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Commit 31d02cdc authored by peastman's avatar peastman
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Merge pull request #363 from peastman/pme 

Added option to explicitly set PME parameters
parents cfc01d01 c9eef8cf
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docs/usersguide/theory.rst
View file @ 31d02cdc
......@@ -417,7 +417,8 @@ and the number of nodes in the mesh along each dimension as
{n}_{\text{mesh}}=\frac{2\alpha d}{{3d}^{1/5}}
where *d* is the width of the periodic box along that dimension. (Note that
where *d* is the width of the periodic box along that dimension. Alternatively,
the user may choose to explicitly set values for these parameters. (Note that
some Platforms may choose to use a larger value of :math:`n_\text{mesh}` than that
given by this equation. For example, some FFT implementations require the mesh
size to be a multiple of certain small prime numbers, so a Platform might round
......
openmmapi/include/openmm/NonbondedForce.h
View file @ 31d02cdc
......@@ -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) 2008-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -182,15 +182,41 @@ public:
* which is acceptable. This value is used to select the reciprocal space cutoff and separation
* parameter so that the average error level will be less than the tolerance. There is not a
* rigorous guarantee that all forces on all atoms will be less than the tolerance, however.
*
* For PME calculations, if setPMEParameters() is used to set alpha to something other than 0,
* this value is ignored.
*/
double getEwaldErrorTolerance() const;
/**
* Get the error tolerance for Ewald summation. This corresponds to the fractional error in the forces
* Set the error tolerance for Ewald summation. This corresponds to the fractional error in the forces
* which is acceptable. This value is used to select the reciprocal space cutoff and separation
* parameter so that the average error level will be less than the tolerance. There is not a
* rigorous guarantee that all forces on all atoms will be less than the tolerance, however.
*
* For PME calculations, if setPMEParameters() is used to set alpha to something other than 0,
* this value is ignored.
*/
void setEwaldErrorTolerance(double tol);
/**
* Get the parameters to use for PME calculations. If alpha is 0 (the default), these parameters are
* ignored and instead their values are chosen based on the Ewald error tolerance.
*
* @param alpha the separation parameter
* @param nx the number of grid points along the X axis
* @param ny the number of grid points along the Y axis
* @param nz the number of grid points along the Z axis
*/
void getPMEParameters(double& alpha, int& nx, int& ny, int& nz) const;
/**
* Set the parameters to use for PME calculations. If alpha is 0 (the default), these parameters are
* ignored and instead their values are chosen based on the Ewald error tolerance.
*
* @param alpha the separation parameter
* @param nx the number of grid points along the X axis
* @param ny the number of grid points along the Y axis
* @param nz the number of grid points along the Z axis
*/
void setPMEParameters(double alpha, int nx, int ny, int nz);
/**
* Add the nonbonded force parameters for a particle. This should be called once for each particle
* in the System. When it is called for the i'th time, it specifies the parameters for the i'th particle.
......@@ -332,9 +358,9 @@ private:
class ParticleInfo;
class ExceptionInfo;
NonbondedMethod nonbondedMethod;
double cutoffDistance, switchingDistance, rfDielectric, ewaldErrorTol;
double cutoffDistance, switchingDistance, rfDielectric, ewaldErrorTol, alpha;
bool useSwitchingFunction, useDispersionCorrection;
int recipForceGroup;
int recipForceGroup, nx, ny, nz;
void addExclusionsToSet(const std::vector<std::set<int> >& bonded12, std::set<int>& exclusions, int baseParticle, int fromParticle, int currentLevel) const;
std::vector<ParticleInfo> particles;
std::vector<ExceptionInfo> exceptions;
......
openmmapi/src/NonbondedForce.cpp
View file @ 31d02cdc
......@@ -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) 2008-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -48,7 +48,7 @@ using std::stringstream;
using std::vector;
NonbondedForce::NonbondedForce() : nonbondedMethod(NoCutoff), cutoffDistance(1.0), switchingDistance(-1.0), rfDielectric(78.3),
ewaldErrorTol(5e-4), useSwitchingFunction(false), useDispersionCorrection(true), recipForceGroup(-1) {
ewaldErrorTol(5e-4), alpha(0.0), useSwitchingFunction(false), useDispersionCorrection(true), recipForceGroup(-1), nx(0), ny(0), nz(0) {
}
NonbondedForce::NonbondedMethod NonbondedForce::getNonbondedMethod() const {
......@@ -95,11 +95,24 @@ double NonbondedForce::getEwaldErrorTolerance() const {
return ewaldErrorTol;
}
void NonbondedForce::setEwaldErrorTolerance(double tol)
{
void NonbondedForce::setEwaldErrorTolerance(double tol) {
ewaldErrorTol = tol;
}
void NonbondedForce::getPMEParameters(double& alpha, int& nx, int& ny, int& nz) const {
alpha = this->alpha;
nx = this->nx;
ny = this->ny;
nz = this->nz;
}
void NonbondedForce::setPMEParameters(double alpha, int nx, int ny, int nz) {
this->alpha = alpha;
this->nx = nx;
this->ny = ny;
this->nz = nz;
}
int NonbondedForce::addParticle(double charge, double sigma, double epsilon) {
particles.push_back(ParticleInfo(charge, sigma, epsilon));
return particles.size()-1;
......
openmmapi/src/NonbondedForceImpl.cpp
View file @ 31d02cdc
......@@ -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) 2008-2010 Stanford University and the Authors. *
* Portions copyright (c) 2008-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -149,16 +149,19 @@ void NonbondedForceImpl::calcEwaldParameters(const System& system, const Nonbond
}
void NonbondedForceImpl::calcPMEParameters(const System& system, const NonbondedForce& force, double& alpha, int& xsize, int& ysize, int& zsize) {
Vec3 boxVectors[3];
system.getDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
double tol = force.getEwaldErrorTolerance();
alpha = (1.0/force.getCutoffDistance())*std::sqrt(-log(2.0*tol));
xsize = (int) ceil(2*alpha*boxVectors[0][0]/(3*pow(tol, 0.2)));
ysize = (int) ceil(2*alpha*boxVectors[1][1]/(3*pow(tol, 0.2)));
zsize = (int) ceil(2*alpha*boxVectors[2][2]/(3*pow(tol, 0.2)));
xsize = max(xsize, 5);
ysize = max(ysize, 5);
zsize = max(zsize, 5);
force.getPMEParameters(alpha, xsize, ysize, zsize);
if (alpha == 0.0) {
Vec3 boxVectors[3];
system.getDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
double tol = force.getEwaldErrorTolerance();
alpha = (1.0/force.getCutoffDistance())*std::sqrt(-log(2.0*tol));
xsize = (int) ceil(2*alpha*boxVectors[0][0]/(3*pow(tol, 0.2)));
ysize = (int) ceil(2*alpha*boxVectors[1][1]/(3*pow(tol, 0.2)));
zsize = (int) ceil(2*alpha*boxVectors[2][2]/(3*pow(tol, 0.2)));
xsize = max(xsize, 5);
ysize = max(ysize, 5);
zsize = max(zsize, 5);
}
}
int NonbondedForceImpl::findZero(const NonbondedForceImpl::ErrorFunction& f, int initialGuess) {
......
platforms/cuda/tests/TestCudaEwald.cpp
View file @ 31d02cdc
......@@ -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) 2008-2012 Stanford University and the Authors. *
* Portions copyright (c) 2008-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -252,6 +252,54 @@ void testErrorTolerance(NonbondedForce::NonbondedMethod method) {
}
}
void testPMEParameters() {
// Create a cloud of random point charges.
const int numParticles = 51;
const double boxWidth = 4.7;
System system;
system.setDefaultPeriodicBoxVectors(Vec3(boxWidth, 0, 0), Vec3(0, boxWidth, 0), Vec3(0, 0, boxWidth));
NonbondedForce* force = new NonbondedForce();
system.addForce(force);
vector<Vec3> positions(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; i++) {
system.addParticle(1.0);
force->addParticle(-1.0+i*2.0/(numParticles-1), 1.0, 0.0);
positions[i] = Vec3(boxWidth*genrand_real2(sfmt), boxWidth*genrand_real2(sfmt), boxWidth*genrand_real2(sfmt));
}
force->setNonbondedMethod(NonbondedForce::PME);
// Compute the energy with an error tolerance of 1e-3.
force->setEwaldErrorTolerance(1e-3);
VerletIntegrator integrator1(0.01);
Context context1(system, integrator1, platform);
context1.setPositions(positions);
double energy1 = context1.getState(State::Energy).getPotentialEnergy();
// Try again with an error tolerance of 1e-4.
force->setEwaldErrorTolerance(1e-4);
VerletIntegrator integrator2(0.01);
Context context2(system, integrator2, platform);
context2.setPositions(positions);
double energy2 = context2.getState(State::Energy).getPotentialEnergy();
// Now explicitly set the parameters. These should match the values that were
// used for tolerance 1e-3.
force->setPMEParameters(2.49291157051793, 32, 32, 32);
VerletIntegrator integrator3(0.01);
Context context3(system, integrator3, platform);
context3.setPositions(positions);
double energy3 = context3.getState(State::Energy).getPotentialEnergy();
ASSERT_EQUAL_TOL(energy1, energy3, 1e-6);
ASSERT(fabs((energy1-energy2)/energy1) > 1e-5);
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
......@@ -261,6 +309,7 @@ int main(int argc, char* argv[]) {
// testEwald2Ions();
testErrorTolerance(NonbondedForce::Ewald);
testErrorTolerance(NonbondedForce::PME);
testPMEParameters();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
......
platforms/opencl/tests/TestOpenCLEwald.cpp
View file @ 31d02cdc
......@@ -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) 2008-2010 Stanford University and the Authors. *
* Portions copyright (c) 2008-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -252,6 +252,54 @@ void testErrorTolerance(NonbondedForce::NonbondedMethod method) {
}
}
void testPMEParameters() {
// Create a cloud of random point charges.
const int numParticles = 51;
const double boxWidth = 4.7;
System system;
system.setDefaultPeriodicBoxVectors(Vec3(boxWidth, 0, 0), Vec3(0, boxWidth, 0), Vec3(0, 0, boxWidth));
NonbondedForce* force = new NonbondedForce();
system.addForce(force);
vector<Vec3> positions(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; i++) {
system.addParticle(1.0);
force->addParticle(-1.0+i*2.0/(numParticles-1), 1.0, 0.0);
positions[i] = Vec3(boxWidth*genrand_real2(sfmt), boxWidth*genrand_real2(sfmt), boxWidth*genrand_real2(sfmt));
}
force->setNonbondedMethod(NonbondedForce::PME);
// Compute the energy with an error tolerance of 1e-3.
force->setEwaldErrorTolerance(1e-3);
VerletIntegrator integrator1(0.01);
Context context1(system, integrator1, platform);
context1.setPositions(positions);
double energy1 = context1.getState(State::Energy).getPotentialEnergy();
// Try again with an error tolerance of 1e-4.
force->setEwaldErrorTolerance(1e-4);
VerletIntegrator integrator2(0.01);
Context context2(system, integrator2, platform);
context2.setPositions(positions);
double energy2 = context2.getState(State::Energy).getPotentialEnergy();
// Now explicitly set the parameters. These should match the values that were
// used for tolerance 1e-3.
force->setPMEParameters(2.49291157051793, 32, 32, 32);
VerletIntegrator integrator3(0.01);
Context context3(system, integrator3, platform);
context3.setPositions(positions);
double energy3 = context3.getState(State::Energy).getPotentialEnergy();
ASSERT_EQUAL_TOL(energy1, energy3, 1e-6);
ASSERT(fabs((energy1-energy2)/energy1) > 1e-5);
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
......@@ -261,6 +309,7 @@ int main(int argc, char* argv[]) {
// testEwald2Ions();
testErrorTolerance(NonbondedForce::Ewald);
testErrorTolerance(NonbondedForce::PME);
testPMEParameters();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
......
platforms/reference/tests/TestReferenceEwald.cpp
View file @ 31d02cdc
......@@ -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) 2008-2010 Stanford University and the Authors. *
* Portions copyright (c) 2008-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -354,6 +354,55 @@ void testErrorTolerance(NonbondedForce::NonbondedMethod method) {
}
}
void testPMEParameters() {
// Create a cloud of random point charges.
const int numParticles = 51;
const double boxWidth = 4.7;
System system;
system.setDefaultPeriodicBoxVectors(Vec3(boxWidth, 0, 0), Vec3(0, boxWidth, 0), Vec3(0, 0, boxWidth));
NonbondedForce* force = new NonbondedForce();
system.addForce(force);
vector<Vec3> positions(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; i++) {
system.addParticle(1.0);
force->addParticle(-1.0+i*2.0/(numParticles-1), 1.0, 0.0);
positions[i] = Vec3(boxWidth*genrand_real2(sfmt), boxWidth*genrand_real2(sfmt), boxWidth*genrand_real2(sfmt));
}
force->setNonbondedMethod(NonbondedForce::PME);
ReferencePlatform platform;
// Compute the energy with an error tolerance of 1e-3.
force->setEwaldErrorTolerance(1e-3);
VerletIntegrator integrator1(0.01);
Context context1(system, integrator1, platform);
context1.setPositions(positions);
double energy1 = context1.getState(State::Energy).getPotentialEnergy();
// Try again with an error tolerance of 1e-4.
force->setEwaldErrorTolerance(1e-4);
VerletIntegrator integrator2(0.01);
Context context2(system, integrator2, platform);
context2.setPositions(positions);
double energy2 = context2.getState(State::Energy).getPotentialEnergy();
// Now explicitly set the parameters. These should match the values that were
// used for tolerance 1e-3.
force->setPMEParameters(2.49291157051793, 32, 32, 32);
VerletIntegrator integrator3(0.01);
Context context3(system, integrator3, platform);
context3.setPositions(positions);
double energy3 = context3.getState(State::Energy).getPotentialEnergy();
ASSERT_EQUAL_TOL(energy1, energy3, 1e-6);
ASSERT(fabs((energy1-energy2)/energy1) > 1e-5);
}
int main() {
try {
testEwaldExact();
......@@ -362,6 +411,7 @@ int main() {
// testWaterSystem();
testErrorTolerance(NonbondedForce::Ewald);
testErrorTolerance(NonbondedForce::PME);
testPMEParameters();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
......
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