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 online_get_phase_graph():
mpr = check_apikey()
compat = MaterialsProjectCompatibility()
print("input the elements list")
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
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.png'
proc_str = "Writing Data to " + filename + " File..."
procs(proc_str, step_count, sp='-->>')
pdp.write_image(filename)
def structure_finger_print():
h_str = "# "
if is_pbc():
struct = readstructure(crystal=True, molecule=False, cano=True)
struct_ana = CrystalAnalysis(struct)
(rdf_x, rdf_species) = struct_ana.fp_oganov()
else:
struct = readstructure(crystal=False, molecule=True, cano=True)
struct_ana = MoleculeAnalysis(struct)
(rdf_x,
rdf_species) = struct_ana.discrete_radial_distribution_function()
data = np.zeros((len(rdf_x), len(rdf_species) + 1))
data[:, 0] = rdf_x
tmp1_str = "#%(key1)+12s"
tmp2_dic = {'key1': 'Distance/A'}
for i, key in enumerate(rdf_species.keys()):
data[:, i + 1] = rdf_species[key]
tmp1_str += "%(key" + str(i + 2) + ")+12s"
if (isinstance(struct, MStructure)):
tmp2_dic["key" + str(i + 2)] = str(key)
if (isinstance(struct, Molecule)):
tmp2_dic["key" + str(i + 2)] = str((key[0].number, key[1].number))
for el in struct.types_of_specie:
h_str += str(el) + ' |->' + str(el.number) + ' '
head_line = h_str + '\n' + tmp1_str % tmp2_dic
filename = "FingerPrint.dat"
proc_str = "Writting data to " + filename + " File ..."
procs(proc_str, 0, sp='-->>')
write_col_data(filename, data, head_line=head_line)
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 online_get_properties():
mpr = check_apikey()
print("input the mp-ID")
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
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='-->>')
json_store(data, filename)
def online_get_banddos():
check_matplotlib()
mpr = check_apikey()
print("input the mp-ID")
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
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)
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)
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 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 structures_difference(distance_tolerance=0.1, rcut=30):
if is_pbc():
structs, fnames = readstructure(crystal=True,
molecule=False,
multi_files=True,
cano=True)
else:
structs, fnames = readstructure(crystal=False,
molecule=True,
multi_files=True,
cano=True)
for i in structs:
print(i)
for i in fnames:
print(i)
n_struct = len(structs)
proc_str = "Total Number of Files are : " + str(n_struct)
procs(proc_str, 0, sp='-->>')
dij = np.zeros((n_struct, n_struct))
for i, j in itertools.combinations(range(n_struct), 2):
struct_i = structs[i]
struct_j = structs[j]
if isinstance(struct_i, MStructure):
dij[i, j] = distance(struct_i, struct_j, rcut, pbc=True)
dij[j, i] = dij[i, j]
else:
dij[i, j] = distance(struct_i, struct_j, rcut, pbc=False)
dij[j, i] = dij[i, j]
filename = "StructureDistance.dat"
proc_str = "Writting data to " + filename + " File ..."
procs(proc_str, 0, sp='-->>')
write_col_data(filename, dij, head_line='')
data = ''
for i, st_name in enumerate(fnames):
data += "%(key1)+5s %(key2)+s" % {
'key1': str(i),
'key2': fnames[i]
} + '\n'
filename = "StructureList.dat"
proc_str = "Writting data to " + filename + " File ..."
procs(proc_str, 0, sp='-->>')
head_line = "#%(key1)+5s %(key2)+s" % {
'key1': 'index',
'key2': 'structure_name'
} + '\n'
data = head_line + data
write_col_data(filename, data, str_data=True)
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 elastic_analysis():
filename = 'OUTCAR'
step_count = 1
check_file(filename)
proc_str = "Reading Data From " + filename + " File ..."
procs(proc_str, step_count, sp='-->>')
outcar = Outcar(filename)
outcar.read_elastic_tensor()
cij_tensor = np.array(outcar.data['elastic_tensor'])
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)
struct0 = vsr.structures[0]
natom = struct0.num_sites
weight = struct0.composition.weight
volume = struct0.lattice.volume
## converting the units
volume *= 1.0e-30 ## from Angstrom to meters
weight *= weight * 1.0e-3 ## from gram to kg
density = weight / (volume * Avogadro)
asa = analyzer.SpacegroupAnalyzer(struct0)
# lat_type=asa.get_crystal_system()
crys_type = asa.get_lattice_type()
## Redefining the Cij matrix into the correct Voigt notation since VASP's OUTCAR has a different order
## In VASP: Columns and rows are listed as: 1, 2, 3, 6, 4, 5
## In this format OUTCAR's C44 values would be actually C66, C55 would be C44, and C66 would be C55.
## OUTCAR follows the below order:
## [C11 C12 C13 C16 C14 C15]
## [C21 C22 C23 C26 C24 C25]
## [C31 C32 C33 C36 C34 C35]
## [C61 C62 C63 C66 C64 C65]
## [C41 C42 C43 C46 C44 C45]
## [C51 C52 C53 C56 C54 C55]
cnew = np.zeros((6, 6))
snew = np.zeros((6, 6))
cnew = np.copy(cij_tensor)
for j in range(0, 6):
cnew[3][j] = cij_tensor[4][j]
cnew[4][j] = cij_tensor[5][j]
cnew[5][j] = cij_tensor[3][j]
ctemp = np.zeros((6, 6))
ctemp = np.copy(cnew)
for i in range(0, 6):
cnew[i][3] = cnew[i][4]
cnew[i][4] = cnew[i][5]
cnew[i][5] = ctemp[i][3]
# Change the units of Cij from kBar to GPa
cnew = cnew / 10.0
proc_str = "\n Modified elastic tensor in correct order (in GPa units)"
print(proc_str)
fmt = "%7.3f " * 6
for i in range(6):
print(fmt % tuple(cnew[i, :]))
def check_symmetric(a, tol=1e-8):
return np.allclose(a, a.T, atol=tol)
print(
'\n Checking if the elastic tensor is symmetric: i.e. Cij = Cji: %5s'
% check_symmetric(cnew))
print("\n Eigen Values of the elastic tensor:")
evals = LA.eigvals(cnew)
print(fmt % tuple(evals))
if np.all(evals) > 0.0:
print("\n All eigen values are positive indicating elastic stability.")
else:
print(
"\n ATTENTION: One or more eigen values are negative indicating elastic instability."
)
calc_elastic_prop(cnew, snew, crys_type, density, weight, natom)
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 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 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 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 online_get_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 = ""
while in_str == "":
in_str = input().strip()
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)
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')
elif choice == 2:
print("input the formula of structure")
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
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)
elif choice == 3:
print("input the elements list")
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
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)
else:
print('unknow choice')
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)
