Add dataclass for Murnaghan (#64)

* Add dataclass for Murnaghan

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* add hdf5 file

* fix values

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: jan-janssen

pyiron_dataclasses/v1/converter.py

@@ -28,6 +28,11 @@
     LammpsOutput,
     LammpsPotential,
 )
+from pyiron_dataclasses.v1.murn import (
+    MurnaghanInput,
+    MurnaghanJob,
+    MurnaghanOutput,
+)
 from pyiron_dataclasses.v1.sphinx import (
     BornOppenheimer,
     PawPot,
@@ -68,6 +73,7 @@ def get_dataclass(job_dict: dict) -> Callable:
         "<class 'pyiron_atomistics.lammps.lammps.Lammps'>": _convert_lammps_job_dict,
         "<class 'pyiron_atomistics.sphinx.sphinx.Sphinx'>": _convert_sphinx_job_dict,
         "<class 'pyiron_atomistics.vasp.vasp.Vasp'>": _convert_vasp_job_dict,
+        "<class 'pyiron_atomistics.atomistics.master.murnaghan.Murnaghan'>": _convert_murnaghan_job_dict,
     }
     return funct_dict[job_dict["TYPE"]](job_dict=job_dict)
 
@@ -920,6 +926,49 @@ def _convert_vasp_job_dict(job_dict):
     )
 
 
+def _convert_murnaghan_job_dict(job_dict):
+    input_dict = _convert_generic_parameters_to_dictionary(
+        generic_parameter_dict=job_dict["input"]["parameters"]
+    )
+    return MurnaghanJob(
+        job_id=job_dict["job_id"],
+        server=Server(
+            user=job_dict["server"]["user"],
+            host=job_dict["server"]["host"],
+            run_mode=job_dict["server"]["run_mode"],
+            queue=job_dict["server"]["queue"],
+            qid=job_dict["server"]["qid"],
+            cores=job_dict["server"]["cores"],
+            threads=job_dict["server"]["threads"],
+            new_hdf=job_dict["server"]["new_hdf"],
+            run_time=job_dict["server"]["run_time"],
+            memory_limit=job_dict["server"]["memory_limit"],
+            accept_crash=job_dict["server"]["accept_crash"],
+        ),
+        status=job_dict["status"],
+        calculation_input=MurnaghanInput(
+            num_points=input_dict["num_points"],
+            fit_type=input_dict["fit_type"],
+            fit_order=input_dict["fit_order"],
+            vol_range=input_dict["vol_range"],
+            axes=input_dict["axes"],
+            strains=input_dict["strains"],
+            allow_aborted=input_dict["allow_aborted"],
+        ),
+        calculation_output=MurnaghanOutput(
+            energy=job_dict["output"]["energy"],
+            equilibrium_b_prime=job_dict["output"]["equilibrium_b_prime"],
+            equilibrium_bulk_modulus=job_dict["output"]["equilibrium_bulk_modulus"],
+            equilibrium_energy=job_dict["output"]["equilibrium_energy"],
+            equilibrium_volume=job_dict["output"]["equilibrium_volume"],
+            error=job_dict["output"]["error"],
+            id=job_dict["output"]["id"],
+            volume=job_dict["output"]["volume"],
+            structure=job_dict["output"]["structure"],
+        ),
+    )
+
+
 def _convert_generic_parameters_to_string(generic_parameter_dict: dict) -> str:
     output_str = ""
     for p, v in zip(

pyiron_dataclasses/v1/murn.py

@@ -0,0 +1,40 @@
+from dataclasses import dataclass
+from typing import Optional
+
+import numpy as np
+
+from pyiron_dataclasses.v1.atomistic import Structure
+from pyiron_dataclasses.v1.job import Executable, Server
+
+
+@dataclass
+class MurnaghanInput:
+    num_points: int
+    fit_type: str
+    fit_order: Optional[int]
+    vol_range: float
+    axes: tuple[str]
+    strains: Optional[list[float]]
+    allow_aborted: bool
+
+
+@dataclass
+class MurnaghanOutput:
+    energy: np.ndarray
+    equilibrium_b_prime: float
+    equilibrium_bulk_modulus: float
+    equilibrium_energy: float
+    equilibrium_volume: float
+    error: np.ndarray
+    id: np.ndarray
+    volume: np.ndarray
+    structure: Structure
+
+
+@dataclass
+class MurnaghanJob:
+    job_id: int
+    server: Server
+    status: str
+    calculation_input: MurnaghanInput
+    calculation_output: MurnaghanOutput

tests/pyiron_atomistics_0_6_13/murn.h5

@@ -117,3 +117,21 @@ def test_lammps_calc_minimize(self):
             job_lammps.calculation_output.generic.energy_tot[-1],
             -13.4486826111902 * ureg.eV,
         )
+
+    def test_murnaghan_lammps(self):
+        job = self.project.create.job.Lammps("lmp")
+        job.structure = self.project.create.structure.bulk("Al", cubic=True)
+        murn = self.project.create.job.Murnaghan("murn")
+        murn.ref_job = job
+        murn.run()
+        job_dict = read_dict_from_hdf(
+            file_name=murn.project_hdf5.file_name,
+            h5_path="/",
+            recursive=True,
+            slash="ignore",
+        )
+        job_murn = get_dataclass(job_dict[murn.job_name])
+        self.assertEqual(
+            job_murn.calculation_output.equilibrium_bulk_modulus,
+            81.0404454580153,
+        )

tests/test_pyiron_atomistics_live.py

@@ -27,9 +27,19 @@ def test_all(self):
                 recursive=True,
                 slash="ignore",
             )[hdf5_file.split(".")[0]]
-            self.assertEqual(
-                get_dataclass(job_dict=job_dict).calculation_output.generic.energy_tot[
-                    -1
-                ],
-                energy_dict[hdf5_file],
-            )
+            if hdf5_file in ["sx.h5", "lmp.h5", "vasp.h5"]:
+                self.assertEqual(
+                    get_dataclass(
+                        job_dict=job_dict
+                    ).calculation_output.generic.energy_tot[-1],
+                    energy_dict[hdf5_file],
+                )
+            elif hdf5_file == "murn.h5":
+                self.assertEqual(
+                    get_dataclass(
+                        job_dict=job_dict
+                    ).calculation_output.equilibrium_bulk_modulus,
+                    81.04044545801592,
+                )
+            else:
+                raise ValueError()