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tsoc
openmm
Commits
0e5d3fb1
Commit
0e5d3fb1
authored
Sep 02, 2011
by
Peter Eastman
Browse files
Using fast approximation for erfc instead of tabulated values
parent
d9029f61
Changes
3
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3 changed files
with
7 additions
and
26 deletions
+7
-26
platforms/opencl/src/OpenCLKernels.cpp
platforms/opencl/src/OpenCLKernels.cpp
+0
-16
platforms/opencl/src/OpenCLKernels.h
platforms/opencl/src/OpenCLKernels.h
+1
-2
platforms/opencl/src/kernels/coulombLennardJones.cl
platforms/opencl/src/kernels/coulombLennardJones.cl
+6
-8
No files found.
platforms/opencl/src/OpenCLKernels.cpp
View file @
0e5d3fb1
...
@@ -41,7 +41,6 @@
...
@@ -41,7 +41,6 @@
#include "lepton/Parser.h"
#include "lepton/Parser.h"
#include "lepton/ParsedExpression.h"
#include "lepton/ParsedExpression.h"
#include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
#include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
#include "openmm/internal/MSVC_erfc.h"
#include <cmath>
#include <cmath>
#include <set>
#include <set>
...
@@ -1154,8 +1153,6 @@ OpenCLCalcNonbondedForceKernel::~OpenCLCalcNonbondedForceKernel() {
...
@@ -1154,8 +1153,6 @@ OpenCLCalcNonbondedForceKernel::~OpenCLCalcNonbondedForceKernel() {
delete
pmeAtomRange
;
delete
pmeAtomRange
;
if
(
pmeAtomGridIndex
!=
NULL
)
if
(
pmeAtomGridIndex
!=
NULL
)
delete
pmeAtomGridIndex
;
delete
pmeAtomGridIndex
;
if
(
erfcTable
!=
NULL
)
delete
erfcTable
;
if
(
sort
!=
NULL
)
if
(
sort
!=
NULL
)
delete
sort
;
delete
sort
;
if
(
fft
!=
NULL
)
if
(
fft
!=
NULL
)
...
@@ -1341,19 +1338,6 @@ void OpenCLCalcNonbondedForceKernel::initialize(const System& system, const Nonb
...
@@ -1341,19 +1338,6 @@ void OpenCLCalcNonbondedForceKernel::initialize(const System& system, const Nonb
}
}
else
else
ewaldSelfEnergy
=
0.0
;
ewaldSelfEnergy
=
0.0
;
// Tabulate values of erfc().
if
(
force
.
getNonbondedMethod
()
==
NonbondedForce
::
Ewald
||
force
.
getNonbondedMethod
()
==
NonbondedForce
::
PME
)
{
const
int
tableSize
=
2048
;
defines
[
"ERFC_TABLE_SCALE"
]
=
doubleToString
((
tableSize
-
1
)
/
(
alpha
*
force
.
getCutoffDistance
()));
erfcTable
=
new
OpenCLArray
<
cl_float
>
(
cl
,
tableSize
,
"ErfcTable"
,
false
,
CL_MEM_READ_ONLY
);
vector
<
cl_float
>
erfcVector
(
tableSize
);
for
(
int
i
=
0
;
i
<
tableSize
;
++
i
)
erfcVector
[
i
]
=
(
float
)
erfc
(
i
*
(
alpha
*
force
.
getCutoffDistance
())
/
(
tableSize
-
1
));
erfcTable
->
upload
(
erfcVector
);
cl
.
getNonbondedUtilities
().
addArgument
(
OpenCLNonbondedUtilities
::
ParameterInfo
(
"erfcTable"
,
"float"
,
1
,
sizeof
(
cl_float
),
erfcTable
->
getDeviceBuffer
()));
}
// Add the interaction to the default nonbonded kernel.
// Add the interaction to the default nonbonded kernel.
...
...
platforms/opencl/src/OpenCLKernels.h
View file @
0e5d3fb1
...
@@ -477,7 +477,7 @@ public:
...
@@ -477,7 +477,7 @@ public:
OpenCLCalcNonbondedForceKernel
(
std
::
string
name
,
const
Platform
&
platform
,
OpenCLContext
&
cl
,
System
&
system
)
:
CalcNonbondedForceKernel
(
name
,
platform
),
OpenCLCalcNonbondedForceKernel
(
std
::
string
name
,
const
Platform
&
platform
,
OpenCLContext
&
cl
,
System
&
system
)
:
CalcNonbondedForceKernel
(
name
,
platform
),
hasInitializedKernel
(
false
),
cl
(
cl
),
sigmaEpsilon
(
NULL
),
exceptionParams
(
NULL
),
exceptionIndices
(
NULL
),
cosSinSums
(
NULL
),
pmeGrid
(
NULL
),
hasInitializedKernel
(
false
),
cl
(
cl
),
sigmaEpsilon
(
NULL
),
exceptionParams
(
NULL
),
exceptionIndices
(
NULL
),
cosSinSums
(
NULL
),
pmeGrid
(
NULL
),
pmeBsplineModuliX
(
NULL
),
pmeBsplineModuliY
(
NULL
),
pmeBsplineModuliZ
(
NULL
),
pmeBsplineTheta
(
NULL
),
pmeBsplineDtheta
(
NULL
),
pmeAtomRange
(
NULL
),
pmeBsplineModuliX
(
NULL
),
pmeBsplineModuliY
(
NULL
),
pmeBsplineModuliZ
(
NULL
),
pmeBsplineTheta
(
NULL
),
pmeBsplineDtheta
(
NULL
),
pmeAtomRange
(
NULL
),
pmeAtomGridIndex
(
NULL
),
erfcTable
(
NULL
),
sort
(
NULL
),
fft
(
NULL
)
{
pmeAtomGridIndex
(
NULL
),
sort
(
NULL
),
fft
(
NULL
)
{
}
}
~
OpenCLCalcNonbondedForceKernel
();
~
OpenCLCalcNonbondedForceKernel
();
/**
/**
...
@@ -511,7 +511,6 @@ private:
...
@@ -511,7 +511,6 @@ private:
OpenCLArray
<
mm_float4
>*
pmeBsplineDtheta
;
OpenCLArray
<
mm_float4
>*
pmeBsplineDtheta
;
OpenCLArray
<
cl_int
>*
pmeAtomRange
;
OpenCLArray
<
cl_int
>*
pmeAtomRange
;
OpenCLArray
<
mm_int2
>*
pmeAtomGridIndex
;
OpenCLArray
<
mm_int2
>*
pmeAtomGridIndex
;
OpenCLArray
<
cl_float
>*
erfcTable
;
OpenCLSort
<
mm_int2
>*
sort
;
OpenCLSort
<
mm_int2
>*
sort
;
OpenCLFFT3D
*
fft
;
OpenCLFFT3D
*
fft
;
cl
::
Kernel
exceptionsKernel
;
cl
::
Kernel
exceptionsKernel
;
...
...
platforms/opencl/src/kernels/coulombLennardJones.cl
View file @
0e5d3fb1
...
@@ -4,15 +4,13 @@ if (!isExcluded || needCorrection) {
...
@@ -4,15 +4,13 @@ if (!isExcluded || needCorrection) {
const float prefactor = 138.935456f*posq1.w*posq2.w*invR;
const float prefactor = 138.935456f*posq1.w*posq2.w*invR;
float alphaR = EWALD_ALPHA*r;
float alphaR = EWALD_ALPHA*r;
float erfcAlphaR = 0.0f;
float erfcAlphaR = 0.0f;
if
(
r2
<
CUTOFF_SQUARED
)
{
if (r2 < CUTOFF_SQUARED
|
|
needCorrection
)
{
float
normalized
=
ERFC_TABLE_SCALE*alphaR
;
//
This
approximation
for
erfc
is
from
Abramowitz
and
Stegun
(
1964
)
p.
299.
They
cite
the
following
as
int
tableIndex
=
(
int
)
normalized
;
//
the
original
source:
C.
Hastings,
Jr.,
Approximations
for
Digital
Computers
(
1955
)
.
float
fract2
=
normalized-tableIndex
;
float
fract1
=
1.0f
-fract2
;
float
t
=
1.0f
/
(
1.0f+0.47047f*alphaR
)
;
erfcAlphaR
=
fract1*erfcTable[tableIndex]
+
fract2*erfcTable[tableIndex+1]
;
erfcAlphaR
=
(
t*
(
0.3480242f+t*
(
-0.0958798f+t*0.7478556f
)))
*exp
(
-alphaR*alphaR
)
;
}
}
else
if
(
needCorrection
)
erfcAlphaR
=
erfc
(
alphaR
)
;
float
tempForce
=
0.0f
;
float
tempForce
=
0.0f
;
if
(
needCorrection
)
{
if
(
needCorrection
)
{
//
Subtract
off
the
part
of
this
interaction
that
was
included
in
the
reciprocal
space
contribution.
//
Subtract
off
the
part
of
this
interaction
that
was
included
in
the
reciprocal
space
contribution.
...
...
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