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Copy pathAction_InfraredSpectrum.cpp
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171 lines (163 loc) · 6.07 KB
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#include "Action_InfraredSpectrum.h"
#include "CpptrajStdio.h"
#include "ProgressBar.h"
#include "Constants.h"
#include "DataSet_double.h"
#include "DataSet_Vector.h"
#include "Corr.h"
#ifdef _OPENMP
# include <omp.h>
#endif
Action_InfraredSpectrum::Action_InfraredSpectrum() :
Vel_(0),
VAC_(0),
currentTop_(0),
tstep_(0.0),
maxLag_(-1),
previousNselected_(-1),
useFFT_(true)
{
SetHidden(true);
}
// Action_InfraredSpectrum::Help()
void Action_InfraredSpectrum::Help() const {
mprintf("\t[<name>] [<mask>] [out <file>] [direct] [maxlag <lag>] [tstep <step>]\n"
"\t[rawout <raw vector>]\n");
}
// Action_InfraredSpectrum::Init()
Action::RetType Action_InfraredSpectrum::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
DataFile* outfile = init.DFL().AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
DataFile* rawfile = init.DFL().AddDataFile( actionArgs.GetStringKey("rawout"), actionArgs );
useFFT_ = !actionArgs.hasKey("direct");
maxLag_ = actionArgs.getKeyInt("maxlag", -1);
tstep_ = actionArgs.getKeyDouble("tstep", 1.0);
if (mask_.SetMaskString( actionArgs.GetMaskNext() )) return Action::ERR;
previousNselected_ = -1;
// DataSet
Vel_ = (DataSet_Vector*)
init.DSL().AddSet(DataSet::VECTOR,
MetaData(actionArgs.GetStringNext(), "raw"), "IR");
if (Vel_ == 0) return Action::ERR;
Vel_->SetupFormat().SetFormatWidthPrecision(12, 4);
if (rawfile != 0) rawfile->AddDataSet( Vel_ );
VAC_ = init.DSL().AddSet(DataSet::DOUBLE, MetaData(Vel_->Meta().Name(), "ac"));
if (VAC_ == 0) return Action::ERR;
if (outfile != 0) outfile->AddDataSet( VAC_ );
Vel_->SetDim(Dimension::X, Dimension(0.0, tstep_, "Time (ps)"));
VAC_->SetDim(Dimension::X, Dimension(0.0, tstep_, "Time (ps)"));
mprintf(" INFRARED SPECTRUM:\n");
mprintf("\tFor atoms in mask '%s'\n", mask_.MaskString());
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");
mprintf("\tAutocorrelation function data in '%s'\n", VAC_->Meta().PrintName().c_str());
if (outfile != 0)
mprintf("\tAutocorrelation function output to '%s'\n", outfile->DataFilename().full());
mprintf("\tRaw velocity*charge vector data in '%s'\n", Vel_->Meta().PrintName().c_str());
if (rawfile != 0)
mprintf("\tRaw velocity*charge vector output to '%s'\n", rawfile->DataFilename().full());
return Action::OK;
}
// Action_InfraredSpectrum::Setup()
Action::RetType Action_InfraredSpectrum::Setup(ActionSetup& setup)
{
if (!setup.CoordInfo().HasVel()) {
mprinterr("Error: No velocity info present in frames.\n");
return Action::ERR;
}
if (setup.Top().SetupIntegerMask( mask_ )) return Action::ERR;
mask_.MaskInfo();
if (mask_.None()) {
mprintf("Warning: No atoms selected by mask.\n");
return Action::SKIP;
}
if (previousNselected_ != -1 && mask_.Nselected() != previousNselected_)
mprintf("Warning: Selected # atoms has changed; was %i, now is %i\n",
previousNselected_, mask_.Nselected());
previousNselected_ = mask_.Nselected();
// TODO: Cache charges?
currentTop_ = setup.TopAddress();
return Action::OK;
}
// Action_InfraredSpectrum::DoAction()
Action::RetType Action_InfraredSpectrum::DoAction(int frameNum, ActionFrame& frm)
{
Vec3 sum(0.0);
for (AtomMask::const_iterator atm = mask_.begin(); atm != mask_.end(); ++atm)
sum += Vec3(frm.Frm().VelXYZ(*atm)) * Constants::AMBERTIME_TO_PS * (*currentTop_)[*atm].Charge();
Vel_->AddVxyz( sum );
return Action::OK;
}
// Action_InfraredSpectrum::Print()
void Action_InfraredSpectrum::Print() {
if (Vel_ == 0 || Vel_->Size() < 1) return;
mprintf(" INFRARED SPECTRUM:\n");
int maxlag;
if (maxLag_ <= 0) {
maxlag = (int)Vel_->Size() / 2;
mprintf("\tSetting maximum lag to 1/2 total frames (%i)\n", maxlag);
} else if (maxLag_ > (int)Vel_->Size()) {
maxlag = (int)Vel_->Size();
mprintf("\tSpecified maximum lag > total length, setting to %i\n", maxlag);
} else
maxlag = maxLag_;
// Allocate space for output correlation function values.
DataSet_double& Ct = static_cast<DataSet_double&>( *VAC_ );
Ct.Resize( maxlag );
if (!useFFT_) {
// DIRECT METHOD
ParallelProgress progress( maxlag );
int t;
unsigned int dtmax, dt;
# ifdef _OPENMP
# pragma omp parallel private(t, dtmax, dt) firstprivate(progress)
{
progress.SetThread(omp_get_thread_num());
# pragma omp for schedule(dynamic)
# endif
for (t = 0; t < maxlag; ++t)
{
progress.Update( t );
dtmax = Vel_->Size() - t;
for (dt = 0; dt < dtmax; ++dt)
Ct[t] += (*Vel_)[dt] * (*Vel_)[dt + t];
Ct[t] /= (double)dtmax;
//mprintf("\tCt[%i]= %f\n", t, Ct[t]); // DEBUG
}
# ifdef _OPENMP
} // END pragma omp parallel
# endif
progress.Finish();
} else {
// FFT METHOD
// Since FFT is cyclic, unroll vectors into a 1D array; in the resulting
// transformed array after FFT, every 3rd value will be the correlation
// via dot products that we want (once it is normalized).
unsigned int total_length = Vel_->Size() * 3;
CorrF_FFT pubfft;
pubfft.CorrSetup( total_length );
ComplexArray data1 = pubfft.Array();
//mprintf("Complex Array Size is %i (%i actual)\n", data1.size(), data1.size()*2);
// Place vector from each frame into 1D array
unsigned int nd = 0; // Will be used to index complex data
for (DataSet_Vector::const_iterator vec = Vel_->begin(); vec != Vel_->end(); ++vec, nd+=6)
{
data1[nd ] = (*vec)[0]; data1[nd+1] = 0.0;
data1[nd+2] = (*vec)[1]; data1[nd+3] = 0.0;
data1[nd+4] = (*vec)[2]; data1[nd+5] = 0.0;
}
data1.PadWithZero( total_length );
pubfft.AutoCorr( data1 );
// Normalization
nd = 0;
for (int t = 0; t < maxlag; t++, nd += 3)
Ct[t] = data1[nd*2] * ( 3.0 / (double)((total_length - nd)) );
}
}