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tsoc
openmm
Commits
29cf1500
Commit
29cf1500
authored
Nov 03, 2009
by
Mark Friedrichs
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parent
b0115d73
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platforms/cuda/src/kernels/kCalculateGBVIForces2.cu
platforms/cuda/src/kernels/kCalculateGBVIForces2.cu
+242
-0
platforms/cuda/src/kernels/kCalculateGBVIForces2.h
platforms/cuda/src/kernels/kCalculateGBVIForces2.h
+374
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platforms/cuda/src/kernels/kCalculateGBVIForces2.cu
0 → 100755
View file @
29cf1500
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2009 Stanford University and the Authors. *
* Authors: Scott Le Grand, Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include <stdio.h>
#include <cuda.h>
#include <vector_functions.h>
#include <cstdlib>
#include <string>
#include <iostream>
#include <fstream>
using
namespace
std
;
#include "gputypes.h"
#include "cudaKernels.h"
struct
Atom
{
float
x
;
float
y
;
float
z
;
float
r
;
float
sr
;
float
fx
;
float
fy
;
float
fz
;
float
fb
;
};
static
__constant__
cudaGmxSimulation
cSim
;
void
SetCalculateGBVIForces2Sim
(
gpuContext
gpu
)
{
cudaError_t
status
;
status
=
cudaMemcpyToSymbol
(
cSim
,
&
gpu
->
sim
,
sizeof
(
cudaGmxSimulation
));
RTERROR
(
status
,
"cudaMemcpyToSymbol: SetSim copy to cSim failed"
);
}
void
GetCalculateGBVIForces2Sim
(
gpuContext
gpu
)
{
cudaError_t
status
;
status
=
cudaMemcpyFromSymbol
(
&
gpu
->
sim
,
cSim
,
sizeof
(
cudaGmxSimulation
));
RTERROR
(
status
,
"cudaMemcpyFromSymbol: SetSim copy from cSim failed"
);
}
#include "kCalculateGBVIAux.h"
/**
* This file contains the kernel for evalauating the second stage of GBSA. It is included
* several times in kCalculateGBVIForces2.cu with different #defines to generate
* different versions of the kernels.
*/
__global__
void
kCalculateGBVIForces2a_kernel
()
{
unsigned
int
pos
=
(
blockIdx
.
x
*
blockDim
.
x
+
threadIdx
.
x
);
if
(
pos
>=
cSim
.
atoms
)
return
;
float4
apos
=
cSim
.
pPosq
[
pos
];
float4
ar
=
cSim
.
pGBVIData
[
pos
];
float
fb
=
cSim
.
pBornForce
[
pos
];
unsigned
int
posJ
=
0
;
float4
force
;
force
.
x
=
force
.
y
=
force
.
z
=
force
.
w
=
0.0
f
;
while
(
posJ
<
cSim
.
atoms
)
{
float4
aposJ
=
cSim
.
pPosq
[
posJ
];
float4
arJ
=
cSim
.
pGBVIData
[
posJ
];
float
fbJ
=
cSim
.
pBornForce
[
posJ
];
float
dx
=
aposJ
.
x
-
apos
.
x
;
float
dy
=
aposJ
.
y
-
apos
.
y
;
float
dz
=
aposJ
.
z
-
apos
.
z
;
float
r2
=
dx
*
dx
+
dy
*
dy
+
dz
*
dz
;
float
r
=
sqrt
(
r2
);
float
dE
=
getGBVI_dE2
(
r
,
ar
.
x
,
arJ
.
y
,
fb
);
dE
=
r
>
1.0e-08
f
?
dE
:
0.0
f
;
//dx = dy = dz = 1.0f;
float
d
=
dx
*
dE
;
force
.
x
-=
d
;
d
=
dy
*
dE
;
force
.
y
-=
d
;
d
=
dz
*
dE
;
force
.
z
-=
d
;
#if 1
dE
=
getGBVI_dE2
(
r
,
arJ
.
x
,
ar
.
y
,
fbJ
);
dE
=
r
>
1.0e-08
f
?
dE
:
0.0
f
;
d
=
dx
*
dE
;
force
.
x
-=
d
;
d
=
dy
*
dE
;
force
.
y
-=
d
;
d
=
dz
*
dE
;
force
.
z
-=
d
;
#endif
posJ
+=
1
;
}
// Write results
cSim
.
pForce4a
[
pos
]
=
force
;
}
// Include versions of the kernels for N^2 calculations.
#define METHOD_NAME(a, b) a##N2##b
#include "kCalculateGBVIForces2.h"
#define USE_OUTPUT_BUFFER_PER_WARP
#undef METHOD_NAME
#define METHOD_NAME(a, b) a##N2ByWarp##b
#include "kCalculateGBVIForces2.h"
// Include versions of the kernels with cutoffs.
#undef METHOD_NAME
#undef USE_OUTPUT_BUFFER_PER_WARP
#define USE_CUTOFF
#define METHOD_NAME(a, b) a##Cutoff##b
#include "kCalculateGBVIForces2.h"
#define USE_OUTPUT_BUFFER_PER_WARP
#undef METHOD_NAME
#define METHOD_NAME(a, b) a##CutoffByWarp##b
#include "kCalculateGBVIForces2.h"
// Include versions of the kernels with periodic boundary conditions.
#undef METHOD_NAME
#undef USE_OUTPUT_BUFFER_PER_WARP
#define USE_PERIODIC
#define METHOD_NAME(a, b) a##Periodic##b
#include "kCalculateGBVIForces2.h"
#define USE_OUTPUT_BUFFER_PER_WARP
#undef METHOD_NAME
#define METHOD_NAME(a, b) a##PeriodicByWarp##b
#include "kCalculateGBVIForces2.h"
void
kCalculateGBVIForces2
(
gpuContext
gpu
)
{
//printf("kCalculateGBVIForces2\n");
size_t
numWithInteractions
;
#if 0
kClearForces(gpu);
(void) fprintf( stderr, "\nkCalculateGBVIForces2: cleared force prior loop2\n" ); (void) fflush( stderr );
kCalculateGBVIForces2a_kernel<<<gpu->sim.blocks, 384>>>();
(void) fprintf( stderr, "\ncalled kCalculateGBVIForces2a\n" ); (void) fflush( stderr );
return;
#endif
switch
(
gpu
->
sim
.
nonbondedMethod
)
{
case
NO_CUTOFF
:
if
(
gpu
->
bOutputBufferPerWarp
)
kCalculateGBVIN2ByWarpForces2_kernel
<<<
gpu
->
sim
.
bornForce2_blocks
,
gpu
->
sim
.
bornForce2_threads_per_block
,
sizeof
(
Atom
)
*
gpu
->
sim
.
bornForce2_threads_per_block
>>>
(
gpu
->
sim
.
pWorkUnit
,
gpu
->
sim
.
workUnits
);
else
kCalculateGBVIN2Forces2_kernel
<<<
gpu
->
sim
.
bornForce2_blocks
,
gpu
->
sim
.
bornForce2_threads_per_block
,
sizeof
(
Atom
)
*
gpu
->
sim
.
bornForce2_threads_per_block
>>>
(
gpu
->
sim
.
pWorkUnit
,
gpu
->
sim
.
workUnits
);
//(void) fprintf( stderr, "\nkCalculateGBVIForces2: Born radii/force forces warp=%u\n", gpu->bOutputBufferPerWarp ); (void) fflush( stderr );
#define GBVI_DEBUG 0
#if ( GBVI_DEBUG == 1 )
(
void
)
fprintf
(
stderr
,
"
\n
kCalculateGBVIForces2: Born radii/force forces:
\n
"
);
(
void
)
fflush
(
stderr
);
gpu
->
psBornForce
->
Download
();
gpu
->
psForce4
->
Download
();
for
(
int
ii
=
0
;
ii
<
gpu
->
natoms
;
ii
++
){
(
void
)
fprintf
(
stderr
,
"%d bF=%14.6e Fa[%14.6e %14.6e %14.6e] Fb[%14.6e %14.6e %14.6e]
\n
"
,
ii
,
gpu
->
psBornForce
->
_pSysStream
[
0
][
ii
],
gpu
->
psForce4
->
_pSysStream
[
0
][
ii
].
x
,
gpu
->
psForce4
->
_pSysStream
[
0
][
ii
].
y
,
gpu
->
psForce4
->
_pSysStream
[
0
][
ii
].
z
,
gpu
->
psForce4
->
_pSysStream
[
1
][
ii
].
x
,
gpu
->
psForce4
->
_pSysStream
[
1
][
ii
].
y
,
gpu
->
psForce4
->
_pSysStream
[
1
][
ii
].
z
);
}
for
(
int
ii
=
0
;
ii
<
gpu
->
sim
.
paddedNumberOfAtoms
*
2
;
ii
++
){
(
void
)
fprintf
(
stderr
,
"%d bF=%14.6e Fa[%14.6e %14.6e %14.6e %14.6e]
\n
"
,
ii
,
gpu
->
psBornForce
->
_pSysStream
[
0
][
ii
],
gpu
->
psForce4
->
_pSysStream
[
0
][
ii
].
x
,
gpu
->
psForce4
->
_pSysStream
[
0
][
ii
].
y
,
gpu
->
psForce4
->
_pSysStream
[
0
][
ii
].
z
,
gpu
->
psForce4
->
_pSysStream
[
0
][
ii
].
w
);
}
#endif
#undef GBVI_DEBUG
break
;
case
CUTOFF
:
numWithInteractions
=
gpu
->
psInteractionCount
->
_pSysData
[
0
];
if
(
gpu
->
bOutputBufferPerWarp
)
kCalculateGBVICutoffByWarpForces2_kernel
<<<
gpu
->
sim
.
bornForce2_blocks
,
gpu
->
sim
.
bornForce2_threads_per_block
,
(
sizeof
(
Atom
)
+
sizeof
(
float3
))
*
gpu
->
sim
.
bornForce2_threads_per_block
>>>
(
gpu
->
sim
.
pInteractingWorkUnit
,
numWithInteractions
);
else
kCalculateGBVICutoffForces2_kernel
<<<
gpu
->
sim
.
bornForce2_blocks
,
gpu
->
sim
.
bornForce2_threads_per_block
,
(
sizeof
(
Atom
)
+
sizeof
(
float3
))
*
gpu
->
sim
.
bornForce2_threads_per_block
>>>
(
gpu
->
sim
.
pInteractingWorkUnit
,
numWithInteractions
);
break
;
case
PERIODIC
:
numWithInteractions
=
gpu
->
psInteractionCount
->
_pSysData
[
0
];
if
(
gpu
->
bOutputBufferPerWarp
)
kCalculateGBVIPeriodicByWarpForces2_kernel
<<<
gpu
->
sim
.
bornForce2_blocks
,
gpu
->
sim
.
bornForce2_threads_per_block
,
(
sizeof
(
Atom
)
+
sizeof
(
float3
))
*
gpu
->
sim
.
bornForce2_threads_per_block
>>>
(
gpu
->
sim
.
pInteractingWorkUnit
,
numWithInteractions
);
else
kCalculateGBVIPeriodicForces2_kernel
<<<
gpu
->
sim
.
bornForce2_blocks
,
gpu
->
sim
.
bornForce2_threads_per_block
,
(
sizeof
(
Atom
)
+
sizeof
(
float3
))
*
gpu
->
sim
.
bornForce2_threads_per_block
>>>
(
gpu
->
sim
.
pInteractingWorkUnit
,
numWithInteractions
);
break
;
}
LAUNCHERROR
(
"kCalculateGBVIForces2"
);
}
platforms/cuda/src/kernels/kCalculateGBVIForces2.h
0 → 100644
View file @
29cf1500
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2009 Stanford University and the Authors. *
* Authors: Scott Le Grand, Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "kCalculateGBVIAux.h"
/**
* This file contains the kernel for evalauating the second stage of GBSA. It is included
* several times in kCalculateGBVIForces2.cu with different #defines to generate
* different versions of the kernels.
*/
__global__
void
METHOD_NAME
(
kCalculateGBVI
,
Forces2_kernel
)(
unsigned
int
*
workUnit
,
unsigned
int
numWorkUnits
)
{
extern
__shared__
Atom
sA
[];
unsigned
int
totalWarps
=
cSim
.
bornForce2_blocks
*
cSim
.
bornForce2_threads_per_block
/
GRID
;
unsigned
int
warp
=
(
blockIdx
.
x
*
blockDim
.
x
+
threadIdx
.
x
)
/
GRID
;
unsigned
int
pos
=
warp
*
numWorkUnits
/
totalWarps
;
unsigned
int
end
=
(
warp
+
1
)
*
numWorkUnits
/
totalWarps
;
#ifdef USE_CUTOFF
float3
*
tempBuffer
=
(
float3
*
)
&
sA
[
cSim
.
bornForce2_threads_per_block
];
#endif
unsigned
int
lasty
=
-
0xFFFFFFFF
;
while
(
pos
<
end
)
{
// Extract cell coordinates from appropriate work unit
unsigned
int
x
=
workUnit
[
pos
];
unsigned
int
y
=
((
x
>>
2
)
&
0x7fff
)
<<
GRIDBITS
;
x
=
(
x
>>
17
)
<<
GRIDBITS
;
unsigned
int
tgx
=
threadIdx
.
x
&
(
GRID
-
1
);
unsigned
int
i
=
x
+
tgx
;
float4
apos
=
cSim
.
pPosq
[
i
];
float4
ar
=
cSim
.
pGBVIData
[
i
];
float
fb
=
cSim
.
pBornForce
[
i
];
unsigned
int
tbx
=
threadIdx
.
x
-
tgx
;
unsigned
int
tj
=
tgx
;
Atom
*
psA
=
&
sA
[
tbx
];
float3
af
;
sA
[
threadIdx
.
x
].
fx
=
af
.
x
=
0
.
0
f
;
sA
[
threadIdx
.
x
].
fy
=
af
.
y
=
0
.
0
f
;
sA
[
threadIdx
.
x
].
fz
=
af
.
z
=
0
.
0
f
;
if
(
x
==
y
)
// Handle diagonals uniquely at 50% efficiency
{
// Read fixed atom data into registers and GRF
sA
[
threadIdx
.
x
].
x
=
apos
.
x
;
sA
[
threadIdx
.
x
].
y
=
apos
.
y
;
sA
[
threadIdx
.
x
].
z
=
apos
.
z
;
sA
[
threadIdx
.
x
].
r
=
ar
.
x
;
sA
[
threadIdx
.
x
].
sr
=
ar
.
y
;
sA
[
threadIdx
.
x
].
fb
=
fb
;
for
(
unsigned
int
j
=
(
tgx
+
1
)
&
(
GRID
-
1
);
j
!=
tgx
;
j
=
(
j
+
1
)
&
(
GRID
-
1
))
{
float
dx
=
psA
[
j
].
x
-
apos
.
x
;
float
dy
=
psA
[
j
].
y
-
apos
.
y
;
float
dz
=
psA
[
j
].
z
-
apos
.
z
;
#ifdef USE_PERIODIC
dx
-=
floor
(
dx
/
cSim
.
periodicBoxSizeX
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeX
;
dy
-=
floor
(
dy
/
cSim
.
periodicBoxSizeY
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeY
;
dz
-=
floor
(
dz
/
cSim
.
periodicBoxSizeZ
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeZ
;
#endif
float
r2
=
dx
*
dx
+
dy
*
dy
+
dz
*
dz
;
float
r
=
sqrt
(
r2
);
// Atom I Born forces and sum
float
dE
=
getGBVI_dE2
(
r
,
ar
.
x
,
psA
[
j
].
sr
,
fb
);
#if defined USE_PERIODIC
if
(
i
>=
cSim
.
atoms
||
x
+
j
>=
cSim
.
atoms
||
r2
>
cSim
.
nonbondedCutoffSqr
)
{
dE
=
0
.
0
f
;
}
#endif
#if defined USE_CUTOFF
if
(
r2
>
cSim
.
nonbondedCutoffSqr
)
{
dE
=
0
.
0
f
;
}
#endif
float
d
=
dx
*
dE
;
af
.
x
-=
d
;
psA
[
j
].
fx
+=
d
;
d
=
dy
*
dE
;
af
.
y
-=
d
;
psA
[
j
].
fy
+=
d
;
d
=
dz
*
dE
;
af
.
z
-=
d
;
psA
[
j
].
fz
+=
d
;
}
// Write results
float4
of
;
#ifdef USE_OUTPUT_BUFFER_PER_WARP
unsigned
int
offset
=
x
+
tgx
+
warp
*
cSim
.
stride
;
of
=
cSim
.
pForce4b
[
offset
];
of
.
x
+=
af
.
x
+
sA
[
threadIdx
.
x
].
fx
;
of
.
y
+=
af
.
y
+
sA
[
threadIdx
.
x
].
fy
;
of
.
z
+=
af
.
z
+
sA
[
threadIdx
.
x
].
fz
;
cSim
.
pForce4b
[
offset
]
=
of
;
#else
unsigned
int
offset
=
x
+
tgx
+
(
x
>>
GRIDBITS
)
*
cSim
.
stride
;
of
=
cSim
.
pForce4b
[
offset
];
of
.
x
+=
af
.
x
+
sA
[
threadIdx
.
x
].
fx
;
of
.
y
+=
af
.
y
+
sA
[
threadIdx
.
x
].
fy
;
of
.
z
+=
af
.
z
+
sA
[
threadIdx
.
x
].
fz
;
of
.
w
=
0
.
0
f
;
cSim
.
pForce4b
[
offset
]
=
of
;
#endif
}
else
{
// Read fixed atom data into registers and GRF
if
(
lasty
!=
y
)
{
unsigned
int
j
=
y
+
tgx
;
float4
temp
=
cSim
.
pPosq
[
j
];
float4
temp1
=
cSim
.
pGBVIData
[
j
];
float
fb
=
cSim
.
pBornForce
[
j
];
sA
[
threadIdx
.
x
].
fb
=
fb
;
sA
[
threadIdx
.
x
].
x
=
temp
.
x
;
sA
[
threadIdx
.
x
].
y
=
temp
.
y
;
sA
[
threadIdx
.
x
].
z
=
temp
.
z
;
sA
[
threadIdx
.
x
].
r
=
temp1
.
x
;
sA
[
threadIdx
.
x
].
sr
=
temp1
.
y
;
}
#ifdef USE_CUTOFF
unsigned
int
flags
=
cSim
.
pInteractionFlag
[
pos
];
if
(
flags
==
0
)
{
// No interactions in this block.
}
else
if
(
flags
==
0xFFFFFFFF
)
#endif
{
// Compute all interactions within this block.
for
(
unsigned
int
j
=
0
;
j
<
GRID
;
j
++
)
{
float
dx
=
psA
[
tj
].
x
-
apos
.
x
;
float
dy
=
psA
[
tj
].
y
-
apos
.
y
;
float
dz
=
psA
[
tj
].
z
-
apos
.
z
;
#ifdef USE_PERIODIC
dx
-=
floor
(
dx
/
cSim
.
periodicBoxSizeX
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeX
;
dy
-=
floor
(
dy
/
cSim
.
periodicBoxSizeY
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeY
;
dz
-=
floor
(
dz
/
cSim
.
periodicBoxSizeZ
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeZ
;
#endif
float
r2
=
dx
*
dx
+
dy
*
dy
+
dz
*
dz
;
float
r
=
sqrt
(
r2
);
float
dE
=
getGBVI_dE2
(
r
,
ar
.
x
,
psA
[
tj
].
sr
,
fb
);
#if defined USE_PERIODIC
if
(
i
>=
cSim
.
atoms
||
y
+
tj
>=
cSim
.
atoms
||
r2
>
cSim
.
nonbondedCutoffSqr
)
{
dE
=
0
.
0
f
;
}
#endif
#if defined USE_CUTOFF
if
(
r2
>
cSim
.
nonbondedCutoffSqr
)
{
dE
=
0
.
0
f
;
}
#endif
float
d
=
dx
*
dE
;
af
.
x
-=
d
;
psA
[
tj
].
fx
+=
d
;
d
=
dy
*
dE
;
af
.
y
-=
d
;
psA
[
tj
].
fy
+=
d
;
d
=
dz
*
dE
;
af
.
z
-=
d
;
psA
[
tj
].
fz
+=
d
;
// Atom J Born sum term
dE
=
getGBVI_dE2
(
r
,
psA
[
tj
].
r
,
ar
.
y
,
psA
[
tj
].
fb
);
#ifdef USE_PERIODIC
if
(
i
>=
cSim
.
atoms
||
y
+
tj
>=
cSim
.
atoms
||
r2
>
cSim
.
nonbondedCutoffSqr
)
{
dE
=
0
.
0
f
;
}
#endif
#if defined USE_CUTOFF
if
(
r2
>
cSim
.
nonbondedCutoffSqr
)
{
dE
=
0
.
0
f
;
}
#endif
dx
*=
dE
;
dy
*=
dE
;
dz
*=
dE
;
psA
[
tj
].
fx
+=
dx
;
psA
[
tj
].
fy
+=
dy
;
psA
[
tj
].
fz
+=
dz
;
af
.
x
-=
dx
;
af
.
y
-=
dy
;
af
.
z
-=
dz
;
tj
=
(
tj
+
1
)
&
(
GRID
-
1
);
}
}
#ifdef USE_CUTOFF
else
{
// Compute only a subset of the interactions in this block.
for
(
unsigned
int
j
=
0
;
j
<
GRID
;
j
++
)
{
if
((
flags
&
(
1
<<
j
))
!=
0
)
{
float
dx
=
psA
[
j
].
x
-
apos
.
x
;
float
dy
=
psA
[
j
].
y
-
apos
.
y
;
float
dz
=
psA
[
j
].
z
-
apos
.
z
;
#ifdef USE_PERIODIC
dx
-=
floor
(
dx
/
cSim
.
periodicBoxSizeX
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeX
;
dy
-=
floor
(
dy
/
cSim
.
periodicBoxSizeY
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeY
;
dz
-=
floor
(
dz
/
cSim
.
periodicBoxSizeZ
+
0
.
5
f
)
*
cSim
.
periodicBoxSizeZ
;
#endif
float
r2
=
dx
*
dx
+
dy
*
dy
+
dz
*
dz
;
float
r
=
sqrt
(
r2
);
// Interleaved Atom I and J Born Forces and sum components
float
dE
=
getGBVI_dE2
(
r
,
ar
.
x
,
psA
[
j
].
sr
,
fb
);
#if defined USE_PERIODIC
if
(
i
>=
cSim
.
atoms
||
y
+
j
>=
cSim
.
atoms
||
r2
>
cSim
.
nonbondedCutoffSqr
)
{
dE
=
0
.
0
f
;
}
#endif
#if defined USE_CUTOFF
if
(
r2
>
cSim
.
nonbondedCutoffSqr
)
{
dE
=
0
.
0
f
;
}
#endif
float
d
=
dx
*
dE
;
af
.
x
-=
d
;
tempBuffer
[
threadIdx
.
x
].
x
=
d
;
d
=
dy
*
dE
;
af
.
y
-=
d
;
tempBuffer
[
threadIdx
.
x
].
y
=
d
;
d
=
dz
*
dE
;
af
.
z
-=
d
;
tempBuffer
[
threadIdx
.
x
].
z
=
d
;
// Atom J Born sum term
dE
=
getGBVI_dE2
(
r
,
psA
[
j
].
r
,
ar
.
y
,
psA
[
j
].
fb
);
#ifdef USE_PERIODIC
if
(
i
>=
cSim
.
atoms
||
y
+
j
>=
cSim
.
atoms
||
r2
>
cSim
.
nonbondedCutoffSqr
)
{
dE
=
0
.
0
f
;
}
#endif
#if defined USE_CUTOFF
if
(
r2
>
cSim
.
nonbondedCutoffSqr
)
{
dE
=
0
.
0
f
;
}
#endif
dx
*=
dE
;
dy
*=
dE
;
dz
*=
dE
;
tempBuffer
[
threadIdx
.
x
].
x
+=
dx
;
tempBuffer
[
threadIdx
.
x
].
y
+=
dy
;
tempBuffer
[
threadIdx
.
x
].
z
+=
dz
;
af
.
x
-=
dx
;
af
.
y
-=
dy
;
af
.
z
-=
dz
;
// Sum the forces on atom j.
if
(
tgx
%
2
==
0
)
{
tempBuffer
[
threadIdx
.
x
].
x
+=
tempBuffer
[
threadIdx
.
x
+
1
].
x
;
tempBuffer
[
threadIdx
.
x
].
y
+=
tempBuffer
[
threadIdx
.
x
+
1
].
y
;
tempBuffer
[
threadIdx
.
x
].
z
+=
tempBuffer
[
threadIdx
.
x
+
1
].
z
;
}
if
(
tgx
%
4
==
0
)
{
tempBuffer
[
threadIdx
.
x
].
x
+=
tempBuffer
[
threadIdx
.
x
+
2
].
x
;
tempBuffer
[
threadIdx
.
x
].
y
+=
tempBuffer
[
threadIdx
.
x
+
2
].
y
;
tempBuffer
[
threadIdx
.
x
].
z
+=
tempBuffer
[
threadIdx
.
x
+
2
].
z
;
}
if
(
tgx
%
8
==
0
)
{
tempBuffer
[
threadIdx
.
x
].
x
+=
tempBuffer
[
threadIdx
.
x
+
4
].
x
;
tempBuffer
[
threadIdx
.
x
].
y
+=
tempBuffer
[
threadIdx
.
x
+
4
].
y
;
tempBuffer
[
threadIdx
.
x
].
z
+=
tempBuffer
[
threadIdx
.
x
+
4
].
z
;
}
if
(
tgx
%
16
==
0
)
{
tempBuffer
[
threadIdx
.
x
].
x
+=
tempBuffer
[
threadIdx
.
x
+
8
].
x
;
tempBuffer
[
threadIdx
.
x
].
y
+=
tempBuffer
[
threadIdx
.
x
+
8
].
y
;
tempBuffer
[
threadIdx
.
x
].
z
+=
tempBuffer
[
threadIdx
.
x
+
8
].
z
;
}
if
(
tgx
==
0
)
{
psA
[
j
].
fx
+=
tempBuffer
[
threadIdx
.
x
].
x
+
tempBuffer
[
threadIdx
.
x
+
16
].
x
;
psA
[
j
].
fy
+=
tempBuffer
[
threadIdx
.
x
].
y
+
tempBuffer
[
threadIdx
.
x
+
16
].
y
;
psA
[
j
].
fz
+=
tempBuffer
[
threadIdx
.
x
].
z
+
tempBuffer
[
threadIdx
.
x
+
16
].
z
;
}
}
}
}
#endif
// Write results
float4
of
;
#ifdef USE_OUTPUT_BUFFER_PER_WARP
unsigned
int
offset
=
x
+
tgx
+
warp
*
cSim
.
stride
;
of
=
cSim
.
pForce4b
[
offset
];
of
.
x
+=
af
.
x
;
of
.
y
+=
af
.
y
;
of
.
z
+=
af
.
z
;
cSim
.
pForce4b
[
offset
]
=
of
;
offset
=
y
+
tgx
+
warp
*
cSim
.
stride
;
of
=
cSim
.
pForce4b
[
offset
];
of
.
x
+=
sA
[
threadIdx
.
x
].
fx
;
of
.
y
+=
sA
[
threadIdx
.
x
].
fy
;
of
.
z
+=
sA
[
threadIdx
.
x
].
fz
;
cSim
.
pForce4b
[
offset
]
=
of
;
#else
unsigned
int
offset
=
x
+
tgx
+
(
y
>>
GRIDBITS
)
*
cSim
.
stride
;
of
=
cSim
.
pForce4b
[
offset
];
of
.
x
+=
af
.
x
;
of
.
y
+=
af
.
y
;
of
.
z
+=
af
.
z
;
of
.
w
=
0
.
0
f
;
cSim
.
pForce4b
[
offset
]
=
of
;
offset
=
y
+
tgx
+
(
x
>>
GRIDBITS
)
*
cSim
.
stride
;
of
=
cSim
.
pForce4b
[
offset
];
of
.
x
+=
sA
[
threadIdx
.
x
].
fx
;
of
.
y
+=
sA
[
threadIdx
.
x
].
fy
;
of
.
z
+=
sA
[
threadIdx
.
x
].
fz
;
cSim
.
pForce4b
[
offset
]
=
of
;
#endif
}
lasty
=
y
;
pos
++
;
}
}
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