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Merge pull request rartino#3 from Vevn/daniel_branch
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Added code for high symmetry parsing
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@danieldevo
danieldevo authored May 5, 2020
2 parents 7d2f771 + eb39503 commit 1c5846c
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Showing 2 changed files with 218 additions and 79 deletions.
13 changes: 12 additions & 1 deletion envisionpy/hdf5parser/h5writer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -100,7 +100,7 @@ def _write_steps(h5file, steps):
h5['/MD'].attrs["steps"] = steps
return

def _write_bandstruct(h5file, band_data, kval_list):
def _write_bandstruct(h5file, band_data, kval_list, parsed_symbols, parsed_coords):
with h5py.File(h5file, "a") as h5:
h5.create_dataset('BandStructure/KPoints', data=np.array(kval_list), dtype = np.float32)
for i, band in enumerate(band_data):
Expand All @@ -110,6 +110,17 @@ def _write_bandstruct(h5file, band_data, kval_list):
dataset.attrs['QuantityName'] = 'Energy'
dataset.attrs['VariableName'] = 'Band {}'.format(i)
dataset.attrs['VariableSymbol'] = '$B_{{{}}}$'.format(i)
for i in range(0, len(parsed_symbols)):
dataset = h5.create_dataset('/Highcoordinates/{}/Symbol'.format(i),
data = np.asarray(parsed_symbols[i],dtype = h5py.string_dtype()))
dataset.attrs['Unit'] = 'NoUnit'
dataset.attrs['QuantitySymbol'] = '$Character$'.format(i)
dataset.attrs['QuantityName'] = 'Symbol of highcoordinate'
dataset.attrs['VariableName'] = 'Symbol of coordinate {}'.format(i)
dataset.attrs['VariableSymbol'] = '$S_{{{}}}$'.format(i)
h5.create_dataset('/Highcoordinates/{}/Coordinates'.format(i),
data = np.array(parsed_coords[i]),
dtype = np.float32)

def _write_fermi_energy(h5file, fermi_energy):
with h5py.File(h5file,"a") as h5:
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284 changes: 206 additions & 78 deletions envisionpy/hdf5parser/vasp/bandstructure.py
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Original file line number Diff line number Diff line change
Expand Up @@ -34,90 +34,218 @@
import h5py
from h5writer import _write_bandstruct
from fermiEnergy import fermi_energy_parser
from unitcell import _find_line, coordinates_re

line_reg_int = re.compile(r'^( *[+-]?[0-9]+){3} *$')
line_reg_float = re.compile(r'( *[+-]?[0-9]*\.[0-9]+(?:[eE][+-]?[0-9]+)? *){4}')

def _parse_lattype(vasp_dir):
"""Retrieves lattice type from OUTCAR file.
Parameters
----------
vasp_dir : string
string containing path to VASP-files
Returns
-------
found_lattype : string
string of lattice type
"""
outcar_file = os.path.join(vasp_dir, 'OUTCAR')
try:
with open(outcar_file, "r") as f:
lattype_re = re.compile(r'(?<=Found a ).*?(?= cell.)')
match = False
found_lattype = []
for line in f:
match = lattype_re.search(line)
if match:
found_lattype = match.group()
except StopIteration:
pass # if EOF is reached here
except OSError:
print('OUTCAR file not in directory.')
return []
return found_lattype

def _parse_kpoints(vasp_dir):
"""Retrives coordinates from KPOINTS file
and removes duplicates.
Parameters
----------
vasp_dir : string
string containing path to VASP-files
Returns
-------
cleaned_coords : list of float
List of parsed coordinates
"""

match = False
kpoints_file = os.path.join(vasp_dir, 'KPOINTS')
try:
with open(kpoints_file, "r") as f:
found_coords = []
match = _find_line(coordinates_re, f)
while match:
coords = [float(coordinate) for coordinate in match.groups()]
found_coords.append(coords)
match = coordinates_re.search(next(f))
if not match:
match = coordinates_re.search(next(f))
except StopIteration:
pass # if EOF is reached here
except OSError:
print('KPOINTS file not in directory.')
return []
sorted_coords = sorted(found_coords)
cleaned_coords = [sorted_coords[i] for i in range(len(sorted_coords)) if i == 0 or sorted_coords[i] != sorted_coords[i-1]]

return cleaned_coords

def symmetry_retriever(vasp_dir):
"""Compares input from OUTCAR and KPOINTS with stored
coordinates and symbols to find a match. Retrieves the
matched combination. The symmetry_points and
symmetry_symbols variables contains high symmetry data
in the following order:
[CUB, BCC, FCC, TET, HEX, ORC, TRI1a/TRI2a, TRI1b/TRI2b]
Parameters
----------
vasp_dir : str
Path to directory containing vasp files
Returns:
--------
result_points: list of float
list of matched symmetry coordinates
result_symbs: list of characters
list of matched symmetry symbols
"""

symmetry_points = [[[0.0, 0.0, 0.0], [0.5, 0.5, 0.0], [0.5, 0.5, 0.5], [0.0, 0.5, 0.0]], [[0.0, 0.0, 0.0], [0.5, -0.5, 0.5], [0.25, 0.25, 0.25], [0.0, 0.0, 0.5]], [[0.0, 0.0, 0.0], [0.375, 0.375, 0.75], [0.5, 0.5, 0.5], [0.625, 0.25, 0.625], [0.5, 0.25, 0.75], [0.5, 0.0, 0.5]], [[0.0, 0.0, 0.0], [0.5, 0.5, 0.5], [0.5, 0.5, 0.0], [0.0, 0.5, 0.5], [0.0, 0.5, 0.0], [0.0, 0.0, 0.5]], [[0.0, 0.0, 0.0], [0.0, 0.0, 0.5], [0.33333, 0.33333, 0.5], [0.33333, 0.33333, 0.0], [0.5, 0.0, 0.5], [0.5, 0.0, 0.0]], [[0.0, 0.0, 0.0], [0.5, 0.5, 0.5], [0.5, 0.5, 0.0], [0.0, 0.5, 0.5], [0.5, 0.0, 0.5], [0.5, 0.0, 0.0], [0.0, 0.5, 0.0], [0.0, 0.0, 0.5]], [[0.0, 0.0, 0.0], [0.5, 0.5, 0.0], [0.0, 0.5, 0.5], [0.5, 0.0, 0.5], [0.5, 0.5, 0.5], [0.5, 0.0, 0.0], [0.0, 0.5, 0.0], [0.0, 0.0, 0.5]], [[0.0, 0.0, 0.0], [0.5, -0.5, 0.0], [0.0, 0.0, 0.5], [-0.5, -0.5, 0.5], [0.0, -0.5, 0.5], [0.0, -0.5, 0.0], [0.5, 0.0, 0.0], [-0.5, 0.0, 0.5]]]

symmetry_symbols = [['\u0393', 'M', 'R', 'X'], ['\u0393', 'H', 'P', 'N'], ['\u0393', 'K', 'L', 'U', 'W', 'X'], ['\u0393', 'A', 'M', 'R', 'X', 'Z'], ['\u0393', 'A', 'H', 'K', 'L', 'M'], ['\u0393', 'R', 'S', 'T', 'U', 'X', 'Y', 'Z'], ['\u0393', 'L', 'M', 'N', 'R', 'X', 'Y', 'Z'], ['\u0393', 'L', 'M', 'N', 'R', 'X', 'Y', 'Z']]

found_points = _parse_kpoints(vasp_dir)
found_lattype = _parse_lattype(vasp_dir)
result_points = []
result_symb = []
for i in range(len(symmetry_points)):
if len(found_points) == 8:
if found_lattype == 'simple orthorhombic':
result_points = symmetry_points[5]
result_symb = symmetry_symbols[5]
return result_points, result_symb
if found_lattype == 'triclinic':
if sorted(symmetry_points[6]) == sorted(found_points):
result_points = symmetry_points[6]
result_symb = symmetry_symbols[6]
return result_points, result_symb
if sorted(symmetry_points[7]) == sorted(found_points):
result_points = symmetry_points[7]
result_symb = symmetry_symbols[7]
return result_points, result_symb
if len(symmetry_points[i]) == len(found_points) and len(found_points) != 8:
if sorted(symmetry_points[i]) == sorted(found_points):
result_points = symmetry_points[i]
result_symb = symmetry_symbols[i]
return result_points, result_symb
return result_points, result_symb

def bandstruct_parse(file_object):
"""
Parses band structure data from EIGENVAL
Parameters
----------
file_object : file object
File object containing data in EIGENVAL
Returns
-------
band_data : list
list containing all the band data
kval_list : list
list containing all the K-points
"""
data = None
kval = None
kval_list = []
band_data = []
i = 0

for line in file_object:
match_float = line_reg_float.match(line)
match_int = line_reg_int.match(line)
if match_int:
data = [int(v) for v in line.split()]
band_data = [[] for _ in range(data[2])]
if data and match_float:
kval = []
for u in range(3):
kval.append(float(line.split()[u]))
elif kval and data:
band_data[i].append(float(line.split()[1]))
i += 1
if i == len(band_data) and kval:
kval_list.append(kval)
kval = None
i = 0
return band_data, kval_list
"""
Parses band structure data from EIGENVAL
Parameters
----------
file_object : file object
File object containing data in EIGENVAL
Returns
-------
band_data : list
list containing all the band data
kval_list : list
list containing all the K-points
"""
data = None
kval = None
kval_list = []
band_data = []
i = 0

for line in file_object:
match_float = line_reg_float.match(line)
match_int = line_reg_int.match(line)
if match_int:
data = [int(v) for v in line.split()]
band_data = [[] for _ in range(data[2])]
if data and match_float:
kval = []
for u in range(3):
kval.append(float(line.split()[u]))
elif kval and data:
band_data[i].append(float(line.split()[1]))
i += 1
if i == len(band_data) and kval:
kval_list.append(kval)
kval = None
i = 0
return band_data, kval_list


def bandstructure(h5file, vasp_dir):
"""
Parses band structure data from EIGENVAL
Parameters
----------
h5file : str
String that asserts which HDF-file to write to
vasp_dir : str
Path to directory containing EIGENVAL file
Returns
-------
bool
Return True if EIGENVAL was parsed, False otherwise
"""
if os.path.isfile(h5file):
with h5py.File(h5file, 'r') as h5:
if '/Bandstructure' in h5:
print('Band structure data already parsed. Skipping.')
return False
try:
with open(os.path.join(vasp_dir, 'EIGENVAL'), 'r') as f:
band_data, kval_list = bandstruct_parse(f)
# Get's the Fermi energy as an int if the DOSCAR file exist.
fermi_energy = fermi_energy_parser(vasp_dir)
for band in band_data:
for data in band:
data -= fermi_energy
if not band_data:
print('EIGENVAL does not contain any data for band structure. Skipping.')
return False
except OSError:
print('EIGENVAL file not in directory. Skipping.')
return False
_write_bandstruct(h5file, band_data, kval_list)
print('Band structure data was parsed successfully.')
return True
"""
Parses band structure data from EIGENVAL and
high symmetry data from OUTCAR and KPOINTS
Parameters
----------
h5file : str
String that asserts which HDF-file to write to
vasp_dir : str
Path to directory containing EIGENVAL file
Returns
-------
bool
Return True if KPOINTS and
EIGENVAL was parsed,
False otherwise
"""
if os.path.isfile(h5file):
with h5py.File(h5file, 'r') as h5:
if '/Bandstructure' and '/Highcoordinates' in h5:
print('Band structure data already parsed. Skipping.')
return False
try:
with open(os.path.join(vasp_dir, 'EIGENVAL'), 'r') as f:
band_data, kval_list = bandstruct_parse(f)
# Get's the Fermi energy as an int if the DOSCAR file exist.
fermi_energy = fermi_energy_parser(vasp_dir)
for band in band_data:
for data in band:
data -= fermi_energy
if not band_data:
print('EIGENVAL does not contain any data for band structure. Skipping.')
return False
except OSError:
print('EIGENVAL file not in directory. Skipping.')
return False

parsed_coords, parsed_symbols = symmetry_retriever(vasp_dir)
if parsed_coords:
_write_bandstruct(h5file, band_data, kval_list, parsed_symbols, parsed_coords)
print('Band structure data was parsed successfully.')
return True
elif not parsed_coords and os.path.isfile(os.path.join(vasp_dir, 'KPOINTS')) and os.path.isfile(os.path.join(vasp_dir, 'OUTCAR')):
print('Cannot interpret data in KPOINTS or OUTCAR')
return False
else:
return False

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