[SIESTA-L] systemlable.band.up and systemlable.band.down
Dear siesta users, I calculate the electronic properties of my supercell by spin polorized calculation.so I set SpinPolarize to true. I dont know how to obtaian the systemlable.band.up and systemlable.band.down. how to modify the gnubands.f to plot the bandstructure for both spins? I look forward any suggestion and help , Thanks in advance. Best Regards, Somayeh Fotoohi
Re: [SIESTA-L] Transiesta: how to avoid writing SCATT.TSGFL?
In the TBTrans_rep version this is not implemented (yet), in this case use the TBTrans version. The easiest thing is to decrease the number of energy-points in the simulation and thus requiring several simulations to get the full energy range you need. 2013/7/22 d.otalv...@utwente.nl Hello everyone, Is there a tag recognized by transiesta (trunk-431) that disables writing the Green Function matrices for both left and right electrodes? Since the Green function has to be calculated for every energy, in my case these files are on the order of 20+GB!! Is there any good reason why I should keep them? If not, how do I disable writing them? You can reuse them for every simulation where the electrode and energy range does not change. In this case you save the computation of the surface Green's functions, and the transmission calculation will be much faster. All the best, Diana Diana M. Otálvaro Doctoral Candidate Computational Material Science MESA+ Institute of Nanotechnology University of Twente. Enschede, Nederland Kind regards Nick
Re: [SIESTA-L] About parallel versions of SIESTA
Just to clarify. The compilation of a program does not per se distinguish where the routines linked are contained. As long as the linking step finds the required routines it will compile. Thus you could easily create one library which contained BLAS, LAPACK, ScaLAPACK and BLACS and just link to that. The compilation will find all the routines needed and that is it. Doing -lscalapack just tells the linker that all routines in that library should be added to the pool of available routines (well, basically anyway :) ). Thus SIESTA cannot tell whether -lfoo is actually scalapack/blas/lapack or something fourth. Hope this clarified the linking step and the compilation of programs with external libraries. Kind regards Nick 2013/7/22 Sebastian Caicedo Davila sebastian.caic...@correounivalle.edu.co Thanks Nick. You're right they're just one library. My concern is mainly whether SIESTA needs an explicit BLACS lib to work or it will just use the routines embedded in th Scalapack library by default. Best regards. Sebastian On 07/22/2013 03:47 AM, Nick Papior Andersen wrote: But if you are using the ScaLAPACK installer it will install the latest ScaLAPACK library, hence you will have BLACS embedded in the ScaLAPACK library. Or is there something I am missing? Embedded libraries does not mean that BLACS routines are deprecated, but rather that instead of 2 libraries (BLACS and ScaLAPACK) they are now 1 library (ScaLAPACK 2.x == ScaLAPACK 1.x + BLACS). Hence when you link you just add the ScaLAPACK with -lscalapack or however you wish to add the library. Kind regards Nick 2013/7/22 Sebastian Caicedo sebastian.caic...@correounivalle.edu.co Hello everyone, I'm trying to build a parallel version of SIESTA and I'm using the Scalapack installer to get the libraries I need. The problem is that since version 2.0 the BLACS library is embedded into the SCALAPACK lib, so I don't know whether SIESTA will work without BLACS or not. Any hints? Thanks in advance Sebastian
[SIESTA-L] optical mesh
Dear siesta users I m trying to calculate the optical properties of an armchair GNR. can any one check my .fdf file and tell me if i defined my parameters correctly.specially my optical mesh. I really appreciate any help. Best regards Somayeh Rudi here is my .fdf file: # AGNR N_a = 5 # SystemLabel AGNR NumberOfSpecies 2 NumberOfAtoms 14 %block ChemicalSpeciesLabel 1 6 C 2 1 H %endblock ChemicalSpeciesLabel %PAO.Basis basis.fdf %PAO.BasisSize SZ %block PAO.BasisSizes C DZP H DZP %endblock PAO.BasisSizes %AtomicCoordinatesFormat ScaledCartesian # Format for coordinates %AtomicCoorFormatOut Ang %block kgrid_Monkhorst_Pack 1 0 0 0.5 0 1 0 0.5 0 0 32 0.5 %endblock kgrid_Monkhorst_Pack MeshCutoff 210. Ry SolutionMethod diagon MaxSCFIterations 200 DM.MixingWeight 0.20 DM.Tolerance 1.d-5 DM.NumberPulay 4 ElectronicTemperature 300 K DM.UseSaveDM true UseSaveData true SpinPolarized false xc.functional LDA xc.authors CA WriteMullikenPop 1 SaveDeltaRho .true. SaveRho .true. SaveElectrostaticPotential .true. SaveTotalPotential .true. %block LocalDensityOfStates -3.0520 -2.8520 eV %endblock LocalDensityOfStates %block BandLines 1 0.00 0.00 0. \Gamma 200 0.00 0.00 1. X %endblock BandLines LatticeConstant 4.26258 Ang %block LatticeVectors 22.82899136 0.000 0.000 0.000 16.00 0.000 0.000 0.000 1.000 %endblock LatticeVectors AtomicCoordinatesFormat NotScaledCartesianAng %block AtomicCoordinatesAndAtomicSpecies 8.95349397 8. 1.42086 1 8.95349397 8. 2.84172 1 10.18399482 8. 3.55215 1 10.18399482 8. 0.71043 1 11.41449568 8. 1.42086 1 11.41449568 8. 2.84172 1 12.64499654 8. 3.55215 1 12.64499654 8. 0.71043 1 13.87549739 8. 1.42086 1 13.87549739 8. 2.84172 1 8. 8. 0.87036 2 8. 8. 3.39222 2 14.82899136 8. 0.87036 2 14.82899136 8. 3.39222 2 %endblock AtomicCoordinatesAndAtomicSpecies # Calculation of dielectric function OpticalCalculation .true. Optical.Broaden 0.1 eV %block Optical.Mesh 1 1 64 %endblock Optical.Mesh #Optical.OffsetMesh .true. Optical.PolarizationType polarized %block Optical.Vector 0.000 0.000 1.000 %endblock Optical.Vector
Re: [SIESTA-L] optical mesh
Dear somayeh. I think Armchair Graphen Nano Ribone has 2D structure .you have to pay attention for griding (kgrid_Monkhorst) your griding is for 1 0 00.5 1D structure along Z Direction . Be sure your structure is 1D or 2 D structure .And 0 1 00.5 0 0 32 0.5 xc.functional GGA , xc.authors PBE Is better and exact approximation i think. On Sun, Jul 28, 2013 at 5:47 PM, somayeh rudi sapphire_b...@yahoo.comwrote: Dear siesta users I m trying to calculate the optical properties of an armchair GNR. can any one check my .fdf file and tell me if i defined my parameters correctly.specially my optical mesh. I really appreciate any help. Best regards Somayeh Rudi here is my .fdf file: # AGNR N_a = 5 # SystemLabel AGNR NumberOfSpecies 2 NumberOfAtoms14 %block ChemicalSpeciesLabel 16 C 21 H %endblock ChemicalSpeciesLabel %PAO.Basis basis.fdf %PAO.BasisSize SZ %block PAO.BasisSizes C DZP H DZP %endblock PAO.BasisSizes %AtomicCoordinatesFormat ScaledCartesian # Format for coordinates %AtomicCoorFormatOut Ang %block kgrid_Monkhorst_Pack 1 0 00.5 0 1 00.5 0 0 32 0.5 %endblock kgrid_Monkhorst_Pack MeshCutoff 210. Ry SolutionMethoddiagon MaxSCFIterations 200 DM.MixingWeight 0.20 DM.Tolerance 1.d-5 DM.NumberPulay 4 ElectronicTemperature 300 K DM.UseSaveDM true UseSaveData true SpinPolarized false xc.functional LDA xc.authorsCA WriteMullikenPop 1 SaveDeltaRho .true. SaveRho .true. SaveElectrostaticPotential.true. SaveTotalPotential.true. %block LocalDensityOfStates -3.0520 -2.8520 eV %endblock LocalDensityOfStates %block BandLines 1 0.00 0.00 0. \Gamma 200 0.00 0.00 1. X %endblock BandLines LatticeConstant 4.26258 Ang %block LatticeVectors 22.82899136 0.000 0.000 0.000 16.00 0.000 0.000 0.000 1.000 %endblock LatticeVectors AtomicCoordinatesFormat NotScaledCartesianAng %block AtomicCoordinatesAndAtomicSpecies 8.95349397 8. 1.42086 1 8.95349397 8. 2.84172 1 10.18399482 8. 3.55215 1 10.18399482 8. 0.71043 1 11.41449568 8. 1.42086 1 11.41449568 8. 2.84172 1 12.64499654 8. 3.55215 1 12.64499654 8. 0.71043 1 13.87549739 8. 1.42086 1 13.87549739 8. 2.84172 1 8. 8. 0.87036 2 8. 8. 3.39222 2 14.82899136 8. 0.87036 2 14.82899136 8. 3.39222 2 %endblock AtomicCoordinatesAndAtomicSpecies # Calculation of dielectric function OpticalCalculation .true. Optical.Broaden 0.1 eV %block Optical.Mesh 1 1 64 %endblock Optical.Mesh #Optical.OffsetMesh .true. Optical.PolarizationType polarized %block Optical.Vector 0.000 0.000 1.000 %endblock Optical.Vector
Re: [SIESTA-L] optical mesh
Dear Mostafa Thanks for your reply. My structure is an 5-armchair graphene nanoribbon along the z direction. i want to know that the optical mesh (1 1 64) that i used is correct or not. i obtained different conductivities for optical mesh (1 1 64) and optical mesh (64 1 1) , i m not sure which one gives the correct conductivity. On Sun, 7/28/13, Mostafa Shabani mostafa.nanophys...@gmail.com wrote: Subject: Re: [SIESTA-L] optical mesh To: siesta-l@uam.es Date: Sunday, July 28, 2013, 10:20 PM Dear somayeh. I think Armchair Graphen Nano Ribone has 2D structure .you have to pay attention for griding (kgrid_Monkhorst) your griding is for 1 0 0 0.5 1D structure along Z Direction . Be sure your structure is 1D or 2 D structure .And 0 1 0 0.5 0 0 32 0.5xc.functional GGA , xc.authors PBE Is better and exact approximation i think. On Sun, Jul 28, 2013 at 5:47 PM, somayeh rudi sapphire_b...@yahoo.com wrote: Dear siesta users I m trying to calculate the optical properties of an armchair GNR. can any one check my .fdf file and tell me if i defined my parameters correctly.specially my optical mesh. I really appreciate any help. Best regards Somayeh Rudi here is my .fdf file: # AGNR N_a = 5 # SystemLabel AGNR NumberOfSpecies 2 NumberOfAtoms 14 %block ChemicalSpeciesLabel 1 6 C 2 1 H %endblock ChemicalSpeciesLabel %PAO.Basis basis.fdf %PAO.BasisSize SZ %block PAO.BasisSizes C DZP H DZP %endblock PAO.BasisSizes %AtomicCoordinatesFormat ScaledCartesian # Format for coordinates %AtomicCoorFormatOut Ang %block kgrid_Monkhorst_Pack 1 0 0 0.5 0 1 0 0.5 0 0 32 0.5 %endblock kgrid_Monkhorst_Pack MeshCutoff 210. Ry SolutionMethod diagon MaxSCFIterations 200 DM.MixingWeight 0.20 DM.Tolerance 1.d-5 DM.NumberPulay 4 ElectronicTemperature 300 K DM.UseSaveDM true UseSaveData true SpinPolarized false xc.functional LDA xc.authors CA WriteMullikenPop 1 SaveDeltaRho .true. SaveRho .true. SaveElectrostaticPotential .true. SaveTotalPotential .true. %block LocalDensityOfStates -3.0520 -2.8520 eV %endblock LocalDensityOfStates %block BandLines 1 0.00 0.00 0. \Gamma 200 0.00 0.00 1. X %endblock BandLines LatticeConstant 4.26258 Ang %block LatticeVectors 22.82899136 0.000 0.000 0.000 16.00 0.000 0.000 0.000 1.000 %endblock LatticeVectors AtomicCoordinatesFormat NotScaledCartesianAng %block AtomicCoordinatesAndAtomicSpecies 8.95349397 8. 1.42086 1 8.95349397 8. 2.84172 1 10.18399482 8. 3.55215 1 10.18399482 8. 0.71043 1 11.41449568 8. 1.42086 1 11.41449568 8. 2.84172 1 12.64499654 8. 3.55215 1 12.64499654 8. 0.71043 1 13.87549739 8. 1.42086 1 13.87549739 8. 2.84172 1 8. 8. 0.87036 2 8. 8. 3.39222 2 14.82899136 8. 0.87036 2 14.82899136 8. 3.39222 2 %endblock AtomicCoordinatesAndAtomicSpecies # Calculation of dielectric function OpticalCalculation .true. Optical.Broaden 0.1 eV %block Optical.Mesh 1 1 64 %endblock Optical.Mesh #Optical.OffsetMesh .true. Optical.PolarizationType polarized %block Optical.Vector 0.000 0.000 1.000 %endblock Optical.Vector
Re: [SIESTA-L] optical mesh
Dear Mostafa Thanks for your reply. My structure is an 5-armchair graphene nanoribbon along the z direction. i want to know that the optical mesh (1 1 64) that i used is correct or not. i obtained different conductivities for optical mesh (1 1 64) and optical mesh (64 1 1) , i m not sure which one gives the correct conductivity. On Sun, 7/28/13, Mostafa Shabani mostafa.nanophys...@gmail.com wrote: Subject: Re: [SIESTA-L] optical mesh To: siesta-l@uam.es Date: Sunday, July 28, 2013, 10:20 PM Dear somayeh. I think Armchair Graphen Nano Ribone has 2D structure .you have to pay attention for griding (kgrid_Monkhorst) your griding is for 1 0 0 0.5 1D structure along Z Direction . Be sure your structure is 1D or 2 D structure .And 0 1 0 0.5 0 0 32 0.5xc.functional GGA , xc.authors PBE Is better and exact approximation i think. On Sun, Jul 28, 2013 at 5:47 PM, somayeh rudi sapphire_b...@yahoo.com wrote: Dear siesta users I m trying to calculate the optical properties of an armchair GNR. can any one check my .fdf file and tell me if i defined my parameters correctly.specially my optical mesh. I really appreciate any help. Best regards Somayeh Rudi here is my .fdf file: # AGNR N_a = 5 # SystemLabel AGNR NumberOfSpecies 2 NumberOfAtoms 14 %block ChemicalSpeciesLabel 1 6 C 2 1 H %endblock ChemicalSpeciesLabel %PAO.Basis basis.fdf %PAO.BasisSize SZ %block PAO.BasisSizes C DZP H DZP %endblock PAO.BasisSizes %AtomicCoordinatesFormat ScaledCartesian # Format for coordinates %AtomicCoorFormatOut Ang %block kgrid_Monkhorst_Pack 1 0 0 0.5 0 1 0 0.5 0 0 32 0.5 %endblock kgrid_Monkhorst_Pack MeshCutoff 210. Ry SolutionMethod diagon MaxSCFIterations 200 DM.MixingWeight 0.20 DM.Tolerance 1.d-5 DM.NumberPulay 4 ElectronicTemperature 300 K DM.UseSaveDM true UseSaveData true SpinPolarized false xc.functional LDA xc.authors CA WriteMullikenPop 1 SaveDeltaRho .true. SaveRho .true. SaveElectrostaticPotential .true. SaveTotalPotential .true. %block LocalDensityOfStates -3.0520 -2.8520 eV %endblock LocalDensityOfStates %block BandLines 1 0.00 0.00 0. \Gamma 200 0.00 0.00 1. X %endblock BandLines LatticeConstant 4.26258 Ang %block LatticeVectors 22.82899136 0.000 0.000 0.000 16.00 0.000 0.000 0.000 1.000 %endblock LatticeVectors AtomicCoordinatesFormat NotScaledCartesianAng %block AtomicCoordinatesAndAtomicSpecies 8.95349397 8. 1.42086 1 8.95349397 8. 2.84172 1 10.18399482 8. 3.55215 1 10.18399482 8. 0.71043 1 11.41449568 8. 1.42086 1 11.41449568 8. 2.84172 1 12.64499654 8. 3.55215 1 12.64499654 8. 0.71043 1 13.87549739 8. 1.42086 1 13.87549739 8. 2.84172 1 8. 8. 0.87036 2 8. 8. 3.39222 2 14.82899136 8. 0.87036 2 14.82899136 8. 3.39222 2 %endblock AtomicCoordinatesAndAtomicSpecies # Calculation of dielectric function OpticalCalculation .true. Optical.Broaden 0.1 eV %block Optical.Mesh 1 1 64 %endblock Optical.Mesh #Optical.OffsetMesh .true. Optical.PolarizationType polarized %block Optical.Vector 0.000 0.000 1.000 %endblock Optical.Vector
