This will not visit all indexes of the array because array indexes begin at 0, not 1. In other words, the first element of the 2D array would be adjacencyMatrix[0][0] so you should start both of your iterations from 0.
If the array has a length of 5, the largest index would therefore be four so be careful how far you iterate.
For example, if you did:
for (int i = 1; i <= number_of_nodes; i++)
for (int j = 1; j <= number_of_nodes; j++)
adjacencyMatrix[i][j] = adjacency_matrix[i][j];
Then it would visit:
adjacencyMatrix[1][1];
adjacencyMatrix[1][2];
adjacencyMatrix[2][1];
adjacencyMatrix[2][2];
etc...
If you did:
for (int i = 1; i <= number_of_nodes; i++)
adjacencyMatrix[i][i] = adjacency_matrix[i][i];
Then it would visit:
adjacencyMatrix[1][1];
adjacencyMatrix[2][2];
adjacencyMatrix[3][3];
adjacencyMatrix[4][4];
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solved Accessing Nested For Loop Indexes