def test_xml_set_first_attribv(inpxml_etree):
from aiida_fleur.tools.xml_util import xml_set_first_attribv, eval_xpath
etree = inpxml_etree(TEST_INP_XML_PATH)
xml_set_first_attribv(etree, '/fleurInput/calculationSetup/cutoffs', 'Gmax', 11.00)
assert float(eval_xpath(etree, '/fleurInput/calculationSetup/cutoffs/@Gmax')) == 11
xml_set_first_attribv(etree, '/fleurInput/atomGroups/atomGroup', 'species', 'TEST-1')
assert eval_xpath(etree, '/fleurInput/atomGroups/atomGroup/@species') == ['TEST-1', 'Pt-1']
def test_fleurinp_modifier2(create_fleurinp, inpxml_etree):
"""Tests if fleurinp_modifier with various other modifations methods,
the detailed tests for method functionality is tested elsewhere."""
from aiida_fleur.tools.xml_util import eval_xpath
fleurinp_tmp = create_fleurinp(inpxmlfilefolder)
etree = inpxml_etree(inpxmlfilefolder)
fm = FleurinpModifier(fleurinp_tmp)
actions = fm.get_avail_actions()
assert isinstance(actions, dict)
new_tag = eval_xpath(etree, '/fleurInput/calculationSetup/scfLoop')
fm.delete_tag('/fleurInput/calculationSetup/scfLoop')
fm.replace_tag('/fleurInput/calculationSetup/cutoffs', new_tag)
fm.delete_att('/fleurInput/calculationSetup/soc', 'theta')
fm.create_tag('/fleurInput/calculationSetup/soc', 'theta')
fm.xml_set_all_text('/fleurInput/cell/symmetryOperations/symOp/row-1', 'test text')
fm.xml_set_text_occ('/fleurInput/cell/symmetryOperations/symOp/row-1', 'test text')
fm.xml_set_text('/fleurInput/cell/symmetryOperations/symOp/row-1', 'test text')
fm.xml_set_all_attribv('/fleurInput/calculationSetup/soc', 'theta', 12)
fm.xml_set_first_attribv('/fleurInput/calculationSetup/soc', 'theta', 12)
fm.xml_set_attribv_occ('/fleurInput/calculationSetup/soc', 'theta', 12)
fm.set_species_label(' 222', {'mtSphere': {'radius': 3.333}})
fm.set_atomgr_att_label(attributedict={'force': [('relaxXYZ', 'FFF')]}, atom_label=' 222')
fm.set_atomgr_att(attributedict={'force': [('relaxXYZ', 'TFF')]}, species='Fe-1')
fm.set_nkpts(500, gamma='T')
fm.set_kpath({'gamma': (0, 0, 0), 'L': (0.1, 0.1, 0.1)}, 300)
fm.add_num_to_att('/fleurInput/calculationSetup/soc', 'theta', 4)
#fm.set_species1
fm.show()
def extract_corelevels(outxmlfile, options=None):
"""
Extracts corelevels out of out.xml files
:params outxmlfile: path to out.xml file
:param options: A dict: 'iteration' : X/'all'
:returns corelevels: A list of the form:
.. code-block:: python
[atomtypes][spin][dict={atomtype : '', corestates : list_of_corestates}]
[atomtypeNumber][spin]['corestates'][corestate number][attribute]
get corelevel energy of first atomtype, spin1, corelevels[0][0]['corestates'][i]['energy']
:example of output:
.. code-block:: python
[[{'atomtype': ' 1',
'corestates': [{'energy': -3.6489930627,
'j': ' 0.5',
'l': ' 0',
'n': ' 1',
'weight': 2.0}],
'eigenvalue_sum': ' -7.2979861254',
'kin_energy': ' 13.4757066163',
'spin': '1'}],
[{'atomtype': ' 2',
'corestates': [{'energy': -3.6489930627,
'j': ' 0.5',
'l': ' 0',
'n': ' 1',
'weight': 2.0}],
'eigenvalue_sum': ' -7.2979861254',
'kin_energy': ' 13.4757066163',
'spin': '1'}]]
"""
##########################################
#1. read out.xml in etree
#2. get all species
#3. get number of atom types and their species
#4 get corelevel dimension from atoms types.
#5 init saving arrays:
#list length number of atom types, which contains dictionaries:
# in the form { 'species' : species, 'coresetup' : '', 'atom' : W , 'corelevels' : []} lists of corelevels from last iteration (Do i want all iterations, optional?) Or do I even want a dictionaries of corelevels? (but coresetup is in atom type info
#6 parse corelevels:
# get last iteration
# fill corelevel list
#######################################
########################
#XPATHS to maintain
species_xpath = '/fleurOutput/inputData/atomSpecies'
iteration_xpath = '/fleurOutput/scfLoop/iteration'
atomgroup_xpath = '/fleurOutput/inputData/atomGroups'
coreconfig_xpath = 'electronConfig/coreConfig/text()'
valenceconfig_xpath = 'electronConfig/valenceConfig/text()'
state_occ_xpath = 'electronConfig/stateOccupation'
relcoreStates_xpath = 'coreStates'
relpos_xpath = 'relPos'
abspos_xpath = 'absPos'
filmpos_xpath = 'filmPos'
#TODO all the attribute names...
######################
#1. read out.xml in etree
# TODO this should be common, moved somewhere else and importet
parsed_data = {}
outfile_broken = False
parse_xml = True
parser = etree.XMLParser(recover=False) #, remove_blank_text=True)
parser_info = {'parser_warnings': [], 'unparsed': []}
try:
tree = etree.parse(outxmlfile, parser)
except etree.XMLSyntaxError:
outfile_broken = True
#print 'broken xml'
parser_info['parser_warnings'].append(
'The out.xml file is broken I try to repair it.')
if outfile_broken:
#repair xmlfile and try to parse what is possible.
parser = etree.XMLParser(recover=True) #, remove_blank_text=True)
try:
tree = etree.parse(outxmlfile, parser)
except etree.XMLSyntaxError:
parser_info['parser_warnings'].append(
'Skipping the parsing of the xml file. Repairing was not possible.'
)
parse_xml = False
#if parse_xml:
root = tree.getroot()
# 2. get all species from input
# get element, name, coreStates
# TODO why can this not be eval_xpath2?
species_nodes = eval_xpath(root, species_xpath, parser_info)
species_atts = {}
species_names = []
for species in species_nodes:
species_name = species.get('name')
species_corestates = species.get('coreStates')
species_element = species.get('element')
species_atomicnumber = species.get('atomicNumber')
species_magMom = species.get('magMom')
#TODO sometimes not in inp.xml... what if it is not there
coreconfig = eval_xpath(species, coreconfig_xpath, parser_info)
valenceconfig = eval_xpath(species, valenceconfig_xpath, parser_info)
state_occ = eval_xpath2(species, state_occ_xpath, parser_info)
#parse state occ
state_results = []
for tag in state_occ: #always a list?
state = tag.get('state')
spinUp = tag.get('spinUp')
spinDown = tag.get('spinDown')
state_results.append({state: [spinUp, spinDown]})
species_atts[species_name] = {
'name': species_name,
'corestates': species_corestates,
'element': species_element,
'atomgroups': [],
'mag_mom': species_magMom,
'atomic_number': species_atomicnumber,
'coreconfig': coreconfig,
'valenceconfig': valenceconfig,
'stateOccupation': state_results
}
species_names.append(species_name)
#3. get number of atom types and their species from input
atomtypes = []
atomgroup_nodes = eval_xpath(root, atomgroup_xpath,
parser_info) #/fleurinp/
# always a list?
for atomgroup in atomgroup_nodes:
types_dict = {}
group_species = atomgroup.get('species')
if group_species in species_names:
species_atts[group_species]['atomgroups'].append(atomgroup)
element = species_atts[group_species]['element']
atomicnumber = int(species_atts[group_species]['atomic_number'])
coreconf = species_atts[group_species]['coreconfig']
valenceconf = species_atts[group_species]['valenceconfig']
stateocc = species_atts[group_species]['stateOccupation']
a = eval_xpath2(
atomgroup, relpos_xpath, parser_info) + eval_xpath2(
atomgroup, abspos_xpath, parser_info) + eval_xpath2(
atomgroup, filmpos_xpath, parser_info) # always list
natoms = len(a)
types_dict = {
'species': group_species,
'element': element,
'atomic_number': atomicnumber,
'coreconfig': coreconf,
'valenceconfig': valenceconf,
'stateOccupation': stateocc,
'natoms': natoms
}
atomtypes.append(types_dict)
#natomgroup = len(atomgroup_nodes)
#print(natomgroup)
corelevels = []
#4 get corelevel dimension from atoms types.
#5 init saving arrays:
#6 parse corelevels:
iteration_nodes = eval_xpath2(root, iteration_xpath, parser_info)
nIteration = len(iteration_nodes)
if nIteration >= 1:
iteration_to_parse = iteration_nodes[-1] #TODO:Optional all or other
#print iteration_to_parse
corestatescards = eval_xpath2(iteration_to_parse, relcoreStates_xpath,
parser_info)
# maybe does not return a list...
for atype in atomtypes: # spin=2 is already in there
corelevels.append([])
for corestatescard in corestatescards:
corelv = parse_state_card(corestatescard, iteration_to_parse,
parser_info)
corelevels[int(corelv['atomtype']) - 1].append(
corelv) # is corelv['atomtype'] always an integer?
#print parser_info
#pprint(corelevels[0][1]['corestates'][2]['energy'])
#corelevels[atomtypeNumber][spin]['corestates'][corestate number][attribute]
return corelevels, atomtypes
def set_nmmpmat(fleurinp_tree_copy, nmmp_lines_copy, species_name, orbital, spin,\
occStates=None, denmat=None, phi=None, theta=None):
"""Routine sets the block in the n_mmp_mat file specified by species_name, orbital and spin
to the desired density matrix
:param fleurinp_tree_copy: an xmltree that represents inp.xml
:param nmmp_lines_copy: list of lines in the n_mmp_mat file
:param species_name: string, name of the species you want to change
:param orbital: integer, orbital quantum number of the LDA+U procedure to be modified
:param spin: integer, specifies which spin block should be modified
:param occStates: list, sets the diagonal elements of the density matrix and everything
else to zero
:param denmat: matrix, specify the density matrix explicitely
:param phi: float, optional angle (radian), by which to rotate the density matrix before writing it
:param theta: float, optional angle (radian), by which to rotate the density matrix before writing it
:raises ValueError: If something in the input is wrong
:raises KeyError: If no LDA+U procedure is found on a species
"""
#All lda+U procedures have to be considered since we need to keep the order
ldau_xpath = '/fleurInput/atomSpecies/species/ldaU'
magnetism_xpath = '/fleurInput/calculationSetup/magnetism'
if species_name == 'all':
species_xpath = '/fleurInput/atomSpecies/species'
elif species_name[:4] == 'all-': #format all-<string>
species_xpath = '/fleurInput/atomSpecies/species[contains(@name,"{}")]'.format(species_name[4:])
else:
species_xpath = '/fleurInput/atomSpecies/species[@name = "{}"]'.format(species_name)
all_species = eval_xpath2(fleurinp_tree_copy, species_xpath)
#Get number of spins (TODO for develop version also read l_mtnocoPot)
mag_elem = eval_xpath(fleurinp_tree_copy, magnetism_xpath)
nspins = convert_to_int(get_xml_attribute(mag_elem, 'jspins'), suc_return=False)
if spin > nspins:
raise ValueError(f'Invalid input: spin {spin} requested, but input has only {nspins} spins')
all_ldau = eval_xpath2(fleurinp_tree_copy, ldau_xpath)
numRows = nspins * 14 * len(all_ldau)
#Check that numRows matches the number of lines in nmmp_lines_copy
#If not either there was an n_mmp_mat file present in Fleurinp before and a lda+u calculation
#was added or removed or the n_mmp_mat file was initialized and after the fact lda+u procedures were added
#or removed. In both cases the resolution of this modification is very involved so we throw an error
if nmmp_lines_copy is not None:
#Remove blank lines
while '' in nmmp_lines_copy:
nmmp_lines_copy.remove('')
if numRows != len(nmmp_lines_copy):
raise ValueError('The number of lines in n_mmp_mat does not match the number expected from '+\
'the inp.xml file. Either remove the existing file before making modifications '+\
'and only use set_nmmpmat after all modifications to the inp.xml')
if phi is not None or theta is not None:
if phi is None:
phi = 0.0
if theta is None:
theta = 0.0
d_wigner = get_wigner_matrix(orbital, phi, theta)
for species in all_species:
current_name = get_xml_attribute(species, 'name')
#Determine the place at which the given U procedure occurs
ldau_index = None
for index, ldau in enumerate(all_ldau):
ldau_species = get_xml_attribute(ldau.getparent(), 'name')
ldau_orbital = convert_to_int(get_xml_attribute(ldau, 'l'), suc_return=False)
if current_name == ldau_species and ldau_orbital == orbital:
ldau_index = index
if ldau_index is None:
raise KeyError(f'No LDA+U procedure found on species {current_name} with l={orbital}')
if occStates is not None:
#diagonal density matrix
denmatpad = np.zeros((7, 7), dtype=complex)
#Fill out the outer states with zero
occStatespad = np.zeros(7, dtype=complex)
occStatespad[3 - orbital:4 + orbital] = occStates[:]
for i, occ in enumerate(occStatespad):
denmatpad[i, i] = occ
elif denmat is not None:
#density matrix is completely specified
denmatpad = np.zeros((7, 7), dtype=complex)
denmatpad[3 - orbital:4 + orbital, 3 - orbital:4 + orbital] = denmat
else:
raise ValueError('Invalid definition of density matrix. Provide either occStates or denmat')
if phi is not None and theta is not None:
#Rotate the density matrix
denmatpad = d_wigner.T.conj().dot(denmatpad.dot(d_wigner))
#check if fleurinp has a specified n_mmp_mat file if not initialize it with 0
if nmmp_lines_copy is None:
nmmp_lines_copy = []
for index in range(numRows):
nmmp_lines_copy.append(''.join(map(str, [f'{0.0:20.13f}' for x in range(7)])))
#Select the right block from n_mmp_mat and overwrite it with denmatpad
startRow = ((spin - 1) * len(all_ldau) + ldau_index) * 14
for index in range(startRow, startRow + 14):
currentLine = index - startRow
currentRow = currentLine // 2
if currentLine % 2 == 0:
#Line ends with a real part
nmmp_lines_copy[index] = ''.join(map(str, [f'{x.real:20.13f}{x.imag:20.13f}'\
for x in denmatpad[currentRow, :3]])) +\
f'{denmatpad[currentRow, 3].real:20.13f}'
else:
#Line begins with a imaginary part
nmmp_lines_copy[index] = f'{denmatpad[currentRow, 3].imag:20.13f}' +\
''.join(map(str, [f'{x.real:20.13f}{x.imag:20.13f}'\
for x in denmatpad[currentRow, 4:]]))
return nmmp_lines_copy
def validate_nmmpmat(fleurinp_tree, nmmp_lines):
"""
Checks that the given nmmp_lines is valid with the given fleurinp_tree
Checks that the number of blocks is as expected from the inp.xml and each
block does not contain non-zero elements outside their size given by the
orbital quantum number in the inp.xml. Additionally the occupations, i.e.
diagonal elements are checked that they are in between 0 and the maximum
possible occupation
:param fleurinp_tree_copy: an xmltree that represents inp.xml
:param nmmp_lines_copy: list of lines in the n_mmp_mat file
:raises ValueError: if any of the above checks are violated.
"""
#First check the number of ldau procedures
ldau_xpath = '/fleurInput/atomSpecies/species/ldaU'
magnetism_xpath = '/fleurInput/calculationSetup/magnetism'
#Get number of spins (TODO for develop version also read l_mtnocoPot)
mag_elem = eval_xpath(fleurinp_tree, magnetism_xpath)
nspins = convert_to_int(get_xml_attribute(mag_elem, 'jspins'), suc_return=False)
all_ldau = eval_xpath2(fleurinp_tree, ldau_xpath)
numRows = nspins * 14 * len(all_ldau)
tol = 0.01
if nspins > 1:
maxOcc = 1.0
else:
maxOcc = 2.0
#Check that numRows matches the number of lines in nmmp_lines
if nmmp_lines is not None:
#Remove blank lines
while '' in nmmp_lines:
nmmp_lines.remove('')
if numRows != len(nmmp_lines):
raise ValueError('The number of lines in n_mmp_mat does not match the number expected from '+\
'the inp.xml file.')
else:
return
#Now check for each block if the numbers make sense
#(no numbers outside the valid area and no nonsensical occupations)
for ldau_index, ldau in enumerate(all_ldau):
orbital = convert_to_int(get_xml_attribute(ldau, 'l'), suc_return=False)
species_name = get_xml_attribute(ldau.getparent(), 'name')
for spin in range(nspins):
startRow = (spin * len(all_ldau) + ldau_index) * 14
for index in range(startRow, startRow + 14):
currentLine = index - startRow
currentRow = currentLine // 2
line = nmmp_lines[index].split(' ')
while '' in line:
line.remove('')
nmmp = np.array([float(x) for x in line])
outside_val = False
if abs(currentRow - 3) > orbital:
if any(np.abs(nmmp) > 1e-12):
outside_val = True
if currentLine % 2 == 0:
#m=-3 to m=0 real part
if any(np.abs(nmmp[:(3 - orbital) * 2]) > 1e-12):
outside_val = True
else:
#m=0 imag part to m=3
if any(np.abs(nmmp[orbital * 2 + 1:]) > 1e-12):
outside_val = True
if outside_val:
raise ValueError(f'Found value outside of valid range in for species {species_name}, spin {spin+1}'
f' and l={orbital}')
invalid_diag = False
if spin < 2:
if currentRow - 3 <= 0 and currentLine % 2 == 0:
if nmmp[currentRow * 2] < -tol or nmmp[currentRow * 2] > maxOcc + tol:
invalid_diag = True
else:
if nmmp[(currentRow - 3) * 2 - 1] < -tol or nmmp[(currentRow - 3) * 2 - 1] > maxOcc + tol:
invalid_diag = True
if invalid_diag:
raise ValueError(f'Found invalid diagonal element for species {species_name}, spin {spin+1}'
f' and l={orbital}')