parser_exciting.py 12.8 KB
Newer Older
1
import setup_paths
2
3
import numpy as np
from nomadcore.simple_parser import SimpleMatcher as SM, mainFunction
4
from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
5
from nomadcore.caching_backend import CachingLevel
Pardini, Lorenzo (lopa)'s avatar
Pardini, Lorenzo (lopa) committed
6
import os, sys, json, exciting_parser_dos,exciting_parser_bandstructure
7

8
9
10
11
12
13
14
15
16
17
18
19
20
21
class ExcitingParserContext(object):

  def startedParsing(self, path, parser):
    self.parser=parser

  def onClose_exciting_section_lattice_vectors(self, backend, gIndex, section):
    latticeX = section["exciting_geometry_lattice_vector_x"]
    latticeY = section["exciting_geometry_lattice_vector_y"]
    latticeZ = section["exciting_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)

22
23
24
  def onClose_section_single_configuration_calculation(self, backend, gIndex, section):
    dirPath = os.path.dirname(self.parser.fIn.name)
    dosFile = os.path.join(dirPath, "dos.xml")
Pardini, Lorenzo (lopa)'s avatar
Pardini, Lorenzo (lopa) committed
25
    bandFile = os.path.join(dirPath, "bandstructure.xml")
26
27
28
    if os.path.exists(dosFile):
      with open(dosFile) as f:
        exciting_parser_dos.parseDos(f, backend)
Pardini, Lorenzo (lopa)'s avatar
Pardini, Lorenzo (lopa) committed
29
30
31
    if os.path.exists(bandFile):
      with open(bandFile) as g:
        exciting_parser_bandstructure.parseBand(g, backend)
32

Pardini, Lorenzo (lopa)'s avatar
Pardini, Lorenzo (lopa) committed
33
34
35
36
37
38
39
40
41
42
43
44
45
  xc_internal_map = {
  2: {'LDA_C_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'+'GGA_X_PBE_SOL'},
  26: {'GGA_X_WC'},
  30: {'GGA_C_AM05'+'GGA_X_AM05'},
  300: {'GGA_C_BGCP'+'GGA_X_BGCP'},
  406: {'HYB_GGA_C_PBEH'+'HYB_GGA_X_PBEH'},
  }
46

Pardini, Lorenzo (lopa)'s avatar
Pardini, Lorenzo (lopa) committed
47
print {'GGA_C_PBE'+'+'+'GGA_X_PBE'}
48
# description of the input
49
50


51
52
53
54
55
56
57
mainFileDescription = \
    SM(name = "root matcher",
       startReStr = "",
       weak = True,
       subMatchers = [
         SM(name = "header",
         startReStr = r"\s*\|\s*EXCITING\s*(?P<program_version>[-a-zA-Z0-9]+)\s*started\s*=",
58
         fixedStartValues={'program_name': 'exciting', 'program_basis_set_type': '(L)APW+lo' },
59
60
61
62
63
         sections = ["section_run"],
         subMatchers = [
	   SM(name = 'input',
              startReStr = r"\|\sStarting initialization",
              endReStr = r"\|\sEnding initialization",
64
              sections = ['section_system'],
65
66
67
68
              subMatchers = [
                SM(startReStr = r"\sLattice vectors \(cartesian\) :",
                sections = ["exciting_section_lattice_vectors"],
                subMatchers = [
69

70
    SM(startReStr = r"\s*(?P<exciting_geometry_lattice_vector_x__bohr>[-+0-9.]+)\s+(?P<exciting_geometry_lattice_vector_y__bohr>[-+0-9.]+)\s+(?P<exciting_geometry_lattice_vector_z__bohr>[-+0-9.]+)", repeats = True)
71
                ]),
Pardini, Lorenzo (lopa)'s avatar
Pardini, Lorenzo (lopa) committed
72
73
74
75
76
77
                SM(startReStr = r"\sReciprocal lattice vectors \(cartesian\) :",
                sections = ["exciting_section_reciprocal_lattice_vectors"],
                subMatchers = [

    SM(startReStr = r"\s*(?P<exciting_geometry_reciprocal_lattice_vector_x__bohr_1>[-+0-9.]+)\s+(?P<exciting_geometry_reciprocal_lattice_vector_y__bohr_1>[-+0-9.]+)\s+(?P<exciting_geometry_reciprocal_lattice_vector_z__bohr_1>[-+0-9.]+)", repeats = True)
                ]),
78
    SM(r"\s*Unit cell volume\s*:\s*(?P<exciting_unit_cell_volume__bohr3>[-0-9.]+)"),
Pardini, Lorenzo (lopa)'s avatar
Pardini, Lorenzo (lopa) committed
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
    SM(r"\s*Brillouin zone volume\s*:\s*(?P<exciting_brillouin_zone_volume__bohr_3>[-0-9.]+)"),
    SM(r"\s*Species\s*:\s*[0-9]\s*\((?P<exciting_geometry_atom_labels>[-a-zA-Z0-9]+)\)", repeats = True,
       subMatchers = [
    SM(r"\s*muffin-tin radius\s*:\s*(?P<exciting_muffin_tin_radius__bohr>[-0-9.]+)"),
    SM(r"\s*# of radial points in muffin-tin\s*:\s*(?P<exciting_muffin_tin_points>[-0-9.]+)"),
    SM(startReStr = r"\s*atomic positions\s*\(lattice\)\s*:\s*",
      subMatchers = [
        SM(r"\s*[0-9]\s*:\s*(?P<exciting_geometry_atom_positions_x__bohr>[-+0-9.]+)\s*(?P<exciting_geometry_atom_positions_y__bohr>[-+0-9.]+)\s*(?P<exciting_geometry_atom_positions_z__bohr>[-+0-9.]+)", repeats = True)
      ])
    ]),
    SM(r"\s*k-point grid\s*:\s*(?P<exciting_number_kpoint_x>[-0-9.]+)\s+(?P<exciting_number_kpoint_y>[-0-9.]+)\s+(?P<exciting_number_kpoint_z>[-0-9.]+)"),
    SM(r"\s*k-point offset\s*:\s*(?P<exciting_kpoint_offset_x>[-0-9.]+)\s+(?P<exciting_kpoint_offset_y>[-0-9.]+)\s+(?P<exciting_kpoint_offset_z>[-0-9.]+)"),
    SM(r"\s*Total number of k-points\s*:\s*(?P<exciting_number_kpoints>[-0-9.]+)"),
    SM(r"\s*R\^MT_min \* \|G\+k\|_max \(rgkmax\)\s*:\s*(?P<exciting_rgkmax__bohr>[-0-9.]+)"),
    SM(r"\s*Maximum \|G\| for potential and density\s*:\s*(?P<exciting_gmaxvr__bohr_1>[-0-9.]+)"),
    SM(r"\s*G-vector grid sizes\s*:\s*(?P<exciting_gvector_size_x>[-0-9.]+)\s+(?P<exciting_gvector_size_y>[-0-9.]+)\s+(?P<exciting_gvector_size_z>[-0-9.]+)"),
    SM(r"\s*Total number of G-vectors\s*:\s*(?P<exciting_gvector_total>[-0-9.]+)"),
    SM(startReStr = r"\s*Maximum angular momentum used for\s*",
        subMatchers = [
          SM(r"\s*APW functions\s*:\s*(?P<exciting_lmaxapw>[-0-9.]+)")
        ]),
    SM(r"\s*Total nuclear charge\s*:\s*(?P<exciting_nuclear_charge>[-0-9.]+)"),
    SM(r"\s*Total electronic charge\s*:\s*(?P<exciting_electronic_charge>[-0-9.]+)"),
    SM(r"\s*Total core charge\s*:\s*(?P<exciting_core_charge>[-0-9.]+)"),
    SM(r"\s*Total valence charge\s*:\s*(?P<exciting_valence_charge>[-0-9.]+)"),
    SM(r"\s*Effective Wigner radius, r_s\s*:\s*(?P<exciting_wigner_radius>[-0-9.]+)"),
    SM(r"\s*Number of empty states\s*:\s*(?P<exciting_empty_states>[-0-9.]+)"),
    SM(r"\s*Total number of valence states\s*:\s*(?P<exciting_valence_states>[-0-9.]+)"),
    SM(r"\s*Maximum Hamiltonian size\s*:\s*(?P<exciting_hamiltonian_size>[-0-9.]+)"),
    SM(r"\s*Maximum number of plane-waves\s*:\s*(?P<exciting_pw>[-0-9.]+)"),
    SM(r"\s*Total number of local-orbitals\s*:\s*(?P<exciting_lo>[-0-9.]+)"),
    SM(r"\s*Smearing scheme\s*:\s*(?P<exciting_smearing_type>[-a-zA-Z0-9]+)"),
    SM(r"\s*Smearing width\s*:\s*(?P<exciting_smearing_width__hartree>[-0-9.]+)"),
    SM(r"\s*Using\s*(?P<exciting_potential_mixing>[-a-zA-Z\s*]+)\s*potential mixing")
113
              ]),
Pardini, Lorenzo (lopa)'s avatar
Pardini, Lorenzo (lopa) committed
114
115
116
117
118
119
120
121
#    SM(name = "functionals",
#    sections = ['section_method'],
#    subMatchers = [
#    SM(startReStr = r"\s*Exchange-correlation type\s*:\s*(?P<exciting_xc_functional>[-0-9.]+)",
#       sections = ['section_XC_functionals'],
#       print  exciting_xc_functional),
#       XC_functional_name = ExcitingParserContext.xc_internal_map.get('exciting_xc_functional'))
#                  ]),
122
123
124
125
126
127
128
129
130
131
            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*SCF iteration number\s*:",
                  sections = ["section_scf_iteration"],
                  repeats = True,
                  subMatchers = [
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
                   SM(r"\s*Total energy\s*:\s*(?P<energy_total_scf_iteration__hartree>[-0-9.]+)"),
                   SM(r"\s*Fermi energy\s*:\s*(?P<exciting_fermi_energy_scf_iteration__hartree>[-0-9.]+)"),
                   SM(r"\s*Kinetic energy\s*:\s*(?P<electronic_kinetic_energy_scf_iteration__hartree>[-0-9.]+)"),
                   SM(r"\s*Coulomb energy\s*:\s*(?P<exciting_coulomb_energy_scf_iteration__hartree>[-0-9.]+)"),
                   SM(r"\s*Exchange energy\s*:\s*(?P<exciting_exchange_energy_scf_iteration__hartree>[-0-9.]+)"),
                   SM(r"\s*Correlation energy\s*:\s*(?P<exciting_correlation_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*Effective potential energy\s*:\s*(?P<exciting_effective_potential_energy_scf_iteration__hartree>[-0-9.]+)"),
                   SM(r"\s*Coulomb potential energy\s*:\s*(?P<exciting_coulomb_potential_energy_scf_iteration__hartree>[-0-9.]+)"),
                   SM(r"\s*xc potential energy\s*:\s*(?P<energy_XC_potential_scf_iteration__hartree>[-0-9.]+)"),
                   SM(r"\s*Hartree energy\s*:\s*(?P<exciting_hartree_energy_scf_iteration__hartree>[-0-9.]+)"),
                   SM(r"\s*Electron-nuclear energy\s*:\s*(?P<exciting_electron_nuclear_energy_scf_iteration__hartree>[-0-9.]+)"),
                   SM(r"\s*Nuclear-nuclear energy\s*:\s*(?P<exciting_nuclear_nuclear_energy_scf_iteration__hartree>[-0-9.]+)"),
                   SM(r"\s*Madelung energy\s*:\s*(?P<exciting_madelung_energy_scf_iteration__hartree>[-0-9.]+)"),
                   SM(r"\s*Core-electron kinetic energy\s*:\s*(?P<exciting_core_electron_kinetic_energy_scf_iteration__hartree>[-0-9.]+)"),
Pardini, Lorenzo (lopa)'s avatar
Pardini, Lorenzo (lopa) committed
147
148
149
150
151
152
153
                   SM(r"\s*Absolute change in total energy   (target)\s*:\s*(?P<energy_change_scf_iteration__hartree>[-0-9.]+)"),
                   SM(r"\s*DOS at Fermi energy \(states\/Ha\/cell\)\s*:\s*(?P<exciting_dos_fermi_scf_iteration__hartree_1>[-0-9.]+)"),
                   SM(r"\s*core leakage\s*:\s*(?P<exciting_core_leakage_scf_iteration>[-0-9.]+)"),
                   SM(r"\s*interstitial\s*:\s*(?P<exciting_interstitial_charge_scf_iteration>[-0-9.]+)"),
                   SM(r"\s*total charge in muffin-tins\s*:\s*(?P<exciting_total_MT_charge_scf_iteration>[-0-9.]+)"),
                   SM(r"\s*Estimated fundamental gap\s*:\s*(?P<exciting_gap_scf_iteration__hartree>[-0-9.]+)"),
                   SM(r"\s*Wall time \(seconds\)\s*:\s*(?P<exciting_time_scf_iteration>[-0-9.]+)")
154
                  ]),
155
                SM(name="final_quantities",
156
157
158
                  startReStr = r"\| Convergence targets achieved. Performing final SCF iteration\s*\+",
                  endReStr = r"\| Self-consistent loop stopped\s*\+",
                   subMatchers = [
159
160
161
162
163
164
165
166
167
168
169
170
171
172
                     SM(r"\s*Total energy\s*:\s*(?P<energy_total__hartree>[-0-9.]+)"),
                     SM(r"\s*Fermi energy\s*:\s*(?P<exciting_fermi_energy__hartree>[-0-9.]+)"),
                     SM(r"\s*Kinetic energy\s*:\s*(?P<electronic_kinetic_energy__hartree>[-0-9.]+)"),
                     SM(r"\s*Coulomb energy\s*:\s*(?P<exciting_coulomb_energy__hartree>[-0-9.]+)"),
                     SM(r"\s*Exchange energy\s*:\s*(?P<exciting_exchange_energy__hartree>[-0-9.]+)"),
                     SM(r"\s*Correlation energy\s*:\s*(?P<exciting_correlation_energy__hartree>[-0-9.]+)"),
                     SM(r"\s*Sum of eigenvalues\s*:\s*(?P<energy_sum_eigenvalues__hartree>[-0-9.]+)"),
                     SM(r"\s*Effective potential energy\s*:\s*(?P<exciting_effective_potential_energy__hartree>[-0-9.]+)"),
                     SM(r"\s*Coulomb potential energy\s*:\s*(?P<exciting_coulomb_potential_energy__hartree>[-0-9.]+)"),
                     SM(r"\s*xc potential energy\s*:\s*(?P<energy_XC_potential__hartree>[-0-9.]+)"),
                     SM(r"\s*Hartree energy\s*:\s*(?P<exciting_hartree_energy__hartree>[-0-9.]+)"),
                     SM(r"\s*Electron-nuclear energy\s*:\s*(?P<exciting_electron_nuclear_energy__hartree>[-0-9.]+)"),
                     SM(r"\s*Nuclear-nuclear energy\s*:\s*(?P<exciting_nuclear_nuclear_energy__hartree>[-0-9.]+)"),
                     SM(r"\s*Madelung energy\s*:\s*(?P<exciting_madelung_energy__hartree>[-0-9.]+)"),
Pardini, Lorenzo (lopa)'s avatar
Pardini, Lorenzo (lopa) committed
173
174
175
176
177
178
                     SM(r"\s*Core-electron kinetic energy\s*:\s*(?P<exciting_core_electron_kinetic_energy__hartree>[-0-9.]+)"),
                     SM(r"\s*DOS at Fermi energy \(states\/Ha\/cell\)\s*:\s*(?P<exciting_dos_fermi__hartree_1>[-0-9.]+)"),
                     SM(r"\s*core leakage\s*:\s*(?P<exciting_core_leakage>[-0-9.]+)"),
                     SM(r"\s*interstitial\s*:\s*(?P<exciting_interstitial_charge>[-0-9.]+)"),
                     SM(r"\s*total charge in muffin-tins\s*:\s*(?P<exciting_total_MT_charge>[-0-9.]+)"),
                     SM(r"\s*Estimated fundamental gap\s*:\s*(?P<exciting_gap__hartree>[-0-9.]+)")
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
                   ])
               ]
            )
          ])
    ])




parserInfo = {
  "name": "exciting_parser",
  "version": "1.0"
}

metaInfoPath = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(__file__)),"../../../../nomad-meta-info/meta_info/nomad_meta_info/exciting.nomadmetainfo.json"))
metaInfoEnv, warnings = loadJsonFile(filePath = metaInfoPath, dependencyLoader = None, extraArgsHandling = InfoKindEl.ADD_EXTRA_ARGS, uri = None)
195

196
197
198
199
200
201
cachingLevelForMetaName = {
                            "exciting_geometry_lattice_vector_x":CachingLevel.Cache,
                            "exciting_geometry_lattice_vector_y":CachingLevel.Cache,
                            "exciting_geometry_lattice_vector_z":CachingLevel.Cache,
                            "exciting_section_lattice_vectors": CachingLevel.Ignore
                          }
202
203

if __name__ == "__main__":
204
205
206
#    for name in metaInfoEnv.infoKinds:
#        print 'nameo', name
    mainFunction(mainFileDescription, metaInfoEnv, parserInfo, cachingLevelForMetaName = cachingLevelForMetaName, superContext=ExcitingParserContext())