[SIESTA-L] Question about spin configuration
Dear all : I have one question about siesta. I used siesta 2.0 version and system is a Ru complex(Creutz-Taube ion) which has two redox site on Ru atom. One is 4d^6 : t2g(dxy + dyz + dxz) was supposed to be 6 electrons, eg(dz2 + dx2-y2) was supposed to be zero . And the other one is 4d^5 : t2g was supposed to be 5 electrons , eg was supposed to be zero . eg --||-- --||----||-- t2g === 4d^6 case eg --||-- --||----|-- t2g === 4d^5 case How could I use command to do this ? __ 付費才容量無上限？Yahoo!奇摩電子信箱2.0免費給你，信件永遠不必刪！ http://tw.mg0.mail.yahoo.com/dc/landing
Re: [SIESTA-L] Question about spin configuration
Dear all : I used siesta 2.0 version and system is a Ru complex(Creutz-Taube ion) which has two redox site on Ru atom. One is 4d^6 : t2g(dxy + dyz + dxz) was supposed to be 6 electrons, eg(dz2 + dx2-y2) was supposed to be zero . And the other one is 4d^5 : t2g was supposed to be 5 electrons , eg was supposed to be zero . How could I use command to do this ? In a rough tuning, you can influence spin moment; your two cases have different spin, so with a bit of luck you'll get the right coordination stabilized in one or another case. In a more sophisticated tuning, you can prepare density matrix, addressing each of d st
Re: [SIESTA-L] Question about spin configuration
On Sun, 30 Mar 2008, Cheng Pin Yen wrote: | Dear all : | I have one question about siesta. | I used siesta 2.0 version and system is a Ru | complex(Creutz-Taube ion) which has two redox site on | Ru atom. | One is 4d^6 : | t2g(dxy + dyz + dxz) was supposed to be 6 | electrons, | eg(dz2 + dx2-y2) was supposed to be zero . | And the other one is 4d^5 : | t2g was supposed to be 5 electrons , | eg was supposed to be zero . | How could I use command to do this ? Dear Cheng Pin Yen: as a rough tuning, you can define spin on each atom directly in the InitSpin block of fdf input. One of your configurations is magnetic and the other not, so with a bit of luck you will be able to stabilize one and another of them. As a more sophisticated tuning, you can hack the density matrix, addressing individual (on-site) terms for each orbital, and pray that these configurations survive in subsequent self-consistent calculation with a prudent mixing. I wrote a tool http://www.home.uni-osnabrueck.de/apostnik/Software/DMtune.tar.gz which, as it is, does not allow to modify occupations of individual orbitals, but it can be easily changed in this sense, I think. Independently on this technical problem, and speaking about Ru ion, I wonder how reasonable your results will be without a spin-orbit... 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/ --+
Re: [SIESTA-L] Segmentation fault in Broyden mixing
I'm running 2.0.2-rc9 on an Intel machine, the flags for ifort are -O3 -ip -tpp7 -xT -axT. No segmentation faults in either Broyden mixing or relaxation. Although I have to admit that the k-point parallelization isn't working, only parallelization over orbitals :) 2008/3/27, Marcos Verissimo Alves [EMAIL PROTECTED]: Hi Vasilii, Broyden mixing or Broyden relaxation (or both)? I had problems using the Broyden mixing scheme, and actually, I still am, even after this fix... Can you pass your compilation options as they are set in the arch.make? Which compiler are you using? Marcos Vous avez écrit / You have written / Lei ha scritto / Você escreveu... Vasilii Artyukhov Strange, I'm using Broyden all the time and never had any segmentation faults there... 2008/3/27, Marcos Verissimo Alves [EMAIL PROTECTED]: Hi all, I was trying to use the Broyden mixing scheme in siesta, in both versions 2.0 and 2.0.2-rc9, and I was getting a segmentation fault when it came to cycling the broyden history. Looking at the code, I saw that in the file m_broyddj.f90, the following lines (86-93) were commented: if (associated(br%dF)) deallocate(br%dF) allocate(br%dF(1:n,0:maxit)) if (associated(br%u)) deallocate(br%u) allocate(br%u(1:n,0:maxit)) if (associated(br%w)) deallocate(br%w) allocate(br%w(0:maxit)) if (associated(br%dFdF)) deallocate(br%dFdF) allocate(br%dFdF(0:maxit,0:maxit)) which was the source of the error. So if you want to use Broyden mixing for the SCF, you have to uncomment them and recompile siesta. Cheers, Marcos -- Dr. Marcos Verissimo Alves Post-Doctoral Fellow Unité de Physico-Chimie et de Physique des Matériaux (PCPM) Université Catholique de Louvain 1 Place Croix du Sud, B-1348 Louvain-la-Neuve Belgique -- Gort, Klaatu barada nikto. Klaatu barada nikto. Klaatu barada nikto. -- Dr. Marcos Verissimo Alves Post-Doctoral Fellow Unité de Physico-Chimie et de Physique des Matériaux (PCPM) Université Catholique de Louvain 1 Place Croix du Sud, B-1348 Louvain-la-Neuve Belgique -- Gort, Klaatu barada nikto. Klaatu barada nikto. Klaatu barada nikto.
[SIESTA-L] Calculation of Si bulk properties
Hi, I am a new user of SIESTA. I have been trying to reproduce the results for Si as mention in Soler et. al 2002 paper, before I go for my actual calculations. I have used the DZP Basis mentioned at http://www.uam.es/departamentos/ciencias/fismateriac/siesta/ Pseudopotential at http://www.uam.es/departamentos/ciencias/fismateriac/siesta/ My calculation for 64-atoms: 1) Lattice Constant: I changed the lattice parameter and find the energy and plotting that I find 5.45 Ang, instead of 5.40 as reported in the paper. Why this so different? 2) Bulk modulus: With B = V*Curvature = V*2c3 = 15 MPa, which is far less than 98.6 MPa? Why? Here, c3 is defined as E =C1 + c2*V + c3*V^2, curve fit to the E vs V curve. 3) Cohesive Energy: I find energy per atom 107.759eV in the bulk. Now to calculate energy per atom I tried to use the suggestions given at http://www.mail-archive.com/siesta-l@listserv.uam.es/msg03118.html I get -7.49eV/atom as pseudopotential calculation, and -576.38eV/atom as ae. So, which one is the energy of the free atom. None is a good one for comparing with the energy I got from bulk to find the cohesive energy. I really tried to search the archive and find solutions to these. I could not find any explicit answers. I am not sure what I am missing. *Some expert's simple directions can solve the problem right away*. I really need this help. Thanks in advance, Sophia Univ. of California - Berkeley Attached fdf file # - # FDF for a cubic c-Si supercell with 64 atoms # # E. Artacho, April 1999 # - SystemName 64-atom Si SystemLabel Si NumberOfAtoms 64 NumberOfSpecies 1 %block ChemicalSpeciesLabel 1 14 Si %endblock ChemicalSpeciesLabel PAO.BasisSize DZP PAO.EnergyShift 20 meV %Block PAO.Basis Si 3 -0.46385 n=3 0 2 E15.42551 4.96988 7.0 4.37722 1.0 1.0 n=3 1 2 E 4.69636 3.83128 7.0 4.09123 1.0 1.0 n=3 2 1 E11.96912 0.03131 4.55426 1.0 %EndBlock PAO.Basis LatticeConstant 5.430 Ang %block LatticeVectors 2.000 0.000 0.000 0.000 2.000 0.000 0.000 0.000 2.000 %endblock LatticeVectors %block kgrid_Monkhorst_Pack 2 0 0 0.0 0 2 0 0.0 0 0 2 0.0 %endblock kgrid_Monkhorst_Pack MeshCutoff 40.0 Ry MaxSCFIterations 100 DM.MixingWeight 0.3 DM.NumberPulay 3 DM.Tolerance 1.d-3 DM.UseSaveDM XC.functional LDA XC.authors CA SolutionMethod diagon ElectronicTemperature 25 meV WriteForces true WriteCoorStep true MD.TypeOfRun cg MD.NumCGsteps 0 MD.MaxCGDispl 0.1 Ang MD.MaxForceTol0.01 eV/Ang # earler 0.04 SaveRho true AtomicCoordinatesFormat ScaledCartesian %block AtomicCoordinatesAndAtomicSpecies 0.0 0.0 0.0 1 0.0 0.5 0.5 1 0.25000 0.25000 0.75000 1 0.25000 0.75000 0.25000 1 0.5 0.0 0.5 1 0.5 0.5 0.0 1 0.75000 0.25000 0.25000 1 0.75000 0.75000 0.75000 1 0.0 0.0 1.0 1 0.0 0.5 1.5 1 0.25000 0.25000 1.75000 1 0.25000 0.75000 1.25000 1 0.5 0.0 1.5 1 0.5 0.5 1.0 1 0.75000 0.25000 1.25000 1 0.75000 0.75000 1.75000 1 0.0 1.0 0.0 1 0.0 1.5 0.5 1 0.25000 1.25000 0.75000 1 0.25000 1.75000 0.25000 1 0.5 1.0 0.5 1 0.5 1.5 0.0 1 0.75000 1.25000 0.25000 1 0.75000 1.75000 0.75000 1 0.0 1.0 1.0 1 0.0 1.5 1.5 1 0.25000 1.25000 1.75000 1 0.25000 1.75000 1.25000 1 0.5 1.0 1.5 1 0.5 1.5 1.0 1 0.75000 1.25000 1.25000 1 0.75000 1.75000 1.75000 1 1.0 0.0 0.0 1 1.0 0.5 0.5 1 1.25000 0.25000 0.75000 1 1.25000 0.75000 0.25000 1 1.5 0.0 0.5 1 1.5 0.5 0.0 1 1.75000 0.25000 0.25000 1 1.75000 0.75000 0.75000 1 1.0 0.0 1.0 1 1.0 0.5 1.5 1 1.25000 0.25000 1.75000 1 1.25000
