Add a couple of parameters, do some tidying

docs/user-guide/xml/xml-filters.tex

@@ -203,6 +203,42 @@ which produces a field file \inlsh{threshold\_max.fld}.
 Performs the same function as the \inltt{ThresholdMax} filter but records the
 time at which the threshold variable drops below a prescribed value.
 
+\subsection{One-dimensional energy}
+
+This filter is designed to output the energy spectrum of one-dimensional
+elements. It transforms the solution field at each timestep into a orthogonal
+basis defined by the functions
+\[
+\psi_p(\xi) = L_p(\xi)
+\]
+where $L_p$ is the $p$-th Legendre polynomial. This can be used to show the
+presence of, for example, oscillations in the underlying field due to numerical
+instability. The resulting output is written into a file called
+\inltt{session.eny} by default. The following parameters are supported:
+
+\begin{center}
+  \begin{tabularx}{0.99\textwidth}{lllX}
+    \toprule
+    \textbf{Option name} & \textbf{Required} & \textbf{Default} &
+    \textbf{Description} \\
+    \midrule
+    \inltt{OutputFile}      & \xmark   & \inltt{session} &
+    Prefix of the output filename to which the energy spectrum is written.\\
+    \inltt{OutputFrequency} & \xmark   & 1 &
+    Number of timesteps after which output is written.\\
+    \bottomrule
+  \end{tabularx}
+\end{center}
+
+An example syntax is given below:
+
+\begin{lstlisting}[style=XMLStyle,gobble=2]
+  <FILTER TYPE="Energy1D">
+      <PARAM NAME="OutputFile">EnergyFile</PARAM>
+      <PARAM NAME="OutputFrequency">10</PARAM>
+  </FILTER>
+\end{lstlisting}
+
 \subsection{Modal energy}
 
 \begin{notebox}

library/SolverUtils/Filters/FilterEnergy1D.cpp

@@ -29,7 +29,7 @@
 // FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 // DEALINGS IN THE SOFTWARE.
 //
-// Description: Outputs solution fields during time-stepping.
+// Description: Outputs orthogonal expansion of 1D elements.
 //
 ///////////////////////////////////////////////////////////////////////////////
 
@@ -46,9 +46,37 @@ namespace Nektar
         FilterEnergy1D::FilterEnergy1D(
             const LibUtilities::SessionReaderSharedPtr &pSession,
             const std::map<std::string, std::string> &pParams) :
-            Filter(pSession)
+            Filter(pSession),
+            m_index(0)
         {
-            m_out.open("energy-out.txt");
+            std::string outName;
+            if (pParams.find("OutputFile") == pParams.end())
+            {
+                outName = m_session->GetSessionName();
+            }
+            else
+            {
+                ASSERTL0(!(pParams.find("OutputFile")->second.empty()),
+                         "Missing parameter 'OutputFile'.");
+                outName = pParams.find("OutputFile")->second;
+            }
+
+            if (pParams.find("OutputFrequency") == pParams.end())
+            {
+                m_outputFrequency = 1;
+            }
+            else
+            {
+                m_outputFrequency =
+                    atoi(pParams.find("OutputFrequency")->second.c_str());
+            }
+
+            outName += ".eny";
+
+            ASSERTL0(pSession->GetComm()->GetSize() == 1,
+                     "The 1D energy filter currently only works in serial.");
+
+            m_out.open(outName);
         }
 
         FilterEnergy1D::~FilterEnergy1D()
@@ -60,15 +88,27 @@ namespace Nektar
             const Array<OneD, const MultiRegions::ExpListSharedPtr> &pFields,
             const NekDouble &time)
         {
+            ASSERTL0(pFields[0]->GetExp(0)->GetNumBases() == 1,
+                     "The Energy 1D filter is only valid in 1D.");
         }
 
         void FilterEnergy1D::v_Update(
             const Array<OneD, const MultiRegions::ExpListSharedPtr> &pFields,
             const NekDouble &time)
         {
+            // Only output every m_outputFrequency
+            if ((m_index++) % m_outputFrequency)
+            {
+                return;
+            }
+
             int nElmt = pFields[0]->GetExpSize();
 
             // Loop over all elements
+            m_out << "##" << endl;
+            m_out << "## Time = " << time << endl;
+            m_out << "##" << endl;
+
             for (int i = 0; i < nElmt; ++i)
             {
                 // Figure out number of modes in this expansion.
@@ -87,7 +127,8 @@ namespace Nektar
                     exp->GetBasis(0)->GetPointsKey());
 
                 // Find coeffs for this element in the list of all coefficients
-                Array<OneD, NekDouble> coeffs = pFields[0]->GetCoeffs() + pFields[0]->GetCoeff_Offset(i);
+                Array<OneD, NekDouble> coeffs =
+                    pFields[0]->GetCoeffs() + pFields[0]->GetCoeff_Offset(i);
 
                 // Storage for orthogonal coefficients
                 Array<OneD, NekDouble> coeffsOrth(nModes);
@@ -96,11 +137,14 @@ namespace Nektar
                 LibUtilities::InterpCoeff1D(bkey, coeffs, bkeyOrth, coeffsOrth);
 
                 // Write coeffs to file
+                m_out << "# Element " << i << " (ID "
+                      << exp->GetGeom()->GetGlobalID() << ")" << endl;
                 for (int j = 0; j < nModes; ++j)
                 {
                     m_out << coeffsOrth[j] << endl;
                 }
             }
+            m_out << endl;
         }
 
         void FilterEnergy1D::v_Finalise(

library/SolverUtils/Filters/FilterEnergy1D.h

 ///////////////////////////////////////////////////////////////////////////////
 //
-// File FilterCheckpoint.h
+// File FilterEnergy1D.h
 //
 // For more information, please see: http://www.nektar.info
 //
@@ -29,12 +29,12 @@
 // FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 // DEALINGS IN THE SOFTWARE.
 //
-// Description: Outputs solution fields during time-stepping.
+// Description: Outputs orthogonal expansion of 1D elements.
 //
 ///////////////////////////////////////////////////////////////////////////////
 
-#ifndef NEKTAR_SOLVERUTILS_FILTERS_FILTERCHECKPOINT_H
-#define NEKTAR_SOLVERUTILS_FILTERS_FILTERCHECKPOINT_H
+#ifndef NEKTAR_SOLVERUTILS_FILTERS_FILTERENERGY1D_H
+#define NEKTAR_SOLVERUTILS_FILTERS_FILTERENERGY1D_H
 
 #include <SolverUtils/Filters/Filter.h>
 
@@ -51,8 +51,8 @@ namespace Nektar
             static FilterSharedPtr create(
                 const LibUtilities::SessionReaderSharedPtr &pSession,
                 const std::map<std::string, std::string> &pParams) {
-                FilterSharedPtr p = MemoryManager<FilterEnergy1D>::AllocateSharedPtr(pSession, pParams);
-                //p->InitObject();
+                FilterSharedPtr p = MemoryManager<FilterEnergy1D>
+                    ::AllocateSharedPtr(pSession, pParams);
                 return p;
             }
 
@@ -65,15 +65,26 @@ namespace Nektar
             SOLVER_UTILS_EXPORT ~FilterEnergy1D();
 
         protected:
-            virtual void v_Initialise(const Array<OneD, const MultiRegions::ExpListSharedPtr> &pFields, const NekDouble &time);
-            virtual void v_Update(const Array<OneD, const MultiRegions::ExpListSharedPtr> &pFields, const NekDouble &time);
-            virtual void v_Finalise(const Array<OneD, const MultiRegions::ExpListSharedPtr> &pFields, const NekDouble &time);
+            virtual void v_Initialise(
+                const Array<OneD, const MultiRegions::ExpListSharedPtr> &pField,
+                const NekDouble                                         &time);
+            virtual void v_Update(
+                const Array<OneD, const MultiRegions::ExpListSharedPtr> &pField,
+                const NekDouble                                         &time);
+            virtual void v_Finalise(
+                const Array<OneD, const MultiRegions::ExpListSharedPtr> &pField,
+                const NekDouble                                         &time);
             virtual bool v_IsTimeDependent();
 
         private:
+            /// Output file.
             ofstream m_out;
+            /// Output frequency.
+            unsigned int m_outputFrequency;
+            /// Current index counter.
+            unsigned int m_index;
         };
     }
 }
 
-#endif /* NEKTAR_SOLVERUTILS_FILTERS_FILTERCHECKPOINT_H */
+#endif