kernel3.cl 14.2 KB
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/*

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.

*/


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__kernel void __attribute__ ((reqd_work_group_size(NUM_OF_THREADS_PER_BLOCK,1,1)))
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perform_LS(		
			char   dockpars_num_of_atoms,
			char   dockpars_num_of_atypes,
			int    dockpars_num_of_intraE_contributors,
			char   dockpars_gridsize_x,
			char   dockpars_gridsize_y,
			char   dockpars_gridsize_z,
			float  dockpars_grid_spacing,
         __global const float* restrict dockpars_fgrids, // This is too large to be allocated in __constant 
	        	int    dockpars_rotbondlist_length,
			float  dockpars_coeff_elec,
			float  dockpars_coeff_desolv,
  	 __global       float* restrict dockpars_conformations_next,
  	 __global 	float* restrict dockpars_energies_next,
  	 __global 	int*   restrict dockpars_evals_of_new_entities,
  	 __global 	uint*  restrict dockpars_prng_states,
			int    dockpars_pop_size,
			int    dockpars_num_of_genes,
			float  dockpars_lsearch_rate,
			uint   dockpars_num_of_lsentities,
			float  dockpars_rho_lower_bound,
			float  dockpars_base_dmov_mul_sqrt3,
			float  dockpars_base_dang_mul_sqrt3,
			uint   dockpars_cons_limit,
			uint   dockpars_max_num_of_iters,
			float  dockpars_qasp,
	     __constant float* atom_charges_const,
             __constant char*  atom_types_const,
	     __constant char*  intraE_contributors_const,
             __constant float* VWpars_AC_const,
             __constant float* VWpars_BD_const,
             __constant float* dspars_S_const,
             __constant float* dspars_V_const,
             __constant int*   rotlist_const,
             __constant float* ref_coords_x_const,
             __constant float* ref_coords_y_const,
             __constant float* ref_coords_z_const,
             __constant float* rotbonds_moving_vectors_const,
             __constant float* rotbonds_unit_vectors_const,
             __constant float* ref_orientation_quats_const
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)
//The GPU global function performs local search on the pre-defined entities of conformations_next.
//The number of blocks which should be started equals to num_of_lsentities*num_of_runs.
//This way the first num_of_lsentities entity of each population will be subjected to local search
//(and each block carries out the algorithm for one entity).
//Since the first entity is always the best one in the current population,
//it is always tested according to the ls probability, and if it not to be
//subjected to local search, the entity with ID num_of_lsentities is selected instead of the first one (with ID 0).
{
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	// 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.
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	__local float genotype_candidate[ACTUAL_GENOTYPE_LENGTH];
	__local float genotype_deviate  [ACTUAL_GENOTYPE_LENGTH];
	__local float genotype_bias     [ACTUAL_GENOTYPE_LENGTH];
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        __local float rho;
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	__local int   cons_succ;
	__local int   cons_fail;
	__local int   iteration_cnt;
	__local float candidate_energy;
	__local int   evaluation_cnt;
	int gene_counter;

	__local float offspring_genotype[ACTUAL_GENOTYPE_LENGTH];
	__local int run_id;
	__local int entity_id;
	__local float offspring_energy;

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	__local float calc_coords_x[MAX_NUM_OF_ATOMS];
	__local float calc_coords_y[MAX_NUM_OF_ATOMS];
	__local float calc_coords_z[MAX_NUM_OF_ATOMS];
	__local float partial_energies[NUM_OF_THREADS_PER_BLOCK];

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	// -------------------------------------------------------------------
	// Calculate gradients (forces) for intermolecular energy
	// Derived from autodockdev/maps.py
	// -------------------------------------------------------------------

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	// Disabling gradient calculation for this kernel
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	__local bool  is_enabled_gradient_calc;
	if (get_local_id(0) == 0) {
		is_enabled_gradient_calc = false;
	}
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	// Variables to store gradient of 
	// the intermolecular energy per each ligand atom
	__local float gradient_inter_x[MAX_NUM_OF_ATOMS];
	__local float gradient_inter_y[MAX_NUM_OF_ATOMS];
	__local float gradient_inter_z[MAX_NUM_OF_ATOMS];

	// Final gradient resulting out of gradient calculation
	__local float gradient_genotype[GENOTYPE_LENGTH_IN_GLOBMEM];
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	// -------------------------------------------------------------------

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	// Determining run ID and entity ID
	// Initializing offspring genotype
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	if (get_local_id(0) == 0)
	{
		run_id = get_group_id(0) / dockpars_num_of_lsentities;
		entity_id = get_group_id(0) % dockpars_num_of_lsentities;

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		// Since entity 0 is the best one due to elitism,
		// it should be subjected to random selection
		if (entity_id == 0) {
			// If entity 0 is not selected according to LS-rate,
			// choosing an other entity
			if (100.0f*gpu_randf(dockpars_prng_states) > dockpars_lsearch_rate) {
				entity_id = dockpars_num_of_lsentities;					
			}
		}
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		offspring_energy = dockpars_energies_next[run_id*dockpars_pop_size+entity_id];
	}

	barrier(CLK_LOCAL_MEM_FENCE);

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  	async_work_group_copy(offspring_genotype,
			      dockpars_conformations_next+(run_id*dockpars_pop_size+entity_id)*GENOTYPE_LENGTH_IN_GLOBMEM,
                              dockpars_num_of_genes, 0);

	for (gene_counter = get_local_id(0);
	     gene_counter < dockpars_num_of_genes;
	     gene_counter+= NUM_OF_THREADS_PER_BLOCK) {
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		   genotype_bias[gene_counter] = 0.0f;
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	}
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	if (get_local_id(0) == 0) {
		rho = 1.0f;
		cons_succ = 0;
		cons_fail = 0;
		iteration_cnt = 0;
		evaluation_cnt = 0;
	}

	barrier(CLK_LOCAL_MEM_FENCE);

	while ((iteration_cnt < dockpars_max_num_of_iters) && (rho > dockpars_rho_lower_bound))
	{
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		// New random deviate
		for (gene_counter = get_local_id(0);
		     gene_counter < dockpars_num_of_genes;
		     gene_counter+= NUM_OF_THREADS_PER_BLOCK)
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		{
			genotype_deviate[gene_counter] = rho*(2*gpu_randf(dockpars_prng_states)-1);

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			// Translation genes
			if (gene_counter <= 2)
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				genotype_deviate[gene_counter] *= dockpars_base_dmov_mul_sqrt3;
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			// Shoemake orientation-genes do not use initial deviation
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			// Torsion genes
			else if (gene_counter >= 6) 
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				genotype_deviate[gene_counter] *= dockpars_base_dang_mul_sqrt3;
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		}

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		// Generating new genotype candidate
		for (gene_counter = get_local_id(0);
		     gene_counter < dockpars_num_of_genes;
		     gene_counter+= NUM_OF_THREADS_PER_BLOCK) {

			// Shoemake genes (u1, u2, u3) ranges between [0,1]
			if ((gene_counter >= 3) && (gene_counter <= 5)) { 
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			   genotype_candidate[gene_counter] = gpu_randf(dockpars_prng_states);
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			}
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			// Other genes: translation and torsions
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			else {
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			   genotype_candidate[gene_counter] = offspring_genotype[gene_counter] + 
							      genotype_deviate[gene_counter]   + 
							      genotype_bias[gene_counter];
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			}
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		}

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		// Evaluating candidate
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		barrier(CLK_LOCAL_MEM_FENCE);

		// ==================================================================
		gpu_calc_energy(dockpars_rotbondlist_length,
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				dockpars_num_of_atoms,
				dockpars_gridsize_x,
				dockpars_gridsize_y,
				dockpars_gridsize_z,
				dockpars_fgrids,
				dockpars_num_of_atypes,
				dockpars_num_of_intraE_contributors,
				dockpars_grid_spacing,
				dockpars_coeff_elec,
				dockpars_qasp,
				dockpars_coeff_desolv,
				genotype_candidate,
				&candidate_energy,
				&run_id,
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				// 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.
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				calc_coords_x,
				calc_coords_y,
				calc_coords_z,
				partial_energies,

				atom_charges_const,
				atom_types_const,
				intraE_contributors_const,
				VWpars_AC_const,
				VWpars_BD_const,
				dspars_S_const,
				dspars_V_const,
				rotlist_const,
				ref_coords_x_const,
				ref_coords_y_const,
				ref_coords_z_const,
				rotbonds_moving_vectors_const,
				rotbonds_unit_vectors_const,
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				ref_orientation_quats_const
			 	// Gradient-related arguments
			 	// Calculate gradients (forces) for intermolecular energy
			 	// Derived from autodockdev/maps.py
				,
				&is_enabled_gradient_calc,
				gradient_inter_x,
				gradient_inter_y,
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				gradient_inter_z,
				gradient_genotype
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				);
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		// =================================================================

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		if (get_local_id(0) == 0) {
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			evaluation_cnt++;
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		}
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		barrier(CLK_LOCAL_MEM_FENCE);

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		if (candidate_energy < offspring_energy)	// If candidate is better, success
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		{
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			for (gene_counter = get_local_id(0);
			     gene_counter < dockpars_num_of_genes;
			     gene_counter+= NUM_OF_THREADS_PER_BLOCK)
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			{
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				// Updating offspring_genotype
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				offspring_genotype[gene_counter] = genotype_candidate[gene_counter];

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				// Updating genotype_bias
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				genotype_bias[gene_counter] = 0.6f*genotype_bias[gene_counter] + 0.4f*genotype_deviate[gene_counter];
			}

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			// Work-item 0 will overwrite the shared variables
			// used in the previous if condition
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			barrier(CLK_LOCAL_MEM_FENCE);

			if (get_local_id(0) == 0)
			{
				offspring_energy = candidate_energy;
				cons_succ++;
				cons_fail = 0;
			}
		}
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		else	// If candidate is worser, check the opposite direction
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		{
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			// Generating the other genotype candidate
			for (gene_counter = get_local_id(0);
			     gene_counter < dockpars_num_of_genes;
			     gene_counter+= NUM_OF_THREADS_PER_BLOCK) {
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				// Shoemake genes (u1, u2, u3) ranges between [0,1]
				if ((gene_counter >= 3) && (gene_counter <= 5)) {
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				   genotype_candidate[gene_counter] =  gpu_randf(dockpars_prng_states);
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				}
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				// Other genes: translation and torsions
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				else {
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				   genotype_candidate[gene_counter] = offspring_genotype[gene_counter] - 
								      genotype_deviate[gene_counter] - 
								      genotype_bias[gene_counter];
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				}
			}

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			//evaluating candidate
			barrier(CLK_LOCAL_MEM_FENCE);

			// =================================================================
			gpu_calc_energy(dockpars_rotbondlist_length,
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					dockpars_num_of_atoms,
					dockpars_gridsize_x,
					dockpars_gridsize_y,
					dockpars_gridsize_z,
					dockpars_fgrids,
					dockpars_num_of_atypes,
					dockpars_num_of_intraE_contributors,
					dockpars_grid_spacing,
					dockpars_coeff_elec,
				        dockpars_qasp,
					dockpars_coeff_desolv,
					genotype_candidate,
					&candidate_energy,
					&run_id,
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					// 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.
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					calc_coords_x,
					calc_coords_y,
					calc_coords_z,
					partial_energies,

					atom_charges_const,
					atom_types_const,
					intraE_contributors_const,
					VWpars_AC_const,
					VWpars_BD_const,
					dspars_S_const,
					dspars_V_const,
					rotlist_const,
					ref_coords_x_const,
					ref_coords_y_const,
					ref_coords_z_const,
					rotbonds_moving_vectors_const,
					rotbonds_unit_vectors_const,
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					ref_orientation_quats_const
				 	// Gradient-related arguments
				 	// Calculate gradients (forces) for intermolecular energy
				 	// Derived from autodockdev/maps.py
					,
					&is_enabled_gradient_calc,
					gradient_inter_x,
					gradient_inter_y,
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					gradient_inter_z,
					gradient_genotype
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					);
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			// =================================================================

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			if (get_local_id(0) == 0) {
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				evaluation_cnt++;
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			}
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			barrier(CLK_LOCAL_MEM_FENCE);

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			if (candidate_energy < offspring_energy) // If candidate is better, success
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			{
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				for (gene_counter = get_local_id(0);
				     gene_counter < dockpars_num_of_genes;
			       	     gene_counter+= NUM_OF_THREADS_PER_BLOCK)
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				{
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					// Updating offspring_genotype
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					offspring_genotype[gene_counter] = genotype_candidate[gene_counter];

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					// Updating genotype_bias
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					genotype_bias[gene_counter] = 0.6f*genotype_bias[gene_counter] - 0.4f*genotype_deviate[gene_counter];
				}

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				// Work-item 0 will overwrite the shared variables
				// used in the previous if condition
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				barrier(CLK_LOCAL_MEM_FENCE);

				if (get_local_id(0) == 0)
				{
					offspring_energy = candidate_energy;
					cons_succ++;
					cons_fail = 0;
				}
			}
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			else	// Failure in both directions
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			{
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				for (gene_counter = get_local_id(0);
				     gene_counter < dockpars_num_of_genes;
				     gene_counter+= NUM_OF_THREADS_PER_BLOCK)
					   // Updating genotype_bias
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					   genotype_bias[gene_counter] = 0.5f*genotype_bias[gene_counter];

				if (get_local_id(0) == 0)
				{
					cons_succ = 0;
					cons_fail++;
				}
			}
		}

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		// Changing rho if needed
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		if (get_local_id(0) == 0)
		{
			iteration_cnt++;

			if (cons_succ >= dockpars_cons_limit)
			{
				rho *= LS_EXP_FACTOR;
				cons_succ = 0;
			}
			else
				if (cons_fail >= dockpars_cons_limit)
				{
					rho *= LS_CONT_FACTOR;
					cons_fail = 0;
				}
		}
		barrier(CLK_LOCAL_MEM_FENCE);
	}

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	// Updating eval counter and energy
	if (get_local_id(0) == 0) {
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		dockpars_evals_of_new_entities[run_id*dockpars_pop_size+entity_id] += evaluation_cnt;
		dockpars_energies_next[run_id*dockpars_pop_size+entity_id] = offspring_energy;
	}

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	// Mapping torsion angles
	for (gene_counter = get_local_id(0);
	     gene_counter < dockpars_num_of_genes;
	     gene_counter+= NUM_OF_THREADS_PER_BLOCK) {
		   if (gene_counter >= 6) {
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			    map_angle(&(offspring_genotype[gene_counter]));
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		   }
	}
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	// Updating old offspring in population
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	barrier(CLK_LOCAL_MEM_FENCE);

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  	async_work_group_copy(dockpars_conformations_next+(run_id*dockpars_pop_size+entity_id)*GENOTYPE_LENGTH_IN_GLOBMEM,
        	              offspring_genotype,
        	              dockpars_num_of_genes,0);
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}