main.py 25.8 KB
Newer Older
Daniel Speckhard's avatar
Daniel Speckhard committed
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 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 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134
# Copyright 2016-2018 Ask Hjorth Larsen, Fawzi Mohamed
#
#   Licensed under the Apache License, Version 2.0 (the "License");
#   you may not use this file except in compliance with the License.
#   You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
#   Unless required by applicable law or agreed to in writing, software
#   distributed under the License is distributed on an "AS IS" BASIS,
#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
#   See the License for the specific language governing permissions and
#   limitations under the License.

#
# Main author and maintainer: Ask Hjorth Larsen <asklarsen@gmail.com>

from __future__ import print_function
import os
import sys
import logging
from glob import glob
import re

import numpy as np
from ase.data import chemical_symbols
from ase import Atoms

from nomadcore.simple_parser import (mainFunction, SimpleMatcher as SM,
                                     AncillaryParser)
from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
from nomadcore.unit_conversion.unit_conversion \
    import register_userdefined_quantity, convert_unit

from siestaparser.inputvars import varlist

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

parser_info = {'name':'siesta-parser', 'version': '1.0'}


def siesta_energy(title, meta, **kwargs):
    return SM(r'siesta:\s*%s\s*=\s*(?P<%s__eV>\S+)' % (title, meta),
              name=meta, **kwargs)


def line_iter(fd, linepattern = re.compile(r'\s*([^#]+)')):
    # Strip off comments and whitespace, return only non-empty strings
    for line in fd:
        match = linepattern.match(line)
        if match:
            line = match.group().rstrip()
            if line:
                yield line


def get_input_metadata(inputvars_file, use_new_format):
    inputvars = {}
    blocks = {}

    varset = set(varlist)

    lower_vars = {}
    for var in varlist:
        lower_vars[var.lower()] = var

    def addvar(tokens):
        name = tokens[0]
        val = ' '.join(tokens[1:])
        name = name.lower()
        if name in lower_vars:
            name = lower_vars[name]
            inputvars[name] = val

    currentblock = None

    with open(inputvars_file) as fd:
        lines = line_iter(fd)

        for line in lines:
            tokens = line.split()
            assert len(tokens) > 0

            if tokens[0].startswith('%'):
                if tokens[0].lower() == '%block':
                    #assert currentblock == None
                    currentblock = []
                    blocks[tokens[1]] = currentblock
                elif tokens[0].lower() == '%endblock':
                    currentblock = None
                else:
                    raise ValueError('Unknown: %s' % tokens[0])
            else:
                if use_new_format:
                    if line.startswith(' '):
                        if currentblock is None:
                            continue  # Ignore.  Probably some warning
                        #assert currentblock is not None, line
                        currentblock.append(tokens)
                    else:
                        currentblock = None
                        addvar(tokens)
                else:
                    if currentblock is not None:
                        currentblock.append(tokens)
                    else:
                        addvar(tokens)

    return inputvars, blocks


"""
%block PAO.Basis                 # Define Basis set
O                     2                    # Species label, number of l-shells
 n=2   0   2                         # n, l, Nzeta
   3.305      2.479
   1.000      1.000
 n=2   1   2 P   1                   # n, l, Nzeta, Polarization, NzetaPol
   3.937      2.542
   1.000      1.000
H                     1                    # Species label, number of l-shells
 n=1   0   2 P   1                   # n, l, Nzeta, Polarization, NzetaPol
   4.709      3.760
   1.000      1.000
%endblock PAO.Basis
"""


class SiestaContext(object):
    def __init__(self):
135 136 137
        self.reset()

    def reset(self):
Daniel Speckhard's avatar
Daniel Speckhard committed
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
        self.fname = None  # The file that we are parsing
        self.dirname = None  # Base directory of calculations
        #self.parser = None  # The parser object
        self.format = None  # 'old' or 'new'; when parsing version

        # label and things determined by label
        self.label = None
        self.files = None  # Dict of files
        self.blocks = None  # Dict of input blocks (coords, cell, etc.)

        self.data = {}
        self.special_input_vars = {}

        self.system_meta = {}
        self.section_refs = {}  # {name: gindex, ...}
        self.simulation_type = None

    def adhoc_format_new(self, parser):
        assert self.format is None
        self.format = 'new'

    def adhoc_format_old(self, parser):
        assert self.format is None
        self.format = 'old'

    def adhoc_set_label(self, parser):
        # ASSUMPTION: the parser fIn is in the 'root' of whatever was uploaded.
        # This may not be true.  Figure out how to do this in general.
        line = parser.fIn.readline()
        assert line.startswith('reinit: System Label:')
        self.label = label = line.split()[-1]
        dirname = self.dirname

        files = {}

        for fileid in ['EIG', 'KP']:
            path = os.path.join(dirname, '%s.%s' % (label, fileid))
            if os.path.isfile(path):
                files[fileid] = path
            # Warn if files are not present?
            #
            # Also: input file
            #       input parser logfile
            #
            # what else?  We already get force/stress/positions from stdout.
        if self.format == 'new':
            inplogfiles = glob('%s/fdf-*.log' % dirname)
            assert len(inplogfiles) == 1
            if inplogfiles:
                inplogfiles.sort()
                files['inputlog'] = inplogfiles[0]
        else:
            assert self.format == 'old', self.format
            files['inputlog'] = os.path.join(dirname, 'out.fdf')
        self.files = files

    def adhoc_set_simulation_type(self, parser):
        line = parser.fIn.readline()

        if self.simulation_type is not None:
            return

        line = line.strip()

        if line.startswith('Single-point'):
            self.simulation_type = 'singlepoint'
        elif 'opt' in line or 'move' in line:
            self.simulation_type = 'optimization'
        else:
            raise ValueError('Todo: recognize simulation type "%s"' % line)

    def startedParsing(self, fname, parser):
        self.fname = fname
        path = os.path.abspath(fname)
212
        self.dirname = os.path.dirname(path)
Daniel Speckhard's avatar
Daniel Speckhard committed
213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675

    #def onClose_x_siesta_section_xc_authors(self, backend, gindex, section):

    def onClose_section_frame_sequence(self, backend, gindex, section):
        backend.addValue('frame_sequence_to_sampling_ref',
                         self.section_refs['sampling_method'])

    def onOpen_section_sampling_method(self, backend, gindex, section):
        self.section_refs['sampling_method'] = gindex

    def onOpen_section_frame_sequence(self, backend, gindex, section):
        self.section_refs['frame_sequence'] = gindex

    def onClose_section_sampling_method(self, backend, gindex, section):
        simtype = self.simulation_type
        assert simtype is not None
        if simtype == 'optimization':
            backend.addValue('sampling_method', 'geometry_optimization')
        elif simtype == 'singlepoint':
            pass
        else:
            raise ValueError('XXX: %s' % simtype)

    def onClose_section_eigenvalues(self, backend, gindex, section):
        self.read_eigenvalues(backend)

    def onOpen_section_method(self, backend, gindex, section):
        self.section_refs['method'] = gindex

    def onClose_section_method(self, backend, gindex, section):
        temp = self.special_input_vars['ElectronicTemperature']
        temp, unit = temp.split()
        assert unit == 'Ry'  # Siesta always converts to Ry here I think
        temp = float(temp)
        temp = convert_unit(temp, 'rydberg')
        backend.addValue('smearing_width', temp)

        #simtype = self.special_input_vars['MD.TypeOfRun']
        #print('SIMTYPE', simtype)
        #sdfsdf

    def onOpen_section_system(self, backend, gindex, section):
        self.section_refs['system'] = gindex

    def onClose_section_system(self, backend, gindex, section):
        data = self.data
        meta = self.system_meta

        latvec = data.pop('block_lattice_vectors', None)
        if latvec is not None:
            latvec = latvec.astype(float)
            size = self.special_input_vars['LatticeConstant']
            size, unit = size.split()
            #assert unit == 'ang', unit
            unit = {'ang': 'angstrom',
                    'Bohr': 'bohr'}[unit]

            size = float(size)
            size = convert_unit(size, unit)
            meta['simulation_cell'] = latvec * size

        cell = data.pop('outcell_ang', None)
        cell2 = data.pop('auto_unit_cell_ang', None)
        if cell2 is not None:
            cell = cell2

        if cell is not None:
            cell = cell.astype(float)
            cell = convert_unit(cell, 'angstrom')
            meta['simulation_cell'] = cell

        labels = data.pop('block_species_label', None)
        if labels is not None:
            assert labels.shape[1] == 1
            labels = labels[:, 0]
            self.labels = labels

        block_coords_and_species = self.data.pop('block_coords_and_species_from_inputlog', None)

        block_coords_and_species = data.pop('block_coords_and_species', block_coords_and_species)
        coords_and_species = data.pop('coords_and_species', None)

        if coords_and_species is None:
            coords_and_species = block_coords_and_species

        if coords_and_species is not None:
            coords = coords_and_species[:, :3].astype(float)

            unit = self.special_input_vars['AtomicCoordinatesFormat']
            if unit == 'Ang':
                coords = convert_unit(coords, 'angstrom')
            elif unit in ['Fractional', 'ScaledCartesian']:
                a = Atoms('%dX' % len(coords),
                          scaled_positions=coords,
                          cell=meta['simulation_cell'])
                coords = a.positions
            else:
                raise ValueError('Unknown: %s' % unit)
            meta['atom_positions'] = coords

            species_index = coords_and_species[:, 3].astype(int)

            atom_labels = np.array([self.labels[i - 1] for i in species_index])
            meta['atom_labels'] = atom_labels

        positions = self.data.pop('outcoord_ang', None)
        if positions is not None:
            positions = convert_unit(positions.astype(float), 'angstrom')
            meta['atom_positions'] = positions

        for key, value in meta.items():
            backend.addArrayValues(key, value)

        backend.addArrayValues('configuration_periodic_dimensions',
                               np.ones(3, bool))

        assert len(self.data) == 0, self.data

    def onClose_section_run(self, backend, gindex, section):
        pass

    def onClose_section_single_configuration_calculation(self, backend,
                                                         gindex, section):
        forces = self.data.pop('forces_ev_ang', None)
        if forces is not None:
            forces = forces.astype(float)
            forces = convert_unit(forces, 'eV/angstrom')
            backend.addArrayValues('atom_forces_free_raw', forces)

        stress = self.data.pop('stress_tensor_ev_ang', None)
        if stress is not None:
            stress = stress.astype(float)
            stress = convert_unit(stress, 'eV/angstrom^3')
            backend.addArrayValues('stress_tensor', stress)

        backend.addValue('single_configuration_to_calculation_method_ref',
                         self.section_refs['method'])
        backend.addValue('single_configuration_calculation_to_system_ref',
                         self.section_refs['system'])

    def onClose_x_siesta_section_input(self, backend, gindex, section):
        inputvars_file = self.files.get('inputlog')
        if inputvars_file is None:
            raise ValueError('no input logfile!')

        inputvars, blocks = get_input_metadata(inputvars_file,
                                               self.format == 'new')
        for varname, value in inputvars.items():
            backend.addValue('x_siesta_input_%s' % varname, value)

        for special_name in ['LatticeConstant',
                             'AtomicCoordinatesFormat',
                             'AtomicCoordinatesFormatOut',
                             'ElectronicTemperature']:
            self.special_input_vars[special_name] = inputvars.get(special_name)

        self.blocks = blocks
        self.data['block_coords_and_species_from_inputlog'] = np.array(blocks['AtomicCoordinatesAndAtomicSpecies'], str)

        authors = section['x_siesta_xc_authors']
        if authors is None:
            raise ValueError('XC authors not found!')

        assert len(authors) == 1
        authors = authors[0]

        # XXX Case sensitive?
        mapping = {'CA': ('LDA_X', 'LDA_C_PZ'),
                   'PZ': ('LDA_X', 'LDA_C_PZ'),
                   'PW92': ('LDA_X', 'LDA_C_PW'),
                   #'PW91': '',
                   'PBE': ('GGA_X_PBE', 'GGA_C_PBE'),
                   'revPBE': ('GGA_X_PBE_R', 'GGA_C_PBE'),
                   'RPBE': ('GGA_X_RPBE', 'GGA_C_PBE'),
                   #'WC': ('GGA_X_WC', ),
                   # Siesta does not mention which correlation is used with
                   # the WC functional.  Is it just the PBE one?
                   'AM05': ('GGA_X_AM05', 'GGA_C_AM05'),
                   'PBEsol': ('GGA_X_PBE_SOL', 'GGA_C_PBE_SOL'),
                   'BLYP': ('GGA_X_B88', 'GGA_C_LYP'),
                   'DF1': ('gga_x_pbe_r', 'vdw_c_df1'),
                   'DRSLL': ('gga_x_pbe_r', 'vdw_c_df1'),
                   'LMKLL': ('gga_x_rpw86', 'vdw_c_df2'),
                   'DF2': ('gga_x_rpw86', 'vdw_c_df2'),
                   'KBM': ('GGA_X_OPTB88_VDW', 'vdw_c_df1'),
                   'C09': ('GGA_X_C09X', 'vdw_c_df1'),
                   'BH': ('GGA_X_LV_RPW86', 'vdw_c_df1'),
        }
        xc = mapping.get(authors)

        if xc is None:
            raise ValueError('XC functional %s unsupported by parser'
                             % authors)

        for funcname in xc:
            gid = backend.openSection('section_XC_functionals')
            backend.addValue('XC_functional_name', funcname)
            backend.closeSection('section_XC_functionals', gid)

    def read_eigenvalues(self, backend):
        eigfile = self.files.get('EIG')
        if eigfile is None:
            return

        with open(eigfile) as fd:
            eFermi = float(next(fd).strip())
            nbands, nspins, nkpts = [int(n) for n in next(fd).split()]

            tokens = []
            for line in fd:
                tokens.extend(line.split())

        tokens = iter(tokens)

        eps = np.empty((nspins, nkpts, nbands))
        for k in range(nkpts):
            kindex = int(next(tokens))
            assert k + 1 == kindex
            for s in range(nspins):
                eps[s, k, :] = [next(tokens) for _ in range(nbands)]
        unread = list(tokens)
        assert len(unread) == 0
        assert s == nspins - 1
        assert k == nkpts - 1

        # Where does SIESTA store the occupations?
        backend.addArrayValues('eigenvalues_values', convert_unit(eps, 'eV'))

        kpfile = self.files.get('KP')
        if kpfile is None:
            return


        with open(kpfile) as fd:
            tokens = fd.read().split()

        nkpts = int(tokens[0])
        data = np.array(tokens[1:], object).reshape(-1, 5)
        coords = data[:, 1:4].astype(float)
        weights = data[:, 4].astype(float)
        backend.addArrayValues('eigenvalues_kpoints', coords)
        # XXX metadata for Fermi level?
        # k-point weights?

    def save_array(self, key, dtype=float, istart=0, iend=None,
                   unit=None):
        return get_array(key, dtype=dtype, istart=istart, iend=iend, unit=unit,
                         storage=self.data)

    def multi_sm(self, name, startpattern, linepattern, endmatcher=None,
                 conflict='fail',  # 'fail', 'keep', 'overwrite'
                 *args, **kwargs):

        pat = re.compile(linepattern)  # XXX how to get compiled pattern?
        ngroups = pat.groups

        allgroups = []
        def addline(parser):
            line = parser.fIn.readline()
            match = pat.match(line)
            assert match is not None
            thislinegroups = match.groups()
            assert len(thislinegroups) == ngroups
            allgroups.append(thislinegroups)

        def savearray(parser):
            arr = np.array(allgroups, dtype=object)
            del allgroups[:]
            if name in self.data:
                if conflict == 'fail':
                    raise ValueError('grrr %s %s' % (name, self.data[name]))
                elif conflict == 'keep':
                    return  # Do not save array
                elif conflict == 'overwrite':
                    pass
                else:
                    raise ValueError('Unknown keyword %s' % conflict)
            if arr.size > 0:
                self.data[name] = arr

        if endmatcher is None:
            endmatcher = r'.*'

        if hasattr(endmatcher, 'swapcase'):
            endmatcher = SM(endmatcher,
                            endReStr='',
                            forwardMatch=True,
                            name='%s-end' % name,
                            adHoc=savearray)

        sm = SM(startpattern,
                name=name,
                subMatchers=[
                    SM(linepattern,
                       name='%s-line' % name,
                       repeats=True,
                       forwardMatch=True,
                       required=True,
                       adHoc=addline),
                    endmatcher,
                ], **kwargs)
        return sm

context = SiestaContext()

def get_header_matcher():
    m = SM(r'',
           name='header',
           fixedStartValues={'program_name': 'Siesta',
                             'program_basis_set_type': 'numeric AOs'},
           weak=True,
           forwardMatch=True,
           subMatchers=[
               SM(r'Siesta Version: (?P<program_version>\S+)',
                  name='version',
                  adHoc=context.adhoc_format_new),
               SM(r'SIESTA\s*(?P<program_version>.+)',
                  name='alt-version', adHoc=context.adhoc_format_old),
               SM(r'Architecture\s*:\s*(?P<x_siesta_arch>.+)', name='arch'),
               SM(r'Compiler flags\s*:\s*(?P<x_siesta_compilerflags>.+)',
                  name='flags'),
           ])
    return m


def anycase(string):
    tokens = []
    for letter in list(string):
        if letter.isalpha():
            tokens.append('[%s%s]' % (letter.upper(),
                                      letter.lower()))
        else:
            tokens.append(letter)
    return ''.join(tokens)

welcome_pattern = r'\s*\*\s*WELCOME TO SIESTA\s*\*'

def get_input_matcher():
    m = SM(welcome_pattern,
           name='welcome',
           sections=['section_method', 'x_siesta_section_input'],
           fixedStartValues={'electronic_structure_method': 'DFT',
                             'smearing_kind': 'fermi'},
           subFlags=SM.SubFlags.Unordered,
           subMatchers=[
               SM(r'NumberOfAtoms\s*(?P<number_of_atoms>\d+)',
                  name='natoms'),
               context.multi_sm('block_species_label',
                                anycase(r'%block ChemicalSpeciesLabel'),
                                r'\s*\d+\s*\d+\s*(\S+)',
                            conflict='keep'),
               context.multi_sm('block_coords_and_species',
                                anycase(r'%block AtomicCoordinatesAndAtomicSpecies'),
                                r'\s*(\S+)\s*(\S+)\s*(\S+)\s*(\d+)'),
               context.multi_sm('block_lattice_vectors',
                                anycase(r'%block LatticeVectors'),
                                r'(?!%)\s*(\S+)\s*(\S+)\s*(\S+)'),
               SM(r'%s\s*(?P<x_siesta_xc_authors>\S+)' % anycase('xc\.authors'),
                  name='xc authors',
                  fixedStartValues={'x_siesta_xc_authors': 'CA'}),
               #SM(r'MD.TypeOfRun\s*(?P<x_siesta_typeofrun>\S+)',
               #   fixedStartValues={'x_siesta_typeofrun': 'none'}),
               SM(r'reinit: System Name:\s*(?P<system_name>.+)',
                  name='sysname'),
               SM(r'reinit: System Label:\s*(?P<x_siesta_system_label>\S+)',
                  name='syslabel', forwardMatch=True,
                  adHoc=context.adhoc_set_label),
               context.multi_sm('coords_and_species',
                                r'siesta: Atomic coordinates \(Bohr\) and species',
                                r'siesta:\s*(\S+)\s*(\S+)\s*(\S+)\s*(\d+)'),
               context.multi_sm('auto_unit_cell_ang',
                                r'siesta: Automatic unit cell vectors \(Ang\):',
                                r'siesta:\s*(\S+)\s*(\S+)\s*(\S+)'),
               # XXX must be an array with number of spin channels!
               #SM(r'Total number of electrons:\s*(?P<number_of_electrons>\S+)',
               #   name='nelectrons'),
       ])
    return m


step_pattern = r'\s*(Single-point calculation|Begin[^=]+=\s*\d+)'

def get_step_matcher():
    m = SM(step_pattern,
           name='step',
           forwardMatch=True,
           adHoc=context.adhoc_set_simulation_type,
           sections=['section_single_configuration_calculation'],
           subFlags=SM.SubFlags.Unordered,
           subMatchers=[
               SM(r'\s*=============+', name='====='),
               context.multi_sm('outcoord_ang',
                                r'outcoor: Atomic coordinates \(Ang\):',
                                r'\s*(\S+)\s*(\S+)\s*(\S+)'),
               context.multi_sm('outcell_ang',
                                r'outcell: Unit cell vectors \(Ang\):',
                                r'\s*(\S+)\s*(\S+)\s*(\S+)'),
               SM(r'siesta: E_KS\(eV\)\s*=\s*(?P<energy_total__eV>\S+)',
                  name='etotal'),
               context.multi_sm('forces_ev_ang',
                                r'siesta: Atomic forces \(eV/Ang\):',
                                r'(?:siesta:)?\s+\d+\s*(\S+)\s*(\S+)\s*(\S+)'),
               context.multi_sm('stress_tensor_ev_ang',
                                r'siesta: Stress tensor \(static\) \(eV/Ang\*\*3\):',
                                r'siesta:\s*(\S+)\s*(\S+)\s*(\S+)'),
               SM(r'siesta: Final energy \(eV\):',
                  endReStr='siesta:\s*Total\s*=\s*\S+',
                  name='Efinal',
                  subMatchers=[
                      siesta_energy('Band Struct\.', 'energy_sum_eigenvalues'),
                      siesta_energy('Kinetic', 'electronic_kinetic_energy'),
                      siesta_energy('Hartree', 'energy_electrostatic'),
                      #siesta_energy('Ext\. field', ''),
                      siesta_energy('Exch\.-corr\.', 'energy_XC'),
                      #siesta_energy('Ion-electron', ''),
                      #siesta_energy('Ion-Ion', ''),
                      #siesta_energy('Ekinion', ''),
                      # energy_total was matched above already
                      #siesta_energy('Total', 'energy_total'),
                      SM(r'', weak=True, name='trigger_readeig',
                         sections=['section_eigenvalues']),
                  ]),
           ])
    return m


mainFileDescription = SM(
    r'',
    name='root',
    #weak=True,
    sections=['section_run'],
    subMatchers=[
        get_header_matcher(),
        SM(r'(%s|%s)' % (welcome_pattern, step_pattern),
           name='system-section',
           #weak=True,
           forwardMatch=True,
           repeats=True,
           required=True,
           sections=['section_system', 'section_frame_sequence', 'section_sampling_method'],
           subMatchers=[
               get_input_matcher(),
               get_step_matcher(),
           ]),
        SM(r'x^',  # Make sure whole file is parsed
           name='end')
    ])


import nomad_meta_info
metaInfoPath = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(nomad_meta_info.__file__)), "siesta.nomadmetainfo.json"))
metaInfoEnv, warnings = loadJsonFile(filePath = metaInfoPath, dependencyLoader = None, extraArgsHandling = InfoKindEl.ADD_EXTRA_ARGS, uri = None)

class SiestaParser():
   """ A proper class envolop for running this parser from within python. """
   def __init__(self, backend, **kwargs):
       self.backend_factory = backend

   def parse(self, mainfile):
       from unittest.mock import patch
       logging.info('siesta parser started')
       logging.getLogger('nomadcore').setLevel(logging.WARNING)
       backend = self.backend_factory(metaInfoEnv)
676
       context.reset()
Daniel Speckhard's avatar
Daniel Speckhard committed
677 678 679 680 681 682
       with patch.object(sys, 'argv', ['<exe>', '--uri', 'nmd://uri', mainfile]):
           mainFunction(
               mainFileDescription,
               metaInfoEnv,
               parser_info,
               cachingLevelForMetaName={},
683
               superContext=context,
Daniel Speckhard's avatar
Daniel Speckhard committed
684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699
               superBackend=backend)

       return backend


def main(**kwargs):
    mainFunction(mainFileDescription=mainFileDescription,
                 metaInfoEnv=metaInfoEnv,
                 parserInfo=parser_info,
                 cachingLevelForMetaName={},
                 superContext=context,
                 **kwargs)

if __name__ == '__main__':
    main()