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