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/) >
-- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
