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Tomoki-YAMASHITA / CrySPY

CrySPY is a crystal structure prediction tool written in Python.
https://tomoki-yamashita.github.io/CrySPY_doc
MIT License
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Too short distance between atoms #54

Closed thienbinh92 closed 1 year ago

thienbinh92 commented 1 year ago

Hello, I would like to ask how to control the minimum distance between atoms. I set mindist in the input file:

mindist = [[1.8, 1.8, 1.8],
           [1.8, 1.8, 1.8],
           [1.8, 1.8, 1.8]]
spgnum = 161
jobcmd = zsh
jobfile = job_cryspy

[structure]
natot = 12
atype = Li Co O
nat = 3 3 6

But the output shows something like the following. O-O distance is too short for a crystal.

[2023-08-29 17:33:50,021][struc_util][INFO] Li - Li: 1.28
[2023-08-29 17:33:50,021][struc_util][INFO] Li - Co: 1.27
[2023-08-29 17:33:50,021][struc_util][INFO] Li - O: 0.99
[2023-08-29 17:33:50,021][struc_util][INFO] Co - Co: 1.26
[2023-08-29 17:33:50,021][struc_util][INFO] Co - O: 0.98
[2023-08-29 17:33:50,021][struc_util][INFO] O - O: 0.7
Tomoki-YAMASHITA commented 1 year ago

Here is an example of mindist for a binary sisytem:

mindist_1 = 2.0 1.8
mindist_2 = 1.8 1.5

The simple instruction is available in https://tomoki-yamashita.github.io/CrySPY_doc/features/restrict_dist/index.html

Could you try to use the following?

mindist_1 = 1.8 1.8 1.8
mindist_2 = 1.8 1.8 1.8
mindist_3 = 1.8 1.8 1.8

Please use github discussion next time.（https://github.com/Tomoki-YAMASHITA/CrySPY/discussions） Any other questions are welcome!

thienbinh92 commented 1 year ago

Thank you for your quick response. I changed the mindist_1, 2, 3, but it still resulted in some structures in which O-O bonds are shorter than 1A. For example, this structure:

ID_3
1.0
   1.8812375913902557    3.2583990893964225   -2.8431659625446426
   1.8812375913902557   -3.2583990893964208   -2.8431659625446430
  -3.7624751827805114   -0.0000000000000018   -2.8431659625446439
Li Co O
3 3 6
direct
   0.0000000000000000    0.0000000000000000    0.0000000000000000 Li
   0.1913043144126091    0.1913043144126091    0.1913043144126092 Li
   0.8086956855873910    0.8086956855873910    0.8086956855873910 Li
   0.4999999999999999    0.0000000000000001    1.0000000000000000 Co
   1.0000000000000000    0.0000000000000000    0.5000000000000000 Co
   0.0000000000000001    0.5000000000000000    1.0000000000000000 Co
   0.9999999999999999    0.5613044041651456    0.4386955958348544 O
   0.5613044041651454    0.4386955958348544    0.0000000000000001 O
   0.4386955958348543    0.9999999999999998    0.5613044041651456 O
   1.0000000000000000    0.4386955958348543    0.5613044041651456 O
   0.4386955958348543    0.5613044041651456    1.0000000000000000 O
   0.5613044041651456    0.0000000000000000    0.4386955958348545 O
Tomoki-YAMASHITA commented 1 year ago

Could you paste log_cryspy here?

thienbinh92 commented 1 year ago

Here you are!

[2023-08-30 09:36:02,636][cryspy_init][INFO] 

Start CrySPY 1.2.0

[2023-08-30 09:36:02,637][cryspy_init][INFO] # ---------- Read input file, cryspy.in
[2023-08-30 09:36:02,638][read_input][INFO] Save input data in cryspy.stat
[2023-08-30 09:36:02,639][cryspy_init][INFO] # ---------- Initial structure generation
[2023-08-30 09:36:02,639][cryspy_init][INFO] Number of MPI processes: 1
[2023-08-30 09:36:02,639][gen_init_struc][INFO] # ------ mindist
[2023-08-30 09:36:02,642][struc_util][INFO] Li - Li: 1.28
[2023-08-30 09:36:02,642][struc_util][INFO] Li - Co: 1.27
[2023-08-30 09:36:02,642][struc_util][INFO] Li - O: 0.99
[2023-08-30 09:36:02,642][struc_util][INFO] Co - Co: 1.26
[2023-08-30 09:36:02,643][struc_util][INFO] Co - O: 0.98
[2023-08-30 09:36:02,643][struc_util][INFO] O - O: 0.7
[2023-08-30 09:36:02,643][gen_init_struc][INFO] # ------ generate structures
[2023-08-30 09:36:02,877][gen_pyxtal][INFO] Structure ID      0 was generated. Space group:  47 -->  47 Pmmm
[2023-08-30 09:36:02,965][gen_pyxtal][INFO] Structure ID      1 was generated. Space group:  35 -->  35 Cmm2
[2023-08-30 09:36:03,020][gen_pyxtal][INFO] Structure ID      2 was generated. Space group: 119 --> 119 I-4m2
[2023-08-30 09:36:03,062][gen_pyxtal][INFO] Structure ID      3 was generated. Space group: 115 --> 115 P-4m2
[2023-08-30 09:36:03,125][gen_pyxtal][INFO] Structure ID      4 was generated. Space group: 166 --> 166 R-3m
[2023-08-30 09:36:03,168][gen_pyxtal][INFO] Structure ID      5 was generated. Space group:  35 -->  35 Cmm2
[2023-08-30 09:36:03,192][gen_pyxtal][INFO] Structure ID      6 was generated. Space group: 156 --> 156 P3m1
[2023-08-30 09:36:03,296][gen_pyxtal][INFO] Structure ID      7 was generated. Space group: 123 --> 123 P4/mmm
[2023-08-30 09:36:03,429][gen_pyxtal][INFO] Structure ID      8 was generated. Space group: 191 --> 191 P6/mmm
[2023-08-30 09:36:03,475][gen_pyxtal][INFO] Structure ID      9 was generated. Space group:  35 -->  35 Cmm2
[2023-08-30 09:36:03,509][gen_pyxtal][INFO] Structure ID     10 was generated. Space group:  16 -->  16 P222
[2023-08-30 09:36:03,730][gen_pyxtal][INFO] Structure ID     11 was generated. Space group:  97 --> 139 I4/mmm
[2023-08-30 09:36:03,834][gen_pyxtal][INFO] Structure ID     12 was generated. Space group:  65 -->  65 Cmmm
[2023-08-30 09:36:04,461][gen_pyxtal][INFO] Structure ID     13 was generated. Space group: 207 --> 221 Pm-3m
[2023-08-30 09:36:05,027][gen_pyxtal][INFO] Structure ID     14 was generated. Space group: 107 --> 107 I4mm
[2023-08-30 09:36:05,152][gen_pyxtal][INFO] Structure ID     15 was generated. Space group: 200 --> 221 Pm-3m
[2023-08-30 09:36:05,164][gen_pyxtal][INFO] Structure ID     16 was generated. Space group: 172 --> 172 P6_4
[2023-08-30 09:36:05,191][gen_pyxtal][INFO] Structure ID     17 was generated. Space group: 157 --> 157 P31m
[2023-08-30 09:36:05,216][gen_pyxtal][INFO] Structure ID     18 was generated. Space group: 175 --> 175 P6/m
[2023-08-30 09:36:05,320][gen_pyxtal][INFO] Structure ID     19 was generated. Space group:  21 -->  21 C222
[2023-08-30 09:36:05,344][gen_pyxtal][INFO] Structure ID     20 was generated. Space group: 168 --> 168 P6
[2023-08-30 09:36:05,359][gen_pyxtal][INFO] Structure ID     21 was generated. Space group: 157 --> 157 P31m
[2023-08-30 09:36:05,390][gen_pyxtal][INFO] Structure ID     22 was generated. Space group: 160 --> 160 R3m
[2023-08-30 09:36:05,422][gen_pyxtal][INFO] Structure ID     23 was generated. Space group: 164 --> 164 P-3m1
[2023-08-30 09:36:05,470][gen_pyxtal][INFO] Structure ID     24 was generated. Space group:  12 -->  12 C2/m
[2023-08-30 09:36:05,569][gen_pyxtal][INFO] Structure ID     25 was generated. Space group:  16 -->  16 P222
[2023-08-30 09:36:05,629][gen_pyxtal][INFO] Structure ID     26 was generated. Space group:  82 -->  82 I-4
[2023-08-30 09:36:05,826][gen_pyxtal][INFO] Structure ID     27 was generated. Space group: 221 --> 221 Pm-3m
[2023-08-30 09:36:05,937][gen_pyxtal][INFO] Structure ID     28 was generated. Space group: 148 --> 148 R-3
[2023-08-30 09:36:05,970][gen_pyxtal][INFO] Structure ID     29 was generated. Space group: 146 --> 146 R3
[2023-08-30 09:36:06,077][gen_pyxtal][INFO] Structure ID     30 was generated. Space group: 139 --> 139 I4/mmm
[2023-08-30 09:36:06,195][gen_pyxtal][INFO] Structure ID     31 was generated. Space group: 139 --> 139 I4/mmm
[2023-08-30 09:36:06,279][gen_pyxtal][INFO] Structure ID     32 was generated. Space group:  97 -->  97 I422
[2023-08-30 09:36:06,292][gen_pyxtal][INFO] Structure ID     33 was generated. Space group: 172 --> 172 P6_4
[2023-08-30 09:36:06,312][gen_pyxtal][INFO] Structure ID     34 was generated. Space group: 183 --> 183 P6mm
[2023-08-30 09:36:06,620][gen_pyxtal][INFO] Structure ID     35 was generated. Space group: 166 --> 166 R-3m
[2023-08-30 09:36:06,660][gen_pyxtal][INFO] Structure ID     36 was generated. Space group:  99 -->  99 P4mm
[2023-08-30 09:36:06,878][gen_pyxtal][INFO] Structure ID     37 was generated. Space group:  82 -->  82 I-4
[2023-08-30 09:36:06,976][gen_pyxtal][INFO] Structure ID     38 was generated. Space group:  65 -->  65 Cmmm
[2023-08-30 09:36:07,028][gen_pyxtal][INFO] Structure ID     39 was generated. Space group:  21 -->  21 C222
[2023-08-30 09:36:07,083][gen_pyxtal][INFO] Structure ID     40 was generated. Space group:  23 -->  23 I222
[2023-08-30 09:36:07,112][gen_pyxtal][INFO] Structure ID     41 was generated. Space group:   5 -->   5 C2
[2023-08-30 09:36:07,162][gen_pyxtal][INFO] Structure ID     42 was generated. Space group: 149 --> 187 P-6m2
[2023-08-30 09:36:07,213][gen_pyxtal][INFO] Structure ID     43 was generated. Space group:  35 -->  35 Cmm2
[2023-08-30 09:36:07,247][gen_pyxtal][INFO] Structure ID     44 was generated. Space group:  35 -->  35 Cmm2
[2023-08-30 09:36:07,476][gen_pyxtal][INFO] Structure ID     45 was generated. Space group: 123 --> 123 P4/mmm
[2023-08-30 09:36:07,544][gen_pyxtal][INFO] Structure ID     46 was generated. Space group: 162 --> 191 P6/mmm
[2023-08-30 09:36:07,602][gen_pyxtal][INFO] Structure ID     47 was generated. Space group: 146 --> 146 R3
[2023-08-30 09:36:11,243][gen_pyxtal][INFO] Structure ID     48 was generated. Space group: 221 --> 221 Pm-3m
[2023-08-30 09:36:11,346][gen_pyxtal][INFO] Structure ID     49 was generated. Space group:  89 --> 123 P4/mmm
[2023-08-30 09:36:11,425][gen_pyxtal][INFO] Structure ID     50 was generated. Space group: 143 --> 143 P3
[2023-08-30 09:36:11,436][gen_pyxtal][INFO] Structure ID     51 was generated. Space group: 154 --> 154 P3_221
[2023-08-30 09:36:11,459][gen_pyxtal][INFO] Structure ID     52 was generated. Space group: 143 --> 143 P3
[2023-08-30 09:36:11,510][gen_pyxtal][INFO] Structure ID     53 was generated. Space group:  35 -->  35 Cmm2
[2023-08-30 09:36:11,555][gen_pyxtal][INFO] Structure ID     54 was generated. Space group: 172 --> 172 P6_4
[2023-08-30 09:36:11,762][gen_pyxtal][INFO] Structure ID     55 was generated. Space group:  47 -->  47 Pmmm
[2023-08-30 09:36:11,802][gen_pyxtal][INFO] Structure ID     56 was generated. Space group: 155 --> 155 R32
[2023-08-30 09:36:11,852][gen_pyxtal][INFO] Structure ID     57 was generated. Space group: 171 --> 171 P6_2
[2023-08-30 09:36:12,751][gen_pyxtal][INFO] Structure ID     58 was generated. Space group:  97 -->  97 I422
[2023-08-30 09:36:13,527][gen_pyxtal][INFO] Structure ID     59 was generated. Space group: 221 --> 221 Pm-3m
[2023-08-30 09:36:13,539][gen_pyxtal][INFO] Structure ID     60 was generated. Space group: 171 --> 171 P6_2
[2023-08-30 09:36:13,571][gen_pyxtal][INFO] Structure ID     61 was generated. Space group: 150 --> 150 P321
[2023-08-30 09:36:13,702][gen_pyxtal][INFO] Structure ID     62 was generated. Space group: 123 --> 123 P4/mmm
[2023-08-30 09:36:15,247][gen_pyxtal][INFO] Structure ID     63 was generated. Space group:  87 --> 139 I4/mmm
[2023-08-30 09:36:15,320][gen_pyxtal][INFO] Structure ID     64 was generated. Space group: 107 --> 107 I4mm
[2023-08-30 09:36:15,427][gen_pyxtal][INFO] Structure ID     65 was generated. Space group: 200 --> 200 Pm-3
[2023-08-30 09:36:15,477][gen_pyxtal][INFO] Structure ID     66 was generated. Space group: 107 --> 107 I4mm
[2023-08-30 09:36:15,640][gen_pyxtal][INFO] Structure ID     67 was generated. Space group: 164 --> 164 P-3m1
[2023-08-30 09:36:15,715][gen_pyxtal][INFO] Structure ID     68 was generated. Space group: 115 --> 115 P-4m2
[2023-08-30 09:36:15,747][gen_pyxtal][INFO] Structure ID     69 was generated. Space group: 150 --> 150 P321
[2023-08-30 09:36:15,763][gen_pyxtal][INFO] Structure ID     70 was generated. Space group: 144 --> 144 P3_1
[2023-08-30 09:36:15,801][gen_pyxtal][INFO] Structure ID     71 was generated. Space group:   6 -->   6 Pm
[2023-08-30 09:36:16,175][gen_pyxtal][INFO] Structure ID     72 was generated. Space group:  99 -->  99 P4mm
[2023-08-30 09:36:16,253][gen_pyxtal][INFO] Structure ID     73 was generated. Space group: 115 --> 115 P-4m2
[2023-08-30 09:36:16,344][gen_pyxtal][INFO] Structure ID     74 was generated. Space group:  47 -->  47 Pmmm
[2023-08-30 09:36:16,395][gen_pyxtal][INFO] Structure ID     75 was generated. Space group: 160 --> 160 R3m
[2023-08-30 09:36:16,428][gen_pyxtal][INFO] Structure ID     76 was generated. Space group: 174 --> 174 P-6
[2023-08-30 09:36:16,472][gen_pyxtal][INFO] Structure ID     77 was generated. Space group: 168 --> 183 P6mm
[2023-08-30 09:36:16,603][gen_pyxtal][INFO] Structure ID     78 was generated. Space group:  21 -->  21 C222
[2023-08-30 09:36:16,687][gen_pyxtal][INFO] Structure ID     79 was generated. Space group: 221 --> 221 Pm-3m
[2023-08-30 09:36:16,708][gen_pyxtal][INFO] Structure ID     80 was generated. Space group: 181 --> 181 P6_422
[2023-08-30 09:36:17,910][gen_pyxtal][INFO] Structure ID     81 was generated. Space group: 200 --> 200 Pm-3
[2023-08-30 09:36:18,088][gen_pyxtal][INFO] Structure ID     82 was generated. Space group: 121 --> 121 I-42m
[2023-08-30 09:36:18,165][gen_pyxtal][INFO] Structure ID     83 was generated. Space group:  22 -->  22 F222
[2023-08-30 09:36:18,528][gen_pyxtal][INFO] Structure ID     84 was generated. Space group: 207 --> 221 Pm-3m
[2023-08-30 09:36:18,590][gen_pyxtal][INFO] Structure ID     85 was generated. Space group:   1 -->   1 P1
[2023-08-30 09:36:19,747][gen_pyxtal][INFO] Structure ID     86 was generated. Space group: 119 --> 119 I-4m2
[2023-08-30 09:36:19,758][gen_pyxtal][INFO] Structure ID     87 was generated. Space group: 153 --> 153 P3_212
[2023-08-30 09:36:19,809][gen_pyxtal][INFO] Structure ID     88 was generated. Space group:  82 -->  82 I-4
[2023-08-30 09:36:19,848][gen_pyxtal][INFO] Structure ID     89 was generated. Space group: 162 --> 191 P6/mmm
[2023-08-30 09:36:19,874][gen_pyxtal][INFO] Structure ID     90 was generated. Space group: 181 --> 181 P6_422
[2023-08-30 09:36:19,932][gen_pyxtal][INFO] Structure ID     91 was generated. Space group: 164 --> 164 P-3m1
[2023-08-30 09:36:20,031][gen_pyxtal][INFO] Structure ID     92 was generated. Space group: 156 --> 156 P3m1
[2023-08-30 09:36:20,182][gen_pyxtal][INFO] Structure ID     93 was generated. Space group: 175 --> 191 P6/mmm
[2023-08-30 09:36:20,311][gen_pyxtal][INFO] Structure ID     94 was generated. Space group: 207 --> 221 Pm-3m
[2023-08-30 09:36:20,329][gen_pyxtal][INFO] Structure ID     95 was generated. Space group: 153 --> 153 P3_212
[2023-08-30 09:36:20,346][gen_pyxtal][INFO] Structure ID     96 was generated. Space group: 144 --> 144 P3_1
[2023-08-30 09:36:20,636][gen_pyxtal][INFO] Structure ID     97 was generated. Space group: 107 --> 107 I4mm
[2023-08-30 09:36:20,695][gen_pyxtal][INFO] Structure ID     98 was generated. Space group: 207 --> 221 Pm-3m
[2023-08-30 09:36:20,817][gen_pyxtal][INFO] Structure ID     99 was generated. Space group: 189 --> 189 P-62m
[2023-08-30 09:36:21,304][cryspy_init][INFO] Elapsed time for structure generation: 0:00:18.664124
[2023-08-30 09:36:29,844][cryspy_restart][INFO] 

Restart CrySPY 1.2.0

[2023-08-30 09:36:29,863][ctrl_job][INFO] # ---------- job status
[2023-08-30 09:36:29,863][ctrl_job][INFO] ID      0: Stage 1 Done!
Tomoki-YAMASHITA commented 1 year ago

mindist_? were not read. Please start from the beginning. (delete all files or make new directory)

thienbinh92 commented 1 year ago

Yes, I tried, but similar things still happened.

[2023-08-30 11:29:38,053][cryspy_init][INFO] 

Start CrySPY 1.2.0

[2023-08-30 11:29:38,054][cryspy_init][INFO] # ---------- Read input file, cryspy.in
[2023-08-30 11:29:38,055][read_input][INFO] Save input data in cryspy.stat
[2023-08-30 11:29:38,057][cryspy_init][INFO] # ---------- Initial structure generation
[2023-08-30 11:29:38,057][cryspy_init][INFO] Number of MPI processes: 1
[2023-08-30 11:29:38,057][gen_init_struc][INFO] # ------ mindist
[2023-08-30 11:29:38,060][struc_util][INFO] Li - Li: 1.28
[2023-08-30 11:29:38,060][struc_util][INFO] Li - Co: 1.27
[2023-08-30 11:29:38,060][struc_util][INFO] Li - O: 0.99
[2023-08-30 11:29:38,060][struc_util][INFO] Co - Co: 1.26
[2023-08-30 11:29:38,060][struc_util][INFO] Co - O: 0.98
[2023-08-30 11:29:38,060][struc_util][INFO] O - O: 0.7
[2023-08-30 11:29:38,060][gen_init_struc][INFO] # ------ generate structures
Tomoki-YAMASHITA commented 1 year ago

Could you give me cryspy.in?

thienbinh92 commented 1 year ago

Here is the whole file:

[basic]
algo = RS
calc_code = ASE
tot_struc = 100
nstage = 1
njob = 2
mindist_1 = 1.8 1.8 1.8
mindist_2 = 1.8 1.8 1.8
mindist_3 = 1.8 1.8 1.8
spgnum = 161
jobcmd = zsh
jobfile = job_cryspy

[structure]
natot = 12
atype = Li Co O
nat = 3 3 6

[ASE]
ase_python = ase_in.py

[option]
Tomoki-YAMASHITA commented 1 year ago

Please move mindist_? and spgnum to [structure section]. For your information, spgnum = 161 is not compatible with the nat. You should change spgnum or nat.

[2023-08-30 14:13:31,490][gen_pyxtal][WARNING] Compoisition [ 9  9 18] not compatible with symmetry 161: spg = 161 retry.
Tomoki-YAMASHITA commented 1 year ago

This is not an issue.