Difference between revisions of "Avogadro/C4/File-Extensions/English-timed"

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|00:05
 
|00:05
|  In this tutorial, we will learn to, Prepare input files for '''computational ''' '''chemistry''' programmes such as:<br/> '''GAMESS, Gaussian, MOPAC, NWChem''' etc.
+
|  In this tutorial, we will learn to prepare: '''input''' files for computational chemistry programmes such as:<br/> '''GAMESS, Gaussian, MOPAC, NWChem''' etc.
  
 
|-
 
|-
 
|00:18
 
|00:18
And view '''Molecular orbitals ''' and  '''calculated IR spectrum''' using output files generated from: '''GAMESS''' and '''Gaussian''' software.
+
and, view '''Molecular orbitals ''' and  '''calculated IR spectrum''' using output files generated from '''GAMESS''' and '''Gaussian''' software.
  
 
|-
 
|-
 
|00:28
 
|00:28
|  Here I am using '''Ubuntu Linux '''OS version. 14.04.
+
|  Here I am using '''Ubuntu Linux '''OS version. 14.04,
  
 
'''Avogadro''' version 1.1.1.
 
'''Avogadro''' version 1.1.1.
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|-
 
|00:49
 
|00:49
|  The example files required for this tutorial are provided as code files.  
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|  The example files required for this tutorial are provided as '''code files'''.  
  
 
|-
 
|-
 
|00:55
 
|00:55
|  Please download and save them in a folder on desktop.
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|  Please download and '''save''' them in a folder on desktop.
  
 
|-
 
|-
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|-
 
|-
 
|01:04
 
|01:04
|  Load a benzene molecule from '''Build''' menu using '''Insert fragment''' library.
+
'''Load''' a benzene molecule from '''Build''' menu, using '''Insert fragment''' library.
  
 
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|-
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|-
 
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|01:23
 
|01:23
|Using '''Avogadro''' we can prepare input files for popular quantum codes such as:
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|Using '''Avogadro''', we can prepare input files for popular '''quantum code'''s such as:
  
 
'''GAMESS'''
 
'''GAMESS'''
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| 01:36
 
| 01:36
|  Click on '''Gaussian''' option.A graphical data input dialog box opens.
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|  Click on '''Gaussian''' option. A graphical data input dialog box opens.
  
 
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|-
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|-
 
|-
 
| 01:55
 
| 01:55
|  '''Avogadro''' by itself cannot calculate '''molecular orbitals.'''
+
|  '''Avogadro''' by itself cannot calculate molecular orbitals.
  
 
|-
 
|-
 
| 01:59
 
| 01:59
| So let us create an Input file to view the '''molecular orbitals''' of '''benzene''' molecule.
+
| So, let us create an input file to view the molecular orbitals of '''benzene''' molecule.
  
 
|-
 
|-
 
|02:05
 
|02:05
|  In '''Gaussian''' input dialog box , type the title as '''Benzene hyphen MO'''.
+
|  In '''Gaussian''' input dialog box , type the '''Title''' as '''Benzene hyphen MO'''.
  
 
|-
 
|-
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'''Format '''as '''cartesian'''
 
'''Format '''as '''cartesian'''
  
Check the''' checkpoint check box.'''
+
Check the''' checkpoint''' check box.
  
 
|-
 
|-
 
|02:40
 
|02:40
|  You can see the preview of the input file at the bottom of the dialog box.
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|  You can see the '''preview''' of the input file at the bottom of the dialog box.
  
 
|-
 
|-
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|03:18
 
|03:18
| Now this file can be used as an input file for the '''Gaussian''' software programme.
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| Now, this file can be used as an input file for the '''Gaussian''' software programme.
  
 
|-
 
|-
|03: 24
+
|03:24
 
|  About '''Gaussian''' software.
 
|  About '''Gaussian''' software.
  
 
|-
 
|-
 
|03:28
 
|03:28
|'''Gaussian''' is a computer programme for '''computational chemistry'''.
+
|'''Gaussian''' is a computer programme for computational chemistry.
  
 
|-
 
|-
 
|03:32
 
|03:32
| It is a commercial software developed and licensed by '''Gaussian Inc.'''
+
| It is a commercial software developed and licensed by '''Gaussian Inc.''' More information is available at the given link. http://www.gaussian.com/
More information is available at the given link. http://www.gaussian.com/
+
  
 
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|-
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|04:01
 
|04:01
|Click on the panel. Optimize the geometry using '''auto-optimization tool'''.
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|Click on the '''panel'''. Optimize the geometry using '''auto-optimization tool'''.
  
 
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|-
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|-
 
|-
 
|04:36
 
|04:36
|'''RHF''', '''Restricted Hartee Fock''' method of '''approximation '''for the determination of '''wave function.'''
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|'''RHF''', '''Restricted Hartee Fock''' method of approximation for the determination of '''wave function.'''
  
 
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|05:24
 
|05:24
|  For now we will keep the default parameters as such.
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|  For now, we will keep the default parameters as such.
  
 
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|-
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|-
 
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|05:42
 
|05:42
|  Choose the file location as '''Desktop'''. Click on '''Save button.'''
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|  Choose the file location as '''Desktop'''. Click on '''Save''' button.
  
 
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|-
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|05:57
 
|05:57
 
| '''GAMESS''' stands for:  '''General Atomic and Molecular Electronic Structure System'''.
 
| '''GAMESS''' stands for:  '''General Atomic and Molecular Electronic Structure System'''.
(GAMESS)It is a general ab initio quantum chemistry package.   
+
(GAMESS) It is a general ab initio quantum chemistry package.   
  
 
|-
 
|-
 
|06:08
 
|06:08
|  It is available at no cost to both academic and industrial users.
+
|  It is available at no cost, to both academic and industrial users.
  
 
|-
 
|-
 
|06:14
 
|06:14
| Information about installation and download is given at the following link.       http://www.msg.ameslab.gov/gamess/download.html
+
| Information about installation and download is given at the following link.
 +
http://www.msg.ameslab.gov/gamess/download.html
  
 
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|06:45
 
|06:45
| Those interested can download '''GAMESS''' software from the given link.
+
| Those interested can download '''GAMESS''' software from the given link. And, load the input file to generate the output file.
And load the input file to generate the output file. http://www.msg.ameslab.gov/gamess/download.htm
+
http://www.msg.ameslab.gov/gamess/download.htm
  
 
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|07:03
 
|07:03
|Lets view these output files in '''avogadro'''.  
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|Let's view these output files in '''avogadro'''.  
  
 
|-
 
|-
 
|07:07
 
|07:07
|  Open a new Avogadro window.
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|  Open a new '''Avogadro''' window.
  
 
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|07:47
 
|07:47
|  To view the '''orbitals,''' click on the '''orbital''' name from the list.
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|  To view the orbitals, click on the '''orbital''' name from the list.
  
 
|-
 
|-
 
|07:54
 
|07:54
|  If you want to change the display of '''orbitals'''....
+
|  If you want to change the display of '''orbitals''',
 
+
click on the '''spanner''' symbol next to surfaces option in the display types.  
Click on the '''spanner''' symbol next to surfaces option in the display types.  
+
  
 
|-
 
|-
 
|08:02
 
|08:02
|  In the''' Surface Setting''' dialog box.Drag the '''slider''' to change the opacity. Observe the panel.
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|  In the''' Surface Setting''' dialog box, drag the '''slider''' to change the '''opacity'''. Observe the '''panel'''.
  
 
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|08:17
|  By default the '''orbitals ''' are rendered as '''fill'''.
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|  By default, the '''orbitals ''' are rendered as '''fill'''.
  
 
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|08:38
| Observe the panel, the colors of the orbitals are now changed. Close the dialog box.
+
| Observe the panel. The colors of the orbitals are now changed. Close the dialog box.
  
 
|-
 
|-
 
|08:45
 
|08:45
|  To remove the orbitals from the structure;Un-check the '''Surfaces''' option in the '''Display Types.'''
+
|  To remove the orbitals from the structure, un-check the '''Surfaces''' option in the '''Display Types.'''
  
 
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|09:13
 
|09:13
|  We can also view the IR spectrum for the structure.
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|  We can also view the IR-spectrum for the structure.
  
 
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|-
 
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|09:47
 
|09:47
|  Let's summarize  
+
|  Let's summarize.
  
 
|-
 
|-
 
|09:49
 
|09:49
| In this tutorial we have learnt to, Prepare the input files for '''computational chemistry''' programmes such as: '''GAMESS and Gaussian.'''
+
| In this tutorial, we have learnt to: prepare the input files for '''computational chemistry''' programmes such as  '''GAMESS and Gaussian''',
  
 
|-
 
|-
 
|09:58
 
|09:58
View '''Molecular orbitals''' for '''benzene''' and '''water''' molecules.
+
view '''Molecular orbitals''' for '''benzene''' and '''water''' molecules,
  
 
|-
 
|-
 
|10:04
 
|10:04
View calculated '''IR spectrum''' for molecules using log files generated from '''Gaussian'''.
+
view calculated '''IR spectrum''' for molecules using log files generated from '''Gaussian'''.
  
 
|-
 
|-
 
|10:11
 
|10:11
|  For Assignment, Open the log file for '''benzene''' molecule from the code files provided.
+
|  For Assignment, open the log file for '''benzene''' molecule from the '''code files''' provided.
  
 
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|10:22
 
|10:22
| Change the display and color of the lobes. Save the image in '''JPEG '''format.
+
| Change the display and color of the lobes. '''Save''' the '''image''' in '''JPEG '''format.
  
 
|-
 
|-
 
|10:29
 
|10:29
| This video summarizes the Spoken Tutorial project If you do not have good bandwidth, you can download and watch it.
+
| This video summarizes the '''Spoken Tutorial''' project. If you do not have good bandwidth, you can download and watch it.
  
 
|-
 
|-

Latest revision as of 12:03, 24 July 2018

Time
Narration
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.

http://www.msg.ameslab.gov/gamess/download.html

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.

http://www.msg.ameslab.gov/gamess/download.htm

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.
10:35 We conduct workshops using Spoken Tutorials and give certificates. Please contact us.
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.

Contributors and Content Editors

Jyotisolanki, PoojaMoolya, Sandhya.np14