Create next generation
2025 June 16
First run
When you run cryspy, the program enters structure generation mode.
It generates the first generation of random structures and then exits.
cryspy
It can be confirmed from the output that structures are generated with the number of atoms within the range specified by ll_nat and ul_nat.
...
[2025-06-16 10:04:45,648][cryspy_init][INFO] # ---------- Initial structure generation
[2025-06-16 10:04:45,648][rs_gen][INFO] # ------ mindist
[2025-06-16 10:04:45,650][struc_util][INFO] Cu - Cu: 1.32
[2025-06-16 10:04:45,650][struc_util][INFO] Cu - Ag: 1.385
[2025-06-16 10:04:45,650][struc_util][INFO] Cu - Au: 1.34
[2025-06-16 10:04:45,650][struc_util][INFO] Ag - Ag: 1.45
[2025-06-16 10:04:45,650][struc_util][INFO] Ag - Au: 1.405
[2025-06-16 10:04:45,650][struc_util][INFO] Au - Au: 1.36
[2025-06-16 10:04:45,650][rs_gen][INFO] # ------ generate structures
[2025-06-16 10:04:45,659][gen_pyxtal][WARNING] Compoisition [1 4] not compatible with symmetry 34: spg = 34 retry.
[2025-06-16 10:04:45,662][gen_pyxtal][WARNING] Compoisition [ 2 2 12] not compatible with symmetry 39: spg = 39 retry.
[2025-06-16 10:04:45,691][gen_pyxtal][INFO] Structure ID 0: (3, 1, 2) Space group: 82 --> 119 I-4m2
[2025-06-16 10:04:45,694][gen_pyxtal][WARNING] Compoisition [6 6 2] not compatible with symmetry 57: spg = 57 retry.
[2025-06-16 10:04:45,749][gen_pyxtal][INFO] Structure ID 1: (1, 8, 5) Space group: 71 --> 71 Immm
[2025-06-16 10:04:45,857][gen_pyxtal][INFO] Structure ID 2: (3, 7, 8) Space group: 174 --> 174 P-6
...
The file cryspy.stat shows that the current generation’s information is being added during the EA process.
[status]
generation = 1
id_queueing = 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
Optimize structures
After running cryspy several times and completing the structure optimization for the first generation, the output will appear as shown below.
...
[2025-06-16 10:25:56,962][ctrl_job][INFO] Done generation 1
[2025-06-16 10:25:56,962][ctrl_job][INFO] Calculate convex hull for generation 1
[2025-06-16 10:25:57,854][ctrl_job][INFO]
EA is ready
Convex hull
At this point, the hull distance data and the convex hull plot have been output to ./data/convex_hull/.
- hull_dist_all_gen_1
ID hull distance (eV/atom) Num_atom
7 0.000000 (0, 2, 6)
14 0.036510 (1, 7, 6)
17 0.064702 (0, 1, 5)
19 0.113649 (0, 0, 8)
16 0.168530 (6, 4, 8)
9 0.186497 (8, 4, 6)
1 0.187379 (1, 8, 5)
11 0.233893 (4, 5, 4)
3 0.273365 (6, 5, 5)
10 0.326759 (1, 4, 4)
2 0.330749 (3, 7, 8)
8 0.359543 (6, 2, 7)
4 0.404169 (4, 4, 2)
18 0.422989 (0, 6, 8)
13 0.428456 (0, 6, 3)
5 0.444792 (7, 4, 7)
6 0.464305 (7, 7, 7)
12 0.556654 (3, 0, 0)
15 0.560062 (6, 7, 1)
0 0.644278 (3, 1, 2)
- conv_hull_gen_1.svg
Create next generation
Once all preparations are complete, running cryspy again automatically creates a backup and starts generating the next-generation structures.
cryspy
...
[2025-06-16 10:37:19,860][ctrl_job][INFO] Done generation 1
[2025-06-16 10:37:20,136][utility][INFO] Backup data
[2025-06-16 10:37:20,173][ea_next_gen][INFO] # ---------- Evolutionary algorithm
[2025-06-16 10:37:20,174][ea_next_gen][INFO] Generation 2
[2025-06-16 10:37:20,174][ea_next_gen][INFO] # ------ natural selection
[2025-06-16 10:37:20,177][ea_next_gen][INFO] ranking without duplication (including elite):
[2025-06-16 10:37:20,177][ea_next_gen][INFO] Structure ID 7, fitness: 0.00000
[2025-06-16 10:37:20,177][ea_next_gen][INFO] Structure ID 14, fitness: 0.03651
[2025-06-16 10:37:20,177][ea_next_gen][INFO] Structure ID 17, fitness: 0.06470
[2025-06-16 10:37:20,177][ea_next_gen][INFO] Structure ID 19, fitness: 0.11365
[2025-06-16 10:37:20,177][ea_next_gen][INFO] Structure ID 16, fitness: 0.16853
[2025-06-16 10:37:20,177][ea_next_gen][INFO] Structure ID 9, fitness: 0.18650
[2025-06-16 10:37:20,177][ea_next_gen][INFO] Structure ID 1, fitness: 0.18738
[2025-06-16 10:37:20,177][ea_next_gen][INFO] Structure ID 11, fitness: 0.23389
[2025-06-16 10:37:20,177][ea_next_gen][INFO] Structure ID 3, fitness: 0.27336
[2025-06-16 10:37:20,177][ea_next_gen][INFO] Structure ID 10, fitness: 0.32676
[2025-06-16 10:37:20,177][ea_next_gen][INFO] # ------ Generate children
[2025-06-16 10:37:20,177][ea_child][INFO] # -- mindist
[2025-06-16 10:37:20,179][struc_util][INFO] Cu - Cu: 1.32
[2025-06-16 10:37:20,179][struc_util][INFO] Cu - Ag: 1.385
[2025-06-16 10:37:20,179][struc_util][INFO] Cu - Au: 1.34
[2025-06-16 10:37:20,179][struc_util][INFO] Ag - Ag: 1.45
[2025-06-16 10:37:20,179][struc_util][INFO] Ag - Au: 1.405
[2025-06-16 10:37:20,179][struc_util][INFO] Au - Au: 1.36
[2025-06-16 10:37:20,217][crossover][INFO] Structure ID 20 (0, 4, 7) was generated from 19 and 14 by crossover. Space group: 1 P1
[2025-06-16 10:37:20,219][crossover][INFO] Structure ID 21 (0, 1, 7) was generated from 7 and 17 by crossover. Space group: 1 P1
[2025-06-16 10:37:20,221][crossover][INFO] Structure ID 22 (3, 0, 8) was generated from 16 and 19 by crossover. Space group: 1 P1
[2025-06-16 10:37:20,225][crossover][INFO] Structure ID 23 (0, 1, 7) was generated from 7 and 17 by crossover. Space group: 1 P1
...
[2025-06-16 10:37:20,809][ea_next_gen][INFO] # ------ Select elites
[2025-06-16 10:37:20,809][ea_next_gen][INFO] Structure ID 7 keeps as the elite
[2025-06-16 10:37:20,809][ea_next_gen][INFO] Structure ID 14 keeps as the elite
After that, simply running cryspy repeatedly will advance the structure search.