Merge pull request #1304 from pyiron/lammps_potential_dict

A workaround to fix reloading potentials with LAMMPS

.ci_support/environment-old.yml

@@ -13,7 +13,7 @@ dependencies:
 - pandas =2.0.3
 - phonopy =2.20.0
 - pint =0.18
-- pyiron_base =0.6.16
+- pyiron_base =0.7.2
 - pylammpsmpi =0.2.7
 - pyscal =2.10.4
 - scikit-learn =1.2.1

.ci_support/environment.yml

@@ -15,7 +15,7 @@ dependencies:
 - pandas =2.2.0
 - phonopy =2.21.0
 - pint =0.23
-- pyiron_base =0.7.1
+- pyiron_base =0.7.2
 - pylammpsmpi =0.2.11
 - pyscal =2.10.18
 - scikit-learn =1.4.0

pyiron_atomistics/lammps/base.py

@@ -742,7 +742,12 @@ def from_hdf(self, hdf=None, group_name=None):  # TODO: group_name should be rem
         self._structure_from_hdf()
         self.input.from_dict(
             data_dict=self._hdf5.read_dict_from_hdf(
-                group_paths=["input", "input/control_inp", "input/potential_inp"]
+                [
+                    "input",
+                    "input/control_inp",
+                    "input/potential_inp",
+                    "input/potential_inp/potential",
+                ]
             )
         )
 
@@ -1082,7 +1087,12 @@ def from_hdf(self, hdf5):
         """
         self.from_dict(
             data_dict=hdf5.read_dict_from_hdf(
-                ["input", "input/control_inp", "input/potential_inp"]
+                [
+                    "input",
+                    "input/control_inp",
+                    "input/potential_inp",
+                    "input/potential_inp/potential",
+                ]
             )
         )
 

pyiron_atomistics/lammps/potential.py

@@ -184,6 +184,30 @@ def get_charge(self, element_symbol):
             )
             raise NameError(msg) from None
 
+    def to_dict(self):
+        super_dict = super(LammpsPotential, self).to_dict()
+        if self._df is not None:
+            super_dict.update(
+                {
+                    "potential/" + key: self._df[key].values[0]
+                    for key in ["Config", "Filename", "Name", "Model", "Species"]
+                }
+            )
+            if "Citations" in self._df.columns.values:
+                super_dict["potential/Citations"] = self._df["Citations"].values[0]
+        return super_dict
+
+    def from_dict(self, obj_dict, version: str = None):
+        super(LammpsPotential, self).from_dict(obj_dict=obj_dict, version=version)
+        if "potential" in obj_dict.keys() and "Config" in obj_dict["potential"].keys():
+            entry_dict = {
+                key: [obj_dict["potential"][key]]
+                for key in ["Config", "Filename", "Name", "Model", "Species"]
+            }
+            if "Citations" in obj_dict["potential"].keys():
+                entry_dict["Citations"] = [obj_dict["potential"]["Citations"]]
+            self._df = pd.DataFrame(entry_dict)
+
     def to_hdf(self, hdf, group_name=None):
         if self._df is not None:
             with hdf.open("potential") as hdf_pot:

pyproject.toml

@@ -35,7 +35,7 @@ dependencies = [
     "pandas==2.2.0",
     "phonopy==2.21.0",
     "pint==0.23",
-    "pyiron_base==0.7.1",
+    "pyiron_base==0.7.2",
     "pylammpsmpi==0.2.11",
     "scipy==1.12.0",
     "scikit-learn==1.4.0",