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tsoc
openmm
Commits
a4020466
"platforms/cuda/tests/TestCudaDPDIntegrator.cpp" did not exist on "68e02e809df6804b76ceb7ac07af73c1efa186cc"
Commit
a4020466
authored
Jul 14, 2009
by
Peter Eastman
Browse files
Renamed OpenMMContext to Context
parent
95b8dbd6
Changes
139
Hide whitespace changes
Inline
Side-by-side
Showing
20 changed files
with
90 additions
and
90 deletions
+90
-90
openmmapi/src/HarmonicBondForceImpl.cpp
openmmapi/src/HarmonicBondForceImpl.cpp
+4
-4
openmmapi/src/LangevinIntegrator.cpp
openmmapi/src/LangevinIntegrator.cpp
+3
-3
openmmapi/src/NonbondedForceImpl.cpp
openmmapi/src/NonbondedForceImpl.cpp
+4
-4
openmmapi/src/OpenMMContext.cpp
openmmapi/src/OpenMMContext.cpp
+23
-23
openmmapi/src/OpenMMContextImpl.cpp
openmmapi/src/OpenMMContextImpl.cpp
+14
-14
openmmapi/src/PeriodicTorsionForceImpl.cpp
openmmapi/src/PeriodicTorsionForceImpl.cpp
+4
-4
openmmapi/src/RBTorsionForceImpl.cpp
openmmapi/src/RBTorsionForceImpl.cpp
+4
-4
openmmapi/src/VariableLangevinIntegrator.cpp
openmmapi/src/VariableLangevinIntegrator.cpp
+3
-3
openmmapi/src/VariableVerletIntegrator.cpp
openmmapi/src/VariableVerletIntegrator.cpp
+3
-3
openmmapi/src/VerletIntegrator.cpp
openmmapi/src/VerletIntegrator.cpp
+3
-3
platforms/brook/include/BrookKernelFactory.h
platforms/brook/include/BrookKernelFactory.h
+1
-1
platforms/brook/include/BrookPlatform.h
platforms/brook/include/BrookPlatform.h
+4
-4
platforms/brook/include/BrookStreamFactory.h
platforms/brook/include/BrookStreamFactory.h
+1
-1
platforms/brook/src/BrookBonded.h
platforms/brook/src/BrookBonded.h
+1
-1
platforms/brook/src/BrookCalcGBSAOBCForceKernel.cpp
platforms/brook/src/BrookCalcGBSAOBCForceKernel.cpp
+4
-4
platforms/brook/src/BrookCalcGBSAOBCForceKernel.h
platforms/brook/src/BrookCalcGBSAOBCForceKernel.h
+2
-2
platforms/brook/src/BrookCalcHarmonicAngleForceKernel.cpp
platforms/brook/src/BrookCalcHarmonicAngleForceKernel.cpp
+4
-4
platforms/brook/src/BrookCalcHarmonicAngleForceKernel.h
platforms/brook/src/BrookCalcHarmonicAngleForceKernel.h
+2
-2
platforms/brook/src/BrookCalcHarmonicBondForceKernel.cpp
platforms/brook/src/BrookCalcHarmonicBondForceKernel.cpp
+4
-4
platforms/brook/src/BrookCalcHarmonicBondForceKernel.h
platforms/brook/src/BrookCalcHarmonicBondForceKernel.h
+2
-2
No files found.
openmmapi/src/HarmonicBondForceImpl.cpp
View file @
a4020466
...
@@ -29,7 +29,7 @@
...
@@ -29,7 +29,7 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
* -------------------------------------------------------------------------- */
#include "openmm/internal/
OpenMM
ContextImpl.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/internal/HarmonicBondForceImpl.h"
#include "openmm/internal/HarmonicBondForceImpl.h"
#include "openmm/kernels.h"
#include "openmm/kernels.h"
...
@@ -44,16 +44,16 @@ HarmonicBondForceImpl::HarmonicBondForceImpl(HarmonicBondForce& owner) : owner(o
...
@@ -44,16 +44,16 @@ HarmonicBondForceImpl::HarmonicBondForceImpl(HarmonicBondForce& owner) : owner(o
HarmonicBondForceImpl
::~
HarmonicBondForceImpl
()
{
HarmonicBondForceImpl
::~
HarmonicBondForceImpl
()
{
}
}
void
HarmonicBondForceImpl
::
initialize
(
OpenMM
ContextImpl
&
context
)
{
void
HarmonicBondForceImpl
::
initialize
(
ContextImpl
&
context
)
{
kernel
=
context
.
getPlatform
().
createKernel
(
CalcHarmonicBondForceKernel
::
Name
(),
context
);
kernel
=
context
.
getPlatform
().
createKernel
(
CalcHarmonicBondForceKernel
::
Name
(),
context
);
dynamic_cast
<
CalcHarmonicBondForceKernel
&>
(
kernel
.
getImpl
()).
initialize
(
context
.
getSystem
(),
owner
);
dynamic_cast
<
CalcHarmonicBondForceKernel
&>
(
kernel
.
getImpl
()).
initialize
(
context
.
getSystem
(),
owner
);
}
}
void
HarmonicBondForceImpl
::
calcForces
(
OpenMM
ContextImpl
&
context
,
Stream
&
forces
)
{
void
HarmonicBondForceImpl
::
calcForces
(
ContextImpl
&
context
,
Stream
&
forces
)
{
dynamic_cast
<
CalcHarmonicBondForceKernel
&>
(
kernel
.
getImpl
()).
executeForces
(
context
);
dynamic_cast
<
CalcHarmonicBondForceKernel
&>
(
kernel
.
getImpl
()).
executeForces
(
context
);
}
}
double
HarmonicBondForceImpl
::
calcEnergy
(
OpenMM
ContextImpl
&
context
)
{
double
HarmonicBondForceImpl
::
calcEnergy
(
ContextImpl
&
context
)
{
return
dynamic_cast
<
CalcHarmonicBondForceKernel
&>
(
kernel
.
getImpl
()).
executeEnergy
(
context
);
return
dynamic_cast
<
CalcHarmonicBondForceKernel
&>
(
kernel
.
getImpl
()).
executeEnergy
(
context
);
}
}
...
...
openmmapi/src/LangevinIntegrator.cpp
View file @
a4020466
...
@@ -30,8 +30,8 @@
...
@@ -30,8 +30,8 @@
* -------------------------------------------------------------------------- */
* -------------------------------------------------------------------------- */
#include "openmm/LangevinIntegrator.h"
#include "openmm/LangevinIntegrator.h"
#include "openmm/
OpenMM
Context.h"
#include "openmm/Context.h"
#include "openmm/internal/
OpenMM
ContextImpl.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/kernels.h"
#include "openmm/kernels.h"
#include <ctime>
#include <ctime>
#include <string>
#include <string>
...
@@ -48,7 +48,7 @@ LangevinIntegrator::LangevinIntegrator(double temperature, double frictionCoeff,
...
@@ -48,7 +48,7 @@ LangevinIntegrator::LangevinIntegrator(double temperature, double frictionCoeff,
setRandomNumberSeed
((
int
)
time
(
NULL
));
setRandomNumberSeed
((
int
)
time
(
NULL
));
}
}
void
LangevinIntegrator
::
initialize
(
OpenMM
ContextImpl
&
contextRef
)
{
void
LangevinIntegrator
::
initialize
(
ContextImpl
&
contextRef
)
{
context
=
&
contextRef
;
context
=
&
contextRef
;
kernel
=
context
->
getPlatform
().
createKernel
(
IntegrateLangevinStepKernel
::
Name
(),
contextRef
);
kernel
=
context
->
getPlatform
().
createKernel
(
IntegrateLangevinStepKernel
::
Name
(),
contextRef
);
dynamic_cast
<
IntegrateLangevinStepKernel
&>
(
kernel
.
getImpl
()).
initialize
(
contextRef
.
getSystem
(),
*
this
);
dynamic_cast
<
IntegrateLangevinStepKernel
&>
(
kernel
.
getImpl
()).
initialize
(
contextRef
.
getSystem
(),
*
this
);
...
...
openmmapi/src/NonbondedForceImpl.cpp
View file @
a4020466
...
@@ -30,7 +30,7 @@
...
@@ -30,7 +30,7 @@
* -------------------------------------------------------------------------- */
* -------------------------------------------------------------------------- */
#include "openmm/OpenMMException.h"
#include "openmm/OpenMMException.h"
#include "openmm/internal/
OpenMM
ContextImpl.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/internal/NonbondedForceImpl.h"
#include "openmm/internal/NonbondedForceImpl.h"
#include "openmm/kernels.h"
#include "openmm/kernels.h"
#include <sstream>
#include <sstream>
...
@@ -47,7 +47,7 @@ NonbondedForceImpl::NonbondedForceImpl(NonbondedForce& owner) : owner(owner) {
...
@@ -47,7 +47,7 @@ NonbondedForceImpl::NonbondedForceImpl(NonbondedForce& owner) : owner(owner) {
NonbondedForceImpl
::~
NonbondedForceImpl
()
{
NonbondedForceImpl
::~
NonbondedForceImpl
()
{
}
}
void
NonbondedForceImpl
::
initialize
(
OpenMM
ContextImpl
&
context
)
{
void
NonbondedForceImpl
::
initialize
(
ContextImpl
&
context
)
{
kernel
=
context
.
getPlatform
().
createKernel
(
CalcNonbondedForceKernel
::
Name
(),
context
);
kernel
=
context
.
getPlatform
().
createKernel
(
CalcNonbondedForceKernel
::
Name
(),
context
);
// Check for errors in the specification of exceptions.
// Check for errors in the specification of exceptions.
...
@@ -86,11 +86,11 @@ void NonbondedForceImpl::initialize(OpenMMContextImpl& context) {
...
@@ -86,11 +86,11 @@ void NonbondedForceImpl::initialize(OpenMMContextImpl& context) {
dynamic_cast
<
CalcNonbondedForceKernel
&>
(
kernel
.
getImpl
()).
initialize
(
context
.
getSystem
(),
owner
);
dynamic_cast
<
CalcNonbondedForceKernel
&>
(
kernel
.
getImpl
()).
initialize
(
context
.
getSystem
(),
owner
);
}
}
void
NonbondedForceImpl
::
calcForces
(
OpenMM
ContextImpl
&
context
,
Stream
&
forces
)
{
void
NonbondedForceImpl
::
calcForces
(
ContextImpl
&
context
,
Stream
&
forces
)
{
dynamic_cast
<
CalcNonbondedForceKernel
&>
(
kernel
.
getImpl
()).
executeForces
(
context
);
dynamic_cast
<
CalcNonbondedForceKernel
&>
(
kernel
.
getImpl
()).
executeForces
(
context
);
}
}
double
NonbondedForceImpl
::
calcEnergy
(
OpenMM
ContextImpl
&
context
)
{
double
NonbondedForceImpl
::
calcEnergy
(
ContextImpl
&
context
)
{
return
dynamic_cast
<
CalcNonbondedForceKernel
&>
(
kernel
.
getImpl
()).
executeEnergy
(
context
);
return
dynamic_cast
<
CalcNonbondedForceKernel
&>
(
kernel
.
getImpl
()).
executeEnergy
(
context
);
}
}
...
...
openmmapi/src/OpenMMContext.cpp
View file @
a4020466
...
@@ -29,51 +29,51 @@
...
@@ -29,51 +29,51 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
* -------------------------------------------------------------------------- */
#include "openmm/
OpenMM
Context.h"
#include "openmm/Context.h"
#include "openmm/internal/
OpenMM
ContextImpl.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/OpenMMException.h"
#include "openmm/OpenMMException.h"
using
namespace
OpenMM
;
using
namespace
OpenMM
;
using
namespace
std
;
using
namespace
std
;
OpenMM
Context
::
OpenMM
Context
(
System
&
system
,
Integrator
&
integrator
)
{
Context
::
Context
(
System
&
system
,
Integrator
&
integrator
)
{
impl
=
new
OpenMM
ContextImpl
(
*
this
,
system
,
integrator
,
0
);
impl
=
new
ContextImpl
(
*
this
,
system
,
integrator
,
0
);
}
}
OpenMM
Context
::
OpenMM
Context
(
System
&
system
,
Integrator
&
integrator
,
Platform
&
platform
)
{
Context
::
Context
(
System
&
system
,
Integrator
&
integrator
,
Platform
&
platform
)
{
impl
=
new
OpenMM
ContextImpl
(
*
this
,
system
,
integrator
,
&
platform
);
impl
=
new
ContextImpl
(
*
this
,
system
,
integrator
,
&
platform
);
}
}
OpenMM
Context
::~
OpenMM
Context
()
{
Context
::~
Context
()
{
delete
impl
;
delete
impl
;
}
}
const
System
&
OpenMM
Context
::
getSystem
()
const
{
const
System
&
Context
::
getSystem
()
const
{
return
impl
->
getSystem
();
return
impl
->
getSystem
();
}
}
System
&
OpenMM
Context
::
getSystem
()
{
System
&
Context
::
getSystem
()
{
return
impl
->
getSystem
();
return
impl
->
getSystem
();
}
}
const
Integrator
&
OpenMM
Context
::
getIntegrator
()
const
{
const
Integrator
&
Context
::
getIntegrator
()
const
{
return
impl
->
getIntegrator
();
return
impl
->
getIntegrator
();
}
}
Integrator
&
OpenMM
Context
::
getIntegrator
()
{
Integrator
&
Context
::
getIntegrator
()
{
return
impl
->
getIntegrator
();
return
impl
->
getIntegrator
();
}
}
const
Platform
&
OpenMM
Context
::
getPlatform
()
const
{
const
Platform
&
Context
::
getPlatform
()
const
{
return
impl
->
getPlatform
();
return
impl
->
getPlatform
();
}
}
Platform
&
OpenMM
Context
::
getPlatform
()
{
Platform
&
Context
::
getPlatform
()
{
return
impl
->
getPlatform
();
return
impl
->
getPlatform
();
}
}
State
OpenMM
Context
::
getState
(
int
types
)
const
{
State
Context
::
getState
(
int
types
)
const
{
State
state
(
impl
->
getTime
(),
impl
->
getSystem
().
getNumParticles
(),
State
::
DataType
(
types
));
State
state
(
impl
->
getTime
(),
impl
->
getSystem
().
getNumParticles
(),
State
::
DataType
(
types
));
if
(
types
&
State
::
Energy
)
if
(
types
&
State
::
Energy
)
state
.
setEnergy
(
impl
->
calcKineticEnergy
(),
impl
->
calcPotentialEnergy
());
state
.
setEnergy
(
impl
->
calcKineticEnergy
(),
impl
->
calcPotentialEnergy
());
...
@@ -92,34 +92,34 @@ State OpenMMContext::getState(int types) const {
...
@@ -92,34 +92,34 @@ State OpenMMContext::getState(int types) const {
return
state
;
return
state
;
}
}
void
OpenMM
Context
::
setTime
(
double
time
)
{
void
Context
::
setTime
(
double
time
)
{
impl
->
setTime
(
time
);
impl
->
setTime
(
time
);
}
}
void
OpenMM
Context
::
setPositions
(
const
vector
<
Vec3
>&
positions
)
{
void
Context
::
setPositions
(
const
vector
<
Vec3
>&
positions
)
{
if
((
int
)
positions
.
size
()
!=
impl
->
getSystem
().
getNumParticles
())
if
((
int
)
positions
.
size
()
!=
impl
->
getSystem
().
getNumParticles
())
throw
OpenMMException
(
"Called setPositions() on a
n OpenMM
Context with the wrong number of positions"
);
throw
OpenMMException
(
"Called setPositions() on a
Context with the wrong number of positions"
);
impl
->
getPositions
().
loadFromArray
(
&
positions
[
0
]);
impl
->
getPositions
().
loadFromArray
(
&
positions
[
0
]);
}
}
void
OpenMM
Context
::
setVelocities
(
const
vector
<
Vec3
>&
velocities
)
{
void
Context
::
setVelocities
(
const
vector
<
Vec3
>&
velocities
)
{
if
((
int
)
velocities
.
size
()
!=
impl
->
getSystem
().
getNumParticles
())
if
((
int
)
velocities
.
size
()
!=
impl
->
getSystem
().
getNumParticles
())
throw
OpenMMException
(
"Called setVelocities() on a
n OpenMM
Context with the wrong number of velocities"
);
throw
OpenMMException
(
"Called setVelocities() on a
Context with the wrong number of velocities"
);
impl
->
getVelocities
().
loadFromArray
(
&
velocities
[
0
]);
impl
->
getVelocities
().
loadFromArray
(
&
velocities
[
0
]);
}
}
double
OpenMM
Context
::
getParameter
(
const
string
&
name
)
{
double
Context
::
getParameter
(
const
string
&
name
)
{
return
impl
->
getParameter
(
name
);
return
impl
->
getParameter
(
name
);
}
}
void
OpenMM
Context
::
setParameter
(
const
string
&
name
,
double
value
)
{
void
Context
::
setParameter
(
const
string
&
name
,
double
value
)
{
impl
->
setParameter
(
name
,
value
);
impl
->
setParameter
(
name
,
value
);
}
}
void
OpenMM
Context
::
reinitialize
()
{
void
Context
::
reinitialize
()
{
System
&
system
=
impl
->
getSystem
();
System
&
system
=
impl
->
getSystem
();
Integrator
&
integrator
=
impl
->
getIntegrator
();
Integrator
&
integrator
=
impl
->
getIntegrator
();
Platform
&
platform
=
impl
->
getPlatform
();
Platform
&
platform
=
impl
->
getPlatform
();
delete
impl
;
delete
impl
;
impl
=
new
OpenMM
ContextImpl
(
*
this
,
system
,
integrator
,
&
platform
);
impl
=
new
ContextImpl
(
*
this
,
system
,
integrator
,
&
platform
);
}
}
openmmapi/src/OpenMMContextImpl.cpp
View file @
a4020466
...
@@ -35,7 +35,7 @@
...
@@ -35,7 +35,7 @@
#include "openmm/System.h"
#include "openmm/System.h"
#include "openmm/kernels.h"
#include "openmm/kernels.h"
#include "openmm/internal/ForceImpl.h"
#include "openmm/internal/ForceImpl.h"
#include "openmm/internal/
OpenMM
ContextImpl.h"
#include "openmm/internal/ContextImpl.h"
#include <map>
#include <map>
#include <vector>
#include <vector>
...
@@ -44,7 +44,7 @@ using std::map;
...
@@ -44,7 +44,7 @@ using std::map;
using
std
::
vector
;
using
std
::
vector
;
using
std
::
string
;
using
std
::
string
;
OpenMM
ContextImpl
::
OpenMM
ContextImpl
(
OpenMM
Context
&
owner
,
System
&
system
,
Integrator
&
integrator
,
Platform
*
platform
)
:
ContextImpl
::
ContextImpl
(
Context
&
owner
,
System
&
system
,
Integrator
&
integrator
,
Platform
*
platform
)
:
owner
(
owner
),
system
(
system
),
owner
(
owner
),
system
(
system
),
integrator
(
integrator
),
platform
(
platform
),
integrator
(
integrator
),
platform
(
platform
),
platformData
(
NULL
)
platformData
(
NULL
)
...
@@ -65,7 +65,7 @@ OpenMMContextImpl::OpenMMContextImpl(OpenMMContext& owner, System& system, Integ
...
@@ -65,7 +65,7 @@ OpenMMContextImpl::OpenMMContextImpl(OpenMMContext& owner, System& system, Integ
if
(
platform
==
0
)
if
(
platform
==
0
)
this
->
platform
=
platform
=
&
Platform
::
findPlatform
(
kernelNames
);
this
->
platform
=
platform
=
&
Platform
::
findPlatform
(
kernelNames
);
else
if
(
!
platform
->
supportsKernels
(
kernelNames
))
else
if
(
!
platform
->
supportsKernels
(
kernelNames
))
throw
OpenMMException
(
"Specified a Platform for a
n OpenMM
Context which does not support all required kernels"
);
throw
OpenMMException
(
"Specified a Platform for a
Context which does not support all required kernels"
);
platform
->
contextCreated
(
*
this
);
platform
->
contextCreated
(
*
this
);
initializeForcesKernel
=
platform
->
createKernel
(
InitializeForcesKernel
::
Name
(),
*
this
);
initializeForcesKernel
=
platform
->
createKernel
(
InitializeForcesKernel
::
Name
(),
*
this
);
dynamic_cast
<
InitializeForcesKernel
&>
(
initializeForcesKernel
.
getImpl
()).
initialize
(
system
);
dynamic_cast
<
InitializeForcesKernel
&>
(
initializeForcesKernel
.
getImpl
()).
initialize
(
system
);
...
@@ -83,58 +83,58 @@ OpenMMContextImpl::OpenMMContextImpl(OpenMMContext& owner, System& system, Integ
...
@@ -83,58 +83,58 @@ OpenMMContextImpl::OpenMMContextImpl(OpenMMContext& owner, System& system, Integ
velocities
.
fillWithValue
(
&
zero
);
velocities
.
fillWithValue
(
&
zero
);
}
}
OpenMM
ContextImpl
::~
OpenMM
ContextImpl
()
{
ContextImpl
::~
ContextImpl
()
{
for
(
int
i
=
0
;
i
<
(
int
)
forceImpls
.
size
();
++
i
)
for
(
int
i
=
0
;
i
<
(
int
)
forceImpls
.
size
();
++
i
)
delete
forceImpls
[
i
];
delete
forceImpls
[
i
];
platform
->
contextDestroyed
(
*
this
);
platform
->
contextDestroyed
(
*
this
);
}
}
double
OpenMM
ContextImpl
::
getTime
()
const
{
double
ContextImpl
::
getTime
()
const
{
return
dynamic_cast
<
const
UpdateTimeKernel
&>
(
updateTimeKernel
.
getImpl
()).
getTime
(
*
this
);
return
dynamic_cast
<
const
UpdateTimeKernel
&>
(
updateTimeKernel
.
getImpl
()).
getTime
(
*
this
);
}
}
void
OpenMM
ContextImpl
::
setTime
(
double
t
)
{
void
ContextImpl
::
setTime
(
double
t
)
{
dynamic_cast
<
UpdateTimeKernel
&>
(
updateTimeKernel
.
getImpl
()).
setTime
(
*
this
,
t
);
dynamic_cast
<
UpdateTimeKernel
&>
(
updateTimeKernel
.
getImpl
()).
setTime
(
*
this
,
t
);
}
}
double
OpenMM
ContextImpl
::
getParameter
(
std
::
string
name
)
{
double
ContextImpl
::
getParameter
(
std
::
string
name
)
{
if
(
parameters
.
find
(
name
)
==
parameters
.
end
())
if
(
parameters
.
find
(
name
)
==
parameters
.
end
())
throw
OpenMMException
(
"Called getParameter() with invalid parameter name"
);
throw
OpenMMException
(
"Called getParameter() with invalid parameter name"
);
return
parameters
[
name
];
return
parameters
[
name
];
}
}
void
OpenMM
ContextImpl
::
setParameter
(
std
::
string
name
,
double
value
)
{
void
ContextImpl
::
setParameter
(
std
::
string
name
,
double
value
)
{
if
(
parameters
.
find
(
name
)
==
parameters
.
end
())
if
(
parameters
.
find
(
name
)
==
parameters
.
end
())
throw
OpenMMException
(
"Called setParameter() with invalid parameter name"
);
throw
OpenMMException
(
"Called setParameter() with invalid parameter name"
);
parameters
[
name
]
=
value
;
parameters
[
name
]
=
value
;
}
}
void
OpenMM
ContextImpl
::
calcForces
()
{
void
ContextImpl
::
calcForces
()
{
dynamic_cast
<
InitializeForcesKernel
&>
(
initializeForcesKernel
.
getImpl
()).
execute
(
*
this
);
dynamic_cast
<
InitializeForcesKernel
&>
(
initializeForcesKernel
.
getImpl
()).
execute
(
*
this
);
for
(
int
i
=
0
;
i
<
(
int
)
forceImpls
.
size
();
++
i
)
for
(
int
i
=
0
;
i
<
(
int
)
forceImpls
.
size
();
++
i
)
forceImpls
[
i
]
->
calcForces
(
*
this
,
forces
);
forceImpls
[
i
]
->
calcForces
(
*
this
,
forces
);
}
}
double
OpenMM
ContextImpl
::
calcKineticEnergy
()
{
double
ContextImpl
::
calcKineticEnergy
()
{
return
dynamic_cast
<
CalcKineticEnergyKernel
&>
(
kineticEnergyKernel
.
getImpl
()).
execute
(
*
this
);
return
dynamic_cast
<
CalcKineticEnergyKernel
&>
(
kineticEnergyKernel
.
getImpl
()).
execute
(
*
this
);
}
}
double
OpenMM
ContextImpl
::
calcPotentialEnergy
()
{
double
ContextImpl
::
calcPotentialEnergy
()
{
double
energy
=
0.0
;
double
energy
=
0.0
;
for
(
int
i
=
0
;
i
<
(
int
)
forceImpls
.
size
();
++
i
)
for
(
int
i
=
0
;
i
<
(
int
)
forceImpls
.
size
();
++
i
)
energy
+=
forceImpls
[
i
]
->
calcEnergy
(
*
this
);
energy
+=
forceImpls
[
i
]
->
calcEnergy
(
*
this
);
return
energy
;
return
energy
;
}
}
void
OpenMM
ContextImpl
::
updateContextState
()
{
void
ContextImpl
::
updateContextState
()
{
for
(
int
i
=
0
;
i
<
(
int
)
forceImpls
.
size
();
++
i
)
for
(
int
i
=
0
;
i
<
(
int
)
forceImpls
.
size
();
++
i
)
forceImpls
[
i
]
->
updateContextState
(
*
this
);
forceImpls
[
i
]
->
updateContextState
(
*
this
);
}
}
void
*
OpenMM
ContextImpl
::
getPlatformData
()
{
void
*
ContextImpl
::
getPlatformData
()
{
return
platformData
;
return
platformData
;
}
}
void
OpenMM
ContextImpl
::
setPlatformData
(
void
*
data
)
{
void
ContextImpl
::
setPlatformData
(
void
*
data
)
{
platformData
=
data
;
platformData
=
data
;
}
}
openmmapi/src/PeriodicTorsionForceImpl.cpp
View file @
a4020466
...
@@ -29,7 +29,7 @@
...
@@ -29,7 +29,7 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
* -------------------------------------------------------------------------- */
#include "openmm/internal/
OpenMM
ContextImpl.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/internal/PeriodicTorsionForceImpl.h"
#include "openmm/internal/PeriodicTorsionForceImpl.h"
#include "openmm/kernels.h"
#include "openmm/kernels.h"
...
@@ -44,16 +44,16 @@ PeriodicTorsionForceImpl::PeriodicTorsionForceImpl(PeriodicTorsionForce& owner)
...
@@ -44,16 +44,16 @@ PeriodicTorsionForceImpl::PeriodicTorsionForceImpl(PeriodicTorsionForce& owner)
PeriodicTorsionForceImpl
::~
PeriodicTorsionForceImpl
()
{
PeriodicTorsionForceImpl
::~
PeriodicTorsionForceImpl
()
{
}
}
void
PeriodicTorsionForceImpl
::
initialize
(
OpenMM
ContextImpl
&
context
)
{
void
PeriodicTorsionForceImpl
::
initialize
(
ContextImpl
&
context
)
{
kernel
=
context
.
getPlatform
().
createKernel
(
CalcPeriodicTorsionForceKernel
::
Name
(),
context
);
kernel
=
context
.
getPlatform
().
createKernel
(
CalcPeriodicTorsionForceKernel
::
Name
(),
context
);
dynamic_cast
<
CalcPeriodicTorsionForceKernel
&>
(
kernel
.
getImpl
()).
initialize
(
context
.
getSystem
(),
owner
);
dynamic_cast
<
CalcPeriodicTorsionForceKernel
&>
(
kernel
.
getImpl
()).
initialize
(
context
.
getSystem
(),
owner
);
}
}
void
PeriodicTorsionForceImpl
::
calcForces
(
OpenMM
ContextImpl
&
context
,
Stream
&
forces
)
{
void
PeriodicTorsionForceImpl
::
calcForces
(
ContextImpl
&
context
,
Stream
&
forces
)
{
dynamic_cast
<
CalcPeriodicTorsionForceKernel
&>
(
kernel
.
getImpl
()).
executeForces
(
context
);
dynamic_cast
<
CalcPeriodicTorsionForceKernel
&>
(
kernel
.
getImpl
()).
executeForces
(
context
);
}
}
double
PeriodicTorsionForceImpl
::
calcEnergy
(
OpenMM
ContextImpl
&
context
)
{
double
PeriodicTorsionForceImpl
::
calcEnergy
(
ContextImpl
&
context
)
{
return
dynamic_cast
<
CalcPeriodicTorsionForceKernel
&>
(
kernel
.
getImpl
()).
executeEnergy
(
context
);
return
dynamic_cast
<
CalcPeriodicTorsionForceKernel
&>
(
kernel
.
getImpl
()).
executeEnergy
(
context
);
}
}
...
...
openmmapi/src/RBTorsionForceImpl.cpp
View file @
a4020466
...
@@ -29,7 +29,7 @@
...
@@ -29,7 +29,7 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
* -------------------------------------------------------------------------- */
#include "openmm/internal/
OpenMM
ContextImpl.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/internal/RBTorsionForceImpl.h"
#include "openmm/internal/RBTorsionForceImpl.h"
#include "openmm/kernels.h"
#include "openmm/kernels.h"
...
@@ -44,16 +44,16 @@ RBTorsionForceImpl::RBTorsionForceImpl(RBTorsionForce& owner) : owner(owner) {
...
@@ -44,16 +44,16 @@ RBTorsionForceImpl::RBTorsionForceImpl(RBTorsionForce& owner) : owner(owner) {
RBTorsionForceImpl
::~
RBTorsionForceImpl
()
{
RBTorsionForceImpl
::~
RBTorsionForceImpl
()
{
}
}
void
RBTorsionForceImpl
::
initialize
(
OpenMM
ContextImpl
&
context
)
{
void
RBTorsionForceImpl
::
initialize
(
ContextImpl
&
context
)
{
kernel
=
context
.
getPlatform
().
createKernel
(
CalcRBTorsionForceKernel
::
Name
(),
context
);
kernel
=
context
.
getPlatform
().
createKernel
(
CalcRBTorsionForceKernel
::
Name
(),
context
);
dynamic_cast
<
CalcRBTorsionForceKernel
&>
(
kernel
.
getImpl
()).
initialize
(
context
.
getSystem
(),
owner
);
dynamic_cast
<
CalcRBTorsionForceKernel
&>
(
kernel
.
getImpl
()).
initialize
(
context
.
getSystem
(),
owner
);
}
}
void
RBTorsionForceImpl
::
calcForces
(
OpenMM
ContextImpl
&
context
,
Stream
&
forces
)
{
void
RBTorsionForceImpl
::
calcForces
(
ContextImpl
&
context
,
Stream
&
forces
)
{
dynamic_cast
<
CalcRBTorsionForceKernel
&>
(
kernel
.
getImpl
()).
executeForces
(
context
);
dynamic_cast
<
CalcRBTorsionForceKernel
&>
(
kernel
.
getImpl
()).
executeForces
(
context
);
}
}
double
RBTorsionForceImpl
::
calcEnergy
(
OpenMM
ContextImpl
&
context
)
{
double
RBTorsionForceImpl
::
calcEnergy
(
ContextImpl
&
context
)
{
return
dynamic_cast
<
CalcRBTorsionForceKernel
&>
(
kernel
.
getImpl
()).
executeEnergy
(
context
);
return
dynamic_cast
<
CalcRBTorsionForceKernel
&>
(
kernel
.
getImpl
()).
executeEnergy
(
context
);
}
}
...
...
openmmapi/src/VariableLangevinIntegrator.cpp
View file @
a4020466
...
@@ -30,8 +30,8 @@
...
@@ -30,8 +30,8 @@
* -------------------------------------------------------------------------- */
* -------------------------------------------------------------------------- */
#include "openmm/VariableLangevinIntegrator.h"
#include "openmm/VariableLangevinIntegrator.h"
#include "openmm/
OpenMM
Context.h"
#include "openmm/Context.h"
#include "openmm/internal/
OpenMM
ContextImpl.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/kernels.h"
#include "openmm/kernels.h"
#include <limits>
#include <limits>
#include <string>
#include <string>
...
@@ -48,7 +48,7 @@ VariableLangevinIntegrator::VariableLangevinIntegrator(double temperature, doubl
...
@@ -48,7 +48,7 @@ VariableLangevinIntegrator::VariableLangevinIntegrator(double temperature, doubl
setRandomNumberSeed
((
int
)
time
(
NULL
));
setRandomNumberSeed
((
int
)
time
(
NULL
));
}
}
void
VariableLangevinIntegrator
::
initialize
(
OpenMM
ContextImpl
&
contextRef
)
{
void
VariableLangevinIntegrator
::
initialize
(
ContextImpl
&
contextRef
)
{
context
=
&
contextRef
;
context
=
&
contextRef
;
kernel
=
context
->
getPlatform
().
createKernel
(
IntegrateVariableLangevinStepKernel
::
Name
(),
contextRef
);
kernel
=
context
->
getPlatform
().
createKernel
(
IntegrateVariableLangevinStepKernel
::
Name
(),
contextRef
);
dynamic_cast
<
IntegrateVariableLangevinStepKernel
&>
(
kernel
.
getImpl
()).
initialize
(
contextRef
.
getSystem
(),
*
this
);
dynamic_cast
<
IntegrateVariableLangevinStepKernel
&>
(
kernel
.
getImpl
()).
initialize
(
contextRef
.
getSystem
(),
*
this
);
...
...
openmmapi/src/VariableVerletIntegrator.cpp
View file @
a4020466
...
@@ -30,8 +30,8 @@
...
@@ -30,8 +30,8 @@
* -------------------------------------------------------------------------- */
* -------------------------------------------------------------------------- */
#include "openmm/VariableVerletIntegrator.h"
#include "openmm/VariableVerletIntegrator.h"
#include "openmm/
OpenMM
Context.h"
#include "openmm/Context.h"
#include "openmm/internal/
OpenMM
ContextImpl.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/kernels.h"
#include "openmm/kernels.h"
#include <limits>
#include <limits>
#include <string>
#include <string>
...
@@ -44,7 +44,7 @@ VariableVerletIntegrator::VariableVerletIntegrator(double errorTol) : errorTol(e
...
@@ -44,7 +44,7 @@ VariableVerletIntegrator::VariableVerletIntegrator(double errorTol) : errorTol(e
setConstraintTolerance
(
1e-4
);
setConstraintTolerance
(
1e-4
);
}
}
void
VariableVerletIntegrator
::
initialize
(
OpenMM
ContextImpl
&
contextRef
)
{
void
VariableVerletIntegrator
::
initialize
(
ContextImpl
&
contextRef
)
{
context
=
&
contextRef
;
context
=
&
contextRef
;
kernel
=
context
->
getPlatform
().
createKernel
(
IntegrateVariableVerletStepKernel
::
Name
(),
contextRef
);
kernel
=
context
->
getPlatform
().
createKernel
(
IntegrateVariableVerletStepKernel
::
Name
(),
contextRef
);
dynamic_cast
<
IntegrateVariableVerletStepKernel
&>
(
kernel
.
getImpl
()).
initialize
(
contextRef
.
getSystem
(),
*
this
);
dynamic_cast
<
IntegrateVariableVerletStepKernel
&>
(
kernel
.
getImpl
()).
initialize
(
contextRef
.
getSystem
(),
*
this
);
...
...
openmmapi/src/VerletIntegrator.cpp
View file @
a4020466
...
@@ -30,8 +30,8 @@
...
@@ -30,8 +30,8 @@
* -------------------------------------------------------------------------- */
* -------------------------------------------------------------------------- */
#include "openmm/VerletIntegrator.h"
#include "openmm/VerletIntegrator.h"
#include "openmm/
OpenMM
Context.h"
#include "openmm/Context.h"
#include "openmm/internal/
OpenMM
ContextImpl.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/kernels.h"
#include "openmm/kernels.h"
#include <string>
#include <string>
...
@@ -44,7 +44,7 @@ VerletIntegrator::VerletIntegrator(double stepSize) {
...
@@ -44,7 +44,7 @@ VerletIntegrator::VerletIntegrator(double stepSize) {
setConstraintTolerance
(
1e-4
);
setConstraintTolerance
(
1e-4
);
}
}
void
VerletIntegrator
::
initialize
(
OpenMM
ContextImpl
&
contextRef
)
{
void
VerletIntegrator
::
initialize
(
ContextImpl
&
contextRef
)
{
context
=
&
contextRef
;
context
=
&
contextRef
;
kernel
=
context
->
getPlatform
().
createKernel
(
IntegrateVerletStepKernel
::
Name
(),
contextRef
);
kernel
=
context
->
getPlatform
().
createKernel
(
IntegrateVerletStepKernel
::
Name
(),
contextRef
);
dynamic_cast
<
IntegrateVerletStepKernel
&>
(
kernel
.
getImpl
()).
initialize
(
contextRef
.
getSystem
(),
*
this
);
dynamic_cast
<
IntegrateVerletStepKernel
&>
(
kernel
.
getImpl
()).
initialize
(
contextRef
.
getSystem
(),
*
this
);
...
...
platforms/brook/include/BrookKernelFactory.h
View file @
a4020466
...
@@ -44,7 +44,7 @@ class BrookKernelFactory : public KernelFactory {
...
@@ -44,7 +44,7 @@ class BrookKernelFactory : public KernelFactory {
public:
public:
KernelImpl
*
createKernelImpl
(
std
::
string
name
,
const
Platform
&
platform
,
OpenMM
ContextImpl
&
context
)
const
;
KernelImpl
*
createKernelImpl
(
std
::
string
name
,
const
Platform
&
platform
,
ContextImpl
&
context
)
const
;
};
};
}
// namespace OpenMM
}
// namespace OpenMM
...
...
platforms/brook/include/BrookPlatform.h
View file @
a4020466
...
@@ -278,17 +278,17 @@ class OPENMM_EXPORT BrookPlatform : public Platform {
...
@@ -278,17 +278,17 @@ class OPENMM_EXPORT BrookPlatform : public Platform {
FILE
*
getLog
(
void
)
const
;
FILE
*
getLog
(
void
)
const
;
/**
/**
* This is called whenever a new
OpenMM
Context is created. It gives the Platform a chance to initialize
* This is called whenever a new Context is created. It gives the Platform a chance to initialize
* the context and store platform-specific data in it.
* the context and store platform-specific data in it.
*/
*/
void
contextCreated
(
OpenMM
ContextImpl
&
context
)
const
;
void
contextCreated
(
ContextImpl
&
context
)
const
;
/**
/**
* This is called whenever a
n OpenMM
Context is deleted. It gives the Platform a chance to clean up
* This is called whenever a
Context is deleted. It gives the Platform a chance to clean up
* any platform-specific data that was stored in it.
* any platform-specific data that was stored in it.
*/
*/
void
contextDestroyed
(
OpenMM
ContextImpl
&
context
)
const
;
void
contextDestroyed
(
ContextImpl
&
context
)
const
;
/**
/**
* Get minSuggestedThreads
* Get minSuggestedThreads
...
...
platforms/brook/include/BrookStreamFactory.h
View file @
a4020466
...
@@ -77,7 +77,7 @@ class OPENMM_EXPORT BrookStreamFactory : public StreamFactory {
...
@@ -77,7 +77,7 @@ class OPENMM_EXPORT BrookStreamFactory : public StreamFactory {
* @return StreamImpl
* @return StreamImpl
*/
*/
StreamImpl
*
createStreamImpl
(
std
::
string
name
,
int
size
,
Stream
::
DataType
type
,
const
Platform
&
platform
,
OpenMM
ContextImpl
&
context
)
const
;
StreamImpl
*
createStreamImpl
(
std
::
string
name
,
int
size
,
Stream
::
DataType
type
,
const
Platform
&
platform
,
ContextImpl
&
context
)
const
;
/**
/**
* Create StreamImpl
* Create StreamImpl
...
...
platforms/brook/src/BrookBonded.h
View file @
a4020466
...
@@ -31,7 +31,7 @@
...
@@ -31,7 +31,7 @@
#include "BrookStreamImpl.h"
#include "BrookStreamImpl.h"
#include "BrookCommon.h"
#include "BrookCommon.h"
#include "openmm/
OpenMM
Context.h"
#include "openmm/Context.h"
#include "BrookBondParameters.h"
#include "BrookBondParameters.h"
namespace
OpenMM
{
namespace
OpenMM
{
...
...
platforms/brook/src/BrookCalcGBSAOBCForceKernel.cpp
View file @
a4020466
...
@@ -172,11 +172,11 @@ void BrookCalcGBSAOBCForceKernel::initialize( const System& system, const GBSAOB
...
@@ -172,11 +172,11 @@ void BrookCalcGBSAOBCForceKernel::initialize( const System& system, const GBSAOB
/**
/**
* Compute forces given particle coordinates
* Compute forces given particle coordinates
*
*
* @param context
OpenMM
ContextImpl context
* @param context ContextImpl context
*
*
*/
*/
void
BrookCalcGBSAOBCForceKernel
::
executeForces
(
OpenMM
ContextImpl
&
context
){
void
BrookCalcGBSAOBCForceKernel
::
executeForces
(
ContextImpl
&
context
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -193,13 +193,13 @@ void BrookCalcGBSAOBCForceKernel::executeForces( OpenMMContextImpl& context ){
...
@@ -193,13 +193,13 @@ void BrookCalcGBSAOBCForceKernel::executeForces( OpenMMContextImpl& context ){
/**
/**
* Execute the kernel to calculate the OBC energy
* Execute the kernel to calculate the OBC energy
*
*
* @param context
OpenMM
ContextImpl context
* @param context ContextImpl context
*
*
* @return energy
* @return energy
*
*
*/
*/
double
BrookCalcGBSAOBCForceKernel
::
executeEnergy
(
OpenMM
ContextImpl
&
context
){
double
BrookCalcGBSAOBCForceKernel
::
executeEnergy
(
ContextImpl
&
context
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
...
platforms/brook/src/BrookCalcGBSAOBCForceKernel.h
View file @
a4020466
...
@@ -72,7 +72,7 @@ class BrookCalcGBSAOBCForceKernel : public CalcGBSAOBCForceKernel {
...
@@ -72,7 +72,7 @@ class BrookCalcGBSAOBCForceKernel : public CalcGBSAOBCForceKernel {
*
*
*/
*/
void
executeForces
(
OpenMM
ContextImpl
&
context
);
void
executeForces
(
ContextImpl
&
context
);
/**
/**
* Execute the kernel to calculate the energy.
* Execute the kernel to calculate the energy.
...
@@ -84,7 +84,7 @@ class BrookCalcGBSAOBCForceKernel : public CalcGBSAOBCForceKernel {
...
@@ -84,7 +84,7 @@ class BrookCalcGBSAOBCForceKernel : public CalcGBSAOBCForceKernel {
*
*
*/
*/
double
executeEnergy
(
OpenMM
ContextImpl
&
context
);
double
executeEnergy
(
ContextImpl
&
context
);
/**
/**
* Set log file reference
* Set log file reference
...
...
platforms/brook/src/BrookCalcHarmonicAngleForceKernel.cpp
View file @
a4020466
...
@@ -171,11 +171,11 @@ void BrookCalcHarmonicAngleForceKernel::initialize( const System& system, const
...
@@ -171,11 +171,11 @@ void BrookCalcHarmonicAngleForceKernel::initialize( const System& system, const
/**
/**
* Compute forces given particle coordinates
* Compute forces given particle coordinates
*
*
* @param context
OpenMM
ContextImpl context
* @param context ContextImpl context
*
*
*/
*/
void
BrookCalcHarmonicAngleForceKernel
::
executeForces
(
OpenMM
ContextImpl
&
context
){
void
BrookCalcHarmonicAngleForceKernel
::
executeForces
(
ContextImpl
&
context
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -195,13 +195,13 @@ void BrookCalcHarmonicAngleForceKernel::executeForces( OpenMMContextImpl& contex
...
@@ -195,13 +195,13 @@ void BrookCalcHarmonicAngleForceKernel::executeForces( OpenMMContextImpl& contex
/**
/**
* Execute the kernel to calculate the energy
* Execute the kernel to calculate the energy
*
*
* @param context
OpenMM
ContextImpl context
* @param context ContextImpl context
*
*
* @return potential energy
* @return potential energy
*
*
*/
*/
double
BrookCalcHarmonicAngleForceKernel
::
executeEnergy
(
OpenMM
ContextImpl
&
context
){
double
BrookCalcHarmonicAngleForceKernel
::
executeEnergy
(
ContextImpl
&
context
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
...
platforms/brook/src/BrookCalcHarmonicAngleForceKernel.h
View file @
a4020466
...
@@ -72,7 +72,7 @@ class BrookCalcHarmonicAngleForceKernel : public CalcHarmonicAngleForceKernel {
...
@@ -72,7 +72,7 @@ class BrookCalcHarmonicAngleForceKernel : public CalcHarmonicAngleForceKernel {
*
*
*/
*/
void
executeForces
(
OpenMM
ContextImpl
&
context
);
void
executeForces
(
ContextImpl
&
context
);
/**
/**
* Execute the kernel to calculate the energy.
* Execute the kernel to calculate the energy.
...
@@ -83,7 +83,7 @@ class BrookCalcHarmonicAngleForceKernel : public CalcHarmonicAngleForceKernel {
...
@@ -83,7 +83,7 @@ class BrookCalcHarmonicAngleForceKernel : public CalcHarmonicAngleForceKernel {
*
*
*/
*/
double
executeEnergy
(
OpenMM
ContextImpl
&
context
);
double
executeEnergy
(
ContextImpl
&
context
);
/**
/**
* Set log file reference
* Set log file reference
...
...
platforms/brook/src/BrookCalcHarmonicBondForceKernel.cpp
View file @
a4020466
...
@@ -177,11 +177,11 @@ void BrookCalcHarmonicBondForceKernel::initialize( const System& system, const H
...
@@ -177,11 +177,11 @@ void BrookCalcHarmonicBondForceKernel::initialize( const System& system, const H
/**
/**
* Compute forces given particle coordinates
* Compute forces given particle coordinates
*
*
* @param context
OpenMM
ContextImpl context
* @param context ContextImpl context
*
*
*/
*/
void
BrookCalcHarmonicBondForceKernel
::
executeForces
(
OpenMM
ContextImpl
&
context
){
void
BrookCalcHarmonicBondForceKernel
::
executeForces
(
ContextImpl
&
context
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -201,13 +201,13 @@ void BrookCalcHarmonicBondForceKernel::executeForces( OpenMMContextImpl& context
...
@@ -201,13 +201,13 @@ void BrookCalcHarmonicBondForceKernel::executeForces( OpenMMContextImpl& context
/**
/**
* Execute the kernel to calculate the energy
* Execute the kernel to calculate the energy
*
*
* @param context
OpenMM
ContextImpl context
* @param context ContextImpl context
*
*
* @return potential energy
* @return potential energy
*
*
*/
*/
double
BrookCalcHarmonicBondForceKernel
::
executeEnergy
(
OpenMM
ContextImpl
&
context
){
double
BrookCalcHarmonicBondForceKernel
::
executeEnergy
(
ContextImpl
&
context
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
...
platforms/brook/src/BrookCalcHarmonicBondForceKernel.h
View file @
a4020466
...
@@ -72,7 +72,7 @@ class BrookCalcHarmonicBondForceKernel : public CalcHarmonicBondForceKernel {
...
@@ -72,7 +72,7 @@ class BrookCalcHarmonicBondForceKernel : public CalcHarmonicBondForceKernel {
*
*
*/
*/
void
executeForces
(
OpenMM
ContextImpl
&
context
);
void
executeForces
(
ContextImpl
&
context
);
/**
/**
* Execute the kernel to calculate the energy.
* Execute the kernel to calculate the energy.
...
@@ -83,7 +83,7 @@ class BrookCalcHarmonicBondForceKernel : public CalcHarmonicBondForceKernel {
...
@@ -83,7 +83,7 @@ class BrookCalcHarmonicBondForceKernel : public CalcHarmonicBondForceKernel {
*
*
*/
*/
double
executeEnergy
(
OpenMM
ContextImpl
&
context
);
double
executeEnergy
(
ContextImpl
&
context
);
/**
/**
* Set log file reference
* Set log file reference
...
...
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