src/gromacs/gmxpreprocess/tomorse.cpp

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  38 /* This file is completely threadsafe - keep it that way! */
  39 #include "gmxpre.h"
  40
  41 #include "tomorse.h"
  42
  43 #include <cctype>
  44 #include <cmath>
  45 #include <cstdlib>
  46 #include <cstring>
  47
  48 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
  49 #include "gromacs/gmxpreprocess/grompp_impl.h"
  50 #include "gromacs/gmxpreprocess/toputil.h"
  51 #include "gromacs/topology/ifunc.h"
  52 #include "gromacs/utility/cstringutil.h"
  53 #include "gromacs/utility/fatalerror.h"
  54 #include "gromacs/utility/futil.h"
  55 #include "gromacs/utility/smalloc.h"
  56
  57 typedef struct
  58 {
  59     char *ai, *aj;
  60     real  e_diss;
  61 } t_2morse;
  62
  63 static t_2morse* read_dissociation_energies(int* n2morse)
  64 {
  65     char        ai[32], aj[32];
  66     double      e_diss;
  67     const char* fn     = "edissoc.dat";
  68     t_2morse*   t2m    = nullptr;
  69     int         maxn2m = 0, n2m = 0;
  70     int         nread;
  71
  72     /* Open the file with dissociation energies */
  73     gmx::FilePtr fp = gmx::openLibraryFile(fn);
  74     do
  75     {
  76         /* Try and read two atom names and an energy term from it */
  77         nread = fscanf(fp.get(), "%s%s%lf", ai, aj, &e_diss);
  78         if (nread == 3)
  79         {
  80             /* If we got three terms, it probably was OK, no further checking */
  81             if (n2m >= maxn2m)
  82             {
  83                 /* Increase memory for 16 at once, some mallocs are stupid */
  84                 maxn2m += 16;
  85                 srenew(t2m, maxn2m);
  86             }
  87             /* Copy the values */
  88             t2m[n2m].ai     = gmx_strdup(ai);
  89             t2m[n2m].aj     = gmx_strdup(aj);
  90             t2m[n2m].e_diss = e_diss;
  91             /* Increment counter */
  92             n2m++;
  93         }
  94         /* If we did not read three items, quit reading */
  95     } while (nread == 3);
  96
  97     /* Set the return values */
  98     *n2morse = n2m;
  99
 100     return t2m;
 101 }
 102
 103 static int nequal(const char* a1, const char* a2)
 104 {
 105     int i;
 106
 107     /* Count the number of (case insensitive) characters that are equal in
 108      * two strings. If they are equally long their respective null characters are
 109      * counted also.
 110      */
 111     for (i = 0; (a1[i] != '\0') && (a2[i] != '\0'); i++)
 112     {
 113         if (toupper(a1[i]) != toupper(a2[i]))
 114         {
 115             break;
 116         }
 117     }
 118     if ((a1[i] == '\0') && (a2[i] == '\0'))
 119     {
 120         i++;
 121     }
 122
 123     return i;
 124 }
 125
 126 static real search_e_diss(int n2m, t_2morse t2m[], const char* ai, const char* aj)
 127 {
 128     int  i;
 129     int  ibest = -1;
 130     int  nii, njj, nbstii = 0, nbstjj = 0;
 131     real ediss = 400;
 132
 133     /* Do a best match search for dissociation energies */
 134     for (i = 0; (i < n2m); i++)
 135     {
 136         /* Check for a perfect match */
 137         if (((gmx_strcasecmp(t2m[i].ai, ai) == 0) && (gmx_strcasecmp(t2m[i].aj, aj) == 0))
 138             || ((gmx_strcasecmp(t2m[i].aj, ai) == 0) && (gmx_strcasecmp(t2m[i].ai, aj) == 0)))
 139         {
 140             ibest = i;
 141             break;
 142         }
 143         else
 144         {
 145             /* Otherwise count the number of equal characters in the strings ai and aj
 146              * and the ones from the file
 147              */
 148             nii = nequal(t2m[i].ai, ai);
 149             njj = nequal(t2m[i].aj, aj);
 150             if (((nii > nbstii) && (njj >= nbstjj)) || ((nii >= nbstii) && (njj > nbstjj)))
 151             {
 152                 if ((nii > 0) && (njj > 0))
 153                 {
 154                     ibest  = i;
 155                     nbstii = nii;
 156                     nbstjj = njj;
 157                 }
 158             }
 159             else
 160             {
 161                 /* Swap ai and aj (at least in counting the number of equal chars) */
 162                 nii = nequal(t2m[i].ai, aj);
 163                 njj = nequal(t2m[i].aj, ai);
 164                 if (((nii > nbstii) && (njj >= nbstjj)) || ((nii >= nbstii) && (njj > nbstjj)))
 165                 {
 166                     if ((nii > 0) && (njj > 0))
 167                     {
 168                         ibest  = i;
 169                         nbstii = nii;
 170                         nbstjj = njj;
 171                     }
 172                 }
 173             }
 174         }
 175     }
 176     /* Return the dissocation energy corresponding to the best match, if we have
 177      * found one.
 178      */
 179     if (ibest == -1)
 180     {
 181         return ediss;
 182     }
 183     else
 184     {
 185         return t2m[ibest].e_diss;
 186     }
 187 }
 188
 189 void convert_harmonics(gmx::ArrayRef<MoleculeInformation> mols, PreprocessingAtomTypes* atype)
 190 {
 191     int       n2m;
 192     t_2morse* t2m;
 193
 194     /* First get the data */
 195     t2m = read_dissociation_energies(&n2m);
 196     if (n2m <= 0)
 197     {
 198         fprintf(stderr, "No dissocation energies read\n");
 199         return;
 200     }
 201
 202     /* For all the molecule types */
 203     int i = 0;
 204     for (auto& mol : mols)
 205     {
 206         /* Check how many morse and harmonic BONDSs there are, increase size of
 207          * morse with the number of harmonics
 208          */
 209         for (int bb = 0; (bb < F_NRE); bb++)
 210         {
 211             if ((interaction_function[bb].flags & IF_BTYPE) && (bb != F_MORSE))
 212             {
 213                 int nrharm = mol.interactions[bb].size();
 214
 215                 /* Now loop over the harmonics, trying to convert them */
 216                 for (auto harmonic = mol.interactions[bb].interactionTypes.begin();
 217                      harmonic != mol.interactions[bb].interactionTypes.end();)
 218                 {
 219                     int  ni   = harmonic->ai();
 220                     int  nj   = harmonic->aj();
 221                     real edis = search_e_diss(n2m, t2m,
 222                                               atype->atomNameFromAtomType(mol.atoms.atom[ni].type),
 223                                               atype->atomNameFromAtomType(mol.atoms.atom[nj].type));
 224                     if (edis != 0)
 225                     {
 226                         real              b0         = harmonic->c0();
 227                         real              kb         = harmonic->c1();
 228                         real              beta       = std::sqrt(kb / (2 * edis));
 229                         std::vector<int>  atoms      = { ni, nj };
 230                         std::vector<real> forceParam = { b0, edis, beta };
 231                         mol.interactions[F_MORSE].interactionTypes.emplace_back(
 232                                 InteractionOfType(atoms, forceParam));
 233                         harmonic = mol.interactions[bb].interactionTypes.erase(harmonic);
 234                     }
 235                     else
 236                     {
 237                         ++harmonic;
 238                     }
 239                 }
 240
 241                 int newHarmonics = mol.interactions[bb].size();
 242                 fprintf(stderr, "Converted %d out of %d %s to morse bonds for mol %d\n",
 243                         nrharm - newHarmonics, nrharm, interaction_function[bb].name, i);
 244             }
 245         }
 246         i++;
 247     }
 248     sfree(t2m);
 249 }