def set_status(self, structure):
self._grid = 0
self._all_done = False
self._workdir = None
self._converged = is_converged(False, structure)
try:
self._grid = read_grid_from_file(s_name(structure) +
".full_res")['grid']
self._all_done = read_grid_from_file(
s_name(structure) + ".full_res")['all_done']
self._workdir = os.path.join(s_name(structure),
'work_' + str(self.grid))
except (IOError, OSError):
pass
def test_read_grid_from_file(self):
"""
Testing the reading the results of a full set of calculations from file
"""
# no full res file case
full_res_read = read_grid_from_file('full_res')
self.assertEqual(full_res_read, {'grid': 0, 'all_done': False})
# file there done case
full_res = {'grid': 2, 'all_done': True}
with open('full_res', 'w') as f:
json.dump(obj=full_res, fp=f)
full_res_read = read_grid_from_file('full_res')
self.assertEqual(full_res_read, full_res)
def store_results(self, name):
folder = name + '.res'
store_conv_results(name, folder)
w = 'w' + str(read_grid_from_file(name + ".full_res")['grid'])
try:
if os.path.isdir(os.path.join(name + ".conv", w, "t11",
"outdata")):
shutil.copyfile(
os.path.join(name + ".conv", w, "t2", "outdata",
"out_GSR.nc"),
os.path.join(folder, "out_GSR.nc"))
shutil.copyfile(
os.path.join(name + ".conv", w, "t11", "outdata",
"out_SIGRES.nc"),
os.path.join(folder, "out_SIGRES.nc"))
else:
shutil.copyfile(
os.path.join(name + ".conv", w, "t9", "outdata",
"out_SIGRES.nc"),
os.path.join(folder, "out_SIGRES.nc"))
except (OSError, IOError): # compatibility issue
shutil.copyfile(
os.path.join(name + ".conv", "work_0", "task_6", "outdata",
"out_SIGRES.nc"),
os.path.join(folder, "out_SIGRES.nc"))
def test_SiC_conv(self):
"""
Testing a full convergence calculation cycle on SiC using precomupted data.
"""
# the current version uses refence data from a run using the production version on zenobe
# once all checks out the run should be done using the input generated using this version to replace the
# reference
wdir = tempfile.mkdtemp()
os.chdir(wdir)
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'] = '.psp8'
os.environ['ABINIT_PS'] = wdir
reference_dir = os.path.join(__reference_dir__, 'SiC_test_case')
if not os.path.isdir(reference_dir): raise RuntimeError('py.test needs to be started in the HTGW root, '
'%s does not exist' % __reference_dir__)
# copy input
print(wdir)
self.assertTrue(os.path.isdir(reference_dir))
src_files = os.listdir(reference_dir)
for file_name in src_files:
full_file_name = os.path.join(reference_dir, file_name)
if os.path.isfile(full_file_name):
shutil.copy(full_file_name, wdir)
self.assertEqual(len(os.listdir(wdir)), 6)
print(os.listdir(wdir))
structure = Structure.from_file('SiC.cif')
structure.item = 'SiC.cif'
print(' ==== generate flow === ')
gwsetup(update=False)
self.assertTrue(os.path.isdir(os.path.join(wdir, 'SiC_SiC.cif')))
print(os.listdir(os.path.join(wdir)))
print(os.listdir(os.path.join(wdir, 'SiC_SiC.cif')))
self.assertTrue(os.path.isfile(os.path.join(wdir, 'SiC_SiC.cif', '__AbinitFlow__.pickle')))
self.assertEqual(len(os.listdir(os.path.join(wdir, 'SiC_SiC.cif', 'w0'))), 48)
print(' ==== copy reference results from first calculation === ')
shutil.rmtree(os.path.join(wdir, 'SiC_SiC.cif'))
shutil.copytree(os.path.join(reference_dir, 'ref_res', 'SiC_SiC.cif'), os.path.join(wdir, 'SiC_SiC.cif'))
self.assertTrue(os.path.isdir(os.path.join(wdir, 'SiC_SiC.cif')))
self.assertEqual(len(os.listdir(os.path.join(wdir, 'SiC_SiC.cif', 'w0'))), 68)
print(' ==== process output === ')
gwoutput()
print(os.listdir('.'))
self.assertTrue(os.path.isfile('plot-fits'))
self.assertTrue(os.path.isfile('plots'))
self.assertEqual(is_converged(hartree_parameters=True, structure=structure, return_values=True),
{u'ecut': 44.0, u'ecuteps': 4.0, u'gap': 6.816130591466406, u'nbands': 60})
self.assertTrue(os.path.isfile('SiC_SiC.cif.full_res'))
print(' ==== generate next flow === ')
print(' version with bandstructure and dos ')
gwsetup(update=False)
self.assertTrue(os.path.isdir('SiC_SiC.cif.conv'))
print(os.listdir(os.path.join(wdir, 'SiC_SiC.cif.conv', 'w0')))
self.assertEqual(len(os.listdir(os.path.join(wdir, 'SiC_SiC.cif.conv', 'w0'))), 15)
print(' ==== copy reference from second flow === ')
time.sleep(1) # the .conv directory should be older than the first one
shutil.rmtree(os.path.join(wdir, 'SiC_SiC.cif.conv'))
shutil.copytree(os.path.join(reference_dir, 'ref_res', 'SiC_SiC.cif.conv'),
os.path.join(wdir, 'SiC_SiC.cif.conv'))
self.assertTrue(os.path.isdir(os.path.join(wdir, 'SiC_SiC.cif.conv')))
self.assertEqual(len(os.listdir(os.path.join(wdir, 'SiC_SiC.cif.conv', 'w0'))), 13)
print(' ==== process output === ')
backup = sys.stdout
sys.stdout = StringIO() # capture output
gwoutput()
out = sys.stdout.getvalue() # release output
sys.stdout.close() # close the stream
sys.stdout = backup # restore original stdout
print('=== *** ====\n'+out+'=== *** ====\n')
gap = 0
for l in out.split('\n'):
if 'values' in l:
gap = float(l.split(' ')[6])
self.assertEqual(gap, 7.114950664158926)
print(os.listdir('.'))
print('processed')
self.assertTrue(os.path.isfile('SiC_SiC.cif.full_res'))
full_res = read_grid_from_file(s_name(structure)+'.full_res')
self.assertEqual(full_res, {u'all_done': True, u'grid': 0})
self.assertTrue(os.path.isdir(os.path.join(wdir, 'SiC_SiC.cif.res')))
self.assertEqual(len(os.listdir(os.path.join(wdir, 'SiC_SiC.cif.res'))), 5)
print(os.listdir(os.path.join(wdir, 'SiC_SiC.cif.res')))
msrf = MySigResFile(os.path.join(wdir, 'SiC_SiC.cif.res', 'out_SIGRES.nc'))
self.assertEqual(msrf.h**o, 6.6843830378711786)
self.assertEqual(msrf.lumo, 8.0650328308487982)
self.assertEqual(msrf.homo_gw, 6.2325949743130034)
self.assertEqual(msrf.lumo_gw, 8.2504215095164763)
self.assertEqual(msrf.fundamental_gap('ks'), msrf.lumo - msrf.h**o)
self.assertEqual(msrf.fundamental_gap('gw'), msrf.lumo_gw - msrf.homo_gw)
self.assertAlmostEqual(msrf.fundamental_gap('gamma'), gap, places=3)
# since we now have a mysigresfile object we test the functionality
msrf.get_scissor()
# return self.qplist_spin[0].build_scissors(domains=[[-200, mid], [mid, 200]], k=1, plot=False)
res = msrf.get_scissor_residues()
self.assertEqual(res, [0.05322754684319431, 0.34320373172956475])
# return sc.residues
#msrf.plot_scissor(title='')
#msrf.plot_qpe(title='')
# to be continued
if temp_ABINIT_PS is not None:
os.environ['ABINIT_PS_EXT'] = temp_ABINIT_PS_EXT
os.environ['ABINIT_PS'] = temp_ABINIT_PS
def create(self):
"""
create single abinit G0W0 flow
"""
# manager = 'slurm' if 'ceci' in self.spec['mode'] else 'shell'
# an AbiStructure object has an overwritten version of get_sorted_structure that sorts according to Z
# this could also be pulled into the constructor of Abistructure
# abi_structure = self.structure.get_sorted_structure()
from abipy import abilab
item = copy.copy(self.structure.item)
self.structure.__class__ = abilab.Structure
self.structure = self.structure.get_sorted_structure_z()
self.structure.item = item
abi_structure = self.structure
manager = TaskManager.from_user_config()
# Initialize the flow.
flow = Flow(self.work_dir, manager, pickle_protocol=0)
# kpoint grid defined over density 40 > ~ 3 3 3
if self.spec['converge'] and not self.all_converged:
# (2x2x2) gamma centered mesh for the convergence test on nbands and ecuteps
# if kp_in is present in the specs a kp_in X kp_in x kp_in mesh is used for the convergence study
print('== here ===')
print(self.spec.__class__)
json.dumps(self.spec.data, indent=2)
if 'kp_in' in self.spec.data.keys():
if self.spec['kp_in'] > 9:
print(
'WARNING:\nkp_in should be < 13 to generate an n x n x n mesh\nfor larger values a grid with '
'density kp_in will be generated')
kppa = self.spec['kp_in']
else:
kppa = 2
else:
# use the specified density for the final calculation with the converged nbands and ecuteps of other
# stand alone calculations
kppa = self.spec['kp_grid_dens']
gamma = True
# 'standard' parameters for stand alone calculation
scf_nband = self.get_bands(self.structure) + 20
# additional bands to accommodate for nbdbuf and a bit extra
nscf_nband = [10 * self.get_bands(self.structure)]
nksmall = None
ecuteps = [8]
extra_abivars = dict()
# read user defined extra abivars from file 'extra_abivars' should be dictionary
extra_abivars.update(read_extra_abivars())
# self.bands_fac = 0.5 if 'gwcomp' in extra_abivars.keys() else 1
# self.convs['nscf_nbands']['test_range'] =
# tuple([self.bands_fac*x for x in self.convs['nscf_nbands']['test_range']])
ecut = extra_abivars.pop('ecut', 44)
ecutsigx = extra_abivars.pop('ecutsigx', 44)
# if npfft is too large or if npfft changes between the nscf calcualtion and the screening / sigma calulations
# strange things can happen
if 'npfft' not in extra_abivars:
extra_abivars['npfft'] = 3
if ecutsigx > ecut:
raise RuntimeError('ecutsigx can not be larger than ecut')
if ecutsigx < max(ecuteps):
raise RuntimeError('ecutsigx < ecuteps this is not realistic')
response_models = ['godby']
if 'ppmodel' in extra_abivars.keys():
response_models = [extra_abivars.pop('ppmodel')]
if self.option is not None:
for k in self.option.keys():
if k == 'ecut':
ecut = self.option[k]
if k in ['ecuteps', 'nscf_nbands']:
pass
else:
extra_abivars.update({k: self.option[k]})
try:
grid = read_grid_from_file(s_name(self.structure) +
".full_res")['grid']
all_done = read_grid_from_file(
s_name(self.structure) + ".full_res")['all_done']
workdir = os.path.join(s_name(self.structure), 'w' + str(grid))
except (IOError, OSError):
grid = 0
all_done = False
workdir = None
if not all_done:
if (self.spec['test']
or self.spec['converge']) and not self.all_converged:
if self.spec['test']:
print('| setting test calculation')
tests = SingleAbinitGWWork(self.structure, self.spec).tests
response_models = []
else:
if grid == 0:
print('| setting convergence calculations for grid 0')
# tests = SingleAbinitGWWorkFlow(self.structure, self.spec).convs
tests = self.convs
else:
print('| extending grid')
# tests = expand(SingleAbinitGWWorkFlow(self.structure, self.spec).convs, grid)
tests = expand(self.convs, grid)
ecuteps = []
nscf_nband = []
for test in tests:
if tests[test]['level'] == 'scf':
if self.option is None:
extra_abivars.update(
{test + '_s': tests[test]['test_range']})
elif test in self.option:
extra_abivars.update({test: self.option[test]})
else:
extra_abivars.update(
{test + '_s': tests[test]['test_range']})
else:
for value in tests[test]['test_range']:
if test == 'nscf_nbands':
nscf_nband.append(
value * self.get_bands(self.structure))
# scr_nband takes nscf_nbands if not specified
# sigma_nband takes scr_nbands if not specified
if test == 'ecuteps':
ecuteps.append(value)
if test == 'response_model':
response_models.append(value)
elif self.all_converged:
print(
'| setting up for testing the converged values at the high kp grid '
)
# add a bandstructure and dos calculation
if os.path.isfile('bands'):
nksmall = -30
# negative value > only bandstructure
else:
nksmall = 30
# in this case a convergence study has already been performed.
# The resulting parameters are passed as option
ecuteps = [
self.option['ecuteps'], self.option['ecuteps'] +
self.convs['ecuteps']['test_range'][1] -
self.convs['ecuteps']['test_range'][0]
]
nscf_nband = [
self.option['nscf_nbands'], self.option['nscf_nbands'] +
self.convs['nscf_nbands']['test_range'][1] -
self.convs['nscf_nbands']['test_range'][0]
]
# for option in self.option:
# if option not in ['ecuteps', 'nscf_nband']:
# extra_abivars.update({option + '_s': self.option[option]})
else:
print('| all is done for this material')
return
logger.info('ecuteps : %s ' % str(ecuteps))
logger.info('extra : %s ' % str(extra_abivars))
logger.info('nscf_nb : %s ' % str(nscf_nband))
inputs = g0w0_convergence_inputs(abi_structure,
self.pseudo_table,
kppa,
nscf_nband,
ecuteps,
ecutsigx,
scf_nband,
ecut,
accuracy="normal",
spin_mode="unpolarized",
smearing=None,
response_models=response_models,
charge=0.0,
gw_qprange=2,
gamma=gamma,
nksmall=nksmall,
extra_abivars=extra_abivars)
work = G0W0Work(scf_inputs=inputs[0],
nscf_inputs=inputs[1],
scr_inputs=inputs[2],
sigma_inputs=inputs[3])
# work = g0w0_extended_work(abi_structure, self.pseudo_table, kppa, nscf_nband, ecuteps, ecutsigx, scf_nband,
# accuracy="normal", spin_mode="unpolarized", smearing=None, response_models=response_models,
# charge=0.0, sigma_nband=None, scr_nband=None, gamma=gamma, nksmall=nksmall, **extra_abivars)
print(workdir)
flow.register_work(work, workdir=workdir)
return flow.allocate()
def execute_flow(self, structure, spec_data):
"""
execute spec prepare input/jobfiles or submit to fw for a given structure
for vasp the different jobs are created into a flow
todo this should actually create and execute a VaspGWWorkFlow(GWWorkflow)
"""
# general part for the base class
grid = 0
all_done = False
converged = is_converged(False, structure)
try:
grid = read_grid_from_file(s_name(structure) + ".full_res")['grid']
all_done = read_grid_from_file(s_name(structure) +
".full_res")['all_done']
except (IOError, OSError):
pass
if all_done:
print('| all is done for this material')
return
# specific part
if spec_data['mode'] == 'fw':
fw_work_flow = VaspGWFWWorkFlow()
else:
fw_work_flow = []
if spec_data['test'] or spec_data['converge']:
if spec_data['test']:
tests_prep = GWscDFTPrepVaspInputSet(structure,
spec_data).tests
tests_prep.update(
GWDFTDiagVaspInputSet(structure, spec_data).tests)
elif spec_data['converge'] and converged:
tests_prep = self.get_conv_res_test(spec_data,
structure)['tests_prep']
else:
tests_prep = GWscDFTPrepVaspInputSet(structure,
spec_data).convs
tests_prep.update(
GWDFTDiagVaspInputSet(structure, spec_data).convs)
if grid > 0:
tests_prep = expand(tests=tests_prep, level=grid)
print(tests_prep)
for test_prep in tests_prep:
print('setting up test for: ' + test_prep)
for value_prep in tests_prep[test_prep]['test_range']:
print("**" + str(value_prep) + "**")
option = {'test_prep': test_prep, 'value_prep': value_prep}
self.create_job(spec_data, structure, 'prep', fw_work_flow,
converged, option)
for job in spec_data['jobs'][1:]:
if job == 'G0W0':
if spec_data['test']:
tests = GWG0W0VaspInputSet(
structure, spec_data).tests
elif spec_data['converge'] and converged:
tests = self.get_conv_res_test(
spec_data, structure)['tests']
else:
tests = GWG0W0VaspInputSet(
structure, spec_data).convs
if grid > 0:
tests = expand(tests=tests, level=grid)
print(tests)
if job in ['GW0', 'scGW0']:
input_set = GWG0W0VaspInputSet(
structure, spec_data)
input_set.gw0_on()
if spec_data['test']:
tests = input_set.tests
else:
tests = input_set.tests
for test in tests:
print(' setting up test for: ' + test)
for value in tests[test]['test_range']:
print(" **" + str(value) + "**")
option.update({'test': test, 'value': value})
self.create_job(spec_data, structure, job,
fw_work_flow, converged,
option)