def main():
"""
The main function. Extracts the data specified in the input arguments.
If no argument is given the default is to get all data.
If a path is given, that will be used as the current directory.
"""
current_path = getcwd()
if len(sys.argv) == 1:
sys.argv = sys.argv + ['kpoints', 'kpoint_type', 'total_kpoints',
'title', 'formula_unit',
'total_energy', 'all_energies',
'total_cpu_time', 'encut', 'surface_area',
'print', 'dos']
elif isdir(sys.argv[1]):
current_path = sys.argv[1]
rf = open('%s/results.csv' % current_path, 'wb')
result_csv_file = writer(rf, delimiter=',', quotechar='|',
quoting=QUOTE_MINIMAL)
written_header = False
paths = Find(current_path, 'OUTCAR')
for path in paths:
if outcar_is_needed(): outcar = Outcar(path)
if oszicar_is_needed(): oszicar = Oszicar(path)
if poscar_is_needed(): poscar = Poscar(path)
if contcar_is_needed(): contcar = Contcar(path)
if kpoints_is_needed(): kpoints = Kpoints(path, extract=True)
if doscar_is_needed(): doscar = Doscar(path)
results = []
col_titles = []
for argument in sys.argv:
if argument == 'title':
if 'Title' not in col_titles:
col_titles.append('Title')
results.append(contcar.title)
elif argument == 'lattice_constant':
if 'a0 [Ang]' not in col_titles:
col_titles.append('a0 [Ang]')
results.append(contcar.supercell.a0)
elif argument == 'coa':
if 'c/a' not in col_titles:
col_titles.append('c/a')
try:
results.append(contcar.coa)
except:
print contcar.path
elif argument == 'average_u':
if '<u>' not in col_titles:
col_titles.append('<u>')
results.append(contcar.calculate_average_u())
elif argument == 'surface_area':
if 'Surface Area [Ang^2]' not in col_titles:
col_titles.append('Surface Area [Ang^2]')
results.append(contcar.surface_area)
elif argument == 'formula_unit':
if 'Formula unit' not in col_titles:
col_titles.append('Formula unit')
results.append(contcar.formula_unit)
elif argument == 'adatom_pos':
found = False
if 'adatom_pos' not in col_titles:
col_titles += ['adatom x', 'adatom y', 'adatom z']
try:
contcar.find_adatoms()
for atom in contcar.supercell.atoms:
if atom.adatom:
if 'real' in sys.argv:
results += list(contcar.supercell.convert_to_real(atom.position))
else:
results += list(atom.position)
found = True
break
except:
print "Error: No CONTCAR found, trying POSCAR instead!"
if not found:
try:
poscar.find_adatoms()
for atom in poscar.supercell.atoms:
if atom.adatom:
if 'real' in sys.argv:
results += list(poscar.supercell.convert_to_real(atom.position))
else:
results += list(atom.position)
break
except:
print "Error: No POSCAR found either!"
elif argument == 'old_adatom_pos':
if 'old_adatom_pos' not in col_titles:
col_titles += ['old-adatom x', 'old-adatom y', 'old-adatom z']
poscar.find_adatoms()
for atom in poscar.supercell.atoms:
if atom.adatom:
if 'real' in sys.argv:
results += list(poscar.supercell.convert_to_real(atom.position))
else:
results += list(atom.position)
break
elif argument == 'total_energy':
if 'Total Energy [eV]' not in col_titles:
col_titles.append('Total Energy [eV]')
results.append(oszicar.total_energy)
elif argument == 'magmom':
if 'Magmom' not in col_titles:
col_titles.append('Magmom')
results.append(oszicar.magmom)
elif argument == 'all_energies':
f = open('%s/all_energies.csv' % current_path, 'wb')
energy_csv_file = writer(f, delimiter=',', quotechar='|',
quoting=QUOTE_MINIMAL)
energy_csv_file.writerow([contcar.title] + oszicar.all_energies)
f.close()
elif argument == 'nodes':
if 'Nodes' not in col_titles:
col_titles.append('Nodes')
results.append(outcar.nodes)
elif argument == 'total_cpu_time':
if 'Total CPU time' not in col_titles:
col_titles.append('Total CPU time')
results.append(outcar.total_cpu_time)
elif argument == 'volume':
if 'Volume [Ang^3]' not in col_titles:
col_titles.append('Volume [Ang^3]')
results.append(outcar.volume)
elif argument == 'total_nr_of_ions':
if 'Nr of ions' not in col_titles:
col_titles.append('Nr of ions')
results.append(outcar.total_nr_of_ions)
elif argument == 'kpoints':
if 'K-points' not in col_titles:
col_titles.append('K-points')
results.append("%ix%ix%i" % outcar.kpoints)
elif argument == 'total_kpoints':
if 'Total K-points' not in col_titles:
col_titles.append('Total K-points')
results.append(outcar.total_kpoints)
elif argument == 'nkpts':
if 'Total K-points' not in col_titles:
col_titles.append('NKPTS')
results.append(outcar.nkpts)
elif argument == 'kpoint_type':
if 'K-mesh type' not in col_titles:
col_titles.append('K-mesh type')
results.append(kpoints.mesh_type)
elif argument == 'encut':
if 'ENCUT' not in col_titles:
col_titles.append('ENCUT')
results.append(outcar.encut)
elif argument == 'bandgap':
if 'Bandgap [eV]' not in col_titles:
col_titles.append('Bandgap [eV]')
results.append(doscar.bandgap)
elif argument == 'dos':
f = open('%s/dos.csv' % current_path, 'w')
f.write("Fermi level,Bandgap\n")
f.write("%f,%f\n" % (doscar.fermi_level, doscar.bandgap))
f.write("Energy,DOS,Integrated DOS\n")
for line in doscar.dos:
f.write("%s,%s,%s\n" % (line[0], line[1], line[2]))
f.close()
elif argument == 'dos_per_atom':
i = 0
line = 0
for count in contcar.counts:
int_dos = [[0] * 3] * doscar.steps
f = open('%s/dos%s.csv' % (current_path, outcar.atom_symbols[i]), 'w')
dos_csv_file = writer(f, delimiter=',', quotechar='|',
quoting=QUOTE_MINIMAL)
dos_csv_file.writerow(['Symbol', 'Count'])
dos_csv_file.writerow([outcar.atom_symbols[i], count])
for atom in range(line, line + count):
for energy in range(0, doscar.steps):
int_dos[energy] = [doscar.dos_per_atom[atom][energy][0],
int_dos[energy][1] + doscar.dos_per_atom[atom][energy][4],
int_dos[energy][2] + doscar.dos_per_atom[atom][energy][5]]
dos_csv_file.writerow(['Energy', 'DOS', 'Integrated DOS'])
for row in int_dos:
dos_csv_file.writerow(row)
f.close()
line += count
i += 1 # Choose correct symbol
if not written_header:
result_csv_file.writerow(col_titles)
written_header = True
result_csv_file.writerow(results)
rf.close()
if 'print' in sys.argv:
system('/bin/cat "%s/results.csv"' % current_path)
def main():
"""
The main function. Extracts the data specified in the input arguments.
If no argument is given the default is to get all data.
If a path is given, that will be used as the current directory.
"""
if "path=" in sys.argv[1]:
current_path = sys.argv[1][5:]
else:
current_path = getcwd()
print current_path
if len(sys.argv) == 1:
sys.argv = sys.argv + ['kpoints', 'kpoint_type', 'total_kpoints',
'title', 'formula_unit',
'total_energy', 'all_energies',
'total_cpu_time', 'encut', 'surface_area',
'print', 'dos']
elif isdir(sys.argv[1]):
current_path = sys.argv[1]
rf = open('%s/results.csv' % current_path, 'wb')
result_csv_file = writer(rf, delimiter=',', quotechar='|',
quoting=QUOTE_MINIMAL)
written_header = False
paths = Find(current_path, ['OUTCAR', 'OUTCAR.gz', 'OUTCAR.bz2'])
for path in paths:
if outcar_is_needed(): outcar = Outcar(path)
if oszicar_is_needed(): oszicar = Oszicar(path)
if poscar_is_needed(): poscar = Poscar(path)
if contcar_is_needed(): contcar = Contcar(path)
if kpoints_is_needed(): kpoints = Kpoints(path, extract=True)
if doscar_is_needed(): doscar = Doscar(path)
results = []
col_titles = []
for argument in sys.argv:
if argument == 'title':
if 'Title' not in col_titles:
col_titles.append('Title')
results.append(contcar.title)
elif argument == 'lattice_constant' or argument =='alat':
if 'a0 [Ang]' not in col_titles:
col_titles.append('a0 [Ang]')
results.append(contcar.supercell.a0)
elif argument == 'coa':
if 'c/a' not in col_titles:
col_titles.append('c/a')
try:
results.append(contcar.coa)
except:
print contcar.path
elif argument == 'average_u':
if '<u>' not in col_titles:
col_titles.append('<u>')
results.append(contcar.calculate_average_u())
elif argument == 'surface_area':
if 'Surface Area [Ang^2]' not in col_titles:
col_titles.append('Surface Area [Ang^2]')
results.append(contcar.surface_area)
elif argument == 'formula_unit':
if 'Formula unit' not in col_titles:
col_titles.append('Formula unit')
results.append(contcar.formula_unit)
elif argument == 'adatom_pos':
found = False
if 'adatom_pos' not in col_titles:
col_titles += ['adatom x', 'adatom y', 'adatom z']
try:
contcar.find_adatoms()
for atom in contcar.supercell.atoms:
if atom.adatom:
if 'real' in sys.argv:
results += list(contcar.supercell.convert_to_real(atom.position))
else:
results += list(atom.position)
found = True
break
except:
print "Error: No CONTCAR found, trying POSCAR instead!"
if not found:
try:
poscar.find_adatoms()
for atom in poscar.supercell.atoms:
if atom.adatom:
if 'real' in sys.argv:
results += list(poscar.supercell.convert_to_real(atom.position))
else:
results += list(atom.position)
break
except:
print "Error: No POSCAR found either!"
elif argument == 'old_adatom_pos':
if 'old_adatom_pos' not in col_titles:
col_titles += ['old-adatom x', 'old-adatom y', 'old-adatom z']
poscar.find_adatoms()
for atom in poscar.supercell.atoms:
if atom.adatom:
if 'real' in sys.argv:
results += list(poscar.supercell.convert_to_real(atom.position))
else:
results += list(atom.position)
break
elif argument == 'total_energy':
if 'Total Energy [eV]' not in col_titles:
col_titles.append('Total Energy [eV]')
results.append(oszicar.total_energy)
elif argument == 'magmom':
if 'Magmom' not in col_titles:
col_titles.append('Magmom')
results.append(oszicar.magmom)
elif argument == 'all_energies':
f = open('%s/all_energies.csv' % current_path, 'wb')
energy_csv_file = writer(f, delimiter=',', quotechar='|',
quoting=QUOTE_MINIMAL)
energy_csv_file.writerow([contcar.title] + oszicar.all_energies)
f.close()
elif argument == 'nodes':
if 'Nodes' not in col_titles:
col_titles.append('Nodes')
results.append(outcar.nodes)
elif argument == 'total_cpu_time':
if 'Total CPU time' not in col_titles:
col_titles.append('Total CPU time')
results.append(outcar.total_cpu_time)
elif argument == 'volume':
if 'Volume [Ang^3]' not in col_titles:
col_titles.append('Volume [Ang^3]')
results.append(outcar.volume)
elif argument == 'total_nr_of_ions':
if 'Nr of ions' not in col_titles:
col_titles.append('Nr of ions')
results.append(outcar.total_nr_of_ions)
elif argument == 'kpoints':
if 'K-points' not in col_titles:
col_titles.append('K-points')
results.append("%ix%ix%i" % outcar.kpoints)
elif argument == 'total_kpoints':
if 'Total K-points' not in col_titles:
col_titles.append('Total K-points')
results.append(outcar.total_kpoints)
elif argument == 'nkpts':
if 'Total K-points' not in col_titles:
col_titles.append('NKPTS')
results.append(outcar.nkpts)
elif argument == 'kpoint_type':
if 'K-mesh type' not in col_titles:
col_titles.append('K-mesh type')
results.append(kpoints.mesh_type)
elif argument == 'encut':
if 'ENCUT' not in col_titles:
col_titles.append('ENCUT')
results.append(outcar.encut)
elif argument == 'bandgap':
if 'Bandgap [eV]' not in col_titles:
col_titles.append('Bandgap [eV]')
results.append(doscar.bandgap)
elif argument == 'dos':
f = open('%s/dos.csv' % current_path, 'w')
f.write("Fermi level,Bandgap\n")
f.write("%f,%f\n" % (doscar.fermi_level, doscar.bandgap))
f.write("Energy,DOS,Integrated DOS\n")
for line in doscar.dos:
f.write("%s,%s,%s\n" % (line[0], line[1], line[2]))
f.close()
elif argument == 'dos_per_atom':
i = 0
line = 0
for count in contcar.counts:
int_dos = [[0] * 3] * doscar.steps
f = open('%s/dos%s.csv' % (current_path, outcar.atom_symbols[i]), 'w')
dos_csv_file = writer(f, delimiter=',', quotechar='|',
quoting=QUOTE_MINIMAL)
dos_csv_file.writerow(['Symbol', 'Count'])
dos_csv_file.writerow([outcar.atom_symbols[i], count])
for atom in range(line, line + count):
for energy in range(0, doscar.steps):
int_dos[energy] = [doscar.dos_per_atom[atom][energy][0],
int_dos[energy][1] + doscar.dos_per_atom[atom][energy][4],
int_dos[energy][2] + doscar.dos_per_atom[atom][energy][5]]
dos_csv_file.writerow(['Energy', 'DOS', 'Integrated DOS'])
for row in int_dos:
dos_csv_file.writerow(row)
f.close()
line += count
i += 1 # Choose correct symbol
elif argument == 'polarization':
if 'p_ionX' not in col_titles:
col_titles = col_titles + ['p_ionX [eAng]', 'p_ionY [eAng]', 'p_ionZ [eAng]',
'p_elX [eAng]', 'p_elY [eAng]', 'p_elZ [eAng]']
results = results + outcar.polarization[0] + outcar.polarization[1]
elif argument == 'ic_piezoelectric_tensor':
f = open('%s/ic_piezoelectric_tensor.csv' % current_path, 'w')
f.write('Ion-clamped Piezoelectric tensor [C/m^2]\n')
pt = outcar.ic_piezo_tensor()
f.write('XX,YY,ZZ,XY,YZ,ZX\n')
for item in pt[0]:
f.write(str(item) + ',')
f.write('\n')
for item in pt[1]:
f.write(str(item) + ',')
f.write('\n')
for item in pt[2]:
f.write(str(item) + ',')
f.write('\n')
f.close()
elif argument == 'ci_e33':
if 'CI e33' not in col_titles:
col_titles.append('CI e33')
results.append(outcar.ci_e33)
elif argument == 'bc_33_average':
if 'Born EC 33 [e]' not in col_titles:
col_titles.append('Born EC 33 [e]')
results.append(outcar.born_charge_33_average)
elif argument == 'iterations':
if 'Iterations' not in col_titles:
col_titles.append('Iterations')
results.append(oszicar.iterations)
elif argument == 'permittivity':
f = open('%s/permittivity.csv' % current_path, 'w')
f.write('MACROSCOPIC STATIC DIELECTRIC TENSOR (including local field effects in DFT)\n')
permittivity = outcar.permittivity
f.write('X,Y,Z\n')
for item in permittivity[0]:
f.write(str(item) + ',')
f.write('\n')
for item in permittivity[1]:
f.write(str(item) + ',')
f.write('\n')
for item in permittivity[2]:
f.write(str(item) + ',')
f.write('\n')
f.close()
if not written_header:
result_csv_file.writerow(col_titles)
written_header = True
result_csv_file.writerow(results)
rf.close()
if 'print' in sys.argv:
system('column -s, -t "%s/results.csv"' % current_path)
