src/gromacs/mdlib/calcvir.cpp

   1 /*
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  37 /* This file is completely threadsafe - keep it that way! */
  38 #include "gmxpre.h"
  39
  40 #include <algorithm>
  41
  42 #include "gromacs/math/vectypes.h"
  43 #include "gromacs/mdlib/force.h"
  44 #include "gromacs/mdlib/gmx_omp_nthreads.h"
  45 #include "gromacs/pbcutil/ishift.h"
  46 #include "gromacs/pbcutil/mshift.h"
  47 #include "gromacs/pbcutil/pbc.h"
  48
  49 #define XXXX    0
  50 #define XXYY    1
  51 #define XXZZ    2
  52 #define YYXX    3
  53 #define YYYY    4
  54 #define YYZZ    5
  55 #define ZZXX    6
  56 #define ZZYY    7
  57 #define ZZZZ    8
  58
  59 static void upd_vir(rvec vir, real dvx, real dvy, real dvz)
  60 {
  61     vir[XX] -= 0.5*dvx;
  62     vir[YY] -= 0.5*dvy;
  63     vir[ZZ] -= 0.5*dvz;
  64 }
  65
  66 void calc_vir(int nxf, rvec x[], rvec f[], tensor vir,
  67               gmx_bool bScrewPBC, matrix box)
  68 {
  69     int      i;
  70     double   dvxx = 0, dvxy = 0, dvxz = 0, dvyx = 0, dvyy = 0, dvyz = 0, dvzx = 0, dvzy = 0, dvzz = 0;
  71
  72 #pragma omp parallel for num_threads(gmx_omp_nthreads_get(emntDefault)) \
  73     schedule(static) \
  74     reduction(+: dvxx, dvxy, dvxz, dvyx, dvyy, dvyz, dvzx, dvzy, dvzz)
  75     for (i = 0; i < nxf; i++)
  76     {
  77         dvxx += x[i][XX]*f[i][XX];
  78         dvxy += x[i][XX]*f[i][YY];
  79         dvxz += x[i][XX]*f[i][ZZ];
  80
  81         dvyx += x[i][YY]*f[i][XX];
  82         dvyy += x[i][YY]*f[i][YY];
  83         dvyz += x[i][YY]*f[i][ZZ];
  84
  85         dvzx += x[i][ZZ]*f[i][XX];
  86         dvzy += x[i][ZZ]*f[i][YY];
  87         dvzz += x[i][ZZ]*f[i][ZZ];
  88
  89         if (bScrewPBC)
  90         {
  91             int isx = IS2X(i);
  92             /* We should correct all odd x-shifts, but the range of isx is -2 to 2 */
  93             if (isx == 1 || isx == -1)
  94             {
  95                 dvyy += box[YY][YY]*f[i][YY];
  96                 dvyz += box[YY][YY]*f[i][ZZ];
  97
  98                 dvzy += box[ZZ][ZZ]*f[i][YY];
  99                 dvzz += box[ZZ][ZZ]*f[i][ZZ];
 100             }
 101         }
 102     }
 103
 104     upd_vir(vir[XX], dvxx, dvxy, dvxz);
 105     upd_vir(vir[YY], dvyx, dvyy, dvyz);
 106     upd_vir(vir[ZZ], dvzx, dvzy, dvzz);
 107 }
 108
 109
 110 static void lo_fcv(int i0, int i1,
 111                    real x[], real f[], tensor vir,
 112                    int is[], real box[], gmx_bool bTriclinic)
 113 {
 114     int      i, i3, tx, ty, tz;
 115     real     xx, yy, zz;
 116     real     dvxx = 0, dvxy = 0, dvxz = 0, dvyx = 0, dvyy = 0, dvyz = 0, dvzx = 0, dvzy = 0, dvzz = 0;
 117
 118     if (bTriclinic)
 119     {
 120         for (i = i0; (i < i1); i++)
 121         {
 122             i3 = DIM*i;
 123             tx = is[i3+XX];
 124             ty = is[i3+YY];
 125             tz = is[i3+ZZ];
 126
 127             xx    = x[i3+XX]-tx*box[XXXX]-ty*box[YYXX]-tz*box[ZZXX];
 128             dvxx += xx*f[i3+XX];
 129             dvxy += xx*f[i3+YY];
 130             dvxz += xx*f[i3+ZZ];
 131
 132             yy    = x[i3+YY]-ty*box[YYYY]-tz*box[ZZYY];
 133             dvyx += yy*f[i3+XX];
 134             dvyy += yy*f[i3+YY];
 135             dvyz += yy*f[i3+ZZ];
 136
 137             zz    = x[i3+ZZ]-tz*box[ZZZZ];
 138             dvzx += zz*f[i3+XX];
 139             dvzy += zz*f[i3+YY];
 140             dvzz += zz*f[i3+ZZ];
 141         }
 142     }
 143     else
 144     {
 145         for (i = i0; (i < i1); i++)
 146         {
 147             i3 = DIM*i;
 148             tx = is[i3+XX];
 149             ty = is[i3+YY];
 150             tz = is[i3+ZZ];
 151
 152             xx    = x[i3+XX]-tx*box[XXXX];
 153             dvxx += xx*f[i3+XX];
 154             dvxy += xx*f[i3+YY];
 155             dvxz += xx*f[i3+ZZ];
 156
 157             yy    = x[i3+YY]-ty*box[YYYY];
 158             dvyx += yy*f[i3+XX];
 159             dvyy += yy*f[i3+YY];
 160             dvyz += yy*f[i3+ZZ];
 161
 162             zz    = x[i3+ZZ]-tz*box[ZZZZ];
 163             dvzx += zz*f[i3+XX];
 164             dvzy += zz*f[i3+YY];
 165             dvzz += zz*f[i3+ZZ];
 166         }
 167     }
 168
 169     upd_vir(vir[XX], dvxx, dvxy, dvxz);
 170     upd_vir(vir[YY], dvyx, dvyy, dvyz);
 171     upd_vir(vir[ZZ], dvzx, dvzy, dvzz);
 172 }
 173
 174 void f_calc_vir(int i0, int i1, rvec x[], rvec f[], tensor vir,
 175                 t_graph *g, matrix box)
 176 {
 177     int start, end;
 178
 179     if (g && (g->nnodes > 0))
 180     {
 181         /* Calculate virial for bonded forces only when they belong to
 182          * this node.
 183          */
 184         start = std::max(i0, g->at_start);
 185         end   = std::min(i1, g->at_end);
 186         lo_fcv(start, end, x[0], f[0], vir, g->ishift[0], box[0], TRICLINIC(box));
 187
 188         /* If not all atoms are bonded, calculate their virial contribution
 189          * anyway, without shifting back their coordinates.
 190          * Note the nifty pointer arithmetic...
 191          */
 192         if (start > i0)
 193         {
 194             calc_vir(start-i0, x + i0, f + i0, vir, FALSE, box);
 195         }
 196         if (end < i1)
 197         {
 198             calc_vir(i1-end, x + end, f + end, vir, FALSE, box);
 199         }
 200     }
 201     else
 202     {
 203         calc_vir(i1-i0, x + i0, f + i0, vir, FALSE, box);
 204     }
 205 }