:orphan:

.. status publishable
.. product MD Phonon
.. sectionauthor David Reith
.. SME David Reith
.. PR Walter 
.. TW Katherine  
.. date 2023

.. _MDphononDTS:

|medea| |mdphonon| Vibrational Properties from Molecular Dynamics Simulations
-----------------------------------------------------------------------------

.. admonition:: **At-a-Glance** 

  |medea|\ :sup:`®`\ [#TM]_ *MD Phonon* calculates vibrational properties from
  velocity auto-correlation functions obtained during molecular dynamics
  simulations and can be efficiently applied to low symmetry
  structures such as crystalline structures with defects, amorphous materials
  and fluids. Based on the vibrational density of states, obtained from the
  velocity auto-correlation functions, 
  thermodynamic properties such as entropy or Helmholtz free
  energy can be calculated accurately and efficiently. 
   

  **Key Benefits**

  * Study systems with low symmetry. For example, temperature stabilized
    structures (*i.e.*, perovskites), amorphous materials, or crystalline structures with defects.
  * Automated plot creation facilitates analysis of results.
  * View the plots for velocity auto-correlation functions of each element in each subset.
  * Study the vibrational density of states, its partial contributions of all elements, and all subsets by automatically generated plots on the JobServer and within |medea|’s analysis tool.
  * Evaluate thermodynamic properties at the chosen temperature such as internal energy, entropy, Helmholtz free energy, and heat capacity.


The vibrational density of states is calculated from velocity auto-correlation
functions  [#Lin2003]_ obtained on-the-fly during LAMMPS microcanonical NVE molecular
dynamic simulations thereby making use of the LAMMPS
engine for efficient performance
on computers from scalar workstations to massively parallel supercomputers.
Based on the density of states thermodynamical properties such as internal energy, entropy,
Helmholtz free energy, and heat capacity are calculated. 
This approach can be applied to crystalline systems, amorphous materials and
fluids facilitating the vibrational study of complex materials.  

The calculated density of states is viewed directly on the *JobServer* or within
the |medea| graphical-user interface. Thermodynamical properties are
reported in the *Job.out* file and are available as variables in the *Flowchart*
environment. 



.. figure:: /Datasheets/images/MDPhonon_TDF.png
   :width: 3.5in
   :align: center

   Thermodynamic functions Helmholtz free energy *A*, potential energy *E* and
   entropy times temperature *- T S* are shown for wurtzite aluminum nitride.  

.. figure:: /Datasheets/images/MDPhonon_Methane.png
   :align: center

   Vibrational density of states for a methane fluid at a temperature of 100 K.  

Properties from *MD Phonon*
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

* Total and partial vibrational density of states
* Zero-point energy
* Thermodynamic properties at a given temperature: 

  * Vibrational part of heat capacity
  * Enthalpy
  * Entropy
  * Helmholtz free energy 

Characteristics
^^^^^^^^^^^^^^^^^^

* Apply |medea| |mdphonon| to amorphous materials, fluids, and crystalline
  structures such as metals, and ceramics.
  Accuracy depends on the quality of the employed forcefield.

* Define subsets (e.g., interface layers, surface layers, nanoparticles, etc.) for which to calculate the partial
  contributions.  

* Plug the |medea| |mdphonon| module into any LAMMPS simulation workflow and
  the vibrational density of states, as well as thermodynamic properties, are
  calculated.

.. add for a column break, adjust where needed
.. raw:: latex

   \newpage

Required Modules
^^^^^^^^^^^^^^^^

* |medea| |menvironment|
* |medea| |mdphonon|
* |medea| |mlammps| |mstdenv|


Recommended  Modules 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

* |medea| |mphonon|


.. Will update find out more after webinar and creation of tutorials.
.. Find Out More [Required]
.. ^^^^^^^^^^^^^^^^^^^^^^^^

.. Include a Call-To-Action (CTA) but avoid saying “call us” or “visit our website.”
.. We will already have that information at the bottom of the datasheet. Use the CTA
.. to direct readers to the next step that would lead them along the sales cycle path
.. or to another valuable and helpful piece of information like the product’s architecture,
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.. [#TM] |regTMinfo|

.. [#Lin2003] S.-T. Lin *et al.*,
   *J. Chem. Phys.* **119**, 11792 (2003)
   (`DOI <https://doi.org/10.1063/1.1624057>`__)

.. only:: html 
 
    :download: :download:`pdf </Datasheets/Datasheet-MDPhonon.pdf>`