Re-enabled automatic peralign call.

utilities/NekMesh/InputModules/InputMCF.cpp

@@ -340,6 +340,7 @@ void InputMCF::Process()
 
     if(m_2D)
     {
+        ////**** 2DGenerator ****////
         m_mesh->m_expDim = 2;
         m_mesh->m_spaceDim = 2;
         mods.push_back(GetModuleFactory().CreateInstance(
@@ -416,54 +417,23 @@ void InputMCF::Process()
         mods.back()->RegisterConfig("r",m_blprog);
     }
 
-    for(int i = 0; i < mods.size(); i++)
+    ////**** Peralign ****////
+    if (m_2D && m_periodic.size())
     {
-        mods[i]->SetDefaults();
-        mods[i]->Process();
-    }
-
-    // Run peralign
-
-    /*if (m_periodic.size())
-    {
-        mods.clear();
-
         vector<string> lines;
         boost::split(lines, m_periodic, boost::is_any_of(":"));
 
         for (vector<string>::iterator il = lines.begin(); il != lines.end();
              ++il)
         {
-            vector<string> tmp(2);
-            vector<unsigned> data(2);
-            boost::split(tmp, *il, boost::is_any_of(","));
-            data[0] = boost::lexical_cast<unsigned>(tmp[0]);
-            data[1] = boost::lexical_cast<unsigned>(tmp[1]);
-
             mods.push_back(GetModuleFactory().CreateInstance(
                 ModuleKey(eProcessModule, "peralign"), m_mesh));
+            
+            vector<string> tmp(2);
+            boost::split(tmp, *il, boost::is_any_of(","));
             mods.back()->RegisterConfig("surf1", tmp[0]);
             mods.back()->RegisterConfig("surf2", tmp[1]);
-
-            Array<OneD, NekDouble> P11 =
-                m_mesh->m_cad->GetCurve(data[0])->GetVertex()[0]->GetLoc();
-            Array<OneD, NekDouble> P12 =
-                m_mesh->m_cad->GetCurve(data[0])->GetVertex()[1]->GetLoc();
-            Array<OneD, NekDouble> P21 =
-                m_mesh->m_cad->GetCurve(data[1])->GetVertex()[0]->GetLoc();
-            Array<OneD, NekDouble> P22 =
-                m_mesh->m_cad->GetCurve(data[1])->GetVertex()[1]->GetLoc();
-
-            Array<OneD, NekDouble> T(2);
-
-            T[0] = (P21[0] + P22[0] - P11[0] - P12[0]) / 2;
-            T[1] = (P21[1] + P22[1] - P11[1] - P12[1]) / 2;
-
-            NekDouble mag = sqrt(T[0] * T[0] + T[1] * T[1]);
-
-            stringstream ss;
-            ss << T[0] / mag << "," << T[1] / mag << "," << 0.0;
-            mods.back()->RegisterConfig("dir", ss.str());
+        }
     }
 
     for(int i = 0; i < mods.size(); i++)
@@ -471,7 +441,6 @@ void InputMCF::Process()
         mods[i]->SetDefaults();
         mods[i]->Process();
     }
-    }*/
 }
 }
 }

utilities/NekMesh/ProcessModules/ProcessPerAlign.cpp

@@ -112,6 +112,18 @@ void ProcessPerAlign::Process()
     NekDouble vec[3];
 
     if (tmp1.size() == 1)
+    {
+        if (!dir.size() && m_mesh->m_spaceDim == 2)
+        {
+            Array<OneD, NekDouble> T =
+                m_mesh->m_cad->GetPeriodicTranslationVector(surf1, surf2);
+            NekDouble mag = sqrt(T[0] * T[0] + T[1] * T[1]);
+
+            vec[0] = T[0] / mag;
+            vec[1] = T[1] / mag;
+            vec[2] = T[2] / mag;
+        }
+        else
         {
             if (dir != "x" && dir != "y" && dir != "z")
             {
@@ -124,6 +136,7 @@ void ProcessPerAlign::Process()
             vec[1] = dir == "y" ? 1.0 : 0.0;
             vec[2] = dir == "z" ? 1.0 : 0.0;
         }
+    }
     else if (tmp1.size() == 3)
     {
         vec[0] = boost::lexical_cast<NekDouble>(tmp1[0]);