Thanks to all your help. I start to understand the problem. I changed the lattice vectors as follows
%block LatticeVectors 1.5 0.5 0 0 1.5 0.5 0.5 0 1.5 %endblock LatticeVectors The program is now running. But i'm getting a very low Fermi Energy (-9.875060 eV) compared to bulk Au Fermi Energy (-5.5eV). Hence i tried to do a supercell block of 2 0 0 0 1 0 0 0 1 When i observe the output, the new unit cell created next to the input cell is pushed above by 0.5 Lattice constant. I think this causes a mismatch of B.C resulting in an erraneous Fermi Energy. I also tried lattice vectors %block LatticeVectors 1. 0. 0 0 1. 0. 0. 0 1. %endblock LatticeVectors This is pushing the newly formed FCC closer to the input cell. *The solution i require is the correct lattice vectors for a FCC unit cell which would provide me the correct periodic boundary conditions.* Any help on this would be greatly appreciated Once again thank you very much to everyone for taking time off your schedule to help me. Regards Ram On Thu, Apr 14, 2011 at 7:21 PM, Prathibha Ramaprasad <prama...@asu.edu>wrote: > Ram, > > I am not sure your approach is correct. Or maybe its not clear to me. > > If you have already done bulk calibration for Au and just want to simulate > the 14 atoms in your fdf, then shouldn't you be running it as a molecule > instead? Enclosed in a vaccum box? In this case your lattice vectors should > reflect this. > > If Au has FCC symmetry then a Au unit cell has 4 atoms only (6 face*1/2 + > 8corners * 1/8 = 4) or has 1 atom in its primitive cell as Dangxin mentioned > because u can replicate it perfectly with the symmetry operations. So, if > you are infact doing bulk simulation, then your 14 atom input is definitely > wrong. As I first mentioned you clearly have extraneous atoms which are > overlapping because siesta does periodic calculation. > > Prat > > > On Thu, Apr 14, 2011 at 3:20 PM, janakiraman balachandran < > jana...@umich.edu> wrote: > >> Thanks Pratiba. I'm sorry but I dont understand your question regarding >> CIF. I gave the input of Au coordinates manually. My interest here is in the >> Hamiltonian and not in the energy or E-k plot. So i need a bigger system to >> solve. >> >> >> >> On Thu, Apr 14, 2011 at 5:41 PM, Prathibha Ramaprasad >> <prama...@asu.edu>wrote: >> >>> Do you have a CIF or any other structure file for Au? >>> >>> Also if Au does not have degenerate symmetries, just providing 2-atom >>> primitive cell should work too. >>> >>> Prat >>> >>> On Thu, Apr 14, 2011 at 2:34 PM, janakiraman balachandran < >>> jana...@umich.edu> wrote: >>> >>>> Dear Dangxin >>>> >>>> Thank you for the reply. Why do you say that i need to give only one >>>> atom? How would the program know the difference between FCC and BCC if i >>>> give only one atom? >>>> >>>> I would prefer to do a bulk calculation with 14 atom FCC since i need >>>> that output somewhere else. >>>> >>>> On Thu, Apr 14, 2011 at 5:29 PM, Dangxin Wu <dangxi...@yahoo.com>wrote: >>>> >>>>> Are you doing a bulk calculation? There should be only one atom in one >>>>> unit cell of FCC according to your input cell parameters (at [0, 0, 0]). >>>>> Looking at the warnings in your output, many of the atoms are repeated >>>>> (they >>>>> are exactly the same atom). >>>>> >>>>> Dangxin >>>>> >>>>> ------------------------------ >>>>> *From:* janakiraman balachandran <jana...@umich.edu> >>>>> >>>>> *To:* siesta-l@uam.es >>>>> *Cc:* Prathibha Ramaprasad <prama...@asu.edu> >>>>> *Sent:* Thu, April 14, 2011 3:19:39 PM >>>>> *Subject:* Re: [SIESTA-L] Au unit cell not converging >>>>> >>>>> Hi >>>>> Thanks for the reply. I use one unit cell of FCC. It has 14 Au atoms. >>>>> Infact i visualized them using molden and computed the distance. I dont >>>>> see >>>>> anything wrong with the input >>>>> >>>>> Ram >>>>> >>>>> On Thu, Apr 14, 2011 at 5:07 PM, Prathibha Ramaprasad < >>>>> prama...@asu.edu> wrote: >>>>> >>>>>> Ram, >>>>>> >>>>>> Most likely you have included more atoms than there should be in the >>>>>> unit cell, for example the ones belonging to an adjacent unit cell (as >>>>>> most >>>>>> crystal viewing tools do). Carefully examine the atoms at the border of >>>>>> your >>>>>> unit cell and remove the extra ones. As siesta uses periodic cells, these >>>>>> atoms overlap and give you the error you have mentioned. >>>>>> >>>>>> Prat >>>>>> >>>>>> >>>>>> On Thu, Apr 14, 2011 at 1:51 PM, janakiraman balachandran < >>>>>> jana...@umich.edu> wrote: >>>>>> >>>>>>> Hi >>>>>>> I'm trying to run a Au unit cell in siesta. However i'm getting a >>>>>>> warning stating the atoms on opposite surfaces are too close (distance >>>>>>> 0). >>>>>>> Subsequently i get an error that says the leading minor is not positive >>>>>>> definite and hence diagonalization cannot be performed. I'm very sure >>>>>>> that i >>>>>>> have used the correct Lattice distance. I'm not sure what causes the >>>>>>> problem. I have attached the fdf file. I have commented the * >>>>>>> kgrid_Monkhorst_Pack* and* BandLines*. But even with them >>>>>>> uncommented, i get the same error >>>>>>> >>>>>>> I need to make it work as soon as possible. Hence any help to sort >>>>>>> this problem would be greatly appreciated >>>>>>> >>>>>>> Thank you >>>>>>> >>>>>>> Regards >>>>>>> Ram >>>>>>> >>>>>> >>>>>> >>>>> >>>> >>> >> >
