From 118e1383844c64d521a04be1c5bb26337af8c97f Mon Sep 17 00:00:00 2001
From: speckhard <dts@stanford.edu>
Date: Fri, 15 Mar 2019 15:16:44 +0100
Subject: [PATCH] Tested and working, nomad-faird.
---
.gitignore | 1 +
.../__init__.py | 15 +--
.../elastic_parser_input_exciting.py | 0
.../elastic_parser_input_wien2k.py | 1 -
.../parser_elastic.py | 112 +++++++++++-------
setup.py | 33 ++++++
.../eu/nomad_lab/parsers/ElasticParser.scala | 58 ---------
.../nomad_lab/parsers/ElasticParserSpec.scala | 33 ------
8 files changed, 109 insertions(+), 144 deletions(-)
rename parser/parser-elastic/setup_paths.py => elasticparser/__init__.py (66%)
rename {parser/parser-elastic => elasticparser}/elastic_parser_input_exciting.py (100%)
rename {parser/parser-elastic => elasticparser}/elastic_parser_input_wien2k.py (99%)
rename {parser/parser-elastic => elasticparser}/parser_elastic.py (96%)
create mode 100644 setup.py
delete mode 100644 src/main/scala/eu/nomad_lab/parsers/ElasticParser.scala
delete mode 100644 src/test/scala/eu/nomad_lab/parsers/ElasticParserSpec.scala
diff --git a/.gitignore b/.gitignore
index 004455a..1325359 100644
--- a/.gitignore
+++ b/.gitignore
@@ -9,6 +9,7 @@ syntax: glob
*.pyc
*.bk
*.swp
+*.egg-info
.DS_Store
*.annotate
diff --git a/parser/parser-elastic/setup_paths.py b/elasticparser/__init__.py
similarity index 66%
rename from parser/parser-elastic/setup_paths.py
rename to elasticparser/__init__.py
index 1872074..9b38a23 100644
--- a/parser/parser-elastic/setup_paths.py
+++ b/elasticparser/__init__.py
@@ -1,20 +1,15 @@
-# Copyright 2017-2018 Fawzi Mohamed
-#
+# 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.
-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)
+from elasticparser.parser_elastic import ElasticParser
diff --git a/parser/parser-elastic/elastic_parser_input_exciting.py b/elasticparser/elastic_parser_input_exciting.py
similarity index 100%
rename from parser/parser-elastic/elastic_parser_input_exciting.py
rename to elasticparser/elastic_parser_input_exciting.py
diff --git a/parser/parser-elastic/elastic_parser_input_wien2k.py b/elasticparser/elastic_parser_input_wien2k.py
similarity index 99%
rename from parser/parser-elastic/elastic_parser_input_wien2k.py
rename to elasticparser/elastic_parser_input_wien2k.py
index 6ea9ed5..9e2494d 100644
--- a/parser/parser-elastic/elastic_parser_input_wien2k.py
+++ b/elasticparser/elastic_parser_input_wien2k.py
@@ -1,5 +1,4 @@
from builtins import object
-import setup_paths
from nomadcore.simple_parser import mainFunction, CachingLevel
from nomadcore.simple_parser import SimpleMatcher as SM
from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
diff --git a/parser/parser-elastic/parser_elastic.py b/elasticparser/parser_elastic.py
similarity index 96%
rename from parser/parser-elastic/parser_elastic.py
rename to elasticparser/parser_elastic.py
index 3fcbd57..1db8de0 100644
--- a/parser/parser-elastic/parser_elastic.py
+++ b/elasticparser/parser_elastic.py
@@ -13,7 +13,6 @@
# limitations under the License.
from builtins import object
-import setup_paths
import numpy as np
from nomadcore.unit_conversion.unit_conversion import convert_unit
from nomadcore.parser_backend import JsonParseEventsWriterBackend
@@ -21,7 +20,10 @@ from nomadcore.simple_parser import mainFunction, AncillaryParser, CachingLevel
from nomadcore.simple_parser import SimpleMatcher as SM
from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
from nomadcore.unit_conversion import unit_conversion
-import os, sys, json, elastic_parser_input_exciting, elastic_parser_input_wien2k
+import os, sys, json
+import logging
+import elasticparser.elastic_parser_input_exciting as elastic_parser_input_exciting
+import elasticparser.elastic_parser_input_wien2k as elastic_parser_input_wien2k
from ase import Atoms
#from pathlib import Path
@@ -34,7 +36,7 @@ def is_number(s):
class SampleContext(object):
- def __init__(self):
+ def __init__(self):
# self.mainFileUri = sys.argv[1] #exciting !!!!!!LOCAL HOME!!!!!!!! OKOKOKOK
self.mainFileUri = sys.argv[2] #exciting !!! FOR NOMAD URI nmd:// or sbt -> zip file!!!!!!!! OKOKKOOK
self.parser = None
@@ -63,7 +65,7 @@ class SampleContext(object):
if self.secMethodIndex is None:
self.secMethodIndex = gIndex
- def onClose_section_run(self, backend, gIndex, section):
+ def onClose_section_run(self, backend, gIndex, section):
backend.addValue('program_name', 'elastic')
backend.addValue('program_version', '1.0')
@@ -72,8 +74,8 @@ class SampleContext(object):
self.SGN = int(section["x_elastic_space_group_number"][0])
mainFile = self.parser.fIn.fIn.name
dirPath = os.path.dirname(mainFile) #####exciting sbt -> zip file#### YES ?????????? sure???? check first OKOKOKKO
- self.mainFile = self.parser.fIn.name
- self.mainFilePath = self.mainFile[0:-12]
+ self.mainFile = self.parser.fIn.name
+ self.mainFilePath = self.mainFile[0:-12]
# dirPath = self.mainFileUri[0:-12] #####exciting LOCAL HOME or from NOMAD URI nmd:// ####### YES OKOKOKOK
for files in os.listdir(dirPath):
if files[-3:] == "xml":
@@ -123,7 +125,7 @@ class SampleContext(object):
posX.append(float(s[1]))
posY.append(float(s[2]))
posZ.append(float(s[3]))
- elif len(s) == 3 and s[1] != "=":
+ elif len(s) == 3 and s[1] != "=":
if is_number(s[0]):
lattice.append([fromB(alat*float(s[0])),fromB(alat*float(s[1])),fromB(alat*float(s[2]))])
else:
@@ -140,14 +142,14 @@ class SampleContext(object):
coord = atoms.get_positions()
backend.addArrayValues('atom_positions', np.asarray(coord))
backend.addArrayValues('atom_labels', np.asarray(atom_labels))
- backend.addValue("simulation_cell", cell)
+ backend.addValue("simulation_cell", cell)
def onClose_section_method(self, backend, gIndex, section):
ha_per_joule = convert_unit(1, "hartree", "J")
giga = 10**9
elCode = section['x_elastic_code']
elasticGIndex = backend.openSection("section_single_configuration_calculation")
- self.mainFilePath = self.mainFileUri[0:-12]
+ self.mainFilePath = self.mainFileUri[0:-12]
questa = os.getcwd()
mdr = float(section['x_elastic_max_lagrangian_strain'][0])
ordr = int(section['x_elastic_elastic_constant_order'][0])
@@ -244,7 +246,7 @@ class SampleContext(object):
physStress_dummy.append([])
os.chdir(Dstn)
- cur_dir = os.getcwd()
+ cur_dir = os.getcwd()
if elCode[0] == 'exciting':
try:
@@ -272,7 +274,7 @@ class SampleContext(object):
except:
pass
- elif elCode[0] == 'WIEN':
+ elif elCode[0] == 'WIEN':
f = open(Dstn+'_Energy.dat', 'r')
while 1:
s = f.readline()
@@ -302,7 +304,7 @@ class SampleContext(object):
s = s.strip()
s = s.split()
if is_number(s[0]):
- dummy_eta = s[0]
+ dummy_eta = s[0]
dummy_LS1 = s[1]
dummy_LS2 = s[2]
dummy_LS3 = s[3]
@@ -311,7 +313,7 @@ class SampleContext(object):
dummy_LS6 = s[6]
eta[-1].append(float(dummy_eta))
LagrStress_dummy[-1].append([float(dummy_LS1),float(dummy_LS2),float(dummy_LS3),float(dummy_LS4),float(dummy_LS5),float(dummy_LS6)])
-
+
g = open(Dstn+'_Physical-stress.dat', 'r')
while 1:
s = g.readline()
@@ -519,7 +521,7 @@ class SampleContext(object):
for i in range(6):
string.append('Dstn'+str(i+1))
stringCV.append('DstnCV'+str(i+1))
-
+
for Dstn in string:
j = string.index(Dstn)
for i in range(1, ECs+1):
@@ -784,7 +786,7 @@ class SampleContext(object):
for i in range(len(LagrStress_dummy[j])):
LagrStress[k][j].append(LagrStress_dummy[j][i][k])
physStress[k][j].append(physStress_dummy[j][i][k])
-
+
for i in range(0,6):
elasticSIndex = backend.openSection("x_elastic_section_strain_diagrams")
backend.addValue("x_elastic_strain_diagram_type", "Lagrangian-stress")
@@ -793,7 +795,7 @@ class SampleContext(object):
backend.addValue("x_elastic_strain_diagram_eta_values", eta)
backend.addValue("x_elastic_strain_diagram_values", LagrStress[i])
backend.closeSection("x_elastic_section_strain_diagrams", elasticSIndex)
-
+
elasticSIndex = backend.openSection("x_elastic_section_strain_diagrams")
backend.addValue("x_elastic_strain_diagram_type", "Physical-stress")
backend.addValue("x_elastic_strain_diagram_stress_Voigt_component", int(i+1))
@@ -855,7 +857,7 @@ class SampleContext(object):
backend.addValue("x_elastic_strain_diagram_eta_values", dS5_eta[i])
backend.addValue("x_elastic_strain_diagram_values", dS5_val[i])
backend.closeSection("x_elastic_section_strain_diagrams", elasticSIndex)
-
+
else:
pass
@@ -946,13 +948,13 @@ class SampleContext(object):
LC = 'RI'
ECs= 14
- A = C111-C222+C112
- B = float(3/4)*C222-float(1/2)*C111-float(1/4)*C112
- C = float(1/2)*C111-float(1/4)*C222-float(1/4)*C112
- D = float(1/2)*(C113-C123)
- E = float(1/2)*(C155-C144)
- F = float(1/2)*(C114+float(3)*C124)
- G =-C114-float(2)*C124
+ A = C111-C222+C112
+ B = float(3/4)*C222-float(1/2)*C111-float(1/4)*C112
+ C = float(1/2)*C111-float(1/4)*C222-float(1/4)*C112
+ D = float(1/2)*(C113-C123)
+ E = float(1/2)*(C155-C144)
+ F = float(1/2)*(C114+float(3)*C124)
+ G =-C114-float(2)*C124
H = float(1/2)*(C114-C124)
ECmat[0][0][0] = C111
@@ -1073,10 +1075,10 @@ class SampleContext(object):
LC = 'HII'
ECs= 12
- A = C111-C222+C112
- B = float(3/4)*C222-float(1/2)*C111-float(1/4)*C112
- C = float(1/2)*C111-float(1/4)*C222-float(1/4)*C112
- D = float(1/2)*(C113-C123)
+ A = C111-C222+C112
+ B = float(3/4)*C222-float(1/2)*C111-float(1/4)*C112
+ C = float(1/2)*C111-float(1/4)*C222-float(1/4)*C112
+ D = float(1/2)*(C113-C123)
E = float(1/2)*(C155-C144)
ECmat[0][0][0] = C111
@@ -1164,10 +1166,10 @@ class SampleContext(object):
LC = 'HI'
ECs= 10
- A = C111-C222+C112
- B = float(3/4)*C222-float(1/2)*C111-float(1/4)*C112
- C = float(1/2)*C111-float(1/4)*C222-float(1/4)*C112
- D = float(1/2)*(C113-C123)
+ A = C111-C222+C112
+ B = float(3/4)*C222-float(1/2)*C111-float(1/4)*C112
+ C = float(1/2)*C111-float(1/4)*C222-float(1/4)*C112
+ D = float(1/2)*(C113-C123)
E = float(1/2)*(C155-C144)
ECmat[0][0][0] = C111
@@ -1311,22 +1313,22 @@ class SampleContext(object):
ECs= 6
ECmat[0][0][0] = C111
- ECmat[0][0][1] = C112
- ECmat[0][0][2] = C112
+ ECmat[0][0][1] = C112
+ ECmat[0][0][2] = C112
ECmat[0][1][0] = C112
ECmat[0][1][1] = C112
ECmat[0][1][2] = C113
- ECmat[0][2][0] = C112
- ECmat[0][2][1] = C123
- ECmat[0][2][2] = C112
- ECmat[0][3][3] = C144
- ECmat[0][4][4] = C155
+ ECmat[0][2][0] = C112
+ ECmat[0][2][1] = C123
+ ECmat[0][2][2] = C112
+ ECmat[0][3][3] = C144
+ ECmat[0][4][4] = C155
ECmat[0][5][5] = C155
ECmat[1][0][0] = C112
ECmat[1][0][1] = C112
ECmat[1][0][2] = C123
- ECmat[1][1][0] = C112
+ ECmat[1][1][0] = C112
ECmat[1][1][1] = C111
ECmat[1][1][2] = C112
ECmat[1][2][0] = C123
@@ -1366,7 +1368,7 @@ class SampleContext(object):
ECmat[4][4][1] = C144
ECmat[4][4][2] = C155
ECmat[4][5][3] = C456
-
+
ECmat[5][0][5] = C155
ECmat[5][1][5] = C155
ECmat[5][2][5] = C144
@@ -1430,9 +1432,35 @@ 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/elastic.nomadmetainfo.json"))
+# metaInfoPath = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(__file__)),"../../../../nomad-meta-info/meta_info/nomad_meta_info/elastic.nomadmetainfo.json"))
+# metaInfoEnv, warnings = loadJsonFile(filePath = metaInfoPath, dependencyLoader = None, extraArgsHandling = InfoKindEl.ADD_EXTRA_ARGS, uri = None)
+
+import nomad_meta_info
+metaInfoPath = os.path.normpath(
+ os.path.join(os.path.dirname(os.path.abspath(nomad_meta_info.__file__)), "elastic.nomadmetainfo.json"))
metaInfoEnv, warnings = loadJsonFile(filePath = metaInfoPath, dependencyLoader = None, extraArgsHandling = InfoKindEl.ADD_EXTRA_ARGS, uri = None)
+class ElasticParser():
+ """ 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('elastic 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=SampleContext(),
+ superBackend=backend)
+
+ return backend
+
+
if __name__ == "__main__":
superContext = SampleContext()
mainFunction(mainFileDescription, metaInfoEnv, parserInfo, superContext = superContext)
diff --git a/setup.py b/setup.py
new file mode 100644
index 0000000..aad6b3f
--- /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='elasticparser',
+ version='0.1',
+ description='NOMAD parser implementation for Elastic.',
+ 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/ElasticParser.scala b/src/main/scala/eu/nomad_lab/parsers/ElasticParser.scala
deleted file mode 100644
index 7d380bf..0000000
--- a/src/main/scala/eu/nomad_lab/parsers/ElasticParser.scala
+++ /dev/null
@@ -1,58 +0,0 @@
-/*
- * Copyright 2017-2018 Fawzi Mohamed
- *
- * 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 ElasticParser extends SimpleExternalParserGenerator(
- name = "ElasticParser",
- parserInfo = jn.JObject(
- ("name" -> jn.JString("ElasticParser")) ::
- ("parserId" -> jn.JString("ElasticParser" + lab.ElasticVersionInfo.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.ElasticVersionInfo.toMap.map {
- case (key, value) =>
- (key -> jn.JString(value.toString))
- }(breakOut): List[(String, jn.JString)])
- )) :: Nil
- ),
- mainFileTypes = Seq("text/.*"),
- mainFileRe = """\s*Order of elastic constants\s*=\s*[0-9]+\s*""".r,
- cmd = Seq(DefaultPythonInterpreter.pythonExe(), "${envDir}/parsers/elastic/parser/parser-elastic/parser_elastic.py",
- "--uri", "${mainFileUri}", "${mainFilePath}"),
- resList = Seq(
- "parser-elastic/parser_elastic.py",
- "parser-elastic/setup_paths.py",
- "parser-elastic/elastic_parser_input_wien2k.py",
- "parser-elastic/elastic_parser_input_exciting.py",
- "nomad_meta_info/public.nomadmetainfo.json",
- "nomad_meta_info/common.nomadmetainfo.json",
- "nomad_meta_info/meta_types.nomadmetainfo.json",
- "nomad_meta_info/elastic.nomadmetainfo.json"
- ) ++ DefaultPythonInterpreter.commonFiles(),
- dirMap = Map(
- "parser-elastic" -> "parsers/elastic/parser/parser-elastic/",
- "nomad_meta_info" -> "nomad-meta-info/meta_info/nomad_meta_info",
- "python" -> "python-common/common/python/nomadcore"
- ) ++ DefaultPythonInterpreter.commonDirMapping()
-)
diff --git a/src/test/scala/eu/nomad_lab/parsers/ElasticParserSpec.scala b/src/test/scala/eu/nomad_lab/parsers/ElasticParserSpec.scala
deleted file mode 100644
index 5f40972..0000000
--- a/src/test/scala/eu/nomad_lab/parsers/ElasticParserSpec.scala
+++ /dev/null
@@ -1,33 +0,0 @@
-/*
- * Copyright 2017-2018 Fawzi Mohamed
- *
- * 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 ElasticParserSpec extends Specification {
-
- "ElasticParser2ndTest" >> {
- "test with json-events" >> {
- ParserRun.parse(ElasticParser, "parsers/elastic/test/examples/2nd/INFO_ElaStic", "json-events") must_== ParseResult.ParseSuccess
- }
- "test with json" >> {
- ParserRun.parse(ElasticParser, "parsers/elastic/test/examples/2nd/INFO_ElaStic", "json") must_== ParseResult.ParseSuccess
- }
-
- }
-
-}
--
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