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37 /* This file is completely threadsafe - keep it that way! */
45 #include "gromacs/gmxpreprocess/grompp_impl.h"
46 #include "gromacs/gmxpreprocess/notset.h"
47 #include "gromacs/gmxpreprocess/readir.h"
48 #include "gromacs/gmxpreprocess/topdirs.h"
49 #include "gromacs/gmxpreprocess/toppush.h"
50 #include "gromacs/gmxpreprocess/toputil.h"
51 #include "gromacs/math/units.h"
52 #include "gromacs/topology/ifunc.h"
53 #include "gromacs/utility/fatalerror.h"
54 #include "gromacs/utility/smalloc.h"
56 static void copy_bond (t_params
*pr
, int to
, int from
)
57 /* copies an entry in a bond list to another position.
58 * does no allocing or freeing of memory
61 /*memcpy((char*) &(pr->param[to]),(char*) &(pr->param[from]),
62 (size_t)sizeof(pr->param[from]));*/
67 range_check(to
, 0, pr
->nr
);
68 range_check(from
, 0, pr
->nr
);
69 for (i
= 0; (i
< MAXATOMLIST
); i
++)
71 pr
->param
[to
].a
[i
] = pr
->param
[from
].a
[i
];
73 for (i
= 0; (i
< MAXFORCEPARAM
); i
++)
75 pr
->param
[to
].c
[i
] = pr
->param
[from
].c
[i
];
77 for (i
= 0; (i
< MAXSLEN
); i
++)
79 pr
->param
[to
].s
[i
] = pr
->param
[from
].s
[i
];
84 static int count_hydrogens (char ***atomname
, int nra
, const int a
[])
90 gmx_fatal(FARGS
, "Cannot call count_hydrogens with no atomname (%s %d)",
95 for (i
= 0; (i
< nra
); i
++)
97 if (toupper(**(atomname
[a
[i
]])) == 'H')
106 void make_shake (t_params plist
[], t_atoms
*atoms
, int nshake
)
108 char ***info
= atoms
->atomname
;
111 t_param p
, *bond
, *ang
;
113 int i
, j
, ftype
, ftype_a
;
116 if (nshake
!= eshNONE
)
121 printf("turning H bonds into constraints...\n");
124 printf("turning all bonds into constraints...\n");
127 printf("turning all bonds and H angles into constraints...\n");
130 printf("turning all bonds and angles into constraints...\n");
133 gmx_fatal(FARGS
, "Invalid option for make_shake (%d)", nshake
);
136 if ((nshake
== eshHANGLES
) || (nshake
== eshALLANGLES
))
138 /* Add all the angles with hydrogens to the shake list
139 * and remove them from the bond list
141 for (ftype
= 0; (ftype
< F_NRE
); ftype
++)
143 if (interaction_function
[ftype
].flags
& IF_BTYPE
)
145 bonds
= &(plist
[ftype
]);
147 for (ftype_a
= 0; (bonds
->nr
> 0 && ftype_a
< F_NRE
); ftype_a
++)
149 if (interaction_function
[ftype_a
].flags
& IF_ATYPE
)
151 pr
= &(plist
[ftype_a
]);
153 for (i
= 0; (i
< pr
->nr
); )
157 ang
= &(pr
->param
[i
]);
159 printf("Angle: %d-%d-%d\n", ang
->ai(), ang
->aj(), ang
->ak());
161 numhydrogens
= count_hydrogens(info
, 3, ang
->a
);
162 if ((nshake
== eshALLANGLES
) ||
163 (numhydrogens
> 1) ||
164 (numhydrogens
== 1 && toupper(**(info
[ang
->a
[1]])) == 'O'))
166 /* Can only add hydrogen angle shake, if the two bonds
168 * append this angle to the shake list
173 /* Calculate length of constraint */
176 for (j
= 0; !bFound
&& (j
< bonds
->nr
); j
++)
178 bond
= &(bonds
->param
[j
]);
179 if (((bond
->ai() == ang
->ai()) &&
180 (bond
->aj() == ang
->aj())) ||
181 ((bond
->ai() == ang
->aj()) &&
182 (bond
->aj() == ang
->ai())))
186 if (((bond
->ai() == ang
->ak()) &&
187 (bond
->aj() == ang
->aj())) ||
188 ((bond
->ai() == ang
->aj()) &&
189 (bond
->aj() == ang
->ak())))
193 bFound
= (b_ij
!= 0.0) && (b_jk
!= 0.0);
197 /* apply law of cosines */
198 p
.c0() = std::sqrt( b_ij
*b_ij
+ b_jk
*b_jk
-
199 2.0*b_ij
*b_jk
*cos(DEG2RAD
*ang
->c0()) );
202 printf("p: %d, q: %d, dist: %12.5e\n", p
.ai(), p
.aj(), p
.c0());
204 add_param_to_list (&(plist
[F_CONSTR
]), &p
);
205 /* move the last bond to this position */
206 copy_bond (pr
, i
, pr
->nr
-1);
207 /* should free memory here!! */
220 } /* if shake angles */
222 /* Add all the bonds with hydrogens to the shake list
223 * and remove them from the bond list
225 for (ftype
= 0; (ftype
< F_NRE
); ftype
++)
227 if (interaction_function
[ftype
].flags
& IF_BTYPE
)
229 pr
= &(plist
[ftype
]);
231 for (i
= 0; i
< pr
->nr
; i
++)
233 if ( (nshake
!= eshHBONDS
) ||
234 (count_hydrogens (info
, 2, pr
->param
[i
].a
) > 0) )
236 /* append this bond to the shake list */
237 p
.ai() = pr
->param
[i
].ai();
238 p
.aj() = pr
->param
[i
].aj();
239 p
.c0() = pr
->param
[i
].c0();
240 p
.c1() = pr
->param
[i
].c2();
241 add_param_to_list (&(plist
[F_CONSTR
]), &p
);
245 copy_bond(pr
, j
++, i
);