Go back to using [] to flatten vectors

Iterators appear to give much slower code, so
revert this change for now.
This reverts commit 656311f.

modules/kernel/include/Vector.h

@@ -113,14 +113,6 @@ class Vector : public Value
     V::insert(V::end(), o.begin(), o.end());
     return *this;
   }
-
-  //! Allocate enough storage for `new_cap` elements
-  /** Makes sure that the vector can contain `new_cap` elements without needing
-      a reallocation. This does not change the reported size of the vector. */
-  void reserve(unsigned int new_cap) {
-    V::reserve(new_cap);
-  }
-
 #if !defined(IMP_DOXYGEN) && !defined(SWIG)
   void show(std::ostream &out = std::cout) const {
     out << "[";

modules/kernel/include/internal/container_helpers.h

@@ -39,21 +39,23 @@ inline bool is_valid(
 template <unsigned int D>
 inline ParticlesTemp flatten(const Vector<
     Array<D, WeakPointer<Particle>, Particle *> > &in) {
-  ParticlesTemp ret;
-  ret.reserve(in.size() * D);
+  ParticlesTemp ret(in.size() * D);
   for (unsigned int i = 0; i < in.size(); ++i) {
-    ret += in[i];
+    for (unsigned int j = 0; j < D; ++j) {
+      ret[i * D + j] = in[i][j];
+    }
   }
   return ret;
 }
 
 template <unsigned int D>
 inline ParticleIndexes flatten(
     const Vector<Array<D, ParticleIndex> > &in) {
-  ParticleIndexes ret;
-  ret.reserve(in.size() * D);
+  ParticleIndexes ret(in.size() * D);
   for (unsigned int i = 0; i < in.size(); ++i) {
-    ret += in[i];
+    for (unsigned int j = 0; j < D; ++j) {
+      ret[i * D + j] = in[i][j];
+    }
   }
   return ret;
 }