| 44 |
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#include "primitives/Molecule.hpp" |
| 45 |
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namespace oopse { |
| 46 |
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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){ |
| 51 |
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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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|
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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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> |
} |
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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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< |
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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< |
//if selection is static, we only need to evaluate it once |
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< |
if (!evaluator1_.isDynamic()) { |
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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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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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|
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|
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< |
/**@todo Fixed 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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|
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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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|
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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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> |
} |
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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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|
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int nblocks = bsMan_->getNBlocks(); |
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|
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for (int i = 0; i < nblocks; ++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_->loadBlock(i); |
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|
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< |
if (i != j) { |
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< |
//if i equals to j, the block is still used, should not unload it |
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< |
bsMan_->unloadBlock(j); |
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< |
} |
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< |
} |
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< |
bsMan_->unloadBlock(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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> |
|
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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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|
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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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|
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< |
int jstart, jend; |
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|
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< |
assert(bsMan_->isBlockActive(block1) && bsMan_->isBlockActive(block2)); |
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> |
int jstart, jend; |
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|
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< |
SnapshotBlock snapshotBlock1 = bsMan_->getSnapshotBlock(block1); |
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< |
SnapshotBlock snapshotBlock2 = bsMan_->getSnapshotBlock(block2); |
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> |
assert(bsMan_->isBlockActive(block1) && bsMan_->isBlockActive(block2)); |
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|
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< |
jend = snapshotBlock2.second; |
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< |
|
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< |
for (int i = snapshotBlock1.first; i < snapshotBlock1.second; ++i) { |
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< |
|
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< |
//evaluate selection if it is dynamic |
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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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< |
} |
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< |
|
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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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> |
SnapshotBlock snapshotBlock1 = bsMan_->getSnapshotBlock(block1); |
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> |
SnapshotBlock snapshotBlock2 = bsMan_->getSnapshotBlock(block2); |
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|
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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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< |
|
| 183 |
< |
for(int j = jstart; j < jend; ++j) { |
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< |
//evaluate selection |
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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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< |
} |
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> |
jend = snapshotBlock2.second; |
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> |
|
| 168 |
> |
for (int i = snapshotBlock1.first; i < snapshotBlock1.second; ++i) { |
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> |
|
| 170 |
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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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< |
|
| 173 |
< |
correlateFrames(i, j); |
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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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> |
jstart = i; |
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> |
} else { |
| 178 |
> |
jstart = snapshotBlock2.first; |
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> |
} |
| 180 |
> |
|
| 181 |
> |
for(int j = jstart; j < jend; ++j) { |
| 182 |
> |
//update the position or velocity of the atoms belong to rigid bodies |
| 183 |
> |
updateFrame(j); |
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> |
|
| 185 |
> |
correlateFrames(i, j); |
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> |
} |
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|
} |
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} |
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– |
} |
| 189 |
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|
| 190 |
< |
void TimeCorrFunc::updateFrame(int frame){ |
| 190 |
> |
void TimeCorrFunc::updateFrame(int frame){ |
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|
Molecule* mol; |
| 192 |
|
RigidBody* rb; |
| 193 |
|
SimInfo::MoleculeIterator mi; |
| 195 |
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|
| 196 |
|
/** @todo need improvement */ |
| 197 |
|
if (storageLayout_ & DataStorage::dslPosition) { |
| 198 |
< |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
| 198 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
| 199 |
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|
| 200 |
< |
//change the positions of atoms which belong to the rigidbodies |
| 201 |
< |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
| 202 |
< |
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 |
| 201 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
| 202 |
> |
rb->updateAtoms(frame); |
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> |
} |
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> |
} |
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|
} |
| 206 |
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|
| 207 |
|
if (storageLayout_ & DataStorage::dslVelocity) { |
| 208 |
< |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
| 208 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
| 209 |
|
|
| 210 |
< |
//change the positions of atoms which belong to the rigidbodies |
| 211 |
< |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
| 212 |
< |
rb->updateAtomVel(frame); |
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< |
} |
| 214 |
< |
} |
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> |
//change the positions of atoms which belong to the rigidbodies |
| 211 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
| 212 |
> |
rb->updateAtomVel(frame); |
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> |
} |
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> |
} |
| 215 |
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|
| 216 |
|
} |
| 217 |
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|
| 218 |
< |
} |
| 218 |
> |
} |
| 219 |
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|
| 220 |
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|
| 221 |
< |
void TimeCorrFunc::preCorrelate() { |
| 221 |
> |
void TimeCorrFunc::preCorrelate() { |
| 222 |
|
std::fill(histogram_.begin(), histogram_.end(), 0.0); |
| 223 |
|
std::fill(count_.begin(), count_.end(), 0); |
| 224 |
< |
} |
| 224 |
> |
} |
| 225 |
|
|
| 226 |
< |
void TimeCorrFunc::postCorrelate() { |
| 226 |
> |
void TimeCorrFunc::postCorrelate() { |
| 227 |
|
for (int i =0 ; i < nTimeBins_; ++i) { |
| 228 |
< |
if (count_[i] > 0) { |
| 229 |
< |
histogram_[i] /= count_[i]; |
| 230 |
< |
} |
| 228 |
> |
if (count_[i] > 0) { |
| 229 |
> |
histogram_[i] /= count_[i]; |
| 230 |
> |
} |
| 231 |
|
} |
| 232 |
< |
} |
| 232 |
> |
} |
| 233 |
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|
| 234 |
|
|
| 235 |
< |
void TimeCorrFunc::writeCorrelate() { |
| 235 |
> |
void TimeCorrFunc::writeCorrelate() { |
| 236 |
|
std::ofstream ofs(outputFilename_.c_str()); |
| 237 |
|
|
| 238 |
|
if (ofs.is_open()) { |
| 239 |
|
|
| 240 |
< |
ofs << "#" << getCorrFuncType() << "\n"; |
| 241 |
< |
ofs << "#selection script1: \"" << selectionScript1_ <<"\"\tselection script2: \"" << selectionScript2_ << "\"\n"; |
| 242 |
< |
ofs << "#extra information: " << extra_ << "\n"; |
| 243 |
< |
ofs << "#time\tcorrVal\n"; |
| 240 |
> |
ofs << "#" << getCorrFuncType() << "\n"; |
| 241 |
> |
ofs << "#selection script1: \"" << selectionScript1_ <<"\"\tselection script2: \"" << selectionScript2_ << "\"\n"; |
| 242 |
> |
ofs << "#extra information: " << extra_ << "\n"; |
| 243 |
> |
ofs << "#time\tcorrVal\n"; |
| 244 |
|
|
| 245 |
< |
for (int i = 0; i < nTimeBins_; ++i) { |
| 246 |
< |
ofs << time_[i] << "\t" << histogram_[i] << "\n"; |
| 247 |
< |
} |
| 245 |
> |
for (int i = 0; i < nTimeBins_; ++i) { |
| 246 |
> |
ofs << time_[i] << "\t" << histogram_[i] << "\n"; |
| 247 |
> |
} |
| 248 |
|
|
| 249 |
|
} else { |
| 250 |
< |
sprintf(painCave.errMsg, |
| 251 |
< |
"TimeCorrFunc::writeCorrelate Error: fail to open %s\n", outputFilename_.c_str()); |
| 252 |
< |
painCave.isFatal = 1; |
| 253 |
< |
simError(); |
| 250 |
> |
sprintf(painCave.errMsg, |
| 251 |
> |
"TimeCorrFunc::writeCorrelate Error: fail to open %s\n", outputFilename_.c_str()); |
| 252 |
> |
painCave.isFatal = 1; |
| 253 |
> |
simError(); |
| 254 |
|
} |
| 255 |
|
|
| 256 |
|
ofs.close(); |
| 257 |
< |
} |
| 257 |
> |
} |
| 258 |
|
|
| 259 |
|
} |
