added intramolecular gradients

Makefile

@@ -198,7 +198,7 @@ odock: check-env-all stringify $(SRC)
 
 # Example
 PDB     := 3ce3
-NRUN    := 200
+NRUN    := 100
 POPSIZE := 2048
 TESTNAME:= test
 

common/calcenergy_basic.h

@@ -27,19 +27,19 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
 
 #include "defines.h"
 
-#define RLIST_ATOMID_MASK 	 0x000000FF
-#define RLIST_RBONDID_MASK 	 0x0000FF00
-#define RLIST_RBONDID_SHIFT  8
-#define RLIST_FIRSTROT_MASK  0x00010000
-#define RLIST_GENROT_MASK 	 0x00020000
-#define RLIST_DUMMY_MASK 	 	 0x00040000
-#define DEG_TO_RAD 					 0.0174533f
+#define RLIST_ATOMID_MASK 	0x000000FF
+#define RLIST_RBONDID_MASK 	0x0000FF00
+#define RLIST_RBONDID_SHIFT  	8
+#define RLIST_FIRSTROT_MASK  	0x00010000
+#define RLIST_GENROT_MASK 	0x00020000
+#define RLIST_DUMMY_MASK 	0x00040000
+#define DEG_TO_RAD 		0.0174533f
 
 // LCG: linear congruential generator constants
-#define RAND_A 							1103515245u
-#define RAND_C 							12345u
+#define RAND_A 			1103515245u
+#define RAND_C 			12345u
 // WARNING: it is supposed that unsigned int is 32 bit long
-#define MAX_UINT 						4294967296.0f
+#define MAX_UINT 		4294967296.0f
 
 // Macro for capturing grid values
 	// Original
@@ -57,6 +57,14 @@ 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])
 
+// Constants for dielelectric term of the intramolecular energy/gradient
+#define DIEL_A 		-8.5525f
+#define DIEL_WAT 	78.4f
+#define DIEL_B 		(DIEL_WAT - DIEL_A)
+#define DIEL_LAMBDA	0.003627f
+#define DIEL_H		DIEL_LAMBDA
+#define DIEL_K		7.7839f
+
 // Used for Shoemake to quternion transformation
 #define PI_TIMES_2 (float)(2.0f*M_PI)
 

common/defines.h

@@ -39,7 +39,7 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
 	#define NUM_OF_THREADS_PER_BLOCK 64
 #endif
 
-#define MAX_NUM_OF_ATOMS 	256
+#define MAX_NUM_OF_ATOMS 	100 // TODO: optimize local arrays in gradient calc to increase this constant up to 256
 #define MAX_NUM_OF_ATYPES 	14
 #define MAX_NUM_OF_ROTBONDS 	32
 #define MAX_INTRAE_CONTRIBUTORS (MAX_NUM_OF_ATOMS * MAX_NUM_OF_ATOMS)

device/kernel_gradient.cl

@@ -160,6 +160,15 @@ gradient_minimizer(
 	__local float gradient_inter_x[MAX_NUM_OF_ATOMS];
 	__local float gradient_inter_y[MAX_NUM_OF_ATOMS];
 	__local float gradient_inter_z[MAX_NUM_OF_ATOMS];
+
+	// Variables to store gradient of 
+	// the intramolecular energy per each ligand atom
+	__local float gradient_intra_x[MAX_NUM_OF_ATOMS];
+	__local float gradient_intra_y[MAX_NUM_OF_ATOMS];
+	__local float gradient_intra_z[MAX_NUM_OF_ATOMS];
+	__local float gradient_per_intracontributor[MAX_INTRAE_CONTRIBUTORS];
+	
+
 	// -------------------------------------------------------------------
 
 	// Variables to store partial energies
@@ -231,6 +240,10 @@ gradient_minimizer(
 				gradient_inter_x,
 				gradient_inter_y,
 				gradient_inter_z,
+				gradient_intra_x,
+				gradient_intra_y,
+				gradient_intra_z,
+				gradient_per_intracontributor,
 				local_gradient
 				);
 		// =============================================================