Avogadro/C4/File-Extensions/English-timed
From Script | Spoken-Tutorial
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| 00:01 | Welcome to this tutorial on File Extensions. |
| 00:05 | In this tutorial, we will learn to prepare: input files for computational chemistry programmes such as: GAMESS, Gaussian, MOPAC, NWChem etc. |
| 00:18 | and, view Molecular orbitals and calculated IR spectrum using output files generated from GAMESS and Gaussian software. |
| 00:28 | Here I am using Ubuntu Linux OS version. 14.04,
Avogadro version 1.1.1. |
| 00:38 | To follow this tutorial you should be familiar with, Avogadro interface. |
| 00:43 | If not, for relevant tutorials, please visit our website. |
| 00:49 | The example files required for this tutorial are provided as code files. |
| 00:55 | Please download and save them in a folder on desktop. |
| 01:00 | Here I have opened the Avogadro window. |
| 01:04 | Load a benzene molecule from Build menu, using Insert fragment library. |
| 01:12 | Optimize the geometry using Auto-optimization tool from the tool bar. |
| 01:20 | Click on the Extensions menu. |
| 01:23 | Using Avogadro, we can prepare input files for popular quantum codes such as:
GAMESS Gaussian MOLPRO MOPAC Q-CHEM etc. |
| 01:36 | Click on Gaussian option. A graphical data input dialog box opens. |
| 01:43 | Let me demonstrate how to generate input file for Gaussian program. |
| 01:49 | We need to fill in the required features shown in the dialog box. |
| 01:55 | Avogadro by itself cannot calculate molecular orbitals. |
| 01:59 | So, let us create an input file to view the molecular orbitals of benzene molecule. |
| 02:05 | In Gaussian input dialog box , type the Title as Benzene hyphen MO. |
| 02:11 | Choose Frequencies from the Calculation drop down.
Processors as 1. Theory as B3LYP. 6-31G(d) as Basis set. Charge zero. Multiplicity 1. Output as Standard. Format as cartesian Check the checkpoint check box. |
| 02:40 | You can see the preview of the input file at the bottom of the dialog box. |
| 02:45 | It will be updated as you change the options. |
| 02:49 | Click on Generate button. |
| 02:52 | A Save input Deck dialog box opens. |
| 02:56 | The Gaussian input file generated will be saved with a dot com extension . |
| 03:02 | Type the file name as Benzene. Choose the location as Desktop. Click on Save button. |
| 03:10 | The file will be saved as Benzene.com on the desktop. Open the file with gedit. |
| 03:18 | Now, this file can be used as an input file for the Gaussian software programme. |
| 03:24 | About Gaussian software. |
| 03:28 | Gaussian is a computer programme for computational chemistry. |
| 03:32 | It is a commercial software developed and licensed by Gaussian Inc. More information is available at the given link. http://www.gaussian.com/ |
| 03:41 | Back to Avogadro window. Close the dialog box. |
| 03:46 | Now let us see how to prepare an input file for GAMESS programme. |
| 03:51 | Open a new window. Click on “New” from the Tools menu. |
| 03:56 | Build a water molecule using Draw tool. Change the element to Oxygen. |
| 04:01 | Click on the panel. Optimize the geometry using auto-optimization tool. |
| 04:08 | Click on Extensions menu. Select GAMESS, Input generator from the sub-menu. |
| 04:16 | A GAMESS input dialog box opens. There are two tabs Basic setup and Advanced setup. |
| 04:24 | As we did with the Gaussian input file, fill in the required information. |
| 04:29 | Under Basic Setup, we will select Equilibrium Geometry under Calculate field. |
| 04:36 | RHF, Restricted Hartee Fock method of approximation for the determination of wave function. |
| 04:44 | Since water is a small molecule, we will select 6-31G(d,p) as Basis set. |
| 04:52 | In gas phase, singlet , because all the electrons are paired. |
| 04:58 | Water is a neutral molecule, so charge will be neutral. |
| 05:02 | Click on Advanced Setup to add some more parameters to control the optimization. |
| 05:08 | Click on Basis if you want to change the set of functions. |
| 05:12 | Click on Data. |
| 05:14 | Type the Title as water-MO. |
| 05:18 | Change the Point Group to CnV. |
| 05:21 | Order of Principal Axis to 2. |
| 05:24 | For now, we will keep the default parameters as such. |
| 05:29 | Click on Generate. A Save Input deck opens. |
| 05:34 | By default, the file extension is dot inp. |
| 05:38 | Type the file name as Water. |
| 05:42 | Choose the file location as Desktop. Click on Save button. |
| 05:48 | The GAMESS input file is saved as Water.inp on the Desktop. |
| 05:55 | About GAMESS |
| 05:57 | GAMESS stands for: General Atomic and Molecular Electronic Structure System.
(GAMESS) It is a general ab initio quantum chemistry package. |
| 06:08 | It is available at no cost, to both academic and industrial users. |
| 06:14 | Information about installation and download is given at the following link. |
| 06:20 | Now we have generated input files for GAMESS and Gaussian programmes. |
| 06:26 | These input files are ready to be loaded into respective programmes. |
| 06:31 | Viewers please note: Gaussian is a commercial software. Hence I will not be able to show the interface to load the input file. |
| 06:41 | As mentioned earlier GAMESS is free software. |
| 06:45 | Those interested can download GAMESS software from the given link. And, load the input file to generate the output file. |
| 06:53 | I have some Gaussian and GAMESS output files on the desktop. |
| 06:58 | I have provided these files as code files along with this tutorial. |
| 07:03 | Let's view these output files in avogadro. |
| 07:07 | Open a new Avogadro window. |
| 07:10 | Click on open icon in the tool bar. |
| 07:13 | Navigate to the file location. Select Benzene.log |
| 07:18 | The file opens, we can see the structure of benzene on the panel. |
| 07:24 | Benzene.log was generated using Gaussian. |
| 07:28 | It contains information about molecular orbitals and C-C and C-H bond stretching. |
| 07:36 | Sometimes the log file may not show orbital information. |
| 07:40 | In such case open the .fchk file provided in the codefiles. |
| 07:47 | To view the orbitals, click on the orbital name from the list. |
| 07:54 | If you want to change the display of orbitals,
click on the spanner symbol next to surfaces option in the display types. |
| 08:02 | In the Surface Setting dialog box, drag the slider to change the opacity. Observe the panel. |
| 08:10 | There are three options in the Render drop-down, fill, lines and points. |
| 08:17 | By default, the orbitals are rendered as fill. |
| 08:21 | There is also an option to change the color of the lobes. |
| 08:25 | Click on the Color tabs next to positive and negative option. |
| 08:30 | A Select Color dialog box opens. |
| 08:33 | Click on any color to select. Click on OK button. |
| 08:38 | Observe the panel. The colors of the orbitals are now changed. Close the dialog box. |
| 08:45 | To remove the orbitals from the structure, un-check the Surfaces option in the Display Types. |
| 08:51 | Click on Vibrations tab to view the vibrational frequencies. |
| 08:56 | In the Vibration window, click on any frequency from the list. |
| 09:01 | Click on Start Animation button present at the bottom of the window. |
| 09:06 | Observe the panel. The stretching of C-C and C-H bonds are animated. |
| 09:13 | We can also view the IR-spectrum for the structure. |
| 09:17 | Click on Show Spectra. |
| 09:20 | A Spectra Visualization window opens. It shows the calculated IR spectrum of Benzene. |
| 09:27 | Open a new window. Open the log file created for water molecule using GAMESS programme. |
| 09:35 | The log file opens with a structure of water and Molecular orbital information. |
| 09:41 | Click on the name of the orbital from the list. The orbital is displayed on the panel. |
| 09:47 | Let's summarize. |
| 09:49 | In this tutorial, we have learnt to: prepare the input files for computational chemistry programmes such as GAMESS and Gaussian, |
| 09:58 | view Molecular orbitals for benzene and water molecules, |
| 10:04 | view calculated IR spectrum for molecules using log files generated from Gaussian. |
| 10:11 | For Assignment, open the log file for benzene molecule from the code files provided. |
| 10:18 | Display any Molecular Orbital from the list. |
| 10:22 | Change the display and color of the lobes. Save the image in JPEG format. |
| 10:29 | This video summarizes the Spoken Tutorial project. If you do not have good bandwidth, you can download and watch it. |
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| 10:42 | The Spoken Tutorial Project is funded by NMEICT, MHRD Government of India. |
| 10:48 | This is Snehalatha from IIT Bombay signing off.
Thank you for joining. |
