def structure_from_ucell(name):
"""Returns a `Structure` from the name of entry in the database."""
try:
return Structure.from_abivars(ucell(name))
except KeyError:
raise KeyError("Cannot find key %s in:\n %s" %
(name, list(_UCELLS.keys())))
def find_all_pp(obj, xc, family, label_dict={},pp_path=pp_path):
symbols = []
if isinstance(obj, collections.Iterable) and (
not isinstance(obj, str)) and isinstance(obj[0], str):
symbols = obj
elif isinstance(obj, str) and os.path.isfile(obj):
structure = Structure.as_structure(obj)
symbols = set(structure.symbol_set)
elif isinstance(obj, Structure):
symbols = obj.symbol_set
elif isinstance(obj, Atoms):
for elem in obj.get_chemical_symbols():
if elem not in symbols:
symbols.append(elem)
else:
raise ValueError(
'obj should be one of these: list of chemical symbols| abipy structure file name| abipy structure| ase atoms.'
)
ppdict = OrderedDict()
for elem in symbols:
if elem not in ppdict:
if elem in label_dict:
label = label_dict
else:
label = ''
ppdict[elem] = find_pp(elem, xc, family, label,pp_path=pp_path)
return list(ppdict.values())
def to_abi_structure(obj, magmoms=False):
ms = None
if isinstance(obj, str) and os.path.isfile(obj):
structure = Structure.as_structure(obj)
elif isinstance(obj, Structure):
structure = obj
elif isinstance(obj, Atoms):
structure = Structure.from_ase_atoms(obj)
if magmoms:
ms = obj.get_initial_magnetic_moments()
else:
raise ValueError(
'obj should be one of these: abipy structure file name| abipy structure| ase atoms.'
)
if magmoms:
return structure, ms
else:
return structure
def test_GWWork(self):
"""
Testing the abstract class GWFWWork
"""
struc = AbiStructure.from_file(abidata.cif_file("si.cif"))
struc.item = 'test'
self.assertIsInstance(struc, AbiStructure)
work = GWWork()
work.set_status(struc)
self.assertEqual(work.workdir, 'Si_test/work_0')
self.assertEqual(work.grid, 0)
self.assertFalse(work.all_done)
def test_GWWork(self):
"""
Testing the abstract class GWFWWork
"""
struc = AbiStructure.from_file(abidata.cif_file("si.cif"))
struc.item = 'test'
self.assertIsInstance(struc, AbiStructure)
work = GWWork()
work.set_status(struc)
self.assertEqual(work.workdir, 'Si_test/work_0')
self.assertEqual(work.grid, 0)
self.assertFalse(work.all_done)
def to_abi_structure(obj,magmoms=False):
ms=None
if isinstance(obj, str) and os.path.isfile(obj):
structure = Structure.as_structure(obj)
elif isinstance(obj, Structure):
structure = obj
elif isinstance(obj, Atoms):
#cell=obj.get_cell()
#acell0=np.linalg.norm(cell[0])
#acell1=np.linalg.norm(cell[1])
#acell2=np.linalg.norm(cell[2])
#cell0=cell[0]/acell0
#cell1=cell[1]/acell1
#cell2=cell[2]/acell2
#acell=[acell0, acell1, acell2]
#rprim=[cell0, cell1, cell2]
#xred=obj.get_scaled_positions()
#znucl=list(set(obj.get_atomic_numbers()))
#ntypat=len(znucl)
#typat=[]
#for z in obj.get_atomic_numbers():
# for i,n in enumerate(znucl):
# if z==n:
# typat.append(i)
#structure = Structure.from_abivars(acell=acell, rprim=rprim, typat=typat, xred=xred, ntypat=ntypat, znucl=znucl)
structure = Structure.from_ase_atoms(obj)
if magmoms:
ms=obj.get_initial_magnetic_moments()
else:
raise ValueError(
'obj should be one of these: abipy structure file name| abipy structure| ase atoms.'
)
if magmoms:
return structure,ms
else:
return structure
def test_expand(self):
"""
Testing helper function to extend the convergence grid
"""
self.maxDiff = None
spec = get_spec('GW')
struc = AbiStructure.from_file(abidata.cif_file("si.cif"))
struc.item = 'test'
wdir = tempfile.mkdtemp()
print('wdir', wdir)
os.chdir(wdir)
shutil.copyfile(abidata.cif_file("si.cif"), os.path.join(wdir, 'si.cif'))
shutil.copyfile(abidata.pseudo("14si.pspnc").path, os.path.join(wdir, 'Si.pspnc'))
shutil.copyfile(os.path.join(abidata.dirpath, 'managers', 'shell_manager.yml'),
os.path.join(wdir, 'manager.yml'))
shutil.copyfile(os.path.join(abidata.dirpath, 'managers', 'scheduler.yml'), os.path.join(wdir, 'scheduler.yml'))
try:
temp_ABINIT_PS_EXT = os.environ['ABINIT_PS_EXT']
temp_ABINIT_PS = os.environ['ABINIT_PS']
except KeyError:
temp_ABINIT_PS_EXT = None
temp_ABINIT_PS = None
os.environ['ABINIT_PS_EXT'] = '.pspnc'
os.environ['ABINIT_PS'] = wdir
tests = SingleAbinitGWWork(struc, spec).convs
tests_out = {'nscf_nbands': {'test_range': (40,),
'control': 'gap', 'method': 'set_bands', 'level': 'nscf'},
'ecut': {'test_range': (50, 48, 46, 44),
'control': 'e_ks_max', 'method': 'direct', 'level': 'scf'},
'ecuteps': {'test_range': (4, 8, 12, 16, 20),
'control': 'gap', 'method': 'direct', 'level': 'sigma'}}
self.assertEqual(expand(tests, 1), tests_out)
spec.data['code'] = 'VASP'
if "VASP_PSP_DIR" in os.environ:
spec.update_code_interface()
tests = GWG0W0VaspInputSet(struc, spec).convs
tests_out = {'ENCUTGW': {'test_range': (200, 400, 600, 800), 'control': 'gap', 'method': 'incar_settings'}}
self.assertEqual(expand(tests, 1), tests_out)
if temp_ABINIT_PS is not None:
os.environ['ABINIT_PS_EXT'] = temp_ABINIT_PS_EXT
os.environ['ABINIT_PS'] = temp_ABINIT_PS
def test_VaspGWFWWorkFlow(self):
"""
Testing the concrete VaspGWFWWorkFlow class
"""
struc = AbiStructure.from_file(abidata.cif_file("si.cif"))
struc.item = 'test'
self.assertIsInstance(struc, AbiStructure)
work = VaspGWFWWorkFlow()
self.assertEqual(len(work.work_list), 0)
self.assertEqual(len(work.connections), 0)
self.assertEqual(work.fw_id, 1)
self.assertEqual(work.prep_id, 1)
self.assertEqual(len(work.wf), 0)
if False:
for job in ['prep', 'G0W0', 'GW0', 'scGW0']:
parameters = dict()
parameters['spec'] = dict()
parameters['spec']['converge'] = True
parameters['job'] = job
work.add_work(parameters=parameters)
def test_VaspGWFWWorkFlow(self):
"""
Testing the concrete VaspGWFWWorkFlow class
"""
struc = AbiStructure.from_file(abidata.cif_file("si.cif"))
struc.item = 'test'
self.assertIsInstance(struc, AbiStructure)
work = VaspGWFWWorkFlow()
self.assertEqual(len(work.work_list), 0)
self.assertEqual(len(work.connections), 0)
self.assertEqual(work.fw_id, 1)
self.assertEqual(work.prep_id, 1)
self.assertEqual(len(work.wf), 0)
if False:
for job in ['prep', 'G0W0', 'GW0', 'scGW0']:
parameters = dict()
parameters['spec'] = dict()
parameters['spec']['converge'] = True
parameters['job'] = job
work.add_work(parameters=parameters)
def test_expand(self):
"""
Testing helper function to extend the convergence grid
"""
self.maxDiff = None
spec = get_spec('GW')
struc = AbiStructure.from_file(abidata.cif_file("si.cif"))
struc.item = 'test'
wdir = tempfile.mkdtemp()
print('wdir', wdir)
os.chdir(wdir)
shutil.copyfile(abidata.cif_file("si.cif"), os.path.join(wdir, 'si.cif'))
shutil.copyfile(abidata.pseudo("14si.pspnc").path, os.path.join(wdir, 'Si.pspnc'))
shutil.copyfile(os.path.join(abidata.dirpath, 'managers', 'shell_manager.yml'),
os.path.join(wdir, 'manager.yml'))
shutil.copyfile(os.path.join(abidata.dirpath, 'managers', 'simple_scheduler.yml'), os.path.join(wdir, 'scheduler.yml'))
temp_ABINIT_PS_EXT = os.environ.get('ABINIT_PS_EXT', None)
temp_ABINIT_PS = os.environ.get('ABINIT_PS', None)
os.environ['ABINIT_PS_EXT'] = '.pspnc'
os.environ['ABINIT_PS'] = wdir
tests = SingleAbinitGWWork(struc, spec).convs
tests_out = {'nscf_nbands': {'test_range': (25,),
'control': 'gap', 'method': 'set_bands', 'level': 'nscf'},
'ecut': {'test_range': (50, 48, 46, 44),
'control': 'e_ks_max', 'method': 'direct', 'level': 'scf'},
'ecuteps': {'test_range': (4, 6, 8, 10, 12),
'control': 'gap', 'method': 'direct', 'level': 'sigma'}}
self.assertEqual(expand(tests, 1), tests_out)
spec.data['code'] = 'VASP'
if temp_ABINIT_PS is not None:
os.environ['ABINIT_PS_EXT'] = temp_ABINIT_PS_EXT
os.environ['ABINIT_PS'] = temp_ABINIT_PS
def structure_from_ucell(name):
"""Returns a `Structure` from the name of entry in the database."""
try:
return Structure.from_abivars(ucell(name))
except KeyError:
raise KeyError("Cannot find key %s in:\n %s" % (name, _UCELLS.keys()))
def test_SingleAbinitGWWork(self):
"""
Testing the concrete SingelAbinitGWWork class
"""
struc = AbiStructure.from_file(abidata.cif_file("si.cif"))
struc.item = 'test'
wdir = tempfile.mkdtemp()
#wdir = '.'
shutil.copyfile(abidata.cif_file("si.cif"),
os.path.join(wdir, 'si.cif'))
shutil.copyfile(
abidata.pseudo("14si.pspnc").path, os.path.join(wdir, 'Si.pspnc'))
shutil.copyfile(
os.path.join(abidata.dirpath, 'managers',
'shell_manager_nompi.yml'),
os.path.join(wdir, 'manager.yml'))
shutil.copyfile(
os.path.join(abidata.dirpath, 'managers', 'scheduler.yml'),
os.path.join(wdir, 'scheduler.yml'))
try:
temp_ABINIT_PS_EXT = os.environ['ABINIT_PS_EXT']
temp_ABINIT_PS = os.environ['ABINIT_PS']
except KeyError:
temp_ABINIT_PS_EXT = None
temp_ABINIT_PS = None
os.environ['ABINIT_PS_EXT'] = '.pspnc'
os.environ['ABINIT_PS'] = wdir
self.assertIsInstance(struc, AbiStructure)
spec = get_spec('GW')
spec.data['kp_grid_dens'] = 100
spec.data['kp_in'] = -100
with open(os.path.join(wdir, 'extra_abivars'), 'w') as f:
f.write('{"ecut": 8, "ecutsigx": 8}')
work = SingleAbinitGWWork(struc, spec)
self.assertEqual(len(work.CONVS), 3)
conv_strings = ['method', 'control', 'level']
for test in work.CONVS:
self.assertIsInstance(work.CONVS[test]['test_range'], tuple)
for item in conv_strings:
self.assertIsInstance(work.CONVS[test][item], unicode)
self.assertEqual(work.work_dir, 'Si_test')
self.assertEqual(len(work.pseudo_table), 1)
self.assertEqual(work.bands_fac, 1)
self.assertEqual(work.get_electrons(struc), 8)
self.assertEqual(work.get_bands(struc), 6)
self.assertGreater(work.get_bands(struc),
work.get_electrons(struc) / 2,
'More electrons than bands, very bad.')
flow = work.create()
print(work.work_dir)
print(flow.workdir)
print(flow[0].workdir)
self.assertIsInstance(flow, Flow)
self.assertEqual(len(flow), 1) # one work
self.assertEqual(len(flow[0]), 4) # with 4 tasks
# self.assertEqual(flow.workdir, 'Si')
self.assertEqual(flow.build_and_pickle_dump(), 0)
# some more tests
flow.rmtree()
spec = get_spec('GW')
spec.data['converge'] = True
struc.item = 'converge'
work = SingleAbinitGWWork(struc, spec)
flow = work.create()
self.assertEqual(len(flow[0]), 45)
self.assertEqual(flow[0][0].__class__, ScfTask)
self.assertEqual(flow[0][1].__class__, ScfTask)
self.assertEqual(flow[0][2].__class__, ScfTask)
self.assertEqual(flow[0][3].__class__, ScfTask)
self.assertEqual(flow[0][4].__class__, NscfTask)
self.assertEqual(flow[0][5].__class__, ScrTask)
self.assertEqual(flow[0][6].__class__, SigmaTask)
ecuts = [
dict(task.input.as_dict()['abi_args'])['ecut'] for task in flow[0]
]
print('ecuts:', ecuts)
# it is essential that the first four are diffent, this is for the convergence study of ecut, and that
# after that is stays the same
self.assertEqual(ecuts, [
50, 48, 46, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44,
44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44,
44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44
])
nbands = [
dict(task.input.as_dict()['abi_args'])['nband'] for task in flow[0]
]
print('nbands:', nbands)
# the firs 4 should be 'low' these are self consistent
# the fifth should be the maximum of what follows
# the 6th and on should always be pairs that are the same, they are combinations of scr and sigma tasks
self.assertEqual(nbands, [
26, 26, 26, 26, 180, 30, 30, 60, 60, 120, 120, 180, 180, 30, 30,
60, 60, 120, 120, 180, 180, 30, 30, 60, 60, 120, 120, 180, 180, 30,
30, 60, 60, 120, 120, 180, 180, 30, 30, 60, 60, 120, 120, 180, 180
])
ecuteps = [
dict(task.input.as_dict()['abi_args']).get('ecuteps', None)
for task in flow[0]
]
print('ecuteps:', ecuteps)
self.assertEqual(ecuteps, [
None, None, None, None, None, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8,
8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 16, 16, 16, 16, 16, 16,
16, 16, 20, 20, 20, 20, 20, 20, 20, 20
])
inplens = [len(task.input.as_dict()['abi_args']) for task in flow[0]]
print(inplens)
self.assertEqual(inplens, [
17, 17, 17, 17, 18, 27, 30, 27, 30, 27, 30, 27, 30, 27, 30, 27, 30,
27, 30, 27, 30, 27, 30, 27, 30, 27, 30, 27, 30, 27, 30, 27, 30, 27,
30, 27, 30, 27, 30, 27, 30, 27, 30, 27, 30
])
ngkpts = [
dict(task.input.as_dict()['abi_args'])['ngkpt'] for task in flow[0]
]
for ngkpt in ngkpts:
self.assertEqual(ngkpt, [2, 2, 2])
self.assertEqual(flow.build_and_pickle_dump(), 0)
# some more tests
flow.rmtree()
if temp_ABINIT_PS is not None:
os.environ['ABINIT_PS_EXT'] = temp_ABINIT_PS_EXT
os.environ['ABINIT_PS'] = temp_ABINIT_PS
def test_SingleAbinitGWWork(self):
"""
Testing the concrete SingelAbinitGWWork class
"""
struc = AbiStructure.from_file(abidata.cif_file("si.cif"))
struc.item = 'test'
wdir = tempfile.mkdtemp()
#wdir = '.'
shutil.copyfile(abidata.cif_file("si.cif"), os.path.join(wdir, 'si.cif'))
shutil.copyfile(abidata.pseudo("14si.pspnc").path, os.path.join(wdir, 'Si.pspnc'))
shutil.copyfile(os.path.join(abidata.dirpath, 'managers', 'shell_manager_nompi.yml'),
os.path.join(wdir, 'manager.yml'))
shutil.copyfile(os.path.join(abidata.dirpath, 'managers', 'scheduler.yml'), os.path.join(wdir, 'scheduler.yml'))
try:
temp_ABINIT_PS_EXT = os.environ['ABINIT_PS_EXT']
temp_ABINIT_PS = os.environ['ABINIT_PS']
except KeyError:
temp_ABINIT_PS_EXT = None
temp_ABINIT_PS = None
os.environ['ABINIT_PS_EXT'] = '.pspnc'
os.environ['ABINIT_PS'] = wdir
self.assertIsInstance(struc, AbiStructure)
spec = get_spec('GW')
spec.data['kp_grid_dens'] = 100
spec.data['kp_in'] = -100
with open(os.path.join(wdir, 'extra_abivars'), 'w') as f:
f.write('{"ecut": 8, "ecutsigx": 8}')
work = SingleAbinitGWWork(struc, spec)
self.assertEqual(len(work.CONVS), 3)
conv_strings = ['method', 'control', 'level']
for test in work.CONVS:
self.assertIsInstance(work.CONVS[test]['test_range'], tuple)
for item in conv_strings:
self.assertIsInstance(work.CONVS[test][item], unicode)
self.assertEqual(work.work_dir, 'Si_test')
self.assertEqual(len(work.pseudo_table), 1)
self.assertEqual(work.bands_fac, 1)
self.assertEqual(work.get_electrons(struc), 8)
self.assertEqual(work.get_bands(struc), 6)
self.assertGreater(work.get_bands(struc), work.get_electrons(struc) / 2, 'More electrons than bands, very bad.')
flow = work.create()
print(work.work_dir)
print(flow.workdir)
print(flow[0].workdir)
self.assertIsInstance(flow, Flow)
self.assertEqual(len(flow), 1) # one work
self.assertEqual(len(flow[0]), 4) # with 4 tasks
# self.assertEqual(flow.workdir, 'Si')
self.assertEqual(flow.build_and_pickle_dump(), 0)
# some more tests
flow.rmtree()
spec = get_spec('GW')
spec.data['converge'] = True
struc.item = 'converge'
work = SingleAbinitGWWork(struc, spec)
flow = work.create()
self.assertEqual(len(flow[0]), 45)
self.assertEqual(flow.build_and_pickle_dump(), 0)
# some more tests
flow.rmtree()
if temp_ABINIT_PS is not None:
os.environ['ABINIT_PS_EXT'] = temp_ABINIT_PS_EXT
os.environ['ABINIT_PS'] = temp_ABINIT_PS
def test_expand(self):
"""
Testing helper function to extend the convergence grid
"""
self.maxDiff = None
spec = get_spec('GW')
struc = AbiStructure.from_file(abidata.cif_file("si.cif"))
struc.item = 'test'
wdir = tempfile.mkdtemp()
print('wdir', wdir)
os.chdir(wdir)
shutil.copyfile(abidata.cif_file("si.cif"),
os.path.join(wdir, 'si.cif'))
shutil.copyfile(
abidata.pseudo("14si.pspnc").path, os.path.join(wdir, 'Si.pspnc'))
shutil.copyfile(
os.path.join(abidata.dirpath, 'managers', 'shell_manager.yml'),
os.path.join(wdir, 'manager.yml'))
shutil.copyfile(
os.path.join(abidata.dirpath, 'managers', 'scheduler.yml'),
os.path.join(wdir, 'scheduler.yml'))
try:
temp_ABINIT_PS_EXT = os.environ['ABINIT_PS_EXT']
temp_ABINIT_PS = os.environ['ABINIT_PS']
except KeyError:
temp_ABINIT_PS_EXT = None
temp_ABINIT_PS = None
os.environ['ABINIT_PS_EXT'] = '.pspnc'
os.environ['ABINIT_PS'] = wdir
tests = SingleAbinitGWWork(struc, spec).convs
tests_out = {
'nscf_nbands': {
'test_range': (40, ),
'control': 'gap',
'method': 'set_bands',
'level': 'nscf'
},
'ecut': {
'test_range': (50, 48, 46, 44),
'control': 'e_ks_max',
'method': 'direct',
'level': 'scf'
},
'ecuteps': {
'test_range': (4, 8, 12, 16, 20),
'control': 'gap',
'method': 'direct',
'level': 'sigma'
}
}
self.assertEqual(expand(tests, 1), tests_out)
spec.data['code'] = 'VASP'
if "VASP_PSP_DIR" in os.environ:
spec.update_code_interface()
tests = GWG0W0VaspInputSet(struc, spec).convs
tests_out = {
'ENCUTGW': {
'test_range': (200, 400, 600, 800),
'control': 'gap',
'method': 'incar_settings'
}
}
self.assertEqual(expand(tests, 1), tests_out)
if temp_ABINIT_PS is not None:
os.environ['ABINIT_PS_EXT'] = temp_ABINIT_PS_EXT
os.environ['ABINIT_PS'] = temp_ABINIT_PS
#!/usr/bin/env python
from __future__ import division
import numpy as np
import abipy.data as data
from abipy.abilab import Structure, StructureModifier, AbiInput
structure = Structure.from_file(data.cif_file("si.cif"))
modifier = StructureModifier(structure)
# From 98% to 102% of the initial volume.
new_structures = modifier.scale_lattice(vol_ratios=np.arange(98, 104, 2) / 100.)
inp = AbiInput(pseudos=data.pseudos("14si.pspnc"), ndtset=len(new_structures))
for (idt, new_structure) in enumerate(new_structures):
inp.set_structure(new_structure, dtset=idt+1)
print(inp)
# Supercell
inp = AbiInput(pseudos=data.pseudos("14si.pspnc"), ndtset=1)
new_structure = modifier.make_supercell(scaling_matrix=[1,2,3])
inp.set_structure(new_structure)
print(inp)
structure = Structure.from_abivars({
# This context manager is required to use the collection name selected in source_db
# By default mongoengine uses the name of the class (in this case RelaxResult) as
# name of the collection to query.
with source_db.switch_collection(RelaxResult) as RelaxResult:
# download from the database the relaxed structure
# This relies on mongoengine (http://mongoengine.org/) to interact with the database.
# See the module abiflows.database.mongoengine.abinit_results for the objects used to store the results
relaxed_results = RelaxResult.objects(mp_id=mp_id)
# Assume that there is one and only one result matching the query. In real cases you might want to check this.
# At this point is an instance of a RelaxResult object
relaxed = relaxed_results[0]
# load the relaxed Structure
structure = Structure.from_dict(relaxed.abinit_output.structure)
# use the same k-point sampling as the one of the relax
kppa = relaxed.abinit_input.kppa
ngkpt = relaxed.abinit_input.ngkpt
# The AbinitInput object used for the relax is stored in the database.
# We get it to use the same approximations used during the relaxation.
relax_input = relaxed.abinit_input.last_input.to_mgobj()
# We use the same k and q point grid
qppa = kppa
extra_abivars = dict(chkprim=1, nstep=100, chksymbreak=1)
# as for the relax workflow, information stored in the database for the calculation. In particular information
# about the source structure.
initialization_info = dict(kppa=kppa, mp_id=mp_id,
relax_db=source_db.as_dict_no_credentials(), relax_id=relaxed.id,
def test_SingleAbinitGWWork(self):
"""
Testing the concrete SingelAbinitGWWork class
"""
struc = AbiStructure.from_file(abidata.cif_file("si.cif"))
struc.item = 'test'
wdir = '.'
shutil.copyfile(abidata.cif_file("si.cif"), os.path.join(wdir, 'si.cif'))
shutil.copyfile(abidata.pseudo("14si.pspnc").path, os.path.join(wdir, 'Si.pspnc'))
shutil.copyfile(os.path.join(abidata.dirpath, 'managers', 'shell_manager_nompi.yml'),
os.path.join(wdir, 'manager.yml'))
shutil.copyfile(os.path.join(abidata.dirpath, 'managers', 'scheduler.yml'), os.path.join(wdir, 'scheduler.yml'))
try:
temp_ABINIT_PS_EXT = os.environ['ABINIT_PS_EXT']
temp_ABINIT_PS = os.environ['ABINIT_PS']
except KeyError:
temp_ABINIT_PS_EXT = None
temp_ABINIT_PS = None
os.environ['ABINIT_PS_EXT'] = '.pspnc'
os.environ['ABINIT_PS'] = wdir
self.assertIsInstance(struc, AbiStructure)
spec = get_spec('GW')
spec.data['kp_grid_dens'] = 100
spec.data['kp_in'] = -100
with open('extra_abivars', 'w') as f:
f.write('{"ecut": 8, "ecutsigx": 8}')
work = SingleAbinitGWWork(struc, spec)
self.assertEqual(len(work.CONVS), 3)
conv_strings = ['method', 'control', 'level']
for test in work.CONVS:
self.assertIsInstance(work.CONVS[test]['test_range'], tuple)
for item in conv_strings:
self.assertIsInstance(work.CONVS[test][item], unicode)
self.assertEqual(work.work_dir, 'Si_test')
self.assertEqual(len(work.pseudo_table), 1)
self.assertEqual(work.bands_fac, 1)
self.assertEqual(work.get_electrons(struc), 8)
self.assertEqual(work.get_bands(struc), 6)
self.assertGreater(work.get_bands(struc), work.get_electrons(struc) / 2, 'More electrons than bands, very bad.')
flow = work.create()
print(work.work_dir)
print(flow.workdir)
print(flow[0].workdir)
self.assertIsInstance(flow, Flow)
self.assertEqual(len(flow), 1) # one work
self.assertEqual(len(flow[0]), 4) # with 4 tasks
# self.assertEqual(flow.workdir, 'Si')
self.assertEqual(flow.build_and_pickle_dump(), 0)
# some more tests
flow.rmtree()
spec = get_spec('GW')
spec.data['converge'] = True
struc.item = 'converge'
work = SingleAbinitGWWork(struc, spec)
flow = work.create()
self.assertEqual(len(flow[0]), 45)
self.assertEqual(flow.build_and_pickle_dump(), 0)
# some more tests
flow.rmtree()
if temp_ABINIT_PS is not None:
os.environ['ABINIT_PS_EXT'] = temp_ABINIT_PS_EXT
os.environ['ABINIT_PS'] = temp_ABINIT_PS
def structure_from_ucell(name):
"""Returns a `Structure` from the name of entry in the database."""
return Structure.from_abivars(ucell(name))