Source code for aiida.orm.calculation.job.quantumespresso.helpers
# -*- coding: utf-8 -*-
import xml.dom.minidom
import os
import difflib
import copy
from aiida.common.exceptions import InputValidationError, InternalError
# Can also try to use LooseVersion instead, if more complicated things are
# required, e.g. with strings. But be careful, check if the behavior in
# this case is the intended one.
from distutils.version import StrictVersion
__copyright__ = u"Copyright (c), This file is part of the AiiDA platform. For further information please visit http://www.aiida.net/. All rights reserved."
__license__ = "MIT license, see LICENSE.txt file."
__authors__ = "The AiiDA team."
__version__ = "0.7.0"
[docs]class QEInputValidationError(InputValidationError):
"""
This class is the exception that is generated by the parser when it
encounters an error while creating the input file of Quantum ESPRESSO.
"""
pass
def _check_and_convert(kw,val,expected_type):
"""
val: the value to be read and converted to a Fortran-friendly string.
expected_type: a string with the expected type. Can be:
INTEGER
REAL
CHARACTER
LOGICAL
"""
# Note that bool should come before integer, because a boolean matches also
# isinstance(...,int)
if expected_type.upper() == "LOGICAL":
if isinstance(val,bool):
outval = val
else:
raise TypeError(
'Expected a boolean for keyword {}, found {} instead'.format(
kw, type(val)))
elif expected_type.upper() == "REAL":
if isinstance(val,(int, long)):
outval = float(val)
elif isinstance(val, float):
outval = val
else:
raise TypeError(
'Expected a float for keyword {}, found {} instead'.format(
kw, type(val)))
elif expected_type.upper() == "INTEGER":
if isinstance(val,(int, long)):
outval = val
else:
raise TypeError(
'Expected an integer for keyword {}, found {} instead'.format(
kw, type(val)))
elif expected_type.upper() == "CHARACTER":
if isinstance(val,basestring):
outval = val
else:
raise TypeError(
'Expected a string for keyword {}, found {} instead'.format(
kw, type(val)))
else:
raise InternalError('Unexpected type check for keyword {}: {})'.format(
kw, expected_type.upper()))
return outval
[docs]def pw_input_helper(input_params, structure,
stop_at_first_error=False, flat_mode=False, version="5.4.0"):
"""
Validate if the input dictionary for Quantum ESPRESSO is valid.
Return the dictionary (possibly with small variations: e.g. convert
integer to float where necessary, recreate the proper structure
if flat_mode is True, ...) to use as input parameters (use_parameters)
for the pw.x calculation.
:param input_params: If flat_mode is True, pass a dictionary
with 'key' = value; use the correct type
(int, bool, ...) for value. If an array is required:
* if its length is fixed: pass a list of the required length
* if its length is 'ntyp': pass a dictionary, associating each
specie to its value.
* (other lengths are not supported)
Example::
{
'calculation': 'vc-relax',
'ecutwfc': 30.,
'hubbard_u': {'O': 1},
}
If instead flat_mode is False, pass a dictionary in the format
expected by AiiDA (keys are namelists, values are in the format
specified above, i.e. key/value pairs for all keywords in the
given namelist).
Example::
{
'CONTROL': {
'calculation': 'vc-relax'
},
'SYSTEM': {
'hubbard_u': {'O': 1.0},
'ecutwfc': 30.,
},
},
:param structure: the StructureData object used as input for QE pw.x
:param stop_at_first_error: if True, stops at the first error.
Otherwise, when, possible, continue and give a global error for all
the issues encountered.
:param flat_mode: if True, instead of passing the dictionary of namelists,
and inside the keywords, pass directly the keywords - this function
will return the correct dictionary to pass to the PwCalculation,
with the keywords arranged in the correct namelist.
:param version: string with version number, used to find the correct XML
file descriptor. If not specified, uses the most recent version
available in the validator. It reads the definitions from the XML files
in the same folder as this python module. If the version is not
recognised, the Exception message will also suggest a close-by version.
:raise QeInputValidationError: (subclass of InputValidationError) if
the input is not considered valid.
"""
errors_list = []
# =========== LIST OF KNOWN NAMELISTS, CARDS, VARIABLES, ... ===============
compulsory_namelists = ['CONTROL', 'SYSTEM', 'ELECTRONS']
valid_calculations_and_opt_namelists = {
'scf':[],
'nscf':[],
'bands':[],
'relax':['IONS'],
'md':['IONS'],
'vc-relax':['IONS', 'CELL'],
'vc-md': ['IONS', 'CELL'],
}
if not isinstance(input_params, dict):
raise QEInputValidationError('input_params must be a dictionary')
# So that if I modify input_params, nothing happens outside
if flat_mode:
input_params_internal = copy.deepcopy(input_params)
else:
input_params_internal = {}
input_original_namelists = {}
all_input_namelists = set()
for nl, content in input_params.iteritems():
if not isinstance(content, dict):
raise QEInputValidationError(
"The content associated to the namelist '{}' must be a "
"dictionary".format(nl))
all_input_namelists.add(nl)
for k, v in content.iteritems():
input_params_internal[k] = copy.deepcopy(v)
if k in input_original_namelists:
err_str = "The keyword '{}' was specified both in the "
"namelist {} and {}.".format(k,
input_original_namelists[k], nl)
if stop_at_first_error:
raise QEInputValidationError(err_str)
else:
errors_list.append(err_str)
input_original_namelists[k] = nl
# List of the keywords that must not appear in the input
# (e.g. because they are automatically filled in by the plugin)
blocked_kws = [i.lower() for i in
["pseudo_dir",
"outdir",
"ibrav",
"celldm",
"nat",
"ntyp",
"prefix",
"a", "b", "c", "cosab", "cosac", "cosbc",
]
]
# TODO: possibly add here above also restart_mode?
# List of the keywords that must ALWAYS appear in the input
compulsory_kws = set([i.lower() for i in
["calculation",
"ecutwfc",
]
])
# ===================== PARSING OF THE XML DEFINITION FILE ===============
module_dir = os.path.dirname(__file__)
if module_dir == '':
module_dir = os.curdir
xml_path = os.path.join(module_dir,'INPUT_PW-{}.xml'.format(version))
try:
with open(xml_path,'r') as f:
dom = xml.dom.minidom.parse(f)
except IOError:
prefix = 'INPUT_PW-'
suffix = '.xml'
versions = [fname[len(prefix):-len(suffix)] for fname
in os.listdir(module_dir) if fname.startswith(prefix)
and fname.endswith(suffix)]
versions = sorted(versions, key=lambda x: StrictVersion(x))
strictversions = versions + [version]
strictversions = sorted(strictversions, key=lambda x: StrictVersion(x))
pos = strictversions.index(version)
if pos == 0:
add_str = " (the version you specified is too old)"
else:
add_str = " (the older, closest version you can use is {})".format(
strictversions[pos-1])
raise QEInputValidationError(
"Unknown Quantum Espresso version: {}. "
"Available versions: {};{}".format(version, ", ".join(versions),
add_str))
# ========== List of known PW variables (from XML file) ===============
known_kws = dom.getElementsByTagName('var')
valid_kws = {}
for kw in known_kws:
if kw in valid_kws:
raise InternalError("Something strange, I found more than one "
"keyword '{}' in the XML description...".format(
kw))
valid_kws[kw.getAttribute('name').lower()] = {}
parent = kw
try:
while True:
parent = parent.parentNode
if parent.tagName == 'namelist':
valid_kws[kw.getAttribute('name').lower()]["namelist"] = \
parent.getAttribute('name').upper()
break
except AttributeError:
# There are also variables in cards instead of namelists:
# I ignore them
pass
# raise QEInputValidationError("Unable to find namelist for "
# "keyword %s." % kw.getAttribute('name'))
expected_type = kw.getAttribute('type')
# Fix for groups of variables
if expected_type == '':
if kw.parentNode.tagName == 'vargroup':
expected_type = kw.parentNode.getAttribute('type')
valid_kws[kw.getAttribute('name').lower()]['expected_type'] = \
expected_type.upper()
# ====== List of known PW 'dimensions' (arrays) (from XML file) ===========
known_dims = dom.getElementsByTagName('dimension')
valid_dims = {}
for dim in known_dims:
if dim in valid_dims:
raise InternalError("Something strange, I found more than one "
"keyword '{}' in the XML description...".format(dim))
valid_dims[dim.getAttribute('name').lower()] = {}
parent = dim
try:
while True:
parent = parent.parentNode
if parent.tagName == 'namelist':
valid_dims[dim.getAttribute('name').lower()]["namelist"] = \
parent.getAttribute('name').upper()
break
except AttributeError:
# There are also variables in cards instead of namelists:
# I ignore them
pass
# raise QEInputValidationError("Unable to find namelist "
# "for keyword %s." % dim.getAttribute('name'))
expected_type = dim.getAttribute('type')
# Fix for groups of variables
if expected_type == '':
if dim.parentNode.tagName == 'vargroup':
expected_type = dim.parentNode.getAttribute('type')
valid_dims[dim.getAttribute('name').lower()]['expected_type'] = \
expected_type.upper()
# I assume start_val is always 1
start_val = dim.getAttribute('start')
if start_val != '1':
raise InternalError(
"Wrong start value '{}' in input array (dimension) {}".format(
(start_val, dim.getAttribute('name'))))
# I save the string as it is; somewhere else I will check for its value
valid_dims[dim.getAttribute('name').lower()]['end_val'] = \
dim.getAttribute('end')
# Used to suggest valid keywords if an unknown one is found
valid_invars_list = list(
set([i.lower() for i in valid_dims.keys()] +
[i.lower() for i in valid_kws.keys()]) - set(blocked_kws))
# =================== Check for blocked keywords ===========================
for kw in input_params_internal.keys():
if kw in blocked_kws:
err_str = "You should not provide explicitly keyword '{}'.".format(
kw)
if stop_at_first_error:
raise QEInputValidationError(err_str)
else:
errors_list.append(err_str)
# from 5.0.2, this CANNOT be specified anymore!
if StrictVersion(version) < StrictVersion('5.0.2'):
# To be sure that things are read in angstrom - not possible in recent
# versions
input_params_internal['a'] = 1.
# Get info on atomic species from the StructureData object
atomic_species_list = [k.name for k in structure.kinds]
try:
calculation_type = input_params_internal['calculation']
except KeyError:
raise QEInputValidationError("Error, you need to specify at least the "
"calculation type (among {})".format(
", ".join(valid_calculations_and_opt_namelists.keys())))
try:
opt_namelists = valid_calculations_and_opt_namelists[calculation_type]
except KeyError:
raise QEInputValidationError("Error, {} is not a valid value for "
"the calculation type (valid values: {})".format(calculation_type,
", ".join(valid_calculations_and_opt_namelists.keys())))
internal_dict = {i: {} for i in compulsory_namelists + opt_namelists}
all_namelists = set(compulsory_namelists)
for namelists in valid_calculations_and_opt_namelists.values():
all_namelists.update(namelists)
if not flat_mode:
# Unexpected namelists specified by the user
additional_namelists = sorted(all_input_namelists - set(all_namelists))
if additional_namelists:
err_str = "Error, the following namelists were specified but are " \
"not expected: {}".format(
", ".join(additional_namelists))
if stop_at_first_error:
raise QEInputValidationError(err_str)
else:
errors_list.append(err_str)
# Empty list that contains the list of provided kws to check for
# the compulsory ones at the end
inserted_kws = []
# I parse each element of the input dictionary
for kw, value in input_params_internal.iteritems():
#print kw, valid_kws[kw.lower()]
kw = kw.lower()
if kw in valid_kws:
# It is a variable
found_var = valid_kws[kw]
namelist_name = found_var['namelist']
if not flat_mode:
input_namelist_name = input_original_namelists[kw]
if namelist_name != input_namelist_name:
err_str = \
"Error, keyword '{}' specified in namelist '{}', " \
"but it should be instead in '{}'".format(
kw, input_namelist_name, namelist_name)
if stop_at_first_error:
raise QEInputValidationError(err_str)
else:
errors_list.append(err_str)
try:
internal_dict[namelist_name][kw] = _check_and_convert(
kw,value, found_var['expected_type'])
except KeyError:
if namelist_name in all_namelists:
err_str = \
"Error, namelist {} not valid for calculation type " \
"{}".format(namelist_name, calculation_type)
if stop_at_first_error:
raise QEInputValidationError(err_str)
else:
errors_list.append(err_str)
else:
err_str = "Error, unknown namelist " \
"{}".format(namelist_name)
if stop_at_first_error:
raise QEInputValidationError(err_str)
else:
errors_list.append(err_str)
except TypeError as e:
if stop_at_first_error:
raise
else:
errors_list.append(e.message)
elif kw in valid_dims:
# It is an array
found_var = valid_dims[kw]
namelist_name = found_var['namelist']
if not flat_mode:
input_namelist_name = input_original_namelists[kw]
if namelist_name != input_namelist_name:
err_str = \
"Error, keyword '{}' specified in namelist '{}', " \
"but it should be instead in '{}'".format(
kw, input_namelist_name, namelist_name)
if stop_at_first_error:
raise QEInputValidationError(err_str)
else:
errors_list.append(err_str)
## I accept only ntyp or an integer as end_val
if found_var['end_val'] == 'ntyp':
if not isinstance(value,dict):
err_str = \
"Error, expecting a dictionary to associate each " \
"specie to a value for keyword '{}'.".format(kw)
if stop_at_first_error:
raise QEInputValidationError(err_str)
else:
errors_list.append(err_str)
continue
outdict = {}
for kindname, found_item in value.iteritems():
if kindname not in atomic_species_list:
err_str = \
"Error, '{}' is not a valid kind name.".format(kindname)
if stop_at_first_error:
raise QEInputValidationError(err_str)
else:
errors_list.append(err_str)
continue
try:
outdict[kindname] = _check_and_convert(kw,found_item,
found_var['expected_type'])
except TypeError:
if stop_at_first_error:
raise
else:
errors_list.append(e.message)
try:
internal_dict[namelist_name][kw] = outdict
except KeyError:
err_str = \
"Error, unknown namelist {}".format(namelist_name)
if stop_at_first_error:
raise QEInputValidationError(err_str)
else:
errors_list.append(err_str)
continue
else:
try:
end_value = int(found_var['end_val'])
except ValueError:
err_str = \
"Error, invalid end value '{}' for keyword '{}'.".format(
(found_var['end_val'], kw))
if stop_at_first_error:
raise QEInputValidationError(err_str)
else:
errors_list.append(err_str)
continue
if not isinstance(value,list) or len(value) != end_value:
err_str = \
"Error, expecting a list of length {} for keyword " \
"'{}'.".format(end_value, kw)
if stop_at_first_error:
raise QEInputValidationError(err_str)
else:
errors_list.append(err_str)
continue
outlist = []
for found_item in value:
if found_item is None:
# skip if the value is None (i.e., not provided)
outlist.append(None)
else:
try:
outlist.append(_check_and_convert(kw,found_item,
found_var['expected_type']))
except TypeError as e:
if stop_at_first_error:
raise
else:
errors_list.append(e.message)
outlist.append(None)
try:
internal_dict[namelist_name][kw] = outlist
except KeyError:
err_str = \
"Error, unknown namelist {}".format(namelist_name)
if stop_at_first_error:
raise QEInputValidationError(err_str)
else:
errors_list.append(err_str)
continue
else:
# Neither a variable nor an array
err_str = "Problem parsing keyword {}. ".format(kw)
similar_kws = difflib.get_close_matches(kw, valid_invars_list)
if len(similar_kws)==1:
err_str += "Maybe you wanted to specify {}?".format(
similar_kws[0])
elif len(similar_kws) > 1:
err_str += "Maybe you wanted to specify one of these: " \
"{}?".format(", ".join(similar_kws))
else:
err_str += "(No similar keywords found...)"
if stop_at_first_error:
raise QEInputValidationError(err_str)
else:
errors_list.append(err_str)
# Used to check if all compulsory variables are set
inserted_kws += [kw]
# ============== I check here compulsory variables ===========
missing_kws = compulsory_kws - set(inserted_kws)
if len(missing_kws) != 0:
err_str = "Missing compulsory variables: {}.".format(
", ".join(missing_kws))
if stop_at_first_error:
raise QEInputValidationError(err_str)
else:
errors_list.append(err_str)
if errors_list:
raise QEInputValidationError(
"Errors! {} issues found:\n* ".format(len(errors_list)) +
"\n* ".join(errors_list))
return internal_dict
if __name__ == "__main__":
# An example of usage
from aiida.orm import load_node
structure = DataFactory('structure')(cell=[[1,0,0],[0,1,0],[0,0,1]])
structure.append_atom(symbols='Si', position=[0,0,0])
structure.append_atom(symbols='O', position=[0.5,0.5,0.5])
try:
print validate_pw_input({
'calculation': 'vc-relax',
'ecutwfc': 30.,
'lda_plus_u': True,
'lda_plus_u_kind': 2,
'ion_temperature': 'a',
# 'hubbard_u': [1, None],
'hubbard_u': {'O': 1},
},
structure, flat_mode = True,
version = '5.1')
except QEInputValidationError as e:
print "*"*72
print "* ERROR !"
print "*"*72
print e.message
try:
print validate_pw_input(
{
'CONTROL': {
'calculation': 'vc-relax'
},
'IONS': {
'ion_temperature': 'a'
},
'CELL': {
},
'ELECTRONS': {
},
'SYSTEM': {
'lda_plus_u_kind': 2,
'ecutwfc': 30.0,
'hubbard_u': {'O': 1.0},
'lda_plus_u': True}
},
structure, flat_mode = False)
except QEInputValidationError as e:
print "*"*72
print "* ERROR !"
print "*"*72
print e.message