src/gromacs/gmxpreprocess/hackblock.cpp

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  38 /* This file is completely threadsafe - keep it that way! */
  39 #include "gmxpre.h"
  40
  41 #include "hackblock.h"
  42
  43 #include <cstring>
  44
  45 #include "gromacs/gmxpreprocess/notset.h"
  46 #include "gromacs/math/vec.h"
  47 #include "gromacs/mdtypes/md_enums.h"
  48 #include "gromacs/topology/atoms.h"
  49 #include "gromacs/topology/symtab.h"
  50 #include "gromacs/utility/arrayref.h"
  51 #include "gromacs/utility/cstringutil.h"
  52 #include "gromacs/utility/exceptions.h"
  53 #include "gromacs/utility/fatalerror.h"
  54 #include "gromacs/utility/gmxassert.h"
  55 #include "gromacs/utility/smalloc.h"
  56 #include "gromacs/utility/stringcompare.h"
  57
  58 /* these MUST correspond to the enum in hackblock.h */
  59 const char* btsNames[ebtsNR] = { "bonds", "angles", "dihedrals", "impropers", "exclusions", "cmap" };
  60 const int   btsNiatoms[ebtsNR] = { 2, 3, 4, 4, 2, 5 };
  61
  62 MoleculePatchType MoleculePatch::type() const
  63 {
  64     if (oname.empty() && !nname.empty())
  65     {
  66         return MoleculePatchType::Add;
  67     }
  68     else if (!oname.empty() && nname.empty())
  69     {
  70         return MoleculePatchType::Delete;
  71     }
  72     else if (!oname.empty() && !nname.empty())
  73     {
  74         return MoleculePatchType::Replace;
  75     }
  76     else
  77     {
  78         GMX_THROW(gmx::InvalidInputError("Unknown type of atom modification"));
  79     }
  80 }
  81
  82 void clearModificationBlock(MoleculePatchDatabase* globalPatches)
  83 {
  84     globalPatches->name.clear();
  85     globalPatches->hack.clear();
  86     for (int i = 0; i < ebtsNR; i++)
  87     {
  88         globalPatches->rb[i].b.clear();
  89     }
  90 }
  91
  92 #define safe_strdup(str) (((str) != NULL) ? gmx_strdup(str) : NULL)
  93
  94 static bool contains_char(const BondedInteraction& s, char c)
  95 {
  96
  97     bool bRet = false;
  98     for (int i = 0; i < MAXATOMLIST; i++)
  99     {
 100         if (!s.a[i].empty() && s.a[i][0] == c)
 101         {
 102             bRet = true;
 103         }
 104     }
 105
 106     return bRet;
 107 }
 108
 109 static int rbonded_find_atoms_in_list(const BondedInteraction&               b,
 110                                       gmx::ArrayRef<const BondedInteraction> blist,
 111                                       int                                    natoms)
 112 {
 113     int foundPos = -1;
 114
 115     for (auto it = blist.begin(); (it != blist.end()) && (foundPos < 0); it++)
 116     {
 117         bool atomsMatch = true;
 118         for (int k = 0; k < natoms && atomsMatch; k++)
 119         {
 120             atomsMatch = atomsMatch && (b.a[k] == it->a[k]);
 121         }
 122         /* Try reverse if forward match did not work */
 123         if (!atomsMatch)
 124         {
 125             atomsMatch = true;
 126             for (int k = 0; k < natoms && atomsMatch; k++)
 127             {
 128                 atomsMatch = atomsMatch && (b.a[k] == it->a[natoms - 1 - k]);
 129             }
 130         }
 131         if (atomsMatch)
 132         {
 133             foundPos = std::distance(blist.begin(), it);
 134             /* If all the atoms AND all the parameters match, it is likely that
 135              * the user made a copy-and-paste mistake (since it would be much cheaper
 136              * to just bump the force constant 2x if you really want it twice).
 137              * Since we only have the unparsed string here we can only detect
 138              * EXACT matches (including identical whitespace).
 139              */
 140             if (b.s == it->s)
 141             {
 142                 gmx_warning("Duplicate line found in or between hackblock and rtp entries");
 143             }
 144         }
 145     }
 146     return foundPos;
 147 }
 148
 149 bool mergeBondedInteractionList(gmx::ArrayRef<const BondedInteractionList> s,
 150                                 gmx::ArrayRef<BondedInteractionList>       d,
 151                                 bool                                       bMin,
 152                                 bool                                       bPlus)
 153 {
 154     bool bBondsRemoved = false;
 155     for (int i = 0; i < ebtsNR; i++)
 156     {
 157         if (!s[i].b.empty())
 158         {
 159             /* Record how many bonds we have in the destination when we start.
 160              *
 161              * If an entry is present in the hackblock (destination), we will
 162              * not add the one from the main rtp, since the point is for hackblocks
 163              * to overwrite it. However, if there is no hackblock entry we do
 164              * allow multiple main rtp entries since some forcefield insist on that.
 165              *
 166              * We accomplish this by checking the position we find an entry in,
 167              * rather than merely checking whether it exists at all.
 168              * If that index is larger than the original (hackblock) destination
 169              * size, it was added from the main rtp, and then we will allow more
 170              * such entries. In contrast, if the entry found has a lower index
 171              * it is a hackblock entry meant to override the main rtp, and then
 172              * we don't add the main rtp one.
 173              */
 174             int nbHackblockStart = d[i].b.size();
 175
 176             for (const auto& b : s[i].b)
 177             {
 178                 /* Check if this bonded string already exists before adding.
 179                  * We are merging from the main RTP to the hackblocks, so this
 180                  * will mean the hackblocks overwrite the man RTP, as intended.
 181                  */
 182                 int index = rbonded_find_atoms_in_list(b, d[i].b, btsNiatoms[i]);
 183                 /* - If we did not find this interaction at all, the index will be -1,
 184                  *   and then we should definitely add it to the merged hackblock and rtp.
 185                  *
 186                  * Alternatively, if it was found, index will be >=0.
 187                  * - In case this index is lower than the original number of entries,
 188                  *   it is already present as a *hackblock* entry, and those should
 189                  *   always override whatever we have listed in the RTP. Thus, we
 190                  *   should just keep that one and not add anything from the RTP.
 191                  * - Finally, if it was found, but with an index higher than
 192                  *   the original number of entries, it comes from the RTP rather
 193                  *   than hackblock, and then we must have added it ourselves
 194                  *   in a previous iteration. In that case it is a matter of
 195                  *   several entries for the same sequence of atoms, and we allow
 196                  *   that in the RTP. In this case we should simply copy all of
 197                  *   them, including this one.
 198                  */
 199                 if (index < 0 || index >= nbHackblockStart)
 200                 {
 201                     if (!(bMin && contains_char(b, '-')) && !(bPlus && contains_char(b, '+')))
 202                     {
 203                         d[i].b.push_back(b);
 204                     }
 205                     else if (i == ebtsBONDS)
 206                     {
 207                         bBondsRemoved = true;
 208                     }
 209                 }
 210                 else
 211                 {
 212                     /* This is the common case where a hackblock entry simply
 213                      * overrides the RTP, so we cannot warn here.
 214                      */
 215                 }
 216             }
 217         }
 218     }
 219     return bBondsRemoved;
 220 }
 221
 222 void copyPreprocessResidues(const PreprocessResidue& s, PreprocessResidue* d, t_symtab* symtab)
 223 {
 224     *d = s;
 225     d->atom.clear();
 226     for (const auto& a : s.atom)
 227     {
 228         d->atom.push_back(a);
 229     }
 230     d->atomname.clear();
 231     for (const auto& a : s.atomname)
 232     {
 233         d->atomname.push_back(put_symtab(symtab, *a));
 234     }
 235     d->cgnr.clear();
 236     for (const auto& c : s.cgnr)
 237     {
 238         d->cgnr.push_back(c);
 239     }
 240     for (int i = 0; i < ebtsNR; i++)
 241     {
 242         d->rb[i].type = s.rb[i].type;
 243         d->rb[i].b.clear();
 244     }
 245     mergeBondedInteractionList(s.rb, d->rb, FALSE, FALSE);
 246 }
 247
 248 void mergeAtomModifications(const MoleculePatchDatabase& s, MoleculePatchDatabase* d)
 249 {
 250     for (const auto& h : s.hack)
 251     {
 252         d->hack.push_back(h);
 253     }
 254 }
 255
 256 void mergeAtomAndBondModifications(const MoleculePatchDatabase& s, MoleculePatchDatabase* d)
 257 {
 258     mergeAtomModifications(s, d);
 259     mergeBondedInteractionList(s.rb, d->rb, FALSE, FALSE);
 260 }
 261
 262 void copyModificationBlocks(const MoleculePatchDatabase& s, MoleculePatchDatabase* d)
 263 {
 264     *d      = s;
 265     d->name = s.name;
 266     d->hack.clear();
 267     for (int i = 0; i < ebtsNR; i++)
 268     {
 269         d->rb[i].b.clear();
 270     }
 271     mergeAtomAndBondModifications(s, d);
 272 }
 273
 274 #undef safe_strdup