Skip to content
GitLab
Commits (1)
Hide whitespace changes
Inline Side-by-side
.gitignore
View file @ f914e0c0
# use glob syntax.
syntax: glob
*.ser
*.class
*~
*.bak
#*.off
*.old
# python
__pycache__
.mypy_cache
*.pyc
*.bk
*.swp
*.annotate
.DS_Store
# logging files
detailed.log
# eclipse conf file
.settings
.classpath
.project
.manager
.scala_dependencies
# idea
.idea
*.iml
# building
target
build
null
tmp*
temp*
dist
test-output
build.log
# other scm
.svn
.CVS
.hg*
# switch to regexp syntax.
# syntax: regexp
# ^\.pc/
#SHITTY output not in target directory
build.log
#emacs TAGS
TAGS
lib/
env/
*.egg-info/
\ No newline at end of file
parser/parser-qbox/setup_paths.py deleted 100644 → 0
View file @ ffebcc60
import sys, os, os.path
baseDir = os.path.dirname(os.path.abspath(__file__))
commonDir = os.path.normpath(os.path.join(baseDir,"../../../../python-common/common/python"))
if not commonDir in sys.path:
sys.path.insert(0, commonDir)
parser/parser-qbox/QboxCommon.py → qboxparser/QboxCommon.py
View file @ f914e0c0
import setup_paths
import numpy as np
from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
from nomadcore.unit_conversion.unit_conversion import convert_unit
......
parser/parser-qbox/QboxInputParser.py → qboxparser/QboxInputParser.py
View file @ f914e0c0
from builtins import object
import setup_paths
import numpy as np
import nomadcore.ActivateLogging
from nomadcore.caching_backend import CachingLevel
......@@ -16,7 +15,7 @@ import logging, os, re, sys
############################################################
###############[1] transfer PARSER CONTEXT #################
############################################################
logger = logging.getLogger("nomad.qboxInputParser")
logger = logging.getLogger("nomad.qboxInputParser")
class QboxInputParserContext(object):
......@@ -32,7 +31,7 @@ class QboxInputParserContext(object):
"""
self.secMethodIndex = None
self.secSystemDescriptionIndex = None
self.singleConfCalcs = []
......@@ -74,20 +73,20 @@ class QboxInputParserContext(object):
def onClose_x_qbox_section_functionals(self, backend, gIndex, section):
functional_list = section["x_qbox_functional_name"]
if not functional_list: # default is LDA in qbox
if not functional_list: # default is LDA in qbox
functional = "LDA"
else :
functional = functional_list[-1] # use the xc appeared the last time
functional = functional_list[-1] # use the xc appeared the last time
if functional:
functionalMap = {
"LDA": ["LDA_X", "LDA_C_PZ"],
"VMN": ["LDA_X", "LDA_C_VWN"],
"PBE": ["GGA_X_PBE","GGA_C_PBE"],
"PBE0": ["GGA_X_PBE","GGA_C_PBE"],
"B3LYP": ["HYB_GGA_XC_B3LYP5"]
#need to be extended to add alpha_PBE0 :coefficient of Hartree-Fock exchange in the PBE0 xc functional
"LDA": ["LDA_X", "LDA_C_PZ"],
"VMN": ["LDA_X", "LDA_C_VWN"],
"PBE": ["GGA_X_PBE","GGA_C_PBE"],
"PBE0": ["GGA_X_PBE","GGA_C_PBE"],
"B3LYP": ["HYB_GGA_XC_B3LYP5"]
#need to be extended to add alpha_PBE0 :coefficient of Hartree-Fock exchange in the PBE0 xc functional
}
# Push the functional string into the backend
nomadNames = functionalMap.get(functional)
......@@ -103,7 +102,7 @@ class QboxInputParserContext(object):
###################################################################
# (3.4) onClose for geometry and force (section_system)
# todo: maybe we can move the force to onClose_section_single_configuration_calculation in the future.
# todo: maybe we can move the force to onClose_section_single_configuration_calculation in the future.
###################################################################
def onOpen_section_method(self, backend, gIndex, section):
# keep track of the latest method section
......@@ -148,7 +147,7 @@ class QboxInputParserContext(object):
if unit_cell:
backend.addArrayValues('simulation_cell', np.asarray(unit_cell))
backend.addArrayValues("configuration_periodic_dimensions", np.ones(3, dtype=bool))
......@@ -163,7 +162,7 @@ class QboxInputParserContext(object):
#############################################################
#################[2] MAIN PARSER STARTS HERE ###############
......@@ -178,7 +177,7 @@ def build_QboxInputFileSimpleMatcher():
which allows nice formating of nested SimpleMatchers in python.
Returns:
SimpleMatcher that parses input file of qbox.
SimpleMatcher that parses input file of qbox.
"""
......@@ -204,18 +203,18 @@ def build_QboxInputFileSimpleMatcher():
SM(r"\s*set\s+atoms_dyn\s+(?P<x_qbox_atoms_dyn>[A-Za-z0-9]+)\s*"),
SM(r"\s*set\s+cell_dyn\s+(?P<x_qbox_cell_dyn>[A-Za-z0-9]+)\s*"),
#--------set xc---------
#--------set xc---------
SM(name = "qboxXC",
startReStr = r"\s*set\s+xc\s+(?P<x_qbox_functional_name>[A-Za-z0-9]+)\s*",
sections = ["x_qbox_section_functionals"]
),
),
#-------set efield---------
SM (r"\s*set\s+e_field\s*(?P<x_qbox_efield_x>[-+0-9.]+)\s+(?P<x_qbox_efield_y>[-+0-9.]+)\s+(?P<x_qbox_efield_z>[-+0-9.]+)\s*",repeats = True)
#???both this version adn qbox_section_efield version could not give mather for efield, need to check.
])
......@@ -231,7 +230,7 @@ def build_QboxInputFileSimpleMatcher():
subMatchers = [
#=============================================================================
# read OUPUT file *.r, the method part comes from INPUT file *.i, so we
# read OUPUT file *.r, the method part comes from INPUT file *.i, so we
# do not need to parser INPUT file, the OUTPUT file contains all information
#=============================================================================
SM (name = 'NewRun',
......@@ -243,11 +242,11 @@ def build_QboxInputFileSimpleMatcher():
fixedStartValues={'program_name': 'qbox', 'program_basis_set_type': 'plane waves'},
sections = ['section_run'],
subMatchers = [
#-----------input method---------------------
calculationMethodSubMatcher
]) # CLOSING SM NewRun
]) # CLOSING SM NewRun
]) # END Root
......@@ -259,7 +258,7 @@ def get_cachingLevelForMetaName(metaInfoEnv):
metaInfoEnv: metadata which is an object of the class InfoKindEnv in nomadcore.local_meta_info.py.
Returns:
Dictionary with metaname as key and caching level as value.
Dictionary with metaname as key and caching level as value.
"""
# manually adjust caching of metadata
cachingLevelForMetaName = {
......
parser/parser-qbox/QboxParser.py → qboxparser/QboxParser.py
View file @ f914e0c0
from builtins import object
import setup_paths
import numpy as np
import nomadcore.ActivateLogging
from nomadcore.caching_backend import CachingLevel
from nomadcore.simple_parser import AncillaryParser, mainFunction
from nomadcore.simple_parser import SimpleMatcher as SM
from QboxCommon import get_metaInfo
import QboxXMLParser
from .QboxCommon import get_metaInfo
from . import QboxXMLParser
import logging, os, re, sys
import nomad_meta_info
############################################################
# This is the parser for the main file of qbox (for the output file *.r) .
############################################################
......@@ -17,7 +18,7 @@ import logging, os, re, sys
############################################################
###############[1] transfer PARSER CONTEXT #################
############################################################
logger = logging.getLogger("nomad.qboxParser")
logger = logging.getLogger("nomad.qboxParser")
class QboxParserContext(object):
......@@ -33,7 +34,7 @@ class QboxParserContext(object):
"""
self.secMethodIndex = None
self.secSystemDescriptionIndex = None
self.singleConfCalcs = []
......@@ -78,9 +79,9 @@ class QboxParserContext(object):
x_qbox_loading_xml_file_list = section['x_qbox_loading_xml_file']
xml_file = x_qbox_loading_xml_file_list[-1]
if xml_file is not None:
xml_file = x_qbox_loading_xml_file_list[-1]
if xml_file is not None:
logger.warning("This output showed this calculation need to load xml file, so we need this xml file ('%s') to read geometry information" % os.path.normpath(xml_file) )
fName = os.path.normpath(xml_file)
......@@ -94,7 +95,7 @@ class QboxParserContext(object):
try:
with open(fName) as fxml:
xmlParser.parseFile(fxml)
except IOError:
logger.warning("Could not find xml file in directory '%s'. " % os.path.dirname(os.path.abspath(self.fName)))
......@@ -102,20 +103,20 @@ class QboxParserContext(object):
def onClose_x_qbox_section_functionals(self, backend, gIndex, section):
functional_list = section["x_qbox_functional_name"]
if not functional_list: # default is LDA in qbox
if not functional_list: # default is LDA in qbox
functional = "LDA"
else :
functional = functional_list[-1] # use the xc appeared the last time
functional = functional_list[-1] # use the xc appeared the last time
if functional:
functionalMap = {
"LDA": ["LDA_X", "LDA_C_PZ"],
"VMN": ["LDA_X", "LDA_C_VWN"],
"PBE": ["GGA_X_PBE","GGA_C_PBE"],
"PBE0": ["GGA_X_PBE","GGA_C_PBE"],
"B3LYP": ["HYB_GGA_XC_B3LYP5"]
#need to be extended to add alpha_PBE0 :coefficient of Hartree-Fock exchange in the PBE0 xc functional
"LDA": ["LDA_X", "LDA_C_PZ"],
"VMN": ["LDA_X", "LDA_C_VWN"],
"PBE": ["GGA_X_PBE","GGA_C_PBE"],
"PBE0": ["GGA_X_PBE","GGA_C_PBE"],
"B3LYP": ["HYB_GGA_XC_B3LYP5"]
#need to be extended to add alpha_PBE0 :coefficient of Hartree-Fock exchange in the PBE0 xc functional
}
# Push the functional string into the backend
nomadNames = functionalMap.get(functional)
......@@ -132,7 +133,7 @@ class QboxParserContext(object):
# #################################################################
# # (3.1) onClose for OUTPUT SCF (section_scf_iteration)
# # (3.1) onClose for OUTPUT SCF (section_scf_iteration)
# #################################################################
# # Storing the total energy of each SCF iteration in an array
# def onClose_section_scf_iteration(self, backend, gIndex, section):
......@@ -140,15 +141,15 @@ class QboxParserContext(object):
# # get cached values for energy_total_scf_iteration
# ev = section['energy_total_scf_iteration']
# self.scfIterNr = len(ev)
#
#
# #self.energy_total_scf_iteration_list.append(ev)
# #backend.addArrayValues('energy_total_scf_iteration_list', np.asarray(ev))
# #backend.addValue('number_of_scf_iterations', self.scfIterNr)
# #-----???shanghui want to know why can not add them.
#################################################################
# (3.2) onClose for OUTPUT eigenvalues (section_eigenvalues)
# (3.2) onClose for OUTPUT eigenvalues (section_eigenvalues)
#################################################################
#def onClose_section_eigenvalues(self, backend, gIndex, section):
# """Trigger called when _section_eigenvalues is closed.
......@@ -158,22 +159,22 @@ class QboxParserContext(object):
# evs = []
# ev = section['qbox_eigenvalue_eigenvalue']
# if ev is not None:
# if ev is not None:
# occ = section['qbox_eigenvalue_occupation']
# occs.append(occ)
# occs.append(occ)
# evs.append(ev)
# self.eigenvalues_occupation = []
# self.eigenvalues_values = []
# #self.eigenvalues_kpoints = []
# #self.eigenvalues_kpoints = []
# self.eigenvalues_occupation.append(occs)
# self.eigenvalues_values.append(evs)
###################################################################
# (3.4) onClose for geometry and force (section_system)
# todo: maybe we can move the force to onClose_section_single_configuration_calculation in the future.
# todo: maybe we can move the force to onClose_section_single_configuration_calculation in the future.
###################################################################
def onOpen_section_method(self, backend, gIndex, section):
# keep track of the latest method section
......@@ -227,7 +228,7 @@ class QboxParserContext(object):
if unit_cell:
backend.addArrayValues('simulation_cell', np.asarray(unit_cell))
backend.addArrayValues("configuration_periodic_dimensions", np.ones(3, dtype=bool))
......@@ -251,10 +252,10 @@ class QboxParserContext(object):
backend.addArrayValues('stress_tensor', np.transpose(np.asarray(x_qbox_stress_tensor)))
#############################################################
#################[2] MAIN PARSER STARTS HERE ###############
......@@ -269,19 +270,19 @@ def build_QboxMainFileSimpleMatcher():
which allows nice formating of nested SimpleMatchers in python.
Returns:
SimpleMatcher that parses main file of qbox.
SimpleMatcher that parses main file of qbox.
"""
#####################################################################
# (1) submatcher for header
#note: we add x_qbox_section_functionals here because we want to add
# a default LDA here even 'set xc' is not shown in *.i file.
#note: we add x_qbox_section_functionals here because we want to add
# a default LDA here even 'set xc' is not shown in *.i file.
#####################################################################
headerSubMatcher = SM(name = 'ProgramHeader',
startReStr = r"\s*I qbox\s+(?P<program_version>[0-9.]+)",
sections = ["x_qbox_section_functionals"],
# sections = ["x_qbox_section_functionals"],
subMatchers = [
SM(r"\s*<nodename>\s+(?P<x_qbox_nodename>[a-zA-Z0-9.-]+)\s+</nodename>")
])
......@@ -308,11 +309,11 @@ def build_QboxMainFileSimpleMatcher():
subMatchers = [
#-----load from xml file-----
# when using 'load *.xml' in *.i file, qbox will read geometry information from xml file,
# here we call a QboxXMLParser to read the geometry information out.
# when using 'load *.xml' in *.i file, qbox will read geometry information from xml file,
# here we call a QboxXMLParser to read the geometry information out.
SM(name = "qboxXMLfile",
startReStr = r"\s*LoadCmd",
forwardMatch = True, #use this or not like qboxXC
forwardMatch = True, #use this or not like qboxXC
sections = ["x_qbox_section_xml_file"],
subMatchers = [
SM(r"\s*LoadCmd:\s*loading from\s+(?P<x_qbox_loading_xml_file>[A-Za-z0-9./-_]+)"),
......@@ -327,17 +328,17 @@ def build_QboxMainFileSimpleMatcher():
SM(r"\s*\[qbox\]\s+<cmd>\s*set\s+atoms_dyn\s+(?P<x_qbox_atoms_dyn>[A-Za-z0-9]+)\s*</cmd>"),
SM(r"\s*\[qbox\]\s+<cmd>\s*set\s+cell_dyn\s+(?P<x_qbox_cell_dyn>[A-Za-z0-9]+)\s*</cmd>"),
#--------set xc---------
#--------set xc---------
SM(name = "qboxXC",
startReStr = r"\s*\[qbox\]\s+<cmd>\s*set\s+xc\s+(?P<x_qbox_functional_name>[A-Za-z0-9]+)\s*</cmd>",
sections = ["x_qbox_section_functionals"]
),
),
#-------set efield---------
SM (r"\s*\[qbox\]\s*\[qbox\]\s*<cmd>\s*set\s+e_field\s*(?P<x_qbox_efield_x>[-+0-9.]+)\s+(?P<x_qbox_efield_y>[-+0-9.]+)\s+(?P<x_qbox_efield_z>[-+0-9.]+)\s*</cmd>",repeats = True)
#???both this version adn qbox_section_efield version could not give mather for efield, need to check.
])
####################################################################
# (3.1) submatcher for OUPUT SCF, this Dmol parser, we need to change to qbox later
####################################################################
......@@ -348,18 +349,18 @@ def build_QboxMainFileSimpleMatcher():
# SM(r"\s*Ef\s+(?P<energy_total_scf_iteration__hartree>[-+0-9.eEdD]+)\s+(?P<dmol3_binding_energy_scf_iteration__hartree>[-+0-9.eEdD]+)\s+(?P<dmol3_convergence_scf_iteration>[-+0-9.eEdD]+)\s+(?P<dmol3_time_scf_iteration>[0-9.eEdD]+)\s+(?P<dmol3_number_scf_iteration>[0-9]+)\s*",
# sections = ['section_scf_iteration'],
# repeats = True)
#
# ])
#
# ])
####################################################################
# (3.2) submatcher for OUPUT eigenvalues, this Dmol parser, we need to change to qbox later
####################################################################
# eigenvalueSubMatcher = SM(name = 'Eigenvalues',
# startReStr = r"\s*state\s+eigenvalue\s+occupation\s*",
# sections = ['section_eigenvalues'],
# subMatchers = [
####################################################################
# eigenvalueSubMatcher = SM(name = 'Eigenvalues',
# startReStr = r"\s*state\s+eigenvalue\s+occupation\s*",
# sections = ['section_eigenvalues'],
# subMatchers = [
# SM(r"\s*[0-9]+\s+[+-]\s+[0-9]+\s+[A-Za-z]+\s+[-+0-9.eEdD]+\s+(?P<dmol3_eigenvalue_e igenvalue__eV>[-+0-9.eEdD]+)\s+(?P<dmol3_eigenvalue_occupation>[0-9.eEdD]+)", repeats = True)
# ])
# ])
#
####################################################################
......@@ -368,9 +369,9 @@ def build_QboxMainFileSimpleMatcher():
totalenergySubMatcher = SM(name = 'Totalenergy',
startReStr = r"\s*<ekin>",
subMatchers = [
SM(r"\s*<etotal>\s+(?P<energy_total__hartree>[-+0-9.eEdD]+)\s+</etotal>",repeats = True )
])
SM(r"\s*<etotal>\s+(?P<energy_total__hartree>[-+0-9.eEdD]+)\s+</etotal>",repeats = True )
])
#####################################################################
# (3.4) submatcher for OUTPUT relaxation_geometry(section_system)
......@@ -439,7 +440,7 @@ def build_QboxMainFileSimpleMatcher():
subMatchers = [
#=============================================================================
# read OUPUT file *.r, the method part comes from INPUT file *.i, so we
# read OUPUT file *.r, the method part comes from INPUT file *.i, so we
# do not need to parser INPUT file, the OUTPUT file contains all information
#=============================================================================
SM (name = 'NewRun',
......@@ -451,15 +452,15 @@ def build_QboxMainFileSimpleMatcher():
fixedStartValues={'program_name': 'qbox', 'program_basis_set_type': 'plane waves'},
sections = ['section_run'],
subMatchers = [
#-----------(1)output: header---------------------
#-----------(1)output: header---------------------
headerSubMatcher,
#-----------(2)output: method---------------------
calculationMethodSubMatcher,
#-----------(2.2) efield----------------------
# efieldSubMatcher,
#-----------(3)output: single configuration-------
#-----------(3)output: single configuration-------
SM(name = "single configuration matcher",
startReStr = r"\s*<iteration count*",
#endReStr = r"\s*</iteration>",
......@@ -479,13 +480,13 @@ def build_QboxMainFileSimpleMatcher():
]
),
#-----------(4)output: properties-------
#-----------(4)output: properties-------
#-----------(4.1) MLWF----------------------
MLWFSubMatcher,
#-----------(4.3) dipole----------------------
dipoleSubMatcher
]) # CLOSING SM NewRun
]) # CLOSING SM NewRun
]) # END Root
......@@ -497,7 +498,7 @@ def get_cachingLevelForMetaName(metaInfoEnv):
metaInfoEnv: metadata which is an object of the class InfoKindEnv in nomadcore.local_meta_info.py.
Returns:
Dictionary with metaname as key and caching level as value.
Dictionary with metaname as key and caching level as value.
"""
# manually adjust caching of metadata
cachingLevelForMetaName = {
......@@ -513,29 +514,45 @@ def get_cachingLevelForMetaName(metaInfoEnv):
return cachingLevelForMetaName
# get main file description
QboxMainFileSimpleMatcher = build_QboxMainFileSimpleMatcher()
# loading metadata from nomad-meta-info/meta_info/nomad_meta_info/qbox.nomadmetainfo.json
metaInfoPath = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(nomad_meta_info.__file__)), "qbox.nomadmetainfo.json"))
metaInfoEnv = get_metaInfo(metaInfoPath)
# set parser info
parserInfo = {'name':'qbox-parser', 'version': '1.0'}
# get caching level for metadata
cachingLevelForMetaName = get_cachingLevelForMetaName(metaInfoEnv)
def main():
"""Main function.
Set up everything for the parsing of the qbox main file and run the parsing.
"""
# get main file description
QboxMainFileSimpleMatcher = build_QboxMainFileSimpleMatcher()
# loading metadata from nomad-meta-info/meta_info/nomad_meta_info/qbox.nomadmetainfo.json
metaInfoPath = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(__file__)), "../../../../nomad-meta-info/meta_info/nomad_meta_info/qbox.nomadmetainfo.json"))
metaInfoEnv = get_metaInfo(metaInfoPath)
# set parser info
parserInfo = {'name':'qbox-parser', 'version': '1.0'}
# get caching level for metadata
cachingLevelForMetaName = get_cachingLevelForMetaName(metaInfoEnv)
# start parsing
mainFunction(mainFileDescription = QboxMainFileSimpleMatcher,
metaInfoEnv = metaInfoEnv,
parserInfo = parserInfo,
cachingLevelForMetaName = cachingLevelForMetaName,
superContext = QboxParserContext())
class QboxParser():
""" 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.debug('qbox parser started')
logging.getLogger('nomadcore').setLevel(logging.WARNING)
backend = self.backend_factory(metaInfoEnv)
with patch.object(sys, 'argv', ['<exe>', '--uri', 'nmd://uri', mainfile]):
mainFunction(
mainFileDescription=QboxMainFileSimpleMatcher,
metaInfoEnv=metaInfoEnv,
parserInfo=parserInfo,
cachingLevelForMetaName=cachingLevelForMetaName,
superContext=QboxParserContext(),
superBackend=backend)
return backend
if __name__ == "__main__":
main()
mainFunction(
mainFileDescription = QboxMainFileSimpleMatcher,
metaInfoEnv = metaInfoEnv,
parserInfo = parserInfo,
cachingLevelForMetaName = cachingLevelForMetaName,
superContext = QboxParserContext())
parser/parser-qbox/QboxXMLParser.py → qboxparser/QboxXMLParser.py
View file @ f914e0c0
from builtins import object
import setup_paths
import numpy as np
import nomadcore.ActivateLogging
from nomadcore.caching_backend import CachingLevel
from nomadcore.simple_parser import mainFunction
from nomadcore.simple_parser import SimpleMatcher as SM
from QboxCommon import get_metaInfo
from .QboxCommon import get_metaInfo
import logging, os, re, sys
#################################################################################
# This is the parser for the *.xml file of qbox to read the geometry information.
# Only needed when 'load *.xml' is used in the *.r file.
# Only needed when 'load *.xml' is used in the *.r file.
###################################################################################
logger = logging.getLogger("nomad.QboxXMLParser")
......
qboxparser/__init__.py 0 → 100644
View file @ f914e0c0
from qboxparser.QboxParser import QboxParser
\ No newline at end of file
setup.py 0 → 100644
View file @ f914e0c0
# Copyright 2016-2018 Fawzi Mohamed, Lauri Himanen, Danio Brambila, Ankit Kariryaa, Henning Glawe
#
# 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.
from setuptools import setup, find_packages
def main():
setup(
name='qboxparser',
version='0.1',
description='NOMAD parser implementation for qbox.',
author='Fawzi Mohamed, Honghui Shang',
license='APACHE 2.0',
packages=find_packages(),
install_requires=[
'nomadcore'
],
)
if __name__ == '__main__':
main()
src/main/scala/eu/nomad_lab/parsers/QboxParser.scala deleted 100644 → 0
View file @ ffebcc60
/*
Copyright 2016-2017 The NOMAD Developers Group
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.
*/
package eu.nomad_lab.parsers
import eu.{ nomad_lab => lab }
import eu.nomad_lab.DefaultPythonInterpreter
import org.{ json4s => jn }
import scala.collection.breakOut
object QboxParser extends SimpleExternalParserGenerator(
name = "QboxParser",
parserInfo = jn.JObject(
("name" -> jn.JString("QboxParser")) ::
("parserId" -> jn.JString("QboxParser" + lab.QboxVersionInfo.version)) ::
("versionInfo" -> jn.JObject(
("nomadCoreVersion" -> jn.JObject(lab.NomadCoreVersionInfo.toMap.map {
case (k, v) => k -> jn.JString(v.toString)
}(breakOut): List[(String, jn.JString)])) ::
(lab.QboxVersionInfo.toMap.map {
case (key, value) =>
(key -> jn.JString(value.toString))
}(breakOut): List[(String, jn.JString)])
)) :: Nil
),
mainFileTypes = Seq("application/xml"),
mainFileRe = """<\?xml version="1.0" encoding="UTF-8"\?>\s*
\s*<fpmd:simulation xmlns:fpmd="http://www.quantum-simulation.org/ns/fpmd/fpmd-1.0">\s*
\s*
\s*=+\s*
\s*I\s*qbox\s*(?<version>[-_.0-9A-Za-z]+).*I
(?:\s*I.+I
)*\s*I\s+http://qboxcode.org\s*I
(?:\s*I.+I
)*\s*=+\s*
""".r,
cmd = Seq(DefaultPythonInterpreter.pythonExe(), "${envDir}/parsers/qbox/parser/parser-qbox/QboxParser.py",
"--uri", "${mainFileUri}", "${mainFilePath}"),
resList = Seq(
"parser-qbox/QboxParser.py",
"parser-qbox/QboxCommon.py",
"parser-qbox/QboxXMLParser.py",
"parser-qbox/setup_paths.py",
"nomad_meta_info/public.nomadmetainfo.json",
"nomad_meta_info/common.nomadmetainfo.json",
"nomad_meta_info/meta_types.nomadmetainfo.json",
"nomad_meta_info/qbox.nomadmetainfo.json"
) ++ DefaultPythonInterpreter.commonFiles(),
dirMap = Map(
"parser-qbox" -> "parsers/qbox/parser/parser-qbox",
"nomad_meta_info" -> "nomad-meta-info/meta_info/nomad_meta_info"
) ++ DefaultPythonInterpreter.commonDirMapping()
)
src/test/scala/eu/nomad_lab/parsers/QboxParserSpec.scala deleted 100644 → 0
View file @ ffebcc60
/*
Copyright 2016-2017 The NOMAD Developers Group
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.
*/
package eu.nomad_lab.parsers
import org.specs2.mutable.Specification
object QboxParserSpec extends Specification {
"QboxParserTest" >> {
"test with json-events" >> {
ParserRun.parse(QboxParser, "parsers/qbox/test/examples/01_h2ogs.r", "json-events") must_== ParseResult.ParseSuccess
}
"test with json" >> {
ParserRun.parse(QboxParser, "parsers/qbox/test/examples/01_h2ogs.r", "json") must_== ParseResult.ParseSuccess
}
}
}