def launch_workflow(code, structure, pseudo_family, kpoints_distance, ecutwfc,
ecutrho, hubbard_u, hubbard_v, hubbard_file_pk,
starting_magnetization, smearing,
automatic_parallelization, clean_workdir, max_num_machines,
max_wallclock_seconds, with_mpi, daemon):
"""Run a `PwBaseWorkChain`."""
from aiida.orm import Bool, Float, Str, Dict
from aiida.plugins import WorkflowFactory
from aiida_quantumespresso.utils.resources import get_default_options, get_automatic_parallelization_options
builder = WorkflowFactory('quantumespresso.pw.base').get_builder()
parameters = {
'SYSTEM': {
'ecutwfc': ecutwfc,
'ecutrho': ecutrho,
},
}
try:
hubbard_file = validate.validate_hubbard_parameters(
structure, parameters, hubbard_u, hubbard_v, hubbard_file_pk)
except ValueError as exception:
raise click.BadParameter(str(exception))
try:
validate.validate_starting_magnetization(structure, parameters,
starting_magnetization)
except ValueError as exception:
raise click.BadParameter(str(exception))
try:
validate.validate_smearing(parameters, smearing)
except ValueError as exception:
raise click.BadParameter(str(exception))
builder.pw.code = code
builder.pw.structure = structure
builder.pw.parameters = Dict(dict=parameters)
builder.pseudo_family = Str(pseudo_family)
builder.kpoints_distance = Float(kpoints_distance)
if hubbard_file:
builder.hubbard_file = hubbard_file
if automatic_parallelization:
automatic_parallelization = get_automatic_parallelization_options(
max_num_machines, max_wallclock_seconds)
builder.automatic_parallelization = Dict(
dict=automatic_parallelization)
else:
builder.pw.metadata.options = get_default_options(
max_num_machines, max_wallclock_seconds, with_mpi)
if clean_workdir:
builder.clean_workdir = Bool(True)
launch.launch_process(builder, daemon)
def launch_workflow(code, structure, pseudo_family, kpoints_distance, ecutwfc,
ecutrho, hubbard_u, hubbard_v, hubbard_file_pk,
starting_magnetization, smearing,
automatic_parallelization, clean_workdir, max_num_machines,
max_wallclock_seconds, with_mpi, daemon, final_scf):
"""Run a `PwRelaxWorkChain`."""
from aiida.orm import Bool, Float, Dict, Str
from aiida.plugins import WorkflowFactory
from qe_tools import CONSTANTS
from aiida_quantumespresso.utils.resources import get_default_options, get_automatic_parallelization_options
builder = WorkflowFactory('quantumespresso.pw.relax').get_builder()
cutoff_wfc, cutoff_rho = pseudo_family.get_recommended_cutoffs(
structure=structure)
parameters = {
'CONTROL': {
'calculation': 'relax',
},
'SYSTEM': {
'ecutwfc': ecutwfc or cutoff_wfc / CONSTANTS.ry_to_ev,
'ecutrho': ecutrho or cutoff_rho / CONSTANTS.ry_to_ev,
},
}
try:
hubbard_file = validate.validate_hubbard_parameters(
structure, parameters, hubbard_u, hubbard_v, hubbard_file_pk)
except ValueError as exception:
raise click.BadParameter(str(exception))
try:
validate.validate_starting_magnetization(structure, parameters,
starting_magnetization)
except ValueError as exception:
raise click.BadParameter(str(exception))
try:
validate.validate_smearing(parameters, smearing)
except ValueError as exception:
raise click.BadParameter(str(exception))
builder.structure = structure
builder.base.kpoints_distance = Float(kpoints_distance)
builder.base.pw.code = code
builder.base.pw.pseudos = pseudo_family.get_pseudos(structure=structure)
builder.base.pw.parameters = Dict(dict=parameters)
if hubbard_file:
builder.base.pw.hubbard_file = hubbard_file
if automatic_parallelization:
automatic_parallelization = get_automatic_parallelization_options(
max_num_machines, max_wallclock_seconds)
builder.base.automatic_parallelization = Dict(
dict=automatic_parallelization)
else:
builder.base.pw.metadata.options = get_default_options(
max_num_machines, max_wallclock_seconds, with_mpi)
if clean_workdir:
builder.clean_workdir = Bool(True)
if final_scf:
builder.base_final_scf.pseudo_family = Str(pseudo_family)
builder.base_final_scf.kpoints_distance = Float(kpoints_distance)
builder.base_final_scf.pw.code = code
builder.base_final_scf.pw.parameters = Dict(dict=parameters)
builder.base_final_scf.pw.metadata.options = get_default_options(
max_num_machines, max_wallclock_seconds, with_mpi)
launch.launch_process(builder, daemon)
def launch(code, structure, pseudo_family, kpoints, max_num_machines,
max_wallclock_seconds, daemon, ecutwfc, ecutrho, hubbard_u,
hubbard_v, hubbard_file_pk, starting_magnetization, smearing,
automatic_parallelization, clean_workdir):
"""
Run the PwBaseWorkChain for a given input structure
"""
from aiida.orm.data.base import Bool, Str
from aiida.orm.data.parameter import ParameterData
from aiida.orm.utils import WorkflowFactory
from aiida.work.launch import run, submit
from aiida_quantumespresso.utils.resources import get_default_options, get_automatic_parallelization_options
PwBaseWorkChain = WorkflowFactory('quantumespresso.pw.base')
parameters = {
'SYSTEM': {
'ecutwfc': ecutwfc,
'ecutrho': ecutrho,
},
}
try:
hubbard_file = validate.validate_hubbard_parameters(
structure, parameters, hubbard_u, hubbard_v, hubbard_file_pk)
except ValueError as exception:
raise click.BadParameter(exception.message)
try:
validate.validate_starting_magnetization(structure, parameters,
starting_magnetization)
except ValueError as exception:
raise click.BadParameter(exception.message)
try:
validate.validate_smearing(parameters, smearing)
except ValueError as exception:
raise click.BadParameter(exception.message)
inputs = {
'code': code,
'structure': structure,
'pseudo_family': Str(pseudo_family),
'kpoints': kpoints,
'parameters': ParameterData(dict=parameters),
}
if automatic_parallelization:
automatic_parallelization = get_automatic_parallelization_options(
max_num_machines, max_wallclock_seconds)
inputs['automatic_parallelization'] = ParameterData(
dict=automatic_parallelization)
else:
options = get_default_options(max_num_machines, max_wallclock_seconds)
inputs['options'] = ParameterData(dict=options)
if clean_workdir:
inputs['clean_workdir'] = Bool(True)
if daemon:
workchain = submit(PwBaseWorkChain, **inputs)
click.echo('Submitted {}<{}> to the daemon'.format(
PwBaseWorkChain.__name__, workchain.pk))
else:
run(PwBaseWorkChain, **inputs)
def run_calculation(
name,
struct,
group,
codename,
pseudo_family,
k_distance=0.20,
scale_element_init_moment={},
input_namelists={},
code_runtime_options=None
):
"""
This function converts a given initial structure into an AiiDA readable format
to perform a static SCF calculation.
Parameters
----------
name : str
The name of the structure or calculations eg. name='Fe'
struct : Structure object
The defect structure
group : str
The name of the group to store AiiDA nodes on AiiDA database. Its advisable to keep track
of this name to make sure you organize your data
codename : str
The name of the code configured on AiiDA database to perform this type of calculations
pseudo_family : str
A pseudopotential family configured on AiiDA database
k_distance : float
The density of k-point mesh use for k-point integration in DFT. For more see this
material cloud page for its usage: https://www.materialscloud.org/work/tools/qeinputgenerator
Default=0.2.
scale_element_init_moment : dict
A user define dictionary type of magnetic ions to scale its magnetic moment.
Default={}.
input_namelists : dict
A user define Quantum ESPRESSO (QE) input namelists. Default={}
mu_plus : bool
If True, to specify a total charge of the system and initialise a
starting charge of muon. Defualt=False
code_runtime_options : None
The HPC requirements of number of nodes and k-points. Depends on the code
configure in `codename`.
Returns
-------
Submit calculation to AiiDA daemon
"""
from aiida_quantumespresso.utils.resources import get_default_options, get_automatic_parallelization_options
from aiida.orm import Group
g, just_created = Group.objects.get_or_create(group)
code = Code.get_from_string(codename)
builder = code.get_builder()
builder.metadata.label = "{} - Unitcell".format(name)
builder.metadata.description = "Magnetic test for - {}".format(name)
StructureData = DataFactory("structure")
labeled_structure, nspin, magnetic_elements_kinds = analyze_pymatgen_structure(struct, mark_muon=False)
builder.structure = StructureData(pymatgen=labeled_structure)
structure_copy = StructureData(pymatgen=labeled_structure)
if nspin == 2:
# Set all polarizations to 0.4
for k in magnetic_elements_kinds.keys():
for idx in magnetic_elements_kinds[k].keys():
magnetic_elements_kinds[k][idx] = magnetic_elements_kinds[k][idx] * scale_element_init_moment.get(k, 1.)
elif nspin == 4:
raise NotImplemented("Non collinear case not implemented.")
Dict = DataFactory('dict')
parameters_dict = {
'CONTROL': {
'calculation': 'scf',
'restart_mode': 'from_scratch',
},
'SYSTEM': {
'ecutwfc': 60.,
'ecutrho': 600.,
'occupations':'smearing',
'smearing': 'm-v',
'degauss' : 0.02,
'nspin': nspin, #
},
'ELECTRONS': {
'conv_thr' : 1.e-7,
'mixing_beta' : 0.30,
'mixing_mode' : 'local-TF'
}
}
#print('Old Dictionary\n', parameters_dict)
#override
parameters_dict=merge(input_namelists, parameters_dict)
#print('New Dictionary\n', parameters_dict)
parameters = Dict(dict=parameters_dict)
builder.parameters = parameters
if nspin == 2:
parameters_dict['SYSTEM']['starting_magnetization'] = merge_dict_of_dicts(magnetic_elements_kinds)
KpointsData = DataFactory('array.kpoints')
#kpoints = KpointsData()
#kpoints.set_kpoints_mesh([2,2,2],offset=(0,0,0))
kpoints = KpointsData()
kpoints.set_cell_from_structure(builder.structure)
kpoints.set_kpoints_mesh_from_density(k_distance, force_parity=False)
kpoints.store()
settings_dict={}
num_k_points = np.prod(kpoints.get_kpoints_mesh()[0])
if num_k_points==1:
settings_dict={'gamma_only': True}
else:
settings_dict={'gamma_only': False}
builder.pseudos = get_pseudos_from_structure(structure_copy, pseudo_family)
#builder.metadata.options.resources = resources
#builder.metadata.options.max_wallclock_seconds = 259200 #86400
builder.parameters = parameters
builder.kpoints = kpoints
# AAAA: automatic_parallelization does not work!!!
automatic_parallelization = False
if automatic_parallelization:
automatic_parallelization = get_automatic_parallelization_options(1, 24*60*60-60*5)
builder.automatic_parallelization = Dict(dict=automatic_parallelization)
else:
if code_runtime_options is None or code_runtime_options == '':
# num machines, time, mpi
default_options = get_default_options(1, 24*60*60-60*5, True)
builder.metadata.options = default_options
else:
exec_options = code_runtime_options.split('|')[0].split()
default_options = get_default_options(int(exec_options[0]), int(exec_options[1]), True)
builder.metadata.options = default_options
if code_runtime_options is None or code_runtime_options == '':
npool = np.min([4, num_k_points])
settings_dict['cmdline'] = ['-nk', str(npool), '-ndiag', '1']
else:
parallel_options = code_runtime_options.split('|')[1]
settings_dict['cmdline'] = parallel_options.strip().split()
clean_workdir = False
final_scf = False
if clean_workdir:
builder.clean_workdir = Bool(True)
if final_scf:
builder.final_scf = Bool(True)
calc = submit(builder)
if not (g is None):
g.add_nodes(calc)
print(name +' magnetic test calculation created with PK = {}'.format(calc.pk))
return calc
def run_wc(
index,
name,
struct,
group,
codename,
pseudo_family,
k_distance=0.20,
scale_element_init_moment={},
input_namelists={},
mu_plus=False,
code_runtime_options=None
):
"""
This function converts a given initial structure into an AiiDA readable format
to runs an AiiDA RELAX Workchain.
Parameters
----------
index : int
An index of the structure supply eg. index=0
name : str
The name of the structure or calculations eg. name='Fe'
struct : Structure object
The defect structure
group : str
The name of the group to store AiiDA nodes on AiiDA database. Its advisable to keep track
of this name to make sure you organize your data
codename : str
The name of the code configured on AiiDA database to perform this type of calculations
pseudo_family : str
A pseudopotential family configured on AiiDA database
k_distance : float
The density of k-point mesh use for k-point integration in DFT. For more see this
material cloud page for its usage: https://www.materialscloud.org/work/tools/qeinputgenerator
Default=0.2.
scale_element_init_moment : dict
A user define dictionary type of magnetic ions to scale its magnetic moment.
Default={}.
input_namelists : dict
A user define Quantum ESPRESSO (QE) input namelists. Default={}
mu_plus : bool
If True, to specify a total charge of the system and initialise a
starting charge of muon. Defualt=False
code_runtime_options : None
The HPC requirements of number of nodes and k-points. Depends on the code
configure in `codename`.
Returns
-------
Submit calculation to AiiDA daemon
"""
from aiida_quantumespresso.utils.resources import get_default_options, get_automatic_parallelization_options
builder = WorkflowFactory('quantumespresso.pw.relax').get_builder()
builder.relaxation_scheme = Str('relax')
builder.metadata.label = "{}-{}".format(name, index)
builder.metadata.description = "Muon site relaxation workchain for {}, with initial position {} {} {}".format(name, *struct[-1].coords.tolist())
#builder.meta_convergence=Bool(False)
StructureData = DataFactory("structure")
#builder.structure = StructureData(pymatgen=struct)
#builder.structure, nspin, magnetic_elements_kinds = pymatgen_to_aiida(struct, StructureData)
labeled_structure, nspin, magnetic_elements_kinds = analyze_pymatgen_structure(struct)
builder.structure = StructureData(pymatgen=labeled_structure)
# Append all type of species, magnetic or not
species = [str(site.specie.symbol) for site in labeled_structure]
distinct_species = list(set(species))
for mag_kinds in magnetic_elements_kinds.values():
distinct_species.append(list(mag_kinds.keys()))
if nspin == 2:
# Set all polarizations to 0.4
for k in magnetic_elements_kinds.keys():
for idx in magnetic_elements_kinds[k].keys():
magnetic_elements_kinds[k][idx] = magnetic_elements_kinds[k][idx] * scale_element_init_moment.get(k, 1.)
elif nspin == 4:
raise NotImplemented("Non collinear case not implemented.")
# Default QE inputs
Dict = DataFactory('dict')
parameters_dict = {
'CONTROL': {
'calculation': 'relax',
'restart_mode': 'from_scratch',
'nstep': 150
# 'forc_conv_thr': 1,
# 'etot_conv_thr': 1000
},
'SYSTEM': {
'ecutwfc': 60.,
'ecutrho': 600.,
'occupations':'smearing',
'smearing': 'gaussian',
'degauss' : 0.02,
'nspin': nspin,
},
'ELECTRONS': {
'electron_maxstep': 500,
'conv_thr' : 1.0e-7,
'mixing_beta' : 0.30,
'mixing_mode' : 'local-TF'
}
}
if nspin == 2:
parameters_dict['SYSTEM']['starting_magnetization'] = merge_dict_of_dicts(magnetic_elements_kinds)
if mu_plus:
parameters_dict['SYSTEM']['starting_charge'] = {'No': 0.6}
parameters_dict['SYSTEM']['tot_charge'] = 1.
input_namelistss = copy.deepcopy(input_namelists)
if input_namelistss:
# Remove some stuff from input namelist
# lets comment the stuffs below
# In my opinion are a mess
# dictionary changes size for each iterations
input_namelistss.pop('CONTROL',0)
input_namelistss.pop('K_POINTS',0)
input_namelistss.pop('CELL_PARAMETERS',0)
input_namelistss.pop('ATOMIC_FORCES',0)
if 'SYSTEM' in input_namelistss.keys():
for kw in ('nat ntyp A B C cosAB cosAC cosBC nbnd tot_charge').split():
r = input_namelistss['SYSTEM'].pop(kw,'')
if r:
print('Your setting for {} has been removed'.format(r))
for kw in input_namelistss['SYSTEM'].keys():
r = ''
if 'celldm' in kw:
r = input_namelistss['SYSTEM'].pop(kw)
if 'starting_' in kw:
r = input_namelistss['SYSTEM'].pop(kw)
if r:
print('Your setting for {} has been removed'.format(r))
# add hubbard parameters
lda_plus_u_kind = 0
if 'Hubbard_U' in input_namelistss['SYSTEM'].keys():
# Get hubbard values from user defined input nameliest
hubbard_dict = input_namelistss['SYSTEM']['Hubbard_U']
# The eligible hubbard elements define by user
hubbard_species = _distinct_species(distinct_species)
# Specify the hubbard parameters
hubbard_parameters = set_hubbard_u_parameters(hubbard_species, hubbard_dict)
input_namelistss['SYSTEM']['Hubbard_U'] = hubbard_parameters
if 'Hubbard_J' in input_namelistss['SYSTEM'].keys():
# Assumed same as Hubbard U parameters
input_namelistss['SYSTEM']['Hubbard_J'] = hubbard_parameters
lda_plus_u_kind = 1
if 'Hubbard_V' in input_namelistss['SYSTEM'].keys():
# Assumed same as Hubbard U parameters
input_namelistss['SYSTEM']['Hubbard_V'] = hubbard_parameters
lda_plus_u_kind = 2
input_namelistss['SYSTEM']['lda_plus_u_kind'] = lda_plus_u_kind
parameters_dict = merge(input_namelistss, parameters_dict)
parameters = Dict(dict=parameters_dict)
builder.base.pseudo_family = Str(pseudo_family)
#builder.base.kpoints_distance = Float(0.4)
KpointsData = DataFactory('array.kpoints')
kpoints = KpointsData()
kpoints.set_cell_from_structure(builder.structure)
#set kpoint mesh based on density
kpoints.set_kpoints_mesh_from_density(k_distance, force_parity=False)
kpoints.store()
settings_dict={}
# Number of k-points to determine K-point integration type
# Gamma or Automatic by Monkhorst-Pack
num_k_points = np.prod(kpoints.get_kpoints_mesh()[0])
if num_k_points==1:
settings_dict={'gamma_only': True}
else:
settings_dict={'gamma_only': False}
builder.base.kpoints = kpoints
builder.base.pw.code = Code.get_from_string(codename)
builder.base.pw.parameters = parameters
#if hubbard_file:
# builder.base.pw.hubbard_file = hubbard_file
# AAAA: automatic_parallelization does not work!!!
automatic_parallelization = False
if automatic_parallelization:
automatic_parallelization = get_automatic_parallelization_options(1, 24*60*60-60*5)
builder.base.automatic_parallelization = Dict(dict=automatic_parallelization)
else:
if code_runtime_options is None or code_runtime_options == '':
# num machines, time, mpi
default_options = get_default_options(1, 24*60*60-60*5, True)
builder.base.pw.metadata.options = default_options
else:
exec_options = code_runtime_options.split('|')[0].split()
#default_options = get_default_options(int(exec_options[0]), int(exec_options[1]), True)
#builder.base.pw.metadata.options = default_options
builder.base.pw.metadata.options.resources={'num_machines': int(exec_options[0])}
builder.base.pw.metadata.options.max_wallclock_seconds = int(exec_options[1])
builder.base.pw.metadata.options.withmpi = True
#builder.base.pw.metadata.options.mpirun_extra_params='--map-by socket:PE=8 --rank-by core'.split()
if code_runtime_options is None or code_runtime_options == '':
npool = np.min([4, num_k_points])
settings_dict['cmdline'] = ['-nk', str(npool), '-ndiag', '1']
else:
parallel_options = code_runtime_options.split('|')[1]
settings_dict['cmdline'] = parallel_options.strip().split()
builder.base.pw.settings = Dict(dict=settings_dict)
clean_workdir = False
final_scf = False
if clean_workdir:
builder.clean_workdir = Bool(True)
if final_scf:
builder.final_scf = Bool(True)
calc = submit(builder)
if not (group is None):
group.add_nodes(calc)
return calc
def launch_workflow(code, structure, pseudo_family, kpoints_distance, ecutwfc,
ecutrho, hubbard_u, hubbard_v, hubbard_file_pk,
starting_magnetization, smearing,
automatic_parallelization, clean_workdir, max_num_machines,
max_wallclock_seconds, with_mpi, daemon):
"""Run a `PwBandsWorkChain`."""
# pylint: disable=too-many-statements
from aiida.orm import Bool, Float, Dict
from aiida.plugins import WorkflowFactory
from aiida_quantumespresso.utils.resources import get_default_options, get_automatic_parallelization_options
builder = WorkflowFactory('quantumespresso.pw.bands').get_builder()
cutoff_wfc, cutoff_rho = pseudo_family.get_recommended_cutoffs(
structure=structure, unit='Ry')
parameters = {
'CONTROL': {
'calculation': 'relax',
},
'SYSTEM': {
'ecutwfc': ecutwfc or cutoff_wfc,
'ecutrho': ecutrho or cutoff_rho,
},
}
try:
hubbard_file = validate.validate_hubbard_parameters(
structure, parameters, hubbard_u, hubbard_v, hubbard_file_pk)
except ValueError as exception:
raise click.BadParameter(str(exception))
try:
validate.validate_starting_magnetization(structure, parameters,
starting_magnetization)
except ValueError as exception:
raise click.BadParameter(str(exception))
try:
validate.validate_smearing(parameters, smearing)
except ValueError as exception:
raise click.BadParameter(str(exception))
pseudos = pseudo_family.get_pseudos(structure=structure)
parameters = Dict(dict=parameters)
builder.structure = structure
builder.relax.base.pw.code = code
builder.relax.base.pw.parameters = parameters
builder.relax.base.pw.pseudos = pseudos
builder.relax.base.kpoints_distance = Float(kpoints_distance)
builder.relax.meta_convergence = Bool(False)
builder.scf.pw.code = code
builder.scf.pw.parameters = parameters
builder.scf.pw.pseudos = pseudos
builder.scf.kpoints_distance = Float(kpoints_distance)
builder.bands.pw.code = code
builder.bands.pw.parameters = parameters
builder.bands.pw.pseudos = pseudos
if hubbard_file:
builder.relax.base.pw.hubbard_file = hubbard_file
builder.scf.base.pw.hubbard_file = hubbard_file
builder.bands.base.pw.hubbard_file = hubbard_file
if automatic_parallelization:
auto_para = Dict(dict=get_automatic_parallelization_options(
max_num_machines, max_wallclock_seconds))
builder.relax.base.automatic_parallelization = auto_para
builder.scf.automatic_parallelization = auto_para
builder.bands.automatic_parallelization = auto_para
else:
metadata_options = get_default_options(max_num_machines,
max_wallclock_seconds, with_mpi)
builder.relax.base.pw.metadata.options = metadata_options
builder.scf.pw.metadata.options = metadata_options
builder.bands.pw.metadata.options = metadata_options
if clean_workdir:
builder.clean_workdir = Bool(True)
launch.launch_process(builder, daemon)