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rework kpath generators
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@condmatr
condmatr committed Jun 3, 2023
1 parent 2593a3d commit 7a812f6
Showing 1 changed file with 74 additions and 94 deletions.
168 changes: 74 additions & 94 deletions elphonpy/bands.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,44 @@
from elphonpy.pseudo import get_pseudos


def distance_kpt_spacing(high_sym_kpoints, line_density):
kpath = []
sym_kpt_idx = []
idx = 0
for i in range(len(high_sym_kpoints)-1):
num_pts = np.int64(np.round(line_density*np.linalg.norm(high_sym_kpoints[i] - high_sym_kpoints[i+1]),0))
kpoints = np.linspace(high_sym_kpoints[i], high_sym_kpoints[i+1], num_pts)
if i == 0:
kpath = kpath + kpoints.tolist()
sym_kpt_idx.append(idx)
idx += num_pts
sym_kpt_idx.append(idx)
else:
kpath = kpath + kpoints[1:].tolist()
idx += num_pts-1
sym_kpt_idx.append(idx)

return kpath, sym_kpt_idx

def distance_kpt_spacing(high_sym_kpoints, line_density):
kpath = []
sym_kpt_idx = []
idx = 0
for i in range(len(high_sym_kpoints)-1):
num_pts = np.int64(np.round(line_density*np.linalg.norm(high_sym_kpoints[i] - high_sym_kpoints[i+1]),0))
kpoints = np.linspace(high_sym_kpoints[i], high_sym_kpoints[i+1], num_pts)
if i == 0:
kpath = kpath + kpoints.tolist()
sym_kpt_idx.append(idx)
idx += num_pts-1
sym_kpt_idx.append(idx)
else:
kpath = kpath + kpoints[1:].tolist()
idx += num_pts-1
sym_kpt_idx.append(idx)

return kpath, sym_kpt_idx

def get_simple_kpath(structure, line_density=100):
"""
Creates kpath for desired structure using SeeKPath, outputs kpath dictionary.
Expand All @@ -21,59 +59,35 @@ def get_simple_kpath(structure, line_density=100):
from pymatgen.symmetry.kpath import KPathSeek as seekpath
import numpy as np
skp = seekpath(structure, symprec=0.01)
kp = skp.get_kpoints(line_density=line_density, coords_are_cartesian=False)

path = skp.kpath
kp_recip_list = list(path['kpoints'].values())

kp_arrays = kp[0]
kp_high_sym_list = kp[1]
kpath = skp.kpath
print(kpath)

high_sym_dummy = []
high_sym_idx = []
high_sym_symbol = []
high_sym_kpt = []

kpt_out = []

for i in range(len(kp_arrays)):
if kp_high_sym_list[i] != '' and kp_high_sym_list[i] != kp_high_sym_list[i-1]:
high_sym_dummy.append(i)
if i-1 in high_sym_dummy:
high_sym_symbol.remove(high_sym_symbol[-1])
high_sym_symbol.remove(high_sym_symbol[-1])
high_sym_symbol.append(f'{kp_high_sym_list[i-1]}|{kp_high_sym_list[i]}')
continue
if kp_high_sym_list[i] == 'GAMMA':
high_sym_symbol.append('$\Gamma$')
high_sym_kpt.append(np.round(kp_arrays[i],8).tolist())
else:
high_sym_symbol.append(kp_high_sym_list[i])
high_sym_kpt.append(np.round(kp_arrays[i],8).tolist())

if not np.array_equal(kp_arrays[i], kp_arrays[i-1]):
kpt_out.append(kp_arrays[i].tolist())
else:
continue

for i in range(len(kpt_out)):
for j in kp_recip_list:
if np.allclose(np.array(kpt_out[i]), np.array(j), rtol=1e-08,atol=1e-08):
high_sym_idx.append(i)

kpath_dict = {'path_symbols':high_sym_symbol,
'path_kpoints':high_sym_kpt,
'path_idx_wrt_kpt':high_sym_idx,
'kpoints':kpt_out}
sym_kpt_list = []

for sym in kpath['path'][0]:
sym_kpt_list.append(kpath['kpoints'][sym])

high_sym_kpoints = np.array(sym_kpt_list)

kpoint_list, sym_idx = distance_kpt_spacing(high_sym_kpoints, line_density)
sym_list = kpath['path'][0]

for i in range(len(sym_list)):
if sym_list[i] == 'GAMMA':
sym_list[i] = '$\Gamma$'

kpath_dict = {'path_symbols':sym_list,
'path_kpoints':sym_kpt_list,
'path_idx_wrt_kpt':sym_idx,
'kpoints':kpoint_list}

return kpath_dict

def get_custom_kpath(structure, symbol_kpoints_dict, line_density=100):
def get_custom_kpath(symbol_kpoints_dict, line_density=100):
"""
Creates kpath for desired structure using SeeKPath, outputs kpath dictionary.
Creates kpath for desired structure using custom kpath, outputs kpath dictionary.
Args:
structure (Pymatgen Structure or IStructure): Input structure.
symbol_kpoints_dict (dict): A dictionary containing 'path_symbols':a list of symbol strings.
'path_kpoints':a list of path kpoints.
e.g.
Expand All @@ -90,58 +104,24 @@ def get_custom_kpath(structure, symbol_kpoints_dict, line_density=100):
Returns:
kpath_dict (dict): Dictionary containing kpath information.
"""
import numpy as np

recip_lat = structure.lattice.reciprocal_lattice

kpoints = np.array(symbol_kpoints_dict['path_kpoints'])

all_kp = []

for i in range(len(kpoints)-1):

kpi = kpoints[i]
kpf = kpoints[i+1]

weight = round(recip_lat.get_all_distances(kpi, kpf)[0][0]*line_density)

kp_section = np.concatenate((np.linspace(kpi[0], kpf[0], weight).reshape(-1,1), np.linspace(kpi[1],kpf[1], weight).reshape(-1,1), np.linspace(kpi[2],kpf[2], weight).reshape(-1,1)), axis=1)
all_kp.append(kp_section)

kp_arrays = np.vstack(all_kp)

kp_sym = symbol_kpoints_dict['path_symbols']
path_kp = symbol_kpoints_dict['path_kpoints']
kp_sym_idx = []
kpt_out = []

j = 0
for i in range(len(kp_arrays)-1):

kpt = kp_arrays[i]

if not np.allclose(kpt, kp_arrays[i+1], rtol=1e-08,atol=1e-08):
kpt_out.append(kpt.tolist())
# print(True)
if np.allclose(kpt, path_kp[j], rtol=1e-08,atol=1e-08):
# print(kpt)
if i == 0:
kp_sym_idx.append(0)
else:
kp_sym_idx.append(i-j+1)
j+=1

kp_sym_idx.append(len(kp_arrays)-j)
kpt_out.append(kp_arrays[-1].tolist())

kpath_dict = {'path_symbols':kp_sym,
'path_kpoints':path_kp,
'path_idx_wrt_kpt':kp_sym_idx,
'kpoints':kpt_out}
sym_list = symbol_kpoints_dict['path_symbols']
sym_kpt_list = symbol_kpoints_dict['path_kpoints']
high_sym_kpoints = np.array(sym_kpt_list)

kpoint_list, sym_idx = distance_kpt_spacing(high_sym_kpoints, line_density)

for i in range(len(sym_list)):
if sym_list[i] == 'GAMMA':
sym_list[i] = '$\Gamma$'

kpath_dict = {'path_symbols':sym_list,
'path_kpoints':sym_kpt_list,
'path_idx_wrt_kpt':sym_idx,
'kpoints':kpoint_list}

return kpath_dict


def bands_input_gen(prefix, structure, pseudo_dict, param_dict_scf, param_dict_bands, kpath_dict, multE=1.0, rhoe=None, workdir='./bands', copy_pseudo=False):
"""
Prepares input files for QE Bands calculation, writes input file to workdir.
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