Merge pull request #25 from pyiron/lammps_triclinic

Lammps: Use change_box when switching from orthogonal box to triclini…
pyiron · Jan 22, 2021 · bc4c321 · bc4c321
2 parents c891995 + 3468bd0
commit bc4c321
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Showing 2 changed files with 35 additions and 7 deletions.
diff --git a/pyiron_atomistics/lammps/interactive.py b/pyiron_atomistics/lammps/interactive.py
@@ -114,26 +114,46 @@ def interactive_cells_setter(self, cell):
             warnings.warn('set_relative() is deprecated as of 2020-02-26. It is not guaranteed from pyiron_atomistics vers. 0.3')
 
         if is_skewed and is_scaled:
+            self._interactive_lib_command(
+                "change_box all triclinic"
+            )
             self._interactive_lib_command(
                 "change_box all x final 0 %f y final 0 %f z final 0 %f \
-                 xy final %f xz final %f yz final %f triclinic remap units box"
+                 xy final %f xz final %f yz final %f remap units box"
                 % (lx, ly, lz, xy, xz, yz)
             )
         elif is_skewed and not is_scaled:
+            self._interactive_lib_command(
+                "change_box all triclinic"
+            )
             self._interactive_lib_command(
                 "change_box all x final 0 %f y final 0 %f z final 0 %f \
-                xy final %f xz final %f yz final %f triclinic units box"
+                xy final %f xz final %f yz final %f units box"
                 % (lx, ly, lz, xy, xz, yz)
             )
         elif not is_skewed and is_scaled:
             self._interactive_lib_command(
-                "change_box all x final 0 %f y final 0 %f z final 0 %f remap units box"
-                % (lx, ly, lz)
+                "change_box all triclinic"
+            )
+            self._interactive_lib_command(
+                "change_box all x final 0 %f y final 0 %f z final 0 %f \
+                xy final %f xz final %f yz final %f remap units box"
+                % (lx, ly, lz, 0.0, 0.0, 0.0)
+            )
+            self._interactive_lib_command(
+                "change_box all ortho"
             )
         else:  # is neither skewed nor scaled
             self._interactive_lib_command(
-                "change_box all x final 0 %f y final 0 %f z final 0 %f units box"
-                % (lx, ly, lz)
+                "change_box all triclinic"
+            )
+            self._interactive_lib_command(
+                "change_box all x final 0 %f y final 0 %f z final 0 %f \
+                xy final %f xz final %f yz final %f units box"
+                % (lx, ly, lz, 0.0, 0.0, 0.0)
+            )
+            self._interactive_lib_command(
+                "change_box all ortho"
             )
 
     def interactive_volume_getter(self):

diff --git a/tests/lammps/test_interactive.py b/tests/lammps/test_interactive.py
@@ -64,9 +64,17 @@ def tearDownClass(cls):
 
     def test_interactive_cells_setter(self):
         self.job.interactive_cells_setter(np.eye(3))
+        self.assertEqual(
+            self.job._interactive_library._command[-3],
+            "change_box all triclinic",
+        )
+        self.assertEqual(
+            self.job._interactive_library._command[-2],
+            "change_box all x final 0 1.000000 y final 0 1.000000 z final 0 1.000000                 xy final 0.000000 xz final 0.000000 yz final 0.000000 units box",
+        )
         self.assertEqual(
             self.job._interactive_library._command[-1],
-            "change_box all x final 0 1.000000 y final 0 1.000000 z final 0 1.000000 units box",
+            "change_box all ortho",
         )
 
     def test_interactive_positions_setter(self):