This option makes simple siesta calculation, I want to do transiesta --- Message initial ---
De : "Shiba Subedi" <shibashib...@gmail.com> Envoyé : 13 février 2015 04:43 A : siesta-l@uam.es Objet : Re: [SIESTA-L] wrong solution method add SolutionMethod diagon in input file On 13 February 2015 at 00:57, toufik esssakhri <tou...@hotmail.fr> wrote: > Ok i will talk to our system administrator to install it > thanks a lot > > ------------------------------ > From: nickpap...@gmail.com > Date: Thu, 12 Feb 2015 19:07:41 +0000 > > To: siesta-l@uam.es > Subject: Re: [SIESTA-L] wrong solution method > > Sorry, that is probably wrong, I do not know what is wrong with pl-5, > however, could you try with this version: > > http://departments.icmab.es/leem/siesta/CodeAccess/Code/siesta-trunk-462.tgz > found here: > http://departments.icmab.es/leem/siesta/CodeAccess/Code/downloads.html > > 2015-02-12 19:04 GMT+00:00 Nick Papior Andersen <nickpap...@gmail.com>: > > I think your system administrator needs to do the previous steps I said, > it seems like you have a corrupt executable. (it reads it in correctly > first, then dies later...) :( > > 2015-02-12 19:00 GMT+00:00 toufik esssakhri <tou...@hotmail.fr>: > > it gives the same error > siesta: ERROR: wrong solution method > ------------------------------ > From: nickpap...@gmail.com > Date: Thu, 12 Feb 2015 18:54:02 +0000 > > To: siesta-l@uam.es > Subject: Re: [SIESTA-L] wrong solution method > > try and change solutionmethod to: > transi > > 2015-02-12 18:44 GMT+00:00 toufik esssakhri <tou...@hotmail.fr>: > > all done by our system administrator > i succeed to other calculations in the same platform, for example > > > > Siesta Version: siesta-3.2-pl-5 > Architecture : x86_64-centos-linux-intel--openmpi > Compiler flags: mpif90 -O0 > PARALLEL version > TRANSIESTA support > > * Running on 64 nodes in parallel > >> Start of run: 15-DEC-2014 11:48:17 > > *********************** > * WELCOME TO SIESTA * > *********************** > > reinit: Reading from standard input > ************************** Dump of input data file > **************************** > SystemName scat-femgo > SystemLabel scat-femgo > ================================================== > .... > .... > elaps: ELAPSED times: > elaps: Routine Calls Time/call Tot.time % > elaps: siesta 1 7856.494 7856.494 100.00 > elaps: Setup 1 0.897 0.897 0.01 > elaps: bands 1 0.002 0.002 0.00 > elaps: writewave 1 0.007 0.007 0.00 > elaps: KSV_init 1 0.001 0.001 0.00 > elaps: IterMD 1 7828.209 7828.209 99.64 > elaps: hsparse 1 0.032 0.032 0.00 > elaps: overlap 1 0.449 0.449 0.01 > elaps: IterSCF 299 26.140 7815.913 99.48 > elaps: kinefsm 2 0.204 0.407 0.01 > elaps: nlefsm 2 1.224 2.447 0.03 > elaps: DHSCF 301 2.937 884.071 11.25 > elaps: DHSCF1 1 2.335 2.335 0.03 > elaps: DHSCF2 1 4.585 4.585 0.06 > elaps: REORD 3327 0.006 19.105 0.24 > elaps: POISON 302 0.869 262.514 3.34 > elaps: DHSCF3 301 2.889 869.714 11.07 > elaps: rhoofd 301 0.083 24.969 0.32 > elaps: cellXC 301 0.288 86.724 1.10 > elaps: vmat 300 0.731 219.307 2.79 > elaps: MolMec 2 0.000 0.000 0.00 > elaps: diagon 70 69.026 4831.847 61.50 > elaps: cdiag 1400 0.395 552.392 7.03 > elaps: cdiag1 1400 0.029 40.251 0.51 > elaps: cdiag2 1400 0.074 104.072 1.32 > elaps: cdiag3 1400 0.267 373.211 4.75 > elaps: cdiag4 1400 0.024 34.288 0.44 > elaps: TS 229 6.532 1495.884 19.04 > elaps: DHSCF4 1 1.252 1.252 0.02 > elaps: dfscf 1 0.910 0.910 0.01 > elaps: overfsm 1 0.005 0.005 0.00 > elaps: optical 1 0.001 0.001 0.00 > > >> End of run: 15-DEC-2014 13:59:13 > > > ------------------------------ > From: nickpap...@gmail.com > Date: Thu, 12 Feb 2015 18:37:50 +0000 > To: siesta-l@uam.es > Subject: Re: [SIESTA-L] wrong solution method > > > Are you sure you have done: > make clean > make transiesta > > Else try and compile transiesta again by doing the above. > > 2015-02-12 18:28 GMT+00:00 toufik esssakhri <tou...@hotmail.fr>: > > Dear all, > > i want to redo examples from > http://departments.icmab.es/leem/siesta/tlv14/ using siesta-3.2-pl-5, > i begun with the first example (00-chain), i do not make any change to the > *fdf files > the first step (electrode) is done correctally and i have the elect.TSHS, > now to do calculation for scattering > the SolutionMethod is set to transiesta, but i have an error : "*siesta: > ERROR: wrong solution method*" > you can check the out file > > Siesta Version: siesta-3.2-pl-5 > Architecture : x86_64-centos-linux-intel--openmpi > Compiler flags: mpif90 -O0 > PARALLEL version > TRANSIESTA support > > * Running on 64 nodes in parallel > >> Start of run: 12-FEB-2015 21:27:26 > > *********************** > * WELCOME TO SIESTA * > *********************** > > reinit: Reading from standard input > ************************** Dump of input data file > **************************** > # Here we list the options used for > # transiesta. > SolutionMethod transiesta > # Define the electrodes (notice they are the same) > TS.HSFileLeft ./elec.TSHS > TS.HSFileRight ./elec.TSHS > # Define the contour: > TS.ComplexContourEmin -30. eV > TS.ComplexContour.NPoles 6 > TS.ComplexContour.NCircle 30 > TS.ComplexContour.NLine 8 > # TBT OPTIONS > TS.TBT.Emin -10. eV > TS.TBT.Emax +10. eV > TS.TBT.NPoints 301 > # Regular SIESTA options: > MD.TypeOfRun CG > MD.NumCGsteps 0 > SystemName Carbon chain > SystemLabel chain-scat > LatticeConstant 1.0 Ang > %block LatticeVectors > 12.0000 0.0000 0.0000 > 0.0000 12.0000 0.0000 > 0.0000 0.0000 28.4000 > %endblock LatticeVectors > NumberOfSpecies 1 > %block ChemicalSpeciesLabel > 1 6 C > %endblock ChemicalSpeciesLabel > NumberOfAtoms 20 > AtomicCoordinatesFormat Ang > %block AtomicCoordinatesAndAtomicSpecies > 0.000 0.000 0.0000 1 # 1 > 0.000 0.000 1.4200 1 # 2 > 0.000 0.000 2.8400 1 # 3 > 0.000 0.000 4.2600 1 # 4 > 0.000 0.000 5.6800 1 # 5 > 0.000 0.000 7.1000 1 # 6 > 0.000 0.000 8.5200 1 # 7 > 0.000 0.000 9.9400 1 # 8 > 0.000 0.000 11.3600 1 # 9 > 0.000 0.000 12.7800 1 # 10 > 0.000 0.000 14.2000 1 # 11 > 0.000 0.000 15.6200 1 # 12 > 0.000 0.000 17.0400 1 # 13 > 0.000 0.000 18.4600 1 # 14 > 0.000 0.000 19.8800 1 # 15 > 0.000 0.000 21.3000 1 # 16 > 0.000 0.000 22.7200 1 # 17 > 0.000 0.000 24.1400 1 # 18 > 0.000 0.000 25.5600 1 # 19 > 0.000 0.000 26.9800 1 # 20 > %endblock AtomicCoordinatesAndAtomicSpecies > %block kgrid_Monkhorst_Pack > 1 0 0 0. > 0 1 0 0. > 0 0 1 0. > %endblock kgrid_Monkhorst_Pack > MeshCutoff 200. Ry > DM.MixingWeight 0.2 > DM.NumberPulay 4 > ************************** End of input data file > ***************************** > > reinit: > ----------------------------------------------------------------------- > reinit: System Name: Carbon chain > reinit: > ----------------------------------------------------------------------- > reinit: System Label: chain-scat > reinit: > ----------------------------------------------------------------------- > > initatom: Reading input for the pseudopotentials and atomic orbitals > ---------- > Species number: 1 Label: C Atomic number: 6 > Ground state valence configuration: 2s02 2p02 > Reading pseudopotential information in formatted form from C.psf > > Valence configuration for pseudopotential generation: > 2s( 2.00) rc: 1.54 > 2p( 2.00) rc: 1.54 > 3d( 0.00) rc: 1.54 > 4f( 0.00) rc: 1.54 > For C, 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. > > <basis_specs> > > =============================================================================== > C Z= 6 Mass= 12.010 Charge= 0.17977+309 > Lmxo=1 Lmxkb= 3 BasisType=split Semic=F > L=0 Nsemic=0 Cnfigmx=2 > n=1 nzeta=2 polorb=0 > splnorm: 0.15000 > vcte: 0.0000 > rinn: 0.0000 > rcs: 0.0000 0.0000 > lambdas: 1.0000 1.0000 > L=1 Nsemic=0 Cnfigmx=2 > n=1 nzeta=2 polorb=1 > 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 > > =============================================================================== > </basis_specs> > > atom: Called for C (Z = 6) > > read_vps: Pseudopotential generation method: > read_vps: ATM3 Troullier-Martins > Total valence charge: 4.00000 > > xc_check: Exchange-correlation functional: > xc_check: Ceperley-Alder > V l=0 = -2*Zval/r beyond r= 1.5227 > V l=1 = -2*Zval/r beyond r= 1.5227 > V l=2 = -2*Zval/r beyond r= 1.5227 > V l=3 = -2*Zval/r beyond r= 1.5038 > All V_l potentials equal beyond r= 1.5227 > This should be close to max(r_c) in ps generation > All pots = -2*Zval/r beyond r= 1.5227 > > VLOCAL1: 99.0% of the norm of Vloc inside 18.722 Ry > VLOCAL1: 99.9% of the norm of Vloc inside 42.668 Ry > atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 1.83678 > atom: Maximum radius for r*vlocal+2*Zval: 1.58088 > 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= 1.747182 el= -1.001948 Ekb= 4.950286 kbcos= 0.319819 > l= 1 rc= 1.747182 el= -0.398598 Ekb= -4.108613 kbcos= -0.367053 > l= 2 rc= 1.930978 el= 0.002326 Ekb= -1.042946 kbcos= -0.009366 > l= 3 rc= 2.055542 el= 0.003420 Ekb= -0.408633 kbcos= -0.001262 > > 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 2s > > SPLIT: PAO cut-off radius determined from an > SPLIT: energy shift= 0.020000 Ry > > izeta = 1 > lambda = 1.000000 > rc = 4.191849 > energy = -0.983897 > kinetic = 0.880927 > potential(screened) = -1.864824 > potential(ionic) = -5.475687 > > izeta = 2 > rmatch = 3.431921 > splitnorm = 0.150000 > energy = -0.853083 > kinetic = 1.298222 > potential(screened) = -2.151305 > potential(ionic) = -5.995890 > > SPLIT: Orbitals with angular momentum L= 1 > > SPLIT: Basis orbitals for state 2p > > SPLIT: PAO cut-off radius determined from an > SPLIT: energy shift= 0.020000 Ry > > izeta = 1 > lambda = 1.000000 > rc = 4.870301 > energy = -0.379093 > kinetic = 2.540023 > potential(screened) = -2.919116 > potential(ionic) = -6.427960 > > izeta = 2 > rmatch = 3.475094 > splitnorm = 0.150000 > energy = -0.215057 > kinetic = 3.814571 > potential(screened) = -4.029628 > potential(ionic) = -7.920250 > > POLgen: Perturbative polarization orbital with L= 2 > > POLgen: Polarization orbital for state 2p > > izeta = 1 > rc = 4.870301 > energy = 1.280996 > kinetic = 2.631310 > potential(screened) = -1.350314 > potential(ionic) = -4.295640 > atom: Total number of Sankey-type orbitals: 13 > > atm_pop: Valence configuration (for local Pseudopot. screening): > 2s( 2.00) > 2p( 2.00) > Vna: chval, zval: 4.00000 4.00000 > > Vna: Cut-off radius for the neutral-atom potential: 4.870301 > > atom: > _________________________________________________________________________ > > prinput: Basis input > ---------------------------------------------------------- > > PAO.BasisType split > > %block ChemicalSpeciesLabel > 1 6 C # Species index, atomic number, species > label > %endblock ChemicalSpeciesLabel > > %block PAO.Basis # Define Basis set > C 2 # Species label, number of > l-shells > n=2 0 2 # n, l, Nzeta > 4.192 3.432 > 1.000 1.000 > n=2 1 2 P 1 # n, l, Nzeta, Polarization, NzetaPol > 4.870 3.475 > 1.000 1.000 > %endblock PAO.Basis > > prinput: > ---------------------------------------------------------------------- > > coor: Atomic-coordinates input format = Cartesian coordinates > coor: (in Angstroms) > > siesta: Atomic coordinates (Bohr) and species > siesta: 0.00000 0.00000 0.00000 1 1 > siesta: 0.00000 0.00000 2.68341 1 2 > siesta: 0.00000 0.00000 5.36682 1 3 > siesta: 0.00000 0.00000 8.05024 1 4 > siesta: 0.00000 0.00000 10.73365 1 5 > siesta: 0.00000 0.00000 13.41706 1 6 > siesta: 0.00000 0.00000 16.10047 1 7 > siesta: 0.00000 0.00000 18.78389 1 8 > siesta: 0.00000 0.00000 21.46730 1 9 > siesta: 0.00000 0.00000 24.15071 1 10 > siesta: 0.00000 0.00000 26.83412 1 11 > siesta: 0.00000 0.00000 29.51753 1 12 > siesta: 0.00000 0.00000 32.20095 1 13 > siesta: 0.00000 0.00000 34.88436 1 14 > siesta: 0.00000 0.00000 37.56777 1 15 > siesta: 0.00000 0.00000 40.25118 1 16 > siesta: 0.00000 0.00000 42.93459 1 17 > siesta: 0.00000 0.00000 45.61801 1 18 > siesta: 0.00000 0.00000 48.30142 1 19 > siesta: 0.00000 0.00000 50.98483 1 20 > > siesta: System type = chain > > initatomlists: Number of atoms, orbitals, and projectors: 20 260 > 320 > > 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 = F > redata: Number of spin components = 1 > redata: Long output = F > redata: Number of Atomic Species = 1 > redata: Charge density info will appear in .RHO file > redata: Write Mulliken Pop. = NO > redata: Mesh Cutoff = 200.0000 Ry > redata: Net charge of the system = 0.0000 |e| > redata: Max. number of SCF Iter = 50 > redata: Performing Pulay mixing using = 4 iterations > redata: Mix DM in first SCF step ? = F > redata: Write Pulay info on disk? = F > redata: Discard 1st Pulay DM after kick = F > redata: New DM Mixing Weight = 0.2000 > 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: Require Harris convergence for SCF = F > redata: DM Harris 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 = Transiesta > 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 = 0.2000 Bohr > redata: Maximum number of CG moves = 0 > redata: Force tolerance = 0.0016 Ry/Bohr > redata: > *********************************************************************** > > ts_read_options: > ************************************************************** > ts_read_options: Save H and S matrices = T > ts_read_options: Mixing Hamiltonian = F > ts_read_options: TranSIESTA Voltage = 0.0000 Volts > ts_read_options: TriDiag = F > ts_read_options: Update DM Contact Reg. only = T > ts_read_options: N. Buffer At. Left = 0 > ts_read_options: N. Buffer At. Right = 0 > ts_read_options: N. Pts. Circle = 30 > ts_read_options: N. Pts. Line = 8 > ts_read_options: N. Poles in Contour = 6 > ts_read_options: N. Pts. Bias Contour = 5 > ts_read_options: Contour E Min. = -2.2049 Ry > ts_read_options: GFEta = 0.000001 Ry > ts_read_options: Electronic Temperature = 0.0019 Ry > ts_read_options: Bias Contour Method = gaussfermi > ts_read_options: Left GF File = Left.GF > ts_read_options: Right GF File = Right.GF > ts_read_options: Calculate GF = T > ts_read_options: Save S and quit (onlyS) = F > ts_read_options: > ************************************************************** > > ************************ Begin: TS CHECKS AND WARNINGS > ************************ > ************************ End: TS CHECKS AND WARNINGS > ************************** > > Total number of electrons: 80.000000 > Total ionic charge: 80.000000 > > * ProcessorY, Blocksize: 8 5 > > Kpoints in: 1 . Kpoints trimmed: 1 > > siesta: k-grid: Number of k-points = 1 > siesta: k-grid: Cutoff (effective) = 6.000 Ang > siesta: k-grid: Supercell and displacements > siesta: k-grid: 1 0 0 0.000 > siesta: k-grid: 0 1 0 0.000 > siesta: k-grid: 0 0 1 0.000 > Kpoints in: 1 . Kpoints trimmed: 1 > > transiesta: ts_k-grid: Number of Transport k-points = 1 > transiesta: ts_k-grid: Supercell and displacements > transiesta: ts_k-grid: 1 0 0 0.000 > transiesta: ts_k-grid: 0 1 0 0.000 > > > * Maximum dynamic memory allocated = 1 MB > > siesta: ============================== > Begin CG move = 0 > ============================== > > outcell: Unit cell vectors (Ang): > 12.000000 0.000000 0.000000 > 0.000000 12.000000 0.000000 > 0.000000 0.000000 28.400000 > > outcell: Cell vector modules (Ang) : 12.000000 12.000000 28.400000 > outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 > outcell: Cell volume (Ang**3) : 4089.6000 > New_DM. Step: 1 > Initializing Density Matrix... > > InitMesh: MESH = 108 x 108 x 250 = 2916000 > InitMesh: Mesh cutoff (required, used) = 200.000 214.163 Ry > > * Maximum dynamic memory allocated = 10 MB > siesta: ERROR: wrong solution method > > > > > -- > Kind regards Nick > > > > > -- > Kind regards Nick > > > > > -- > Kind regards Nick > > > > > -- > Kind regards Nick > -- Your Sincerely Shiba Subedi Central Department of Physics, Tribhuvan University Kathmandu, Nepal
