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tsoc
openmm
Commits
f4f5b568
Commit
f4f5b568
authored
Aug 15, 2013
by
peastman
Browse files
Avoid nans when using PME with Drude particles
parent
8f6d3ec1
Changes
3
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3 changed files
with
24 additions
and
18 deletions
+24
-18
platforms/cuda/src/kernels/coulombLennardJones.cu
platforms/cuda/src/kernels/coulombLennardJones.cu
+4
-2
platforms/opencl/src/kernels/coulombLennardJones.cl
platforms/opencl/src/kernels/coulombLennardJones.cl
+4
-2
platforms/reference/src/SimTKReference/ReferenceLJCoulombIxn.cpp
...ms/reference/src/SimTKReference/ReferenceLJCoulombIxn.cpp
+16
-14
No files found.
platforms/cuda/src/kernels/coulombLennardJones.cu
View file @
f4f5b568
...
...
@@ -22,9 +22,11 @@ if ((!isExcluded && r2 < CUTOFF_SQUARED) || needCorrection) {
if
(
needCorrection
)
{
// Subtract off the part of this interaction that was included in the reciprocal space contribution.
if
(
1
-
erfcAlphaR
>
1e-6
)
{
tempForce
=
-
prefactor
*
((
1.0
f
-
erfcAlphaR
)
-
alphaR
*
expAlphaRSqr
*
TWO_OVER_SQRT_PI
);
tempEnergy
+=
-
prefactor
*
(
1.0
f
-
erfcAlphaR
);
}
}
else
{
#if HAS_LENNARD_JONES
real
sig
=
sigmaEpsilon1
.
x
+
sigmaEpsilon2
.
x
;
...
...
platforms/opencl/src/kernels/coulombLennardJones.cl
View file @
f4f5b568
...
...
@@ -22,9 +22,11 @@ if ((!isExcluded && r2 < CUTOFF_SQUARED) || needCorrection) {
if
(
needCorrection
)
{
//
Subtract
off
the
part
of
this
interaction
that
was
included
in
the
reciprocal
space
contribution.
if
(
1-erfcAlphaR
>
1e-6
)
{
tempForce
=
-prefactor*
((
1.0f-erfcAlphaR
)
-alphaR*expAlphaRSqr*TWO_OVER_SQRT_PI
)
;
tempEnergy
+=
-prefactor*
(
1.0f-erfcAlphaR
)
;
}
}
else
{
#
if
HAS_LENNARD_JONES
real
sig
=
sigmaEpsilon1.x
+
sigmaEpsilon2.x
;
...
...
platforms/reference/src/SimTKReference/ReferenceLJCoulombIxn.cpp
View file @
f4f5b568
...
...
@@ -432,6 +432,7 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec>
RealOpenMM
r
=
deltaR
[
0
][
ReferenceForce
::
RIndex
];
RealOpenMM
inverseR
=
one
/
(
deltaR
[
0
][
ReferenceForce
::
RIndex
]);
RealOpenMM
alphaR
=
alphaEwald
*
r
;
if
(
erf
(
alphaR
)
>
1e-6
)
{
RealOpenMM
dEdR
=
(
RealOpenMM
)
(
ONE_4PI_EPS0
*
atomParameters
[
ii
][
QIndex
]
*
atomParameters
[
jj
][
QIndex
]
*
inverseR
*
inverseR
*
inverseR
);
dEdR
=
(
RealOpenMM
)
(
dEdR
*
(
erf
(
alphaR
)
-
2
*
alphaR
*
exp
(
-
alphaR
*
alphaR
)
/
SQRT_PI
));
...
...
@@ -454,6 +455,7 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec>
}
}
}
}
if
(
totalEnergy
)
*
totalEnergy
-=
totalExclusionEnergy
;
...
...
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