From 83a4de4efa40731f7e192c795fc1e82f00f27fc8 Mon Sep 17 00:00:00 2001
From: speckhard <dts@stanford.edu>
Date: Fri, 22 Feb 2019 12:34:16 +0100
Subject: [PATCH] Added Orca to Nomad-Faird framework.
---
.gitignore | 2 +
orcaparser.egg-info/PKG-INFO | 10 +++
orcaparser.egg-info/SOURCES.txt | 10 +++
orcaparser.egg-info/dependency_links.txt | 1 +
orcaparser.egg-info/requires.txt | 1 +
orcaparser.egg-info/top_level.txt | 1 +
orcaparser/__init__.py | 15 +++++
.../orca_parser.py => orcaparser/parser.py | 46 ++++++++++----
.../parser-orca => orcaparser}/setup_paths.py | 0
setup.py | 33 ++++++++++
.../eu/nomad_lab/parsers/OrcaParser.scala | 61 -------------------
.../eu/nomad_lab/parsers/OrcaParserSpec.scala | 30 ---------
12 files changed, 106 insertions(+), 104 deletions(-)
create mode 100644 orcaparser.egg-info/PKG-INFO
create mode 100644 orcaparser.egg-info/SOURCES.txt
create mode 100644 orcaparser.egg-info/dependency_links.txt
create mode 100644 orcaparser.egg-info/requires.txt
create mode 100644 orcaparser.egg-info/top_level.txt
create mode 100644 orcaparser/__init__.py
rename parser/parser-orca/orca_parser.py => orcaparser/parser.py (97%)
rename {parser/parser-orca => orcaparser}/setup_paths.py (100%)
create mode 100644 setup.py
delete mode 100644 src/main/scala/eu/nomad_lab/parsers/OrcaParser.scala
delete mode 100644 src/test/scala/eu/nomad_lab/parsers/OrcaParserSpec.scala
diff --git a/.gitignore b/.gitignore
index a6cb8b6..5f92ac3 100644
--- a/.gitignore
+++ b/.gitignore
@@ -9,6 +9,8 @@ syntax: glob
*.pyc
*.bk
*.swp
+*.egg-info
+
.DS_Store
# logging files
diff --git a/orcaparser.egg-info/PKG-INFO b/orcaparser.egg-info/PKG-INFO
new file mode 100644
index 0000000..cfdc984
--- /dev/null
+++ b/orcaparser.egg-info/PKG-INFO
@@ -0,0 +1,10 @@
+Metadata-Version: 1.0
+Name: orcaparser
+Version: 0.1
+Summary: NOMAD parser implementation for Orca.
+Home-page: UNKNOWN
+Author: UNKNOWN
+Author-email: UNKNOWN
+License: APACHE 2.0
+Description: UNKNOWN
+Platform: UNKNOWN
diff --git a/orcaparser.egg-info/SOURCES.txt b/orcaparser.egg-info/SOURCES.txt
new file mode 100644
index 0000000..acef332
--- /dev/null
+++ b/orcaparser.egg-info/SOURCES.txt
@@ -0,0 +1,10 @@
+README.md
+setup.py
+./orcaparser/__init__.py
+./orcaparser/parser.py
+./orcaparser/setup_paths.py
+./orcaparser.egg-info/PKG-INFO
+./orcaparser.egg-info/SOURCES.txt
+./orcaparser.egg-info/dependency_links.txt
+./orcaparser.egg-info/requires.txt
+./orcaparser.egg-info/top_level.txt
\ No newline at end of file
diff --git a/orcaparser.egg-info/dependency_links.txt b/orcaparser.egg-info/dependency_links.txt
new file mode 100644
index 0000000..8b13789
--- /dev/null
+++ b/orcaparser.egg-info/dependency_links.txt
@@ -0,0 +1 @@
+
diff --git a/orcaparser.egg-info/requires.txt b/orcaparser.egg-info/requires.txt
new file mode 100644
index 0000000..f23d347
--- /dev/null
+++ b/orcaparser.egg-info/requires.txt
@@ -0,0 +1 @@
+nomadcore
diff --git a/orcaparser.egg-info/top_level.txt b/orcaparser.egg-info/top_level.txt
new file mode 100644
index 0000000..9a96c6e
--- /dev/null
+++ b/orcaparser.egg-info/top_level.txt
@@ -0,0 +1 @@
+orcaparser
diff --git a/orcaparser/__init__.py b/orcaparser/__init__.py
new file mode 100644
index 0000000..31bf698
--- /dev/null
+++ b/orcaparser/__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 orcaparser.parser import OrcaParser
diff --git a/parser/parser-orca/orca_parser.py b/orcaparser/parser.py
similarity index 97%
rename from parser/parser-orca/orca_parser.py
rename to orcaparser/parser.py
index c3f9546..88b958b 100644
--- a/parser/parser-orca/orca_parser.py
+++ b/orcaparser/parser.py
@@ -1,11 +1,11 @@
# Copyright 2016-2018 Sebastian Alarcon Villaseca, Sebastián Alarcón Villaseca, Fawzi Mohamed, Micael Oliveira, Ankit Kariryaa, Danio Brambila
-#
+#
# 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.
@@ -14,7 +14,6 @@
# -*- coding: utf-8 -*
from builtins import object
-import setup_paths
import numpy as np
from nomadcore.simple_parser import SimpleMatcher, mainFunction
from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
@@ -88,7 +87,7 @@ class OrcaContext(object):
#***************************************
# Local functionals
#***************************************
- # HFS: Hartree-Fock Slater
+ # HFS: Hartree-Fock Slater
"HF": ["HF_X"],
"HFS": ["HF_X"],
# XAlpha: The famous old Slater Xa theory
@@ -151,7 +150,7 @@ class OrcaContext(object):
"TPSS": ["LDA_X", "MGGA_X_TPSS", "LDA_C_PW", "MGGA_C_TPSS"],
# TPSSh: The hybrid version of TPSS (10% HF exchange)
"TPSSh": ["HYB_MGGA_XC_TPSSH"],
- # TPSS0: A 25% exchange version of TPSSh that yields improved energetics
+ # TPSS0: A 25% exchange version of TPSSh that yields improved energetics
# compared to TPSSh but is otherwise not well tested
# "TPSS0": ["HYB_MGGA_XC_TPSSH"],
# M06L: The Minnesota M06-L meta-GGA functional
@@ -285,7 +284,7 @@ def build_OrcaMainFileSimpleMatcher():
which allows nice formating of nested SimpleMatchers in python.
Returns:
- SimpleMatcher that parses main file of ORCA.
+ SimpleMatcher that parses main file of ORCA.
"""
#
# a) SimpleMatcher for header and ORCA version:
@@ -333,7 +332,7 @@ def buildSinglePointSubMatchers():
subMatchers = [
SM(r"\s+(?P<x_orca_atom_labels>[a-zA-Z]+)\s+(?P<x_orca_atom_positions_x__angstrom>[-+0-9.]+)\s+(?P<x_orca_atom_positions_y__angstrom>[-+0-9.]+)\s+(?P<x_orca_atom_positions_z__angstrom>[-+0-9.]+)", repeats = True)
]
- ),
+ ),
# Get basis set information:
SM(name = 'Basis set information',
startReStr = r"BASIS SET INFORMATION\s*",
@@ -349,7 +348,7 @@ def buildSinglePointSubMatchers():
SM(r"\s*Group\s+[0-9]+\s+Type\s+(?P<x_orca_basis_set_atom_labels>[a-zA-Z]+)\s+:\s+(?P<x_orca_auxiliary_basis_set>[0-9a-z]+)\s+contracted\s+to\s+(?P<x_orca_auxiliary_basis_set_contracted>[0-9a-z]+)\s+pattern\s+\{[0-9/]+\}", repeats = True)
]
)
- ]
+ ]
),
# Basis set statistics and startup info:
SM(name = 'Basis set statistics and startup info',
@@ -544,7 +543,7 @@ def buildGeoOptMatcher():
#
# c) SimpleMatcher for geometry optimization:
# *******************************************
-#
+#
return SM(name = 'Geometry optimization',
startReStr = r"\s*\* Geometry Optimization Run \*\s*",
sections = ["section_sampling_method"],
@@ -570,7 +569,7 @@ def buildGeoOptMatcher():
sections = ["x_orca_final_geometry"],
subMatchers = [
SM(r"\s+(?P<x_orca_atom_labels_geo_opt>[a-zA-Z]+)\s+(?P<x_orca_atom_positions_x_geo_opt__angstrom>[-+0-9.]+)\s+(?P<x_orca_atom_positions_y_geo_opt__angstrom>[-+0-9.]+)\s+(?P<x_orca_atom_positions_z_geo_opt__angstrom>[-+0-9.]+)", repeats = True)
- ]
+ ]
),
# *** FINAL ENERGY EVALUATION AT THE STATIONARY POINT ***
#
@@ -586,7 +585,7 @@ def buildMp2Matcher():
#
# d) Post-processing calculations:
# ********************************
-#
+#
# MP2 Calculation (post-proc):
return SM(name = 'mp2',
startReStr = r"\s*ORCA MP2 CALCULATION\s*",
@@ -711,8 +710,29 @@ parserInfo = {
"version": "1.0"
}
-metaInfoPath = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(__file__)),"../../../../nomad-meta-info/meta_info/nomad_meta_info/orca.nomadmetainfo.json"))
+import nomad_meta_info
+metaInfoPath = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(nomad_meta_info.__file__)), "orca.nomadmetainfo.json"))
metaInfoEnv, warnings = loadJsonFile(filePath = metaInfoPath, dependencyLoader = None, extraArgsHandling = InfoKindEl.ADD_EXTRA_ARGS, uri = None)
+class OrcaParser():
+ """ 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('orca 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,
+ metaInfoEnv,
+ parserInfo,
+ superContext=OrcaContext(),
+ superBackend=backend)
+
+ return backend
+
if __name__ == "__main__":
mainFunction(mainFileDescription, metaInfoEnv, parserInfo, superContext=OrcaContext())
diff --git a/parser/parser-orca/setup_paths.py b/orcaparser/setup_paths.py
similarity index 100%
rename from parser/parser-orca/setup_paths.py
rename to orcaparser/setup_paths.py
diff --git a/setup.py b/setup.py
new file mode 100644
index 0000000..7444433
--- /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='orcaparser',
+ version='0.1',
+ description='NOMAD parser implementation for Orca.',
+ 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/OrcaParser.scala b/src/main/scala/eu/nomad_lab/parsers/OrcaParser.scala
deleted file mode 100644
index ba0f4dc..0000000
--- a/src/main/scala/eu/nomad_lab/parsers/OrcaParser.scala
+++ /dev/null
@@ -1,61 +0,0 @@
-/*
- * Copyright 2016-2018 Sebastian Alarcon Villaseca, Sebastián Alarcón Villaseca, Fawzi Mohamed, Micael Oliveira, Ankit Kariryaa, Danio Brambila
- *
- * 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 OrcaParser extends SimpleExternalParserGenerator(
- name = "OrcaParser",
- parserInfo = jn.JObject(
- ("name" -> jn.JString("OrcaParser")) ::
- ("parserId" -> jn.JString("OrcaParser" + lab.OrcaVersionInfo.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.OrcaVersionInfo.toMap.map {
- case (key, value) =>
- (key -> jn.JString(value.toString))
- }(breakOut): List[(String, jn.JString)])
- )) :: Nil
- ),
- mainFileTypes = Seq("text/.*"),
- mainFileRe = """\s+\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\**\s*
-\s+\* O R C A \*\s*
-\s+\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\**\s*
-\s*
-\s*--- An Ab Initio, DFT and Semiempirical electronic structure package ---\s*
-""".r,
- cmd = Seq(DefaultPythonInterpreter.pythonExe(), "${envDir}/parsers/orca/parser/parser-orca/orca_parser.py",
- "--uri", "${mainFileUri}", "${mainFilePath}"),
- resList = Seq(
- "parser-orca/orca_parser.py",
- "parser-orca/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/orca.nomadmetainfo.json"
- ) ++ DefaultPythonInterpreter.commonFiles(),
- dirMap = Map(
- "parser-orca" -> "parsers/orca/parser/parser-orca",
- "nomad_meta_info" -> "nomad-meta-info/meta_info/nomad_meta_info"
- ) ++ DefaultPythonInterpreter.commonDirMapping(),
- metaInfoEnv = Some(lab.meta.KnownMetaInfoEnvs.orca)
-)
diff --git a/src/test/scala/eu/nomad_lab/parsers/OrcaParserSpec.scala b/src/test/scala/eu/nomad_lab/parsers/OrcaParserSpec.scala
deleted file mode 100644
index c8f4c0a..0000000
--- a/src/test/scala/eu/nomad_lab/parsers/OrcaParserSpec.scala
+++ /dev/null
@@ -1,30 +0,0 @@
-/*
- * Copyright 2016-2018 Sebastian Alarcon Villaseca, Sebastián Alarcón Villaseca, Fawzi Mohamed, Micael Oliveira, Ankit Kariryaa, Danio Brambila
- *
- * 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 OrcaParserSpec extends Specification {
- "OrcaParserTest" >> {
- "test with json-events" >> {
- ParserRun.parse(OrcaParser, "parsers/orca/test/examples/output_files/orca3.2706823.out", "json-events") must_== ParseResult.ParseSuccess
- }
- "test with json" >> {
- ParserRun.parse(OrcaParser, "parsers/orca/test/examples/output_files/orca3.2706823.out", "json") must_== ParseResult.ParseSuccess
- }
- }
-}
--
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