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Commit d251789a authored by lvs's avatar lvs
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gradients converted from shoemake into axisangle

parent 17b12c3f
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Makefile
View file @ d251789a
......@@ -203,14 +203,14 @@ odock: check-env-all stringify $(SRC)
# 3tmn: for testing gradients of torsion genes (1 torsion)
PDB := 3ce3
NRUN := 200
POPSIZE := 500
NRUN := 100
POPSIZE := 150
TESTNAME := test
TESTLS := fire
test: odock
$(BIN_DIR)/$(TARGET) -ffile ./input/$(PDB)/derived/$(PDB)_protein.maps.fld -lfile ./input/$(PDB)/derived/$(PDB)_ligand.pdbqt -nrun $(NRUN) -psize $(POPSIZE) -resnam $(TESTNAME) -gfpop 0 -lsmet $(TESTLS)
$(BIN_DIR)/$(TARGET) -ffile ./input/$(PDB)/derived/$(PDB)_protein.maps.fld -lfile ./input/$(PDB)/derived/$(PDB)_ligand.pdbqt -nrun $(NRUN) -psize $(POPSIZE) -resnam $(TESTNAME) -gfpop 0 -lsmet $(TESTLS) -lsit 10
ASTEX_PDB := 2bsm
ASTEX_NRUN:= 10
......
common/calcenergy_basic.h
View file @ d251789a
......@@ -70,6 +70,7 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
// Used for Shoemake to quaternion transformation
#define PI_TIMES_2 (float)(2.0f*M_PI)
#define PI_FLOAT (float)(M_PI)
// -------------------------------------------
......@@ -98,7 +99,8 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
#define STEP_DECREASE 0.2f
#define STEP_START 1E3 // Starting step size. This might look gigantic but will cap
#define MAX_DEV_TRANSLATION 2.0f // 2 Angstrom, but must be divided by the gridspacing (store in variable)
#define MAX_DEV_ROTATION 0.2f // Shoemake range [0, 1]
//#define MAX_DEV_ROTATION 0.2f // Shoemake range [0, 1]
#define MAX_DEV_ROTATION 0.5f/DEG_TO_RAD // 0.5f RAD
#define MAX_DEV_TORSION 0.5f/DEG_TO_RAD // 0.5f RAD
......
device/calcenergy.cl
View file @ d251789a
......@@ -98,6 +98,17 @@ void gpu_calc_energy(
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;
......@@ -132,57 +143,54 @@ void gpu_calc_energy(
}
// 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
{
// Rotational genes in the Shoemake space expressed in radians
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_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;
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];
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 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];
}
// 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
......@@ -468,7 +476,7 @@ if (get_local_id (0) == 0) {
// Getting smoothed distance
// smoothed_distance = function(atomic_distance, opt_distance)
float smoothed_distance;
float delta_distance = 0.5f*dockpars_smooth;
float delta_distance = 0.5f*dockpars_smooth;
if (atomic_distance <= (opt_distance - delta_distance)) {
smoothed_distance = atomic_distance + delta_distance;
......
device/calcgradient.cl
View file @ d251789a
......@@ -39,6 +39,20 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
//#define DEBUG_GRAD_TORSION_GENES
void map_priv_angle(float* angle)
// The GPU device function maps
// the input parameter to the interval 0...360
// (supposing that it is an angle).
{
while (*angle >= 360.0f) {
*angle -= 360.0f;
}
while (*angle < 0.0f) {
*angle += 360.0f;
}
}
// Atomic operations used in gradients of intra contributors.
// Only atomic_cmpxchg() works on floats.
// So for atomic add on floats, this link was used:
......@@ -127,6 +141,10 @@ void gpu_calc_gradient(
__constant int* rotbonds_const,
__constant int* rotbonds_atoms_const,
__constant int* num_rotating_atoms_per_rotbond_const
,
__constant float* angle_const,
__constant float* dependence_on_theta_const,
__constant float* dependence_on_rotangle_const
// Gradient-related arguments
// Calculate gradients (forces) for intermolecular energy
......@@ -168,6 +186,17 @@ void gpu_calc_gradient(
}
barrier(CLK_LOCAL_MEM_FENCE);
// 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;
......@@ -202,57 +231,54 @@ void gpu_calc_gradient(
}
// 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
{
// Rotational genes in the Shoemake space are expressed in radians
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_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;
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];
float 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 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];
}
// 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
......@@ -899,26 +925,46 @@ void gpu_calc_gradient(
printf("%-20s %-10.5f %-10.5f %-10.5f %-10.5f\n", "quat_torque (w,x,y,z): ", quat_torque.w, quat_torque.x, quat_torque.y, quat_torque.z);
#endif
// Converting quaternion gradients into Shoemake gradients
// Converting quaternion gradients into orientation gradients
// Derived from autodockdev/motion.py/_get_cube3_gradient
// This is where we are in Shoemake space
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];
// This is where we are in the orientation axis-angle space
// Equivalent to "current_oclacube" in autodockdev/motions.py
// TODO: Check very initial input orientation genes
float current_phi, current_theta, current_rotangle;
current_phi = genotype[3]; // phi (in sexagesimal (DEG) unbounded)
current_theta = genotype[4]; // theta (in sexagesimal (DEG) unbounded)
current_rotangle = genotype[5]; // rotangle (in sexagesimal (DEG) unbounded)
map_priv_angle(&current_phi); // phi (in DEG bounded within [0, 360])
map_priv_angle(&current_theta); // theta (in DEG bounded within [0, 360])
map_priv_angle(&current_rotangle); // rotangle (in DEG bounded within [0, 360])
current_phi = current_phi * DEG_TO_RAD; // phi (in RAD)
current_theta = current_theta * DEG_TO_RAD; // theta (in RAD)
current_rotangle = current_rotangle * DEG_TO_RAD; // rotangle (in RAD)
bool is_theta_gt_pi = (current_theta > PI_FLOAT) ? true: false;
#if defined (DEBUG_GRAD_ROTATION_GENES)
printf("%-30s %-10.5f %-10.5f %-10.5f\n", "current_u (1,2,3): ", genotype[3], genotype[4], genotype[5]);
printf("%-30s %-10.5f %-10.5f %-10.5f\n", "current_axisangle (1,2,3): ", current_phi, current_theta, current_rotangle);
#endif
// This is where we are in quaternion space
// current_q = cube3_to_quaternion(current_u)
// current_q = oclacube_to_quaternion(angles)
float4 current_q;
current_q.w = native_sqrt(1-current_u1) * native_sin(PI_TIMES_2*current_u2);
current_q.x = native_sqrt(1-current_u1) * native_cos(PI_TIMES_2*current_u2);
current_q.y = native_sqrt(current_u1) * native_sin(PI_TIMES_2*current_u3);
current_q.z = native_sqrt(current_u1) * native_cos(PI_TIMES_2*current_u3);
// Axis of rotation
float rotaxis_x = native_sin(current_theta) * native_cos(current_phi);
float rotaxis_y = native_sin(current_theta) * native_sin(current_phi);
float rotaxis_z = native_cos(current_theta);
float ang;
ang = current_rotangle * 0.5f;
current_q.w = native_cos(ang);
current_q.x = rotaxis_x * native_sin(ang);
current_q.y = rotaxis_y * native_sin(ang);
current_q.z = rotaxis_z * native_sin(ang);
#if defined (DEBUG_GRAD_ROTATION_GENES)
printf("%-30s %-10.8f %-10.8f %-10.8f %-10.8f\n", "current_q (w,x,y,z): ", current_q.w, current_q.x, current_q.y, current_q.z);
......@@ -938,23 +984,33 @@ void gpu_calc_gradient(
printf("%-30s %-10.8f %-10.8f %-10.8f %-10.8f\n", "target_q (w,x,y,z): ", target_q.w, target_q.x, target_q.y, target_q.z);
#endif
// This is where we want to be in Shoemake space
float target_u1, target_u2, target_u3;
// This is where we want to be in the orientation axis-angle space
float target_phi, target_theta, target_rotangle;
// 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_q.y*target_q.y + target_q.z*target_q.z;
target_u2 = atan2(target_q.w, target_q.x);
target_u3 = atan2(target_q.y, target_q.z);
if (target_u2 < 0.0f) { target_u2 += PI_TIMES_2; }
if (target_u2 > PI_TIMES_2) { target_u2 -= PI_TIMES_2; }
if (target_u3 < 0.0f) { target_u3 += PI_TIMES_2; }
if (target_u3 > PI_TIMES_2) { target_u3 -= PI_TIMES_2; }
// target_oclacube = quaternion_to_oclacube(target_q, theta_larger_than_pi)
// Derived from autodockdev/motions.py/quaternion_to_oclacube()
// In our terms means quaternion_to_oclacube(target_q{w|x|y|z}, theta_larger_than_pi)
ang = acos(target_q.w);
target_rotangle = 2.0f * ang;
float inv_sin_ang = native_recip(native_sin(ang));
rotaxis_x = target_q.x * inv_sin_ang;
rotaxis_y = target_q.y * inv_sin_ang;
rotaxis_z = target_q.z * inv_sin_ang;
target_theta = acos(rotaxis_z);
if (is_theta_gt_pi == false) {
target_phi = remainder((atan2( rotaxis_y, rotaxis_x) + PI_TIMES_2), PI_TIMES_2);
}
else {
target_phi = remainder((atan2(-rotaxis_y, -rotaxis_x) + PI_TIMES_2), PI_TIMES_2);
target_theta = PI_TIMES_2 - target_theta;
}
#if defined (DEBUG_GRAD_ROTATION_GENES)
printf("%-30s %-10.8f %-10.8f %-10.8f\n", "target_u (1,2,3) - after mapping: ", target_u1, target_u2, target_u3);
printf("%-30s %-10.8f %-10.8f %-10.8f\n", "target_axisangle (1,2,3) - after mapping: ", target_phi, target_theta, target_rotangle);
#endif
// The infinitesimal rotation will produce an infinitesimal displacement
......@@ -963,40 +1019,120 @@ void gpu_calc_gradient(
// The correct amount of displacement in shoemake space is obtained
// by multiplying the infinitesimal displacement by shoemake_scaling:
//float shoemake_scaling = native_divide(torque_length, INFINITESIMAL_RADIAN/*infinitesimal_radian*/);
float shoemake_scaling = torque_length * INV_INFINITESIMAL_RADIAN;
float orientation_scaling = torque_length * INV_INFINITESIMAL_RADIAN;
// Derivates in cube3
// "current_u2" and "current_u3" are mapped into
// the same range [0, 2PI] of "target_u2" and "target_u3"
float grad_u1, grad_u2, grad_u3;
grad_u1 = shoemake_scaling * (target_u1 - current_u1);
grad_u2 = shoemake_scaling * (target_u2 - current_u2 * PI_TIMES_2);
grad_u3 = shoemake_scaling * (target_u3 - current_u3 * PI_TIMES_2);
float grad_phi, grad_theta, grad_rotangle;
/*
grad_phi = orientation_scaling * (target_phi - current_phi);
grad_theta = orientation_scaling * (target_theta - current_theta);
grad_rotangle = orientation_scaling * (target_rotangle - current_rotangle);
*/
grad_phi = orientation_scaling * (remainder(target_phi - current_phi + PI_FLOAT, PI_TIMES_2) - PI_FLOAT);
grad_theta = orientation_scaling * (remainder(target_theta - current_theta + PI_FLOAT, PI_TIMES_2) - PI_FLOAT);
grad_rotangle = orientation_scaling * (remainder(target_rotangle - current_rotangle + PI_FLOAT, PI_TIMES_2) - PI_FLOAT);
#if defined (DEBUG_GRAD_ROTATION_GENES)
printf("%-30s %-10.8f %-10.8f %-10.8f\n", "grad_u (1,2,3) - before emp. scaling: ", grad_u1, grad_u2, grad_u3);
printf("%-30s %-10.8f %-10.8f %-10.8f\n", "grad_axisangle (1,2,3) - before emp. scaling: ", grad_phi, grad_theta, grad_rotangle);
#endif
// Empirical scaling
float temp_u1 = genotype[3];
if ((0.0f < temp_u1) && (temp_u1 < 1.0f)){
grad_u1 *= (native_divide(1.0f, temp_u1) + native_divide(1.0f, (1.0f-temp_u1)));
// Corrections of derivatives
// Constant arrays have 1000 elements.
// Each array spans approximatedly from 0.0 to 2*PI.
// The distance between each x-point (angle-delta) is 2*PI/1000.
const float angle_delta = 0.00628353f;
const float inv_angle_delta = 159.154943;
// Correcting theta gradients interpolating
// values from correction look-up-tables
// (X0,Y0) and (X1,Y1) are known points
// How to find the Y value in the straight line between Y0 and Y1,
// corresponding to a certain X?
/*
| dependence_on_theta_const
| dependence_on_rotangle_const
|
|
| Y1
|
| Y=?
| Y0
|_________________________________ angle_const
X0 X X1
*/
// Finding the index-position of "grad_delta" in the "angle_const" array
//uint index_theta = floor(native_divide(current_theta - angle_const[0], angle_delta));
//uint index_rotangle = floor(native_divide(current_rotangle - angle_const[0], angle_delta));
uint index_theta = floor((current_theta - angle_const[0]) * inv_angle_delta);
uint index_rotangle = floor((current_rotangle - angle_const[0]) * inv_angle_delta);
// Interpolating theta values
// X0 -> index - 1
// X1 -> index + 1
// Expresed as weighted average:
// Y = [Y0 * ((X1 - X) / (X1-X0))] + [Y1 * ((X - X0) / (X1-X0))]
// Simplified for GPU (less terms):
// Y = [Y0 * (X1 - X) + Y1 * (X - X0)] / (X1 - X0)
// Taking advantage of constant:
// Y = [Y0 * (X1 - X) + Y1 * (X - X0)] * inv_angle_delta
float X0_theta, Y0_theta;
float X1_theta, Y1_theta;
float X_theta;
float dependence_on_theta; //Y = dependence_on_theta
X_theta = current_theta;
// Using interpolation on out-of-bounds elements results in hang
if (index_theta <= 0) {
//printf("WARNING: index_theta: %u\n", index_theta);
dependence_on_theta = dependence_on_theta_const[0];
}
else if (index_theta >= 999){
//printf("WARNING: index_theta: %u\n", index_theta);
dependence_on_theta = dependence_on_theta_const[999];
}
else {
X0_theta = angle_const[index_theta];
Y0_theta = dependence_on_theta_const[index_theta];
X1_theta = angle_const[index_theta+1];
Y1_theta = dependence_on_theta_const[index_theta+1];
}
grad_u2 *= 4.0f * (1.0f-temp_u1);
grad_u3 *= 4.0f * temp_u1;
dependence_on_theta = (Y0_theta * (X1_theta-X_theta) + Y1_theta * (X_theta-X0_theta)) * inv_angle_delta;
// Interpolating rotangle values
float X0_rotangle, Y0_rotangle;
float X1_rotangle, Y1_rotangle;
float X_rotangle;
float dependence_on_rotangle; //Y = dependence_on_rotangle
X_rotangle = current_rotangle;
// Using interpolation on previous and/or next elements results in hang
if (index_rotangle <= 0) {
//printf("WARNING: index_rotangle: %u\n", index_rotangle);
dependence_on_rotangle = dependence_on_rotangle_const[0];
}
else if (index_rotangle >= 999){
//printf("WARNING: index_rotangle: %u\n", index_rotangle);
dependence_on_rotangle = dependence_on_rotangle_const[999];
}
else {
X0_rotangle = angle_const[index_rotangle];
Y0_rotangle = dependence_on_rotangle_const[index_rotangle];
X1_rotangle = angle_const[index_rotangle+1];
Y1_rotangle = dependence_on_rotangle_const[index_rotangle+1];
}
dependence_on_rotangle = (Y0_rotangle * (X1_rotangle-X_rotangle) + Y1_rotangle * (X_rotangle-X0_rotangle)) * inv_angle_delta;
#if defined (DEBUG_GRAD_ROTATION_GENES)
printf("%-30s %-10.8f %-10.8f %-10.8f\n", "grad_u (1,2,3) - after emp. scaling: ", grad_u1, grad_u2, grad_u3);
printf("%-30s %-10.8f %-10.8f %-10.8f\n", "grad_axisangle (1,2,3) - after emp. scaling: ", grad_phi, grad_theta, grad_rotangle);
#endif
// Setting gradient rotation-related genotypes in cube3.
// Scaling gradient for u2 and u3 genes as
// their corresponding gradients were calculated in the space where u2/3 are within [0, 2PI]
// but OCLaDock u2/3 genes are within [0, 1]
gradient_genotype[3] = grad_u1;
gradient_genotype[4] = grad_u2 * PI_TIMES_2;
gradient_genotype[5] = grad_u3 * PI_TIMES_2;
// Setting gradient rotation-related genotypes in cube
// Multiplicating by DEG_TO_RAD is to make it uniform to DEG (see torsion gradients)
gradient_genotype[3] = native_divide(grad_phi, (dependence_on_theta * dependence_on_rotangle)) * DEG_TO_RAD;
gradient_genotype[4] = native_divide(grad_theta, dependence_on_rotangle) * DEG_TO_RAD;
gradient_genotype[5] = grad_rotangle * DEG_TO_RAD;
}
// ------------------------------------------
......
device/kernel3.cl
View file @ d251789a
......@@ -166,32 +166,22 @@ perform_LS(
genotype_deviate[gene_counter] = rho*(2*gpu_randf(dockpars_prng_states)-1);
// Translation genes
if (gene_counter <= 2)
if (gene_counter < 3) {
genotype_deviate[gene_counter] *= dockpars_base_dmov_mul_sqrt3;
// Shoemake orientation-genes do not use initial deviation
// Torsion genes
else if (gene_counter >= 6)
}
// Orientation and torsion genes
else {
genotype_deviate[gene_counter] *= dockpars_base_dang_mul_sqrt3;
}
}
// 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)) {
genotype_candidate[gene_counter] = gpu_randf(dockpars_prng_states);
}
// Other genes: translation and torsions
else {
genotype_candidate[gene_counter] = offspring_genotype[gene_counter] +
genotype_deviate[gene_counter] +
genotype_bias[gene_counter];
}
}
// Evaluating candidate
......@@ -294,17 +284,9 @@ perform_LS(
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)) {
genotype_candidate[gene_counter] = gpu_randf(dockpars_prng_states);
}
// Other genes: translation and torsions
else {
genotype_candidate[gene_counter] = offspring_genotype[gene_counter] -
genotype_deviate[gene_counter] -
genotype_bias[gene_counter];
}
}
// Evaluating candidate
......@@ -447,7 +429,7 @@ perform_LS(
for (gene_counter = get_local_id(0);
gene_counter < dockpars_num_of_genes;
gene_counter+= NUM_OF_THREADS_PER_BLOCK) {
if (gene_counter >= 6) {
if (gene_counter >= 3) {
map_angle(&(offspring_genotype[gene_counter]));
}
}
......
device/kernel4.cl
View file @ d251789a
......@@ -233,14 +233,10 @@ gpu_gen_and_eval_newpops(
if (/*100.0f**/gpu_randf(dockpars_prng_states) < dockpars_mutation_rate)
{
// Translation genes
if (gene_counter <= 2) {
if (gene_counter < 3) {
offspring_genotype[gene_counter] += dockpars_abs_max_dmov*(2*gpu_randf(dockpars_prng_states)-1);
}
// Shoemake genes (u1, u2, u3) ranges between [0,1]
else if (gene_counter <= 5) {
offspring_genotype[gene_counter] = gpu_randf(dockpars_prng_states);
}
// Torsion genes
// Orientation and torsion genes
else {
offspring_genotype[gene_counter] += dockpars_abs_max_dang*(2*gpu_randf(dockpars_prng_states)-1);
map_angle(&(offspring_genotype[gene_counter]));
......
device/kernel_fire.cl
View file @ d251789a
......@@ -62,6 +62,10 @@ gradient_minFire(
__constant int* rotbonds_const,
__constant int* rotbonds_atoms_const,
__constant int* num_rotating_atoms_per_rotbond_const
,
__constant float* angle_const,
__constant float* dependence_on_theta_const,
__constant float* dependence_on_rotangle_const
)
//The GPU global function performs gradient-based minimization on (some) entities of conformations_next.
//The number of OpenCL compute units (CU) which should be