def __init__(self, bandstructure_path, info_path, results_path):
r"""
Initialises an instance of the :class:`~effmass.inputs.Data` class and checks data using :meth:`check_data`.
Args:
bandStructure_path (str): The path to the bandstructure file.
info_path (str): The path to the info file.
results_path (str): The path to the results.out file.
Returns:
None.
"""
super().__init__()
assert (type(bandstructure_path) == str), "The bandStructure path must be a string"
assert (type(info_path) == str), "The info path must be a string"
assert (type(results_path) == str), "The results path must be a string"
# load the Octopus data
band_struct = bandstructure.Bandstructure(bandstructure_path)
self.number_of_kpoints = band_struct.num_kpoints
info_data = info.Info(info_path)
results_data = results.Results(results_path, self.number_of_kpoints)
# unpack the reciprocal lattice vector
lattice_vectors = info_data.get_lattice_vectors()
lattice_vector, reciprocal_lattice = zip(*lattice_vectors)
reciprocal_lattice_split = [lattice.split() for lattice in reciprocal_lattice]
self.reciprocal_lattice = [[float(v) for v in vector] for vector in reciprocal_lattice_split]
self.spin_channels = 1
self.number_of_bands = band_struct.num_bands
# load energies and occupancies from bandstructure file
octo_data_energies, octo_data_occupancies = band_struct.get_eigenvalues()
# change to shape (num kpoints, num bands)
self.energies = octo_data_energies.T
self.occupancy = octo_data_occupancies.T
# handle negative occupancy values
if np.any(self.occupancy < 0):
warnings.warn("One or more occupancies in your data are negative. All negative occupancies will be set to zero.")
self.occupancy[ self.occupancy < 0 ] = 0.0
# load kpoints from bandstructure file and into an numpy array
kpoints = band_struct.kpoints
kx, ky, kz = zip(*kpoints)
kpoints = np.array([kx, ky, kz])
# change to shape (number_of_kpoints, 3)
self.kpoints = kpoints.T
self.CBM = extrema._calc_CBM(self.occupancy, self.energies)
self.VBM = extrema._calc_VBM(self.occupancy, self.energies)
self.fermi_energy = (self.CBM + self.VBM) / 2
self.check_data(self.spin_channels, self.number_of_kpoints, self.number_of_bands,
self.CBM, self.VBM, self.fermi_energy, self.occupancy)
def test_bandedge_energy(toy_segments, toy_data_object):
assert math.isclose(
toy_segments[0]._bandedge_energy(toy_data_object),
extrema._calc_VBM(toy_data_object.occupancy, toy_data_object.energies))
assert math.isclose(
toy_segments[1]._bandedge_energy(toy_data_object),
extrema._calc_CBM(toy_data_object.occupancy, toy_data_object.energies))
assert math.isclose(
toy_segments[2]._bandedge_energy(toy_data_object),
extrema._calc_CBM(toy_data_object.occupancy, toy_data_object.energies))
def __init__(self, outcar_path, procar_path, ignore=0):
r"""
Initialises an instance of the :class:`~effmass.inputs.Data` class and checks data using :meth:`check_data`.
Args:
outcar_path (str): The path to the OUTCAR file
procar_path (str): The path to the PROCAR file
ignore (int): The number of kpoints to ignore at the beginning of the bandstructure slice through kspace (useful for hybrid calculations where zero weightings are appended to a previous self-consistent calculation).
Returns:
None.
"""
assert (type(outcar_path) == str), "The OUTCAR path must be a string"
assert (type(procar_path) == str), "The PROCAR path must be a string"
assert (type(ignore) == int and ignore >= 0
), "The number of kpoints to ignore must be a positive integer"
reciprocal_lattice = outcar.reciprocal_lattice_from_outcar(outcar_path)
vasp_data = procar.Procar()
vasp_data.read_from_file(procar_path)
if vasp_data.calculation[
'spin_polarised']: # to account for the change in PROCAR format for calculations with 2 spin channels (1 k-point block ---> 2 k-point blocks)
blocks = 2
else:
blocks = 1
self.spin_channels = vasp_data.spin_channels
self.number_of_kpoints = vasp_data.number_of_k_points - ignore
self.number_of_bands = vasp_data.number_of_bands
self.number_of_ions = vasp_data.number_of_ions
self.kpoints = vasp_data.k_points[ignore:]
self.energies = vasp_data.bands[self.number_of_bands * ignore:,
1:].reshape(
self.number_of_kpoints,
self.number_of_bands * blocks).T
self.occupancy = vasp_data.occupancy[self.number_of_bands * ignore:,
1:].reshape(
self.number_of_kpoints,
self.number_of_bands *
blocks).T
self.reciprocal_lattice = reciprocal_lattice * 2 * math.pi
self.CBM = extrema._calc_CBM(self.occupancy, self.energies)
self.VBM = extrema._calc_VBM(self.occupancy, self.energies)
self.fermi_energy = (self.CBM + self.VBM) / 2
self.dos = []
self.integrated_dos = []
self.check_data()
def __init__(self, directory_path, output_name='calculation.out'):
r"""
Initialises an instance of the :class:`~effmass.inputs.DataAims` class and checks data using :meth:`check_data`.
Args:
directory_path (str): The path to the directory containing output, geometry.in, control.in and bandstructure files
output_name (str): Name of the output file - contrary to the rest of the files, this is chosen by the user during an Aims run. Defaults to 'aims.out'.
Returns:
None.
"""
super().__init__()
assert (type(directory_path) == str), "The file path must be a string"
"Finding reciprocal lattice vectors"
latvec = []
for line in open("{}/geometry.in".format(directory_path)):
line = line.split("\t")[0]
words = line.split()
if len(words) == 0:
continue
if words[0] == "lattice_vector":
if len(words) != 4:
raise Exception("geometry.in: Syntax error in line '"+line+"'")
latvec.append(np.array(words[1:4]))
if len(latvec) != 3:
raise Exception("geometry.in: Must contain exactly 3 lattice vectors")
latvec = np.asarray(latvec)
latvec = latvec.astype(np.float)
#Calculate reciprocal lattice vectors
rlatvec = []
volume = (np.dot(latvec[0,:],np.cross(latvec[1,:],latvec[2,:])))
rlatvec.append(np.array(2*math.pi*np.cross(latvec[1,:],latvec[2,:])/volume))
rlatvec.append(np.array(2*math.pi*np.cross(latvec[2,:],latvec[0,:])/volume))
rlatvec.append(np.array(2*math.pi*np.cross(latvec[0,:],latvec[1,:])/volume))
reciprocal_lattice = np.asarray(rlatvec)
self.reciprocal_lattice = reciprocal_lattice
"Finding spin channels"
spin_channels = 0
for line in open("{}/{}".format(directory_path, output_name)):
line = line.split("\t")[0]
if "include_spin_orbit" in line:
spin_channels = 4
break
elif "Number of spin channels" in line:
words = line.split()
spin_channels = int(words[-1])
break
self.spin_channels = spin_channels
"Finding number of bands"
number_of_bands = 0
for line in open("{}/{}".format(directory_path, output_name)):
line = line.split("\t")[0]
if "Number of Kohn-Sham" in line:
words = line.split()
number_of_bands = int(words[-1])
break
if spin_channels == 2 or spin_channels == 4: #Doubling for spin-polarised calculation
number_of_bands = 2*number_of_bands
self.number_of_bands = number_of_bands
"Finding number of kpoints and determining number of BZ paths"
number_of_kpoints = 0
number_of_BZ_paths = 0
path_list = []
for line in open("{}/{}".format(directory_path, output_name)):
line = line.split("\n")[0]
if not line.startswith("#") and "output" in line:
if "band" in line:
words = line.split()
if words[0]=="output" and words[1]=="band":
path_list.append(int(words[8]))
number_of_BZ_paths += 1
number_of_kpoints = sum(path_list)
"Reading out bandstructure files to determine kpoint, energy and occupation matrices"
kpoints = np.zeros([number_of_kpoints,3])
energies = np.zeros([number_of_bands,number_of_kpoints])
occupancy = np.zeros([number_of_bands,number_of_kpoints])
path_counter = 0
if spin_channels == 1 or spin_channels == 4:
kpoint_counter = 0
while path_counter<number_of_BZ_paths:
kpoint_counter = sum(path_list[:path_counter])
for line in open("{}/band1{:03d}.out".format(directory_path, path_counter+1)):
line = line.split("\t")[0]
words = line.split()
kpoints[int(kpoint_counter),0] = float(words[1])
kpoints[int(kpoint_counter),1] = float(words[2])
kpoints[int(kpoint_counter),2] = float(words[3])
for i in range(number_of_bands):
energies[i,int(kpoint_counter)] = float(words[5+2*i])
occupancy[i,int(kpoint_counter)] = float(words[4+2*i])
kpoint_counter += 1
path_counter +=1
if spin_channels == 2:
while path_counter<number_of_BZ_paths:
kpoint_counter = int(sum(path_list[:path_counter]))
for line in open("{}/band1{:03d}.out".format(directory_path, path_counter+1)):
line = line.split("\t")[0]
words = line.split()
kpoints[int(kpoint_counter),0] = float(words[1])
kpoints[int(kpoint_counter),1] = float(words[2])
kpoints[int(kpoint_counter),2] = float(words[3])
for i in range(number_of_bands//2):
energies[i,int(kpoint_counter)] = float(words[5+2*i])
occupancy[i,int(kpoint_counter)] = float(words[4+2*i])
kpoint_counter += 1
kpoint_counter = int(sum(path_list[:path_counter]))
for line in open("{}/band2{:03d}.out".format(directory_path, path_counter+1)):
line = line.split("\t")[0]
words = line.split()
for i in range(number_of_bands//2):
energies[number_of_bands//2+i,kpoint_counter] = float(words[5+2*i])
occupancy[number_of_bands//2+i,kpoint_counter] = float(words[4+2*i])
kpoint_counter += 1
path_counter += 1
"Delete double kpoints at path edges"
index_count = len(kpoints)
index = 0
while index < index_count-1:
if np.array_equal(kpoints[index],kpoints[index+1]):
kpoints = np.delete(kpoints,index+1,axis=0)
energies = np.delete(energies,index+1,axis=1)
occupancy = np.delete(occupancy,index+1,axis=1)
index_count = len(kpoints)
index += 1
self.number_of_kpoints = len(kpoints)
self.CBM = extrema._calc_CBM(occupancy, energies)
self.VBM = extrema._calc_VBM(occupancy, energies)
self.fermi_energy = (self.CBM + self.VBM) / 2
"Cutting energy values in a range of 30 eV above and below the Fermi level. FHI AIMS is all electron, but not all states are needed for a meaningful effmass calculation"
index_count = len(occupancy)
index = 0
while index < index_count-1:
if all(item < self.fermi_energy - 30 for item in energies[index]):
energies = np.delete(energies, index, axis = 0)
occupancy = np.delete(occupancy, index, axis = 0)
index_count = len(occupancy)
elif all(item > self.fermi_energy + 30 for item in energies[index]):
energies = np.delete(energies, index, axis = 0)
occupancy = np.delete(occupancy, index, axis = 0)
index_count = len(occupancy)
else:
index += 1
self.energies = energies
self.occupancy = occupancy
self.kpoints = kpoints
self.check_data(self.spin_channels, self.number_of_kpoints, self.number_of_bands,
self.CBM, self.VBM, self.fermi_energy, self.occupancy)
def __init__(self, outcar_path, procar_path, ignore=0, **kwargs):
r"""
Initialises an instance of the :class:`~effmass.inputs.Data` class and checks data using :meth:`check_data`.
Args:
outcar_path (str): The path to the OUTCAR file
procar_path (:obj:`str` or :obj:`list`): The path(s) to one or more PROCAR files.
ignore (int): The number of kpoints to ignore at the beginning of the bandstructure slice through kspace (useful for hybrid calculations where zero weightings are appended to a previous self-consistent calculation).
**kwargs: Additional keyword arguments for reading the PROCAR file(s).
Returns:
None.
"""
super().__init__()
assert (type(outcar_path) == str), "The OUTCAR path must be a string"
assert (type(ignore) == int and ignore >= 0
), "The number of kpoints to ignore must be a positive integer"
reciprocal_lattice = outcar.reciprocal_lattice_from_outcar(outcar_path)
if isinstance(procar_path, list):
vasp_data = procar.Procar.from_files(procar_path, **kwargs)
elif isinstance(procar_path, str):
vasp_data = procar.Procar.from_file(procar_path, **kwargs)
else:
raise TypeError('procar_path must be a string or list of strings')
self.spin_channels = vasp_data.spin_channels
self.number_of_bands = vasp_data.number_of_bands
number_of_kpoints = vasp_data.number_of_k_points
vasp_data_energies = np.array( [ band.energy for band in np.ravel( vasp_data.bands ) ] )
vasp_data_occupancies = np.array( [ band.occupancy for band in np.ravel( vasp_data.bands ) ] )
if vasp_data.calculation['spin_polarised']: # to account for the change in PROCAR format for calculations with 2 spin channels (1 k-point block ---> 2 k-point blocks)
energies = np.zeros([self.number_of_bands*2,number_of_kpoints]) # This is a very ugly way to slice 'n' dice. Should avoid creating new array and use array methods instead. But it does the job so will keep for now.
for i in range(self.number_of_bands):
energies[i] = vasp_data_energies.reshape(
number_of_kpoints*2, # factor of 2 for each kpoint block
self.number_of_bands).T[i][:number_of_kpoints]
energies[self.number_of_bands+i] = vasp_data_energies.reshape(
number_of_kpoints*2,
self.number_of_bands).T[i][number_of_kpoints:]
occupancy = np.zeros([self.number_of_bands*2,number_of_kpoints])
for i in range(self.number_of_bands):
occupancy[i] = vasp_data_occupancies.reshape(
number_of_kpoints*2,
self.number_of_bands).T[i][:number_of_kpoints]
occupancy[self.number_of_bands+i] = vasp_data_occupancies.reshape(
number_of_kpoints*2,
self.number_of_bands).T[i][number_of_kpoints:]
else:
energies = vasp_data_energies.reshape(
number_of_kpoints,
self.number_of_bands).T
occupancy = vasp_data_occupancies.reshape(
number_of_kpoints,
self.number_of_bands).T
# remove values which are from the self-consistent calculation prior to the bandstructure calculation (workflow for hybrid functionals)
self.energies = np.delete(energies,list(range(ignore)),1)
self.occupancy = np.delete(occupancy,list(range(ignore)),1)
self.number_of_kpoints = number_of_kpoints - ignore
# handle negative occupancy values
if np.any(self.occupancy < 0):
warnings.warn("One or more occupancies in your PROCAR file are negative. All negative occupancies will be set to zero.")
self.occupancy[ self.occupancy < 0 ] = 0.0
self.kpoints = np.array( [ kp.frac_coords
for kp in vasp_data.k_points[ignore:vasp_data.number_of_k_points] ] )
self.reciprocal_lattice = reciprocal_lattice * 2 * math.pi
self.CBM = extrema._calc_CBM(self.occupancy, self.energies)
self.VBM = extrema._calc_VBM(self.occupancy, self.energies)
self.fermi_energy = (self.CBM + self.VBM) / 2
self.dos = []
self.integrated_dos = []
self.check_data(self.spin_channels, self.number_of_kpoints, self.number_of_bands,
self.CBM, self.VBM, self.fermi_energy, self.occupancy)
def test_calc_VBM(toy_data_object):
assert extrema._calc_VBM(toy_data_object.occupancy,toy_data_object.energies) == 0.5
def __init__(self, outcar_path, procar_path, ignore=0):
r"""
Initialises an instance of the :class:`~effmass.inputs.Data` class and checks data using :meth:`check_data`.
Args:
outcar_path (str): The path to the OUTCAR file
procar_path (str): The path to the PROCAR file
ignore (int): The number of kpoints to ignore at the beginning of the bandstructure slice through kspace (useful for hybrid calculations where zero weightings are appended to a previous self-consistent calculation).
Returns:
None.
"""
assert (type(outcar_path) == str), "The OUTCAR path must be a string"
assert (type(procar_path) == str), "The PROCAR path must be a string"
assert (type(ignore) == int and ignore >= 0
), "The number of kpoints to ignore must be a positive integer"
reciprocal_lattice = outcar.reciprocal_lattice_from_outcar(outcar_path)
vasp_data = procar.Procar()
vasp_data.read_from_file(procar_path)
self.spin_channels = vasp_data.spin_channels
self.number_of_bands = vasp_data.number_of_bands
self.number_of_ions = vasp_data.number_of_ions
number_of_kpoints = vasp_data.number_of_k_points
if vasp_data.calculation[
'spin_polarised']: # to account for the change in PROCAR format for calculations with 2 spin channels (1 k-point block ---> 2 k-point blocks)
energies = np.zeros(
[self.number_of_bands * 2, number_of_kpoints]
) # This is a very ugly way to slice 'n' dice. Should avoid creating new array and use array methods instead. But it does the job so will keep for now.
for i in range(self.number_of_bands):
energies[i] = vasp_data.bands[:, 1:].reshape(
number_of_kpoints * 2, # factor or 2 for each kpoint block
self.number_of_bands).T[i][:number_of_kpoints]
energies[self.number_of_bands +
i] = vasp_data.bands[:, 1:].reshape(
number_of_kpoints * 2,
self.number_of_bands).T[i][number_of_kpoints:]
occupancy = np.zeros([self.number_of_bands * 2, number_of_kpoints])
for i in range(self.number_of_bands):
occupancy[i] = vasp_data.occupancy[:, 1:].reshape(
number_of_kpoints * 2,
self.number_of_bands).T[i][:number_of_kpoints]
occupancy[self.number_of_bands +
i] = vasp_data.occupancy[:, 1:].reshape(
number_of_kpoints * 2,
self.number_of_bands).T[i][number_of_kpoints:]
else:
energies = vasp_data.bands[:, 1:].reshape(number_of_kpoints,
self.number_of_bands).T
occupancy = vasp_data.occupancy[:, 1:].reshape(
number_of_kpoints, self.number_of_bands).T
# remove values which are from the self-consistent calculation prior to the bandstructure calculation (workflow for hybrid functionals)
self.energies = np.delete(energies, list(range(ignore)), 1)
self.occupancy = np.delete(occupancy, list(range(ignore)), 1)
self.number_of_kpoints = number_of_kpoints - ignore
self.kpoints = vasp_data.k_points[ignore:vasp_data.number_of_k_points]
self.reciprocal_lattice = reciprocal_lattice * 2 * math.pi
self.CBM = extrema._calc_CBM(self.occupancy, self.energies)
self.VBM = extrema._calc_VBM(self.occupancy, self.energies)
self.fermi_energy = (self.CBM + self.VBM) / 2
self.dos = []
self.integrated_dos = []
self.check_data()