diff --git a/parser/parser-gromacs/GromacsParser.py b/parser/parser-gromacs/GromacsParser.py index 0aa2f3733ceb5138b05cf28b7629751d63cb15ad..76070b986779640f4813b5ca9845288572561296 100644 --- a/parser/parser-gromacs/GromacsParser.py +++ b/parser/parser-gromacs/GromacsParser.py @@ -595,11 +595,13 @@ class GromacsParser(SmartParser.ParserBase): self.MDnextstep = steps[-1] + 1 if self.MDcurrentstep in logsteps: self.MDlogstep = self.MDcurrentstep - self.MDlogsteps.pop(0) + if len(self.MDlogsteps)>1: + self.MDlogsteps.pop(0) if len(self.MDlogsteps)>0: self.MDnextlogstep=self.MDlogsteps[0] else: - self.MDnextlogstep=logsteps[-1] + 1 + if len(logsteps)>0: + self.MDnextlogstep=logsteps[-1] self.stepcontrolDict.update({"nextlogsteps" : logsteps}) self.stepcontrolDict.update({"MDcurrentstep" : self.MDcurrentstep}) self.stepcontrolDict.update({"MDcurrenttime" : self.MDcurrentstep*timestep}) diff --git a/src/test/scala/eu/nomad_lab/parsers/GromacsParserSpec.scala b/src/test/scala/eu/nomad_lab/parsers/GromacsParserSpec.scala index 164d2f1224d23da26317f81fae87d16388231af1..f38025fea6a89cf6f5db250e8f9739d1116f7d8b 100644 --- a/src/test/scala/eu/nomad_lab/parsers/GromacsParserSpec.scala +++ b/src/test/scala/eu/nomad_lab/parsers/GromacsParserSpec.scala @@ -3,34 +3,52 @@ package eu.nomad_lab.parsers import org.specs2.mutable.Specification object GromacsParserTests extends Specification { - "GromacsParserTest" >> { -// "[aminoacids] test with json-events" >> { -// ParserRun.parse(GromacsParser, "parsers/gromacs/test/examples/aminoacids/md.log", "json-events") must_== ParseResult.ParseSuccess -// } -// "[aminoacids] test with json" >> { -// ParserRun.parse(GromacsParser, "parsers/gromacs/test/examples/aminoacids/md.log", "json") must_== ParseResult.ParseSuccess -// } -// "[argon] test with json-events" >> { -// ParserRun.parse(GromacsParser, "parsers/gromacs/test/examples/argon/md.log", "json-events") must_== ParseResult.ParseSuccess -// } -// "[argon] test with json" >> { -// ParserRun.parse(GromacsParser, "parsers/gromacs/test/examples/argon/md.log", "json") must_== ParseResult.ParseSuccess -// } -// "[water] test with json-events" >> { -// ParserRun.parse(GromacsParser, "parsers/gromacs/test/examples/water/md.log", "json-events") must_== ParseResult.ParseSuccess -// } -// "[water] test with json" >> { -// ParserRun.parse(GromacsParser, "parsers/gromacs/test/examples/water/md.log", "json") must_== ParseResult.ParseSuccess -// } -// "[tip4p] test with json-events" >> { -// ParserRun.parse(GromacsParser, "parsers/gromacs/test/examples/tip4p/md.log", "json-events") must_== ParseResult.ParseSuccess -// } -// "[tip4p] test with json" >> { -// ParserRun.parse(GromacsParser, "parsers/gromacs/test/examples/tip4p/md.log", "json") must_== ParseResult.ParseSuccess -// } + "GromacsParserTest_1" >> { + "[aminoacids] test with json-events" >> { + ParserRun.parse(GromacsParser, "parsers/gromacs/test/examples/aminoacids/md.log", "json-events") must_== ParseResult.ParseSuccess + } + } + "GromacsParserTest_2" >> { + "[aminoacids] test with json" >> { + ParserRun.parse(GromacsParser, "parsers/gromacs/test/examples/aminoacids/md.log", "json") must_== ParseResult.ParseSuccess + } + } + "GromacsParserTest_3" >> { + "[argon] test with json-events" >> { + ParserRun.parse(GromacsParser, "parsers/gromacs/test/examples/argon/md.log", "json-events") must_== ParseResult.ParseSuccess + } + } + "GromacsParserTest_4" >> { + "[argon] test with json" >> { + ParserRun.parse(GromacsParser, "parsers/gromacs/test/examples/argon/md.log", "json") must_== ParseResult.ParseSuccess + } + } + "GromacsParserTest_5" >> { + "[water] test with json-events" >> { + ParserRun.parse(GromacsParser, "parsers/gromacs/test/examples/water/md.log", "json-events") must_== ParseResult.ParseSuccess + } + } + "GromacsParserTest_6" >> { + "[water] test with json" >> { + ParserRun.parse(GromacsParser, "parsers/gromacs/test/examples/water/md.log", "json") must_== ParseResult.ParseSuccess + } + } + "GromacsParserTest_7" >> { + "[tip4p] test with json-events" >> { + ParserRun.parse(GromacsParser, "parsers/gromacs/test/examples/tip4p/md.log", "json-events") must_== ParseResult.ParseSuccess + } + } + "GromacsParserTest_8" >> { + "[tip4p] test with json" >> { + ParserRun.parse(GromacsParser, "parsers/gromacs/test/examples/tip4p/md.log", "json") must_== ParseResult.ParseSuccess + } + } + "GromacsParserTest_9" >> { "[Fe] test with json-events" >> { ParserRun.parse(GromacsParser, "parsers/gromacs/test/examples/fe_test/md.log", "json-events") must_== ParseResult.ParseSuccess } + } + "GromacsParserTest_10" >> { "[Fe] test with json" >> { ParserRun.parse(GromacsParser, "parsers/gromacs/test/examples/fe_test/md.log", "json") must_== ParseResult.ParseSuccess }