From ae97cd460788eaa1ff52b5e55f5fc812c63c42f0 Mon Sep 17 00:00:00 2001
From: speckhard <dts@stanford.edu>
Date: Mon, 25 Feb 2019 15:46:12 +0100
Subject: [PATCH] Ready for Nomad-Faird
---
.gitignore | 1 +
.../SimpleDL_POLYParser.py | 91 +++++++++-----
dlpolyparser/__init__.py | 15 +++
.../dlPolyParser.py | 114 ++++++++++++------
.../libDlPolyParser.py | 0
.../libMomo.py | 0
.../setup_paths.py | 0
setup.py | 33 +++++
.../eu/nomad_lab/parsers/DlPolyParser.scala | 57 ---------
.../nomad_lab/parsers/DlPolyParserSpec.scala | 30 -----
10 files changed, 184 insertions(+), 157 deletions(-)
rename {parser/parser-dl_poly => dlpolyparser}/SimpleDL_POLYParser.py (73%)
create mode 100644 dlpolyparser/__init__.py
rename {parser/parser-dl_poly => dlpolyparser}/dlPolyParser.py (83%)
rename {parser/parser-dl_poly => dlpolyparser}/libDlPolyParser.py (100%)
rename {parser/parser-dl_poly => dlpolyparser}/libMomo.py (100%)
rename {parser/parser-dl_poly => dlpolyparser}/setup_paths.py (100%)
create mode 100644 setup.py
delete mode 100644 src/main/scala/eu/nomad_lab/parsers/DlPolyParser.scala
delete mode 100644 src/test/scala/eu/nomad_lab/parsers/DlPolyParserSpec.scala
diff --git a/.gitignore b/.gitignore
index cae25f9..e3efb3a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -9,6 +9,7 @@ syntax: glob
*.pyc
*.bk
*.swp
+*.egg-info
.DS_Store
# eclipse conf file
diff --git a/parser/parser-dl_poly/SimpleDL_POLYParser.py b/dlpolyparser/SimpleDL_POLYParser.py
similarity index 73%
rename from parser/parser-dl_poly/SimpleDL_POLYParser.py
rename to dlpolyparser/SimpleDL_POLYParser.py
index 019bbfb..a4149ba 100644
--- a/parser/parser-dl_poly/SimpleDL_POLYParser.py
+++ b/dlpolyparser/SimpleDL_POLYParser.py
@@ -1,11 +1,11 @@
# Copyright 2016-2018 Carl Poelking, Fawzi Mohamed, Ankit Kariryaa
-#
+#
# 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.
@@ -15,7 +15,6 @@
from __future__ import print_function
from builtins import range
from builtins import object
-import setup_paths
import numpy as np
import math
from nomadcore.simple_parser import mainFunction
@@ -38,7 +37,7 @@ class DL_POLYParserContext(object):
def onClose_section_system(self, backend, gIndex, section):
print("<onClose_section_system>")
return
- def onClose_dl_poly_section_md_molecule_type(self, backend, gIndex, section):
+ def onClose_x_dl_poly_section_md_molecule_type(self, backend, gIndex, section):
print("<onClose_molecule_type>")
return
@@ -55,7 +54,7 @@ mainFileDescription = SM(name = 'root',
weak = True,
startReStr = "",
subMatchers = [
-
+
SM(name = 'newRun',
startReStr = r" \*\* DL_POLY \*\* authors: i.t.todorov & w.smith \** P \**",
repeats = False,
@@ -67,26 +66,26 @@ mainFileDescription = SM(name = 'root',
SM(name = 'progHeader',
startReStr = r" \*\* DL_POLY \*\* authors: i.t.todorov & w.smith \** P \**",
subMatchers = [
- SM(r"\s*\*\*\s*\*\* version: (?P<program_version>[0-9a-zA-Z_.]*) / \s* (?P<dl_poly_program_version_date>[\w]*\s*[\w]*)\s*\** O \**"),
+ SM(r"\s*\*\*\s*\*\* version: (?P<program_version>[0-9a-zA-Z_.]*) / \s* (?P<x_dl_poly_program_version_date>[\w]*\s*[\w]*)\s*\** O \**"),
SM(r"\s*\** when publishing research data obtained using (?P<program_name>[0-9a-zA-Z_.]*) \**"),
- SM(r"\s*\**\s*(?P<dl_poly_system_description>[0-9a-zA-Z_()]*)\s*\**")
+ SM(r"\s*\**\s*(?P<x_dl_poly_system_description>[0-9a-zA-Z_()]*)\s*\**")
]),
SM(name = 'mdParams',
startReStr = r"\s*SIMULATION CONTROL PARAMETERS\s*",
required = True,
sections = ['section_method'],
subMatchers = [
- SM(r"\s*simulation temperature \(K\)\s*(?P<dl_poly_thermostat_temperature>[-+0-9.eEdD]*)\s*"),
- SM(r"\s*equilibration period \(steps\)\s*(?P<dl_poly_step_number_equilibration>[0-9]*)\s*"),
- SM(r"\s*selected number of timesteps\s*(?P<dl_poly_step_number>[0-9]*)\s*")
+ SM(r"\s*simulation temperature \(K\)\s*(?P<x_dl_poly_thermostat_temperature>[-+0-9.eEdD]*)\s*"),
+ SM(r"\s*equilibration period \(steps\)\s*(?P<x_dl_poly_step_number_equilibration>[0-9]*)\s*"),
+ SM(r"\s*selected number of timesteps\s*(?P<x_dl_poly_step_number>[0-9]*)\s*")
]),
-
+
# Open system
# ... open topology
# ... ... store <numberofmoleculetypes>
# ... ... open molecule type id1
# ... ... open molecule type ...
-
+
SM(name = 'mdSystem',
startReStr = r"\s*SYSTEM SPECIFICATION\s*",
required = True,
@@ -96,18 +95,18 @@ mainFileDescription = SM(name = 'root',
startReStr = r"\s*number of molecular types\s*[0-9]*\s*",
required = True,
forwardMatch = True,
- sections = ['dl_poly_section_md_topology'],
+ sections = ['x_dl_poly_section_md_topology'],
subMatchers = [
- SM(r"\s*number of molecular types\s*(?P<dl_poly_md_molecular_types>[0-9]*)"),
+ SM(r"\s*number of molecular types\s*(?P<x_dl_poly_md_molecular_types>[0-9]*)"),
SM(name = 'mdTopologyMolecule',
startReStr = r"\s*molecular species type\s*[0-9]*\s*",
repeats = True,
required = True,
forwardMatch = True,
- sections = ['dl_poly_section_md_molecule_type'],
+ sections = ['x_dl_poly_section_md_molecule_type'],
subMatchers = [
- SM(r"\s*molecular species type\s*(?P<dl_poly_md_molecule_type_id>[0-9]*)\s*"),
- SM(r"\s*name of species:\s*(?P<dl_poly_md_molecule_type_name>[\w]* [\w]*)\s*")
+ SM(r"\s*molecular species type\s*(?P<x_dl_poly_md_molecule_type_id>[0-9]*)\s*"),
+ SM(r"\s*name of species:\s*(?P<x_dl_poly_md_molecule_type_name>[\w]* [\w]*)\s*")
])
])
#SM(r"\s*number of molecular types\s*(?P<dl_poly_molecular_types_number>[0-9]*)\s*"),
@@ -118,7 +117,7 @@ mainFileDescription = SM(name = 'root',
#sections = ['dl_poly_section_molecule_types'],
#subMatchers = [\
#])
- ])
+ ])
])
])
@@ -182,11 +181,11 @@ mainFileDescription = SM(name = 'root',
]), # CLOSING section_eigenvalues
]), # CLOSING section_eigenvalues_group
-
+
]), # CLOSING section_single_configuration_calculation
-
+
]), # CLOSING section_system
-
+
]), # CLOSING SM newRun
@@ -196,22 +195,50 @@ mainFileDescription = SM(name = 'root',
# THIS PARSER
parserInfo = {'name':'dl_poly-parser', 'version': '0.0'}
-# LOAD METADATA
-metaInfoPath = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(__file__)),"../../../../nomad-meta-info/meta_info/nomad_meta_info/dl_poly.nomadmetainfo.json"))
-metaInfoEnv, warnings = loadJsonFile(filePath = metaInfoPath, dependencyLoader = None, extraArgsHandling = InfoKindEl.ADD_EXTRA_ARGS, uri = None)
+# # LOAD METADATA
+# metaInfoPath = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(__file__)),"../../../../nomad-meta-info/meta_info/nomad_meta_info/dl_poly.nomadmetainfo.json"))
+# metaInfoEnv, warnings = loadJsonFile(filePath = metaInfoPath, dependencyLoader = None, extraArgsHandling = InfoKindEl.ADD_EXTRA_ARGS, uri = None)
# CUSTOMIZE CACHING
cachingLevelForMetaName = {}
+import nomad_meta_info
+metaInfoPath = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(nomad_meta_info.__file__)), "dl_poly.nomadmetainfo.json"))
+metaInfoEnv, warnings = loadJsonFile(filePath = metaInfoPath, dependencyLoader = None, extraArgsHandling = InfoKindEl.ADD_EXTRA_ARGS, uri = None)
+
+class DlPolyParser():
+ """ 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.info('dl-poly 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=mainFileDescription,
+ metaInfoEnv=metaInfoEnv,
+ parserInfo = parserInfo,
+ cachingLevelForMetaName = cachingLevelForMetaName,
+ superContext=DL_POLYParserContext(),
+ superBackend=backend,
+ onClose = {},
+ defaultSectionCachingLevel = True)
+
+ return backend
+
+
if __name__ == "__main__":
- mainFunction(mainFileDescription,
- metaInfoEnv,
- parserInfo,
- superContext = DL_POLYParserContext(),
- cachingLevelForMetaName = cachingLevelForMetaName,
+ mainFunction(mainFileDescription,
+ metaInfoEnv,
+ parserInfo,
+ superContext = DL_POLYParserContext(),
+ cachingLevelForMetaName = cachingLevelForMetaName,
onClose = {},
defaultSectionCachingLevel = False)
-
-
+
+
diff --git a/dlpolyparser/__init__.py b/dlpolyparser/__init__.py
new file mode 100644
index 0000000..562628c
--- /dev/null
+++ b/dlpolyparser/__init__.py
@@ -0,0 +1,15 @@
+# Copyright 2015-2018 Lauri Himanen, Fawzi Mohamed, Ankit Kariryaa
+#
+# 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 dlpolyparser.dlPolyParser import DlPolyParserWrapper
diff --git a/parser/parser-dl_poly/dlPolyParser.py b/dlpolyparser/dlPolyParser.py
similarity index 83%
rename from parser/parser-dl_poly/dlPolyParser.py
rename to dlpolyparser/dlPolyParser.py
index 4c54d69..4b8fa3a 100644
--- a/parser/parser-dl_poly/dlPolyParser.py
+++ b/dlpolyparser/dlPolyParser.py
@@ -1,11 +1,11 @@
# Copyright 2016-2018 Carl Poelking, Fawzi Mohamed, Ankit Kariryaa
-#
+#
# 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.
@@ -17,30 +17,29 @@ import os
import sys
import re
import json
-#import logging
-import setup_paths
+import logging
import numpy as np
from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
from nomadcore.parser_backend import JsonParseEventsWriterBackend
from contextlib import contextmanager
-from libDlPolyParser import *
+from dlpolyparser.libDlPolyParser import *
try:
- from libMomo import osio, endl, flush
+ from dlpolyparser.libMomo import osio, endl, flush
osio.ConnectToFile('parser.osio.log')
green = osio.mg
except:
osio = endl = flush = None
green = None
-
-parser_info = {
- "name": "parser-dl-poly",
- "version": "0.0",
- "json": "../../../../nomad-meta-info/meta_info/nomad_meta_info/dl_poly.nomadmetainfo.json"
-}
+
+# parser_info = {
+# "name": "parser-dl-poly",
+# "version": "0.0",
+# "json": "../../../../nomad-meta-info/meta_info/nomad_meta_info/dl_poly.nomadmetainfo.json"
+# }
# LOGGING
def log(msg, highlight=None, enter=endl):
@@ -54,7 +53,7 @@ def log(msg, highlight=None, enter=endl):
def open_section(p, name):
gid = p.openSection(name)
yield gid
- p.closeSection(name, gid)
+ p.closeSection(name, gid)
def push(jbe, terminal, key1, fct=lambda x: x.As(), key2=None, conv=None):
if key2 == None: key2 = key1
@@ -82,27 +81,64 @@ def push_value(jbe, value, key, conv=None):
return value
def push_array_values(jbe, value, key, conv=None):
- if conv:
+ if conv:
jbe.addArrayValues(key, value*conv)
else:
jbe.addArrayValues(key, value)
return value
-def parse(output_file_name):
- jbe = JsonParseEventsWriterBackend(meta_info_env)
+
+# class DlPolyParser():
+# """ A proper class envolop for running this parser from within python. """
+# def __init__(self, backend, **kwargs):
+# self.backend_factory = backend
+
+# from unittest.mock import patch
+# logging.info('dl-poly parser started')
+# logging.getLogger('nomadcore').setLevel(logging.WARNING)
+# backend = self.backend_factory(metaInfoEnv)
+# # Rename parser
+# def parse(self, mainfile):
+
+
+logger = logging.getLogger("nomad.DLPolyParser")
+
+
+class DlPolyParserWrapper():
+ """ A proper class envolop for running this parser using Noamd-FAIRD infra. """
+ def __init__(self, backend, **kwargs):
+ self.backend_factory = backend
+
+ def parse(self, mainfile):
+ import nomad_meta_info
+ metaInfoPath = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(nomad_meta_info.__file__)), "dl_poly.nomadmetainfo.json"))
+ metaInfoEnv, warnings = loadJsonFile(filePath = metaInfoPath, dependencyLoader = None, extraArgsHandling = InfoKindEl.ADD_EXTRA_ARGS, uri = None)
+ from unittest.mock import patch
+ logging.info('dl-poly parser started')
+ logging.getLogger('nomadcore').setLevel(logging.WARNING)
+ backend = self.backend_factory(metaInfoEnv)
+ # Call the old parser without a class.
+ parserInfo = {'name': 'dl_poly-parser', 'version': '0.0'}
+ backend = parse_without_class(mainfile, backend, parserInfo)
+ return backend
+
+
+def parse_without_class(output_file_name, backend, parser_info):
+ """ Parse method to parse mainfile and write output to backend."""
+ jbe = backend
jbe.startedParsingSession(output_file_name, parser_info)
-
+
base_dir = os.path.dirname(os.path.abspath(output_file_name))
# PARSE CONTROLS ...
ctrl_file_name = os.path.join(base_dir, 'CONTROL')
terminal_ctrls = DlPolyControls(osio)
- terminal_ctrls.ParseControls(ctrl_file_name)
+ terminal_ctrls.ParseControls(ctrl_file_name)
# PARSE OUTPUT / TOPOLOGY ...
output_file_name = os.path.join(base_dir, 'OUTPUT')
terminal = DlPolyParser(osio)
- terminal.ParseOutput(output_file_name)
+ terminal.ParseOutput(output_file_name)
# PARSE CONFIG ...
cfg_file_name = os.path.join(base_dir, 'CONFIG')
@@ -126,7 +162,7 @@ def parse(output_file_name):
out = terminal
top = terminal.topology
cfg = terminal_cfg
- trj = terminal_trj
+ trj = terminal_trj
terminals = [ctr, out, top, cfg, trj]
# ESTABLISH (ENERGY) UNITS
@@ -143,13 +179,13 @@ def parse(output_file_name):
ofs.write('[%s] %s = %s\n' % (t.logtag, key, t[key].As(str)))
ofs.write('\n')
ofs.close()
-
+
# PUSH TO BACKEND
with open_section(jbe, 'section_run') as gid_run:
push(jbe, out, 'program_name')
push(jbe, out, 'program_version')
#push(jbe, out, 'program_info', key2='program_version_date')
-
+
# TOPOLOGY SECTION
with open_section(jbe, 'section_topology') as gid_top:
# Cross-referencing is done on-the-fly (as gid's become available)
@@ -157,7 +193,7 @@ def parse(output_file_name):
# b) <atom_in_molecule_to_atom_type_ref> : shape=(number_of_atoms_in_molecule, [<gid>])
# c) <atom_to_molecule> : shape=(number_of_topology_atoms, [<molidx>, <atomidx>])
push(jbe, top, 'number_of_topology_molecules', lambda s: s.As(int))
- push(jbe, top, 'number_of_topology_atoms', lambda s: s.As(int))
+ push(jbe, top, 'number_of_topology_atoms', lambda s: s.As(int))
# Atom types
mol_type_atom_type_id_to_atom_type_gid = {}
for mol in top.molecules:
@@ -170,7 +206,7 @@ def parse(output_file_name):
mol_type_atom_type_id_to_atom_type_gid[mol_name][atom_id] = gid_atom
push(jbe, atom, 'atom_type_name', lambda s: s.As(), 'atom_name')
push(jbe, atom, 'atom_type_mass', lambda s: s.As(float), 'atom_mass', conv=UNITCONV_DLPOLY_TO_SI['mass'])
- push(jbe, atom, 'atom_type_charge', lambda s: s.As(float), 'atom_charge', conv=UNITCONV_DLPOLY_TO_SI['charge'])
+ push(jbe, atom, 'atom_type_charge', lambda s: s.As(float), 'atom_charge', conv=UNITCONV_DLPOLY_TO_SI['charge'])
# Molecule types
molecule_type_name_to_type_gid = {}
for mol in top.molecules:
@@ -181,12 +217,12 @@ def parse(output_file_name):
for atom in mol.atoms:
atom_id = atom['atom_id'].As(int)
atom_gid_list.append(atom_type_id_to_atom_type_gid[atom_id])
- # Add molecule
+ # Add molecule
with open_section(jbe, 'section_molecule_type') as gid_mol:
molecule_type_name_to_type_gid[mol['molecule_type_name'].As()] = gid_mol
push(jbe, mol, 'molecule_type_name')
push(jbe, mol, 'number_of_atoms_in_molecule', lambda s: s.As(int))
-
+
push_array(jbe, mol, 'atom_in_molecule_name')
push_array(jbe, mol, 'atom_in_molecule_charge', conv=UNITCONV_DLPOLY_TO_SI['charge'])
push_array_values(jbe, np.asarray(atom_gid_list), 'atom_in_molecule_to_atom_type_ref')
@@ -219,7 +255,7 @@ def parse(output_file_name):
with open_section(jbe, 'section_sampling_method') as gid_sec_sampling_method:
sec_sampling_method_ref = gid_sec_sampling_method
# Ensemble
- ensemble = push(jbe, out, 'ensemble_type', lambda s: s.As().split()[0].upper())
+ ensemble = push(jbe, out, 'ensemble_type', lambda s: s.As().split()[0].upper())
# Method
push(jbe, out, 'sampling_method')
push(jbe, out, 'x_dl_poly_integrator_type')
@@ -230,7 +266,7 @@ def parse(output_file_name):
push(jbe, out, 'x_dl_poly_thermostat_target_temperature', lambda s: s.As(float), conv=UNITCONV_DLPOLY_TO_SI['temperature'])
push(jbe, out, 'x_dl_poly_thermostat_tau', lambda s: s.As(float))
pass
- if 'P' in ensemble:
+ if 'P' in ensemble:
push(jbe, out, 'x_dl_poly_barostat_target_pressure', lambda s: s.As(float), conv=UNITCONV_DLPOLY_TO_SI['pressure_katm'])
push(jbe, out, 'x_dl_poly_barostat_tau', lambda s: s.As(float), conv=UNITCONV_DLPOLY_TO_SI['time'])
pass
@@ -241,19 +277,21 @@ def parse(output_file_name):
with open_section(jbe, 'section_method') as gid_sec_method:
sec_method_ref = gid_sec_method
push_value(jbe, 'force_field', 'calculation_method')
-
+
# TODO Store state variables in frames/system description (temperature, pressure)
# TODO Store interactions
-
+
# SYSTEM DESCRIPTION
refs_system_description = []
all_frames = [cfg] + trj.frames # <- Initial config + trajectory
for frame in all_frames:
with open_section(jbe, 'section_system') as gid:
- refs_system_description.append(gid)
+ refs_system_description.append(gid)
# Configuration core
- atom_labels = np.array([ atom['atom_name'].As() for atom in frame.atoms ])
+ atom_labels = np.array(
+ [ atom['atom_name'].As().replace('+','').replace('-','') for atom in frame.atoms ])
push_array_values(jbe, atom_labels, 'atom_labels')
+ # push_array_values(jbe, atom_species, 'atom_atom_numbers')
push_array_values(jbe, frame.position_matrix, 'atom_positions', conv=UNITCONV_DLPOLY_TO_SI['length'])
push_array_values(jbe, frame.box_matrix, 'simulation_cell', conv=UNITCONV_DLPOLY_TO_SI['length'])
push_array_values(jbe, frame.pbc_booleans, 'configuration_periodic_dimensions')
@@ -263,7 +301,7 @@ def parse(output_file_name):
# TODO Wouldn't it be simpler if forces were added here?
pass
pass
-
+
# SINGLE CONFIGURATIONS
refs_single_configuration = []
i_frame = -1
@@ -282,8 +320,8 @@ def parse(output_file_name):
push_array_values(jbe, frame.force_matrix, 'atom_forces', conv=UNITCONV_DLPOLY_TO_SI['mass']*UNITCONV_DLPOLY_TO_SI['length']/UNITCONV_DLPOLY_TO_SI['time']**2)
# Method reference
push_value(jbe, sec_method_ref, 'single_configuration_to_calculation_method_ref')
- pass
-
+ pass
+
# FRAME-SEQUENCE SECTION
with open_section(jbe, 'section_frame_sequence'):
push_value(jbe, len(all_frames), 'number_of_frames_in_sequence')
@@ -296,7 +334,7 @@ def parse(output_file_name):
pass
jbe.finishedParsingSession("ParseSuccess", None)
- return
+ return jbe
if __name__ == '__main__':
@@ -316,5 +354,5 @@ if __name__ == '__main__':
output_file_name = sys.argv[1]
parse(output_file_name)
-
+
diff --git a/parser/parser-dl_poly/libDlPolyParser.py b/dlpolyparser/libDlPolyParser.py
similarity index 100%
rename from parser/parser-dl_poly/libDlPolyParser.py
rename to dlpolyparser/libDlPolyParser.py
diff --git a/parser/parser-dl_poly/libMomo.py b/dlpolyparser/libMomo.py
similarity index 100%
rename from parser/parser-dl_poly/libMomo.py
rename to dlpolyparser/libMomo.py
diff --git a/parser/parser-dl_poly/setup_paths.py b/dlpolyparser/setup_paths.py
similarity index 100%
rename from parser/parser-dl_poly/setup_paths.py
rename to dlpolyparser/setup_paths.py
diff --git a/setup.py b/setup.py
new file mode 100644
index 0000000..be54ef3
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,33 @@
+# Copyright 2015-2018 Lorenzo Pardini
+#
+# 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='dlpolyparser',
+ version='0.1',
+ description='NOMAD parser implementation for DL-Poly.',
+ license='APACHE 2.0',
+ package_dir={'': './'},
+ packages=find_packages(),
+ install_requires=[
+ 'nomadcore'
+ ],
+ )
+
+
+if __name__ == '__main__':
+ main()
diff --git a/src/main/scala/eu/nomad_lab/parsers/DlPolyParser.scala b/src/main/scala/eu/nomad_lab/parsers/DlPolyParser.scala
deleted file mode 100644
index a052383..0000000
--- a/src/main/scala/eu/nomad_lab/parsers/DlPolyParser.scala
+++ /dev/null
@@ -1,57 +0,0 @@
-/*
- * Copyright 2016-2018 Carl Poelking, Fawzi Mohamed, Ankit Kariryaa
- *
- * 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 DlPolyParser extends SimpleExternalParserGenerator(
- name = "DlPolyParser",
- parserInfo = jn.JObject(
- ("name" -> jn.JString("DlPolyParser")) ::
- ("parserId" -> jn.JString("DlPolyParser" + lab.DlPolyVersionInfo.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.DlPolyVersionInfo.toMap.map {
- case (key, value) =>
- (key -> jn.JString(value.toString))
- }(breakOut): List[(String, jn.JString)])
- )) :: Nil
- ),
- mainFileTypes = Seq("text/.*"),
- mainFileRe = """ DL_POLY """.r,
- cmd = Seq(DefaultPythonInterpreter.pythonExe(), "${envDir}/parsers/dl_poly/parser/parser-dl_poly/dlPolyParser.py",
- "${mainFilePath}"),
- resList = Seq(
- "parser-dl_poly/dlPolyParser.py",
- "parser-dl_poly/libDlPolyParser.py",
- "parser-dl_poly/libMomo.py",
- "parser-dl_poly/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/dl_poly.nomadmetainfo.json"
- ) ++ DefaultPythonInterpreter.commonFiles(),
- dirMap = Map(
- "parser-dl_poly" -> "parsers/dl_poly/parser/parser-dl_poly",
- "nomad_meta_info" -> "nomad-meta-info/meta_info/nomad_meta_info"
- ) ++ DefaultPythonInterpreter.commonDirMapping()
-)
diff --git a/src/test/scala/eu/nomad_lab/parsers/DlPolyParserSpec.scala b/src/test/scala/eu/nomad_lab/parsers/DlPolyParserSpec.scala
deleted file mode 100644
index 6759e57..0000000
--- a/src/test/scala/eu/nomad_lab/parsers/DlPolyParserSpec.scala
+++ /dev/null
@@ -1,30 +0,0 @@
-/*
- * Copyright 2016-2018 Carl Poelking, Fawzi Mohamed, Ankit Kariryaa
- *
- * 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 DlPolyParserSpec extends Specification {
- "DlPolyParserTest" >> {
- "test with json-events" >> {
- ParserRun.parse(DlPolyParser, "parsers/dl-poly/test/examples/dl-poly-test1/OUTPUT", "json-events") must_== ParseResult.ParseSuccess
- }
- "test with json" >> {
- ParserRun.parse(DlPolyParser, "parsers/dl-poly/test/examples/dl-poly-test1/OUTPUT", "json") must_== ParseResult.ParseSuccess
- }
- }
-}
--
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