/* -------------------------------------------------------------------------- *
 *                                   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  *
 * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
 * 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:       *
 *                                                                            *
 * The above copyright notice and this permission notice shall be included in *
 * all copies or substantial portions of the Software.                        *
 *                                                                            *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
 * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
 * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
 * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
 * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
 * -------------------------------------------------------------------------- */

kernel void kupdate_md_verlet( 
		float dt,
		float3 posq<>, 
		float3 v<>, 
		float3 f<>,
		float invmass<>,
		out float3 vnew<>, 
		out float3 posqp<> ){

	vnew   = v + f*invmass*dt;
	posqp  = posq + vnew*dt;
}

kernel void kupdate_md1_berendsen( 
		float dt,
		float3 lg, //Berendsen coupling, assuming only one group
		float3 uold, //Mean velocity from previous step
		float4 posq<>, 
		float3 v<>, 
		float3 f<>,
		float invmass<>,
		out float3 vnew<>, 
		out float4 posqp<> )
{
	float3 vb;
	float3 one;
	posqp = posq;

	one = float3( 1.0f, 1.0f, 1.0f );

	vb = ( one - lg ) * uold;
	
	vnew = lg* ( v + f * invmass * dt ) + vb;
 	
	posqp.xyz += vnew * dt;
}

//Nose-Hoover / Parinello Rahman
kernel void kupdate_md1_extended (
		float dt,
		float3 lg, 
		float xi,
		float3 M0, 
		float3 M1,
		float3 M2,
		float3 uold,
		float4 posq<>, 
		float3 v<>, 
		float3 f<>,
		float invmass<>,
		out float3 vnew<>, 
		out float4 posqp<> )
{
	float3 vrel, vnrel;
	float3 vtrans;

	vrel  = v - uold;
	vtrans = float3( dot(M0, vrel), dot(M1, vrel), dot(M2, vrel) );
	vrel += dt * ( invmass * f - xi * vrel - vtrans );
	vnew = uold + lg * vrel;
	posqp = posq;
	posqp.xyz += vnew * dt;
}

		
kernel void kupdate_md2(
		float dtinv, //1/dt
		float4 posqp<>, //positions after constraints
		float4 posq<>,  //positions before update
		out float3 vnew<>, //Corrected velocities
		out float4 posqnew<> //equal to posqp, avoids an extra call to copy
		)
{
	posqnew = posqp;
	vnew = ( posqp - posq ) * dtinv;
}

/* Version that handles terms of order dt more carefully
 * Update1 computes deltax's rather than x + deltax 
 * Corresponding shake implementation modifies the delta's
 * Update2 adds the constrained deltas to x.
 * */

kernel void kupdate_md1_berendsen_fix1( 
		float dt,
		float3 lg, //Berendsen coupling, assuming only one group
		float3 uold, //Mean velocity from previous step
		float4 posq<>, 
		float3 v<>, 
		float3 f<>,
		float invmass<>,
		out float3 vnew<>, 
		out float4 posqp<> )
{
	float3 vb;
	float3 one;

	one = float3( 1.0f, 1.0f, 1.0f );

	vb = ( one - lg ) * uold;
	
	vnew = lg* ( v + f * invmass * dt ) + vb;
 	
	posqp.xyz = vnew * dt;
	posqp.w = posq.w;
}

//Nose-Hoover / Parinello Rahman
kernel void kupdate_md1_extended_fix1 (
		float dt,
		float3 lg, 
		float xi,
		float3 M0, 
		float3 M1,
		float3 M2,
		float3 uold,
		float4 posq<>, 
		float3 v<>, 
		float3 f<>,
		float invmass<>,
		out float3 vnew<>, 
		out float4 posqp<> )
{
	float3 vrel, vnrel;
	float3 vtrans;

	vrel  = v - uold;
	vtrans = float3( dot(M0, vrel), dot(M1, vrel), dot(M2, vrel) );
	vrel += dt * ( invmass * f - xi * vrel - vtrans );
	vnew = uold + lg * vrel;
	posqp.w = posq.w;
	posqp.xyz = vnew * dt;
}

kernel void kupdate_md2_fix1(
		float dtinv, //1/dt
		float4 posqp<>, //positions after constraints
		float4 posq<>,  //positions before update
		out float3 vnew<>, //Corrected velocities
		out float4 posqnew<> //equal to posqp, avoids an extra call to copy
		)
{
	posqnew.xyz = posq.xyz + posqp.xyz;
	posqnew.w   = posq.w;
	vnew = posqp.xyz * dtinv;
}