stack
=====


The stack command is used to stack the current structure. The type of stacking depends on the current structure.
Currently available structures:

* graphene/boronnitride (creates a stack of sheets)
* cnt (creates a periodic stack of parallel cnts)

Depending on which structure is stacked, different arguments and commands for further customization are available:

graphene/boronnitride stacking
-------------------------------

``interlayer_spacing``
^^^^^^^^^^^^^^^^^^^^^^^^

the interlayer_spacing arg sets the distance between adjacent sheets Angstrom. the arg requires one floating point value.
example: ``interlayer_spacing=5.0``. The default for graphene is ``interlayer_spacing=3.35``,  the default for boronnitride ``interlayer_spacing=3.5``.
graphene will have ABA stacking and boronnitride will have AA' stacking.

``number_of_layers``
^^^^^^^^^^^^^^^^^^^^^

the number_of_layers arg sets the number of sheets that the stack will contain. the arg requires one integer value.
example: ``number_of_layers=5``.


Example build:

.. code-block:: none

     CONAN-build: build type=graphene
     CONAN-build: stack interlayer_spacing=5.0 number_of_layers=5


will yield the following structure:

.. image:: ../../pictures/basic_graphene_stack.png
   :width: 40%
   :alt: Graphene_stacked

cnt stacking
------------

Cnt stacking will create a periodic boox of parallel cnts

``multiplicity``
^^^^^^^^^^^^^^^^^

the multiplicity arg sets the number of unit cells in x and y directions. the arg requires two integer values.
example: ``multiplicity=2 3``.

``tube_distance=``
^^^^^^^^^^^^^^^^^^

the tube_distance arg sets the distance between parallel tubes in Angstrom. the arg requires one floating point value.
example: ``tube_distance=1.0``.


example build:

.. code-block:: none

     CONAN-build: build type=cnt armchair tube_size=8 tube_length=10.0
     CONAN-build: stack multiplcity=2 2 tube_distance=1.0


will yield the following structure:

.. image:: ../../pictures/cnt_stacked.png
   :width: 40%
   :alt: cnt_stacked


add
===

the add command is used to place functional groups at a specific position. Functional groups are
taken from the .xyz files in /current_version/structures/ and selected with the ``group`` argument. ``group=OH`` will search for
a file called "OH.xyz" in the structures folder and add its contents to the sheet. The position can be specified using the ``position``,
which takes in the index of the atom the group should be placed on. When using VMD the indices can be shown using the ``vmd show_index`` command in conan.
The command tries to take into account the local topology of the structure, so placements on curved surfaces (like the inside of a Pore) are possible.


undo
====

The last command can be reset using the ``undo`` command.