Merging develop into master

Nightly Bot · cwsmith · commit ecc64db4e488 · 2018-08-15T00:18:24.000-04:00
diff --git a/apf/apf.cc b/apf/apf.cc
@@ -463,6 +463,13 @@ Field* createUserField(Mesh* m, const char* name, int valueType, FieldShape* s,
   return makeField(m, name, valueType, 0, s, new UserData(f));
 }
 
+void updateUserField(Field* field, Function* newFunc)
+{
+  UserData* ud = dynamic_cast<UserData*>(field->getData());
+  // ud will be null if the data is not user data
+  if (ud) ud->setFunction(newFunc);
+}
+
 void copyData(Field* to, Field* from)
 {
   copyFieldData(from->getData(), to->getData());
diff --git a/apf/apf.h b/apf/apf.h
@@ -668,14 +668,22 @@ struct Function
   virtual void eval(MeshEntity* e, double* result) = 0;
 };
 
-/** \brief Create a Field from a user's analytic function.
-  \details This field will use no memory, has values on all
-  nodes, and calls the user Function for all value queries.
-  Writing to this field does nothing.
-  */
+/* \brief Create a Field from a user's analytic function.
+ * \details This field will use no memory, has values on all
+ * nodes, and calls the user Function for all value queries.
+ * Writing to this field does nothing.
+ * \warning if you copy the mesh with apf::convert you may want to use
+ * apf::updateUserField to update function that this field refers to. This is
+ * extremely important if the analytic function you use references user fields.
+ */
 Field* createUserField(Mesh* m, const char* name, int valueType, FieldShape* s,
     Function* f);
 
+/* \brief update the analytic function from a user field
+ * \details this field updates the apf::Function which the UserField refers to
+ */
+void updateUserField(Field* field, Function* newFunc);
+
 /** \brief Compute a nodal gradient field from a nodal input field
   \details given a nodal field, compute approximate nodal gradient
   values by giving each node a volume-weighted average of the
diff --git a/apf/apfArrayData.cc b/apf/apfArrayData.cc
@@ -79,6 +79,14 @@ class ArrayDataOf : public FieldDataOf<T>
     T* getDataArray() {
       return this->dataArray;
     }
+    virtual FieldData* clone() {
+      //FieldData* newData = new TagDataOf<double>();
+      FieldData* newData = new ArrayDataOf<T>();
+      newData->init(this->field);
+      copyFieldData(static_cast<FieldDataOf<T>*>(newData),
+                    static_cast<FieldDataOf<T>*>(this->field->getData()));
+      return newData;
+    }
 
   private:
     /* data variables go here */
diff --git a/apf/apfConvert.cc b/apf/apfConvert.cc
@@ -7,6 +7,8 @@
 #include "apfNumbering.h"
 #include <map>
 #include <pcu_util.h>
+#include <iostream>
+#include <cstdlib>
 
 namespace apf {
 
@@ -31,6 +33,9 @@ class Converter
       convertFields();
       convertNumberings();
       convertGlobalNumberings();
+      // this must be called after anything that might create tags e.g. fields
+      // or numberings to avoid problems with tag duplication
+      convertTags();
       outMesh->acceptChanges();
     }
     ModelEntity* getNewModelFromOld(ModelEntity* oldC)
@@ -210,6 +215,48 @@ class Converter
         }
       }
     }
+    void convertTag(Mesh* inMesh, MeshTag* in, Mesh* outMesh, MeshTag* out)
+    {
+      for (int d = 0; d <= 3; ++d) {
+        int tagType = inMesh->getTagType(in);
+        int tagSize = inMesh->getTagSize(in);
+        PCU_DEBUG_ASSERT(tagType == outMesh->getTagType(out));
+        PCU_DEBUG_ASSERT(tagSize == outMesh->getTagSize(out));
+        MeshIterator* it = inMesh->begin(d);
+        MeshEntity* e;
+        while ((e = inMesh->iterate(it))) {
+          if(inMesh->hasTag(e, in)) {
+            // these initializations cannot go into the cases due to compiler
+            // warnings on gcc 7.3.0
+            double* dblData;
+            int* intData;
+            long* lngData; 
+            switch (tagType) {
+              case apf::Mesh::DOUBLE:
+                dblData = new double[tagSize];
+                inMesh->getDoubleTag(e, in, dblData);
+                outMesh->setDoubleTag(newFromOld[e], out, dblData);
+                break;
+              case apf::Mesh::INT:
+                intData = new int[tagSize];
+                inMesh->getIntTag(e, in, intData);
+                outMesh->setIntTag(newFromOld[e], out, intData);
+                break;
+              case apf::Mesh::LONG:
+                lngData = new long[tagSize];
+                inMesh->getLongTag(e, in, lngData);
+                outMesh->setLongTag(newFromOld[e], out, lngData);
+                break;
+              default:
+                std::cerr << "Tried to convert unknown tag type\n";
+                abort();
+                break;
+            }
+        }
+        }
+        inMesh->end(it);
+      }
+    }
     void convertFields()
     {
       for (int i = 0; i < inMesh->countFields(); ++i) {
@@ -222,20 +269,76 @@ class Converter
     {
       for (int i = 0; i < inMesh->countNumberings(); ++i) {
         Numbering* in = inMesh->getNumbering(i);
-        Numbering* out = createNumbering(outMesh,
-            getName(in), getShape(in), countComponents(in));
+        Numbering* out;
+        if (getField(in)) {
+          // here we assume that the fields have already been copied into the
+          // mesh
+          Field* outField = outMesh->findField(getName(getField(in)));
+          PCU_DEBUG_ASSERT(outField);
+          out = createNumbering(outField);
+        }
+        else {
+          out = createNumbering(outMesh, getName(in), getShape(in),
+                                countComponents(in));
+        }
         convertNumbering(in, out);
       }
     }
     void convertGlobalNumberings()
     {
       for (int i = 0; i < inMesh->countGlobalNumberings(); ++i) {
         GlobalNumbering* in = inMesh->getGlobalNumbering(i);
-        GlobalNumbering* out = createGlobalNumbering(outMesh,
-            getName(in), getShape(in), countComponents(in));
+        GlobalNumbering* out;
+        if (getField(in)) {
+          // here we assume that the fields have already been copied into the
+          // mesh
+          Field* outField = outMesh->findField(getName(getField(in)));
+          PCU_DEBUG_ASSERT(outField);
+          out = createGlobalNumbering(outField);
+        }
+        else {
+          out = createGlobalNumbering(outMesh, getName(in), getShape(in),
+                                      countComponents(in));
+        }
         convertGlobalNumbering(in, out);
       }
     }
+    void convertTags()
+    {
+      DynamicArray<MeshTag*> tags;
+      inMesh->getTags(tags);
+      for (std::size_t i = 0; i < tags.getSize(); ++i) {
+        apf::MeshTag* in = tags[i];
+        PCU_DEBUG_ASSERT(in);
+        // create a new tag on the outMesh
+        int tagType = inMesh->getTagType(in);
+        int tagSize = inMesh->getTagSize(in);
+        const char* tagName = inMesh->getTagName(in);
+        PCU_DEBUG_ASSERT(tagName);
+        // need to make sure that the tag wasn't already created by a field or
+        // numbering
+        if (!outMesh->findTag(tagName)) {
+          apf::MeshTag* out = NULL;
+          switch (tagType) {
+            case apf::Mesh::DOUBLE:
+              out = outMesh->createDoubleTag(tagName, tagSize);
+              break;
+            case apf::Mesh::INT:
+              out = outMesh->createIntTag(tagName, tagSize);
+              break;
+            case apf::Mesh::LONG:
+              out = outMesh->createLongTag(tagName, tagSize);
+              break;
+            default:
+              std::cerr << "Tried to convert unknown tag type\n";
+              abort();
+          }
+          PCU_DEBUG_ASSERT(out);
+          // copy the tag on the inMesh to the outMesh
+          convertTag(inMesh, in, outMesh, out);
+        }
+      }
+    }
     void convertQuadratic()
     {
       if (inMesh->getShape() != getLagrange(2) && inMesh->getShape() != getSerendipity())
diff --git a/apf/apfCoordData.cc b/apf/apfCoordData.cc
@@ -11,6 +11,14 @@
 
 namespace apf {
 
+FieldData* CoordData::clone() {
+  FieldData* newData = new CoordData();
+  newData->init(field);
+  copyFieldData(static_cast<FieldDataOf<double>*>(newData),
+                static_cast<FieldDataOf<double>*>(field->getData()));
+  return newData;
+
+}
 void CoordData::init(FieldBase* f)
 {
   FieldData::field = f;
diff --git a/apf/apfCoordData.h b/apf/apfCoordData.h
@@ -33,6 +33,7 @@ class CoordData : public FieldDataOf<double>
     virtual void get(MeshEntity* e, double* data);
     virtual void set(MeshEntity* e, double const* data);
     virtual bool isFrozen() { return false; }
+    virtual FieldData* clone();
   private:
     Mesh* mesh;
     FieldShape* shape;
diff --git a/apf/apfFieldData.cc b/apf/apfFieldData.cc
@@ -10,11 +10,6 @@ FieldData::~FieldData()
 {
 }
 
-FieldData* FieldData::clone()
-{
-  abort();
-}
-
 void FieldData::rename(const char*)
 {
   abort();
diff --git a/apf/apfFieldData.h b/apf/apfFieldData.h
@@ -22,7 +22,7 @@ class FieldData
     virtual bool hasEntity(MeshEntity* e) = 0;
     virtual void removeEntity(MeshEntity* e) = 0;
     virtual bool isFrozen() = 0;
-    virtual FieldData* clone();
+    virtual FieldData* clone() = 0;
     virtual void rename(const char* newName);
     FieldBase* getField() {return field;}
   protected:
@@ -55,6 +55,7 @@ class FieldDataOf : public FieldData
     void setNodeComponents(MeshEntity* e, int node, T const* components);
     void getNodeComponents(MeshEntity* e, int node, T* components);
     int getElementData(MeshEntity* entity, NewArray<T>& data);
+    virtual FieldData* clone()=0;
 };
 
 } //namespace apf
diff --git a/apf/apfNumbering.cc b/apf/apfNumbering.cc
@@ -461,6 +461,14 @@ GlobalNumbering* createGlobalNumbering(
   return n;
 }
 
+GlobalNumbering* createGlobalNumbering(Field* f)
+{
+  GlobalNumbering* n = new GlobalNumbering();
+  n->init(f);
+  f->getMesh()->addGlobalNumbering(n);
+  return n;
+}
+
 FieldShape* getShape(GlobalNumbering* n)
 {
   return n->getShape();
@@ -601,5 +609,5 @@ void getNodes(GlobalNumbering* n, DynamicArray<Node>& nodes)
   getFieldNodes(n,nodes);
 }
 
+Field* getField(GlobalNumbering* n) { return n->getField(); }
 }
-
diff --git a/apf/apfNumbering.h b/apf/apfNumbering.h
@@ -159,6 +159,11 @@ GlobalNumbering* createGlobalNumbering(
     const char* name,
     FieldShape* shape,
     int components=1);
+
+/** \brief Create a Numbering of degrees of freedom of a Field.
+ */
+GlobalNumbering* createGlobalNumbering(Field* f);
+
 FieldShape* getShape(GlobalNumbering* n);
 const char* getName(GlobalNumbering* n);
 /** \brief get the mesh associated with a global numbering */
@@ -176,6 +181,9 @@ long getNumber(GlobalNumbering* n, MeshEntity* e, int node, int component=0);
 /** \brief get an element's global node numbers */
 int getElementNumbers(GlobalNumbering* n, MeshEntity* e,
     NewArray<long>& numbers);
+/** \brief get the field being numbered
+ */
+Field* getField(GlobalNumbering* n);
 
 /** \brief converts a local numbering into a global numbering.
   \param destroy Should the input Numbering* be destroyed?
diff --git a/apf/apfUserData.cc b/apf/apfUserData.cc
@@ -42,4 +42,13 @@ bool UserData::isFrozen()
   return false;
 }
 
+FieldData* UserData::clone()
+{
+  FieldData* newData = new UserData(function);
+  newData->init(field);
+  copyFieldData(static_cast<FieldDataOf<double>*>(newData),
+                static_cast<FieldDataOf<double>*>(field->getData()));
+  return newData;
+}
+
 }
diff --git a/apf/apfUserData.h b/apf/apfUserData.h
@@ -21,11 +21,15 @@ struct UserData : public FieldDataOf<double>
   void get(MeshEntity* e, double* data);
   void set(MeshEntity* e, double const* data);
   bool isFrozen();
+  virtual FieldData* clone();
+  // using const * const gives an error on gcc/7.3.0 because the return is an
+  // r-value which cannot be modified anyways
+  Function const* getFunction() const { return function; }
+  void setFunction(Function* func) { function = func; }
+  private:
   Function* function;
 };
 
 }
 
 #endif
-
-
diff --git a/cmake/FindSimModSuite.cmake b/cmake/FindSimModSuite.cmake
@@ -74,7 +74,7 @@ string(REGEX REPLACE
   "${SIM_VERSION}")
 
 set(MIN_VALID_SIM_VERSION 11.0.170826)
-set(MAX_VALID_SIM_VERSION 12.0.180713)
+set(MAX_VALID_SIM_VERSION 12.0.180811)
 if( (SIM_DOT_VERSION VERSION_LESS MIN_VALID_SIM_VERSION) OR
     (SIM_DOT_VERSION VERSION_GREATER MAX_VALID_SIM_VERSION) )
   MESSAGE(FATAL_ERROR 
diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt
@@ -20,6 +20,7 @@ util_exe_func(describe describe.cc)
 test_exe_func(quality quality.cc)
 test_exe_func(writeVtxPtn writeVtxPtn.cc)
 test_exe_func(verify_2nd_order_shapes verify_2nd_order_shapes.cc)
+test_exe_func(verify_convert verify_convert.cc)
 
 # Geometric model utilities
 if(ENABLE_SIMMETRIX)
diff --git a/test/testing.cmake b/test/testing.cmake
@@ -33,6 +33,7 @@ mpi_test(integrate 1 ./integrate)
 mpi_test(qr_test 1 ./qr)
 mpi_test(base64 1 ./base64)
 mpi_test(tensor_test 1 ./tensor)
+mpi_test(verify_convert 1 ./verify_convert)
 
 if(ENABLE_SIMMETRIX)
   mpi_test(in_closure_of 1
diff --git a/test/verify_convert.cc b/test/verify_convert.cc

Original file line number	Diff line number	Diff line change
`@@ -463,6 +463,13 @@ Field* createUserField(Mesh* m, const char* name, int valueType, FieldShape* s,`
`463`	`463`	`return makeField(m, name, valueType, 0, s, new UserData(f));`
`464`	`464`	`}`
`465`	`465`
	`466`	`+void updateUserField(Field* field, Function* newFunc)`
	`467`	`+{`
	`468`	`+ UserData* ud = dynamic_cast<UserData*>(field->getData());`
	`469`	`+ // ud will be null if the data is not user data`
	`470`	`+ if (ud) ud->setFunction(newFunc);`
	`471`	`+}`
	`472`	`+`
`466`	`473`	`void copyData(Field* to, Field* from)`
`467`	`474`	`{`
`468`	`475`	`copyFieldData(from->getData(), to->getData());`
Original file line number	Diff line number	Diff line change
`@@ -10,11 +10,6 @@ FieldData::~FieldData()`
`10`	`10`	`{`
`11`	`11`	`}`
`12`	`12`
`13`		`-FieldData* FieldData::clone()`
`14`		`-{`
`15`		`- abort();`
`16`		`-}`
`17`		`-`
`18`	`13`	`void FieldData::rename(const char*)`
`19`	`14`	`{`
`20`	`15`	`abort();`
Original file line number	Diff line number	Diff line change
`@@ -461,6 +461,14 @@ GlobalNumbering* createGlobalNumbering(`
`461`	`461`	`return n;`
`462`	`462`	`}`
`463`	`463`
	`464`	`+GlobalNumbering* createGlobalNumbering(Field* f)`
	`465`	`+{`
	`466`	`+ GlobalNumbering* n = new GlobalNumbering();`
	`467`	`+ n->init(f);`
	`468`	`+ f->getMesh()->addGlobalNumbering(n);`
	`469`	`+ return n;`
	`470`	`+}`
	`471`	`+`
`464`	`472`	`FieldShape* getShape(GlobalNumbering* n)`
`465`	`473`	`{`
`466`	`474`	`return n->getShape();`
`@@ -601,5 +609,5 @@ void getNodes(GlobalNumbering* n, DynamicArray<Node>& nodes)`
`601`	`609`	`getFieldNodes(n,nodes);`
`602`	`610`	`}`
`603`	`611`
	`612`	`+Field* getField(GlobalNumbering* n) { return n->getField(); }`
`604`	`613`	`}`
`605`		`-`