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Commit 21ab85f0 authored by Leonardo Solis's avatar Leonardo Solis
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redefined Shoemake genes limits all [0,1]

parent 7f3818e0
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common/calcenergy_basic.h
View file @ 21ab85f0
......@@ -57,4 +57,9 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
cube[0][0][1]*weights[0][0][1] +cube[1][0][1]*weights[1][0][1] + \
cube[0][1][1]*weights[0][1][1] +cube[1][1][1]*weights[1][1][1])
// Used for Shoemake to quternion transformation
#define PI_TIMES_2 (float)(2.0f*M_PI)
#endif /* CALCENERGY_BASIC_H_ */
device/calcenergy.cl
View file @ 21ab85f0
......@@ -107,13 +107,14 @@ void gpu_calc_energy( int dockpars_rotbondlist_length,
}
}
#if 0
// Rotational genes in the Shoemake space expressed in radians
float u1, u2, u3;
u1 = genotype[3];
u2 = genotype[4]*DEG_TO_RAD;
u3 = genotype[5]*DEG_TO_RAD;
u2 = genotype[4]/**DEG_TO_RAD*/;
u3 = genotype[5]/**DEG_TO_RAD*/;
#endif
#if defined (IMPROVE_GRID)
// INTERMOLECULAR for-loop (intermediate results)
......@@ -182,11 +183,18 @@ void gpu_calc_energy( int dockpars_rotbondlist_length,
// FIXME: add precision choices with preprocessor directives:
// NATIVE_PRECISION, HALF_PRECISION, Full precision
// u1 should be within the valid range [0,1]
quatrot_left_q = native_sqrt(1 - u1) * native_sin(u2);
quatrot_left_x = native_sqrt(1 - u1) * native_cos(u2);
quatrot_left_y = native_sqrt(u1) * native_sin(u3);
quatrot_left_z = native_sqrt(u1) * native_cos(u3);
// Rotational genes in the Shoemake space expressed in radians
float u1, u2, u3;
u1 = genotype[3];
u2 = genotype[4]/**DEG_TO_RAD*/;
u3 = genotype[5]/**DEG_TO_RAD*/;
// 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];
......@@ -705,7 +713,7 @@ void gpu_calc_energy( int dockpars_rotbondlist_length,
dockpars_gridsize_y,
dockpars_gridsize_z,
atom_typeid, z_low, y_low, x_low);
cube [1][0][0] = GETGRIDVALUE(dockpars_fgrids,
cube [1][0][0] = GETGRIDVALUE(dockpars_fgridsu2,
dockpars_gridsize_x,
dockpars_gridsize_y,
dockpars_gridsize_z,
......@@ -966,10 +974,10 @@ void gpu_calc_energy( int dockpars_rotbondlist_length,
// where we are in quaternion space
// 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(u2);
current_qx = native_sqrt(1-current_u1) * native_cos(u2);
current_qy = native_sqrt(current_u1) * native_sin(u3);
current_qz = native_sqrt(current_u1) * native_cos(u3);
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);
// where we want to be in quaternion space
float target_qw, target_qx, target_qy, target_qz;
......@@ -989,8 +997,8 @@ void gpu_calc_energy( int dockpars_rotbondlist_length,
// 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 = atan2pi(target_qw, target_qx)*180.0f; // in sexagesimal
target_u3 = atan2pi(target_qy, target_qz)*180.0f; // in sexagesimal
target_u2 = atan2pi(target_qw, target_qx)/PI_TIMES_2;
target_u3 = atan2pi(target_qy, target_qz)/PI_TIMES_2;
// derivates in cube3
float grad_u1, grad_u2, grad_u3;
......
device/kernel3.cl
View file @ 21ab85f0
......@@ -228,8 +228,8 @@ perform_LS( char dockpars_num_of_atoms,
for (gene_counter=get_local_id(0);
gene_counter<dockpars_num_of_genes;
gene_counter += NUM_OF_THREADS_PER_BLOCK) {
if (gene_counter == 3) {
genotype_candidate[gene_counter] = /*0.2f**/gpu_randf(dockpars_prng_states);
if ((gene_counter > 2) || (gene_counter < 6)) { // Shoemake genes: u1, u2, u3
genotype_candidate[gene_counter] = gpu_randf(dockpars_prng_states);
}
else {
genotype_candidate[gene_counter] = offspring_genotype[gene_counter] + genotype_deviate[gene_counter] + genotype_bias[gene_counter];
......@@ -348,8 +348,8 @@ perform_LS( char dockpars_num_of_atoms,
gene_counter<dockpars_num_of_genes;
gene_counter += NUM_OF_THREADS_PER_BLOCK) {
if (gene_counter == 3) {
genotype_candidate[gene_counter] = /*0.2f**/gpu_randf(dockpars_prng_states);
if ((gene_counter > 2) || (gene_counter < 6)) { // Shoemake genes: u1, u2, u3
genotype_candidate[gene_counter] = gpu_randf(dockpars_prng_states);
}
else {
genotype_candidate[gene_counter] = offspring_genotype[gene_counter] - genotype_deviate[gene_counter] - genotype_bias[gene_counter];
......
device/kernel4.cl
View file @ 21ab85f0
......@@ -276,27 +276,9 @@ gpu_gen_and_eval_newpops(char dockpars_num_of_atoms,
*/
if (gene_counter < 3)
offspring_genotype[gene_counter] += dockpars_abs_max_dmov*(2*gpu_randf(dockpars_prng_states)-1);
else if (gene_counter == 3) {// u1, FIXME: hardcoded
offspring_genotype[gene_counter] = /*0.2f**/gpu_randf(dockpars_prng_states);
/*
offspring_genotype[gene_counter] += 0.2f*(2*gpu_randf(dockpars_prng_states)-1);
if (offspring_genotype[gene_counter] > 1.0f) { // clamp it
offspring_genotype[gene_counter] = 0.9f;
}
if (offspring_genotype[gene_counter] < 0.0f) { // clamp it
offspring_genotype[gene_counter] = 0.1f;
}
//printf("mutation - offspring_genotype[gene_counter]: %f\n", offspring_genotype[gene_counter]);
*/
}
else if (gene_counter < 6) { // u2&3, FIXME: hardcoded
offspring_genotype[gene_counter] += 90.0f*(2*gpu_randf(dockpars_prng_states)-1);
map_angle(&(offspring_genotype[gene_counter]));
else if (gene_counter < 6) { // Shoemake genes: u1, u2, 23
offspring_genotype[gene_counter] = gpu_randf(dockpars_prng_states);
}
else
{
......
host/src/calcenergy.cpp
View file @ 21ab85f0
......@@ -256,13 +256,13 @@ int prepare_const_fields_for_gpu(Liganddata* myligand_reference,
float u1, u2, u3;
u1 = cpu_ref_ori_angles[3*i];
u2 = cpu_ref_ori_angles[3*i+1]*DEG_TO_RAD;
u3 = cpu_ref_ori_angles[3*i+2]*DEG_TO_RAD;
u2 = cpu_ref_ori_angles[3*i+1];
u3 = cpu_ref_ori_angles[3*i+2];
ref_orientation_quats[4*i] = sqrt(1-u1) * sinf(u2); //q
ref_orientation_quats[4*i+1] = sqrt(1-u1) * cosf(u2); //x
ref_orientation_quats[4*i+2] = sqrt(u1) * sinf(u3); //y
ref_orientation_quats[4*i+3] = sqrt(u1) * cosf(u3); //z
ref_orientation_quats[4*i] = sqrt(1-u1) * sinf(2*PI*u2); //q
ref_orientation_quats[4*i+1] = sqrt(1-u1) * cosf(2*PI*u2); //x
ref_orientation_quats[4*i+2] = sqrt(u1) * sinf(2*PI*u3); //y
ref_orientation_quats[4*i+3] = sqrt(u1) * cosf(2*PI*u3); //z
//printf("Precalculated quaternion for run %d: %f %f %f %f\n", i, ref_orientation_quats[4*i], ref_orientation_quats[4*i+1], ref_orientation_quats[4*i+2], ref_orientation_quats[4*i+3]);
}
......
host/src/getparameters.cpp
View file @ 21ab85f0
......@@ -648,19 +648,19 @@ void gen_initpop_and_reflig(Dockpars* mypars,
#if defined (REPRO)
init_populations[entity_id*GENOTYPE_LENGTH_IN_GLOBMEM+gene_id] = 22.0452;
#else
init_populations[entity_id*GENOTYPE_LENGTH_IN_GLOBMEM+gene_id] = ((float) rand()/ (float) RAND_MAX)*360;
init_populations[entity_id*GENOTYPE_LENGTH_IN_GLOBMEM+gene_id] = ((float) rand()/ (float) RAND_MAX);
#endif
else if (gene_id == 5) // u3 (Shoemake)
#if defined (REPRO)
init_populations[entity_id*GENOTYPE_LENGTH_IN_GLOBMEM+gene_id] = 26.0555;
#else
init_populations[entity_id*GENOTYPE_LENGTH_IN_GLOBMEM+gene_id] = ((float) rand()/ (float) RAND_MAX)*360;
init_populations[entity_id*GENOTYPE_LENGTH_IN_GLOBMEM+gene_id] = ((float) rand()/ (float) RAND_MAX);
#endif
else // torsions
#if defined (REPRO)
init_populations[entity_id*GENOTYPE_LENGTH_IN_GLOBMEM+gene_id] = 22.0452;
#else
init_populations[entity_id*GENOTYPE_LENGTH_IN_GLOBMEM+gene_id] = ((float) rand()/ (float) RAND_MAX)*360;
init_populations[entity_id*GENOTYPE_LENGTH_IN_GLOBMEM+gene_id] = ((float) rand()/ (float) RAND_MAX);
#endif
......@@ -700,9 +700,9 @@ void gen_initpop_and_reflig(Dockpars* mypars,
mypars->ref_ori_angles[1] = 190.279;
mypars->ref_ori_angles[2] = 190.279;
#else
mypars->ref_ori_angles[0] = floor( (float) rand()/ (float) RAND_MAX); // u1
mypars->ref_ori_angles[1] = floor(((float) rand()/ (float) RAND_MAX)*360); // u2
mypars->ref_ori_angles[2] = floor(((float) rand()/ (float) RAND_MAX)*360); // u3
mypars->ref_ori_angles[0] = floor((float) rand()/ (float) RAND_MAX); // u1
mypars->ref_ori_angles[1] = floor((float) rand()/ (float) RAND_MAX); // u2
mypars->ref_ori_angles[2] = floor((float) rand()/ (float) RAND_MAX); // u3
#endif
......@@ -787,8 +787,8 @@ void gen_initpop_and_reflig(Dockpars* mypars,
ref_ori_angles[3*i+2] = 190.279;
#else
ref_ori_angles[3*i] = ((float) rand()/ (float) RAND_MAX); // u1
ref_ori_angles[3*i+1] = ((float) rand()/ (float) RAND_MAX)*360; // u2
ref_ori_angles[3*i+2] = ((float) rand()/ (float) RAND_MAX)*360; // u3
ref_ori_angles[3*i+1] = ((float) rand()/ (float) RAND_MAX); // u2
ref_ori_angles[3*i+2] = ((float) rand()/ (float) RAND_MAX); // u3
//printf("u1, u2, u3: %10f %10f %10f \n", ref_ori_angles[3*i], ref_ori_angles[3*i+1], ref_ori_angles[3*i+2]);
#endif
}
......
host/src/processligand.cpp
View file @ 21ab85f0
......@@ -1281,12 +1281,12 @@ void change_conform_f(Liganddata* myligand,
genotype [i] = genotype_f [i];
shoemake [0] = (genotype [3]);
shoemake [1] = (genotype [4])*(PI/180);
shoemake [2] = (genotype [5])*(PI/180);
shoemake [1] = (genotype [4])*(2*PI);
shoemake [2] = (genotype [5])*(2*PI);
refori_shoemake [0] = (cpu_ref_ori_angles [0]);
refori_shoemake [1] = (cpu_ref_ori_angles [1])*(PI/180);
refori_shoemake [2] = (cpu_ref_ori_angles [2])*(PI/180);
refori_shoemake [1] = (cpu_ref_ori_angles [1])*(2*PI);
refori_shoemake [2] = (cpu_ref_ori_angles [2])*(2*PI);
// +++++++++++++++++++++++++++++++++++++++
// OCLADock
......
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