include/constr.h

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  36
  37 #ifndef _constr_h
  38 #define _constr_h
  39 #include "visibility.h"
  40 #include "typedefs.h"
  41 #include "types/commrec.h"
  42
  43 #ifdef __cplusplus
  44 extern "C" {
  45 #endif
  46
  47 enum
  48 {
  49     econqCoord,         /* Constrain coordinates (mass weighted)           */
  50     econqVeloc,         /* Constrain velocities (mass weighted)            */
  51     econqDeriv,         /* Constrain a derivative (mass weighted),         *
  52                          * for instance velocity or acceleration,          *
  53                          * constraint virial can not be calculated.        */
  54     econqDeriv_FlexCon, /* As econqDeriv, but only output flex. con.       */
  55     econqForce,         /* Constrain forces (non mass-weighted)            */
  56     econqForceDispl     /* Constrain forces (mass-weighted 1/0 for freeze) */
  57 };
  58
  59 GMX_LIBMD_EXPORT
  60 int n_flexible_constraints(struct gmx_constr *constr);
  61 /* Returns the total number of flexible constraints in the system */
  62
  63 void too_many_constraint_warnings(int eConstrAlg,int warncount);
  64 /* Generate a fatal error because of too many LINCS/SETTLE warnings */
  65
  66 gmx_shakedata_t shake_init();
  67 /* Initializes and return the SHAKE data structure */
  68
  69 gmx_bool bshakef(FILE *log,             /* Log file                     */
  70                     gmx_shakedata_t shaked, /* SHAKE data */
  71                     int natoms,         /* Total number of atoms        */
  72                     real invmass[],     /* Atomic masses                */
  73                     int nblocks,        /* The number of shake blocks   */
  74                     int sblock[],       /* The shake blocks             */
  75                     t_idef *idef,       /* The interaction def          */
  76                     t_inputrec *ir,     /* Input record                 */
  77                     rvec x_s[],         /* Coords before update         */
  78                     rvec prime[],               /* Output coords                */
  79                     t_nrnb *nrnb,       /* Performance measure          */
  80                     real *lagr,         /* The Lagrange multipliers     */
  81                     real lambda,        /* FEP lambda                   */
  82                     real *dvdlambda,    /* FEP force                    */
  83                     real invdt,         /* 1/delta_t                    */
  84                     rvec *v,            /* Also constrain v if v!=NULL  */
  85                     gmx_bool bCalcVir,  /* Calculate r x m delta_r      */
  86                     tensor vir_r_m_dr,  /* sum r x m delta_r            */
  87                     gmx_bool bDumpOnError,  /* Dump debugging stuff on error*/
  88                     int econq,         /* which type of constrainint is occurring */
  89                     t_vetavars *vetavar);           /* veta for pressure control */
  90 /* Shake all the atoms blockwise. It is assumed that all the constraints
  91  * in the idef->shakes field are sorted, to ascending block nr. The
  92  * sblock array points into the idef->shakes.iatoms field, with block 0
  93  * starting
  94  * at sblock[0] and running to ( < ) sblock[1], block n running from
  95  * sblock[n] to sblock[n+1]. Array sblock should be large enough.
  96  * Return TRUE when OK, FALSE when shake-error
  97  */
  98
  99 gmx_settledata_t settle_init(real mO,real mH,real invmO,real invmH,
 100                                     real dOH,real dHH);
 101 /* Initializes and returns a structure with SETTLE parameters */
 102
 103 void csettle(gmx_settledata_t settled,
 104              int nsettle,       /* Number of settles            */
 105              t_iatom iatoms[],  /* The settle iatom list        */
 106              const t_pbc *pbc,   /* PBC data pointer, can be NULL  */
 107              real b4[],         /* Old coordinates              */
 108              real after[],      /* New coords, to be settled    */
 109              real invdt,         /* 1/delta_t                    */
 110              real *v,            /* Also constrain v if v!=NULL  */
 111              int calcvir_atom_end, /* Calculate r x m delta_r up to this atom */
 112              tensor vir_r_m_dr,  /* sum r x m delta_r            */
 113              int *xerror,
 114              t_vetavars *vetavar     /* variables for pressure control */
 115     );
 116
 117 void settle_proj(FILE *fp,
 118                  gmx_settledata_t settled,int econq,
 119                  int nsettle, t_iatom iatoms[],
 120                  const t_pbc *pbc,   /* PBC data pointer, can be NULL  */
 121                  rvec x[],
 122                  rvec *der,rvec *derp,
 123                  int CalcVirAtomEnd,tensor vir_r_m_dder,
 124                  t_vetavars *vetavar);
 125 /* Analytical algorithm to subtract the components of derivatives
 126  * of coordinates working on settle type constraint.
 127  */
 128
 129 void cshake(atom_id iatom[],int ncon,int *nnit,int maxnit,
 130                    real dist2[],real xp[],real rij[],real m2[],real omega,
 131                    real invmass[],real tt[],real lagr[],int *nerror);
 132 /* Regular iterative shake */
 133
 134 void crattle(atom_id iatom[],int ncon,int *nnit,int maxnit,
 135                     real dist2[],real vp[],real rij[],real m2[],real omega,
 136                     real invmass[],real tt[],real lagr[],int *nerror,real invdt,t_vetavars *vetavar);
 137
 138 gmx_bool constrain(FILE *log,gmx_bool bLog,gmx_bool bEner,
 139                    gmx_constr_t constr,
 140                    t_idef *idef,
 141                    t_inputrec *ir,
 142                    gmx_ekindata_t *ekind,
 143                    t_commrec *cr,
 144                    gmx_large_int_t step,int delta_step,
 145                    t_mdatoms *md,
 146                    rvec *x,rvec *xprime,rvec *min_proj,
 147                    gmx_bool bMolPBC,matrix box,
 148                    real lambda,real *dvdlambda,
 149                    rvec *v,tensor *vir,
 150                    t_nrnb *nrnb,int econq, gmx_bool bPscal, real veta, real vetanew);
 151 /*
 152  * When econq=econqCoord constrains coordinates xprime using th
 153  * directions in x, min_proj is not used.
 154  *
 155  * When econq=econqDeriv, calculates the components xprime in
 156  * the constraint directions and subtracts these components from min_proj.
 157  * So when min_proj=xprime, the constraint components are projected out.
 158  *
 159  * When econq=econqDeriv_FlexCon, the same is done as with econqDeriv,
 160  * but only the components of the flexible constraints are stored.
 161  *
 162  * When bMolPBC=TRUE, assume that molecules might be broken: correct PBC.
 163  *
 164  * delta_step is used for determining the constraint reference lengths
 165  * when lenA != lenB or will the pull code with a pulling rate.
 166  * step + delta_step is the step at which the final configuration
 167  * is meant to be; for update delta_step = 1.
 168  *
 169  * If v!=NULL also constrain v by adding the constraint corrections / dt.
 170  *
 171  * If vir!=NULL calculate the constraint virial.
 172  *
 173  * if veta != NULL, constraints are done assuming isotropic pressure control
 174  * (i.e. constraining rdot.r = (v + veta*r).r = 0 instead of v
 175  *
 176  * Init_constraints must have be called once, before calling constrain.
 177  *
 178  * Return TRUE if OK, FALSE in case of shake error
 179  *
 180  */
 181
 182 GMX_LIBMD_EXPORT
 183 gmx_constr_t init_constraints(FILE *log,
 184                                      gmx_mtop_t *mtop,t_inputrec *ir,
 185                                      gmx_edsam_t ed,t_state *state,
 186                                      t_commrec *cr);
 187 /* Initialize constraints stuff */
 188
 189 GMX_LIBMD_EXPORT
 190 void set_constraints(gmx_constr_t constr,
 191                                                         gmx_localtop_t *top,
 192                                                         t_inputrec *ir,
 193                                                         t_mdatoms *md,
 194                                                         t_commrec *cr);
 195 /* Set up all the local constraints for the node */
 196
 197 /* The at2con t_blocka struct returned by the routines below
 198  * contains a list of constraints per atom.
 199  * The F_CONSTRNC constraints in this structure number consecutively
 200  * after the F_CONSTR constraints.
 201  */
 202
 203 t_blocka make_at2con(int start,int natoms,
 204                             t_ilist *ilist,t_iparams *iparams,
 205                             gmx_bool bDynamics,int *nflexiblecons);
 206 /* Returns a block struct to go from atoms to constraints */
 207
 208 const t_blocka *atom2constraints_moltype(gmx_constr_t constr);
 209 /* Returns the an array of atom to constraints lists for the moltypes */
 210
 211 const int **atom2settle_moltype(gmx_constr_t constr);
 212 /* Returns the an array of atom to settle for the moltypes */
 213
 214 #define constr_iatomptr(nconstr,iatom_constr,iatom_constrnc,con) ((con) < (nconstr) ? (iatom_constr)+(con)*3 : (iatom_constrnc)+(con-nconstr)*3)
 215 /* Macro for getting the constraint iatoms for a constraint number con
 216  * which comes from a list where F_CONSTR and F_CONSTRNC constraints
 217  * are concatenated.
 218  */
 219
 220 gmx_bool inter_charge_group_constraints(const gmx_mtop_t *mtop);
 221 /* Returns if there are inter charge group constraints */
 222
 223 gmx_bool inter_charge_group_settles(const gmx_mtop_t *mtop);
 224 /* Returns if there are inter charge group settles */
 225
 226 real *constr_rmsd_data(gmx_constr_t constr);
 227 /* Return the data for determining constraint RMS relative deviations.
 228  * Returns NULL when LINCS is not used.
 229  */
 230
 231 GMX_LIBMD_EXPORT
 232 real constr_rmsd(gmx_constr_t constr,gmx_bool bSD2);
 233 /* Return the RMSD of the constraint, bSD2 selects the second SD step */
 234
 235 real *lincs_rmsd_data(gmx_lincsdata_t lincsd);
 236 /* Return the data for determining constraint RMS relative deviations */
 237
 238 real lincs_rmsd(gmx_lincsdata_t lincsd,gmx_bool bSD2);
 239 /* Return the RMSD of the constraint, bSD2 selects the second SD step */
 240
 241 gmx_lincsdata_t init_lincs(FILE *fplog,gmx_mtop_t *mtop,
 242                            int nflexcon_global,t_blocka *at2con,
 243                            gmx_bool bPLINCS,int nIter,int nProjOrder);
 244 /* Initializes and returns the lincs data struct */
 245
 246 void set_lincs(t_idef *idef,t_mdatoms *md,
 247                       gmx_bool bDynamics,t_commrec *cr,
 248                       gmx_lincsdata_t li);
 249 /* Initialize lincs stuff */
 250
 251 void set_lincs_matrix(gmx_lincsdata_t li,real *invmass,real lambda);
 252 /* Sets the elements of the LINCS constraint coupling matrix */
 253
 254 real constr_r_max(FILE *fplog,gmx_mtop_t *mtop,t_inputrec *ir);
 255 /* Returns an estimate of the maximum distance between atoms
 256  * required for LINCS.
 257  */
 258
 259 gmx_bool
 260 constrain_lincs(FILE *log,gmx_bool bLog,gmx_bool bEner,
 261                             t_inputrec *ir,
 262                             gmx_large_int_t step,
 263                             gmx_lincsdata_t lincsd,t_mdatoms *md,
 264                 t_commrec *cr,
 265                             rvec *x,rvec *xprime,rvec *min_proj,
 266                 matrix box,t_pbc *pbc,
 267                             real lambda,real *dvdlambda,
 268                             real invdt,rvec *v,
 269                             gmx_bool bCalcVir,tensor vir_r_m_dr,
 270                             int econ,
 271                             t_nrnb *nrnb,
 272                             int maxwarn,int *warncount);
 273 /* Returns if the constraining succeeded */
 274
 275
 276 /* helper functions for andersen temperature control, because the
 277  * gmx_constr construct is only defined in constr.c. Return the list
 278  * of blocks (get_sblock) and the number of blocks (get_nblocks).  */
 279
 280 int *get_sblock(struct gmx_constr *constr);
 281
 282 int get_nblocks(struct gmx_constr *constr);
 283
 284 #ifdef __cplusplus
 285 }
 286 #endif
 287 #endif