Questions tagged [sparse-arrays]

Questions on the construction and manipulation of sparse arrays in Mathematica, with functions like SparseArray[] and Band[].

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3
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1answer
85 views

How to write correctly some arguments in SparseArray

I am struggling to put an argument in SparseArray. Let's consider the following example ...
0
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0answers
35 views

Automation procces of a sparse matrix

I have his set of equations obtained by the finite difference method. The variables represent the grid points of a rectangular grid. The size of the rectangular grid is 3*3. ...
1
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0answers
47 views

Parallelizing construction of sparsearray

I'm constructing sparse arrays where blocks of each array are results of the integral defined in integralList ...
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2answers
95 views

Improving large array manipulation

I am doing an iterative program, which uses large arrays/vectors and where the output of one round is used as an input for the next steps but works slowly when dimensions are bigger. In brief, we ...
0
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0answers
41 views

sparse matrix multiplication

Say I have a sparse matrix $M$ with $\sim 50.000 .000$ non zero elements. What is the fastest way to make operations such as : $$M^k X$$ where $X$ is a given vector. Is the operation $MX$ ...
1
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1answer
34 views

Fastest way to convert two associations into a sparse matrix

I have two association $N$ and $C$ $N$ has this form : $N=<|x_1\rightarrow \{x_{1,1},...x_{1,p_1}\},x_2\rightarrow \{x_{2,1},...x_{2,p_2}\}...,x_D\rightarrow \{x_{D1},...x_{Dp_D}\} |>$ $C$ has ...
8
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1answer
111 views

Efficiently populate a Sparsearray for a set of rules for a constrained basis

I want to populate quite a large SparseArray(10^6 x10^6) efficiently. It is basically a spin system Hamiltonian with a constrained Hilbert space. Unlike the examples I have looked at in this forum ...
1
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0answers
75 views

Fast definition of sparse tensor

I'm defining a sparse array through ...
1
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1answer
72 views

Lowest Eigenvalue of a large sparse matrix without choking up the RAM (Corrected) [closed]

I am trying to find the lowest eigenvalue of a large sparse matrix of dimension N (=$3^n$, where n is number of particles in system ) using ...
3
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1answer
82 views

Memory leak when creating a SparseArray

Problem: I have a list e={u,v,w} and wish to construct a sparse matrix with entries {u[i],v[i]}->w[i]. Note that the same ...
2
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0answers
66 views

What is the fastest way to get the lowest eigenvalue and corresponding eigenstate in Mathematica?

I tried to use the Arnoldi method to get the smallest eigenvalue and corresponding eigenstate for large matrix. However, Arnoldi did not give me the desired result: ...
6
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1answer
99 views

Efficient construction of a SparseArray from LIL (list of lists of column entries)

In Python scipy.sparse, there are methods to convert between CSR, CSC, LIL, DOK, etc. implementations of a sparse matrix. What is the most efficient way in Mathematica to construct a ...
4
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0answers
100 views

Insufficient memory problem in Mathematica

I am trying to initialize a 48600 x 48600 packed array from a sparse matrix and a diagonal matrix in Mathematica 8. If S1 is a sparsearray of that size then and S2 is list of 48600 length, then I am ...
3
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2answers
79 views

How to efficiently upsample a greyscale image to generate a representative binary image

I want to create binary images by upsampling a series of greyscale images (192 x 144 resolution) by a factor of 10 with the new pixel values being a pseudorandom distribution of 0's & 1's based on ...
3
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2answers
101 views

Creating a block matrix from arrays of blocks

I am trying to generate a matrix from square blocks. Effectively, I have a $n×n$ matrix polynomial $P(l)$, the $qth$ derivative of $P(l)$ with respect to $l$, which is denoted by $P^{(q)} (l)$, and a ...
5
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2answers
184 views

Permute association key and generate a sparse array

Imagine having an Association Av = <|{1, 4, 2, 3} -> a, {2, 4, 2, 4} -> b|> It can be much longer. I am searching ...
0
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1answer
57 views

How can I define a function using ArrayFlatten without using SetDelayed?

I created a matrix F2 using SparseArray and ArrayFlatten as follows: ...
0
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0answers
59 views

Seeming inconsistencies with “Eigenfunction” [duplicate]

I am working on a problem which involves calculating the spectrum of a family of 2970x2970 Hermitian matrices. I have done similar things with Mathematica in the past, but this time there is an odd, ...
-1
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1answer
61 views

Construct a matrix from blocks of matrices [closed]

I am trying to find eigen values of a matrix system where entries of the matrix are also matrix. This is how my matrix looks: $$ M=\begin{bmatrix} H[j,j] & T[j,j+1] & 0 &0 &....
2
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2answers
103 views

Elegant way to construct a matrix with symbolic entries

I would like to construct a matrix $G$ composed of block matrices $G^{(i)}$ as defined entry-wise below stacked vertically as $$G = \begin{bmatrix} G^{(1)} \\ G^{(2)} \\ \vdots \\ G^{(i)} \\ \vdots \\ ...
3
votes
1answer
48 views

How do I pass indices to a function when constructing a SparseArray?

I am trying to speed up my Mathematica code, so instead of testing and calculating the same thing again and again I want to save the result in a SparseArray. The goal is to generate a matrix which I ...
0
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1answer
76 views

Import and export a list of SparseArrays efficiently?

I have a list of integers dims and a list of SparseArrays bdrs (representing a chain complex ...
0
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0answers
50 views

How to find the rank of a sparse-array list without memory leaks?

I have a very wide list of sparse arrays (I basically just used the numbers as an encoding mechanism for vectors of polynomials), and I want to find out whether they're linearly independent. How ...
7
votes
1answer
191 views

Efficiently populate sparse matrix with band structure

I'm trying to efficiently populate elements of a very large (2^20 x 2^20) symmetric matrix with 1s - luckily the matrix is very sparse, <0.1% filling. Further, the matrix has a very well defined ...
9
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3answers
240 views

Multiplying two complex SparseArray objects, yielding empty SparseArray crashes kernel

Problem: When I multiply together two sparse matrices that should give back the 0 matrix, where at least one element among the two is complex and at least one is not an exact number, the kernel ...
8
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1answer
184 views

SparseArray to list of lists (column entries) efficiently?

Suppose we have a very big very sparse matrix, e.g.: ...
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0answers
55 views

How to apply PolynomialMod to a SparseArray?

I have a list bdrs of SparseArrays, whose entries are polynomials in the variable t with ...
10
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2answers
217 views

`Count` for `SparseArray`

Why does Count not work with SparseArrays, and is there any function I can use to replace it? What would be an efficient ...
7
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0answers
110 views

Memory usage for smallest eigenvalues

I have a bunch of hermitian matrices which are huge (of order 2^17 x 2^17) but extremely sparse so that, when I build the matrices, the usage of RAM is low (say of order 1 GB or similar). The ...
8
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1answer
343 views

Reusing PARDISO symbolic factorization

Is there a way to do this natively in Mathematica? I read in several places that this is possible with LibraryLink, but I don't have a lot of experience with C and so I'm having trouble implementing ...
2
votes
1answer
141 views

Arnoldi method misses eigenvalues degeneracies for very sparse matrices

I am here to signal a problem very very similar to the one already discussed here Wrong eigenvalues from a sparse matrix In particular, I have a very sparse matrix and I am asking just few dominant ...
3
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1answer
107 views

How to speed up my code using Sparse-array possibly?

I created two loops using Parallel table and a table. The outer loop causes a (nstates by nstates) dimension matrix and the inner loop calculates the matrix elements based on their position in the ...
5
votes
1answer
71 views

Create block matrix with secondary diagonals using Band function

Given matrices m1, ... , mk and matrices n1, ... , nk-1, I would like to define a block matrix $$ m=\left( \begin{array}{rrrr}m1 ...
3
votes
1answer
53 views

Fastest way to ArrayFlatten a 2D array of 2D arrays, both for Sparse and Dense

I am using Mathematica 12 and want to know what is the fastest way to transform a 2D array of 2D arrays both for dense and sparse arrays. I remember looking for this a few versions of Mathematica ago, ...
5
votes
1answer
109 views

How to speed up this SparseArray construction

This code is (obviously) getting slower with the growing number of trials, currently running over 5 hours. This stylised example takes 2.5 minutes. It is not entirel illustrative as the real situation ...
1
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0answers
74 views

Why did LinearSolve give me two different results?

Given that I have a sparse array as follows: ...
6
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1answer
60 views

NearestTo causes a kernel crash when applied to a list of SparseArrays [closed]

Nearest and NearestTo cause a kernel crash on Mathematica 12.0.0 for Mac OS X. (running on OS X 10.11.6) when operating on a list of SparseArray vectors. Here's my minimal breaking example: ...
1
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1answer
84 views

How does Indexed work in terms of sparse array

I want to use indexed given that s is an element [0,500] but I am unsure how to write that without getting a format error or a tensor error. ...
0
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0answers
118 views

Determining the price of an option using Black-Scholes

Code for randomly generated interest rates: ...
3
votes
1answer
42 views

Condition in SparseArray does not check the condition for some matrix elements

Consider the following MWE: SparseArray[{{i_, j_} /; (IntegerDigits[i - 1, 2, 2][[1]] == 0) :> 1}, {4, 4}] This should give a $4\times 4$ matrix in which the ...
2
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1answer
43 views

How can I create SparseArray by imposing conditions?

I have two lists: one for directed links list1 and another list2 for the values associated with the links. ...
7
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2answers
252 views

Fastest way to update rows of an array of SparseArrays

I have an array of sparse arrays (check update 3 below for a concrete example that has the same qualitative features as what I use in my real code) , say ...
0
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0answers
44 views

Filling Regions (Blocks) of a Binary Matrix with Different Probabilities

This is an extension of the following question: How to generate binary array whose elements with values 1 are randomly drawn, where the most elegant answer was posted in the comments: ...
7
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1answer
199 views

Efficiently calculating matrix exponential of a recursively generated matrix

Given a matrix $A$ of size $N \times N$, I want to evaluate the function \begin{equation} F(t) = |\operatorname{Tr}(\exp(-i A t))|^2 \end{equation} as a function of $t$. Here, $A[n]$ is constructed ...
2
votes
1answer
53 views

Efficient Linear Operators on SparseArrays

I have a rank four SparseArray of dimension {40, 40, 40, 40}. I wish to apply a linear operator to it, whose form I know abstractly. That is, I have a simple closed form for the action of the operator ...
2
votes
1answer
170 views

How to RowReduce a sparse matrix?

I want to compute the reduced row echelon form of a sparse matrix, but RowReduce returns a dense matrix. Is there a build-in function that computes the reduced form ...
4
votes
3answers
108 views

Sparse matrix processing: flip sign of top-left entries of the matrix

I have a 12k X 12k sparse array (~1% density) and I need to: take the square root of all the elements flip the sign of all the elements in the top-left half of the matrix For example, say that the ...
8
votes
1answer
423 views

Finding the null space of a large sparse matrix

I am trying to compute the null space of a large $n\times n$ sparse matrix. No matter how large the dimension of the matrix is, it will always look like as below: The figure on the left shows the ...
4
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0answers
79 views

ParametricNDSolveValue with SparseArrays

I want to solve large, sparse matrix systems with ParametricNDSolveValue and was hoping to use SparseArray to speed up the computation. However I find that ParametricNDSolveValue doesn't seem to work ...
3
votes
1answer
105 views

Signed cell adjacency matrices (boundary operators)

In How to obtain the cell-adjacency graph of a mesh? there are some great answers that show how to obtain the cell adjacency matrix of a mesh. How would one generalize these to incorporate the ...

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