diff --git a/src/mdevaluate/coordinates.py b/src/mdevaluate/coordinates.py index 1e3b623..9841875 100755 --- a/src/mdevaluate/coordinates.py +++ b/src/mdevaluate/coordinates.py @@ -646,7 +646,7 @@ def next_neighbors( return distances_new, indices_new else: atoms_pbc, atoms_pbc_index = pbc_points( - query_atoms, box, thickness=distance_upper_bound + 0.1, index=True, **kwargs + atoms, box, thickness=distance_upper_bound + 0.1, index=True, **kwargs ) tree = KDTree(atoms_pbc) distances, indices = tree.query( @@ -692,12 +692,16 @@ def number_of_neighbors( elif not distinct: dnn = 1 + print(atoms[:5]) + print(query_atoms[:5]) + print(" ") + box = atoms.box if np.all(np.diag(np.diag(box)) == box): atoms = atoms % np.diag(box) tree = KDTree(atoms, boxsize=np.diag(box)) else: - atoms_pbc = pbc_points(query_atoms, box, thickness=r_max + 0.1, **kwargs) + atoms_pbc = pbc_points(atoms, box, thickness=r_max + 0.1, **kwargs) tree = KDTree(atoms_pbc) num_of_neighbors = tree.query_ball_point(query_atoms, r_max, return_length=True) diff --git a/src/mdevaluate/distribution.py b/src/mdevaluate/distribution.py index cb20d21..6aa09fd 100644 --- a/src/mdevaluate/distribution.py +++ b/src/mdevaluate/distribution.py @@ -126,6 +126,9 @@ def rdf( particles_in_volume = int( np.max(number_of_neighbors(atoms_a, query_atoms=atoms_b, r_max=bins[-1])) * 1.1 ) + print(atoms_a[:5]) + print(atoms_b[:5]) + print(" ") distances, indices = next_neighbors( atoms_a, atoms_b, @@ -147,9 +150,9 @@ def rdf( distances = [d for dist in distances for d in dist] hist, bins = np.histogram(distances, bins=bins, range=(0, bins[-1]), density=False) - hist = hist / len(atoms_a) + hist = hist / len(atoms_b) hist = hist / (4 / 3 * np.pi * bins[1:] ** 3 - 4 / 3 * np.pi * bins[:-1] ** 3) - n = len(atoms_b) / np.prod(np.diag(atoms_b.box)) + n = len(atoms_a) / np.prod(np.diag(atoms_a.box)) hist = hist / n return hist