-/* -*- 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 file is part of Gromacs Copyright (c) 1991-2008
- * David van der Spoel, Erik Lindahl, Berk Hess, University of Groningen.
+ * Copyright (c) 2009,2010,2014, 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.
*
- * 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
+ * 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.
*
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+ *
* To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org
- *
- * And Hey:
- * Gnomes, ROck Monsters And Chili Sauce
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include "typedefs.h"
-#include "vec.h"
-#include "pbc.h"
-#include "domdec.h"
-#include "domdec_network.h"
-#include "nsgrid.h"
-#include "network.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/domdec_network.h"
+#include "gromacs/legacyheaders/nsgrid.h"
+#include "gromacs/legacyheaders/network.h"
-static void calc_cgcm_av_stddev(t_block *cgs,int n,rvec *x,rvec av,rvec stddev,
+#include "gromacs/utility/fatalerror.h"
+
+static void calc_cgcm_av_stddev(t_block *cgs, int n, rvec *x, rvec av, rvec stddev,
t_commrec *cr_sum)
{
- int *cgindex;
- dvec s1,s2;
+ int *cgindex;
+ dvec s1, s2;
double buf[7];
- int cg,d,k0,k1,k,nrcg;
- real inv_ncg;
- rvec cg_cm;
+ int cg, d, k0, k1, k, nrcg;
+ real inv_ncg;
+ rvec cg_cm;
clear_dvec(s1);
clear_dvec(s2);
cgindex = cgs->index;
- for(cg=0; cg<n; cg++)
+ for (cg = 0; cg < n; cg++)
{
k0 = cgindex[cg];
k1 = cgindex[cg+1];
nrcg = k1 - k0;
if (nrcg == 1)
{
- copy_rvec(x[k0],cg_cm);
+ copy_rvec(x[k0], cg_cm);
}
else
{
inv_ncg = 1.0/nrcg;
-
+
clear_rvec(cg_cm);
- for(k=k0; (k<k1); k++)
+ for (k = k0; (k < k1); k++)
{
- rvec_inc(cg_cm,x[k]);
+ rvec_inc(cg_cm, x[k]);
}
- for(d=0; (d<DIM); d++)
+ for (d = 0; (d < DIM); d++)
{
cg_cm[d] *= inv_ncg;
}
}
- for(d=0; d<DIM; d++)
+ for (d = 0; d < DIM; d++)
{
s1[d] += cg_cm[d];
s2[d] += cg_cm[d]*cg_cm[d];
if (cr_sum != NULL)
{
- for(d=0; d<DIM; d++)
+ for (d = 0; d < DIM; d++)
{
buf[d] = s1[d];
buf[DIM+d] = s2[d];
}
buf[6] = n;
- gmx_sumd(7,buf,cr_sum);
- for(d=0; d<DIM; d++)
+ gmx_sumd(7, buf, cr_sum);
+ for (d = 0; d < DIM; d++)
{
s1[d] = buf[d];
s2[d] = buf[DIM+d];
n = (int)(buf[6] + 0.5);
}
- dsvmul(1.0/n,s1,s1);
- dsvmul(1.0/n,s2,s2);
+ dsvmul(1.0/n, s1, s1);
+ dsvmul(1.0/n, s2, s2);
- for(d=0; d<DIM; d++)
+ for (d = 0; d < DIM; d++)
{
av[d] = s1[d];
stddev[d] = sqrt(s2[d] - s1[d]*s1[d]);
}
}
-static void set_tric_dir(ivec *dd_nc,gmx_ddbox_t *ddbox,matrix box)
+static void set_tric_dir(ivec *dd_nc, gmx_ddbox_t *ddbox, matrix box)
{
- int npbcdim,d,i,j;
- rvec *v,*normal;
- real dep,inv_skew_fac2;
-
+ int npbcdim, d, i, j;
+ rvec *v, *normal;
+ real dep, inv_skew_fac2;
+
npbcdim = ddbox->npbcdim;
normal = ddbox->normal;
- for(d=0; d<DIM; d++)
+ for (d = 0; d < DIM; d++)
{
ddbox->tric_dir[d] = 0;
- for(j=d+1; j<npbcdim; j++)
+ for (j = d+1; j < npbcdim; j++)
{
if (box[j][d] != 0)
{
ddbox->tric_dir[d] = 1;
if (dd_nc != NULL && (*dd_nc)[j] > 1 && (*dd_nc)[d] == 1)
{
- gmx_fatal(FARGS,"Domain decomposition has not been implemented for box vectors that have non-zero components in directions that do not use domain decomposition: ncells = %d %d %d, box vector[%d] = %f %f %f",
- dd_nc[XX],dd_nc[YY],dd_nc[ZZ],
- j+1,box[j][XX],box[j][YY],box[j][ZZ]);
+ gmx_fatal(FARGS, "Domain decomposition has not been implemented for box vectors that have non-zero components in directions that do not use domain decomposition: ncells = %d %d %d, box vector[%d] = %f %f %f",
+ dd_nc[XX], dd_nc[YY], dd_nc[ZZ],
+ j+1, box[j][XX], box[j][YY], box[j][ZZ]);
}
}
}
-
+
/* Convert box vectors to orthogonal vectors for this dimension,
* for use in distance calculations.
* Set the trilinic skewing factor that translates
if (ddbox->tric_dir[d])
{
inv_skew_fac2 = 1;
- v = ddbox->v[d];
+ v = ddbox->v[d];
if (d == XX || d == YY)
{
/* Normalize such that the "diagonal" is 1 */
- svmul(1/box[d+1][d+1],box[d+1],v[d+1]);
- for(i=0; i<d; i++)
+ svmul(1/box[d+1][d+1], box[d+1], v[d+1]);
+ for (i = 0; i < d; i++)
{
v[d+1][i] = 0;
}
if (d == XX)
{
/* Normalize such that the "diagonal" is 1 */
- svmul(1/box[d+2][d+2],box[d+2],v[d+2]);
- for(i=0; i<d; i++)
+ svmul(1/box[d+2][d+2], box[d+2], v[d+2]);
+ for (i = 0; i < d; i++)
{
v[d+2][i] = 0;
}
/* Make vector [d+2] perpendicular to vector [d+1],
* this does not affect the normalization.
*/
- dep = iprod(v[d+1],v[d+2])/norm2(v[d+1]);
- for(i=0; i<DIM; i++)
+ dep = iprod(v[d+1], v[d+2])/norm2(v[d+1]);
+ for (i = 0; i < DIM; i++)
{
v[d+2][i] -= dep*v[d+1][i];
}
inv_skew_fac2 += sqr(v[d+2][d]);
-
- cprod(v[d+1],v[d+2],normal[d]);
+
+ cprod(v[d+1], v[d+2], normal[d]);
}
else
{
}
if (debug)
{
- fprintf(debug,"box[%d] %.3f %.3f %.3f\n",
- d,box[d][XX],box[d][YY],box[d][ZZ]);
- for(i=d+1; i<DIM; i++)
+ fprintf(debug, "box[%d] %.3f %.3f %.3f\n",
+ d, box[d][XX], box[d][YY], box[d][ZZ]);
+ for (i = d+1; i < DIM; i++)
{
- fprintf(debug," v[%d] %.3f %.3f %.3f\n",
- i,v[i][XX],v[i][YY],v[i][ZZ]);
+ fprintf(debug, " v[%d] %.3f %.3f %.3f\n",
+ i, v[i][XX], v[i][YY], v[i][ZZ]);
}
}
}
ddbox->skew_fac[d] = 1.0/sqrt(inv_skew_fac2);
/* Set the normal vector length to skew_fac */
dep = ddbox->skew_fac[d]/norm(normal[d]);
- svmul(dep,normal[d],normal[d]);
+ svmul(dep, normal[d], normal[d]);
if (debug)
{
- fprintf(debug,"skew_fac[%d] = %f\n",d,ddbox->skew_fac[d]);
- fprintf(debug,"normal[%d] %.3f %.3f %.3f\n",
- d,normal[d][XX],normal[d][YY],normal[d][ZZ]);
+ fprintf(debug, "skew_fac[%d] = %f\n", d, ddbox->skew_fac[d]);
+ fprintf(debug, "normal[%d] %.3f %.3f %.3f\n",
+ d, normal[d][XX], normal[d][YY], normal[d][ZZ]);
}
}
else
{
ddbox->skew_fac[d] = 1;
-
- for(i=0; i<DIM; i++)
+
+ for (i = 0; i < DIM; i++)
{
clear_rvec(ddbox->v[d][i]);
ddbox->v[d][i][i] = 1;
- }
+ }
clear_rvec(normal[d]);
normal[d][d] = 1;
}
}
}
-static void low_set_ddbox(t_inputrec *ir,ivec *dd_nc,matrix box,
- gmx_bool bCalcUnboundedSize,int ncg,t_block *cgs,rvec *x,
+static void low_set_ddbox(t_inputrec *ir, ivec *dd_nc, matrix box,
+ gmx_bool bCalcUnboundedSize, int ncg, t_block *cgs, rvec *x,
t_commrec *cr_sum,
gmx_ddbox_t *ddbox)
{
- rvec av,stddev;
- real b0,b1;
+ rvec av, stddev;
+ real b0, b1;
int d;
ddbox->npbcdim = ePBC2npbcdim(ir->ePBC);
ddbox->nboundeddim = inputrec2nboundeddim(ir);
- for(d=0; d<ddbox->nboundeddim; d++)
+ for (d = 0; d < ddbox->nboundeddim; d++)
{
ddbox->box0[d] = 0;
ddbox->box_size[d] = box[d][d];
if (ddbox->nboundeddim < DIM && bCalcUnboundedSize)
{
- calc_cgcm_av_stddev(cgs,ncg,x,av,stddev,cr_sum);
+ calc_cgcm_av_stddev(cgs, ncg, x, av, stddev, cr_sum);
/* GRID_STDDEV_FAC * stddev
* gives a uniform load for a rectangular block of cg's.
* For a sphere it is not a bad approximation for 4x1x1 up to 4x2x2.
*/
- for(d=ddbox->nboundeddim; d<DIM; d++)
+ for (d = ddbox->nboundeddim; d < DIM; d++)
{
b0 = av[d] - GRID_STDDEV_FAC*stddev[d];
b1 = av[d] + GRID_STDDEV_FAC*stddev[d];
if (debug)
{
- fprintf(debug,"Setting global DD grid boundaries to %f - %f\n",
- b0,b1);
+ fprintf(debug, "Setting global DD grid boundaries to %f - %f\n",
+ b0, b1);
}
ddbox->box0[d] = b0;
ddbox->box_size[d] = b1 - b0;
}
}
- set_tric_dir(dd_nc,ddbox,box);
+ set_tric_dir(dd_nc, ddbox, box);
}
-void set_ddbox(gmx_domdec_t *dd,gmx_bool bMasterState,t_commrec *cr_sum,
- t_inputrec *ir,matrix box,
- gmx_bool bCalcUnboundedSize,t_block *cgs,rvec *x,
+void set_ddbox(gmx_domdec_t *dd, gmx_bool bMasterState, t_commrec *cr_sum,
+ t_inputrec *ir, matrix box,
+ gmx_bool bCalcUnboundedSize, t_block *cgs, rvec *x,
gmx_ddbox_t *ddbox)
{
if (!bMasterState || DDMASTER(dd))
{
- low_set_ddbox(ir,&dd->nc,box,bCalcUnboundedSize,
- bMasterState ? cgs->nr : dd->ncg_home,cgs,x,
+ low_set_ddbox(ir, &dd->nc, box, bCalcUnboundedSize,
+ bMasterState ? cgs->nr : dd->ncg_home, cgs, x,
bMasterState ? NULL : cr_sum,
ddbox);
}
if (bMasterState)
{
- dd_bcast(dd,sizeof(gmx_ddbox_t),ddbox);
+ dd_bcast(dd, sizeof(gmx_ddbox_t), ddbox);
}
}
-void set_ddbox_cr(t_commrec *cr,ivec *dd_nc,
- t_inputrec *ir,matrix box,t_block *cgs,rvec *x,
+void set_ddbox_cr(t_commrec *cr, ivec *dd_nc,
+ t_inputrec *ir, matrix box, t_block *cgs, rvec *x,
gmx_ddbox_t *ddbox)
{
if (MASTER(cr))
{
- low_set_ddbox(ir,dd_nc,box,TRUE,cgs->nr,cgs,x,NULL,ddbox);
+ low_set_ddbox(ir, dd_nc, box, TRUE, cgs->nr, cgs, x, NULL, ddbox);
}
- gmx_bcast(sizeof(gmx_ddbox_t),ddbox,cr);
+ gmx_bcast(sizeof(gmx_ddbox_t), ddbox, cr);
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff