c/////////////////////////////////////////////////////////////////////// c c Author: M. Shiga c Last updated: Dec 18, 2020 by M. Shiga c Description: default values for input.dat c c/////////////////////////////////////////////////////////////////////// c======================================================================= c get_nprocs_2.F c======================================================================= c----------------------------------------------------------------------- c /* */ c /* Parallel parameters: */ c /* */ c /* np_beads is the number of beads computed in each cycle */ c /* np_force is the parallel number for each bead */ c /* */ c /* Default: np_beads = -1, means min(nbead,nprocs) */ c /* np_force = -1, means (nprocs/np_beads) */ c /* */ c /* Either np_beads or no_force could be changed */ c /* (when both are changed it goes back to default) */ c /* */ c /* when np_beads is changed it is assumed that */ c /* np_force = nprocs / np_beads */ c /* */ c /* when np_force is changed it is assumed that */ c /* np_beads = nprocs / np_force */ c /* */ c /* N = np_beads*np_force is processes used in each cycle */ c /* */ c /* Number of cycles = nbead/N + min(1,mod(nbead,N)) */ c /* */ c /* Number of processes (nprocs) must be set equal to N */ c /* (processes are fully used except for the last cycle) */ c /* */ c /* Thus, nprocs must be a multiple of np_beads and np_force */ c /* */ c /* Example: nbead=4 could be run with */ c /* nprocs np_beads np_force */ c /* 8 4 2 */ c /* 6 3 2 */ c /* */ c----------------------------------------------------------------------- c----------------------------------------------------------------------- c /* bead parallel parameter (-1: default) */ c----------------------------------------------------------------------- -1 c----------------------------------------------------------------------- c /* force parallel parameter (-1: default) */ c----------------------------------------------------------------------- -1 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----------------------------------------------------------------------- NEW 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 = ABINIT-MP abinitmp 5.0. (embedded) */ c /* ipotential = ABINIT-MP5 abinitmp 5.0. (system call) */ c /* ipotential = EAM eam. */ c /* ipotential = G03 gaussian 03. */ c /* ipotential = G98 gaussian 98. */ c /* ipotential = GAMESS gamess. */ c /* ipotential = HARMONIC harmonic potential. */ c /* ipotential = MM mm force field. */ c /* ipotential = MOLPRO molpro. */ c /* ipotential = MOPAC mopac. */ c /* ipotential = ONIOM oniom. */ c /* ipotential = ORCA orca 3.0. (system call) */ c /* ipotential = QE quantum espresso (embedded). */ c /* ipotential = QMMM qm/mm. */ c /* ipotential = SMASH smash 2.2.0. */ c /* ipotential = SPLINE spline function. */ c /* ipotential = TURBOMOLE turbomole. */ c /* ipotential = VASP vasp 5.0. (embedded) */ c /* ipotential = VASP5 vasp 5.0. (system call) */ c /* ipotential = USER user defined. */ c /* ipotential = WATER water. */ c /* */ c----------------------------------------------------------------------- not_available c----------------------------------------------------------------------- c /* */ c /* QM potential model in QM/MM method */ c /* */ c /* qmmm_potential = SMASH smash 2.2.0. */ c /* */ c----------------------------------------------------------------------- SMASH c----------------------------------------------------------------------- c /* */ c /* QM embedding model in QM/MM method */ c /* */ c /* qmmm_embedding = EE electronic embedding. */ c /* qmmm_embedding = ME mechanical embedding. */ c /* */ c----------------------------------------------------------------------- EE c----------------------------------------------------------------------- c /* */ c /* High precision potential model in ONIOM method */ c /* */ c /* oniom_hi_potential = SMASH smash 2.2.0. */ c /* */ c----------------------------------------------------------------------- SMASH c----------------------------------------------------------------------- c /* */ c /* Low precision potential model in ONIOM method */ c /* */ c /* oniom_lo_potential = MM mm force field. */ c /* */ c----------------------------------------------------------------------- MM c======================================================================= c setup_me.F, setup_ee.F c======================================================================= c----------------------------------------------------------------------- c /* */ c /* input directory for QM calculations in QM/MM method */ c /* */ c----------------------------------------------------------------------- dat c----------------------------------------------------------------------- c /* */ c /* scratch directory in QM/MM method */ c /* */ c----------------------------------------------------------------------- scr c----------------------------------------------------------------------- c /* print interval: QM/MM energy contributions (qmmm.out) */ c----------------------------------------------------------------------- 1 c----------------------------------------------------------------------- c /* charge variation of QM atoms in image cell (0: fixed) */ c----------------------------------------------------------------------- 0 c======================================================================= c setup_oniom.F c======================================================================= c----------------------------------------------------------------------- c /* */ c /* input directories in ONIOM method */ c /* */ c----------------------------------------------------------------------- dat_1 dat_2 dat_3 c----------------------------------------------------------------------- c /* */ c /* scratch directories in ONIOM method */ c /* */ c----------------------------------------------------------------------- scr_1 scr_2 scr_3 c----------------------------------------------------------------------- c /* print interval: ONIOM energy contributions (qmmm.out) */ c----------------------------------------------------------------------- 1 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 gethess.F c======================================================================= c----------------------------------------------------------------------- c /* output interval: hessian */ 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: radial distributions of centroid */ c /* (rdf_cent.out) calculated as the mean of the distance */ c /* between atoms in all beads in the frame */ c----------------------------------------------------------------------- -1 c----------------------------------------------------------------------- c /* output interval: radial distributions */ c /* of each bead (rdf_bead.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: xsf file (trj.xsf) */ c----------------------------------------------------------------------- -1 c----------------------------------------------------------------------- c /* output interval: xsf file (trj.xsf) */ 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 /* ikind_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 setup_pimd.F, etc. c======================================================================= -1.d0 c======================================================================= c force_g16.F c======================================================================= c----------------------------------------------------------------------- c /* g16 command */ c----------------------------------------------------------------------- 'g16' 'formchk' c----------------------------------------------------------------------- c /* g16 gradient */ c----------------------------------------------------------------------- 1 c----------------------------------------------------------------------- c /* g16 oniom */ c----------------------------------------------------------------------- 0 c----------------------------------------------------------------------- c /* g16 dipole */ 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 /* mech_type = CLUSTER: cluster boundary condition. */ c /* */ c----------------------------------------------------------------------- NONE c----------------------------------------------------------------------- c /* */ c /* For mech_type = EFEI */ c /* */ c /* atom 1, atom 2, force [au] */ c /* */ c----------------------------------------------------------------------- not_available c----------------------------------------------------------------------- c /* */ c /* For mech_type = CLUSTER */ c /* */ c /* distance from center of mass [au], force constant [au] */ c /* */ c----------------------------------------------------------------------- not_available c----------------------------------------------------------------------- c /* print interval of energy components (mech.out) */ c----------------------------------------------------------------------- 1 c----------------------------------------------------------------------- c /* */ c /* freeze: */ c /* */ c /* OFF: all atoms are free to move */ c /* ON: atoms specified by the following line, with */ c /* the first and the last atoms, are frozen */ c /* */ c----------------------------------------------------------------------- OFF 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----------------------------------------------------------------------- DIST 0.100d0 ANGL 5.000d0 DIH 10.000d0 DIFF 0.100d0 CN 0.100d0 DCN 0.100d0 XYZ 0.100d0 DXYZ 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----------------------------------------------------------------------- DIST 2.0 5.0 0.1 ANGL 0.0 180.0 6.0 DIH 0.0 360.0 12.0 DIFF -3.0 3.0 0.2 CN 0.0 3.0 0.1 DCN -2.0 2.0 0.1 XYZ 2.0 5.0 0.1 DXYZ 2.0 5.0 0.1 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 /* addition of new hills in metadynamics */ c /* */ c /* ioption = 0 add gaussian when walker is displaced */ c /* ioption = 1 add gaussian with equal timing */ c /* */ c----------------------------------------------------------------------- 0 c----------------------------------------------------------------------- c /* */ c /* cut off parameter in hill reconstruction of 3D metadynamics */ c /* */ c----------------------------------------------------------------------- 100.d0 c----------------------------------------------------------------------- c /* */ c /* reference temperature of metadynamics in kelvin */ c /* */ c /* dtemp_meta = 0.0 conventional metadynamics */ c /* dtemp_meta = nonzero well tempered metadynamics */ c /* */ c /* this is the only option in well tempered metadynamics */ c /* */ c----------------------------------------------------------------------- 0.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 force_best.F c======================================================================= c----------------------------------------------------------------------- c /* */ c /* best method */ c /* */ c /* ioption_best = 0 : off */ c /* ioption_best = 1 : on */ c /* */ c----------------------------------------------------------------------- 0 c----------------------------------------------------------------------- c /* iobest = solute (central atom) in best method */ c----------------------------------------------------------------------- 0 c----------------------------------------------------------------------- c /* iobest = solvent (common species) in best method */ c----------------------------------------------------------------------- 1 c----------------------------------------------------------------------- c /* force constant in best method in hartree/bohr**2 */ c----------------------------------------------------------------------- 25.0 c----------------------------------------------------------------------- c /* cut off energy in hartree */ c----------------------------------------------------------------------- 1.d-16 c----------------------------------------------------------------------- c /* print interval for best */ c----------------------------------------------------------------------- 1 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, line, column */ c----------------------------------------------------------------------- 'FREE ENERGIE OF THE ION-ELECTRON SYSTEM (eV)', 2, 5 c----------------------------------------------------------------------- c /* VASP energy gradient keyword, line, column */ c----------------------------------------------------------------------- 'POSITION TOTAL-FORCE (eV/Angst)', 2, 4 c----------------------------------------------------------------------- c /* VASP energy stress keyword, line, column */ c----------------------------------------------------------------------- 'FORCE on cell =-STRESS in cart. coord. units (eV):', 14, 3 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 /* dftb+ version: 19.1 or 18.2 */ c----------------------------------------------------------------------- '19.1' c======================================================================= c force_libdftb.F c======================================================================= c----------------------------------------------------------------------- c /* output options for the lib version of CP2K c----------------------------------------------------------------------- 0 c======================================================================= c c======================================================================= 1 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 /* interval of adjusting number of md steps per mc cycle */ c----------------------------------------------------------------------- -1 c----------------------------------------------------------------------- c /* (minimum) number of md steps per mc cycle */ c----------------------------------------------------------------------- 2 c----------------------------------------------------------------------- c /* maximum number of md steps per mc cycle */ c----------------------------------------------------------------------- 128 c----------------------------------------------------------------------- c /* magnifying factor of md steps per mc cycle */ c----------------------------------------------------------------------- 2 c----------------------------------------------------------------------- c /* lower bound of target acceptance ratio */ c----------------------------------------------------------------------- 0.05 c----------------------------------------------------------------------- c /* upper bound of target acceptance ratio */ c----------------------------------------------------------------------- 0.20 c======================================================================= c setup_dual.F c======================================================================= c----------------------------------------------------------------------- c /* methods of high and low levels */ c----------------------------------------------------------------------- MM MM c----------------------------------------------------------------------- c /* data directories of high and low levels */ c----------------------------------------------------------------------- dat_hi dat_lo c----------------------------------------------------------------------- c /* scratch directories of high and low levels */ c----------------------------------------------------------------------- scr_hi scr_lo 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 3000.0 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 1000.d0 c======================================================================= c setup_alchem.F c======================================================================= c----------------------------------------------------------------------- c /* alchemical potentials */ c----------------------------------------------------------------------- MM MM c----------------------------------------------------------------------- c /* input directories for alchemical potentials */ c----------------------------------------------------------------------- alchem_1 alchem_2 c----------------------------------------------------------------------- c /* scratch directories for alchemical potentials */ c----------------------------------------------------------------------- scr_1 scr_2 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 /* automatic step control in string method, ON or OFF. */ c----------------------------------------------------------------------- ON c======================================================================= c analysis_rehmc.F c======================================================================= 1 c======================================================================= c force_smash.F (#ifdef smash: with direct link to smash) c======================================================================= 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 force_smash.F (#ifndef smash: without direct link to smash) c======================================================================= c----------------------------------------------------------------------- c /* smash execution command */ c----------------------------------------------------------------------- 'smash' c----------------------------------------------------------------------- c /* option for the gradient (forces) calculation */ c /* */ c /* smash_grad = 1 : ON */ c /* = 0 : OFF */ c /* */ c----------------------------------------------------------------------- 1 c----------------------------------------------------------------------- c /* option for the dipole moment calculation */ c /* */ c /* smash_dip = 1 : ON */ c /* = 0 : OFF */ c /* */ c----------------------------------------------------------------------- 1 c----------------------------------------------------------------------- c /* number of treads for smash calculation */ c----------------------------------------------------------------------- 1 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----------------------------------------------------------------------- DIST 5.0d+0 ANGL 5.0d-2 DIH 5.0d-3 DIFF 2.5d+0 CN 1.0d+0 DCN 1.0d+0 XYZ 5.0d+0 DXYZ 5.0d+0 c======================================================================= c setup_om.F, setup_omopt.F c======================================================================= c----------------------------------------------------------------------- c /* overdamped or underdamped */ c----------------------------------------------------------------------- OVERDAMPED c----------------------------------------------------------------------- c /* time increment of OM action [fs] */ c----------------------------------------------------------------------- 0.625d0 c----------------------------------------------------------------------- c /* friction constant [1/fs] */ c----------------------------------------------------------------------- 0.00625d0 c======================================================================= c read_species.f c======================================================================= taken from http://www.nist.gov/pml/data/comp.cfm a.w.: atomic weight n.a.: not available taken from https://en.wikipedia.org/wiki/Covalent_radius cov : covalent radius of single bond [angstrom] cutoff radius of intramolecular bonds defined by rad = cov/0.52918*1.45 [bohr] 246 ! no atomic mass rad cov species H 1 1.00782503223 0.88 ! 0.32 1H He 2 4.00260325413 1.26 ! 0.46 4He Li 3 7.0160034366 3.64 ! 1.33 7Li Be 4 9.012183065 2.79 ! 1.02 9Be B 5 6.9675 2.33 ! 0.85 a.w. C 6 12.000000000 2.06 ! 0.75 12C N 7 14.00307400443 1.92 ! 0.70 14N O 8 15.99491461957 1.73 ! 0.63 16O F 9 18.99840316273 1.75 ! 0.64 19F Ne 10 19.9924401762 1.84 ! 0.67 20Ne Na 11 22.9897692820 4.25 ! 1.55 23Na Mg 12 24.3055 3.81 ! 1.39 a.w. Al 13 26.98153853 3.45 ! 1.26 27Al Si 14 27.97692653465 3.18 ! 1.16 28Si P 15 30.97376199842 3.04 ! 1.11 31P S 16 31.9720711744 2.82 ! 1.03 32S Cl 17 35.4515 2.71 ! 0.99 a.w. Ar 18 39.9623831237 2.63 ! 0.96 40Ar K 19 38.9637064864 5.37 ! 1.96 39K Ca 20 39.962590863 4.69 ! 1.71 40Ca Sc 21 44.95590828 4.06 ! 1.48 45Sc Ti 22 47.867 3.73 ! 1.36 a.w. V 23 50.94395704 3.67 ! 1.34 51V Cr 24 51.9961 3.34 ! 1.22 a.w. Mn 25 54.93804391 3.26 ! 1.19 55Mn Fe 26 55.845 3.18 ! 1.16 a.w. Co 27 58.93319429 3.04 ! 1.11 59Co Ni 28 58.6934 3.01 ! 1.10 a.w. Cu 29 63.546 3.07 ! 1.12 a.w. Zn 30 65.38 3.23 ! 1.18 a.w. Ga 31 69.723 3.40 ! 1.24 a.w. Ge 32 72.630 3.40 ! 1.24 a.w. As 33 74.92159457 3.32 ! 1.21 75As Se 34 78.971 3.18 ! 1.16 a.w. Br 35 79.904 3.12 ! 1.14 a.w. Kr 36 83.798 3.21 ! 1.17 a.w. Rb 37 85.4678 5.75 ! 2.10 a.w. Sr 38 87.62 5.07 ! 1.85 a.w. Y 39 88.9058403 4.47 ! 1.63 89Y Zr 40 89.9046977 4.22 ! 1.54 90Zr Nb 41 92.9063730 4.03 ! 1.47 93Nb Mo 42 95.95 3.78 ! 1.38 a.w. Tc 43 98.0 3.51 ! 1.28 a.w. Ru 44 101.07 3.43 ! 1.25 a.w. Rh 45 102.9054980 3.43 ! 1.25 103Rh Pd 46 106.42 3.29 ! 1.20 a.w. Ag 47 107.8682 3.51 ! 1.28 a.w. Cd 48 112.414 3.73 ! 1.36 a.w. In 49 114.903878776 3.89 ! 1.42 115In Sn 50 118.710 3.84 ! 1.40 a.w. Sb 51 121.760 3.84 ! 1.40 a.w. Te 52 127.60 3.73 ! 1.36 a.w. I 53 126.9044719 3.64 ! 1.33 127I Xe 54 131.293 3.59 ! 1.31 a.w. Cs 55 132.9054519610 6.36 ! 2.32 133Cs Ba 56 137.327 5.37 ! 1.96 a.w. La 57 138.9063563 4.93 ! 1.80 139La Ce 58 140.116 4.47 ! 1.63 a.w. Pr 59 140.9076576 4.82 ! 1.76 141Pr Nd 60 144.242 4.77 ! 1.74 a.w. Pm 61 145.0 4.74 ! 1.73 a.w. Sm 62 150.36 4.71 ! 1.72 a.w. Eu 63 151.964 4.60 ! 1.68 a.w. Gd 64 157.25 4.63 ! 1.69 a.w. Tb 65 158.9253547 4.60 ! 1.68 159Tb Dy 66 162.500 4.58 ! 1.67 a.w. Ho 67 164.9303288 4.55 ! 1.66 165Ho Er 68 167.259 4.52 ! 1.65 a.w. Tm 69 168.9342179 4.49 ! 1.64 169Tm Yb 70 173.054 4.66 ! 1.70 a.w. Lu 71 174.9407752 4.44 ! 1.62 175Lu Hf 72 178.49 4.16 ! 1.52 a.w. Ta 73 180.9479958 4.00 ! 1.46 181Ta W 74 183.84 3.75 ! 1.37 a.w. Re 75 186.207 3.59 ! 1.31 a.w. Os 76 190.23 3.53 ! 1.29 a.w. Ir 77 192.217 3.34 ! 1.22 a.w. Pt 78 195.084 3.37 ! 1.23 a.w. Au 79 196.96656879 3.40 ! 1.24 197Au Hg 80 200.592 3.64 ! 1.33 a.w. Tl 81 204.3835 3.95 ! 1.44 a.w. Pb 82 207.2 3.95 ! 1.44 a.w. Bi 83 208.9803991 4.14 ! 1.51 209Bi Po 84 209.0 3.97 ! 1.45 a.w. At 85 210.0 4.03 ! 1.47 a.w. Rn 86 222.0 3.89 ! 1.42 a.w. Fr 87 223.0197360 6.11 ! 2.23 223Fr Ra 88 226.0 5.51 ! 2.01 226Ra Ac 89 227.0277523 5.10 ! 1.86 227Ac Th 90 232.0380558 4.80 ! 1.75 232Th Pa 91 231.0358842 4.63 ! 1.69 231Pa U 92 238.0507884 4.66 ! 1.70 238U Np 93 237.0 4.69 ! 1.71 a.w. Pu 94 244.0 4.71 ! 1.72 a.w. Am 95 241.0 4.55 ! 1.66 n.a Cm 96 243.0 4.55 ! 1.66 n.a Bk 97 247.0 4.55 ! 1.66 n.a Cf 98 249.0 4.60 ! 1.68 n.a Es 99 252.082980 4.52 ! 1.65 n.a Fm 100 257.0951061 4.58 ! 1.67 n.a Md 101 258.0 4.74 ! 1.73 n.a No 102 259.10103 4.82 ! 1.76 n.a Lr 103 262.10961 4.41 ! 1.61 n.a Rf 104 267.12179 4.30 ! 1.57 n.a Db 105 268.12567 4.08 ! 1.49 n.a Sg 106 271.13393 3.92 ! 1.43 n.a Bh 107 272.13826 3.86 ! 1.41 n.a Hs 108 270.13429 3.67 ! 1.34 n.a Mt 109 276.15159 3.53 ! 1.29 n.a Ds 110 281.16451 3.51 ! 1.28 n.a Rg 111 280.16514 3.32 ! 1.21 n.a Cn 112 285.17712 3.34 ! 1.22 n.a Nh 113 284.17873 3.73 ! 1.36 n.a Fl 114 289.19042 3.92 ! 1.43 n.a Mc 115 288.19274 4.44 ! 1.62 n.a Lv 116 293.20449 4.80 ! 1.75 n.a Ts 117 292.20746 4.52 ! 1.65 n.a Og 118 294.21392 4.30 ! 1.57 n.a 1 1 1.00782503223 0.88 ! 0.32 1H 2 2 4.00260325413 1.26 ! 0.46 4He 3 3 7.0160034366 3.64 ! 1.33 7Li 4 4 9.012183065 2.79 ! 1.02 9Be 5 5 6.9675 2.33 ! 0.85 a.w. 6 6 12.000000000 2.06 ! 0.75 12C 7 7 14.00307400443 1.92 ! 0.70 14N 8 8 15.99491461957 1.73 ! 0.63 16O 9 9 18.99840316273 1.75 ! 0.64 19F 10 10 19.9924401762 1.84 ! 0.67 20Ne 11 11 22.9897692820 4.25 ! 1.55 23Na 12 12 24.3055 3.81 ! 1.39 a.w. 13 13 26.98153853 3.45 ! 1.26 27Al 14 14 27.97692653465 3.18 ! 1.16 28Si 15 15 30.97376199842 3.04 ! 1.11 31P 16 16 31.9720711744 2.82 ! 1.03 32S 17 17 35.4515 2.71 ! 0.99 a.w. 18 18 39.9623831237 2.63 ! 0.96 40Ar 19 19 38.9637064864 5.37 ! 1.96 39K 20 20 39.962590863 4.69 ! 1.71 40Ca 21 21 44.95590828 4.06 ! 1.48 45Sc 22 22 47.867 3.73 ! 1.36 a.w. 23 23 50.94395704 3.67 ! 1.34 51V 24 24 51.9961 3.34 ! 1.22 a.w. 25 25 54.93804391 3.26 ! 1.19 55Mn 26 26 55.845 3.18 ! 1.16 a.w. 27 27 58.93319429 3.04 ! 1.11 59Co 28 28 58.6934 3.01 ! 1.10 a.w. 29 29 63.546 3.07 ! 1.12 a.w. 30 30 65.38 3.23 ! 1.18 a.w. 31 31 69.723 3.40 ! 1.24 a.w. 32 32 72.630 3.40 ! 1.24 a.w. 33 33 74.92159457 3.32 ! 1.21 75As 34 34 78.971 3.18 ! 1.16 a.w. 35 35 79.904 3.12 ! 1.14 a.w. 36 36 83.798 3.21 ! 1.17 a.w. 37 37 85.4678 5.75 ! 2.10 a.w. 38 38 87.62 5.07 ! 1.85 a.w. 39 39 88.9058403 4.47 ! 1.63 89Y 40 40 89.9046977 4.22 ! 1.54 90Zr 41 41 92.9063730 4.03 ! 1.47 93Nb 42 42 95.95 3.78 ! 1.38 a.w. 43 43 98.0 3.51 ! 1.28 a.w. 44 44 101.07 3.43 ! 1.25 a.w. 45 45 102.9054980 3.43 ! 1.25 103Rh 46 46 106.42 3.29 ! 1.20 a.w. 47 47 107.8682 3.51 ! 1.28 a.w. 48 48 112.414 3.73 ! 1.36 a.w. 49 49 114.903878776 3.89 ! 1.42 115In 50 50 118.710 3.84 ! 1.40 a.w. 51 51 121.760 3.84 ! 1.40 a.w. 52 52 127.60 3.73 ! 1.36 a.w. 53 53 126.9044719 3.64 ! 1.33 127I 54 54 131.293 3.59 ! 1.31 a.w. 55 55 132.9054519610 6.36 ! 2.32 133Cs 56 56 137.327 5.37 ! 1.96 a.w. 57 57 138.9063563 4.93 ! 1.80 139La 58 58 140.116 4.47 ! 1.63 a.w. 59 59 140.9076576 4.82 ! 1.76 141Pr 60 60 144.242 4.77 ! 1.74 a.w. 61 61 145.0 4.74 ! 1.73 a.w. 62 62 150.36 4.71 ! 1.72 a.w. 63 63 151.964 4.60 ! 1.68 a.w. 64 64 157.25 4.63 ! 1.69 a.w. 65 65 158.9253547 4.60 ! 1.68 159Tb 66 66 162.500 4.58 ! 1.67 a.w. 67 67 164.9303288 4.55 ! 1.66 165Ho 68 68 167.259 4.52 ! 1.65 a.w. 69 69 168.9342179 4.49 ! 1.64 169Tm 70 70 173.054 4.66 ! 1.70 a.w. 71 71 174.9407752 4.44 ! 1.62 175Lu 72 72 178.49 4.16 ! 1.52 a.w. 73 73 180.9479958 4.00 ! 1.46 181Ta 74 74 183.84 3.75 ! 1.37 a.w. 75 75 186.207 3.59 ! 1.31 a.w. 76 76 190.23 3.53 ! 1.29 a.w. 77 77 192.217 3.34 ! 1.22 a.w. 78 78 195.084 3.37 ! 1.23 a.w. 79 79 196.96656879 3.40 ! 1.24 197Au 80 80 200.592 3.64 ! 1.33 a.w. 81 81 204.3835 3.95 ! 1.44 a.w. 82 82 207.2 3.95 ! 1.44 a.w. 83 83 208.9803991 4.14 ! 1.51 209Bi 84 84 209.0 3.97 ! 1.45 a.w. 85 85 210.0 4.03 ! 1.47 a.w. 86 86 222.0 3.89 ! 1.42 a.w. 87 87 223.0197360 6.11 ! 2.23 223Fr 88 88 226.0 5.51 ! 2.01 226Ra 89 89 227.0277523 5.10 ! 1.86 227Ac 90 90 232.0380558 4.80 ! 1.75 232Th 91 91 231.0358842 4.63 ! 1.69 231Pa 92 92 238.0507884 4.66 ! 1.70 238U 93 93 237.0 4.69 ! 1.71 a.w. 94 94 244.0 4.71 ! 1.72 a.w. 95 95 241.0 4.55 ! 1.66 n.a 96 96 243.0 4.55 ! 1.66 n.a 97 97 247.0 4.55 ! 1.66 n.a 98 98 249.0 4.60 ! 1.68 n.a 99 99 252.082980 4.52 ! 1.65 n.a 100 100 257.0951061 4.58 ! 1.67 n.a 101 101 258.0 4.74 ! 1.73 n.a 102 102 259.10103 4.82 ! 1.76 n.a 103 103 262.10961 4.41 ! 1.61 n.a 104 104 267.12179 4.30 ! 1.57 n.a 105 105 268.12567 4.08 ! 1.49 n.a 106 106 271.13393 3.92 ! 1.43 n.a 107 107 272.13826 3.86 ! 1.41 n.a 108 108 270.13429 3.67 ! 1.34 n.a 109 109 276.15159 3.53 ! 1.29 n.a 110 110 281.16451 3.51 ! 1.28 n.a 111 111 280.16514 3.32 ! 1.21 n.a 112 112 285.17712 3.34 ! 1.22 n.a 113 113 284.17873 3.73 ! 1.36 n.a 114 114 289.19042 3.92 ! 1.43 n.a 115 115 288.19274 4.44 ! 1.62 n.a 116 116 293.20449 4.80 ! 1.75 n.a 117 117 292.20746 4.52 ! 1.65 n.a 118 118 294.21392 4.30 ! 1.57 n.a D 1 2.01410177812 0.88 ! 0.32 2H T 1 3.0160492779 0.88 ! 0.32 3H Mu 1 0.1134289257 0.88 ! 0.32 muon HW 1 1.00782503223 0.88 ! 0.32 TIP3P hydrogen OW 8 15.99491461957 1.73 ! 0.63 TIP3P oxygen M 1 1.00782503223 1.73 ! 0.63 dummy atom: TIP4P etc. L 1 1.00782503223 0.00 ! 0.00 dummy atom: link atom etc. X 1 1.00782503223 0.00 ! 0.00 dummy atom: rotor etc. e 0 0.00054857989 0.00 ! 0.00 electron E 0 3.5977449e+51 0.00 ! 0.00 planet earth c======================================================================= c setup_afed.f c======================================================================= c----------------------------------------------------------------------- c /* afed_type = GRAD: free energy gradient */ c /* = TEST: convergence test */ c /* = DESCENT: descent trajectory */ c /* = ASCENT: ascent trajectory */ c /* = AUTO: automated search */ c /* = TAMD: temperature accelerated MD */ c /* = LOGMFD: logarithmatic mean force dynamics */ c----------------------------------------------------------------------- GRAD c----------------------------------------------------------------------- c /* algo_ascent_afed = GAD: gentlest ascent */ c /* = EVF: eigenvector following */ c----------------------------------------------------------------------- GAD c----------------------------------------------------------------------- c /* maximum number of AFED iterations (AFED steps) */ c----------------------------------------------------------------------- 200 c----------------------------------------------------------------------- c /* number of steps in preliminary MD runs */ c----------------------------------------------------------------------- 1000 c----------------------------------------------------------------------- c /* number of steps in productive MD runs */ c----------------------------------------------------------------------- 2000 c----------------------------------------------------------------------- c /* maximum step size in ascent trajectories */ c----------------------------------------------------------------------- 1.d0 c----------------------------------------------------------------------- c /* maximum step size in descent trajectories */ c----------------------------------------------------------------------- 0.5d0 c----------------------------------------------------------------------- c /* converged step size in ascent and descent trajectories */ c----------------------------------------------------------------------- 0.05d0 c----------------------------------------------------------------------- c /* damping factor of step size when converging */ c----------------------------------------------------------------------- 0.7d0 c----------------------------------------------------------------------- c /* parameter gamma in ascent trajectory */ c----------------------------------------------------------------------- 0.0025d0 c----------------------------------------------------------------------- c /* interval of explicit hessian computation in gad */ c----------------------------------------------------------------------- 20 c----------------------------------------------------------------------- c /* iterations switching from gad to evf */ c----------------------------------------------------------------------- 80 c----------------------------------------------------------------------- c /* maximum free energy */ c----------------------------------------------------------------------- 0.16d0 c----------------------------------------------------------------------- c /* radius of landmark in automated search */ c----------------------------------------------------------------------- 2.5d0 c----------------------------------------------------------------------- c /* maximum number of shots from minimum in automated search */ c----------------------------------------------------------------------- 20 c----------------------------------------------------------------------- c /* maximum number of consecutive misses in automated search */ c----------------------------------------------------------------------- 10 c----------------------------------------------------------------------- c /* parameter set of each cv used in AFED */ c----------------------------------------------------------------------- DIST 0.08d0 2.0d0 10.0d0 ANGL 3.00d0 0.0d0 180.0d0 DIH 5.00d0 -180.0d0 180.0d0 DIFF 0.08d0 -4.0d0 4.0d0 CN 0.04d0 0.0d0 4.0d0 DCN 0.04d0 -2.0d0 2.0d0 XYZ 0.08d0 2.0d0 10.0d0 DXYZ 0.08d0 2.0d0 10.0d0 c----------------------------------------------------------------------- c /* bead sampling for ascent: analytical or numerical */ c----------------------------------------------------------------------- NUMERICAL c----------------------------------------------------------------------- c /* finite difference parameter for numerical hessian */ c----------------------------------------------------------------------- 5.d0 c----------------------------------------------------------------------- c /* print interval in convergence test */ c----------------------------------------------------------------------- 100 c----------------------------------------------------------------------- c /* print interval of snapshots in xyz format */ c----------------------------------------------------------------------- 1 c----------------------------------------------------------------------- c /* tamd type */ c----------------------------------------------------------------------- NVT c----------------------------------------------------------------------- c /* step size in tamd */ c----------------------------------------------------------------------- 1.d0 c----------------------------------------------------------------------- c /* temperature in tamd */ c----------------------------------------------------------------------- 3000.d0 c----------------------------------------------------------------------- c /* initial free energy in tamd */ c----------------------------------------------------------------------- 0.d0 c----------------------------------------------------------------------- c /* logmfd type */ c----------------------------------------------------------------------- NVE c----------------------------------------------------------------------- c /* step size in logmfd */ c----------------------------------------------------------------------- 1.d0 c----------------------------------------------------------------------- c /* alpha in logmfd */ c----------------------------------------------------------------------- 4.d0 c----------------------------------------------------------------------- c /* gamma in logmfd */ c----------------------------------------------------------------------- -1.d0 c----------------------------------------------------------------------- c /* initial free energy in logmfd */ c----------------------------------------------------------------------- 0.005d0 c----------------------------------------------------------------------- c /* parameter for thermostat mass in nvt-tamd and logmfd */ c----------------------------------------------------------------------- 100 c----------------------------------------------------------------------- c /* parameter for eigenvalue calculations */ c----------------------------------------------------------------------- 1 c----------------------------------------------------------------------- c /* molecular dynamics cycle for productive runs */ c----------------------------------------------------------------------- NVE c----------------------------------------------------------------------- c /* initial cv position and velocity */ c----------------------------------------------------------------------- AUTOMATIC c----------------------------------------------------------------------- c /* initial cv position and velocity in logmfd */ c----------------------------------------------------------------------- MANUAL 0.0 0.0 c----------------------------------------------------------------------- c /* initial mass position and velocity in logmfd */ c----------------------------------------------------------------------- AUTOMATIC c----------------------------------------------------------------------- c /* 1: average, or 2: weighted average in logmfd and tamd */ c----------------------------------------------------------------------- 1 c======================================================================= c force_user.f c======================================================================= c----------------------------------------------------------------------- c /* execution command */ c----------------------------------------------------------------------- not_available c----------------------------------------------------------------------- c /* input file (atomic positions) */ c----------------------------------------------------------------------- not_available c----------------------------------------------------------------------- c /* output file (potential, forces, virial) */ c----------------------------------------------------------------------- not_available c======================================================================= c gadcycle.f c======================================================================= c----------------------------------------------------------------------- c /* GAD gamma value in atomic unit */ c----------------------------------------------------------------------- 0.1d0 c----------------------------------------------------------------------- c /* GAD maximum energy value in hartree */ c----------------------------------------------------------------------- 1.0e+100 c----------------------------------------------------------------------- c /* print interval of potential energy */ c----------------------------------------------------------------------- 1 c======================================================================= c scancycle.F c======================================================================= c----------------------------------------------------------------------- c /* file name of post process: name.001.sh, ... */ c----------------------------------------------------------------------- " " c======================================================================= c setup_multi.f c======================================================================= c----------------------------------------------------------------------- c /* inner cycles for multiple time scale method */ c----------------------------------------------------------------------- 100 c======================================================================= c init_molcomp.f c======================================================================= c----------------------------------------------------------------------- c /* number of molecular components */ c----------------------------------------------------------------------- 0 c----------------------------------------------------------------------- c /* number of molecules */ c----------------------------------------------------------------------- 0 c======================================================================= c setup_tass.f c======================================================================= c----------------------------------------------------------------------- c /* parameter set of each cv used in TASS */ c----------------------------------------------------------------------- 100 c----------------------------------------------------------------------- c /* print interval: free energy reconstruction */ c----------------------------------------------------------------------- 100 c----------------------------------------------------------------------- c /* print interval: energy components */ c----------------------------------------------------------------------- 1 c----------------------------------------------------------------------- c /* print interval: cv trajectory */ c----------------------------------------------------------------------- 1 c----------------------------------------------------------------------- c /* tamd temperature in tass (= temperature if negative) */ c----------------------------------------------------------------------- -1.d0 c----------------------------------------------------------------------- c /* cv dimension of reconstruction (= ntass if negative) */ c----------------------------------------------------------------------- -1 c======================================================================= c setup_polymers.f c======================================================================= c----------------------------------------------------------------------- c /* */ c /* Number of polymer images */ c /* */ c----------------------------------------------------------------------- 16 c----------------------------------------------------------------------- c /* */ c /* Parallelization number for polymers */ c /* */ c----------------------------------------------------------------------- 1 c----------------------------------------------------------------------- c /* */ c /* The step size for polymer moves */ c /* */ c----------------------------------------------------------------------- 0.d0 c----------------------------------------------------------------------- c /* */ c /* End polymers */ c /* */ c /* ends_poly = FIXED: both ends are fixed. */ c /* ends_poly = FREE: both ends are free to move. */ c /* */ c----------------------------------------------------------------------- FIXED c----------------------------------------------------------------------- c /* */ c /* Print interval of mean forces */ c /* */ c----------------------------------------------------------------------- 10 c----------------------------------------------------------------------- c /* */ c /* Number of cycles for polymer moves */ c /* */ c----------------------------------------------------------------------- 1 c----------------------------------------------------------------------- c /* */ c /* Guess of polymers */ c /* */ c /* guess_poly = LINE: linear interpolation. */ c /* guess_poly = SPLINE: spline interpolation. */ c /* */ c----------------------------------------------------------------------- LINE c----------------------------------------------------------------------- c /* */ c /* Projection of mean forces */ c /* */ c /* projcmf_poly = OFF: apply. */ c /* projcmf_poly = ON: do not apply. */ c /* */ c----------------------------------------------------------------------- OFF c----------------------------------------------------------------------- c /* */ c /* Number of grids for interpolation */ c /* */ c----------------------------------------------------------------------- 10 c======================================================================= c force_aenet.f c======================================================================= c----------------------------------------------------------------------- c /* */ c /* Atomic types for AENET */ c /* */ c----------------------------------------------------------------------- 0 c----------------------------------------------------------------------- c /* */ c /* Generate input for AENET */ c /* */ c----------------------------------------------------------------------- not available c----------------------------------------------------------------------- c /* */ c /* Train input for AENET */ c /* */ c----------------------------------------------------------------------- not available c----------------------------------------------------------------------- c /* */ c /* xsf print interval for AENET */ c /* */ c----------------------------------------------------------------------- -1 c----------------------------------------------------------------------- c /* */ c /* generate/train step interval for AENET */ c /* */ c----------------------------------------------------------------------- -1 c----------------------------------------------------------------------- c /* */ c /* save step interval for the trained AENET potentials */ c /* */ c----------------------------------------------------------------------- -1 c----------------------------------------------------------------------- c /* */ c /* last generate/train step for AENET */ c /* */ c----------------------------------------------------------------------- 99999999 c----------------------------------------------------------------------- c /* */ c /* minimum number of xsf files to train AENET */ c /* */ c----------------------------------------------------------------------- 300 c----------------------------------------------------------------------- c /* */ c /* option of xsf files - 0: accepted, 1: accepted+rejected */ c /* */ c----------------------------------------------------------------------- 1 c----------------------------------------------------------------------- c /* */ c /* scratch directory of trained networks for AENET */ c /* */ c----------------------------------------------------------------------- "trained_networks" c----------------------------------------------------------------------- c /* */ c /* directory of the periodically saved trained AENET networks */ c /* */ c----------------------------------------------------------------------- "saved_networks" c----------------------------------------------------------------------- c /* */ c /* delay time for hard disk access of AENET */ c /* */ c----------------------------------------------------------------------- "0.25" c======================================================================= c print_minfo.f c======================================================================= c----------------------------------------------------------------------- c /* */ c /* Should we output minfo files with ES information */ c /* Only used in SCAN, STATIC and NMA methods */ c /* */ c /* iprint_minfo = -1 : Do not print */ c /* iprint_minfo != -1 : Print Minfor files */ c /* */ c----------------------------------------------------------------------- -1 c======================================================================= c force_qe.f c======================================================================= c----------------------------------------------------------------------- c /* QE command */ c----------------------------------------------------------------------- 'qe.x' c----------------------------------------------------------------------- c /* frequency of quantum espresso output */ c----------------------------------------------------------------------- 0 1 c----------------------------------------------------------------------- c /* filename of quantum espresso output */ c----------------------------------------------------------------------- qe.dat c======================================================================= c adjust_fictmass_hmc.f, adjust_physmass_rehmc.f c======================================================================= c----------------------------------------------------------------------- c /* number of atoms picked in a trial move (-1: all atoms) */ c----------------------------------------------------------------------- -1 c======================================================================= c judge_ax_hmc.f, judge_ax_rehmc.f c======================================================================= c----------------------------------------------------------------------- c /* step interval of atomic exchange (-1: no exchange) */ c----------------------------------------------------------------------- -1 c----------------------------------------------------------------------- c /* number of kinds for atomic exchange */ c----------------------------------------------------------------------- 0 c======================================================================= c predict_aenet_MPI.f c======================================================================= c----------------------------------------------------------------------- c /* neighbor list skin parameter for aenet (angstrom) */ c----------------------------------------------------------------------- 2.0 c----------------------------------------------------------------------- c /* print interval of heat flux trajectory for aenet */ c----------------------------------------------------------------------- -1