INitial commit of CAC code

docs/Commands/group.md

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+# group
+
+```sh
+group id selection shape ...
+```
+
+## Inputs 
+
+`id` - assigned id for the group.
+
+`selection` - either `atoms`, `elements`, or `all`. 
+
+`shape` - either `block`, `sphere`, or `type`.
+
+**Additional arguments depend on the group shape passed and are listed below:** 
+
+```sh
+group id selection block xlo xhi ylo yhi zlo zhi
+```
+where `{x,y,z}lo` are the lower bounds along `x,y,z` and `{x,y,z}hi` are the upper bounds along `x,y,z`.
+
+```sh
+group id selection sphere x y z r
+```
+where `x y z` define the centroid of the sphere and `r` defines the radius of the sphere.
+
+```sh
+group id selection type n
+```
+where `n` is a number which selects the `n`th atom type.
+
+## Examples
+```sh
+group tophalf all block -inf inf -inf inf inf*0.5 inf
+group precip atoms sphere 100 78 78 10
+group Ni atoms type 2
+```
+
+## Description
+
+The group option is used in conjunction with other commands which require a group input. 
+**A default `all` group is defined which contains all atoms and elements.**
+A subsection of all atoms or elements can be selected using the group command.
+`id` is used to refer to the group in other commands.
+`selection` determines which element types are selected within the group. 
+A group can be defined containing only `atoms`, `elements`, or `both`. 
+If element types are within the bounds of the group but are not specified with `selection` they are not defined as members of the group.
+
+All positions for the group command can be specified using position specifications described [here](../Misc/position.md).
+
+
+