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)", __FILE__, __LINE__);
  63     }
  64
  65     nh = 0;
  66     for (int i = 0; (i < nra); i++)
  67     {
  68         if (toupper(**(atomname[a[i]])) == 'H')
  69         {
  70             nh++;
  71         }
  72     }
  73
  74     return nh;
  75 }
  76
  77 void make_shake(gmx::ArrayRef<InteractionsOfType> plist, t_atoms* atoms, int nshake)
  78 {
  79     char*** info = atoms->atomname;
  80     real    b_ij, b_jk;
  81     if (nshake != eshNONE)
  82     {
  83         switch (nshake)
  84         {
  85             case eshHBONDS: printf("turning H bonds into constraints...\n"); break;
  86             case eshALLBONDS: printf("turning all bonds into constraints...\n"); break;
  87             case eshHANGLES: printf("turning all bonds and H angles into constraints...\n"); break;
  88             case eshALLANGLES: printf("turning all bonds and angles into constraints...\n"); break;
  89             default: gmx_fatal(FARGS, "Invalid option for make_shake (%d)", nshake);
  90         }
  91
  92         if ((nshake == eshHANGLES) || (nshake == eshALLANGLES))
  93         {
  94             /* Add all the angles with hydrogens to the shake list
  95              * and remove them from the bond list
  96              */
  97             for (int ftype = 0; (ftype < F_NRE); ftype++)
  98             {
  99                 if (interaction_function[ftype].flags & IF_CHEMBOND)
 100                 {
 101                     InteractionsOfType* bonds = &(plist[ftype]);
 102
 103                     for (int ftype_a = 0; (gmx::ssize(*bonds) > 0 && ftype_a < F_NRE); ftype_a++)
 104                     {
 105                         if (interaction_function[ftype_a].flags & IF_ATYPE)
 106                         {
 107                             InteractionsOfType* pr = &(plist[ftype_a]);
 108
 109                             for (auto parm = pr->interactionTypes.begin();
 110                                  parm != pr->interactionTypes.end();)
 111                             {
 112                                 const InteractionOfType* ang = &(*parm);
 113 #ifdef DEBUG
 114                                 printf("Angle: %d-%d-%d\n", ang->ai(), ang->aj(), ang->ak());
 115 #endif
 116                                 int numhydrogens = count_hydrogens(info, 3, ang->atoms());
 117                                 if ((nshake == eshALLANGLES) || (numhydrogens > 1)
 118                                     || (numhydrogens == 1 && toupper(**(info[ang->aj()])) == 'O'))
 119                                 {
 120                                     /* Can only add hydrogen angle shake, if the two bonds
 121                                      * are constrained.
 122                                      * append this angle to the shake list
 123                                      */
 124                                     std::vector<int> atomNumbers = { ang->ai(), ang->ak() };
 125
 126                                     /* Calculate length of constraint */
 127                                     bool bFound = false;
 128                                     b_ij = b_jk = 0.0;
 129                                     for (const auto& bond : bonds->interactionTypes)
 130                                     {
 131                                         if (((bond.ai() == ang->ai()) && (bond.aj() == ang->aj()))
 132                                             || ((bond.ai() == ang->aj()) && (bond.aj() == ang->ai())))
 133                                         {
 134                                             b_ij = bond.c0();
 135                                         }
 136                                         if (((bond.ai() == ang->ak()) && (bond.aj() == ang->aj()))
 137                                             || ((bond.ai() == ang->aj()) && (bond.aj() == ang->ak())))
 138                                         {
 139                                             b_jk = bond.c0();
 140                                         }
 141                                         bFound = (b_ij != 0.0) && (b_jk != 0.0);
 142                                     }
 143                                     if (bFound)
 144                                     {
 145                                         real param = std::sqrt(b_ij * b_ij + b_jk * b_jk
 146                                                                - 2.0 * b_ij * b_jk
 147                                                                          * cos(DEG2RAD * ang->c0()));
 148                                         std::vector<real> forceParm = { param, param };
 149                                         if (ftype == F_CONNBONDS || ftype_a == F_CONNBONDS)
 150                                         {
 151                                             gmx_fatal(FARGS,
 152                                                       "Can not constrain all angles when they "
 153                                                       "involved bonds of type %s",
 154                                                       interaction_function[F_CONNBONDS].longname);
 155                                         }
 156                                         /* apply law of cosines */
 157 #ifdef DEBUG
 158                                         printf("p: %d, q: %d, dist: %12.5e\n", atomNumbers[0],
 159                                                atomNumbers[1], forceParm[0]);
 160 #endif
 161                                         add_param_to_list(&(plist[F_CONSTR]),
 162                                                           InteractionOfType(atomNumbers, forceParm));
 163                                         /* move the last bond to this position */
 164                                         *parm = *(pr->interactionTypes.end() - 1);
 165                                         pr->interactionTypes.erase(pr->interactionTypes.end() - 1);
 166                                     }
 167                                 }
 168                                 else
 169                                 {
 170                                     ++parm;
 171                                 }
 172                             }
 173                         } /* if IF_ATYPE */
 174                     }     /* for ftype_A */
 175                 }         /* if IF_BTYPE */
 176             }             /* for ftype */
 177         }                 /* if shake angles */
 178
 179         /* Add all the bonds with hydrogens to the shake list
 180          * and remove them from the bond list
 181          */
 182         for (int ftype = 0; (ftype < F_NRE); ftype++)
 183         {
 184             if (interaction_function[ftype].flags & IF_BTYPE)
 185             {
 186                 InteractionsOfType* pr = &(plist[ftype]);
 187                 for (auto parm = pr->interactionTypes.begin(); parm != pr->interactionTypes.end();)
 188                 {
 189                     if ((nshake != eshHBONDS) || (count_hydrogens(info, 2, parm->atoms()) > 0))
 190                     {
 191                         /* append this bond to the shake list */
 192                         std::vector<int>  atomNumbers = { parm->ai(), parm->aj() };
 193                         std::vector<real> forceParm   = { parm->c0(), parm->c2() };
 194                         add_param_to_list(&(plist[F_CONSTR]), InteractionOfType(atomNumbers, forceParm));
 195                         parm = pr->interactionTypes.erase(parm);
 196                     }
 197                     else
 198                     {
 199                         ++parm;
 200                     }
 201                 }
 202             }
 203         }
 204     }
 205 }