add structure override option

pyiron · Nov 9, 2023 · c34b0bb · c34b0bb
1 parent 4dbc822
commit c34b0bb
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/pyiron_contrib/atomistics/mean_field/core/bond_analysis.py b/pyiron_contrib/atomistics/mean_field/core/bond_analysis.py
@@ -426,7 +426,8 @@ def validate_ready_to_run(self):
         if self.input.md_job is not None:
             self.input.md_trajectory = self.input.md_job.output.unwrapped_positions[self.input.thermalize_snapshots:]
             self.input.md_cells = self.input.md_job.output.cells[self.input.thermalize_snapshots:]
-            self.input.structure = self.input.md_job.structure.copy()
+            if self.input.structure is None:
+                self.input.structure = self.input.md_job.structure.copy()
 
         if (self.input.md_trajectory is None) | (self.input.md_cells is None):
             raise AttributeError('Either <job>.input.md_job or <job>.input.md_trajectory and <job>.input.md_cells must be set')

diff --git a/pyiron_contrib/atomistics/mean_field/core/mean_field.py b/pyiron_contrib/atomistics/mean_field/core/mean_field.py
@@ -348,7 +348,7 @@ def virial(args):
                 _, _, b_eps = self.find_virial_quant(bonds=bonds, meshes=meshes, temperature=temperature, eps=eps, lm=args, 
                                                      fix=fix, Veff=Veff)
                 return np.abs(self.b_0*eps-b_eps)
-            solver = root_scalar(virial, x0=lm, x1=lm+0.001, method='lm', rtol=1e-20)
+            solver = root_scalar(virial, x0=lm, x1=lm+0.001, rtol=1e-20)
             eff_temp, lm = temperature, solver.root
         virial_q = self.find_virial_quant(bonds=bonds, meshes=meshes, temperature=eff_temp, eps=eps, lm=lm, fix=fix, 
                                           Veff=Veff, return_rho_1=True)