On 07/02/2011 12:35 AM, Zahra Talebi wrote:
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.
That fdf read in coordination from another file, i.e, ben+h2_z.xyz, thanks to fdf's powerful capability. You can see the following line to know this thing:
> %block AtomicCoordinatesAndAtomicSpecies < ben+h2_z.xyz
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
-- Hongyi Zhao <[email protected]> Institute of Semiconductors, Chinese Academy of Sciences GnuPG DSA: 0xD108493
