Add the 'evalplateau' command. Other misc. fixes. (#821)

* DRR - Initial incarnation of evalequilibration

* DRR - Enable evalequil

* DRR - Start to determine direction of relaxation

* DRR - Use forward declares.

* DRR - Fix up includes for forward declares in Array1D.h

* DRR - use Array1D

* DRR - Add non linear curve fitting and final curve output

* DRR - Add nonlinear fit stats printout

* DRR - Ensure A1 parameter guess starts out < 0 (improves convergence)

* DRR - Try adding an offset to X. I think the incoming X values will need to be shifted as well.

* DRR - Use an offset so that when fitting, the first X value is always 1. With the addition of the A2 parameter, we're saying we dont know exactly where on the exponential curve the data starts.

* DRR - Allow stats to be redirected to a file.

* DRR - Add some documentation

* DRR - More docs

* DRR - Start adding results

* DRR - Make blocks respect noexitonerror

* DRR - Add calculation of difference of last half of data from long-time estimate

* DRR - New forms of exponentials that are more consistent with each other and with first order decay. Bounded by A0 OP A2 (where OP is + for decay and - for inverse) and A2 at times 0 and infinity

* DRR - Remove obsolete code

* DRR - Make it easier to add more results data sets

* DRR - Add final fit parameters to results

* DRR - Add determination of equilibrated via cutoffs

* DRR - Add slope calculation

* DRR - Fix equation forms in output

* DRR - Add 1st half avg calc. Make sure printing to statsout

* DRR - Add equil. time

* DRR - Get F value from regression

* DRR - Save regression F value

* DRR - Use offset so X values start at 0. This gives proper weight to the t=0 case where the first value should be close to A0+A2 or A2-A0

* DRR - Try out new equation

* DRR - Use average of first 10% of data as a guess for A0

* DRR - Remove old functions

* DRR - Add comment

* DRR - Add slope criterion in final determination. Add more output when criteria not satisfied.

* DRR - In for loops with files, warn if an expression with wildcards does not expand to a file, dont add it.

* DRR - Revision bump for evalquil. May need to be updated in the future since the command is not fully ready yet.

* DRR - When output from actions/analyses is directed to stdout, ensure it is properly directed to output file if one has been specified.

* DRR - Ensure residue IsTerminal info is preserved on strip so things like 'pdbter' still work properly

* DRR - Use not isdigit so single wildcard is properly handled

* DRR - Add gamma function code. Use cmath version if c++11 support available, otherwise use an approximation

* DRR - Add C11_SUPPORT define when c++11 support available

* DRR - Add GammaFn to build

* DRR - Add file for calculating chi squared PDF

* DRR - Create default cut

* DRR - Improve strip warning message

* DRR - Add topresnum keyword for pdb output to use topology residue numbering instead of original

* DRR - Update pdb trajout documentation

* DRR - Fix missing include from forward declare

* DRR - Analysis_EvalEquilibration -> EvalPlateau; better name for what it actually does.

* DRR - Ignore mkl.h (helpme_standalone.h)

* DRR - Update for EvalPlateau

* DRR - Recast everything as plateau

* Add evalplateau test

* Add to list of tests.

* DRR - Ended up not needing the chi^2 function yet. Remove for now.

* Revision bump for evalplateau

* Hide evalplateau, not quite ready for prime time. Add onboard help.

* Revamp how hidden commands are defined. Instead of making a separate category, add a flag that marks the command as hidden. This allows the command to retain its underlying category and so things like 'runanalysis' work as intended with hidden commands.

Co-authored-by: Daniel R. Roe <daniel.roe@nih.gov>

configure

@@ -681,6 +681,7 @@ SetupFinalFlags() {
   if [ $USE_SINGLEENSEMBLE -ne 0 ] ; then DIRECTIVES="$DIRECTIVES -DENABLE_SINGLE_ENSEMBLE" ; fi
   if [ ! -z "$LFS"               ] ; then DIRECTIVES="$DIRECTIVES $LFS" ; fi
   if [ "$C11_SUPPORT" = 'yes'    ] ; then
+    DIRECTIVES="$DIRECTIVES -DC11_SUPPORT"
     if [ "${LIB_STAT[$LFFTW3]}" != 'off' ] ; then
       DIRECTIVES="$DIRECTIVES -DLIBPME -DHAVE_FFTWD=1"
     fi

doc/cpptraj.lyx

@@ -15170,35 +15170,38 @@ vdw PQR format; write charges and vdW radii to occupancy/B-factor columns.
 \end_layout
 
 \begin_layout Description
-pdbres: Use PDB V3 residue names.
+pdbres Use PDB V3 residue names.
  Will write a default chain ID ('Z') for each residue if the corresponding
  topology does not have chain ID information.
 \end_layout
 
 \begin_layout Description
-pdbatom: Use PDB V3 atom names.
+pdbatom Use PDB V3 atom names.
 \end_layout
 
 \begin_layout Description
-pdbv3: Use PDB V3 residue/atom names.
+pdbv3 Use PDB V3 residue/atom names.
  Same as specifying 'pdbres' and 'pdbatom'.
 \end_layout
 
 \begin_layout Description
-teradvance: Increment record (atom) number for TER records (not done by
- default).
+topresnum Use topology residue numbers; otherwise use original residue numbers.
 \end_layout
 
 \begin_layout Description
-terbyres: Print TER cards based on residue sequence instead of molecules.
+teradvance Increment record (atom) number for TER records (not done by default).
 \end_layout
 
 \begin_layout Description
-pdbter: Print TER cards according to original PDB TER (if available).
+terbyres Print TER cards based on residue sequence instead of molecules.
 \end_layout
 
 \begin_layout Description
-noter: Do not write TER cards.
+pdbter Print TER cards according to original PDB TER (if available).
+\end_layout
+
+\begin_layout Description
+noter Do not write TER cards.
 \end_layout
 
 \begin_layout Description
@@ -15363,7 +15366,7 @@ cpptraj
 \end_layout
 
 \begin_layout Description
-highprecision: (EXPERT USE ONLY) Write with 8.6 precision instead of 8.3.
+highprecision (EXPERT USE ONLY) Write with 8.6 precision instead of 8.3.
  Note that since the width does not change, the precision of large coords
  may be lower than 6.
 \end_layout

src/Action.h

@@ -28,8 +28,6 @@ class Action : public DispatchObject {
   public:
     /// Constructor
     Action() : DispatchObject(ACTION) {}
-    /// Constructor - override ACTION (e.g. HIDDEN)
-    Action(DispatchObject::Otype o) : DispatchObject(o) {}
     /// Enumerate potential return states from Init, Setup, and DoAction.
     enum RetType { OK=0, ///< Everything OK, normal return.
                    ERR,  ///< Problem occurred.

src/Action_Channel.cpp

@@ -4,8 +4,12 @@
 #include "DataSet_GridFlt.h"
 
 // CONSTRUCTOR
-Action_Channel::Action_Channel() : Action(HIDDEN),
-  grid_(0), dxyz_(-1.0) {}
+Action_Channel::Action_Channel() :
+  grid_(0),
+  dxyz_(-1.0)
+{
+  SetHidden(true);
+}
 
 void Action_Channel::Help() const {
   mprintf("\t<solute mask> [<solvent mask>] [out <file>] [dx <dx> [dy <dy>] [dz <dz>]]\n");

src/Action_DNAionTracker.cpp

@@ -4,12 +4,14 @@
 #include "CpptrajStdio.h"
 
 // CONSTRUCTOR
-Action_DNAionTracker::Action_DNAionTracker() : Action(HIDDEN), 
+Action_DNAionTracker::Action_DNAionTracker() :
   distance_(0),
   bintype_(COUNT),
   poffset_(0),
   useMass_(true)
-{ }
+{
+  SetHidden(true);
+}
 
 void Action_DNAionTracker::Help() const {
   mprintf("\tname mask_p1 mask_p2 mask_base mask_ions\n"

src/Action_Diffusion.cpp

@@ -494,7 +494,8 @@ void Action_Diffusion::CalcDiffusionConst(unsigned int& set, DataSet* ds, int Nd
   double Factor = 10.0 / ((double)Ndim * 2.0);
   double slope, intercept, corr;
   double Dval = 0.0;
-  if (data.LinearRegression( slope, intercept, corr, 0 ) == 0)
+  double Fval = 0;
+  if (data.LinearRegression( slope, intercept, corr, Fval, 0 ) == 0)
     Dval = slope * Factor;
   if (diffout_ == 0)
     mprintf("\t'%s' D= %g  Slope= %g  Int= %g  Corr= %g\n", data.legend(), Dval,

src/Action_FilterByData.cpp

@@ -1,5 +1,6 @@
 #include "Action_FilterByData.h"
 #include "CpptrajStdio.h"
+#include "DataSet_1D.h"
 
 void Action_FilterByData::Help() const {
   mprintf("\t{<dataset arg> min <min> max <max> ...} [out <file>] [name <setname>]\n"

src/Action_GridFreeEnergy.cpp

@@ -7,11 +7,13 @@
 #include "Constants.h" // GASK_KCAL, SMALL
 
 // CONSTRUCTOR
-Action_GridFreeEnergy::Action_GridFreeEnergy() : Action(HIDDEN),
+Action_GridFreeEnergy::Action_GridFreeEnergy() :
   maxVoxelOccupancyCount_(600), // NOTE: See header for comments.
   tempInKevin_(293.0),
   grid_(0)
-{}
+{
+  SetHidden(true);
+}
 
 void Action_GridFreeEnergy::Help() const {
   mprintf("\t<filename>\n%s\n\t<mask>\n", GridAction::HelpText);

src/Action_InfraredSpectrum.cpp

@@ -9,15 +9,17 @@
 #  include <omp.h>
 #endif
 
-Action_InfraredSpectrum::Action_InfraredSpectrum() : Action(HIDDEN),
+Action_InfraredSpectrum::Action_InfraredSpectrum() :
   Vel_(0),
   VAC_(0),
   currentTop_(0),
   tstep_(0.0),
   maxLag_(-1),
   previousNselected_(-1),
   useFFT_(true)
-{}
+{
+  SetHidden(true);
+}
 
 // Action_InfraredSpectrum::Help()
 void Action_InfraredSpectrum::Help() const {

src/Action_Matrix.cpp

@@ -3,6 +3,7 @@
 #include "CpptrajStdio.h"
 #include "DistRoutines.h"
 #include "Constants.h" // DEGRAD
+#include "DataSet_1D.h"
 
 // CONSTRUCTOR
 Action_Matrix::Action_Matrix() :

src/Action_NMRrst.cpp

@@ -11,13 +11,25 @@
 #include "BufferedLine.h"
 
 // CONSTRUCTOR
-Action_NMRrst::Action_NMRrst() : Action(HIDDEN),
-   findOutput_(0), specOutput_(0), masterDSL_(0), numNoePairs_(0), max_cut_(6.0),
-   strong_cut_(2.9), medium_cut_(3.5), weak_cut_(5.0),
-   resOffset_(0), debug_(0), nframes_(0), useMass_(false),
-   findNOEs_(false), series_(false),
+Action_NMRrst::Action_NMRrst() :
+   findOutput_(0),
+   specOutput_(0),
+   masterDSL_(0),
+   numNoePairs_(0),
+   max_cut_(6.0),
+   strong_cut_(2.9),
+   medium_cut_(3.5),
+   weak_cut_(5.0),
+   resOffset_(0),
+   debug_(0),
+   nframes_(0),
+   useMass_(false),
+   findNOEs_(false),
+   series_(false),
    rsttop_(0)
-{} 
+{
+  SetHidden(true);
+} 
 
 void Action_NMRrst::Help() const {
   mprintf("\t[file <rstfile>] [name <dataname>] [geom] [noimage] [resoffset <r>]\n"

src/Action_Projection.cpp

@@ -3,6 +3,7 @@
 #include "CpptrajStdio.h"
 #include "StringRoutines.h" // integerToString
 #include "Constants.h" // DEGRAD
+#include "DataSet_1D.h"
 
 // CONSTRUCTOR
 Action_Projection::Action_Projection() :

src/Action_Spam.cpp

@@ -14,7 +14,7 @@
 #include "DataSet_Mesh.h"
 
 // CONSTRUCTOR
-Action_Spam::Action_Spam() : Action(HIDDEN),
+Action_Spam::Action_Spam() :
   debug_(0),
   DG_BULK_(-30.3), // Free energy of bulk SPCE water
   DH_BULK_(-22.2), // Enthalpy of bulk SPCE water

src/Action_Strip.cpp

@@ -56,15 +56,15 @@ Action::RetType Action_Strip::Init(ArgList& actionArgs, ActionInit& init, int de
 Action::RetType Action_Strip::Setup(ActionSetup& setup) {
   if (setup.Top().SetupIntegerMask( M1_ )) return Action::ERR;
   if (M1_.None()) {
-    mprintf("Warning: strip: Mask [%s] has no atoms.\n",M1_.MaskString());
+    // If no atoms will be kept, no need for this command. SKIP.
+    mprintf("Warning: Mask [%s] would strip all atoms. Skipping.\n", M1_.MaskString());
     return Action::SKIP;
   }
   int numStripped = setup.Top().Natom() - M1_.Nselected();
   mprintf("\tStripping %i atoms.\n", numStripped);
-  // If no atoms will be stripped, no need to use this command. SKIP
+  // SANITY CHECK: If no atoms will be stripped, no need to use this command. SKIP
   if ( numStripped == 0 ) {
-    mprintf("Warning: No atoms to strip. Skipping 'strip' for topology '%s'\n",
-            setup.Top().c_str());
+    mprintf("Warning: No atoms to strip. Skipping.\n");
     return Action::SKIP;
   }
 

src/Analysis.h

@@ -11,8 +11,6 @@ class Analysis : public DispatchObject {
   public:
     /// Constructor
     Analysis() : DispatchObject(ANALYSIS) {}
-    /// Constructor - override ANALYSIS (e.g. HIDDEN)
-    Analysis(DispatchObject::Otype o) : DispatchObject(o) {}
     /// Enumerate potential return stats from Setup and Analyze.
     enum RetType { OK = 0, ERR };
     /// Destructor - virtual since this class is inherited

src/Analysis_AmdBias.cpp

@@ -2,12 +2,14 @@
 #include "CpptrajStdio.h"
 #include "DataSet_double.h"
 
-Analysis_AmdBias::Analysis_AmdBias() : Analysis(HIDDEN),  
+Analysis_AmdBias::Analysis_AmdBias() :
   ds1_(0), 
   Ethresh_(0.0),
   alpha_(0.0),
   bias_(0)
-{}
+{
+  SetHidden(true);
+}
 
 void Analysis_AmdBias::Help() const {
   mprintf("\tds <Edata> ethresh <Ethresh> alpha <alpha> out <filename>\n");

src/Analysis_Average.cpp

@@ -1,6 +1,7 @@
 #include <cmath>
 #include "Analysis_Average.h"
 #include "CpptrajStdio.h"
+#include "DataSet_1D.h"
 
 Analysis_Average::Analysis_Average() :
   avgOfSets_(0),