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 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 is_pbc():
print('your choice ?')
print('{} >>> {}'.format('1', 'crystal'))
print('{} >>> {}'.format('2', 'molecule/cluster'))
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
choice = int(in_str)
assert choice in [1, 2]
if choice == 1:
return True
else:
return False
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 select_function(choice):
# structure operation
if choice == "a1":
random_operation()
elif choice == "a2":
covert_operation()
elif choice == "a3":
build_operation()
elif choice == "a4":
cleave_operation()
elif choice == "a5":
strain_operation()
elif choice == 'a6':
twoD_operation()
# structure analysis
elif choice == "b1":
structure_symmetry()
elif choice == "b2":
structure_finger_print()
elif choice == "b3":
structures_difference()
elif choice == "b4":
get_primitive_cell()
elif choice == "b5":
get_conventional_cell()
elif choice == "b6":
get_xrd()
# vasp in/out tools
elif choice == "c1":
struct = readstructure(crystal=True,
molecule=False,
filename='POSCAR',
cano=False)
sepline(ch=' prepare intput files ', sp='-')
print('your choce ?')
print('{} >>> {}'.format('1', 'prepare all files automatically'))
print('{} >>> {}'.format('2', 'prepare INCAR file'))
print('{} >>> {}'.format('3', 'prepare KPOINTS file'))
print('{} >>> {}'.format('4', 'prepare POTCAR file'))
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
choice = int(in_str)
if choice == 1:
generate_all_input(struct)
elif choice == 2:
generate_incar(struct)
elif choice == 3:
generate_kpoint(struct)
elif choice == 4:
generate_potcar(struct)
else:
print("unknown choice")
elif choice == "cxx":
sepline(ch=' summary output files ', sp='=')
print('{} >>> {}'.format('1', 'describe OUCAR file'))
print('{} >>> {}'.format('2', 'describe OSICAR file'))
print('{} >>> {}'.format('3', 'describe vasprun.xml file'))
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
choice = int(in_str)
if choice == 1:
describe_outcar()
elif choice == 2:
describe_OSICAR()
elif choice == 3:
describe_vasprun()
else:
print("unknow choice")
elif choice == "c2":
sepline(ch=' vasp output analysis ', sp='-')
print('{} >>> {}'.format('1 ', 'total density of states'))
print('{} >>> {}'.format('2 ', 'projected density of states'))
print('{} >>> {}'.format('3 ', 'band structure'))
print('{} >>> {}'.format('4 ', 'projected band structure'))
print('{} >>> {}'.format('5 ', 'select one band structure'))
print('{} >>> {}'.format('6 ', 'charge density'))
print('{} >>> {}'.format('7 ', 'spin density'))
print('{} >>> {}'.format('8 ', 'charge density difference'))
print('{} >>> {}'.format('9 ', 'spin density component: up/down'))
print('{} >>> {}'.format('10', 'average charge density/potential'))
print('{} >>> {}'.format('11', 'optics analysis'))
print('{} >>> {}'.format('12', 'mechanical analysis'))
print('{} >>> {}'.format('13',
'ab initio molecular dynamics analysis'))
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
choice = int(in_str)
if choice == 1:
total_dos()
elif choice == 2:
projected_dos()
elif choice == 3:
band_structure()
elif choice == 4:
projected_band_structure()
elif choice == 5:
select_one_band_structure()
elif choice == 6:
charge_density()
elif choice == 7:
spin_density()
elif choice == 8:
charge_density_diff()
elif choice == 9:
spin_density_component()
elif choice == 10:
chg_locp_average()
elif choice == 11:
optics_analysis()
elif choice == 12:
elastic_analysis()
elif choice == 13:
aimd_analysis()
else:
print("unknow choice")
# online exctraction
elif choice == "e1":
online_get_banddos()
elif choice == "e2":
online_get_structure()
elif choice == "e3":
online_get_properties()
elif choice == "e4":
online_get_phase_graph()
elif choice == "88":
return
else:
print("unknow choice")
return
def readstructure(crystal=True,
molecule=False,
filename=None,
multi_files=False,
cano=False):
if multi_files:
if crystal:
print('input the full file names seperated by space')
print('supported format 1: a.vasp')
print('supported format 2: a.cif')
print('supported format 3: a.vasp b.vasp')
print('supported format 4: *.vasp')
print('supported format 5: *.cif')
structs = []
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
if '*' in in_str:
fnames = glob.glob(in_str)
else:
fnames = in_str.split()
#print(fnames)
for fname in fnames:
if 'vasp' in fname:
try:
struct = MStructure.from_file(fname)
except:
nfname = str(uuid.uuid4()) + '_POSCAR'
os.symlink(fname, nfname)
mpt_log.debug("linke file for %s is %s" %
(fname, nfname))
fname = nfname
struct = MStructure.from_file(fname)
os.unlink(fname)
else:
try:
#print(fname)
struct = MStructure.from_file(fname)
except:
raise Exception("Unknown format")
#print(struct)
#print(type(struct))
if cano:
struct.canonical_form()
structs.append(struct)
return structs, fnames
if molecule:
print(
'input the full file names seperated by space (only for .xyz format)'
)
print('supported format 1: a.xyz b.xyz')
print('supported format 2: *.xyz')
structs = []
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
if '*' in in_str:
fnames = glob.glob(in_str)
else:
fnames = in_str.split()
for fname in fnames:
struct = MMolecule.from_file(fname)
if cano:
struct.canonical_form()
structs.append(struct)
return structs, fnames
if filename is not None:
try:
struct = MStructure.from_file(filename)
if cano:
struct.canonical_form()
except:
struct = MMolecule.from_file(filename)
if cano:
struct.canonical_form()
return struct
# sepline(ch='Read Structure',sp='=')
print('your choice ?')
print('{} >>> {}'.format('0', 'specific the file name!'))
if crystal:
print('{} >>> {}'.format('1', 'POSCAR'))
print('{} >>> {}'.format('2', 'CONTCAR'))
print('{} >>> {}'.format('3', 'CHGCAR'))
print('{} >>> {}'.format('4', 'LOCPOT'))
print('{} >>> {}'.format('5', NAME + '.cif'))
print('{} >>> {}'.format('6', NAME + '.xsf'))
print('{} >>> {}'.format('7', NAME + '.nc'))
print('{} >>> {}'.format('8', NAME + '.yaml'))
print('{} >>> {}'.format('9', NAME + '.json'))
if molecule:
print('{} >>> {}'.format('1', NAME + '.xyz'))
print('{} >>> {}'.format('2', NAME + '.mol'))
print('{} >>> {}'.format('3', NAME + '.nc'))
print('{} >>> {}'.format('4', NAME + '.yaml'))
print('{} >>> {}'.format('5', NAME + '.json'))
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
fstin = int(in_str)
if crystal:
if fstin == 0:
print('input the full file name')
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
fname = in_str
if fname.endswith('.vasp'):
nfname = str(uuid.uuid4()) + '_POSCAR'
os.symlink(fname, nfname)
fname = nfname
else:
fname = infile_list_c[fstin - 1]
struct = MStructure.from_file(fname)
if cano:
struct.canonical_form()
if molecule:
if fstin == 0:
print('input the full file name')
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
fname = in_str
else:
fname = infile_list_m[fstin - 1]
struct = MMolecule.from_file(fname)
if cano:
struct.canonical_form()
return struct
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 print_menu():
sepline(ch=" structural operation ", sp='=')
print('{} >>> {}'.format('a1', 'random operation'))
print('{} >>> {}'.format('a2', 'covert operation'))
print('{} >>> {}'.format('a3', 'build operation'))
print('{} >>> {}'.format('a4', 'cleave operation'))
print('{} >>> {}'.format('a5', 'strain operation'))
print('{} >>> {}'.format('a6', '2D structure operation'))
sepline(ch=" structural analysis ", sp='=')
print('{} >>> {}'.format('b1', 'structure symmetry'))
print('{} >>> {}'.format('b2', 'structure finger print'))
print('{} >>> {}'.format('b3', 'structure difference'))
print('{} >>> {}'.format('b4', 'get primitive cell'))
print('{} >>> {}'.format('b5', 'get conventional cell'))
print('{} >>> {}'.format('b6', 'get XRD pattern'))
sepline(ch=" vasp in/out tools ", sp='=')
print('{} >>> {}'.format('c1', 'prepare input files'))
print('{} >>> {}'.format('c2', 'analysis output files'))
# print('{} >>> {}'.format('c3','summary output files'))
#sepline(ch=" vasp auto calculation ",sp='=')
#print('{} >>> {}'.format('d1','optimize structure'))
#print('{} >>> {}'.format('d2','calculate band structure'))
#print('{} >>> {}'.format('d3','calculate band structure HSE06'))
#print('{} >>> {}'.format('d4','calculate dos'))
#print('{} >>> {}'.format('d5','calculate dos by HSE06'))
#print('{} >>> {}'.format('d6','calculate elastic properties'))
#print('{} >>> {}'.format('d7','calculate phonon'))
#print('{} >>> {}'.format('d8','execute MD simulation'))
sepline(ch=" online retrieve ", sp='=')
print('{} >>> {}'.format('e1', 'get band/dos by mp-ID'))
print('{} >>> {}'.format('e2',
'get structure from materialsproject database'))
print('{} >>> {}'.format('e3', 'get properties by mp-ID'))
print('{} >>> {}'.format('e4', 'get phase graph'))
sepline(ch="=", sp='=')
#TODO
# sepline(ch=" siesta tools ",sp='=')
# print('{} >>> {}'.format('si1','prepare input files'))
# sepline(ch=" gaussian tools ",sp='=')
# print('{} >>> {}'.format('gi1','prepare input files'))
# sepline(ch=" nwchem tools ",sp='=')
# print('{} >>> {}'.format('ni1','prepare input files'))
# sepline(ch=" quantum espresso tools ",sp='=')
# print('{} >>> {}'.format('qi1','prepare input files'))
# sepline(ch=" lammps tools ",sp='=')
# print('{} >>> {}'.format('li1','prepare input files'))
print("")
print("")
print("88 >>> exit")
print("your choice ?")
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
select_function(in_str)
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 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