From 8f80ec98b36be628cdc98d90334213c1409e1c3c Mon Sep 17 00:00:00 2001
From: Fawzi Mohamed <fawzi.mohamed@fhi-berlin.mpg.de>
Date: Fri, 25 Jan 2019 23:05:13 +0100
Subject: [PATCH] meta 2.0 changes
---
parser/parser-dftb+/parser_dftb_plus.py | 6 ++++--
src/main/scala/eu/nomad_lab/parsers/DftbPlusParser.scala | 2 +-
.../scala/eu/nomad_lab/parsers/DftbPlusParserSpec.scala | 4 ++--
3 files changed, 7 insertions(+), 5 deletions(-)
diff --git a/parser/parser-dftb+/parser_dftb_plus.py b/parser/parser-dftb+/parser_dftb_plus.py
index 47a1e65..87034de 100644
--- a/parser/parser-dftb+/parser_dftb_plus.py
+++ b/parser/parser-dftb+/parser_dftb_plus.py
@@ -62,7 +62,9 @@ class dftb_plusContext(object):
if forces is not None:
atom_force.append(forces)
if atom_force:
+ fId = backend.openSection('section_atom_forces')
backend.addArrayValues('atom_forces', np.transpose(np.asarray(atom_force)))
+ backend.closeSection('section_atom_forces', fId)
def onClose_section_system(self, backend, gIndex, section):
@@ -101,7 +103,7 @@ mainFileDescription = SM(
sections = ['section_system','section_topology','section_molecule_type'],
subMatchers = [
SM(r"\s*Coordinates of moved atoms\s*\(?(au)?\)?:"),
- SM(r"\s*(?P<atom>\d+)\s*(?P<x_dftbp_atom_positions_X__bohr>[+-]?\d+\.\d+)\s*(?P<x_dftbp_atom_positions_Y__bohr>[+-]?\d+\.\d+)\s*(?P<x_dftbp_atom_positions_Z__bohr>[+-]?\d+\.\d+)\s*", repeats = True),
+ SM(r"\s*(?P<atom>\d+)\s*(?P<x_dftbp_atom_positions_x__bohr>[+-]?\d+\.\d+)\s*(?P<x_dftbp_atom_positions_y__bohr>[+-]?\d+\.\d+)\s*(?P<x_dftbp_atom_positions_z__bohr>[+-]?\d+\.\d+)\s*", repeats = True),
],
),
SM(name = 'charges',
@@ -159,7 +161,7 @@ mainFileDescription = SM(
sections = ['section_single_configuration_calculation'],
subMatchers = [
SM(r"\s*Total Forces*"),
- SM(r"\s*(?P<x_dftbp_atom_forces_X__forceAu>[+-]?\d+\.\d+E?[+-]?\d+)\s*(?P<x_dftbp_atom_forces_Y__forceAu>[+-]?\d+\.\d+E?[+-]?\d+)\s*(?P<x_dftbp_atom_forces_Z__forceAu>[+-]?\d+\.\d+E?[+-]?\d+)\s*", repeats = True),
+ SM(r"\s*(?P<x_dftbp_atom_forces_x__forceAu>[+-]?\d+\.\d+E?[+-]?\d+)\s*(?P<x_dftbp_atom_forces_y__forceAu>[+-]?\d+\.\d+E?[+-]?\d+)\s*(?P<x_dftbp_atom_forces_z__forceAu>[+-]?\d+\.\d+E?[+-]?\d+)\s*", repeats = True),
SM(r"\s*Maximal derivative component:\s*(?P<x_dftbp_force_max__forceAu>[+-]?\d+\.\d+E?[+-]?\d+)\s*(au)?"),
SM(r"\s*Max force for moved atoms::\s*(?P<x_dftbp_force_max_mov__forceAu>[+-]?\d+\.\d+E?[+-]?\d+)\s*(au)?"),
],
diff --git a/src/main/scala/eu/nomad_lab/parsers/DftbPlusParser.scala b/src/main/scala/eu/nomad_lab/parsers/DftbPlusParser.scala
index d00eefe..5a5c2ca 100644
--- a/src/main/scala/eu/nomad_lab/parsers/DftbPlusParser.scala
+++ b/src/main/scala/eu/nomad_lab/parsers/DftbPlusParser.scala
@@ -48,7 +48,7 @@ object DftbPlusParser extends SimpleExternalParserGenerator(
"parser-dftb+/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/meta.nomadmetainfo.json",
"nomad_meta_info/dftb_plus.nomadmetainfo.json"
) ++ DefaultPythonInterpreter.commonFiles(),
dirMap = Map(
diff --git a/src/test/scala/eu/nomad_lab/parsers/DftbPlusParserSpec.scala b/src/test/scala/eu/nomad_lab/parsers/DftbPlusParserSpec.scala
index 227b4f2..5fa4c92 100644
--- a/src/test/scala/eu/nomad_lab/parsers/DftbPlusParserSpec.scala
+++ b/src/test/scala/eu/nomad_lab/parsers/DftbPlusParserSpec.scala
@@ -21,10 +21,10 @@ import org.specs2.mutable.Specification
object DftbPlusTests extends Specification {
"DftbPlusParserTest" >> {
"test with json-events" >> {
- ParserRun.parse(DftbPlusParser, "parsers/dftbPlus/test/examples/detailed.out", "json-events") must_== ParseResult.ParseSuccess
+ ParserRun.parse(DftbPlusParser, "parsers/dftb-plus/test/examples/detailed.out", "json-events") must_== ParseResult.ParseSuccess
}
"test with json" >> {
- ParserRun.parse(DftbPlusParser, "parsers/dftbPlus/test/examples/detailed.out", "json") must_== ParseResult.ParseSuccess
+ ParserRun.parse(DftbPlusParser, "parsers/dftb-plus/test/examples/detailed.out", "json") must_== ParseResult.ParseSuccess
}
}
}
--
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