Vibrational frequencies and IR spectrum of ethane
*************************************************

ADF Spectroscopy Geometry optimization Vibrational frequencies IR
spectrum Normal modes


Create an ethane molecule
=========================

   **1.** Open AMSinput

Next we create an ethane molecule:

   **1.** Select the C-tool ([image: CTool][image])
   **2.** Click once in the molecule drawing area to make a carbon atom
   **3.** Click again to make a second carbon atom
   **4.** Select **Atoms → Add Hydrogens**
   **5.** And do it again: **Atoms → Add Hydrogens**
   **6.** Pre-optimize by clicking on [image: PreOptimTool][image]
   **7.** Click the Symmetrize button [image: SymmTool][image]

   [image]

You need to add hydrogen twice: the first time one carbon atom was
selected. Thus, the 'Add Hydrogen' command added the hydrogen to that
selected atom only. By repeating the 'Add Hydrogen' command the
hydrogens are added in all possible places.

The symmetrization should have enforced perfect D(3D) symmetry, using
the Symmol program (see the help balloon on that button for details).


Geometry optimization and vibrational frequencies calculation
=============================================================

We will now set up a geometry optimization followed by a frequency
calculation:

   In the main ADF panel:
   **1.** Select **Task → Geometry Optimization**
   **2.** Check the **Frequencies** check-box

   [image]

Now run the calculation:

   In AMSinput
   **1.** In the **menu bar**, select **File → Run** (give your calculation a nice name, e.g.  'ethane')
   Wait for the calculation to finish (check the logfile)...
   **2.** Click the 'Update molecule' button that pops up in the AMSinput window to update the geometry


Visualize the IR-spectrum, normal modes
=======================================

The IR spectrum can be visualized using the AMSspectra module.

   In AMSinput
   **1.** In the **menu bar** Select **SCM → Spectra**
 [image]

On the left side of the window the molecule (Ethane) is shown.

On the right side the IR spectrum is shown.

Tip:

  * save a picture (of the IR spectrum) as an image: **File → Save
    Image...** (PNG by default)

  * export the xy coordinates of the spectrum to a plain text file:
    **File → Export XY Values...**.

  * export the peak positions and intensities to a plain text file:
    **File → Export XY Peaks...**.

  * Increase the spectral linewidth (Width box beneath spectrum) to
    obtain a spectrum that looks better.

Below the spectrum window a table is shown with details about the
peaks.

You can click on a peak in the spectrum, or select a line in the
table:

   **1.** Click on the mode with the intensity (approximately 58 km/mol) in the table
 [image]

The atoms of the molecule should be animated according to the selected
normal mode (see also the options in the **Play** menu in the menu
bar).

To view another normal mode, you can use the left and right arrow keys
to move through them.

You can make the displacements larger or smaller via menu commands
(**Play → Configure Displacements**), or via the up and down arrow
keys on the keyboard (after clicking in the graph or molecule window).

To show the normal mode as vectors:

   **1.** Click in the molecule window to make sure it has input focus
   **2.** Click on **Play → Displacement Vectors** to visualize the normal mode with vectors
 [image]

You can make the vectors larger or smaller using the same
ctrl/cmd-L/K, or arrow up and down.

You can also visualize the normal mode in AMSmovie (which offers some
extra options, e.g. you can make an mpg movie showing the mode)

   In the menu bar, select **Play → Open Mode In AMSmovie**

In AMSmovie you have some extra advanced options, for example you can
make an mpg movie showing the mode.

See also: Partial Vibrational Spectra (PVDOS)

You can close all open AMS-GUI windows by selecting in the menu bar
**SCM → Quit All**,
