Tutorial: Single Point Calculation

In this tutorial we will show how to perform an ab-initio single point calculation using the PySurf framework. If you have any other electronic structure program installed that is supported by PySurf, you can just use it. Otherwise you can download the PySCF program package and install it via:

pip install pyscf

PySCF is free of charge. In this tutorial we use it to do a TDDFT calculation.

Next you need a folder for the calculation and an xyz file. There is an example (where?) of a $SO_2$ geometry. Go to your favorite place and make a folder for the test calculation and copy your coordinate file:

mkdir test_so2
cd test_so2
cp <so2.xyz> ./

<so2.xyz> stands for the path of your so2 coordinate file.

Finally you have to run the sp_calc.py workflow for a single point calculation. <pysurf> is the path where your PySurf package is installed

python <pysurf>/bin/sp_calc.py so2.xyz 2 energy

The sp_calc.py script takes three positional arguments. The first is the path of the coordinate file, the second is the number of states and the third is a list of the properties that you want to calculate. If you also want to have the gradients you have to write:

python <pysurf>/bin/sp_calc.py so2.xyz 2 "energy, gradient"

For help text of the script type:

python <pysurf>/bin/sp_calc.py -h

Subsequently PySurf will guide you through all the questions of the SurfacePointProvider and the electronic structure interface. You can take the defaults or choose your own. The Colt framework helps you that your answers are consistent. In this case, we accept all the defaults up to the point for the software. There we choose PySCF. Subsequently we take the defaults again. The PySCF calculation is started and the output is printed to the screen. The results are saved in the database that was put in the input (the default is just db.dat). To see all the parameters of your calculation, you can open the spp.inp file, where the whole input is stored. If you want to repeat the calculation with the same settings for a different geometry, you can just exchange the coordinate file. Typing again:

python <pysurf>/bin/sp_calc.py so2.xyz 2 "energy, gradient"

Will start a new calculation. This time no questions will be asked, but all the answers are read from the spp.inp file. See the other tutorials how to setup multiple calculations.

Congratualtions, you just performed your first single point calculation with PySurf!