Re: [SIESTA-L] Is it appropriate to use a same basis set for a junction when it is stretched?
Look for information on Basis Set Superposition Error (BSSE). SIESTA uses atom-centred basis sets, so BSSE does affect calculations. Basically you get an unphysical attractive force that favours shorter distances. Herbert On 16/01/13 05:29, Guangping Zhang wrote: Dear siesta users: I now use siesta to investigate the elongation of a molecular junction. When the molecular junction is stretched, the number of atoms is unchanged, also the basis set is the same. My question is : is there any problem to use the same basis set during the elongation of the moleuclar junction? Can this affect the energy? Can the energies be compared between different stretch? Any advice is welcome. Guangping 2013-01-16 Guangping Zhang -- Herbert Fruchtl Senior Scientific Computing Officer School of Chemistry, School of Mathematics and Statistics University of St Andrews -- The University of St Andrews is a charity registered in Scotland: No SC013532
Re: [SIESTA-L] why my running did stop.
Your message is on the list now!
Camps
On Wednesday, January 16, 2013, Mostafa Shabani wrote:
hi miss talebi.
how can i ask my question like you from siesta mailing list
i have problem with my fdf file.i register to mailing list but i can not
see my questions and answer to them
please help mr thanks.
On Tue, Jan 15, 2013 at 7:55 PM, Abraham Hmiel
abehm...@gmail.comjavascript:_e({}, 'cvml', 'abehm...@gmail.com');
wrote:
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.comjavascript:_e({}, 'cvml', 'talebi_z2...@yahoo.com');
wrote:
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
--
[]'s,
@mps
Re: Fw: [SIESTA-L] why my running did stop.
hi miss talebi. how can i ask my question like you from siesta mailing list i have problem with my fdf file.i register to mailing list but i can not see my questions and answer to them please help mr thanks. On Tue, Jan 15, 2013 at 7:55 PM, Abraham Hmiel abehm...@gmail.com wrote: 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
[SIESTA-L] Pseudopotential reading error
Hello, I am experiencing an error, I am not able to determine more closely than: The program aborts while using the SPLIT program for the pseudopotential verification of Nitrogen while trying to do some crystal structure optimisations. The main program parses Abort, and the last lines of output are as follows: === /basis_specs atom: Called for N_gga (Z = 7) read_vps: Pseudopotential generation method: read_vps: ATM3 Troullier-Martins Total valence charge:5.0 read_vps: Pseudopotential includes a core correction: read_vps: Pseudo-core for xc-correction xc_check: Exchange-correlation functional: xc_check: GGA Perdew, Burke Ernzerhof 1996 V l=0 = -2*Zval/r beyond r= 1.4606 V l=1 = -2*Zval/r beyond r= 1.4606 V l=2 = -2*Zval/r beyond r= 1.4606 V l=3 = -2*Zval/r beyond r= 1.4606 All V_l potentials equal beyond r= 1.4606 This should be close to max(r_c) in ps generation All pots = -2*Zval/r beyond r= 1.4606 VLOCAL1: 99.0% of the norm of Vloc inside 20.347 Ry VLOCAL1: 99.9% of the norm of Vloc inside 46.372 Ry atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge1.76189 atom: Maximum radius for r*vlocal+2*Zval:1.53550 GHOST: No ghost state for L = 0 GHOST: No ghost state for L = 1 GHOST: No ghost state for L = 2 GHOST: No ghost state for L = 3 KBgen: Kleinman-Bylander projectors: l= 0 rc= 1.634559 el= -1.363963 Ekb= 5.296955 kbcos= 0.335621 l= 1 rc= 1.614250 el= -0.521451 Ekb= -5.259161 kbcos= -0.433408 l= 2 rc= 1.718383 el= 0.001991 Ekb= -1.271464 kbcos= -0.007566 l= 3 rc= 1.761893 el= 0.003093 Ekb= -0.494769 kbcos= -0.001015 KBgen: Total number of Kleinman-Bylander projectors: 16 atom: - atom: SANKEY-TYPE ORBITALS: atom: Selected multiple-zeta basis: split SPLIT: Orbitals with angular momentum L= 0 SPLIT: Basis orbitals for state 2s SPLIT: PAO cut-off radius determined from an SPLIT: energy shift= 0.01 Ry izeta = 1 lambda =1.00 rc =3.970931 energy = -1.354621 kinetic =1.185116 potential(screened) = -2.539737 potential(ionic) = -8.071102 izeta = 2 rmatch =2.905100 splitnorm =0.15 energy = -1.158092 It stops at the one line or the other, but always in that region. I have tried the LDA(ca) and the GGA(PBE) pseudos from the website with their corresponding calculations, but this gives always the same result. I would be very happy, if you could give me a hint how to work around this problem. Thanks a lot Joachim -- Joachim Breternitz PhD student School of Chemistry University of Glasgow joac...@chem.gla.ac.uk
Re: Re: [SIESTA-L] Is it appropriate to use a same basis set for a junction when it is stretched?
Dear Herbert, Thanks for your suggestion. As I known, the BSSE is always used in the investigation of adsorption of a molecule on a surface or the interaction of two or more subsystems. Otherwise, I may misunderstand your meaning. If so, can you give some more details? In my case, the system keeps the same, only for each configuration, the atomic coordinates are changed by fraction of Angstrom. Is BSEE also need to be carried on at this time? If so, when we do an geometry optimization in SIESTA, the BSSE should be taken care of and I think it is not necessary to do so in the geometry optimization. I intend to mean that in the elongation of the molecular junction, the center of each basis orbital is changed, is there some issues to take care of for this. Thanks for your suggestion. Best Guangping 2013-01-17 Guangping Zhang 发件人：Herbert Fruchtl 发送时间：2013-01-16 17:37 主题：Re: [SIESTA-L] Is it appropriate to use a same basis set for a junction when it is stretched? 收件人：siesta-lsiesta-l@uam.es 抄送： Look for information on Basis Set Superposition Error (BSSE). SIESTA uses atom-centred basis sets, so BSSE does affect calculations. Basically you get an unphysical attractive force that favours shorter distances. Herbert On 16/01/13 05:29, Guangping Zhang wrote: Dear siesta users: I now use siesta to investigate the elongation of a molecular junction. When the molecular junction is stretched, the number of atoms is unchanged, also the basis set is the same. My question is : is there any problem to use the same basis set during the elongation of the moleuclar junction? Can this affect the energy? Can the energies be compared between different stretch? Any advice is welcome. Guangping 2013-01-16 Guangping Zhang -- Herbert Fruchtl Senior Scientific Computing Officer School of Chemistry, School of Mathematics and Statistics University of St Andrews -- The University of St Andrews is a charity registered in Scotland: No SC013532
