hint 2-2 inline code reference check

Author: kcpearce

Project#01/hints/hint1-3.md

@@ -6,32 +6,15 @@ double x[50], y[50], z[50];
 
 A more elegant solution is to allocate the memory dynamically for each array once you know the number of atoms:
 ```c++
-#include <iostream>
-#include <fstream>
-#include <iomanip>
+int natom;
+input >> natom;
 
-...
+int *zval = new int[natom];
+double *x = new double[natom];
+double *y = new double[natom];
+double *z = new double[natom];
 
-int main()
-{  
-  ifstream input("geom.dat");
-
-  int natom;
-  input >> natom;
-
-  input.close();
-  
-  int *zval = new int[natom];
-  double *x = new double[natom];
-  double *y = new double[natom];
-  double *z = new double[natom];
-
-  ...
-
-  delete[] zval;  delete[] x;  delete[] y;  delete[] z;
-
-  return 0;
-}
+delete[] zval;  delete[] x;  delete[] y;  delete[] z;
 ```
 
 Don't forget to delete[] the memory after you're finished!

Project#01/hints/hint2-1.md

@@ -0,0 +1,18 @@
+If we choose to store the matrix of bond distances, we need to allocate the necessary memory, either as a static two-dimensional array:
+```c++
+double R[50][50];
+```
+
+or via dynamic allocation using the [Molecule class](https://github.com/CrawfordGroup/ProgrammingProjects/wiki/Classes-and-Objects):
+```c++
+double **R = new double* [mol.natom];
+for(int i=0; i < mol.natom; i++)
+  R[i] = new double[mol.natom];
+```
+
+Don't forget to delete[] the memory at the end of the program:
+```c++
+for(int i=0; i < mol.natom; i++)
+  delete[] R[i];
+delete[] R;
+```

Project#01/hints/hint2-2.md

@@ -0,0 +1,17 @@
+To build the distance matrix, we need a loop for each index:
+```c++
+  ...
+  #include <cmath>
+  ...
+  
+  for(int i=0; i < mol.natom; i++) {
+    for(int j=0; j < mol.natom; j++) {
+        R[i][j] = sqrt(
+            (mol.geom[i][0]-mol.geom[j][0])*(mol.geom[i][0]-mol.geom[j][0])
+          + (mol.geom[i][1]-mol.geom[j][1])*(mol.geom[i][1]-mol.geom[j][1])
+          + (mol.geom[i][2]-mol.geom[j][2])*(mol.geom[i][2]-mol.geom[j][2])
+                      );
+    }
+  }
+```
+Note also that the `sqrt()` function is part of the C math library; thus we need the `#include <cmath>` directive.