void Action_Diffusion::Help() const {
ShortHelp();
mprintf(" Compute a mean square displacement plot for the atoms in the <mask>.\n"
" By default the average displacements are calculated unless 'individual'\n"
" is specified. Diffusion constants will be calculated from best-fit linear\n"
" regression lines of MSDs vs time unless 'nocalc' is specified.\n");
}
void Action_Diffusion::Help() const {
ShortHelp();
mprintf(" Compute a mean square displacement plot for the atoms in the <mask>.\n"
" The following files are produced:\n"
" x_<suffix>: Mean square displacement(s) in the X direction (in Å^2).\n"
" y_<suffix>: Mean square displacement(s) in the Y direction (in Å^2).\n"
" z_<suffix>: Mean square displacement(s) in the Z direction (in Å^2).\n"
" r_<suffix>: Overall mean square displacement(s) (in Å^2).\n"
" a_<suffix>: Total distance travelled (in Å).\n");
}
// Action_Diffusion::Init()
Action::RetType Action_Diffusion::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
# ifdef MPI
trajComm_ = init.TrajComm();
# endif
debug_ = debugIn;
image_.InitImaging( !(actionArgs.hasKey("noimage")) );
// Determine if this is old syntax or new.
if (actionArgs.Nargs() > 2 && actionArgs.ArgIsMask(1) && validDouble(actionArgs[2]))
{
// Old syntax: <mask> <time per frame> [average] [<prefix>]
printIndividual_ = !(actionArgs.hasKey("average"));
calcDiffConst_ = false;
mprintf("Warning: Deprecated syntax for 'diffusion'. Consider using new syntax:\n");
ShortHelp();
mask_.SetMaskString( actionArgs.GetMaskNext() );
time_ = actionArgs.getNextDouble(1.0);
if (CheckTimeArg(time_)) return Action::ERR;
std::string outputNameRoot = actionArgs.GetStringNext();
// Default filename: 'diffusion'
if (outputNameRoot.empty())
outputNameRoot.assign("diffusion");
// Open output files
ArgList oldArgs("prec 8.3 noheader");
DataFile::DataFormatType dft = DataFile::DATAFILE;
outputx_ = init.DFL().AddDataFile(outputNameRoot+"_x.xmgr", dft, oldArgs);
outputy_ = init.DFL().AddDataFile(outputNameRoot+"_y.xmgr", dft, oldArgs);
outputz_ = init.DFL().AddDataFile(outputNameRoot+"_z.xmgr", dft, oldArgs);
outputr_ = init.DFL().AddDataFile(outputNameRoot+"_r.xmgr", dft, oldArgs);
outputa_ = init.DFL().AddDataFile(outputNameRoot+"_a.xmgr", dft, oldArgs);
} else {
// New syntax: [{separateout <suffix> | out <filename>}] [time <time per frame>]
// [<mask>] [<set name>] [individual] [diffout <filename>] [nocalc]
printIndividual_ = actionArgs.hasKey("individual");
calcDiffConst_ = !(actionArgs.hasKey("nocalc"));
std::string suffix = actionArgs.GetStringKey("separateout");
std::string outname = actionArgs.GetStringKey("out");
if (!outname.empty() && !suffix.empty()) {
mprinterr("Error: Specify either 'out' or 'separateout', not both.\n");
return Action::ERR;
}
diffout_ = init.DFL().AddDataFile(actionArgs.GetStringKey("diffout"));
time_ = actionArgs.getKeyDouble("time", 1.0);
if (CheckTimeArg(time_)) return Action::ERR;
mask_.SetMaskString( actionArgs.GetMaskNext() );
// Open output files.
if (!suffix.empty()) {
FileName FName( suffix );
outputx_ = init.DFL().AddDataFile(FName.PrependFileName("x_"), actionArgs);
outputy_ = init.DFL().AddDataFile(FName.PrependFileName("y_"), actionArgs);
outputz_ = init.DFL().AddDataFile(FName.PrependFileName("z_"), actionArgs);
outputr_ = init.DFL().AddDataFile(FName.PrependFileName("r_"), actionArgs);
outputa_ = init.DFL().AddDataFile(FName.PrependFileName("a_"), actionArgs);
if (diffout_ == 0 && calcDiffConst_)
diffout_ = init.DFL().AddDataFile(FName.PrependFileName("diff_"), actionArgs);
} else if (!outname.empty()) {
outputr_ = init.DFL().AddDataFile( outname, actionArgs );
outputx_ = outputy_ = outputz_ = outputa_ = outputr_;
}
}
if (diffout_ != 0) calcDiffConst_ = true;
// Add DataSets
dsname_ = actionArgs.GetStringNext();
if (dsname_.empty())
dsname_ = init.DSL().GenerateDefaultName("Diff");
avg_x_ = init.DSL().AddSet(DataSet::DOUBLE, MetaData(dsname_, "X"));
avg_y_ = init.DSL().AddSet(DataSet::DOUBLE, MetaData(dsname_, "Y"));
avg_z_ = init.DSL().AddSet(DataSet::DOUBLE, MetaData(dsname_, "Z"));
avg_r_ = init.DSL().AddSet(DataSet::DOUBLE, MetaData(dsname_, "R"));
avg_a_ = init.DSL().AddSet(DataSet::DOUBLE, MetaData(dsname_, "A"));
if (avg_x_ == 0 || avg_y_ == 0 || avg_z_ == 0 || avg_r_ == 0 || avg_a_ == 0)
return Action::ERR;
if (outputr_ != 0) outputr_->AddDataSet( avg_r_ );
if (outputx_ != 0) outputx_->AddDataSet( avg_x_ );
if (outputy_ != 0) outputy_->AddDataSet( avg_y_ );
if (outputz_ != 0) outputz_->AddDataSet( avg_z_ );
if (outputa_ != 0) outputa_->AddDataSet( avg_a_ );
// Set X dim
Xdim_ = Dimension(0.0, time_, "Time");
avg_x_->SetDim(Dimension::X, Xdim_);
avg_y_->SetDim(Dimension::X, Xdim_);
avg_z_->SetDim(Dimension::X, Xdim_);
avg_r_->SetDim(Dimension::X, Xdim_);
avg_a_->SetDim(Dimension::X, Xdim_);
// Add DataSets for diffusion constant calc
if (calcDiffConst_) {
MetaData::tsType ts = MetaData::NOT_TS;
diffConst_ = init.DSL().AddSet(DataSet::DOUBLE, MetaData(dsname_, "D", ts));
diffLabel_ = init.DSL().AddSet(DataSet::STRING, MetaData(dsname_, "Label", ts));
diffSlope_ = init.DSL().AddSet(DataSet::DOUBLE, MetaData(dsname_, "Slope", ts));
diffInter_ = init.DSL().AddSet(DataSet::DOUBLE, MetaData(dsname_, "Intercept", ts));
diffCorrl_ = init.DSL().AddSet(DataSet::DOUBLE, MetaData(dsname_, "Corr", ts));
if (diffConst_ == 0 || diffLabel_ == 0 || diffSlope_ == 0 || diffInter_ == 0 ||
diffCorrl_ == 0)
return Action::ERR;
# ifdef MPI
// No sync needed since these are not time series
diffConst_->SetNeedsSync( false );
diffLabel_->SetNeedsSync( false );
diffSlope_->SetNeedsSync( false );
diffInter_->SetNeedsSync( false );
diffCorrl_->SetNeedsSync( false );
# endif
if (diffout_ != 0) {
diffout_->AddDataSet( diffConst_ );
diffout_->AddDataSet( diffSlope_ );
diffout_->AddDataSet( diffInter_ );
diffout_->AddDataSet( diffCorrl_ );
diffout_->AddDataSet( diffLabel_ );
}
Dimension Ddim( 1, 1, "Set" );
diffConst_->SetDim(Dimension::X, Ddim);
diffLabel_->SetDim(Dimension::X, Ddim);
diffSlope_->SetDim(Dimension::X, Ddim);
diffInter_->SetDim(Dimension::X, Ddim);
diffCorrl_->SetDim(Dimension::X, Ddim);
}
// Save master data set list, needed when printIndividual_
masterDSL_ = init.DslPtr();
mprintf(" DIFFUSION:\n");
mprintf("\tAtom Mask is [%s]\n", mask_.MaskString());
if (printIndividual_)
mprintf("\tBoth average and individual diffusion will be calculated.\n");
else
mprintf("\tOnly average diffusion will be calculated.\n");
mprintf("\tData set base name: %s\n", avg_x_->Meta().Name().c_str());
if (image_.UseImage())
mprintf("\tCorrections for imaging enabled.\n");
else
mprintf("\tCorrections for imaging disabled.\n");
// If one file defined, assume all are.
if (outputx_ != 0) {
mprintf("\tOutput files:\n"
"\t %s: (x) Mean square displacement(s) in the X direction (in Ang.^2).\n"
"\t %s: (y) Mean square displacement(s) in the Y direction (in Ang.^2).\n"
"\t %s: (z) Mean square displacement(s) in the Z direction (in Ang.^2).\n"
"\t %s: (r) Overall mean square displacement(s) (in Ang.^2).\n"
"\t %s: (a) Total distance travelled (in Ang.).\n",
outputx_->DataFilename().full(), outputy_->DataFilename().full(),
outputz_->DataFilename().full(), outputr_->DataFilename().full(),
outputa_->DataFilename().full());
}
mprintf("\tThe time between frames is %g ps.\n", time_);
if (calcDiffConst_) {
mprintf("\tCalculating diffusion constants by fitting slope to MSD vs time\n"
"\t and multiplying by 10.0/2*N (where N is # of dimensions), units\n"
"\t are 1x10^-5 cm^2/s.\n");
if (diffout_ != 0)
mprintf("\tDiffusion constant output to '%s'\n", diffout_->DataFilename().full());
else
mprintf("\tDiffusion constant output to STDOUT.\n");
} else
mprintf("\tTo calculate diffusion constant from mean squared displacement plots,\n"
"\t calculate the slope of MSD vs time and multiply by 10.0/2*N (where N\n"
"\t is # of dimensions); this will give units of 1x10^-5 cm^2/s.\n");
return Action::OK;
}