bug correction and documentation

src/tools/Pbc.cpp

@@ -159,7 +159,7 @@ void Pbc::apply(std::vector<Vector>& dlist, unsigned max_index) const {
   apply(mdMemoryView< -1,3>(&dlist[0][0],dlist.size()),max_index);
 }
 
-void Pbc::apply(mdMemoryView< -1,3>dlist, unsigned max_index) const {
+void Pbc::apply(mdMemoryView< -1,3> dlist, unsigned max_index) const {
   if (max_index==0) max_index=dlist.size();
   if(type==unset) {
     // do nothing
@@ -183,17 +183,17 @@ void Pbc::apply(mdMemoryView< -1,3>dlist, unsigned max_index) const {
   } else if(type==generic) {
     for(unsigned k=0; k<max_index; ++k) {
       auto t =distance(Vector(0.0,0.0,0.0),
-                         Vector(dlist[k][0],dlist[k][1],dlist[k][2]));
+      {dlist[k][0],dlist[k][1],dlist[k][2]});
       dlist[k][0]  = t[0];
       dlist[k][1]  = t[1];
       dlist[k][2]  = t[2];
     }
   } else plumed_merror("unknown pbc type");
 }
 
-Vector Pbc::distance(const Vector&v1, Vector d,int*nshifts)const {
+Vector Pbc::distance(const Vector&v1, Vector d, int*nshifts) const {
   //d is copy/move constructed
-  //when possible d will be RVOed 
+  //when possible d will be RVOed
   //it is equivalent to declare Vector d ad assigning it to the difference
   //between the inputs
   d-=v1;

src/tools/Pbc.h

@@ -30,25 +30,33 @@
 namespace PLMD {
 
 //this more or less mocks c++20 span with fixed size
-template < int N=3>
-  class MemoryView {
-    double *ptr_;
-    public:
-    MemoryView(double* p) :ptr_(p){}
-    constexpr size_t size()const {return N;}
-    double & operator[](size_t i) { return ptr_ [i];}
-  };
+template < std::size_t N=3>
+class MemoryView {
+  double *ptr_;
+public:
+  MemoryView(double* p) :ptr_(p) {}
+  constexpr size_t size()const {return N;}
+  constexpr size_t extent = N;
+  double & operator[](size_t i) { return ptr_[i];}
+};
 
-//this more or less mocks c++23 mdspan
-template < int N=-1,int STRIDE=3>
-  class mdMemoryView {
-    double *ptr_;
-    size_t size_;
-    public:
-    mdMemoryView(double* p, size_t s) :ptr_(p), size_(s){}
-    size_t size()const {return size_;}
-    MemoryView<STRIDE> operator[](size_t i) { return MemoryView<STRIDE>(ptr_ + i *N);}
-  };
+//this more or less mocks c++23 mdspan without the fancy multi-indexed operator[]
+//the idea is to take an address that you know to be strided in a certain way and 
+//make it avaiable to any interface (like using the data from a nunmpy.ndarray in
+//a function thought for a std::vector<PLMD::Vector> )
+//the N=-1 is there for mocking the run time size from the span (where a 
+//dynamic extent is size_t(-))
+template < std::size_t N=-1, std::size_t STRIDE=3>
+class mdMemoryView {
+  double *ptr_;
+  size_t size_;
+public:
+  mdMemoryView(double* p, size_t s) :ptr_(p), size_(s) {}
+  size_t size()const {return size_;}
+  constexpr size_t extent = N;
+  constexpr size_t stride = STRIDE;
+  MemoryView<STRIDE> operator[](size_t i) { return MemoryView<STRIDE>(ptr_ + i * STRIDE);}
+};
 
 /*
 Tool to deal with periodic boundary conditions.