Dear Matias,
That's a very good point. To address it, I just looked at this paper: Guillermo Román-Pérez and José M. Soler Phys. Rev. Lett. 103, 096102 – Published 27 August 2009 and saw they benchmarked carbon nanotubes. I suggest to look at papers by Cooper, Soler, and other teams developing vdw pseudos, and see if they benchmarked water. You can also look at other quantum chemistry works beyond the DFT level and see what they report for water in terms of binding energy and bond lengths, to say something. I believe Fernandez-Serra has worked with water using vdw pseudos as well, so have a look at some of her papers too. The last leg of this process thus involves some literature search, but I am glad to read that your pseudos are ghost-free at the moment. As indicated before, it would be great if you share your results and benchmarks with us. Cheers! -Salvador ________________________________ From: [email protected] <[email protected]> on behalf of Matías Soto C. <[email protected]> Sent: Tuesday, October 6, 2015 1:02 PM To: [email protected] Subject: Re: [SIESTA-L] Question about pseudopotential vdw for Hydrogen atom Thanks for the advice Salvador. It takes a little bit to change the radius and test the new pseudo for no ghost states and then test it for water molecule bond lengths and bond angle. But it compares well to experimental bond lengths and bond angle. However, I have a question: how do you ensure eigenvalues and spin polarization look good? I can look at the eigenvalues and compare to those from GGA and LDA, but other than that I don't know if there's a more straightforward way of comparison. Thanks again, -- Matias Soto Matias Soto C. Ph.D. Program MSNE Department Rice University On Thu, Oct 1, 2015 at 10:52 AM, Salvador Barraza-Lopez <[email protected]<mailto:[email protected]>> wrote: Indeed, I have encountered similar phenomena: For instance, working with the BH vdw exchange-correlation potential, I documented ghost states for Te when taking the INP from the webpage. I feel that the expectation that plugging a new xc flag on the INP file should not be expected to hold always (and why should it?)... So you have to put some time to get it done. H should not be problematic, and that may be the reason you have not received a file yet... I may say, increase/decrease the radius for the second component (down the INP file) by about 10% and get a pseudo. Plug that pseudo back into your calculation and see if it shows no ghosts. If not, just ensure bond lengths and eigenvalues, and maybe spin polarization look good. Then you should be good to go. There is some work involved, but there are things to learn as well. As I said, it may not be that difficult. Could put you back one day, but it will be worth doing it. Again, it may be that someone in the list could send you the file you need. But while you wait, it may be worth giving it a go yourself. Or in other words, why wait if you can do it. You could then share your own INP, so that others know what rs to use. Cheers! -Salvador ________________________________ From: [email protected]<mailto:[email protected]> <[email protected]<mailto:[email protected]>> on behalf of Matías Soto C. <[email protected]<mailto:[email protected]>> Sent: Thursday, October 1, 2015 10:10 AM To: [email protected]<mailto:[email protected]> Subject: Re: [SIESTA-L] Question about pseudopotential vdw for Hydrogen atom Thanks for your reply Salvador. The pseudo was taken from the siesta database which uses the cutoff radii shown. Such pseudopotential does not show any ghost states when running under LDA or GGA. I've seen other messages in this listserve where people had similar problems but the solution is not shown. Hopefully I can follow your advice and develop my own pseudpotential for Hydrogen in van der waals DFT. However, I was hoping that someone had already found a solution to the same problem and was willing to share the pseudopotential. Thank, -- Matias Matias Soto C. Ph.D. Program MSNE Department Rice University On Wed, Sep 30, 2015 at 1:10 PM, Salvador Barraza-Lopez <[email protected]<mailto:[email protected]>> wrote: Dear Matias, Let me provide the following advice. The channel showing ghosts is the p-one (L=1), so it is not that relevant for the problem, L=0 is not giving you ghosts. So I suggest that you vary the radii for the L=1 channel on the INP file. I could not tell you how to change it, since one has to try by hand. Then, you would want to run a calculation with these pseudos on known environments (water molecule, and so on), and see if you match all-electron results (bond distances, eigenvalues). That way you would know your pseudo is good, or you could improve if it is not. Of course, there may be somebody who could provide a working one for you; I've not worked with that element and that pseudo. But even in that case, you may want to ask the person who is giving it to you, or you may want to look at it yourself, as of how the pseudo is performing. I hope these comments are helpful. Best regards, -Salvador ________________________________________ From: [email protected]<mailto:[email protected]> <[email protected]<mailto:[email protected]>> on behalf of Matias Soto <[email protected]<mailto:[email protected]>> Sent: Wednesday, September 30, 2015 12:59 PM To: [email protected]<mailto:[email protected]> Subject: [SIESTA-L] Question about pseudopotential vdw for Hydrogen atom Hello SIESTA users, I know this question has been asked before but I couldn't find the message where the solution has been shown. I need to generate psf file for hydrogen. I changed from ca to vw in inp file when generating psf file in ATOM program. When I run calculation for single hydrogen atom using siesta-trunk-462 I get messages about ghost states: atom: Called for H (Z = 1) read_vps: Pseudopotential generation method: read_vps: ATM3.3.2 Troullier-Martins Total valence charge: 1.00000 xc_check: Exchange-correlation functional: xc_check: VDW Dion-Rydberg-Schroeder-Langreth-Lundqvist V l=0 = -2*Zval/r beyond r= 1.3816 V l=1 = -2*Zval/r beyond r= 1.3816 V l=2 = -2*Zval/r beyond r= 1.3644 All V_l potentials equal beyond r= 1.2977 This should be close to max(r_c) in ps generation All pots = -2*Zval/r beyond r= 1.3816 VLOCAL1: 99.0% of the norm of Vloc inside 25.776 Ry VLOCAL1: 99.9% of the norm of Vloc inside 58.745 Ry atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 1.52711 atom: Maximum radius for r*vlocal+2*Zval: 1.28155 GHOST: No ghost state for L = 0 GHOST: WARNING: Ghost state for L = 1 GHOST: No ghost state for L = 2 KBgen: WARNING: Ghost states have been detected KBgen: WARNING: Some parameter should be changed in the KBgen: WARNING: pseudopotential generation procedure. Stopping Program from Node: 0 I am using: XC.functional VDW XC.authors DRSLL If someone could please provide working parameters for hydrogen pseudopotential for van der waals exchange-correlation. Thank you! Matias Soto C. Ph.D. Program MSNE Department Rice University
