src/gromacs/mdlib/calcvir.cpp

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  37 /* This file is completely threadsafe - keep it that way! */
  38 #include "gmxpre.h"
  39
  40 #include "calcvir.h"
  41
  42 #include "config.h" /* for GMX_MAX_OPENMP_THREADS */
  43
  44 #include <algorithm>
  45
  46 #include "gromacs/math/vec.h"
  47 #include "gromacs/math/vectypes.h"
  48 #include "gromacs/mdlib/gmx_omp_nthreads.h"
  49 #include "gromacs/pbcutil/ishift.h"
  50 #include "gromacs/pbcutil/mshift.h"
  51 #include "gromacs/pbcutil/pbc.h"
  52 #include "gromacs/utility/gmxassert.h"
  53
  54 #define XXXX    0
  55 #define XXYY    1
  56 #define XXZZ    2
  57 #define YYXX    3
  58 #define YYYY    4
  59 #define YYZZ    5
  60 #define ZZXX    6
  61 #define ZZYY    7
  62 #define ZZZZ    8
  63
  64 static void upd_vir(rvec vir, real dvx, real dvy, real dvz)
  65 {
  66     vir[XX] -= 0.5*dvx;
  67     vir[YY] -= 0.5*dvy;
  68     vir[ZZ] -= 0.5*dvz;
  69 }
  70
  71 static void calc_x_times_f(int nxf, const rvec x[], const rvec f[],
  72                            gmx_bool bScrewPBC, const matrix box,
  73                            matrix x_times_f)
  74 {
  75     clear_mat(x_times_f);
  76
  77     for (int i = 0; i < nxf; i++)
  78     {
  79         for (int d = 0; d < DIM; d++)
  80         {
  81             for (int n = 0; n < DIM; n++)
  82             {
  83                 x_times_f[d][n] += x[i][d]*f[i][n];
  84             }
  85         }
  86
  87         if (bScrewPBC)
  88         {
  89             int isx = IS2X(i);
  90             /* We should correct all odd x-shifts, but the range of isx is -2 to 2 */
  91             if (isx == 1 || isx == -1)
  92             {
  93                 for (int d = 0; d < DIM; d++)
  94                 {
  95                     for (int n = 0; n < DIM; n++)
  96                     {
  97                         x_times_f[d][n] += box[d][d]*f[i][n];
  98                     }
  99                 }
 100             }
 101         }
 102     }
 103 }
 104
 105 void calc_vir(int nxf, const rvec x[], const rvec f[], tensor vir,
 106               bool bScrewPBC, const matrix box)
 107 {
 108     matrix x_times_f;
 109
 110     int    nthreads = gmx_omp_nthreads_get_simple_rvec_task(emntDefault, nxf*9);
 111
 112     GMX_ASSERT(nthreads >= 1, "Avoids uninitialized x_times_f (warning)");
 113
 114     if (nthreads == 1)
 115     {
 116         calc_x_times_f(nxf, x, f, bScrewPBC, box, x_times_f);
 117     }
 118     else
 119     {
 120         /* Use a buffer on the stack for storing thread-local results.
 121          * We use 2 extra elements (=18 reals) per thread to separate thread
 122          * local data by at least a cache line. Element 0 is not used.
 123          */
 124         matrix xf_buf[GMX_OPENMP_MAX_THREADS*3];
 125
 126 #pragma omp parallel for num_threads(nthreads) schedule(static)
 127         for (int thread = 0; thread < nthreads; thread++)
 128         {
 129             int start = (nxf*thread)/nthreads;
 130             int end   = std::min(nxf*(thread + 1)/nthreads, nxf);
 131
 132             calc_x_times_f(end - start, x + start, f + start, bScrewPBC, box,
 133                            thread == 0 ? x_times_f : xf_buf[thread*3]);
 134         }
 135
 136         for (int thread = 1; thread < nthreads; thread++)
 137         {
 138             m_add(x_times_f, xf_buf[thread*3], x_times_f);
 139         }
 140     }
 141
 142     for (int d = 0; d < DIM; d++)
 143     {
 144         upd_vir(vir[d], x_times_f[d][XX], x_times_f[d][YY], x_times_f[d][ZZ]);
 145     }
 146 }
 147
 148
 149 static void lo_fcv(int i0, int i1,
 150                    const real x[], const real f[], tensor vir,
 151                    const int is[], const real box[], gmx_bool bTriclinic)
 152 {
 153     int      i, i3, tx, ty, tz;
 154     real     xx, yy, zz;
 155     real     dvxx = 0, dvxy = 0, dvxz = 0, dvyx = 0, dvyy = 0, dvyz = 0, dvzx = 0, dvzy = 0, dvzz = 0;
 156
 157     if (bTriclinic)
 158     {
 159         for (i = i0; (i < i1); i++)
 160         {
 161             i3 = DIM*i;
 162             tx = is[i3+XX];
 163             ty = is[i3+YY];
 164             tz = is[i3+ZZ];
 165
 166             xx    = x[i3+XX]-tx*box[XXXX]-ty*box[YYXX]-tz*box[ZZXX];
 167             dvxx += xx*f[i3+XX];
 168             dvxy += xx*f[i3+YY];
 169             dvxz += xx*f[i3+ZZ];
 170
 171             yy    = x[i3+YY]-ty*box[YYYY]-tz*box[ZZYY];
 172             dvyx += yy*f[i3+XX];
 173             dvyy += yy*f[i3+YY];
 174             dvyz += yy*f[i3+ZZ];
 175
 176             zz    = x[i3+ZZ]-tz*box[ZZZZ];
 177             dvzx += zz*f[i3+XX];
 178             dvzy += zz*f[i3+YY];
 179             dvzz += zz*f[i3+ZZ];
 180         }
 181     }
 182     else
 183     {
 184         for (i = i0; (i < i1); i++)
 185         {
 186             i3 = DIM*i;
 187             tx = is[i3+XX];
 188             ty = is[i3+YY];
 189             tz = is[i3+ZZ];
 190
 191             xx    = x[i3+XX]-tx*box[XXXX];
 192             dvxx += xx*f[i3+XX];
 193             dvxy += xx*f[i3+YY];
 194             dvxz += xx*f[i3+ZZ];
 195
 196             yy    = x[i3+YY]-ty*box[YYYY];
 197             dvyx += yy*f[i3+XX];
 198             dvyy += yy*f[i3+YY];
 199             dvyz += yy*f[i3+ZZ];
 200
 201             zz    = x[i3+ZZ]-tz*box[ZZZZ];
 202             dvzx += zz*f[i3+XX];
 203             dvzy += zz*f[i3+YY];
 204             dvzz += zz*f[i3+ZZ];
 205         }
 206     }
 207
 208     upd_vir(vir[XX], dvxx, dvxy, dvxz);
 209     upd_vir(vir[YY], dvyx, dvyy, dvyz);
 210     upd_vir(vir[ZZ], dvzx, dvzy, dvzz);
 211 }
 212
 213 void f_calc_vir(int i0, int i1, const rvec x[], const rvec f[], tensor vir,
 214                 const t_graph *g, const matrix box)
 215 {
 216     int start, end;
 217
 218     if (g && (g->nnodes > 0))
 219     {
 220         /* Calculate virial for bonded forces only when they belong to
 221          * this node.
 222          */
 223         start = std::max(i0, g->at_start);
 224         end   = std::min(i1, g->at_end);
 225         lo_fcv(start, end, x[0], f[0], vir, g->ishift[0], box[0], TRICLINIC(box));
 226
 227         /* If not all atoms are bonded, calculate their virial contribution
 228          * anyway, without shifting back their coordinates.
 229          * Note the nifty pointer arithmetic...
 230          */
 231         if (start > i0)
 232         {
 233             calc_vir(start-i0, x + i0, f + i0, vir, FALSE, box);
 234         }
 235         if (end < i1)
 236         {
 237             calc_vir(i1-end, x + end, f + end, vir, FALSE, box);
 238         }
 239     }
 240     else
 241     {
 242         calc_vir(i1-i0, x + i0, f + i0, vir, FALSE, box);
 243     }
 244 }