kupdatemd.br

/****************************************************************
* This file is part of the gpu acceleration library for gromacs.
* Author: V. Vishal
* Copyright (C) Pande Group, Stanford, 2006
*****************************************************************/

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;
}