diff --git a/.github/workflows/merge-gate.yml b/.github/workflows/merge-gate.yml
index bdb3a047bf..e707ce0eef 100644
--- a/.github/workflows/merge-gate.yml
+++ b/.github/workflows/merge-gate.yml
@@ -141,18 +141,19 @@ jobs:
     - name: Set up Python 3.8
       uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: '3.8'
     - name: Add conda to system path
       run: |
         # $CONDA is an environment variable pointing to the root of the miniconda directory
         echo $CONDA/bin >> $GITHUB_PATH
     - name: Install conda packages
       run: |
-        conda install setuptools cython numpy pytest mock curl 
+        conda env update --file devtools/ci/environment.yml --name base
     - name: Install cpptraj
       run: |
         export PATH=$HOME/bin:${PATH}
         export LD_LIBRARY_PATH=$HOME/lib:${LD_LIBRARY_PATH}
+        export MAKE_COMMAND="make -j2"
         ./configure --buildlibs -openmp -shared gnu
         source cpptraj.sh
         make -j2 libcpptraj
diff --git a/configure b/configure
index 31e4cb7aa3..b635608b99 100755
--- a/configure
+++ b/configure
@@ -1031,7 +1031,7 @@ EOF
     fi
   elif [ "$MKL_FFTW" = 'yes' ] ; then
     # Using FFTW from MKL
-    TestProgram "  Checking FFTW3" "$CXX" "$CXXFLAGS ${LIB_INCL[$LBLAS]}" testp.cpp "${LIB_FLAG[$LBLAS]}"
+    TestProgram "  Checking MKL FFTW3" "$CXX" "$CXXFLAGS ${LIB_INCL[$LBLAS]}" testp.cpp "${LIB_FLAG[$LBLAS]}"
   else
     TestProgram silent "  Checking FFTW3" "$CXX" "$CXXFLAGS ${LIB_INCL[$LFFTW3]}" testp.cpp "${LIB_FLAG[$LFFTW3]}"
     if [ $? -ne 0 ] ; then
diff --git a/devtools/ci/environment.yml b/devtools/ci/environment.yml
index 34d6a61f6f..4bff2d813b 100644
--- a/devtools/ci/environment.yml
+++ b/devtools/ci/environment.yml
@@ -1,10 +1,11 @@
 channels:
-    - defaults 
+    - conda-forge
 dependencies:
     - python=3.8
+    - pyflakes
     - numpy
-    - mock
-    - pytest
     - cython
     - setuptools
-    - curl 
+    - pytest
+    - mock
+    - curl
diff --git a/doc/cpptraj.lyx b/doc/cpptraj.lyx
index c54a2db1f6..6641ba7a18 100644
--- a/doc/cpptraj.lyx
+++ b/doc/cpptraj.lyx
@@ -8341,7 +8341,7 @@ The following general commands are available:
 \begin_layout Standard
 \align center
 \begin_inset Tabular
-<lyxtabular version="3" rows="34" columns="2">
+<lyxtabular version="3" rows="35" columns="2">
 <features tabularvalignment="middle">
 <column alignment="center" valignment="top">
 <column alignment="center" valignment="top">
@@ -8734,6 +8734,26 @@ parallelanalysis
 <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
 \begin_inset Text
 
+\begin_layout Plain Layout
+parsedata
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Parse timing data from CPPTRAJ output.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
 \begin_layout Plain Layout
 precision
 \end_layout
@@ -11455,6 +11475,175 @@ noprefix "false"
 .
 \end_layout
 
+\begin_layout Subsection
+parsedata
+\end_layout
+
+\begin_layout LyX-Code
+parsetiming <filename args> ...
+ [out <file>] [name <setname>]
+\end_layout
+
+\begin_layout LyX-Code
+        	[sortby {time|cores|filename}] [includebad] [showdetails]
+\end_layout
+
+\begin_layout LyX-Code
+        	[type {trajproc|trajread|actframe}] [reverse]
+\end_layout
+
+\begin_layout LyX-Code
+        	[groupout <file> [grouptype {prefix|name|kind}]]
+\end_layout
+
+\begin_deeper
+\begin_layout Description
+<filename
+\begin_inset space ~
+\end_inset
+
+args> Files containing CPPTRAJ output to get timing data from.
+\end_layout
+
+\begin_layout Description
+[out
+\begin_inset space ~
+\end_inset
+
+<file>] Write total sorted timing sets to <file>.
+\end_layout
+
+\begin_layout Description
+[name
+\begin_inset space ~
+\end_inset
+
+<setname>] Set name for timing data sets.
+\end_layout
+
+\begin_layout Description
+[sortby
+\begin_inset space ~
+\end_inset
+
+{time|cores|filename}] Sort timing data sets by either time, number of cores
+ (MPI processes * OpenMP threads), or file name.
+\end_layout
+
+\begin_layout Description
+[includebad] If specified, include run output for which timing data cannot
+ be extracted (e.g.
+ an incomplete/failed run).
+\end_layout
+
+\begin_layout Description
+[showdetails] If specified, details about each run will be printed to STDOUT.
+\end_layout
+
+\begin_layout Description
+[type
+\begin_inset space ~
+\end_inset
+
+{trajproc|trajread|actframe} If specified, report time other than the total
+ time (which is the default):
+\end_layout
+
+\begin_deeper
+\begin_layout Description
+trajproc Total trajectory processing time (trajectory I/O plus action frame
+ time).
+\end_layout
+
+\begin_layout Description
+trajread Trajectory read time (requires compiling with '-timer' configure
+ option/-DTIMER compiler define).
+\end_layout
+
+\begin_layout Description
+actframe Action frame time (requires compiling with '-timer' configure option/-D
+TIMER compiler define).
+\end_layout
+
+\end_deeper
+\begin_layout Description
+[reverse] Instead of longest time to shortest time, sort shortest time to
+ longest time.
+\end_layout
+
+\begin_layout Description
+[groupout
+\begin_inset space ~
+\end_inset
+
+<file>] Group run output by a property and write to a file.
+ Additional details will be written like speedup and efficiency (relative
+ to the slowest run).
+\end_layout
+
+\begin_deeper
+\begin_layout Description
+[grouptype
+\begin_inset space ~
+\end_inset
+
+{prefix|name|kind}] Property to group runs by in group output file.
+\end_layout
+
+\begin_deeper
+\begin_layout Description
+prefix Group by directory prefix.
+\end_layout
+
+\begin_layout Description
+name Group by run type name (see 
+\emph on
+<setname>[name]
+\emph default
+ below).
+\end_layout
+
+\begin_layout Description
+kind Group by run type name; OpenMP runs are separated by number of OpenMP
+ threads.
+\end_layout
+
+\end_deeper
+\end_deeper
+\begin_layout Standard
+DataSets Created:
+\end_layout
+
+\begin_layout Description
+<setname> Set containing sorted run times.
+\end_layout
+
+\begin_layout Description
+<setname>[name] Set containing shortedhand run names.
+ Consists of a prefix (S for serial, O for OpenMP, M for MPI, H for hybrid
+ MPI/OpenMP) followed by numbers indicating number of MPI processes 'x'
+ OpenMP threads; e.g., H16x4 means a hybrid run consisting of 16 MPI processes
+ and 4 OpenMP threads per process.
+ If CUDA is active, the name will be wrapped in 'G()', e.g.
+ G(H16x4).
+\end_layout
+
+\begin_layout Description
+<setname>[dir] Set containing output directory prefixes.
+ If no directory prefix, just contains output file name.
+\end_layout
+
+\end_deeper
+\begin_layout Standard
+The 
+\series bold
+\emph on
+parsedata
+\series default
+\emph default
+ command can be used to extract timing data from CPPTRAJ output.
+\end_layout
+
 \begin_layout Subsection
 precision
 \end_layout
diff --git a/src/Analysis_TICA.cpp b/src/Analysis_TICA.cpp
new file mode 100644
index 0000000000..a7204be90f
--- /dev/null
+++ b/src/Analysis_TICA.cpp
@@ -0,0 +1,157 @@
+#include "Analysis_TICA.h"
+#include "CpptrajStdio.h"
+#include "Matrix.h" // TODO DataSet?
+#include <cmath> // sqrt
+
+/** CONSTRUCTOR */
+Analysis_TICA::Analysis_TICA() :
+  TgtTraj_(0),
+  lag_(0),
+  useMass_(false)
+{
+  SetHidden(true);
+}
+
+// Analysis_TICA::Help()
+void Analysis_TICA::Help() const {
+  mprintf("[crdset <set name>] [lag <time lag>] [mask <mask>] [mass]\n");
+}
+
+// Analysis_TICA::Setup()
+Analysis::RetType Analysis_TICA::Setup(ArgList& analyzeArgs, AnalysisSetup& setup, int debugIn)
+{
+  // Attempt to get coords dataset from datasetlist
+  std::string setname = analyzeArgs.GetStringKey("crdset");
+  TgtTraj_ = (DataSet_Coords*)setup.DSL().FindCoordsSet( setname );
+  if (TgtTraj_ == 0) {
+    mprinterr("Error: Could not locate COORDS set corresponding to %s\n",
+              setname.c_str());
+    Help();
+    return Analysis::ERR;
+  }
+  // Other keywords
+  lag_ = analyzeArgs.getKeyInt("lag", 1);
+  std::string maskstr = analyzeArgs.GetStringKey("mask");
+  if (mask1_.SetMaskString( maskstr )) {
+    mprinterr("Error: Could not set atom mask string '%s'\n", maskstr.c_str());
+    return Analysis::ERR;
+  }
+  useMass_ = analyzeArgs.hasKey("mass");
+
+  // Print analysis info
+  mprintf("    TICA: Time independent correlation analysis.\n");
+  mprintf("\tUsing coordinates from set '%s'\n", TgtTraj_->legend());
+  mprintf("\tUsing atoms selected by mask '%s'\n", mask1_.MaskString());
+  mprintf("\tTime lag: %i frames.\n", lag_);
+  if (useMass_)
+    mprintf("\tMass-weighted.\n");
+  else
+    mprintf("\tNot mass-weighted.\n");
+
+  return Analysis::OK;
+}
+
+// Analysis_TICA::Analyze()
+Analysis::RetType Analysis_TICA::Analyze() {
+  unsigned int Nframes = TgtTraj_->Size();
+  if (Nframes < 1) {
+    mprinterr("Error: No frames to analyze.\n");
+    return Analysis::ERR;
+  }
+  // Evaluate mask
+  if ( TgtTraj_->Top().SetupIntegerMask( mask1_ ) ) {
+    mprinterr("Error: Could not evaluate atom mask '%s'\n", mask1_.MaskString());
+    return Analysis::ERR;
+  }
+  mask1_.MaskInfo();
+  if (mask1_.None()) {
+    mprinterr("Error: No atoms selected by mask '%s'\n", mask1_.MaskString());
+    return Analysis::ERR;
+  }
+  // Allocate frames
+  Frame coords0;
+  coords0.SetupFrameFromMask( mask1_, TgtTraj_->Top().Atoms(), TgtTraj_->CoordsInfo() );
+  Frame coords1 = coords0;
+  // Diagonal vectors
+  typedef std::vector<Vec3> Varray;
+  Varray vect(mask1_.Nselected(), Vec3(0.0));
+  //Varray vect2(mask1_.Nselected(), Vec3(0.0));
+  // Matrix - half
+  Matrix<double> covarMatrix;
+  covarMatrix.resize( mask1_.Nselected()*3, 0 );
+  // Loop over frames
+  for (unsigned int frm0 = 0; frm0 < Nframes; frm0++) {
+    mprintf("DEBUG: Frame %i\n", frm0);
+    TgtTraj_->GetFrame(frm0, coords0, mask1_);
+    // Covariance
+    Matrix<double>::iterator mat = covarMatrix.begin();
+    for (int idx1 = 0; idx1 < mask1_.Nselected(); idx1++) {
+      Vec3 XYZi( coords0.XYZ(idx1) );
+      // Store veci and veci^2
+      vect[idx1] += XYZi;
+      //vect2[idx1] += XYZi.Squared();
+      // Loop over X, Y, and Z of veci
+      for (int iidx = 0; iidx < 3; iidx++) {
+        double Vi = XYZi[iidx];
+        // Diagonal
+        for (int jidx = iidx; jidx < 3; jidx++)
+          *(mat++) += Vi * XYZi[jidx]; // Vi * j{0,1,2}, Vi * j{1,2}, Vi * j{2}
+        // Inner loop
+        for (int idx2 = idx1 + 1; idx2 < mask1_.Nselected(); idx2++) {
+          Vec3 XYZj( coords0.XYZ(idx2) );
+          *(mat++) += Vi * XYZj[0];
+          *(mat++) += Vi * XYZj[1];
+          *(mat++) += Vi * XYZj[2];
+        } // END inner loop over idx2
+      } // END loop over x y z of veci
+    } // END outer loop over idx1
+  } // END loop over frames
+
+  // Normalize
+  double norm = 1.0 / (double)TgtTraj_->Size();
+  for (Varray::iterator it = vect.begin(); it != vect.end(); ++it)
+    *it *= norm;
+  for (Matrix<double>::iterator it = covarMatrix.begin(); it != covarMatrix.end(); ++it)
+    *it *= norm;
+  // Calc <riri> - <ri><ri>
+  //for (int k = 0; k < mask1_.Nselected(); k++) {
+  //  vect2[k][0] -= (vect[k][0] * vect[k][0]);
+  //  vect2[k][1] -= (vect[k][1] * vect[k][1]);
+  //  vect2[k][2] -= (vect[k][2] * vect[k][2]);
+  //}
+  // Calc <rirj> - <ri><rj>
+  double Mass = 1.0;
+  double mass1 = 1.0;
+  Matrix<double>::iterator mat = covarMatrix.begin();
+  for (int idx1 = 0; idx1 < mask1_.Nselected(); idx1++) {
+    if (useMass_)
+      mass1 = coords0.Mass(idx1);
+    for (int iidx = 0; iidx < 3; iidx++) {
+      double Vi = vect[idx1][iidx];
+      for (int idx2 = idx1; idx2 < mask1_.Nselected(); idx2++) {
+        if (useMass_)
+          Mass = sqrt( mass1 * coords0.Mass(idx2) );
+        if (idx1 == idx2) {
+          // Self
+          for (int jidx = iidx; jidx < 3; jidx++) {
+            *mat = (*mat - (Vi * vect[idx2][jidx])) * Mass;
+            ++mat;
+          }
+        } else {
+          for (int jidx = 0; jidx < 3; jidx++) {
+            *mat = (*mat - (Vi * vect[idx2][jidx])) * Mass;
+            ++mat;
+          }
+        }
+      } // END inner loop over idx2
+    } // END loop over elements of vect[idx1]
+  } // END outer loop over idx1
+  // DEBUG PRINT
+  for (int row = 0; row < mask1_.Nselected()*3; row++) {
+    for (int col = 0; col < mask1_.Nselected()*3; col++) {
+      mprintf(" %6.3f", covarMatrix.element(col, row));
+    }
+    mprintf("\n");
+  }
+  return Analysis::OK;
+}
diff --git a/src/Analysis_TICA.h b/src/Analysis_TICA.h
new file mode 100644
index 0000000000..fe44df32af
--- /dev/null
+++ b/src/Analysis_TICA.h
@@ -0,0 +1,19 @@
+#ifndef INC_ANALYSIS_TICA_H
+#define INC_ANALYSIS_TICA_H
+#include "Analysis.h"
+/// <Enter description of Analysis_TICA here>
+class Analysis_TICA : public Analysis {
+  public:
+    Analysis_TICA();
+    DispatchObject* Alloc() const { return (DispatchObject*)new Analysis_TICA(); }
+    void Help() const;
+
+    Analysis::RetType Setup(ArgList&, AnalysisSetup&, int);
+    Analysis::RetType Analyze();
+  private:
+    DataSet_Coords* TgtTraj_; ///< Input trajectory
+    int lag_; ///< TICA time lag
+    AtomMask mask1_; ///< Atoms to use in matrix calc
+    bool useMass_; ///< Control whether to mass-weight
+};
+#endif
diff --git a/src/Command.cpp b/src/Command.cpp
index 1c20c508b9..158e2d5fb2 100644
--- a/src/Command.cpp
+++ b/src/Command.cpp
@@ -39,6 +39,7 @@
 #include "Exec_Show.h"
 #include "Exec_Random.h"
 #include "Exec_CompareClusters.h"
+#include "Exec_ParseTiming.h"
 // ----- SYSTEM ----------------------------------------------------------------
 #include "Exec_System.h"
 // ----- COORDS ----------------------------------------------------------------
@@ -199,6 +200,7 @@
 #include "Analysis_HausdorffDistance.h"
 #include "Analysis_Slope.h"
 #include "Analysis_EvalPlateau.h"
+#include "Analysis_TICA.h"
 #include "Analysis_CalcDiffusion.h"
 
 CmdList Command::commands_ = CmdList();
@@ -235,6 +237,7 @@ void Command::Init() {
   Command::AddCmd( new Exec_NoExitOnError(),   Cmd::EXE, 1, "noexitonerror" );
   Command::AddCmd( new Exec_NoProgress(),      Cmd::EXE, 1, "noprogress" );
   Command::AddCmd( new Exec_ParallelAnalysis(),Cmd::EXE, 1, "parallelanalysis" );
+  Command::AddCmd( new Exec_ParseTiming(),     Cmd::EXE, 1, "parsetiming" );
   Command::AddCmd( new Exec_Precision(),       Cmd::EXE, 1, "precision" );
   Command::AddCmd( new Exec_PrintData(),       Cmd::EXE, 1, "printdata" );
   Command::AddCmd( new Exec_QuietBlocks(),     Cmd::EXE, 1, "quietblocks" );
@@ -432,6 +435,7 @@ void Command::Init() {
   Command::AddCmd( new Analysis_Spline(),      Cmd::ANA, 1, "spline" );
   Command::AddCmd( new Analysis_Statistics(),  Cmd::ANA, 2, "stat", "statistics" );
   Command::AddCmd( new Analysis_TI(),          Cmd::ANA, 1, "ti" );
+  Command::AddCmd( new Analysis_TICA(),        Cmd::ANA, 1, "tica" ); // hidden
   Command::AddCmd( new Analysis_Timecorr(),    Cmd::ANA, 1, "timecorr" );
   Command::AddCmd( new Analysis_VectorMath(),  Cmd::ANA, 1, "vectormath" );
   Command::AddCmd( new Analysis_Wavelet(),     Cmd::ANA, 1, "wavelet" );
diff --git a/src/Exec_ParseTiming.cpp b/src/Exec_ParseTiming.cpp
new file mode 100644
index 0000000000..6e94685176
--- /dev/null
+++ b/src/Exec_ParseTiming.cpp
@@ -0,0 +1,564 @@
+#include "Exec_ParseTiming.h"
+#include "CpptrajStdio.h"
+#include "FileName.h"
+#include "BufferedLine.h"
+#include "DataSet_Mesh.h"
+#include "StringRoutines.h"
+#include <cstring> // strncmp
+#include <algorithm> // std::sort
+
+/** CONSTRUCTOR */
+Exec_ParseTiming::Exec_ParseTiming() :
+  Exec(GENERAL)
+{
+}
+
+// -----------------------------------------------------------------------------
+/** Hold run timing and details. */
+class Exec_ParseTiming::RunTiming {
+  public:
+    /// CONSTRUCTOR - blank
+    RunTiming() : version_major_(-1), version_minor_(-1), version_revision_(-1),
+                  isMPI_(false), isOpenMP_(false), isCUDA_(false),
+                  nprocs_(-1), nthreads_(-1), t_total_(-1), t_traj_proc_(-1) {}
+    /// CONSTRUCTOR - filename
+    RunTiming(std::string const& name) : filename_(name),
+                  version_major_(-1), version_minor_(-1), version_revision_(-1),
+                  isMPI_(false), isOpenMP_(false), isCUDA_(false),
+                  nprocs_(-1), nthreads_(-1), t_total_(-1), t_traj_proc_(-1)
+    {
+      // Get directory prefix.
+      std::string dirprefix( filename_.DirPrefix_NoSlash() );
+      FileName fname( filename_ );
+      while (!dirprefix.empty()) {
+        fname.SetFileName_NoExpansion( fname.DirPrefix_NoSlash() );
+        dirprefix = fname.DirPrefix_NoSlash();
+      }
+      prefix_ = fname.Base();
+      //FileName dirprefix2( dirprefix1.Full() );
+      //mprintf("DEBUG: '%s' Dirprefix= '%s' name= '%s'\n", filename_.full(), fname.full(), fname.base());
+    }
+
+    void SetVersionAndType(std::string const& vstr, bool isM, bool isO, bool isC) {
+      isMPI_ = isM;
+      isOpenMP_ = isO;
+      isCUDA_ = isC;
+      ArgList varg( vstr, "V." );
+      version_major_ = varg.getNextInteger(-1);
+      version_minor_ = varg.getNextInteger(-1);
+      version_revision_ = varg.getNextInteger(-1);
+    }
+
+    void SetNprocs(int n) { nprocs_ = n; }
+    void SetNthreads(int n) { nthreads_ = n; }
+    void SetTotalTime(double t) { t_total_ = t; }
+    void SetTrajProcTime(double t) { t_traj_proc_ = t; }
+    void AddTrajReadTime(double t) { t_traj_read_.push_back( t ); }
+    void AddActionFrameTime(double t) { t_action_frame_.push_back( t ); }
+
+    int Nthreads() const { return nthreads_; }
+    double TotalTime() const { return t_total_; }
+    double TrajProcTime() const { return t_traj_proc_; }
+
+    double TrajReadTime() const {
+      double t = 0;
+      for (Darray::const_iterator it = t_traj_read_.begin(); it != t_traj_read_.end(); ++it)
+        if (*it > t) t = *it;
+      return t;
+    }
+
+    double ActionFrameTime() const {
+      double t = 0;
+      for (Darray::const_iterator it = t_action_frame_.begin(); it != t_action_frame_.end(); ++it)
+        if (*it > t) t = *it;
+      return t;
+    }
+
+    int TotalCores() const {
+      if (isMPI_ && isOpenMP_)
+        return nprocs_ * nthreads_;
+      else if (isMPI_)
+        return nprocs_;
+      else if (isOpenMP_)
+        return nthreads_;
+      else
+        return 1;
+    }
+
+    bool HasDetailedTiming() const { return !(t_traj_read_.empty() || t_action_frame_.empty()); }
+
+    FileName const& Filename() const { return filename_; }
+    std::string const& Prefix() const { return prefix_; }
+    std::string const& Directory() const {
+      if (filename_.DirPrefix().empty())
+        return filename_.Full();
+      else
+        return filename_.DirPrefix();
+    }
+
+    std::string Name() const {
+      std::string out;
+      if (isMPI_ && isOpenMP_)
+        out.assign("H" + integerToString(nprocs_) + "x" + integerToString(nthreads_));
+      else if (isMPI_)
+        out.assign("M" + integerToString(nprocs_));
+      else if (isOpenMP_)
+        out.assign("O" + integerToString(nthreads_));
+      else
+        out.assign("S");
+      if (isCUDA_) {
+        std::string tmp = out;
+        out.assign( "G(" + tmp + ")" );
+      }
+      return out;
+    }
+
+    void Print() const {
+      mprintf("%s Version %i.%i.%i mpi=%i omp=%i cuda=%i nprocs=%i nthreads=%i ncores=%i t_total=%g t_traj_proc=%g",
+              filename_.full(), version_major_, version_minor_, version_revision_,
+              (int)isMPI_, (int)isOpenMP_, (int)isCUDA_, nprocs_, nthreads_, TotalCores(), t_total_, t_traj_proc_);
+      if (!t_traj_read_.empty()) {
+        mprintf(" t_traj_read={");
+        for (Darray::const_iterator it = t_traj_read_.begin(); it != t_traj_read_.end(); ++it)
+          mprintf(" %g", *it);
+        mprintf("}");
+      }
+      if (!t_action_frame_.empty()) {
+        mprintf(" t_action_frame={");
+        for (Darray::const_iterator it = t_action_frame_.begin(); it != t_action_frame_.end(); ++it)
+          mprintf(" %g", *it);
+        mprintf("}");
+      }
+      mprintf("\n");
+    }
+
+    bool IsBad() {
+      errMsg_.clear();
+      if (filename_.empty()) { errMsg_.assign("Empty run name."); return true; }
+      if (t_total_ < 0) { errMsg_.assign("Empty run time."); return true; }
+      if (isMPI_ && nprocs_ < 1) { errMsg_.assign("MPI && procs < 1."); return true; }
+      if (isOpenMP_ && nthreads_ < 1) { errMsg_.assign("OpenMP && threads < 1."); return true; }
+      return false;
+    }
+
+    /** \return last error message set by IsBad() */
+    std::string const& ErrMsg() const { return errMsg_; }
+
+    /** Sort by total time, longest first. */
+    struct sort_by_total_time {
+      inline bool operator()(RunTiming const& first, RunTiming const& second) const {
+        return (first.TotalTime() > second.TotalTime());
+      }
+    };
+
+    /** Sort by total cores, then time. */
+    struct sort_by_cores {
+      inline bool operator()(RunTiming const& first, RunTiming const& second) const {
+        int first_cores = first.TotalCores();
+        int second_cores = second.TotalCores();
+        if (first_cores == second_cores)
+          return (first.TotalTime() > second.TotalTime());
+        else
+          return (first_cores < second_cores);
+      }
+    };
+
+    /** Sort by file name. */
+    struct sort_by_filename {
+      inline bool operator()(RunTiming const& first, RunTiming const& second) const {
+        if (first.filename_.Full() == second.filename_.Full())
+          return (first.TotalTime() > second.TotalTime());
+        else
+          return (first.filename_.Full() < second.filename_.Full());
+      }
+    };
+  private:
+    FileName filename_;
+    std::string prefix_; ///< Filename prefix
+    int version_major_;
+    int version_minor_;
+    int version_revision_;
+    bool isMPI_;
+    bool isOpenMP_;
+    bool isCUDA_;
+    int nprocs_;
+    int nthreads_;
+    double t_total_;
+    double t_traj_proc_; 
+    Darray t_traj_read_;
+    Darray t_action_frame_;
+    std::string errMsg_;
+};
+// -----------------------------------------------------------------------------
+
+/** Execute command. */
+Exec_ParseTiming::RunTiming Exec_ParseTiming::read_cpptraj_output(std::string const& fname) {
+  BufferedLine infile;
+
+
+  RunTiming thisRun( fname );
+  if (infile.OpenFileRead( fname )) {
+    mprinterr("Error: Could not open '%s'\n", fname.c_str());
+    return thisRun;
+  }
+  const char* ptr = infile.Line();
+  while (ptr != 0) {
+    if (ptr[0] == 'C') {
+      if (strncmp(ptr, "CPPTRAJ: Trajectory Analysis.", 29)==0) {
+        //mprintf("DEBUG: Title: %s\n", ptr);
+        ArgList titleArg( ptr+29, " " );
+        //mprintf("DEBUG: TitleArg: %s\n", title.ArgLine());
+        // Version should be the first arg
+        std::string versionStr = titleArg.GetStringNext();
+        bool isMPI = titleArg.hasKey("MPI");
+        bool isOpenMP = titleArg.hasKey("OpenMP");
+        bool isCUDA = titleArg.hasKey("CUDA");
+        thisRun.SetVersionAndType(versionStr, isMPI, isOpenMP, isCUDA);
+      }
+    } else if (ptr[0] == '|') {
+      ArgList infoArg(ptr+1, " ");
+      if (infoArg.Nargs() == 4 && infoArg[0] == "Running" && infoArg[1] == "on") {
+        // processes should be the next integer arg
+        thisRun.SetNprocs( infoArg.getNextInteger(-1) );
+      } else if (infoArg.Nargs() == 4 && infoArg[1] == "OpenMP" &&  infoArg[2] == "threads") {
+        //mprintf("DEBUG: OpenMP threads. %s\n", ptr);
+        // threads should be the next integer arg
+        thisRun.SetNthreads( infoArg.getNextInteger(-1) );
+      }
+    } else if (ptr[0] == 'T') {
+      if (strncmp(ptr, "TIME:", 5) == 0) {
+        ArgList timeArg( ptr, " \t" );
+        //timeArg.PrintDebug();
+        if (timeArg.Nargs() == 6 && timeArg[1] == "Total" && timeArg[2] == "execution")
+          thisRun.SetTotalTime( timeArg.getKeyDouble("time:", -1) );
+        else if (timeArg.Nargs() >= 6 && timeArg[1] == "Trajectory" && timeArg[2] == "Process")
+          thisRun.SetTrajProcTime( timeArg.getKeyDouble(":", -1) );
+        else if (timeArg.Nargs() > 3 && timeArg[1] == "Trajectory" && timeArg[2] == "read:")
+          thisRun.AddTrajReadTime( timeArg.getNextDouble(-1) );
+        else if (timeArg.Nargs() > 4 && timeArg[1] == "Action" && timeArg[2] == "frame" && timeArg[3] == "processing:")
+          thisRun.AddActionFrameTime( timeArg.getNextDouble(-1) );
+      } // END TIME:
+    }
+    ptr = infile.Line();
+  }
+  //thisRun.Print();
+  infile.CloseFile();
+  return thisRun;
+}
+
+/** \return Y value according to yvar */
+double Exec_ParseTiming::YVAL(Ytype yvar, RunTiming const& run)
+{
+  double Y = 0;
+  switch (yvar) {
+    case Y_T_TOTAL    : Y = run.TotalTime(); break;
+    case Y_T_TRAJPROC : Y = run.TrajProcTime(); break;
+    case Y_T_TRAJREAD : Y = run.TrajReadTime(); break;
+    case Y_T_ACTFRAME : Y = run.ActionFrameTime(); break;
+  }
+  return Y;
+}
+
+/** Make an output data set for RunArray */
+int Exec_ParseTiming::create_output_set(RunArray const& Runs, DataSetList& DSL,
+                                        DataFile* outfile, std::string const& dsname,
+                                        Dimension const& Xdim, Xtype xvar, Ytype yvar)
+const
+{
+  // Create DataSet
+
+  DataSet* ds = DSL.AddSet( DataSet::XYMESH, MetaData(dsname) );
+  if (ds == 0) {
+    mprinterr("Error: Could not allocate output set.\n");
+    return 1;
+  }
+  if (outfile != 0) outfile->AddDataSet( ds );
+  DataSet_Mesh& outset = static_cast<DataSet_Mesh&>( *ds );
+  outset.Allocate( DataSet::SizeArray(1, Runs.size()) );
+  outset.SetDim(Dimension::X, Xdim);
+  //outset.SetDim(Dimension::Y, Ydim);
+
+  DataSet* nameSet = DSL.AddSet(DataSet::STRING, MetaData(dsname, "name"));
+  if (nameSet == 0) {
+    mprinterr("Error: Could not allocate output names set.\n");
+    return 1;
+  }
+  if (outfile != 0) outfile->AddDataSet( nameSet );
+  nameSet->Allocate( DataSet::SizeArray(1, Runs.size()) );
+  nameSet->SetDim(Dimension::X, Xdim);
+
+  DataSet* dirNameSet = DSL.AddSet(DataSet::STRING, MetaData(dsname, "dir"));
+  if (dirNameSet == 0) {
+    mprinterr("Error: Could not allocate directory names set.\n");
+    return 1;
+  }
+  if (outfile != 0) outfile->AddDataSet( dirNameSet );
+  dirNameSet->Allocate( DataSet::SizeArray(1, Runs.size()) );
+  dirNameSet->SetDim(Dimension::X, Xdim);
+
+  for (RunArray::const_iterator it = Runs.begin(); it != Runs.end(); ++it) {
+    double X = 0;
+    switch (xvar) {
+      case X_INDEX : X = (double)(it - Runs.begin()); break;
+      case X_CORES : X = (double)it->TotalCores(); break;
+    }
+    double Y = YVAL( yvar, *it );
+
+    outset.AddXY(X, Y);
+    nameSet->Add(it - Runs.begin(), it->Name().c_str());
+    dirNameSet->Add(it - Runs.begin(), it->Directory().c_str());
+    //it->Print();
+  }
+  return 0;
+}
+
+/** Write a run group to file. */
+void Exec_ParseTiming::write_to_file(CpptrajFile& outfile, RunArray const& Runs, Xtype xvar, Ytype yvar,
+                                     double refy, double refcores)
+const
+{
+  //double refy = 0;
+  //double refcores = 0;
+  for (RunArray::const_iterator it = Runs.begin(); it != Runs.end(); ++it) {
+    double X = 0;
+    switch (xvar) {
+      case X_INDEX : X = (double)(it - Runs.begin()); break;
+      case X_CORES : X = (double)it->TotalCores(); break;
+    }
+    double Y = YVAL( yvar, *it );
+    
+    //if (it == Runs.begin()) {
+    //  refy = Y;
+    //  refcores = (double)it->TotalCores();
+    //}
+    double speedup = refy / Y;
+    int totalCores = it->TotalCores();
+    double ideal_speedup = (double)totalCores / refcores;
+    double efficiency = speedup / ideal_speedup;
+    outfile.Printf("%12.4f %12.4f %6.2f %6i %6.2f %12s %s\n", X, Y, speedup, totalCores, efficiency, it->Name().c_str(), it->Directory().c_str());
+  }
+}
+
+// Exec_ParseTiming::Help()
+void Exec_ParseTiming::Help() const
+{
+  mprintf("\t<filename args> ... [out <file>] [name <setname>]\n"
+          "\t[sortby {time|cores|filename}] [includebad] [showdetails]\n"
+          "\t[type {trajproc|trajread|actframe}] [reverse]\n"
+          "\t[groupout <file> [grouptype {prefix|name|kind}]]\n"
+          "  Parse cpptraj output for timing data.\n"
+         );
+}
+
+// Exec_ParseTiming::Execute()
+Exec::RetType Exec_ParseTiming::Execute(CpptrajState& State, ArgList& argIn)
+{
+  enum SortType { SORT_T_TOTAL = 0, SORT_CORES, SORT_FILENAME };
+  const char* SortTypeStr[] = {"time", "total # cores", "file name"};
+  SortType sort = SORT_T_TOTAL;
+  std::string sortarg = argIn.GetStringKey("sortby");
+  if (!sortarg.empty()) {
+    if (sortarg == "time")
+      sort = SORT_T_TOTAL;
+    else if (sortarg == "cores")
+      sort = SORT_CORES;
+    else if (sortarg == "filename")
+      sort = SORT_FILENAME;
+    else {
+      mprinterr("Error: Unrecognized sort: %s\n", sortarg.c_str());
+      return CpptrajState::ERR;
+    }
+  }
+  mprintf("\tSort by %s.\n", SortTypeStr[sort]);
+
+  bool reverse_sort = argIn.hasKey("reverse");
+  if (reverse_sort)
+    mprintf("\tPerforming reverse sort.\n");
+
+  bool showdetails = argIn.hasKey("showdetails");
+  if (showdetails)
+    mprintf("\tWill print details for each run to STDOUT.\n");
+
+  bool include_bad = argIn.hasKey("includebad");
+  if (include_bad)
+    mprintf("\tIncluding bad results.\n");
+
+  DataFile* outfile = State.DFL().AddDataFile( argIn.GetStringKey("out"), argIn );
+  if (outfile != 0)
+    mprintf("\tOutput to file '%s'\n", outfile->DataFilename().full());
+
+  std::string groupOutArg = argIn.GetStringKey("groupout");
+  CpptrajFile* groupout = 0;
+  GroupType groupOpt = GROUPBY_PREFIX;
+  if (!groupOutArg.empty()) {
+    groupout = State.DFL().AddCpptrajFile(groupOutArg, "Timing by group", DataFileList::TEXT);
+    if (groupout == 0) {
+      mprinterr("Error: Could not add file '%s'\n", groupOutArg.c_str());
+      return CpptrajState::ERR;
+    }
+    mprintf("\tGroup output to '%s'\n", groupout->Filename().full());
+    // NOTE: groupby is already a keyword for standard data file output
+    std::string grouptypeArg = argIn.GetStringKey("grouptype");
+    if (!grouptypeArg.empty()) {
+      if (grouptypeArg == "prefix")
+        groupOpt = GROUPBY_PREFIX;
+      else if (grouptypeArg == "name")
+        groupOpt = GROUPBY_NAME;
+      else if (grouptypeArg == "kind")
+        groupOpt = GROUPBY_KIND;
+      else {
+        mprinterr("Error: Unrecognized option for 'grouptype': %s\n", grouptypeArg.c_str());
+        return CpptrajState::ERR;
+      }
+    }
+    static const char* GroupTypeStr[] = { "directory prefix", "run type name", "run kind" };
+    mprintf("\tGroup by %s.\n", GroupTypeStr[groupOpt]);
+  }
+
+  std::string dsname = argIn.GetStringKey("name");
+  if (dsname.empty())
+    dsname = State.DSL().GenerateDefaultName("TIMING");
+  mprintf("\tDataSet name: %s\n", dsname.c_str());
+
+  Xtype xvar;
+  Ytype yvar = Y_T_TOTAL;
+  Dimension Xdim;
+  //Dimension Ydim;
+
+  if (sort == SORT_CORES) {
+    xvar = X_CORES;
+    Xdim.SetLabel("Cores");
+  } else {
+    xvar = X_INDEX;
+    Xdim.SetLabel("Run");
+  }
+
+  bool needsDetailedTiming = false;
+  const char* YtypeStr[] = { "Total", "Trajectory Process", "Trajectory Read", "Action Frame" };
+  std::string typearg = argIn.GetStringKey("type");
+  if (typearg.empty())
+    yvar = Y_T_TOTAL;
+  else if (typearg == "trajproc")
+    yvar = Y_T_TRAJPROC;
+  else if (typearg == "trajread") {
+    yvar = Y_T_TRAJREAD;
+    needsDetailedTiming = true;
+  } else if (typearg == "actframe") {
+    yvar = Y_T_ACTFRAME;
+    needsDetailedTiming = true;
+  }
+  mprintf("\tUsing %s time.\n", YtypeStr[yvar]);
+  //Ydim.SetLabel("TotalTime");
+
+  // ----- Only file name args below here --------
+  File::NameArray FileNameList;
+
+  std::string filearg = argIn.GetStringNext();
+  while (!filearg.empty()) {
+    File::NameArray fnames = File::ExpandToFilenames( filearg );
+    if (fnames.empty()) {
+      mprintf("Warning: No files matching '%s'\n", filearg.c_str());
+    } else {
+      for (File::NameArray::const_iterator it = fnames.begin(); it != fnames.end(); ++it)
+        FileNameList.push_back( *it );
+    }
+    filearg = argIn.GetStringNext();
+  }
+
+  typedef std::vector<RunTiming> RunArray;
+  RunArray Runs;
+  Runs.reserve( FileNameList.size() );
+  for (File::NameArray::const_iterator it = FileNameList.begin(); it != FileNameList.end(); ++it) {
+    //mprintf("\t%s\n", it->full());
+    RunTiming thisRun = read_cpptraj_output( it->Full() );
+    if (thisRun.IsBad()) {
+      mprintf("Warning: Problem reading cpptraj output from '%s' : %s\n", it->full(), thisRun.ErrMsg().c_str());
+      if (include_bad)
+        Runs.push_back( thisRun );
+      //return CpptrajState::ERR;
+    } else {
+      Runs.push_back( thisRun );
+    }
+    //Runs.back().Print();
+    //mprintf("\n");
+  }
+  mprintf("\t%zu runs.\n", Runs.size());
+
+  // Check Runs
+  for (RunArray::const_iterator it = Runs.begin(); it != Runs.end(); ++it) {
+    if (needsDetailedTiming && !it->HasDetailedTiming()) {
+      mprinterr("Error: Detailed timing requested but output %s does not contain detailed timing.\n",
+                it->Filename().full());
+      //it->Print();
+      return CpptrajState::ERR;
+    }
+  }
+
+  // Sort runs
+  switch (sort) {
+    case SORT_T_TOTAL  : std::sort(Runs.begin(), Runs.end(), RunTiming::sort_by_total_time()); break;
+    case SORT_CORES    : std::sort(Runs.begin(), Runs.end(), RunTiming::sort_by_cores()); break;
+    case SORT_FILENAME : std::sort(Runs.begin(), Runs.end(), RunTiming::sort_by_filename()); break;
+  }
+
+  if (reverse_sort)
+    std::reverse( Runs.begin(), Runs.end() );
+
+  // Group runs - TODO use pointers?
+  if (groupout != 0) {
+    //groupout.OpenWrite("");
+    typedef std::map<std::string, RunArray> RunMap;
+    RunMap groupByPrefix;
+    // Reference Y for speedup will be the largest Y
+    double refY = 0;
+    double refCores = 0;
+    for (RunArray::const_iterator it = Runs.begin(); it != Runs.end(); ++it)
+    {
+      // Determine reference
+      double runY = YVAL(yvar, *it);
+      if (runY > refY) {
+        refY = runY;
+        refCores = (double)it->TotalCores();
+      }
+      // Insert into map by desired group type
+      std::string key;
+      switch (groupOpt) {
+        case GROUPBY_PREFIX : key = it->Prefix(); break;
+        case GROUPBY_NAME   : key = it->Name(); break;
+        case GROUPBY_KIND   :
+          key = it->Name()[0];
+          if (key[0] == 'H')
+            key.append(integerToString(it->Nthreads())); 
+          break;
+      }
+      RunMap::iterator jt = groupByPrefix.lower_bound( key );
+      if (jt == groupByPrefix.end() || jt->first != key )
+      {
+        // New group
+        jt = groupByPrefix.insert( jt, std::pair<std::string,RunArray>( key, RunArray() ) );
+      }
+      jt->second.push_back( *it );
+    }
+    mprintf("\tFound %zu groups.\n", groupByPrefix.size());
+    for (RunMap::const_iterator jt = groupByPrefix.begin(); jt != groupByPrefix.end(); ++jt)
+    {
+      groupout->Printf("#\t\t%s\n", jt->first.c_str());
+      write_to_file(*groupout, jt->second, xvar, yvar, refY, refCores);
+      //for (RunArray::const_iterator it = jt->second.begin(); it != jt->second.end(); ++it)
+      //  mprintf("\t\t\t%s\n", it->Filename().DirPrefix().c_str());
+    }
+  }
+
+  // Create DataSet
+  if (create_output_set(Runs, State.DSL(), outfile, dsname, Xdim, xvar, yvar))
+    return CpptrajState::ERR;
+  // Print details
+  if (showdetails) {
+    mprintf("\tRun details:\n");
+    for (RunArray::const_iterator it = Runs.begin(); it != Runs.end(); ++it) {
+      mprintf("\t\t");
+      it->Print();
+    }
+  }
+  return CpptrajState::OK;
+}
diff --git a/src/Exec_ParseTiming.h b/src/Exec_ParseTiming.h
new file mode 100644
index 0000000000..b89e147134
--- /dev/null
+++ b/src/Exec_ParseTiming.h
@@ -0,0 +1,30 @@
+#ifndef INC_EXEC_PARSETIMING_H
+#define INC_EXEC_PARSETIMING_H
+#include "Exec.h"
+/// For extracting and parsing timing data from cpptraj output 
+class Exec_ParseTiming : public Exec {
+  public:
+    Exec_ParseTiming();
+    void Help() const;
+    DispatchObject* Alloc() const { return (DispatchObject*)new Exec_ParseTiming(); }
+    RetType Execute(CpptrajState&, ArgList&);
+  private:
+    typedef std::vector<double> Darray;
+    class RunTiming;
+    typedef std::vector<RunTiming> RunArray;
+
+    // Which variables to plot
+    enum Xtype { X_INDEX=0, X_CORES };
+    enum Ytype { Y_T_TOTAL=0, Y_T_TRAJPROC, Y_T_TRAJREAD, Y_T_ACTFRAME };
+    // Groupo types. NOTE: Update GroupTypeStr in Exec_ParseTiming.cpp
+    enum GroupType { GROUPBY_PREFIX = 0, GROUPBY_NAME, GROUPBY_KIND };
+
+    static inline double YVAL(Ytype, RunTiming const&);
+
+    RunTiming read_cpptraj_output(std::string const&);
+    int create_output_set(RunArray const&, DataSetList&, DataFile*,
+                          std::string const&, Dimension const&,
+                          Xtype, Ytype) const;
+    void write_to_file(CpptrajFile&, RunArray const&, Xtype, Ytype, double, double) const;
+};
+#endif
diff --git a/src/FileName.h b/src/FileName.h
index 5a70641e75..8ac9f6eb27 100644
--- a/src/FileName.h
+++ b/src/FileName.h
@@ -28,15 +28,28 @@ class FileName {
     void clear();
     /// \return true if string matches full or base file name.
     bool MatchFullOrBase(std::string const&) const;
-
+    /// \return the full file path
     const std::string& Full()      const { return fullPathName_;         }
+    /// \return only the base file name
     const std::string& Base()      const { return baseName_;             }
+    /// \return only the base file name extension
     const std::string& Ext()       const { return extension_;            }
+    /// \return the full file path (const char*)
     const char* full()             const { return fullPathName_.c_str(); }
+    /// \return only the base file name (const char*)
     const char* base()             const { return baseName_.c_str();     }
+    /// \return only the base file name extension (const char*)
     const char* ext()              const { return extension_.c_str();    }
+    /// \return Recognized compression extension if present
     const std::string& Compress()  const { return compressExt_;          }
+    /// \return the directory prefix, including the trailing slash
     const std::string& DirPrefix() const { return dirPrefix_;            }
+    /// \return the directory prefix, no trailing slash
+    std::string DirPrefix_NoSlash() const {
+      if (dirPrefix_.empty()) return dirPrefix_;
+      return dirPrefix_.substr(0, dirPrefix_.size()-1);
+    }
+    /// \return true if the file name is not set
     bool empty()                   const { return fullPathName_.empty(); }
   private:
     std::string fullPathName_;
diff --git a/src/Frame.cpp b/src/Frame.cpp
index abd8d91c1d..ef3f206fcc 100644
--- a/src/Frame.cpp
+++ b/src/Frame.cpp
@@ -484,6 +484,20 @@ int Frame::SetupFrameFromMask(AtomMask const& maskIn, std::vector<Atom> const& a
   return 0; 
 }
 
+/** Set up frame to hold # selected atoms in given mask based on
+  * given array of atoms and coordinate info.
+  */
+int Frame::SetupFrameFromMask(AtomMask const& maskIn, std::vector<Atom> const& atoms,
+                              CoordinateInfo const& cinfo)
+{
+  setupFrame( maskIn.Nselected(), cinfo );
+  Mass_.clear();
+  Mass_.reserve( maskIn.Nselected() );
+  for (AtomMask::const_iterator atom = maskIn.begin(); atom != maskIn.end(); ++atom) 
+    Mass_.push_back( atoms[ *atom ].Mass() );
+  return 0;
+}
+
 // ---------- FRAME Add/remove components --------------------------------------
 int Frame::AddVelocities(Darray const& vIn) {
   if ((int)vIn.size() != ncoord_) {
diff --git a/src/Frame.h b/src/Frame.h
index 5f543fdb23..041ade57e0 100644
--- a/src/Frame.h
+++ b/src/Frame.h
@@ -154,6 +154,8 @@ class Frame {
     int SetupFrameV(std::vector<Atom> const&, CoordinateInfo const&);
     /// Allocate frame for selected # atoms, coords/mass only.
     int SetupFrameFromMask(AtomMask const&, std::vector<Atom> const&);
+    /// Allocate frame for selected # atoms and coordinate info.
+    int SetupFrameFromMask(AtomMask const&, std::vector<Atom> const&, CoordinateInfo const&);
     // ----- Add/remove components from Frame ----
     int AddVelocities(Darray const&);
     void RemoveVelocities();
diff --git a/src/Vec3.h b/src/Vec3.h
index 4fe4e960ff..eea7c70d3d 100644
--- a/src/Vec3.h
+++ b/src/Vec3.h
@@ -94,6 +94,10 @@ class Vec3 {
                    (V_[2]*rhs.V_[0]) - (V_[0]*rhs.V_[2]),   // UZVX+UXVZ
                    (V_[0]*rhs.V_[1]) - (V_[1]*rhs.V_[0]) ); // UXVY+UYVX
     }
+    /// \return New vector with each element squared
+    Vec3 Squared() const {
+      return Vec3(V_[0]*V_[0], V_[1]*V_[1], V_[2]*V_[2]);
+    }
     // TODO: Make const ref only?
     double  operator[](int idx) const { return V_[idx]; }
     double& operator[](int idx)       { return V_[idx]; }
diff --git a/src/Version.h b/src/Version.h
index cc77287f99..5cac8ee66b 100644
--- a/src/Version.h
+++ b/src/Version.h
@@ -12,7 +12,7 @@
  * Whenever a number that precedes <revision> is incremented, all subsequent
  * numbers should be reset to 0.
  */
-#define CPPTRAJ_INTERNAL_VERSION "V6.20.2"
+#define CPPTRAJ_INTERNAL_VERSION "V6.20.3"
 /// PYTRAJ relies on this
 #define CPPTRAJ_VERSION_STRING CPPTRAJ_INTERNAL_VERSION
 #endif
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index fc2b98a05b..f08f79a7a3 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -131,6 +131,7 @@ Analysis_Spline.o : Analysis_Spline.cpp ActionState.h Analysis.h AnalysisState.h
 Analysis_State.o : Analysis_State.cpp ActionState.h Analysis.h AnalysisState.h Analysis_State.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Analysis_Statistics.o : Analysis_Statistics.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Statistics.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_float.h DataSet_integer.h DataSet_string.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Analysis_TI.o : Analysis_TI.cpp ActionState.h Analysis.h AnalysisState.h Analysis_TI.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_TICA.o : Analysis_TICA.cpp ActionState.h Analysis.h AnalysisState.h Analysis_TICA.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Analysis_Timecorr.o : Analysis_Timecorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Timecorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Analysis_VectorMath.o : Analysis_VectorMath.cpp ActionState.h Analysis.h AnalysisState.h Analysis_VectorMath.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Analysis_Wavelet.o : Analysis_Wavelet.cpp ActionFrameCounter.h ActionState.h Analysis.h AnalysisState.h Analysis_Wavelet.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ClusterMap.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h ProgressBar.h ProgressTimer.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
@@ -185,7 +186,7 @@ ClusterMap.o : ClusterMap.cpp AssociatedData.h ClusterMap.h Constants.h CpptrajF
 Cmd.o : Cmd.cpp Cmd.h DispatchObject.h
 CmdInput.o : CmdInput.cpp CmdInput.h StringRoutines.h
 CmdList.o : CmdList.cpp Cmd.h CmdList.h DispatchObject.h
-Command.o : Command.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h ActionTopWriter.h Action_Align.h Action_Angle.h Action_AreaPerMol.h Action_AtomMap.h Action_AtomicCorr.h Action_AtomicFluct.h Action_AutoImage.h Action_Average.h Action_AvgBox.h Action_Bounds.h Action_Box.h Action_Center.h Action_Channel.h Action_CheckChirality.h Action_CheckStructure.h Action_Closest.h Action_ClusterDihedral.h Action_Contacts.h Action_CreateCrd.h Action_CreateReservoir.h Action_DNAionTracker.h Action_DSSP.h Action_Density.h Action_Diffusion.h Action_Dihedral.h Action_DihedralRMS.h Action_Dipole.h Action_DistRmsd.h Action_Distance.h Action_Energy.h Action_Esander.h Action_FilterByData.h Action_FixAtomOrder.h Action_FixImagedBonds.h Action_GIST.h Action_Grid.h Action_GridFreeEnergy.h Action_HydrogenBond.h Action_Image.h Action_InfraredSpectrum.h Action_Jcoupling.h Action_Keep.h Action_LESsplit.h Action_LIE.h Action_LipidOrder.h Action_MakeStructure.h Action_Mask.h Action_Matrix.h Action_MinImage.h Action_Molsurf.h Action_MultiDihedral.h Action_MultiPucker.h Action_MultiVector.h Action_NAstruct.h Action_NMRrst.h Action_NativeContacts.h Action_OrderParameter.h Action_Outtraj.h Action_PairDist.h Action_Pairwise.h Action_Principal.h Action_Projection.h Action_Pucker.h Action_Radgyr.h Action_Radial.h Action_RandomizeIons.h Action_Remap.h Action_ReplicateCell.h Action_Rmsd.h Action_Rotate.h Action_RunningAvg.h Action_STFC_Diffusion.h Action_Scale.h Action_SetVelocity.h Action_Spam.h Action_Strip.h Action_Surf.h Action_SymmetricRmsd.h Action_Temperature.h Action_Time.h Action_ToroidalDiffusion.h Action_Translate.h Action_Unstrip.h Action_Unwrap.h Action_Vector.h Action_VelocityAutoCorr.h Action_Volmap.h Action_Volume.h Action_Watershell.h Action_XtalSymm.h Analysis.h AnalysisList.h AnalysisState.h Analysis_AmdBias.h Analysis_AutoCorr.h Analysis_Average.h Analysis_CalcDiffusion.h Analysis_Clustering.h Analysis_ConstantPHStats.h Analysis_Corr.h Analysis_CrankShaft.h Analysis_CrdFluct.h Analysis_CrossCorr.h Analysis_CurveFit.h Analysis_Divergence.h Analysis_EvalPlateau.h Analysis_FFT.h Analysis_HausdorffDistance.h Analysis_Hist.h Analysis_IRED.h Analysis_Integrate.h Analysis_KDE.h Analysis_Lifetime.h Analysis_LowestCurve.h Analysis_Matrix.h Analysis_MeltCurve.h Analysis_Modes.h Analysis_MultiHist.h Analysis_Multicurve.h Analysis_Overlap.h Analysis_PhiPsi.h Analysis_Regression.h Analysis_RemLog.h Analysis_Rms2d.h Analysis_RmsAvgCorr.h Analysis_Rotdif.h Analysis_RunningAvg.h Analysis_Slope.h Analysis_Spline.h Analysis_State.h Analysis_Statistics.h Analysis_TI.h Analysis_Timecorr.h Analysis_VectorMath.h Analysis_Wavelet.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h AxisType.h BaseIOtype.h Box.h BoxArgs.h BufferedLine.h CharMask.h Cluster/Algorithm.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DrawGraph.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Sieve.h Cluster/Silhouette.h ClusterMap.h Cmd.h CmdInput.h CmdList.h Command.h CompactFrameArray.h ComplexArray.h Constants.h Constraints.h ControlBlock.h ControlBlock_For.h CoordinateInfo.h Corr.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_RemLog.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h Deprecated.h DiffusionResults.h DihedralSearch.h Dimension.h DispatchObject.h Energy.h Energy_Sander.h EnsembleIn.h EnsembleOutList.h Ewald.h EwaldOptions.h Ewald_ParticleMesh.h ExclusionArray.h Exec.h Exec_AddMissingRes.h Exec_Analyze.h Exec_Calc.h Exec_CatCrd.h Exec_Change.h Exec_ClusterMap.h Exec_CombineCoords.h Exec_Commands.h Exec_CompareClusters.h Exec_CompareEnergy.h Exec_CompareTop.h Exec_CrdAction.h Exec_CrdOut.h Exec_CreateSet.h Exec_DataFile.h Exec_DataFilter.h Exec_DataSetCmd.h Exec_Emin.h Exec_Flatten.h Exec_GenerateAmberRst.h Exec_Graft.h Exec_Help.h Exec_HmassRepartition.h Exec_LoadCrd.h Exec_LoadTraj.h Exec_ParallelAnalysis.h Exec_ParmBox.h Exec_ParmSolvent.h Exec_ParmStrip.h Exec_ParmWrite.h Exec_PermuteDihedrals.h Exec_Precision.h Exec_PrepareForLeap.h Exec_PrintData.h Exec_Random.h Exec_ReadData.h Exec_ReadEnsembleData.h Exec_ReadInput.h Exec_RotateDihedral.h Exec_RunAnalysis.h Exec_ScaleDihedralK.h Exec_SequenceAlign.h Exec_Set.h Exec_Show.h Exec_SortEnsembleData.h Exec_SplitCoords.h Exec_System.h Exec_Top.h Exec_Traj.h Exec_UpdateParameters.h Exec_ViewRst.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h GIST_PME.h Grid.h GridAction.h GridBin.h HistBin.h Hungarian.h ImageOption.h ImageTypes.h InputTrajCommon.h MapAtom.h MaskArray.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h OnlineVarT.h OutputTrajCommon.h PDBfile.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h RPNcalc.h Random.h Range.h ReferenceAction.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h SplineFxnTable.h StructureCheck.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/GistCudaSetup.cuh helpme_standalone.h molsurf.h
+Command.o : Command.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h ActionTopWriter.h Action_Align.h Action_Angle.h Action_AreaPerMol.h Action_AtomMap.h Action_AtomicCorr.h Action_AtomicFluct.h Action_AutoImage.h Action_Average.h Action_AvgBox.h Action_Bounds.h Action_Box.h Action_Center.h Action_Channel.h Action_CheckChirality.h Action_CheckStructure.h Action_Closest.h Action_ClusterDihedral.h Action_Contacts.h Action_CreateCrd.h Action_CreateReservoir.h Action_DNAionTracker.h Action_DSSP.h Action_Density.h Action_Diffusion.h Action_Dihedral.h Action_DihedralRMS.h Action_Dipole.h Action_DistRmsd.h Action_Distance.h Action_Energy.h Action_Esander.h Action_FilterByData.h Action_FixAtomOrder.h Action_FixImagedBonds.h Action_GIST.h Action_Grid.h Action_GridFreeEnergy.h Action_HydrogenBond.h Action_Image.h Action_InfraredSpectrum.h Action_Jcoupling.h Action_Keep.h Action_LESsplit.h Action_LIE.h Action_LipidOrder.h Action_MakeStructure.h Action_Mask.h Action_Matrix.h Action_MinImage.h Action_Molsurf.h Action_MultiDihedral.h Action_MultiPucker.h Action_MultiVector.h Action_NAstruct.h Action_NMRrst.h Action_NativeContacts.h Action_OrderParameter.h Action_Outtraj.h Action_PairDist.h Action_Pairwise.h Action_Principal.h Action_Projection.h Action_Pucker.h Action_Radgyr.h Action_Radial.h Action_RandomizeIons.h Action_Remap.h Action_ReplicateCell.h Action_Rmsd.h Action_Rotate.h Action_RunningAvg.h Action_STFC_Diffusion.h Action_Scale.h Action_SetVelocity.h Action_Spam.h Action_Strip.h Action_Surf.h Action_SymmetricRmsd.h Action_Temperature.h Action_Time.h Action_ToroidalDiffusion.h Action_Translate.h Action_Unstrip.h Action_Unwrap.h Action_Vector.h Action_VelocityAutoCorr.h Action_Volmap.h Action_Volume.h Action_Watershell.h Action_XtalSymm.h Analysis.h AnalysisList.h AnalysisState.h Analysis_AmdBias.h Analysis_AutoCorr.h Analysis_Average.h Analysis_CalcDiffusion.h Analysis_Clustering.h Analysis_ConstantPHStats.h Analysis_Corr.h Analysis_CrankShaft.h Analysis_CrdFluct.h Analysis_CrossCorr.h Analysis_CurveFit.h Analysis_Divergence.h Analysis_EvalPlateau.h Analysis_FFT.h Analysis_HausdorffDistance.h Analysis_Hist.h Analysis_IRED.h Analysis_Integrate.h Analysis_KDE.h Analysis_Lifetime.h Analysis_LowestCurve.h Analysis_Matrix.h Analysis_MeltCurve.h Analysis_Modes.h Analysis_MultiHist.h Analysis_Multicurve.h Analysis_Overlap.h Analysis_PhiPsi.h Analysis_Regression.h Analysis_RemLog.h Analysis_Rms2d.h Analysis_RmsAvgCorr.h Analysis_Rotdif.h Analysis_RunningAvg.h Analysis_Slope.h Analysis_Spline.h Analysis_State.h Analysis_Statistics.h Analysis_TI.h Analysis_TICA.h Analysis_Timecorr.h Analysis_VectorMath.h Analysis_Wavelet.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h AxisType.h BaseIOtype.h Box.h BoxArgs.h BufferedLine.h CharMask.h Cluster/Algorithm.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DrawGraph.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Sieve.h Cluster/Silhouette.h ClusterMap.h Cmd.h CmdInput.h CmdList.h Command.h CompactFrameArray.h ComplexArray.h Constants.h Constraints.h ControlBlock.h ControlBlock_For.h CoordinateInfo.h Corr.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_RemLog.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h Deprecated.h DiffusionResults.h DihedralSearch.h Dimension.h DispatchObject.h Energy.h Energy_Sander.h EnsembleIn.h EnsembleOutList.h Ewald.h EwaldOptions.h Ewald_ParticleMesh.h ExclusionArray.h Exec.h Exec_AddMissingRes.h Exec_Analyze.h Exec_Calc.h Exec_CatCrd.h Exec_Change.h Exec_ClusterMap.h Exec_CombineCoords.h Exec_Commands.h Exec_CompareClusters.h Exec_CompareEnergy.h Exec_CompareTop.h Exec_CrdAction.h Exec_CrdOut.h Exec_CreateSet.h Exec_DataFile.h Exec_DataFilter.h Exec_DataSetCmd.h Exec_Emin.h Exec_Flatten.h Exec_GenerateAmberRst.h Exec_Graft.h Exec_Help.h Exec_HmassRepartition.h Exec_LoadCrd.h Exec_LoadTraj.h Exec_ParallelAnalysis.h Exec_ParmBox.h Exec_ParmSolvent.h Exec_ParmStrip.h Exec_ParmWrite.h Exec_ParseTiming.h Exec_PermuteDihedrals.h Exec_Precision.h Exec_PrepareForLeap.h Exec_PrintData.h Exec_Random.h Exec_ReadData.h Exec_ReadEnsembleData.h Exec_ReadInput.h Exec_RotateDihedral.h Exec_RunAnalysis.h Exec_ScaleDihedralK.h Exec_SequenceAlign.h Exec_Set.h Exec_Show.h Exec_SortEnsembleData.h Exec_SplitCoords.h Exec_System.h Exec_Top.h Exec_Traj.h Exec_UpdateParameters.h Exec_ViewRst.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h GIST_PME.h Grid.h GridAction.h GridBin.h HistBin.h Hungarian.h ImageOption.h ImageTypes.h InputTrajCommon.h MapAtom.h MaskArray.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h OnlineVarT.h OutputTrajCommon.h PDBfile.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h RPNcalc.h Random.h Range.h ReferenceAction.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h SplineFxnTable.h StructureCheck.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/GistCudaSetup.cuh helpme_standalone.h molsurf.h
 CompactFrameArray.o : CompactFrameArray.cpp Box.h CompactFrameArray.h CoordinateInfo.h CpptrajStdio.h Matrix_3x3.h Parallel.h ReplicaDimArray.h Vec3.h
 ComplexArray.o : ComplexArray.cpp ArrayIterator.h ComplexArray.h
 Constraints.o : Constraints.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
@@ -308,6 +309,7 @@ Exec_ParmBox.o : Exec_ParmBox.cpp Action.h ActionList.h ActionState.h Analysis.h
 Exec_ParmSolvent.o : Exec_ParmSolvent.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmSolvent.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_ParmStrip.o : Exec_ParmStrip.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmStrip.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_ParmWrite.o : Exec_ParmWrite.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmWrite.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_ParseTiming.o : Exec_ParseTiming.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParseTiming.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_PermuteDihedrals.o : Exec_PermuteDihedrals.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h DistRoutines.h EnsembleIn.h EnsembleOutList.h ExclusionArray.h Exec.h Exec_PermuteDihedrals.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Precision.o : Exec_Precision.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Precision.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_PrepareForLeap.o : Exec_PrepareForLeap.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_PrepareForLeap.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h LeapInterface.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h Structure/Disulfide.h Structure/HisProt.h Structure/ResStatArray.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarToken.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
diff --git a/src/cpptrajfiles b/src/cpptrajfiles
index d26287fa65..cca042ad42 100644
--- a/src/cpptrajfiles
+++ b/src/cpptrajfiles
@@ -134,6 +134,7 @@ COMMON_SOURCES= \
         Analysis_State.cpp \
         Analysis_Statistics.cpp \
         Analysis_TI.cpp \
+        Analysis_TICA.cpp \
         Analysis_Timecorr.cpp \
         Analysis_VectorMath.cpp \
         Analysis_Wavelet.cpp \
@@ -278,6 +279,7 @@ COMMON_SOURCES= \
         Exec_ParmSolvent.cpp \
         Exec_ParmStrip.cpp \
         Exec_ParmWrite.cpp \
+        Exec_ParseTiming.cpp \
         Exec_PermuteDihedrals.cpp \
         Exec_Precision.cpp \
         Exec_PrepareForLeap.cpp \
diff --git a/test/Makefile b/test/Makefile
index 02acb7ddd8..efc11e1fd6 100644
--- a/test/Makefile
+++ b/test/Makefile
@@ -521,6 +521,9 @@ test.tordiff:
 test.calcdiffusion:
 	@-cd Test_CalcDiffusion && ./RunTest.sh $(OPT)
 
+test.parsetiming:
+	@-cd Test_ParseTiming && ./RunTest.sh $(OPT)
+
 # Every test target should go here.
 COMPLETETESTS=test.general \
               test.strip \
@@ -685,7 +688,8 @@ COMPLETETESTS=test.general \
               test.compareenergy \
               test.avgbox \
               test.tordiff \
-              test.calcdiffusion
+              test.calcdiffusion \
+              test.parsetiming
 
 test.all:
 	$(MAKE) test.complete summary
diff --git a/test/Test_ParseTiming/RunTest.sh b/test/Test_ParseTiming/RunTest.sh
new file mode 100755
index 0000000000..ec72199851
--- /dev/null
+++ b/test/Test_ParseTiming/RunTest.sh
@@ -0,0 +1,22 @@
+#!/bin/bash
+
+. ../MasterTest.sh
+
+TESTNAME='Parse timing tests'
+
+CleanFiles parse.in parse.dat parse.out
+
+INPUT='-i parse.in'
+
+UNITNAME='Parse timing test'
+cat > parse.in <<EOF
+parsetiming hpod13-n.16-N.4-c.4.out hpod13-n.4-N.1-c.4.out hpod13-n.8-N.2-c.4.out \
+  sortby time out parse.dat includebad groupout parse.out grouptype kind showdetails name Run
+list
+EOF
+RunCpptraj "$UNITNAME"
+DoTest parse.dat.save parse.dat
+DoTest parse.out.save parse.out
+
+EndTest
+
diff --git a/test/Test_ParseTiming/hpod13-n.16-N.4-c.4.out b/test/Test_ParseTiming/hpod13-n.16-N.4-c.4.out
new file mode 100644
index 0000000000..bfced0a4da
--- /dev/null
+++ b/test/Test_ParseTiming/hpod13-n.16-N.4-c.4.out
@@ -0,0 +1,157 @@
+JobID: 19616409
+NodeList: p13n[1-4]
+SLURM_NODELIST=p13n[1-4]
+SLURM_JOB_NAME=t.gcc_8.2-cuda_11.8.0-mvapich2_2.3.7.hpod13-n.16-N.4-c.4
+SLURMD_NODENAME=p13n1
+SLURM_TOPOLOGY_ADDR=p13n1
+SLURM_PRIO_PROCESS=0
+SLURM_NODE_ALIASES=(null)
+SLURM_JOB_QOS=normal
+SLURM_TOPOLOGY_ADDR_PATTERN=node
+SLURM_NNODES=4
+SLURM_JOBID=19616409
+SLURM_NTASKS=16
+SLURM_TASKS_PER_NODE=4(x4)
+SLURM_WORKING_CLUSTER=lobos:slurmctl:6817:9728:109
+SLURM_CONF=/usr/local/slurm-22.05.8/etc/slurm.conf
+SLURM_JOB_ID=19616409
+SLURM_CPUS_PER_TASK=4
+SLURM_JOB_USER=droe
+SLURM_JOB_UID=27798
+SLURM_NODEID=0
+SLURM_SUBMIT_DIR=/u/droe/Benchmarks/Cpptraj_calcdiffusion/Cpptraj_calcrdf_MpiBenchmarks.hpod13.forTalk/test.gcc_8.2-cuda_11.8.0-mvapich2_2.3.7/hpod13-n.16-N.4-c.4
+SLURM_TASK_PID=29469
+SLURM_NPROCS=16
+SLURM_CPUS_ON_NODE=32
+SLURM_PROCID=0
+SLURM_JOB_NODELIST=p13n[1-4]
+SLURM_LOCALID=0
+SLURM_JOB_GID=9000
+SLURM_JOB_CPUS_PER_NODE=32(x4)
+SLURM_CLUSTER_NAME=lobos
+SLURM_GTIDS=0
+SLURM_SUBMIT_HOST=tesla2.lobos.nih.gov
+SLURM_JOB_PARTITION=hpod13
+SLURM_JOB_ACCOUNT=cbs
+SLURM_JOB_NUM_NODES=4
+LMOD_FAMILY_CUDA=cuda
+LMOD_FAMILY_CUDA_VERSION=11.8.0
+CUDA_HOME=/v/apps/cuda/11.8.0
+OPENMM_CUDA_COMPILER=/v/apps/cuda/11.8.0/bin/nvcc
+
+CPPTRAJ: Trajectory Analysis. V6.20.2 (GitHub) MPI OpenMP
+    ___  ___  ___  ___
+     | \/ | \/ | \/ | 
+    _|_/\_|_/\_|_/\_|_
+
+| Running on 16 processes.
+| 4 OpenMP threads available.
+| Date/time: 08/09/23 10:34:15
+| Available memory: 30.530 GB
+
+INPUT: Reading input from 'cpptraj.in'
+  [parm /u/rvenable/RvProj/Unwrap/Water/box34x.psf]
+	Reading '/u/rvenable/RvProj/Unwrap/Water/box34x.psf' as Charmm PSF
+    Reading Charmm PSF file box34x.psf as topology file.
+Warning: PSF has no dihedrals.
+Warning: PSF has no impropers.
+	PSF contains 4020 atoms, 1340 residues.
+Warning: Determining bond length parameters from element types for 'box34x.psf'.
+  [set PREFIX = fromtraj.nvt]
+	Variable 'PREFIX' set to 'fromtraj.nvt'
+  [trajin /u/droe/Local_work/For/Rick/npt.diffusion/nvt.unwrap.dcd 1 30000 1]
+	Reading '/u/droe/Local_work/For/Rick/npt.diffusion/nvt.unwrap.dcd' as Charmm DCD
+	Version >= 22; assuming shape matrix is stored.
+Warning: Trajectory box type is 'Cubic' but topology box type is 'None'.
+Warning: Setting topology box information from trajectory.
+  [rdf out fromtraj.nvt.wato.agr :TIP3@OH2 0.1 12]
+    RADIAL: Calculating RDF for atoms in mask1 [:TIP3@OH2] to atoms in mask2 [:TIP3@OH2]
+	Output to fromtraj.nvt.wato.agr.
+	Histogram max 12.000000, spacing 0.100000, bins 120.
+	Normalizing using particle density of 0.033456 molecules/Ang^3.
+	Parallelizing RDF calculation with 4 threads.
+---------- RUN BEGIN -------------------------------------------------
+
+PARAMETER FILES (1 total):
+ 0: box34x.psf, 4020 atoms, 1340 res, box: Cubic, 1340 mol, 1340 solvent
+
+INPUT TRAJECTORIES (1 total):
+ 0: 'nvt.unwrap.dcd' is a CHARMM DCD file (coords) Little Endian 32 bit, Parm box34x.psf (Cubic box) (reading 30000 of 1010000)
+  Coordinate processing will occur on 30000 frames.
+
+PARALLEL INFO:
+  Process 0 will handle 1875 frames.
+  Process 1 will handle 1875 frames.
+  Process 2 will handle 1875 frames.
+  Process 3 will handle 1875 frames.
+  Process 4 will handle 1875 frames.
+  Process 5 will handle 1875 frames.
+  Process 6 will handle 1875 frames.
+  Process 7 will handle 1875 frames.
+  Process 8 will handle 1875 frames.
+  Process 9 will handle 1875 frames.
+  Process 10 will handle 1875 frames.
+  Process 11 will handle 1875 frames.
+  Process 12 will handle 1875 frames.
+  Process 13 will handle 1875 frames.
+  Process 14 will handle 1875 frames.
+  Process 15 will handle 1875 frames.
+.....................................................
+ACTION SETUP FOR PARM 'box34x.psf' (1 actions):
+  0: [rdf out fromtraj.nvt.wato.agr :TIP3@OH2 0.1 12]
+	1340 atoms in Mask1, 1340 atoms in Mask2
+	Imaging on.
+
+BEGIN PARALLEL TRAJECTORY PROCESSING:
+ 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
+TIME: Rank 0 throughput= 130.1740 frames / second.
+TIME: Rank 1 throughput= 98.4571 frames / second.
+TIME: Rank 2 throughput= 89.5782 frames / second.
+TIME: Rank 3 throughput= 84.6900 frames / second.
+TIME: Rank 4 throughput= 80.6405 frames / second.
+TIME: Rank 5 throughput= 78.1665 frames / second.
+TIME: Rank 6 throughput= 76.6285 frames / second.
+TIME: Rank 7 throughput= 74.9952 frames / second.
+TIME: Rank 8 throughput= 73.1935 frames / second.
+TIME: Rank 9 throughput= 71.8725 frames / second.
+TIME: Rank 10 throughput= 70.3985 frames / second.
+TIME: Rank 11 throughput= 69.6566 frames / second.
+TIME: Rank 12 throughput= 68.7572 frames / second.
+TIME: Rank 13 throughput= 67.8059 frames / second.
+TIME: Rank 14 throughput= 66.6708 frames / second.
+TIME: Rank 15 throughput= 65.8386 frames / second.
+TIME: Avg. throughput= 1053.4124 frames / second.
+
+ACTION OUTPUT:
+    RADIAL: 30000 frames, # in mask1= 1340, # in mask2 = 1340, # in common = 1340
+	Density is 44.797584 distances / Ang^3.
+TIME: Analyses took 0.0000 seconds.
+
+DATASETS (2 total):
+	PREFIX "PREFIX" (string variable), size is 1 (0.044 kB)
+	g(r)_00002 ":TIP3@OH2 => :TIP3@OH2" (double), size is 120 (0.960 kB)
+    Total data set memory usage is at least 1.004 kB
+
+DATAFILES (1 total):
+  fromtraj.nvt.wato.agr (Grace File):  :TIP3@OH2 => :TIP3@OH2
+
+RUN TIMING:
+TIME:		Init               : 0.0017 s (  0.01%)
+TIME:		Trajectory Process : 28.4789 s ( 99.99%)
+TIME:		Data Set Sync      : 0.0002 s (  0.00%)
+TIME:		Action Post        : 0.0001 s (  0.00%)
+TIME:		Analysis           : 0.0000 s (  0.00%)
+TIME:		Data File Write    : 0.0014 s (  0.00%)
+TIME:		Other              : 0.0010 s (  0.00%)
+TIME:	Run Total 28.4831 s
+---------- RUN END ---------------------------------------------------
+TIME: Total execution time: 28.5628 seconds.
+--------------------------------------------------------------------------------
+To cite CPPTRAJ use:
+Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for
+  Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem.
+  Theory Comput., 2013, 9 (7), pp 3084-3095.
+Daniel R. Roe and Thomas E. Cheatham, III, "Parallelization of CPPTRAJ enables
+  large scale analysis of molecular dynamics trajectory data". J. Comp.
+  Chem., 2018, DOI: 10.1002/jcc25382.
+
diff --git a/test/Test_ParseTiming/hpod13-n.4-N.1-c.4.out b/test/Test_ParseTiming/hpod13-n.4-N.1-c.4.out
new file mode 100644
index 0000000000..abc87e7b40
--- /dev/null
+++ b/test/Test_ParseTiming/hpod13-n.4-N.1-c.4.out
@@ -0,0 +1,129 @@
+JobID: 19615041
+NodeList: p13n1
+SLURM_NODELIST=p13n1
+SLURM_JOB_NAME=t.gcc_8.2-cuda_11.8.0-mvapich2_2.3.7.hpod13-n.4-N.1-c.4
+SLURMD_NODENAME=p13n1
+SLURM_TOPOLOGY_ADDR=p13n1
+SLURM_PRIO_PROCESS=0
+SLURM_NODE_ALIASES=(null)
+SLURM_JOB_QOS=normal
+SLURM_TOPOLOGY_ADDR_PATTERN=node
+SLURM_NNODES=1
+SLURM_JOBID=19615041
+SLURM_NTASKS=4
+SLURM_TASKS_PER_NODE=4
+SLURM_WORKING_CLUSTER=lobos:slurmctl:6817:9728:109
+SLURM_CONF=/usr/local/slurm-22.05.8/etc/slurm.conf
+SLURM_JOB_ID=19615041
+SLURM_CPUS_PER_TASK=4
+SLURM_JOB_USER=droe
+SLURM_JOB_UID=27798
+SLURM_NODEID=0
+SLURM_SUBMIT_DIR=/u/droe/Benchmarks/Cpptraj_calcdiffusion/Cpptraj_calcrdf_MpiBenchmarks.hpod13.forTalk/test.gcc_8.2-cuda_11.8.0-mvapich2_2.3.7/hpod13-n.4-N.1-c.4
+SLURM_TASK_PID=15466
+SLURM_NPROCS=4
+SLURM_CPUS_ON_NODE=32
+SLURM_PROCID=0
+SLURM_JOB_NODELIST=p13n1
+SLURM_LOCALID=0
+SLURM_JOB_GID=9000
+SLURM_JOB_CPUS_PER_NODE=32
+SLURM_CLUSTER_NAME=lobos
+SLURM_GTIDS=0
+SLURM_SUBMIT_HOST=tesla2.lobos.nih.gov
+SLURM_JOB_PARTITION=hpod13
+SLURM_JOB_ACCOUNT=cbs
+SLURM_JOB_NUM_NODES=1
+
+CPPTRAJ: Trajectory Analysis. V6.20.2 (GitHub) MPI OpenMP
+    ___  ___  ___  ___
+     | \/ | \/ | \/ | 
+    _|_/\_|_/\_|_/\_|_
+
+| Running on 4 processes.
+| 4 OpenMP threads available.
+| Date/time: 08/08/23 13:33:15
+| Available memory: 31.007 GB
+
+INPUT: Reading input from 'cpptraj.in'
+  [parm /u/rvenable/RvProj/Unwrap/Water/box34x.psf]
+	Reading '/u/rvenable/RvProj/Unwrap/Water/box34x.psf' as Charmm PSF
+    Reading Charmm PSF file box34x.psf as topology file.
+Warning: PSF has no dihedrals.
+Warning: PSF has no impropers.
+	PSF contains 4020 atoms, 1340 residues.
+Warning: Determining bond length parameters from element types for 'box34x.psf'.
+  [set PREFIX = fromtraj.nvt]
+	Variable 'PREFIX' set to 'fromtraj.nvt'
+  [trajin /u/droe/Local_work/For/Rick/npt.diffusion/nvt.unwrap.dcd 1 30000 1]
+	Reading '/u/droe/Local_work/For/Rick/npt.diffusion/nvt.unwrap.dcd' as Charmm DCD
+	Version >= 22; assuming shape matrix is stored.
+Warning: Trajectory box type is 'Cubic' but topology box type is 'None'.
+Warning: Setting topology box information from trajectory.
+  [rdf out fromtraj.nvt.wato.agr :TIP3@OH2 0.1 12]
+    RADIAL: Calculating RDF for atoms in mask1 [:TIP3@OH2] to atoms in mask2 [:TIP3@OH2]
+	Output to fromtraj.nvt.wato.agr.
+	Histogram max 12.000000, spacing 0.100000, bins 120.
+	Normalizing using particle density of 0.033456 molecules/Ang^3.
+	Parallelizing RDF calculation with 4 threads.
+---------- RUN BEGIN -------------------------------------------------
+
+PARAMETER FILES (1 total):
+ 0: box34x.psf, 4020 atoms, 1340 res, box: Cubic, 1340 mol, 1340 solvent
+
+INPUT TRAJECTORIES (1 total):
+ 0: 'nvt.unwrap.dcd' is a CHARMM DCD file (coords) Little Endian 32 bit, Parm box34x.psf (Cubic box) (reading 30000 of 1010000)
+  Coordinate processing will occur on 30000 frames.
+
+PARALLEL INFO:
+  Process 0 will handle 7500 frames.
+  Process 1 will handle 7500 frames.
+  Process 2 will handle 7500 frames.
+  Process 3 will handle 7500 frames.
+.....................................................
+ACTION SETUP FOR PARM 'box34x.psf' (1 actions):
+  0: [rdf out fromtraj.nvt.wato.agr :TIP3@OH2 0.1 12]
+	1340 atoms in Mask1, 1340 atoms in Mask2
+	Imaging on.
+
+BEGIN PARALLEL TRAJECTORY PROCESSING:
+ 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
+TIME: Rank 0 throughput= 97.9603 frames / second.
+TIME: Rank 1 throughput= 77.7931 frames / second.
+TIME: Rank 2 throughput= 71.8034 frames / second.
+TIME: Rank 3 throughput= 68.0942 frames / second.
+TIME: Avg. throughput= 272.3767 frames / second.
+
+ACTION OUTPUT:
+    RADIAL: 30000 frames, # in mask1= 1340, # in mask2 = 1340, # in common = 1340
+	Density is 44.797584 distances / Ang^3.
+TIME: Analyses took 0.0000 seconds.
+
+DATASETS (2 total):
+	PREFIX "PREFIX" (string variable), size is 1 (0.044 kB)
+	g(r)_00002 ":TIP3@OH2 => :TIP3@OH2" (double), size is 120 (0.960 kB)
+    Total data set memory usage is at least 1.004 kB
+
+DATAFILES (1 total):
+  fromtraj.nvt.wato.agr (Grace File):  :TIP3@OH2 => :TIP3@OH2
+
+RUN TIMING:
+TIME:		Init               : 0.0017 s (  0.00%)
+TIME:		Trajectory Process : 110.1416 s (100.00%)
+TIME:		Data Set Sync      : 0.0001 s (  0.00%)
+TIME:		Action Post        : 0.0001 s (  0.00%)
+TIME:		Analysis           : 0.0000 s (  0.00%)
+TIME:		Data File Write    : 0.0015 s (  0.00%)
+TIME:		Other              : 0.0009 s (  0.00%)
+TIME:	Run Total 110.1459 s
+---------- RUN END ---------------------------------------------------
+TIME: Total execution time: 110.2056 seconds.
+--------------------------------------------------------------------------------
+To cite CPPTRAJ use:
+Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for
+  Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem.
+  Theory Comput., 2013, 9 (7), pp 3084-3095.
+Daniel R. Roe and Thomas E. Cheatham, III, "Parallelization of CPPTRAJ enables
+  large scale analysis of molecular dynamics trajectory data". J. Comp.
+  Chem., 2018, DOI: 10.1002/jcc25382.
+
diff --git a/test/Test_ParseTiming/hpod13-n.8-N.2-c.4.out b/test/Test_ParseTiming/hpod13-n.8-N.2-c.4.out
new file mode 100644
index 0000000000..963d3af27d
--- /dev/null
+++ b/test/Test_ParseTiming/hpod13-n.8-N.2-c.4.out
@@ -0,0 +1,141 @@
+JobID: 19615144
+NodeList: p13n[1-2]
+SLURM_NODELIST=p13n[1-2]
+SLURM_JOB_NAME=t.gcc_8.2-cuda_11.8.0-mvapich2_2.3.7.hpod13-n.8-N.2-c.4
+SLURMD_NODENAME=p13n1
+SLURM_TOPOLOGY_ADDR=p13n1
+SLURM_PRIO_PROCESS=0
+SLURM_NODE_ALIASES=(null)
+SLURM_JOB_QOS=normal
+SLURM_TOPOLOGY_ADDR_PATTERN=node
+SLURM_NNODES=2
+SLURM_JOBID=19615144
+SLURM_NTASKS=8
+SLURM_TASKS_PER_NODE=4(x2)
+SLURM_WORKING_CLUSTER=lobos:slurmctl:6817:9728:109
+SLURM_CONF=/usr/local/slurm-22.05.8/etc/slurm.conf
+SLURM_JOB_ID=19615144
+SLURM_CPUS_PER_TASK=4
+SLURM_JOB_USER=droe
+SLURM_JOB_UID=27798
+SLURM_NODEID=0
+SLURM_SUBMIT_DIR=/u/droe/Benchmarks/Cpptraj_calcdiffusion/Cpptraj_calcrdf_MpiBenchmarks.hpod13.forTalk/test.gcc_8.2-cuda_11.8.0-mvapich2_2.3.7/hpod13-n.8-N.2-c.4
+SLURM_TASK_PID=21507
+SLURM_NPROCS=8
+SLURM_CPUS_ON_NODE=32
+SLURM_PROCID=0
+SLURM_JOB_NODELIST=p13n[1-2]
+SLURM_LOCALID=0
+SLURM_JOB_GID=9000
+SLURM_JOB_CPUS_PER_NODE=32(x2)
+SLURM_CLUSTER_NAME=lobos
+SLURM_GTIDS=0
+SLURM_SUBMIT_HOST=tesla2.lobos.nih.gov
+SLURM_JOB_PARTITION=hpod13
+SLURM_JOB_ACCOUNT=cbs
+SLURM_JOB_NUM_NODES=2
+LMOD_FAMILY_CUDA=cuda
+LMOD_FAMILY_CUDA_VERSION=11.8.0
+CUDA_HOME=/v/apps/cuda/11.8.0
+OPENMM_CUDA_COMPILER=/v/apps/cuda/11.8.0/bin/nvcc
+
+CPPTRAJ: Trajectory Analysis. V6.20.2 (GitHub) MPI OpenMP
+    ___  ___  ___  ___
+     | \/ | \/ | \/ | 
+    _|_/\_|_/\_|_/\_|_
+
+| Running on 8 processes.
+| 4 OpenMP threads available.
+| Date/time: 08/08/23 14:57:36
+| Available memory: 30.896 GB
+
+INPUT: Reading input from 'cpptraj.in'
+  [parm /u/rvenable/RvProj/Unwrap/Water/box34x.psf]
+	Reading '/u/rvenable/RvProj/Unwrap/Water/box34x.psf' as Charmm PSF
+    Reading Charmm PSF file box34x.psf as topology file.
+Warning: PSF has no dihedrals.
+Warning: PSF has no impropers.
+	PSF contains 4020 atoms, 1340 residues.
+Warning: Determining bond length parameters from element types for 'box34x.psf'.
+  [set PREFIX = fromtraj.nvt]
+	Variable 'PREFIX' set to 'fromtraj.nvt'
+  [trajin /u/droe/Local_work/For/Rick/npt.diffusion/nvt.unwrap.dcd 1 30000 1]
+	Reading '/u/droe/Local_work/For/Rick/npt.diffusion/nvt.unwrap.dcd' as Charmm DCD
+	Version >= 22; assuming shape matrix is stored.
+Warning: Trajectory box type is 'Cubic' but topology box type is 'None'.
+Warning: Setting topology box information from trajectory.
+  [rdf out fromtraj.nvt.wato.agr :TIP3@OH2 0.1 12]
+    RADIAL: Calculating RDF for atoms in mask1 [:TIP3@OH2] to atoms in mask2 [:TIP3@OH2]
+	Output to fromtraj.nvt.wato.agr.
+	Histogram max 12.000000, spacing 0.100000, bins 120.
+	Normalizing using particle density of 0.033456 molecules/Ang^3.
+	Parallelizing RDF calculation with 4 threads.
+---------- RUN BEGIN -------------------------------------------------
+
+PARAMETER FILES (1 total):
+ 0: box34x.psf, 4020 atoms, 1340 res, box: Cubic, 1340 mol, 1340 solvent
+
+INPUT TRAJECTORIES (1 total):
+ 0: 'nvt.unwrap.dcd' is a CHARMM DCD file (coords) Little Endian 32 bit, Parm box34x.psf (Cubic box) (reading 30000 of 1010000)
+  Coordinate processing will occur on 30000 frames.
+
+PARALLEL INFO:
+  Process 0 will handle 3750 frames.
+  Process 1 will handle 3750 frames.
+  Process 2 will handle 3750 frames.
+  Process 3 will handle 3750 frames.
+  Process 4 will handle 3750 frames.
+  Process 5 will handle 3750 frames.
+  Process 6 will handle 3750 frames.
+  Process 7 will handle 3750 frames.
+.....................................................
+ACTION SETUP FOR PARM 'box34x.psf' (1 actions):
+  0: [rdf out fromtraj.nvt.wato.agr :TIP3@OH2 0.1 12]
+	1340 atoms in Mask1, 1340 atoms in Mask2
+	Imaging on.
+
+BEGIN PARALLEL TRAJECTORY PROCESSING:
+ 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
+TIME: Rank 0 throughput= 112.0884 frames / second.
+TIME: Rank 1 throughput= 86.1163 frames / second.
+TIME: Rank 2 throughput= 80.1873 frames / second.
+TIME: Rank 3 throughput= 76.0794 frames / second.
+TIME: Rank 4 throughput= 72.5535 frames / second.
+TIME: Rank 5 throughput= 70.3294 frames / second.
+TIME: Rank 6 throughput= 68.3018 frames / second.
+TIME: Rank 7 throughput= 66.5251 frames / second.
+TIME: Avg. throughput= 532.1992 frames / second.
+
+ACTION OUTPUT:
+    RADIAL: 30000 frames, # in mask1= 1340, # in mask2 = 1340, # in common = 1340
+	Density is 44.797584 distances / Ang^3.
+TIME: Analyses took 0.0000 seconds.
+
+DATASETS (2 total):
+	PREFIX "PREFIX" (string variable), size is 1 (0.044 kB)
+	g(r)_00002 ":TIP3@OH2 => :TIP3@OH2" (double), size is 120 (0.960 kB)
+    Total data set memory usage is at least 1.004 kB
+
+DATAFILES (1 total):
+  fromtraj.nvt.wato.agr (Grace File):  :TIP3@OH2 => :TIP3@OH2
+
+RUN TIMING:
+TIME:		Init               : 0.0017 s (  0.00%)
+TIME:		Trajectory Process : 56.3699 s ( 99.99%)
+TIME:		Data Set Sync      : 0.0001 s (  0.00%)
+TIME:		Action Post        : 0.0002 s (  0.00%)
+TIME:		Analysis           : 0.0000 s (  0.00%)
+TIME:		Data File Write    : 0.0016 s (  0.00%)
+TIME:		Other              : 0.0014 s (  0.00%)
+TIME:	Run Total 56.3749 s
+---------- RUN END ---------------------------------------------------
+TIME: Total execution time: 56.4351 seconds.
+--------------------------------------------------------------------------------
+To cite CPPTRAJ use:
+Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for
+  Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem.
+  Theory Comput., 2013, 9 (7), pp 3084-3095.
+Daniel R. Roe and Thomas E. Cheatham, III, "Parallelization of CPPTRAJ enables
+  large scale analysis of molecular dynamics trajectory data". J. Comp.
+  Chem., 2018, DOI: 10.1002/jcc25382.
+
diff --git a/test/Test_ParseTiming/parse.dat.save b/test/Test_ParseTiming/parse.dat.save
new file mode 100644
index 0000000000..46896d8ed8
--- /dev/null
+++ b/test/Test_ParseTiming/parse.dat.save
@@ -0,0 +1,4 @@
+#Run              Run Run[name]                Run[dir]
+   0.000     110.2056      H4x4  hpod13-n.4-N.1-c.4.out
+   1.000      56.4351      H8x4  hpod13-n.8-N.2-c.4.out
+   2.000      28.5628     H16x4 hpod13-n.16-N.4-c.4.out
diff --git a/test/Test_ParseTiming/parse.out.save b/test/Test_ParseTiming/parse.out.save
new file mode 100644
index 0000000000..8c252c1a9f
--- /dev/null
+++ b/test/Test_ParseTiming/parse.out.save
@@ -0,0 +1,4 @@
+#		H4
+      0.0000     110.2056   1.00     16   1.00         H4x4 hpod13-n.4-N.1-c.4.out
+      1.0000      56.4351   1.95     32   0.98         H8x4 hpod13-n.8-N.2-c.4.out
+      2.0000      28.5628   3.86     64   0.96        H16x4 hpod13-n.16-N.4-c.4.out
diff --git a/test/Test_TICA/RunTest.sh b/test/Test_TICA/RunTest.sh
new file mode 100755
index 0000000000..f6b16f9227
--- /dev/null
+++ b/test/Test_TICA/RunTest.sh
@@ -0,0 +1,24 @@
+#!/bin/bash
+
+. ../MasterTest.sh
+
+CleanFiles tica.in
+
+INPUT='-i tica.in'
+
+cat > tica.in <<EOF
+parm ../tz2.parm7
+loadcrd ../tz2.crd name TZ2
+
+set MASK = :1-3@CA
+
+crdaction TZ2 matrix name M1 mwcovar out M1.dat \$MASK
+
+runanalysis tica crdset TZ2 mask \$MASK lag 1 mass
+
+list dataset
+EOF
+RunCpptraj "TICA test."
+
+EndTest
+exit 0