OK,I don't write this block directly with the coordinate datas,instead I use another file *.xyz to hold the position datas.And in *.fdf it only needs to tell the block the file's name like this :
%block AtomicCoordinatesAndAtomicSpecies < ben+h2_z.xyz %endblock AtomicCoordinatesAndAtomicSpecies and it also work as you write it in directly. Because in my test there are hundreds of atoms in the cluster ,it is convenient and clearly to use this format. 2011/7/2 Zahra Talebi <[email protected]> > Hi, > I am a new user of siesta and by reading your e-mail a question came to my > mind. can you tell me that why your fdf doesn`t have the atom coordination > block. > thank you > > ------------------------------ > *From:* Robin H <[email protected]> > *To:* [email protected] > *Sent:* Fri, July 1, 2011 11:32:53 AM > *Subject:* [SIESTA-L] problem with Siesta, cannot describe benzene-H2 > binding: big error > > Dear siesta users,I'm now puzzled with the results by siesta in > calculating the interaction energy of benzene and molecule > hydrogen.According to a reference(Fabien Tran et al,J. Phys. Chem. B 2002, > 106, 8689-8696),they used the Gaussian packages,and got the results much > agreed with the experiment datas:when the orientation of the H2 axis is > parallel to X axis ,the interation energy is 0.42 kcal/mol,and when the > orientation is parallel to Z axis,the interaction energy is 0.72 > kcal/mol.But I tried with siesta (the parameters has been kept the same as > possible as I can ),the former results is 3.7997kcal/mol,and the latter is > becoming to 4.252kcal/mol.Both of the calculation has a big difference after > I checked all the possible reasons.I could't understand why siesta can't > make an accurate results.So I want to know is there any possible reason > about the precision of siesta? > *the following is an input file of two examples:* > SystemName Ben+h2_z > SystemLabel ben+h2_z > NumberOfAtoms 14 > NumberOfSpecies 2 > %block ChemicalSpeciesLabel > 1 6 C > 2 1 H > %endblock ChemicalSpeciesLabel > #%block PAO.BasisSizes > # O DZP > # Zn DZP > # C DZP > # H DZP > #%endblock PAO.BasisSizes > %block PAO.Basis > C 2 > n=2 0 3 > 4.088 3.347 3.002 > 1.000 1.000 1.000 > n=2 1 3 P 1 > 4.870 3.347 3.002 > 1.000 1.000 1.000 > H 1 > n=1 0 3 P 1 > 4.593 3.713 3.002 > 1.000 1.000 1.000 > %endblock PAO.Basis > #PAO.BasisSize DZP > PAO.EnergyShift 100 meV > PAO.BasisType split > LatticeConstant 15.000 Ang > #%block LatticeParameters > # 2.460 2.460 6.800 90.000 90.000 120.000 > #%endblock LatticeParameters > %block LatticeVectors > 1.000 0.000 0.000 > 0.000 1.000 0.000 > 0.000 0.000 1.000 > %endblock LatticeVectors > > #Kgrid_cutoff 5.00000 Ang > %block kgrid_Monkhorst_Pack > 1 0 0 0.0 > 0 1 0 0.0 > 0 0 1 0.0 > %endblock kgrid_Monkhorst_Pack > # %block BandLines > # 1 0.000 0.000 -1.000 > # 100 0.000 0.000 1.000 > # %endblock BandLines > #%block GeometryConstraints > # position from 1 to 424 > #%endblock GeometryConstraints > > #SPIN options > XC.functional GGA > XC.authors PBE > NetCharge 0 > SpinPolarized F > FixSpin F > TotalSpin 0.0 > MeshCutoff 300.0 Ry > FilterCutoff 100. Ry > # SCF options > #%block DM.InitSpin > #%endblock DM.InitSpin > MaxSCFIterations 100 # Maximum number of SCF iter > DM.MixingWeight 0.10 # New DM amount for next SCF cycle > DM.NumberPulay 10 > DM.Tolerance 1.d-4 # Tolerance in maximum difference between > input and output DM > DM.UseSaveDM T # to use continuation files > DM.MixSCF1 F > DM.PulayOnFile F # Store in memory ('F') or in files ('T') > SolutionMethod diagon # OrderN or Diagon > ElectronicTemperature 100.0 K #Temp. for Fermi smearing > > # MD options > > MD.TypeOfRun cg > MD.NumCGsteps 150 > MD.MaxCGDispl 0.1 Ang > MD.MaxForceTol 0.01 eV/Ang > MD.VariableCell F > MD.MaxStressTol 0.05 GPa > #MD.TypeOfRun fc > #MD.FCDispl 0.04 Ang > #MD.FCfirst 1 > #MD.FClast 200 > AtomicCoordinatesFormat Ang > %block AtomicCoordinatesAndAtomicSpecies < ben+h2_z.xyz > %endblock AtomicCoordinatesAndAtomicSpecies > # OUTPUT options > WriteCoorInitial T > WriteCoorStep T > WriteCoorXmol T > WriteForces T > WriteEigenvalues T # If .false., it writes them in the > file Systemlabel.EIG > WriteMullikenPop 1 # Write Mulliken Population > Analysis > #WriteKpoints T > #WriteKbands T > #WriteBands T > WriteMDCoorXmol F > WriteMDhistory F > # options for saving or reading information > MD.UseSaveZM F # Use stored positions and velocities > MD.UseSaveCG F # Use stored positions and velocities > SaveRho T # Write valence pseudocharge at the mesh > #SaveDeltaRho T # Write RHOscf-RHOatm at the mesh > #SaveElectrostaticPotential T # Write the total elect. pot. at the > mesh > # (local pseudopotential + Hartree) > SaveHS T > SaveTotalPotential T # write the valence total effective local > potential > # (local pseudopotential + Hartree + Vxc) > #WriteSiestaDim T # Write minimum dim to siesta.h and stop > #WriteDenchar T # Write information for DENCHAR > >
