Initial work on Broombridge v.0.3

.github/workflows/devskim.yml

@@ -0,0 +1,31 @@
+name: DevSkim
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+  workflow_dispatch:
+  schedule:
+    # set schedule to run at 2AM PT on Saturdays
+    - cron: '0 9 * * Sat'
+
+jobs:
+  lint:
+    name: DevSkim
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Run DevSkim scanner
+        uses: microsoft/DevSkim-Action@v1
+
+      - name: Upload DevSkim scan results to GitHub Security tab
+        uses: github/codeql-action/upload-sarif@v2
+        with:
+          sarif_file: devskim-results.sarif

.github/workflows/gh-sync.yml

@@ -0,0 +1,38 @@
+name: Sync GitHub with ADO
+
+on: 
+  issues:
+    types: [closed, edited, deleted, reopened, assigned, unassigned, labeled, unlabeled]
+  issue_comment:
+
+concurrency: 
+  group: ${{ github.event.issue.number }}
+  cancel-in-progress: true
+
+jobs:
+  sync-issues:
+    name: Run gh-sync from GitHub action
+    if: ${{ github.event.label.name == 'tracking' || contains(github.event.issue.labels.*.name, 'tracking') }}
+    runs-on: ubuntu-latest
+    steps:
+      - name: Login to Azure
+        uses: Azure/login@v1
+        with:
+          creds: ${{ secrets.AZURE_CREDENTIALS }}
+
+      - id: AzureKeyVault
+        uses: Azure/get-keyvault-secrets@v1
+        with:
+          keyvault: 'kv-qdk-build'
+          secrets: 'ghSyncBuildPAT'
+
+      - name: 'Trigger gh-sync'
+        uses: microsoft/gh-sync@main
+        with:
+          ado-organization-url: ${{ secrets.ADO_URL }}
+          ado-project: ${{ secrets.ADO_PROJECT }}
+          ado-area-path: ${{ secrets.ADO_AREA_PATH }}
+          github-repo: 'microsoft/QuantumLibraries'
+          issue-number: ${{ github.event.issue.number }}
+          ado-token: ${{ steps.AzureKeyVault.outputs.ghSyncBuildPAT }}
+          github-token: ${{ secrets.GITHUB_TOKEN }}

.sscignore

@@ -0,0 +1,3 @@
+{
+  "cfs": ["CFS0012", "CFS0013"]
+}

Build/manifest.ps1

@@ -38,7 +38,7 @@ $artifacts = @{
         ".\Chemistry\src\DataModel\bin\$Env:BUILD_CONFIGURATION\netstandard2.1\Microsoft.Quantum.Chemistry.DataModel.dll",
         ".\Chemistry\src\Jupyter\bin\$Env:BUILD_CONFIGURATION\netstandard2.1\Microsoft.Quantum.Chemistry.Jupyter.dll",
         ".\Chemistry\src\Runtime\bin\$Env:BUILD_CONFIGURATION\netstandard2.1\Microsoft.Quantum.Chemistry.Runtime.dll",
-        ".\Chemistry\src\Tools\bin\$Env:BUILD_CONFIGURATION\netcoreapp3.1\qdk-chem.dll"
+        ".\Chemistry\src\Tools\bin\$Env:BUILD_CONFIGURATION\net6.0\qdk-chem.dll"
     ) | ForEach-Object { Join-Path $PSScriptRoot (Join-Path ".." $_) };
 } 
 

Build/props/tests.props

@@ -7,7 +7,7 @@
   </PropertyGroup>
 
   <ItemGroup>
-    <PackageReference Include="Microsoft.Quantum.Xunit" Version="0.13.201118141-beta" />
+    <PackageReference Include="Microsoft.Quantum.Xunit" Version="0.26.233415" />
     <PackageReference Include="Microsoft.NET.Test.Sdk" Version="16.4.0" />
     <PackageReference Include="xunit" Version="2.4.1" />
     <PackageReference Include="xunit.runner.visualstudio" Version="2.4.1" />

Build/steps.yml

@@ -1,10 +1,10 @@
 steps:
 
 - task: UseDotNet@2
-  displayName: 'Use .NET Core SDK 3.1.300'
+  displayName: 'Use .NET Core SDK 6.0.x'
   inputs:
     packageType: sdk
-    version: '3.1.300'
+    version: '6.0.x'
 
 
 - task: UsePythonVersion@0

Chemistry.sln

@@ -1,7 +1,7 @@
 
 Microsoft Visual Studio Solution File, Format Version 12.00
-# Visual Studio Version 16
-VisualStudioVersion = 16.0.28803.156
+# Visual Studio Version 17
+VisualStudioVersion = 17.3.32929.385
 MinimumVisualStudioVersion = 10.0.40219.1
 Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "Documentation", "Documentation", "{561759D2-4D2D-4EE3-9565-9AAEC4A7D64B}"
 	ProjectSection(SolutionItems) = preProject
@@ -24,23 +24,27 @@ Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "Standard", "Standard\src\St
 EndProject
 Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "BroombridgeExamples", "BroombridgeExamples", "{F25F3396-EDE5-4A9F-A428-643EB138F00F}"
 	ProjectSection(SolutionItems) = preProject
-		Chemistry\tests\BroombridgeExamples\broombridge_v0.1.yaml = Chemistry\tests\BroombridgeExamples\broombridge_v0.1.yaml
-		Chemistry\tests\BroombridgeExamples\broombridge_v0.2.yaml = Chemistry\tests\BroombridgeExamples\broombridge_v0.2.yaml
-		Chemistry\tests\BroombridgeExamples\hydrogen_0.1.yaml = Chemistry\tests\BroombridgeExamples\hydrogen_0.1.yaml
-		Chemistry\tests\BroombridgeExamples\hydrogen_0.2.yaml = Chemistry\tests\BroombridgeExamples\hydrogen_0.2.yaml
-		Chemistry\tests\BroombridgeExamples\LiH_0.1.yaml = Chemistry\tests\BroombridgeExamples\LiH_0.1.yaml
-		Chemistry\tests\BroombridgeExamples\LiH_0.2.yaml = Chemistry\tests\BroombridgeExamples\LiH_0.2.yaml
+		Chemistry\tests\TestData\Broombridge\broombridge_v0.1.yaml = Chemistry\tests\TestData\Broombridge\broombridge_v0.1.yaml
+		Chemistry\tests\TestData\Broombridge\broombridge_v0.2.yaml = Chemistry\tests\TestData\Broombridge\broombridge_v0.2.yaml
+		Chemistry\tests\TestData\Broombridge\H2O-6_fourfold_v0.3.yaml = Chemistry\tests\TestData\Broombridge\H2O-6_fourfold_v0.3.yaml
+		Chemistry\tests\TestData\Broombridge\H2O-6_trivial_v0.3.yaml = Chemistry\tests\TestData\Broombridge\H2O-6_trivial_v0.3.yaml
+		Chemistry\tests\TestData\Broombridge\hydrogen_0.1.yaml = Chemistry\tests\TestData\Broombridge\hydrogen_0.1.yaml
+		Chemistry\tests\TestData\Broombridge\hydrogen_0.2.yaml = Chemistry\tests\TestData\Broombridge\hydrogen_0.2.yaml
+		Chemistry\tests\TestData\Broombridge\LiH_0.1.yaml = Chemistry\tests\TestData\Broombridge\LiH_0.1.yaml
+		Chemistry\tests\TestData\Broombridge\LiH_0.2.yaml = Chemistry\tests\TestData\Broombridge\LiH_0.2.yaml
 	EndProjectSection
 EndProject
 Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "SamplesTests", "Chemistry\tests\SamplesTests\SamplesTests.csproj", "{2A0E61DB-7187-4359-B5C7-C30FCB1D6800}"
 EndProject
-Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "Metapackage", "Chemistry\src\Metapackage\Metapackage.csproj", "{E8268248-FC5B-4F4E-82FF-5C8CC40950BB}"
+Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "Metapackage", "Chemistry\src\Metapackage\Metapackage.csproj", "{E8268248-FC5B-4F4E-82FF-5C8CC40950BB}"
 EndProject
 Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "Chemistry", "Chemistry", "{43A9F607-5884-4CB9-A455-01E98F5532E2}"
 EndProject
 Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "src", "src", "{812F2D11-792D-4305-8427-01B632A92299}"
 EndProject
-Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "Tools", "Chemistry\src\Tools\Tools.csproj", "{3EF5845F-B348-4DC9-A905-23A6FB9AB421}"
+Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "Tools", "Chemistry\src\Tools\Tools.csproj", "{3EF5845F-B348-4DC9-A905-23A6FB9AB421}"
+EndProject
+Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "DataModelTests", "Chemistry\tests\DataModelTests\DataModelTests.csproj", "{B86DDA60-44F0-4C05-837E-CEA84DBCADF7}"
 EndProject
 Global
 	GlobalSection(SolutionConfigurationPlatforms) = preSolution
@@ -80,6 +84,10 @@ Global
 		{3EF5845F-B348-4DC9-A905-23A6FB9AB421}.Debug|Any CPU.Build.0 = Debug|Any CPU
 		{3EF5845F-B348-4DC9-A905-23A6FB9AB421}.Release|Any CPU.ActiveCfg = Release|Any CPU
 		{3EF5845F-B348-4DC9-A905-23A6FB9AB421}.Release|Any CPU.Build.0 = Release|Any CPU
+		{B86DDA60-44F0-4C05-837E-CEA84DBCADF7}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+		{B86DDA60-44F0-4C05-837E-CEA84DBCADF7}.Debug|Any CPU.Build.0 = Debug|Any CPU
+		{B86DDA60-44F0-4C05-837E-CEA84DBCADF7}.Release|Any CPU.ActiveCfg = Release|Any CPU
+		{B86DDA60-44F0-4C05-837E-CEA84DBCADF7}.Release|Any CPU.Build.0 = Release|Any CPU
 	EndGlobalSection
 	GlobalSection(SolutionProperties) = preSolution
 		HideSolutionNode = FALSE
@@ -93,6 +101,7 @@ Global
 		{E8268248-FC5B-4F4E-82FF-5C8CC40950BB} = {F561BE56-63D8-4C33-A3B3-CF2685BC7A5C}
 		{812F2D11-792D-4305-8427-01B632A92299} = {43A9F607-5884-4CB9-A455-01E98F5532E2}
 		{3EF5845F-B348-4DC9-A905-23A6FB9AB421} = {812F2D11-792D-4305-8427-01B632A92299}
+		{B86DDA60-44F0-4C05-837E-CEA84DBCADF7} = {595D5855-8820-48D7-B5E1-9C88215A866A}
 	EndGlobalSection
 	GlobalSection(ExtensibilityGlobals) = postSolution
 		SolutionGuid = {6869E5BF-551A-40F1-9B6B-D1B27A5676CB}

Chemistry/src/DataModel/DataModel.csproj

@@ -34,7 +34,7 @@
     <PackageReference Include="Microsoft.Extensions.Logging" Version="3.0.0" />
     <PackageReference Include="Microsoft.Extensions.Logging.Console" Version="3.0.0" />
     <PackageReference Include="Microsoft.Extensions.Logging.Debug" Version="3.0.0" />
-    <PackageReference Include="Newtonsoft.Json" Version="12.0.3" />
+    <PackageReference Include="Newtonsoft.Json" Version="13.0.1" />
     <PackageReference Include="YamlDotNet" Version="8.1.2" />
     <PackageReference Include="Serilog.Extensions.Logging.File" Version="1.1.0" />
   </ItemGroup>

Chemistry/src/DataModel/OrbitalIntegral/OrbitalIntegral.cs

@@ -24,6 +24,17 @@ public enum Convention
             Dirac, Mulliken
         }
 
+        // NB [Design note]: this intentionally duplicates the corresponding
+        //                   enum in the V0_3 class, allowing forward versions
+        //                   to add or modify permutation symmetries without
+        //                   retroactively changing the definition of V0_3.
+        public enum PermutationSymmetry
+        {
+            Eightfold,
+            Fourfold,
+            Trivial
+        }
+
         /// <summary>
         /// Indices of orbitals in the overlap integral.
         /// </summary>
@@ -34,28 +45,35 @@ public enum Convention
         /// </summary>
         public double Coefficient;
 
+        /// <summary>
+        /// Symmetry of the orbital overlap integral.
+        /// </summary>
+        public PermutationSymmetry Symmetry = PermutationSymmetry.Eightfold;
+
         /// <summary>
         /// Parameterless constructors. Sets this as an empty OrbitalIntegral with coefficient 0.0
         /// </summary>
         public OrbitalIntegral() : this(0.0)
         {
         }
 
-        public OrbitalIntegral(double coefficient)
+        /// <param name="coefficient">coefficient of orbital integral.</param>
+        /// <param name="symmetry">Convention of symmetry of orbital indices.</param>
+        public OrbitalIntegral(double coefficient, PermutationSymmetry symmetry = PermutationSymmetry.Eightfold) : this(new int[] { }, coefficient, symmetry)
         {
-            OrbitalIndices = new int[] { };
-            Coefficient = coefficient;
         }
 
         /// <summary>
         /// Constructor for orbital integral object.
         /// </summary>
         /// <param name="orbitalIndices">Array of orbital indices in Dirac notation.</param>
         /// <param name="coefficient">coefficient of orbital integral.</param>
-        public OrbitalIntegral(IEnumerable<int> orbitalIndices, double coefficient = 0.0) 
+        /// <param name="symmetry">Convention of symmetry of orbital indices.</param>
+        public OrbitalIntegral(IEnumerable<int> orbitalIndices, double coefficient = 0.0, PermutationSymmetry symmetry = PermutationSymmetry.Eightfold) 
         {
             OrbitalIndices = orbitalIndices.ToArray();
             Coefficient = coefficient;
+            Symmetry = symmetry;
         }
 
         /// <summary>
@@ -64,10 +82,12 @@ public OrbitalIntegral(IEnumerable<int> orbitalIndices, double coefficient = 0.0
         /// <param name="orbitalIndices">Array of orbital indices.</param>
         /// <param name="coefficient">coefficient of orbital integral.</param>
         /// <param name="convention">Convention for ordering of orbital indices.</param>
-        public OrbitalIntegral(IEnumerable<int> orbitalIndices, double coefficient, Convention convention = Convention.Mulliken)
+        /// <param name="symmetry">Convention of symmetry of orbital indices.</param>
+        public OrbitalIntegral(IEnumerable<int> orbitalIndices, double coefficient, PermutationSymmetry symmetry, Convention convention = Convention.Mulliken)
         {
             OrbitalIndices = ConvertIndices(orbitalIndices, convention, Convention.Dirac);
             Coefficient = coefficient;
+            Symmetry = symmetry;
         }
 
         public TermType.OrbitalIntegral TermType
@@ -107,6 +127,40 @@ public void ResetSign()
         /// <returns>Length of orbital indices.</returns>
         public int Length => OrbitalIndices.Length;
 
+        private static int[][] EnumerateTwoBodyPermutations(PermutationSymmetry symmetry, int i, int j, int k, int l) =>
+            symmetry switch
+            {
+                // In Mulliken notation,
+                // (ij|kl) = (ij|lk) = (ji|kl) = (ji|lk) =
+                // (kl|ij) = (lk|ij) = (kl|ji) = (lk|ji)
+                // Orbital indices are in Dirac notation.
+                PermutationSymmetry.Eightfold => new int[][]
+                {
+                    new int[] { i, j, k, l }, // 0123 
+                    new int[] { j, i, l, k }, // 1032
+                    new int[] { k, l, i, j }, // 2301
+                    new int[] { l, k, j, i }, // 3210
+                    new int[] { i, k, j, l }, // 0213
+                    new int[] { k, i, l, j }, // 2031
+                    new int[] { j, l, i, k }, // 1302
+                    new int[] { l, j, k, i }  // 3120
+                },
+                // In Mulliken notation,
+                // (ij|kl) = (ji|lk) = (kl|ij) = (lk|ji) 
+                // Orbital indices are in Dirac notation.
+                PermutationSymmetry.Fourfold => new int[][]
+                {
+                    new int[] { i, j, k, l }, // Identity
+                    new int[] { l, k, j, i }, // Complex conjugation
+                    new int[] { j, i, l, k }, // Change of variables
+                    new int[] { k, l, i, j }, // Complex conjugation & Change of variables
+                },
+                PermutationSymmetry.Trivial => new int[][]
+                {
+                    new int[] { i, j, k, l }
+                },
+                _ => throw new Exception($"Permutation symmetry {symmetry} is not valid for two-body permutations.")
+            };
 
         /// <summary>
         /// Enumerates over all orbital integrals with the same coefficient
@@ -128,25 +182,13 @@ public OrbitalIntegral[] EnumerateOrbitalSymmetries()
                     new int[] {i, j},
                     new int[] {j, i}
                 };
-                return symmetries.Distinct(new ArrayEqualityComparer<int>()).Select(o => new OrbitalIntegral(o, coefficient)).ToArray();
+                return symmetries.Distinct(new ArrayEqualityComparer<int>()).Select(o => new OrbitalIntegral(o, coefficient, Symmetry)).ToArray();
             }
             else if (OrbitalIndices.Length == 4)
             {
-                var i = OrbitalIndices[0];
-                var j = OrbitalIndices[1];
-                var k = OrbitalIndices[2];
-                var l = OrbitalIndices[3];
-                var symmetries = new int[][] {
-                    new int[] { i, j, k, l }, // 0123
-                    new int[] { j, i, l, k }, // 1032
-                    new int[] { k, l, i, j }, // 2301
-                    new int[] { l, k, j, i }, // 3210
-                    new int[] { i, k, j, l }, // 0213
-                    new int[] { k, i, l, j }, // 2031
-                    new int[] { j, l, i, k }, // 1302
-                    new int[] { l, j, k, i }  // 3120
-                };
-                return symmetries.Distinct(new ArrayEqualityComparer<int>()).Select(o => new OrbitalIntegral(o, coefficient)).ToArray();
+                return EnumerateTwoBodyPermutations(Symmetry, OrbitalIndices[0], OrbitalIndices[1], OrbitalIndices[2], OrbitalIndices[3])
+                    .Distinct(new ArrayEqualityComparer<int>())
+                    .Select(o => new OrbitalIntegral(o, coefficient, Symmetry)).ToArray();
             }
             else
             {
@@ -160,7 +202,7 @@ public OrbitalIntegral[] EnumerateOrbitalSymmetries()
         public OrbitalIntegral Clone()
         {
             var newArray = OrbitalIndices.Clone<int>();
-            return new OrbitalIntegral(newArray, Coefficient);
+            return new OrbitalIntegral(newArray, Coefficient, Symmetry);
         }
 
         /// <summary>
@@ -172,14 +214,14 @@ public OrbitalIntegral ToCanonicalForm()
         {
             var symmetries = EnumerateOrbitalSymmetries().Select(o => o.OrbitalIndices).ToList();
             symmetries.Sort(new ArrayLexicographicComparer<int>());
-            return new OrbitalIntegral(symmetries.First(), Coefficient);
+            return new OrbitalIntegral(symmetries.First(), Coefficient, Symmetry);
         }
 
         /// <summary>
         /// Checks of this orbital integral has indices sorted in canonical order.
         /// </summary>
         /// <returns>Returns <see cref="bool"/> if the orbital integral indices are canonically sorted
-        /// and <see cref="false"/> otherwise.
+        /// and <c>false</c> otherwise.
         /// </returns>
         public bool IsInCanonicalOrder()
         {

Chemistry/src/DataModel/OrbitalIntegral/OrbitalIntegralExtensions.cs

@@ -20,7 +20,6 @@ namespace Microsoft.Quantum.Chemistry.OrbitalIntegrals
     /// </summary>
     public static partial class Extensions
     {
-
         /// <summary>
         /// Method for constructing a fermion Hamiltonian from an orbital integral Hamiltonian.
         /// </summary>
@@ -34,7 +33,7 @@ public static partial class Extensions
             var nOrbitals = sourceHamiltonian.SystemIndices.Max() + 1;
             var hamiltonian = new FermionHamiltonian();
             Func<OrbitalIntegral, double, IEnumerable<(HermitianFermionTerm, DoubleCoeff)>> conversion = 
-                (orb, coeff) => new OrbitalIntegral(orb.OrbitalIndices, coeff).ToHermitianFermionTerms(nOrbitals, indexConvention)
+                (orb, coeff) => new OrbitalIntegral(orb.OrbitalIndices, coeff, orb.Symmetry).ToHermitianFermionTerms(nOrbitals, indexConvention)
                 .Select(o => (o.Item1, o.Item2.ToDoubleCoeff()));
 
             foreach (var termType in sourceHamiltonian.Terms)
@@ -49,7 +48,6 @@ public static partial class Extensions
             return hamiltonian;
         }
 
-
         /// <summary>
         /// Creates all fermion terms generated by all symmetries of an orbital integral.
         /// </summary>
@@ -95,7 +93,9 @@ public static partial class Extensions
         {
             // One-electron orbital integral symmetries
             // ij = ji
-            var pqSpinOrbitals = orbitalIntegral.EnumerateOrbitalSymmetries().EnumerateSpinOrbitals();
+            var pqSpinOrbitals = orbitalIntegral
+                .EnumerateOrbitalSymmetries()
+                .EnumerateSpinOrbitals();
 
             var coefficient = orbitalIntegral.Coefficient;
 

Chemistry/src/DataModel/OrbitalIntegral/OrbitalIntegralHamiltonian.cs

@@ -32,7 +32,7 @@ public OrbitalIntegralHamiltonian(IEnumerable<OrbitalIntegral> terms) : base()
         /// <param name="orbitalIntegral">Orbital integral to add to Hamiltonian.</param>
         public void Add(OrbitalIntegral orbitalIntegral)
         {
-            Add(new OrbitalIntegral(orbitalIntegral.OrbitalIndices), orbitalIntegral.Coefficient);
+            Add(new OrbitalIntegral(orbitalIntegral.OrbitalIndices, symmetry: orbitalIntegral.Symmetry), orbitalIntegral.Coefficient);
         }
 
         /// <summary>