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tsoc
openmm
Commits
b456b980
Commit
b456b980
authored
Jan 28, 2020
by
peastman
Browse files
Fixed error on CPU platform when forces disagree about whether the system is periodic
parent
45f8c022
Changes
1
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1 changed file
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6 additions
and
6 deletions
+6
-6
platforms/cpu/src/CpuKernels.cpp
platforms/cpu/src/CpuKernels.cpp
+6
-6
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platforms/cpu/src/CpuKernels.cpp
View file @
b456b980
...
@@ -614,7 +614,7 @@ void CpuCalcNonbondedForceKernel::initialize(const System& system, const Nonbond
...
@@ -614,7 +614,7 @@ void CpuCalcNonbondedForceKernel::initialize(const System& system, const Nonbond
dispersionCoefficient
=
NonbondedForceImpl
::
calcDispersionCorrection
(
system
,
force
);
dispersionCoefficient
=
NonbondedForceImpl
::
calcDispersionCorrection
(
system
,
force
);
else
else
dispersionCoefficient
=
0.0
;
dispersionCoefficient
=
0.0
;
data
.
isPeriodic
=
(
nonbondedMethod
==
CutoffPeriodic
||
nonbondedMethod
==
Ewald
||
nonbondedMethod
==
PME
||
nonbondedMethod
==
LJPME
);
data
.
isPeriodic
|
=
(
nonbondedMethod
==
CutoffPeriodic
||
nonbondedMethod
==
Ewald
||
nonbondedMethod
==
PME
||
nonbondedMethod
==
LJPME
);
}
}
double
CpuCalcNonbondedForceKernel
::
execute
(
ContextImpl
&
context
,
bool
includeForces
,
bool
includeEnergy
,
bool
includeDirect
,
bool
includeReciprocal
)
{
double
CpuCalcNonbondedForceKernel
::
execute
(
ContextImpl
&
context
,
bool
includeForces
,
bool
includeEnergy
,
bool
includeDirect
,
bool
includeReciprocal
)
{
...
@@ -923,7 +923,7 @@ void CpuCalcCustomNonbondedForceKernel::initialize(const System& system, const C
...
@@ -923,7 +923,7 @@ void CpuCalcCustomNonbondedForceKernel::initialize(const System& system, const C
force
.
getInteractionGroupParameters
(
i
,
set1
,
set2
);
force
.
getInteractionGroupParameters
(
i
,
set1
,
set2
);
interactionGroups
.
push_back
(
make_pair
(
set1
,
set2
));
interactionGroups
.
push_back
(
make_pair
(
set1
,
set2
));
}
}
data
.
isPeriodic
=
(
nonbondedMethod
==
CutoffPeriodic
);
data
.
isPeriodic
|
=
(
nonbondedMethod
==
CutoffPeriodic
);
nonbonded
=
new
CpuCustomNonbondedForce
(
energyExpression
,
forceExpression
,
parameterNames
,
exclusions
,
energyParamDerivExpressions
,
data
.
threads
);
nonbonded
=
new
CpuCustomNonbondedForce
(
energyExpression
,
forceExpression
,
parameterNames
,
exclusions
,
energyParamDerivExpressions
,
data
.
threads
);
if
(
interactionGroups
.
size
()
>
0
)
if
(
interactionGroups
.
size
()
>
0
)
nonbonded
->
setInteractionGroups
(
interactionGroups
);
nonbonded
->
setInteractionGroups
(
interactionGroups
);
...
@@ -1016,7 +1016,7 @@ void CpuCalcGBSAOBCForceKernel::initialize(const System& system, const GBSAOBCFo
...
@@ -1016,7 +1016,7 @@ void CpuCalcGBSAOBCForceKernel::initialize(const System& system, const GBSAOBCFo
obc
.
setSurfaceAreaEnergy
((
float
)
force
.
getSurfaceAreaEnergy
());
obc
.
setSurfaceAreaEnergy
((
float
)
force
.
getSurfaceAreaEnergy
());
if
(
force
.
getNonbondedMethod
()
!=
GBSAOBCForce
::
NoCutoff
)
if
(
force
.
getNonbondedMethod
()
!=
GBSAOBCForce
::
NoCutoff
)
obc
.
setUseCutoff
((
float
)
force
.
getCutoffDistance
());
obc
.
setUseCutoff
((
float
)
force
.
getCutoffDistance
());
data
.
isPeriodic
=
(
force
.
getNonbondedMethod
()
==
GBSAOBCForce
::
CutoffPeriodic
);
data
.
isPeriodic
|
=
(
force
.
getNonbondedMethod
()
==
GBSAOBCForce
::
CutoffPeriodic
);
}
}
double
CpuCalcGBSAOBCForceKernel
::
execute
(
ContextImpl
&
context
,
bool
includeForces
,
bool
includeEnergy
)
{
double
CpuCalcGBSAOBCForceKernel
::
execute
(
ContextImpl
&
context
,
bool
includeForces
,
bool
includeEnergy
)
{
...
@@ -1190,7 +1190,7 @@ void CpuCalcCustomGBForceKernel::initialize(const System& system, const CustomGB
...
@@ -1190,7 +1190,7 @@ void CpuCalcCustomGBForceKernel::initialize(const System& system, const CustomGB
ixn
=
new
CpuCustomGBForce
(
numParticles
,
exclusions
,
valueExpressions
,
valueDerivExpressions
,
valueGradientExpressions
,
valueParamDerivExpressions
,
ixn
=
new
CpuCustomGBForce
(
numParticles
,
exclusions
,
valueExpressions
,
valueDerivExpressions
,
valueGradientExpressions
,
valueParamDerivExpressions
,
valueNames
,
valueTypes
,
energyExpressions
,
energyDerivExpressions
,
energyGradientExpressions
,
energyParamDerivExpressions
,
energyTypes
,
valueNames
,
valueTypes
,
energyExpressions
,
energyDerivExpressions
,
energyGradientExpressions
,
energyParamDerivExpressions
,
energyTypes
,
particleParameterNames
,
data
.
threads
);
particleParameterNames
,
data
.
threads
);
data
.
isPeriodic
=
(
force
.
getNonbondedMethod
()
==
CustomGBForce
::
CutoffPeriodic
);
data
.
isPeriodic
|
=
(
force
.
getNonbondedMethod
()
==
CustomGBForce
::
CutoffPeriodic
);
}
}
double
CpuCalcCustomGBForceKernel
::
execute
(
ContextImpl
&
context
,
bool
includeForces
,
bool
includeEnergy
)
{
double
CpuCalcCustomGBForceKernel
::
execute
(
ContextImpl
&
context
,
bool
includeForces
,
bool
includeEnergy
)
{
...
@@ -1252,7 +1252,7 @@ void CpuCalcCustomManyParticleForceKernel::initialize(const System& system, cons
...
@@ -1252,7 +1252,7 @@ void CpuCalcCustomManyParticleForceKernel::initialize(const System& system, cons
ixn
=
new
CpuCustomManyParticleForce
(
force
,
data
.
threads
);
ixn
=
new
CpuCustomManyParticleForce
(
force
,
data
.
threads
);
nonbondedMethod
=
CalcCustomManyParticleForceKernel
::
NonbondedMethod
(
force
.
getNonbondedMethod
());
nonbondedMethod
=
CalcCustomManyParticleForceKernel
::
NonbondedMethod
(
force
.
getNonbondedMethod
());
cutoffDistance
=
force
.
getCutoffDistance
();
cutoffDistance
=
force
.
getCutoffDistance
();
data
.
isPeriodic
=
(
nonbondedMethod
==
CutoffPeriodic
);
data
.
isPeriodic
|
=
(
nonbondedMethod
==
CutoffPeriodic
);
}
}
double
CpuCalcCustomManyParticleForceKernel
::
execute
(
ContextImpl
&
context
,
bool
includeForces
,
bool
includeEnergy
)
{
double
CpuCalcCustomManyParticleForceKernel
::
execute
(
ContextImpl
&
context
,
bool
includeForces
,
bool
includeEnergy
)
{
...
@@ -1295,7 +1295,7 @@ CpuCalcGayBerneForceKernel::~CpuCalcGayBerneForceKernel() {
...
@@ -1295,7 +1295,7 @@ CpuCalcGayBerneForceKernel::~CpuCalcGayBerneForceKernel() {
void
CpuCalcGayBerneForceKernel
::
initialize
(
const
System
&
system
,
const
GayBerneForce
&
force
)
{
void
CpuCalcGayBerneForceKernel
::
initialize
(
const
System
&
system
,
const
GayBerneForce
&
force
)
{
ixn
=
new
CpuGayBerneForce
(
force
);
ixn
=
new
CpuGayBerneForce
(
force
);
data
.
isPeriodic
=
(
force
.
getNonbondedMethod
()
==
GayBerneForce
::
CutoffPeriodic
);
data
.
isPeriodic
|
=
(
force
.
getNonbondedMethod
()
==
GayBerneForce
::
CutoffPeriodic
);
if
(
force
.
getNonbondedMethod
()
!=
GayBerneForce
::
NoCutoff
)
{
if
(
force
.
getNonbondedMethod
()
!=
GayBerneForce
::
NoCutoff
)
{
double
cutoff
=
force
.
getCutoffDistance
();
double
cutoff
=
force
.
getCutoffDistance
();
data
.
requestNeighborList
(
cutoff
,
0.1
*
cutoff
,
true
,
ixn
->
getExclusions
());
data
.
requestNeighborList
(
cutoff
,
0.1
*
cutoff
,
true
,
ixn
->
getExclusions
());
...
...
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