Random Search (RS)

Info

ASE is easy to start for beginners because when you install CrySPY (csp-cryspy), ASE is also automatically installed.

Preparation of input files

Follow any one of the examples and then go to “Running CrySPY” section.

Running CrySPY

Loading external data

Only if calc_code == ext.

Load external data

ASE in your local PC

2023 July 10

ASE provides interfaces to different codes. ASE also includes Pure Python EMT calculator, which is suitable for testing CrySPY because of its fast and easy structure optimization.

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

Assumption

Here, we assume the following conditions:

CrySPY 1.2.0 or later in your local PC
CrySPY job filename: job_cryspy
ase input filename: ase_in.py

Input files

Move to your working directory, and copy the example files by one of the following methods.

Download from cryspy_utility/examples/ase_Cu8_RS
Copy from CrySPY utility that you installed

cd ase_Cu8_RS
tree

.
├── calc_in
│   ├── ase_in.py_1
│   └── job_cryspy
└── cryspy.in

cryspy.in

cryspy.in is the input file of CrySPY.

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

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

[ASE]
ase_python = ase_in.py

[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 as a background job internally.

[ASE] section is required when you use ASE.

You can name the following files whatever you want:

jobfile: job_cryspy
ase_python: ase_in.py

The other input variables are discussed later.

calc_in directory

The job file and input files for ASE 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

# ---------- ASE
python3 ase_in.py

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

You can specify the input (ase_in.py) file names, but it must match the values of ase_python in cryspy.in. You must add sed -i -e '3 s/^.*$/done/' stat_job at the end of the file in CrySPY.

Note

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

Tip

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 ASE

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 in this ASE tutorial, so we need only ase_in.py_1. ase_in.py_1 is listed below. Refer to the ASE documentation for details.

from ase.constraints import ExpCellFilter, StrainFilter
from ase.calculators.emt import EMT
from ase.calculators.lj import LennardJones
from ase.optimize.sciopt import SciPyFminCG
from ase.optimize import BFGS
from ase.spacegroup.symmetrize import FixSymmetry
import numpy as np
from ase.io import read, write

# ---------- input structure
# CrySPY outputs 'POSCAR' as an input file in work/xxxxxx directory
atoms = read('POSCAR', format='vasp')

# ---------- setting and run
atoms.calc = EMT()
atoms.set_constraint([FixSymmetry(atoms)])
atoms = ExpCellFilter(atoms, hydrostatic_strain=False)
opt = BFGS(atoms)
#opt=SciPyFminCG(atoms)
opt.run()

# ---------- opt. structure and energy
# [rule in ASE interface]
# output file for energy: 'log.tote' in eV/cell
#                         CrySPY reads the last line of 'log.tote'
# output file for structure: 'CONTCAR' in vasp format
e = atoms.atoms.get_total_energy()
with open('log.tote', mode='w') as f:
    f.write(str(e))

write('CONTCAR', atoms.atoms, format='vasp')

Unlike VASP and QE, the ASE input (python script) is more flexible. CrySPY has two rules:

Energy is output in units of eV/cell to log.tote file. CrySPY reads the last line of it.
Optimized structure is output to `CONTCAR`` file in the VASP format.

Running CrySPY

Go to Running CrySPY

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:

(only version 0.10.3 or earlier) 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 by one of the following methods.

Download from cryspy_utility/examples/soiap_Si8_RS
Copy from CrySPY utility that you installed
(only version 0.10.3 or earlier) 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 as a background job 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.

Note

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

Tip

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

VASP

2024 April 24

In this tutorial, we try to use CrySPY in a PC cluster with a job scheduler system such as PBS. Here we employ VASP. The target system is Na8Cl8, 16 atoms.

Assumption

Here, we assume the following conditions:

CrySPY 1.2.0 or later in your PC cluster
CrySPY job command: qsub
CrySPY job filename: job_cryspy
executable file, vasp_std in your PC cluster

Input files

Move to your working directory, and copy the example files by one of the following methods.

Download from cryspy_utility/examples/vasp_Na8Cl8_RS
Copy from CrySPY utility that you installed

cd vasp_Na8Cl8_RS
tree

.
├── calc_in
│   ├── INCAR_1
│   ├── INCAR_2
│   ├── POTCAR
│   ├── POTCAR_is_dummy
│   └── job_cryspy
└── cryspy.in

cryspy.in

cryspy.in is the input file of CrySPY.

[basic]
algo = RS
calc_code = VASP
tot_struc = 5
nstage = 2
njob = 2
jobcmd = qsub
jobfile = job_cryspy

[structure]
natot = 16
atype = Na Cl
nat = 8 8
mindist_1 = 2.5 1.5
mindist_2 = 1.5 2.5

[VASP]
kppvol = 40 80

[option]

In [basic] section, jobcmd = qsub can be changed in accordance with your environment. CrySPY runs qsub job_cryspy as a background job internally in this setting. You can name the following file whatever you want:

jobfile

We adopt a stage-based system for structure optimization calculations. Here, we use nstage = 2. For example, users can configure the following settings. In the first stage, only the ionic positions are relaxed, fixing the cell shape, with low k-point grid density. Next, the ionic positions and cell shape are fully relaxed with high accuracy in the second stage.

[VASP] section is required when you use VASP. You have to specify k-point grid density (Å^-3) for each stage in kppvol.

Info

See Input file > Kpoint for details of kppvol

The other input variables are discussed later.

calc_in directory

The job file and input files for VASP 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
#$ -cwd
#$ -V -S /bin/bash
####$ -V -S /bin/zsh
#$ -N Na8Cl8_CrySPY_ID
#$ -pe smp 20
####$ -q ibis1.q
####$ -q ibis2.q
####$ -q ibis3.q
####$ -q ibis4.q

# ---------- vasp
VASPROOT=/usr/local/vasp/vasp.6.4.2/bin
mpirun -np $NSLOTS $VASPROOT/vasp_std

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

Change VASPROOT to the appropriate path suitable for your environment. 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.

Note

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

Tip

Input for VASP

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 = 2, so we need INCAR_1 and INCAR_2. Here, INCAR_1 is set to fix the cell and relax only the ionic positions, while INCAR_2 is configured to fully relax both the cell and ionic positions.

INCAR_1

SYSTEM = NaCl
!!!LREAL = Auto
Algo = Fast
NSW = 40

LWAVE = .FALSE.
!LCHARG = .FALSE.

ISPIN =  1

ISMEAR = 0
SIGMA = 0.1

IBRION = 2
ISIF = 2

EDIFF = 1e-5
EDIFFG = -0.01

INCAR_2

SYSTEM = NaCl
!!LREAL = Auto
Algo = Fast
NSW = 200

ENCUT = 341

!!LWAVE = .FALSE.
!!LCHARG = .FALSE.


ISPIN =  1

ISMEAR = 0
SIGMA = 0.1

IBRION = 2
ISIF = 3

EDIFF = 1e-5
EDIFFG = -0.01

CrySPY automatically generates POSCAR and KPOINTS files. You have to prepare POTCAR file yourself. The POTCAR included in this example file is empty, so please be aware of that.

Warning

POTCAR in this example is empty. We cannot distribute it.

Running CrySPY

Go to Running CrySPY

QE

2024 April 24, updated

In this tutorial, we try to use CrySPY in a machine with a job scheduler system such as PBS. Here we employ QUANTUM ESPRESSO. (QE). The target system is Si 8 atoms.

Assumption

Here, we assume the following conditions:

CrySPY job command: qsub
CrySPY job filename: job_cryspy
QE executable file: /usr/local/qe-6.5/bin/pw.x
QE input filename: pwscf.in
QE output filename: pwscf.out

Input files

Move to your working directory, and copy input example files by one of the following methods.

Download from cryspy_utility/examples/qe_Si8_RS
Copy from CrySPY utility that you installed
(only version 0.10.3 or earlier) cp -r ~/CrySPY_root/CrySPY-0.9.0/example/v0.9.0/QE_Si8_RS .

cd QE_RS_Si8
tree

.
├── calc_in
│   ├── job_cryspy
│   ├── pwscf.in_1
│   └── pwscf.in_2
└── cryspy.in

cryspy.in

cryspy.in is the input file of CrySPY.

[basic]
algo = RS
calc_code = QE
tot_struc = 5
nstage = 2
njob = 2
jobcmd = qsub
jobfile = job_cryspy

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

[QE]
qe_infile = pwscf.in
qe_outfile = pwscf.out
kppvol =  40  80

[option]

In [basic] section, jobcmd = qsub can be changed in accordance with your environment. CrySPY runs qsub job_cryspy as a background job internally in this setting.

[QE] section is required when you use QE. You have to specify k-point grid density (Å^-3) for each stage in kppvol.

Info

See Input file > Kpoint for details of kppvol

You can name the following files whatever you want:

jobfile
qe_infile
qe_outfile

The other input variables are discussed later.

calc_in directory

The job file and input files for QE 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
#$ -cwd
#$ -V -S /bin/bash
####$ -V -S /bin/zsh
#$ -N Si8_CrySPY_ID
#$ -pe smp 20
####$ -q ibis1.q
####$ -q ibis2.q

mpirun -np $NSLOTS /path/to/pw.x < pwscf.in > pwscf.out


if [ -e "CRASH" ]; then
    sed -i -e '3 s/^.*$/skip/' stat_job
    exit 1
fi

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

Change /path/to/pw.x to the appropriate path suitable for your environment. You can specify the input (pwscf.in) and output (pwscf.out) file names, but they must match the values of qe_infile and qe_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.

Note

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

Tip

Input for QE

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 = 2, so we need pwscf.in_1 and pwscf.in_2. Here, pwscf.in_1 is set to fix the cell and relax only the ionic positions, while pwscf.in_2 is configured to fully relax both the cell and ionic positions.

pwscf.in_1

 &control
    title = 'Si8'
    calculation = 'relax'
    nstep = 100
    restart_mode = 'from_scratch',
    pseudo_dir = '/usr/local/pslibrary.1.0.0/pbe/PSEUDOPOTENTIALS/'
    outdir='./out.d/'
 /

 &system
    ibrav = 0
    nat = 8
    ntyp = 1
    ecutwfc = 44.0
    occupations = 'smearing'
    degauss = 0.01
 /

 &electrons
 /

 &ions
 /

 &cell
 /

ATOMIC_SPECIES
  Si  28.086  Si.pbe-n-kjpaw_psl.1.0.0.UPF

pwscf.in_2

 &control
    title = 'Si8'
    calculation = 'vc-relax'
    nstep = 200
    restart_mode = 'from_scratch',
    pseudo_dir = '/usr/local/pslibrary.1.0.0/pbe/PSEUDOPOTENTIALS/'
    outdir='./out.d/'
 /

 &system
    ibrav = 0
    nat = 8
    ntyp = 1
    ecutwfc = 44.0
    occupations = 'smearing'
    degauss = 0.01
 /

 &electrons
 /

 &ions
 /

 &cell
 /

ATOMIC_SPECIES
  Si  28.086  Si.pbe-n-kjpaw_psl.1.0.0.UPF

Change pseudo_dir to your suitable directory. Inputs for structure data and k-point such as ATOMIC_POSITIONS and K_POINTS are automatically appended by CrySPY with pymatgen. Users do not have to prepare them in pwscf.in_x.

Running CrySPY

Go to Running CrySPY

OpenMX

Coming soon.

LAMMPS

Coming soon.

External program

Available from CrySPY 0.11.0.

If you use an external program not supported by CrySPY, the optimized energy and structure data can be loaded semi-manually in CrySPY. You have to prepare two files, ext_opt_struc_data.pkl and ext_energy_data.pkl.

Assumption

Here, we assume the following conditions:

(version 0.10.3 or earlier) CrySPY main script: ~/CrySPY_root/CrySPY-0.11.0/cryspy.py

(calc_in directory is not required.)

Input files

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

version 1.0.0 or later
- Copy from CrySPY utility
version 0.10.3 or earlier
- cp -r ~/CrySPY_root/CrySPY-0.9.0/example/ext_Si8_RS .

cd ext_Si8_RS
tree

.
└── cryspy.in

cryspy.in

cryspy.in is the input file of CrySPY.

[basic]
algo = RS
calc_code = ext
tot_struc = 5

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

[option]

If calc_code == ext, nstage, njob, jobcmd, and jobfile are ignored.

Running CrySPY

This mode is different from the normal use of CrySPY. Go to Load external data.

Check cryspy.in

See Input file in detail.

Let’s take a look at cryspy.in again. This may be slightly different depending on calc_code you chose.

[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]

[basic] section

algo: Algorithm. Set RS for Random Search.
calc_code: Structure optimizer. Choose from VASP, QE, OMX, soiap, LAMMPS
tot_struc: The total number of structures. In this case, 5 random structures are generated at 1st run.
nstage: The number of stages. It’s up to you.
njob: The number of jobs running at the same time. In this example, CrySPY sets 2 slots for structure optimization, in other words, optimizes every 2 structures.
jobcmd: Command for jobs. Use bash, zsh, qsub, and so on.
jobfile: File name of the job file.

[structure] section

natot: The total number of atoms. e.g. for Na8Cl8: natot = 16.
atype: Atom type. e.g. for Na8Cl8: atype = Na Cl.
nat: The number of each atom. e.g. for Na8Cl8: nat = 8 8

Script to run

Note

For version 1.0.0 or later, skip this page. The executable script is automatically installed.

Assumption

Here, we assume the following condition:

CrySPY main script: ~/CrySPY_root/CrySPY-0.9.0/cryspy.py

Make script

Let’s make a convenient shell script to avoid typing long commands over and over again. Here, we create the script, cryspy (any file name will do).

$ emacs cryspy
$ chmod 744 cryspy
$ cat cryspy

#!/bin/sh

python3 -u ~/CrySPY_root/CrySPY-0.9.0/cryspy.py 1>> log 2>> err

-u option (unbuffered option) can be omitted.

You can put this script in your $PATH, or just use like bash ./cryspy.

Firsrt run

2023 July 10, update

Make sure you have the following in your working directory.

calc_in/
(cryspy)
cryspy.in

$ ls
calc_in/  cryspy.in

Then, run CyrSPY!

cryspy

If you use old version (0.10.3 or earlier):

bash ./cryspy

At the first run, CrySPY goes into structure generation mode. CrySPY stops after 5 structure generation.

If it worked properly, the following output appears on the screen:

[2023-07-10 18:40:54,389][cryspy_init][INFO] 


Start CrySPY 1.2.0


[2023-07-10 18:40:54,389][cryspy_init][INFO] # ---------- Read input file, cryspy.in
[2023-07-10 18:40:54,390][read_input][INFO] Save input data in cryspy.stat
[2023-07-10 18:40:54,391][cryspy_init][INFO] # ---------- Initial structure generation
[2023-07-10 18:40:54,391][cryspy_init][INFO] Number of MPI processes: 1
[2023-07-10 18:40:54,391][gen_init_struc][INFO] # ------ mindist
[2023-07-10 18:40:54,395][struc_util][INFO] Cu - Cu: 1.32
[2023-07-10 18:40:54,395][gen_init_struc][INFO] # ------ generate structures
[2023-07-10 18:40:54,481][gen_pyxtal][INFO] Structure ID      0 was generated. Space group:   1 -->   1 P1
[2023-07-10 18:40:54,493][gen_pyxtal][INFO] Structure ID      1 was generated. Space group:  28 -->  28 Pma2
[2023-07-10 18:40:54,498][gen_pyxtal][INFO] Structure ID      2 was generated. Space group:  29 -->  29 Pca2_1
[2023-07-10 18:40:54,704][gen_pyxtal][INFO] Structure ID      3 was generated. Space group: 137 --> 137 P4_2/nmc
[2023-07-10 18:40:54,725][gen_pyxtal][INFO] Structure ID      4 was generated. Space group: 212 --> 214 I4_132
[2023-07-10 18:40:54,800][cryspy_init][INFO] Elapsed time for structure generation: 0:00:00.408367
cryspy  4.35s user 1.04s system 145% cpu 3.697 total

Several output files are also generated.

(cryspy.out): Short log. only version 0.10.3 or earlier.
cryspy.stat: Status file.
data/init_POSCARS: Initial struture file in POSCAR format. You can open this file using VESTA
data/pkl_data: Directory to save pickled data.
log_cryspy: log.
err_cryspy: error and warning.

Let’s take a look at cryspy.stat file.

...
(omit)
...
[status]
id_queueing = 0 1 2 3 4

Structure ID 0 – 4 are queueing because we just generated structures, and have not submitted yet.

Tip

Check the initial structures, if the distances between atoms are too close, you should set the mindist in cryspy.in.

Features > Restriction on interatomic distances

Submit job

2023 July 10, update

Continue

CrySPY continues the simulation if you have cryspy.stat file.

Tip

Continue if you have crypy.stat
Start from the beginning if you don’t have cryspy.stat

Submit job

Run CyrSPY again.

cryspy

Check the screen or log_cryspy file.

[2023-07-10 18:52:51,859][cryspy_restart][INFO] 


Restart CrySPY 1.2.0


[2023-07-10 18:52:51,869][ctrl_job][INFO] # ---------- job status
[2023-07-10 18:52:51,904][ctrl_job][INFO] ID      0: submit job, Stage 1
[2023-07-10 18:52:51,931][ctrl_job][INFO] ID      1: submit job, Stage 1

And also cryspy.stat file.

...
(omit)
...
[status]
id_queueing = 2 3 4
id      0 = Stage 1
id      1 = Stage 1

CrySPY submitted two jobs for structure ID 0 and 1 as you set njob = 2 in cryspy.in. Calculations are performed in the work directory. These directory names correspond to their structure ID.

tree -d work

work
├── 000000
├── 000001
└── fin

When the two jobs are done, run CrySPY again.

cryspy

[2023-07-10 18:55:01,053][cryspy_restart][INFO] 


Restart CrySPY 1.2.0


[2023-07-10 18:55:01,058][ctrl_job][INFO] # ---------- job status
[2023-07-10 18:55:01,058][ctrl_job][INFO] ID      0: Stage 1 Done!
[2023-07-10 18:55:01,093][ctrl_job][INFO]     collect results: E = -0.00696997755502915 eV/atom
[2023-07-10 18:55:01,132][ctrl_job][INFO] ID      1: Stage 1 Done!
[2023-07-10 18:55:01,133][ctrl_job][INFO]     collect results: E = 0.4934076667166454 eV/atom
[2023-07-10 18:55:01,144][cryspy][INFO] 

recheck 1

[2023-07-10 18:55:01,145][ctrl_job][INFO] # ---------- job status
[2023-07-10 18:55:01,153][ctrl_job][INFO] ID      2: submit job, Stage 1
[2023-07-10 18:55:01,161][ctrl_job][INFO] ID      3: submit job, Stage 1

If you set nstage = 2 (more than 2), new jobs on stage 2 for ID 0 and 1 are submitted. If you set nstage = 1, CrySPY collects calculation data of ID 0 and 1, then submits next ID’s jobs. Directories of the finished structure are moved to the fin directory.

Repeat cryspy several times until all 5 structures are done. You can delete the work directory when the simulation is done if you do not need it.

The auto script (repeat_cryspy) may help you.

Check results

Move to data directory. There should be a few more files.

$ cd data
$ ls
cryspy_rslt  cryspy_rslt_energy_asc  init_POSCARS  opt_POSCARS  pkl_data/

cryspy_rslt: Result file.
cryspy_rslt_energy_asc: Result file sorted in energy ascending order.
init_POSCARS: Initial struture file in POSCAR format.
opt_POSCARS: Optimized structure file in POSCAR format.
pkl_data/: Directory to save pickled data.

The results are written to text files, cryspy_rslt and cryspy_rslt_energy_asc (and also saved in pickle data in pkl_data directory).

Each result appends to cryspy_rslt file in the order in which one finished earlier.

cat cryspy_rslt

   Spg_num Spg_sym  Spg_num_opt Spg_sym_opt  E_eV_atom  Magmom      Opt
0      139  I4/mmm          139      I4/mmm  -3.000850     NaN     done
1       98  I4_122           12        C2/m  -3.978441     NaN  not_yet
2       16    P222           16        P222  -3.348616     NaN  not_yet
3       36  Cmc2_1           36      Cmc2_1  -3.520306     NaN  not_yet
4       36  Cmc2_1            4        P2_1  -3.304168     NaN  not_yet

Info

Not ID order in cryspy_rslt

In cryspy_rslt_energy_asc file, the results are sorted in energy ascending order.

cat cryspy_rslt_energy_asc

   Spg_num Spg_sym  Spg_num_opt Spg_sym_opt  E_eV_atom  Magmom      Opt
1       98  I4_122           12        C2/m  -3.978441     NaN  not_yet
3       36  Cmc2_1           36      Cmc2_1  -3.520306     NaN  not_yet
2       16    P222           16        P222  -3.348616     NaN  not_yet
4       36  Cmc2_1            4        P2_1  -3.304168     NaN  not_yet
0      139  I4/mmm          139      I4/mmm  -3.000850     NaN     done

Spg_num and Spg_sym show space group information on initial structures. Spg_num_opt and Spg_sym_opt are those of optimized structures. The last column Opt indicates whether or not optimization reached required accuracy.

Append structures

Of course only 5 structures are not enough to find stable structures. You can append structures whenever you want. Here let’s append more 5 structures.

For Si-Si mindist, the default value of 1.11 Å is used in the first structure generation (see log_cryspy), which is a little too close. Let us try to set the mindist to 2.0 Å.

Info

For mindist, see also Features > Restriction on interatomic distances.

Edit cryspy.in and change the value of tot_struc into 10, and add mindist_1 = 2.0

emacs cryspy.in
cat cryspy.in

[basic]
algo = RS
calc_code = soiap
tot_struc = 10
nstage = 1
njob = 2
jobcmd = zsh
jobfile = job_cryspy

[structure]
natot = 8
atype = Si
nat = 8
mindist_1 = 2.0

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

[option]

Then run cryspy, and check log_cryspy file.

cryspy &
cat log_cryspy

...
(omit)
...

2023/03/19 00:01:47
CrySPY 1.0.0
Restart cryspy.py


Changed tot_struc from 5 to 10
Changed mindist from None to [[2.0]]

Backup data

# ---------- Append structures
# ------ mindist
Si - Si 2.0
Structure ID      5 was generated. Space group: 218 --> 221 Pm-3m
Structure ID      6 was generated. Space group:  86 --> 129 P4/nmm
Structure ID      7 was generated. Space group: 129 --> 129 P4/nmm
Structure ID      8 was generated. Space group: 191 --> 191 P6/mmm
Structure ID      9 was generated. Space group:  31 -->  31 Pmn2_1

Remember that CrySPY goes into structure generation mode whenever you change the value of tot_struc. In this mode, CrySPY does not do any other action such as collecting data, submitting jobs, and so on.

Note

Structure generation mode whenever you change the value of tot_struc.
From version 1.0.0, CrySPY automatically backs up when adding structures. See features/backup.

Repeat cryspy & several times until all appended structures are done. The auto script (repeat_cryspy) may help you.

Analysis and visualization

Download the data

It is assumed here that you analyze and visualize CrySPY data in your local PC. If you use CrySPY in super computers or workstations, download the data in your local PC. You can delete the work and backup directory if you do not need it because the file size could be very large.

jupyter notebook

Move to the data/ directory in results you just download. Then copy cryspy_analyzer_RS.ipynb from CrySPY utility.

$ ls
calc_in/ cryspy.in cryspy.stat  data/  err_cryspy  log_cryspy

$ cd data
$ ls
cryspy_rslt  cryspy_rslt_energy_asc  init_POSCARS  opt_CIFS.cif  opt_POSCARS  pkl_data/

cp /path/to/CrySPY_utility/cryspy_analyzer_RS.ipynb .

Run jupyter. (VScode, jupyter lab, jupyter notebook, and so on.) You can get the following figure by simply running the steps in order.

Load external data

You need only cryspy.in.

$ ls
cryspy.in

Then, run CyrSPY.

cryspy &

At the first run, CrySPY goes into structure generation mode as usual. CrySPY stops after 5 structure generation.

If it worked properly, log_cryspy would look like this.

2022/07/14 19:41:41
CrySPY 1.0.0
Start cryspy.py

Read input file, cryspy.in
Write input data in cryspy.out
Save input data in cryspy.stat

# --------- Generate initial structures
# ------ mindist
Si - Si 1.11
Structure ID      0 was generated. Space group:  88 --> 141 I4_1/amd
Structure ID      1 was generated. Space group: 101 --> 101 P4_2cm
Structure ID      2 was generated. Space group: 204 --> 229 Im-3m
Structure ID      3 was generated. Space group: 199 --> 199 I2_13
Structure ID      4 was generated. Space group:  12 -->  12 C2/m

Unlike normal use, a directory named ext was created. Only the stat_job file exists in ext/.

$ cat ext/stat_job
out

If you run cryspy when “out” is written in the stat_job file, queueing structure files (cif format) are exported in ext/queue.

cryspy &

$ ls ext/queue
0.cif  1.cif  2.cif  3.cif  4.cif

The number in the file name is structure ID. The fist line of stat_job was automatically changed.

$ cat ext/stat_job
submitted

Perform structure optimization and energy evaluation in an external program using the output cif files. Once that calculation is done, prepare the optimized structure and energy data in the pickle data format, ext_opt_struc_data.pkl and ext_energy_data.pkl.

The data format of ext_opt_struc_data.pkl is the same as init_struc_data.pkl and opt_struc_data.pkl, see Data format/Initial and optimized structure data.

The data format of ext_energy_data.pkl is similar to ext_opt_struc_data.pkl. Just change the value from the structure data into the energy. An example of the energy data (dict type) is shown below.

key: structure ID
value: energy

{0: -0.7139331910805997,
 1: -0.5643404689832622,
 2: -0.5832404287259171,
 3: -0.535037327286169,
 4: -0.6316663459586607}

The ext/calc_data directory should be automatically generated, so put the two pickle files here.

$ ls ext/calc_data
ext_energy_data.pkl  ext_opt_struc_data.pkl

When ready, replace the first line of the stat_job file with “done” and run CrySPY.

$ emacs /ext/stat_job
$ cat /ext/stat_job
done

cryspy &

CrySPY collects the result data.

Random Search (RS)

Preparation of input files

Running CrySPY

Loading external data

Subsections of Random Search (RS)

ASE in your local PC

Assumption

Input files

cryspy.in

calc_in directory

Job file

Input for ASE

Running CrySPY

soiap in your local PC

Assumption

Input files

cryspy.in

calc_in directory

Job file

Input for soiap

Running CrySPY

VASP

Assumption

Input files

cryspy.in

calc_in directory

Job file

Input for VASP

Running CrySPY

QE

Assumption

Input files

cryspy.in

calc_in directory

Job file

Input for QE

Running CrySPY

OpenMX

LAMMPS

External program

Assumption

Input files

cryspy.in

Running CrySPY

Check cryspy.in

[basic] section

[structure] section

Script to run

Assumption

Make script

Firsrt run

Submit job

Continue

Submit job

Check results

Append structures

Analysis and visualization

Download the data

jupyter notebook

Load external data