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docking
ocladock
Commits
13cf53f5
Commit
13cf53f5
authored
Jan 18, 2018
by
lvs
Browse files
solved #10
parent
bcf40428
Changes
4
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common/defines.h
View file @
13cf53f5
...
...
@@ -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
View file @
13cf53f5
...
...
@@ -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
View file @
13cf53f5
...
...
@@ -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
View file @
13cf53f5
...
...
@@ -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
*
);
...
...
Leonardo Solis
@solis
mentioned in merge request
!2 (closed)
·
Jan 18, 2018
mentioned in merge request
!2 (closed)
mentioned in merge request !2
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