From 3e58c0dd55681c6f719b80dac3eeade2da9a3608 Mon Sep 17 00:00:00 2001
From: Fawzi Mohamed <fawzi.mohamed@fhi-berlin.mpg.de>
Date: Tue, 29 Jan 2019 14:53:12 +0100
Subject: [PATCH] meta 2.0 changes
---
parser/parser-qbox/QboxInputParser.py | 12 +++++-----
parser/parser-qbox/QboxParser.py | 22 ++++++++++---------
.../eu/nomad_lab/parsers/QboxParser.scala | 2 +-
3 files changed, 19 insertions(+), 17 deletions(-)
diff --git a/parser/parser-qbox/QboxInputParser.py b/parser/parser-qbox/QboxInputParser.py
index 12c10dca..9e232dbb 100644
--- a/parser/parser-qbox/QboxInputParser.py
+++ b/parser/parser-qbox/QboxInputParser.py
@@ -79,8 +79,8 @@ class QboxInputParserContext(object):
backend.addValue("sampling_method", sampling_method)
backend.closeSection("section_sampling_method", samplingGIndex)
frameSequenceGIndex = backend.openSection("section_frame_sequence")
- backend.addValue("frame_sequence_to_sampling_ref", samplingGIndex)
- backend.addArrayValues("frame_sequence_local_frames_ref", np.asarray(self.singleConfCalcs))
+ backend.addValue("frame_sequence_to_sampling_method_ref", samplingGIndex)
+ backend.addArrayValues("frame_sequence_to_frames_ref", np.asarray(self.singleConfCalcs))
backend.closeSection("section_frame_sequence", frameSequenceGIndex)
@@ -108,9 +108,9 @@ class QboxInputParserContext(object):
if not nomadNames:
raise Exception("Unhandled xc functional %s found" % functional)
for name in nomadNames:
- s = backend.openSection("section_XC_functionals")
- backend.addValue('XC_functional_name', name)
- backend.closeSection("section_XC_functionals", s)
+ s = backend.openSection("section_xc_functionals")
+ backend.addValue('xc_functional_name', name)
+ backend.closeSection("section_xc_functionals", s)
@@ -171,7 +171,7 @@ class QboxInputParserContext(object):
def onClose_section_single_configuration_calculation(self, backend, gIndex, section):
# write the references to section_method and section_system
- backend.addValue('single_configuration_to_calculation_method_ref', self.secMethodIndex)
+ backend.addValue('single_configuration_calculation_to_method_ref', self.secMethodIndex)
backend.addValue('single_configuration_calculation_to_system_ref', self.secSystemDescriptionIndex)
diff --git a/parser/parser-qbox/QboxParser.py b/parser/parser-qbox/QboxParser.py
index a65db215..d19c2dfb 100644
--- a/parser/parser-qbox/QboxParser.py
+++ b/parser/parser-qbox/QboxParser.py
@@ -80,8 +80,8 @@ class QboxParserContext(object):
backend.addValue("sampling_method", sampling_method)
backend.closeSection("section_sampling_method", samplingGIndex)
frameSequenceGIndex = backend.openSection("section_frame_sequence")
- backend.addValue("frame_sequence_to_sampling_ref", samplingGIndex)
- backend.addArrayValues("frame_sequence_local_frames_ref", np.asarray(self.singleConfCalcs))
+ backend.addValue("frame_sequence_to_sampling_method_ref", samplingGIndex)
+ backend.addArrayValues("frame_sequence_to_frames_ref", np.asarray(self.singleConfCalcs))
backend.closeSection("section_frame_sequence", frameSequenceGIndex)
@@ -136,9 +136,9 @@ class QboxParserContext(object):
if not nomadNames:
raise Exception("Unhandled xc functional %s found" % functional)
for name in nomadNames:
- s = backend.openSection("section_XC_functionals")
- backend.addValue('XC_functional_name', name)
- backend.closeSection("section_XC_functionals", s)
+ s = backend.openSection("section_xc_functionals")
+ backend.addValue('xc_functional_name', name)
+ backend.closeSection("section_xc_functionals", s)
@@ -229,7 +229,9 @@ class QboxParserContext(object):
atom_force.append(api)
if atom_force:
# need to transpose array since its shape is [number_of_atoms,3] in the metadata
- backend.addArrayValues('atom_forces', np.transpose(np.asarray(atom_force)))
+ fId = backend.openSection('section_atom_forces')
+ backend.addArrayValues('atom_forces', np.transpose(np.asarray(atom_force)))
+ backend.closeSection('section_atom_forces', fId)
#----4. unit_cell
@@ -250,7 +252,7 @@ class QboxParserContext(object):
def onClose_section_single_configuration_calculation(self, backend, gIndex, section):
# write the references to section_method and section_system
- backend.addValue('single_configuration_to_calculation_method_ref', self.secMethodIndex)
+ backend.addValue('single_configuration_calculation_to_method_ref', self.secMethodIndex)
backend.addValue('single_configuration_calculation_to_system_ref', self.secSystemDescriptionIndex)
@@ -421,13 +423,13 @@ def build_QboxMainFileSimpleMatcher():
])
####################################################################
- # (4.1) submatcher for properties : MLWF (x_qbox_section_MLWF)
+ # (4.1) submatcher for properties : MLWF (x_qbox_section_mlwf)
####################################################################
MLWFSubMatcher = SM(name = 'MLWF',
startReStr = r"\s*<mlwfs>",
- sections = ["x_qbox_section_MLWF"],
+ sections = ["x_qbox_section_mlwf"],
subMatchers = [
- SM (r"\s*<mlwf center=\"\s*(?P<x_qbox_geometry_MLWF_atom_positions_x__bohr>[-+0-9.]+)\s+(?P<x_qbox_geometry_MLWF_atom_positions_y__bohr>[-+0-9.]+)\s+(?P<x_qbox_geometry_MLWF_atom_positions_z__bohr>[-+0-9.]+)\s*\"\s+spread=\"\s*(?P<x_qbox_geometry_MLWF_atom_spread__bohr>[-+0-9.]+)\s*\"", repeats = True)
+ SM (r"\s*<mlwf center=\"\s*(?P<x_qbox_geometry_mlwf_atom_positions_x__bohr>[-+0-9.]+)\s+(?P<x_qbox_geometry_mlwf_atom_positions_y__bohr>[-+0-9.]+)\s+(?P<x_qbox_geometry_mlwf_atom_positions_z__bohr>[-+0-9.]+)\s*\"\s+spread=\"\s*(?P<x_qbox_geometry_mlwf_atom_spread__bohr>[-+0-9.]+)\s*\"", repeats = True)
])
diff --git a/src/main/scala/eu/nomad_lab/parsers/QboxParser.scala b/src/main/scala/eu/nomad_lab/parsers/QboxParser.scala
index 162fcc79..5448980b 100644
--- a/src/main/scala/eu/nomad_lab/parsers/QboxParser.scala
+++ b/src/main/scala/eu/nomad_lab/parsers/QboxParser.scala
@@ -56,7 +56,7 @@ object QboxParser extends SimpleExternalParserGenerator(
"parser-qbox/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/qbox.nomadmetainfo.json"
) ++ DefaultPythonInterpreter.commonFiles(),
dirMap = Map(
--
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