Added aflow parser, minor fix to metainfo

Author: ladinesa

.gitmodules

@@ -207,3 +207,6 @@
 [submodule "dependencies/parsers/xps"]
 	path = dependencies/parsers/xps
 	url = https://github.com/nomad-coe/nomad-parser-xps.git
+[submodule "dependencies/parsers/aflow"]
+	path = dependencies/parsers/aflow
+	url = https://github.com/nomad-coe/nomad-parser-aflow.git

dependencies/parsers/aflow

@@ -1472,7 +1472,7 @@ class BaseCalculation(MSection):
         categories=[FastAccess])
 
     n_references = Quantity(
-        type=np.dtype(np.float64),
+        type=np.dtype(np.int32),
         shape=[],
         description='''
          Number of references to the current section calculation.

nomad/datamodel/metainfo/simulation/calculation.py

@@ -24,7 +24,7 @@
 from nomad.datamodel.metainfo.simulation.method import Method
 from nomad.datamodel.metainfo.simulation.system import System
 from nomad.datamodel.metainfo.simulation.calculation import Calculation
-
+from nomad.datamodel.metainfo.common import FastAccess
 
 m_package = Package()
 
@@ -175,41 +175,6 @@ class MessageRun(MSection):
         ''')
 
 
-class RunReference(MSection):
-    '''
-    Section that describes the relationship between the current section to other run
-    sections.
-
-    The kind of relationship between the the current section and the referenced section
-    run is described by kind. The referenced section is given by value (typically used for
-    a run section in the same archive) or external_url.
-    '''
-
-    m_def = Section(validate=False)
-
-    external_url = Quantity(
-        type=str,
-        shape=[],
-        description='''
-        URL used to reference an externally stored run section.
-        ''')
-
-    kind = Quantity(
-        type=str,
-        shape=[],
-        description='''
-        Defines the kind of relationship between the referenced section run with the
-        present section.
-        ''')
-
-    value = Quantity(
-        type=Reference(SectionProxy('Run')),
-        shape=[],
-        description='''
-        Value of the referenced section run.
-        ''')
-
-
 class Run(MSection):
     '''
     Every section run represents a single call of a program.
@@ -240,6 +205,31 @@ class Run(MSection):
         An optional calculation id, if one is found in the code input/output files.
         ''')
 
+    starting_run_ref = Quantity(
+        type=Reference(SectionProxy('Run')),
+        shape=[],
+        description='''
+        Links the current section run to a section run containing the calculations from
+        which the current section starts.
+        ''',
+        categories=[FastAccess])
+
+    n_references = Quantity(
+        type=np.dtype(np.int32),
+        shape=[],
+        description='''
+         Number of references to the current section calculation.
+        ''')
+
+    runs_ref = Quantity(
+        type=Reference(SectionProxy('Run')),
+        shape=['n_references'],
+        description='''
+        Links the the current section to other run sections. Such a link is necessary for
+        example for workflows that may contain a series of runs.
+        ''',
+        categories=[FastAccess])
+
     program = SubSection(sub_section=Program.m_def)
 
     time_run = SubSection(sub_section=TimeRun.m_def)
@@ -252,7 +242,5 @@ class Run(MSection):
 
     calculation = SubSection(sub_section=Calculation.m_def, repeats=True)
 
-    run_ref = SubSection(sub_section=RunReference.m_def, repeats=True)
-
 
 m_package.__init_metainfo__()

nomad/datamodel/metainfo/simulation/run.py

@@ -6,7 +6,7 @@
     Reference, MEnum, derived)
 from nomad.metainfo.search_extension import Search
 from nomad.datamodel.metainfo.simulation.calculation import Calculation
-from nomad.datamodel.metainfo.simulation.run import RunReference
+from nomad.datamodel.metainfo.simulation.run import Run
 from .common import FastAccess
 
 
@@ -1141,40 +1141,6 @@ class SinglePoint(MSection):
         ''')
 
 
-class WorkflowReference(MSection):
-    '''
-    Section that provides a link between a section to a section workflow. Such a link is
-    necessary for example between an Debye model that uses a the poisson ratio calculated
-    from an elastic workflow. The relationship should be described by kind and the
-    referred section workflow is given by value. An external url can also be provided in
-    place of value.
-    '''
-
-    m_def = Section(validate=False)
-
-    kind = Quantity(
-        type=str,
-        shape=[],
-        description='''
-        Defines the relationship between the referenced section workflow and the present
-        section.
-        ''')
-
-    external_url = Quantity(
-        type=str,
-        shape=[],
-        description='''
-        URL used to reference an externally stored section workflow.
-        ''')
-
-    value = Quantity(
-        type=Reference(SectionProxy('Workflow')),
-        shape=[],
-        description='''
-        Value of the referenced section wofklow.
-        ''')
-
-
 class Workflow(MSection):
     '''
     Section containing the  results of a workflow.
@@ -1224,6 +1190,31 @@ class Workflow(MSection):
         simulation.
         ''')
 
+    run_ref = Quantity(
+        type=Reference(Run.m_def),
+        shape=[],
+        description='''
+        Links the section workflow to the section run that contains the calculations.
+        ''',
+        categories=[FastAccess])
+
+    n_references = Quantity(
+        type=np.dtype(np.int32),
+        shape=[],
+        description='''
+         Number of references to the current section workflow.
+        ''')
+
+    workflows_ref = Quantity(
+        type=Reference(SectionProxy('Workflow')),
+        shape=['n_references'],
+        description='''
+        Links the the current section to other workflow sections. Such a link is necessary
+        for example between an Debye model that uses a the poisson ratio calculated
+        from an elastic workflow.
+        ''',
+        categories=[FastAccess])
+
     single_point = SubSection(
         sub_section=SinglePoint.m_def,
         # TODO determine if there is a need for this to be a repeating section
@@ -1280,9 +1271,3 @@ class Workflow(MSection):
     thermodynamics = SubSection(
         sub_section=Thermodynamics.m_def,
         repeats=False)
-
-    workflow_ref = SubSection(
-        sub_section=WorkflowReference.m_def, repeats=True)
-
-    run_ref = SubSection(
-        sub_section=RunReference.m_def, repeats=True)

nomad/datamodel/metainfo/workflow.py

@@ -383,7 +383,7 @@ def set_thermo_property(name):
                         values.append(quantity.magnitude if hasattr(quantity, 'magnitude') else quantity)
                 except Exception:
                     pass
-            unit = quantity.unit if hasattr(quantity, 'unit') else 1.0
+            unit = quantity.units if hasattr(quantity, 'units') else 1.0
             setattr(self.section, name, np.array(values) * unit)
 
         if not self.section.temperature:

nomad/normalizing/workflow.py

@@ -72,6 +72,7 @@
 from openkimparser import OpenKIMParser
 from xpsparser import XPSParser
 from eelsdbparser import EELSDBParser
+from aflowparser import AFLOWParser
 # TODO
 # from mpesparser import MPESParser
 # from aptfimparser import APTFIMParser
@@ -216,6 +217,7 @@ def match_parser(mainfile_path: str, strict=True) -> Parser:
     # APTFIMParser(),
     EELSDBParser(),
     XPSParser(),
+    AFLOWParser(),
     ArchiveParser()
 ]