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Commit a8fb9077 authored by lvs's avatar lvs
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corrected smoothing with vdw index

parent 9b20069a
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Makefile
View file @ a8fb9077
......@@ -206,10 +206,10 @@ NRUN := 100
POPSIZE := 150
TESTNAME := test
TESTLS := sd
NUM_LSIT := 300
NUM_LSIT := 30
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 1 -lsmet $(TESTLS) -lsit $(NUM_LSIT) -smooth 0.0
$(BIN_DIR)/$(TARGET) -ffile ./input/$(PDB)/derived/$(PDB)_protein.maps.fld -lfile ./input/$(PDB)/derived/$(PDB)_ligand.pdbqt -nrun $(NRUN) -psize $(POPSIZE) -resnam $(TESTNAME) -gfpop 1 -lsmet $(TESTLS) -lsit $(NUM_LSIT) -smooth 0.5
ASTEX_PDB := 2bsm
ASTEX_NRUN:= 10
......
device/calcenergy.cl
View file @ a8fb9077
......@@ -21,9 +21,7 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*/
//#define DEBUG_ENERGY_KERNEL1
//#define DEBUG_ENERGY_KERNEL4
//#define DEBUG_ENERGY_KERNEL3
//#define DEBUG_ENERGY_KERNEL
#include "calcenergy_basic.h"
......@@ -59,7 +57,7 @@ void gpu_calc_energy(
__local float* calc_coords_z,
__local float* partial_energies,
#if defined (DEBUG_ENERGY_KERNEL1) || defined (DEBUG_ENERGY_KERNEL4) || defined (DEBUG_ENERGY_KERNEL3)
#if defined (DEBUG_ENERGY_KERNEL)
__local float* partial_interE,
__local float* partial_intraE,
#endif
......@@ -67,9 +65,14 @@ void gpu_calc_energy(
__constant float* atom_charges_const,
__constant char* atom_types_const,
__constant char* intraE_contributors_const,
#if 0
bool debug,
#endif
float dockpars_smooth,
__constant float* reqm,
__constant float* reqm_hbond,
__constant uint* atom1_types_reqm,
__constant uint* atom2_types_reqm,
__constant float* VWpars_AC_const,
__constant float* VWpars_BD_const,
__constant float* dspars_S_const,
......@@ -90,7 +93,7 @@ void gpu_calc_energy(
{
partial_energies[get_local_id(0)] = 0.0f;
#if defined (DEBUG_ENERGY_KERNEL1) || defined (DEBUG_ENERGY_KERNEL4) || defined (DEBUG_ENERGY_KERNEL3)
#if defined (DEBUG_ENERGY_KERNEL)
partial_interE[get_local_id(0)] = 0.0f;
partial_intraE[get_local_id(0)] = 0.0f;
#endif
......@@ -269,7 +272,7 @@ void gpu_calc_energy(
|| (z >= dockpars_gridsize_z-1)){
partial_energies[get_local_id(0)] += 16777216.0f; //100000.0f;
#if defined (DEBUG_ENERGY_KERNEL1) || defined (DEBUG_ENERGY_KERNEL4) || defined (DEBUG_ENERGY_KERNEL3)
#if defined (DEBUG_ENERGY_KERNEL)
partial_interE[get_local_id(0)] += 16777216.0f;
#endif
}
......@@ -328,7 +331,7 @@ void gpu_calc_energy(
// Calculating affinity energy
partial_energies[get_local_id(0)] += TRILININTERPOL(cube, weights);
#if defined (DEBUG_ENERGY_KERNEL1) || defined (DEBUG_ENERGY_KERNEL4) || defined (DEBUG_ENERGY_KERNEL3)
#if defined (DEBUG_ENERGY_KERNEL)
partial_interE[get_local_id(0)] += TRILININTERPOL(cube, weights);
#endif
......@@ -348,7 +351,7 @@ void gpu_calc_energy(
// Calculating electrostatic energy
partial_energies[get_local_id(0)] += q * TRILININTERPOL(cube, weights);
#if defined (DEBUG_ENERGY_KERNEL1) || defined (DEBUG_ENERGY_KERNEL4) || defined (DEBUG_ENERGY_KERNEL3)
#if defined (DEBUG_ENERGY_KERNEL)
partial_interE[get_local_id(0)] += q * TRILININTERPOL(cube, weights);
#endif
......@@ -368,7 +371,7 @@ void gpu_calc_energy(
// Calculating desolvation energy
partial_energies[get_local_id(0)] += fabs(q) * TRILININTERPOL(cube, weights);
#if defined (DEBUG_ENERGY_KERNEL1) || defined (DEBUG_ENERGY_KERNEL4) || defined (DEBUG_ENERGY_KERNEL3)
#if defined (DEBUG_ENERGY_KERNEL)
partial_interE[get_local_id(0)] += fabs(q) * TRILININTERPOL(cube, weights);
#endif
}
......@@ -376,7 +379,7 @@ void gpu_calc_energy(
} // End atom_id for-loop (INTERMOLECULAR ENERGY)
#if defined (DEBUG_ENERGY_KERNEL1) || defined (DEBUG_ENERGY_KERNEL4) || defined (DEBUG_ENERGY_KERNEL3)
#if defined (DEBUG_ENERGY_KERNEL)
barrier(CLK_LOCAL_MEM_FENCE);
if (get_local_id(0) == 0)
......@@ -408,7 +411,24 @@ void gpu_calc_energy(
for (uint contributor_counter = get_local_id(0);
contributor_counter < dockpars_num_of_intraE_contributors;
contributor_counter +=NUM_OF_THREADS_PER_BLOCK)
#if 0
if (get_local_id (0) == 0) {
for (uint contributor_counter = 0;
contributor_counter < dockpars_num_of_intraE_contributors;
contributor_counter ++)
#endif
{
#if 0
// Only for testing smoothing
float smoothed_intraE = 0.0f;
float raw_intraE_vdw_hb = 0.0f;
float raw_intraE_el = 0.0f;
float raw_intraE_sol = 0.0f;
float raw_intraE = 0.0f;
#endif
// Getting atom IDs
uint atom1_id = intraE_contributors_const[3*contributor_counter];
uint atom2_id = intraE_contributors_const[3*contributor_counter+1];
......@@ -423,12 +443,17 @@ void gpu_calc_energy(
float atomic_distance = native_sqrt(subx*subx + suby*suby + subz*subz)*dockpars_grid_spacing;
// Calculating energy contributions
/*
if (atomic_distance < 8.0f)
{
*/
// Getting type IDs
uint atom1_typeid = atom_types_const[atom1_id];
uint atom2_typeid = atom_types_const[atom2_id];
uint atom1_type_vdw_hb = atom1_types_reqm [atom1_typeid];
uint atom2_type_vdw_hb = atom2_types_reqm [atom2_typeid];
// 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
......@@ -438,11 +463,17 @@ void gpu_calc_energy(
if (intraE_contributors_const[3*contributor_counter+2] == 1) //H-bond
{
#if 0
opt_distance = reqm_hbond [atom1_typeid] + reqm_hbond [atom2_typeid];
#endif
opt_distance = reqm_hbond [atom1_type_vdw_hb] + reqm_hbond [atom2_type_vdw_hb];
}
else //van der Waals
{
#if 0
opt_distance = 0.5f*(reqm [atom1_typeid] + reqm [atom2_typeid]);
#endif
opt_distance = 0.5f*(reqm [atom1_type_vdw_hb] + reqm [atom2_type_vdw_hb]);
}
// Getting smoothed distance
......@@ -460,38 +491,33 @@ void gpu_calc_energy(
smoothed_distance = atomic_distance - delta_distance;
}
/*
if (get_local_id (0) == 0) {
if (intraE_contributors_const[3*contributor_counter+2] == 1) //H-bond
{
printf("%-5s %u %u %f %f %f %f %f %f\n", "hbond", atom1_typeid, atom2_typeid, reqm_hbond [atom1_typeid], reqm_hbond [atom2_typeid], opt_distance, delta_distance, atomic_distance, smoothed_distance);
}
else //van der Waals
{
printf("%-5s %u %u %f %f %f %f %f %f\n", "vdw", atom1_typeid, atom2_typeid, reqm [atom1_typeid], reqm [atom2_typeid], opt_distance, delta_distance, atomic_distance, smoothed_distance);
}
}
*/
// Calculating van der Waals / hydrogen bond term
partial_energies[get_local_id(0)] += native_divide(VWpars_AC_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(smoothed_distance/*atomic_distance*/,12));
#if defined (DEBUG_ENERGY_KERNEL1) || defined (DEBUG_ENERGY_KERNEL4) || defined (DEBUG_ENERGY_KERNEL3)
#if 0
smoothed_intraE = native_divide(VWpars_AC_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(smoothed_distance,12));
raw_intraE_vdw_hb = native_divide(VWpars_AC_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(atomic_distance ,12));
#endif
#if defined (DEBUG_ENERGY_KERNEL)
partial_intraE[get_local_id(0)] += native_divide(VWpars_AC_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(smoothed_distance/*atomic_distance*/,12));
#endif
if (intraE_contributors_const[3*contributor_counter+2] == 1) { //H-bond
partial_energies[get_local_id(0)] -= native_divide(VWpars_BD_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(smoothed_distance/*atomic_distance*/,10));
#if defined (DEBUG_ENERGY_KERNEL1) || defined (DEBUG_ENERGY_KERNEL4) || defined (DEBUG_ENERGY_KERNEL3)
#if 0
smoothed_intraE -= native_divide(VWpars_BD_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(smoothed_distance,10));
raw_intraE_vdw_hb -= native_divide(VWpars_BD_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(atomic_distance ,10));
#endif
#if defined (DEBUG_ENERGY_KERNEL)
partial_intraE[get_local_id(0)] -= native_divide(VWpars_BD_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(smoothed_distance/*atomic_distance*/,10));
#endif
}
else { //van der Waals
partial_energies[get_local_id(0)] -= native_divide(VWpars_BD_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(smoothed_distance/*atomic_distance*/,6));
#if defined (DEBUG_ENERGY_KERNEL1) || defined (DEBUG_ENERGY_KERNEL4) || defined (DEBUG_ENERGY_KERNEL3)
#if 0
smoothed_intraE -= native_divide(VWpars_BD_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(smoothed_distance,6));
raw_intraE_vdw_hb -= native_divide(VWpars_BD_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(atomic_distance ,6));
#endif
#if defined (DEBUG_ENERGY_KERNEL)
partial_intraE[get_local_id(0)] -= native_divide(VWpars_BD_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(smoothed_distance/*atomic_distance*/,6));
#endif
}
......@@ -501,8 +527,19 @@ void gpu_calc_energy(
dockpars_coeff_elec * atom_charges_const[atom1_id] * atom_charges_const[atom2_id],
atomic_distance * (DIEL_A + native_divide(DIEL_B,(1.0f + DIEL_K*native_exp(-DIEL_B_TIMES_H*atomic_distance))))
);
#if defined (DEBUG_ENERGY_KERNEL1) || defined (DEBUG_ENERGY_KERNEL4) || defined (DEBUG_ENERGY_KERNEL3)
#if 0
smoothed_intraE += native_divide (
dockpars_coeff_elec * atom_charges_const[atom1_id] * atom_charges_const[atom2_id],
atomic_distance * (DIEL_A + native_divide(DIEL_B,(1.0f + DIEL_K*native_exp(-DIEL_B_TIMES_H*atomic_distance))))
);
raw_intraE_el = native_divide (
dockpars_coeff_elec * atom_charges_const[atom1_id] * atom_charges_const[atom2_id],
atomic_distance * (DIEL_A + native_divide(DIEL_B,(1.0f + DIEL_K*native_exp(-DIEL_B_TIMES_H*atomic_distance))))
);
#endif
#if defined (DEBUG_ENERGY_KERNEL)
partial_intraE[get_local_id(0)] += native_divide (
dockpars_coeff_elec * atom_charges_const[atom1_id] * atom_charges_const[atom2_id],
atomic_distance * (DIEL_A + native_divide(DIEL_B,(1.0f + DIEL_K*native_exp(-DIEL_B_TIMES_H*atomic_distance))))
......@@ -517,7 +554,20 @@ void gpu_calc_energy(
dockpars_qasp*fabs(atom_charges_const[atom2_id]))*dspars_V_const[atom1_typeid]) *
dockpars_coeff_desolv*native_exp(-0.03858025f*native_powr(atomic_distance, 2));
#if defined (DEBUG_ENERGY_KERNEL1) || defined (DEBUG_ENERGY_KERNEL4) || defined (DEBUG_ENERGY_KERNEL3)
#if 0
smoothed_intraE += ((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*native_exp(-0.03858025f*native_powr(atomic_distance, 2));
raw_intraE_sol = ((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*native_exp(-0.03858025f*native_powr(atomic_distance, 2));
#endif
#if defined (DEBUG_ENERGY_KERNEL)
partial_intraE[get_local_id(0)] += ((dspars_S_const[atom1_typeid] +
dockpars_qasp*fabs(atom_charges_const[atom1_id]))*dspars_V_const[atom2_typeid] +
(dspars_S_const[atom2_typeid] +
......@@ -527,9 +577,61 @@ void gpu_calc_energy(
}
#if 0
raw_intraE = raw_intraE_vdw_hb + raw_intraE_el + raw_intraE_sol;
if (debug == true) {
///*
//if (get_local_id (0) == 0) {
if (intraE_contributors_const[3*contributor_counter+2] == 1) //H-bond
{
// diogos table
// printf("%3u %-5s %3u %3u %3.5f %3.5f %3.5f %3.5f %3.5f %3.5f %3.5f\n", contributor_counter, "hbond", atom1_id, atom2_id, reqm_hbond [atom1_type_vdw_hb], reqm_hbond [atom2_type_vdw_hb], opt_distance, atomic_distance, smoothed_distance, smoothed_intraE, raw_intraE);
printf("%3u %-5s %3u %3u %3.5f %3.5f %3.5f %3.5f %3.5f %3.5f %3.5f %3.5f %3.5f %3.5f\n", contributor_counter, "hbond", atom1_id, atom2_id, reqm_hbond [atom1_type_vdw_hb], reqm_hbond [atom2_type_vdw_hb], opt_distance, atomic_distance, smoothed_distance, smoothed_intraE, raw_intraE, raw_intraE_vdw_hb, raw_intraE_el, raw_intraE_sol);
}
else //van der Waals
{
// diogos table
// printf("%3u %-5s %3u %3u %3.5f %3.5f %3.5f %3.5f %3.5f %3.5f %3.5f\n", contributor_counter, "vdw", atom1_id, atom2_id, reqm [atom1_type_vdw_hb], reqm [atom2_type_vdw_hb], opt_distance, atomic_distance, smoothed_distance, smoothed_intraE, raw_intraE);
printf("%3u %-5s %3u %3u %3.5f %3.5f %3.5f %3.5f %3.5f %3.5f %3.5f %3.5f %3.5f %3.5f\n", contributor_counter, "vdw", atom1_id, atom2_id, reqm [atom1_type_vdw_hb], reqm [atom2_type_vdw_hb], opt_distance, atomic_distance, smoothed_distance, smoothed_intraE, raw_intraE, raw_intraE_vdw_hb, raw_intraE_el, raw_intraE_sol);
};
//}
//*/
}
#endif
/*
} // if (atomic_distance < 8.0f)
*/
} // End contributor_counter for-loop (INTRAMOLECULAR ENERGY)
#if 0
} // if (get_local_id (0) == 0) {
#endif
barrier(CLK_LOCAL_MEM_FENCE);
if (get_local_id(0) == 0)
......@@ -546,7 +648,7 @@ void gpu_calc_energy(
barrier(CLK_LOCAL_MEM_FENCE);
#if defined (DEBUG_ENERGY_KERNEL1) || defined (DEBUG_ENERGY_KERNEL4) || defined (DEBUG_ENERGY_KERNEL3)
#if defined (DEBUG_ENERGY_KERNEL)
if (get_local_id(0) == 0)
{
float energy_intraE = partial_intraE[0];
......
device/calcgradient.cl
View file @ a8fb9077
......@@ -37,7 +37,7 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
//#define DEBUG_GRAD_TRANSLATION_GENES
//#define DEBUG_GRAD_ROTATION_GENES
//#define DEBUG_GRAD_TORSION_GENES
//#define DEBUG_ENERGY_KERNEL5
// Atomic operations used in gradients of intra contributors.
// Only atomic_cmpxchg() works on floats.
......@@ -111,6 +111,8 @@ void gpu_calc_gradient(
float dockpars_smooth,
__constant float* reqm,
__constant float* reqm_hbond,
__constant uint* atom1_types_reqm,
__constant uint* atom2_types_reqm,
__constant float* VWpars_AC_const,
__constant float* VWpars_BD_const,
__constant float* dspars_S_const,
......@@ -609,6 +611,9 @@ void gpu_calc_gradient(
// Getting type IDs
uint atom1_typeid = atom_types_const[atom1_id];
uint atom2_typeid = atom_types_const[atom2_id];
uint atom1_type_vdw_hb = atom1_types_reqm [atom1_typeid];
uint atom2_type_vdw_hb = atom2_types_reqm [atom2_typeid];
//printf ("%-5u %-5u %-5u\n", contributor_counter, atom1_id, atom2_id);
// Getting optimum pair distance (opt_distance) from reqm and reqm_hbond
......@@ -620,11 +625,17 @@ void gpu_calc_gradient(
if (intraE_contributors_const[3*contributor_counter+2] == 1) //H-bond
{
/*
opt_distance = reqm_hbond [atom1_typeid] + reqm_hbond [atom2_typeid];
*/
opt_distance = reqm_hbond [atom1_type_vdw_hb] + reqm_hbond [atom2_type_vdw_hb];
}
else //van der Waals
{
/*
opt_distance = 0.5f*(reqm [atom1_typeid] + reqm [atom2_typeid]);
*/
opt_distance = 0.5f*(reqm [atom1_type_vdw_hb] + reqm [atom2_type_vdw_hb]);
}
// Getting smoothed distance
......
device/kernel1.cl
View file @ a8fb9077
......@@ -47,6 +47,8 @@ gpu_calc_initpop(
float dockpars_smooth,
__constant float* reqm,
__constant float* reqm_hbond,
__constant uint* atom1_types_reqm,
__constant uint* atom2_types_reqm,
__constant float* VWpars_AC_const,
__constant float* VWpars_BD_const,
__constant float* dspars_S_const,
......@@ -71,7 +73,7 @@ gpu_calc_initpop(
__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];
#if defined (DEBUG_ENERGY_KERNEL1)
#if defined (DEBUG_ENERGY_KERNEL)
__local float partial_interE[NUM_OF_THREADS_PER_BLOCK];
__local float partial_intraE[NUM_OF_THREADS_PER_BLOCK];
#endif
......@@ -119,7 +121,7 @@ gpu_calc_initpop(
calc_coords_y,
calc_coords_z,
partial_energies,
#if defined (DEBUG_ENERGY_KERNEL1)
#if defined (DEBUG_ENERGY_KERNEL)
partial_interE,
partial_intraE,
#endif
......@@ -127,9 +129,14 @@ gpu_calc_initpop(
atom_charges_const,
atom_types_const,
intraE_contributors_const,
#if 0
false,
#endif
dockpars_smooth,
reqm,
reqm_hbond,
atom1_types_reqm,
atom2_types_reqm,
VWpars_AC_const,
VWpars_BD_const,
dspars_S_const,
......@@ -148,7 +155,7 @@ gpu_calc_initpop(
dockpars_energies_current[get_group_id(0)] = energy;
dockpars_evals_of_new_entities[get_group_id(0)] = 1;
#if defined (DEBUG_ENERGY_KERNEL1)
#if defined (DEBUG_ENERGY_KERNEL)
printf("%-18s [%-5s]---{%-5s} [%-10.8f]---{%-10.8f}\n", "-ENERGY-KERNEL1-", "GRIDS", "INTRA", partial_interE[0], partial_intraE[0]);
#endif
}
......
device/kernel3.cl
View file @ a8fb9077
......@@ -58,6 +58,8 @@ perform_LS(
float dockpars_smooth,
__constant float* reqm,
__constant float* reqm_hbond,
__constant uint* atom1_types_reqm,
__constant uint* atom2_types_reqm,
__constant float* VWpars_AC_const,
__constant float* VWpars_BD_const,
__constant float* dspars_S_const,
......@@ -103,7 +105,7 @@ perform_LS(
__local float calc_coords_z[MAX_NUM_OF_ATOMS];
__local float partial_energies[NUM_OF_THREADS_PER_BLOCK];
#if defined (DEBUG_ENERGY_KERNEL3)
#if defined (DEBUG_ENERGY_KERNEL)
__local float partial_interE [NUM_OF_THREADS_PER_BLOCK];
__local float partial_intraE [NUM_OF_THREADS_PER_BLOCK];
#endif
......@@ -222,7 +224,7 @@ perform_LS(
calc_coords_y,
calc_coords_z,
partial_energies,
#if defined (DEBUG_ENERGY_KERNEL3)
#if defined (DEBUG_ENERGY_KERNEL)
partial_interE,
partial_intraE,
#endif
......@@ -230,9 +232,14 @@ perform_LS(
atom_charges_const,
atom_types_const,
intraE_contributors_const,
#if 0
false,
#endif
dockpars_smooth,
reqm,
reqm_hbond,
atom1_types_reqm,
atom2_types_reqm,
VWpars_AC_const,
VWpars_BD_const,
dspars_S_const,
......@@ -250,7 +257,7 @@ perform_LS(
if (get_local_id(0) == 0) {
evaluation_cnt++;
#if defined (DEBUG_ENERGY_KERNEL3)
#if defined (DEBUG_ENERGY_KERNEL)
printf("%-18s [%-5s]---{%-5s} [%-10.8f]---{%-10.8f}\n", "-ENERGY-KERNEL3-", "GRIDS", "INTRA", partial_interE[0], partial_intraE[0]);
#endif
}
......@@ -330,7 +337,7 @@ perform_LS(
calc_coords_y,
calc_coords_z,
partial_energies,
#if defined (DEBUG_ENERGY_KERNEL3)
#if defined (DEBUG_ENERGY_KERNEL)
partial_interE,
partial_intraE,
#endif
......@@ -338,9 +345,14 @@ perform_LS(
atom_charges_const,
atom_types_const,
intraE_contributors_const,
#if 0
false,
#endif
dockpars_smooth,
reqm,
reqm_hbond,
atom1_types_reqm,
atom2_types_reqm,
VWpars_AC_const,
VWpars_BD_const,
dspars_S_const,
......@@ -358,7 +370,7 @@ perform_LS(
if (get_local_id(0) == 0) {
evaluation_cnt++;
#if defined (DEBUG_ENERGY_KERNEL3)
#if defined (DEBUG_ENERGY_KERNEL)
printf("%-18s [%-5s]---{%-5s} [%-10.8f]---{%-10.8f}\n", "-ENERGY-KERNEL3-", "GRIDS", "INTRA", partial_interE[0], partial_intraE[0]);
#endif
}
......
device/kernel4.cl
View file @ a8fb9077
......@@ -58,6 +58,8 @@ gpu_gen_and_eval_newpops(
float dockpars_smooth,
__constant float* reqm,
__constant float* reqm_hbond,
__constant uint* atom1_types_reqm,
__constant uint* atom2_types_reqm,
__constant float* VWpars_AC_const,
__constant float* VWpars_BD_const,
__constant float* dspars_S_const,
......@@ -95,7 +97,7 @@ gpu_gen_and_eval_newpops(
__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];
#if defined (DEBUG_ENERGY_KERNEL4)
#if defined (DEBUG_ENERGY_KERNEL)
__local float partial_interE [NUM_OF_THREADS_PER_BLOCK];
__local float partial_intraE [NUM_OF_THREADS_PER_BLOCK];
#endif
......@@ -277,7 +279,7 @@ gpu_gen_and_eval_newpops(
calc_coords_y,
calc_coords_z,
partial_energies,
#if defined (DEBUG_ENERGY_KERNEL4)
#if defined (DEBUG_ENERGY_KERNEL)
partial_interE,
partial_intraE,
#endif
......@@ -285,9 +287,14 @@ gpu_gen_and_eval_newpops(
atom_charges_const,
atom_types_const,
intraE_contributors_const,
#if 0
false,
#endif
dockpars_smooth,
reqm,
reqm_hbond,
atom1_types_reqm,
atom2_types_reqm,
VWpars_AC_const,
VWpars_BD_const,
dspars_S_const,
......@@ -306,7 +313,7 @@ gpu_gen_and_eval_newpops(
dockpars_evals_of_new_entities[get_group_id(0)] = 1;
dockpars_energies_next[get_group_id(0)] = energy;
#if defined (DEBUG_ENERGY_KERNEL4)
#if defined (DEBUG_ENERGY_KERNEL)
printf("%-18s [%-5s]---{%-5s} [%-10.8f]---{%-10.8f}\n", "-ENERGY-KERNEL4-", "GRIDS", "INTRA", partial_interE[0], partial_intraE[0]);
#endif
}
......
device/kernel_gradient.cl
View file @ a8fb9077
......@@ -32,6 +32,8 @@ gradient_minimizer(
float dockpars_smooth,
__constant float* reqm,
__constant float* reqm_hbond,
__constant uint* atom1_types_reqm,
__constant uint* atom2_types_reqm,
__constant float* VWpars_AC_const,
__constant float* VWpars_BD_const,
__constant float* dspars_S_const,
......@@ -142,7 +144,7 @@ gradient_minimizer(
__local float calc_coords_z[MAX_NUM_OF_ATOMS];
__local float partial_energies[NUM_OF_THREADS_PER_BLOCK];
#if defined (DEBUG_ENERGY_KERNEL5)
#if defined (DEBUG_ENERGY_KERNEL)
__local float partial_interE[NUM_OF_THREADS_PER_BLOCK];
__local float partial_intraE[NUM_OF_THREADS_PER_BLOCK];
#endif
......@@ -362,6 +364,8 @@ gradient_minimizer(
dockpars_smooth,
reqm,
reqm_hbond,
atom1_types_reqm,
atom2_types_reqm,
VWpars_AC_const,
VWpars_BD_const,
dspars_S_const,
......@@ -432,7 +436,7 @@ gradient_minimizer(
dockpars_coeff_elec,
dockpars_qasp,
dockpars_coeff_desolv,
candidate_genotype,
/*candidate_genotype,*/genotype, /*use genotype only for reproduce results*/
&candidate_energy,
&run_id,
// Some OpenCL compilers don't allow declaring
......@@ -443,7 +447,7 @@ gradient_minimizer(
calc_coords_y,
calc_coords_z,
partial_energies,
#if defined (DEBUG_ENERGY_KERNEL5)
#if defined (DEBUG_ENERGY_KERNEL)
partial_interE,
partial_intraE,
#endif
......@@ -451,9 +455,14 @@ gradient_minimizer(
atom_charges_const,
atom_types_const,
intraE_contributors_const,
#if 0
true,
#endif
dockpars_smooth,
reqm,
reqm_hbond,
atom1_types_reqm,
atom2_types_reqm,
VWpars_AC_const,
VWpars_BD_const,
dspars_S_const,
......@@ -468,6 +477,16 @@ gradient_minimizer(
);
// =============================================================
#if defined (DEBUG_ENERGY_KERNEL)
if ((get_group_id(0) == 0) && (get_local_id(0) == 0)) {
for(uint i = 0; i < dockpars_num_of_genes; i++) {
printf("genotype[%u]=%f \n", i, genotype[i]);
}
printf("partial_interE=%f \n", partial_interE[0]);
printf("partial_intraE=%f \n", partial_intraE[0]);
}
#endif
// Checking if E(candidate_genotype) < E(genotype)
if (candidate_energy < energy){
......@@ -507,7 +526,7 @@ gradient_minimizer(
printf("# minimizer-iters: %-3u, stepsize: %10.7f, E: %10.7f\n", iteration_cnt, stepsize, energy);
#endif
#if defined (DEBUG_ENERGY_KERNEL5)
#if defined (DEBUG_ENERGY_KERNEL)
printf("%-18s [%-5s]---{%-5s} [%-10.7f]---{%-10.7f}\n", "-ENERGY-KERNEL5-", "GRIDS", "INTRA", partial_interE[0], partial_intraE[0]);
#endif