Initial commit for NAMD parser

7fd449a0 · Berk Onat · 7fd449a0 · 7fd449a0 · 7fd449a0 · 7fd449a0
Commit 7fd449a0 authored Jan 18, 2018 by Berk Onat
20 changed files
--- a/README.md
+++ b/README.md
+# NAMD Parser
+[NOMAD Laboratory CoE](http://nomad-coe.eu) parser for [NAMD](http://www.ks.uiuc.edu/Research/namd/)
+## Version 0.0.1
+
+This is the parser for NAMD Molecular Dynamics (namd2) in [NAMD](http://www.ks.uiuc.edu/Research/namd/).
+The official version lives at:
+
+    git@gitlab.mpcdf.mpg.de:nomad-lab/parser-namd.git
+
+You can browse it at:
+
+    https://gitlab.rzg.mpg.de/nomad-lab/parser-namd
+
+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/namd 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
+NAMD md (namd2 executable) log output files can be parsed with:
+
+    python NAMDParser.py [path/toFile]
+
+### Test Files
+Example log output files of NAMD can be found in the directory test/examples.
+More details about the calculations and files will be explained in this README file.
+
--- a/parser/.DS_Store
+++ b/parser/.DS_Store
--- a/parser/parser-namd/.DS_Store
+++ b/parser/parser-namd/.DS_Store
--- a/parser/parser-namd/.idea/misc.xml
+++ b/parser/parser-namd/.idea/misc.xml
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\ No newline at end of file
--- a/parser/parser-namd/.idea/modules.xml
+++ b/parser/parser-namd/.idea/modules.xml
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\ No newline at end of file
--- a/parser/parser-namd/.idea/parser-amber.iml
+++ b/parser/parser-namd/.idea/parser-amber.iml
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\ No newline at end of file
--- a/parser/parser-namd/.idea/workspace.xml
+++ b/parser/parser-namd/.idea/workspace.xml
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\ No newline at end of file
--- a/parser/parser-namd/NAMDCommon.py
+++ b/parser/parser-namd/NAMDCommon.py
+import logging
+import os
+
+PARSERNAME = "NAMD"
+PROGRAMNAME = "namd"
+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-namd/NAMDDictionary.py
+++ b/parser/parser-namd/NAMDDictionary.py
--- a/parser/parser-namd/NAMDParser.py
+++ b/parser/parser-namd/NAMDParser.py
--- a/parser/parser-namd/setup_paths.py
+++ b/parser/parser-namd/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/NAMDParser.scala
+++ b/src/main/scala/eu/nomad_lab/parsers/NAMDParser.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 NAMDParser extends SimpleExternalParserGenerator(
+  name = "NAMDParser",
+  parserInfo = jn.JObject(
+    ("name" -> jn.JString("NAMDParser")) ::
+      ("parserId" -> jn.JString("NAMDParser" + lab.NAMDVersionInfo.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.NAMDVersionInfo.toMap.map {
+            case (key, value) =>
+              (key -> jn.JString(value.toString))
+          }(breakOut): List[(String, jn.JString)])
+      )) :: Nil
+  ),
+  mainFileTypes = Seq("text/.*"),
+  mainFileRe = """\s*Info:\s*NAMD\s*[0-9.]+\s*for\s*""".r,
+  cmd = Seq(DefaultPythonInterpreter.pythonExe(), "${envDir}/parsers/gromacs/parser/parser-namd/NAMDParser.py",
+    "${mainFilePath}"),
+  resList = Seq(
+    "parser-namd/NAMDParser.py",
+    "parser-namd/NAMDDictionary.py",
+    "parser-namd/NAMDCommon.py",
+    "parser-namd/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/namd.nomadmetainfo.json"
+  ) ++ DefaultPythonInterpreter.commonFiles(),
+  dirMap = Map(
+    "parser-namd" -> "parsers/namd/parser/parser-namd",
+    "nomad_meta_info" -> "nomad-meta-info/meta_info/nomad_meta_info",
+    "python" -> "python-common/common/python/nomadcore"
+  ) ++ DefaultPythonInterpreter.commonDirMapping(),
+  metaInfoEnv = Some(lab.meta.KnownMetaInfoEnvs.gromacs)
+)
+
--- a/src/test/scala/eu/nomad_lab/parsers/NAMDParserSpec.scala
+++ b/src/test/scala/eu/nomad_lab/parsers/NAMDParserSpec.scala
+package eu.nomad_lab.parsers
+
+import org.specs2.mutable.Specification
+
+object NAMDParserTests extends Specification {
+  "NAMDParserTest" >> {
+    "[tiny with 507 atoms] test with json-events" >> {
+      ParserRun.parse(NAMDParser, "parsers/gromacs/test/examples/tiny/tiny.log", "json-events") must_== ParseResult.ParseSuccess
+    }
+    "[tiny with 507 atoms] test with json" >> {
+      ParserRun.parse(NAMDParser, "parsers/gromacs/test/examples/tiny/tiny.log", "json") must_== ParseResult.ParseSuccess
+    }
+    "[apoa1-trajectory with 92224 atoms] test with json-events" >> {
+      ParserRun.parse(NAMDParser, "parsers/gromacs/test/examples/apoa1-trajectory/apoa1.log", "json-events") must_== ParseResult.ParseSuccess
+    }
+    "[apoa1-trajectory with 92224 atoms] test with json" >> {
+      ParserRun.parse(NAMDParser, "parsers/gromacs/test/examples/apoa1-trajectory/apoa1.log", "json") must_== ParseResult.ParseSuccess
+    }
+  }
+}
--- a/test/examples/README.md
+++ b/test/examples/README.md
+# Tests:
+### Source of Tests:
+
+The tests are taken from NAMD (version 2.12) examples in [NAMD](http://www.ks.uiuc.edu/Research/namd/utilities/).
+
+### Example Tests:
+
+#### ApoA1 benchmark 
+92224 atoms, periodic, PME [NAMD home link](http://www.ks.uiuc.edu/Research/namd/utilities/apoa1/)
+#### tiny benchmark 
+507 atoms, periodic, PME [NAMD home link](http://www.ks.uiuc.edu/Research/namd/utilities/tiny/)
+#### Interactive BPTI benchmark 
+882 atoms, small [NAMD home link](http://www.ks.uiuc.edu/Research/namd/utilities/bpti_imd/)
+#### ER-GRE benchmark 
+36573 atoms, spherical [NAMD home link](http://www.ks.uiuc.edu/Research/namd/utilities/er-gre/)
--- a/test/examples/apoa1-andersen/FFTW_NAMD_2.12_Linux-x86_64-MPI.txt
+++ b/test/examples/apoa1-andersen/FFTW_NAMD_2.12_Linux-x86_64-MPI.txt
+(FFTW-2.1.3 (108 537 1 0 123 1 1 209 0) (36 537 1 0 123 1 1 77 0) (12 537 1 0 123 1 0 276 0) (4 537 1 0 123 1 0 100 0) (54 537 1 0 123 1 1 143 0) (18 537 1 0 123 1 1 77 0) (6 537 1 0 123 1 0 144 0) (2 537 1 0 123 1 0 56 0) (27 537 1 0 123 1 1 77 0) (9 537 1 0 123 1 0 210 0) (3 537 1 0 123 1 0 78 0) (108 537 1 0 287 1 1 209 0) (36 537 1 0 287 1 1 77 0) (12 537 1 0 287 1 0 276 0) (4 537 1 0 287 1 0 100 0) (54 537 1 0 287 1 1 209 0) (18 537 1 0 287 1 1 77 0) (6 537 1 0 287 1 0 144 0) (2 537 1 0 287 1 0 56 0) (27 537 1 0 287 1 1 77 0) (9 537 1 0 287 1 0 210 0) (3 537 1 0 287 1 0 78 0) (108 537 -1 0 123 1 1 198 0) (36 537 -1 0 123 1 1 66 0) (12 537 -1 0 123 1 0 265 0) (4 537 -1 0 123 1 0 89 0) (54 537 -1 0 123 1 1 198 0) (18 537 -1 0 123 1 1 66 0) (6 537 -1 0 123 1 0 133 0) (2 537 -1 0 123 1 0 45 0) (27 537 -1 0 123 1 1 66 0) (9 537 -1 0 123 1 0 199 0) (3 537 -1 0 123 1 0 67 0) (108 537 -1 0 287 1 1 198 0) (36 537 -1 0 287 1 1 66 0) (12 537 -1 0 287 1 0 265 0) (4 537 -1 0 287 1 0 89 0) (54 537 -1 0 287 1 1 198 0) (18 537 -1 0 287 1 1 66 0) (6 537 -1 0 287 1 0 133 0) (2 537 -1 0 287 1 0 45 0) (27 537 -1 0 287 1 1 66 0) (9 537 -1 0 287 1 0 199 0) (3 537 -1 0 287 1 0 67 0) (5 529 -1 1 1 1 4 112 0) (2 529 -1 1 1 1 4 46 0) (10 529 -1 1 1 1 4 222 0) (4 529 -1 1 1 1 4 90 0) (20 529 -1 1 1 1 6 47 0) (8 529 -1 1 1 1 4 178 0) (40 529 -1 1 1 1 6 91 0) (16 529 -1 1 1 1 4 354 0) (80 529 -1 1 1 1 6 113 0) (3 537 -1 0 41 1 0 67 0) (9 537 -1 0 41 1 0 199 0) (27 537 -1 0 41 1 1 66 0) (2 537 -1 0 41 1 0 45 0) (6 537 -1 0 41 1 0 133 0) (18 537 -1 0 41 1 1 66 0) (54 537 -1 0 41 1 1 198 0) (4 537 -1 0 41 1 0 89 0) (12 537 -1 0 41 1 0 265 0) (36 537 -1 0 41 1 1 132 0) (108 537 -1 0 41 1 1 198 0) (3 537 -1 0 1107 1 0 67 0) (9 537 -1 0 1107 1 0 199 0) (27 537 -1 0 1107 1 1 66 0) (2 537 -1 0 1107 1 0 45 0) (6 537 -1 0 1107 1 0 133 0) (18 537 -1 0 1107 1 1 66 0) (54 537 -1 0 1107 1 1 198 0) (4 537 -1 0 1107 1 0 89 0) (12 537 -1 0 1107 1 0 265 0) (36 537 -1 0 1107 1 1 66 0) (108 537 -1 0 1107 1 1 198 0) (3 537 1 0 1107 1 0 78 0) (9 537 1 0 1107 1 0 210 0) (27 537 1 0 1107 1 1 77 0) (2 537 1 0 1107 1 0 56 0) (6 537 1 0 1107 1 0 144 0) (18 537 1 0 1107 1 1 77 0) (54 537 1 0 1107 1 1 209 0) (4 537 1 0 1107 1 0 100 0) (12 537 1 0 1107 1 0 276 0) (36 537 1 0 1107 1 1 77 0) (108 537 1 0 1107 1 1 209 0) (5 529 1 1 1 1 5 125 0) (2 529 1 1 1 1 5 59 0) (10 529 1 1 1 1 5 235 0) (4 529 1 1 1 1 5 103 0) (20 529 1 1 1 1 6 58 0) (8 529 1 1 1 1 5 191 0) (40 529 1 1 1 1 6 102 0) (16 529 1 1 1 1 5 367 0) (80 529 1 1 1 1 6 234 0) (3 537 1 0 41 1 0 78 0) (9 537 1 0 41 1 0 210 0) (27 537 1 0 41 1 1 77 0) (2 537 1 0 41 1 0 56 0) (6 537 1 0 41 1 0 144 0) (18 537 1 0 41 1 1 77 0) (54 537 1 0 41 1 1 209 0) (4 537 1 0 41 1 0 100 0) (12 537 1 0 41 1 0 276 0) (36 537 1 0 41 1 1 77 0) (108 537 1 0 41 1 1 209 0))
\ No newline at end of file
--- a/test/examples/apoa1-andersen/FFTW_NAMD_2.12_MacOSX-x86_64-multicore.txt
+++ b/test/examples/apoa1-andersen/FFTW_NAMD_2.12_MacOSX-x86_64-multicore.txt
+(FFTW-2.1.3 (5 529 -1 1 1 1 4 112 0) (2 529 -1 1 1 1 4 46 0) (10 529 -1 1 1 1 4 222 0) (4 529 -1 1 1 1 4 90 0) (20 529 -1 1 1 1 6 47 0) (8 529 -1 1 1 1 4 178 0) (40 529 -1 1 1 1 6 91 0) (16 529 -1 1 1 1 4 354 0) (80 529 -1 1 1 1 6 179 0) (3 537 -1 0 41 1 0 67 0) (9 537 -1 0 41 1 0 199 0) (27 537 -1 0 41 1 1 66 0) (2 537 -1 0 41 1 0 45 0) (6 537 -1 0 41 1 0 133 0) (18 537 -1 0 41 1 1 66 0) (54 537 -1 0 41 1 1 132 0) (4 537 -1 0 41 1 0 89 0) (12 537 -1 0 41 1 0 265 0) (36 537 -1 0 41 1 1 66 0) (108 537 -1 0 41 1 1 198 0) (3 537 -1 0 4428 1 0 67 0) (9 537 -1 0 4428 1 0 199 0) (27 537 -1 0 4428 1 1 66 0) (2 537 -1 0 4428 1 0 45 0) (6 537 -1 0 4428 1 0 133 0) (18 537 -1 0 4428 1 1 66 0) (54 537 -1 0 4428 1 1 132 0) (4 537 -1 0 4428 1 0 89 0) (12 537 -1 0 4428 1 0 265 0) (36 537 -1 0 4428 1 1 66 0) (108 537 -1 0 4428 1 1 198 0) (3 537 1 0 4428 1 0 78 0) (9 537 1 0 4428 1 0 210 0) (27 537 1 0 4428 1 1 77 0) (2 537 1 0 4428 1 0 56 0) (6 537 1 0 4428 1 0 144 0) (18 537 1 0 4428 1 1 55 0) (54 537 1 0 4428 1 1 143 0) (4 537 1 0 4428 1 0 100 0) (12 537 1 0 4428 1 0 276 0) (36 537 1 0 4428 1 1 77 0) (108 537 1 0 4428 1 1 209 0) (5 529 1 1 1 1 5 125 0) (2 529 1 1 1 1 5 59 0) (10 529 1 1 1 1 5 235 0) (4 529 1 1 1 1 5 103 0) (20 529 1 1 1 1 6 58 0) (8 529 1 1 1 1 5 191 0) (40 529 1 1 1 1 6 102 0) (16 529 1 1 1 1 5 367 0) (80 529 1 1 1 1 6 190 0) (3 537 1 0 41 1 0 78 0) (9 537 1 0 41 1 0 210 0) (27 537 1 0 41 1 1 77 0) (2 537 1 0 41 1 0 56 0) (6 537 1 0 41 1 0 144 0) (18 537 1 0 41 1 1 77 0) (54 537 1 0 41 1 1 143 0) (4 537 1 0 41 1 0 100 0) (12 537 1 0 41 1 0 276 0) (36 537 1 0 41 1 1 77 0) (108 537 1 0 41 1 1 209 0))
\ No newline at end of file
--- a/test/examples/apoa1-andersen/apoa1-out.coor
+++ b/test/examples/apoa1-andersen/apoa1-out.coor
--- a/test/examples/apoa1-andersen/apoa1-out.vel
+++ b/test/examples/apoa1-andersen/apoa1-out.vel
--- a/test/examples/apoa1-andersen/apoa1-out.xsc
+++ b/test/examples/apoa1-andersen/apoa1-out.xsc
+# NAMD extended system configuration output file
+#$LABELS step a_x a_y a_z b_x b_y b_z c_x c_y c_z o_x o_y o_z
+500 106.961377282 0 0 0 106.961377282 0 0 0 76.4009837728 0 0 0
--- a/test/examples/apoa1-andersen/apoa1.log
+++ b/test/examples/apoa1-andersen/apoa1.log