def main():
"""
main gw output processing
"""
if os.path.isfile('plots'):
os.remove('plots')
if os.path.isfile('plot-fits'):
os.remove('plot-fits')
spec = get_spec('GW')
spec.read_from_file('spec.in')
print('Found setup for ', spec.get_code())
counters = spec.loop_structures('o')
return counters
def test_store_empty(self):
"""
Testing loop_structures store mode s empty case
"""
wdir = tempfile.mkdtemp()
print('wdir', wdir)
os.chdir(wdir)
shutil.copyfile(abidata.cif_file("si.cif"), os.path.join(wdir, 'si.cif'))
spec_in = get_spec('GW')
self.assertIsInstance(spec_in, GWSpecs)
spec_in.data['source'] = 'cif'
return_value = spec_in.loop_structures('s')
self.assertEqual(return_value[0], 0)
self.assertEqual(return_value[1], 1)
self.assertEqual(return_value[2], {u'Si_si.cif': 'no data found to insert in db'})
def test_output_empty(self):
"""
Testing loop_structures output parsing mode o empty case
"""
wdir = tempfile.mkdtemp()
print('wdir', wdir)
os.chdir(wdir)
shutil.copyfile(abidata.cif_file("si.cif"), os.path.join(wdir, 'si.cif'))
spec_in = get_spec('GW')
self.assertIsInstance(spec_in, GWSpecs)
spec_in.data['source'] = 'cif'
spec_in.data['converge'] = True
return_value = spec_in.loop_structures('o')
self.assertEqual(return_value[0], 0)
self.assertEqual(return_value[1], 1)
self.assertEqual(return_value[2], {u'Si_si.cif': u'calculation stage could not be determined for convergence calculation'})
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 main(update=True):
"""
main gw setup
"""
spec_in = get_spec('GW')
try:
spec_in.read_from_file('spec.in')
except (IOError, OSError):
try:
spec_in.read_from_file('$HOME/.abinit/abipy/spec.in')
except (IOError, OSError):
pass
pass
if update:
# in testing mode there should not be interactive updating
spec_in.update_interactive()
spec_in.test()
spec_in.write_to_file('spec.in')
counters = spec_in.loop_structures('i')
return counters
def test_setup_single(self):
"""
Testing the main functions called in the abiGWsetup script for a single shot calculation
"""
spec_in = get_spec('GW')
self.assertIsInstance(spec_in, GWSpecs)
self.assert_equal(spec_in.test(), 0)
self.assert_equal(len(spec_in.to_dict()), 10)
self.assert_equal(spec_in.get_code(), 'ABINIT')
spec_in.data['source'] = 'cif'
self.assert_equal(spec_in.hash_str(), "code:ABINIT;source:cifjobs:['prep', 'G0W0'];mode:ceci;functional:PBE;kp_grid_dens:500prec:m;tol:0.0001;test:False;converge:False")
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
spec_in.data['source'] = 'cif'
print('dirpath', abidata.dirpath)
spec_in.write_to_file('spec.in')
self.assertTrue(os.path.isfile(os.path.join(wdir, 'spec.in')))
spec_in.loop_structures('i')
if temp_ABINIT_PS is not None:
os.environ['ABINIT_PS_EXT'] = temp_ABINIT_PS_EXT
os.environ['ABINIT_PS'] = temp_ABINIT_PS
ls = os.listdir('.')
print(ls)
self.assertEqual(ls, [u'job_collection', u'manager.yml', u'scheduler.yml', u'si.cif', u'Si.pspnc',
u'Si_si.cif', u'spec.in'])
ls2 = os.listdir('Si_si.cif/')
print(ls2)
self.assertEqual(ls2, [u'.nodeid', u'__AbinitFlow__.pickle', u'indata', u'outdata', u'tmpdata', u'w0'])
ls3 = os.listdir('Si_si.cif/w0/')
print(ls3)
self.assertEqual(ls3, [u'indata', u'outdata', u't0', u't1', u't2', u't3', u'tmpdata'])
with open('Si_si.cif/w0/t0/run.abi') as f:
abi = f.readlines()
for x in [' ecut 44\n', ' tolvrs 1e-08\n', ' kptopt 1\n', ' ngkpt 6 6 6\n', ' nshiftk 1\n', ' nband 26\n']:
self.assertIn(x, abi)
with open('Si_si.cif/w0/t1/run.abi') as f:
abi = f.readlines()
for x in [' ecut 44\n', ' tolwfr 1e-17\n', ' kptopt 1\n', ' iscf -2\n']:
self.assertIn(x, abi)
with open('Si_si.cif/w0/t2/run.abi') as f:
abi = f.readlines()
for x in [' kptopt 1\n', ' shiftk 0 0 0\n', ' ngkpt 6 6 6\n', ' nshiftk 1\n', ' iscf -2\n', ' nband 60\n',
' nsppol 1\n', ' ecut 44\n', ' toldfe 1e-08\n',' gwmem 10\n', ' inclvkb 2\n', '\n', ' symsigma 1\n',
' ecuteps 8\n']:
self.assertIn(x, abi)
with open('Si_si.cif/w0/t3/run.abi') as f:
abi = f.readlines()
for x in [' kptopt 1\n', ' shiftk 0 0 0\n', ' ngkpt 6 6 6\n', ' nshiftk 1\n', ' iscf -2\n', ' nband 60\n',
' nsppol 1\n', ' ecut 44\n', ' toldfe 1e-08\n', ' gwmem 10\n', ' inclvkb 2\n', '\n', ' symsigma 1\n',
' ecutsigx 44\n', ' ecuteps 8\n', ' gw_qprange 2\n', ' ppmodel 1\n', ' gwcalctyp 00\n']:
self.assertIn(x, abi)
def test_GWget_spec(self):
"""
Testing the factory function get_specs()
"""
spec = get_spec('GW')
self.assertIsInstance(spec, GWSpecs)
def test_SingleAbinitGWWork(self):
"""
Testing the concrete SingleAbinitGWWork class
"""
struc = AbiStructure.from_file(abidata.cif_file("si.cif"))
struc.item = 'test'
wdir = tempfile.mkdtemp()
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_nompi_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
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], str)
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, 120, 30, 30, 60, 60, 90, 90, 120, 120, 30, 30, 60, 60, 90, 90, 120,
120, 30, 30, 60, 60, 90, 90, 120, 120, 30, 30, 60, 60, 90, 90, 120, 120, 30, 30, 60,
60, 90, 90, 120, 120])
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, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8,
8, 8, 8, 8, 8, 8, 10, 10, 10, 10, 10, 10, 10, 10, 12, 12, 12, 12, 12, 12, 12, 12])
inplens = [len(task.input.as_dict()['abi_args']) for task in flow[0]]
print(inplens)
self.assertEqual(inplens, [18, 18, 18, 18, 19, 29, 31, 29, 31, 29, 31, 29, 31, 29, 31, 29, 31, 29, 31, 29, 31,
29, 31, 29, 31, 29, 31, 29, 31, 29, 31, 29, 31, 29, 31, 29, 31, 29, 31, 29, 31, 29,
31, 29, 31])
ngkpts = [dict(task.input.as_dict()['abi_args'])['ngkpt'] for task in flow[0]]
for ngkpt in ngkpts:
self.assertEqual(ngkpt, [2, 2, 2])
npffts = [dict(task.input.as_dict()['abi_args'])['npfft'] for task in flow[0]]
self.assertTrue(all(x == 3 for x in npffts))
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 main():
spec_in = get_spec('GW')
spec_in.read_from_file('spec.in')
counters = spec_in.loop_structures('s')
return counters