def excecute_flow(self, structure, spec_data):
"""
excecute spec prepare input/jobfiles or submit to fw for a given structure
for abinit a flow is created using abinitio
"""
if spec_data['converge'] and is_converged(self.hartree_parameters, structure):
option = is_converged(self.hartree_parameters, structure, return_values=True)
else:
option = None
print(option)
work_flow = SingleAbinitGWWork(structure, spec_data, option)
flow = work_flow.create()
if flow is not None:
flow.build_and_pickle_dump()
work_flow.create_job_file()
def execute_flow(self, structure, spec_data):
"""
execute spec prepare input/jobfiles or submit to fw for a given structure
for abinit a flow is created using abinitio
"""
if spec_data['converge'] and is_converged(self.hartree_parameters,
structure):
option = is_converged(self.hartree_parameters,
structure,
return_values=True)
else:
option = None
work_flow = SingleAbinitGWWork(structure, spec_data, option)
flow = work_flow.create()
print('flow')
if flow is not None:
flow.build_and_pickle_dump()
work_flow.create_job_file()
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 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