Merge pull request #41 from robinzyb/devel

convert npt_i cell to angstrom when parsing from cp2k output

cp2kdata/block_parser/cells.py

@@ -127,6 +127,9 @@ def parse_all_md_cells(output_file: List[str],
                     match["alpha"], match["beta"], match["gamma"]]
             cell = np.array(cell, dtype=float)
             cell[3:] = init_cell_angles
+            # convert bohr to angstrom
+            cell[:3] = cell[:3] * au2A
+            # make sure cell length are in angstrom and cell angles are in degree before sent to cellpar_to_cell
             cell = cellpar_to_cell(cell)
             all_md_cells.append(cell)
 

tests/test_cube/test_cube.py

@@ -56,8 +56,19 @@ def test_mav(self, cube_and_answer):
         mav_answer = np.load(os.path.join(answer_dir, "mav.npy"))
         mav_x_answer = mav_answer[0]
         mav_answer = mav_answer[1]
-        assert np.all(mav == mav_answer)
-        assert np.all(mav_x == mav_x_answer)
+
+        np.testing.assert_almost_equal(mav, 
+                                       mav_answer, 
+                                       decimal=8,
+                                       err_msg = 'mav failed'
+                                       )
+        np.testing.assert_almost_equal(mav_x,
+                                        mav_x_answer,
+                                        decimal=8,
+                                        err_msg = 'mav_x failed'
+                                        )
+        #assert np.all(mav == mav_answer)
+        #assert np.all(mav_x == mav_x_answer)