solved #10

common/defines.h

@@ -37,11 +37,11 @@ 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 				90
+#define MAX_NUM_OF_ATOMS 				256
 #define MAX_NUM_OF_ATYPES 			14
-#define MAX_INTRAE_CONTRIBUTORS 8128
-#define MAX_NUM_OF_ROTATIONS 		4096
 #define MAX_NUM_OF_ROTBONDS 		32
+#define MAX_INTRAE_CONTRIBUTORS MAX_NUM_OF_ATOMS * MAX_NUM_OF_ATOMS
+#define MAX_NUM_OF_ROTATIONS 		MAX_NUM_OF_ATOMS * MAX_NUM_OF_ROTBONDS
 #define MAX_POPSIZE 						2048
 #define MAX_NUM_OF_RUNS 				1000
 

device/calcenergy.cl

@@ -46,7 +46,7 @@ void gpu_calc_energy(	    int    dockpars_rotbondlist_length,
 		    __local float* genotype,
 		    __local float* energy,
 		    __local int*   run_id,
-	
+
                     // Some OpenCL compilers don't allow local var outside kernels
 		    // so this local vars are passed from a kernel
 		    __local float* calc_coords_x,
@@ -76,7 +76,7 @@ void gpu_calc_energy(	    int    dockpars_rotbondlist_length,
 //determines which reference orientation should be used.
 {
 	int contributor_counter;
-	char atom1_id, atom2_id, atom1_typeid, atom2_typeid;
+	/*char*/uint atom1_id, atom2_id, atom1_typeid, atom2_typeid;
 
 	// Name changed to distance_leo to avoid
 	// errors as "distance" is the name of OpenCL function

host/inc/processgrid.h

@@ -40,6 +40,7 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
 // http://ask.systutorials.com/681/get-the-directory-path-and-file-name-from-absolute-path-linux
 #endif
 
+#include "defines.h"
 #include "miscellaneous.h"
 
 #define getvalue_4Darr(mempoi, grinf, t, z, y, x)                  *(mempoi + (grinf).size_xyz[0] * (y + (grinf).size_xyz[1] * (z + (grinf).size_xyz[2]*t)) + x)
@@ -63,7 +64,7 @@ typedef struct
 	int    size_xyz [3];
 	double spacing;
 	double size_xyz_angstr [3];
-	char   grid_types [16][3];
+	char   grid_types [MAX_NUM_OF_ATYPES+2][3]; // The additional two are the electrostatic and the desolvation types
 	int    num_of_atypes;
 	double origo_real_xyz [3];
 } Gridinfo;

host/inc/processligand.h

@@ -85,24 +85,24 @@ typedef struct
 	int 	num_of_atoms;
 	int 	num_of_atypes;
 	int 	num_of_rotbonds;
-	char 	atom_types [14][3];	//in the case of arrays, the first index is called row index,
-	double 	atom_idxyzq [256][5];	//the second is called column index
-	int 	rotbonds [32][2];
-	char 	atom_rotbonds [256][32];
-	int 	atom_rigid_structures [256];
-	char 	bonds [256][256];
-	char 	intraE_contributors [256][256];
-	double 	VWpars_A [14][14];
-	double	VWpars_B [14][14];
-	double 	VWpars_C [14][14];
-	double 	VWpars_D [14][14];
-	double 	volume [14];
-	double 	solpar [14];
+	char 	atom_types [MAX_NUM_OF_ATYPES][3];	//in the case of arrays, the first index is called row index,
+	double 	atom_idxyzq [MAX_NUM_OF_ATOMS][5];	//the second is called column index
+	int 	rotbonds [MAX_NUM_OF_ROTBONDS][2];
+	char 	atom_rotbonds [MAX_NUM_OF_ATOMS][MAX_NUM_OF_ROTBONDS];
+	int 	atom_rigid_structures [MAX_NUM_OF_ATOMS];
+	char 	bonds [MAX_NUM_OF_ATOMS][MAX_NUM_OF_ATOMS];
+	char 	intraE_contributors [MAX_NUM_OF_ATOMS][MAX_NUM_OF_ATOMS];
+	double 	VWpars_A [MAX_NUM_OF_ATYPES][MAX_NUM_OF_ATYPES];
+	double	VWpars_B [MAX_NUM_OF_ATYPES][MAX_NUM_OF_ATYPES];
+	double 	VWpars_C [MAX_NUM_OF_ATYPES][MAX_NUM_OF_ATYPES];
+	double 	VWpars_D [MAX_NUM_OF_ATYPES][MAX_NUM_OF_ATYPES];
+	double 	volume [MAX_NUM_OF_ATYPES];
+	double 	solpar [MAX_NUM_OF_ATYPES];
 	int 	num_of_rotations_required;
 	int 	num_of_intraE_contributors;
 	int 	num_of_rotcyc;
-	double 	rotbonds_moving_vectors [32][3];
-	double 	rotbonds_unit_vectors [32][3];
+	double 	rotbonds_moving_vectors [MAX_NUM_OF_ROTBONDS][3];
+	double 	rotbonds_unit_vectors [MAX_NUM_OF_ROTBONDS][3];
 } Liganddata;
 
 int init_liganddata(const char*, Liganddata*, Gridinfo*);