include/constr.h

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