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tsoc
openmm
Commits
16bd6601
Commit
16bd6601
authored
May 24, 2013
by
peastman
Browse files
Created OpenCL implementation of DrudeSCFIntegrator
parent
c78efcbd
Changes
6
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6 changed files
with
434 additions
and
1 deletion
+434
-1
plugins/drude/platforms/cuda/src/CudaDrudeKernels.cpp
plugins/drude/platforms/cuda/src/CudaDrudeKernels.cpp
+2
-0
plugins/drude/platforms/cuda/src/CudaDrudeKernels.h
plugins/drude/platforms/cuda/src/CudaDrudeKernels.h
+1
-1
plugins/drude/platforms/opencl/src/OpenCLDrudeKernelFactory.cpp
...s/drude/platforms/opencl/src/OpenCLDrudeKernelFactory.cpp
+3
-0
plugins/drude/platforms/opencl/src/OpenCLDrudeKernels.cpp
plugins/drude/platforms/opencl/src/OpenCLDrudeKernels.cpp
+239
-0
plugins/drude/platforms/opencl/src/OpenCLDrudeKernels.h
plugins/drude/platforms/opencl/src/OpenCLDrudeKernels.h
+45
-0
plugins/drude/platforms/opencl/tests/TestOpenCLDrudeSCFIntegrator.cpp
...e/platforms/opencl/tests/TestOpenCLDrudeSCFIntegrator.cpp
+144
-0
No files found.
plugins/drude/platforms/cuda/src/CudaDrudeKernels.cpp
View file @
16bd6601
...
...
@@ -334,6 +334,8 @@ private:
};
CudaIntegrateDrudeSCFStepKernel
::~
CudaIntegrateDrudeSCFStepKernel
()
{
if
(
minimizerPos
!=
NULL
)
lbfgs_free
(
minimizerPos
);
}
void
CudaIntegrateDrudeSCFStepKernel
::
initialize
(
const
System
&
system
,
const
DrudeSCFIntegrator
&
integrator
,
const
DrudeForce
&
force
)
{
...
...
plugins/drude/platforms/cuda/src/CudaDrudeKernels.h
View file @
16bd6601
...
...
@@ -122,7 +122,7 @@ private:
class
CudaIntegrateDrudeSCFStepKernel
:
public
IntegrateDrudeSCFStepKernel
{
public:
CudaIntegrateDrudeSCFStepKernel
(
std
::
string
name
,
const
Platform
&
platform
,
CudaContext
&
cu
)
:
IntegrateDrudeSCFStepKernel
(
name
,
platform
),
cu
(
cu
)
{
IntegrateDrudeSCFStepKernel
(
name
,
platform
),
cu
(
cu
)
,
minimizerPos
(
NULL
)
{
}
~
CudaIntegrateDrudeSCFStepKernel
();
/**
...
...
plugins/drude/platforms/opencl/src/OpenCLDrudeKernelFactory.cpp
View file @
16bd6601
...
...
@@ -43,6 +43,7 @@ extern "C" void registerKernelFactories() {
OpenCLDrudeKernelFactory
*
factory
=
new
OpenCLDrudeKernelFactory
();
platform
.
registerKernelFactory
(
CalcDrudeForceKernel
::
Name
(),
factory
);
platform
.
registerKernelFactory
(
IntegrateDrudeLangevinStepKernel
::
Name
(),
factory
);
platform
.
registerKernelFactory
(
IntegrateDrudeSCFStepKernel
::
Name
(),
factory
);
}
catch
(
std
::
exception
ex
)
{
// Ignore
...
...
@@ -65,5 +66,7 @@ KernelImpl* OpenCLDrudeKernelFactory::createKernelImpl(std::string name, const P
return
new
OpenCLCalcDrudeForceKernel
(
name
,
platform
,
cl
);
if
(
name
==
IntegrateDrudeLangevinStepKernel
::
Name
())
return
new
OpenCLIntegrateDrudeLangevinStepKernel
(
name
,
platform
,
cl
);
if
(
name
==
IntegrateDrudeSCFStepKernel
::
Name
())
return
new
OpenCLIntegrateDrudeSCFStepKernel
(
name
,
platform
,
cl
);
throw
OpenMMException
((
std
::
string
(
"Tried to create kernel with illegal kernel name '"
)
+
name
+
"'"
).
c_str
());
}
plugins/drude/platforms/opencl/src/OpenCLDrudeKernels.cpp
View file @
16bd6601
...
...
@@ -42,6 +42,13 @@
using
namespace
OpenMM
;
using
namespace
std
;
static
void
setPosqCorrectionArg
(
OpenCLContext
&
cl
,
cl
::
Kernel
&
kernel
,
int
index
)
{
if
(
cl
.
getUseMixedPrecision
())
kernel
.
setArg
<
cl
::
Buffer
>
(
index
,
cl
.
getPosqCorrection
().
getDeviceBuffer
());
else
kernel
.
setArg
<
void
*>
(
index
,
NULL
);
}
class
OpenCLDrudeForceInfo
:
public
OpenCLForceInfo
{
public:
OpenCLDrudeForceInfo
(
const
DrudeForce
&
force
)
:
OpenCLForceInfo
(
0
),
force
(
force
)
{
...
...
@@ -310,3 +317,235 @@ void OpenCLIntegrateDrudeLangevinStepKernel::execute(ContextImpl& context, const
double
OpenCLIntegrateDrudeLangevinStepKernel
::
computeKineticEnergy
(
ContextImpl
&
context
,
const
DrudeLangevinIntegrator
&
integrator
)
{
return
cl
.
getIntegrationUtilities
().
computeKineticEnergy
(
0.5
*
integrator
.
getStepSize
());
}
class
OpenCLIntegrateDrudeSCFStepKernel
::
ReorderListener
:
public
OpenCLContext
::
ReorderListener
{
public:
ReorderListener
(
OpenCLContext
&
cl
,
const
vector
<
int
>&
drudeParticles
,
vector
<
int
>&
reorderedDrudeParticles
)
:
cl
(
cl
),
drudeParticles
(
drudeParticles
),
reorderedDrudeParticles
(
reorderedDrudeParticles
)
{
}
void
execute
()
{
const
vector
<
int
>&
order
=
cl
.
getAtomIndex
();
int
numParticles
=
order
.
size
();
vector
<
int
>
inverseOrder
(
numParticles
);
for
(
int
i
=
0
;
i
<
numParticles
;
i
++
)
inverseOrder
[
order
[
i
]]
=
i
;
int
numDrudeParticles
=
drudeParticles
.
size
();
for
(
int
i
=
0
;
i
<
numDrudeParticles
;
i
++
)
reorderedDrudeParticles
[
i
]
=
inverseOrder
[
drudeParticles
[
i
]];
}
private:
OpenCLContext
&
cl
;
const
vector
<
int
>&
drudeParticles
;
vector
<
int
>&
reorderedDrudeParticles
;
};
OpenCLIntegrateDrudeSCFStepKernel
::~
OpenCLIntegrateDrudeSCFStepKernel
()
{
if
(
minimizerPos
!=
NULL
)
lbfgs_free
(
minimizerPos
);
}
void
OpenCLIntegrateDrudeSCFStepKernel
::
initialize
(
const
System
&
system
,
const
DrudeSCFIntegrator
&
integrator
,
const
DrudeForce
&
force
)
{
cl
.
getPlatformData
().
initializeContexts
(
system
);
// Identify Drude particles.
for
(
int
i
=
0
;
i
<
force
.
getNumParticles
();
i
++
)
{
int
p
,
p1
,
p2
,
p3
,
p4
;
double
charge
,
polarizability
,
aniso12
,
aniso34
;
force
.
getParticleParameters
(
i
,
p
,
p1
,
p2
,
p3
,
p4
,
charge
,
polarizability
,
aniso12
,
aniso34
);
drudeParticles
.
push_back
(
p
);
reorderedDrudeParticles
.
push_back
(
p
);
}
cl
.
addReorderListener
(
new
ReorderListener
(
cl
,
drudeParticles
,
reorderedDrudeParticles
));
// Initialize the energy minimizer.
minimizerPos
=
lbfgs_malloc
(
drudeParticles
.
size
()
*
3
);
if
(
minimizerPos
==
NULL
)
throw
OpenMMException
(
"DrudeSCFIntegrator: Failed to allocate memory"
);
lbfgs_parameter_init
(
&
minimizerParams
);
minimizerParams
.
linesearch
=
LBFGS_LINESEARCH_BACKTRACKING_STRONG_WOLFE
;
// Create the kernels.
cl
::
Program
program
=
cl
.
createProgram
(
OpenCLKernelSources
::
verlet
,
""
);
kernel1
=
cl
::
Kernel
(
program
,
"integrateVerletPart1"
);
kernel2
=
cl
::
Kernel
(
program
,
"integrateVerletPart2"
);
prevStepSize
=
-
1.0
;
}
void
OpenCLIntegrateDrudeSCFStepKernel
::
execute
(
ContextImpl
&
context
,
const
DrudeSCFIntegrator
&
integrator
)
{
OpenCLIntegrationUtilities
&
integration
=
cl
.
getIntegrationUtilities
();
int
numAtoms
=
cl
.
getNumAtoms
();
double
dt
=
integrator
.
getStepSize
();
if
(
!
hasInitializedKernels
)
{
hasInitializedKernels
=
true
;
kernel1
.
setArg
<
cl_int
>
(
0
,
numAtoms
);
kernel1
.
setArg
<
cl
::
Buffer
>
(
1
,
cl
.
getIntegrationUtilities
().
getStepSize
().
getDeviceBuffer
());
kernel1
.
setArg
<
cl
::
Buffer
>
(
2
,
cl
.
getPosq
().
getDeviceBuffer
());
setPosqCorrectionArg
(
cl
,
kernel1
,
3
);
kernel1
.
setArg
<
cl
::
Buffer
>
(
4
,
cl
.
getVelm
().
getDeviceBuffer
());
kernel1
.
setArg
<
cl
::
Buffer
>
(
5
,
cl
.
getForce
().
getDeviceBuffer
());
kernel1
.
setArg
<
cl
::
Buffer
>
(
6
,
integration
.
getPosDelta
().
getDeviceBuffer
());
kernel2
.
setArg
<
cl_int
>
(
0
,
numAtoms
);
kernel2
.
setArg
<
cl
::
Buffer
>
(
1
,
cl
.
getIntegrationUtilities
().
getStepSize
().
getDeviceBuffer
());
kernel2
.
setArg
<
cl
::
Buffer
>
(
2
,
cl
.
getPosq
().
getDeviceBuffer
());
setPosqCorrectionArg
(
cl
,
kernel2
,
3
);
kernel2
.
setArg
<
cl
::
Buffer
>
(
4
,
cl
.
getVelm
().
getDeviceBuffer
());
kernel2
.
setArg
<
cl
::
Buffer
>
(
5
,
integration
.
getPosDelta
().
getDeviceBuffer
());
}
if
(
dt
!=
prevStepSize
)
{
if
(
cl
.
getUseDoublePrecision
()
||
cl
.
getUseMixedPrecision
())
{
vector
<
mm_double2
>
stepSizeVec
(
1
);
stepSizeVec
[
0
]
=
mm_double2
(
dt
,
dt
);
cl
.
getIntegrationUtilities
().
getStepSize
().
upload
(
stepSizeVec
);
}
else
{
vector
<
mm_float2
>
stepSizeVec
(
1
);
stepSizeVec
[
0
]
=
mm_float2
((
cl_float
)
dt
,
(
cl_float
)
dt
);
cl
.
getIntegrationUtilities
().
getStepSize
().
upload
(
stepSizeVec
);
}
prevStepSize
=
dt
;
}
// Call the first integration kernel.
cl
.
executeKernel
(
kernel1
,
numAtoms
);
// Apply constraints.
integration
.
applyConstraints
(
integrator
.
getConstraintTolerance
());
// Call the second integration kernel.
cl
.
executeKernel
(
kernel2
,
numAtoms
);
// Update the positions of virtual sites and Drude particles.
integration
.
computeVirtualSites
();
minimize
(
context
,
integrator
.
getMinimizationErrorTolerance
());
// Update the time and step count.
cl
.
setTime
(
cl
.
getTime
()
+
dt
);
cl
.
setStepCount
(
cl
.
getStepCount
()
+
1
);
// Reduce UI lag.
#ifdef WIN32
cl
.
getQueue
().
flush
();
#endif
}
double
OpenCLIntegrateDrudeSCFStepKernel
::
computeKineticEnergy
(
ContextImpl
&
context
,
const
DrudeSCFIntegrator
&
integrator
)
{
return
cl
.
getIntegrationUtilities
().
computeKineticEnergy
(
0.5
*
integrator
.
getStepSize
());
}
struct
MinimizerData
{
ContextImpl
&
context
;
OpenCLContext
&
cl
;
vector
<
int
>&
reorderedDrudeParticles
;
MinimizerData
(
ContextImpl
&
context
,
OpenCLContext
&
cl
,
vector
<
int
>&
reorderedDrudeParticles
)
:
context
(
context
),
cl
(
cl
),
reorderedDrudeParticles
(
reorderedDrudeParticles
)
{}
};
static
lbfgsfloatval_t
evaluate
(
void
*
instance
,
const
lbfgsfloatval_t
*
x
,
lbfgsfloatval_t
*
g
,
const
int
n
,
const
lbfgsfloatval_t
step
)
{
MinimizerData
*
data
=
reinterpret_cast
<
MinimizerData
*>
(
instance
);
ContextImpl
&
context
=
data
->
context
;
OpenCLContext
&
cl
=
data
->
cl
;
vector
<
int
>&
reorderedDrudeParticles
=
data
->
reorderedDrudeParticles
;
int
numDrudeParticles
=
reorderedDrudeParticles
.
size
();
// Set the particle positions.
cl
.
getPosq
().
download
(
cl
.
getPinnedBuffer
());
mm_double4
periodicBoxSize
=
cl
.
getPeriodicBoxSizeDouble
();
if
(
cl
.
getUseDoublePrecision
())
{
mm_double4
*
posq
=
(
mm_double4
*
)
cl
.
getPinnedBuffer
();
for
(
int
i
=
0
;
i
<
numDrudeParticles
;
++
i
)
{
mm_double4
&
p
=
posq
[
reorderedDrudeParticles
[
i
]];
mm_int4
offset
=
cl
.
getPosCellOffsets
()[
reorderedDrudeParticles
[
i
]];
p
.
x
=
x
[
3
*
i
]
+
offset
.
x
*
periodicBoxSize
.
x
;
p
.
y
=
x
[
3
*
i
+
1
]
+
offset
.
y
*
periodicBoxSize
.
y
;
p
.
z
=
x
[
3
*
i
+
2
]
+
offset
.
z
*
periodicBoxSize
.
z
;
}
}
else
{
mm_float4
*
posq
=
(
mm_float4
*
)
cl
.
getPinnedBuffer
();
for
(
int
i
=
0
;
i
<
numDrudeParticles
;
++
i
)
{
mm_float4
&
p
=
posq
[
reorderedDrudeParticles
[
i
]];
mm_int4
offset
=
cl
.
getPosCellOffsets
()[
reorderedDrudeParticles
[
i
]];
p
.
x
=
x
[
3
*
i
]
+
offset
.
x
*
periodicBoxSize
.
x
;
p
.
y
=
x
[
3
*
i
+
1
]
+
offset
.
y
*
periodicBoxSize
.
y
;
p
.
z
=
x
[
3
*
i
+
2
]
+
offset
.
z
*
periodicBoxSize
.
z
;
}
}
cl
.
getPosq
().
upload
(
cl
.
getPinnedBuffer
());
// Compute the forces and energy for this configuration.
double
energy
=
context
.
calcForcesAndEnergy
(
true
,
true
);
cl
.
getForce
().
download
(
cl
.
getPinnedBuffer
());
if
(
cl
.
getUseDoublePrecision
())
{
mm_double4
*
force
=
(
mm_double4
*
)
cl
.
getPinnedBuffer
();
for
(
int
i
=
0
;
i
<
numDrudeParticles
;
++
i
)
{
int
index
=
reorderedDrudeParticles
[
i
];
g
[
3
*
i
]
=
-
force
[
index
].
x
;
g
[
3
*
i
+
1
]
=
-
force
[
index
].
y
;
g
[
3
*
i
+
2
]
=
-
force
[
index
].
z
;
}
}
else
{
mm_float4
*
force
=
(
mm_float4
*
)
cl
.
getPinnedBuffer
();
for
(
int
i
=
0
;
i
<
numDrudeParticles
;
++
i
)
{
int
index
=
reorderedDrudeParticles
[
i
];
g
[
3
*
i
]
=
-
force
[
index
].
x
;
g
[
3
*
i
+
1
]
=
-
force
[
index
].
y
;
g
[
3
*
i
+
2
]
=
-
force
[
index
].
z
;
}
}
return
energy
;
}
void
OpenCLIntegrateDrudeSCFStepKernel
::
minimize
(
ContextImpl
&
context
,
double
tolerance
)
{
// Record the initial positions.
int
numDrudeParticles
=
reorderedDrudeParticles
.
size
();
cl
.
getPosq
().
download
(
cl
.
getPinnedBuffer
());
mm_double4
periodicBoxSize
=
cl
.
getPeriodicBoxSizeDouble
();
if
(
cl
.
getUseDoublePrecision
())
{
mm_double4
*
posq
=
(
mm_double4
*
)
cl
.
getPinnedBuffer
();
for
(
int
i
=
0
;
i
<
numDrudeParticles
;
++
i
)
{
mm_double4
p
=
posq
[
reorderedDrudeParticles
[
i
]];
mm_int4
offset
=
cl
.
getPosCellOffsets
()[
reorderedDrudeParticles
[
i
]];
minimizerPos
[
3
*
i
]
=
p
.
x
-
offset
.
x
*
periodicBoxSize
.
x
;
minimizerPos
[
3
*
i
+
1
]
=
p
.
y
-
offset
.
y
*
periodicBoxSize
.
y
;
minimizerPos
[
3
*
i
+
2
]
=
p
.
z
-
offset
.
z
*
periodicBoxSize
.
z
;
}
}
else
{
mm_float4
*
posq
=
(
mm_float4
*
)
cl
.
getPinnedBuffer
();
for
(
int
i
=
0
;
i
<
numDrudeParticles
;
++
i
)
{
mm_float4
p
=
posq
[
reorderedDrudeParticles
[
i
]];
mm_int4
offset
=
cl
.
getPosCellOffsets
()[
reorderedDrudeParticles
[
i
]];
minimizerPos
[
3
*
i
]
=
p
.
x
-
offset
.
x
*
periodicBoxSize
.
x
;
minimizerPos
[
3
*
i
+
1
]
=
p
.
y
-
offset
.
y
*
periodicBoxSize
.
y
;
minimizerPos
[
3
*
i
+
2
]
=
p
.
z
-
offset
.
z
*
periodicBoxSize
.
z
;
}
minimizerParams
.
xtol
=
1e-7
;
}
// Determine a normalization constant for scaling the tolerance.
double
norm
=
0.0
;
for
(
int
i
=
0
;
i
<
3
*
numDrudeParticles
;
i
++
)
norm
+=
minimizerPos
[
i
]
*
minimizerPos
[
i
];
norm
/=
numDrudeParticles
;
norm
=
(
norm
<
1
?
1
:
sqrt
(
norm
));
minimizerParams
.
epsilon
=
tolerance
/
norm
;
// Perform the minimization.
lbfgsfloatval_t
fx
;
MinimizerData
data
(
context
,
cl
,
reorderedDrudeParticles
);
lbfgs
(
numDrudeParticles
*
3
,
minimizerPos
,
&
fx
,
evaluate
,
NULL
,
&
data
,
&
minimizerParams
);
}
\ No newline at end of file
plugins/drude/platforms/opencl/src/OpenCLDrudeKernels.h
View file @
16bd6601
...
...
@@ -35,6 +35,7 @@
#include "openmm/DrudeKernels.h"
#include "OpenCLContext.h"
#include "OpenCLArray.h"
#include "lbfgs.h"
namespace
OpenMM
{
...
...
@@ -116,6 +117,50 @@ private:
cl
::
Kernel
kernel1
,
kernel2
;
};
/**
* This kernel is invoked by DrudeSCFIntegrator to take one time step
*/
class
OpenCLIntegrateDrudeSCFStepKernel
:
public
IntegrateDrudeSCFStepKernel
{
public:
OpenCLIntegrateDrudeSCFStepKernel
(
std
::
string
name
,
const
Platform
&
platform
,
OpenCLContext
&
cl
)
:
IntegrateDrudeSCFStepKernel
(
name
,
platform
),
cl
(
cl
),
hasInitializedKernels
(
false
),
minimizerPos
(
NULL
)
{
}
~
OpenCLIntegrateDrudeSCFStepKernel
();
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param integrator the DrudeSCFIntegrator this kernel will be used for
* @param force the DrudeForce to get particle parameters from
*/
void
initialize
(
const
System
&
system
,
const
DrudeSCFIntegrator
&
integrator
,
const
DrudeForce
&
force
);
/**
* Execute the kernel.
*
* @param context the context in which to execute this kernel
* @param integrator the DrudeSCFIntegrator this kernel is being used for
*/
void
execute
(
ContextImpl
&
context
,
const
DrudeSCFIntegrator
&
integrator
);
/**
* Compute the kinetic energy.
*
* @param context the context in which to execute this kernel
* @param integrator the DrudeSCFIntegrator this kernel is being used for
*/
double
computeKineticEnergy
(
ContextImpl
&
context
,
const
DrudeSCFIntegrator
&
integrator
);
private:
class
ReorderListener
;
void
minimize
(
ContextImpl
&
context
,
double
tolerance
);
OpenCLContext
&
cl
;
bool
hasInitializedKernels
;
double
prevStepSize
;
std
::
vector
<
int
>
drudeParticles
;
std
::
vector
<
int
>
reorderedDrudeParticles
;
lbfgsfloatval_t
*
minimizerPos
;
lbfgs_parameter_t
minimizerParams
;
cl
::
Kernel
kernel1
,
kernel2
;
};
}
// namespace OpenMM
#endif
/*OPENCL_DRUDE_KERNELS_H_*/
plugins/drude/platforms/opencl/tests/TestOpenCLDrudeSCFIntegrator.cpp
0 → 100644
View file @
16bd6601
/* -------------------------------------------------------------------------- *
* 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) 2013 Stanford University and the Authors. *
* Authors: 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. *
* -------------------------------------------------------------------------- */
/**
* This tests the OpenCL implementation of DrudeSCFIntegrator.
*/
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "openmm/NonbondedForce.h"
#include "openmm/Platform.h"
#include "openmm/System.h"
#include "openmm/VirtualSite.h"
#include "openmm/DrudeForce.h"
#include "openmm/DrudeSCFIntegrator.h"
#include "SimTKUtilities/SimTKOpenMMUtilities.h"
#include <iostream>
#include <vector>
using
namespace
OpenMM
;
using
namespace
std
;
extern
"C"
OPENMM_EXPORT
void
registerDrudeOpenCLKernelFactories
();
void
testWater
()
{
// Create a box of SWM4-NDP water molecules. This involves constraints, virtual sites,
// and Drude particles.
const
int
gridSize
=
4
;
const
int
numMolecules
=
gridSize
*
gridSize
*
gridSize
;
const
double
spacing
=
0.6
;
const
double
boxSize
=
spacing
*
(
gridSize
+
1
);
System
system
;
NonbondedForce
*
nonbonded
=
new
NonbondedForce
();
DrudeForce
*
drude
=
new
DrudeForce
();
system
.
addForce
(
nonbonded
);
system
.
addForce
(
drude
);
system
.
setDefaultPeriodicBoxVectors
(
Vec3
(
boxSize
,
0
,
0
),
Vec3
(
0
,
boxSize
,
0
),
Vec3
(
0
,
0
,
boxSize
));
nonbonded
->
setNonbondedMethod
(
NonbondedForce
::
CutoffPeriodic
);
nonbonded
->
setCutoffDistance
(
1.0
);
for
(
int
i
=
0
;
i
<
numMolecules
;
i
++
)
{
int
startIndex
=
system
.
getNumParticles
();
system
.
addParticle
(
15.6
);
// O
system
.
addParticle
(
0.4
);
// D
system
.
addParticle
(
1.0
);
// H1
system
.
addParticle
(
1.0
);
// H2
system
.
addParticle
(
0.0
);
// M
nonbonded
->
addParticle
(
1.71636
,
0.318395
,
0.21094
*
4.184
);
nonbonded
->
addParticle
(
-
1.71636
,
1
,
0
);
nonbonded
->
addParticle
(
0.55733
,
1
,
0
);
nonbonded
->
addParticle
(
0.55733
,
1
,
0
);
nonbonded
->
addParticle
(
-
1.11466
,
1
,
0
);
for
(
int
j
=
0
;
j
<
5
;
j
++
)
for
(
int
k
=
0
;
k
<
j
;
k
++
)
nonbonded
->
addException
(
startIndex
+
j
,
startIndex
+
k
,
0
,
1
,
0
);
system
.
addConstraint
(
startIndex
,
startIndex
+
2
,
0.09572
);
system
.
addConstraint
(
startIndex
,
startIndex
+
3
,
0.09572
);
system
.
addConstraint
(
startIndex
+
2
,
startIndex
+
3
,
0.15139
);
system
.
setVirtualSite
(
startIndex
+
4
,
new
ThreeParticleAverageSite
(
startIndex
,
startIndex
+
2
,
startIndex
+
3
,
0.786646558
,
0.106676721
,
0.106676721
));
drude
->
addParticle
(
startIndex
+
1
,
startIndex
,
-
1
,
-
1
,
-
1
,
-
1.71636
,
1.71636
*
1.71636
/
(
100000
*
4.184
),
1
,
1
);
}
vector
<
Vec3
>
positions
;
for
(
int
i
=
0
;
i
<
gridSize
;
i
++
)
for
(
int
j
=
0
;
j
<
gridSize
;
j
++
)
for
(
int
k
=
0
;
k
<
gridSize
;
k
++
)
{
Vec3
pos
(
i
*
spacing
,
j
*
spacing
,
k
*
spacing
);
positions
.
push_back
(
pos
);
positions
.
push_back
(
pos
);
positions
.
push_back
(
pos
+
Vec3
(
0.09572
,
0
,
0
));
positions
.
push_back
(
pos
+
Vec3
(
-
0.023999
,
0.092663
,
0
));
positions
.
push_back
(
pos
);
}
// Simulate it and check energy conservation and the total force on the Drude particles.
DrudeSCFIntegrator
integ
(
0.0005
);
Platform
&
platform
=
Platform
::
getPlatformByName
(
"OpenCL"
);
Context
context
(
system
,
integ
,
platform
);
context
.
setPositions
(
positions
);
context
.
applyConstraints
(
1e-5
);
context
.
setVelocitiesToTemperature
(
300.0
);
State
state
=
context
.
getState
(
State
::
Energy
);
double
initialEnergy
;
int
numSteps
=
1000
;
double
maxNorm
=
(
platform
.
getPropertyValue
(
context
,
"OpenCLPrecision"
)
==
"double"
?
1.0
:
5.0
);
for
(
int
i
=
0
;
i
<
numSteps
;
i
++
)
{
integ
.
step
(
1
);
state
=
context
.
getState
(
State
::
Energy
|
State
::
Forces
);
if
(
i
==
0
)
initialEnergy
=
state
.
getPotentialEnergy
()
+
state
.
getKineticEnergy
();
else
ASSERT_EQUAL_TOL
(
initialEnergy
,
state
.
getPotentialEnergy
()
+
state
.
getKineticEnergy
(),
0.01
);
const
vector
<
Vec3
>&
force
=
state
.
getForces
();
double
norm
=
0.0
;
for
(
int
j
=
1
;
j
<
(
int
)
force
.
size
();
j
+=
5
)
norm
+=
sqrt
(
force
[
j
].
dot
(
force
[
j
]));
norm
=
(
norm
/
numMolecules
);
ASSERT
(
norm
<
maxNorm
);
}
}
int
main
(
int
argc
,
char
*
argv
[])
{
try
{
registerDrudeOpenCLKernelFactories
();
if
(
argc
>
1
)
Platform
::
getPlatformByName
(
"OpenCL"
).
setPropertyDefaultValue
(
"OpenCLPrecision"
,
string
(
argv
[
1
]));
testWater
();
}
catch
(
const
std
::
exception
&
e
)
{
std
::
cout
<<
"exception: "
<<
e
.
what
()
<<
std
::
endl
;
std
::
cout
<<
"FAIL - ERROR. Test failed."
<<
std
::
endl
;
return
1
;
}
std
::
cout
<<
"Done"
<<
std
::
endl
;
return
0
;
}
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