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#include "primitives/Molecule.hpp" |
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namespace oopse { |
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|
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< |
TimeCorrFunc::TimeCorrFunc(SimInfo* info, const std::string& filename, |
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< |
const std::string& sele1, const std::string& sele2, int storageLayout) |
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> |
TimeCorrFunc::TimeCorrFunc(SimInfo* info, const std::string& filename, |
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> |
const std::string& sele1, const std::string& sele2, int storageLayout) |
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: info_(info), storageLayout_(storageLayout), dumpFilename_(filename), selectionScript1_(sele1), |
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selectionScript2_(sele2), evaluator1_(info), evaluator2_(info), seleMan1_(info), seleMan2_(info){ |
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|
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< |
int nAtoms = info->getNGlobalAtoms(); |
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int nRigidBodies = info->getNGlobalRigidBodies(); |
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< |
int nStuntDoubles = nAtoms + nRigidBodies; |
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> |
int nAtoms = info->getNGlobalAtoms(); |
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> |
int nRigidBodies = info->getNGlobalRigidBodies(); |
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> |
int nStuntDoubles = nAtoms + nRigidBodies; |
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|
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< |
std::set<AtomType*> atomTypes = info->getUniqueAtomTypes(); |
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< |
std::set<AtomType*>::iterator i; |
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bool hasDirectionalAtom = false; |
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bool hasMultipole = false; |
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for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
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> |
std::set<AtomType*> atomTypes = info->getUniqueAtomTypes(); |
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> |
std::set<AtomType*>::iterator i; |
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> |
bool hasDirectionalAtom = false; |
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> |
bool hasMultipole = false; |
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> |
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
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if ((*i)->isDirectional()){ |
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< |
hasDirectionalAtom = true; |
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> |
hasDirectionalAtom = true; |
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} |
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if ((*i)->isMultipole()){ |
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< |
hasMultipole = true; |
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> |
hasMultipole = true; |
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} |
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< |
} |
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> |
} |
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< |
if (nRigidBodies > 0 || hasDirectionalAtom) { |
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> |
if (nRigidBodies > 0 || hasDirectionalAtom) { |
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storageLayout_ |= DataStorage::dslAmat; |
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< |
} |
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< |
if (hasMultipole) { |
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> |
} |
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> |
if (hasMultipole) { |
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storageLayout_ |= DataStorage::dslElectroFrame; |
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if (nRigidBodies > 0) { |
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< |
storageLayout_ |= DataStorage::dslAngularMomentum; |
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> |
storageLayout_ |= DataStorage::dslAngularMomentum; |
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} |
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< |
} |
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if(nRigidBodies > 0 && storageLayout_ & DataStorage::dslVelocity) { |
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> |
} |
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> |
if(nRigidBodies > 0 && storageLayout_ & DataStorage::dslVelocity) { |
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storageLayout_ |= DataStorage::dslAngularMomentum; |
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< |
} |
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> |
} |
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|
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< |
bsMan_ = new BlockSnapshotManager(info, dumpFilename_, storageLayout_); |
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info_->setSnapshotManager(bsMan_); |
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> |
bsMan_ = new BlockSnapshotManager(info, dumpFilename_, storageLayout_); |
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> |
info_->setSnapshotManager(bsMan_); |
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|
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< |
evaluator1_.loadScriptString(selectionScript1_); |
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evaluator2_.loadScriptString(selectionScript2_); |
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> |
evaluator1_.loadScriptString(selectionScript1_); |
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> |
evaluator2_.loadScriptString(selectionScript2_); |
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|
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< |
//if selection is static, we only need to evaluate it once |
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if (!evaluator1_.isDynamic()) { |
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> |
//if selection is static, we only need to evaluate it once |
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> |
if (!evaluator1_.isDynamic()) { |
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seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
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validateSelection(seleMan1_); |
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} else { |
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sprintf(painCave.errMsg, |
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> |
} else { |
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> |
sprintf(painCave.errMsg, |
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"TimeCorrFunc Error: dynamic selection is not supported\n"); |
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< |
painCave.isFatal = 1; |
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simError(); |
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} |
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> |
painCave.isFatal = 1; |
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> |
simError(); |
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> |
} |
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|
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< |
if (!evaluator2_.isDynamic()) { |
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> |
if (!evaluator2_.isDynamic()) { |
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seleMan2_.setSelectionSet(evaluator2_.evaluate()); |
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validateSelection(seleMan2_); |
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} else { |
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< |
sprintf(painCave.errMsg, |
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> |
} else { |
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> |
sprintf(painCave.errMsg, |
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"TimeCorrFunc Error: dynamic selection is not supported\n"); |
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< |
painCave.isFatal = 1; |
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simError(); |
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} |
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> |
painCave.isFatal = 1; |
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> |
simError(); |
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> |
} |
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/**@todo Fix Me */ |
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Globals* simParams = info_->getSimParams(); |
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if (simParams->haveSampleTime()){ |
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> |
/**@todo Fix Me */ |
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> |
Globals* simParams = info_->getSimParams(); |
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> |
if (simParams->haveSampleTime()){ |
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deltaTime_ = simParams->getSampleTime(); |
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} else { |
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sprintf(painCave.errMsg, |
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> |
} else { |
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> |
sprintf(painCave.errMsg, |
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"TimeCorrFunc::writeCorrelate Error: can not figure out deltaTime\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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> |
painCave.isFatal = 1; |
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> |
simError(); |
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> |
} |
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< |
int nframes = bsMan_->getNFrames(); |
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< |
nTimeBins_ = nframes; |
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histogram_.resize(nTimeBins_); |
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count_.resize(nTimeBins_); |
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time_.resize(nTimeBins_); |
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> |
int nframes = bsMan_->getNFrames(); |
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> |
nTimeBins_ = nframes; |
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> |
histogram_.resize(nTimeBins_); |
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> |
count_.resize(nTimeBins_); |
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> |
time_.resize(nTimeBins_); |
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for (int i = 0; i < nTimeBins_; ++i) { |
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for (int i = 0; i < nTimeBins_; ++i) { |
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time_[i] = i * deltaTime_; |
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} |
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> |
} |
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< |
} |
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> |
} |
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< |
void TimeCorrFunc::doCorrelate() { |
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> |
void TimeCorrFunc::doCorrelate() { |
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preCorrelate(); |
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int nblocks = bsMan_->getNBlocks(); |
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for (int i = 0; i < nblocks; ++i) { |
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bsMan_->loadBlock(i); |
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> |
bsMan_->loadBlock(i); |
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for (int j = i; j < nblocks; ++j) { |
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bsMan_->loadBlock(j); |
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< |
correlateBlocks(i, j); |
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< |
bsMan_->unloadBlock(j); |
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} |
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> |
for (int j = i; j < nblocks; ++j) { |
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> |
bsMan_->loadBlock(j); |
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> |
correlateBlocks(i, j); |
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> |
bsMan_->unloadBlock(j); |
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} |
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bsMan_->unloadBlock(i); |
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> |
bsMan_->unloadBlock(i); |
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} |
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postCorrelate(); |
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writeCorrelate(); |
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} |
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> |
} |
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< |
void TimeCorrFunc::correlateBlocks(int block1, int block2) { |
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> |
void TimeCorrFunc::correlateBlocks(int block1, int block2) { |
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int jstart, jend; |
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for (int i = snapshotBlock1.first; i < snapshotBlock1.second; ++i) { |
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//update the position or velocity of the atoms belong to rigid bodies |
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updateFrame(i); |
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//update the position or velocity of the atoms belong to rigid bodies |
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> |
updateFrame(i); |
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|
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// if the two blocks are the same, we don't want to correlate |
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< |
// backwards in time, so start j at the same frame as i |
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< |
if (block1 == block2) { |
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> |
// if the two blocks are the same, we don't want to correlate |
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> |
// backwards in time, so start j at the same frame as i |
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> |
if (block1 == block2) { |
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jstart = i; |
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} else { |
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jstart = snapshotBlock2.first; |
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} |
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> |
} else { |
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> |
jstart = snapshotBlock2.first; |
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} |
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< |
for(int j = jstart; j < jend; ++j) { |
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< |
//update the position or velocity of the atoms belong to rigid bodies |
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< |
updateFrame(j); |
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> |
for(int j = jstart; j < jend; ++j) { |
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> |
//update the position or velocity of the atoms belong to rigid bodies |
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> |
updateFrame(j); |
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< |
correlateFrames(i, j); |
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< |
} |
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> |
correlateFrames(i, j); |
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> |
} |
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} |
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< |
} |
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> |
} |
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< |
void TimeCorrFunc::updateFrame(int frame){ |
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> |
void TimeCorrFunc::updateFrame(int frame){ |
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Molecule* mol; |
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RigidBody* rb; |
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SimInfo::MoleculeIterator mi; |
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/** @todo need improvement */ |
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if (storageLayout_ & DataStorage::dslPosition) { |
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< |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
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> |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
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< |
//change the positions of atoms which belong to the rigidbodies |
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< |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
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< |
rb->updateAtoms(frame); |
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< |
} |
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< |
} |
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> |
//change the positions of atoms which belong to the rigidbodies |
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> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
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> |
rb->updateAtoms(frame); |
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> |
} |
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> |
} |
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} |
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if (storageLayout_ & DataStorage::dslVelocity) { |
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< |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
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> |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
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|
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< |
//change the positions of atoms which belong to the rigidbodies |
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< |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
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< |
rb->updateAtomVel(frame); |
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< |
} |
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< |
} |
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> |
//change the positions of atoms which belong to the rigidbodies |
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> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
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> |
rb->updateAtomVel(frame); |
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> |
} |
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> |
} |
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} |
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< |
} |
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> |
} |
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< |
void TimeCorrFunc::preCorrelate() { |
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> |
void TimeCorrFunc::preCorrelate() { |
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std::fill(histogram_.begin(), histogram_.end(), 0.0); |
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std::fill(count_.begin(), count_.end(), 0); |
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< |
} |
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> |
} |
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|
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< |
void TimeCorrFunc::postCorrelate() { |
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> |
void TimeCorrFunc::postCorrelate() { |
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for (int i =0 ; i < nTimeBins_; ++i) { |
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< |
if (count_[i] > 0) { |
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< |
histogram_[i] /= count_[i]; |
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< |
} |
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> |
if (count_[i] > 0) { |
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> |
histogram_[i] /= count_[i]; |
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> |
} |
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} |
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< |
} |
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> |
} |
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|
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|
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< |
void TimeCorrFunc::writeCorrelate() { |
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> |
void TimeCorrFunc::writeCorrelate() { |
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std::ofstream ofs(outputFilename_.c_str()); |
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|
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if (ofs.is_open()) { |
| 239 |
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|
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< |
ofs << "#" << getCorrFuncType() << "\n"; |
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< |
ofs << "#selection script1: \"" << selectionScript1_ <<"\"\tselection script2: \"" << selectionScript2_ << "\"\n"; |
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< |
ofs << "#extra information: " << extra_ << "\n"; |
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< |
ofs << "#time\tcorrVal\n"; |
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> |
ofs << "#" << getCorrFuncType() << "\n"; |
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> |
ofs << "#selection script1: \"" << selectionScript1_ <<"\"\tselection script2: \"" << selectionScript2_ << "\"\n"; |
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> |
ofs << "#extra information: " << extra_ << "\n"; |
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> |
ofs << "#time\tcorrVal\n"; |
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|
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< |
for (int i = 0; i < nTimeBins_; ++i) { |
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< |
ofs << time_[i] << "\t" << histogram_[i] << "\n"; |
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< |
} |
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> |
for (int i = 0; i < nTimeBins_; ++i) { |
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> |
ofs << time_[i] << "\t" << histogram_[i] << "\n"; |
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> |
} |
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|
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} else { |
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< |
sprintf(painCave.errMsg, |
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< |
"TimeCorrFunc::writeCorrelate Error: fail to open %s\n", outputFilename_.c_str()); |
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< |
painCave.isFatal = 1; |
| 253 |
< |
simError(); |
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> |
sprintf(painCave.errMsg, |
| 251 |
> |
"TimeCorrFunc::writeCorrelate Error: fail to open %s\n", outputFilename_.c_str()); |
| 252 |
> |
painCave.isFatal = 1; |
| 253 |
> |
simError(); |
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} |
| 255 |
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|
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ofs.close(); |
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< |
} |
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> |
} |
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|
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} |
