diff --git a/doc/cpptraj.bib b/doc/cpptraj.bib
index 412af4f063..96e77b003d 100644
--- a/doc/cpptraj.bib
+++ b/doc/cpptraj.bib
@@ -444,3 +444,29 @@ @article{Roe2022a
 title = {{ Quantifying the Effects of Lossy Compression on Energies Calculated from Molecular Dynamics Trajectories}},
 year = {2022}
 }
+
+@article{Perez2013,
+author = {P{\'e}rez-Hern{\'a}ndez, Guillermo and Paul, Fabian and Giorgino, Toni and De Fabritiis, Gianni and No{\'e}, Frank},
+    title = "{Identification of slow molecular order parameters for Markov model construction}",
+    journal = {The Journal of Chemical Physics},
+    volume = {139},
+    number = {1},
+    pages = {015102},
+    year = {2013},
+    month = {07},
+    issn = {0021-9606},
+    doi = {10.1063/1.4811489},
+    url = {https://doi.org/10.1063/1.4811489},
+}
+
+@article{Noe2016,
+author = {No{\'e}, Frank and Banisch, Ralf and Clementi, Cecilia},
+title = {Commute Maps: Separating Slowly Mixing Molecular Configurations for Kinetic Modeling},
+journal = {Journal of Chemical Theory and Computation},
+volume = {12},
+number = {11},
+pages = {5620-5630},
+year = {2016},
+doi = {10.1021/acs.jctc.6b00762},
+URL = { https://doi.org/10.1021/acs.jctc.6b00762 },
+}
diff --git a/doc/cpptraj.lyx b/doc/cpptraj.lyx
index 0c372e355a..3f1f3b0bef 100644
--- a/doc/cpptraj.lyx
+++ b/doc/cpptraj.lyx
@@ -20011,7 +20011,7 @@ Mod
 \begin_layout Standard
 \align center
 \begin_inset Tabular
-<lyxtabular version="3" rows="90" columns="3">
+<lyxtabular version="3" rows="91" columns="3">
 <features islongtable="true" longtabularalignment="center">
 <column alignment="center" valignment="top" width="25text%">
 <column alignment="center" valignment="top" width="65text%">
@@ -21416,6 +21416,36 @@ Calculate a matrix of the specified type from input coordinates.
 <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
 \begin_inset Text
 
+\begin_layout Plain Layout
+mindist/maxdist
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Calculate the minimum or maximum distance between pairs of atoms/residues/molecu
+les.
+\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
+
+\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
 minimage
 \end_layout
@@ -34322,24 +34352,128 @@ matrix dist @CA out distmat.dat
 \end_layout
 
 \begin_layout Subsection
-mindist
+mindist/maxdist
 \end_layout
 
-\begin_layout Standard
-This functionality is now part of the 
+\begin_layout LyX-Code
+{min|max}dist mask1 <mask1> [mask2 <mask2>] [{byatom|byres|bymol}]
+\end_layout
+
+\begin_layout LyX-Code
+              [noimage] [name <setname>] [out <file>] [resoffset <#>]
+\end_layout
+
+\begin_deeper
+\begin_layout Description
+mask1
+\begin_inset space ~
+\end_inset
+
+<mask1> First mask for selecting atoms.
+\end_layout
+
+\begin_layout Description
+[mask2
+\begin_inset space ~
+\end_inset
+
+<mask2>] Optional second mask for selecting atoms.
+\end_layout
+
+\begin_layout Description
+[{byatom|byres|bymol}]
+\end_layout
+
+\begin_deeper
+\begin_layout Description
+byatom Report the minimum or maximum distance between atoms in <mask1> or
+ between atoms in <mask1> and atoms in <mask2>.
+\end_layout
+
+\begin_layout Description
+byres Report the minimum or maximum distance between all residue pairs selected
+ by <mask1>, or pairs of residues selected by <mask1> and residues selected
+ by <mask2> (excluding certain pairs, see 
 \series bold
-\emph on
-nativecontacts
+resoffset
 \series default
-\emph default
- command; see 
-\begin_inset CommandInset ref
-LatexCommand vref
-reference "subsec:cpptraj-nativecontacts"
+).
+\end_layout
+
+\begin_layout Description
+bymol Report the minimum or maximum distance between all molecule pairs
+ selected by <mask1>, or pairs of molecules selected by <mask1> and molecules
+ selected by <mask2>.
+\end_layout
+
+\end_deeper
+\begin_layout Description
+[noimage] Do not use the minimum image convention for distances.
+\end_layout
 
+\begin_layout Description
+[name
+\begin_inset space ~
 \end_inset
 
-.
+<setname>] Output data set name.
+\end_layout
+
+\begin_layout Description
+[out
+\begin_inset space ~
+\end_inset
+
+<file>] Write data to <file>.
+\end_layout
+
+\begin_layout Description
+[resoffset
+\begin_inset space ~
+\end_inset
+
+<#>] For 
+\series bold
+byres
+\series default
+, ignore residue pairs if the difference in residue numbers is greater than
+ the cutoff (default 1).
+\end_layout
+
+\begin_layout Standard
+Data Sets Created:
+\end_layout
+
+\begin_layout Description
+<name> For 
+\series bold
+byatom
+\series default
+, a set containing the minimum or maximum distance for each frame.
+\end_layout
+
+\begin_layout Description
+<name>[<#>_<#>] For 
+\series bold
+byres
+\series default
+/
+\series bold
+b
+\series default
+ymol, a set containing the minimum or maximum distance between the residue/molec
+ule pair specified by the numbers in the aspect, e.g.
+ '<name>[1_3]' for 
+\series bold
+byres
+\series default
+ would be between residues 1 and 3.
+\end_layout
+
+\end_deeper
+\begin_layout Standard
+Calculate the minimum or maximum distance in Angstroms between atoms or
+ residue/molecule pairs.
 \end_layout
 
 \begin_layout Subsection
@@ -37122,6 +37256,13 @@ principal :1-76 dorotation out principal.dat
 
 \begin_layout Subsection
 projection
+\begin_inset CommandInset label
+LatexCommand label
+name "subsec:cpptraj-projection"
+
+\end_inset
+
+
 \end_layout
 
 \begin_layout LyX-Code
@@ -37130,7 +37271,7 @@ projection [<name>] evecs <dataset name> [out <outfile>] [beg <beg>] [end
 \end_layout
 
 \begin_layout LyX-Code
-           [<mask>] [dihedrals <dataset arg>]
+           {[<mask>] | [dihedrals <dataset arg>] | [data <dataset arg> ...]}
 \end_layout
 
 \begin_layout LyX-Code
@@ -37200,6 +37341,21 @@ arg>] (Dihedral covariance only) Dihedral data sets to use in projection;
  MUST CORRESPOND TO HOW EIGENVECTORS WERE GENERATED.
 \end_layout
 
+\begin_layout Description
+[data
+\begin_inset space ~
+\end_inset
+
+<dataset
+\begin_inset space ~
+\end_inset
+
+arg>] (Data covariance only, e.g.
+ from TICA).
+ 1D data sets to use in projection; MUST CORRESPOND TO HOW EIGENVECTORS
+ WERE GENERATED.
+\end_layout
+
 \begin_layout Description
 [start
 \begin_inset space ~
@@ -37263,6 +37419,12 @@ Projects snapshots onto eigenvectors obtained by diagonalizing covariance
 diagmatrix
 \series default
 \shape default
+/
+\series bold
+\emph on
+tica
+\series default
+\emph default
 ) or previously read-in (e.g.
  with 
 \series bold
@@ -37283,9 +37445,11 @@ readdata
 
 \family sans
 \series bold
+\emph on
 matrix
 \family default
 \series default
+\emph default
 
 \begin_inset Quotes erd
 \end_inset
@@ -37305,6 +37469,23 @@ projection
 \series default
 \emph default
  command.
+ If only 1D data sets need to be projected, see the 
+\series bold
+\emph on
+projectdata
+\series default
+\emph default
+ analysis command, 
+\begin_inset CommandInset ref
+LatexCommand vref
+reference "subsec:cpptraj-projectdata"
+plural "false"
+caps "false"
+noprefix "false"
+
+\end_inset
+
+.
 \end_layout
 
 \begin_layout Subsection
@@ -43058,7 +43239,7 @@ trajin
 \begin_layout Standard
 \align center
 \begin_inset Tabular
-<lyxtabular version="3" rows="48" columns="3">
+<lyxtabular version="3" rows="50" columns="3">
 <features islongtable="true" longtabularalignment="center">
 <column alignment="center" valignment="top" width="25text%">
 <column alignment="center" valignment="top" width="50text%">
@@ -44096,6 +44277,35 @@ N phi/psi dihedrals
 <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
 \begin_inset Text
 
+\begin_layout Plain Layout
+projectdata
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Project data along eigenmodes.
+\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
+eigenmodes, N 1D scalar
+\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
 regress
 \end_layout
@@ -44364,6 +44574,35 @@ N 1D scalar
 <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
 \begin_inset Text
 
+\begin_layout Plain Layout
+tica
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Perform time-independent correlation analysis.
+\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
+COORDS, N 1D scalar
+\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
 timecorr
 \end_layout
@@ -48219,7 +48458,7 @@ name "subsec:diagmatrix-|-analyze"
 \end_layout
 
 \begin_layout LyX-Code
-diagmatrix <name> [out <filename>] [thermo [outthermo <filename>]]
+diagmatrix <matrix name> [out <filename>] [thermo [outthermo <filename>]]
 \end_layout
 
 \begin_layout LyX-Code
@@ -48238,7 +48477,11 @@ diagmatrix <name> [out <filename>] [thermo [outthermo <filename>]]
 \begin_layout Description
 
 \series bold
-<name>
+<matrix
+\begin_inset space ~
+\end_inset
+
+name>
 \series default
  Name of symmetric matrix to diagonalize.
 \end_layout
@@ -51556,6 +51799,130 @@ run
 phipsi DPDP[phi] DPDP[psi] out phipsi.dat resrange 1-22
 \end_layout
 
+\begin_layout Subsection
+projectdata
+\begin_inset CommandInset label
+LatexCommand label
+name "subsec:cpptraj-projectdata"
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout LyX-Code
+projectdata evecs <evecs dataset> [name <name>] [out <outfile>] [beg <beg>]
+ [end <end>]
+\end_layout
+
+\begin_layout LyX-Code
+            {[dihedrals <dataset arg>] | [data <dataset arg> ...]}
+\end_layout
+
+\begin_deeper
+\begin_layout Description
+evecs
+\begin_inset space ~
+\end_inset
+
+<dataset
+\begin_inset space ~
+\end_inset
+
+name> Data set containing eigenvectors (modes).
+\end_layout
+
+\begin_layout Description
+[name
+\begin_inset space ~
+\end_inset
+
+<name>] Output data set name.
+\end_layout
+
+\begin_layout Description
+[out
+\begin_inset space ~
+\end_inset
+
+<outfile>] Write projections to <outfile>.
+\end_layout
+
+\begin_layout Description
+[beg
+\begin_inset space ~
+\end_inset
+
+<beg>] First eigenvector/mode to use (default 1).
+\end_layout
+
+\begin_layout Description
+[end
+\begin_inset space ~
+\end_inset
+
+<end>] Final eigenvector/mode to use (default 2).
+\end_layout
+
+\begin_layout Description
+[dihedrals
+\begin_inset space ~
+\end_inset
+
+<dataset
+\begin_inset space ~
+\end_inset
+
+arg>] (Dihedral covariance only) Dihedral data sets to use in projection;
+ MUST CORRESPOND TO HOW EIGENVECTORS WERE GENERATED.
+\end_layout
+
+\begin_layout Description
+[data
+\begin_inset space ~
+\end_inset
+
+<dataset
+\begin_inset space ~
+\end_inset
+
+arg>] (Data covariance only, e.g.
+ from TICA).
+ 1D data sets to use in projection; MUST CORRESPOND TO HOW EIGENVECTORS
+ WERE GENERATED.
+\end_layout
+
+\begin_layout Standard
+Data Sets Created:
+\end_layout
+
+\begin_layout Description
+<name>:<#> Projection data set for mode <#>.
+\end_layout
+
+\end_deeper
+\begin_layout Standard
+Project data along previously generated eigenmodes from e.g.
+ PCA or TICA.
+ This is a faster alternative to the 
+\series bold
+\emph on
+projection
+\series default
+\emph default
+ command (
+\begin_inset CommandInset ref
+LatexCommand vref
+reference "subsec:cpptraj-projection"
+plural "false"
+caps "false"
+noprefix "false"
+
+\end_inset
+
+) if only 1D data sets need to be projected.
+\end_layout
+
 \begin_layout Subsection
 regress
 \end_layout
@@ -53661,6 +54028,172 @@ ti TIdata nq 9 name Curve out skip.agr curveout curve.agr nskip 0,5,10,15,20,30,
 ,50
 \end_layout
 
+\begin_layout Subsection
+tica
+\end_layout
+
+\begin_layout LyX-Code
+tica { crdset <COORDS set name> [mask <mask>] |
+\end_layout
+
+\begin_layout LyX-Code
+       data <input set arg1> ...
+ }
+\end_layout
+
+\begin_layout LyX-Code
+     [lag <time lag>] [map {kinetic|commute|none}]
+\end_layout
+
+\begin_layout LyX-Code
+     [name <output set name>] [out <file>] [cumvarout <file>]
+\end_layout
+
+\begin_deeper
+\begin_layout Description
+crdset
+\begin_inset space ~
+\end_inset
+
+<COORDS
+\begin_inset space ~
+\end_inset
+
+set
+\begin_inset space ~
+\end_inset
+
+name> Input coordinates (COORDS) data set.
+\end_layout
+
+\begin_deeper
+\begin_layout Description
+mask
+\begin_inset space ~
+\end_inset
+
+<mask> Selected atoms in input coordinates (COORDS) data set.
+\end_layout
+
+\end_deeper
+\begin_layout Description
+data
+\begin_inset space ~
+\end_inset
+
+<input
+\begin_inset space ~
+\end_inset
+
+set
+\begin_inset space ~
+\end_inset
+
+arg1> Input 1D data set name(s), may specify more than once.
+ If any data set is periodic, all need to be periodic.
+\end_layout
+
+\begin_layout Description
+lag
+\begin_inset space ~
+\end_inset
+
+<time
+\begin_inset space ~
+\end_inset
+
+lag> TICA lag time in frames.
+\end_layout
+
+\begin_layout Description
+map
+\begin_inset space ~
+\end_inset
+
+{kinetic|commute|none} How to transform the resulting eigenvectors.
+\end_layout
+
+\begin_deeper
+\begin_layout Description
+kinetic (default) Scale eigenvectors by eigenvalues so that distances in
+ the transformed data approximate kinetic distances; particularly useful
+ if using the projections to cluster.
+\end_layout
+
+\begin_layout Description
+commute Scale eigenvectors by regularized time scales, sqrt(timescale_i
+ / 2), so that distances in the transformed data will approximate commute
+ distances.
+ Timescales smaller than the lag time are dampened.
+\begin_inset CommandInset citation
+LatexCommand citep
+key "Noe2016"
+literal "true"
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Description
+none Do not scale eigenvectors.
+\end_layout
+
+\end_deeper
+\begin_layout Description
+name
+\begin_inset space ~
+\end_inset
+
+<output
+\begin_inset space ~
+\end_inset
+
+set
+\begin_inset space ~
+\end_inset
+
+name> Output data set name.
+\end_layout
+
+\begin_layout Description
+out
+\begin_inset space ~
+\end_inset
+
+<file> File to write TICA modes to.
+\end_layout
+
+\begin_layout Description
+cumvarout
+\begin_inset space ~
+\end_inset
+
+<file> File to write eigenvalue cumulative variance to.
+\end_layout
+
+\end_deeper
+\begin_layout Standard
+Perform time-independent correlation analysis (TICA).
+ Similar to principal component analysis (PCA), TICA calculates eigenvectors/eig
+envalues (i.e.
+ eigenmodes) from input data sets (either coordinates or a combination of
+ other 1D data sets).
+ Whereas the eigenvectors from PCA describe the variance in the input data,
+ the eigenvectors from TICA describe the maximal autocorrelation in the
+ input data at the given lag time.
+\begin_inset CommandInset citation
+LatexCommand citep
+key "Perez2013"
+literal "true"
+
+\end_inset
+
+ The analysis can be performed on either coordinates or 1D data sets; the
+ data sets can either be all periodic (in which case they will be converted
+ to cos/sin form) or not.
+\end_layout
+
 \begin_layout Subsection
 timecorr
 \end_layout
diff --git a/src/Action_Matrix.cpp b/src/Action_Matrix.cpp
index e4192516aa..aaf571e86f 100644
--- a/src/Action_Matrix.cpp
+++ b/src/Action_Matrix.cpp
@@ -853,6 +853,10 @@ void Action_Matrix::FinishCovariance(size_t element_size) {
   double Mass = 1.0;
   double mass2 = 1.0;
 
+//  mprintf("DEBUG: First 3 elements: %f %f %f\n",
+//          Mat_->GetElement(0, 0),
+//          Mat_->GetElement(1, 0),
+//          Mat_->GetElement(2, 0));
   DataSet_MatrixDbl::iterator mat = Mat_->begin();
   // Calc <riri> - <ri><ri>
   Vect2MinusVect(); // Is vect2 used?
@@ -862,6 +866,14 @@ void Action_Matrix::FinishCovariance(size_t element_size) {
     M_iterator m2 = mass2_.begin();
     // Position for mask2 halfway through vect/vect2
     v_iterator v1idx2begin = Mat_->v1begin() + Mat_->Ncols();
+//    mprintf("DEBUG: First 3 elements of V1: %f %f %f\n",
+//            *(Mat_->v1begin()),
+//            *(Mat_->v1begin() + 1),
+//            *(Mat_->v1begin() + 2));
+//    mprintf("DEBUG: First 3 elements of V2: %f %f %f\n",
+//            *(v1idx2begin),
+//            *(v1idx2begin + 1),
+//            *(v1idx2begin + 2));
     for (v_iterator v1idx2 = v1idx2begin; v1idx2 != Mat_->v1end(); v1idx2 += element_size)
     {
       if (Mat_->Meta().ScalarType() == MetaData::MWCOVAR)
@@ -874,6 +886,7 @@ void Action_Matrix::FinishCovariance(size_t element_size) {
           if (Mat_->Meta().ScalarType() == MetaData::MWCOVAR)
             Mass = sqrt( mass2 * *(m1++) );
           for (unsigned int idx = 0; idx < element_size; ++idx) {
+            //mprintf("mat = (%f - (%f * %f)) * %f\n", *mat, Vi, *(v1idx1+idx), Mass); // DEBUG
             *mat = (*mat - (Vi * *(v1idx1+idx))) * Mass;
             ++mat;
           }
diff --git a/src/Action_MinMaxDist.cpp b/src/Action_MinMaxDist.cpp
new file mode 100644
index 0000000000..88f6388240
--- /dev/null
+++ b/src/Action_MinMaxDist.cpp
@@ -0,0 +1,448 @@
+#include "Action_MinMaxDist.h"
+#include "CharMask.h"
+#include "CpptrajStdio.h"
+#include "DistRoutines.h"
+#include "StringRoutines.h" // integerToString
+#include <limits> // Max double
+#include <cmath> // sqrt
+
+/** CONSTRUCTOR */
+Action_MinMaxDist::Action_MinMaxDist() :
+  mode_(NO_MODE),
+  distType_(NO_DIST),
+  outfile_(0),
+  byAtomSet_(0),
+  masterDSL_(0),
+  debug_(0),
+  resOffset_(0)
+{}
+
+const char* Action_MinMaxDist::modeStr_[] = {
+  "atoms",
+  "residues",
+  "molecules",
+  0
+};
+
+const char* Action_MinMaxDist::distTypeStr_[] = {
+  "minimum",
+  "maximum",
+  "minimum and maximum",
+  0
+};
+
+// Action_MinMaxDist::Help()
+void Action_MinMaxDist::Help() const {
+  mprintf("\tmask1 <mask1> [mask2 <mask2>] [{byatom|byres|bymol}]\n"
+          "\t[noimage] [name <setname>] [out <file>] [resoffset <#>]\n"
+          "  Record the min/max distance between atoms/residues/molecules.\n"
+         );
+}
+
+// Action_MinMaxDist::Init()
+Action::RetType Action_MinMaxDist::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
+{
+  debug_ = debugIn;
+  // Get Keywords
+  imageOpt_.InitImaging( !(actionArgs.hasKey("noimage")) );
+  resOffset_ = actionArgs.getKeyInt("resoffset", 1);
+  // Mask Keywords
+  std::string mask1str = actionArgs.GetStringKey("mask1");
+  if (mask1str.empty()) {
+    mprinterr("Error: Must specify at least 'mask1'\n");
+    return Action::ERR;
+  }
+  if (mask1_.SetMaskString( mask1str )) {
+    mprinterr("Error: Could not set mask1 '%s'\n", mask1str.c_str());
+    return Action::ERR;
+  }
+  std::string mask2str = actionArgs.GetStringKey("mask2");
+  if (!mask2str.empty()) {
+    if (mask2_.SetMaskString( mask2str )) {
+      mprinterr("Error: Could not set mask2 '%s'\n", mask2str.c_str());
+      return Action::ERR;
+    }
+  }
+  // File args
+  outfile_ = init.DFL().AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
+  // Mode args
+  if (actionArgs.hasKey("byatom"))
+    mode_ = BY_ATOM;
+  else if (actionArgs.hasKey("byres"))
+    mode_ = BY_RES;
+  else if (actionArgs.hasKey("bymol"))
+    mode_ = BY_MOL;
+  // Distance calc type args
+  // TODO This action is a little different in that it looks at the 
+  //      command name to figure out if user wants minimum or maximum
+  //      distance. May break if command name is updated and this isnt.
+  //bool calc_mindist = (actionArgs.hasKey("mindist") || (actionArgs[0] == "mindist"));
+  //bool calc_maxdist = (actionArgs.hasKey("maxdist") || (actionArgs[0] == "maxdist"));
+  bool calc_mindist = (actionArgs[0][0] == 'm' && actionArgs[0][1] == 'i' && actionArgs[0][2] == 'n');
+  bool calc_maxdist = (actionArgs[0][0] == 'm' && actionArgs[0][1] == 'a' && actionArgs[0][2] == 'x');
+  //if (actionArgs.hasKey("bothdist"))
+  //  distType_ = BOTH_DIST;
+  // DataSet Name
+  dsname_ = actionArgs.GetStringKey("name");
+  // Default name
+  if (dsname_.empty())
+    dsname_ = init.DSL().GenerateDefaultName("MINMAXDIST");
+  // Default mode
+  if (mode_ == NO_MODE)
+    mode_ = BY_ATOM;
+  // Default distance calc type
+  if (distType_ == NO_DIST) {
+    if (calc_mindist && calc_maxdist) {
+      //distType_ = BOTH_DIST;
+      mprinterr("Error: Can only have 'mindist' or 'maxdist', not both.\n");
+      return Action::ERR;
+    } else if (calc_mindist)
+      distType_ = MIN_DIST;
+    else if (calc_maxdist)
+      distType_ = MAX_DIST;
+    else {
+      mprinterr("Internal Error: No distance type specified and command name '%s' unrecognized.\n",
+                actionArgs[0].c_str());
+      return Action::ERR;
+    }
+  }
+  // Checks
+  if (mode_ == BY_ATOM && distType_ == MIN_DIST && !mask2_.MaskStringSet())
+    mprintf("Warning: Minimum by atom distance for a single mask will always be the shortest bond distance.\n");
+  // Save master data set list
+  masterDSL_ = init.DslPtr();
+  // Allocate by atom set
+  if (mode_ == BY_ATOM) {
+    byAtomSet_ = init.DSL().AddSet(DataSet::FLOAT, MetaData(dsname_));
+    if (byAtomSet_ == 0) {
+      mprinterr("Error: Could not allocate set '%s'\n", dsname_.c_str());
+      return Action::ERR;
+    }
+    if (outfile_ != 0)
+      outfile_->AddDataSet( byAtomSet_ );
+  }
+
+  mprintf("    MINMAXDIST: Calculating %s distance for selected %s.\n",
+          distTypeStr_[distType_], modeStr_[mode_]);
+  if (mode_ == BY_RES)
+    mprintf("\tResidue offset: %i\n", resOffset_);
+  mprintf("\tMask1: %s\n", mask1_.MaskString());
+  if (mask2_.MaskStringSet()) {
+    mprintf("\tMask2: %s\n", mask2_.MaskString());
+  }
+  if (imageOpt_.UseImage())
+    mprintf("\tDistances will use minimum image convention if box info present.\n");
+  else
+    mprintf("\tDistances will not be imaged.\n");
+  mprintf("\tData set name: %s\n", dsname_.c_str());
+  if (outfile_ != 0)
+    mprintf("\tData file name: %s\n", outfile_->DataFilename().full());
+
+  return Action::OK;
+}
+
+/** For DEBUG, print selected atoms in entity array., */
+void Action_MinMaxDist::printEntities(Earray const& entities, AtomMask const& maskIn) const {
+  mprintf("DEBUG: Selected %s in mask %s\n",
+          modeStr_[mode_], maskIn.MaskString());
+  for (Earray::const_iterator it = entities.begin(); it != entities.end(); ++it) {
+    mprintf("\t%s %i :", it->name_.c_str(), it->num_ + 1);
+    for (AtomMask::const_iterator at = it->emask_.begin(); at != it->emask_.end(); ++at)
+      mprintf(" %i", *at + 1);
+    mprintf("\n");
+  }
+}
+
+/** Set up entities for atoms selected in given mask. */
+int Action_MinMaxDist::setupEntityArray(Earray& entities, AtomMask const& maskIn,
+                                        Topology const& topIn)
+const
+{
+  entities.clear();
+  CharMask cmask(maskIn.ConvertToCharMask(), maskIn.Nselected());
+
+  if (mode_ == BY_RES) {
+    //entities.reserve(topIn.Nres());
+    for (int ires = 0; ires < topIn.Nres(); ires++) {
+      Residue const& Res = topIn.Res(ires);
+      bool needs_alloc = true;
+      for (int at = Res.FirstAtom(); at != Res.LastAtom(); at++) {
+        if (cmask.AtomInCharMask( at )) {
+          if (needs_alloc) {
+            entities.push_back( Entity(Res.Name().Truncated(), ires) );
+            needs_alloc = false;
+          }
+          Entity& currentEntity = entities.back();
+          currentEntity.emask_.AddSelectedAtom( at );
+        }
+      }
+    } // END loop over residues
+  } else if (mode_ == BY_MOL) {
+    for (int imol = 0; imol < topIn.Nmol(); imol++) {
+      Molecule const& Mol = topIn.Mol(imol);
+      bool needs_alloc = true;
+      for (Unit::const_iterator seg = Mol.MolUnit().segBegin();
+                                seg != Mol.MolUnit().segEnd(); ++seg)
+      {
+        for (int at = seg->Begin(); at < seg->End(); ++at) {
+          if (cmask.AtomInCharMask( at )) {
+            if (needs_alloc) {
+              int rnum = topIn[at].ResNum();
+              entities.push_back( Entity(topIn.Res(rnum).Name().Truncated(), imol) );
+              needs_alloc = false;
+            }
+            Entity& currentEntity = entities.back();
+            currentEntity.emask_.AddSelectedAtom( at );
+          }
+        }
+      } // END loop over molecule segments
+    } // END loop over molecules
+  } else {
+    mprinterr("Internal Error: Action_MinMaxDist::setupEntityArray() Unhandled mode\n");
+    return 1;
+  }
+  // DEBUG - print entities
+  if (debug_ > 0)
+    printEntities(entities, maskIn);
+  mprintf("\t%zu %s selected by mask '%s'\n", entities.size(), modeStr_[mode_], maskIn.MaskString());
+  return 0;
+}
+
+/// Aspect for BY_RES/BY_MOL
+inline static std::string entity_aspect(int r0, int r1)
+{
+  return std::string( integerToString(r0+1) + "_" + integerToString(r1+1) );
+}
+
+// Action_MinMaxDist::Setup()
+Action::RetType Action_MinMaxDist::Setup(ActionSetup& setup)
+{
+  // Set up imaging info for this topology 
+  imageOpt_.SetupImaging( setup.CoordInfo().TrajBox().HasBox() );
+  if (imageOpt_.ImagingEnabled())
+    mprintf("\tDistance imaging on.\n");
+  else
+    mprintf("\tDistance imaging off.\n");
+  // Set up masks
+  if (setup.Top().SetupIntegerMask( mask1_ )) {
+    mprinterr("Error: Could not set up mask '%s'\n", mask1_.MaskString());
+    return Action::OK;
+  }
+  mask1_.MaskInfo();
+  if (mask1_.None()) {
+    mprintf("Warning: Nothing selected by mask '%s'\n", mask1_.MaskString());
+    return Action::SKIP;
+  }
+  if (mask2_.MaskStringSet()) {
+    if (setup.Top().SetupIntegerMask( mask2_ )) {
+      mprinterr("Error: Could not set up mask '%s'\n", mask2_.MaskString());
+      return Action::OK;
+    }
+    mask2_.MaskInfo();
+    if (mask2_.None()) {
+      mprintf("Warning: Nothing selected by mask '%s'\n", mask2_.MaskString());
+      return Action::SKIP;
+    }
+  }
+  // By residue/molecule interaction pair data set setup
+  activeSets_.clear();
+  if (mode_ != BY_ATOM) {
+    if (setupEntityArray(entities1_, mask1_, setup.Top())) {
+      mprinterr("Error: Could not set up %s for mask '%s'\n",
+                modeStr_[mode_], mask1_.MaskString());
+      return Action::ERR;
+    }
+    if (mask2_.MaskStringSet()) {
+      if (setupEntityArray(entities2_, mask2_, setup.Top())) {
+        mprinterr("Error: Could not set up %s for mask '%s'\n",
+                  modeStr_[mode_], mask2_.MaskString());
+        return Action::ERR;
+      }
+      // Check if entity numbers overlap
+      std::vector<bool> entity_selected;
+      if (mode_ == BY_RES)
+        entity_selected.assign( setup.Top().Nres(), false );
+      else if (mode_ == BY_MOL)
+        entity_selected.assign( setup.Top().Nmol(), false );
+      for (Earray::const_iterator it1 = entities1_.begin(); it1 != entities1_.end(); ++it1)
+        entity_selected[it1->num_] = true;
+      for (Earray::const_iterator it2 = entities2_.begin(); it2 != entities2_.end(); ++it2) {
+        if (entity_selected[it2->num_]) {
+          mprinterr("Error: %s selected by mask2 '%s' must not overlap those selected by mask1 '%s'\n",
+                    modeStr_[mode_], mask2_.MaskString(), mask1_.MaskString());
+          return Action::ERR;
+        }
+      }
+      // Set up DataSets for each entity pair
+      int tgtOffset = 0;
+      if (mode_ == BY_RES)
+        tgtOffset = resOffset_;
+      for (Earray::const_iterator it1 = entities1_.begin(); it1 != entities1_.end(); ++it1)
+      {
+        for (Earray::const_iterator it2 = entities2_.begin(); it2 != entities2_.end(); ++it2)
+        {
+          int offset = it1->num_ - it2->num_;
+          if (offset < 0) offset = -offset;
+          if (offset > tgtOffset) {
+            if (debug_ > 1)
+              mprintf("DEBUG: Pair %i - %i\n", it1->num_ + 1, it2->num_ + 1);
+            MetaData meta(dsname_, entity_aspect(it1->num_, it2->num_));
+            DataSet* ds = interactionSets_.AddInteractionSet(*masterDSL_, DataSet::FLOAT, meta, it2->num_, it1->num_, outfile_);
+            if (ds == 0) {
+              mprinterr("Error: Could not allocate data set %s[%s]\n",
+                        meta.Name().c_str(), meta.Aspect().c_str());
+              return Action::ERR;
+            }
+            activeSets_.push_back( ActiveSet(ds, it1, it2) );
+          }
+        }
+      }
+    } else {
+      // Set up DataSets for each entity pair
+      int tgtOffset = 0;
+      if (mode_ == BY_RES)
+        tgtOffset = resOffset_;
+      for (Earray::const_iterator it1 = entities1_.begin(); it1 != entities1_.end(); ++it1)
+      {
+        for (Earray::const_iterator it2 = it1 + 1; it2 != entities1_.end(); ++it2)
+        {
+          int offset = it1->num_ - it2->num_;
+          if (offset < 0) offset = -offset;
+          if (offset > tgtOffset) {
+            if (debug_ > 1)
+              mprintf("DEBUG: Pair %i - %i\n", it1->num_ + 1, it2->num_ + 1);
+            MetaData meta(dsname_, entity_aspect(it1->num_, it2->num_));
+            DataSet* ds = interactionSets_.AddInteractionSet(*masterDSL_, DataSet::FLOAT, meta, it2->num_, it1->num_, outfile_);
+            if (ds == 0) {
+              mprinterr("Error: Could not allocate data set %s[%s]\n",
+                        meta.Name().c_str(), meta.Aspect().c_str());
+              return Action::ERR;
+            }
+            activeSets_.push_back( ActiveSet(ds, it1, it2) );
+          }
+        }
+      }
+    }
+    mprintf("\t%zu active pairs of %s\n", activeSets_.size(), modeStr_[mode_]);
+    if (debug_ > 0) {
+      mprintf("DEBUG: Active sets:\n");
+      for (DSarray::const_iterator it = activeSets_.begin(); it != activeSets_.end(); ++it)
+        mprintf("\t%s\n", it->ds_->legend());
+    }
+    if (activeSets_.empty()) {
+      mprintf("Warning: No active interaction pairs. Skipping.\n");
+      return Action::SKIP;
+    }
+  } // END BY_RES, BY_MOL
+
+  return Action::OK;
+}
+
+/** Get min distance between all atom pairs */
+double Action_MinMaxDist::get_min_dist(AtomMask const& mask1, AtomMask const& mask2, Frame const& frameIn)
+const
+{
+  double min_dist2 = std::numeric_limits<double>::max(); 
+  for (AtomMask::const_iterator at1 = mask1.begin(); at1 != mask1.end(); ++at1) {
+    const double* XYZ1 = frameIn.XYZ(*at1);
+    for (AtomMask::const_iterator at2 = mask2.begin(); at2 != mask2.end(); ++at2) {
+      if (*at1 != *at2) {
+        const double* XYZ2 = frameIn.XYZ(*at2);
+        double dist2 = DIST2(imageOpt_.ImagingType(), XYZ1, XYZ2, frameIn.BoxCrd());
+        //mprintf("DEBUG: get_min_dist(m1,m2) %i %i = %f\n", *at1 + 1, *at2 + 1, sqrt(dist2));
+        if (dist2 < min_dist2)
+          min_dist2 = dist2;
+      }
+    }
+  }
+  return sqrt(min_dist2);
+}
+
+/** Get min distance between all atoms pairs */
+double Action_MinMaxDist::get_min_dist(AtomMask const& mask1, Frame const& frameIn)
+const
+{
+  double min_dist2 = std::numeric_limits<double>::max(); 
+  for (AtomMask::const_iterator at1 = mask1.begin(); at1 != mask1.end(); ++at1) {
+    const double* XYZ1 = frameIn.XYZ(*at1);
+    for (AtomMask::const_iterator at2 = at1 + 1; at2 != mask1.end(); ++at2) {
+      const double* XYZ2 = frameIn.XYZ(*at2);
+      double dist2 = DIST2(imageOpt_.ImagingType(), XYZ1, XYZ2, frameIn.BoxCrd());
+      if (dist2 < min_dist2)
+        min_dist2 = dist2;
+    }
+  }
+  return sqrt(min_dist2);
+}
+
+/** Get max distance between all atom pairs */
+double Action_MinMaxDist::get_max_dist(AtomMask const& mask1, AtomMask const& mask2, Frame const& frameIn)
+const
+{
+  double max_dist2 = 0;
+  for (AtomMask::const_iterator at1 = mask1.begin(); at1 != mask1.end(); ++at1) {
+    const double* XYZ1 = frameIn.XYZ(*at1);
+    for (AtomMask::const_iterator at2 = mask2.begin(); at2 != mask2.end(); ++at2) {
+      if (*at1 != *at2) {
+        const double* XYZ2 = frameIn.XYZ(*at2);
+        double dist2 = DIST2(imageOpt_.ImagingType(), XYZ1, XYZ2, frameIn.BoxCrd());
+        if (dist2 > max_dist2)
+          max_dist2 = dist2;
+      }
+    }
+  }
+  return sqrt(max_dist2);
+}
+
+/** Get max distance between all atoms pairs */
+double Action_MinMaxDist::get_max_dist(AtomMask const& mask1, Frame const& frameIn)
+const
+{
+  double max_dist2 = 0; 
+  for (AtomMask::const_iterator at1 = mask1.begin(); at1 != mask1.end(); ++at1) {
+    const double* XYZ1 = frameIn.XYZ(*at1);
+    for (AtomMask::const_iterator at2 = at1 + 1; at2 != mask1.end(); ++at2) {
+      const double* XYZ2 = frameIn.XYZ(*at2);
+      double dist2 = DIST2(imageOpt_.ImagingType(), XYZ1, XYZ2, frameIn.BoxCrd());
+      if (dist2 > max_dist2)
+        max_dist2 = dist2;
+    }
+  }
+  return sqrt(max_dist2);
+}
+
+// Action_MinMaxDist::DoAction()
+Action::RetType Action_MinMaxDist::DoAction(int frameNum, ActionFrame& frm)
+{
+  if (imageOpt_.ImagingEnabled())
+    imageOpt_.SetImageType( frm.Frm().BoxCrd().Is_X_Aligned_Ortho() );
+
+  if (mode_ == BY_ATOM) {
+    float dist;
+    if (mask2_.MaskStringSet()) {
+      if (distType_ == MIN_DIST)
+        dist = get_min_dist(mask1_, mask2_, frm.Frm());
+      else if (distType_ == MAX_DIST)
+        dist = get_max_dist(mask1_, mask2_, frm.Frm());
+    } else {
+       if (distType_ == MIN_DIST)
+        dist = get_min_dist(mask1_, frm.Frm());
+      else if (distType_ == MAX_DIST)
+        dist = get_max_dist(mask1_, frm.Frm());
+    }
+    byAtomSet_->Add( frameNum, &dist );
+  } else {
+    // BY_RES / BY_MOL
+    for (DSarray::const_iterator set = activeSets_.begin(); set != activeSets_.end(); ++set) {
+      float dist;
+      if (distType_ == MIN_DIST)
+        dist = get_min_dist(set->it1_->emask_, set->it2_->emask_, frm.Frm());
+      else if (distType_ == MAX_DIST)
+        dist = get_max_dist(set->it1_->emask_, set->it2_->emask_, frm.Frm());
+    
+      set->ds_->Add( frameNum, &dist );
+    }
+  }
+   
+  return Action::OK;
+}
diff --git a/src/Action_MinMaxDist.h b/src/Action_MinMaxDist.h
new file mode 100644
index 0000000000..9fbcd1aa4d
--- /dev/null
+++ b/src/Action_MinMaxDist.h
@@ -0,0 +1,77 @@
+#ifndef INC_ACTION_MINMAXDIST_H
+#define INC_ACTION_MINMAXDIST_H
+#include "Action.h"
+#include "ImageOption.h"
+#include "InteractionData.h"
+/// Record the min/max distance between atoms/residues/molecules 
+class Action_MinMaxDist : public Action {
+  public:
+    /// CONSTRUCTOR
+    Action_MinMaxDist();
+    /// ALLOCATOR
+    DispatchObject* Alloc() const { return (DispatchObject*)new Action_MinMaxDist(); }
+    /// HELP
+    void Help() const;
+  private:
+    enum ModeType {BY_ATOM = 0, BY_RES, BY_MOL, NO_MODE};
+    enum DistType { MIN_DIST = 0, MAX_DIST, BOTH_DIST, NO_DIST };
+
+    static const char* modeStr_[];
+    static const char* distTypeStr_[];
+
+    /// Used to track residues/molecules
+    class Entity {
+      public:
+        Entity(std::string const& na, int nu) : name_(na), num_(nu) {}
+        AtomMask emask_;   ///< Selected atoms in entity.
+        std::string name_; ///< residue/molecule name
+        int num_;          ///< residue/molecule number
+    };
+    typedef std::vector<Entity> Earray;
+
+    /// Used to track active sets and corresponding entities
+    class ActiveSet {
+      public:
+        ActiveSet(DataSet* ds, Earray::const_iterator const& it1, Earray::const_iterator const& it2) :
+          ds_(ds), it1_(it1), it2_(it2) {}
+        DataSet* ds_;
+        Earray::const_iterator it1_;
+        Earray::const_iterator it2_;
+    };
+    typedef std::vector<ActiveSet> DSarray;
+
+    Action::RetType Init(ArgList&, ActionInit&, int);
+    Action::RetType Setup(ActionSetup&);
+    Action::RetType DoAction(int, ActionFrame&);
+    void Print() {}
+
+    /// For debug, print entities to STDOUT
+    void printEntities(Earray const&, AtomMask const&) const;
+    /// Set up entity array for current mode
+    int setupEntityArray(Earray&, AtomMask const&, Topology const&) const;
+    /// Get minimum distance between atoms in masks
+    double get_min_dist(AtomMask const&, AtomMask const&, Frame const&) const;
+    /// Get minimum distance between atoms in mask
+    double get_min_dist(AtomMask const&, Frame const&) const;
+    /// Get maximum distance between atoms in masks
+    double get_max_dist(AtomMask const&, AtomMask const&, Frame const&) const;
+    /// Get maximum distance between atoms in mask
+    double get_max_dist(AtomMask const&, Frame const&) const;
+
+    AtomMask mask1_;
+    AtomMask mask2_;
+    ModeType mode_;
+    DistType distType_;
+    ImageOption imageOpt_; ///< Used to determine if imaging should be used.
+    Earray entities1_; ///< Entities corresponding to mask1_
+    Earray entities2_; ///< Entities corresponding to mask2_
+    std::string dsname_; ///< Data set name
+    DataFile* outfile_;  ///< Output data file
+    DataSet* byAtomSet_; ///< By atom output data set
+    DataSetList* masterDSL_; ///< Pointer to master data set list
+    Cpptraj::InteractionData interactionSets_; ///< Hold interaction sets
+    DSarray activeSets_;                       ///< Hold active interaction sets
+    int debug_;
+    int resOffset_;          ///< If BY_RES, do not look at pairs separated by less than resOffset_ in sequence
+};
+#endif
diff --git a/src/Action_Projection.cpp b/src/Action_Projection.cpp
index 7d1d151ef9..d275af5e97 100644
--- a/src/Action_Projection.cpp
+++ b/src/Action_Projection.cpp
@@ -4,6 +4,7 @@
 #include "StringRoutines.h" // integerToString
 #include "Constants.h" // DEGRAD
 #include "DataSet_1D.h"
+#include "DataSet_Modes.h"
 
 // CONSTRUCTOR
 Action_Projection::Action_Projection() :
@@ -14,7 +15,7 @@ Action_Projection::Action_Projection() :
 
 void Action_Projection::Help() const {
   mprintf("\t[<name>] evecs <evecs dataset> [out <outfile>] [beg <beg>] [end <end>]\n"
-          "\t[<mask>] [dihedrals <dataset arg>]\n\t%s\n"
+          "\t{[<mask>] | [dihedrals <dataset arg>] | [data <dataset arg> ...]}\n\t%s\n"
           "  Calculate projection along given eigenvectors.\n", ActionFrameCounter::HelpText);
 }
 
@@ -65,9 +66,10 @@ Action::RetType Action_Projection::Init(ArgList& actionArgs, ActionInit& init, i
   if (modinfo_->Meta().ScalarType() != MetaData::COVAR &&
       modinfo_->Meta().ScalarType() != MetaData::MWCOVAR &&
       modinfo_->Meta().ScalarType() != MetaData::DIHCOVAR &&
-      modinfo_->Meta().ScalarType() != MetaData::IDEA)
+      modinfo_->Meta().ScalarType() != MetaData::IDEA &&
+      modinfo_->Meta().ScalarType() != MetaData::DATACOVAR)
   {
-    mprinterr("Error: evecs type is not COVAR, MWCOVAR, DIHCOVAR, or IDEA.\n");
+    mprinterr("Error: evecs type is not COVAR, MWCOVAR, DIHCOVAR, DATACOVAR, or IDEA.\n");
     return Action::ERR;
   }
 
@@ -90,6 +92,16 @@ Action::RetType Action_Projection::Init(ArgList& actionArgs, ActionInit& init, i
                 " number of average elements %i\n", DihedralSets_.size()*2, modinfo_->NavgCrd());
       return Action::ERR;
     }
+  } else if (modinfo_->Meta().ScalarType() == MetaData::DATACOVAR) {
+    DihedralSets_.clear();
+    std::string dataarg = actionArgs.GetStringKey("data");
+    while (!dataarg.empty()) {
+      if (DihedralSets_.AppendSetsFromArgs( ArgList(dataarg), init.DSL() )) {
+        mprinterr("Error: Could not add data sets using argument '%s'\n", dataarg.c_str());
+        return Action::ERR;
+      }
+      dataarg = actionArgs.GetStringKey("data");
+    }
   } else {
     // Get mask
     if (mask_.SetMaskString( actionArgs.GetMaskNext() )) return Action::ERR;
@@ -129,6 +141,8 @@ Action::RetType Action_Projection::Init(ArgList& actionArgs, ActionInit& init, i
   FrameCounterInfo();
   if (modinfo_->Meta().ScalarType() == MetaData::DIHCOVAR)
     mprintf("\t%zu dihedral data sets.\n", DihedralSets_.size());
+  else if (modinfo_->Meta().ScalarType() == MetaData::DATACOVAR)
+    mprintf("\t%zu data sets.\n", DihedralSets_.size());
   else
     mprintf("\tAtom Mask: [%s]\n", mask_.MaskString());
 
@@ -137,7 +151,9 @@ Action::RetType Action_Projection::Init(ArgList& actionArgs, ActionInit& init, i
 
 // Action_Projection::Setup()
 Action::RetType Action_Projection::Setup(ActionSetup& setup) {
-  if (modinfo_->Meta().ScalarType() != MetaData::DIHCOVAR) {
+  if (modinfo_->Meta().ScalarType() != MetaData::DIHCOVAR &&
+      modinfo_->Meta().ScalarType() != MetaData::DATACOVAR)
+  {
     // Setup mask
     if (setup.Top().SetupIntegerMask( mask_ )) return Action::ERR;
     if (mask_.None()) {
@@ -227,6 +243,20 @@ Action::RetType Action_Projection::DoAction(int frameNum, ActionFrame& frm) {
       float fproj = (float)proj;
       project_[mode]->Add( frameNum, &fproj );
     }
+  } else if (modinfo_->Meta().ScalarType() == MetaData::DATACOVAR ) {
+    for (int mode = beg_; mode < end_; ++mode) {
+      DataSet_Modes::AvgIt Avg = modinfo_->AvgBegin();
+      double proj = 0.0;
+      for (Array1D::const_iterator it = DihedralSets_.begin();
+                                   it != DihedralSets_.end(); ++it)
+      {
+        double dval = (*it)->Dval( frm.TrajoutNum() ) - *(Avg++);
+        proj += (dval * *Vec);
+        Vec++;
+      }
+      float fproj = (float)proj;
+      project_[mode]->Add( frameNum, &fproj );
+    }
   } else { // if modinfo_.ScalarType() == IDEA
     int ip = 0;
     for (int mode = beg_; mode < end_; ++mode) {
diff --git a/src/Action_Projection.h b/src/Action_Projection.h
index d74cce3e26..05f263b270 100644
--- a/src/Action_Projection.h
+++ b/src/Action_Projection.h
@@ -1,9 +1,9 @@
 #ifndef INC_ACTION_PROJECTION_H
 #define INC_ACTION_PROJECTION_H
 #include "Action.h"
-#include "DataSet_Modes.h"
 #include "ActionFrameCounter.h"
 #include "Array1D.h"
+class DataSet_Modes;
 /// project snapshots on normal modes
 class Action_Projection : public Action, ActionFrameCounter {
   public:
diff --git a/src/Analysis_Matrix.cpp b/src/Analysis_Matrix.cpp
index 2dddabcbe7..452735ba9e 100644
--- a/src/Analysis_Matrix.cpp
+++ b/src/Analysis_Matrix.cpp
@@ -17,7 +17,7 @@ Analysis_Matrix::Analysis_Matrix() :
 {}
 
 void Analysis_Matrix::Help() const {
-  mprintf("\t<name> [out <filename>] [thermo [outthermo <filename>] [temp <T>]]\n"
+  mprintf("\t<matrix name> [out <filename>] [thermo [outthermo <filename>] [temp <T>]]\n"
           "\t[vecs <#>] [name <modesname>] [reduce]\n"
           "\t[ nmwiz [nmwizvecs <n>] [nmwizfile <file>] %s\n"
           "\t  nmwizmask <mask> ]\n"
diff --git a/src/Analysis_Project.cpp b/src/Analysis_Project.cpp
new file mode 100644
index 0000000000..3245f358b0
--- /dev/null
+++ b/src/Analysis_Project.cpp
@@ -0,0 +1,183 @@
+#include "Analysis_Project.h"
+#include "CpptrajStdio.h"
+#include "DataSet_1D.h"
+#include "DataSet_Modes.h"
+#include "StringRoutines.h"
+
+// Analysis_Project::Help()
+void Analysis_Project::Help() const {
+  mprintf("\tevecs <evecs dataset> [name <name>] [out <outfile>] [beg <beg>] [end <end>]\n"
+          "\t{[dihedrals <dataset arg>] | [data <dataset arg> ...]}\n"
+          "  Calculate projection along given eigenvectors.\n");
+}
+
+// Analysis_Project::Setup()
+Analysis::RetType Analysis_Project::Setup(ArgList& analyzeArgs, AnalysisSetup& setup, int debugIn)
+{
+  beg_ = analyzeArgs.getKeyInt("beg", 1) - 1;
+  end_ = analyzeArgs.getKeyInt("end", 2);
+
+  std::string modesname = analyzeArgs.GetStringKey("evecs");
+  if (modesname.empty()) {
+    mprinterr("Error: No eigenvectors data set specified ('evecs <name>').\n");
+    return Analysis::ERR;
+  }
+
+  // Check if DataSet exists
+  modinfo_ = (DataSet_Modes*)setup.DSL().FindSetOfType( modesname, DataSet::MODES );
+  if (modinfo_ == 0) {
+    mprinterr("Error: No modes set '%s' found.\n", modesname.c_str());
+    return Analysis::ERR;
+  }
+
+  // Output Filename
+  DataFile* DF = setup.DFL().AddDataFile( analyzeArgs.GetStringKey("out"), analyzeArgs );
+
+  Sets_.clear();
+  std::string diharg = analyzeArgs.GetStringKey("dihedrals");
+  std::string dataarg = analyzeArgs.GetStringKey("data");
+  if (!diharg.empty() && !dataarg.empty()) {
+    mprinterr("Error: Specify either 'dihedrals' or 'data', not both.\n");
+    return Analysis::ERR;
+  }
+  if (!diharg.empty()) {
+    // Get dihedral data sets
+    Sets_.AddTorsionSets( setup.DSL().GetMultipleSets( diharg ) );
+    if ( Sets_.empty() ) {
+      mprinterr("Error: No valid data sets found.\n");
+      return Analysis::ERR;
+    }
+  }
+  if (!dataarg.empty()) {
+    while (!dataarg.empty()) {
+      if (Sets_.AppendSetsFromArgs( ArgList(dataarg), setup.DSL() )) {
+        mprinterr("Error: Could not add data sets using argument '%s'\n", dataarg.c_str());
+        return Analysis::ERR;
+      }
+      dataarg = analyzeArgs.GetStringKey("data");
+    }
+  }
+  if (Sets_.empty()) {
+    mprinterr("Error: No input data sets.\n");
+    return Analysis::ERR;
+  }
+
+  // Set up data sets
+  std::string setname = analyzeArgs.GetStringKey("name");
+  if (setname.empty())
+    setname = setup.DSL().GenerateDefaultName("Proj");
+  for (int mode = beg_; mode < end_; ++mode) {
+    int imode = mode + 1;
+    DataSet* dout = setup.DSL().AddSet( DataSet::FLOAT, MetaData(setname, imode) );
+    if (dout == 0) {
+      mprinterr("Error: Could not create output dataset for mode %i\n", imode);
+      return Analysis::ERR;
+    }
+    dout->SetLegend("Mode"+integerToString(imode));
+    project_.push_back( dout );
+    if (DF != 0) DF->AddDataSet( dout );
+  }
+
+  mprintf("    PROJECTION: Calculating projection using eigenvectors %i to %i of %s\n",
+          beg_+1, end_, modinfo_->legend());
+  if (DF != 0)
+    mprintf("\tResults are written to %s\n", DF->DataFilename().full());
+  mprintf("\t%zu input data sets.\n", Sets_.size());
+
+  return Analysis::OK;
+}
+
+// Analysis_Project::Analyze()
+Analysis::RetType Analysis_Project::Analyze() {
+  if (modinfo_->Nmodes() < 1) {
+    mprinterr("Error: modes set '%s' is empty.\n", modinfo_->legend());
+    return Analysis::ERR;
+  }
+  // Check if beg and end are in bounds.
+  if (end_ > modinfo_->Nmodes()) {
+    mprintf("Warning: 'end' %i is greater than # evecs (%i); setting end to %i\n",
+            end_, modinfo_->Nmodes(), modinfo_->Nmodes());
+    end_ = modinfo_->Nmodes();
+  }
+  if (beg_ < 0 || beg_ >= end_) {
+    mprinterr("Error: 'beg' %i out of bounds.\n", beg_+1);
+    return Analysis::ERR;
+  }
+  // Check Modes type
+  if (modinfo_->Meta().ScalarType() == MetaData::DIHCOVAR) {
+    if ((int)Sets_.size() * 2 != modinfo_->VectorSize()) {
+      mprinterr("Error: Number of dihedral data sets %zu does not correspond to"
+                " number of eigenvectors %i\n", Sets_.size()*2, modinfo_->VectorSize());
+      return Analysis::ERR;
+    } else if ((int)Sets_.size() * 2 != modinfo_->NavgCrd()) {
+      mprinterr("Error: Number of dihedral data sets %zu does not correspond to"
+                " number of average elements %i\n", Sets_.size()*2, modinfo_->NavgCrd());
+      return Analysis::ERR;
+    }
+  } else if (modinfo_->Meta().ScalarType() == MetaData::DATACOVAR) {
+    if ((int)Sets_.size() != modinfo_->VectorSize()) {
+      mprinterr("Error: Number of data sets %zu does not correspond to"
+                " number of eigenvectors %i\n", Sets_.size(), modinfo_->VectorSize());
+      return Analysis::ERR;
+    } else if ((int)Sets_.size() != modinfo_->NavgCrd()) {
+      mprinterr("Error: Number of data sets %zu does not correspond to"
+                " number of average elements %i\n", Sets_.size(), modinfo_->NavgCrd());
+      return Analysis::ERR;
+    }
+  } else {
+    mprinterr("Error: Can only do data or dihedral modes currently.\n");
+    return Analysis::ERR; // FIXME this check should be earlier
+  }
+
+  // Check that sets have same size
+  unsigned int maxFrames = 0;
+  if (!Sets_.empty()) {
+    maxFrames = Sets_.Array().front()->Size();
+    for (Array1D::const_iterator it = Sets_.begin(); it != Sets_.end(); ++it)
+    {
+      if ((*it)->Size() != maxFrames) {
+        mprinterr("Error: Set '%s' does not have same size (%zu) as first set (%u)\n",
+                  (*it)->legend(), (*it)->Size(), maxFrames);
+        return Analysis::ERR;
+      }
+    }
+  } 
+  // Loop over frames
+  for (unsigned int idx = 0; idx < maxFrames; idx++) {
+    // Always start at first eigenvector element of first mode.
+    const double* Vec = modinfo_->Eigenvector(beg_);
+    if (modinfo_->Meta().ScalarType() == MetaData::DIHCOVAR ) {
+      for (int mode = beg_; mode < end_; ++mode) {
+        DataSet_Modes::AvgIt Avg = modinfo_->AvgBegin();
+        double proj = 0.0;
+        for (Array1D::const_iterator dih = Sets_.begin();
+                                     dih != Sets_.end(); ++dih)
+        {
+          double theta = (*dih)->Dval( idx ) * Constants::DEGRAD;
+          proj += (cos(theta) - *(Avg++)) * Vec[0];
+          proj += (sin(theta) - *(Avg++)) * Vec[1];
+          Vec += 2;
+        }
+        // TODO: Convert to degrees?
+        float fproj = (float)proj;
+        project_[mode]->Add( idx, &fproj );
+      }
+    } else if (modinfo_->Meta().ScalarType() == MetaData::DATACOVAR ) {
+      for (int mode = beg_; mode < end_; ++mode) {
+        DataSet_Modes::AvgIt Avg = modinfo_->AvgBegin();
+        double proj = 0.0;
+        for (Array1D::const_iterator it = Sets_.begin();
+                                     it != Sets_.end(); ++it)
+        {
+          double dval = (*it)->Dval( idx ) - *(Avg++);
+          proj += (dval * *Vec);
+          Vec++;
+        }
+        float fproj = (float)proj;
+        project_[mode]->Add( idx, &fproj );
+      }
+    }
+  } // END loop over frames
+
+  return Analysis::OK;
+}
diff --git a/src/Analysis_Project.h b/src/Analysis_Project.h
new file mode 100644
index 0000000000..a6f7a57fc5
--- /dev/null
+++ b/src/Analysis_Project.h
@@ -0,0 +1,22 @@
+#ifndef INC_ANALYSIS_PROJECT_H
+#define INC_ANALYSIS_PROJECT_H
+#include "Analysis.h"
+#include "Array1D.h"
+class DataSet_Modes;
+/// <Enter description of Analysis_Project here>
+class Analysis_Project : public Analysis {
+  public:
+    Analysis_Project() {}
+    DispatchObject* Alloc() const { return (DispatchObject*)new Analysis_Project(); }
+    void Help() const;
+
+    Analysis::RetType Setup(ArgList&, AnalysisSetup&, int);
+    Analysis::RetType Analyze();
+  private:
+    int beg_;
+    int end_;
+    DataSet_Modes* modinfo_; ///< Modes to project on
+    Array1D Sets_; ///< Input data sets to project
+    std::vector<DataSet*> project_; ///< Hold output projections for each mode
+};
+#endif
diff --git a/src/Analysis_TICA.cpp b/src/Analysis_TICA.cpp
index a7204be90f..61d799d0fd 100644
--- a/src/Analysis_TICA.cpp
+++ b/src/Analysis_TICA.cpp
@@ -1,58 +1,1106 @@
 #include "Analysis_TICA.h"
+#ifdef CPPTRAJ_DEBUG_TICA
+#include "CoordCovarMatrix_Full.h"
+#include "CoordCovarMatrix_Half.h"
+#endif
+#include "Constants.h" // PI
 #include "CpptrajStdio.h"
-#include "Matrix.h" // TODO DataSet?
-#include <cmath> // sqrt
+#include "DataSet_1D.h"
+#include "DataSet_double.h"
+#include "DataSet_MatrixDbl.h"
+#include "DataSet_Modes.h"
+#include "ProgressBar.h"
+#include <cmath> //sqrt, fabs, log
+#include <algorithm> // std::max
 
 /** CONSTRUCTOR */
 Analysis_TICA::Analysis_TICA() :
   TgtTraj_(0),
   lag_(0),
-  useMass_(false)
+  debug_(0),
+  calcType_(COORDS),
+  useMass_(false),
+  evectorScale_(NO_SCALING),
+  ticaModes_(0),
+  cumulativeVariance_(0)
+# ifdef CPPTRAJ_DEBUG_TICA
+  ,debugC0_(0),
+  debugCT_(0)
+# endif
 {
-  SetHidden(true);
+}
+
+/** DESTRUCTOR */
+Analysis_TICA::~Analysis_TICA() {
+  for (std::vector<DataSet_1D*>::iterator it = cossin_.begin(); it != cossin_.end(); ++it)
+    delete *it;
 }
 
 // Analysis_TICA::Help()
 void Analysis_TICA::Help() const {
-  mprintf("[crdset <set name>] [lag <time lag>] [mask <mask>] [mass]\n");
+  mprintf("\t{ crdset <COORDS set name> [mask <mask>] |\n"
+          "\t  data <input set arg1> ... }\n"
+          "\t[lag <time lag>] [map {kinetic|commute|none}]\n"
+          "\t[name <output set name>] [out <file>] [cumvarout <file>]\n"
+          "  Perform time-independent correlation analysis for either coordinates\n"
+          "  or 1D data sets; the data sets can either be all periodic (in which case\n"
+          "  they will be converted to cos/sin form) or not.\n"
+         );
+          
 }
 
 // Analysis_TICA::Setup()
 Analysis::RetType Analysis_TICA::Setup(ArgList& analyzeArgs, AnalysisSetup& setup, int debugIn)
 {
-  // Attempt to get coords dataset from datasetlist
+  debug_ = debugIn;
+  // Attempt to get coords dataset or datasets from datasetlist
+  TgtTraj_ = 0;
+  sets_.clear();
   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();
+  std::string dataarg = analyzeArgs.GetStringKey("data");
+  if (!setname.empty() && !dataarg.empty()) {
+    mprinterr("Error: Specify either 'crdset' or 'data', not both.\n");
+    return Analysis::ERR;
+  }
+  if (!setname.empty()) {
+    calcType_ = COORDS;
+    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;
+    }
+  } else if (!dataarg.empty()) {
+    calcType_ = DATA;
+    while (!dataarg.empty()) {
+      if (sets_.AppendSetsFromArgs( ArgList(dataarg), setup.DSL() )) {
+        mprinterr("Error: Could not add data sets using argument '%s'\n", dataarg.c_str());
+        return Analysis::ERR;
+      }
+      dataarg = analyzeArgs.GetStringKey("data");
+    }
+    // Check if sets are periodic or not
+    if (!sets_.empty()) {
+      Array1D::const_iterator setit = sets_.begin();
+      bool isTorsion = (*setit)->Meta().IsTorsionArray();
+      for (; setit != sets_.end(); ++setit) {
+        if (isTorsion != (*setit)->Meta().IsTorsionArray()) {
+          mprinterr("Error: If one set is periodic, all must be periodic (%s).\n", (*setit)->legend());
+          return Analysis::ERR;
+        }
+      }
+      if (isTorsion)
+        calcType_ = PERIODIC;
+    }
+  } else {
+    mprinterr("Error: Must specify either 'crdset' or 'data'.\n");
     return Analysis::ERR;
   }
   // Other keywords
-  lag_ = analyzeArgs.getKeyInt("lag", 1);
+  std::string maparg = analyzeArgs.GetStringKey("map");
+  if (!maparg.empty()) {
+    if (maparg == "kinetic")
+      evectorScale_ = KINETIC_MAP;
+    else if (maparg == "commute")
+      evectorScale_ = COMMUTE_MAP;
+    else if (maparg == "none")
+      evectorScale_ = NO_SCALING;
+    else {
+      mprinterr("Error: Unrecognized keyword for 'map' argument: %s\n", maparg.c_str());
+      return Analysis::ERR;
+    }
+  } else
+    evectorScale_ = KINETIC_MAP;
+  lag_ = analyzeArgs.getKeyInt("lag", 10);
   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");
+# ifdef CPPTRAJ_DEBUG_TICA
+  maskstr = analyzeArgs.GetStringKey("mask2");
+  if (!maskstr.empty()) {
+    mprintf("DEBUG: Second mask detected.\n");
+    if (mask2_.SetMaskString( maskstr )) {
+      mprinterr("Error: Could not set second atom mask string '%s'\n", maskstr.c_str());
+      return Analysis::ERR;
+    }
+  }
+# endif
+  //useMass_ = analyzeArgs.hasKey("mass"); // TODO enable
+
+  // Allocate data sets/data file
+  std::string dsname = analyzeArgs.GetStringKey("name");
+  ticaModes_ = (DataSet_Modes*)setup.DSL().AddSet( DataSet::MODES, dsname, "TICA" );
+  if (ticaModes_ == 0) {
+    mprinterr("Error: Could not allocate output TICA modes.\n");
+    return Analysis::ERR;
+  }
+  DataFile* outfile = setup.DFL().AddDataFile( analyzeArgs.GetStringKey("out"), analyzeArgs);
+  if (outfile != 0)
+    outfile->AddDataSet( ticaModes_ );
 
+  cumulativeVariance_ = (DataSet_1D*)setup.DSL().AddSet(DataSet::DOUBLE, MetaData(ticaModes_->Meta().Name(), "cumvar"));
+  if (cumulativeVariance_ == 0) {
+    mprinterr("Error: Could not allocate output cumulative variance.\n");
+    return Analysis::ERR;
+  }
+  cumulativeVariance_->ModifyDim(Dimension::X).SetLabel("Mode");
+  // Change default precision
+  cumulativeVariance_->SetupFormat().SetFormatWidthPrecision(12,8);
+  DataFile* cvoutfile = setup.DFL().AddDataFile( analyzeArgs.GetStringKey("cumvarout"), analyzeArgs);
+  if (cvoutfile != 0)
+    cvoutfile->AddDataSet( cumulativeVariance_ );
+# ifdef CPPTRAJ_DEBUG_TICA
+  debugC0_ = setup.DFL().AddCpptrajFile(analyzeArgs.GetStringKey("debugc0"), "TICA C0 debug",
+                                                                   DataFileList::TEXT, true);
+  if (debugC0_ == 0) {
+    mprinterr("Error: Could not open C0 debug file.\n");
+    return Analysis::ERR;
+  }
+  debugCT_ = setup.DFL().AddCpptrajFile(analyzeArgs.GetStringKey("debugct"), "TICA CT debug",
+                                                                   DataFileList::TEXT, true);
+  if (debugCT_ == 0) {
+    mprinterr("Error: Could not open CT debug file.\n");
+    return Analysis::ERR;
+  }
+# else
+  std::string tmparg = analyzeArgs.GetStringKey("debugc0");
+  if (!tmparg.empty()) mprintf("Warning: Not compiled with -DCPPTRAJ_DEBUG_TICA, ignoring 'debugc0'\n");
+  tmparg = analyzeArgs.GetStringKey("debugct");
+  if (!tmparg.empty()) mprintf("Warning: Not compiled with -DCPPTRAJ_DEBUG_TICA, ignoring 'debugct'\n");
+# endif
   // 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());
+  if (TgtTraj_ != 0) {
+    mprintf("\tUsing coordinates from set '%s'\n", TgtTraj_->legend());
+    mprintf("\tUsing atoms selected by mask '%s'\n", mask1_.MaskString());
+    //if (useMass_)
+    //  mprintf("\tMass-weighted.\n");
+    //else
+    //  mprintf("\tNot mass-weighted.\n");
+  }
+  if (!sets_.empty()) {
+    mprintf("\tUsing %zu data sets:", sets_.size());
+    for (Array1D::const_iterator it = sets_.begin(); it != sets_.end(); ++it)
+      mprintf(" %s", (*it)->legend());
+    mprintf("\n");
+    if (calcType_ == PERIODIC)
+      mprintf("\tSets are periodic (torsions).\n");
+    else
+      mprintf("\tSets are not periodic.\n");
+  }
   mprintf("\tTime lag: %i frames.\n", lag_);
-  if (useMass_)
-    mprintf("\tMass-weighted.\n");
-  else
-    mprintf("\tNot mass-weighted.\n");
+# ifdef CPPTRAJ_DEBUG_TICA
+  if (debugC0_ != 0)
+    mprintf("\tDebug C0 output to %s\n", debugC0_->Filename().full());
+  if (debugCT_ != 0)
+    mprintf("\tDebug CT output to %s\n", debugCT_->Filename().full());
+# endif
+  switch (evectorScale_) {
+    case NO_SCALING  : mprintf("\tNot scaling eigenvectors.\n"); break;
+    case KINETIC_MAP : mprintf("\tScaling eigenvectors by eigenvalues.\n"); break;
+    case COMMUTE_MAP : mprintf("\tScaling eigenvectors by regularized time scales.\n"); break;
+  }
+  mprintf("\tTICA data set: %s\n", ticaModes_->legend());
+  if (outfile != 0)
+    mprintf("\tTICA data set written to '%s'\n", outfile->DataFilename().full());
+  mprintf("\tCumulative variance set: %s\n", cumulativeVariance_->legend());
+  if (cvoutfile != 0)
+    mprintf("\tCumulative variance written to '%s'\n", cvoutfile->DataFilename().full());
 
   return Analysis::OK;
 }
 
 // Analysis_TICA::Analyze()
 Analysis::RetType Analysis_TICA::Analyze() {
+  if (TgtTraj_ != 0) {
+    // 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;
+    }
+  }
+
+  // Check that sets have same size
+  unsigned int maxFrames = 0;
+  if (!sets_.empty()) {
+    maxFrames = sets_.Array().front()->Size();
+    for (DSarray::const_iterator it = sets_.begin(); it != sets_.end(); ++it)
+    {
+      if ((*it)->Size() != maxFrames) {
+        mprinterr("Error: Set '%s' does not have same size (%zu) as first set (%u)\n",
+                  (*it)->legend(), (*it)->Size(), maxFrames);
+        return Analysis::ERR;
+      }
+    }
+  } else if (TgtTraj_ != 0) {
+    maxFrames = TgtTraj_->Size();
+  } else {
+    // Sanity check
+    mprinterr("Internal Error: Unhandled calculation type in Analysis_TICA::Analyze().\n");
+    return Analysis::ERR;
+  }
+  if (maxFrames < 1) {
+    mprinterr("Error: No frames to analyze.\n");
+    return Analysis::ERR;
+  }
+  // Calculate start and end times for C0 and CT
+  if ( (unsigned int)lag_ >= maxFrames ) {
+    mprinterr("Error: lag %i >= max frames %u\n", lag_, maxFrames);
+    return Analysis::ERR;
+  }
+
+  // Split each periodic set into a cos/sin pair TODO do this prior for the mean calc
+  cossin_.clear();
+  if (calcType_ == PERIODIC) {
+    cossin_.reserve(sets_.size() * 2);
+    for (Array1D::const_iterator it = sets_.begin(); it != sets_.end(); ++it)
+    {
+      DataSet_double* CosSet = new DataSet_double();
+      CosSet->Allocate(DataSet::SizeArray(1, (*it)->Size()));
+      DataSet_double* SinSet = new DataSet_double();
+      SinSet->Allocate(DataSet::SizeArray(1, (*it)->Size()));
+      for (unsigned int ii = 0; ii < (*it)->Size(); ii++) {
+        double theta = (*it)->Dval(ii) * Constants::DEGRAD;
+        CosSet->AddElement( cos(theta) );
+        SinSet->AddElement( sin(theta) );
+      }
+      cossin_.push_back( (DataSet_1D*)CosSet );
+      cossin_.push_back( (DataSet_1D*)SinSet );
+    }
+  }
+
+  if (calcMatrices(maxFrames)) return Analysis::ERR;
+
+  if (evectorScale_ == KINETIC_MAP) {
+    // Weight eigenvectors by eigenvalues
+    for (int ii = 0; ii < ticaModes_->Nmodes(); ii++)
+      ticaModes_->MultiplyEvecByFac( ii, ticaModes_->Eigenvalue(ii) );
+  } else if (evectorScale_ == COMMUTE_MAP) {
+    // Weight eigenvectors by regularized time scales
+    for (int ii = 0; ii < ticaModes_->Nmodes(); ii++) {
+      double ts = 1 - lag_ / log(fabs(ticaModes_->Eigenvalue(ii)));
+      double dval = tanh(Constants::PI * ((ts - lag_) / lag_) + 1);
+      dval = std::max(dval, 0.0);
+      double rts = 0.5 * ts * dval;
+      ticaModes_->MultiplyEvecByFac( ii, sqrt(rts / 2.0) );
+    }
+  }
+
+  // Calculate cumulative variance
+  cumulativeVariance_->Allocate(DataSet::SizeArray(1, ticaModes_->Nmodes()));
+  double cumulativeSum = 0;
+  for (int ii = 0; ii < ticaModes_->Nmodes(); ii++) {
+    double dval = fabs(ticaModes_->Eigenvalue(ii));
+    dval *= dval;
+    cumulativeSum += dval;
+    cumulativeVariance_->Add(ii, &cumulativeSum);
+  }
+  // Normalize the cumulative variance
+  DataSet_double& cvset = static_cast<DataSet_double&>( *cumulativeVariance_ );
+  for (int ii = 0; ii < ticaModes_->Nmodes(); ii++)
+    cvset[ii] /= cumulativeSum;
+
+  //if (TgtTraj_ != 0)
+  //  return analyze_crdset();
+  //else if (!sets_.empty())
+  //  return analyze_datasets();
+
+  return Analysis::OK;
+}
+
+// -----------------------------------------------------------------------------
+#ifdef CPPTRAJ_DEBUG_TICA
+/// FOR DEBUG
+static inline void printDarray(const char* desc, std::vector<double> const& arrayIn, const char* fmt)
+{
+  //static const char* fmt = "%15.8f";
+  mprintf("DEBUG: %s:  [", desc);
+  int col = 0;
+  for (std::vector<double>::const_iterator it = arrayIn.begin(); it != arrayIn.end(); ++it)
+  {
+    mprintf(fmt, *it);
+    if ( (it+1) == arrayIn.end() ) mprintf("]");
+    col++;
+    if (col==4) {
+      mprintf("\n");
+      col = 0;
+    }
+  }
+  if (col != 0)
+    mprintf("\n");
+}
+
+/// For debugging - print eigenvalues to file
+static void printEvals(DataSet_Modes const& modes, const char* fname) {
+  CpptrajFile outfile;
+  if (outfile.OpenWrite(fname)) {
+    mprinterr("Internal Error: printEvals: could not open file %s\n", fname);
+    return;
+  }
+  for (int ii = 0; ii < modes.Nmodes(); ii++)
+    outfile.Printf("%12.8f\n", modes.Eigenvalue(ii));
+  outfile.CloseFile();
+}
+
+/// For debugging - print eigenvectors to file
+static void printEvecs(DataSet_Modes const& modes, const char* fname) {
+  CpptrajFile outfile;
+  if (outfile.OpenWrite(fname)) {
+    mprinterr("Internal Error: printEvals: could not open file %s\n", fname);
+    return;
+  }
+  for (int ii = 0; ii < modes.Nmodes(); ii++) {
+    const double* evec = modes.Eigenvector(ii);
+    for (int jj = 0; jj < modes.VectorSize(); jj++)
+      outfile.Printf("%12.8f", evec[jj]);
+    outfile.Printf("\n");
+  }
+  outfile.CloseFile();
+}
+
+/// For debugging. Print matrix to file
+static void printMatrix(const char* fname, DataSet_2D& matR, ArgList& tmpArgs,
+                        int width, int precision, TextFormat::FmtType fmt)
+{
+  if (width > 0) {
+    matR.SetupFormat().SetFormatWidthPrecision( width, precision );
+    matR.SetupFormat().SetFormatType( fmt );
+  }
+  DataFile outfile8;
+  outfile8.SetupDatafile(fname, tmpArgs, 0);
+  outfile8.AddDataSet( &matR );
+  outfile8.WriteDataOut();
+  tmpArgs.SetAllUnmarked();
+}
+
+/// For debugging. Print matrix to file
+static void printMatrix(const char* fname, DataSet_2D& matR, ArgList& tmpArgs)
+{
+  printMatrix(fname, matR, tmpArgs, -1, -1, TextFormat::DOUBLE);
+}
+#endif /* CPPTRAJ_DEBUG_TICA */
+// -----------------------------------------------------------------------------
+/** Calculate combined effective sums for tau=0 and tau=lag for 1D data sets. */
+void Analysis_TICA::calc_sums_from1Dsets(Darray& means, std::vector<DataSet_1D*> const& setsIn,
+                                         unsigned int lagIn, unsigned int end1)
+{
+  means.assign( setsIn.size(), 0 );
+  for (unsigned int idx = 0; idx != setsIn.size(); ++idx) {
+    DataSet_1D* seti = setsIn[idx];
+    //unsigned int end1 = seti->Size() - lag_;
+    unsigned int k2 = lagIn;
+    for (unsigned int k1 = 0; k1 < end1; k1++, k2++) {
+      means[idx] += (seti->Dval(k1) + seti->Dval(k2));
+    }
+  }
+}
+
+/** Calculate combined effective sums for tau=0 and tau=lag for COORDS set. */
+void Analysis_TICA::calc_sums_fromCoordsSet(Darray& means, unsigned int end1) const {
+  // Allocate frames
+  Frame coords1;
+  coords1.SetupFrameFromMask( mask1_ );
+  Frame coords2 = coords1;
+  //Frame coords1 = TgtTraj_->AllocateFrame();
+  //Frame coords2 = TgtTraj_->AllocateFrame();
+
+  means.assign( mask1_.Nselected() * 3, 0 );
+  unsigned int k2 = lag_;
+  for (unsigned int k1 = 0; k1 < end1; k1++, k2++) {
+    //TgtTraj_->GetFrame(k1, coords1);
+    //TgtTraj_->GetFrame(k2, coords2);
+    TgtTraj_->GetFrame(k1, coords1, mask1_);
+    TgtTraj_->GetFrame(k2, coords2, mask1_);
+    unsigned int jdx = 0;
+    //for (int idx = 0; idx != mask1_.Nselected(); ++idx, jdx += 3)
+    for (int idx = 0; idx != mask1_.Nselected(); ++idx, jdx += 3)
+    {
+      //int at = mask1_[idx];
+      const double* xyz1 = coords1.XYZ( idx );
+      const double* xyz2 = coords2.XYZ( idx );
+      means[jdx  ] += (xyz1[0] + xyz2[0]);
+      means[jdx+1] += (xyz1[1] + xyz2[1]);
+      means[jdx+2] += (xyz1[2] + xyz2[2]);
+    }
+  }
+}
+
+/** Calculate total weight */
+double Analysis_TICA::calc_total_weight(Darray const& weights, unsigned int end1) {
+  // Total weight is times 2 because symmetric
+  double total_weight = 0;
+  if (!weights.empty()) {
+    for (Darray::const_iterator it = weights.begin(); it != weights.end(); ++it)
+      total_weight += *it;
+    total_weight *= 2;
+  } else
+    total_weight = end1 * 2;
+  return total_weight;
+}
+
+/** Create XXYY and XYYX matrices. */
+void Analysis_TICA::create_matrices_from1Dsets( std::vector<DataSet_1D*> const& setsIn,
+                                                DataSet_2D* matXXYY,
+                                                DataSet_2D* matXYYX,
+                                                Darray const& means,
+                                                unsigned int lagIn,
+                                                unsigned int end1 )
+{
+  unsigned int Nrows = matXXYY->Nrows();
+  unsigned int Ncols = matXXYY->Ncols();
+  unsigned int xxyyIdx = 0;
+  unsigned int xyyxIdx = 0;
+
+  ParallelProgress progress(Nrows);
+
+  for (unsigned int row = 0; row < Nrows; row++) {
+    progress.Update(row);
+    for (unsigned int col = row; col < Ncols; col++) {
+      DataSet_1D* seti = setsIn[row];
+      double offi = means[row];
+      DataSet_1D* setj = setsIn[col];
+      double offj = means[col];
+      double sum = 0;
+      double sumxx = 0;
+      unsigned int k2 = lagIn;
+      for (unsigned int k1 = 0; k1 < end1; k1++, k2++) {
+        double dvali1 = seti->Dval(k1) - offi;
+        double dvalj2 = setj->Dval(k2) - offj;
+        double dvali2 = seti->Dval(k2) - offi;
+        double dvalj1 = setj->Dval(k1) - offj;
+        //if (row == 0 && col == 0) mprintf("DBG1: %u %u %u %g %g\n", row, col, k1, dvali, dvalj);
+        // XYYX
+        sum += (dvali1 * dvalj2);
+        sum += (dvali2 * dvalj1);
+        // XXYY
+        sumxx += (dvali1 * dvalj1);
+        sumxx += (dvalj2 * dvali2);
+      }
+      matXYYX->SetElement(xyyxIdx++, sum);
+      matXXYY->SetElement(xxyyIdx++, sumxx);
+    }
+  }
+  progress.Finish();
+}
+
+/** Create XXYY and XYYX matrices. */
+void Analysis_TICA::create_matrices_from1Dsets( DataSet_2D* matXXYY,
+                                                DataSet_2D* matXYYX,
+                                                Darray const& means,
+                                                unsigned int end1 )
+const
+{
+  MetaData md = ticaModes_->Meta();
+  md.SetScalarMode( MetaData::M_MATRIX );
+  md.SetScalarType( MetaData::DATACOVAR );
+  ticaModes_->SetMeta( md );
+  unsigned int Ncols = sets_.size();
+
+  matXXYY->AllocateHalf( Ncols );
+  matXYYX->AllocateHalf( Ncols );
+
+  create_matrices_from1Dsets( sets_.Array(), matXXYY, matXYYX, means, lag_, end1 );
+}
+
+/** Create XXYY and XYYX matrices for periodic 1D sets. */
+void Analysis_TICA::create_matrices_fromPeriodicSets( DataSet_2D* matXXYY, DataSet_2D* matXYYX,
+                                                Darray const& means, unsigned int end1 )
+const
+{
+  MetaData md = ticaModes_->Meta();
+  md.SetScalarMode( MetaData::M_MATRIX );
+  md.SetScalarType( MetaData::DIHCOVAR );
+  ticaModes_->SetMeta( md );
+  unsigned int Ncols = sets_.size() * 2;
+
+  matXXYY->AllocateHalf( Ncols );
+  matXYYX->AllocateHalf( Ncols );
+
+  create_matrices_from1Dsets( cossin_, matXXYY, matXYYX, means, lag_, end1 );
+}
+
+/** Create XXYY and XYYX matrices for COORDS set. */
+void Analysis_TICA::create_matrices_fromCoordsSet(DataSet_2D* matXXYY, DataSet_2D* matXYYX,
+                                                Darray const& means, unsigned int end1 )
+const
+{
+  MetaData md = ticaModes_->Meta();
+  md.SetScalarMode( MetaData::M_MATRIX );
+  md.SetScalarType( MetaData::COVAR );
+  ticaModes_->SetMeta( md );
+  unsigned int Ncols = mask1_.Nselected() * 3;
+  unsigned int Nrows = Ncols;
+
+  matXXYY->AllocateHalf( Ncols );
+  matXYYX->AllocateHalf( Ncols );
+
+  // Allocate frames
+  Frame coords1;
+  coords1.SetupFrameFromMask( mask1_ );
+  Frame coords2 = coords1;
+  //Frame coords1 = TgtTraj_->AllocateFrame();
+  //Frame coords2 = TgtTraj_->AllocateFrame();
+
+  ParallelProgress progress( end1 );
+  unsigned int k2 = lag_;
+  for (unsigned int k1 = 0; k1 < end1; k1++, k2++) {
+    progress.Update( k1 );
+    //TgtTraj_->GetFrame(k1, coords1);
+    //TgtTraj_->GetFrame(k2, coords2);
+    TgtTraj_->GetFrame(k1, coords1, mask1_);
+    TgtTraj_->GetFrame(k2, coords2, mask1_);
+
+    //unsigned int xxyyIdx = 0;
+    //unsigned int xyyxIdx = 0;
+    unsigned int Idx = 0;
+    for (unsigned int row = 0; row < Nrows; row++) {
+      for (unsigned int col = row; col < Ncols; col++) {
+        double offi = means[row];
+        double offj = means[col];
+
+        double dvali1 = coords1[row] - offi;
+        double dvalj2 = coords2[col] - offj;
+        double dvali2 = coords2[row] - offi;
+        double dvalj1 = coords1[col] - offj;
+
+        // XYYX
+        matXYYX->UpdateElement(Idx, (dvali1 * dvalj2) +
+                                    (dvali2 * dvalj1));
+        // XXYY
+        matXXYY->UpdateElement(Idx, (dvali1 * dvalj1) +
+                                    (dvalj2 * dvali2));
+
+        Idx++;
+      } // END loop over cols
+    } // END loop over rows
+  } // END loop over frames
+  progress.Finish();
+}
+
+// -----------------------------------------------------------------------------
+/** Calculate XXYY and XYYX matrices. */
+int Analysis_TICA::calcMatrices(unsigned int maxFrames) const {
+  mprintf("\tCalculating C0 and CT matrices.\n");
+  unsigned int c0end = maxFrames - (unsigned int)lag_;
+  if (debug_ > 0)
+    mprintf("DEBUG: C0 start = %u end = %u\n", 0, c0end);
+
+  // Calculate means 
+  Darray means;
+  switch (calcType_) {
+    case DATA     : calc_sums_from1Dsets( means, sets_.Array(), lag_, c0end ); break;
+    case PERIODIC : calc_sums_from1Dsets( means, cossin_, lag_, c0end ); break;
+    case COORDS   : calc_sums_fromCoordsSet( means, c0end ); break;
+  }
+
+  // Calculate total weight
+  double total_weight = calc_total_weight( Darray(), c0end );
+  for (Darray::iterator it = means.begin(); it != means.end(); ++it)
+    *it /= total_weight;
+# ifdef CPPTRAJ_DEBUG_TICA
+  CpptrajFile meanout; // DEBUG
+  if (meanout.OpenWrite("test.mean.dat")) {
+    mprinterr("Error: Could not open test.mean.dat\n");
+    return 1;
+  }
+  for (Darray::const_iterator it = means.begin(); it != means.end(); ++it) {
+    meanout.Printf("%12.8f\n", *it); // DEBUG
+  }
+  meanout.CloseFile();
+#endif
+
+  // Calculate matrices
+  DataSet_MatrixDbl matXXYY, matXYYX;
+  matXXYY.SetMeta(MetaData("C0"));
+  switch (calcType_) {
+    case DATA :
+      create_matrices_from1Dsets(static_cast<DataSet_2D*>(&matXXYY), static_cast<DataSet_2D*>(&matXYYX), means, c0end);
+      break;
+    case PERIODIC :
+      create_matrices_fromPeriodicSets(static_cast<DataSet_2D*>(&matXXYY), static_cast<DataSet_2D*>(&matXYYX), means, c0end);
+      break;
+    case COORDS :
+      create_matrices_fromCoordsSet(static_cast<DataSet_2D*>(&matXXYY), static_cast<DataSet_2D*>(&matXYYX), means, c0end);
+      break;
+  }
+# ifdef CPPTRAJ_DEBUG_TICA
+  ArgList tmpArgs("square2d noheader");
+  printMatrix("test.xxyy.dat", matXXYY, tmpArgs, 12, 6, TextFormat::DOUBLE);
+  printMatrix("test.xyyx.dat", matXYYX, tmpArgs, 12, 6, TextFormat::DOUBLE);
+# endif
+  // Normalize
+  matXXYY.Normalize( 1.0 / total_weight );
+  matXYYX.Normalize( 1.0 / total_weight );
+# ifdef CPPTRAJ_DEBUG_TICA
+  printMatrix("test.xxyy.norm.dat", matXXYY, tmpArgs);
+  printMatrix("test.xyyx.norm.dat", matXYYX, tmpArgs);
+# endif
+  // Calculate TICA eigenmodes
+  if (calculateTICA( means, matXXYY, matXYYX)) {
+    mprinterr("Error: Caclulation of TICA modes failed.\n");
+    return 1;
+  }
+
+  return 0;
+}
+
+/** Calculate TICA eigenvalues/eigenvectors from C0 and CT matrices. */
+int Analysis_TICA::calculateTICA(Darray const& meanX, DataSet_2D const& CXXYY, DataSet_2D const& Cxy) const {
+  // ---------------------------------------------
+  // Get C0 eigenvectors/eigenvalues
+  DataSet_Modes C0_Modes;
+  C0_Modes.SetAvgCoords( meanX );
+  // Want all eigenvectors
+  if (C0_Modes.CalcEigen( CXXYY, CXXYY.Ncols() )) {
+    mprinterr("Error: Could not calculate eigenvectors and eigenvales for C0 matrix.\n");
+    return 1;
+  }
+  // Eigenvec/vals should come out of CalcEigen sorted from largest Eigenval to smallest.
+  // Determine cutoff; C0 is symmetric positive-definite so select
+  // cutoff so that negative eigenvalues vanish.
+  double min_eval = C0_Modes.Eigenvalue(C0_Modes.Nmodes()-1);
+  if (debug_ > 0)
+    mprintf("DEBUG: Min C0 eigenvalue= %g\n", min_eval);
+  double epsilon = 1e-6; // FIXME TODO make user-definable
+  if (min_eval < 0) {
+    epsilon = std::max(epsilon, -min_eval + 1e-16);
+  }
+  // Get the absolute value of each eigenvector
+  Darray abs_c0_evals;
+  abs_c0_evals.reserve( C0_Modes.Nmodes() );
+  for (int ii = 0; ii < C0_Modes.Nmodes(); ii++)
+    abs_c0_evals.push_back( fabs( C0_Modes.Eigenvalue(ii) ) );
+  // Find the index of the first abs(eigenvalue) smaller than epsilon
+  int idx_first_smaller = 0;
+  for (; idx_first_smaller < C0_Modes.Nmodes(); idx_first_smaller++) {
+    if ( abs_c0_evals[idx_first_smaller] < epsilon ) {
+      //mprintf("%g < %g\n", abs_c0_evals[idx_first_smaller], epsilon ); // DEBUG
+      break;
+    }
+  }
+  if (debug_ > 0)
+    mprintf("DEBUG: Index of eigenvalue smaller than %g %i\n", epsilon, idx_first_smaller);
+  C0_Modes.ResizeModes( idx_first_smaller );
+  // Enforce canonical eigenvector signs
+  C0_Modes.SetCanonicalEvecSigns();
+# ifdef CPPTRAJ_DEBUG_TICA
+  // DEBUG - print eigenvalues/eigenvectors
+  printEvals(C0_Modes, "sm.dat");
+  printEvecs(C0_Modes, "Vm.dat");
+# endif
+  // Create matrix Ltrans, where rows are eigenvectors of C0 times eigenvalues of C0
+  DataSet_MatrixDbl matLtrans;
+  matLtrans.Allocate2D( C0_Modes.VectorSize(), C0_Modes.Nmodes() );
+  unsigned int idx = 0;
+  for (int ii = 0; ii < C0_Modes.Nmodes(); ii++) {
+    double fac = 1.0 / sqrt(C0_Modes.Eigenvalue(ii));
+    const double* evec = C0_Modes.Eigenvector(ii);
+    for (int jj = 0; jj < C0_Modes.VectorSize(); ++jj)
+      matLtrans.SetElement(idx++, evec[jj] * fac);
+  }
+# ifdef CPPTRAJ_DEBUG_TICA
+  // DEBUG - write unnormalized matrix
+  ArgList tmpArgs("square2d noheader"); // DEBUG
+  printMatrix("matLtrans.dat", matLtrans, tmpArgs, 12, 8, TextFormat::DOUBLE);
+# endif
+  // L is transposed already (eigenvectors are in rows)
+  // Calculate L^T * Ct
+  DataSet_MatrixDbl matLtransCt;
+  DataSet_2D::RetType ret = matLtransCt.Multiply(matLtrans, Cxy);
+  if (ret != DataSet_2D::OK) {
+    mprinterr("Error: Could not multiply L^T x CT\n");
+    return 1;
+  }
+# ifdef CPPTRAJ_DEBUG_TICA
+  // DEBUG - write unnormalized matrix
+  printMatrix("matLCt.dat", matLtransCt, tmpArgs, 15, 8, TextFormat::SCIENTIFIC);
+# endif
+  // Calculate (L^T * Ct) * L
+  // Need to use transpose of Ltrans to get L
+  DataSet_MatrixDbl Ct_trans;
+  Ct_trans.SetMeta(MetaData("CT"));
+  ret = Ct_trans.Multiply_M2transpose(matLtransCt, matLtrans);
+  if (ret != DataSet_2D::OK) {
+    mprinterr("Error: Could not multiply (L^T x CT) x L\n");
+    return 1;
+  }
+# ifdef CPPTRAJ_DEBUG_TICA
+  // DEBUG - write unnormalized matrix
+  printMatrix("Ct_trans.dat", Ct_trans, tmpArgs, 12, 8, TextFormat::DOUBLE);
+# endif
+  DataSet_Modes Ct_Modes;
+  Ct_Modes.SetAvgCoords( meanX );
+  // Want all eigenvectors
+  if (Cxy.IsSymmetric()) {
+    mprintf("\tCT is symmetric.\n");
+    if (Ct_Modes.CalcEigen( Ct_trans, Ct_trans.Ncols() )) {
+      mprinterr("Error: Could not calculate eigenvectors and eigenvalues for CT matrix.\n");
+      return 1;
+    }
+  } else {
+    mprintf("\tCT is not symmetric.\n");
+    if (Ct_Modes.CalcEigen_General( Ct_trans )) {
+      mprinterr("Error: Could not calculate eigenvectors and eigenvalues for CT matrix (non-symmetric).\n");
+      return 1;
+    }
+  }
+  // Sort by abs(eigenvalue)
+  Ct_Modes.SortByAbsEigenvalue();
+# ifdef CPPTRAJ_DEBUG_TICA
+  printEvals(Ct_Modes, "ctvals.dat");
+  printEvecs(Ct_Modes, "ctvecs.dat");
+# endif
+  // Calculate R^T * L^T to get (LR)^T
+  DataSet_MatrixDbl ctm; // FIXME DataSet_Modes eigenvectors should be in a DataSet_MatrixDbl?
+  ctm.Allocate2D( Ct_Modes.VectorSize(), Ct_Modes.Nmodes() );
+  std::copy( Ct_Modes.Eigenvectors(),
+             Ct_Modes.Eigenvectors() + (Ct_Modes.Nmodes() * Ct_Modes.VectorSize()),
+             (double*)ctm.MatrixPtr() );
+  DataSet_MatrixDbl matRt;
+  matRt.Multiply( ctm, matLtrans );
+# ifdef CPPTRAJ_DEBUG_TICA
+  printMatrix("matRt.dat", matRt, tmpArgs, 12, 8, TextFormat::DOUBLE);
+# endif
+  //DataSet_Modes matRmodes;
+  ticaModes_->SetAvgCoords( Ct_Modes.AvgCrd() );
+  ticaModes_->SetModes(false, Ct_Modes.Nmodes(), Ct_Modes.VectorSize(),
+                       Ct_Modes.EigenvaluePtr(), (const double*)matRt.MatrixPtr());
+  ticaModes_->SetCanonicalEvecSigns();
+  //DataFile outfile9;
+  //outfile9.SetupDatafile("matRmodes.dat", 0);
+  //outfile9.AddDataSet( ticaModes_ );
+  //outfile9.WriteDataOut();
+/*
+  // The following is to test the math in the same exact order as L x Ct_Modes^T
+  DataSet_MatrixDbl matL;
+  ret = matL.TransposeOf( matLtrans );
+  if (ret != DataSet_2D::OK) {
+    mprinterr("Error: Could not get transpose of L^T\n");
+    if ( ret == DataSet_2D::ALLOC_ERR) mprinterr("Error: Allocation error.\n");
+    return 1;
+  }
+  // DEBUG - write unnormalized matrix
+  printMatrix("matL.dat", matL, tmpArgs, 12, 8, TextFormat::DOUBLE);
+
+  // Put eigenvectors in columns
+  DataSet_MatrixDbl R_trans;
+  if (R_trans.Allocate2D( Ct_Modes.Nmodes(), Ct_Modes.VectorSize() )) {
+    mprinterr("Error: Could not allocate matrix for Ct eigenvectors.\n");
+    return 1;
+  }
+  idx = 0;
+  for (unsigned int row = 0; row < R_trans.Nrows(); row++) {
+    for (unsigned int col = 0; col < R_trans.Ncols(); col++) {
+      const double* evec = Ct_Modes.Eigenvector(col);
+      R_trans[idx++] = evec[row];
+    }
+  }
+  // DEBUG - write unnormalized matrix
+  printMatrix("R_trans.dat", R_trans, tmpArgs, 12, 8, TextFormat::DOUBLE);
+
+  // Calculate L * R^T
+  // TODO calculate R^T * L^T to get (LR)^T instead?
+  DataSet_MatrixDbl matR;
+  matR.Multiply( matL, R_trans );
+
+  // Change eigenvector (in columns) signs
+  for (unsigned int col = 0; col < matR.Ncols(); col++) {
+    // Find the maximum absolute value of the eigenvector (in column)
+    double abs_maxval = 0;
+    unsigned int abs_maxidx = 0;
+    for (unsigned int row = 0; row < matR.Nrows(); row++) {
+      double dval = fabs( matR.GetElement( col, row ) );
+      if (dval > abs_maxval) {
+        abs_maxval = dval;
+        abs_maxidx = row;
+      }
+    }
+    double elt = matR.GetElement(col, abs_maxidx);
+    mprintf("argmax %u %u %g\n", col, abs_maxidx, elt);
+    double sign;
+    if (elt < 0)
+      sign = -1.0;
+    else
+      sign = 1.0;
+    // Multiply all elements of eigenvector (in column) by sign of max abs element
+    for (unsigned int row = 0; row < matR.Nrows(); row++) {
+      double dval = matR.GetElement( col, row ) * sign;
+      matR.SetElement( col, row, dval );
+    }
+  }
+  // DEBUG - write unnormalized matrix
+  printMatrix("matR.dat", matR, tmpArgs, 12, 8, TextFormat::DOUBLE);
+*/
+  return 0;
+}
+
+#ifdef CPPTRAJ_DEBUG_TICA
+// =============================================================================
+/// Calculate sum over each set TODO weights
+static inline void calculate_sum(std::vector<double>& sumX,
+                                 std::vector<DataSet_1D*> const& sets, 
+                                 unsigned int nelt_,
+                                 unsigned int startFrame, unsigned int endFrame)
+{
+  sumX.assign( sets.size() * nelt_, 0 );
+
+  if (nelt_ == 2) {
+    mprinterr("Internal Error: CoordCovarMatrix_Half::AddDataToMatrix_C0CT(): Not implemented.\n");
+    return;
+  } else if (nelt_ == 1) {
+    for (unsigned int jdx = 0; jdx < sets.size(); jdx++) {
+      for (unsigned int idx = startFrame; idx < endFrame; idx++) {
+        sumX[jdx] += sets[jdx]->Dval(idx);
+      }
+    }
+  }
+}
+
+/// Subtract the set mean from every element of the set
+static inline void subtract_mean(DataSet_double& out,
+                                 DataSet_1D const* in,
+                                 unsigned int nelt_,
+                                 double total_weight,
+                                 double sumX,
+                                 unsigned int startFrame, unsigned int endFrame)
+{
+//  DataSet_double& out = static_cast<DataSet_double&>( *outPtr );
+  //out.clear();
+  out.Allocate(DataSet::SizeArray(1, endFrame - startFrame));
+  //out.reserve(endFrame - startFrame);
+  double mean = sumX / total_weight;
+  for (unsigned int idx = startFrame; idx != endFrame; idx++) {
+    out.AddElement( in->Dval(idx) - mean );
+    //out.push_back( in->Dval(idx) - mean );
+  }
+}
+
+/// Multiply transpose of matrix by matrix TODO since the resulting matrix is supposed to be symmetric we can speed this up
+static void matT_times_mat( DataSet_2D* out,
+                            std::vector<DataSet_double> const& M1,
+                            std::vector<DataSet_double> const& M2)
+{
+  unsigned int Nrows = M1.size();
+  unsigned int Ncols = M2.size();
+  out->Allocate2D( Ncols, Nrows );
+  unsigned int idx = 0;
+  for (unsigned int row = 0; row < Nrows; row++) {
+    DataSet_double const& seti = M1[row];
+    for (unsigned int col = 0; col < Ncols; col++) {
+      DataSet_double const& setj = M2[col];
+      // seti->Size() must equal setj->Size()
+      double sum = 0;
+      for (unsigned int k = 0; k < seti.Size(); k++) {
+        //if (row == 0 && col == 0) mprintf("DBG0: %u %u %u %g %g\n", row, col, k, seti.Dval(k), setj.Dval(k));
+        sum += (seti.Dval(k) * setj.Dval(k));
+      }
+      out->SetElement(idx++, sum);
+      //mprintf(" %12.4f", sum);
+    }
+    //mprintf("\n");
+  }
+}
+
+/// For eaach matrix, Multiply transpose of matrix by matrix, then sum
+static void matT_times_mat_symmetric( DataSet_2D* out,
+                                      std::vector<DataSet_double> const& M1,
+                                      std::vector<DataSet_double> const& M2 )
+{
+  if (M1.size() != M2.size()) {
+    mprinterr("Internal Error: matT_times_mat_symmetric: Different # of sets.\n");
+    return;
+  }
+  out->AllocateHalf( M1.size() );
+  unsigned int Nrows = M1.size();
+  unsigned int Ncols = Nrows;
+  unsigned int idx = 0;
+  for (unsigned int row = 0; row < Nrows; row++) {
+    DataSet_double const& seti1 = M1[row];
+    DataSet_double const& seti2 = M2[row];
+    for (unsigned int col = row; col < Ncols; col++) {
+      DataSet_double const& setj1 = M1[col];
+      DataSet_double const& setj2 = M2[col];
+      double sum = 0;
+      // ALL SETS MUST HAVE SAME SIZE
+      unsigned int nframes = seti1.Size();
+      for (unsigned int k = 0; k < nframes; k++) {
+        sum += (seti1.Dval(k) * setj1.Dval(k));
+        sum += (seti2.Dval(k) * setj2.Dval(k));
+      }
+      out->SetElement(idx++, sum);
+      //mprintf(" %12.4f", sum);
+    }
+    //mprintf("\n");
+  }
+}
+
+
+/** Calculate instantaneous covariance and lagged covariance arrays */
+int Analysis_TICA::calculateCovariance_C0CT(DSarray const& sets)
+const
+{
+  static unsigned int nelt_ = 1;
+  // Check that sets have same size
+  unsigned int maxFrames = sets.front()->Size();
+  for (DSarray::const_iterator it = sets.begin(); it != sets.end(); ++it)
+  {
+    if ((*it)->Size() != maxFrames) {
+      mprinterr("Error: Set '%s' does not have same size (%zu) as first set (%u)\n",
+                (*it)->legend(), (*it)->Size(), maxFrames);
+      return 1;
+    }
+  }
+  // Calculate start and end times for C0 and CT
+  if ( (unsigned int)lag_ >= maxFrames ) {
+    mprinterr("Error: lag %i >= max frames %u\n", lag_, maxFrames);
+    return 1;
+  }
+  unsigned int c0end = maxFrames - (unsigned int)lag_;
+  mprintf("DEBUG: C0 start = %u end = %u\n", 0, c0end);
+  unsigned int ctstart = (unsigned int)lag_;
+  mprintf("DEBUG: CT start = %u end = %u\n", ctstart, maxFrames);
+  // Calculate sum over each set
+  Darray sumX;
+  calculate_sum(sumX, sets, nelt_, 0, c0end);
+  printDarray("sx_raw", sumX, "%15.8f");
+
+  Darray sumY;
+  calculate_sum(sumY, sets, nelt_, ctstart, maxFrames);
+  printDarray("sy_raw", sumY, "%15.8f");
+
+  // Sanity check
+  if (sumX.size() != sumY.size()) {
+    mprinterr("Internal Error: Analysis_TICA::calculateCovariance_C0CT(): sumX size != sumY size\n");
+    return 1;
+  }
+
+  // Calculate effective sum (symmetric)
+  Darray sx;
+  sx.reserve( sumX.size() );
+  for (unsigned int jdx = 0; jdx != sumX.size(); jdx++)
+    sx.push_back( sumX[jdx] + sumY[jdx] );
+
+  // Total weight is times 2 because symmetric
+  //double total_weight = 0;
+  //for (Darray::const_iterator it = weights.begin(); it != weights.end(); ++it)
+  //  total_weight += *it;
+  //total_weight *= 2;
+  double total_weight = c0end * 2;
+  mprintf("DEBUG: Total weight= %f\n", total_weight);
+  // DEBUG - print mean
+  CpptrajFile meanout;
+  if (meanout.OpenWrite("debug.mean.dat")) {
+    mprinterr("Error: Could not open debug.mean.dat\n");
+    return 1;
+  }
+  Darray meanX;
+  meanX.reserve( sx.size() );
+  for (Darray::const_iterator it = sx.begin(); it != sx.end(); ++it) {
+    meanX.push_back( *it / total_weight);
+    meanout.Printf("%12.6f\n", meanX.back()); // DEBUG
+  }
+  meanout.CloseFile();
+
+
+  // Center TODO sx_centered and sy_centered may not need to be calced
+  Darray sx_centered, sy_centered;
+  sx_centered.reserve( sumX.size() );
+  sy_centered.reserve( sumY.size() );
+  for (unsigned int idx = 0; idx != sumX.size(); idx++)
+  {
+    sx_centered.push_back( sumX[idx] - (0.5 * sx[idx]) );
+    sy_centered.push_back( sumY[idx] - (0.5 * sx[idx]) );
+  }
+  printDarray("sx_raw_centered", sx_centered, "%16.8e");
+  printDarray("sy_raw_centered", sy_centered, "%16.8e");
+
+  // Remove mean
+  typedef std::vector<DataSet_double> DDArray;
+  DDArray CenteredX(sets.size());
+  DDArray CenteredY(sets.size());
+
+  Darray tmpx, tmpy; // DEBUG
+  // Because symmetric, sy = sx //TODO use meanX set
+  Darray const& sy = sx;
+  for (unsigned int jdx = 0; jdx != sets.size(); jdx++) {
+    subtract_mean(CenteredX[jdx], sets[jdx], nelt_, total_weight, sx[jdx], 0, c0end);
+    subtract_mean(CenteredY[jdx], sets[jdx], nelt_, total_weight, sy[jdx], ctstart, maxFrames);
+    tmpx.push_back( CenteredX[jdx].Dval(0) ); // DEBUG
+    tmpy.push_back( CenteredY[jdx].Dval(0) ); // DEBUG
+  }
+  printDarray("X0", tmpx, "%16.8e");
+  printDarray("Y0", tmpy, "%16.8e");
+
+  // ---------------------------------------------
+  ArgList tmpArgs("square2d noheader");
+  // Calculate Cxxyy
+  DataSet_MatrixDbl CXXYY;// = (DataSet_2D*)new DataSet_MatrixDbl();
+  matT_times_mat_symmetric(static_cast<DataSet_2D*>(&CXXYY), CenteredX, CenteredY);
+  // DEBUG - write unnormalized matrix
+  printMatrix("cxxyy.dat", CXXYY, tmpArgs, 12, 6, TextFormat::DOUBLE);
+
+  // Calculate Cxyyx
+  DataSet_MatrixDbl Cxy, Cyx;
+  matT_times_mat(static_cast<DataSet_2D*>(&Cxy), CenteredX, CenteredY);
+  matT_times_mat(static_cast<DataSet_2D*>(&Cyx), CenteredY, CenteredX);
+  for (unsigned int idx = 0; idx != Cxy.Size(); idx++) {
+    double sum = Cxy.GetElement(idx) + Cyx.GetElement(idx);
+    Cxy.SetElement(idx, sum);
+  }
+  // DEBUG - write unnormalized matrix
+  printMatrix("cxyyx.dat", Cxy, tmpArgs, 12, 6, TextFormat::DOUBLE);
+
+  // Normalize
+  CXXYY.Normalize( 1.0 / total_weight );
+  Cxy.Normalize( 1.0 / total_weight );
+  // DEBUG - write normalized matrices
+  printMatrix("cxxyy.norm.dat", CXXYY, tmpArgs);
+  printMatrix("cxyyx.norm.dat", Cxy, tmpArgs);
+
+  // ---------------------------------------------
+  if (calculateTICA( meanX, CXXYY, Cxy)) {
+    mprinterr("Error: Caclulation of TICA modes failed.\n");
+    return 1;
+  }
+
+  return 0;
+}
+
+/** Analyze multiple 1D data sets. */
+Analysis::RetType Analysis_TICA::analyze_datasets() {
+  if (calculateCovariance_C0CT( sets_.Array() ) || ticaModes_ == 0) {
+    mprinterr("Error: Could not calculate C0/CT matrices.\n");
+    return Analysis::ERR;
+  }
+  
+/*  // Matrix - half
+  CoordCovarMatrix_Half covarMatrix;
+  if (covarMatrix.SetupMatrix( sets_.Array() )) {
+    mprinterr("Error: Could not set up C0 matrix for data sets.\n");
+    return Analysis::ERR;
+  }
+  covarMatrix.AddDataToMatrix( sets_.Array() );
+  // Normalize
+  if (covarMatrix.FinishMatrix()) {
+    mprinterr("Error: Could not normalize coordinate covariance matrix for C0.\n");
+    return Analysis::ERR;
+  }
+  // DEBUG PRINT
+  covarMatrix.DebugPrint("C0", *debugC0_, " %12.6f");*/
+
+  return Analysis::OK;
+}
+
+/** Analyze coordinates data set. */
+Analysis::RetType Analysis_TICA::analyze_crdset() {
   unsigned int Nframes = TgtTraj_->Size();
   if (Nframes < 1) {
     mprinterr("Error: No frames to analyze.\n");
@@ -68,90 +1116,71 @@ Analysis::RetType Analysis_TICA::Analyze() {
     mprinterr("Error: No atoms selected by mask '%s'\n", mask1_.MaskString());
     return Analysis::ERR;
   }
+  // DEBUG
+  if (mask2_.MaskStringSet()) {
+    if ( TgtTraj_->Top().SetupIntegerMask( mask2_ ) ) {
+      mprinterr("Error: Could not evaluate second atom mask '%s'\n", mask2_.MaskString());
+      return Analysis::ERR;
+    }
+    mask2_.MaskInfo();
+    if (mask2_.None()) {
+      mprinterr("Error: No atoms selected by second mask '%s'\n", mask2_.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));
+  Frame coords0 = TgtTraj_->AllocateFrame();
+  //coords0.SetupFrameFromMask( mask1_, TgtTraj_->Top().Atoms(), TgtTraj_->CoordsInfo() );
+  //Frame coords1 = coords0;
   // Matrix - half
-  Matrix<double> covarMatrix;
-  covarMatrix.resize( mask1_.Nselected()*3, 0 );
+  CoordCovarMatrix_Half covarMatrix;
+  if (covarMatrix.SetupMatrix(TgtTraj_->Top().Atoms(), mask1_, useMass_ )) {
+    mprinterr("Error: Could not set up C0 matrix for '%s'.\n", TgtTraj_->legend());
+    return Analysis::ERR;
+  }
   // Loop over frames
   for (unsigned int frm0 = 0; frm0 < Nframes; frm0++) {
-    mprintf("DEBUG: Frame %i\n", frm0);
-    TgtTraj_->GetFrame(frm0, coords0, mask1_);
+    //mprintf("DEBUG: Frame %i\n", frm0);
+    //TgtTraj_->GetFrame(frm0, coords0, mask1_);
+    TgtTraj_->GetFrame(frm0, coords0);
     // 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
+    covarMatrix.AddFrameToMatrix( coords0, mask1_ );
   } // 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
+  if (covarMatrix.FinishMatrix()) {
+    mprinterr("Error: Could not normalize coordinate covariance matrix for C0.\n");
+    return Analysis::ERR;
+  }
+
   // 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));
+  covarMatrix.DebugPrint("C0", *debugC0_);
+
+  if (mask2_.MaskStringSet()) {
+    // DEBUG
+    // Matrix - full
+    CoordCovarMatrix_Full CT;
+    CT.SetupMatrix(TgtTraj_->Top().Atoms(), mask1_,
+                   TgtTraj_->Top().Atoms(), mask2_, useMass_);
+    // Loop over frames
+    for (unsigned int frm0 = 0; frm0 < Nframes; frm0++) {
+      //mprintf("DEBUG: Frame %i\n", frm0);
+      //TgtTraj_->GetFrame(frm0, coords0, mask1_);
+      TgtTraj_->GetFrame(frm0, coords0);
+      // Covariance
+      CT.AddFrameToMatrix( coords0, mask1_, coords0, mask2_ );
+    } // END loop over frames
+
+    // Normalize
+    if (CT.FinishMatrix()) {
+      mprinterr("Error: Could not normalize coordinate covariance matrix for CT.\n");
+      return Analysis::ERR;
     }
-    mprintf("\n");
+
+    // DEBUG PRINT
+    CT.DebugPrint("CT", *debugCT_);
   }
+
   return Analysis::OK;
 }
+#endif /* CPPTRAJ_DEBUG_TICA */
diff --git a/src/Analysis_TICA.h b/src/Analysis_TICA.h
index fe44df32af..f8acbbaea0 100644
--- a/src/Analysis_TICA.h
+++ b/src/Analysis_TICA.h
@@ -1,19 +1,77 @@
 #ifndef INC_ANALYSIS_TICA_H
 #define INC_ANALYSIS_TICA_H
 #include "Analysis.h"
-/// <Enter description of Analysis_TICA here>
+#include "Array1D.h"
+class DataSet_2D;
+class DataSet_Modes;
+/// Perform time-independent correlation analysis 
 class Analysis_TICA : public Analysis {
   public:
     Analysis_TICA();
+    ~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
+    enum EvectorScaleType {
+      NO_SCALING = 0, ///< Do not scale eigenvectors
+      KINETIC_MAP,    ///< Scale eigenvectors by eigenvalues
+      COMMUTE_MAP     ///< Scale eigenvectors by regularized time scales
+    };
+    enum CalcType {
+      COORDS = 0, ///< Use XYZ coordinates
+      DATA,       ///< Use 1D data sets
+      PERIODIC    ///< Use 1D periodic data sets
+    };
+
+    typedef std::vector<DataSet_1D*> DSarray;
+    typedef std::vector<double> Darray;
+
+    /// Calculate total weight
+    static double calc_total_weight(Darray const&, unsigned int);
+    /// Calculate sums of X and Y for 1D data sets in a single pass
+    static void calc_sums_from1Dsets(Darray&, std::vector<DataSet_1D*> const&, unsigned int, unsigned int);
+    /// Calculate sums of X and Y for COORDS sets in a single pass
+    void calc_sums_fromCoordsSet(Darray&, unsigned int) const;
+    /// Create XXYY and XYYX matrices from an array of 1D sets
+    static void create_matrices_from1Dsets(std::vector<DataSet_1D*> const&, DataSet_2D*, DataSet_2D*,
+                                           Darray const&, unsigned int, unsigned int);
+    /// Create XXYY and XYYX matrices from an array of 1D sets in a single pass
+    void create_matrices_from1Dsets(DataSet_2D*, DataSet_2D*, Darray const&, unsigned int) const;
+    /// Create XXYY and XYYX matrices from an array of periodic 1D sets in a single pass
+    void create_matrices_fromPeriodicSets(DataSet_2D*, DataSet_2D*, Darray const&, unsigned int) const;
+    /// Create XXYY and XYYX matrices from COORDS set in a single pass
+    void create_matrices_fromCoordsSet(DataSet_2D*, DataSet_2D*, Darray const&, unsigned int) const;
+    /// Calculate TICA matrices
+    int calcMatrices(unsigned int) const;
+    /// Calculate TICA modes
+    int calculateTICA(Darray const&, DataSet_2D const&, DataSet_2D const&) const;
+#   ifdef CPPTRAJ_DEBUG_TICA
+    /// Analyze using coordinates data set (TgtTraj_)
+    Analysis::RetType analyze_crdset();
+    /// Analyze using 1D data sets (sets_)
+    Analysis::RetType analyze_datasets();
+    /// Calculate instantaneous and lagged covariance matrices
+    int calculateCovariance_C0CT(DSarray const&) const;
+#   endif
+
+    Array1D sets_;                   ///< Input 1D data sets (data)
+    DSarray cossin_;                 ///< Input 1D periodic sets converted to cos/sin pairs (data)
+    DataSet_Coords* TgtTraj_;        ///< Input trajectory (crdset)
+    AtomMask mask1_;                 ///< Atoms to use in matrix calc (crdset)
+    int lag_;                        ///< TICA time lag
+    int debug_;
+    CalcType calcType_;              ///< Type of calculation (TODO allow mixed data types)
+    bool useMass_;                   ///< Control whether to mass-weight TODO enable
+    EvectorScaleType evectorScale_;  ///< Eigenvector scaling type
+    DataSet_Modes* ticaModes_;       ///< Output TICA modes
+    DataSet_1D* cumulativeVariance_; ///< Hold output cumulative variance
+#   ifdef CPPTRAJ_DEBUG_TICA
+    AtomMask mask2_;                 ///< Second atom mask for debugging full covar matrix
+    CpptrajFile* debugC0_;           ///< Debug output for C0
+    CpptrajFile* debugCT_;           ///< Debug output for CT
+#   endif
 };
 #endif
diff --git a/src/ArgList.cpp b/src/ArgList.cpp
index 873259ea0f..14ae587156 100644
--- a/src/ArgList.cpp
+++ b/src/ArgList.cpp
@@ -494,3 +494,8 @@ bool ArgList::Contains(const char *key) const {
     }
   return false;
 }
+
+/** Make all arguments unmarked. */
+void ArgList::SetAllUnmarked() {
+  marked_.assign( marked_.size(), false );
+}
diff --git a/src/ArgList.h b/src/ArgList.h
index f05b7dda26..9f2fe9421e 100644
--- a/src/ArgList.h
+++ b/src/ArgList.h
@@ -59,6 +59,8 @@ class ArgList {
     void AddArg(std::string const&);
     /// Mark given argument
     void MarkArg(int);
+    /// Set all arguments as unmarked
+    void SetAllUnmarked();
     /// Print a warning if not all arguments are marked
     bool CheckForMoreArgs() const;
     /// Print the argument list
diff --git a/src/Array1D.cpp b/src/Array1D.cpp
index 468f9f4ac1..424e5ec0f3 100644
--- a/src/Array1D.cpp
+++ b/src/Array1D.cpp
@@ -64,8 +64,20 @@ int Array1D::AddTorsionSets(DataSetList const& SetList) {
   return 0;
 }
 
+/** Add sets from arguments, clear the list first. */
+int Array1D::AddSetsFromArgs(ArgList const& dsetArgs, DataSetList const& DSLin)
+{
+  return addSetsFromArgs(dsetArgs, DSLin, false);
+}
+
+/** Append sets from arguments to the list. */
+int Array1D::AppendSetsFromArgs(ArgList const& dsetArgs, DataSetList const& DSLin)
+{
+  return addSetsFromArgs(dsetArgs, DSLin, true);
+}
+
 // Array1D::AddSetsFromArgs()
-int Array1D::AddSetsFromArgs(ArgList const& dsetArgs, DataSetList const& DSLin) {
+int Array1D::addSetsFromArgs(ArgList const& dsetArgs, DataSetList const& DSLin, bool append) {
   DataSetList input_dsl;
   for (ArgList::const_iterator dsa = dsetArgs.begin(); dsa != dsetArgs.end(); ++dsa)
     input_dsl += DSLin.GetMultipleSets( *dsa );
@@ -74,7 +86,8 @@ int Array1D::AddSetsFromArgs(ArgList const& dsetArgs, DataSetList const& DSLin)
     return 1;
   }
   // Add to main list
-  array_.clear();
+  if (!append)
+    array_.clear();
   if (AddDataSets( input_dsl ))
     return 1;
   return 0;
diff --git a/src/Array1D.h b/src/Array1D.h
index e3da93a8d2..fd144c5211 100644
--- a/src/Array1D.h
+++ b/src/Array1D.h
@@ -24,8 +24,15 @@ class Array1D {
     void SortArray1D();
     int AddDataSets(DataSetList const&);
     int AddTorsionSets(DataSetList const&);
+    /// Add sets to the list, clear first
     int AddSetsFromArgs(ArgList const&, DataSetList const&);
+    /// Append sets to the list
+    int AppendSetsFromArgs(ArgList const&, DataSetList const&);
+    /// \return the internal array
+    std::vector<DataSet_1D*> const& Array() const { return array_; }
   private:
+    int addSetsFromArgs(ArgList const&, DataSetList const&, bool);
+
     std::vector<DataSet_1D*> array_;
 };
 #endif
diff --git a/src/Command.cpp b/src/Command.cpp
index e098f8c9bd..d2730f07ca 100644
--- a/src/Command.cpp
+++ b/src/Command.cpp
@@ -162,6 +162,7 @@
 #include "Action_Keep.h"
 #include "Action_AvgBox.h"
 #include "Action_ToroidalDiffusion.h"
+#include "Action_MinMaxDist.h"
 // ----- ANALYSIS --------------------------------------------------------------
 #include "Analysis_Hist.h"
 #include "Analysis_Corr.h"
@@ -206,6 +207,7 @@
 #include "Analysis_EvalPlateau.h"
 #include "Analysis_TICA.h"
 #include "Analysis_CalcDiffusion.h"
+#include "Analysis_Project.h"
 
 CmdList Command::commands_ = CmdList();
 
@@ -362,6 +364,7 @@ void Command::Init() {
   Command::AddCmd( new Action_MakeStructure(), Cmd::ACT, 1, "makestructure" );
   Command::AddCmd( new Action_Mask(),          Cmd::ACT, 1, "mask" );
   Command::AddCmd( new Action_Matrix(),        Cmd::ACT, 1, "matrix" );
+  Command::AddCmd( new Action_MinMaxDist(),    Cmd::ACT, 2, "mindist", "maxdist" );
   Command::AddCmd( new Action_MinImage(),      Cmd::ACT, 1, "minimage" );
   Command::AddCmd( new Action_Molsurf(),       Cmd::ACT, 1, "molsurf" );
   Command::AddCmd( new Action_MultiDihedral(), Cmd::ACT, 1, "multidihedral" );
@@ -433,6 +436,7 @@ void Command::Init() {
   Command::AddCmd( new Analysis_MultiHist(),   Cmd::ANA, 1, "multihist" );
   Command::AddCmd( new Analysis_Overlap(),     Cmd::ANA, 1, "overlap" ); // hidden 
   Command::AddCmd( new Analysis_PhiPsi(),      Cmd::ANA, 1, "phipsi" );
+  Command::AddCmd( new Analysis_Project(),     Cmd::ANA, 1, "projectdata" );
   Command::AddCmd( new Analysis_Regression(),  Cmd::ANA, 1, "regress" );
   Command::AddCmd( new Analysis_RemLog(),      Cmd::ANA, 1, "remlog" );
   Command::AddCmd( new Analysis_Rms2d(),       Cmd::ANA, 2, "2drms", "rms2d" );
@@ -443,7 +447,7 @@ 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_TICA(),        Cmd::ANA, 1, "tica" );
   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" );
@@ -455,7 +459,6 @@ void Command::Init() {
   Command::AddCmd( new Deprecated_AvgCoord(),    Cmd::DEP, 1, "avgcoord" );
   Command::AddCmd( new Deprecated_DihScan(),     Cmd::DEP, 1, "dihedralscan" );
   Command::AddCmd( new Deprecated_Hbond(),       Cmd::DEP, 2, "acceptor", "donor" );
-  Command::AddCmd( new Deprecated_MinDist(),     Cmd::DEP, 2, "mindist", "maxdist" );
   Command::AddCmd( new Deprecated_ParmBondInfo(),Cmd::DEP, 1, "parmbondinfo" );
   Command::AddCmd( new Deprecated_ParmMolInfo(), Cmd::DEP, 1, "parmmolinfo" );
   Command::AddCmd( new Deprecated_ParmResInfo(), Cmd::DEP, 1, "parmresinfo" );
diff --git a/src/CoordCovarMatrix.cpp b/src/CoordCovarMatrix.cpp
new file mode 100644
index 0000000000..6e62b76b71
--- /dev/null
+++ b/src/CoordCovarMatrix.cpp
@@ -0,0 +1,74 @@
+#include "CoordCovarMatrix.h"
+#include "Atom.h"
+#include "AtomMask.h"
+#include "CpptrajFile.h"
+#include "CpptrajStdio.h"
+#include "Frame.h"
+
+/** CONSTRUCTOR - number of elements */
+CoordCovarMatrix::CoordCovarMatrix() :
+  nframes_(0),
+  nelt_(0),
+  useMass_(false)
+{}
+
+/** Clear the matrix */
+void CoordCovarMatrix::Clear() {
+  covarMatrix_.clear();
+  nframes_ = 0;
+  clearMat();
+}
+
+/** Setup mass array */
+void CoordCovarMatrix::set_mass_array(Darray& mass, std::vector<Atom> const& atoms,
+                                      AtomMask const& maskIn, bool useMassIn)
+{
+  nframes_ = 0;
+  useMass_ = useMassIn;
+  mass.clear();
+  mass.reserve( maskIn.Nselected() );
+  if (useMassIn) {
+    for (AtomMask::const_iterator at = maskIn.begin(); at != maskIn.end(); ++at)
+      mass.push_back( atoms[*at].Mass() );
+  } else {
+    for (int idx = 0; idx < maskIn.Nselected(); idx++)
+      mass.push_back( 1.0 );
+  }
+}
+
+/** Debug print to file with default format. */
+void CoordCovarMatrix::DebugPrint(const char* desc, CpptrajFile& outfile) const {
+  DebugPrint(desc, outfile, " %6.3f");
+}
+
+/** Debug print to file */
+void CoordCovarMatrix::DebugPrint(const char* desc, CpptrajFile& outfile, const char* fmt) const {
+  if (desc != 0)
+    outfile.Printf("DEBUG: CoordCovarMatrix: %s\n", desc);
+  for (unsigned int row = 0; row < covarMatrix_.Nrows(); row++) {
+    for (unsigned int col = 0; col < covarMatrix_.Ncols(); col++) {
+      outfile.Printf(fmt, covarMatrix_.element(col, row));
+    }
+    outfile.Printf("\n");
+  }
+}
+
+/** \return True if incoming array size is divisible by nelt_ */
+bool CoordCovarMatrix::has_valid_size(Darray const& arrayIn) const {
+  return ( (arrayIn.size() % nelt_) == 0);
+}
+
+/** Extract coordinates from given Frame into specified array. */
+void CoordCovarMatrix::get_frame_coords(Darray& arrayIn, Frame const& frameIn, AtomMask const& maskIn)
+const
+{
+  arrayIn.clear();
+  unsigned int arraySize = (unsigned int)maskIn.Nselected() * nelt_;
+  arrayIn.reserve( arraySize );
+  for (AtomMask::const_iterator at = maskIn.begin(); at != maskIn.end(); ++at) {
+    const double* XYZ = frameIn.XYZ(*at);
+    arrayIn.push_back( XYZ[0] );
+    arrayIn.push_back( XYZ[1] );
+    arrayIn.push_back( XYZ[2] );
+  }
+}
diff --git a/src/CoordCovarMatrix.h b/src/CoordCovarMatrix.h
new file mode 100644
index 0000000000..29bbee3bf5
--- /dev/null
+++ b/src/CoordCovarMatrix.h
@@ -0,0 +1,51 @@
+#ifndef INC_COORDCOVARMATRIX_H
+#define INC_COORDCOVARMATRIX_H
+#include "Matrix.h"
+#include <vector>
+class Atom;
+class AtomMask;
+class CpptrajFile;
+class DataSet_1D;
+class Frame;
+/// Coordinate covariance matrix abstract base class
+class CoordCovarMatrix {
+  public:
+    /// CONSTRUCTOR
+    CoordCovarMatrix();
+    /// DESTRUCTOR - virtual since inherited
+    virtual ~CoordCovarMatrix() {}
+    // --------------------------------- 
+    /// Finish calculating the matrix (normalize, calc <rirj> - <ri><rj>)
+    virtual int FinishMatrix() = 0;
+    // ---------------------------------
+    /// Clear the matrix
+    void Clear();
+
+    /// Print matrix elements to STDOUT for debug with default format
+    void DebugPrint(const char*, CpptrajFile&) const;
+    /// Print matrix elements to STDOUT for debug with given format
+    void DebugPrint(const char*, CpptrajFile&, const char*) const;
+  protected:
+    typedef Matrix<double> MatType;
+    typedef std::vector<double> Darray;
+    typedef std::vector<DataSet_1D*> DSarray;
+
+    /// clear internal variables
+    virtual void clearMat() = 0;
+
+    /// set mass array
+    void set_mass_array(Darray&, std::vector<Atom> const&, AtomMask const&, bool);
+
+    /// \return True if incoming Darray size is divisible by nelt_
+    bool has_valid_size(Darray const&) const;
+
+    /// Place coordinates from selected atoms in Frame into an array
+    void get_frame_coords(Darray&, Frame const&, AtomMask const&) const;
+  //private: // TODO all private
+
+    MatType covarMatrix_;  ///< Coordinate covariance matrix
+    unsigned int nframes_; ///< Number of frames added to the matrix
+    unsigned int nelt_;    ///< Number of elements per i,j entry
+    bool useMass_;         ///< If true use mass weighting
+};
+#endif
diff --git a/src/CoordCovarMatrix_Full.cpp b/src/CoordCovarMatrix_Full.cpp
new file mode 100644
index 0000000000..202c128adf
--- /dev/null
+++ b/src/CoordCovarMatrix_Full.cpp
@@ -0,0 +1,186 @@
+#include "CoordCovarMatrix_Full.h"
+#include "AtomMask.h"
+#include "CpptrajStdio.h"
+#include <cmath> //sqrt
+
+/** CONSTRUCTOR */
+CoordCovarMatrix_Full::CoordCovarMatrix_Full()
+{}
+
+/** Clear the matrix */
+void CoordCovarMatrix_Full::clearMat() {
+  vect_1_.clear();
+  vect_2_.clear();
+  mass1_.clear();
+  mass2_.clear();
+}
+
+/** Set up array sizess and masses. */
+int CoordCovarMatrix_Full::SetupMatrix(std::vector<Atom> const& atoms1,
+                                       AtomMask const& maskIn1,
+                                       std::vector<Atom> const& atoms2,
+                                       AtomMask const& maskIn2, bool useMassIn)
+{
+  nelt_ = 3; // xyz
+  unsigned int arraySize1 = (unsigned int)maskIn1.Nselected() * nelt_;
+  unsigned int arraySize2 = (unsigned int)maskIn2.Nselected() * nelt_;
+  // Matrix - full
+  covarMatrix_.resize( arraySize1, arraySize2 );
+
+  vect_1_.assign(arraySize1, 0);
+  vect_2_.assign(arraySize2, 0);
+  set_mass_array( mass1_, atoms1, maskIn1, useMassIn );
+  set_mass_array( mass2_, atoms2, maskIn2, useMassIn );
+
+  return 0;
+}
+
+/** Store diagonal (average and average^2) */
+/*static inline void store_diagonal(std::vector<double>& vect,
+//                                  std::vector<Vec3>& vect2,
+                                  unsigned int nelt,
+                                  Frame const& frameIn,
+                                  AtomMask const& maskIn)
+{
+  for (int idx = 0; idx < maskIn.Nselected(); idx++)
+  {
+    const double* XYZ = frameIn.XYZ( maskIn[idx] );
+    int eidx = idx * nelt;
+    for (unsigned int ii = 0; ii < nelt; ii++) {
+      vect[eidx+ii]  += XYZ[ii];
+//      vect2[idx][ii] += (XYZ[ii] * XYZ[ii]);
+    }
+  }
+}*/
+
+/** Store average */
+static inline void store_diagonal(std::vector<double>& vect, std::vector<double> const& arrayIn)
+{
+  for (unsigned int idx = 0; idx < arrayIn.size(); ++idx)
+    vect[idx] += arrayIn[idx];
+}
+
+/** Add selected atoms in given Frames to the matrix. */
+void CoordCovarMatrix_Full::AddFrameToMatrix(Frame const& frameIn1, AtomMask const& maskIn1,
+                                             Frame const& frameIn2, AtomMask const& maskIn2)
+{
+  Darray array1, array2; // TODO make class vars
+  get_frame_coords(array1, frameIn1, maskIn1);
+  get_frame_coords(array2, frameIn2, maskIn2);
+  AddToMatrix(array1, array2);
+}
+
+/** Add elements to the matrix. */
+void CoordCovarMatrix_Full::AddToMatrix(Darray const& array1, Darray const& array2) {
+  // sanity checks
+  if (!has_valid_size(array1)) {
+    mprinterr("Internal Error: CoordCovarMatrix_Full::AddToMatrix(): Incoming array1 size %zu not divisible by %u\n",
+              array1.size(), nelt_);
+    return;
+  }
+  if (!has_valid_size(array2)) {
+    mprinterr("Internal Error: CoordCovarMatrix_Full::AddToMatrix(): Incoming array2 size %zu not divisible by %u\n",
+              array2.size(), nelt_);
+    return;
+  }
+
+  //MatType::iterator mat = covarMatrix_.begin();
+  for (unsigned int idx2 = 0; idx2 < mass2_.size(); idx2++)
+  {
+    unsigned int eidx2 = idx2 * nelt_;
+    Matrix<double>::iterator mat = covarMatrix_.begin() + (eidx2*covarMatrix_.Ncols()); // NX
+    const double* XYZj = (&array2[0]) + eidx2;
+    for (unsigned int ny = 0; ny < nelt_; ny++) {
+      double Vj = XYZj[ny];
+      for (unsigned int idx1 = 0; idx1 < mass1_.size(); idx1++)
+      {
+        unsigned int eidx1 = idx1 * nelt_;
+        const double* XYZi = (&array1[0]) + eidx1;
+        for (unsigned int nx = 0; nx < nelt_; nx++) {
+          *(mat++) += Vj * XYZi[nx];
+        }
+      }
+    }
+  }
+  // Mask1/mask2 diagonal
+//  store_diagonal(vect_1_, vect2_1_, frameIn1, maskIn1);
+//  store_diagonal(vect_2_, vect2_2_, frameIn2, maskIn2);
+//  store_diagonal(vect_1_, nelt_, frameIn1, maskIn1);
+//  store_diagonal(vect_2_, nelt_, frameIn2, maskIn2);
+  store_diagonal(vect_1_, array1);
+  store_diagonal(vect_2_, array2);
+  nframes_++;
+}
+
+/** Calculate <v^2> - <v><v> */
+/*static inline void vect2_minus_vect(std::vector<Vec3>& vect2, std::vector<Vec3> const& vect)
+{
+  // Sanity check
+  if (vect2.size() != vect.size()) {
+    mprinterr("Internal Error: CoordCovarMatrix_Full: Vect2 size (%zu) != Vect size (%zu)\n",
+              vect2.size(), vect.size());
+    return;
+  }
+  for (unsigned int idx = 0; idx != vect2.size(); idx++) {
+    Vec3& V2 = vect2[idx];
+    Vec3 const& V1 = vect[idx];
+    for (int ny = 0; ny < 3; ny++)
+      V2[ny] -= (V1[ny] * V1[ny]);
+  }
+}*/
+
+/** Finish processing covariance matrix */
+int CoordCovarMatrix_Full::FinishMatrix() {
+  if (nframes_ < 1) {
+    mprinterr("Error: No frames in coordinate covariance matrix.\n");
+    return 1;
+  }
+  // Normalize
+  double norm = 1.0 / (double)nframes_;
+  for (Darray::iterator it = vect_1_.begin(); it != vect_1_.end(); ++it)
+    *it *= norm;
+  for (Darray::iterator it = vect_2_.begin(); it != vect_2_.end(); ++it)
+    *it *= norm;
+//  for (Varray::iterator it = vect2_1_.begin(); it != vect2_1_.end(); ++it)
+//    *it *= norm;
+//  for (Varray::iterator it = vect2_2_.begin(); it != vect2_2_.end(); ++it)
+//    *it *= norm;
+  for (MatType::iterator it = covarMatrix_.begin(); it != covarMatrix_.end(); ++it)
+    *it *= norm;
+  mprintf("DEBUG: First 3 elements: %f %f %f\n",
+          covarMatrix_.element(0, 0),
+          covarMatrix_.element(1, 0),
+          covarMatrix_.element(2, 0));
+  mprintf("DEBUG: First 3 elements of V1: %f %f %f\n",
+          vect_1_[0],
+          vect_1_[1],
+          vect_1_[2]);
+  mprintf("DEBUG: First 3 elements of V2: %f %f %f\n",
+          vect_2_[0],
+          vect_2_[1],
+          vect_2_[2]);
+  // Calc <riri> - <ri><ri>
+//  vect2_minus_vect(vect2_1_, vect_1_);
+//  vect2_minus_vect(vect2_2_, vect_2_);
+  // Calc <rirj> - <rj><rj>
+  Matrix<double>::iterator mat = covarMatrix_.begin();
+  for (unsigned int idx2 = 0; idx2 < mass2_.size(); idx2++)
+  {
+    double mass2 = mass2_[idx2];
+    unsigned int eidx2 = idx2 * nelt_;
+    for (unsigned int ny = 0; ny < nelt_; ny++) {
+      double V2 = vect_2_[eidx2+ny];
+      for (unsigned int idx1 = 0; idx1 < mass1_.size(); idx1++) {
+        double Mass = sqrt(mass2 * mass1_[idx1]);
+        unsigned int eidx1 = idx1 * nelt_;
+        for (unsigned int nx = 0; nx < nelt_; nx++) {
+          double V1 = vect_1_[eidx1+nx];
+          mprintf("mat = (%f - (%f * %f)) * %f\n", *mat, V2, V1, Mass);
+          *mat = (*mat - (V2 * V1)) * Mass;
+          ++mat;
+        }
+      } // END loop over vect_1_
+    }
+  } // END loop over vect_2_
+  return 0;
+}
diff --git a/src/CoordCovarMatrix_Full.h b/src/CoordCovarMatrix_Full.h
new file mode 100644
index 0000000000..f115a07034
--- /dev/null
+++ b/src/CoordCovarMatrix_Full.h
@@ -0,0 +1,30 @@
+#ifndef INC_COORDCOVARMATRIX_FULL_H
+#define INC_COORDCOVARMATRIX_FULL_H
+#include "CoordCovarMatrix.h"
+/// Coordinate covanriance full matrix
+class CoordCovarMatrix_Full : public CoordCovarMatrix {
+  public:
+    CoordCovarMatrix_Full();
+    /// Finish calculating the matrix (normalize, calc <rirj> - <ri><rj>)
+    int FinishMatrix();
+    // ---------------------------------
+    /// Set up matrix for 2 masks
+    int SetupMatrix(std::vector<Atom> const&, AtomMask const&,
+                    std::vector<Atom> const&, AtomMask const&, bool);
+    /// Add selected atoms in Frame to matrix
+    void AddFrameToMatrix(Frame const&, AtomMask const&,
+                          Frame const&, AtomMask const&);
+  private:
+    /// Clear the matrix
+    void clearMat();
+    /// Set up the covariance matrix for selected atoms
+    int setupMat(std::vector<Atom> const&, AtomMask const&);
+    /// Add elements to the matrix
+    void AddToMatrix(Darray const&, Darray const&);
+
+    Darray vect_1_; ///< Hold average of elements in mask1
+    Darray vect_2_; ///< Hold average of elements in mask2
+    Darray mass1_; ///< Hold masses of atoms in mask1
+    Darray mass2_; ///< Hold masses of atoms in mask2
+};
+#endif
diff --git a/src/CoordCovarMatrix_Half.cpp b/src/CoordCovarMatrix_Half.cpp
new file mode 100644
index 0000000000..3cae1185e3
--- /dev/null
+++ b/src/CoordCovarMatrix_Half.cpp
@@ -0,0 +1,243 @@
+#include "CoordCovarMatrix_Half.h"
+#include "AtomMask.h"
+#include "Constants.h"
+#include "CpptrajStdio.h"
+#include "DataSet_1D.h"
+#include <cmath> // sqrt
+
+/** CONSTRUCTOR */
+CoordCovarMatrix_Half::CoordCovarMatrix_Half()
+{}
+
+/** Clear the matrix */
+void CoordCovarMatrix_Half::clearMat() {
+  vect_.clear();
+  mass_.clear();
+}
+
+/** Set up array for incoming data sets. */
+int CoordCovarMatrix_Half::SetupMatrix(DSarray const& sets)
+{
+  int is_periodic = -1;
+  
+  for (DSarray::const_iterator it = sets.begin(); it != sets.end(); ++it)
+  {
+    if ((*it)->Meta().IsTorsionArray()) {
+      if (is_periodic == -1)
+        is_periodic = 1;
+      else if (is_periodic != 1) {
+        mprinterr("Error: If one set is not periodic all must be. Set '%s' is periodic.\n",
+                  (*it)->legend());
+        return 1;
+      }
+    } else {
+      if (is_periodic == -1)
+        is_periodic = 0;
+      else if (is_periodic != 0) {
+        mprinterr("Error: If one set is periodic all must be. Set '%'s is not periodic.\n",
+                  (*it)->legend());
+        return 1;
+      }
+    }
+  }
+  if (is_periodic) {
+    mprintf("\tPeriodic data sets detected.\n");
+    nelt_ = 2;
+  } else {
+    mprintf("\tNon-periodic data sets detected.\n");
+    nelt_ = 1;
+  }
+  unsigned int matSize = sets.size() * nelt_;
+  // Matrix - half
+  covarMatrix_.resize( matSize, 0 );
+
+  vect_.assign( matSize, 0 );
+
+  mass_.resize( sets.size(), 1.0 );
+
+  return 0;
+}
+
+/** Set up array sizess and masses. */
+int CoordCovarMatrix_Half::SetupMatrix(std::vector<Atom> const& atoms,
+                                       AtomMask const& maskIn, bool useMassIn)
+{
+  nelt_ = 3; // xyz
+  unsigned int arraySize = (unsigned int)maskIn.Nselected() * nelt_;
+  // Matrix - half
+  covarMatrix_.resize( arraySize, 0 );
+
+  vect_.assign( arraySize, 0 );
+
+  set_mass_array(mass_, atoms, maskIn, useMassIn);
+
+  return 0;
+}
+
+/** Add data from sets to the matrix. */
+void CoordCovarMatrix_Half::AddDataToMatrix(DSarray const& sets)
+{
+  // TODO check empty input array
+  // Check that sets have same size
+  unsigned int maxFrames = sets.front()->Size();
+  for (DSarray::const_iterator it = sets.begin(); it != sets.end(); ++it)
+  {
+    if ((*it)->Size() != maxFrames) {
+      mprinterr("Error: Set '%s' does not have same size (%zu) as first set (%u)\n",
+                (*it)->legend(), (*it)->Size(), maxFrames);
+      return;
+    }
+  }
+  Darray arrayIn;
+  arrayIn.resize( sets.size() * nelt_ );
+  if (nelt_ == 2) {
+    for (unsigned int idx = 0; idx < maxFrames; idx++) {
+      unsigned int jdx = 0;
+      for (DSarray::const_iterator it = sets.begin(); it != sets.end(); ++it, jdx += 2)
+      {
+        double dval = (*it)->Dval(idx) * Constants::DEGRAD;
+        arrayIn[jdx  ] = cos( dval );
+        arrayIn[jdx+1] = sin( dval );
+      }
+      AddToMatrix(arrayIn);
+    }
+  } else if (nelt_ == 1) {
+    for (unsigned int idx = 0; idx < maxFrames; idx++) {
+      for (unsigned int jdx = 0; jdx < sets.size(); jdx++) {
+        arrayIn[jdx] = sets[jdx]->Dval(idx);
+      }
+      AddToMatrix(arrayIn);
+    }
+  } else {
+    // Sanity check
+    mprinterr("Internal Error: CoordCovarMatrix_Half::AddDataToMatrix(): Unsupported nelt %u\n", nelt_);
+  }
+}
+
+/** Add selected atoms in given Frame to the matrix. */
+void CoordCovarMatrix_Half::AddFrameToMatrix(Frame const& frameIn, AtomMask const& maskIn)
+{
+  Darray arrayIn; // TODO class array?
+  get_frame_coords(arrayIn, frameIn, maskIn);
+  AddToMatrix(arrayIn);
+}
+
+/** Add elements to the matrix. */
+void CoordCovarMatrix_Half::AddToMatrix(Darray const& arrayIn) {
+  // sanity check
+  if (!has_valid_size(arrayIn)) {
+    mprinterr("Internal Error: CoordCovarMatrix_Half::AddToMatrix(): Incoming array size %zu not divisible by %u\n",
+              arrayIn.size(), nelt_);
+    return;
+  }
+  // Covariance
+  MatType::iterator mat = covarMatrix_.begin();
+  for (unsigned int idx2 = 0; idx2 < mass_.size(); idx2++) {
+    unsigned int eidx2 = idx2 * nelt_;
+    const double* XYZj = (&arrayIn[0]) + eidx2;
+    // Store average 
+    for (unsigned int ej = 0; ej < nelt_; ej++)
+      vect_[eidx2+ej] += XYZj[ej];
+    //XYZj.Print("XYZj");
+    // Loop over X, Y, and Z of vecj
+    for (unsigned int jidx = 0; jidx < nelt_; jidx++) {
+      double Vj = XYZj[jidx];
+      // Diagonal
+      for (unsigned int ej = jidx; ej < nelt_; ej++)
+        *(mat++) += Vj * XYZj[ej]; // Vj * j{0,1,2}, Vj * j{1,2}, Vj * j{2}
+      // Inner loop
+      for (unsigned int idx1 = idx2 + 1; idx1 < mass_.size(); idx1++) {
+        unsigned int eidx1 = idx1 * nelt_;
+        const double* XYZi = (&arrayIn[0]) + eidx1;
+        for (unsigned int ei = 0; ei < nelt_; ei++) {
+          *(mat++) += Vj * XYZi[ei];
+        }
+      } // END inner loop over idx1
+    } // END loop over x y z of vecj
+  } // END outer loop over idx2
+  nframes_++;
+}
+
+/** Add given Frame to the matrix. */
+/*void CoordCovarMatrix_Half::AddFrameToMatrix(Frame const& frameIn)
+{
+  // Covariance
+  MatType::iterator mat = covarMatrix_.begin();
+  for (int idx1 = 0; idx1 < frameIn.Natom(); idx1++) {
+    Vec3 XYZi( frameIn.XYZ(idx1) );
+    // Store veci and veci^2
+    vect_[idx1] += XYZi;
+    //XYZi.Print("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 < frameIn.Natom(); idx2++) {
+        Vec3 XYZj( frameIn.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
+  nframes_++;
+}*/
+
+/** Finish the matrix. */
+int CoordCovarMatrix_Half::FinishMatrix() {
+  if (nframes_ < 1) {
+    mprinterr("Error: No frames in coordinate covariance matrix.\n");
+    return 1;
+  }
+  // Normalize
+  double norm = 1.0 / (double)nframes_;
+  for (Darray::iterator it = vect_.begin(); it != vect_.end(); ++it)
+    *it *= norm;
+  for (MatType::iterator it = covarMatrix_.begin(); it != covarMatrix_.end(); ++it)
+    *it *= norm;
+  // DEBUG print mean
+  CpptrajFile outfile;
+  outfile.OpenWrite("debug.mean.dat");
+  for (Darray::iterator it = vect_.begin(); it != vect_.end(); ++it)
+    outfile.Printf("%12.6f\n", *it);
+  outfile.CloseFile();
+  // 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>
+  MatType::iterator mat = covarMatrix_.begin();
+//  double TwoN = (double)( covarMatrix_->Ncols() * 2 );
+  for (unsigned int idx2 = 0; idx2 < mass_.size(); idx2++) {
+    double mass2 = mass_[idx2];
+    for (unsigned int jidx = 0; jidx < nelt_; jidx++) {
+      unsigned int eidx2 = idx2*nelt_;
+//      d_m2_idx = (double)eidx2;
+//      mat = Mat_->begin() + (int)(0.5*d_m2_idx*(TwoN-d_m2_idx-1.0)+d_m2_idx);
+      double Vj = vect_[eidx2 + jidx];
+      for (unsigned int idx1 = idx2; idx1 < mass_.size(); idx1++) {
+        double Mass = sqrt( mass2 * mass_[idx1] );
+        if (idx2 == idx1) {
+          // Self
+          for (unsigned int ej = jidx; ej < nelt_; ej++) {
+            *mat = (*mat - (Vj * vect_[eidx2 + ej])) * Mass;
+            ++mat;
+          }
+        } else {
+          unsigned int eidx1 = idx1*nelt_;
+          for (unsigned int iidx = 0; iidx < nelt_; iidx++) {
+            *mat = (*mat - (Vj * vect_[eidx1 + iidx])) * Mass;
+            ++mat;
+          }
+        }
+      } // END inner loop over idx1
+    } // END loop over elements of vect_[idx2]
+  } // END outer loop over idx2
+  return 0;
+}
diff --git a/src/CoordCovarMatrix_Half.h b/src/CoordCovarMatrix_Half.h
new file mode 100644
index 0000000000..a63d412509
--- /dev/null
+++ b/src/CoordCovarMatrix_Half.h
@@ -0,0 +1,33 @@
+#ifndef INC_COORDCOVARMATRIX_HALF_H
+#define INC_COORDCOVARMATRIX_HALF_H
+#include "CoordCovarMatrix.h"
+/// Coordinate covariance half (self) matrix
+class CoordCovarMatrix_Half : public CoordCovarMatrix {
+  public:
+    /// CONSTRUCTOR 
+    CoordCovarMatrix_Half();
+    // ---------------------------------
+    /// Finish calculating the matrix (normalize, calc <rirj> - <ri><rj>)
+    int FinishMatrix();
+    // ---------------------------------
+    /// Set up half matrix for coordinates
+    int SetupMatrix(std::vector<Atom> const&, AtomMask const&, bool);
+    /// Set up half matrix for data sets
+    int SetupMatrix(DSarray const&);
+    /// Add selected atoms in Frame to matrix
+    void AddFrameToMatrix(Frame const&, AtomMask const&);
+    /// Add Frame to matrix
+    //void AddFrameToMatrix(Frame const&);
+    /// Add data in sets to matrix
+    void AddDataToMatrix(DSarray const&);
+  private:
+    /// Add elements to the matrix
+    void AddToMatrix(Darray const&);
+    /// Clear the matrix
+    void clearMat();
+
+    Darray vect_;
+    Darray mass_;
+
+};
+#endif
diff --git a/src/DataFile.cpp b/src/DataFile.cpp
index b215286b34..fdff22684b 100644
--- a/src/DataFile.cpp
+++ b/src/DataFile.cpp
@@ -292,6 +292,16 @@ int DataFile::SetupDatafile(FileName const& fnameIn, ArgList& argIn,
     dfType_ = (DataFormatType)FileTypes::GetTypeFromExtension(DF_WriteKeyArray, filename_.Ext(),
                                                               DATAFILE);
   // Set up DataIO based on format.
+  std::vector<DataSet*> previousSets;
+  if (dataio_ != 0) {
+    delete dataio_;
+    if (!SetList_.empty()) {
+      // Save current sets so they can be re-added with the new DataIO object
+      for (DataSetList::const_iterator it = SetList_.begin(); it != SetList_.end(); ++it)
+        previousSets.push_back( *it );
+    }
+    SetList_.ClearAll();
+  }
   dataio_ = (DataIO*)FileTypes::AllocIO( DF_AllocArray, dfType_, false );
   if (dataio_ == 0) return Error("Error: Data file allocation failed.\n");
   dataio_->SetDebug( debug_ );
@@ -301,6 +311,15 @@ int DataFile::SetupDatafile(FileName const& fnameIn, ArgList& argIn,
 # endif
   if (!argIn.empty())
     ProcessArgs( argIn );
+  // Re-add sets if necessary
+  if (!previousSets.empty()) {
+    for (std::vector<DataSet*>::const_iterator it = previousSets.begin(); it != previousSets.end(); ++it) {
+      if ( AddDataSet( *it ) ) {
+        mprinterr("Error: Could not add set '%s' to file '%s'\n", (*it)->legend(), filename_.full());
+        return 1;
+      }
+    }
+  }
   return 0;
 }
 
@@ -616,6 +635,8 @@ void DataFile::SetDataFilePrecision(int widthIn, int precisionIn) {
   default_width_ = widthIn;
   default_precision_ = precisionIn;
   SetList_.SetPrecisionOfDataSets("*", widthIn, precisionIn);
+  // Indicate file needs to be written
+  dflWrite_ = true;
 }
 
 // DataFile::DataSetNames()
diff --git a/src/DataIO_Evecs.cpp b/src/DataIO_Evecs.cpp
index e7934096e9..6deaed9a94 100644
--- a/src/DataIO_Evecs.cpp
+++ b/src/DataIO_Evecs.cpp
@@ -50,6 +50,7 @@ const char* DataIO_Evecs::MatrixOutputString(MetaData::scalarType typeIn) {
     case MetaData::IDEA :      ptr = "IDEA"; break;
     case MetaData::IREDMAT  :  ptr = "IRED"; break;
     case MetaData::DIHCOVAR :  ptr = "DIHCOVAR"; break;
+    case MetaData::DATACOVAR : ptr = "DATACOVAR"; break;
     default:                  ptr = "UNKNOWN";
   }
   return ptr;
diff --git a/src/DataSet_2D.cpp b/src/DataSet_2D.cpp
new file mode 100644
index 0000000000..67e839e30a
--- /dev/null
+++ b/src/DataSet_2D.cpp
@@ -0,0 +1,24 @@
+#include "DataSet_2D.h"
+#include <cmath> // fabs
+
+/** Check that the given matrix is symmetric. 
+  * This will work similar to numpy.allclose.
+  * https://numpy.org/doc/stable/reference/generated/numpy.allclose.html
+  */
+bool DataSet_2D::IsSymmetric() const {
+  if (MatrixKind() == HALF || MatrixKind() == TRI) return true;
+  if (Ncols() != Nrows()) return false;
+
+  static const double rtol = 1e-5;
+  static const double atol = 1e-8;
+
+  for (unsigned int row = 0; row != Nrows(); row++) {
+    for (unsigned int col = row+1; col < Ncols(); col++) {
+      double a = GetElement(col, row);
+      double b = GetElement(row, col);
+      bool is_equiv = ((fabs(a - b) <= (atol + rtol * fabs(b))));
+      if (!is_equiv) return false;
+    }
+  }
+  return true;
+}
diff --git a/src/DataSet_2D.h b/src/DataSet_2D.h
index f14bd61c5d..dc39d86501 100644
--- a/src/DataSet_2D.h
+++ b/src/DataSet_2D.h
@@ -24,8 +24,12 @@ class DataSet_2D : public DataSet {
 
     /// Add given value to element at specified col/row
     virtual void UpdateElement(size_t, size_t, double) = 0;
+    /// Add given value to element at specified 1D index
+    virtual void UpdateElement(size_t, double) = 0;
     /// Set element at specified col/row to given value
     virtual void SetElement(size_t, size_t, double) = 0;
+    /// Set element at specified 1D index to given value
+    virtual void SetElement(size_t, double) = 0;
 
     /// \return Data from matrix at col/row 
     virtual double GetElement(size_t, size_t) const = 0;
@@ -43,6 +47,91 @@ class DataSet_2D : public DataSet {
     virtual const void* MatrixPtr() const = 0;
     /// \return pointer to underlying matrix.
     virtual void* MatrixPtr() = 0;
+    /// Clear matrix
+    virtual void Clear() = 0;
+    /// Normalize matrix
+    virtual void Normalize(double) = 0;
+    // -------------------------------------------
+    enum RetType { OK = 0, DIM_MISMATCH, ALLOC_ERR, ERR };
+    /// Set this matrix with the result of M1 x M2
+    RetType Multiply(DataSet_2D const& M1, DataSet_2D const& M2) {
+      if (M1.Ncols() != M2.Nrows()) return DIM_MISMATCH;
+      unsigned int len = M1.Ncols();
+      if (Allocate2D( M2.Ncols(), M1.Nrows() )) return ALLOC_ERR;
+      unsigned int idx = 0;
+      for (unsigned int row = 0; row != Nrows(); row++) {
+        for (unsigned int col = 0; col != Ncols(); col++) {
+          double sum = 0;
+          for (unsigned int k = 0; k != len; k++)
+            sum += M1.GetElement(k, row) * M2.GetElement(col, k);
+          SetElement(idx++, sum);
+        }
+      }
+      return OK;
+    }
+    /// Set this matrix with the result of M1 x M2^T
+    RetType Multiply_M2transpose(DataSet_2D const& M1, DataSet_2D const& M2) {
+      if (M1.Ncols() != M2.Ncols()) return DIM_MISMATCH;
+      unsigned int len = M1.Ncols();
+      if (Allocate2D( M2.Nrows(), M1.Nrows() )) return ALLOC_ERR;
+      unsigned int idx = 0;
+      for (unsigned int row = 0; row != Nrows(); row++) {
+        for (unsigned int col = 0; col != Ncols(); col++) {
+          double sum = 0;
+          for (unsigned int k = 0; k != len; k++)
+            sum += M1.GetElement(k, row) * M2.GetElement(k, col);
+          SetElement(idx++, sum);
+        }
+      }
+      return OK;
+    }
+    /// Set this matrix with the result of M1^T x M2
+    RetType Multiply_M1transpose(DataSet_2D const& M1, DataSet_2D const& M2) {
+      if (M1.Nrows() != M2.Nrows()) return DIM_MISMATCH;
+      unsigned int len = M1.Nrows();
+      if (Allocate2D( M2.Ncols(), M1.Ncols() )) return ALLOC_ERR;
+      unsigned int idx = 0;
+      for (unsigned int row = 0; row != Nrows(); row++) {
+        for (unsigned int col = 0; col != Ncols(); col++) {
+          double sum = 0;
+          for (unsigned int k = 0; k != len; k++)
+            sum += M1.GetElement(row, k) * M2.GetElement(col, k);
+          SetElement(idx++, sum);
+        }
+      }
+      return OK;
+    }
+
+    /// Set this matrix with the result of M1^T
+    RetType TransposeOf(DataSet_2D const& M1) {
+      RetType ret = ERR;
+      MatrixKindType m1kind = M1.MatrixKind();
+      if (m1kind == FULL) {
+        if (Allocate2D( M1.Nrows(), M1.Ncols() )) return ALLOC_ERR;
+        ret = OK;
+        for (unsigned int row = 0; row < M1.Nrows(); row++) {
+          for (unsigned int col = 0; col < M1.Ncols(); col++)
+            SetElement( row, col, M1.GetElement(col, row) );
+        }
+      } else if (m1kind == HALF) {
+        if (AllocateHalf( M1.Ncols() )) return ALLOC_ERR;
+        ret = OK;
+        for (unsigned int row = 0; row < M1.Nrows(); row++) {
+          for (unsigned int col = row; col < M1.Ncols(); col++)
+            SetElement( row, col, M1.GetElement(col, row) );
+        }
+      } else if (m1kind == TRI) {
+        if (AllocateTriangle( M1.Ncols() )) return ALLOC_ERR;
+        ret = OK;
+        for (unsigned int row = 0; row < M1.Nrows(); row++) {
+          for (unsigned int col = row + 1; col < M1.Ncols(); col++)
+            SetElement( row, col, M1.GetElement(col, row) );
+        }
+      }
+      return ret;
+    }
+    /// \return True if matrix is symmetric
+    bool IsSymmetric() const;
     // -------------------------------------------
     // TODO: Remove this. Only needed by DataSet_1D.h
     void Add(size_t,const void*) { }
diff --git a/src/DataSet_MatrixDbl.cpp b/src/DataSet_MatrixDbl.cpp
index 122ae55794..d6553a2fb4 100644
--- a/src/DataSet_MatrixDbl.cpp
+++ b/src/DataSet_MatrixDbl.cpp
@@ -14,6 +14,21 @@ double* DataSet_MatrixDbl::MatrixArray() const {
   return matOut;
 }
 
+/** Clear the matrix. */
+void DataSet_MatrixDbl::Clear() {
+  mat_.clear();
+  vect_.clear();
+  mass_.clear();
+  //kind_;
+  snap_ = 0;
+}
+
+/** Normalize the matrix. */
+void DataSet_MatrixDbl::Normalize(double norm) {
+  for (Matrix<double>::iterator it = mat_.begin(); it != mat_.end(); ++it)
+    *it *= norm;
+}
+
 #ifdef MPI
 int DataSet_MatrixDbl::Sync(size_t total, std::vector<int> const& rank_frames,
                             Parallel::Comm const& commIn)
diff --git a/src/DataSet_MatrixDbl.h b/src/DataSet_MatrixDbl.h
index f8fca7f711..5c46c90393 100644
--- a/src/DataSet_MatrixDbl.h
+++ b/src/DataSet_MatrixDbl.h
@@ -25,7 +25,9 @@ class DataSet_MatrixDbl : public DataSet_2D {
     int AllocateHalf(size_t x)                 { kind_=HALF; return mat_.resize(x,0); }
     int AllocateTriangle(size_t x)             { kind_=TRI;  return mat_.resize(0,x); }
     void UpdateElement(size_t x,size_t y,double v) { mat_.updateElement(x,y,v); }
+    void UpdateElement(size_t i, double d)         { mat_[i] += d; }
     void SetElement(size_t x,size_t y,double d)    { mat_.setElement(x,y,d);    }
+    void SetElement(size_t i, double d)            { mat_[i] = d; }
     double GetElement(size_t x,size_t y) const { return mat_.element(x,y); }
     double GetElement(size_t i)          const { return mat_[i];           }
     size_t Nrows()                       const { return mat_.Nrows();      }
@@ -34,6 +36,8 @@ class DataSet_MatrixDbl : public DataSet_2D {
     MatrixKindType MatrixKind()          const { return kind_;             }
     const void* MatrixPtr()              const { return mat_.Ptr();        }
     void* MatrixPtr()                          { return mat_.Ptr();        }
+    void Clear();
+    void Normalize(double);
     // -------------------------------------------
     unsigned int Nsnapshots()            const { return snap_;              }
     void IncrementSnapshots()                  { ++snap_;                   }
diff --git a/src/DataSet_MatrixFlt.cpp b/src/DataSet_MatrixFlt.cpp
index 9eabeeac10..d2ae8fecc8 100644
--- a/src/DataSet_MatrixFlt.cpp
+++ b/src/DataSet_MatrixFlt.cpp
@@ -14,6 +14,22 @@ double* DataSet_MatrixFlt::MatrixArray() const {
     matOut[i] = (double)mat_[i];
   return matOut;
 }
+
+/** Clear the matrix */
+void DataSet_MatrixFlt::Clear() {
+  mat_.clear();
+  // kind_;
+}
+
+/** Normalize the matrix */
+void DataSet_MatrixFlt::Normalize(double norm) {
+  for (Matrix<float>::iterator it = mat_.begin(); it != mat_.end(); ++it)
+  {
+    double newElt = ((double)*it) * norm;
+    *it = (float)newElt;
+  }
+}
+
 #ifdef MPI
 int DataSet_MatrixFlt::Sync(size_t total, std::vector<int> const& rank_frames,
                             Parallel::Comm const& commIn)
diff --git a/src/DataSet_MatrixFlt.h b/src/DataSet_MatrixFlt.h
index 7a0cf6f01c..26c1186043 100644
--- a/src/DataSet_MatrixFlt.h
+++ b/src/DataSet_MatrixFlt.h
@@ -24,7 +24,9 @@ class DataSet_MatrixFlt : public DataSet_2D {
     int AllocateHalf(size_t x)                 { kind_=HALF; return mat_.resize(x,0); }
     int AllocateTriangle(size_t x)             { kind_=TRI;  return mat_.resize(0,x); }
     void UpdateElement(size_t x,size_t y,double v) { mat_.updateElement(x,y,v); }
+    void UpdateElement(size_t i, double d)         { mat_[i] += (float)d; }
     void SetElement(size_t x,size_t y,double d)    { mat_.setElement(x,y,d);    }
+    void SetElement(size_t i, double d)            { mat_[i] = d; }
     double GetElement(size_t x,size_t y) const { return (double)mat_.element(x,y); }
     double GetElement(size_t i)          const { return (double)mat_[i];           }
     size_t Nrows()                       const { return mat_.Nrows(); }
@@ -33,6 +35,8 @@ class DataSet_MatrixFlt : public DataSet_2D {
     MatrixKindType MatrixKind()          const { return kind_;        }
     const void* MatrixPtr()              const { return mat_.Ptr();        }
     void* MatrixPtr()                          { return mat_.Ptr();        }
+    void Clear();
+    void Normalize(double);
     // -------------------------------------------
     int AddElement(float d)                    { return mat_.addElement(d); }
     /// Type definition of iterator over matrix elements.
diff --git a/src/DataSet_Modes.cpp b/src/DataSet_Modes.cpp
index 96eb490aaa..5cfafe9efd 100644
--- a/src/DataSet_Modes.cpp
+++ b/src/DataSet_Modes.cpp
@@ -1,15 +1,21 @@
-#include <cmath> // sqrt
 #include "DataSet_Modes.h"
-#include "CpptrajStdio.h"
 #include "ArgList.h"
 #include "Constants.h" // PI, TWOPI
+#include "CpptrajStdio.h"
+#include "DataSet_2D.h"
+#include "DataSet_MatrixDbl.h"
 #include "Frame.h"
+#include <cmath> // sqrt, fabs
+#include <algorithm> // std::sort
 
 #ifndef NO_MATHLIB
 // Definition of Fortran subroutines called from this class
 extern "C" {
   // LAPACK
+  /// Compute the eigenvalues and (optionally) the left and/or right eigenvectors for a symmetric matrix
   void dspev_(char&, char&, int&, double*, double*, double*, int&, double*, int&);
+  /// Compute the eigenvalues and (optionally) the left and/or right eigenvectors for a general matrix
+  void dgeev_(char&, char&, int&, double*, int&, double*, double*, double*, int&, double*, int&, double*, int&, int&);
   // ARPACK
   void dsaupd_(int&, char&, int&, char*, int&, double&, double*,
                int&, double*, int&, int*, int*, double*, double*,
@@ -23,7 +29,7 @@ extern "C" {
 
 const char* DataSet_Modes::DeprecateFileMsg = "Modes should be read in prior to this command with 'readdata'\n";
 
-// CONSTRUCTOR
+/** CONSTRUCTOR */
 DataSet_Modes::DataSet_Modes() :
   // 0 dim indicates DataSet-specific write
   DataSet(MODES, GENERIC, TextFormat(TextFormat::DOUBLE, 10, 5), 0),
@@ -56,6 +62,12 @@ size_t DataSet_Modes::MemUsageInBytes() const {
   return mySize;
 }
 
+/** Set average coords */
+int DataSet_Modes::SetAvgCoords(std::vector<double> const& avgIn) {
+  avgcrd_ = avgIn;
+  return 0;
+}
+
 // DataSet_Modes::SetAvgCoords()
 int DataSet_Modes::SetAvgCoords(DataSet_2D const& mIn) {
   avgcrd_.clear();
@@ -133,8 +145,29 @@ int DataSet_Modes::AllocateModes(unsigned int n_eigenvalues, unsigned int evects
   return 0;
 }
 
-/** Get n_to_calc eigenvectors and eigenvalues from given matrix. They will be
-  * stored in descending order (largest eigenvalue first).
+/** Get all eigenvectors and eigenvalues from given matrix. They
+  * will be stored in descending order (largest eigenvalue first).
+  */
+int DataSet_Modes::CalcEigen_General(DataSet_2D const& mIn) {
+# ifdef NO_MATHLIB
+  mprinterr("Error: Compiled without LAPACK/BLAS routines.\n");
+  return 1;
+# else
+  int n_to_calc = mIn.Ncols();
+
+  if (mIn.IsSymmetric()) {
+    return CalcEigen(mIn, n_to_calc);
+  }
+
+  // If we are here, mIn is not symmetric. Need to solve general eigenvalue problem.
+  mprinterr("Internal Error: DataSet_Modes::CalcEigen: Non-symmetric matrix calc not yet implemented.\n");
+
+  return 1;
+# endif /* NO_MATHLIB */
+}
+
+/** Get n_to_calc eigenvectors and eigenvalues from given symmetric matrix.
+  * They will be stored in descending order (largest eigenvalue first).
   */
 int DataSet_Modes::CalcEigen(DataSet_2D const& mIn, int n_to_calc) {
 # ifdef NO_MATHLIB
@@ -144,9 +177,33 @@ int DataSet_Modes::CalcEigen(DataSet_2D const& mIn, int n_to_calc) {
   bool eigenvaluesOnly = false;
   int info = 0;
   int ncols = (int)mIn.Ncols();
-  if (mIn.MatrixKind() != DataSet_2D::HALF) {
-    mprinterr("Error: Eigenvector/value calc only for symmetric matrices.\n");
-    return 1;
+  double* mat = 0;
+  // Create copy of matrix since call to dspev destroys it
+  if (mIn.MatrixKind() == DataSet_2D::HALF) {
+    mat = mIn.MatrixArray();
+  } else {
+    // FULL or TRI matrix. Convert to HALF form.
+    // Check that Matrix is symmetric.
+    if (mIn.Nrows() != mIn.Ncols()) {
+      mprinterr("Error: # of rows in '%s' != # of columns; cannot calculate eigenvectors/values.\n",
+                mIn.legend());
+      return 1;
+    }
+    if (!mIn.IsSymmetric()) {
+      mprintf("Warning: DataSet_Modes::CalcEigen(): Matrix '%s' does not appear to be symmetric.\n",
+              mIn.legend());
+      // TODO report most dissimilar i,j pair?
+    }
+    //mprinterr("Error: Eigenvector/value calc only for symmetric matrices.\n");
+    //return 1;
+    unsigned int matsize = mIn.Ncols() * (mIn.Ncols() + 1) / 2;
+    mat = new double[matsize];
+    unsigned int idx = 0;
+    for (unsigned int row = 0; row < mIn.Nrows(); row++) {
+      for (unsigned int col = row; col < mIn.Ncols(); col++) {
+        mat[idx++] = mIn.GetElement(row, col); // row,col is lower, col,row is upper
+      }
+    }
   }
   // If number to calc is 0, assume we want eigenvalues only
   if (n_to_calc < 1) {
@@ -169,9 +226,9 @@ int DataSet_Modes::CalcEigen(DataSet_2D const& mIn, int n_to_calc) {
   }
 # endif
   if (eigenvaluesOnly)
-    mprintf("\tCalculating eigenvalues only.\n");
+    mprintf("\tCalculating eigenvalues only for %s.\n", mIn.legend());
   else
-    mprintf("\tCalculating eigenvectors and eigenvalues.\n");
+    mprintf("\tCalculating eigenvectors and eigenvalues for %s.\n", mIn.legend());
   // -----------------------------------------------------------------
   if (calcAll) {
     mprintf("\tCalculating all eigenmodes.\n");
@@ -192,8 +249,7 @@ int DataSet_Modes::CalcEigen(DataSet_2D const& mIn, int n_to_calc) {
     // Set up space to hold eigenvalues
     if (evalues_ != 0) delete[] evalues_;
     evalues_ = new double[ ncols ];
-    // Create copy of matrix since call to dspev destroys it
-    double* mat = mIn.MatrixArray();
+
     // Lower triangle; not upper since fortran array layout is inverted w.r.t. C/C++
     char uplo = 'L'; 
     // Allocate temporary workspace
@@ -434,6 +490,107 @@ int DataSet_Modes::MassWtEigvect() {
   return 0;
 }
 
+/** Resize so that only the first N modes are saved. */
+int DataSet_Modes::ResizeModes(int NtoSave) {
+  if (NtoSave < 1) {
+    mprinterr("Internal Error: DataSet_Modes::ResizeModes: # of modes to save < 1\n");
+    return 1;
+  }
+  if (NtoSave >= nmodes_) {
+    mprintf("\tNo need to resize modes %s; # to keep (%i) >= # modes (%i)\n",
+            legend(), NtoSave, nmodes_);
+    return 0;
+  }
+  // Resize values
+  double* newEvals = new double[ NtoSave ];
+  std::copy( evalues_, evalues_ + NtoSave, newEvals );
+  delete[] evalues_;
+  evalues_ = newEvals;
+  // Resize vectors
+  unsigned int newSize = NtoSave * vecsize_;
+  double* newEvecs = new double[ newSize ];
+  std::copy( evectors_, evectors_ + newSize, newEvecs );
+  delete[] evectors_;
+  evectors_ = newEvecs;
+
+  nmodes_ = NtoSave;
+  return 0;
+}
+
+/** Multiply all elements of specified eigenvector by a factor */
+void DataSet_Modes::MultiplyEvecByFac(int nvec, double fac) {
+  double* evec = evectors_ + (nvec * vecsize_);
+  for (int jj = 0; jj < vecsize_; jj++)
+    evec[jj] *= fac;
+}
+
+/// Class used to sort eigenvalue/index pairs
+class DataSet_Modes::EvIdxPair {
+  public:
+    EvIdxPair(double e, int i) : eval_(e), idx_(i) {}
+
+    bool operator<(EvIdxPair const& rhs) const {
+      return (eval_ > rhs.eval_);
+    }
+    double Eval() const { return eval_; }
+    int Idx() const { return idx_; }
+  private:
+    double eval_;
+    int idx_;
+};
+
+/** Sort eigenvectors and eigenvalues in descending order of abs(eigenvalue) */
+void DataSet_Modes::SortByAbsEigenvalue() {
+  // Create eigenvalue/index pairs
+  typedef std::vector<EvIdxPair> Earray;
+
+  Earray Pairs;
+  for (int ii = 0; ii < nmodes_; ii++)
+    Pairs.push_back( EvIdxPair(fabs(evalues_[ii]), ii) );
+  // Sort by abs(eigenvalue)
+  std::sort( Pairs.begin(), Pairs.end() );
+  // Recreate the vectors array, sorted
+  double* newEvals = new double[ nmodes_ ];
+  double* newEvecs = new double[ nmodes_ * vecsize_ ];
+  for (Earray::const_iterator it = Pairs.begin(); it != Pairs.end(); ++it) {
+    newEvals[it - Pairs.begin()] = evalues_[it->Idx()];
+    double* evecNew = newEvecs + ((it - Pairs.begin()) * vecsize_);
+    const double* evecOld = evectors_ + (it->Idx() * vecsize_);
+    std::copy( evecOld, evecOld + vecsize_, evecNew );
+  }
+  delete[] evectors_;
+  delete[] evalues_;
+  evalues_ = newEvals;
+  evectors_ = newEvecs;
+}
+
+/** Enforce canonical eigenvector signs by multiplying every element of each
+  * eigenvector by the sign of the element with the greatest absolute value.
+  */
+void DataSet_Modes::SetCanonicalEvecSigns() {
+  for (int ii = 0; ii < Nmodes(); ii++) {
+    // Find the maximum absolute value of the eigenvector
+    double abs_maxval = 0;
+    int abs_maxidx = 0;
+    const double* evec = Eigenvector(ii);
+    for (int jj = 0; jj < VectorSize(); jj++) {
+      double dval = fabs( evec[jj] );
+      if ( dval > abs_maxval ) {
+        abs_maxval = dval;
+        abs_maxidx = jj;
+      }
+    }
+    //mprintf("argmax %i %i %g\n", ii, abs_maxidx, evec[abs_maxidx]); // DEBUG
+    double sign;
+    if ( evec[abs_maxidx] < 0 )
+      sign = -1.0;
+    else
+      sign =  1.0;
+    // Multiply all elements of the eigenvector by the sign of the max abs element
+    MultiplyEvecByFac( ii, sign );
+  }
+}
+
 // DataSet_Modes::ReduceVectors() 
 int DataSet_Modes::ReduceVectors() {
   if (evectors_ == 0) {
diff --git a/src/DataSet_Modes.h b/src/DataSet_Modes.h
index 06b842dc55..e8ad130e1d 100644
--- a/src/DataSet_Modes.h
+++ b/src/DataSet_Modes.h
@@ -1,6 +1,7 @@
 #ifndef INC_DATASET_MODES_H
 #define INC_DATASET_MODES_H
-#include "DataSet_MatrixDbl.h"
+#include "DataSet.h"
+class DataSet_2D;
 /// Hold eigenvalues/eigenvectors and optionally averaged coords.
 class DataSet_Modes : public DataSet {
   public:
@@ -38,14 +39,26 @@ class DataSet_Modes : public DataSet {
     double* EvectPtr()                     { return evectors_; }
 
     int SetAvgCoords(DataSet_2D const&);
+    int SetAvgCoords(std::vector<double> const&); // TODO deprecate above version for this one
     int SetModes(bool, int, int, const double*, const double*);
     /// Allocate memory for modes data
     int AllocateModes(unsigned int, unsigned int, unsigned int, unsigned int);
+    /// Calculate all eigenvalues/eigenvectors for given matrix
+    int CalcEigen_General(DataSet_2D const&);
+    /// Calculate specific # of eigenvalues/eigenvectors for given symmetric matrix
     int CalcEigen(DataSet_2D const&,int);
+    /// Multiply all elements of the specified eigenvector by given value
+    void MultiplyEvecByFac(int, double);
+    /// Descending sort by absolute value of eigenvalues
+    void SortByAbsEigenvalue();
+    /// Set canonical eigenvector signs
+    void SetCanonicalEvecSigns();
     void PrintModes();
     int EigvalToFreq(double);
     int MassWtEigvect();
     int ReduceVectors();
+    /// Resize so that only the first N modes are saved
+    int ResizeModes(int);
     int Thermo(CpptrajFile&, int, double, double) const;
 
     double Eigenvalue(int i)         const { return evalues_[i];                } // IRED
@@ -58,6 +71,9 @@ class DataSet_Modes : public DataSet {
     bool EvecsAreMassWtd()           const { return evecsAreMassWtd_;           }
     bool EvalsAreFreq()              const { return evalsAreFreq_;              }
   private:
+    /// Class used to sort eigenvalue/index pairs
+    class EvIdxPair;
+
     int ReduceCovar();
     int ReduceDistCovar();
 
diff --git a/src/Deprecated.cpp b/src/Deprecated.cpp
index 012f810b56..fa8496e006 100644
--- a/src/Deprecated.cpp
+++ b/src/Deprecated.cpp
@@ -1,10 +1,6 @@
 #include "Deprecated.h"
 #include "CpptrajStdio.h"
 
-void Deprecated_MinDist::Help() const {
-  mprinterr("  Use the 'nativecontacts' action instead.\n");
-}
-
 void Deprecated_Hbond::Help() const {
   mprinterr("  Hydrogen bond acceptors and donors are defined within the 'hbond' action.\n");
 }
diff --git a/src/Deprecated.h b/src/Deprecated.h
index 9d8dab7732..a0cce51ba9 100644
--- a/src/Deprecated.h
+++ b/src/Deprecated.h
@@ -8,7 +8,6 @@ class Deprecated : public DispatchObject {
     DispatchObject* Alloc() const { return 0; }
 };
 
-class Deprecated_MinDist      : public Deprecated { public: void Help() const; };
 class Deprecated_Hbond        : public Deprecated { public: void Help() const; };
 class Deprecated_TopSearch    : public Deprecated { public: void Help() const; };
 class Deprecated_ParmBondInfo : public Deprecated { public: void Help() const; };
diff --git a/src/Frame.cpp b/src/Frame.cpp
index 8a63853801..efae5a7473 100644
--- a/src/Frame.cpp
+++ b/src/Frame.cpp
@@ -498,6 +498,15 @@ int Frame::SetupFrameFromMask(AtomMask const& maskIn, std::vector<Atom> const& a
   return 0;
 }
 
+/** Set up frame to hold selected number of atoms in given mask.
+  * All masses will be 1.0.
+  */
+int Frame::SetupFrameFromMask(AtomMask const& maskIn) {
+  ReallocateX( maskIn.Nselected() );
+  Mass_.assign( maskIn.Nselected(), 1.0 );
+  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 041ade57e0..2247b78806 100644
--- a/src/Frame.h
+++ b/src/Frame.h
@@ -156,6 +156,8 @@ class Frame {
     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&);
+    /// Allocate frame for selected # atoms
+    int SetupFrameFromMask(AtomMask const&);
     // ----- Add/remove components from Frame ----
     int AddVelocities(Darray const&);
     void RemoveVelocities();
diff --git a/src/InteractionData.cpp b/src/InteractionData.cpp
new file mode 100644
index 0000000000..85dc65fbdb
--- /dev/null
+++ b/src/InteractionData.cpp
@@ -0,0 +1,40 @@
+#include "InteractionData.h"
+#include "CpptrajStdio.h"
+#include "DataFile.h"
+#include "DataSetList.h"
+
+using namespace Cpptraj;
+
+/** CONSTRUCTOR */
+InteractionData::InteractionData()
+{}
+
+/** Add set tracking interaction between the two given indices. */
+DataSet* InteractionData::AddInteractionSet(DataSetList& dsl, DataSet::DataType typeIn,
+                                            MetaData const& metaIn, int i0, int i1,
+                                            DataFile* outfile)
+{
+  // Check for existing interaction
+  Ipair interaction;
+  if (i1 < i0) {
+    interaction.first = i1;
+    interaction.second = i0;
+  } else {
+    interaction.first = i0;
+    interaction.second = i1;
+  }
+  MapType::const_iterator it = setMap_.lower_bound(interaction);
+  if (it == setMap_.end() || it->first != interaction)
+  {
+    // New interaction
+    DataSet* ds = dsl.AddSet(typeIn, metaIn);
+    if (ds == 0) {
+      mprinterr("Error: Could not allocate data set %s\n", metaIn.PrintName().c_str());
+      return 0;
+    }
+    if (outfile != 0) outfile->AddDataSet( ds );
+    it = setMap_.insert(it, PairType(interaction, ds));
+  }
+  // TODO check existing set for issues?
+  return it->second;
+}
diff --git a/src/InteractionData.h b/src/InteractionData.h
new file mode 100644
index 0000000000..087e00d07f
--- /dev/null
+++ b/src/InteractionData.h
@@ -0,0 +1,24 @@
+#ifndef INC_INTERACTIONDATA_H
+#define INC_INTERACTIONDATA_H
+#include "DataSet.h" // DataType
+#include <map>
+class DataFile;
+class DataSetList;
+class MetaData;
+namespace Cpptraj {
+/// Hold data sets corresponding to interactions between entities.
+class InteractionData {
+  public:
+    InteractionData();
+
+    /// Add interaction pair data set
+    DataSet* AddInteractionSet(DataSetList&, DataSet::DataType, MetaData const&, int, int, DataFile*);
+  private:
+    typedef std::pair<int,int> Ipair;
+    typedef std::pair<Ipair,DataSet*> PairType;
+    typedef std::map<Ipair,DataSet*> MapType;
+
+    MapType setMap_; ///< Hold map of interaction #s to data sets
+};
+}
+#endif
diff --git a/src/MetaData.cpp b/src/MetaData.cpp
index f3a5b560a6..8f81c7237d 100644
--- a/src/MetaData.cpp
+++ b/src/MetaData.cpp
@@ -16,7 +16,7 @@ const char* MetaData::Stypes[] = {
   // Matrix
   "distance",    "covariance",          "mass-weighted covariance",
   "correlation", "distance covariance", "IDEA",
-  "IRED",        "dihedral covariance",
+  "IRED",        "dihedral covariance", "data covariance",
   // Vector
   "IRED",
   "notype" };
@@ -29,7 +29,7 @@ const MetaData::scalarMode MetaData::TypeModes[] = {
   M_DISTANCE,
   M_MATRIX,  M_MATRIX, M_MATRIX,
   M_MATRIX,  M_MATRIX, M_MATRIX,
-  M_MATRIX,  M_MATRIX,
+  M_MATRIX,  M_MATRIX, M_MATRIX,
   M_VECTOR,
   UNKNOWN_MODE };
 
diff --git a/src/MetaData.h b/src/MetaData.h
index fb56b41ac4..beb87ca66a 100644
--- a/src/MetaData.h
+++ b/src/MetaData.h
@@ -27,7 +27,7 @@ class MetaData {
       NOE,
       DIST,    COVAR,     MWCOVAR,
       CORREL,  DISTCOVAR, IDEA,
-      IREDMAT, DIHCOVAR,
+      IREDMAT, DIHCOVAR, DATACOVAR,
       IREDVEC,
       UNDEFINED
     };
diff --git a/src/Version.h b/src/Version.h
index 38e4d0f4ed..5f4b12966a 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 "V6.24.0"
+#define CPPTRAJ_INTERNAL_VERSION "V6.24.1"
 /// PYTRAJ relies on this
 #define CPPTRAJ_VERSION_STRING CPPTRAJ_INTERNAL_VERSION
 #endif
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 024bbea344..c59cdf0f6e 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -50,6 +50,7 @@ Action_MakeStructure.o : Action_MakeStructure.cpp Action.h ActionState.h Action_
 Action_Mask.o : Action_Mask.cpp Action.h ActionFrameCounter.h ActionState.h Action_Mask.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.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_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.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 TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Action_Matrix.o : Action_Matrix.cpp Action.h ActionFrameCounter.h ActionState.h Action_Matrix.h ArgList.h Array1D.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_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Vector.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 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
 Action_MinImage.o : Action_MinImage.cpp Action.h ActionState.h Action_MinImage.h ArgList.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_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
+Action_MinMaxDist.o : Action_MinMaxDist.cpp Action.h ActionState.h Action_MinMaxDist.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.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 DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h InteractionData.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 StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Action_Molsurf.o : Action_Molsurf.cpp Action.h ActionState.h Action_Molsurf.h ArgList.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_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 molsurf.h
 Action_MultiDihedral.o : Action_MultiDihedral.cpp Action.h ActionState.h Action_MultiDihedral.h ArgList.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 DihedralSearch.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 StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Action_MultiPucker.o : Action_MultiPucker.cpp Action.h ActionState.h Action_MultiPucker.h ArgList.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_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
@@ -62,7 +63,7 @@ Action_Outtraj.o : Action_Outtraj.cpp Action.h ActionFrameCounter.h ActionState.
 Action_PairDist.o : Action_PairDist.cpp Action.h ActionState.h Action_PairDist.h ArgList.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 DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.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
 Action_Pairwise.o : Action_Pairwise.cpp Action.h ActionFrameCounter.h ActionState.h Action_Pairwise.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_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h DispatchObject.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.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
 Action_Principal.o : Action_Principal.cpp Action.h ActionState.h Action_Principal.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_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_Vector.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
-Action_Projection.o : Action_Projection.cpp Action.h ActionFrameCounter.h ActionState.h Action_Projection.h ArgList.h Array1D.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_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.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 StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Projection.o : Action_Projection.cpp Action.h ActionFrameCounter.h ActionState.h Action_Projection.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_Modes.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 StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Action_Pucker.o : Action_Pucker.cpp Action.h ActionState.h Action_Pucker.h ArgList.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_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 TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Action_Radgyr.o : Action_Radgyr.cpp Action.h ActionState.h Action_Radgyr.h ArgList.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_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
 Action_Radial.o : Action_Radial.cpp Action.h ActionState.h Action_Radial.h ArgList.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 DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h Gpu.h ImageOption.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 cuda_kernels/kernel_rdf.cuh
@@ -115,11 +116,12 @@ Analysis_Lifetime.o : Analysis_Lifetime.cpp ActionState.h Analysis.h AnalysisSta
 Analysis_LowestCurve.o : Analysis_LowestCurve.cpp ActionState.h Analysis.h AnalysisState.h Analysis_LowestCurve.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 Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.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_Matrix.o : Analysis_Matrix.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Matrix.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_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.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_MeltCurve.o : Analysis_MeltCurve.cpp ActionState.h Analysis.h AnalysisState.h Analysis_MeltCurve.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 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_Modes.o : Analysis_Modes.cpp ActionFrameCounter.h ActionState.h Analysis.h AnalysisState.h Analysis_Modes.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_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.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 OutputTrajCommon.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 TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_Modes.o : Analysis_Modes.cpp ActionFrameCounter.h ActionState.h Analysis.h AnalysisState.h Analysis_Modes.h ArgList.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 DataSet_Modes.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.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 TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Analysis_MultiHist.o : Analysis_MultiHist.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Hist.h Analysis_KDE.h Analysis_MultiHist.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 Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.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 TrajectoryFile.h TypeNameHolder.h Unit.h Vec3.h
 Analysis_Multicurve.o : Analysis_Multicurve.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CurveFit.h Analysis_Multicurve.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_Coords.h DataSet_Coords_REF.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_Overlap.o : Analysis_Overlap.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Overlap.h ArgList.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 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_PhiPsi.o : Analysis_PhiPsi.cpp ActionState.h Analysis.h AnalysisState.h Analysis_PhiPsi.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 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_Project.o : Analysis_Project.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Project.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_Modes.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 StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Analysis_Regression.o : Analysis_Regression.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Regression.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 Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Analysis_RemLog.o : Analysis_RemLog.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Lifetime.h Analysis_RemLog.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 DataSet_RemLog.h DataSet_integer.h DataSet_integer_mem.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 ProgressBar.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_Rms2d.o : Analysis_Rms2d.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Rms2d.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.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_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h QuaternionRMSD.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TypeNameHolder.h Unit.h Vec3.h
@@ -131,7 +133,7 @@ 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 AssociatedData_NOE.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_TICA.o : Analysis_TICA.cpp ActionState.h Analysis.h AnalysisState.h Analysis_TICA.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordCovarMatrix.h CoordCovarMatrix_Full.h CoordCovarMatrix_Half.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h DataSet_double.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 ProgressBar.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
@@ -186,11 +188,14 @@ 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_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_CrdTransform.h Exec_CreateSet.h Exec_DataFile.h Exec_DataFilter.h Exec_DataSetCmd.h Exec_Emin.h Exec_ExtendedComparison.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_Sequence.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 Exec_Zmatrix.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h GIST_PME.h Grid.h GridAction.h GridBin.h GridMover.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_MinMaxDist.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_Project.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_CrdTransform.h Exec_CreateSet.h Exec_DataFile.h Exec_DataFilter.h Exec_DataSetCmd.h Exec_Emin.h Exec_ExtendedComparison.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_Sequence.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 Exec_Zmatrix.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h GIST_PME.h Grid.h GridAction.h GridBin.h GridMover.h HistBin.h Hungarian.h ImageOption.h ImageTypes.h InputTrajCommon.h InteractionData.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
 ControlBlock_For.o : ControlBlock_For.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 ControlBlock.h ControlBlock_For.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 FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_dataSetBlocks.h ForLoop_inData.h ForLoop_integer.h ForLoop_list.h ForLoop_mask.h ForLoop_overSets.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
+CoordCovarMatrix.o : CoordCovarMatrix.cpp ArrayIterator.h Atom.h AtomMask.h Box.h CoordCovarMatrix.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Unit.h Vec3.h
+CoordCovarMatrix_Full.o : CoordCovarMatrix_Full.cpp ArrayIterator.h Atom.h AtomMask.h CoordCovarMatrix.h CoordCovarMatrix_Full.h CpptrajStdio.h MaskToken.h Matrix.h Molecule.h NameType.h Residue.h Segment.h SymbolExporting.h Unit.h
+CoordCovarMatrix_Half.o : CoordCovarMatrix_Half.cpp ArrayIterator.h AssociatedData.h Atom.h AtomMask.h Constants.h CoordCovarMatrix.h CoordCovarMatrix_Half.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h Dimension.h FileIO.h FileName.h MaskToken.h Matrix.h MetaData.h Molecule.h NameType.h Parallel.h Range.h Residue.h Segment.h SymbolExporting.h TextFormat.h Unit.h
 CoordinateInfo.o : CoordinateInfo.cpp Box.h CoordinateInfo.h CpptrajStdio.h Matrix_3x3.h Parallel.h ReplicaDimArray.h Vec3.h
 Corr.o : Corr.cpp ArrayIterator.h ComplexArray.h Corr.h PubFFT.h
 Cph.o : Cph.cpp Cph.h NameType.h
@@ -214,7 +219,7 @@ DataIO_CharmmRtfPrm.o : DataIO_CharmmRtfPrm.cpp ArgList.h AssociatedData.h Atom.
 DataIO_Cmatrix_Binary.o : DataIO_Cmatrix_Binary.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/Cframes.h Cluster/Cmatrix_Binary.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Cmatrix_Binary.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h Dimension.h FileIO.h FileName.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
 DataIO_Cmatrix_NC.o : DataIO_Cmatrix_NC.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/Cframes.h Cluster/Cmatrix_NC.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Cmatrix_NC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h Dimension.h FileIO.h FileName.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
 DataIO_Cpout.o : DataIO_Cpout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Cpout.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_pH.h Dimension.h FileIO.h FileName.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
-DataIO_Evecs.o : DataIO_Evecs.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Evecs.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h Dimension.h FileIO.h FileName.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
+DataIO_Evecs.o : DataIO_Evecs.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Evecs.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Modes.h Dimension.h FileIO.h FileName.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
 DataIO_Gnuplot.o : DataIO_Gnuplot.cpp ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Gnuplot.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.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
 DataIO_Grace.o : DataIO_Grace.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Grace.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_string.h Dimension.h FileIO.h FileName.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
 DataIO_Mdout.o : DataIO_Mdout.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Mdout.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.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 StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
@@ -230,6 +235,7 @@ DataIO_Xplor.o : DataIO_Xplor.cpp ArgList.h ArrayIterator.h AssociatedData.h Ato
 DataSet.o : DataSet.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
 DataSetList.o : DataSetList.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Cluster/Cframes.h Cluster/Cmatrix_NC.h CompactFrameArray.h ComplexArray.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_FRM.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_GridDbl.h DataSet_GridFlt.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_PairwiseCache_NC.h DataSet_Parameters.h DataSet_RemLog.h DataSet_StringVar.h DataSet_Tensor.h DataSet_Topology.h DataSet_Vector.h DataSet_Vector_Scalar.h DataSet_Zmatrix.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_disk.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h InputTrajCommon.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 Spline.h StringRoutines.h SymbolExporting.h SymmetricTensor.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TypeNameHolder.h Unit.h Vec3.h
 DataSet_1D.o : DataSet_1D.cpp ArrayIterator.h AssociatedData.h ComplexArray.h Constants.h Corr.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h PubFFT.h Range.h TextFormat.h
+DataSet_2D.o : DataSet_2D.cpp AssociatedData.h CpptrajFile.h DataSet.h DataSet_2D.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
 DataSet_3D.o : DataSet_3D.cpp AssociatedData.h Box.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_3D.h Dimension.h FileIO.h FileName.h GridBin.h Matrix_3x3.h MetaData.h Parallel.h Range.h TextFormat.h Vec3.h
 DataSet_Coords.o : DataSet_Coords.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataSet_Coords_CRD.o : DataSet_Coords_CRD.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_CRD.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
@@ -371,6 +377,7 @@ Image_List_Mask.o : Image_List_Mask.cpp Atom.h AtomMask.h AtomType.h Box.h Const
 Image_List_Pair.o : Image_List_Pair.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h Image_List.h Image_List_Pair.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
 Image_List_Unit.o : Image_List_Unit.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h Image_List.h Image_List_Unit.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
 InputTrajCommon.o : InputTrajCommon.cpp CpptrajStdio.h FileName.h InputTrajCommon.h TrajFrameCounter.h
+InteractionData.o : InteractionData.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h InteractionData.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
 KDE.o : KDE.cpp AssociatedData.h Constants.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_double.h Dimension.h FileIO.h FileName.h HistBin.h KDE.h MetaData.h Parallel.h Range.h TextFormat.h
 LeapInterface.o : LeapInterface.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h File_TempName.h Frame.h LeapInterface.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 StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 MapAtom.o : MapAtom.cpp Atom.h MapAtom.h NameType.h SymbolExporting.h
diff --git a/src/cpptrajfiles b/src/cpptrajfiles
index a5b3bb4419..816fc0592d 100644
--- a/src/cpptrajfiles
+++ b/src/cpptrajfiles
@@ -52,6 +52,7 @@ COMMON_SOURCES= \
         Action_MakeStructure.cpp \
         Action_Mask.cpp \
         Action_Matrix.cpp \
+        Action_MinMaxDist.cpp \
         Action_MinImage.cpp \
         Action_Molsurf.cpp \
         Action_MultiDihedral.cpp \
@@ -123,6 +124,7 @@ COMMON_SOURCES= \
         Analysis_MultiHist.cpp \
         Analysis_Overlap.cpp \
         Analysis_PhiPsi.cpp \
+        Analysis_Project.cpp \
         Analysis_Regression.cpp \
         Analysis_RemLog.cpp \
         Analysis_Rms2d.cpp \
@@ -163,6 +165,9 @@ COMMON_SOURCES= \
         ComplexArray.cpp \
         Constraints.cpp \
         ControlBlock_For.cpp \
+        CoordCovarMatrix.cpp \
+        CoordCovarMatrix_Full.cpp \
+        CoordCovarMatrix_Half.cpp \
         CoordinateInfo.cpp \
         Corr.cpp \
         Cph.cpp \
@@ -201,6 +206,7 @@ COMMON_SOURCES= \
         DataSet.cpp \
         DataSetList.cpp \
         DataSet_1D.cpp \
+        DataSet_2D.cpp \
         DataSet_3D.cpp \
         DataSet_Coords.cpp \
         DataSet_Coords_CRD.cpp \
@@ -339,6 +345,7 @@ COMMON_SOURCES= \
         Image_List_Mask.cpp \
         Image_List_Pair.cpp \
         Image_List_Unit.cpp \
+        InteractionData.cpp \
         InputTrajCommon.cpp \
         KDE.cpp \
         LeapInterface.cpp \
diff --git a/test/Makefile b/test/Makefile
index 5c97316457..d518104090 100644
--- a/test/Makefile
+++ b/test/Makefile
@@ -539,6 +539,9 @@ test.readoff:
 test.sequence:
 	@-cd Test_Sequence && ./RunTest.sh $(OPT)
 
+test.tica:
+	@-cd Test_TICA && ./RunTest.sh $(OPT)
+
 # Every test target should go here.
 COMPLETETESTS=test.general \
               test.strip \
@@ -709,7 +712,8 @@ COMPLETETESTS=test.general \
               test.readprep \
               test.zmatrix \
               test.readoff \
-              test.sequence
+              test.sequence \
+              test.tica
 
 test.all:
 	$(MAKE) test.complete summary
diff --git a/test/Test_MinMaxDist/RunTest.sh b/test/Test_MinMaxDist/RunTest.sh
new file mode 100755
index 0000000000..a456241f74
--- /dev/null
+++ b/test/Test_MinMaxDist/RunTest.sh
@@ -0,0 +1,57 @@
+#!/bin/bash
+
+. ../MasterTest.sh
+
+CleanFiles mmdist.in tz2.byatom.dat temp.dat tz2.byatom.1.dat \
+           tz2.byres.?.dat tz2.bymol.?.dat
+
+TESTNAME='Min/max distance tests'
+
+INPUT='-i mmdist.in'
+cat > mmdist.in <<EOF
+parm ../tz2.parm7
+trajin ../tz2.crd
+
+mindist name Min mask1 :2 mask2 :11 byatom out tz2.byatom.dat
+maxdist name Max mask1 :2 mask2 :11 byatom out tz2.byatom.dat
+mindist name Min1 mask1 ^1 byatom out tz2.byatom.1.dat
+maxdist name Max1 mask1 ^1 byatom out tz2.byatom.1.dat
+
+
+#nativecontacts :2 :11 savenonnative mindist out temp.dat
+#nativecontacts :2 :11 savenonnative maxdist out temp.dat
+#nativecontacts ^1 maxdist out temp.dat
+#precision temp.dat 8 3
+EOF
+RunCpptraj "Min/max distance by atom tests"
+DoTest tz2.byatom.dat.save tz2.byatom.dat
+DoTest tz2.byatom.1.dat.save tz2.byatom.1.dat
+
+cat > mmdist.in <<EOF
+parm ../tz2.truncoct.parm7
+trajin ../tz2.truncoct.crd
+
+mindist name ResMin1 mask1 :1-7 byres out tz2.byres.1.dat
+maxdist name ResMax1 mask1 :1-7 byres out tz2.byres.1.dat
+mindist name ResMin2 mask1 :2-4 mask2 :9-11 byres out tz2.byres.2.dat
+maxdist name ResMax2 mask1 :2-4 mask2 :9-11 byres out tz2.byres.2.dat
+EOF
+RunCpptraj "Min/max distance by residue tests"
+DoTest tz2.byres.1.dat.save tz2.byres.1.dat
+DoTest tz2.byres.2.dat.save tz2.byres.2.dat
+
+cat > mmdist.in <<EOF
+parm ../tz2.truncoct.parm7
+trajin ../tz2.truncoct.crd
+
+mindist name MolMin1 mask1 ^1-10 bymol out tz2.bymol.1.dat
+maxdist name MolMax1 mask1 ^1-10 bymol out tz2.bymol.1.dat
+mindist name MolMin2 mask1 ^1 mask2 ^342,567,638,1026,1560,1846&@O bymol out tz2.bymol.2.dat
+maxdist name MolMax2 mask1 ^1 mask2 ^342,567,638,1026,1560,1846&@O bymol out tz2.bymol.2.dat
+#closest 1 ^1 first closestout temp.dat
+EOF
+RunCpptraj "Min/max distance by molecule tests"
+DoTest tz2.bymol.1.dat.save tz2.bymol.1.dat
+DoTest tz2.bymol.2.dat.save tz2.bymol.2.dat
+EndTest
+exit 0
diff --git a/test/Test_MinMaxDist/tz2.byatom.1.dat.save b/test/Test_MinMaxDist/tz2.byatom.1.dat.save
new file mode 100644
index 0000000000..861d119f04
--- /dev/null
+++ b/test/Test_MinMaxDist/tz2.byatom.1.dat.save
@@ -0,0 +1,102 @@
+#Frame       Min1     Max1
+       1    0.959   29.560
+       2    0.960   31.131
+       3    0.960   32.325
+       4    0.960   32.440
+       5    0.960   31.348
+       6    0.959   28.216
+       7    0.959   27.023
+       8    0.959   23.612
+       9    0.960   24.375
+      10    0.960   27.513
+      11    0.960   27.557
+      12    0.960   30.501
+      13    0.960   32.133
+      14    0.959   32.323
+      15    0.959   33.343
+      16    0.960   34.470
+      17    0.959   35.838
+      18    0.960   34.234
+      19    0.960   32.854
+      20    0.959   34.537
+      21    0.960   35.645
+      22    0.959   34.742
+      23    0.959   35.677
+      24    0.960   34.868
+      25    0.959   34.064
+      26    0.960   34.548
+      27    0.960   35.434
+      28    0.960   34.917
+      29    0.960   35.334
+      30    0.959   35.459
+      31    0.959   35.445
+      32    0.960   34.742
+      33    0.960   35.095
+      34    0.960   35.290
+      35    0.959   36.271
+      36    0.960   35.242
+      37    0.959   34.260
+      38    0.959   34.176
+      39    0.960   35.634
+      40    0.960   34.780
+      41    0.960   35.336
+      42    0.960   34.803
+      43    0.959   35.657
+      44    0.960   35.948
+      45    0.960   36.171
+      46    0.960   35.008
+      47    0.960   34.428
+      48    0.960   36.054
+      49    0.959   34.814
+      50    0.960   32.669
+      51    0.959   32.266
+      52    0.959   33.559
+      53    0.959   33.480
+      54    0.960   33.088
+      55    0.960   35.290
+      56    0.959   34.990
+      57    0.960   34.632
+      58    0.960   34.045
+      59    0.960   33.619
+      60    0.960   34.294
+      61    0.959   34.022
+      62    0.960   32.532
+      63    0.960   32.119
+      64    0.959   32.826
+      65    0.960   32.418
+      66    0.960   25.888
+      67    0.960   25.829
+      68    0.959   29.411
+      69    0.959   30.604
+      70    0.959   30.652
+      71    0.959   27.995
+      72    0.959   28.355
+      73    0.959   29.949
+      74    0.960   31.380
+      75    0.959   30.183
+      76    0.960   26.756
+      77    0.960   24.256
+      78    0.960   24.976
+      79    0.960   26.517
+      80    0.960   24.725
+      81    0.960   24.195
+      82    0.959   22.932
+      83    0.959   24.066
+      84    0.960   24.288
+      85    0.960   26.077
+      86    0.960   23.975
+      87    0.960   24.564
+      88    0.960   23.422
+      89    0.960   23.691
+      90    0.959   23.900
+      91    0.960   23.307
+      92    0.960   24.221
+      93    0.959   22.923
+      94    0.960   22.561
+      95    0.959   23.657
+      96    0.959   23.353
+      97    0.959   23.879
+      98    0.960   24.223
+      99    0.960   24.409
+     100    0.960   22.941
+     101    0.959   22.305
diff --git a/test/Test_MinMaxDist/tz2.byatom.dat.save b/test/Test_MinMaxDist/tz2.byatom.dat.save
new file mode 100644
index 0000000000..f1a4ac7a05
--- /dev/null
+++ b/test/Test_MinMaxDist/tz2.byatom.dat.save
@@ -0,0 +1,102 @@
+#Frame        Min      Max
+       1   16.832   29.560
+       2   16.994   31.131
+       3   15.454   32.325
+       4   16.799   32.440
+       5   15.520   26.784
+       6    9.051   22.231
+       7    6.890   19.366
+       8    6.781   18.893
+       9    7.781   18.518
+      10    9.176   22.143
+      11   10.302   23.494
+      12   14.470   28.019
+      13   17.874   30.868
+      14   19.335   31.336
+      15   17.044   29.557
+      16   15.038   26.845
+      17   16.976   26.513
+      18   15.697   29.211
+      19   16.756   29.435
+      20   18.963   32.001
+      21   19.200   33.112
+      22   21.893   32.471
+      23   22.746   33.068
+      24   19.250   30.703
+      25   12.535   27.839
+      26   14.665   29.039
+      27   19.802   32.571
+      28   21.793   34.303
+      29   23.472   35.334
+      30   23.315   35.376
+      31   21.210   35.445
+      32   20.510   32.619
+      33   18.098   30.957
+      34   19.678   32.354
+      35   21.165   32.896
+      36   17.102   31.552
+      37   19.106   30.728
+      38   17.709   28.729
+      39   15.801   28.428
+      40   15.159   28.964
+      41   14.524   28.928
+      42   16.886   30.371
+      43   21.605   34.871
+      44   23.761   34.666
+      45   23.335   36.171
+      46   20.948   35.008
+      47   20.303   33.340
+      48   21.583   36.054
+      49   21.935   32.728
+      50   16.862   27.774
+      51   17.052   28.464
+      52   16.411   28.740
+      53   17.338   31.498
+      54   18.244   31.205
+      55   17.448   31.562
+      56   18.000   31.164
+      57   20.647   32.347
+      58   21.222   33.369
+      59   20.412   28.697
+      60   19.844   32.103
+      61   18.602   30.913
+      62   13.814   27.843
+      63   16.121   29.308
+      64   17.694   26.411
+      65   13.935   21.474
+      66    7.686   20.481
+      67    9.249   20.474
+      68   12.675   20.765
+      69   15.262   25.604
+      70   15.591   25.169
+      71   15.143   23.985
+      72   13.601   25.347
+      73   13.119   26.871
+      74   18.300   29.319
+      75   16.242   27.181
+      76   14.465   26.449
+      77   11.234   22.230
+      78    3.062   16.829
+      79    2.152   11.610
+      80    2.581   13.083
+      81    3.001   11.534
+      82    3.701   13.606
+      83    3.019   15.709
+      84    4.208   16.080
+      85    3.429   18.271
+      86    3.018   14.184
+      87    2.701   13.893
+      88    2.049   15.222
+      89    3.039   18.237
+      90    5.283   15.833
+      91    2.526   12.824
+      92    2.926   12.024
+      93    2.913   10.493
+      94    2.431   11.998
+      95    2.445   12.481
+      96    2.666   13.132
+      97    2.795   11.449
+      98    3.095   13.293
+      99    2.267   12.293
+     100    2.171   12.067
+     101    2.487   13.073
diff --git a/test/Test_MinMaxDist/tz2.bymol.1.dat.save b/test/Test_MinMaxDist/tz2.bymol.1.dat.save
new file mode 100644
index 0000000000..88e7dc73ba
--- /dev/null
+++ b/test/Test_MinMaxDist/tz2.bymol.1.dat.save
@@ -0,0 +1,11 @@
+#Frame   MolMin1[1_2] MolMin1[1_3] MolMin1[1_4] MolMin1[1_5] MolMin1[1_6] MolMin1[1_7] MolMin1[1_8] MolMin1[1_9] MolMin1[1_10] MolMin1[2_3] MolMin1[2_4] MolMin1[2_5] MolMin1[2_6] MolMin1[2_7] MolMin1[2_8] MolMin1[2_9] MolMin1[2_10] MolMin1[3_4] MolMin1[3_5] MolMin1[3_6] MolMin1[3_7] MolMin1[3_8] MolMin1[3_9] MolMin1[3_10] MolMin1[4_5] MolMin1[4_6] MolMin1[4_7] MolMin1[4_8] MolMin1[4_9] MolMin1[4_10] MolMin1[5_6] MolMin1[5_7] MolMin1[5_8] MolMin1[5_9] MolMin1[5_10] MolMin1[6_7] MolMin1[6_8] MolMin1[6_9] MolMin1[6_10] MolMin1[7_8] MolMin1[7_9] MolMin1[7_10] MolMin1[8_9] MolMin1[8_10] MolMin1[9_10] MolMax1[1_2] MolMax1[1_3] MolMax1[1_4] MolMax1[1_5] MolMax1[1_6] MolMax1[1_7] MolMax1[1_8] MolMax1[1_9] MolMax1[1_10] MolMax1[2_3] MolMax1[2_4] MolMax1[2_5] MolMax1[2_6] MolMax1[2_7] MolMax1[2_8] MolMax1[2_9] MolMax1[2_10] MolMax1[3_4] MolMax1[3_5] MolMax1[3_6] MolMax1[3_7] MolMax1[3_8] MolMax1[3_9] MolMax1[3_10] MolMax1[4_5] MolMax1[4_6] MolMax1[4_7] MolMax1[4_8] MolMax1[4_9] MolMax1[4_10] MolMax1[5_6] MolMax1[5_7] MolMax1[5_8] MolMax1[5_9] MolMax1[5_10] MolMax1[6_7] MolMax1[6_8] MolMax1[6_9] MolMax1[6_10] MolMax1[7_8] MolMax1[7_9] MolMax1[7_10] MolMax1[8_9] MolMax1[8_10] MolMax1[9_10]
+       1       13.486        2.533       12.878       10.481       14.375        7.036       13.229       13.127        14.343       20.358       16.017       21.753       17.814        7.317       16.434       21.506        13.842       23.555       20.202       22.752       12.044       20.697       14.397        23.677       11.804        9.543       17.458       17.894       13.491         1.895        7.432       24.710       17.788       16.394        10.513       22.335       19.993       17.691         7.743       14.291       17.710        16.239       10.815        20.588        15.229       26.495       16.764       26.355       24.419       25.822       24.631       26.865       26.559        26.825       22.576       18.203       23.396       19.816        9.371       17.851       23.350        16.196       25.590       21.863       24.004       14.521       22.633       16.161        25.824       13.947       11.388       19.357       20.132       15.071         3.747        8.917       25.687       19.392       18.327        12.966       24.964       22.044       20.152         9.847       15.542       18.257        18.274       12.149        22.677        16.897
+       2       11.959        3.133       11.750       10.641       13.873        7.480       13.168       12.054        13.082       22.466       16.039       20.993       14.080        8.731       14.280       21.929        14.070       24.659       19.634       21.584       12.847       20.554       13.541        24.670       11.608        7.831       18.667       19.853       15.666         1.760        9.420       25.198       18.362       16.039        10.265       20.183       22.021       18.437         5.983       11.816       16.999        17.342       12.471        22.609        17.341       26.278       16.568       25.869       25.473       25.713       23.942       27.114       27.122        26.846       23.239       18.413       22.299       16.017       10.330       16.818       24.003        16.235       25.774       21.184       23.218       14.825       21.573       15.381        26.690       12.717        9.814       20.607       21.386       16.703         3.972       11.101       26.005       19.697       17.758        11.609       22.782       23.948       20.215         7.626       13.831       18.933        19.691       14.570        23.617        18.499
+       3       12.722        2.863       11.333       11.175       13.892        7.113       12.134       14.374        14.690       21.637       15.831       21.201       14.008        9.118       14.280       21.709        13.411       24.866       18.144       21.409       12.772       20.198       15.230        23.372       12.248        7.312       19.176       20.191       15.451         1.972        9.367       24.065       17.793       15.547        12.153       20.846       21.850       19.689         5.886       10.454       18.020        16.695       10.866        21.829        15.214       26.331       16.014       25.989       25.231       25.819       22.657       26.676       26.488        27.133       23.991       18.284       22.782       15.074       10.651       16.160       24.252        14.802       26.302       19.917       22.471       14.698       22.133       16.866        25.926       13.073        9.226       21.958       21.990       16.162         4.017       11.192       25.830       18.780       16.881        14.022       22.846       23.263       21.018         8.521       13.129       20.309        19.007       13.348        24.038        17.255
+       4       11.354        3.055       10.570       10.641       14.493        7.933       11.674       14.588        13.448       23.087       15.897       20.636       15.018        9.525       14.271       22.641        13.251       23.760       18.382       20.835       13.931       19.912       15.163        22.750       11.800        9.647       18.414       20.060       13.883         2.548       10.079       23.869       19.877       17.824        12.242       22.030       19.726       17.695         8.048       10.469       18.709        16.128       11.414        21.866        14.391       26.439       17.239       26.532       26.061       25.708       24.423       25.601       26.645        26.849       24.555       18.332       22.174       17.152       10.675       16.651       24.585        15.133       25.829       20.663       22.354       16.039       22.320       16.190        25.293       13.144       11.528       21.163       21.462       15.517         3.885       11.791       25.494       21.112       19.315        13.730       24.771       21.661       19.880        10.864       12.572       20.414        18.784       13.623        23.661        16.298
+       5       10.854        3.128       11.336       11.476       13.882        7.774       11.902       14.173        13.481       22.116       15.258       17.903       14.061        9.246       15.148       21.961        12.324       22.008       18.956       21.633       13.946       20.892       13.754        22.998       11.057       10.167       18.478       18.861       12.931         3.673        9.086       24.402       19.631       18.421        11.438       21.912       19.307       18.449         7.167       11.515       18.874        16.913       11.182        21.887        15.161       26.305       17.425       26.176       25.716       25.843       24.639       26.409       26.633        26.598       23.215       16.841       18.890       15.994       10.866       17.161       23.570        14.272       24.071       21.521       23.080       15.724       22.508       15.381        25.192       12.602       11.222       21.050       20.008       15.021         4.472       10.974       25.791       21.424       20.336        12.385       24.362       22.011       20.156         8.934       12.512       20.447        19.653       12.694        22.831        16.944
+       6       10.923        2.881       10.654       11.133       12.883        7.785       10.867       14.546        13.279       21.942       16.957       18.498       14.519       10.204       17.032       23.756        12.937       23.008       18.886       21.854       14.645       19.893       14.065        24.712       11.698        8.774       20.372       18.877       14.124         4.602        9.938       23.740       17.735       16.831        11.975       22.345       18.980       18.117         4.797       11.329       19.992        18.777       10.557        22.662        17.082       26.211       17.549       25.975       25.835       25.853       24.571       26.648       25.806        26.247       23.640       18.227       20.911       15.869       11.513       18.217       25.581        14.254       25.011       20.880       24.252       15.870       22.367       15.637        26.256       13.100       10.854       22.200       20.742       16.152         6.490       11.333       25.351       19.672       18.379        13.492       24.502       21.065       20.898         7.227       12.979       21.610        20.032       12.254        24.756        19.471
+       7        8.052        3.736       11.508       10.789       11.532        7.069       10.425       14.226        13.515       21.127       17.768       17.590       17.173       12.722       18.403       24.717        13.475       21.237       19.357       22.483       13.933       20.762       11.938        24.061       10.121        9.948       20.461       17.520       13.822         4.943        7.378       24.393       18.293       17.975         9.380       22.210       17.693       17.975         6.173       13.252       18.802        19.321       10.426        22.389        17.634       25.734       17.890       26.407       24.920       24.254       23.199       27.066       26.393        26.962       23.189       20.157       19.623       18.275       14.210       19.400       26.499        15.942       22.012       21.554       24.762       14.821       22.753       14.061        24.559       11.831       11.742       22.095       20.148       14.786         7.053        8.560       26.117       19.538       19.062        10.707       24.017       19.808       20.237         7.580       15.188       20.351        20.903       12.517        25.024        18.743
+       8        9.405        3.798       10.872       11.059       10.817        6.582       11.949       14.152        12.777       20.883       16.773       16.234       15.457       13.314       18.362       24.527        12.011       21.965       19.375       23.205       13.042       20.884       13.917        23.506       11.332        9.654       20.434       16.581       13.639         5.452        7.824       24.406       18.969       17.469         9.602       22.080       18.310       17.693         5.743       13.951       18.733        18.855        8.794        22.145        17.790       26.192       17.137       26.171       25.474       23.628       23.334       27.059       26.650        26.474       22.236       19.123       18.251       17.420       14.648       19.847       26.199        14.570       23.182       22.171       24.931       14.275       23.134       15.926        25.270       13.392       11.373       22.299       18.170       14.768         6.550        9.122       25.446       19.646       18.592        10.926       24.255       19.933       19.837         8.058       15.804       21.017        21.164       11.144        23.550        19.266
+       9        7.473        2.589       11.632       10.924        9.412        7.068       10.826       14.235        14.262       18.669       17.214       18.149       18.157       13.934       17.422       25.121        13.255       23.402       18.306       22.512       14.733       21.316       14.211        23.307       11.588        9.570       20.722       17.854       13.805         4.251        6.530       23.829       17.039       16.819         9.122       20.505       17.272       18.132         7.619       12.989       20.573        19.809        9.399        22.909        17.980       25.762       16.205       25.693       24.980       22.541       22.790       27.052       25.761        26.833       20.195       19.372       19.930       19.895       15.549       18.605       26.225        14.943       24.534       20.283       23.909       15.703       23.620       16.013        25.400       13.627       10.680       22.446       20.253       15.338         5.912        8.543       25.016       18.881       17.570        10.788       22.527       18.843       19.214         8.664       15.061       22.134        21.011       11.136        24.976        19.219
+      10        8.760        3.973       11.055       12.623       11.360        7.563       11.808       15.198        13.499       21.856       20.749       20.337       19.702       12.767       14.393       22.081        16.448       20.539       17.031       20.209       15.057       22.371       13.420        23.662       13.225       10.946       20.207       16.718       12.000         5.125        6.600       23.221       18.701       17.135         9.649       22.087       17.446       16.289         7.172       13.176       19.050        19.413       10.063        22.485        16.981       25.498       18.219       25.851       25.919       23.273       23.655       26.541       26.418        26.585       23.075       22.213       22.015       21.664       13.674       16.490       23.809        18.230       23.199       18.622       21.881       16.003       23.226       15.446        24.762       15.087       13.036       22.329       18.290       14.729         6.704        9.314       24.143       20.983       19.198        11.727       24.347       19.237       18.319         8.423       15.032       21.435        20.894       11.294        23.928        19.221
diff --git a/test/Test_MinMaxDist/tz2.bymol.2.dat.save b/test/Test_MinMaxDist/tz2.bymol.2.dat.save
new file mode 100644
index 0000000000..20a7a37050
--- /dev/null
+++ b/test/Test_MinMaxDist/tz2.bymol.2.dat.save
@@ -0,0 +1,11 @@
+#Frame   MolMin2[1_342] MolMin2[1_567] MolMin2[1_638] MolMin2[1_1026] MolMin2[1_1560] MolMin2[1_1846] MolMax2[1_342] MolMax2[1_567] MolMax2[1_638] MolMax2[1_1026] MolMax2[1_1560] MolMax2[1_1846]
+       1          2.058          2.391          2.112           2.709           1.826           2.472         14.549         19.358         18.529          18.242          19.008          14.598
+       2          1.756          2.653          1.883           2.586           1.978           1.857         14.064         18.597         19.116          17.606          18.844          14.594
+       3          2.120          2.728          1.783           3.001           2.300           2.386         14.744         17.790         19.430          17.388          19.347          15.086
+       4          1.708          2.825          1.959           2.570           3.048           2.256         14.383         18.227         18.796          16.982          19.249          15.116
+       5          1.780          3.537          2.080           1.788           2.560           2.124         13.544         18.700         19.248          15.840          19.041          15.255
+       6          1.869          3.473          1.880           2.184           2.533           1.855         13.900         19.086         18.417          15.255          19.930          14.854
+       7          1.705          3.149          1.744           1.748           2.343           2.340         13.747         19.494         18.106          15.606          18.541          14.762
+       8          1.935          1.707          1.853           1.817           1.887           2.061         14.095         18.106         16.979          15.792          18.559          14.015
+       9          1.907          1.794          1.939           2.052           2.455           2.216         13.787         18.797         16.865          16.447          18.943          13.838
+      10          3.151          2.656          2.654           1.792           2.665           2.691         14.748         18.928         18.023          16.979          19.506          15.040
diff --git a/test/Test_MinMaxDist/tz2.byres.1.dat.save b/test/Test_MinMaxDist/tz2.byres.1.dat.save
new file mode 100644
index 0000000000..98ccfed344
--- /dev/null
+++ b/test/Test_MinMaxDist/tz2.byres.1.dat.save
@@ -0,0 +1,11 @@
+#Frame   ResMin1[1_3] ResMin1[1_4] ResMin1[1_5] ResMin1[1_6] ResMin1[1_7] ResMin1[2_4] ResMin1[2_5] ResMin1[2_6] ResMin1[2_7] ResMin1[3_5] ResMin1[3_6] ResMin1[3_7] ResMin1[4_6] ResMin1[4_7] ResMin1[5_7] ResMax1[1_3] ResMax1[1_4] ResMax1[1_5] ResMax1[1_6] ResMax1[1_7] ResMax1[2_4] ResMax1[2_5] ResMax1[2_6] ResMax1[2_7] ResMax1[3_5] ResMax1[3_6] ResMax1[3_7] ResMax1[4_6] ResMax1[4_7] ResMax1[5_7]
+       1        3.194        7.532        8.957       12.744       13.509        4.546        7.034       10.736        9.729        2.336        6.212        7.392        4.035        3.144        3.130       10.306       18.470       15.076       19.082       18.962       16.070       15.777       20.095       16.824        9.094       13.337       13.293       12.858        9.842       11.237
+       2        4.044        7.591        9.034       12.969       13.773        4.581        6.987       10.661        9.553        2.231        6.521        7.846        4.484        3.077        3.184       10.671       18.909       15.451       19.183       19.503       16.166       15.321       19.366       16.990        9.614       13.253       14.021       12.223       10.406       11.160
+       3        4.030        7.615        9.231       13.082       13.743        4.630        7.394       10.896        9.591        2.839        6.732        7.893        4.343        3.077        3.507       10.952       19.004       15.624       19.325       19.550       16.673       15.830       19.281       17.134        9.787       13.600       14.038       11.608       10.612       11.086
+       4        4.378        8.088        9.397       13.339       13.909        4.563        7.039       10.800        9.864        2.936        6.352        7.616        4.212        2.597        3.217       11.119       19.239       15.675       19.448       19.396       16.135       16.025       19.299       16.686        9.578       13.283       13.398       11.948        9.795       11.429
+       5        4.214        8.128        9.855       13.553       13.988        4.774        7.629       11.268       10.900        2.708        6.815        7.443        4.668        2.910        2.478       10.441       19.222       15.622       18.999       19.633       17.487       16.229       19.353       18.196        9.568       13.240       13.587       12.437       10.121       11.430
+       6        4.372        8.215        9.630       13.417       14.340        4.703        7.101       10.790       11.100        2.225        5.853        7.285        4.344        2.495        2.883       11.243       19.338       15.523       19.484       19.653       17.118       16.177       20.581       18.047        8.946       13.459       13.290       12.392       10.147       11.747
+       7        4.266        8.060        9.075       13.039       14.012        4.604        6.727       10.577       10.312        2.292        5.812        7.350        4.294        2.701        2.709       11.276       19.280       15.462       18.852       19.615       16.751       15.564       18.743       17.543        9.295       12.901       13.600       11.616       10.134       11.411
+       8        3.685        7.348        9.095       12.722       13.623        4.471        7.437       11.069       10.649        2.508        6.360        7.568        4.397        2.932        2.822       10.438       18.735       15.403       18.821       19.224       16.709       16.482       19.132       17.442        9.645       13.162       13.341       12.289        9.773       11.149
+       9        3.475        7.532        9.064       12.975       13.907        4.513        7.441       11.114       11.045        2.609        6.491        7.804        4.646        2.658        2.841       10.149       18.651       15.233       18.771       19.245       17.093       16.813       19.064       17.791        9.551       13.203       13.575       12.117       10.059       10.970
+      10        3.698        7.849        9.515       13.156       13.650        4.635        7.462       10.916       10.854        2.574        6.400        6.976        4.563        2.693        2.465       10.226       19.061       15.166       18.862       19.024       17.532       16.152       19.519       17.876        9.202       12.887       13.044       12.834        9.159       11.043
diff --git a/test/Test_MinMaxDist/tz2.byres.2.dat.save b/test/Test_MinMaxDist/tz2.byres.2.dat.save
new file mode 100644
index 0000000000..de556da024
--- /dev/null
+++ b/test/Test_MinMaxDist/tz2.byres.2.dat.save
@@ -0,0 +1,11 @@
+#Frame   ResMin2[2_9] ResMin2[2_10] ResMin2[2_11] ResMin2[3_9] ResMin2[3_10] ResMin2[3_11] ResMin2[4_9] ResMin2[4_10] ResMin2[4_11] ResMax2[2_9] ResMax2[2_10] ResMax2[2_11] ResMax2[3_9] ResMax2[3_10] ResMax2[3_11] ResMax2[4_9] ResMax2[4_10] ResMax2[4_11]
+       1        2.625         2.802         2.675        2.256         1.890         3.924        2.536         3.808         7.424       10.912        11.855         9.767       11.983         8.937        12.261       10.266        12.552        19.866
+       2        2.274         2.459         2.726        2.798         2.008         4.000        2.631         3.671         7.401       11.517        11.253         9.992       11.309         8.713        13.017       10.186        12.054        20.548
+       3        2.642         2.816         2.681        2.557         1.858         4.032        2.386         3.506         7.356       11.370        11.352        10.328       10.857         8.660        13.208       10.395        12.253        20.841
+       4        3.111         2.360         2.611        2.699         2.148         4.104        2.434         3.848         7.763       11.000        11.393        10.290       11.295         8.763        13.613       10.460        12.983        21.299
+       5        3.407         2.545         2.496        2.633         1.784         3.840        2.439         3.324         7.308       12.473        11.749        10.536       11.302         8.189        12.989       10.282        12.299        21.045
+       6        3.186         2.534         2.851        2.660         1.913         4.234        2.406         3.505         7.327       11.681        12.155        10.287       11.173         8.309        13.494       10.067        12.404        20.863
+       7        2.814         2.360         2.768        2.972         1.932         4.168        2.611         3.586         7.577       11.812        11.362        10.078       11.817         8.687        13.748       10.852        12.533        21.108
+       8        2.729         2.618         2.726        2.337         1.744         4.176        2.440         3.542         7.347       11.654        11.992         9.914       10.875         8.380        12.691       10.420        12.741        20.665
+       9        2.761         2.470         2.620        2.464         1.961         3.708        2.328         3.582         7.463       12.127        12.073         9.908       11.117         8.506        12.734       10.389        12.612        20.726
+      10        2.829         2.507         2.535        2.394         1.930         3.738        2.505         3.876         7.577       12.838        11.511         9.795       11.041         8.615        12.766       10.276        12.950        21.186
diff --git a/test/Test_TICA/RunTest.sh b/test/Test_TICA/RunTest.sh
index f6b16f9227..339031e7d9 100755
--- a/test/Test_TICA/RunTest.sh
+++ b/test/Test_TICA/RunTest.sh
@@ -2,23 +2,81 @@
 
 . ../MasterTest.sh
 
-CleanFiles tica.in
+CleanFiles tica.in ticadebug.dat M?.dat ticadebug.m?.dat \
+           tz2.*.dat crd.*.dat dih.*.dat
 
 INPUT='-i tica.in'
 
+#MASS=mass
+#cat > tica.in <<EOF
+#parm ../tz2.parm7
+#loadcrd ../tz2.crd name TZ2
+#
+#set MASK = :1-3@N,CA,C
+#
+#crdaction TZ2 matrix name M1 mwcovar out M1.dat \$MASK $MASS
+#
+#runanalysis tica crdset TZ2 mask \$MASK lag 1 debugc0 ticadebug.m1.dat $MASS
+#
+#crdaction TZ2 matrix name M2 mwcovar out M2.dat :1-3@N,CA :1-3@C,O $MASS
+#
+#runanalysis tica crdset TZ2 mask :1-3@N,CA mask2 :1-3@C,O lag 1 debugct ticadebug.m2.dat $MASS
+#
+#list dataset
+#EOF
 cat > tica.in <<EOF
 parm ../tz2.parm7
-loadcrd ../tz2.crd name TZ2
+trajin ../tz2.crd
+#createcrd TZ2
+distance d1.12 :1@CA :12@CA
+distance d2.11 :2@CA :11@CA
+distance d3.10 :3@CA :10@CA
+distance d4.9  :4@CA :9@CA
+distance d5.8  :5@CA :8@CA
+rms R0 first @CA
+tica data R0 data d* name TICA lag 10 out tz2.ticamodes.dat cumvarout tz2.cumvar.dat
+tica data R0 data d* name TICA2 lag 10 map commute out tz2.tica2modes.dat
+run
+writedata tz2.raw.dat R0 d*
 
-set MASK = :1-3@CA
-
-crdaction TZ2 matrix name M1 mwcovar out M1.dat \$MASK
+#projection Evec out tz2.project.dat evecs TICA data R0 data d*
+runanalysis projectdata name Evec out tz2.project.dat evecs TICA data R0 data d*
+run
+EOF
+RunCpptraj "TICA test, 1D data sets."
+DoTest tz2.ticamodes.dat.save tz2.ticamodes.dat
+DoTest tz2.cumvar.dat.save tz2.cumvar.dat
+DoTest tz2.project.dat.save tz2.project.dat
+DoTest tz2.tica2modes.dat.save tz2.tica2modes.dat
 
-runanalysis tica crdset TZ2 mask \$MASK lag 1 mass
+cat > tica.in <<EOF
+parm ../tz2.parm7
+loadcrd ../tz2.crd name MyCrd
+tica crdset MyCrd mask @CA name TICA lag 10 out crd.ticamodes.dat cumvarout crd.cumvar.dat
+run
+# DEBUG
+#crdaction MyCrd strip !@CA
+#runanalysis tica crdset MyCrd name TICA2 lag 10 out crd.tica2modes.dat cumvarout crd.cumvar2.dat
+EOF
+RunCpptraj "TICA test, coordinates."
+DoTest crd.ticamodes.dat.save crd.ticamodes.dat
+DoTest crd.cumvar.dat.save crd.cumvar.dat
 
-list dataset
+cat > tica.in <<EOF
+parm ../tz2.parm7
+trajin ../tz2.crd
+dihedral d1 :1@C :2@N :2@CA :2@C
+dihedral d2 :2@N :2@CA :2@C :3@N
+createcrd MyCrd
+tica data d1 data d2 name TICA lag 10 out dih.ticamodes.dat cumvarout dih.cumvar.dat
+run
 EOF
-RunCpptraj "TICA test."
+RunCpptraj "TICA test, dihedrals."
+DoTest dih.ticamodes.dat.save dih.ticamodes.dat
+DoTest dih.cumvar.dat.save dih.cumvar.dat
+
+#diff M1.dat ticadebug.m1.dat
+#diff M2.dat ticadebug.m2.dat
 
 EndTest
 exit 0
diff --git a/test/Test_TICA/crd.cumvar.dat.save b/test/Test_TICA/crd.cumvar.dat.save
new file mode 100644
index 0000000000..bf4e8879c6
--- /dev/null
+++ b/test/Test_TICA/crd.cumvar.dat.save
@@ -0,0 +1,37 @@
+#Mode    TICA[cumvar]
+       1   0.09423424
+       2   0.17453684
+       3   0.24243192
+       4   0.30905635
+       5   0.37380235
+       6   0.43478321
+       7   0.48923433
+       8   0.54210563
+       9   0.58778965
+      10   0.63198711
+      11   0.67257062
+      12   0.70892034
+      13   0.74302738
+      14   0.77416622
+      15   0.80405702
+      16   0.83327440
+      17   0.85987041
+      18   0.88259828
+      19   0.90160100
+      20   0.91699753
+      21   0.93103666
+      22   0.94455705
+      23   0.95570115
+      24   0.96433226
+      25   0.97217102
+      26   0.97965685
+      27   0.98434620
+      28   0.98856732
+      29   0.99256107
+      30   0.99478638
+      31   0.99671443
+      32   0.99797534
+      33   0.99898308
+      34   0.99960061
+      35   0.99999292
+      36   1.00000000
diff --git a/test/Test_TICA/crd.ticamodes.dat.save b/test/Test_TICA/crd.ticamodes.dat.save
new file mode 100644
index 0000000000..cdd3792166
--- /dev/null
+++ b/test/Test_TICA/crd.ticamodes.dat.save
@@ -0,0 +1,296 @@
+ Eigenvector file: COVAR nmodes 36 width 11
+   36   36
+   -2.16585   10.46799    2.84118   -0.30047    9.59902    3.45799   -0.36873
+    7.52547    1.11224   -0.08867    8.05757   -1.82734   -0.45848    5.36836
+   -3.49360   -2.62743    3.78713   -2.45055   -2.40556    0.93847   -2.35715
+   -3.10766   -2.22973   -1.41519   -0.82904   -4.05838    0.00015   -0.72778
+   -7.19796   -0.21329    0.57981   -9.11418    1.89087    2.09110  -11.72096
+    1.25470
+ ****
+    1     0.90735
+   -0.01527    0.01627    0.02771    0.01106    0.00882    0.06976    0.08412
+   -0.13262    0.04661    0.02639    0.27149   -0.10913   -0.05049    0.14457
+    0.00517    0.12046   -0.02745    0.04658   -0.17463    0.01253    0.06757
+    0.46550   -0.11452    0.11339   -0.22810    0.41493   -0.44167    0.03219
+   -0.10675    0.14039    0.10014   -0.03759   -0.33058    0.08715    0.07034
+   -0.15160
+ ****
+    2    -0.83760
+   -0.08929   -0.12566    0.26888    0.60277   -0.30025   -0.61363   -0.09203
+   -0.68438   -0.48001   -0.33795    0.17114    0.75254    0.17947   -1.04252
+    0.35138   -0.38761    0.92328    0.22161    0.31008   -0.80846   -0.25728
+   -0.28713    0.40001    0.02598    0.60505   -0.78985    0.56918   -0.94358
+    0.87222   -0.72048    0.96206   -0.66250    0.72535    0.01887   -0.44938
+   -0.22399
+ ****
+    3     0.77018
+   -0.19337   -0.18828   -0.04517    0.61559   -0.47806    0.81750   -0.10945
+    0.87396   -0.39361    0.31925   -0.60621    1.10855    0.71594   -0.37213
+   -0.46925   -0.37881   -0.94258    0.66207    0.39115    0.50785   -0.28546
+   -0.41374   -0.68433   -0.21426    0.94231   -0.66493    1.08899   -0.54296
+    1.10163   -0.78102    0.65748   -0.68743    1.24266    0.06886   -0.34573
+    0.39538
+ ****
+    4    -0.76293
+   -0.21838   -0.16623    0.25060    0.45181   -0.07103   -0.96480    0.18885
+    0.19494    0.08799   -0.05157   -0.87458   -0.72327    0.10714    1.16679
+    0.06570   -0.01715   -1.29274   -0.26828    0.11459    1.22032   -0.07996
+   -0.70843   -0.99907   -0.09295    0.94735    0.06851    0.01640   -0.27928
+   -0.74552   -0.03732    0.43124    0.50684   -0.25605    0.30659   -0.19059
+   -0.33843
+ ****
+    5    -0.75210
+    0.16162    0.13212   -0.05283   -0.05410   -0.45225   -0.09431    0.15491
+    0.25568    0.30947   -0.31941   -0.42968   -0.06296    0.05225    0.17649
+    0.17026   -0.27394   -0.18430   -0.04852   -0.14364    0.29748   -0.07944
+   -0.49894    0.35861    0.00274    0.23086   -0.31580   -0.42838   -0.12461
+    0.66503   -0.07840   -0.57158   -0.90268    0.26179   -0.48549    0.05429
+   -0.39245
+ ****
+    6     0.72991
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+   -0.11724   -0.23781   -0.72193    0.24724    0.39570    0.57520   -0.46219
+   -0.31814   -0.42761   -0.10441    0.34238    0.11651   -0.00148   -0.00955
+   -0.85116    1.23313   -0.41761    0.68076   -0.94316    0.38500   -0.44685
+   -0.04796    0.05629    0.39720   -0.01438    0.22861   -0.04035    0.19468
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+ ****
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+   -0.41233   -0.03272   -0.12854    0.97717    0.16571   -0.12025   -0.08052
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+ ****
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+   -0.29162    0.09667   -0.06906   -0.21268   -0.16713    0.54619   -0.39850
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+   -0.25063   -0.41679    0.39502   -0.76214    0.36338    0.23636    0.03572
+   -0.17460
+ ****
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+    0.88701    0.01833    0.32777   -1.11408   -0.29994    0.41531    0.21107
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+ ****
+   10     0.62140
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+   -0.81677   -0.91083    0.10561    0.75498   -0.05263    0.63279   -0.31447
+    0.08301   -0.57726    0.52033    0.40527    0.21869    0.06582   -0.15028
+    0.17011
+ ****
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+ ****
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+    0.18084
+ ****
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+   -0.18848   -0.29848    0.45657    0.24818    0.10653   -0.00981   -0.05519
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+ ****
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+ ****
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+   -0.53553   -0.69836   -0.25863    0.03484    0.30239    0.24513   -0.13171
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+ ****
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+ ****
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+ ****
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+    0.04583    0.05002   -0.08011   -0.09428   -0.02537   -0.01799    0.14826
+   -0.05551    0.04338   -0.05775    0.04660   -0.07163   -0.01153   -0.02229
+    0.05681   -0.00994    0.02517   -0.13300    0.05223    0.05570   -0.05573
+   -0.04148   -0.01476    0.01479    0.00460   -0.00535   -0.04224    0.00297
+    0.04537
+ ****
+   33    -0.09383
+    0.02101   -0.00475    0.00811   -0.04999   -0.07510   -0.04459    0.05319
+    0.04747    0.03882   -0.09773   -0.00854   -0.08570    0.04173    0.03260
+    0.07047    0.02643    0.01381   -0.07110    0.01635   -0.03737    0.00311
+   -0.04305   -0.04759    0.03872   -0.04407    0.08179   -0.04258    0.08945
+   -0.11165    0.04669    0.07710    0.03877   -0.01366    0.02031   -0.04423
+   -0.00431
+ ****
+   34     0.07345
+   -0.01379    0.01679   -0.03683   -0.00404   -0.06852    0.03324    0.01336
+    0.03667    0.04066   -0.06782   -0.02124    0.01074    0.04560    0.00586
+    0.05025   -0.05440   -0.02401    0.02245   -0.01424   -0.00673   -0.00574
+    0.08990   -0.00882    0.03039   -0.08553   -0.02269    0.07221    0.00004
+   -0.03975    0.00276   -0.00136    0.06102    0.01150   -0.00004   -0.03661
+    0.03895
+ ****
+   35     0.05854
+   -0.00558    0.02510    0.00146   -0.00786   -0.04989    0.02320   -0.02275
+   -0.02194    0.02857    0.04593    0.02096    0.03422    0.00034    0.02592
+   -0.01746    0.02517   -0.00371   -0.00340   -0.05270   -0.04151    0.04519
+    0.09388   -0.06465    0.03012   -0.06357    0.06165   -0.06610   -0.02206
+    0.01621    0.04281   -0.02769   -0.06972   -0.01447    0.02389   -0.00103
+    0.00061
+ ****
+   36    -0.00786
+    0.00195   -0.00143    0.00314   -0.00083   -0.00290   -0.00402   -0.00110
+   -0.00230    0.00522   -0.00013    0.00233   -0.00928   -0.00120    0.00005
+   -0.00054    0.01103   -0.00101    0.00066   -0.01232   -0.00723    0.00567
+    0.00416    0.00634   -0.00250    0.00213   -0.00649   -0.00054    0.00094
+    0.00358   -0.00163    0.00588   -0.00274    0.00275    0.00059   -0.00403
+    0.00017
diff --git a/test/Test_TICA/dih.cumvar.dat.save b/test/Test_TICA/dih.cumvar.dat.save
new file mode 100644
index 0000000000..c8e20c7385
--- /dev/null
+++ b/test/Test_TICA/dih.cumvar.dat.save
@@ -0,0 +1,5 @@
+#Mode    TICA[cumvar]
+       1   0.43645404
+       2   0.82003795
+       3   0.98477491
+       4   1.00000000
diff --git a/test/Test_TICA/dih.ticamodes.dat.save b/test/Test_TICA/dih.ticamodes.dat.save
new file mode 100644
index 0000000000..bcd8ec99fb
--- /dev/null
+++ b/test/Test_TICA/dih.ticamodes.dat.save
@@ -0,0 +1,15 @@
+ Eigenvector file: DIHCOVAR nmodes 4 width 11
+    4    4
+    0.07085   -0.90791    0.67080   -0.72203
+ ****
+    1    -0.31252
+    0.53237   -3.00623   -2.25109    0.57789
+ ****
+    2     0.29298
+   -0.26695   -1.41123    4.64628   -3.33765
+ ****
+    3     0.19200
+    0.34305    0.37563    0.17782    0.65989
+ ****
+    4    -0.05837
+    0.03172    0.10191    1.31799   -1.56690
diff --git a/test/Test_TICA/tz2.cumvar.dat.save b/test/Test_TICA/tz2.cumvar.dat.save
new file mode 100644
index 0000000000..83758ce1d7
--- /dev/null
+++ b/test/Test_TICA/tz2.cumvar.dat.save
@@ -0,0 +1,7 @@
+#Mode    TICA[cumvar]
+       1   0.68193247
+       2   0.82647376
+       3   0.93987867
+       4   0.97878005
+       5   0.99437209
+       6   1.00000000
diff --git a/test/Test_TICA/tz2.project.dat.save b/test/Test_TICA/tz2.project.dat.save
new file mode 100644
index 0000000000..fe870169b7
--- /dev/null
+++ b/test/Test_TICA/tz2.project.dat.save
@@ -0,0 +1,102 @@
+#Frame      Mode1    Mode2
+       1    0.094    1.739
+       2    0.107    1.215
+       3    0.304    0.651
+       4    0.604    0.883
+       5    0.402    0.715
+       6    0.170   -0.114
+       7   -0.203   -0.398
+       8   -0.368    0.500
+       9   -0.298    0.798
+      10   -0.213    0.434
+      11   -0.321    0.557
+      12    0.248    0.687
+      13    0.366    0.591
+      14    0.336    0.488
+      15    0.569    0.106
+      16    0.571   -0.268
+      17    0.386   -0.467
+      18    0.518   -0.520
+      19    0.389   -0.050
+      20    0.766    0.397
+      21    0.838    0.332
+      22    0.715    0.151
+      23    0.653   -0.136
+      24    0.502   -0.094
+      25    0.387   -0.429
+      26    0.502   -0.303
+      27    0.495   -0.132
+      28    0.594   -0.271
+      29    0.796   -0.134
+      30    0.778   -0.022
+      31    0.692   -0.180
+      32    0.709    0.151
+      33    0.560   -0.225
+      34    0.627    0.097
+      35    0.729   -0.281
+      36    0.782   -0.161
+      37    0.498    0.096
+      38    0.399   -0.445
+      39    0.522   -0.425
+      40    0.395   -0.187
+      41    0.435   -0.361
+      42    0.560   -0.102
+      43    0.638   -0.078
+      44    0.749   -0.179
+      45    0.836   -0.188
+      46    0.641   -0.077
+      47    0.811    0.363
+      48    0.756    0.295
+      49    0.738   -0.014
+      50    0.518   -0.259
+      51    0.428   -0.324
+      52    0.238   -0.274
+      53    0.381    0.163
+      54    0.536    0.062
+      55    0.545   -0.046
+      56    0.597   -0.373
+      57    0.667   -0.404
+      58    0.667    0.010
+      59    0.650   -0.008
+      60    0.665    0.095
+      61    0.658    0.130
+      62    0.425    0.033
+      63    0.193   -0.170
+      64    0.081    0.080
+      65   -0.285    0.083
+      66   -0.449   -0.136
+      67   -1.220   -0.410
+      68   -0.908    0.006
+      69   -0.569    0.885
+      70   -0.957    0.413
+      71   -0.371   -0.147
+      72   -0.743   -0.388
+      73   -0.494    0.050
+      74   -0.418    0.048
+      75   -0.493   -0.098
+      76   -0.612    0.101
+      77   -0.963    0.038
+      78   -1.459   -0.510
+      79   -1.355   -0.112
+      80   -1.070    0.374
+      81   -1.303   -0.050
+      82   -1.165   -0.250
+      83   -0.982   -0.148
+      84   -1.189   -0.171
+      85   -0.871    0.045
+      86   -0.872    0.311
+      87   -0.947    0.312
+      88   -1.109    0.081
+      89   -0.888    0.089
+      90   -1.006   -0.272
+      91   -1.153   -0.316
+      92   -1.169    0.195
+      93   -1.460   -0.275
+      94   -1.166    0.186
+      95   -1.232   -0.174
+      96   -0.990   -0.089
+      97   -1.349   -0.260
+      98   -0.972    0.097
+      99   -1.374   -0.221
+     100   -0.924    0.036
+     101   -1.091   -0.174
diff --git a/test/Test_TICA/tz2.tica2modes.dat.save b/test/Test_TICA/tz2.tica2modes.dat.save
new file mode 100644
index 0000000000..0ce845b5e9
--- /dev/null
+++ b/test/Test_TICA/tz2.tica2modes.dat.save
@@ -0,0 +1,21 @@
+ Eigenvector file: DATACOVAR nmodes 6 width 11
+    6    6
+    4.18412   22.94287   18.96758   14.92085   12.85960    9.02956
+ ****
+    1     0.73901
+    0.06899   -0.06928    0.23780   -0.20663    0.74276    0.23602
+ ****
+    2     0.34023
+   -1.17547   -0.45850    0.34233    0.29094   -0.71231    1.30193
+ ****
+    3    -0.30137
+   -0.80104    0.42778   -0.83677    1.05293   -0.71665    1.38608
+ ****
+    4    -0.17651
+    0.00000   -0.00000    0.00000   -0.00000   -0.00000    0.00000
+ ****
+    5     0.11175
+    0.00000   -0.00000   -0.00000    0.00000    0.00000   -0.00000
+ ****
+    6     0.06714
+    0.00000   -0.00000    0.00000    0.00000   -0.00000   -0.00000
diff --git a/test/Test_TICA/tz2.ticamodes.dat.save b/test/Test_TICA/tz2.ticamodes.dat.save
new file mode 100644
index 0000000000..4d79da05ae
--- /dev/null
+++ b/test/Test_TICA/tz2.ticamodes.dat.save
@@ -0,0 +1,21 @@
+ Eigenvector file: DATACOVAR nmodes 6 width 11
+    6    6
+    4.18412   22.94287   18.96758   14.92085   12.85960    9.02956
+ ****
+    1     0.73901
+    0.01747   -0.01754    0.06022   -0.05233    0.18810    0.05977
+ ****
+    2     0.34023
+   -0.27975   -0.10912    0.08147    0.06924   -0.16952    0.30985
+ ****
+    3    -0.30137
+    0.19457   -0.10391    0.20325   -0.25576    0.17408   -0.33668
+ ****
+    4    -0.17651
+   -0.27124    0.01260   -0.09091    0.04572    0.14182   -0.35407
+ ****
+    5     0.11175
+    0.01193   -0.00537   -0.05896    0.02849    0.08431   -0.05691
+ ****
+    6     0.06714
+    0.05992   -0.02404    0.00754    0.05443   -0.02240   -0.04258