次世代の生成
2025年4月6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
...
[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
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
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．
...
[2025-04-06 09:20:26,218][ctrl_job][INFO] Done generation 1
[2025-04-06 09:20:26,218][ctrl_job][INFO]
EA is ready
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
...
[2025-04-06 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
あとはcryspyの実行を繰り返せば，探索が進む．