Hello everyone!
I am trying to get the Radial and Angular Distribution Functions (RDF, ADF) from the AUTO-FOX package.
from FOX import MultiMolecule, example_xyz
sys = MultiMolecule.from_xyz(r'C:\Users\bnzmi\OneDrive - Northeastern University\Lustig Lab\RDF Attempts\hybrid7-pos-1.xyz')
rdf = sys.init_rdf(atom_subset=('Al', 'C', 'O'))
adf = sys.init_adf(r_max=13, weight=None, atom_subset=('O',))
adf_weighted = sys.init_adf(r_max=13, atom_subset=('O',))
rdf.plot(title='RDF')
adf.plot(title='ADF')
adf_weighted.plot(title='Distance-weighted ADF')
When I run this script, I get this error message:
[rest of the directory path]\LocalCache\local-packages\Python312\site-packages\FOX\functions\rdf.py:103: RuntimeWarning: divide by zero encountered in divide
dens_mean = dist_shape[2] / ((4/3) * np.pi * (0.5 * dist.max(axis=(1, 2)))**3)
What I tried to do:
- I consulted the documentation (Radial & Angular Distribution Function — Auto-FOX 1.0.0b2.dev85+ga7fd4e5 documentation), but could not really understand what the issue is. I have a script checking the positions of all my atoms in the system, and none of them are close to zero (the shortest distance is around 1.5 A).
I even checked the source code for RDF (auto-FOX/FOX/functions/rdf.py at master · nlesc-nano/auto-FOX · GitHub), but I am not sure what dist.max is, as it is not defined.
- I am also wondering if my issue is not using floats. How does that apply to my code?
I tried to print my “sys”, and all of the elements in it seem to be floats? See below:
[[[ 7.25600514 8.72794805 12.02820221]
[14.95928393 7.84438621 11.64682185]
[10.96354716 11.067581 8.55290687]
[13.90091624 15.56398689 8.76734726]
[16.80418492 13.57377941 9.60267977]
[ 6.33053393 15.84933413 2.60828572]
[ 8.21413187 13.2309031 2.91318796]
[ 8.93575675 16.15589859 2.44320707]
[12.40698335 7.84374698 2.77464373]
[11.92339275 11.34323094 11.80519698]
[ 7.52861562 7.56520827 9.78788325]
[13.10538581 6.73522015 13.76295514]
[10.82989723 12.10437062 10.06084028]
[12.87908469 5.32888489 8.22080132]
[ 1.07778236 3.09234291 7.15402912]
[11.63654902 5.60199583 5.58738808]
[-0.53486586 -2.17915618 2.59191956]
[10.4356729 6.42491477 -4.42810484]
[ 6.95128157 3.39314284 3.37684836]
[16.97975178 6.60982909 10.6174393 ]
[10.95329605 1.27074336 4.52390992]
[12.78397904 3.05412743 7.09692838]
[12.33656654 -0.65409041 3.08627917]
[13.65578941 -2.15069691 -0.16165908]
[-3.27092597 11.92237014 1.83463317]
[-0.70312332 10.78231393 16.58499829]
[ 6.72650307 6.72909033 5.89401978]
[ 6.77745953 17.59925813 5.79215546]
[ 8.18637451 15.31592535 6.88374314]
[10.62893379 5.7730726 1.53417611]
[ 8.09091963 8.34391673 3.42659414]
[ 9.28725088 10.65364402 2.57004451]
[ 9.68928304 8.9113796 -2.40555176]
[ 0.12624191 10.68564384 -5.81805456]
[ 6.95518149 9.61098255 14.58827988]
[ 1.34611275 6.57618174 14.35029969]
[ 7.43603734 4.32365274 7.0977121 ]
[ 5.64086131 8.31555877 7.7967102 ]
[ 6.49595398 7.75162723 4.2642536 ]
[ 2.99617441 2.12574957 9.26036517]
[ 9.89495245 3.3401569 4.96679085]
[ 5.32812313 7.77853996 3.58329398]
[ 8.90244357 5.55354152 3.44017076]
[ 3.98327179 8.70742134 2.4366657 ]
[ 7.99312455 5.80399956 12.53134304]
[ 4.80430815 3.6943093 6.22870122]
[ 3.79232246 -0.26922842 7.11844103]
[ 0.2173818 -0.18838547 4.90822017]
[ 6.72185774 2.32004651 0.57268472]
[ 5.34912678 15.38046439 8.50277079]
[-1.66035381 10.66112395 9.72699782]
[ 1.38628949 12.2795194 2.9465908 ]
[ 1.79612442 9.38067778 4.49232811]
[ 3.45818308 13.71276208 1.42855228]
[-2.95126372 8.42249247 10.882055 ]
[ 3.37256262 9.23874181 9.09710981]
[ 1.42387917 7.15022174 5.21559012]
[-0.3821581 2.22427304 5.02820014]
[ 2.92760917 5.93451299 3.44801565]
[ 3.35133044 0.67449708 12.96943685]
[ 2.80663569 3.07975794 12.07405559]
[ 2.73693849 5.37196875 6.55851118]
[ 6.48900074 19.04488274 11.43837073]
[ 4.61299704 15.57958535 10.99807735]
[-0.42402647 16.55842749 11.79872831]
[13.69741641 6.05368799 16.70948865]
[10.59075766 1.04084036 7.31630451]
[ 5.78341624 2.39498415 9.49620596]]]
I would love some input! Thank you kindly!