All Option Keywords
========================

Here, we describe all option keywords in ABPolymer input file. You can find an input file containing all options here: :doc:`input`.

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charmm
--------

.. option:: scaling14

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      * - Value
        - A real number
      * - Default
        - ``1.0``
   
   Define the scaling factor for electrostatic interactions of 1-4 term.

.. option:: rcutoff

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      * - Value
        - A real number
      * - Default
        - ``15.0``
    
   Define the distance in Angstrom to cutoff non-bonded interactions.

   If ``rswitch`` is larger than ``rcutoff``, switching function will not be used and no cutoff is applied on long range forces.	

.. option:: rswitch

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      * - Value
        - A real number
      * - Default
        - ``10.0``
   
   Define the distance in Angstrom to activate switching function.
   
   If ``rswitch`` is larger than ``rcutoff``, switching function will not be used and no cutoff is applied on long range forces.	

opt
----

This option controls the geometry optimization details.

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.. option:: num_steps

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      * - Value
        - An integer
      * - Default
        - ``1000``
   
   The maximum number of geometry optimization steps.

.. option:: epsilon

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      * - Value
        - A real number
      * - Default
        - ``1.E-2``
   
   The convergence condition. If the ratio of gradient norm to coordinate norm is less than ``epsilon``, then the optimization is assumed to be converged.

md
------

This option controls the NVT molecular dynamics (MD) simulation details.

.. option:: dt

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      * - Value
        - A real number 
      * - Default
        - ``0.0005``

   The time step in ps. For systems not containing hydrogen atoms, ``dt`` can be set to ``0.001`` ps.

.. option:: num_steps

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      * - Value
        - An integer
      * - Default
        - ``10000``
   
   The number of MD steps to be run.

.. option:: output_freq

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      * - Value
        - An integer
      * - Default
        - ``100``

   The number of steps that MD information is output. The trajectory will be output to disk. 

.. option:: temp

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      * - Value
        - A real number
      * - Default
        - ``300``
   
   Define the target temperature for NVT simulation.

.. option:: temp_nhc_length

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      * - Value
        - An integer
      * - Default
        - ``5``
   
   The length of Nose-Hoover chain to control the temperature. Usually an integer larger than 2 is enough.

.. option:: temp_nhc_tau

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      * - Value
        - A real number
      * - Default
        - ``0.05``
   
   The time-constant of Nose-Hoover chain to control the temperature in ps.

grow
------

This option controls the amorphous material growth details.

.. option:: dir_fn

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      * - Value
        - A directory name
      * - Default
        - ``x``
  
   The folder to store all intermediate files during the simulation. This directory should have **NOT** already existed, otherwise ABPolymer will raise an error like ``Cannot create directory "x" to save intermediates``.

.. option:: num_steps

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      * - Value
        - An integer
      * - Default
        - ``-1``

If a positive number is given, the growing will be performed for ``num_steps``  steps. If ``-1`` is given, the growing will stop when all units are depleted.

.. option:: r_intra

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      * - Value
        - A real number
      * - Default
        - ``4``

Define the distance in Angstrom at which an intramolecular bond may form.

If 2 reactive sites of the same molecule are within this distance, a bond **MAY** form between them. So, if you set it to a negative value like ``-4``, no intramolecular polymerization will occur.

.. option:: md_freq

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      * - Value
        - An integer
      * - Default
        - ``10``

   The frequency to do MD information. For example, if you set ``md_freq`` to ``10``, then every 10 growing steps, an NVT MD (controlled by the ``md`` block) will be performed.

unit
------

This option gives the components of the amorphous material. A typical input is:

.. code-block:: 
    :linenos:
    
    unit 
        paf1.xyz           100
        myunits/paf80.xyz  10
    end

This means that the amorphous material contains ``100`` monomers defined by ``paf1.xyz`` and ``10`` monomers defined by ``myunits/paf80.xyz``. The order does not matter, since ABPolymer will grow with a random monomer in each step.

For details of preparing monomer file ``*.xyz``, see :doc:`monomer`.