src/gromacs/gmxpreprocess/topshake.cpp

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   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/math/utilities.h"
  53 #include "gromacs/topology/ifunc.h"
  54 #include "gromacs/utility/fatalerror.h"
  55 #include "gromacs/utility/logger.h"
  56 #include "gromacs/utility/smalloc.h"
  57
  58 static int count_hydrogens(char*** atomname, int nra, gmx::ArrayRef<const int> a)
  59 {
  60     int nh;
  61
  62     if (!atomname)
  63     {
  64         gmx_fatal(FARGS, "Cannot call count_hydrogens with no atomname (%s %d)", __FILE__, __LINE__);
  65     }
  66
  67     nh = 0;
  68     for (int i = 0; (i < nra); i++)
  69     {
  70         if (toupper(**(atomname[a[i]])) == 'H')
  71         {
  72             nh++;
  73         }
  74     }
  75
  76     return nh;
  77 }
  78
  79 void make_shake(gmx::ArrayRef<InteractionsOfType> plist, t_atoms* atoms, int nshake, const gmx::MDLogger& logger)
  80 {
  81     char*** info = atoms->atomname;
  82     real    b_ij, b_jk;
  83     if (nshake != eshNONE)
  84     {
  85         switch (nshake)
  86         {
  87             case eshHBONDS:
  88                 GMX_LOG(logger.info)
  89                         .asParagraph()
  90                         .appendTextFormatted("turning H bonds into constraints...");
  91                 break;
  92             case eshALLBONDS:
  93                 GMX_LOG(logger.info)
  94                         .asParagraph()
  95                         .appendTextFormatted("turning all bonds into constraints...");
  96                 break;
  97             case eshHANGLES:
  98                 GMX_LOG(logger.info)
  99                         .asParagraph()
 100                         .appendTextFormatted("turning all bonds and H angles into constraints...");
 101                 break;
 102             case eshALLANGLES:
 103                 GMX_LOG(logger.info)
 104                         .asParagraph()
 105                         .appendTextFormatted("turning all bonds and angles into constraints...");
 106                 break;
 107             default: gmx_fatal(FARGS, "Invalid option for make_shake (%d)", nshake);
 108         }
 109
 110         if ((nshake == eshHANGLES) || (nshake == eshALLANGLES))
 111         {
 112             /* Add all the angles with hydrogens to the shake list
 113              * and remove them from the bond list
 114              */
 115             for (int ftype = 0; (ftype < F_NRE); ftype++)
 116             {
 117                 if (interaction_function[ftype].flags & IF_CHEMBOND)
 118                 {
 119                     InteractionsOfType* bonds = &(plist[ftype]);
 120
 121                     for (int ftype_a = 0; (gmx::ssize(*bonds) > 0 && ftype_a < F_NRE); ftype_a++)
 122                     {
 123                         if (interaction_function[ftype_a].flags & IF_ATYPE)
 124                         {
 125                             InteractionsOfType* pr = &(plist[ftype_a]);
 126
 127                             for (auto parm = pr->interactionTypes.begin();
 128                                  parm != pr->interactionTypes.end();)
 129                             {
 130                                 const InteractionOfType* ang = &(*parm);
 131 #ifdef DEBUG
 132                                 GMX_LOG(logger.info)
 133                                         .asParagraph()
 134                                         .appendTextFormatted(
 135                                                 "Angle: %d-%d-%d", ang->ai(), ang->aj(), ang->ak());
 136 #endif
 137                                 int numhydrogens = count_hydrogens(info, 3, ang->atoms());
 138                                 if ((nshake == eshALLANGLES) || (numhydrogens > 1)
 139                                     || (numhydrogens == 1 && toupper(**(info[ang->aj()])) == 'O'))
 140                                 {
 141                                     /* Can only add hydrogen angle shake, if the two bonds
 142                                      * are constrained.
 143                                      * append this angle to the shake list
 144                                      */
 145                                     std::vector<int> atomNumbers = { ang->ai(), ang->ak() };
 146
 147                                     /* Calculate length of constraint */
 148                                     bool bFound = false;
 149                                     b_ij = b_jk = 0.0;
 150                                     for (const auto& bond : bonds->interactionTypes)
 151                                     {
 152                                         if (((bond.ai() == ang->ai()) && (bond.aj() == ang->aj()))
 153                                             || ((bond.ai() == ang->aj()) && (bond.aj() == ang->ai())))
 154                                         {
 155                                             b_ij = bond.c0();
 156                                         }
 157                                         if (((bond.ai() == ang->ak()) && (bond.aj() == ang->aj()))
 158                                             || ((bond.ai() == ang->aj()) && (bond.aj() == ang->ak())))
 159                                         {
 160                                             b_jk = bond.c0();
 161                                         }
 162                                         bFound = (b_ij != 0.0) && (b_jk != 0.0);
 163                                     }
 164                                     if (bFound)
 165                                     {
 166                                         real param = std::sqrt(
 167                                                 b_ij * b_ij + b_jk * b_jk
 168                                                 - 2.0 * b_ij * b_jk * cos(gmx::c_deg2Rad * ang->c0()));
 169                                         std::vector<real> forceParm = { param, param };
 170                                         if (ftype == F_CONNBONDS || ftype_a == F_CONNBONDS)
 171                                         {
 172                                             gmx_fatal(FARGS,
 173                                                       "Can not constrain all angles when they "
 174                                                       "involved bonds of type %s",
 175                                                       interaction_function[F_CONNBONDS].longname);
 176                                         }
 177                                         /* apply law of cosines */
 178 #ifdef DEBUG
 179                                         GMX_LOG(logger.info)
 180                                                 .asParagraph()
 181                                                 .appendTextFormatted("p: %d, q: %d, dist: %12.5e",
 182                                                                      atomNumbers[0],
 183                                                                      atomNumbers[1],
 184                                                                      forceParm[0]);
 185 #endif
 186                                         add_param_to_list(&(plist[F_CONSTR]),
 187                                                           InteractionOfType(atomNumbers, forceParm));
 188                                         /* move the last bond to this position */
 189                                         *parm = *(pr->interactionTypes.end() - 1);
 190                                         pr->interactionTypes.erase(pr->interactionTypes.end() - 1);
 191                                     }
 192                                 }
 193                                 else
 194                                 {
 195                                     ++parm;
 196                                 }
 197                             }
 198                         } /* if IF_ATYPE */
 199                     }     /* for ftype_A */
 200                 }         /* if IF_BTYPE */
 201             }             /* for ftype */
 202         }                 /* if shake angles */
 203
 204         /* Add all the bonds with hydrogens to the shake list
 205          * and remove them from the bond list
 206          */
 207         for (int ftype = 0; (ftype < F_NRE); ftype++)
 208         {
 209             if (interaction_function[ftype].flags & IF_BTYPE)
 210             {
 211                 InteractionsOfType* pr = &(plist[ftype]);
 212                 for (auto parm = pr->interactionTypes.begin(); parm != pr->interactionTypes.end();)
 213                 {
 214                     if ((nshake != eshHBONDS) || (count_hydrogens(info, 2, parm->atoms()) > 0))
 215                     {
 216                         /* append this bond to the shake list */
 217                         std::vector<int>  atomNumbers = { parm->ai(), parm->aj() };
 218                         std::vector<real> forceParm   = { parm->c0(), parm->c2() };
 219                         add_param_to_list(&(plist[F_CONSTR]), InteractionOfType(atomNumbers, forceParm));
 220                         parm = pr->interactionTypes.erase(parm);
 221                     }
 222                     else
 223                     {
 224                         ++parm;
 225                     }
 226                 }
 227             }
 228         }
 229     }
 230 }