include/types/inputrec.h

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  35 #ifndef _inputrec_h_
  36 #define _inputrec_h_
  37
  38
  39 #ifdef HAVE_CONFIG_H
  40 #include <config.h>
  41 #endif
  42
  43
  44 #include "types/simple.h"
  45
  46 typedef struct {
  47   int  n;               /* Number of terms                              */
  48   real *a;              /* Coeffients (V / nm )                         */
  49   real *phi;            /* Phase angles                                 */
  50 } t_cosines;
  51
  52 typedef struct {
  53   real E0;              /* Field strength (V/nm)                        */
  54   real omega;           /* Frequency (1/ps)                             */
  55   real t0;              /* Centre of the Gaussian pulse (ps)            */
  56   real sigma;           /* Width of the Gaussian pulse (FWHM) (ps)      */
  57 } t_efield;
  58
  59 #define EGP_EXCL  (1<<0)
  60 #define EGP_TABLE (1<<1)
  61
  62 typedef struct {
  63   int     ngtc;                  /* # T-Coupl groups                        */
  64   int     nhchain_num;           /* # of nose-hoover chains per group       */
  65   int     ngacc;                 /* # Accelerate groups                     */
  66   int     ngfrz;                 /* # Freeze groups                         */
  67   int     ngener;                /* # Ener groups                           */
  68   real    *nrdf;                 /* Nr of degrees of freedom in a group     */
  69   double  *vscale_nhc;           /* scaling term for velocities in NHC      */
  70   real    *ref_t;                /* Coupling temperature        per group   */
  71   int     *annealing;            /* No/simple/periodic SA for each group    */
  72   int     *anneal_npoints;       /* Number of annealing time points per grp */
  73   real    **anneal_time;         /* For ea. group: Time points              */
  74   real    **anneal_temp;         /* For ea. grp: Temperature at these times */
  75                                  /* Final temp after all intervals is ref_t */
  76   real    *tau_t;                /* Tau coupling time                       */
  77   rvec    *acc;                  /* Acceleration per group                  */
  78   ivec    *nFreeze;              /* Freeze the group in each direction ?    */
  79   int     *egp_flags;            /* Exclusions/tables of energy group pairs */
  80
  81   /* QMMM stuff */
  82   int     ngQM;         /* nr of QM groups                              */
  83   int     *QMmethod;    /* Level of theory in the QM calculation        */
  84   int     *QMbasis;     /* Basisset in the QM calculation               */
  85   int     *QMcharge;    /* Total charge in the QM region                */
  86   int     *QMmult;      /* Spin multiplicicty in the QM region          */
  87   bool    *bSH;         /* surface hopping (diabatic hop only)          */
  88   int     *CASorbitals; /* number of orbiatls in the active space       */
  89   int     *CASelectrons;/* number of electrons in the active space      */
  90   real    *SAon;        /* at which gap (A.U.) the SA is switched on    */
  91   real    *SAoff;
  92   int     *SAsteps;     /* in how many steps SA goes from 1-1 to 0.5-0.5*/
  93   bool    *bOPT;
  94   bool    *bTS;
  95 } t_grpopts;
  96
  97 enum { epgrppbcNONE, epgrppbcREFAT, epgrppbcCOS };
  98
  99 typedef struct {
 100   int        nat;      /* Number of atoms in the pull group */
 101   atom_id    *ind;     /* The global atoms numbers */
 102   int        nat_loc;  /* Number of local pull atoms */
 103   int        nalloc_loc; /* Allocation size for ind_loc and weight_loc */
 104   atom_id    *ind_loc; /* Local pull indices */
 105   int        nweight;  /* The number of weights (0 or nat) */
 106   real       *weight;  /* Weights (use all 1 when weight==NULL) */
 107   real       *weight_loc; /* Weights for the local indices */
 108   int        epgrppbc; /* The type of pbc for this pull group, see enum above */
 109   atom_id    pbcatom;  /* The reference atom for pbc (global number) */
 110   rvec       vec;      /* The pull vector, direction or position */
 111   rvec       init;     /* Initial reference displacement */
 112   real       rate;     /* Rate of motion (nm/ps) */
 113   real       k;        /* force constant */
 114   real       kB;       /* force constant for state B */
 115   real       wscale;   /* scaling factor for the weights: sum w m/sum w w m */
 116   real       invtm;    /* inverse total mass of the group: 1/wscale sum w m */
 117   dvec       x;        /* center of mass before update */
 118   dvec       xp;       /* center of mass after update before constraining */
 119   dvec       dr;       /* The distance from the reference group */
 120   double     f_scal;   /* Scalar force for directional pulling */
 121   dvec       f;        /* force due to the pulling/constraining */
 122 } t_pullgrp;
 123
 124 typedef struct {
 125   int        ngrp;        /* number of groups */
 126   int        eGeom;       /* pull geometry */
 127   ivec       dim;         /* used to select components for constraint */
 128   real       cyl_r1;      /* radius of cylinder for dynamic COM */
 129   real       cyl_r0;      /* radius of cylinder including switch length */
 130   real       constr_tol;  /* absolute tolerance for constraints in (nm) */
 131   int        nstxout;     /* Output frequency for pull x */
 132   int        nstfout;     /* Output frequency for pull f */
 133   int        ePBC;        /* the boundary conditions */
 134   int        npbcdim;     /* do pbc in dims 0 <= dim < npbcdim */
 135   bool       bRefAt;      /* do we need reference atoms for a group COM ? */
 136   int        cosdim;      /* dimension for cosine weighting, -1 if none */
 137   bool       bVirial;     /* do we need to add the pull virial? */
 138   t_pullgrp  *grp;        /* groups to pull/restrain/etc/ */
 139   t_pullgrp  *dyna;       /* dynamic groups for use with local constraints */
 140   rvec       *rbuf;       /* COM calculation buffer */
 141   dvec       *dbuf;       /* COM calculation buffer */
 142   double     *dbuf_cyl;   /* cylinder ref. groups COM calculation buffer */
 143
 144   FILE       *out_x;      /* output file for pull data */
 145   FILE       *out_f;      /* output file for pull data */
 146 } t_pull;
 147
 148 typedef struct {
 149   int  eI;              /* Integration method                           */
 150   gmx_large_int_t nsteps;       /* number of steps to be taken                  */
 151   int  simulation_part; /* Used in checkpointing to separate chunks */
 152   gmx_large_int_t init_step;    /* start at a stepcount >0 (used w. tpbconv)    */
 153   int  nstcalcenergy;   /* fequency of energy calc. and T/P coupl. upd. */
 154   int  ns_type;         /* which ns method should we use?               */
 155   int  nstlist;         /* number of steps before pairlist is generated */
 156   int  ndelta;          /* number of cells per rlong                    */
 157   int  nstcomm;         /* number of steps after which center of mass   */
 158                         /* motion is removed                            */
 159   int  comm_mode;       /* Center of mass motion removal algorithm      */
 160   int nstcheckpoint;    /* checkpointing frequency                      */
 161   int nstlog;           /* number of steps after which print to logfile */
 162   int nstxout;          /* number of steps after which X is output      */
 163   int nstvout;          /* id. for V                                    */
 164   int nstfout;          /* id. for F                                    */
 165   int nstenergy;        /* number of steps after which energies printed */
 166   int nstxtcout;        /* id. for compressed trj (.xtc)                */
 167   double init_t;        /* initial time (ps)                            */
 168   double delta_t;       /* time step (ps)                               */
 169   real xtcprec;         /* precision of xtc file                        */
 170   int  nkx,nky,nkz;     /* number of k vectors in each spatial dimension*/
 171                         /* for fourier methods for long range electrost.*/
 172   int  pme_order;       /* interpolation order for PME                  */
 173   real ewald_rtol;      /* Real space tolerance for Ewald, determines   */
 174                         /* the real/reciprocal space relative weight    */
 175   int  ewald_geometry;  /* normal/3d ewald, or pseudo-2d LR corrections */
 176   real epsilon_surface; /* Epsilon for PME dipole correction            */
 177   bool bOptFFT;         /* optimize the fft plan at start               */
 178   int  ePBC;            /* Type of periodic boundary conditions         */
 179   int  bPeriodicMols;   /* Periodic molecules                           */
 180   bool bContinuation;   /* Continuation run: starting state is correct  */
 181   int  etc;             /* temperature coupling                         */
 182   int  epc;             /* pressure coupling                            */
 183   int  epct;            /* pressure coupling type                       */
 184   real tau_p;           /* pressure coupling time (ps)                  */
 185   tensor ref_p;         /* reference pressure (kJ/(mol nm^3))           */
 186   tensor compress;      /* compressability ((mol nm^3)/kJ)              */
 187   int  refcoord_scaling;/* How to scale absolute reference coordinates  */
 188   rvec posres_com;      /* The COM of the posres atoms                  */
 189   rvec posres_comB;     /* The B-state COM of the posres atoms          */
 190   int  andersen_seed;   /* Random seed for Andersen thermostat.         */
 191   real rlist;           /* short range pairlist cut-off (nm)            */
 192   real rlistlong;       /* long range pairlist cut-off (nm)             */
 193   real rtpi;            /* Radius for test particle insertion           */
 194   int  coulombtype;     /* Type of electrostatics treatment             */
 195   real rcoulomb_switch; /* Coulomb switch range start (nm)              */
 196   real rcoulomb;        /* Coulomb cutoff (nm)                          */
 197   real epsilon_r;       /* relative dielectric constant                 */
 198   real epsilon_rf;      /* relative dielectric constant of the RF       */
 199   int  implicit_solvent;/* No (=explicit water), or GBSA solvent models */
 200   int  gb_algorithm;    /* Algorithm to use for calculation Born radii  */
 201   int  nstgbradii;      /* Frequency of updating Generalized Born radii */
 202   real rgbradii;        /* Cutoff for GB radii calculation              */
 203   real gb_saltconc;     /* Salt concentration (M) for GBSA models       */
 204   real gb_epsilon_solvent; /* dielectric coeff. of implicit solvent     */
 205   real gb_obc_alpha;    /* 1st scaling factor for Bashford-Case GB      */
 206   real gb_obc_beta;     /* 2nd scaling factor for Bashford-Case GB      */
 207   real gb_obc_gamma;    /* 3rd scaling factor for Bashford-Case GB      */
 208   real gb_dielectric_offset; /* Dielectric offset for Still/HCT/OBC     */
 209   int  sa_algorithm;    /* Algorithm for SA part of GBSA                */
 210   real sa_surface_tension; /* Energy factor for SA part of GBSA */
 211   int  vdwtype;         /* Type of Van der Waals treatment              */
 212   real rvdw_switch;     /* Van der Waals switch range start (nm)        */
 213   real rvdw;                /* Van der Waals cutoff (nm)                */
 214   int  eDispCorr;       /* Perform Long range dispersion corrections    */
 215   real tabext;          /* Extension of the table beyond the cut-off,   *
 216                          * as well as the table length for 1-4 interac. */
 217   real shake_tol;       /* tolerance for shake                          */
 218   int  efep;            /* free energy interpolation no/yes             */
 219   double init_lambda;   /* initial value for perturbation variable      */
 220   double delta_lambda;  /* change of lambda per time step (1/dt)        */
 221   int  n_flambda;       /* The number of foreign lambda points          */
 222   double *flambda;      /* The foreign lambda values                    */
 223   real sc_alpha;        /* free energy soft-core parameter              */
 224   int  sc_power;        /* lambda power for soft-core interactions      */
 225   real sc_sigma;        /* free energy soft-core sigma when c6 or c12=0 */
 226   int  nstdhdl;         /* The frequency for calculating dhdl           */
 227   int  eDisre;          /* Type of distance restraining                 */
 228   real dr_fc;               /* force constant for ta_disre                      */
 229   int  eDisreWeighting; /* type of weighting of pairs in one restraints */
 230   bool bDisreMixed;     /* Use comb of time averaged and instan. viol's */
 231   int  nstdisreout;     /* frequency of writing pair distances to enx   */
 232   real dr_tau;              /* time constant for memory function in disres      */
 233   real orires_fc;           /* force constant for orientational restraints  */
 234   real orires_tau;          /* time constant for memory function in orires      */
 235   int  nstorireout;     /* frequency of writing tr(SD) to enx           */
 236   real dihre_fc;        /* force constant for dihedral restraints       */
 237   real em_stepsize;         /* The stepsize for updating                        */
 238   real em_tol;              /* The tolerance                            */
 239   int  niter;           /* Number of iterations for convergence of      */
 240                         /* steepest descent in relax_shells             */
 241   real fc_stepsize;     /* Stepsize for directional minimization        */
 242                         /* in relax_shells                              */
 243   int  nstcgsteep;      /* number of steps after which a steepest       */
 244                         /* descents step is done while doing cg         */
 245   int  nbfgscorr;       /* Number of corrections to the hessian to keep */
 246   int  eConstrAlg;      /* Type of constraint algorithm                 */
 247   int  nProjOrder;      /* Order of the LINCS Projection Algorithm      */
 248   real LincsWarnAngle;  /* If bond rotates more than %g degrees, warn   */
 249   int  nLincsIter;      /* Number of iterations in the final Lincs step */
 250   bool bShakeSOR;       /* Use successive overrelaxation for shake      */
 251   real bd_fric;         /* Friction coefficient for BD (amu/ps)         */
 252   int  ld_seed;         /* Random seed for SD and BD                    */
 253   int  nwall;           /* The number of walls                          */
 254   int  wall_type;       /* The type of walls                            */
 255   real wall_r_linpot;   /* The potentail is linear for r<=wall_r_linpot */
 256   int  wall_atomtype[2];/* The atom type for walls                      */
 257   real wall_density[2]; /* Number density for walls                     */
 258   real wall_ewald_zfac; /* Scaling factor for the box for Ewald         */
 259   int  ePull;           /* Type of pulling: no, umbrella or constraint  */
 260   t_pull *pull;         /* The data for center of mass pulling          */
 261   real cos_accel;       /* Acceleration for viscosity calculation       */
 262   tensor deform;        /* Triclinic deformation velocities (nm/ps)     */
 263   int  userint1;        /* User determined parameters                   */
 264   int  userint2;
 265   int  userint3;
 266   int  userint4;
 267   real userreal1;
 268   real userreal2;
 269   real userreal3;
 270   real userreal4;
 271   t_grpopts opts;       /* Group options                                */
 272   t_cosines ex[DIM];    /* Electric field stuff (spatial part)          */
 273   t_cosines et[DIM];    /* Electric field stuff (time part)             */
 274   bool bQMMM;           /* QM/MM calculation                            */
 275   int  QMconstraints;   /* constraints on QM bonds                      */
 276   int  QMMMscheme;      /* Scheme: ONIOM or normal                      */
 277   real scalefactor;     /* factor for scaling the MM charges in QM calc.*/
 278 } t_inputrec;
 279
 280 #define DEFORM(ir) ((ir).deform[XX][XX]!=0 || (ir).deform[YY][YY]!=0 || (ir).deform[ZZ][ZZ]!=0 || (ir).deform[YY][XX]!=0 || (ir).deform[ZZ][XX]!=0 || (ir).deform[ZZ][YY]!=0)
 281
 282 #define DYNAMIC_BOX(ir) ((ir).epc!=epcNO || (ir).eI==eiTPI || DEFORM(ir))
 283
 284 #define PRESERVE_SHAPE(ir) ((ir).epc != epcNO && (ir).deform[XX][XX] == 0 && ((ir).epct == epctISOTROPIC || (ir).epct == epctSEMIISOTROPIC))
 285
 286 #define NEED_MUTOT(ir) (((ir).coulombtype==eelEWALD || EEL_PME((ir).coulombtype)) && ((ir).ewald_geometry==eewg3DC || (ir).epsilon_surface!=0))
 287
 288 #define IR_TWINRANGE(ir) ((ir).rlist > 0 && ((ir).rlistlong == 0 || (ir).rlistlong > (ir).rlist))
 289
 290 #define IR_ELEC_FIELD(ir) ((ir).ex[XX].n > 0 || (ir).ex[YY].n > 0 || (ir).ex[ZZ].n > 0)
 291
 292 #define IR_EXCL_FORCES(ir) (EEL_FULL((ir).coulombtype) || (EEL_RF((ir).coulombtype) && (ir).coulombtype != eelRF_NEC) || (ir).implicit_solvent != eisNO)
 293 /* use pointer definitions of ir here, since that's what's usually used in the code */
 294 #define IR_NVT_TROTTER(ir) (((ir)->eI == eiVV) && ((ir)->etc == etcNOSEHOOVER))
 295
 296 #define IR_NPT_TROTTER(ir) (((ir)->eI == eiVV) && ((ir)->epc == epcMTTK))
 297
 298 #endif