2.8 Running USPEX examples: a mini-tutorial

Once you have downloaded the USPEX package and installed it, you can run the first USPEX example. The description of the examples is listed in Appendix 9.1. The required external codes to run the examples (except EX13) are shown below:

GULP: EX02, EX03, EX08, EX12, EX15 (VCNEB), EX16, EX18, EX21(META), EX22(Generalized META), EX23

VASP: EX01, EX07, EX09, EX14 (META), EX17, EX19, EX24, EX29, EX30, EX31

QE: EX33

LAMMPS: EX04, EX26 (TPS)

ATK: EX05

CASTEP: EX06

DMACRYS: EX10

Tinker: EX11

MOPAC: EX20

DFTB: EX25

FHIaims: EX27, EX28

Now, let us start our first USPEX experience:

Test the USPEX python runner

To get the version information, you can use the following command:

>> USPEX -v

You should get something like this:

  USPEX Version 10.2 (19/01/2019)

Run the EX13-3D_special_quasirandom_structure_TiCoO2

EX13 does not require any external code, you can run it to get familiar with the USPEX running procedure. The calculation would take $\sim$ 30 minutes. To start the calculation, first create a test folder, copy the example files and then run the calculation through the USPEX Python runner, with the following commands:

>> mkdir EX13
>> cd EX13
>> USPEX -c 13
>> USPEX -r

Meanwhile you have some time to get more details about example EX13. In EX13, the structural order is optimized (minimized) with the evolutionary algorithm to yield a generalized special quasirandom structure (gSQS). Therefore in INPUT.txt the following is set:

USPEX : calculationMethod
% optType
-4  
% EndOptType

and these parameters are used below:

300   : calculationType

% atomType
Co Ti O
% EndAtomType

% numSpecies
16 16 64
% EndNumSpecies

which specifies that we deal with the Co $_{16}$ Ti $_{16}$ O $_{64}$ system.

Since you do not need to use any external code, you can simply set

% abinitioCode
0
% ENDabinit

The Seeds/POSCARS file contains the initial Ti $_{16}$ Co $_{16}$ O $_{64}$ structure.

When you find the USPEX_IS_DONE file, congratulations, you have successfully finished your first USPEX example. Next, you can run calculations which require external codes.

Run an example using external code

In this step, we suggest to run examples interfaced with GULP or VASP, starting from EX02 or EX01. Use USPEX runner to get the example information of EX02, create a separate folder and copy the files, with commands:

>> mkdir EX02
>> cd EX02
>> USPEX -c 2

Since in example EX02 GULP code is used, set:

% abinitioCode
3 3 3 3
% ENDabinit

To run a serial job without a job batch system, you should change the following parameters in the INPUT.txt below:

1     : whichCluster
1     : numParallelCalcs

In the example INPUT.txt, you will see whichCluster=QSH, where QSH is name of our group’s cluster name. User can specify their own cluster: for the details, please see Section 8.8.

% commandExecutable
gulp < input > output
% EndExecutable

But make sure, that this command also works on your machine. If you want to run EX01 with a parallel version of VASP, you should set something like:

% abinitioCode
1 1 1 1
% ENDabinit

% commandExecutable
mpirun -np 8 vasp
% EndExecutable

With wrong commandExecutable settings, you will not able to run your calculation. Finally, do not forget to suitably modify submitJob_remote.py and checkStatus_remote.py files for your computer/supercomputer.

When everything is set correctly, we can run the calculation through USPEX runner using the command:

>> USPEX -r

Checking the results

After starting the command, you can check the output files in results1/ folder.

Now, you have a basic experience of using USPEX to run simple calculations. Please read the following sections of this manual to get more insight into USPEX. When analyzing results, it is essential that you visualize the structures (for visualization, see section 8.1).