def get_mp_phase_graph():
mpr = check_apikey()
compat = MaterialsProjectCompatibility()
print("input the elements list")
wait_sep()
in_str = wait()
elements = in_str.split()
web = "materials.org"
proc_str = "Reading Data From " + web + " ..."
step_count = 1
procs(proc_str, step_count, sp='-->>')
unprocessed_entries = mpr.get_entries_in_chemsys(elements)
processed_entries = compat.process_entries(unprocessed_entries)
pd = PhaseDiagram(processed_entries)
pdp = PDPlotter(pd, show_unstable=True)
try:
pdp.show()
except:
pass
finally:
step_count += 1
filename = 'phase' + '-'.join(elements) + '.png'
proc_str = "Writing Data to " + filename + " File..."
procs(proc_str, step_count, sp='-->>')
pdp.write_image(filename)
return True
def charge_density_diff():
print("input the name of charge density file like this")
print("file_A file_B, or")
print("it means rho(A)-rho(B))")
print("file_A file_B file_C")
print("it means rho(A)-rho(B)-rho(C)")
wait_sep()
in_str=""
while in_str=="":
in_str=input().strip()
filenames=in_str.split()
len_file=len(filenames)
chg=[None]*len_file
if len_file>=2:
for i in range(len_file):
fchg=filenames[i]
proc_str="Reading Charge Density From "+fchg+" File ..."
procs(proc_str,i+1,sp='-->>')
chg[i] = CHGCAR.from_file(fchg)
diff_chg=copy(chg[0])
for j in range(len_file-1):
diff_chg-=chg[j+1]
proc_str="Writing Charge Density Difference to Diff.vasp File ..."
procs(proc_str,i+2,sp='-->>')
diff_chg.write_file('Diff.vasp','total')
else:
print("you must input at least 2 files")
def charge_density():
proc_str="Reading Charge Density From CHG File ..."
procs(proc_str,1,sp='-->>')
chg = CHGCAR.from_file("CHG")
proc_str="Writing Charge Density To CHARGE.vasp File ..."
procs(proc_str,2,sp='-->>')
chg.write_file('CHGARGE.vasp','total')
def chg_locp_average():
chg=False
print("which file would like to average: CHG or LOCPOT ?")
wait_sep()
in_str=""
while in_str=="":
in_str=input().strip()
if in_str.lower()=='chg':
filename='CHG'
check_file(filename)
grid_data = CHGCAR.from_file(filename)
head_line="#%(key1)+s %(key2)+s"%{'key1':'Distance/Ang','key2':'Average Charge/(e/Ang**3)'}
chg=True
elif in_str.lower()=='locpot':
filename='LOCPOT'
check_file(filename)
grid_data = Locpot.from_file(filename)
head_line="#%(key1)+s %(key2)+s"%{'key1':'Distance/Ang','key2':'Average Potential/(eV)'}
else:
print('unknown file file: '+in_str)
os._exit()
step_count=1
check_file(filename)
proc_str="Reading Data From "+ filename +" File ..."
procs(proc_str,step_count,sp='-->>')
volume=grid_data.structure.volume
print("which direction would like to average: x y or z ?")
wait_sep()
in_str=""
while in_str=="":
in_str=input().strip().lower()
if in_str=="x":
selected_dir=0
elif in_str=='y':
selected_dir=1
elif in_str=='z':
selected_dir=2
else:
print("Unknow Direction!")
return
axis_grid=grid_data.get_axis_grid(selected_dir)
if chg:
aver_grid=grid_data.get_average_along_axis(selected_dir)/volume
else:
aver_grid=grid_data.get_average_along_axis(selected_dir)
data=np.vstack((axis_grid,aver_grid)).T
step_count+=1
if chg:
filename="average_CHG_"+in_str+'.dat'
else:
filename="average_LOCPOT_"+in_str+'.dat'
proc_str="Writting Average Data to "+ filename +" File ..."
procs(proc_str,step_count,sp='-->>')
write_col_data(filename,data,head_line)
def get_mp_properties():
mpr = check_apikey()
print("input the mp-ID")
wait_sep()
in_str = wait()
mp_id = in_str
proc_str = "Reading Data From " + web + " ..."
step_count = 1
procs(proc_str, step_count, sp='-->>')
data = mpr.get_data(mp_id)
filename = mp_id + '.json'
proc_str = "Writing Data To " + filename + " File ..."
step_count += 1
procs(proc_str, step_count, sp='-->>')
dumpfn(data, filename)
return True
def get_mp_banddos():
check_matplotlib()
mpr = check_apikey()
print("input the mp-ID")
wait_sep()
in_str = wait()
mp_id = in_str
step_count = 1
proc_str = "Reading Data From " + web + " ..."
procs(proc_str, step_count, sp='-->>')
data = mpr.get_entry_by_material_id(mp_id)
sepline()
print(data)
sepline()
step_count += 1
proc_str = "Reading Band Data From " + web + " ..."
procs(proc_str, step_count, sp='-->>')
band = mpr.get_bandstructure_by_material_id(mp_id)
if band is None:
print("No data obtained online, stop now!")
os.exit(0)
step_count += 1
filename = mp_id + '_band.png'
proc_str = "Writing Data to " + filename + " File..."
bsp = BSPlotter(band)
procs(proc_str, step_count, sp='-->>')
bsp.save_plot(filename=filename, img_format="png")
step_count += 1
proc_str = "Reading DOS Data From " + web + " ..."
procs(proc_str, step_count, sp='-->>')
dos = mpr.get_dos_by_material_id(mp_id)
if dos is None:
print("No data obtained online, stop now!")
step_count += 1
filename = mp_id + '_dos.png'
proc_str = "Writing Data to " + filename + " File..."
dsp = DosPlotter()
dsp.add_dos('Total', dos)
procs(proc_str, step_count, sp='-->>')
dsp.save_plot(filename=filename, img_format="png")
def get_oqmd_structure():
print('{} >>> {}'.format('1', 'get a structure by oqmd-ID'))
print('{} >>> {}'.format('2', 'get structures by fomular'))
print('{} >>> {}'.format('3', 'get structures by elements'))
print('{} >>> {}'.format('4', 'get structures by filters'))
wait_sep()
in_str = wait()
choice = in_str
qr = QMPYRester()
if choice == "1":
print("input the oqmd-ID")
wait_sep()
in_str = wait()
oqmd_id = int(in_str)
step_count = 1
proc_str = "Reading Data From " + web + " ..."
procs(proc_str, step_count, sp='-->>')
data = qr.get_optimade_structure_by_id(oqmd_id)
if data is None:
print("Unknown OQMD-ID, check the OQMD-ID")
return None
else:
struct = data_to_structure(data)
filename = str(oqmd_id) + '.vasp'
step_count += 1
proc_str = "Writing Data to " + filename + " File..."
procs(proc_str, step_count, sp='-->>')
struct.to(filename=filename, fmt='POSCAR')
return True
elif choice == "2":
print("Not supported now!")
os._exit(0)
elif choice == "3":
print("Not supported now!")
os._exit(0)
elif choice == "4":
print("Not supported now!")
os._exit(0)
#print("elements=O AND ( _oqmd_stability<-0.1 OR _oqmd_delta_e<-0.5)")
else:
print('Unknow choice')
return None
def spin_density():
proc_str="Reading Spin Charge Density From CHG File ..."
procs(proc_str,1,sp='-->>')
chg = CHGCAR.from_file("CHG")
assert(chg.is_spin_polarized)
proc_str="Writing Total Charge Density To Total.vasp File ..."
procs(proc_str,2,sp='-->>')
chg.write_file('Total.vasp','total')
proc_str="Writing Spin Charge Density To Spin.vasp File ..."
procs(proc_str,3,sp='-->>')
chg.write_file('Spin.vasp','diff')
def spin_density_component():
proc_str="Reading Spin Up/Down Density From CHG File ..."
procs(proc_str,1,sp='-->>')
chg = CHGCAR.from_file("CHG")
assert(chg.is_spin_polarized)
data=chg.spin_data.copy()
chg.data={'spinup':data[Spin.up],'spindown':data[Spin.down]}
proc_str="Writing Spin Up Density To Spinup.vasp File ..."
procs(proc_str,2,sp='-->>')
chg.write_file('Spinup.vasp','spinup')
proc_str="Writing Spin Down Density To Spindown.vasp File ..."
procs(proc_str,3,sp='-->>')
chg.write_file('Spindown.vasp','spindown')
def optics_analysis():
filename='vasprun.xml'
step_count=1
check_file(filename)
proc_str="Reading Data From "+ filename +" File ..."
procs(proc_str,step_count,sp='-->>')
vsr=Vasprun(filename,parse_eigen=False)
try:
energy=np.array(vsr.dielectric[0])
freq=energy/H
real=np.array(vsr.dielectric[1])
imag=np.array(vsr.dielectric[2])
except:
print('extracing data failed ')
return
head_line="#%(key1)+12s%(key2)+12s%(key3)+12s%(key4)+12s%(key5)+12s%(key6)+12s%(key7)+12s"%\
{'key1':'Energy','key2':'xx','key3':'yy','key4':'zz','key5':'xy','key6':'yz','key7':'zx'}
step_count+=1
filename="AbsorbSpectrum.dat"
proc_str="Writing Data To "+ filename +" File ..."
procs(proc_str,step_count,sp='-->>')
Absorb=np.zeros((len(freq),6))
for i in range(6):
Absorb[:,i]=1.4142*freq*(np.sqrt(-real[:,i]+np.sqrt(imag[:,i]*imag[:,i]+real[:,i]*real[:,i])))/(C0*100)
data=np.vstack((energy,Absorb.T)).T
write_col_data(filename,data,head_line,e_fmt=True)
step_count+=1
filename="RefractiveSpectrum.dat"
proc_str="Writing Data To "+ filename +" File ..."
procs(proc_str,step_count,sp='-->>')
Refrac=np.zeros((len(freq),6))
for i in range(6):
Refrac[:,i]=(np.sqrt(real[:,i]+np.sqrt(imag[:,i]*imag[:,i]+real[:,i]*real[:,i])))/1.4142
data=np.vstack((energy,Refrac.T)).T
write_col_data(filename,data,head_line,e_fmt=True)
step_count+=1
filename="EnergyLossSpectrum.dat"
proc_str="Writing Data To "+ filename +" File ..."
procs(proc_str,step_count,sp='-->>')
EnergyLoss=np.zeros((len(freq),6))
for i in range(6):
EnergyLoss[:,i]=imag[:,i]/(imag[:,i]*imag[:,i]+real[:,i]*real[:,i])
data=np.vstack((energy,EnergyLoss.T)).T
write_col_data(filename,data,head_line,e_fmt=True)
step_count+=1
filename="ExtictionSpectrum.dat"
proc_str="Writing Data To "+ filename +" File ..."
procs(proc_str,step_count,sp='-->>')
Extic=np.zeros((len(freq),6))
for i in range(6):
Extic[:,i]=(np.sqrt(-real[:,i]+np.sqrt(imag[:,i]*imag[:,i]+real[:,i]*real[:,i])))/1.4142
data=np.vstack((energy,Extic.T)).T
write_col_data(filename,data,head_line,e_fmt=True)
step_count+=1
filename="ReflectivitySpectrum.dat"
proc_str="Writing Data To "+ filename +" File ..."
procs(proc_str,step_count,sp='-->>')
Reflect=np.zeros((len(freq),6))
for i in range(6):
Reflect[:,i]=((Refrac[:,i]-1)*(Refrac[:,i]-1)+Extic[:,i]*Extic[:,i])/((Refrac[:,i]+1)*(Refrac[:,i]+1)+Extic[:,i]*Extic[:,i])
data=np.vstack((energy,Reflect.T)).T
write_col_data(filename,data,head_line,e_fmt=True)
def select_one_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)
nelect=vsr.parameters['NELECT']
nbands=bands.nb_bands
if vsr.is_spin:
proc_str="This Is a Spin-polarized Calculation."
procs(proc_str,0,sp='-->>')
ISPIN=2
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
proc_str="Total band number is "+str(nbands)
procs(proc_str,0,sp='-->>')
proc_str="Total electron number is "+str(nelect)
procs(proc_str,0,sp='-->>')
print("which band would like to select ?")
wait_sep()
in_str=""
while in_str=="":
in_str=input().strip()
selected_band=int(in_str)
step_count+=1
filename="BAND_"+str(selected_band)+'.dat'
proc_str="Writting Selected Band Structure Data to "+ filename +" File ..."
procs(proc_str,step_count,sp='-->>')
if ISPIN==1 or ISPIN==3:
band_data=bands.bands[Spin.up][selected_band-1]-vsr.efermi
data=np.vstack((bands.distance,band_data)).T
head_line="#%(key1)+12s%(key2)+13s"%{'key1':'K-Distance','key2':'Energy(ev)'}
write_col_data(filename,data,head_line,len(band_data))
else:
band_data_up=bands.bands[Spin.up][selected_band-1]-vsr.efermi
band_data_down=bands.bands[Spin.down][selected_band-1]-vsr.efermi
data=np.vstack((bands.distance,band_data_up,band_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,len(band_data_up))
return
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 total_dos():
check_matplotlib()
filename='vasprun.xml'
check_file(filename)
proc_str="Reading Data From "+ filename +" File ..."
procs(proc_str,1,sp='-->>')
vsr=Vasprun(filename,parse_eigen=False)
tdos=vsr.tdos
idos=vsr.idos
E=tdos.energies-tdos.efermi
if vsr.is_spin:
proc_str="This Is a Spin-polarized Calculation."
procs(proc_str,0,sp='-->>')
proc_str="Writting TDOS.dat File ..."
TDOSUP=tdos.densities[Spin.up]
TDOSDOWN=tdos.densities[Spin.down]
ETDOS=np.vstack((E,TDOSUP,TDOSDOWN))
head_line="#%(key1)+12s%(key2)+12s%(key3)+12s"%{'key1':'Energy(eV)','key2':'SpinUp','key3':'SpinDown'}
write_col_data('TDOS.dat',ETDOS.T,head_line)
proc_str="Writting IDOS.dat File ..."
procs(proc_str,3,sp='-->>')
IDOSUP=idos.densities[Spin.up]
IDOSDOWN=idos.densities[Spin.down]
EIDOS=np.vstack((E,IDOSUP,IDOSDOWN))
head_line="#%(key1)+12s%(key2)+12s%(key3)+12s"%{'key1':'Energy(eV)','key2':'IntSpinUp','key3':'IntSpinDown'}
write_col_data('IDOS.dat',EIDOS.T,head_line)
plt1=DosPlotter()
plt2=DosPlotter()
plt1.add_dos('Total DOS',tdos)
plt2.add_dos('Total DOS',idos)
try:
# plt1.show()
plt1.save_plot('TotalDOS.png', img_format="png")
# plt2.show()
plt2.save_plot('IntegratedDOS.png', img_format="png")
except:
print("pls use gnuplot to plot TDOS.dat and IDOS.dat")
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='-->>')
proc_str="Writting TDOS.dat File ..."
procs(proc_str,2,sp='-->>')
TDOS=tdos.densities[Spin.up]
ETDOS=np.vstack((E,TDOS))
head_line="#%(key1)+12s%(key2)+12s"%{'key1':'Energy(eV)','key2':'TotalDOS'}
write_col_data('TDOS.dat',ETDOS.T,head_line)
proc_str="Writting IDOS.dat File ..."
procs(proc_str,3,sp='-->>')
IDOS=idos.densities[Spin.up]
EIDOS=np.vstack((E,IDOS))
head_line="#%(key1)+12s%(key2)+13s"%{'key1':'Energy(eV)','key2':'IntegratedDOS'}
write_col_data('IDOS.dat',EIDOS.T,head_line)
plt1=DosPlotter()
plt2=DosPlotter()
plt1.add_dos('Total DOS',tdos)
plt2.add_dos('Integrated DOS',idos)
filename4="TotalDOS.png IntegratedDOS.png"
proc_str="Saving Plot to "+ filename4 +" File ..."
procs(proc_str,4,sp='-->>')
try:
# plt1.show()
plt1.save_plot('TotalDOS.png', img_format="png")
# plt2.show()
plt2.save_plot('IntegratedDOS.png', img_format="png")
except:
print("pls use gnuplot to plot TDOS.dat and IDOS.dat")
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 !!!")
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)
def get_mp_structure():
mpr = check_apikey()
print('your choice ?')
print('{} >>> {}'.format('1', 'get a structure by mp-ID'))
print('{} >>> {}'.format('2', 'get a structure by fomular'))
print('{} >>> {}'.format('3', 'get a structure by elements'))
wait_sep()
in_str = wait()
choice = int(in_str)
if choice == 1:
print("input the mp-ID")
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
mp_id = in_str
struct = mpr.get_structure_by_material_id(mp_id)
if isinstance(struct, Structure):
pass
else:
print("Unknown mp-ID, check the mp-ID")
return None
web = "materials.org"
step_count = 1
proc_str = "Reading Data From " + web + " ..."
procs(proc_str, step_count, sp='-->>')
filename = mp_id + '.vasp'
step_count += 1
proc_str = "Writing Data to " + filename + " File..."
procs(proc_str, step_count, sp='-->>')
struct.to(filename=filename, fmt='POSCAR')
return True
elif choice == 2:
print("input the formula of structure")
wait_sep()
in_str = wait()
formula = in_str
mpid = mpr.query(criteria={'pretty_formula': formula},
properties=['material_id'])
web = "materials.org"
proc_str = "Reading Data From " + web + " ..."
step_count = 1
procs(proc_str, step_count, sp='-->>')
for i in range(len(mpid)):
sid = mpid[i]['material_id']
struct = mpr.get_structure_by_material_id(sid)
filename = sid + '.cif'
step_count += 1
proc_str = "Writing Data to " + filename + " File..."
procs(proc_str, step_count, sp='-->>')
struct.to(fmt='cif', filename=filename)
return True
elif choice == 3:
print("input the elements list")
wait_sep()
in_str = wait()
elements = in_str.split()
data = mpr.get_entries_in_chemsys(elements=elements)
web = "materials.org"
proc_str = "Reading Data From " + web + " ..."
step_count = 1
procs(proc_str, step_count, sp='-->>')
for i in range(len(data)):
if len(data[i].composition) == len(elements):
sid = data[i].entry_id
struct = mpr.get_structure_by_material_id(sid)
filename = sid + '.cif'
step_count += 1
proc_str = "Writing Data to " + filename + " File..."
procs(proc_str, step_count, sp='-->>')
struct.to(fmt='cif', filename=filename)
return True
else:
print('unknow choice')
return None