include/constr.h

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  36 #ifdef HAVE_CONFIG_H
  37 #include<config.h>
  38 #endif
  39
  40 #include "typedefs.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 extern int n_flexible_constraints(struct gmx_constr *constr);
  59 /* Returns the total number of flexible constraints in the system */
  60
  61 extern void too_many_constraint_warnings(int eConstrAlg,int warncount);
  62 /* Generate a fatal error because of too many LINCS/SETTLE warnings */
  63
  64 extern gmx_shakedata_t shake_init();
  65 /* Initializes and return the SHAKE data structure */
  66
  67 extern 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                     matrix box,         /* The box                      */
  76                     rvec x_s[],         /* Coords before update         */
  77                     rvec xp[],          /* Output coords                */
  78                     t_nrnb *nrnb,       /* Performance measure          */
  79                     real *lagr,         /* The Lagrange multipliers     */
  80                     real lambda,        /* FEP lambda                   */
  81                     real *dvdlambda,    /* FEP force                    */
  82                     real invdt,         /* 1/delta_t                    */
  83                     rvec *v,            /* Also constrain v if v!=NULL  */
  84                     bool bCalcVir,      /* Calculate r x m delta_r      */
  85                     tensor rmdr,        /* sum r x m delta_r            */
  86                     bool bDumpOnError); /* Dump debugging stuff on error*/
  87 /* Shake all the atoms blockwise. It is assumed that all the constraints
  88  * in the idef->shakes field are sorted, to ascending block nr. The
  89  * sblock array points into the idef->shakes.iatoms field, with block 0
  90  * starting
  91  * at sblock[0] and running to ( < ) sblock[1], block n running from
  92  * sblock[n] to sblock[n+1]. Array sblock should be large enough.
  93  * Return TRUE when OK, FALSE when shake-error
  94  */
  95
  96 extern gmx_settledata_t settle_init(real mO,real mH,real invmO,real invmH,
  97                                     real dOH,real dHH);
  98 /* Initializes and returns a structure with SETTLE parameters */
  99
 100 extern void csettle(gmx_settledata_t settled,
 101                     int nsettle,        /* Number of settles            */
 102                     t_iatom iatoms[],   /* The settle iatom list        */
 103                     real b4[],          /* Old coordinates              */
 104                     real after[],       /* New coords, to be settled    */
 105                     real invdt,         /* 1/delta_t                    */
 106                     real *v,            /* Also constrain v if v!=NULL  */
 107                     bool bCalcVir,      /* Calculate r x m delta_r      */
 108                     tensor rmdr,        /* sum r x m delta_r            */
 109                     int *xerror);
 110
 111 extern void settle_proj(FILE *fp,
 112                         gmx_settledata_t settled,int econq,
 113                         int nsettle, t_iatom iatoms[],rvec x[],
 114                         rvec *der,rvec *derp,
 115                         bool bCalcVir,tensor rmdder);
 116 /* Analytical algorithm to subtract the components of derivatives
 117  * of coordinates working on settle type constraint.
 118  */
 119
 120 extern void cshake(atom_id iatom[],int ncon,int *nnit,int maxnit,
 121                    real dist2[],real xp[],real rij[],real m2[],real omega,
 122                    real invmass[],real tt[],real lagr[],int *nerror);
 123 /* Regular iterative shake */
 124
 125 extern bool constrain(FILE *log,bool bLog,bool bEner,
 126                       gmx_constr_t constr,
 127                       t_idef *idef,
 128                       t_inputrec *ir,
 129                       t_commrec *cr,
 130                       gmx_large_int_t step,int delta_step,
 131                       t_mdatoms *md,
 132                       rvec *x,rvec *xprime,rvec *min_proj,matrix box,
 133                       real lambda,real *dvdlambda,
 134                       rvec *v,tensor *vir,
 135                       t_nrnb *nrnb,int econq);
 136 /*
 137  * When econq=econqCoord constrains coordinates xprime using th
 138  * directions in x, min_proj is not used.
 139  *
 140  * When econq=econqDeriv, calculates the components xprime in
 141  * the constraint directions and subtracts these components from min_proj.
 142  * So when min_proj=xprime, the constraint components are projected out.
 143  *
 144  * When econq=econqDeriv_FlexCon, the same is done as with econqDeriv,
 145  * but only the components of the flexible constraints are stored.
 146  *
 147  * delta_step is used for determining the constraint reference lengths
 148  * when lenA != lenB or will the pull code with a pulling rate.
 149  * step + delta_step is the step at which the final configuration
 150  * is meant to be; for update delta_step = 1.
 151  *
 152  * If v!=NULL also constrain v by adding the constraint corrections / dt.
 153  *
 154  * If vir!=NULL calculate the constraint virial.
 155  *
 156  * Init_constraints must have be called once, before calling constrain.
 157  *
 158  * Return TRUE if OK, FALSE in case of shake error
 159  *
 160  */
 161
 162 extern gmx_constr_t init_constraints(FILE *log,
 163                                      gmx_mtop_t *mtop,t_inputrec *ir,
 164                                      gmx_edsam_t ed,t_state *state,
 165                                      t_commrec *cr);
 166 /* Initialize constraints stuff */
 167
 168 extern void set_constraints(gmx_constr_t constr,
 169                                                         gmx_localtop_t *top,
 170                                                         t_inputrec *ir,
 171                                                         t_mdatoms *md,
 172                                                         t_commrec *cr);
 173 /* Set up all the local constraints for the node */
 174
 175 /* The at2con t_blocka struct returned by the routines below
 176  * contains a list of constraints per atom.
 177  * The F_CONSTRNC constraints in this structure number consecutively
 178  * after the F_CONSTR constraints.
 179  */
 180
 181 extern t_blocka make_at2con(int start,int natoms,
 182                             t_ilist *ilist,t_iparams *iparams,
 183                             bool bDynamics,int *nflexiblecons);
 184 /* Returns a block struct to go from atoms to constraints */
 185
 186 extern t_blocka *atom2constraints_moltype(gmx_constr_t constr);
 187 /* Returns the an arry of atom to constraints lists for the moltypes */
 188
 189 #define constr_iatomptr(nconstr,iatom_constr,iatom_constrnc,con) ((con) < (nconstr) ? (iatom_constr)+(con)*3 : (iatom_constrnc)+(con-nconstr)*3)
 190 /* Macro for getting the constraint iatoms for a constraint number con
 191  * which comes from a list where F_CONSTR and F_CONSTRNC constraints
 192  * are concatenated.
 193  */
 194
 195 extern bool inter_charge_group_constraints(gmx_mtop_t *mtop);
 196 /* Returns if there are inter charge group constraints */
 197
 198 extern real *constr_rmsd_data(gmx_constr_t constr);
 199 /* Return the data for determining constraint RMS relative deviations.
 200  * Returns NULL when LINCS is not used.
 201  */
 202
 203 extern real constr_rmsd(gmx_constr_t constr,bool bSD2);
 204 /* Return the RMSD of the constraint, bSD2 selects the second SD step */
 205
 206 extern real *lincs_rmsd_data(gmx_lincsdata_t lincsd);
 207 /* Return the data for determining constraint RMS relative deviations */
 208
 209 extern real lincs_rmsd(gmx_lincsdata_t lincsd,bool bSD2);
 210 /* Return the RMSD of the constraint, bSD2 selects the second SD step */
 211
 212 gmx_lincsdata_t init_lincs(FILE *fplog,gmx_mtop_t *mtop,
 213                            int nflexcon_global,t_blocka *at2con,
 214                            bool bPLINCS,int nIter,int nProjOrder);
 215 /* Initializes and returns the lincs data struct */
 216
 217 extern void set_lincs(t_idef *idef,t_mdatoms *md,
 218                       bool bDynamics,t_commrec *cr,
 219                       gmx_lincsdata_t li);
 220 /* Initialize lincs stuff */
 221
 222 extern void set_lincs_matrix(gmx_lincsdata_t li,real *invmass,real lambda);
 223 /* Sets the elements of the LINCS constraint coupling matrix */
 224
 225 extern real constr_r_max(FILE *fplog,gmx_mtop_t *mtop,t_inputrec *ir);
 226 /* Returns an estimate of the maximum distance between atoms
 227  * required for LINCS.
 228  */
 229
 230 extern bool constrain_lincs(FILE *log,bool bLog,bool bEner,
 231                             t_inputrec *ir,
 232                             gmx_large_int_t step,
 233                             gmx_lincsdata_t lincsd,t_mdatoms *md,
 234                             t_commrec *cr,
 235                             rvec *x,rvec *xprime,rvec *min_proj,matrix box,
 236                             real lambda,real *dvdlambda,
 237                             real invdt,rvec *v,
 238                             bool bCalcVir,tensor rmdr,
 239                             int econ,
 240                             t_nrnb *nrnb,
 241                             int maxwarn,int *warncount);
 242 /* Returns if the constraining succeeded */
 243
 244 #ifdef __cplusplus
 245 }
 246 #endif