chore: Remove original I/O - part 2 (#2534)

Co-authored-by: Tristan Youngs <trisyoungs@googlemail.com>

Author: trisyoungs

CMakeLists.txt

@@ -293,7 +293,6 @@ set(BASIC_LINK_LIBS
     main
     classes
     kernels
-    potentials
     neta
     analyser
     keywords

src/classes/CMakeLists.txt

@@ -13,7 +13,6 @@ add_library(
   configuration_box.cpp
   configuration_contents.cpp
   configuration_io.cpp
-  configuration_potentials.cpp
   configuration_sites.cpp
   configuration_upkeep.cpp
   configurationAtom.cpp
@@ -49,7 +48,6 @@ add_library(
   species_atomic.cpp
   species_common.cpp
   species_intra.cpp
-  species_io.cpp
   species_isotopologues.cpp
   species_site.cpp
   species_transform.cpp

src/classes/configuration.h

@@ -10,7 +10,6 @@
 #include "classes/configurationAtom.h"
 #include "classes/molecule.h"
 #include "classes/siteStack.h"
-#include "kernels/potentials/base.h"
 #include <map>
 #include <memory>
 #include <vector>
@@ -177,27 +176,6 @@ class Configuration : public Serialisable<const CoreData &>
     // Scale Box, Cells, and Molecule geometric centres according to current size factor
     void applySizeFactor(const EnergyKernel *kernel);
 
-    /*
-     * External Potentials
-     */
-    private:
-    // Defined global potentials
-    std::vector<std::unique_ptr<ExternalPotential>> globalPotentials_;
-    // Defined targeted potentials
-    std::vector<std::unique_ptr<ExternalPotential>> targetedPotentials_;
-
-    public:
-    // Add global potential
-    void addGlobalPotential(std::unique_ptr<ExternalPotential> potential);
-    // Return vector of defined global potentials
-    const std::vector<std::unique_ptr<ExternalPotential>> &globalPotentials() const;
-    // Add targeted potential
-    void addTargetedPotential(std::unique_ptr<ExternalPotential> potential);
-    // Return vector of defined targeted potentials
-    const std::vector<std::unique_ptr<ExternalPotential>> &targetedPotentials() const;
-    // Link targeted potentials to atoms
-    void linkTargetedPotentials();
-
     /*
      * Upkeep
      */

src/classes/configurationAtom.cpp

@@ -42,19 +42,3 @@ SpeciesAtom::ScaledInteractionDefinition ConfigurationAtom::scaling(const Config
 
     return speciesAtom_->scaling(j->speciesAtom());
 }
-
-/*
- * Targeted Potentials
- */
-
-// Add targeted potential to this atom
-void ConfigurationAtom::addTargetedPotential(const ExternalPotential *potential)
-{
-    targetedPotentials_.emplace_back(potential);
-}
-
-// Clear all targeted potentials from this Atom
-void ConfigurationAtom::clearTargetedPotentials() { targetedPotentials_.clear(); }
-
-// Return list of targeted potentials for this atom
-const std::vector<const ExternalPotential *> &ConfigurationAtom::targetedPotentials() const { return targetedPotentials_; }

src/classes/configurationAtom.h

@@ -6,7 +6,6 @@
 #include "classes/atom.h"
 #include "classes/speciesAtom.h"
 #include "classes/speciesBond.h"
-#include "kernels/potentials/base.h"
 #include <memory>
 #include <vector>
 
@@ -48,19 +47,4 @@ class ConfigurationAtom : public Atom<SpeciesBond>
     public:
     // Return scaling type and factors (electrostatic, van der Waals) to employ with specified Atom
     SpeciesAtom::ScaledInteractionDefinition scaling(const ConfigurationAtom *j) const;
-
-    /*
-     * Targeted External Potentials
-     */
-    private:
-    // Vector of targeted potentials affecting this atom
-    std::vector<const ExternalPotential *> targetedPotentials_;
-
-    public:
-    // Add targeted potential to this atom
-    void addTargetedPotential(const ExternalPotential *potential);
-    // Clear all targeted potentials from this Atom
-    void clearTargetedPotentials();
-    // Return list of targeted potentials for this atom
-    const std::vector<const ExternalPotential *> &targetedPotentials() const;
 };

src/classes/configuration_contents.cpp

@@ -41,8 +41,6 @@ void Configuration::empty()
     atoms_.clear();
     appliedSizeFactor_ = std::nullopt;
     speciesPopulations_.clear();
-    globalPotentials_.clear();
-    targetedPotentials_.clear();
     cells_.clear();
 
     ++version_;

src/classes/configuration_io.cpp

@@ -8,7 +8,6 @@
 #include "classes/coreData.h"
 #include "classes/pairPotential.h"
 #include "classes/species.h"
-#include "kernels/potentials/producer.h"
 #include <algorithm>
 
 // Write through specified LineParser
@@ -62,24 +61,6 @@ bool Configuration::serialise(LineParser &parser) const
             return false;
     }
 
-    // If there are no defined external potentials we are done
-    if (globalPotentials_.empty() && targetedPotentials_.empty())
-        return true;
-
-    // Write global potentials
-    if (!parser.writeLineF("{}  # nGlobalPotentials\n", globalPotentials_.size()))
-        return false;
-    for (auto &pot : globalPotentials_)
-        if (!pot->serialise(parser, ""))
-            return false;
-
-    // Write targeted potentials
-    if (!parser.writeLineF("{}  # nTargetedPotentials\n", targetedPotentials_.size()))
-        return false;
-    for (auto &pot : targetedPotentials_)
-        if (!pot->serialise(parser, ""))
-            return false;
-
     return true;
 }
 
@@ -168,77 +149,5 @@ bool Configuration::deserialise(LineParser &parser, const CoreData &coreData, bo
     if (!hasPotentials)
         return true;
 
-    // Read in global potentials
-    if (parser.getArgsDelim(LineParser::Defaults) != LineParser::Success)
-        return false;
-    globalPotentials_.resize(parser.argi(0));
-    for (auto &pot : globalPotentials_)
-    {
-        // First line contains potential type
-        if (parser.getArgsDelim(LineParser::Defaults) != LineParser::Success)
-            return false;
-        auto potentialType = ExternalPotentialTypes::isType(parser.argsv(0));
-        if (!potentialType)
-            return Messenger::error("Unrecognised external potential type '{}' found in Configuration '{}' in restart file.\n",
-                                    parser.argsv(0), name());
-
-        // Create new external potential
-        pot = ExternalPotentialProducer::create(*potentialType);
-        if (!pot->deserialise(parser, coreData))
-            return false;
-    }
-
-    // Get atom types present in configuration
-    auto atomTypes = atomTypeVector();
-
-    // Read in targeted potentials
-    if (parser.getArgsDelim(LineParser::Defaults) != LineParser::Success)
-        return false;
-    targetedPotentials_.resize(parser.argi(0));
-    for (auto &pot : targetedPotentials_)
-    {
-        // First line contains potential type
-        if (parser.getArgsDelim(LineParser::Defaults) != LineParser::Success)
-            return false;
-        auto potentialType = ExternalPotentialTypes::isType(parser.argsv(0));
-        if (!potentialType)
-            return Messenger::error("Unrecognised external potential type '{}' found in Configuration '{}' in restart file.\n",
-                                    parser.argsv(0), name());
-
-        // Create new external potential
-        pot = ExternalPotentialProducer::create(*potentialType);
-
-        // Additional arguments after the potential type correspond to targets for the potential
-        for (auto n = 1; n < parser.nArgs(); ++n)
-        {
-            // Plain number - corresponds to a specific atom in the configuration
-            if (DissolveSys::isNumber(parser.args(n)))
-            {
-                auto i = parser.argi(n);
-                if (i < 0 || i >= atoms_.size())
-                    Messenger::exception("Atom index {} for targeted potential is out of range.\n", i);
-                pot->addTargetAtomIndex(i);
-            }
-            else if (std::ranges::find_if(atomTypes, [&](const auto at)
-                                          { return DissolveSys::sameString(at->name(), parser.args(n)); }) != atomTypes.end())
-            {
-                auto it = std::ranges::find_if(atomTypes, [&](const auto at)
-                                               { return DissolveSys::sameString(at->name(), parser.args(n)); });
-                pot->addTargetAtomType(*it);
-            }
-            else if (coreData.findSpecies(DissolveSys::niceName(parser.args(n))))
-                pot->addTargetSpecies(coreData.findSpecies(DissolveSys::niceName(parser.args(n))));
-            else
-                Messenger::exception("Unrecognised target '{}' for potential.\n", parser.args(n));
-        }
-
-        // Read in the rest of the potential
-        if (!pot->deserialise(parser, coreData))
-            return false;
-    }
-
-    // Link targeted potentials to atoms
-    linkTargetedPotentials();
-
     return true;
 }

src/classes/configuration_potentials.cpp

@@ -304,40 +304,6 @@ class Species : public Serialisable<>
      * Serialisation
      */
     public:
-    // Species Block Keyword Enum
-    enum class SpeciesKeyword
-    {
-        Angle,          /* 'Angle' - Defines an Angle joining three atoms */
-        Atom,           /* 'Atom' - Specifies an Atom in the Species */
-        Bond,           /* 'Bond' - Defines a Bond joining two atoms */
-        BondType,       /* 'BondType' - Sets the type of a specific bond */
-        BoxAngles,      /* 'BoxAngles' - Specify unit cell angles for the species */
-        BoxLengths,     /* 'BoxLengths' - Specify unit cell lengths for the species */
-        Charge,         /* 'Charge' - Specifies the atomic charge for an individual atom */
-        CommonAngle,    /* 'CommonAngle' - Define a common angle (added for transition to Dissolve2) */
-        CommonBond,     /* 'CommonBond' - Define a common angle (added for transition to Dissolve2) */
-        CommonImproper, /* 'CommonImproper' - Define a common angle (added for transition to Dissolve2) */
-        CommonTorsion,  /* 'CommonTorsion' - Define a common angle (added for transition to Dissolve2) */
-        EndSpecies,     /* 'EndSpecies' - Signals the end of the current Species */
-        Forcefield,     /* 'Forcefield' - Sets the Forcefield from which to (re)generate or set terms */
-        Improper,       /* 'Improper' - Define an Improper interaction between four atoms */
-        Isotopologue,   /* 'Isotopologue' - Add an isotopologue to the Species */
-        NAngles,        /* 'NAngles' - Hint at the total number of angles in the Species */
-        NAtoms,         /* 'NAtoms' - Hint at the total number of atoms in the Species */
-        NBonds,         /* 'NBonds' - Hint at the total number of bonds in the Species */
-        NImpropers,     /* 'NImpropers' - Hint at the total number of impropers in the Species */
-        NTorsions,      /* 'NTorsions' - Hint at the total number of torsions in the Species */
-        Scaling14,      /* 'Scaling14' - Specify 1-4 scaling factors for torsion terms */
-        Site,           /* 'Site' - Define an analysis site within the Species */
-        Torsion         /* 'Torsion' - Define a Torsion interaction between four atoms */
-    };
-    // Return enum option info for SpeciesKeyword
-    static EnumOptions<Species::SpeciesKeyword> keywords();
-    // Read Species definition from specified LineParser
-    bool read(LineParser &parser, CoreData &coreData);
-    // Write Species definition to specified LineParser
-    bool write(LineParser &parser, std::string_view prefix);
-
     // Express as a serialisable value
     void serialise(std::string tag, SerialisedValue &target) const override;
     // Read values from a serialisable value