euro-hpc-pl · lpawela · Apr 9, 2024 · Sep 8, 2021 · Sep 9, 2021 · Oct 18, 2021
diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -1,48 +1,41 @@
 name: CI
 on:
-  - push
-  - pull_request
+  pull_request:
+    branches:
+      - master
+  push:
 jobs:
   test:
-    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }}
-    runs-on: ${{ matrix.os }}
+    name: Julia ${{ matrix.version }}
+    runs-on: [self-hosted,titan,gpu]
     strategy:
       fail-fast: false
       matrix:
         version:
           - '1.9'
           - '1.10'
-        os:
-          - ubuntu-latest
-          - macOS-latest
-        arch:
-          - x64
     steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@v1
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
-          arch: ${{ matrix.arch }}
       - uses: julia-actions/julia-buildpkg@latest
       - uses: julia-actions/julia-runtest@latest
         env:
           JULIA_NUM_THREADS: 4
       - uses: julia-actions/julia-processcoverage@v1
-      # - uses: codecov/codecov-action@v1
-      #   with:
-      #     file: lcov.info
       - uses: coverallsapp/github-action@master
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}
           path-to-lcov: lcov.info
-          flag-name: job-${{ matrix.version }}-${{ matrix.os }}-${{ matrix.arch }}
           parallel: true
-
+          flag-name: run-${{ matrix.version }}
   finish:
     needs: test
-    runs-on: ubuntu-latest
+    runs-on: [self-hosted,titan]
     steps:
-      - uses: coverallsapp/github-action@master
+      - name: Close parallel build
+        uses: coverallsapp/github-action@v1
         with:
-          github-token: ${{ secrets.GITHUB_TOKEN }}
           parallel-finished: true
+          carryforward: "run-1.9,run-1.10"
diff --git a/Project.toml b/Project.toml
@@ -1,22 +1,34 @@
 name = "SpinGlassNetworks"
 uuid = "b7f6bd3e-55dc-4da6-96a9-ef9dbec6ac19"
-authors = ["Krzysztof Domino <[email protected]>", "Anna Maria Dziubyna <annamariadziubyna@gmail.com>", "Bartłomiej Gardas <[email protected]>", "Konrad Jałowiecki <[email protected]>", "Łukasz Pawela <[email protected]>", "Marek M. Rams <[email protected]>"]
-version = "0.3.2"
+authors = ["Anna Maria Dziubyna <[email protected]>", "Tomasz Śmierzchalski <smierzchalski.tomek@gmail.com>", "Bartłomiej Gardas <[email protected]>", "Konrad Jałowiecki <[email protected]>", "Łukasz Pawela <[email protected]>", "Marek M. Rams <[email protected]>"]
+version = "1.0.0"
 
 [deps]
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
+CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
+HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
+JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 LabelledGraphs = "605abd48-4d17-4660-b914-d4df33194460"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+MKL = "33e6dc65-8f57-5167-99aa-e5a354878fb2"
 MetaGraphs = "626554b9-1ddb-594c-aa3c-2596fe9399a5"
+SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+SpinGlassTensors = "7584fc6a-5a23-4eeb-8277-827aab0146ea"
 
 [compat]
-CSV = "0.8 - 0.10"
-DocStringExtensions = "0.8"
-Graphs = "1.9"
-LabelledGraphs = "^0.4.4"
-MetaGraphs = "0.7.2"
+CSV = "0.8"
+CUDA = "4.4"
+DocStringExtensions = "0.9"
+Graphs = "1.9.0"
+HDF5 = "0.17"
+JLD2 = "0.4"
+LabelledGraphs = "0.4.4"
+MKL = "0.4.2"
+MetaGraphs = "0.7"
+SparseArrays = "1.9"
+SpinGlassTensors = "1"
 julia = "1.9, 1.10"
 
 [extras]

diff --git a/README.md b/README.md
@@ -1,2 +1,5 @@
 [![Coverage Status](https://coveralls.io/repos/github/iitis/SpinGlassNetworks.jl/badge.svg?branch=master)](https://coveralls.io/github/iitis/SpinGlassNetworks.jl?branch=master)
 # SpinGlassNetworks.jl
+Part of SpinGlassPEPS package. It constitutes the basis for the preparation of tensors and operations on them.
+
+We don't expect the user to interact with this package, as it is more of a "back-end" type. Nevertheless, we provide API references should the need arise.
diff --git a/docs/make.jl b/docs/make.jl
@@ -1,21 +1,23 @@
 using Documenter, SpinGlassNetworks
 
 _pages = [
-    "Introduction" => "index.md",
     "User guide" => "userguide.md",
-    "API Reference" => "api.md"
+    "Ising graph" => "ising.md",
+    "Lattice geometries" => "lattice.md",
+    "Clustered hamiltonian" => "clh.md",
+    "Local dimensional reduction" => "bp.md",
+    "API Reference for auxiliary functions" => "api.md",
 ]
 
 # ============================
-format = Documenter.HTML(edit_link = "master",
-                         prettyurls = get(ENV, "CI", nothing) == "true",
-)
+format =
+    Documenter.HTML(edit_link = "master", prettyurls = get(ENV, "CI", nothing) == "true")
 
 # format = Documenter.LaTeX(platform="none")
 
 makedocs(
-    sitename="SpinGlassNetworks.jl",
+    sitename = "SpinGlassNetworks.jl",
     modules = [SpinGlassNetworks],
     pages = _pages,
-    format = format
-    )
+    format = format,
+)
diff --git a/docs/src/api.md b/docs/src/api.md
@@ -1,36 +1,66 @@
 # Library
 
----
-
 ```@meta
 CurrentModule = SpinGlassNetworks
 ```
 
 ## Ising Graphs
-
 ```@docs
-ising_graph
-biases
-couplings
-cluster
+inter_cluster_edges
 prune
-rank_vec
+couplings
 ```
 
-## Factor Graphs
+## Clustered Hamiltonian
+```@docs
+split_into_clusters
+decode_clustered_hamiltonian_state
+rank_reveal
+energy
+energy_2site
+cluster_size
+bond_energy
+exact_cond_prob
+truncate_clustered_hamiltonian
+```
 
+## Belief propagation
 ```@docs
-factor_graph
-decode_factor_graph_state
+local_energy
+interaction_energy
+get_neighbors
+MergedEnergy
+update_message
+merge_vertices_cl_h
+projector
+SparseCSC
 ```
 
-## Auxiliary Functions
+## Projectors
+```@docs
+PoolOfProjectors
+get_projector!
+add_projector!
+empty!
+```
 
+## Spectrum
 ```@docs
-brute_force
-energy
-full_spectrum
+Spectrum
+matrix_to_integers
 gibbs_tensor
-rank_reveal
-super_square_lattice
+brute_force
+```
+
+## Truncate
+```@docs
+truncate_clustered_hamiltonian_1site_BP
+truncate_clustered_hamiltonian_2site_energy
+select_numstate_best
+```
+
+## Auxiliary Functions
+```@docs
+zephyr_to_linear
+load_openGM
 ```
diff --git a/docs/src/bp.md b/docs/src/bp.md
@@ -0,0 +1,9 @@
+## Belief propagation
+
+Local dimensional reduction can be achieved by selectively choosing states in the clustered Hamiltonian that have the lowest local energy in the cluster. This approach aims to reduce the dimensionality of the problem by focusing on the most relevant and energetically favorable states. It can be done by truncation based on energy or truncation based on Loopy Belief Propagation.
+
+```@docs
+clustered_hamiltonian_2site
+belief_propagation
+truncate_clustered_hamiltonian_2site_BP
+```
diff --git a/docs/src/clh.md b/docs/src/clh.md
@@ -0,0 +1,24 @@
+# Introduction
+A clustered Hamiltonian is a graphical representation that allows for a convenient and intuitive way to describe the structure of a network.
+
+The concept of a clustered Hamiltonian within `SpinGlassNetworks.jl` introduces a mechanism for organizing spins into desired geometries, facilitating a structured approach to modeling complex spin systems. Analogous to a standard factor graph, the clustered Hamiltonian involves nodes that represent tensors within the underlying network. The edges connecting these nodes in the clustered Hamiltonian correspond to the indices shared between the respective tensors in the tensor network.
+
+```@docs
+clustered_hamiltonian
+```
+
+## Simple example
+
+```@example
+using SpinGlassNetworks
+
+# Prepare simple instance
+instance = "$(@__DIR__)/../../src/instances/square_diagonal/5x5/diagonal.txt"
+ig = ising_graph(instance)
+
+# Create clustered Hamiltonian
+cl_h = clustered_hamiltonian(
+    ig,
+    cluster_assignment_rule = super_square_lattice((5,5,4))
+)
+```
diff --git a/docs/src/images/annealing.png b/docs/src/images/annealing.png
diff --git a/docs/src/images/bb.png b/docs/src/images/bb.png
diff --git a/docs/src/images/branch_bound.png b/docs/src/images/branch_bound.png
diff --git a/docs/src/images/clustering.png b/docs/src/images/clustering.png
diff --git a/docs/src/images/contract.png b/docs/src/images/contract.png
diff --git a/docs/src/images/explain.png b/docs/src/images/explain.png
diff --git a/docs/src/images/graphs.png b/docs/src/images/graphs.png
diff --git a/docs/src/images/lattice.png b/docs/src/images/lattice.png
diff --git a/docs/src/images/layout.png b/docs/src/images/layout.png
diff --git a/docs/src/images/peg.png b/docs/src/images/peg.png
diff --git a/docs/src/images/pegasus.png b/docs/src/images/pegasus.png
diff --git a/docs/src/images/peps_graph.png b/docs/src/images/peps_graph.png
diff --git a/docs/src/images/prob.png b/docs/src/images/prob.png
diff --git a/docs/src/images/sd.png b/docs/src/images/sd.png
diff --git a/docs/src/images/square_cross_double.png b/docs/src/images/square_cross_double.png
diff --git a/docs/src/images/square_cross_single.png b/docs/src/images/square_cross_single.png
diff --git a/docs/src/images/square_diag.png b/docs/src/images/square_diag.png
diff --git a/docs/src/images/square_double.png b/docs/src/images/square_double.png
diff --git a/docs/src/images/square_single.png b/docs/src/images/square_single.png
diff --git a/docs/src/images/svd_truncate.png b/docs/src/images/svd_truncate.png
diff --git a/docs/src/images/trans.png b/docs/src/images/trans.png
diff --git a/docs/src/images/zep.png b/docs/src/images/zep.png
diff --git a/docs/src/images/zephyr.png b/docs/src/images/zephyr.png
diff --git a/docs/src/images/zipper.png b/docs/src/images/zipper.png
diff --git a/docs/src/ising.md b/docs/src/ising.md
@@ -0,0 +1,25 @@
+# Ising model
+
+The Ising model is a mathematical model used to describe the behavior of interacting particles, such as atoms or molecules, in a magnetic field. In the Ising model, each particle is represented as a binary variable $s_i$ that can take on the values of either +1 or -1. The total energy of the system is given by the Hamiltonian:
+
+$H =  \sum_{(i,j) \in \mathcal{E}} J_{ij} s_i s_j + \sum_{i} h_i s_i$
+
+where $J_{ij}$ is the coupling constant between particles $i$ and $j$, $h_i$ is the external magnetic field at particle $i$, and the sum is taken over all pairs of particles and all particles in the system $\mathcal{E}$, respectively.
+
+In `SpinGlassPEPS.jl` package, an Ising graph can be created using the command `ising_graph`.
+```@docs
+ising_graph
+```
+
+## Simple example
+In this simple example below we show how to create Ising graph of a instance given as txt file in a format (i, j, Jij). The resulting graph has vertices corresponding to positions of spins in the system and edges defining coupling strength between spins. Each vertex contains information about local field.
+
+```@example
+using SpinGlassNetworks
+# Create Ising instance
+instance = "$(@__DIR__)/../../src/instances/square_diagonal/5x5/diagonal.txt"
+ig = ising_graph(instance)
+
+# View graph properties
+@show biases(ig), couplings(ig)
+```