/* -------------------------------------------------------------------------- *
 *                                   OpenMM                                   *
 * -------------------------------------------------------------------------- *
 * This is part of the OpenMM molecular simulation toolkit originating from   *
 * Simbios, the NIH National Center for Physics-Based Simulation of           *
 * Biological Structures at Stanford, funded under the NIH Roadmap for        *
 * Medical Research, grant U54 GM072970. See https://simtk.org.               *
 *                                                                            *
 * Portions copyright (c) 2008 Stanford University and the Authors.           *
 * Authors: Peter Eastman, Mark Friedrichs, Chris Bruns                       *
 * Contributors:                                                              *
 *                                                                            *
 * Permission is hereby granted, free of charge, to any person obtaining a    *
 * copy of this software and associated documentation files (the "Software"), *
 * to deal in the Software without restriction, including without limitation  *
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 * and/or sell copies of the Software, and to permit persons to whom the      *
 * Software is furnished to do so, subject to the following conditions:       *
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 * The above copyright notice and this permission notice shall be included in *
 * all copies or substantial portions of the Software.                        *
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 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
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 * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
 * -------------------------------------------------------------------------- */

//Harmonic bonds kernel
//Input is a stream of i, j pairs
//parms is float2( b0, kA )
//Output is two streams of forces fi, fj
//Can be optimized as necessary
kernel void kbonds_harmonic(
		float xstrwidth, //atom stream width
		float2 atoms<>,
		float2 parms<>,
		float4 posq[][],
		out float3 fi<>,
		out float3 fj<>
		) {
	float2 ai, aj;
	float3 rij;
	float rinv;
	
	ai.y = floor( atoms.x / xstrwidth );
	ai.x = atoms.x - ai.y * xstrwidth;

	aj.y = floor( atoms.y / xstrwidth );
	aj.x = atoms.y - aj.y * xstrwidth;

	rij = posq[ai].xyz - posq[aj].xyz; //3
	rinv = rsqrt( dot(rij, rij) ); //6
	fi = -parms.y * ( 1.0f - parms.x * rinv ) * rij; //6
	fj = -fi; 

	//Total: 15 flops
}