def MP_db():
sepline(ch=" Materials Project database ", sp='=')
print('''\
e1 >>> get band/dos by mp-ID
e2 >>> get structure from materialsproject database
e3 >>> get properties by mp-ID
e4 >>> get phase graph''')
def menu():
"""show the first class menu
function description:
Args:
None
Returns:
None
"""
label.input
structural_operation()
structural_analysis()
vasp_inout()
vasp_workflow()
MP_db()
local_db()
sepline(ch="=", sp='=')
print("")
print("")
your_choice()
in_str = wait()
ret = select_function(in_str)
if ret is None:
goto.input
def local_db():
sepline(ch=" local database ", sp='=')
print('''\
f1 >>> check local database
f2 >>> get entry by l-ID
f3 >>> get entry by formula
f4 >>> get entry by element
f5 >>> insert entry into database''')
def structural_analysis():
sepline(ch=" structural analysis ", sp='=')
print('''\
b1 >>> structure symmetry
b2 >>> structure finger print
b3 >>> structure difference
b4 >>> get primitive cell
b5 >>> get conventional cell
b6 >>> get XRD pattern''')
def structural_operation():
sepline(ch=" structural operation ", sp='=')
print('''\
a1 >>> random operation
a2 >>> convert operation
a3 >>> build operation
a4 >>> cleave opeartion
a5 >>> strain operation
a6 >>> 2D structure operation''')
def MP_db():
sepline(ch=" On-line database ",sp='=')
print('''\
e1 >>> (MP) get band/dos by mp-ID
e2 >>> (MP) get structure by mp-ID/elements/formula
e3 >>> (MP) get properties by mp-ID
e4 >>> (MP) get phase graph
e5 >>> (OQMD) get structure by ID/elements/formula''',
)
def vasp_workflow():
sepline(ch=" vasp calclation workflow", sp='=')
print('''\
d1 >>> optimize structure
d2 >>> calculate band structure
d3 >>> calculate band structure HSE06
d4 >>> calculate dos
d5 >>> calculate dos by HSE06
d6 >>> calculate elastic properties
d7 >>> calculate phonon
d8 >>> execute MD simulation''')
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 structure_symmetry():
structs, fnames = read_structures()
multi_structs(structs, fnames)
for struct, fname in zip(structs, fnames):
if isinstance(struct, Structure):
sa = SpacegroupAnalyzer(struct)
print("file name: {}".format(fname))
print("{} : {}".format('Structure Type', 'periodicity'))
print("{} : {}".format('Lattice Type', sa.get_lattice_type()))
print("{} : {}".format('Space Group ID',
sa.get_space_group_number()))
print("{} : {}".format('International Symbol',
sa.get_space_group_symbol()))
print("{} : {}".format('Hall Symbol', sa.get_hall()))
sepline()
if isinstance(struct, Molecule):
print("file name: {}".format(fname))
sa = PointGroupAnalyzer(struct)
print("{} : {}".format('Structure Type', 'non-periodicity'))
print("{} : {}".format('International Symbol',
ast.get_pointgroup()))
return True
def get_conventional_cell():
structs, fnames = read_structures()
multi_structs(structs, fnames)
for struct, fname in zip(structs, fnames):
sepline(ch='conventional cell', sp='-')
ast = SpacegroupAnalyzer(struct)
conv_st = ast.get_conventional_standard_structure()
print(conv_st)
sepline()
print('save to ' + NAME + '_convention_' + fname + '.vasp')
conv_st.to(filename=NAME + '_conventional_' + fname + '.vasp',
fmt='poscar')
sepline()
return True
def get_primitive_cell():
structs, fnames = read_structures()
multi_structs(structs, fnames)
for struct, fname in zip(structs, fnames):
sepline(ch='Primitive Cell', sp='-')
ast = SpacegroupAnalyzer(struct)
prim_st = ast.find_primitive()
print(prim_st)
sepline()
print('save to ' + NAME + '_primitive_' + fname + '.vasp')
prim_st.to(filename=NAME + '_primitive_' + fname + '.vasp',
fmt='poscar')
sepline()
return True
def vasp_inout():
sepline(ch=" vasp in/out tools ", sp='=')
print('''\
c1 >>> prepare input files
c2 >>> analysis output files
c3 >>> summary output files''')
def select_function(choice):
r"""
submenu for selecting function
"""
# structure operation
if choice == "a1":
print('{} >>> {}'.format('1', 'random structure generating'))
print('{} >>> {}'.format('2', 'random perturbation for atom index'))
print('{} >>> {}'.format('3', 'random disturbing for lattice matrix'))
print('{} >>> {}'.format('4', 'random disturbing for atom position'))
your_choice()
in_str = wait()
if in_str == "0":
return None
return random_operation(in_str)
elif choice == "a2":
return covert_operation()
elif choice == "a3":
print('{} >>> {}'.format('1', 'build supercell'))
print('{} >>> {}'.format('2', 'build nanotube'))
print('{} >>> {}'.format('3', 'build absorption configuration'))
your_choice()
in_str = wait()
if in_str == "0":
return None
return build_operation(in_str)
elif choice == "a4":
print('{} >>> {}'.format('1', 'cleave surface'))
print('{} >>> {}'.format('2', 'cleave sphere cluster'))
print('{} >>> {}'.format('3', 'cleave shell structure'))
your_choice()
in_str = wait()
if in_str == "0":
return None
return cleave_operation(in_str)
elif choice == "a5":
return strain_operation()
elif choice == 'a6':
print('{} >>> {}'.format('1', 'build rippled structure'))
print('{} >>> {}'.format('2', 'build multi-layered structure'))
print('{} >>> {}'.format('3', 'split multi-layered structure'))
print('{} >>> {}'.format('4', 'resize vacuum layer'))
print('{} >>> {}'.format('5', 'center atomic-layer along z direction'))
print('{} >>> {}'.format('6',
'apply strain along different direction'))
print('{} >>> {}'.format('7', 'constrain atom in specific range'))
print('{} >>> {}'.format(
'8', 'get a substrate for 2D material (online!!!)'))
your_choice()
in_str = wait()
if in_str == "0":
return None
return twod_operation(in_str)
# structure analysis
elif choice == "b1":
return structure_symmetry()
elif choice == "b2":
return structure_finger_print()
elif choice == "b3":
return structures_difference()
elif choice == "b4":
return get_primitive_cell()
elif choice == "b5":
return get_conventional_cell()
elif choice == "b6":
return get_xrd()
# vasp in/out tools
elif choice == "c1":
structs, fnames = read_structures()
if structs is None:
return None
multi_structs(structs, fnames)
sepline(ch=' prepare intput files ', sp='-')
your_choice()
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'))
label.input1
wait_sep()
choice = wait()
if choice == "0":
return None
elif choice == "1":
return generate_all_input(structs, fnames)
elif choice == "2":
return generate_incar(structs, fnames)
elif choice == "3":
return generate_kpoint(structs, fnames)
elif choice == "4":
return generate_potcar(structs, fnames)
else:
print("unknown choice, check the input")
goto.input1
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'))
label.input2
wait_sep()
choice = wait()
if choice == "0":
return None
if choice == "1":
return describe_OUTCAR()
elif choice == "2":
return describe_OSICAR()
elif choice == "3":
return describe_vasprun()
else:
print("unknown choice, check the input")
goto.input2
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'))
label.input3
wait_sep()
choice = wait()
if choice == "0":
return None
if choice == "1":
return total_dos()
elif choice == "2":
return projected_dos()
elif choice == "3":
return band_structure()
elif choice == "4":
return projected_band_structure()
elif choice == "5":
return select_one_band_structure()
elif choice == "6":
return charge_density()
elif choice == "7":
return spin_density()
elif choice == "8":
return charge_density_diff()
elif choice == "9":
return spin_density_component()
elif choice == "10":
return chg_locp_average()
elif choice == "11":
return optics_analysis()
elif choice == "12":
return elastic_analysis()
elif choice == "13":
return aimd_analysis()
else:
print("unknown choice, check the input")
goto.input3
# online exctraction
elif choice == "e1":
return get_mp_banddos()
elif choice == "e2":
return get_mp_structure()
elif choice == "e3":
return get_mp_properties()
elif choice == "e4":
return get_mp_phase_graph()
elif choice == "e5":
return get_oqmd_structure()
elif choice == "88":
os._exit(0)
else:
print("unknown choice, return now")
return None
