Add vectormath average keyword (#1155)

* Add vectormath average

* Add vectormath average test

* Add vectormath average entry and dataset aspects for vectormath.

* Remove extra unneeded variable that was causing problems generating the manual pdf

* Update manual pdf

* 6.29.19. Revision bump for vectormath average.

Author: drroe

doc/CpptrajManual.pdf

@@ -1,3 +1,3 @@
 b37726e7a841f6fc695ecd7fb040ffbf  CpptrajDevelopmentGuide.lyx
-8fe330adac3e61d024fceb51b814a8ba  cpptraj.lyx
+5af47ac2cb73a9c7cd83fc82c1d2f421  cpptraj.lyx
 5d9b5b5ed47a3ded57b6464df99b3585  CpptrajManual.lyx

doc/DocumentChecksums.txt

@@ -6,12 +6,6 @@
 \origin unavailable
 \textclass article
 \begin_preamble
-% Added by lyx2lyx
-%% Variable width box for table cells
-\newenvironment{cellvarwidth}[1][t]
-    {\begin{varwidth}[#1]{\linewidth}}
-    {\@finalstrut\@arstrutbox\end{varwidth}}
-% Added by lyx2lyx
 \usepackage{varwidth}
 \end_preamble
 \use_default_options true
@@ -20918,36 +20912,11 @@ Calculate the dihedral angle using four points.
 \begin_inset Text
 
 \begin_layout Plain Layout
-\begin_inset ERT
-status collapsed
-
-\begin_layout Plain Layout
-
-
-\backslash
-begin{cellvarwidth}
-\end_layout
-
-\end_inset
-
-dihrms
+dihrms, 
 \end_layout
 
 \begin_layout Plain Layout
 dihedralrms
-\begin_inset ERT
-status collapsed
-
-\begin_layout Plain Layout
-
-
-\backslash
-end{cellvarwidth}
-\end_layout
-
-\end_inset
-
-
 \end_layout
 
 \end_inset
@@ -55231,7 +55200,8 @@ vectormath vec1 <vecname1> vec2 <vecname2> [out <filename>] [norm] [name
 \end_layout
 
 \begin_layout LyX-Code
-           [ dotproduct | dotangle | crossproduct | magnitude ]
+           [ dotproduct | dotangle | crossproduct | magnitude | average
+ ]
 \begin_inset Separator latexpar
 \end_inset
 
@@ -55271,6 +55241,24 @@ vec2
  Name of file to write output to.
 \end_layout
 
+\begin_layout Description
+[norm] Normalize the vectors; this will affect any subsequent calculations
+ with the vectors.
+ This is turned on automatically if 
+\series bold
+dotangle/magnitude
+\series default
+ specified.
+\end_layout
+
+\begin_layout Description
+[name
+\begin_inset space ~
+\end_inset
+
+<setname>] Output data set name.
+\end_layout
+
 \begin_layout Description
 [dotproduct] (Default) Calculate the dot-product of the two vectors.
 \end_layout
@@ -55297,13 +55285,59 @@ vec2
 \end_layout
 
 \begin_layout Description
-[norm] Normalize the vectors; this will affect any subsequent calculations
- with the vectors.
- This is turned on automatically if 
+[average] Calculate the average (over frames) of vectors selected by 
 \series bold
-dotangle/magnitude
+vec1
 \series default
- specified.
+ (no need to specify 
+\series bold
+vec2
+\series default
+).
+\end_layout
+
+\begin_layout Standard
+DataSets created:
+\end_layout
+
+\begin_layout Description
+<setname>[Dot] (double) Vector dot product (
+\series bold
+dotproduct
+\series default
+ only).
+\end_layout
+
+\begin_layout Description
+<setname>[Angle] (double) Angle in degrees from vector dot product (
+\series bold
+dotangle
+\series default
+ only).
+\end_layout
+
+\begin_layout Description
+<setname>[Cross] (vector) Cross product (
+\series bold
+crossproduct
+\series default
+ only).
+\end_layout
+
+\begin_layout Description
+<setname>[Mag] (double) Magnitude (
+\series bold
+magnitude
+\series default
+ only).
+\end_layout
+
+\begin_layout Description
+<setname>[Avg] (vector) Average vector (
+\series bold
+average
+\series default
+ only).
 \end_layout
 
 \end_deeper

doc/cpptraj.lyx

@@ -8,7 +8,7 @@
 
 /// Strings corresponding to modes, used in output.
 const char* Analysis_VectorMath::ModeString[] = {
-  "Dot product", "Angle from dot product", "Cross product", "Magnitude" };
+  "Dot product", "Angle from dot product", "Cross product", "Magnitude", "Average" };
 
 // CONSTRUCTOR
 Analysis_VectorMath::Analysis_VectorMath() :
@@ -18,12 +18,12 @@ Analysis_VectorMath::Analysis_VectorMath() :
 
 void Analysis_VectorMath::Help() const {
   mprintf("\tvec1 <vecname1> vec2 <vecname2> [out <filename>] [norm] [name <setname>]\n"
-          "\t[ dotproduct | dotangle | crossproduct | magnitude ]\n"
+          "\t[ dotproduct | dotangle | crossproduct | magnitude | average ]\n"
           "  Calculate dot product, angle from dot product (degrees), or cross product\n"
           "  for specified vectors. Either vec1 or vec2 can be size 1, otherwise they\n"
-          "  must both be the same size. If 'magnitude' is specified, just calculate\n"
-          "  the magnitudes of the vectors selected by 'vec1' (no need to specify\n"
-          "  'vec2').\n");
+          "  must both be the same size.\n"
+          "  If 'magnitude' or 'average' is specified, just calculate the magnitudes\n"
+          "  or averages of the vector selected by 'vec1' (no need to specify 'vec2').\n");
 }
 
 // Analysis_VectorMath::Setup()
@@ -54,6 +54,11 @@ Analysis::RetType Analysis_VectorMath::Setup(ArgList& analyzeArgs, AnalysisSetup
       mprintf("Warning: 'norm' does not make sense with 'magnitude', ignoring.\n");
       norm_ = false;
     }
+  } else if (analyzeArgs.hasKey("average")) {
+    mode_ = AVERAGE;
+    dtype = DataSet::VECTOR;
+    dname = "Avg";
+    requires_two_vecs = false;
   }
 
   // Get Vectors
@@ -145,6 +150,26 @@ const
   return 0;
 }
 
+/** Calculate the average vector. */
+int Analysis_VectorMath::Average(DataSet* Dout, DataSet_Vector const& V1)
+const
+{
+  DataSet_Vector& Out = static_cast<DataSet_Vector&>( *Dout );
+  Vec3 VXYZ(0.0, 0.0, 0.0);
+  for (unsigned int idx = 0; idx < V1.Size(); idx++)
+    VXYZ += V1[idx];
+  VXYZ /= (double)V1.Size();
+  if (V1.HasOrigins()) {
+    Vec3 OXYZ(0.0, 0.0, 0.0);
+    for (unsigned int idx = 0; idx < V1.Size(); idx++)
+      OXYZ += V1.OXYZ(idx);
+    OXYZ /= (double)V1.Size();
+    Out.AddVxyzo( VXYZ, OXYZ );
+  } else
+    Out.AddVxyz( VXYZ );
+  return 0;
+}
+
 // Analysis_VectorMath::DotProduct()
 int Analysis_VectorMath::DotProduct(DataSet* Dout, DataSet_Vector& V1, DataSet_Vector& V2,
                                     unsigned int vmax, unsigned int v1inc, unsigned int v2inc)
@@ -235,6 +260,8 @@ Analysis::RetType Analysis_VectorMath::Analyze() {
       int err = 1;
       if (mode_ == MAGNITUDE)
         err = Magnitude( DataOut_[ii], *(vinfo1_[ii]) );
+      else if (mode_ == AVERAGE)
+        err = Average( DataOut_[ii], *(vinfo1_[ii]) );
       if (err != 0) {
         mprinterr("Error: A problem occurred when performing vector math for set '%s'\n",
                   vinfo1_[ii]->legend());

src/Analysis_VectorMath.cpp

@@ -11,10 +11,11 @@ class Analysis_VectorMath : public Analysis {
     Analysis::RetType Setup(ArgList&, AnalysisSetup&, int);
     Analysis::RetType Analyze();
   private:
-    enum ModeType {  DOTPRODUCT = 0, DOTANGLE, CROSSPRODUCT, MAGNITUDE };
+    enum ModeType {  DOTPRODUCT = 0, DOTANGLE, CROSSPRODUCT, MAGNITUDE, AVERAGE };
     static const char* ModeString[];
 
     int Magnitude(DataSet*, DataSet_Vector const&) const;
+    int Average(DataSet*, DataSet_Vector const&) const;
     int DotProduct(DataSet*, DataSet_Vector&, DataSet_Vector&,
                    unsigned int, unsigned int, unsigned int) const;
     int CrossProduct(DataSet*, DataSet_Vector&, DataSet_Vector&,

src/Analysis_VectorMath.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 "V6.29.18"
+#define CPPTRAJ_INTERNAL_VERSION "V6.29.19"
 /// PYTRAJ relies on this
 #define CPPTRAJ_VERSION_STRING CPPTRAJ_INTERNAL_VERSION
 #endif

src/Version.h

@@ -0,0 +1,2 @@
+#Frame                                                  V12avg
+       1  13.1965 -12.6155   3.4216   6.7847   0.1828 -13.8070

test/Test_VectorMath/Average.dat.save

@@ -2,7 +2,8 @@
 
 . ../MasterTest.sh
 
-CleanFiles vectors.dat dotproduct.dat corr.in v1init_dot_v1.dat Magnitude.dat
+CleanFiles vectors.dat dotproduct.dat corr.in v1init_dot_v1.dat Magnitude.dat \
+           Average.dat
 
 INPUT="corr.in"
 TOP=../tz2.parm7
@@ -37,5 +38,13 @@ EOF
 RunCpptraj "$UNITNAME"
 DoTest Magnitude.dat.save Magnitude.dat
 
+UNITNAME='Vector average tests'
+cat > corr.in <<EOF
+readdata ../Test_Vector/vtest.dat.12.save as dat vector magnitude name V12
+runanalysis vectormath vec1 V12 average out Average.dat name V12avg
+EOF
+RunCpptraj "$UNITNAME"
+DoTest Average.dat.save Average.dat
+
 EndTest
 exit 0