c*********************************************************************** c c default values for input.dat c c*********************************************************************** c======================================================================= c setparams.F c======================================================================= c----------------------------------------------------------------------- c /* */ c /* style in reading initial geometry */ c /* */ c /* input_style = OLD: read from centroid.dat. */ c /* input_style = NEW: read from structure.dat. */ c /* */ c----------------------------------------------------------------------- OLD c----------------------------------------------------------------------- c /* */ c /* calculational method */ c /* */ c /* method = STATIC static. */ c /* method = TESTFORCE test forces. */ c /* method = TESTVIRIAL test virial. */ c /* method = GEOOPT geometry optimization. */ c /* method = NMA normal mode analysis. */ c /* method = SD steepest descent. */ c /* method = BOXOPT box optimization. */ c /* method = MD classical molecular dynamics. */ c /* method = PIMD path integral md. */ c /* method = PIHMC path integral hybrid monte carlo. */ c /* method = CMD centroid md. */ c /* method = RPMD ring polymer md. */ c /* method = MTD metadynamics. */ c /* method = REHMC replica exchange hmc. */ c /* method = STRING string method. */ c /* method = PHONON phonon calculation. */ c /* method = OMOPT optimization of OM action. */ c /* method = TESTOM test OM force. */ c /* */ c----------------------------------------------------------------------- STATIC c----------------------------------------------------------------------- c /* */ c /* statistical ensemble */ c /* */ c /* ensemble = NONE not specified. */ c /* ensemble = NVE constant volume and energy. */ c /* ensemble = NVT constant volume and temperature. */ c /* ensemble = NPT constant pressure and temperature */ c /* ensemble = NTT constant tension and temperature. */ c /* ensemble = NPH constant pressure and enthalpy. */ c /* ensemble = NTH constant tension and enthalpy. */ c /* */ c----------------------------------------------------------------------- NONE c----------------------------------------------------------------------- c /* number of atoms */ c----------------------------------------------------------------------- 0 c----------------------------------------------------------------------- c /* number of atomic species */ c----------------------------------------------------------------------- 0 c----------------------------------------------------------------------- c /* number of beads */ c----------------------------------------------------------------------- 1 c----------------------------------------------------------------------- c /* multiple time step for harmonic forces */ c----------------------------------------------------------------------- 1 c----------------------------------------------------------------------- c /* multiple time step for thermostats */ c----------------------------------------------------------------------- 5 c----------------------------------------------------------------------- c /* */ c /* type of thermostat */ c /* */ c /* bath_type = NONE no thermostat. */ c /* bath_type = NHC Nose-Hoover chain. */ c /* bath_type = NHCS Nose-Hoover chains (multiple) */ c /* bath_type = MNHC massive Nose-Hoover chain. */ c /* */ c /* usage: */ c /* */ c /* bath_type = MNHC for PIMD (NVT). */ c /* bath_type = MNHC for CMD. */ c /* bath_type = NONE for RPMD. */ c /* */ c----------------------------------------------------------------------- NONE c----------------------------------------------------------------------- c /* multiplicity of massive Nose-Hoover chain thermostats */ c----------------------------------------------------------------------- 1 c----------------------------------------------------------------------- c /* chain length of massive Nose-Hoover chain thermostat */ c----------------------------------------------------------------------- 4 c----------------------------------------------------------------------- c /* */ c /* type of potential model */ c /* */ c /* ipotential = WATER water. */ c /* ipotential = HARMONIC harmonic potential. */ c /* ipotential = SPLINE spline function. */ c /* ipotential = MM mm force field. */ c /* ipotential = EAM eam. */ c /* ipotential = MOPAC mopac. */ c /* ipotential = G03 gaussian 03. */ c /* ipotential = G98 gaussian 98. */ c /* ipotential = TURBOMOLE turbomole. */ c /* ipotential = GAMESS gamess. */ c /* ipotential = MOLPRO molpro. */ c /* ipotential = ABINIT-MP abinitmp 5.0. (embedded) */ c /* ipotential = ABINIT-MP5 abinitmp 5.0. (system call) */ c /* ipotential = VASP vasp 5.0. (embedded) */ c /* ipotential = VASP5 vasp 5.0. (system call) */ c /* ipotential = SMASH smash 1.1.0 */ c /* ipotential = ORCA orca 3.0 (system call) */ c /* */ c----------------------------------------------------------------------- not_available c======================================================================= c setcondition.F c======================================================================= c----------------------------------------------------------------------- c /* */ c /* translational and rotational corrections */ c /* */ c /* itrans_start = 0 ... no translational correction */ c /* = 1 ... subtract at initial step */ c /* = 2 ... correct each time step */ c /* */ c /* irot_start = 0 ... no rotational correction */ c /* = 1 ... subtract at initial step */ c /* = 2 ... correct each time step */ c /* */ c----------------------------------------------------------------------- 0 0 c----------------------------------------------------------------------- c /* number of MD steps */ c----------------------------------------------------------------------- 4 c----------------------------------------------------------------------- c /* time step size in [fs] */ c-----------------------------------------------------------------------
0.25d0 c----------------------------------------------------------------------- c /* temperature in [K] */ c----------------------------------------------------------------------- 300.d0 c----------------------------------------------------------------------- c /* pressure in [MPa] */ c----------------------------------------------------------------------- 0.101325d0 c----------------------------------------------------------------------- c /* characteristic time scale of thermostat [fs] */ c----------------------------------------------------------------------- 10.d0 c----------------------------------------------------------------------- c /* characteristic time scale of barostat [fs] */ c----------------------------------------------------------------------- 1000.d0 c----------------------------------------------------------------------- c /* temperature for bead spread [K] (valid for initial run) */ c----------------------------------------------------------------------- 500.d0 c----------------------------------------------------------------------- c /* PIMD execution command */ c----------------------------------------------------------------------- 'pimd.x' c======================================================================= c softexit.F c======================================================================= c----------------------------------------------------------------------- c /* read interval of exit.dat */ c----------------------------------------------------------------------- 10 c======================================================================= c standard.F c======================================================================= c----------------------------------------------------------------------- c /* output interval: standard output (standard.out) */ c----------------------------------------------------------------------- 1 c======================================================================= c analysis.F c======================================================================= c----------------------------------------------------------------------- c /* output interval: bond lengths (bond.out) */ c----------------------------------------------------------------------- -1 c----------------------------------------------------------------------- c /* output interval: radius of gyration (rgy.out) */ c----------------------------------------------------------------------- -1 c----------------------------------------------------------------------- c /* output interval: energy averages (eavg.out) */ c----------------------------------------------------------------------- -1 c----------------------------------------------------------------------- c /* output interval: radial distributions (rdf.out) */ c----------------------------------------------------------------------- -1 c----------------------------------------------------------------------- c /* output interval: trajectory in regular format */ c----------------------------------------------------------------------- -1 c----------------------------------------------------------------------- c /* */ c /* format for trajectory output */ c /* */ c /* iformat_trj = 1 double precision */ c /* = 2 single presision */ c /* */ c----------------------------------------------------------------------- 1 c----------------------------------------------------------------------- c /* output interval: xyz file (trj.xyz) */ c----------------------------------------------------------------------- -1 c----------------------------------------------------------------------- c /* output interval: box trajectory (box.out) */ c----------------------------------------------------------------------- -1 c----------------------------------------------------------------------- c /* */ c /* format of xyz file */ c /* */ c /* iformat_xyz = 1 each bead separately */ c /* = 2 all beads together */ c /* = 3 centroid only */ c /* */ c----------------------------------------------------------------------- 2 c----------------------------------------------------------------------- c /* */ c /* first species and last species to be printed in xyz file */ c /* */ c /* ispec_xyz = 1 first species */ c /* = 2 second species */ c /* = -1 last species */ c /* */ c----------------------------------------------------------------------- 1 -1 c----------------------------------------------------------------------- c /* output interval: dipole moment ( dipole.out) */ c----------------------------------------------------------------------- -1 c----------------------------------------------------------------------- c /* output interval: linear/angular momentum (momentum.out) */ c----------------------------------------------------------------------- -1 c----------------------------------------------------------------------- c /* output interval: update restart files (*.ini) */ c----------------------------------------------------------------------- 10 c----------------------------------------------------------------------- c /* */ c /* radial distributions (rdf.out) */ c /* */ c /* lower bound, upper bound, increment in [bohr] */ c /* */ c----------------------------------------------------------------------- 1.d0 20.d0 0.01d0 c======================================================================= c analysis_string.F c======================================================================= c----------------------------------------------------------------------- c /* output interval: string.xyz, string_pot.out */ c----------------------------------------------------------------------- 1 c======================================================================= c boundary.F c======================================================================= c----------------------------------------------------------------------- c /* */ c /* boundary condition */ c /* */ c /* iboundary = 0 free */ c /* = 1 periodic */ c /* */ c /* for periodic boundary, the box matrix is provided */ c /* */ c /* ( ax, bx, cx ) */ c /* H = ( ay, by, cy ) */ c /* ( az, bz, cz ) */ c /* */ c /* where a, b, c are lattice vectors of the box */ c /* */ c----------------------------------------------------------------------- 0 c----------------------------------------------------------------------- c /* central atom in periodic boundary condition */ c----------------------------------------------------------------------- 1 c======================================================================= c force_g09.F c======================================================================= c----------------------------------------------------------------------- c /* g09 command */ c----------------------------------------------------------------------- 'g09' 'formchk' c----------------------------------------------------------------------- c /* g09 gradient */ c----------------------------------------------------------------------- 1 c----------------------------------------------------------------------- c /* g09 oniom */ c----------------------------------------------------------------------- 0 c----------------------------------------------------------------------- c /* g09 dipole */ c----------------------------------------------------------------------- 1 c======================================================================= c force_g03.F c======================================================================= c----------------------------------------------------------------------- c /* g03 command */ c----------------------------------------------------------------------- 'g03' 'formchk' c----------------------------------------------------------------------- c /* g03 gradient */ c----------------------------------------------------------------------- 1 c----------------------------------------------------------------------- c /* g03 dipole */ c----------------------------------------------------------------------- 1 c======================================================================= c force_g98.F c======================================================================= c----------------------------------------------------------------------- c /* g98 command */ c----------------------------------------------------------------------- 'g98' 'formchk' c----------------------------------------------------------------------- c /* g98 gradient */ c----------------------------------------------------------------------- 1 c----------------------------------------------------------------------- c /* g98 dipole */ c----------------------------------------------------------------------- 1 c======================================================================= c force_mopac.F c======================================================================= c----------------------------------------------------------------------- c /* mopac command */ c----------------------------------------------------------------------- 'nohup /opt/mopac/mopac/MOPAC2007.out' c======================================================================= c force_turbo.F c======================================================================= c----------------------------------------------------------------------- c /* turbomole commands */ c----------------------------------------------------------------------- dscf control.1 grad control.2 c----------------------------------------------------------------------- c /* */ c /* turbomole guess option */ c /* */ c /* turbo_guess = PREVIOUS : mo's from previous step */ c /* = PULAY : Pulay's fourth order extrapolation */ c /* = KOLAFA : Kolafa's sixth order extrapolation */ c /* */ c----------------------------------------------------------------------- 1 c======================================================================= c lbfgscycle.F c======================================================================= c----------------------------------------------------------------------- c /* */ c /* convergence criteria for limited memory BFGS method */ c /* */ c /* rms displacement, max displacement, */ c /* rms gradient, max gradient */ c /* */ c----------------------------------------------------------------------- 1.d-4, 1.d-5, 1.d-5, 1.d-6 c======================================================================= c random.F c======================================================================= c----------------------------------------------------------------------- c /* */ c /* option for random number generator */ c /* */ c /* irandom = 0 seed is zero. */ c /* = 1 seed is at random. */ c /* */ c----------------------------------------------------------------------- 0 c======================================================================= c force_mech.F c======================================================================= c----------------------------------------------------------------------- c /* */ c /* mech_type : mechanochemistry */ c /* */ c /* mech_type = NONE: no external force. */ c /* mech_type = EFEI: external force explicitly included. */ c /* */ c----------------------------------------------------------------------- NONE c----------------------------------------------------------------------- c /* */ c /* For mech_type = EFEI */ c /* */ c /* atom 1, atom 2, force [au] */ c /* */ c----------------------------------------------------------------------- not_available c----------------------------------------------------------------------- c /* print interval of energy components (mech.out) */ c----------------------------------------------------------------------- 1 c======================================================================= c testforce.F, testvirial.F, freq.F, boxopt.F c======================================================================= c----------------------------------------------------------------------- c /* finite difference shift parameter */ c----------------------------------------------------------------------- 1.d-4 c======================================================================= c force_gamess.F c======================================================================= c----------------------------------------------------------------------- c /* gamess execution command */ c----------------------------------------------------------------------- 'rungms gamess 00 1' c======================================================================= c force_orca.F c======================================================================= c----------------------------------------------------------------------- c /* orca execution command */ c----------------------------------------------------------------------- 'orca' c======================================================================= c metacycle.F / pimd_hills.F c======================================================================= c----------------------------------------------------------------------- c /* maximum number of gaussians */ c----------------------------------------------------------------------- 50000 c----------------------------------------------------------------------- c /* */ c /* parameters of collective variables */ c /* */ c /* 1st line: number of collective variables */ c /* 2nd line: type and parameters for the 1st cv */ c /* 3rd line: type and parameters for the 2nd cv */ c /* nth line: type and parameters for the (n-1)th cv */ c /* */ c /* type 1: bond distance */ c /* 1, atom #1, atom #2 */ c /* */ c /* type 2: bond angle */ c /* 2, atom #1, atom #2, atom #3 */ c /* */ c /* type 3: dihedral angle */ c /* 3, atom #1, atom #2, atom #3, atom #4 */ c /* */ c /* type 4: bond difference */ c /* 4, atom #1, atom #2, atom #3 */ c /* */ c /* type 5: coordination number */ c /* 5, spec #1, spec #2, mu, nu, distance [bohr] */ c /* */ c----------------------------------------------------------------------- not_available c----------------------------------------------------------------------- c /* number of reference steps for harmonic potential */ c----------------------------------------------------------------------- 10 c----------------------------------------------------------------------- c /* gaussian height [kelvin] */ c----------------------------------------------------------------------- 150.d0 c----------------------------------------------------------------------- c /* */ c /* gaussian width */ c /* */ c /* type 1: bond distance, width [bohr] */ c /* type 2: bond angle, width [deg] */ c /* type 3: dihedral angle, width [deg] */ c /* type 4: bond difference, width [bohr] */ c /* type 5: coordination, width [no unit] */ c /* */ c----------------------------------------------------------------------- 1 0.100d0 2 5.000d0 3 10.000d0 4 0.100d0 5 0.100d0 c----------------------------------------------------------------------- c /* */ c /* time scale of diffusion of collective variables [fs] */ c /* */ c /* = time scale of adding new gaussian */ c /* */ c /* the mass of fictitious particle is set by */ c /* */ c /* fictmass_meta = t_cv_meta**2 / (1.5*gw_meta)**2 / beta */ c /* */ c----------------------------------------------------------------------- 75.0 c----------------------------------------------------------------------- c /* */ c /* time scale of oscillation of collective variables [fs] */ c /* */ c /* = period of oscillation for the harmonic term */ c /* */ c /* fc_meta = 4 * pi**2 * fictmass_meta / time_fc_meta**2 */ c /* */ c /* note: set nref_meta such that */ c /* */ c /* dt/nref_meta * 100 > time_fc_meta */ c /* */ c----------------------------------------------------------------------- 30.d0 c----------------------------------------------------------------------- c /* */ c /* time limit of adding a new hill [fs] */ c /* */ c /* note: set time_limit_meta at least more than three times */ c /* as large as time_cv_meta */ c /* */ c----------------------------------------------------------------------- 225.0 c----------------------------------------------------------------------- c /* */ c /* characteristic time scale of cv thermostat [fs] */ c /* */ c /* note: this must be large enough */ c /* */ c----------------------------------------------------------------------- 1000.d0 c----------------------------------------------------------------------- c /* print interval: energy components */ c----------------------------------------------------------------------- 1 c----------------------------------------------------------------------- c /* print interval: hills reconstruction */ c----------------------------------------------------------------------- 100 c----------------------------------------------------------------------- c /* print interval: cv trajectory */ c----------------------------------------------------------------------- 1 c----------------------------------------------------------------------- c /* */ c /* parameters for hills reconstruction */ c /* */ c /* type 1: min, max, mesh of bond distance [bohr] */ c /* type 2: min, max, mesh of bond angle [deg] */ c /* type 3: min, max, mesh of dihedral angle [deg] */ c /* type 4: min, max, mesh of bond difference [bohr] */ c /* type 5: min, max, mesh of coordination [no unit] */ c /* */ c----------------------------------------------------------------------- 1 1.0 6.0 0.02 2 0.0 180.0 1.00 3 0.0 360.0 2.00 4 -3.0 3.0 0.02 5 0.0 4.0 0.02 c----------------------------------------------------------------------- c /* */ c /* addition of hills in multiple walker metadynamics */ c /* */ c /* ioption = 0 simply add for all walkers */ c /* ioption = 1 choose walkers that are well separated */ c /* */ c----------------------------------------------------------------------- 1 c----------------------------------------------------------------------- c /* */ c /* cut off parameter in hill reconstruction of 3D metadynamics */ c /* */ c----------------------------------------------------------------------- 100.d0 c======================================================================= c force_water.F c======================================================================= c----------------------------------------------------------------------- c /* */ c /* water model: */ c /* */ c /* model_water = 1 spc/f */ c /* = 2 rwk */ c /* */ c----------------------------------------------------------------------- 1 c======================================================================= c setup_oniom.F c======================================================================= c----------------------------------------------------------------------- c /* */ c /* ONIOM data */ c /* */ c /* number species of layer A, link atom, layer B */ c /* high level and low level potentials */ c /* directory 1 */ c /* directory 2 */ c /* directory 3 */ c /* number of link atoms */ c /* bonded atoms and bond distance of each link atom */ c /* */ c----------------------------------------------------------------------- not_available c----------------------------------------------------------------------- c /* print interval: ONIOM energy contributions (oniom.out) */ c----------------------------------------------------------------------- 1 c----------------------------------------------------------------------- c /* */ c /* definition of dipole moment in ONIOM */ c /* */ c /* idipole_oniom = 1 value of layer A */ c /* 2 value of the whole system */ c /* */ c----------------------------------------------------------------------- 1 c----------------------------------------------------------------------- c /* */ c /* the use of BEST method in ONIOM method (old format) */ c /* */ c /* 0 off */ c /* 1 on */ c /* */ c /* if on, */ c /* */ c /* central species and identical species in layers A, B */ c /* */ c----------------------------------------------------------------------- 0 c----------------------------------------------------------------------- c /* */ c /* the use of BEST method in ONIOM and QM/MM method */ c /* (new format) */ c /* */ c /* 0 off */ c /* 1 on */ c /* */ c /* if on, */ c /* */ c /* central species and identical species in layers A, B */ c /* */ c----------------------------------------------------------------------- 0 c======================================================================= c force_qmmm.F c======================================================================= c----------------------------------------------------------------------- c /* */ c /* qmmm data */ c /* */ c /* number species of layer A, link atom, layer B */ c /* high level and low level potentials */ c /* directory 1 */ c /* directory 2 */ c /* directory 3 */ c /* number of link atoms */ c /* bonded atoms and bond distance of each link atom */ c /* */ c----------------------------------------------------------------------- not_available c----------------------------------------------------------------------- c /* print interval: QM/MM energy contributions (qmmm.out) */ c----------------------------------------------------------------------- 1 c----------------------------------------------------------------------- c /* */ c /* definition of dipole moment in QM/MM */ c /* */ c /* idipole_qmmm = 1 value of layer A */ c /* 2 value of whole system */ c /* */ c----------------------------------------------------------------------- 1 c----------------------------------------------------------------------- c /* */ c /* the use of best method QM/MM method (old format) */ c /* */ c /* 0 off */ c /* 1 on */ c /* */ c /* if on, */ c /* */ c /* central species and identical species in layer A, B */ c /* */ c----------------------------------------------------------------------- 0 c======================================================================= c setup_multi.F c======================================================================= c----------------------------------------------------------------------- c /* multiple time step parameter */ c----------------------------------------------------------------------- 100 c======================================================================= c force_vasp.F c======================================================================= c----------------------------------------------------------------------- c /* VASP output file options */ c----------------------------------------------------------------------- 0 1 c----------------------------------------------------------------------- c /* if 1, MO of previous step is used as initial guess */ c----------------------------------------------------------------------- 1 c======================================================================= c force_vasp5.F c======================================================================= c----------------------------------------------------------------------- c /* VASP command */ c----------------------------------------------------------------------- 'mpirun -np 4 vasp > output.vasp' c----------------------------------------------------------------------- c /* VASP energy keyword */ c----------------------------------------------------------------------- 'FREE ENERGIE OF THE ION-ELECTRON SYSTEM (eV)' c----------------------------------------------------------------------- c /* VASP energy gradient keyword */ c----------------------------------------------------------------------- 'POSITION TOTAL-FORCE (eV/Angst)' c======================================================================= c force_molpro.F c======================================================================= c----------------------------------------------------------------------- c /* molpro command */ c----------------------------------------------------------------------- 'molpro' c======================================================================= c force_dftb.F c======================================================================= c----------------------------------------------------------------------- c /* dftb command */ c----------------------------------------------------------------------- 'dftb+' c======================================================================= c force_abinit_mp4.F, force_abinit_mp5.F c======================================================================= c----------------------------------------------------------------------- c /* abinit_mp command */ c----------------------------------------------------------------------- 'abinitmp' c======================================================================= c force_abinit_mp.F c======================================================================= c----------------------------------------------------------------------- c /* abinit_mp input file */ c----------------------------------------------------------------------- 'input.ajf' c----------------------------------------------------------------------- c /* abinit_mp output file */ c----------------------------------------------------------------------- 'output.abi' 0 1 c----------------------------------------------------------------------- c /* if 1, MO of previous step is used as initial guess */ c----------------------------------------------------------------------- 1 0 0 c======================================================================= c setup_tfs.F, setup_mfe.F c======================================================================= c----------------------------------------------------------------------- c /* number of states */ c----------------------------------------------------------------------- 1 c----------------------------------------------------------------------- c /* initial state number */ c----------------------------------------------------------------------- 1 c----------------------------------------------------------------------- c /* output interval: tully' fewest switches (tfs.out) */ c----------------------------------------------------------------------- 1 c----------------------------------------------------------------------- c /* output interval: mean field ehrenfest (mfe.out) */ c----------------------------------------------------------------------- 1 c----------------------------------------------------------------------- c /* output interval: nonadiabatic coupling (nac.out) */ c----------------------------------------------------------------------- 1 c======================================================================= c setup_pihmc.F c======================================================================= c----------------------------------------------------------------------- c /* */ c /* Suzuki-Trotter expansion */ c /* */ c /* iorder_hmc = 2 second order */ c /* iorder_hmc = 4 fourth order */ c /* */ c----------------------------------------------------------------------- 2 c======================================================================= c setup_pihmc.F, setup_rehmc.F c======================================================================= c----------------------------------------------------------------------- c /* number of md steps per mc cycle */ c----------------------------------------------------------------------- 1 c======================================================================= c setup_dual.F c======================================================================= c----------------------------------------------------------------------- c /* methods of high and low levels */ c /* directories of high and low levels */ c----------------------------------------------------------------------- not_available, not_available not_available, not_available c----------------------------------------------------------------------- c /* print interval: energy components (dual.out) */ c----------------------------------------------------------------------- 1 c======================================================================= c setup_nph.F, setup_npt.F, setup_nth.F, setup_ntt.F c======================================================================= c----------------------------------------------------------------------- c /* */ c /* nph_type: type of flexible box for NPH ensemble */ c /* */ c /* = CUBIC1 cubic box (Andersen) */ c /* = CUBIC2 cubic box (Martyna-Tuckerman-Klein) */ c /* = PPHEX parallel piped hexagonal (Parrinello-Rahman) */ c /* */ c----------------------------------------------------------------------- CUBIC2 c----------------------------------------------------------------------- c /* */ c /* npt_type: type of flexible box for NPT ensemble */ c /* */ c /* = CUBIC1 cubic box (Andersen) */ c /* = CUBIC2 cubic box (Martyna-Tuckerman-Klein) */ c /* = PPHEX parallel piped hexagonal (Parrinello-Rahman) */ c /* */ c----------------------------------------------------------------------- CUBIC2 c----------------------------------------------------------------------- c /* */ c /* nth_type: type of flexible box for NtH ensemble */ c /* */ c /* = CUBIC1 cubic box (Andersen) */ c /* = CUBIC2 cubic box (Martyna-Tuckerman-Klein) */ c /* = PPHEX parallel piped hexagonal (Parrinello-Rahman) */ c /* */ c----------------------------------------------------------------------- PPHEX c----------------------------------------------------------------------- c /* */ c /* ntt_type: type of flexible box for NtT ensemble */ c /* */ c /* = CUBIC1 cubic box (Andersen) */ c /* = CUBIC2 cubic box (Martyna-Tuckerman-Klein) */ c /* = PPHEX parallel piped hexagonal (Parrinello-Rahman) */ c /* */ c----------------------------------------------------------------------- PPHEX c----------------------------------------------------------------------- c /* tension for NtH and NtT ensembles */ c----------------------------------------------------------------------- 0.d0 0.d0 0.d0 0.d0 0.d0 0.d0 0.d0 0.d0 0.d0 c======================================================================= c phonon.F c======================================================================= c----------------------------------------------------------------------- c /* number of primitive cells per supercell */ c----------------------------------------------------------------------- 1 1 1 c----------------------------------------------------------------------- c /* k-points for phonon dispersion */ c----------------------------------------------------------------------- 1 0.0 0.0 0.0 c----------------------------------------------------------------------- c /* k-point sampling for phonon density of states */ c----------------------------------------------------------------------- 1 1 1 c----------------------------------------------------------------------- c /* phonon dos range */ c----------------------------------------------------------------------- 0.0 5000.0 5.0 c----------------------------------------------------------------------- c /* temperature range for phonon energies */ c----------------------------------------------------------------------- 0.0 1000.0 10.0 c======================================================================= c setup_cmd.F c======================================================================= c----------------------------------------------------------------------- c /* adiabaticity parameter for cmd */ c----------------------------------------------------------------------- 10 c======================================================================= c setup_rehmc.F c======================================================================= c----------------------------------------------------------------------- c /* */ c /* type of replica exchange method */ c /* */ c /* irem_type = T no exchange between temperatures */ c /* irem_type = TX allow exchanges between temperatures */ c /* irem_type = HX hamiltonian exchanges for alchemistry */ c /* */ c----------------------------------------------------------------------- TX c----------------------------------------------------------------------- c /* minimum and maximum temperatures in TP or TX */ c----------------------------------------------------------------------- 300.d0 300.d0 c======================================================================= c setup_string.F c======================================================================= c----------------------------------------------------------------------- c /* both ends in string method FREE or FIXED. */ c----------------------------------------------------------------------- FIXED c----------------------------------------------------------------------- c /* grid parameter in string method */ c----------------------------------------------------------------------- 11 c======================================================================= c analysis_rehmc.F c======================================================================= 1 c======================================================================= c force_dftb.F c======================================================================= c----------------------------------------------------------------------- c /* dftb command */ c----------------------------------------------------------------------- 'dftb+' c======================================================================= c force_smash.F c======================================================================= c----------------------------------------------------------------------- c /* smash execution command */ c /* */ c /* note: this option is obsolete */ c----------------------------------------------------------------------- smash c----------------------------------------------------------------------- c /* iexe_smash_grad: option for force calculation in smash */ c /* = 0: off */ c /* = 1: on */ c /* */ c /* note: this option is obsolete */ c----------------------------------------------------------------------- 1 c----------------------------------------------------------------------- c /* iexe_smash_dip: option for dipole calculation in smash */ c /* = 0: off */ c /* = 1: on */ c /* */ c /* note: this option is obsolete */ c----------------------------------------------------------------------- 0 c----------------------------------------------------------------------- c /* smash_threads: number of openmp threads for smash */ c /* */ c /* note: this option is obsolete */ c----------------------------------------------------------------------- 1 c----------------------------------------------------------------------- c /* smash_options: smash standard input (without geometry) */ c----------------------------------------------------------------------- job method=hf basis=6-31g(d) memory=1gb charge=0 control iprint=1 c----------------------------------------------------------------------- c /* */ c /* smash guess option */ c /* */ c /* smash_guess = PREVIOUS : mo's from previous step */ c /* = PULAY : Pulay's fourth order extrapolation */ c /* = KOLAFA : Kolafa's sixth order extrapolation */ c /* */ c----------------------------------------------------------------------- PREVIOUS c======================================================================= c setup_conv.F c======================================================================= c----------------------------------------------------------------------- c /* number of constraints */ c----------------------------------------------------------------------- 0 c----------------------------------------------------------------------- c /* output interval: constraints (cons.out) */ c----------------------------------------------------------------------- 1 c----------------------------------------------------------------------- c /* */ c /* parameters for constraints */ c /* */ c /* type 1: bond distance [bohr] */ c /* type 2: bond angle [deg] */ c /* type 3: dihedral angle [deg] */ c /* type 4: bond difference [bohr] */ c /* type 5: coordination [no unit] */ c /* */ c----------------------------------------------------------------------- 1 1.d0 2 4.d-4 3 1.d-4 4 1.d0 5 1.d0 c======================================================================= c setup_om.F, setup_omopt.F c======================================================================= c----------------------------------------------------------------------- c /* overdamped or underdamped */ c----------------------------------------------------------------------- OVERDAMPED c----------------------------------------------------------------------- c /* time increment of OM action */ c----------------------------------------------------------------------- 0.625d0 c----------------------------------------------------------------------- c /* friction constant [1/fs] */ c----------------------------------------------------------------------- 0.00625098366d0 c======================================================================= c read_species.f c======================================================================= taken from http://www.nist.gov/pml/data/comp.cfm a.w.: atomic weight n.a.: not available 121 L 1 1.00782503223 link atom H 1 1.00782503223 1H D 1 2.01410177812 2H T 1 3.0160492779 3H He 2 4.00260325413 4He Li 3 7.0160034366 7Li Be 4 9.012183065 9Be B 5 6.9675 a.w. C 6 12.000000000 12C N 7 14.00307400443 14N O 8 15.99491461957 16O F 9 18.99840316273 19F Ne 10 19.9924401762 20Ne Na 11 22.9897692820 23Na Mg 12 24.3055 a.w. Al 13 26.98153853 27Al Si 14 27.97692653465 28Si P 15 30.97376199842 31P S 16 31.9720711744 32S Cl 17 35.4515 a.w. Ar 18 39.9623831237 40Ar K 19 38.9637064864 39K Ca 20 39.962590863 40Ca Sc 21 44.95590828 45Sc Ti 22 47.867 a.w. V 23 50.94395704 51V Cr 24 51.9961 a.w. Mn 25 54.93804391 55Mn Fe 26 55.845 a.w. Co 27 58.93319429 59Co Ni 28 58.6934 a.w. Cu 29 63.546 a.w. Zn 30 65.38 a.w. Ga 31 69.723 a.w. Ge 32 72.630 a.w. As 33 74.92159457 75As Se 34 78.971 a.w. Br 35 79.904 a.w. Kr 36 83.798 a.w. Rb 37 85.4678 a.w. Sr 38 87.62 a.w. Y 39 88.9058403 89Y Zr 40 89.9046977 90Zr Nb 41 92.9063730 93Nb Mo 42 95.95 a.w. Tc 43 98.0 a.w. Ru 44 101.07 a.w. Rh 45 102.9054980 103Rh Pd 46 106.42 a.w. Ag 47 107.8682 a.w. Cd 48 112.414 a.w. In 49 114.903878776 115In Sn 50 118.710 a.w. Sb 51 121.760 a.w. Te 52 127.60 a.w. I 53 126.9044719 127I Xe 54 131.293 a.w. Cs 55 132.9054519610 133Cs Ba 56 137.327 a.w. La 57 138.9063563 139La Ce 58 140.116 a.w. Pr 59 140.9076576 141Pr Nd 60 144.242 a.w. Pm 61 145.0 a.w. Sm 62 150.36 a.w. Eu 63 151.964 a.w. Gd 64 157.25 a.w. Tb 65 158.9253547 159Tb Dy 66 162.500 a.w. Ho 67 164.9303288 165Ho Er 68 167.259 a.w. Tm 69 168.9342179 169Tm Yb 70 173.054 a.w. Lu 71 174.9407752 175Lu Hf 72 178.49 a.w. Ta 73 180.9479958 181Ta W 74 183.84 a.w. Re 75 186.207 a.w. Os 76 190.23 a.w. Ir 77 192.217 a.w. Pt 78 195.084 a.w. Au 79 196.96656879 197Au Hg 80 200.592 a.w. Tl 81 204.3835 a.w. Pb 82 207.2 a.w. Bi 83 208.9803991 209Bi Po 84 209.0 a.w. At 85 210.0 a.w. Rn 86 222.0 a.w. Fr 87 223.0197360 223Fr Ra 88 226.0 226Ra Ac 89 227.0277523 227Ac Th 90 232.0380558 232Th Pa 91 231.0358842 231Pa U 92 238.0507884 238U Np 93 237.0 a.w. Pu 94 244.0 a.w. Am 95 241.0 n.a Cm 96 243.0 n.a Bk 97 247.0 n.a Cf 98 249.0 n.a Es 99 252.082980 n.a Fm 100 257.0951061 n.a Md 101 258.0 n.a No 102 259.10103 n.a Lr 103 262.10961 n.a Rf 104 267.12179 n.a Db 105 268.12567 n.a Sg 106 271.13393 n.a Bh 107 272.13826 n.a Hs 108 270.13429 n.a Mt 109 276.15159 n.a Ds 110 281.16451 n.a Rg 111 280.16514 n.a Cn 112 285.17712 n.a Uut 113 284.17873 n.a Fl 114 289.19042 n.a Uup 115 288.19274 n.a Lv 116 293.20449 n.a Uus 117 292.20746 n.a Uuo 118 294.21392 n.a