*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2018,2019, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/utility/gmxassert.h"
-#define XXXX 0
-#define XXYY 1
-#define XXZZ 2
-#define YYXX 3
-#define YYYY 4
-#define YYZZ 5
-#define ZZXX 6
-#define ZZYY 7
-#define ZZZZ 8
+#define XXXX 0
+#define XXYY 1
+#define XXZZ 2
+#define YYXX 3
+#define YYYY 4
+#define YYZZ 5
+#define ZZXX 6
+#define ZZYY 7
+#define ZZZZ 8
static void upd_vir(rvec vir, real dvx, real dvy, real dvz)
{
- vir[XX] -= 0.5*dvx;
- vir[YY] -= 0.5*dvy;
- vir[ZZ] -= 0.5*dvz;
+ vir[XX] -= 0.5 * dvx;
+ vir[YY] -= 0.5 * dvy;
+ vir[ZZ] -= 0.5 * dvz;
}
-static void calc_x_times_f(int nxf, const rvec x[], const rvec f[],
- gmx_bool bScrewPBC, const matrix box,
- matrix x_times_f)
+static void calc_x_times_f(int nxf, const rvec x[], const rvec f[], gmx_bool bScrewPBC, const matrix box, matrix x_times_f)
{
clear_mat(x_times_f);
{
for (int n = 0; n < DIM; n++)
{
- x_times_f[d][n] += x[i][d]*f[i][n];
+ x_times_f[d][n] += x[i][d] * f[i][n];
}
}
{
for (int n = 0; n < DIM; n++)
{
- x_times_f[d][n] += box[d][d]*f[i][n];
+ x_times_f[d][n] += box[d][d] * f[i][n];
}
}
}
}
}
-void calc_vir(int nxf, const rvec x[], const rvec f[], tensor vir,
- bool bScrewPBC, const matrix box)
+void calc_vir(int nxf, const rvec x[], const rvec f[], tensor vir, bool bScrewPBC, const matrix box)
{
matrix x_times_f;
- int nthreads = gmx_omp_nthreads_get_simple_rvec_task(emntDefault, nxf*9);
+ int nthreads = gmx_omp_nthreads_get_simple_rvec_task(emntDefault, nxf * 9);
GMX_ASSERT(nthreads >= 1, "Avoids uninitialized x_times_f (warning)");
* We use 2 extra elements (=18 reals) per thread to separate thread
* local data by at least a cache line. Element 0 is not used.
*/
- matrix xf_buf[GMX_OPENMP_MAX_THREADS*3];
+ matrix xf_buf[GMX_OPENMP_MAX_THREADS * 3];
#pragma omp parallel for num_threads(nthreads) schedule(static)
for (int thread = 0; thread < nthreads; thread++)
{
- int start = (nxf*thread)/nthreads;
- int end = std::min(nxf*(thread + 1)/nthreads, nxf);
+ int start = (nxf * thread) / nthreads;
+ int end = std::min(nxf * (thread + 1) / nthreads, nxf);
calc_x_times_f(end - start, x + start, f + start, bScrewPBC, box,
- thread == 0 ? x_times_f : xf_buf[thread*3]);
+ thread == 0 ? x_times_f : xf_buf[thread * 3]);
}
for (int thread = 1; thread < nthreads; thread++)
{
- m_add(x_times_f, xf_buf[thread*3], x_times_f);
+ m_add(x_times_f, xf_buf[thread * 3], x_times_f);
}
}
}
-static void lo_fcv(int i0, int i1,
- const real x[], const real f[], tensor vir,
- const int is[], const real box[], gmx_bool bTriclinic)
+static void
+lo_fcv(int i0, int i1, const real x[], const real f[], tensor vir, const int is[], const real box[], gmx_bool bTriclinic)
{
- int i, i3, tx, ty, tz;
- real xx, yy, zz;
- real dvxx = 0, dvxy = 0, dvxz = 0, dvyx = 0, dvyy = 0, dvyz = 0, dvzx = 0, dvzy = 0, dvzz = 0;
+ int i, i3, tx, ty, tz;
+ real xx, yy, zz;
+ real dvxx = 0, dvxy = 0, dvxz = 0, dvyx = 0, dvyy = 0, dvyz = 0, dvzx = 0, dvzy = 0, dvzz = 0;
if (bTriclinic)
{
for (i = i0; (i < i1); i++)
{
- i3 = DIM*i;
- tx = is[i3+XX];
- ty = is[i3+YY];
- tz = is[i3+ZZ];
-
- xx = x[i3+XX]-tx*box[XXXX]-ty*box[YYXX]-tz*box[ZZXX];
- dvxx += xx*f[i3+XX];
- dvxy += xx*f[i3+YY];
- dvxz += xx*f[i3+ZZ];
-
- yy = x[i3+YY]-ty*box[YYYY]-tz*box[ZZYY];
- dvyx += yy*f[i3+XX];
- dvyy += yy*f[i3+YY];
- dvyz += yy*f[i3+ZZ];
-
- zz = x[i3+ZZ]-tz*box[ZZZZ];
- dvzx += zz*f[i3+XX];
- dvzy += zz*f[i3+YY];
- dvzz += zz*f[i3+ZZ];
+ i3 = DIM * i;
+ tx = is[i3 + XX];
+ ty = is[i3 + YY];
+ tz = is[i3 + ZZ];
+
+ xx = x[i3 + XX] - tx * box[XXXX] - ty * box[YYXX] - tz * box[ZZXX];
+ dvxx += xx * f[i3 + XX];
+ dvxy += xx * f[i3 + YY];
+ dvxz += xx * f[i3 + ZZ];
+
+ yy = x[i3 + YY] - ty * box[YYYY] - tz * box[ZZYY];
+ dvyx += yy * f[i3 + XX];
+ dvyy += yy * f[i3 + YY];
+ dvyz += yy * f[i3 + ZZ];
+
+ zz = x[i3 + ZZ] - tz * box[ZZZZ];
+ dvzx += zz * f[i3 + XX];
+ dvzy += zz * f[i3 + YY];
+ dvzz += zz * f[i3 + ZZ];
}
}
else
{
for (i = i0; (i < i1); i++)
{
- i3 = DIM*i;
- tx = is[i3+XX];
- ty = is[i3+YY];
- tz = is[i3+ZZ];
-
- xx = x[i3+XX]-tx*box[XXXX];
- dvxx += xx*f[i3+XX];
- dvxy += xx*f[i3+YY];
- dvxz += xx*f[i3+ZZ];
-
- yy = x[i3+YY]-ty*box[YYYY];
- dvyx += yy*f[i3+XX];
- dvyy += yy*f[i3+YY];
- dvyz += yy*f[i3+ZZ];
-
- zz = x[i3+ZZ]-tz*box[ZZZZ];
- dvzx += zz*f[i3+XX];
- dvzy += zz*f[i3+YY];
- dvzz += zz*f[i3+ZZ];
+ i3 = DIM * i;
+ tx = is[i3 + XX];
+ ty = is[i3 + YY];
+ tz = is[i3 + ZZ];
+
+ xx = x[i3 + XX] - tx * box[XXXX];
+ dvxx += xx * f[i3 + XX];
+ dvxy += xx * f[i3 + YY];
+ dvxz += xx * f[i3 + ZZ];
+
+ yy = x[i3 + YY] - ty * box[YYYY];
+ dvyx += yy * f[i3 + XX];
+ dvyy += yy * f[i3 + YY];
+ dvyz += yy * f[i3 + ZZ];
+
+ zz = x[i3 + ZZ] - tz * box[ZZZZ];
+ dvzx += zz * f[i3 + XX];
+ dvzy += zz * f[i3 + YY];
+ dvzz += zz * f[i3 + ZZ];
}
}
upd_vir(vir[ZZ], dvzx, dvzy, dvzz);
}
-void f_calc_vir(int i0, int i1, const rvec x[], const rvec f[], tensor vir,
- const t_graph *g, const matrix box)
+void f_calc_vir(int i0, int i1, const rvec x[], const rvec f[], tensor vir, const t_graph* g, const matrix box)
{
int start, end;
*/
if (start > i0)
{
- calc_vir(start-i0, x + i0, f + i0, vir, FALSE, box);
+ calc_vir(start - i0, x + i0, f + i0, vir, FALSE, box);
}
if (end < i1)
{
- calc_vir(i1-end, x + end, f + end, vir, FALSE, box);
+ calc_vir(i1 - end, x + end, f + end, vir, FALSE, box);
}
}
else
{
- calc_vir(i1-i0, x + i0, f + i0, vir, FALSE, box);
+ calc_vir(i1 - i0, x + i0, f + i0, vir, FALSE, box);
}
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff