src/gromacs/gmxpreprocess/topshake.cpp

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   6  * Copyright (c) 2013,2014,2015,2018,2019, 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/smalloc.h"
  55
  56 static int count_hydrogens (char ***atomname, int nra, gmx::ArrayRef<const int> a)
  57 {
  58     int  nh;
  59
  60     if (!atomname)
  61     {
  62         gmx_fatal(FARGS, "Cannot call count_hydrogens with no atomname (%s %d)",
  63                   __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)
  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                 printf("turning H bonds into constraints...\n");
  88                 break;
  89             case eshALLBONDS:
  90                 printf("turning all bonds into constraints...\n");
  91                 break;
  92             case eshHANGLES:
  93                 printf("turning all bonds and H angles into constraints...\n");
  94                 break;
  95             case eshALLANGLES:
  96                 printf("turning all bonds and angles into constraints...\n");
  97                 break;
  98             default:
  99                 gmx_fatal(FARGS, "Invalid option for make_shake (%d)", nshake);
 100         }
 101
 102         if ((nshake == eshHANGLES) || (nshake == eshALLANGLES))
 103         {
 104             /* Add all the angles with hydrogens to the shake list
 105              * and remove them from the bond list
 106              */
 107             for (int ftype = 0; (ftype < F_NRE); ftype++)
 108             {
 109                 if (interaction_function[ftype].flags & IF_BTYPE)
 110                 {
 111                     InteractionsOfType *bonds = &(plist[ftype]);
 112
 113                     for (int ftype_a = 0; (gmx::ssize(*bonds) > 0 && ftype_a < F_NRE); ftype_a++)
 114                     {
 115                         if (interaction_function[ftype_a].flags & IF_ATYPE)
 116                         {
 117                             InteractionsOfType *pr = &(plist[ftype_a]);
 118
 119                             for (auto parm = pr->interactionTypes.begin(); parm != pr->interactionTypes.end(); )
 120                             {
 121                                 const InteractionOfType *ang = &(*parm);
 122 #ifdef DEBUG
 123                                 printf("Angle: %d-%d-%d\n", ang->ai(), ang->aj(), ang->ak());
 124 #endif
 125                                 int numhydrogens = count_hydrogens(info, 3, ang->atoms());
 126                                 if ((nshake == eshALLANGLES) ||
 127                                     (numhydrogens > 1) ||
 128                                     (numhydrogens == 1 && toupper(**(info[ang->aj()])) == 'O'))
 129                                 {
 130                                     /* Can only add hydrogen angle shake, if the two bonds
 131                                      * are constrained.
 132                                      * append this angle to the shake list
 133                                      */
 134                                     std::vector<int> atomNumbers = {ang->ai(), ang->ak()};
 135
 136                                     /* Calculate length of constraint */
 137                                     bool bFound = false;
 138                                     b_ij   = b_jk = 0.0;
 139                                     for (const auto &bond : bonds->interactionTypes)
 140                                     {
 141                                         if (((bond.ai() == ang->ai()) &&
 142                                              (bond.aj() == ang->aj())) ||
 143                                             ((bond.ai() == ang->aj()) &&
 144                                              (bond.aj() == ang->ai())))
 145                                         {
 146                                             b_ij = bond.c0();
 147                                         }
 148                                         if (((bond.ai() == ang->ak()) &&
 149                                              (bond.aj() == ang->aj())) ||
 150                                             ((bond.ai() == ang->aj()) &&
 151                                              (bond.aj() == ang->ak())))
 152                                         {
 153                                             b_jk = bond.c0();
 154                                         }
 155                                         bFound = (b_ij != 0.0) && (b_jk != 0.0);
 156                                     }
 157                                     if (bFound)
 158                                     {
 159                                         real              param = std::sqrt( b_ij*b_ij + b_jk*b_jk -
 160                                                                              2.0*b_ij*b_jk*cos(DEG2RAD*ang->c0()));
 161                                         std::vector<real> forceParm = {param, param};
 162                                         /* apply law of cosines */
 163 #ifdef DEBUG
 164                                         printf("p: %d, q: %d, dist: %12.5e\n", atomNumbers[0],
 165                                                atomNumbers[1], forceParm[0]);
 166 #endif
 167                                         add_param_to_list (&(plist[F_CONSTR]), InteractionOfType(atomNumbers, forceParm));
 168                                         /* move the last bond to this position */
 169                                         *parm = *(pr->interactionTypes.end() - 1);
 170                                         pr->interactionTypes.erase(pr->interactionTypes.end() - 1);
 171                                     }
 172                                 }
 173                                 else
 174                                 {
 175                                     ++parm;
 176                                 }
 177                             }
 178                         } /* if IF_ATYPE */
 179                     }     /* for ftype_A */
 180                 }         /* if IF_BTYPE */
 181             }             /* for ftype */
 182         }                 /* if shake angles */
 183
 184         /* Add all the bonds with hydrogens to the shake list
 185          * and remove them from the bond list
 186          */
 187         for (int ftype = 0; (ftype < F_NRE); ftype++)
 188         {
 189             if (interaction_function[ftype].flags & IF_BTYPE)
 190             {
 191                 InteractionsOfType *pr = &(plist[ftype]);
 192                 for (auto parm = pr->interactionTypes.begin(); parm != pr->interactionTypes.end(); )
 193                 {
 194                     if ( (nshake != eshHBONDS) ||
 195                          (count_hydrogens (info, 2, parm->atoms()) > 0) )
 196                     {
 197                         /* append this bond to the shake list */
 198                         std::vector<int>  atomNumbers = {parm->ai(), parm->aj()};
 199                         std::vector<real> forceParm   = { parm->c0(), parm->c2()};
 200                         add_param_to_list (&(plist[F_CONSTR]), InteractionOfType(atomNumbers, forceParm));
 201                         parm = pr->interactionTypes.erase(parm);
 202                     }
 203                     else
 204                     {
 205                         ++parm;
 206                     }
 207                 }
 208             }
 209         }
 210     }
 211 }