Jtdcftul

In the context of resistor networks and finding the (equivalent) resistance between two arbitrary nodes, I am trying to learn how to write
a generic approach in Mathematica, generic as in an approach that also lends itself to large spatially randomly distributed graphs as well (not just lattices), where then one has to deal
with sparse matrices. Before getting there, I've tried simply recreating a piece of algorithm written in Julia for solving an example on a square grid, with all resistances set to 1.

Here's the grid where each edge depicts a resistor between its incident nodes (all resistance values are assumed to be $1 Omega$) and two arbitrary nodes ($A$ at {2,2} and $B$ at {7,8}) are highlighted, question is to find the resistance between them.

In the Julia's code snippet, the approach of injecting a current and measuring the voltages at the two nodes is adopted, as shown below: (source)

N = 10

D1 = speye(N-1,N) - spdiagm(ones(N-1),1,N-1,N)

D = [ kron(D1, speye(N)); kron(speye(N), D1) ]

i, j = N*1 + 2, N*7+7

b = zeros(N^2); b[i], b[j] = 1, -1

v = (D' * D)  b

v[i] - v[j]

Output: 1.6089912417307288

I've tried to recreate exactly the same approach in Mathematica, here's what I have done:

n = 10;

grid = GridGraph[{n, n}];

i = n*1 + 2;

j = n*7 + 7;

b = ConstantArray[0, {n*n, 1}];

b[[i]] = {1};

b[[j]] = {-1};

incidenceMat = IncidenceMatrix[grid];

matrixA = incidenceMat.Transpose[incidenceMat];

v = LinearSolve[matrixA, b]

I feel very silly, but I must be missing something probably very obvious as LinearSolve does not manage to find a solution (for the chosen nodes the answer is know to be $1.608991...$, which is obtained by taking the potential difference between A and B since the current is set to 1).

Questions

• Have I mis-interpreted something in my replication of the algorithm sample written in Julia?




• It would be very interesting and useful if someone could comment on how extensible these approaches are to more general systems (2d, 3d and not only for lattices). For instance, which
  approaches would be more suitable to adopt in Mathematica for larger resistor networks (in terms of efficiency, as one would have to deal with very sparse matrices probably).

As a side-note, on the same Rosetta article, there are two alternative code snippets provided for Mathematica (which follows Maxima's approach, essentially similar to the one written Julia).
In case someone is interested I include them here: (source for both)

gridresistor[p_, q_, ai_, aj_, bi_, bj_] := 

  Block[{A, B, k, c, V}, A = ConstantArray[0, {p*q, p*q}];

   Do[k = (i - 1) q + j;

    If[{i, j} == {ai, aj}, A[[k, k]] = 1, c = 0;

     If[1 <= i + 1 <= p && 1 <= j <= q, c++; A[[k, k + q]] = -1];

     If[1 <= i - 1 <= p && 1 <= j <= q, c++; A[[k, k - q]] = -1];

     If[1 <= i <= p && 1 <= j + 1 <= q, c++; A[[k, k + 1]] = -1];

     If[1 <= i <= p && 1 <= j - 1 <= q, c++; A[[k, k - 1]] = -1];

     A[[k, k]] = c], {i, p}, {j, q}];

   B = SparseArray[(k = (bi - 1) q + bj) -> 1, p*q];

   LinearSolve[A, B][[k]]];

N[gridresistor[10, 10, 2, 2, 8, 7], 40]

Alternatively:

graphresistor[g_, a_, b_] := 

  LinearSolve[

    SparseArray[{{a, a} -> 1, {i_, i_} :> Length@AdjacencyList[g, i], 

      Alternatives @@ Join[#, Reverse /@ #] &[

        List @@@ EdgeList[VertexDelete[g, a]]] -> -1}, {VertexCount[

       g], VertexCount[g]}], SparseArray[b -> 1, VertexCount[g]]][[b]];

N[graphresistor[GridGraph[{10, 10}], 12, 77], 40]

In addition to Carl Woll's post:

Computing the pseudoinverse of a the graph Laplacian matrix (a.k.a. the KirchhoffMatrix) is very expensive and in general leads to a dense matrix that, if the graph is too large, cannot be stored in RAM. In the case that you have to compute only a comparatively small block of the resistance distance matrix, you can employ sparse methods as follows:

Generating a graph with 160000 vertices.

g = GridGraph[{400, 400}, GraphLayout -> None];

L = N@KirchhoffMatrix[g];

Notice that the kernel of the Kirchhoff matrix consists solely of constant vectors and its image is the orthogonal complement of constant vectors. Hence, by adding orthogonality to the constant vectors as additional constraint, we may constructing utitilize the following sparse saddle point matrix A and its LinearSolveFunction S for computing the pseudoinverse of the Kirchhoff matrix (works this way only for connected graphs!).

A = With[{a = SparseArray[ConstantArray[1., {1, VertexCount[g]}]]},

   ArrayFlatten[{{L, a[Transpose]}, {a, 0.}}]

   ];

S = LinearSolve[A]; // AbsoluteTiming

Applying the pseudoinverse of L to a vector b is now equivalent to

b = RandomReal[{-1, 1}, VertexCount[g]];

x = S[Join[b, {0.}]][[1 ;; -2]];

We may exploit that via the following helper function; internally, incomputes only few columns of the pseudoinverse and returns the corresponding resistance graph matrix.

resitanceDistanceMatrix[S_LinearSolveFunction, idx_List] := 

  Module[{n, basis, Γ},

   n = S[[1, 1]];

   basis = SparseArray[

     Transpose[{idx, Range[Length[idx]]}] -> 1.,

     {n, Length[idx]}

     ];

   Γ = S[basis][[idx]];

   Outer[Plus, Diagonal[Γ], 

     Diagonal[Γ]] - Γ - 

    Transpose[Γ]

   ];

Let's compute the resistance distance matrix for 5 random vertices:

SeedRandom[123];

idx = RandomSample[1 ;; VertexCount[g], 5];

resitanceDistanceMatrix[S, idx] // MatrixForm

$$left(
begin{array}{ccccc}
0. & 2.65527 & 2.10199 & 2.20544 & 2.76988 \
2.65527 & 0. & 2.98857 & 2.85428 & 2.3503 \
2.10199 & 2.98857 & 0. & 2.63996 & 3.05817 \
2.20544 & 2.85428 & 2.63996 & 0. & 3.04984 \
2.76988 & 2.3503 & 3.05817 & 3.04984 & 0. \
end{array}
right)$$

This requires $k$ linear solves for $k (k-1) /2 $ distances, so it is even more efficient than the method you posted (which needs one linear solve per distance).

The most expensive part of the code is to generate the LinearSolveFunction S. Thus, I designed the code so that S can be reused.

Under the hood, a sparse LU-factorization is computed via UMFPACK. Since the graph g is planar, this is guaranteed to be very quick compared to computing the whole pseudoinverse.

For nonplanar graphs, things become complicated. Often, using LU-factorization will work in reasonable time. But that is not guaranteed. If you have for example a cubical grid in 3D, LU-factorization will take much longer than a 2D-problem of similar size even if you measure size by the number of nonzero entries. In such cases, iterative linear solvers with suitable preconditioners may perform much better. One such method (with somewhat built-in preconditioner) is the (geometric or algebraic) multigrid method. I've posted one here. For a timing comparison of linear solves on a cubical grid topology see here. The drawback of this method is that you have to create a nested hierarchy of graphs on your own (e.g. by edge collapse). You may find more info on the topic by googling for "multigrid"+"graph".

Based on rcampion2012's answer to Efficient Implementation of Resistance Distance for graphs?, you could use:

resistanceGraph[g_] := With[{Γ = PseudoInverse[N @ KirchhoffMatrix[g]]},

    Outer[Plus, Diagonal[Γ], Diagonal[Γ]] - Γ - Transpose[Γ]

]

Then, you can find the resistance using:

r = resistanceGraph[GridGraph[{10, 10}]];

r[[12, 68]]

1.60899