include/types/inputrec.h

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  35 #ifndef _inputrec_h_
  36 #define _inputrec_h_
  37
  38
  39 #include "simple.h"
  40 #include "../sysstuff.h"
  41
  42 #ifdef __cplusplus
  43 extern "C" {
  44 #endif
  45
  46
  47 typedef struct {
  48   int  n;               /* Number of terms                              */
  49   real *a;              /* Coeffients (V / nm )                         */
  50   real *phi;            /* Phase angles                                 */
  51 } t_cosines;
  52
  53 typedef struct {
  54   real E0;              /* Field strength (V/nm)                        */
  55   real omega;           /* Frequency (1/ps)                             */
  56   real t0;              /* Centre of the Gaussian pulse (ps)            */
  57   real sigma;           /* Width of the Gaussian pulse (FWHM) (ps)      */
  58 } t_efield;
  59
  60 #define EGP_EXCL  (1<<0)
  61 #define EGP_TABLE (1<<1)
  62
  63 typedef struct {
  64   int     ngtc;                  /* # T-Coupl groups                        */
  65   int     nhchainlength;         /* # of nose-hoover chains per group       */
  66   int     ngacc;                 /* # Accelerate groups                     */
  67   int     ngfrz;                 /* # Freeze groups                         */
  68   int     ngener;                /* # Ener groups                           */
  69   real    *nrdf;                 /* Nr of degrees of freedom in a group     */
  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   gmx_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   gmx_bool    *bOPT;
  94   gmx_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   gmx_bool       bRefAt;      /* do we need reference atoms for a group COM ? */
 136   int        cosdim;      /* dimension for cosine weighting, -1 if none */
 137   gmx_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     *grpcnt;    /* Number of home atoms in each freeze group */
 150     real    *mass;  /* Total mass of the home atoms of each freeze group */
 151     rvec    *force; /* Total force on the home atoms of each freeze group for the last stepcnt steps */
 152     rvec    *vel;   /* Velocity of each freeze group, calculated using the force summed over all threads */
 153     double  *dbuf;  /* Buffer for summing over all threads */
 154     int     stepcnt;    /* Number of steps since the last summation and update */
 155 } t_rigid;
 156
 157 typedef struct {
 158   int  eI;              /* Integration method                           */
 159   gmx_large_int_t nsteps;       /* number of steps to be taken                  */
 160   int  simulation_part; /* Used in checkpointing to separate chunks */
 161   gmx_large_int_t init_step;    /* start at a stepcount >0 (used w. tpbconv)    */
 162   int  nstcalcenergy;   /* fequency of energy calc. and T/P coupl. upd. */
 163   int  ns_type;         /* which ns method should we use?               */
 164   int  nstlist;         /* number of steps before pairlist is generated */
 165   int  ndelta;          /* number of cells per rlong                    */
 166   int  nstcomm;         /* number of steps after which center of mass   */
 167                         /* motion is removed                            */
 168   int  comm_mode;       /* Center of mass motion removal algorithm      */
 169   int nstcheckpoint;    /* checkpointing frequency                      */
 170   int nstlog;           /* number of steps after which print to logfile */
 171   int nstxout;          /* number of steps after which X is output      */
 172   int nstvout;          /* id. for V                                    */
 173   int nstfout;          /* id. for F                                    */
 174   int nstenergy;        /* number of steps after which energies printed */
 175   int nstxtcout;        /* id. for compressed trj (.xtc)                */
 176   double init_t;        /* initial time (ps)                            */
 177   double delta_t;       /* time step (ps)                               */
 178   real xtcprec;         /* precision of xtc file                        */
 179   int  nkx,nky,nkz;     /* number of k vectors in each spatial dimension*/
 180                         /* for fourier methods for long range electrost.*/
 181   int  pme_order;       /* interpolation order for PME                  */
 182   real ewald_rtol;      /* Real space tolerance for Ewald, determines   */
 183                         /* the real/reciprocal space relative weight    */
 184   int  ewald_geometry;  /* normal/3d ewald, or pseudo-2d LR corrections */
 185   real epsilon_surface; /* Epsilon for PME dipole correction            */
 186   gmx_bool bOptFFT;         /* optimize the fft plan at start               */
 187   int  ePBC;            /* Type of periodic boundary conditions         */
 188   int  bPeriodicMols;   /* Periodic molecules                           */
 189   gmx_bool bContinuation;   /* Continuation run: starting state is correct      */
 190   int  etc;             /* temperature coupling                         */
 191   int  nsttcouple;      /* interval in steps for temperature coupling   */
 192   int  epc;             /* pressure coupling                            */
 193   int  epct;            /* pressure coupling type                       */
 194   int  nstpcouple;      /* interval in steps for pressure coupling      */
 195   real tau_p;           /* pressure coupling time (ps)                  */
 196   tensor ref_p;         /* reference pressure (kJ/(mol nm^3))           */
 197   tensor compress;      /* compressability ((mol nm^3)/kJ)              */
 198   int  refcoord_scaling;/* How to scale absolute reference coordinates  */
 199   rvec posres_com;      /* The COM of the posres atoms                  */
 200   rvec posres_comB;     /* The B-state COM of the posres atoms          */
 201   int  andersen_seed;   /* Random seed for Andersen thermostat.         */
 202   real rlist;           /* short range pairlist cut-off (nm)            */
 203   real rlistlong;       /* long range pairlist cut-off (nm)             */
 204   real rtpi;            /* Radius for test particle insertion           */
 205   int  coulombtype;     /* Type of electrostatics treatment             */
 206   real rcoulomb_switch; /* Coulomb switch range start (nm)              */
 207   real rcoulomb;        /* Coulomb cutoff (nm)                          */
 208   real epsilon_r;       /* relative dielectric constant                 */
 209   real epsilon_rf;      /* relative dielectric constant of the RF       */
 210   int  implicit_solvent;/* No (=explicit water), or GBSA solvent models */
 211   int  gb_algorithm;    /* Algorithm to use for calculation Born radii  */
 212   int  nstgbradii;      /* Frequency of updating Generalized Born radii */
 213   real rgbradii;        /* Cutoff for GB radii calculation              */
 214   real gb_saltconc;     /* Salt concentration (M) for GBSA models       */
 215   real gb_epsilon_solvent; /* dielectric coeff. of implicit solvent     */
 216   real gb_obc_alpha;    /* 1st scaling factor for Bashford-Case GB      */
 217   real gb_obc_beta;     /* 2nd scaling factor for Bashford-Case GB      */
 218   real gb_obc_gamma;    /* 3rd scaling factor for Bashford-Case GB      */
 219   real gb_dielectric_offset; /* Dielectric offset for Still/HCT/OBC     */
 220   int  sa_algorithm;    /* Algorithm for SA part of GBSA                */
 221   real sa_surface_tension; /* Energy factor for SA part of GBSA */
 222   int  vdwtype;         /* Type of Van der Waals treatment              */
 223   real rvdw_switch;     /* Van der Waals switch range start (nm)        */
 224   real rvdw;                /* Van der Waals cutoff (nm)                */
 225   int  eDispCorr;       /* Perform Long range dispersion corrections    */
 226   real tabext;          /* Extension of the table beyond the cut-off,   *
 227                          * as well as the table length for 1-4 interac. */
 228   real shake_tol;       /* tolerance for shake                          */
 229   int  efep;            /* free energy interpolation no/yes             */
 230   double init_lambda;   /* initial value for perturbation variable      */
 231   double delta_lambda;  /* change of lambda per time step (1/dt)        */
 232   int  n_flambda;       /* The number of foreign lambda points          */
 233   double *flambda;      /* The foreign lambda values                    */
 234   real sc_alpha;        /* free energy soft-core parameter              */
 235   int  sc_power;        /* lambda power for soft-core interactions      */
 236   real sc_sigma;        /* free energy soft-core sigma when c6 or c12=0 */
 237   real sc_sigma_min;    /* minimum FE sc sigma (default: =sg_sigma)     */
 238   int  nstdhdl;         /* The frequency for writing to dhdl.xvg        */
 239   int  separate_dhdl_file; /* whether to write a separate dhdl.xvg file
 240                               note: NOT a gmx_bool, but an enum */
 241   int  dhdl_derivatives;/* whether to calculate+write dhdl derivatives
 242                               note: NOT a gmx_bool, but an enum */
 243   int  dh_hist_size;    /* The maximum size for the dH histogram        */
 244   double dh_hist_spacing; /* The spacing for the dH histogram           */
 245   int  eDisre;          /* Type of distance restraining                 */
 246   real dr_fc;               /* force constant for ta_disre                      */
 247   int  eDisreWeighting; /* type of weighting of pairs in one restraints */
 248   gmx_bool bDisreMixed;     /* Use comb of time averaged and instan. viol's     */
 249   int  nstdisreout;     /* frequency of writing pair distances to enx   */
 250   real dr_tau;              /* time constant for memory function in disres      */
 251   real orires_fc;           /* force constant for orientational restraints  */
 252   real orires_tau;          /* time constant for memory function in orires      */
 253   int  nstorireout;     /* frequency of writing tr(SD) to enx           */
 254   real dihre_fc;        /* force constant for dihedral restraints       */
 255   real em_stepsize;         /* The stepsize for updating                        */
 256   real em_tol;              /* The tolerance                            */
 257   int  niter;           /* Number of iterations for convergence of      */
 258                         /* steepest descent in relax_shells             */
 259   real fc_stepsize;     /* Stepsize for directional minimization        */
 260                         /* in relax_shells                              */
 261   int  nstcgsteep;      /* number of steps after which a steepest       */
 262                         /* descents step is done while doing cg         */
 263   int  nbfgscorr;       /* Number of corrections to the hessian to keep */
 264   int  eConstrAlg;      /* Type of constraint algorithm                 */
 265   int  nProjOrder;      /* Order of the LINCS Projection Algorithm      */
 266   real LincsWarnAngle;  /* If bond rotates more than %g degrees, warn   */
 267   int  nLincsIter;      /* Number of iterations in the final Lincs step */
 268   gmx_bool bShakeSOR;       /* Use successive overrelaxation for shake      */
 269   real bd_fric;         /* Friction coefficient for BD (amu/ps)         */
 270   int  ld_seed;         /* Random seed for SD and BD                    */
 271   int  nwall;           /* The number of walls                          */
 272   int  wall_type;       /* The type of walls                            */
 273   real wall_r_linpot;   /* The potentail is linear for r<=wall_r_linpot */
 274   int  wall_atomtype[2];/* The atom type for walls                      */
 275   real wall_density[2]; /* Number density for walls                     */
 276   real wall_ewald_zfac; /* Scaling factor for the box for Ewald         */
 277   int  ePull;           /* Type of pulling: no, umbrella or constraint  */
 278   t_pull *pull;         /* The data for center of mass pulling          */
 279   t_rigid *rigid;       /* The data for rigid body motion               */
 280   real cos_accel;       /* Acceleration for viscosity calculation       */
 281   tensor deform;        /* Triclinic deformation velocities (nm/ps)     */
 282   int  userint1;        /* User determined parameters                   */
 283   int  userint2;
 284   int  userint3;
 285   int  userint4;
 286   real userreal1;
 287   real userreal2;
 288   real userreal3;
 289   real userreal4;
 290   t_grpopts opts;       /* Group options                                */
 291   t_cosines ex[DIM];    /* Electric field stuff (spatial part)          */
 292   t_cosines et[DIM];    /* Electric field stuff (time part)             */
 293   gmx_bool bQMMM;           /* QM/MM calculation                            */
 294   int  QMconstraints;   /* constraints on QM bonds                      */
 295   int  QMMMscheme;      /* Scheme: ONIOM or normal                      */
 296   real scalefactor;     /* factor for scaling the MM charges in QM calc.*/
 297 } t_inputrec;
 298
 299 #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)
 300
 301 #define DYNAMIC_BOX(ir) ((ir).epc!=epcNO || (ir).eI==eiTPI || DEFORM(ir))
 302
 303 #define PRESERVE_SHAPE(ir) ((ir).epc != epcNO && (ir).deform[XX][XX] == 0 && ((ir).epct == epctISOTROPIC || (ir).epct == epctSEMIISOTROPIC))
 304
 305 #define NEED_MUTOT(ir) (((ir).coulombtype==eelEWALD || EEL_PME((ir).coulombtype)) && ((ir).ewald_geometry==eewg3DC || (ir).epsilon_surface!=0))
 306
 307 #define IR_TWINRANGE(ir) ((ir).rlist > 0 && ((ir).rlistlong == 0 || (ir).rlistlong > (ir).rlist))
 308
 309 #define IR_ELEC_FIELD(ir) ((ir).ex[XX].n > 0 || (ir).ex[YY].n > 0 || (ir).ex[ZZ].n > 0)
 310
 311 #define IR_EXCL_FORCES(ir) (EEL_FULL((ir).coulombtype) || (EEL_RF((ir).coulombtype) && (ir).coulombtype != eelRF_NEC) || (ir).implicit_solvent != eisNO)
 312 /* use pointer definitions of ir here, since that's what's usually used in the code */
 313 #define IR_NVT_TROTTER(ir) ((((ir)->eI == eiVV) || ((ir)->eI == eiVVAK)) && ((ir)->etc == etcNOSEHOOVER))
 314
 315 #define IR_NPT_TROTTER(ir) ((((ir)->eI == eiVV) || ((ir)->eI == eiVVAK)) && ((ir)->epc == epcMTTK))
 316
 317 #ifdef __cplusplus
 318 }
 319 #endif
 320
 321
 322 #endif