-fast flag increases performance, it is transformed into -O3 I guess but not sure. Try also using -fastsse instead of fast - it worked for me also, but depends on your processor.
On 21/02/07, bipul rakshit <[EMAIL PROTECTED]> wrote:
hello sir, now it works, and give me the right results.. thanks a lot... but can you tell me what if i use fast and what if not.... Yurko Natanzon <[EMAIL PROTECTED]> wrote: Dear bipul rakshit, I see you are using Portland compiler with -fast flag. It is known for causing problems like crashes and bad results for siesta 2.0 at least. I suggest to play with optimization flags, for example, change to -O2, -O1 or so. On 21/02/07, bipul rakshit wrote: > hello siesta user, > i am running siesta in parallel. As a test i run the same problem in > parallel which i already run in serial. But now the energy of the system in > parallel become very large as compared to the same system when i run in > serial...... > can anybody suggest me what is the problem > i am sending the two output file as > tmse.serial and tmse.parallel for serial and parallel results respec... > > thanks > > ________________________________ > Here's a new way to find what you're looking for - Yahoo! Answers > --0-2002543467-1172055332=:51085-- > > > Siesta Version: siesta-2.0-release > Architecture : i686-pc-linux-gnu--Portland > Compiler flags: mpif90 -g -fast > PARALLEL version > > * Running in serial mode with MPI > >> Start of run: 21-FEB-2007 11:44:07 > > *********************** > * WELCOME TO SIESTA * > *********************** > > reinit: Reading from standard input > ************************** Dump of input data file > **************************** > # $Id: ptn.fdf,v 1.1 1999/04/20 14:43:44 emilio Exp $ > # > ----------------------------------------------------------------------------- > # FDF fo > # > # E. Artacho, April 1999 > # > ----------------------------------------------------------------------------- > SystemName tmse > SystemLabel tmse > NumberOfAtoms 2 > NumberOfSpecies 2 > %block ChemicalSpeciesLabel > 1 69 Tm > 2 34 Se > %endblock ChemicalSpeciesLabel > PAO.BasisType split > #PAO.BasisSize DZP > PAO.EnergyShift 0.1 eV > PAO.SplitNorm 0.2000 > %block PAO.Basis # Define Basis set > Tm 2 # Species label, number of l-shells > n=6 0 2 P 1 # n, l, Nzeta, Polarization, NzetaPol > 6.982 5.645 > 1.000 1.000 > # n=5 2 2 # n, l, Nzeta > # 5.044 2.803 > # 1.000 1.000 > n=4 3 2 P > 6.982 5.645 > 1.000 1.000 > Se 2 > n=4 0 2 > 5.64483 3.02914 > 1.00 1.00 > n=4 1 2 > 7.25855 2.85547 > 1.00 1.00 > %endblock PAO.Basis > LatticeConstant 5.6900 Ang > #%block LatticeParameters > # 3.92 3.92 3.92 60.0 60.0 60.0 > #%endblock LatticeParameters > %block LatticeVectors > 0.5 0.5 0.0 > 0.5 0.0 0.5 > 0.0 0.5 0.5 > %endblock LatticeVectors > MeshCutoff 250.00 Ry > # SCF options > MaxSCFIterations 200 # Maximum number of SCF iter > DM.MixingWeight 0.3 # New DM amount for next SCF cycle > DM.Tolerance 1.d-4 # Tolerance in maximum difference > DM.NumberPulay 8 # Number of pulay mixing steps > DM.UseSaveDM .false. # tells if already existing density > matrix is to be used or not > WriteCoorXmol > WriteMullikenPop 1 > WriteForces .true. > ElectronicTemperature 30 meV > xc.functional LDA > xc.authors CA > # WriteCoorStep .true. > #AtomCoorFormatOut Ang > SolutionMethod Diagon # OrderN or Diagon > AtomicCoordinatesFormat Fractional > %block AtomicCoordinatesAndAtomicSpecies > 0.0000 0.0000 0.0000 1 > 0.5000 0.5000 0.5000 2 > %endblock AtomicCoordinatesAndAtomicSpecies > MD.TypeOfRun CG # Type of dynamics: > MD.NumCGsteps 180 # Number of CG steps for > MD.MaxCGDispl 0.4 Ang # Maximum atomic displacement > MD.MaxForceTol 0.01 eV/Ang # Tolerance in the maximum > MD.MaxStressTol 0.1 GPa > MD.VariableCell .true. > %block kgrid_Monkhorst_Pack > 12 0 0 0.0 > 0 12 0 0.0 > 0 0 12 0.0 > %endblock kgrid_Monkhorst_Pack > Diag.DivideAndConquer .false. > ************************** End of input data file > ***************************** > > reinit: > ----------------------------------------------------------------------- > reinit: System Name: tmse > reinit: > ----------------------------------------------------------------------- > reinit: System Label: tmse > reinit: > ----------------------------------------------------------------------- > > initatom: Reading input for the pseudopotentials and atomic orbitals > ---------- > Species number: 1 Label: Tm Atomic number: 69 > Species number: 2 Label: Se Atomic number: 34 > Ground state valence configuration: 6s02 4f13 > Reading pseudopotential information in formatted form from Tm.psf > Ground state valence configuration: 4s02 4p04 > Reading pseudopotential information in formatted form from Se.psf > For Tm, standard SIESTA heuristics set lmxkb to 5 > (one more than the basis l, including polarization orbitals). > Use PS.lmax or PS.KBprojectors blocks to override. > Warning: For Tm lmxkb would have been set to 5 > Setting it to maximum value of 3 (f projector) > Warning: Empty PAO shell. l = 1 > Will have a KB projector anyway... > Warning: Empty PAO shell. l = 2 > Will have a KB projector anyway... > For Se, standard SIESTA heuristics set lmxkb to 2 > (one more than the basis l, including polarization orbitals). > Use PS.lmax or PS.KBprojectors blocks to override. > > > =============================================================================== > Tm Z= 69 Mass= 168.93 Charge= 0.00000 > Lmxo=3 Lmxkb=3 BasisType=split Semic=F > L=0 Nsemic=0 Cnfigmx=6 > n=1 nzeta=2 polorb=1 > vcte: 0.00000 > rinn: 0.00000 > rcs: 6.9820 5.6450 > lambdas: 1.0000 1.0000 > L=1 Nsemic=0 Cnfigmx=6 > L=2 Nsemic=0 Cnfigmx=5 > L=3 Nsemic=0 Cnfigmx=4 > n=1 nzeta=2 polorb=1 > vcte: 0.00000 > rinn: 0.00000 > rcs: 6.9820 5.6450 > 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 > =============================================================================== > > > atom: Called for Tm (Z = 69) > > read_vps: Pseudopotential generation method: > read_vps: ATM 3.2.2 Troullier-Martins > > read_vps: Pseudopotential generated from a relativistic atomic calculation > read_vps: There are spin-orbit pseudopotentials available > read_vps: Spin-orbit interaction is not included in this calculation > > read_vps: Valence configuration (pseudopotential and basis set generation): > 6s( 2.00) rc: 3.97 > 6p( 0.00) rc: 3.97 > 5d( 0.00) rc: 3.97 > 4f(13.00) rc: 4.17 > Total valence charge: 15.00000 > > xc_check: Exchange-correlation functional: > xc_check: Ceperley-Alder > V l=0 = -2*Zval/r beyond r= 5.4925 > V l=1 = -2*Zval/r beyond r= 5.4925 > V l=2 = -2*Zval/r beyond r= 5.4925 > V l=3 = -2*Zval/r beyond r= 5.4925 > All V_l potentials equal beyond r= 4.1201 > This should be close to max(r_c) in ps generation > All pots = -2*Zval/r beyond r= 5.4925 > Using large-core scheme for Vlocal > > atom: Estimated core radius 5.49252 > > atom: Including non-local core corrections could be a good idea > atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 5.84676 > atom: Maximum radius for r*vlocal+2*Zval: 5.56161 > GHOST: No ghost state for L = 0 > GHOST: No ghost state for L = 1 > GHOST: No ghost state for L = 2 > GHOST: No ghost state for L = 3 > > KBgen: Kleinman-Bylander projectors: > l= 0 rc= 4.277570 el= -0.296039 Ekb= -0.622965 kbcos= -0.594473 > l= 1 rc= 4.277570 el= -0.086738 Ekb= -0.619196 kbcos= -0.226166 > l= 2 rc= 4.224433 el= -0.071792 Ekb= -4.063882 kbcos= -0.589249 > l= 3 rc= 4.120130 el= -0.251699 Ekb=-12.164449 kbcos= -0.886908 > > KBgen: Total number of Kleinman-Bylander projectors: 16 > atom: > ------------------------------------------------------------------------- > > atom: SANKEY-TYPE ORBITALS: > atom: Selected multiple-zeta basis: split > > SPLIT: Orbitals with angular momentum L= 0 > > SPLIT: Basis orbitals for state 6s > > izeta = 1 > lambda = 1.000000 > rc = 6.964935 > energy = -0.261274 > kinetic = 0.241240 > potential(screened) = -0.502514 > potential(ionic) = -9.172153 > > izeta = 2 > rmatch = 5.702400 > splitnorm = 0.552865 > energy = 0.042306 > kinetic = 0.687590 > potential(screened) = -0.645284 > potential(ionic) = -9.732488 > > SPLIT: Orbitals with angular momentum L= 3 > > SPLIT: Basis orbitals for state 4f > > izeta = 1 > lambda = 1.000000 > rc = 6.964935 > energy = -0.251906 > kinetic = 8.040232 > potential(screened) = -8.292139 > potential(ionic) = -23.259849 > > izeta = 2 > rmatch = 5.702400 > splitnorm = 0.000455 > energy = -0.251408 > kinetic = 8.068044 > potential(screened) = -8.319452 > potential(ionic) = -23.307249 > > POLgen: Perturbative polarization orbital with L= 1 > > POLgen: Polarization orbital for state 6s > > izeta = 1 > rc = 6.964935 > energy = -0.049206 > kinetic = 0.458911 > potential(screened) = -0.508117 > potential(ionic) = -8.638323 > > POLgen: Perturbative polarization orbital with L= 4 > > POLgen: Polarization orbital for state 4f > > izeta = 1 > rc = 6.964935 > energy = 3.369074 > kinetic = 10.268329 > potential(screened) = -6.899255 > potential(ionic) = -21.197479 > atom: Total number of Sankey-type orbitals: 28 > > atm_pop: Valence configuration(local Pseudopot. screening): > 6s( 2.00) > 6p( 0.00) > 5d( 0.00) > 4f(13.00) > Vna: chval, zval: 15.00000 15.00000 > > Vna: Cut-off radius for the neutral-atom potential: 6.964935 > > atom: > _________________________________________________________________________ > > > =============================================================================== > Se Z= 34 Mass= 78.960 Charge= 0.00000 > Lmxo=1 Lmxkb=2 BasisType=split Semic=F > L=0 Nsemic=0 Cnfigmx=4 > n=1 nzeta=2 polorb=0 > vcte: 0.00000 > rinn: 0.00000 > rcs: 5.6448 3.0291 > lambdas: 1.0000 1.0000 > L=1 Nsemic=0 Cnfigmx=4 > n=1 nzeta=2 polorb=0 > vcte: 0.00000 > rinn: 0.00000 > rcs: 7.2586 2.8555 > 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 > =============================================================================== > > > atom: Called for Se (Z = 34) > > read_vps: Pseudopotential generation method: > read_vps: ATM 3.2.2 Troullier-Martins > > read_vps: Pseudopotential generated from a relativistic atomic calculation > read_vps: There are spin-orbit pseudopotentials available > read_vps: Spin-orbit interaction is not included in this calculation > > read_vps: Valence configuration (pseudopotential and basis set generation): > 4s( 2.00) rc: 1.80 > 4p( 4.00) rc: 2.09 > 4d( 0.00) rc: 1.89 > Total valence charge: 6.00000 > > xc_check: Exchange-correlation functional: > xc_check: Ceperley-Alder > V l=0 = -2*Zval/r beyond r= 3.1935 > V l=1 = -2*Zval/r beyond r= 3.1935 > V l=2 = -2*Zval/r beyond r= 3.1935 > All V_l potentials equal beyond r= 2.0619 > This should be close to max(r_c) in ps generation > All pots = -2*Zval/r beyond r= 3.1935 > Using large-core scheme for Vlocal > > atom: Estimated core radius 3.19350 > > atom: Including non-local core corrections could be a good idea > atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 3.52937 > atom: Maximum radius for r*vlocal+2*Zval: 3.23367 > GHOST: No ghost state for L = 0 > GHOST: No ghost state for L = 1 > GHOST: No ghost state for L = 2 > > KBgen: Kleinman-Bylander projectors: > l= 0 rc= 2.140641 el= -1.282149 Ekb= 7.514714 kbcos= 0.238681 > l= 1 rc= 2.140641 el= -0.489584 Ekb= 2.689557 kbcos= 0.242169 > l= 2 rc= 2.140641 el= 0.002371 Ekb= 7.497228 kbcos= 0.019395 > > KBgen: Total number of Kleinman-Bylander projectors: 9 > atom: > ------------------------------------------------------------------------- > > atom: SANKEY-TYPE ORBITALS: > atom: Selected multiple-zeta basis: split > > SPLIT: Orbitals with angular momentum L= 0 > > SPLIT: Basis orbitals for state 4s > > izeta = 1 > lambda = 1.000000 > rc = 5.746706 > energy = -1.281402 > kinetic = 0.781756 > potential(screened) = -2.063158 > potential(ionic) = -6.675439 > > izeta = 2 > rmatch = 3.075956 > splitnorm = 0.366048 > energy = -0.797323 > kinetic = 1.874138 > potential(screened) = -2.671461 > potential(ionic) = -7.590957 > > SPLIT: Orbitals with angular momentum L= 1 > > SPLIT: Basis orbitals for state 4p > > izeta = 1 > lambda = 1.000000 > rc = 7.378937 > energy = -0.488435 > kinetic = 1.123771 > potential(screened) = -1.612206 > potential(ionic) = -5.763251 > > izeta = 2 > rmatch = 2.853693 > splitnorm = 0.582656 > energy = 0.370860 > kinetic = 2.968627 > potential(screened) = -2.597767 > potential(ionic) = -7.551113 > atom: Total number of Sankey-type orbitals: 8 > > atm_pop: Valence configuration(local Pseudopot. screening): > 4s( 2.00) > 4p( 4.00) > Vna: chval, zval: 6.00000 6.00000 > > Vna: Cut-off radius for the neutral-atom potential: 7.378937 > > atom: > _________________________________________________________________________ > > prinput: Basis input > ---------------------------------------------------------- > > PAO.BasisType split > > %block ChemicalSpeciesLabel > 1 69 Tm # Species index, atomic number, species > label > 2 34 Se # Species index, atomic number, species > label > %endblock ChemicalSpeciesLabel > > %block PAO.Basis # Define Basis set > Tm 2 # Species label, number of l-shells > n=6 0 2 P 1 # n, l, Nzeta, Polarization, NzetaPol > 6.965 5.702 > 1.000 1.000 > n=4 3 2 P 1 # n, l, Nzeta, Polarization, NzetaPol > 6.965 5.702 > 1.000 1.000 > Se 2 # Species label, number of l-shells > n=4 0 2 # n, l, Nzeta > 5.747 3.076 > 1.000 1.000 > n=4 1 2 # n, l, Nzeta > 7.379 2.854 > 1.000 1.000 > %endblock PAO.Basis > > prinput: > ---------------------------------------------------------------------- > > > 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: > coor: Atomic-coordinates input format = Fractional > redata: Number of spin components = 1 > redata: Long output = F > redata: Number of Atomic Species = 2 > redata: Charge density info will appear in .RHO file > redata: Write Mulliken Pop. = Atomic and Orbital charges > redata: Mesh Cutoff = 250.0000 Ry > redata: Net charge of the system = 0.0000 |e| > redata: Max. number of SCF Iter = 200 > redata: Performing Pulay mixing using = 8 iterations > redata: Mix DM in first SCF step ? = F > redata: Write Pulay info on disk? = F > redata: New DM Mixing Weight = 0.3000 > 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 = 0.000100 > redata: Require Energy convergence for SCF = F > redata: DM Energy tolerance for SCF = 0.000100 eV > redata: Using Saved Data (generic) = F > redata: Use continuation files for DM = F > redata: Neglect nonoverlap interactions = F > redata: Method of Calculation = Diagonalization > redata: Divide and Conquer = F > redata: Electronic Temperature = 0.0022 Ry > redata: Fix the spin of the system = F > redata: Dynamics option = CG coord. optimization > redata: Variable cell = T > redata: Use continuation files for CG = F > redata: Max atomic displ per move = 0.7559 Bohr > redata: Maximum number of CG moves = 180 > redata: Force tolerance = 0.0004 Ry/Bohr > redata: Stress tolerance = 0.1000 GPa > redata: > *********************************************************************** > > siesta: Atomic coordinates (Bohr) and species > siesta: 0.00000 0.00000 0.00000 1 1 > siesta: 5.37627 5.37627 5.37627 2 2 > > initatomlists: Number of atoms, orbitals, and projectors: 2 36 25 > > siesta: System type = bulk > > * ProcessorY, Blocksize: 1 24 > > > siesta: k-grid: Number of k-points = 1008 > siesta: k-grid: Cutoff = 24.141 Ang > siesta: k-grid: Supercell and displacements > siesta: k-grid: 12 0 0 0.000 > siesta: k-grid: 0 12 0 0.000 > siesta: k-grid: 0 0 12 0.000 > > superc: Internal auxiliary supercell: 7 x 7 x 7 = 343 > superc: Number of atoms, orbitals, and projectors: 686 12348 8575 > > * Maximum dynamic memory allocated = 2 MB > > siesta: ============================== > Begin CG move = 0 > ============================== > > superc: Internal auxiliary supercell: 7 x 7 x 7 = 343 > superc: Number of atoms, orbitals, and projectors: 686 12348 8575 > > outcell: Unit cell vectors (Ang): > 2.845000 2.845000 0.000000 > 2.845000 0.000000 2.845000 > 0.000000 2.845000 2.845000 > > outcell: Cell vector modules (Ang) : 4.023438 4.023438 4.023438 > outcell: Cell angles (23,13,12) (deg): 60.0000 60.0000 60.0000 > outcell: Cell volume (Ang**3) : 46.0550 > > InitMesh: MESH = 32 x 32 x 32 = 32768 > InitMesh: Mesh cutoff (required, used) = 250.000 262.240 Ry > > * Maximum dynamic memory allocated = 66 MB > > stepf: Fermi-Dirac step function > > siesta: Program's energy decomposition (eV): > siesta: Eions = 1578.050130 > siesta: Ena = -128022.794811 > siesta: Ekin = 1511.164452 > siesta: Enl = -1682.384356 > siesta: DEna = 0.000000 > siesta: DUscf = 0.000000 > siesta: DUext = 0.000000 > siesta: Exc = -274.846537 > siesta: eta*DQ = 0.000000 === message truncated === ________________________________ Here�s a new way to find what you're looking for - Yahoo! Answers
-- 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]
