include/constr.h

   1 /* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
   2  *
   3  *
   4  *                This source code is part of
   5  *
   6  *                 G   R   O   M   A   C   S
   7  *
   8  *          GROningen MAchine for Chemical Simulations
   9  *
  10  *                        VERSION 3.2.0
  11  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  12  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  13  * Copyright (c) 2001-2004, The GROMACS development team,
  14  * check out http://www.gromacs.org for more information.
  15
  16  * This program is free software; you can redistribute it and/or
  17  * modify it under the terms of the GNU General Public License
  18  * as published by the Free Software Foundation; either version 2
  19  * of the License, or (at your option) any later version.
  20  *
  21  * If you want to redistribute modifications, please consider that
  22  * scientific software is very special. Version control is crucial -
  23  * bugs must be traceable. We will be happy to consider code for
  24  * inclusion in the official distribution, but derived work must not
  25  * be called official GROMACS. Details are found in the README & COPYING
  26  * files - if they are missing, get the official version at www.gromacs.org.
  27  *
  28  * To help us fund GROMACS development, we humbly ask that you cite
  29  * the papers on the package - you can find them in the top README file.
  30  *
  31  * For more info, check our website at http://www.gromacs.org
  32  *
  33  * And Hey:
  34  * Gromacs Runs On Most of All Computer Systems
  35  */
  36
  37 #include "typedefs.h"
  38
  39 #ifdef __cplusplus
  40 extern "C" {
  41 #endif
  42
  43 enum
  44 {
  45     econqCoord,         /* Constrain coordinates (mass weighted)           */
  46     econqVeloc,         /* Constrain velocities (mass weighted)            */
  47     econqDeriv,         /* Constrain a derivative (mass weighted),         *
  48                          * for instance velocity or acceleration,          *
  49                          * constraint virial can not be calculated.        */
  50     econqDeriv_FlexCon, /* As econqDeriv, but only output flex. con.       */
  51     econqForce,         /* Constrain forces (non mass-weighted)            */
  52     econqForceDispl     /* Constrain forces (mass-weighted 1/0 for freeze) */
  53 };
  54
  55 int n_flexible_constraints(struct gmx_constr *constr);
  56 /* Returns the total number of flexible constraints in the system */
  57
  58 void too_many_constraint_warnings(int eConstrAlg,int warncount);
  59 /* Generate a fatal error because of too many LINCS/SETTLE warnings */
  60
  61 gmx_shakedata_t shake_init();
  62 /* Initializes and return the SHAKE data structure */
  63
  64 gmx_bool bshakef(FILE *log,             /* Log file                     */
  65                     gmx_shakedata_t shaked, /* SHAKE data */
  66                     int natoms,         /* Total number of atoms        */
  67                     real invmass[],     /* Atomic masses                */
  68                     int nblocks,        /* The number of shake blocks   */
  69                     int sblock[],       /* The shake blocks             */
  70                     t_idef *idef,       /* The interaction def          */
  71                     t_inputrec *ir,     /* Input record                 */
  72                     matrix box,         /* The box                      */
  73                     rvec x_s[],         /* Coords before update         */
  74                     rvec prime[],               /* Output coords                */
  75                     t_nrnb *nrnb,       /* Performance measure          */
  76                     real *lagr,         /* The Lagrange multipliers     */
  77                     real lambda,        /* FEP lambda                   */
  78                     real *dvdlambda,    /* FEP force                    */
  79                     real invdt,         /* 1/delta_t                    */
  80                     rvec *v,            /* Also constrain v if v!=NULL  */
  81                     gmx_bool bCalcVir,      /* Calculate r x m delta_r      */
  82                     tensor rmdr,        /* sum r x m delta_r            */
  83                     gmx_bool bDumpOnError,  /* Dump debugging stuff on error*/
  84                     int econq,         /* which type of constrainint is occurring */
  85                     t_vetavars *vetavar);           /* veta for pressure control */
  86 /* Shake all the atoms blockwise. It is assumed that all the constraints
  87  * in the idef->shakes field are sorted, to ascending block nr. The
  88  * sblock array points into the idef->shakes.iatoms field, with block 0
  89  * starting
  90  * at sblock[0] and running to ( < ) sblock[1], block n running from
  91  * sblock[n] to sblock[n+1]. Array sblock should be large enough.
  92  * Return TRUE when OK, FALSE when shake-error
  93  */
  94
  95 gmx_settledata_t settle_init(real mO,real mH,real invmO,real invmH,
  96                                     real dOH,real dHH);
  97 /* Initializes and returns a structure with SETTLE parameters */
  98
  99 void csettle(gmx_settledata_t settled,
 100                     int nsettle,        /* Number of settles            */
 101                     t_iatom iatoms[],   /* The settle iatom list        */
 102                     real b4[],          /* Old coordinates              */
 103                     real after[],       /* New coords, to be settled    */
 104                     real invdt,         /* 1/delta_t                    */
 105                     real *v,            /* Also constrain v if v!=NULL  */
 106                     gmx_bool bCalcVir,      /* Calculate r x m delta_r      */
 107                     tensor rmdr,        /* sum r x m delta_r            */
 108                     int *xerror,
 109                     t_vetavars *vetavar     /* variables for pressure control */
 110     );
 111
 112 void settle_proj(FILE *fp,
 113                         gmx_settledata_t settled,int econq,
 114                         int nsettle, t_iatom iatoms[],rvec x[],
 115                         rvec *der,rvec *derp,
 116                         gmx_bool bCalcVir,tensor rmdder, t_vetavars *vetavar);
 117 /* Analytical algorithm to subtract the components of derivatives
 118  * of coordinates working on settle type constraint.
 119  */
 120
 121 void cshake(atom_id iatom[],int ncon,int *nnit,int maxnit,
 122                    real dist2[],real xp[],real rij[],real m2[],real omega,
 123                    real invmass[],real tt[],real lagr[],int *nerror);
 124 /* Regular iterative shake */
 125
 126 void crattle(atom_id iatom[],int ncon,int *nnit,int maxnit,
 127                     real dist2[],real vp[],real rij[],real m2[],real omega,
 128                     real invmass[],real tt[],real lagr[],int *nerror,real invdt,t_vetavars *vetavar);
 129
 130 gmx_bool constrain(FILE *log,gmx_bool bLog,gmx_bool bEner,
 131                       gmx_constr_t constr,
 132                       t_idef *idef,
 133                       t_inputrec *ir,
 134                       gmx_ekindata_t *ekind,
 135                       t_commrec *cr,
 136                       gmx_large_int_t step,int delta_step,
 137                       t_mdatoms *md,
 138                       rvec *x,rvec *xprime,rvec *min_proj,matrix box,
 139                       real lambda,real *dvdlambda,
 140                       rvec *v,tensor *vir,
 141                       t_nrnb *nrnb,int econq, gmx_bool bPscal, real veta, real vetanew);
 142 /*
 143  * When econq=econqCoord constrains coordinates xprime using th
 144  * directions in x, min_proj is not used.
 145  *
 146  * When econq=econqDeriv, calculates the components xprime in
 147  * the constraint directions and subtracts these components from min_proj.
 148  * So when min_proj=xprime, the constraint components are projected out.
 149  *
 150  * When econq=econqDeriv_FlexCon, the same is done as with econqDeriv,
 151  * but only the components of the flexible constraints are stored.
 152  *
 153  * delta_step is used for determining the constraint reference lengths
 154  * when lenA != lenB or will the pull code with a pulling rate.
 155  * step + delta_step is the step at which the final configuration
 156  * is meant to be; for update delta_step = 1.
 157  *
 158  * If v!=NULL also constrain v by adding the constraint corrections / dt.
 159  *
 160  * If vir!=NULL calculate the constraint virial.
 161  *
 162  * if veta != NULL, constraints are done assuming isotropic pressure control
 163  * (i.e. constraining rdot.r = (v + veta*r).r = 0 instead of v
 164  *
 165  * Init_constraints must have be called once, before calling constrain.
 166  *
 167  * Return TRUE if OK, FALSE in case of shake error
 168  *
 169  */
 170
 171 gmx_constr_t init_constraints(FILE *log,
 172                                      gmx_mtop_t *mtop,t_inputrec *ir,
 173                                      gmx_edsam_t ed,t_state *state,
 174                                      t_commrec *cr);
 175 /* Initialize constraints stuff */
 176
 177 void set_constraints(gmx_constr_t constr,
 178                                                         gmx_localtop_t *top,
 179                                                         t_inputrec *ir,
 180                                                         t_mdatoms *md,
 181                                                         t_commrec *cr);
 182 /* Set up all the local constraints for the node */
 183
 184 /* The at2con t_blocka struct returned by the routines below
 185  * contains a list of constraints per atom.
 186  * The F_CONSTRNC constraints in this structure number consecutively
 187  * after the F_CONSTR constraints.
 188  */
 189
 190 t_blocka make_at2con(int start,int natoms,
 191                             t_ilist *ilist,t_iparams *iparams,
 192                             gmx_bool bDynamics,int *nflexiblecons);
 193 /* Returns a block struct to go from atoms to constraints */
 194
 195 t_blocka *atom2constraints_moltype(gmx_constr_t constr);
 196 /* Returns the an arry of atom to constraints lists for the moltypes */
 197
 198 #define constr_iatomptr(nconstr,iatom_constr,iatom_constrnc,con) ((con) < (nconstr) ? (iatom_constr)+(con)*3 : (iatom_constrnc)+(con-nconstr)*3)
 199 /* Macro for getting the constraint iatoms for a constraint number con
 200  * which comes from a list where F_CONSTR and F_CONSTRNC constraints
 201  * are concatenated.
 202  */
 203
 204 gmx_bool inter_charge_group_constraints(gmx_mtop_t *mtop);
 205 /* Returns if there are inter charge group constraints */
 206
 207 real *constr_rmsd_data(gmx_constr_t constr);
 208 /* Return the data for determining constraint RMS relative deviations.
 209  * Returns NULL when LINCS is not used.
 210  */
 211
 212 real constr_rmsd(gmx_constr_t constr,gmx_bool bSD2);
 213 /* Return the RMSD of the constraint, bSD2 selects the second SD step */
 214
 215 real *lincs_rmsd_data(gmx_lincsdata_t lincsd);
 216 /* Return the data for determining constraint RMS relative deviations */
 217
 218 real lincs_rmsd(gmx_lincsdata_t lincsd,gmx_bool bSD2);
 219 /* Return the RMSD of the constraint, bSD2 selects the second SD step */
 220
 221 gmx_lincsdata_t init_lincs(FILE *fplog,gmx_mtop_t *mtop,
 222                            int nflexcon_global,t_blocka *at2con,
 223                            gmx_bool bPLINCS,int nIter,int nProjOrder);
 224 /* Initializes and returns the lincs data struct */
 225
 226 void set_lincs(t_idef *idef,t_mdatoms *md,
 227                       gmx_bool bDynamics,t_commrec *cr,
 228                       gmx_lincsdata_t li);
 229 /* Initialize lincs stuff */
 230
 231 void set_lincs_matrix(gmx_lincsdata_t li,real *invmass,real lambda);
 232 /* Sets the elements of the LINCS constraint coupling matrix */
 233
 234 real constr_r_max(FILE *fplog,gmx_mtop_t *mtop,t_inputrec *ir);
 235 /* Returns an estimate of the maximum distance between atoms
 236  * required for LINCS.
 237  */
 238
 239 gmx_bool constrain_lincs(FILE *log,gmx_bool bLog,gmx_bool bEner,
 240                             t_inputrec *ir,
 241                             gmx_large_int_t step,
 242                             gmx_lincsdata_t lincsd,t_mdatoms *md,
 243                             t_commrec *cr,
 244                             rvec *x,rvec *xprime,rvec *min_proj,matrix box,
 245                             real lambda,real *dvdlambda,
 246                             real invdt,rvec *v,
 247                             gmx_bool bCalcVir,tensor rmdr,
 248                             int econ,
 249                             t_nrnb *nrnb,
 250                             int maxwarn,int *warncount);
 251 /* Returns if the constraining succeeded */
 252
 253 #ifdef __cplusplus
 254 }
 255 #endif