次世代の生成
最終更新日：2026年10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．
...
[2026-07-07 15:18:02,548][cryspy_init][INFO] # ---------- Initial structure generation
[2026-07-07 15:18:02,548][rs_gen][INFO] # ------ mindist
[2026-07-07 15:18:02,549][struc_util][INFO] Cu - Cu: 1.32
[2026-07-07 15:18:02,549][struc_util][INFO] Cu - Ag: 1.385
[2026-07-07 15:18:02,549][struc_util][INFO] Cu - Au: 1.34
[2026-07-07 15:18:02,549][struc_util][INFO] Ag - Ag: 1.45
[2026-07-07 15:18:02,549][struc_util][INFO] Ag - Au: 1.405
[2026-07-07 15:18:02,549][struc_util][INFO] Au - Au: 1.36
[2026-07-07 15:18:02,549][rs_gen][INFO] # ------ Generate random structures
[2026-07-07 15:18:02,712][gen_pyxtal][INFO] Structure ID 0: (6, 6, 2) Space group: 196 --> 216 F-43m
[2026-07-07 15:18:02,721][gen_pyxtal][WARNING] Compoisition [7 5 3] not compatible with symmetry 224: spg = 224 retry.
[2026-07-07 15:18:02,726][gen_pyxtal][WARNING] Compoisition [3 3] not compatible with symmetry 134: spg = 134 retry.
[2026-07-07 15:18:02,733][gen_pyxtal][WARNING] Compoisition [ 6 4 16] not compatible with symmetry 140: spg = 140 retry.
[2026-07-07 15:18:02,822][gen_pyxtal][INFO] Structure ID 1: (1, 4, 3) Space group: 23 --> 71 Immm
[2026-07-07 15:18:02,839][gen_pyxtal][INFO] Structure ID 2: (2, 2, 8) Space group: 150 --> 150 P321
...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．
...
[2026-07-07 15:21:18,273][ea_next_gen][INFO] Done generation 1
[2026-07-07 15:21:18,273][ea_next_gen][INFO] Calculate convex hull for generation 1
Ignoring fixed y limits to fulfill fixed data aspect with adjustable data limits.
[2026-07-07 15:21:18,772][ea_next_gen][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
14 0.000000 (0, 1, 3)
9 0.088493 (2, 8, 8)
15 0.105278 (8, 7, 5)
10 0.200962 (8, 0, 7)
8 0.210806 (0, 3, 3)
13 0.247862 (5, 6, 8)
19 0.258563 (6, 6, 1)
5 0.261977 (2, 6, 4)
6 0.269711 (7, 7, 2)
18 0.290792 (1, 6, 6)
11 0.292541 (8, 3, 1)
16 0.356158 (6, 2, 4)
2 0.373888 (2, 2, 8)
7 0.514507 (0, 4, 4)
12 0.548770 (3, 4, 4)
1 0.617685 (1, 4, 3)
3 0.761585 (1, 0, 8)
17 0.934091 (6, 4, 7)
4 0.955053 (2, 8, 4)
0 1.019078 (6, 6, 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，次世代構造の生成が始まる．
デフォルト（backup_interval = 1）では，次世代構造を生成する直前に自動バックアップが実行される．
v1.5.0以降は，[option]セクションのbackup_intervalで間隔（世代数）を変更でき，0で自動バックアップを無効にする．詳細は機能 > バックアップを参照．
cryspy...
[2026-07-07 15:29:32,182][ea_next_gen][INFO] Done generation 1
[2026-07-07 15:29:32,505][utility][INFO] Backup data
[2026-07-07 15:29:32,512][ea_next_gen][INFO] # ---------- Evolutionary algorithm
[2026-07-07 15:29:32,512][ea_next_gen][INFO] Generation 2
[2026-07-07 15:29:32,512][ea_next_gen][INFO] # ------ Apply nat/composition constraints
[2026-07-07 15:29:32,512][ea_next_gen][INFO] Current candidates after constraint filter: 20
[2026-07-07 15:29:32,513][ea_next_gen][INFO] Elite structures after constraint filter: 0
[2026-07-07 15:29:32,513][ea_next_gen][INFO] # ------ natural selection
[2026-07-07 15:29:32,515][ea_next_gen][INFO] ranking without duplication (including elite):
[2026-07-07 15:29:32,515][ea_next_gen][INFO] Structure ID 14, fitness: 0.00000
[2026-07-07 15:29:32,515][ea_next_gen][INFO] Structure ID 9, fitness: 0.08849
[2026-07-07 15:29:32,515][ea_next_gen][INFO] Structure ID 15, fitness: 0.10528
[2026-07-07 15:29:32,515][ea_next_gen][INFO] Structure ID 10, fitness: 0.20096
[2026-07-07 15:29:32,515][ea_next_gen][INFO] Structure ID 8, fitness: 0.21081
[2026-07-07 15:29:32,515][ea_next_gen][INFO] Structure ID 13, fitness: 0.24786
[2026-07-07 15:29:32,515][ea_next_gen][INFO] Structure ID 19, fitness: 0.25856
[2026-07-07 15:29:32,515][ea_next_gen][INFO] Structure ID 5, fitness: 0.26198
[2026-07-07 15:29:32,515][ea_next_gen][INFO] Structure ID 6, fitness: 0.26971
[2026-07-07 15:29:32,515][ea_next_gen][INFO] Structure ID 18, fitness: 0.29079
[2026-07-07 15:29:32,515][ea_next_gen][INFO] # ------ Generate children
[2026-07-07 15:29:32,515][ea_child][INFO] # -- mindist
[2026-07-07 15:29:32,517][struc_util][INFO] Cu - Cu: 1.32
[2026-07-07 15:29:32,517][struc_util][INFO] Cu - Ag: 1.385
[2026-07-07 15:29:32,517][struc_util][INFO] Cu - Au: 1.34
[2026-07-07 15:29:32,517][struc_util][INFO] Ag - Ag: 1.45
[2026-07-07 15:29:32,517][struc_util][INFO] Ag - Au: 1.405
[2026-07-07 15:29:32,517][struc_util][INFO] Au - Au: 1.36
[2026-07-07 15:29:32,521][ea_child][INFO] eligible candidates for crossover and strain: 10
[2026-07-07 15:29:32,521][ea_child][INFO] eligible candidates for permutation: 10
[2026-07-07 15:29:32,521][ea_child][INFO] eligible candidates for addition: 10
[2026-07-07 15:29:32,522][ea_child][INFO] eligible candidates for elimination: 10
[2026-07-07 15:29:32,522][ea_child][INFO] eligible candidates for substitution: 10
[2026-07-07 15:29:32,527][crossover][WARNING] remove_within_mindist: some atoms within mindist. retry.
[2026-07-07 15:29:32,532][crossover][WARNING] remove_within_mindist: some atoms within mindist. retry.
[2026-07-07 15:29:32,537][crossover][WARNING] remove_within_mindist: some atoms within mindist. retry.
[2026-07-07 15:29:32,541][crossover][WARNING] remove_within_mindist: some atoms within mindist. retry.
[2026-07-07 15:29:32,547][crossover][WARNING] remove_within_mindist: some atoms within mindist. retry.
[2026-07-07 15:29:32,551][crossover][WARNING] remove_within_mindist: some atoms within mindist. retry.
[2026-07-07 15:29:32,556][crossover][WARNING] remove_within_mindist: some atoms within mindist. retry.
[2026-07-07 15:29:32,561][crossover][WARNING] remove_within_mindist: some atoms within mindist. retry.
[2026-07-07 15:29:32,564][crossover][WARNING] remove_within_mindist: some atoms within mindist. retry.
[2026-07-07 15:29:32,569][crossover][WARNING] remove_within_mindist: some atoms within mindist. retry.
[2026-07-07 15:29:32,592][crossover][WARNING] remove_within_mindist: some atoms within mindist. retry.
[2026-07-07 15:29:32,622][crossover][WARNING] remove_within_mindist: some atoms within mindist. retry.
[2026-07-07 15:29:32,644][crossover][WARNING] remove_within_mindist: some atoms within mindist. retry.
[2026-07-07 15:29:32,667][crossover][INFO] Structure ID 20 (8, 3, 5) was generated from 10 and 15 by crossover. Space group: 1 P1
[2026-07-07 15:29:32,668][crossover][INFO] Structure ID 21 (0, 1, 5) was generated from 14 and 8 by crossover. Space group: 1 P1
...
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...
[2026-07-07 15:29:33,401][ea_next_gen][INFO] # ------ Apply nat/composition constraints to elite candidates
[2026-07-07 15:29:33,401][ea_next_gen][INFO] Elite candidates after constraint filter: 20
[2026-07-07 15:29:33,401][ea_next_gen][INFO] Structure ID 14 keeps as the elite
[2026-07-07 15:29:33,401][ea_next_gen][INFO] Structure ID 9 keeps as the eliteあとはcryspyの実行を繰り返せば，探索が進む．