Update waves

Created by: acrovato

Context

This pull request brings the last developments from the flow module as well as some upgrade to waves.

Major changes in flow

• flow is now able to compute 3D flows
• The Jacobian (tangent) matrix for the Netwton method is now fully analytical
• The adjacent elements identification is now based on ```std::unordered_set````

Major changes in waves

• tbox and fwk are now included in a namespace
• waves is now fully included in a namespace
• All elements now have a private memory (Mem) which can be publicly accessed
• All elements now have a cache including Gauss points (Gauss) which can be publicly accessed
• MshDeformation now uses a linear elasticity solver
• MshCrack class implemented (creates duplicate internal boundaries in meshes)

Test

The ctest battery has been run on gaston, 100% tests passed under 110s.

Future work

• Use automated indentation rules for the whole code
• Move methods using VTK outside of MshData
• Clean tbox (mainly MshData, Tri3, Tera4 and Hex8)

tbox/src/wMshDeformation.cpp

@@ -200,9 +200,11 @@ void MshDeformation::initializeMoving(std::vector<Group *> bndGrp)
 {
     // Create vector of boundary nodes
     for (auto bnd : bndGrp)
-        for (auto e : bnd->tag->elems)
+        for (auto e : bnd->tag->elems) {
+            movBndElems.push_back(e);
             for (auto n : e->nodes)
                 movBndNodes.push_back(n);
+        }
     // Get unique
     std::sort(movBndNodes.begin(), movBndNodes.end());
     auto iterator = std::unique(movBndNodes.begin(), movBndNodes.end());
@@ -217,12 +219,16 @@ void MshDeformation::initializeInternal(Link * intBndLnk)
 {
     // Temporary container for nodes
     std::vector<Node *> nodes0, nodes1;
-    for(auto e : intBndLnk->tags[0]->elems)
+    for(auto e : intBndLnk->tags[0]->elems) {
+        intBndElems.push_back(e);
         for(auto n : e->nodes)
             nodes0.push_back(n);
-    for(auto e : intBndLnk->tags[1]->elems)
+    }
+    for(auto e : intBndLnk->tags[1]->elems) {
+        intBndElems.push_back(e);
         for(auto n : e->nodes)
             nodes1.push_back(n);
+    }
     // Get unique
     std::sort (nodes0.begin(), nodes0.end());
     auto it = std::unique (nodes0.begin(), nodes0.end());
@@ -362,19 +368,31 @@ void MshDeformation::deform()
         n->pos.x[m] -= q[nDim*(n->row)+m];
     }
     // Update element memory and check the Jacobian (only implemented for Tri3)
-    for (auto e : fldElems) {
-        if (e->type() == ELTYPE::TRI3){
-            Mem &m = e->getVMem();
-            m.update();
-            for (int k = 0; k < m.getGPn() ; k++) {
-                if (m.getDetJ(k) <= 0) {
-                    std::stringstream err;
-                    err << "Negative jacobian detected for element: " << *e << "\n";
-                    throw std::runtime_error(err.str());
-                }
-            }
-        }
-    }
+    //for (auto e : fldElems) {
+    //    if (e->type() == ELTYPE::TRI3){
+    //        Mem &m = e->getVMem();
+    //        m.update();
+    //        for (int k = 0; k < m.getGPn() ; k++) {
+    //            if (m.getDetJ(k) <= 0) {
+    //                std::stringstream err;
+    //                err << "Negative jacobian detected for element: " << *e << "\n";
+    //                throw std::runtime_error(err.str());
+    //            }
+    //        }
+    //    }
+    //}
+    //for (auto e : msh->elems) {
+    //    if (e->type() == ELTYPE::TRI3 || e->type() == ELTYPE::LINE2){
+    //        e->getVMem().update();
+    //    }
+    //}
+    for (auto e : fldElems)
+        e->getVMem().update();
+    for (auto e : movBndElems)
+        e->getVMem().update();
+    for (auto e : intBndElems)
+        e->getVMem().update();        
+
 }
 
 void MshDeformation::write(std::ostream &out) const