Computational Basics

Joseph Schneider
jeschneider@uchicago.edu
Calculating Wavefunctions –
What’s so Hard?

Easy Hard

You need the wavefunction to solve for the wavefunction!

 How Computers Think: The SCF
Algorithm
Guess orbitals Most error is introduced in:
• The way electron repulsion is
“Solve” a simplified calculated (the functional for
Schrodinger equation DFT)
• The way atomic orbitals are
Is it No “Step” represented (the basis set)
“Self Consistent”? the orbitals
Yes
• The numerical integration grid

Do things with
the orbitals
Each step of this process can be controlled
 Translating the Input File

Guess orbitals
Functional

“Solve” a simplified
Schrodinger equation

Is it No “Step”
“Self Consistent”? the orbitals
Yes

Do things with
the orbitals
 Translating the Input File

Guess orbitals
Basis Set

“Solve” a simplified
Schrodinger equation

Is it No “Step”
“Self Consistent”? the orbitals
Yes

Do things with
the orbitals
 Translating the Input File

Guess orbitals

Optimize
“Solve” a simplified
Geometry
Schrodinger equation

Is it No “Step”
“Self Consistent”? the orbitals
Yes

Do things with
the orbitals
 Translating the Input File

Guess orbitals

“Solve” a simplified Print the orbitals

when done
Schrodinger equation

Is it No “Step”
“Self Consistent”? the orbitals
Yes

Do things with
the orbitals
 Translating the Input File

Guess orbitals

“Solve” a simplified Coordinates of Atoms

Schrodinger equation

Is it No “Step”
“Self Consistent”? the orbitals
Yes

Do things with
the orbitals
 Translating the Input File

Guess orbitals

“Solve” a simplified Charge of -1

Schrodinger equation

Is it No “Step”
“Self Consistent”? the orbitals
Yes

Do things with
the orbitals
 Translating the Input File

Guess orbitals

“Solve” a simplified Singlet

Schrodinger equation

Is it No “Step”
“Self Consistent”? the orbitals
Yes

Do things with
the orbitals
Submitting the Job

The RCC Website has good instructions on what

programs you will need and what goes into this
sbatch file
A More Complex Calculation
 A More Complex Calculation
Guess the Result of
Previous Calculations

Guess orbitals

“Solve” a simplified
Schrodinger equation

Is it No “Step”
“Self Consistent”? the orbitals
Yes

Do things with
the orbitals
 A More Complex Calculation
Where to find
Guess orbitals this guess

“Solve” a simplified
Schrodinger equation

Is it No “Step”
“Self Consistent”? the orbitals
Yes

Do things with
the orbitals
 A More Complex Calculation

Guess orbitals
The Functional

“Solve” a simplified
Schrodinger equation

Is it No “Step”
“Self Consistent”? the orbitals
Yes

Do things with
the orbitals
 A More Complex Calculation

Guess orbitals
Use Implicit
Solvation
“Solve” a simplified
Schrodinger equation

Is it No “Step”
“Self Consistent”? the orbitals
Yes

Do things with
the orbitals
 A More Complex Calculation

Guess orbitals
The Basis

“Solve” a simplified
Schrodinger equation

Is it No “Step”
“Self Consistent”? the orbitals
Yes

Do things with
the orbitals
 A More Complex Calculation

Guess orbitals
Use the Resolution of
“Solve” a simplified Identity approximation to
Schrodinger equation speed up calculation of
electron repulsion

Is it No “Step”
“Self Consistent”? the orbitals
Yes

Do things with
the orbitals
 A More Complex Calculation

Guess orbitals

The auxiliary basis set for

“Solve” a simplified the RI approximation
Schrodinger equation

Is it No “Step”
“Self Consistent”? the orbitals
Yes

Do things with
the orbitals
 A More Complex Calculation

Guess orbitals

“Solve” a simplified Use a different (larger)

Schrodinger equation basis set for the pesky
transition metal

Is it No “Step”
“Self Consistent”? the orbitals
Yes

Do things with
the orbitals
 A More Complex Calculation

Guess orbitals

Use tight criterion for

“Solve” a simplified when convergence is
Schrodinger equation reached

Is it No “Step”
“Self Consistent”? the orbitals
Yes

Do things with
the orbitals
 A More Complex Calculation

Guess orbitals

“Solve” a simplified Use the KDIIS algorithm to

determine the step to take
Schrodinger equation

Is it No “Step”
“Self Consistent”? the orbitals
Yes

Do things with
the orbitals
 A More Complex Calculation

Guess orbitals

“Solve” a simplified Take small steps

Schrodinger equation

Is it No “Step”
“Self Consistent”? the orbitals
Yes

Do things with
the orbitals
 A More Complex Calculation

Guess orbitals

Finish with
“Solve” a simplified Second Order SCF
Schrodinger equation

Is it No “Step”
“Self Consistent”? the orbitals
Yes

Do things with
the orbitals
 A More Complex Calculation

Guess orbitals

“Solve” a simplified
Schrodinger equation

When to start
Is it No “Step” using SOSCF
“Self Consistent”? the orbitals
Yes

Do things with
the orbitals
 A More Complex Calculation

Guess orbitals

“Solve” a simplified Save the electron

Schrodinger equation density files

Is it No “Step”
“Self Consistent”? the orbitals
Yes

Do things with
the orbitals
 A More Complex Calculation

Guess orbitals

“Solve” a simplified
Schrodinger equation

Is it No “Step”
“Self Consistent”? the orbitals
Yes
Take coordinates
from a .xyz file
Do things with
the orbitals
 A More Complex Calculation

Guess orbitals

“Solve” a simplified
Schrodinger equation

Is it No “Step”
“Self Consistent”? the orbitals
Yes Neutral

Do things with
the orbitals
 A More Complex Calculation

Guess orbitals

“Solve” a simplified
Schrodinger equation

Is it No “Step”
“Self Consistent”? the orbitals
Yes Triplet

Do things with
the orbitals
 A More Complex Calculation

Guess orbitals

“Solve” a simplified
Schrodinger equation

Is it No “Step”
“Self Consistent”? the orbitals
Yes Here’s the
xyz file
Do things with
the orbitals
 What the Calculation Spits Out

Stores the Orbitals

The Energy, MO Energies,

Charge/Spin location, etc.

Final Coordinates
Looking into the Output File

• The final energy is all the way at the bottom

• Reported in Hartrees; 1 Hartree = 627.5 kcal/mol
• There is a lot of error in this number! You want to
use energy differences so you get error canceling
Visualizing the Orbitals
 Visualizing the Spin Density
• Printing in the output is convenient, but:
• Can make output files clumsily large
• Avogadro is finnicky with open shelled systems
• Another option is to use orca_plot
 Visualizing the Spin Density
• Load the same ORCA
version the calculation
was done in
• Avogadro reads
Gaussian Cube (select
with “7”)
• It will ask for certain
files – if you don’t have
them, it can remake
them
Resources
• Practical Resources:
• ORCA Input Library:
https://sites.google.com/site/orcainputlibrary/home
• A guide on how to set up calculations in ORCA
• Also gives concise, practical help on functional and basis set choice
• ORCA Manual: Linked from the input library
• More in-depth documentation for how to use ORCA
• Email me for a copy if the links on the above site don’t work
• Gaussian Manual: https://gaussian.com/man/
• Seems to be the Gaussian equivalent to the ORCA resources I use
• UChicago’s Research Computing Cluster:
https://rcc.uchicago.edu/accounts-allocations
• Instructions on getting an account, logging on, and submitting jobs
• Theoretical Help
• Prof. Mazziotti’s class Winter Term
• Introduction to Computational Chemistry by Jenson
• Density functional theory: An introduction by Argaman
and Makov
• https://aapt.scitation.org/doi/pdf/10.1119/1.19375?class=pdf
• An introduction to DFT theory that I particularly like
• Jacob’s Ladder of Density Functional Approximations for
the Exchange-Correlation Energy by Perdew and
Schmidt
• https://aip.scitation.org/doi/pdf/10.1063/1.1390175
• A classic description of different types of DFT functionals