calcgradient.cl 34.3 KB
Newer Older
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
/*

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.

*/

/*
#include "calcenergy_basic.h"
*/
// All related pragmas are in defines.h (accesible by host and device code)

Leonardo Solis's avatar
Leonardo Solis committed
29
30
31
32
33
34
35
36

// The GPU device function calculates the energy's gradient (forces or derivatives) 
// of the entity described by genotype, dockpars and the ligand-data
// arrays in constant memory and returns it in the "gradient_genotype" 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 get_group_id(0)), 
// since this determines which reference orientation should be used.

37
38
39
40
41
42
43
44
45
46
47
48
49
void gpu_calc_gradient(	    
				int    dockpars_rotbondlist_length,
				char   dockpars_num_of_atoms,
			    	char   dockpars_gridsize_x,
			    	char   dockpars_gridsize_y,
			    	char   dockpars_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,
Leonardo Solis's avatar
Leonardo Solis committed
50
51
52
53
				// 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.
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
		    	__local float* genotype,
		    	__local int*   run_id,

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

	             __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

		    // Gradient-related arguments
		    // Calculate gradients (forces) for intermolecular energy
		    // Derived from autodockdev/maps.py
		
		    // "is_enabled_gradient_calc": enables gradient calculation.
		    // In Genetic-Generation: no need for gradients
		    // In Gradient-Minimizer: must calculate gradients
			,
			    int    dockpars_num_of_genes,
	    	    __local float* gradient_inter_x,
	            __local float* gradient_inter_y,
	            __local float* gradient_inter_z,
88
89
90
91
		    __local float* gradient_intra_x,
		    __local float* gradient_intra_y,
		    __local float* gradient_intra_z,
	            __local float* gradient_per_intracontributor,
92
93
94
		    __local float* gradient_genotype			
)
{
95
	// Initializing gradients (forces) 
96
97
98
99
	// Derived from autodockdev/maps.py
	for (uint atom_id = get_local_id(0);
		  atom_id < dockpars_num_of_atoms;
		  atom_id+= NUM_OF_THREADS_PER_BLOCK) {
100
		// Intermolecular gradients
101
102
103
		gradient_inter_x[atom_id] = 0.0f;
		gradient_inter_y[atom_id] = 0.0f;
		gradient_inter_z[atom_id] = 0.0f;
104
105
106
107
108
109
		// Intramolecular gradients
		gradient_intra_x[atom_id] = 0.0f;
		gradient_intra_y[atom_id] = 0.0f;
		gradient_intra_z[atom_id] = 0.0f;
	}

Leonardo Solis's avatar
Leonardo Solis committed
110
	// Initializing gradients per intramolecular contributor pairs 
111
112
113
114
	for (uint intracontrib_atompair_id = get_local_id(0);
		  intracontrib_atompair_id < dockpars_num_of_intraE_contributors;
		  intracontrib_atompair_id+= NUM_OF_THREADS_PER_BLOCK) {
		gradient_per_intracontributor[intracontrib_atompair_id] = 0.0f;
115
116
	}

Leonardo Solis's avatar
Leonardo Solis committed
117
118
119
120
121
122
123
124
125
	// Initializing gradient genotypes
	for (uint gene_cnt = get_local_id(0);
		  gene_cnt < dockpars_num_of_genes;
		  gene_cnt+= NUM_OF_THREADS_PER_BLOCK) {
		gradient_genotype[gene_cnt] = 0.0f;
	}

	barrier(CLK_LOCAL_MEM_FENCE);

126
127
128
129
130
131
	uchar g1 = dockpars_gridsize_x;
	uint  g2 = dockpars_gridsize_x * dockpars_gridsize_y;
  	uint  g3 = dockpars_gridsize_x * dockpars_gridsize_y * dockpars_gridsize_z;


	// ================================================
Leonardo Solis's avatar
Leonardo Solis committed
132
	// CALCULATING ATOMIC POSITIONS AFTER ROTATIONS
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
	// ================================================
	for (uint rotation_counter = get_local_id(0);
	          rotation_counter < dockpars_rotbondlist_length;
	          rotation_counter+=NUM_OF_THREADS_PER_BLOCK)
	{
		int rotation_list_element = 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] = ref_coords_x_const[atom_id];
				atom_to_rotate[1] = ref_coords_y_const[atom_id];
				atom_to_rotate[2] = 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_movingvec[3];

			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
			{
Leonardo Solis's avatar
Leonardo Solis committed
168
				// Rotational genes in the Shoemake space are expressed in radians
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
				float u1 = genotype[3];
				float u2 = genotype[4];
				float u3 = genotype[5];

				// u1, u2, u3 should be within their valid range of [0,1]
				quatrot_left_q = native_sqrt(1 - u1) * native_sin(PI_TIMES_2*u2); 
				quatrot_left_x = native_sqrt(1 - u1) * native_cos(PI_TIMES_2*u2);
				quatrot_left_y = native_sqrt(u1)     * native_sin(PI_TIMES_2*u3);
				quatrot_left_z = native_sqrt(u1)     * native_cos(PI_TIMES_2*u3);

				rotation_movingvec[0] = genotype[0];
				rotation_movingvec[1] = genotype[1];
				rotation_movingvec[2] = genotype[2];
			}
			else	// If rotating around rotatable bond
			{
				uint rotbond_id = (rotation_list_element & RLIST_RBONDID_MASK) >> RLIST_RBONDID_SHIFT;

				float rotation_unitvec[3];
				rotation_unitvec[0] = rotbonds_unit_vectors_const[3*rotbond_id];
				rotation_unitvec[1] = rotbonds_unit_vectors_const[3*rotbond_id+1];
				rotation_unitvec[2] = rotbonds_unit_vectors_const[3*rotbond_id+2];
				float rotation_angle = genotype[6+rotbond_id]*DEG_TO_RAD;

				rotation_movingvec[0] = rotbonds_moving_vectors_const[3*rotbond_id];
				rotation_movingvec[1] = rotbonds_moving_vectors_const[3*rotbond_id+1];
				rotation_movingvec[2] = rotbonds_moving_vectors_const[3*rotbond_id+2];

				// 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 torsion angles into quaternions
				// FIXME: add precision choices with preprocessor directives: 
				// NATIVE_PRECISION, HALF_PRECISION, Full precision
				rotation_angle  = native_divide(rotation_angle, 2.0f);
				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*ref_orientation_quats_const[4*(*run_id)]-
						 quatrot_temp_x*ref_orientation_quats_const[4*(*run_id)+1]-
						 quatrot_temp_y*ref_orientation_quats_const[4*(*run_id)+2]-
						 quatrot_temp_z*ref_orientation_quats_const[4*(*run_id)+3];
				quatrot_left_x = quatrot_temp_q*ref_orientation_quats_const[4*(*run_id)+1]+
						 ref_orientation_quats_const[4*(*run_id)]*quatrot_temp_x+
						 quatrot_temp_y*ref_orientation_quats_const[4*(*run_id)+3]-
						 ref_orientation_quats_const[4*(*run_id)+2]*quatrot_temp_z;
				quatrot_left_y = quatrot_temp_q*ref_orientation_quats_const[4*(*run_id)+2]+
						 ref_orientation_quats_const[4*(*run_id)]*quatrot_temp_y+
						 ref_orientation_quats_const[4*(*run_id)+1]*quatrot_temp_z-
						 quatrot_temp_x*ref_orientation_quats_const[4*(*run_id)+3];
				quatrot_left_z = quatrot_temp_q*ref_orientation_quats_const[4*(*run_id)+3]+
						 ref_orientation_quats_const[4*(*run_id)]*quatrot_temp_z+
						 quatrot_temp_x*ref_orientation_quats_const[4*(*run_id)+2]-
						 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

	// ================================================
Leonardo Solis's avatar
Leonardo Solis committed
286
	// CALCULATING INTERMOLECULAR GRADIENTS
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
	// ================================================
	for (uint atom_id = get_local_id(0);
	          atom_id < dockpars_num_of_atoms;
	          atom_id+= NUM_OF_THREADS_PER_BLOCK)
	{
		uint atom_typeid = 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 = 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)){
			
			// Setting gradients (forces) penalties.
			// These are valid as long as they are high
			gradient_inter_x[atom_id] += 16777216.0f;
			gradient_inter_y[atom_id] += 16777216.0f;
			gradient_inter_z[atom_id] += 16777216.0f;
		}
		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;

			// 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);

			// -------------------------------------------------------------------
			// Deltas dx, dy, dz are already normalized 
			// (by host/src/getparameters.cpp) in OCLaDock.
			// The correspondance between vertices in xyz axes is:
			// 0, 1, 2, 3, 4, 5, 6, 7  and  000, 100, 010, 001, 101, 110, 011, 111
			// -------------------------------------------------------------------
			/*
			    deltas: (x-x0)/(x1-x0), (y-y0...
			    vertices: (000, 100, 010, 001, 101, 110, 011, 111)        

				  Z
				  '
				  3 - - - - 6
				 /.        /|
				4 - - - - 7 |
				| '       | |
				| 0 - - - + 2 -- Y
				'/        |/
				1 - - - - 5
			       /
			      X
			*/

			// Intermediate values for vectors in x-direction
			float x10, x52, x43, x76;
			float vx_z0, vx_z1;

			// Intermediate values for vectors in y-direction
			float y20, y51, y63, y74;
			float vy_z0, vy_z1;

			// Intermediate values for vectors in z-direction
			float z30, z41, z62, z75;
			float vz_y0, vz_y1;

			// -------------------------------------------------------------------
			// Calculating gradients (forces) corresponding to 
			// "atype" intermolecular energy
			// Derived from autodockdev/maps.py
			// -------------------------------------------------------------------

Leonardo Solis's avatar
Leonardo Solis committed
390
			// Vector in x-direction
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
			/*
			x10 = grid[int(vertices[1])] - grid[int(vertices[0])] # z = 0
			x52 = grid[int(vertices[5])] - grid[int(vertices[2])] # z = 0
			x43 = grid[int(vertices[4])] - grid[int(vertices[3])] # z = 1
			x76 = grid[int(vertices[7])] - grid[int(vertices[6])] # z = 1
			vx_z0 = (1-yd) * x10 + yd * x52     #  z = 0
			vx_z1 = (1-yd) * x43 + yd * x76     #  z = 1
			gradient[0] = (1-zd) * vx_z0 + zd * vx_z1 
			*/

			x10 = cube [1][0][0] - cube [0][0][0]; // z = 0
			x52 = cube [1][1][0] - cube [0][1][0]; // z = 0
			x43 = cube [1][0][1] - cube [0][0][1]; // z = 1
			x76 = cube [1][1][1] - cube [0][1][1]; // z = 1
			vx_z0 = (1 - dy) * x10 + dy * x52;     // z = 0
			vx_z1 = (1 - dy) * x43 + dy * x76;     // z = 1
			gradient_inter_x[atom_id] += (1 - dz) * vx_z0 + dz * vx_z1;

Leonardo Solis's avatar
Leonardo Solis committed
409
			// Vector in y-direction
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
			/*
			y20 = grid[int(vertices[2])] - grid[int(vertices[0])] # z = 0
			y51 = grid[int(vertices[5])] - grid[int(vertices[1])] # z = 0
			y63 = grid[int(vertices[6])] - grid[int(vertices[3])] # z = 1
			y74 = grid[int(vertices[7])] - grid[int(vertices[4])] # z = 1
			vy_z0 = (1-xd) * y20 + xd * y51     #  z = 0
			y_z1 = (1-xd) * y63 + xd * y74     #  z = 1
			gradient[1] = (1-zd) * vy_z0 + zd * vy_z1
			*/

			y20 = cube[0][1][0] - cube [0][0][0];	// z = 0
			y51 = cube[1][1][0] - cube [1][0][0];	// z = 0
			y63 = cube[0][1][1] - cube [0][0][1];	// z = 1
			y74 = cube[1][1][1] - cube [1][0][1];	// z = 1
			vy_z0 = (1 - dx) * y20 + dx * y51;	// z = 0
			vy_z1 = (1 - dx) * y63 + dx * y74;	// z = 1
			gradient_inter_y[atom_id] += (1 - dz) * vy_z0 + dz * vy_z1;

Leonardo Solis's avatar
Leonardo Solis committed
428
			// Vectors in z-direction
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
			/*	
			z30 = grid[int(vertices[3])] - grid[int(vertices[0])] # y = 0
			z41 = grid[int(vertices[4])] - grid[int(vertices[1])] # y = 0
			z62 = grid[int(vertices[6])] - grid[int(vertices[2])] # y = 1
			z75 = grid[int(vertices[7])] - grid[int(vertices[5])] # y = 1
			vz_y0 = (1-xd) * z30 + xd * z41     # y = 0
			vz_y1 = (1-xd) * z62 + xd * z75     # y = 1
			gradient[2] = (1-yd) * vz_y0 + yd * vz_y1
			*/

			z30 = cube [0][0][1] - cube [0][0][0];	// y = 0
			z41 = cube [1][0][1] - cube [1][0][0];	// y = 0
			z62 = cube [0][1][1] - cube [0][1][0];	// y = 1 
			z75 = cube [1][1][1] - cube [1][1][0];	// y = 1
			vz_y0 = (1 - dx) * z30 + dx * z41;	// y = 0
			vz_y1 = (1 - dx) * z62 + dx * z75;	// y = 1
			gradient_inter_z[atom_id] += (1 - dy) * vz_y0 + dy * vz_y1;

			// -------------------------------------------------------------------
			// Calculating gradients (forces) corresponding to 
			// "elec" intermolecular energy
			// Derived from autodockdev/maps.py
			// -------------------------------------------------------------------

			// 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);

Leonardo Solis's avatar
Leonardo Solis committed
466
			// Vector in x-direction
467
468
469
470
471
472
473
474
			x10 = cube [1][0][0] - cube [0][0][0]; // z = 0
			x52 = cube [1][1][0] - cube [0][1][0]; // z = 0
			x43 = cube [1][0][1] - cube [0][0][1]; // z = 1
			x76 = cube [1][1][1] - cube [0][1][1]; // z = 1
			vx_z0 = (1 - dy) * x10 + dy * x52;     // z = 0
			vx_z1 = (1 - dy) * x43 + dy * x76;     // z = 1
			gradient_inter_x[atom_id] += (1 - dz) * vx_z0 + dz * vx_z1;

Leonardo Solis's avatar
Leonardo Solis committed
475
			// Vector in y-direction
476
477
478
479
480
481
482
483
			y20 = cube[0][1][0] - cube [0][0][0];	// z = 0
			y51 = cube[1][1][0] - cube [1][0][0];	// z = 0
			y63 = cube[0][1][1] - cube [0][0][1];	// z = 1
			y74 = cube[1][1][1] - cube [1][0][1];	// z = 1
			vy_z0 = (1 - dx) * y20 + dx * y51;	// z = 0
			vy_z1 = (1 - dx) * y63 + dx * y74;	// z = 1
			gradient_inter_y[atom_id] += (1 - dz) * vy_z0 + dz * vy_z1;

Leonardo Solis's avatar
Leonardo Solis committed
484
			// Vectors in z-direction
485
486
487
488
489
490
491
492
493
			z30 = cube [0][0][1] - cube [0][0][0];	// y = 0
			z41 = cube [1][0][1] - cube [1][0][0];	// y = 0
			z62 = cube [0][1][1] - cube [0][1][0];	// y = 1 
			z75 = cube [1][1][1] - cube [1][1][0];	// y = 1
			vz_y0 = (1 - dx) * z30 + dx * z41;	// y = 0
			vz_y1 = (1 - dx) * z62 + dx * z75;	// y = 1
			gradient_inter_z[atom_id] += (1 - dy) * vz_y0 + dy * vz_y1;

			// -------------------------------------------------------------------
Leonardo Solis's avatar
Leonardo Solis committed
494
			// Calculating gradients (forces) corresponding to 
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
			// "dsol" intermolecular energy
			// Derived from autodockdev/maps.py
			// -------------------------------------------------------------------

			// 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);

Leonardo Solis's avatar
Leonardo Solis committed
512
			// Vector in x-direction
513
514
515
516
517
518
519
520
			x10 = cube [1][0][0] - cube [0][0][0]; // z = 0
			x52 = cube [1][1][0] - cube [0][1][0]; // z = 0
			x43 = cube [1][0][1] - cube [0][0][1]; // z = 1
			x76 = cube [1][1][1] - cube [0][1][1]; // z = 1
			vx_z0 = (1 - dy) * x10 + dy * x52;     // z = 0
			vx_z1 = (1 - dy) * x43 + dy * x76;     // z = 1
			gradient_inter_x[atom_id] += (1 - dz) * vx_z0 + dz * vx_z1;

Leonardo Solis's avatar
Leonardo Solis committed
521
			// Vector in y-direction
522
523
524
525
526
527
528
529
			y20 = cube[0][1][0] - cube [0][0][0];	// z = 0
			y51 = cube[1][1][0] - cube [1][0][0];	// z = 0
			y63 = cube[0][1][1] - cube [0][0][1];	// z = 1
			y74 = cube[1][1][1] - cube [1][0][1];	// z = 1
			vy_z0 = (1 - dx) * y20 + dx * y51;	// z = 0
			vy_z1 = (1 - dx) * y63 + dx * y74;	// z = 1
			gradient_inter_y[atom_id] += (1 - dz) * vy_z0 + dz * vy_z1;

Leonardo Solis's avatar
Leonardo Solis committed
530
			// Vectors in z-direction
531
532
533
534
535
536
537
538
539
540
541
542
543
			z30 = cube [0][0][1] - cube [0][0][0];	// y = 0
			z41 = cube [1][0][1] - cube [1][0][0];	// y = 0
			z62 = cube [0][1][1] - cube [0][1][0];	// y = 1 
			z75 = cube [1][1][1] - cube [1][1][0];	// y = 1
			vz_y0 = (1 - dx) * z30 + dx * z41;	// y = 0
			vz_y1 = (1 - dx) * z62 + dx * z75;	// y = 1
			gradient_inter_z[atom_id] += (1 - dy) * vz_y0 + dy * vz_y1;

			// -------------------------------------------------------------------
		}

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

544
545
546
547
	// Inter- and intra-molecular energy calculation
	// are independent from each other, so NO barrier is needed here.
  	// As these two require different operations,
	// they can be executed only sequentially on the GPU.
548
549

	// ================================================
Leonardo Solis's avatar
Leonardo Solis committed
550
	// CALCULATING INTRAMOLECULAR GRADIENTS
551
552
553
	// ================================================
	for (uint contributor_counter = get_local_id(0);
	          contributor_counter < dockpars_num_of_intraE_contributors;
Leonardo Solis's avatar
Leonardo Solis committed
554
	          contributor_counter+= NUM_OF_THREADS_PER_BLOCK)
555
	{
556
		// Getting atom IDs
557
558
559
		uint atom1_id = intraE_contributors_const[3*contributor_counter];
		uint atom2_id = intraE_contributors_const[3*contributor_counter+1];

Leonardo Solis's avatar
Leonardo Solis committed
560
561
562
563
564
		// 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];
565

566
		// Calculating atomic distance
567
568
569
570
571
		float atomic_distance = native_sqrt(subx*subx + suby*suby + subz*subz)*dockpars_grid_spacing;

		if (atomic_distance < 1.0f)
			atomic_distance = 1.0f;

572
		// Calculating gradient contributions
573
574
575
576
577
578
		if ((atomic_distance < 8.0f) && (atomic_distance < 20.48f))
		{
			// Getting type IDs
			uint atom1_typeid = atom_types_const[atom1_id];
			uint atom2_typeid = atom_types_const[atom2_id];

579
580
581
582
			// Calculating van der Waals / hydrogen bond term
			gradient_per_intracontributor[contributor_counter] += native_divide (-12*VWpars_AC_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],
									                     native_powr(atomic_distance, 13)
									       		    );
583

584
585
586
587
588
589
590
591
592
593
			if (intraE_contributors_const[3*contributor_counter+2] == 1) {	//H-bond
				gradient_per_intracontributor[contributor_counter] += native_divide (10*VWpars_BD_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],
										                     native_powr(atomic_distance, 11)
										                    );
			}
			else {	//van der Waals
				gradient_per_intracontributor[contributor_counter] += native_divide (6*VWpars_BD_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],
										                     native_powr(atomic_distance, 7)
										                    );
			}
594

595
596
			// Calculating electrostatic term
			// http://www.wolframalpha.com/input/?i=1%2F(x*(A%2B(B%2F(1%2BK*exp(-h*B*x)))))
Leonardo Solis's avatar
Leonardo Solis committed
597
			float upper = DIEL_A*native_powr(native_exp(DIEL_B_TIMES_H*atomic_distance) + DIEL_K, 2) + (DIEL_B)*native_exp(DIEL_B_TIMES_H*atomic_distance)*(DIEL_B_TIMES_H_TIMES_K*atomic_distance + native_exp(DIEL_B_TIMES_H*atomic_distance) + DIEL_K);
598
		
Leonardo Solis's avatar
Leonardo Solis committed
599
			float lower = native_powr(atomic_distance, 2) * native_powr(DIEL_A * (native_exp(DIEL_B_TIMES_H*atomic_distance) + DIEL_K) + DIEL_B * native_exp(DIEL_B_TIMES_H*atomic_distance), 2);
600

Leonardo Solis's avatar
Leonardo Solis committed
601
        		gradient_per_intracontributor[contributor_counter] +=  -dockpars_coeff_elec * atom_charges_const[atom1_id] * atom_charges_const[atom2_id] * native_divide (upper, lower);
602

603
604
605
606
607
608
			// Calculating desolvation term
			gradient_per_intracontributor[contributor_counter] += (
									       (dspars_S_const[atom1_typeid] + dockpars_qasp*fabs(atom_charges_const[atom1_id])) * dspars_V_const[atom2_typeid] +
							                       (dspars_S_const[atom2_typeid] + dockpars_qasp*fabs(atom_charges_const[atom2_id])) * dspars_V_const[atom1_typeid]
				        				      ) *
					                       			dockpars_coeff_desolv * -0.07716049382716049 * atomic_distance * native_exp(-0.038580246913580245*native_powr(atomic_distance, 2));
609

610
611
		}
	} // End contributor_counter for-loop (INTRAMOLECULAR ENERGY)
612

613
	barrier(CLK_LOCAL_MEM_FENCE);
614

615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
	// Accumulating gradients of each atom from "gradient_per_intracontributor"
	if (get_local_id(0) == 0) {
		for (uint contributor_counter = 0;
			  contributor_counter < dockpars_num_of_intraE_contributors;
			  contributor_counter ++) {

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

			// Calculating xyz distances in Angstroms
			// between"atom1_id"-to-"atom2_id"
			float subx = (calc_coords_x[atom1_id] - calc_coords_x[atom2_id]) * dockpars_grid_spacing;
			float suby = (calc_coords_y[atom1_id] - calc_coords_y[atom2_id]) * dockpars_grid_spacing;
			float subz = (calc_coords_z[atom1_id] - calc_coords_z[atom2_id]) * dockpars_grid_spacing;

			// Calculating gradients in xyz components.
			// Gradients for both atoms in a single contributor pair
			// have the same magnitude, but opposite directions
			gradient_intra_x[atom1_id] += gradient_per_intracontributor[contributor_counter] * subx;
			gradient_intra_y[atom1_id] += gradient_per_intracontributor[contributor_counter] * suby;
			gradient_intra_z[atom1_id] += gradient_per_intracontributor[contributor_counter] * subz;

			gradient_intra_x[atom2_id] -= gradient_per_intracontributor[contributor_counter] * subx;
			gradient_intra_y[atom2_id] -= gradient_per_intracontributor[contributor_counter] * suby;
			gradient_intra_z[atom2_id] -= gradient_per_intracontributor[contributor_counter] * subz;
		}
	}
	
644
645
646

	barrier(CLK_LOCAL_MEM_FENCE);

647
	// Accumulating inter- and intramolecular gradients
Leonardo Solis's avatar
Leonardo Solis committed
648
	// simply into "gradient_inter_{x|y|z}"
649
650
651
652
653
654
	for (uint atom_cnt = get_local_id(0);
		  atom_cnt < dockpars_num_of_atoms;
		  atom_cnt+= NUM_OF_THREADS_PER_BLOCK) {
		gradient_inter_x[atom_cnt] = gradient_inter_x[atom_cnt] + gradient_intra_x[atom_cnt];
		gradient_inter_y[atom_cnt] = gradient_inter_y[atom_cnt] + gradient_intra_y[atom_cnt];
		gradient_inter_z[atom_cnt] = gradient_inter_z[atom_cnt] + gradient_intra_z[atom_cnt];
655
656
	}

657
658
	barrier(CLK_LOCAL_MEM_FENCE);

659
	// ------------------------------------------
Leonardo Solis's avatar
Leonardo Solis committed
660
	// Obtaining translation-related gradients
661
662
663
664
665
	// ------------------------------------------
	if (get_local_id(0) == 0) {
		for (uint lig_atom_id = 0;
			  lig_atom_id<dockpars_num_of_atoms;
			  lig_atom_id++) {
Leonardo Solis's avatar
Leonardo Solis committed
666
667
668
			gradient_genotype[0] += gradient_inter_x[lig_atom_id]; // gradient for gene 0: gene x
			gradient_genotype[1] += gradient_inter_y[lig_atom_id]; // gradient for gene 1: gene y
			gradient_genotype[2] += gradient_inter_z[lig_atom_id]; // gradient for gene 2: gene z
669
		}
670
671
672
673
674
675

		/*
		printf("gradient_x:%f\n", gradient_genotype [0]);
		printf("gradient_y:%f\n", gradient_genotype [1]);
		printf("gradient_z:%f\n", gradient_genotype [2]);
		*/
676
677
678
	}

	// ------------------------------------------
Leonardo Solis's avatar
Leonardo Solis committed
679
680
	// Obtaining rotation-related gradients
	// ------------------------------------------ 
681
682
683
684
685
686
687
688
689
690
691
				
	// Transform gradients_inter_{x|y|z} 
	// into local_gradients[i] (with four quaternion genes)
	// Derived from autodockdev/motions.py/forces_to_delta_genes()

	// Transform local_gradients[i] (with four quaternion genes)
	// into local_gradients[i] (with three Shoemake genes)
	// Derived from autodockdev/motions.py/_get_cube3_gradient()
	// ------------------------------------------
	if (get_local_id(0) == 1) {

692
		float3 torque_rot = (float3)(0.0f, 0.0f, 0.0f);
693

Leonardo Solis's avatar
Leonardo Solis committed
694
		// Center of rotation 
695
696
		// In getparameters.cpp, it indicates 
		// translation genes are in grid spacing (instead of Angstroms)
Leonardo Solis's avatar
Leonardo Solis committed
697
698
699
700
		float3 about;
		about.x = genotype[0]; 
		about.y = genotype[1];
		about.z = genotype[2];
701
		
702
703
704
		// Temporal variable to calculate translation differences.
		// They are converted back to Angstroms here
		float3 r;
705
			
706
707
708
		for (uint lig_atom_id = 0;
			  lig_atom_id<dockpars_num_of_atoms;
			  lig_atom_id++) {
Leonardo Solis's avatar
Leonardo Solis committed
709
710
711
			r.x = (calc_coords_x[lig_atom_id] - about.x) * dockpars_grid_spacing; 
			r.y = (calc_coords_y[lig_atom_id] - about.y) * dockpars_grid_spacing;  
			r.z = (calc_coords_z[lig_atom_id] - about.z) * dockpars_grid_spacing; 
712
713
			torque_rot += cross(r, torque_rot);
		}
714

715
716
717
718
719
720
721
722
723
724
725
726
		const float rad = 1E-8;
		const float rad_div_2 = native_divide(rad, 2);

		float quat_w, quat_x, quat_y, quat_z;

		// Derived from rotation.py/axisangle_to_q()
		// genes[3:7] = rotation.axisangle_to_q(torque, rad)
		torque_rot = fast_normalize(torque_rot);
		quat_x = torque_rot.x;
		quat_y = torque_rot.y;
		quat_z = torque_rot.z;

Leonardo Solis's avatar
Leonardo Solis committed
727
		// Rotation-related gradients are expressed here in quaternions
728
729
730
731
732
		quat_w = native_cos(rad_div_2);
		quat_x = quat_x * native_sin(rad_div_2);
		quat_y = quat_y * native_sin(rad_div_2);
		quat_z = quat_z * native_sin(rad_div_2);

Leonardo Solis's avatar
Leonardo Solis committed
733
		// Converting quaternion gradients into Shoemake gradients 
734
735
		// Derived from autodockdev/motion.py/_get_cube3_gradient

Leonardo Solis's avatar
Leonardo Solis committed
736
		// This is where we are in cube3
737
738
739
740
741
		float current_u1, current_u2, current_u3;
		current_u1 = genotype[3]; // check very initial input Shoemake genes
		current_u2 = genotype[4];
		current_u3 = genotype[5];

Leonardo Solis's avatar
Leonardo Solis committed
742
		// This is where we are in quaternion space
743
744
745
746
747
748
749
		// current_q = cube3_to_quaternion(current_u)
		float current_qw, current_qx, current_qy, current_qz;
		current_qw = native_sqrt(1-current_u1) * native_sin(PI_TIMES_2*current_u2);
		current_qx = native_sqrt(1-current_u1) * native_cos(PI_TIMES_2*current_u2);
		current_qy = native_sqrt(current_u1)   * native_sin(PI_TIMES_2*current_u3);
		current_qz = native_sqrt(current_u1)   * native_cos(PI_TIMES_2*current_u3);

Leonardo Solis's avatar
Leonardo Solis committed
750
		// This is where we want to be in quaternion space
751
752
753
754
755
756
757
758
759
760
		float target_qw, target_qx, target_qy, target_qz;

		// target_q = rotation.q_mult(q, current_q)
		// Derived from autodockdev/rotation.py/q_mult()
		// In our terms means q_mult(quat_{w|x|y|z}, current_q{w|x|y|z})
		target_qw = quat_w*current_qw - quat_x*current_qx - quat_y*current_qy - quat_z*current_qz;// w
		target_qx = quat_w*current_qx + quat_x*current_qw + quat_y*current_qz - quat_z*current_qy;// x
		target_qy = quat_w*current_qy + quat_y*current_qw + quat_z*current_qx - quat_x*current_qz;// y
		target_qz = quat_w*current_qz + quat_z*current_qw + quat_x*current_qy - quat_y*current_qx;// z

Leonardo Solis's avatar
Leonardo Solis committed
761
		// This is where we want to be in cube3
762
763
764
765
766
767
768
769
770
		float target_u1, target_u2, target_u3;

		// target_u = quaternion_to_cube3(target_q)
		// Derived from autodockdev/motions.py/quaternion_to_cube3()
		// In our terms means quaternion_to_cube3(target_q{w|x|y|z})
		target_u1 = target_qy*target_qy + target_qz*target_qz;
		target_u2 = atan2(target_qw, target_qx);
		target_u3 = atan2(target_qy, target_qz);

Leonardo Solis's avatar
Leonardo Solis committed
771
		// Derivates in cube3
772
773
774
775
		float grad_u1, grad_u2, grad_u3;
		grad_u1 = target_u1 - current_u1;
		grad_u2 = target_u2 - current_u2;
		grad_u3 = target_u3 - current_u3;
776
			
Leonardo Solis's avatar
Leonardo Solis committed
777
		// Empirical scaling
778
		float temp_u1 = genotype[3];
779
			
780
781
782
783
784
		if ((temp_u1 > 1.0f) || (temp_u1 < 0.0f)){
			grad_u1 *= ((1/temp_u1) + (1/(1-temp_u1)));
		}
		grad_u2 *= 4 * (1-temp_u1);
		grad_u3 *= 4 * temp_u1;
785
			
Leonardo Solis's avatar
Leonardo Solis committed
786
		// Setting gradient rotation-related genotypes in cube3
787
788
789
790
791
792
793
794
795
		gradient_genotype[3] = grad_u1;
		gradient_genotype[4] = grad_u2;
		gradient_genotype[5] = grad_u3;

		/*
		printf("gradient_shoemake_u1:%f\n", gradient_genotype [3]);
		printf("gradient_shoemake_u2:%f\n", gradient_genotype [4]);
		printf("gradient_shoemake_u3:%f\n", gradient_genotype [5]);
		*/
796
797
	}

Leonardo Solis's avatar
Leonardo Solis committed
798
799
800
	// ------------------------------------------
	// Obtaining torsion-related gradients
	// ------------------------------------------
801
802
803
804
805
806
807
808
809
810
811
812
813
814
	if (get_local_id(0) == 2) {

		for (uint rotbond_id = 0;
			  rotbond_id < dockpars_num_of_genes-6;
			  rotbond_id ++) {

			float3 rotation_unitvec;
			rotation_unitvec.x = rotbonds_unit_vectors_const[3*rotbond_id];
			rotation_unitvec.y = rotbonds_unit_vectors_const[3*rotbond_id+1];
			rotation_unitvec.z = rotbonds_unit_vectors_const[3*rotbond_id+2];

			// Torque of torsions
			float3 torque_tor = (float3)(0.0f, 0.0f, 0.0f);

815
			// Iterating over each ligand atom
816
817
818
819
			for (uint lig_atom_id = 0;
				  lig_atom_id<dockpars_num_of_atoms;
				  lig_atom_id++) {

Leonardo Solis's avatar
Leonardo Solis committed
820
				// Calculating torque on point "A" 
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
				// (could be any other point "B" along the rotation axis)
				float3 atom_coords = {calc_coords_x[lig_atom_id], 
					              calc_coords_y[lig_atom_id], 
					              calc_coords_z[lig_atom_id]};

				float3 atom_force  = {gradient_inter_x[lig_atom_id],
					              gradient_inter_y[lig_atom_id],
				                      gradient_inter_z[lig_atom_id]};

				float3 rotation_movingvec;
				rotation_movingvec.x = rotbonds_moving_vectors_const[3*rotbond_id];
				rotation_movingvec.y = rotbonds_moving_vectors_const[3*rotbond_id+1];
				rotation_movingvec.z = rotbonds_moving_vectors_const[3*rotbond_id+2];

				torque_tor = cross((atom_coords-rotation_movingvec), atom_force);
			}

838
			// Projecting torque on rotation axis
839
840
841
842
843
			float torque_on_axis = dot(rotation_unitvec, torque_tor);

			// Assignment of gene-based gradient
			gradient_genotype[rotbond_id+6] = torque_on_axis;

844
845
846
847
			/*
			printf("gradient_torsion [%u] :%f\n", rotbond_id+6, gradient_genotype [rotbond_id+6]);
			*/
		} // End of iterations over rotatable bonds
848
849
850
	}

}