minor corrections

Makefile

@@ -211,11 +211,11 @@ test: odock
 
 ASTEX_PDB := 2bsm
 ASTEX_NRUN:= 100
-ASTEX_POPSIZE := 150
+ASTEX_POPSIZE := 500
 ASTEX_TESTNAME := test_astex
 
 astex: odock
-	$(BIN_DIR)/$(TARGET) -ffile ./input_tsri/search-set-astex/$(ASTEX_PDB)/protein.maps.fld -lfile ./input_tsri/search-set-astex/$(ASTEX_PDB)/flex-xray.pdbqt -nrun $(ASTEX_NRUN) -psize $(ASTEX_POPSIZE) -resnam $(ASTEX_TESTNAME) -gfpop 0
+	$(BIN_DIR)/$(TARGET) -ffile ./input_tsri/search-set-astex/$(ASTEX_PDB)/protein.maps.fld -lfile ./input_tsri/search-set-astex/$(ASTEX_PDB)/flex-xray.pdbqt -nrun $(ASTEX_NRUN) -psize $(ASTEX_POPSIZE) -resnam $(ASTEX_TESTNAME) -gfpop 1
 
 
 #	$(BIN_DIR)/$(TARGET) -ffile ./input_tsri/search-set-astex/$(ASTEX_PDB)/protein.maps.fld -lfile ./input_tsri/search-set-astex/$(ASTEX_PDB)/flex-xray.pdbqt -nrun $(ASTEX_NRUN) -psize $(ASTEX_POPSIZE) -resnam $(ASTEX_TESTNAME) -gfpop 1 | tee ./input_tsri/search-set-astex/intrapairs/$(ASTEX_PDB)_intrapair.txt

common/defines.h

@@ -58,6 +58,6 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
 //#define NATIVE_PRECISION
 #define MAPPED_COPY
 
-//#define GRADIENT_ENABLED
+#define GRADIENT_ENABLED
 
 #endif /* DEFINES_H_ */

device/kernel_gradient.cl

@@ -78,16 +78,16 @@ gradient_minimizer(
 	if (get_local_id(0) == 0)
 	{
 		// Choosing a random entity out of the entire population
-///*
+/*
 		run_id = get_group_id(0);
-		entity_id = (uint)(dockpars_pop_size * gpu_randf(dockpars_prng_states));
-		//entity_id = 0;
-//*/
+		//entity_id = (uint)(dockpars_pop_size * gpu_randf(dockpars_prng_states));
+		entity_id = 0;
+*/
 
-/*
+///*
 		run_id = get_group_id(0) / dockpars_num_of_lsentities;
 		entity_id = get_group_id(0) % dockpars_num_of_lsentities;
-*/
+//*/
 		
 		energy = dockpars_energies_next[run_id*dockpars_pop_size+entity_id];
 

host/src/performdocking.cpp

@@ -409,8 +409,8 @@ filled with clock() */
 	// Setup here (temporarily?) the gradient and associated parameters.
 	// This should be ultimately configurable by the user as program exec. flags.
 	Gradientparameters gradientpars;
-	gradientpars.max_num_of_iters = 100;
-	gradientpars.max_num_of_consec_fails = gradientpars.max_num_of_iters / 5;
+	gradientpars.max_num_of_iters = 30;
+	gradientpars.max_num_of_consec_fails = (unsigned int)(0.05 * gradientpars.max_num_of_iters);
 	gradientpars.alpha = 0.000001f; //0.001f; // TODO: find out why 0.001f, 0.0001f (100 runs, 500 popsize) throws segmentation fault
 
 	// Set minimum values for input conformation (translation genes as x, y, z)
@@ -434,16 +434,16 @@ filled with clock() */
 	mallocBufferObject(context, CL_MEM_READ_ONLY, size_conformation_min_perturbation, &mem_gradpars_conformation_min_perturbation);
 	memcopyBufferObjectToDevice(command_queue, mem_gradpars_conformation_min_perturbation, gradientpars.conformation_min_perturbation, size_conformation_min_perturbation);
 
-/*
+///*
 	// Initially, the number of entities that undergo gradient-minimization,
 	// by default, it is the same as the number of entities that undergo gradient-based minimizer
 	blocksPerGridForEachGradMinimizerEntity = dockpars.num_of_lsentities*mypars->num_of_runs;
-*/
+//*/
 
-///*
+/*
 	// test, only one entity per reach run, undergoes gradient minimization
 	blocksPerGridForEachGradMinimizerEntity = mypars->num_of_runs;
-//*/
+*/
 
 	clock_start_docking = clock();