def unitcell(h5file, vasp_dir, elements=None, poscar_equiv='POSCAR'):
"""POSCAR parser
Reads lattice vectors and atom positions from POSCAR file and writes data to an HDF5 file.
If no element symbols are given as an argument, the parser looks for them in the POTCAR file,
or in POSCAR if no POTCAR file is found.
If POSCAR uses cartesian coordinates, they will be transformed.
If the given HDF5 file already contains unit cell data, nothing is parsed.
Parameters
----------
h5file : str
Path to HDF5 file
vasp_dir : str
Path to directory containing POSCAR file
elements : list of str
(Default value = None)
List of element symbols
Returns
-------
bool
True if POSCAR was parsed, False otherwise.
"""
if os.path.isfile(h5file):
with h5py.File(h5file, 'r') as h5:
if "/UnitCell" in h5:
print("Already parsed. Skipping.")
return True
try:
# Parses lattice vectors and atom positions from POSCAR
with open(os.path.join(vasp_dir,poscar_equiv), "r") as f:
scaling_factor, basis = _parse_lattice(f)
elements, atoms = _find_elements(f, elements, vasp_dir)
coords_list = _parse_coordinates(
f,
sum(atoms),
_cartesian(f),
np.linalg.inv(basis)
)
_write_basis(h5file, basis)
_write_scaling_factor(h5file, scaling_factor)
_write_coordinates(
h5file,
atoms,
coords_list,
elements,
'/UnitCell'
)
return True
except FileNotFoundError:
print("POSCAR file not found.")
return False
def md(h5_path, vasp_dir, elements=None):
"""XDATCAR parser
Reads atom positions for each time step and lattice vectors from XDATCAR file and writes data
to an HDF5 file. If no element symbols are given as an argument, the parser looks for them
in the POTCAR file, or in XDATCAR if no POTCAR file is found.
If the given HDF5 file already contains molecular dynamics data, nothing is parsed.
Parameters
----------
h5_path : str
Path to HDF5 file
vasp_dir : str
Path to directory containing XDATCAR file
elements : list of str
(Default value = None)
List of element symbols
Returns
-------
bool
True if XDATCAR was parsed, False otherwise.
"""
if os.path.isfile(h5_path):
with h5py.File(h5_path, 'r') as h5:
if "/MD" in h5:
print("Already parsed. Skipping.")
return False
try:
with open(os.path.join(vasp_dir, 'XDATCAR'), "r") as f:
scaling_factor, basis = _parse_lattice(f)
elements, atoms = _find_elements(f, elements, vasp_dir)
_write_basis(h5_path, scaling_factor * basis)
step = 0
while True:
coords_list = []
try:
coords_list = _parse_coordinates(f, sum(atoms))
except Exception as instance:
text, length = instance.args
if length != 0:
raise
return False
if not coords_list:
break
_write_md(h5_path, atoms, coords_list, elements, step)
step += 1
_write_steps(h5_path, step)
return True
except FileNotFoundError:
print("XDATCAR file not found.")
return False
def unitcell_parser(h5file, ELK_dir):
elements, number_of_atoms = find_elements(ELK_dir)
scaling_factor, basis = parse_lattice(ELK_dir)
coords_list = parse_coordinates(ELK_dir, number_of_atoms)
#with open(os.path.join(ELK_dir,info_equiv), "r") as f:
_write_basis(h5file, basis)
_write_scaling_factor(h5file, scaling_factor=1)
_write_coordinates(h5file, number_of_atoms, coords_list, elements,
'/UnitCell')
return
def parse_elf(h5file, ELK_dir):
scaling_factor, basis = parse_lattice(ELK_dir)
_write_basis(h5file, basis)
_write_scaling_factor(h5file, scaling_factor=1)
ELK_file = Path(ELK_dir).joinpath('ELF3D.OUT')
with open(ELK_file, "r+") as f:
for i in itertools.count():
array, data_dim = parse_vol(f)
if not _write_volume(h5file, i, array, data_dim, "ELF"):
return False
if not array:
break
return True
def volume(h5file, hdfgroup, vasp_dir, vasp_file):
"""
Reads volume data from vasp_file, either CHG or ELFCAR,
and stores it in an HDF-file.
Parameters
----------
h5file : str
String that asserts which HDF-file to write to
hdfgroup : str
String that asserts which group to write to in HDF-file
vasp_dir : str
Path to directory containing volume file
vasp_file : str
String that asserts which file to open in the directory
Returns
-------
bool
True if volume file was parsed, False otherwise.
"""
if os.path.isfile(h5file):
with h5py.File(h5file, 'r') as h5:
if '/{}'.format(hdfgroup) in h5:
print(vasp_file + ' already parsed. Skipping.')
return False
try:
with open(os.path.join(vasp_dir, 'POSCAR'), 'r') as f:
scaling_factor, basis = _parse_lattice(f)
_write_basis(h5file, basis)
_write_scaling_factor(h5file, scaling_factor)
except FileNotFoundError:
print("POSCAR file not in directory. Skipping.")
try:
with open(os.path.join(vasp_dir, vasp_file), "r") as f:
for i in itertools.count():
array, data_dim = parse_volume(f, hdfgroup)
if not _write_volume(h5file, i, array, data_dim, hdfgroup):
return False
if not array:
break
except FileNotFoundError:
print(vasp_file + ' file not in directory. Skipping.')
return False
print(vasp_file + ' was parsed successfully.')
return True
def parse_force_elk(h5file, elk_dir, inviwo=False, elements=None):
elements, atoms = find_elements(elk_dir)
coordinates = parse_coordinates(elk_dir, atoms)
scaling_factor, basis = parse_lattice(elk_dir)
force_tips = parse_force(elk_dir, coordinates)
if os.path.isfile(h5file):
with h5py.File(h5file, 'r') as h5:
if "/UnitCell" not in h5:
_write_basis(h5file, basis)
_write_scaling_factor(h5file, scaling_factor=1)
_write_coordinates(h5file, atoms, coordinates, elements,
'/UnitCell')
_write_forces(h5file, atoms, force_tips, '/Forces')
return True
else:
_write_basis(h5file, basis)
_write_scaling_factor(h5file, scaling_factor=1)
_write_coordinates(h5file, atoms, coordinates, elements, '/UnitCell')
_write_forces(h5file, atoms, force_tips, '/Forces')
return True
def force_parser(h5file,
vasp_dir,
inviwo=False,
elements=None,
poscar_equiv='POSCAR'):
if has_been_parsed("force_parser", h5file, vasp_dir) and inviwo:
print("Already Parsed, skipping")
return True
try:
# Parses lattice vectors and atom positions from POSCAR
with open(os.path.join(vasp_dir, poscar_equiv), "r") as f:
scaling_factor, basis = _parse_lattice(f)
elements, atoms = _find_elements(f, elements, vasp_dir)
coords_list = _parse_coordinates(f, sum(atoms), _cartesian(f),
np.linalg.inv(basis))
force_list = _parse_forces(vasp_dir, True, coords_list)
if os.path.isfile(h5file):
with h5py.File(h5file, 'r') as h5:
if "/UnitCell" in h5:
h5.close()
_write_forces(h5file, atoms, force_list, '/Forces')
return True
else:
h5.close()
_write_basis(h5file, basis)
_write_scaling_factor(h5file, scaling_factor)
_write_coordinates(h5file, atoms, coords_list,
elements, '/UnitCell')
else:
_write_basis(h5file, basis)
_write_scaling_factor(h5file, scaling_factor)
_write_coordinates(h5file, atoms, coords_list, elements,
'/UnitCell')
_write_forces(h5file, atoms, force_list, '/Forces')
return True
except FileNotFoundError:
print("POSCAR file not found........")
return False