File behaviour for restarts and diagnostics (take 2)

core/src/ModelMetadata.cpp

@@ -196,6 +196,21 @@ void ModelMetadata::setDimensionsFromFile(const std::string& filename)
             if (dim.isNull()) {
                 dim = ncFile.getDim(dimensionSpec.altName);
             }
+#ifdef USE_XIOS
+            // Account for the fact that XIOS writes dimensions differently if only one
+            // discretisation is written out. If the dimension is still null at this point then we
+            // assume that the only discretisation used is HDomain-based, i.e., HField, DGField, or
+            // DGSField.
+            if (dim.isNull()) {
+                if (dimensionSpec.name == "x_dim") {
+                    dim = ncFile.getDim("x");
+                } else if (dimensionSpec.name == "y_dim") {
+                    dim = ncFile.getDim("y");
+                } else {
+                    continue;
+                }
+            }
+#endif
             // If we didn't find a dimension with the dimensions name or altName, throw.
             if (dim.isNull()) {
                 throw std::out_of_range(

core/src/include/Xios.hpp

@@ -83,40 +83,18 @@ class Xios : public Configured<Xios> {
     ModelArray::Type getFieldType(const std::string& fieldId);
     void setFieldType(const std::string& fieldId, const ModelArray::Type& type);
 
-    /* File */
-    void createFile(const std::string& fileId, const int& fieldType);
-    void setFileType(const std::string& fileId, const std::string& fileType);
-    void setFileOutputFreq(const std::string& fileId, const Duration& outputFreq);
-    void setFileParAccess(const std::string& fileId, const std::string& parAccess);
-    std::string getFileType(const std::string& fileId);
-    Duration getFileOutputFreq(const std::string& fileId);
-    std::string getFileMode(const std::string& fileId);
-    std::string getFileParAccess(const std::string& fileId);
-    void fileAddField(const std::string& fileId, const std::string& fieldId);
-    std::vector<std::string> fileGetFieldIds(const std::string& fileId);
-
     enum {
         ENABLED_KEY,
         OUTPUT_FIELD_NAMES_KEY,
-        OUTPUT_SPLITFREQ_KEY,
         INPUT_FIELD_NAMES_KEY,
         DIAGNOSTIC_PERIOD_KEY,
         DIAGNOSTIC_FILE_KEY,
         DIAGNOSTIC_FIELD_NAMES_KEY,
-        DIAGNOSTIC_SPLITFREQ_KEY,
         FORCING_PERIOD_KEY,
         FORCING_FILE_KEY,
         FORCING_FIELD_NAMES_KEY,
     };
 
-    // TODO: Make the following enum private
-    enum {
-        OUTPUT_RESTART,
-        INPUT_RESTART,
-        DIAGNOSTIC,
-        FORCING,
-    };
-
 protected:
     bool isConfigured;
 
@@ -192,20 +170,37 @@ class Xios : public Configured<Xios> {
     /* File */
     xios::CFileGroup* getFileGroup();
     xios::CFile* getFile(const std::string& fileId);
-    void setFileMode(const std::string& fileId, const std::string& mode);
     std::string outputFileId;
+    std::string outputFormatStr = "%y-%mo-%dT%h:%mi:%sZ";
     std::string inputFileId;
     std::string diagnosticFilename;
     std::string diagnosticFileId;
+    std::string diagnosticFormatStr = "%y-%mo-%dT%h:%mi:%sZ";
     std::string forcingFilename;
     std::string forcingFileId;
+    enum {
+        OUTPUT_RESTART,
+        INPUT_RESTART,
+        DIAGNOSTIC,
+        FORCING,
+    };
     const std::map<int, std::string&> fileMap = {
         { OUTPUT_RESTART, outputFileId },
         { INPUT_RESTART, inputFileId },
         { DIAGNOSTIC, diagnosticFileId },
         { FORCING, forcingFileId },
     };
     void setupFiles();
+    void createFile(const std::string& fileId);
+    void fileAddField(const std::string& fileId, const std::string& fieldId);
+    std::vector<std::string> fileGetFieldIds(const std::string& fileId);
+    const std::map<std::string, std::string> formatStrMap = {
+        { "%Y", "%y" },
+        { "%m-", "%mo-" },
+        { "%H", "%h" },
+        { "%M", "%mi" },
+        { "%S", "%s" },
+    };
 
     /* I/O */
     void read(const std::string& fieldId, ModelArray& modelarray);

core/src/include/xios_c_interface.hpp

@@ -146,16 +146,15 @@ void cxios_set_file_output_freq(xios::CFile* file_hdl, cxios_duration output_fre
 void cxios_set_file_split_freq(xios::CFile* file_hdl, cxios_duration split_freq_c);
 void cxios_set_file_mode(xios::CFile* file_hdl, const char* mode, int mode_size);
 void cxios_set_file_par_access(xios::CFile* file_hdl, const char* par_access, int par_access_size);
-void cxios_get_file_type(xios::CFile* file_hdl, char* type, int type_size);
-void cxios_get_file_output_freq(xios::CFile* file_hdl, cxios_duration* output_freq_c);
-void cxios_get_file_mode(xios::CFile* file_hdl, char* mode, int mode_size);
-void cxios_get_file_par_access(xios::CFile* file_hdl, char* par_access, int par_access_size);
+void cxios_set_file_split_freq_format(
+    xios::CFile* file_hdl, const char* split_freq_format, int split_freq_format_size);
 bool cxios_is_defined_file_name(xios::CFile* file_hdl);
 bool cxios_is_defined_file_type(xios::CFile* file_hdl);
 bool cxios_is_defined_file_output_freq(xios::CFile* file_hdl);
 bool cxios_is_defined_file_split_freq(xios::CFile* file_hdl);
 bool cxios_is_defined_file_mode(xios::CFile* file_hdl);
 bool cxios_is_defined_file_par_access(xios::CFile* file_hdl);
+bool cxios_is_defined_file_split_freq_format(xios::CFile* file_hdl);
 void cxios_xml_tree_add_fieldtofile(
     xios::CFile* file, xios::CField** field, const char* _id, int _id_len);
 

core/test/CMakeLists.txt

@@ -217,63 +217,103 @@ if(ENABLE_MPI)
         )
         target_link_libraries(testXiosField_MPI3 PRIVATE nextsimlib doctest::doctest)
 
-        add_executable(testXiosFile_MPI2 "XiosFile_test.cpp" "MainMPI.cpp")
-        target_compile_definitions(testXiosFile_MPI2 PRIVATE USE_XIOS)
+        add_executable(testXiosReadForcing_MPI2 "XiosReadForcing_test.cpp" "MainMPI.cpp")
+        target_compile_definitions(testXiosReadForcing_MPI2
+            PRIVATE
+                USE_XIOS
+                TEST_FILES_DIR=\"${CMAKE_CURRENT_BINARY_DIR}\"
+        )
+        target_include_directories(
+            testXiosReadForcing_MPI2
+            PRIVATE
+                ${PHYSICS_INCLUDE_DIRS}
+                "${MODEL_INCLUDE_DIR}"
+                "${XIOS_INCLUDE_LIST}"
+                "${ModulesRoot}/StructureModule"
+        )
+        target_link_libraries(testXiosReadForcing_MPI2 PRIVATE nextsimlib doctest::doctest)
+
+        add_executable(testXiosReadDiagnostic_MPI2 "XiosReadDiagnostic_test.cpp" "MainMPI.cpp")
+        target_compile_definitions(testXiosReadDiagnostic_MPI2
+            PRIVATE
+                USE_XIOS
+                TEST_FILES_DIR=\"${CMAKE_CURRENT_BINARY_DIR}\"
+        )
+        target_include_directories(
+            testXiosReadDiagnostic_MPI2
+            PRIVATE
+                ${PHYSICS_INCLUDE_DIRS}
+                "${MODEL_INCLUDE_DIR}"
+                "${XIOS_INCLUDE_LIST}"
+                "${ModulesRoot}/StructureModule"
+        )
+        target_link_libraries(testXiosReadDiagnostic_MPI2 PRIVATE nextsimlib doctest::doctest)
+
+        add_executable(testXiosReadRestart_MPI2 "XiosReadRestart_test.cpp" "MainMPI.cpp")
+        target_compile_definitions(testXiosReadRestart_MPI2
+            PRIVATE
+                USE_XIOS
+                TEST_FILES_DIR=\"${CMAKE_CURRENT_BINARY_DIR}\"
+        )
         target_include_directories(
-            testXiosFile_MPI2
+            testXiosReadRestart_MPI2
             PRIVATE
                 ${PHYSICS_INCLUDE_DIRS}
                 "${MODEL_INCLUDE_DIR}"
                 "${XIOS_INCLUDE_LIST}"
                 "${ModulesRoot}/StructureModule"
         )
-        target_link_libraries(testXiosFile_MPI2 PRIVATE nextsimlib doctest::doctest)
+        target_link_libraries(testXiosReadRestart_MPI2 PRIVATE nextsimlib doctest::doctest)
 
-        add_executable(testXiosRead_MPI2 "XiosRead_test.cpp" "MainMPI.cpp")
-        target_compile_definitions(testXiosRead_MPI2
+        add_executable(testXiosWriteDiagnostic_MPI2 "XiosWriteDiagnostic_test.cpp" "MainMPI.cpp")
+        target_compile_definitions(testXiosWriteDiagnostic_MPI2
             PRIVATE
                 USE_XIOS
                 TEST_FILES_DIR=\"${CMAKE_CURRENT_BINARY_DIR}\"
         )
         target_include_directories(
-            testXiosRead_MPI2
+            testXiosWriteDiagnostic_MPI2
             PRIVATE
                 ${PHYSICS_INCLUDE_DIRS}
                 "${MODEL_INCLUDE_DIR}"
                 "${XIOS_INCLUDE_LIST}"
                 "${ModulesRoot}/StructureModule"
         )
-        target_link_libraries(testXiosRead_MPI2 PRIVATE nextsimlib doctest::doctest)
+        target_link_libraries(testXiosWriteDiagnostic_MPI2 PRIVATE nextsimlib doctest::doctest)
 
-        add_executable(testXiosWrite_MPI2 "XiosWrite_test.cpp" "MainMPI.cpp")
-        target_compile_definitions(testXiosWrite_MPI2
+        add_executable(testXiosWriteRestart_MPI2 "XiosWriteRestart_test.cpp" "MainMPI.cpp")
+        target_compile_definitions(testXiosWriteRestart_MPI2
             PRIVATE
                 USE_XIOS
                 TEST_FILES_DIR=\"${CMAKE_CURRENT_BINARY_DIR}\"
         )
         target_include_directories(
-            testXiosWrite_MPI2
+            testXiosWriteRestart_MPI2
             PRIVATE
                 ${PHYSICS_INCLUDE_DIRS}
                 "${MODEL_INCLUDE_DIR}"
                 "${XIOS_INCLUDE_LIST}"
                 "${ModulesRoot}/StructureModule"
         )
-        target_link_libraries(testXiosWrite_MPI2 PRIVATE nextsimlib doctest::doctest)
+        target_link_libraries(testXiosWriteRestart_MPI2 PRIVATE nextsimlib doctest::doctest)
 
         set(XIOS_TESTS
             testXiosCalendar_MPI1
             testXiosAxis_MPI3
             testXiosField_MPI3
-            testXiosFile_MPI2
-            testXiosRead_MPI2
-            testXiosWrite_MPI2
+            testXiosReadForcing_MPI2
+            testXiosReadDiagnostic_MPI2
+            testXiosReadRestart_MPI2
+            testXiosWriteDiagnostic_MPI2
+            testXiosWriteRestart_MPI2
         )
 
         add_mpi_test("${XIOS_TESTS}")
 
-        # Ensure XiosWrite_test is run before XiosRead_test
-        set_tests_properties(testXiosRead_MPI2 PROPERTIES DEPENDS testXiosWrite_MPI2)
+        # Ensure XiosWrite<Diagnostic/Restart>_test are run before XiosRead<Diagnostic/Restart>_test
+        set_tests_properties(testXiosReadRestart_MPI2 PROPERTIES DEPENDS testXiosWriteRestart_MPI2)
+        set_tests_properties(testXiosReadDiagnostic_MPI2
+                             PROPERTIES DEPENDS testXiosWriteDiagnostic_MPI2)
     else()
         add_executable(testHaloExchangeCB_MPI3
             "HaloExchangeCB_test.cpp"