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37 /* This file is completely threadsafe - keep it that way! */
45 #include "gromacs/legacyheaders/typedefs.h"
46 #include "gromacs/utility/cstringutil.h"
47 #include "grompp-impl.h"
48 #include "gromacs/utility/futil.h"
49 #include "gromacs/utility/smalloc.h"
51 #include "gromacs/utility/fatalerror.h"
52 #include "gpp_atomtype.h"
61 static t_2morse *read_dissociation_energies(int *n2morse)
66 const char *fn = "edissoc.dat";
68 int maxn2m = 0, n2m = 0;
71 /* Open the file with dissociation energies */
75 /* Try and read two atom names and an energy term from it */
76 nread = fscanf(fp, "%s%s%lf", ai, aj, &e_diss);
79 /* If we got three terms, it probably was OK, no further checking */
82 /* Increase memory for 16 at once, some mallocs are stupid */
87 t2m[n2m].ai = gmx_strdup(ai);
88 t2m[n2m].aj = gmx_strdup(aj);
89 t2m[n2m].e_diss = e_diss;
90 /* Increment counter */
93 /* If we did not read three items, quit reading */
98 /* Set the return values */
104 static int nequal(char *a1, char *a2)
108 /* Count the number of (case insensitive) characters that are equal in
109 * two strings. If they are equally long their respective null characters are
112 for (i = 0; (a1[i] != '\0') && (a2[i] != '\0'); i++)
114 if (toupper(a1[i]) != toupper(a2[i]))
119 if ((a1[i] == '\0') && (a2[i] == '\0'))
127 static real search_e_diss(int n2m, t_2morse t2m[], char *ai, char *aj)
131 int nii, njj, nbstii = 0, nbstjj = 0;
134 /* Do a best match search for dissociation energies */
135 for (i = 0; (i < n2m); i++)
137 /* Check for a perfect match */
138 if (((gmx_strcasecmp(t2m[i].ai, ai) == 0) && (gmx_strcasecmp(t2m[i].aj, aj) == 0)) ||
139 ((gmx_strcasecmp(t2m[i].aj, ai) == 0) && (gmx_strcasecmp(t2m[i].ai, aj) == 0)))
146 /* Otherwise count the number of equal characters in the strings ai and aj
147 * and the ones from the file
149 nii = nequal(t2m[i].ai, ai);
150 njj = nequal(t2m[i].aj, aj);
151 if (((nii > nbstii) && (njj >= nbstjj)) ||
152 ((nii >= nbstii) && (njj > nbstjj)))
154 if ((nii > 0) && (njj > 0))
163 /* Swap ai and aj (at least in counting the number of equal chars) */
164 nii = nequal(t2m[i].ai, aj);
165 njj = nequal(t2m[i].aj, ai);
166 if (((nii > nbstii) && (njj >= nbstjj)) ||
167 ((nii >= nbstii) && (njj > nbstjj)))
169 if ((nii > 0) && (njj > 0))
179 /* Return the dissocation energy corresponding to the best match, if we have
180 * found one. Do some debug output anyway.
186 fprintf(debug, "MORSE: Couldn't find E_diss for bond %s - %s, using default %g\n", ai, aj, ediss);
194 fprintf(debug, "MORSE: Dissoc. E (%10.3f) for bond %4s-%4s taken from bond %4s-%4s\n",
195 t2m[ibest].e_diss, ai, aj, t2m[ibest].ai, t2m[ibest].aj);
197 return t2m[ibest].e_diss;
201 void convert_harmonics(int nrmols, t_molinfo mols[], gpp_atomtype_t atype)
206 int i, j, k, last, ni, nj;
207 int nrharm, nrmorse, bb;
208 real edis, kb, b0, beta;
209 gmx_bool *bRemoveHarm;
211 /* First get the data */
212 t2m = read_dissociation_energies(&n2m);
215 fprintf(debug, "MORSE: read %d dissoc energies\n", n2m);
219 fprintf(stderr, "No dissocation energies read\n");
223 /* For all the molecule types */
224 for (i = 0; (i < nrmols); i++)
226 /* Check how many morse and harmonic BONDSs there are, increase size of
227 * morse with the number of harmonics
229 nrmorse = mols[i].plist[F_MORSE].nr;
231 for (bb = 0; (bb < F_NRE); bb++)
233 if ((interaction_function[bb].flags & IF_BTYPE) && (bb != F_MORSE))
235 nrharm = mols[i].plist[bb].nr;
236 pr_alloc(nrharm, &(mols[i].plist[F_MORSE]));
237 snew(bRemoveHarm, nrharm);
239 /* Now loop over the harmonics, trying to convert them */
240 for (j = 0; (j < nrharm); j++)
242 ni = mols[i].plist[bb].param[j].AI;
243 nj = mols[i].plist[bb].param[j].AJ;
245 search_e_diss(n2m, t2m,
246 get_atomtype_name(mols[i].atoms.atom[ni].type, atype),
247 get_atomtype_name(mols[i].atoms.atom[nj].type, atype));
250 bRemoveHarm[j] = TRUE;
251 b0 = mols[i].plist[bb].param[j].c[0];
252 kb = mols[i].plist[bb].param[j].c[1];
253 beta = sqrt(kb/(2*edis));
254 mols[i].plist[F_MORSE].param[nrmorse].a[0] = ni;
255 mols[i].plist[F_MORSE].param[nrmorse].a[1] = nj;
256 mols[i].plist[F_MORSE].param[nrmorse].c[0] = b0;
257 mols[i].plist[F_MORSE].param[nrmorse].c[1] = edis;
258 mols[i].plist[F_MORSE].param[nrmorse].c[2] = beta;
262 mols[i].plist[F_MORSE].nr = nrmorse;
264 /* Now remove the harmonics */
265 for (j = last = 0; (j < nrharm); j++)
269 /* Copy it to the last position */
270 for (k = 0; (k < MAXATOMLIST); k++)
272 mols[i].plist[bb].param[last].a[k] =
273 mols[i].plist[bb].param[j].a[k];
275 for (k = 0; (k < MAXFORCEPARAM); k++)
277 mols[i].plist[bb].param[last].c[k] =
278 mols[i].plist[bb].param[j].c[k];
283 /* cppcheck-suppress uninitvar Fixed in cppcheck 1.65 */
285 fprintf(stderr, "Converted %d out of %d %s to morse bonds for mol %d\n",
286 nrharm-last, nrharm, interaction_function[bb].name, i);
287 mols[i].plist[bb].nr = last;