Update master

Created by: acrovato

Context and description

This PR consists in bringing the latest development into master. They consist of the following:

• class enum ELTYPE member names have been modified from EL_NAME to NAME
• override keyword have been added for flow module
• flow module and part of tbox module have been documented
• Various refactoring for the following classes:
  • Pt
  • Link
  • MshDeformation
  • flow::Wake
  • flow::Kutta
• CMakeLists have been updated so that each module finds its own required packages. This is a first implementation but it can be further improved
• nogui options has been added to some fdtd module testcase to supress plot output when using ctest. This is a temporary solution
• Add sph test
• Minor changes and cleaning

Warning

Kim features (mrstlnos) have not been built and are more than likely completely broken...

Checklist

• compilation (ubuntu)
• compilation (windows)
• compilation (macOS)
• battery testing (ubuntu)
• battery testing (windows)
• battery testing (macOS)
• formatting

flow/src/wKutta.cpp

@@ -2,9 +2,8 @@
 #include <algorithm>
 using namespace flow;
 
-Kutta::Kutta(std::shared_ptr<MshData> _msh, int no0, int no1, int no2, int no3,
-             double _tolX, double _tolY, double _tolZ) : Link(_msh, no0, no1, no2, no3),
-             tolX(_tolX), tolY(_tolY), tolZ(_tolZ)
+Kutta::Kutta(std::shared_ptr<MshData> _msh, int no0, int no1, int no2, int no3)
+            : Link(_msh, no0, no1, no2, no3)
 {
     if (tag0->elems.size() != tag1->elems.size()) {
         std::ostringstream err;
@@ -17,9 +16,8 @@ Kutta::Kutta(std::shared_ptr<MshData> _msh, int no0, int no1, int no2, int no3,
 }
 
 Kutta::Kutta(std::shared_ptr<MshData> _msh, std::string const &name0,
-             std::string const &name1, std::string const &name2, std::string const &name3,
-             double _tolX, double _tolY, double _tolZ) : Link(_msh, name0, name1, name2, name3),
-             tolX(_tolX), tolY(_tolY), tolZ(_tolZ)
+             std::string const &name1, std::string const &name2,
+             std::string const &name3) : Link(_msh, name0, name1, name2, name3)
 {
     if (tag0->elems.size() != tag1->elems.size()) {
         std::ostringstream err;
@@ -68,7 +66,7 @@ void Kutta::connectNodes()
         //std::cout << "MASTER: " << nUp->pos.x[0] << ',' << nUp->pos.x[1] << ',' << nUp->pos.x[2] << std::endl;
         for (auto nLw : nodesLw) {
             //std::cout << "    SLAVE: " << nLw->pos.x[0] << ',' << nLw->pos.x[1] << ',' << nLw->pos.x[2] << std::endl;
-            if (comparePos(nUp->pos, nLw->pos)) {
+            if (nUp->pos.compare(nLw->pos)) {
                 nodMap[i] = std::pair<Node *, Node *> (nUp, nLw);
                 break;
             }
@@ -187,21 +185,6 @@ void Kutta::connectVolElements(std::vector<std::pair<Element *, Element *>> &sur
     }
 }
 
-/**
- * @brief Compare two positions
- * @authors Adrien Crovato
- */
-bool Kutta::comparePos(Pt posA, Pt posB) const
-{
-    double deltaX = std::abs(posA.x[0] - posB.x[0]);
-    double deltaY = std::abs(posA.x[1] - posB.x[1]);
-    double deltaZ = std::abs(posA.x[2] - posB.x[2]);
-    if (deltaX <= tolX && deltaY <= tolY && deltaZ <= tolZ)
-        return true;
-    else 
-        return false;
-}
-
 void Kutta::write(std::ostream &out) const
 {
     out << "flow::Kutta on " << *tag0 << " and " << *tag1 << "\n";