File: factories.py

package info (click to toggle)
python-ase 3.21.1-2
  • links: PTS, VCS
  • area: main
  • in suites: bullseye
  • size: 13,936 kB
  • sloc: python: 122,428; xml: 946; makefile: 111; javascript: 47
file content (694 lines) | stat: -rw-r--r-- 20,441 bytes parent folder | download
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
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
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
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
import os
import re
from pathlib import Path
from typing import Mapping
import configparser

import pytest

from ase.calculators.calculator import (names as calculator_names,
                                        get_calculator_class)


class NotInstalled(Exception):
    pass


def get_testing_executables():
    # TODO: better cross-platform support (namely Windows),
    # and a cross-platform global config file like /etc/ase/ase.conf
    paths = [Path.home() / '.config' / 'ase' / 'ase.conf']
    try:
        paths += [Path(x) for x in os.environ['ASE_CONFIG'].split(':')]
    except KeyError:
        pass
    conf = configparser.ConfigParser()
    conf['executables'] = {}
    effective_paths = conf.read(paths)
    return effective_paths, conf['executables']


factory_classes = {}


def factory(name):
    def decorator(cls):
        cls.name = name
        factory_classes[name] = cls
        return cls

    return decorator


def make_factory_fixture(name):
    @pytest.fixture(scope='session')
    def _factory(factories):
        factories.require(name)
        return factories[name]

    _factory.__name__ = '{}_factory'.format(name)
    return _factory


@factory('abinit')
class AbinitFactory:
    def __init__(self, executable, pp_paths):
        self.executable = executable
        self.pp_paths = pp_paths
        self._version = None

    def version(self):
        from ase.calculators.abinit import get_abinit_version
        # XXX Ugly
        if self._version is None:
            self._version = get_abinit_version(self.executable)
        return self._version

    def is_legacy_version(self):
        version = self.version()
        major_ver = int(version.split('.')[0])
        return major_ver < 9

    def _base_kw(self, v8_legacy_format):
        if v8_legacy_format:
            command = f'{self.executable} < PREFIX.files > PREFIX.log'
        else:
            command = f'{self.executable} PREFIX.in > PREFIX.log'

        return dict(command=command,
                    v8_legacy_format=v8_legacy_format,
                    pp_paths=self.pp_paths,
                    ecut=150,
                    chksymbreak=0,
                    toldfe=1e-3)

    def calc(self, **kwargs):
        from ase.calculators.abinit import Abinit
        legacy = kwargs.pop('v8_legacy_format', None)
        if legacy is None:
            legacy = self.is_legacy_version()

        kw = self._base_kw(legacy)
        kw.update(kwargs)
        return Abinit(**kw)

    @classmethod
    def fromconfig(cls, config):
        factory = AbinitFactory(config.executables['abinit'],
                                config.datafiles['abinit'])
        # XXX Hack
        factory._version = factory.version()
        return factory


@factory('asap')
class AsapFactory:
    importname = 'asap3'

    def calc(self, **kwargs):
        from asap3 import EMT
        return EMT(**kwargs)

    def version(self):
        import asap3
        return asap3.__version__

    @classmethod
    def fromconfig(cls, config):
        # XXXX TODO Clean this up.  Copy of GPAW.
        # How do we design these things?
        import importlib
        spec = importlib.util.find_spec('asap3')
        if spec is None:
            raise NotInstalled('asap3')
        return cls()


@factory('cp2k')
class CP2KFactory:
    def __init__(self, executable):
        self.executable = executable

    def version(self):
        from ase.calculators.cp2k import Cp2kShell
        shell = Cp2kShell(self.executable, debug=False)
        return shell.version

    def calc(self, **kwargs):
        from ase.calculators.cp2k import CP2K
        return CP2K(command=self.executable, **kwargs)

    @classmethod
    def fromconfig(cls, config):
        return CP2KFactory(config.executables['cp2k'])


@factory('dftb')
class DFTBFactory:
    def __init__(self, executable):
        self.executable = executable

    def version(self):
        stdout = read_stdout([self.executable])
        match = re.search(r'DFTB\+ release\s*(\S+)', stdout, re.M)
        return match.group(1)

    def calc(self, **kwargs):
        from ase.calculators.dftb import Dftb
        # XXX datafiles should be imported from datafiles project
        # We should include more datafiles for DFTB there, and remove them
        # from ASE's own datadir.
        command = f'{self.executable} > PREFIX.out'
        datadir = Path(__file__).parent / 'testdata'
        assert datadir.exists()
        return Dftb(
            command=command,
            slako_dir=str(datadir) + '/',  # XXX not obvious
            **kwargs)

    @classmethod
    def fromconfig(cls, config):
        return cls(config.executables['dftb'])


@factory('dftd3')
class DFTD3Factory:
    def __init__(self, executable):
        self.executable = executable

    def calc(self, **kwargs):
        from ase.calculators.dftd3 import DFTD3
        return DFTD3(command=self.executable, **kwargs)

    @classmethod
    def fromconfig(cls, config):
        return cls(config.executables['dftd3'])


def read_stdout(args, createfile=None):
    import tempfile
    from subprocess import Popen, PIPE
    with tempfile.TemporaryDirectory() as directory:
        if createfile is not None:
            path = Path(directory) / createfile
            path.touch()
        proc = Popen(args,
                     stdout=PIPE,
                     stderr=PIPE,
                     stdin=PIPE,
                     cwd=directory,
                     encoding='ascii')
        stdout, _ = proc.communicate()
        # Exit code will be != 0 because there isn't an input file
    return stdout


@factory('elk')
class ElkFactory:
    def __init__(self, executable, species_dir):
        self.executable = executable
        self.species_dir = species_dir

    def version(self):
        output = read_stdout([self.executable])
        match = re.search(r'Elk code version (\S+)', output, re.M)
        return match.group(1)

    def calc(self, **kwargs):
        from ase.calculators.elk import ELK
        command = f'{self.executable} > elk.out'
        return ELK(command=command, species_dir=self.species_dir, **kwargs)

    @classmethod
    def fromconfig(cls, config):
        return cls(config.executables['elk'], config.datafiles['elk'][0])


@factory('espresso')
class EspressoFactory:
    def __init__(self, executable, pseudo_dir):
        self.executable = executable
        self.pseudo_dir = pseudo_dir

    def _base_kw(self):
        from ase.units import Ry
        return dict(ecutwfc=300 / Ry)

    def version(self):
        stdout = read_stdout([self.executable])
        match = re.match(r'\s*Program PWSCF\s*(\S+)', stdout, re.M)
        assert match is not None
        return match.group(1)

    def calc(self, **kwargs):
        from ase.calculators.espresso import Espresso
        command = '{} -in PREFIX.pwi > PREFIX.pwo'.format(self.executable)
        pseudopotentials = {}
        for path in self.pseudo_dir.glob('*.UPF'):
            fname = path.name
            # Names are e.g. si_lda_v1.uspp.F.UPF
            symbol = fname.split('_', 1)[0].capitalize()
            pseudopotentials[symbol] = fname

        kw = self._base_kw()
        kw.update(kwargs)
        return Espresso(command=command,
                        pseudo_dir=str(self.pseudo_dir),
                        pseudopotentials=pseudopotentials,
                        **kw)

    @classmethod
    def fromconfig(cls, config):
        paths = config.datafiles['espresso']
        assert len(paths) == 1
        return cls(config.executables['espresso'], paths[0])


@factory('exciting')
class ExcitingFactory:
    def __init__(self, executable):
        # XXX species path
        self.executable = executable

    def calc(self, **kwargs):
        from ase.calculators.exciting import Exciting
        return Exciting(bin=self.executable, **kwargs)

    @classmethod
    def fromconfig(cls, config):
        return cls(config.executables['exciting'])


@factory('vasp')
class VaspFactory:
    def __init__(self, executable):
        self.executable = executable

    def calc(self, **kwargs):
        from ase.calculators.vasp import Vasp
        # XXX We assume the user has set VASP_PP_PATH
        if Vasp.VASP_PP_PATH not in os.environ:
            # For now, we skip with a message that we cannot run the test
            pytest.skip(
                'No VASP pseudopotential path set. Set the ${} environment variable to enable.'
                .format(Vasp.VASP_PP_PATH))
        return Vasp(command=self.executable, **kwargs)

    @classmethod
    def fromconfig(cls, config):
        return cls(config.executables['vasp'])


@factory('gpaw')
class GPAWFactory:
    importname = 'gpaw'

    def calc(self, **kwargs):
        from gpaw import GPAW
        return GPAW(**kwargs)

    def version(self):
        import gpaw
        return gpaw.__version__

    @classmethod
    def fromconfig(cls, config):
        import importlib
        spec = importlib.util.find_spec('gpaw')
        # XXX should be made non-pytest dependent
        if spec is None:
            raise NotInstalled('gpaw')
        return cls()


@factory('gromacs')
class GromacsFactory:
    def __init__(self, executable):
        self.executable = executable

    def version(self):
        from ase.calculators.gromacs import get_gromacs_version
        return get_gromacs_version(self.executable)

    def calc(self, **kwargs):
        from ase.calculators.gromacs import Gromacs
        return Gromacs(command=self.executable, **kwargs)

    @classmethod
    def fromconfig(cls, config):
        return cls(config.executables['gromacs'])


class BuiltinCalculatorFactory:
    def calc(self, **kwargs):
        from ase.calculators.calculator import get_calculator_class
        cls = get_calculator_class(self.name)
        return cls(**kwargs)

    @classmethod
    def fromconfig(cls, config):
        return cls()


@factory('emt')
class EMTFactory(BuiltinCalculatorFactory):
    pass


@factory('lammpsrun')
class LammpsRunFactory:
    def __init__(self, executable):
        self.executable = executable

    def version(self):
        stdout = read_stdout([self.executable])
        match = re.match(r'LAMMPS\s*\((.+?)\)', stdout, re.M)
        return match.group(1)

    def calc(self, **kwargs):
        from ase.calculators.lammpsrun import LAMMPS
        return LAMMPS(command=self.executable, **kwargs)

    @classmethod
    def fromconfig(cls, config):
        return cls(config.executables['lammpsrun'])


@factory('lammpslib')
class LammpsLibFactory:
    def __init__(self, potentials_path):
        # Set the path where LAMMPS will look for potential parameter files
        os.environ["LAMMPS_POTENTIALS"] = str(potentials_path)
        self.potentials_path = potentials_path

    def version(self):
        import lammps
        cmd_args = [
            "-echo", "log", "-log", "none", "-screen", "none", "-nocite"
        ]
        lmp = lammps.lammps(name="", cmdargs=cmd_args, comm=None)
        try:
            return lmp.version()
        finally:
            lmp.close()

    def calc(self, **kwargs):
        from ase.calculators.lammpslib import LAMMPSlib
        return LAMMPSlib(**kwargs)

    @classmethod
    def fromconfig(cls, config):
        return cls(config.datafiles['lammps'][0])


@factory('openmx')
class OpenMXFactory:
    def __init__(self, executable, data_path):
        self.executable = executable
        self.data_path = data_path

    def version(self):
        from ase.calculators.openmx.openmx import parse_omx_version
        dummyfile = 'omx_dummy_input'
        stdout = read_stdout([self.executable, dummyfile],
                             createfile=dummyfile)
        return parse_omx_version(stdout)

    def calc(self, **kwargs):
        from ase.calculators.openmx import OpenMX
        return OpenMX(command=self.executable,
                      data_path=str(self.data_path),
                      **kwargs)

    @classmethod
    def fromconfig(cls, config):
        return cls(config.executables['openmx'],
                   data_path=config.datafiles['openmx'][0])


@factory('octopus')
class OctopusFactory:
    def __init__(self, executable):
        self.executable = executable

    def version(self):
        stdout = read_stdout([self.executable, '--version'])
        match = re.match(r'octopus\s*(.+)', stdout)
        return match.group(1)

    def calc(self, **kwargs):
        from ase.calculators.octopus import Octopus
        command = f'{self.executable} > stdout.log'
        return Octopus(command=command, **kwargs)

    @classmethod
    def fromconfig(cls, config):
        return cls(config.executables['octopus'])


@factory('siesta')
class SiestaFactory:
    def __init__(self, executable, pseudo_path):
        self.executable = executable
        self.pseudo_path = pseudo_path

    def version(self):
        from ase.calculators.siesta.siesta import get_siesta_version
        full_ver = get_siesta_version(self.executable)
        m = re.match(r'siesta-(\S+)', full_ver, flags=re.I)
        if m:
            return m.group(1)
        return full_ver

    def calc(self, **kwargs):
        from ase.calculators.siesta import Siesta
        command = '{} < PREFIX.fdf > PREFIX.out'.format(self.executable)
        return Siesta(command=command,
                      pseudo_path=str(self.pseudo_path),
                      **kwargs)

    @classmethod
    def fromconfig(cls, config):
        paths = config.datafiles['siesta']
        assert len(paths) == 1
        path = paths[0]
        return cls(config.executables['siesta'], str(path))


@factory('nwchem')
class NWChemFactory:
    def __init__(self, executable):
        self.executable = executable

    def version(self):
        stdout = read_stdout([self.executable], createfile='nwchem.nw')
        match = re.search(
            r'Northwest Computational Chemistry Package \(NWChem\) (\S+)',
            stdout, re.M)
        return match.group(1)

    def calc(self, **kwargs):
        from ase.calculators.nwchem import NWChem
        command = f'{self.executable} PREFIX.nwi > PREFIX.nwo'
        return NWChem(command=command, **kwargs)

    @classmethod
    def fromconfig(cls, config):
        return cls(config.executables['nwchem'])


class NoSuchCalculator(Exception):
    pass


class Factories:
    all_calculators = set(calculator_names)
    builtin_calculators = {'eam', 'emt', 'ff', 'lj', 'morse', 'tip3p', 'tip4p'}
    autoenabled_calculators = {'asap'} | builtin_calculators

    # TODO: Port calculators to use factories.  As we do so, remove names
    # from list of calculators that we monkeypatch:
    monkeypatch_calculator_constructors = {
        'ace',
        'aims',
        'amber',
        'castep',
        'crystal',
        'demon',
        'demonnano',
        'dftd3',
        'dmol',
        'exciting',
        'fleur',
        'gamess_us',
        'gaussian',
        'gulp',
        'hotbit',
        'lammpslib',
        'mopac',
        'onetep',
        'orca',
        'Psi4',
        'qchem',
        'turbomole',
    }

    def __init__(self, requested_calculators):
        executable_config_paths, executables = get_testing_executables()
        assert isinstance(executables, Mapping), executables
        self.executables = executables
        self.executable_config_paths = executable_config_paths

        datafiles_module = None
        datafiles = {}

        try:
            import asetest as datafiles_module
        except ImportError:
            pass
        else:
            datafiles.update(datafiles_module.datafiles.paths)
            datafiles_module = datafiles_module

        self.datafiles_module = datafiles_module
        self.datafiles = datafiles

        factories = {}

        for name, cls in factory_classes.items():
            try:
                factory = cls.fromconfig(self)
            except (NotInstalled, KeyError):
                pass
            else:
                factories[name] = factory

        self.factories = factories

        requested_calculators = set(requested_calculators)
        if 'auto' in requested_calculators:
            requested_calculators.remove('auto')
            requested_calculators |= set(self.factories)
        self.requested_calculators = requested_calculators

        for name in self.requested_calculators:
            if name not in self.all_calculators:
                raise NoSuchCalculator(name)

    def installed(self, name):
        return name in self.builtin_calculators | set(self.factories)

    def is_adhoc(self, name):
        return name not in factory_classes

    def optional(self, name):
        return name not in self.builtin_calculators

    def enabled(self, name):
        auto = name in self.autoenabled_calculators and self.installed(name)
        return auto or (name in self.requested_calculators)

    def require(self, name):
        # XXX This is for old-style calculator tests.
        # Newer calculator tests would depend on a fixture which would
        # make them skip.
        # Older tests call require(name) explicitly.
        assert name in calculator_names
        if not self.installed(name) and not self.is_adhoc(name):
            pytest.skip(f'Not installed: {name}')
        if name not in self.requested_calculators:
            pytest.skip(f'Use --calculators={name} to enable')

    def __getitem__(self, name):
        return self.factories[name]

    def monkeypatch_disabled_calculators(self):
        test_calculator_names = (self.autoenabled_calculators
                                 | self.builtin_calculators
                                 | self.requested_calculators)
        disable_names = self.monkeypatch_calculator_constructors - test_calculator_names
        #disable_names = self.all_calculators - test_calculator_names

        for name in disable_names:
            try:
                cls = get_calculator_class(name)
            except ImportError:
                pass
            else:

                def get_mock_init(name):
                    def mock_init(obj, *args, **kwargs):
                        pytest.skip(f'use --calculators={name} to enable')

                    return mock_init

                def mock_del(obj):
                    pass

                cls.__init__ = get_mock_init(name)
                cls.__del__ = mock_del


def get_factories(pytestconfig):
    opt = pytestconfig.getoption('--calculators')
    requested_calculators = opt.split(',') if opt else []
    return Factories(requested_calculators)


def parametrize_calculator_tests(metafunc):
    """Parametrize tests using our custom markers.

    We want tests marked with @pytest.mark.calculator(names) to be
    parametrized over the named calculator or calculators."""
    calculator_inputs = []

    for marker in metafunc.definition.iter_markers(name='calculator'):
        calculator_names = marker.args
        kwargs = dict(marker.kwargs)
        marks = kwargs.pop('marks', [])
        for name in calculator_names:
            param = pytest.param((name, kwargs), marks=marks)
            calculator_inputs.append(param)

    if calculator_inputs:
        metafunc.parametrize('factory',
                             calculator_inputs,
                             indirect=True,
                             ids=lambda input: input[0])


class CalculatorInputs:
    def __init__(self, factory, parameters=None):
        if parameters is None:
            parameters = {}
        self.parameters = parameters
        self.factory = factory

    @property
    def name(self):
        return self.factory.name

    def __repr__(self):
        cls = type(self)
        return '{}({}, {})'.format(cls.__name__, self.name, self.parameters)

    def new(self, **kwargs):
        kw = dict(self.parameters)
        kw.update(kwargs)
        return CalculatorInputs(self.factory, kw)

    def calc(self, **kwargs):
        param = dict(self.parameters)
        param.update(kwargs)
        return self.factory.calc(**param)


class ObsoleteFactoryWrapper:
    # We use this for transitioning older tests to the new framework.
    def __init__(self, name):
        self.name = name

    def calc(self, **kwargs):
        from ase.calculators.calculator import get_calculator_class
        cls = get_calculator_class(self.name)
        return cls(**kwargs)