Re: [SIESTA-L] SCF convergence issue
Have a look at the distances your nuclei are moving per CG step. Try reducing your MD.MaxCGDispl if many of them are moving that far. It'll increase the number of CG steps you'll need, but it might stabilise your system. Edan. Cherry Y. Yates wrote: snipped
Re: [SIESTA-L] Pseudopotential, can not start(VPSOUT)
I sometimes get this error when I input bad radii (usually when they're way too short). If you show us your input file, we'll have a better idea of whether its the program or your input. vikas thakur wrote: Dear all, I m a new user to siesta2.0.1. I try to find the pseudopotential for O . I follow the process as given in mannual. but there is message as follow [EMAIL PROTECTED] O]# sh ../pg.sh O.tm2.inp ../pg.sh: line 33: 2838 segmentation fault $ prog cp: cannot stat 'VPSOUT': No such file or directory cp: cannot stat 'VPSFMT': No such file or directory ==Output data in directory O.tm2 ==Pseudopotential in O.tm2.vsp and O.tm2.psf There is a directory created O.tm2 but there is no file or directory named O.tm2.vsp and O.tm2.psf. What is this problem and how can i resolve it. thank you all. With best wishes Vikas Thakur [EMAIL PROTECTED] Jiwaji University, Gwalior M.P. India. Take the Internet to Go: Yahoo!Go puts the Internet in your pocket: mail, news, photos more.
Re: [SIESTA-L] atom Program and Pseudopotential error
You have to be careful with whitespace in the input file. The following works for me: pg Li TM2 Pseudopotencial GS ref tm2 Li ca 0.0 1 2 2 0 1.00 2 1 0.00 1.54 1.54 0.00 0.00 12345678901234567890123456789012345678901234567890 Ruler Also, as Bipul said, you'll probably get errors in an actual SIESTA calculation unless you add some more angular momenta: 1 4 2 0 1.00 2 1 0.00 3 2 0.00 4 3 0.00 Alternatively, you should be able to avoid that by adding a PS.lmax block to your .fdf file (the SIESTA user guide shows you how). Edan. Saswata Bhattacharya wrote: dear friends, i have got a typical problem for the last few months.whenever i go to run atom program for Li i use the following input given below--- pg Li TM2 Pseudopotencial GS ref tm2 Li ca 0.0 0.0 0.0 0.0 1 2 2 0 1.00 2 1 0.00 1.54 1.54 0 0 12345678901234567890123456789012345678901234567890 Ruler but each time i get the same output message given below--- cp: cannot stat `VPSOUT': No such file or directory cp: cannot stat `VPSFMT': No such file or directory i cant understand what is just happend and i shall be highly grateful if anybody tells me about the actual mistake i have done.. with regards, Saswata Heres a new way to find what you're looking for - Yahoo! Answers
Re: [SIESTA-L] Making siesta work with fractional electrons invalence orbitals
On Fri, 2008-06-06 at 13:59 -0600, M Bharat Kumar wrote: Hi Siesta users, I need help in making siesta work with fractional electrons in valence orbitals. I am attaching input for atom program and input output of siesta. I was not able to understand the warning messages in siesta output. Any help is appreciated and thanks in advance. Bharat I'm not sure what you mean by fractional electrons ... do you mean you want to set NetCharge in your system to some non-integer (which is totally allowed and I do it all the time), or some kind of excited charge-neutral state with a fraction of an electron excited? Anyway, I made a different pseudopotential and your input .fdf worked, so the problem is most likely in your pseudo definition. Here's what I tried: pe Gold tm2 4.0 n=Au c=pbr 0.0 0.0 0.0 0.0 0.0 0.0 124 60 1.00 0.00 61 0.00 0.00 52 10.00 0.00 53 0.00 0.00 2.00 2.50 1.00 2.00 1.00 1.40 #23456789012345678901234567890123456789012345678901234567890 I changed: * c=pbr (was c=pb, you probably want relativistic corrections enabled for gold). * Changed the population of the valence orbitals (you might not need to mess around with exciting the pseudopotential populations to get a decent excited state calculation, your mileage may vary and I've never calculated gold before, let alone in bizarre charge states). * Messed around with the r_c values. Your pseudofunctions were overshooting the all-electron charge density peaks. ATOM produces .gps files which you can feed into gnuplot to get .ps files with pretty graphs showing how well each L channel in your pseudo corresponds to their all-electron analogs. I picked new r_c values from these graphs. Any combination of these changes may be what you need to make your calculation work, so good luck with that. Edan.
Re: [SIESTA-L] grid2cube error
Javad, The code is converting your lattice vectors from Angstroms to Bohrs (watch out for this with things like nuclear positions too). I don't know what's going on with your recompiled grid2cube problem, but on the plus side you can ignore it and go back to the older build that gave you the right answer. Edan. Dear SIESTA users, Hello and good day! I am trying to get the isosurface of a nanotube usind grid2cube tool and LDOS. The problem is that I am getting wrong values for my unit-cell vectors like 75.58907511097422 0.000 0.000 0.000 56.69180633323067 0.000 0.000 0.000 37.24840648781031 while my unit-cell vectors are 40.000 0. 0. 0. 30.000 0. 0. 0. 19.7110 snipped
Re: [SIESTA-L] ./configure: Permission denied
In the absence of any other information and assuming your compiler is working fine, did you check that the configure file is executable? Edit: sorry for the accidental extra post. Edan. On 15/05/2009, at 10:18 AM, Jonas Baltrusaitis wrote: Hi, I am not sure why, but when I download, unpack siesta-2.0.2 cd into Src and try ./configure it gives me [r...@mr9540 Src]# ./configure -bash: ./configure: Permission denied [r...@mr9540 Src]# I am loged in as a root so now I am puzzled why is the permission denied. Does it have anything to do with the code itself? thanks Jonas
Re: [SIESTA-L] Severe Error
I'm guessing the problem lies in your AtomicCoordinatesAndAtomicSpecies block. Try removing the last two things in each line, i.e. instead of 58.594000 47.2540000.793000 3 N 1 use 58.594000 47.2540000.793000 3 Edan. On 30/05/2009, at 7:45 AM, Eric Perim wrote: snipped
