Re: [SIESTA-L] Graphene based study using Siesta
Dear Rajan, Although SIESTA has a well-documented history of studying graphene's transport and interface properties, one caveat regarding the locality of the LCAO basis set and its consequences is written about here in this article by Derek Stewart of Cornell: https://courses.cit.cornell.edu/das248/index_files/cautionary_tale_of_two_basis_sets_and_graphene.pdf Cheers, Abraham Hmiel On Thu, Sep 17, 2015 at 1:12 AM, Monica Garcia <m.gar...@simune.eu> wrote: > Dear Rajan, > > Here you have some references in which SIESTA was used to simulate > different Graphene properties, > > - Comparison of the electronic transport properties of metallic graphene > and silicene nanoribbons; S. Yamacli, J. Nanopart. Res. (2014) 16. > > - The interaction of metallic clusters on reduced graphene oxide; E. > Gracia Espino, G. Hu, A. Shchukarev, and T. Wagberg, J. Am. Chem. Soc. > (2014), 136, 6626. > > - Quantum transport in chemically modified two-dimensional graphene; N. > Leconte, A. Lherbier, F. Varchon, P. Ordejon, S. Roche, and J.-C. Charlier, > Phys. Rev. B 84, (2011) 235420. > > - The potential of graphene nanoribbons (GNR’s) as molecular-scale > sensors; R. Chowdhury, S. Adhikari, P. Rees, S. P. Wilks and F. Scarpa, > Phys. Rev. B 83, (2011) 045401. > > I hope you find them useful, > > Regards, > Mónica > > > Mónica García-Mota > Simulations Manager > Tolosa Hiribidea 76 | 20018 Donostia - San Sebastián | Spain > T.: +34 943 57 40 68 | m.gar...@simune.eu <m.gar...@simune.eu> | > www.simune.eu[image: SIMUNE Atomistic Simulations] <http://www.simune.eu/> > > On 17 Sep 2015, at 09:51, RAJAN SINGH <singhrajan.i...@gmail.com> wrote: > > Dear Sir/Madam > > I want to use Siesta for my research work. I want to use it for study the > Graphene and its interface with different materials. Can you suggest me > some tutorials regarding that. I also want to know what are the limitations > of using Siesta for Graphene interface study? > > Please enlighten me with your comments. > > Thank You. > > > -- *Abraham Hmiel, Ph. D.* http://abehmiel.net/about
Re: [SIESTA-L] PAO-basis block for As
My guess regarding the compilation errors: there's no need to use sudo for this install, and your compiler in the makefile is pointing to f77, is it that the same compiler you used to install SIESTA? It doesn't have to be, but if SIESTA compiles you should use what works there. Your FC line should be pointing to f90, or whatever fortran compiler (pg90, ifort, ifc, gfortran, etc.) you used in the SIESTA install. Check your Obj/ folder in the SIESTA source tree for the arch.make. I could not reproduce your error when I used my own f77 compiler or f90 or gfortran so that's strange. Try using gfortran, perhaps? You should not have to edit the source code to get this utility to work. Just try a different compiler until you can get it to work. My gfortran is: GNU Fortran 95 (GCC) 4.1.2 20070115 and it compiles without error. Swarm is Open-MP enabled, so you could compile it in parallel as well. On Thu, Jun 11, 2015 at 6:29 AM, Ludwig, Stephan stephan.lud...@pi1.physik.uni-stuttgart.de wrote: Hello Abraham, thank you for your suggestion. Unfortunately I have proplems to install the optimization programm. typing 'make swarm simplex' I receive the error message i1@QuanQal2:/home/siesta-3.2-pl-5/Util/Optimizer$ sudo make swarm simplex f77 -c io.f io_assign: Error on line 2: syntax error Warning on line 13: ignoring text after end. Warning on line 13: local variable out never used Warning on line 13: local variable intend never used Error on line 13: Declaration error for intend: adjustable dimension on non-argument /usr/bin/f77: aborting compilation make: *** [io.o] Fehler 25 The io.f file looks like this SUBROUTINE io_assign(lun) integer intend(out) :: lun logical used integer iostat c c Looks for a free unit and assigns it to lun c do lun= 10, 99 inquire(unit=lun, opened=used, iostat=iostat) if (iostat .ne. 0) used = .true. if (.not. used) return enddo end SUBROUTINE io_assign Can you help me to find the syntax error? Best regards Stephan -Original message- *From:* Abraham Hmiel abehm...@gmail.com *Sent:* Wednesday 10th June 2015 17:42 *To:* Siesta, Self-Consistent DFT LCAO program, http://www.uam.es/siesta siesta-l@uam.es *Subject:* Re: [SIESTA-L] PAO-basis block for As Stephan, Creating a PAO basis set from scratch is a nontrivial exercise even for experts. The way I usually use involves the simplex tetrahedral method, which allows you to vary several parameters at a time and find their optimized values. There is an implementation included with SIESTA. Look in the Util/Optimizer folder of the siesta source tree. There are some examples there which will allow you to use the simplex method code in a basic manner for a water molecule to optimize basis set parameters. Take a look at the files and study them and run the example calculations. They're pretty quick. From there, it's not a big stretch to apply the principles to arsenic. You will still have to figure out the format of the PAO basis block corresponding to your pseudopotential and desired size of the basis set. You might try using As2S3 or solid arsenic as input, and optimize for bond length and total energy minimization. I'd offer that you might learn more doing it this way. Kind regards, On Wed, Jun 10, 2015 at 7:27 AM, Nick Papior Andersen nickpap...@gmail.com wrote: I would suggest you ask your supervisor/professor (I suspect you have one?). 2015-06-10 16:24 GMT+02:00 Ludwig, Stephan stephan.lud...@pi1.physik.uni-stuttgart.de: Hello everybody, I'm an absolute beginner in DFT calculations (I'm a Master student) and now I have to cope with a material containing Arsenid. The pseudopotential of As in the database has a semicore state so I have to implement the PAO-basis block in the fdf-file. I have no idea how to choose the parameters of this block to obtain reasonable results. I was able to start siesta by using a PAO-basis block which was originally designed for iron: %block PAO.Basis # Define Basis set As 1 # Species label, number of l-shells n=3 2 2 # n, l, Nzeta 6.000 0.000 1.000 1.000 %endblock PAO.Basis Can anybody please deliver a suitable PAO-basis and a pseudopotential for As. Or can anybody help me to find a suitable PAO-basis for the pseudopotential I use. You can find it in the attachment It would be a great help and I would learn a lot through it Thanks and regards Stephan Ludwig -- Kind regards Nick -- *Abraham Hmiel, Ph. D.* http://abehmiel.net/about -Original message- *From:* Abraham Hmiel abehm...@gmail.com *Sent:* Wednesday 10th June 2015 17:42 *To:* Siesta, Self-Consistent DFT LCAO program, http://www.uam.es/siesta siesta-l@uam.es *Subject:* Re: [SIESTA-L] PAO-basis block for As Stephan, Creating a PAO basis set from scratch is a nontrivial exercise even
Re: [SIESTA-L] PAO-basis block for As
Stephan, Creating a PAO basis set from scratch is a nontrivial exercise even for experts. The way I usually use involves the simplex tetrahedral method, which allows you to vary several parameters at a time and find their optimized values. There is an implementation included with SIESTA. Look in the Util/Optimizer folder of the siesta source tree. There are some examples there which will allow you to use the simplex method code in a basic manner for a water molecule to optimize basis set parameters. Take a look at the files and study them and run the example calculations. They're pretty quick. From there, it's not a big stretch to apply the principles to arsenic. You will still have to figure out the format of the PAO basis block corresponding to your pseudopotential and desired size of the basis set. You might try using As2S3 or solid arsenic as input, and optimize for bond length and total energy minimization. I'd offer that you might learn more doing it this way. Kind regards, On Wed, Jun 10, 2015 at 7:27 AM, Nick Papior Andersen nickpap...@gmail.com wrote: I would suggest you ask your supervisor/professor (I suspect you have one?). 2015-06-10 16:24 GMT+02:00 Ludwig, Stephan stephan.lud...@pi1.physik.uni-stuttgart.de: Hello everybody, I'm an absolute beginner in DFT calculations (I'm a Master student) and now I have to cope with a material containing Arsenid. The pseudopotential of As in the database has a semicore state so I have to implement the PAO-basis block in the fdf-file. I have no idea how to choose the parameters of this block to obtain reasonable results. I was able to start siesta by using a PAO-basis block which was originally designed for iron: %block PAO.Basis # Define Basis set As 1 # Species label, number of l-shells n=3 2 2 # n, l, Nzeta 6.000 0.000 1.000 1.000 %endblock PAO.Basis Can anybody please deliver a suitable PAO-basis and a pseudopotential for As. Or can anybody help me to find a suitable PAO-basis for the pseudopotential I use. You can find it in the attachment It would be a great help and I would learn a lot through it Thanks and regards Stephan Ludwig -- Kind regards Nick -- *Abraham Hmiel, Ph. D.* http://abehmiel.net/about
Re: [SIESTA-L] Energy levels for a single fullerene
68.9985269.00356 69.0070069.8322669.8333469.8386670.10739 70.1077370.1100370.1127270.1251170.40924 70.4122370.4140072.1514372.1525772.16014 72.1630573.1207773.1250373.1335673.13520 73.1388374.9945274.9971975.0033975.01031 75.0107176.8235476.8279076.8432976.86721 76.8700776.8749476.8772376.9185876.92214 76.9288677.5347377.5387277.5585077.66816 77.6707077.6721277.6796177.6814978.95244 78.9544278.9567178.9601780.6100680.61769 80.6184980.6208281.6730281.6762881.67931 84.3271884.3320984.3384384.3458484.34987 90.6700590.6752090.6823390.6945993.87314 93.8788993.8792693.8827593.88424 101.09874 101.10956 101.11326 101.11994 101.37630 101.37675 101.38497 103.36522 103.37822 103.38777 103.38884 104.33887 104.34513 104.34915 104.35560 104.36248 -- *Abraham Hmiel, Ph. D.* http://abehmiel.net/about
Re: [SIESTA-L] Why don't appear the electric density of Al in my simulation?
Hello, I'm pretty sure that in your case, the electronic charge density is indeed printed volumetrically, but it's inside the radius of the aluminum atom in your molecular visualizer, which is opaque. So, you have some options: 1) reduce the radius of your atomic sphere models 2) lower the threshold of the charge density isosurface 3) plot the charge density heat map in planar cross-sections, without sphere models (this is the manner that I see most often in publications) 4) change the opacity of your atomic models (depends on the visualizer) Any one of those should work in your case. Kind regards, On Tue, May 5, 2015 at 9:30 AM, Guilherme Maia Sawyer guisaw...@yahoo.com.br wrote: *Ab initio* calculations in the *AlFeO*3 compound have been performed using the SIESTA program package. Calculations of atomic geometry and electronic structure were performed within first-principles of Dendity-Functional Theory (DFT) under the generalized gradient approximation (GGA) of Perdew, Burke, and Ernzerhof (PBE) including spin polarization. A 490 Ry cutoff was employed for the plane wave basis, and integrations over the Brillouin zone of the orthorhombic crystal were sampled with a 5 X 5 X 5 k-points mesh. My question is, Why don't appear the electron density for the Al? Appear for the O, and Fe... but not for the Al!! Anyone can help me with this issue?! *Why don't appear the electric density of Al in my simulation?*. ___ Guilherme Maia Santos Doutorando (PhD student) Multifunctional Devices Development Lab - MDDL Departamento de Física - DF (Departament of physics) Universidade Estadual de Maringá - UEM (State University of Maringá) University of Texas at San Antonio - UTSA -- *Abraham Hmiel, Ph. D.* http://abehmiel.net/about
Re: [SIESTA-L] Fwd: Antiferromagnetic system calculations
Anita, It would be helpful to the list to see your input file and which version of siesta you are running, along with the context of where your error occurs in the program's output. ZPOTRF is a LAPACK/SCALAPACK routine that computes the cholesky factorization of a real hermitian matrix that is positive definite. According to the routine's help page http://www.netlib.org/lapack/explore-html/da/d7a/_v_a_r_i_a_n_t_s_2cholesky_2_r_l_2zpotrf_8f.html, the error thrown seems to be an invalid number for the leading dimension. My guess is that something is amiss in your input file which is causing this behavior. Perhaps someone with more experience than me with magnetism in SIESTA can help you once you give us the information that we need to look deeper into your problem. Best regards, On Wed, Jun 18, 2014 at 2:49 PM, Anita Rani ranianit...@gmail.com wrote: Hello to all siesta users I want to study magnetic properties of (GaMn)As calculations for 32 atoms. (15Ga 1Mn 16As) but at the end of run i got the problem i.e. On entry to ZPOTRF parameter number 4 had an illegal value I could not understand what the problem was. I have given same parameters for FM calculations. There was no problem like this. plz give some suggestions. If anybody have Input file Regarding Antiferromagnetic properties .Plz send me. Thanks alot. with Regards -- // \\ Anita Sharma // \\ Assistant Professor in Physics // ... \\Guru Nanak College for Girls // \\ Sri Muktsar Sahib, (Punjab) (9465305760) -- // \\ Anita Sharma // \\ Assistant Professor in Physics // ... \\Guru Nanak College for Girls // \\ Sri Muktsar Sahib, (Punjab) (9465305760) -- *Abraham Hmiel* Katherine Belz Groves Fellow in Nanoscience Xue Group, SUNY College of Nanoscale Science and Engineering http://abehmiel.net/about
Re: [SIESTA-L] Structure does not converge
Tobias, I'm curious, what do the results of the following commands look like? 1) fgrep constrained 1.out 2) fgrep outcell: Cell vector modules (Ang) 1.out *where 1.out is the name of the output log file You don't have to print them and send them our way, as they'll be very large, but what can you say about them in general? Are the forces fluctuating about a small amount that isn't quite as small as the threshold you've chosen? Are the lattice parameters very different from what you started with? Is everything blowing up? In general, this is what I do. Instead of doing one relaxation with a very large number of CG steps, perform several in steps, making sure the UseSaveData flag is set to true so that you don't have to come up with a new density matrix each time and can use the previous CG trajectory information as well: 1) Do one with MD.NumCGSteps ~ 10 and MD.MaxCGDispl ~ 0.15 Ang, to perform a very coarse relaxation (it is unlikely you will meet the threshold, and that's okay. You're not done). Call the output file 1.out or something like that. 2) Do one with MD.NumCGSteps ~ 20 and MD.MaxCGDispl ~ 0.05 Ang, to perform a coarse relaxation. Call the output file 2.out 3) Do one with MD.NumCGSteps ~ 20 and MD.MaxCGDispl ~ 0.01 Ang, to perform a finer relaxation. Call the output file 3.out ... as many successive steps as you need with as much fineness as desired or until you meet your force convergence criteria, at which point you will have a relaxed structure. If 'everything is blowing up' then you may have to take another look at your simulation parameters. Sometimes choosing the wrong Pulay mixing parameters will prevent your simulation from falling into a convergence basin, so another look at that may be helpful. Transition metals sometimes call for using small (~0.01 or smaller) DM.MixingWeight with a kick every several steps (see the manual). Warm regards, -- *Abraham Hmiel* Katherine Belz Groves Fellow in Nanoscience Xue Group, SUNY College of Nanoscale Science and Engineering http://abehmiel.net/about On Fri, Jan 24, 2014 at 1:09 PM, Kraemer, Tobias t.krae...@hw.ac.uk wrote: Dear SIESTA users, I am very new to the SIESTA code, so to start with I am familiarising myself with the protocols involved to run calculations with the code. I am trying to reproduce some numbers from a paper, where a crystal structure (triclinic system) of a Ru-allyl complex was relaxed (Organometallics, 2013, 32, 3784). I have set up a SIESTA input for relaxing this structure, using PBE with the default DZP basis sets for all atoms, along with pseudopotentials from the SIESTA database (I am aware that this might not be the best choice, but to start with it might be a fair option). The calculation seems to fail to converge to a minimum structure and stops after the default 500 opt cycles. This makes me suspicious, since my feeling is that the structure should have converged within 500 cycles. The SCF cycles converge fine. I have attached my input file below, the structure is read in from an external xyz file (attached). I have used as many default settings for the moment as possible. I would appreciate if you could share your experience and advice on this subject. Is such an input in principle a good starting point for the task at hand? What could I improve? Would the use of a Monkhorst-Pack grid be a better choice? There are some other Questions regarding dispersion corrections but first I need to play around with what I understand from the manual. Kind regards, thanks for everybody’s help. Really trying to learn how to get reliable results. Tobias SystemName [Ru(AcCN)2(Cp*)(eta3-phenylallyl) unit cell SystemLabel ru_allyl NumberOfAtoms 160 NumberOfSpecies 7 WriteMullikenPop1 %block ChemicalSpeciesLabel 1 44 Ru # Species index, atomic number, species label 2 15 P 3 9 F 4 8 O 5 7 N 6 6 C 7 1 H %endblock ChemicalSpeciesLabel MeshCutoff 400.0 Ry NetCharge 0.00 XC.functional GGA XC.authors PBE SpinPolarized.false. DM.NumberPulay4 DM.MixingWeight 0.3 DM.UseSaveDM .true. NeglNonOverlapInt False AtomicCoordinatesFormat NotScaledCartesianAng AtomicCoordinatesAndAtomicSpecies ru_allylinput.xyz LatticeConstant 1.0 Ang %block LatticeParameters 9.5347 11.7495 15.8787 109.395 96.719 100.965 %endblock LatticeParameters WriteCoorXmol True WriteForces .true. WriteMullikenPop 1 SaveDeltaRho .true. MD.TypeOfRun cg # Type of dynamics: Conjugate gradients MD.NumCGsteps 500 # number of CG steps MD.MaxCGDispl 0.15 Ang MD.MaxForceTol 0.04 eV/Ang MD.UseSaveXV yes MD.VariableCell.true. Dr. Tobias Kraemer Research Associate Institute
Re: [SIESTA-L] atoms
Suman,
I think the answer you're looking for is 42. Only 42-atom simulations are
considered by peer review ;)
But joking aside, you should look to previously-published ab-initio results
in your system of interest or something close to it. Even if such results
exist, you should perform methodological checks on system size, i.e.
size-convergence simulations with respect to: the number of layers in a
surface slab, or supercell dimensions if you're simulating a bulk compound
(perhaps with a defect or other non-homogeneity), different sizes of
nanowire, etc. Some of the most important current problems in nanoscience
involve quantum size-effects, and you don't really know how many atoms a
good simulation requires until you try it- the physics of a particular
solid-state system can vary dramatically based on small size increments!
So, to answer the question you posed, no real number of atoms guideline
exists. Use what is feasible and timely for your computational setup while
giving trustworthy, meaningful, repeatable results! By the way, the T in
siesta stands for Thousands (but this only really makes sense with the
order-N functional). The number of atoms in a SIESTA simulation could be
anywhere in the range {10^0, 10^4}.
--
*Abraham Hmiel*
Katherine Belz Groves Fellow in Nanoscience
Xue Group, SUNY College of Nanoscale Science and Engineering
http://abehmiel.net/about
On Fri, Jan 24, 2014 at 8:21 AM, Suman Chowdhury sumanchowdhur...@gmail.com
wrote:
Dear all,
what is the typical number of atoms one should use for publishable results
using SIESTA?
Re: [SIESTA-L] reciprocal lattice vectors in SIESTA
Hello Diana, As far as I'm aware, SIESTA doesn't print the reciprocal lattice vectors by default and no keyword exists to print them. However, it is relatively easy to create a short script in python or Matlab or such a program that will calculate them by inputting the unit cell vectors and then taking cross products (http://www.lcst-cn.org/Solid%20State%20Physics/Ch22.html) or, if you're ambitious, you can modify the code to print them in a new file or something. Regards, *Abraham Hmiel* Katherine Belz Groves Fellow in Nanoscience Xue Group, SUNY College of Nanoscale Science and Engineering http://abehmiel.net/about
Re: [SIESTA-L] Re: Question
Mohammad, First, you don't need mpirun to run gnubands. The program only takes a few moments to run, even with very large systems and there is no parallelization implemented. It just reshapes the band structure arrays into something more easily plotted. Just use: $ gnubands QD.bands QD_bands.dat Second, if you navigate to the directory where gnubands.f lies and open gnubands.f with your favorite file editor, you will see that there are some maximum limits that can halt the program. (the line - if(overflow) stop...) Adjusting, for example, maxb upwards to a higher value (perhaps a MUCH higher value) where it is originally declared as 100, then recompiling gnubands, will fix your issue with the program. Likewise, if you continue to obtain the same error, perhaps you have breached the maxk limit for the number of k-points in your plot. Friendly regards, -- *Abraham Hmiel* Katherine Belz Groves Fellow in Nanoscience Xue Group, College of Nanoscale Science and Engineering at SUNY Albany http://abehmiel.net/about
Re: [SIESTA-L] BiYO3 optimization
Dear Ulas, I've looked at your .out file and it seems to me that your method is mostly good, but I do have a suggestion and I hope it helps, regarding your basis set: with transition metal oxides, I have found that the inclusion of semicore states is at times absolutely essential to find the correct global energy minima. That could be your problem here. In your case I would include 4p semicore states for Y and the 4f and 5d states for Bi. For help on how to do this, take a look at this basis input for Bi with semicore states included (or other elements, or search SIESTA-L): http://www.icmab.es/leem/siesta/Databases/BasisSets/Bi/gga/ - you will need to explicitly specify the basis of all your atoms in the fdf file and also need to create a new pseudopotential files for Y and Bi, created with the atom program. For O, you can look for a basis set inside a metal oxide as well. You can try to approach a reasonable lattice constant first, then use the simplex method in siesta-xxx-/Util/Optimizer to fine tune the soft confinement parameters and cutoff radii of the basis with your half-optimized crystal structure, then relax the lattice vectors again using your optimized basis. There are ample tutorials on the simplex method, both included in SIESTA's documentation in the Optimizer directory and also elsewhere on SIESTA-L. I'm pretty sure the inclusion of semicore states with correct pseudopotentials and a well-defined optimized basis set will get you to where you want to be just fine. Hearty cheers! On Tue, Aug 6, 2013 at 9:43 AM, Ulas Koroglu ulaskoro...@gmail.com wrote: Dear Siesta Users and Developers, I try to optimize BiYO3 crystal that has the cubic structure. While experimental value of lattice parameter is a=5.484 Angstrom, but I found a=4.095 Angstrom during the geometry optimization in Siesta 3.1. There is a big different between the two (experimental and theoretical) values. I used many ways to correct the theoretical result ( a=4.095 Angstrom) but, I didn't achieve. I did not understand what problem is. If you can suggest me a solution, I would be very appreciated. I have attached the input and output files. Best regards. Ulas Koroglu. -- *Abraham Hmiel* Katherine Belz Groves Fellow in Nanoscience Xue Group, College of Nanoscale Science and Engineering at SUNY Albany http://abehmiel.net/about
Re: [SIESTA-L] Charge transfer Calculation from an atom to the other
Kiarash, To add to Ruslan's response, two and a half years ago on SIESTA-L there was a correspondence between Gao Min and Martin Zoloff on how to create charge density difference plots- http://www.mail-archive.com/siesta-l@uam.es/msg02700.html - Martin made a fortran code for creating charge density difference plots from .RHO files. It is quite useful and I find myself using it often. Just make sure you use the same grid, system size, etc. for all 3 pieces. Other options you can look into are Bader and Hirschfield charge analysis, but I would definitely start with charge density difference. Cheers, -- *Abraham Hmiel* Katherine Belz Groves Fellow in Nanoscience Xue Group, College of Nanoscale Science and Engineering at SUNY Albany http://abehmiel.net/about On Fri, Jul 26, 2013 at 5:58 AM, Руслан Жачук zhac...@gmail.com wrote: The best way is to do like this: 1) Calculate charge density of isolated atom, n_at 2) Calculate charge density of another isolated system, which you are interested, for example, surface, n_surf 3) Calculate charge density of combined system , atom on the surface, n_combined Then charge transfer is: delta_n = n_combined - n_at - n_surf Check out PhysRevB 81, 165424 ( 2010 ) for details. Regards Ruslan Zhachuk 2013/7/26 Kiarash Hosseini kiarash.hosse...@gmail.com Dear All, Good time. I want to compute the charge transfer from an atom to the other in an ensemble quantitatively. As far as I am concerned I have two choices: 1. Using Local Density of states (LDOS). 2. Using *Mulliken population* analysis. Please let me know if any of the above mentioned options work? Also please suggest any other way to compute charge transfer from among specific atoms. Thank you in advance. -- Yours Sincerely, Kiarash Hosseini Mechanical Engineering MSc Tehran Iran
Re: [SIESTA-L] Selective Van Der Waals interactions
Ian, You can turn on/off the a posteriori vdW Grimme correction for only the atoms and species that you want, but as far as I know the self-consistent vdW is applied to the entire simulation box like any other xc-functional. Other than that, I think if you're using a vdW-xc functional that gets the correct geometric and electronic structure of the bulk form of your substrate, you should be in good hands (except for the matter of increased computational time). Cheers, *Abraham Hmiel* Katherine Belz Groves Fellow in Nanoscience Xue Group, College of Nanoscale Science and Engineering at SUNY Albany On Fri, Jul 26, 2013 at 8:16 AM, Ian Shuttleworth shuttleworth@gmail.com wrote: Siesterers I am using siesta-trunk-421 / 433. Is there any way to turn on van der Waals interactions for just a specific part of the system you're looking at? For example, organics adsorbed on a surface : I want to investigate vdW between the adsorbates but I dont want to use vdW for the substrate. The only command I can find it XC.hybrid which seems to apply to all species. Thanks Ian Shuttleworth
Re: [SIESTA-L] Binding energy of argon dimer overestimated
Vitor, Although I agree that you will have to perform a counterpoise correction on the energy, that will only lower the binding energy by about 0.1-0.2 eV. So, something else is wrong here. I took another look at the original Grimme paper and found that you're using too high of a Grimme potential parameter. Supposing C6 for Argon is 4.61 (Table 1) from the paper J. Comput. Chem. Vol 27, 1787-1799 (2006), the geometric average of C6 for two Argon atoms (eq. 13) is, unsuprisingly, 4.61 and that is the value you should use in your MM.Potentials Block, rather than 47.85. There is a parameter, MM.Grimme.S6, missing in your input file. Experience suggests that the default value for this parameter is usually not good enough to capture the physics of the vdW interaction. As Herbert said, plotting Ar-Ar distance versus the binding energy will clearly show you the trend (you will have to perform a ghost atom calculation for each distance, look elsewhere on the list for help with that, I believe I answered a similar question some time ago). You should see that the PBE functional does not bind Ar-Ar together, with no minimum in Binding E vs distance, and the DFT-D+PBE scheme will probably bind it slightly. Increasing your basis set size is going to play a big role in how your calculation comes out. If you don't want to use the simplex method to optimize your basis, try out TZDP or a similar, larger basis. You must declare your own basis set if you wish to include diffuse orbitals (s-like orbitals of higher principal quantum number). Cheers! On Thu, Jun 27, 2013 at 8:25 PM, Vitor Damiao vitordam...@gmail.com wrote: Hi Abraham, follows the file .fdf to see if you can help me. argon dimer calculations showed acceptable results with the vasp and g03 programs. thanks, Vitor. 2013/6/27 Abraham Hmiel abehm...@gmail.com Hello Vitor, GGA functionals typically do a poor job of capturing the physics of systems with strong van der Waals character like the Ar dimer. Typically LDA performs better than GGA because of fortunate cancellation of error, but is still far from correct. Try installing a recent version of SIESTA's development trunk, available from the website. You will be able to use the vdW-DF (DRSLL), vdW-DF2 (LMKLL), and opt-b88 (KBM) functionals which may significantly improve your Ar-Ar bond distance and binding energy at the expense of additional time spent calculating the xc energy. There is a decent pool of computational results in the literature to draw from here, as well. Furthermore, these self-consistent vdW functionals will give you the tools to engineer a better optimized basis for Ar. Using an optimized basis rather than the automatically-generated ones can be useful and it probably couldn't hurt to add additional zetas, polarization orbitals and diffuse orbitals to your basis. Without your .fdf file though, it's difficult to give you a more exact perscription, but using some form of vdW-DF could be a decent start, I feel. Best of luck, On Thu, Jun 27, 2013 at 2:28 PM, Vitor Damiao vitordam...@gmail.comwrote: Hi all, Have anybody calculated the argon dimer with SIESTA program? It appears that the binding energy (BE) is overestimated. Please, see a DFT-PBE calculation using a DZP basis set for Ar---Ar: BE (DFT) = 1.3 kcal/mol BE (DFT+D) = 2.4 kcal/mol BE (Expt.) = 0.28 kcal/mol I have tried using different pseudopotentials schemes, but the binding energies appears to be too high. I would be grateful if someone could explain me this trouble. Thanks in advance Vitor -- *Abraham Hmiel* Katherine Belz Groves Fellow in Nanoscience Xue Group, College of Nanoscale Science and Engineering at SUNY Albany http://abehmiel.net/about -- *Abraham Hmiel* Katherine Belz Groves Fellow in Nanoscience Xue Group, College of Nanoscale Science and Engineering at SUNY Albany http://abehmiel.net/about
Re: [SIESTA-L] Fwd: Error
Hello Mohammad, We'd like to help you solve your problem, but we are going to need more information from you. You should attach: 1) the last ~10 lines of your output file which can provide a guide for us to see where the program halted 2) a copy of the .fdf you used to run SIESTA 3) a copy of the arch.make file that was used to compile SIESTA, if you can 4) tell us the bash shell command that you used to run SIESTA Any or all of that information would be appreciated. In the meantime, check with your sysadmin to make sure there is no limit placed on how much CPU time you are allowed to use on your cluster and that the memory required by SIESTA is something that you are able to furnish, as both a user on a node (ulimit -a) and on the cluster's hardware itself. Can you reproduce the error if you use fewer processors or a totally different system? Best regards, On Tue, Jun 11, 2013 at 11:25 AM, mohammad mahdi Tavakoli mehdy.tavak...@gmail.com wrote: Dear siesta users Hi I have an error which is killed my run. mpirun noticed that process rank 3 with PID 3026 on node user-virtual-machine exited on signal 9 (Killed). Can you guide me? Thanks. -- *Abraham Hmiel* Katherine Belz Groves Fellow in Nanoscience Xue Group, College of Nanoscale Science and Engineering at SUNY Albany http://abehmiel.net/about
[SIESTA-L] Re: defining k path for surfaces
plane, for example, for the (110) plane. I think (but I may be wrong) that if I put a path from the bulk when calculating the surface, I will waste computing resource, and some bands in the direction perpendicular to the plane will be null or flat. Regards, Hatuey -- *On Wed, Jun 5, 2013 at 10:19 PM, Abraham Hmiel abehm...@gmail.comwrote: Hi Hatuey,* What you're looking for is here: http://www.cryst.ehu.es/** cryst/get_kvec.html http://www.cryst.ehu.es/cryst/get_kvec.html - find the space group for SnO2 and enter it in the box. The k-vector coordinates that SIESTA uses in a band structure calculation are in the first set of columns, CDML. If you input coordinates this way, it is important to use BandlinesScale ReciprocalLatticeVectors in your .fdf file. Then, the manual page http://www.icmab.es/leem/** siesta/Documentation/Manuals/**siesta-3.1-manual/node55.htmlhttp://www.icmab.es/leem/siesta/Documentation/Manuals/siesta-3.1-manual/node55.html **for information on how to define the path in k-space which will of course be implemented in your .fdf file. Defining the path in k-space has no implications for the density of states calculation. I always use the projected density of states output options, as I have a lot more control over what orbitals I'm looking at for my own analysis. That particular page is here: http://www.icmab.es/** leem/siesta/Documentation/**Manuals/siesta-3.1-manual/**node60.htmlhttp://www.icmab.es/leem/siesta/Documentation/Manuals/siesta-3.1-manual/node60.html With PDOS, it is usually a good idea to have a finer k-grid than your SCF calculation. For example, if you are simulating a surface with a converged k-grid of: %block kgrid_Monkhorst_pack 6 0 0 0.0 0 6 0 0.0 0 0 1 0.0 %block kgrid_Monkhorst_pack The following k-grid may be suitable for a PDOS calculation: %block PDOS.kgrid_Monkhorst_pack 16 0 0 0.0 0 16 0 0.0 0 0 1 0.0 %block PDOS.kgrid_Monkhorst_pack * De:* Hatuey Hack hatuey_h...@yahoo.com.br *Para:* siesta-l@uam.es siesta-l@uam.es *Enviadas:* Quarta-feira, 5 de Junho de 2013 11:17 *Assunto:* defining k path for surfaces Dear all, I am trying to calculate the band structure for different 2D systems. My systems consist in nanosheets of SnO2 obtained in the 101 and 110 direction from a tetragonal structure grown in the xy plane with the vacum in the z direction. I would like to know how to define the k path in the Brillouin zone for electronic band and DOS calculation. Best regards, Hatuey -- *Abraham Hmiel* Katherine Belz Groves Fellow in Nanoscience Xue Group, College of Nanoscale Science and Engineering at SUNY Albany http://abehmiel.net/about
[SIESTA-L] Re: defining k path for surfaces
Sorry, I already realize I've made a proofreading mistake:
'use X for the reciprocal short direction, X' for the reciprocal long
direction, and M as the vector composition of both X and X'. The reciprocal
short direction is parallel to the surface unit cell long direction,
correct?'
should instead read:
'use X for the reciprocal long direction, X' for the reciprocal short
direction, and M as the vector composition of both X and X'. The reciprocal
short direction is parallel to the surface unit cell long direction,
correct?'
apologies.
On Thu, Jun 6, 2013 at 10:08 AM, Abraham Hmiel abehm...@gmail.com wrote:
Hello again Hatuey,
Yes, the k-band utility from Bilbao will give you the band paths for the
bulk. For a surface, it is indeed a little different but not really any
more difficult. The question you asked is not especially relevant to
SIESTA, but I will answer it anyway because it's a good pedagogical example.
I am using this paper as a sample reference for your case:
http://www.cmdmc.com.br/redecmdmc/lab/arquivos_publicacoes/2781_Density%20Functional%20Theory%20Study%20on%20the%20Structural%20and%20Electronic%20Properties%20of%20Low%20Index.pdf
-- they are dealing with composite TiO2//SnO2 rutile surfaces but in the
same Miller index planes that you are interested in, and also TiO2 and SnO2
individually so it makes for a good example. Usually it is a good idea to
adopt the conventions of previously published research, especially if you
are making direct comparisons to them.
Draw your attention to pages 8948 and 8949 where they depict the
calculated band structure. They also show the Brillouin zone of the
surface. The surface Brillouin zone ought to be a rectangle for this
material because we are dealing with a cubic crystal cut along a face
diagonal, so one dimension of the surface Brillouin zone will be longer
than the other. The labels M and X, now, are NOT the same as the bulk M and
X high-symmetry points.
Consider the (110) plane case: If you make a cut to the bulk crystal along
(110) and then orient your viewpoint so that [110] is normal to your line
of sight (the z-direction, like in your simulation), one choice of lattice
vectors that yield a rectangular surface unit cell is: {1 -1 0} and {0 0
1}. You are probably already using this in your surface unit cell. The
paper, and its predecessor on which the label conventions are based (
http://prb.aps.org/pdf/PRB/v64/i7/e075407) use X for the reciprocal
short direction, X' for the reciprocal long direction, and M as the
vector composition of both X and X'. The reciprocal short direction is
parallel to the surface unit cell long direction, correct? So now, for
the SnO2 rutile (110) case, we arrive at the conclusion that X is along [0
0 1] and X' is along [1 -1 0], and M is along [1 -1 1]. Pretty simple,
right? But we're not done because we need to tell SIESTA what to do with
this information and it doesn't care about the bulk crystal, just the
surface unit cell for the purposes of finding reciprocal lattice vectors
and so on. In this unit cell, the x direction is along [0 0 1], and the
y-direction is along [1 -1 0] in the bulk crystal.
We need to remember that the 1st Brillouin zone's boundary is half the
length of the reciprocal cell vectors (see
http://upload.wikimedia.org/wikipedia/commons/2/22/Brillouin_zone.svg for
a graphical example), so, for the surface unit cell of (110) Rutile SnO2:
The Gamma point is at [0 0 0] (that's easy)
The X' point is at [0 0.5 0] (because it's parallel to the y-direction,
the reciprocal short direction)
The M point is at [0.5 0.5 0] (because it's the sum of vectors X' and X,
therefore x+y unit vectors)
The X point is at [0.5 0 0] (again, the x-direction in the surface unit
cell, the reciprocal long direction)
And then, creating this path in reciprocal space in a way SIESTA can
understand (and I'm estimating the number of points in each line):
WriteBands .true.
BandLinesScaleReciprocalLatticeVectors
%block BandLines
10 0 0 \Gamma
20 0.5 0 0 Xprime
50 0.5 0.5 0 M
20 0 0.5 0 X
50 0 0 0 \Gamma
%endblock BandLines
Then, run: (assuming your systemlabel is SnO2_110)
bash gnubands SnO2_110.bands SnO2_110_bands.dat
When plotted with software like matplotlib or gnuplot, this should create
a plot that is similar to figure 2b in the 1st reference I gave you once
you choose the correct viewing window. Keep in mind that your energies will
be with respect to the program's energy zero and not the VBM, Fermi energy,
or vacuum level unless you write a script to subtract that energy from the
second column of SnO2_110_bands.dat.
If you calculate the lengths of each reciprocal lattice vector in 1/bohr
or Angstrom you can probably make a more consistent band lines scale than
the one I used above for the number of points along each line, but I'll
leave that as an exercise for you. Also another exercise for you: do you
have
Re: [SIESTA-L] defining k path for surfaces
Hi Hatuey, What you're looking for is here: http://www.cryst.ehu.es/cryst/get_kvec.html - find the space group for SnO2 and enter it in the box. The k-vector coordinates that SIESTA uses in a band structure calculation are in the first set of columns, CDML. If you input coordinates this way, it is important to use BandlinesScale ReciprocalLatticeVectors in your .fdf file. Then, the manual page http://www.icmab.es/leem/siesta/Documentation/Manuals/siesta-3.1-manual/node55.html for information on how to define the path in k-space which will of course be implemented in your .fdf file. Defining the path in k-space has no implications for the density of states calculation. I always use the projected density of states output options, as I have a lot more control over what orbitals I'm looking at for my own analysis. That particular page is here: http://www.icmab.es/leem/siesta/Documentation/Manuals/siesta-3.1-manual/node60.html With PDOS, it is usually a good idea to have a finer k-grid than your SCF calculation. For example, if you are simulating a surface with a converged k-grid of: %block kgrid_Monkhorst_pack 6 0 0 0.0 0 6 0 0.0 0 0 1 0.0 %block kgrid_Monkhorst_pack The following k-grid may be suitable for a PDOS calculation: %block PDOS.kgrid_Monkhorst_pack 16 0 0 0.0 0 16 0 0.0 0 0 1 0.0 %block PDOS.kgrid_Monkhorst_pack Best regards, *Abraham Hmiel* Katherine Belz Groves Fellow in Nanoscience Xue Group, College of Nanoscale Science and Engineering at SUNY Albany http://abehmiel.net/about
Re: [SIESTA-L] Convergence for charged system...
Hi Luigi, A few suggestions: 1) Your MaxCGsteps and MaxSCFIterations are both very large, convergence in many problems can be adequately approached by using a small number of CG updates, like 10-50 to perform a stepwise convergence, changing mixing parameters slightly between runs, observing how the forces change between CG steps and using UseSaveData = .true. to use saved DM's, XV's and so on. MaxSCFIterations could be around 100-250, much more than that and you're wasting your time, might I add. 2) Try using more Pulay convergence parameters. This will probably get you to convergence if you choose them right. You will have to modify them until you attain something that works. For starters, try: DM.NumberPulay 5 DM.MixingWeight 0.002 DM.NumberKick 12 DM.KickMixingWeight0.0766 I've found that oftentimes the Pulay kick will knock your SCF cycle into a convergence basin, especially with charged systems or hard pseudopotentials. Look in the manual to see how these are defined. 3) I'm not sure why SimulateDoping would help you, it seems unphysical to me in a molecule rather than a solid. Your meshcutoff also seems low, but it won't help your convergence problem. Look into converging that value once you can close your SCF loop. 4) 30x30x30A cell is a big box for a small molecule, perhaps there may be a benefit to using a smaller cell, since a Madelung correction term is applied for molecules? If you go to a 20x20x20 cell does the convergence issue get worse? That's all I can think of for now, definitely look into the Pulay convergence acceleration though. Warm regards, *Abraham Hmiel* Katherine Belz Groves Fellow in Nanoscience Xue Group, College of Nanoscale Science and Engineering at SUNY Albany http://abehmiel.net/about
[***Posible SPAM***]Re: [SIESTA-L] DOS ploting
Jafar, I think you're using the wrong unix pipe command. Try: $ ./Eig2DOS Si.EIG Si.dos Or you can try using the %ProjectedDensityOfStates block, which will give you much more valuable information, in my opinion. See the manual for details. You may want to do some basic bash shell/unix pipe tutorials because your questions in this thread have little to do with SIESTA and more to do with proper shell command syntax. Look here for a beginner's introduction: http://arachnoid.com/linux/shell_programming.html Best, -- *Abraham Hmiel* Katherine Belz Groves Fellow in Nanoscience Xue Group, College of Nanoscale Science and Engineering at SUNY Albany http://abehmiel.net/about
Re: [SIESTA-L] DOS ploting
Jafar, Upon closer inspection, it seems that you have the correct command syntax. Sorry for the confusion. You wrote it the wrong way once and the right way once in your message. I'm still having trouble replicating your error, though. Have you copied the eig2dos file to $HOME/usr/bin or some other directory that is within the scope of your $PATH environment variable (in .bashrc or .profile in your home directory)? If you do this, you don't need to use ./ to run the executable and you don't need to have the executable in the same directory as your data. I am curious, from what version of siesta did you build the eig2dos utility? Did you use the same fortran compiler that you used to build siesta? Are you sure that you're using the correct spelling and case of the filenames? Cheers, On Tue, Apr 30, 2013 at 11:17 AM, Abraham Hmiel abehm...@gmail.com wrote: Jafar, I think you're using the wrong unix pipe command. Try: $ ./Eig2DOS Si.EIG Si.dos Or you can try using the %ProjectedDensityOfStates block, which will give you much more valuable information, in my opinion. See the manual for details. You may want to do some basic bash shell/unix pipe tutorials because your questions in this thread have little to do with SIESTA and more to do with proper shell command syntax. Look here for a beginner's introduction: http://arachnoid.com/linux/shell_programming.html Best, -- *Abraham Hmiel* Katherine Belz Groves Fellow in Nanoscience Xue Group, College of Nanoscale Science and Engineering at SUNY Albany http://abehmiel.net/about -- *Abraham Hmiel* Katherine Belz Groves Fellow in Nanoscience Xue Group, College of Nanoscale Science and Engineering at SUNY Albany http://abehmiel.net/about
Re: [SIESTA-L] Error in Cholesky... (Abraham Hmiel)
Hamidreza, You're trying to fit 20 atoms into a 2.159Ax2.169A rhomboid unit cell in a flat geometry? That sounds like a pretty bad idea to me. Like I said before, rethink your atomic positions. You are getting an error because when your atomic positions are translated back into your primary unit cell, they overlap with one another and introduce a ridiculous electron density distribution which throws off the diagonalization algorithm. How have you 'converged' your k-point grid and meshcutoff with respect to total energy if you are getting errors like this? I refuse to believe that the 'best Meshcutoff' for this system occurs at zero. I have performed this simulation myself and obtained an optimal value around 300 Ry. Same with k-points. If you are looking to reproduce the Dirac Cone in the band structure, you are not going to get anywhere with the k-point mesh you are using. This is a very well-studied problem. Please search the list for more help and double-check your input files to make sure they make sense. Best, Abraham Hmiel On Sun, Mar 31, 2013 at 8:06 AM, Hamidreza Balangi hamidrezabala...@yahoo.com wrote: Hi ** My friend Abraham Hmiel Idid input file (fdf) according to the manual, and email list. While convergence Lattice Constant, PAO.Basis, kgrid_Monkhorst, cut off obtain with respect to total energy The following error appeared to converge better with smaller LatticeConstant *Error in Cholesky factorisation in cdiag error stop from Node: 0* *Finally*, 1 - The atomic coordinates of obtained with AutoCAD software*** * 2 - the best cut off appear at zero 3 - In case the error is not explained in the manual and mailing list is not given the correct answer to this question. 4 - I have Input file attachment for you. please help me in this problem. With thanks and best wishes to you hamidreza balangi ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** -- *Abraham Hmiel* Katherine Belz Groves Fellow in Nanoscience Xue Group, College of Nanoscale Science and Engineering at SUNY Albany http://abehmiel.net/about
Re: [SIESTA-L] Fw: This is an error Cholesky on run sheet Graphene
Hamidreza, I'd like to help you solve your problem, but it seems like you have not read the manual to learn how to perform a proper calculation. Please do so. Additionally, if you search the mailing list archives, you will find working graphene input .fdf files that yield plausible results because this question has been asked dozens of times. For example: http://www.mail-archive.com/siesta-l@listserv.uam.es/msg02155.html Here is what comes to mind when I read your input file: 1. Why are you using siesta 2.0.2? The most recent version is profoundly better and has more features. Unless there is a specific reason to use 2.0.2, you should upgrade to the new version. 2. For an infinite graphene sheet, 10x10x1 M-P k-point grid is not good enough because it is too coarse around graphene's dirac points in the BZ. You will need at least 48x48x1 from experience. 3. 20 Ry is way too small for the MeshCutoff. Try at least 10 times this value, and you will need to converge this value with respect to total energy. 4. (The reason why your simulation is not working) you have no atoms listed inside your AtomicCoordinatesAndAtomicSpecies block. If you have no species listed here, I believe the program will make the coordinates of everything (0,0,0), hence why it prints that warning that specific atoms are too close together. Finally, when attaching items in an email to the list, please use plain text (or .png for figures) from now on. I'm also not sure why you posted your message five times to the list, it is mildly irritating to see such a thing in my inbox and might make people less willing to help you. Hope this helps and good luck with your calculation, -- *Abraham Hmiel* Katherine Belz Groves Fellow in Nanoscience Xue Group, College of Nanoscale Science and Engineering at SUNY Albany http://abehmiel.net/about
Re: [SIESTA-L] problem
Zahra, You've posted to the list before with regards to this system. Why are you still plotting a band structure path in reciprocal space of a molecule? Please prove to us that you can explain what you're trying to do and then we can help you solve your issue. By the way, it's always helpful to include the relevant figures in your email to show us what you mean. No one really wants to run this system ourselves to see your result (not that we could, without knowing which pseudopotentials you're using). Best, On Wed, Jan 30, 2013 at 2:07 PM, Zahra Talebi talebi_z2...@yahoo.comwrote: hi every body, I runned this fdf with siesta but I don`t know why my DOS diagram doesn`t show the same band gap as my band structure showes. Can any body tell me about that. or guid me that how can I solve this question. regards -- *Abraham Hmiel* Katherine Belz Groves Fellow in Nanoscience Xue Group, College of Nanoscale Science and Engineering at SUNY Albany http://abehmiel.net/about
Re: Fw: [SIESTA-L] why my running did stop.
I found the line, # MD.NumCGsteps 550 # Number of CG steps for which is out-commented. (550 steps is very large, by the way! Try 20 or 30 at a time) Remove the '#' to perform a geometry relaxation. If you don't specify the number of steps, the computer will just assume I am going to do a single-point energy calculation. Also, because you are simulating a molecule (a graphene flake passivated by H, it seems), you do not need nearly as many k-points as you are using and the band lines you are using don't really make any sense because of the 0D symmetry. Also, you might want to upgrade to the latest version of SIESTA. Go to the home page for the newest release. http://icmab.cat/leem/siesta/ Best, On Tue, Jan 15, 2013 at 9:47 AM, Zahra Talebi talebi_z2...@yahoo.comwrote: hi every body, I attached my out file after running a siesta, can any body explain for me that why the running stoped. best regurds -- *Abraham Hmiel* Katherine Belz Groves Fellow in Nanoscience Xue Group, College of Nanoscale Science and Engineering at SUNY Albany http://abehmiel.net/about
Re: [SIESTA-L] Siesta: System type = molecule
Hakkim, SIESTA will automatically detect the molecule, chain, slab, or bulk type depending on how close the images of each atom are across the x, y, and z dimensions of your simulation cell. This is done in the shaper.f subroutine. If your unit cell is big enough in all 3 dimensions such that no orbitals interact (in a certain range) in your atom list's periodic image, you will have a molecule. If they interact in one dimension, you will have a chain (or nanowire), two, a slab, and all three dimensions, a bulk system. If you are seeking to do a force minimization calculation on a bulk system and you are getting System type = molecule in the output, you need to check the dimensions of your unit cell to make sure it is small enough that image atoms in all three dimensions will interact with the atoms whose position you've explicitly declared in the unit cell. Maybe your dimensions are proportionally correct to the crystal you'd like to simulate but your lattice constant is too big. On Wed, Nov 14, 2012 at 9:36 AM, Hakkim Vovusha hakkim.vovu...@physics.uu.se wrote: HI, I am doing force minimization calculation (periodic system) in siesta and I have found in the output Siesta: System type = molecule but i need to change the molecule into bulk i.e. Siesta: System type = bulk. Can any one help how to change these molecule into bulk. with regards hakkim -- *Abraham Hmiel* Katherine Belz Groves Fellow in Nanoscience Xue Group, College of Nanoscale Science and Engineering at SUNY Albany http://abehmiel.net/about
Re: Re: Re: [SIESTA-L] post-processing the energy band
Liu, I have tried to run your input file with siesta-trunk-364, siesta-3.1pl-9, and siesta-trunk-411, and it seems that trunk-411 is hanging at the writewavefunctions step for me. It's not printing out any 'maxk' business, just not completing the wavefunction-writing output in 30 minutes when it took 45 seconds in the other codes I've tried. If you are not using the vdw-xc that is included in the trunk versions, why not just use a different version of siesta to write the wavefunctions? Have you tried a more recent trunk version? I have checked the changelog and saw that writewave.f has been amended to include greater functionality at trunk-414, you might wish to try trunk-424 and see if that version will write the wavefunctions correctly. Also, unrelated to your issue, I noticed you may want to tighten up your Monkhorst-Pack k-point grid to at least 30x30x1 to get a good description of the dispersion of the energy bands close to the K point in the BZ. It may make the difference between a band structure that makes sense and one that looks like garbage. Best, On Thu, Nov 8, 2012 at 1:42 AM, liuyunlong0902 liuyunlong0...@126.comwrote: Thanks for your suggestion. Here I include the input and output file, which is just an example for calculating graphene energyband. This work can run well on the old version 'siesta-3.0-rc2' ,but not the new version 'siesta-trunk-411'. I check the 'maxk' in 'writewave.F' of both version, but find nothing difference. Best, -- Liu At 2012-11-08 09:54:03,Abraham Hmiel abehm...@gmail.com wrote: What follows is a general explanation for what to do in this case and ones like it. In this case, what I did is to run the following command in the /Src/ directory of my SIESTA build to see where all the instances of 'maxk' were (I'm using trunk-364 at the moment, it shouldn't be too different, though): [Src] grep 'maxk' * and the output found files that use 'maxk' in a bunch of the files. There is a lot of output here, and I'll spare you the whole list, but one of these files has the error message you specificed, so take a look at 'writewave.F' to see if you're doing anything wrong. You didn't include your input file with your message, and it would help to diagnose the problem. I would double-check that you're using the correct syntax for the WaveFuncKPoints fdf block by examining the source core for the initwave and wwave subroutines. There is no substitute for reading the source code :) On Wed, Nov 7, 2012 at 11:34 AM, liuyunlong0902 liuyunlong0...@126.comwrote: Dear Abraham Hmiel, Thanks for your help! Besides, I have another problem in running SIESTA new version 'siesta-trunk-411', when submit a siesta work, the output file give the warning Writing Wavefunction: parameter Maxk too small, So how I can change the parameter 'Maxk' ? Thanks again. Best, -- Liu At 2012-11-05 19:33:31,Abraham Hmiel abehm...@gmail.com wrote: Liu, Try increasing the value of the 'maxb' parameter in gnubands.f, (increasing from 100 to something like 5000) and then re-compiling gnubands.f and then trying it again. Best, On Mon, Nov 5, 2012 at 6:15 AM, liuyunlong0902 liuyunlong0...@126.comwrote: Dear all, I have difficulty in post-processing the energy band. When the generated '*.bands' file is handled by 'gnubands', warning is that 'Dimensions in gnubands too small'. Would anyone help me solve the problem? Regards, --- Liu -- *Abraham Hmiel* Katherine Belz Groves Fellow in Nanoscience Xue Group, College of Nanoscale Science and Engineering at SUNY Albany http://abehmiel.net/about -- *Abraham Hmiel* Katherine Belz Groves Fellow in Nanoscience Xue Group, College of Nanoscale Science and Engineering at SUNY Albany http://abehmiel.net/about -- *Abraham Hmiel* Katherine Belz Groves Fellow in Nanoscience Xue Group, College of Nanoscale Science and Engineering at SUNY Albany http://abehmiel.net/about
Re: [SIESTA-L] SIESTA-L-fdf format
Hakkim, What I believe Sergio was asking you is, what is the shell command you use to run siesta? For example, mpirun -np 8 siesta input.fdf 1.out Best, On Mon, Nov 5, 2012 at 4:14 AM, Hakkim Vovusha hakkim.vovu...@physics.uu.se wrote: I have generate fdf file for my molecule from xyz coord using GDIS then i started to run the siesta. I have attached the fdf file. regards hakkim On 11/2/2012 6:25 PM, Sergio Ferrari wrote: Hi Hakkim, How exactly do you run Siesta? Regards, Sergio Ferrari 2012/11/2 Hakkim Vovusha hakkim.vovu...@physics.uu.se Hi, I have generated fdf file from the link GDIS http://gdis.sourceforge.net/. then I start to run siesta (md calculation) its running but i havenot find nothing in the output file. can any one help in this regards with regards hakkim -- *Abraham Hmiel* Katherine Belz Groves Fellow in Nanoscience Xue Group, College of Nanoscale Science and Engineering at SUNY Albany http://abehmiel.net/about
Re: [SIESTA-L] SIESTA-L-fdf format
Hakkim, You have not told SIESTA what to do in your .fdf file. Therefore, I don't really know what you want to do either but you need some lines like this: MD.TypeOfRun Nose MD.InitialTImeStep 1 MD.FinalTimeStep 1000 MD.LengthTimeStep1.0 fs MD.VariableCell .false. MD.TargetTemperature 278.0 K MD.InitialTemperature278.0 K MD.NoseMass 100.0 Ry*fs**2 Also, I see in your .fdf file that you did not define the LatticeVectors block. You need to tell SIESTA the size of the simulation cell, she can't guess this automatically. You need to read the manual, especially the pages on Molecular Dynamics parameters Best, On Mon, Nov 5, 2012 at 6:26 AM, Abraham Hmiel abehm...@gmail.com wrote: Hakkim, What I believe Sergio was asking you is, what is the shell command you use to run siesta? For example, mpirun -np 8 siesta input.fdf 1.out Best, On Mon, Nov 5, 2012 at 4:14 AM, Hakkim Vovusha hakkim.vovu...@physics.uu.se wrote: I have generate fdf file for my molecule from xyz coord using GDIS then i started to run the siesta. I have attached the fdf file. regards hakkim On 11/2/2012 6:25 PM, Sergio Ferrari wrote: Hi Hakkim, How exactly do you run Siesta? Regards, Sergio Ferrari 2012/11/2 Hakkim Vovusha hakkim.vovu...@physics.uu.se Hi, I have generated fdf file from the link GDIS http://gdis.sourceforge.net/. then I start to run siesta (md calculation) its running but i havenot find nothing in the output file. can any one help in this regards with regards hakkim -- *Abraham Hmiel* Katherine Belz Groves Fellow in Nanoscience Xue Group, College of Nanoscale Science and Engineering at SUNY Albany http://abehmiel.net/about -- *Abraham Hmiel* Katherine Belz Groves Fellow in Nanoscience Xue Group, College of Nanoscale Science and Engineering at SUNY Albany http://abehmiel.net/about
Re: [SIESTA-L] Negative phonon frequency problem.
Saikat, Your issue here is that you are using the default value of: MD.MaxForceTol0.04 eV/Ang because you are not using it in your fdf file. For what you are trying to accomplish, I think a MD.MaxForceTol of about 0.001 eV/Ang is more appropriate.This is a good target for small molecules. Try using far fewer MD.NumCGsteps too, I usually use about 30-50 at a time so that if something goes wrong you can trace it without waiting forever, a good practice if you're moving from small molecules to molecules adsorbed onto a surface or something. MaxSCFiterations is very high as well, should something unfortunate happen with your convergence. It won't affect anything here, though. You can also use: UseSaveData .true. To restart simulations that go to the full # of CG steps using saved density matrices and atomic positions, and recent CG history. The reason why you were seeing negative frequencies is because your geometry optimization is not finding the global minimum, so that when atoms are displaced in the FC step by very small amounts, it might find a lower energy state. This topic is discussed at length elsewhere on the list. -- Abraham Hmiel Katherine Belz Groves Fellow in Nanoscience Xue Group, College of Nanoscale Science and Engineering at SUNY Albany
Re: [SIESTA-L] mpi error while running siesta
Dear Karan, We are going to need a lot more information than the error message you provided to solve your problem. What is the command you used to invoke the program? What are the contents of your arch.make file and the input fdf file? What few things have you tried, exactly? Does the invocation of siesta work in serial mode? Has siesta with mpi ever successfully run? Is this a chronic problem or does it happen seemingly at random? The more information you put forward to the listserv, the more able we are to help you. Best, On Sat, Jun 23, 2012 at 10:19 AM, karan deep kara_nd...@yahoo.co.in wrote: Dear users i m suddenly getting this error while running siesta Fatal error in MPI_Comm_group: Invalid communicator, error stack: MPI_Comm_group(150): MPI_Comm_group(comm=0x0, group=0x7fff0c620494) failed MPI_Comm_group(74).: Invalid communicator i try few things but nothing is working -- Abraham Hmiel Katherine Belz Groves Fellow in Nanoscience Xue Group, College of Nanoscale Science and Engineering at SUNY Albany
Re: [SIESTA-L] siesta relaxation question
Personally I would only trust an 100 Ry cutoff calculation to provide a starting point for a geometric configuration destined for further relaxation. My experience tells me if you use oxygen you should always be using 350 Ry or more, and typically for some materials I've been simulating recently, as high as 550Ry. Incidentally, depending on your simulation cell, any cutoff will set the *actual* grid used to be higher, sometimes much higher. If you take a stable geometry and perform a single-point energy (0 CG steps) convergence test with respect to the meshcutoff, try and see what happens when you increment the mesh cutoff by steps of about 100 Ry or so all the way to about 2000 Ry- you should find that the energy won't change by much after a certain point, and the cutoff you should choose will balance being respectably close to that converged energy. Always record the meshcutoff used by siesta, not the one in your input file. For example, a while ago with bulk TiO2, I found that the difference in total energy between a ~1400 Ry cutoff and a ~550 Ry cutoff was about the same as the difference between ~450 Ry and ~550 Ry. I chose the 550 Ry grid as it was 'sufficiently converged' for my purposes, did an egg-box test, printed the proof in a couple quick plots and saved it somewhere accessible. Having a tight grid that is balanced by its memory usage is a trick you kind of have to get a knack for. It is true that some problems really do require tight expensive grids and a lot of memory, and it might seem to squeeze a lot of the time benefits out of using LCAO-based approach (vdW xc-functionals come to mind). In these cases your parallelization scheme and how you select initial reference geometries will make a lot of difference! The egg-box convergence test is another one you will find yourself doing often to check the reliability of your numerical grid, look elsewhere on the list for that. The bottom line is, I would always explicitly include the MeshCutoff as an input in an fdf of mine for research purposes. Even when I need a 'quick and dirty' estimate of something or perhaps a stepping stone to a reference geometry to iron out some of the more expensive force-fluctuation math. On Wed, Apr 11, 2012 at 6:36 PM, Yi Gao yigao1...@gmail.com wrote: Dear siesta users, Recently I have been using siesta to find optimized structure of crystal such as anatase. According to what I have found, if we run the CG or Broyden method to search for atom positions with least forces, say, 0.02 eV/Ang, the default MeshCutoff (e.g., 100.0 Ry) gives a configuration. However, if I simply displace the origin of my lattice from somewhere to some atom, keeping the primitive vectors unchanged, the forces exerted on each atom will change, which is unphysical. What I can do is to increase the MeshCutoff to try to get converged results, i.e., displacing the origin of the lattice does not change the forces on each atom, and finally in agreement with experiments. But it turns out to be MeshCutoff = 500.0 Ry, so large that it is difficult to extend to larger systems. My question is that how can I trust the atom configuration with the default MeshCutoff? Is it always necessary to set MeshCutoff to an exceedingly large value to get converged results? Best wishes! Yi -- Abraham Hmiel Katherine Belz Groves Fellow in Nanoscience Xue Group, College of Nanoscale Science and Engineering at SUNY Albany
Re: [SIESTA-L] how to explain
Zahra, When you calculated DOS with SIESTA, what method did you use? Did you use EIG2DOS or did you use a PDOS utility (then sum the PDOS on each atom and orbital), or something else? I would trust your 'band' energy diagrams for this molecule. The DOS calculation uses a Gaussian smearing parameter that you set yourself. If the HOMO-LUMO gap around the Fermi energy is close to your smearing parameter, what you show in the DOS you shared will happen. Try lowering the value for the smearing parameter (According to your plots it looks like it is around 0.250). If you used eig2dos with a first line like this: -3.4561 0.25 1000 -10 10 reduce the second number to something less than, about 0.05. How you would plot a DOS curve is something of a personal preference, considering clarity and value of information presented. A smaller smearing width will change how the curve looks somewhat. Change the parameters until you get something you are satisfied with. Also, using many k-points when calculating an isolated molecule is not usually a good idea. Use a 1x1x1 k-point mesh for a molecule and only worry about convergence with respect to the real space mesh cutoff. Best of Luck, Abraham Hmiel Katherine Belz Groves Fellow in Nanoscience Xue Group, College of Nanoscale Science and Engineering at SUNY Albany On Mon, Oct 10, 2011 at 8:45 AM, Zahra Talebi talebi_z2...@yahoo.comwrote: hi dear siesta usrs, t first I hope to be able to ask my question in a right way, because my english isnot good. I just did some run and got the result as band structure and dos for the special run of siesta. As you notic I attached them to my e-mail. my band structure showes a very smal band gap arround gama and because I am running for molecule, the band structure must be the same in other path of beriloan zone too, by such a band strucute I expect to see a very small gap in my DOS arrround fermi energy but not only I don`t have any gap there is a tick near fermi energy. can any body tell me why this happen. if you need my fdf I can send it for you. also I have some other run too which Ihave the same problem for them. I mean I have a gap arround fermi energy in my band structure but in my DOS diagram I can see the DENSITy arround the frmi energy. Thanks for your help.
Re: [SIESTA-L] no gradient calculation
Robert, It is absolutely possible to do this, the total energy is printed a few times when the run ends. To calculate single point energy, use: MD.TypeOfRun cg MD.NumCGsteps 0 So that atoms are frozen in place, then once the run is finished either look for a siesta: total Energy line in the output file, or you can use grep to look for the specific line in the file. Try: fgrep siesta: FreeEng if you want the free energy or fgrep siesta: Etot for the total energy (in many instances, they will be the same). The grep command used this way will return two values, the first is the (unconverged) total energy from the beginning of the run, and the second is the converged energy at the end of the cg/scf loop. Towards the end of the output file, you can also find lines like these: siesta: Final energy (eV): siesta: Band Struct. = -28113.082516 siesta: Kinetic = 62511.903467 siesta: Hartree = 1851209.928718 siesta:Ext. field = 0.00 siesta: Exch.-corr. = -19076.142766 siesta: Ion-electron =-3768244.293672 siesta: Ion-ion = 1753136.700291 siesta: Ekinion = 0.00 siesta: Total = -120461.903961 Where the energy is partitioned into all of its components. You have to carry the calculation through to completion, either by satisfying some atomic force convergence condition or a maximum of conjugate gradient steps to get this information, so you won't see it if you are interrupting the calculation somehow. Best of luck, Abraham Hmiel Katherine Belz Groves Fellow in Nanoscience Xue Group, College of Nanoscale Science and Engineering at SUNY Albany On Tue, Oct 4, 2011 at 7:53 AM, robert.sed...@marge.uochb.cas.cz wrote: Hello SiestaUsers, I'm new member of SiestaUsers family. I have one small question, is it possible to calculate only single point (electronic) energy with siesta ... . In my output I can see also gradients, but I would like to calculate only energy. Thanks in advance. Best Regards Robert Sedlak
Re: [SIESTA-L] Band Identification
Hello Abbas, This is usually a multi-step process. At a general level, you need to look at the quantities derived from orbital populations. Projected density of states is an important one. If you use the pdos utility or a special script you write, you can separate the PDOS data file into PDOS aggregated onto a specific atom, group of atoms, orbital, or selected orbitals on selected atoms. You should re-read the section in the manual about PDOS, how to create it, etc. The other thing you can look at is the crystal orbital overlap population by running the COOP utility mprop. Look elsewhere on the list for information in how to set that data file, basically, you select pairwise atoms/orbitals and a range of distances and it will calculate COOP. You will have to manually prepare a lot of data and look at it side by side to determine which orbitals are interacting strongly at what energies. From that, you can see a general energy range of where to look for the local (spatial) electronic density of states (plotted with grid2cube), which can be supplied as a range of energies in the fdf. The other way to do is is to plot a lot of wavefunctions and use the denchar utility to make .cube files then plot isosurfaces of the complex wavefunction at a particular grid density using a program of your choosing. If you look at them side by side in sequence, you can discern characteristics that mark the spatial patterns of what you're looking for. Unfortunately, sometimes these visualization files can get quite large and cumbersome for some computers to handle, but either way you should then have a pretty good idea of which band since they are numbered sequentially up from the lowest energy state. It's not going to tell you BEEP: THIS BAND IS PI* but it is a judgment you will have to make. And then have the band structure handy for reference to put everything in perspective. You should write a script or something that can identify an energy band in the k-range you specify in a crystal. Combined, these things are all ingredients of good convincing arguments in a publication. Best of luck, -- Abraham Hmiel Katherine Belz Groves Fellow in Nanoscience Xue Group, College of Nanoscale Science and Engineering at SUNY Albany On Thu, Sep 29, 2011 at 9:54 PM, Abbas Ebnonnasir aebno...@mymail.mines.edu wrote: Dear SIESTA users, I'm trying to find out how I can identify each band in band structure plot, resulted from SIESTA, i.e, I need to know which band belongs to which molecular/crystal orbital (which one is Pi, which one is Pi*, Sigma). Any comment will be appreciated. Thank you in advance. All the wishes, -Abbas
Re: [SIESTA-L] graphene
Zahra, The cause of your incorrect DOS is due to the fact that in graphene, there are only a few ways of sampling the Brillouin zone while keeping the Dirac Point as a member of the mesh. When you go from exactly describing the desired k-point grid with the %block kgrid_monkhorst_pack to using kgrid_cutoff, you no longer demand specific points in the mesh so you might end up avoiding the area of reciprocal space around the dirac point, which is responsible for a lot of the physics. You need a pretty dense mesh to get the DOS correct because of the special feature at the Dirac point which must include the Dirac Point, and SIESTA doesn't 'know' to do this when you use a numerical cutoff value. It has less to do with graphene being 2D and more to do with its Fermi surface being just a single point which should be sampled densely and the k-mesh chosen carefully. A related question appears on another thread and you should observe the answer given there: http://www.mail-archive.com/siesta-l@uam.es/msg00935.html - for starters, a 21x21x1 mesh seems to do a good job, presuming the rest of the input file is nearly the same style as the one in that thread. Best, Abraham Hmiel Katherine Belz Groves Fellow in Nanoscience Xue Group, College of Nanoscale Science and Engineering at SUNY Albany On Thu, Sep 1, 2011 at 4:45 AM, Zahra Talebi talebi_z2...@yahoo.com wrote: Hi dear users I am working on graphene. before this I used kgrid Mokharest pack in my fdf file but just recently I tried kgrid cutoff. it caused that I don`t get the right DOS. why this happen? Is it because graphene is two dimention and I cannot use kgrid cutoff for that. If any body knows the answer please let me know. regards, Zahra.
Re: [SIESTA-L] Can siesta preform the nudged elastic band (NEB) calculation?
There is not an implementation within the SIESTA code as of now for nudged elastic band, but there is an implementation in the python package 'ASE' - google 'atomic simulation environment' for more info. Basically, you can use SIESTA as a calculator for the total energies and forces and let ASE perform the set of minimizations along the chain of images. Abe On Jul 16, 2011 8:17 AM, Jingbin Li jingbin...@gmail.com wrote: Hi Hongyi, As far as I know, there is no NEB implementation in Siesta yet. Thanks, On Sat, Jul 16, 2011 at 1:49 AM, Hongyi Zhao hongyi.z...@gmail.com wrote: Hi all, I know that VASP can do the NEB calculation for finding saddle points and minimum energy paths between known reactants and products. But don't know whether we can perform the similar job within siesta? Regards -- Hongyi Zhao hongyi.z...@gmail.com Institute of Semiconductors, Chinese Academy of Sciences GnuPG DSA: 0xD108493
Re: [SIESTA-L] question about post-process output file .PDOS
If I understand your question correctly, you're having trouble getting useful information out of a PDOS file. There is a PDOS parsing utility in the main /Util directory, but I usually don't use it. Look elsewhere on the list for help with that. This is the way I peel the tag garbage off: If you know exactly how many orbitals for atom, number of bins, and you make a separate list of the indexes of the atoms, you can remove all the xml tags with this unix command: bash$ grep -ve \ -ve \ -ve = systemlabel.PDOS systemlabel_PDOS.dat then use the remaining file with a matlab or python script to chop up that large PDOS file into atoms of like orbitals, etc. This requires you to be consistent in your indexing scheme and you should become very familiar with your basis set if you do it this way. Best, Abraham Hmiel Katherine Belz Groves Fellow in Nanoscience Xue Group, College of Nanoscale Science and Engineering at SUNY Albany On Fri, Jul 15, 2011 at 4:40 PM, lily zheng lilyclem...@gmail.com wrote: Dear all, How to give those parameters which show up as the head of .PDOS file? pdos nspin1/nspin norbitals 6/norbitals energy_values units=eV It seems that we need modify them, otherwise, it gives us the error message like: At line 53 of file eig2dos.f (unit = 5, file = 'stdin') Fortran runtime error: Bad real number in item 1 of list input Any hint would be much appreciated! Lily --
Re: [SIESTA-L] Single point energy calculation within SIESTA.
Hongyi, MD.TypeOfRun cg MD.NumCGsteps 0 Will provide you with a single-point energy calculation. It tells the conjugate gradient minimum-finder algorithm to stop after achieving convergence in the Self-Consistent Field loop no matter what the forces on the atoms are. Use more than 0 steps for a geometry relaxation, and increment your number of CG steps carefully if you run into issues with wrong geometries, failed convergence, or oscillating forces so that you can diagnose problems. Best, Abraham Hmiel Katherine Belz Groves Graduate Fellow in Nanoscience, Xue Group The College of Nanoscale Science and Engineering at SUNY Albany Clouds are not spheres, mountains are not cones, coastlines are not circles, and bark is not smooth, nor does lightning travel in a straight line. - Benoit Mandelbrot On Wed, May 25, 2011 at 12:36 PM, Hongyi Zhao hongyi.z...@gmail.com wrote: Hi all, I've learned that the single point energy calculation should be the most appropriate method for any type of convergence testings (whether that be k-point, cutoff, fine grid or cell size). I want to know if there are keywords/flags within SIESTA for single point energy calculation? Regards. -- Hongyi Zhao hongyi.z...@gmail.com Institute of Semiconductors, Chinese Academy of Sciences GnuPG DSA: 0xD108493
Re: Re: [SIESTA-L] about basis-set superposition error (BSSE)
Should I set a ghost atom between the molecule and the nanotube ? No, this is what you must do: You've already got the relaxed structure of the nanowire + adsorbed molecule system, right? Let's call this system A and its total energy is E-A You need 6 more calculations to complete the puzzle this is pretty much what you should do: 1 calculation with the same k-point grid, mesh grid, and cell size as system A, but only for the nanotube, fully relaxed to a similar tolerance as system A. Find its total energy. Call this E-NT. 1 calculation with the same k-point grid, mesh grid, and cell size as system A, but only for the adsorbed molecule, fully relaxed to a similar tolerance as system A. Find its total energy. Call this E-AD 1 single-point calculation (0 CG steps) of the nanowire in the relaxed geometry of system A (use the final .XV file or .xyz file or whatever you want but remove the adsorbed molecule). Find its total energy. Call this E-noghost-NT 1 single-point calculation (0 CG steps) of the adsorbed molecule in the relaxed geometry of system A (use the final .XV file or .xyz file or whatever you want but remove the adsorbed molecule). Find its total energy. Call this E-noghost-AD 1 single-point calculation (0 CG steps) of the nanowire in the relaxed geometry of system A, except replace any adsorbate chemical species with ghost atoms. If you have species in the adsorbate that are present in the nanowire, for example, a simulation of H2O on a hydrogen-passivated SiNW (or C in methane on a CNT), then copy the H.psf file to a new file like H_ghost.psf and then create a new chemical species H_ghost with atomic number -1 and a different atomic species index. Replace any index of the H in the adsorbate with the new index, and introduce a new basis set for H_ghost that is identical to the one you used for H (except for the label H_ghost). Find its total energy. Call this E-ghost-NT 1 single-point calculation (0 CG steps) of the adsorbed molecule in the relaxed geometry of system A, except replace any nanowire chemical species with ghost atoms and follow the procedure above if you have any species in the adsorbate that are also present in the nanowire. Find its total energy. Call this E-ghost-AD The counterpoise correction is: (E-ghost-AD - E-noghost-AD + E-ghost-NT - E-noghost-NT) call this E-CC. It should be a fraction of an eV, have a negative sign and very sensitive to the adsorption site geometry. The BSSE should _reduce_ the adsorption energy... and the energy of adsorption is: E-NT + E-AD - E-A + E-CC And that is how you do the counterpoise correction with SIESTA. Best, Abraham Hmiel Katherine Belz Groves Graduate Fellow in Nanoscience, Xue Group The College of Nanoscale Science and Engineering at SUNY Albany Clouds are not spheres, mountains are not cones, coastlines are not circles, and bark is not smooth, nor does lightning travel in a straight line. - Benoit Mandelbrot On Wed, Mar 30, 2011 at 12:09 AM, yf liu liuyf1...@gmail.com wrote: Dear Herbert Fruchtl: thank you very much for your reply. I have read the manual carefully, but find little message about the ghost atoms. the new question is: How can I use the ghost atom to correct the binding energy etc. ? For example, I want correct the calculation about the molecule adsorption on the nanotube. Should I set a ghost atom between the molecule and the nanotube ? looking forward your reply. 2011/3/20 Wei Hu gyrw4...@mail.ustc.edu.cn I am sorry, I am a freshman about the siesta. The input is listed in the following. My calculations about the binding energy do not meet the experimental results,so,I have to check the ghost atoms calculations.Now,The impact is acceptable. Another problem is how to get the chemical potential or total energy of free C or N atom. Does it need to calculate the the ghost atoms affected by the supercell? SystemName C62N_ghost SystemLabel C62N_ghost NumberOfSpecies 3 %block ChemicalSpeciesLabel 1 6 C 2 7 N 3 -6 Cg %endblock ChemicalSpeciesLabel %block PS.lmax C 1 %endblock PS.lmax %include coord.fdf PAO.BasisSize DZP #SolutionMethod dm_on SolutionMethod diagon MeshCutoff 200.000 Ry #MD.TypeOfRun Broyden #MD.TypeOfRun CG #MD.NumCGsteps 500 WriteForces MD.MaxForceTol 0.04 eV/Ang #DM.UseSaveDM T MaxSCFIterations 100 DM.MixingWeight 0.1 DM.NumberPulay 6 #DM.MixingWeight 0.25 #DM.NumberPulay 0 SpinPolarized .true. #FixSpin .true. #TotalSpin 2.0 WriteMullikenPop 1 NetCharge -1.0 %block kgrid_Monkhorst_Pack 2 0 0 0.0 0 2 0 0.0 0 0 2 0.0 %endblock kgrid_Monkhorst_Pack -Original E-mail- From: Herbert Fruchtl herbert.fruc...@st-andrews.ac.uk Sent Time: 2011-3-18 20:06:46 To: siesta-l@uam.es Cc: Subject: Re: [SIESTA-L] about basis-set superposition error (BSSE) From the energy part of the output alone we can't tell if the input
Re: Re: [SIESTA-L] about basis-set superposition error (BSSE)
An edit to my post: the line. 1 single-point calculation (0 CG steps) of the adsorbed molecule in the relaxed geometry of system A (use the final .XV file or .xyz file or whatever you want but remove the adsorbed molecule). Find its total energy. Call this E-noghost-AD should actually read 1 single-point calculation (0 CG steps) of the adsorbed molecule in the relaxed geometry of system A (use the final .XV file or .xyz file or whatever you want but remove the NANOTUBE). Find its total energy. Call this E-noghost-AD By the way, BSSE corrections should ALWAYS be performed in SIESTA because it uses an incomplete basis set (atomic orbitals), not just when your adsorption energy calculations are different than experiment or you want to lower your adsorption energy to make your calculations look nice for a paper. If you are still seeing vast differences between your adsorption energy calculations and experiments, it may be a good idea to look into different functionals like the van-der-Waals functionals implemented in the SIESTA-trunk version. Or, additionally, you can try to use diffuse basis functions (s-like) to help complete the basis set in the region corresponding to adsorption. On Wed, Mar 30, 2011 at 12:50 AM, Abraham Hmiel abehm...@gmail.com wrote: Should I set a ghost atom between the molecule and the nanotube ? No, this is what you must do: You've already got the relaxed structure of the nanowire + adsorbed molecule system, right? Let's call this system A and its total energy is E-A You need 6 more calculations to complete the puzzle this is pretty much what you should do: 1 calculation with the same k-point grid, mesh grid, and cell size as system A, but only for the nanotube, fully relaxed to a similar tolerance as system A. Find its total energy. Call this E-NT. 1 calculation with the same k-point grid, mesh grid, and cell size as system A, but only for the adsorbed molecule, fully relaxed to a similar tolerance as system A. Find its total energy. Call this E-AD 1 single-point calculation (0 CG steps) of the nanowire in the relaxed geometry of system A (use the final .XV file or .xyz file or whatever you want but remove the adsorbed molecule). Find its total energy. Call this E-noghost-NT 1 single-point calculation (0 CG steps) of the adsorbed molecule in the relaxed geometry of system A (use the final .XV file or .xyz file or whatever you want but remove the adsorbed molecule). Find its total energy. Call this E-noghost-AD 1 single-point calculation (0 CG steps) of the nanowire in the relaxed geometry of system A, except replace any adsorbate chemical species with ghost atoms. If you have species in the adsorbate that are present in the nanowire, for example, a simulation of H2O on a hydrogen-passivated SiNW (or C in methane on a CNT), then copy the H.psf file to a new file like H_ghost.psf and then create a new chemical species H_ghost with atomic number -1 and a different atomic species index. Replace any index of the H in the adsorbate with the new index, and introduce a new basis set for H_ghost that is identical to the one you used for H (except for the label H_ghost). Find its total energy. Call this E-ghost-NT 1 single-point calculation (0 CG steps) of the adsorbed molecule in the relaxed geometry of system A, except replace any nanowire chemical species with ghost atoms and follow the procedure above if you have any species in the adsorbate that are also present in the nanowire. Find its total energy. Call this E-ghost-AD The counterpoise correction is: (E-ghost-AD - E-noghost-AD + E-ghost-NT - E-noghost-NT) call this E-CC. It should be a fraction of an eV, have a negative sign and very sensitive to the adsorption site geometry. The BSSE should _reduce_ the adsorption energy... and the energy of adsorption is: E-NT + E-AD - E-A + E-CC And that is how you do the counterpoise correction with SIESTA. Best, Abraham Hmiel Katherine Belz Groves Graduate Fellow in Nanoscience, Xue Group The College of Nanoscale Science and Engineering at SUNY Albany Clouds are not spheres, mountains are not cones, coastlines are not circles, and bark is not smooth, nor does lightning travel in a straight line. - Benoit Mandelbrot On Wed, Mar 30, 2011 at 12:09 AM, yf liu liuyf1...@gmail.com wrote: Dear Herbert Fruchtl: thank you very much for your reply. I have read the manual carefully, but find little message about the ghost atoms. the new question is: How can I use the ghost atom to correct the binding energy etc. ? For example, I want correct the calculation about the molecule adsorption on the nanotube. Should I set a ghost atom between the molecule and the nanotube ? looking forward your reply. 2011/3/20 Wei Hu gyrw4...@mail.ustc.edu.cn I am sorry, I am a freshman about the siesta. The input is listed in the following. My calculations about the binding energy do not meet the experimental results,so,I
Re: [SIESTA-L] Strange halting behavior after DM initialization due to mesh?
This problem has been solved. The offense is a stack size parameter in my user setting that was too low. The command: ulimit -s unlimited should be added to your .bashrc settings if you are having similar problems, or increase the stack size to something high enough. It appears that large-scale DFT calculations may frequently exceed default user memory limits and is not discussed in the manual. Thanks and cheers for the responses, Abe
Re: [SIESTA-L] ifort+mpich2 compiling error
Hi Reza, From your errors in compiling the FoX library, it seems that you might be using v11 of ifort, which has problems. If you haven't seen this yet, follow these instructions to remove the FoX libraries from the compilations: http://www.icmab.es/siesta/SIESTA/News/IntelV11 The only thing this will affect are xml output, not the SIESTA method. Or, you can use less aggressive optimization options for the FoX library and still compile it. Instructions for that are on that link, too. The only other piece of advice I'd tell you to try is to roll back the intel compiler to v10, or use gfortran4.4 openmpi. Best, Abe Hmiel
Re: [SIESTA-L] Blocks about geometry of graphene
Clersson, Please do not be impatient. Followers of this list are busy and you sent us two nearly identical messages in two hours. With regards to your fdf file, I saw some errors. First of all I don't think your Atomic coordinates are right. What you should do if you feel unsure about this is set up a for loop in the programming language of your choice and print out the atomic coordinates, and then use Xmol or avogadro or something to visualize them. If your graphene lattice vectors are in the first and fourth quadrants making a 30 degree angle with the x-axis as in your file, your atomic coordinates block should be a basis of two carbon atoms lying on a line parallel to the x-axis (again, plot it out if you have to). This is not what you have. You need to make sure you're keeping track of units, too. The units in your coordinates block are in Angstrom. That means that two carbon atoms in your file are separated by sqrt(2*1/3^2) angstroms, less than 1/2 an angstrom. I plotted a sketch of what your system is and attached it. It is highly suspect, I would recommend you fix the coordinates and lattice vectors. It seems that you included an extra factor of the lattice parameter in the block LatticeVectors to me, but other than that I won't tell you the right answer. Besides that, you need to specify some lattice vector in the c-plane. You can't just use zero. Use at least 12 angstroms so you have no overlap. Your kgrid mesh looks fine. The bandlines block is also wrong, the number at the beginning of the line should be the index of that point on the x-axis of your band plot, so instead of 1 50 50 100 you should have something like 1 51 101 151 if you want 50 points per high symmetry direction. MD.NumCGSteps = 0 is what you do for a single-point energy calculation, but you need to relax the geometry of your system before you can get anything meaningful out of it. And finally, why are you including all the transport flags in the relaxation? You haven't even performed the relaxation yet, so save all the transiesta stuff (and maybe the PDOS and LDOS as well) until after you've attained the electronic ground state. You might even want to use MD.Variablecell to relax the lattice vectors along with the coordinates and you might need to tune the mixingweight and numberpulay to hasten convergence. And please do the tutorial exercises and try to search the mailing list archives next time before you ask the community twice for anything. DFT is not an easy field to get into and you need to understand what you're doing before you just jump in and calculate the band structure of graphene. Which, by the way, is not an easy task once you've got everything right judging from the activity on this list for such a pedagogical example, so you'll probably need to play around with a lot more parameters. This is the matlab script I whipped up in a couple minutes to check your geometry. I essentially ignored the c-lattice parameter and left it as all zeroes. latt = 2.42; imax=3; jmax=3; coords = zeros(imax*jmax*2,3); basis1 = [0.0 0.0 0.0] basis2 = [0. 0. 0.0]; latt1 = [2.13 1.2297]; latt2 = [2.13 -1.2297]; index=1; for i=0:imax for j=0:jmax coords(index,1) = basis1(1)+i*latt1(1)*latt+j*latt2(1)*latt; coords(index+1,1) = basis2(1)+i*latt1(1)*latt+j*latt2(1)*latt; coords(index,2) = basis1(2)+i*latt1(2)*latt+j*latt2(2)*latt; coords(index+1,2) = basis2(2)+i*latt1(2)*latt+j*latt2(2)*latt; index=index+2; end end %to plot in an xyz file, you have to add the character 'C' to the beginning %of each line with atomic data and then print the total number of atoms as %the first line, then skip a line (or use for comment), then begin with %coordinates on the third line. This must be in Angstrom. Please print out a copy of the latest version of the SIESTA manual for your reference and do and read the tutorial exercises. It makes a world of difference. If you still need help with convergence and attaining a proper band structure of graphene, this topic has been beaten 9/10s to death on the SIESTA-L list already so please check there first. I hope this helps point you in the right direction for your research and future SIESTA exploits. Best of luck to you. Abraham Hmiel Ph.D. student at CNSE, SUNY Albany On Mon, Oct 25, 2010 at 1:35 PM, Clersson Nascimento clerisson...@gmail.com wrote: dear siesta users, I'm interested in to calculate the band structure of graphene but i have some doubts about how to construct the blocks that refer to geometry structure. I have the following block: %block AtomicCoordinatesAndAtomicSpecies 0. 0. 0. 1 0. 0. 0. 1 %endblock AtomicCoordinatesAndAtomicSpecies so, i made the following blocks %block LatticeVectors 2.13 1.2297560733739 0.00 2.13-1.2297560733739 0.00 0.00 0.000.00 %endblock LatticeVectors %block
Re: [SIESTA-L] Blocks about geometry of graphene
Ok, no problem, glad I could help out and sorry for being a little abrasive if I came off that way. No harm was meant. For some good texts on electronic structure, I found Richard Martin's book very helpful, as well as Jorge Kohanoff's book, Electronic Structure Calculations for Solids and Molecules. You should read the original SIESTA paper to get a handle on their method and the things that go into the computation, and of course, be very astute about what you're putting into your files. It really helps to be able to quickly generate geometry files and then display them with a piece of software or export them into a format that can be read by SIESTA or other programs. I end up using spreadsheets and emacs a lot. It seems from the file you're interested in doing some transport calculations. I would definitely get up to speed on the proper details as to how to obtain electronic structure data from the geometry relaxation first and how this relates to the physics in your systems before your foray into transport with this software. Building good pseudopotentials and basis sets and testing them are also not really discussed in the SIESTA manual either, and they are learned skills that come about with practice so for this it is very important to know the right terminology and what all these little parameters mean so you don't use oodles of supercomputer time crunching nonphysical things. This community and list is very helpful but always remember to check the archives first and be creative in your search terms, and double-and-triple-check your fdf files. Best of luck to you on your journey, Abraham On Mon, Oct 25, 2010 at 4:24 PM, Clersson Nascimento clerisson...@gmail.com wrote: Dear Abrahan, First, my apologies for send two e-mails. That was my first e-mail to mail list and i was not sure the e-mail had been sent. Actually, I thought I should have gotten the message(since I was also a member of the list), for this I sent it twice. With regards your answer, I am very grateful for your patient explanation about my mistakes. These are my first steps in the field of eletronic structure. I'm still looking where to find information in this turbulent beginning of my research. So your answer was providential. Thaks again, Best regards. Clerisson Nascimento
