From: Egon Willighagen <egonw@us...>  20020817 11:58:34

Update of /cvsroot/jmol/Jmol/samples In directory uswprcvs1:/tmp/cvsserv19242/samples Added Files: HfO2_mol_opt.in HfO2_on_Si_relax.in bulk_Si.in slab_7Si_3Vac_2x.in t54.in Log Message: Added Fabian Dortu's ABINITReader contribution, including a few example files. Also updated documention about this.  NEW FILE: HfO2_mol_opt.in  # H2 molecule in a big box # # This file will optimize automatically the interatomic distance #Define the methodology to find the minimum ionmov 3 # Use the modified Broyden algorithm ntime 20 # Maximum number of Broyden "timesteps" tolmxf 5.0d4 # Stopping criterion for the geometry optimization : when # the residual forces are less than tolmxf, the Broyden # algorithm can stop xcart 0.0 0.0 0.0 # Hf 0.7 0.7 0.0 # O 0.7 0.7 0.0 # O toldff 5.0d5 # Will stop the SCF cycle when, twice in a row, # the difference between two consecutive evaluations of # forces differ by less than toldff (in Hartree/Bohr) #nband 1 # Only one band is occupied. In order to get the energy, # forces ..., there is no need to compute more than one band. # #The rest of this file is similar to the t11.in file, except #that xcart has been moved above, and that toldfe has been replaced #by toldff, see above. #Definition of the unit cell acell 15 15 15 # The keyword "acell" refers to the # lengths of the primitive vectors (in Bohr) # The priitive cell is cubic by default #Definition of the atom types ntype 2 # There is only 2 type of atom zatnum 72 8 # The keyword "zatnum" refers to the atomic number of the # possible type(s) of atom. The pseudopotential(s) # mentioned in the "files" file must correspond # to the type(s) of atom. Here, the only type is Hydrogen. #Definition of the atoms natom 3 # There are 3 atoms type 1 2 2 # HfO2 #Definition of the planewave basis set ecut 40.0 # Maximal kinetic energy cutoff, in Hartree #Definition of the kpoint grid nkpt 1 # Only one k point is needed for isolated system, # taken by default to be 0.0 0.0 0.0 #Definition of the SCF procedure nstep 20 # Maximal number of SCF cycles #toldfe is no more defined, as toldff is used above... diemac 1.0 # Although this is not mandatory, it is worth to # precondition the SCF cycle. The model dielectric diemix 0.5 # function used as the standard preconditioner # is described in the "dielng" input variable section. # Here, we follow the prescriptions for molecules # in a big box  NEW FILE: HfO2_on_Si_relax.in  # Study of relaxed HfO2 on Silicon [100] non relaxed # Dynamic optcell 0 # This is the default. Don't optimize unit cell ionmov 3 # Relaxation BroydenFletcher tolmxf 1.0d6 # Force tolerance ntime 30 # Definition of the kpoint grids kptopt 1 # Option for the automatic generation of k points, # taking into account the symmetries. ngkpt 4 4 1 # unneccessary to sample in the z direction nshiftk 2 shiftk 0.5 0.0 0.0 0.0 0.5 0.0 # Definition of the unit cell acell 3*10.216 # Lattice parameters of bulk silicon in Bohr(optimized) rprim 0.5 0.5 0.0 # These values will define a tetragonal cell with 4 atoms, 1.0 1.0 0.0 # NONprimitive, with a different orientation 0.0 0.0 2.5 # than the primitive cell which is rhombohedral. chkprim 0 # This input variable allows to use nonprimitive # unit cells. # Definition of the atom types ntype 3 # There is only one type of atom zatnum 14 72 8 # Atomic number of silicon,Hafnium and Oxygen # Definition of the atoms natom 20 # There are 20 atoms in the unit cell type 14*1 2 2 4*3 # They are of type 1, silicon, 2 Hf, 3 O. xcart # I use xcart (in Bohr) instead of xred because it will # be easier in the case of a slab of varying # Silicon and vacuum thickness. 0.0 0.0 0.0 # atom at the corner 2.554 2.554 2.554 # 2.554=a_cell/4 5.108 0.0 5.108 # 5.108=a_cell/2 7.662 2.554 7.662 # 7.662=3*a_cell/4 0.0 0.0 10.216 2.554 2.554 12.770 # 12.770=a_cell*5/4 5.108 0.0 15.324 # 15.324=a_cell*3/2 5.108 5.108 0.0 # expanding in x,y direction 7.662 7.662 2.554 10.216 5.108 5.108 12.77 7.662 7.662 5.108 5.108 10.216 7.662 7.662 12.770 10.216 5.108 15.324 5.108 5.108 15.324 # adding the Hf on top of Si 10.216 10.216 15.324 # idem in adjacent cell 2.554 2.554 15.324 # adding oxygens 7.662 2.554 15.324 12.77 5.108 15.324 7.662 5.108 15.324 # Definition of the planewave basis set #ecut 8.0 # Maximal kinetic energy cutoff, in Hartree # Convergence was not very good ecut 35.0 # Definition of the SCF procedure nstep 20 # Maximal number of SCF cycles. toldfe 1.0d6 # Will stop when, twice in a row, the difference # between two consecutive evaluations of total # energy differ by less then toldfe (Ha) diemac 12.0 # precondition the SCF cycle (12 is good for bulk Si)  NEW FILE: bulk_Si.in  # Crystalline silicon : computation of the total energy # Convergence with respect to the number of k points. #Definition of the kpoint grids kptopt 1 # Option for the automatic generation of k points, taking # into account the symmetry nshiftk 4 shiftk 0.5 0.5 0.5 # These shifts will be the same for all grids 0.5 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.5 ngkpt 8 8 8 # Definition of the different grids #Definition of the unit cell acell 3*10.18 # This is equivalent to 10.18 10.18 10.18 rprim 0.0 0.5 0.5 # FCC primitive vectors (to be scaled by acell) 0.5 0.0 0.5 0.5 0.5 0.0 #Definition of the atom types ntype 1 # There is only one type of atom zatnum 14 # The keyword "zatnum" refers to the atomic number of the # possible type(s) of atom. The pseudopotential(s) # mentioned in the "files" file must correspond # to the type(s) of atom. Here, the only type is Silicon. #Definition of the atoms natom 2 # There are two atoms type 1 1 # They both are of type 1, that is, Silicon. xred # This keyword indicate that the location of the atoms # will follow, one triplet of number for each atom 0.0 0.0 0.0 # Triplet giving the REDUCED coordinate of atom 1. 0.25 0.25 0.25 # Triplet giving the REDUCED coordinate of atom 2. #Definition of the planewave basis set ecut 8.0 # Maximal kinetic energy cutoff, in Hartree #Definition of the SCF procedure nstep 10 # Maximal number of SCF cycles toldfe 1.0d6 # Will stop when, twice in a row, the difference # between two consecutive evaluations of total energy # differ by less than toldfe (in Hartree) diemac 12.0 # Although this is not mandatory, it is worth to # precondition the SCF cycle. The model dielectric # function used as the standard preconditioner # is described in the "dielng" input variable section. # Here, we follow the prescription for bulk silicon.  NEW FILE: slab_7Si_3Vac_2x.in  # Crystalline silicon # # In the next simulations, we will compute the surface energy # of the [001] Si slab. # So we have to change the orientation of the cell. # Here we compute the bulk silicon energy with this new # unit cell. It should gave the same result as the classical # rhombohedral unit cell (per atom of course) # Definition of the kpoint grids kptopt 1 # Option for the automatic generation of k points, # taking into account the symmetries. ngkpt 4 4 4 nshiftk 2 shiftk 0.5 0.0 0.5 0.0 0.5 0.5 # Definition of the unit cell acell 3*10.216 # Lattice parameters of bulk silicon in Bohr(optimized) rprim 0.5 0.5 0.0 # These values will define a tetragonal cell with 4 atoms, 1.0 1.0 0.0 # NONprimitive, with a different orientation 0.0 0.0 2.5 # than the primitive cell which is rhombohedral. chkprim 0 # This input variable allows to use nonprimitive # unit cells. # Definition of the atom types ntype 1 # There is only one type of atom zatnum 14 # Atomic number of silicon # Definition of the atoms natom 14 # There are 4 atoms in the unit cell type 14*1 # They are of type 1, silicon. xcart # I use xcart (in Bohr) instead of xred because it will # be easier in the case of a slab of varying # Silicon and vacuum thickness. 0.0 0.0 0.0 # atom at the corner 2.554 2.554 2.554 # 2.554=a_cell/4 5.108 0.0 5.108 # 5.108=a_cell/2 7.662 2.554 7.662 # 7.662=3*a_cell/4 0.0 0.0 10.216 2.554 2.554 12.770 # 12.770=a_cell*5/4 5.108 0.0 15.324 # 15.324=a_cell*3/2 5.108 5.108 0.0 # expanding in x,y direction 7.662 7.662 2.554 10.216 5.108 5.108 12.77 7.662 7.662 5.108 5.108 10.216 7.662 7.662 12.770 10.216 5.108 15.324 # Definition of the planewave basis set ecut 8.0 # Maximal kinetic energy cutoff, in Hartree # Definition of the SCF procedure nstep 20 # Maximal number of SCF cycles. toldfe 1.0d6 # Will stop when, twice in a row, the difference # between two consecutive evaluations of total # energy differ by less then toldfe (Ha) diemac 12.0 # precondition the SCF cycle (12 is good for bulk Si)  NEW FILE: t54.in  # Crystalline AlAs : computation of the dynamical matrix at Gamma # #Responsefunction calculation, with q=0 rfphon 1 # Will consider phonontype perturbation rfatpol 1 2 # All the atoms will be displaced rfdir 1 1 1 # Along all reduced coordinate axis nqpt 1 # One wavevector is to be considered qpt 0 0 0 # This wavevector is q=0 (Gamma) kptopt 2 # Automatic generation of k points, taking # into account the timereversal symmetry only tolvrs 1.0d8 # SCF stopping criterion iscf 5 # Selfconsistent calculation, using algorithm 5 irdwfk 1 # Read the groundstate wavefunctions ####################################################################### #Common input variables #Definition of the unit cell acell 3*10.61 # This is equivalent to 10.61 10.61 10.61 rprim 0.0 0.5 0.5 # In lessons 1 and 2, these primitive vectors 0.5 0.0 0.5 # (to be scaled by acell) were 1 0 0 0 1 0 0 0 1 0.5 0.5 0.0 # that is, the default. #Definition of the atom types ntype 2 # There are two types of atom zatnum 13 33 # The keyword "zatnum" refers to the atomic number of the # possible type(s) of atom. The pseudopotential(s) # mentioned in the "files" file must correspond # to the type(s) of atom. Here, type 1 is the Aluminum, # type 2 is the Arsenic. #Definition of the atoms natom 2 # There are two atoms type 1 2 # The first is of type 1 (Al), the second is of type 2 (As). xred # This keyword indicate that the location of the atoms # will follow, one triplet of number for each atom 0.0 0.0 0.0 # Triplet giving the REDUCED coordinate of atom 1. 0.25 0.25 0.25 # Triplet giving the REDUCED coordinate of atom 2. #Gives the number of band, explicitely (do not take the default) nband 4 # For an insulator (if described correctly as an insulator # by DFT), there is no need to include conduction bands # in responsefunction calculations #Definition of the planewave basis set ecut 3.0 # Maximal kinetic energy cutoff, in Hartree #Definition of the kpoint grid kptrlatt 4 4 4 # In cartesian coordinates, this grid is simple cubic, and 4 4 4 # actually corresponds to the socalled 8x8x8 MonkhorstPack grid. 4 4 4 # It might as well be obtained through the use of # ngkpt, nshiftk and shiftk . #Definition of the SCF procedure nstep 15 # Maximal number of SCF cycles diemac 9.0 # Although this is not mandatory, it is worth to # precondition the SCF cycle. The model dielectric # function used as the standard preconditioner # is described in the "dielng" input variable section. # The dielectric constant of AlAs is smaller that the one of Si (=12). 