include/constr.h

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  36
  37 #ifndef _constr_h
  38 #define _constr_h
  39 #include "typedefs.h"
  40 #include "types/commrec.h"
  41
  42 #ifdef __cplusplus
  43 extern "C" {
  44 #endif
  45
  46 enum
  47 {
  48     econqCoord,         /* Constrain coordinates (mass weighted)           */
  49     econqVeloc,         /* Constrain velocities (mass weighted)            */
  50     econqDeriv,         /* Constrain a derivative (mass weighted),         *
  51                          * for instance velocity or acceleration,          *
  52                          * constraint virial can not be calculated.        */
  53     econqDeriv_FlexCon, /* As econqDeriv, but only output flex. con.       */
  54     econqForce,         /* Constrain forces (non mass-weighted)            */
  55     econqForceDispl     /* Constrain forces (mass-weighted 1/0 for freeze) */
  56 };
  57
  58 int n_flexible_constraints(struct gmx_constr *constr);
  59 /* Returns the total number of flexible constraints in the system */
  60
  61 void too_many_constraint_warnings(int eConstrAlg,int warncount);
  62 /* Generate a fatal error because of too many LINCS/SETTLE warnings */
  63
  64 gmx_shakedata_t shake_init();
  65 /* Initializes and return the SHAKE data structure */
  66
  67 gmx_bool bshakef(FILE *log,             /* Log file                     */
  68                     gmx_shakedata_t shaked, /* SHAKE data */
  69                     int natoms,         /* Total number of atoms        */
  70                     real invmass[],     /* Atomic masses                */
  71                     int nblocks,        /* The number of shake blocks   */
  72                     int sblock[],       /* The shake blocks             */
  73                     t_idef *idef,       /* The interaction def          */
  74                     t_inputrec *ir,     /* Input record                 */
  75                     rvec x_s[],         /* Coords before update         */
  76                     rvec prime[],               /* Output coords                */
  77                     t_nrnb *nrnb,       /* Performance measure          */
  78                     real *lagr,         /* The Lagrange multipliers     */
  79                     real lambda,        /* FEP lambda                   */
  80                     real *dvdlambda,    /* FEP force                    */
  81                     real invdt,         /* 1/delta_t                    */
  82                     rvec *v,            /* Also constrain v if v!=NULL  */
  83                     gmx_bool bCalcVir,      /* Calculate r x m delta_r      */
  84                     tensor rmdr,        /* sum r x m delta_r            */
  85                     gmx_bool bDumpOnError,  /* Dump debugging stuff on error*/
  86                     int econq,         /* which type of constrainint is occurring */
  87                     t_vetavars *vetavar);           /* veta for pressure control */
  88 /* Shake all the atoms blockwise. It is assumed that all the constraints
  89  * in the idef->shakes field are sorted, to ascending block nr. The
  90  * sblock array points into the idef->shakes.iatoms field, with block 0
  91  * starting
  92  * at sblock[0] and running to ( < ) sblock[1], block n running from
  93  * sblock[n] to sblock[n+1]. Array sblock should be large enough.
  94  * Return TRUE when OK, FALSE when shake-error
  95  */
  96
  97 gmx_settledata_t settle_init(real mO,real mH,real invmO,real invmH,
  98                                     real dOH,real dHH);
  99 /* Initializes and returns a structure with SETTLE parameters */
 100
 101 void csettle(gmx_settledata_t settled,
 102              int nsettle,       /* Number of settles            */
 103              t_iatom iatoms[],  /* The settle iatom list        */
 104              const t_pbc *pbc,   /* PBC data pointer, can be NULL  */
 105              real b4[],         /* Old coordinates              */
 106              real after[],      /* New coords, to be settled    */
 107              real invdt,         /* 1/delta_t                    */
 108              real *v,            /* Also constrain v if v!=NULL  */
 109              int calcvir_atom_end, /* Calculate r x m delta_r up to this atom */
 110              tensor rmdr,        /* sum r x m delta_r            */
 111              int *xerror,
 112              t_vetavars *vetavar     /* variables for pressure control */
 113     );
 114
 115 void settle_proj(FILE *fp,
 116                  gmx_settledata_t settled,int econq,
 117                  int nsettle, t_iatom iatoms[],
 118                  const t_pbc *pbc,   /* PBC data pointer, can be NULL  */
 119                  rvec x[],
 120                  rvec *der,rvec *derp,
 121                  int CalcVirAtomEnd,tensor rmdder, t_vetavars *vetavar);
 122 /* Analytical algorithm to subtract the components of derivatives
 123  * of coordinates working on settle type constraint.
 124  */
 125
 126 void cshake(atom_id iatom[],int ncon,int *nnit,int maxnit,
 127                    real dist2[],real xp[],real rij[],real m2[],real omega,
 128                    real invmass[],real tt[],real lagr[],int *nerror);
 129 /* Regular iterative shake */
 130
 131 void crattle(atom_id iatom[],int ncon,int *nnit,int maxnit,
 132                     real dist2[],real vp[],real rij[],real m2[],real omega,
 133                     real invmass[],real tt[],real lagr[],int *nerror,real invdt,t_vetavars *vetavar);
 134
 135 gmx_bool constrain(FILE *log,gmx_bool bLog,gmx_bool bEner,
 136                    gmx_constr_t constr,
 137                    t_idef *idef,
 138                    t_inputrec *ir,
 139                    gmx_ekindata_t *ekind,
 140                    t_commrec *cr,
 141                    gmx_large_int_t step,int delta_step,
 142                    t_mdatoms *md,
 143                    rvec *x,rvec *xprime,rvec *min_proj,
 144                    gmx_bool bMolPBC,matrix box,
 145                    real lambda,real *dvdlambda,
 146                    rvec *v,tensor *vir,
 147                    t_nrnb *nrnb,int econq, gmx_bool bPscal, real veta, real vetanew);
 148 /*
 149  * When econq=econqCoord constrains coordinates xprime using th
 150  * directions in x, min_proj is not used.
 151  *
 152  * When econq=econqDeriv, calculates the components xprime in
 153  * the constraint directions and subtracts these components from min_proj.
 154  * So when min_proj=xprime, the constraint components are projected out.
 155  *
 156  * When econq=econqDeriv_FlexCon, the same is done as with econqDeriv,
 157  * but only the components of the flexible constraints are stored.
 158  *
 159  * When bMolPBC=TRUE, assume that molecules might be broken: correct PBC.
 160  *
 161  * delta_step is used for determining the constraint reference lengths
 162  * when lenA != lenB or will the pull code with a pulling rate.
 163  * step + delta_step is the step at which the final configuration
 164  * is meant to be; for update delta_step = 1.
 165  *
 166  * If v!=NULL also constrain v by adding the constraint corrections / dt.
 167  *
 168  * If vir!=NULL calculate the constraint virial.
 169  *
 170  * if veta != NULL, constraints are done assuming isotropic pressure control
 171  * (i.e. constraining rdot.r = (v + veta*r).r = 0 instead of v
 172  *
 173  * Init_constraints must have be called once, before calling constrain.
 174  *
 175  * Return TRUE if OK, FALSE in case of shake error
 176  *
 177  */
 178
 179 gmx_constr_t init_constraints(FILE *log,
 180                                      gmx_mtop_t *mtop,t_inputrec *ir,
 181                                      gmx_edsam_t ed,t_state *state,
 182                                      t_commrec *cr);
 183 /* Initialize constraints stuff */
 184
 185 void set_constraints(gmx_constr_t constr,
 186                                                         gmx_localtop_t *top,
 187                                                         t_inputrec *ir,
 188                                                         t_mdatoms *md,
 189                                                         t_commrec *cr);
 190 /* Set up all the local constraints for the node */
 191
 192 /* The at2con t_blocka struct returned by the routines below
 193  * contains a list of constraints per atom.
 194  * The F_CONSTRNC constraints in this structure number consecutively
 195  * after the F_CONSTR constraints.
 196  */
 197
 198 t_blocka make_at2con(int start,int natoms,
 199                             t_ilist *ilist,t_iparams *iparams,
 200                             gmx_bool bDynamics,int *nflexiblecons);
 201 /* Returns a block struct to go from atoms to constraints */
 202
 203 const t_blocka *atom2constraints_moltype(gmx_constr_t constr);
 204 /* Returns the an array of atom to constraints lists for the moltypes */
 205
 206 const int **atom2settle_moltype(gmx_constr_t constr);
 207 /* Returns the an array of atom to settle for the moltypes */
 208
 209 #define constr_iatomptr(nconstr,iatom_constr,iatom_constrnc,con) ((con) < (nconstr) ? (iatom_constr)+(con)*3 : (iatom_constrnc)+(con-nconstr)*3)
 210 /* Macro for getting the constraint iatoms for a constraint number con
 211  * which comes from a list where F_CONSTR and F_CONSTRNC constraints
 212  * are concatenated.
 213  */
 214
 215 gmx_bool inter_charge_group_constraints(const gmx_mtop_t *mtop);
 216 /* Returns if there are inter charge group constraints */
 217
 218 gmx_bool inter_charge_group_settles(const gmx_mtop_t *mtop);
 219 /* Returns if there are inter charge group settles */
 220
 221 real *constr_rmsd_data(gmx_constr_t constr);
 222 /* Return the data for determining constraint RMS relative deviations.
 223  * Returns NULL when LINCS is not used.
 224  */
 225
 226 real constr_rmsd(gmx_constr_t constr,gmx_bool bSD2);
 227 /* Return the RMSD of the constraint, bSD2 selects the second SD step */
 228
 229 real *lincs_rmsd_data(gmx_lincsdata_t lincsd);
 230 /* Return the data for determining constraint RMS relative deviations */
 231
 232 real lincs_rmsd(gmx_lincsdata_t lincsd,gmx_bool bSD2);
 233 /* Return the RMSD of the constraint, bSD2 selects the second SD step */
 234
 235 gmx_lincsdata_t init_lincs(FILE *fplog,gmx_mtop_t *mtop,
 236                            int nflexcon_global,t_blocka *at2con,
 237                            gmx_bool bPLINCS,int nIter,int nProjOrder);
 238 /* Initializes and returns the lincs data struct */
 239
 240 void set_lincs(t_idef *idef,t_mdatoms *md,
 241                       gmx_bool bDynamics,t_commrec *cr,
 242                       gmx_lincsdata_t li);
 243 /* Initialize lincs stuff */
 244
 245 void set_lincs_matrix(gmx_lincsdata_t li,real *invmass,real lambda);
 246 /* Sets the elements of the LINCS constraint coupling matrix */
 247
 248 real constr_r_max(FILE *fplog,gmx_mtop_t *mtop,t_inputrec *ir);
 249 /* Returns an estimate of the maximum distance between atoms
 250  * required for LINCS.
 251  */
 252
 253 gmx_bool
 254 constrain_lincs(FILE *log,gmx_bool bLog,gmx_bool bEner,
 255                             t_inputrec *ir,
 256                             gmx_large_int_t step,
 257                             gmx_lincsdata_t lincsd,t_mdatoms *md,
 258                 t_commrec *cr,
 259                             rvec *x,rvec *xprime,rvec *min_proj,
 260                 matrix box,t_pbc *pbc,
 261                             real lambda,real *dvdlambda,
 262                             real invdt,rvec *v,
 263                             gmx_bool bCalcVir,tensor rmdr,
 264                             int econ,
 265                             t_nrnb *nrnb,
 266                             int maxwarn,int *warncount);
 267 /* Returns if the constraining succeeded */
 268
 269
 270 /* helper functions for andersen temperature control, because the
 271  * gmx_constr construct is only defined in constr.c. Return the list
 272  * of blocks (get_sblock) and the number of blocks (get_nblocks).  */
 273
 274 int *get_sblock(struct gmx_constr *constr);
 275
 276 int get_nblocks(struct gmx_constr *constr);
 277
 278 #ifdef __cplusplus
 279 }
 280 #endif
 281 #endif