From 6e2683ed490d00c9603a75050e46a90a60ec6065 Mon Sep 17 00:00:00 2001
From: Lauri Himanen <6513318+lauri-codes@users.noreply.github.com>
Date: Thu, 10 Oct 2024 20:50:11 +0300
Subject: [PATCH] Fixing overlap issue. (#30)

---
 matid/clustering/sbc.py      |  2 +-
 matid/core/periodicfinder.py | 10 +++++++---
 2 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/matid/clustering/sbc.py b/matid/clustering/sbc.py
index 26a62c1b..e5a647c4 100644
--- a/matid/clustering/sbc.py
+++ b/matid/clustering/sbc.py
@@ -28,7 +28,7 @@ def get_clusters(
         merge_threshold=0.5,
         merge_radius=1,
         bond_threshold=0.65,
-        overlap_threshold=-0.1,
+        overlap_threshold=-0.4,
         radii="covalent",
         seed=7,
     ):
diff --git a/matid/core/periodicfinder.py b/matid/core/periodicfinder.py
index e729f64b..23bc7a4e 100644
--- a/matid/core/periodicfinder.py
+++ b/matid/core/periodicfinder.py
@@ -61,7 +61,7 @@ def get_region(
         max_cell_size,
         pos_tol,
         bond_threshold=None,
-        overlap_threshold=-0.1,
+        overlap_threshold=-0.6,
         distances: Distances = None,
         return_mask: bool = False,
     ):
@@ -530,11 +530,15 @@ def _find_proto_cell(
 
         # Check that the final proto cell atoms don't overlap
         if proto_cell is not None:
-            dist_proto_cell = matid.geometry.get_distances(proto_cell).dist_matrix_mic
-            dist_proto_cell = dist_proto_cell[np.triu_indices(dist_proto_cell.shape[0])]
+            dist_proto_cell = matid.geometry.get_distances(proto_cell).dist_matrix_radii_mic
+            dist_proto_cell = dist_proto_cell[np.triu_indices(dist_proto_cell.shape[0], 1)]
+            print(dist_proto_cell.min(), overlap_threshold)
             if dist_proto_cell.min() < overlap_threshold:
                 return None, None, None, None
 
+        from ase.visualize import view
+        view(proto_cell)
+
         return proto_cell, offset, n_spans, n_periodic_spans_selected
 
     def _find_graphs(