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BandDOS: Add automatic adjustments of numbands to reach given energy ... #174

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8ac370e
BandDOS: Add automatic adjustments of numbands to reach given energy ...
janssenhenning May 20, 2022
af476b6
Fix wrong name
janssenhenning May 20, 2022
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222 changes: 152 additions & 70 deletions aiida_fleur/workflows/banddos.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,12 +19,13 @@
import numpy as np

from aiida.orm import Code, Dict, RemoteData, KpointsData
from aiida.orm import load_node, CalcJobNode, FolderData, BandsData, XyData
from aiida.engine import WorkChain, ToContext, if_
from aiida.orm import FolderData, BandsData, XyData
from aiida.engine import WorkChain, ToContext, if_, while_
from aiida.engine import calcfunction as cf
from aiida.common.exceptions import NotExistent
from aiida.common import AttributeDict
from aiida.tools.data.array.kpoints import get_explicit_kpoints_path
from aiida.engine import ExitCode

from aiida_fleur.workflows.scf import FleurScfWorkChain
from aiida_fleur.workflows.base_fleur import FleurBaseWorkChain
Expand All @@ -33,6 +34,8 @@
from aiida_fleur.tools.common_fleur_wf import test_and_get_codenode
from aiida_fleur.data.fleurinp import FleurinpData, get_fleurinp_from_remote_data

from masci_tools.util.schema_dict_util import evaluate_attribute


class FleurBandDosWorkChain(WorkChain):
'''
Expand All @@ -44,8 +47,10 @@ class FleurBandDosWorkChain(WorkChain):
# wf_parameters: { 'tria', 'nkpts', 'sigma', 'emin', 'emax'}
# defaults : tria = True, nkpts = 800, sigma=0.005, emin= , emax =

_workflowversion = '0.5.2'
_workflowversion = '0.6.0'

#These are the files that are expected for a BandDOS calculation
_BANDFILES = ['banddos.hdf', 'bands.1', 'bands.2', 'Local.1', 'Local.2']
_default_options = {
'resources': {
'num_machines': 1,
Expand All @@ -65,6 +70,10 @@ class FleurBandDosWorkChain(WorkChain):
'kpoints_distance': None,
'kpoints_explicit': None, #dictionary containing a list of kpoints, weights
#and additional arguments to pass to set_kpointlist
'bands_energy_above_fermi': None, #Up to which energy the bands should be calculated
#If the workflow can adjust numBands it will do so
#until the minimum of the highest band is above this
#parameter (in Htr)
'sigma': 0.005,
'emin': -0.50,
'emax': 0.90,
Expand Down Expand Up @@ -95,10 +104,9 @@ def define(cls, spec):
spec.outline(cls.start,
if_(cls.scf_needed)(
cls.converge_scf,
cls.banddos_after_scf,
).else_(
cls.banddos_wo_scf,
), cls.return_results)
cls.inspect_scf,
),
while_(cls.not_enough_bands)(cls.run_banddos, cls.inspect_banddos), cls.return_results)

spec.output('output_banddos_wc_para', valid_type=Dict)
spec.output('last_calc_retrieved', valid_type=FolderData)
Expand All @@ -114,6 +122,10 @@ def define(cls, spec):
spec.exit_code(236, 'ERROR_INVALID_INPUT_FILE', message="Input file was corrupted after user's modifications.")
spec.exit_code(334, 'ERROR_SCF_CALCULATION_FAILED', message='SCF calculation failed.')
spec.exit_code(335, 'ERROR_SCF_CALCULATION_NOREMOTE', message='Found no SCF calculation remote repository.')
spec.exit_code(344, 'ERROR_BANDDOS_CALCULATION_FAILED', message='BandDOS calculation failed.')
spec.exit_code(345,
'ERROR_BANDDOS_NOT_ENOUGH_BANDS',
message='BandDOS calculation failed. Requested bands energy maximum cannot be reached')

def start(self):
'''
Expand All @@ -135,6 +147,11 @@ def start(self):
self.ctx.warnings = []
self.ctx.errors = []

self.ctx.banddos_code_hdf5 = False
self.ctx.numbands_input = None
self.ctx.numbands_bands = None
self.ctx.highest_band_minimum = 0

inputs = self.inputs

wf_default = copy.deepcopy(self._default_wf_para)
Expand Down Expand Up @@ -332,6 +349,11 @@ def change_fleurinp(self):
change_dict = {'band': True, 'minEnergy': emin, 'maxEnergy': emax, 'sigma': sigma}
fleurmode.set_inpchanges(change_dict)

if self.ctx.numbands_bands is not None and self.ctx.numbands_input != 'all':
#Here we already ran the Band calculation and did not have enough
#bands. For now we just double the bands to calculate
fleurmode.set_inpchanges({'numbands': 2 * self.ctx.numbands_bands})

try:
fleurmode.show(display=False, validate=True)
except etree.DocumentInvalid:
Expand All @@ -353,6 +375,14 @@ def scf_needed(self):
"""
return self.ctx.scf_needed

def get_inputs_scf(self):
"""
Initialize inputs for scf workflow:
wf_param, options, calculation parameters, codes, structure
"""
input_scf = AttributeDict(self.exposed_inputs(FleurScfWorkChain, namespace='scf'))
return input_scf

def converge_scf(self):
"""
Converge charge density.
Expand All @@ -361,12 +391,11 @@ def converge_scf(self):
res = self.submit(FleurScfWorkChain, **inputs)
return ToContext(scf=res)

def banddos_after_scf(self):
def inspect_scf(self):
"""
This method submits the BandDOS calculation after the initial SCF calculation
Make sure the SCF calculation succeeded
"""
calc = self.ctx.scf

if not calc.is_finished_ok:
message = ('The SCF calculation was not successful.')
self.control_end_wc(message)
Expand All @@ -386,6 +415,11 @@ def banddos_after_scf(self):
self.control_end_wc(message)
return self.exit_codes.ERROR_SCF_CALCULATION_FAILED

def run_banddos(self):
"""
This method submits the BandDOS FleurCalculation
"""

self.report('INFO: run BandDOS calculation')

status = self.change_fleurinp()
Expand All @@ -401,27 +435,26 @@ def banddos_after_scf(self):
# Do not copy mixing_history* files from the parent
settings = {'remove_from_remotecopy_list': ['mixing_history*']}

# Retrieve remote folder of the reference calculation
pk_last = 0
scf_ref_node = load_node(calc.pk)
for i in scf_ref_node.called:
if i.node_type == 'process.workflow.workchain.WorkChainNode.':
if i.process_class is FleurBaseWorkChain:
if pk_last < i.pk:
pk_last = i.pk
try:
remote = load_node(pk_last).outputs.remote_folder
except AttributeError:
message = ('Found no remote folder of the reference scf calculation.')
self.control_end_wc(message)
return self.exit_codes.ERROR_SCF_CALCULATION_NOREMOTE
if self.ctx.scf_needed:
try:
remote = self.ctx.scf.outputs.last_calc.remote_folder
except (NotExistent, AttributeError):
message = ('Found no remote folder of the reference scf calculation.')
self.control_end_wc(message)
return self.exit_codes.ERROR_SCF_CALCULATION_NOREMOTE
else:
remote = self.inputs.remote

label = 'bansddos_calculation'
label = 'banddos_calculation'
description = 'Bandstructure or DOS is calculated for the given structure'

code = self.inputs.fleur
options = self.ctx.options.copy()

self.ctx.banddos_code_hdf5 = code.description is not None and 'hdf5' in code.description.lower()
xmltree, schema_dict = fleurin.load_inpxml()
self.ctx.numbands_input = evaluate_attribute(xmltree, schema_dict, 'numbands')

inputs_builder = get_inputs_fleur(code,
remote,
fleurin,
Expand All @@ -433,52 +466,67 @@ def banddos_after_scf(self):
future = self.submit(FleurBaseWorkChain, **inputs_builder)
return ToContext(banddos_calc=future)

def banddos_wo_scf(self):
def not_enough_bands(self):
"""
This method submits the BandDOS calculation without a previous SCF calculation
Return whether the band calculation produced enough
bands for the requested energy window
"""
self.report('INFO: run BandDOS calculation')
# Is this the first run?
if not self.ctx.banddos_calc:
return True

status = self.change_fleurinp()
if status:
return status

fleurin = self.ctx.fleurinp_banddos
if fleurin is None:
error = ('ERROR: Creating BandDOS Fleurinp failed for an unknown reason')
self.control_end_wc(error)
return self.exit_codes.ERROR_CHANGING_FLEURINPUT_FAILED

# Do not copy mixing_history* files from the parent
settings = {'remove_from_remotecopy_list': ['mixing_history*']}

# Retrieve remote folder from the inputs
remote = self.inputs.remote
wf_dict = self.ctx.wf_dict
#For non-hdf5 codes we do not adjust the bands
if not self.ctx.banddos_code_hdf5:
if wf_dict['bands_above_fermi_energy'] is not None:
self.report('The number of bands is only adjusted if the Fleur code '
'for the BandDOS calculation is compiled with HDF5')
return False

return wf_dict['mode'] == 'band' \
and wf_dict['bands_energy_above_fermi'] is not None \
and self.ctx.numbands_input != 'all' \
and self.ctx.highest_band_minimum < wf_dict['bands_above_fermi_energy']

def inspect_banddos(self):
"""
Inspect the results of the BandDOS calculation
"""
calc = self.ctx.banddos_calc
if not calc.is_finished_ok:
message = ('The BandDOS calculation was not successful.')
self.control_end_wc(message)
return self.exit_codes.ERROR_BANDDOS_CALCULATION_FAILED

label = 'bansddos_calculation'
description = 'Bandstructure or DOS is calculated for the given structure'
try:
outpara_node = calc.outputs.output_parameters
except NotExistent:
message = ('The BandDOS calculation failed, no output node.')
self.control_end_wc(message)
return self.exit_codes.ERROR_BANDDOS_CALCULATION_FAILED

code = self.inputs.fleur
options = self.ctx.options.copy()
retrieved = calc.outputs.retrieved

inputs_builder = get_inputs_fleur(code,
remote,
fleurin,
options,
label,
description,
settings,
add_comp_para=self.ctx.wf_dict['add_comp_para'])
future = self.submit(FleurBaseWorkChain, **inputs_builder)
return ToContext(banddos_calc=future)

def get_inputs_scf(self):
"""
Initialize inputs for scf workflow:
wf_param, options, calculation parameters, codes, structure
"""
input_scf = AttributeDict(self.exposed_inputs(FleurScfWorkChain, namespace='scf'))
return input_scf
if not any(file in retrieved.list_object_names() for file in self._BANDFILES):
message = ('The BandDOS calculation failed, no band/DOS files were produced.')
self.control_end_wc(message)
return self.exit_codes.ERROR_BANDDOS_CALCULATION_FAILED

if self.ctx.banddos_code_hdf5 and self.ctx.wf_dict['bands_energy_above_fermi'] is not None:
res = get_highest_band_minimum(retrieved)
if isinstance(res, ExitCode):
message = ('Failed to retrieve band information from banddos.hdf')
self.control_end_wc(message)
return self.exit_codes.ERROR_BANDDOS_CALCULATION_FAILED
nbands, self.ctx.highest_band_minimum = res
if nbands == self.ctx.numbands_bands:
#We doubled the number of bands but got no more bands
#this means the energy given is unreasonable and we cannot
#Get more bands
message = ('Requested energy window cannot be calculated. Cannot retrieve more bands')
self.control_end_wc(message)
return self.exit_codes.ERROR_BANDDOS_NOT_ENOUGH_BANDS
self.ctx.numbands_bands = nbands

def return_results(self):
'''
Expand Down Expand Up @@ -514,13 +562,11 @@ def return_results(self):

#check if band file exists: if not succesful = False
#TODO be careful with general bands.X
bandfiles = ['bands.1', 'bands.2', 'banddos.hdf', 'Local.1', 'Local.2']

bandfile_res = []
if retrieved:
bandfile_res = retrieved.list_object_names()

for name in bandfiles:
for name in self._BANDFILES:
if name in bandfile_res:
self.ctx.successful = True
if not self.ctx.successful:
Expand Down Expand Up @@ -641,7 +687,7 @@ def create_aiida_bands_data(fleurinp, retrieved):
"""
from masci_tools.io.parsers.hdf5 import HDF5Reader, HDF5TransformationError
from masci_tools.io.parsers.hdf5.recipes import FleurSimpleBands #no projections only eigenvalues for now
from aiida.engine import ExitCode
from aiida.engine import ExitCode #pylint: disable=reimported,redefined-outer-name

try:
kpoints = fleurinp.get_kpointsdata_ncf(only_used=True)
Expand Down Expand Up @@ -690,7 +736,7 @@ def create_aiida_dos_data(retrieved):
"""
from masci_tools.io.parsers.hdf5 import HDF5Reader, HDF5TransformationError
from masci_tools.io.parsers.hdf5.recipes import FleurDOS #only standard DOS for now
from aiida.engine import ExitCode
from aiida.engine import ExitCode #pylint: disable=reimported,redefined-outer-name

if 'banddos.hdf' in retrieved.list_object_names():
try:
Expand All @@ -715,3 +761,39 @@ def create_aiida_dos_data(retrieved):
'Contains XyData for the density of states calculation with total, interstitial, atom and orbital weights')

return dos


def get_highest_band_minimum(retrieved):
"""
Gets the number of bands calculated and the highest band minimum
of the calculated bands

:param retrieved: :py:class:`aiida.orm.FolderData` for the bandstructure calculation

:returns: number of bands and the band minimum of the highest band

:raises: ExitCode 300, banddos.hdf file is missing
:raises: ExitCode 310, banddos.hdf reading failed
"""
from masci_tools.io.parsers.hdf5 import HDF5Reader, HDF5TransformationError
from masci_tools.io.parsers.hdf5.recipes import FleurSimpleBands #no projections only eigenvalues for now
from aiida.engine import ExitCode #pylint: disable=reimported,redefined-outer-name

if 'banddos.hdf' in retrieved.list_object_names():
try:
with retrieved.open('banddos.hdf', 'rb') as f:
with HDF5Reader(f) as reader:
data, attributes = reader.read(recipe=FleurSimpleBands)
except (HDF5TransformationError, ValueError) as exc:
return ExitCode(310, message=f'banddos.hdf reading failed with: {exc}')
else:
return ExitCode(300, message='banddos.hdf file not in the retrieved files')

nkpts, nbands = attributes['nkpts'], attributes['nbands']
eigenvalues = data['eigenvalues_up'].reshape((nkpts, nbands))
highest_band_minimum = np.nanmin(eigenvalues[:, -1])
if 'eigenvalues_down' in data:
eigenvalues = data['eigenvalues_down'].reshape((nkpts, nbands))
highest_band_minimum = min(np.nanmin(eigenvalues[:, -1]), highest_band_minimum)

return nbands, highest_band_minimum