Add the 'time' action (#722)

* DRR - Cpptraj: Initial incarnation of the time action.

* DRR - Cpptraj: Enable time command

* DRR - Cpptraj: Add basic time addition test

* DRR - Cpptraj: Clean up error message. Return MODIFY_TOPOLOGY even though we are not really modifying the topology so that if 'time' is used with 'crdaction' the warning about COORDS data sets not storing time values is printed.

* DRR - Cpptraj: Add time to trajectory test

* DRR - Cpptraj: Modify time info test

* DRR - Cpptraj: Change 'notime' to 'remove' - just makes more sense.

* DRR - Cpptraj: Add test for removing time info

* DRR - Cpptraj: Add test to makefile

* DRR - Cpptraj: Revision bump for adding 'time' action

* DRR - Cpptraj: Update manual.

* DRR - Cpptraj: Want TrajoutNum(), not incoming frameNum.

* DRR - Cpptraj: Test that writes netcdf in parallel requires parallel netcdf

doc/cpptraj.lyx

@@ -14508,7 +14508,7 @@ Mod
 \begin_layout Standard
 \align center
 \begin_inset Tabular
-<lyxtabular version="3" rows="84" columns="3">
+<lyxtabular version="3" rows="85" columns="3">
 <features islongtable="true" longtabularalignment="center">
 <column alignment="center" valignment="top" width="1.3in">
 <column alignment="center" valignment="top" width="4.5in">
@@ -16724,6 +16724,35 @@ Calculate system temperature using velocities of specified atoms.
 <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
 \begin_inset Text
 
+\begin_layout Plain Layout
+time
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Add/remove/modify time information in frames.
+\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
+X
+\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
 trans, translate
 \end_layout
@@ -31756,7 +31785,57 @@ Calculate temperature in frame based on velocity information.
 \series default
  is specified just use frame temperature (read in from e.g.
  REMD trajectory).
-
+\end_layout
+
+\begin_layout Subsection
+time
+\end_layout
+
+\begin_layout LyX-Code
+time {time0 <initial time> dt <step> [update] | remove}
+\end_layout
+
+\begin_deeper
+\begin_layout Description
+time0
+\begin_inset space ~
+\end_inset
+
+<initial
+\begin_inset space ~
+\end_inset
+
+time> Time of the first frame (ps).
+\end_layout
+
+\begin_layout Description
+dt
+\begin_inset space ~
+\end_inset
+
+<step> Time step between frames (ps).
+\end_layout
+
+\begin_layout Description
+[update] If specified, modify any existing time info.
+\end_layout
+
+\begin_layout Description
+remove Remove any time info from frame.
+\end_layout
+
+\end_deeper
+\begin_layout Standard
+Either add time information to frames, modify existing time information
+ in frames, or remove existing time information from frames.
+ Note that currently COORDS data sets do not store time information, so
+ using this command with the 
+\series bold
+\emph on
+crdaction
+\series default
+\emph default
+ command will have no effect.
 \end_layout
 
 \begin_layout Subsection

src/Action_Time.cpp

@@ -0,0 +1,98 @@
+#include "Action_Time.h"
+#include "CpptrajStdio.h"
+
+/// CONSTRUCTOR
+Action_Time::Action_Time() :
+  time0_(0.0),
+  dt_(0.001),
+  mode_(ADD)
+{}
+
+// Action_Time::Help()
+void Action_Time::Help() const {
+  mprintf("\t{time0 <initial time> dt <step> [update] | remove}\n"
+          "  Add, modify, or remove time information from each frame.\n"
+          "    time0 <initial time> : Time of the first frame (ps).\n"
+          "    dt <step>            : Time step between frames (ps).\n"
+          "    update               : If specified, modify any existing time info.\n"
+          "    remove               : Remove any time info from frame.\n");
+}
+
+// Action_Time::Init()
+Action::RetType Action_Time::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
+{
+  /// Make sure that something has been specified.
+  if (actionArgs.hasKey("remove"))
+    mode_ = REMOVE;
+  else {
+    if (!actionArgs.Contains("time0") &&
+        !actionArgs.Contains("dt"))
+    {
+      mprinterr("Error: Must specify either 'time0', 'dt', or both if 'remove' not specified.\n");
+      return Action::ERR;
+    }
+    time0_ = actionArgs.getKeyDouble("time0", 0.0);
+    dt_    = actionArgs.getKeyDouble("dt", 0.001);
+    if (actionArgs.hasKey("update"))
+      mode_ = MODIFY;
+    else
+      mode_ = ADD;
+  }
+
+  mprintf("    TIME:");
+  if (mode_ == REMOVE)
+    mprintf(" Removing all time information from frames.\n");
+  else {
+    if (mode_ == MODIFY)
+      mprintf(" Updating time information in frames.\n");
+    else
+      mprintf(" Adding/overwriting time information in frames.\n");
+    mprintf("\tInitial time = %g ps\n", time0_);
+    mprintf("\tTime step    = %g ps\n", dt_);
+  }
+  return Action::OK;
+}
+
+// Action_Time::Setup()
+Action::RetType Action_Time::Setup(ActionSetup& setup)
+{
+  cInfo_ = setup.CoordInfo();
+  if (!cInfo_.HasTime()) {
+    if (mode_ == MODIFY)
+      mprintf("Warning: 'update' specified but no time info in frame. Adding time info.\n");
+    else if (mode_ == REMOVE) {
+      mprintf("Warning: 'remove' specified but no time info in frame. Skipping.\n");
+      return Action::SKIP;
+    } else if (mode_ == ADD)
+      mprintf("\tAdding time information to frames.\n");
+  } else {
+    if (mode_ == MODIFY)
+      mprintf("\tUpdating time information in frames.\n");
+    else if (mode_ == REMOVE)
+      mprintf("\tRemoving time information in frames.\n");
+    else if (mode_ == ADD)
+      mprintf("\tOverwriting time information in frames.\n");
+  }
+  if (mode_ == REMOVE)
+    cInfo_.SetTime( false );
+  else
+    cInfo_.SetTime( true );
+  setup.SetCoordInfo( &cInfo_ );
+  return Action::MODIFY_TOPOLOGY;
+}
+
+// Action_Time::DoAction()
+Action::RetType Action_Time::DoAction(int frameNum, ActionFrame& frm)
+{
+  double currTime = 0.0;
+  double newTime  = 0.0;
+  switch (mode_) {
+    case REMOVE : frm.ModifyFrm().SetTime( currTime ); break;
+    case MODIFY : currTime = frm.Frm().Time();
+    case ADD    :
+      newTime = currTime + time0_ + ((double)frm.TrajoutNum() * dt_);
+      frm.ModifyFrm().SetTime( newTime );
+      break;
+  }
+  return Action::MODIFY_COORDS;
+}

src/Action_Time.h

@@ -0,0 +1,22 @@
+#ifndef INC_ACTION_TIME_H
+#define INC_ACTION_TIME_H
+#include "Action.h"
+/// Add/remove/modify time information in frame. 
+class Action_Time : public Action {
+  public:
+    Action_Time();
+    DispatchObject* Alloc() const { return (DispatchObject*)new Action_Time(); }
+    void Help() const;
+  private:
+    Action::RetType Init(ArgList&, ActionInit&, int);
+    Action::RetType Setup(ActionSetup&);
+    Action::RetType DoAction(int, ActionFrame&);
+    void Print() {}
+
+    double time0_;         ///< Initial time
+    double dt_;            ///< Time step.
+    enum ModeType { ADD = 0, MODIFY, REMOVE };
+    ModeType mode_;        ///< Modification mode.
+    CoordinateInfo cInfo_; ///< The modified CoordinateInfo
+};
+#endif

src/Command.cpp

@@ -138,6 +138,7 @@
 #include "Action_LipidOrder.h"
 #include "Action_InfraredSpectrum.h"
 #include "Action_XtalSymm.h"
+#include "Action_Time.h"
 // ----- ANALYSIS --------------------------------------------------------------
 #include "Analysis_Hist.h"
 #include "Analysis_Corr.h"
@@ -348,6 +349,7 @@ void Command::Init() {
   Command::AddCmd( new Action_Surf(),          Cmd::ACT, 1, "surf" );
   Command::AddCmd( new Action_SymmetricRmsd(), Cmd::ACT, 1, "symmrmsd" );
   Command::AddCmd( new Action_Temperature(),   Cmd::ACT, 1, "temperature" );
+  Command::AddCmd( new Action_Time(),          Cmd::ACT, 1, "time" );
   Command::AddCmd( new Action_Translate(),     Cmd::ACT, 2, "trans", "translate" );
   Command::AddCmd( new Action_Unstrip(),       Cmd::ACT, 1, "unstrip" );
   Command::AddCmd( new Action_Unwrap(),        Cmd::ACT, 1, "unwrap" );

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 "V4.14.2"
+#define CPPTRAJ_INTERNAL_VERSION "V4.14.3"
 /// PYTRAJ relies on this
 #define CPPTRAJ_VERSION_STRING CPPTRAJ_INTERNAL_VERSION
 #endif