Re: [SIESTA-L] pseudopotential question
Dear all, As you know, there is a pseudopotential file database in this website. Are pseudopotential files in the database reasonable? As I tested a simple h2o calculation to compare H and O pseudopotential files in siesta with H and O pseudopotential files in the database, the Energy value is a quite different. As I checked those output files, the cutoff raidus is different from each other. Dear HeeSung Choi, it is usually useless to judge by the absolute value of total energy (not only in Siesta but in all-electron codes as well) What you should compare are physically meaningful differences. When testing a psedopotential you do it by looking at the difference values of total energy between different test configurations. In calculation of real systems this would be, say, binding energy, or energy differences between given magnetic configurations. I think such physical results produced by the (H,O) pseudopots from Siesta package and from the Abinit database will be very close. In any case it is always a user's responsibility to decide where these or that pseudos are reasonable (depending on, for which particular problem). Best regards Andrei Postnikov I put those Energy values from two output files. Plases let me know your opnions. Thank you. 1) h2o calculation with pseudopotential file from database siesta: Program's energy decomposition (eV): siesta: Eions = 674.103101 siesta: Ena =85.208373 siesta: Ekin= 340.284488 siesta: Enl = -100.636934 siesta: DEna=-3.485784 siesta: DUscf = 0.772125 siesta: DUext = 0.00 siesta: Exc = -113.071379 siesta: eta*DQ = 0.00 siesta: Emadel = 0.00 siesta: Ekinion = 0.00 siesta: Eharris = -465.035046 siesta: Etot= -465.032213 siesta: FreeEng = -465.032213 siesta: Final energy (eV): siesta: Kinetic = 340.284488 siesta: Hartree = 384.329642 siesta:Ext. field = 0.00 siesta: Exch.-corr. =-113.071379 siesta: Ion-electron = -1065.070924 siesta: Ion-ion = -11.504041 siesta: Ekinion = 0.00 siesta: Total =-465.032213 2) h2o calculation with pseudopotential file from siesta package siesta: Program's energy decomposition (eV): siesta: Eions = 815.854478 siesta: Ena = 175.154321 siesta: Ekin= 353.755904 siesta: Enl = -63.083659 siesta: DEna=-3.346061 siesta: DUscf = 0.755426 siesta: DUext = 0.00 siesta: Exc = -113.203337 siesta: eta*DQ = 0.00 siesta: Emadel = 0.00 siesta: Ekinion = 0.00 siesta: Eharris = -465.824667 siesta: Etot= -465.821884 siesta: FreeEng = -465.821884 siesta: Final energy (eV): siesta: Kinetic = 353.755904 siesta: Hartree = 385.159853 siesta:Ext. field = 0.00 siesta: Exch.-corr. =-113.203337 siesta: Ion-electron = -1080.056603 siesta: Ion-ion = -11.477701 siesta: Ekinion = 0.00 siesta: Total =-465.821884
[SIESTA-L] pseudopotential file in the website
Dear all, As you know, there is a pseudopotential file database in this website. Are pseudopotential files in the database reasonable? As I tested a simple h2o calculation to compare H and O pseudopotential files in siesta with H and O pseudopotential files in the database, the Energy value is a quite different. As I checked those output files, the cutoff raidus is different from each other. I put those Energy values from two output files. Plases let me know your opnions. Thank you. 1) h2o calculation with pseudopotential file from database siesta: Program's energy decomposition (eV): siesta: Eions = 674.103101 siesta: Ena =85.208373 siesta: Ekin= 340.284488 siesta: Enl = -100.636934 siesta: DEna=-3.485784 siesta: DUscf = 0.772125 siesta: DUext = 0.00 siesta: Exc = -113.071379 siesta: eta*DQ = 0.00 siesta: Emadel = 0.00 siesta: Ekinion = 0.00 siesta: Eharris = -465.035046 siesta: Etot= -465.032213 siesta: FreeEng = -465.032213 siesta: Final energy (eV): siesta: Kinetic = 340.284488 siesta: Hartree = 384.329642 siesta:Ext. field = 0.00 siesta: Exch.-corr. =-113.071379 siesta: Ion-electron = -1065.070924 siesta: Ion-ion = -11.504041 siesta: Ekinion = 0.00 siesta: Total =-465.032213 2) h2o calculation with pseudopotential file from database siesta: Program's energy decomposition (eV): siesta: Eions = 815.854478 siesta: Ena = 175.154321 siesta: Ekin= 353.755904 siesta: Enl = -63.083659 siesta: DEna=-3.346061 siesta: DUscf = 0.755426 siesta: DUext = 0.00 siesta: Exc = -113.203337 siesta: eta*DQ = 0.00 siesta: Emadel = 0.00 siesta: Ekinion = 0.00 siesta: Eharris = -465.824667 siesta: Etot= -465.821884 siesta: FreeEng = -465.821884 siesta: Final energy (eV): siesta: Kinetic = 353.755904 siesta: Hartree = 385.159853 siesta:Ext. field = 0.00 siesta: Exch.-corr. =-113.203337 siesta: Ion-electron = -1080.056603 siesta: Ion-ion = -11.477701 siesta: Ekinion = 0.00 siesta: Total =-465.821884 ==
[SIESTA-L] pseudopotential question
Dear all, As you know, there is a pseudopotential file database in this website. Are pseudopotential files in the database reasonable? As I tested a simple h2o calculation to compare H and O pseudopotential files in siesta with H and O pseudopotential files in the database, the Energy value is a quite different. As I checked those output files, the cutoff raidus is different from each other. I put those Energy values from two output files. Plases let me know your opnions. Thank you. 1) h2o calculation with pseudopotential file from database siesta: Program's energy decomposition (eV): siesta: Eions = 674.103101 siesta: Ena =85.208373 siesta: Ekin= 340.284488 siesta: Enl = -100.636934 siesta: DEna=-3.485784 siesta: DUscf = 0.772125 siesta: DUext = 0.00 siesta: Exc = -113.071379 siesta: eta*DQ = 0.00 siesta: Emadel = 0.00 siesta: Ekinion = 0.00 siesta: Eharris = -465.035046 siesta: Etot= -465.032213 siesta: FreeEng = -465.032213 siesta: Final energy (eV): siesta: Kinetic = 340.284488 siesta: Hartree = 384.329642 siesta:Ext. field = 0.00 siesta: Exch.-corr. =-113.071379 siesta: Ion-electron = -1065.070924 siesta: Ion-ion = -11.504041 siesta: Ekinion = 0.00 siesta: Total =-465.032213 2) h2o calculation with pseudopotential file from siesta package siesta: Program's energy decomposition (eV): siesta: Eions = 815.854478 siesta: Ena = 175.154321 siesta: Ekin= 353.755904 siesta: Enl = -63.083659 siesta: DEna=-3.346061 siesta: DUscf = 0.755426 siesta: DUext = 0.00 siesta: Exc = -113.203337 siesta: eta*DQ = 0.00 siesta: Emadel = 0.00 siesta: Ekinion = 0.00 siesta: Eharris = -465.824667 siesta: Etot= -465.821884 siesta: FreeEng = -465.821884 siesta: Final energy (eV): siesta: Kinetic = 353.755904 siesta: Hartree = 385.159853 siesta:Ext. field = 0.00 siesta: Exch.-corr. =-113.203337 siesta: Ion-electron = -1080.056603 siesta: Ion-ion = -11.477701 siesta: Ekinion = 0.00 siesta: Total =-465.821884
[SIESTA-L] Pseudopotential issue
Dear Users, I am trying to use the program atom to generate pseudopotentials for siesta. However, I cannot generate them for elements like Mo and Ta. Is there a restriction on the maximum number of electrons or maximum main quantum number? Here is an example my input: pg Mo with 4d states in valence tm22.6 n=Mo c=car 0.0 0.0 0.0 0.0 0.0 0.0 83 50 1.00 0.00 51 0.00 0.00 42 5.00 0.00 1.90 1.90 1.90 Here is what sh ../pg.sh Mo.4d5s5ptm2.inp spits out: cp: cannot stat `VPSOUT': No such file or directory cp: cannot stat `VPSFMT': No such file or directory == Output data in directory Mo.4d5s5ptm2 == Pseudopotential in Mo.4d5s5ptm2.vps and Mo.4d5s5ptm2.psf But no psf or vps files are generated. The OUT file ends like this: kinetic energy * 2 =16715.70921324 potential energy = -16438.34858294 virial correction = 22.23021351 - virial sum= 299.59084381 Mo pseudopotential generation: Troullier-Martins nlseigenvalue rc cdrc delta error in gamfind (aka v0pp) - delta not found stop parameter =861 Please advise me on what I am doing wrong. Or is it even possible to generate pseudopotentials for heavier elements? Sincerely, Anastassia --- Anastassia Alexandrova, Ph.D. Yale University Department of Chemistry 225 Prospect Street New Haven, CT 06520-8107 Phone: 203-432-6288 Fax: 203-432-6144 [EMAIL PROTECTED] http://zarbi.chem.yale.edu/~anastassia/ --- Go one more mile...
Re: [SIESTA-L] Pseudopotential issue
The error you are getting is because of the format of the input file. The atom program is very very sensitive to the format of the input file. Use the ruler and compare the exact spacing etc of the the rc and all other parameters. It will work.Sanjay. --- On Mon, 5/19/08, Anastassia Alexandrova [EMAIL PROTECTED] wrote:From: Anastassia Alexandrova [EMAIL PROTECTED]Subject: [SIESTA-L] Pseudopotential issueTo: SIESTA-L@listserv.uam.esDate: Monday, May 19, 2008, 11:09 AMDear Users,I am trying to use the program atom to generate pseudopotentials for siesta.However, I cannot generate them for elements like Mo and Ta. Is there arestriction on the maximum number of electrons or maximum main quantum number?Here is an example my input: pg Mo with 4d states in valencetm22.6 n=Mo c=car 0.0 0.0 0.0 0.0 0.0 0.08350 1.00 0.0051 0.00 0.0042 5.00 0.00 1.90 1.90 1.90Here is what "sh ../pg.sh Mo.4d5s5ptm2.inp" spits out:cp: cannot stat `VPSOUT': No such file or directorycp: cannot stat `VPSFMT': No such file or directory== Output data in directory Mo.4d5s5ptm2== Pseudopotential in Mo.4d5s5ptm2.vps and Mo.4d5s5ptm2.psfBut no psf or vps files are generated. The OUT file ends like this: kinetic energy * 2 =16715.70921324 potential energy = -16438.34858294 virial correction = 22.23021351 - virial sum = 299.59084381 Mo pseudopotential generation: Troullier-Martins nlseigenvalue rc cdrc deltaerror in gamfind (aka v0pp) - delta not foundstop parameter =861Please advise me on what I am doing wrong. Or is it even possible to generatepseudopotentials for heavier elements?Sincerely,Anastassia--- Anastassia Alexandrova, Ph.D. Yale University Department of Chemistry 225 Prospect Street New Haven, CT 06520-8107 Phone: 203-432-6288 Fax: 203-432-6144[EMAIL PROTECTED]http://zarbi.chem.yale.edu/~anastassia/---Go one more mile...
Re: [SIESTA-L] Pseudopotential and basis for Co
Hi Ali, In the webpage there are LDA GGA pseudos, but I have no basis sets. http://www.uam.es/departamentos/ciencias/fismateriac/siesta/periodictable-intro.html Regards, Eduardo
[SIESTA-L] Pseudopotential and basis for Co
Dear SIESTA users, I need a pseudopotential and Basis for Cobalt (Co) atom. I hope that someone among you, has already worked on the Cobalt send me the pseudopotential and the basis for Cobalt (Co) thanks in advance Ali.
Re: [SIESTA-L] Pseudopotential
let's see your C.tm2.inp ,or it's because you have not in the directory of C.tm2.inp.
[SIESTA-L] Pseudopotential
Dear Users, When i genereate i have an error message in siesta 2.0.1 version, can anyone tell what is the exact problem??? cp: cannot stat `C.tm2.inp': No such file or directory forrtl: No such file or directory forrtl: severe (29): file not found, unit 5, file /export/home/jcgreen/nkugan/C.tm2/INP Image PCRoutineLineSource atm004C893A Unknown Unknown Unknown atm004C7B3A Unknown Unknown Unknown atm00480E26 Unknown Unknown Unknown atm00446999 Unknown Unknown Unknown atm00446286 Unknown Unknown Unknown atm00455869 Unknown Unknown Unknown atm00403424 Unknown Unknown Unknown atm00403322 Unknown Unknown Unknown libc.so.6 2ACAFF63A154 Unknown Unknown Unknown atm00403269 Unknown Unknown Unknown cp: cannot stat `VPSOUT': No such file or directory cp: cannot stat `VPSFMT': No such file or directory == Output data in directory C.tm2 == Pseudopotential in C.tm2.vps and C.tm2.psf Thanks in advance cheers kugan Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ
Re: [SIESTA-L] Pseudopotential
pg Indium tm2 0.00 n=In c=pbr 0.0 0.0 0.0 0.0 0.0 0.0 94 50 2.00 0.00 51 1.00 0.00 52 0.00 0.00 43 0.00 0.00 2.65 2.65 2.65 2.65 2008/1/26, karim rezouali [EMAIL PROTECTED]: Dear SIESTA users, I need a GGA pseudopotential for Indium atom (In.tm2.inp). Is there somebody which has the kindness to send it to me. thanks in advance Karim _ Ne gardez plus qu'une seule adresse mail ! Copiez vos mails vers Yahoo! Mail http://mail.yahoo.fr -- Gökhan SÜRÜCÜ
[SIESTA-L] Pseudopotential
Dear SIESTA users, I need a GGA pseudopotential for Indium atom (In.tm2.inp). Is there somebody which has the kindness to send it to me. thanks in advance Karim _ Ne gardez plus qu'une seule adresse mail ! Copiez vos mails vers Yahoo! Mail http://mail.yahoo.fr
Re: [SIESTA-L] pseudopotential for Pt
Dear Mohammad, there was a question about pseudopotential for platinum before. I think Javier Junquera gave an input for the ATOM program to create LDA pseudopotential for platinum and also a basis set for platinum. So here it is: INPUT FOR ATOM: pe Platinum tm2 n=Pt c=car 0.0 0.0 0.0 0.0 0.0 0.0 124 60 1.00 0.00 61 0.00 0.00 52 9.00 0.00 53 0.00 0.00 2.35 2.50 1.24 2.35 0.0 1.7 and basis set: %block PAO.Basis Pt 3 0.06506 n=6 0 2 E35.28484 6.29031 6.85818 5.34263 1.0 1.0 n=6 1 1 E10.02220 2.26448 7.56445 1.0 n=5 2 2 E30.91888 6.56288 7.13150 5.56464 1.0 1.0 %EndBlock PAO.Basis When you use ATOM, be careful about the format of the input file, it is quite rigid. Good luck Bozidar
[SIESTA-L] pseudopotential for Pt
Dear Siesta users, Does anyone have a pseudopotential for platinum? Thanks a lot for your help. Mohammad
Re: [SIESTA-L] pseudopotential for Ga and As
Dear Cherry , you can figure out from url below http://lorax.chem.upenn.edu/Research/psp_lda.html as i said before, opium package can easily generate psps for siesta with psf format. On Nov 30, 2007 3:27 PM, Cherry Y. Yates [EMAIL PROTECTED] wrote: Please send them to me if you happen to have these pseudopotentials. Thanks!!! Cherry Be a better sports nut! Let your teams follow you with Yahoo Mobile. Try it now. http://mobile.yahoo.com/sports;_ylt=At9_qDKvtAbMuh1G1SQtBI7ntAcJ -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 [EMAIL PROTECTED], [EMAIL PROTECTED]
[SIESTA-L] pseudopotential for Ga and As
Please send them to me if you happen to have these pseudopotentials. Thanks!!! Cherry Be a better sports nut! Let your teams follow you with Yahoo Mobile. Try it now. http://mobile.yahoo.com/sports;_ylt=At9_qDKvtAbMuh1G1SQtBI7ntAcJ
Re: [SIESTA-L] pseudopotential for gold (Au)
thanks a lot. will do tests. CYY --- Varadharajan Srinivasan [EMAIL PROTECTED] wrote: I made one recently but haven't tested it completely. I attach it with this email. Please test it before use and do let me know if there's something wrong. Best regards, Vardha Srinivasan. Computational Nanoscience Group Univ. of California, Berkeley. On Nov 15, 2007, at 1:52 PM, Cherry Y. Yates wrote: Does any one have a good pseudopotential for gold (Au)? Thanks. __ __ Get easy, one-click access to your favorites. Make Yahoo! your homepage. http://www.yahoo.com/r/hs Get easy, one-click access to your favorites. Make Yahoo! your homepage. http://www.yahoo.com/r/hs
Re: [SIESTA-L] pseudopotential for gold (Au)
I made one recently but haven't tested it completely. I attach it with this email. Please test it before use and do let me know if there's something wrong. Best regards, Vardha Srinivasan. Computational Nanoscience Group Univ. of California, Berkeley. Au_SV.psf Description: Binary data On Nov 15, 2007, at 1:52 PM, Cherry Y. Yates wrote: Does any one have a good pseudopotential for gold (Au)? Thanks. __ __ Get easy, one-click access to your favorites. Make Yahoo! your homepage. http://www.yahoo.com/r/hs
[SIESTA-L] pseudopotential for gold (Au)
Does any one have a good pseudopotential for gold (Au)? Thanks. Get easy, one-click access to your favorites. Make Yahoo! your homepage. http://www.yahoo.com/r/hs
Re: [SIESTA-L] Pseudopotential
Dear John, u just need to replace pb with pbr (r stands for relativistic calculation + polarized). See the ATOM manual. John Appleton [EMAIL PROTECTED] wrote: Dear users, To generate non-spin polarized PBE pseudopotential by the atom utility, I use the following input: pe Oxygen tm2 0.0 Opb 0.0 0.0 0.0 0.0 0.0 0.0 14 20 2.00 0.00 21 4.00 0.00 32 0.00 0.00 43 0.00 0.00 1.25 1.25 1.25 1.25 0.00 1.50 === Now I wish to know what to change on line 3 to get spin polarized/relativistic. Should pb on line 3 be replaced with pbs or rp? For example for the LDA Ceperly-Alder parametrization, NSP and SP would correspond to ca and cas respectively on line 3. Secondly, I would like to know the correct way to I run SP and NSP calculations for the same system: (a) do I use one pseudopotential for the both calculations? OR (B) for each calculation I use the corresponding pseudo-potential, that is, SP pseudo for SP calculations and NSP pseudo for NSP calculations. Thank you. J. A. __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com
Re: [SIESTA-L] pseudopotential basis for Sulfur.
dear Jingbin, the problem is that atom program is very sensitive to the input file format. the number of spaces and position of all the parameter should not change. Try taking one of the sample input file from siesta/pseudo/atom/Tutorial and modify them for your purpose. On 28/09/2007, Jingbin Li [EMAIL PROTECTED] wrote: Dear Friend, I succeeded in produing the pseudopotential basis for Carbon atom under /Pseudo/atom/Tutorial directory and now I am trying to produce my own pseudopotential basis for Sulfur atom. I copy the parameters from atom_table.txt in dir /Pseudo/atom/Contrib. The S.tm2.inp file is like following, ## pg Sulfur Guess Ecut ~ 25Ryl=0,1,2 as local tm2 n=S c=ca 0.0 0.0 0.0 0.0 0.0 0.0 33 30 2.00 0.00 31 4.00 0.00 32 0.00 0.00 1.70 1.70 1.70 # And when I run sh ../pg.sh S.tm2.inp I got the following message cp: cannot stat `VPSOUT': No such file or directory cp: cannot stat `VPSFMT': No such file or directory == Output data in directory S.tm2 == Pseudopotential in S.tm2.vps and S.tm2.psf and I could not find the S.tm2.vps and S.tm2.psf files. How could I fix this ? Thanks Best, Jingbin -- Yurko Natanzon PhD Student Henryk Niewodniczański Institute of Nuclear Physics Polish Academy of Sciences ul. Radzikowskiego 152, 31-342 Kraków, Poland Email: [EMAIL PROTECTED], [EMAIL PROTECTED]
[SIESTA-L] Pseudopotential and basis for Zinc
Dear Siesters, I would need a Zn pseudo with basis at GGA PBE. Please share with me! Many thanks, Giac -- * * * * * * * * * * * * * * * * * * * * * * * * * * Giacomo Giorgi * * Ph.D. * * Dipartimento di Chimica e Istituto di * * Scienze e Tecnologie Molecolari ISTM-CNR* * Universita' degli Studi di Perugia * * Via Elce di Sotto 8 06123 Perugia Italia * * Tel: +39 075-5855618 Fax: +39 075-5855606 * * E-mail: giac_at_thch.unipg.it * * * * * * * * * * * * * * * * * * * * * * * * * * Oltre le illusioni di Timbuctu' e le gambe lunghe di Babalu' c'era questa strada... Questa strada zitta che vola via come una farfalla, una nostalgia, nostalgia al gusto di curacao... Forse un giorno meglio mi spieghero'... (Paolo Conte, Hemingway)
Re: [SIESTA-L] pseudopotential and basis set for S and Ag
S 3 n=3 0 2 6.0 3.205 n=3 1 2 7.594 3.543 n=3 2 1 3.25 pe Sulfur tm2 1.7 S pbr 0.0 0.0 0.0 0.0 0.0 0.0 34 30 2.00 0.00 31 4.00 0.00 32 0.00 0.00 43 0.00 0.00 1.50 1.70 1.70 1.80 1.10 1.00 #2345678901234567890123456789012345678901234567890
[SIESTA-L] pseudopotential and basis set for S and Ag
Dear all, Does anybody have a GGA pseudopotential and basis set for Sulfur and for Silver that you could share? Thank you, Natalia -- Natalia Martsinovich Department of Physics Tel: (+44) (0)20 7848 1315 King's College London Fax: (+44) (0)20 7848 2420 Strand Room Q45 London WC2R 2LS, UK [EMAIL PROTECTED]
Re: [SIESTA-L] Pseudopotential for Fe and Bi
Dear Swaroop try this http://www.tddft.org/programs/octopus/pseudo.php On 6/3/07, M.Sairam Swaroop [EMAIL PROTECTED] wrote: Hi all Could someone share pseudopotentials (LDA flavor) for Bi(Bismuth) and Fe. Thanks Swaroop -- M.Sairam Swaroop Theoretical Sciences Unit JNCASR,Jakkur Bangalore-64 INDIA -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 [EMAIL PROTECTED], [EMAIL PROTECTED]
[SIESTA-L] Pseudopotential for Fe and Bi
Hi all Could someone share pseudopotentials (LDA flavor) for Bi(Bismuth) and Fe. Thanks Swaroop -- M.Sairam Swaroop Theoretical Sciences Unit JNCASR,Jakkur Bangalore-64 INDIA
Re: [SIESTA-L] Pseudopotential, can not start(VPSOUT)
Dear Sir, Thank you for your response. Actually we are getting error message while we are compiling our siesta-2.0.1 code. We first configure the code by ./configure and then give the command make. This is the case (make) after which we r getting the error. I think we do not have a proper makefile for this. Perhaps my input file for Pseudopotential for O is the, as it as given in example for O which is as follow. pg Oxygen tm2 2.0 n=O c=ca 0.0 0.0 0.0 0.0 0.0 0.0 14 20 2.00 0.00 21 4.00 0.00 32 0.00 0.00 43 0.00 0.00 1.15 1.15 1.15 1.15 Thank you Sir. Vikas thakur - Sick sense of humor? Visit Yahoo! TV's Comedy with an Edge to see what's on, when.
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] Pseudopotential, can not start(VPSOUT)
The program crashed because of the memory allocation(perhaps)! perhaps, some bugs in the compiler? In your mail: From: vikas thakur [EMAIL PROTECTED] Reply-To: Siesta, Self-Consistent DFT LCAO program,http://www.uam.es/siesta; [EMAIL PROTECTED] To: SIESTA-L@listserv.uam.es Subject: [SIESTA-L] Pseudopotential, can not start(VPSOUT) Date:Mon, 28 May 2007 22:09:00 -0700 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. Powered by UESTC SMG SPAM, virus-free and secure email https://smg.uestc.edu.cn
[SIESTA-L] Pseudopotential, can not start(VPSOUT)
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] pseudopotential and basis set for Zn with semicorestates
Zn is not a good example of using SZ for semicore Well, it's easy to check - just take SZ and then DZ and compare total energy. If the impact of DZ is similar to that of DZ for s and p states, then it is worth using DZ. Of course checking for exact properties of interest would be more precise but longer.
Re: [SIESTA-L] pseudopotential and basis set for Zn with semicorestates
Yes, Andrei is absolutely right: Zn is not a good example of using SZ for semicore - it's d-states overlap with s-band, and therefore should be more considered as valence. SZ should be OK for such elements as As or Ga, where these states are located deeper in energy, and therefore are more localized. But in any case, as Andrei pointed out, everything depends on what you would like to obtain, and you should always check your particular desired quantity for convergence. (I saw results of big supercell calculations, where people freeze Zn 3d, putting it in pseudopotential. However, I would not recomment that ...) Thanks for your comment, Andrei! Vladimir. Andrei Postnikov wrote: On Fri, 26 Jan 2007, Vladimir Timochevski wrote: | Usually semicore states are quite localized, and from my experience a SZ-type | of orbitals is sufficient for them. So, in case of Zn (3d10 semicore states) | put something like | %block PAO.Basis | Zn 2 | n=4 0 2 P | 0.0 0.0 | 1.0 1.0 | n=3 2 1 | 0.0 | 1.0 | %endblock PAO.Basis | This will give you 2 4s-orbitals, 3 4p-orbitals, and 5 3d-orbitals. Cutoff | radii will be generated automatically. Dear Vladimir: This is indeed a quite risky advise... of course the final decision depends on what you are doing and level of accuracy you need. You'll probably get the position of Zn3d band right with SZ, but lattice parameter, elastic propeties, and phonons could be quite off. 3d of Zn is hardly a good semicore, it is really too close and contribute substantially to bondings. Best regards, Andrei
Re: [SIESTA-L] pseudopotential and basis set for Zn with semicore states
I also have some questions about the semicore pseudo potential and basis. You know, generally, when we generate a psf, we can use the Default DZP basis to check whether or not the psf is good enough by checking the standard band (for examle, got from LAPW calculation), and also calculate the lattice constant,compard with the experimental data. However, if we generate a semicore psf, we have also to specify the basis set ourself. How to make sure the basis you specify is the good one? So, any tricky things here? Thank you! On 1/23/07, karim rezouali [EMAIL PROTECTED] wrote: Dear siesta Users, I need a pseudopotential (and basis-set) for zinc with semicore states. Thank you in advance K.Rezouali ___ Découvrez une nouvelle façon d'obtenir des réponses à toutes vos questions ! Profitez des connaissances, des opinions et des expériences des internautes sur Yahoo! Questions/Réponses http://fr.answers.yahoo.com
[SIESTA-L] pseudopotential and basis set for Zn with semicore states
Dear siesta Users, I need a pseudopotential (and basis-set) for zinc with semicore states. Thank you in advance K.Rezouali ___ Découvrez une nouvelle façon d'obtenir des réponses à toutes vos questions ! Profitez des connaissances, des opinions et des expériences des internautes sur Yahoo! Questions/Réponses http://fr.answers.yahoo.com
[SIESTA-L] Pseudopotential for Li
dear friends, can anybody give me pseudopotential for Li? thanx in advance. regards, Saswata Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download Now! http://messenger.yahoo.com/download.php
Re: [SIESTA-L] Pseudopotential wanted
Hello Siesta users Does any body has good GGA pseudopotentail and Basis of Be,O,Al,Si. Thank you. Mic. __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com
[SIESTA-L] Pseudopotential and basis set for Mo?
Hi, Can anyone please provide a Pseudopotential for Mo? Furthermore I'd like to optimize the basis set for MoO2. It seems there is a way to do this with a simplex algorithm for Siesta. Is this approach documented anywhere? Thanks, Kevin
[SIESTA-L] Pseudopotential for Bi
Dear All, Does anyone have a working pseudopotential for Bi? I would greatly appreciate receiving your help and cooperation. Thanks in advance, A. Sen
Re: [SIESTA-L] Pseudopotential help
Respected Sir, thanks a lot for replying me.actually i am very much new in this field and so i didnt able to get the meaning what you have suggested me.I got one mistake that i have done is that the no of valence orbital that is there in the line # 5,but what did you mean by pp file format and what r those parameters that should be modified?please reply, regards, Saswata Bhattacharya. lan haiping [EMAIL PROTECTED] wrote: hi atom routine is sensitive to pp file format.. Try to start with a correct format file ,and modify its parameters.. hope help regards. hai-ping On 11/7/06, Saswata Bhattacharya [EMAIL PROTECTED] wrote: Dear all, i am trying to run atom program for Boron Pseudopotential and my .tm2.inp file looks like pg Boron tm23.0 n=B c=ca 0.0 0.0 0.0 0.0 0.0 0.0 13 20 2.00 0.00 21 1.00 0.00 30 0.00 0.00 31 0.00 0.00 1.60 1.60 1.60 1.60 now with this i cant able to get .psf file,if anybody shows me the point where i am doing the mistake i will be highly thakful to him... Regards, Saswata Bhattacharya - Find out what India is talking about on - Yahoo! Answers India Send FREE SMS to your friend's mobile from Yahoo! Messenger Version 8. Get it NOW - Find out what India is talking about on - Yahoo! Answers India Send FREE SMS to your friend's mobile from Yahoo! Messenger Version 8. Get it NOW
Re: [SIESTA-L] Pseudopotential help
Saswata Bhattacharya wrote: Dear all, i am trying to run atom program for Boron Pseudopotential and my .tm2.inp file looks like pg Boron tm23.0 n=B c=ca 0.0 0.0 0.0 0.0 0.0 0.0 13 20 2.00 0.00 21 1.00 0.00 30 0.00 0.00 31 0.00 0.00 1.60 1.60 1.60 1.60 now with this i cant able to get .psf file,if anybody shows me the point where i am doing the mistake i will be highly thakful to him... Regards, Saswata Bhattacharya Find out what India is talking about on - Yahoo! Answers India http://us.rd.yahoo.com/mail/in/yanswers/*http://in.answers.yahoo.com/ Send FREE SMS to your friend's mobile from Yahoo! Messenger Version 8. Get it NOW http://us.rd.yahoo.com/mail/in/messengertagline/*http://in.messenger.yahoo.com Hi Saswata, you are using 2s, 2p 3s and 3p as valence orbitals so you have to put 1 * *4instead of 1 3 Good luck. Bozidar
Re: [SIESTA-L] Pseudopotential help
hi atom routine is sensitive to pp file format.. Try to start with a correct format file ,and modify its parameters.. hope help regards. hai-ping On 11/7/06, Saswata Bhattacharya [EMAIL PROTECTED] wrote: Dear all, i am trying to run atom program for Boron Pseudopotential and my .tm2.inp file looks like pg Boron tm23.0 n=B c=ca 0.0 0.0 0.0 0.0 0.0 0.0 13 20 2.00 0.00 21 1.00 0.00 30 0.00 0.00 31 0.00 0.00 1.60 1.60 1.60 1.60 now with this i cant able to get .psf file,if anybody shows me the point where i am doing the mistake i will be highly thakful to him... Regards, Saswata Bhattacharya -- Find out what India is talking about on - Yahoo! Answers Indiahttp://us.rd.yahoo.com/mail/in/yanswers/*http://in.answers.yahoo.com/ Send FREE SMS to your friend's mobile from Yahoo! Messenger Version 8. Get it NOWhttp://us.rd.yahoo.com/mail/in/messengertagline/*http://in.messenger.yahoo.com
[SIESTA-L] Pseudopotential needed
Dear all, Due some calculation I need Pseudopotential of Boron.Can anybody please help me with sending me that B.psf file to my email address [EMAIL PROTECTED] have created some .tm2.inp files but those are not working with atom program.I shall be highly obliged if anybody send me a Pseudopotential file of Boron along with .tm2.inp. regards, Saswata - Find out what India is talking about on - Yahoo! Answers India Send FREE SMS to your friend's mobile from Yahoo! Messenger Version 8. Get it NOW
Re: [SIESTA-L] pseudopotential problem
Hi, I would add the following option to what Marcos says: You can start with a standard atom inp file. See the atom manual for details. Then do an all electron calculation with atm. So you really want an ae.inp kind of file. Keep in mind, atm, unlike siesta, has a very *rigid* readout format, so *keep all spacings in your input files as in the template ae.inp file* that you can get, for instance on the Tutorial directory of atom. Otherwise you will get all kind of errors during the ae.sh script run. Once you have a successful atm calculation, go to your Bi.ae.inp directory, that will be created if a successful run did happen, and opent the OUT file. In this file you will have a bunch of data. Go to the channels you want your pseudo to have and dismiss the previous channels (you get all channels here 'cause this is an all-electron calculation). Check the biggest r extr for the channels you are interested in. For instance, from one of my files: . . . n = 5 l = 1 s = 0.5 a extr 0.290 -0.408 0.601 -1.120 b extr-0.055 0.022 -0.013 0.008 r extr 0.037 0.138 0.351 0.979 r zero 0.075 0.216 0.528 r 90/99 % 1.597 2.266 . . . (and assuming I wanted the 5p orbital to be in the valence) I would write down 0.97 as a starting point for my rc in my pseudo. You get the idea. Please PLOT the radial part of your all electron result. Your rc must be away enough from parts where your wavefunctions cross the r axis (ie, bigger than the biggest r zero value). Okay, suppose you wrote down your r extrs. Now take a template pg (or pe for that matter) file. Replace the rcs in that file (and the atomic number as well as the pseudo flavor to suit!) by the ones you just got. Sometimes is safe to choose one of your r_extrs for all rcs (the smallest, the biggest, some value in between,...) Run the pg.sh script. Go back to your output dir (something like Bi.pe.inp) and plot the wavefuncions once more. pg(pe) wavefunctions should overlap outside rc. On a more stringent test of your pseudo, you can check in the atom manual how to test for transferability. All this is good but, -sometimes atm changes your input radii (See OUT file for actual taken values). -even though you are happy with your pseudo, siesta discovers GHOST states (...and crashes). Then you have to go back to your pseudo inp file and modify some options slightly. -if your pseudo makes for a sucessful siesta run, do *check* some bulk properties: Lattice constants and the like. Bottom line is, it will take you a couple of days to get comfortable with the process of generating pseudos but it is worth (and perhaps even necessary if you consider using SIESTA in the long run) the effort. Best regards, Salvador. On Thursday 05 October 2006 09:08, Marcos Verissimo Alves wrote: Hi Bozo, Hi Marcos thanks for your mail and sorry for not giving full information, I just wanted to keep mail as short as possible so people can go quickly through it. Don't keep the e-mail short when you have a problem whose cause you cannot identify. In some cases, a more lengthy (but not too lengthy) explanation is necessary, in order to identify possible sources of error. So, what I did is: I went to SIESTA webpage, then to LINKS and there you can find ABINIT with the list of pseudopotentials that Siesta can use. So I simply downloaded GGA (PBE) Hartwigsen_Goedecker-Hutter pseudopotentil for Bi as a text file. I named it Bi.psf. So there is your problem. If you look at the abinit pseudopotential format and the .psf format, you will see that they are completely different. What the link means is that siesta can use thses potentials because they are norm-conserving, but they have to be in the appropriate format. If you can find (or anyone in the list can provide) a format conversion tool from the abinit format to the siesta format, it will be great. Otherwise, you can do: a) See if, in the abinit file, the core radii are specified. I don't remember if siesta has HGH pseudopotential generation (probably not), but you could use the rc's from HGH as a starting point for generating your own TM GGA pseudo using atom, testing it on elemental Bi. If this is not good, you can do b) a search in the literature, find some paper with calculations for Bi which states the channels and core radii for the GGA TM pseudopotential are used, and generate your own pseudo from those. Or, c) you could ask, on the list, if anyone has a good pseudo for Bi. I had pseudopotential for Si from before. And then started simulation. I know that pseudopotential for Si is ok, because I did some calculations with silicon in diamond before, and everything worked fine. Probably because the pseudo was in the right file format (.psf). In simulation I am using generalized gradient approximation and also PBE parametrization of the
Re: [SIESTA-L] pseudopotential problem
Hi Bozidar, That really depends on the kind of error you are obtaining on the reading of the pesudo by siesta. There are several points in which your e-mail provides incomplete information: 1) Have you downloaded the pseudopotential itself? If it's giving an error, then it might be corrupted. Difficult to happen, but could be. 2) Have you downloaded the input file and then generated the pseudo using atom? If so, then you may (inappropriately) be getting ghost states and this is the kind of error Chun is referring to; it has been discussed on the list a while ago. If this is the case (ghost states from a pseudo which is known to have none), then you should recompile atom with a good compiler (intel is very good), with -O2 optimization, and NOT -O3, which is known to, in some cases, induce to numerical errors. So, to really help you, you should provide more information on what you have actually done. Best regards, Marcos Hi, I think you must have used the different compilers to make the siesta and the atom. You can recompile the atom using the same compiler you used to make siesta, than generate the pseudopotential again. Good luck. Chun - Original Message - From: Bozidar Butorac [EMAIL PROTECTED] To: SIESTA-L@listserv.uam.es Sent: Thursday, October 05, 2006 4:48 PM Subject: [SIESTA-L] pseudopotential problem Dear Siesta users I started calculation about Bismuth in Silicon. I downloaded pseudopotential for Bi from the SIESTA webpage, but after siesta reads input file, the calculation suddenly stops when the pseudopotentil for Bi is being read. I know that pseudopotential for Si is ok, because I did some simulations involving silicon before and everything was good. I think the problem is about the format of pseudopotential file for Bi, but I don't know how to fix it. Does anybody have an idea how to solve it? I also attached the output file. Thank you very much in advance. Cheers, Bozo -- Dr. Marcos Verissimo Alves Post-Doctoral Fellow Condensed Matter and Statistical Physics Sector International Centre for Theoretical Physics Trieste, Italy I have become so addicted to vi that I try to exit OpenOffice by typing :wq!
[SIESTA-L] pseudopotential problem
Dear Siesta users I started calculation about Bismuth in Silicon. I downloaded pseudopotential for Bi from the SIESTA webpage, but after siesta reads input file, the calculation suddenly stops when the pseudopotentil for Bi is being read. I know that pseudopotential for Si is ok, because I did some simulations involving silicon before and everything was good. I think the problem is about the format of pseudopotential file for Bi, but I don't know how to fix it. Does anybody have an idea how to solve it? I also attached the output file. Thank you very much in advance. Cheers, Bozo Taking nodenames from /home/bozidar/Marshall/Bi_in_Si/244.node00.kcl.ac.uk.conf, number of nodes specified by -np /opt/scali/bin/mpimon -stdin all /home/bozidar/bin/siesta -- n02 1 n02 1 SIESTA 1.3-- [Release] (30 Jul 2003) Architecture : pgf90-mpich Compiler flags: mpif90 -fast PARALLEL version * Running on2 nodes in parallel Start of run: 5-OCT-2006 7:28:58 *** * WELCOME TO SIESTA * *** WARNING: Siesta is reading its input from file INPUT_DEBUG ** Dump of input data file # Label SystemLabel Bi_in_Si # Optimisation MD.TypeOfRun CG MD.NumCGSteps 150 MD.MaxForceTol 0.01 eV/Ang MD.VariableCell true MD.MaxStressTol 100 bar # SCF SolutionMethod diagon kgrid_cutoff 1.0 Ang MaxSCFIterations 200 DM.MixingWeight 0.10 DM.NumberPulay 3 SpinPolarized false # Basis set MeshCutoff 170 Ry PAO.EnergyShift 0.01 Ry PAO.BasisSize DZP #PAO.SplitNorm 0.15 # Functional XC.Functional GGA XC.Authors PBE # I/O LongOutput true UseSaveData false NumberOfSpecies 2 NumberOfAtoms 64 %block ChemicalSpeciesLabel 1 14 Si 2 83 Bi %endblock ChemicalSpeciesLabel LatticeConstant1.0 Ang %block LatticeVectors 11.0430140.00 0.00 0.0011.043014 0.00 0.00 0.00 11.043009 %endblock LatticeVectors AtomicCoordinatesFormat Ang %block AtomicCoordinatesAndAtomicSpecies -0.0567 -0.0859 -0.2005 1 # Si 1 1.380382351.380378231.38036897 1 # Si 2 2.760758482.76075650 -0.1971 1 # Si 3 4.141121824.141122501.38037668 1 # Si 4 -0.07752.760756062.76075324 1 # Si 5 1.380386384.141122884.14112765 1 # Si 6 2.76075870 -0.11452.76075387 1 # Si 7 4.141122201.380382664.14112805 1 # Si 8 5.52150958 -0.1113 -0.1881 1 # Si 9 6.901887851.380375211.38036817 1 # Si10 8.282252162.76075320 -0.2085 1 # Si11 9.662616254.141120391.38037155 1 # Si12 5.521511762.760752772.76075210 1 # Si13 6.901891504.141121114.14112799 1 # Si14 8.28225312 -0.14672.76075230 1 # Si15 9.662614361.380379474.14112697 1 # Si16 -0.08105.52151198 -0.1950 1 # Si17 1.380379226.901891041.38036724 1 # Si18 2.760754868.28225329 -0.2255 1 # Si19 4.141121049.662614561.38036914 1 # Si20 -0.10738.282253702.76075032 1 # Si21 1.380383589.662612584.14112543 1 # Si22 2.760755455.521513472.76075143 1 # Si23 4.141121296.901892614.14112751 1 # Si24 5.521508225.52150909 -0.1749 1 # Si25 6.901887146.901890421.38036878 1 # Si26 8.282249168.28224996 -0.2361 1 # Si27 9.662615849.662613541.38036341 1 # Si28 5.521508668.282250812.76074921 1 # Si29 6.901887429.662611614.14112649 1 # Si30 8.282250615.521510382.76074955 1 # Si31 9.662613266.901890364.14112617 1 # Si32 -0.0608 -0.09945.52151657 1 # Si33 1.380380871.380375956.90189628 1 # Si34 2.760756952.760753625.52152168 1 # Si35 4.141123294.141121756.90189933 1 # Si36 -0.08932.760753408.28225115 1 # Si37 1.380386734.141119879.66260137 1 # Si38 2.76075754 -0.14568.28225184 1 # Si39 4.141121541.380380479.66260173 1 # Si40 5.52150922 -0.12495.52151529 1 # Si41 6.901885831.380372506.90189468 1 # Si42 8.282251182.760750185.52152044 1 # Si43 9.662615574.141120726.90189703 1 # Si44 5.521510482.760750718.28225032 1 # Si45 6.901886824.141123439.66260728 1 # Si46 8.28225125
[SIESTA-L] pseudopotential
Dear Siesta users, I am supposed to do some calculations with Bismuth, so does anybody have a pseudopotential for it. Cheers Bozo
Re: [SIESTA-L] pseudopotential problem?
hi, the input file of atm routine should be strict in format .. so , you can modify some good input files , and set parameters for C element hope help regards, hai-ping On 9/1/06, Chun Li [EMAIL PROTECTED] wrote: Dear all: I need help eagerly. I encouter a problem after generating the Pseudopotential of Carbon, which makes the calculation can't run rightly. A error [forrtl: severe (41): insufficient virtual memory] always arises.My C.tm2.inp is : pg C Pseudopotencial tm2 2.00 Cca 0 12 20 2.00 21 2.00 1.24 1.24 0.0 0.0 0.0 # #2345678901234567890123456789012345678901234567890 Ruler Please help me! Regards Zhuhua Zhang
[SIESTA-L] pseudopotential problem?
Dear all: I need help eagerly. I encouter a problem after generating the Pseudopotential of Carbon, which makes the calculation can't run rightly. A error [forrtl: severe (41): insufficient virtual memory] always arises.My C.tm2.inp is : pg C Pseudopotencial tm2 2.00 Cca 0 12 20 2.00 21 2.00 1.24 1.24 0.0 0.0 0.0 # #2345678901234567890123456789012345678901234567890 Ruler Please help me! Regards Zhuhua Zhang
[SIESTA-L] Pseudopotential for Bromine
Hi everybody! I have a system with C,H,O and Br. The bromine atom is attached to an aromatic ring. Could anyone provide me a pseudopotential for Bromine or give me any hint to build up it? Thanks Tomás
[SIESTA-L] Pseudopotential for S
Dear Siesta Users, I will be very thankful for sending me pseudopotential for S or information on where I could get it. Regards, Bohdan Andriyevsky
Re: [SIESTA-L] pseudopotential for Platinum
Here's a start pg Platinum tm2 n=Pt c=car 0.0 0.0 0.0 0.0 0.0 0.0 12 4 60 1.00 0.00 61 0.00 0.00 52 9.00 0.00 53 0.00 0.00 2.25 2.25 2.25 2.25 Steve Dr. Steve. Bailey. Lancs. Cumb. IoP Branch Secretary. Department of Physics, Lancaster University, Lancaster, LA14YB, UK. [EMAIL PROTECTED] Tel 01524592844 Fax (01524)844037 - Original Message - From: Sergey Lisenkov [EMAIL PROTECTED] To: SIESTA-L@LISTSERV.UAM.ES Sent: Wednesday, January 26, 2005 3:56 PM Subject: [SIESTA-L] pseudopotential for Platinum Dear Users, Does anybody has a pseudopotential for Platinum? I cannot generate it. Thanks, Salomon __ Do you Yahoo!? The all-new My Yahoo! - What will yours do? http://my.yahoo.com
[SIESTA-L] pseudopotential for Platinum
Dear Users, Does anybody has a pseudopotential for Platinum? I cannot generate it. Thanks, Salomon __ Do you Yahoo!? The all-new My Yahoo! - What will yours do? http://my.yahoo.com
[SIESTA-L] Pseudopotential Charge Density Issue
Hello Everyone, Over the past few months I have been trying to resolve an issue related to the total integrated charge density. I have been trying to create pseudopotentials for Cd and recently Si using the atom program. Atom produces two files AECHARGE and PSCHARGE. Now one of the test conditions of a good pseudopotential is that the total integrated charge density for each wavefunction should agree within a given rc (which means that the pseudopotentail duplicates the correct core charge). According to the Atom manual you can do some basic math and get the total charge as a function of the radius. Then I should be able to simple sum up all the point to Log Der radius. My isues is this it seems that I usully get a total integrated charge desnisty for the pseudopotential case that is 10-13% less than the AE case. They do match at the specified LogDer Radius. Why does this occur? Does SIESTA renormalize the pseudopotentials. If this is so how do you check the pseudopotental for the necessary test condition before performing a run in SIESTA?
Re: [SIESTA-L] Pseudopotential core correction
Hi Ranier, I the original paper by Louie et. al (PRB 26, 1728 (1982)) suggests that: ... r_o may chosen as the radius where the core charge density is from 1 to 2 times larger than the valence charge density. The ATOM program chooses r_o so that the core charge density is equal to the valence charge density. A more recent paper by Porezag et. al (PRB 60, 14132 (1999)) argues that this is not the best choice for r_o in general. Bests, On Sun, 2004-11-21 at 21:17, Rainer Hoft wrote: Dear Siesta users, is there a general rule for how large the core correction radius should be for generating pseudopotentials? Thanks! Rainer -- UTS CRICOS Provider Code: 00099F DISCLAIMER: This email message and any accompanying attachments may contain confidential information. If you are not the intended recipient, do not read, use, disseminate, distribute or copy this message or attachments. If you have received this message in error, please notify the sender immediately and delete this message. Any views expressed in this message are those of the individual sender, except where the sender expressly, and with authority, states them to be the views the University of Technology Sydney. Before opening any attachments, please check them for viruses and defects. -- Nichols A. Romero 4-133 ESB, MC 704 508 East Michigan Avenue 1110 West Green Street Apartment 12 Urbana, IL 61801-3080 Urbana, IL 61801-5176 (217) 333-6108 (217) 417-5210
Re: [SIESTA-L] Pseudopotential input for W (Tungsten)
On Wed, Nov 17, 2004 at 11:30:39AM +0800, Chunsheng Guo wrote: Hello, Anybody has experience with pseudopotential generation of W element? Your information is greatly appreciated. Hi - I've recently published a paper using SIESTA on the doping behaviour of WO3; it includes full details of the pseudopotentials I used. http://scitation.aip.org/dbt/dbt.jsp?KEY=PRBMDOVolume=70Issue=16 is the link to the issue index: the reference is Density-functional study of charge doping in WO3 Andrew D. Walkingshaw, Nicola A. Spaldin, and Emilio Artacho Published 25 October 2004 (7 pages) Physical Review B 70, 165110 Best wishes, Andrew -- Dept of Earth Sciences, Univ. Cambridge ::: http://www.esc.cam.ac.uk/ email: [EMAIL PROTECTED]::: http://www.lexical.org.uk/blog/ Random Walk, 10pm Wednesdays, CUR1350 ::: http://www.cur1350.co.uk/
[SIESTA-L] Pseudopotential input for W (Tungsten)
Hello, Anybody has experience with pseudopotential generation of W element? Your information is greatly appreciated.
Re: [SIESTA-L] Pseudopotential input for S (sulphur)
Hello data pseudopotential generation of S element pg Sulfur tm20.00 n=S c=ca 0.0 0.0 0.0 0.0 0.0 0.0 34 30 2.000 0.000 31 4.000 0.000 32 0.000 0.000 43 0.000 0.000 1.700 1.700 1.700 1.700 Best regards Xiang-Yang (Benjamin) Liu [EMAIL PROTECTED] dedi: Hello, Anybody has experience with pseudopotential generation of S element? Your information is greatly appreciated. Best regards, Benjamin Liu --
[SIESTA-L] Pseudopotential input for S (sulphur)
Hello, Anybody has experience with pseudopotential generation of S element? Your information is greatly appreciated. Best regards, Benjamin Liu
Re: [SIESTA-L] pseudopotential Pb
On Monday 21 June 2004 04:24 am, you wrote: Dear all, could anyone suggest me an input file for the generation of psuedopotential for Pb without semicore shells ? Hi Try this pg tm2 Pb car 0.000 0.000 0.000 0.000 0.000 0.000 132 60 2.000 0.000 0.000 61 2.000 0.000 0.000 3.18000 3.18000 0.0 0.0 0.0 0.0 0.0 Of course you may add a d orbital with 0 occupation Regards, Carlos.
[SIESTA-L] pseudopotential Pb
Dear all, could anyone suggest me an input file for the generation of psuedopotential for Pb without semicore shells ? with : pg Lead tm20.00 n=Pb c=car 0.0 0.0 0.0 0.0 0.0 0.0 134 60 2.000 0.000 61 2.000 0.000 62 0.000 0.000 53 0.000 0.000 2.450 2.450 2.450 2.450 I obtain the following: cp: cannot stat `VPSOUT': No such file or directory cp: cannot stat `VPSFMT': No such file or directory == Output data in directory Pb == Pseudopotential in Pb.vps and Pb.psf cp: cannot stat `../..//charge.gp*': No such file or directory cp: cannot stat `../..//vcharge.gp*': No such file or directory cp: cannot stat `../..//vspin.gp*': No such file or directory cp: cannot stat `../..//coreq.gp*': No such file or directory cp: cannot stat `../..//pots.gp*': No such file or directory cp: cannot stat `../..//pseudo.gp*': No such file or directory cp: cannot stat `../..//scrpots.gp*': No such file or directory cp: cannot stat `../..//subps.gp*': No such file or directory what is the core radius for Pb ? best regards, Raffaele Buffa _ Personalizza MSN Messenger con sfondi e fotografie! http://www.ilovemessenger.msn.it/
[SIESTA-L] Pseudopotential format
Dear Siesta users, I'm new in the list and the use of Siesta, and would like to make a remark in the atom doc manual. Il is written (page 6) that the pseudo files can be readable by either Siesta and PW. Could anyone tell me what is PW? An other Plan Wave program ? One more thing about the nlcc nonlinear core correction in those files, could you please tell me the format of this block in the file ? (true charge, density, derivativesof charge or density) ? Thank you in advance. Frédéric Bouyer
[SIESTA-L] pseudopotential problem!
Hi All: I am trying to do some calculations on a palladium cluster. Irrespective of the kind of pseudopotential I use, I always end up with the following error.. ~~ POLgen: Perturbative polarization orbital with L= 1 POLgen: Polarization orbital for state 5s POLARIZATION: Iteration to find the polarization orbital has failed ! Please try with a Rc no bigger than 0.00E+00 Bohr Stopping Program ~~ I have tried with different values of rc, but I always get the above error. Any suggestions would be welcome. Thanks, Tarakeshwar --- The input for the pseudopotential file is given below.. pg Palladium tm2 2.500 n=Pd c=car 0.0 0.0 0.0 0.0 0.0 0.0 84 50 1.000 0.000 51 0.000 0.000 42 9.000 0.000 43 0.000 0.000 2.1002.7002.002.00
[SIESTA-L] pseudopotential and unbound reference states
Hi. This is more of question on generating TM pseudopotentials in general and is not necessarily specific to SIESTA. When using the polarization orbitals in your basis, it is necessary to have a pseudopotential for the next higher angular momentum state. For example, same I'm doing Zr: n l occ - 5 0 2.0 5 1 0.0 4 2 2.0 4 3 0.0 If I want to have polarization orbitals for the 4d e-, I need to have the pseudopotential for the 4f. Now, the real 4f orbitals are unbound in neutral Zr and I know that SIESTA merely uses orbitals with f symmetry. How does one choose an appropriate r_c for the 4f orbital? Usually, r_c should be picked so that its after the last node of the AE wavefunction. But there is only an unbound reference state. So it has no nodes. Bests, -- Nichols A. Romero 4-133 ESB, MC 704 508 East Michigan Avenue 1110 West Green Street Apartment 12 Urbana, IL 61801-3080 Urbana, IL 61801-5176 (217) 333-6108 (217) 417-5210
Re: [SIESTA-L] pseudopotential generation problem
Check the spacing of the input file, make sure the numbers are spaced just like those in one of the examples, otherwise it won't work, since fortran has a fixed format input, Jordan On Tue, 2004-02-10 at 03:43, PengGang Yin wrote: Dears all, I meet a problem when I generate pseudopotential. The erro message is as follows. cp: cannot stat `VPSOUT': No such file or directory cp: cannot stat `VPSFMT': No such file or directory == Output data in directory C.tm2 == Pseudopotential in C.tm2.vps and C.tm2.psf How do I deal with this problem? Thank you for your help in advance. Penggang Yin 2.10 _ Do You Yahoo!? 完全å…è´¹çš„é›…è™Žç”µé‚®ï¼Œé©¬ä¸ æ³¨å†ŒèŽ·èµ é¢å¤–60兆网络å˜å‚¨ç©ºé—´ http://cn.rd.yahoo.com/mail_cn/tag/?http://cn.mail.yahoo.com
[SIESTA-L] pseudopotential generation problem
Dears all, I meet a problem when I generate pseudopotential. The erro message is as follows. cp: cannot stat `VPSOUT': No such file or directory cp: cannot stat `VPSFMT': No such file or directory == Output data in directory C.tm2 == Pseudopotential in C.tm2.vps and C.tm2.psf How do I deal with this problem? Thank you for your help in advance. Penggang Yin 2.10 _ Do You Yahoo!? ê
[SIESTA-L] Pseudopotential read error
Hello, I will very much appreciate some help as I still cannot read pseudopotential files (both vps and psf). I send the screen dump for the psf one and the file itself. Thank you in advance. Orlin Blajiev Best regards, Orlin Blajiev -- Orlin Blajiev Department of Metallurgy, Electrochemistry and Materials Science Faculty of Applied Science Vrije Universiteit Brussel Pleinlaan 2, B-1050 Brussels Belgium http://wwwtw.vub.ac.be/meta/ tel.: 32-(0)2-6293538 fax : 32-(0)2-6293200 Attachment Converted: c:\cygwin\home\paz\e-mail\attach\screen.png Cu ca rel nc ATM3 11-tte-03 Troullier-Martins 4s 1.00r r= 2.08/4p 0.00r r= 2.30/3d10.00r r= 2.08/ 3 2 1132 0.854742129885E-04 0.1250E-01 11.00 Radial grid follows 0.107513324605E-05 0.216379000353E-05 0.326614037729E-05 0.438235661180E-05 0.551261311812E-05 0.665708650114E-05 0.781595558715E-05 0.898940145179E-05 0.101776074484E-04 0.113807592365E-04 0.125990448111E-04 0.138326545318E-04 0.150817811525E-04 0.163466198520E-04 0.176273682637E-04 0.189242265072E-04 0.202373972193E-04 0.215670855856E-04 0.229134993726E-04 0.242768489601E-04 0.256573473744E-04 0.270552103210E-04 0.284706562190E-04 0.299039062347E-04 0.313551843162E-04 0.328247172287E-04 0.343127345897E-04 0.358194689050E-04 0.373451556049E-04 0.388900330810E-04 0.404543427236E-04 0.420383289592E-04 0.436422392889E-04 0.452663243270E-04 0.469108378400E-04 0.485760367865E-04 0.502621813573E-04 0.519695350159E-04 0.536983645398E-04 0.554489400620E-04 0.572215351136E-04 0.59016421E-04 0.608338951751E-04 0.626742246237E-04 0.645377025670E-04 0.664246201773E-04 0.683352722894E-04 0.702699574464E-04 0.722289779470E-04 0.742126398920E-04 0.762212532326E-04 0.782551318188E-04 0.803145934482E-04 0.823999599160E-04 0.845115570648E-04 0.866497148360E-04 0.888147673211E-04 0.910070528140E-04 0.932269138637E-04 0.954746973281E-04 0.977507544279E-04 0.100055440802E-03 0.102389116561E-03 0.104752146348E-03 0.107144899391E-03 0.109567749562E-03 0.112021075436E-03 0.114505260351E-03 0.117020692465E-03 0.119567764821E-03 0.122146875403E-03 0.124758427202E-03 0.127402828279E-03 0.130080491826E-03 0.132791836235E-03 0.135537285158E-03 0.138317267578E-03 0.141132217871E-03 0.143982575881E-03 0.146868786980E-03 0.149791302146E-03 0.152750578027E-03 0.155747077017E-03 0.158781267324E-03 0.161853623046E-03 0.164964624247E-03 0.168114757025E-03 0.171304513595E-03 0.174534392364E-03 0.177804898007E-03 0.181116541546E-03 0.184469840433E-03 0.187865318628E-03 0.191303506680E-03 0.194784941815E-03 0.198310168012E-03 0.201879736097E-03 0.205494203820E-03 0.209154135951E-03 0.212860104360E-03 0.216612688114E-03 0.220412473561E-03 0.224260054424E-03 0.228156031898E-03 0.232101014735E-03 0.236095619347E-03 0.240140469900E-03 0.244236198410E-03 0.248383444842E-03 0.252582857212E-03 0.256835091688E-03 0.261140812689E-03 0.265500692992E-03 0.269915413839E-03 0.274385665038E-03 0.278912145075E-03 0.283495561222E-03 0.288136629647E-03 0.292836075526E-03 0.297594633158E-03 0.302413046076E-03 0.307292067167E-03 0.312232458789E-03 0.317234992887E-03 0.322300451118E-03 0.327429624970E-03 0.332623315887E-03 0.337882335393E-03 0.343207505221E-03 0.348599657440E-03 0.354059634585E-03 0.359588289787E-03 0.365186486910E-03 0.370855100685E-03 0.376595016844E-03 0.382407132260E-03 0.388292355088E-03 0.394251604906E-03 0.400285812859E-03 0.406395921805E-03 0.412582886459E-03 0.418847673549E-03 0.425191261960E-03 0.431614642890E-03 0.438118820006E-03 0.444704809598E-03 0.451373640742E-03 0.458126355455E-03 0.464964008862E-03 0.471887669362E-03 0.478898418790E-03 0.485997352589E-03 0.493185579984E-03 0.500464224148E-03 0.507834422386E-03 0.515297326304E-03 0.522854101998E-03 0.530505930229E-03 0.538254006611E-03 0.546099541795E-03 0.554043761664E-03 0.562087907518E-03 0.570233236270E-03 0.578481020646E-03 0.586832549377E-03 0.595289127408E-03 0.603852076096E-03 0.612522733419E-03 0.621302454184E-03 0.630192610243E-03 0.639194590698E-03 0.648309802128E-03 0.657539668803E-03 0.666885632910E-03 0.676349154772E-03 0.685931713086E-03 0.695634805145E-03 0.705459947078E-03 0.715408674082E-03 0.725482540667E-03 0.735683120894E-03 0.746012008626E-03 0.756470817771E-03 0.767061182540E-03 0.84757700E-03 0.788643218830E-03 0.799638262587E-03 0.810771606969E-03 0.822044991583E-03 0.833460177920E-03 0.845018949625E-03 0.856723112780E-03 0.868574496184E-03 0.880574951640E-03 0.892726354243E-03 0.905030602675E-03 0.917489619500E-03 0.930105351463E-03 0.942879769801E-03 0.955814870540E-03 0.968912674817E-03 0.982175229190E-03 0.995604605961E-03 0.100920290350E-02 0.102297224656E-02 0.103691478664E-02 0.105103270228E-02 0.106532819944E-02 0.107980351181E-02 0.109446090121E-02 0.110930265786E-02 0.112433110083E-02
