their species is and
# their positions are.
# Then we append them to the new structureData
all_atom_groups = root.xpath(all_atom_groups_xpath)
for atom_group in all_atom_groups:
current_species = atom_group.get(atom_group_attrib_species)
group_atom_positions_abs = atom_group.xpath(atom_group_tag_abspos)
group_atom_positions_rel = atom_group.xpath(atom_group_tag_relpos)
group_atom_positions_film = atom_group.xpath(atom_group_tag_filmpos)
if group_atom_positions_abs: # we have absolute positions
for atom in group_atom_positions_abs:
postion_a = atom.text.split()
# allow for math *, /
for i, pos in enumerate(postion_a):
if '/' in pos:
temppos = pos.split('/')
postion_a[i] = float(temppos[0]) / float(temppos[1])
elif '*' in pos:
temppos = pos.split('*')
postion_a[i] = float(temppos[0]) * float(temppos[1])
else:
postion_a[i] = float(pos)
postion_a[i] = postion_a[i] * BOHR_A
# append atom to StructureData
struc.append_atom(position=postion_a, symbols=species_dict[current_species][species_attrib_element])
elif group_atom_positions_rel: # we have relative positions
# TODO: check if film or 1D calc, because this is not allowed! I guess
for atom in group_atom_positions_rel:
postion_r = atom.text.split()
# allow for math * /
for i, pos in enumerate(postion_r):
if '/' in pos:
temppos = pos.split('/')
postion_r[i] = float(temppos[0]) / float(temppos[1])
elif '*' in pos:
temppos = pos.split('*')
postion_r[i] = float(temppos[0]) * float(temppos[1])
else:
postion_r[i] = float(pos)
# now transform to absolute Positions
new_abs_pos = rel_to_abs(postion_r, cell)
# append atom to StructureData
struc.append_atom(position=new_abs_pos,
symbols=species_dict[current_species][species_attrib_element])
elif group_atom_positions_film: # Do we support mixture always, or only in film case?
# either support or throw error
for atom in group_atom_positions_film:
# film pos are rel rel abs, therefore only transform first two coordinates
postion_f = atom.text.split()
# allow for math * /
for i, pos in enumerate(postion_f):
if '/' in pos:
temppos = pos.split('/')
postion_f[i] = float(temppos[0]) / float(temppos[1])
elif '*' in postion_f[i]:
temppos = pos.split('*')
postion_f[i] = float(temppos[0]) * float(temppos[1])
else:
postion_f[i] = float(pos)
# now transform to absolute Positions
postion_f[2] = postion_f[2] * BOHR_A
new_abs_pos = rel_to_abs_f(postion_f, cell)
# append atom to StructureData
struc.append_atom(position=new_abs_pos,
symbols=species_dict[current_species][species_attrib_element])
else:
# TODO throw error
print('I should never get here, 1D not supported yet, ' 'I only know relPos, absPos, filmPos')
# TODO throw error
# TODO DATA-DATA links are not wanted, you might want to use a cf instead
#struc.add_link_from(self, label='self.structure', link_type=LinkType.CREATE)
# label='self.structure'
# return {label : struc}
return struc
[docs] @cf
def get_structuredata(self):
"""
This routine return an AiiDA Structure Data type produced from the ``inp.xml``
file. If this was done before, it returns the existing structure data node.
This is a calcfunction and therefore keeps the provenance.
:param fleurinp: a FleurinpData instance to be parsed into a StructureData
:returns: StructureData node
"""
return self.get_structuredata_ncf()
[docs] def get_kpointsdata_ncf(self):
"""
This routine returns an AiiDA :class:`~aiida.orm.KpointsData` type produced from the
``inp.xml`` file. This only works if the kpoints are listed in the in inpxml.
This is NOT a calcfunction and does not keep the provenance!
:returns: :class:`~aiida.orm.KpointsData` node
"""
from aiida.orm import KpointsData
# HINT, TODO:? in this routine, the 'cell' you might get in an other way
# exp: StructureData.cell, but for this you have to make a structureData Node,
# which might take more time for structures with lots of atoms.
# then just parsing the cell from the inp.xml
# as in the routine get_structureData
# Disclaimer: this routine needs some xpath expressions.
# these are hardcoded here, therefore maintainance might be needed,
# if you want to circumvent this, you have
# to get all the paths from somewhere.
#######
# all hardcoded xpaths used and attributes names:
bravaismatrix_bulk_xpath = '/fleurInput/cell/bulkLattice/bravaisMatrix/'
bravaismatrix_film_xpath = '/fleurInput/cell/filmLattice/bravaisMatrix/'
kpointlist_xpath = '/fleurInput/calculationSetup/bzIntegration/kPointList/'
kpoint_tag = 'kPoint'
kpointlist_attrib_posscale = 'posScale'
kpointlist_attrib_weightscale = 'weightScale'
#kpointlist_attrib_count = 'count'
kpoint_attrib_weight = 'weight'
row1_tag_name = 'row-1'
row2_tag_name = 'row-2'
row3_tag_name = 'row-3'
########
if 'inp.xml' not in self.files:
print('cannot get a KpointsData because fleurinpdata has no inp.xml file yet')
# TODO what to do in this case?
return False
# else read in inpxml
if self._schema_file_path: # Schema there, parse with schema
xmlschema_doc = etree.parse(self._schema_file_path)
xmlschema = etree.XMLSchema(xmlschema_doc)
parser = etree.XMLParser(attribute_defaults=True, encoding='utf-8')
with self.open(path='inp.xml', mode='r') as inpxmlfile:
tree = etree.parse(inpxmlfile, parser)
tree.xinclude()
# remove comments from inp.xml
comments = tree.xpath('//comment()')
for c in comments:
p = c.getparent()
p.remove(c)
if not xmlschema.validate(tree):
raise ValueError('Input file is not validated against the schema.')
else: # schema not there, parse without
print('parsing inp.xml without XMLSchema')
with self.open(path='inp.xml', mode='r') as inpxmlfile:
tree = etree.parse(inpxmlfile)
tree.xinclude()
# remove comments from inp.xml
comments = tree.xpath('//comment()')
for c in comments:
p = c.getparent()
p.remove(c)
root = tree.getroot()
# get cell matrix from inp.xml
cell = None
row1 = root.xpath(bravaismatrix_bulk_xpath + row1_tag_name) # [0].text.split()
if row1: # bulk calculation
row1 = row1[0].text.split()
row2 = root.xpath(bravaismatrix_bulk_xpath + row2_tag_name)[0].text.split()
row3 = root.xpath(bravaismatrix_bulk_xpath + row3_tag_name)[0].text.split()
# TODO? allow math?
for i, cor in enumerate(row1):
row1[i] = float(cor) * BOHR_A
for i, cor in enumerate(row2):
row2[i] = float(cor) * BOHR_A
for i, cor in enumerate(row3):
row3[i] = float(cor) * BOHR_A
cell = [row1, row2, row3]
# set boundary conditions
pbc1 = [True, True, True]
elif root.xpath(bravaismatrix_film_xpath + row1_tag_name):
# film calculation
row1 = root.xpath(bravaismatrix_film_xpath + row1_tag_name)[0].text.split()
row2 = root.xpath(bravaismatrix_film_xpath + row2_tag_name)[0].text.split()
row3 = root.xpath(bravaismatrix_film_xpath + row3_tag_name)[0].text.split()
for i, cor in enumerate(row1):
row1[i] = float(cor) * BOHR_A
for i, cor in enumerate(row2):
row2[i] = float(cor) * BOHR_A
for i, cor in enumerate(row3):
row3[i] = float(cor) * BOHR_A
# row3 = [0, 0, 0]#? TODO:what has it to be in this case?
cell = [row1, row2, row3]
pbc1 = [True, True, False]
if cell is None:
print('Could not extract Bravias matrix out of inp.xml. Is the '
'Bravias matrix explicitly given? i.e Latnam definition '
'not supported.')
return None
# get kpoints only works if kpointlist in inp.xml
kpoints = root.xpath(kpointlist_xpath + kpoint_tag)
if kpoints:
posscale = root.xpath(kpointlist_xpath + '@' + kpointlist_attrib_posscale)
weightscale = root.xpath(kpointlist_xpath + '@' + kpointlist_attrib_weightscale)
#count = root.xpath(kpointlist_xpath + '@' + kpointlist_attrib_count)
kpoints_pos = []
kpoints_weight = []
for kpoint in kpoints:
kpoint_pos = kpoint.text.split()
for i, kval in enumerate(kpoint_pos):
kpoint_pos[i] = float(kval) / float(posscale[0])
kpoint_weight = float(kpoint.get(kpoint_attrib_weight)) / float(weightscale[0])
kpoints_pos.append(kpoint_pos)
kpoints_weight.append(kpoint_weight)
totalw = 0
for weight in kpoints_weight:
totalw = totalw + weight
kps = KpointsData()
kps.set_cell(cell)
kps.pbc = pbc1
kps.set_kpoints(kpoints_pos, cartesian=False, weights=kpoints_weight)
#kps.add_link_from(self, label='fleurinp.kpts', link_type=LinkType.CREATE)
kps.label = 'fleurinp.kpts'
# return {label: kps}
return kps
else: # TODO parser other kpoints formats, if they fit in an AiiDA node
print('No kpoint list in inp.xml')
return None
[docs] @cf
def get_kpointsdata(self):
"""
This routine returns an AiiDA :class:`~aiida.orm.KpointsData` type produced from the
``inp.xml`` file. This only works if the kpoints are listed in the in inpxml.
This is a calcfunction and keeps the provenance!
:returns: :class:`~aiida.orm.KpointsData` node
"""
return self.get_kpointsdata_ncf()
[docs] def get_parameterdata_ncf(self):
"""
This routine returns an AiiDA :class:`~aiida.orm.Dict` type produced from the ``inp.xml``
file. This node can be used for inpgen as `calc_parameters`.
This is NOT a calcfunction and does NOT keep the provenance!
:returns: :class:`~aiida.orm.Dict` node
"""
from aiida_fleur.tools.xml_util import get_inpgen_paranode_from_xml
if 'inp.xml' not in self.files:
print('cannot get a StructureData because fleurinpdata has no inp.xml file yet')
# TODO what to do in this case?
return False
# read in inpxml
with self.open(path='inp.xml', mode='r') as inpxmlfile:
new_parameters = get_inpgen_paranode_from_xml(etree.parse(inpxmlfile))
return new_parameters
# Is there a way to give self to calcfunctions?
[docs] @staticmethod
@cf
def get_parameterdata(fleurinp):
"""
This routine returns an AiiDA :class:`~aiida.orm.Dict` type produced from the ``inp.xml``
file. The returned node can be used for inpgen as `calc_parameters`.
This is a calcfunction and keeps the provenance!
:returns: :class:`~aiida.orm.Dict` node
"""
return fleurinp.get_parameterdata_ncf()
[docs] @cf
def set_kpointsdata(self, fleurinp_orgi, KpointsDataNode):
"""
This calc function writes the all the kpoints from a :class:`~aiida.orm.KpointsData` node
in the ``inp.xml`` file as a kpointslist. It replaces kpoints written in the
``inp.xml`` file. The output :class:`~aiida_fleur.data.fleurinp.FleurinpData` is stored in
the database.
Currently it is the users resposibility to provide a full
:class:`~aiida.orm.KpointsData` node with weights.
:param KpointsDataNode: :class:`~aiida.orm.KpointsData` node to be written into ``inp.xml``
:returns: modified :class:`~aiida_fleur.data.fleurinp.FleurinpData` node
"""
from aiida.orm import KpointsData
#from aiida.common.exceptions import InputValidationError
# all hardcoded xpaths used and attributes names:
fleurinp = fleurinp_orgi.copy()
kpointlist_xpath = '/fleurInput/calculationSetup/bzIntegration/kPointList'
#kpoint_tag = 'kPoint'
#kpointlist_attrib_posscale = 'posScale'
#kpointlist_attrib_weightscale = 'weightScale'
#kpointlist_attrib_count = 'count'
#kpoint_attrib_weight = 'weight'
#### method layout: #####
# Check if Kpoints node
# get kpoints, weights, inp.xml
# replace the kpoints tag.(delete old write new)
# kpoint list posScale, wightScale, count
# <kPointList posScale="36.00000000" weightScale="324.00000000" count="324">
# <kPoint weight=" 1.000000"> 17.000000 0.000000 0.000000</kPoint>
# add new inp.xml to fleurinpdata
if not isinstance(KpointsDataNode, KpointsData):
raise InputValidationError('The node given is not a valid KpointsData node.')
if 'inp.xml' in fleurinp.files:
# read in inpxml
if fleurinp._schema_file_path: # Schema there, parse with schema
xmlschema_doc = etree.parse(fleurinp._schema_file_path)
xmlschema = etree.XMLSchema(xmlschema_doc)
parser = etree.XMLParser(schema=xmlschema,
attribute_defaults=True,
remove_blank_text=True,
encoding='utf-8')
with fleurinp.open(path='inp.xml', mode='r') as inpxmlfile:
tree = etree.parse(inpxmlfile, parser)
else: # schema not there, parse without
print('parsing inp.xml without XMLSchema')
parser = etree.XMLParser(attribute_defaults=True, remove_blank_text=True, encoding='utf-8')
with self.open(path='inp.xml', mode='r') as inpxmlfile:
tree = etree.parse(inpxmlfile, parser)
#root = tree.getroot()
else:
raise InputValidationError('No inp.xml file yet specified, to add kpoints to.')
#cell_k = KpointsDataNode.cell
# TODO: shall we check if cell is the same as cell from structure?
# or is that to narrow?
kpoint_list = KpointsDataNode.get_kpoints(also_weights=True, cartesian=False)
nkpts = len(kpoint_list[0])
totalw = 0
for weight in kpoint_list[1]:
totalw = totalw + weight
#weightscale = totalw
new_kpo = etree.Element('kPointList', posScale='1.000', weightScale='1.0', count='{}'.format(nkpts))
for i, kpos in enumerate(kpoint_list[0]):
new_k = etree.Element('kPoint', weight='{}'.format(kpoint_list[1][i]))
new_k.text = '{} {} {}'.format(kpos[0], kpos[1], kpos[2])
new_kpo.append(new_k)
new_tree = replace_tag(tree, kpointlist_xpath, new_kpo)
# use _write_new_fleur_xmlinp_file(fleurinp, inp_file_xmltree, fleur_change_dic):
# TODO this should be sourced out to other methods.
# somehow directly writing inp.xml does not work, create new one
inpxmlfile = os.path.join(fleurinp._get_folder_pathsubfolder.abspath, 'temp_inp.xml')
# write new inp.xml, schema evaluation will be done when the file gets added
new_tree.write(inpxmlfile, pretty_print=True)
print(('wrote tree to' + str(inpxmlfile)))
# delete old inp.xml file, not needed anymore
# TODO maybe do some checks before
fleurinp.del_file('inp.xml')
# now the new inp.xml file is added and with that the inpxml_dict will
# be overwritten, and the file validated
fleurinp._add_path(str(inpxmlfile), 'inp.xml')
# remove temporary inp.xml file
os.remove(inpxmlfile)
return fleurinp
[docs] def get_tag(self, xpath):
"""
Tries to evaluate an xpath expression for ``inp.xml`` file. If it fails it logs it.
:param xpath: an xpath expression
:returns: A node list retrived using given xpath
"""
if 'inp.xml' in self.files:
# read in inpxml
if self._schema_file_path: # Schema there, parse with schema
#xmlschema_doc = etree.parse(self._schema_file_path)
#xmlschema = etree.XMLSchema(xmlschema_doc)
#parser = etree.XMLParser(schema=xmlschema, attribute_defaults=True)
with self.open(path='inp.xml', mode='r') as inpxmlfile:
tree = etree.parse(inpxmlfile) # , parser)
else: # schema not there, parse without
print('parsing inp.xml without XMLSchema')
with self.open(path='inp.xml', mode='r') as inpxmlfile:
tree = etree.parse(inpxmlfile)
root = tree.getroot()
else:
raise InputValidationError('No inp.xml file yet specified, to get a tag from')
try:
return_value = root.xpath(xpath)
except etree.XPathEvalError:
raise InputValidationError('There was a XpathEvalError on the xpath: {} \n Either it does '
'not exist, or something is wrong with the expression.'
''.format(xpath))
if len(return_value) == 1:
return return_value
else:
return return_value