pbc correctly handled when trasferring to json and back Issue #210 (#211

)

* pbc correctly handled when trasferring to json and back

also fix ASEComputeBonds which previously modified atoms

also add .vscode to gitognore

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* store PBC key

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Fabian <[email protected]>

.gitignore

@@ -160,3 +160,4 @@ cython_debug/
 .idea/
 
 tmp/
+.vscode

tests/test_data.py

@@ -0,0 +1,12 @@
+import pytest
+from ase.build import bulk, molecule
+
+from zndraw.data import atoms_from_json, atoms_to_json
+
+
+@pytest.mark.parametrize(
+    "atoms", [(molecule("C6H6")), (molecule("H2O")), (bulk("Cu", "fcc", a=3.6))]
+)
+def test_atoms_from_and_to_json_return_unchanged_atoms_object(atoms):
+    atom_copy = atoms.copy()
+    assert atom_copy == atoms_from_json(atoms_to_json(atoms))

zndraw/bonds/__init__.py

@@ -17,12 +17,13 @@ def build_graph(self, atoms: ase.Atoms):
             self.double_bond_multiplier,
             self.triple_bond_multiplier,
         ]
-        connectivity_matrix = np.zeros((len(atoms), len(atoms)), dtype=int)
-        atoms.pbc = False
-        distance_matrix = atoms.get_all_distances(mic=False)
+        atoms_copy = atoms.copy()
+        connectivity_matrix = np.zeros((len(atoms_copy), len(atoms_copy)), dtype=int)
+        atoms_copy.pbc = False
+        distance_matrix = atoms_copy.get_all_distances(mic=False)
         np.fill_diagonal(distance_matrix, np.inf)
         for cutoff in cutoffs:
-            cutoffs = np.array(natural_cutoffs(atoms, mult=cutoff))
+            cutoffs = np.array(natural_cutoffs(atoms_copy, mult=cutoff))
             cutoffs = cutoffs[:, None] + cutoffs[None, :]
             connectivity_matrix[distance_matrix <= cutoffs] += 1
         G = nx.from_numpy_array(connectivity_matrix)

zndraw/data.py

@@ -62,7 +62,7 @@ def atoms_from_json(data: dict) -> ase.Atoms:
     atoms = ase.Atoms(
         numbers=data["numbers"],
         cell=data["cell"],
-        pbc=True,
+        pbc=data["pbc"],
         positions=data["positions"],
     )
 

zndraw/static/pycom/Cache.js

@@ -11,14 +11,24 @@ class Atom {
 }
 
 class Atoms {
-  constructor({ positions, cell, numbers, colors, radii, connectivity, calc }) {
+  constructor({
+    positions,
+    cell,
+    numbers,
+    colors,
+    radii,
+    connectivity,
+    calc,
+    pbc,
+  }) {
     this.positions = positions;
     this.cell = cell;
     this.numbers = numbers;
     this.colors = colors;
     this.radii = radii;
     this.connectivity = connectivity;
     this.calc = calc;
+    this.pbc = pbc;
 
     this.length = this.positions.length;
   }
@@ -65,6 +75,7 @@ class Cache {
           radii: data[key].radii,
           connectivity: data[key].connectivity,
           calc: data[key].calc,
+          pbc: data[key].pbc,
         });
       });
       const slider = document.getElementById("frame-slider");