Coverage for /builds/ericyuan00000/ase/ase/io/elk.py: 86.33%
256 statements
« prev ^ index » next coverage.py v7.5.3, created at 2025-06-18 01:20 +0000
1# fmt: off
3import collections
4from pathlib import Path
6import numpy as np
8from ase import Atoms
9from ase.units import Bohr, Hartree
10from ase.utils import reader, writer
12elk_parameters = {'swidth': Hartree}
15@reader
16def read_elk(fd):
17 """Import ELK atoms definition.
19 Reads unitcell, atom positions, magmoms from elk.in/GEOMETRY.OUT file.
20 """
22 lines = fd.readlines()
24 scale = np.ones(4) # unit cell scale
25 positions = []
26 cell = []
27 symbols = []
28 magmoms = []
30 # find cell scale
31 for n, line in enumerate(lines):
32 if line.split() == []:
33 continue
34 if line.strip() == 'scale':
35 scale[0] = float(lines[n + 1])
36 elif line.startswith('scale'):
37 scale[int(line.strip()[-1])] = float(lines[n + 1])
38 for n, line in enumerate(lines):
39 if line.split() == []:
40 continue
41 if line.startswith('avec'):
42 cell = np.array(
43 [[float(v) * scale[1] for v in lines[n + 1].split()],
44 [float(v) * scale[2] for v in lines[n + 2].split()],
45 [float(v) * scale[3] for v in lines[n + 3].split()]])
46 if line.startswith('atoms'):
47 lines1 = lines[n + 1:] # start subsearch
48 spfname = []
49 natoms = []
50 atpos = []
51 bfcmt = []
52 for n1, line1 in enumerate(lines1):
53 if line1.split() == []:
54 continue
55 if 'spfname' in line1:
56 spfnamenow = lines1[n1].split()[0]
57 spfname.append(spfnamenow)
58 natomsnow = int(lines1[n1 + 1].split()[0])
59 natoms.append(natomsnow)
60 atposnow = []
61 bfcmtnow = []
62 for line in lines1[n1 + 2:n1 + 2 + natomsnow]:
63 atposnow.append([float(v) for v in line.split()[0:3]])
64 if len(line.split()) == 6: # bfcmt present
65 bfcmtnow.append(
66 [float(v) for v in line.split()[3:]])
67 atpos.append(atposnow)
68 bfcmt.append(bfcmtnow)
69 # symbols, positions, magmoms based on ELK spfname, atpos, and bfcmt
70 symbols = ''
71 positions = []
72 magmoms = []
73 for n, s in enumerate(spfname):
74 symbols += str(s[1:].split('.')[0]) * natoms[n]
75 positions += atpos[n] # assumes fractional coordinates
76 if len(bfcmt[n]) > 0:
77 # how to handle cases of magmoms being one or three dim array?
78 magmoms += [m[-1] for m in bfcmt[n]]
79 atoms = Atoms(symbols, scaled_positions=positions, cell=[1, 1, 1])
80 if len(magmoms) > 0:
81 atoms.set_initial_magnetic_moments(magmoms)
82 # final cell scale
83 cell = cell * scale[0] * Bohr
85 atoms.set_cell(cell, scale_atoms=True)
86 atoms.pbc = True
87 return atoms
90@writer
91def write_elk_in(fd, atoms, parameters=None):
92 if parameters is None:
93 parameters = {}
95 parameters = dict(parameters)
96 species_path = parameters.pop('species_dir', None)
98 if parameters.get('spinpol') is None:
99 if atoms.get_initial_magnetic_moments().any():
100 parameters['spinpol'] = True
102 if 'xctype' in parameters:
103 if 'xc' in parameters:
104 raise RuntimeError("You can't use both 'xctype' and 'xc'!")
106 if parameters.get('autokpt'):
107 if 'kpts' in parameters:
108 raise RuntimeError("You can't use both 'autokpt' and 'kpts'!")
109 if 'ngridk' in parameters:
110 raise RuntimeError(
111 "You can't use both 'autokpt' and 'ngridk'!")
112 if 'ngridk' in parameters:
113 if 'kpts' in parameters:
114 raise RuntimeError("You can't use both 'ngridk' and 'kpts'!")
116 if parameters.get('autoswidth'):
117 if 'smearing' in parameters:
118 raise RuntimeError(
119 "You can't use both 'autoswidth' and 'smearing'!")
120 if 'swidth' in parameters:
121 raise RuntimeError(
122 "You can't use both 'autoswidth' and 'swidth'!")
124 inp = {}
125 inp.update(parameters)
127 if 'xc' in parameters:
128 xctype = {'LDA': 3, # PW92
129 'PBE': 20,
130 'REVPBE': 21,
131 'PBESOL': 22,
132 'WC06': 26,
133 'AM05': 30,
134 'mBJLDA': (100, 208, 12)}[parameters['xc']]
135 inp['xctype'] = xctype
136 del inp['xc']
138 if 'kpts' in parameters:
139 # XXX should generalize kpts handling.
140 from ase.calculators.calculator import kpts2mp
141 mp = kpts2mp(atoms, parameters['kpts'])
142 inp['ngridk'] = tuple(mp)
143 vkloff = [] # is this below correct?
144 for nk in mp:
145 if nk % 2 == 0: # shift kpoint away from gamma point
146 vkloff.append(0.5)
147 else:
148 vkloff.append(0)
149 inp['vkloff'] = vkloff
150 del inp['kpts']
152 if 'smearing' in parameters:
153 name = parameters.smearing[0].lower()
154 if name == 'methfessel-paxton':
155 stype = parameters.smearing[2]
156 else:
157 stype = {'gaussian': 0,
158 'fermi-dirac': 3,
159 }[name]
160 inp['stype'] = stype
161 inp['swidth'] = parameters.smearing[1]
162 del inp['smearing']
164 # convert keys to ELK units
165 for key, value in inp.items():
166 if key in elk_parameters:
167 inp[key] /= elk_parameters[key]
169 # write all keys
170 for key, value in inp.items():
171 fd.write(f'{key}\n')
172 if isinstance(value, bool):
173 fd.write(f'.{("false", "true")[value]}.\n\n')
174 elif isinstance(value, (int, float)):
175 fd.write(f'{value}\n\n')
176 else:
177 fd.write('%s\n\n' % ' '.join([str(x) for x in value]))
179 # cell
180 fd.write('avec\n')
181 for vec in atoms.cell:
182 fd.write('%.14f %.14f %.14f\n' % tuple(vec / Bohr))
183 fd.write('\n')
185 # atoms
186 species = {}
187 symbols = []
188 for a, (symbol, m) in enumerate(
189 zip(atoms.get_chemical_symbols(),
190 atoms.get_initial_magnetic_moments())):
191 if symbol in species:
192 species[symbol].append((a, m))
193 else:
194 species[symbol] = [(a, m)]
195 symbols.append(symbol)
196 fd.write('atoms\n%d\n' % len(species))
197 # scaled = atoms.get_scaled_positions(wrap=False)
198 scaled = np.linalg.solve(atoms.cell.T, atoms.positions.T).T
199 for symbol in symbols:
200 fd.write(f"'{symbol}.in' : spfname\n")
201 fd.write('%d\n' % len(species[symbol]))
202 for a, m in species[symbol]:
203 fd.write('%.14f %.14f %.14f 0.0 0.0 %.14f\n' %
204 (tuple(scaled[a]) + (m,)))
206 # if sppath is present in elk.in it overwrites species blocks!
208 # Elk seems to concatenate path and filename in such a way
209 # that we must put a / at the end:
210 if species_path is not None:
211 fd.write(f"sppath\n'{species_path}/'\n\n")
214class ElkReader:
215 def __init__(self, path):
216 self.path = Path(path)
218 def _read_everything(self):
219 yield from self._read_energy()
221 with (self.path / 'INFO.OUT').open() as fd:
222 yield from parse_elk_info(fd)
224 with (self.path / 'EIGVAL.OUT').open() as fd:
225 yield from parse_elk_eigval(fd)
227 with (self.path / 'KPOINTS.OUT').open() as fd:
228 yield from parse_elk_kpoints(fd)
230 def read_everything(self):
231 dct = dict(self._read_everything())
233 # The eigenvalue/occupation tables do not say whether there are
234 # two spins, so we have to reshape them from 1 x K x SB to S x K x B:
235 spinpol = dct.pop('spinpol')
236 if spinpol:
237 for name in 'eigenvalues', 'occupations':
238 array = dct[name]
239 _, nkpts, nbands_double = array.shape
240 assert _ == 1
241 assert nbands_double % 2 == 0
242 nbands = nbands_double // 2
243 newarray = np.empty((2, nkpts, nbands))
244 newarray[0, :, :] = array[0, :, :nbands]
245 newarray[1, :, :] = array[0, :, nbands:]
246 if name == 'eigenvalues':
247 # Verify that eigenvalues are still sorted:
248 diffs = np.diff(newarray, axis=2)
249 assert all(diffs.flat[:] > 0)
250 dct[name] = newarray
251 return dct
253 def _read_energy(self):
254 txt = (self.path / 'TOTENERGY.OUT').read_text()
255 tokens = txt.split()
256 energy = float(tokens[-1]) * Hartree
257 yield 'free_energy', energy
258 yield 'energy', energy
261def parse_elk_kpoints(fd):
262 header = next(fd)
263 lhs, rhs = header.split(':', 1)
264 assert 'k-point, vkl, wkpt' in rhs, header
265 nkpts = int(lhs.strip())
267 kpts = np.empty((nkpts, 3))
268 weights = np.empty(nkpts)
270 for ikpt in range(nkpts):
271 line = next(fd)
272 tokens = line.split()
273 kpts[ikpt] = np.array(tokens[1:4]).astype(float)
274 weights[ikpt] = float(tokens[4])
275 yield 'ibz_kpoints', kpts
276 yield 'kpoint_weights', weights
279def parse_elk_info(fd):
280 dct = collections.defaultdict(list)
281 fd = iter(fd)
283 spinpol = None
284 converged = False
285 actually_did_not_converge = False
286 # Legacy code kept track of both these things, which is strange.
287 # Why could a file both claim to converge *and* not converge?
289 # We loop over all lines and extract also data that occurs
290 # multiple times (e.g. in multiple SCF steps)
291 for line in fd:
292 # "name of quantity : 1 2 3"
293 tokens = line.split(':', 1)
294 if len(tokens) == 2:
295 lhs, rhs = tokens
296 dct[lhs.strip()].append(rhs.strip())
298 elif line.startswith('Convergence targets achieved'):
299 converged = True
300 elif 'reached self-consistent loops maximum' in line.lower():
301 actually_did_not_converge = True
303 if 'Spin treatment' in line:
304 # (Somewhat brittle doing multi-line stuff here.)
305 line = next(fd)
306 spinpol = line.strip() == 'spin-polarised'
308 yield 'converged', converged and not actually_did_not_converge
309 if spinpol is None:
310 raise RuntimeError('Could not determine spin treatment')
311 yield 'spinpol', spinpol
313 if 'Fermi' in dct:
314 yield 'fermi_level', float(dct['Fermi'][-1]) * Hartree
316 if 'total force' in dct:
317 forces = []
318 for line in dct['total force']:
319 forces.append(line.split())
320 yield 'forces', np.array(forces, float) * (Hartree / Bohr)
323def parse_elk_eigval(fd):
325 def match_int(line, word):
326 number, colon, word1 = line.split()
327 assert word1 == word
328 assert colon == ':'
329 return int(number)
331 def skip_spaces(line=''):
332 while not line.strip():
333 line = next(fd)
334 return line
336 line = skip_spaces()
337 nkpts = match_int(line, 'nkpt') # 10 : nkpts
338 line = next(fd)
339 nbands = match_int(line, 'nstsv') # 15 : nstsv
341 eigenvalues = np.empty((nkpts, nbands))
342 occupations = np.empty((nkpts, nbands))
343 kpts = np.empty((nkpts, 3))
345 for ikpt in range(nkpts):
346 line = skip_spaces()
347 tokens = line.split()
348 assert tokens[-1] == 'vkl', tokens
349 assert ikpt + 1 == int(tokens[0])
350 kpts[ikpt] = np.array(tokens[1:4]).astype(float)
352 line = next(fd) # "(state, eigenvalue and occupancy below)"
353 assert line.strip().startswith('(state,'), line
354 for iband in range(nbands):
355 line = next(fd)
356 tokens = line.split() # (band number, eigenval, occ)
357 assert iband + 1 == int(tokens[0])
358 eigenvalues[ikpt, iband] = float(tokens[1])
359 occupations[ikpt, iband] = float(tokens[2])
361 yield 'ibz_kpoints', kpts
362 yield 'eigenvalues', eigenvalues[None] * Hartree
363 yield 'occupations', occupations[None]