Minor metainfo refactor, new parsers

atomistic @ 725ed6ca

-Subproject commit ef6209c60f3a4a92b5411f9bdef1dd7a326ed32c
+Subproject commit 725ed6ca3b65fe44e7ab9023ded2db5f84a6a880

electronic @ d1eaaf31

-Subproject commit eee9bd051c3c52e3560cdb8092f79488dee05009
+Subproject commit d1eaaf31da27402c33d90559d3f21af7ee9a2294

workflow @ e1dc7c53

-Subproject commit 4050431cce67d80793e548e7f79e44de7e95ecb8
+Subproject commit e1dc7c53061d5cf282e3784578d43c38bc972c82

nomad/datamodel/metainfo/simulation/calculation.py

@@ -126,6 +126,7 @@ class AtomicValues(MSection):
 
     m_def = Section(validate=False)
 
+    # TODO rename this to spin_channel
     spin = Quantity(
         type=np.dtype(np.int32),
         shape=[],
@@ -210,6 +211,7 @@ class EnergyEntry(Atomic):
         cell.
         ''')
 
+    # TODO rename this to value_atomic
     values_per_atom = Quantity(
         type=np.dtype(np.float64),
         shape=['n_atoms'],
@@ -409,6 +411,38 @@ class Energy(MSection):
         ''',
         repeats=True)
 
+    enthalpy = Quantity(
+        type=np.dtype(np.float64),
+        shape=[],
+        unit='joule',
+        description='''
+        Value of the calculated enthalpy per cell i.e. energy_total + pressure * volume.
+        ''')
+
+    entropy = Quantity(
+        type=np.dtype(np.float64),
+        shape=[],
+        unit='joule / kelvin',
+        description='''
+        Value of the entropy.
+        ''')
+
+    chemical_potential = Quantity(
+        type=np.dtype(np.float64),
+        shape=[],
+        unit='joule',
+        description='''
+        Value of the chemical potential.
+        ''')
+
+    internal = Quantity(
+        type=np.dtype(np.float64),
+        shape=[],
+        unit='joule',
+        description='''
+        Value of the internal energy.
+        ''')
+
     # TODO remove this should be be entropy.correction
     correction_entropy = SubSection(
         sub_section=EnergyEntry.m_def,
@@ -529,38 +563,6 @@ class Forces(MSection):
         corresponding to the minus gradient of energy_T0.
         ''')
 
-    enthalpy = Quantity(
-        type=np.dtype(np.float64),
-        shape=[],
-        unit='joule',
-        description='''
-        Value of the calculated enthalpy per cell i.e. energy_total + pressure * volume.
-        ''')
-
-    entropy = Quantity(
-        type=np.dtype(np.float64),
-        shape=[],
-        unit='joule / kelvin',
-        description='''
-        Value of the entropy.
-        ''')
-
-    chemical_potential = Quantity(
-        type=np.dtype(np.float64),
-        shape=[],
-        unit='joule',
-        description='''
-        Value of the chemical potential.
-        ''')
-
-    internal = Quantity(
-        type=np.dtype(np.float64),
-        shape=[],
-        unit='joule',
-        description='''
-        Value of the internal energy.
-        ''')
-
     contributions = SubSection(
         sub_section=ForcesEntry.m_def,
         description='''
@@ -646,6 +648,20 @@ class ChargesValue(AtomicValues):
         Value of the charge projected on atom and orbital.
         ''')
 
+    n_electrons = Quantity(
+        type=np.dtype(np.float64),
+        shape=[],
+        description='''
+        Value of the number of electrons projected on atom and orbital.
+        ''')
+
+    spin_z = Quantity(
+        type=np.dtype(np.float64),
+        shape=[],
+        description='''
+        Value of the azimuthal spin projected on atom and orbital.
+        ''')
+
 
 class Charges(Atomic):
     '''
@@ -670,6 +686,15 @@ class Charges(Atomic):
         Value of the atomic charges calculated through analysis_method.
         ''')
 
+    n_electrons = Quantity(
+        type=np.dtype(np.float64),
+        shape=['n_atoms'],
+        description='''
+        Value of the number of electrons on the atoms.
+        ''')
+
+    # TODO should this be on a separate section magnetic_moments or charges should be
+    # renamed population
     spins = Quantity(
         type=np.dtype(np.float64),
         shape=['n_atoms'],
@@ -1428,7 +1453,7 @@ class ExcitedStates(MSection):
         ''')
 
 
-class VibrationsValues(MSection):
+class VibrationalFrequenciesValues(MSection):
     '''
     Section describing a vibrational spectrum.
     '''
@@ -1472,7 +1497,7 @@ class VibrationsValues(MSection):
         ''')
 
 
-class Vibrations(MSection):
+class VibrationalFrequencies(MSection):
     '''
     Section containing results related to vibrational frequencies.
     '''
@@ -1491,12 +1516,14 @@ class Vibrations(MSection):
         shape=['n_frequencies'],
         unit='1 / meter',
         description='''
-        Values of vibration Frequenices (cm-1)
+        Values of vibrational frequencies (m-1)
         ''')
 
-    raman = SubSection(sub_section=VibrationsValues.m_def, repeats=False)
+    # TODO add normal modes
+
+    raman = SubSection(sub_section=VibrationalFrequenciesValues.m_def, repeats=False)
 
-    infrared = SubSection(sub_section=VibrationsValues.m_def, repeats=False)
+    infrared = SubSection(sub_section=VibrationalFrequenciesValues.m_def, repeats=False)
 
 
 class BaseCalculation(MSection):
@@ -1649,7 +1676,7 @@ class BaseCalculation(MSection):
 
     excited_states = SubSection(sub_section=ExcitedStates.m_def, repeats=True)
 
-    vibrational_frequencies = SubSection(sub_section=Vibrations.m_def, repeats=True)
+    vibrational_frequencies = SubSection(sub_section=VibrationalFrequencies.m_def, repeats=True)
 
     potential = SubSection(sub_section=Potential.m_def, repeats=True)