Skip to content
GitLab
Menu
Projects
Groups
Snippets
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
tsoc
openmm
Commits
b723e4af
Commit
b723e4af
authored
Mar 22, 2013
by
Peter Eastman
Browse files
Replaced lots of tabs with spaces
parent
93c467b2
Changes
33
Hide whitespace changes
Inline
Side-by-side
Showing
20 changed files
with
138 additions
and
138 deletions
+138
-138
CMakeLists.txt
CMakeLists.txt
+2
-2
platforms/cuda/include/windowsExportCuda.h
platforms/cuda/include/windowsExportCuda.h
+2
-2
platforms/cuda/src/CudaBondedUtilities.cpp
platforms/cuda/src/CudaBondedUtilities.cpp
+1
-1
platforms/cuda/src/CudaContext.cpp
platforms/cuda/src/CudaContext.cpp
+5
-5
platforms/cuda/src/CudaParallelKernels.cpp
platforms/cuda/src/CudaParallelKernels.cpp
+1
-1
platforms/cuda/src/CudaPlatform.cpp
platforms/cuda/src/CudaPlatform.cpp
+7
-7
platforms/cuda/src/kernels/pme.cu
platforms/cuda/src/kernels/pme.cu
+21
-21
platforms/cuda/tests/TestCudaEwald.cpp
platforms/cuda/tests/TestCudaEwald.cpp
+4
-4
platforms/opencl/include/windowsExportOpenCL.h
platforms/opencl/include/windowsExportOpenCL.h
+2
-2
platforms/opencl/src/OpenCLParallelKernels.cpp
platforms/opencl/src/OpenCLParallelKernels.cpp
+1
-1
platforms/opencl/src/kernels/customGBEnergyN2.cl
platforms/opencl/src/kernels/customGBEnergyN2.cl
+1
-1
platforms/opencl/src/kernels/customGBEnergyN2_cpu.cl
platforms/opencl/src/kernels/customGBEnergyN2_cpu.cl
+1
-1
platforms/reference/src/ReferenceKernels.cpp
platforms/reference/src/ReferenceKernels.cpp
+8
-8
platforms/reference/src/SimTKReference/PME.h
platforms/reference/src/SimTKReference/PME.h
+11
-11
platforms/reference/src/SimTKReference/ReferenceBondIxn.cpp
platforms/reference/src/SimTKReference/ReferenceBondIxn.cpp
+7
-7
platforms/reference/src/SimTKReference/ReferenceLJCoulomb14.cpp
...rms/reference/src/SimTKReference/ReferenceLJCoulomb14.cpp
+2
-2
platforms/reference/src/SimTKReference/ReferenceLJCoulombIxn.cpp
...ms/reference/src/SimTKReference/ReferenceLJCoulombIxn.cpp
+5
-5
platforms/reference/src/SimTKReference/fftpack.cpp
platforms/reference/src/SimTKReference/fftpack.cpp
+55
-55
platforms/reference/src/SimTKReference/fftpack.h
platforms/reference/src/SimTKReference/fftpack.h
+1
-1
platforms/reference/src/gbsa/CpuGBVI.cpp
platforms/reference/src/gbsa/CpuGBVI.cpp
+1
-1
No files found.
CMakeLists.txt
View file @
b723e4af
...
...
@@ -167,7 +167,7 @@ SET(OPENMM_SVN_REVISION "${OPENMM_SVN_REVISION}" CACHE STRING "subversion reposi
ADD_DEFINITIONS
(
-DOPENMM_LIBRARY_NAME=
${
OPENMM_LIBRARY_NAME
}
-DOPENMM_MAJOR_VERSION=
${
OPENMM_MAJOR_VERSION
}
-DOPENMM_MINOR_VERSION=
${
OPENMM_MINOR_VERSION
}
-DOPENMM_BUILD_VERSION=
${
OPENMM_BUILD_VERSION
}
)
-DOPENMM_BUILD_VERSION=
${
OPENMM_BUILD_VERSION
}
)
# CMake quotes automatically when building Visual Studio projects but we need
# to add them ourselves for Linux or Cygwin. Two cases to avoid duplicate quotes
...
...
@@ -251,7 +251,7 @@ SET(API_REL_INCLUDE_FILES) # start these out empty
SET
(
API_ABS_INCLUDE_FILES
)
FOREACH
(
dir
${
API_INCLUDE_DIRS
}
)
FILE
(
GLOB fullpaths
${
dir
}
/*.h
)
# returns full pathnames
FILE
(
GLOB fullpaths
${
dir
}
/*.h
)
# returns full pathnames
SET
(
API_ABS_INCLUDE_FILES
${
API_ABS_INCLUDE_FILES
}
${
fullpaths
}
)
FOREACH
(
pathname
${
fullpaths
}
)
...
...
platforms/cuda/include/windowsExportCuda.h
View file @
b723e4af
...
...
@@ -30,9 +30,9 @@
#if defined(OPENMM_CUDA_BUILDING_SHARED_LIBRARY)
#define OPENMM_EXPORT_CUDA __declspec(dllexport)
#elif defined(OPENMM_CUDA_BUILDING_STATIC_LIBRARY) || defined(OPENMM_CUDA_USE_STATIC_LIBRARIES)
#define OPENMM_EXPORT_CUDA
#define OPENMM_EXPORT_CUDA
#else
#define OPENMM_EXPORT_CUDA __declspec(dllimport) // i.e., a client of a shared library
#define OPENMM_EXPORT_CUDA __declspec(dllimport) // i.e., a client of a shared library
#endif
#else
#define OPENMM_EXPORT_CUDA // Linux, Mac
...
...
platforms/cuda/src/CudaBondedUtilities.cpp
View file @
b723e4af
...
...
@@ -79,7 +79,7 @@ void CudaBondedUtilities::initialize(const System& system) {
int
startAtom
=
0
;
while
(
startAtom
<
numAtoms
)
{
int
width
=
min
(
numAtoms
-
startAtom
,
4
);
int
paddedWidth
=
(
width
==
3
?
4
:
width
);
int
paddedWidth
=
(
width
==
3
?
4
:
width
);
vector
<
unsigned
int
>
indexVec
(
paddedWidth
*
numBonds
);
for
(
int
bond
=
0
;
bond
<
numBonds
;
bond
++
)
{
for
(
int
atom
=
0
;
atom
<
width
;
atom
++
)
...
...
platforms/cuda/src/CudaContext.cpp
View file @
b723e4af
...
...
@@ -322,11 +322,11 @@ static bool compileInWindows(const string &command) {
ZeroMemory
(
&
pi
,
sizeof
(
pi
)
);
vector
<
char
>
args
(
std
::
max
(
1000
,
(
int
)
fullcommand
.
size
()
+
1
));
strcpy
(
&
args
[
0
],
fullcommand
.
c_str
());
si
.
dwFlags
=
STARTF_USESHOWWINDOW
;
si
.
dwFlags
=
STARTF_USESHOWWINDOW
;
si
.
wShowWindow
=
SW_HIDE
;
if
(
!
CreateProcess
(
NULL
,
&
args
[
0
],
NULL
,
NULL
,
FALSE
,
0
,
NULL
,
NULL
,
&
si
,
&
pi
))
{
return
-
1
;
}
if
(
!
CreateProcess
(
NULL
,
&
args
[
0
],
NULL
,
NULL
,
FALSE
,
0
,
NULL
,
NULL
,
&
si
,
&
pi
))
{
return
-
1
;
}
WaitForSingleObject
(
pi
.
hProcess
,
INFINITE
);
return
0
;
}
...
...
@@ -933,7 +933,7 @@ void CudaContext::reorderAtomsImpl(bool enforcePeriodic) {
Real4
padding
=
{
0
,
0
,
0
,
0
};
vector
<
Real4
>
oldPosq
(
paddedNumAtoms
,
padding
);
vector
<
Real4
>
oldPosqCorrection
(
paddedNumAtoms
,
padding
);
Mixed4
paddingMixed
=
{
0
,
0
,
0
,
0
};
Mixed4
paddingMixed
=
{
0
,
0
,
0
,
0
};
vector
<
Mixed4
>
oldVelm
(
paddedNumAtoms
,
paddingMixed
);
posq
->
download
(
oldPosq
);
velm
->
download
(
oldVelm
);
...
...
platforms/cuda/src/CudaParallelKernels.cpp
View file @
b723e4af
...
...
@@ -45,7 +45,7 @@ if (result != CUDA_SUCCESS) { \
#include <Windows.h>
static
long
long
getTime
()
{
FILETIME
ft
;
GetSystemTimeAsFileTime
(
&
ft
);
// 100-nanoseconds since 1-1-1601
GetSystemTimeAsFileTime
(
&
ft
);
// 100-nanoseconds since 1-1-1601
ULARGE_INTEGER
result
;
result
.
LowPart
=
ft
.
dwLowDateTime
;
result
.
HighPart
=
ft
.
dwHighDateTime
;
...
...
platforms/cuda/src/CudaPlatform.cpp
View file @
b723e4af
...
...
@@ -86,18 +86,18 @@ CudaPlatform::CudaPlatform() {
setPropertyDefaultValue
(
CudaPrecision
(),
"single"
);
#ifdef _MSC_VER
char
*
bindir
=
getenv
(
"CUDA_BIN_PATH"
);
string
nvcc
=
(
bindir
==
NULL
?
"nvcc.exe"
:
string
(
bindir
)
+
"
\\
nvcc.exe"
);
string
nvcc
=
(
bindir
==
NULL
?
"nvcc.exe"
:
string
(
bindir
)
+
"
\\
nvcc.exe"
);
int
length
=
GetShortPathName
(
nvcc
.
c_str
(),
NULL
,
0
);
if
(
length
>
0
)
{
vector
<
char
>
shortName
(
length
);
GetShortPathName
(
nvcc
.
c_str
(),
&
shortName
[
0
],
length
);
nvcc
=
string
(
&
shortName
[
0
]);
}
if
(
length
>
0
)
{
vector
<
char
>
shortName
(
length
);
GetShortPathName
(
nvcc
.
c_str
(),
&
shortName
[
0
],
length
);
nvcc
=
string
(
&
shortName
[
0
]);
}
setPropertyDefaultValue
(
CudaCompiler
(),
nvcc
);
setPropertyDefaultValue
(
CudaTempDirectory
(),
string
(
getenv
(
"TEMP"
)));
#else
char
*
compiler
=
getenv
(
"OPENMM_CUDA_COMPILER"
);
string
nvcc
=
(
compiler
==
NULL
?
"/usr/local/cuda/bin/nvcc"
:
string
(
compiler
));
string
nvcc
=
(
compiler
==
NULL
?
"/usr/local/cuda/bin/nvcc"
:
string
(
compiler
));
setPropertyDefaultValue
(
CudaCompiler
(),
nvcc
);
char
*
tmpdir
=
getenv
(
"TMPDIR"
);
string
tmp
=
(
tmpdir
==
NULL
?
string
(
P_tmpdir
)
:
string
(
tmpdir
));
...
...
platforms/cuda/src/kernels/pme.cu
View file @
b723e4af
...
...
@@ -165,31 +165,31 @@ gridEvaluateEnergy(real2* __restrict__ halfcomplex_pmeGrid, real* __restrict__ e
int
remainder
=
index
-
kx
*
GRID_SIZE_Y
*
(
GRID_SIZE_Z
);
int
ky
=
remainder
/
(
GRID_SIZE_Z
);
int
kz
=
remainder
-
ky
*
(
GRID_SIZE_Z
);
int
mx
=
(
kx
<
(
GRID_SIZE_X
+
1
)
/
2
)
?
kx
:
(
kx
-
GRID_SIZE_X
);
int
my
=
(
ky
<
(
GRID_SIZE_Y
+
1
)
/
2
)
?
ky
:
(
ky
-
GRID_SIZE_Y
);
int
mz
=
(
kz
<
(
GRID_SIZE_Z
+
1
)
/
2
)
?
kz
:
(
kz
-
GRID_SIZE_Z
);
real
mhx
=
mx
*
invPeriodicBoxSize
.
x
;
real
mhy
=
my
*
invPeriodicBoxSize
.
y
;
real
mhz
=
mz
*
invPeriodicBoxSize
.
z
;
real
m2
=
mhx
*
mhx
+
mhy
*
mhy
+
mhz
*
mhz
;
real
bx
=
pmeBsplineModuliX
[
kx
];
real
by
=
pmeBsplineModuliY
[
ky
];
real
bz
=
pmeBsplineModuliZ
[
kz
];
real
denom
=
m2
*
bx
*
by
*
bz
;
real
eterm
=
recipScaleFactor
*
EXP
(
-
RECIP_EXP_FACTOR
*
m2
)
/
denom
;
int
mx
=
(
kx
<
(
GRID_SIZE_X
+
1
)
/
2
)
?
kx
:
(
kx
-
GRID_SIZE_X
);
int
my
=
(
ky
<
(
GRID_SIZE_Y
+
1
)
/
2
)
?
ky
:
(
ky
-
GRID_SIZE_Y
);
int
mz
=
(
kz
<
(
GRID_SIZE_Z
+
1
)
/
2
)
?
kz
:
(
kz
-
GRID_SIZE_Z
);
real
mhx
=
mx
*
invPeriodicBoxSize
.
x
;
real
mhy
=
my
*
invPeriodicBoxSize
.
y
;
real
mhz
=
mz
*
invPeriodicBoxSize
.
z
;
real
m2
=
mhx
*
mhx
+
mhy
*
mhy
+
mhz
*
mhz
;
real
bx
=
pmeBsplineModuliX
[
kx
];
real
by
=
pmeBsplineModuliY
[
ky
];
real
bz
=
pmeBsplineModuliZ
[
kz
];
real
denom
=
m2
*
bx
*
by
*
bz
;
real
eterm
=
recipScaleFactor
*
EXP
(
-
RECIP_EXP_FACTOR
*
m2
)
/
denom
;
if
(
kz
>=
(
GRID_SIZE_Z
/
2
+
1
))
{
kx
=
((
kx
==
0
)
?
kx
:
GRID_SIZE_X
-
kx
);
ky
=
((
ky
==
0
)
?
ky
:
GRID_SIZE_Y
-
ky
);
kz
=
GRID_SIZE_Z
-
kz
;
if
(
kz
>=
(
GRID_SIZE_Z
/
2
+
1
))
{
kx
=
((
kx
==
0
)
?
kx
:
GRID_SIZE_X
-
kx
);
ky
=
((
ky
==
0
)
?
ky
:
GRID_SIZE_Y
-
ky
);
kz
=
GRID_SIZE_Z
-
kz
;
}
int
indexInHalfComplexGrid
=
kz
+
ky
*
(
GRID_SIZE_Z
/
2
+
1
)
+
kx
*
(
GRID_SIZE_Y
*
(
GRID_SIZE_Z
/
2
+
1
));
real2
grid
=
halfcomplex_pmeGrid
[
indexInHalfComplexGrid
];
if
(
kx
!=
0
||
ky
!=
0
||
kz
!=
0
)
{
energy
+=
eterm
*
(
grid
.
x
*
grid
.
x
+
grid
.
y
*
grid
.
y
);
int
indexInHalfComplexGrid
=
kz
+
ky
*
(
GRID_SIZE_Z
/
2
+
1
)
+
kx
*
(
GRID_SIZE_Y
*
(
GRID_SIZE_Z
/
2
+
1
));
real2
grid
=
halfcomplex_pmeGrid
[
indexInHalfComplexGrid
];
if
(
kx
!=
0
||
ky
!=
0
||
kz
!=
0
)
{
energy
+=
eterm
*
(
grid
.
x
*
grid
.
x
+
grid
.
y
*
grid
.
y
);
}
}
energyBuffer
[
blockIdx
.
x
*
blockDim
.
x
+
threadIdx
.
x
]
+=
0.5
f
*
energy
;
energyBuffer
[
blockIdx
.
x
*
blockDim
.
x
+
threadIdx
.
x
]
+=
0.5
f
*
energy
;
}
extern
"C"
__global__
...
...
platforms/cuda/tests/TestCudaEwald.cpp
View file @
b723e4af
...
...
@@ -58,10 +58,10 @@ void testEwaldPME(bool includeExceptions) {
// Use amorphous NaCl system for the tests
const
int
numParticles
=
894
;
const
double
cutoff
=
1.2
;
const
double
boxSize
=
3.00646
;
double
tol
=
1e-5
;
const
int
numParticles
=
894
;
const
double
cutoff
=
1.2
;
const
double
boxSize
=
3.00646
;
double
tol
=
1e-5
;
ReferencePlatform
reference
;
System
system
;
...
...
platforms/opencl/include/windowsExportOpenCL.h
View file @
b723e4af
...
...
@@ -30,9 +30,9 @@
#if defined(OPENMM_OPENCL_BUILDING_SHARED_LIBRARY)
#define OPENMM_EXPORT_OPENCL __declspec(dllexport)
#elif defined(OPENMM_OPENCL_BUILDING_STATIC_LIBRARY) || defined(OPENMM_OPENCL_USE_STATIC_LIBRARIES)
#define OPENMM_EXPORT_OPENCL
#define OPENMM_EXPORT_OPENCL
#else
#define OPENMM_EXPORT_OPENCL __declspec(dllimport) // i.e., a client of a shared library
#define OPENMM_EXPORT_OPENCL __declspec(dllimport) // i.e., a client of a shared library
#endif
#else
#define OPENMM_EXPORT_OPENCL // Linux, Mac
...
...
platforms/opencl/src/OpenCLParallelKernels.cpp
View file @
b723e4af
...
...
@@ -36,7 +36,7 @@ using namespace std;
#include <Windows.h>
static
long
long
getTime
()
{
FILETIME
ft
;
GetSystemTimeAsFileTime
(
&
ft
);
// 100-nanoseconds since 1-1-1601
GetSystemTimeAsFileTime
(
&
ft
);
// 100-nanoseconds since 1-1-1601
ULARGE_INTEGER
result
;
result
.
LowPart
=
ft
.
dwLowDateTime
;
result
.
HighPart
=
ft
.
dwHighDateTime
;
...
...
platforms/opencl/src/kernels/customGBEnergyN2.cl
View file @
b723e4af
...
...
@@ -17,7 +17,7 @@ __kernel void computeN2Energy(
__global
real4*
restrict
forceBuffers,
#
endif
__global
real*
restrict
energyBuffer,
__local
real4*
restrict
local_force,
__global
const
real4*
restrict
posq,
__local
real4*
restrict
local_posq,
__global
const
unsigned
int*
restrict
exclusions,
__global
const
real4*
restrict
posq,
__local
real4*
restrict
local_posq,
__global
const
unsigned
int*
restrict
exclusions,
__global
const
ushort2*
exclusionTiles,
#
ifdef
USE_CUTOFF
__global
const
ushort2*
restrict
tiles,
__global
const
unsigned
int*
restrict
interactionCount,
real4
periodicBoxSize,
real4
invPeriodicBoxSize,
unsigned
int
maxTiles,
__global
const
real4*
restrict
blockCenter,
__global
const
int*
restrict
interactingAtoms
...
...
platforms/opencl/src/kernels/customGBEnergyN2_cpu.cl
View file @
b723e4af
...
...
@@ -17,7 +17,7 @@ __kernel void computeN2Energy(
__global
real4*
restrict
forceBuffers,
#
endif
__global
real*
restrict
energyBuffer,
__local
real4*
restrict
local_force,
__global
const
real4*
restrict
posq,
__local
real4*
restrict
local_posq,
__global
const
unsigned
int*
restrict
exclusions,
__global
const
real4*
restrict
posq,
__local
real4*
restrict
local_posq,
__global
const
unsigned
int*
restrict
exclusions,
__global
const
ushort2*
exclusionTiles,
#
ifdef
USE_CUTOFF
__global
const
ushort2*
restrict
tiles,
__global
const
unsigned
int*
restrict
interactionCount,
real4
periodicBoxSize,
real4
invPeriodicBoxSize,
unsigned
int
maxTiles,
__global
const
real4*
restrict
blockCenter,
__global
const
int*
restrict
interactingAtoms
...
...
platforms/reference/src/ReferenceKernels.cpp
View file @
b723e4af
...
...
@@ -1756,10 +1756,10 @@ void ReferenceIntegrateLangevinStepKernel::execute(ContextImpl& context, const L
}
RealOpenMM
tau
=
static_cast
<
RealOpenMM
>
(
friction
==
0.0
?
0.0
:
1.0
/
friction
);
dynamics
=
new
ReferenceStochasticDynamics
(
context
.
getSystem
().
getNumParticles
(),
static_cast
<
RealOpenMM
>
(
stepSize
),
static_cast
<
RealOpenMM
>
(
tau
),
static_cast
<
RealOpenMM
>
(
temperature
)
);
context
.
getSystem
().
getNumParticles
(),
static_cast
<
RealOpenMM
>
(
stepSize
),
static_cast
<
RealOpenMM
>
(
tau
),
static_cast
<
RealOpenMM
>
(
temperature
)
);
vector
<
ReferenceCCMAAlgorithm
::
AngleInfo
>
angles
;
findAnglesForCCMA
(
context
.
getSystem
(),
angles
);
constraints
=
new
ReferenceCCMAAlgorithm
(
context
.
getSystem
().
getNumParticles
(),
numConstraints
,
constraintIndices
,
constraintDistances
,
masses
,
angles
,
(
RealOpenMM
)
integrator
.
getConstraintTolerance
());
...
...
@@ -1823,10 +1823,10 @@ void ReferenceIntegrateBrownianStepKernel::execute(ContextImpl& context, const B
delete
constraints
;
}
dynamics
=
new
ReferenceBrownianDynamics
(
context
.
getSystem
().
getNumParticles
(),
static_cast
<
RealOpenMM
>
(
stepSize
),
static_cast
<
RealOpenMM
>
(
friction
),
static_cast
<
RealOpenMM
>
(
temperature
)
);
context
.
getSystem
().
getNumParticles
(),
static_cast
<
RealOpenMM
>
(
stepSize
),
static_cast
<
RealOpenMM
>
(
friction
),
static_cast
<
RealOpenMM
>
(
temperature
)
);
vector
<
ReferenceCCMAAlgorithm
::
AngleInfo
>
angles
;
findAnglesForCCMA
(
context
.
getSystem
(),
angles
);
constraints
=
new
ReferenceCCMAAlgorithm
(
context
.
getSystem
().
getNumParticles
(),
numConstraints
,
constraintIndices
,
constraintDistances
,
masses
,
angles
,
(
RealOpenMM
)
integrator
.
getConstraintTolerance
());
...
...
platforms/reference/src/SimTKReference/PME.h
View file @
b723e4af
...
...
@@ -54,11 +54,11 @@ pme_t;
*/
int
pme_init
(
pme_t
*
ppme
,
RealOpenMM
ewaldcoeff
,
int
natoms
,
const
int
ngrid
[
3
],
int
pme_order
,
RealOpenMM
epsilon_r
);
RealOpenMM
ewaldcoeff
,
int
natoms
,
const
int
ngrid
[
3
],
int
pme_order
,
RealOpenMM
epsilon_r
);
/*
* Evaluate reciprocal space PME energy and forces.
...
...
@@ -75,12 +75,12 @@ pme_init(pme_t * ppme,
*/
int
pme_exec
(
pme_t
pme
,
std
::
vector
<
OpenMM
::
RealVec
>&
atomCoordinates
,
std
::
vector
<
OpenMM
::
RealVec
>&
forces
,
RealOpenMM
**
atomParameters
,
const
RealOpenMM
periodicBoxSize
[
3
],
RealOpenMM
*
energy
,
RealOpenMM
pme_virial
[
3
][
3
]);
std
::
vector
<
OpenMM
::
RealVec
>&
atomCoordinates
,
std
::
vector
<
OpenMM
::
RealVec
>&
forces
,
RealOpenMM
**
atomParameters
,
const
RealOpenMM
periodicBoxSize
[
3
],
RealOpenMM
*
energy
,
RealOpenMM
pme_virial
[
3
][
3
]);
...
...
platforms/reference/src/SimTKReference/ReferenceBondIxn.cpp
View file @
b723e4af
...
...
@@ -95,8 +95,8 @@ ReferenceBondIxn::~ReferenceBondIxn( ){
Do computation in double?
@param vector1
first vector
@param vector2
second vector
@param vector1
first vector
@param vector2
second vector
@param hasREntry if set, then vector1[ReferenceForce::RIndex] = norm of vector
defaults to 0 (i.e., R unavailable)
...
...
@@ -175,8 +175,8 @@ RealOpenMM ReferenceBondIxn::getNormedDotProduct( RealOpenMM* vector1, RealOpenM
Get angle between two vectors
@param vector1
first vector
@param vector2
second vector
@param vector1
first vector
@param vector2
second vector
@param outputDotProduct output cosine of angle between two vectors (optional)
@param hasREntry if set, then vector1[ReferenceForce::RIndex] = norm of vector
defaults to 0 -> R unavailable
...
...
@@ -228,9 +228,9 @@ RealOpenMM ReferenceBondIxn::getAngleBetweenTwoVectors( RealOpenMM* vector1, Rea
Get dihedral angle between three vectors
@param vector1
first vector
@param vector2
second vector
@param vector3
third vector
@param vector1
first vector
@param vector2
second vector
@param vector3
third vector
@param outputCrossProduct output cross product vectors
@param cosineOfAngle cosine of angle (output)
@param signVector vector to test sign (optional)
...
...
platforms/reference/src/SimTKReference/ReferenceLJCoulomb14.cpp
View file @
b723e4af
...
...
@@ -74,8 +74,8 @@ ReferenceLJCoulomb14::~ReferenceLJCoulomb14( ){
@param atomCoordinates atom coordinates
@param parameters three parameters:
parameters[0]= (c12/c6)**1/6 (sigma)
parameters[1]= c6*c6/c12 (4*epsilon)
parameters[2]= epsfac*q1*q2
parameters[1]= c6*c6/c12 (4*epsilon)
parameters[2]= epsfac*q1*q2
@param forces force array (forces added to current values)
@param totalEnergy if not null, the energy will be added to this
...
...
platforms/reference/src/SimTKReference/ReferenceLJCoulombIxn.cpp
View file @
b723e4af
...
...
@@ -216,14 +216,14 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec>
// PME
if
(
pme
&&
includeReciprocal
)
{
pme_t
pmedata
;
/* abstract handle for PME data */
RealOpenMM
virial
[
3
][
3
];
pme_t
pmedata
;
/* abstract handle for PME data */
RealOpenMM
virial
[
3
][
3
];
pme_init
(
&
pmedata
,
alphaEwald
,
numberOfAtoms
,
meshDim
,
5
,
1
);
pme_init
(
&
pmedata
,
alphaEwald
,
numberOfAtoms
,
meshDim
,
5
,
1
);
pme_exec
(
pmedata
,
atomCoordinates
,
forces
,
atomParameters
,
periodicBoxSize
,
&
recipEnergy
,
virial
);
pme_exec
(
pmedata
,
atomCoordinates
,
forces
,
atomParameters
,
periodicBoxSize
,
&
recipEnergy
,
virial
);
if
(
totalEnergy
)
if
(
totalEnergy
)
*
totalEnergy
+=
recipEnergy
;
if
(
energyByAtom
)
...
...
platforms/reference/src/SimTKReference/fftpack.cpp
View file @
b723e4af
...
...
@@ -669,8 +669,8 @@ fftpack_transpose_2d(t_complex * in_data,
int
nx
,
int
ny
)
{
t_complex
*
src
;
int
i
,
j
;
t_complex
*
src
;
int
i
,
j
;
if
(
nx
<
2
||
ny
<
2
)
{
...
...
@@ -682,45 +682,45 @@ fftpack_transpose_2d(t_complex * in_data,
}
if
(
in_data
==
out_data
)
{
src
=
(
t_complex
*
)
malloc
(
sizeof
(
t_complex
)
*
nx
*
ny
);
memcpy
(
src
,
in_data
,
sizeof
(
t_complex
)
*
nx
*
ny
);
}
else
{
src
=
in_data
;
}
for
(
i
=
0
;
i
<
nx
;
i
++
)
{
for
(
j
=
0
;
j
<
ny
;
j
++
)
{
out_data
[
j
*
nx
+
i
].
re
=
src
[
i
*
ny
+
j
].
re
;
out_data
[
j
*
nx
+
i
].
im
=
src
[
i
*
ny
+
j
].
im
;
}
}
if
(
src
!=
in_data
)
{
free
(
src
);
}
return
0
;
{
src
=
(
t_complex
*
)
malloc
(
sizeof
(
t_complex
)
*
nx
*
ny
);
memcpy
(
src
,
in_data
,
sizeof
(
t_complex
)
*
nx
*
ny
);
}
else
{
src
=
in_data
;
}
for
(
i
=
0
;
i
<
nx
;
i
++
)
{
for
(
j
=
0
;
j
<
ny
;
j
++
)
{
out_data
[
j
*
nx
+
i
].
re
=
src
[
i
*
ny
+
j
].
re
;
out_data
[
j
*
nx
+
i
].
im
=
src
[
i
*
ny
+
j
].
im
;
}
}
if
(
src
!=
in_data
)
{
free
(
src
);
}
return
0
;
}
static
int
fftpack_transpose_2d_nelem
(
t_complex
*
in_data
,
t_complex
*
out_data
,
int
nx
,
int
ny
,
t_complex
*
out_data
,
int
nx
,
int
ny
,
int
nelem
)
{
t_complex
*
src
;
int
ncopy
;
int
i
,
j
;
t_complex
*
src
;
int
ncopy
;
int
i
,
j
;
ncopy
=
nelem
*
sizeof
(
t_complex
);
ncopy
=
nelem
*
sizeof
(
t_complex
);
if
(
nx
<
2
||
ny
<
2
)
{
...
...
@@ -732,28 +732,28 @@ fftpack_transpose_2d_nelem(t_complex * in_data,
}
if
(
in_data
==
out_data
)
{
src
=
(
t_complex
*
)
malloc
(
nx
*
ny
*
ncopy
);
memcpy
(
src
,
in_data
,
nx
*
ny
*
ncopy
);
}
else
{
src
=
in_data
;
}
for
(
i
=
0
;
i
<
nx
;
i
++
)
{
for
(
j
=
0
;
j
<
ny
;
j
++
)
{
memcpy
(
out_data
+
(
j
*
nx
+
i
)
*
nelem
,
src
+
(
i
*
ny
+
j
)
*
nelem
,
ncopy
);
}
}
if
(
src
!=
in_data
)
{
free
(
src
);
}
return
0
;
{
src
=
(
t_complex
*
)
malloc
(
nx
*
ny
*
ncopy
);
memcpy
(
src
,
in_data
,
nx
*
ny
*
ncopy
);
}
else
{
src
=
in_data
;
}
for
(
i
=
0
;
i
<
nx
;
i
++
)
{
for
(
j
=
0
;
j
<
ny
;
j
++
)
{
memcpy
(
out_data
+
(
j
*
nx
+
i
)
*
nelem
,
src
+
(
i
*
ny
+
j
)
*
nelem
,
ncopy
);
}
}
if
(
src
!=
in_data
)
{
free
(
src
);
}
return
0
;
}
...
...
@@ -877,7 +877,7 @@ fftpack_init_3d(fftpack_t * pfft,
*
pfft
=
fft
;
return
0
;
return
0
;
};
...
...
platforms/reference/src/SimTKReference/fftpack.h
View file @
b723e4af
...
...
@@ -229,7 +229,7 @@ fftpack_exec_3d (fftpack_t setup,
* Destroy setup and release all allocated memory.
*
* \param setup Setup returned from fftpack_init_1d(), or one
*
of the other initializers.
*
of the other initializers.
*
*/
void
...
...
platforms/reference/src/gbsa/CpuGBVI.cpp
View file @
b723e4af
...
...
@@ -170,7 +170,7 @@ void CpuGBVI::computeBornRadiiUsingQuinticSpline( RealOpenMM atomicRadius3, Real
// (A - V)*dS/dV - S(V) = (A-V)*d(qSpline) + (A-V)*U/(A-V)**2 - qSpline - U/(A-V)
// = (A-V)*d(qSpline) - qSpline L < V < A**(-3)
// = (A-V)*d(qSpline) - qSpline L < V < A**(-3)
// (A - V)*dS/dV - S(V) = (A-V)*U*/(A-V)**2 - U/(A-V) = 0 U < V
...
...
Prev
1
2
Next
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment