Initial commit for complete parser

0cd794a4 · Berk Onat · 0cd794a4 · 0cd794a4 · 0cd794a4 · 0cd794a4
Commit 0cd794a4 authored Mar 22, 2018 by Berk Onat
--- a/README.md
+++ b/README.md
+# GROMOS Parser
+[NOMAD Laboratory CoE](http://nomad-coe.eu) parser for [GROMOS]()
+## Version 0.0.1
+
+This is the parser for GROMOS in [GROMOS]().
+The official version lives at:
+
+    git@gitlab.mpcdf.mpg.de:nomad-lab/parser-gromos.git
+
+You can browse it at:
+
+    https://gitlab.rzg.mpg.de/nomad-lab/parser-gromos
+
+It relies on having the nomad-meta-info and the python-common repositories one level higher.
+The simplest way to have this is to check out nomad-lab-base recursively:
+
+    git clone --recursive git@gitlab.mpcdf.mpg.de:nomad-lab/nomad-lab-base.git
+
+This parser will be in the directory parsers/gromos of this repository.
+
+## Running and Testing the Parser
+### Requirements
+The required python packages can be installed with (see [python-common](https://gitlab.rzg.mpg.de/nomad-lab/python-common)):
+
+    pip install -r nomad-lab-base/python-common/requirements.txt
+
+### Usage
+GROMOS MD log output files can be parsed with:
+
+    python GROMOSParser.py [path/toFile]
+
+### Test Files
+Example log output files of GROMOS can be found in the directory test/examples.
+More details about the calculations and files are explained in README file of test/examples.
+
--- a/parser/.DS_Store
+++ b/parser/.DS_Store
--- a/parser/parser-gromos/.DS_Store
+++ b/parser/parser-gromos/.DS_Store
--- a/parser/parser-gromos/.idea/misc.xml
+++ b/parser/parser-gromos/.idea/misc.xml
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+</project>
\ No newline at end of file
--- a/parser/parser-gromos/.idea/modules.xml
+++ b/parser/parser-gromos/.idea/modules.xml
+<?xml version="1.0" encoding="UTF-8"?>
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+</project>
\ No newline at end of file
--- a/parser/parser-gromos/.idea/parser-amber.iml
+++ b/parser/parser-gromos/.idea/parser-amber.iml
+<?xml version="1.0" encoding="UTF-8"?>
+<module type="PYTHON_MODULE" version="4">
+  <component name="NewModuleRootManager">
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+    <orderEntry type="inheritedJdk" />
+    <orderEntry type="sourceFolder" forTests="false" />
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+  <component name="TestRunnerService">
+    <option name="projectConfiguration" value="Nosetests" />
+    <option name="PROJECT_TEST_RUNNER" value="Nosetests" />
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+</module>
\ No newline at end of file
--- a/parser/parser-gromos/.idea/workspace.xml
+++ b/parser/parser-gromos/.idea/workspace.xml
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+      <option name="PARENT_ENVS" value="true" />
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\ No newline at end of file
--- a/parser/parser-gromos/GROMOSCommon.py
+++ b/parser/parser-gromos/GROMOSCommon.py
+import logging
+import os
+
+PARSERNAME = "GROMOS"
+PROGRAMNAME = "gromos"
+PARSERVERSION = "0.0.1"
+PARSERMETANAME = PARSERNAME.lower()
+PARSERTAG = 'x_' + PARSERMETANAME
+
+PARSER_INFO_DEFAULT = {
+        'name'   : PARSERMETANAME+'-parser', 
+        'version': PARSERVERSION
+}
+
+META_INFO_PATH = os.path.normpath(os.path.join(
+    os.path.dirname(os.path.abspath(__file__)), 
+    "../../../../nomad-meta-info/meta_info/nomad_meta_info/"+PARSERMETANAME+".nomadmetainfo.json"))
+
+LOGGER = logging.getLogger("nomad."+PROGRAMNAME+"Parser")
+
+def set_excludeList(self):
+    """Sets the exclude list for x_
+
+    Returns:
+        the list of names
+    """
+    excludelist = [
+        PARSERTAG+'_mdin_verbatim_writeout',
+        PARSERTAG+'_dumm_text',
+        PARSERTAG+'_dummy',
+        PARSERTAG+'_mdin_wt'
+        ]
+    excludelist.extend([PARSERTAG+'_mdin_file_%s' % fileNL.lower() for fileNL in self.fileDict.keys()])
+    excludelist.extend([PARSERTAG+'_mdin_%s' % cntrlNL.lower() for cntrlNL in self.cntrlDict.keys()])
+    excludelist.extend([PARSERTAG+'_mdin_%s' % ewaldNL.lower() for ewaldNL in self.ewaldDict.keys()])
+    excludelist.extend([PARSERTAG+'_mdin_%s' % qmmmNL.lower() for qmmmNL in self.qmmmDict.keys()])
+    return excludelist
+
+def set_includeList():
+    """Sets the include list for x_
+
+    Returns:
+        the list of names
+    """
+    includelist = []
+    return includelist
+
+
--- a/parser/parser-gromos/GROMOSDictionary.py
+++ b/parser/parser-gromos/GROMOSDictionary.py
--- a/parser/parser-gromos/GROMOSParser.py
+++ b/parser/parser-gromos/GROMOSParser.py
--- a/parser/parser-gromos/setup_paths.py
+++ b/parser/parser-gromos/setup_paths.py
+import sys
+import os
+import 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)
--- a/src/main/scala/eu/nomad_lab/parsers/GromosParser.scala
+++ b/src/main/scala/eu/nomad_lab/parsers/GromosParser.scala
+package eu.nomad_lab.parsers
+
+import eu.nomad_lab
+import eu.nomad_lab.DefaultPythonInterpreter
+import org.{ json4s => jn }
+import eu.{ nomad_lab => lab }
+import scala.collection.breakOut
+
+object GromosParser extends SimpleExternalParserGenerator(
+  name = "GromosParser",
+  parserInfo = jn.JObject(
+    ("name" -> jn.JString("GromosParser")) ::
+      ("parserId" -> jn.JString("GromosParser" + lab.GromosVersionInfo.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.GromosVersionInfo.toMap.map {
+            case (key, value) =>
+              (key -> jn.JString(value.toString))
+          }(breakOut): List[(String, jn.JString)])
+      )) :: Nil
+  ),
+  mainFileTypes = Seq("text/.*"),
+  mainFileRe = """^MD\+\+\s*\s*""".r,
+  cmd = Seq(DefaultPythonInterpreter.pythonExe(), "${envDir}/parsers/gromos/parser/parser-gromos/GROMOSParser.py",
+    "${mainFilePath}"),
+  resList = Seq(
+    "parser-gromos/GROMOSParser.py",
+    "parser-gromos/GROMOSDictionary.py",
+    "parser-gromos/GROMOSCommon.py",
+    "parser-gromos/setup_paths.py",
+    "nomad_meta_info/public.nomadmetainfo.json",
+    "nomad_meta_info/common.nomadmetainfo.json",
+    "nomad_meta_info/meta_types.nomadmetainfo.json"
+  ) ++ DefaultPythonInterpreter.commonFiles(),
+  dirMap = Map(
+    "parser-gromos" -> "parsers/gromos/parser/parser-gromos",
+    "nomad_meta_info" -> "nomad-meta-info/meta_info/nomad_meta_info",
+    "python" -> "python-common/common/python/nomadcore"
+  ) ++ DefaultPythonInterpreter.commonDirMapping(),
+  metaInfoEnv = Some(lab.meta.KnownMetaInfoEnvs.gromos)
+)
+
--- a/src/test/scala/eu/nomad_lab/parsers/GromosParserSpec.scala
+++ b/src/test/scala/eu/nomad_lab/parsers/GromosParserSpec.scala
+package eu.nomad_lab.parsers
+
+import org.specs2.mutable.Specification
+
+object GromosParserTests extends Specification {
+  "GromosParserTest" >> {
+    "[Peptide in Water with 2792 atoms] test with json-events" >> {
+      ParserRun.parse(NAMDParser, "parsers/gromos/test/examples/eq/eq_peptide_1.omd", "json-events") must_== ParseResult.ParseSuccess
+    }
+    "[Peptide in Water with 2792 atoms] test with json" >> {
+      ParserRun.parse(NAMDParser, "parsers/gromos/test/examples/eq/eq_peptide_1.omd", "json") must_== ParseResult.ParseSuccess
+    }
+  }
+}
--- a/test/.DS_Store
+++ b/test/.DS_Store
--- a/test/examples/.DS_Store
+++ b/test/examples/.DS_Store
--- a/test/examples/README.md
+++ b/test/examples/README.md
+# Tests:
+### Source of Tests:
+
+The tests are taken from Gromos Tutorial in [GROMOS](http://www.gromos.net).
+
+### Example Tests:
+
+#### Peptide in Water benchmark 
+2792 atoms, 908 water molecules as Solvent and 7 Solute residues
--- a/test/examples/eq/eq_peptide_1.cnf
+++ b/test/examples/eq/eq_peptide_1.cnf
--- a/test/examples/eq/eq_peptide_1.imd
+++ b/test/examples/eq/eq_peptide_1.imd
+TITLE
+	Automatically generated input file
+	essmpc Mon Mar 12 14:31:13 2018
+END
+SYSTEM
+#      NPM      NSM
+         1      908
+END
+STEP
+#   NSTLIM         T        DT
+     10000         0     0.002
+END
+BOUNDCOND
+#      NTB    NDFMIN
+         1         3
+END
+MULTIBATH
+# ALGORITHM:
+#      weak-coupling:      use weak-coupling scheme
+#      nose-hoover:        use Nose Hoover scheme
+#      nose-hoover-chains: use Nose Hoover chains scheme
+# NUM: number of chains in Nose Hoover chains scheme
+#      !! only specify NUM when needed !!
+# NBATHS: number of temperature baths to couple to
+#          ALGORITHM
+                   0
+#  NBATHS
+         2
+# TEMP0(1 ... NBATHS)  TAU(1 ... NBATHS)
+        60       0.1
+        60       0.1
+
+#   DOFSET: number of distinguishable sets of d.o.f.
+         2
+# LAST(1 ... DOFSET)  COMBATH(1 ... DOFSET)  IRBATH(1 ... DOFSET)
+        73         1         1      2797         2         2
+END
+FORCE
+#      NTF array
+# bonds    angles   imp.     dihe     charge nonbonded
+  0        1        1        1        1        1
+# NEGR    NRE(1)    NRE(2)    ...      NRE(NEGR)
+     4
+       71       72       73     2797
+END
+COVALENTFORM
+#    NTBBH    NTBAH     NTBDN
+         0         0         0
+END
+CONSTRAINT
+# NTC
+    3
+#      NTCP  NTCP0(1)
+          1    0.0001
+#      NTCS  NTCS0(1)
+          1    0.0001
+END
+PAIRLIST
+# algorithm    NSNB   RCUTP   RCUTL    SIZE    TYPE
+          1       5     0.8     1.4     0.4       0
+END
+NONBONDED
+# NLRELE
+         1
+#  APPAK    RCRF   EPSRF    NSLFEXCL
+         0       1.4        61         1
+# NSHAPE  ASHAPE  NA2CLC   TOLA2   EPSLS
+         3       1.4         2     1e-10         0
+#    NKX     NKY     NKZ   KCUT
+        10        10        10       100
+#    NGX     NGY     NGZ  NASORD  NFDORD  NALIAS  NSPORD
+        32        32        32         3         2         3         4
+# NQEVAL  FACCUR  NRDGRD  NWRGRD
+    100000       1.6         0         0
+#  NLRLJ  SLVDNS
+         0      33.3
+END
+INITIALISE
+# Default values for NTI values: 0
+#   NTIVEL    NTISHK    NTINHT    NTINHB
+         1         0         0         0
+#   NTISHI    NTIRTC    NTICOM
+         1         0         0
+#   NTISTI
+         0
+#       IG     TEMPI
+    210185        60
+END
+COMTRANSROT
+#     NSCM
+      1000
+END
+POSITIONRES
+#     values for NTPOR
+#     0: no position re(con)straining
+#     1: use CPOR
+#     2: use CPOR/ ATOMIC B-FACTORS
+#     3: position constraining
+#    NTPOR    NTPORB  NTPORS      CPOR
+         1         1         0     25000
+END
+PRINTOUT
+#NTPR: print out energies, etc. every NTPR steps
+#NTPP: =1 perform dihedral angle transition monitoring
+#     NTPR      NTPP
+       100         0
+END
+WRITETRAJ
+#    NTWX     NTWSE      NTWV      NTWF      NTWE      NTWG      NTWB
+      100         0         0         0       100         0         0
+END
--- a/test/examples/eq/eq_peptide_1.omd
+++ b/test/examples/eq/eq_peptide_1.omd
--- a/test/examples/eq/eq_peptide_1.run
+++ b/test/examples/eq/eq_peptide_1.run
+#!/bin/sh
+
+# first we set some variables
+NAME=`whoami`
+PROGRAM=../../../BUILD/bin/md
+SIMULDIR=/home/eng/essmpc/GROMOS/TESTS/peptide/eq
+
+# create temporary directory
+WORKDIR=${SIMULDIR}
+mkdir -p ${WORKDIR}
+cd       ${WORKDIR}
+
+# set the input files
+TOPO=${SIMULDIR}/peptide_2Cl_54a7.top
+IUNIT=${SIMULDIR}/eq_peptide_1.imd
+INPUTCRD=${SIMULDIR}/peptide_2Cl_h2o.cnf
+REFPOS=${SIMULDIR}/peptide_2Cl_h2o.rpr
+POSRESSPEC=${SIMULDIR}/peptide_2Cl_h2o.por
+
+#set the output files
+OUNIT=eq_peptide_1.omd
+OUTPUTCRD=eq_peptide_1.cnf
+OUTPUTTRX=eq_peptide_1.trc
+OUTPUTTRE=eq_peptide_1.tre
+
+
+MDOK=1
+
+${PROGRAM} \
+	@topo        ${TOPO} \
+	@conf        ${INPUTCRD} \
+	@input       ${IUNIT} \
+	@posresspec  ${POSRESSPEC} \
+	@refpos      ${REFPOS} \
+	@fin         ${OUTPUTCRD} \
+	@trc         ${OUTPUTTRX} \
+	@tre         ${OUTPUTTRE}\
+	>            ${OUNIT}
+grep "finished successfully" ${OUNIT} > /dev/null || MDOK=0
+
+uname -a >> ${OUNIT}
+
+# compress some files
+#gzip ${OUTPUTTRX}
+#gzip ${OUTPUTTRE}
+
+# copy the files back
+OK=1
+cp ${OUNIT}               ${SIMULDIR} || OK=0
+cp ${OUTPUTCRD}           ${SIMULDIR} || OK=0
+cp ${OUTPUTTRX}           ${SIMULDIR} || OK=0
+cp ${OUTPUTTRE}           ${SIMULDIR} || OK=0
+
+# clean up after successful run
+if `test ${OK} -eq 0`; then
+  uname -a > mess;
+  echo 'cp failed for eq_peptide, run 1' >> mess;
+  Mail -s "ERROR" ${NAME} < mess;
+  cd ${SIMULDIR};
+else
+  cd ${SIMULDIR};
+#  rm ${WORKDIR}/*;
+#  rmdir ${WORKDIR};
+fi
+
+# stop if MD was not succesfull
+if `test ${MDOK} -eq 0`; then
+  exit
+fi
+
+# perform last command (usually submit next job)
+cd ${SIMULDIR}
+