def test_make_perfect_band_edge_state_from_vasp(vasp_files):
procar = Procar(vasp_files / "MgO_2x2x2_perfect" / "PROCAR")
vasprun = Vasprun(vasp_files / "MgO_2x2x2_perfect" / "vasprun.xml")
outcar = Outcar(vasp_files / "MgO_2x2x2_perfect" / "OUTCAR")
actual = make_perfect_band_edge_state_from_vasp(procar, vasprun, outcar)
vbm_info = EdgeInfo(band_idx=127,
kpt_coord=(0.25, 0.25, 0.25),
orbital_info=OrbitalInfo(energy=2.7746,
orbitals={
'Mg':
[0.0, 0.0, 0.0, 0.0],
'O':
[0.0, 0.704, 0.0, 0.0]
},
occupation=1.0))
cbm_info = EdgeInfo(band_idx=128,
kpt_coord=(0.25, 0.25, 0.25),
orbital_info=OrbitalInfo(energy=8.2034,
orbitals={
'Mg':
[0.192, 0.0, 0.0, 0.0],
'O':
[0.224, 0.096, 0.0, 0.0]
},
occupation=0.0))
expected = PerfectBandEdgeState(vbm_info=vbm_info, cbm_info=cbm_info)
assert actual == expected
def make_perfect_band_edge_state(args):
procar = Procar(args.dir / defaults.procar)
vasprun = Vasprun(args.dir / defaults.vasprun)
outcar = Outcar(args.dir / defaults.outcar)
perfect_band_edge_state = \
make_perfect_band_edge_state_from_vasp(procar, vasprun, outcar)
perfect_band_edge_state.to_json_file(args.dir /
"perfect_band_edge_state.json")
def setUp(self) -> None:
procar_perfect = Procar(self.DEFECTS_MGO_DIR / "perfect" / "PROCAR")
structure_perfect = self.get_structure_by_name("MgO64atoms")
procar_va_o_2 = Procar(self.DEFECTS_MGO_DIR / "Va_O1_2" / "PROCAR")
structure_va_o_2 = self.get_structure_by_name("MgO64atoms-Va_O1_2")
# MgO vbm
self.orbital_1 = calc_orbital_character(procar=procar_perfect,
structure=structure_perfect,
spin=Spin.up,
band_index=127,
kpoint_index=0)
# MgO vbm
self.orbital_2 = calc_orbital_character(procar=procar_va_o_2,
structure=structure_va_o_2,
spin=Spin.up,
band_index=123,
kpoint_index=0)
def test_calc_participation_ratio(self):
procar = Procar(self.DEFECTS_MGO_DIR / "Va_O1_2" / "PROCAR")
actual = calc_participation_ratio(procar=procar,
spin=Spin.up,
band_index=0,
atom_indices=[32, 33])
# 33 0.051 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.051
# 34 0.051 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.051
# tot 0.732 0.001 0.001 0.001 0.000 0.000 0.000 0.000 0.000 0.736
expected = 0.051 * 2 / 0.736
self.assertAlmostEqual(expected, actual, 2)
def make_edge_characters(args):
for d in args.dirs:
logger.info(f"Parsing data in {d} ...")
vasprun = Vasprun(d / defaults.vasprun)
procar = Procar(d / defaults.procar)
outcar = Outcar(d / defaults.outcar)
calc_results = loadfn(d / "calc_results.json")
structure_analyzer = DefectStructureAnalyzer(
calc_results.structure, args.perfect_calc_results.structure)
edge_characters = MakeEdgeCharacters(
procar, vasprun, outcar,
structure_analyzer.neighboring_atom_indices).edge_characters
edge_characters.to_json_file(d / "edge_characters.json")
def test_band_edge_properties_orbital_contributions(test_data_files):
procar = Procar(test_data_files / "MgO_band_PROCAR")
structure = Structure(
Lattice.cubic(1), species=["Mg", "O"], coords=[[0]*3, [0.5]*3])
vbm_info = BandEdge.from_dict({'energy': 3.0663, 'spin': 1, 'band_index': 3,
'kpoint_index': 0,
'kpoint_coords': [0.0, 0.0, 0.0]})
cbm_info = BandEdge.from_dict({'energy': 7.726, 'spin': 1, 'band_index': 4,
'kpoint_index': 0,
'kpoint_coords': [0.0, 0.0, 0.0]})
vbm, cbm = edge_orbital_contributions(procar, structure, vbm_info, cbm_info)
assert vbm["O"]["p"] == 0.753
assert cbm["Mg"]["s"] == 0.238
def _inner(_dir: Path):
try:
defect_entry = loadfn(_dir / "defect_entry.json")
title = defect_entry.name
except FileNotFoundError:
title = "No name"
procar = Procar(_dir / defaults.procar)
vasprun = Vasprun(_dir / defaults.vasprun)
str_info = loadfn(_dir / "defect_structure_info.json")
band_edge_orb_chars = make_band_edge_orbital_infos(
procar, vasprun, supercell_vbm, supercell_cbm, str_info)
band_edge_orb_chars.to_json_file(_dir / "band_edge_orbital_infos.json")
plotter = EigenvalueMplPlotter(title=title,
band_edge_orb_infos=band_edge_orb_chars,
supercell_vbm=supercell_vbm,
supercell_cbm=supercell_cbm)
plotter.construct_plot()
plotter.plt.savefig(fname=_dir / "eigenvalues.pdf")
plotter.plt.clf()
def test_calc_orbital_character(self):
procar = Procar(self.DEFECTS_MGO_DIR / "Va_O1_2" / "PROCAR")
structure = self.get_structure_by_name("MgO64atoms-Va_O1_2")
actual = calc_orbital_character(procar=procar,
structure=structure,
spin=Spin.up,
band_index=0,
kpoint_index=0)
mg_sum = (0.002 + 0.001 + 0.001 + 0.001 + 0.002 + 0.001 + 0.001 +
0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 +
0.001 + 0.001 + 0.002 + 0.002 + 0.001 + 0.001 + 0.001 +
0.001 + 0.001 + 0.001 + 0.002 + 0.001 + 0.002 + 0.001 +
0.001 + 0.001 + 0.001 + 0.001)
o_sum = (0.051 + 0.051 + 0.017 + 0.051 + 0.017 + 0.017 + 0.008 +
0.028 + 0.024 + 0.024 + 0.028 + 0.014 + 0.014 + 0.014 +
0.014 + 0.024 + 0.028 + 0.014 + 0.014 + 0.028 + 0.024 +
0.014 + 0.014 + 0.024 + 0.014 + 0.028 + 0.014 + 0.028 +
0.014 + 0.024 + 0.014)
expected = {
'Mg': {
's': mg_sum,
'p': 0.0,
'd': 0.0,
'f': 0.0
},
'O': {
's': o_sum,
'p': 0.0,
'd': 0.0,
'f': 0.0
}
}
self.assertAlmostEqual(expected["Mg"]["s"], actual["Mg"]["s"], 4)
self.assertAlmostEqual(expected["O"]["s"], actual["O"]["s"], 4)
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 projected_dos():
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)
nedos=vsr.parameters['NEDOS']
struct=vsr.final_structure
pdos=vsr.pdos
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
(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='-->>')
contrib=np.zeros((nedos,norbitals+1,2))
energies=vsr.tdos.energies-vsr.efermi
for ispin in [0,1]:
if ispin==0:
spin=Spin.up
s_name='Up'
else:
spin=Spin.down
s_name='Down'
contrib[:,0,ispin]=energies
for i in atom_index:
for j in range(norbitals):
contrib[:,j+1,ispin]=contrib[:,j+1,ispin]+pdos[i][Orbital(j)][spin]
step_count+=1
filename="PDOS_"+s_name+".dat"
proc_str="Writting Projected DOS Data to "+ filename +" File ..."
procs(proc_str,step_count,sp='-->>')
tmp1_str="#%%(key1)+12s"
tmp2_dic={'key1':'Energy(ev)'}
for i in range(norbitals):
tmp1_str+="%(key"+str(i+2)+")+12s"
tmp2_dic["key"+str(i+2)]=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,contrib[:,:,ispin],head_line)
else:
if vsr.parameters['LNONCOLLINEAR']:
proc_str="This Is a Non-Collinear Calculation."
procs(proc_str,0,sp='-->>')
else:
proc_str="This Is a Non-Spin Calculation."
procs(proc_str,0,sp='-->>')
contrib=np.zeros((nedos,norbitals+1))
energies=vsr.tdos.energies-vsr.efermi
contrib[:,0]=energies
for i in atom_index:
for j in range(norbitals):
contrib[:,j+1]=contrib[:,j+1]+pdos[i][Orbital(j)][Spin.up]
step_count+=1
filename="PDOS.dat"
proc_str="Writting Projected DOS Data to "+ filename +" File ..."
procs(proc_str,step_count,sp='-->>')
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,contrib,head_line)