From f23b06e7f0ea77e66bad9c4e6057a70634c89bfa Mon Sep 17 00:00:00 2001
From: Joe Wallwork <jw2423@cam.ac.uk>
Date: Mon, 9 Dec 2024 15:18:28 +0000
Subject: [PATCH 1/4] Set up ParaGridIO_Xios as a copy of ParaGridIO for now

---
 core/src/CMakeLists.txt                       |   8 +-
 core/src/ParaGridIO.cpp                       |   4 +-
 core/src/ParaGridIO_Xios.cpp                  | 530 ++++++++++++++++++
 core/src/StructureFactory.cpp                 |   7 +-
 core/src/include/ParaGridIO.hpp               |   4 +-
 core/src/include/ParaGridIO_Xios.hpp          | 138 +++++
 core/test/CMakeLists.txt                      |  81 +--
 core/test/ParaGrid_test.cpp                   |   9 +-
 core/test/XiosReadWrite_test.cpp              |   4 +-
 .../ERA5Atmosphere.cpp                        |   6 +-
 .../OceanBoundaryModule/TOPAZOcean.cpp        |   8 +-
 11 files changed, 747 insertions(+), 52 deletions(-)
 create mode 100644 core/src/ParaGridIO_Xios.cpp
 create mode 100644 core/src/include/ParaGridIO_Xios.hpp

diff --git a/core/src/CMakeLists.txt b/core/src/CMakeLists.txt
index b3d973f76..0c230d58c 100644
--- a/core/src/CMakeLists.txt
+++ b/core/src/CMakeLists.txt
@@ -1,5 +1,11 @@
 # Sources for the main neXtSIM model
 
+if(ENABLE_XIOS)
+  set(ParaGridIO_Impl "ParaGridIO_Xios")
+else()
+  set(ParaGridIO_Impl "ParaGridIO")
+endif()
+
 set(BaseSources
     "Logged.cpp"
     "ModelConfig.cpp"
@@ -11,7 +17,7 @@ set(BaseSources
     "CommandLineParser.cpp"
     "CommonRestartMetadata.cpp"
     "RectGridIO.cpp"
-    "ParaGridIO.cpp"
+    "${ParaGridIO_Impl}.cpp"
     "FileCallbackCloser.cpp"
     "Finalizer.cpp"
     "DevStep.cpp"
diff --git a/core/src/ParaGridIO.cpp b/core/src/ParaGridIO.cpp
index 63f47cb48..9b6842692 100644
--- a/core/src/ParaGridIO.cpp
+++ b/core/src/ParaGridIO.cpp
@@ -1,10 +1,11 @@
 /*!
  * @file ParaGridIO.cpp
  *
- * @date Oct 24, 2022
+ * @date 09 Dec 2024
  * @author Tim Spain <timothy.spain@nersc.no>
  */
 
+#ifndef USE_XIOS
 #include "include/ParaGridIO.hpp"
 
 #include "include/CommonRestartMetadata.hpp"
@@ -513,3 +514,4 @@ void ParaGridIO::closeAllFiles()
 }
 
 } /* namespace Nextsim */
+#endif /* not USE_XIOS */
diff --git a/core/src/ParaGridIO_Xios.cpp b/core/src/ParaGridIO_Xios.cpp
new file mode 100644
index 000000000..3aeea3154
--- /dev/null
+++ b/core/src/ParaGridIO_Xios.cpp
@@ -0,0 +1,530 @@
+/*!
+ * @file ParaGridIO_Xios.cpp
+ *
+ * @date 09 Dec 2024
+ * @author Tim Spain <timothy.spain@nersc.no>
+ * @author Joe Wallwork <jw2423@cam.ac.uk>
+ */
+
+#ifdef USE_XIOS
+#include "include/ParaGridIO_Xios.hpp"
+
+#include "include/CommonRestartMetadata.hpp"
+#include "include/FileCallbackCloser.hpp"
+#include "include/Finalizer.hpp"
+#include "include/MissingData.hpp"
+#include "include/NZLevels.hpp"
+#include "include/gridNames.hpp"
+
+#include <ncDim.h>
+#include <ncException.h>
+#include <ncFile.h>
+#include <ncGroup.h>
+#include <ncVar.h>
+
+#include <algorithm>
+#include <cstdlib>
+#include <map>
+#include <stdexcept>
+#include <string>
+
+namespace Nextsim {
+
+// TODO: XIOS implementation
+ParaGridIO::ParaGridIO(ParametricGrid& grid)
+    : IParaGridIO(grid)
+    , openFilesAndIndices(getOpenFilesAndIndices())
+    , dimensionKeys({
+          // clang-format off
+          // Accept post-May 2024 (xdim, ydim, zdim) dimension names and pre-May 2024 (x, y, z)
+        { "yx", ModelArray::Type::H },
+        { "ydimxdim", ModelArray::Type::H },
+        { "zyx", ModelArray::Type::Z },
+        { "zdimydimxdim", ModelArray::Type::Z },
+        { "yxdg_comp", ModelArray::Type::DG },
+        { "ydimxdimdg_comp", ModelArray::Type::DG },
+        { "yxdgstress_comp", ModelArray::Type::DGSTRESS },
+        { "ydimxdimdgstress_comp", ModelArray::Type::DGSTRESS },
+        { "ycgxcg", ModelArray::Type::CG },
+        { "yvertexxvertexncoords", ModelArray::Type::VERTEX },
+          // clang-format on
+      })
+    , isDG({
+          // clang-format off
+        { ModelArray::Dimension::X, false },
+        { ModelArray::Dimension::Y, false },
+        { ModelArray::Dimension::Z, false },
+        { ModelArray::Dimension::XCG, true },
+        { ModelArray::Dimension::YCG, true },
+        { ModelArray::Dimension::DG, true },
+        { ModelArray::Dimension::DGSTRESS, true },
+        // NCOORDS is a number of components, but not in the same way as the DG components.
+        { ModelArray::Dimension::NCOORDS, false },
+          // clang-format on
+      })
+    , dimCompMap({
+          // clang-format off
+        { ModelArray::componentMap.at(ModelArray::Type::DG), ModelArray::Type::DG },
+        { ModelArray::componentMap.at(ModelArray::Type::DGSTRESS), ModelArray::Type::DGSTRESS },
+        { ModelArray::componentMap.at(ModelArray::Type::VERTEX), ModelArray::Type::VERTEX },
+          // clang-format on
+      })
+{
+    Logged::warning("XIOS integration has not yet been completed");
+    static bool doneOnce = doOnce();
+}
+
+bool ParaGridIO::doOnce()
+{
+    // TODO: Setup XIOS in this method
+
+    // Register the finalization function here
+    Finalizer::registerUnique(closeAllFiles);
+    // Since it should only ever run once, do further one-off initialization: allow distant
+    // classes to close files via a callback.
+    FileCallbackCloser::onClose(close);
+
+    return true;
+}
+
+ParaGridIO::~ParaGridIO() = default;
+
+#ifdef USE_MPI
+ModelState ParaGridIO::getModelState(const std::string& filePath, ModelMetadata& metadata)
+#else
+ModelState ParaGridIO::getModelState(const std::string& filePath)
+#endif
+{
+    // TODO: XIOS implementation
+    ModelState state;
+
+    try {
+#ifdef USE_MPI
+        netCDF::NcFilePar ncFile(filePath, netCDF::NcFile::read, metadata.mpiComm);
+#else
+        netCDF::NcFile ncFile(filePath, netCDF::NcFile::read);
+#endif
+        netCDF::NcGroup metaGroup(ncFile.getGroup(IStructure::metadataNodeName()));
+        netCDF::NcGroup dataGroup(ncFile.getGroup(IStructure::dataNodeName()));
+
+        // Dimensions and DG components
+        std::multimap<std::string, netCDF::NcDim> dimMap = dataGroup.getDims();
+        for (auto entry : ModelArray::definedDimensions) {
+            auto dimType = entry.first;
+            if (dimCompMap.count(dimType) > 0)
+                // TODO Assertions that DG in the file equals the compile time DG in the model. See
+                // #205
+                continue;
+
+            ModelArray::DimensionSpec& dimensionSpec = entry.second;
+            // Find dimensions in the netCDF file by their name in the ModelArray details
+            netCDF::NcDim dim = dataGroup.getDim(dimensionSpec.name);
+            // Also check the old name
+            if (dim.isNull()) {
+                dim = dataGroup.getDim(dimensionSpec.altName);
+            }
+            // If we didn't find a dimension with the dimensions name or altName, throw.
+            if (dim.isNull()) {
+                throw std::out_of_range(
+                    std::string("No netCDF dimension found corresponding to the dimension named ")
+                    + dimensionSpec.name + std::string(" or ") + dimensionSpec.altName);
+            }
+            if (dimType == ModelArray::Dimension::Z) {
+                // A special case, as the number of levels in the file might not be
+                // the number that the selected ice thermodynamics requires.
+#ifdef USE_MPI
+                ModelArray::setDimension(dimType, NZLevels::get(), NZLevels::get(), 0);
+#else
+                ModelArray::setDimension(dimType, NZLevels::get());
+#endif
+            } else {
+#ifdef USE_MPI
+                auto dimName = dim.getName();
+                size_t localLength = 0;
+                size_t start = 0;
+                if (dimType == ModelArray::Dimension::X) {
+                    localLength = metadata.localExtentX;
+                    start = metadata.localCornerX;
+                } else if (dimType == ModelArray::Dimension::Y) {
+                    localLength = metadata.localExtentY;
+                    start = metadata.localCornerY;
+                } else if (dimType == ModelArray::Dimension::XVERTEX) {
+                    localLength = metadata.localExtentX + 1;
+                    start = metadata.localCornerX;
+                } else if (dimType == ModelArray::Dimension::YVERTEX) {
+                    localLength = metadata.localExtentY + 1;
+                    start = metadata.localCornerY;
+                } else {
+                    localLength = dim.getSize();
+                    start = 0;
+                }
+                ModelArray::setDimension(dimType, dim.getSize(), localLength, start);
+#else
+                ModelArray::setDimension(dimType, dim.getSize());
+#endif
+            }
+        }
+
+        // Get all vars in the data group, and load them into a new ModelState
+
+        for (auto entry : dataGroup.getVars()) {
+            const std::string& varName = entry.first;
+            netCDF::NcVar& var = entry.second;
+            // Determine the type from the dimensions
+            std::vector<netCDF::NcDim> varDims = var.getDims();
+            std::string dimKey = "";
+            for (netCDF::NcDim& dim : varDims) {
+                dimKey += dim.getName();
+            }
+            if (!dimensionKeys.count(dimKey)) {
+                throw std::out_of_range(
+                    std::string("No ModelArray::Type corresponds to the dimensional key ")
+                    + dimKey);
+            }
+            ModelArray::Type type = dimensionKeys.at(dimKey);
+            state.data[varName] = ModelArray(type);
+            ModelArray& data = state.data.at(varName);
+            data.resize();
+
+            std::vector<size_t> start;
+            std::vector<size_t> count;
+            if (ModelArray::hasDoF(type)) {
+                auto ncomps = data.nComponents();
+                start.push_back(0);
+                count.push_back(ncomps);
+            }
+            for (ModelArray::Dimension dt : ModelArray::typeDimensions.at(type)) {
+                auto dim = ModelArray::definedDimensions.at(dt);
+                start.push_back(dim.start);
+                count.push_back(dim.localLength);
+            }
+            // dims are looped in [dg], x, y, [z] order so start and count
+            // order must be reveresed to match order netcdf expects
+            std::reverse(start.begin(), start.end());
+            std::reverse(count.begin(), count.end());
+
+            var.getVar(start, count, &data[0]);
+        }
+        ncFile.close();
+    } catch (const netCDF::exceptions::NcException& nce) {
+        std::string ncWhat(nce.what());
+        ncWhat += ": " + filePath;
+        throw std::runtime_error(ncWhat);
+    }
+    return state;
+}
+
+ModelState ParaGridIO::readForcingTimeStatic(
+    const std::set<std::string>& forcings, const TimePoint& time, const std::string& filePath)
+{
+    // TODO: XIOS implementation
+
+    ModelState state;
+
+    try {
+        netCDF::NcFile ncFile(filePath, netCDF::NcFile::read);
+        netCDF::NcGroup metaGroup(ncFile.getGroup(IStructure::metadataNodeName()));
+        netCDF::NcGroup dataGroup(ncFile.getGroup(IStructure::dataNodeName()));
+
+        // Read the time axis
+        netCDF::NcDim timeDim = dataGroup.getDim(timeName);
+        // Read the time variable
+        netCDF::NcVar timeVar = dataGroup.getVar(timeName);
+        // Calculate the index of the largest time value on the axis below our target
+        size_t targetTIndex;
+        // Get the time axis as a vector
+        std::vector<double> timeVec(timeDim.getSize());
+        timeVar.getVar(timeVec.data());
+        // Get the index of the largest TimePoint less than the target.
+        targetTIndex = std::find_if(std::begin(timeVec), std::end(timeVec), [time](double t) {
+            return (TimePoint() + Duration(t)) > time;
+        }) - timeVec.begin();
+        // Rather than the first that is greater than, get the last that is less
+        // than or equal to. But don't go out of bounds.
+        if (targetTIndex > 0)
+            --targetTIndex;
+        // ASSUME all forcings are HFields: finite volume fields on the same
+        // grid as ice thickness
+        std::vector<size_t> indexArray = { targetTIndex };
+        std::vector<size_t> extentArray = { 1 };
+
+        // Loop over the dimensions of H
+        const std::vector<ModelArray::Dimension>& dimensions
+            = ModelArray::typeDimensions.at(ModelArray::Type::H);
+        for (auto riter = dimensions.rbegin(); riter != dimensions.rend(); ++riter) {
+            indexArray.push_back(0);
+            extentArray.push_back(ModelArray::definedDimensions.at(*riter).localLength);
+        }
+
+        for (const std::string& varName : forcings) {
+            netCDF::NcVar var = dataGroup.getVar(varName);
+            state.data[varName] = ModelArray(ModelArray::Type::H);
+            ModelArray& data = state.data.at(varName);
+            data.resize();
+
+            var.getVar(indexArray, extentArray, &data[0]);
+        }
+        ncFile.close();
+    } catch (const netCDF::exceptions::NcException& nce) {
+        std::string ncWhat(nce.what());
+        ncWhat += ": " + filePath;
+        throw std::runtime_error(ncWhat);
+    }
+    return state;
+}
+
+void ParaGridIO::dumpModelState(
+    const ModelState& state, const ModelMetadata& metadata, const std::string& filePath)
+{
+    // TODO: XIOS implementation
+
+#ifdef USE_MPI
+    netCDF::NcFilePar ncFile(filePath, netCDF::NcFile::replace, metadata.mpiComm);
+#else
+    netCDF::NcFile ncFile(filePath, netCDF::NcFile::replace);
+#endif
+
+    CommonRestartMetadata::writeStructureType(ncFile, metadata);
+    netCDF::NcGroup metaGroup = ncFile.addGroup(IStructure::metadataNodeName());
+    netCDF::NcGroup dataGroup = ncFile.addGroup(IStructure::dataNodeName());
+    CommonRestartMetadata::writeRestartMetadata(metaGroup, metadata);
+
+    // Dump the dimensions and number of components
+    std::map<ModelArray::Dimension, netCDF::NcDim> ncFromMAMap;
+    for (auto entry : ModelArray::definedDimensions) {
+        ModelArray::Dimension dim = entry.first;
+        size_t dimSz = (dimCompMap.count(dim)) ? ModelArray::nComponents(dimCompMap.at(dim))
+                                               : dimSz = entry.second.globalLength;
+        ncFromMAMap[dim] = dataGroup.addDim(entry.second.name, dimSz);
+        // TODO Do I need to add data, even if it is just integers 0...n-1?
+    }
+
+    // Also create the sets of dimensions to be connected to the data fields
+    std::map<ModelArray::Type, std::vector<netCDF::NcDim>> dimMap;
+    for (auto entry : ModelArray::typeDimensions) {
+        ModelArray::Type type = entry.first;
+        std::vector<netCDF::NcDim> ncDims;
+        for (auto iter = entry.second.rbegin(); iter != entry.second.rend(); ++iter) {
+            ModelArray::Dimension& maDim = *iter;
+            ncDims.push_back(ncFromMAMap.at(maDim));
+        }
+        dimMap[type] = ncDims;
+    }
+
+    // Everything that has components needs that dimension, too. This always varies fastest, and so
+    // is last in the vector of dimensions.
+    for (auto entry : dimCompMap) {
+        dimMap.at(entry.second).push_back(ncFromMAMap.at(entry.first));
+    }
+
+    std::set<std::string> restartFields = { hiceName, ciceName, hsnowName, ticeName, sstName,
+        sssName, maskName, coordsName, xName, yName, longitudeName, latitudeName, gridAzimuthName,
+        uName, vName, damageName }; // TODO and others
+    // If the above fields are found in the supplied ModelState, output them
+    for (auto entry : state.data) {
+        if (restartFields.count(entry.first)) {
+            // Get the type, then relevant vector of NetCDF dimensions
+            ModelArray::Type type = entry.second.getType();
+            std::vector<size_t> start;
+            std::vector<size_t> count;
+            if (ModelArray::hasDoF(type)) {
+                auto ncomps = entry.second.nComponents();
+                start.push_back(0);
+                count.push_back(ncomps);
+            }
+            for (ModelArray::Dimension dt : entry.second.typeDimensions.at(type)) {
+                auto dim = entry.second.definedDimensions.at(dt);
+                start.push_back(dim.start);
+                count.push_back(dim.localLength);
+            }
+            // dims are looped in [dg], x, y, [z] order so start and count
+            // order must be reveresed to match order netcdf expects
+            std::reverse(start.begin(), start.end());
+            std::reverse(count.begin(), count.end());
+
+            std::vector<netCDF::NcDim>& ncDims = dimMap.at(type);
+            netCDF::NcVar var(dataGroup.addVar(entry.first, netCDF::ncDouble, ncDims));
+            var.putAtt(mdiName, netCDF::ncDouble, MissingData::value());
+            var.putVar(start, count, entry.second.getData());
+        }
+    }
+
+    ncFile.close();
+}
+
+void ParaGridIO::writeDiagnosticTime(
+    const ModelState& state, const ModelMetadata& meta, const std::string& filePath)
+{
+    // TODO: XIOS implementation
+
+    bool isNew = openFilesAndIndices.count(filePath) <= 0;
+    size_t nt = (isNew) ? 0 : ++openFilesAndIndices.at(filePath).second;
+    if (isNew) {
+        // Open a new file and emplace it in the map of open files.
+        // Set the initial time to be zero (assigned above)
+        // Piecewise construction is necessary to correctly construct the file handle/time index
+        // pair
+#ifdef USE_MPI
+        openFilesAndIndices.emplace(std::piecewise_construct, std::make_tuple(filePath),
+            std::forward_as_tuple(std::piecewise_construct,
+                std::forward_as_tuple(filePath, netCDF::NcFile::replace, meta.mpiComm),
+                std::forward_as_tuple(nt)));
+#else
+        openFilesAndIndices.emplace(std::piecewise_construct, std::make_tuple(filePath),
+            std::forward_as_tuple(std::piecewise_construct,
+                std::forward_as_tuple(filePath, netCDF::NcFile::replace),
+                std::forward_as_tuple(nt)));
+#endif
+    }
+    // Get the file handle
+    NetCDFFileType& ncFile = openFilesAndIndices.at(filePath).first;
+
+    // Get the netCDF groups, creating them if necessary
+    netCDF::NcGroup metaGroup = (isNew) ? ncFile.addGroup(IStructure::metadataNodeName())
+                                        : ncFile.getGroup(IStructure::metadataNodeName());
+    netCDF::NcGroup dataGroup = (isNew) ? ncFile.addGroup(IStructure::dataNodeName())
+                                        : ncFile.getGroup(IStructure::dataNodeName());
+
+    if (isNew) {
+        // Write the common structure and time metadata
+        CommonRestartMetadata::writeStructureType(ncFile, meta);
+        CommonRestartMetadata::writeRestartMetadata(metaGroup, meta);
+    }
+    // Get the unlimited time dimension, creating it if necessary
+    netCDF::NcDim timeDim = (isNew) ? dataGroup.addDim(timeName) : dataGroup.getDim(timeName);
+
+    // All of the dimensions defined by the data at a particular timestep.
+    std::map<ModelArray::Dimension, netCDF::NcDim> ncFromMAMap;
+    for (auto entry : ModelArray::definedDimensions) {
+        ModelArray::Dimension dim = entry.first;
+        size_t dimSz = (dimCompMap.count(dim)) ? ModelArray::nComponents(dimCompMap.at(dim))
+                                               : dimSz = entry.second.globalLength;
+        ncFromMAMap[dim] = (isNew) ? dataGroup.addDim(entry.second.name, dimSz)
+                                   : dataGroup.getDim(entry.second.name);
+    }
+
+    // Also create the sets of dimensions to be connected to the data fields
+    std::map<ModelArray::Type, std::vector<netCDF::NcDim>> dimMap;
+    // Create the index and size arrays
+    std::map<ModelArray::Type, std::vector<size_t>> startMap;
+    std::map<ModelArray::Type, std::vector<size_t>> countMap;
+    for (auto entry : ModelArray::typeDimensions) {
+        ModelArray::Type type = entry.first;
+        std::vector<netCDF::NcDim> ncDims;
+        std::vector<size_t> start;
+        std::vector<size_t> count;
+
+        // Everything that has components needs that dimension, too
+        if (ModelArray::hasDoF(type)) {
+            if (type == ModelArray::Type::VERTEX && !isNew)
+                continue;
+            auto ncomps = ModelArray::nComponents(type);
+            auto dim = ModelArray::componentMap.at(type);
+            ncDims.push_back(ncFromMAMap.at(dim));
+            start.push_back(0);
+            count.push_back(ncomps);
+        }
+        for (auto dt : entry.second) {
+            auto dim = ModelArray::definedDimensions.at(dt);
+            ncDims.push_back(ncFromMAMap.at(dt));
+            start.push_back(dim.start);
+            count.push_back(dim.localLength);
+        }
+
+        // Deal with VERTEX in each case
+        // Add the time dimension for all types that are not VERTEX
+        if (type != ModelArray::Type::VERTEX) {
+            ncDims.push_back(timeDim);
+            start.push_back(nt);
+            count.push_back(1UL);
+        } else if (!isNew) {
+            // For VERTEX in an existing file, there is nothing more to be done
+            continue;
+        }
+
+        std::reverse(ncDims.begin(), ncDims.end());
+        std::reverse(start.begin(), start.end());
+        std::reverse(count.begin(), count.end());
+
+        dimMap[type] = ncDims;
+        startMap[type] = start;
+        countMap[type] = count;
+    }
+
+    // Create a special timeless set of dimensions for the landmask
+    std::vector<netCDF::NcDim> maskDims;
+    std::vector<size_t> maskIndexes;
+    std::vector<size_t> maskExtents;
+    if (isNew) {
+        for (ModelArray::Dimension& maDim : ModelArray::typeDimensions.at(ModelArray::Type::H)) {
+            maskDims.push_back(ncFromMAMap.at(maDim));
+        }
+        maskIndexes = { 0, 0 };
+        maskExtents = { ModelArray::definedDimensions
+                            .at(ModelArray::typeDimensions.at(ModelArray::Type::H)[0])
+                            .localLength,
+            ModelArray::definedDimensions.at(ModelArray::typeDimensions.at(ModelArray::Type::H)[1])
+                .localLength };
+    }
+
+    // Put the time axis variable
+    std::vector<netCDF::NcDim> timeDimVec = { timeDim };
+    netCDF::NcVar timeVar((isNew) ? dataGroup.addVar(timeName, netCDF::ncDouble, timeDimVec)
+                                  : dataGroup.getVar(timeName));
+    double secondsSinceEpoch = (meta.time() - TimePoint()).seconds();
+#ifdef USE_MPI
+    netCDF::setVariableCollective(timeVar, dataGroup);
+#endif
+    timeVar.putVar({ nt }, { 1 }, &secondsSinceEpoch);
+
+    // Write the data
+    for (auto entry : state.data) {
+        ModelArray::Type type = entry.second.getType();
+        // Skip timeless fields (mask, coordinates) on existing files
+        if (!isNew && (entry.first == maskName || type == ModelArray::Type::VERTEX))
+            continue;
+        if (entry.first == maskName) {
+            // Land mask in a new file (since it was skipped above in existing files)
+            netCDF::NcVar var(dataGroup.addVar(maskName, netCDF::ncDouble, maskDims));
+            // No missing data
+#ifdef USE_MPI
+            netCDF::setVariableCollective(var, dataGroup);
+#endif
+            var.putVar(maskIndexes, maskExtents, entry.second.getData());
+
+        } else {
+            std::vector<netCDF::NcDim>& ncDims = dimMap.at(type);
+            // Get the variable object, either creating a new one or getting the existing one
+            netCDF::NcVar var((isNew) ? dataGroup.addVar(entry.first, netCDF::ncDouble, ncDims)
+                                      : dataGroup.getVar(entry.first));
+            if (isNew)
+                var.putAtt(mdiName, netCDF::ncDouble, MissingData::value());
+#ifdef USE_MPI
+            netCDF::setVariableCollective(var, dataGroup);
+#endif
+            var.putVar(startMap.at(type), countMap.at(type), entry.second.getData());
+        }
+    }
+}
+
+// TODO: This method will likely be dropped in the XIOS implementation
+void ParaGridIO::close(const std::string& filePath)
+{
+    if (getOpenFilesAndIndices().count(filePath) > 0) {
+        getOpenFilesAndIndices().at(filePath).first.close();
+        getOpenFilesAndIndices().erase(filePath);
+    }
+}
+
+// TODO: This method will likely be dropped in the XIOS implementation
+void ParaGridIO::closeAllFiles()
+{
+    std::cout << "ParaGridIO::closeAllFiles: closing " << getOpenFilesAndIndices().size()
+              << " files" << std::endl;
+    while (getOpenFilesAndIndices().size() > 0) {
+        close(getOpenFilesAndIndices().begin()->first);
+    }
+}
+
+} /* namespace Nextsim */
+#endif /* USE_XIOS */
diff --git a/core/src/StructureFactory.cpp b/core/src/StructureFactory.cpp
index fb893e796..e3a5cd269 100644
--- a/core/src/StructureFactory.cpp
+++ b/core/src/StructureFactory.cpp
@@ -1,7 +1,7 @@
 /*!
  * @file StructureFactory.cpp
  *
- * @date Jan 18, 2022
+ * @date 09 Dec 2024
  * @author Tim Spain <timothy.spain@nersc.no>
  * @author Kacper Kornet <kk562@cam.ac.uk>
  */
@@ -13,8 +13,11 @@
 #include "include/NextsimModule.hpp"
 
 #include "include/RectGridIO.hpp"
-
+#ifdef USE_XIOS
+#include "include/ParaGridIO_Xios.hpp"
+#else
 #include "include/ParaGridIO.hpp"
+#endif
 
 #include <ncFile.h>
 #include <ncGroup.h>
diff --git a/core/src/include/ParaGridIO.hpp b/core/src/include/ParaGridIO.hpp
index 34e803b24..5db8fe9b0 100644
--- a/core/src/include/ParaGridIO.hpp
+++ b/core/src/include/ParaGridIO.hpp
@@ -1,10 +1,11 @@
 /*!
  * @file ParaGridIO.hpp
  *
- * @date Oct 24, 2022
+ * @date 09 Dec 2024
  * @author Tim Spain <timothy.spain@nersc.no>
  */
 
+#ifndef USE_XIOS
 #ifndef PARAGRIDIO_HPP
 #define PARAGRIDIO_HPP
 
@@ -125,3 +126,4 @@ class ParaGridIO : public ParametricGrid::IParaGridIO {
 } /* namespace Nextsim */
 
 #endif /* PARAGRIDIO_HPP */
+#endif /* not USE_XIOS */
diff --git a/core/src/include/ParaGridIO_Xios.hpp b/core/src/include/ParaGridIO_Xios.hpp
new file mode 100644
index 000000000..6495fe518
--- /dev/null
+++ b/core/src/include/ParaGridIO_Xios.hpp
@@ -0,0 +1,138 @@
+/*!
+ * @file ParaGridIO.hpp
+ *
+ * @date 09 Dec 2024
+ * @author Tim Spain <timothy.spain@nersc.no>
+ */
+
+#ifdef USE_XIOS
+#ifndef PARAGRIDIO_HPP
+#define PARAGRIDIO_HPP
+
+#include "StructureModule/include/ParametricGrid.hpp"
+#include "include/Xios.hpp"
+
+#ifdef USE_MPI
+#include "ParallelNetcdfFile.hpp"
+#endif
+#include <map>
+#include <ncFile.h>
+#include <string>
+
+namespace Nextsim {
+
+/*!
+ * A class to perform input and output for the ParametricGrid class using XIOS.
+ * Unlike the other GridIO classes, this will hold non-restart files open to
+ * accumulate data until closed using the close function.
+ */
+class ParaGridIO : public ParametricGrid::IParaGridIO {
+public:
+// TODO: This member will likely be dropped in the XIOS implementation
+#ifdef USE_MPI
+    using NetCDFFileType = netCDF::NcFilePar;
+#else
+    using NetCDFFileType = netCDF::NcFile;
+#endif
+
+    ParaGridIO(ParametricGrid& grid);
+    virtual ~ParaGridIO();
+
+    /*!
+     * Retrieves the ModelState from a restart file of the parametric_grid type
+     * using XIOS.
+     *
+     * @param filePath The file path containing the file to be read.
+     */
+#ifdef USE_MPI
+    ModelState getModelState(const std::string& filePath, ModelMetadata& metadata) override;
+#else
+    ModelState getModelState(const std::string& filePath) override;
+#endif
+
+    /*!
+     * @brief Writes the ModelState to a given file location from the provided
+     * model data and metadata using XIOS.
+     *
+     * @params state The model state and configuration object.
+     * @params metadata The model metadata (principally the initial file
+     * creation model time).
+     * @params filePath The path for the restart file.
+     */
+    void dumpModelState(
+        const ModelState& state, const ModelMetadata& meta, const std::string& filePath) override;
+
+    /*!
+     * @brief Reads forcings from a ParameticGrid flavoured file using XIOS.
+     *
+     * @param forcings The names of the forcings required.
+     * @param time The time for which to get the forcings.
+     * @param filePath Path to the file to read.
+     */
+    ModelState readForcingTime(const std::set<std::string>& forcings, const TimePoint& time,
+        const std::string& filePath) override
+    {
+        return readForcingTimeStatic(forcings, time, filePath);
+    }
+
+    /*!
+     * @brief Writes diagnostic data to a file using XIOS.
+     *
+     * @param state The state to write to the file.
+     * @param time The time of the passed data.
+     * @param filePath Path of the file to write to.
+     */
+    void writeDiagnosticTime(
+        const ModelState& state, const ModelMetadata& meta, const std::string& filePath) override;
+
+    // TODO: This method will likely be dropped in the XIOS implementation
+    /*!
+     * Closes an open diagnostic file Does nothing when provided with a
+     * restart file name.
+     *
+     * @param filePath The path to the file to be closed.
+     */
+    static void close(const std::string& filePath);
+
+    static ModelState readForcingTimeStatic(
+        const std::set<std::string>& forcings, const TimePoint& time, const std::string& filePath);
+
+private:
+    typedef std::map<std::string, std::pair<NetCDFFileType, size_t>> FileAndIndexMap;
+
+    ParaGridIO() = delete;
+    ParaGridIO(const ParaGridIO& other) = delete;
+    ParaGridIO& operator=(const ParaGridIO& other) = delete;
+
+    // TODO: These members will likely be dropped in the XIOS implementation
+    const std::map<std::string, ModelArray::Type> dimensionKeys;
+    const std::map<ModelArray::Dimension, bool> isDG;
+    const std::map<ModelArray::Dimension, ModelArray::Type> dimCompMap;
+
+    // Ensures that static variables are created in the correct order.
+    // TODO: This method will likely be dropped in the XIOS implementation
+    static void makeDimCompMap();
+
+    // Closes all still-open NetCDF files
+    // TODO: This method will likely be dropped in the XIOS implementation
+    static void closeAllFiles();
+
+    // Existing or open files are a property of the computer outside the individual
+    // class instance, so they are singletons.
+    // TODO: This member will likely be dropped in the XIOS implementation
+    FileAndIndexMap& openFilesAndIndices;
+    // TODO: This method will likely be dropped in the XIOS implementation
+    inline static FileAndIndexMap& getOpenFilesAndIndices()
+    {
+        static FileAndIndexMap fim;
+        return fim;
+    }
+
+    //! Performs some one-time initialization for the class. Returns true.
+    static bool doOnce();
+};
+
+} /* namespace Nextsim */
+
+#endif /* PARAGRIDIO_HPP */
+#endif /* USE_XIOS */
diff --git a/core/test/CMakeLists.txt b/core/test/CMakeLists.txt
index ed8e02992..e43f5199e 100644
--- a/core/test/CMakeLists.txt
+++ b/core/test/CMakeLists.txt
@@ -38,39 +38,6 @@ if(ENABLE_MPI)
         DEPENDS partition_metadata_3.nc partition_metadata_2.nc
     )
 
-    add_executable(testRectGrid_MPI3 "RectGrid_test.cpp" "MainMPI.cpp")
-    target_compile_definitions(
-        testRectGrid_MPI3
-        PRIVATE TEST_FILES_DIR=\"${CMAKE_CURRENT_BINARY_DIR}\"
-    )
-    target_include_directories(
-        testRectGrid_MPI3
-        PRIVATE ${MODEL_INCLUDE_DIR} "${ModulesRoot}/StructureModule"
-    )
-    target_link_libraries(testRectGrid_MPI3 PRIVATE nextsimlib doctest::doctest)
-
-    add_executable(testParaGrid_MPI2 "ParaGrid_test.cpp" "MainMPI.cpp")
-    target_compile_definitions(
-        testParaGrid_MPI2
-        PRIVATE
-            USE_MPI
-            TEST_FILES_DIR=\"${CMAKE_CURRENT_BINARY_DIR}\"
-            TEST_FILE_SOURCE=\"${CMAKE_CURRENT_SOURCE_DIR}\"
-    )
-    target_include_directories(
-        testParaGrid_MPI2
-        PRIVATE ${MODEL_INCLUDE_DIR} "${ModulesRoot}/StructureModule"
-    )
-    target_link_libraries(testParaGrid_MPI2 PRIVATE nextsimlib doctest::doctest)
-
-    add_executable(testConfigOutput_MPI2 "ConfigOutput_test.cpp" "MainMPI.cpp")
-    target_compile_definitions(
-        testConfigOutput_MPI2
-        PRIVATE USE_MPI TEST_FILES_DIR=\"${CMAKE_CURRENT_BINARY_DIR}\"
-    )
-    target_include_directories(testConfigOutput_MPI2 PRIVATE ${MODEL_INCLUDE_DIR})
-    target_link_libraries(testConfigOutput_MPI2 PRIVATE nextsimlib doctest::doctest)
-
     if(ENABLE_XIOS)
         file(
             CREATE_LINK
@@ -89,12 +56,13 @@ if(ENABLE_MPI)
             "${xios_EXTERNS}/blitz/"
             "${xios_EXTERNS}/rapidxml/include"
         )
+        set(MODEL_INCLUDE_DIR "${MODEL_INCLUDE_DIR}" "${XIOS_INCLUDE_LIST}")
 
         add_executable(testXiosCalendar_MPI2 "XiosCalendar_test.cpp" "MainMPI.cpp")
         target_compile_definitions(testXiosCalendar_MPI2 PRIVATE USE_XIOS)
         target_include_directories(
             testXiosCalendar_MPI2
-            PRIVATE "${MODEL_INCLUDE_DIR}" "${XIOS_INCLUDE_LIST}" "${ModulesRoot}/StructureModule"
+            PRIVATE "${MODEL_INCLUDE_DIR}" "${ModulesRoot}/StructureModule"
         )
         target_link_libraries(testXiosCalendar_MPI2 PRIVATE nextsimlib doctest::doctest)
 
@@ -102,7 +70,7 @@ if(ENABLE_MPI)
         target_compile_definitions(testXiosAxis_MPI2 PRIVATE USE_XIOS)
         target_include_directories(
             testXiosAxis_MPI2
-            PRIVATE "${MODEL_INCLUDE_DIR}" "${XIOS_INCLUDE_LIST}" "${ModulesRoot}/StructureModule"
+            PRIVATE "${MODEL_INCLUDE_DIR}" "${ModulesRoot}/StructureModule"
         )
         target_link_libraries(testXiosAxis_MPI2 PRIVATE nextsimlib doctest::doctest)
 
@@ -110,7 +78,7 @@ if(ENABLE_MPI)
         target_compile_definitions(testXiosDomain_MPI2 PRIVATE USE_XIOS)
         target_include_directories(
             testXiosDomain_MPI2
-            PRIVATE "${MODEL_INCLUDE_DIR}" "${XIOS_INCLUDE_LIST}" "${ModulesRoot}/StructureModule"
+            PRIVATE "${MODEL_INCLUDE_DIR}" "${ModulesRoot}/StructureModule"
         )
         target_link_libraries(testXiosDomain_MPI2 PRIVATE nextsimlib doctest::doctest)
 
@@ -118,7 +86,7 @@ if(ENABLE_MPI)
         target_compile_definitions(testXiosGrid_MPI2 PRIVATE USE_XIOS)
         target_include_directories(
             testXiosGrid_MPI2
-            PRIVATE "${MODEL_INCLUDE_DIR}" "${XIOS_INCLUDE_LIST}" "${ModulesRoot}/StructureModule"
+            PRIVATE "${MODEL_INCLUDE_DIR}" "${ModulesRoot}/StructureModule"
         )
         target_link_libraries(testXiosGrid_MPI2 PRIVATE nextsimlib doctest::doctest)
 
@@ -126,7 +94,7 @@ if(ENABLE_MPI)
         target_compile_definitions(testXiosField_MPI2 PRIVATE USE_XIOS)
         target_include_directories(
             testXiosField_MPI2
-            PRIVATE "${MODEL_INCLUDE_DIR}" "${XIOS_INCLUDE_LIST}" "${ModulesRoot}/StructureModule"
+            PRIVATE "${MODEL_INCLUDE_DIR}" "${ModulesRoot}/StructureModule"
         )
         target_link_libraries(testXiosField_MPI2 PRIVATE nextsimlib doctest::doctest)
 
@@ -134,7 +102,7 @@ if(ENABLE_MPI)
         target_compile_definitions(testXiosFile_MPI2 PRIVATE USE_XIOS)
         target_include_directories(
             testXiosFile_MPI2
-            PRIVATE "${MODEL_INCLUDE_DIR}" "${XIOS_INCLUDE_LIST}" "${ModulesRoot}/StructureModule"
+            PRIVATE "${MODEL_INCLUDE_DIR}" "${ModulesRoot}/StructureModule"
         )
         target_link_libraries(testXiosFile_MPI2 PRIVATE nextsimlib doctest::doctest)
 
@@ -142,10 +110,43 @@ if(ENABLE_MPI)
         target_compile_definitions(testXiosReadWrite_MPI2 PRIVATE USE_XIOS)
         target_include_directories(
             testXiosReadWrite_MPI2
-            PRIVATE "${MODEL_INCLUDE_DIR}" "${XIOS_INCLUDE_LIST}" "${ModulesRoot}/StructureModule"
+            PRIVATE "${MODEL_INCLUDE_DIR}" "${ModulesRoot}/StructureModule"
         )
         target_link_libraries(testXiosReadWrite_MPI2 PRIVATE nextsimlib doctest::doctest)
     endif()
+
+    add_executable(testRectGrid_MPI3 "RectGrid_test.cpp" "MainMPI.cpp")
+    target_compile_definitions(
+        testRectGrid_MPI3
+        PRIVATE TEST_FILES_DIR=\"${CMAKE_CURRENT_BINARY_DIR}\"
+    )
+    target_include_directories(
+        testRectGrid_MPI3
+        PRIVATE ${MODEL_INCLUDE_DIR} "${ModulesRoot}/StructureModule"
+    )
+    target_link_libraries(testRectGrid_MPI3 PRIVATE nextsimlib doctest::doctest)
+
+    add_executable(testParaGrid_MPI2 "ParaGrid_test.cpp" "MainMPI.cpp")
+    target_compile_definitions(
+        testParaGrid_MPI2
+        PRIVATE
+            USE_MPI
+            TEST_FILES_DIR=\"${CMAKE_CURRENT_BINARY_DIR}\"
+            TEST_FILE_SOURCE=\"${CMAKE_CURRENT_SOURCE_DIR}\"
+    )
+    target_include_directories(
+        testParaGrid_MPI2
+        PRIVATE ${MODEL_INCLUDE_DIR} "${ModulesRoot}/StructureModule"
+    )
+    target_link_libraries(testParaGrid_MPI2 PRIVATE nextsimlib doctest::doctest)
+
+    add_executable(testConfigOutput_MPI2 "ConfigOutput_test.cpp" "MainMPI.cpp")
+    target_compile_definitions(
+        testConfigOutput_MPI2
+        PRIVATE USE_MPI TEST_FILES_DIR=\"${CMAKE_CURRENT_BINARY_DIR}\"
+    )
+    target_include_directories(testConfigOutput_MPI2 PRIVATE ${MODEL_INCLUDE_DIR})
+    target_link_libraries(testConfigOutput_MPI2 PRIVATE nextsimlib doctest::doctest)
 else()
     add_executable(testRectGrid "RectGrid_test.cpp")
     target_compile_definitions(testRectGrid PRIVATE TEST_FILES_DIR=\"${CMAKE_CURRENT_BINARY_DIR}\")
diff --git a/core/test/ParaGrid_test.cpp b/core/test/ParaGrid_test.cpp
index f4e41e0c1..74f7c6f59 100644
--- a/core/test/ParaGrid_test.cpp
+++ b/core/test/ParaGrid_test.cpp
@@ -1,7 +1,7 @@
 /*!
  * @file ParaGrid_test.cpp
  *
- * @date 24 Sep 2024
+ * @date 09 Dec 2024
  * @author Tim Spain <timothy.spain@nersc.no>
  */
 
@@ -9,6 +9,7 @@
 #include <cstdlib>
 #ifdef USE_MPI
 #include <doctest/extensions/doctest_mpi.h>
+#undef INFO
 #else
 #define DOCTEST_CONFIG_IMPLEMENT_WITH_MAIN
 #include <doctest/doctest.h>
@@ -17,10 +18,14 @@
 #include "include/Configurator.hpp"
 #include "include/ConfiguredModule.hpp"
 #include "include/NZLevels.hpp"
+#ifdef USE_XIOS
+#include "include/ParaGridIO_Xios.hpp"
+#else
 #include "include/ParaGridIO.hpp"
-#include "include/ParametricGrid.hpp"
+#endif
 #include "include/IStructure.hpp"
 #include "include/NextsimModule.hpp"
+#include "include/ParametricGrid.hpp"
 #include "include/gridNames.hpp"
 
 #include <cmath>
diff --git a/core/test/XiosReadWrite_test.cpp b/core/test/XiosReadWrite_test.cpp
index aaab7da45..51ac403e6 100644
--- a/core/test/XiosReadWrite_test.cpp
+++ b/core/test/XiosReadWrite_test.cpp
@@ -1,7 +1,7 @@
 /*!
  * @file    XiosReadWrite_test.cpp
  * @author  Joe Wallwork <jw2423@cam.ac.uk>
- * @date    19 Nov 2024
+ * @date    09 Dec 2024
  * @brief   Tests for XIOS write method
  * @details
  * This test is designed to test the read and write methods of the C++
@@ -13,7 +13,7 @@
 
 #include "StructureModule/include/ParametricGrid.hpp"
 #include "include/NextsimModule.hpp"
-#include "include/ParaGridIO.hpp"
+#include "include/ParaGridIO_Xios.hpp"
 #include "include/Xios.hpp"
 
 #include <filesystem>
diff --git a/physics/src/modules/AtmosphereBoundaryModule/ERA5Atmosphere.cpp b/physics/src/modules/AtmosphereBoundaryModule/ERA5Atmosphere.cpp
index 75ee026f7..011bb21f7 100644
--- a/physics/src/modules/AtmosphereBoundaryModule/ERA5Atmosphere.cpp
+++ b/physics/src/modules/AtmosphereBoundaryModule/ERA5Atmosphere.cpp
@@ -1,7 +1,7 @@
 /*!
  * @file ERA5Atmosphere.cpp
  *
- * @date 24 Sep 2024
+ * @date 09 Dec 2024
  * @author Tim Spain <timothy.spain@nersc.no>
  */
 
@@ -9,7 +9,11 @@
 
 #include "include/Finalizer.hpp"
 #include "include/NextsimModule.hpp"
+#ifdef USE_XIOS
+#include "include/ParaGridIO_Xios.hpp"
+#else
 #include "include/ParaGridIO.hpp"
+#endif
 
 namespace Nextsim {
 
diff --git a/physics/src/modules/OceanBoundaryModule/TOPAZOcean.cpp b/physics/src/modules/OceanBoundaryModule/TOPAZOcean.cpp
index 70eb86bae..8137a0ae1 100644
--- a/physics/src/modules/OceanBoundaryModule/TOPAZOcean.cpp
+++ b/physics/src/modules/OceanBoundaryModule/TOPAZOcean.cpp
@@ -1,17 +1,21 @@
 /*!
  * @file TOPAZOcean.cpp
  *
- * @date 24 Sep 2024
+ * @date 09 Dec 2024
  * @author Tim Spain <timothy.spain@nersc.no>
  */
 
 #include "include/TOPAZOcean.hpp"
 
 #include "include/Finalizer.hpp"
-#include "include/IIceOceanHeatFlux.hpp"
 #include "include/IFreezingPoint.hpp"
+#include "include/IIceOceanHeatFlux.hpp"
 #include "include/NextsimModule.hpp"
+#ifdef USE_XIOS
+#include "include/ParaGridIO_Xios.hpp"
+#else
 #include "include/ParaGridIO.hpp"
+#endif
 #include "include/constants.hpp"
 
 namespace Nextsim {

From ddd19f3e32f4f5e6b60887aec92378284c984044 Mon Sep 17 00:00:00 2001
From: Joe Wallwork <jw2423@cam.ac.uk>
Date: Mon, 9 Dec 2024 18:07:52 +0000
Subject: [PATCH 2/4] Add extra workflow job for testing without XIOS

---
 .github/workflows/test_suite.yml | 40 ++++++++++++++++++++++++++++----
 1 file changed, 36 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/test_suite.yml b/.github/workflows/test_suite.yml
index 3056b53e5..f7c502653 100644
--- a/.github/workflows/test_suite.yml
+++ b/.github/workflows/test_suite.yml
@@ -50,9 +50,43 @@ jobs:
         cd test
         python3 ThermoIntegration_test.py
         ./run_test_jan2010_integration_test.sh python3
-        cd -
 
-  test-ubuntu-mpi:
+  test-ubuntu-mpi-noxios:
+
+    runs-on: ubuntu-22.04
+    container:
+      image: ghcr.io/nextsimhub/nextsimdg-dev-env:latest
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: build and compile with MPI but not XIOS
+      run: |
+        . /opt/spack-environment/activate.sh
+        mkdir -p build && cd build
+        cmake -DENABLE_MPI=ON -DENABLE_XIOS=OFF -DCMAKE_CXX_COMPILER="$(which mpic++)" ..
+        make -j 4
+
+    - name: run MPI tests
+      run: |
+        . /opt/spack-environment/activate.sh
+        apt update
+        apt install -y wget
+        cd build
+        (cd core/test && wget "ftp://ftp.nersc.no/nextsim/netCDF/partition_metadata_1.nc")
+        for component in core physics dynamics
+        do
+            cd $component/test
+            for file in $(find test* -maxdepth 0 -type f)
+            do
+              echo $file
+              nprocs=$(echo $file | sed -r "s/.*MPI([0-9]+)/\1/")
+              mpirun --allow-run-as-root --oversubscribe -n $nprocs ./$file
+            done
+            cd -
+        done
+
+  test-ubuntu-mpi-xios:
 
     runs-on: ubuntu-22.04
     container:
@@ -86,7 +120,6 @@ jobs:
             done
             cd -
         done
-        cd -
 
   test-mac-serial:
 
@@ -138,4 +171,3 @@ jobs:
         cd test
         python ThermoIntegration_test.py
         ./run_test_jan2010_integration_test.sh python
-        cd -

From 1291ae453cfc581d90c42d677709715070466f1e Mon Sep 17 00:00:00 2001
From: Joe Wallwork <jw2423@cam.ac.uk>
Date: Tue, 10 Dec 2024 10:45:37 +0000
Subject: [PATCH 3/4] Drop ParaGridIO_Xios.hpp

---
 core/src/CMakeLists.txt                       |   6 +-
 core/src/ParaGridIO_Xios.cpp                  |   5 +-
 core/src/StructureFactory.cpp                 |   8 +-
 core/src/include/ParaGridIO.hpp               |   4 +-
 core/src/include/ParaGridIO_Xios.hpp          | 138 ------------------
 core/test/ParaGrid_test.cpp                   |  10 +-
 core/test/XiosReadWrite_test.cpp              |   4 +-
 .../ERA5Atmosphere.cpp                        |   6 +-
 .../OceanBoundaryModule/TOPAZOcean.cpp        |   6 +-
 9 files changed, 16 insertions(+), 171 deletions(-)
 delete mode 100644 core/src/include/ParaGridIO_Xios.hpp

diff --git a/core/src/CMakeLists.txt b/core/src/CMakeLists.txt
index 0c230d58c..97ce23c67 100644
--- a/core/src/CMakeLists.txt
+++ b/core/src/CMakeLists.txt
@@ -1,9 +1,9 @@
 # Sources for the main neXtSIM model
 
 if(ENABLE_XIOS)
-  set(ParaGridIO_Impl "ParaGridIO_Xios")
+  set(ParaGridIO_Impl "ParaGridIO_Xios.cpp")
 else()
-  set(ParaGridIO_Impl "ParaGridIO")
+  set(ParaGridIO_Impl "ParaGridIO.cpp")
 endif()
 
 set(BaseSources
@@ -17,7 +17,7 @@ set(BaseSources
     "CommandLineParser.cpp"
     "CommonRestartMetadata.cpp"
     "RectGridIO.cpp"
-    "${ParaGridIO_Impl}.cpp"
+    "${ParaGridIO_Impl}"
     "FileCallbackCloser.cpp"
     "Finalizer.cpp"
     "DevStep.cpp"
diff --git a/core/src/ParaGridIO_Xios.cpp b/core/src/ParaGridIO_Xios.cpp
index 3aeea3154..902ed0a45 100644
--- a/core/src/ParaGridIO_Xios.cpp
+++ b/core/src/ParaGridIO_Xios.cpp
@@ -1,17 +1,18 @@
 /*!
  * @file ParaGridIO_Xios.cpp
  *
- * @date 09 Dec 2024
+ * @date 10 Dec 2024
  * @author Tim Spain <timothy.spain@nersc.no>
  * @author Joe Wallwork <jw2423@cam.ac.uk>
  */
 
 #ifdef USE_XIOS
-#include "include/ParaGridIO_Xios.hpp"
+#include "include/ParaGridIO.hpp"
 
 #include "include/CommonRestartMetadata.hpp"
 #include "include/FileCallbackCloser.hpp"
 #include "include/Finalizer.hpp"
+#include "include/Logged.hpp"
 #include "include/MissingData.hpp"
 #include "include/NZLevels.hpp"
 #include "include/gridNames.hpp"
diff --git a/core/src/StructureFactory.cpp b/core/src/StructureFactory.cpp
index e3a5cd269..f41b95441 100644
--- a/core/src/StructureFactory.cpp
+++ b/core/src/StructureFactory.cpp
@@ -1,7 +1,7 @@
 /*!
  * @file StructureFactory.cpp
  *
- * @date 09 Dec 2024
+ * @date 10 Dec 2024
  * @author Tim Spain <timothy.spain@nersc.no>
  * @author Kacper Kornet <kk562@cam.ac.uk>
  */
@@ -12,12 +12,8 @@
 #include "include/IStructure.hpp"
 #include "include/NextsimModule.hpp"
 
-#include "include/RectGridIO.hpp"
-#ifdef USE_XIOS
-#include "include/ParaGridIO_Xios.hpp"
-#else
 #include "include/ParaGridIO.hpp"
-#endif
+#include "include/RectGridIO.hpp"
 
 #include <ncFile.h>
 #include <ncGroup.h>
diff --git a/core/src/include/ParaGridIO.hpp b/core/src/include/ParaGridIO.hpp
index 5db8fe9b0..89fc4ec02 100644
--- a/core/src/include/ParaGridIO.hpp
+++ b/core/src/include/ParaGridIO.hpp
@@ -1,11 +1,10 @@
 /*!
  * @file ParaGridIO.hpp
  *
- * @date 09 Dec 2024
+ * @date 10 Dec 2024
  * @author Tim Spain <timothy.spain@nersc.no>
  */
 
-#ifndef USE_XIOS
 #ifndef PARAGRIDIO_HPP
 #define PARAGRIDIO_HPP
 
@@ -126,4 +125,3 @@ class ParaGridIO : public ParametricGrid::IParaGridIO {
 } /* namespace Nextsim */
 
 #endif /* PARAGRIDIO_HPP */
-#endif /* not USE_XIOS */
diff --git a/core/src/include/ParaGridIO_Xios.hpp b/core/src/include/ParaGridIO_Xios.hpp
deleted file mode 100644
index 6495fe518..000000000
--- a/core/src/include/ParaGridIO_Xios.hpp
+++ /dev/null
@@ -1,138 +0,0 @@
-/*!
- * @file ParaGridIO.hpp
- *
- * @date 09 Dec 2024
- * @author Tim Spain <timothy.spain@nersc.no>
- */
-
-#ifdef USE_XIOS
-#ifndef PARAGRIDIO_HPP
-#define PARAGRIDIO_HPP
-
-#include "StructureModule/include/ParametricGrid.hpp"
-#include "include/Xios.hpp"
-
-#ifdef USE_MPI
-#include "ParallelNetcdfFile.hpp"
-#endif
-#include <map>
-#include <ncFile.h>
-#include <string>
-
-namespace Nextsim {
-
-/*!
- * A class to perform input and output for the ParametricGrid class using XIOS.
- * Unlike the other GridIO classes, this will hold non-restart files open to
- * accumulate data until closed using the close function.
- */
-class ParaGridIO : public ParametricGrid::IParaGridIO {
-public:
-// TODO: This member will likely be dropped in the XIOS implementation
-#ifdef USE_MPI
-    using NetCDFFileType = netCDF::NcFilePar;
-#else
-    using NetCDFFileType = netCDF::NcFile;
-#endif
-
-    ParaGridIO(ParametricGrid& grid);
-    virtual ~ParaGridIO();
-
-    /*!
-     * Retrieves the ModelState from a restart file of the parametric_grid type
-     * using XIOS.
-     *
-     * @param filePath The file path containing the file to be read.
-     */
-#ifdef USE_MPI
-    ModelState getModelState(const std::string& filePath, ModelMetadata& metadata) override;
-#else
-    ModelState getModelState(const std::string& filePath) override;
-#endif
-
-    /*!
-     * @brief Writes the ModelState to a given file location from the provided
-     * model data and metadata using XIOS.
-     *
-     * @params state The model state and configuration object.
-     * @params metadata The model metadata (principally the initial file
-     * creation model time).
-     * @params filePath The path for the restart file.
-     */
-    void dumpModelState(
-        const ModelState& state, const ModelMetadata& meta, const std::string& filePath) override;
-
-    /*!
-     * @brief Reads forcings from a ParameticGrid flavoured file using XIOS.
-     *
-     * @param forcings The names of the forcings required.
-     * @param time The time for which to get the forcings.
-     * @param filePath Path to the file to read.
-     */
-    ModelState readForcingTime(const std::set<std::string>& forcings, const TimePoint& time,
-        const std::string& filePath) override
-    {
-        return readForcingTimeStatic(forcings, time, filePath);
-    }
-
-    /*!
-     * @brief Writes diagnostic data to a file using XIOS.
-     *
-     * @param state The state to write to the file.
-     * @param time The time of the passed data.
-     * @param filePath Path of the file to write to.
-     */
-    void writeDiagnosticTime(
-        const ModelState& state, const ModelMetadata& meta, const std::string& filePath) override;
-
-    // TODO: This method will likely be dropped in the XIOS implementation
-    /*!
-     * Closes an open diagnostic file Does nothing when provided with a
-     * restart file name.
-     *
-     * @param filePath The path to the file to be closed.
-     */
-    static void close(const std::string& filePath);
-
-    static ModelState readForcingTimeStatic(
-        const std::set<std::string>& forcings, const TimePoint& time, const std::string& filePath);
-
-private:
-    typedef std::map<std::string, std::pair<NetCDFFileType, size_t>> FileAndIndexMap;
-
-    ParaGridIO() = delete;
-    ParaGridIO(const ParaGridIO& other) = delete;
-    ParaGridIO& operator=(const ParaGridIO& other) = delete;
-
-    // TODO: These members will likely be dropped in the XIOS implementation
-    const std::map<std::string, ModelArray::Type> dimensionKeys;
-    const std::map<ModelArray::Dimension, bool> isDG;
-    const std::map<ModelArray::Dimension, ModelArray::Type> dimCompMap;
-
-    // Ensures that static variables are created in the correct order.
-    // TODO: This method will likely be dropped in the XIOS implementation
-    static void makeDimCompMap();
-
-    // Closes all still-open NetCDF files
-    // TODO: This method will likely be dropped in the XIOS implementation
-    static void closeAllFiles();
-
-    // Existing or open files are a property of the computer outside the individual
-    // class instance, so they are singletons.
-    // TODO: This member will likely be dropped in the XIOS implementation
-    FileAndIndexMap& openFilesAndIndices;
-    // TODO: This method will likely be dropped in the XIOS implementation
-    inline static FileAndIndexMap& getOpenFilesAndIndices()
-    {
-        static FileAndIndexMap fim;
-        return fim;
-    }
-
-    //! Performs some one-time initialization for the class. Returns true.
-    static bool doOnce();
-};
-
-} /* namespace Nextsim */
-
-#endif /* PARAGRIDIO_HPP */
-#endif /* USE_XIOS */
diff --git a/core/test/ParaGrid_test.cpp b/core/test/ParaGrid_test.cpp
index 74f7c6f59..8f47d76f9 100644
--- a/core/test/ParaGrid_test.cpp
+++ b/core/test/ParaGrid_test.cpp
@@ -1,7 +1,7 @@
 /*!
  * @file ParaGrid_test.cpp
  *
- * @date 09 Dec 2024
+ * @date 10 Dec 2024
  * @author Tim Spain <timothy.spain@nersc.no>
  */
 
@@ -17,14 +17,10 @@
 
 #include "include/Configurator.hpp"
 #include "include/ConfiguredModule.hpp"
-#include "include/NZLevels.hpp"
-#ifdef USE_XIOS
-#include "include/ParaGridIO_Xios.hpp"
-#else
-#include "include/ParaGridIO.hpp"
-#endif
 #include "include/IStructure.hpp"
+#include "include/NZLevels.hpp"
 #include "include/NextsimModule.hpp"
+#include "include/ParaGridIO.hpp"
 #include "include/ParametricGrid.hpp"
 #include "include/gridNames.hpp"
 
diff --git a/core/test/XiosReadWrite_test.cpp b/core/test/XiosReadWrite_test.cpp
index 51ac403e6..05be6c985 100644
--- a/core/test/XiosReadWrite_test.cpp
+++ b/core/test/XiosReadWrite_test.cpp
@@ -1,7 +1,7 @@
 /*!
  * @file    XiosReadWrite_test.cpp
  * @author  Joe Wallwork <jw2423@cam.ac.uk>
- * @date    09 Dec 2024
+ * @date    10 Dec 2024
  * @brief   Tests for XIOS write method
  * @details
  * This test is designed to test the read and write methods of the C++
@@ -13,7 +13,7 @@
 
 #include "StructureModule/include/ParametricGrid.hpp"
 #include "include/NextsimModule.hpp"
-#include "include/ParaGridIO_Xios.hpp"
+#include "include/ParaGridIO.hpp"
 #include "include/Xios.hpp"
 
 #include <filesystem>
diff --git a/physics/src/modules/AtmosphereBoundaryModule/ERA5Atmosphere.cpp b/physics/src/modules/AtmosphereBoundaryModule/ERA5Atmosphere.cpp
index 011bb21f7..d6acd250a 100644
--- a/physics/src/modules/AtmosphereBoundaryModule/ERA5Atmosphere.cpp
+++ b/physics/src/modules/AtmosphereBoundaryModule/ERA5Atmosphere.cpp
@@ -1,7 +1,7 @@
 /*!
  * @file ERA5Atmosphere.cpp
  *
- * @date 09 Dec 2024
+ * @date 10 Dec 2024
  * @author Tim Spain <timothy.spain@nersc.no>
  */
 
@@ -9,11 +9,7 @@
 
 #include "include/Finalizer.hpp"
 #include "include/NextsimModule.hpp"
-#ifdef USE_XIOS
-#include "include/ParaGridIO_Xios.hpp"
-#else
 #include "include/ParaGridIO.hpp"
-#endif
 
 namespace Nextsim {
 
diff --git a/physics/src/modules/OceanBoundaryModule/TOPAZOcean.cpp b/physics/src/modules/OceanBoundaryModule/TOPAZOcean.cpp
index 8137a0ae1..bb871da3c 100644
--- a/physics/src/modules/OceanBoundaryModule/TOPAZOcean.cpp
+++ b/physics/src/modules/OceanBoundaryModule/TOPAZOcean.cpp
@@ -1,7 +1,7 @@
 /*!
  * @file TOPAZOcean.cpp
  *
- * @date 09 Dec 2024
+ * @date 10 Dec 2024
  * @author Tim Spain <timothy.spain@nersc.no>
  */
 
@@ -11,11 +11,7 @@
 #include "include/IFreezingPoint.hpp"
 #include "include/IIceOceanHeatFlux.hpp"
 #include "include/NextsimModule.hpp"
-#ifdef USE_XIOS
-#include "include/ParaGridIO_Xios.hpp"
-#else
 #include "include/ParaGridIO.hpp"
-#endif
 #include "include/constants.hpp"
 
 namespace Nextsim {

From 306f8e954dc3301929f15ebeff1d508ed6d37dff Mon Sep 17 00:00:00 2001
From: Joe Wallwork <jw2423@cam.ac.uk>
Date: Tue, 10 Dec 2024 10:48:44 +0000
Subject: [PATCH 4/4] Revert minor changes

---
 core/src/StructureFactory.cpp                 |  5 +-
 core/src/include/ParaGridIO.hpp               |  2 +-
 core/test/CMakeLists.txt                      | 81 +++++++++----------
 core/test/ParaGrid_test.cpp                   |  7 +-
 core/test/XiosReadWrite_test.cpp              |  2 +-
 .../ERA5Atmosphere.cpp                        |  2 +-
 .../OceanBoundaryModule/TOPAZOcean.cpp        |  4 +-
 7 files changed, 51 insertions(+), 52 deletions(-)

diff --git a/core/src/StructureFactory.cpp b/core/src/StructureFactory.cpp
index f41b95441..fb893e796 100644
--- a/core/src/StructureFactory.cpp
+++ b/core/src/StructureFactory.cpp
@@ -1,7 +1,7 @@
 /*!
  * @file StructureFactory.cpp
  *
- * @date 10 Dec 2024
+ * @date Jan 18, 2022
  * @author Tim Spain <timothy.spain@nersc.no>
  * @author Kacper Kornet <kk562@cam.ac.uk>
  */
@@ -12,9 +12,10 @@
 #include "include/IStructure.hpp"
 #include "include/NextsimModule.hpp"
 
-#include "include/ParaGridIO.hpp"
 #include "include/RectGridIO.hpp"
 
+#include "include/ParaGridIO.hpp"
+
 #include <ncFile.h>
 #include <ncGroup.h>
 #include <ncGroupAtt.h>
diff --git a/core/src/include/ParaGridIO.hpp b/core/src/include/ParaGridIO.hpp
index 89fc4ec02..34e803b24 100644
--- a/core/src/include/ParaGridIO.hpp
+++ b/core/src/include/ParaGridIO.hpp
@@ -1,7 +1,7 @@
 /*!
  * @file ParaGridIO.hpp
  *
- * @date 10 Dec 2024
+ * @date Oct 24, 2022
  * @author Tim Spain <timothy.spain@nersc.no>
  */
 
diff --git a/core/test/CMakeLists.txt b/core/test/CMakeLists.txt
index e43f5199e..ed8e02992 100644
--- a/core/test/CMakeLists.txt
+++ b/core/test/CMakeLists.txt
@@ -38,6 +38,39 @@ if(ENABLE_MPI)
         DEPENDS partition_metadata_3.nc partition_metadata_2.nc
     )
 
+    add_executable(testRectGrid_MPI3 "RectGrid_test.cpp" "MainMPI.cpp")
+    target_compile_definitions(
+        testRectGrid_MPI3
+        PRIVATE TEST_FILES_DIR=\"${CMAKE_CURRENT_BINARY_DIR}\"
+    )
+    target_include_directories(
+        testRectGrid_MPI3
+        PRIVATE ${MODEL_INCLUDE_DIR} "${ModulesRoot}/StructureModule"
+    )
+    target_link_libraries(testRectGrid_MPI3 PRIVATE nextsimlib doctest::doctest)
+
+    add_executable(testParaGrid_MPI2 "ParaGrid_test.cpp" "MainMPI.cpp")
+    target_compile_definitions(
+        testParaGrid_MPI2
+        PRIVATE
+            USE_MPI
+            TEST_FILES_DIR=\"${CMAKE_CURRENT_BINARY_DIR}\"
+            TEST_FILE_SOURCE=\"${CMAKE_CURRENT_SOURCE_DIR}\"
+    )
+    target_include_directories(
+        testParaGrid_MPI2
+        PRIVATE ${MODEL_INCLUDE_DIR} "${ModulesRoot}/StructureModule"
+    )
+    target_link_libraries(testParaGrid_MPI2 PRIVATE nextsimlib doctest::doctest)
+
+    add_executable(testConfigOutput_MPI2 "ConfigOutput_test.cpp" "MainMPI.cpp")
+    target_compile_definitions(
+        testConfigOutput_MPI2
+        PRIVATE USE_MPI TEST_FILES_DIR=\"${CMAKE_CURRENT_BINARY_DIR}\"
+    )
+    target_include_directories(testConfigOutput_MPI2 PRIVATE ${MODEL_INCLUDE_DIR})
+    target_link_libraries(testConfigOutput_MPI2 PRIVATE nextsimlib doctest::doctest)
+
     if(ENABLE_XIOS)
         file(
             CREATE_LINK
@@ -56,13 +89,12 @@ if(ENABLE_MPI)
             "${xios_EXTERNS}/blitz/"
             "${xios_EXTERNS}/rapidxml/include"
         )
-        set(MODEL_INCLUDE_DIR "${MODEL_INCLUDE_DIR}" "${XIOS_INCLUDE_LIST}")
 
         add_executable(testXiosCalendar_MPI2 "XiosCalendar_test.cpp" "MainMPI.cpp")
         target_compile_definitions(testXiosCalendar_MPI2 PRIVATE USE_XIOS)
         target_include_directories(
             testXiosCalendar_MPI2
-            PRIVATE "${MODEL_INCLUDE_DIR}" "${ModulesRoot}/StructureModule"
+            PRIVATE "${MODEL_INCLUDE_DIR}" "${XIOS_INCLUDE_LIST}" "${ModulesRoot}/StructureModule"
         )
         target_link_libraries(testXiosCalendar_MPI2 PRIVATE nextsimlib doctest::doctest)
 
@@ -70,7 +102,7 @@ if(ENABLE_MPI)
         target_compile_definitions(testXiosAxis_MPI2 PRIVATE USE_XIOS)
         target_include_directories(
             testXiosAxis_MPI2
-            PRIVATE "${MODEL_INCLUDE_DIR}" "${ModulesRoot}/StructureModule"
+            PRIVATE "${MODEL_INCLUDE_DIR}" "${XIOS_INCLUDE_LIST}" "${ModulesRoot}/StructureModule"
         )
         target_link_libraries(testXiosAxis_MPI2 PRIVATE nextsimlib doctest::doctest)
 
@@ -78,7 +110,7 @@ if(ENABLE_MPI)
         target_compile_definitions(testXiosDomain_MPI2 PRIVATE USE_XIOS)
         target_include_directories(
             testXiosDomain_MPI2
-            PRIVATE "${MODEL_INCLUDE_DIR}" "${ModulesRoot}/StructureModule"
+            PRIVATE "${MODEL_INCLUDE_DIR}" "${XIOS_INCLUDE_LIST}" "${ModulesRoot}/StructureModule"
         )
         target_link_libraries(testXiosDomain_MPI2 PRIVATE nextsimlib doctest::doctest)
 
@@ -86,7 +118,7 @@ if(ENABLE_MPI)
         target_compile_definitions(testXiosGrid_MPI2 PRIVATE USE_XIOS)
         target_include_directories(
             testXiosGrid_MPI2
-            PRIVATE "${MODEL_INCLUDE_DIR}" "${ModulesRoot}/StructureModule"
+            PRIVATE "${MODEL_INCLUDE_DIR}" "${XIOS_INCLUDE_LIST}" "${ModulesRoot}/StructureModule"
         )
         target_link_libraries(testXiosGrid_MPI2 PRIVATE nextsimlib doctest::doctest)
 
@@ -94,7 +126,7 @@ if(ENABLE_MPI)
         target_compile_definitions(testXiosField_MPI2 PRIVATE USE_XIOS)
         target_include_directories(
             testXiosField_MPI2
-            PRIVATE "${MODEL_INCLUDE_DIR}" "${ModulesRoot}/StructureModule"
+            PRIVATE "${MODEL_INCLUDE_DIR}" "${XIOS_INCLUDE_LIST}" "${ModulesRoot}/StructureModule"
         )
         target_link_libraries(testXiosField_MPI2 PRIVATE nextsimlib doctest::doctest)
 
@@ -102,7 +134,7 @@ if(ENABLE_MPI)
         target_compile_definitions(testXiosFile_MPI2 PRIVATE USE_XIOS)
         target_include_directories(
             testXiosFile_MPI2
-            PRIVATE "${MODEL_INCLUDE_DIR}" "${ModulesRoot}/StructureModule"
+            PRIVATE "${MODEL_INCLUDE_DIR}" "${XIOS_INCLUDE_LIST}" "${ModulesRoot}/StructureModule"
         )
         target_link_libraries(testXiosFile_MPI2 PRIVATE nextsimlib doctest::doctest)
 
@@ -110,43 +142,10 @@ if(ENABLE_MPI)
         target_compile_definitions(testXiosReadWrite_MPI2 PRIVATE USE_XIOS)
         target_include_directories(
             testXiosReadWrite_MPI2
-            PRIVATE "${MODEL_INCLUDE_DIR}" "${ModulesRoot}/StructureModule"
+            PRIVATE "${MODEL_INCLUDE_DIR}" "${XIOS_INCLUDE_LIST}" "${ModulesRoot}/StructureModule"
         )
         target_link_libraries(testXiosReadWrite_MPI2 PRIVATE nextsimlib doctest::doctest)
     endif()
-
-    add_executable(testRectGrid_MPI3 "RectGrid_test.cpp" "MainMPI.cpp")
-    target_compile_definitions(
-        testRectGrid_MPI3
-        PRIVATE TEST_FILES_DIR=\"${CMAKE_CURRENT_BINARY_DIR}\"
-    )
-    target_include_directories(
-        testRectGrid_MPI3
-        PRIVATE ${MODEL_INCLUDE_DIR} "${ModulesRoot}/StructureModule"
-    )
-    target_link_libraries(testRectGrid_MPI3 PRIVATE nextsimlib doctest::doctest)
-
-    add_executable(testParaGrid_MPI2 "ParaGrid_test.cpp" "MainMPI.cpp")
-    target_compile_definitions(
-        testParaGrid_MPI2
-        PRIVATE
-            USE_MPI
-            TEST_FILES_DIR=\"${CMAKE_CURRENT_BINARY_DIR}\"
-            TEST_FILE_SOURCE=\"${CMAKE_CURRENT_SOURCE_DIR}\"
-    )
-    target_include_directories(
-        testParaGrid_MPI2
-        PRIVATE ${MODEL_INCLUDE_DIR} "${ModulesRoot}/StructureModule"
-    )
-    target_link_libraries(testParaGrid_MPI2 PRIVATE nextsimlib doctest::doctest)
-
-    add_executable(testConfigOutput_MPI2 "ConfigOutput_test.cpp" "MainMPI.cpp")
-    target_compile_definitions(
-        testConfigOutput_MPI2
-        PRIVATE USE_MPI TEST_FILES_DIR=\"${CMAKE_CURRENT_BINARY_DIR}\"
-    )
-    target_include_directories(testConfigOutput_MPI2 PRIVATE ${MODEL_INCLUDE_DIR})
-    target_link_libraries(testConfigOutput_MPI2 PRIVATE nextsimlib doctest::doctest)
 else()
     add_executable(testRectGrid "RectGrid_test.cpp")
     target_compile_definitions(testRectGrid PRIVATE TEST_FILES_DIR=\"${CMAKE_CURRENT_BINARY_DIR}\")
diff --git a/core/test/ParaGrid_test.cpp b/core/test/ParaGrid_test.cpp
index 8f47d76f9..f4e41e0c1 100644
--- a/core/test/ParaGrid_test.cpp
+++ b/core/test/ParaGrid_test.cpp
@@ -1,7 +1,7 @@
 /*!
  * @file ParaGrid_test.cpp
  *
- * @date 10 Dec 2024
+ * @date 24 Sep 2024
  * @author Tim Spain <timothy.spain@nersc.no>
  */
 
@@ -9,7 +9,6 @@
 #include <cstdlib>
 #ifdef USE_MPI
 #include <doctest/extensions/doctest_mpi.h>
-#undef INFO
 #else
 #define DOCTEST_CONFIG_IMPLEMENT_WITH_MAIN
 #include <doctest/doctest.h>
@@ -17,11 +16,11 @@
 
 #include "include/Configurator.hpp"
 #include "include/ConfiguredModule.hpp"
-#include "include/IStructure.hpp"
 #include "include/NZLevels.hpp"
-#include "include/NextsimModule.hpp"
 #include "include/ParaGridIO.hpp"
 #include "include/ParametricGrid.hpp"
+#include "include/IStructure.hpp"
+#include "include/NextsimModule.hpp"
 #include "include/gridNames.hpp"
 
 #include <cmath>
diff --git a/core/test/XiosReadWrite_test.cpp b/core/test/XiosReadWrite_test.cpp
index 05be6c985..aaab7da45 100644
--- a/core/test/XiosReadWrite_test.cpp
+++ b/core/test/XiosReadWrite_test.cpp
@@ -1,7 +1,7 @@
 /*!
  * @file    XiosReadWrite_test.cpp
  * @author  Joe Wallwork <jw2423@cam.ac.uk>
- * @date    10 Dec 2024
+ * @date    19 Nov 2024
  * @brief   Tests for XIOS write method
  * @details
  * This test is designed to test the read and write methods of the C++
diff --git a/physics/src/modules/AtmosphereBoundaryModule/ERA5Atmosphere.cpp b/physics/src/modules/AtmosphereBoundaryModule/ERA5Atmosphere.cpp
index d6acd250a..75ee026f7 100644
--- a/physics/src/modules/AtmosphereBoundaryModule/ERA5Atmosphere.cpp
+++ b/physics/src/modules/AtmosphereBoundaryModule/ERA5Atmosphere.cpp
@@ -1,7 +1,7 @@
 /*!
  * @file ERA5Atmosphere.cpp
  *
- * @date 10 Dec 2024
+ * @date 24 Sep 2024
  * @author Tim Spain <timothy.spain@nersc.no>
  */
 
diff --git a/physics/src/modules/OceanBoundaryModule/TOPAZOcean.cpp b/physics/src/modules/OceanBoundaryModule/TOPAZOcean.cpp
index bb871da3c..70eb86bae 100644
--- a/physics/src/modules/OceanBoundaryModule/TOPAZOcean.cpp
+++ b/physics/src/modules/OceanBoundaryModule/TOPAZOcean.cpp
@@ -1,15 +1,15 @@
 /*!
  * @file TOPAZOcean.cpp
  *
- * @date 10 Dec 2024
+ * @date 24 Sep 2024
  * @author Tim Spain <timothy.spain@nersc.no>
  */
 
 #include "include/TOPAZOcean.hpp"
 
 #include "include/Finalizer.hpp"
-#include "include/IFreezingPoint.hpp"
 #include "include/IIceOceanHeatFlux.hpp"
+#include "include/IFreezingPoint.hpp"
 #include "include/NextsimModule.hpp"
 #include "include/ParaGridIO.hpp"
 #include "include/constants.hpp"