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
