Hi dear all,
I did adsorption between four different graphenes (including pristine, B or N
doped and defective graphenes) and gas molecules (CO, NO, NO2 and NH3) were
investigated by using siesta.the first several fdf files and xyz files you've
Attached
I can refer to points happens in other papers But I can not get the results in
the output of the system.
the first with different distances Molecules are put on top of graphene. But in
any case, the molecules are placed at far from of graphene sheet. which bond
length is large, due to strong coupling between atom N(Molecule) and B (boron
atoms in graphene sheet) that was mentioned in the papers, does not occur.
It also seems to be no charge transfer between the molecule and the graphene
does not occur
Therefore, I do not understand reason the problems
Thank you in advance for your help.
hamidrtezabalangi
SystemName graphene
SystemLabel graphene
NumberOfAtoms 51
NumberOfSpecies 4
%block ChemicalSpeciesLabel
1 6 C # Species index, atomic number, species label
2 7 N
3 8 O
4 5 B
%endblock ChemicalSpeciesLabel
LatticeConstant 2.475 Ang ## This is only valid for graphene case
PAO.BasisSize DZP
%block LatticeVectors
3.976 0.0 0.0
0.0 5.164 0.0
0.0 0.0 10.0
%endblock LatticeVectors
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
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1.229998 10.650007 -0.000000 1
2.460000 11.360010 -0.000000 1
3.690000 10.650007 -0.000000 1
4.920000 11.360010 0.000000 1
6.149999 10.650007 -0.000000 1
7.380001 11.360010 -0.000000 1
8.610006 10.650009 -0.000000 1
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1.229999 9.229929 -0.000000 1
2.460000 8.519724 0.000000 1
3.690000 9.229930 -0.000000 1
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6.150000 9.229930 0.000000 1
7.380000 8.519723 -0.000000 1
8.610007 9.229928 0.000000 1
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4.919999 7.078492 0.000000 1
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7.380000 7.078492 -0.000000 1
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4.919973 -0.000009 0.000000 1
6.149999 0.709977 0.000000 1
7.379970 -0.000008 -0.000000 1
8.610006 0.709975 0.000000 1
4.919000 7.100000 3.200000 2
5.237100 5.912900 3.400000 3
3.790300 7.586100 3.400000 3
%endblock AtomicCoordinatesAndAtomicSpecies
%block kgrid_Monkhorst_Pack
10 0 0 0.0
0 10 0 0.0
0 0 1 0.0
%endblock kgrid_Monkhorst_Pack
XC.functional LDA
XC.authors CA
SpinPolarized false
MaxSCFIterations 500 # Maximum number of SCF iter
DM.Tolerance 0.0001 # Tolerance in maximum difference
DM.MixingWeight 0.12 # New DM amount for next SCF cycle
DM.NumberPulay 4
SolutionMethod Diagon # OrderN or Diagon
MeshCutoff 200.0 Ry
DM.UseSaveDM true
DM.UseSaveData true
WriteMullikenPop 1
MD.TypeOfRun CG
MD.VariableCell true
MD.NumCGsteps 8480
MD.MaxForceTol 0.0400 eV/Ang
MD.ConstantVolume T
WriteForces T
SaveRho true
SaveDeltaRho true
SaveElectrostaticPotential true
SaveTotalPotential true
LocalDensityOfStates true
WriteDenchar true
%block ProjectedDensityOfStates
-10.00 10.00 0.2 5000 eV
%endblock ProjectedDensityOfStates
WriteBands True
BandLinesScale pi/a # Default Value
%block BandLines
1 1.000000 0.577350 0.0000 M
25 0.000000 0.000000 0.0000 \Gamma
20 0.666667 1.154700 0.0000 K
10 1.000000 0.577350 0.0000 M
%endblock BandLines
WriteCoorXmol true
MD.UseSaveXV true
52
C 0.001144 11.309441 0.135832
C 1.229193 10.603743 0.106836
C 2.453105 11.314542 0.106705
C 3.677811 10.605278 0.067001
C 4.902951 11.314179 0.077250
C 6.127860 10.605056 0.058471
C 7.352663 11.314591 0.092089
C 8.576399 10.603942 0.086099
C 0.000809 8.481194 0.049843
C 1.229088 9.186941 0.063044
C 2.453822 8.476371 0.019648
C 3.676288 9.189752 0.017288
C 4.902802 8.481091 -0.032390
C 6.129103 9.189889 0.008410
C 7.351259 8.476953 0.005203
C 8.576359 9.187343 0.042370
C 0.000805 7.067468 0.017546
C 1.227945 6.358528 0.001238
C 2.455626 7.057561 -0.014524
C 3.686794 6.348843 -0.051370
C 4.902471 7.071185 -0.071293
C 6.117577 6.348475 -0.059413
C 7.349243 7.057698 -0.027714
C 8.577073 6.358747 -0.018449
C 0.000627 4.238083 0.024774
C 1.232578 4.945795 0.006913
C 2.462521 4.236132 0.000068
C 3.692915 4.936345 -0.027599
N 4.902569 4.237710 -0.026523
C 6.111686 4.936329 -0.036413
C 7.341934 4.236418 -0.015218
C 8.572377 4.946121 -0.013847
C 0.000605 2.827812 0.038908
C 1.227680 2.119410 0.031058
C 2.449289 2.822852 0.012018
C 3.682758 2.130224 -0.005152
C 4.902460 2.844911 -0.014874
C 6.121800 2.130317 -0.012684
C 7.355514 2.822945 -0.002577
C 8.576907 2.119614 0.010502
C 0.000665 -0.007028 0.021349
C 1.227253 0.701582 0.021131
C 2.452832 0.001085 -0.007193
C 3.682964 0.711769 -0.014636
C 4.902325 -0.001860 -0.033633
C 6.122023 0.711824 -0.021965
C 7.351947 0.001111 -0.021338
C 8.577708 0.702031 0.000764
N 4.893611 7.135278 2.923419
H 4.465411 7.985882 2.538378
H 4.347329 6.341335 2.569584
H 5.833526 7.063592 2.515101
