Added a check that masses/charges are actually passed from MD

This is related to the closed issue #162

I think that with standard usage of PLUMED all the actions should be
active at step zero, and so all the masses and charges should be requested
to codes like NAMD or OPENMM. Anyway,this fix will double check for it
adding an overhead only at the first simulation step.

src/core/Atoms.cpp

@@ -28,6 +28,7 @@
 #include <algorithm>
 #include <iostream>
 #include <string>
+#include <cmath>
 
 using namespace std;
 
@@ -191,6 +192,8 @@ void Atoms::share(const std::set<AtomNumber>& unique){
   int ndata=3;
   if(!massAndChargeOK){
     ndata=5;
+    masses.assign(masses.size(),NAN);
+    charges.assign(charges.size(),NAN);
     mdatoms->getCharges(gatindex,charges);
     mdatoms->getMasses(gatindex,masses);
   }