Example (XMOLECULE): Dynamics of |H2O+| with a classical electron
=================================================================

In this example, the dynamics of an ionized water molecule and an electron in its vicinity is described.
The example investigates the interaction of the molecule ion and a photoelectron during a photoionization process.

See::

   Examples/xpyder/H2O+_and_el/


Preparation
-----------

Make sure you have installed xmolecule in your local python environment.
See Installation instructions.

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

   xpyder -i input_electron_fssh -d electron_fssh

Details of the Inputfile
------------------------
The ``input_electron_fssh`` is the input file used for the calculation: ::

   $SYSTEM
     qchemistry = xmolecule
     xunit = bohr
   $END

   $xmolecule
     MOM=yes
     gto=6-31G
     HF=yes
     gs_occ=yes
     occ=22221
     charge=1
     R_softcore=0.32
   $end

   $trajectory
     dt = 0.001   fs
     tf = 1.0   fs
   $end

   $quantum
     type = fssh
     nstates = 4
     istate  = 3
     rescaling = nac
   $end

   $mmregion
     dt = 0.001  fs
   $end


   $cartPOS
     O  -0.000000    -0.000000     0.116743
     H  -0.000000    -1.498103     1.205793
     H  -0.000000     1.498103     1.205793
   $end

   $cartVEL
     O     0.000000     0.000000     0.000000
     H     0.000000     0.000000     0.000000
     H     0.000000     0.000000     0.000000
   $end

   $cartPOS_MM
     e    0.000000     0.600000     0.600000
   $end

   $cartVEL_MM
     e    0.000000     0.100000     0.600000
   $end


1. ``$SYSTEM``
   
   - ``qchemistry = xmolecule`` specifies the quantum chemistry tool. 

2. ``$xmolecule`` gives input details 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. ``$quantum``
   
   - ``type = fssh`` specifies the type of surface hopping. ``fssh`` denotes Tully's Fewest Switches Surface hoping.

   - ``istate`` and ``nstate`` gives the initial state at which the trajectory starts and the number of states that are used, respectively.

   - ``rescaling = nac`` specifies the type of rescaling done. 

4. ``$mm_region`` indicates that there is a classical particle in the simulation

5. ``$cartPos`` / ``$cartPos_MM`` / ``$cartVEL`` / ``$cartVEL_MM``

   - these section specify the initial position and velocities of the atoms and the electron
   
Output data
-----------
The folder ``electron_fssh`` 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 of the states.
3. ``V_ad.log`` gives the adiabatic potential energies for all the states.
4. ``R.log`` gives the position of the atoms and the electron.
5. ``V.log`` gives the velocity of the atoms.
6. ``S.log`` gives the state at which the trajectory is at every time step.
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 more details about the hopping.
10. ``partial.log`` shows partial charges of each atom (Mulliken charges).


   .. figure :: exampleH2OElFSSH.png
      :width: 600
      :alt: Electronic state populations as a function of time

      Electronic state populations as a function of time.

The figure shows the electronic state populations as a function of time computed for a single FSSH trajectory.
As one can see, the flying away electron induces strong couplings between the states that leads to strong changes in the state populations.


.. |H2O+| replace:: H\ :sub:`2`\ O\ :sup:`+`