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Commit 0a1cd99c authored by Ask Hjorth Larsen's avatar Ask Hjorth Larsen
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read more stuff. Better error msgs when things to wrong

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parser/parser-siesta/parser.py
+ 125
− 38
View file @ 0a1cd99c
......@@ -11,7 +11,7 @@ from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
from nomadcore.unit_conversion.unit_conversion \
import register_userdefined_quantity, convert_unit
from util import floating
from util import floating, integer
arg = sys.argv[1]
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"))
......@@ -24,7 +24,7 @@ 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),
return SM(r'siesta:\s*%s\s*=\s*(?P<%s__eV>\S+)' % (title, meta),
name=meta, **kwargs)
......@@ -40,7 +40,7 @@ def ArraySM(header, row, build, **kwargs):
sm = SM(header,
name='startarray',
name=kwargs.pop('name', 'startarray'),
required=True,
subFlags=SM.SubFlags.Sequenced,
subMatchers=[
......@@ -54,25 +54,66 @@ def ArraySM(header, row, build, **kwargs):
return sm
def errprint(func):
def wrapper(backend, lines):
try:
func(backend, lines)
except Exception:
print('Error in %s: %d lines' % (func.__name__,
len(lines)))
for line in lines:
print(line, file=sys.stderr)
raise
return wrapper
def tokenize(lines):
return np.array([line.split() for line in lines], object)
@errprint
def build_cell(backend, lines):
cell = tokenize(lines).astype(float)
backend.addArrayValues('simulation_cell', convert_unit(cell, 'angstrom'))
@errprint
def get_forces(backend, lines):
forces = tokenize(lines)[:, 2:].astype(float)
if len(lines) == 0:
# Siesta sometimes, stupidly, writes a Forces header.
# It then proceeds to not write any forces.
# Thus we ignore that silliness
return
forces = tokenize(lines)[:, 1:].astype(float)
assert forces.shape[1] == 3
backend.addArrayValues('atom_forces', convert_unit(forces, 'eV/angstrom'))
@errprint
def get_stress(backend, lines):
stress = tokenize(lines)[:, 1:].astype(float)
assert stress.shape == (3, 3)
backend.addArrayValues('atom_stress', convert_unit(stress, 'eV/angstrom**3'))
@errprint
def get_dipole(backend, lines):
assert len(lines) == 1
dipole = tokenize(lines)[:, -3:].astype(float)
# Hmm. There is no common metadata for dipole moment for some reason.
#print('dipole', dipole)
def get_array(metaname, dtype, istart=0, iend=None, unit=None):
@errprint
def buildarray(backend, lines):
arr = tokenize(lines)
if iend is None:
arr = arr[:, istart:]
else:
arr = arr[:, istart:iend]
arr = arr.astype(dtype)
if unit is not None:
arr = convert_unit(arr, unit)
backend.addArrayValues(metaname, arr)
return buildarray
@errprint
def add_positions_and_labels(backend, lines):
matrix = tokenize(lines)
positions = matrix[:, 1:4].astype(float)
......@@ -81,33 +122,77 @@ def add_positions_and_labels(backend, lines):
backend.addArrayValues('atom_labels', labels)
# .EIG file:
#fermi level
# nstates nspins nkpts
# kptnumber spin1eps1 spin1eps2.... spin1epsN spin2eps1 spin2eps2... spin2epsN
"""
%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
"""
infoFileDescription = SM(
name='root',
weak=True,
startReStr='',
fixedStartValues={'program_name': 'siesta'},
# In SIESTA, the calculations are always periodic
fixedStartValues={'program_name': 'siesta',
'configuration_periodic_dimensions': np.ones(3, bool)},
sections=['section_run'],
subFlags=SM.SubFlags.Sequenced, # sequenced or not?
subMatchers=[
SM(r'Siesta Version: (?P<program_name>siesta)-(?P<program_version>\S*)',
SM(r'Siesta Version: (?P<program_name>siesta)-(?P<program_version>\S+)',
name='name&version', required=True),
ArraySM(r'siesta: Atomic coordinates \(Bohr\) and species',
r'siesta:\s*\S+\s+\S+\s+\S+\s+\S+\s+\S+',
add_positions_and_labels),
SM(r'\s*Single-point calculation',
ArraySM(r'siesta: Automatic unit cell vectors \(Ang\):',
r'siesta:\s*\S+\s*\S+\s*\S+',
get_array('simulation_cell', float, 1, 4, unit='angstrom')),
SM(r'\s*Single-point calculation|\s*Begin \S+ opt\.',
name='singleconfig',
repeats=True,
# XXX some of the matchers should not be in single config calculation
sections=['section_single_configuration_calculation'],
subFlags=SM.SubFlags.Sequenced,
subMatchers=[
ArraySM(r'outcoor: Atomic coordinates \(Ang\):',
r'\s*\S+\s*\S+\s*\S+',
get_array('atom_positions', float, 0, 3, unit='angstrom')),
ArraySM(r'outcell: Unit cell vectors \(Ang\):',
r'\s*\S+\s*\S+\s*\S+',
build_cell),
SM(r'\s*scf:\s*iscf', name='scf', required=True),
SM(r'SCF cycle converged after\s*%s\s*iterations'
% integer('number_of_scf_iterations'), name='scf-iterations'),
SM(r'siesta: E_KS\(eV\)\s*=\s*%s' % floating('energy_free__eV'),
name='E_KS'),
ArraySM(r'siesta: Atomic forces \(eV/Ang\):',
r'\s*[0-9]+\s+\S+\s+\S+\s+\S+',
get_forces, name='forces-in-opt-step'),
SM(r'Target enthalpy', name='end-singleconfig'),
SM(r'', weak=True, name='After singleconfigs',
subFlags=SM.SubFlags.Sequenced,
subMatchers=[
# There is a stupid header in the middle of nowhere which is
# equal to a later header, so we swallow it here:
SM(r'siesta: Atomic forces \(eV/Ang\):'),
#SM(r'siesta: Atomic forces \(eV/Ang\):'),
ArraySM(r'siesta: Atomic forces \(eV/Ang\):',
r'siesta:\s*[0-9]+\s+\S+\s+\S+\s+\S+',
get_forces, name='forces-in-single-calc'),
SM(r'siesta: Program\'s energy decomposition \(eV\):',
name='energy header 1',
weak=True,
......@@ -127,15 +212,17 @@ infoFileDescription = SM(
#siesta_energy('Ekinion', ''),
siesta_energy('Total', 'energy_total'),
]),
ArraySM(r'siesta: Atomic forces \(eV/Ang\):',
r'siesta:\s*[0-9]+\s+\S+\s+\S+\s+\S+',
get_forces),
ArraySM(r'siesta: Stress tensor ',#\(static\) \(eV/Ang**3\):',
ArraySM(r'siesta: Stress tensor \(static\) \(eV/Ang\*\*3\):',
r'siesta:\s*\S+\s+\S+\s+\S+',
get_stress),
ArraySM(r'siesta: Electric dipole \(Debye\)\s*=',
r'siesta: Electric dipole \(Debye\)\s*=',
get_dipole,
forwardMatch=True),
# The purpose of the following matcher is to parse all lines
SM(r'x^', name='end')
])
]),
])
class SiestaContext(object):
......
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