Skip to content

GitLab

Commit 07afe544 authored by peastman's avatar peastman
Browse files

Merge pull request #1171 from peastman/hardwall 

Hard wall constraints for DrudeLangevinIntegrator
parents 59bd8d19 fce85f6d
Show whitespace changes
Inline Side-by-side
Showing with 368 additions and 16 deletions
plugins/drude/openmmapi/include/openmm/DrudeLangevinIntegrator.h
View file @ 07afe544
......@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2013 Stanford University and the Authors. *
* Portions copyright (c) 2008-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -45,6 +45,10 @@ namespace OpenMM {
* A second thermostat, typically with a much lower temperature, is applied to the relative internal
* displacement of each pair.
*
* This integrator can optionally set an upper limit on how far any Drude particle is ever allowed to
* get from its parent particle. This can sometimes help to improve stability. The limit is enforced
* with a hard wall constraint.
*
* This Integrator requires the System to include a DrudeForce, which it uses to identify the Drude
* particles.
*/
......@@ -129,6 +133,16 @@ public:
void setDrudeFriction(double coeff) {
drudeFriction = coeff;
}
/**
* Get the maximum distance a Drude particle can ever move from its parent particle, measured in nm. This is implemented
* with a hard wall constraint. If this distance is set to 0 (the default), the hard wall constraint is omitted.
*/
double getMaxDrudeDistance() const;
/**
* Set the maximum distance a Drude particle can ever move from its parent particle, measured in nm. This is implemented
* with a hard wall constraint. If this distance is set to 0 (the default), the hard wall constraint is omitted.
*/
void setMaxDrudeDistance(double distance);
/**
* Get the random number seed. See setRandomNumberSeed() for details.
*/
......@@ -181,7 +195,7 @@ protected:
*/
double computeKineticEnergy();
private:
double temperature, friction, drudeTemperature, drudeFriction;
double temperature, friction, drudeTemperature, drudeFriction, maxDrudeDistance;
int randomNumberSeed;
Kernel kernel;
};
......
plugins/drude/openmmapi/src/DrudeLangevinIntegrator.cpp
View file @ 07afe544
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2013 Stanford University and the Authors. *
* Portions copyright (c) 2008-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -46,11 +46,22 @@ DrudeLangevinIntegrator::DrudeLangevinIntegrator(double temperature, double fric
setFriction(frictionCoeff);
setDrudeTemperature(drudeTemperature);
setDrudeFriction(drudeFrictionCoeff);
setMaxDrudeDistance(0);
setStepSize(stepSize);
setConstraintTolerance(1e-5);
setRandomNumberSeed(0);
}
double DrudeLangevinIntegrator::getMaxDrudeDistance() const {
return maxDrudeDistance;
}
void DrudeLangevinIntegrator::setMaxDrudeDistance(double distance) {
if (distance < 0)
throw OpenMMException("setMaxDrudeDistance: Distance cannot be negative");
maxDrudeDistance = distance;
}
void DrudeLangevinIntegrator::initialize(ContextImpl& contextRef) {
if (owner != NULL && &contextRef.getOwner() != owner)
throw OpenMMException("This Integrator is already bound to a context");
......
plugins/drude/platforms/cuda/src/CudaDrudeKernels.cpp
View file @ 07afe544
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2013 Stanford University and the Authors. *
* Portions copyright (c) 2013-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -279,6 +279,7 @@ void CudaIntegrateDrudeLangevinStepKernel::initialize(const System& system, cons
CUmodule module = cu.createModule(CudaKernelSources::vectorOps+CudaDrudeKernelSources::drudeLangevin, defines, "");
kernel1 = cu.getKernel(module, "integrateDrudeLangevinPart1");
kernel2 = cu.getKernel(module, "integrateDrudeLangevinPart2");
hardwallKernel = cu.getKernel(module, "applyHardWallConstraints");
prevStepSize = -1.0;
}
......@@ -296,6 +297,8 @@ void CudaIntegrateDrudeLangevinStepKernel::execute(ContextImpl& context, const D
double vscaleDrude = exp(-stepSize*integrator.getDrudeFriction());
double fscaleDrude = (1-vscaleDrude)/integrator.getDrudeFriction()/(double) 0x100000000;
double noisescaleDrude = sqrt(2*BOLTZ*integrator.getDrudeTemperature()*integrator.getDrudeFriction())*sqrt(0.5*(1-vscaleDrude*vscaleDrude)/integrator.getDrudeFriction());
double maxDrudeDistance = integrator.getMaxDrudeDistance();
double hardwallscaleDrude = sqrt(BOLTZ*integrator.getDrudeTemperature());
if (stepSize != prevStepSize) {
if (cu.getUseDoublePrecision() || cu.getUseMixedPrecision()) {
double2 ss = make_double2(0, stepSize);
......@@ -316,7 +319,9 @@ void CudaIntegrateDrudeLangevinStepKernel::execute(ContextImpl& context, const D
float vscaleDrudeFloat = (float) vscaleDrude;
float fscaleDrudeFloat = (float) fscaleDrude;
float noisescaleDrudeFloat = (float) noisescaleDrude;
void *vscalePtr, *fscalePtr, *noisescalePtr, *vscaleDrudePtr, *fscaleDrudePtr, *noisescaleDrudePtr;
float maxDrudeDistanceFloat =(float) maxDrudeDistance;
float hardwallscaleDrudeFloat = (float) hardwallscaleDrude;
void *vscalePtr, *fscalePtr, *noisescalePtr, *vscaleDrudePtr, *fscaleDrudePtr, *noisescaleDrudePtr, *maxDrudeDistancePtr, *hardwallscaleDrudePtr;
if (cu.getUseDoublePrecision() || cu.getUseMixedPrecision()) {
vscalePtr = &vscale;
fscalePtr = &fscale;
......@@ -324,6 +329,8 @@ void CudaIntegrateDrudeLangevinStepKernel::execute(ContextImpl& context, const D
vscaleDrudePtr = &vscaleDrude;
fscaleDrudePtr = &fscaleDrude;
noisescaleDrudePtr = &noisescaleDrude;
maxDrudeDistancePtr = &maxDrudeDistance;
hardwallscaleDrudePtr = &hardwallscaleDrude;
}
else {
vscalePtr = &vscaleFloat;
......@@ -332,6 +339,8 @@ void CudaIntegrateDrudeLangevinStepKernel::execute(ContextImpl& context, const D
vscaleDrudePtr = &vscaleDrudeFloat;
fscaleDrudePtr = &fscaleDrudeFloat;
noisescaleDrudePtr = &noisescaleDrudeFloat;
maxDrudeDistancePtr = &maxDrudeDistanceFloat;
hardwallscaleDrudePtr = &hardwallscaleDrudeFloat;
}
// Call the first integration kernel.
......@@ -352,6 +361,12 @@ void CudaIntegrateDrudeLangevinStepKernel::execute(ContextImpl& context, const D
void* args2[] = {&cu.getPosq().getDevicePointer(), &posCorrection, &integration.getPosDelta().getDevicePointer(),
&cu.getVelm().getDevicePointer(), &integration.getStepSize().getDevicePointer()};
cu.executeKernel(kernel2, args2, numAtoms);
// Apply hard wall constraints.
void* hardwallArgs[] = {&cu.getPosq().getDevicePointer(), &posCorrection, &cu.getVelm().getDevicePointer(),
&pairParticles->getDevicePointer(), &integration.getStepSize().getDevicePointer(), maxDrudeDistancePtr, hardwallscaleDrudePtr};
cu.executeKernel(hardwallKernel, hardwallArgs, pairParticles->getSize());
integration.computeVirtualSites();
// Update the time and step count.
......
plugins/drude/platforms/cuda/src/CudaDrudeKernels.h
View file @ 07afe544
......@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2013 Stanford University and the Authors. *
* Portions copyright (c) 2013-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -113,7 +113,7 @@ private:
double prevStepSize;
CudaArray* normalParticles;
CudaArray* pairParticles;
CUfunction kernel1, kernel2;
CUfunction kernel1, kernel2, hardwallKernel;
};
/**
......
plugins/drude/platforms/cuda/src/kernels/drudeLangevin.cu
View file @ 07afe544
......@@ -101,3 +101,111 @@ extern "C" __global__ void integrateDrudeLangevinPart2(real4* __restrict__ posq,
index += blockDim.x*gridDim.x;
}
}
/**
* Apply hard wall constraints
*/
extern "C" __global__ void applyHardWallConstraints(real4* __restrict__ posq, real4* __restrict__ posqCorrection, mixed4* __restrict__ velm,
const int2* __restrict__ pairParticles, const mixed2* __restrict__ dt, mixed maxDrudeDistance, mixed hardwallscaleDrude) {
mixed stepSize = dt[0].y;
for (int i = blockIdx.x*blockDim.x+threadIdx.x; i < NUM_PAIRS; i += blockDim.x*gridDim.x) {
int2 particles = pairParticles[i];
#ifdef USE_MIXED_PRECISION
real4 posReal1 = posq[particles.x];
real4 posReal2 = posq[particles.y];
real4 posCorr1 = posqCorrection[particles.x];
real4 posCorr2 = posqCorrection[particles.y];
mixed4 pos1 = make_mixed4(posReal1.x+(mixed)posCorr1.x, posReal1.y+(mixed)posCorr1.y, posReal1.z+(mixed)posCorr1.z, posReal1.w);
mixed4 pos2 = make_mixed4(posReal2.x+(mixed)posCorr2.x, posReal2.y+(mixed)posCorr2.y, posReal2.z+(mixed)posCorr2.z, posReal2.w);
#else
mixed4 pos1 = posq[particles.x];
mixed4 pos2 = posq[particles.y];
#endif
mixed4 delta = pos1-pos2;
mixed r = SQRT(delta.x*delta.x + delta.y*delta.y + delta.z*delta.z);
mixed rInv = RECIP(r);
if (rInv*maxDrudeDistance < 1) {
// The constraint has been violated, so make the inter-particle distance "bounce"
// off the hard wall.
mixed4 bondDir = delta*rInv;
mixed4 vel1 = velm[particles.x];
mixed4 vel2 = velm[particles.y];
mixed mass1 = RECIP(vel1.w);
mixed mass2 = RECIP(vel2.w);
mixed deltaR = r-maxDrudeDistance;
mixed deltaT = stepSize;
mixed dotvr1 = vel1.x*bondDir.x + vel1.y*bondDir.y + vel1.z*bondDir.z;
mixed4 vb1 = bondDir*dotvr1;
mixed4 vp1 = vel1-vb1;
if (vel2.w == 0) {
// The parent particle is massless, so move only the Drude particle.
if (dotvr1 != 0)
deltaT = deltaR/fabs(dotvr1);
if (deltaT > stepSize)
deltaT = stepSize;
dotvr1 = -dotvr1*hardwallscaleDrude/(fabs(dotvr1)*SQRT(mass1));
mixed dr = -deltaR + deltaT*dotvr1;
pos1.x += bondDir.x*dr;
pos1.y += bondDir.y*dr;
pos1.z += bondDir.z*dr;
#ifdef USE_MIXED_PRECISION
posq[particles.x] = make_real4((real) pos1.x, (real) pos1.y, (real) pos1.z, (real) pos1.w);
posqCorrection[particles.x] = make_real4(pos1.x-(real) pos1.x, pos1.y-(real) pos1.y, pos1.z-(real) pos1.z, 0);
#else
posq[particles.x] = pos1;
#endif
vel1.x = vp1.x + bondDir.x*dotvr1;
vel1.y = vp1.y + bondDir.y*dotvr1;
vel1.z = vp1.z + bondDir.z*dotvr1;
velm[particles.x] = vel1;
}
else {
// Move both particles.
mixed invTotalMass = RECIP(mass1+mass2);
mixed dotvr2 = vel2.x*bondDir.x + vel2.y*bondDir.y + vel2.z*bondDir.z;
mixed4 vb2 = bondDir*dotvr2;
mixed4 vp2 = vel2-vb2;
mixed vbCMass = (mass1*dotvr1 + mass2*dotvr2)*invTotalMass;
dotvr1 -= vbCMass;
dotvr2 -= vbCMass;
if (dotvr1 != dotvr2)
deltaT = deltaR/fabs(dotvr1-dotvr2);
if (deltaT > stepSize)
deltaT = stepSize;
mixed vBond = hardwallscaleDrude/SQRT(mass1);
dotvr1 = -dotvr1*vBond*mass2*invTotalMass/fabs(dotvr1);
dotvr2 = -dotvr2*vBond*mass1*invTotalMass/fabs(dotvr2);
mixed dr1 = -deltaR*mass2*invTotalMass + deltaT*dotvr1;
mixed dr2 = deltaR*mass1*invTotalMass + deltaT*dotvr2;
dotvr1 += vbCMass;
dotvr2 += vbCMass;
pos1.x += bondDir.x*dr1;
pos1.y += bondDir.y*dr1;
pos1.z += bondDir.z*dr1;
pos2.x += bondDir.x*dr2;
pos2.y += bondDir.y*dr2;
pos2.z += bondDir.z*dr2;
#ifdef USE_MIXED_PRECISION
posq[particles.x] = make_real4((real) pos1.x, (real) pos1.y, (real) pos1.z, (real) pos1.w);
posq[particles.y] = make_real4((real) pos2.x, (real) pos2.y, (real) pos2.z, (real) pos2.w);
posqCorrection[particles.x] = make_real4(pos1.x-(real) pos1.x, pos1.y-(real) pos1.y, pos1.z-(real) pos1.z, 0);
posqCorrection[particles.y] = make_real4(pos2.x-(real) pos2.x, pos2.y-(real) pos2.y, pos2.z-(real) pos2.z, 0);
#else
posq[particles.x] = pos1;
posq[particles.y] = pos2;
#endif
vel1.x = vp1.x + bondDir.x*dotvr1;
vel1.y = vp1.y + bondDir.y*dotvr1;
vel1.z = vp1.z + bondDir.z*dotvr1;
vel2.x = vp2.x + bondDir.x*dotvr2;
vel2.y = vp2.y + bondDir.y*dotvr2;
vel2.z = vp2.z + bondDir.z*dotvr2;
velm[particles.x] = vel1;
velm[particles.y] = vel2;
}
}
}
}
plugins/drude/platforms/cuda/tests/TestCudaDrudeLangevinIntegrator.cpp
View file @ 07afe544
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2013 Stanford University and the Authors. *
* Portions copyright (c) 2013-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -60,6 +60,7 @@ void testSinglePair() {
const double mass2 = 0.1;
const double totalMass = mass1+mass2;
const double reducedMass = (mass1*mass2)/(mass1+mass2);
const double maxDistance = 0.05;
System system;
system.addParticle(mass1);
system.addParticle(mass2);
......@@ -70,6 +71,7 @@ void testSinglePair() {
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(0, 0, 0);
DrudeLangevinIntegrator integ(temperature, 20.0, temperatureDrude, 20.0, 0.003);
integ.setMaxDrudeDistance(maxDistance);
Platform& platform = Platform::getPlatformByName("CUDA");
Context context(system, integ, platform);
context.setPositions(positions);
......@@ -84,12 +86,15 @@ void testSinglePair() {
int numSteps = 10000;
for (int i = 0; i < numSteps; i++) {
integ.step(10);
State state = context.getState(State::Velocities);
State state = context.getState(State::Velocities | State::Positions);
const vector<Vec3>& vel = state.getVelocities();
Vec3 velCM = vel[0]*(mass1/totalMass) + vel[1]*(mass2/totalMass);
keCM += 0.5*totalMass*velCM.dot(velCM);
Vec3 velInternal = vel[0]-vel[1];
keInternal += 0.5*reducedMass*velInternal.dot(velInternal);
Vec3 delta = state.getPositions()[0]-state.getPositions()[1];
double distance = sqrt(delta.dot(delta));
ASSERT(distance <= maxDistance*(1+1e-6));
}
ASSERT_USUALLY_EQUAL_TOL(3*0.5*BOLTZ*temperature, keCM/numSteps, 0.1);
ASSERT_USUALLY_EQUAL_TOL(3*0.5*BOLTZ*temperatureDrude, keInternal/numSteps, 0.01);
......
plugins/drude/platforms/opencl/src/OpenCLDrudeKernels.cpp
View file @ 07afe544
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2013 Stanford University and the Authors. *
* Portions copyright (c) 2013-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -284,6 +284,7 @@ void OpenCLIntegrateDrudeLangevinStepKernel::initialize(const System& system, co
cl::Program program = cl.createProgram(OpenCLDrudeKernelSources::drudeLangevin, defines, "");
kernel1 = cl::Kernel(program, "integrateDrudeLangevinPart1");
kernel2 = cl::Kernel(program, "integrateDrudeLangevinPart2");
hardwallKernel = cl::Kernel(program, "applyHardWallConstraints");
prevStepSize = -1.0;
}
......@@ -307,6 +308,14 @@ void OpenCLIntegrateDrudeLangevinStepKernel::execute(ContextImpl& context, const
kernel2.setArg<cl::Buffer>(2, integration.getPosDelta().getDeviceBuffer());
kernel2.setArg<cl::Buffer>(3, cl.getVelm().getDeviceBuffer());
kernel2.setArg<cl::Buffer>(4, integration.getStepSize().getDeviceBuffer());
hardwallKernel.setArg<cl::Buffer>(0, cl.getPosq().getDeviceBuffer());
if (cl.getUseMixedPrecision())
hardwallKernel.setArg<cl::Buffer>(1, cl.getPosqCorrection().getDeviceBuffer());
else
hardwallKernel.setArg<void*>(1, NULL);
hardwallKernel.setArg<cl::Buffer>(2, cl.getVelm().getDeviceBuffer());
hardwallKernel.setArg<cl::Buffer>(3, pairParticles->getDeviceBuffer());
hardwallKernel.setArg<cl::Buffer>(4, integration.getStepSize().getDeviceBuffer());
}
// Compute integrator coefficients.
......@@ -318,6 +327,8 @@ void OpenCLIntegrateDrudeLangevinStepKernel::execute(ContextImpl& context, const
double vscaleDrude = exp(-stepSize*integrator.getDrudeFriction());
double fscaleDrude = (1-vscaleDrude)/integrator.getDrudeFriction();
double noisescaleDrude = sqrt(2*BOLTZ*integrator.getDrudeTemperature()*integrator.getDrudeFriction())*sqrt(0.5*(1-vscaleDrude*vscaleDrude)/integrator.getDrudeFriction());
double maxDrudeDistance = integrator.getMaxDrudeDistance();
double hardwallscaleDrude = sqrt(BOLTZ*integrator.getDrudeTemperature());
if (stepSize != prevStepSize) {
if (cl.getUseDoublePrecision() || cl.getUseMixedPrecision()) {
mm_double2 ss = mm_double2(0, stepSize);
......@@ -336,6 +347,8 @@ void OpenCLIntegrateDrudeLangevinStepKernel::execute(ContextImpl& context, const
kernel1.setArg<cl_double>(9, vscaleDrude);
kernel1.setArg<cl_double>(10, fscaleDrude);
kernel1.setArg<cl_double>(11, noisescaleDrude);
hardwallKernel.setArg<cl_double>(5, maxDrudeDistance);
hardwallKernel.setArg<cl_double>(6, hardwallscaleDrude);
}
else {
kernel1.setArg<cl_float>(6, (cl_float) vscale);
......@@ -344,6 +357,8 @@ void OpenCLIntegrateDrudeLangevinStepKernel::execute(ContextImpl& context, const
kernel1.setArg<cl_float>(9, (cl_float) vscaleDrude);
kernel1.setArg<cl_float>(10, (cl_float) fscaleDrude);
kernel1.setArg<cl_float>(11, (cl_float) noisescaleDrude);
hardwallKernel.setArg<cl_float>(5, (cl_float) maxDrudeDistance);
hardwallKernel.setArg<cl_float>(6, (cl_float) hardwallscaleDrude);
}
// Call the first integration kernel.
......@@ -358,6 +373,10 @@ void OpenCLIntegrateDrudeLangevinStepKernel::execute(ContextImpl& context, const
// Call the second integration kernel.
cl.executeKernel(kernel2, numAtoms);
// Apply hard wall constraints.
cl.executeKernel(hardwallKernel, pairParticles->getSize());
integration.computeVirtualSites();
// Update the time and step count.
......
plugins/drude/platforms/opencl/src/OpenCLDrudeKernels.h
View file @ 07afe544
......@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2013 Stanford University and the Authors. *
* Portions copyright (c) 2013-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -114,7 +114,7 @@ private:
double prevStepSize;
OpenCLArray* normalParticles;
OpenCLArray* pairParticles;
cl::Kernel kernel1, kernel2;
cl::Kernel kernel1, kernel2, hardwallKernel;
};
/**
......
plugins/drude/platforms/opencl/src/kernels/drudeLangevin.cl
View file @ 07afe544
......@@ -101,3 +101,99 @@ __kernel void integrateDrudeLangevinPart2(__global real4* restrict posq, __globa
index += get_global_size(0);
}
}
/**
* Apply hard wall constraints
*/
__kernel void applyHardWallConstraints(__global real4* restrict posq, __global real4* restrict posqCorrection, __global mixed4* restrict velm,
__global const int2* restrict pairParticles, __global const mixed2* restrict dt, mixed maxDrudeDistance, mixed hardwallscaleDrude) {
mixed stepSize = dt[0].y;
for (int i = get_global_id(0); i < NUM_PAIRS; i += get_global_size(0)) {
int2 particles = pairParticles[i];
#ifdef USE_MIXED_PRECISION
real4 posReal1 = posq[particles.x];
real4 posReal2 = posq[particles.y];
real4 posCorr1 = posqCorrection[particles.x];
real4 posCorr2 = posqCorrection[particles.y];
mixed4 pos1 = (mixed4) (posReal1.x+(mixed)posCorr1.x, posReal1.y+(mixed)posCorr1.y, posReal1.z+(mixed)posCorr1.z, posReal1.w);
mixed4 pos2 = (mixed4) (posReal2.x+(mixed)posCorr2.x, posReal2.y+(mixed)posCorr2.y, posReal2.z+(mixed)posCorr2.z, posReal2.w);
#else
mixed4 pos1 = posq[particles.x];
mixed4 pos2 = posq[particles.y];
#endif
mixed4 delta = pos1-pos2;
mixed r = sqrt(delta.x*delta.x + delta.y*delta.y + delta.z*delta.z);
mixed rInv = 1/r;
if (rInv*maxDrudeDistance < 1) {
// The constraint has been violated, so make the inter-particle distance "bounce"
// off the hard wall.
mixed4 bondDir = delta*rInv;
mixed4 vel1 = velm[particles.x];
mixed4 vel2 = velm[particles.y];
mixed mass1 = 1/vel1.w;
mixed mass2 = 1/vel2.w;
mixed deltaR = r-maxDrudeDistance;
mixed deltaT = stepSize;
mixed dotvr1 = vel1.x*bondDir.x + vel1.y*bondDir.y + vel1.z*bondDir.z;
mixed4 vb1 = bondDir*dotvr1;
mixed4 vp1 = vel1-vb1;
if (vel2.w == 0) {
// The parent particle is massless, so move only the Drude particle.
if (dotvr1 != 0)
deltaT = deltaR/fabs(dotvr1);
if (deltaT > stepSize)
deltaT = stepSize;
dotvr1 = -dotvr1*hardwallscaleDrude/(fabs(dotvr1)*sqrt(mass1));
mixed dr = -deltaR + deltaT*dotvr1;
pos1.xyz += bondDir.xyz*dr;
#ifdef USE_MIXED_PRECISION
posq[particles.x] = (real4) ((real) pos1.x, (real) pos1.y, (real) pos1.z, (real) pos1.w);
posqCorrection[particles.x] = (real4) (pos1.x-(real) pos1.x, pos1.y-(real) pos1.y, pos1.z-(real) pos1.z, 0);
#else
posq[particles.x] = pos1;
#endif
vel1.xyz = vp1.xyz + bondDir.xyz*dotvr1;
velm[particles.x] = vel1;
}
else {
// Move both particles.
mixed invTotalMass = 1/(mass1+mass2);
mixed dotvr2 = vel2.x*bondDir.x + vel2.y*bondDir.y + vel2.z*bondDir.z;
mixed4 vb2 = bondDir*dotvr2;
mixed4 vp2 = vel2-vb2;
mixed vbCMass = (mass1*dotvr1 + mass2*dotvr2)*invTotalMass;
dotvr1 -= vbCMass;
dotvr2 -= vbCMass;
if (dotvr1 != dotvr2)
deltaT = deltaR/fabs(dotvr1-dotvr2);
if (deltaT > stepSize)
deltaT = stepSize;
mixed vBond = hardwallscaleDrude/sqrt(mass1);
dotvr1 = -dotvr1*vBond*mass2*invTotalMass/fabs(dotvr1);
dotvr2 = -dotvr2*vBond*mass1*invTotalMass/fabs(dotvr2);
mixed dr1 = -deltaR*mass2*invTotalMass + deltaT*dotvr1;
mixed dr2 = deltaR*mass1*invTotalMass + deltaT*dotvr2;
dotvr1 += vbCMass;
dotvr2 += vbCMass;
pos1.xyz += bondDir.xyz*dr1;
pos2.xyz += bondDir.xyz*dr2;
#ifdef USE_MIXED_PRECISION
posq[particles.x] = (real4) ((real) pos1.x, (real) pos1.y, (real) pos1.z, (real) pos1.w);
posq[particles.y] = (real4) ((real) pos2.x, (real) pos2.y, (real) pos2.z, (real) pos2.w);
posqCorrection[particles.x] = (real4) (pos1.x-(real) pos1.x, pos1.y-(real) pos1.y, pos1.z-(real) pos1.z, 0);
posqCorrection[particles.y] = (real4) (pos2.x-(real) pos2.x, pos2.y-(real) pos2.y, pos2.z-(real) pos2.z, 0);
#else
posq[particles.x] = pos1;
posq[particles.y] = pos2;
#endif
vel1.xyz = vp1.xyz + bondDir.xyz*dotvr1;
vel2.xyz = vp2.xyz + bondDir.xyz*dotvr2;
velm[particles.x] = vel1;
velm[particles.y] = vel2;
}
}
}
}
plugins/drude/platforms/opencl/tests/TestOpenCLDrudeLangevinIntegrator.cpp
View file @ 07afe544
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2013 Stanford University and the Authors. *
* Portions copyright (c) 2013-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -60,6 +60,7 @@ void testSinglePair() {
const double mass2 = 0.1;
const double totalMass = mass1+mass2;
const double reducedMass = (mass1*mass2)/(mass1+mass2);
const double maxDistance = 0.05;
System system;
system.addParticle(mass1);
system.addParticle(mass2);
......@@ -70,6 +71,7 @@ void testSinglePair() {
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(0, 0, 0);
DrudeLangevinIntegrator integ(temperature, 20.0, temperatureDrude, 20.0, 0.003);
integ.setMaxDrudeDistance(maxDistance);
Platform& platform = Platform::getPlatformByName("OpenCL");
Context context(system, integ, platform);
context.setPositions(positions);
......@@ -84,12 +86,15 @@ void testSinglePair() {
int numSteps = 10000;
for (int i = 0; i < numSteps; i++) {
integ.step(10);
State state = context.getState(State::Velocities);
State state = context.getState(State::Velocities | State::Positions);
const vector<Vec3>& vel = state.getVelocities();
Vec3 velCM = vel[0]*(mass1/totalMass) + vel[1]*(mass2/totalMass);
keCM += 0.5*totalMass*velCM.dot(velCM);
Vec3 velInternal = vel[0]-vel[1];
keInternal += 0.5*reducedMass*velInternal.dot(velInternal);
Vec3 delta = state.getPositions()[0]-state.getPositions()[1];
double distance = sqrt(delta.dot(delta));
ASSERT(distance <= maxDistance*(1+1e-6));
}
ASSERT_USUALLY_EQUAL_TOL(3*0.5*BOLTZ*temperature, keCM/numSteps, 0.1);
ASSERT_USUALLY_EQUAL_TOL(3*0.5*BOLTZ*temperatureDrude, keInternal/numSteps, 0.01);
......
plugins/drude/platforms/reference/src/ReferenceDrudeKernels.cpp
View file @ 07afe544
......@@ -235,7 +235,6 @@ void ReferenceIntegrateDrudeLangevinStepKernel::initialize(const System& system,
// Identify particle pairs and ordinary particles.
set<int> particles;
vector<RealOpenMM> particleMass;
for (int i = 0; i < system.getNumParticles(); i++) {
particles.insert(i);
double mass = system.getParticleMass(i);
......@@ -325,6 +324,75 @@ void ReferenceIntegrateDrudeLangevinStepKernel::execute(ContextImpl& context, co
pos[i] = xPrime[i];
}
}
// Apply hard wall constraints.
const RealOpenMM maxDrudeDistance = integrator.getMaxDrudeDistance();
if (maxDrudeDistance > 0) {
const RealOpenMM hardwallscaleDrude = sqrt(kTDrude);
for (int i = 0; i < (int) pairParticles.size(); i++) {
int p1 = pairParticles[i].first;
int p2 = pairParticles[i].second;
RealVec delta = pos[p1]-pos[p2];
RealOpenMM r = sqrt(delta.dot(delta));
RealOpenMM rInv = 1/r;
if (rInv*maxDrudeDistance < 1.0) {
// The constraint has been violated, so make the inter-particle distance "bounce"
// off the hard wall.
if (rInv*maxDrudeDistance < 0.5)
throw OpenMMException("Drude particle moved too far beyond hard wall constraint");
RealVec bondDir = delta*rInv;
RealVec vel1 = vel[p1];
RealVec vel2 = vel[p2];
RealOpenMM mass1 = particleMass[p1];
RealOpenMM mass2 = particleMass[p2];
RealOpenMM deltaR = r-maxDrudeDistance;
RealOpenMM deltaT = dt;
RealOpenMM dotvr1 = vel1.dot(bondDir);
RealVec vb1 = bondDir*dotvr1;
RealVec vp1 = vel1-vb1;
if (mass2 == 0) {
// The parent particle is massless, so move only the Drude particle.
if (dotvr1 != 0.0)
deltaT = deltaR/abs(dotvr1);
if (deltaT > dt)
deltaT = dt;
dotvr1 = -dotvr1*hardwallscaleDrude/(abs(dotvr1)*sqrt(mass1));
RealOpenMM dr = -deltaR + deltaT*dotvr1;
pos[p1] += bondDir*dr;
vel[p1] = vp1 + bondDir*dotvr1;
}
else {
// Move both particles.
RealOpenMM invTotalMass = pairInvTotalMass[i];
RealOpenMM dotvr2 = vel2.dot(bondDir);
RealVec vb2 = bondDir*dotvr2;
RealVec vp2 = vel2-vb2;
RealOpenMM vbCMass = (mass1*dotvr1 + mass2*dotvr2)*invTotalMass;
dotvr1 -= vbCMass;
dotvr2 -= vbCMass;
if (dotvr1 != dotvr2)
deltaT = deltaR/abs(dotvr1-dotvr2);
if (deltaT > dt)
deltaT = dt;
RealOpenMM vBond = hardwallscaleDrude/sqrt(mass1);
dotvr1 = -dotvr1*vBond*mass2*invTotalMass/abs(dotvr1);
dotvr2 = -dotvr2*vBond*mass1*invTotalMass/abs(dotvr2);
RealOpenMM dr1 = -deltaR*mass2*invTotalMass + deltaT*dotvr1;
RealOpenMM dr2 = deltaR*mass1*invTotalMass + deltaT*dotvr2;
dotvr1 += vbCMass;
dotvr2 += vbCMass;
pos[p1] += bondDir*dr1;
pos[p2] += bondDir*dr2;
vel[p1] = vp1 + bondDir*dotvr1;
vel[p2] = vp2 + bondDir*dotvr2;
}
}
}
}
ReferenceVirtualSites::computePositions(context.getSystem(), pos);
data.time += integrator.getStepSize();
data.stepCount++;
......
plugins/drude/platforms/reference/src/ReferenceDrudeKernels.h
View file @ 07afe544
......@@ -115,6 +115,7 @@ private:
ReferencePlatform::PlatformData& data;
std::vector<int> normalParticles;
std::vector<std::pair<int, int> > pairParticles;
std::vector<double> particleMass;
std::vector<double> particleInvMass;
std::vector<double> pairInvTotalMass;
std::vector<double> pairInvReducedMass;
......@@ -158,6 +159,7 @@ private:
std::vector<double> particleInvMass;
lbfgsfloatval_t *minimizerPos;
lbfgs_parameter_t minimizerParams;
double maxDrudeDistance;
};
} // namespace OpenMM
......
plugins/drude/platforms/reference/tests/TestReferenceDrudeLangevinIntegrator.cpp
View file @ 07afe544
......@@ -60,6 +60,7 @@ void testSinglePair() {
const double mass2 = 0.1;
const double totalMass = mass1+mass2;
const double reducedMass = (mass1*mass2)/(mass1+mass2);
const double maxDistance = 0.05;
System system;
system.addParticle(mass1);
system.addParticle(mass2);
......@@ -70,6 +71,7 @@ void testSinglePair() {
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(0, 0, 0);
DrudeLangevinIntegrator integ(temperature, 20.0, temperatureDrude, 20.0, 0.003);
integ.setMaxDrudeDistance(maxDistance);
Platform& platform = Platform::getPlatformByName("Reference");
Context context(system, integ, platform);
context.setPositions(positions);
......@@ -84,12 +86,15 @@ void testSinglePair() {
int numSteps = 10000;
for (int i = 0; i < numSteps; i++) {
integ.step(10);
State state = context.getState(State::Velocities);
State state = context.getState(State::Velocities | State::Positions);
const vector<Vec3>& vel = state.getVelocities();
Vec3 velCM = vel[0]*(mass1/totalMass) + vel[1]*(mass2/totalMass);
keCM += 0.5*totalMass*velCM.dot(velCM);
Vec3 velInternal = vel[0]-vel[1];
keInternal += 0.5*reducedMass*velInternal.dot(velInternal);
Vec3 delta = state.getPositions()[0]-state.getPositions()[1];
double distance = sqrt(delta.dot(delta));
ASSERT(distance <= maxDistance*(1+1e-6));
}
ASSERT_USUALLY_EQUAL_TOL(3*0.5*BOLTZ*temperature, keCM/numSteps, 0.1);
ASSERT_USUALLY_EQUAL_TOL(3*0.5*BOLTZ*temperatureDrude, keInternal/numSteps, 0.01);
......
wrappers/python/src/swig_doxygen/swigInputConfig.py
View file @ 07afe544
......@@ -425,6 +425,7 @@ UNITS = {
("System", "getForce") : (None, ()),
("System", "getVirtualSite") : (None, ()),
("DrudeLangevinIntegrator", "getDrudeTemperature") : ("unit.kelvin", ()),
("DrudeLangevinIntegrator", "getMaxDrudeDistance") : ("unit.nanometer", ()),
("MonteCarloMembraneBarostat", "getXYMode") : (None, ()),
("MonteCarloMembraneBarostat", "getZMode") : (None, ()),
("DrudeLangevinIntegrator", "getDrudeFriction") : ("1/unit.picosecond", ()),
......
wrappers/python/tests/TestAPIUnits.py
View file @ 07afe544
......@@ -1200,6 +1200,9 @@ class TestAPIUnits(unittest.TestCase):
self.assertEqual(integrator.getStepSize(), 0.1*femtosecond)
integrator.setStepSize(0.0005)
self.assertEqual(integrator.getStepSize(), 0.0005*picosecond)
self.assertEqual(integrator.getMaxDrudeDistance(), 0*nanometer)
integrator.setMaxDrudeDistance(0.05)
self.assertEqual(integrator.getMaxDrudeDistance(), 0.05*nanometer)
def testCustomIntegrator(self):
""" Tests the CustomIntegrator API features """
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment