def test_skparplot(self):
"""Can we plot a band-structure objectives?"""
env = {}
database = Database()
latticeinfo = {'type': 'FCC', 'param': 5.4315}
model = 'Si.bs'
filename = '_workdir/test_plot/bs1.pdf'
get_bandstructure(env,
database,
'test_dftbutils/Si/bs/',
model,
latticeinfo=latticeinfo)
modeldb = database.get(model)
bands = modeldb['bands']
eps = 0.25
jitter = eps * (0.5 - random(bands.shape))
altbands = bands + jitter
if os.path.exists(filename):
os.remove(filename)
else:
os.makedirs('_workdir/test_plot', exist_ok=True)
skparplot(modeldb['kvector'], [altbands, bands],
filename=filename,
xticklabels=modeldb['kticklabels'],
xlabel='wave-vector',
ylabel='Energy, eV',
linelabels=['ref', 'model'],
ylim=(-13, 6))
self.assertTrue(os.path.exists(filename))
def test_get_special_Ek_options(self):
"""Get E(k) for explicitly given, and multiple bands"""
env = {}
database = Database()
model = 'test.Ek'
src = 'test_dftbutils/Si/bs'
get_bandstructure(env,
database,
src,
model,
latticeinfo={
'type': 'FCC',
'param': 5.431
})
dst = database.get(model)
get_special_Ek(env,
database,
model,
model,
sympts=['K', 'L'],
extract={
'cb': [0, 2, 4, 6],
'vb': [0, 2, 4, 6]
})
self.assertAlmostEqual(dst['Ec_L_4'], 2.8089, places=3)
self.assertAlmostEqual(dst['Ec_L_0'], 0.3995, places=3)
self.assertAlmostEqual(dst['Ec_K_0'], 0.6915, places=3)
#
self.assertAlmostEqual(dst['Ev_L_0'], -2.5016, places=3)
self.assertAlmostEqual(dst['Ev_L_4'], -7.842, places=3)
self.assertAlmostEqual(dst['Ev_L_6'], -11.3369, places=3)
self.assertAlmostEqual(dst['Ev_K_0'], -3.5884, places=3)
self.assertAlmostEqual(dst['Ev_K_2'], -4.963, places=3)
self.assertAlmostEqual(dst['Ev_K_4'], -8.694, places=3)
self.assertAlmostEqual(dst['Ev_K_6'], -9.8759, places=3)
def test_get_special_Ek(self):
"""Get E(k) for k obtained from the kLines"""
env = {}
database = Database()
model = 'test.Ek'
src = 'test_dftbutils/Si/bs'
get_bandstructure(env,
database,
src,
model,
latticeinfo={
'type': 'FCC',
'param': 5.431
})
dst = database.get(model)
get_special_Ek(env, database, model, model)
self.assertAlmostEqual(dst['Ec_L_0'], 0.4, places=3)
self.assertAlmostEqual(dst['Ec_G_0'], 1.616, places=3)
self.assertAlmostEqual(dst['Ec_X_0'], 0.2025, places=3)
self.assertAlmostEqual(dst['Ec_U_0'], 0.6915, places=3)
self.assertAlmostEqual(dst['Ec_K_0'], 0.6915, places=3)
#
self.assertAlmostEqual(dst['Ev_L_0'], -2.5016, places=3)
self.assertAlmostEqual(dst['Ev_G_0'], -1.1289, places=3)
self.assertAlmostEqual(dst['Ev_X_0'], -3.9592, places=3)
self.assertAlmostEqual(dst['Ev_U_0'], -3.5885, places=3)
self.assertAlmostEqual(dst['Ev_K_0'], -3.5885, places=3)
def test_get_bandstructure(self):
"""Can we get the bandstructure and gap/cb/vb details?"""
env = {}
database = Database()
src = 'test_dftbutils/bs'
dst = 'test.bs'
get_bandstructure(env, database, src, dst)
modeldict = database.get(dst)
nptest.assert_array_almost_equal(modeldict['bands'], self.ref_bands)
self.assertEqual(modeldict['nkpts'], self.ref_nk)
self.assertEqual(modeldict['nbands'], self.ref_nb)
self.assertEqual(modeldict['Ef'], self.ref_Ef)
self.assertEqual(modeldict['Egap'], self.ref_Eg)
self.assertEqual(modeldict['Ecb'], self.ref_Ec)
self.assertEqual(modeldict['Evb'], self.ref_Ev)
def test_get_kvec_abscissa2(self):
"""Can we get the bandstructure and extract the kvector info"""
latticeinfo = {'type': 'FCC', 'param': 1.}
lat = Lattice(latticeinfo)
database = Database()
src = 'test_dftbutils/bs'
get_bandstructure({'workroot': '.'}, database, src, 'test', latticeinfo=latticeinfo)
kLines = database.get_item('test', 'kLines')
bands = database.get_item('test', 'bands')
logger.debug('Bands.shape: {}'.format(bands.shape))
logger.debug('kLines : {}'.format(kLines))
xx, xt, xl = get_kvec_abscissa(lat, kLines)
refxl = ['X', 'Γ', 'K', 'L', 'Γ']
refxt = [0, 6.28319, 12.94751, 16.79516, 22.23656]
self.assertListEqual(xl, refxl)
nptest.assert_almost_equal(xt, refxt, 5)
self.assertAlmostEqual(xx[-1], xt[-1])
self.assertEqual(len(xx), kLines[-1][-1]+1)
def test_get_effmasses_default(self):
"""Can we get effective masses in addition to band-structure, with default settings?"""
env = {}
database = Database()
src = 'test_dftbutils/Si/bs'
model = 'test.meff'
get_bandstructure(env,
database,
src,
model,
latticeinfo={
'type': 'FCC',
'param': 5.431
})
dst = database.get(model)
# the values below are in oldskpar.debug.log in the above dir
self.assertTrue(dst['withSOC'])
self.assertEqual(dst['ivbtop'], 7)
self.assertEqual(dst['nkpts'], 206)
self.assertEqual(dst['nbands'], 36)
self.assertAlmostEqual(dst['Ef'], -3.0621, places=3)
self.assertAlmostEqual(dst['Egap'], 1.1289, places=3)
self.assertAlmostEqual(dst['Ecb'], -3.06221, places=3)
self.assertAlmostEqual(dst['Evb'], -4.19099, places=3)
#
ref_klines = [('L', 0), ('Gamma', 53), ('X', 113), ('U', 141),
('K', 142), ('Gamma', 205)]
ref_klinesdict = {
'K': [142],
'X': [113],
'Gamma': [53, 205],
'L': [0],
'U': [141]
}
self.assertListEqual(dst['kLines'], ref_klines)
self.assertDictEqual(dst['kLinesDict'], ref_klinesdict)
get_effmasses(env, database, model, model)
ref_meff_tags = ['me_LG', 'me_GX', 'me_XU', 'me_KG']
ref_meff_tags.extend(['mh_LG', 'mh_GX', 'mh_XU', 'mh_KG'])
self.assertTrue(all([key in dst for key in ref_meff_tags]))
def main_bands(args):
"""
Chain the relevant tasks for obtaining band-structure and execute.
"""
# setup logger
# -------------------------------------------------------------------
loglevel = logging.DEBUG if args.verbose else logging.INFO
logger = get_logger(name='dftbutils',
filename='dftbutils.bands.log',
verbosity=loglevel)
#logger.info(args)
# deal with bands-specific arguments if any
# --------------------------------------------------
workroot = '.'
workdir = abspath(expanduser(args.workdir))
sccdir = abspath(joinpath(workdir, 'scc'))
sccchg = abspath(joinpath(sccdir, 'charges.bin'))
bsdir = abspath(joinpath(workdir, 'bs'))
dftb = args.dftb
dftblog = 'dftb.log'
bands = args.bands
if args.dos:
dos = args.dos
bandslog = 'dp_bands.log'
if not args.plot_only:
# Execute the necessary commands
# scc calculation
execute(cmd=dftb, workdir=sccdir, outfile=dftblog)
# check log
execute(cmd=['check_dftblog', dftblog],
workdir=sccdir,
outfile='chk.log')
# extract dos for plotting
if args.dos:
execute(cmd=[dos, 'band.out', 'dos_total.dat'],
workdir=sccdir,
outfile=bandslog)
# copy charges for klines calculation
execute(cmd=['cp', '-f', sccchg, bsdir], workdir='.', outfile=None)
# klines calculation
execute(cmd=dftb, workdir=bsdir, outfile=dftblog)
# check log
execute(cmd=['check_dftblog', dftblog],
workdir=sccdir,
outfile='chk.log')
# extract bands for plotting
execute(cmd=[bands, 'band.out', 'bands'],
workdir=bsdir,
outfile=bandslog)
if args.plot or args.plot_only:
# hack the plotting directly, not via tasks, to avoid needing objectives
database = {}
implargs = {'workroot': workroot}
get_bandstructure(implargs,
database,
bsdir,
'dftb',
latticeinfo=args.latticeinfo)
bsdata = database.get('dftb')
logger.info('Band-gap (eV) = {:.3f}'.format(bsdata['Egap']))
yy1 = bsdata['bands'] - bsdata['Evb']
if args.latticeinfo:
xx1 = bsdata['kvector']
xtl = bsdata['kticklabels']
else:
xx1 = np.asarray(range(yy1.shape[1]))
xtl = None
filename = os.path.join(workroot, workdir, 'bs.pdf')
plot_bs(xx1, yy1, filename=filename, ylim=args.ylim, xticklabels=xtl)
def test_get_effmasses_select(self):
"""Can we get select effective masses with a control options?"""
env = {}
database = Database()
model = 'test.meff'
# NOTABENE: the refdata here is from SOC calculation!!!
src = 'test_dftbutils/Si/bs'
get_bandstructure(env,
database,
src,
model,
latticeinfo={
'type': 'FCC',
'param': 5.431
})
dst = database.get(model)
directions = ['Gamma-X', 'Gamma-L', 'Gamma-K']
# Example how to extract different masses over a different energy window:
# Note that subsequent extractions overwrite final data in dst, so we start with
# the deepest bands, and than reduce the number of bands, towards to top of VB
# The energy window should be adjusted depending on the anticipated curvature of the band
get_effmasses(env,
database,
model,
model,
directions=directions,
carriers='e',
nb=1,
Erange=0.005,
usebandindex=True)
# get the lowest band masses: (spin-orbit); forceErange seems to not work properly?
get_effmasses(env,
database,
model,
model,
directions=directions,
carriers='h',
nb=5,
Erange=0.0015,
forceErange=True)
# get the light hole bands (3 and 4)
get_effmasses(env,
database,
model,
model,
directions=directions,
carriers='h',
nb=3,
Erange=0.008)
# get the top two (heavy hole) bands (1 and 2); enforce indexing! (i.e. add _0)
get_effmasses(env,
database,
model,
model,
directions=directions,
carriers='h',
nb=1,
Erange=0.002,
usebandindex=True)
self.assertAlmostEqual(dst['me_GX_0'], 0.935, places=3)
self.assertAlmostEqual(dst['mh_GX_0'], -0.278, places=2)
self.assertAlmostEqual(dst['mh_GK_0'], -1.891, places=3)
self.assertAlmostEqual(dst['mh_GL_0'], -0.633, places=3)
self.assertAlmostEqual(dst['mh_GX_2'], -0.286, places=3)
self.assertAlmostEqual(dst['mh_GK_2'], -0.362, places=3)
self.assertAlmostEqual(dst['mh_GL_2'], -2.2426, places=3)
self.assertAlmostEqual(dst['mh_GX_4'], -0.1389, places=3)
self.assertAlmostEqual(dst['mh_GK_4'], -0.095, places=3)
self.assertAlmostEqual(dst['mh_GL_4'], -0.086, places=3)
self.assertAlmostEqual(dst['cbminpos_GX_0'], 0.817, places=2)