soiap in your local PC

soiap is Structure Optimization with InterAtomic Potential. It is suitable for testing CrySPY because of its fast structure optimization. See instructions to install soiap.

In this tutorial, we try to use CrySPY in your local PC (Mac or Linux). The target system is Si 8 atoms.

Assumption

Here, we assume the following conditions:

  • CrySPY main script: ~/CrySPY_root/CrySPY-0.9.0/cryspy.py
  • CrySPY job filename: job_cryspy
  • soiap executable file: ~/local/soiap-0.3.0/src/soiap
  • soiap input filename: soiap.in
  • soiap output filename: soiap.out
  • soiap input structure filename: initial.cif

Input files

Move to your working directory, and copy input example files.

$ cp -r ~/CrySPY_root/CrySPY-0.9.0/example/v0.9.0/soiap_RS_Si8 .
$ cd soiap_RS_Si8
$ tree
.
├── calc_in
│   ├── job_cryspy
│   └── soiap.in_1
└── cryspy.in

cryspy.in

cryspy.in is the input file of CrySPY.

[basic]
algo = RS
calc_code = soiap
tot_struc = 5
nstage = 1
njob = 2
jobcmd = zsh
jobfile = job_cryspy

[structure]
natot = 8
atype = Si
nat = 8

[soiap]
soiap_infile = soiap.in
soiap_outfile = soiap.out
soiap_cif = initial.cif

[option]

In [basic] section, jobcmd = zsh can be changed to jobcmd = sh or jobcmd = bash in accordance with your environment. CrySPY runs zsh job_cryspy internally.

[soiap] section is required when you use soiap.

You can name the following files whatever you want:

  • jobfile
  • soiap_infile
  • soiap_outfile
  • soiap_cif

The other input variables are discussed later.

calc_in directory

The job file and input files for soiap are prepared in this directory.

Job file

The name of the job file must match the value of jobfile in cryspy.in. The example of job file (here, job_cryspy) is shown below.

#!/bin/sh

# ---------- soiap
EXEPATH=/path/to/soiap
$EXEPATH/soiap soiap.in 2>&1 > soiap.out

# ---------- CrySPY
sed -i -e '3 s/^.*$/done/' stat_job

Change /path/to/soiap into right path suitable for your environment. You can specify the input (soiap.in) and output (soiap.out) file names, but they must match the values of soiap_infile and soiap_outfile in cryspy.in. The job file is written in the same way as the one you usually use except for the last line. You must add sed -i -e '3 s/^.*$/done/' stat_job at the end of the file in CrySPY.

sed -i -e '3 s/^.*$/done/' stat_job is required at the end of the job file.

In the job file of CrySPY, the string “CrySPY_ID” is automatically replaced with the structure ID. When you use a job scheduler such as PBS and SLURM, it is useful to set the structure ID to the job name. For example, in the PBS system, #PBS -N Si_CrySPY_ID in ID 10 is replaced with #PBS -N Si_10. Note that starting with a number will result in an error. You should add a prefix like Si_.

Input for soiap

Input files based on the number of stages (nstage in cryspy.in) are required. Name the input file(s) with a suffix _x. Here x means the stage number.

We are using nstage = 1, so we need only soiap.in_1.

soiap.in_1 is listed below.

crystal initial.cif ! CIF file for the initial structure
symmetry 1 ! 0: not symmetrize displacements of the atoms or 1: symmetrize

md_mode_cell 3 ! cell-relaxation method
               ! 0: FIRE, 2: quenched MD, or 3: RFC5
number_max_relax_cell 100 ! max. number of the cell relaxation
number_max_relax 1 ! max. number of the atom relaxation
max_displacement 0.1 ! max. displacement of atoms in Bohr

external_stress_v 0.0 0.0 0.0 ! external pressure in GPa

th_force 5d-5 ! convergence threshold for the force in Hartree a.u.
th_stress 5d-7 ! convergence threshold for the stress in Hartree a.u.

force_field 1 ! force field
              ! 1: Stillinger-Weber for Si, 2: Tsuneyuki potential for SiO2,
              ! 3: ZRL for Si-O-N-H, 4: ADP for Nd-Fe-B, 5: Jmatgen, or
              ! 6: Lennard-Jones

The input structure file is specified at the first line. Use the same name as the value of soiap_cif in cryspy.in.

Running CrySPY

Go to Running CrySPY