Sorry I did a mistake and the input file didn't appear correctly in my previous mail.... oups! The input file is attached to this mail.
Simon > Dear Siesta Users, > > I would like to use the ZMatrix format in order to impose complex > constraints during the structural relaxation of molecular junctions. As a > first test, I tried to relax the bond length Au-Au of bulk gold (the input > is below). Well, the geometry of the system changes during the calculation > but do not relax towards the equilibrium one. As an example, the forces > evolves as > Max 0.508665 constrained (step 0) > Max 0.298118 constrained (step ~60) > Max 3.732910 constrained (step 180). > > Do I mis something ? > Every suggestions are welcome.... > > Best regards, > Simon > > --- input --- > > SystemName cond > SystemLabel cond > > NumberOfAtoms 48 > NumberOfSpecies 4 > > %block ChemicalSpeciesLabel > 1 79 Au > 2 1 H > 3 6 C > 4 16 S > %endblock ChemicalSpeciesLabel > > LatticeConstant 1.0 Ang > %block LatticeVectors > 11.78039897907284 0 0 > 5.89019946947620 10.20212478179412 0 > 0.51961524227066 0.30000000000000 32.82762500000000 > %endblock LatticeVectors > > %block kgrid_Monkhorst_Pack > 1 0 0 0.0 > 0 1 0 0.0 > 0 0 1 0.0 > %endblock kgrid_Monkhorst_Pack > > ZM.UnitsLength Ang > ZM.UnitsAngle deg > ZM.ForceTolLength 0.1e-01 eV/Ang > ZM.ForceTolAngle 0.5e-01 eV/deg > ZM.MaxDisplLength 0.001 Ang > ZM.MaxDisplAngle 0.001 deg > > %block Zmatrix > molecule > 1 0 0 0 0.00 0.000000 0.000000 0 0 0 1 > 1 0 0 daa 90.000000 00.000000 1 0 0 1 1 2 > 0 daa 60.000000 0.000000 1 0 0 1 2 3 1 > daa 120.000000 180.000000 1 0 0 1 3 1 2 daa > 120.000000 0.000000 1 0 0 1 3 2 1 daa > 120.000000 180.000000 1 0 0 1 4 5 3 daa > 120.000000 180.000000 1 0 0 1 5 6 3 daa > 120.000000 180.000000 1 0 0 1 6 3 2 daa > 120.000000 0.000000 1 0 0 1 6 5 3 daa > 120.000000 180.000000 1 0 0 1 8 9 6 daa > 120.000000 180.000000 1 0 0 1 9 10 6 daa > 120.000000 180.000000 1 0 0 1 10 6 5 daa > 120.000000 0.000000 1 0 0 1 12 13 10 daa > 120.000000 180.000000 1 0 0 1 13 9 6 daa > 120.000000 180.000000 1 0 0 1 15 12 9 daa > 120.000000 180.000000 1 0 0 1 1 3 2 daa > 60.000000 -70.528779 1 0 0 1 2 1 3 daa > 120.000000 -70.528779 1 0 0 1 3 1 2 daa > 120.000000 70.528779 1 0 0 1 4 2 3 daa > 120.000000 -70.528779 1 0 0 1 5 3 1 daa > 120.000000 109.471221 1 0 0 1 6 3 2 daa > 120.000000 70.528779 1 0 0 1 7 4 5 daa > 120.000000 -70.528779 1 0 0 1 8 5 6 daa > 120.000000 -70.528779 1 0 0 1 9 6 3 daa > 120.000000 109.471221 1 0 0 1 10 6 5 daa > 120.000000 70.528779 1 0 0 1 11 8 9 daa > 120.000000 -70.528779 1 0 0 1 12 9 10 daa > 120.000000 -70.528779 1 0 0 1 13 10 6 daa > 120.000000 109.471221 1 0 0 1 14 12 13 daa > 120.000000 -70.528779 1 0 0 1 15 13 9 daa > 120.000000 109.471221 1 0 0 1 16 15 12 daa > 120.000000 109.471221 1 0 0 1 17 3 1 daa > 120.000000 180.000000 1 0 0 1 18 5 3 daa > 120.000000 125.264389 1 0 0 1 19 6 3 daa > 120.000000 -180.000000 1 0 0 1 20 8 5 daa > 120.000000 125.264389 1 0 0 1 21 9 6 daa > 120.000000 125.264389 1 0 0 1 22 10 6 daa > 120.000000 180.000000 1 0 0 1 23 11 8 daa > 120.000000 125.264389 1 0 0 1 24 12 9 daa > 120.000000 125.264389 1 0 0 1 25 13 10 daa > 120.000000 125.264389 1 0 0 1 26 13 10 daa > 120.000000 180.000000 1 0 0 1 27 14 12 daa > 120.000000 125.264389 1 0 0 1 28 15 13 daa > 120.000000 125.264389 1 0 0 1 29 15 13 daa > 120.000000 180.000000 1 0 0 1 30 16 15 daa > 120.000000 125.264389 1 0 0 1 31 16 15 daa > 120.000000 -180.000000 1 0 0 1 32 31 15 daa > 120.000000 180.000000 1 0 0 > variables > daa 2.90 > %endblock Zmatrix > > %block PAO.Basis # Define Basis set > Au 2 # Species label, number of l-shells > n=6 0 2 P 1 # n, l, Nzeta, Polarization, NzetaPol > 6.893 5.302 > 1.000 1.000 > n=5 2 1 # n, l, Nzeta > 4.858 > 1.000 > H 1 # Species label, number of l-shells > n=1 0 2 P 1 # n, l, Nzeta, Polarization, NzetaPol > 5.205 3.359 > 1.000 1.000 > C 2 # Species label, number of l-shells > n=2 0 2 # n, l, Nzeta > 4.518 3.029 > 1.000 1.000 > n=2 1 2 P 1 # n, l, Nzeta, Polarization, NzetaPol > 5.519 3.105 > 1.000 1.000 > S 2 # Species label, number of l-shells > n=3 0 2 # n, l, Nzeta > 4.492 3.166 > 1.000 1.000 > n=3 1 2 P 2 # n, l, Nzeta, Polarization, NzetaPol > 5.487 3.455 > 1.000 1.000 > %endblock PAO.Basis > > MeshCutoff 200. Ry # 80. Ry OK for gold (see Emilio) > PAO.BasisType split # Type of PAO basis set > SpinPolarized F # 'T', 'F' > FixSpin F > TotalSpin 0.0 > NonCollinearSpin F > > XC.functional GGA > XC.authors PBE > > SolutionMethod diagon > NetCharge 0.0 > ElectronicTemperature 300 K > OccupationFunction FD > > MaxSCFIterations 140 > DM.MixingWeight 0.04 > DM.Tolerance 0.00005 > DM.NumberPulay 5 > DM.UseSaveDM .true. > UseSaveData .true. > > MD.TypeOfRun CG > MD.NumCGsteps 200 > MD.MaxForceTol 0.1e-01 eV/Ang > MD.MaxCGDispl 0.01 Ang > MD.VariableCell .true. > MD.MaxStressTol 0.005 GPa > > SaveElectrostaticPotential T > SaveRho T > WriteDM T > WriteCoorInitial T > WriteMDhistory T > WriteCoorXmol T > WriteForces T > WriteCoorStep T > WriteMDXmol T > SaveHS T > > > -- > Simon Dubois > > PhD Student > Ecole Polytechnique de Louvain > Unité de Physico-Chimie et de Physique des Matériaux (PCPM) > Place Croix du Sud, 1 > B-1348 Louvain-La-Neuve (Belgium) > Tel. 010/47.28.38 > > > > -- > Simon Dubois > > PhD Student > Ecole Polytechnique de Louvain > Unité de Physico-Chimie et de Physique des Matériaux (PCPM) > Place Croix du Sud, 1 > B-1348 Louvain-La-Neuve (Belgium) > Tel. 010/47.28.38 > --
input.fdf
Description: application/vnd.fdf
