Molecule insertion 
=====================
.. |Angstrom|   unicode:: U+00C5 

This script was designed for adding molecules into the simulation box with existing atoms inside. 
It is suitable for inserting molecules inside porous materials such as metal organic frameworks (MOFs). 
The positions and the orientations will be randomly determined 
considering the overlap with the existing and the pre-added 
atoms. CO2 and H2O are explicitly defined in the scripts, while the other molecular types are needed to be added 
by modifying the script. 

Input 
---------

optional arguments:

* ``--help``
   Show helping message and exit

* ``-frame`` 
   Input framework structure from any format to ASE reader

* ``-h2o`` 
   The number of H2O molecules inserted in framework

* ``-co2``
   The number of CO2 molecules inserted in framework

* ``-maxiter`` 
   Max iteration when placing each molecules

* ``-threshold`` 
   Threshold for minimum intermolecular distance when placing molecules

* ``-l_fix_framework``
   Fix framework or not

* ``-l_sort_mol`` 
   Sort molecule layer or not

* ``-seed`` 
   Seed for random (in case you want the same structure)

* ``-outfile`` 
   The name of file to be written out

* ``-format``
   The format of output file to be written out





Example 
---------

.. code-block:: shell 

    $ python ./src/insertmolecules.py \
            -frame ./structure/calf20.vasp \
            -h2o 4 \
            -co2 2 \
            -outfile output_calf 
            -format vasp \
            -l_fix_framework True \
            -threshold 2.1