def test_joins3_user_group(self):
from aiida.orm.user import User
from aiida.orm.querybuilder import QueryBuilder
# Create another user
new_email = "[email protected]"
user = self.backend.users.create(email=new_email)
user.store()
# Create a group that belongs to that user
from aiida.orm.group import Group
group = Group(name="node_group")
group.user = user
group.store()
# Search for the group of the user
qb = QueryBuilder()
qb.append(User, tag='user', filters={'id': {'==': user.id}})
qb.append(Group, belongs_to='user', filters={'id': {'==': group.id}})
self.assertEquals(
qb.count(), 1, "The expected group that belongs to "
"the selected user was not found.")
# Search for the user that owns a group
qb = QueryBuilder()
qb.append(Group, tag='group', filters={'id': {'==': group.id}})
qb.append(User, owner_of='group', filters={'id': {'==': user.id}})
self.assertEquals(
qb.count(), 1, "The expected user that owns the "
"selected group was not found.")
def create_cif_data(cls):
"""Create CifData object."""
with tempfile.NamedTemporaryFile(mode='w+') as fhandle:
filename = fhandle.name
fhandle.write(cls.valid_sample_cif_str)
fhandle.flush()
a_cif = CifData(file=filename,
source={
'version': '1234',
'db_name': 'COD',
'id': '0000001'
})
a_cif.store()
g_ne = Group(label='non_empty_group')
g_ne.store()
g_ne.add_nodes(a_cif)
g_e = Group(label='empty_group')
g_e.store()
cls.cif = a_cif
return {
DummyVerdiDataListable.NODE_ID_STR: a_cif.id,
DummyVerdiDataListable.NON_EMPTY_GROUP_ID_STR: g_ne.id,
DummyVerdiDataListable.EMPTY_GROUP_ID_STR: g_e.id
}
def add_to_group(node):
try:
g = Group.get_from_string('examples')
except NotExistent:
g = Group(name='examples')
g.store()
g.add_nodes(node)
def get_group():
try:
g = Group.get_from_string('examples')
except NotExistent:
g = Group(name='examples')
g.store()
return g
def create_trajectory_data():
"""Create TrajectoryData object with two arrays."""
traj = TrajectoryData()
# I create sample data
stepids = np.array([60, 70])
times = stepids * 0.01
cells = np.array([[[
2.,
0.,
0.,
], [
0.,
2.,
0.,
], [
0.,
0.,
2.,
]], [[
3.,
0.,
0.,
], [
0.,
3.,
0.,
], [
0.,
0.,
3.,
]]])
symbols = ['H', 'O', 'C']
positions = np.array([[[0., 0., 0.], [0.5, 0.5, 0.5], [1.5, 1.5, 1.5]],
[[0., 0., 0.], [0.5, 0.5, 0.5], [1.5, 1.5, 1.5]]])
velocities = np.array([[[0., 0., 0.], [0., 0., 0.], [0., 0., 0.]],
[[0.5, 0.5, 0.5], [0.5, 0.5, 0.5], [-0.5, -0.5, -0.5]]])
# I set the node
traj.set_trajectory(
stepids=stepids, cells=cells, symbols=symbols, positions=positions, times=times, velocities=velocities
)
traj.store()
# Create 2 groups and add the data to one of them
g_ne = Group(label='non_empty_group')
g_ne.store()
g_ne.add_nodes(traj)
g_e = Group(label='empty_group')
g_e.store()
return {
DummyVerdiDataListable.NODE_ID_STR: traj.id,
DummyVerdiDataListable.NON_EMPTY_GROUP_ID_STR: g_ne.id,
DummyVerdiDataListable.EMPTY_GROUP_ID_STR: g_e.id
}
def create_structure_bands():
"""Create bands structure object."""
alat = 4. # angstrom
cell = [
[
alat,
0.,
0.,
],
[
0.,
alat,
0.,
],
[
0.,
0.,
alat,
],
]
strct = StructureData(cell=cell)
strct.append_atom(position=(0., 0., 0.), symbols='Fe')
strct.append_atom(position=(alat / 2., alat / 2., alat / 2.),
symbols='O')
strct.store()
@calcfunction
def connect_structure_bands(strct): # pylint: disable=unused-argument
alat = 4.
cell = np.array([
[alat, 0., 0.],
[0., alat, 0.],
[0., 0., alat],
])
kpnts = KpointsData()
kpnts.set_cell(cell)
kpnts.set_kpoints([[0., 0., 0.], [0.1, 0.1, 0.1]])
bands = BandsData()
bands.set_kpointsdata(kpnts)
bands.set_bands([[1.0, 2.0], [3.0, 4.0]])
return bands
bands = connect_structure_bands(strct)
# Create 2 groups and add the data to one of them
g_ne = Group(label='non_empty_group')
g_ne.store()
g_ne.add_nodes(bands)
g_e = Group(label='empty_group')
g_e.store()
return {
DummyVerdiDataListable.NODE_ID_STR: bands.id,
DummyVerdiDataListable.NON_EMPTY_GROUP_ID_STR: g_ne.id,
DummyVerdiDataListable.EMPTY_GROUP_ID_STR: g_e.id
}
def create_structure_bands():
alat = 4. # angstrom
cell = [
[
alat,
0.,
0.,
],
[
0.,
alat,
0.,
],
[
0.,
0.,
alat,
],
]
s = StructureData(cell=cell)
s.append_atom(position=(0., 0., 0.), symbols='Fe')
s.append_atom(position=(alat / 2., alat / 2., alat / 2.), symbols='O')
s.store()
@calcfunction
def connect_structure_bands(structure):
alat = 4.
cell = np.array([
[alat, 0., 0.],
[0., alat, 0.],
[0., 0., alat],
])
k = KpointsData()
k.set_cell(cell)
k.set_kpoints([[0., 0., 0.], [0.1, 0.1, 0.1]])
b = BandsData()
b.set_kpointsdata(k)
b.set_bands([[1.0, 2.0], [3.0, 4.0]])
return b
b = connect_structure_bands(s)
# Create 2 groups and add the data to one of them
g_ne = Group(label='non_empty_group')
g_ne.store()
g_ne.add_nodes(b)
g_e = Group(label='empty_group')
g_e.store()
return {
TestVerdiDataListable.NODE_ID_STR: b.id,
TestVerdiDataListable.NON_EMPTY_GROUP_ID_STR: g_ne.id,
TestVerdiDataListable.EMPTY_GROUP_ID_STR: g_e.id
}
def create_structure_data():
"""Create StructureData object."""
alat = 4. # angstrom
cell = [
[
alat,
0.,
0.,
],
[
0.,
alat,
0.,
],
[
0.,
0.,
alat,
],
]
# BaTiO3 cubic structure
struc = StructureData(cell=cell)
struc.append_atom(position=(0., 0., 0.), symbols='Ba')
struc.append_atom(position=(alat / 2., alat / 2., alat / 2.),
symbols='Ti')
struc.append_atom(position=(alat / 2., alat / 2., 0.), symbols='O')
struc.append_atom(position=(alat / 2., 0., alat / 2.), symbols='O')
struc.append_atom(position=(0., alat / 2., alat / 2.), symbols='O')
struc.store()
# Create 2 groups and add the data to one of them
g_ne = Group(label='non_empty_group')
g_ne.store()
g_ne.add_nodes(struc)
g_e = Group(label='empty_group')
g_e.store()
return {
DummyVerdiDataListable.NODE_ID_STR: struc.id,
DummyVerdiDataListable.NON_EMPTY_GROUP_ID_STR: g_ne.id,
DummyVerdiDataListable.EMPTY_GROUP_ID_STR: g_e.id
}
def upload_basisset_family(cls,
folder,
group_name,
group_description,
stop_if_existing=True,
extension=".basis",
dry_run=False):
"""
Upload a set of Basis Set files in a given group.
:param folder: a path containing all Basis Set files to be added.
Only files ending in the set extension (case-insensitive) are considered.
:param group_name: the name of the group to create. If it exists and is
non-empty, a UniquenessError is raised.
:param group_description: a string to be set as the group description.
Overwrites previous descriptions, if the group was existing.
:param stop_if_existing: if True, check for the md5 of the files and,
if the file already exists in the DB, raises a MultipleObjectsError.
If False, simply adds the existing BasisSetData node to the group.
:param extension: the filename extension to look for
:param dry_run: If True, do not change the database.
"""
from aiida.common import aiidalogger
from aiida.orm import Group
from aiida.common.exceptions import UniquenessError, NotExistent
from aiida_crystal17.aiida_compatability import get_automatic_user
automatic_user = get_automatic_user()
if not os.path.isdir(folder):
raise ValueError("folder must be a directory")
# only files, and only those ending with specified exension;
# go to the real file if it is a symlink
files = [
os.path.realpath(os.path.join(folder, i))
for i in os.listdir(folder)
if os.path.isfile(os.path.join(folder, i))
and i.lower().endswith(extension)
]
nfiles = len(files)
try:
group = Group.get(name=group_name, type_string=BASISGROUP_TYPE)
group_created = False
except NotExistent:
group = Group(name=group_name,
type_string=BASISGROUP_TYPE,
user=automatic_user)
group_created = True
if group.user.email != automatic_user.email:
raise UniquenessError(
"There is already a BasisFamily group with name {}"
", but it belongs to user {}, therefore you "
"cannot modify it".format(group_name, group.user.email))
# Always update description, even if the group already existed
group.description = group_description
# NOTE: GROUP SAVED ONLY AFTER CHECKS OF UNICITY
basis_and_created = _retrieve_basis_sets(files, stop_if_existing)
# check whether basisset are unique per element
elements = [(i[0].element, i[0].md5sum) for i in basis_and_created]
# If group already exists, check also that I am not inserting more than
# once the same element
if not group_created:
for aiida_n in group.nodes:
# Skip non-basis sets
if not isinstance(aiida_n, BasisSetData):
continue
elements.append((aiida_n.element, aiida_n.md5sum))
elements = set(
elements) # Discard elements with the same MD5, that would
# not be stored twice
elements_names = [e[0] for e in elements]
if not len(elements_names) == len(set(elements_names)):
duplicates = set(
[x for x in elements_names if elements_names.count(x) > 1])
duplicates_string = ", ".join(i for i in duplicates)
raise UniquenessError(
"More than one Basis found for the elements: " +
duplicates_string + ".")
# At this point, save the group, if still unstored
if group_created and not dry_run:
group.store()
# save the basis set in the database, and add them to group
for basisset, created in basis_and_created:
if created:
if not dry_run:
basisset.store()
aiidalogger.debug("New node {0} created for file {1}".format( # pylint: disable=logging-format-interpolation
basisset.uuid, basisset.filename))
else:
aiidalogger.debug("Reusing node {0} for file {1}".format( # pylint: disable=logging-format-interpolation
basisset.uuid, basisset.filename))
# Add elements to the group all together
if not dry_run:
group.add_nodes(basis for basis, created in basis_and_created)
nuploaded = len([_ for _, created in basis_and_created if created])
return nfiles, nuploaded
def upload_psf_family(folder,
group_name,
group_description,
stop_if_existing=True):
"""
Upload a set of PSF files in a given group.
:param folder: a path containing all PSF files to be added.
Only files ending in .PSF (case-insensitive) are considered.
:param group_name: the name of the group to create. If it exists and is
non-empty, a UniquenessError is raised.
:param group_description: a string to be set as the group description.
Overwrites previous descriptions, if the group was existing.
:param stop_if_existing: if True, check for the md5 of the files and,
if the file already exists in the DB, raises a MultipleObjectsError.
If False, simply adds the existing PsfData node to the group.
"""
import os
import aiida.common
from aiida.common import aiidalogger
from aiida.orm import Group
from aiida.common.exceptions import UniquenessError, NotExistent
from aiida.backends.utils import get_automatic_user
from aiida.orm.querybuilder import QueryBuilder
if not os.path.isdir(folder):
raise ValueError("folder must be a directory")
# only files, and only those ending with .psf or .PSF;
# go to the real file if it is a symlink
files = [
os.path.realpath(os.path.join(folder, i)) for i in os.listdir(folder)
if os.path.isfile(os.path.join(folder, i))
and i.lower().endswith('.psf')
]
nfiles = len(files)
try:
group = Group.get(name=group_name, type_string=PSFGROUP_TYPE)
group_created = False
except NotExistent:
group = Group(name=group_name,
type_string=PSFGROUP_TYPE,
user=get_automatic_user())
group_created = True
if group.user != get_automatic_user():
raise UniquenessError("There is already a PsfFamily group with name {}"
", but it belongs to user {}, therefore you "
"cannot modify it".format(
group_name, group.user.email))
# Always update description, even if the group already existed
group.description = group_description
# NOTE: GROUP SAVED ONLY AFTER CHECKS OF UNICITY
pseudo_and_created = []
for f in files:
md5sum = aiida.common.utils.md5_file(f)
qb = QueryBuilder()
qb.append(PsfData, filters={'attributes.md5': {'==': md5sum}})
existing_psf = qb.first()
#existing_psf = PsfData.query(dbattributes__key="md5",
# dbattributes__tval = md5sum)
if existing_psf is None:
# return the psfdata instances, not stored
pseudo, created = PsfData.get_or_create(f,
use_first=True,
store_psf=False)
# to check whether only one psf per element exists
# NOTE: actually, created has the meaning of "to_be_created"
pseudo_and_created.append((pseudo, created))
else:
if stop_if_existing:
raise ValueError("A PSF with identical MD5 to "
" {} cannot be added with stop_if_existing"
"".format(f))
existing_psf = existing_psf[0]
pseudo_and_created.append((existing_psf, False))
# check whether pseudo are unique per element
elements = [(i[0].element, i[0].md5sum) for i in pseudo_and_created]
# If group already exists, check also that I am not inserting more than
# once the same element
if not group_created:
for aiida_n in group.nodes:
# Skip non-pseudos
if not isinstance(aiida_n, PsfData):
continue
elements.append((aiida_n.element, aiida_n.md5sum))
elements = set(elements) # Discard elements with the same MD5, that would
# not be stored twice
elements_names = [e[0] for e in elements]
if not len(elements_names) == len(set(elements_names)):
duplicates = set(
[x for x in elements_names if elements_names.count(x) > 1])
duplicates_string = ", ".join(i for i in duplicates)
raise UniquenessError("More than one PSF found for the elements: " +
duplicates_string + ".")
# At this point, save the group, if still unstored
if group_created:
group.store()
# save the psf in the database, and add them to group
for pseudo, created in pseudo_and_created:
if created:
pseudo.store()
aiidalogger.debug("New node {} created for file {}".format(
pseudo.uuid, pseudo.filename))
else:
aiidalogger.debug("Reusing node {} for file {}".format(
pseudo.uuid, pseudo.filename))
# Add elements to the group all togetehr
group.add_nodes(pseudo for pseudo, created in pseudo_and_created)
nuploaded = len([_ for _, created in pseudo_and_created if created])
return nfiles, nuploaded
class TbmodelWorkflow(Workflow):
'''
AiiDA workflow to get tight binding model of a material using VASP and
wannier90.
Necessary steps are:
* selfconsistent run with few kpoints
* nonselfconsistent run with lwannier90
* lwannier90 run with projections block
* wannier.x run with hr_plot = True
'''
def __init__(self, **kwargs):
super(TbmodelWorkflow, self).__init__(**kwargs)
self.group = None
try:
self.group = Group.get_from_string('tbmodel')
except NotExistent:
self.group = Group(name='tbmodel')
self.group.store()
def get_calc_maker(self):
'''
return an VaspMaker instance.
'''
from aiida.orm import Code
params = self.get_parameters()
maker = VaspMaker(structure=params['structure'])
maker.add_settings(icharg=0,
istart=0,
lorbit=11,
lsorbit=True,
sigma=0.05,
ismear=0,
gga='PE',
gga_compat=False)
maker.code = Code.get_from_string(params['vasp'])
# ~ maker.computer = maker.code.get_computer()
maker.label = params.get('name')
return maker
@Workflow.step
def start(self):
'''
prepare, store and attach the selfconsistent run
to get the charge density.
'''
params = self.get_parameters()
maker = VaspMaker(structure=params['structure'], calc_cls='vasp.scf')
maker.rewrite_settings(**params['settings'])
kp = params['kpmesh']
maker.kpoints.set_kpoints_mesh(kp)
maker.code = Code.get_from_string(params['vasp'])
maker.queue = params['queue']
maker.resources['num_machines'] = 4
maker.resources['num_mpiprocs_per_machine'] = 2
maker.label = params.get('name') + ': sc run'
calc = maker.new()
calc.description = '{}: selfconsistent run'.format(params.get('name'))
calc.store_all()
calc.set_extras({'experiment': 'tight-binding'})
self.group.add_nodes(calc)
self.attach_calculation(calc)
self.append_to_report(
'{}: starting selfconsistent run, PK={}, uuid={}'.format(
params.get('name'), calc.pk, calc.uuid))
self.add_attributes({'scstep': {'pk': calc.pk, 'uuid': calc.uuid}})
self.next(self.winrun)
@Workflow.step
def winrun(self):
'''
prepare, store and attach the non-selfconsistent run
to get the wannier input file
'''
params = self.get_parameters()
# get chgcar from previous step
scstep = self.get_attributes()['scstep']
prev = self.get_step_calculations(self.start)
sccalc = prev.get(uuid=scstep['uuid'])
self.append_to_report('{}: retrieved sc step calculation'.format(
params.get('name')))
# set up band structure step
maker = VaspMaker(calc_cls='vasp.nscf', continue_from=sccalc)
maker.add_settings(lwannier90=True, icharg=11)
maker.label = params.get('name') + ': win run'
calc = maker.new()
calc.description = '{}: win run'.format(params.get('name'))
calc.store_all()
calc.set_extras({'experiment': 'tight-binding'})
self.group.add_nodes(calc)
self.attach_calculation(calc)
self.append_to_report('{}: starting win run, PK={}, uuid={}'.format(
params.get('name'), calc.pk, calc.uuid))
self.add_attributes({'winstep': {'pk': calc.pk, 'uuid': calc.uuid}})
self.next(self.amnrun)
@Workflow.step
def amnrun(self):
params = self.get_parameters()
winstep = self.get_attributes()['winstep']
prev = self.get_step_calculations(self.winrun)
wincalc = prev.get(uuid=winstep['uuid'])
self.append_to_report('{}: retrieved nscf calculation'.format(
params.get('name')))
maker = VaspMaker(calc_cls='vasp.amn', copy_from=wincalc)
maker.wannier_settings = wincalc.out.wannier_settings.copy()
# ~ maker.wannier_data = wincalc.out.wannier_data
num_bands = maker.wannier_settings.get_dict()['num_wann']
maker.wannier_settings.update_dict({'num_bands': num_bands})
maker.wannier_settings.update_dict(params['win'])
maker.label = params.get('name') + ': amn run'
calc = maker.new()
calc.description = '{}: amn run'.format(params.get('name'))
calc.store_all()
calc.set_extras({'experiment': 'tight-binding'})
self.group.add_nodes(calc)
self.attach_calculation(calc)
self.append_to_report('{}: starting amn run, PK={}, uuid={}'.format(
params.get('name'), calc.pk, calc.uuid))
self.add_attributes({'amnstep': {'pk': calc.pk, 'uuid': calc.uuid}})
self.next(self.wannrun)
@Workflow.step
def wannrun(self):
params = self.get_parameters()
amnstep = self.get_attributes()['amnstep']
prev = self.get_step_calculations(self.amnrun)
amncalc = prev.get(uuid=amnstep['uuid'])
self.append_to_report('{}: retrieved amn calculation'.format(
params.get('name')))
calc = CalculationFactory('vasp.wannier')()
code = Code.get_from_string(params['wannier_x'])
calc.use_code(code)
calc.set_computer(code.get_computer())
calc.use_settings(amncalc.inp.wannier_settings)
calc.use_data(amncalc.out.wannier_data)
calc.label = params.get('name') + ': wannier run'
calc.set_resources({'num_machines': 1})
calc.set_queue_name(amncalc.get_queue_name())
calc.description = calc.label
calc.store_all()
calc.set_extras({'experiment': 'tight-binding'})
self.group.add_nodes(calc)
self.attach_calculation(calc)
self.add_result('wannier_run', calc)
self.append_to_report(
'{}: starting wannier run, PK={}, uuid={}'.format(
params.get('name'), calc.pk, calc.uuid))
self.add_attributes({'wannstep': {'pk': calc.pk, 'uuid': calc.uuid}})
self.next(self.exit)
