Hi, In this it seems you don't need the filtering that macroave is capable of. In that case you can use sisl to create the data for you.
The command would be something like this: sgrid siesta.VH --average 0 --average 1 --out VH_z.dat which will write a 2 column data file with z coordinates (in Ang) as the first and the plane-averaged potential in the 2nd column (in eV). Note this is accessible in the latest sisl development, so you'll need to install the development version ( http://zerothi.github.io/sisl/docs/latest/installation.html#development-version ). The macroave calculations have only recently been added (by an external contributor, see https://github.com/zerothi/sisl/pull/230), but we haven't made a tutorial for this yet. ;) Den man. 31. aug. 2020 kl. 22.00 skrev Boubacar Traore < bt.bouba...@gmail.com>: > Hi, > >> 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 >> <https://protection.puc.rediris.es/fmlurlsvc/?fewReq=:B:JVw4MzE7OCR0PzMsMiRrZj8yMzgyMyRxa2VsY3Z3cGc/MWY1YTA6YDJjY2dnM2EwZ2MyNzEwZzY0Z2EzZ2YwZDRnNDMyMjRkNyR2PzM3Ozo6NDE6NzUkc2tmPzI1VDprZ0xvMjM1NjoxLzI1VDprZ0xtMjM1NjoxJHBhcnY/cWtncXZjL25Cd2NvLGdxJGE/OzI=&url=http%3a%2f%2fmacroave.in> >> file. But there are some queries that I have not understood regarding the >> macroave.in >> <https://protection.puc.rediris.es/fmlurlsvc/?fewReq=:B:JVw4MzE7OCR0PzMsMiRrZj8yMzgyMyRxa2VsY3Z3cGc/MWY1YTA6YDJjY2dnM2EwZ2MyNzEwZzY0Z2EzZ2YwZDRnNDMyMjRkNyR2PzM3Ozo6NDE6NzUkc2tmPzI1VDprZ0xvMjM1NjoxLzI1VDprZ0xtMjM1NjoxJHBhcnY/cWtncXZjL25Cd2NvLGdxJGE/OzI=&url=http%3a%2f%2fmacroave.in> >> file. And I would be very glad if any one could help me in this regard. > > It's the .VH file that is needed in your case. > > >> 1. In the fourth line of macroave.in >> <https://protection.puc.rediris.es/fmlurlsvc/?fewReq=:B:JVw4MzE7OCR0PzMsMiRrZj8yMzgyMyRxa2VsY3Z3cGc/MWY1YTA6YDJjY2dnM2EwZ2MyNzEwZzY0Z2EzZ2YwZDRnNDMyMjRkNyR2PzM3Ozo6NDE6NzUkc2tmPzI1VDprZ0xvMjM1NjoxLzI1VDprZ0xtMjM1NjoxJHBhcnY/cWtncXZjL25Cd2NvLGdxJGE/OzI=&url=http%3a%2f%2fmacroave.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? >> > Your bi-layer system consists of layers of the same type. So, "surface" > should do the job. "Interface" is for heterstructures or hetero-layers with > different materials. Anyway, you may try both and see the difference. > > >> 2. In the Fifth and Sixth line of macroave.in >> <https://protection.puc.rediris.es/fmlurlsvc/?fewReq=:B:JVw4MzE7OCR0PzMsMiRrZj8yMzgyMyRxa2VsY3Z3cGc/MWY1YTA6YDJjY2dnM2EwZ2MyNzEwZzY0Z2EzZ2YwZDRnNDMyMjRkNyR2PzM3Ozo6NDE6NzUkc2tmPzI1VDprZ0xvMjM1NjoxLzI1VDprZ0xtMjM1NjoxJHBhcnY/cWtncXZjL25Cd2NvLGdxJGE/OzI=&url=http%3a%2f%2fmacroave.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? >> > What macroave does is nothing but averaging the potential/density in the > plane and filtering it out let's say along z-direction. The two functions > ( for interface) or one function (for surface) are for the filtering > purpose. In the filtering step, macroave performs convolutions. The length > is about the unit cell length or cell period along z. See this reference > paper of Junquera et al. for more detail: 10.1088/0953-8984/19/21/213203 > <https://doi.org/10.1088/0953-8984/19/21/213203> > > >> 3.In the 7th line, of macroave.in >> <https://protection.puc.rediris.es/fmlurlsvc/?fewReq=:B:JVw4MzE7OCR0PzMsMiRrZj8yMzgyMyRxa2VsY3Z3cGc/MWY1YTA6YDJjY2dnM2EwZ2MyNzEwZzY0Z2EzZ2YwZDRnNDMyMjRkNyR2PzM3Ozo6NDE6NzUkc2tmPzI1VDprZ0xvMjM1NjoxLzI1VDprZ0xtMjM1NjoxJHBhcnY/cWtncXZjL25Cd2NvLGdxJGE/OzI=&url=http%3a%2f%2fmacroave.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? >> > Yes, but in carbon you have 4 valence electrons. Remember that this is > important only when you use macroave with charge densities (.RHO file); it > is used for normalization. To get the total number of electrons, you can > also do : > grep "Total number of electrons" SystemLabel.out > > 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? >> > PAV : is the averaged density/potential in the plane of the system along z. > MAV : is the filtered or nano smoothed density/potential along z. Here, > the oscillatory part is removed and the filter functions are used for that. > > Best, > Boubacar > > On Sat, 29 Aug 2020 at 20:56, Harkishan Dua <hdua.p...@gmail.com> wrote: > >> 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 >> <https://protection.puc.rediris.es/fmlurlsvc/?fewReq=:B:JVw4MzE7OCR0PzMsMiRrZj8yMzgyMyRxa2VsY3Z3cGc/MWY1YTA6YDJjY2dnM2EwZ2MyNzEwZzY0Z2EzZ2YwZDRnNDMyMjRkNyR2PzM3Ozo6NDE6NzUkc2tmPzI1VDprZ0xvMjM1NjoxLzI1VDprZ0xtMjM1NjoxJHBhcnY/cWtncXZjL25Cd2NvLGdxJGE/OzI=&url=http%3a%2f%2fmacroave.in> >> file. But there are some queries that I have not understood regarding the >> macroave.in >> <https://protection.puc.rediris.es/fmlurlsvc/?fewReq=:B:JVw4MzE7OCR0PzMsMiRrZj8yMzgyMyRxa2VsY3Z3cGc/MWY1YTA6YDJjY2dnM2EwZ2MyNzEwZzY0Z2EzZ2YwZDRnNDMyMjRkNyR2PzM3Ozo6NDE6NzUkc2tmPzI1VDprZ0xvMjM1NjoxLzI1VDprZ0xtMjM1NjoxJHBhcnY/cWtncXZjL25Cd2NvLGdxJGE/OzI=&url=http%3a%2f%2fmacroave.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 >> <https://protection.puc.rediris.es/fmlurlsvc/?fewReq=:B:JVw4MzE7OCR0PzMsMiRrZj8yMzgyMyRxa2VsY3Z3cGc/MWY1YTA6YDJjY2dnM2EwZ2MyNzEwZzY0Z2EzZ2YwZDRnNDMyMjRkNyR2PzM3Ozo6NDE6NzUkc2tmPzI1VDprZ0xvMjM1NjoxLzI1VDprZ0xtMjM1NjoxJHBhcnY/cWtncXZjL25Cd2NvLGdxJGE/OzI=&url=http%3a%2f%2fmacroave.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 >> <https://protection.puc.rediris.es/fmlurlsvc/?fewReq=:B:JVw4MzE7OCR0PzMsMiRrZj8yMzgyMyRxa2VsY3Z3cGc/MWY1YTA6YDJjY2dnM2EwZ2MyNzEwZzY0Z2EzZ2YwZDRnNDMyMjRkNyR2PzM3Ozo6NDE6NzUkc2tmPzI1VDprZ0xvMjM1NjoxLzI1VDprZ0xtMjM1NjoxJHBhcnY/cWtncXZjL25Cd2NvLGdxJGE/OzI=&url=http%3a%2f%2fmacroave.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 >> <https://protection.puc.rediris.es/fmlurlsvc/?fewReq=:B:JVw4MzE7OCR0PzMsMiRrZj8yMzgyMyRxa2VsY3Z3cGc/MWY1YTA6YDJjY2dnM2EwZ2MyNzEwZzY0Z2EzZ2YwZDRnNDMyMjRkNyR2PzM3Ozo6NDE6NzUkc2tmPzI1VDprZ0xvMjM1NjoxLzI1VDprZ0xtMjM1NjoxJHBhcnY/cWtncXZjL25Cd2NvLGdxJGE/OzI=&url=http%3a%2f%2fmacroave.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/) > -- Kind regards Nick
-- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
