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 namespace gmx
  56 {
  57
  58 //! Recursing function to help find all adjacent constraints.
  59 static void constr_recur(const t_blocka *at2con,
  60                          const t_ilist *ilist, const t_iparams *iparams,
  61                          gmx_bool bTopB,
  62                          int at, int depth, int nc, int *path,
  63                          real r0, real r1, real *r2max,
  64                          int *count)
  65 {
  66     int      ncon1;
  67     t_iatom *ia1, *ia2;
  68     int      c, con, a1;
  69     gmx_bool bUse;
  70     t_iatom *ia;
  71     real     len, rn0, rn1;
  72
  73     (*count)++;
  74
  75     ncon1 = ilist[F_CONSTR].nr/3;
  76     ia1   = ilist[F_CONSTR].iatoms;
  77     ia2   = ilist[F_CONSTRNC].iatoms;
  78
  79     /* Loop over all constraints connected to this atom */
  80     for (c = at2con->index[at]; c < at2con->index[at+1]; c++)
  81     {
  82         con = at2con->a[c];
  83         /* Do not walk over already used constraints */
  84         bUse = TRUE;
  85         for (a1 = 0; a1 < depth; a1++)
  86         {
  87             if (con == path[a1])
  88             {
  89                 bUse = FALSE;
  90             }
  91         }
  92         if (bUse)
  93         {
  94             ia = constr_iatomptr(ncon1, 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, "Found longer constraint distance: r0 %5.3f r1 %5.3f rmax %5.3f\n", rn0, rn1, sqrt(*r2max));
 122                     for (a1 = 0; a1 < depth; a1++)
 123                     {
 124                         fprintf(debug, " %d %5.3f",
 125                                 path[a1],
 126                                 iparams[constr_iatomptr(ncon1, ia1, ia2, con)[0]].constr.dA);
 127                     }
 128                     fprintf(debug, " %d %5.3f\n", con, len);
 129                 }
 130             }
 131             /* Limit the number of recursions to 1000*nc,
 132              * so a call does not take more than a second,
 133              * even for highly connected systems.
 134              */
 135             if (depth + 1 < nc && *count < 1000*nc)
 136             {
 137                 if (ia[1] == at)
 138                 {
 139                     a1 = ia[2];
 140                 }
 141                 else
 142                 {
 143                     a1 = ia[1];
 144                 }
 145                 /* Recursion */
 146                 path[depth] = con;
 147                 constr_recur(at2con, ilist, iparams,
 148                              bTopB, a1, depth+1, nc, path, rn0, rn1, r2max, count);
 149                 path[depth] = -1;
 150             }
 151         }
 152     }
 153 }
 154
 155 //! Find the interaction radius needed for constraints for this molecule type.
 156 static real constr_r_max_moltype(const gmx_moltype_t *molt,
 157                                  const t_iparams     *iparams,
 158                                  const t_inputrec    *ir)
 159 {
 160     int      natoms, *path, at, count;
 161
 162     t_blocka at2con;
 163     real     r0, r1, r2maxA, r2maxB, rmax, lam0, lam1;
 164
 165     if (molt->ilist[F_CONSTR].nr   == 0 &&
 166         molt->ilist[F_CONSTRNC].nr == 0)
 167     {
 168         return 0;
 169     }
 170
 171     natoms = molt->atoms.nr;
 172
 173     at2con = make_at2con(natoms, molt->ilist, iparams,
 174                          flexibleConstraintTreatment(EI_DYNAMICS(ir->eI)));
 175     snew(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,
 189                      FALSE, at, 0, 1+ir->nProjOrder, path, r0, r1, &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,
 204                          TRUE, at, 0, 1+ir->nProjOrder, path, r0, 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     done_blocka(&at2con);
 220     sfree(path);
 221
 222     return rmax;
 223 }
 224
 225 real constr_r_max(FILE *fplog, const gmx_mtop_t *mtop, const t_inputrec *ir)
 226 {
 227     real rmax = 0;
 228     for (const gmx_moltype_t &molt : mtop->moltype)
 229     {
 230         rmax = std::max(rmax,
 231                         constr_r_max_moltype(&molt,
 232                                              mtop->ffparams.iparams, ir));
 233     }
 234
 235     if (fplog)
 236     {
 237         fprintf(fplog, "Maximum distance for %d constraints, at 120 deg. angles, all-trans: %.3f nm\n", 1+ir->nProjOrder, rmax);
 238     }
 239
 240     return rmax;
 241 }
 242
 243 } // namespace