Merge branch 'new-parsers' into 'v1.0.7'

Implemented new full parsers, minor metainfo updates

See merge request !593

atomistic @ 7a57120d

-Subproject commit 958d4f2ef91563791ebfe6b329fae5615d992024
+Subproject commit 7a57120d6b4845f471577af75ad3e205ee503ea5

electronic @ eee9bd05

-Subproject commit 122d8347e79cd4e77adfcc6db4962b10b6075801
+Subproject commit eee9bd051c3c52e3560cdb8092f79488dee05009

workflow @ 4050431c

-Subproject commit d9d499b873b1bd1847a13376acc48a928661036a
+Subproject commit 4050431cce67d80793e548e7f79e44de7e95ecb8

nomad/datamodel/metainfo/simulation/calculation.py

@@ -310,7 +310,7 @@ class Energy(MSection):
         energy calculated with the functional stored in XC_functional.
         ''')
 
-    # TODO Could potential be generalized for other energy types
+    # TODO Remove this should use xc.potential
     xc_potential = SubSection(
         sub_section=EnergyEntry.m_def,
         description='''
@@ -335,6 +335,7 @@ class Energy(MSection):
         energy.
         ''')
 
+    # TODO remove this or electrostatic
     coulomb = SubSection(
         sub_section=EnergyEntry.m_def,
         description='''
@@ -528,6 +529,38 @@ 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='''
@@ -1129,6 +1162,7 @@ class Multipoles(MSection):
     higher_order = SubSection(sub_section=MultipolesEntry.m_def, repeats=True)
 
 
+# TODO remove this section
 class Thermodynamics(MSection):
     '''
     Section containing results related to a thermodynamics calculation.
@@ -1564,6 +1598,37 @@ class BaseCalculation(MSection):
         contamination in spin-unrestricted calculations.
         ''')
 
+    pressure = Quantity(
+        type=np.dtype(np.float64),
+        shape=[],
+        unit='pascal',
+        description='''
+        Value of the pressure of the system.
+        ''')
+
+    temperature = Quantity(
+        type=np.dtype(np.float64),
+        shape=[],
+        unit='kelvin',
+        description='''
+        Value of the temperature of the system at which the properties are calculated.
+        ''')
+
+    time_physical = Quantity(
+        type=np.dtype(np.int32),
+        shape=[],
+        unit='second',
+        description='''
+        The elapsed time with respect to the start of the simulation.
+        ''')
+
+    time_step = Quantity(
+        type=np.dtype(np.int32),
+        shape=[],
+        description='''
+        The number of time steps with respect to the start of the simulation.
+        ''')
+
     energy = SubSection(sub_section=Energy.m_def, categories=[FastAccess])
 
     forces = SubSection(sub_section=Forces.m_def)

nomad/datamodel/metainfo/simulation/method.py

@@ -232,7 +232,7 @@ class MoleculeParameters(MSection):
         Number of atoms in the molecule.
         ''')
 
-    atoms = SubSection(sub_section=AtomParameters.m_def, repeats=True)
+    atom_parameters = SubSection(sub_section=AtomParameters.m_def, repeats=True)
 
 
 class GaussianBasisGroup(MSection):
@@ -432,8 +432,7 @@ class Interaction(MSection):
         type=str,
         shape=[],
         description='''
-        Denotes the classification of the potential. Could be one of pair, LJ, Morse, EAM,
-        MEAM.
+        Denotes the classification of the potential.
         ''')
 
     name = Quantity(
@@ -444,16 +443,24 @@ class Interaction(MSection):
         cut-offs, potential versions.
         ''')
 
+    n_atoms = Quantity(
+        type=np.dtype(np.int32),
+        shape=[],
+        description='''
+        Number of atoms included in the interaction
+        '''
+    )
+
     atom_labels = Quantity(
         type=str,
-        shape=[2],
+        shape=['n_atoms'],
         description='''
         Labels of the atoms described by the interaction.
         ''')
 
     atom_indices = Quantity(
         type=np.dtype(np.int32),
-        shape=[2],
+        shape=['n_atoms'],
         description='''
         Indices of the atoms in the system described by the interaction.
         ''')

nomad/datamodel/metainfo/simulation/system.py

@@ -399,7 +399,7 @@ class Constraint(MSection):
         Number of atoms involved in this constraint.
         ''')
 
-    indices = Quantity(
+    atom_indices = Quantity(
         type=np.dtype(np.int32),
         shape=['n_constraints', 'n_atoms'],
         description='''