src/gromacs/gmxpreprocess/add_par.cpp

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  37 /* This file is completely threadsafe - keep it that way! */
  38 #include "gmxpre.h"
  39
  40 #include "add_par.h"
  41
  42 #include <cstring>
  43
  44 #include <algorithm>
  45
  46 #include "gromacs/gmxpreprocess/grompp_impl.h"
  47 #include "gromacs/gmxpreprocess/notset.h"
  48 #include "gromacs/gmxpreprocess/toputil.h"
  49 #include "gromacs/utility/cstringutil.h"
  50 #include "gromacs/utility/fatalerror.h"
  51 #include "gromacs/utility/smalloc.h"
  52
  53 #include "hackblock.h"
  54
  55 void add_param(InteractionsOfType        *ps,
  56                int                        ai,
  57                int                        aj,
  58                gmx::ArrayRef<const real>  c,
  59                const char                *s)
  60 {
  61     if ((ai < 0) || (aj < 0))
  62     {
  63         gmx_fatal(FARGS, "Trying to add impossible atoms: ai=%d, aj=%d", ai, aj);
  64     }
  65     std::vector<int>  atoms = {ai, aj};
  66     std::vector<real> forceParm(c.begin(), c.end());
  67
  68     ps->interactionTypes.emplace_back(InteractionOfType(atoms, forceParm, s ? s : ""));
  69 }
  70
  71 void add_imp_param(InteractionsOfType *ps, int ai, int aj, int ak, int al, real c0, real c1,
  72                    const char *s)
  73 {
  74     std::vector<int>  atoms     = {ai, aj, ak, al};
  75     std::vector<real> forceParm = {c0, c1};
  76     ps->interactionTypes.emplace_back(InteractionOfType(atoms, forceParm, s ? s : ""));
  77 }
  78
  79 void add_dih_param(InteractionsOfType *ps, int ai, int aj, int ak, int al, real c0, real c1,
  80                    real c2, const char *s)
  81 {
  82     std::vector<int>  atoms     = {ai, aj, ak, al};
  83     std::vector<real> forceParm = {c0, c1, c2};
  84     ps->interactionTypes.emplace_back(InteractionOfType(atoms, forceParm, s ? s : ""));
  85 }
  86
  87 void add_cmap_param(InteractionsOfType *ps, int ai, int aj, int ak, int al, int am, const char *s)
  88 {
  89     std::vector<int> atoms = {ai, aj, ak, al, am};
  90     ps->interactionTypes.emplace_back(InteractionOfType(atoms, {}, s ? s : ""));
  91 }
  92
  93 void add_vsite2_atoms(InteractionsOfType *ps, int ai, int aj, int ak)
  94 {
  95     std::vector<int> atoms = {ai, aj, ak};
  96     ps->interactionTypes.emplace_back(InteractionOfType(atoms, {}));
  97 }
  98
  99 void add_vsite2_param(InteractionsOfType *ps, int ai, int aj, int ak, real c0)
 100 {
 101     std::vector<int>  atoms     = {ai, aj, ak};
 102     std::vector<real> forceParm = {c0};
 103     ps->interactionTypes.emplace_back(InteractionOfType(atoms, forceParm));
 104 }
 105
 106 void add_vsite3_param(InteractionsOfType *ps, int ai, int aj, int ak, int al,
 107                       real c0, real c1)
 108 {
 109     std::vector<int>  atoms     = {ai, aj, ak, al};
 110     std::vector<real> forceParm = {c0, c1};
 111     ps->interactionTypes.emplace_back(InteractionOfType(atoms, forceParm));
 112 }
 113
 114 void add_vsite3_atoms(InteractionsOfType *ps, int ai, int aj, int ak, int al, bool bSwapParity)
 115 {
 116     std::vector<int>  atoms = {ai, aj, ak, al};
 117     ps->interactionTypes.emplace_back(InteractionOfType(atoms, {}));
 118
 119     if (bSwapParity)
 120     {
 121         ps->interactionTypes.back().setForceParameter(1, -1);
 122     }
 123 }
 124
 125 void add_vsite4_atoms(InteractionsOfType *ps, int ai, int aj, int ak, int al, int am)
 126 {
 127     std::vector<int> atoms = {ai, aj, ak, al, am};
 128     ps->interactionTypes.emplace_back(InteractionOfType(atoms, {}));
 129 }
 130
 131 int search_jtype(const PreprocessResidue &localPpResidue, const char *name, bool bNterm)
 132 {
 133     int    niter, jmax;
 134     size_t k, kmax, minstrlen;
 135     char  *rtpname, searchname[12];
 136
 137     strcpy(searchname, name);
 138
 139     /* Do a best match comparison */
 140     /* for protein N-terminus, allow renaming of H1, H2 and H3 to H */
 141     if (bNterm && (strlen(searchname) == 2) && (searchname[0] == 'H') &&
 142         ( (searchname[1] == '1') || (searchname[1] == '2') ||
 143           (searchname[1] == '3') ) )
 144     {
 145         niter = 2;
 146     }
 147     else
 148     {
 149         niter = 1;
 150     }
 151     kmax = 0;
 152     jmax = -1;
 153     for (int iter = 0; (iter < niter && jmax == -1); iter++)
 154     {
 155         if (iter == 1)
 156         {
 157             /* Try without the hydrogen number in the N-terminus */
 158             searchname[1] = '\0';
 159         }
 160         for (int j = 0; (j < localPpResidue.natom()); j++)
 161         {
 162             rtpname = *(localPpResidue.atomname[j]);
 163             if (gmx_strcasecmp(searchname, rtpname) == 0)
 164             {
 165                 jmax = j;
 166                 kmax = strlen(searchname);
 167                 break;
 168             }
 169             if (iter == niter - 1)
 170             {
 171                 minstrlen = std::min(strlen(searchname), strlen(rtpname));
 172                 for (k = 0; k < minstrlen; k++)
 173                 {
 174                     if (searchname[k] != rtpname[k])
 175                     {
 176                         break;
 177                     }
 178                 }
 179                 if (k > kmax)
 180                 {
 181                     kmax = k;
 182                     jmax = j;
 183                 }
 184             }
 185         }
 186     }
 187     if (jmax == -1)
 188     {
 189         gmx_fatal(FARGS, "Atom %s not found in rtp database in residue %s",
 190                   searchname, localPpResidue.resname.c_str());
 191     }
 192     if (kmax != strlen(searchname))
 193     {
 194         gmx_fatal(FARGS, "Atom %s not found in rtp database in residue %s, "
 195                   "it looks a bit like %s",
 196                   searchname, localPpResidue.resname.c_str(), *(localPpResidue.atomname[jmax]));
 197     }
 198     return jmax;
 199 }