Difference between revisions of "ORCA---Computational-Chemistry/C2/Run-an-Input--File/English"

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(Created page with "'''Title of the script''': '''Run Orca Input file ''' '''Author: '''Arup Sarkar, Raj Singh and Madhuri Ganapathi '''Keywords: '''ORCA, Avogadro, water, xyz file, xyz coordi...")
 
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'''Summary'''
 
'''Summary'''
 
|| In this tutorial, we have  
 
|| In this tutorial, we have  
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* Ran an''' '''input file in the''' ORCA''' environment using the terminal.  
+
* Ran an input file in the ''' ORCA''' environment using the terminal.  
 
* Generated an output file.
 
* Generated an output file.
 
* Compared the bond length and bond angle before and after optimization in '''ORCA'''.
 
* Compared the bond length and bond angle before and after optimization in '''ORCA'''.
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* Open the input files of cyclohexane and benzene generated in previous assignment
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* Open the input files of '''cyclohexane''' and '''benzene''' generated in the previous assignment
−
 
+
 
* Run the input files in the '''ORCA''' environment using the terminal
 
* Run the input files in the '''ORCA''' environment using the terminal
 
* Generate the output files.
 
* Generate the output files.

Revision as of 18:16, 30 April 2024

Title of the script: Run Orca Input file

Author: Arup Sarkar, Raj Singh and Madhuri Ganapathi


Keywords: ORCA, Avogadro, water, xyz file, xyz coordinates, input file, output file, bond length, bond angle, video tutorial.


Visual Cue Narration
Slide Number 1

Title slide

Welcome to this spoken tutorial on

Run an Input File using ORCA.

Slide Number 2

Learning Objectives

In this tutorial, we will learn to,
  • Run an input file in the ORCA environment.
  • Generate an output file.
  • Compare the bond length and bond angle before and after optimization in ORCA.
  • Analyse the generated output
Slide Number 3

System Requirement

To record this tutorial, I am using;

Ubuntu Linux OS version 20.04

ORCA version 5.0.4

Gedit text editor version 3.36.2

Avogadro version 1.2.0

Slide Number 4

Pre-requisites


https://spoken-tutorial.org

To follow this tutorial,

Learner, should be familiar with Avogadro software and

Learner, should have installed ORCA version 5.0.4


If not please access the relevant tutorials from this website.

Slide Number 5

Code Files

The files used in this tutorial are provided in the Code files link.

Please download and extract the files.

Make a copy and then use them while practising.

Cursor in the Home folder.

Double-click to open the Water folder.

Let us go to the Home directory and open the water folder.
Point to water.xyz and water.inp file in the water folder. Learners please note:

The water folder was created earlier while practising the prerequisite tutorial.

Please refer to the prerequisite tutorial for more information.

Press Ctrl + A to select the files.

Right-click >> copy

Right-click >> paste,

Let us make a copy of the files present in the water folder.


Rename the copied files as waterA.xyz and waterA.inp.


Users can rename the files as desired.

This helps to compare the xyz coordinates after the input file is run using ORCA.

Right-click and select Open With Text Editor. Now let’s open the water.inp file using a text editor.

Windows users may use a notepad or any other text editor to open the input file.

Point to the xyz coordinates of the molecule. Notice the xyz coordinates of the molecule.

They are obtained after auto optimization of the molecule in Avogadro.

Point to # and line next to it. The lines after the hash(#) symbol will be treated as comments.

ORCA will not execute these lines.

So skip the lines.

Point to line ! RHF OPT def2-SVP

Point to !.

The program code starts with an exclamatory(!) mark.
Point to RHF

Point to def2-SVP

Point to OPT

Here RHF is the Restricted Hartree Fock method.


Using this method we will run a geometry optimization of water molecule.


def2-SVP is the Basis set in ORCA.


The OPT keyword is used to optimize the molecule in ORCA.

Point to * xyz 0 1

Point to the asterisk at the start and end.

Here xyz specifies the coordinates of the molecule in Angstrom units.

0 is the charge and

1 is the spin multiplicity(2S+1)

The coordinates should start and end with an asterisk (*).

Point to the Close button.

Click the Close button.

All the command lines are correct.

You can close the input file.

Run the Input File in ORCA Now we will run the water.inp file in the ORCA environment.
Point to the ORCA file in the Home folder.

Double-click to open the orca folder.

I have already installed and extracted the ORCA 5.0.4 file to my Home directory.

I will open the orca folder.

Move the cursor on the files in the folder.

Point to the orca program.

Here, all the files are already compiled and are in executable format.


All calculations will run using the orca executable file.

Show the water and orca directories are in the home directory. Both orca and water directories are in the Home directory.
Press Ctrl + Alt + T keys together to open the terminal. Open the terminal by pressing Ctrl, Alt and T keys together.
Let’s create an alias for the path to fetch the orca program.
Type gedit .bashrc

>> press Enter.


Type gedit space .bashrc and press Enter to edit the bashrc file.

The file opens.

Show the alias command in the .bashrc file. In the file, I have added the path in the alias command to fetch orca.

Users please the type file path as per your file loaction.

Click on the X button to close the file. Close the .bashrc file.
Type source .bashrc at the prompt.

Press Enter.

Let us go back to the terminal, to source the file.

At the prompt type, source space .bashrc and Press Enter.

From now on, instead of typing the full path just type orca at the prompt.

Cursor on the terminal. Now we will run the input file in ORCA.
Type orca space ~/Water/water.inp


Highlight file location.

Type orca space ~/water/water.inp, as we are in the water folder.
Type > ~/Water/water.out

Press Enter

Please give a space after typing the path of the input file.

Now type greater than(>) sign.

Here greater than(>) sign is used to channel the output to the same folder.


Press space bar again


To save the output file in the current directory, type ~/water/water.out


This will direct the output to a text file.


Please type the file path as per your file location.


Press Enter to run the command.

Point to the files in the water folder.


Open the water folder along with the terminal to see the files.

Observe that some temporary files are generated in the folder.

These files are generated as the input file runs in ORCA.


The temporary files are removed after output files are generated.


The generation of the output takes a few seconds.

Double click on the water.out file.


Scroll down to show the output.


Point to the FINAL SINGLE POINT ENERGY


-75.961333016443 Eh

Double click on the water.out

file to open it.


Scroll down the file to see the output.


Here is the final single point energy after the Hartree Fock optimization.


This number may vary a little for the learners.


Single point energy is the lowest energy solution to Schrödinger's equation.

Show the Converged cycles. When the input file runs in ORCA it creates different converge cycles.


Then optimises the structure.


So the xyz coordinates change after the optimisation is done.

Click on the X button to close the file. Let us now close the file.
Cursor on water.xyz file.

Double click on the files to open them.

Click on water.xyz file.

Point to the coordinates.

Let’s open the files water.xyz and waterA.xyz.


Here we can compare the values of the xyz coordinates in the xyz files.


Observe the change in values of XYZ coordinates.

Point to the coordinates. The coordinates have changed after the structure converged in orca.


This indicates that the structure is better converged in the ORCA environment.

Click on the X button. Let us close the files.
Point to the file.

Right-click on the file, select the option Open With Other Application

Let us open the xyz file in Avogadro.


Right-click on water.xyz file.

Select Open With Other Application option.

Point to the dialog box.

From the Recommended Applications select Avogadro.

Click on the Select button at the top right corner of the dialog box.


Point to the water molecule in the Avogadro panel.

Select Application dialog box opens.


From the Recommended Applications select Avogadro.

Click on Select button at the top right corner of the dialog box.


Water molecule is loaded in the panel.

Click on Click to Measure tool on the toolbar.


Click on Hydrogen and then on Oxygen atom to measure the bond length.


Point to the bond length at the bottom.


Show text box: with bond length after auto optimization in Avogadro.

Now click the Click to Measure tool on the toolbar.


Click on Hydrogen and then on click oxygen atom to measure the bond length.


Observe that the bond length is 0.945 A0


This value is close to the experimental value suggested in literature.


In the prerequisite tutorial we have determined the bond length as 0.969 A0.

This value was obtained after auto optimization of the structure in Avogadro.

Click on Second hydrogen atom.


Point to the bond angle at the bottom left.


Show text box: with bond angle after auto optimization in Avogadro.

Click on the next hydrogen atom to measure the bond angle.

Observe that the bond angle is 105.1 degrees

This value is close to the experimental value suggested in literature.

In the prerequisite tutorial we have determined the bond angle as 104.0 degrees.

This value was obtained after auto optimization of the structure in Avogadro.

Click on the X button to close. Close the Avogadro interface.
Now we will analyse the output.
Right-click on the water folder, select the option Open in Terminal.

Point to the folder in the terminal.

Right-click on the water folder and select the option Open in Terminal.


Folder opens in the terminal.

Type ls at the prompt.

Press Enter

Point to the list of files.

Point to water.out

Type ls at the prompt and Press Enter to see the list files.

Here we have the water.out file.

Point to water.out.

Type vi <space> water.out and press Enter.

Point to the output.

Point to the cursor.

Now let us open this file using the vi editor.

Type vi <space> water.out and press Enter.

Output is shown on the terminal.

Observe that the cursor is at the top left corner.

Press Shift + G. Press Shift and G keys togther to go to the bottom of the terminal output.
Point to time. Here we can see the time taken to generate the output in the orca environment.
Type ?Item, press Enter.

Point to Item keyword.

Type ?Item and press Enter.

It searches for the Item keyword.

In this section, the file has converged to show the geometry optimization.

Type ?TOTAL and press Enter.

Point to total SCF energy.

Type ?TOTAL all in capital letters and press Enter.

Search shows the total SCF energy.

Here SCF is a self-consistent field method to calculate energy.

Type ?FINAL and press Enter.

Point to the Final single point energy.

Type ?FINAL all in capital letters and press Enter.

Search shows the Final Single Point energy after optimization.

Press :q to quit the process.

Type cd ..

Press colonq(:q) and press Enter to quit the process.


Type cd <space> <dot> <dot> (cd ..) to go back to the Home folder.

With this, we come to the end of this tutorial.

Let us summarize.

Slide Number 6

Summary

In this tutorial, we have
  • Ran an input file in the ORCA environment using the terminal.
  • Generated an output file.
  • Compared the bond length and bond angle before and after optimization in ORCA.
  • Analysed the generated output
Slide Number 7 + 8

Assignment

As an assignment,


  • Open the input files of cyclohexane and benzene generated in the previous assignment
  • Run the input files in the ORCA environment using the terminal
  • Generate the output files.
  • Compare the bond lengths and bond angles before and after optimization in ORCA.
Slide Number 9

Spoken Tutorial project

The video at the following link summarizes the Spoken Tutorial project.

Please download and watch it.

Slide number 10

Spoken Tutorial workshop

The spoken tutorial project team conducts workshops and gives certificates.

For more details, please write to us.

Slide Number 11

Spoken Tutorial forum

Please post your timed queries in this forum.
Slide number 12

Acknowledgement

Spoken Tutorial Project was established by the Ministry of Education Government of India.
Thank you The tutorial is contributed by Arup Sarkar, Raj Singh and Madhuri Ganapathi from FOSSEE, IIT Bombay.

Thank you for joining.

Contributors and Content Editors

Madhurig, Snehalathak

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