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37 /* This file is completely threadsafe - keep it that way! */
48 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
49 #include "gromacs/gmxpreprocess/grompp-impl.h"
50 #include "gromacs/gmxpreprocess/toputil.h"
51 #include "gromacs/legacyheaders/types/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"
62 static t_2morse
*read_dissociation_energies(int *n2morse
)
67 const char *fn
= "edissoc.dat";
69 int maxn2m
= 0, n2m
= 0;
72 /* Open the file with dissociation energies */
76 /* Try and read two atom names and an energy term from it */
77 nread
= fscanf(fp
, "%s%s%lf", ai
, aj
, &e_diss
);
80 /* If we got three terms, it probably was OK, no further checking */
83 /* Increase memory for 16 at once, some mallocs are stupid */
88 t2m
[n2m
].ai
= gmx_strdup(ai
);
89 t2m
[n2m
].aj
= gmx_strdup(aj
);
90 t2m
[n2m
].e_diss
= e_diss
;
91 /* Increment counter */
94 /* If we did not read three items, quit reading */
99 /* Set the return values */
105 static int nequal(char *a1
, char *a2
)
109 /* Count the number of (case insensitive) characters that are equal in
110 * two strings. If they are equally long their respective null characters are
113 for (i
= 0; (a1
[i
] != '\0') && (a2
[i
] != '\0'); i
++)
115 if (toupper(a1
[i
]) != toupper(a2
[i
]))
120 if ((a1
[i
] == '\0') && (a2
[i
] == '\0'))
128 static real
search_e_diss(int n2m
, t_2morse t2m
[], char *ai
, char *aj
)
132 int nii
, njj
, nbstii
= 0, nbstjj
= 0;
135 /* Do a best match search for dissociation energies */
136 for (i
= 0; (i
< n2m
); i
++)
138 /* Check for a perfect match */
139 if (((gmx_strcasecmp(t2m
[i
].ai
, ai
) == 0) && (gmx_strcasecmp(t2m
[i
].aj
, aj
) == 0)) ||
140 ((gmx_strcasecmp(t2m
[i
].aj
, ai
) == 0) && (gmx_strcasecmp(t2m
[i
].ai
, aj
) == 0)))
147 /* Otherwise count the number of equal characters in the strings ai and aj
148 * and the ones from the file
150 nii
= nequal(t2m
[i
].ai
, ai
);
151 njj
= nequal(t2m
[i
].aj
, aj
);
152 if (((nii
> nbstii
) && (njj
>= nbstjj
)) ||
153 ((nii
>= nbstii
) && (njj
> nbstjj
)))
155 if ((nii
> 0) && (njj
> 0))
164 /* Swap ai and aj (at least in counting the number of equal chars) */
165 nii
= nequal(t2m
[i
].ai
, aj
);
166 njj
= nequal(t2m
[i
].aj
, ai
);
167 if (((nii
> nbstii
) && (njj
>= nbstjj
)) ||
168 ((nii
>= nbstii
) && (njj
> nbstjj
)))
170 if ((nii
> 0) && (njj
> 0))
180 /* Return the dissocation energy corresponding to the best match, if we have
181 * found one. Do some debug output anyway.
187 fprintf(debug
, "MORSE: Couldn't find E_diss for bond %s - %s, using default %g\n", ai
, aj
, ediss
);
195 fprintf(debug
, "MORSE: Dissoc. E (%10.3f) for bond %4s-%4s taken from bond %4s-%4s\n",
196 t2m
[ibest
].e_diss
, ai
, aj
, t2m
[ibest
].ai
, t2m
[ibest
].aj
);
198 return t2m
[ibest
].e_diss
;
202 void convert_harmonics(int nrmols
, t_molinfo mols
[], gpp_atomtype_t atype
)
207 int i
, j
, k
, last
, ni
, nj
;
208 int nrharm
, nrmorse
, bb
;
209 real edis
, kb
, b0
, beta
;
210 gmx_bool
*bRemoveHarm
;
212 /* First get the data */
213 t2m
= read_dissociation_energies(&n2m
);
216 fprintf(debug
, "MORSE: read %d dissoc energies\n", n2m
);
220 fprintf(stderr
, "No dissocation energies read\n");
224 /* For all the molecule types */
225 for (i
= 0; (i
< nrmols
); i
++)
227 /* Check how many morse and harmonic BONDSs there are, increase size of
228 * morse with the number of harmonics
230 nrmorse
= mols
[i
].plist
[F_MORSE
].nr
;
232 for (bb
= 0; (bb
< F_NRE
); bb
++)
234 if ((interaction_function
[bb
].flags
& IF_BTYPE
) && (bb
!= F_MORSE
))
236 nrharm
= mols
[i
].plist
[bb
].nr
;
237 pr_alloc(nrharm
, &(mols
[i
].plist
[F_MORSE
]));
238 snew(bRemoveHarm
, nrharm
);
240 /* Now loop over the harmonics, trying to convert them */
241 for (j
= 0; (j
< nrharm
); j
++)
243 ni
= mols
[i
].plist
[bb
].param
[j
].ai();
244 nj
= mols
[i
].plist
[bb
].param
[j
].aj();
246 search_e_diss(n2m
, t2m
,
247 get_atomtype_name(mols
[i
].atoms
.atom
[ni
].type
, atype
),
248 get_atomtype_name(mols
[i
].atoms
.atom
[nj
].type
, atype
));
251 bRemoveHarm
[j
] = TRUE
;
252 b0
= mols
[i
].plist
[bb
].param
[j
].c
[0];
253 kb
= mols
[i
].plist
[bb
].param
[j
].c
[1];
254 beta
= std::sqrt(kb
/(2*edis
));
255 mols
[i
].plist
[F_MORSE
].param
[nrmorse
].a
[0] = ni
;
256 mols
[i
].plist
[F_MORSE
].param
[nrmorse
].a
[1] = nj
;
257 mols
[i
].plist
[F_MORSE
].param
[nrmorse
].c
[0] = b0
;
258 mols
[i
].plist
[F_MORSE
].param
[nrmorse
].c
[1] = edis
;
259 mols
[i
].plist
[F_MORSE
].param
[nrmorse
].c
[2] = beta
;
263 mols
[i
].plist
[F_MORSE
].nr
= nrmorse
;
265 /* Now remove the harmonics */
266 for (j
= last
= 0; (j
< nrharm
); j
++)
270 /* Copy it to the last position */
271 for (k
= 0; (k
< MAXATOMLIST
); k
++)
273 mols
[i
].plist
[bb
].param
[last
].a
[k
] =
274 mols
[i
].plist
[bb
].param
[j
].a
[k
];
276 for (k
= 0; (k
< MAXFORCEPARAM
); k
++)
278 mols
[i
].plist
[bb
].param
[last
].c
[k
] =
279 mols
[i
].plist
[bb
].param
[j
].c
[k
];
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
;