次世代の生成
2025年6月16日
初回実行
cryspyを実行すると，構造生成モードになり，第一世代のランダム構造が生成されて，一旦プログラムは終了する．
cryspy
出力をみると，ll_natとul_natの範囲の原子数で構造が生成されているのが確認できる．
...
[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
...
cryspy.statを見ると，EAでは現在の世代の情報が追加されている．
[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
構造最適化
何度かcryspyを実行して，第一世代の構造最適化を終わらせると，下記のように出力される．
...
[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
凸包
この時点で，./data/convex_hull/にhull distanceの情報とconvex hullのグラフが出力されている．
- 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
次世代生成
準備ができた状態でもう一度cryspyを実行すると，バックアップが実行されてから，次世代構造の生成が始まる．
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
あとはcryspyの実行を繰り返せば，探索が進む．