/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
*
- *
+ *
* 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.
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* 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.
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+ *
* 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.
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+ *
* For more info, check our website at http://www.gromacs.org
- *
+ *
* And Hey:
* GROningen Mixture of Alchemy and Childrens' Stories
*/
#include "pbc.h"
#include "gstat.h"
#include "futil.h"
-#include "vec.h"
+#include "vec.h"
typedef struct {
- int natoms;
+ int natoms;
t_graph *gr;
} rmpbc_graph_t;
typedef struct gmx_rmpbc {
t_idef *idef;
- int natoms_init;
- int ePBC;
- int ngraph;
+ int natoms_init;
+ int ePBC;
+ int ngraph;
rmpbc_graph_t *graph;
} koeiepoep;
-static t_graph *gmx_rmpbc_get_graph(gmx_rmpbc_t gpbc,int ePBC,int natoms)
+static t_graph *gmx_rmpbc_get_graph(gmx_rmpbc_t gpbc, int ePBC, int natoms)
{
- int i;
+ int i;
rmpbc_graph_t *gr;
if (ePBC == epbcNONE
}
gr = NULL;
- for(i=0; i<gpbc->ngraph; i++)
+ for (i = 0; i < gpbc->ngraph; i++)
{
if (natoms == gpbc->graph[i].natoms)
{
*/
if (natoms > gpbc->natoms_init)
{
- gmx_fatal(FARGS,"Structure or trajectory file has more atoms (%d) than the topology (%d)",natoms,gpbc->natoms_init);
+ gmx_fatal(FARGS, "Structure or trajectory file has more atoms (%d) than the topology (%d)", natoms, gpbc->natoms_init);
}
gpbc->ngraph++;
- srenew(gpbc->graph,gpbc->ngraph);
- gr = &gpbc->graph[gpbc->ngraph-1];
+ srenew(gpbc->graph, gpbc->ngraph);
+ gr = &gpbc->graph[gpbc->ngraph-1];
gr->natoms = natoms;
- gr->gr = mk_graph(NULL,gpbc->idef,0,natoms,FALSE,FALSE);
+ gr->gr = mk_graph(NULL, gpbc->idef, 0, natoms, FALSE, FALSE);
}
return gr->gr;
}
-gmx_rmpbc_t gmx_rmpbc_init(t_idef *idef,int ePBC,int natoms,
+gmx_rmpbc_t gmx_rmpbc_init(t_idef *idef, int ePBC, int natoms,
matrix box)
{
gmx_rmpbc_t gpbc;
-
- snew(gpbc,1);
+
+ snew(gpbc, 1);
gpbc->natoms_init = natoms;
-
+
/* This sets pbc when we now it,
* otherwise we guess it from the instantaneous box in the trajectory.
*/
if (NULL != gpbc)
{
- for(i=0; i<gpbc->ngraph; i++)
+ for (i = 0; i < gpbc->ngraph; i++)
{
done_graph(gpbc->graph[i].gr);
}
}
}
-static int gmx_rmpbc_ePBC(gmx_rmpbc_t gpbc,matrix box)
+static int gmx_rmpbc_ePBC(gmx_rmpbc_t gpbc, matrix box)
{
if (NULL != gpbc && gpbc->ePBC >= 0)
{
}
}
-void gmx_rmpbc(gmx_rmpbc_t gpbc,int natoms,matrix box,rvec x[])
+void gmx_rmpbc(gmx_rmpbc_t gpbc, int natoms, matrix box, rvec x[])
{
- int ePBC;
+ int ePBC;
t_graph *gr;
-
- ePBC = gmx_rmpbc_ePBC(gpbc,box);
- gr = gmx_rmpbc_get_graph(gpbc,ePBC,natoms);
+
+ ePBC = gmx_rmpbc_ePBC(gpbc, box);
+ gr = gmx_rmpbc_get_graph(gpbc, ePBC, natoms);
if (gr != NULL)
{
- mk_mshift(stdout,gr,ePBC,box,x);
- shift_self(gr,box,x);
+ mk_mshift(stdout, gr, ePBC, box, x);
+ shift_self(gr, box, x);
}
}
-void gmx_rmpbc_copy(gmx_rmpbc_t gpbc,int natoms,matrix box,rvec x[],rvec x_s[])
+void gmx_rmpbc_copy(gmx_rmpbc_t gpbc, int natoms, matrix box, rvec x[], rvec x_s[])
{
- int ePBC;
+ int ePBC;
t_graph *gr;
- int i;
+ int i;
- ePBC = gmx_rmpbc_ePBC(gpbc,box);
- gr = gmx_rmpbc_get_graph(gpbc,ePBC,natoms);
+ ePBC = gmx_rmpbc_ePBC(gpbc, box);
+ gr = gmx_rmpbc_get_graph(gpbc, ePBC, natoms);
if (gr != NULL)
{
- mk_mshift(stdout,gr,ePBC,box,x);
- shift_x(gr,box,x,x_s);
+ mk_mshift(stdout, gr, ePBC, box, x);
+ shift_x(gr, box, x, x_s);
}
else
{
- for(i=0; i<natoms; i++)
+ for (i = 0; i < natoms; i++)
{
- copy_rvec(x[i],x_s[i]);
+ copy_rvec(x[i], x_s[i]);
}
}
}
-void gmx_rmpbc_trxfr(gmx_rmpbc_t gpbc,t_trxframe *fr)
+void gmx_rmpbc_trxfr(gmx_rmpbc_t gpbc, t_trxframe *fr)
{
- int ePBC;
+ int ePBC;
t_graph *gr;
if (fr->bX && fr->bBox)
{
- ePBC = gmx_rmpbc_ePBC(gpbc,fr->box);
- gr = gmx_rmpbc_get_graph(gpbc,ePBC,fr->natoms);
+ ePBC = gmx_rmpbc_ePBC(gpbc, fr->box);
+ gr = gmx_rmpbc_get_graph(gpbc, ePBC, fr->natoms);
if (gr != NULL)
{
- mk_mshift(stdout,gr,ePBC,fr->box,fr->x);
- shift_self(gr,fr->box,fr->x);
+ mk_mshift(stdout, gr, ePBC, fr->box, fr->x);
+ shift_self(gr, fr->box, fr->x);
}
}
}
-void rm_gropbc(t_atoms *atoms,rvec x[],matrix box)
+void rm_gropbc(t_atoms *atoms, rvec x[], matrix box)
{
real dist;
- int n,m,d;
-
+ int n, m, d;
+
/* check periodic boundary */
- for(n=1;(n<atoms->nr);n++)
+ for (n = 1; (n < atoms->nr); n++)
{
- for(m=DIM-1; m>=0; m--)
+ for (m = DIM-1; m >= 0; m--)
{
dist = x[n][m]-x[n-1][m];
if (fabs(dist) > 0.9*box[m][m])
{
- if ( dist > 0 )
+ if (dist > 0)
{
- for(d=0; d<=m; d++)
+ for (d = 0; d <= m; d++)
{
x[n][d] -= box[m][d];
}
}
else
{
- for(d=0; d<=m; d++)
+ for (d = 0; d <= m; d++)
{
x[n][d] += box[m][d];
}
}
- }
+ }
}
}
}
-
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff