2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 1991-2001
5 * BIOSON Research Institute, Dept. of Biophysical Chemistry
6 * University of Groningen, The Netherlands
7 * Copyright (c) 2012,2013, by the GROMACS development team, led by
8 * David van der Spoel, Berk Hess, Erik Lindahl, and including many
9 * others, as listed in the AUTHORS file in the top-level source
10 * directory and at http://www.gromacs.org.
12 * GROMACS is free software; you can redistribute it and/or
13 * modify it under the terms of the GNU Lesser General Public License
14 * as published by the Free Software Foundation; either version 2.1
15 * of the License, or (at your option) any later version.
17 * GROMACS is distributed in the hope that it will be useful,
18 * but WITHOUT ANY WARRANTY; without even the implied warranty of
19 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
20 * Lesser General Public License for more details.
22 * You should have received a copy of the GNU Lesser General Public
23 * License along with GROMACS; if not, see
24 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
25 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
27 * If you want to redistribute modifications to GROMACS, please
28 * consider that scientific software is very special. Version
29 * control is crucial - bugs must be traceable. We will be happy to
30 * consider code for inclusion in the official distribution, but
31 * derived work must not be called official GROMACS. Details are found
32 * in the README & COPYING files - if they are missing, get the
33 * official version at http://www.gromacs.org.
35 * To help us fund GROMACS development, we humbly ask that you cite
36 * the research papers on the package. Check out http://www.gromacs.org.
43 * Routines for Filters and convolutions
48 #include "dens_filter.h"
53 #define EXP(x) (exp(x))
55 #define EXP(x) (expf(x))
58 /* Modulo function assuming y>0 but with arbitrary INTEGER x */
59 static int MOD(int x, int y){
65 gmx_bool convolution(int dataSize,real *x, int kernelSize, real* kernel)
70 /* check validity of params */
71 if(!x || !kernel) return FALSE;
72 if(dataSize <=0 || kernelSize <= 0) return FALSE;
74 /* start convolution from out[kernelSize-1] to out[dataSize-1] (last) */
75 for(i = kernelSize-1; i < dataSize; ++i)
77 for(j = i, k = 0; k < kernelSize; --j, ++k)
78 out[i] += x[j] * kernel[k];
81 /* convolution from out[0] to out[kernelSize-2] */
82 for(i = 0; i < kernelSize - 1; ++i)
84 for(j = i, k = 0; j >= 0; --j, ++k)
85 out[i] += x[j] * kernel[k];
88 for(i=0;i<dataSize;i++) x[i]=out[i];
93 /* Assuming kernel is shorter than x */
95 gmx_bool periodic_convolution(int datasize, real *x, int kernelsize,
101 if (!x || !kernel) return FALSE;
102 if (kernelsize<=0|| datasize<=0|| kernelsize > datasize) return FALSE;
104 snew(filtered,datasize);
106 for(i=0;(i<datasize); i++){
107 for(j=0; (j<kernelsize); j++){
108 filtered[i] += kernel[j]*x[MOD((i-j),datasize)];
111 for(i=0; i<datasize; i++) x[i]=filtered[i];
118 /* returns discrete gaussian kernel of size n in *out, where n=2k+1=3,5,7,9,11 and k=1,2,3 is the order
119 * NO checks are performed
121 void gausskernel(real *out, int n, real var){
126 for(i=-k; i<=k; i++){
128 tot+=out[j++]=EXP(-arg);