How did you do it? How were your unit conversions etc.? Remember that sisl automatically converts to eV and Ang when reading siesta files.
Den man. 21. sep. 2020 kl. 15.22 skrev Harkishan Dua <hdua.p...@gmail.com>: > We are working on a system similar to the paper attached. In the paper it > can be seen in Figure 1.(b) (page 15328) the potential plot where the > potential difference is visible. and with that they have made the Table 1 > (page 15331) where they have taken the potential difference in volts. > In our work, we are creating the potential plots using SISL, > But in our work, even though we are getting potential difference which is > very small to be seen directly from the graph, yet when we convert it into > volts, we get a very large number. please help me with my doubt > > Regards > Harkishan Dua > PhD student > Department of Physics > Assam University Silchar. > > On Mon, Sep 7, 2020 at 12:24 PM Nick Papior <nickpap...@gmail.com> wrote: > >> Hi, >> >> Den søn. 6. sep. 2020 kl. 16.36 skrev Harkishan Dua <hdua.p...@gmail.com >> >: >> >>> Dear sir, >>> I am trying to generate the potential plot for monolayer CdS and Bilayer >>> CdS systems using sisl. and with that I am getting the plots of the ones I >>> have attached with this mail.There are some queries that I wished to >>> clarify: >>> 1. As both structures are planar Z coordinates are fixed for all the >>> atoms. So how I am getting potential for variation of Z near the proximity >>> of the regions where the atoms reside. As these are regions of empty space. >>> >> The plot you show is just the potential with respect to Z coordinate. So >> your atoms Z-coordinate can be directly transferred to this plot. >> >>> 2. When measuring distance between the two dips we are getting slightly >>> different values than that of the interlayer distance of the structure. As >>> per my knowledge these two values should be the same. >>> I will be glad if you help me in this regard. >>> >> What does "slightly different" mean? The real-space grid is not >> infinitely precise, and so each voxel (3D box) occupies a finite space >> resulting in a finite discretization of the potential/density. I think >> you'll find that the voxel spacing (along Z) should correspond nicely with >> your mismatch. >> >>> >>> Attached with this email are the plots for CdS monolayer and Bilayer >>> systems. >>> >>> On Wed, Sep 2, 2020 at 2:11 PM Boubacar Traore <bt.bouba...@gmail.com> >>> wrote: >>> >>>> Thanks Nick for this update on sisl :-) >>>> >>>> On Tue, 1 Sep 2020 at 22:00, Nick Papior <nickpap...@gmail.com> wrote: >>>> >>>>> 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/) >>>>> >>>> >> >> -- >> Kind regards Nick >> > -- 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/)
