src/gromacs/mdlib/constraintrange.cpp

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  37 /* This file is completely threadsafe - keep it that way! */
  38 #include "gmxpre.h"
  39
  40 #include "constraintrange.h"
  41
  42 #include <cmath>
  43
  44 #include <algorithm>
  45
  46 #include "gromacs/mdlib/constr.h"
  47 #include "gromacs/mdtypes/inputrec.h"
  48 #include "gromacs/topology/block.h"
  49 #include "gromacs/topology/mtop_util.h"
  50 #include "gromacs/utility/basedefinitions.h"
  51 #include "gromacs/utility/fatalerror.h"
  52 #include "gromacs/utility/real.h"
  53 #include "gromacs/utility/smalloc.h"
  54
  55 static void constr_recur(const t_blocka *at2con,
  56                          const t_ilist *ilist, const t_iparams *iparams,
  57                          gmx_bool bTopB,
  58                          int at, int depth, int nc, int *path,
  59                          real r0, real r1, real *r2max,
  60                          int *count)
  61 {
  62     int      ncon1;
  63     t_iatom *ia1, *ia2;
  64     int      c, con, a1;
  65     gmx_bool bUse;
  66     t_iatom *ia;
  67     real     len, rn0, rn1;
  68
  69     (*count)++;
  70
  71     ncon1 = ilist[F_CONSTR].nr/3;
  72     ia1   = ilist[F_CONSTR].iatoms;
  73     ia2   = ilist[F_CONSTRNC].iatoms;
  74
  75     /* Loop over all constraints connected to this atom */
  76     for (c = at2con->index[at]; c < at2con->index[at+1]; c++)
  77     {
  78         con = at2con->a[c];
  79         /* Do not walk over already used constraints */
  80         bUse = TRUE;
  81         for (a1 = 0; a1 < depth; a1++)
  82         {
  83             if (con == path[a1])
  84             {
  85                 bUse = FALSE;
  86             }
  87         }
  88         if (bUse)
  89         {
  90             ia = constr_iatomptr(ncon1, ia1, ia2, con);
  91             /* Flexible constraints currently have length 0, which is incorrect */
  92             if (!bTopB)
  93             {
  94                 len = iparams[ia[0]].constr.dA;
  95             }
  96             else
  97             {
  98                 len = iparams[ia[0]].constr.dB;
  99             }
 100             /* In the worst case the bond directions alternate */
 101             if (nc % 2 == 0)
 102             {
 103                 rn0 = r0 + len;
 104                 rn1 = r1;
 105             }
 106             else
 107             {
 108                 rn0 = r0;
 109                 rn1 = r1 + len;
 110             }
 111             /* Assume angles of 120 degrees between all bonds */
 112             if (rn0*rn0 + rn1*rn1 + rn0*rn1 > *r2max)
 113             {
 114                 *r2max = rn0*rn0 + rn1*rn1 + r0*rn1;
 115                 if (debug)
 116                 {
 117                     fprintf(debug, "Found longer constraint distance: r0 %5.3f r1 %5.3f rmax %5.3f\n", rn0, rn1, sqrt(*r2max));
 118                     for (a1 = 0; a1 < depth; a1++)
 119                     {
 120                         fprintf(debug, " %d %5.3f",
 121                                 path[a1],
 122                                 iparams[constr_iatomptr(ncon1, ia1, ia2, con)[0]].constr.dA);
 123                     }
 124                     fprintf(debug, " %d %5.3f\n", con, len);
 125                 }
 126             }
 127             /* Limit the number of recursions to 1000*nc,
 128              * so a call does not take more than a second,
 129              * even for highly connected systems.
 130              */
 131             if (depth + 1 < nc && *count < 1000*nc)
 132             {
 133                 if (ia[1] == at)
 134                 {
 135                     a1 = ia[2];
 136                 }
 137                 else
 138                 {
 139                     a1 = ia[1];
 140                 }
 141                 /* Recursion */
 142                 path[depth] = con;
 143                 constr_recur(at2con, ilist, iparams,
 144                              bTopB, a1, depth+1, nc, path, rn0, rn1, r2max, count);
 145                 path[depth] = -1;
 146             }
 147         }
 148     }
 149 }
 150
 151 static real constr_r_max_moltype(const gmx_moltype_t *molt,
 152                                  const t_iparams     *iparams,
 153                                  const t_inputrec    *ir)
 154 {
 155     int      natoms, nflexcon, *path, at, count;
 156
 157     t_blocka at2con;
 158     real     r0, r1, r2maxA, r2maxB, rmax, lam0, lam1;
 159
 160     if (molt->ilist[F_CONSTR].nr   == 0 &&
 161         molt->ilist[F_CONSTRNC].nr == 0)
 162     {
 163         return 0;
 164     }
 165
 166     natoms = molt->atoms.nr;
 167
 168     at2con = make_at2con(0, natoms, molt->ilist, iparams,
 169                          EI_DYNAMICS(ir->eI), &nflexcon);
 170     snew(path, 1+ir->nProjOrder);
 171     for (at = 0; at < 1+ir->nProjOrder; at++)
 172     {
 173         path[at] = -1;
 174     }
 175
 176     r2maxA = 0;
 177     for (at = 0; at < natoms; at++)
 178     {
 179         r0 = 0;
 180         r1 = 0;
 181
 182         count = 0;
 183         constr_recur(&at2con, molt->ilist, iparams,
 184                      FALSE, at, 0, 1+ir->nProjOrder, path, r0, r1, &r2maxA, &count);
 185     }
 186     if (ir->efep == efepNO)
 187     {
 188         rmax = sqrt(r2maxA);
 189     }
 190     else
 191     {
 192         r2maxB = 0;
 193         for (at = 0; at < natoms; at++)
 194         {
 195             r0    = 0;
 196             r1    = 0;
 197             count = 0;
 198             constr_recur(&at2con, molt->ilist, iparams,
 199                          TRUE, at, 0, 1+ir->nProjOrder, path, r0, r1, &r2maxB, &count);
 200         }
 201         lam0 = ir->fepvals->init_lambda;
 202         if (EI_DYNAMICS(ir->eI))
 203         {
 204             lam0 += ir->init_step*ir->fepvals->delta_lambda;
 205         }
 206         rmax = (1 - lam0)*sqrt(r2maxA) + lam0*sqrt(r2maxB);
 207         if (EI_DYNAMICS(ir->eI))
 208         {
 209             lam1 = ir->fepvals->init_lambda + (ir->init_step + ir->nsteps)*ir->fepvals->delta_lambda;
 210             rmax = std::max(rmax, (1 - lam1)*std::sqrt(r2maxA) + lam1*std::sqrt(r2maxB));
 211         }
 212     }
 213
 214     done_blocka(&at2con);
 215     sfree(path);
 216
 217     return rmax;
 218 }
 219
 220 real constr_r_max(FILE *fplog, const gmx_mtop_t *mtop, const t_inputrec *ir)
 221 {
 222     real rmax = 0;
 223     for (const gmx_moltype_t &molt : mtop->moltype)
 224     {
 225         rmax = std::max(rmax,
 226                         constr_r_max_moltype(&molt,
 227                                              mtop->ffparams.iparams, ir));
 228     }
 229
 230     if (fplog)
 231     {
 232         fprintf(fplog, "Maximum distance for %d constraints, at 120 deg. angles, all-trans: %.3f nm\n", 1+ir->nProjOrder, rmax);
 233     }
 234
 235     return rmax;
 236 }