Initial working commit with bug in delete command

README.md

@@ -245,6 +245,24 @@ This allows the user to specify the boundary conditions for the model being outp
 
 **Example:** `-boundary psp`
 
+### Option Delete
+
+```
+-delete keywords
+```
+
+Delete requires the usage of additional keywords to specify which delete action will be taken. These additional keywords are below:
+
+**overlap**
+
+```
+-delete overlap rc_off
+```
+
+This command will delete all overlapping atoms within a specific cutoff radius `rc_off`. This currently does not affect elements. 
+
+****
+
 ## Position Specification
 
 Specifying positions in cacmb can be done through a variety of ways. Examples of each format is shown below.