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qiqi2926

铜虫 (小有名气)

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虫号: 1004137
注册: 2010-04-23
性别: GG
专业: 原子和分子物理

[求助] 利用siesta做verlet MD时出现问题siesta: WARNING: Atoms

在利用siesta做verlet MD，用Si8做的时候顺利结束，但是换成LiBH4或者NH3BH3时，均出现siesta: WARNING: Atoms  1880  2366 too close: rij = 0.288938 Ang之类的错误警告，不知道是怎么回事？
现将输入文件附上：
SystemName       libh4
SystemLabel       libh4

NumberOfAtoms    24
NumberOfSpecies    3

%block ChemicalSpeciesLabel
1  1  H
2  3  Li
3  5  B
%endblock ChemicalSpeciesLabel

PAO.BasisSize    SZ
PAO.EnergyShift    300 meV

LatticeConstant    6.4494  Ang

%block LatticeVectors
   1.000000000000000    0.000000000000000    0.000000000000000
   0.000000000000000    0.822867243000000    0.000000000000000
   0.000000000000000    0.000000000000000    0.820525940000000
%endblock LatticeVectors
MeshCutoff       130.0 Ry

%block kgrid_Monkhorst_Pack
6  0  0  0.0
0  6  0  0.0
0  0  6  0.0
%endblock kgrid_Monkhorst_Pack

MaxSCFIterations 50
DM.MixingWeight    0.3
DM.NumberPulay    4
DM.Tolerance       1.d-4
DM.UseSaveDM

SolutionMethod    diagon
ElectronicTemperature  25 meV

MD.TypeOfRun       Verlet
MD.InitialTimeStep 1
MD.FinalTimeStep    200
MD.LengthTimeStep          3.0 fs
MD.InitialTemperature 10.0 K

WriteMDHistory T

AtomicCoordinatesFormat  Fractional

%block AtomicCoordinatesAndAtomicSpecies
0.0949999988079071 0.3339999914169312 0.0740000009536743 1 h
0.0949999988079071 0.8339999914169313 0.5740000009536742 1 h
-0.0949999988079071  -0.3339999914169312 0.0740000009536743 1 h
-0.0949999988079071 0.1660000085830689 0.5740000009536743 1 h
0.5949999988079071  -0.3339999914169312 0.0740000009536743 1 h
0.5949999988079071 0.1660000085830688 0.5740000009536743 1 h
0.4050000011920930 0.3339999914169312 0.0740000009536743 1 h
0.4050000011920930 0.8339999914169310 0.5740000009536743 1 h
0.2500000000000000 0.0496999993920326 0.1831000000238419 1 h
0.2500000000000000 0.3510000109672546 0.3802999854087830 1 h
0.2500000000000000 0.5496999993920326 0.6831000000238418 1 h
0.2500000000000000 0.8510000109672545 0.8802999854087830 1 h
-0.2500000000000000  -0.0496999993920326 0.1831000000238419 1 h
-0.2500000000000000  -0.3510000109672546 0.3802999854087830 1 h
-0.2500000000000000 0.4503000006079674 0.6831000000238419 1 h
-0.2500000000000000 0.1489999890327454 0.8802999854087829 1 h
0.0000000000000000 0.0000000000000000 0.0000000000000000 2 li
0.0000000000000000 0.5000000000000000 0.4999999999999999 2 li
0.5000000000000000  -0.0000000000000000  -0.0000000000000000 2 li
0.5000000000000000 0.4999999999999999 0.5000000000000000 2 li
0.2500000000000000 0.2712000012397766 0.1729999929666519 3 b
0.2500000000000000 0.7712000012397767 0.6729999929666518 3 b
-0.2500000000000000  -0.2712000012397766 0.1729999929666519 3 b
-0.2500000000000000 0.2287999987602234 0.6729999929666519 3 b
%endblock AtomicCoordinatesAndAtomicSpecies
如需要输出文件，请留言告知
谢谢

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