Dear sir/ma'am
I am trying to generate the potential plot using macroave and for that I
have taken the .XV file and made it to run it with the macroave.in file.
But there are some queries that I have not understood regarding the
macroave.in file. And I would be very glad if any one could help me in this
regard.
1. In the fourth line of macroave.in file we need to mention how many step
functions we need to smooth. And I am working on a bilayer system so I wish
to know whether I should take surface or interface calculation in this
regard (appeded below is the fdf file of the calculation that I am
running). What would be the case for trilayer system?
2. In the Fifth and Sixth line of macroave.in file we need to mention the
width of the two functions like planar lattice spacing. I am not able to
understand what quantity it is asking. Should I specify the the interlayer
distance? what should be these values for my input given below? What would
be the case for multilayer system? and if the system has buckling, then how
should I chose these values?
3.In the 7th line, of macroave.in file we need to specify the number of
electrons in the slab. Here I wanted to know that suppose I am working on a
carbon based bilayer system, do I need to take the valence electrons or all
the 6 electrons and multiply it with the number of carbon atoms on each
layer?
4. And in running the macroave calculation, I am getting two generated
files with the calculation with extensions MAV and PAV. what is the
difference between macroscopic average and the planar average files?
appended below is the fdf file
# System Descriptor
SystemName Au-m-GGA
SystemLabel Au-m-GGA
NumberOfAtoms 36
NumberOfSpecies 1
%block Chemical_Species_Label
1 6 C
%endblock Chemical_Species_Label
%block PAO.BasisSizes
C DZP
%endblock PAO.BasisSizes
AtomicCoordinatesFormat Ang
AtomicCoorFormatOut Ang
%block AtomicCoordinatesAndAtomicSpecies
2.73256850 4.73073748 8.34901293 1 1 C
0.33859744 0.58458484 8.34912362 1 2 C
-0.85804026 2.65775355 8.34874884 1 3 C
3.92917251 2.65751886 8.34898485 1 4 C
2.73233932 0.58476470 8.34903393 1 5 C
0.33877634 4.73053116 8.34871091 1 6 C
0.82428376 1.42604781 9.53348231 1 7 C
0.11321792 2.65772943 9.53337950 1 8 C
2.95787834 2.65763647 9.53348398 1 9 C
2.24672706 1.42590432 9.53355328 1 10 C
0.82436502 3.88944295 9.53333025 1 11 C
2.24666573 3.88939178 9.53337329 1 12 C
0.82483542 3.88883163 7.16411390 1 13 C
2.24657899 3.88894521 7.16435350 1 14 C
2.24653140 1.42631958 7.16432757 1 15 C
2.95739219 2.65752906 7.16429019 1 16 C
0.11396438 2.65763067 7.16415136 1 17 C
0.82463967 1.42629661 7.16443629 1 18 C
2.73291473 4.73053968 14.14109530 1 19 C
0.33894801 0.58439532 14.14115704 1 20 C
-0.85769340 2.65763741 14.14124979 1 21 C
3.92955252 2.65738270 14.14146264 1 22 C
2.73272063 0.58460272 14.14145918 1 23 C
0.33914193 4.73040180 14.14121034 1 24 C
0.82486919 1.42621461 15.32582034 1 25 C
0.11415085 2.65758543 15.32595201 1 26 C
2.95757515 2.65747612 15.32604007 1 27 C
2.24668741 1.42628537 15.32605337 1 28 C
0.82500484 3.88880084 15.32591913 1 29 C
2.24685285 3.88886448 15.32578554 1 30 C
0.82480401 3.88921354 12.95669401 1 31 C
2.24717950 3.88910615 12.95674799 1 32 C
2.24716059 1.42567539 12.95683394 1 33 C
2.95832448 2.65739945 12.95681228 1 34 C
0.11365578 2.65750271 12.95674170 1 35 C
0.82477007 1.42578489 12.95679594 1 36 C
%endblock AtomicCoordinatesAndAtomicSpecies
LatticeConstant 1.00 Ang
%block LatticeVectors
6.138500 0.000081 0.000273
-3.068830 5.316279 -0.000326
0.001847 -0.001238 22.490288
%endblock LatticeVectors
%block kgrid_Monkhorst_Pack
10 0 0 0.0
0 10 0 0.0
0 0 2 0.0
%endblock kgrid_Monkhorst_Pack
XC.functional VDW
XC.authors LMKLL
SpinPolarized .true.
MeshCutoff 320. Ry
MaxSCFIterations 300
DM.MixingWeight 0.05
DM.Tolerance 5.d-5
DM.NumberPulay 5
SolutionMethod diagon
ElectronicTemperature 300 K
MD.TypeOfRun cg
MD.VariableCell .true.
MD.NumCGsteps 800
MD.MaxForceTol 0.01 eV/Ang
WriteCoorInitial
WriteCoorStep
WriteCoorXmol .true.
WriteKpoints .true.
WriteEigenvalues .true.
WriteKbands .true.
WriteBands .true.
WriteMullikenPop 1
WriteMDCoorXmol .false.
WriteMDhistory .false.
DM.UseSaveDM
MD.UseSaveXV .true.
SaveRho
SaveDeltaRho
SaveElectrostaticPotential .true.
WriteSiestaDim .true.
SaveHS .true.
On Sat, Aug 29, 2020 at 1:30 AM Boubacar Traore <bt.bouba...@gmail.com>
wrote:
> Hi,
>
> For this, you need to activate this tag "SaveElectrostaticPotential" to
> true for siesta to generate the total electrostatic potential file named
> SystemLabel.VH. Then you use siesta utility "macroave" from Util/macroave
> directory to plot the variation of the potential along the layers.
> Best,
> Boubacar
>
>
> On Wed, 26 Aug 2020 at 22:00, Harkishan Dua <hdua.p...@gmail.com> wrote:
>
>> Dear Sir/Ma’am
>>
>> I am new to siesta, and I wish to find the variation of potential in a
>> bilayer system with respect to the distance between the layers. Could you
>> please tell me how I can do that with siesta? I wish to generate a plot
>> similar to the one attached along with this mail which was reported in the
>> paper
>>
>> https://doi.org/10.1021/jp403706e
>>
>> --
>> SIESTA is supported by the Spanish Research Agency (AEI) and by the
>> European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
>>
>
> --
> SIESTA is supported by the Spanish Research Agency (AEI) and by the
> European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
>
--
SIESTA is supported by the Spanish Research Agency (AEI) and by the European
H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
