Added possibility to use more images with pbc_points.

mdevaluate/pbc.py

@@ -199,27 +199,37 @@ def nojump(frame, usecache=True):
         ).T) * frame.box.diagonal()
     return frame - delta
 
-def pbc_points(coordinates, box, thickness=0, index=False, shear=False):
+
+def pbc_points(coordinates, box, thickness=0, index=False, shear=False,
+               extra_image=False):
     """
     Returns the points their first periodic images. Does not fold 
     them back into the box.
     Thickness 0 means all 27 boxes. Positive means the box+thickness. 
     Negative values mean that less than the box is returned.
-    index=True also returns the indices with indices of images being their originals values.
+    index=True also returns the indices with indices of images being their
+    originals values.
     """
     if shear:
-        box[2,0] = box[2,0]%box[0,0]
-    grid = np.array([ [i, j, k] for k in [-1,0,1] for j in [1,0,-1] for i in [-1,0,1] ])
-    coordinatesPBC = np.concatenate([coordinates+v@box for v in grid], axis=0)
+        box[2, 0] = box[2, 0] % box[0, 0]
+    if shear or extra_image:
+        grid = np.array([[i, j, k] for k in [-2, -1, 0, 1, 2]
+                         for j in [2, 1, 0, -1, -2] for i in [-2, -1, 0, 1, 2]])
+        indices = np.tile(np.arange(len(coordinates)), 125)
+    else:
+        grid = np.array([[i, j, k] for k in [-1, 0, 1] for j in [1, 0, -1]
+                         for i in [-1, 0, 1]])
+        indices = np.tile(np.arange(len(coordinates)), 27)
+    coordinates_pbc = np.concatenate([coordinates+v@box for v in grid], axis=0)
     size = np.diag(box)
-    indices = np.tile(np.arange(len(coordinates)),(27))
+
     if thickness != 0:
-        mask = np.all(coordinatesPBC > -thickness, axis=1)
-        coordinatesPBC = coordinatesPBC[mask]
+        mask = np.all(coordinates_pbc > -thickness, axis=1)
+        coordinates_pbc = coordinates_pbc[mask]
         indices = indices[mask]
-        mask = np.all(coordinatesPBC < size+thickness, axis=1)
-        coordinatesPBC = coordinatesPBC[mask]
+        mask = np.all(coordinates_pbc < size+thickness, axis=1)
+        coordinates_pbc = coordinates_pbc[mask]
         indices = indices[mask]
     if index:
-        return coordinatesPBC, indices
-    return coordinatesPBC    
+        return coordinates_pbc, indices
+    return coordinates_pbc

requirements.txt

@@ -6,5 +6,5 @@ pandas
 dask
 sqlalchemy
 psycopg2-binary
-ipyvlume
+ipyvolume
 jupyter_contrib_nbextensions