src/gromacs/gmxpreprocess/topshake.cpp

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   6  * Copyright (c) 2013,2014,2015,2018,2019,2020, by the GROMACS development team, led by
   7  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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  37 /* This file is completely threadsafe - keep it that way! */
  38 #include "gmxpre.h"
  39
  40 #include "topshake.h"
  41
  42 #include <cctype>
  43 #include <cmath>
  44
  45 #include "gromacs/gmxpreprocess/grompp_impl.h"
  46 #include "gromacs/gmxpreprocess/notset.h"
  47 #include "gromacs/gmxpreprocess/readir.h"
  48 #include "gromacs/gmxpreprocess/topdirs.h"
  49 #include "gromacs/gmxpreprocess/toppush.h"
  50 #include "gromacs/gmxpreprocess/toputil.h"
  51 #include "gromacs/math/units.h"
  52 #include "gromacs/topology/ifunc.h"
  53 #include "gromacs/utility/fatalerror.h"
  54 #include "gromacs/utility/logger.h"
  55 #include "gromacs/utility/smalloc.h"
  56
  57 static int count_hydrogens(char*** atomname, int nra, gmx::ArrayRef<const int> a)
  58 {
  59     int nh;
  60
  61     if (!atomname)
  62     {
  63         gmx_fatal(FARGS, "Cannot call count_hydrogens with no atomname (%s %d)", __FILE__, __LINE__);
  64     }
  65
  66     nh = 0;
  67     for (int i = 0; (i < nra); i++)
  68     {
  69         if (toupper(**(atomname[a[i]])) == 'H')
  70         {
  71             nh++;
  72         }
  73     }
  74
  75     return nh;
  76 }
  77
  78 void make_shake(gmx::ArrayRef<InteractionsOfType> plist, t_atoms* atoms, int nshake, const gmx::MDLogger& logger)
  79 {
  80     char*** info = atoms->atomname;
  81     real    b_ij, b_jk;
  82     if (nshake != eshNONE)
  83     {
  84         switch (nshake)
  85         {
  86             case eshHBONDS:
  87                 GMX_LOG(logger.info)
  88                         .asParagraph()
  89                         .appendTextFormatted("turning H bonds into constraints...");
  90                 break;
  91             case eshALLBONDS:
  92                 GMX_LOG(logger.info)
  93                         .asParagraph()
  94                         .appendTextFormatted("turning all bonds into constraints...");
  95                 break;
  96             case eshHANGLES:
  97                 GMX_LOG(logger.info)
  98                         .asParagraph()
  99                         .appendTextFormatted("turning all bonds and H angles into constraints...");
 100                 break;
 101             case eshALLANGLES:
 102                 GMX_LOG(logger.info)
 103                         .asParagraph()
 104                         .appendTextFormatted("turning all bonds and angles into constraints...");
 105                 break;
 106             default: gmx_fatal(FARGS, "Invalid option for make_shake (%d)", nshake);
 107         }
 108
 109         if ((nshake == eshHANGLES) || (nshake == eshALLANGLES))
 110         {
 111             /* Add all the angles with hydrogens to the shake list
 112              * and remove them from the bond list
 113              */
 114             for (int ftype = 0; (ftype < F_NRE); ftype++)
 115             {
 116                 if (interaction_function[ftype].flags & IF_CHEMBOND)
 117                 {
 118                     InteractionsOfType* bonds = &(plist[ftype]);
 119
 120                     for (int ftype_a = 0; (gmx::ssize(*bonds) > 0 && ftype_a < F_NRE); ftype_a++)
 121                     {
 122                         if (interaction_function[ftype_a].flags & IF_ATYPE)
 123                         {
 124                             InteractionsOfType* pr = &(plist[ftype_a]);
 125
 126                             for (auto parm = pr->interactionTypes.begin();
 127                                  parm != pr->interactionTypes.end();)
 128                             {
 129                                 const InteractionOfType* ang = &(*parm);
 130 #ifdef DEBUG
 131                                 GMX_LOG(logger.info)
 132                                         .asParagraph()
 133                                         .appendTextFormatted(
 134                                                 "Angle: %d-%d-%d", ang->ai(), ang->aj(), ang->ak());
 135 #endif
 136                                 int numhydrogens = count_hydrogens(info, 3, ang->atoms());
 137                                 if ((nshake == eshALLANGLES) || (numhydrogens > 1)
 138                                     || (numhydrogens == 1 && toupper(**(info[ang->aj()])) == 'O'))
 139                                 {
 140                                     /* Can only add hydrogen angle shake, if the two bonds
 141                                      * are constrained.
 142                                      * append this angle to the shake list
 143                                      */
 144                                     std::vector<int> atomNumbers = { ang->ai(), ang->ak() };
 145
 146                                     /* Calculate length of constraint */
 147                                     bool bFound = false;
 148                                     b_ij = b_jk = 0.0;
 149                                     for (const auto& bond : bonds->interactionTypes)
 150                                     {
 151                                         if (((bond.ai() == ang->ai()) && (bond.aj() == ang->aj()))
 152                                             || ((bond.ai() == ang->aj()) && (bond.aj() == ang->ai())))
 153                                         {
 154                                             b_ij = bond.c0();
 155                                         }
 156                                         if (((bond.ai() == ang->ak()) && (bond.aj() == ang->aj()))
 157                                             || ((bond.ai() == ang->aj()) && (bond.aj() == ang->ak())))
 158                                         {
 159                                             b_jk = bond.c0();
 160                                         }
 161                                         bFound = (b_ij != 0.0) && (b_jk != 0.0);
 162                                     }
 163                                     if (bFound)
 164                                     {
 165                                         real param = std::sqrt(b_ij * b_ij + b_jk * b_jk
 166                                                                - 2.0 * b_ij * b_jk
 167                                                                          * cos(DEG2RAD * ang->c0()));
 168                                         std::vector<real> forceParm = { param, param };
 169                                         if (ftype == F_CONNBONDS || ftype_a == F_CONNBONDS)
 170                                         {
 171                                             gmx_fatal(FARGS,
 172                                                       "Can not constrain all angles when they "
 173                                                       "involved bonds of type %s",
 174                                                       interaction_function[F_CONNBONDS].longname);
 175                                         }
 176                                         /* apply law of cosines */
 177 #ifdef DEBUG
 178                                         GMX_LOG(logger.info)
 179                                                 .asParagraph()
 180                                                 .appendTextFormatted("p: %d, q: %d, dist: %12.5e",
 181                                                                      atomNumbers[0],
 182                                                                      atomNumbers[1],
 183                                                                      forceParm[0]);
 184 #endif
 185                                         add_param_to_list(&(plist[F_CONSTR]),
 186                                                           InteractionOfType(atomNumbers, forceParm));
 187                                         /* move the last bond to this position */
 188                                         *parm = *(pr->interactionTypes.end() - 1);
 189                                         pr->interactionTypes.erase(pr->interactionTypes.end() - 1);
 190                                     }
 191                                 }
 192                                 else
 193                                 {
 194                                     ++parm;
 195                                 }
 196                             }
 197                         } /* if IF_ATYPE */
 198                     }     /* for ftype_A */
 199                 }         /* if IF_BTYPE */
 200             }             /* for ftype */
 201         }                 /* if shake angles */
 202
 203         /* Add all the bonds with hydrogens to the shake list
 204          * and remove them from the bond list
 205          */
 206         for (int ftype = 0; (ftype < F_NRE); ftype++)
 207         {
 208             if (interaction_function[ftype].flags & IF_BTYPE)
 209             {
 210                 InteractionsOfType* pr = &(plist[ftype]);
 211                 for (auto parm = pr->interactionTypes.begin(); parm != pr->interactionTypes.end();)
 212                 {
 213                     if ((nshake != eshHBONDS) || (count_hydrogens(info, 2, parm->atoms()) > 0))
 214                     {
 215                         /* append this bond to the shake list */
 216                         std::vector<int>  atomNumbers = { parm->ai(), parm->aj() };
 217                         std::vector<real> forceParm   = { parm->c0(), parm->c2() };
 218                         add_param_to_list(&(plist[F_CONSTR]), InteractionOfType(atomNumbers, forceParm));
 219                         parm = pr->interactionTypes.erase(parm);
 220                     }
 221                     else
 222                     {
 223                         ++parm;
 224                     }
 225                 }
 226             }
 227         }
 228     }
 229 }