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‎tilde/core/api.py‎

Lines changed: 86 additions & 22 deletions
Original file line numberDiff line numberDiff line change
@@ -2,7 +2,7 @@
22
# Functionality exposed as an API
33
# Author: Evgeny Blokhin
44

5-
__version__ = "0.9.1"
5+
__version__ = "0.9.3"
66

77
import os, sys
88
import re
@@ -34,7 +34,28 @@
3434
class API:
3535
version = __version__
3636
__shared_state = {}
37-
formula_sequence = ['Fr','Cs','Rb','K','Na','Li', 'Be','Mg','Ca','Sr','Ba','Ra', 'Sc','Y','La','Ce','Pr','Nd','Pm','Sm','Eu','Gd','Tb','Dy','Ho','Er','Tm','Yb', 'Ac','Th','Pa','U','Np','Pu', 'Ti','Zr','Hf', 'V','Nb','Ta', 'Cr','Mo','W', 'Fe','Ru','Os', 'Co','Rh','Ir', 'Mn','Tc','Re', 'Ni','Pd','Pt', 'Cu','Ag','Au', 'Zn','Cd','Hg', 'B','Al','Ga','In','Tl', 'Pb','Sn','Ge','Si','C', 'N','P','As','Sb','Bi', 'H', 'Po','Te','Se','S','O', 'At','I','Br','Cl','F', 'He','Ne','Ar','Kr','Xe','Rn']
37+
formula_sequence = [
38+
'Fr','Cs','Rb','K','Na','Li',
39+
'Be','Mg','Ca','Sr','Ba','Ra',
40+
'Sc','Y','La','Ce','Pr','Nd','Pm','Sm','Eu','Gd','Tb','Dy','Ho','Er','Tm','Yb',
41+
'Ac','Th','Pa','U','Np','Pu',
42+
'Ti','Zr','Hf',
43+
'V','Nb','Ta',
44+
'Cr','Mo','W',
45+
'Fe','Ru','Os',
46+
'Co','Rh','Ir',
47+
'Mn','Tc','Re',
48+
'Ni','Pd','Pt',
49+
'Cu','Ag','Au',
50+
'Zn','Cd','Hg',
51+
'B','Al','Ga','In','Tl',
52+
'Pb','Sn','Ge','Si','C',
53+
'N','P','As','Sb','Bi',
54+
'H',
55+
'Po','Te','Se','S','O',
56+
'At','I','Br','Cl','F',
57+
'He','Ne','Ar','Kr','Xe','Rn'
58+
]
3859

3960
def __init__(self, settings=settings):
4061
self.settings = settings
@@ -58,14 +79,14 @@ def __init__(self, settings=settings):
5879
if not os.path.isfile( os.path.realpath(BASE_DIR + '/../parsers') + '/' + parsername + '/' + parsername + '.py' ):
5980
raise RuntimeError('Parser API Error: Parser code for ' + parsername + ' is missing!')
6081
try:
61-
parsermanifest = json.loads( open( os.path.realpath(BASE_DIR + '/../parsers') + '/' + parsername + '/manifest.json' ).read() )
82+
parsermanifest = json.loads(open( os.path.realpath(BASE_DIR + '/../parsers') + '/' + parsername + '/manifest.json' ).read())
6283
except:
6384
raise RuntimeError('Parser API Error: Parser manifest for ' + parsername + ' has corrupted format!')
6485

6586
if (not 'enabled' in parsermanifest or not parsermanifest['enabled']) and not self.settings['debug_regime']:
6687
continue
6788

68-
All_parsers[parsername] = importlib.import_module('tilde.parsers.' + parsername + '.' + parsername) # all imported modules will be stored here
89+
All_parsers[parsername] = importlib.import_module('tilde.parsers.' + parsername + '.' + parsername) # all imported modules will be here
6990

7091
# replace modules by classes and check *fingerprints* method
7192
for parser, module in All_parsers.items():
@@ -101,7 +122,7 @@ def __init__(self, settings=settings):
101122
raise RuntimeError('Module API Error: no appdata tag for ' + appname + '!')
102123
if 'onprocess' in appmanifest:
103124
try:
104-
app = __import__('tilde.apps.' + appname + '.' + appname, fromlist=[appname.capitalize()]) # this means: from foo import Foo
125+
app = __import__('tilde.apps.' + appname + '.' + appname, fromlist=[appname.capitalize()]) # from foo import Foo
105126
except ImportError:
106127
raise RuntimeError('Module API Error: module ' + appname + ' is invalid or not found!')
107128
self.Apps[appname] = {
@@ -285,7 +306,7 @@ def _parse(self, parsable, parser_name):
285306
error = "routine %s parser error in %s: %s" % ( parser_name, parsable, e )
286307
except:
287308
exc_type, exc_value, exc_tb = sys.exc_info()
288-
error = "unexpected %s parser error in %s:\n %s" % ( parser_name, parsable, "".join(traceback.format_exception( exc_type, exc_value, exc_tb )) )
309+
error = "unexpected %s parser error in %s:\n %s" % (parser_name, parsable, "".join(traceback.format_exception( exc_type, exc_value, exc_tb )))
289310
yield None, error
290311

291312
def parse(self, parsable):
@@ -549,7 +570,7 @@ def postprocess(self, calc, with_module=None, dry_run=None):
549570
AppInstance = appclass['appmodule'](calc)
550571
except:
551572
exc_type, exc_value, exc_tb = sys.exc_info()
552-
errmsg = "Fatal error in %s module:\n %s" % ( appname, " ".join(traceback.format_exception( exc_type, exc_value, exc_tb )) )
573+
errmsg = "Fatal error in %s module:\n %s" % (appname, " ".join(traceback.format_exception( exc_type, exc_value, exc_tb )))
553574
calc.apps[appname]['error'] = errmsg
554575
calc.warning( errmsg )
555576
else:
@@ -601,9 +622,15 @@ def save(self, calc, session):
601622
# re-orientate eigenvectors
602623
for i in range(0, len(calc.phonons['ph_eigvecs'][bzpoint])):
603624
for j in range(0, len(calc.phonons['ph_eigvecs'][bzpoint][i])//3):
604-
eigv = array([calc.phonons['ph_eigvecs'][bzpoint][i][j*3], calc.phonons['ph_eigvecs'][bzpoint][i][j*3+1], calc.phonons['ph_eigvecs'][bzpoint][i][j*3+2]])
625+
eigv = array([
626+
calc.phonons['ph_eigvecs'][bzpoint][i][j*3],
627+
calc.phonons['ph_eigvecs'][bzpoint][i][j*3+1],
628+
calc.phonons['ph_eigvecs'][bzpoint][i][j*3+2]
629+
])
605630
R = dot( eigv, calc.structures[-1].cell ).tolist()
606-
calc.phonons['ph_eigvecs'][bzpoint][i][j*3], calc.phonons['ph_eigvecs'][bzpoint][i][j*3+1], calc.phonons['ph_eigvecs'][bzpoint][i][j*3+2] = [round(x, 3) for x in R]
631+
calc.phonons['ph_eigvecs'][bzpoint][i][j*3], \
632+
calc.phonons['ph_eigvecs'][bzpoint][i][j*3+1], \
633+
calc.phonons['ph_eigvecs'][bzpoint][i][j*3+2] = [round(x, 3) for x in R]
607634

608635
try: irreps = calc.phonons['irreps'][bzpoint]
609636
except KeyError:
@@ -612,7 +639,7 @@ def save(self, calc, session):
612639
empty.append('')
613640
irreps = empty
614641

615-
phonons_json.append({ 'bzpoint':bzpoint, 'freqs':frqset, 'irreps':irreps, 'ph_eigvecs':calc.phonons['ph_eigvecs'][bzpoint] })
642+
phonons_json.append({'bzpoint':bzpoint, 'freqs':frqset, 'irreps':irreps, 'ph_eigvecs':calc.phonons['ph_eigvecs'][bzpoint]})
616643
if bzpoint == '0 0 0':
617644
phonons_json[-1]['ir_active'] = calc.phonons['ir_active']
618645
phonons_json[-1]['raman_active'] = calc.phonons['raman_active']
@@ -641,8 +668,15 @@ def save(self, calc, session):
641668

642669
# construct ORM for other props
643670
calc.related_files = list(map(virtualize_path, calc.related_files))
644-
ormcalc.meta_data = model.Metadata(location=calc.info['location'], finished=calc.info['finished'], raw_input=calc.info['input'], modeling_time=calc.info['duration'], chemical_formula=html_formula(calc.info['standard']), download_size=calc.download_size, filenames=json.dumps(calc.related_files))
645-
671+
ormcalc.meta_data = model.Metadata(
672+
location=calc.info['location'],
673+
finished=calc.info['finished'],
674+
raw_input=calc.info['input'],
675+
modeling_time=calc.info['duration'],
676+
chemical_formula=html_formula(calc.info['standard']),
677+
download_size=calc.download_size,
678+
filenames=json.dumps(calc.related_files)
679+
)
646680
codefamily = model.Codefamily.as_unique(session, content = calc.info['framework'])
647681
codeversion = model.Codeversion.as_unique(session, content=calc.info['prog'])
648682

@@ -651,17 +685,30 @@ def save(self, calc, session):
651685

652686
pot = model.Pottype.as_unique(session, name=calc.info['H'])
653687
pot.instances.append(ormcalc)
654-
ormcalc.recipinteg = model.Recipinteg(kgrid=calc.info['k'], kshift=calc.info['kshift'], smearing=calc.info['smear'], smeartype=calc.info['smeartype'])
688+
ormcalc.recipinteg = model.Recipinteg(
689+
kgrid=calc.info['k'],
690+
kshift=calc.info['kshift'],
691+
smearing=calc.info['smear'],
692+
smeartype=calc.info['smeartype']
693+
)
655694
ormcalc.basis = model.Basis(
656695
kind=calc.info['ansatz'],
657-
content=_json.dumps(calc.electrons['basis_set']) if calc.electrons['basis_set'] else None # NB. ujson fails on NaN
696+
content=_json.dumps(calc.electrons['basis_set']) if calc.electrons['basis_set'] else None # NB. ujson fails here on NaN
658697
)
659698
ormcalc.energy = model.Energy(convergence=json.dumps(calc.convergence), total=calc.info['energy'])
660699

661700
ormcalc.spacegroup = model.Spacegroup(n=calc.info['ng'])
662-
ormcalc.struct_ratios = model.Struct_ratios(chemical_formula=calc.info['standard'], formula_units=calc.info['expanded'], nelem=calc.info['nelem'], dimensions=calc.info['dims'])
701+
ormcalc.struct_ratios = model.Struct_ratios(
702+
chemical_formula=calc.info['standard'],
703+
formula_units=calc.info['expanded'],
704+
nelem=calc.info['nelem'],
705+
dimensions=calc.info['dims']
706+
)
663707
if len(calc.tresholds) > 1:
664-
ormcalc.struct_optimisation = model.Struct_optimisation(tresholds=json.dumps(calc.tresholds), ncycles=json.dumps(calc.ncycles))
708+
ormcalc.struct_optimisation = model.Struct_optimisation(
709+
tresholds=_json.dumps(calc.tresholds), # NB. ujson fails here on NaN
710+
ncycles=json.dumps(calc.ncycles)
711+
)
665712

666713
for n, ase_repr in enumerate(calc.structures):
667714
is_final = True if n == len(calc.structures)-1 else False
@@ -678,7 +725,7 @@ def save(self, calc, session):
678725
charges = ase_repr.get_array('charges') if 'charges' in ase_repr.arrays else [None for j in range(len(ase_repr))]
679726
magmoms = ase_repr.get_array('magmoms') if 'magmoms' in ase_repr.arrays else [None for j in range(len(ase_repr))]
680727
for n, i in enumerate(ase_repr):
681-
struct.atoms.append( model.Atom( number=chemical_symbols.index(i.symbol), x=i.x, y=i.y, z=i.z, charge=charges[n], magmom=magmoms[n] ) )
728+
struct.atoms.append(model.Atom(number=chemical_symbols.index(i.symbol), x=i.x, y=i.y, z=i.z, charge=charges[n], magmom=magmoms[n]))
682729

683730
ormcalc.structures.append(struct)
684731
# TODO Forces
@@ -773,7 +820,10 @@ def purge(self, session, checksum):
773820

774821
# for all types of entries
775822
if len(C.references):
776-
left_references = [ int(i[0]) for i in session.query(model.Reference.reference_id).join(model.metadata_references, model.Reference.reference_id == model.metadata_references.c.reference_id).filter(model.metadata_references.c.checksum == checksum).all() ]
823+
left_references = [ int(i[0]) for i in session.query(model.Reference.reference_id).join(
824+
model.metadata_references,
825+
model.Reference.reference_id == model.metadata_references.c.reference_id
826+
).filter(model.metadata_references.c.checksum == checksum).all() ]
777827
session.execute( model.delete( model.metadata_references ).where( model.metadata_references.c.checksum == checksum ) )
778828

779829
# remove the whole citation?
@@ -804,8 +854,15 @@ def merge(self, session, checksums, title):
804854

805855
cur_depth = 0
806856

807-
for nested_depth, grid_item, download_size in session.query(model.Calculation.nested_depth, model.Grid.info, model.Metadata.download_size).filter(model.Calculation.checksum == model.Grid.checksum, model.Grid.checksum == model.Metadata.checksum, model.Calculation.checksum.in_(checksums)).all():
808-
857+
for nested_depth, grid_item, download_size in session.query(
858+
model.Calculation.nested_depth,
859+
model.Grid.info,
860+
model.Metadata.download_size
861+
).filter(
862+
model.Calculation.checksum == model.Grid.checksum,
863+
model.Grid.checksum == model.Metadata.checksum,
864+
model.Calculation.checksum.in_(checksums)
865+
).all():
809866
if nested_depth > cur_depth: cur_depth = nested_depth
810867

811868
grid_item = json.loads(grid_item)
@@ -881,8 +938,15 @@ def augment(self, session, parent, addendum):
881938
parent_grid = session.query(model.Grid).get(parent)
882939
info_obj = json.loads(parent_grid.info)
883940

884-
for nested_depth, grid_item, download_size in session.query(model.Calculation.nested_depth, model.Grid.info, model.Metadata.download_size).filter(model.Calculation.checksum == model.Grid.checksum, model.Grid.checksum == model.Metadata.checksum, model.Calculation.checksum.in_(filtered_addendum)).all():
885-
941+
for nested_depth, grid_item, download_size in session.query(
942+
model.Calculation.nested_depth,
943+
model.Grid.info,
944+
model.Metadata.download_size
945+
).filter(
946+
model.Calculation.checksum == model.Grid.checksum,
947+
model.Grid.checksum == model.Metadata.checksum,
948+
model.Calculation.checksum.in_(filtered_addendum)
949+
).all():
886950
if nested_depth >= parent_calc.nested_depth:
887951
parent_calc.nested_depth = nested_depth + 1
888952

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