def fundamental_gaps(self, query=None, sort='system'):
"""
print the gap info for all the systems in the database
:param query:
:param sort: default sort per system
:return:
"""
mp_key = os.environ['MP_KEY']
if query is None:
query = {}
for item in self.col.find(query).sort(sort):
print('')
print('System : ', item['system'].split('_')[0])
print('Ps : ', item['ps'])
print('extra : ', item['extra_vars'])
print('gwresults : ', item['gw_results'])
print('item : ', item['item'])
if 'mp-' in item['item']:
try:
with MPRester(mp_key) as mp_database:
gap = {}
bandstructure = mp_database.get_bandstructure_by_material_id(
item['item'])
gap['vbm_l'] = bandstructure.kpoints[
bandstructure.get_vbm()['kpoint_index'][0]].label
gap['cbm_l'] = bandstructure.kpoints[
bandstructure.get_cbm()['kpoint_index'][0]].label
gap['vbm_e'] = bandstructure.get_vbm()['energy']
gap['cbm_e'] = bandstructure.get_cbm()['energy']
gap['cbm'] = tuple(
bandstructure.kpoints[bandstructure.get_cbm(
)['kpoint_index'][0]].frac_coords)
gap['vbm'] = tuple(
bandstructure.kpoints[bandstructure.get_vbm(
)['kpoint_index'][0]].frac_coords)
except (MPRestError, IndexError, KeyError) as err:
print(err.message)
gap = None
else:
gap = None
if gap:
print(gap['cbm_l'], gap['vbm_l'])
print(gap['cbm'], gap['vbm'])
try:
data = self.gfs.get(item['results_file']).read()
if len(data) > 1000:
srf = MySigResFile(data)
srf.print_gap_info()
except IOError:
print('No Sigres file in DataBase')
def sigres_plots(self, query=None, sort='system'):
"""
Plot the scissor operators for all the systems in the DB
:param query:
:param sort:
:return:
"""
if query is None:
query = {}
for item in self.col.find(query).sort(sort):
print('System : ', item['system'].split('_')[0])
print('Ps : ', item['ps'])
print('extra : ', item['extra_vars'])
print('gwresults : ', item['gw_results'])
try:
print('data : ', item['results_file'])
data = self.gfs.get(item['results_file']).read()
if len(data) > 1000:
srf = MySigResFile(data)
title = "QPState corrections of " + str(item['system']) + "\nusing "\
+ str(item['ps'].split('/')[-2])
if item['extra_vars'] is not None:
title += ' and ' + str(
self.fix_extra(item['extra_vars']))
fig = srf.plot_scissor(title=title)
srf.print_gap_info()
sc = srf.get_scissor()
try:
if not item['tgwgap']:
bands_data = self.gfs.get(item['ksbands_file'])
ks_bands = MyBandsFile(bands_data)
item['tkshomo'] = ks_bands.h**o
item['tkslumo'] = ks_bands.lumo
item['tksgap'] = ks_bands.lumo - ks_bands.h**o
item['tgwhomo'] = ks_bands.h**o + sc.apply(
ks_bands.h**o)
item['tgwlumo'] = ks_bands.lumo + sc.apply(
ks_bands.lumo)
item['tgwgap'] = item['tgwlumo'] - item['tgwhomo']
self.col.save(item)
except KeyError:
pass
except IOError:
print('No Sigres file in DataBase')
try:
return fig
except UnboundLocalError:
return None
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 band_plots(self, query=None, sort='system'):
"""
Plot the scissored bands for all the systems in the DB
:param query:
:param sort:
:return:
"""
if query is None:
query = {}
for item in self.col.find(query).sort(sort):
exclude = ['ZnO_mp-2133', 'K3Sb_mp-14017', 'NiP2_mp-486', 'OsS2_mp-20905', 'PbO_mp-1336', 'Rb3Sb_mp-16319',
'As2Os_mp-2455']
if item['system'] in exclude:
continue
if False:
print('System : ', item['system'].split('_mp-')[0])
print('Ps : ', item['ps'])
print('extra : ', item['extra_vars'])
print('gwresults : ', item['gw_results'])
try:
data = self.gfs.get(item['results_file']).read()
if len(data) > 1000:
srf = MySigResFile(data)
title = "QPState corrections of " + str(item['system']) + "\nusing " \
+ str(item['ps'].split('/')[-2])
if item['extra_vars'] is not None:
title += ' and ' + str(self.fix_extra(item['extra_vars']))
srf.plot_scissor(title=title)
srf.print_gap_info()
sc = srf.get_scissor()
with self.gfs.get(item['ksbands_file']) as f:
ksb = MyBandsFile(f.read()).ebands
qpb = ksb.apply_scissors(sc)
# Plot the LDA and the QPState band structure with matplotlib.
plotter = ElectronBandsPlotter()
plotter.add_ebands("KS", ksb)
plotter.add_ebands("KS+scissors(e)", qpb)
fig = plotter.plot(align='cbm', ylim=(-5, 10), title="%s Bandstructure" %
item['system'].split('_mp-')[0])
try:
if not item['tgwgap']:
bands_data = self.gfs.get(item['ksbands_file'])
ks_bands = MyBandsFile(bands_data)
item['tkshomo'] = ks_bands.h**o
item['tkslumo'] = ks_bands.lumo
item['tksgap'] = ks_bands.lumo - ks_bands.h**o
item['tgwhomo'] = ks_bands.h**o + sc.apply(ks_bands.h**o)
item['tgwlumo'] = ks_bands.lumo + sc.apply(ks_bands.lumo)
item['tgwgap'] = item['tgwlumo'] - item['tgwhomo']
self.col.save(item)
except KeyError:
pass
except (KeyError, IOError, NoFile):
print('No Sigres file in DataBase')
try:
return fig
except UnboundLocalError:
return None
def get_data_set(self, query=None, sigresdata=False, update=False):
"""
method to retrieve a data set from database
"""
self.data_set = []
if sigresdata:
print('may need to parse nc files, this may take some time')
if query is None:
query = {}
for item in self.col.find(query):
try:
mpid = item['system'].split('_mp-')[1]
except IndexError:
mpid = 0
try:
entry = {'system': item['system'].split('_mp-')[0],
'id': "mp-%s" % mpid,
'ps': item['ps'].split('/')[-2],
'xc': item['spec']['functional'],
'kp_in': item['spec'].get('kp_in', None),
'extra': self.fix_extra(item['extra_vars']),
'data': item['gw_results']}
print("id: %s" % entry['id'])
mp_id = entry['id'].split('mp-')[1]
try:
for exp_result in self.col_external.exp.find({'MP_id': str(mp_id)}):
expgap = exp_result['band_gap']
icsd = exp_result['icsd_data']['icsd_id']
entry['expgap'] = expgap
for pbe_result in self.col_external.GGA_BS.find({'transformations.history.0.id': icsd}):
pbegap = pbe_result['analysis']['bandgap']
entry['pbegap'] = pbegap
except:
print(str(mp_id))
expgap = None
icsd = None
pbegap = None
if sigresdata:
try:
if update:
raise KeyError
if 'max_en' not in item['srf_data'].keys():
raise KeyError
entry['data'].update(item['srf_data'])
sys.stdout.write(".")
sys.stdout.flush()
except KeyError:
sys.stdout.write(":")
sys.stdout.flush()
try:
print('getting srfdata')
srf = MySigResFile(self.gfs.get(item['results_file']).read())
srf_data = {'gwfgap': srf.fundamental_gap('gw'),
'ksfgap': srf.fundamental_gap('ks'),
'gwggap': srf.fundamental_gap('gamma'),
'gwhomo': srf.homo_gw,
'kshomo': srf.h**o,
'gwlumo': srf.lumo_gw,
'kslumo': srf.lumo,
'max_en': srf.en_max_band,
'scissor_residues': srf.scissor_residues}
entry['data'].update(srf_data)
except: # (IOError, OSError, NetcdfReaderError):
srf_data = {'gwfgap': 0,
'ksfgap': 0,
'gwhomo': 0,
'kshomo': 0,
'gwlumo': 0,
'kslumo': 0,
'max_en': 0,
'scissor_residues': [0, 0]}
entry['data'].update(srf_data)
item['srf_data'] = srf_data
self.col.save(item)
if item['system'] not in []:
print('bands for', item['system'])
try:
if item['bs_data']['gwbgap'] is None:
raise KeyError
entry['data'].update(item['bs_data'])
sys.stdout.write(".")
sys.stdout.flush()
except KeyError:
try:
t0 = time.time()
if item['system'] in ['As2Os_mp-2455', 'AgI_mp-22894', 'PbO_mp-20878', 'Cu2O_mp-361']:
raise KeyError
with self.gfs.get(item['ksbands_file']) as f:
ksb = MyBandsFile(f.read())
t = time.time() - t0
print('reading bands : %s' % t)
t0 = time.time()
with self.gfs.get(item['results_file']) as g:
srf = MySigResFile(g.read())
t = time.time() - t0
print('reading srf : %s' % t)
t0 = time.time()
scissor = srf.get_scissor()
gwbhomo = ksb.h**o + scissor.apply(ksb.h**o)
gwblumo = ksb.lumo + scissor.apply(ksb.lumo)
bs_data = {'ksbgap': ksb.lumo - ksb.h**o,
'ksbhomo': ksb.h**o,
'gwbhomo': gwbhomo,
'ksblumo': ksb.lumo,
'gwblumo': gwblumo,
'gwbgap': gwblumo - gwbhomo}
entry['data'].update(bs_data)
t = time.time() - t0
print('making updating : %s' % t)
print('got ksbandsdata')
except (NoFile, KeyError, ValueError, KeyboardInterrupt):
print('failed getting ksbandsdata')
bs_data = {'ksbgap': None,
'ksbhomo': None,
'gwbhomo': None,
'gwblumo': None,
'ksblumo': None,
'gwbgap': None}
item['bs_data'] = bs_data
self.col.save(item)
self.data_set.append(entry)
except CursorNotFound:
print('cursonotfound')
print('\n')