Spectroscopy
=============

It is available for MLatom to simulate different kinds of spectra. 
Here we will show how to use MLatom for power spectra and IR spectra.

- :ref:`Power spectra <Power spectra>`
- :ref:`IR spectra <IR spectra>`

.. _Power spectra:

Power spectra
~~~~~~~~~~~~~

MD trajectory can be used to generate the power spectra. Here we choose ethanol as example. 
To generate the power spectrum of ethanol in command line, we should prepare the input file 
:download:`ethanol_ps.inp <files/ethanol_ps.inp>` and the auxiliary file :download:`ethanol_traj.h5 <files/ethanol_traj.h5>` 
documenting the molecular dynamics trajectory of ethanol.

.. code-block::

   # ethanol_ps.inp
   MD2vibr                     # Calculate vibrational spectrum from MD 
   trajH5MDin=ethanol_traj.h5  # Read MD trajectory
   output=ps                   # Calculate power spectrum

Run it.

.. code-block::

   mlatom ethanol_ps.inp

Import a specific module in Python so that the result will appear in ``.png`` format.

.. code-block::

   from IPython.display import Image
   Image(filename='ps.png') 

.. _IR spectra:

IR spectra
~~~~~~~~~~~

MD trajectory can also be used to generate IR spectra. Similar with the power spectra, in command line we need to 
prepare the input file :download:`ethanol_ir.inp <files/ethanol_ir.inp>` and the MD trajectory :download:`ethanol_traj.h5 <files/ethanol_traj.h5>`.

.. code-block::

   # ethanol_ir.inp
   MD2vibr                     # Calculate vibrational spectrum from MD 
   trajH5MDin=ethanol_traj.h5  # Read MD trajectory
   output=ir                   # Calculate infrared spectrum

Run the input file.

.. code-block::

   mlatom ethanol_ir.inp

Import a specific module in Python so that the result will appear in ``.png`` format.

.. code-block::

   from IPython.display import Image
   Image(filename='ir.png') 

There is the code for simulating IR spectra in Python.

You can see the spectrum (``ir.png``) in your folder after the computation is finished:

.. figure:: _static/ir-aiqm1.png
   :width: 100%
   :align: center

Below, for comparison, is the spectrum from the NIST database:

.. figure:: _static/ir-nist.png
   :width: 100%
   :align: center

.. code-block::

   import mlatom as ml

   traj = ml.data.molecular_trajectory() 
   traj.load('ethanol_traj.h5',format='h5md')
   dt = traj.steps[1].time - traj.steps[0].time
   moldb = ml.data.molecular_database() 
   moldb.molecules = [each.molecule for each in traj.steps]

   vib = ml.vibrational_spectrum(molecular_database=moldb, dt=dt)
   vib.plot_infrared_spectrum(filename='ir_api.png')

   from IPython.display import Image
   Image(filename='ir_api.png') 

.. include:: ml-nea.rst

.. include:: ml-tpa.rst