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 prime[],               /* 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                     int econq,         /* which type of constrainint is occurring */
  88                     t_vetavars *vetavar);           /* veta for pressure control */
  89 /* Shake all the atoms blockwise. It is assumed that all the constraints
  90  * in the idef->shakes field are sorted, to ascending block nr. The
  91  * sblock array points into the idef->shakes.iatoms field, with block 0
  92  * starting
  93  * at sblock[0] and running to ( < ) sblock[1], block n running from
  94  * sblock[n] to sblock[n+1]. Array sblock should be large enough.
  95  * Return TRUE when OK, FALSE when shake-error
  96  */
  97
  98 extern gmx_settledata_t settle_init(real mO,real mH,real invmO,real invmH,
  99                                     real dOH,real dHH);
 100 /* Initializes and returns a structure with SETTLE parameters */
 101
 102 extern void csettle(gmx_settledata_t settled,
 103                     int nsettle,        /* Number of settles            */
 104                     t_iatom iatoms[],   /* The settle iatom list        */
 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                     bool bCalcVir,      /* Calculate r x m delta_r      */
 110                     tensor rmdr,        /* sum r x m delta_r            */
 111                     int *xerror,
 112                     t_vetavars *vetavar     /* variables for pressure control */
 113     );
 114
 115 extern void settle_proj(FILE *fp,
 116                         gmx_settledata_t settled,int econq,
 117                         int nsettle, t_iatom iatoms[],rvec x[],
 118                         rvec *der,rvec *derp,
 119                         bool bCalcVir,tensor rmdder, t_vetavars *vetavar);
 120 /* Analytical algorithm to subtract the components of derivatives
 121  * of coordinates working on settle type constraint.
 122  */
 123
 124 extern void cshake(atom_id iatom[],int ncon,int *nnit,int maxnit,
 125                    real dist2[],real xp[],real rij[],real m2[],real omega,
 126                    real invmass[],real tt[],real lagr[],int *nerror);
 127 /* Regular iterative shake */
 128
 129 extern void crattle(atom_id iatom[],int ncon,int *nnit,int maxnit,
 130                     real dist2[],real vp[],real rij[],real m2[],real omega,
 131                     real invmass[],real tt[],real lagr[],int *nerror,real invdt,t_vetavars *vetavar);
 132
 133 extern bool constrain(FILE *log,bool bLog,bool bEner,
 134                       gmx_constr_t constr,
 135                       t_idef *idef,
 136                       t_inputrec *ir,
 137                       gmx_ekindata_t *ekind,
 138                       t_commrec *cr,
 139                       gmx_large_int_t step,int delta_step,
 140                       t_mdatoms *md,
 141                       rvec *x,rvec *xprime,rvec *min_proj,matrix box,
 142                       real lambda,real *dvdlambda,
 143                       rvec *v,tensor *vir,
 144                       t_nrnb *nrnb,int econq, bool bPscal, real veta, real vetanew);
 145 /*
 146  * When econq=econqCoord constrains coordinates xprime using th
 147  * directions in x, min_proj is not used.
 148  *
 149  * When econq=econqDeriv, calculates the components xprime in
 150  * the constraint directions and subtracts these components from min_proj.
 151  * So when min_proj=xprime, the constraint components are projected out.
 152  *
 153  * When econq=econqDeriv_FlexCon, the same is done as with econqDeriv,
 154  * but only the components of the flexible constraints are stored.
 155  *
 156  * delta_step is used for determining the constraint reference lengths
 157  * when lenA != lenB or will the pull code with a pulling rate.
 158  * step + delta_step is the step at which the final configuration
 159  * is meant to be; for update delta_step = 1.
 160  *
 161  * If v!=NULL also constrain v by adding the constraint corrections / dt.
 162  *
 163  * If vir!=NULL calculate the constraint virial.
 164  *
 165  * if veta != NULL, constraints are done assuming isotropic pressure control
 166  * (i.e. constraining rdot.r = (v + veta*r).r = 0 instead of v
 167  *
 168  * Init_constraints must have be called once, before calling constrain.
 169  *
 170  * Return TRUE if OK, FALSE in case of shake error
 171  *
 172  */
 173
 174 extern gmx_constr_t init_constraints(FILE *log,
 175                                      gmx_mtop_t *mtop,t_inputrec *ir,
 176                                      gmx_edsam_t ed,t_state *state,
 177                                      t_commrec *cr);
 178 /* Initialize constraints stuff */
 179
 180 extern void set_constraints(gmx_constr_t constr,
 181                                                         gmx_localtop_t *top,
 182                                                         t_inputrec *ir,
 183                                                         t_mdatoms *md,
 184                                                         t_commrec *cr);
 185 /* Set up all the local constraints for the node */
 186
 187 /* The at2con t_blocka struct returned by the routines below
 188  * contains a list of constraints per atom.
 189  * The F_CONSTRNC constraints in this structure number consecutively
 190  * after the F_CONSTR constraints.
 191  */
 192
 193 extern t_blocka make_at2con(int start,int natoms,
 194                             t_ilist *ilist,t_iparams *iparams,
 195                             bool bDynamics,int *nflexiblecons);
 196 /* Returns a block struct to go from atoms to constraints */
 197
 198 extern t_blocka *atom2constraints_moltype(gmx_constr_t constr);
 199 /* Returns the an arry of atom to constraints lists for the moltypes */
 200
 201 #define constr_iatomptr(nconstr,iatom_constr,iatom_constrnc,con) ((con) < (nconstr) ? (iatom_constr)+(con)*3 : (iatom_constrnc)+(con-nconstr)*3)
 202 /* Macro for getting the constraint iatoms for a constraint number con
 203  * which comes from a list where F_CONSTR and F_CONSTRNC constraints
 204  * are concatenated.
 205  */
 206
 207 extern bool inter_charge_group_constraints(gmx_mtop_t *mtop);
 208 /* Returns if there are inter charge group constraints */
 209
 210 extern real *constr_rmsd_data(gmx_constr_t constr);
 211 /* Return the data for determining constraint RMS relative deviations.
 212  * Returns NULL when LINCS is not used.
 213  */
 214
 215 extern real constr_rmsd(gmx_constr_t constr,bool bSD2);
 216 /* Return the RMSD of the constraint, bSD2 selects the second SD step */
 217
 218 extern real *lincs_rmsd_data(gmx_lincsdata_t lincsd);
 219 /* Return the data for determining constraint RMS relative deviations */
 220
 221 extern real lincs_rmsd(gmx_lincsdata_t lincsd,bool bSD2);
 222 /* Return the RMSD of the constraint, bSD2 selects the second SD step */
 223
 224 gmx_lincsdata_t init_lincs(FILE *fplog,gmx_mtop_t *mtop,
 225                            int nflexcon_global,t_blocka *at2con,
 226                            bool bPLINCS,int nIter,int nProjOrder);
 227 /* Initializes and returns the lincs data struct */
 228
 229 extern void set_lincs(t_idef *idef,t_mdatoms *md,
 230                       bool bDynamics,t_commrec *cr,
 231                       gmx_lincsdata_t li);
 232 /* Initialize lincs stuff */
 233
 234 extern void set_lincs_matrix(gmx_lincsdata_t li,real *invmass,real lambda);
 235 /* Sets the elements of the LINCS constraint coupling matrix */
 236
 237 extern real constr_r_max(FILE *fplog,gmx_mtop_t *mtop,t_inputrec *ir);
 238 /* Returns an estimate of the maximum distance between atoms
 239  * required for LINCS.
 240  */
 241
 242 extern bool constrain_lincs(FILE *log,bool bLog,bool bEner,
 243                             t_inputrec *ir,
 244                             gmx_large_int_t step,
 245                             gmx_lincsdata_t lincsd,t_mdatoms *md,
 246                             t_commrec *cr,
 247                             rvec *x,rvec *xprime,rvec *min_proj,matrix box,
 248                             real lambda,real *dvdlambda,
 249                             real invdt,rvec *v,
 250                             bool bCalcVir,tensor rmdr,
 251                             int econ,
 252                             t_nrnb *nrnb,
 253                             int maxwarn,int *warncount);
 254 /* Returns if the constraining succeeded */
 255
 256 #ifdef __cplusplus
 257 }
 258 #endif