renamed kernel_minimizer to kernel_sd

Makefile

@@ -50,7 +50,7 @@ K1_NAME="gpu_calc_initpop"
 K2_NAME="gpu_sum_evals"
 K3_NAME="perform_LS"
 K4_NAME="gpu_gen_and_eval_newpops"
-K5_NAME="gradient_minimizer"
+K5_NAME="gradient_minSD"
 K6_NAME="gradient_minFire"
 K_NAMES=-DK1=$(K1_NAME) -DK2=$(K2_NAME) -DK3=$(K3_NAME) -DK4=$(K4_NAME) -DK5=$(K5_NAME) -DK6=$(K6_NAME)
 # Kernel flags

device/calcenergy.cl

@@ -695,5 +695,5 @@ if (get_local_id (0) == 0) {
 #include "kernel4.cl"
 #include "kernel3.cl"
 #include "calcgradient.cl"
-#include "kernel_gradient.cl"
+#include "kernel_sd.cl"
 #include "kernel_fire.cl"

device/kernel_gradient.cl → device/kernel_sd.cl

@@ -16,7 +16,7 @@
 //#define DEBUG_INITIAL_2BRT
 
 __kernel void __attribute__ ((reqd_work_group_size(NUM_OF_THREADS_PER_BLOCK,1,1)))
-gradient_minimizer(	
+gradient_minSD(	
 			    char   dockpars_num_of_atoms,
 			    char   dockpars_num_of_atypes,
 			    int    dockpars_num_of_intraE_contributors,

host/src/performdocking.cpp

@@ -44,7 +44,7 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
 #define KRNL3 K3
 #define KRNL4 K4
 #define KRNL5 K5
-#define KRNL5 K6
+#define KRNL6 K6
 #endif
 
 #define INC " -I " KRNL_FOLDER " -I " KRNL_COMMON

stringify_ocl_krnls.sh

@@ -19,7 +19,7 @@ IN_KERNELa=$KERNEL_DIR/"auxiliary_genetic.cl"
 IN_KERNEL3=$KERNEL_DIR/"kernel3.cl"
 IN_KERNEL4=$KERNEL_DIR/"kernel4.cl"
 IN_KERNELb=$KERNEL_DIR/"calcgradient.cl"
-IN_KERNEL5=$KERNEL_DIR/"kernel_gradient.cl"
+IN_KERNEL5=$KERNEL_DIR/"kernel_sd.cl"
 IN_KERNEL6=$KERNEL_DIR/"kernel_fire.cl"
 
 echo " "

[Leonardo Solis]

@diogo.martins here I am adding a discussion for a previously bug observed with PDB=5kao.

As you can see in the initial implementation, there is a wrong assignment to KRNL5 (variable holding the SD kernel-name). So, its name was being overwritten, and therefore referring to KRNL6 (FIRE) instead.

#define KRNL5 K5
#define KRNL5 K6

So, although I didn't verify that after this commit the 5kao-bug was gone, (due to the required very specific code setting), I think this pretty much has solved it.