tomoki-yamashita/cryspy

CrySPY is a crystal structure prediction tool written in Python.

cryspy's Issues

I encounted the error when i use the cryspy with QE6.8

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.

Too short distance between atoms

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

How to calculate RMSE for a predicted a structure and a true structure?

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?

How to create the executable file of find_wy after installing the find_wy?

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.

Possible to use with CIF files?

CIFs as inputs

Initial structures

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?

empty POTCAR

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.

Documentation empty in certain places?

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

OSError: [Errno 8] Exec format 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.

Could CrySPY generate 2D crystals?

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

The structures with an element Bk can not be produced.

Hello,

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

gs.

The QE input is formatted incorrectly

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.