kshakeh.br

/* -------------------------------------------------------------------------- *
 *                                   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.                                     *
 * -------------------------------------------------------------------------- */

/*
 * This kernel constrains bonds involving hydrogen using an unrolled
 * shake implementation. We assume that a heavy atom can have at most 
 * 3 hydrogens attached. The hydrogens are expected to be identical
 *
 * For atoms that have ewer than 3 hydrogens
 *
 * Also we don't check the constraints!
 *  
 * We do a fixed number of iterations without checking for convergence
 * to avoid stalling
 * *************************************************************/

/*
kernel void
kshakeh(
		float nit,      //number of iterations
		float strwidth, //stream width of posq
		float invmH,    //inverse mass of hydrogen
		float omega,    //parameter from gromacs, possibly unused
		float4 atoms<>, //heavy0, h1, h2, h3
		float4 posq[][], //positions before update
		float4 posqp[][], //positions after update
		float4 params<>, // (1/m0, mu/2, blensq, 0.0f )
		out float4 cposq0<>, //constrained position for heavy atom
		out float4 cposq1<>, //ditto for h1
		out float4 cposq2<>, //ditto for h2
		out float4 cposq3<> //ditto for h3
		) {
	float2 ai, aj1, aj2, aj3; //2d indices, can be precalc.
	float i; //iteration count
	float3 xi, xj1, xj2, xj3; //coordinates
	float3 xpi, xpj1, xpj2, xpj3; //coordinates
	float3 rij1, rij2, rij3, rpij, dr;
	float rpsqij, rrpr, acor;
	float mask2, mask3;
	float diff;
	
	ai.y  = floor( atoms.x / strwidth );
	ai.x  = atoms.x - ai.y * strwidth;

	aj1.y = floor( atoms.y / strwidth );
	aj1.x = atoms.y - aj1.y * strwidth;

	//If further hydrogens are absent,
	//just set to the coordinates of the first
	//so we don't have any junk memory accesses
	//or nans/infs in the calcs.	
	if ( atoms.z > -0.5f ) {
		aj2.y = floor( atoms.z / strwidth );
		aj2.x = atoms.z - aj2.y * strwidth;
		mask2 = 1.0f;
	}
	else {
		aj2 = aj1; 
		mask2 = 0.0f;
	}

	if ( atoms.w > -0.5f ) {	
		aj3.y = floor( atoms.w / strwidth );
		aj3.x = atoms.w - aj3.y * strwidth;
		mask3 = 1.0f;
	}
	else {
		aj3 = aj1;
		mask3 = 0.0f;
	}


	cposq0 = posq[ai];
	cposq1 = posq[aj1];
	cposq2 = posq[aj2];
	cposq3 = posq[aj3];
	
	
	xi  = cposq0.xyz;
	xj1 = cposq1.xyz;
	xj2 = cposq2.xyz;
	xj3 = cposq3.xyz;
	
	rij1 = xi - xj1;
	rij2 = xi - xj2;
	rij3 = xi - xj3;

	xpi  = posqp[ai].xyz;
	xpj1 = posqp[aj1].xyz;
	xpj2 = posqp[aj2].xyz;
	xpj3 = posqp[aj3].xyz;

	i = 0.0f;
	while ( i < 15.0f ) {
		//First hydrogen
		rpij   = xpi - xpj1;
		rpsqij = dot( rpij, rpij );
		rrpr   = dot( rij1, rpij );
		//for debugging only
		diff = abs( params.z - rpsqij ) / (params.z * 2 * 1e-4 );
		if ( diff < 1.0f )
			acor = 0.0f;
		else
			//params.y = mu/2, params.z = blen*blen
			acor = omega * ( params.z - rpsqij ) * params.y / rrpr ;
		dr   = rij1 * acor;
		xpi  += dr * params.x;
		xpj1 -= dr * invmH;

		//Second hydrogen
		rpij   = xpi - xpj2;
		rpsqij = dot( rpij, rpij );
		rrpr   = dot( rij2, rpij );
		//for debugging only
		diff = abs( params.z - rpsqij ) / (params.z * 2 * 1e-4 );
		if ( diff < 1.0f )
			acor = 0.0f;
		else
			//params.y = mu/2, params.z = blen*blen
			acor = mask2 * omega * ( params.z - rpsqij ) * params.y / rrpr ;
		dr   = rij2 * acor;
		xpi  += dr * params.x;
		xpj2 -= dr * invmH;

		//Third hydrogen
		rpij   = xpi - xpj3;
		rpsqij = dot( rpij, rpij );
		rrpr   = dot( rij3, rpij );
		//for debugging only
		diff = abs( params.z - rpsqij ) / (params.z * 2 * 1e-4 );
		if ( diff < 1.0f )
			acor = 0.0f;
		else
			//params.y = mu/2, params.z = blen*blen
			acor = mask3 * omega * ( params.z - rpsqij ) * params.y / rrpr ;
		dr   = rij3 * acor;
		xpi  += dr * params.x;
		xpj3 -= dr * invmH;
		
		i += 1.0f;
	}

	cposq0.xyz = xpi;
	cposq1.xyz = xpj1;
	cposq2.xyz = xpj2;
	cposq3.xyz = xpj3;
} */

/*Applies the updated positions
 *Each atom occurs at one and only one position
 * */
/*
kernel void kshakeh_update( 
		float strwidth, //width of cposq streams
		float2 invmap<>,    //shakeh inverse map
		float4 posq<>,     //untouched positions
		float4 cposq0[][], //constrained position for heavy atom
		float4 cposq1[][], //ditto for h1
		float4 cposq2[][], //ditto for h2
		float4 cposq3[][], //ditto for h3
		out float4 oposq<> //updated positions
		){
	float2 atom;
	
	atom.y = floor( invmap.x / strwidth );
	atom.x = invmap.x - atom.y * strwidth;
	
	if ( invmap.y < 0 )
		oposq = posq;
	else if ( invmap.y < 0.5f ) 
		oposq = cposq0[ atom ];
	else if ( invmap.y < 1.5f )
		oposq = cposq1[ atom ];
	else if ( invmap.y < 2.5f )
		oposq = cposq2[ atom ];
	else if ( invmap.y < 3.5f )
		oposq = cposq3[ atom ];
} */

/* Fix for precision of terms first order in dt
 * To be used with corresponding update kernels
 * The input posqp is now changes to posq rather than
 * posq+changes
 * */
kernel void
kshakeh_fix1(
		float nit,      //number of iterations
		float strwidth, //stream width of posq
		float invmH,    //inverse mass of hydrogen
		float omega,    //parameter from gromacs, possibly unused
		float4 atoms<>, //heavy0, h1, h2, h3
		float3 posq[][], //positions before update
		float3 posqp[][], //changes to positions
		float4 params<>, // (1/m0, mu/2, blensq, 0.0f )
		out float3 cposq0<>, //constrained position for heavy atom
		out float3 cposq1<>, //ditto for h1
		out float3 cposq2<>, //ditto for h2
		out float3 cposq3<> //ditto for h3
		) {
	float2 ai, aj1, aj2, aj3; //2d indices, can be precalc.
	float i; //iteration count
	float3 xi, xj1, xj2, xj3; //coordinates
	float3 xpi, xpj1, xpj2, xpj3; //coordinates
	float3 rij1, rij2, rij3, rpij, dr;
	float rpsqij, rrpr, acor;
	float mask2, mask3;
	float diff;
	float rij1sq, rij2sq, rij3sq;
	float ld1, ld2, ld3;
	
	// ai.y  = floor( atoms.x / strwidth );
   ai.y  = round( (atoms.x - fmod( atoms.x, strwidth ))/strwidth );
	ai.x  = atoms.x - ai.y * strwidth;

	// aj1.y = floor( atoms.y / strwidth );
   aj1.y  = round( (atoms.y - fmod( atoms.y, strwidth ))/strwidth );
	aj1.x = atoms.y - aj1.y * strwidth;

	//If further hydrogens are absent,
	//just set to the coordinates of the first
	//so we don't have any junk memory accesses
	//or nans/infs in the calcs.	
	if ( atoms.z > -0.5f ) {
		// aj2.y = floor( atoms.z / strwidth );
		aj2.y = round( (atoms.z - fmod( atoms.z, strwidth ))/strwidth );
		aj2.x = atoms.z - aj2.y * strwidth;
		mask2 = 1.0f;
	}
	else {
		aj2 = aj1; 
		mask2 = 0.0f;
	}

	if ( atoms.w > -0.5f ) {	
		// aj3.y = floor( atoms.w / strwidth );
		aj3.y = round( (atoms.w - fmod( atoms.w, strwidth ))/strwidth );
		aj3.x = atoms.w - aj3.y * strwidth;
		mask3 = 1.0f;
	}
	else {
		aj3 = aj1;
		mask3 = 0.0f;
	}

	cposq0 = posq[ai];
	cposq1 = posq[aj1];
	cposq2 = posq[aj2];
	cposq3 = posq[aj3];
	
	xi  = cposq0;
	xj1 = cposq1;
	xj2 = cposq2;
	xj3 = cposq3;
	
	rij1 = xi - xj1;
	rij2 = xi - xj2;
	rij3 = xi - xj3;

	rij1sq = dot( rij1, rij1 );
	rij2sq = dot( rij2, rij2 );
	rij3sq = dot( rij3, rij3 );

	ld1 = params.z - rij1sq;
	ld2 = params.z - rij2sq;
	ld3 = params.z - rij3sq;

/*
	xpi  = posqp[ai];
	xpj1 = posqp[aj1];
	xpj2 = posqp[aj2];
	xpj3 = posqp[aj3];
*/


	xpi  = posqp[ai]   - xi;
	xpj1 = posqp[aj1]  - xj1;
	xpj2 = posqp[aj2]  - xj2;
	xpj3 = posqp[aj3]  - xj3;


// XXX
	// cposq0 = posqp[ai];
	// cposq1 = posqp[aj1];
	// cposq2 = posqp[aj2];
	// cposq3 = posqp[aj3];
// OK
// XXX
	


	i = 0.0f;
	while ( i < 15.0f ) {
		//First hydrogen
		rpij   = xpi - xpj1; //This is really rpij - rij
		rpsqij = dot( rpij, rpij ); //This is really deltar ^ 2
		rrpr   = dot( rij1, rpij ); //This is r.deltar
		//for debugging only
		//params.y = mu/2, params.z = blen*blen
		diff = abs( ld1 - 2 * rrpr - rpsqij ) / (params.z * 2 * 1e-4f );
		if ( diff < 1.0f )
		  acor = 0.0f;
		 else
			acor = omega * ( ld1 - 2 * rrpr - rpsqij ) * params.y / ( rrpr + rij1sq ) ;
		dr   = rij1 * acor;
		xpi  += dr * params.x;
		xpj1 -= dr * invmH;

		//Second hydrogen
		rpij   = xpi - xpj2;
		rpsqij = dot( rpij, rpij );
		rrpr   = dot( rij2, rpij );
		//for debugging only
		diff = abs( ld2 - 2 * rrpr - rpsqij ) / (params.z * 2 * 1e-4f );
		if ( diff < 1.0f )
			acor = 0.0f;
		else
			acor = mask2 * omega * ( ld2 - 2 * rrpr - rpsqij ) * params.y / ( rrpr + rij2sq ) ;
		dr   = rij2 * acor;
		xpi  += dr * params.x;
		xpj2 -= dr * invmH;

		//Third hydrogen
		rpij   = xpi - xpj3;
		rpsqij = dot( rpij, rpij );
		rrpr   = dot( rij3, rpij );
		diff = abs( ld3 - 2 * rrpr - rpsqij ) / (params.z * 2 * 1e-4f );
		// for debugging only
		if ( diff < 1.0f )
			 acor = 0.0f;
		else
			acor = mask3 * omega * ( ld3 - 2 * rrpr - rpsqij ) * params.y / ( rrpr + rij3sq ) ;
		dr   = rij3 * acor;
		xpi  += dr * params.x;
		xpj3 -= dr * invmH;
		
		i += 1.0f;
	}

	//Output modified delta's
	cposq0 = xpi;
	cposq1 = xpj1;
	cposq2 = xpj2;
	cposq3 = xpj3;

}

kernel void
kshakeh_fix2(
		float nit,      //number of iterations
		float strwidth, //stream width of posq
		float invmH,    //inverse mass of hydrogen
		float omega,    //parameter from gromacs, possibly unused
		float4 atoms<>, //heavy0, h1, h2, h3
		float3 posq[][], //positions before update
		float3 posqp[][], //changes to positions
		float4 params<>, // (1/m0, mu/2, blensq, 0.0f )
		out float3 cposq0<>, //constrained position for heavy atom
		out float3 cposq1<>, //ditto for h1
		out float3 cposq2<>, //ditto for h2
		out float3 cposq3<> //ditto for h3
		) {
	float2 ai, aj1, aj2, aj3; //2d indices, can be precalc.
	float i; //iteration count
	float3 xi, xj1, xj2, xj3; //coordinates
	float3 xpi, xpj1, xpj2, xpj3; //coordinates
	float3 rij1, rij2, rij3, rpij, dr;
	float rpsqij, rrpr, acor;
	float mask2, mask3;
	float diff;
	float rij1sq, rij2sq, rij3sq;
	float ld1, ld2, ld3;
	
	// ai.y  = floor( atoms.x / strwidth );
   ai.y  = round( (atoms.x - fmod( atoms.x, strwidth ))/strwidth );
	ai.x  = atoms.x - ai.y * strwidth;

	// aj1.y = floor( atoms.y / strwidth );
   aj1.y  = round( (atoms.y - fmod( atoms.y, strwidth ))/strwidth );
	aj1.x = atoms.y - aj1.y * strwidth;

	//If further hydrogens are absent,
	//just set to the coordinates of the first
	//so we don't have any junk memory accesses
	//or nans/infs in the calcs.	
	if ( atoms.z > -0.5f ) {
		// aj2.y = floor( atoms.z / strwidth );
		aj2.y = round( (atoms.z - fmod( atoms.z, strwidth ))/strwidth );
		aj2.x = atoms.z - aj2.y * strwidth;
		mask2 = 1.0f;
	}
	else {
		aj2 = aj1; 
		mask2 = 0.0f;
	}

	if ( atoms.w > -0.5f ) {	
		// aj3.y = floor( atoms.w / strwidth );
		aj3.y = round( (atoms.w - fmod( atoms.w, strwidth ))/strwidth );
		aj3.x = atoms.w - aj3.y * strwidth;
		mask3 = 1.0f;
	}
	else {
		aj3 = aj1;
		mask3 = 0.0f;
	}


	cposq0 = posq[ai];
	cposq1 = posq[aj1];
	cposq2 = posq[aj2];
	cposq3 = posq[aj3];
	
	xi  = cposq0;
	xj1 = cposq1;
	xj2 = cposq2;
	xj3 = cposq3;
	
	rij1 = xi - xj1;
	rij2 = xi - xj2;
	rij3 = xi - xj3;

	rij1sq = dot( rij1, rij1 );
	rij2sq = dot( rij2, rij2 );
	rij3sq = dot( rij3, rij3 );

	ld1 = params.z - rij1sq;
	ld2 = params.z - rij2sq;
	ld3 = params.z - rij3sq;

	xpi  = posqp[ai];
	xpj1 = posqp[aj1];
	xpj2 = posqp[aj2];
	xpj3 = posqp[aj3];


/*
	xpi  = posqp[ai]   - xi;
	xpj1 = posqp[aj1]  - xj1;
	xpj2 = posqp[aj2]  - xj2;
	xpj3 = posqp[aj3]  - xj3;

*/

// XXX
	// cposq0 = posqp[ai];
	// cposq1 = posqp[aj1];
	// cposq2 = posqp[aj2];
	// cposq3 = posqp[aj3];
// OK
// XXX
	


	i = 0.0f;
	while ( i < 15.0f ) {
		//First hydrogen
		rpij   = xpi - xpj1; //This is really rpij - rij
		rpsqij = dot( rpij, rpij ); //This is really deltar ^ 2
		rrpr   = dot( rij1, rpij ); //This is r.deltar
		//for debugging only
		//params.y = mu/2, params.z = blen*blen
		diff = abs( ld1 - 2 * rrpr - rpsqij ) / (params.z * 2 * 1e-4f );
		if ( diff < 1.0f )
		  acor = 0.0f;
		 else
			acor = omega * ( ld1 - 2 * rrpr - rpsqij ) * params.y / ( rrpr + rij1sq ) ;
		dr   = rij1 * acor;
		xpi  += dr * params.x;
		xpj1 -= dr * invmH;

		//Second hydrogen
		rpij   = xpi - xpj2;
		rpsqij = dot( rpij, rpij );
		rrpr   = dot( rij2, rpij );
		//for debugging only
		diff = abs( ld2 - 2 * rrpr - rpsqij ) / (params.z * 2 * 1e-4f );
		if ( diff < 1.0f )
			acor = 0.0f;
		else
			acor = mask2 * omega * ( ld2 - 2 * rrpr - rpsqij ) * params.y / ( rrpr + rij2sq ) ;
		dr   = rij2 * acor;
		xpi  += dr * params.x;
		xpj2 -= dr * invmH;

		//Third hydrogen
		rpij   = xpi - xpj3;
		rpsqij = dot( rpij, rpij );
		rrpr   = dot( rij3, rpij );
		diff = abs( ld3 - 2 * rrpr - rpsqij ) / (params.z * 2 * 1e-4f );
		// for debugging only
		if ( diff < 1.0f )
			 acor = 0.0f;
		else
			acor = mask3 * omega * ( ld3 - 2 * rrpr - rpsqij ) * params.y / ( rrpr + rij3sq ) ;
		dr   = rij3 * acor;
		xpi  += dr * params.x;
		xpj3 -= dr * invmH;
		
		i += 1.0f;
	}

	//Output modified delta's
	cposq0 = xpi;
	cposq1 = xpj1;
	cposq2 = xpj2;
	cposq3 = xpj3;

}

/*Applies the updated delta's
 *Each atom occurs at one and only one position
 * */
kernel void kshakeh_update1_fix1Old( 
		float strwidth, //width of cposq streams
		float2 invmap<>,    //shakeh inverse map
		float3 posq<>,     //constrained deltas
		float3 cposq0[][], //constrained delta for heavy atom
		float3 cposq1[][], //ditto for h1
		float3 cposq2[][], //ditto for h2
		float3 cposq3[][], //ditto for h3
		out float3 oposq<> //updated deltas
		){
	float2 atom;
	
	//atom.y = floor( invmap.x / strwidth );
   atom.y  = round( (invmap.x - fmod( invmap.x, strwidth ))/strwidth );
	atom.x = invmap.x - atom.y * strwidth;
	
	if ( invmap.y < 0 )
		oposq = posq;
	else if ( invmap.y < 0.5f ) 
		oposq = cposq0[ atom ];
	else if ( invmap.y < 1.5f )
		oposq = cposq1[ atom ];
	else if ( invmap.y < 2.5f )
		oposq = cposq2[ atom ];
	else if ( invmap.y < 3.5f )
		oposq = cposq3[ atom ];
}

kernel void kshakeh_update2_fix1( 
		float strwidth, //width of cposq streams
		float2 invmap<>,    //shakeh inverse map
		float3 posq<>,     //old positions
		float3 posqp<>,    //deltas from sd2
		float3 cposq0[][], //constrained delta for heavy atom
		float3 cposq1[][], //ditto for h1
		float3 cposq2[][], //ditto for h2
		float3 cposq3[][], //ditto for h3
		out float3 oposq<> //updated deltas
		){
	float2 atom;
	
	// atom.y = floor( invmap.x / strwidth );
   atom.y  = round( (invmap.x - fmod( invmap.x, strwidth ))/strwidth );
	atom.x = invmap.x - atom.y * strwidth;
	
	if ( invmap.y < 0 ){
		oposq = posqp - posq;
	} else if ( invmap.y < 0.5f ) 
		oposq = cposq0[ atom ];
	else if ( invmap.y < 1.5f)
		oposq = cposq1[ atom ];
	else if ( invmap.y < 2.5f )
		oposq = cposq2[ atom ];
	else if ( invmap.y < 3.5f )
		oposq = cposq3[ atom ];

	oposq += posq;
}

kernel void kshakeh_update1_fix1( 
		float strwidth, //width of cposq streams
      float sdFactor,
		float2 invmap<>,    //shakeh inverse map
		float3 posq<>,     //old positions
		float3 posqp<>,    //deltas from sd2
		float3 vp<>,    //deltas from sd2
		float3 cposq0[][], //constrained delta for heavy atom
		float3 cposq1[][], //ditto for h1
		float3 cposq2[][], //ditto for h2
		float3 cposq3[][], //ditto for h3
		out float3 oposq<> //updated deltas
		){
	float2 atom;
	
	// atom.y = floor( invmap.x / strwidth );
   atom.y  = round( (invmap.x - fmod( invmap.x, strwidth ))/strwidth );
	atom.x = invmap.x - atom.y * strwidth;
	
	oposq = posq;
	if ( invmap.y < 0 ){
		oposq = posqp;
	} else if ( invmap.y < 0.5f ) 
		oposq += cposq0[ atom ];
	else if ( invmap.y < 1.5f )
		oposq += cposq1[ atom ];
	else if ( invmap.y < 2.5f )
		oposq += cposq2[ atom ];
	else if ( invmap.y < 3.5f )
		oposq += cposq3[ atom ];

}