void NonbondedForceImpl::calcPMEParameters(const System& system, const NonbondedForce& force, double& alpha, int& xsize, int& ysize, int& zsize, bool lj) {
if (lj)
force.getLJPMEParameters(alpha, xsize, ysize, zsize);
else
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));
if (lj) {
xsize = (int) ceil(alpha*boxVectors[0][0]/(3*pow(tol, 0.2)));
ysize = (int) ceil(alpha*boxVectors[1][1]/(3*pow(tol, 0.2)));
zsize = (int) ceil(alpha*boxVectors[2][2]/(3*pow(tol, 0.2)));
}
else {
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, 6);
ysize = max(ysize, 6);
zsize = max(zsize, 6);
}
}
void testSerialization() {
// Create a Force.
NonbondedForce force;
force.setNonbondedMethod(NonbondedForce::CutoffPeriodic);
force.setCutoffDistance(2.0);
force.setEwaldErrorTolerance(1e-3);
force.setReactionFieldDielectric(50.0);
force.setUseDispersionCorrection(false);
force.addParticle(1, 0.1, 0.01);
force.addParticle(0.5, 0.2, 0.02);
force.addParticle(-0.5, 0.3, 0.03);
force.addException(0, 1, 2, 0.5, 0.1);
force.addException(1, 2, 0.2, 0.4, 0.2);
// Serialize and then deserialize it.
stringstream buffer;
XmlSerializer::serialize<NonbondedForce>(&force, "Force", buffer);
NonbondedForce* copy = XmlSerializer::deserialize<NonbondedForce>(buffer);
// Compare the two forces to see if they are identical.
NonbondedForce& force2 = *copy;
ASSERT_EQUAL(force.getNonbondedMethod(), force2.getNonbondedMethod());
ASSERT_EQUAL(force.getCutoffDistance(), force2.getCutoffDistance());
ASSERT_EQUAL(force.getEwaldErrorTolerance(), force2.getEwaldErrorTolerance());
ASSERT_EQUAL(force.getReactionFieldDielectric(), force2.getReactionFieldDielectric());
ASSERT_EQUAL(force.getUseDispersionCorrection(), force2.getUseDispersionCorrection());
ASSERT_EQUAL(force.getNumParticles(), force2.getNumParticles());
for (int i = 0; i < force.getNumParticles(); i++) {
double charge1, sigma1, epsilon1;
double charge2, sigma2, epsilon2;
force.getParticleParameters(i, charge1, sigma1, epsilon1);
force2.getParticleParameters(i, charge2, sigma2, epsilon2);
ASSERT_EQUAL(charge1, charge2);
ASSERT_EQUAL(sigma1, sigma2);
ASSERT_EQUAL(epsilon1, epsilon2);
}
ASSERT_EQUAL(force.getNumExceptions(), force2.getNumExceptions());
for (int i = 0; i < force.getNumExceptions(); i++) {
int a1, a2, b1, b2;
double charge1, sigma1, epsilon1;
double charge2, sigma2, epsilon2;
force.getExceptionParameters(i, a1, b1, charge1, sigma1, epsilon1);
force2.getExceptionParameters(i, a2, b2, charge2, sigma2, epsilon2);
ASSERT_EQUAL(a1, a2);
ASSERT_EQUAL(b1, b2);
ASSERT_EQUAL(charge1, charge2);
ASSERT_EQUAL(sigma1, sigma2);
ASSERT_EQUAL(epsilon1, epsilon2);
}
}
void ValidateOpenMM::writeNonbondedForce( FILE* filePtr, const NonbondedForce & nonbondedForce ) const {
// charge and vdw parameters
(void) fprintf( filePtr, "NonbondedForce %d\n", nonbondedForce.getNumParticles() );
for(int ii = 0; ii < nonbondedForce.getNumParticles(); ii++ ){
double charge, sigma, epsilon;
nonbondedForce.getParticleParameters( ii, charge, sigma, epsilon );
(void) fprintf( filePtr, "%8d %14.7e %14.7e %14.7e\n", ii, charge, sigma, epsilon );
}
// cutoff, dielectric, Ewald tolerance
(void) fprintf( filePtr, "CutoffDistance %14.7e\n", nonbondedForce.getCutoffDistance() );
(void) fprintf( filePtr, "RFDielectric %14.7e\n", nonbondedForce.getReactionFieldDielectric() );
(void) fprintf( filePtr, "EwaldRTolerance %14.7e\n", nonbondedForce.getEwaldErrorTolerance() );
// cutoff mode
std::string nonbondedForceMethod;
switch( nonbondedForce.getNonbondedMethod() ){
case NonbondedForce::NoCutoff:
nonbondedForceMethod = "NoCutoff";
break;
case NonbondedForce::CutoffNonPeriodic:
nonbondedForceMethod = "CutoffNonPeriodic";
break;
case NonbondedForce::CutoffPeriodic:
nonbondedForceMethod = "CutoffPeriodic";
break;
case NonbondedForce::Ewald:
nonbondedForceMethod = "Ewald";
break;
case NonbondedForce::PME:
nonbondedForceMethod = "PME";
break;
default:
nonbondedForceMethod = "Unknown";
}
(void) fprintf( filePtr, "NonbondedForceMethod %s\n", nonbondedForceMethod.c_str() );
(void) fprintf( filePtr, "NonbondedForceExceptions %d\n", nonbondedForce.getNumExceptions() );
for(int ii = 0; ii < nonbondedForce.getNumExceptions(); ii++ ){
int particle1, particle2;
double chargeProd, sigma, epsilon;
nonbondedForce.getExceptionParameters( ii, particle1, particle2, chargeProd, sigma, epsilon );
(void) fprintf( filePtr, "%8d %8d %8d %14.7e %14.7e %14.7e\n", ii, particle1, particle2, chargeProd, sigma, epsilon );
}
}
void NonbondedForceImpl::calcEwaldParameters(const System& system, const NonbondedForce& force, double& alpha, int& kmaxx, int& kmaxy, int& kmaxz) {
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));
kmaxx = findZero(EwaldErrorFunction(boxVectors[0][0], alpha, tol), 10);
kmaxy = findZero(EwaldErrorFunction(boxVectors[1][1], alpha, tol), 10);
kmaxz = findZero(EwaldErrorFunction(boxVectors[2][2], alpha, tol), 10);
if (kmaxx%2 == 0)
kmaxx++;
if (kmaxy%2 == 0)
kmaxy++;
if (kmaxz%2 == 0)
kmaxz++;
}
void testSerialization() {
// Create a Force.
NonbondedForce force;
force.setForceGroup(3);
force.setNonbondedMethod(NonbondedForce::CutoffPeriodic);
force.setSwitchingDistance(1.5);
force.setUseSwitchingFunction(true);
force.setCutoffDistance(2.0);
force.setEwaldErrorTolerance(1e-3);
force.setReactionFieldDielectric(50.0);
force.setUseDispersionCorrection(false);
double alpha = 0.5;
int nx = 3, ny = 5, nz = 7;
force.setPMEParameters(alpha, nx, ny, nz);
double dalpha = 0.8;
int dnx = 4, dny = 6, dnz = 7;
force.setLJPMEParameters(dalpha, dnx, dny, dnz);
force.addParticle(1, 0.1, 0.01);
force.addParticle(0.5, 0.2, 0.02);
force.addParticle(-0.5, 0.3, 0.03);
force.addException(0, 1, 2, 0.5, 0.1);
force.addException(1, 2, 0.2, 0.4, 0.2);
force.addGlobalParameter("scale1", 1.0);
force.addGlobalParameter("scale2", 2.0);
force.addParticleParameterOffset("scale1", 2, 1.5, 2.0, 2.5);
force.addExceptionParameterOffset("scale2", 1, -0.1, -0.2, -0.3);
// Serialize and then deserialize it.
stringstream buffer;
XmlSerializer::serialize<NonbondedForce>(&force, "Force", buffer);
NonbondedForce* copy = XmlSerializer::deserialize<NonbondedForce>(buffer);
// Compare the two forces to see if they are identical.
NonbondedForce& force2 = *copy;
ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force.getNonbondedMethod(), force2.getNonbondedMethod());
ASSERT_EQUAL(force.getSwitchingDistance(), force2.getSwitchingDistance());
ASSERT_EQUAL(force.getUseSwitchingFunction(), force2.getUseSwitchingFunction());
ASSERT_EQUAL(force.getCutoffDistance(), force2.getCutoffDistance());
ASSERT_EQUAL(force.getEwaldErrorTolerance(), force2.getEwaldErrorTolerance());
ASSERT_EQUAL(force.getReactionFieldDielectric(), force2.getReactionFieldDielectric());
ASSERT_EQUAL(force.getUseDispersionCorrection(), force2.getUseDispersionCorrection());
ASSERT_EQUAL(force.getNumParticles(), force2.getNumParticles());
ASSERT_EQUAL(force.getNumExceptions(), force2.getNumExceptions());
ASSERT_EQUAL(force.getNumGlobalParameters(), force2.getNumGlobalParameters());
ASSERT_EQUAL(force.getNumParticleParameterOffsets(), force2.getNumParticleParameterOffsets());
ASSERT_EQUAL(force.getNumExceptionParameterOffsets(), force2.getNumExceptionParameterOffsets());
double alpha2;
int nx2, ny2, nz2;
force2.getPMEParameters(alpha2, nx2, ny2, nz2);
ASSERT_EQUAL(alpha, alpha2);
ASSERT_EQUAL(nx, nx2);
ASSERT_EQUAL(ny, ny2);
ASSERT_EQUAL(nz, nz2);
double dalpha2;
int dnx2, dny2, dnz2;
force2.getLJPMEParameters(dalpha2, dnx2, dny2, dnz2);
ASSERT_EQUAL(dalpha, dalpha2);
ASSERT_EQUAL(dnx, dnx2);
ASSERT_EQUAL(dny, dny2);
ASSERT_EQUAL(dnz, dnz2);
for (int i = 0; i < force.getNumGlobalParameters(); i++) {
ASSERT_EQUAL(force.getGlobalParameterName(i), force2.getGlobalParameterName(i));
ASSERT_EQUAL(force.getGlobalParameterDefaultValue(i), force2.getGlobalParameterDefaultValue(i));
}
for (int i = 0; i < force.getNumParticleParameterOffsets(); i++) {
int index1, index2;
string param1, param2;
double charge1, sigma1, epsilon1;
double charge2, sigma2, epsilon2;
force.getParticleParameterOffset(i, param1, index1, charge1, sigma1, epsilon1);
force2.getParticleParameterOffset(i, param2, index2, charge2, sigma2, epsilon2);
ASSERT_EQUAL(index1, index1);
ASSERT_EQUAL(param1, param2);
ASSERT_EQUAL(charge1, charge2);
ASSERT_EQUAL(sigma1, sigma2);
ASSERT_EQUAL(epsilon1, epsilon2);
}
for (int i = 0; i < force.getNumExceptionParameterOffsets(); i++) {
int index1, index2;
string param1, param2;
double charge1, sigma1, epsilon1;
double charge2, sigma2, epsilon2;
force.getExceptionParameterOffset(i, param1, index1, charge1, sigma1, epsilon1);
force2.getExceptionParameterOffset(i, param2, index2, charge2, sigma2, epsilon2);
ASSERT_EQUAL(index1, index1);
ASSERT_EQUAL(param1, param2);
ASSERT_EQUAL(charge1, charge2);
ASSERT_EQUAL(sigma1, sigma2);
ASSERT_EQUAL(epsilon1, epsilon2);
}
for (int i = 0; i < force.getNumParticles(); i++) {
double charge1, sigma1, epsilon1;
double charge2, sigma2, epsilon2;
force.getParticleParameters(i, charge1, sigma1, epsilon1);
force2.getParticleParameters(i, charge2, sigma2, epsilon2);
ASSERT_EQUAL(charge1, charge2);
ASSERT_EQUAL(sigma1, sigma2);
ASSERT_EQUAL(epsilon1, epsilon2);
}
ASSERT_EQUAL(force.getNumExceptions(), force2.getNumExceptions());
for (int i = 0; i < force.getNumExceptions(); i++) {
int a1, a2, b1, b2;
double charge1, sigma1, epsilon1;
double charge2, sigma2, epsilon2;
force.getExceptionParameters(i, a1, b1, charge1, sigma1, epsilon1);
force2.getExceptionParameters(i, a2, b2, charge2, sigma2, epsilon2);
ASSERT_EQUAL(a1, a2);
ASSERT_EQUAL(b1, b2);
ASSERT_EQUAL(charge1, charge2);
ASSERT_EQUAL(sigma1, sigma2);
ASSERT_EQUAL(epsilon1, epsilon2);
}
}
