tomoki-yamashita / cryspy Goto Github PK

Dear Sir,
Following the step of documents, I download the folder of find_wy just from the github. But, I do not know how to create the executable file of find_wy from this folder. Thank you for helping.

Hello,

When the Si is replaced by Bk, the QE_Si8_RS example do not run. May the actinides element is absent.

gs.

Am I correct that I can supply initial structures to CrysPy to help to generate new structures based on them?

I tried to use CrysPy_utility to do so and supplied 1 experimental structure as initial guess. However, cryspy utility always stops with error message saying that total number of structures (20 in my case) is different than loaded number of structures from pkl file (1).

Is it an expected behavior?

Hello, I have taken great interest in your code and have tried running it with QE but have ran into multiple problems. For example in the code for interface/QE/strucuture.py, the code has it that the order of the elements are wrong. This is the example QE file I get from CRYSPY for a RS.

`
&control
title = 'Si8'
calculation = 'relax'
nstep = 100
restart_mode = 'from_scratch',
pseudo_dir = '~/calculations/subbig/pseudo'
outdir='./out.d/'
/

&system
ibrav = 0
nat = 8
ntyp = 1
ecutwfc = 44.0
occupations = 'smearing'
degauss = 0.01
/

&electrons
/

&ions
/

&cell
/

ATOMIC_SPECIES
C 6 C.pbesol-n-kjpaw_psl.1.0.0.UPF
N 7 N.pbesol-theos.UPF
O 8 O.pbesol-n-kjpaw_psl.0.1.UPF
H 1 H.pbesol-rrkjus_psl.1.0.0.UPF
CELL_PARAMETERS angstrom
8.1848068865698647 0.7595598784348114 -3.3614435519497508
0.0000000000000000 4.4085364017832651 1.5179270290575053
0.0000000000000000 0.0000000000000000 8.4052731466826653
ATOMIC_POSITIONS crystal
H 1.0272744478181299 0.2627384881289004 0.0937040858057427
H 0.7599491902187562 0.4420509409689334 -0.0379224401397704
H 1.3007095992936761 -0.1762893569218246 0.1301253103079126
H 1.3893435394195548 -0.0918628105280647 0.3098480415925064
H 0.4922202182767800 0.4226243674907904 -0.0430278705054866
H 1.2803379384555376 0.1694080055216949 0.1230441804720760
H 0.4340795085209237 0.0087842692283943 0.1757403461623094
H 0.6500865178911813 -0.3590159214232218 0.4058724455370528
H 0.9157461409670384 -0.3277890657827509 0.4067927517420840
C 0.6714343797682183 -0.1906154698147080 0.3120322805532349
C 0.8609280385192991 0.0556383934057273 0.1807914373508377
C 1.1426173714168577 -0.1350332890639422 0.2454986051209205
C 0.7357180528581425 0.2795152402424241 0.0506878208188995
C 0.5793394500253902 0.2630572865696528 0.0503723761544435
C 1.2879407348735656 -0.0447281851573187 0.1963193557811781
C 0.5462998709944149 0.0248704954110217 0.1798608171398284
C 0.8290013795207284 -0.1775005144063645 0.3144883205869253
N 1.0157177154294088 0.0828068224690623 0.1677794035480051
O 1.1406391373372478 -0.3925329060627208 0.3486125988670675
K_POINTS automatic
2 4 2 0 0 0
`

1. After each section there shouldn't be a line break , it should end with forward slash only.
2. The order for the input is Atomic species, ATOMIC_positions angstrom, K_points automatic, and in the end cell_parameters.

With the input file provided from the code I get the following error:
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error in routine read_cards (1):
species H in ATOMIC_POSITIONS is nonexistent
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Most likely due to the wrong order of the elements in the code.

Thank you so much for anything, any way I can help please reach out to me.

Dear Dr. Yamashita,

When searching my systems (combing with QE7.3 code), it repeats the selections many many times, i.e., the laqa_select_id file puts out the following information from the 66th step,

So, how to solve this issue, would you like to give any suggestions? The laqa_select_id and cryspy.in (part information) files are attached.

Selection ID
........
66 1 90 39 28
67 1 90 39 28
68 1 90 39 28
69 1 90 39 28
70 1 90 39 28
71 1 90 39 28
72 1 90 39 28
73 1 90 39 28
74 1 90 39 28
75 1 90 39 28
76 1 90 39 28
77 1 90 39 28
78 1 90 39 28
79 1 90 39 28
80 1 90 39 28
81 1 90 39 28
82 1 90 39 28
83 1 90 39 28
84 1 90 39 28
85 1 90 39 28
86 1 90 39 28
87 1 90 39 28
88 1 90 39 28
89 1 90 39 28
90 1 90 39 28
91 1 90 39 28
92 1 90 39 28
93 1 90 39 28
94 1 90 39 28
95 1 90 39 28
96 1 90 39 28
97 1 90 39 28
98 1 90 39 28
99 1 90 39 28
100 1 90 39 28
101 1 90 39 28
102 1 90 39 28
103 1 90 39 28
104 1 90 39 28
105 1 90 39 28
106 1 90 39 28
107 1 90 39 28
108 1 90 39 28
109 1 90 39 28
110 1 90 39 28
111 1 90 39 28
112 1 90 39 28
113 1 90 39 28
114 1 90 39 28
115 1 90 39 28
116 90 39 1 28
117 90 39 1 28
118 90 39 1 28
119 90 39 1 28
120 90 39 1 28
121 90 39 1 28
122 90 39 1 28
123 90 39 1 28
124 90 39 1 28
125 90 39 1 28
126 90 39 1 28
127 90 39 1 28
128 90 39 1 28
129 90 39 1 28
130 90 39 1 28
131 90 1 39 28
132 90 1 39 28
133 90 1 39 28
134 90 1 39 28
135 90 1 39 28
136 90 1 39 28
137 90 1 39 28
138 90 1 39 28
139 90 1 39 28
140 90 1 39 28
141 90 1 39 28
142 90 1 39 28
143 1 90 39 28
144 1 90 39 28
145 1 90 39 28
146 1 90 39 28
147 1 90 39 28
148 1 90 39 28
149 1 90 39 28
150 1 90 39 28
151 1 90 39 28
152 1 90 39 28
153 1 90 39 28
154 1 90 39 28
155 1 90 39 28
156 1 90 39 28

Uploading cryspy.in…
Uploading laqa_select_id…

Dear Developers,

Is it possible for CrySPY to search the two-dimensional materials such as by LAQA methods? If so, would you like to share some examples?

Thanks so much.

Roc

HTU

CIFs as inputs

Thank you for developing a so nice tool to predict the structure of crystals.
I install the cryspy 0.10.0 and quantum espresso 6.8 on centos 7.
The combo, pyxtal, pymatgen were also installed normally.
But I can not run the QE_benzene_2_RS_mol example in the folder of cryspy.
The cryspy can generate the structure of benzene, but when i run the command "./crpspy &" for the second time. The cryspy can not be running normally.
In the file of ~/QE_benzene_2_RS_mol/work/000000/job_cryspy.e4000, I got this message "/var/spool/torque/mom_priv/jobs/4000.node01.SC:行8：pwscf.in: 没有那个文件或目录
sed: 无法读取 stat_job:没有那个文件或目录"

I want to know how to deal with this error.

I am getting this error OSError: [Errno 8] Exec format error: '/home/sadman/Desktop/CrySPY/CrySPY/f-fingerprint/cal_fingerprint.f90' which is called in the subprocess.

e.g. https://tomoki-yamashita.github.io/CrySPY_doc/tutorial/bo/

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

Hi. Could CrySPY generate 2D crystals randomly and how?

Hi, I'm new to CSP, I installed CrySPY and try to reproduce some example. I choosed the VASP_qsub_EA_Na8Cl8 example, but I found the POTCAR in the calc_in folder is empty, when I submit an job, there is an error:
POSCAR found type information on POSCAR Na Cl
POSCAR found : 2 types and 16 ions
scaLAPACK will be used
ERROR: number of potentials on File POTCAR incompatible with number of species
INCAR : 2 POTCAR: 0
I'm using vasp5.4.4 now, I tried switch to vasp5.4.1 but the same error occured.

numpy ==2.0.0 run cryspy print follow messa：
ImportError: numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()' after cimporting numpy; use 'numpy._import_array' to disable if you are certain you don't need it)

need to intall numpy==1.26.4 or other vision

Usually, we need to do some kind of evaluation to check the performance of the CSP algorithm.
This can be done by calculating the RMSE distance between the predicted structure and the predicted structure... Does CrySPY has such a function?