/*
* Read potential parameters from file.
*/
void LocalLamellarOrderingExternal::readParameters(std::istream &in)
{
if (nAtomType_ == 0) {
UTIL_THROW("nAtomType must be set before readParam");
}
if (!boundaryPtr_) {
UTIL_THROW("Boundary must be set before readParam");
}
// Read parameters
read<int>(in, "perpDirection", perpDirection_);
if (perpDirection_ < 0 || perpDirection_ >= Dimension) {
UTIL_THROW("Invalid index for perpendicular direction.");
}
read<int>(in, "parallelDirection", parallelDirection_);
if (parallelDirection_ < 0 || parallelDirection_ >= Dimension) {
UTIL_THROW("Invalid index for parallel direction.");
}
read<double>(in, "fraction", fraction_);
prefactor_.allocate(nAtomType_);
readDArray<double>(in, "prefactor", prefactor_, nAtomType_);
read<double>(in, "externalParameter", externalParameter_);
read<double>(in, "interfaceWidth", width_);
read<int>(in, "periodicity", periodicity_);
isInitialized_ = true;
}
/*
* Read potential parameters from file.
*/
void PeriodicExternal::readParameters(std::istream &in)
{
if (nAtomType_ == 0) {
UTIL_THROW("nAtomType must be set before readParam");
}
if (!boundaryPtr_) {
UTIL_THROW("Boundary must be set before readParam");
}
// Read parameters
prefactor_.allocate(nAtomType_);
readDArray<double>(in, "prefactor", prefactor_, nAtomType_);
read<double>(in, "externalParameter", externalParameter_);
read<int>(in, "nWaveVectors", nWaveVectors_);
read<double>(in, "C", C_);
waveVectors_.allocate(nWaveVectors_);
readDArray<Vector>(in, "waveVectors", waveVectors_, nWaveVectors_);
phases_.allocate(nWaveVectors_);
readDArray<double>(in, "phases", phases_, nWaveVectors_);
read<Vector>(in, "shift", shift_);
read<double>(in, "interfaceWidth", interfaceWidth_);
read<int>(in, "periodicity", periodicity_);
isInitialized_ = true;
}
void McSimulation::load(const std::string& filename)
{
if (isInitialized_) {
UTIL_THROW("Error: Called load when already initialized");
}
if (!isRestarting_) {
UTIL_THROW("Error: Called load without restart option");
}
// Load from archive
Serializable::IArchive ar;
std::ios_base::openmode mode = std::ios_base::in | std::ios_base::binary;
fileMaster().openRestartIFile(filename, ar.file(), mode);
load(ar);
ar.file().close();
#ifdef UTIL_MPI
#ifdef MCMD_PERTURB
if (system().hasPerturbation()) {
// Read one command file, after reading multiple restart files.
Util::Log::file() << "Set to use a single command file"
<< std::endl;
setIoCommunicator();
}
#endif
#endif
isInitialized_ = true;
}
/*
* Remove all ghosts.
*/
void AtomStorage::clearGhosts()
{
// Precondition
if (locked_)
UTIL_THROW("AtomStorage is locked");
// Clear ghosts from the map
map_.clearGhosts(ghostSet_);
// Transfer ghosts from the set to the reservoir
Atom* atomPtr;
while (ghostSet_.size() > 0) {
atomPtr = &ghostSet_.pop();
ghostReservoir_.push(*atomPtr);
}
if (ghostSet_.size() != 0) {
UTIL_THROW("Nonzero ghostSet size at end of clearGhosts");
}
if (map_.nGhost() != 0) {
UTIL_THROW("Nonzero nGhost in map at end of clearGhosts");
}
if (map_.nGhostDistinct() != 0) {
UTIL_THROW("Nonzero nGhostDistinct at end of clearGhosts");
}
}
/*
* Load state from an archive.
*/
void ClusterHistogram::loadParameters(Serializable::IArchive& ar)
{
// Load interval and outputFileName
Analyzer::loadParameters(ar);
loadParameter<int>(ar,"speciesId", speciesId_);
if (speciesId_ < 0) {
UTIL_THROW("Negative speciesId");
}
if (speciesId_ >= system().simulation().nSpecies()) {
UTIL_THROW("speciesId > nSpecies");
}
loadParameter<int>(ar, "atomTypeId", atomTypeId_);
if (atomTypeId_ < 0) {
UTIL_THROW("Negative atomTypeId");
}
loadParameter<double>(ar, "cutoff", cutoff_);
if (cutoff_ < 0) {
UTIL_THROW("Negative cutoff");
}
identifier_.initialize(speciesId_, atomTypeId_, cutoff_);
loadParameter<int>(ar, "histMin", histMin_);
loadParameter<int>(ar, "histMax", histMax_);
ar >> hist_;
ar >> nSample_;
isInitialized_ = true;
}
/*
* Load internal state from an archive.
*/
void McSimulation::loadParameters(Serializable::IArchive &ar)
{
if (isInitialized_) {
UTIL_THROW("Error: Called readParam when already initialized");
}
#ifdef UTIL_MPI
if (hasIoCommunicator()) {
UTIL_THROW("Error: Has a param communicator in loadParameters");
}
#endif
Simulation::loadParameters(ar);
loadParamComposite(ar, system());
loadParamComposite(ar, *mcMoveManagerPtr_);
loadParamComposite(ar, analyzerManager());
loadParameter<int>(ar, "saveInterval", saveInterval_);
if (saveInterval_ > 0) {
loadParameter<std::string>(ar, "saveFileName", saveFileName_);
}
system().loadConfig(ar);
ar >> iStep_;
isValid();
isInitialized_ = true;
}
/*
* Load state from an archive.
*/
void StructureFactor::loadParameters(Serializable::IArchive& ar)
{
Analyzer::loadParameters(ar);
ar & nAtomType_;
loadParameter<int>(ar, "nMode", nMode_);
loadDMatrix<double>(ar, "modes", modes_, nMode_, nAtomType_);
loadParameter<int>(ar, "nWave", nWave_);
loadDArray<IntVector>(ar, "waveIntVectors", waveIntVectors_, nWave_);
ar & structureFactors_;
ar & nSample_;
// Validate
if (nAtomType_ != system().simulation().nAtomType()) {
UTIL_THROW("Inconsistent values of nAtomType_");
}
if (modes_.capacity1() != nMode_) {
UTIL_THROW("Inconsistent capacity1 for modes array");
}
if (modes_.capacity2() != nAtomType_) {
UTIL_THROW("Inconsistent capacity2 for modes array");
}
if (waveIntVectors_.capacity() != nWave_) {
UTIL_THROW("Inconsistent capacity for waveIntVector");
}
// Allocate temporary data structures
waveVectors_.allocate(nWave_);
fourierModes_.allocate(nWave_, nMode_);
isInitialized_ = true;
}
/*
* Read and execute commands from a specified command file.
*/
void McSimulation::readCommands(std::istream &in)
{
if (!isInitialized_) {
UTIL_THROW("McSimulation is not initialized");
}
std::string command;
std::string filename;
std::ifstream inputFile;
std::ofstream outputFile;
#ifndef UTIL_MPI
std::istream& inBuffer = in;
#else
std::stringstream inBuffer;
std::string line;
#endif
bool readNext = true;
while (readNext) {
// iffdef UTIL_MPI, read a line and copy to stringstream inBuffer
// ifndef UTIL_MPI, inBuffer is simply a reference to istream in.
#ifdef UTIL_MPI
// Read a command line, and broadcast if necessary.
if (!hasIoCommunicator() || isIoProcessor()) {
getNextLine(in, line);
}
if (hasIoCommunicator()) {
bcast<std::string>(communicator(), line, 0);
}
// Copy the command line to inBuffer.
inBuffer.clear();
for (unsigned i=0; i < line.size(); ++i) {
inBuffer.put(line[i]);
}
#endif
inBuffer >> command;
Log::file() << command;
if (isRestarting_) {
if (command == "RESTART") {
int endStep;
inBuffer >> endStep;
Log::file() << " " << iStep_ << " to "
<< endStep << std::endl;
simulate(endStep, isRestarting_);
isRestarting_ = false;
} else {
UTIL_THROW("Missing RESTART command");
}
} else {
void ScoreFeatureManager::configure(const std::vector<std::string> args)
{
bool domainAdded = false;
bool sparseDomainAdded = false;
for (size_t i = 0; i < args.size(); ++i) {
if (args[i] == "--IgnoreSentenceId") {
m_includeSentenceId = true;
} else if (args[i].substr(0,8) == "--Domain") {
string type = args[i].substr(8);
++i;
UTIL_THROW_IF(i == args.size(), ScoreFeatureArgumentException, "Missing domain file");
string domainFile = args[i];
UTIL_THROW_IF(domainAdded, ScoreFeatureArgumentException,
"Only allowed one domain feature");
if (type == "Subset") {
m_features.push_back(ScoreFeaturePtr(new SubsetDomainFeature(domainFile)));
} else if (type == "Ratio") {
m_features.push_back(ScoreFeaturePtr(new RatioDomainFeature(domainFile)));
} else if (type == "Indicator") {
m_features.push_back(ScoreFeaturePtr(new IndicatorDomainFeature(domainFile)));
} else {
UTIL_THROW(ScoreFeatureArgumentException, "Unknown domain feature type " << type);
}
domainAdded = true;
m_includeSentenceId = true;
} else if (args[i].substr(0,14) == "--SparseDomain") {
string type = args[i].substr(14);
++i;
UTIL_THROW_IF(i == args.size(), ScoreFeatureArgumentException, "Missing domain file");
string domainFile = args[i];
UTIL_THROW_IF(sparseDomainAdded, ScoreFeatureArgumentException,
"Only allowed one sparse domain feature");
if (type == "Subset") {
m_features.push_back(ScoreFeaturePtr(new SparseSubsetDomainFeature(domainFile)));
} else if (type == "Ratio") {
m_features.push_back(ScoreFeaturePtr(new SparseRatioDomainFeature(domainFile)));
} else if (type == "Indicator") {
m_features.push_back(ScoreFeaturePtr(new SparseIndicatorDomainFeature(domainFile)));
} else {
UTIL_THROW(ScoreFeatureArgumentException, "Unknown domain feature type " << type);
}
sparseDomainAdded = true;
m_includeSentenceId = true;
} else if(args[i] == "--GHKMFeatureSparse"){
//MARIA
m_features.push_back(ScoreFeaturePtr(new InternalStructFeatureSparse()));
} else if(args[i] == "--GHKMFeatureDense"){
//MARIA
m_features.push_back(ScoreFeaturePtr(new InternalStructFeatureDense()));
} else {
UTIL_THROW(ScoreFeatureArgumentException,"Unknown score argument " << args[i]);
}
}
}
/*
* Set nAtomType
*/
void PeriodicExternal::setNAtomType(int nAtomType)
{
if (nAtomType <= 0) {
UTIL_THROW("nAtomType <= 0");
}
if (nAtomType > MaxAtomType) {
UTIL_THROW("nAtomType > PeriodicExternal::MaxAtomType");
}
nAtomType_ = nAtomType;
}
/*
* Set nAtomType
*/
void LocalLamellarOrderingExternal::setNAtomType(int nAtomType)
{
if (nAtomType <= 0) {
UTIL_THROW("nAtomType <= 0");
}
if (nAtomType > MaxAtomType) {
UTIL_THROW("nAtomType > LocalLamellarOrderingExternal::MaxAtomType");
}
nAtomType_ = nAtomType;
}
/*
* Set nAtomType
*/
void OrthoBoxExternal::setNAtomType(int nAtomType)
{
if (nAtomType <= 0) {
UTIL_THROW("nAtomType <= 0");
}
if (nAtomType > MaxAtomType) {
UTIL_THROW("nAtomType > OrthoBoxExternal::MaxAtomType");
}
nAtomType_ = nAtomType;
}
/*
* Set nAtomType
*/
void NucleationExternal::setNAtomType(int nAtomType)
{
if (nAtomType <= 0) {
UTIL_THROW("nAtomType <= 0");
}
if (nAtomType > MaxAtomType) {
UTIL_THROW("nAtomType > NucleationExternal::MaxAtomType");
}
nAtomType_ = nAtomType;
}
/*
* Clear memory block (reset to empty state).
*/
void MemoryIArchive::clear()
{
if (!isAllocated()) {
UTIL_THROW("Archive is not allocated");
}
if (!ownsData_) {
UTIL_THROW("Archive does not own data");
}
cursor_ = begin();
end_ = begin();
}
void OnDiskWrapper::BeginLoad(const std::string &filePath)
{
if (!OpenForLoad(filePath)) {
UTIL_THROW(util::FileOpenException, "Couldn't open for loading: " << filePath);
}
if (!m_vocab.Load(*this))
UTIL_THROW(util::FileOpenException, "Couldn't load vocab");
UINT64 rootFilePos = GetMisc("RootNodeOffset");
m_rootSourceNode = new PhraseNode(rootFilePos, *this);
}
/*
* Finalize receiving block, check consistency.
*/
void Buffer::endRecvBlock()
{
if (recvSize_ != 0) {
UTIL_THROW("Error: Recv counter != 0 at end of block");
}
if (recvPtr_ != recvBlockEnd_) {
UTIL_THROW("Error: Inconsistent recv cursor at end of block");
}
recvBlockBegin_ = 0;
recvBlockEnd_ = 0;
recvSize_ = 0;
recvType_ = NONE;
}
/*
* Clear accumulators.
*/
void McMuExchange::setup()
{
nMolecule_ = system().nMolecule(speciesId_);
if (nMolecule_ > accumulators_.capacity()) {
UTIL_THROW("nMolecule > capacity");
}
if (nMolecule_ <= 0) {
UTIL_THROW("nMolecule <= 0");
}
for (int iMol = 0; iMol < nMolecule_; ++iMol) {
accumulators_[iMol].clear();
}
}
/*
* Read saveInterval and saveFileName.
*/
void Integrator::readParameters(std::istream& in)
{
read<int>(in, "saveInterval", saveInterval_);
if (saveInterval_ > 0) {
if (Analyzer::baseInterval > 0) {
if (saveInterval_ % Analyzer::baseInterval != 0) {
UTIL_THROW("saveInterval is not a multiple of baseInterval");
}
} else {
UTIL_THROW("Analyzer::baseInterval is not positive");
}
read<std::string>(in, "saveFileName", saveFileName_);
}
}
/*
* Return address for a new ghost Atom.
*/
Atom* AtomStorage::newGhostPtr()
{
// Preconditions
if (newGhostPtr_ != 0)
UTIL_THROW("Unregistered newGhostPtr_ still active");
if (locked_ )
UTIL_THROW("AtomStorage is locked");
if (ghostReservoir_.size() == 0)
UTIL_THROW("Atom to pop from empty atomReservoir");
newGhostPtr_ = &ghostReservoir_.pop();
newGhostPtr_->clear();
newGhostPtr_->setIsGhost(true);
return newGhostPtr_;
}
/*
* Reset cursor to beginning, prepare to reread.
*/
void MemoryIArchive::reset()
{
if (!isAllocated()) {
UTIL_THROW("Archive is not allocated");
}
cursor_ = begin();
}
void ConstrainedDecoding::Load()
{
const StaticData &staticData = StaticData::Instance();
bool addBeginEndWord = (staticData.GetSearchAlgorithm() == ChartDecoding) || (staticData.GetSearchAlgorithm() == ChartIncremental);
InputFileStream constraintFile(m_path);
std::string line;
long sentenceID = staticData.GetStartTranslationId() - 1;
while (getline(constraintFile, line)) {
vector<string> vecStr = Tokenize(line, "\t");
Phrase phrase(0);
if (vecStr.size() == 1) {
sentenceID++;
phrase.CreateFromString(Output, staticData.GetOutputFactorOrder(), vecStr[0], staticData.GetFactorDelimiter(), NULL);
} else if (vecStr.size() == 2) {
sentenceID = Scan<long>(vecStr[0]);
phrase.CreateFromString(Output, staticData.GetOutputFactorOrder(), vecStr[1], staticData.GetFactorDelimiter(), NULL);
} else {
UTIL_THROW(util::Exception, "Reference file not loaded");
}
if (addBeginEndWord) {
phrase.InitStartEndWord();
}
m_constraints.insert(make_pair(sentenceID,phrase));
}
}
/*
* Allocate and initialize all containers (private).
*/
void AtomStorage::allocate()
{
// Precondition
if (isInitialized_) {
UTIL_THROW("AtomStorage can only be initialized once");
}
atoms_.allocate(atomCapacity_);
atomReservoir_.allocate(atomCapacity_);
atomSet_.allocate(atoms_);
int i;
for (i = atomCapacity_ - 1; i >=0; --i) {
atomReservoir_.push(atoms_[i]);
}
ghosts_.allocate(ghostCapacity_);
ghostReservoir_.allocate(ghostCapacity_);
ghostSet_.allocate(ghosts_);
for (i = ghostCapacity_ - 1; i >=0; --i) {
ghostReservoir_.push(ghosts_[i]);
}
map_.allocate(totalAtomCapacity_);
snapshot_.allocate(atomCapacity_);
isInitialized_ = true;
}
/*
* Determine whether an atom exchange and reneighboring is needed.
*/
bool Integrator::isExchangeNeeded(double skin)
{
if (!atomStorage().isCartesian()) {
UTIL_THROW("Error: Coordinates not Cartesian in isExchangeNeeded");
}
// Calculate maximum square displacment on this node
double maxSqDisp = atomStorage().maxSqDisplacement();
int needed = 0;
if (sqrt(maxSqDisp) > 0.5*skin) {
needed = 1;
}
timer_.stamp(CHECK);
#if UTIL_MPI
int neededAll;
domain().communicator().Allreduce(&needed, &neededAll,
1, MPI::INT, MPI::MAX);
timer_.stamp(ALLREDUCE);
return bool(neededAll);
#else
return bool(needed);
#endif
}
/*
* Determine whether an atom exchange and reneighboring is needed.
*/
bool Integrator::isExchangeNeeded(double skin)
{
if (!atomStorage().isCartesian()) {
UTIL_THROW("Error: Coordinates not Cartesian in isExchangeNeeded");
}
// Calculate maximum square displacment on this node
double maxSqDisp = atomStorage().maxSqDisplacement();
timer_.stamp(CHECK);
// Decide on master node if maximum exceeds threshhold.
int needed;
#if UTIL_MPI
double maxSqDispAll; // global maximum
domain().communicator().Reduce(&maxSqDisp, &maxSqDispAll, 1,
MPI::DOUBLE, MPI::MAX, 0);
if (domain().communicator().Get_rank() == 0) {
needed = 0;
if (sqrt(maxSqDispAll) > 0.5*skin) {
needed = 1;
}
}
domain().communicator().Bcast(&needed, 1, MPI::INT, 0);
timer_.stamp(ALLREDUCE);
#else
if (sqrt(maxSqDisp) > 0.5*skin) {
needed = 1;
}
#endif
return bool(needed);
}
GlobalLexicalModelUnlimited::GlobalLexicalModelUnlimited(const std::string &line)
:StatelessFeatureFunction(0, line)
{
UTIL_THROW(util::Exception,
"GlobalLexicalModelUnlimited hasn't been refactored for new feature function framework yet"); // TODO need to update arguments to key=value
const vector<string> modelSpec = Tokenize(line);
for (size_t i = 0; i < modelSpec.size(); i++ ) {
bool ignorePunctuation = true, biasFeature = false, restricted = false;
size_t context = 0;
string filenameSource, filenameTarget;
vector< string > factors;
vector< string > spec = Tokenize(modelSpec[i]," ");
// read optional punctuation and bias specifications
if (spec.size() > 0) {
if (spec.size() != 2 && spec.size() != 3 && spec.size() != 4 && spec.size() != 6) {
std::cerr << "Format of glm feature is <factor-src>-<factor-tgt> [ignore-punct] [use-bias] "
<< "[context-type] [filename-src filename-tgt]";
//return false;
}
factors = Tokenize(spec[0],"-");
if (spec.size() >= 2)
ignorePunctuation = Scan<size_t>(spec[1]);
if (spec.size() >= 3)
biasFeature = Scan<size_t>(spec[2]);
if (spec.size() >= 4)
context = Scan<size_t>(spec[3]);
if (spec.size() == 6) {
filenameSource = spec[4];
filenameTarget = spec[5];
restricted = true;
}
} else
factors = Tokenize(modelSpec[i],"-");
if ( factors.size() != 2 ) {
std::cerr << "Wrong factor definition for global lexical model unlimited: " << modelSpec[i];
//return false;
}
const vector<FactorType> inputFactors = Tokenize<FactorType>(factors[0],",");
const vector<FactorType> outputFactors = Tokenize<FactorType>(factors[1],",");
throw runtime_error("GlobalLexicalModelUnlimited should be reimplemented as a stateful feature");
GlobalLexicalModelUnlimited* glmu = NULL; // new GlobalLexicalModelUnlimited(inputFactors, outputFactors, biasFeature, ignorePunctuation, context);
if (restricted) {
cerr << "loading word translation word lists from " << filenameSource << " and " << filenameTarget << endl;
if (!glmu->Load(filenameSource, filenameTarget)) {
std::cerr << "Unable to load word lists for word translation feature from files "
<< filenameSource
<< " and "
<< filenameTarget;
//return false;
}
}
}
}
LanguageModelKen<lm::ngram::ProbingModel>& InMemoryPerSentenceOnDemandLM::GetPerThreadLM() const
{
LanguageModelKen<lm::ngram::ProbingModel> *lm;
lm = m_perThreadLM.get();
if (lm == NULL) {
lm = new LanguageModelKen<lm::ngram::ProbingModel>();
string* filename = m_tmpFilename.get();
if (filename == NULL) {
UTIL_THROW(util::Exception, "Can't get a thread-specific LM because no temporary filename has been set for this thread\n");
} else {
lm->LoadModel(*filename, util::POPULATE_OR_READ);
}
VERBOSE(1, filename);
VERBOSE(1, "\tLM initialized\n");
m_perThreadLM.reset(lm);
}
assert(lm);
return *lm;
}
FFState* CoveredReferenceFeature::EvaluateWhenApplied(
const ChartHypothesis& /* cur_hypo */,
int /* featureID - used to index the state in the previous hypotheses */,
ScoreComponentCollection* accumulator) const
{
UTIL_THROW(util::Exception, "Not implemented");
}
/*
* Set the nBondType_ member
*/
void HarmonicBond::setNBondType(int nBondType)
{
if (nBondType > MaxNBondType) {
UTIL_THROW("nBondType > HarmonicBond::MaxNBondType");
}
nBondType_ = nBondType;
}
/*
* Set the nAngleType_ member.
*/
void CosineSqAngle::setNAngleType(int nAngleType)
{
if (nAngleType > MaxNAngleType) {
UTIL_THROW("nAngleType > CosineSqAngle::MaxNAngleType");
}
nAngleType_ = nAngleType;
}
const TargetPhraseCollectionWithSourcePhrase* PhraseDictionary::
GetTargetPhraseCollectionLegacy(InputType const& src,WordsRange const& range) const
{
UTIL_THROW(util::Exception, "Legacy method not implemented");
//Phrase phrase = src.GetSubString(range);
//return GetTargetPhraseCollection(phrase);
}