-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+/*
+ * This file is part of the GROMACS molecular simulation package.
*
- *
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * VERSION 3.2.0
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
-
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2012,2014, 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.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
- *
- * If you want to redistribute modifications, please consider that
- * scientific software is very special. Version control is crucial -
- * bugs must be traceable. We will be happy to consider code for
- * inclusion in the official distribution, but derived work must not
- * be called official GROMACS. Details are found in the README & COPYING
- * files - if they are missing, get the official version at www.gromacs.org.
- *
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
* To help us fund GROMACS development, we humbly ask that you cite
- * the papers on the package - you can find them in the top README file.
- *
- * For more info, check our website at http://www.gromacs.org
- *
- * And Hey:
- * GROningen Mixture of Alchemy and Childrens' Stories
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
#include <math.h>
#include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
#include "gmx_fatal.h"
#include "calcgrid.h"
-#define facNR 4
-const int factor[facNR] = {2,3,5,7};
+/* The grid sizes below are based on timing of a 3D cubic grid in fftw
+ * compiled with SSE using 4 threads in fft5d.c.
+ * A grid size is removed when a larger grid is faster.
+ */
-static void make_list(int start_fac,int *ng,int ng_max,int *n_list,int **list)
-{
- int i,fac;
-
- if (*ng < ng_max)
- {
- if (*n_list % 100 == 0)
- {
- srenew(*list,*n_list+100);
- }
- (*list)[*n_list] = *ng;
- (*n_list)++;
-
- for(i=start_fac; i<facNR; i++)
- {
- fac = factor[i];
- /* The choice of grid size is based on benchmarks of fftw
- * and the need for a lot of factors for nice DD decomposition.
- * The base criterion is that a grid size is not included
- * when there is a larger grid size that produces a faster 3D FFT.
- * Allow any power for 2, two for 3 and 5, but only one for 7.
- * Three for 3 are ok when there is also a factor of 2.
- * Two factors of 5 are not allowed with a factor of 3 or 7.
- * A factor of 7 does not go with a factor of 5, 7 or 9.
- */
- if ((fac == 2) ||
- (fac == 3 && (*ng % 9 != 0 ||
- (*ng % 2 == 0 && *ng % 27 != 0))) ||
- (fac == 5 && *ng % 15 != 0 && *ng % 25 != 0) ||
- (fac == 7 && *ng % 5 != 0 && *ng % 7 != 0 && *ng % 9 != 0))
- {
- *ng *= fac;
- make_list(i,ng,ng_max,n_list,list);
- *ng /= fac;
- }
- }
- }
-}
+/* Small grid size array */
+#define g_initNR 15
+const int grid_init[g_initNR] = { 6, 8, 10, 12, 14, 16, 20, 24, 25, 28, 32, 36, 40, 42, 44 };
-static int list_comp(const void *a,const void *b)
-{
- return (*((int *)a) - *((int *)b));
-}
+/* For larger grid sizes, a prefactor with any power of 2 can be added.
+ * Only sizes divisible by 4 should be used, 90 is allowed, 140 not.
+ */
+#define g_baseNR 14
+const int grid_base[g_baseNR] = { 45, 48, 50, 52, 54, 56, 60, 64, 70, 72, 75, 80, 81, 84 };
-real calc_grid(FILE *fp,matrix box,real gr_sp,
- int *nx,int *ny,int *nz)
+real calc_grid(FILE *fp, matrix box, real gr_sp,
+ int *nx, int *ny, int *nz)
{
- int d,n[DIM];
- int i,j,nmin[DIM];
- rvec box_size,spacing;
+ int d, n[DIM];
+ int i;
+ rvec box_size;
+ int nmin, fac2, try;
+ rvec spacing;
real max_spacing;
- int ng_max,ng;
- int n_list,*list;
- if (gr_sp <= 0)
+ if ((*nx <= 0 || *ny <= 0 || *nz <= 0) && gr_sp <= 0)
+ {
+ gmx_fatal(FARGS, "invalid fourier grid spacing: %g", gr_sp);
+ }
+
+ if (grid_base[g_baseNR-1] % 4 != 0)
{
- gmx_fatal(FARGS,"invalid fourier grid spacing: %g",gr_sp);
+ gmx_incons("the last entry in grid_base is not a multiple of 4");
}
/* New grid calculation setup:
*
* /Erik Lindahl, 20060402.
*/
- for(d=0; d<DIM; d++)
+ for (d = 0; d < DIM; d++)
{
box_size[d] = 0;
- for(i=0;i<DIM;i++)
+ for (i = 0; i < DIM; i++)
{
box_size[d] += box[d][i]*box[d][i];
}
box_size[d] = sqrt(box_size[d]);
}
-
+
n[XX] = *nx;
n[YY] = *ny;
n[ZZ] = *nz;
-
- ng = 1;
- ng_max = 1;
- for(d=0; d<DIM; d++)
- {
- nmin[d] = (int)(box_size[d]/gr_sp + 0.999);
- if (2*nmin[d] > ng_max)
- {
- ng_max = 2*nmin[d];
- }
- }
- n_list=0;
- list=NULL;
- make_list(0,&ng,ng_max,&n_list,&list);
-
- if ((*nx<=0) || (*ny<=0) || (*nz<=0))
+
+ if ((*nx <= 0) || (*ny <= 0) || (*nz <= 0))
{
if (NULL != fp)
{
- fprintf(fp,"Calculating fourier grid dimensions for%s%s%s\n",
- *nx > 0 ? "":" X",*ny > 0 ? "":" Y",*nz > 0 ? "":" Z");
+ fprintf(fp, "Calculating fourier grid dimensions for%s%s%s\n",
+ *nx > 0 ? "" : " X", *ny > 0 ? "" : " Y", *nz > 0 ? "" : " Z");
}
}
-
- qsort(list,n_list,sizeof(list[0]),list_comp);
- if (debug)
- {
- for(i=0; i<n_list; i++)
- fprintf(debug,"grid: %d\n",list[i]);
- }
-
- for(d=0; d<DIM; d++)
+
+ max_spacing = 0;
+ for (d = 0; d < DIM; d++)
{
- for(i=0; (i<n_list) && (n[d]<=0); i++)
+ if (n[d] <= 0)
{
- if (list[i] >= nmin[d])
+ nmin = (int)(box_size[d]/gr_sp + 0.999);
+
+ i = g_initNR - 1;
+ if (grid_init[i] >= nmin)
{
- n[d] = list[i];
+ /* Take the smallest possible grid in the list */
+ while (i > 0 && grid_init[i-1] >= nmin)
+ {
+ i--;
+ }
+ n[d] = grid_init[i];
+ }
+ else
+ {
+ /* Determine how many pre-factors of 2 we need */
+ fac2 = 1;
+ i = g_baseNR - 1;
+ while (fac2*grid_base[i] < nmin)
+ {
+ fac2 *= 2;
+ }
+ /* Find the smallest grid that is >= nmin */
+ do
+ {
+ try = fac2*grid_base[i];
+ /* We demand a factor of 4, avoid 140, allow 90 */
+ if (((try % 4 == 0 && try != 140) || try == 90) &&
+ try >= nmin)
+ {
+ n[d] = try;
+ }
+ i--;
+ }
+ while (i > 0);
}
}
- }
-
- sfree(list);
-
- max_spacing = 0;
- for(d=0; d<DIM; d++)
- {
+
spacing[d] = box_size[d]/n[d];
if (spacing[d] > max_spacing)
{
*nz = n[ZZ];
if (NULL != fp)
{
- fprintf(fp,"Using a fourier grid of %dx%dx%d, spacing %.3f %.3f %.3f\n",
- *nx,*ny,*nz,spacing[XX],spacing[YY],spacing[ZZ]);
+ fprintf(fp, "Using a fourier grid of %dx%dx%d, spacing %.3f %.3f %.3f\n",
+ *nx, *ny, *nz, spacing[XX], spacing[YY], spacing[ZZ]);
}
return max_spacing;
}
-
-
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff