/* $Revision$ $Author$ $Date$
*
* Copyright (C) 2005-2007 Violeta Labarta <vlabarta@users.sf.net>
*
* Contact: cdk-devel@lists.sourceforge.net
*
* This program 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.
*
* This program 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 this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
*/
package org.openscience.cdk.modeling.forcefield;
/**
* Cutoffs and Smoothing Functions.
*
*@author vlabarta
*@cdk.created February 28, 2005
*@cdk.module forcefield
* @cdk.githash
*/
public class SmoothingFunctions {
double[] s = null; // Smoothing function
double cutoffr0 = 5; // For Smoothing function (s)
double cutoffr1 = 6; // For Smoothing function (s)
double dampingFactor = 1; // For Smoothing function (s)
/**
* Constructor for the SmoothingFunctions object
*/
public SmoothingFunctions() {}
/**
* Calculate the smoothing function from atom distances.
*
*
*@param atomDistances 3d distance between the atoms.
*/
public void setSmoothingFunction(double[] atomDistances) {
s = new double[atomDistances.length];
for (int i=0; i<atomDistances.length; i++) {
if (atomDistances[i] < cutoffr0) {
s[i] = 1;
} else if (atomDistances[i] > cutoffr1) {
s[i] = 0;
} else {
s[i] = 1 - dampingFactor * ((atomDistances[i] - cutoffr0) / (cutoffr1 - cutoffr0));
}
//logger.debug("s[" + i + "] = " + s[i]);
}
}
/**
* Get the smoothing function value for every atom distance.
*
*
*@return smoothing function value for every atom distance.
*/
public double[] getSmoothingFunction() {
return s;
}
}