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37 /* This file is completely threadsafe - keep it that way! */
48 static void upd_vir(rvec vir, real dvx, real dvy, real dvz)
55 void calc_vir(int nxf, rvec x[], rvec f[], tensor vir,
56 gmx_bool bScrewPBC, matrix box)
59 double dvxx = 0, dvxy = 0, dvxz = 0, dvyx = 0, dvyy = 0, dvyz = 0, dvzx = 0, dvzy = 0, dvzz = 0;
61 for (i = 0; (i < nxf); i++)
63 dvxx += x[i][XX]*f[i][XX];
64 dvxy += x[i][XX]*f[i][YY];
65 dvxz += x[i][XX]*f[i][ZZ];
67 dvyx += x[i][YY]*f[i][XX];
68 dvyy += x[i][YY]*f[i][YY];
69 dvyz += x[i][YY]*f[i][ZZ];
71 dvzx += x[i][ZZ]*f[i][XX];
72 dvzy += x[i][ZZ]*f[i][YY];
73 dvzz += x[i][ZZ]*f[i][ZZ];
78 /* We should correct all odd x-shifts, but the range of isx is -2 to 2 */
79 if (isx == 1 || isx == -1)
81 dvyy += box[YY][YY]*f[i][YY];
82 dvyz += box[YY][YY]*f[i][ZZ];
84 dvzy += box[ZZ][ZZ]*f[i][YY];
85 dvzz += box[ZZ][ZZ]*f[i][ZZ];
90 upd_vir(vir[XX], dvxx, dvxy, dvxz);
91 upd_vir(vir[YY], dvyx, dvyy, dvyz);
92 upd_vir(vir[ZZ], dvzx, dvzy, dvzz);
96 static void lo_fcv(int i0, int i1,
97 real x[], real f[], tensor vir,
98 int is[], real box[], gmx_bool bTriclinic)
100 int i, i3, tx, ty, tz;
102 real dvxx = 0, dvxy = 0, dvxz = 0, dvyx = 0, dvyy = 0, dvyz = 0, dvzx = 0, dvzy = 0, dvzz = 0;
106 for (i = i0; (i < i1); i++)
113 xx = x[i3+XX]-tx*box[XXXX]-ty*box[YYXX]-tz*box[ZZXX];
118 yy = x[i3+YY]-ty*box[YYYY]-tz*box[ZZYY];
123 zz = x[i3+ZZ]-tz*box[ZZZZ];
131 for (i = i0; (i < i1); i++)
138 xx = x[i3+XX]-tx*box[XXXX];
143 yy = x[i3+YY]-ty*box[YYYY];
148 zz = x[i3+ZZ]-tz*box[ZZZZ];
155 upd_vir(vir[XX], dvxx, dvxy, dvxz);
156 upd_vir(vir[YY], dvyx, dvyy, dvyz);
157 upd_vir(vir[ZZ], dvzx, dvzy, dvzz);
160 static void lo_fcv2(int i0, int i1,
161 rvec x[], rvec f[], tensor vir,
162 ivec is[], matrix box, gmx_bool bTriclinic)
164 int i, gg, tx, ty, tz;
166 real dvxx = 0, dvxy = 0, dvxz = 0, dvyx = 0, dvyy = 0, dvyz = 0, dvzx = 0, dvzy = 0, dvzz = 0;
170 for (i = i0, gg = 0; (i < i1); i++, gg++)
176 xx = x[i][XX]-tx*box[XX][XX]-ty*box[YY][XX]-tz*box[ZZ][XX];
181 yy = x[i][YY]-ty*box[YY][YY]-tz*box[ZZ][YY];
186 zz = x[i][ZZ]-tz*box[ZZ][ZZ];
194 for (i = i0, gg = 0; (i < i1); i++, gg++)
200 xx = x[i][XX]-tx*box[XX][XX];
205 yy = x[i][YY]-ty*box[YY][YY];
210 zz = x[i][ZZ]-tz*box[ZZ][ZZ];
217 upd_vir(vir[XX], dvxx, dvxy, dvxz);
218 upd_vir(vir[YY], dvyx, dvyy, dvyz);
219 upd_vir(vir[ZZ], dvzx, dvzy, dvzz);
222 void f_calc_vir(int i0, int i1, rvec x[], rvec f[], tensor vir,
223 t_graph *g, matrix box)
227 if (g && (g->nnodes > 0))
229 /* Calculate virial for bonded forces only when they belong to
232 start = max(i0, g->at_start);
233 end = min(i1, g->at_end);
235 lo_fcv2(start, end, x, f, vir, g->ishift, box, TRICLINIC(box));
237 lo_fcv(start, end, x[0], f[0], vir, g->ishift[0], box[0], TRICLINIC(box));
240 /* If not all atoms are bonded, calculate their virial contribution
241 * anyway, without shifting back their coordinates.
242 * Note the nifty pointer arithmetic...
246 calc_vir(start-i0, x + i0, f + i0, vir, FALSE, box);
250 calc_vir(i1-end, x + end, f + end, vir, FALSE, box);
255 calc_vir(i1-i0, x + i0, f + i0, vir, FALSE, box);