MusicRipperSettings::MusicRipperSettings(void)
{
VerticalConfigurationGroup* rippersettings = new VerticalConfigurationGroup(false);
rippersettings->setLabel(QObject::tr("CD Ripper Settings"));
rippersettings->addChild(ParanoiaLevel());
rippersettings->addChild(FilenameTemplate());
rippersettings->addChild(NoWhitespace());
rippersettings->addChild(PostCDRipScript());
rippersettings->addChild(EjectCD());
addChild(rippersettings);
VerticalConfigurationGroup* encodersettings = new VerticalConfigurationGroup(false);
encodersettings->setLabel(QObject::tr("CD Ripper Settings (part 2)"));
encodersettings->addChild(EncoderType());
encodersettings->addChild(DefaultRipQuality());
encodersettings->addChild(Mp3UseVBR());
addChild(encodersettings);
}
/** Set up variable with value. In this case allow any amount of whitespace,
* so re-tokenize the original argument line (minus the command).
*/
CpptrajState::RetType
Control_Set::SetupControl(CpptrajState& State, ArgList& argIn, Varray& CurrentVars)
{
ArgList remaining = argIn.RemainingArgs();
size_t pos0 = remaining.ArgLineStr().find_first_of("=");
if (pos0 == std::string::npos) {
mprinterr("Error: Expected <var>=<value>\n");
return CpptrajState::ERR;
}
size_t pos1 = pos0;
bool append = false;
if (pos0 > 0 && remaining.ArgLineStr()[pos0-1] == '+') {
pos0--;
append = true;
}
std::string variable = NoWhitespace( remaining.ArgLineStr().substr(0, pos0) );
if (variable.empty()) {
mprinterr("Error: No variable name.\n");
return CpptrajState::ERR;
}
ArgList equals( NoLeadingWhitespace(remaining.ArgLineStr().substr(pos1+1)) );
std::string value;
if (equals.Contains("inmask")) {
AtomMask mask( equals.GetStringKey("inmask") );
Topology* top = State.DSL().GetTopByIndex( equals );
if (top == 0) return CpptrajState::ERR;
if (top->SetupIntegerMask( mask )) return CpptrajState::ERR;
if (equals.hasKey("atoms"))
value = integerToString( mask.Nselected() );
else if (equals.hasKey("residues")) {
int curRes = -1;
int nres = 0;
for (AtomMask::const_iterator at = mask.begin(); at != mask.end(); ++at) {
int res = (*top)[*at].ResNum();
if (res != curRes) {
nres++;
curRes = res;
}
}
value = integerToString( nres );
} else if (equals.hasKey("molecules")) {
int curMol = -1;
int nmol = 0;
for (AtomMask::const_iterator at = mask.begin(); at != mask.end(); ++at) {
int mol = (*top)[*at].MolNum();
if (mol != curMol) {
nmol++;
curMol = mol;
}
}
value = integerToString( nmol );
} else {
mprinterr("Error: Expected 'atoms', 'residues', or 'molecules'.\n");
return CpptrajState::ERR;
}
} else if (equals.hasKey("trajinframes")) {
value = integerToString(State.InputTrajList().MaxFrames());
} else
value = equals.ArgLineStr();
if (append)
CurrentVars.AppendVariable( "$" + variable, value );
else
CurrentVars.UpdateVariable( "$" + variable, value );
mprintf("\tVariable '%s' set to '%s'\n", variable.c_str(), value.c_str());
for (int iarg = 0; iarg < argIn.Nargs(); iarg++)
argIn.MarkArg( iarg );
return CpptrajState::OK;
}
// Action_Density::Init()
Action::RetType Action_Density::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
# ifdef MPI
trajComm_ = init.TrajComm();
# endif
DataFile* outfile = init.DFL().AddDataFile(actionArgs.GetStringKey("out"), actionArgs);
std::string dsname = actionArgs.GetStringKey("name");
if (actionArgs.hasKey("x") ) {
axis_ = DX;
area_coord_[0] = DY;
area_coord_[1] = DZ;
} else if (actionArgs.hasKey("y") ) {
axis_ = DY;
area_coord_[0] = DX;
area_coord_[1] = DZ;
} else if (actionArgs.hasKey("z") ) {
axis_ = DZ;
area_coord_[0] = DX;
area_coord_[1] = DY;
}
property_ = NUMBER;
if (actionArgs.hasKey("number") ) property_ = NUMBER;
else if (actionArgs.hasKey("mass") ) property_ = MASS;
else if (actionArgs.hasKey("charge") ) property_ = CHARGE;
else if (actionArgs.hasKey("electron") ) property_ = ELECTRON;
binType_ = CENTER;
if (actionArgs.hasKey("bincenter")) binType_ = CENTER;
else if (actionArgs.hasKey("binedge") ) binType_ = EDGE;
delta_ = actionArgs.getKeyDouble("delta", 0.01);
if (delta_ <= 0) {
mprinterr("Error: Delta must be > 0.0\n");
return Action::ERR;
}
// for compatibility with ptraj, ignored because we rely on the atom code to
// do the right thing, see Atom.{h,cpp}
if (actionArgs.hasKey("efile"))
mprintf("Warning: The 'efile' keyword is deprecated.\n");
// read the rest of the command line as a series of masks
std::string maskstr;
unsigned int idx = 1;
while ( (maskstr = actionArgs.GetMaskNext() ) != emptystring) {
masks_.push_back( AtomMask(maskstr) );
if (dsname.empty())
dsname = init.DSL().GenerateDefaultName("DENSITY");
MetaData MD(dsname, "avg", idx);
MD.SetTimeSeries( MetaData::NOT_TS );
// Hold average density
DataSet* ads = init.DSL().AddSet( DataSet::DOUBLE, MD );
if (ads == 0) return Action::ERR;
ads->SetLegend( NoWhitespace(masks_.back().MaskExpression()) );
AvSets_.push_back( ads );
if (outfile != 0) outfile->AddDataSet( ads );
// Hold SD density
MD.SetAspect("sd");
DataSet* sds = init.DSL().AddSet( DataSet::DOUBLE, MD );
if (sds == 0) return Action::ERR;
sds->SetLegend( NoWhitespace("sd(" + masks_.back().MaskExpression() + ")") );
SdSets_.push_back( sds );
if (outfile != 0) outfile->AddDataSet( sds );
# ifdef MPI
ads->SetNeedsSync( false ); // Populated in Print()
sds->SetNeedsSync( false );
# endif
idx++;
}
if (masks_.empty()) {
// If no masks assume we want total system density.
if (dsname.empty())
dsname = actionArgs.GetStringNext();
density_ = init.DSL().AddSet(DataSet::DOUBLE, dsname, "DENSITY");
if (density_ == 0) return Action::ERR;
if (outfile != 0) outfile->AddDataSet( density_ );
image_.InitImaging( true );
// Hijack delta for storing sum of masses
delta_ = 0.0;
} else {
// Density selected by mask(s) along an axis
density_ = 0;
histograms_.resize(masks_.size() );
}
mprintf(" DENSITY:");
if (density_ == 0) {
const char* binStr[] = {"center", "edge"};
mprintf(" Determining %s density for %zu masks.\n", PropertyStr_[property_], masks_.size());
mprintf("\troutine version: %s\n", ROUTINE_VERSION_STRING);
mprintf("\tDelta is %f\n", delta_);
mprintf("\tAxis is %s\n", AxisStr_[axis_]);
mprintf("\tData set name is '%s'\n", dsname.c_str());
mprintf("\tData set aspect [avg] holds the mean, aspect [sd] holds standard deviation.\n");
mprintf("\tBin coordinates will be to bin %s.\n", binStr[binType_]);
} else {
mprintf(" No masks specified, calculating total system density in g/cm^3.\n");
mprintf("\tData set name is '%s'\n", density_->legend());
}
if (outfile != 0)
mprintf("\tOutput to '%s'\n", outfile->DataFilename().full());
return Action::OK;
}
// Action_Density::Init()
Action::RetType Action_Density::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
# ifdef MPI
if (init.TrajComm().Size() > 1) {
mprinterr("Error: 'density' action does not work with > 1 thread (%i threads currently).\n",
init.TrajComm().Size());
return Action::ERR;
}
# endif
DataFile* outfile = init.DFL().AddDataFile(actionArgs.GetStringKey("out"), actionArgs);
std::string dsname = actionArgs.GetStringKey("name");
if (dsname.empty())
dsname = init.DSL().GenerateDefaultName("DENSITY");
if (actionArgs.hasKey("x") ) {
axis_ = DX;
area_coord_[0] = DY;
area_coord_[1] = DZ;
} else if (actionArgs.hasKey("y") ) {
axis_ = DY;
area_coord_[0] = DX;
area_coord_[1] = DZ;
} else if (actionArgs.hasKey("z") ) {
axis_ = DZ;
area_coord_[0] = DX;
area_coord_[1] = DY;
}
property_ = NUMBER;
if (actionArgs.hasKey("number") ) property_ = NUMBER;
if (actionArgs.hasKey("mass") ) property_ = MASS;
if (actionArgs.hasKey("charge") ) property_ = CHARGE;
if (actionArgs.hasKey("electron") ) property_ = ELECTRON;
delta_ = actionArgs.getKeyDouble("delta", 0.01);
// for compatibility with ptraj, ignored because we rely on the atom code to
// do the right thing, see Atom.{h,cpp}
if (actionArgs.hasKey("efile"))
mprintf("Warning: The 'efile' keyword is deprecated.\n");
// read the rest of the command line as a series of masks
std::string maskstr;
unsigned int idx = 1;
while ( (maskstr = actionArgs.GetMaskNext() ) != emptystring) {
masks_.push_back( AtomMask(maskstr) );
MetaData MD(dsname, "avg", idx);
MD.SetTimeSeries( MetaData::NOT_TS );
// Hold average density
DataSet* ads = init.DSL().AddSet( DataSet::DOUBLE, MD );
if (ads == 0) return Action::ERR;
ads->SetLegend( NoWhitespace(masks_.back().MaskExpression()) );
AvSets_.push_back( ads );
if (outfile != 0) outfile->AddDataSet( ads );
// Hold SD density
MD.SetAspect("sd");
DataSet* sds = init.DSL().AddSet( DataSet::DOUBLE, MD );
if (sds == 0) return Action::ERR;
sds->SetLegend( NoWhitespace("sd(" + masks_.back().MaskExpression() + ")") );
SdSets_.push_back( sds );
if (outfile != 0) outfile->AddDataSet( sds );
# ifdef MPI
ads->SetNeedsSync( false ); // Populated in Print()
sds->SetNeedsSync( false );
# endif
idx++;
}
if (masks_.empty()) {
mprinterr("Error: No masks specified.\n");
return Action::ERR;
}
minus_histograms_.resize(masks_.size() );
plus_histograms_.resize(masks_.size() );
mprintf(" DENSITY: Determining %s density for %zu masks.\n", PropertyStr_[property_],
masks_.size());
mprintf("\troutine version: %s\n", ROUTINE_VERSION_STRING);
mprintf("\tDelta is %f\n", delta_);
mprintf("\tAxis is %s\n", AxisStr_[axis_]);
mprintf("\tData set name is '%s'\n", dsname.c_str());
if (outfile != 0)
mprintf("\tOutput to '%s'\n", outfile->DataFilename().full());
return Action::OK;
}