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 vir_r_m_dr,  /* 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 vir_r_m_dr,  /* 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 vir_r_m_dder,
 122                  t_vetavars *vetavar);
 123 /* Analytical algorithm to subtract the components of derivatives
 124  * of coordinates working on settle type constraint.
 125  */
 126
 127 void cshake(atom_id iatom[],int ncon,int *nnit,int maxnit,
 128                    real dist2[],real xp[],real rij[],real m2[],real omega,
 129                    real invmass[],real tt[],real lagr[],int *nerror);
 130 /* Regular iterative shake */
 131
 132 void crattle(atom_id iatom[],int ncon,int *nnit,int maxnit,
 133                     real dist2[],real vp[],real rij[],real m2[],real omega,
 134                     real invmass[],real tt[],real lagr[],int *nerror,real invdt,t_vetavars *vetavar);
 135
 136 gmx_bool constrain(FILE *log,gmx_bool bLog,gmx_bool bEner,
 137                    gmx_constr_t constr,
 138                    t_idef *idef,
 139                    t_inputrec *ir,
 140                    gmx_ekindata_t *ekind,
 141                    t_commrec *cr,
 142                    gmx_large_int_t step,int delta_step,
 143                    t_mdatoms *md,
 144                    rvec *x,rvec *xprime,rvec *min_proj,
 145                    gmx_bool bMolPBC,matrix box,
 146                    real lambda,real *dvdlambda,
 147                    rvec *v,tensor *vir,
 148                    t_nrnb *nrnb,int econq, gmx_bool bPscal, real veta, real vetanew);
 149 /*
 150  * When econq=econqCoord constrains coordinates xprime using th
 151  * directions in x, min_proj is not used.
 152  *
 153  * When econq=econqDeriv, calculates the components xprime in
 154  * the constraint directions and subtracts these components from min_proj.
 155  * So when min_proj=xprime, the constraint components are projected out.
 156  *
 157  * When econq=econqDeriv_FlexCon, the same is done as with econqDeriv,
 158  * but only the components of the flexible constraints are stored.
 159  *
 160  * When bMolPBC=TRUE, assume that molecules might be broken: correct PBC.
 161  *
 162  * delta_step is used for determining the constraint reference lengths
 163  * when lenA != lenB or will the pull code with a pulling rate.
 164  * step + delta_step is the step at which the final configuration
 165  * is meant to be; for update delta_step = 1.
 166  *
 167  * If v!=NULL also constrain v by adding the constraint corrections / dt.
 168  *
 169  * If vir!=NULL calculate the constraint virial.
 170  *
 171  * if veta != NULL, constraints are done assuming isotropic pressure control
 172  * (i.e. constraining rdot.r = (v + veta*r).r = 0 instead of v
 173  *
 174  * Init_constraints must have be called once, before calling constrain.
 175  *
 176  * Return TRUE if OK, FALSE in case of shake error
 177  *
 178  */
 179
 180 gmx_constr_t init_constraints(FILE *log,
 181                                      gmx_mtop_t *mtop,t_inputrec *ir,
 182                                      gmx_edsam_t ed,t_state *state,
 183                                      t_commrec *cr);
 184 /* Initialize constraints stuff */
 185
 186 void set_constraints(gmx_constr_t constr,
 187                                                         gmx_localtop_t *top,
 188                                                         t_inputrec *ir,
 189                                                         t_mdatoms *md,
 190                                                         t_commrec *cr);
 191 /* Set up all the local constraints for the node */
 192
 193 /* The at2con t_blocka struct returned by the routines below
 194  * contains a list of constraints per atom.
 195  * The F_CONSTRNC constraints in this structure number consecutively
 196  * after the F_CONSTR constraints.
 197  */
 198
 199 t_blocka make_at2con(int start,int natoms,
 200                             t_ilist *ilist,t_iparams *iparams,
 201                             gmx_bool bDynamics,int *nflexiblecons);
 202 /* Returns a block struct to go from atoms to constraints */
 203
 204 const t_blocka *atom2constraints_moltype(gmx_constr_t constr);
 205 /* Returns the an array of atom to constraints lists for the moltypes */
 206
 207 const int **atom2settle_moltype(gmx_constr_t constr);
 208 /* Returns the an array of atom to settle for the moltypes */
 209
 210 #define constr_iatomptr(nconstr,iatom_constr,iatom_constrnc,con) ((con) < (nconstr) ? (iatom_constr)+(con)*3 : (iatom_constrnc)+(con-nconstr)*3)
 211 /* Macro for getting the constraint iatoms for a constraint number con
 212  * which comes from a list where F_CONSTR and F_CONSTRNC constraints
 213  * are concatenated.
 214  */
 215
 216 gmx_bool inter_charge_group_constraints(const gmx_mtop_t *mtop);
 217 /* Returns if there are inter charge group constraints */
 218
 219 gmx_bool inter_charge_group_settles(const gmx_mtop_t *mtop);
 220 /* Returns if there are inter charge group settles */
 221
 222 real *constr_rmsd_data(gmx_constr_t constr);
 223 /* Return the data for determining constraint RMS relative deviations.
 224  * Returns NULL when LINCS is not used.
 225  */
 226
 227 real constr_rmsd(gmx_constr_t constr,gmx_bool bSD2);
 228 /* Return the RMSD of the constraint, bSD2 selects the second SD step */
 229
 230 real *lincs_rmsd_data(gmx_lincsdata_t lincsd);
 231 /* Return the data for determining constraint RMS relative deviations */
 232
 233 real lincs_rmsd(gmx_lincsdata_t lincsd,gmx_bool bSD2);
 234 /* Return the RMSD of the constraint, bSD2 selects the second SD step */
 235
 236 gmx_lincsdata_t init_lincs(FILE *fplog,gmx_mtop_t *mtop,
 237                            int nflexcon_global,t_blocka *at2con,
 238                            gmx_bool bPLINCS,int nIter,int nProjOrder);
 239 /* Initializes and returns the lincs data struct */
 240
 241 void set_lincs(t_idef *idef,t_mdatoms *md,
 242                       gmx_bool bDynamics,t_commrec *cr,
 243                       gmx_lincsdata_t li);
 244 /* Initialize lincs stuff */
 245
 246 void set_lincs_matrix(gmx_lincsdata_t li,real *invmass,real lambda);
 247 /* Sets the elements of the LINCS constraint coupling matrix */
 248
 249 real constr_r_max(FILE *fplog,gmx_mtop_t *mtop,t_inputrec *ir);
 250 /* Returns an estimate of the maximum distance between atoms
 251  * required for LINCS.
 252  */
 253
 254 gmx_bool
 255 constrain_lincs(FILE *log,gmx_bool bLog,gmx_bool bEner,
 256                             t_inputrec *ir,
 257                             gmx_large_int_t step,
 258                             gmx_lincsdata_t lincsd,t_mdatoms *md,
 259                 t_commrec *cr,
 260                             rvec *x,rvec *xprime,rvec *min_proj,
 261                 matrix box,t_pbc *pbc,
 262                             real lambda,real *dvdlambda,
 263                             real invdt,rvec *v,
 264                             gmx_bool bCalcVir,tensor vir_r_m_dr,
 265                             int econ,
 266                             t_nrnb *nrnb,
 267                             int maxwarn,int *warncount);
 268 /* Returns if the constraining succeeded */
 269
 270
 271 /* helper functions for andersen temperature control, because the
 272  * gmx_constr construct is only defined in constr.c. Return the list
 273  * of blocks (get_sblock) and the number of blocks (get_nblocks).  */
 274
 275 int *get_sblock(struct gmx_constr *constr);
 276
 277 int get_nblocks(struct gmx_constr *constr);
 278
 279 #ifdef __cplusplus
 280 }
 281 #endif
 282 #endif