Merge branch 'master' into 'release'

Zeta normalization was applied twice in tests.

See merge request luechow-group/inPsights!8

.gitlab/issue_templates/Bug Report.md

@@ -0,0 +1,18 @@
+## Problem Definition
+
+<!-- Provide a description of what is the current problem and why you are raising this issue.
+If it's a bug please describe what was the unexpected thing that occured and what was the
+expected behaviour. -->
+
+## Files and Logs
+
+<!-- Provide files and logs of an (minimal) example 
+together with an instruction on how to reproduce the error. -->
+
+
+### System Description
+
+
+Operating system:
+
+inPsights version:

.gitlab/issue_templates/Feature Request.md

@@ -0,0 +1,14 @@
+## Abstract
+
+<!-- Please describe by example what problem you see in the current Amolqc implementation 
+that you would like addressed.-->
+
+## Motivation
+
+<!-- Why do you think this feature should be addressed. 
+What is the value added to the users of Amolqc and why would they want to have it implemented? -->
+
+## Specification
+
+<!-- If the feature is technical in nature 
+please write as detailed as possible a specification of what needs to be built. -->

src/BaseLib/resources/TestMolecules.h

@@ -209,10 +209,13 @@ namespace TestMolecules {
     }
 
     namespace HeH {
+        const MolecularGeometry nuclei = {
+                AtomsVector({
+                                    {Element::He, {0, 0, 0.37}},
+                                    {Element::H, {0, 0, -0.37}}}),{}};
         namespace ElectronsInCores {
             const MolecularGeometry normal = {
-                    AtomsVector({{Element::He,{0, 0, 0.37}},
-                                 {Element::H, {0, 0,-0.37}}}),
+                    nuclei.atoms(),
                     ElectronsVector({{Spin::alpha,{0, 0, 0.37}},
                                      {Spin::alpha,{0, 0, 0.37}},
                                      {Spin::beta, {0, 0,-0.37}}})};

src/Methods/StructuralSimilarity/SOAP/include/LocalSimilarity.h

@@ -29,6 +29,10 @@ namespace SOAP {
                       const TypeSpecificNeighborhoodsAtOneCenter &expansions2,
                       double zeta = General::settings.zeta());
 
+        double kernelDistance(const Environment &e1,
+                              const Environment &e2,
+                              double zeta = General::settings.zeta());
+
         double kernelDistance(const TypeSpecificNeighborhoodsAtOneCenter &expansions1,
                               const TypeSpecificNeighborhoodsAtOneCenter &expansions2,
                               double zeta = General::settings.zeta());

src/Methods/StructuralSimilarity/SOAP/source/LocalSimilarity.cpp

@@ -14,7 +14,7 @@ namespace SOAP {
             auto expansion1 = expander.computeParticularExpansions(e1);
             auto expansion2 = expander.computeParticularExpansions(e2);
 
-            return pow(kernel(expansion1, expansion2), zeta);
+            return kernel(expansion1, expansion2, zeta);
         }
 
         double unnormalizedKernel(const Environment &e1, const Environment &e2) {
@@ -110,9 +110,19 @@ namespace SOAP {
         double kernelDistance(const TypeSpecificNeighborhoodsAtOneCenter &expansions1,
                               const TypeSpecificNeighborhoodsAtOneCenter &expansions2, double zeta) {
 
-            return sqrt(2.0 - 2.0 * kernel(expansions1, expansions1, zeta));
+            return sqrt(2.0 - 2.0 * kernel(expansions1, expansions2, zeta));
         }
 
+        double kernelDistance(const Environment &e1, const Environment &e2, double zeta) {
+            assert(zeta > 0 && "Zeta must be positive.");
+            NeighborhoodExpander expander;
+            auto expansion1 = expander.computeParticularExpansions(e1);
+            auto expansion2 = expander.computeParticularExpansions(e2);
+
+            return kernelDistance(expansion1, expansion2, zeta);
+        }
+
+
 
         double internal::typeAgnostic(const TypeSpecificNeighborhoodsAtOneCenter &expansions) {
             int noneType = 0;

src/Methods/StructuralSimilarity/SOAP/tests/ALocalSimilarityTest.cpp

@@ -24,6 +24,32 @@ class ALocalSimilarityTest : public ::testing::Test {
     };
 };
 
+TEST_F(ALocalSimilarityTest, LocalSimilarityMaxSimilarityBound) {
+    General::settings.mode = General::Mode::chemical;
+    ParticleKit::create(TestMolecules::H2::nuclei);
+
+    auto H2 = TestMolecules::H2::nuclei;
+
+    Environment h0(H2, EnumeratedType<int>(int(Element::H), 0));
+    Environment h1(H2, EnumeratedType<int>(int(Element::H), 1));
+
+    ASSERT_NEAR(LocalSimilarity::kernel(h0, h1), 1.0, eps);
+    ASSERT_NEAR(LocalSimilarity::kernelDistance(h0, h1), 0.0, eps);
+}
+
+TEST_F(ALocalSimilarityTest, LocalSimilarityMinSimilarityBound) {
+    General::settings.mode = General::Mode::chemical;
+    ParticleKit::create(TestMolecules::HeH::nuclei);
+
+    auto HeH = TestMolecules::HeH::nuclei;
+
+    Environment he0(HeH, EnumeratedType<int>(int(Element::He), 0));
+    Environment h0(HeH, EnumeratedType<int>(int(Element::H), 0));
+
+    ASSERT_NEAR(LocalSimilarity::kernel(he0, h0), 0.0, eps);
+    ASSERT_NEAR(LocalSimilarity::kernelDistance(he0, h0), std::sqrt(2.0), eps);
+}
+
 TEST_F(ALocalSimilarityTest, GenericNormalization) {
     ParticleKit::create(molecule);
     General::settings.mode = General::Mode::typeAgnostic;