Day 9-11: First principles: CRYSTAL Tutorials

We will use tutorials from the CRYSTAL tutorial web site https://tutorials.crystalsolutions.eu for the exercises.

Exercise 1 - Single point energy calculations (day 9)

Initially you should familiarise yourself with converging an SCF calculation by working through at least one of the example systems in the Basic - Single point energy calculation https://tutorials.crystalsolutions.eu/tutorial.html?td=totalenergy&tf=total_energy_tut tutorial. There are zip files containing example inputs for each of the structures attached to the tutorial. You should read the section below on running CRYSTAL. You may also wish to try viewing the structure with DLV.

Should you need more detailed descriptions of the input and output you can look at the Getting acquainted with CRYSTAL section of the tutorials

Exercise 2 - One electron properties

You should try running a Band structure and Density of States from the results of exercise 1. A description of these can be found in the tutorial, One-electron properties - Band structure etc https://tutorials.crystalsolutions.eu/tutorial.html?td=properties&tf=properties_tut You can run these from the command line (instructions below) and display with the CRYSPLOT web tool https://crysplot.crystalsolutions.eu.

Alternatively you can try displaying the calculations with DLV. You may also like to try plotting a 3D charge density and/or electrostatic potential with DLV, https://bmgcsc.gitlab.io/dl-visualize-v3/tutorials/calcs/crystal/3dcd.html . (Note: the charge density of a system with covalent bonds, e.g. Si, will probably show more structure than an ionic system, e.g. MgO.) You will need to use the ECH3/POT3 commands in the manual for this.

Exercise 3 - Advanced calculations

How to model Surfaces is an example of 2D slab calculations which can be used be used to model crystalline surfaces or 2D materials such as graphene. It can be more intuitive to explore the different surface planes and their termination with a visualisation tool, such as DLV, before running a calculation.

Alternatively you may prefer to try one of the other How to model… tutorials if it is more closely related to your project work.

Notes on using CRYSTAL and DLV

Running CRYSTAL SCF calculations

There is a demo copy of CRYSTAL on the virtual machine that will allow you to run the smaller calculations on your local machine. You can run CRYSTAL on the local machine via:

crystal <inputfile

or:

crystal <inputfile >outputfile

Larger examples will need to be run on the SCARF cluster. You should read the notes on setting up your environment on SCARF. There is an example job script (scf.slurm) in the crystal subdirectory of /work4/training/ccp5 on the machine.

Viewing the geometry with DLV

You can view the structure of the system you are calculating with DLV on the virtual machine. To do this you need to add the keyword:

EXTPRT

to the geometry section of your input file, before the END or BASISSET keyword. This will save a version of the geometry in a file named fort.34 which can be read via the Calculate - CRYSTAL - Load file menu option. An example of reading this file is in the tutorials in the DLV documentation at https://bmgcsc.gitlab.io/dl-visualize-v3/tutorials/tutorials.html.

DLV is not in the default PATH of the virtual machine so you will need to use:

/opt/dlv/bin/dlv

to run it.

Generating the geometry with DLV

It is also possible to use DLV to generate the geometry for your CRYSTAL calculation. In the DLV documentation there are examples of creating structures in the Creating and Editing Models section. Once you have created your structure you can save it via the Calculate - CRYSTAL - Save structure menu option. E.g. for MgO with an input file mgo.inp, you might save mgo.str. In this case the geometry section of your input file is just:

EXTERNAL
END

as the entire geometry is now read from the other file (e.g. mgo.str). When running on the local machine this file needs to be copied to fort.34 in the same folder as your input. An example SCARF script for this is scf-ext.slurm.

Running one electron properties with CRYSTAL

Properties are run with the second executable in the CRYSTAL package. Use:

properties <inputfile

on the local machine or the props.slurm eample script on SCARF. They require an input file and density produced by the single point energy calculation for the analysis (fort.9, saved as file.f9 by the scarf scf.slurm script).

Viewing one electron properties

Some of the tools mentioned in the tutorial are out of date. Instead there are a couple of alternatives available.

  • some files can be uploaded to the web tool CRYSPLOT (the link is at the top of the tutorial).

  • DOSS.DAT and BAND.DAT files from the density of states and band structure calculations can be viewed in the virtual machine with the xmgrace tool.

  • Output files can be viewed with DLV by following the Loading properties tutorial for CRYSTAL in the DLV documentation.

(Ignore this - running jobs from DLV doesn’t seem to work on the VM)

DLV also has tutorials which will allow you to automatically generate properties input files, run the calculation and view the results without having to create the input file yourself. To do this you need to start with the Analysing Previous Calculations link to attach the binary fort.9 file (alternatively you could save and use the default ascii fort.98). You may like to try this for a 3D charge density volume, rather than use the 2D plots described in the tutorial. The Displaying and Editing data section of the DLV tutorials shows how to view 3D data or take a 2D slice.

The CRYSTAL manual can be found here: https://www.crystal.unito.it/Manuals/crystal23.pdf

CRYSTAL Home: https://www.crystal.unito.it/index.php

CRYSTAL Basis sets: https://www.crystal.unito.it/basis-sets.php