Added new style documentation for FourierTransform and fixed some iss…

…ues in example inputs in refdist

src/fourier/FourierTransform.cpp

@@ -34,33 +34,43 @@ namespace fourier {
 /*
 Compute the Discrete Fourier Transform (DFT) by means of FFTW of data stored on a 2D grid.
 
-This action can operate on any other action that outputs scalar data on a two-dimensional grid.
-
-Up to now, even if the input data are purely real the action uses a complex DFT.
-
-Just as a quick reference, given a 1D array \f$\mathbf{X}\f$ of size \f$n\f$, this action computes the vector \f$\mathbf{Y}\f$ given by
-
-\f[
-Y_k = \sum_{j=0}^{n-1} X_j e^{2\pi\, j k \sqrt{-1}/n}.
-\f]
-
-This can be easily extended to more than one dimension. All the other details can be found at http://www.fftw.org/doc/What-FFTW-Really-Computes.html#What-FFTW-Really-Computes.
-
-The keyword "FOURIER_PARAMETERS" deserves just a note on the usage. This keyword specifies how the Fourier transform will be normalized. The keyword takes two numerical parameters (\f$a,\,b\f$) that define the normalization according to the following expression
-
-\f[
+This action takes a function on a two-dimensional grid as input and computes a fourier transform upon the input function using [FFTW](https://www.fftw.org).
+Currently, this actions performs a complex fourier transition even if the input data is real.  The functionality here was developed and used in the paper cited
+below. The following input was used in that paper:
+
+```plumed
+UNITS NATURAL
+
+# These two commands calculate one symmetry function for each atom.  These 
+# symmetry functions tell us whether the environment around each atom resembles 
+# the environment in the solid or the environment in the liquid.
+fcc: FCCUBIC SPECIES=1-20736 SWITCH={CUBIC D_0=1.2 D_MAX=1.5} ALPHA=27 
+smapfcc: MORE_THAN ARG=fcc SWITCH={SMAP R_0=0.5 A=8 B=8} 
+smapfcc_grp: GROUP ATOMS=1-20736
+# This calculates the position of the center of the solid region of the simulation box.  What we are computing here a weighted average position 
+# the weights are the order parameters computed using the two commands above.
+center: CENTER PHASES ATOMS=fcc WEIGHTS=smapfcc
+# This calculates the phase field that tells us whether the structure in each part of the simulation box is solid-like or liquid like.
+dens: MULTICOLVARDENS DATA=smapfcc ORIGIN=center DIR=xyz NBINS=50,80,80 BANDWIDTH=1.0,1.0,1.0 GRID_MIN=0.0,auto,auto GRID_MAX=20.0,auto,auto STRIDE=1 CLEAR=1
+# This finds the instantaneous location of the interface between the solid and liquid phases
+contour: FIND_CONTOUR_SURFACE ARG=dens CONTOUR=0.5 SEARCHDIR=dens_dist.x 
+DUMPGRID ARG=contour FILE=contour.dat
+# This does the fourier transform of the location of the interface.  We can extract the interfacial stiffness from the average of this fourier transform
+ft: FOURIER_TRANSFORM ARG=contour FT_TYPE=norm FOURIER_PARAMETERS=-1,1
+DUMPGRID ARG=ft FILE=fourier.dat STRIDE=10
+```
+
+We do not think this action has been used in any other paper. If you are interested in using the functionality here we would recommend you carefully 
+read the documentation for the FFTW library.  You may find it necessary to modify the code in this action for your particular purpose.  
+
+To what FFTW computes we would recommend reading [this page](http://www.fftw.org/doc/What-FFTW-Really-Computes.html#What-FFTW-Really-Computes).
+
+Notice that the keyword "FOURIER_PARAMETERS" specifies how the Fourier transform will be normalized. The keyword takes two numerical parameters $a$ and $b$ that are both set equal to one by default.  
+The normalization is then defined as:
+
+$$
 \frac{1}{n^{(1-a)/2}} \sum_{j=0}^{n-1} X_j e^{2\pi b\, j k \sqrt{-1}/n}
-\f]
-
-The default values of these parameters are: \f$a=1\f$ and \f$b=1\f$.
-
-\par Examples
-
-The following example tells Plumed to compute the complex 2D 'backward' Discrete Fourier Transform by taking the data saved on a grid called 'density', and normalizing the output by \f$ \frac{1}{\sqrt{N_x\, N_y}}\f$, where \f$N_x\f$ and \f$N_y\f$ are the number of data on the grid (it can be the case that \f$N_x\neq N_y\f$):
-
-\plumedfile
-FOURIER_TRANSFORM STRIDE=1 GRID=density FT_TYPE=complex FOURIER_PARAMETERS=0,-1
-\endplumedfile
+$$
 
 */
 //+ENDPLUMEDOC
@@ -96,6 +106,7 @@ void FourierTransform::registerKeywords( Keywords& keys ) {
   keys.addOutputComponent("real","FT_TYPE","grid","the real part of the function");
   keys.addOutputComponent("imag","FT_TYPE","grid","the imaginary part of the function");
   keys.setValueDescription("grid","the fourier transform of the input grid");
+  keys.addDOI("10.1088/1361-648X/aa893d");
 }
 
 FourierTransform::FourierTransform(const ActionOptions&ao):

src/matrixtools/TransposeMatrix.cpp

@@ -103,7 +103,11 @@ TransposeMatrix::TransposeMatrix(const ActionOptions& ao):
   else if( getPntrToArgument(0)->getRank()==1 ) { shape.resize(2); shape[0]=1; shape[1]=getPntrToArgument(0)->getShape()[0]; }
   else if( getPntrToArgument(0)->getShape()[0]==1 ) { shape.resize(1); shape[0] = getPntrToArgument(0)->getShape()[1]; }
   else { shape.resize(2); shape[0]=getPntrToArgument(0)->getShape()[1]; shape[1]=getPntrToArgument(0)->getShape()[0]; }
-  addValue( shape ); setNotPeriodic(); getPntrToComponent(0)->buildDataStore();
+  addValue( shape ); 
+  if( getPntrToArgument(0)->isPeriodic() ) {
+      std::string smin, smax; getPntrToArgument(0)->getDomain( smin, smax ); setPeriodic( smin, smax );
+  } else setNotPeriodic();
+  getPntrToComponent(0)->buildDataStore();
   if( shape.size()==2 ) getPntrToComponent(0)->reshapeMatrixStore( shape[1] );
 }
 

src/refdist/Kernel.cpp

@@ -67,8 +67,13 @@ k: KERNEL ARG=d TYPE=gaussian CENTER=1 SIGMA=0.1
 ```
 
 The [NORMALIZED_EUCLIDEAN_DISTANCE](NORMALIZED_EUCLIDEAN_DISTANCE.md) between the instantaneous distance and the point 1 is evaluated here.
-The metric vector that is used to evaluate this distance is taking the reciprocal of the square of the input SIGMA value. Lastly, the weight, $w$,
-in the expression above is set equal to one.
+The metric vector that is used to evaluate this distance is taking the reciprocal of the square of the input SIGMA value. Lastly, the height of the Gaussian, $w$,
+in the expression above is set equal to one.  If you would like the total volume of the Gaussian to be equal to one you use the `NORMALIZED` keyword as shown here:
+
+```plumed
+d: DISTANCE ATOMS=1,2
+k: KERNEL ARG=d TYPE=gaussian CENTER=1 SIGMA=0.1 NORMALIZED
+```
 
 If your Kernel is a function of two arguments you can use the [NORMALIZED_EUCLIDEAN_DISTANCE](NORMALIZED_EUCLIDEAN_DISTANCE.md) to evaluate the 
 distance as is done in the following example:
@@ -285,7 +290,7 @@ Kernel::Kernel(const ActionOptions&ao):
     // And the (suitably normalized) kernel
     readInputLine( getShortcutLabel() + ": CUSTOM ARG=" + getShortcutLabel() + "_dist_2," + getShortcutLabel() + "_vol FUNC=" + wstr + "*exp(-x/2)/y PERIODIC=NO");
   } else {
-    readInputLine( getShortcutLabel() + ": CUSTOM ARG1=" + getShortcutLabel() + "_dist_2 FUNC=" + wstr + "*" + func_str + " PERIODIC=NO");
+    readInputLine( getShortcutLabel() + ": CUSTOM ARG=" + getShortcutLabel() + "_dist_2 FUNC=" + wstr + "*" + func_str + " PERIODIC=NO");
   }
   checkRead();
 

src/refdist/MahalanobisDistance.cpp

@@ -231,7 +231,9 @@ MahalanobisDistance::MahalanobisDistance( const ActionOptions& ao):
     // Transpose sines to get a row vector
     readInputLine( getShortcutLabel() + "_sinediff: TRANSPOSE ARG=" + getShortcutLabel() + "_sinediffT");
     // Compute the off diagonal elements
-    readInputLine( getShortcutLabel() + "_matvec: MATRIX_PRODUCT ARG=" + getShortcutLabel() + "_offdiagmet," + getShortcutLabel() +"_sinediffT");
+    ActionWithValue* avs=plumed.getActionSet().selectWithLabel<ActionWithValue*>( getShortcutLabel() + "_sinediffT" ); plumed_assert( avs && avs->getNumberOfComponents()==1 );
+    if( (avs->copyOutput(0))->getRank()==1 ) readInputLine( getShortcutLabel() + "_matvec: MATRIX_VECTOR_PRODUCT ARG=" + metstr + "," + getShortcutLabel() +"_sinediffT"); 
+    else readInputLine( getShortcutLabel() + "_matvec: MATRIX_PRODUCT ARG=" + getShortcutLabel() + "_offdiagmet," + getShortcutLabel() +"_sinediffT");
     readInputLine( getShortcutLabel() + "_offdiag: MATRIX_PRODUCT_DIAGONAL ARG=" + getShortcutLabel() + "_sinediff," + getShortcutLabel() +"_matvec");
     // Sort out the metric for the diagonal elements
     std::string metstr2 = getShortcutLabel() + "_diagmet";

src/tools/Keywords.cpp

@@ -649,7 +649,7 @@ bool Keywords::checkArgumentType( const std::size_t& rank, const bool& hasderiv
     if( rank==1 && x.second.find("vector")!=std::string::npos ) return true;
     if( rank==2 && x.second.find("matrix")!=std::string::npos ) return true;
   }
-  plumed_merror("WARNING: type for input argument has not been specified");
+  if( argument_types.size()==0 ) plumed_merror("WARNING: type for input argument has not been specified");
   return false;
 }