From 11d83dbed5472c2053e3f54a81c3b8a1e37926bc Mon Sep 17 00:00:00 2001
From: Berk Onat <b.onat@warwick.ac.uk>
Date: Wed, 24 Jan 2018 10:22:12 +0000
Subject: [PATCH] Fixed bug at step counter. Adding non-threaded tests.
---
parser/parser-gromacs/GromacsParser.py | 6 +-
.../nomad_lab/parsers/GromacsParserSpec.scala | 68 ++++++++++++-------
2 files changed, 47 insertions(+), 27 deletions(-)
diff --git a/parser/parser-gromacs/GromacsParser.py b/parser/parser-gromacs/GromacsParser.py
index 0aa2f37..76070b9 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 164d2f1..f38025f 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
}
--
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