src/gromacs/mdlib/constraintrange.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   5  * Copyright (c) 2001-2004, The GROMACS development team.
   6  * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
   7  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   8  * and including many others, as listed in the AUTHORS file in the
   9  * top-level source directory and at http://www.gromacs.org.
  10  *
  11  * GROMACS is free software; you can redistribute it and/or
  12  * modify it under the terms of the GNU Lesser General Public License
  13  * as published by the Free Software Foundation; either version 2.1
  14  * of the License, or (at your option) any later version.
  15  *
  16  * GROMACS is distributed in the hope that it will be useful,
  17  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  18  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  19  * Lesser General Public License for more details.
  20  *
  21  * You should have received a copy of the GNU Lesser General Public
  22  * License along with GROMACS; if not, see
  23  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  24  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  25  *
  26  * If you want to redistribute modifications to GROMACS, please
  27  * consider that scientific software is very special. Version
  28  * control is crucial - bugs must be traceable. We will be happy to
  29  * consider code for inclusion in the official distribution, but
  30  * derived work must not be called official GROMACS. Details are found
  31  * in the README & COPYING files - if they are missing, get the
  32  * official version at http://www.gromacs.org.
  33  *
  34  * To help us fund GROMACS development, we humbly ask that you cite
  35  * the research papers on the package. Check out http://www.gromacs.org.
  36  */
  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/logger.h"
  53 #include "gromacs/utility/real.h"
  54 #include "gromacs/utility/smalloc.h"
  55
  56 namespace gmx
  57 {
  58
  59 //! Recursing function to help find all adjacent constraints.
  60 static void constr_recur(const t_blocka *at2con,
  61                          const InteractionLists &ilist,
  62                          gmx::ArrayRef<const t_iparams> iparams,
  63                          gmx_bool bTopB,
  64                          int at, int depth, int nc, int *path,
  65                          real r0, real r1, real *r2max,
  66                          int *count)
  67 {
  68     int      c, con, a1;
  69     gmx_bool bUse;
  70     real     len, rn0, rn1;
  71
  72     (*count)++;
  73
  74     gmx::ArrayRef<const int> ia1 = ilist[F_CONSTR].iatoms;
  75     gmx::ArrayRef<const int> ia2 = ilist[F_CONSTRNC].iatoms;
  76
  77     /* Loop over all constraints connected to this atom */
  78     for (c = at2con->index[at]; c < at2con->index[at+1]; c++)
  79     {
  80         con = at2con->a[c];
  81         /* Do not walk over already used constraints */
  82         bUse = TRUE;
  83         for (a1 = 0; a1 < depth; a1++)
  84         {
  85             if (con == path[a1])
  86             {
  87                 bUse = FALSE;
  88             }
  89         }
  90         if (bUse)
  91         {
  92             const int *ia = constr_iatomptr(ia1, ia2, con);
  93             /* Flexible constraints currently have length 0, which is incorrect */
  94             if (!bTopB)
  95             {
  96                 len = iparams[ia[0]].constr.dA;
  97             }
  98             else
  99             {
 100                 len = iparams[ia[0]].constr.dB;
 101             }
 102             /* In the worst case the bond directions alternate */
 103             if (nc % 2 == 0)
 104             {
 105                 rn0 = r0 + len;
 106                 rn1 = r1;
 107             }
 108             else
 109             {
 110                 rn0 = r0;
 111                 rn1 = r1 + len;
 112             }
 113             /* Assume angles of 120 degrees between all bonds */
 114             if (rn0*rn0 + rn1*rn1 + rn0*rn1 > *r2max)
 115             {
 116                 *r2max = rn0*rn0 + rn1*rn1 + r0*rn1;
 117                 if (debug)
 118                 {
 119                     fprintf(debug, "Found longer constraint distance: r0 %5.3f r1 %5.3f rmax %5.3f\n", rn0, rn1, sqrt(*r2max));
 120                     for (a1 = 0; a1 < depth; a1++)
 121                     {
 122                         fprintf(debug, " %d %5.3f",
 123                                 path[a1],
 124                                 iparams[constr_iatomptr(ia1, ia2, con)[0]].constr.dA);
 125                     }
 126                     fprintf(debug, " %d %5.3f\n", con, len);
 127                 }
 128             }
 129             /* Limit the number of recursions to 1000*nc,
 130              * so a call does not take more than a second,
 131              * even for highly connected systems.
 132              */
 133             if (depth + 1 < nc && *count < 1000*nc)
 134             {
 135                 if (ia[1] == at)
 136                 {
 137                     a1 = ia[2];
 138                 }
 139                 else
 140                 {
 141                     a1 = ia[1];
 142                 }
 143                 /* Recursion */
 144                 path[depth] = con;
 145                 constr_recur(at2con, ilist, iparams,
 146                              bTopB, a1, depth+1, nc, path, rn0, rn1, r2max, count);
 147                 path[depth] = -1;
 148             }
 149         }
 150     }
 151 }
 152
 153 //! Find the interaction radius needed for constraints for this molecule type.
 154 static real constr_r_max_moltype(const gmx_moltype_t            *molt,
 155                                  gmx::ArrayRef<const t_iparams>  iparams,
 156                                  const t_inputrec               *ir)
 157 {
 158     int      natoms, *path, at, count;
 159
 160     t_blocka at2con;
 161     real     r0, r1, r2maxA, r2maxB, rmax, lam0, lam1;
 162
 163     if (molt->ilist[F_CONSTR].size()   == 0 &&
 164         molt->ilist[F_CONSTRNC].size() == 0)
 165     {
 166         return 0;
 167     }
 168
 169     natoms = molt->atoms.nr;
 170
 171     at2con = make_at2con(*molt, iparams,
 172                          flexibleConstraintTreatment(EI_DYNAMICS(ir->eI)));
 173     snew(path, 1+ir->nProjOrder);
 174     for (at = 0; at < 1+ir->nProjOrder; at++)
 175     {
 176         path[at] = -1;
 177     }
 178
 179     r2maxA = 0;
 180     for (at = 0; at < natoms; at++)
 181     {
 182         r0 = 0;
 183         r1 = 0;
 184
 185         count = 0;
 186         constr_recur(&at2con, molt->ilist, iparams,
 187                      FALSE, at, 0, 1+ir->nProjOrder, path, r0, r1, &r2maxA, &count);
 188     }
 189     if (ir->efep == efepNO)
 190     {
 191         rmax = sqrt(r2maxA);
 192     }
 193     else
 194     {
 195         r2maxB = 0;
 196         for (at = 0; at < natoms; at++)
 197         {
 198             r0    = 0;
 199             r1    = 0;
 200             count = 0;
 201             constr_recur(&at2con, molt->ilist, iparams,
 202                          TRUE, at, 0, 1+ir->nProjOrder, path, r0, r1, &r2maxB, &count);
 203         }
 204         lam0 = ir->fepvals->init_lambda;
 205         if (EI_DYNAMICS(ir->eI))
 206         {
 207             lam0 += ir->init_step*ir->fepvals->delta_lambda;
 208         }
 209         rmax = (1 - lam0)*sqrt(r2maxA) + lam0*sqrt(r2maxB);
 210         if (EI_DYNAMICS(ir->eI))
 211         {
 212             lam1 = ir->fepvals->init_lambda + (ir->init_step + ir->nsteps)*ir->fepvals->delta_lambda;
 213             rmax = std::max(rmax, (1 - lam1)*std::sqrt(r2maxA) + lam1*std::sqrt(r2maxB));
 214         }
 215     }
 216
 217     done_blocka(&at2con);
 218     sfree(path);
 219
 220     return rmax;
 221 }
 222
 223 real constr_r_max(const MDLogger &mdlog, const gmx_mtop_t *mtop, const t_inputrec *ir)
 224 {
 225     real rmax = 0;
 226     for (const gmx_moltype_t &molt : mtop->moltype)
 227     {
 228         rmax = std::max(rmax,
 229                         constr_r_max_moltype(&molt,
 230                                              mtop->ffparams.iparams, ir));
 231     }
 232
 233     GMX_LOG(mdlog.info).appendTextFormatted(
 234             "Maximum distance for %d constraints, at 120 deg. angles, all-trans: %.3f nm",
 235             1+ir->nProjOrder, rmax);
 236
 237     return rmax;
 238 }
 239
 240 }  // namespace gmx