[SIESTA-L] Queries about reliability of SIESTA under LDA
Dear Users, I have computed the high pressure properties and electronic structure calculations of a semiconducting heavy earth compounds with LDA and non-relativistic, alongwith polarization orbitals : perturbative polarization. I got underestimated results on phase transition and enrergy gap by an amount of 2-3 %, which seems to be within the limits of DFT - LDA. Is it necessary that LDA not capable to describe the strong correlations in heavy earth compounds with f electrons if one doesnot include spin effect during calculations ? Does it mean that we might have got the right answer for a wrong reason using SIESTA with LDA ? If so, what may be the causes ? May someone answer these queries for my satisfaction ? Thanks in anticipation, Nidhi - Unlimited freedom, unlimited storage. Get it now
Re: [SIESTA-L] Magnetic properties using siesta
Resected Dr. Richardo Faccio, Many thanks for your mail. I wish to calculate ferro-magnetic to anti-ferromagnetic transition along with structural transition. I have computed structural phase transition without spin. But in case of the material I wish to study eg. Ce compounds (which shows magnetic as well as structural transition. I wish to calculate curie temperature, suseptibility and other realted proeprties which lead to magnetic as well as structural transition under pressure as well as at high temperatures. In what units (bohr magnetron ?) the magnetic moment is reported in .out file ? Regards, Nidhi Ricardo Faccio [EMAIL PROTECTED] wrote: Dear Nidhi I think we need a little more information about which type of transition are you looking for ... in order to help you in this task. But, in principle, setting up a spinpolarized .true. could lead to a magnetic solution, you can check the total magnetic moment per cell looking at Q(up-down)... as you said. A Mulliken population analysis could give an idea of the partial magnetic moment in different atoms. Regards Ricardo - -Dr. Ricardo Faccio Mail: Cryssmat-Lab., Cátedra de Física, DETEMA Facultad de Química, Universidad de la República Av. Gral. Flores 2124, C.C. 1157 C.P. 11800, Montevideo, Uruguay. E-mail: [EMAIL PROTECTED] Phone: 598 2 9241860 Int. 109 598 2 9290705 Fax:598 2 9241906 Web: http://cryssmat.fq.edu.uy/ricardo/ricardo.htm - Original Message - From:NidhiSharma To: SIESTA-L@listserv.uam.es Sent: Thursday, August 07, 2008 2:55AM Subject: [SIESTA-L] Magnetic propertiesusing siesta Hi to all, I am trying to compute the magneticproperties of CdTe at 0 temperature as well as at high temperature. Todo this I have used SPIN POLARIZATION .true. in the .fdf file. Is anyother patch should I insert in .fdf file except spin polarization. Howcan I compute the magnetic to non-magnetic transition in this compound. One more thing that I found in the .out file is that it reports some value forQ(up-down). Is it magnetic dipole moment in units of bohrmagneton. Any suggestions are welcome. - Did you know? You can CHAT without downloading messenger. Clickhere - Check out the all-new face of Yahoo! India. Click here.
[SIESTA-L] Magnetic properties using siesta
Hi to all, I am trying to compute the magnetic properties of CdTe at 0 temperature as well as at high temperature. To do this I have used SPIN POLARIZATION .true. in the .fdf file. Is any other patch should I insert in .fdf file except spin polarization. How can I compute the magnetic to non-magnetic transition in this compound. One more thing that I found in the .out file is that it reports some value for Q(up-down). Is it magnetic dipole moment in units of bohr magneton. Any suggestions are welcome. - Did you know? You can CHAT without downloading messenger. Click here
[SIESTA-L] Convergence test for the mesh cut-off and k-point
Hi to all, Will anybody please guide me how to perform the convergence test for mesh-cut-off and k-point (Mohnkorst-Pack scheme)? For this what changes should make in the .fdf file ? Thanks, Nidhi - Bring your gang together. Do your thing. Find your favourite Yahoo! Group.
Re: [SIESTA-L] How to define Bulk Modulus
Respected Sir (Prof.(s) Dr. S. Auluck and Andrei Postnikov) Many thanks for giving me proper guidelines to execute mur_fit.f. As I defined unit cell volume in Bohr^3. Is it same to (a.u.)^3 ? It is reporting one value as BP. Does it mean B' (dB/dP) ? Regards, Sushil Auluck [EMAIL PROTECTED] wrote: nidhi, try ifort.. s.auluck -- Prof. Sushil Auluck Phone: +91-512-6798177(Home) Department of Physics+91-512-6796148/7092(Work) Indian Institute of Technology Mobile: +91-9305548667 Kanpur 208016 (UP) e-mail: [EMAIL PROTECTED] Indiae-mail: [EMAIL PROTECTED] http://www.iitk.ac.in/phy/People/phy_facvis.html http://www.iitk.ac.in/phy/New01/profile_SA.html - Forgot the famous last words? Access your message archive online. Click here.
Re: [SIESTA-L] How to define Bulk Modulus
Respected Andrei Sir, I have run mur_fit.f this program on the bash shell using f77 complier. It displays the following error mur_fit.f: In program `mur_fit': mur_fit.f:117: call lmdif(murna,m,n,x,y,ftol,ftol,ftol,maxfev,epsfcn,diag,mode, ^ Invalid declaration of or reference to symbol `murna' at (^) [initially seen at (^)] mur_fit.f: In subroutine `lmdif': mur_fit.f:117: warning: call lmdif(murna,m,n,x,y,ftol,ftol,ftol,maxfev,epsfcn,diag,mode, 1 mur_fit.f:222: (continued): subroutine lmdif(fcn,m,n,x,fvec,ftol,xtol,gtol,maxfev,epsfcn, 2 Argument #1 (named `fcn') of `lmdif' is a subroutine at (2) but is passed by reference at (1) [info -f g77 M GLOBALS] [EMAIL PROTECTED] Desktop]$ f77 mur_fit.f mur_fit.f: In program `mur_fit': mur_fit.f:117: call lmdif(murna,m,n,x,y,ftol,ftol,ftol,maxfev,epsfcn,diag,mode, ^ Invalid declaration of or reference to symbol `murna' at (^) [initially seen at (^)] mur_fit.f: In subroutine `lmdif': mur_fit.f:117: warning: call lmdif(murna,m,n,x,y,ftol,ftol,ftol,maxfev,epsfcn,diag,mode, 1 mur_fit.f:222: (continued): subroutine lmdif(fcn,m,n,x,fvec,ftol,xtol,gtol,maxfev,epsfcn, 2 Argument #1 (named `fcn') of `lmdif' is a subroutine at (2) but is passed by reference at (1) [info -f g77 M GLOBALS] Is error because of bash shell or compiler. If yes then which compiler should I use ? Please guide me. Regards, Nidhi Andrei Postnikov [EMAIL PROTECTED] wrote: Nidhi: if you are only interested in the E(a) curve, why are you doing MD annealing? You only need a sequence of ~10 static calculations MD.TypeOfRun CG# Default value MD.NumCGsteps 0 (the TypeOfRun does not really matter, but you do not need more than the initial step in whatever kind of MD!) for values of lattice constants within several % around the equilibrium, then you fit the results (total energy) to the Murnaghan (or other) equation of state and you get bulk modulus and its derivative immediately from the fit. If you don't have your favourite fitting progran use mine, http://www.home.uni-osnabrueck.de/apostnik/Software/mur_fit.f (have a look at the fitting curve vs. your data points before believing in the numbers you get from the fit!) The interval of A= 5 to 7 Ang might be OK to localize the minimum, but for a clean fit you'd need much more densely situated points just around the minimum. Good luck, Andrei +-- Dr. Andrei Postnikov Tel. +33-387315873 - mobile +33-666784053 ---+ | Paul Verlaine University - Institute de Chimie, Physique et Mat\'eriaux, | | Laboratoire de Physique des Milieux Denses, 1 Bd Arago, F-57078 Metz, France | +-- [EMAIL PROTECTED] -- http://www.home.uni-osnabrueck.de/apostnik/ --+ On Wed, 23 Apr 2008, Nidhi Sharma wrote: | Dear users, | | I am trying to find the Energy vs alat curve for the B1 phase of LaAs. For this I set the MD. type of run Anneal and Target pressure set to 0.0 GPa and vary the value of alat from 5 to 7 Ang in steps of 0.1. | | MD.TypeOfRun Anneal | MD.AnnealOption Pressure | MD.TargetPressure 0.0 GPa | MD.TauRelax 100.0 fs | MD.BulkModulus100.0 Ry/Bohr**3 | MD.MaxStressTol 0.1 GPa | MD.VariableCell .true. | | I have given default value of Bulk Modulus in .fdf file. What values should I given for MD.BulkModulus in .fdf file. | I got the different energies and pressure for different alat and got the optimal alat. The .out file also report some data in Ry/Bohr**3. I think it is bulk modulus and how we will get the first pressure derivative of Bulk Modulus ? | | Please guide me. | | Thanks in anticipation, | | Nidhi Sharma | - Bring your gang together. Do your thing. Find your favourite Yahoo! Group.
Re: [SIESTA-L] How to define Bulk Modulus
Respeted Andrei Sir, I tried it again with g77 (earlier tried with f77) and got the error as listed below [EMAIL PROTECTED] Desktop]$ g77 mur_fit.f mur_fit.f: In program `mur_fit': mur_fit.f:117: call lmdif(murna,m,n,x,y,ftol,ftol,ftol,maxfev,epsfcn,diag,mode, ^ Invalid declaration of or reference to symbol `murna' at (^) [initially seen at (^)] mur_fit.f: In subroutine `lmdif': mur_fit.f:117: warning: call lmdif(murna,m,n,x,y,ftol,ftol,ftol,maxfev,epsfcn,diag,mode, 1 mur_fit.f:222: (continued): subroutine lmdif(fcn,m,n,x,fvec,ftol,xtol,gtol,maxfev,epsfcn, 2 Argument #1 (named `fcn') of `lmdif' is a subroutine at (2) but is passed by reference at (1) [info -f g77 M GLOBALS] I again request you to spare your time to help solving this problem. Regards, - From Chandigarh to Chennai - find friends all over India. Click here.
[SIESTA-L] How to define Bulk Modulus
Dear users, I am trying to find the Energy vs alat curve for the B1 phase of LaAs. For this I set the MD. type of run Anneal and Target pressure set to 0.0 GPa and vary the value of alat from 5 to 7 Ang in steps of 0.1. MD.TypeOfRun Anneal MD.AnnealOption Pressure MD.TargetPressure 0.0 GPa MD.TauRelax 100.0 fs MD.BulkModulus100.0 Ry/Bohr**3 MD.MaxStressTol 0.1 GPa MD.VariableCell .true. I have given default value of Bulk Modulus in .fdf file. What values should I given for MD.BulkModulus in .fdf file. I got the different energies and pressure for different alat and got the optimal alat. The .out file also report some data in Ry/Bohr**3. I think it is bulk modulus and how we will get the first pressure derivative of Bulk Modulus ? Please guide me. Thanks in anticipation, Nidhi Sharma - Bring your gang together. Do your thing. Find your favourite Yahoo! Group.
Re: [SIESTA-L] PAO basis of Sm and Te
Dr. Andrei Postnikov, Many thanks for sharing valuable information with us. Regards, Nidhi [EMAIL PROTECTED] wrote: Sir, As per your instructions to include 5d in the basis of Te Nidhi: who ever gave you instructions to include 5d in the basis of Te? The previous discussion was about Sm5d, which you now included. As for d-states of Te - there might be a good reason to include some if you find it necessary; but these must be semicore 4d states (in which case, also taken as valence ones in the generation of pseudopotential). Te5d are too far away and not bound, as SIESTA correctly informs you: SPLIT: Basis orbitals for state 5d SPLIT: ERROR Orbital with angular momentum L= 2 not bound in the atom Note that you'd probably need Te4d (if at all) only in order to get good elastic properties, otherwise the basis with Te 5s+5p (add polarization orbitals on Te5p!) could be quite good. Best regards Andrei Postnikov When I define the PAO basis as Sm 4 # Label, l-shells n=6 0 2 P 1 # n, l, Nzeta, Polarization, NzetaPol 0.000 0.000 1.000 1.000 n=6 1 2 0.000 0.000 1.000 1.000 n=5 2 2 0.000 0.000 1.000 1.000 n=4 3 2 0.000 0.000 1.000 1.000 Te 3# Species label, number of l-shells n=5 0 2 P 1 # n, l, Nzeta, Polarization, NzetaPol 0.000 0.000 1.000 1.000 n=5 1 2 # n, l, Nzeta 0.000 0.000 1.000 1.000 n=5 2 2 0.000 0.000 1.000 1.000 it displayed the following error for Te SPLIT: Orbitals with angular momentum L= 2 SPLIT: Basis orbitals for state 5d SPLIT: ERROR Orbital with angular momentum L= 2 not bound in the atom SPLIT: ERROR a cut off radius must be explicitely given Stopping Program from Node:0 But when I remove the 5d in the basis of Te it ran successfully. Please guide me how can I define 5d in the basis of Te. Regards and thanks, Nidhi - Best Jokes, Best Friends, Best Food. Get all this and more on Best of Yahoo! Groups.
Re: [SIESTA-L] PAO basis of Sm and Te
Sir, As per your instructions to include 5d in the basis of Te When I define the PAO basis as Sm 4 # Label, l-shells n=6 0 2 P 1 # n, l, Nzeta, Polarization, NzetaPol 0.000 0.000 1.000 1.000 n=6 1 2 0.000 0.000 1.000 1.000 n=5 2 2 0.000 0.000 1.000 1.000 n=4 3 2 0.000 0.000 1.000 1.000 Te 3# Species label, number of l-shells n=5 0 2 P 1 # n, l, Nzeta, Polarization, NzetaPol 0.000 0.000 1.000 1.000 n=5 1 2 # n, l, Nzeta 0.000 0.000 1.000 1.000 n=5 2 2 0.000 0.000 1.000 1.000 it displayed the following error for Te SPLIT: Orbitals with angular momentum L= 2 SPLIT: Basis orbitals for state 5d SPLIT: ERROR Orbital with angular momentum L= 2 not bound in the atom SPLIT: ERROR a cut off radius must be explicitely given Stopping Program from Node:0 But when I remove the 5d in the basis of Te it ran successfully. Please guide me how can I define 5d in the basis of Te. Regards and thanks, Nidhi [EMAIL PROTECTED] wrote: Hi, I have made the changes according to u and defined the pseudo of Sm as Hi - If u refers to me, mind that I never advised you on the pseudo radii for Sm... I only meant that inclusing 4f is technically no error - but it will probably lead to physically wrong results. Whatever... Regarding your problems with calculations which sometimes stop at an error in basis block, sometimes not: you should carefully read the SIESTA doc file about the syntaxis of the basis block. Namely: but when I define the PAO basis like %block PAO.Basis Sm 2 # Label, l-shells n=6 0 2 P 1 # n, l, Nzeta, Polarization,NzetaPol 0.000 0.000 1.000 1.000 n=6 1 2 0.000 0.000 1.000 1.000 n=5 2 2 0.000 0.000 1.000 1.000 n=4 3 2 0.000 0.000 1.000 1.000 - yes, it fails, because you declared 2 l-shells (1st line of the Sm block) but in the following you pass the info for 4 l-shells. I thought we were already past this problem... Again I mabe the changes in PAO basis as %block PAO.Basis Sm 2 # Label, l-shells n=6 0 2 P 1 # n, l, Nzeta, Polarization, NzetaPol 0.000 0.000 1.000 1.000 n=4 3 2 0.000 0.000 1.000 1.000 Te 2# Species label, number of l-shells n=5 0 2 P 1 # n, l, Nzeta, Polarization, NzetaPol 0.000 0.000 1.000 1.000 n=5 1 2 # n, l, Nzeta 0.000 0.000 1.000 1.000 %endblock PAO.Basis then the program run successfully but lattice parameter and band gap is far from our expt values. Now this is formally correct (number of l-shells declared equals number of l-shells passed), but the basis (at least for Sm) is not complete enough - you'd need 5d in the basis. And after you do this, do not expect to get band structure right, because 4f states will most probably be at a wrong energy... Good luck Andrei Postnikov - Get the freedom to save as many mails as you wish. Click here to know how.
[SIESTA-L] Body centred tetragonal structure
Hi to all, Will anybody please guide me how to define LatticeConstant, %block LatticeVectors, %block AtomicCoordinatesAndAtomicSpecies, %block BandLines for Body centred tetragonal structure. Thanks in advance. Nidhi - From Chandigarh to Chennai - find friends all over India. Click here.
[SIESTA-L] Valence configuration of samarium
Hi to all, Dear users, as we know the valence configuration of Sm is 4f6,6s2. In order to combine it with chalcogenides it is necessary to make the net ionic charge of Sm to 2, means we have to consider the 4f6 in the core. When we define the PAO basis set as %block PAO.Basis Sm 2 # Label, l-shells n=6 0 2 P 1 # n, l, Nzeta, Polarization, NzetaPol 0.000 0.000 1.000 1.000 Te 2# Species label, number of l-shells n=5 0 2 P 1 # n, l, Nzeta, Polarization, NzetaPol 0.000 0.000 1.000 1.000 n=5 1 2 # n, l, Nzeta 0.000 0.000 1.000 1.000 %endblock PAO.Basis it will display the following message reinit: --- reinit: System Name: SmTe reinit: --- reinit: System Label: SmTe reinit: --- initatom: Reading input for the pseudopotentials and atomic orbitals -- Species number:1 Label: Sm Atomic number: 62 Species number:2 Label: Te Atomic number: 52 Ground state valence configuration: 6s02 4f06 Reading pseudopotential information in formatted form from Sm.psf Ground state valence configuration: 5s02 5p04 Reading pseudopotential information in formatted form from Te.psf Bad format of (n), l, nzeta line in PAO.Basis Stopping Program from Node:0 If I include the 4f6 in basis set it will make the net charge 8 and behave as a semi core. If I use a already generated pseudo file of Te which include 5s2, 5p4, 4d0 and 4f0 But how can 4d0 is possible although it contains 10 electrons. When I use this file then we get results but band gap in B1 phase is ~10eV which is quite far from the expt 0.67eV. Please help me how can i resolve the problem of valence charge . Thanks in advance. Nidhi - Did you know? You can CHAT without downloading messenger. Click here
[SIESTA-L] how to define the value of rc to generate pseudo potential
Hi, As I am trying to generate pseudopotential for Sm. Will any body please spare your valuable time to guide me that how to calculate the last line in the pseuopotential input file [rc(s) rc(p) rc(d) rc(f) rcore_flag rcore] eg., it is given in the atom user manual for silicon on page 5. 1.901.901.901.90 0.000.00 rc(s)rc(p)rc(d)rc(f)rcore_flagrcore as I used the already generated pseudo potential from pseudo and bases but it shows the valence configuration of Sm as 6s( 2.00) rc: 3.11 6p( 0.00) rc: 4.10 5d( 0.00) rc: 3.11 5f( 0.00) rc: 3.11 There is no discussion of 4f states even it is also apart of valence states. So I just want to generate my own pseudo potential. So please help me that how I can define rc's for Sm. Is we can choose this value randomly? Regards, Nidhi Sharma - Download prohibited? No problem. CHAT from any browser, without download.
Re: [SIESTA-L] pseudo database; Zn configuration
Hi to all, I am trying to generate the pseudo potential of Sm and S. I am not able to define the last line of pseudo potential input file [rc(s) rc(p) rc(d) rc(f) rcore_flag rcore.] If this data is fixed then from where I can collect this data? Regards, Nidhi Yurko Natanzon [EMAIL PROTECTED] wrote: Dear Andrei, On 13/03/2008, Andrei Postnikov wrote: Many thanks for Eduardo Anglada for uploading the ABINIT pseudos! Just two related questions: 1. Does somebody know whether there s a way to see from the .psf file if the core correction is included, and with which radius? yes, the first line has such an info: #Zr pb nrl nc nc = no core correction pcec - core correction exchange you may find this from the link below by playing with parameters and cheking the changes in first line of output psf: http://www.tddft.org/programs/octopus/pseudo.php (or by using atom for this purposes) I don't know about the radius, it seems that some standard value is used. +-- Dr. Andrei Postnikov Tel. +33-387315873 - mobile +33-666784053 ---+ | Paul Verlaine University - Institute de Chimie, Physique et Mat\'eriaux, | | Laboratoire de Physique des Milieux Denses, 1 Bd Arago, F-57078 Metz, France | +-- [EMAIL PROTECTED] -- http://www.home.uni-osnabrueck.de/apostnik/ --+ -- Yurko (aka Yuriy, Iurii, Jurij etc) Natanzon PhD Student Henryk Niewodniczan`ski Institute of Nuclear Physics Polish Academy of Sciences ul. Radzikowskiego 152, 31-342 Krako`w, Poland Email: [EMAIL PROTECTED], [EMAIL PROTECTED] - Why delete messages? Unlimited storage is just a click away.
Re: [SIESTA-L] difference between spin- and nonspoin- polarized .psf ?
Hi to all, Will anybody guide me that how to modify the .fdf file to get the data for energy vs. lattice constant for computing phase transformation. In which file we can obtained this information? Regards, Nidhi reza behnam [EMAIL PROTECTED] wrote: Dear all, I am testing a ppt for hcp-co by energy minimization with lattice constant and a fixed c/a. with non-polarization option in fdf file it converge very well and I am getting a reasonable lattice constant but when I set the SpinPolarized T , it dose not converge! dose it mean that there is a difference between spin- and nonspoin- polarized .psf ? How can I fix this problem? any advice would be appreciated. Best Regards, Reza Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs - Why delete messages? Unlimited storage is just a click away.
