More significant digits for coordinate files (coord and *.xyz) (#118

) * more significant digits for coordinates Signed-off-by: Marcel Müller <[email protected]> * adapt CHANGELOG.md Signed-off-by: Marcel Müller <[email protected]> * fix coord file writing Signed-off-by: Marcel Müller <[email protected]> --------- Signed-off-by: Marcel Müller <[email protected]>
grimme-lab · Jan 30, 2025 · 55ff200 · 55ff200
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -23,6 +23,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 - version string is now correctly formatted and printed
+- precision (# significant digits) of the coordinate files (`get_coord_str` and `get_xyz_str`) increased from 7 to 14
 
 ## [0.5.0] - 2024-12-16
 ### Changed

diff --git a/src/mindlessgen/molecules/molecule.py b/src/mindlessgen/molecules/molecule.py
@@ -394,9 +394,9 @@ def get_xyz_str(self) -> str:
         for i in range(self.num_atoms):
             xyz_str += (
                 f"{PSE[self.ati[i] + 1]:<5} "
-                + f"{self.xyz[i, 0]:>12.7f} "
-                + f"{self.xyz[i, 1]:>12.7f} "
-                + f"{self.xyz[i, 2]:>12.7f}\n"
+                + f"{self.xyz[i, 0]:>20.14f} "
+                + f"{self.xyz[i, 1]:>20.14f} "
+                + f"{self.xyz[i, 2]:>20.14f}\n"
             )
         return xyz_str
 
@@ -478,9 +478,9 @@ def get_coord_str(self) -> str:
         coord_str = "$coord\n"
         for i in range(self.num_atoms):
             coord_str += (
-                f"{self.xyz[i, 0] / BOHR2AA:>12.7f} "
-                + f"{self.xyz[i, 1] / BOHR2AA:>12.7f} "
-                + f"{self.xyz[i, 2] / BOHR2AA:>12.7f} "
+                f"{self.xyz[i, 0] / BOHR2AA:>20.14f} "
+                + f"{self.xyz[i, 1] / BOHR2AA:>20.14f} "
+                + f"{self.xyz[i, 2] / BOHR2AA:>20.14f} "
                 + f"{PSE[self.ati[i] + 1]:>5}\n"
             )
         coord_str += "$end\n"

diff --git a/test/test_molecules/test_molecule.py b/test/test_molecules/test_molecule.py
@@ -255,8 +255,8 @@ def test_write_coord_to_file(tmp_path):
     mol.xyz = np.array([[0.0, 0.0, 0.0], [1.0, 0.0, 0.0]])
 
     expected_content = """$coord
-0.0000000 0.0000000 0.0000000 H
-1.8897261 0.0000000 0.0000000 F
+0.00000000000000 0.00000000000000 0.00000000000000 H
+1.88972612590778 0.00000000000000 0.00000000000000 F
 $end
 """