bool OME::interpolateResponse(const RealVec &freqs)
{
if(freqs.empty())
{
LOUDNESS_ERROR("OME: Input vector has no elements.");
return 0;
}
else
{
response_.resize(freqs.size(), 0.0);
//load the data into vectors
getData();
//the spline
spline s;
//middle ear
if(middleEarType_ != NONE)
{
s.set_points(middleEarFreqPoints_, middleEardB_);
for (uint i=0; i < freqs.size(); i++)
{
if((freqs[i]<=75) && (middleEarType_ == ANSIS342007_MIDDLE_EAR_HPF))
response_[i] = -14.6; //Post HPF correction
else if(freqs[i] >= middleEarFreqPoints_[40])
response_[i] = middleEardB_[40];
else
response_[i] = s(freqs[i]);
}
}
else
{
LOUDNESS_WARNING("OME: No middle ear filter used.");
}
//outer ear
if(outerEarType_ != NONE)
{
Real lastFreq = outerEarFreqPoints_.back();
Real lastDataPoint = outerEardB_.back();
s.set_points(outerEarFreqPoints_, outerEardB_);
for(uint i = 0; i < freqs.size(); i++)
{
if(freqs[i] >= lastFreq)
response_[i] += lastDataPoint;
else
response_[i] += s(freqs[i]);
}
}
else
{
LOUDNESS_WARNING("OME: No outer ear filter used.");
}
return 1;
}
}
//Window functions:
void Window::hann(RealVec &window, bool periodic)
{
unsigned int N = window.size();
int denom = N-1;//produces zeros on both sides
if(periodic)//Harris (1978) Eq 27b
denom = N;
for(uint i=0; i<window.size(); i++)
{
window[i] = 0.5 - 0.5 * cos(2.0*PI*i/denom);
}
}
// return a vector of the top k indices of a
void topk(RealVec a, vector<size_t> & indtop){
multimap<real, size_t> m; // mapping from value to its index
RealVecItr it;
for (it = a.begin(); it != a.end(); ++it)
m.insert(make_pair(*it, it - a.begin()));
multimap<real, size_t>::reverse_iterator itm; // mapping from value to its index
size_t indx=0;
for (itm = m.rbegin(); itm != m.rend(); ++itm){
//cout << itm->first <<" , "<< itm->second << endl;
indtop[indx]=itm->second;
indx++;
}
}
double ReferenceIntegrateRPMDStepKernel::computeKineticEnergy(ContextImpl& context, const RPMDIntegrator& integrator) {
const System& system = context.getSystem();
int numParticles = system.getNumParticles();
vector<RealVec>& velData = extractVelocities(context);
double energy = 0.0;
for (int i = 0; i < numParticles; ++i) {
double mass = system.getParticleMass(i);
if (mass > 0) {
RealVec v = velData[i];
energy += mass*(v.dot(v));
}
}
return 0.5*energy;
}
void Window::normaliseWindow(RealVec &window, const Normalisation& normalisation)
{
if (normalisation != NONE)
{
double x = 0.0;
double sum = 0.0, sumSquares = 0.0;
double normFactor = 1.0;
uint wSize = window.size();
for(uint i=0; i < wSize; i++)
{
x = window[i];
sum += x;
sumSquares += x*x;
}
switch (normalisation)
{
case (ENERGY):
normFactor = sqrt(wSize/sumSquares);
LOUDNESS_DEBUG(name_ << ": Normalising for energy.");
break;
case (AMPLITUDE):
normFactor = wSize/sum;
LOUDNESS_DEBUG(name_ << ": Normalising for amplitude.");
break;
default:
normFactor = sqrt(wSize/sumSquares);
}
LOUDNESS_DEBUG(name_ << ": Normalising window using factor: " << normFactor);
for(uint i=0; i < wSize; i++)
window[i] *= normFactor;
}
}
MatrixXd Scalar<Element>::computeSourceTerm(const double time, const PetscInt time_idx) {
mSource.setZero();
for (auto &source : Element::Sources()) {
RealVec pnt;
if (Element::NumDim() == 2) {
pnt.resize(2);
pnt << source->LocR(), source->LocS();
}
if (Element::NumDim() == 3) {
pnt.resize(3);
pnt << source->LocR(), source->LocS(), source->LocT();
}
mSource += (Element::getDeltaFunctionCoefficients(pnt) * source->fire(time, time_idx));
}
return Element::applyTestAndIntegrate(mSource);
}
void MCMCGRDiagnosticPSRF::outputResults(
const std::string& filenameGRScalars,
const RealVec& sampledInd,
int precData) const
{
/* sampledInd may contain more values than we monitored */
RealVec::const_iterator it;
advance(it, scalars.size());
RealVec sampledIndTmp(sampledInd.begin(), it);
std::vector < std::string > colNames;
getScalarColNames(colNames);
colNames.push_back("W");
colNames.push_back("B");
colNames.push_back("estVarV");
colNames.push_back("rhat");
colNames.push_back("rhatFlag");
colNames.push_back("sampled?");
std::vector < const RealVec* > data;
addDataPtrs(data, scalars);
data.push_back(&Ws);
data.push_back(&Bs);
data.push_back(&estVarV);
data.push_back(&rhat);
data.push_back(&rhatFlag);
data.push_back(&sampledIndTmp);
outputToFileVertical(data, colNames,
filenameGRScalars, precData);
}
void TriangleFunction::apply( RealVec& inputs, RealVec& outputs ) {
// --- out <- 2.0*( (x-c)/a-floor((x-c)/a+0.5) )
for( int i=0; i<(int)inputs.size(); i++ ) {
Real sawtooth = (inputs[i]-phasev)/spanv-floor((inputs[i]-phasev)/spanv+0.5);
outputs[i] = amplitudev*( 1.0 - fabs( sawtooth ) );
}
}
void PowerSpectrumAndSpatialDetection::hannWindow(RealVec &w, int fftSize)
{
int windowSize = (int)w.size();
Real norm = sqrt(2.0/(fftSize*windowSize*0.375*2e-5*2e-5));
for(int i=0; i< windowSize; i++)
w[i] = norm*(0.5+0.5*cos(2*PI*(i-0.5*(windowSize-1))/windowSize));
}
// fill a vector with probabilities as reals
cxsc::real EquiProbProposal::EquiProbProposal::fillNodeProposalProbs(
const size_t nLeaf,
const size_t nCherry,
RealVec& probs) const
{
cxsc::real retSum = 0.0;
probs.reserve(nLeaf + nCherry);
if (nLeaf + nCherry > 0) {
cxsc::real pNode = 1.0/(nLeaf + nCherry);
retSum += pNode*(1.0*nLeaf + 1.0*nCherry);
probs.assign(nLeaf+nCherry, pNode);
}
return retSum;
}
// fill a vector with probabilities as reals
cxsc::real UniformSSMProposal::fillNodeProposalProbs(
const size_t nLeaf, const size_t nCherry,
RealVec& probs) const
{
cxsc::real retSum = 0.0;
probs.reserve(nLeaf + nCherry);
if (nLeaf > 0) {
cxsc::real pLeaf = probSplitMerge/nLeaf;
retSum += (1.0*nLeaf * pLeaf);
probs.assign(nLeaf, pLeaf);
}
if (nCherry > 0) {
cxsc::real pCherry = probSplitMerge/nCherry;
retSum += (1.0*nCherry * pCherry);
probs.insert(probs.end(), nCherry, pCherry);
}
return retSum;
}
void ReferenceIntegrateDrudeSCFStepKernel::minimize(ContextImpl& context, double tolerance) {
// Record the initial positions and determine a normalization constant for scaling the tolerance.
vector<RealVec>& pos = extractPositions(context);
int numDrudeParticles = drudeParticles.size();
double norm = 0.0;
for (int i = 0; i < numDrudeParticles; i++) {
RealVec p = pos[drudeParticles[i]];
minimizerPos[3*i] = p[0];
minimizerPos[3*i+1] = p[1];
minimizerPos[3*i+2] = p[2];
norm += p.dot(p);
}
norm /= numDrudeParticles;
norm = (norm < 1 ? 1 : sqrt(norm));
minimizerParams.epsilon = tolerance/norm;
// Perform the minimization.
lbfgsfloatval_t fx;
MinimizerData data(context, drudeParticles);
lbfgs(numDrudeParticles*3, minimizerPos, &fx, evaluate, NULL, &data, &minimizerParams);
}
int MCMCGRDiagnosticPSRF::calcDiagnosticsForLoop()
{
if (keepLogs) {
// store the current runningSumAllChains as well
runningSumOverall.push_back(runningSumAllChains);
}
// convergence diagnostics calculations for v's
// the Ws: average, over chains, of sample variance of scalar value
cxsc::real thisW = sumOfSampleVariancesOverChains/(chains * 1.0);
#ifdef MYDEBUG_CALCS_EXTRA
cout << "and thisW = " << thisW << endl;
#endif
Ws.push_back(thisW);
// the Bs
size_t statesForCalcs = states - statesNotInCalcs;
cxsc::real thisB = (1.0/( (chains - 1) * statesForCalcs )
* ( sumOfSquaresOfRunningSums
- (runningSumAllChains
* runningSumAllChains/(chains * 1.0)) ) );
Bs.push_back(thisB);
#ifdef MYDEBUG_CALCS
//check thisB is correct, doing it the long way
// runningSumPtr has one running sum for each chain
RealVec chainAverages;
cxsc::real accRunningSums(0.0);
for (RealVecItr it = runningSum.begin(); it < runningSum.end(); ++it) {
cxsc::real thisChainRunningSum = (*it);
cxsc::real thisChainAv = thisChainRunningSum/(statesForCalcs * 1.0);
chainAverages.push_back(thisChainAv);
accRunningSums+=thisChainRunningSum;
}
cxsc::real overallAv = accRunningSums/(statesForCalcs * chains * 1.0);
cxsc::dotprecision accDiffs(0.0);
for (RealVecItr it = chainAverages.begin(); it < chainAverages.end(); ++it) {
cxsc::real thisDiff = (*it) - overallAv;
// sum up the squares of the differences compared to overall average
cxsc::accumulate(accDiffs, thisDiff, thisDiff);
}
cxsc::real altB = rnd(accDiffs)*( statesForCalcs/(chains - 1.0) );
cout << "\nthisB for v's is\t" << thisB << endl;
cout << "altB for v's is\t" << altB << endl;
//assert(thisB == altB);
#endif
// the estimated var(v)
cxsc::real thisVarV(0.0);
if (statesForCalcs > 1) {
thisVarV = statesForCalcs/(statesForCalcs-1.0)
* thisW + (1.0/statesForCalcs)*thisB;
}
#ifndef OLDCALCMETHOD
if (statesForCalcs > 1) thisVarV +=thisB/(1.0*chains*statesForCalcs);
#endif
estVarV.push_back(thisVarV);
// the rhats
cxsc::real thisRhat(0.0);
// allow division by 0 if w = 0 when var does not
if (thisW > 0.0 || thisVarV > 0.0) {
thisRhat = thisVarV/thisW;
}
rhat.push_back(thisRhat);
#ifdef MYDEBUG_CALCS_EXTRA
cout << "thisRhat = " << thisRhat << " - press any key " << endl;
getchar();
#endif
if ( (thisRhat <= 1.0 + tol)
&& (thisRhat >= 1.0 - tol) ) {
// if we have not been converged before on this scalar value
if (!rhatDiagnosticFlag) {
#ifdef MYDEBUG
cout << "\n" << getScalarsName()
<< " convergence test satisfied in state "
<< states << " (states in calcs = "
<< statesForCalcs << ")"<< endl;
#endif
// set the flag for this scalar value
rhatDiagnosticFlag = 1;
}
}
else { // not converged on this scalar value
// if we were okay on this scalar value before
if (rhatDiagnosticFlag) {
#ifdef MYDEBUG
cout << "\n--------- Note: " << getScalarsName()
<< " convergence test now NOT satisfied in state "
<< states << endl;
#endif
rhatDiagnosticFlag = 0; // update the flag
}
}
if (keepLogs) {
// store the flag as well, as a real, which is a fudge...
rhatFlag.push_back(rhatDiagnosticFlag);
}
// end of checking diagnostic for v's
return rhatDiagnosticFlag;
} // end calculations
void SawtoothFunction::apply( RealVec& inputs, RealVec& outputs ) {
// --- out <- 2.0*( (x-c)/a-floor((x-c)/a+0.5) )
for( int i=0; i<(int)inputs.size(); i++ ) {
outputs[i] = amplitudev*( (inputs[i]-phasev)/spanv-floor((inputs[i]-phasev)/spanv+0.5) );
}
}
void PseudoGaussFunction::apply( RealVec& inputs, RealVec& outputs ) {
for( int i=0; i<(int)inputs.size(); i++ ) {
outputs[i] = 0.5*amplitudev*( sin( 2.0*PI_GRECO*((inputs[i]-phasev)/spanv+0.25) ) + 1.0 );
}
}
void SinFunction::apply( RealVec& inputs, RealVec& outputs ) {
for( int i=0; i<(int)inputs.size(); i++ ) {
outputs[i] = amplitudev*sin(2.0*PI_GRECO*(inputs[i]/spanv)-PI_GRECO*phasev);
}
}
double CpuCalcNonbondedForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy, bool includeDirect, bool includeReciprocal) {
if (!hasInitializedPme) {
hasInitializedPme = true;
useOptimizedPme = false;
if (nonbondedMethod == PME) {
// If available, use the optimized PME implementation.
try {
optimizedPme = getPlatform().createKernel(CalcPmeReciprocalForceKernel::Name(), context);
optimizedPme.getAs<CalcPmeReciprocalForceKernel>().initialize(gridSize[0], gridSize[1], gridSize[2], numParticles, ewaldAlpha);
useOptimizedPme = true;
}
catch (OpenMMException& ex) {
// The CPU PME plugin isn't available.
}
}
}
AlignedArray<float>& posq = data.posq;
vector<RealVec>& posData = extractPositions(context);
vector<RealVec>& forceData = extractForces(context);
RealVec boxSize = extractBoxSize(context);
float floatBoxSize[3] = {(float) boxSize[0], (float) boxSize[1], (float) boxSize[2]};
double energy = (includeReciprocal ? ewaldSelfEnergy : 0.0);
bool ewald = (nonbondedMethod == Ewald);
bool pme = (nonbondedMethod == PME);
if (nonbondedMethod != NoCutoff) {
// Determine whether we need to recompute the neighbor list.
double padding = 0.15*nonbondedCutoff;
bool needRecompute = false;
double closeCutoff2 = 0.25*padding*padding;
double farCutoff2 = 0.5*padding*padding;
int maxNumMoved = numParticles/10;
vector<int> moved;
for (int i = 0; i < numParticles; i++) {
RealVec delta = posData[i]-lastPositions[i];
double dist2 = delta.dot(delta);
if (dist2 > closeCutoff2) {
moved.push_back(i);
if (dist2 > farCutoff2 || moved.size() > maxNumMoved) {
needRecompute = true;
break;
}
}
}
if (!needRecompute && moved.size() > 0) {
// Some particles have moved further than half the padding distance. Look for pairs
// that are missing from the neighbor list.
int numMoved = moved.size();
double cutoff2 = nonbondedCutoff*nonbondedCutoff;
double paddedCutoff2 = (nonbondedCutoff+padding)*(nonbondedCutoff+padding);
for (int i = 1; i < numMoved && !needRecompute; i++)
for (int j = 0; j < i; j++) {
RealVec delta = posData[moved[i]]-posData[moved[j]];
if (delta.dot(delta) < cutoff2) {
// These particles should interact. See if they are in the neighbor list.
RealVec oldDelta = lastPositions[moved[i]]-lastPositions[moved[j]];
if (oldDelta.dot(oldDelta) > paddedCutoff2) {
needRecompute = true;
break;
}
}
}
}
if (needRecompute) {
neighborList->computeNeighborList(numParticles, posq, exclusions, floatBoxSize, data.isPeriodic, nonbondedCutoff+padding, data.threads);
lastPositions = posData;
}
nonbonded->setUseCutoff(nonbondedCutoff, *neighborList, rfDielectric);
}
if (data.isPeriodic) {
double minAllowedSize = 1.999999*nonbondedCutoff;
if (boxSize[0] < minAllowedSize || boxSize[1] < minAllowedSize || boxSize[2] < minAllowedSize)
throw OpenMMException("The periodic box size has decreased to less than twice the nonbonded cutoff.");
nonbonded->setPeriodic(floatBoxSize);
}
if (ewald)
nonbonded->setUseEwald(ewaldAlpha, kmax[0], kmax[1], kmax[2]);
if (pme)
nonbonded->setUsePME(ewaldAlpha, gridSize);
if (useSwitchingFunction)
nonbonded->setUseSwitchingFunction(switchingDistance);
double nonbondedEnergy = 0;
if (includeDirect)
nonbonded->calculateDirectIxn(numParticles, &posq[0], posData, particleParams, exclusions, data.threadForce, includeEnergy ? &nonbondedEnergy : NULL, data.threads);
if (includeReciprocal) {
if (useOptimizedPme) {
PmeIO io(&posq[0], &data.threadForce[0][0], numParticles);
Vec3 periodicBoxSize(boxSize[0], boxSize[1], boxSize[2]);
optimizedPme.getAs<CalcPmeReciprocalForceKernel>().beginComputation(io, periodicBoxSize, includeEnergy);
nonbondedEnergy += optimizedPme.getAs<CalcPmeReciprocalForceKernel>().finishComputation(io);
}
else
nonbonded->calculateReciprocalIxn(numParticles, &posq[0], posData, particleParams, exclusions, forceData, includeEnergy ? &nonbondedEnergy : NULL);
}
energy += nonbondedEnergy;
if (includeDirect) {
ReferenceBondForce refBondForce;
ReferenceLJCoulomb14 nonbonded14;
refBondForce.calculateForce(num14, bonded14IndexArray, posData, bonded14ParamArray, forceData, includeEnergy ? &energy : NULL, nonbonded14);
if (data.isPeriodic)
energy += dispersionCoefficient/(boxSize[0]*boxSize[1]*boxSize[2]);
}
return energy;
}
double ReferenceCalcDrudeForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
vector<RealVec>& pos = extractPositions(context);
vector<RealVec>& force = extractForces(context);
int numParticles = particle.size();
double energy = 0;
// Compute the interactions from the harmonic springs.
for (int i = 0; i < numParticles; i++) {
int p = particle[i];
int p1 = particle1[i];
int p2 = particle2[i];
int p3 = particle3[i];
int p4 = particle4[i];
RealOpenMM a1 = (p2 == -1 ? 1 : aniso12[i]);
RealOpenMM a2 = (p3 == -1 || p4 == -1 ? 1 : aniso34[i]);
RealOpenMM a3 = 3-a1-a2;
RealOpenMM k3 = charge[i]*charge[i]/(polarizability[i]*a3);
RealOpenMM k1 = charge[i]*charge[i]/(polarizability[i]*a1) - k3;
RealOpenMM k2 = charge[i]*charge[i]/(polarizability[i]*a2) - k3;
// Compute the isotropic force.
RealVec delta = pos[p]-pos[p1];
RealOpenMM r2 = delta.dot(delta);
energy += 0.5*k3*r2;
force[p] -= delta*k3;
force[p1] += delta*k3;
// Compute the first anisotropic force.
if (p2 != -1) {
RealVec dir = pos[p1]-pos[p2];
RealOpenMM invDist = 1.0/sqrt(dir.dot(dir));
dir *= invDist;
RealOpenMM rprime = dir.dot(delta);
energy += 0.5*k1*rprime*rprime;
RealVec f1 = dir*(k1*rprime);
RealVec f2 = (delta-dir*rprime)*(k1*rprime*invDist);
force[p] -= f1;
force[p1] += f1-f2;
force[p2] += f2;
}
// Compute the second anisotropic force.
if (p3 != -1 && p4 != -1) {
RealVec dir = pos[p3]-pos[p4];
RealOpenMM invDist = 1.0/sqrt(dir.dot(dir));
dir *= invDist;
RealOpenMM rprime = dir.dot(delta);
energy += 0.5*k2*rprime*rprime;
RealVec f1 = dir*(k2*rprime);
RealVec f2 = (delta-dir*rprime)*(k2*rprime*invDist);
force[p] -= f1;
force[p1] += f1;
force[p3] -= f2;
force[p4] += f2;
}
}
// Compute the screened interaction between bonded dipoles.
int numPairs = pair1.size();
for (int i = 0; i < numPairs; i++) {
int dipole1 = pair1[i];
int dipole2 = pair2[i];
int dipole1Particles[] = {particle[dipole1], particle1[dipole1]};
int dipole2Particles[] = {particle[dipole2], particle1[dipole2]};
for (int j = 0; j < 2; j++)
for (int k = 0; k < 2; k++) {
int p1 = dipole1Particles[j];
int p2 = dipole2Particles[k];
RealOpenMM chargeProduct = charge[dipole1]*charge[dipole2]*(j == k ? 1 : -1);
RealVec delta = pos[p1]-pos[p2];
RealOpenMM r = sqrt(delta.dot(delta));
RealOpenMM u = r*pairThole[i]/pow(polarizability[dipole1]*polarizability[dipole2], 1.0/6.0);
RealOpenMM screening = 1.0 - (1.0+0.5*u)*exp(-u);
energy += ONE_4PI_EPS0*chargeProduct*screening/r;
RealVec f = delta*(ONE_4PI_EPS0*chargeProduct*screening/(r*r*r));
force[p1] += f;
force[p2] -= f;
}
}
return energy;
}
bool CompressSpectrum::initializeInternal(const SignalBank &input)
{
LOUDNESS_ASSERT(input.getNChannels() > 1, name_ << ": Insufficient number of channels.");
/*
* This code is sloppy due to along time spent figuring how
* to implement the damn thing.
* It's currently in two parts, one that searches for the limits of each
* summation range in order to satisfy summation criterion.
* The other that finds the average Centre frequencies per compressed band.
*/
int nChannels = input.getNChannels();
int i=0, binIdxPrev = 0;
Real dif = hertzToCam(input.getCentreFreq(1)) -
hertzToCam(input.getCentreFreq(0));
int groupSize = max(2.0, std::floor(alpha_/(dif)));
int groupSizePrev = groupSize;
vector<int> groupSizeStore, binIdx;
while(i < nChannels-1)
{
//compute different between adjacent bins on Cam scale
dif = hertzToCam(input.getCentreFreq(i+1)) - hertzToCam(input.getCentreFreq(i));
//Check if we can sum bins in group size
if(dif < (alpha_/double(groupSize)))
{
/*
* from here we can group bins in groupSize
* whilst maintaining alpha spacing
*/
//Check we have zero idx
if((binIdx.size() < 1) && (i>0))
{
binIdx.push_back(0);
groupSizeStore.push_back(1);
}
/*
* This line ensures the next group starts at the next multiple of the previous
* groupSize above the previous starting position.
* This is why you sometimes get finer resolution than the criterion
*/
int store = ceil((i-binIdxPrev)/double(groupSizePrev))*groupSizePrev+binIdxPrev;
/*
* This line is cheeky; it re-evaluates the groupSize at the new multiple
* in attempt to maintain alpha spacing, I'm not 100% but the algorithm
* seems to satisfy various criteria
*/
if((store > 0) && (store < nChannels))
{
dif = hertzToCam(input.getCentreFreq(store)) -
hertzToCam(input.getCentreFreq(store-1));
groupSize = max((double)groupSize, std::floor(alpha_/dif));
}
//fill variables
groupSizePrev = groupSize;
binIdxPrev = store;
//storage
binIdx.push_back(store);
groupSizeStore.push_back(groupSize);
//print "Bin: %d, Binnew: %d, composite bin size: %d" % (i, store, groupSize)
//Move i along
i = store+groupSize;
//increment groupSize for wider group
groupSize += 1;
}
else
i += 1;
}
//add the final frequency
if(binIdx[binIdx.size()-1] < nChannels)
binIdx.push_back(nChannels);
//PART 2
//compressed spectrum
RealVec cfs;
Real fa = 0;
int count = 0;
int j = 0;
i = 0;
while(i < nChannels)
{
//bounds check out?
if(i<binIdx[j+1])
{
fa += input.getCentreFreq(i);
count++;
if (count==groupSizeStore[j])
{
//upper limit
upperBandIdx_.push_back(i+1); //+1 for < conditional
//set the output frequency
cfs.push_back(fa/count);
count = 0;
fa = 0;
}
i++;
}
else
j++;
}
//add the final component if it didn't make it
if (count>0)
{
cfs.push_back(fa/count);
upperBandIdx_.push_back(i);
}
//check
#if defined(DEBUG)
Real freqLimit = 0.0;
for(unsigned int i=0; i<cfs.size()-1; i++)
{
if((hertzToCam(cfs[i+1]) - hertzToCam(cfs[i])) > alpha_)
freqLimit = cfs[i];
}
LOUDNESS_DEBUG("CompressSpectrum: Criterion satisfied above " << freqLimit << " Hz.");
#endif
//set output SignalBank
output_.initialize(input.getNSources(),
input.getNEars(),
cfs.size(),
1,
input.getFs());
output_.setCentreFreqs(cfs);
output_.setFrameRate(input.getFrameRate());
LOUDNESS_DEBUG(name_ << ": Number of bins comprising the compressed spectrum: "
<< output_.getNChannels());
return 1;
}
void ReferenceIntegrateDrudeLangevinStepKernel::execute(ContextImpl& context, const DrudeLangevinIntegrator& integrator) {
vector<RealVec>& pos = extractPositions(context);
vector<RealVec>& vel = extractVelocities(context);
vector<RealVec>& force = extractForces(context);
// Update velocities of ordinary particles.
const RealOpenMM vscale = exp(-integrator.getStepSize()*integrator.getFriction());
const RealOpenMM fscale = (1-vscale)/integrator.getFriction();
const RealOpenMM kT = BOLTZ*integrator.getTemperature();
const RealOpenMM noisescale = sqrt(2*kT*integrator.getFriction())*sqrt(0.5*(1-vscale*vscale)/integrator.getFriction());
for (int i = 0; i < (int) normalParticles.size(); i++) {
int index = normalParticles[i];
RealOpenMM invMass = particleInvMass[index];
if (invMass != 0.0) {
RealOpenMM sqrtInvMass = sqrt(invMass);
for (int j = 0; j < 3; j++)
vel[index][j] = vscale*vel[index][j] + fscale*invMass*force[index][j] + noisescale*sqrtInvMass*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
}
}
// Update velocities of Drude particle pairs.
const RealOpenMM vscaleDrude = exp(-integrator.getStepSize()*integrator.getDrudeFriction());
const RealOpenMM fscaleDrude = (1-vscaleDrude)/integrator.getDrudeFriction();
const RealOpenMM kTDrude = BOLTZ*integrator.getDrudeTemperature();
const RealOpenMM noisescaleDrude = sqrt(2*kTDrude*integrator.getDrudeFriction())*sqrt(0.5*(1-vscaleDrude*vscaleDrude)/integrator.getDrudeFriction());
for (int i = 0; i < (int) pairParticles.size(); i++) {
int p1 = pairParticles[i].first;
int p2 = pairParticles[i].second;
RealOpenMM mass1fract = pairInvTotalMass[i]/particleInvMass[p1];
RealOpenMM mass2fract = pairInvTotalMass[i]/particleInvMass[p2];
RealOpenMM sqrtInvTotalMass = sqrt(pairInvTotalMass[i]);
RealOpenMM sqrtInvReducedMass = sqrt(pairInvReducedMass[i]);
RealVec cmVel = vel[p1]*mass1fract+vel[p2]*mass2fract;
RealVec relVel = vel[p2]-vel[p1];
RealVec cmForce = force[p1]+force[p2];
RealVec relForce = force[p2]*mass1fract - force[p1]*mass2fract;
for (int j = 0; j < 3; j++) {
cmVel[j] = vscale*cmVel[j] + fscale*pairInvTotalMass[i]*cmForce[j] + noisescale*sqrtInvTotalMass*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
relVel[j] = vscaleDrude*relVel[j] + fscaleDrude*pairInvReducedMass[i]*relForce[j] + noisescaleDrude*sqrtInvReducedMass*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
}
vel[p1] = cmVel-relVel*mass2fract;
vel[p2] = cmVel+relVel*mass1fract;
}
// Update the particle positions.
int numParticles = particleInvMass.size();
vector<RealVec> xPrime(numParticles);
RealOpenMM dt = integrator.getStepSize();
for (int i = 0; i < numParticles; i++)
if (particleInvMass[i] != 0.0)
xPrime[i] = pos[i]+vel[i]*dt;
// Apply constraints.
extractConstraints(context).apply(pos, xPrime, particleInvMass, integrator.getConstraintTolerance());
// Record the constrained positions and velocities.
RealOpenMM dtInv = 1.0/dt;
for (int i = 0; i < numParticles; i++) {
if (particleInvMass[i] != 0.0) {
vel[i] = (xPrime[i]-pos[i])*dtInv;
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++;
}
//-----------------------------------------------------------------------
// optimizing over smoothing parameter Temp -
// getting best histogram over parameter in [t_lo, t_hi] by max/minmising
// a CV based score
//-----------------------------------------------------------------------
// this is a slower and generic K-fold CV method -- USE Leave1Out for Histograms!!!
// CAUTON: held out Lkl is used as an example and should be replaced
//with the appropriate scoring rule for maximization over parameter in [t_lo, t_hi]
bool selectPriorByLlkCV (RVecData & transformedData, size_t K, double t_lo, double t_hi,
int LocalMaxTempIterations, int MaxTempIterations,
RealVec & AvgHeldOutLkls, vector<double> & Temperatures,
double & t_opt, double & AvgHeldOutLkls_opt,
size_t minPoints, int chooseStarts, int keep,
bool stopOnMaxPosterior, string postFileName,
string checkPostFileNameBase, int precPQ,
unsigned long int seedStarts)
{
RealVec AvgHeldOutEmpiricalDeviations;
// first get a root box containing all points
AdaptiveHistogram adhA0;//main hist object
bool successfulInsertion = false;
successfulInsertion = adhA0.insertFromRVec(transformedData);//insert transformed data
if (!successfulInsertion) throw std::runtime_error("Failed to insert transformed data");
//transformedData.clear();//keep the transformed data!!
size_t n = adhA0.getRootCounter();
size_t d = adhA0.getDimensions ();
//cout << "transformed data: n = " << n << endl; getchar();
bool success=false;
const size_t N = adhA0.getRootCounter();//size of successfully inserted transformed data
const size_t KofN = N/K; //cout << KofN << endl; getchar();
size_t nTrain;
adhA0.clearAllHistData();//clear the transformed data to make space during CV
RVecData transformedDataT;//container to keep the transformed Training data from first burst
RVecData transformedDataV;//container to keep the transformed Validation data from first burst
// set up for permutations
const gsl_rng_type * T;
gsl_rng * r;
gsl_permutation * p = gsl_permutation_alloc (N);
gsl_permutation * q = gsl_permutation_alloc (N);
gsl_rng_env_setup();
T = gsl_rng_default;
r = gsl_rng_alloc (T);
//printf ("initial permutation:");
gsl_permutation_init (p);
//gsl_permutation_fprintf (stdout, p, " %u"); printf ("\n"); getchar();
////////////////////////////////////////////////////////////////////////////////////////////////
int TempIterations=0;
std::vector<double> LocalTemperatures;
do{// outer temp iterations
if (TempIterations!=0){
std::vector<size_t> indtop(AvgHeldOutLkls.size());
topk(AvgHeldOutLkls, indtop);
double tBest =Temperatures[indtop[0]];
double t2ndBest =Temperatures[indtop[1]];
double t3rdBest =Temperatures[indtop[2]];
double tWorst = max(abs(tBest-t2ndBest),abs(tBest-t3rdBest));
t_lo = max(0.00001,tBest-tWorst); t_hi = tBest+tWorst;
// cout << t_lo << " , " << t_hi << " : "<< tBest << " , " << t2ndBest << " , " << t3rdBest << endl; getchar();
if (t_hi-t_lo<0.001 ||
abs(AvgHeldOutLkls[indtop[0]]-AvgHeldOutLkls[indtop[1]])<0.01) {
cout << "reaching temp values < 0.001 or likl diff < 1.0"<<endl; getchar(); break;
}
}
double t_Delta=(t_hi-t_lo)/double(LocalMaxTempIterations-1);
LocalTemperatures.clear();
for(int i=0; i<LocalMaxTempIterations; i++){
Temperatures.push_back(t_lo+(double(i))*t_Delta);
LocalTemperatures.push_back(t_lo+(double(i))*t_Delta);
}
int LocalTempIterations=0;
do
{
//LogTemperaturePrior logPrior(Temperatures[TempIterations]);//t_lo);
LogTemperaturePrior logPrior(LocalTemperatures[LocalTempIterations]);//t_lo);
seedStarts += TempIterations;
real HeldOutLkl = 0.0;
real HeldOutEmpiricalDeviation = 0.0;
// a container for our histograms at various temperatures
AdaptiveHistogram adhA0cv(adhA0.getRootBox()); // make adh for CV with root box from adhA0
for (int cvI=1; cvI<K; cvI++)//K-fold CV loop
{
gsl_ran_shuffle (r, p->data, N, sizeof(size_t));
successfulInsertion = false;
std::vector< subpavings::AdaptiveHistogram* > histsT;
adhA0cv.clearAllHistData();//clear the cv histogram before insertion
adhA0cv.mergeUp();//Merge the possibly multileaf cv histogram up to just root.
transformedDataV.clear(); transformedDataT.clear();//clear Cv containers
for(size_t i=0; i<KofN; i++) transformedDataV.push_back(transformedData[gsl_permutation_get(p,i)]);
for(size_t i=KofN; i<N; i++) transformedDataT.push_back(transformedData[gsl_permutation_get(p,i)]);
successfulInsertion = adhA0cv.insertFromRVec(transformedDataT);//insert transformed data
if (!successfulInsertion) throw std::runtime_error("Failed to insert transformed data");
/* some guesses for max points in a node to stop posterior queue */
nTrain = adhA0cv.getRootCounter(); //cout << "nTrain = " << nTrain << endl; getchar();
size_t critSEB = static_cast<size_t>(std::log(static_cast<double>(nTrain)));//can be as low as 1
/* some guesses for maximum leaves we'll let SEB queue go to */
size_t maxLeavesSEB = nTrain/2;// / critSEB; // integer division
size_t maxLeavesCarving = maxLeavesSEB / 3; // integer division
SPSNodeMeasureVolMassMinus compCarving(nTrain);
AdaptiveHistogram::PrioritySplitQueueEvaluator evaluatorCarving(compCarving, maxLeavesCarving);
SPSNodeMeasureCount compSEB;
AdaptiveHistogram::PrioritySplitQueueEvaluator evaluatorSEB(compSEB, critSEB, maxLeavesSEB);
CarverSEB::findStartingPointsBest(adhA0cv, histsT, evaluatorCarving, evaluatorSEB, logPrior,
minPoints, chooseStarts, keep, stopOnMaxPosterior,
postFileName, checkPostFileNameBase, precPQ, seedStarts);
PiecewiseConstantFunction pcfT(*histsT[0]);
pcfT.smearZeroValues(0.0000001);
//assert (pcfT.getTotalIntegral() == cxsc::real(1.0));
histsT[0]->clearAllHistData();//clear the data from training big burst
histsT[0]->insertFromRVec(transformedDataV);//insert validation data
HeldOutLkl += pcfT.getLogLikelihood(*histsT[0]);
PiecewiseConstantFunction pcfV(*histsT[0]);
//if(pcfT.getTotalIntegral() != cxsc::real(1.0)) {cout << "433!!!"; getchar();}
//histsT[0]->clearAllHistData();//clear the data from validation big burst
//histsT[0]->mergeUp();//merge up to root
HeldOutEmpiricalDeviation += pcfT.getL1Distance(pcfV);
//cout << HeldOutLkl << '\t' << HeldOutEmpiricalDeviation << endl; getchar();
//to free all the contents of histsT at the end
for (size_t i = 0; i < histsT.size(); ++i)
{
if (NULL != histsT[i]) delete histsT[i];
histsT[i] = NULL;
}
}
//cout << "Avg HeldOutLkl = " << HeldOutLkl/double(K) << '\n'
// << "Avg HeldOutEmpiricalDeviation = " << HeldOutEmpiricalDeviation/double(K) << endl; getchar();
AvgHeldOutLkls.push_back(HeldOutLkl/double(K));
AvgHeldOutEmpiricalDeviations.push_back(HeldOutEmpiricalDeviation/double(K));
LocalTempIterations++;
}
while (LocalTempIterations<LocalMaxTempIterations);// && CVgain>0.1);
TempIterations++;
}
while (TempIterations<MaxTempIterations);// && CVgain>0.1);
////////////////////////////////////////////////////////////////////////////////////////////////
cout << Temperatures << endl;
cout << AvgHeldOutLkls << endl << AvgHeldOutEmpiricalDeviations << endl;
cout << "Temp Iteration Number " << TempIterations << endl; getchar();
cout << "MaxTempIterations = " << MaxTempIterations << endl; getchar();
vector<size_t> indtop(AvgHeldOutLkls.size());
topk(AvgHeldOutLkls, indtop);
t_opt = _double(Temperatures[indtop[0]]);
AvgHeldOutLkls_opt = _double(AvgHeldOutLkls[indtop[0]]);
gsl_permutation_free (p);
gsl_rng_free (r);
success=true;
return success;
}
//-----------------------------------------------------------------------
// optimizing over smoothing parameter Temp -
// getting best histogram over parameter in [t_lo, t_hi] by max/minmising
// a CV based score
//-----------------------------------------------------------------------
bool selectPriorByLv1OutCV (RVecData & Data, double t_lo, double t_hi,
int LocalMaxTempIterations, int MaxTempIterations,
RealVec & Lv1OutCVScores, vector<double> & Temperatures,
double & t_opt, double & Lv1OutCVScores_opt,
size_t minPoints, double minVolume, int chooseStarts, int keep,
bool stopOnMaxPosterior, string postFileName,
string checkPostFileNameBase, string burstsFileBaseName,
bool printHist, int precPQ,
bool CarvingMaxPosterior,
unsigned long int seedStarts)
{
bool success=false;
int TempIterations=0;
std::vector<double> LocalTemperatures;
do{// outer temp iterations
if (TempIterations!=0){
std::vector<size_t> indtop(Lv1OutCVScores.size());
topk(Lv1OutCVScores, indtop);
double tBest =Temperatures[indtop[0]];
double t2ndBest =Temperatures[indtop[1]];
double t3rdBest =Temperatures[indtop[2]];
double tWorst = max(abs(tBest-t2ndBest),abs(tBest-t3rdBest));
t_lo = max(t_lo,tBest-tWorst); t_hi = tBest+tWorst;
// cout << t_lo << " , " << t_hi << " : "<< tBest << " , " << t2ndBest << " , " << t3rdBest << endl; getchar();
if (t_hi-t_lo<0.001){
//|| abs(Lv1OutCVScores[indtop[0]]-Lv1OutCVScores[indtop[1]])<0.00001) {
cout << "reaching temp values < 0.001 or Lv1OutCVScores diff < 0.00001"<<endl;
getchar();
break;
}
}
double t_Delta=(t_hi-t_lo)/double(LocalMaxTempIterations-1);
LocalTemperatures.clear();
for(int i=0; i<LocalMaxTempIterations; i++){
Temperatures.push_back(t_lo+(double(i))*t_Delta);
LocalTemperatures.push_back(t_lo+(double(i))*t_Delta);
}
int LocalTempIterations=0;
do
{
//LogTemperaturePrior logPrior(Temperatures[TempIterations]);//t_lo);
//LogTemperaturePrior logPrior(LocalTemperatures[LocalTempIterations]);//t_lo);
double temperatureNow = LocalTemperatures[LocalTempIterations];
seedStarts += TempIterations;
// a container for our histograms
std::vector< subpavings::AdaptiveHistogram* > hists;
// a container for our PCFs of histograms
std::vector< subpavings::PiecewiseConstantFunction* > pcfs;
bool succPQMCopt = false;
//ostringstream strs; strs << temperatureNow;
//string burstsFileBaseNameNow = burstsFileBaseName+"_"+strs.str();
succPQMCopt = optPQMCAdapHist (Data, temperatureNow, hists, pcfs,
minPoints, minVolume, chooseStarts, keep,
stopOnMaxPosterior, postFileName,
checkPostFileNameBase, burstsFileBaseName, printHist, precPQ,
CarvingMaxPosterior, seedStarts);
real lv1outCVScore = pcfs[0]->getLeave1OutCVScore(*hists[0]);
Lv1OutCVScores.push_back(-1.0*lv1outCVScore);// -1.0* so we want to max to be min
LocalTempIterations++;
//to free all the contents of pcfs at the end
for (size_t i = 0; i < pcfs.size(); ++i)
{ if (NULL != pcfs[i]) delete pcfs[i]; pcfs[i] = NULL;}
//to free all the contents of hists at the end
if(CarvingMaxPosterior)
{ for (size_t i = 0; i < hists.size(); ++i)
{ if (NULL != hists[i]) delete hists[i]; hists[i] = NULL;}
}
}
while (LocalTempIterations<LocalMaxTempIterations);// && CVgain>0.1);
TempIterations++;
}
while (TempIterations<MaxTempIterations);// && CVgain>0.1);
////////////////////////////////////////////////////////////////////////////////////////////////
cout << "Temperatures:" << endl;
cout << Temperatures << endl;
cout << "- Lv1OutCVScores: (looking for maximum of -1.0*Lv1OutCVScores)" << endl;
cout << Lv1OutCVScores << endl << endl;
cout << "Temp Iteration Number " << TempIterations << endl; //getchar();
cout << "MaxTempIterations = " << MaxTempIterations << endl; //getchar();
vector<size_t> indtop(Lv1OutCVScores.size());
topk(Lv1OutCVScores, indtop);
t_opt = _double(Temperatures[indtop[0]]);
Lv1OutCVScores_opt = _double(Lv1OutCVScores[indtop[0]]);
success=true;
return success;
}
