src/gromacs/mdlib/constraintrange.cpp

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  38 /* This file is completely threadsafe - keep it that way! */
  39 #include "gmxpre.h"
  40
  41 #include "constraintrange.h"
  42
  43 #include <cmath>
  44
  45 #include <algorithm>
  46
  47 #include "gromacs/mdlib/constr.h"
  48 #include "gromacs/mdtypes/inputrec.h"
  49 #include "gromacs/topology/mtop_util.h"
  50 #include "gromacs/utility/basedefinitions.h"
  51 #include "gromacs/utility/fatalerror.h"
  52 #include "gromacs/utility/listoflists.h"
  53 #include "gromacs/utility/logger.h"
  54 #include "gromacs/utility/real.h"
  55
  56 namespace gmx
  57 {
  58
  59 //! Recursing function to help find all adjacent constraints.
  60 static void constr_recur(const ListOfLists<int>&        at2con,
  61                          const InteractionLists&        ilist,
  62                          gmx::ArrayRef<const t_iparams> iparams,
  63                          gmx_bool                       bTopB,
  64                          int                            at,
  65                          int                            depth,
  66                          int                            nc,
  67                          ArrayRef<int>                  path,
  68                          real                           r0,
  69                          real                           r1,
  70                          real*                          r2max,
  71                          int*                           count)
  72 {
  73     gmx_bool bUse;
  74     real     len, rn0, rn1;
  75
  76     (*count)++;
  77
  78     gmx::ArrayRef<const int> ia1 = ilist[F_CONSTR].iatoms;
  79     gmx::ArrayRef<const int> ia2 = ilist[F_CONSTRNC].iatoms;
  80
  81     /* Loop over all constraints connected to this atom */
  82     for (const int con : at2con[at])
  83     {
  84         /* Do not walk over already used constraints */
  85         bUse = TRUE;
  86         for (int a1 = 0; a1 < depth; a1++)
  87         {
  88             if (con == path[a1])
  89             {
  90                 bUse = FALSE;
  91             }
  92         }
  93         if (bUse)
  94         {
  95             const int* ia = constr_iatomptr(ia1, ia2, con);
  96             /* Flexible constraints currently have length 0, which is incorrect */
  97             if (!bTopB)
  98             {
  99                 len = iparams[ia[0]].constr.dA;
 100             }
 101             else
 102             {
 103                 len = iparams[ia[0]].constr.dB;
 104             }
 105             /* In the worst case the bond directions alternate */
 106             if (nc % 2 == 0)
 107             {
 108                 rn0 = r0 + len;
 109                 rn1 = r1;
 110             }
 111             else
 112             {
 113                 rn0 = r0;
 114                 rn1 = r1 + len;
 115             }
 116             /* Assume angles of 120 degrees between all bonds */
 117             if (rn0 * rn0 + rn1 * rn1 + rn0 * rn1 > *r2max)
 118             {
 119                 *r2max = rn0 * rn0 + rn1 * rn1 + r0 * rn1;
 120                 if (debug)
 121                 {
 122                     fprintf(debug,
 123                             "Found longer constraint distance: r0 %5.3f r1 %5.3f rmax %5.3f\n", rn0,
 124                             rn1, sqrt(*r2max));
 125                     for (int a1 = 0; a1 < depth; a1++)
 126                     {
 127                         fprintf(debug, " %d %5.3f", path[a1],
 128                                 iparams[constr_iatomptr(ia1, ia2, con)[0]].constr.dA);
 129                     }
 130                     fprintf(debug, " %d %5.3f\n", con, len);
 131                 }
 132             }
 133             /* Limit the number of recursions to 1000*nc,
 134              * so a call does not take more than a second,
 135              * even for highly connected systems.
 136              */
 137             if (depth + 1 < nc && *count < 1000 * nc)
 138             {
 139                 int a1;
 140                 if (ia[1] == at)
 141                 {
 142                     a1 = ia[2];
 143                 }
 144                 else
 145                 {
 146                     a1 = ia[1];
 147                 }
 148                 /* Recursion */
 149                 path[depth] = con;
 150                 constr_recur(at2con, ilist, iparams, bTopB, a1, depth + 1, nc, path, rn0, rn1, r2max, count);
 151                 path[depth] = -1;
 152             }
 153         }
 154     }
 155 }
 156
 157 //! Find the interaction radius needed for constraints for this molecule type.
 158 static real constr_r_max_moltype(const gmx_moltype_t*           molt,
 159                                  gmx::ArrayRef<const t_iparams> iparams,
 160                                  const t_inputrec*              ir)
 161 {
 162     int natoms, at, count;
 163
 164     real r0, r1, r2maxA, r2maxB, rmax, lam0, lam1;
 165
 166     if (molt->ilist[F_CONSTR].empty() && molt->ilist[F_CONSTRNC].empty())
 167     {
 168         return 0;
 169     }
 170
 171     natoms = molt->atoms.nr;
 172
 173     const ListOfLists<int> at2con =
 174             make_at2con(*molt, iparams, flexibleConstraintTreatment(EI_DYNAMICS(ir->eI)));
 175     std::vector<int> path(1 + ir->nProjOrder);
 176     for (at = 0; at < 1 + ir->nProjOrder; at++)
 177     {
 178         path[at] = -1;
 179     }
 180
 181     r2maxA = 0;
 182     for (at = 0; at < natoms; at++)
 183     {
 184         r0 = 0;
 185         r1 = 0;
 186
 187         count = 0;
 188         constr_recur(at2con, molt->ilist, iparams, FALSE, at, 0, 1 + ir->nProjOrder, path, r0, r1,
 189                      &r2maxA, &count);
 190     }
 191     if (ir->efep == efepNO)
 192     {
 193         rmax = sqrt(r2maxA);
 194     }
 195     else
 196     {
 197         r2maxB = 0;
 198         for (at = 0; at < natoms; at++)
 199         {
 200             r0    = 0;
 201             r1    = 0;
 202             count = 0;
 203             constr_recur(at2con, molt->ilist, iparams, TRUE, at, 0, 1 + ir->nProjOrder, path, r0,
 204                          r1, &r2maxB, &count);
 205         }
 206         lam0 = ir->fepvals->init_lambda;
 207         if (EI_DYNAMICS(ir->eI))
 208         {
 209             lam0 += ir->init_step * ir->fepvals->delta_lambda;
 210         }
 211         rmax = (1 - lam0) * sqrt(r2maxA) + lam0 * sqrt(r2maxB);
 212         if (EI_DYNAMICS(ir->eI))
 213         {
 214             lam1 = ir->fepvals->init_lambda + (ir->init_step + ir->nsteps) * ir->fepvals->delta_lambda;
 215             rmax = std::max(rmax, (1 - lam1) * std::sqrt(r2maxA) + lam1 * std::sqrt(r2maxB));
 216         }
 217     }
 218
 219     return rmax;
 220 }
 221
 222 real constr_r_max(const MDLogger& mdlog, const gmx_mtop_t* mtop, const t_inputrec* ir)
 223 {
 224     real rmax = 0;
 225     for (const gmx_moltype_t& molt : mtop->moltype)
 226     {
 227         rmax = std::max(rmax, constr_r_max_moltype(&molt, mtop->ffparams.iparams, ir));
 228     }
 229
 230     GMX_LOG(mdlog.info)
 231             .appendTextFormatted(
 232                     "Maximum distance for %d constraints, at 120 deg. angles, all-trans: %.3f nm",
 233                     1 + ir->nProjOrder, rmax);
 234
 235     return rmax;
 236 }
 237
 238 } // namespace gmx