View source for ORCA---Computational-Chemistry/C2/Run-an-Input--File/English

'''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.


{| border=1
|-
||'''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 location.
|-
|| 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 '''Selec'''t''' '''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 '''Selec'''t''' '''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 A<sup>0</sup>


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


In the prerequisite tutorial we have determined the bond length as 0.969 A<sup>0</sup>.

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.
|-
|}