def prepare_ts(work_dir, finished_dirs):
result_path = os.path.join(work_dir, 'prepare_ts.xu')
if not os.path.exists(result_path):
print('Start!')
else:
print('%s exists!' % (result_path))
os.system(r'rm %s' % (result_path))
print('%s is removed!' % (result_path))
###
for dir in finished_dirs:
suf_dir = os.path.join(dir, 'suf')
ts_dir = os.path.join(dir, 'ts')
if os.path.exists(ts_dir):
if not os.path.exists(os.path.join(ts_dir, 'print-out')):
shutil.rmtree(ts_dir)
os.system(r'echo %s rming and making ts >> %s' %
(ts_dir, result_path))
os.mkdir(ts_dir)
mC.create_VASPsp(dir, suf_dir, ts_dir)
mC.create_INCAR(dir, suf_dir, ts_dir, '1')
shutil.copyfile(os.path.join(suf_dir, 'KPOINTS'),
os.path.join(ts_dir, 'KPOINTS'))
create_POSCAR(dir, suf_dir, ts_dir)
mC.create_POTCAR(ts_dir, './potpaw_PBE.54')
create_fort188(dir, suf_dir, ts_dir)
else:
os.system(r'echo %s making ts >> %s' % (ts_dir, result_path))
os.mkdir(ts_dir)
mC.create_VASPsp(dir, suf_dir, ts_dir)
mC.create_INCAR(dir, suf_dir, ts_dir, '1')
shutil.copyfile(os.path.join(suf_dir, 'KPOINTS'),
os.path.join(ts_dir, 'KPOINTS'))
create_POSCAR(dir, suf_dir, ts_dir)
mC.create_POTCAR(ts_dir, './potpaw_PBE.54')
create_fort188(dir, suf_dir, ts_dir)
def make_dopdirs(work_dir):
numbers = ['22', '23', '32', '42', '44', '45', '76', '77', '82']
elements = ['Ti', 'V', 'Ge', 'Mo', 'Ru', 'Rh', 'Os', 'Ir', 'Pb']
for base_element in elements:
suf_dir = os.path.join(work_dir, base_element + 'O2')
contcar = os.path.join(suf_dir, 'CONTCAR')
for dop_element in elements:
dop_dirname = 'dop' + base_element + 'O2' + '_' + dop_element
dop_dir = os.path.join(work_dir, dop_dirname)
dopsuf_dir = os.path.join(dop_dir, 'suf')
if not os.path.exists(dopsuf_dir):
os.mkdir(dop_dir)
os.mkdir(dopsuf_dir)
shutil.copyfile(os.path.join(suf_dir, 'INCAR'),
os.path.join(dopsuf_dir, 'INCAR'))
mS.set_INCAR(os.path.join(dopsuf_dir, 'INCAR'), 'SYSTEM',
dop_dirname + '_suf', 1)
shutil.copyfile(os.path.join(suf_dir, 'POSCAR'),
os.path.join(dopsuf_dir, 'POSCAR'))
change_POSCAR(os.path.join(dopsuf_dir, 'POSCAR'), base_element,
dop_element)
shutil.copyfile(os.path.join(suf_dir, 'KPOINTS'),
os.path.join(dopsuf_dir, 'KPOINTS'))
shutil.copyfile(os.path.join(suf_dir, 'vasp.script'),
os.path.join(dopsuf_dir, 'vasp.script'))
mC.create_POTCAR(dopsuf_dir, './data/potpaw_PBE.54')
def prepare_ab(work_dir, finished_dirs):
result_path = os.path.join(work_dir, 'prepare_Hab_sp2.xu')
if not os.path.exists(result_path):
print('Start!')
else:
print('%s exists!' % (result_path))
os.system(r'rm %s' % (result_path))
print('%s is removed!' % (result_path))
###
for dir in finished_dirs:
suf_dir = os.path.join(dir, 'suf')
ab_dir = os.path.join(dir, 'Hab_sp2')
if os.path.exists(ab_dir):
print(ab_dir)
if not os.path.exists(os.path.join(ab_dir, 'print-out')):
shutil.rmtree(ab_dir)
os.system(r'echo %s rming and making ab >> %s' %
(ab_dir, result_path))
os.mkdir(ab_dir)
mC.create_VASPsp(dir, suf_dir, ab_dir)
mC.create_INCAR(dir, suf_dir, ab_dir, '2')
shutil.copyfile(os.path.join(suf_dir, 'KPOINTS'),
os.path.join(ab_dir, 'KPOINTS'))
create_POSCAR(dir, suf_dir, ab_dir)
mC.create_POTCAR(ab_dir, './data/potpaw_PBE.54')
else:
print(ab_dir)
os.system(r'echo %s making ab >> %s' % (ab_dir, result_path))
os.mkdir(ab_dir)
mC.create_VASPsp(dir, suf_dir, ab_dir)
mC.create_INCAR(dir, suf_dir, ab_dir, '2')
shutil.copyfile(os.path.join(suf_dir, 'KPOINTS'),
os.path.join(ab_dir, 'KPOINTS'))
create_POSCAR(dir, suf_dir, ab_dir)
mC.create_POTCAR(ab_dir, './data/potpaw_PBE.54')
def prepare_fs(work_dir, finished_dirs):
result_path = os.path.join(work_dir, 'prepare_fs_M.xu')
if not os.path.exists(result_path):
print('Start!')
else:
print('%s exists!' % (result_path))
os.system(r'rm %s' % (result_path))
print('%s is removed!' % (result_path))
###
for dir in finished_dirs:
ts_dir = os.path.join(dir, 'ts')
fs_dir = os.path.join(dir, 'fs')
if os.path.exists(fs_dir):
if not os.path.exists(os.path.join(fs_dir, 'print-out')):
print(fs_dir)
shutil.rmtree(fs_dir)
os.system(r'echo %s rming and making fs >> %s' %
(fs_dir, result_path))
os.mkdir(fs_dir)
mC.create_VASPsp(dir, ts_dir, fs_dir)
mC.create_INCAR(dir, ts_dir, fs_dir, '2')
shutil.copyfile(os.path.join(ts_dir, 'CONTCAR'),
os.path.join(fs_dir, 'POSCAR'))
shutil.copyfile(os.path.join(ts_dir, 'KPOINTS'),
os.path.join(fs_dir, 'KPOINTS'))
mC.create_POTCAR(fs_dir, './data/potpaw_PBE.54')
else:
print(fs_dir)
os.system(r'echo %s making fs >> %s' % (fs_dir, result_path))
os.mkdir(fs_dir)
mC.create_VASPsp(dir, ts_dir, fs_dir)
mC.create_INCAR(dir, ts_dir, fs_dir, '2')
shutil.copyfile(os.path.join(ts_dir, 'KPOINTS'),
os.path.join(fs_dir, 'KPOINTS'))
shutil.copyfile(os.path.join(ts_dir, 'CONTCAR'),
os.path.join(fs_dir, 'POSCAR'))
mC.create_POTCAR(fs_dir, './data/potpaw_PBE.54')