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tsoc
openmm
Commits
14d3c584
Commit
14d3c584
authored
Aug 15, 2014
by
peastman
Browse files
Finished CPU implementation of CustomManyParticleForce
parent
be0d5cbe
Changes
6
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6 changed files
with
124 additions
and
155 deletions
+124
-155
openmmapi/include/openmm/internal/vectorize_sse.h
openmmapi/include/openmm/internal/vectorize_sse.h
+2
-2
platforms/cpu/include/CpuCustomManyParticleForce.h
platforms/cpu/include/CpuCustomManyParticleForce.h
+54
-60
platforms/cpu/src/CpuCustomManyParticleForce.cpp
platforms/cpu/src/CpuCustomManyParticleForce.cpp
+66
-56
platforms/cpu/src/CpuKernels.cpp
platforms/cpu/src/CpuKernels.cpp
+1
-2
platforms/cpu/tests/TestCpuCustomManyParticleForce.cpp
platforms/cpu/tests/TestCpuCustomManyParticleForce.cpp
+0
-35
tests/TestVectorize.cpp
tests/TestVectorize.cpp
+1
-0
No files found.
openmmapi/include/openmm/internal/vectorize_sse.h
View file @
14d3c584
...
...
@@ -250,8 +250,8 @@ static inline float dot4(const fvec4& v1, const fvec4& v2) {
}
static
inline
fvec4
cross
(
const
fvec4
&
v1
,
const
fvec4
&
v2
)
{
fvec4
temp
=
_mm_mul_ps
(
v
2
,
_mm_shuffle_ps
(
v
1
,
v
1
,
_MM_SHUFFLE
(
3
,
0
,
2
,
1
)))
-
_mm_mul_ps
(
v
1
,
_mm_shuffle_ps
(
v
2
,
v
2
,
_MM_SHUFFLE
(
3
,
0
,
2
,
1
)));
fvec4
temp
=
_mm_mul_ps
(
v
1
,
_mm_shuffle_ps
(
v
2
,
v
2
,
_MM_SHUFFLE
(
3
,
0
,
2
,
1
)))
-
_mm_mul_ps
(
v
2
,
_mm_shuffle_ps
(
v
1
,
v
1
,
_MM_SHUFFLE
(
3
,
0
,
2
,
1
)));
return
_mm_shuffle_ps
(
temp
,
temp
,
_MM_SHUFFLE
(
3
,
0
,
2
,
1
));
}
...
...
platforms/cpu/include/CpuCustomManyParticleForce.h
View file @
14d3c584
...
...
@@ -50,7 +50,7 @@ private:
class
DihedralTermInfo
;
class
ComputeForceTask
;
class
ThreadData
;
int
numParticlesPerSet
,
numPerParticleParameters
,
numTypes
;
int
numParticles
,
numParticlesPerSet
,
numPerParticleParameters
,
numTypes
;
bool
useCutoff
,
usePeriodic
;
RealOpenMM
cutoffDistance
;
RealOpenMM
periodicBoxSize
[
3
];
...
...
@@ -62,9 +62,7 @@ private:
std
::
vector
<
std
::
vector
<
int
>
>
particleOrder
;
std
::
vector
<
ThreadData
*>
threadData
;
// The following variables are used to make information accessible to the individual threads.
int
numParticles
;
float
*
posq
;
RealVec
const
*
atomCoordinates
;
RealOpenMM
**
particleParameters
;
const
std
::
map
<
std
::
string
,
double
>*
globalParameters
;
std
::
vector
<
AlignedArray
<
float
>
>*
threadForce
;
...
...
@@ -76,6 +74,10 @@ private:
*/
void
threadComputeForce
(
ThreadPool
&
threads
,
int
threadIndex
);
/**
* This is called recursively to loop over all possible combination of a set of particles and evaluate the
* interaction for each one.
*/
void
loopOverInteractions
(
std
::
vector
<
int
>&
availableParticles
,
std
::
vector
<
int
>&
particleSet
,
int
loopIndex
,
int
startIndex
,
RealOpenMM
**
particleParameters
,
float
*
forces
,
ThreadData
&
data
,
const
fvec4
&
boxSize
,
const
fvec4
&
invBoxSize
);
...
...
@@ -85,82 +87,72 @@ private:
@param particleSet the indices of the particles
@param posq atom coordinates in float format
@param atomCoordinates atom coordinates
@param particleParameters particle parameter values (particleParameters[particleIndex][parameterIndex])
@param forces force array (forces added)
@param totalEnergy total energy
--------------------------------------------------------------------------------------- */
void
calculateOneIxn
(
std
::
vector
<
int
>&
particleSet
,
RealOpenMM
**
particleParameters
,
float
*
forces
,
ThreadData
&
data
,
const
fvec4
&
boxSize
,
const
fvec4
&
invBoxSize
);
/**
* Calculate the interaction for one set of particles
*
* @param particleSet the indices of the particles
* @param particleParameters particle parameter values (particleParameters[particleIndex][parameterIndex])
* @param data information and workspace for the current thread
* @param boxSize the size of the periodic box
* @param invBoxSize the inverse size of the periodic box
*/
void
calculateOneIxn
(
std
::
vector
<
int
>&
particleSet
,
RealOpenMM
**
particleParameters
,
float
*
forces
,
ThreadData
&
data
,
const
fvec4
&
boxSize
,
const
fvec4
&
invBoxSize
);
/**
* Compute the displacement and squared distance between two points, optionally using
* periodic boundary conditions.
*/
void
getDeltaR
(
const
fvec4
&
posI
,
const
fvec4
&
posJ
,
fvec4
&
deltaR
,
float
&
r2
,
const
fvec4
&
boxSize
,
const
fvec4
&
invBoxSize
)
const
;
void
computeDelta
(
int
atom1
,
int
atom2
,
RealOpenMM
*
delta
,
const
OpenMM
::
RealVec
*
atomCoordinates
)
const
;
static
RealOpenMM
computeAngle
(
RealOpenMM
*
vec1
,
RealOpenMM
*
vec2
,
float
sign
);
void
computeDelta
(
const
fvec4
&
posI
,
const
fvec4
&
posJ
,
fvec4
&
deltaR
,
float
&
r2
,
const
fvec4
&
boxSize
,
const
fvec4
&
invBoxSize
)
const
;
static
float
computeAngle
(
const
fvec4
&
vi
,
const
fvec4
&
vj
,
float
v2i
,
float
v2j
,
float
sign
);
static
float
getDihedralAngleBetweenThreeVectors
(
const
fvec4
&
v1
,
const
fvec4
&
v2
,
const
fvec4
&
v3
,
fvec4
&
cross1
,
fvec4
&
cross2
,
const
fvec4
&
signVector
);
public:
/**---------------------------------------------------------------------------------------
Constructor
--------------------------------------------------------------------------------------- */
/**
* Create a new CpuCustomManyParticleForce.
*
* @param force the CustomManyParticleForce to create it for
* @param threads the thread pool to use
*/
CpuCustomManyParticleForce
(
const
OpenMM
::
CustomManyParticleForce
&
force
,
ThreadPool
&
threads
);
/**---------------------------------------------------------------------------------------
Destructor
--------------------------------------------------------------------------------------- */
~
CpuCustomManyParticleForce
();
/**---------------------------------------------------------------------------------------
Set the force to use a cutoff.
@param distance the cutoff distance
--------------------------------------------------------------------------------------- */
/**
* Set the force to use a cutoff.
*
* @param distance the cutoff distance
*/
void
setUseCutoff
(
RealOpenMM
distance
);
/**---------------------------------------------------------------------------------------
Set the force to use periodic boundary conditions. This requires that a cutoff has
already been set, and the smallest side of the periodic box is at least twice the cutoff
distance.
@param boxSize the X, Y, and Z widths of the periodic box
--------------------------------------------------------------------------------------- */
/**
* Set the force to use periodic boundary conditions. This requires that a cutoff has
* already been set, and the smallest side of the periodic box is at least twice the cutoff
* distance.
*
* @param boxSize the X, Y, and Z widths of the periodic box
*/
void
setPeriodic
(
OpenMM
::
RealVec
&
boxSize
);
/**---------------------------------------------------------------------------------------
Calculate the interaction
@param posq atom coordinates in float format
@param atomCoordinates atom coordinates
@param particleParameters particle parameter values (particleParameters[particleIndex][parameterIndex])
@param globalParameters the values of global parameters
@param forces force array (forces added)
@param totalEnergy total energy
--------------------------------------------------------------------------------------- */
void
calculateIxn
(
AlignedArray
<
float
>&
posq
,
std
::
vector
<
OpenMM
::
RealVec
>&
atomCoordinates
,
RealOpenMM
**
particleParameters
,
const
std
::
map
<
std
::
string
,
double
>&
globalParameters
,
/**
* Calculate the interaction.
*
* @param posq atom coordinates in float format
* @param particleParameters particle parameter values (particleParameters[particleIndex][parameterIndex])
* @param globalParameters the values of global parameters
* @param threadForce the collection of arrays for each thread to add forces to
* @param includeForce whether to compute forces
* @param includeEnergy whether to compute energy
* @param energy the total energy is added to this
*/
void
calculateIxn
(
AlignedArray
<
float
>&
posq
,
RealOpenMM
**
particleParameters
,
const
std
::
map
<
std
::
string
,
double
>&
globalParameters
,
std
::
vector
<
AlignedArray
<
float
>
>&
threadForce
,
bool
includeForces
,
bool
includeEnergy
,
double
&
energy
);
};
...
...
@@ -198,8 +190,7 @@ public:
int
p1
,
p2
,
p3
,
p4
,
variableIndex
;
Lepton
::
CompiledExpression
forceExpression
;
int
delta1
,
delta2
,
delta3
;
mutable
RealOpenMM
cross1
[
3
];
mutable
RealOpenMM
cross2
[
3
];
mutable
fvec4
cross1
,
cross2
;
DihedralTermInfo
(
const
std
::
string
&
name
,
const
std
::
vector
<
int
>&
atoms
,
const
Lepton
::
CompiledExpression
&
forceExpression
,
ThreadData
&
data
);
};
...
...
@@ -213,6 +204,9 @@ public:
std
::
vector
<
DistanceTermInfo
>
distanceTerms
;
std
::
vector
<
AngleTermInfo
>
angleTerms
;
std
::
vector
<
DihedralTermInfo
>
dihedralTerms
;
AlignedArray
<
fvec4
>
delta
;
std
::
vector
<
float
>
normDelta
;
std
::
vector
<
float
>
norm2Delta
;
double
energy
;
ThreadData
(
const
CustomManyParticleForce
&
force
,
Lepton
::
ParsedExpression
&
energyExpr
,
std
::
map
<
std
::
string
,
std
::
vector
<
int
>
>&
distances
,
std
::
map
<
std
::
string
,
std
::
vector
<
int
>
>&
angles
,
std
::
map
<
std
::
string
,
std
::
vector
<
int
>
>&
dihedrals
);
...
...
platforms/cpu/src/CpuCustomManyParticleForce.cpp
View file @
14d3c584
...
...
@@ -51,6 +51,7 @@ public:
CpuCustomManyParticleForce
::
CpuCustomManyParticleForce
(
const
CustomManyParticleForce
&
force
,
ThreadPool
&
threads
)
:
threads
(
threads
),
useCutoff
(
false
),
usePeriodic
(
false
),
neighborList
(
NULL
)
{
numParticles
=
force
.
getNumParticles
();
numParticlesPerSet
=
force
.
getNumParticlesPerSet
();
numPerParticleParameters
=
force
.
getNumPerParticleParameters
();
...
...
@@ -98,14 +99,12 @@ CpuCustomManyParticleForce::~CpuCustomManyParticleForce() {
delete
threadData
[
i
];
}
void
CpuCustomManyParticleForce
::
calculateIxn
(
AlignedArray
<
float
>&
posq
,
vector
<
RealVec
>&
atomCoordinates
,
RealOpenMM
**
particleParameters
,
void
CpuCustomManyParticleForce
::
calculateIxn
(
AlignedArray
<
float
>&
posq
,
RealOpenMM
**
particleParameters
,
const
map
<
string
,
double
>&
globalParameters
,
vector
<
AlignedArray
<
float
>
>&
threadForce
,
bool
includeForces
,
bool
includeEnergy
,
double
&
energy
)
{
// Record the parameters for the threads.
this
->
numParticles
=
atomCoordinates
.
size
();
this
->
posq
=
&
posq
[
0
];
this
->
atomCoordinates
=
&
atomCoordinates
[
0
];
this
->
particleParameters
=
particleParameters
;
this
->
globalParameters
=
&
globalParameters
;
this
->
threadForce
=
&
threadForce
;
...
...
@@ -220,7 +219,7 @@ void CpuCustomManyParticleForce::loopOverInteractions(vector<int>& availablePart
float
r2
;
for
(
int
j
=
0
;
j
<
loopIndex
&&
include
;
j
++
)
{
fvec4
pos2
(
posq
+
4
*
particleSet
[
j
]);
get
Delta
R
(
pos1
,
pos2
,
deltaR
,
r2
,
boxSize
,
invBoxSize
);
compute
Delta
(
pos1
,
pos2
,
deltaR
,
r2
,
boxSize
,
invBoxSize
);
include
&=
(
r2
<
cutoff2
);
}
}
...
...
@@ -266,29 +265,33 @@ void CpuCustomManyParticleForce::calculateOneIxn(vector<int>& particleSet, RealO
// Compute inter-particle deltas.
int
numDeltas
=
data
.
deltaPairs
.
size
();
RealOpenMM
delta
[
numDeltas
][
ReferenceForce
::
LastDeltaRIndex
];
for
(
int
i
=
0
;
i
<
numDeltas
;
i
++
)
computeDelta
(
permutedParticles
[
data
.
deltaPairs
[
i
].
first
],
permutedParticles
[
data
.
deltaPairs
[
i
].
second
],
delta
[
i
],
atomCoordinates
);
AlignedArray
<
fvec4
>&
delta
=
data
.
delta
;
vector
<
float
>&
normDelta
=
data
.
normDelta
;
vector
<
float
>&
norm2Delta
=
data
.
norm2Delta
;
for
(
int
i
=
0
;
i
<
numDeltas
;
i
++
)
{
int
p1
=
permutedParticles
[
data
.
deltaPairs
[
i
].
first
];
int
p2
=
permutedParticles
[
data
.
deltaPairs
[
i
].
second
];
computeDelta
(
fvec4
(
posq
+
4
*
p1
),
fvec4
(
posq
+
4
*
p2
),
delta
[
i
],
norm2Delta
[
i
],
boxSize
,
invBoxSize
);
normDelta
[
i
]
=
sqrtf
(
norm2Delta
[
i
]);
}
// Compute all of the variables the energy can depend on.
for
(
int
i
=
0
;
i
<
(
int
)
data
.
particleTerms
.
size
();
i
++
)
{
const
ParticleTermInfo
&
term
=
data
.
particleTerms
[
i
];
expressionSet
.
setVariable
(
term
.
variableIndex
,
atomCoordinates
[
permutedParticles
[
term
.
atom
]
][
term
.
component
]);
expressionSet
.
setVariable
(
term
.
variableIndex
,
posq
[
4
*
permutedParticles
[
term
.
atom
]
+
term
.
component
]);
}
for
(
int
i
=
0
;
i
<
(
int
)
data
.
distanceTerms
.
size
();
i
++
)
{
const
DistanceTermInfo
&
term
=
data
.
distanceTerms
[
i
];
expressionSet
.
setVariable
(
term
.
variableIndex
,
d
elta
[
term
.
delta
]
[
ReferenceForce
::
RIndex
]
);
expressionSet
.
setVariable
(
term
.
variableIndex
,
normD
elta
[
term
.
delta
]);
}
for
(
int
i
=
0
;
i
<
(
int
)
data
.
angleTerms
.
size
();
i
++
)
{
const
AngleTermInfo
&
term
=
data
.
angleTerms
[
i
];
expressionSet
.
setVariable
(
term
.
variableIndex
,
computeAngle
(
delta
[
term
.
delta1
],
delta
[
term
.
delta2
],
term
.
delta1Sign
*
term
.
delta2Sign
));
expressionSet
.
setVariable
(
term
.
variableIndex
,
computeAngle
(
delta
[
term
.
delta1
],
delta
[
term
.
delta2
],
norm2Delta
[
term
.
delta1
],
norm2Delta
[
term
.
delta2
],
term
.
delta1Sign
*
term
.
delta2Sign
));
}
for
(
int
i
=
0
;
i
<
(
int
)
data
.
dihedralTerms
.
size
();
i
++
)
{
const
DihedralTermInfo
&
term
=
data
.
dihedralTerms
[
i
];
RealOpenMM
dotDihedral
,
signOfDihedral
;
RealOpenMM
*
crossProduct
[]
=
{
term
.
cross1
,
term
.
cross2
};
expressionSet
.
setVariable
(
term
.
variableIndex
,
ReferenceBondIxn
::
getDihedralAngleBetweenThreeVectors
(
delta
[
term
.
delta1
],
delta
[
term
.
delta2
],
delta
[
term
.
delta3
],
crossProduct
,
&
dotDihedral
,
delta
[
term
.
delta1
],
&
signOfDihedral
,
1
));
expressionSet
.
setVariable
(
term
.
variableIndex
,
getDihedralAngleBetweenThreeVectors
(
delta
[
term
.
delta1
],
delta
[
term
.
delta2
],
delta
[
term
.
delta3
],
term
.
cross1
,
term
.
cross2
,
delta
[
term
.
delta1
]));
}
if
(
includeForces
)
{
...
...
@@ -309,8 +312,8 @@ void CpuCustomManyParticleForce::calculateOneIxn(vector<int>& particleSet, RealO
for
(
int
i
=
0
;
i
<
(
int
)
data
.
distanceTerms
.
size
();
i
++
)
{
const
DistanceTermInfo
&
term
=
data
.
distanceTerms
[
i
];
RealOpenMM
dEdR
=
(
RealOpenMM
)
(
term
.
forceExpression
.
evaluate
()
*
term
.
deltaSign
/
(
d
elta
[
term
.
delta
]
[
ReferenceForce
::
RIndex
]
));
fvec4
force
=
-
dEdR
*
fvec4
((
float
)
delta
[
term
.
delta
]
[
0
],
(
float
)
delta
[
term
.
delta
][
1
],
(
float
)
delta
[
term
.
delta
][
2
],
0.0
f
)
;
float
dEdR
=
(
float
)
(
term
.
forceExpression
.
evaluate
()
*
term
.
deltaSign
/
(
normD
elta
[
term
.
delta
]));
fvec4
force
=
-
dEdR
*
delta
[
term
.
delta
];
f
[
term
.
p1
]
-=
force
;
f
[
term
.
p2
]
+=
force
;
}
...
...
@@ -319,17 +322,15 @@ void CpuCustomManyParticleForce::calculateOneIxn(vector<int>& particleSet, RealO
for
(
int
i
=
0
;
i
<
(
int
)
data
.
angleTerms
.
size
();
i
++
)
{
const
AngleTermInfo
&
term
=
data
.
angleTerms
[
i
];
RealOpenMM
dEdTheta
=
(
RealOpenMM
)
term
.
forceExpression
.
evaluate
();
fvec4
delta1
((
float
)
delta
[
term
.
delta1
][
0
],
(
float
)
delta
[
term
.
delta1
][
1
],
(
float
)
delta
[
term
.
delta1
][
2
],
0.0
f
);
fvec4
delta2
((
float
)
delta
[
term
.
delta2
][
0
],
(
float
)
delta
[
term
.
delta2
][
1
],
(
float
)
delta
[
term
.
delta2
][
2
],
0.0
f
);
fvec4
thetaCross
=
cross
(
delta1
,
delta2
);
float
dEdTheta
=
(
float
)
term
.
forceExpression
.
evaluate
();
fvec4
thetaCross
=
cross
(
delta
[
term
.
delta1
],
delta
[
term
.
delta2
]);
float
lengthThetaCross
=
sqrtf
(
dot3
(
thetaCross
,
thetaCross
));
if
(
lengthThetaCross
<
1.0e-6
f
)
lengthThetaCross
=
1.0e-6
f
;
RealOpenMM
termA
=
dEdTheta
*
term
.
delta2Sign
/
(
d
elta
[
term
.
delta1
]
[
ReferenceForce
::
R2Index
]
*
lengthThetaCross
);
RealOpenMM
termC
=
-
dEdTheta
*
term
.
delta1Sign
/
(
d
elta
[
term
.
delta2
]
[
ReferenceForce
::
R2Index
]
*
lengthThetaCross
);
fvec4
deltaCross1
=
cross
(
delta
1
,
thetaCross
);
fvec4
deltaCross2
=
cross
(
delta
2
,
thetaCross
);
float
termA
=
dEdTheta
*
term
.
delta2Sign
/
(
norm2D
elta
[
term
.
delta1
]
*
lengthThetaCross
);
float
termC
=
-
dEdTheta
*
term
.
delta1Sign
/
(
norm2D
elta
[
term
.
delta2
]
*
lengthThetaCross
);
fvec4
deltaCross1
=
cross
(
delta
[
term
.
delta1
]
,
thetaCross
);
fvec4
deltaCross2
=
cross
(
delta
[
term
.
delta2
]
,
thetaCross
);
fvec4
force1
=
termA
*
deltaCross1
;
fvec4
force3
=
termC
*
deltaCross2
;
fvec4
force2
=
-
(
force1
+
force3
);
...
...
@@ -342,20 +343,19 @@ void CpuCustomManyParticleForce::calculateOneIxn(vector<int>& particleSet, RealO
for
(
int
i
=
0
;
i
<
(
int
)
data
.
dihedralTerms
.
size
();
i
++
)
{
const
DihedralTermInfo
&
term
=
data
.
dihedralTerms
[
i
];
RealOpenMM
dEdTheta
=
(
RealOpenMM
)
term
.
forceExpression
.
evaluate
();
RealOpenMM
internalF
[
4
][
3
];
RealOpenMM
forceFactors
[
4
];
RealOpenMM
normCross1
=
DOT3
(
term
.
cross1
,
term
.
cross1
);
RealOpenMM
normBC
=
delta
[
term
.
delta2
][
ReferenceForce
::
RIndex
];
float
dEdTheta
=
(
float
)
term
.
forceExpression
.
evaluate
();
float
normCross1
=
dot3
(
term
.
cross1
,
term
.
cross1
);
float
normBC
=
normDelta
[
term
.
delta2
];
float
forceFactors
[
4
];
forceFactors
[
0
]
=
(
-
dEdTheta
*
normBC
)
/
normCross1
;
RealOpenMM
normCross2
=
DOT
3
(
term
.
cross2
,
term
.
cross2
);
float
normCross2
=
dot
3
(
term
.
cross2
,
term
.
cross2
);
forceFactors
[
3
]
=
(
dEdTheta
*
normBC
)
/
normCross2
;
forceFactors
[
1
]
=
DOT
3
(
delta
[
term
.
delta1
],
delta
[
term
.
delta2
]);
forceFactors
[
1
]
/=
d
elta
[
term
.
delta2
]
[
ReferenceForce
::
R2Index
]
;
forceFactors
[
2
]
=
DOT
3
(
delta
[
term
.
delta3
],
delta
[
term
.
delta2
]);
forceFactors
[
2
]
/=
d
elta
[
term
.
delta2
]
[
ReferenceForce
::
R2Index
]
;
fvec4
force1
=
forceFactors
[
0
]
*
fvec4
((
float
)
term
.
cross1
[
0
],
(
float
)
term
.
cross1
[
1
],
(
float
)
term
.
cross1
[
2
],
0.0
f
)
;
fvec4
force4
=
forceFactors
[
3
]
*
fvec4
((
float
)
term
.
cross2
[
0
],
(
float
)
term
.
cross2
[
1
],
(
float
)
term
.
cross2
[
2
],
0.0
f
)
;
forceFactors
[
1
]
=
dot
3
(
delta
[
term
.
delta1
],
delta
[
term
.
delta2
]);
forceFactors
[
1
]
/=
norm2D
elta
[
term
.
delta2
];
forceFactors
[
2
]
=
dot
3
(
delta
[
term
.
delta3
],
delta
[
term
.
delta2
]);
forceFactors
[
2
]
/=
norm2D
elta
[
term
.
delta2
];
fvec4
force1
=
forceFactors
[
0
]
*
term
.
cross1
;
fvec4
force4
=
forceFactors
[
3
]
*
term
.
cross2
;
fvec4
s
=
forceFactors
[
1
]
*
force1
-
forceFactors
[
2
]
*
force4
;
f
[
term
.
p1
]
+=
force1
;
f
[
term
.
p2
]
-=
force1
-
s
;
...
...
@@ -377,27 +377,7 @@ void CpuCustomManyParticleForce::calculateOneIxn(vector<int>& particleSet, RealO
data
.
energy
+=
data
.
energyExpression
.
evaluate
();
}
void
CpuCustomManyParticleForce
::
computeDelta
(
int
atom1
,
int
atom2
,
RealOpenMM
*
delta
,
const
OpenMM
::
RealVec
*
atomCoordinates
)
const
{
if
(
usePeriodic
)
ReferenceForce
::
getDeltaRPeriodic
(
atomCoordinates
[
atom1
],
atomCoordinates
[
atom2
],
periodicBoxSize
,
delta
);
else
ReferenceForce
::
getDeltaR
(
atomCoordinates
[
atom1
],
atomCoordinates
[
atom2
],
delta
);
}
RealOpenMM
CpuCustomManyParticleForce
::
computeAngle
(
RealOpenMM
*
vec1
,
RealOpenMM
*
vec2
,
float
sign
)
{
RealOpenMM
dot
=
DOT3
(
vec1
,
vec2
)
*
sign
;
RealOpenMM
cosine
=
dot
/
SQRT
((
vec1
[
ReferenceForce
::
R2Index
]
*
vec2
[
ReferenceForce
::
R2Index
]));
RealOpenMM
angle
;
if
(
cosine
>=
1
)
angle
=
0
;
else
if
(
cosine
<=
-
1
)
angle
=
PI_M
;
else
angle
=
ACOS
(
cosine
);
return
angle
;
}
void
CpuCustomManyParticleForce
::
getDeltaR
(
const
fvec4
&
posI
,
const
fvec4
&
posJ
,
fvec4
&
deltaR
,
float
&
r2
,
const
fvec4
&
boxSize
,
const
fvec4
&
invBoxSize
)
const
{
void
CpuCustomManyParticleForce
::
computeDelta
(
const
fvec4
&
posI
,
const
fvec4
&
posJ
,
fvec4
&
deltaR
,
float
&
r2
,
const
fvec4
&
boxSize
,
const
fvec4
&
invBoxSize
)
const
{
deltaR
=
posJ
-
posI
;
if
(
usePeriodic
)
{
fvec4
base
=
round
(
deltaR
*
invBoxSize
)
*
boxSize
;
...
...
@@ -406,6 +386,32 @@ void CpuCustomManyParticleForce::getDeltaR(const fvec4& posI, const fvec4& posJ,
r2
=
dot3
(
deltaR
,
deltaR
);
}
float
CpuCustomManyParticleForce
::
computeAngle
(
const
fvec4
&
vi
,
const
fvec4
&
vj
,
float
v2i
,
float
v2j
,
float
sign
)
{
float
dot
=
dot3
(
vi
,
vj
)
*
sign
;
float
cosine
=
dot
/
sqrtf
(
v2i
*
v2j
);
if
(
cosine
>
0.99
f
||
cosine
<
-
0.99
f
)
{
// We're close to the singularity in acos(), so take the cross product and use asin() instead.
fvec4
cross12
=
cross
(
vi
,
vj
);
float
scale
=
v2i
*
v2j
;
float
angle
=
asinf
(
sqrtf
(
dot3
(
cross12
,
cross12
)
/
scale
));
if
(
cosine
<
0.0
f
)
angle
=
(
float
)
(
M_PI
-
angle
);
return
angle
;
}
return
acosf
(
cosine
);
}
float
CpuCustomManyParticleForce
::
getDihedralAngleBetweenThreeVectors
(
const
fvec4
&
v1
,
const
fvec4
&
v2
,
const
fvec4
&
v3
,
fvec4
&
cross1
,
fvec4
&
cross2
,
const
fvec4
&
signVector
)
{
cross1
=
cross
(
v1
,
v2
);
cross2
=
cross
(
v2
,
v3
);
float
angle
=
computeAngle
(
cross1
,
cross2
,
dot3
(
cross1
,
cross1
),
dot3
(
cross2
,
cross2
),
1.0
f
);
float
dotProduct
=
dot3
(
signVector
,
cross2
);
if
(
dotProduct
<
0
)
angle
=
-
angle
;
return
angle
;
}
CpuCustomManyParticleForce
::
ParticleTermInfo
::
ParticleTermInfo
(
const
string
&
name
,
int
atom
,
int
component
,
const
Lepton
::
CompiledExpression
&
forceExpression
,
ThreadData
&
data
)
:
name
(
name
),
atom
(
atom
),
component
(
component
),
forceExpression
(
forceExpression
)
{
variableIndex
=
data
.
expressionSet
.
getVariableIndex
(
name
);
...
...
@@ -471,6 +477,10 @@ CpuCustomManyParticleForce::ThreadData::ThreadData(const CustomManyParticleForce
expressionSet
.
registerExpression
(
angleTerms
[
i
].
forceExpression
);
for
(
int
i
=
0
;
i
<
dihedralTerms
.
size
();
i
++
)
expressionSet
.
registerExpression
(
dihedralTerms
[
i
].
forceExpression
);
int
numDeltas
=
deltaPairs
.
size
();
delta
.
resize
(
numDeltas
);
normDelta
.
resize
(
numDeltas
);
norm2Delta
.
resize
(
numDeltas
);
}
void
CpuCustomManyParticleForce
::
ThreadData
::
requestDeltaPair
(
int
p1
,
int
p2
,
int
&
pairIndex
,
float
&
pairSign
,
bool
allowReversed
)
{
...
...
platforms/cpu/src/CpuKernels.cpp
View file @
14d3c584
...
...
@@ -869,7 +869,6 @@ void CpuCalcCustomManyParticleForceKernel::initialize(const System& system, cons
}
double
CpuCalcCustomManyParticleForceKernel
::
execute
(
ContextImpl
&
context
,
bool
includeForces
,
bool
includeEnergy
)
{
vector
<
RealVec
>&
posData
=
extractPositions
(
context
);
map
<
string
,
double
>
globalParameters
;
for
(
int
i
=
0
;
i
<
(
int
)
globalParameterNames
.
size
();
i
++
)
globalParameters
[
globalParameterNames
[
i
]]
=
context
.
getParameter
(
globalParameterNames
[
i
]);
...
...
@@ -881,7 +880,7 @@ double CpuCalcCustomManyParticleForceKernel::execute(ContextImpl& context, bool
ixn
->
setPeriodic
(
box
);
}
double
energy
=
0
;
ixn
->
calculateIxn
(
data
.
posq
,
posData
,
particleParamArray
,
globalParameters
,
data
.
threadForce
,
includeForces
,
includeEnergy
,
energy
);
ixn
->
calculateIxn
(
data
.
posq
,
particleParamArray
,
globalParameters
,
data
.
threadForce
,
includeForces
,
includeEnergy
,
energy
);
return
energy
;
}
...
...
platforms/cpu/tests/TestCpuCustomManyParticleForce.cpp
View file @
14d3c584
...
...
@@ -464,40 +464,6 @@ void testTypeFilters() {
ASSERT_EQUAL_TOL
(
expectedEnergy
,
state
.
getPotentialEnergy
(),
1e-5
);
}
#include <sys/time.h>
void
benchmark
()
{
int
numParticles
=
5000
;
double
boxSize
=
5.0
;
CustomManyParticleForce
*
force
=
new
CustomManyParticleForce
(
3
,
"C*(1+3*cos(theta1)*cos(theta2)*cos(theta3))/(r12*r13*r23)^3;"
"theta1=angle(p1,p2,p3); theta2=angle(p2,p3,p1); theta3=angle(p3,p1,p2);"
"r12=distance(p1,p2); r13=distance(p1,p3); r23=distance(p2,p3)"
);
force
->
addGlobalParameter
(
"C"
,
1.5
);
force
->
setNonbondedMethod
(
CustomManyParticleForce
::
CutoffPeriodic
);
force
->
setCutoffDistance
(
0.6
);
vector
<
double
>
params
;
vector
<
Vec3
>
positions
;
System
system
;
OpenMM_SFMT
::
SFMT
sfmt
;
init_gen_rand
(
0
,
sfmt
);
for
(
int
i
=
0
;
i
<
numParticles
;
i
++
)
{
force
->
addParticle
(
params
);
positions
.
push_back
(
Vec3
(
genrand_real2
(
sfmt
),
genrand_real2
(
sfmt
),
genrand_real2
(
sfmt
))
*
boxSize
);
system
.
addParticle
(
1.0
);
}
system
.
setDefaultPeriodicBoxVectors
(
Vec3
(
boxSize
,
0
,
0
),
Vec3
(
0
,
boxSize
,
0
),
Vec3
(
0
,
0
,
boxSize
));
system
.
addForce
(
force
);
VerletIntegrator
integrator
(
0.001
);
CpuPlatform
platform
;
Context
context
(
system
,
integrator
,
platform
);
context
.
setPositions
(
positions
);
timeval
t1
,
t2
;
gettimeofday
(
&
t1
,
NULL
);
State
state
=
context
.
getState
(
State
::
Forces
|
State
::
Energy
);
gettimeofday
(
&
t2
,
NULL
);
printf
(
"%g %g
\n
"
,
state
.
getPotentialEnergy
(),
(
t2
.
tv_sec
-
t1
.
tv_sec
)
+
1e-6
*
(
t2
.
tv_usec
-
t1
.
tv_usec
));
}
int
main
()
{
try
{
testNoCutoff
();
...
...
@@ -508,7 +474,6 @@ int main() {
testParameters
();
testTabulatedFunctions
();
testTypeFilters
();
benchmark
();
}
catch
(
const
exception
&
e
)
{
cout
<<
"exception: "
<<
e
.
what
()
<<
endl
;
...
...
tests/TestVectorize.cpp
View file @
14d3c584
...
...
@@ -153,6 +153,7 @@ void testMathFunctions() {
ASSERT
(
any
(
f1
>
0.5
));
ASSERT
(
!
any
(
f1
>
2.0
));
ASSERT_VEC4_EQUAL
(
blend
(
f1
,
f2
,
ivec4
(
-
1
,
0
,
-
1
,
0
)),
1.1
,
1.9
,
1.3
,
-
3.8
);
ASSERT_VEC4_EQUAL
(
cross
(
f1
,
f2
),
3.91
,
-
1.84
,
-
1.61
,
0.0
);
}
void
testTranspose
()
{
...
...
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