Commit 29c95f9d authored by Leonardo Solis's avatar Leonardo Solis
Browse files

added smoothing

parent dcd12a25

ofdock_taskpar_alt/Makefile

+2 −2
Original line number Diff line number Diff line
@@ -741,8 +741,8 @@ $(TARGET_DIR)/$(TARGET) : Makefile $(SRCS) $(INCS) $(TARGET_DIR) 
# Following values are used only for emulation

# to have a short but still a representative test

PDB  := 1stp

NRUN := 10

NEV  := 50000 

NRUN := 5

NEV  := 100000 



# Project name

PROJECT_NAME := ofdock_taskpar_alt

ofdock_taskpar_alt/device/Krnl_IntraE.cl

+81 −28
Original line number Diff line number Diff line
@@ -18,6 +18,13 @@ void Krnl_IntraE( 
 	     __constant     char*  restrict KerConstStatic_atom_types_const,



	     __global const char3* restrict KerConstStatic_intraE_contributors_const,



			float 				 DockConst_smooth,

	     __constant     float* restrict KerConstStatic_reqm,

	     __constant     float* restrict KerConstStatic_reqm_hbond,    

	     __constant     uint*  restrict KerConstStatic_atom1_types_reqm,

	     __constant     uint*  restrict KerConstStatic_atom2_types_reqm,   



	     __constant     float* restrict KerConstStatic_VWpars_AC_const,

	     __constant     float* restrict KerConstStatic_VWpars_BD_const,

	     __constant     float* restrict KerConstStatic_dspars_S_const,
@@ -112,53 +119,101 @@ while(active) { 
		float suby = loc_coords_atid1.y - loc_coords_atid2.y;

		float subz = loc_coords_atid1.z - loc_coords_atid2.z;



		//distance_leo = sqrt(subx*subx + suby*suby + subz*subz)*DockConst_grid_spacing;

		float distance_leo = sqrt_custom(subx*subx + suby*suby + subz*subz)*DockConst_grid_spacing;

		//atomic_distance = sqrt(subx*subx + suby*suby + subz*subz)*DockConst_grid_spacing;

		float atomic_distance = sqrt_custom(subx*subx + suby*suby + subz*subz)*DockConst_grid_spacing;



		if (distance_leo < 1.0f) {

/*

		if (atomic_distance < 1.0f) {

			#if defined (DEBUG_KRNL_INTRAE)

			printf("\n\nToo low distance (%f) between atoms %u and %u\n", distance_leo, atom1_id, atom2_id);

			printf("\n\nToo low distance (%f) between atoms %u and %u\n", atomic_distance, atom1_id, atom2_id);

			#endif

			//return HIGHEST_ENERGY;	// Returning maximal value

			distance_leo = 1.0f;

			atomic_distance = 1.0f;

		}

*/



		#if defined (DEBUG_KRNL_INTRAE)

		printf("\n\nCalculating energy contribution of atoms %u and %u\n", atom1_id+1, atom2_id+1);

		printf("Distance: %f\n", distance_leo);

		printf("Distance: %f\n", atomic_distance);

		#endif



/*

		float partialE1;

		float partialE2;

		float partialE3;

		float partialE4;

*/



		// But only if the distance is less than distance cutoff value and 20.48A (because of the tables)

		//if ((distance_leo < 8.0f) && (distance_leo < 20.48f))

		if (distance_leo < 8.0f) 

		{

			float distance_pow_2  = distance_leo*distance_leo; 

			float inverse_distance_pow_2  = native_divide(1.0f, distance_pow_2);

			float inverse_distance_pow_4  = inverse_distance_pow_2 * inverse_distance_pow_2;

			float inverse_distance_pow_6  = inverse_distance_pow_4 * inverse_distance_pow_2;

			float inverse_distance_pow_10 = inverse_distance_pow_6 * inverse_distance_pow_4;

			float inverse_distance_pow_12 = inverse_distance_pow_6 * inverse_distance_pow_6;

		float partialE1 = 0.0f;

		float partialE2 = 0.0f;

		float partialE3 = 0.0f;

		float partialE4 = 0.0f;



 		// Getting types ids

		char atom1_typeid = KerConstStatic_atom_types_const [atom1_id];

		char atom2_typeid = KerConstStatic_atom_types_const [atom2_id];



		// 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;



		uint atom1_type_vdw_hb = KerConstStatic_atom1_types_reqm [atom1_typeid];

     	        uint atom2_type_vdw_hb = KerConstStatic_atom2_types_reqm [atom2_typeid];



		if (ref_intraE_contributors_const.z == 1)	// H-bond

		{

			opt_distance = KerConstStatic_reqm_hbond [atom1_type_vdw_hb] + KerConstStatic_reqm_hbond [atom2_type_vdw_hb];

		}

		else	// Van der Waals

		{

			opt_distance = 0.5f*(KerConstStatic_reqm [atom1_type_vdw_hb] + KerConstStatic_reqm [atom2_type_vdw_hb]);

		}



		// Getting smoothed distance

		// smoothed_distance = function(atomic_distance, opt_distance)

		float smoothed_distance;

		float delta_distance = 0.5f*DockConst_smooth;



		/*printf("delta_distance: %f\n", delta_distance);*/



		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;

		}



		float distance_pow_2  = atomic_distance*atomic_distance; 



		float smoothed_distance_pow_2 = smoothed_distance*smoothed_distance; 

		float inverse_smoothed_distance_pow_2  = native_divide(1.0f, smoothed_distance_pow_2);

		float inverse_smoothed_distance_pow_4  = inverse_smoothed_distance_pow_2 * inverse_smoothed_distance_pow_2;

		float inverse_smoothed_distance_pow_6  = inverse_smoothed_distance_pow_4 * inverse_smoothed_distance_pow_2;

		float inverse_smoothed_distance_pow_10 = inverse_smoothed_distance_pow_6 * inverse_smoothed_distance_pow_4;

		float inverse_smoothed_distance_pow_12 = inverse_smoothed_distance_pow_6 * inverse_smoothed_distance_pow_6;



		if (atomic_distance < 8.0f) 

		{

			// Calculating van der Waals / hydrogen bond term

			partialE1 = KerConstStatic_VWpars_AC_const [atom1_typeid*DockConst_num_of_atypes+atom2_typeid]*inverse_distance_pow_12;

			partialE1 = KerConstStatic_VWpars_AC_const [atom1_typeid*DockConst_num_of_atypes+atom2_typeid]*inverse_smoothed_distance_pow_12;



			float tmp_pE2 = KerConstStatic_VWpars_BD_const [atom1_typeid*DockConst_num_of_atypes+atom2_typeid];



			if (ref_intraE_contributors_const.z == 1)	// H-bond

				partialE2 = tmp_pE2 * inverse_distance_pow_10;

				partialE2 = tmp_pE2 * inverse_smoothed_distance_pow_10;

			else	// Van der Waals

				partialE2 = tmp_pE2 * inverse_distance_pow_6;

				partialE2 = tmp_pE2 * inverse_smoothed_distance_pow_6;



		} // End of if: if (dist < dcutoff)	



		// Calculating electrostatic term

			partialE3 = native_divide(  (DockConst_coeff_elec*KerConstStatic_atom_charges_const[atom1_id]*KerConstStatic_atom_charges_const[atom2_id]) , (distance_leo*(-8.5525f + native_divide(86.9525f, (1.0f + 7.7839f*native_exp(-0.3154f*distance_leo)))))       );

		partialE3 = native_divide(  (DockConst_coeff_elec*KerConstStatic_atom_charges_const[atom1_id]*KerConstStatic_atom_charges_const[atom2_id]) , (atomic_distance*(-8.5525f + native_divide(86.9525f, (1.0f + 7.7839f*native_exp(-0.3154f*atomic_distance)))))       );



		// Calculating desolvation term

		partialE4 = (
@@ -166,8 +221,6 @@ while(active) { 
			  (KerConstStatic_dspars_S_const [atom2_typeid] + DockConst_qasp*fabs(KerConstStatic_atom_charges_const[atom2_id])) * KerConstStatic_dspars_V_const [atom1_typeid]) * 

			 DockConst_coeff_desolv*native_exp(-0.0386f*distance_pow_2);

	

		} // End of if: if ((dist < dcutoff) && (dist < 20.48))	

	

		#if defined (FIXED_POINT_INTRAE)

		//shift_intraE[32] = shift_intraE[0] + partialE1 + partialE2 + partialE3 + partialE4;

		shift_intraE[32] = shift_intraE[0] + fixedpt64_fromfloat(partialE1) +

ofdock_taskpar_alt/host/inc/calcenergy.h

+10 −2
Original line number Diff line number Diff line
@@ -60,6 +60,9 @@ typedef struct 
	float  		abs_max_dmov;

	float  		abs_max_dang;

	float  		lsearch_rate;



	float 		smooth;



	unsigned int 	num_of_lsentities;

	float  		rho_lower_bound;

	float  		base_dmov_mul_sqrt3;
@@ -128,6 +131,11 @@ typedef struct 
*/

	cl_char3  intraE_contributors_const[MAX_INTRAE_CONTRIBUTORS]  __attribute__ ((aligned (32768)));



        float reqm_const [ATYPE_NUM]				      __attribute__ ((aligned (64)));

        float reqm_hbond_const [ATYPE_NUM]			      __attribute__ ((aligned (64)));

        unsigned int  atom1_types_reqm_const [ATYPE_NUM]	      __attribute__ ((aligned (64)));

        unsigned int  atom2_types_reqm_const [ATYPE_NUM]	      __attribute__ ((aligned (64)));



       	float VWpars_AC_const   [MAX_NUM_OF_ATYPES*MAX_NUM_OF_ATYPES] __attribute__ ((aligned (1024)));

       	float VWpars_BD_const   [MAX_NUM_OF_ATYPES*MAX_NUM_OF_ATYPES] __attribute__ ((aligned (1024)));

      	float dspars_S_const    [MAX_NUM_OF_ATYPES]                   __attribute__ ((aligned (64)));

ofdock_taskpar_alt/host/inc/getparameters.h

+3 −0
Original line number Diff line number Diff line
@@ -38,6 +38,9 @@ typedef struct 
		float mutation_rate;

		float crossover_rate;

		float lsearch_rate;



		float smooth;



	unsigned long num_of_ls;

		float tournament_rate;

		float rho_lower_bound;

ofdock_taskpar_alt/host/inc/processligand.h

+9 −0
Original line number Diff line number Diff line
@@ -77,6 +77,15 @@ typedef struct 
	int 	atom_rigid_structures [256];

	char 	bonds [256][256];

	char 	intraE_contributors [256][256];



	// Sizes are hardcoded, ATYPE_NUM=22 float elements as in

	// https://git.esa.informatik.tu-darmstadt.de/docking/ocladock/blob/master/host/src/processligand.cpp#L456

	// See "User Guide AutoDock 4.2" (page 34)

	double  reqm [ATYPE_NUM];

	double  reqm_hbond [ATYPE_NUM];

	unsigned int  atom1_types_reqm [ATYPE_NUM];

	unsigned int  atom2_types_reqm [ATYPE_NUM];



	double 	VWpars_A [14][14];

	double	VWpars_B [14][14];

	double 	VWpars_C [14][14];