Re: [Wien] wien2venus.py problem
Dear Yasir Ali Please use XCrysden for calculating the 3D electron density distribution in WIEN2k. It can handle spin polarized cases as well. Regards Sharat Chandra On Thu, 18 Jul 2013, Yasir Ali wrote: Date: Thu, 18 Jul 2013 22:16:35 -0700 (PDT) From: Yasir Ali Reply-To: A Mailing list for WIEN2k users To: wien Subject: [Wien] wien2venus.py problem I am facing problem in wien2venus.py. i used "wien2venus.py 50 50 50 "to generate case.rho3d file of electron density. When i used to plot this generated file, i.e., case.rho3d in VESTA, it does not give plot but only give an empty cube. So any one can tell me what is the problem? Regards: Yasir Ali ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Calculations at moderate T
If the bulk thermal expansion is anisotropic it would also mean that we will have to take the appropriate values. In the case of a surface it might be anisotropic even if that for the bulk material is isotropic. On Tue, 9 Apr 2013, Laurence Marks wrote: Date: Tue, 9 Apr 2013 18:50:16 -0500 From: Laurence Marks Reply-To: A Mailing list for WIEN2k users To: A Mailing list for WIEN2k users Subject: Re: [Wien] Calculations at moderate T Thanks. Method a) is the only reasonable one, coupled with extrapolating the bulk reference lattice parameters. This would have to be done by a uniform volume expansion without relaxation of course. On Tue, Apr 9, 2013 at 3:03 PM, Peter Blaha wrote: a) Simply empirically extrapolate a0 to a possible value at 1200 K. b) Ab initio: quasiharmonic approximation. Calculate phonons (wien2k + ponon or phonopy, see u supported sw) and resulting -TS at various lattice parameters and search for the minimum of the free energy as function of a0 at the desired T Of course, for a surface this is more difficult. Of course one can use the expanded a,b lattice constants, but relaxation of z will still corrsepond to t=0. It is more a simulation of an epitactically expanded lattice. Am 09.04.2013 19:38, schrieb Laurence Marks: Does anyone know of methods to do calculations at T~1200K taking account of bulk thermal expansion? I am interested in a surface calculation where I suspect that it may be important to consider this, and a moderately rational approach to doing this that has been tested/published would be useful. -- - Peter Blaha Inst. Materials Chemistry, TU Vienna Getreidemarkt 9, A-1060 Vienna, Austria Tel: +43-1-5880115671 Fax: +43-1-5880115698 email: pbl...@theochem.tuwien.ac.at - ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html -- Dr. Sharat Chandra %%%_%%___%%% Home Address %%% Scientist & Asst. Prof. HBNI (_) ___ ___ / _ \ ___ 117, Fifth Avenue Materials Science Group, | |/ _ \ / __\| |_| |' _ \ DAE Township IGCAR, Kalpakkam,| | (_) | |__,| _ | | \| Kalpakkam 603102, Tamil Nadu, INDIA|_|\__/ |\___/|_| |_|_|603102 TN INDIA Ph: +91 44 27480500*22167 / /| | +91 44 27481521 email: sha...@igcar.gov.in | |_| | shara...@gmail.com \___/%%% ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
[Wien] Initialization issue with core leak out of sphere And RMT Sums Greater than NN-DIST
Have you given the lattice parameters in Bohr units or in nm units? I Bohr = 0.5291772108 A On Mon, 5 Dec 2011, Qiwen YAO wrote: > Date: Mon, 05 Dec 2011 19:24:36 +0900 > From: Qiwen YAO > Reply-To: A Mailing list for WIEN2k users > To: A Mailing list for WIEN2k users > Subject: [Wien] Initialization issue with core leak out of sphere And RMT Sums > Greater than NN-DIST > > Dear all, > I have been facing a few compounds that I am unable to do the initialization > (using w2web) for the calculation. > > The problem is: > I was facing both "core leak out of sphere, and RMT Sums Greater than > NN-DIST" at the same time. > > A recent example: I am trying to do an calculation initialization on the > LuFe2O4 (R-3m group) crystal (cell parameters are from the Pearson's Crystal > Data sheet 382676, a=b=0.3435nm, c=2.525nm, Alpha=Beta=90 degree, Theta=120 > degree. Atomic positions: > O1: 0 0 0.1295 > Fe: 0 0 0.2141 > O2: 0 0 0.2914 > Lu: 0 0 0 > ). > > Using the WIEN default RMT values and the default ENERGY to separate core and > valence states (-6) , I was facing core electrons leak out of MT-sphere > message for all four atoms. So I go back to the step and change the > separation energy to the lowest possible value (-10 in this case) - if going > any lower than -10, I will be seeing the error message after running start>, like these: > > forrtl: severe (24): end-of-file during read, unit -4, file stdin > error: command /home/wen/WIEN2K11/wien2k11install/lstart lstart.def failed > > So, the natural step I took next is to increase the RMT values for the atoms > correspondingly (according to each atom's core leak value). Then I am facing > an another problem: If I am to increase the RMT values too large, then in > the step I will be seeing errors like > > ERROR !!! > RMT( 1)=0.53000 AND RMT( 1)=0.53000 > SUMS TO 1.06000 GT NNN-DIST= 0.84061 > > But if the RMT value is not increased enough then the core leaking message > will still be there. > > So how would I solve such problems? I have been facing these for a few > compounds - for example, the other compound I tried was BiAlO3 which would > lead me to the same bottle-neck problem. > > Is there an automatic approaching way that I can take to get rid of both > error message at the same time? For cases like these, if there is no > practical solution to the initialization would that means the unit cell > parameters were out of touch (reality)? > > Thank you for reading. I have been searching the archive for a solution but > no luck. > > Kind regards, > Wen > > ** > > Dr QiWen YAO > JSPS Fellow > Multifunctional Materials Group > Optical and Electronic Materials Unit > Environment and Energy Materials Research Division > > National Institute for Materials Science > > 1-2-1 Sengen, Tsukuba, Ibaraki 305-0047, Japan > Phone: +81-29-851-3354, ext. no. 6482, Fax: +81-29-859-2501 > > ****** > > ___ > Wien mailing list > Wien at zeus.theochem.tuwien.ac.at > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > -- Dr. Sharat Chandra %%%_%%___%%% Home Address %%% Scientist & Asst. Prof. HBNI (_) ___ ___ / _ \ ___ 117, Fifth Avenue Materials Science Group, | |/ _ \ / __\| |_| |' _ \ DAE Township IGCAR, Kalpakkam,| | (_) | |__,| _ | | \| Kalpakkam 603102, Tamil Nadu, INDIA|_|\__/ |\___/|_| |_|_|603102 TN INDIA Ph: +91 44 27480500*22167 / /| | +91 44 27481521 email: sharat at igcar.gov.in | |_| | sharat.c at gmail.com \___/%%%
[Wien] About optic code in WIEN2k_11.1 (Release 5/4/2011)
Hi I have a report to make about the optic code included in WIEN2k_11.1 (Release 5/4/2011). I am using the WIEN2k on a Fedora 12 system with ifort (IFORT) 10.1 20080602. I am calculating the optical constants for Si diamond structure crystal. (lattice parameter 10.270700 atu, Si at (1/8,1/8,1/8). My Si.inop file is given below (just the default file from case.inop, where I have put the proper number of bands in line 2 for NBvalMAX): --- 9 1 number of k-points, first k-point -5.0 3.0 4Emin, Emax for matrix elements, NBvalMAX 2 number of choices (columns in *outmat): 1 Re xx 3 Re zz OFF ON/OFF writes MME to unit 4 Choices: 1..Re 2..Re 3..Re 4..Re 5..Re 6..Re 7..Im 8..Im 9..Im - When I run the command: x optic, I get the following error: emin,emax,nbvalmax -5.00 3.00 4 creating ust kmin,kmax -16 -16 -16 16 16 16 forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PCRoutineLineSource optic 00428975 planew_ 166 planew_tmp.f optic 0043AAA7 mom_mat_ 588 sph-UP_tmp.f optic 0047 MAIN__447 opmain.f optic 0040328E Unknown Unknown Unknown libc.so.6 0030BE61EB1D Unknown Unknown Unknown optic 004031A9 Unknown Unknown Unknown 8.090u 0.232s 0:08.33 99.8% 0+0k 0+5840io 0pf+0w error: command /usr/local/wien2k111/optic optic.def failed -- This input file runs properly with the optic package included in WIEN2k_09.2 (Release 29/9/2009). I am not able to understand where is the error coming from as the codes in both the versions are quite different. Regards Sharat Chandra
[Wien] charge density of a single atom
Hi I am interested in obtaining the variation in the charge density with respect to r, for isolated Y atom. For this I have seen the convergence of total energy with respect to the unit cell length, RMT*kmax and Gmax and I use a single k-point for all the calculations. I obtain 15 a.u. as the converged unit cell parameter. I have put the atom in the centre of the unit cell. scf shows that there are 11 electrons in the valence band, ie., 4s2, 4p6, 4d1, 5s2. The input for lapw2 in electron density calculation is the range of the valence electrons energy obtained in the scf file. I carry out the calculation of the 3D charge density using XCrysden, using RHO, ANG, VAL, NODEBUG as the inputs for lapw5 program. I calculate the the distribution of the charge density from the (1/2,1/2,1/2) to (1,1/2,1/2) direction along the single line to get the rho(r) versus r on a 300 point grid from the xsf data save by XCrysden. When I perform an integration of this data (by integrating the r versus 4*pi*r^2*rho(r) data) to obtain the total charge, I get ~20 electrons. I should be getting either 11 electrons, or 39 electrons, which is the atomic number of Y, what I get is neither here nor there. Can you please tell me what I am doing wrong? Is it that I have to use AIM to get the real charge density, or any other method is to be used? Regards Sharat Chandra
[Wien] charge density of a single atom
Hi I am interested in obtaining the variation in the charge density with respect to r, for isolated Y atom. For this I have seen the convergence of total energy with respect to the unit cell length, RMT*kmax and Gmax and I use a single k-point for all the calculations. I obtain 15 a.u. as the converged unit cell parameter. I have put the atom in the centre of the unit cell. scf shows that there are 11 electrons in the valence band, ie., 4s2, 4p6, 4d1, 5s2. The input for lapw2 in electron density calculation is the range of the valence electrons energy obtained in the scf file. I carry out the calculation of the 3D charge density using XCrysden, using RHO, ANG, VAL, NODEBUG as the inputs for lapw5 program. I calculate the the distribution of the charge density from the (1/2,1/2,1/2) to (1,1/2,1/2) direction along the single line to get the rho(r) versus r on a 300 point grid from the xsf data save by XCrysden. When I perform an integration of this data (by integrating the r versus 4*pi*r^2*rho(r) data) to obtain the total charge, I get ~20 electrons. I should be getting either 11 electrons, or 39 electrons, which is the atomic number of Y, what I get is neither here nor there. Can you please tell me what I am doing wrong? Is it that I have to use AIM to get the real charge density, or any other method is to be used? Regards Sharat Chandra
[Wien] mpich2 with Wien2k
Dear Lawrence We have been able to get the WIEN working only with the mpich1 till now and we too get the same error as you have reported. The error is mainly due to the error in the devices that get made during the compilation of mpich2. However, WIEN works properly with lammpi package. We have the mpich1/2 and lam on our 64 node cluster machine with Redhat 4E and Intel ifort 9/mkl8 compilers. Till now we have found the mpich1 or lam mpi to be compatible with most of the dft packages. Hope this helps you. Regards Sharat Chandra On Fri, 18 Apr 2008, Laurence Marks wrote: > Has anyone got this working? I'm getting an error in CALL > SL_INIT(ICTXTALL, 1, NPE) in lapw1 of > > Fatal error in MPI_Comm_size: Invalid communicator, error stack: > MPI_Comm_size(110): MPI_Comm_size(comm=0x5b, size=0xa4ee68) failed > MPI_Comm_size(69).: Invalid communicator > > (it might be some bad hardware/drivers)
[Wien] Where is the MKL?
Hi You have to run the proper mklvars*.sh or mklvars*.csh file depending on your shell (whether bash or csh/tcsh) at the login time (put it in the .bashrc or .tcshrc). Regards Sharat Chandra
