View source for ORCA---Computational-Chemistry/C2/Generate--Molecular-Orbitals-of-Water/English


'''Title of the script''': '''Generate Molecular Orbitals of Water'''


'''Author: '''Madhuri Ganapathi, Raj Singh, Snehalatha Kaliappan

'''Keywords''':  orca, molecular orbitals of water, gedit text editor, auto optimization, molecular orbitals, homo, lumo,  ucsf chimera, computational chemistry, video tutorial.


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|| '''Visual Cue'''
|| '''Narration'''
|-
|| '''Slide Number 1 '''

'''Title slide '''
|| Welcome to the Spoken tutorial on '''Generate Molecular Orbitals of Water'''.
|-
|| '''Slide Number 2 '''

'''Learning Objectives'''

|| In this tutorial, we will learn to,
* Open the XYZ file.
* Add commands to create the input file.
* Run the input file in ORCA environment to get the ORCA output.
* View the molecular orbital data in the output file.

|-
|| '''Slide Number 3'''

'''System Requirements'''
|| To record this tutorial, I am using;
* '''Ubuntu Linux OS '''version 22.04
* '''ORCA '''version 6.0.1
* '''Gedit Text Editor''' version 41.0

Windows users may use notepad or any other text editor.

|-
|| '''Slide Number 4'''

'''Pre-requisites'''

|| To follow this tutorial, learners should be familiar with '''ORCA software'''. 

|-
|| '''Slide Number 5'''

'''Code Files'''

The following code file is required to practice this tutorial

1.'''water.xyz'''

2. '''commands.txt'''

These files are provided in the Code Files link of this tutorial page

|| The following code files are required to practice this tutorial.

These files are provided in the Code Files link of this tutorial page.
|-
|| Show the downloaded and extracted file to Home directory
|| Download and extract '''water''' folder from the '''Code files''' link to the '''Home directory'''.
|-
|| Right-click on the file 

From the context menu select Open With Text Editor.
|| Let us open the '''water.xyz '''file using a text editor.
|-
|| Select and Delete 3 from the first row.

Press Ctrl+ S to save the file.
|| Delete 3 from the first row and save the file.
|-
|| Right-click on the commands.txt file and '''Open With Text Editor'''
|| Now we will open '''commands.txt''' file using a text editor.

|-
|| Copy the commands(Ctrl+ C)

Paste in the water.xyz(Ctrl+V)

|| Copy and paste the commands from the file in the first row of the '''water.xyz '''file.

|-
|| Type * at the end of the coordinates.
|| At the end of the coordinates row type an '''asterisk''' (*)

We will now go through the code.
|-
|| '''! B3LYP def2-SVP TightSCF Opt'''

'''Highlight !'''

'''Highlight B3LYP'''

'''! B3LYP def2-SVP '''

'''Highlight def2-SVP'''

'''Highlight TightSCF Opt'''
|| The command line starts with an exclamation mark.

Here '''B3LYP''' is the''' dft functional'''.

'''def2-SVP '''is the''' basis set'''.

'''TightSCF Opt''' is the command for geometry optimization.
|-
|| '''%output'''

'''Print[P_MOs] 1'''

'''end'''

|| This block of code is used to print the molecular orbitals of water.

|-
|| Point to * xyz 0 1

* 

Point to the asterisk at the start and end.

|| Here '''xyz '''specifies the coordinates of the molecule.

0 is the charge and 1 is the spin multiplicity.

The coordinates start and end with an '''asterisk''' (*).
|-
|| Point to the numbers and xyz coordinates.

Highlight the xyz coordinates. 

Point to the entire code.
|| The numbers in rows are the '''xyz''' coordinates of the atoms in '''Angstrom '''units.

This is the ORCA input file for generating molecular orbitals of water.

|-
|| Click on the '''3 lines''' icon next '''Save''' button.

In the drop down menu select '''Save As '''option.

Delete '''.xyz '''and '''.inp '''as the extension.

In the '''Save '''dialog box type the file name as '''water.inp'''.

Choose location as '''water folder'''.

Click on the '''Save''' button.

|| Let us now save the file as an input file.

Click on the 3 lines icon next to the '''Save '''button. 

In the drop down menu select '''Save As '''option.

In the '''Save''' dialog box type the file name as '''water.inp'''.

Choose the '''water''' folder to save the file.

Click the '''Save''' button.

|-
|| Open the''' Home''' directory

Open the water folder by double clicking on it.
|| Let us go to the '''Home''' directory and open the''' water '''folder.

It contains the '''water.inp''' file.
|-
|| To open the terminal in water folder,

Right-click and from the context menu 

select Open in Terminal.
|| Let us now open the terminal in '''water '''folder.

Right-click and from the context menu 

select '''Open in Terminal'''.

|-
|| type at the prompt''' file water.inp'''

point to the output

'''water.inp: Unicode text, UTF-8 (with BOM) text '''
|| To check the file format of '''water.inp,''' at the prompt''' '''type''' file water.inp'''

Press''' Enter'''.

'''Terminal '''shows the below output.

If the''' terminal '''shows '''water.inp: ASCII text '''as output, please skip the following steps.

|-
|| Copy paste the command at the prompt 

'''sed -i '1s/^\xEF\xBB\xBF//' water.inp'''

'''Press Ctrl + Shift +V to paste in the terminal'''

Press Enter.
|| We need to convert the Unicode text to '''ASCII'''

text as '''ORCA '''reads only the '''ASCII''' text file.

Let’s open the '''commands.txt''' file again.

Copy and paste the command from commands.txt file to the terminal.

Press Enter
|-
|| Type '''file water.inp'''

Point to the output.

'''water.inp: ASCII text'''

|| To check the file format of '''water.inp''' at the prompt''' '''type '''file water.inp'''

This time terminal shows the below output.
Now let us run the input file in ORCA.

|-
|| Type '''orca water.inp > water.out'''

Press Enter
|| Type '''orca space water.inp space > space water.out'''

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

Press''' Enter'''.
|-
|| Point to files in the water folder, in the HOME directory
|| After the calculation is complete the output file '''water.out''' is generated.

The output file is available in the '''water''' folder in the '''HOME''' directory. 

|-
|| Type 

'''less water.out'''

The .out file opens on the terminal and then press “/” and write in capital “'''ORBITAL ENERGIES'''” and press “Enter”.

|| At the prompt type '''less space water.out'''.

The '''.out''' file opens on the terminal.

Now let us search for the keyword '''ORBITAL ENERGIES.'''

At the colon prompt on the terminal, 

Press back slash (/) and then type in capital letters '''ORBITAL ENERGIES'''.

Press Enter.

|-
|| The Orbital energies Table will appear.

point to the table.

|| The orbital energies table is displayed on the terminal. 

|-
|| '''highlight the Second column''' which tells about the population and '''the first column''' which tells about the Orbital Number. 

point to the second column.

point to orbital 4 and its population.

|| In this table, look at the second column. 

It tells us about the population of the orbitals.

Note that for the water molecule the highest occupied orbital number 4 has least energy.

It has the last highest population of 2.0000.

Number 4 orbital is HOMO. 

|-
|| point to orbital 5 and its population.
|| Now observe orbital number 5. 

It has the first least population and least energy among the unoccupied orbitals.

Number 5 orbital is LUMO.

|-
|| point to HOMO and LUMO
|| We will visualize HOMO and LUMO orbitals using Chimera in the upcoming tutorial.

|-
|| Only Narration
|| Please refer to the additional reading material to learn more about the molecular orbitals of water.
|-
 
|| With this we come to the end of this tutorial.
|-
|| '''Slide Number 6'''

'''Summary'''

In this tutorial, we have learnt to,

* Open the XYZ file.
* Add commands to create the input file.
* Run the input file in '''ORCA''' environment to get the '''ORCA''' Output.
* View molecular orbital data in the output file.

|| Let us summarize.
|-
|| '''Slide Number 7'''

'''Assignment '''

* Create '''ORCA''' input files for carbon monoxide and ammonia.
* Run the''' '''input files in '''ORCA''' environment using the terminal to generate the output files.
* View HOMO and LUMO orbital data in the output files.

|| As an assignment please do the following.

|-
||
|| Thank you for joining.
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