Example (GAMESSUS): Dynamics of |H2+| Fewest Switches Surface Hopping.
======================================================================

This is an example of a fewest-switches-surface-hopping calculation for an ionized hydrogen molecule (|H2+|).
See the directory::

    Examples/xpyder/h2+/

Preparation
-----------
1. set your environment variable CDTK_GAMESSUS to the path of the gamessus directory. For example::

      export CDTK_GAMESSUS=$HOME/gamess/

   Instead of '$HOME/gamess/' insert the actual path of your gamess installation.
2. Depending on your gamess installation, output is written to the scratch file folder. This is configured in the ``rungms`` script in your gamess installation.
   Edit the script ``rungms`` accordingly so that the output is written in the current working directory. You may want to comment out the lines
   ``set SCR=~/gamess/restart`` and ``#set USERSCR=~/gamess/restart``,
   instead, set the SCR and USERSCR environment variables to ``.``. For example::

     export SCR=.
     export USERSCR=.

   Note that the local directory in which the simulation is run should be a rapidly accessible disk (i.e., a local folder or ramdisk) - otherwise there will be huge performance losses.

Running
-------
To run the example, execute::

   xpyder -i input_h2+_dynamics_no_field -d H2+_dynamics_no_field


Details of the Inputfile
------------------------
The file ``input_h2+_dynamics_no_field`` is the input file used for the calculation: ::

    $SYSTEM
      qchemistry  = gamess
      xunit       = an
      rseed       = 1
      keepinp
      keeplog
    $END

    $gamess
      memddi = 2
      mwords = 2
      gbasis = TZV
      icharg = 1
      mult = 2
      ncore = 0
      nact = 2
      nels = 1
      wstate = 1.0,1.0
      nstate = 2
      sz = 0.5
      mxxpan = 100
      fullnr = .true.
    $end

    $trajectory
      dt =  0.01   fs
      tf =  6.0   fs
    $end

    $quantum
      type      = fssh
      rescaling = nac
      istate    = 1 
      nstates   = 2
      first_step = 1.0
    $end

    $cartPOS
      H    0.0   0.0   -0.5292344732
      H    0.0   0.0    0.5292344732 
    $end

    $cartVEL
      H  0.0  0.0    0.00
      H  0.0  0.0   -0.00
    $end



   
1. ``$SYSTEM``
   
   - ``qchemistry = gamess`` specifies the quantum chemistry tool.
   - ``xunit = an`` specifies the unit in the coordinates of the atom is specified. "an" refers to Angstrom
   - ``rseed = 1`` gives the initial seed value for the random number generator used for the calculations.
   - ``keepinp`` and ``keeplog`` will keep the input and the outputput files of the quatum chemistry tool.
     (If you do not give this option, then it will remove the files)

2. ``$gamess``
   
   - this gives the input detials such as the basis used, active space etc., for the electronic structure
     calculation.

3. ``$trajectory``
   - "dt" is for the time step used for the calculation (in fs).
   - "tf" is the final time ie., the time till the calculation will last (in fs).

4. ``cartPOS`` and ``cartVEL``
   - this gives the intial position and velicity of the atoms.

5. ``quantum``
   
   - ``type = fssh`` specifies the type of surface hopping. "fssh" denotes Tully's Fewest Switches Surface hoping.
     (one can give "nohop" to avoid the surface hopping dynamics).
   - ``istate`` and ``nstate`` gives the initial state at which the trajectory present and no. of states respectively.
   - ``rescaling`` specifies the type of rescaling when a hop is performed.
     The parameter ``nac`` specifies rescaling based on non-adiabatic 
     coupling vectors, commonly used for surface hopping.
     Alternatively, one can give ``grd`` for rescaling based on the gradiant.

Output data
-----------
The folder ``H2+_dynamics_no_field`` contains all the output files.

1. ``P.log`` gives the population of the states by solving the time dependent Schroedinger equation.
2. ``C.log`` gives the co-efficients for the electronic states.
3. ``V_ad.log`` gives the adiabatic potential energies for all the states.
4. ``R.log`` gives the position of the atoms at the end of the calculation.
5. ``V.log`` gives the velocity of the atoms.
6. ``S.log`` gives the active surface of the trajectory.
7. ``NAC.log`` gives the coupling terms, i.e., the off diagonal terms of the Hamiltonian.
8. ``E.log`` gives the potential energy, kinetic energy and totol energy of the trajectory.
9. ``Switch.log`` gives the details of the hopping, its probability, the random number used and also the reason for the hopping.

Note: apart from all the above files, there will be output and input files of the eletronic structure calculations based on the input option.

.. |H2+| replace:: H\ :sub:`2`:sup:`+`