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Inconsistent results for the identical system with different order of coordinates #1069
Comments
The problem lies in the incorrect By default, To fix it, I suggest changing |
Also, the problem is not related to GB model itself, but is rooted in SASA. Another problem, although not related to the issue, is that the |
@FanGuozheng thanks, I can reproduce it, I'll try to fix it. @tsihyoung Thanks for the hints, they are very valuable. As almost all parts of DFTB+ work with the asymmetric neighbor list, I'll probably try to fix the SASA instead. |
This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. |
This stale issue has been automatically closed. |
@aradi is this still a live issue? |
Sure, it is still an issue. |
Describe the bug
For an identical system, when only switching orders of coordinates, the DFTB+ results with solvation effect, including charges, energies are different. This only exists when using GeneralizedBorn. If we turn off GeneralizedBorn or switch to COSMO or Vacuum, the DFTB+ results are the same, and which should be the same.
To Reproduce
DFTB input:
Geometry = genFormat {
<<< geo.gen
}
Hamiltonian = DFTB {
SCC = Yes
SCCTolerance = 1.0E-5
ShellResolvedSCC = No
MaxSCCIterations = 500
Mixer = Broyden {
MixingParameter = 0.2
}
Filling = Fermi {
Temperature [K] = 310.15
}
MaxAngularMomentum = {
H = "s"
C = "p"
N = "p"
O = "p"
}
HubbardDerivs = {
N = -0.1535
C = -0.1492
O = -0.1575
H = -0.1857
}
ThirdOrderFull = Yes
HCorrection = Damping {
Exponent = 4.00
}
Solvation = GeneralizedBorn { # GFN2-xTB/GBSA(water)
Solvent = fromConstants {
Epsilon = 80.2
MolecularMass [amu] = 18.0
Density [kg/l] = 1.0
}
Temperature = 0.0009821802
FreeEnergyShift [kcal/mol] = 1.16556316
BornScale = 1.55243817
BornOffset = 2.462811043694508E-02
Radii = vanDerWaalsRadiiD3 {}
Descreening = Values {
H = 0.71893869
C = 0.74298311
N = 0.90261230
O = 0.75369019
}
SASA {
ProbeRadius = 1.843075777670416
Radii = vanDerWaalsRadiiD3 {}
SurfaceTension = Values {
H = -3.34983060E-01
C = -7.47690650E-01
N = -2.31291292E+00
O = 9.17979110E-01
}
}
HBondCorr = Yes
HBondStrength = Values {
H = -7.172800544988973E-02
C = -2.548469535762511E-03
N = -1.976849501504001E-02
O = -8.462476828587280E-03
}
}
SlaterKosterFiles = Type2FileNames {
Prefix = "../3ob-3-1/"
Separator = "-"
Suffix = ".skf"
}
Solver = MAGMA {}
Charge = -1
}
Options = {
WriteChargesAsText = Yes
}
First geometry input:
38 C
C O N H
1 1 2.9822000000E+01 -5.2810000000E+00 -1.2905000000E+01
2 1 3.0345000000E+01 -5.0570000000E+00 -1.1492000000E+01
3 1 2.9876000000E+01 -3.7380000000E+00 -1.0890000000E+01
4 1 3.0048000000E+01 -3.7880000000E+00 -9.3770000000E+00
5 1 3.0641000000E+01 -2.5090000000E+00 -8.7970000000E+00
6 1 3.0065000000E+01 -2.2350000000E+00 -7.4200000000E+00
7 2 2.9035000000E+01 -2.7470000000E+00 -6.9990000000E+00
8 3 3.0751000000E+01 -1.3950000000E+00 -6.6690000000E+00
9 2 3.0551000000E+01 -1.3740000000E+00 -5.4510000000E+00
10 1 2.9305000000E+01 -3.9800000000E+00 -1.3503000000E+01
11 1 2.7835000000E+01 -4.1240000000E+00 -1.3816000000E+01
12 2 2.6977000000E+01 -3.7640000000E+00 -1.3019000000E+01
13 3 2.7571000000E+01 -4.6270000000E+00 -1.5027000000E+01
14 1 2.6416000000E+01 -4.5080000000E+00 -1.5727000000E+01
15 1 2.5566000000E+01 -5.6240000000E+00 -1.5775000000E+01
16 1 2.4365000000E+01 -5.5660000000E+00 -1.6482000000E+01
17 1 2.4019000000E+01 -4.3890000000E+00 -1.7147000000E+01
18 1 2.4874000000E+01 -3.2750000000E+00 -1.7109000000E+01
19 1 2.6077000000E+01 -3.3310000000E+00 -1.6405000000E+01
20 4 2.9082300000E+01 -6.0869000000E+00 -1.2886300000E+01
21 4 3.0634900000E+01 -5.6745000000E+00 -1.3518500000E+01
22 4 3.1436200000E+01 -5.0833000000E+00 -1.1489600000E+01
23 4 3.0026300000E+01 -5.9002000000E+00 -1.0875500000E+01
24 4 2.8822600000E+01 -3.5199000000E+00 -1.1073600000E+01
25 4 3.0484300000E+01 -2.9221000000E+00 -1.1284900000E+01
26 4 3.0710700000E+01 -4.6018000000E+00 -9.0740000000E+00
27 4 2.9074900000E+01 -4.0708000000E+00 -8.9702000000E+00
28 4 3.0367400000E+01 -1.6483000000E+00 -9.4096000000E+00
29 4 3.1731800000E+01 -2.5520000000E+00 -8.7841000000E+00
30 4 3.1578100000E+01 -9.4740000000E-01 -7.0362000000E+00
31 4 2.9825100000E+01 -3.8755000000E+00 -1.4458200000E+01
32 4 2.9515000000E+01 -2.9982000000E+00 -1.3092600000E+01
33 4 2.8350400000E+01 -4.9973000000E+00 -1.5549900000E+01
34 4 2.5830000000E+01 -6.5356000000E+00 -1.5257600000E+01
35 4 2.3708400000E+01 -6.4231000000E+00 -1.6512600000E+01
36 4 2.3089500000E+01 -4.3345000000E+00 -1.7694400000E+01
37 4 2.4598500000E+01 -2.3692000000E+00 -1.7628700000E+01
38 4 2.6730000000E+01 -2.4705000000E+00 -1.6378600000E+01
second geometry input (move first 10 atoms in above geometry to the end in this geometry):
38 C
C O N H
1 1 2.7835000000E+01 -4.1240000000E+00 -1.3816000000E+01
2 2 2.6977000000E+01 -3.7640000000E+00 -1.3019000000E+01
3 3 2.7571000000E+01 -4.6270000000E+00 -1.5027000000E+01
4 1 2.6416000000E+01 -4.5080000000E+00 -1.5727000000E+01
5 1 2.5566000000E+01 -5.6240000000E+00 -1.5775000000E+01
6 1 2.4365000000E+01 -5.5660000000E+00 -1.6482000000E+01
7 1 2.4019000000E+01 -4.3890000000E+00 -1.7147000000E+01
8 1 2.4874000000E+01 -3.2750000000E+00 -1.7109000000E+01
9 1 2.6077000000E+01 -3.3310000000E+00 -1.6405000000E+01
10 4 2.9082300000E+01 -6.0869000000E+00 -1.2886300000E+01
11 4 3.0634900000E+01 -5.6745000000E+00 -1.3518500000E+01
12 4 3.1436200000E+01 -5.0833000000E+00 -1.1489600000E+01
13 4 3.0026300000E+01 -5.9002000000E+00 -1.0875500000E+01
14 4 2.8822600000E+01 -3.5199000000E+00 -1.1073600000E+01
15 4 3.0484300000E+01 -2.9221000000E+00 -1.1284900000E+01
16 4 3.0710700000E+01 -4.6018000000E+00 -9.0740000000E+00
17 4 2.9074900000E+01 -4.0708000000E+00 -8.9702000000E+00
18 4 3.0367400000E+01 -1.6483000000E+00 -9.4096000000E+00
19 4 3.1731800000E+01 -2.5520000000E+00 -8.7841000000E+00
20 4 3.1578100000E+01 -9.4740000000E-01 -7.0362000000E+00
21 4 2.9825100000E+01 -3.8755000000E+00 -1.4458200000E+01
22 4 2.9515000000E+01 -2.9982000000E+00 -1.3092600000E+01
23 4 2.8350400000E+01 -4.9973000000E+00 -1.5549900000E+01
24 4 2.5830000000E+01 -6.5356000000E+00 -1.5257600000E+01
25 4 2.3708400000E+01 -6.4231000000E+00 -1.6512600000E+01
26 4 2.3089500000E+01 -4.3345000000E+00 -1.7694400000E+01
27 4 2.4598500000E+01 -2.3692000000E+00 -1.7628700000E+01
28 4 2.6730000000E+01 -2.4705000000E+00 -1.6378600000E+01
29 1 2.9822000000E+01 -5.2810000000E+00 -1.2905000000E+01
30 1 3.0345000000E+01 -5.0570000000E+00 -1.1492000000E+01
31 1 2.9876000000E+01 -3.7380000000E+00 -1.0890000000E+01
32 1 3.0048000000E+01 -3.7880000000E+00 -9.3770000000E+00
33 1 3.0641000000E+01 -2.5090000000E+00 -8.7970000000E+00
34 1 3.0065000000E+01 -2.2350000000E+00 -7.4200000000E+00
35 2 2.9035000000E+01 -2.7470000000E+00 -6.9990000000E+00
36 3 3.0751000000E+01 -1.3950000000E+00 -6.6690000000E+00
37 2 3.0551000000E+01 -1.3740000000E+00 -5.4510000000E+00
38 1 2.9305000000E+01 -3.9800000000E+00 -1.3503000000E+01
Error output:
The Mulliken charge for the same atom will have 1E-1 e level difference, to minimize the text here, the following part show the total energy difference.
First geometry:
Total energy: -45.8655611501 H -1248.0654 eV
Second geometry:
Total energy: -45.8708466853 H -1248.2092 eV
Expected behaviour
Get the same results for the identical system with different order of coordinates when using GeneralizedBorn.
Additional context
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