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Commit ee8dfe6b authored by Ask Hjorth Larsen's avatar Ask Hjorth Larsen
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clean up vestigial code from certain octopus parser modules, moving the... 

clean up vestigial code from certain octopus parser modules, moving the remainder into the main module
parent 1153f1db
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parser/parser-octopus/octopus_info_parser.py deleted 100644 → 0
View file @ 1153f1db
from __future__ import print_function
from builtins import object
import logging
import setup_paths
from nomadcore.simple_parser import SimpleMatcher as SM
from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
from nomadcore.unit_conversion.unit_conversion \
import register_userdefined_quantity, convert_unit
import os, sys, json
from util import OCT_ENERGY_UNIT_NAME, f_num, i_num, numpattern, integer,\
parse_file_without_decorations
# Match lines like: " Total = -7.05183\n"
def oct_energy_sm(octname, nomadname):
pattern = (r'\s*%(octname)s\s*=\s*%(pattern)s'
% dict(octname=octname,
pattern=numpattern(nomadname,
unit=OCT_ENERGY_UNIT_NAME)))
#print 'oct energy sm', pattern
return SM(pattern,
name=octname)
sm_scfconv = SM(r'SCF converged in\s*%s\s*iterations'
% integer('x_octopus_info_scf_converged_iterations'),
sections=['section_run'])
sm_energy = SM(r'Energy \[(H|eV)\]:', required=True, name='energy_header',
subMatchers=[
oct_energy_sm('Total', 'energy_total'),
oct_energy_sm('Free', 'energy_free'),
oct_energy_sm('Ion-ion', 'x_octopus_info_energy_ion_ion'),
oct_energy_sm('Eigenvalues', 'energy_sum_eigenvalues'),
oct_energy_sm('Hartree', 'energy_electrostatic'),
#oct_energy_sm(r'Int\[n.v_xc\]', ''),
oct_energy_sm('Exchange', 'energy_X'),
oct_energy_sm('Correlation', 'energy_C'),
oct_energy_sm('vanderWaals', 'energy_van_der_Waals'),
oct_energy_sm('-TS', 'energy_correction_entropy'),
oct_energy_sm('Kinetic', 'electronic_kinetic_energy')
])
infoFileDescription = SM(
name='root',
weak=True,
startReStr='',
fixedStartValues={'program_name': 'octopus'},
sections=['section_single_configuration_calculation'],
subFlags=SM.SubFlags.Sequenced,
subMatchers=[
sm_scfconv,
sm_energy,
])
parserInfo = {
"name": "info_parser_octopus",
"version": "1.0"
}
class OctopusParserContext(object):
"""main place to keep the parser status, open ancillary files,..."""
def __init__(self):
self.scfIterNr = 0
# just examples, you probably want to remove the following two triggers
def startedParsing(self, name, parser):
pass
def onClose_section_single_configuration_calculation(self, backend, gIndex, section):
"""trigger called when section_single_configuration_calculation is closed"""
pass
#backend.addValue("", self.scfIterNr)
#logging.getLogger("nomadcore.parsing").info("closing section_single_configuration_calculation gIndex %d %s", gIndex, section.simpleValues)
#self.scfIterNr = 0
def onClose_section_scf_iteration(self, backend, gIndex, section):
"""trigger called when section_scf_iteration is closed"""
pass
#logging.getLogger("nomadcore.parsing").info("closing section_scf_iteration bla gIndex %d %s", gIndex, section.simpleValues)
#self.scfIterNr += 1
#def parse_infofile(meta_info_env, pew, fname):
# parse_file_without_decorations(pew, meta_info_env, infoFileDescription,
# parserInfo, OctopusParserContext(), fname)
def parse_infofile(meta_info_env, pew, fname):
with open(fname) as fd:
for line in fd:
if line.startswith('SCF converged'):
iterations = int(line.split()[-2])
pew.addValue('x_octopus_info_scf_converged_iterations',
iterations)
break
for line in fd: # Jump down to energies:
if line.startswith('Energy ['):
octunit = line.strip().split()[-1].strip('[]:')
nomadunit = {'eV': 'eV', 'H': 'hartree'}[octunit]
break
names = {'Total': 'energy_total',
'Free': 'energy_free',
'Ion-ion': 'x_octopus_info_energy_ion_ion',
'Eigenvalues': 'energy_sum_eigenvalues',
'Hartree': 'energy_electrostatic',
'Exchange': 'energy_X',
'Correlation': 'energy_C',
'vanderWaals': 'energy_van_der_Waals',
'-TS': 'energy_correction_entropy',
'Kinetic': 'electronic_kinetic_energy'}
for line in fd:
if line.startswith('---'):
continue
tokens = line.split()
if len(tokens) < 3:
break
if tokens[0] in names:
pew.addValue(names[tokens[0]],
convert_unit(float(tokens[2]), nomadunit))
parser/parser-octopus/octopus_logfile_parser.py deleted 100644 → 0
View file @ 1153f1db
from nomadcore.simple_parser import mainFunction, SimpleMatcher as SM
from util import numpattern, i_num, f_num, e_num, word, integer, \
parse_file_without_decorations
parserInfo = {
"name": "logfile_parser_octopus",
"version": "1.0"
}
logFileDescription = SM(
name='root',
weak=True,
startReStr='',
fixedStartValues={'program_name': 'octopus'},
#sections=['section_run'],
subFlags=SM.SubFlags.Sequenced,
subMatchers=[
SM(r'Version\s*:\s*%s' % word('program_version')),
#SM(r'Revision\s*:\s*%s' % integer('x_octopus_log_svn_revision')),
]
)
class OctopusLogFileParserContext(object):
def startedParsing(self, name, parser):
pass
def parse_logfile(meta_info_env, pew, fname):
# XXX this is just a hack until we decide to do more
maxlines = 100
with open(fname) as fd:
for i, line in enumerate(fd):
if i > maxlines:
break
if line.startswith('Version'):
version = line.split()[-1]
pew.addValue('program_version', version)
elif line.startswith('Revision'):
revision = int(line.split()[-1])
pew.addValue('x_octopus_log_svn_revision', revision)
# XXX more info
#def parse_logfile(meta_info_env, pew, fname):
# parse_file_without_decorations(pew, meta_info_env, logFileDescription,
# parserInfo, OctopusLogFileParserContext(),
# fname)
parser/parser-octopus/parser_octopus.py
View file @ ee8dfe6b
......@@ -13,12 +13,9 @@ import setup_paths
from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
from nomadcore.parser_backend import JsonParseEventsWriterBackend
from nomadcore.unit_conversion.unit_conversion import convert_unit, \
register_userdefined_quantity
from nomadcore.unit_conversion.unit_conversion import convert_unit
from aseoct import Octopus, parse_input_file
from octopus_info_parser import parse_infofile
from octopus_logfile_parser import parse_logfile
"""This is the Octopus parser.
......@@ -43,6 +40,57 @@ is largely irrelevant.
"""
def parse_infofile(meta_info_env, pew, fname):
with open(fname) as fd:
for line in fd:
if line.startswith('SCF converged'):
iterations = int(line.split()[-2])
pew.addValue('x_octopus_info_scf_converged_iterations',
iterations)
break
for line in fd: # Jump down to energies:
if line.startswith('Energy ['):
octunit = line.strip().split()[-1].strip('[]:')
nomadunit = {'eV': 'eV', 'H': 'hartree'}[octunit]
break
names = {'Total': 'energy_total',
'Free': 'energy_free',
'Ion-ion': 'x_octopus_info_energy_ion_ion',
'Eigenvalues': 'energy_sum_eigenvalues',
'Hartree': 'energy_electrostatic',
'Exchange': 'energy_X',
'Correlation': 'energy_C',
'vanderWaals': 'energy_van_der_Waals',
'-TS': 'energy_correction_entropy',
'Kinetic': 'electronic_kinetic_energy'}
for line in fd:
if line.startswith('---'):
continue
tokens = line.split()
if len(tokens) < 3:
break
if tokens[0] in names:
pew.addValue(names[tokens[0]],
convert_unit(float(tokens[2]), nomadunit))
def parse_logfile(meta_info_env, pew, fname):
maxlines = 100
with open(fname) as fd:
for i, line in enumerate(fd):
if i > maxlines:
break
if line.startswith('Version'):
version = line.split()[-1]
pew.addValue('program_version', version)
elif line.startswith('Revision'):
revision = int(line.split()[-1])
pew.addValue('x_octopus_log_svn_revision', revision)
def parse_gridinfo(metaInfoEnv, pew, fname):
results = {}
......@@ -88,8 +136,6 @@ def parse_gridinfo(metaInfoEnv, pew, fname):
def parse_coordinates_from_parserlog(fname):
results = {}
units = 'bohr'
def buildblock(block):
imax = 1 + max(b[0] for b in block)
jmax = 1 + max(b[1] for b in block)
......@@ -167,10 +213,6 @@ def parse_coordinates_from_parserlog(fname):
def normalize_names(names):
return [name.lower() for name in names]
#ENERGY_UNIT = 'usrOctEnergyUnit'
#LENGTH_UNIT = 'usrOctLengthUnit'
metaInfoPath = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(__file__)),
"../../../../nomad-meta-info/meta_info/nomad_meta_info/octopus.nomadmetainfo.json"))
metaInfoEnv, warnings = loadJsonFile(filePath=metaInfoPath,
......@@ -182,7 +224,6 @@ metaInfoEnv, warnings = loadJsonFile(filePath=metaInfoPath,
metaInfoKinds = metaInfoEnv.infoKinds.copy()
all_metadata_names = list(metaInfoKinds.keys())
normalized2real = dict(zip(normalize_names(all_metadata_names), all_metadata_names))
#assert 'x_octopus_info_scf_converged_iterations' in metaInfoKinds, '\n'.join(list(sorted(metaInfoKinds.keys())))
# We need access to this information because we want/need to dynamically convert
# extracted metadata to its correct type. Thus we need to know the type.
# Also since input is case insensitive, we need to convert normalized (lowercase)
......@@ -211,26 +252,22 @@ def read_parser_log(path):
if ' ' in name:
# Not a real name
continue
#print(name)
# Octopus questionably writes this one twice
#if name != 'speciesprojectorspherethreshold':
exec_kwargs[name] = value
return exec_kwargs
def is_octopus_logfile(fname):
fd = open(fname)
for n, line in enumerate(fd):
if n > 20:
break
if '|0) ~ (0) |' in line: # Eyes from Octopus logo
return True
with open(fname) as fd:
for n, line in enumerate(fd):
if n > 20:
break
if '|0) ~ (0) |' in line: # Eyes from Octopus logo
return True
return False
def find_octopus_logfile(dirname):
allfnames = glob('%s/*' % dirname)
for fname in allfnames:
for fname in os.listdir(dirname):
if os.path.isfile(fname) and is_octopus_logfile(fname):
return fname
return None
......@@ -275,28 +312,6 @@ def override_keywords(kwargs, parser_log_kwargs, fd):
return outkwargs
def register_units(kwargs, fd):
units = kwargs.get('units', 'atomic').lower()
if units == 'atomic':
length_unit = 'bohr'
energy_unit = 'hartree'
elif units == 'ev_angstrom':
length_unit = 'angstrom'
energy_unit = 'eV'
else:
raise ValueError('Unknown units: %s' % units)
if 'unitsinput' in kwargs:
raise ValueError('UnitsInput not supported')
if 'unitsoutput' in kwargs:
raise ValueError('UnitsOutput not supported')
print('Set units: energy=%s, length=%s' % (energy_unit, length_unit),
file=fd)
register_userdefined_quantity(ENERGY_UNIT, energy_unit)
register_userdefined_quantity(LENGTH_UNIT, length_unit)
metadata_dtypes = {'b': bool,
'C': str,
'f': float} # Integer?
......@@ -375,19 +390,12 @@ def parse(fname, fd):
print('Override certain keywords with processed keywords', file=fd)
kwargs = override_keywords(kwargs, parser_log_kwargs, fd)
#register_units(kwargs, fd)
print('Read as ASE calculator', file=fd)
calc = Octopus(dirname, check_keywords=False)
#atoms = calc.get_atoms()
with open_section('section_basis_set_cell_dependent') as basis_set_cell_dependent_gid:
pew.addValue('basis_set_cell_dependent_kind', 'realspace_grids')
# XXX FIXME spacing can very rarely be 3 numbers!
# uuh there is no meaningful way to set grid spacing
# pass
#cubefiles = glob('staticdirname/*.cube')
#cubefiles.sort()
# How does nomad want grid spacing?
nbands = calc.get_number_of_bands()
nspins = calc.get_number_of_spins()
......@@ -506,16 +514,17 @@ def parse(fname, fd):
float(parser_log_kwargs['excesscharge']))
oct_theory_level = kwargs.get('theorylevel', 'dft')
theory_levels = dict(#independent_particles='',
#hartree='',
#hartree_fock='',
dft='DFT')
#classical='',
#rdmft='')
theory_levels = dict(independent_particles='independent_particles', # not defined by Nomad
hartree='Hartree', # not defined by Nomad
hartree_fock='DFT', # nomad wants it that way
dft='DFT',
classical='Classical', # Not defined by Nomad
rdmft='RDMFT') # Not defined by Nomad
# TODO how do we warn if we get an unexpected theory level?
# Currently: KeyError
nomad_theory_level = theory_levels[oct_theory_level]
pew.addValue('electronic_structure_method', 'DFT')
pew.addValue('electronic_structure_method', nomad_theory_level)
if oct_theory_level == 'dft':
ndim = int(kwargs.get('dimensions', 3))
......
src/main/scala/eu/nomad_lab/parsers/OctopusParser.scala
View file @ ee8dfe6b
......@@ -48,10 +48,8 @@ Simulation Box:
resList = Seq(
"parser-octopus/parser_octopus.py",
"parser-octopus/aseoct.py",
"parser-octopus/octopus_logfile_parser.py",
"parser-octopus/generate-octopus-json.py",
"parser-octopus/util.py",
"parser-octopus/octopus_info_parser.py",
"parser-octopus/setup_paths.py",
"nomad_meta_info/public.nomadmetainfo.json",
"nomad_meta_info/common.nomadmetainfo.json",
......
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