diff --git a/dependencies/parsers/vasp b/dependencies/parsers/vasp
index 8776a0bc7b32fb51e98ea8fe7af7d5630240edd3..2c8b7763eae8a27e7c1ca3a8ce86533978f42f73 160000
--- a/dependencies/parsers/vasp
+++ b/dependencies/parsers/vasp
@@ -1 +1 @@
-Subproject commit 8776a0bc7b32fb51e98ea8fe7af7d5630240edd3
+Subproject commit 2c8b7763eae8a27e7c1ca3a8ce86533978f42f73
diff --git a/nomad/cli/parse.py b/nomad/cli/parse.py
index cadec1d8dbea1979337a44dd0db4a98b18b6575f..32f8b5ab80f8e5e34ceec99577fb0ce3f2af496e 100644
--- a/nomad/cli/parse.py
+++ b/nomad/cli/parse.py
@@ -48,8 +48,9 @@ def parse(
if isinstance(parser_backend, MSection):
backend = Backend(parser._metainfo_env, parser.domain)
- root_section = str(datamodel.domains[parser.domain]['root_section'])
- setattr(backend.entry_archive, root_section, parser_backend)
+ root_section = parser_backend.m_def.name
+ section_def = getattr(datamodel.EntryArchive, root_section)
+ backend.entry_archive.m_add_sub_section(section_def, parser_backend)
backend.resource.add(parser_backend)
parser_backend = backend
diff --git a/nomad/datamodel/metainfo/public.py b/nomad/datamodel/metainfo/public.py
index fda3cf773ba7753971c2007e25c3e1a7bb50e4b3..8bef14b727bfbdb6f2bd03c0a509fff22771d08a 100644
--- a/nomad/datamodel/metainfo/public.py
+++ b/nomad/datamodel/metainfo/public.py
@@ -3439,6 +3439,11 @@ class section_run(MSection):
repeats=True,
a_legacy=LegacyDefinition(name='section_system'))
+ section_workflow = SubSection(
+ sub_section=SectionProxy('section_workflow'),
+ repeats=True
+ )
+
class section_sampling_method(MSection):
'''
@@ -5575,4 +5580,37 @@ class section_XC_functionals(MSection):
a_legacy=LegacyDefinition(name='XC_functional_weight'))
+class section_workflow(MSection):
+ '''
+ Section containing the results of a workflow.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_workflow'))
+
+ workflow_type = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ The type of calculation workflow. Can be one of relaxation, elastic, phonon,
+ molecular dynamics.
+ ''',
+ a_legacy=LegacyDefinition(name='workflow_type'))
+
+ relaxation_energy_tolerance = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ The tolerance value in the energy between relaxation steps for convergence.
+ ''',
+ a_legacy=LegacyDefinition(name='relaxation_energy_tolerance'))
+
+ workflow_final_calculation_ref = Quantity(
+ type=Reference(SectionProxy('section_single_configuration_calculation')),
+ shape=[],
+ description='''
+ Reference to last calculation step.
+ ''')
+
+
m_package.__init_metainfo__()
diff --git a/nomad/parsing/legacy.py b/nomad/parsing/legacy.py
index 2cabcf9389bdb7aaad77cf68f2e56b0be3eb3071..0fdd0cfeab3b1de9cd5d645188f19d45b6a94952 100644
--- a/nomad/parsing/legacy.py
+++ b/nomad/parsing/legacy.py
@@ -244,11 +244,14 @@ class Backend(AbstractParserBackend):
if section_def.extends_base_section:
section_def = section_def.base_sections[0]
+ section = self.__open_sections.get((section_def, -1), None)
+ if not section:
+ section = self.open_sections[(section_def, -1)]
if isinstance(property_def, Quantity):
- return self.__open_sections[(section_def, -1)].m_get(property_def)
+ return section.m_get(property_def)
elif isinstance(property_def, SubSection):
- return self.__open_sections[(section_def, -1)].m_get_sub_sections(property_def)
+ return section.m_get_sub_sections(property_def)
def metaInfoEnv(self):
if self.__legacy_env is None:
@@ -302,6 +305,12 @@ class Backend(AbstractParserBackend):
section = self.resolve_context(context_uri)
self.__close(section)
+ @property
+ def open_sections(self):
+ for section in self.entry_archive.m_all_contents():
+ self.__open(section)
+ return self.__open_sections
+
def __open(self, section):
if section.m_parent_index != -1:
self.__open_sections[(section.m_def, section.m_parent_index)] = section
@@ -357,7 +366,9 @@ class Backend(AbstractParserBackend):
if section_def.extends_base_section:
section_def = section_def.base_sections[0]
- section = self.__open_sections[(section_def, g_index)]
+ section = self.__open_sections.get((section_def, g_index), None)
+ if not section:
+ section = self.open_sections[(section_def, g_index)]
return section, quantity_def
diff --git a/nomad/parsing/parsers.py b/nomad/parsing/parsers.py
index c477e0dcbe9d706f6212a4c418f8b25aa91aefce..fa142373b3637313323ad49dbfd402870f61c66d 100644
--- a/nomad/parsing/parsers.py
+++ b/nomad/parsing/parsers.py
@@ -24,6 +24,7 @@ from .artificial import EmptyParser, GenerateRandomParser, TemplateParser, Chaos
from eelsparser import EelsParser
from mpesparser import MPESParser
from aptfimparser import APTFIMParser
+from vaspparser import VASPParser
try:
# these packages are not available without parsing extra, which is ok, if the
@@ -121,18 +122,7 @@ parsers = [
# mainfile_contents_re=r'', # Empty regex since this code calls other DFT codes.
mainfile_name_re=(r'.*/phonopy-FHI-aims-displacement-0*1/control.in$')
),
- LegacyParser(
- name='parsers/vasp', code_name='VASP', code_homepage='https://www.vasp.at/',
- parser_class_name='vaspparser.VASPRunParser',
- mainfile_mime_re=r'(application/.*)|(text/.*)',
- mainfile_contents_re=(
- r'^\s*<\?xml version="1\.0" encoding="ISO-8859-1"\?>\s*'
- r'?\s*<modeling>'
- r'?\s*<generator>'
- r'?\s*<i name="program" type="string">\s*vasp\s*</i>'
- r'?'),
- supported_compressions=['gz', 'bz2', 'xz']
- ),
+ VASPParser(),
VaspOutcarParser(
name='parsers/vasp-outcar', code_name='VASP', code_homepage='https://www.vasp.at/',
parser_class_name='vaspparser.VaspOutcarParser',
diff --git a/nomad/processing/data.py b/nomad/processing/data.py
index fc51648500eda6195bf6ef4c009c829596785d00..4bed0ae4eccb1a9d3e0188eb8c5dca03974d2528 100644
--- a/nomad/processing/data.py
+++ b/nomad/processing/data.py
@@ -388,8 +388,9 @@ class Calc(Proc):
if isinstance(self._parser_backend, MSection):
backend = Backend(parser._metainfo_env, parser.domain)
- root_section = datamodel.domains[parser.domain]['root_section']
- setattr(backend.entry_archive, root_section, self._parser_backend)
+ root_section = self._parser_backend.m_def.name
+ section_def = getattr(datamodel.EntryArchive, root_section)
+ backend.entry_archive.m_add_sub_section(section_def, self._parser_backend)
backend.resource.add(self._parser_backend)
self._parser_backend = backend
diff --git a/tests/test_parsing.py b/tests/test_parsing.py
index 64520336f469c8689c0df97808948efcd3f2ff0a..4378f0c0e763063ab3fa39103f5465393d269057 100644
--- a/tests/test_parsing.py
+++ b/tests/test_parsing.py
@@ -289,13 +289,22 @@ def create_reference(data, pretty):
return json.dumps(data, separators=(',', ':'))
-def assert_parser_result(backend, error=False):
- status, errors = backend.status
- assert status == 'ParseSuccess'
- if error:
- assert len(errors) > 0
- else:
- assert errors is None or len(errors) == 0
+@pytest.fixture(scope='function')
+def assert_parser_result(caplog):
+ def _assert(backend, error=False):
+ status, errors = backend.status
+ assert status == 'ParseSuccess'
+ if error:
+ if not errors:
+ errors = []
+ for record in caplog.get_records(when='call'):
+ if record.levelname in ['WARNING', 'ERROR', 'CRITICAL']:
+ errors.append(record.msg)
+ assert len(errors) > 0
+ else:
+ assert errors is None or len(errors) == 0
+
+ return _assert
def assert_parser_dir_unchanged(previous_wd, current_wd):
@@ -308,8 +317,9 @@ def run_parser(parser_name, mainfile):
result = parser.run(mainfile, logger=utils.get_logger(__name__))
if isinstance(result, MSection):
backend = Backend(parser._metainfo_env, parser.domain)
- root_section = datamodel.domains[parser.domain]['root_section']
- setattr(backend.entry_archive, root_section, result)
+ root_section = result.m_def.name
+ section_def = getattr(datamodel.EntryArchive, root_section)
+ backend.entry_archive.m_add_sub_section(section_def, result)
backend.resource.add(result)
result = backend
result.domain = parser.domain
@@ -357,7 +367,7 @@ def add_calculation_info(backend: Backend, **kwargs) -> Backend:
@pytest.mark.parametrize('parser_name, mainfile', parser_examples)
-def test_parser(parser_name, mainfile):
+def test_parser(parser_name, mainfile, assert_parser_result):
previous_wd = os.getcwd() # Get Working directory before parsing.
parsed_example = run_parser(parser_name, mainfile)
assert_parser_result(parsed_example)
@@ -365,7 +375,7 @@ def test_parser(parser_name, mainfile):
assert_parser_dir_unchanged(previous_wd, current_wd=os.getcwd())
-def test_broken_xml_vasp():
+def test_broken_xml_vasp(assert_parser_result):
parser_name, mainfile = 'parsers/vasp', 'tests/data/parsers/vasp/broken.xml'
previous_wd = os.getcwd() # Get Working directory before parsing.
parsed_example = run_parser(parser_name, mainfile)