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Can't manually setup neighbor list for GFN-FF #1157

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qihexiang opened this issue Jan 12, 2025 · 0 comments
Open

Can't manually setup neighbor list for GFN-FF #1157

qihexiang opened this issue Jan 12, 2025 · 0 comments
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@Thomas3R
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method: GFN-FF Related to the GFN-FF method unconfirmed This report has not yet been confirmed by the developers

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@qihexiang
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Describe the bug
The $ffnb section doesn't make sense during GFN-FF optimization. I followed the guide in the Manual neighbor list setup, but the atom 2 and 8 still exist in neighbor list of atom 1.

To Reproduce

Running with xTB-6.7.1.

The input files La-Complex.xyz and xcontrol are copied from the document.

La-Complex.xyz

41

La           0.72786000000000        0.12391000000000       -0.08628000000000
N            1.00416000000000        2.77325000000000       -0.22511000000000
C           -0.38824000000000        3.25084000000000       -0.25618000000000
C           -1.08765000000000        2.78027000000000       -1.51853000000000
N           -1.11782000000000        1.31094000000000       -1.64701000000000
C           -2.43618000000000        0.67362000000000       -1.46323000000000
C           -2.68421000000000        0.23921000000000       -0.03208000000000
N           -1.66632000000000       -0.73533000000000        0.37904000000000
H            1.42751000000000        3.03853000000000        0.66748000000000
H            1.55240000000000        3.24148000000000       -0.94974000000000
H           -0.45253000000000        4.35033000000000       -0.18966000000000
H           -0.89219000000000        2.85336000000000        0.64062000000000
H           -0.56916000000000        3.20001000000000       -2.39649000000000
H           -2.10911000000000        3.19478000000000       -1.54298000000000
H           -0.79182000000000        1.05191000000000       -2.57777000000000
H           -2.46498000000000       -0.21568000000000       -2.11269000000000
H           -3.24634000000000        1.34395000000000       -1.79772000000000
H           -3.70449000000000       -0.17241000000000        0.04822000000000
H           -2.64135000000000        1.09662000000000        0.66000000000000
H           -1.77601000000000       -1.60108000000000       -0.15808000000000
H           -1.78341000000000       -0.97444000000000        1.37351000000000
S           -1.18295000000000       -0.59297000000000        3.85809000000000
C           -0.22699000000000        0.31138000000000        2.94360000000000
N            0.46256000000000        0.95064000000000        2.20256000000000
C            3.53573000000000       -3.44259000000000       -1.04159000000000
O            3.35606000000000       -3.31729000000000        0.36847000000000
P            2.85469000000000       -1.95320000000000        1.04260000000000
O            1.17475000000000       -2.11560000000000        1.07406000000000
C            0.51020000000000       -3.30623000000000        1.53102000000000
O            3.27039000000000       -2.34141000000000        2.54426000000000
C            2.98605000000000       -1.46746000000000        3.63325000000000
H            4.22423000000000       -4.28154000000000       -1.19720000000000
H            3.97428000000000       -2.52981000000000       -1.47479000000000
H            2.57747000000000       -3.65186000000000       -1.53820000000000
H            0.05574000000000       -3.81208000000000        0.66768000000000
H           -0.25298000000000       -3.00813000000000        2.26220000000000
H            1.23665000000000       -3.97515000000000        2.01184000000000
H            1.94096000000000       -1.58083000000000        3.96023000000000
H            3.17021000000000       -0.41383000000000        3.36804000000000
H            3.65610000000000       -1.75312000000000        4.45272000000000
Cl           2.54962000000000        0.34758000000000       -1.62990000000000

xcontrol

$ffnb
  nb = 1:5, 24, 27, 28, 41
  nb = 2:3,  9, 10
  nb = 8:7, 20, 21
$end

and execute xtb La-complex.xyz --gfnff --input xcontrol --wrtopo nb --opt.

In the output, the atom 2 and atom 8 still connected to atom 1. In the gfnff_list.json, they are still in neighbor list of atom 1.

gfnff_lists.json

{
   "nb":[
   [      2,      5,      8,     24,     27,     28,     41,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      7],
   [      1,      3,      9,     10,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      1,      4],
   [      2,      4,     11,     12,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      4],
   [      3,      5,     13,     14,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      4],
   [      1,      4,      6,     15,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      1,      4],
   [      5,      7,     16,     17,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      4],
   [      6,      8,     18,     19,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      4],
   [      1,      7,     20,     21,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      1,      4],
   [      2,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      1],
   [      2,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      1],
   [      3,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      1],
   [      3,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      1],
   [      4,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      1],
   [      4,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      1],
   [      5,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      1],
   [      6,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      1],
   [      6,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      1],
   [      7,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      1],
   [      7,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      1],
   [      8,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      1],
   [      8,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      1],
   [     23,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      1],
   [     22,     24,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      2],
   [      1,     23,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      2],
   [     26,     32,     33,     34,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      4],
   [     25,     27,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      2],
   [      1,     26,     28,     30,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      4],
   [      1,     27,     29,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      1,      3],
   [     28,     35,     36,     37,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      4],
   [     27,     31,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      2],
   [     30,     38,     39,     40,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      4],
   [     25,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      1],
   [     25,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      1],
   [     25,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      1],
   [     29,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      1],
   [     29,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      1],
   [     29,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      1],
   [     31,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      1],
   [     31,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      1],
   [     31,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      1],
   [      1,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      0,      1]
   ],
   "program call": "xtb La-complex.xyz --gfnff --input xcontrol --wrtopo nb --opt --verbose",
   "method": "GFN-FF",
   "xtb version": "6.7.1 (edcfbbe)"
}

The verbose output are uploaded verbose.log, there is a warning:

[WARNING] Runtime exception occurred
-1- gfnff_setup: Could not read topology file.

Expected behaviour

The atom 2 and 8 dissociating during optimization.

Additional context

The problem can be reproduced in 6.7.1, 6.7.0 and 6.6.1.

gfnff_lists.json
verbose.log
@qihexiang qihexiang added the unconfirmed This report has not yet been confirmed by the developers label Jan 12, 2025
@marvinfriede marvinfriede added the method: GFN-FF Related to the GFN-FF method label Feb 7, 2025
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@Thomas3R Thomas3R

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@Thomas3R @qihexiang @marvinfriede