parser_elk.py 15.7 KB
Newer Older
1
2
from builtins import object
import setup_paths
3
import numpy as np
4
5
6
from nomadcore.simple_parser import mainFunction, AncillaryParser, CachingLevel
from nomadcore.simple_parser import SimpleMatcher as SM
from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
Pardini, Lorenzo (lopa)'s avatar
Pardini, Lorenzo (lopa) committed
7
8
from nomadcore.unit_conversion import unit_conversion
import os, sys, json, logging
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25

class ElkContext(object):
    """context for elk parser"""

    def __init__(self):
        self.parser = None

    def initialize_values(self):
        """allows to reset values if the same superContext is used to parse different files"""
        self.metaInfoEnv = self.parser.parserBuilder.metaInfoEnv

    def startedParsing(self, path, parser):
        """called when parsing starts"""
        self.parser = parser
        # allows to reset values if the same superContext is used to parse different files
        self.initialize_values()

26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
    def onClose_x_elk_section_lattice_vectors(self, backend, gIndex, section):
      latticeX = section["x_elk_geometry_lattice_vector_x"]
      latticeY = section["x_elk_geometry_lattice_vector_y"]
      latticeZ = section["x_elk_geometry_lattice_vector_z"]
      cell = [[latticeX[0],latticeY[0],latticeZ[0]],
              [latticeX[1],latticeY[1],latticeZ[1]],
              [latticeX[2],latticeY[2],latticeZ[2]]]
      backend.addValue("simulation_cell", cell)

    def onClose_x_elk_section_reciprocal_lattice_vectors(self, backend, gIndex, section):
      recLatticeX = section["x_elk_geometry_reciprocal_lattice_vector_x"]
      recLatticeY = section["x_elk_geometry_reciprocal_lattice_vector_y"]
      recLatticeZ = section["x_elk_geometry_reciprocal_lattice_vector_z"]
      recCell = [[recLatticeX[0],recLatticeY[0],recLatticeZ[0]],
              [recLatticeX[1],recLatticeY[1],recLatticeZ[1]],
              [recLatticeX[2],recLatticeY[2],recLatticeZ[2]]]
      backend.addValue("x_elk_simulation_reciprocal_cell", recCell)

44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
    def onClose_x_elk_section_xc(self, backend, gIndex, section):
      xcNr = section["x_elk_xc_functional"][0]
      xc_internal_map = {
        2: ['LDA_C_PZ', 'LDA_X_PZ'],
        3: ['LDA_C_PW'],
        4: ['LDA_C_XALPHA'],
        5: ['LDA_C_VBH'],
        20: ['GGA_C_PBE'],
        21: ['GGA_X_PBE_R'],
        22: ['GGA_C_PBE_SOL'],
        26: ['GGA_X_WC'],
        30: ['GGA_C_AM05']
        }
      for xcName in xc_internal_map[xcNr]:
        gi = backend.openSection("section_XC_functionals")
        backend.addValue("XC_functional_name", xcName)
        backend.closeSection("section_XC_functionals", gi)

Pardini, Lorenzo (lopa)'s avatar
Pardini, Lorenzo (lopa) committed
62
63
64
    def onClose_section_single_configuration_calculation(self, backend, gIndex, section):
      dirPath = os.path.dirname(self.parser.fIn.name)
      dosFile = os.path.join(dirPath, "TDOS.OUT")
Pardini, Lorenzo (lopa)'s avatar
Pardini, Lorenzo (lopa) committed
65
      eigvalFile = os.path.join(dirPath, "EIGVAL.OUT")
Pardini, Lorenzo (lopa)'s avatar
Pardini, Lorenzo (lopa) committed
66
      if os.path.exists(dosFile):
Pardini, Lorenzo (lopa)'s avatar
Pardini, Lorenzo (lopa) committed
67
        dosGIndex=backend.openSection("section_dos")
Pardini, Lorenzo (lopa)'s avatar
Pardini, Lorenzo (lopa) committed
68
        with open(dosFile) as f:
Pardini, Lorenzo (lopa)'s avatar
Pardini, Lorenzo (lopa) committed
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
            dosE=[]
            dosV=[]
            fromH = unit_conversion.convert_unit_function("hartree", "J")
            while True:
                line = f.readline()
                if not line: break
                nrs = list(map(float,line.split()))
                if len(nrs) == 2:
                    dosV.append(nrs[1])
                    dosE.append(fromH(nrs[0]))
                elif len(nrs) != 0:
                    raise Exception("Found more than two values in dos file %s" % dosFile)
            backend.addArrayValues("dos_values", np.asarray(dosV))
            backend.addArrayValues("dos_energies", np.asarray(dosE))
        backend.closeSection("section_dos", dosGIndex)
Pardini, Lorenzo (lopa)'s avatar
Pardini, Lorenzo (lopa) committed
84
85
86
87
      if os.path.exists(eigvalFile):
        eigvalGIndex = backend.openSection("section_eigenvalues")
        with open(eigvalFile) as g:
            eigvalKpoint=[]
88
            eigvalVal=[[],[]]
Pardini, Lorenzo (lopa)'s avatar
Pardini, Lorenzo (lopa) committed
89
            eigvalOcc=[[],[]]
Pardini, Lorenzo (lopa)'s avatar
Pardini, Lorenzo (lopa) committed
90
91
92
93
94
            fromH = unit_conversion.convert_unit_function("hartree", "J")
            while 1:
              s = g.readline()
              if not s: break
              s = s.strip()
95
#              print ("s= ", s)
96
#              print ("len(s)= ", len(s))
97
98
99
100
101
              if len(s) < 20:
                continue
              elif len(s) > 50:
                eigvalVal[0].append([])
                eigvalVal[1].append([])
Pardini, Lorenzo (lopa)'s avatar
Pardini, Lorenzo (lopa) committed
102
103
                eigvalOcc[0].append([])
                eigvalOcc[1].append([])
Pardini, Lorenzo (lopa)'s avatar
Pardini, Lorenzo (lopa) committed
104
                eigvalKpoint.append(list(map(float, s.split()[1:4])))
105
106
107
108
109
110
111
112
#                print ("eigvalKpoint= ", eigvalKpoint)
              else:
                try: int(s[0])
                except ValueError:
                  continue
                else:
                  n, e, occ = s.split()
                  eigvalVal[0][-1].append(int(n))
113
                  eigvalVal[1][-1].append(fromH(float(e)))
Pardini, Lorenzo (lopa)'s avatar
Pardini, Lorenzo (lopa) committed
114
115
116
                  eigvalOcc[0][-1].append(int(n))
                  eigvalOcc[1][-1].append(float(occ))
#                  print ("eigvalOcc= ", eigvalOcc)
Pardini, Lorenzo (lopa)'s avatar
Pardini, Lorenzo (lopa) committed
117
            backend.addArrayValues("eigenvalues_kpoints", np.asarray(eigvalKpoint))
118
            backend.addArrayValues("eigenvalues_values", np.asarray(eigvalVal))
Pardini, Lorenzo (lopa)'s avatar
Pardini, Lorenzo (lopa) committed
119
            backend.addArrayValues("eigenvalues_occupation", np.asarray(eigvalOcc))
Pardini, Lorenzo (lopa)'s avatar
Pardini, Lorenzo (lopa) committed
120
121
122
123

    def onClose_section_system(self, backend, gIndex, section):
      backend.addArrayValues('configuration_periodic_dimensions', np.asarray([True, True, True]))

124
# description of the input
125
126
127
128
129
130
mainFileDescription = \
    SM(name = "root matcher",
       startReStr = "",
       weak = True,
       subMatchers = [
         SM(name = "header",
131
         startReStr = r"\s*\|\s*Elk version\s*(?P<program_version>[-a-zA-Z0-9\.]+)\s*started\s*",
132
133
134
135
         fixedStartValues={'program_name': 'elk', 'program_basis_set_type': '(L)APW+lo' },
            sections = ["section_run", "section_method"],
         subMatchers = [
           SM(name = 'input',
136
137
              startReStr = r"\|\sGround-state run starting from atomic densities\s\|\s",
              endReStr = r"\|\sDensity and potential initialised from atomic data\s",
138
139
              sections = ['section_system'],
              subMatchers = [
140
141
142
143
144
145
146
147
148
149
150
151
                SM(startReStr = r"\s*Lattice vectors :",
                sections = ["x_elk_section_lattice_vectors"],
                subMatchers = [

    SM(startReStr = r"\s*(?P<x_elk_geometry_lattice_vector_x__bohr>[-+0-9.]+)\s+(?P<x_elk_geometry_lattice_vector_y__bohr>[-+0-9.]+)\s+(?P<x_elk_geometry_lattice_vector_z__bohr>[-+0-9.]+)", repeats = True)
                ]),
                SM(startReStr = r"Reciprocal lattice vectors :",
                sections = ["x_elk_section_reciprocal_lattice_vectors"],
                subMatchers = [

    SM(startReStr = r"\s*(?P<x_elk_geometry_reciprocal_lattice_vector_x__bohr_1>[-+0-9.]+)\s+(?P<x_elk_geometry_reciprocal_lattice_vector_y__bohr_1>[-+0-9.]+)\s+(?P<x_elk_geometry_reciprocal_lattice_vector_z__bohr_1>[-+0-9.]+)", repeats = True)
                ]),
152
    SM(r"\s*Unit cell volume\s*:\s*(?P<x_elk_unit_cell_volume__bohr3>[-0-9.]+)"),
Pardini, Lorenzo (lopa)'s avatar
Pardini, Lorenzo (lopa) committed
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
    SM(r"\s*Brillouin zone volume\s*:\s*(?P<x_elk_brillouin_zone_volume__bohr_3>[-0-9.]+)"),
    SM(r"\s*Species\s*:\s*[0-9]\s*\((?P<x_elk_geometry_atom_labels>[-a-zA-Z0-9]+)\)", repeats = True,
       subMatchers = [
    SM(r"\s*muffin-tin radius\s*:\s*(?P<x_elk_muffin_tin_radius__bohr>[-0-9.]+)"),
    SM(r"\s*number of radial points in muffin-tin\s*:\s*(?P<x_elk_muffin_tin_points>[-0-9.]+)"),
    SM(startReStr = r"\s*atomic positions\s*\(lattice\)\, magnetic fields \(Cartesian\)\s*:\s*",
      subMatchers = [
        SM(r"\s*(?P<x_elk_geometry_atom_number>[+0-9]+)\s*:\s*(?P<x_elk_geometry_atom_positions_x__bohr>[-+0-9.]+)\s*(?P<x_elk_geometry_atom_positions_y__bohr>[-+0-9.]+)\s*(?P<x_elk_geometry_atom_positions_z__bohr>[-+0-9.]+)", repeats = True)
      ])
    ]),
    SM(r"\s*k-point grid\s*:\s*(?P<x_elk_number_kpoint_x>[-0-9.]+)\s+(?P<x_elk_number_kpoint_y>[-0-9.]+)\s+(?P<x_elk_number_kpoint_z>[-0-9.]+)"),
    SM(r"\s*k-point offset\s*:\s*(?P<x_elk_kpoint_offset_x>[-0-9.]+)\s+(?P<x_elk_kpoint_offset_y>[-0-9.]+)\s+(?P<x_elk_kpoint_offset_z>[-0-9.]+)"),
    SM(r"\s*Total number of k-points\s*:\s*(?P<x_elk_number_kpoints>[-0-9.]+)"),
    SM(r"\s*Muffin-tin radius times maximum \|G\+k\|\s*:\s*(?P<x_elk_rgkmax__bohr>[-0-9.]+)"),
    SM(r"\s*Maximum \|G\+k\| for APW functions\s*:\s*(?P<x_elk_gkmax__bohr_1>[-0-9.]+)"),
    SM(r"\s*Maximum \|G\| for potential and density\s*:\s*(?P<x_elk_gmaxvr__bohr_1>[-0-9.]+)"),
    SM(r"\s*G-vector grid sizes\s*:\s*(?P<x_elk_gvector_size_x>[-0-9.]+)\s+(?P<x_elk_gvector_size_y>[-0-9.]+)\s+(?P<x_elk_gvector_size_z>[-0-9.]+)"),
    SM(r"\s*Number of G-vectors\s*:\s*(?P<x_elk_gvector_total>[-0-9.]+)"),
    SM(startReStr = r"\s*Maximum angular momentum used for\s*",
        subMatchers = [
          SM(r"\s*APW functions\s*:\s*(?P<x_elk_lmaxapw>[-0-9.]+)")
        ]),
175
176
177
178
179
180
181
182
183
184
    SM(r"\s*Total nuclear charge\s*:\s*(?P<x_elk_nuclear_charge>[-0-9.]+)"),
    SM(r"\s*Total core charge\s*:\s*(?P<x_elk_core_charge>[-0-9.]+)"),
    SM(r"\s*Total valence charge\s*:\s*(?P<x_elk_valence_charge>[-0-9.]+)"),
    SM(r"\s*Total electronic charge\s*:\s*(?P<x_elk_electronic_charge>[-0-9.]+)"),
    SM(r"\s*Effective Wigner radius, r_s\s*:\s*(?P<x_elk_wigner_radius>[-0-9.]+)"),
    SM(r"\s*Number of empty states\s*:\s*(?P<x_elk_empty_states>[-0-9.]+)"),
    SM(r"\s*Total number of valence states\s*:\s*(?P<x_elk_valence_states>[-0-9.]+)"),
    SM(r"\s*Total number of core states\s*:\s*(?P<x_elk_core_states>[-0-9.]+)"),
    SM(r"\s*Total number of local-orbitals\s*:\s*(?P<x_elk_lo>[-0-9.]+)"),
    SM(r"\s*Smearing width\s*:\s*(?P<x_elk_smearing_width__hartree>[-0-9.]+)"),
185
186
    SM(startReStr = r"\s*Exchange-correlation functional\s*:\s*(?P<x_elk_xc_functional>[-0-9.]+)",
       sections = ['x_elk_section_xc'])
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
           ]),
            SM(name = "single configuration iteration",
              startReStr = r"\|\s*Self-consistent loop started\s*\|",
              sections = ["section_single_configuration_calculation"],
              repeats = True,
              subMatchers = [
                SM(name = "scfi totE",
                 startReStr =r"\|\s*Loop number\s*:",
                  sections = ["section_scf_iteration"],
                  repeats = True,
                  subMatchers = [
                   SM(r"\s*Fermi\s*:\s*(?P<x_elk_fermi_energy_scf_iteration__hartree>[-0-9.]+)"),
                   SM(r"\s*sum of eigenvalues\s*:\s*(?P<energy_sum_eigenvalues_scf_iteration__hartree>[-0-9.]+)"),
                   SM(r"\s*electron kinetic\s*:\s*(?P<electronic_kinetic_energy_scf_iteration__hartree>[-0-9.]+)"),
                   SM(r"\s*core electron kinetic\s*:\s*(?P<x_elk_core_electron_kinetic_energy_scf_iteration__hartree>[-0-9.]+)"),
                   SM(r"\s*Coulomb\s*:\s*(?P<x_elk_coulomb_energy_scf_iteration__hartree>[-0-9.]+)"),
                   SM(r"\s*Coulomb potential\s*:\s*(?P<x_elk_coulomb_potential_energy_scf_iteration__hartree>[-0-9.]+)"),
                   SM(r"\s*nuclear-nuclear\s*:\s*(?P<x_elk_nuclear_nuclear_energy_scf_iteration__hartree>[-0-9.]+)"),
                   SM(r"\s*electron-nuclear\s*:\s*(?P<x_elk_electron_nuclear_energy_scf_iteration__hartree>[-0-9.]+)"),
                   SM(r"\s*Hartree\s*:\s*(?P<x_elk_hartree_energy_scf_iteration__hartree>[-0-9.]+)"),
                   SM(r"\s*Madelung\s*:\s*(?P<x_elk_madelung_energy_scf_iteration__hartree>[-0-9.]+)"),
                   SM(r"\s*xc potential\s*:\s*(?P<energy_XC_potential_scf_iteration__hartree>[-0-9.]+)"),
                   SM(r"\s*exchange\s*:\s*(?P<x_elk_exchange_energy_scf_iteration__hartree>[-0-9.]+)"),
                   SM(r"\s*correlation\s*:\s*(?P<x_elk_correlation_energy_scf_iteration__hartree>[-0-9.]+)"),
                   SM(r"\s*electron entropic\s*:\s*(?P<x_elk_electron_entropic_energy_scf_iteration__hartree>[-0-9.]+)"),
                   SM(r"\s*total energy\s*:\s*(?P<energy_total_scf_iteration__hartree>[-0-9.]+)"),
                   SM(r"\s*Density of states at Fermi energy\s*:\s*(?P<x_elk_dos_fermi_scf_iteration__hartree_1>[-0-9.]+)"),
                   SM(r"\s*Estimated indirect band gap\s*:\s*(?P<x_elk_indirect_gap_scf_iteration__hartree>[-0-9.]+)"),
                   SM(r"\s*Estimated direct band gap\s*:\s*(?P<x_elk_direct_gap_scf_iteration__hartree>[-0-9.]+)"),
                   SM(r"\s*core\s*:\s*(?P<x_elk_core_charge_scf_iteration>[-0-9.]+)"),
                   SM(r"\s*valence\s*:\s*(?P<x_elk_valence_charge_scf_iteration>[-0-9.]+)"),
                   SM(r"\s*interstitial\s*:\s*(?P<x_elk_interstitial_charge_scf_iteration>[-0-9.]+)"),
                  ]),
                SM(name="final_quantities",
                  startReStr = r"\sConvergence targets achieved\s*\+",
                  endReStr = r"\| Self-consistent loop stopped\s*\|\+",
                   subMatchers = [
                   SM(r"\s*Fermi\s*:\s*(?P<x_elk_fermi_energy__hartree>[-0-9.]+)"),
                   SM(r"\s*sum of eigenvalues\s*:\s*(?P<energy_sum_eigenvalues__hartree>[-0-9.]+)"),
                   SM(r"\s*electron kinetic\s*:\s*(?P<electronic_kinetic_energy__hartree>[-0-9.]+)"),
                   SM(r"\s*core electron kinetic\s*:\s*(?P<x_elk_core_electron_kinetic_energy__hartree>[-0-9.]+)"),
                   SM(r"\s*Coulomb\s*:\s*(?P<x_elk_coulomb_energy__hartree>[-0-9.]+)"),
                   SM(r"\s*Coulomb potential\s*:\s*(?P<x_elk_coulomb_potential_energy__hartree>[-0-9.]+)"),
                   SM(r"\s*nuclear-nuclear\s*:\s*(?P<x_elk_nuclear_nuclear_energy__hartree>[-0-9.]+)"),
                   SM(r"\s*electron-nuclear\s*:\s*(?P<x_elk_electron_nuclear_energy__hartree>[-0-9.]+)"),
                   SM(r"\s*Hartree\s*:\s*(?P<x_elk_hartree_energy__hartree>[-0-9.]+)"),
                   SM(r"\s*Madelung\s*:\s*(?P<x_elk_madelung_energy__hartree>[-0-9.]+)"),
                   SM(r"\s*xc potential\s*:\s*(?P<energy_XC_potential__hartree>[-0-9.]+)"),
                   SM(r"\s*exchange\s*:\s*(?P<x_elk_exchange_energy__hartree>[-0-9.]+)"),
                   SM(r"\s*correlation\s*:\s*(?P<x_elk_correlation_energy__hartree>[-0-9.]+)"),
                   SM(r"\s*electron entropic\s*:\s*(?P<x_elk_electron_entropic_energy__hartree>[-0-9.]+)"),
                   SM(r"\s*total energy\s*:\s*(?P<energy_total__hartree>[-0-9.]+)"),
                   SM(r"\s*Density of states at Fermi energy\s*:\s*(?P<x_elk_dos_fermi__hartree_1>[-0-9.]+)"),
                   SM(r"\s*Estimated indirect band gap\s*:\s*(?P<x_elk_indirect_gap__hartree>[-0-9.]+)"),
                   SM(r"\s*Estimated direct band gap\s*:\s*(?P<x_elk_direct_gap__hartree>[-0-9.]+)"),
                   SM(r"\s*core\s*:\s*(?P<x_elk_core_charge_final>[-0-9.]+)"),
                   SM(r"\s*valence\s*:\s*(?P<x_elk_valence_charge_final>[-0-9.]+)"),
                   SM(r"\s*interstitial\s*:\s*(?P<x_elk_interstitial_charge_final>[-0-9.]+)")
                   ])
               ]
            )
248
          ])
249
250
251
252
253
254
255
256
257
    ])

parserInfo = {
  "name": "Elk"
}

metaInfoPath = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(__file__)),"../../../../nomad-meta-info/meta_info/nomad_meta_info/elk.nomadmetainfo.json"))
metaInfoEnv, warnings = loadJsonFile(filePath = metaInfoPath, dependencyLoader = None, extraArgsHandling = InfoKindEl.ADD_EXTRA_ARGS, uri = None)

258
259
260
261
262
263
264
265
266
267
268
cachingLevelForMetaName = {
                            "x_elk_geometry_lattice_vector_x":CachingLevel.Cache,
                            "x_elk_geometry_lattice_vector_y":CachingLevel.Cache,
                            "x_elk_geometry_lattice_vector_z":CachingLevel.Cache,
                            "x_elk_section_lattice_vectors": CachingLevel.Ignore,
                            "x_elk_geometry_reciprocal_lattice_vector_x":CachingLevel.Cache,
                            "x_elk_geometry_reciprocal_lattice_vector_y":CachingLevel.Cache,
                            "x_elk_geometry_reciprocal_lattice_vector_z":CachingLevel.Cache,
                            "x_elk_section_reciprocal_lattice_vectors": CachingLevel.Ignore
                          }

269
270
271
if __name__ == "__main__":
    superContext = ElkContext()
    mainFunction(mainFileDescription, metaInfoEnv, parserInfo, superContext = superContext)