Merge pull request #30 from pyiron/master

Update from master

.ci_support/environment.yml

@@ -1,7 +1,7 @@
 channels:
   - conda-forge
 dependencies:
-  - ase >=3.20.1
+  - ase >=3.21.0
   - coveralls
   - coverage
   - codacy-coverage

pyiron_atomistics/atomistics/master/phonopy.py

@@ -124,10 +124,28 @@ def modify_job(self, job, parameter):
 
 class PhonopyJob(AtomisticParallelMaster):
     """
+    Phonopy wrapper for the calculation of free energy in the framework of quasi harmonic approximation.
 
-    Args:
-        project:
-        job_name:
+    Example:
+
+    >>> from pyiron_atomistics import Project
+    >>> pr = Project('my_project')
+    >>> lmp = pr.create_job('Lammps', 'lammps')
+    >>> lmp.structure = pr.create_structure('Fe', 'bcc', 2.832)
+    >>> phono = lmp.create_job('PhonopyJob', 'phonopy')
+    >>> phono.run()
+
+    Get output via `get_thermal_properties()`.
+
+    Note:
+
+    - This class does not consider the thermal expansion. For this, use `QuasiHarmonicJob` (find more in its
+        docstring)
+    - Depending on the value given in `job.input['interaction_range']`, this class automatically changes the number of
+        atoms. The input parameters of the reference job might have to be set appropriately (e.g. use `k_mesh_density`
+        for DFT instead of setting k-points directly).
+    - The structure used in the reference job should be a relaxed structure.
+    - Theory behind it: https://en.wikipedia.org/wiki/Quasi-harmonic_approximation
     """
 
     def __init__(self, project, job_name):
@@ -318,7 +336,7 @@ def get_thermal_properties(self, t_min=1, t_max=1500, t_step=50, temperatures=No
 
         Args:
             t_min (float): minimum sample temperature
-            t_max (float): minimum sample temperature
+            t_max (float): maximum sample temperature
             t_step (int):  tempeature sample interval
             temperatures (array_like, float):  custom array of temperature samples, if given t_min, t_max, t_step are
                                                ignored.

pyiron_atomistics/lammps/base.py

@@ -171,9 +171,11 @@ def potential(self, potential_filename):
         self.input.potential.df = potential
         if "Citations" in potential.columns.values:
             pot_pub_dict = {}
-            for p in ast.literal_eval(potential["Citations"].values[0]):
-                for k in p.keys():
-                    pot_pub_dict[k] = p[k]
+            pub_lst = potential["Citations"].values[0]
+            if isinstance(pub_lst, str):
+                for p in ast.literal_eval(pub_lst):
+                    for k in p.keys():
+                        pot_pub_dict[k] = p[k]
             s.publication_add({"lammps_potential": pot_pub_dict})
         for val in ["units", "atom_style", "dimension"]:
             v = self.input.potential[val]

pyiron_atomistics/project.py

@@ -192,18 +192,6 @@ def create_object(object_type):
         obj = ObjectType(object_type, project=None, job_name=None)
         return obj
 
-    def copy(self):
-        """
-        Copy the project object - copying just the Python object but maintaining the same pyiron path
-
-        Returns:
-            Project: copy of the project object
-        """
-        new = Project(path=self.path, user=self.user, sql_query=self.sql_query)
-        new._filter = self._filter
-        new._inspect_mode = self._inspect_mode
-        return new
-
     def load_from_jobpath(self, job_id=None, db_entry=None, convert_to_object=True):
         """
         Internal function to load an existing job either based on the job ID or based on the database entry dictionary.
@@ -221,7 +209,7 @@ def load_from_jobpath(self, job_id=None, db_entry=None, convert_to_object=True):
         job = super(Project, self).load_from_jobpath(
             job_id=job_id, db_entry=db_entry, convert_to_object=convert_to_object
         )
-        job.project_hdf5._project = Project(path=job.project_hdf5.file_path)
+        job.project_hdf5._project = self.__class__(path=job.project_hdf5.file_path)
         return job
 
     def load_from_jobpath_string(self, job_path, convert_to_object=True):

setup.py

@@ -31,7 +31,7 @@
     keywords='pyiron',
     packages=find_packages(exclude=["*tests*", "*docs*", "*binder*", "*conda*", "*notebooks*", "*.ci_support*"]),
     install_requires=[
-        'ase>=3.20.1',
+        'ase>=3.21.0',
         'defusedxml>=0.6.0',
         'future>=0.18.2',
         'h5py>=3.1.0',

tests/atomistics/structure/test_atoms.py

@@ -450,19 +450,19 @@ def test_rotate_euler(self):
             elements="AlFe", positions=[3 * [0], 3 * [1]], cell=2 * np.eye(3)
         )
         basis = unitcell.copy()
-        basis.rotate_euler(phi=0.1 * np.pi)
+        basis.euler_rotate(phi=0.1 * 180)
         self.assertAlmostEqual(np.arccos(basis.positions[1, :2].sum() / 2) / np.pi, 0.1)
         basis = unitcell.copy()
         center_of_mass = basis.get_center_of_mass()
-        basis.rotate_euler(phi=0.1 * np.pi, center="com")
+        basis.euler_rotate(phi=0.1 * 180, center="com")
         self.assertTrue(np.allclose(basis.get_center_of_mass(), center_of_mass))
         basis = unitcell.copy()
         center_of_positions = basis.positions.mean(axis=0)
-        basis.rotate_euler(phi=0.1 * np.pi, center="cop")
+        basis.euler_rotate(phi=0.1 * 180, center="cop")
         self.assertTrue(np.allclose(center_of_positions, basis.positions.mean(axis=0)))
         basis = unitcell.copy()
         position = basis.positions[1]
-        basis.rotate_euler(phi=0.1 * np.pi, center="cou")
+        basis.euler_rotate(phi=0.1 * 180, center="cou")
         self.assertTrue(np.allclose(position, basis.positions[1]))
 
     def test_set_initial_magnetic_moments(self):