calcenergy.cl

/*

OCLADock, an OpenCL implementation of AutoDock 4.2 running a Lamarckian Genetic Algorithm
Copyright (C) 2017 TU Darmstadt, Embedded Systems and Applications Group, Germany. All rights reserved.

AutoDock is a Trade Mark of the Scripps Research Institute.

This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
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 General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.

*/

//#define DEBUG_ENERGY_KERNEL

#include "calcenergy_basic.h"

typedef struct
{
       float atom_charges_const[MAX_NUM_OF_ATOMS];
       char  atom_types_const  [MAX_NUM_OF_ATOMS];
} kernelconstant_interintra;

typedef struct
{
       char  intraE_contributors_const[3*MAX_INTRAE_CONTRIBUTORS];
} kernelconstant_intracontrib;

typedef struct
{
       float reqm_const [ATYPE_NUM];
       float reqm_hbond_const [ATYPE_NUM];
       unsigned int  atom1_types_reqm_const [ATYPE_NUM];
       unsigned int  atom2_types_reqm_const [ATYPE_NUM];
       float VWpars_AC_const   [MAX_NUM_OF_ATYPES*MAX_NUM_OF_ATYPES];
       float VWpars_BD_const   [MAX_NUM_OF_ATYPES*MAX_NUM_OF_ATYPES];
       float dspars_S_const    [MAX_NUM_OF_ATYPES];
       float dspars_V_const    [MAX_NUM_OF_ATYPES];
} kernelconstant_intra;

typedef struct
{
       int   rotlist_const     [MAX_NUM_OF_ROTATIONS];
} kernelconstant_rotlist;

typedef struct
{
       float ref_coords_x_const[MAX_NUM_OF_ATOMS];
       float ref_coords_y_const[MAX_NUM_OF_ATOMS];
       float ref_coords_z_const[MAX_NUM_OF_ATOMS];
       float rotbonds_moving_vectors_const[3*MAX_NUM_OF_ROTBONDS];
       float rotbonds_unit_vectors_const  [3*MAX_NUM_OF_ROTBONDS];
       float ref_orientation_quats_const  [4*MAX_NUM_OF_RUNS];
} kernelconstant_conform;

// All related pragmas are in defines.h (accesible by host and device code)

void gpu_calc_energy(	    
				int    dockpars_rotbondlist_length,
				char   dockpars_num_of_atoms,
			    	char   dockpars_gridsize_x,
			    	char   dockpars_gridsize_y,
			    	char   dockpars_gridsize_z,
								    		// g1 = gridsize_x
				uint   dockpars_gridsize_x_times_y, 		// g2 = gridsize_x * gridsize_y
				uint   dockpars_gridsize_x_times_y_times_z,	// g3 = gridsize_x * gridsize_y * gridsize_z
		 __global const float* restrict dockpars_fgrids, // This is too large to be allocated in __constant 
		            	char   dockpars_num_of_atypes,
		            	int    dockpars_num_of_intraE_contributors,
			    	float  dockpars_grid_spacing,
			    	float  dockpars_coeff_elec,
			    	float  dockpars_qasp,
			    	float  dockpars_coeff_desolv,
				float  dockpars_smooth,

                    // Some OpenCL compilers don't allow declaring 
		    // local variables within non-kernel functions.
		    // These local variables must be declared in a kernel, 
		    // and then passed to non-kernel functions.
		    	__local float* genotype,
		   	__local float* energy,
		    	__local int*   run_id,

		    	__local float* calc_coords_x,
		    	__local float* calc_coords_y,
		    	__local float* calc_coords_z,
		    	__local float* partial_energies,

			#if defined (DEBUG_ENERGY_KERNEL)
			__local float* partial_interE,
			__local float* partial_intraE,
			#endif
#if 0
 				bool   debug,
#endif
		   __constant     kernelconstant_interintra* 		kerconst_interintra,
		   __global const kernelconstant_intracontrib*  	kerconst_intracontrib,
		   __constant     kernelconstant_intra*			kerconst_intra,
		   __constant     kernelconstant_rotlist*   		kerconst_rotlist,
		   __constant     kernelconstant_conform*		kerconst_conform
)

//The GPU device function calculates the energy of the entity described by genotype, dockpars and the liganddata
//arrays in constant memory and returns it in the energy parameter. The parameter run_id has to be equal to the ID
//of the run whose population includes the current entity (which can be determined with blockIdx.x), since this
//determines which reference orientation should be used.
{
	partial_energies[get_local_id(0)] = 0.0f;

	#if defined (DEBUG_ENERGY_KERNEL)
	partial_interE[get_local_id(0)] = 0.0f;
	partial_intraE[get_local_id(0)] = 0.0f;
	#endif

	// Convert orientation genes from sex. to radians
	float phi         = genotype[3] * DEG_TO_RAD;
	float theta       = genotype[4] * DEG_TO_RAD;
	float genrotangle = genotype[5] * DEG_TO_RAD;

	float genrot_unitvec [3];
	float sin_angle = native_sin(theta);
	genrot_unitvec [0] = sin_angle*native_cos(phi);
	genrot_unitvec [1] = sin_angle*native_sin(phi);
	genrot_unitvec [2] = native_cos(theta);

	uchar g1 = dockpars_gridsize_x;
	uint  g2 = dockpars_gridsize_x_times_y;
  	uint  g3 = dockpars_gridsize_x_times_y_times_z;

	// ================================================
	// CALCULATING ATOMIC POSITIONS AFTER ROTATIONS
	// ================================================
	for (uint rotation_counter = get_local_id(0);
	          rotation_counter < dockpars_rotbondlist_length;
	          rotation_counter+=NUM_OF_THREADS_PER_BLOCK)
	{
		int rotation_list_element = kerconst_rotlist->rotlist_const[rotation_counter];

		if ((rotation_list_element & RLIST_DUMMY_MASK) == 0)	// If not dummy rotation
		{
			uint atom_id = rotation_list_element & RLIST_ATOMID_MASK;

			// Capturing atom coordinates
			float atom_to_rotate[3];

			if ((rotation_list_element & RLIST_FIRSTROT_MASK) != 0)	// If first rotation of this atom
			{
				atom_to_rotate[0] = kerconst_conform->ref_coords_x_const[atom_id];
				atom_to_rotate[1] = kerconst_conform->ref_coords_y_const[atom_id];
				atom_to_rotate[2] = kerconst_conform->ref_coords_z_const[atom_id];
			}
			else
			{
				atom_to_rotate[0] = calc_coords_x[atom_id];
				atom_to_rotate[1] = calc_coords_y[atom_id];
				atom_to_rotate[2] = calc_coords_z[atom_id];
			}

			// Capturing rotation vectors and angle
			float rotation_unitvec[3];
			float rotation_movingvec[3];
			float rotation_angle;

			float quatrot_left_x, quatrot_left_y, quatrot_left_z, quatrot_left_q;
			float quatrot_temp_x, quatrot_temp_y, quatrot_temp_z, quatrot_temp_q;

			if ((rotation_list_element & RLIST_GENROT_MASK) != 0)	// If general rotation
			{
				rotation_unitvec[0] = genrot_unitvec[0];
				rotation_unitvec[1] = genrot_unitvec[1];
				rotation_unitvec[2] = genrot_unitvec[2];

				rotation_movingvec[0] = genotype[0];
				rotation_movingvec[1] = genotype[1];
				rotation_movingvec[2] = genotype[2];

				rotation_angle = genrotangle;
			}
			else	// If rotating around rotatable bond
			{
				uint rotbond_id = (rotation_list_element & RLIST_RBONDID_MASK) >> RLIST_RBONDID_SHIFT;

				rotation_unitvec[0] = kerconst_conform->rotbonds_unit_vectors_const[3*rotbond_id];
				rotation_unitvec[1] = kerconst_conform->rotbonds_unit_vectors_const[3*rotbond_id+1];
				rotation_unitvec[2] = kerconst_conform->rotbonds_unit_vectors_const[3*rotbond_id+2];
				
				rotation_movingvec[0] = kerconst_conform->rotbonds_moving_vectors_const[3*rotbond_id];
				rotation_movingvec[1] = kerconst_conform->rotbonds_moving_vectors_const[3*rotbond_id+1];
				rotation_movingvec[2] = kerconst_conform->rotbonds_moving_vectors_const[3*rotbond_id+2];

				rotation_angle = genotype[6+rotbond_id]*DEG_TO_RAD;

				// Performing additionally the first movement which 
				// is needed only if rotating around rotatable bond
				atom_to_rotate[0] -= rotation_movingvec[0];
				atom_to_rotate[1] -= rotation_movingvec[1];
				atom_to_rotate[2] -= rotation_movingvec[2];
			}

			// Transforming orientation and torsion angles into quaternions
			rotation_angle  = rotation_angle * 0.5f;
			float sin_angle = native_sin(rotation_angle);
			quatrot_left_q  = native_cos(rotation_angle);
			quatrot_left_x  = sin_angle*rotation_unitvec[0];
			quatrot_left_y  = sin_angle*rotation_unitvec[1];
			quatrot_left_z  = sin_angle*rotation_unitvec[2];

			// Performing rotation
			if ((rotation_list_element & RLIST_GENROT_MASK) != 0)	// If general rotation,
										// two rotations should be performed
										// (multiplying the quaternions)
			{
				// Calculating quatrot_left*ref_orientation_quats_const,
				// which means that reference orientation rotation is the first
				quatrot_temp_q = quatrot_left_q;
				quatrot_temp_x = quatrot_left_x;
				quatrot_temp_y = quatrot_left_y;
				quatrot_temp_z = quatrot_left_z;

				quatrot_left_q = quatrot_temp_q*kerconst_conform->ref_orientation_quats_const[4*(*run_id)]-
						 quatrot_temp_x*kerconst_conform->ref_orientation_quats_const[4*(*run_id)+1]-
						 quatrot_temp_y*kerconst_conform->ref_orientation_quats_const[4*(*run_id)+2]-
						 quatrot_temp_z*kerconst_conform->ref_orientation_quats_const[4*(*run_id)+3];
				quatrot_left_x = quatrot_temp_q*kerconst_conform->ref_orientation_quats_const[4*(*run_id)+1]+
						 kerconst_conform->ref_orientation_quats_const[4*(*run_id)]*quatrot_temp_x+
						 quatrot_temp_y*kerconst_conform->ref_orientation_quats_const[4*(*run_id)+3]-
						 kerconst_conform->ref_orientation_quats_const[4*(*run_id)+2]*quatrot_temp_z;
				quatrot_left_y = quatrot_temp_q*kerconst_conform->ref_orientation_quats_const[4*(*run_id)+2]+
						 kerconst_conform->ref_orientation_quats_const[4*(*run_id)]*quatrot_temp_y+
						 kerconst_conform->ref_orientation_quats_const[4*(*run_id)+1]*quatrot_temp_z-
						 quatrot_temp_x*kerconst_conform->ref_orientation_quats_const[4*(*run_id)+3];
				quatrot_left_z = quatrot_temp_q*kerconst_conform->ref_orientation_quats_const[4*(*run_id)+3]+
						 kerconst_conform->ref_orientation_quats_const[4*(*run_id)]*quatrot_temp_z+
						 quatrot_temp_x*kerconst_conform->ref_orientation_quats_const[4*(*run_id)+2]-
						 kerconst_conform->ref_orientation_quats_const[4*(*run_id)+1]*quatrot_temp_y;
			}

			quatrot_temp_q = 0 -
					 quatrot_left_x*atom_to_rotate [0] -
					 quatrot_left_y*atom_to_rotate [1] -
					 quatrot_left_z*atom_to_rotate [2];
			quatrot_temp_x = quatrot_left_q*atom_to_rotate [0] +
					 quatrot_left_y*atom_to_rotate [2] -
					 quatrot_left_z*atom_to_rotate [1];
			quatrot_temp_y = quatrot_left_q*atom_to_rotate [1] -
					 quatrot_left_x*atom_to_rotate [2] +
					 quatrot_left_z*atom_to_rotate [0];
			quatrot_temp_z = quatrot_left_q*atom_to_rotate [2] +
					 quatrot_left_x*atom_to_rotate [1] -
					 quatrot_left_y*atom_to_rotate [0];

			atom_to_rotate [0] = 0 -
					  quatrot_temp_q*quatrot_left_x +
					  quatrot_temp_x*quatrot_left_q -
					  quatrot_temp_y*quatrot_left_z +
					  quatrot_temp_z*quatrot_left_y;
			atom_to_rotate [1] = 0 -
					  quatrot_temp_q*quatrot_left_y +
					  quatrot_temp_x*quatrot_left_z +
					  quatrot_temp_y*quatrot_left_q -
					  quatrot_temp_z*quatrot_left_x;
			atom_to_rotate [2] = 0 -
					  quatrot_temp_q*quatrot_left_z -
					  quatrot_temp_x*quatrot_left_y +
					  quatrot_temp_y*quatrot_left_x +
					  quatrot_temp_z*quatrot_left_q;

			// Performing final movement and storing values
			calc_coords_x[atom_id] = atom_to_rotate [0] + rotation_movingvec[0];
			calc_coords_y[atom_id] = atom_to_rotate [1] + rotation_movingvec[1];
			calc_coords_z[atom_id] = atom_to_rotate [2] + rotation_movingvec[2];

		} // End if-statement not dummy rotation

		barrier(CLK_LOCAL_MEM_FENCE);

	} // End rotation_counter for-loop

	// ================================================
	// CALCULATING INTERMOLECULAR ENERGY
	// ================================================
	for (uint atom_id = get_local_id(0);
	          atom_id < dockpars_num_of_atoms;
	          atom_id+= NUM_OF_THREADS_PER_BLOCK)
	{
		uint atom_typeid = kerconst_interintra->atom_types_const[atom_id];
		float x = calc_coords_x[atom_id];
		float y = calc_coords_y[atom_id];
		float z = calc_coords_z[atom_id];
		float q = kerconst_interintra->atom_charges_const[atom_id];

		if ((x < 0) || (y < 0) || (z < 0) || (x >= dockpars_gridsize_x-1)
				                  || (y >= dockpars_gridsize_y-1)
						  || (z >= dockpars_gridsize_z-1)){
			partial_energies[get_local_id(0)] += 16777216.0f; //100000.0f;
	
			#if defined (DEBUG_ENERGY_KERNEL)
			partial_interE[get_local_id(0)] += 16777216.0f;
			#endif
		}
		else
		{
			// Getting coordinates
			int x_low  = (int)floor(x); 
			int y_low  = (int)floor(y); 
			int z_low  = (int)floor(z);
			int x_high = (int)ceil(x); 
			int y_high = (int)ceil(y); 
			int z_high = (int)ceil(z);
			float dx = x - x_low; 
			float dy = y - y_low; 
			float dz = z - z_low;

			// Calculating interpolation weights
			float weights[2][2][2];
			weights [0][0][0] = (1-dx)*(1-dy)*(1-dz);
			weights [1][0][0] = dx*(1-dy)*(1-dz);
			weights [0][1][0] = (1-dx)*dy*(1-dz);
			weights [1][1][0] = dx*dy*(1-dz);
			weights [0][0][1] = (1-dx)*(1-dy)*dz;
			weights [1][0][1] = dx*(1-dy)*dz;
			weights [0][1][1] = (1-dx)*dy*dz;
			weights [1][1][1] = dx*dy*dz;

			// Capturing affinity values
			uint ylow_times_g1  = y_low*g1;
			uint yhigh_times_g1 = y_high*g1;
		  	uint zlow_times_g2  = z_low*g2;
			uint zhigh_times_g2 = z_high*g2;

			// Grid offset
			uint offset_cube_000 = x_low  + ylow_times_g1  + zlow_times_g2;
			uint offset_cube_100 = x_high + ylow_times_g1  + zlow_times_g2;
			uint offset_cube_010 = x_low  + yhigh_times_g1 + zlow_times_g2;
			uint offset_cube_110 = x_high + yhigh_times_g1 + zlow_times_g2;
			uint offset_cube_001 = x_low  + ylow_times_g1  + zhigh_times_g2;
			uint offset_cube_101 = x_high + ylow_times_g1  + zhigh_times_g2;
			uint offset_cube_011 = x_low  + yhigh_times_g1 + zhigh_times_g2;
			uint offset_cube_111 = x_high + yhigh_times_g1 + zhigh_times_g2;

			uint mul_tmp = atom_typeid*g3;

			float cube[2][2][2];
			cube [0][0][0] = *(dockpars_fgrids + offset_cube_000 + mul_tmp);
			cube [1][0][0] = *(dockpars_fgrids + offset_cube_100 + mul_tmp);
			cube [0][1][0] = *(dockpars_fgrids + offset_cube_010 + mul_tmp);
		        cube [1][1][0] = *(dockpars_fgrids + offset_cube_110 + mul_tmp);
		        cube [0][0][1] = *(dockpars_fgrids + offset_cube_001 + mul_tmp);
			cube [1][0][1] = *(dockpars_fgrids + offset_cube_101 + mul_tmp);
                        cube [0][1][1] = *(dockpars_fgrids + offset_cube_011 + mul_tmp);
                        cube [1][1][1] = *(dockpars_fgrids + offset_cube_111 + mul_tmp);

			// Calculating affinity energy
			partial_energies[get_local_id(0)] += TRILININTERPOL(cube, weights);

			#if defined (DEBUG_ENERGY_KERNEL)
			partial_interE[get_local_id(0)] += TRILININTERPOL(cube, weights);
			#endif

			// Capturing electrostatic values
			atom_typeid = dockpars_num_of_atypes;

			mul_tmp = atom_typeid*g3;
			cube [0][0][0] = *(dockpars_fgrids + offset_cube_000 + mul_tmp);
			cube [1][0][0] = *(dockpars_fgrids + offset_cube_100 + mul_tmp);
      			cube [0][1][0] = *(dockpars_fgrids + offset_cube_010 + mul_tmp);
      			cube [1][1][0] = *(dockpars_fgrids + offset_cube_110 + mul_tmp);
		       	cube [0][0][1] = *(dockpars_fgrids + offset_cube_001 + mul_tmp);
		        cube [1][0][1] = *(dockpars_fgrids + offset_cube_101 + mul_tmp);
		        cube [0][1][1] = *(dockpars_fgrids + offset_cube_011 + mul_tmp);
		        cube [1][1][1] = *(dockpars_fgrids + offset_cube_111 + mul_tmp);

			// Calculating electrostatic energy
			partial_energies[get_local_id(0)] += q * TRILININTERPOL(cube, weights);

			#if defined (DEBUG_ENERGY_KERNEL)
			partial_interE[get_local_id(0)] += q * TRILININTERPOL(cube, weights);
			#endif

			// Capturing desolvation values
			atom_typeid = dockpars_num_of_atypes+1;

			mul_tmp = atom_typeid*g3;
			cube [0][0][0] = *(dockpars_fgrids + offset_cube_000 + mul_tmp);
			cube [1][0][0] = *(dockpars_fgrids + offset_cube_100 + mul_tmp);
      			cube [0][1][0] = *(dockpars_fgrids + offset_cube_010 + mul_tmp);
      			cube [1][1][0] = *(dockpars_fgrids + offset_cube_110 + mul_tmp);
      			cube [0][0][1] = *(dockpars_fgrids + offset_cube_001 + mul_tmp);
      			cube [1][0][1] = *(dockpars_fgrids + offset_cube_101 + mul_tmp);
      			cube [0][1][1] = *(dockpars_fgrids + offset_cube_011 + mul_tmp);
      			cube [1][1][1] = *(dockpars_fgrids + offset_cube_111 + mul_tmp);

			// Calculating desolvation energy
			partial_energies[get_local_id(0)] += fabs(q) * TRILININTERPOL(cube, weights);

			#if defined (DEBUG_ENERGY_KERNEL)
			partial_interE[get_local_id(0)] += fabs(q) * TRILININTERPOL(cube, weights);
			#endif
		}

	} // End atom_id for-loop (INTERMOLECULAR ENERGY)


	#if defined (DEBUG_ENERGY_KERNEL)
	barrier(CLK_LOCAL_MEM_FENCE);

	if (get_local_id(0) == 0)
	{
		float energy_interE = partial_interE[0];

		for (uint contributor_counter=1;
		          contributor_counter<NUM_OF_THREADS_PER_BLOCK;
		          contributor_counter++)
		{
			energy_interE += partial_interE[contributor_counter];
		}
		partial_interE[0] = energy_interE;
		//printf("%-20s %-10.8f\n", "energy_interE: ", energy_interE);
	}

	barrier(CLK_LOCAL_MEM_FENCE);
	#endif


	// In paper: intermolecular and internal energy calculation
	// are independent from each other, -> NO BARRIER NEEDED
  	// but require different operations,
	// thus, they can be executed only sequentially on the GPU.

	// ================================================
	// CALCULATING INTRAMOLECULAR ENERGY
	// ================================================
	for (uint contributor_counter = get_local_id(0);
	          contributor_counter < dockpars_num_of_intraE_contributors;
	          contributor_counter +=NUM_OF_THREADS_PER_BLOCK)

#if 0
if (get_local_id (0) == 0) {
	for (uint contributor_counter = 0;
	          contributor_counter < dockpars_num_of_intraE_contributors;
	          contributor_counter ++)
#endif
	{
#if 0
		// Only for testing smoothing
		float smoothed_intraE = 0.0f;

		float raw_intraE_vdw_hb = 0.0f;
		float raw_intraE_el     = 0.0f;
		float raw_intraE_sol    = 0.0f;
		float raw_intraE        = 0.0f;
#endif

		// Getting atom IDs
		uint atom1_id = kerconst_intracontrib->intraE_contributors_const[3*contributor_counter];
		uint atom2_id = kerconst_intracontrib->intraE_contributors_const[3*contributor_counter+1];

		// Calculating vector components of vector going
		// from first atom's to second atom's coordinates
		float subx = calc_coords_x[atom1_id] - calc_coords_x[atom2_id];
		float suby = calc_coords_y[atom1_id] - calc_coords_y[atom2_id];
		float subz = calc_coords_z[atom1_id] - calc_coords_z[atom2_id];

		// Calculating atomic_distance
		float atomic_distance = native_sqrt(subx*subx + suby*suby + subz*subz)*dockpars_grid_spacing;

		// Getting type IDs
		uint atom1_typeid = kerconst_interintra->atom_types_const[atom1_id];
		uint atom2_typeid = kerconst_interintra->atom_types_const[atom2_id];

		uint atom1_type_vdw_hb = kerconst_intra->atom1_types_reqm_const [atom1_typeid];
     	        uint atom2_type_vdw_hb = kerconst_intra->atom2_types_reqm_const [atom2_typeid];

		// Getting optimum pair distance (opt_distance) from reqm and reqm_hbond
		// reqm: equilibrium internuclear separation 
		//       (sum of the vdW radii of two like atoms (A)) in the case of vdW
		// reqm_hbond: equilibrium internuclear separation
		//  	 (sum of the vdW radii of two like atoms (A)) in the case of hbond 
		float opt_distance;

		if (kerconst_intracontrib->intraE_contributors_const[3*contributor_counter+2] == 1)	//H-bond
		{
			opt_distance = kerconst_intra->reqm_hbond_const [atom1_type_vdw_hb] + kerconst_intra->reqm_hbond_const [atom2_type_vdw_hb];
		}
		else	//van der Waals
		{
			opt_distance = 0.5f*(kerconst_intra->reqm_const [atom1_type_vdw_hb] + kerconst_intra->reqm_const [atom2_type_vdw_hb]);
		}

		// Getting smoothed distance
		// smoothed_distance = function(atomic_distance, opt_distance)
		float smoothed_distance;
		float delta_distance = 0.5f*dockpars_smooth; 

		if (atomic_distance <= (opt_distance - delta_distance)) {
			smoothed_distance = atomic_distance + delta_distance;
		}
		else if (atomic_distance < (opt_distance + delta_distance)) {
			smoothed_distance = opt_distance;
		}
		else { // else if (atomic_distance >= (opt_distance + delta_distance))
			smoothed_distance = atomic_distance - delta_distance;
		}

		// Calculating energy contributions
		// Cuttoff1: internuclear-distance at 8A only for vdw and hbond.
		if (atomic_distance < 8.0f)
		{
			// Calculating van der Waals / hydrogen bond term
			partial_energies[get_local_id(0)] += native_divide(kerconst_intra->VWpars_AC_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(smoothed_distance/*atomic_distance*/,12));

			#if 0
			smoothed_intraE = native_divide(kerconst_intra->VWpars_AC_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(smoothed_distance,12));
			raw_intraE_vdw_hb      = native_divide(kerconst_intra->VWpars_AC_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(atomic_distance  ,12)); 
			#endif

			#if defined (DEBUG_ENERGY_KERNEL)
			partial_intraE[get_local_id(0)] += native_divide(kerconst_intra->VWpars_AC_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(smoothed_distance/*atomic_distance*/,12));
			#endif

			if (kerconst_intracontrib->intraE_contributors_const[3*contributor_counter+2] == 1) {	//H-bond
				partial_energies[get_local_id(0)] -= native_divide(kerconst_intra->VWpars_BD_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(smoothed_distance/*atomic_distance*/,10));

				#if 0
				smoothed_intraE -= native_divide(kerconst_intra->VWpars_BD_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(smoothed_distance,10));
				raw_intraE_vdw_hb 	-= native_divide(kerconst_intra->VWpars_BD_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(atomic_distance  ,10));
				#endif

				#if defined (DEBUG_ENERGY_KERNEL)
				partial_intraE[get_local_id(0)] -= native_divide(kerconst_intra->VWpars_BD_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(smoothed_distance/*atomic_distance*/,10));
				#endif
			}
			else {	//van der Waals
				partial_energies[get_local_id(0)] -= native_divide(kerconst_intra->VWpars_BD_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(smoothed_distance/*atomic_distance*/,6));

				#if 0
				smoothed_intraE -= native_divide(kerconst_intra->VWpars_BD_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(smoothed_distance,6));
				raw_intraE_vdw_hb      -= native_divide(kerconst_intra->VWpars_BD_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(atomic_distance  ,6));
				#endif

				#if defined (DEBUG_ENERGY_KERNEL)
				partial_intraE[get_local_id(0)] -= native_divide(kerconst_intra->VWpars_BD_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(smoothed_distance/*atomic_distance*/,6));
				#endif
			}
		} // if cuttoff1 - internuclear-distance at 8A	

		// Calculating energy contributions
		// Cuttoff2: internuclear-distance at 20.48A only for el and sol.
		if (atomic_distance < 20.48f)
		{
			// Calculating electrostatic term
	       		partial_energies[get_local_id(0)] += native_divide (
		                                                     dockpars_coeff_elec * kerconst_interintra->atom_charges_const[atom1_id] * kerconst_interintra->atom_charges_const[atom2_id],
		                                                     atomic_distance * (DIEL_A + native_divide(DIEL_B,(1.0f + DIEL_K*native_exp(-DIEL_B_TIMES_H*atomic_distance))))
		                                                     );
			#if 0
			smoothed_intraE += native_divide (
						      dockpars_coeff_elec * kerconst_interintra->atom_charges_const[atom1_id] * kerconst_interintra->atom_charges_const[atom2_id],
						      atomic_distance * (DIEL_A + native_divide(DIEL_B,(1.0f + DIEL_K*native_exp(-DIEL_B_TIMES_H*atomic_distance))))
						     );

			raw_intraE_el 	= native_divide (
						      dockpars_coeff_elec * kerconst_interintra->atom_charges_const[atom1_id] * kerconst_interintra->atom_charges_const[atom2_id],
						      atomic_distance * (DIEL_A + native_divide(DIEL_B,(1.0f + DIEL_K*native_exp(-DIEL_B_TIMES_H*atomic_distance))))
						     );
			#endif

			#if defined (DEBUG_ENERGY_KERNEL)
			partial_intraE[get_local_id(0)] += native_divide (
		                                                     dockpars_coeff_elec * kerconst_interintra->kerconst_interintra->atom_charges_const[atom1_id] * kerconst_interintra->atom_charges_const[atom2_id],
		                                                     atomic_distance * (DIEL_A + native_divide(DIEL_B,(1.0f + DIEL_K*native_exp(-DIEL_B_TIMES_H*atomic_distance))))
		                                                     );
			#endif

			// Calculating desolvation term
			// 1/25.92 = 0.038580246913580245
			partial_energies[get_local_id(0)] += ((kerconst_intra->dspars_S_const[atom1_typeid] +
								       dockpars_qasp*fabs(kerconst_interintra->atom_charges_const[atom1_id]))*kerconst_intra->dspars_V_const[atom2_typeid] +
							               (kerconst_intra->dspars_S_const[atom2_typeid] +
								       dockpars_qasp*fabs(kerconst_interintra->atom_charges_const[atom2_id]))*kerconst_intra->dspars_V_const[atom1_typeid]) *
							               dockpars_coeff_desolv*native_exp(-0.03858025f*native_powr(atomic_distance, 2));

			#if 0
			smoothed_intraE += ((kerconst_intra->dspars_S_const[atom1_typeid] +
					dockpars_qasp*fabs(kerconst_interintra->atom_charges_const[atom1_id]))*kerconst_intra->dspars_V_const[atom2_typeid] +
				       (kerconst_intra->dspars_S_const[atom2_typeid] +
				       dockpars_qasp*fabs(kerconst_interintra->atom_charges_const[atom2_id]))*kerconst_intra->dspars_V_const[atom1_typeid]) *
				       dockpars_coeff_desolv*native_exp(-0.03858025f*native_powr(atomic_distance, 2));

			raw_intraE_sol = ((kerconst_intra->dspars_S_const[atom1_typeid] +
					dockpars_qasp*fabs(kerconst_interintra->atom_charges_const[atom1_id]))*kerconst_intra->dspars_V_const[atom2_typeid] +
				       (kerconst_intra->dspars_S_const[atom2_typeid] +
				       dockpars_qasp*fabs(kerconst_interintra->atom_charges_const[atom2_id]))*kerconst_intra->dspars_V_const[atom1_typeid]) *
				       dockpars_coeff_desolv*native_exp(-0.03858025f*native_powr(atomic_distance, 2));
			#endif

			#if defined (DEBUG_ENERGY_KERNEL)
			partial_intraE[get_local_id(0)] += ((kerconst_intra->dspars_S_const[atom1_typeid] +
							       dockpars_qasp*fabs(kerconst_interintra->atom_charges_const[atom1_id]))*kerconst_intra->dspars_V_const[atom2_typeid] +
						               (kerconst_intra->dspars_S_const[atom2_typeid] +
							       dockpars_qasp*fabs(kerconst_interintra->atom_charges_const[atom2_id]))*kerconst_intra->dspars_V_const[atom1_typeid]) *
						               dockpars_coeff_desolv*native_exp(-0.03858025f*native_powr(atomic_distance, 2));
			#endif
		} // if cuttoff2 - internuclear-distance at 20.48A



#if 0
			raw_intraE = raw_intraE_vdw_hb + raw_intraE_el + raw_intraE_sol;

			if (debug == true) {
///*
			//if (get_local_id (0) == 0) {

				if (kerconst_intracontrib->intraE_contributors_const[3*contributor_counter+2] == 1)	//H-bond
				{
					// diogos table
//					printf("%3u %-5s %3u %3u %3.5f %3.5f %3.5f %3.5f %3.5f %3.5f %3.5f\n", contributor_counter, "hbond", atom1_id, atom2_id, kerconst_intra->reqm_hbond_const [atom1_type_vdw_hb], kerconst_intra->reqm_hbond_const [atom2_type_vdw_hb], opt_distance, atomic_distance, smoothed_distance, smoothed_intraE, raw_intraE);

					printf("%3u %-5s %3u %3u %3.5f %3.5f %3.5f %3.5f %3.5f %3.5f %3.5f %3.5f %3.5f %3.5f\n", contributor_counter, "hbond", atom1_id, atom2_id, kerconst_intra->reqm_hbond_const [atom1_type_vdw_hb], kerconst_intra->reqm_hbond_const [atom2_type_vdw_hb], opt_distance, atomic_distance, smoothed_distance, smoothed_intraE, raw_intraE, raw_intraE_vdw_hb, raw_intraE_el, raw_intraE_sol);




				}
				else	//van der Waals
				{
					// diogos table
//					printf("%3u %-5s %3u %3u %3.5f %3.5f %3.5f %3.5f %3.5f %3.5f %3.5f\n", contributor_counter, "vdw", atom1_id, atom2_id, kerconst_intra->reqm_const [atom1_type_vdw_hb], kerconst_intra->reqm_const [atom2_type_vdw_hb], opt_distance, atomic_distance, smoothed_distance, smoothed_intraE, raw_intraE);

					printf("%3u %-5s %3u %3u %3.5f %3.5f %3.5f %3.5f %3.5f %3.5f %3.5f %3.5f %3.5f %3.5f\n", contributor_counter, "vdw", atom1_id, atom2_id, kerconst_intra->reqm_const [atom1_type_vdw_hb], kerconst_intra->reqm_const [atom2_type_vdw_hb], opt_distance, atomic_distance, smoothed_distance, smoothed_intraE, raw_intraE, raw_intraE_vdw_hb, raw_intraE_el, raw_intraE_sol);


				}; 
			//}
//*/
			}
#endif

	} // End contributor_counter for-loop (INTRAMOLECULAR ENERGY)

#if 0
} // if (get_local_id (0) == 0) {
#endif

	barrier(CLK_LOCAL_MEM_FENCE);

	if (get_local_id(0) == 0)
	{
		*energy = partial_energies[0];

		for (uint contributor_counter=1;
		          contributor_counter<NUM_OF_THREADS_PER_BLOCK;
		          contributor_counter++)
		{
			*energy += partial_energies[contributor_counter];
		}
	}

	barrier(CLK_LOCAL_MEM_FENCE);

	#if defined (DEBUG_ENERGY_KERNEL)
	if (get_local_id(0) == 0)
	{
		float energy_intraE = partial_intraE[0];

		for (uint contributor_counter=1;
		          contributor_counter<NUM_OF_THREADS_PER_BLOCK;
		          contributor_counter++)
		{
			energy_intraE += partial_intraE[contributor_counter];
		}
		partial_intraE[0] = energy_intraE;
		//printf("%-20s %-10.8f\n", "energy_intraE: ", energy_intraE);

	}
	barrier(CLK_LOCAL_MEM_FENCE);
	#endif

}

#include "kernel1.cl"
#include "kernel2.cl"
#include "auxiliary_genetic.cl"
#include "kernel4.cl"
#include "kernel3.cl"
#include "calcgradient.cl"
#include "kernel_sd.cl"
#include "kernel_fire.cl"