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Commit 99ef4344 authored by Lee-Ping Wang's avatar Lee-Ping Wang
Browse files

Merge branch 'master' of github.com:SimTk/openmm

parents 471bea82 79fd69c3
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plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.cpp
View file @ 99ef4344
......@@ -1639,6 +1639,24 @@ void CudaCalcAmoebaMultipoleForceKernel::ensureMultipolesValid(ContextImpl& cont
context.calcForcesAndEnergy(false, false, -1);
}
void CudaCalcAmoebaMultipoleForceKernel::getInducedDipoles(ContextImpl& context, vector<Vec3>& dipoles) {
ensureMultipolesValid(context);
int numParticles = cu.getNumAtoms();
dipoles.resize(numParticles);
if (cu.getUseDoublePrecision()) {
vector<double> d;
inducedDipole->download(d);
for (int i = 0; i < numParticles; i++)
dipoles[i] = Vec3(d[3*i], d[3*i+1], d[3*i+2]);
}
else {
vector<float> d;
inducedDipole->download(d);
for (int i = 0; i < numParticles; i++)
dipoles[i] = Vec3(d[3*i], d[3*i+1], d[3*i+2]);
}
}
void CudaCalcAmoebaMultipoleForceKernel::getElectrostaticPotential(ContextImpl& context, const vector<Vec3>& inputGrid, vector<double>& outputElectrostaticPotential) {
ensureMultipolesValid(context);
int numPoints = inputGrid.size();
......
plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.h
View file @ 99ef4344
......@@ -327,6 +327,13 @@ public:
* @return the potential energy due to the force
*/
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
/**
* Get the induced dipole moments of all particles.
*
* @param context the Context for which to get the induced dipoles
* @param dipoles the induced dipole moment of particle i is stored into the i'th element
*/
void getInducedDipoles(ContextImpl& context, std::vector<Vec3>& dipoles);
/**
* Execute the kernel to calculate the electrostatic potential
*
......
plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaMultipoleForce.cpp
View file @ 99ef4344
......@@ -2700,6 +2700,40 @@ static void testPMEMutualPolarizationLargeWater( FILE* log ) {
}
// test querying particle induced dipoles
static void testParticleInducedDipoles() {
int numberOfParticles = 8;
int inputPmeGridDimension = 0;
double cutoff = 9000000.0;
std::vector<Vec3> forces;
double energy;
System system;
AmoebaMultipoleForce* amoebaMultipoleForce = new AmoebaMultipoleForce();;
setupMultipoleAmmonia(system, amoebaMultipoleForce, AmoebaMultipoleForce::NoCutoff, AmoebaMultipoleForce::Mutual,
cutoff, inputPmeGridDimension);
LangevinIntegrator integrator(0.0, 0.1, 0.01);
Context context(system, integrator, Platform::getPlatformByName("CUDA"));
getForcesEnergyMultipoleAmmonia(context, forces, energy);
std::vector<Vec3> dipole;
amoebaMultipoleForce->getInducedDipoles(context, dipole);
// Compare to values calculated by TINKER.
std::vector<Vec3> expectedDipole(numberOfParticles);
expectedDipole[0] = Vec3(0.0031710288, 9.3687453e-7, -0.0006919963);
expectedDipole[1] = Vec3(8.0279737504e-5, -0.000279376, 4.778060103e-5);
expectedDipole[2] = Vec3(0.000079322, 0.0002789804, 4.8696656126e-5);
expectedDipole[3] = Vec3(-0.0001407394, 1.540638116e-6, -0.0007077775);
expectedDipole[4] = Vec3(0.0019564439, -1.0409717e-7, 0.0007332188);
expectedDipole[5] = Vec3(0.0008213891, -0.0007749618, -0.0003883865);
expectedDipole[6] = Vec3(0.0046133992, -7.2868019e-7, 0.0002500622);
expectedDipole[7] = Vec3(0.0008204731, 0.0007772727, -0.0003856176);
for (int i = 0; i < numberOfParticles; i++)
ASSERT_EQUAL_VEC(expectedDipole[i], dipole[i], 1e-4);
}
// test computation of system multipole moments
static void testSystemMultipoleMoments( FILE* log ) {
......@@ -2963,6 +2997,10 @@ int main(int argc, char* argv[]) {
testMultipoleIonsAndWaterPMEMutualPolarization( log );
testMultipoleIonsAndWaterPMEDirectPolarization( log );
// test querying induced dipoles
testParticleInducedDipoles();
// test computation of system multipole moments
testSystemMultipoleMoments( log );
......
plugins/amoeba/platforms/reference/src/AmoebaReferenceKernels.cpp
View file @ 99ef4344
......@@ -683,6 +683,25 @@ double ReferenceCalcAmoebaMultipoleForceKernel::execute(ContextImpl& context, bo
return static_cast<double>(energy);
}
void ReferenceCalcAmoebaMultipoleForceKernel::getInducedDipoles(ContextImpl& context, vector<Vec3>& outputDipoles) {
int numParticles = context.getSystem().getNumParticles();
outputDipoles.resize(numParticles);
// Create an AmoebaReferenceMultipoleForce to do the calculation.
AmoebaReferenceMultipoleForce* amoebaReferenceMultipoleForce = setupAmoebaReferenceMultipoleForce( context );
vector<RealVec>& posData = extractPositions(context);
// Retrieve the induced dipoles.
vector<RealVec> inducedDipoles;
amoebaReferenceMultipoleForce->calculateInducedDipoles(posData, charges, dipoles, quadrupoles, tholes,
dampingFactors, polarity, axisTypes, multipoleAtomZs, multipoleAtomXs, multipoleAtomYs, multipoleAtomCovalentInfo, inducedDipoles);
for (int i = 0; i < numParticles; i++)
outputDipoles[i] = inducedDipoles[i];
delete amoebaReferenceMultipoleForce;
}
void ReferenceCalcAmoebaMultipoleForceKernel::getElectrostaticPotential(ContextImpl& context, const std::vector< Vec3 >& inputGrid,
std::vector< double >& outputElectrostaticPotential ){
......@@ -704,8 +723,6 @@ void ReferenceCalcAmoebaMultipoleForceKernel::getElectrostaticPotential(ContextI
}
delete amoebaReferenceMultipoleForce;
return;
}
void ReferenceCalcAmoebaMultipoleForceKernel::getSystemMultipoleMoments(ContextImpl& context, std::vector< double >& outputMultipoleMoments){
......@@ -726,8 +743,6 @@ void ReferenceCalcAmoebaMultipoleForceKernel::getSystemMultipoleMoments(ContextI
multipoleAtomCovalentInfo, outputMultipoleMoments );
delete amoebaReferenceMultipoleForce;
return;
}
void ReferenceCalcAmoebaMultipoleForceKernel::copyParametersToContext(ContextImpl& context, const AmoebaMultipoleForce& force) {
......
plugins/amoeba/platforms/reference/src/AmoebaReferenceKernels.h
View file @ 99ef4344
......@@ -366,6 +366,13 @@ public:
* @return the potential energy due to the force
*/
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
/**
* Get the induced dipole moments of all particles.
*
* @param context the Context for which to get the induced dipoles
* @param dipoles the induced dipole moment of particle i is stored into the i'th element
*/
void getInducedDipoles(ContextImpl& context, std::vector<Vec3>& dipoles);
/**
* Calculate the electrostatic potential given vector of grid coordinates.
*
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceMultipoleForce.cpp
View file @ 99ef4344
......@@ -1563,6 +1563,28 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateForceAndEnergy( const std::ve
return energy;
}
void AmoebaReferenceMultipoleForce::calculateInducedDipoles(const std::vector<RealVec>& particlePositions,
const std::vector<RealOpenMM>& charges,
const std::vector<RealOpenMM>& dipoles,
const std::vector<RealOpenMM>& quadrupoles,
const std::vector<RealOpenMM>& tholes,
const std::vector<RealOpenMM>& dampingFactors,
const std::vector<RealOpenMM>& polarity,
const std::vector<int>& axisTypes,
const std::vector<int>& multipoleAtomZs,
const std::vector<int>& multipoleAtomXs,
const std::vector<int>& multipoleAtomYs,
const std::vector< std::vector< std::vector<int> > >& multipoleAtomCovalentInfo,
std::vector<RealVec>& outputInducedDipoles) {
// setup, including calculating induced dipoles
std::vector<MultipoleParticleData> particleData;
setup( particlePositions, charges, dipoles, quadrupoles, tholes,
dampingFactors, polarity, axisTypes, multipoleAtomZs, multipoleAtomXs, multipoleAtomYs,
multipoleAtomCovalentInfo, particleData );
outputInducedDipoles = _inducedDipole;
}
void AmoebaReferenceMultipoleForce::calculateAmoebaSystemMultipoleMoments( const std::vector<RealOpenMM>& masses,
const std::vector<RealVec>& particlePositions,
const std::vector<RealOpenMM>& charges,
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceMultipoleForce.h
View file @ 99ef4344
......@@ -471,6 +471,38 @@ public:
const std::vector< std::vector< std::vector<int> > >& multipoleAtomCovalentInfo,
std::vector<OpenMM::RealVec>& forces );
/**
* Calculate particle induced dipoles.
*
* @param masses particle masses
* @param particlePositions Cartesian coordinates of particles
* @param charges scalar charges for each particle
* @param dipoles molecular frame dipoles for each particle
* @param quadrupoles molecular frame quadrupoles for each particle
* @param tholes Thole factors for each particle
* @param dampingFactors dampling factors for each particle
* @param polarity polarity for each particle
* @param axisTypes axis type (Z-then-X, ... ) for each particle
* @param multipoleAtomZs indicies of particle specifying the molecular frame z-axis for each particle
* @param multipoleAtomXs indicies of particle specifying the molecular frame x-axis for each particle
* @param multipoleAtomYs indicies of particle specifying the molecular frame y-axis for each particle
* @param multipoleAtomCovalentInfo covalent info needed to set scaling factors
* @param outputMultipoleMoments output multipole moments
*/
void calculateInducedDipoles(const std::vector<OpenMM::RealVec>& particlePositions,
const std::vector<RealOpenMM>& charges,
const std::vector<RealOpenMM>& dipoles,
const std::vector<RealOpenMM>& quadrupoles,
const std::vector<RealOpenMM>& tholes,
const std::vector<RealOpenMM>& dampingFactors,
const std::vector<RealOpenMM>& polarity,
const std::vector<int>& axisTypes,
const std::vector<int>& multipoleAtomZs,
const std::vector<int>& multipoleAtomXs,
const std::vector<int>& multipoleAtomYs,
const std::vector< std::vector< std::vector<int> > >& multipoleAtomCovalentInfo,
std::vector<RealVec>& outputInducedDipoles);
/**
* Calculate system multipole moments.
*
......
plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaMultipoleForce.cpp
View file @ 99ef4344
......@@ -2605,6 +2605,40 @@ static void testPMEMutualPolarizationLargeWater( FILE* log ) {
}
// test querying particle induced dipoles
static void testParticleInducedDipoles() {
int numberOfParticles = 8;
int inputPmeGridDimension = 0;
double cutoff = 9000000.0;
std::vector<Vec3> forces;
double energy;
System system;
AmoebaMultipoleForce* amoebaMultipoleForce = new AmoebaMultipoleForce();;
setupMultipoleAmmonia(system, amoebaMultipoleForce, AmoebaMultipoleForce::NoCutoff, AmoebaMultipoleForce::Mutual,
cutoff, inputPmeGridDimension);
LangevinIntegrator integrator(0.0, 0.1, 0.01);
Context context(system, integrator, Platform::getPlatformByName("Reference"));
getForcesEnergyMultipoleAmmonia(context, forces, energy);
std::vector<Vec3> dipole;
amoebaMultipoleForce->getInducedDipoles(context, dipole);
// Compare to values calculated by TINKER.
std::vector<Vec3> expectedDipole(numberOfParticles);
expectedDipole[0] = Vec3(0.0031710288, 9.3687453e-7, -0.0006919963);
expectedDipole[1] = Vec3(8.0279737504e-5, -0.000279376, 4.778060103e-5);
expectedDipole[2] = Vec3(0.000079322, 0.0002789804, 4.8696656126e-5);
expectedDipole[3] = Vec3(-0.0001407394, 1.540638116e-6, -0.0007077775);
expectedDipole[4] = Vec3(0.0019564439, -1.0409717e-7, 0.0007332188);
expectedDipole[5] = Vec3(0.0008213891, -0.0007749618, -0.0003883865);
expectedDipole[6] = Vec3(0.0046133992, -7.2868019e-7, 0.0002500622);
expectedDipole[7] = Vec3(0.0008204731, 0.0007772727, -0.0003856176);
for (int i = 0; i < numberOfParticles; i++)
ASSERT_EQUAL_VEC(expectedDipole[i], dipole[i], 1e-4);
}
// test computation of system multipole moments
static void testSystemMultipoleMoments( FILE* log ) {
......@@ -2778,6 +2812,10 @@ int main( int numberOfArguments, char* argv[] ) {
testMultipoleAmmoniaDirectPolarization( log );
// test querying induced dipoles
testParticleInducedDipoles();
// test mutual polarization, no cutoff
testMultipoleAmmoniaMutualPolarization( log );
......
plugins/cpupme/src/CpuPmeKernels.cpp
View file @ 99ef4344
......@@ -34,9 +34,10 @@
#endif
#include "CpuPmeKernels.h"
#include "SimTKOpenMMRealType.h"
#include "openmm/internal/hardware.h"
#include "openmm/internal/vectorize.h"
#include <cmath>
#include <cstring>
#include <smmintrin.h>
using namespace OpenMM;
using namespace std;
......@@ -46,145 +47,73 @@ static const int PME_ORDER = 5;
bool CpuCalcPmeReciprocalForceKernel::hasInitializedThreads = false;
int CpuCalcPmeReciprocalForceKernel::numThreads = 0;
#define EXTRACT_FLOAT(v, element) _mm_cvtss_f32(_mm_shuffle_ps(v, v, _MM_SHUFFLE(0, 0, 0, element)))
// Define function to get the number of processors.
#ifdef __APPLE__
#include <sys/sysctl.h>
#include <dlfcn.h>
#else
#ifdef WIN32
#include <windows.h>
#else
#include <dlfcn.h>
#include <unistd.h>
#endif
#endif
static int getNumProcessors() {
#ifdef __APPLE__
int ncpu;
size_t len = 4;
if (sysctlbyname("hw.logicalcpu", &ncpu, &len, NULL, 0) == 0)
return ncpu;
else
return 1;
#else
#ifdef WIN32
SYSTEM_INFO siSysInfo;
int ncpu;
GetSystemInfo(&siSysInfo);
ncpu = siSysInfo.dwNumberOfProcessors;
if (ncpu < 1)
ncpu = 1;
return ncpu;
#else
long nProcessorsOnline = sysconf(_SC_NPROCESSORS_ONLN);
if (nProcessorsOnline == -1)
return 1;
else
return (int) nProcessorsOnline;
#endif
#endif
}
// Define a function to check the CPU's capabilities.
#ifdef _WIN32
#define cpuid __cpuid
#else
static void cpuid(int cpuInfo[4], int infoType){
#ifdef __LP64__
__asm__ __volatile__ (
"cpuid":
"=a" (cpuInfo[0]),
"=b" (cpuInfo[1]),
"=c" (cpuInfo[2]),
"=d" (cpuInfo[3]) :
"a" (infoType)
);
#else
__asm__ __volatile__ (
"pushl %%ebx\n"
"cpuid\n"
"movl %%ebx, %1\n"
"popl %%ebx\n" :
"=a" (cpuInfo[0]),
"=r" (cpuInfo[1]),
"=c" (cpuInfo[2]),
"=d" (cpuInfo[3]) :
"a" (infoType)
);
#endif
}
#endif
static void spreadCharge(int start, int end, float* posq, float* grid, int gridx, int gridy, int gridz, int numParticles, Vec3 periodicBoxSize) {
float temp[4];
__m128 boxSize = _mm_set_ps(0, (float) periodicBoxSize[2], (float) periodicBoxSize[1], (float) periodicBoxSize[0]);
__m128 invBoxSize = _mm_set_ps(0, (float) (1/periodicBoxSize[2]), (float) (1/periodicBoxSize[1]), (float) (1/periodicBoxSize[0]));
__m128 gridSize = _mm_set_ps(0, gridz, gridy, gridx);
__m128i gridSizeInt = _mm_set_epi32(0, gridz, gridy, gridx);
__m128 one = _mm_set1_ps(1);
__m128 scale = _mm_set1_ps(1.0f/(PME_ORDER-1));
fvec4 boxSize((float) periodicBoxSize[0], (float) periodicBoxSize[1], (float) periodicBoxSize[2], 0);
fvec4 invBoxSize((float) (1/periodicBoxSize[0]), (float) (1/periodicBoxSize[1]), (float) (1/periodicBoxSize[2]), 0);
fvec4 gridSize(gridx, gridy, gridz, 0);
ivec4 gridSizeInt(gridx, gridy, gridz, 0);
fvec4 one(1);
fvec4 scale(1.0f/(PME_ORDER-1));
const float epsilonFactor = sqrt(ONE_4PI_EPS0);
memset(grid, 0, sizeof(float)*gridx*gridy*gridz);
for (int i = start; i < end; i++) {
// Find the position relative to the nearest grid point.
__m128 pos = _mm_loadu_ps(&posq[4*i]);
__m128 posFloor = _mm_floor_ps(_mm_mul_ps(pos, invBoxSize));
__m128 posInBox = _mm_sub_ps(pos, _mm_mul_ps(boxSize, posFloor));
__m128 t = _mm_mul_ps(_mm_mul_ps(posInBox, invBoxSize), gridSize);
__m128i ti = _mm_cvttps_epi32(t);
__m128 dr = _mm_sub_ps(t, _mm_cvtepi32_ps(ti));
__m128i gridIndex = _mm_sub_epi32(ti, _mm_and_si128(gridSizeInt, _mm_cmpeq_epi32(ti, gridSizeInt)));
fvec4 pos(&posq[4*i]);
fvec4 posFloor = floor(pos*invBoxSize);
fvec4 posInBox = pos-boxSize*posFloor;
fvec4 t = posInBox*invBoxSize*gridSize;
ivec4 ti = t;
fvec4 dr = t-ti;
ivec4 gridIndex = ti-(gridSizeInt&ti==gridSizeInt);
// Compute the B-spline coefficients.
__m128 data[PME_ORDER];
data[PME_ORDER-1] = _mm_setzero_ps();
fvec4 data[PME_ORDER];
data[PME_ORDER-1] = 0.0f;
data[1] = dr;
data[0] = _mm_sub_ps(one, dr);
data[0] = one-dr;
for (int j = 3; j < PME_ORDER; j++) {
__m128 div = _mm_set1_ps(1.0f/(j-1));
data[j-1] = _mm_mul_ps(_mm_mul_ps(div, dr), data[j-2]);
fvec4 div(1.0f/(j-1));
data[j-1] = div*dr*data[j-2];
for (int k = 1; k < j-1; k++)
data[j-k-1] = _mm_mul_ps(div, _mm_add_ps(_mm_mul_ps(_mm_add_ps(dr, _mm_set1_ps(k)), data[j-k-2]), _mm_mul_ps(_mm_sub_ps(_mm_set1_ps(j-k), dr), data[j-k-1])));
data[0] = _mm_mul_ps(_mm_mul_ps(div, _mm_sub_ps(one, dr)), data[0]);
data[j-k-1] = div*((dr+k)*data[j-k-2]+(fvec4(j-k)-dr)*data[j-k-1]);
data[0] = div*(one-dr)*data[0];
}
data[PME_ORDER-1] = _mm_mul_ps(_mm_mul_ps(scale, dr), data[PME_ORDER-2]);
data[PME_ORDER-1] = scale*dr*data[PME_ORDER-2];
for (int j = 1; j < (PME_ORDER-1); j++)
data[PME_ORDER-j-1] = _mm_mul_ps(scale, _mm_add_ps(_mm_mul_ps(_mm_add_ps(dr, _mm_set1_ps(j)), data[PME_ORDER-j-2]), _mm_mul_ps(_mm_sub_ps(_mm_set1_ps(PME_ORDER-j), dr), data[PME_ORDER-j-1])));
data[0] = _mm_mul_ps(_mm_mul_ps(scale, _mm_sub_ps(one, dr)), data[0]);
data[PME_ORDER-j-1] = scale*((dr+j)*data[PME_ORDER-j-2]+(fvec4(PME_ORDER-j)-dr)*data[PME_ORDER-j-1]);
data[0] = scale*(one-dr)*data[0];
// Spread the charges.
int gridIndexX = _mm_extract_epi32(gridIndex, 0);
int gridIndexY = _mm_extract_epi32(gridIndex, 1);
int gridIndexZ = _mm_extract_epi32(gridIndex, 2);
int gridIndexX = gridIndex[0];
int gridIndexY = gridIndex[1];
int gridIndexZ = gridIndex[2];
if (gridIndexX < 0)
return; // This happens when a simulation blows up and coordinates become NaN.
int zindex[PME_ORDER];
for (int j = 0; j < PME_ORDER; j++) {
zindex[j] = gridIndexZ+j;
zindex[j] -= (zindex[j] >= gridz ? gridz : 0);
}
float charge = epsilonFactor*posq[4*i+3];
__m128 zdata0to3 = _mm_set_ps(EXTRACT_FLOAT(data[3], 2), EXTRACT_FLOAT(data[2], 2), EXTRACT_FLOAT(data[1], 2), EXTRACT_FLOAT(data[0], 2));
float zdata4 = EXTRACT_FLOAT(data[4], 2);
fvec4 zdata0to3(data[0][2], data[1][2], data[2][2], data[3][2]);
float zdata4 = data[4][2];
if (gridIndexZ+4 < gridz) {
for (int ix = 0; ix < PME_ORDER; ix++) {
int xbase = gridIndexX+ix;
xbase -= (xbase >= gridx ? gridx : 0);
xbase = xbase*gridy*gridz;
float xdata = charge*EXTRACT_FLOAT(data[ix], 0);
float xdata = charge*data[ix][0];
for (int iy = 0; iy < PME_ORDER; iy++) {
int ybase = gridIndexY+iy;
ybase -= (ybase >= gridy ? gridy : 0);
ybase = xbase + ybase*gridz;
float multiplier = xdata*EXTRACT_FLOAT(data[iy], 1);
__m128 add0to3 = _mm_mul_ps(zdata0to3, _mm_set1_ps(multiplier));
_mm_storeu_ps(&grid[ybase+gridIndexZ], _mm_add_ps(_mm_loadu_ps(&grid[ybase+gridIndexZ]), add0to3));
float multiplier = xdata*data[iy][1];
fvec4 add0to3 = zdata0to3*multiplier;
(fvec4(&grid[ybase+gridIndexZ])+add0to3).store(&grid[ybase+gridIndexZ]);
grid[ybase+zindex[4]] += multiplier*zdata4;
}
}
......@@ -194,14 +123,14 @@ static void spreadCharge(int start, int end, float* posq, float* grid, int gridx
int xbase = gridIndexX+ix;
xbase -= (xbase >= gridx ? gridx : 0);
xbase = xbase*gridy*gridz;
float xdata = charge*EXTRACT_FLOAT(data[ix], 0);
float xdata = charge*data[ix][0];
for (int iy = 0; iy < PME_ORDER; iy++) {
int ybase = gridIndexY+iy;
ybase -= (ybase >= gridy ? gridy : 0);
ybase = xbase + ybase*gridz;
float multiplier = xdata*EXTRACT_FLOAT(data[iy], 1);
__m128 add0to3 = _mm_mul_ps(zdata0to3, _mm_set1_ps(multiplier));
_mm_store_ps(temp, add0to3);
float multiplier = xdata*data[iy][1];
fvec4 add0to3 = zdata0to3*multiplier;
add0to3.store(temp);
grid[ybase+zindex[0]] += temp[0];
grid[ybase+zindex[1]] += temp[1];
grid[ybase+zindex[2]] += temp[2];
......@@ -314,84 +243,86 @@ static void reciprocalConvolution(int start, int end, fftwf_complex* grid, int g
}
static void interpolateForces(int start, int end, float* posq, float* force, float* grid, int gridx, int gridy, int gridz, int numParticles, Vec3 periodicBoxSize) {
__m128 boxSize = _mm_set_ps(0, (float) periodicBoxSize[2], (float) periodicBoxSize[1], (float) periodicBoxSize[0]);
__m128 invBoxSize = _mm_set_ps(0, (float) (1/periodicBoxSize[2]), (float) (1/periodicBoxSize[1]), (float) (1/periodicBoxSize[0]));
__m128 gridSize = _mm_set_ps(0, gridz, gridy, gridx);
__m128i gridSizeInt = _mm_set_epi32(0, gridz, gridy, gridx);
__m128 one = _mm_set1_ps(1);
__m128 scale = _mm_set1_ps(1.0f/(PME_ORDER-1));
fvec4 boxSize((float) periodicBoxSize[0], (float) periodicBoxSize[1], (float) periodicBoxSize[2], 0);
fvec4 invBoxSize((float) (1/periodicBoxSize[0]), (float) (1/periodicBoxSize[1]), (float) (1/periodicBoxSize[2]), 0);
fvec4 gridSize(gridx, gridy, gridz, 0);
ivec4 gridSizeInt(gridx, gridy, gridz, 0);
fvec4 one(1);
fvec4 scale(1.0f/(PME_ORDER-1));
const float epsilonFactor = sqrt(ONE_4PI_EPS0);
for (int i = start; i < end; i++) {
// Find the position relative to the nearest grid point.
__m128 pos = _mm_loadu_ps(&posq[4*i]);
__m128 posFloor = _mm_floor_ps(_mm_mul_ps(pos, invBoxSize));
__m128 posInBox = _mm_sub_ps(pos, _mm_mul_ps(boxSize, posFloor));
__m128 t = _mm_mul_ps(_mm_mul_ps(posInBox, invBoxSize), gridSize);
__m128i ti = _mm_cvttps_epi32(t);
__m128 dr = _mm_sub_ps(t, _mm_cvtepi32_ps(ti));
__m128i gridIndex = _mm_sub_epi32(ti, _mm_and_si128(gridSizeInt, _mm_cmpeq_epi32(ti, gridSizeInt)));
fvec4 pos(&posq[4*i]);
fvec4 posFloor = floor(pos*invBoxSize);
fvec4 posInBox = pos-boxSize*posFloor;
fvec4 t = posInBox*invBoxSize*gridSize;
ivec4 ti = t;
fvec4 dr = t-ti;
ivec4 gridIndex = ti-(gridSizeInt&ti==gridSizeInt);
// Compute the B-spline coefficients.
__m128 data[PME_ORDER];
__m128 ddata[PME_ORDER];
data[PME_ORDER-1] = _mm_setzero_ps();
fvec4 data[PME_ORDER];
fvec4 ddata[PME_ORDER];
data[PME_ORDER-1] = 0.0f;
data[1] = dr;
data[0] = _mm_sub_ps(one, dr);
data[0] = one-dr;
for (int j = 3; j < PME_ORDER; j++) {
__m128 div = _mm_set1_ps(1.0f/(j-1));
data[j-1] = _mm_mul_ps(_mm_mul_ps(div, dr), data[j-2]);
fvec4 div(1.0f/(j-1));
data[j-1] = div*dr*data[j-2];
for (int k = 1; k < j-1; k++)
data[j-k-1] = _mm_mul_ps(div, _mm_add_ps(_mm_mul_ps(_mm_add_ps(dr, _mm_set1_ps(k)), data[j-k-2]), _mm_mul_ps(_mm_sub_ps(_mm_set1_ps(j-k), dr), data[j-k-1])));
data[0] = _mm_mul_ps(_mm_mul_ps(div, _mm_sub_ps(one, dr)), data[0]);
data[j-k-1] = div*((dr+k)*data[j-k-2]+(fvec4(j-k)-dr)*data[j-k-1]);
data[0] = div*(one-dr)*data[0];
}
ddata[0] = _mm_sub_ps(_mm_set1_ps(0), data[0]);
ddata[0] = -data[0];
for (int j = 1; j < PME_ORDER; j++)
ddata[j] = _mm_sub_ps(data[j-1], data[j]);
data[PME_ORDER-1] = _mm_mul_ps(_mm_mul_ps(scale, dr), data[PME_ORDER-2]);
ddata[j] = data[j-1]-data[j];
data[PME_ORDER-1] = scale*dr*data[PME_ORDER-2];
for (int j = 1; j < (PME_ORDER-1); j++)
data[PME_ORDER-j-1] = _mm_mul_ps(scale, _mm_add_ps(_mm_mul_ps(_mm_add_ps(dr, _mm_set1_ps(j)), data[PME_ORDER-j-2]), _mm_mul_ps(_mm_sub_ps(_mm_set1_ps(PME_ORDER-j), dr), data[PME_ORDER-j-1])));
data[0] = _mm_mul_ps(_mm_mul_ps(scale, _mm_sub_ps(one, dr)), data[0]);
data[PME_ORDER-j-1] = scale*((dr+j)*data[PME_ORDER-j-2]+(fvec4(PME_ORDER-j)-dr)*data[PME_ORDER-j-1]);
data[0] = scale*(one-dr)*data[0];
// Compute the force on this atom.
int gridIndexX = _mm_extract_epi32(gridIndex, 0);
int gridIndexY = _mm_extract_epi32(gridIndex, 1);
int gridIndexZ = _mm_extract_epi32(gridIndex, 2);
int gridIndexX = gridIndex[0];
int gridIndexY = gridIndex[1];
int gridIndexZ = gridIndex[2];
if (gridIndexX < 0)
return; // This happens when a simulation blows up and coordinates become NaN.
int zindex[PME_ORDER];
for (int j = 0; j < PME_ORDER; j++) {
zindex[j] = gridIndexZ+j;
zindex[j] -= (zindex[j] >= gridz ? gridz : 0);
}
__m128 zdata[PME_ORDER];
fvec4 zdata[PME_ORDER];
for (int j = 0; j < PME_ORDER; j++)
zdata[j] = _mm_set_ps(0, EXTRACT_FLOAT(ddata[j], 2), EXTRACT_FLOAT(data[j], 2), EXTRACT_FLOAT(data[j], 2));
__m128 f = _mm_set1_ps(0);
zdata[j] = fvec4(data[j][2], data[j][2], ddata[j][2], 0);
fvec4 f = 0.0f;
for (int ix = 0; ix < PME_ORDER; ix++) {
int xbase = gridIndexX+ix;
xbase -= (xbase >= gridx ? gridx : 0);
xbase = xbase*gridy*gridz;
float dx = EXTRACT_FLOAT(data[ix], 0);
float ddx = EXTRACT_FLOAT(ddata[ix], 0);
__m128 xdata = _mm_set_ps(0, dx, dx, ddx);
float dx = data[ix][0];
float ddx = ddata[ix][0];
fvec4 xdata(ddx, dx, dx, 0);
for (int iy = 0; iy < PME_ORDER; iy++) {
int ybase = gridIndexY+iy;
ybase -= (ybase >= gridy ? gridy : 0);
ybase = xbase + ybase*gridz;
float dy = EXTRACT_FLOAT(data[iy], 1);
float ddy = EXTRACT_FLOAT(ddata[iy], 1);
__m128 xydata = _mm_mul_ps(xdata, _mm_set_ps(0, dy, ddy, dy));
float dy = data[iy][1];
float ddy = ddata[iy][1];
fvec4 xydata = xdata*fvec4(dy, ddy, dy, 0);
for (int iz = 0; iz < PME_ORDER; iz++) {
__m128 gridValue = _mm_set1_ps(grid[ybase+zindex[iz]]);
f = _mm_add_ps(f, _mm_mul_ps(xydata, _mm_mul_ps(zdata[iz], gridValue)));
fvec4 gridValue(grid[ybase+zindex[iz]]);
f = f+xydata*zdata[iz]*gridValue;
}
}
}
f = _mm_mul_ps(invBoxSize, _mm_mul_ps(gridSize, _mm_mul_ps(f, _mm_set1_ps(-epsilonFactor*posq[4*i+3]))));
_mm_store_ps(&force[4*i], f);
f = invBoxSize*gridSize*f*(-epsilonFactor*posq[4*i+3]);
f.store(&force[4*i]);
}
}
......@@ -576,10 +507,10 @@ void CpuCalcPmeReciprocalForceKernel::runThread(int index) {
threadWait();
int numGrids = threadData.size();
for (int i = gridStart; i < gridEnd; i += 4) {
__m128 sum = _mm_load_ps(&realGrid[i]);
fvec4 sum(&realGrid[i]);
for (int j = 1; j < numGrids; j++)
sum = _mm_add_ps(sum, _mm_load_ps(&threadData[j]->tempGrid[i]));
_mm_store_ps(&realGrid[i], sum);
sum += fvec4(&threadData[j]->tempGrid[i]);
sum.store(&realGrid[i]);
}
threadWait();
if (lastBoxSize != periodicBoxSize) {
......
plugins/drude/platforms/reference/src/ReferenceDrudeKernels.cpp
View file @ 99ef4344
......@@ -34,7 +34,7 @@
#include "openmm/OpenMMException.h"
#include "openmm/internal/ContextImpl.h"
#include "SimTKOpenMMUtilities.h"
#include "ReferenceCCMAAlgorithm.h"
#include "ReferenceConstraints.h"
#include "ReferenceVirtualSites.h"
#include <set>
......@@ -56,20 +56,6 @@ static vector<RealVec>& extractForces(ContextImpl& context) {
return *((vector<RealVec>*) data->forces);
}
static void findAnglesForCCMA(const System& system, vector<ReferenceCCMAAlgorithm::AngleInfo>& angles) {
for (int i = 0; i < system.getNumForces(); i++) {
const HarmonicAngleForce* force = dynamic_cast<const HarmonicAngleForce*>(&system.getForce(i));
if (force != NULL) {
for (int j = 0; j < force->getNumAngles(); j++) {
int atom1, atom2, atom3;
double angle, k;
force->getAngleParameters(j, atom1, atom2, atom3, angle, k);
angles.push_back(ReferenceCCMAAlgorithm::AngleInfo(atom1, atom2, atom3, (RealOpenMM)angle));
}
}
}
}
static double computeShiftedKineticEnergy(ContextImpl& context, vector<double>& inverseMasses, double timeShift, ReferenceConstraintAlgorithm* constraints) {
const System& system = context.getSystem();
int numParticles = system.getNumParticles();
......@@ -91,7 +77,7 @@ static double computeShiftedKineticEnergy(ContextImpl& context, vector<double>&
if (constraints != NULL) {
constraints->setTolerance(1e-4);
constraints->applyToVelocities(numParticles, posData, shiftedVel, inverseMasses);
constraints->applyToVelocities(posData, shiftedVel, inverseMasses);
}
// Compute the kinetic energy.
......@@ -271,21 +257,19 @@ void ReferenceIntegrateDrudeLangevinStepKernel::initialize(const System& system,
// Prepare constraints.
int numConstraints = system.getNumConstraints();
if (numConstraints > 0) {
vector<pair<int, int> > constraintIndices(numConstraints);
vector<RealOpenMM> constraintDistances(numConstraints);
for (int i = 0; i < numConstraints; ++i) {
if (system.getNumConstraints() > 0) {
vector<pair<int, int> > constraintIndices;
vector<RealOpenMM> constraintDistances;
for (int i = 0; i < system.getNumConstraints(); ++i) {
int particle1, particle2;
double distance;
system.getConstraintParameters(i, particle1, particle2, distance);
constraintIndices[i].first = particle1;
constraintIndices[i].second = particle2;
constraintDistances[i] = static_cast<RealOpenMM>(distance);
if (system.getParticleMass(particle1) != 0 || system.getParticleMass(particle2) != 0) {
constraintIndices.push_back(make_pair(particle1, particle2));
constraintDistances.push_back(distance);
}
}
vector<ReferenceCCMAAlgorithm::AngleInfo> angles;
findAnglesForCCMA(system, angles);
constraints = new ReferenceCCMAAlgorithm(system.getNumParticles(), numConstraints, constraintIndices, constraintDistances, particleMass, angles, (RealOpenMM)integrator.getConstraintTolerance());
constraints = new ReferenceConstraints(system, (RealOpenMM) integrator.getConstraintTolerance());
}
}
......@@ -347,7 +331,7 @@ void ReferenceIntegrateDrudeLangevinStepKernel::execute(ContextImpl& context, co
// Apply constraints.
if (constraints != NULL)
constraints->apply(numParticles, pos, xPrime, particleInvMass);
constraints->apply(pos, xPrime, particleInvMass);
// Record the constrained positions and velocities.
......@@ -395,21 +379,19 @@ void ReferenceIntegrateDrudeSCFStepKernel::initialize(const System& system, cons
// Prepare constraints.
int numConstraints = system.getNumConstraints();
if (numConstraints > 0) {
vector<pair<int, int> > constraintIndices(numConstraints);
vector<RealOpenMM> constraintDistances(numConstraints);
for (int i = 0; i < numConstraints; ++i) {
if (system.getNumConstraints() > 0) {
vector<pair<int, int> > constraintIndices;
vector<RealOpenMM> constraintDistances;
for (int i = 0; i < system.getNumConstraints(); ++i) {
int particle1, particle2;
double distance;
system.getConstraintParameters(i, particle1, particle2, distance);
constraintIndices[i].first = particle1;
constraintIndices[i].second = particle2;
constraintDistances[i] = static_cast<RealOpenMM>(distance);
if (system.getParticleMass(particle1) != 0 || system.getParticleMass(particle2) != 0) {
constraintIndices.push_back(make_pair(particle1, particle2));
constraintDistances.push_back(distance);
}
}
vector<ReferenceCCMAAlgorithm::AngleInfo> angles;
findAnglesForCCMA(system, angles);
constraints = new ReferenceCCMAAlgorithm(system.getNumParticles(), numConstraints, constraintIndices, constraintDistances, particleMass, angles, (RealOpenMM)integrator.getConstraintTolerance());
constraints = new ReferenceConstraints(system, (RealOpenMM) integrator.getConstraintTolerance());
}
// Initialize the energy minimizer.
......@@ -443,7 +425,7 @@ void ReferenceIntegrateDrudeSCFStepKernel::execute(ContextImpl& context, const D
// Apply constraints.
if (constraints != NULL)
constraints->apply(numParticles, pos, xPrime, particleInvMass);
constraints->apply(pos, xPrime, particleInvMass);
// Record the constrained positions and velocities.
......
plugins/rpmd/openmmapi/include/openmm/RPMDIntegrator.h
View file @ 99ef4344
......@@ -47,6 +47,9 @@ namespace OpenMM {
* springs to form a ring. This allows certain quantum mechanical effects to be efficiently
* simulated.
*
* By default this Integrator applies a PILE thermostat to the system to simulate constant
* temperature dynamics. You can disable the thermostat by calling setApplyThermostat(false).
*
* Because this Integrator simulates many copies of the System at once, it must be used
* differently from other Integrators. Instead of setting positions and velocities by
* calling methods of the Context, you should use the corresponding methods of the Integrator
......@@ -127,6 +130,18 @@ public:
void setFriction(double coeff) {
friction = coeff;
}
/**
* Get whether a thermostat is applied to the system.
*/
bool getApplyThermostat() const {
return applyThermostat;
}
/**
* Set whether a thermostat is applied to the system.
*/
void setApplyThermostat(bool apply) {
applyThermostat = apply;
}
/**
* Get the random number seed. See setRandomNumberSeed() for details.
*/
......@@ -213,6 +228,7 @@ protected:
private:
double temperature, friction;
int numCopies, randomNumberSeed;
bool applyThermostat;
std::map<int, int> contractions;
bool forcesAreValid, hasSetPosition, hasSetVelocity, isFirstStep;
Kernel kernel;
......
plugins/rpmd/openmmapi/src/RPMDIntegrator.cpp
View file @ 99ef4344
......@@ -42,7 +42,7 @@ using namespace OpenMM;
using namespace std;
RPMDIntegrator::RPMDIntegrator(int numCopies, double temperature, double frictionCoeff, double stepSize, const map<int, int>& contractions) :
numCopies(numCopies), contractions(contractions), forcesAreValid(false), hasSetPosition(false), hasSetVelocity(false), isFirstStep(true) {
numCopies(numCopies), applyThermostat(true), contractions(contractions), forcesAreValid(false), hasSetPosition(false), hasSetVelocity(false), isFirstStep(true) {
setTemperature(temperature);
setFriction(frictionCoeff);
setStepSize(stepSize);
......@@ -51,7 +51,7 @@ RPMDIntegrator::RPMDIntegrator(int numCopies, double temperature, double frictio
}
RPMDIntegrator::RPMDIntegrator(int numCopies, double temperature, double frictionCoeff, double stepSize) :
numCopies(numCopies), forcesAreValid(false), hasSetPosition(false), hasSetVelocity(false), isFirstStep(true) {
numCopies(numCopies), applyThermostat(true), forcesAreValid(false), hasSetPosition(false), hasSetVelocity(false), isFirstStep(true) {
setTemperature(temperature);
setFriction(frictionCoeff);
setStepSize(stepSize);
......
plugins/rpmd/platforms/cuda/src/CudaRpmdKernels.cpp
View file @ 99ef4344
......@@ -205,6 +205,7 @@ void CudaIntegrateRPMDStepKernel::execute(ContextImpl& context, const RPMDIntegr
void* frictionPtr = (useDoublePrecision ? (void*) &friction : (void*) &frictionFloat);
int randomIndex = integration.prepareRandomNumbers(numParticles*numCopies);
void* pileArgs[] = {&velocities->getDevicePointer(), &integration.getRandom().getDevicePointer(), &randomIndex, dtPtr, kTPtr, frictionPtr};
if (integrator.getApplyThermostat())
cu.executeKernel(pileKernel, pileArgs, numParticles*numCopies, workgroupSize);
// Update positions and velocities.
......@@ -223,8 +224,10 @@ void CudaIntegrateRPMDStepKernel::execute(ContextImpl& context, const RPMDIntegr
// Apply the PILE-L thermostat again.
if (integrator.getApplyThermostat()) {
randomIndex = integration.prepareRandomNumbers(numParticles*numCopies);
cu.executeKernel(pileKernel, pileArgs, numParticles*numCopies, workgroupSize);
}
// Update the time and step count.
......
plugins/rpmd/platforms/cuda/tests/TestCudaRpmd.cpp
View file @ 99ef4344
......@@ -431,6 +431,71 @@ void testContractions() {
ASSERT_USUALLY_EQUAL_TOL(expectedKE, meanKE, 1e-2);
}
void testWithoutThermostat() {
const int numParticles = 20;
const int numCopies = 10;
const double temperature = 300.0;
const double mass = 2.0;
// Create a chain of particles.
System system;
HarmonicBondForce* bonds = new HarmonicBondForce();
system.addForce(bonds);
for (int i = 0; i < numParticles; i++) {
system.addParticle(mass);
if (i > 0)
bonds->addBond(i-1, i, 1.0, 1000.0);
}
RPMDIntegrator integ(numCopies, temperature, 1.0, 0.001);
integ.setApplyThermostat(false);
Platform& platform = Platform::getPlatformByName("CUDA");
Context context(system, integ, platform);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<vector<Vec3> > positions(numCopies);
for (int i = 0; i < numCopies; i++) {
positions[i].resize(numParticles);
for (int j = 0; j < numParticles; j++)
positions[i][j] = Vec3(0.95*j, 0.01*genrand_real2(sfmt), 0.01*genrand_real2(sfmt));
integ.setPositions(i, positions[i]);
}
// Simulate it and see if the energy remains constant.
double initialEnergy;
int numSteps = 100;
const double hbar = 1.054571628e-34*AVOGADRO/(1000*1e-12);
const double wn = numCopies*BOLTZ*temperature/hbar;
const double springConstant = mass*wn*wn;
for (int i = 0; i < numSteps; i++) {
integ.step(1);
// Sum the energies of all the copies.
double energy = 0.0;
for (int j = 0; j < numCopies; j++) {
State state = integ.getState(j, State::Positions | State::Energy);
positions[j] = state.getPositions();
energy += state.getPotentialEnergy()+state.getKineticEnergy();
}
// Add the energy from the springs connecting copies.
for (int j = 0; j < numCopies; j++) {
int previous = (j == 0 ? numCopies-1 : j-1);
for (int k = 0; k < numParticles; k++) {
Vec3 delta = positions[j][k]-positions[previous][k];
energy += 0.5*springConstant*delta.dot(delta);
}
}
if (i == 0)
initialEnergy = energy;
else
ASSERT_EQUAL_TOL(initialEnergy, energy, 1e-4);
}
}
int main(int argc, char* argv[]) {
try {
registerRPMDCudaKernelFactories();
......@@ -441,6 +506,7 @@ int main(int argc, char* argv[]) {
testCMMotionRemoval();
testVirtualSites();
testContractions();
testWithoutThermostat();
}
catch(const std::exception& e) {
std::cout << "exception: " << e.what() << std::endl;
......
plugins/rpmd/platforms/opencl/src/OpenCLRpmdKernels.cpp
View file @ 99ef4344
......@@ -223,6 +223,7 @@ void OpenCLIntegrateRPMDStepKernel::execute(ContextImpl& context, const RPMDInte
stepKernel.setArg<cl_float>(4, (cl_float) (integrator.getTemperature()*BOLTZ));
velocitiesKernel.setArg<cl_float>(2, (cl_float) dt);
}
if (integrator.getApplyThermostat())
cl.executeKernel(pileKernel, numParticles*numCopies, workgroupSize);
// Update positions and velocities.
......@@ -238,8 +239,10 @@ void OpenCLIntegrateRPMDStepKernel::execute(ContextImpl& context, const RPMDInte
// Apply the PILE-L thermostat again.
if (integrator.getApplyThermostat()) {
pileKernel.setArg<cl_uint>(2, integration.prepareRandomNumbers(numParticles*numCopies));
cl.executeKernel(pileKernel, numParticles*numCopies, workgroupSize);
}
// Update the time and step count.
......
plugins/rpmd/platforms/opencl/tests/TestOpenCLRpmd.cpp
View file @ 99ef4344
......@@ -432,6 +432,71 @@ void testContractions() {
ASSERT_USUALLY_EQUAL_TOL(expectedKE, meanKE, 1e-2);
}
void testWithoutThermostat() {
const int numParticles = 20;
const int numCopies = 10;
const double temperature = 300.0;
const double mass = 2.0;
// Create a chain of particles.
System system;
HarmonicBondForce* bonds = new HarmonicBondForce();
system.addForce(bonds);
for (int i = 0; i < numParticles; i++) {
system.addParticle(mass);
if (i > 0)
bonds->addBond(i-1, i, 1.0, 1000.0);
}
RPMDIntegrator integ(numCopies, temperature, 1.0, 0.001);
integ.setApplyThermostat(false);
Platform& platform = Platform::getPlatformByName("OpenCL");
Context context(system, integ, platform);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<vector<Vec3> > positions(numCopies);
for (int i = 0; i < numCopies; i++) {
positions[i].resize(numParticles);
for (int j = 0; j < numParticles; j++)
positions[i][j] = Vec3(0.95*j, 0.01*genrand_real2(sfmt), 0.01*genrand_real2(sfmt));
integ.setPositions(i, positions[i]);
}
// Simulate it and see if the energy remains constant.
double initialEnergy;
int numSteps = 100;
const double hbar = 1.054571628e-34*AVOGADRO/(1000*1e-12);
const double wn = numCopies*BOLTZ*temperature/hbar;
const double springConstant = mass*wn*wn;
for (int i = 0; i < numSteps; i++) {
integ.step(1);
// Sum the energies of all the copies.
double energy = 0.0;
for (int j = 0; j < numCopies; j++) {
State state = integ.getState(j, State::Positions | State::Energy);
positions[j] = state.getPositions();
energy += state.getPotentialEnergy()+state.getKineticEnergy();
}
// Add the energy from the springs connecting copies.
for (int j = 0; j < numCopies; j++) {
int previous = (j == 0 ? numCopies-1 : j-1);
for (int k = 0; k < numParticles; k++) {
Vec3 delta = positions[j][k]-positions[previous][k];
energy += 0.5*springConstant*delta.dot(delta);
}
}
if (i == 0)
initialEnergy = energy;
else
ASSERT_EQUAL_TOL(initialEnergy, energy, 1e-4);
}
}
int main(int argc, char* argv[]) {
try {
registerRPMDOpenCLKernelFactories();
......@@ -442,6 +507,7 @@ int main(int argc, char* argv[]) {
testCMMotionRemoval();
testVirtualSites();
testContractions();
testWithoutThermostat();
}
catch(const std::exception& e) {
std::cout << "exception: " << e.what() << std::endl;
......
plugins/rpmd/platforms/reference/src/ReferenceRpmdKernels.cpp
View file @ 99ef4344
......@@ -135,6 +135,7 @@ void ReferenceIntegrateRPMDStepKernel::execute(ContextImpl& context, const RPMDI
const RealOpenMM twown = 2.0*nkT/hbar;
const RealOpenMM c1_0 = exp(-halfdt*integrator.getFriction());
const RealOpenMM c2_0 = sqrt(1.0-c1_0*c1_0);
if (integrator.getApplyThermostat()) {
for (int particle = 0; particle < numParticles; particle++) {
if (system.getParticleMass(particle) == 0.0)
continue;
......@@ -167,6 +168,7 @@ void ReferenceIntegrateRPMDStepKernel::execute(ContextImpl& context, const RPMDI
velocities[k][particle][component] = scale*v[k].re;
}
}
}
// Update velocities.
......@@ -220,6 +222,7 @@ void ReferenceIntegrateRPMDStepKernel::execute(ContextImpl& context, const RPMDI
// Apply the PILE-L thermostat again.
if (integrator.getApplyThermostat()) {
for (int particle = 0; particle < numParticles; particle++) {
if (system.getParticleMass(particle) == 0.0)
continue;
......@@ -252,6 +255,7 @@ void ReferenceIntegrateRPMDStepKernel::execute(ContextImpl& context, const RPMDI
velocities[k][particle][component] = scale*v[k].re;
}
}
}
// Update the time.
......
plugins/rpmd/platforms/reference/tests/TestReferenceRpmd.cpp
View file @ 99ef4344
......@@ -313,12 +313,78 @@ void testContractions() {
ASSERT_USUALLY_EQUAL_TOL(expectedKE, meanKE, 1e-2);
}
void testWithoutThermostat() {
const int numParticles = 20;
const int numCopies = 10;
const double temperature = 300.0;
const double mass = 2.0;
// Create a chain of particles.
System system;
HarmonicBondForce* bonds = new HarmonicBondForce();
system.addForce(bonds);
for (int i = 0; i < numParticles; i++) {
system.addParticle(mass);
if (i > 0)
bonds->addBond(i-1, i, 1.0, 1000.0);
}
RPMDIntegrator integ(numCopies, temperature, 1.0, 0.001);
integ.setApplyThermostat(false);
Platform& platform = Platform::getPlatformByName("Reference");
Context context(system, integ, platform);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<vector<Vec3> > positions(numCopies);
for (int i = 0; i < numCopies; i++) {
positions[i].resize(numParticles);
for (int j = 0; j < numParticles; j++)
positions[i][j] = Vec3(0.95*j, 0.01*genrand_real2(sfmt), 0.01*genrand_real2(sfmt));
integ.setPositions(i, positions[i]);
}
// Simulate it and see if the energy remains constant.
double initialEnergy;
int numSteps = 100;
const double hbar = 1.054571628e-34*AVOGADRO/(1000*1e-12);
const double wn = numCopies*BOLTZ*temperature/hbar;
const double springConstant = mass*wn*wn;
for (int i = 0; i < numSteps; i++) {
integ.step(1);
// Sum the energies of all the copies.
double energy = 0.0;
for (int j = 0; j < numCopies; j++) {
State state = integ.getState(j, State::Positions | State::Energy);
positions[j] = state.getPositions();
energy += state.getPotentialEnergy()+state.getKineticEnergy();
}
// Add the energy from the springs connecting copies.
for (int j = 0; j < numCopies; j++) {
int previous = (j == 0 ? numCopies-1 : j-1);
for (int k = 0; k < numParticles; k++) {
Vec3 delta = positions[j][k]-positions[previous][k];
energy += 0.5*springConstant*delta.dot(delta);
}
}
if (i == 0)
initialEnergy = energy;
else
ASSERT_EQUAL_TOL(initialEnergy, energy, 1e-4);
}
}
int main() {
try {
testFreeParticles();
testCMMotionRemoval();
testVirtualSites();
testContractions();
testWithoutThermostat();
}
catch(const std::exception& e) {
std::cout << "exception: " << e.what() << std::endl;
......
tests/TestParser.cpp
View file @ 99ef4344
......@@ -56,6 +56,12 @@ void verifyEvaluation(const string& expression, double expectedValue) {
ExpressionProgram program = parsed.createProgram();
value = program.evaluate();
ASSERT_EQUAL_TOL(expectedValue, value, 1e-10);
// Create a CompiledExpression and see if that also gives the same result.
CompiledExpression compiled = parsed.createCompiledExpression();
value = compiled.evaluate();
ASSERT_EQUAL_TOL(expectedValue, value, 1e-10);
}
/**
......@@ -86,6 +92,16 @@ void verifyEvaluation(const string& expression, double x, double y, double expec
value = program.evaluate(variables);
ASSERT_EQUAL_TOL(expectedValue, value, 1e-10);
// Create a CompiledExpression and see if that also gives the same result.
CompiledExpression compiled = parsed.createCompiledExpression();
if (compiled.getVariables().find("x") != compiled.getVariables().end())
compiled.getVariableReference("x") = x;
if (compiled.getVariables().find("y") != compiled.getVariables().end())
compiled.getVariableReference("y") = y;
value = compiled.evaluate();
ASSERT_EQUAL_TOL(expectedValue, value, 1e-10);
// Make sure that variable renaming works.
variables.clear();
......
wrappers/python/setup.py
View file @ 99ef4344
......@@ -85,6 +85,7 @@ version = '%(version)s'
full_version = '%(full_version)s'
git_revision = '%(git_revision)s'
release = %(isrelease)s
openmm_library_path = '%(path)s'
if not release:
version = full_version
......@@ -113,7 +114,8 @@ if not release:
a.write(cnt % {'version': version,
'full_version' : full_version,
'git_revision' : git_revision,
'isrelease': str(IS_RELEASED)})
'isrelease': str(IS_RELEASED),
'path': os.getenv('OPENMM_LIB_PATH')})
finally:
a.close()
......@@ -197,7 +199,7 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
macVersion = [int(x) for x in platform.mac_ver()[0].split('.')]
if tuple(macVersion) < (10, 6):
os.environ['MACOSX_DEPLOYMENT_TARGET']='10.5'
extra_link_args.append('-Wl,-rpath,@loader_path/OpenMM')
extra_link_args.append('-Wl,-rpath,'+openmm_lib_path)
library_dirs=[openmm_lib_path]
......@@ -209,6 +211,7 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
include_dirs = include_dirs,
define_macros = define_macros,
library_dirs = library_dirs,
runtime_library_dirs = library_dirs,
libraries = libraries,
extra_compile_args=extra_compile_args,
extra_link_args=extra_link_args,
......@@ -238,8 +241,8 @@ def main():
uninstall()
except:
pass
writeVersionPy()
setupKeywords=buildKeywordDictionary()
writeVersionPy()
setup(**setupKeywords)
if __name__ == '__main__':
......
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