Add page on neighbor definition

rosswhitfield · Sep 22, 2017 · bc1e476 · bc1e476
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diff --git a/docs/images/README.md b/docs/images/README.md
@@ -0,0 +1,5 @@
+To create svg from fig:
+
+```
+fig2dev -L svg src/neighbors.fig neighbors.svg
+```
diff --git a/docs/images/neighbors.svg b/docs/images/neighbors.svg
diff --git a/docs/images/src/neighbors.fig b/docs/images/src/neighbors.fig
@@ -0,0 +1,85 @@
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diff --git a/docs/tutorials.rst b/docs/tutorials.rst
@@ -8,3 +8,4 @@ Tutorials
    tutorials/discus
    tutorials/ase
    tutorials/diffpy
+   tutorials/neighbors
diff --git a/docs/tutorials/neighbors.rst b/docs/tutorials/neighbors.rst
@@ -0,0 +1,29 @@
+==================================
+Neighbors definition in Javelin
+==================================
+
+.. image:: ../images/neighbors.svg
+
+The neighbors above are created in javelin by (starting at 12 o'clock
+and working clockwise):
+
+>>> from javelin.neighborlist import NeighborList
+>>> nl = NeighborList([[0, 0, 0, 2, 0],
+...                    [0, 1, 0, 0, 0],
+...		       [0, 0, 1, 0, 0],
+...                    [0, 0, 2,-1, 0],
+...                    [0, 1,-2,-1, 0]])
+>>> nl
+NeighborList([[ 0  0  0  2  0]
+              [ 0  1  0  0  0]
+              [ 0  0  1  0  0]
+              [ 0  0  2 -1  0]
+              [ 0  1 -2 -1  0]])
+>>> print(nl)
+      |     site      |    vector
+index | origin target |   i   j   k
+    0 |      0      0 |   0   2   0
+    1 |      0      1 |   0   0   0
+    2 |      0      0 |   1   0   0
+    3 |      0      0 |   2  -1   0
+    4 |      0      1 |  -2  -1   0