Add fragment patch, fix importing of occ elat results

resources/surface_description.json

@@ -113,9 +113,9 @@
       "description": "<p>Difference between the alpha and beta electron densities</p>"
     },
     "fragment_patch": {
-      "cmap": "Qualitative14Dark",
+      "cmap": "Turbo",
       "displayName": "Fragment Patch",
-      "occName": "fragment",
+      "occName": "fragment_patch",
       "description": "<p>The index of the associated neighbouring fragment/molecule</p>"
     },
     "de_idx": {

src/core/chemicalstructure.cpp

@@ -10,9 +10,15 @@
 #include <occ/core/kdtree.h>
 
 namespace impl {
-template <typename Index>
+
+MaybeFragment getFragmentForAtom(const ChemicalStructure &structure,
+                                 GenericAtomIndex atomIndex) {
+  auto fragIndex = structure.fragmentIndexForGeneralAtom(atomIndex);
+  return structure.getFragment(fragIndex);
+}
+
 MaybeFragment getFragmentForAtom(const ChemicalStructure &structure,
-                                 Index atomIndex) {
+                                 int atomIndex) {
   auto fragIndex = structure.fragmentIndexForAtom(atomIndex);
   return structure.getFragment(fragIndex);
 }
@@ -572,7 +578,7 @@ FragmentIndex ChemicalStructure::fragmentIndexForAtom(int atomIndex) const {
 }
 
 FragmentIndex
-ChemicalStructure::fragmentIndexForAtom(GenericAtomIndex idx) const {
+ChemicalStructure::fragmentIndexForGeneralAtom(GenericAtomIndex idx) const {
   return fragmentIndexForAtom(genericIndexToIndex(idx));
 }
 
@@ -627,7 +633,7 @@ QColor ChemicalStructure::atomColor(GenericAtomIndex atomIndex) const {
       return Qt::black;
   }
   case AtomColoring::Fragment: {
-    auto fragIndex = fragmentIndexForAtom(atomIndex);
+    auto fragIndex = fragmentIndexForGeneralAtom(atomIndex);
     return getFragmentColor(fragIndex);
   }
   case AtomColoring::Index:
@@ -1163,9 +1169,10 @@ QString ChemicalStructure::getFragmentLabelForAtoms(
     return "None";
 
   // Get unique fragment indices for the atoms
-  ankerl::unordered_dense::set<FragmentIndex, FragmentIndexHash> uniqueFragments;
+  ankerl::unordered_dense::set<FragmentIndex, FragmentIndexHash>
+      uniqueFragments;
   for (const auto &idx : idxs) {
-    uniqueFragments.insert(fragmentIndexForAtom(idx));
+    uniqueFragments.insert(fragmentIndexForGeneralAtom(idx));
   }
 
   // Get chemical formula for these atoms

src/core/chemicalstructure.h

@@ -187,7 +187,7 @@ class ChemicalStructure : public QObject {
 
   inline size_t numberOfFragments() const { return m_fragments.size(); }
   FragmentIndex fragmentIndexForAtom(int) const;
-  FragmentIndex fragmentIndexForAtom(GenericAtomIndex) const;
+  virtual FragmentIndex fragmentIndexForGeneralAtom(GenericAtomIndex) const;
 
   MaybeFragment getFragmentForAtom(int) const;
   MaybeFragment getFragmentForAtom(GenericAtomIndex) const;

src/crystal/crystalstructure.cpp

@@ -599,6 +599,7 @@ void CrystalStructure::completeFragmentContaining(GenericAtomIndex index) {
   }
   updateBondGraph();
 }
+
 void CrystalStructure::completeFragmentContaining(int atomIndex) {
   if (atomIndex < 0 || atomIndex >= numberOfAtoms())
     return;
@@ -1098,6 +1099,17 @@ const FragmentMap &CrystalStructure::symmetryUniqueFragments() const {
   return m_symmetryUniqueFragments;
 }
 
+FragmentIndex
+CrystalStructure::fragmentIndexForGeneralAtom(GenericAtomIndex index) const {
+  if(m_unitCellAtomFragments.size() == 0) return ChemicalStructure::fragmentIndexForGeneralAtom(index);
+  qDebug() << m_unitCellAtomFragments.size() << index.unique;
+  FragmentIndex fragmentIndex = m_unitCellAtomFragments.at(index.unique);
+  fragmentIndex.h += index.x;
+  fragmentIndex.k += index.y;
+  fragmentIndex.l += index.z;
+  return fragmentIndex;
+}
+
 Fragment::State CrystalStructure::getSymmetryUniqueFragmentState(
     FragmentIndex fragmentIndex) const {
   const auto kv = m_symmetryUniqueFragments.find(fragmentIndex);
@@ -1331,7 +1343,9 @@ void CrystalStructure::setPairInteractionsFromDimerAtoms(
       params.fragmentDimer = ud;
       params.nearestAtomDistance = d.nearestAtomDistance;
       params.centroidDistance = d.centroidDistance;
-      params.hasInversionSymmetry = false;
+      // TODO better handling of inversion symmetry
+      QString modelName = pair->interactionModel();
+      params.hasInversionSymmetry = !(modelName == "cg" || modelName.startsWith("crystalclear"));
       pair->setParameters(params);
       p->add(pair);
     }

src/crystal/crystalstructure.h

@@ -43,6 +43,7 @@ class CrystalStructure : public ChemicalStructure {
   inline const auto &spaceGroup() const { return m_crystal.space_group(); }
   occ::Mat3N convertCoordinates(const occ::Mat3N &pos, ChemicalStructure::CoordinateConversion) const override;
 
+  FragmentIndex fragmentIndexForGeneralAtom(GenericAtomIndex) const override;
   void deleteFragmentContainingAtomIndex(int atomIndex) override;
   void deleteIncompleteFragments() override;
   void deleteAtoms(const std::vector<GenericAtomIndex> &) override;

src/crystalx.cpp

@@ -883,6 +883,10 @@ void Crystalx::loadExternalFileData(QString filename) {
     showStatusMessage(
         QString("Loading crystal clear output from %1").arg(filename));
     project->loadCrystalClearJson(filename);
+  }
+  if (filename.endsWith("elat_results.json")) {
+    showStatusMessage(QString("Loading occ elat output from %1").arg(filename));
+    project->loadCrystalClearJson(filename);
   } else if (filename.endsWith("surface.json")) {
     showStatusMessage(QString("Loading crystal surface from %1").arg(filename));
     project->loadCrystalClearSurfaceJson(filename);

src/graphics/scene.cpp

@@ -238,7 +238,8 @@ void Scene::setSelectStatusForAtomDoubleClick(int atom) {
   auto atomIndex = m_structure->indexToGenericIndex(atom);
   if (m_structure->testAtomFlag(atomIndex, AtomFlag::Contact))
     return;
-  const auto fragmentIndex = m_structure->fragmentIndexForAtom(atomIndex);
+  const auto fragmentIndex =
+      m_structure->fragmentIndexForGeneralAtom(atomIndex);
   const auto &atomIndices = m_structure->atomIndicesForFragment(fragmentIndex);
   auto idx = m_structure->indexToGenericIndex(atom);
   m_structure->setAtomFlag(idx, AtomFlag::Selected, true);
@@ -1424,7 +1425,7 @@ void Scene::generateAllExternalFragments() {
     qDebug() << "Generate external fragment";
     if (!mesh)
       return;
-    occ::IVec de_idxs = mesh->vertexProperty("de_idx").cast<int>();
+    occ::IVec de_idxs = mesh->vertexProperty("External atom index").cast<int>();
     qDebug() << "num de_idxs" << de_idxs.size();
     ankerl::unordered_dense::set<int> unique(de_idxs.data(),
                                              de_idxs.data() + de_idxs.size());
@@ -1540,7 +1541,7 @@ void Scene::colorSelectedAtoms(const QColor &color, bool fragments) {
   auto idxs = m_structure->atomsWithFlags(AtomFlag::Selected);
   if (fragments) {
     for (const auto &idx : idxs) {
-      const auto frag = m_structure->fragmentIndexForAtom(idx);
+      const auto frag = m_structure->fragmentIndexForGeneralAtom(idx);
       m_structure->setFragmentColor(frag, color);
     }
   } else {

src/io/crystalclear.cpp

@@ -56,10 +56,15 @@ CrystalStructure *loadCrystalClearJson(const QString &filename) {
     return nullptr;
 
   occ::crystal::Crystal crystal = loadOccCrystal(json["crystal"]);
+  // TODO check if it's cg and then set symmetry of interactions
 
   QList<PairInteractions::PairInteractionList> interactions;
   QList<QList<DimerAtoms>> atomIndices;
 
+  QString modelName = "cg";
+  if(json.contains("model")) {
+    modelName = QString::fromStdString(json["model"]);
+  }
   // Parse neighbor energies
   auto pairsArray = json["pairs"];
   interactions.resize(pairsArray.size());
@@ -69,7 +74,7 @@ CrystalStructure *loadCrystalClearJson(const QString &filename) {
     auto &neighbors = interactions[i];
     auto &offsets = atomIndices[i];
     for (int j = 0; j < siteEnergies.size(); ++j) {
-      auto *pair = new PairInteraction("cg");
+      auto *pair = new PairInteraction(modelName);
       auto dimerObj = siteEnergies[j];
       auto energiesObj = dimerObj["energies"];
       pair->setLabel(QString::number(j + 1));

src/volume/isosurface_calculator.cpp

@@ -134,6 +134,37 @@ QString IsosurfaceCalculator::surfaceName() {
       .arg(m_parameters.isovalue);
 }
 
+void setFragmentPatchForMesh(Mesh * mesh, ChemicalStructure *structure) {
+  if(!mesh) return;
+  if(!structure) return;
+  ankerl::unordered_dense::map<FragmentIndex, int, FragmentIndexHash> fragmentIndices;
+
+  Mesh::ScalarPropertyValues fragmentPatch(mesh->numberOfVertices());
+  fragmentPatch.setConstant(-1.0);
+  occ::IVec de_idxs = mesh->vertexProperty("External atom index").cast<int>();
+  auto atomIndices = mesh->atomsOutside();
+  for (int i = 0; i < de_idxs.size(); i++) {
+    int idx = de_idxs(i);
+    if (idx >= atomIndices.size()) {
+        continue;
+    }
+    const auto &genericIndex = atomIndices[idx];
+    FragmentIndex fidx = structure->fragmentIndexForGeneralAtom(genericIndex);
+    if(fidx.u == -1)  {
+      continue;
+    }
+    const auto kv = fragmentIndices.find(fidx);
+    if(kv != fragmentIndices.end()) {
+      fragmentPatch(i) = kv->second;
+    }
+    else {
+      fragmentPatch(i) = fragmentIndices.size();
+      fragmentIndices.insert({fidx, fragmentIndices.size()});
+    }
+  }
+  mesh->setVertexProperty("Fragment Patch", fragmentPatch);
+}
+
 void IsosurfaceCalculator::surfaceComplete() {
   qDebug() << "Task" << m_name << "finished in IsosurfaceCalculator";
   QList<Mesh *> meshes = io::loadMeshes(m_fileNames);
@@ -155,6 +186,7 @@ void IsosurfaceCalculator::surfaceComplete() {
     }
     mesh->setAtomsInside(m_atomsInside);
     mesh->setAtomsOutside(m_atomsOutside);
+    setFragmentPatchForMesh(mesh, params.structure);
     mesh->setParent(m_structure);
     // create the child instance that will be shown
     MeshInstance *instance = new MeshInstance(mesh);