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37 /* This file is completely threadsafe - keep it that way! */
45 #include "gromacs/math/vectypes.h"
46 #include "gromacs/pbcutil/ishift.h"
47 #include "gromacs/pbcutil/mshift.h"
48 #include "gromacs/pbcutil/pbc.h"
60 static void upd_vir(rvec vir, real dvx, real dvy, real dvz)
67 void calc_vir(int nxf, rvec x[], rvec f[], tensor vir,
68 gmx_bool bScrewPBC, matrix box)
71 double dvxx = 0, dvxy = 0, dvxz = 0, dvyx = 0, dvyy = 0, dvyz = 0, dvzx = 0, dvzy = 0, dvzz = 0;
73 for (i = 0; (i < nxf); i++)
75 dvxx += x[i][XX]*f[i][XX];
76 dvxy += x[i][XX]*f[i][YY];
77 dvxz += x[i][XX]*f[i][ZZ];
79 dvyx += x[i][YY]*f[i][XX];
80 dvyy += x[i][YY]*f[i][YY];
81 dvyz += x[i][YY]*f[i][ZZ];
83 dvzx += x[i][ZZ]*f[i][XX];
84 dvzy += x[i][ZZ]*f[i][YY];
85 dvzz += x[i][ZZ]*f[i][ZZ];
90 /* We should correct all odd x-shifts, but the range of isx is -2 to 2 */
91 if (isx == 1 || isx == -1)
93 dvyy += box[YY][YY]*f[i][YY];
94 dvyz += box[YY][YY]*f[i][ZZ];
96 dvzy += box[ZZ][ZZ]*f[i][YY];
97 dvzz += box[ZZ][ZZ]*f[i][ZZ];
102 upd_vir(vir[XX], dvxx, dvxy, dvxz);
103 upd_vir(vir[YY], dvyx, dvyy, dvyz);
104 upd_vir(vir[ZZ], dvzx, dvzy, dvzz);
108 static void lo_fcv(int i0, int i1,
109 real x[], real f[], tensor vir,
110 int is[], real box[], gmx_bool bTriclinic)
112 int i, i3, tx, ty, tz;
114 real dvxx = 0, dvxy = 0, dvxz = 0, dvyx = 0, dvyy = 0, dvyz = 0, dvzx = 0, dvzy = 0, dvzz = 0;
118 for (i = i0; (i < i1); i++)
125 xx = x[i3+XX]-tx*box[XXXX]-ty*box[YYXX]-tz*box[ZZXX];
130 yy = x[i3+YY]-ty*box[YYYY]-tz*box[ZZYY];
135 zz = x[i3+ZZ]-tz*box[ZZZZ];
143 for (i = i0; (i < i1); i++)
150 xx = x[i3+XX]-tx*box[XXXX];
155 yy = x[i3+YY]-ty*box[YYYY];
160 zz = x[i3+ZZ]-tz*box[ZZZZ];
167 upd_vir(vir[XX], dvxx, dvxy, dvxz);
168 upd_vir(vir[YY], dvyx, dvyy, dvyz);
169 upd_vir(vir[ZZ], dvzx, dvzy, dvzz);
172 static void lo_fcv2(int i0, int i1,
173 rvec x[], rvec f[], tensor vir,
174 ivec is[], matrix box, gmx_bool bTriclinic)
176 int i, gg, tx, ty, tz;
178 real dvxx = 0, dvxy = 0, dvxz = 0, dvyx = 0, dvyy = 0, dvyz = 0, dvzx = 0, dvzy = 0, dvzz = 0;
182 for (i = i0, gg = 0; (i < i1); i++, gg++)
188 xx = x[i][XX]-tx*box[XX][XX]-ty*box[YY][XX]-tz*box[ZZ][XX];
193 yy = x[i][YY]-ty*box[YY][YY]-tz*box[ZZ][YY];
198 zz = x[i][ZZ]-tz*box[ZZ][ZZ];
206 for (i = i0, gg = 0; (i < i1); i++, gg++)
212 xx = x[i][XX]-tx*box[XX][XX];
217 yy = x[i][YY]-ty*box[YY][YY];
222 zz = x[i][ZZ]-tz*box[ZZ][ZZ];
229 upd_vir(vir[XX], dvxx, dvxy, dvxz);
230 upd_vir(vir[YY], dvyx, dvyy, dvyz);
231 upd_vir(vir[ZZ], dvzx, dvzy, dvzz);
234 void f_calc_vir(int i0, int i1, rvec x[], rvec f[], tensor vir,
235 t_graph *g, matrix box)
239 if (g && (g->nnodes > 0))
241 /* Calculate virial for bonded forces only when they belong to
244 start = max(i0, g->at_start);
245 end = min(i1, g->at_end);
247 lo_fcv2(start, end, x, f, vir, g->ishift, box, TRICLINIC(box));
249 lo_fcv(start, end, x[0], f[0], vir, g->ishift[0], box[0], TRICLINIC(box));
252 /* If not all atoms are bonded, calculate their virial contribution
253 * anyway, without shifting back their coordinates.
254 * Note the nifty pointer arithmetic...
258 calc_vir(start-i0, x + i0, f + i0, vir, FALSE, box);
262 calc_vir(i1-end, x + end, f + end, vir, FALSE, box);
267 calc_vir(i1-i0, x + i0, f + i0, vir, FALSE, box);