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Commit a87df3ad authored by peastman's avatar peastman
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Merged upstream changes

parents 1c604fe4 9db70803
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Showing with 48 additions and 47 deletions
.travis.yml
View file @ a87df3ad
......@@ -6,7 +6,8 @@ before_install:
- sudo apt-get update -qq
- sudo apt-get install -qq libpcre3 libpcre3-dev gromacs
- sudo apt-get install -qq swig doxygen llvm-3.3
- sudo apt-get install -qq python-numpy python-scipy python-nose
- sudo apt-get install -qq python-numpy python-scipy python-pip
- sudo pip install nose
- export ASAN_SYMBOLIZER_PATH=/usr/bin/llvm-symbolizer-3.3
script:
......
platforms/cuda/src/kernels/customGBEnergyN2.cu
View file @ a87df3ad
......@@ -190,7 +190,7 @@ extern "C" __global__ void computeN2Energy(unsigned long long* __restrict__ forc
// Extract the coordinates of this tile.
unsigned int x, y;
int x, y;
bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles) {
......@@ -203,7 +203,7 @@ extern "C" __global__ void computeN2Energy(unsigned long long* __restrict__ forc
else
#endif
{
y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
......
platforms/cuda/src/kernels/customGBValueN2.cu
View file @ a87df3ad
......@@ -166,7 +166,7 @@ extern "C" __global__ void computeN2Value(const real4* __restrict__ posq, const
// Extract the coordinates of this tile.
unsigned int x, y;
int x, y;
bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles) {
......@@ -179,7 +179,7 @@ extern "C" __global__ void computeN2Value(const real4* __restrict__ posq, const
else
#endif
{
y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
......
platforms/cuda/src/kernels/gbsaObc1.cu
View file @ a87df3ad
......@@ -226,7 +226,7 @@ extern "C" __global__ void computeBornSum(unsigned long long* __restrict__ globa
// Extract the coordinates of this tile.
unsigned int x, y;
int x, y;
bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles) {
......@@ -239,7 +239,7 @@ extern "C" __global__ void computeBornSum(unsigned long long* __restrict__ globa
else
#endif
{
y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
......@@ -590,7 +590,7 @@ extern "C" __global__ void computeGBSAForce1(unsigned long long* __restrict__ fo
// Extract the coordinates of this tile.
unsigned int x, y;
int x, y;
bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles) {
......@@ -603,7 +603,7 @@ extern "C" __global__ void computeGBSAForce1(unsigned long long* __restrict__ fo
else
#endif
{
y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
......
platforms/cuda/src/kernels/nonbonded.cu
View file @ a87df3ad
......@@ -333,7 +333,7 @@ extern "C" __global__ void computeNonbonded(
bool includeTile = true;
// Extract the coordinates of this tile.
unsigned int x, y;
int x, y;
bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles) {
......@@ -346,7 +346,7 @@ extern "C" __global__ void computeNonbonded(
else
#endif
{
y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
......
platforms/opencl/src/kernels/customGBEnergyN2.cl
View file @ a87df3ad
......@@ -200,7 +200,7 @@ __kernel void computeN2Energy(
// Extract the coordinates of this tile.
unsigned int x, y;
int x, y;
bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles) {
......@@ -213,7 +213,7 @@ __kernel void computeN2Energy(
else
#endif
{
y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
......
platforms/opencl/src/kernels/customGBEnergyN2_cpu.cl
View file @ a87df3ad
......@@ -216,7 +216,7 @@ __kernel void computeN2Energy(
// Extract the coordinates of this tile.
unsigned int x, y;
int x, y;
bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles) {
......@@ -229,7 +229,7 @@ __kernel void computeN2Energy(
else
#endif
{
y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
......
platforms/opencl/src/kernels/customGBValueN2.cl
View file @ a87df3ad
......@@ -174,7 +174,7 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
// Extract the coordinates of this tile.
unsigned int x, y;
int x, y;
bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles) {
......@@ -187,7 +187,7 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
else
#endif
{
y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
......
platforms/opencl/src/kernels/customGBValueN2_cpu.cl
View file @ a87df3ad
......@@ -184,7 +184,7 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
// Extract the coordinates of this tile.
unsigned int x, y;
int x, y;
bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles) {
......@@ -197,7 +197,7 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
else
#endif
{
y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
......
platforms/opencl/src/kernels/gbsaObc.cl
View file @ a87df3ad
......@@ -186,7 +186,7 @@ __kernel void computeBornSum(
// Extract the coordinates of this tile.
unsigned int x, y;
int x, y;
bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles) {
......@@ -199,7 +199,7 @@ __kernel void computeBornSum(
else
#endif
{
y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
......@@ -574,7 +574,7 @@ __kernel void computeGBSAForce1(
// Extract the coordinates of this tile.
unsigned int x, y;
int x, y;
bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles) {
......@@ -587,7 +587,7 @@ __kernel void computeGBSAForce1(
else
#endif
{
y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
......
platforms/opencl/src/kernels/gbsaObc_cpu.cl
View file @ a87df3ad
......@@ -192,7 +192,7 @@ __kernel void computeBornSum(
// Extract the coordinates of this tile.
unsigned int x, y;
int x, y;
bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles) {
......@@ -205,7 +205,7 @@ __kernel void computeBornSum(
else
#endif
{
y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
......@@ -607,7 +607,7 @@ __kernel void computeGBSAForce1(
// Extract the coordinates of this tile.
unsigned int x, y;
int x, y;
bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles) {
......@@ -620,7 +620,7 @@ __kernel void computeGBSAForce1(
else
#endif
{
y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
......
platforms/opencl/src/kernels/nonbonded.cl
View file @ a87df3ad
......@@ -213,7 +213,7 @@ __kernel void computeNonbonded(
// Extract the coordinates of this tile.
unsigned int x, y;
int x, y;
bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles) {
......@@ -226,7 +226,7 @@ __kernel void computeNonbonded(
else
#endif
{
y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
......
platforms/opencl/src/kernels/nonbonded_cpu.cl
View file @ a87df3ad
......@@ -230,7 +230,7 @@ __kernel void computeNonbonded(
// Extract the coordinates of this tile.
unsigned int x, y;
int x, y;
bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles) {
......@@ -243,7 +243,7 @@ __kernel void computeNonbonded(
else
#endif
{
y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
......
plugins/amoeba/openmmapi/include/openmm/AmoebaMultipoleForce.h
View file @ a87df3ad
......@@ -126,7 +126,7 @@ public:
*
* @return the cutoff distance, measured in nm
*/
double getCutoffDistance(void) const;
double getCutoffDistance() const;
/**
* Set the cutoff distance (in nm) being used for nonbonded interactions. If the NonbondedMethod in use
......
plugins/amoeba/openmmapi/include/openmm/AmoebaVdwForce.h
View file @ a87df3ad
......@@ -191,7 +191,7 @@ public:
/**
* Get the cutoff distance.
*/
double getCutoff(void) const;
double getCutoff() const;
/**
* Get the method used for handling long range nonbonded interactions.
......
plugins/amoeba/openmmapi/src/AmoebaMultipoleForce.cpp
View file @ a87df3ad
......@@ -61,7 +61,7 @@ void AmoebaMultipoleForce::setPolarizationType( AmoebaMultipoleForce::Polarizati
polarizationType = type;
}
double AmoebaMultipoleForce::getCutoffDistance( void ) const {
double AmoebaMultipoleForce::getCutoffDistance() const {
return cutoffDistance;
}
......
plugins/amoeba/openmmapi/src/AmoebaVdwForce.cpp
View file @ a87df3ad
......@@ -106,7 +106,7 @@ void AmoebaVdwForce::setCutoff( double inputCutoff ){
cutoff = inputCutoff;
}
double AmoebaVdwForce::getCutoff( void ) const {
double AmoebaVdwForce::getCutoff() const {
return cutoff;
}
......
plugins/amoeba/platforms/cuda/src/kernels/amoebaGk.cu
View file @ a87df3ad
......@@ -97,11 +97,11 @@ extern "C" __global__ void computeBornSum(unsigned long long* __restrict__ bornS
// Extract the coordinates of this tile
const unsigned int tgx = threadIdx.x & (TILE_SIZE-1);
const unsigned int tbx = threadIdx.x - tgx;
unsigned int x, y;
int x, y;
AtomData1 data;
data.bornSum = 0;
if (pos < end) {
y = (unsigned int) floor(NUM_BLOCKS+0.5f-sqrt((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
y = (int) floor(NUM_BLOCKS+0.5f-sqrt((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
......@@ -232,10 +232,10 @@ extern "C" __global__ void computeGKForces(
// Extract the coordinates of this tile
const unsigned int tgx = threadIdx.x & (TILE_SIZE-1);
const unsigned int tbx = threadIdx.x - tgx;
unsigned int x, y;
int x, y;
AtomData2 data;
if (pos < end) {
y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
......@@ -471,10 +471,10 @@ extern "C" __global__ void computeChainRuleForce(
// Extract the coordinates of this tile
const unsigned int tgx = threadIdx.x & (TILE_SIZE-1);
const unsigned int tbx = threadIdx.x - tgx;
unsigned int x, y;
int x, y;
AtomData3 data;
if (pos < end) {
y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
......@@ -766,8 +766,8 @@ extern "C" __global__ void computeEDiffForce(
while (pos < end) {
// Extract the coordinates of this tile.
unsigned int x, y;
y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
int x, y;
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
......
plugins/amoeba/platforms/cuda/src/kernels/amoebaWcaForce.cu
View file @ a87df3ad
......@@ -207,10 +207,10 @@ extern "C" __global__ void computeWCAForce(unsigned long long* __restrict__ forc
const unsigned int tgx = threadIdx.x & (TILE_SIZE-1);
const unsigned int tbx = threadIdx.x - tgx;
const unsigned int localGroupIndex = threadIdx.x/TILE_SIZE;
unsigned int x, y;
int x, y;
AtomData data;
if (pos < end) {
y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
......
plugins/amoeba/platforms/cuda/src/kernels/multipoleElectrostatics.cu
View file @ a87df3ad
......@@ -234,14 +234,14 @@ extern "C" __global__ void computeElectrostatics(
// Extract the coordinates of this tile.
unsigned int x, y;
int x, y;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles)
x = tiles[pos];
else
#endif
{
y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
......
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