Fix orbital moments (#166)

* Fix: VASP does not write charge component for orbital moments
* Rename Calculations -> Batch
* Rename topology -> stoichiometry

.github/workflows/test_full.yml

@@ -26,7 +26,7 @@ jobs:
       run: |
         python --version
         python -m pip install --progress-bar=off --upgrade pip
-        pip install --progress-bar=off "poetry!=1.4.1"
+        pip install --progress-bar=off "poetry<2"
     - name: Install py4vasp
       shell: bash -el {0}
       run: |

src/py4vasp/__init__.py

@@ -1,10 +1,10 @@
 # Copyright © VASP Software GmbH,
 # Licensed under the Apache License 2.0 (http://www.apache.org/licenses/LICENSE-2.0)
 from py4vasp._analysis.mlff import MLFFErrorAnalysis
-from py4vasp._calculations import Calculations
+from py4vasp._batch import Batch
+from py4vasp._calculation import Calculation, calculation
 from py4vasp._third_party.graph import plot
 from py4vasp._third_party.interactive import set_error_handling
-from py4vasp.calculation._class import Calculation
 
 __version__ = "0.10.0"
 set_error_handling("Minimal")

src/py4vasp/_analysis/mlff.py

@@ -50,9 +50,9 @@ def __init__(self, *args, **kwargs):
         self.dft = SimpleNamespace()
 
     @classmethod
-    def _from_data(cls, _calculations):
+    def _from_data(cls, batch):
         mlff_error_analysis = cls(_internal=True)
-        mlff_error_analysis._calculations = _calculations
+        mlff_error_analysis._batch = batch
         set_appropriate_attrs(mlff_error_analysis)
         return mlff_error_analysis
 
@@ -72,10 +72,8 @@ def from_paths(cls, dft_data, mlff_data):
             Path to the MLFF data. Accepts wildcards.
         """
         mlff_error_analysis = cls(_internal=True)
-        calculations = py4vasp.Calculations.from_paths(
-            dft_data=dft_data, mlff_data=mlff_data
-        )
-        mlff_error_analysis._calculations = calculations
+        batch = py4vasp.Batch.from_paths(dft_data=dft_data, mlff_data=mlff_data)
+        mlff_error_analysis._batch = batch
         set_appropriate_attrs(mlff_error_analysis)
         return mlff_error_analysis
 
@@ -95,10 +93,8 @@ def from_files(cls, dft_data, mlff_data):
             Path to the MLFF data. Accepts wildcards.
         """
         mlff_error_analysis = cls(_internal=True)
-        calculations = py4vasp.Calculations.from_files(
-            dft_data=dft_data, mlff_data=mlff_data
-        )
-        mlff_error_analysis._calculations = calculations
+        batch = py4vasp.Batch.from_files(dft_data=dft_data, mlff_data=mlff_data)
+        mlff_error_analysis._batch = batch
         set_appropriate_attrs(mlff_error_analysis)
         return mlff_error_analysis
 
@@ -213,7 +209,7 @@ def set_number_of_configurations(cls):
     cls : MLFFErrorAnalysis
         An instance of MLFFErrorAnalysis.
     """
-    number_of_calculations = cls._calculations.number_of_calculations()
+    number_of_calculations = cls._batch.number_of_calculations()
     cls.dft.nconfig = number_of_calculations["dft_data"]
     cls.mlff.nconfig = number_of_calculations["mlff_data"]
 
@@ -229,7 +225,7 @@ def set_number_of_ions(cls):
     cls : MLFFErrorAnalysis
         An instance of MLFFErrorAnalysis.
     """
-    force_data = cls._calculations.forces.read()
+    force_data = cls._batch.forces.read()
     structures_dft = _dict_to_list(force_data["dft_data"], "structure")
     structures_mlff = _dict_to_list(force_data["mlff_data"], "structure")
     elements_dft = _dict_to_array(structures_dft, "elements")
@@ -252,11 +248,11 @@ def set_paths_and_files(cls):
     cls : MLFFErrorAnalysis
         An instance of MLFFErrorAnalysis.
     """
-    paths = cls._calculations.paths()
+    paths = cls._batch.paths()
     cls.dft.paths = paths["dft_data"]
     cls.mlff.paths = paths["mlff_data"]
-    if hasattr(cls._calculations, "_files"):
-        files = cls._calculations.files()
+    if hasattr(cls._batch, "_files"):
+        files = cls._batch.files()
         cls.dft.files = files["dft_data"]
         cls.mlff.files = files["mlff_data"]
 
@@ -273,7 +269,7 @@ def set_energies(cls):
         An instance of MLFFErrorAnalysis.
     """
     tag = "free energy    TOTEN"
-    energies_data = cls._calculations.energies.read()
+    energies_data = cls._batch.energies.read()
     cls.mlff.energies = _dict_to_array(energies_data["mlff_data"], tag)
     cls.dft.energies = _dict_to_array(energies_data["dft_data"], tag)
 
@@ -298,7 +294,7 @@ def set_force_related_attributes(cls):
     cls : MLFFErrorAnalysis
         An instance of MLFFErrorAnalysis.
     """
-    force_data = cls._calculations.forces.read()
+    force_data = cls._batch.forces.read()
     cls.dft.forces = _dict_to_array(force_data["dft_data"], "forces")
     cls.mlff.forces = _dict_to_array(force_data["mlff_data"], "forces")
     dft_structures = _dict_to_list(force_data["dft_data"], "structure")
@@ -320,6 +316,6 @@ def set_stresses(cls):
     cls : MLFFErrorAnalysis
         An instance of MLFFErrorAnalysis.
     """
-    stress_data = cls._calculations.stresses.read()
+    stress_data = cls._batch.stresses.read()
     cls.dft.stresses = _dict_to_array(stress_data["dft_data"], "stress")
     cls.mlff.stresses = _dict_to_array(stress_data["mlff_data"], "stress")

src/py4vasp/_calculations.py → src/py4vasp/_batch.py

@@ -8,17 +8,17 @@
 from py4vasp._util import convert
 
 
-class Calculations:
-    """A class to handle multiple Calculations all at once.
+class Batch:
+    """A class to handle batch of multiple calculations at once.
 
     This class combines the functionality of the Calculation class for more than one
-    calculation. Create a Calculations object using either a wildcard for a set of
+    calculation. Create a Batch object using either a wildcard for a set of
     paths or files or pass in paths and files directly. Then you can access the
     properties of all calculations via the attributes of the object.
 
     Examples
     --------
-    >>> calcs = Calculations.from_paths(calc1="path_to_calc1", calc2="path_to_calc2")
+    >>> calcs = Batch.from_paths(calc1="path_to_calc1", calc2="path_to_calc2")
     >>> calcs.energies.read() # returns a dictionary with the energies of calc1 and calc2
     >>> calcs.forces.read()   # returns a dictionary with the forces of calc1 and calc2
     >>> calcs.stresses.read() # returns a dictionary with the stresses of calc1 and calc2
@@ -34,8 +34,8 @@ class Calculations:
     def __init__(self, *args, **kwargs):
         if not kwargs.get("_internal"):
             message = """\
-Please setup new CompareCalculations instance using the classmethod CompareCalculations.from_paths()
-or CompareCalculations.from_files() instead of the constructor CompareCalculations()."""
+Please setup new Batch instance using the classmethod Batch.from_paths()
+or Batch.from_files() instead of the constructor Batch()."""
             raise exception.IncorrectUsage(message)
 
     def _path_finder(**kwargs):
@@ -53,7 +53,7 @@ def _path_finder(**kwargs):
 
     @classmethod
     def from_paths(cls, **kwargs):
-        """Set up a Calculations object for paths.
+        """Set up a Batch object for paths.
 
         Setup a calculation for paths by passing in a dictionary with the name of the
         calculation as key and the path to the calculation as value.
@@ -75,7 +75,7 @@ def from_paths(cls, **kwargs):
 
     @classmethod
     def from_files(cls, **kwargs):
-        """Set up a Calculations object from files.
+        """Set up a Batch object from files.
 
         Setup a calculation for files by passing in a dictionary with the name of the
         calculation as key and the path to the calculation as value. Note that this

src/py4vasp/calculation/_CONTCAR.py → src/py4vasp/_calculation/_CONTCAR.py

@@ -1,20 +1,20 @@
 # Copyright © VASP Software GmbH,
 # Licensed under the Apache License 2.0 (http://www.apache.org/licenses/LICENSE-2.0)
 from py4vasp import calculation
+from py4vasp._calculation import base, structure
 from py4vasp._third_party import view
 from py4vasp._util import convert
-from py4vasp.calculation import _base, _structure
 
 
-class CONTCAR(_base.Refinery, view.Mixin, _structure.Mixin):
+class CONTCAR(base.Refinery, view.Mixin, structure.Mixin):
     """CONTCAR contains structural restart-data after a relaxation or MD simulation.
 
     The CONTCAR contains the final structure of the VASP calculation. It can be used as
     input for the next calculation if desired. Depending on the particular setup the
     CONTCAR might contain additional information about the system such as the ion
     and lattice velocities."""
 
-    @_base.data_access
+    @base.data_access
     def to_dict(self):
         """Extract the structural data and the available additional data to a dictionary.
 
@@ -36,7 +36,7 @@ def _read(self, key):
         data = getattr(self._raw_data, key)
         return {key: data[:]} if not data.is_none() else {}
 
-    @_base.data_access
+    @base.data_access
     def to_view(self, supercell=None):
         """Generate a visualization of the final structure.
 
@@ -52,7 +52,7 @@ def to_view(self, supercell=None):
         """
         return self._structure.plot(supercell)
 
-    @_base.data_access
+    @base.data_access
     def __str__(self):
         return "\n".join(self._line_generator())
 
@@ -62,16 +62,18 @@ def _line_generator(self):
         selective_dynamics = self._raw_data.selective_dynamics
         yield convert.text_to_string(self._raw_data.system)
         yield from _cell_lines(cell)
-        yield self._topology().to_POSCAR()
+        yield self._stoichiometry().to_POSCAR()
         if not selective_dynamics.is_none():
             yield "Selective dynamics"
         yield "Direct"
         yield from _ion_position_lines(positions, selective_dynamics)
         yield from _lattice_velocity_lines(self._raw_data.lattice_velocities, cell)
         yield from _ion_velocity_lines(self._raw_data.ion_velocities)
 
-    def _topology(self):
-        return calculation.topology.from_data(self._raw_data.structure.topology)
+    def _stoichiometry(self):
+        return calculation._stoichiometry.from_data(
+            self._raw_data.structure.stoichiometry
+        )
 
 
 def _cell_lines(cell):