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

From Script | Spoken-Tutorial
Jump to: navigation, search
Line 9: Line 9:
 
|-
 
|-
 
|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.
Line 31: Line 31:
 
|-
 
|-
 
|00:49
 
|00:49
−
|  The example files required for this tutorial are provided as code files.  
+
|  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.
+
|  Please download and '''save''' them in a folder on desktop.
  
 
|-
 
|-
Line 43: Line 43:
 
|-
 
|-
 
|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.
  
 
|-
 
|-
Line 55: Line 55:
 
|-
 
|-
 
|01:23
 
|01:23
−
|Using '''Avogadro''' we can prepare input files for popular quantum codes such as:
+
|Using '''Avogadro''', we can prepare input files for popular '''quantum code'''s such as:
  
 
'''GAMESS'''
 
'''GAMESS'''
Line 69: Line 69:
 
|-
 
|-
 
| 01:36
 
| 01:36
−
|  Click on '''Gaussian''' option.A graphical data input dialog box opens.
+
|  Click on '''Gaussian''' option. A graphical data input dialog box opens.
  
 
|-
 
|-
Line 81: Line 81:
 
|-
 
|-
 
| 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.
  
 
|-
 
|-
Line 109: Line 109:
 
'''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.
+
|  You can see the '''preview''' of the input file at the bottom of the dialog box.
  
 
|-
 
|-
Line 141: Line 141:
 
|-
 
|-
 
|03:18
 
|03:18
−
| Now this file can be used as an input file for the '''Gaussian''' software programme.
+
| Now, this file can be used as an input file for the '''Gaussian''' software programme.
  
 
|-
 
|-
Line 149: Line 149:
 
|-
 
|-
 
|03:28
 
|03:28
−
|'''Gaussian''' is a computer programme for '''computational chemistry'''.
+
|'''Gaussian''' is a computer programme for computational chemistry.
  
 
|-
 
|-
Line 174: Line 174:
 
|-
 
|-
 
|04:01
 
|04:01
−
|Click on the panel. Optimize the geometry using '''auto-optimization tool'''.
+
|Click on the '''panel'''. Optimize the geometry using '''auto-optimization tool'''.
  
 
|-
 
|-
Line 194: Line 194:
 
|-
 
|-
 
|04:36
 
|04:36
−
|'''RHF''', '''Restricted Hartee Fock''' method of '''approximation '''for the determination of '''wave function.'''
+
|'''RHF''', '''Restricted Hartee Fock''' method of approximation for the determination of '''wave function.'''
  
 
|-
 
|-
Line 234: Line 234:
 
|-
 
|-
 
|05:24
 
|05:24
−
|  For now we will keep the default parameters as such.
+
|  For now, we will keep the default parameters as such.
  
 
|-
 
|-
Line 250: Line 250:
 
|-
 
|-
 
|05:42
 
|05:42
−
|  Choose the file location as '''Desktop'''. Click on '''Save button.'''
+
|  Choose the file location as '''Desktop'''. Click on '''Save''' button.
  
 
|-
 
|-
Line 263: Line 263:
 
|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
  
 
|-
 
|-
Line 292: Line 293:
 
|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. http://www.msg.ameslab.gov/gamess/download.htm
+
And load the input file to generate the output file.
 +
http://www.msg.ameslab.gov/gamess/download.htm
  
 
|-
 
|-
Line 304: Line 306:
 
|-
 
|-
 
|07:03
 
|07:03
−
|Lets view these output files in '''avogadro'''.  
+
|Let's view these output files in '''avogadro'''.  
  
 
|-
 
|-
 
|07:07
 
|07:07
−
|  Open a new Avogadro window.
+
|  Open a new '''Avogadro''' window.
  
 
|-
 
|-
Line 340: Line 342:
 
|-
 
|-
 
|07:47
 
|07:47
−
|  To view the '''orbitals,''' click on the '''orbital''' name from the list.
+
|  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.
+
|  In the''' Surface Setting''' dialog box, drag the '''slider''' to change the '''opacity'''. Observe the '''panel'''.
  
 
|-
 
|-
Line 358: Line 360:
 
|-
 
|-
 
|08:17
 
|08:17
−
|  By default the '''orbitals ''' are rendered as '''fill'''.
+
|  By default, the '''orbitals ''' are rendered as '''fill'''.
  
 
|-
 
|-
Line 378: Line 380:
 
|-
 
|-
 
|08:38
 
|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.'''
  
 
|-
 
|-
Line 402: Line 404:
 
|-
 
|-
 
|09:13
 
|09:13
−
|  We can also view the IR spectrum for the structure.
+
|  We can also view the IR-spectrum for the structure.
  
 
|-
 
|-
Line 426: Line 428:
 
|-
 
|-
 
|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.
  
 
|-
 
|-
Line 450: Line 452:
 
|-
 
|-
 
|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.
  
 
|-
 
|-

Revision as of 11:50, 6 June 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

Retrieved from "https://script.spoken-tutorial.org/index.php?title=Avogadro/C4/File-Extensions/English-timed&oldid=43352"