def get_kpt_labels(self, bs):
bsplot = BSPlotter(bs)
## get unique K-points
labels = bsplot.get_ticks()["label"]
labelspos = bsplot.get_ticks()["distance"]
labels_uniq = [labels[0]]
labelspos_uniq = [labelspos[0]]
for i in range(1, len(labels)):
if labels[i] != labels[i - 1]:
labels_uniq.append(labels[i])
labelspos_uniq.append(labelspos[i])
labels_uniq = [label.replace("$\mid$", "|") for label in labels_uniq]
## hack for dash which can't display latex :(
labels_uniq = [label.replace("$\Gamma$", u"\u0393") for label in labels_uniq]
return labels_uniq, labelspos_uniq
dosplotter = DosPlotter()
Totaldos = dosplotter.add_dos('Total DOS', tdos)
Integrateddos = dosplotter.add_dos('Integrated DOS', idos)
#Pdos = dosplotter.add_dos('Partial DOS',pdos)
#Spd_dos = dosplotter.add_dos('spd DOS',spd_dos)
#Element_dos = dosplotter.add_dos('Element DOS',element_dos)
#Element_spd_dos = dosplotter.add_dos('Element_spd DOS',element_spd_dos)
dos_dict = {
'Total DOS': tdos,
'Integrated DOS': idos
} #'Partial DOS':pdos,'spd DOS':spd_dos,'Element DOS':element_dos}#'Element_spd DOS':element_spd_dos
add_dos_dict = dosplotter.add_dos_dict(dos_dict)
get_dos_dict = dosplotter.get_dos_dict()
dos_plot = dosplotter.get_plot()
##dosplotter.save_plot("MAPbI3_dos",img_format="png")
##dos_plot.show()
bsplotter = BSPlotter(bs)
bs_plot_data = bsplotter.bs_plot_data()
bs_plot = bsplotter.get_plot()
#bsplotter.save_plot("MAPbI3_bs",img_format="png")
#bsplotter.show()
ticks = bsplotter.get_ticks()
print ticks
bsplotter.plot_brillouin()
bsdos = BSDOSPlotter(
tick_fontsize=10,
egrid_interval=20,
dos_projection="orbitals",
bs_legend=None) #bs_projection="HPbCIN",dos_projection="HPbCIN")
bds = bsdos.get_plot(bs, cdos)
def projected_band_structure():
step_count=1
filename='vasprun.xml'
check_file(filename)
proc_str="Reading Data From "+ filename +" File ..."
procs(proc_str,step_count,sp='-->>')
vsr=Vasprun(filename)
filename='PROCAR'
check_file(filename)
step_count+=1
proc_str="Reading Data From "+ filename +" File ..."
procs(proc_str,step_count,sp='-->>')
procar=Procar(filename)
nbands=procar.nbands
nions=procar.nions
norbitals=len(procar.orbitals)
nkpoints=procar.nkpoints
step_count+=1
filename='KPOINTS'
check_file(filename)
proc_str="Reading Data From "+ filename +" File ..."
procs(proc_str,step_count,sp='-->>')
bands = vsr.get_band_structure(filename, line_mode=True, efermi=vsr.efermi)
struct=vsr.final_structure
(atom_index,in_str)=atom_selection(struct)
if len(atom_index)==0:
print("No atoms selected!")
return
# print(atom_index)
if vsr.is_spin:
proc_str="This Is a Spin-polarized Calculation."
procs(proc_str,0,sp='-->>')
ISPIN=2
contrib=np.zeros((nkpoints,nbands,norbitals,2))
for i in atom_index:
contrib[:,:,:,0]=contrib[:,:,:,0]+procar.data[Spin.up][:,:,i,:]
contrib[:,:,:,1]=contrib[:,:,:,1]+procar.data[Spin.down][:,:,i,:]
for ispin in range(2):
proj_band=contrib[:,:,:,ispin].reshape(nkpoints*nbands,norbitals)
step_count+=1
if ispin==0:
filename="PBAND_Up.dat"
else:
filename="PBAND_Down.dat"
proc_str="Writting Projected Band Structure Data to "+ filename +" File ..."
procs(proc_str,step_count,sp='-->>')
band_data=bands.bands[Spin.up]
y_data=band_data.reshape(1,nbands*nkpoints)[0]-vsr.efermi #shift fermi level to 0
x_data=np.array(bands.distance*nbands)
data=np.vstack((x_data,y_data,proj_band.T)).T
tmp1_str="#%(key1)+12s%(key2)+12s"
tmp2_dic={'key1':'K-Distance','key2':'Energy(ev)'}
for i in range(norbitals):
tmp1_str+="%(key"+str(i+3)+")+12s"
tmp2_dic["key"+str(i+3)]=procar.orbitals[i]
# print(tmp1_str)
atom_index_str=[str(x+1) for x in atom_index]
head_line1="#String: "+in_str+'\n#Selected atom: ' +' '.join(atom_index_str)+'\n'
head_line2=tmp1_str % tmp2_dic
head_line=head_line1+head_line2
write_col_data(filename,data,head_line,nkpoints)
else:
if vsr.parameters['LNONCOLLINEAR']:
proc_str="This Is a Non-Collinear Calculation."
procs(proc_str,0,sp='-->>')
ISPIN=3
else:
proc_str="This Is a Non-Spin Calculation."
procs(proc_str,0,sp='-->>')
ISPIN=1
contrib=np.zeros((nkpoints,nbands,norbitals))
for i in atom_index:
contrib[:,:,:]=contrib[:,:,:]+procar.data[Spin.up][:,:,i,:]
proj_band=contrib.reshape(nkpoints*nbands,norbitals)
step_count+=1
filename="PBAND.dat"
proc_str="Writting Projected Band Structure Data to "+ filename +" File ..."
procs(proc_str,step_count,sp='-->>')
band_data=bands.bands[Spin.up]
y_data=band_data.reshape(1,nbands*nkpoints)[0]-vsr.efermi #shift fermi level to 0
x_data=np.array(bands.distance*nbands)
data=np.vstack((x_data,y_data,proj_band.T)).T
tmp1_str="#%(key1)+12s%(key2)+12s"
tmp2_dic={'key1':'K-Distance','key2':'Energy(ev)'}
for i in range(norbitals):
tmp1_str+="%(key"+str(i+3)+")+12s"
tmp2_dic["key"+str(i+3)]=procar.orbitals[i]
# print(tmp1_str)
atom_index_str=[str(x+1) for x in atom_index]
head_line1="#String: "+in_str+'\n#Selected atom: ' +' '.join(atom_index_str)+'\n'
head_line2=tmp1_str % tmp2_dic
head_line=head_line1+head_line2
write_col_data(filename,data,head_line,nkpoints)
step_count+=1
bsp=BSPlotter(bands)
filename="HighSymmetricPoints.dat"
proc_str="Writting Label infomation to "+ filename +" File ..."
procs(proc_str,step_count,sp='-->>')
head_line="#%(key1)+12s%(key2)+12s%(key3)+12s"%{'key1':'index','key2':'label','key3':'position'}
line=head_line+'\n'
for i,label in enumerate(bsp.get_ticks()['label']):
new_line="%(key1)12d%(key2)+12s%(key3)12f\n"%{'key1':i,'key2':label,'key3':bsp.get_ticks()['distance'][i]}
line+=new_line
write_col_data(filename,line,'',str_data=True)
def band_structure():
check_matplotlib()
step_count=1
filename='vasprun.xml'
check_file(filename)
proc_str="Reading Data From "+ filename +" File ..."
procs(proc_str,step_count,sp='-->>')
vsr=Vasprun(filename)
step_count+=1
filename='KPOINTS'
check_file(filename)
proc_str="Reading Data From "+ filename +" File ..."
procs(proc_str,step_count,sp='-->>')
bands = vsr.get_band_structure(filename, line_mode=True, efermi=vsr.efermi)
step_count+=1
filename='OUTCAR'
check_file(filename)
proc_str="Reading Data From "+ filename +" File ..."
procs(proc_str,step_count,sp='-->>')
outcar=Outcar('OUTCAR')
mag=outcar.as_dict()['total_magnetization']
if vsr.is_spin:
proc_str="This Is a Spin-polarized Calculation."
procs(proc_str,0,sp='-->>')
tdos=vsr.tdos
SpinUp_gap=tdos.get_gap(spin=Spin.up)
cbm_vbm_up=tdos.get_cbm_vbm(spin=Spin.up)
SpinDown_gap=tdos.get_gap(spin=Spin.down)
cbm_vbm_down=tdos.get_cbm_vbm(spin=Spin.up)
if SpinUp_gap > min_gap and SpinDown_gap > min_gap:
is_metal=False
is_semimetal=False
elif SpinUp_gap > min_gap and SpinDown_gap < min_gap:
is_metal=False
is_semimetal=True
elif SpinUp_gap < min_gap and SpinDown_gap > min_gap:
is_metal=False
is_semimetal=True
elif SpinUp_gap < min_gap and SpinDown_gap < min_gap:
is_metal=True
is_semimetal=False
if is_metal:
proc_str="This Material Is a Metal."
procs(proc_str,0,sp='-->>')
if not is_metal and is_semimetal:
proc_str="This Material Is a Semimetal."
procs(proc_str,0,sp='-->>')
else:
proc_str="This Material Is a Semiconductor."
procs(proc_str,0,sp='-->>')
proc_str="Total magnetization is "+str(mag)
procs(proc_str,0,sp='-->>')
if mag > min_mag:
proc_str="SpinUp : vbm=%f eV cbm=%f eV gap=%f eV"%(cbm_vbm_up[1],cbm_vbm_up[0],SpinUp_gap)
procs(proc_str,0,sp='-->>')
proc_str="SpinDown: vbm=%f eV cbm=%f eV gap=%f eV"%(cbm_vbm_down[1],cbm_vbm_down[0],SpinUp_gap)
procs(proc_str,0,sp='-->>')
else:
proc_str="SpinUp : vbm=%f eV cbm=%f eV gap=%f eV"%(cbm_vbm_up[1],cbm_vbm_up[0],SpinUp_gap)
procs(proc_str,0,sp='-->>')
step_count+=1
filename="BAND.dat"
proc_str="Writting Band Structure Data to "+ filename +" File ..."
procs(proc_str,step_count,sp='-->>')
band_data_up=bands.bands[Spin.up]
band_data_down=bands.bands[Spin.down]
y_data_up=band_data_up.reshape(1,band_data_up.shape[0]*band_data_up.shape[1])[0]-vsr.efermi #shift fermi level to 0
y_data_down=band_data_down.reshape(1,band_data_down.shape[0]*band_data_down.shape[1])[0]-vsr.efermi #shift fermi level to 0
x_data=np.array(bands.distance*band_data_up.shape[0])
data=np.vstack((x_data,y_data_up,y_data_down)).T
head_line="#%(key1)+12s%(key2)+13s%(key3)+15s"%{'key1':'K-Distance','key2':'UpEnergy(ev)','key3':'DownEnergy(ev)'}
write_col_data(filename,data,head_line,band_data_up.shape[1])
else:
if vsr.parameters['LNONCOLLINEAR']:
proc_str="This Is a Non-Collinear Calculation."
else:
proc_str="This Is a Non-Spin Calculation."
procs(proc_str,0,sp='-->>')
cbm=bands.get_cbm()['energy']
vbm=bands.get_vbm()['energy']
gap=bands.get_band_gap()['energy']
if not bands.is_metal():
proc_str="This Material Is a Semiconductor."
procs(proc_str,0,sp='-->>')
proc_str="vbm=%f eV cbm=%f eV gap=%f eV"%(vbm,cbm,gap)
procs(proc_str,0,sp='-->>')
else:
proc_str="This Material Is a Metal."
procs(proc_str,0,sp='-->>')
step_count+=1
filename3="BAND.dat"
proc_str="Writting Band Structure Data to "+ filename3 +" File ..."
procs(proc_str,step_count,sp='-->>')
band_data=bands.bands[Spin.up]
y_data=band_data.reshape(1,band_data.shape[0]*band_data.shape[1])[0]-vsr.efermi #shift fermi level to 0
x_data=np.array(bands.distance*band_data.shape[0])
data=np.vstack((x_data,y_data)).T
head_line="#%(key1)+12s%(key2)+13s"%{'key1':'K-Distance','key2':'Energy(ev)'}
write_col_data(filename3,data,head_line,band_data.shape[1])
step_count+=1
bsp=BSPlotter(bands)
filename4="HighSymmetricPoints.dat"
proc_str="Writting Label infomation to "+ filename4 +" File ..."
procs(proc_str,step_count,sp='-->>')
head_line="#%(key1)+12s%(key2)+12s%(key3)+12s"%{'key1':'index','key2':'label','key3':'position'}
line=head_line+'\n'
for i,label in enumerate(bsp.get_ticks()['label']):
new_line="%(key1)12d%(key2)+12s%(key3)12f\n"%{'key1':i,'key2':label,'key3':bsp.get_ticks()['distance'][i]}
line+=new_line
line+='\n'
write_col_data(filename4,line,'',str_data=True)
try:
step_count+=1
filename5="BAND.png"
proc_str="Saving Plot to "+ filename5 +" File ..."
procs(proc_str,step_count,sp='-->>')
bsp.save_plot(filename5, img_format="png")
except:
print("Figure output fails !!!")
class BSPlotterTest(unittest.TestCase):
def setUp(self):
with open(os.path.join(test_dir, "CaO_2605_bandstructure.json"),
"r",
encoding="utf-8") as f:
d = json.loads(f.read())
self.bs = BandStructureSymmLine.from_dict(d)
self.plotter = BSPlotter(self.bs)
self.assertEqual(len(self.plotter._bs), 1,
"wrong number of band objects")
with open(os.path.join(test_dir, "N2_12103_bandstructure.json"),
"r",
encoding="utf-8") as f:
d = json.loads(f.read())
self.sbs_sc = BandStructureSymmLine.from_dict(d)
with open(os.path.join(test_dir, "C_48_bandstructure.json"),
"r",
encoding="utf-8") as f:
d = json.loads(f.read())
self.sbs_met = BandStructureSymmLine.from_dict(d)
self.plotter_multi = BSPlotter([self.sbs_sc, self.sbs_met])
self.assertEqual(len(self.plotter_multi._bs), 2,
"wrong number of band objects")
self.assertEqual(self.plotter_multi._nb_bands, [96, 96],
"wrong number of bands")
warnings.simplefilter("ignore")
def tearDown(self):
warnings.simplefilter("default")
def test_add_bs(self):
self.plotter_multi.add_bs(self.sbs_sc)
self.assertEqual(len(self.plotter_multi._bs), 3,
"wrong number of band objects")
self.assertEqual(self.plotter_multi._nb_bands, [96, 96, 96],
"wrong number of bands")
def test_get_branch_steps(self):
steps_idx = BSPlotter._get_branch_steps(self.sbs_sc.branches)
self.assertEqual(steps_idx, [0, 121, 132, 143],
"wrong list of steps idx")
def test_rescale_distances(self):
rescaled_distances = self.plotter_multi._rescale_distances(
self.sbs_sc, self.sbs_met)
self.assertEqual(
len(rescaled_distances),
len(self.sbs_met.distance),
"wrong lenght of distances list",
)
self.assertEqual(rescaled_distances[-1], 6.5191398067252875,
"wrong last distance value")
self.assertEqual(
rescaled_distances[148],
self.sbs_sc.distance[19],
"wrong distance at high symm k-point",
)
def test_interpolate_bands(self):
data = self.plotter.bs_plot_data()
d = data["distances"]
en = data["energy"]["1"]
int_distances, int_energies = self.plotter._interpolate_bands(d, en)
self.assertEqual(len(int_distances), 10,
"wrong lenght of distances list")
self.assertEqual(len(int_distances[0]), 100,
"wrong lenght of distances in a branch")
self.assertEqual(len(int_energies), 10,
"wrong lenght of distances list")
self.assertEqual(int_energies[0].shape, (16, 100),
"wrong lenght of distances list")
def test_bs_plot_data(self):
self.assertEqual(
len(self.plotter.bs_plot_data()["distances"]),
10,
"wrong number of sequences of branches",
)
self.assertEqual(
len(self.plotter.bs_plot_data()["distances"][0]),
16,
"wrong number of distances in the first sequence of branches",
)
self.assertEqual(
sum([len(e) for e in self.plotter.bs_plot_data()["distances"]]),
160,
"wrong number of distances",
)
lenght = len(
self.plotter.bs_plot_data(split_branches=False)["distances"][0])
self.assertEqual(
lenght, 144,
"wrong number of distances in the first sequence of branches")
lenght = len(
self.plotter.bs_plot_data(split_branches=False)["distances"])
self.assertEqual(
lenght, 2,
"wrong number of distances in the first sequence of branches")
self.assertEqual(self.plotter.bs_plot_data()["ticks"]["label"][5], "K",
"wrong tick label")
self.assertEqual(
len(self.plotter.bs_plot_data()["ticks"]["label"]),
19,
"wrong number of tick labels",
)
def test_get_ticks(self):
self.assertEqual(self.plotter.get_ticks()["label"][5], "K",
"wrong tick label")
self.assertEqual(
self.plotter.get_ticks()["distance"][5],
2.406607625322699,
"wrong tick distance",
)
# Minimal baseline testing for get_plot. not a true test. Just checks that
# it can actually execute.
def test_get_plot(self):
# zero_to_efermi = True, ylim = None, smooth = False,
# vbm_cbm_marker = False, smooth_tol = None
# Disabling latex is needed for this test to work.
from matplotlib import rc
rc("text", usetex=False)
plt = self.plotter.get_plot()
self.assertEqual(plt.ylim(), (-4.0, 7.6348), "wrong ylim")
plt = self.plotter.get_plot(smooth=True)
plt = self.plotter.get_plot(vbm_cbm_marker=True)
self.plotter.save_plot("bsplot.png")
self.assertTrue(os.path.isfile("bsplot.png"))
os.remove("bsplot.png")
plt.close("all")
# test plotter with 2 bandstructures
plt = self.plotter_multi.get_plot()
self.assertEqual(len(plt.gca().get_lines()), 874,
"wrong number of lines")
self.assertEqual(plt.ylim(), (-10.0, 10.0), "wrong ylim")
plt = self.plotter_multi.get_plot(zero_to_efermi=False)
self.assertEqual(plt.ylim(), (-15.2379, 12.67141266), "wrong ylim")
plt = self.plotter_multi.get_plot(smooth=True)
self.plotter_multi.save_plot("bsplot.png")
self.assertTrue(os.path.isfile("bsplot.png"))
os.remove("bsplot.png")
plt.close("all")
