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37 /* This file is completely threadsafe - keep it that way! */
45 #include "gromacs/math/units.h"
47 #include "gromacs/legacyheaders/typedefs.h"
52 #include "gromacs/utility/smalloc.h"
53 #include "gromacs/utility/fatalerror.h"
55 static void copy_bond (t_params *pr, int to, int from)
56 /* copies an entry in a bond list to another position.
57 * does no allocing or freeing of memory
60 /*memcpy((char*) &(pr->param[to]),(char*) &(pr->param[from]),
61 (size_t)sizeof(pr->param[from]));*/
66 range_check(to, 0, pr->nr);
67 range_check(from, 0, pr->nr);
68 for (i = 0; (i < MAXATOMLIST); i++)
70 pr->param[to].a[i] = pr->param[from].a[i];
72 for (i = 0; (i < MAXFORCEPARAM); i++)
74 pr->param[to].c[i] = pr->param[from].c[i];
76 for (i = 0; (i < MAXSLEN); i++)
78 pr->param[to].s[i] = pr->param[from].s[i];
83 static int count_hydrogens (char ***atomname, int nra, atom_id a[])
89 gmx_fatal(FARGS, "Cannot call count_hydrogens with no atomname (%s %d)",
94 for (i = 0; (i < nra); i++)
96 if (toupper(**(atomname[a[i]])) == 'H')
105 void make_shake (t_params plist[], t_atoms *atoms, int nshake)
107 char ***info = atoms->atomname;
110 t_param p, *bond, *ang;
112 int nb, b, i, j, ftype, ftype_a;
115 if (nshake != eshNONE)
120 printf("turning H bonds into constraints...\n");
123 printf("turning all bonds into constraints...\n");
126 printf("turning all bonds and H angles into constraints...\n");
129 printf("turning all bonds and angles into constraints...\n");
132 gmx_fatal(FARGS, "Invalid option for make_shake (%d)", nshake);
135 if ((nshake == eshHANGLES) || (nshake == eshALLANGLES))
137 /* Add all the angles with hydrogens to the shake list
138 * and remove them from the bond list
140 for (ftype = 0; (ftype < F_NRE); ftype++)
142 if (interaction_function[ftype].flags & IF_BTYPE)
144 bonds = &(plist[ftype]);
146 for (ftype_a = 0; (bonds->nr > 0 && ftype_a < F_NRE); ftype_a++)
148 if (interaction_function[ftype_a].flags & IF_ATYPE)
150 pr = &(plist[ftype_a]);
152 for (i = 0; (i < pr->nr); )
156 ang = &(pr->param[i]);
158 printf("Angle: %d-%d-%d\n", ang->AI, ang->AJ, ang->AK);
160 numhydrogens = count_hydrogens(info, 3, ang->a);
161 if ((nshake == eshALLANGLES) ||
162 (numhydrogens > 1) ||
163 (numhydrogens == 1 && toupper(**(info[ang->a[1]])) == 'O'))
165 /* Can only add hydrogen angle shake, if the two bonds
167 * append this angle to the shake list
172 /* Calculate length of constraint */
175 for (j = 0; !bFound && (j < bonds->nr); j++)
177 bond = &(bonds->param[j]);
178 if (((bond->AI == ang->AI) &&
179 (bond->AJ == ang->AJ)) ||
180 ((bond->AI == ang->AJ) &&
181 (bond->AJ == ang->AI)))
185 if (((bond->AI == ang->AK) &&
186 (bond->AJ == ang->AJ)) ||
187 ((bond->AI == ang->AJ) &&
188 (bond->AJ == ang->AK)))
192 bFound = (b_ij != 0.0) && (b_jk != 0.0);
196 /* apply law of cosines */
197 p.C0 = sqrt( b_ij*b_ij + b_jk*b_jk -
198 2.0*b_ij*b_jk*cos(DEG2RAD*ang->C0) );
201 printf("p: %d, q: %d, dist: %12.5e\n", p.AI, p.AJ, p.C0);
203 add_param_to_list (&(plist[F_CONSTR]), &p);
204 /* move the last bond to this position */
205 copy_bond (pr, i, pr->nr-1);
206 /* should free memory here!! */
219 } /* if shake angles */
221 /* Add all the bonds with hydrogens to the shake list
222 * and remove them from the bond list
224 for (ftype = 0; (ftype < F_NRE); ftype++)
226 if (interaction_function[ftype].flags & IF_BTYPE)
228 pr = &(plist[ftype]);
230 for (i = 0; i < pr->nr; i++)
232 if ( (nshake != eshHBONDS) ||
233 (count_hydrogens (info, 2, pr->param[i].a) > 0) )
235 /* append this bond to the shake list */
236 p.AI = pr->param[i].AI;
237 p.AJ = pr->param[i].AJ;
238 p.C0 = pr->param[i].C0;
239 p.C1 = pr->param[i].C2;
240 add_param_to_list (&(plist[F_CONSTR]), &p);
244 copy_bond(pr, j++, i);