CrySPY

1. Introduction

CrySPY is a software package that searches and optimizes crystal structures based on a given composition. It uses first-principles or molecular dynamics software to evaluate structural energies. In this tutorial, we introduce a calculation using the Docker version of MateriApps LIVE! with Random Search to find the optimal structure for a composition of 12 hydrogen atoms and 12 carbon atoms (expected to yield the benzene structure). The energy evaluation of structures is performed using QUANTUM ESPRESSO, which is pre-installed in MateriApps LIVE!. This article is based on the following tutorial:

https://tomoki-yamashita.github.io/CrySPY_doc/index.html

2. Installation

Run the following command to install CrySPY:

pip3 install csp-cryspy

Many scripts will be installed automatically during this process. Since we will use the cryspy command, check its installation with the following command:

which cryspy

If it is not found, refer to the installation log and add the path to the scripts directory to your PATH environment variable:

echo 'export PATH=$PATH:/home/user/.local/bin' >> ~/.bashrc
source ~/.bashrc

3. Preparing Input Files

Download the benzene example from the official CrySPY manual and place it in a working directory. The directory contents should look like this:

cd qe_benzene_2_RS_mol
tree

.
|-- README
|-- calc_in
|   |-- job_cryspy
|   |-- pwscf.in_1
|   `-- pwscf.in_2
`-- cryspy.in

1 directory, 5 files

Modify the job command in cryspy.in to suit your environment. Here, we use jobcmd = bash.

In job_cryspy, replace /path/to/pw.x with the correct path for your environment. If the path is already set, simply using pw.x is sufficient.

In pwscf.in_1 and pwscf.in_2, specify the directory containing pseudopotentials in the pseudo_dir parameter. In this example, we create a directory named pseudo in the home directory and place the files there: pseudo_dir = '/home/user/pseudo/'.

Next, prepare the pseudopotentials. The files pwscf.in_1 and pwscf.in_2 reference H.pbe-kjpaw_psl.1.0.0.UPF and C.pbe-n-kjpaw_psl.1.0.0.UPF. Download the same files from the official QUANTUM ESPRESSO pseudopotential database and place them in the pseudo directory.

4. Execution

First, specify the number of parallel processes to use:

export NSLOTS=1

While in the qe_benzene_2_RS_mol directory, execute:

cryspy

This will generate six structures. Run cryspy again to evaluate the energies of two structures at a time. Continue executing cryspy until the message Done all structures! appears.

Alternatively, you can use the repeat-execution script for cryspy, which automates this process. The entire computation took approximately six hours and twenty minutes to complete.

5. Results

Check the results in the cryspy_rslt_energy_asc file inside the data directory:

   Spg_num   Spg_sym  Spg_num_opt Spg_sym_opt   E_eV_atom  Magmom   Opt
0       58      Pnnm           58        Pnnm -133.439385     NaN  done
2       71      Immm           71        Immm -133.436956     NaN  done
3      136  P4_2/mnm          136    P4_2/mnm -133.436394     NaN  done
5       53      Pmna           53        Pmna -133.433717     NaN  done
4      136  P4_2/mnm           65        Cmmm -133.429064     NaN  done
1      132  P4_2/mcm          132    P4_2/mcm -133.427469     NaN  done

The structures are listed in ascending order of total energy. Visualizing opt_CIFS.cif with VESTA reveals that the structure with ID 0 (the lowest energy) corresponds to the expected benzene structure, as shown below.

6. Conclusion

In this example, we used Random Search, but CrySPY also supports other structure-search methods such as evolutionary algorithms, Bayesian optimization, and Look Ahead based on Quadratic Approximation (LAQA), which can perform more efficient explorations.