parser_gaussian.py 24.9 KB
Newer Older
1
import setup_paths
2
from nomadcore.simple_parser import mainFunction, SimpleMatcher as SM
3
from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
4
5
6
from nomadcore.caching_backend import CachingLevel
import os, sys, json, logging
import numpy as np
7
import ase
8

Rosendo Valero Montero's avatar
Rosendo Valero Montero committed
9
# description of the output
10
11
12
mainFileDescription = SM(
    name = 'root',
    weak = True,
13
    forwardMatch = True, 
14
15
16
    startReStr = "",
    subMatchers = [
        SM(name = 'newRun',
17
18
           startReStr = r"\s*Cite this work as:",
#           endReStr = r"\s*Normal termination of Gaussian",
19
20
21
           repeats = True,
           required = True,
           forwardMatch = True,
22
23
           fixedStartValues={ 'program_name': 'Gaussian', 'program_basis_set_type': 'gaussians' },
           sections   = ['section_run'],
24
25
           subMatchers = [
               SM(name = 'header',
26
27
                  startReStr = r"\s*Cite this work as:",
                  forwardMatch = True,
28
29
30
31
                  subMatchers = [
                      SM(r"\s*Cite this work as:"),
                      SM(r"\s*Gaussian [0-9]+, Revision [A-Za-z0-9.]*,"),
                      SM(r"\s\*\*\*\*\*\*\*\*\*\*\*\**"),
32
33
                      SM(r"\s*(?P<program_name>Gaussian)\s*(?P<program_version>[0-9]+):\s*(?P<x_gaussian_program_implementation>[A-Za-z0-9-.]+)\s*(?P<x_gaussian_program_release_date>[0-9][0-9]?\-[A-Z][a-z][a-z]\-[0-9]+)"),
                      SM(r"\s*(?P<x_gaussian_program_execution_date>[0-9][0-9]?\-[A-Z][a-z][a-z]\-[0-9]+)"),
34
                      ]
35
             ),
36
37
38
39
40
               SM(name = 'globalparams',
                  startReStr = r"\s*%\w*=",
                  subFlags = SM.SubFlags.Unordered,
                  forwardMatch = True,
                  subMatchers = [
41
42
43
                      SM(r"\s*%[Cc]hk=(?P<x_gaussian_chk_file>[A-Za-z0-9.]*)"),
                      SM(r"\s*%[Mm]em=(?P<x_gaussian_memory>[A-Za-z0-9.]*)"),
                      SM(r"\s*%[Nn][Pp]roc=(?P<x_gaussian_number_of_processors>[A-Za-z0-9.]*)")
44
                      ]
45
46
47
             ),
               SM(name = 'charge_multiplicity_natoms',
               sections  = ['x_gaussian_section_system'],
Rosendo Valero Montero's avatar
Rosendo Valero Montero committed
48
49
50
51
		  startReStr = r"\s*Charge =",
                  subFlags = SM.SubFlags.Sequenced,
                  forwardMatch = True,
                  subMatchers = [
52
53
                      SM(r"\s*Charge =\s*(?P<x_gaussian_total_charge>[-+0-9]+) Multiplicity =\s*(?P<x_gaussian_spin_target_multiplicity>[0-9]+)"),
                      SM(r"\s*NAtoms=(?P<x_gaussian_natoms>[0-9]+)"),
54
                      ]
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
             ),
               SM(name = 'atomic masses',
                  sections = ['x_gaussian_section_atomic_masses'],
                  startReStr = r"\s*AtmWgt=",
                  endReStr = r"\s*Leave Link  101",
                  forwardMatch = True,
                  subMatchers = [
                      SM(r"\s*AtmWgt=\s+(?P<x_gaussian_atomic_masses>[0-9.]+(\s+[0-9.]+)(\s+[0-9.]+)?(\s+[0-9.]+)?(\s+[0-9.]+)?(\s+[0-9.]+)?(\s+[0-9.]+)?(\s+[0-9.]+)?(\s+[0-9.]+)?(\s+[0-9.]+)?)", repeats = True)
                      ]
             ),
            # this SimpleMatcher groups a single configuration calculation together with output after SCF convergence from relaxation
            SM (name = 'SingleConfigurationCalculationWithSystemDescription',
                startReStr = "\s*Standard orientation:",
#                endReStr = "\s*Link1:  Proceeding to internal job step number",
                repeats = False,
                forwardMatch = True,
                subMatchers = [
                # the actual section for a single configuration calculation starts here
                SM (name = 'SingleConfigurationCalculation',
                  startReStr = "\s*Standard orientation:",
                  repeats = True,
                  forwardMatch = True,
                  sections = ['x_gaussian_section_single_configuration_calculation'],
                  subMatchers = [
                  SM(name = 'geometry',
                   sections  = ['x_gaussian_section_geometry'],
                   startReStr = r"\s*Standard orientation",
                   endReStr = r"\s*Rotational constants",
83
                      subMatchers = [
84
                      SM(r"\s+[0-9]+\s+(?P<x_gaussian_atomic_number>[0-9]+)\s+[0-9]+\s+(?P<x_gaussian_atom_x_coord__angstrom>[-+0-9EeDd.]+)\s+(?P<x_gaussian_atom_y_coord__angstrom>[-+0-9EeDd.]+)\s+(?P<x_gaussian_atom_z_coord__angstrom>[-+0-9EeDd.]+)",repeats = True),
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
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
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
                      SM(r"\s*Rotational constants")
                    ]
                ),
                    SM(name = 'TotalEnergyScfGaussian',
                    sections  = ['x_gaussian_section_scf_iteration'],
                    startReStr = r"\s*Cycle\s+[0-9]+",
                    forwardMatch = True,
                    repeats = True, 
                    subMatchers = [
                    SM(r"\s*Cycle\s+[0-9]+"),
                    SM(r"\s*E=\s*(?P<x_gaussian_energy_total_scf_iteration__hartree>[-+0-9.]+)\s*Delta-E=\s*(?P<x_gaussian_delta_energy_total_scf_iteration__hartree>[-+0-9.]+)")
                    ]
                ), 
                    SM(name = 'TotalEnergyScfConverged',
                    sections  = ['x_gaussian_section_total_scf_one_geometry'],
                    startReStr = r"\s*SCF Done",
                    forwardMatch = True,
                    subMatchers = [
                    SM(r"\s*(?P<x_gaussian_single_configuration_calculation_converged>SCF Done):\s*[()A-Za-z0-9-]+\s*=\s*(?P<x_gaussian_energy_total_scf_converged__hartree>[-+0-9.]+)")
                    ]  
                ),
                    SM(name = 'RealSpinValue',
                    sections  = ['x_gaussian_section_real_spin_squared'],
                    startReStr = r"\s*Convg\s*=",
                    forwardMatch = True,
                    subMatchers = [
                     SM(r"\s*[A-Z][*][*][0-9]\s*=\s*(?P<x_gaussian_spin_S2>[0-9.]+)"),
                     SM(r"\s*Annihilation of the first spin contaminant"),
                     SM(r"\s*[A-Z][*][*][0-9]\s*before annihilation\s*[0-9.,]+\s*after\s*(?P<x_gaussian_after_annihilation_spin_S2>[0-9.]+)")
                     ]
                ),
                   SM(name = 'ForcesScfGaussian',
                   sections  = ['x_gaussian_section_atom_forces'],
                   startReStr = "\s*Center\s+Atomic\s+Forces ",
                   forwardMatch = True,
                   subMatchers = [
                    SM(r"\s*Center\s+Atomic\s+Forces "),
                    SM(r"\s+[0-9]+\s+[0-9]+\s+(?P<x_gaussian_atom_x_force__hartree_bohr_1>[-+0-9EeDd.]+)\s+(?P<x_gaussian_atom_y_force__hartree_bohr_1>[-+0-9EeDd.]+)\s+(?P<x_gaussian_atom_z_force__hartree_bohr_1>[-+0-9EeDd.]+)",repeats = True),
                    SM(r"\s*Cartesian Forces:\s+")
                    ]
                ),
                  SM(name = 'Geometry_optimization',
                  startReStr = r"\s*Optimization completed.",
                  subMatchers = [
                  SM(r"\s*(?P<x_gaussian_geometry_optimization_converged>Optimized Parameters)"),
                  SM(r"\s*(?P<x_gaussian_geometry_optimization_converged>Optimization stopped)"),
                  SM(r"\s+[0-9]+\s+[0-9]+\s+[0-9]+\s+[-+0-9EeDd.]+\s+[-+0-9EeDd.]+\s+[-+0-9EeDd.]+",repeats = True),
                  SM(r"\s*Distance matrix|\s*Rotational constants|\s*Stoichiometry")
                    ]
               ),
                SM(name = 'Orbital symmetries',
                sections = ['x_gaussian_section_orbital_symmetries'],
                startReStr = r"\s+Population analysis",
                subFlags = SM.SubFlags.Sequenced,
                subMatchers = [
                      SM(r"\s*Orbital symmetries"), 
                      SM(r"\s*Alpha Orbitals"),
                      SM(r"\s*Occupied\s+(?P<x_gaussian_alpha_occ_symmetry_values>\((.+)\))?"),
                      SM(r"\s+(?P<x_gaussian_alpha_occ_symmetry_values>\((.+)\)?)", repeats = True),
                      SM(r"\s*Virtual\s+(?P<x_gaussian_alpha_vir_symmetry_values>\((.+)\))?"),
                      SM(r"\s+(?P<x_gaussian_alpha_vir_symmetry_values>\((.+)\)?)", repeats = True),
                      SM(r"\s*Beta Orbitals"),
                      SM(r"\s*Occupied\s+(?P<x_gaussian_beta_occ_symmetry_values>\((.+)\))?"),
                      SM(r"\s+(?P<x_gaussian_beta_occ_symmetry_values>\((.+)\)?)", repeats = True),
                      SM(r"\s*Virtual\s+(?P<x_gaussian_beta_vir_symmetry_values>\((.+)\))?"),
                      SM(r"\s+(?P<x_gaussian_beta_vir_symmetry_values>\((.+)\)?)", repeats = True),
                      ]
             ),
                SM(name = 'Electronicstatesymmetry',
                sections = ['x_gaussian_section_symmetry'],
                startReStr = r"\s*The electronic state is",
                forwardMatch = True,
                subMatchers = [
                      SM(r"\s*The electronic state is\s*(?P<x_gaussian_elstate_symmetry>[A-Z0-9-]+)[.]")
                      ]
             ),
                SM(name = 'Eigenvalues',
                sections = ['x_gaussian_section_eigenvalues'],
                startReStr = r"\s*Alpha  occ. eigenvalues --",
                forwardMatch = True,
                subFlags = SM.SubFlags.Sequenced,
                subMatchers = [
                      SM(r"\s*Alpha  occ. eigenvalues --\s+(?P<x_gaussian_alpha_occ_eigenvalues_values>(.+)?)", repeats = True), 
                      SM(r"\s*Alpha virt. eigenvalues --\s+(?P<x_gaussian_alpha_vir_eigenvalues_values>(.+)?)", repeats = True),
                      SM(r"\s*Beta  occ. eigenvalues --\s+(?P<x_gaussian_beta_occ_eigenvalues_values>(.+)?)", repeats = True),
                      SM(r"\s*Beta virt. eigenvalues --\s+(?P<x_gaussian_beta_vir_eigenvalues_values>(.+)?)", repeats = True),
                      SM(r"\s*- Condensed to atoms (all electrons)"),
                      ]
             ),
                SM(name = 'Multipoles',
                  sections = ['x_gaussian_section_molecular_multipoles'],
                  startReStr = r"\s*Charge=",
                  forwardMatch = True,
                  subMatchers = [
                      SM(r"\s*Dipole moment "), 
                      SM(r"\s+\w+=\s+(?P<dipole_moment_x>[-+0-9EeDd.]+)\s+\w+=\s+(?P<dipole_moment_y>[-+0-9EeDd.]+)\s+\w+=\s+(?P<dipole_moment_z>[-+0-9EeDd.]+)"),
                      SM(r"\s*Quadrupole moment"), 
                      SM(r"\s+\w+=\s+(?P<quadrupole_moment_xx>[0-9-.]+)\s+\w+=\s+(?P<quadrupole_moment_yy>[0-9-.]+)\s+\w+=\s+(?P<quadrupole_moment_zz>[0-9-.]+)"), 
                      SM(r"\s+\w+=\s+(?P<quadrupole_moment_xy>[0-9-.]+)\s+\w+=\s+(?P<quadrupole_moment_xz>[0-9-.]+)\s+\w+=\s+(?P<quadrupole_moment_yz>[0-9-.]+)"),
                      SM(r"\s*Traceless Quadrupole moment"),
                      SM(r"\s+\w+=\s+[0-9-.]+\s+\w+=\s+[0-9-.]+\s+\w+=\s+[0-9-.]+"),
                      SM(r"\s+\w+=\s+[0-9-.]+\s+\w+=\s+[0-9-.]+\s+\w+=\s+[0-9-.]+"),
                      SM(r"\s*Octapole moment"),
                      SM(r"\s+\w+=\s+(?P<octapole_moment_xxx>[-+0-9EeDd.]+)\s+\w+=\s+(?P<octapole_moment_yyy>[-+0-9EeDd.]+)\s+\w+=\s+(?P<octapole_moment_zzz>[-+0-9EeDd.]+)\s+\w+=\s+(?P<octapole_moment_xyy>[-+0-9EeDd.]+)"),
                      SM(r"\s+\w+=\s+(?P<octapole_moment_xxy>[-+0-9EeDd.]+)\s+\w+=\s+(?P<octapole_moment_xxz>[-+0-9EeDd.]+)\s+\w+=\s+(?P<octapole_moment_xzz>[-+0-9EeDd.]+)\s+\w+=\s+(?P<octapole_moment_yzz>[-+0-9EeDd.]+)"),
                      SM(r"\s+\w+=\s+(?P<octapole_moment_yyz>[-+0-9EeDd.]+)\s+\w+=\s+(?P<octapole_moment_xyz>[-+0-9EeDd.]+)"),
                      SM(r"\s*Hexadecapole moment"),
                      SM(r"\s+\w+=\s+(?P<hexadecapole_moment_xxxx>[-+0-9EeDd.]+)\s+\w+=\s+(?P<hexadecapole_moment_yyyy>[-+0-9EeDd.]+)\s+\w+=\s+(?P<hexadecapole_moment_zzzz>[-+0-9EeDd.]+)\s+\w+=\s+(?P<hexadecapole_moment_xxxy>[-+0-9EeDd.]+)"),
                      SM(r"\s+\w+=\s+(?P<hexadecapole_moment_xxxz>[-+0-9EeDd.]+)\s+\w+=\s+(?P<hexadecapole_moment_yyyx>[-+0-9EeDd.]+)\s+\w+=\s+(?P<hexadecapole_moment_yyyz>[-+0-9EeDd.]+)\s+\w+=\s+(?P<hexadecapole_moment_zzzx>[-+0-9EeDd.]+)"),
                      SM(r"\s+\w+=\s+(?P<hexadecapole_moment_zzzy>[-+0-9EeDd.]+)\s+\w+=\s+(?P<hexadecapole_moment_xxyy>[-+0-9EeDd.]+)\s+\w+=\s+(?P<hexadecapole_moment_xxzz>[-+0-9EeDd.]+)\s+\w+=\s+(?P<hexadecapole_moment_yyzz>[-+0-9EeDd.]+)"),
                      SM(r"\s+\w+=\s+(?P<hexadecapole_moment_xxyz>[-+0-9EeDd.]+)\s+\w+=\s+(?P<hexadecapole_moment_yyxz>[-+0-9EeDd.]+)\s+\w+=\s+(?P<hexadecapole_moment_zzxy>[-+0-9EeDd.]+)")
                      ]
             ),    
                SM(name = 'Frequencies',
                sections = ['x_gaussian_section_frequencies'],
                startReStr = r"\s*Frequencies --",
                forwardMatch = True,
                subFlags = SM.SubFlags.Sequenced,
                subMatchers = [
                      SM(r"\s*Frequencies --\s*(?P<x_gaussian_frequency_values>(.+)?)", repeats = True),
                      SM(r"\s*- Thermochemistry -"),
                      ]
             ),
                SM(name = 'run times',
                  sections = ['x_gaussian_section_times'],
                  startReStr = r"\s*Job cpu time:",
                  forwardMatch = True,
                  subMatchers = [
                      SM(r"\s*Job cpu time:\s*(?P<x_gaussian_program_cpu_time>\s*[0-9]+\s*[a-z]+\s*[0-9]+\s*[a-z]+\s*[0-9]+\s*[a-z]+\s*[0-9.]+\s*[a-z]+)"),
                      SM(r"\s*Normal termination of Gaussian\s*[0-9]+\s* at \s*(?P<x_gaussian_program_termination_date>[A-Za-z]+\s*[A-Za-z]+\s*[0-9]+\s*[0-9:]+\s*[0-9]+)"),
215
                      ]
216
217
218
219
220
221
             )
          ])
        ])
      ])
    ])

222
223
224
225
226
227
228
229
230
231

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

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

232
class GaussianParserContext(object):
233
234
235
236
237
238
239
240
241
242
243
244
245
246
      """Context for parsing Gaussian output file.

        This class keeps tracks of several Gaussian settings to adjust the parsing to them.
        The onClose_ functions allow processing and writing of cached values after a section is closed.
        They take the following arguments:
        backend: Class that takes care of writing and caching of metadata.
        gIndex: Index of the section that is closed.
        section: The cached values and sections that were found in the section that is closed.
      """
      def __init__(self):
        # dictionary of energy values, which are tracked between SCF iterations and written after convergence
        self.totalEnergyList = {
                                'energy_XC_potential': None
                               }
247

248
249
250
251
252
253
254
255
256
257
258
259
260
261
      def initialize_values(self):
        """Initializes the values of certain variables.

        This allows a consistent setting and resetting of the variables,
        when the parsing starts and when a section_run closes.
        """
        # start with -1 since zeroth iteration is the initialization
        self.scfIterNr = -1
        self.scfConvergence = False
        self.geoConvergence = None
        self.geoCrashed = None
        self.scfenergyconverged = 0.0

      def startedParsing(self, path, parser):
262
        self.parser = parser
263
264
        # allows to reset values if the same superContext is used to parse different files
        self.initialize_values()
265

266
267
268
      def onClose_x_gaussian_section_geometry(self, backend, gIndex, section):
        xCoord = section["x_gaussian_atom_x_coord"]
        yCoord = section["x_gaussian_atom_y_coord"]
269
270
        zCoord = section["x_gaussian_atom_z_coord"]
        numbers = section["x_gaussian_atomic_number"]
271
        atom_coords = np.zeros((len(xCoord),3), dtype=float)
272
        atom_numbers = np.zeros(len(xCoord), dtype=int)
273
        atomic_symbols = np.empty((len(xCoord)), dtype=object)
274
        for i in range(len(xCoord)):
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
           atom_coords[i,0] = xCoord[i]
           atom_coords[i,1] = yCoord[i]
           atom_coords[i,2] = zCoord[i]
        for i in range(len(xCoord)):
          atom_numbers[i] = numbers[i]
          atomic_symbols[i] = ase.data.chemical_symbols[atom_numbers[i]]
        backend.addArrayValues("x_gaussian_atom_labels", atomic_symbols)
        backend.addArrayValues("x_gaussian_atom_positions", atom_coords)

      def onClose_x_gaussian_section_atom_forces(self, backend, gIndex, section):
        xForce = section["x_gaussian_atom_x_force"]
        yForce = section["x_gaussian_atom_y_force"]
        zForce = section["x_gaussian_atom_z_force"]
        atom_forces = np.zeros((len(xForce),3), dtype=float)
        for i in range(len(xForce)):
           atom_forces[i,0] = xForce[i]
           atom_forces[i,1] = yForce[i]
           atom_forces[i,2] = zForce[i]
        backend.addArrayValues("x_gaussian_atom_forces", atom_forces)

      def onClose_section_run(self, backend, gIndex, section):
        """Trigger called when section_run is closed.
        """
                # write geometry optimization convergence
        gIndexTmp = backend.openSection('x_gaussian_section_single_configuration_calculation')
        if self.geoConvergence is not None:
            backend.addValue('x_gaussian_geometry_optimization_converged', self.geoConvergence)
        # use values of control.in which was parsed in section_method
        backend.closeSection('x_gaussian_section_single_configuration_calculation', gIndexTmp)

      def onClose_x_gaussian_section_single_configuration_calculation(self, backend, gIndex, section):
        """Trigger called when section_single_configuration_calculation is closed.
         Write number of SCF iterations and convergence.
         Check for convergence of geometry optimization.
        """
        # write number of SCF iterations
        self.scfenergyconverged = section['x_gaussian_energy_total_scf_converged']
        backend.addValue('x_gaussian_number_of_scf_iterations', self.scfIterNr)
        # write SCF convergence and reset
        backend.addValue('x_gaussian_single_configuration_calculation_converged', self.scfConvergence)
        backend.addValue('x_gaussian_energy_total_scf_converged', self.scfenergyconverged)
        self.scfConvergence = False
        # check for geometry optimization convergence
        if section['x_gaussian_geometry_optimization_converged'] is not None:
            if section['x_gaussian_geometry_optimization_converged'][-1] == 'Optimization completed':
               self.geoConvergence = True
            else:
               if section['x_gaussian_geometry_optimization_converged'][-1] == 'Optimization stopped':
                  self.geoConvergence = False
        if section['x_gaussian_geometry_optimization_converged'] is not None:
             if section['x_gaussian_geometry_optimization_converged'][-1] == 'Optimization stopped':
               self.geoCrashed = True
             else:
               self.geoCrashed = False
        # start with -1 since zeroth iteration is the initialization
        self.scfIterNr = -1

      def onClose_x_gaussian_section_scf_iteration(self, backend, gIndex, section):
        # count number of SCF iterations
        self.scfIterNr += 1
        # check for SCF convergence
        if section['x_gaussian_single_configuration_calculation_converged'] is not None:
            self.scfConvergence = True

      def onClose_x_gaussian_section_frequencies(self, backend, gIndex, section):
          frequencies = str(section["x_gaussian_frequency_values"])
          vibfreqs = []
          freqs = [float(f) for f in frequencies[1:].replace("'","").replace(",","").replace("]","").split()]
          vibfreqs = np.append(vibfreqs, freqs)
          backend.addArrayValues("x_gaussian_frequencies", vibfreqs)

      def onClose_x_gaussian_section_atomic_masses(self, backend, gIndex, section):
          atomicmasses = str(section["x_gaussian_atomic_masses"])
          atmass = []
          mass = [float(f) for f in atomicmasses[1:].replace("'","").replace(",","").replace("]","").split()]
          atmass = np.append(atmass, mass)
          backend.addArrayValues("x_gaussian_masses", atmass)   
       
      def onClose_x_gaussian_section_eigenvalues(self, backend, gIndex, section):
          eigenenergies = str(section["x_gaussian_alpha_occ_eigenvalues_values"])
          eigenen1 = []
          energy = [float(f) for f in eigenenergies[1:].replace("'","").replace(",","").replace("]","").split()]
          eigenen1 = np.append(eigenen1, energy)
          occoccupationsalp = np.ones(len(eigenen1), dtype=float)
          eigenenergies = str(section["x_gaussian_alpha_vir_eigenvalues_values"])
          eigenen2 = []
          energy = [float(f) for f in eigenenergies[1:].replace("'","").replace(",","").replace("]","").split()]
          eigenen2 = np.append(eigenen2, energy)
          viroccupationsalp = np.zeros(len(eigenen2), dtype=float)
          eigenencon = np.zeros(len(eigenen1) + len(eigenen2))
          eigenencon = np.concatenate((eigenen1,eigenen2), axis=0)
          occupcon = np.concatenate((occoccupationsalp, viroccupationsalp), axis=0)
          backend.addArrayValues("x_gaussian_alpha_eigenvalues", eigenencon)
          backend.addArrayValues("x_gaussian_alpha_occupations", occupcon)

          eigenenergies = str(section["x_gaussian_beta_occ_eigenvalues_values"])
          eigenen1 = []
          energy = [float(f) for f in eigenenergies[1:].replace("'","").replace(",","").replace("]","").split()]
          eigenen1 = np.append(eigenen1, energy)
          occoccupationsbet = np.ones(len(eigenen1), dtype=float)
          eigenenergies = str(section["x_gaussian_beta_vir_eigenvalues_values"])
          eigenen2 = []
          energy = [float(f) for f in eigenenergies[1:].replace("'","").replace(",","").replace("]","").split()]
          eigenen2 = np.append(eigenen2, energy)
          viroccupationsbet = np.zeros(len(eigenen2), dtype=float)
          eigenencon = np.zeros(len(eigenen1) + len(eigenen2))
          eigenencon = np.concatenate((eigenen1,eigenen2), axis=0)
          occupcon = np.concatenate((occoccupationsbet, viroccupationsbet), axis=0)
          backend.addArrayValues("x_gaussian_beta_eigenvalues", eigenencon)
          backend.addArrayValues("x_gaussian_beta_occupations", occupcon)

      def onClose_x_gaussian_section_orbital_symmetries(self, backend, gIndex, section):
          symoccalpha = str(section["x_gaussian_alpha_occ_symmetry_values"])
          symviralpha = str(section["x_gaussian_alpha_vir_symmetry_values"])
          symoccbeta = str(section["x_gaussian_beta_occ_symmetry_values"])
          symvirbeta = str(section["x_gaussian_beta_vir_symmetry_values"])
          symmetry = [str(f) for f in symoccalpha[1:].replace("'","").replace(",","").replace("(","").replace(")","").replace("]","").split()]
          sym1 = []
          sym1 = np.append(sym1, symmetry)  
          symmetry = [str(f) for f in symviralpha[1:].replace("'","").replace(",","").replace("(","").replace(")","").replace("]","").split()]
          sym2 = []
          sym2 = np.append(sym2, symmetry)
          symmetrycon = np.concatenate((sym1, sym2), axis=0)
          backend.addArrayValues("x_gaussian_alpha_symmetries", symmetrycon) 
          symmetry = [str(f) for f in symoccbeta[1:].replace("'","").replace(",","").replace("(","").replace(")","").replace("]","").split()]
          sym1 = []
          sym1 = np.append(sym1, symmetry)
          symmetry = [str(f) for f in symvirbeta[1:].replace("'","").replace(",","").replace("(","").replace(")","").replace("]","").split()]
          sym2 = []
          sym2 = np.append(sym2, symmetry)
          symmetrycon = np.concatenate((sym1, sym2), axis=0)
          backend.addArrayValues("x_gaussian_beta_symmetries", symmetrycon)
407
408

# which values to cache or forward (mapping meta name -> CachingLevel)
409
cachingLevelForMetaName = {
410
        "x_gaussian_atom_x_coord": CachingLevel.Cache,
411
412
413
        "x_gaussian_atom_y_coord": CachingLevel.Cache,
        "x_gaussian_atom_z_coord": CachingLevel.Cache,
        "x_gaussian_atomic_number": CachingLevel.Cache,
414
415
416
417
418
419
420
421
422
423
424
425
426
        "x_gaussian_section_geometry": CachingLevel.Ignore,
        "x_gaussian_section_total_scf_one_geometry": CachingLevel.Cache,
        "x_gaussian_geometry_optimization_converged": CachingLevel.Cache,
        "x_gaussian_section_scf_iteration": CachingLevel.Cache,
        "x_gaussian_single_configuration_calculation_converged": CachingLevel.Ignore,
        "x_gaussian_atom_x_force": CachingLevel.Cache,
        "x_gaussian_atom_y_force": CachingLevel.Cache,
        "x_gaussian_atom_z_force": CachingLevel.Cache,
        "x_gaussian_section_atom_forces": CachingLevel.Ignore, 
        "x_gaussian_section_frequencies": CachingLevel.Cache,
        "x_gaussian_atomic_masses": CachingLevel.Cache, 
        "x_gaussian_section_eigenvalues": CachingLevel.Cache,
        "x_gaussian_section_orbital_symmetries": CachingLevel.Cache,
427
}
428
429

if __name__ == "__main__":
430
431
    mainFunction(mainFileDescription, metaInfoEnv, parserInfo,
                 cachingLevelForMetaName = cachingLevelForMetaName,
Mohamed, Fawzi Roberto (fawzi)'s avatar
cleanup    
Mohamed, Fawzi Roberto (fawzi) committed
432
                 superContext = GaussianParserContext())