Follow one of the instructions below, then proceed to the section on running CrySPY.
2025 April 5
The files used in this tutorial can be downloaded from CrySPY_utility/examples/ase_Cu8Au8_EA. This tutorial demonstrates a test run on a local machine using ASE’s lightweight Pure Python EMT calculator. The target system is Cu8Au8.
Example of cryspy.in.
[basic]
algo = EA
calc_code = ASE
nstage = 1
njob = 5
jobcmd = zsh
jobfile = job_cryspy
[structure]
atype = Cu Au
nat = 8 8
[EA]
n_pop = 10
n_crsov = 5
n_perm = 2
n_strain = 2
n_rand = 1
n_elite = 1
n_fittest = 5
slct_func = TNM
t_size = 2
maxgen_ea = 0
[ASE]
ase_python = ase_in.py
[option]
algo = EA.jobcmd to bash.tot_struc is not used. The number of structures is determined by n_pop.n_pop = n_crsov + n_perm + n_strain + n_randThe contents under calc_in/ are the same as in Tutorial > Random Search (RS) > ASE in your local PC.
from ase.constraints import FixSymmetry
from ase.filters import FrechetCellFilter
from ase.calculators.emt import EMT
from ase.optimize import BFGS
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)])
cell_filter = FrechetCellFilter(atoms, hydrostatic_strain=False)
opt = BFGS(cell_filter)
opt.run(fmax=0.01, steps=2000)
# ---------- 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 = cell_filter.atoms.get_total_energy()
with open('log.tote', mode='w') as f:
f.write(str(e))
# ------ write structure
opt_atoms = cell_filter.atoms.copy()
opt_atoms.set_constraint(None) # remove constraint for pymatgen
write('CONTCAR', opt_atoms, format='vasp', direct=True)
#!/bin/sh
# ---------- ASE
python3 ase_in.py > out.log
# ---------- CrySPY
sed -i -e '3 s/^.*$/done/' stat_job
2025 April 6
When you run cryspy, the program enters structure generation mode.
It generates the first generation of random structures and then exits.
cryspy
log
...
[2025-04-06 09:15:34,720][ea_init][INFO] # ---------- Initialize evolutionary algorithm
[2025-04-06 09:15:34,720][ea_init][INFO] # ------ Generation 1
[2025-04-06 09:15:34,720][ea_init][INFO] 10 structures by random
In EA, running cryspy appends the current generation’s information to cryspy.stat.
[status]
generation = 1
id_queueing = 0 1 2 3 4 5 6 7 8 9
After running cryspy several times and completing the structure optimization for the first generation, the output will appear as shown below.
...
[2025-04-06 09:20:26,218][ctrl_job][INFO] Done generation 1
[2025-04-06 09:20:26,218][ctrl_job][INFO]
EA is ready
Once all preparations are complete, running cryspy again automatically creates a backup and starts generating the next-generation structures.
cryspy
...
[2025-04-06 09:35:11,546][cryspy_restart][INFO] read input, cryspy.in
[2025-04-06 09:35:11,554][ctrl_job][INFO] # ---------- job status
[2025-04-06 09:35:11,554][ctrl_job][INFO] Done generation 1
[2025-04-06 09:35:11,554][utility][INFO] Backup data
[2025-04-06 09:35:11,611][ea_next_gen][INFO] # ---------- Evolutionary algorithm
[2025-04-06 09:35:11,611][ea_next_gen][INFO] Generation 2
[2025-04-06 09:35:11,613][ea_next_gen][INFO] # ------ natural selection
[2025-04-06 09:35:11,687][ea_next_gen][INFO] ranking without duplication (including elite):
[2025-04-06 09:35:11,687][ea_next_gen][INFO] Structure ID 1, fitness: -0.00530
[2025-04-06 09:35:11,687][ea_next_gen][INFO] Structure ID 3, fitness: 0.01490
[2025-04-06 09:35:11,687][ea_next_gen][INFO] Structure ID 4, fitness: 0.04485
[2025-04-06 09:35:11,687][ea_next_gen][INFO] Structure ID 7, fitness: 0.11501
[2025-04-06 09:35:11,687][ea_next_gen][INFO] Structure ID 8, fitness: 0.15254
[2025-04-06 09:35:11,687][ea_next_gen][INFO] # ------ Generate children
[2025-04-06 09:35:11,687][ea_child][INFO] # -- mindist
[2025-04-06 09:35:11,689][struc_util][INFO] Cu - Cu: 1.32
[2025-04-06 09:35:11,689][struc_util][INFO] Cu - Au: 1.34
[2025-04-06 09:35:11,689][struc_util][INFO] Au - Au: 1.36
[2025-04-06 09:35:11,740][crossover][INFO] Structure ID 10 (8, 8) was generated from 3 and 1 by crossover. Space group: 1 P1
[2025-04-06 09:35:11,764][crossover][WARNING] remove_within_mindist: some atoms within mindist. retry.
[2025-04-06 09:35:11,774][crossover][INFO] Structure ID 11 (8, 8) was generated from 3 and 1 by crossover. Space group: 1 P1
[2025-04-06 09:35:11,789][crossover][INFO] Structure ID 12 (8, 8) was generated from 1 and 4 by crossover. Space group: 1 P1
[2025-04-06 09:35:11,833][crossover][INFO] Structure ID 13 (8, 8) was generated from 1 and 3 by crossover. Space group: 1 P1
[2025-04-06 09:35:11,852][crossover][WARNING] mindist in _add_border_line: Cu - Cu, 0.567032320824818. retry.
[2025-04-06 09:35:11,861][crossover][INFO] Structure ID 14 (8, 8) was generated from 7 and 1 by crossover. Space group: 1 P1
[2025-04-06 09:35:11,875][permutation][INFO] Structure ID 15 (8, 8) was generated from 1 by permutation. Space group: 146 R3
[2025-04-06 09:35:11,888][permutation][INFO] Structure ID 16 (8, 8) was generated from 3 by permutation. Space group: 1 P1
[2025-04-06 09:35:11,890][strain][WARNING] mindist in strain: Cu - Cu, 1.3050485787603692. retry.
[2025-04-06 09:35:11,903][strain][INFO] Structure ID 17 (8, 8) was generated from 3 by strain. Space group: 1 P1
[2025-04-06 09:35:11,917][strain][INFO] Structure ID 18 (8, 8) was generated from 1 by strain. Space group: 1 P1
[2025-04-06 09:35:12,513][ea_child][INFO] # ------ Random structure generation
[2025-04-06 09:35:12,513][rs_gen][INFO] # ------ mindist
[2025-04-06 09:35:12,515][struc_util][INFO] Cu - Cu: 1.32
[2025-04-06 09:35:12,515][struc_util][INFO] Cu - Au: 1.34
[2025-04-06 09:35:12,515][struc_util][INFO] Au - Au: 1.36
[2025-04-06 09:35:12,516][rs_gen][INFO] # ------ generate structures
[2025-04-06 09:35:12,530][gen_pyxtal][INFO] Structure ID 19: (8, 8) Space group: 86 --> 86 P4_2/n
[2025-04-06 09:35:12,533][ea_next_gen][INFO] # ------ Select elites
[2025-04-06 09:35:12,533][ea_next_gen][INFO] Structure ID 9 keeps as the elite
After that, simply running cryspy repeatedly will advance the structure search.
The following is an example of cryspy_rslt after completing calculations up to the third generation.
In EA, generation information (Gen) is also included.
Gen Spg_num Spg_sym Spg_num_opt Spg_sym_opt E_eV_atom Magmom Opt
0 1 214 I4_132 230 Ia-3d 1.168743 NaN no_file
1 1 198 P2_13 198 P2_13 -0.005303 NaN no_file
2 1 95 P4_322 95 P4_322 0.389566 NaN no_file
3 1 27 Pcc2 27 Pcc2 0.014898 NaN no_file
4 1 60 Pbcn 60 Pbcn 0.044852 NaN no_file
5 1 116 P-4c2 116 P-4c2 0.403246 NaN no_file
6 1 187 P-6m2 187 P-6m2 1.054706 NaN no_file
7 1 161 R3c 160 R3m 0.115009 NaN no_file
8 1 146 R3 146 R3 0.152535 NaN no_file
9 1 60 Pbcn 47 Pmmm -0.005676 NaN no_file
10 2 1 P1 1 P1 0.026070 NaN no_file
11 2 1 P1 7 Pc 0.005898 NaN no_file
12 2 1 P1 1 P1 0.005208 NaN no_file
13 2 1 P1 1 P1 0.005506 NaN no_file
14 2 1 P1 1 P1 0.024364 NaN no_file
15 2 146 R3 146 R3 0.011525 NaN no_file
16 2 1 P1 1 P1 0.014590 NaN no_file
17 2 1 P1 1 P1 0.015236 NaN no_file
18 2 1 P1 2 P-1 -0.012335 NaN no_file
19 2 86 P4_2/n 140 I4/mcm 0.274548 NaN no_file
20 3 1 P1 1 P1 0.013611 NaN no_file
21 3 1 P1 10 P2/m -0.014166 NaN no_file
22 3 1 P1 1 P1 0.019472 NaN no_file
23 3 1 P1 1 P1 0.011641 NaN no_file
24 3 1 P1 1 P1 0.000297 NaN no_file
25 3 1 P1 1 P1 0.005596 NaN no_file
26 3 1 P1 1 P1 0.013374 NaN no_file
27 3 1 P1 2 P-1 0.005055 NaN no_file
28 3 2 P-1 12 C2/m -0.012396 NaN no_file
29 3 182 P6_322 182 P6_322 0.711472 NaN no_file
The EA parameters used in each generation are recorded in ea_info.
Gen Population Crossover Permutation Strain Random Elite crs_lat slct_func
1 10 0 0 0 10 0 random TNM
2 10 5 2 2 1 1 random TNM
3 10 5 2 2 1 1 random TNM
Information about the structure generation method and parent individuals is output to ea_origin.
Gen Struc_ID Operation Parent
1 0 random None
1 1 random None
1 2 random None
1 3 random None
1 4 random None
1 5 random None
1 6 random None
1 7 random None
1 8 random None
1 9 random None
2 10 crossover (3, 1)
2 11 crossover (3, 1)
2 12 crossover (1, 4)
2 13 crossover (1, 3)
2 14 crossover (7, 1)
2 15 permutation (1,)
2 16 permutation (3,)
2 17 strain (3,)
2 18 strain (1,)
2 19 random None
2 9 elite elite
3 20 crossover (18, 12)
3 21 crossover (12, 9)
3 22 crossover (12, 18)
3 23 crossover (18, 9)
3 24 crossover (13, 18)
3 25 permutation (18,)
3 26 permutation (9,)
3 27 strain (18,)
3 28 strain (18,)
3 29 random None
3 18 elite elite
It is assumed here that you analyze and visualize CrySPY data on your local PC.
If you use CrySPY on a supercomputer or workstation, download the data to your local machine.
You can delete the work and backup directories if they are not needed, as their file size can be very large.
Move to the data/ directory in the results you downloaded earlier.
Then, if the CrySPY utility has already been downloaded locally, copy cryspy_analyzer_EA.ipynb.
Alternatively, you can download it directly from GitHub (CrySPY_utility/notebook/).
Launch Jupyter (e.g., VS Code, Jupyter Lab, or Jupyter Notebook),
and simply run the cells in order to obtain a figure like the one shown below.
