bool Settings::LoadSettings()
////////////////////////////////////////////////////////////////////////
{
#define GETSTRING(a,b) if (settingsfile.GetString(a, tempstring)) Set##b(tempstring);
#define GETBOOL(a,b) if (settingsfile.GetBool(a, tempbool)) Set##b(tempbool);
#define GETINT(a,b) if (settingsfile.GetInteger(a, tempint)) Set##b(tempint);
BString tempstring;
bool tempbool;
int tempint;
DataFile settingsfile;
if (settingsfile.LoadDataFile(GetSettingsFile()))
{
if (settingsfile.GetBool("ASKONEXIT", tempbool))
SetAskOnExit(tempbool);
if (settingsfile.GetString("LANGUAGE", tempstring))
SetLanguage(tempstring);
if (settingsfile.GetInteger("WINDOWLEFT", tempint))
SetWindowLeft(tempint);
GETINT("WINDOWTOP", WindowTop);
GETINT("WINDOWWIDTH", WindowWidth);
GETINT("WINDOWHEIGHT", WindowHeight);
GETSTRING("TERMINALWINDOW", TerminalWindow);
GETSTRING("LEFTPANELPATH", LeftPanelPath);
GETSTRING("RIGHTPANELPATH", RightPanelPath);
return true;
}
else
return false;
}
void ExtentManager::flushFiles( bool sync ) {
DEV Lock::assertAtLeastReadLocked( _dbname );
for( vector<DataFile*>::iterator i = _files.begin(); i != _files.end(); i++ ) {
DataFile *f = *i;
f->flush(sync);
}
}
// Action_Angle::init()
Action::RetType Action_Angle::Init(ArgList& actionArgs, TopologyList* PFL, DataSetList* DSL, DataFileList* DFL, int debugIn)
{
// Get keywords
DataFile* outfile = DFL->AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
useMass_ = actionArgs.hasKey("mass");
// Get Masks
std::string mask1 = actionArgs.GetMaskNext();
std::string mask2 = actionArgs.GetMaskNext();
std::string mask3 = actionArgs.GetMaskNext();
if (mask1.empty() || mask2.empty() || mask3.empty()) {
mprinterr("Error: angle: Requires 3 masks\n");
return Action::ERR;
}
Mask1_.SetMaskString(mask1);
Mask2_.SetMaskString(mask2);
Mask3_.SetMaskString(mask3);
// Dataset to store angles
ang_ = DSL->AddSet(DataSet::DOUBLE, MetaData(actionArgs.GetStringNext(),MetaData::M_ANGLE),"Ang");
if (ang_==0) return Action::ERR;
// Add dataset to data file list
if (outfile != 0) outfile->AddDataSet( ang_ );
mprintf(" ANGLE: [%s]-[%s]-[%s]\n",Mask1_.MaskString(), Mask2_.MaskString(),
Mask3_.MaskString());
if (useMass_)
mprintf("\tUsing center of mass of atoms in masks.\n");
return Action::OK;
}
DiskLoc MmapV1ExtentManager::_createExtent( OperationContext* txn,
int size,
bool enforceQuota ) {
size = quantizeExtentSize( size );
if ( size > maxSize() )
size = maxSize();
verify( size < DataFile::maxSize() );
for ( int i = numFiles() - 1; i >= 0; i-- ) {
DataFile* f = _getOpenFile(i);
invariant(f);
if ( f->getHeader()->unusedLength >= size ) {
return _createExtentInFile( txn, i, f, size, enforceQuota );
}
}
_checkQuota( enforceQuota, numFiles() );
// no space in an existing file
// allocate files until we either get one big enough or hit maxSize
for ( int i = 0; i < 8; i++ ) {
DataFile* f = _addAFile( txn, size, false );
if ( f->getHeader()->unusedLength >= size ) {
return _createExtentInFile( txn, numFiles() - 1, f, size, enforceQuota );
}
}
// callers don't check for null return code, so assert
msgasserted(14810, "couldn't allocate space for a new extent" );
}
Extent* ExtentManager::createExtent(const char *ns, int size, bool newCapped, bool enforceQuota ) {
size = quantizeExtentSize( size );
for ( int i = numFiles() - 1; i >= 0; i-- ) {
DataFile* f = getFile( i );
if ( f->getHeader()->unusedLength >= size ) {
return _createExtentInFile( i, f, ns, size, newCapped, enforceQuota );
}
}
// no space in an existing file
// allocate files until we either get one big enough or hit maxSize
for ( int i = 0; i < 8; i++ ) {
DataFile* f = addAFile( size, false );
if ( f->getHeader()->unusedLength >= size ||
f->getHeader()->fileLength >= DataFile::maxSize() ) {
return _createExtentInFile( numFiles() - 1, f, ns, size, newCapped, enforceQuota );
}
}
// callers don't check for null return code, so assert
msgasserted(14810, "couldn't allocate space for a new extent" );
}
Exec::RetType Exec_Precision::Execute(CpptrajState& State, ArgList& argIn) {
// Next string is DataSet(s)/DataFile that command pertains to.
std::string name1 = argIn.GetStringNext();
if (name1.empty()) {
mprinterr("Error: No filename/setname given.\n");
return CpptrajState::ERR;
}
// This will break if dataset name starts with a digit...
int width = argIn.getNextInteger(12);
if (width < 1) {
mprintf("Error: Cannot set width < 1 (%i).\n", width);
return CpptrajState::ERR;
}
int precision = argIn.getNextInteger(4);
if (precision < 0) precision = 0;
DataFile* df = State.DFL().GetDataFile(name1);
if (df != 0) {
mprintf("\tSetting precision for all sets in %s to %i.%i\n", df->DataFilename().base(),
width, precision);
df->SetDataFilePrecision(width, precision);
} else {
State.DSL().SetPrecisionOfDataSets( name1, width, precision );
}
return CpptrajState::OK;
}
void
MissionSelector::loadMission(string fileName)
{
if(fileName == "") return;
Mission* oldMission = rMain()->getMission();
Orbit* orbitScreen = static_cast<Orbit*>(rMain()->getScreenManager().getState(Main::ORBIT_SCREEN));
orbitScreen->enterReadyState();
DataFile* dataFile = new DataFile(stringToWString(fileName));
if(dataFile->getRootItem() != NULL) {
Mission* mission = dataFile->getRootItem()->castToClass<Mission>();
if(mission != NULL) {
rMain()->setMission(mission);
if(oldMission != NULL) {
if (oldMission == ConfigManager::getPlayer()->getHomeBase()) {
ConfigManager::getSingleton().savePlayer();
}
else {
delete oldMission->getDataFile();
}
}
}
}
}
void sqlLoadCode( const Database &db ,
const SqlApiBindProgramId &programid ,
int nr ,
VirtualCode &vc ) {
DataFile datafile ( db, SYSTEM_CODEDATA_FNAME, DBFMODE_READONLY);
KeyFile indexfile ( db, SYSTEM_CODEKEY_FNAME , DBFMODE_READONLY);
KeyFileDefinition keydef(indexfile);
KeyType key;
keydef.put(key,0,String(programid.m_fileName));
keydef.put(key,1,nr);
bool found = indexfile.searchMin( RELOP_EQ, key, 2);
#ifdef DEBUGMODULE
_tprintf(_T("loading code for <%s>,%d\n"),programid.filename,nr);
#endif
if(!found)
throwSqlError(SQL_UNKNOWN_PROGRAMID,_T("Unknown programfile:<%s>"),programid.m_fileName);
datafile.readRecord( keydef.getRecordAddr(key), &vc, sizeof(VirtualCode));
if(_tcscmp(vc.getProgramId().m_timestamp,programid.m_timestamp) != 0)
throwSqlError(SQL_TIMESTAMP_MISMATCH,_T("Timestamp mismatch on <%s>"),programid.m_fileName);
}
/** Called once before traj processing. Set up reference info. */
Action::RetType Action_DistRmsd::Init(ArgList& actionArgs, TopologyList* PFL, DataSetList* DSL, DataFileList* DFL, int debugIn)
{
// Check for keywords
DataFile* outfile = DFL->AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
// Reference keywords
// TODO: Can these just be put in the InitRef call?
bool first = actionArgs.hasKey("first");
ReferenceFrame REF = DSL->GetReferenceFrame( actionArgs );
std::string reftrajname = actionArgs.GetStringKey("reftraj");
Topology* RefParm = PFL->GetParm( actionArgs );
// Get the RMS mask string for target
std::string mask0 = actionArgs.GetMaskNext();
TgtMask_.SetMaskString(mask0);
// Get the RMS mask string for reference
std::string mask1 = actionArgs.GetMaskNext();
if (mask1.empty())
mask1 = mask0;
// Initialize reference
if (refHolder_.InitRef(false, first, false, false, reftrajname, REF, RefParm,
mask1, actionArgs, "distrmsd"))
return Action::ERR;
// Set up the RMSD data set
drmsd_ = DSL->AddSet(DataSet::DOUBLE, actionArgs.GetStringNext(),"DRMSD");
if (drmsd_==0) return Action::ERR;
// Add dataset to data file list
if (outfile != 0) outfile->AddDataSet( drmsd_ );
mprintf(" DISTRMSD: (%s), reference is %s\n",TgtMask_.MaskString(),
refHolder_.RefModeString());
return Action::OK;
}
Action::RetType Action_Channel::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
// Keywords.
DataFile* outfile = init.DFL().AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
dxyz_[0] = actionArgs.getKeyDouble("dx", 0.35);
dxyz_[1] = actionArgs.getKeyDouble("dy", dxyz_[0]);
dxyz_[2] = actionArgs.getKeyDouble("dz", dxyz_[1]);
// solute mask
std::string sMask = actionArgs.GetMaskNext();
if (sMask.empty()) {
mprinterr("Error: No solute mask specified.\n");
return Action::ERR;
}
soluteMask_.SetMaskString( sMask );
// solvent mask
sMask = actionArgs.GetMaskNext();
if (sMask.empty())
sMask.assign(":WAT@O");
solventMask_.SetMaskString( sMask );
// Grid Data Set
grid_ = init.DSL().AddSet(DataSet::GRID_FLT, actionArgs.GetStringNext(), "Channel");
if (grid_ == 0) return Action::ERR;
if (outfile != 0) outfile->AddDataSet( grid_ );
mprintf("Warning: *** THIS ACTION IS EXPERIMENTAL AND NOT FULLY IMPLEMENTED. ***\n");
mprintf(" CHANNEL: Solute mask [%s], solvent mask [%s]\n",
soluteMask_.MaskString(), solventMask_.MaskString());
mprintf("\tSpacing: XYZ={ %g %g %g }\n", dxyz_[0], dxyz_[1], dxyz_[2]);
return Action::OK;
}
// Action_AreaPerMol::Init()
Action::RetType Action_AreaPerMol::Init(ArgList& actionArgs, TopologyList* PFL, DataSetList* DSL, DataFileList* DFL, int debugIn)
{
// Get keywords
DataFile* outfile = DFL->AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
if (actionArgs.hasKey("xy")) areaType_ = XY;
else if (actionArgs.hasKey("xz")) areaType_ = XZ;
else if (actionArgs.hasKey("yz")) areaType_ = YZ;
else areaType_ = XY;
Nmols_ = (double)actionArgs.getKeyInt("nmols", -1);
// Get Masks
if (Nmols_ < 0.0) {
Nlayers_ = (double)actionArgs.getKeyInt("nlayers", 1);
if (Nlayers_ < 1.0) {
mprinterr("Error: Number of layers must be > 0\n");
return Action::ERR;
}
Mask1_.SetMaskString( actionArgs.GetMaskNext() );
}
// DataSet
area_per_mol_ = DSL->AddSet(DataSet::DOUBLE, actionArgs.GetStringNext(),"APM");
if (area_per_mol_==0) return Action::ERR;
// Add DataSet to DataFileList
if (outfile != 0) outfile->AddDataSet( area_per_mol_ );
mprintf(" AREAPERMOL: Calculating %s area per molecule", APMSTRING[areaType_]);
if (Mask1_.MaskStringSet())
mprintf(" using mask '%s', %.0f layers.\n", Mask1_.MaskString(), Nlayers_);
else
mprintf(" for %.0f mols\n", Nmols_);
return Action::OK;
}
// todo: this is called a lot. streamline the common case
DataFile* MmapV1ExtentManager::getFile( TransactionExperiment* txn,
int n,
int sizeNeeded ,
bool preallocateOnly) {
verify(this);
DEV Lock::assertAtLeastReadLocked( _dbname );
if ( n < 0 || n >= DiskLoc::MaxFiles ) {
log() << "getFile(): n=" << n << endl;
massert( 10295 , "getFile(): bad file number value (corrupt db?)."
" See http://dochub.mongodb.org/core/data-recovery", false);
}
DEV {
if ( n > 100 ) {
log() << "getFile(): n=" << n << endl;
}
}
DataFile* p = 0;
if ( !preallocateOnly ) {
while ( n >= (int) _files.size() ) {
verify(this);
if( !Lock::isWriteLocked(_dbname) ) {
log() << "error: getFile() called in a read lock, yet file to return is not yet open";
log() << " getFile(" << n << ") _files.size:" <<_files.size() << ' ' << fileName(n).string();
invariant(false);
}
_files.push_back(0);
}
p = _files[n];
}
if ( p == 0 ) {
if ( n == 0 ) audit::logCreateDatabase( currentClient.get(), _dbname );
DEV Lock::assertWriteLocked( _dbname );
boost::filesystem::path fullName = fileName( n );
string fullNameString = fullName.string();
p = new DataFile(n);
int minSize = 0;
if ( n != 0 && _files[ n - 1 ] )
minSize = _files[ n - 1 ]->getHeader()->fileLength;
if ( sizeNeeded + DataFileHeader::HeaderSize > minSize )
minSize = sizeNeeded + DataFileHeader::HeaderSize;
try {
Timer t;
p->open( txn, fullNameString.c_str(), minSize, preallocateOnly );
if ( t.seconds() > 1 ) {
log() << "MmapV1ExtentManager took " << t.seconds()
<< " seconds to open: " << fullNameString;
}
}
catch ( AssertionException& ) {
delete p;
throw;
}
if ( preallocateOnly )
delete p;
else
_files[n] = p;
}
return preallocateOnly ? 0 : p;
}
bool DealWithMatch(const vector <string> &LineList, const boost::regex &RegExpress, const DataFile &TypeEntry, ofstream &TableStream,
const size_t FilingIndex)
// MAJOR robustness issues here! See notes in this function.
{
// cerr << "Going into DealWithMatch()\n";
bool IsSuccessful;
const vector <string> Captures = ObtainCaptures(RegExpress, LineList[0], TypeEntry.PatternExplainCount() + 1);
// cerr << "Got Captures\n";
const vector <string> Descriptors = GatherInfo(LineList, Captures, TypeEntry.GiveAllPatternExplains(),
TypeEntry.GiveAllAssignExpressions(), IsSuccessful);
// cerr << "Got Descriptors\n";
// May need to put in controls of some sort to determine whether something should be quoted or not.
if (IsSuccessful)
{
TableStream << GiveDelimitedList(LineList, ',') << ',' << FilingIndex << ',' << GiveDelimitedList(Descriptors, ',') << "\n";
}
// This above segment prints to the appropriate subcatalogue file the following info:
// Filename, File Group number, Volume Name, FileSize, FilingIndex, and Date information for the file, and any other descriptor information.
// there is always DateTime_Info for Descriptors[0]
return(TableStream.good());
}
void
MissionSelector::startMission(unsigned num)
{
Entry missionEntry;
if(mCurrentCampaign == NULL) {
// FIXME: we should fall back to station school in case a first timer plays
missionEntry = mMissions[0];
}
else {
if(num < 0 || num >= static_cast<int>(mCurrentMissions.size())) return;
mMissionNum = num;
missionEntry = mCurrentMissions[num];
}
Mission* oldMission = rMain()->getMission();
Orbit* orbitScreen = static_cast<Orbit*>(rMain()->getScreenManager().getState(Main::ORBIT_SCREEN));
orbitScreen->enterReadyState();
DataFile* dataFile = new DataFile();
Mission* mission = new Mission(dataFile);
dataFile->setRootItem(mission);
rMain()->setMission(mission);
mission->initScriptFile(missionEntry.script);
if(oldMission != NULL) {
if (oldMission == ConfigManager::getPlayer()->getHomeBase()) {
ConfigManager::getSingleton().savePlayer();
}
else {
delete oldMission->getDataFile();
}
}
}
// Action_FilterByData::Init()
Action::RetType Action_FilterByData::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
maxmin_ = init.DSL().AddSet( DataSet::INTEGER, actionArgs.GetStringKey("name"), "Filter" );
if (maxmin_ == 0) return Action::ERR;
DataFile* maxminfile = init.DFL().AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
if (maxminfile != 0)
maxminfile->AddDataSet( maxmin_ );
// Get min and max args.
while (actionArgs.Contains("min"))
Min_.push_back( actionArgs.getKeyDouble("min", 0.0) );
while (actionArgs.Contains("max"))
Max_.push_back( actionArgs.getKeyDouble("max", 0.0) );
if (Min_.empty()) {
mprinterr("Error: At least one 'min' arg must be specified.\n");
return Action::ERR;
}
if (Max_.empty()) {
mprinterr("Error: At least one 'max' arg must be specified.\n");
return Action::ERR;
}
if (Min_.size() != Max_.size()) {
mprinterr("Error: # of 'min' args (%zu) != # of 'max' args (%zu)\n",
Min_.size(), Max_.size());
return Action::ERR;
}
// Get DataSets from remaining arguments
Dsets_.AddSetsFromArgs( actionArgs.RemainingArgs(), init.DSL() );
if (Dsets_.empty()) {
mprinterr("Error: No data sets specified.\n");
return Action::ERR;
}
if ( Dsets_.size() < Min_.size() ) {
mprinterr("Error: More 'min'/'max' args (%zu) than data sets (%zu).\n",
Min_.size(), Dsets_.size());
return Action::ERR;
}
if ( Dsets_.size() > Min_.size() ) {
unsigned int Nremaining = Dsets_.size() - Min_.size();
double useMin = Min_.back();
double useMax = Max_.back();
mprintf("Warning: More data sets than 'min'/'max' args.\n"
"Warning: Using min=%f and max=%f for last %zu data sets.\n",
useMin, useMax, Nremaining);
for (unsigned int ds = 0; ds < Nremaining; ++ds) {
Min_.push_back( useMin );
Max_.push_back( useMax );
}
}
mprintf(" FILTER: Filtering out frames using %zu data sets.\n", Dsets_.size());
for (unsigned int ds = 0; ds < Dsets_.size(); ds++)
mprintf("\t%.4f < '%s' < %.4f\n", Min_[ds], Dsets_[ds]->legend(), Max_[ds]);
if (maxminfile != 0)
mprintf("\tFilter frame info will be written to %s\n", maxminfile->DataFilename().full());
return Action::OK;
}
// Action_Grid::Init()
Action::RetType Action_Grid::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
debug_ = debugIn;
nframes_ = 0;
// Get output filename
std::string filename = actionArgs.GetStringKey("out");
// Get grid options
grid_ = GridInit( "GRID", actionArgs, init.DSL() );
if (grid_ == 0) return Action::ERR;
# ifdef MPI
if (ParallelGridInit(init.TrajComm(), grid_)) return Action::ERR;
# endif
// Get extra options
max_ = actionArgs.getKeyDouble("max", 0.80);
madura_ = actionArgs.getKeyDouble("madura", 0);
smooth_ = actionArgs.getKeyDouble("smoothdensity", 0);
invert_ = actionArgs.hasKey("invert");
pdbfile_ = init.DFL().AddCpptrajFile(actionArgs.GetStringKey("pdb"),"Grid PDB",DataFileList::PDB,true);
density_ = actionArgs.getKeyDouble("density",0.033456);
if (actionArgs.hasKey("normframe")) normalize_ = TO_FRAME;
else if (actionArgs.hasKey("normdensity")) normalize_ = TO_DENSITY;
else normalize_ = NONE;
if (normalize_ != NONE && (smooth_ > 0.0 || madura_ > 0.0)) {
mprinterr("Error: Normalize options are not compatible with smoothdensity/madura options.\n");
init.DSL().RemoveSet( grid_ );
return Action::ERR;
}
// Get mask
std::string maskexpr = actionArgs.GetMaskNext();
if (maskexpr.empty()) {
mprinterr("Error: GRID: No mask specified.\n");
init.DSL().RemoveSet( grid_ );
return Action::ERR;
}
mask_.SetMaskString(maskexpr);
// Setup output file
// For backwards compat., if no 'out' assume next string is filename
if (filename.empty() && actionArgs.Nargs() > 1 && !actionArgs.Marked(1))
filename = actionArgs.GetStringNext();
DataFile* outfile = init.DFL().AddDataFile(filename, actionArgs);
if (outfile != 0) outfile->AddDataSet((DataSet*)grid_);
// Info
mprintf(" GRID:\n");
GridInfo( *grid_ );
if (outfile != 0) mprintf("\tGrid will be printed to file %s\n", outfile->DataFilename().full());
mprintf("\tGrid data set: '%s'\n", grid_->legend());
mprintf("\tMask expression: [%s]\n",mask_.MaskString());
if (pdbfile_ != 0)
mprintf("\tPseudo-PDB will be printed to %s\n", pdbfile_->Filename().full());
if (normalize_ == TO_FRAME)
mprintf("\tGrid will be normalized by number of frames.\n");
else if (normalize_ == TO_DENSITY)
mprintf("\tGrid will be normalized to a density of %g molecules/Ang^3.\n", density_);
// TODO: print extra options
return Action::OK;
}
DoubleCache::DoubleCache(DataFile& dataFile)
: m_first(new Cache(dataFile.cachePageOne())),
m_second(new Cache(dataFile.cachePageTwo())),
m_current(m_first),
m_filled(NULL)
{
}
// Action_VelocityAutoCorr::Init()
Action::RetType Action_VelocityAutoCorr::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
if (actionArgs.hasKey("usevelocity")) {
mprinterr("Error: The 'usevelocity' keyword is deprecated. Velocity information\n"
"Error: is now used by default if present. To force cpptraj to use\n"
"Error: coordinates to estimate velocities (not recommended) use the\n"
"Error: 'usecoords' keyword.\n");
return Action::ERR;
}
useVelInfo_ = !actionArgs.hasKey("usecoords");
if (mask_.SetMaskString( actionArgs.GetMaskNext() )) return Action::ERR;
DataFile* outfile = init.DFL().AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
diffout_ = init.DFL().AddCpptrajFile( actionArgs.GetStringKey("diffout"),
"VAC diffusion constants", DataFileList::TEXT, true );
maxLag_ = actionArgs.getKeyInt("maxlag", -1);
tstep_ = actionArgs.getKeyDouble("tstep", 1.0);
useFFT_ = !actionArgs.hasKey("direct");
normalize_ = actionArgs.hasKey("norm");
// Set up output data set
VAC_ = init.DSL().AddSet(DataSet::DOUBLE, actionArgs.GetStringNext(), "VAC");
if (VAC_ == 0) return Action::ERR;
// TODO: This should just be a scalar
diffConst_ = init.DSL().AddSet(DataSet::DOUBLE,
MetaData(VAC_->Meta().Name(), "D", MetaData::NOT_TS));
if (diffConst_ == 0) return Action::ERR;
if (outfile != 0) outfile->AddDataSet( VAC_ );
# ifdef MPI
trajComm_ = init.TrajComm();
if (trajComm_.Size() > 1 && !useVelInfo_)
mprintf("\nWarning: When calculating velocities between consecutive frames,\n"
"\nWarning: 'velocityautocorr' in parallel will not work correctly if\n"
"\nWarning: coordinates have been modified by previous actions (e.g. 'rms').\n\n");
diffConst_->SetNeedsSync( false );
# endif
mprintf(" VELOCITYAUTOCORR:\n"
"\tCalculate velocity auto-correlation function for atoms in mask '%s'\n",
mask_.MaskString());
if (useVelInfo_)
mprintf("\tUsing velocity information present in frames.\n");
else
mprintf("\tCalculating velocities between consecutive frames from coordinates.\n");
if (outfile != 0)
mprintf("\tOutput velocity autocorrelation function '%s' to '%s'\n", VAC_->legend(),
outfile->DataFilename().full());
mprintf("\tWriting diffusion constants to '%s'\n", diffout_->Filename().full());
if (maxLag_ < 1)
mprintf("\tMaximum lag will be half total # of frames");
else
mprintf("\tMaximum lag is %i frames", maxLag_);
mprintf(", time step between frames is %f ps\n", tstep_);
if (useFFT_)
mprintf("\tUsing FFT to calculate autocorrelation function.\n");
else
mprintf("\tUsing direct method to calculate autocorrelation function.\n");
if (normalize_)
mprintf("\tNormalizing autocorrelation function to 1.0\n");
return Action::OK;
}
// Analysis_Wavelet::Setup
Analysis::RetType Analysis_Wavelet::Setup(ArgList& analyzeArgs, DataSetList* datasetlist,
TopologyList* PFLin, DataFileList* DFLin, int debugIn)
{
// Attempt to get COORDS DataSet from DataSetList. If none specified the
// default COORDS set will be used.
std::string setname = analyzeArgs.GetStringKey("crdset");
coords_ = (DataSet_Coords*)datasetlist->FindCoordsSet( setname );
if (coords_ == 0) {
mprinterr("Error: Could not locate COORDS set corresponding to %s\n", setname.c_str());
return Analysis::ERR;
}
// Get keywords
DataFile* outfile = DFLin->AddDataFile( analyzeArgs.GetStringKey("out"), analyzeArgs );
setname = analyzeArgs.GetStringKey("name");
// TODO: Check defaults
nb_ = analyzeArgs.getKeyInt("nb", 0); // FIXME: Should be more descriptive? nscale?
if (nb_ < 1) {
mprinterr("Error: Scaling number must be > 0\n");
return Analysis::ERR;
}
S0_ = analyzeArgs.getKeyDouble("s0", 0.2);
ds_ = analyzeArgs.getKeyDouble("ds", 1.0/3.0);
correction_ = analyzeArgs.getKeyDouble("correction", 1.01);
chival_ = analyzeArgs.getKeyDouble("chival", 0.2231);
// Wavelet type: default to Morlet
std::string wavelet_name = analyzeArgs.GetStringKey("type");
if (wavelet_name.empty())
wavelet_type_ = W_MORLET;
else {
wavelet_type_ = W_NONE;
for (int itoken = 0; itoken != (int)W_NONE; itoken++)
if (wavelet_name.compare(Tokens_[itoken].key_) == 0) {
wavelet_type_ = (WaveletType)itoken;
break;
}
if (wavelet_type_ == W_NONE) {
mprinterr("Error: Unrecognized wavelet type: %s\n", wavelet_name.c_str());
return Analysis::ERR;
}
}
// Atom mask
mask_.SetMaskString( analyzeArgs.GetMaskNext() );
// Set up output data set
output_ = datasetlist->AddSet( DataSet::MATRIX_FLT, setname, "WAVELET" );
if (output_ == 0) return Analysis::ERR;
if (outfile != 0) outfile->AddDataSet( output_ );
mprintf(" WAVELET: Using COORDS set '%s', wavelet type %s\n",
coords_->legend(), Tokens_[wavelet_type_].description_);
mprintf("\tCalculating for atoms in mask '%s'\n", mask_.MaskString());
mprintf("\tScaling wavelet %i times starting from %g with delta of %g\n",
nb_, S0_, ds_);
mprintf("\tCorrection: %g\n", correction_);
mprintf("\tChiVal: %g\n", chival_);
if (outfile != 0) mprintf("\tOutput to '%s'\n", outfile->DataFilename().full());
return Analysis::OK;
}
void Bug_Popout::writeMetaToBug3File(const DataFile &df, const DAQ::BugTask::BlockMetaData &m/*, int fudge*/)
{
QString fname (df.metaFileName());
static const QString metaExt(".meta");
if (fname.toLower().endsWith(metaExt)) fname = fname.left(fname.size()-metaExt.size()) + ".bug3";
QFile f(fname);
if (!df.scanCount()) {
f.open(QIODevice::WriteOnly|QIODevice::Truncate|QIODevice::Text);
Debug() << "Bug3 'extra data' file created: " << fname;
} else {
f.open(QIODevice::WriteOnly|QIODevice::Append|QIODevice::Text);
f.seek(f.size()); // got to end?
}
QTextStream ts(&f);
ts << "[ block " << m.blockNum << " ]\n";
ts << "framesThisBlock = " << DAQ::BugTask::FramesPerBlock << "\n";
ts << "spikeGL_DataFile_ScanCount = " << (df.scanCount()/*+u64(fudge/task->numChans())*/) << "\n";
ts << "spikeGL_DataFile_SampleCount = " << (df.sampleCount()/*+u64(fudge)*/) << "\n";
ts << "spikeGL_ScansInBlock = " << DAQ::BugTask::SpikeGLScansPerBlock << "\n";
ts << "boardFrameCounter = ";
for (int i = 0; i < DAQ::BugTask::FramesPerBlock; ++i) {
if (i) ts << ",";
ts << m.boardFrameCounter[i];
}
ts << "\n";
ts << "boardFrameTimer = ";
for (int i = 0; i < DAQ::BugTask::FramesPerBlock; ++i) {
if (i) ts << ",";
ts << m.boardFrameTimer[i];
}
ts << "\n";
ts << "chipFrameCounter = ";
for (int i = 0; i < DAQ::BugTask::FramesPerBlock; ++i) {
if (i) ts << ",";
ts << m.chipFrameCounter[i];
}
ts << "\n";
ts << "chipID = ";
for (int i = 0; i < DAQ::BugTask::FramesPerBlock; ++i) {
if (i) ts << ",";
ts << m.chipID[i];
}
ts << "\n";
ts << "frameMarkerCorrelation = ";
for (int i = 0; i < DAQ::BugTask::FramesPerBlock; ++i) {
if (i) ts << ",";
ts << m.frameMarkerCorrelation[i];
}
ts << "\n";
ts << "missingFrameCount = " << m.missingFrameCount << "\n";
ts << "falseFrameCount = " << m.falseFrameCount << "\n";
ts << "BER = " << m.BER << "\n";
ts << "WER = " << m.WER << "\n";
ts << "avgVunreg = " << m.avgVunreg << "\n";
ts.flush();
}
size_t CookiePath::WriteCookiesL(DataFile &fp, time_t this_time, BOOL dry_run)
{
size_t size = 0;
Cookie* ck = (Cookie*) cookie_list.First();
while (ck)
{
if(ck->Persistent(this_time))
{
DataFile_Record rec(TAG_COOKIE_ENTRY);
ANCHOR(DataFile_Record,rec);
rec.SetRecordSpec(fp.GetRecordSpec());
ck->FillDataFileRecordL(rec);
if (dry_run)
size += rec.CalculateLength();
else
rec.WriteRecordL(&fp);
}
ck = ck->Suc();
}
CookiePath* cp = (CookiePath*) FirstChild();
while (cp)
{
if (cp->HasCookies(this_time))
{
DataFile_Record rec(TAG_COOKIE_PATH_ENTRY);
ANCHOR(DataFile_Record,rec);
rec.SetRecordSpec(fp.GetRecordSpec());
rec.AddRecordL(TAG_COOKIE_PATH_NAME, cp->PathPart());
if (dry_run)
size += rec.CalculateLength();
else
rec.WriteRecordL(&fp);
size += cp->WriteCookiesL(fp, this_time, dry_run);
}
cp = cp->Suc();
}
{
DataFile_Record rec(TAG_COOKIE_PATH_END);
// spec is a pointer to existing field of object fp, there is no need to assert that it's not null
const DataRecord_Spec *spec = fp.GetRecordSpec();
rec.SetRecordSpec(spec);
if (dry_run)
size += ((rec.GetTag() & MSB_VALUE) == MSB_VALUE) ? spec->idtag_len : rec.CalculateLength();
else
rec.WriteRecordL(&fp);
}
return size;
}
DataHeader *get_dataheader(const stdString &dir, const stdString &file,
FileOffset offset)
{
DataFile *datafile = DataFile::reference(dir, file, false);
if (!datafile)
return 0;
DataHeader *header = datafile->getHeader(offset);
datafile->release(); // ref'ed by header
return header; // might be NULL
}
// Action_AtomicFluct::Init()
Action::RetType Action_AtomicFluct::Init(ArgList& actionArgs, TopologyList* PFL, DataSetList* DSL, DataFileList* DFL, int debugIn)
{
// Get frame # keywords
if (InitFrameCounter(actionArgs)) return Action::ERR;
// Get other keywords
bfactor_ = actionArgs.hasKey("bfactor");
calc_adp_ = actionArgs.hasKey("calcadp");
adpoutfile_ = DFL->AddCpptrajFile(actionArgs.GetStringKey("adpout"), "PDB w/ADP",
DataFileList::PDB);;
if (adpoutfile_!=0) calc_adp_ = true; // adpout implies calcadp
if (calc_adp_ && !bfactor_) bfactor_ = true;
DataFile* outfile = DFL->AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
if (actionArgs.hasKey("byres"))
outtype_ = BYRES;
else if (actionArgs.hasKey("bymask"))
outtype_ = BYMASK;
else if (actionArgs.hasKey("byatom") || actionArgs.hasKey("byatm"))
outtype_ = BYATOM;
// Get Mask
Mask_.SetMaskString( actionArgs.GetMaskNext() );
// Get DataSet name
std::string setname = actionArgs.GetStringNext();
// Add output dataset
MetaData md( setname );
md.SetTimeSeries( MetaData::NOT_TS );
if (bfactor_)
md.SetLegend("B-factors");
else
md.SetLegend("AtomicFlx");
dataout_ = DSL->AddSet( DataSet::XYMESH, md, "Fluct" );
if (dataout_ == 0) {
mprinterr("Error: AtomicFluct: Could not allocate dataset for output.\n");
return Action::ERR;
}
if (outfile != 0)
outfile->AddDataSet( dataout_ );
mprintf(" ATOMICFLUCT: calculating");
if (bfactor_)
mprintf(" B factors");
else
mprintf(" atomic positional fluctuations");
if (outfile != 0)
mprintf(", output to file %s", outfile->DataFilename().full());
mprintf("\n Atom mask: [%s]\n",Mask_.MaskString());
FrameCounterInfo();
if (calc_adp_) {
mprintf("\tCalculating anisotropic displacement parameters.\n");
if (adpoutfile_!=0) mprintf("\tWriting PDB with ADP to '%s'\n", adpoutfile_->Filename().full());
}
if (!setname.empty())
mprintf("\tData will be saved to set named %s\n", setname.c_str());
return Action::OK;
}
// TODO: Accept const ArgList so arguments are not reset?
CpptrajFile* DataFileList::AddCpptrajFile(FileName const& nameIn,
std::string const& descrip,
CFtype typeIn, bool allowStdout)
{
// If no filename and stdout not allowed, no output desired.
if (nameIn.empty() && !allowStdout) return 0;
FileName name;
CpptrajFile* Current = 0;
int currentIdx = -1;
if (!nameIn.empty()) {
name = nameIn;
// Append ensemble number if set.
if (ensembleNum_ != -1)
name.Append( "." + integerToString(ensembleNum_) );
// Check if filename in use by DataFile.
DataFile* df = GetDataFile(name);
if (df != 0) {
mprinterr("Error: Text output file name '%s' already in use by data file '%s'.\n",
nameIn.full(), df->DataFilename().full());
return 0;
}
// Check if this filename already in use
currentIdx = GetCpptrajFileIdx( name );
if (currentIdx != -1) Current = cfList_[currentIdx];
}
// If no CpptrajFile associated with name, create new CpptrajFile
if (Current==0) {
switch (typeIn) {
case TEXT: Current = new CpptrajFile(); break;
case PDB: Current = (CpptrajFile*)(new PDBfile()); break;
}
Current->SetDebug(debug_);
// Set up file for writing.
//if (Current->SetupWrite( name, debug_ ))
if (Current->OpenWrite( name ))
{
mprinterr("Error: Setting up text output file %s\n", name.full());
delete Current;
return 0;
}
cfList_.push_back( Current );
cfData_.push_back( CFstruct(descrip, typeIn) );
} else {
// If Current type does not match typeIn do not allow.
if (typeIn != cfData_[currentIdx].Type()) {
mprinterr("Error: Cannot change type of text output for '%s'.\n", Current->Filename().full());
return 0;
}
Current->SetDebug(debug_);
// Update description
if (!descrip.empty())
cfData_[currentIdx].UpdateDescrip( descrip );
}
return Current;
}
Record* ExtentManager::recordFor( const DiskLoc& loc ) {
loc.assertOk();
DataFile* df = getFile( loc.a() );
int ofs = loc.getOfs();
if ( ofs < DataFileHeader::HeaderSize ) {
df->badOfs(ofs); // will uassert - external call to keep out of the normal code path
}
return reinterpret_cast<Record*>( df->p() + ofs );
}
Analysis::RetType Analysis_AutoCorr::Setup(ArgList& analyzeArgs, DataSetList* datasetlist,
TopologyList* PFLin, DataFileList* DFLin, int debugIn)
{
const char* calctype;
std::string setname = analyzeArgs.GetStringKey("name");
DataFile* outfile = DFLin->AddDataFile( analyzeArgs.GetStringKey("out"), analyzeArgs );
lagmax_ = analyzeArgs.getKeyInt("lagmax",-1);
calc_covar_ = !analyzeArgs.hasKey("nocovar");
usefft_ = !analyzeArgs.hasKey("direct");
// Select datasets from remaining args
ArgList dsetArgs = analyzeArgs.RemainingArgs();
for (ArgList::const_iterator dsa = dsetArgs.begin(); dsa != dsetArgs.end(); ++dsa)
dsets_ += datasetlist->GetMultipleSets( *dsa );
if (dsets_.empty()) {
mprinterr("Error: autocorr: No data sets selected.\n");
return Analysis::ERR;
}
// If setname is empty generate a default name
if (setname.empty())
setname = datasetlist->GenerateDefaultName( "autocorr" );
// Setup output datasets
int idx = 0;
MetaData md( setname );
for (DataSetList::const_iterator DS = dsets_.begin(); DS != dsets_.end(); ++DS) {
md.SetIdx( idx++ );
DataSet* dsout = datasetlist->AddSet( DataSet::DOUBLE, md );
if (dsout==0) return Analysis::ERR;
dsout->SetLegend( (*DS)->Meta().Legend() );
outputData_.push_back( dsout );
// Add set to output file
if (outfile != 0) outfile->AddDataSet( outputData_.back() );
}
if (calc_covar_)
calctype = "covariance";
else
calctype = "correlation";
mprintf(" AUTOCORR: Calculating auto-%s for %i data sets:\n", calctype, dsets_.size());
dsets_.List();
if (lagmax_!=-1)
mprintf("\tLag max= %i\n", lagmax_);
if ( !setname.empty() )
mprintf("\tSet name: %s\n", setname.c_str() );
if ( outfile != 0 )
mprintf("\tOutfile name: %s\n", outfile->DataFilename().base());
if (usefft_)
mprintf("\tUsing FFT to calculate %s.\n", calctype);
else
mprintf("\tUsing direct method to calculate %s.\n", calctype);
return Analysis::OK;
}
// Action_Dihedral::init()
Action::RetType Action_Dihedral::Init(ArgList& actionArgs, TopologyList* PFL, FrameList* FL,
DataSetList* DSL, DataFileList* DFL, int debugIn)
{
// Get keywords
DataFile* outfile = DFL->AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
useMass_ = actionArgs.hasKey("mass");
DataSet::scalarType stype = DataSet::UNDEFINED;
range360_ = actionArgs.hasKey("range360");
std::string stypename = actionArgs.GetStringKey("type");
if ( stypename == "alpha" ) stype = DataSet::ALPHA;
else if ( stypename == "beta" ) stype = DataSet::BETA;
else if ( stypename == "gamma" ) stype = DataSet::GAMMA;
else if ( stypename == "delta" ) stype = DataSet::DELTA;
else if ( stypename == "epsilon" ) stype = DataSet::EPSILON;
else if ( stypename == "zeta" ) stype = DataSet::ZETA;
else if ( stypename == "chi" ) stype = DataSet::CHI;
else if ( stypename == "c2p" ) stype = DataSet::C2P;
else if ( stypename == "h1p" ) stype = DataSet::H1P;
else if ( stypename == "phi" ) stype = DataSet::PHI;
else if ( stypename == "psi" ) stype = DataSet::PSI;
else if ( stypename == "pchi" ) stype = DataSet::PCHI;
// Get Masks
std::string mask1 = actionArgs.GetMaskNext();
std::string mask2 = actionArgs.GetMaskNext();
std::string mask3 = actionArgs.GetMaskNext();
std::string mask4 = actionArgs.GetMaskNext();
if (mask1.empty() || mask2.empty() || mask3.empty() || mask4.empty()) {
mprinterr("Error: dihedral: Requires 4 masks\n");
return Action::ERR;
}
M1_.SetMaskString(mask1);
M2_.SetMaskString(mask2);
M3_.SetMaskString(mask3);
M4_.SetMaskString(mask4);
// Setup dataset
dih_ = DSL->AddSet(DataSet::DOUBLE, actionArgs.GetStringNext(),"Dih");
if (dih_==0) return Action::ERR;
dih_->SetScalar( DataSet::M_TORSION, stype );
// Add dataset to datafile list
if (outfile != 0) outfile->AddSet( dih_ );
mprintf(" DIHEDRAL: [%s]-[%s]-[%s]-[%s]\n", M1_.MaskString(),
M2_.MaskString(), M3_.MaskString(), M4_.MaskString());
if (useMass_)
mprintf(" Using center of mass of atoms in masks.\n");
if (range360_)
mprintf(" Output range is 0 to 360 degrees.\n");
else
mprintf(" Output range is -180 to 180 degrees.\n");
return Action::OK;
}
DataFile *DataFile::reference(const stdString &req_dirname,
const stdString &req_basename, bool for_write)
{
DataFile *datafile = 0;
stdString dirname, basename, filename;
Filename::build(req_dirname, req_basename, filename);
Filename::getDirname(filename, dirname);
Filename::getBasename(filename, basename);
#ifdef LOG_DATAFILE
LOG_MSG("reference('%s', '%s', %s)\n",
req_dirname.c_str(),
req_basename.c_str(),
(for_write ? "read/write" : "read-only"));
LOG_MSG("normalized: '%s' + '%s' = '%s')\n",
dirname.c_str(), basename.c_str(), filename.c_str());
#endif
stdList<DataFile *>::iterator i = open_data_files.begin();
for (/**/; i != open_data_files.end (); ++i)
{
datafile = *i;
if (datafile->getFilename() == filename &&
datafile->for_write == for_write)
{
#ifdef LOG_DATAFILE
LOG_MSG("DataFile %s (%c) is cached (%d)\n",
filename.c_str(),
(for_write?'W':'R'), datafile->ref_count);
#endif
datafile->reference();
// When it was put in the cache, it might
// have been a new file.
// But now it's one that already existed,
// so reset is_new_file:
datafile->is_new_file = false;
return datafile;
}
}
try
{
datafile = new DataFile(dirname, basename, filename, for_write);
datafile->reopen();
open_data_files.push_back(datafile);
return datafile;
}
catch (...)
{
if (datafile)
delete datafile;
throw GenericException(__FILE__, __LINE__, "Cannot reference '%s'",
filename.c_str());
}
}
// Either sets header to new dirname/basename/offset
// or returns false
DataHeader *OldDataReader::getHeader(const stdString &dirname,
const stdString &basename,
FileOffset offset)
{
if (!Filename::isValid(basename))
return 0;
DataFile *datafile =
DataFile::reference(dirname, basename, false);
DataHeader *new_header = datafile->getHeader(offset);
datafile->release(); // now ref'ed by header
return new_header;
}
// todo: this is called a lot. streamline the common case
DataFile* ExtentManager::getFile( int n, int sizeNeeded , bool preallocateOnly) {
verify(this);
DEV Lock::assertAtLeastReadLocked( _dbname );
if ( n < 0 || n >= DiskLoc::MaxFiles ) {
log() << "getFile(): n=" << n << endl;
massert( 10295 , "getFile(): bad file number value (corrupt db?): run repair", false);
}
DEV {
if ( n > 100 ) {
log() << "getFile(): n=" << n << endl;
}
}
DataFile* p = 0;
if ( !preallocateOnly ) {
while ( n >= (int) _files.size() ) {
verify(this);
if( !Lock::isWriteLocked(_dbname) ) {
log() << "error: getFile() called in a read lock, yet file to return is not yet open" << endl;
log() << " getFile(" << n << ") _files.size:" <<_files.size() << ' ' << fileName(n).string() << endl;
log() << " context ns: " << cc().ns() << endl;
verify(false);
}
_files.push_back(0);
}
p = _files[n];
}
if ( p == 0 ) {
DEV Lock::assertWriteLocked( _dbname );
boost::filesystem::path fullName = fileName( n );
string fullNameString = fullName.string();
p = new DataFile(n);
int minSize = 0;
if ( n != 0 && _files[ n - 1 ] )
minSize = _files[ n - 1 ]->getHeader()->fileLength;
if ( sizeNeeded + DataFileHeader::HeaderSize > minSize )
minSize = sizeNeeded + DataFileHeader::HeaderSize;
try {
p->open( fullNameString.c_str(), minSize, preallocateOnly );
}
catch ( AssertionException& ) {
delete p;
throw;
}
if ( preallocateOnly )
delete p;
else
_files[n] = p;
}
return preallocateOnly ? 0 : p;
}
