disorderedmaterials · trisyoungs · Jul 8, 2026 · Jul 6, 2026 · Jul 6, 2026 · Jul 6, 2026
diff --git a/src/base/version.h b/src/base/version.h
@@ -3,9 +3,6 @@
 
 #pragma once
 
-// Forward Declarations
-class CoreData;
-
 // Version Counter
 class VersionCounter
 {

diff --git a/src/classes/configuration.h b/src/classes/configuration.h
@@ -223,10 +223,6 @@ class Configuration : public Serialisable
      * Serialisation
      */
     public:
-    // Write through specified LineParser
-    bool serialise(LineParser &parser) const;
-    // Read from specified LineParser
-    bool deserialise(LineParser &parser, const CoreData &coreData, bool hasPotentials);
     // Express as a serialisable value
     void serialise(std::string tag, SerialisedValue &target) const override;
     // Read values from a serialisable value

diff --git a/src/classes/isotopologue.h b/src/classes/isotopologue.h
@@ -15,7 +15,6 @@
 // Forward Declarations
 class AtomType;
 class Species;
-class CoreData;
 
 /*
  * Isotopologue Definition

diff --git a/src/classes/kVector.h b/src/classes/kVector.h
@@ -8,7 +8,6 @@
 
 // Forward Declarations
 class BraggReflection;
-class CoreData;
 
 // K-Vector
 class KVector

diff --git a/src/classes/speciesAtom.h b/src/classes/speciesAtom.h
@@ -13,7 +13,6 @@
 
 // Forward Declarations
 class AtomType;
-class CoreData;
 class SpeciesAngle;
 class SpeciesBond;
 class SpeciesImproper;

diff --git a/src/classes/speciesSite.h b/src/classes/speciesSite.h
@@ -187,7 +187,7 @@ class SpeciesSite : public Serialisable
     // Express as a serialisable value
     void serialise(std::string tag, SerialisedValue &target) const override;
     // Read values from a serialisable value
-    void deserialise(const SerialisedValue &node);
+    void deserialise(const SerialisedValue &node) override;
 };
 
 template <> struct Context<const SpeciesSite *>

diff --git a/src/gui/getConfigurationNameDialog.h b/src/gui/getConfigurationNameDialog.h
@@ -7,7 +7,6 @@
 #include <QDialog>
 
 // Forward Declarations
-class CoreData;
 class Configuration;
 
 // Get Configuration Name Dialog

diff --git a/src/gui/getModuleLayerNameDialog.h b/src/gui/getModuleLayerNameDialog.h
@@ -7,7 +7,6 @@
 #include <QDialog>
 
 // Forward Declarations
-class CoreData;
 class ModuleLayer;
 
 // Get Layer Name Dialog

diff --git a/src/gui/getSpeciesNameDialog.h b/src/gui/getSpeciesNameDialog.h
@@ -7,7 +7,6 @@
 #include <QDialog>
 
 // Forward Declarations
-class CoreData;
 class Species;
 
 // Get Species Name Dialog

diff --git a/src/gui/getTabNameDialog.h b/src/gui/getTabNameDialog.h
@@ -7,7 +7,6 @@
 #include <QDialog>
 
 // Forward Declarations
-class CoreData;
 class MainTab;
 
 // Get MainTab Name Dialog

diff --git a/src/math/sampledDouble.h b/src/math/sampledDouble.h
@@ -6,7 +6,6 @@
 #include "base/serialiser.h"
 
 // Forward Declarations
-class CoreData;
 class LineParser;
 class ProcessPool;
 

diff --git a/src/math/sampledVector.h b/src/math/sampledVector.h
@@ -7,7 +7,6 @@
 #include <vector>
 
 // Forward Declarations
-class CoreData;
 class LineParser;
 
 // Vector of double values with sampling

diff --git a/src/nodes/md.cpp b/src/nodes/md.cpp
@@ -22,7 +22,6 @@ MDNode::MDNode(Graph *parentGraph) : Node(parentGraph)
     addOption("RandomVelocities", "Whether random velocities should always be assigned before beginning MD simulation",
               randomVelocities_);
 
-    addOption("RestrictToSpecies", "Restrict the calculation to the specified Species", restrictToSpecies_);
     addOption("OnlyWhenEnergyStable", "Only run MD when target Configuration energies are stable", onlyWhenEnergyStable_);
 
     addOption("EnergyFrequency", "Frequency at which to calculate total system energy", energyFrequency_);
@@ -156,9 +155,6 @@ NodeConstants::ProcessResult MDNode::process()
         message("Summary will be written every {} step(s).\n", outputFrequency);
     else
         message("Summary will not be written.\n");
-    if (!restrictToSpecies_.empty())
-        message("Calculation will be restricted to species: {}\n",
-                joinStrings(restrictToSpecies_, "  ", [](const auto &sp) { return sp->name(); }));
     message("\n");
 
     // Create kernels
@@ -195,22 +191,6 @@ NodeConstants::ProcessResult MDNode::process()
     double tInstant, ke, tScale;
     Kernel::EnergyResult pe;
 
-    // Determine target molecules from the restrictedSpecies vector (if any)
-    std::vector<const Molecule *> targetMolecules;
-    std::vector<int> free(targetConfiguration_->nAtoms(), 0);
-    if (restrictToSpecies_.empty())
-    {
-        std::fill(free.begin(), free.end(), 1);
-    }
-    else
-        for (const auto &mol : targetConfiguration_->molecules())
-            if (std::find(restrictToSpecies_.begin(), restrictToSpecies_.end(), mol->species()) != restrictToSpecies_.end())
-            {
-                targetMolecules.push_back(mol.get());
-                auto offset = mol->globalAtomOffset();
-                std::fill(free.begin() + offset, free.begin() + offset + mol->atoms().size(), 1);
-            }
-
     /*
      * Calculation Begins
      */
@@ -227,12 +207,9 @@ NodeConstants::ProcessResult MDNode::process()
 
         Messenger::print("Random initial velocities will be assigned.\n");
         velocities.resize(targetConfiguration_->nAtoms(), Vector3());
-        for (auto &&[v, iFree] : zip(velocities, free))
+        for (auto &v : velocities)
         {
-            if (iFree)
-                v.set(exp(DissolveMath::random() - 0.5), exp(DissolveMath::random() - 0.5), exp(DissolveMath::random() - 0.5));
-            else
-                v.zero();
+            v.set(exp(DissolveMath::random() - 0.5), exp(DissolveMath::random() - 0.5), exp(DissolveMath::random() - 0.5));
             v /= sqrt(2.0 * M_PI);
         }
     }
@@ -256,23 +233,18 @@ NodeConstants::ProcessResult MDNode::process()
     // Calculate total velocity and mass over all atoms
     Vector3 vCom;
     auto massSum = 0.0;
-    for (auto &&[v, m, iFree] : zip(velocities, mass, free))
+    for (auto &&[v, m] : zip(velocities, mass))
     {
-        if (!iFree)
-            continue;
         vCom += v * m;
         massSum += m;
     }
 
     // Finalise initial velocities (unless considering intramolecular forces only)
     if (!intramolecularForcesOnly_)
     {
-        // Remove any velocity shift, and re-zero velocities on fixed atoms
+        // Remove any velocity shift
         vCom /= massSum;
         std::transform(velocities.begin(), velocities.end(), velocities.begin(), [vCom](auto vel) { return vel - vCom; });
-        for (auto &&[v, iFree] : zip(velocities, free))
-            if (!iFree)
-                v.zero();
 
         // Calculate instantaneous temperature
         ke = 0.0;
@@ -313,17 +285,11 @@ NodeConstants::ProcessResult MDNode::process()
     // If we're not using a fixed timestep the forces need to be available immediately
     if (timestepType_ != TimestepType::Fixed)
     {
-        // Calculate forces
-        if (targetMolecules.empty())
-        {
-            if (intramolecularForcesOnly_)
-                forceKernel->totalForces(pairPotentialForces, geometryForces,
-                                         {Kernel::ExcludeInterMolecularPairPotential, Kernel::ExcludeExtended});
-            else
-                forceKernel->totalForces(pairPotentialForces, geometryForces);
-        }
+        if (intramolecularForcesOnly_)
+            forceKernel->totalForces(pairPotentialForces, geometryForces,
+                                     {Kernel::ExcludeInterMolecularPairPotential, Kernel::ExcludeExtended});
         else
-            throw(std::runtime_error("Forces calculation on a set of molecules is currently not available.\n"));
+            forceKernel->totalForces(pairPotentialForces, geometryForces);
 
         // Check for suitable timestep
         if (!determineTimeStep(timestepType_, fixedTimestep, pairPotentialForces, geometryForces))
@@ -365,16 +331,12 @@ NodeConstants::ProcessResult MDNode::process()
         targetConfiguration_->updateAtomLocations();
 
         // Calculate forces
-        if (targetMolecules.empty())
-        {
-            if (intramolecularForcesOnly_)
-                forceKernel->totalForces(pairPotentialForces, geometryForces,
-                                         {Kernel::ExcludeInterMolecularPairPotential, Kernel::ExcludeExtended});
-            else
-                forceKernel->totalForces(pairPotentialForces, geometryForces);
-        }
+        if (intramolecularForcesOnly_)
+            forceKernel->totalForces(pairPotentialForces, geometryForces,
+                                     {Kernel::ExcludeInterMolecularPairPotential, Kernel::ExcludeExtended});
         else
-            throw(std::runtime_error("Forces calculation on a set of molecules is currently not available.\n"));
+            forceKernel->totalForces(pairPotentialForces, geometryForces);
+
         // Cap forces
         if (capForces_)
             nCapped = capForces(maxForce, pairPotentialForces, geometryForces);

diff --git a/src/nodes/md.h b/src/nodes/md.h
@@ -63,8 +63,6 @@ class MDNode : public Node
     std::optional<Number> outputFrequency_{5};
     // Whether random velocities should always be assigned before beginning MD simulation
     bool randomVelocities_{false};
-    // Species to restrict calculation to
-    std::vector<const Species *> restrictToSpecies_;
     // Write frequency for trajectory file
     std::optional<Number> trajectoryFrequency_;
     // Velocities

diff --git a/src/nodes/parameter.h b/src/nodes/parameter.h
@@ -562,10 +562,6 @@ template <typename DataClass> class SerialisableParameter : public Parameter<Dat
     {
     };
 
-    template <serialisablePointer E> struct is_ptr_vector<std::vector<E>> : std::true_type
-    {
-    };
-
     /*
      * Serialisation
      */
@@ -587,8 +583,6 @@ template <typename DataClass> class SerialisableParameter : public Parameter<Dat
             if (Parameter<DataClass>::data_)
                 result["data"] = *Parameter<DataClass>::data_;
         }
-        else if constexpr (serialisablePointer<DataClass>)
-            Parameter<DataClass>::data_->serialise("data", result);
         else
             result["data"] = Parameter<DataClass>::data_;
 
@@ -629,11 +623,6 @@ template <typename DataClass> class SerialisableParameter : public Parameter<Dat
             else
                 Parameter<DataClass>::data_ = {};
         }
-        else if constexpr (serialisablePointer<DataClass>)
-        {
-            CoreData coreData; // Temporary patch until we fix up the deserialisation
-            Parameter<DataClass>::data_->deserialise(node.at("data"), coreData);
-        }
         else
         {
             Parameter<DataClass>::data_ = toml::find<DataClass>(node, "data");

diff --git a/tests/gui/optionalDoubleKeyword.cpp b/tests/gui/optionalDoubleKeyword.cpp
diff --git a/tests/gui/optionalIntegerKeyword.cpp b/tests/gui/optionalIntegerKeyword.cpp
diff --git a/tests/nodes/graph.cpp b/tests/nodes/graph.cpp
@@ -56,7 +56,6 @@ class GraphCoreTest : public ::testing::Test
     }
 
     protected:
-    // We need a CoreData and Dissolve definition to properly instantiate DissolveGraph at present.
     DissolveGraph root_;
     AddNode *x_{nullptr}, *y_{nullptr}, *z_{nullptr};
 };

diff --git a/tests/nodes/loop.cpp b/tests/nodes/loop.cpp
@@ -64,7 +64,6 @@ class IterableGraphTest : public ::testing::Test
     }
 
     protected:
-    // We need a CoreData and Dissolve definition to properly instantiate DissolveGraph at present.
     DissolveGraph root_;
     NumberNode *i_{nullptr};
     AddNode *x_{nullptr}, *y_{nullptr};