Merge branch 'master' into 'feature/mc-extrude'

# Conflicts:
#   CHANGELOG.md

CHANGELOG.md

@@ -48,6 +48,7 @@ v4.4.0
 **FieldConvert:**
 - Allow equi-spaced output for 1D and 2DH1D fields (!613)
 - Update quality metric to include scaled Jacobian output (!695)
+- Allow multiple XML files to be specified in InterpField module (!705)
 
 **NekMesh:**
 - Modify curve module to allow for spline input (!628)
@@ -69,6 +70,8 @@ v4.4.0
 - Bug fix to get two meshgen regression tests working (!700)
 - Remove libANN in deference to boost::geometry (!703)
 - 2D to 3D mesh extrusion module (!715)
+- Add a mesh extract option to the linearise module to visualise the result 
+  (!712)
 
 **FieldConvert:**
 - Move all modules to a new library, FieldUtils, to support post-processing
@@ -83,6 +86,7 @@ v4.3.5
 - Fix bug in DG with hybrid meshes (!694)
 - Fix issue with parallel output (!699)
 - Fix performance issue with iterative full solver (!693)
+- Enforced precision on history point output (!706)
 
 **Documentation**
 - Update build instructions in user guide for Windows (!692)

library/FieldUtils/ProcessModules/ProcessInterpField.cpp

@@ -90,7 +90,7 @@ void ProcessInterpField::Process(po::variables_map &vm)
     std::vector<std::string> files;
 
     // set up session file for from field
-    files.push_back(m_config["fromxml"].as<string>());
+    ParseUtils::GenerateOrderedStringVector(m_config["fromxml"].as<string>().c_str(), files);
     m_fromField->m_session =
         LibUtilities::SessionReader::CreateInstance(0, 0, files);
 

library/FieldUtils/ProcessModules/ProcessInterpPoints.cpp

@@ -445,8 +445,8 @@ void ProcessInterpPoints::Process(po::variables_map &vm)
     FieldSharedPtr fromField = boost::shared_ptr<Field>(new Field());
 
     std::vector<std::string> files;
+    ParseUtils::GenerateOrderedStringVector(m_config["fromxml"].as<string>().c_str(), files);
     // set up session file for from field
-    files.push_back(m_config["fromxml"].as<string>());
     fromField->m_session =
         LibUtilities::SessionReader::CreateInstance(0, 0, files);
 

library/SolverUtils/Filters/FilterHistoryPoints.cpp

@@ -402,9 +402,9 @@ void FilterHistoryPoints::v_Initialise(
                                             gloCoord[2]);
 
             m_outputStream << "# " << boost::format("%6.0f") % i;
-            m_outputStream << " " << boost::format("%25e") % gloCoord[0];
-            m_outputStream << " " << boost::format("%25e") % gloCoord[1];
-            m_outputStream << " " << boost::format("%25e") % gloCoord[2];
+            m_outputStream << " " << boost::format("%25.19e") % gloCoord[0];
+            m_outputStream << " " << boost::format("%25.19e") % gloCoord[1];
+            m_outputStream << " " << boost::format("%25.19e") % gloCoord[2];
             m_outputStream << endl;
         }
 
@@ -575,10 +575,10 @@ void FilterHistoryPoints::v_Update(const Array<OneD, const MultiRegions::ExpList
         // Write data values point by point
         for (k = 0; k < m_historyPoints.size(); ++k)
         {
-            m_outputStream << boost::format("%25e") % time;
+            m_outputStream << boost::format("%25.19e") % time;
             for (int j = 0; j < numFields; ++j)
             {
-                m_outputStream << " " << boost::format("%25e") % data[k*numFields+j];
+                m_outputStream << " " << boost::format("%25.19e") % data[k*numFields+j];
             }
             m_outputStream << endl;
         }

utilities/NekMesh/ProcessModules/ProcessLinear.cpp

@@ -55,6 +55,8 @@ ProcessLinear::ProcessLinear(MeshSharedPtr m) : ProcessModule(m)
         ConfigOption(false, "0", "remove curve nodes if element is invalid.");
     m_config["prismonly"] =
         ConfigOption(false, "", "only acts on prims");
+    m_config["extract"] =
+        ConfigOption(false, "", "dump a mesh of the extracted elements");
 }
 
 ProcessLinear::~ProcessLinear()
@@ -138,6 +140,8 @@ void ProcessLinear::Process()
         vector<NodeSharedPtr> zeroNodes;
         boost::unordered_set<int> clearedEdges, clearedFaces, clearedElmts;
 
+        vector<ElementSharedPtr> dumpEls;
+
         // Iterate over list of elements of expansion dimension.
         while(el.size() > 0)
         {
@@ -153,6 +157,7 @@ void ProcessLinear::Process()
 
                 if (Invalid(el[i],thr))//(!gfac->IsValid())
                 {
+                    dumpEls.push_back(el[i]);
                     clearedElmts.insert(el[i]->GetId());;
                     el[i]->SetVolumeNodes(zeroNodes);
 
@@ -216,6 +221,26 @@ void ProcessLinear::Process()
                  << " elements (" << clearedEdges.size() << " edges, "
                  << clearedFaces.size() << " faces)" << endl;
         }
+
+        if(m_config["extract"].beenSet)
+        {
+            MeshSharedPtr dmp = boost::shared_ptr<Mesh>(new Mesh());
+            dmp->m_expDim     = 3;
+            dmp->m_spaceDim   = 3;
+            dmp->m_nummode    = 2;
+
+            dmp->m_element[3] = dumpEls;
+
+            ModuleSharedPtr mod = GetModuleFactory().CreateInstance(
+                ModuleKey(eOutputModule, "xml"), dmp);
+            mod->RegisterConfig("outfile", m_config["extract"].as<string>().c_str());
+            mod->ProcessVertices();
+            mod->ProcessEdges();
+            mod->ProcessFaces();
+            mod->ProcessElements();
+            mod->ProcessComposites();
+            mod->Process();
+        }
     }
 }