Pseudopotentials depend on the original functional and not on the "+U" value. You can find several peudopotentials here http://charter.cnf.cornell.edu/dd_search.php?frmxcprox=&frmxctype=&frmspclass=TM or here (for GGA pseudopotentials) http://departments.icmab.es/leem/siesta/Databases/Pseudopotentials/periodictable-gga-abinit.html or you can create your own one (if you know how to) using the program atom.
> Hello sir > I am doing calculations for Mn using lda+u . I got the problem with pseudo > potential of Mn. If u have the pseudo potential for Mn compatible with > lda+u.plz send me. > On 15 Mar 2015 10:47, <fthe...@iesl.forth.gr> wrote: > >> Same problem for me, but never resolved.... >> >> >> > Dear Siesta users and developers, >> > >> > >> > >> > I want to do some LDA+U calculations by the ldau version of siesta. I >> > compiled it with the same makefile as I used for siesta-3.2. I have >> tested >> > the example of Fe_ldau in the subdirectory of Siesta. However, it >> turned >> > out >> > that when I use only 1 core the execution is successful but if I use >> more >> > cores the code seems pausing at the following lines not moving on but >> it >> > never stops prompted an error. By the way, I can run normal >> calculations >> > without LDA+U with the ldau version of siesta with many cores >> > successfully. >> > So, What is the problem? Any advice and comment will be appreciated. >> > >> > >> > >> > Siesta Version: >> > siesta-2.6.8--ldau-reference-6-dm-fix >> > >> > Architecture : x86_64-unknown-linux-gnu--Intel >> > >> > Compiler flags: mpif90 -g -O2 >> > >> > PARALLEL version >> > >> > >> > >> > * Running on 3 nodes in parallel >> > >> >>> Start of run: 14-MAR-2015 17:39:52 >> > >> > >> > >> > *********************** >> > >> > * WELCOME TO SIESTA * >> > >> > *********************** >> > >> > >> > >> > reinit: Reading from standard input >> > >> > ************************** Dump of input data file >> > **************************** >> > >> > # $Id: Fe.fdf,v 1.1 1999/04/20 12:52:43 emilio Exp $ >> > >> > # >> > >> ---------------------------------------------------------------------------- >> > - >> > >> > # FDF for bcc iron >> > >> > # >> > >> > # GGA, Ferromagnetic. >> > >> > # Scalar-relativistic pseudopotential with non-linear partial-core >> > correction >> > >> > # >> > >> > # E. Artacho, April 1999 >> > >> > # >> > >> ---------------------------------------------------------------------------- >> > - >> > >> > SystemName bcc Fe ferro GGA # Descriptive name of the system >> > >> > SystemLabel Fe # Short name for naming files >> > >> > # Output options >> > >> > WriteCoorStep >> > >> > WriteMullikenPop 1 >> > >> > # Species and atoms >> > >> > NumberOfSpecies 1 >> > >> > NumberOfAtoms 1 >> > >> > %block ChemicalSpeciesLabel >> > >> > 1 26 Fe >> > >> > %endblock ChemicalSpeciesLabel >> > >> > # Basis >> > >> > PAO.EnergyShift 50 meV >> > >> > PAO.BasisSize DZP >> > >> > %block PAO.Basis >> > >> > Fe 2 >> > >> > 0 2 P >> > >> > 6. 0. >> > >> > 2 2 >> > >> > 0. 0. >> > >> > %endblock PAO.Basis >> > >> > LatticeConstant 2.87 Ang >> > >> > %block LatticeVectors >> > >> > 0.50000 0.500000 0.500000 >> > >> > 0.50000 -0.500000 0.500000 >> > >> > 0.50000 0.500000 -0.500000 >> > >> > %endblock LatticeVectors >> > >> > KgridCutoff 15. Ang >> > >> > %block BandLines >> > >> > 1 0.00000 0.000000 0.000000 \Gamma >> > >> > 40 2.00000 0.000000 0.000000 H >> > >> > 28 1.00000 1.000000 0.000000 N >> > >> > 28 0.00000 0.000000 0.000000 \Gamma >> > >> > 34 1.00000 1.000000 1.000000 P >> > >> > %endblock BandLines >> > >> > xc.functional GGA # Exchange-correlation functional >> > >> > xc.authors PBE # Exchange-correlation version >> > >> > SpinPolarized true # Logical parameters are: yes or >> no >> > >> > MeshCutoff 150. Ry # Mesh cutoff. real space mesh >> > >> > # SCF options >> > >> > MaxSCFIterations 40 # Maximum number of SCF iter >> > >> > DM.MixingWeight 0.1 # New DM amount for next SCF cycle >> > >> > DM.Tolerance 1.d-3 # Tolerance in maximum difference >> > >> > # between input and output DM >> > >> > DM.UseSaveDM true # to use continuation files >> > >> > DM.NumberPulay 3 >> > >> > SolutionMethod diagon # OrderN or Diagon >> > >> > ElectronicTemperature 25 meV # Temp. for Fermi smearing >> > >> > # MD options >> > >> > MD.TypeOfRun cg # Type of dynamics: >> > >> > MD.NumCGsteps 0 # Number of CG steps for >> > >> > # coordinate optimization >> > >> > MD.MaxCGDispl 0.1 Ang # Maximum atomic displacement >> > >> > # in one CG step (Bohr) >> > >> > MD.MaxForceTol 0.04 eV/Ang # Tolerance in the maximum >> > >> > # atomic force (Ry/Bohr) >> > >> > # Atomic coordinates >> > >> > AtomicCoordinatesFormat Fractional >> > >> > %block AtomicCoordinatesAndAtomicSpecies >> > >> > 0.000000000000 0.000000000000 0.000000000000 1 >> > >> > %endblock AtomicCoordinatesAndAtomicSpecies >> > >> > LDAU.FirstIteration .false. >> > >> > LDAU.PopTol 5.0d-4 >> > >> > LDAU.ThresholdTol 1.0d-2 >> > >> > LDAU.ProjectorGenerationMethod 2 >> > >> > %block LDAU.proj >> > >> > Fe 1 # number of shells of projectors >> > >> > n=3 2 # n, l >> > >> > 2.00 0.0000 # U(eV), J(eV) >> > >> > 0.000 0.0000 # rc, \omega >> > >> > %endblock LDAU.proj >> > >> > ************************** End of input data file >> > ***************************** >> > >> > >> > >> > reinit: >> > ----------------------------------------------------------------------- >> > >> > reinit: System Name: bcc Fe ferro GGA >> > >> > reinit: >> > ----------------------------------------------------------------------- >> > >> > reinit: System Label: Fe >> > >> > >> > reinit: >> > ----------------------------------------------------------------------- >> > >> > >> > >> > initatom: Reading input for thepseudopotentials and atomic orbitals >> > >> > Species number: 1 Label: Fe Atomic number: 26 >> > >> > Ground state valence configuration: 4s02 3d06 >> > >> > Reading pseudopotential information in formatted form from Fe.psf >> > >> > >> > >> > Valence configuration for pseudopotential generation: >> > >> > 4s( 2.00) rc: 2.41 >> > >> > 4p( 0.00) rc: 2.53 >> > >> > 3d( 6.00) rc: 2.29 >> > >> > 4f( 0.00) rc: 2.29 >> > >> > >> > >> > Repaobasis: processing %block PAO.Basis >> > >> > Repaobasis: species: Fe >> > >> > Repaobasis: Number of shells= 2 >> > >> > Repaobasis: Shell with n,l= 4 0 >> > >> > Repaobasis: Shell with n,l= 3 2 >> > >> > For Fe, standard SIESTA heuristics set lmxkb to 3 >> > >> > (one more than the basis l, including polarization orbitals). >> > >> > Use PS.lmax or PS.KBprojectors blocks to override. >> > >> > >> > >> > Reldauproj: processing %block LDAU.proj >> > >> > Reldauproj: species: Fe >> > >> > Reldauproj: Number of shells= 1 >> > >> > Reldauproj: Shell with n,l= 3 2 >> > >> > Reldauproj: end processing %block LDAU.proj >> > >> > >> > >> > <basis_specs> >> > >> > >> ============================================================================ >> > === >> > >> > = >> > >> > Fe Z= 26 Mass= 55.850 Charge= 0.0000 >> > >> > Lmxo=2 Lmxkb= 3 BasisType=split Semic=F >> > >> > L=0 Nsemic=0 >> > >> > n=4 nzeta=2 polorb= F >> > >> > splnorm: 0.15000 >> > >> > vcte: 0.0000 >> > >> > rinn: 0.0000 >> > >> > rcs: 6.0000 0.0000 >> > >> > lambdas: 1.0000 1.0000 >> > >> > L=1 Nsemic=0 >> > >> > n=4 nzeta=1 polorb= T >> > >> > splnorm: 0.15000 >> > >> > vcte: 0.0000 >> > >> > rinn: 0.0000 >> > >> > rcs: 0.0000 >> > >> > lambdas: 1.0000 >> > >> > L=2 Nsemic=0 >> > >> > n=3 nzeta=2 polorb= F >> > >> > splnorm: 0.15000 >> > >> > vcte: 0.0000 >> > >> > rinn: 0.0000 >> > >> > rcs: 0.0000 0.0000 >> > >> > lambdas: 1.0000 1.0000 >> > >> > - >> > >> > L=0 Nkbl=1 erefs: 0.17977+309 >> > >> > L=1 Nkbl=1 erefs: 0.17977+309 >> > >> > L=2 Nkbl=1 erefs: 0.17977+309 >> > >> > L=3 Nkbl=1 erefs: 0.17977+309 >> > >> > - >> > >> > L=2 Nldau_semic=1 >> > >> > n=3 >> > >> > U, J=: 0.14700 0.0000 >> > >> > vcte: 0.0000 >> > >> > rinn: 0.0000 >> > >> > rcs: 0.0000 >> > >> > lambdas: 1.0000 >> > >> > = >> > >> > </basis_specs> >> > >> > >> > >> > ATOM: Species begin__________________________ >> > >> > ATOM: Called for Fe (Z = 26) >> > >> > >> > >> > read_Read: Pseudopotential generation method: >> > >> > read_vps: ATM 3.2.2 Troullier-Martins >> > >> > Total valence charge: 8.00000 >> > >> > >> > >> > ATOM: Pseudopotential generated from an ionic configuration >> > >> > ATOM: with net charge 0.00 >> > >> > >> > >> > xc_check: Exchange-correlation functional: >> > >> > xc_check: GGA Perdew, Burke & Ernzerhof 1996 >> > >> > V l=0 =-2*Zval/r beyond r= 2.3499 >> > >> > V l=1 =-2*Zval/r beyond r= 2.4704 >> > >> > V l=2 =-2*Zval/r beyond r= 2.2353 >> > >> > V l=3 =-2*Zval/r beyond r= 2.2353 >> > >> > All V_l potentials equal beyond r= 2.4704 >> > >> > This should be close to max(r_c) in ps generation >> > >> > All pots = -2*Zval/r beyond r= 2.4704 >> > >> > >> > >> > VLOCAL1: 99.0% of the norm of Vloc inside 7.113 Ry >> > >> > VLOCAL1: 99.9% of the norm of Vloc inside 16.210 Ry >> > >> > ATOM: Maximum radius for 4*pi*r*r*local-pseudopot. charge 2.97985 >> > >> > atom: Maximum radius for r*vlocal+2*Zval: 2.87017 >> > >> > >> > >> > -------------------------------------------- >> > >> > KB: Generation of KB projectors >> > >> > KB: L= 0 >> > >> > KB: Number of Kleinman-Bylander projectors: 1 >> > >> > KB: Generating projector: 1 >> > >> > KB: Projector kind: standard >> > >> > radial_log schro: updating the rc to: 25.5822751650800 >> > >> > GHOST: No ghost state for L = 0 >> > >> > KB: L= 1 >> > >> > KB: Number of Kleinman-Bylander projectors: 1 >> > >> > KB: Generating projector: 1 >> > >> > KB: Projector kind: standard >> > >> > radial_log schro: updating the rc to: 46.6140229130900 >> > >> > GHOST: No ghost state for L = 1 >> > >> > KB: L= 2 >> > >> > KB: Number of Kleinman-Bylander projectors: 1 >> > >> > KB: Generating projector: 1 >> > >> > KB: Projector kind: standard >> > >> > radial_log schro: updating the rc to: 18.9517908592700 >> > >> > GHOST: No ghost state for L = 2 >> > >> > KB: L= 3 >> > >> > KB: Number of Kleinman-Bylander projectors: 1 >> > >> > KB: Generating projector: 1 >> > >> > KB: Projector kind: standard >> > >> > radial_log schro: updating the rc to: 120.530480482200 >> > >> > GHOST: No ghost state for L = 3 >> > >> > >> > >> > KBgen: Kleinman-Bylander projectors: >> > >> > l= 0 rc= 2.764525 el= -0.389815 Ekb= 3.431041 kbcos= >> > 0.254043 >> > >> > l= 1 rc= 2.799300 el= -0.098222 Ekb= 1.732346 kbcos= >> > 0.192007 >> > >> > l= 2 rc= 2.564764 el= -0.551796 Ekb=-12.271205 kbcos= >> > -0.715516 >> > >> > l= 3 rc= 2.870167 el= 0.003006 Ekb= -1.371972 kbcos= >> > 0.000000 >> > >> > >> > >> > KBgen: Total number of Kleinman-Bylander projectors: 16 >> > >> > >> > >> > -------------------------------------------- >> > >> > >> > >> > BASIS_GEN begin >> > >> > >> > >> > SPLIT: Orbitals with angular momentum L= 0 >> > >> > >> > >> > SPLIT: Basis orbitals for state 4s >> > >> > radial_log schro: updating the rc to: 6.00076868208500 >> > >> > >> > >> > izeta = 1 >> > >> > lambda = 1.000000 >> > >> > rc = 6.000769 >> > >> > Total energy = -0.361656 >> > >> > kinetic = 0.369283 >> > >> > potential(screened) = -0.730939 >> > >> > potential(ionic) = -6.228540 >> > >> > >> > >> > izeta = 2 >> > >> > rmatch = 5.926225 >> > >> > splitnorm = 0.150000 >> > >> > Total energy = -0.304336 >> > >> > kinetic = 0.545465 >> > >> > potential(screened) = -0.849801 >> > >> > potential(ionic) = -6.653009 >> > >> > >> > >> > POLgen: Polarization orbital for state 4s >> > >> > >> > >> > izeta = 1 >> > >> > lambda = 1.000000 >> > >> > rc = 6.000769 >> > >> > Total energy = 0.018885 >> > >> > kinetic = 0.674242 >> > >> > potential(screened) = -0.655358 >> > >> > potential(ionic) = -5.783059 >> > >> > >> > >> > SPLIT: Orbitals with angular momentum L= 2 >> > >> > radial_log schro: updating the rc to: 18.9517908592700 >> > >> > >> > >> > SPLIT: PAO cut-off radius determinated from an >> > >> > SPLIT: energy shift= 0.003675 Ry >> > >> > >> > >> > SPLIT: Basis orbitals for state 3d >> > >> > radial_log schro: updating the rc to: 4.79169190888500 >> > >> > >> > >> > izeta = 1 >> > >> > lambda = 1.000000 >> > >> > rc = 4.791692 >> > >> > Total energy = -0.548667 >> > >> > kinetic = 8.561292 >> > >> > potential(screened) = -9.109958 >> > >> > potential(ionic) = -18.089190 >> > >> > >> > >> > izeta = 2 >> > >> > rmatch = 2.291856 >> > >> > splitnorm = 0.150000 >> > >> > Total energy = -0.137047 >> > >> > kinetic = 11.793848 >> > >> > potential(screened) = -11.930895 >> > >> > potential(ionic) = -21.624702 >> > >> > >> > >> > Basis: Total Species Charge = 8.0000 >> > >> > Basis: Species Exc (eV) = -105.1478 >> > >> > >> > >> > BASISgen end >> > >> > >> > >> > LDAUprojgen begin >> > >> > >> > >> > LDAUprojs with angular momentum L= 2 >> > >> > LDAUproj generation method 2 >> > >> > >> > >> > LDAUproj corresponding to state 3d >> > >> > radial_log schro: updating the rc to: 18.9517908592700 >> > >> > LDAUproj cut-off radious determined from a >> > >> > cutoff norm parameter = 0.900000 >> > >> > LDAUproj is an extended PAO orbital cut off with a >> > >> > Fermi function 1/[1+exp(r-rc)/w] with >> > >> > rc= 2.022544 >> > >> > w = 0.050000 >> > >> > LDAUproj cutoff radious 2.320685 >> > >> > >> > >> > LDAUprojgen end >> > >> > >> > >> > ATOM: Species end_____________________________ >> > >> > na: Computing Vna for species 1 >> > >> > Vna: chval, zval: 8.00000 8.00000 >> > >> > >> > >> > Vna: Cut-off radius for the neutral-atom potential: 6.000769 >> > >> > na: Finished computing Vna for species 1 >> > >> > >> > >> > prinput: Basis input >> > ---------------------------------------------------------- >> > >> > >> > >> > PAO.BasisType split >> > >> > >> > >> > %block ChemicalSpeciesLabel >> > >> > 1 26 Fe # Species index, atomic number, >> species >> > label >> > >> > %endblock ChemicalSpeciesLabel >> > >> > >> > >> > %block PAO.Basis # Define Basis set >> > >> > Fe 3 # Species label, number of l-shells >> > >> > n=4 0 2 P 1 # n, l, Nzeta, Polarization, >> NzetaPol >> > >> > 6.001 5.926 >> > >> > 1.000 1.000 >> > >> > n=3 2 2 # n, l, Nzeta >> > >> > 4.792 2.292 >> > >> > 1.000 1.000 >> > >> > %endblock PAO.Basis >> > >> > >> > >> > prinput: >> > ---------------------------------------------------------------------- >> > >> > >> > >> > coor: Atomic-coordinates input format = Fractional >> > >> > >> > >> > siesta: Atomic coordinates (Bohr) and species >> > >> > siesta: 0.00000 0.00000 0.00000 1 1 >> > >> > >> > >> > siesta: System type = bulk >> > >> > >> > >> > initatomlists: Number of atoms, orbitals, and projectors: 1 15 >> > 16 >> > >> > >> > >> > siesta: ******************** Simulation parameters >> > **************************** >> > >> > siesta: >> > >> > siesta: The following are some of the parameters of the simulation. >> > >> > siesta: A complete list of the parameters used, including default >> values, >> > >> > siesta: can be found in file out.fdf >> > >> > siesta: >> > >> > redata: Non-Collinear-spin run = F >> > >> > redata: SpinPolarized (Up/Down) run = T >> > >> > redata: Number of spin components = 2 >> > >> > redata: Long output = F >> > >> > redata: Maximum wall-clock time = unlimited >> > >> > redata: Number of Atomic Species = 1 >> > >> > redata: Charge density info will appear in .RHO file >> > >> > redata: Write Mulliken Pop. = Atomic and Orbital >> charges >> > >> > redata: Mesh Cutoff = 150.0000 Ry >> > >> > redata: Net charge of the system = 0.0000 |e| >> > >> > redata: Max. number of SCF Iter = 40 >> > >> > redata: Performing Pulay mixing using = 3 iterations >> > >> > redata: Mix DM in first SCF step ? = F >> > >> > redata: Write Pulay info on disk? = F >> > >> > redata: New DM Mixing Weight = 0.1000 >> > >> > redata: New DM Occupancy tolerance = 0.000000000001 >> > >> > redata: No kicks to SCF >> > >> > redata: DM Mixing Weight for Kicks = 0.5000 >> > >> > redata: DM Tolerance for SCF = 0.001000 >> > >> > redata: Require Energy convergence for SCF = F >> > >> > redata: DM Energy tolerance for SCF = 0.000100 eV >> > >> > redata: Require Harris convergence for SCF = F >> > >> > redata: DM Harris energy tolerance for SCF = 0.000100 eV >> > >> > redata: Antiferro initial spin density = F >> > >> > redata: Using Saved Data (generic) = F >> > >> > redata: Use continuation files for DM = T >> > >> > redata: Neglect nonoverlap interactions = F >> > >> > redata: Method of Calculation = Diagonalization >> > >> > redata: Divide and Conquer = T >> > >> > redata: Electronic Temperature = 0.0018 Ry >> > >> > redata: Fix the spin of the system = F >> > >> > redata: Dynamics option = CG coord. optimization >> > >> > redata: Variable cell = F >> > >> > redata: Use continuation files for CG = F >> > >> > redata: Max atomic displ per move = 0.1890 Bohr >> > >> > redata: Maximum number of CG moves = 0 >> > >> > redata: Force tolerance = 0.0016 Ry/Bohr >> > >> > redata: >> > *********************************************************************** >> > >> > Total number of electrons: 8.000000 >> > >> > Total ionic charge: 8.000000 >> > >> > >> > >> > * ProcessorY, Blocksize: 1 5 >> > >> > >> > >> > Kpoints in: 1183 . Kpoints trimmed: 1099 >> > >> > >> > >> > siesta: k-grid: Number of k-points = 1099 >> > >> > siesta: k-grid: Cutoff (effective) = 16.156 Ang >> > >> > siesta: k-grid: Supercell and displacements >> > >> > siesta: k-grid: 0 13 0 0.000 >> > >> > siesta: k-grid: 0 0 13 0.000 >> > >> > siesta: k-grid: 13 0 0 0.000 >> > >> > Naive supercell factors: 8 8 8 >> > >> > >> > >> > superc: Internal auxiliary supercell: 8 x 8 x 8 = 512 >> > >> > superc: Number of atoms, orbitals, and projectors: 512 7680 8192 >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > Best, >> > >> > >> > >> > Xiaoming Wang >> > >> > Postdoc >> > >> > Rutgers >> > >> > >> >> >> ********************************************************* >> Dr Zacharias G. Fthenakis >> Research Associate >> Institute of Electronic Structure and Laser (I.E.S.L.) >> Foundation for Research and Technology Hellas (FO.R.T.H.) >> Vassilika Vouton P.O. Box 1527 71003 Heraklion Crete Greece >> Phone +30 2810 391824 >> FAX +30 2810 391305 >> webpage: http://esperia.iesl.forth.gr/~fthenak >> ********************************************************** >> >> > ********************************************************* Dr Zacharias G. Fthenakis Research Associate Institute of Electronic Structure and Laser (I.E.S.L.) Foundation for Research and Technology Hellas (FO.R.T.H.) Vassilika Vouton P.O. Box 1527 71003 Heraklion Crete Greece Phone +30 2810 391824 FAX +30 2810 391305 webpage: http://esperia.iesl.forth.gr/~fthenak **********************************************************
