turn addfieldfromstring into fieldfromstring and enable modifying existing fields

docs/user-guide/utilities/fieldconvert.tex

@@ -157,7 +157,7 @@ Specifically, FieldConvert has these additional functionalities
 \item \inltt{QCriterion}: Computes the Q-Criterion for a given output file;
 \item \inltt{L2Criterion}: Computes the Lambda 2 Criterion for a given output file;
 \item \inltt{addcompositeid}: Adds the composite ID of an element as an additional field;
-\item \inltt{addfieldfromstring}: Adds a new field from an expression involving the existing fields;
+\item \inltt{fieldfromstring}: Modifies or adds a new field from an expression involving the existing fields;
 \item \inltt{addFld}: Sum two .fld files;
 \item \inltt{combineAvg}: Combine two \nekpp binary output (.chk or .fld) field file containing averages of fields (and
 possibly also Reynolds stresses) into single file;
@@ -286,18 +286,18 @@ obtained through the \nm \inltt{extract} module (see section
 %
 %
 %
-\subsection{Add new field: \textit{addfieldfromstring} module}
-To create a new field using an expression involving the existing fields, one can
-use the \inltt{addfieldfromstring} module of FieldConvert
+\subsection{Add new field: \textit{fieldfromstring} module}
+To modify or create a new field using an expression involving the existing fields, one can
+use the \inltt{fieldfromstring} module of FieldConvert
 %
 \begin{lstlisting}[style=BashInputStyle]
-  FieldConvert -m addfieldfromstring:fieldstr="x+y+u":fieldname="result" \
+  FieldConvert -m fieldfromstring:fieldstr="x+y+u":fieldname="result" \
   file1.xml file2.fld file3.fld
 \end{lstlisting}
 %
 In this case \inltt{fieldstr} is a required parameter describing a function of
 the coordinates and the existing variables, and \inltt{fieldname} is an optional
-parameter defining the name of the new field (the default is newfield).
+parameter defining the name of the new or modified field (the default is newfield).
 \inltt{file3.fld} is the output containing both the original and the new fields,
 and can be processed in a similar way as described
 in section \ref{s:utilities:fieldconvert:sub:convert} to visualise

library/FieldUtils/CMakeLists.txt

@@ -17,7 +17,7 @@ SET(FieldUtilsHeaders
     OutputModules/OutputPts.h
     OutputModules/OutputXml.h
     ProcessModules/ProcessAddCompositeID.h
-    ProcessModules/ProcessAddFieldFromString.h
+    ProcessModules/ProcessFieldFromString.h
     ProcessModules/ProcessAddFld.h
     ProcessModules/ProcessBoundaryExtract.h
     ProcessModules/ProcessCombineAvg.h
@@ -73,7 +73,7 @@ SET(FieldUtilsSources
     OutputModules/OutputPts.cpp
     OutputModules/OutputXml.cpp
     ProcessModules/ProcessAddCompositeID.cpp
-    ProcessModules/ProcessAddFieldFromString.cpp
+    ProcessModules/ProcessFieldFromString.cpp
     ProcessModules/ProcessAddFld.cpp
     ProcessModules/ProcessBoundaryExtract.cpp
     ProcessModules/ProcessCombineAvg.cpp

library/FieldUtils/ProcessModules/ProcessAddFieldFromString.cpp → library/FieldUtils/ProcessModules/ProcessFieldFromString.cpp

 ///////////////////////////////////////////////////////////////////////////////
 //
-//  File: ProcessAddFieldFromString.cpp
+//  File: ProcessFieldFromString.cpp
 //
 //  For more information, please see: http://www.nektar.info/
 //
@@ -29,14 +29,14 @@
 //  FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 //  DEALINGS IN THE SOFTWARE.
 //
-//  Description: Add a new field from a string based on existing variable
+//  Description: Modify an existing or add a new field from a string based on existing variable
 //
 ///////////////////////////////////////////////////////////////////////////////
 #include <iostream>
 #include <string>
 using namespace std;
 
-#include "ProcessAddFieldFromString.h"
+#include "ProcessFieldFromString.h"
 
 #include <LibUtilities/BasicUtils/ParseUtils.h>
 #include <LibUtilities/BasicUtils/SharedArray.hpp>
@@ -46,28 +46,30 @@ namespace Nektar
 namespace FieldUtils
 {
 
-ModuleKey ProcessAddFieldFromString::className =
+ModuleKey ProcessFieldFromString::className =
     GetModuleFactory().RegisterCreatorFunction(
-        ModuleKey(eProcessModule, "addfieldfromstring"),
-        ProcessAddFieldFromString::create,
-        "Create a new field from the existing fields as specified by a string"
-        " using a required argument of the form fieldstr=\"x + y + u\" ");
+        ModuleKey(eProcessModule, "fieldfromstring"),
+        ProcessFieldFromString::create,
+        "Modify an existing or create a new field from the existing fields as "
+        "specified by a string using a required argument of the form "
+        "fieldstr=\"x + y + u\" ");
 
-ProcessAddFieldFromString::ProcessAddFieldFromString(FieldSharedPtr f)
+ProcessFieldFromString::ProcessFieldFromString(FieldSharedPtr f)
     : ProcessModule(f)
 {
     m_config["fieldstr"] = ConfigOption(
-        false, "NotSet", "string of new field to be added (required)");
+        false, "NotSet", "Analytic expression");
     m_config["fieldname"] =
-        ConfigOption(false, "newfield",
-                     "name for new field, default is newfield (optional)");
+        ConfigOption(false,
+                     "newfield",
+                     "name for modified new field, default is \"newfield\" (optional)");
 }
 
-ProcessAddFieldFromString::~ProcessAddFieldFromString(void)
+ProcessFieldFromString::~ProcessFieldFromString(void)
 {
 }
 
-void ProcessAddFieldFromString::Process(po::variables_map &vm)
+void ProcessFieldFromString::Process(po::variables_map &vm)
 {
     // Check if required parameter fieldstr was provided
     ASSERTL0(m_config["fieldstr"].m_beenSet, "fieldstr must be specified");
@@ -77,7 +79,6 @@ void ProcessAddFieldFromString::Process(po::variables_map &vm)
 
     // Set up new field name
     string fieldName = m_config["fieldname"].as<string>();
-    m_f->m_variables.push_back(fieldName);
 
     // Skip in case of empty partition
     if (m_f->m_exp[0]->GetNumElmts() == 0)
@@ -91,13 +92,29 @@ void ProcessAddFieldFromString::Process(po::variables_map &vm)
     ASSERTL0(nstrips == 1,
              "Routine is currently only setup for non-strip files");
 
-    // Create new expansion
-    m_f->m_exp.resize(nfields + 1);
-    m_f->m_exp[nfields] = m_f->AppendExpList(m_f->m_numHomogeneousDir);
+    int fieldID;
+    // check if field exists
+    auto it =
+        std::find(m_f->m_variables.begin(), m_f->m_variables.end(), fieldName);
+    if (it != m_f->m_variables.end())
+    {
+        // modify existing field
+        fieldID = std::distance(m_f->m_variables.begin(), it);
+    }
+    else
+    {
+        // create new field
+        m_f->m_variables.push_back(fieldName);
+
+        // Create new expansion
+        m_f->m_exp.resize(nfields + 1);
+        fieldID             = nfields;
+        m_f->m_exp[fieldID] = m_f->AppendExpList(m_f->m_numHomogeneousDir);
+    }
 
     // Variables for storing names and values for evaluating the function
     string varstr;
-    vector<Array<OneD, const NekDouble>> interpfields;
+    vector<Array<OneD, const NekDouble> > interpfields;
 
     // Add the coordinate values
     varstr += "x y z";
@@ -124,11 +141,11 @@ void ProcessAddFieldFromString::Process(po::variables_map &vm)
     exprId          = strEval.DefineFunction(varstr.c_str(), fieldstr);
 
     // Evaluate function
-    strEval.Evaluate(exprId, interpfields, m_f->m_exp[nfields]->UpdatePhys());
+    strEval.Evaluate(exprId, interpfields, m_f->m_exp[fieldID]->UpdatePhys());
 
     // Update coeffs
-    m_f->m_exp[nfields]->FwdTrans_IterPerExp(
-        m_f->m_exp[nfields]->GetPhys(), m_f->m_exp[nfields]->UpdateCoeffs());
+    m_f->m_exp[fieldID]->FwdTrans_IterPerExp(
+        m_f->m_exp[fieldID]->GetPhys(), m_f->m_exp[fieldID]->UpdateCoeffs());
 }
 }
 }

library/FieldUtils/ProcessModules/ProcessAddFieldFromString.h → library/FieldUtils/ProcessModules/ProcessFieldFromString.h

 ///////////////////////////////////////////////////////////////////////////////
 //
-//  File: ProcessAddFieldFromString.h
+//  File: ProcessFieldFromString.h
 //
 //  For more information, please see: http://www.nektar.info/
 //
@@ -33,8 +33,8 @@
 //
 ////////////////////////////////////////////////////////////////////////////////
 
-#ifndef FIELDUTILS_PROCESSADDNEWFIELDFROMSTR
-#define FIELDUTILS_PROCESSADDNEWFIELDFROMSTR
+#ifndef FIELDUTILS_PROCESSFIELDFROMSTR
+#define FIELDUTILS_PROCESSFIELDFROMSTR
 
 #include "../Module.h"
 
@@ -46,24 +46,24 @@ namespace FieldUtils
 /**
  * @brief This processing module adds a new field from a string definition
  */
-class ProcessAddFieldFromString : public ProcessModule
+class ProcessFieldFromString : public ProcessModule
 {
 public:
     /// Creates an instance of this class
     static std::shared_ptr<Module> create(FieldSharedPtr f)
     {
-        return MemoryManager<ProcessAddFieldFromString>::AllocateSharedPtr(f);
+        return MemoryManager<ProcessFieldFromString>::AllocateSharedPtr(f);
     }
     static ModuleKey className;
 
-    ProcessAddFieldFromString(FieldSharedPtr f);
-    virtual ~ProcessAddFieldFromString();
+    ProcessFieldFromString(FieldSharedPtr f);
+    virtual ~ProcessFieldFromString();
 
     virtual void Process(po::variables_map &vm);
 
     virtual std::string GetModuleName()
     {
-        return "ProcessAddFieldFromString";
+        return "ProcessFieldFromString";
     }
 
     virtual std::string GetModuleDescription()