MetOffice · phlndrwd · Oct 25, 2023 · Oct 24, 2023 · Oct 24, 2023 · Oct 24, 2023
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,10 +1,10 @@
 ###############################################################################
 # MONIO - Met Office NetCDF Input Output                                      #
 #                                                                             #
-# (C) Crown Copyright 2023, Met Office.                                       #
+# (C) Crown Copyright 2023, Met Office. All rights reserved.                  #
 #                                                                             #
-# This software is licensed under the terms of the Apache Licence Version 2.0 #
-# which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.        #
+# This software is licensed under the terms of the 3-Clause BSD License       #
+# which can be obtained from https://opensource.org/license/bsd-3-clause/.    #
 ###############################################################################
 
 cmake_minimum_required(VERSION 3.12)

diff --git a/LICENSE b/LICENSE
@@ -0,0 +1,28 @@
+BSD 3-Clause License
+
+Copyright (c) 2023, Met Office
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/README.md b/README.md
@@ -61,7 +61,15 @@ Where `localFieldSet` is the `atlas::FieldSet` to be populated with data from th
 
 ### Writing Increment Files
 
-Writing of an LFRic-compatible, time-independent, increment file can be carried out with the following call:
+Writing of an LFRic-compatible, time-independent, increment file is dependent on geometry data and other metadata being available at the resolution you intend to write. These will be available if MONIO has already been used to read LFRic-compatible data at the same resolution you intend to write (see the read functions described above). If MONIO has not been used for reading, writing will first require that geometry and metadata are copied from an appropriate input file using the following call:
+
+```
+monio::Monio::get().initialiseFile(grid, filePath); 
+```
+
+Where `grid` is a reference to the `atlas::CubedSphereGrid` used to setup the geometry of the `atlas::FieldSet`, `filePath` is a `std::string` defining a valid path to the file to be read. This particular function call returns an `int` that determines the variable naming convention used in the input file. However, it is necessary to capture and use that `int` here. 
+
+Following this, or if MONIO was also used to read LFRic-compatible data, writing of an LFRic-compatible, time-independent, increment file can be carried out with the following call:
 
 ```
 monio::Monio::get().writeIncrements(localFieldSet, fieldMetadataVec, filePath, isLFRicNaming);
@@ -71,7 +79,15 @@ Where `localFieldSet` is the `atlas::FieldSet` containing the data to be written
 
 ### Writing State Files
 
-_This method is intended for use with tests only_. Writing of an LFRic-compatible, time-independent, state file can be carried out with the following call:
+_This method is intended for use with tests only_. Writing of an LFRic-compatible, time-independent, state file is dependent on geometry data and other metadata being available at the resolution you intend to write. These will be available if MONIO has already been used to read LFRic-compatible data at the same resolution you intend to write (see the read functions described above). If MONIO has not been used for reading, writing will first require that geometry and metadata are copied from an appropriate input file using the following call:
+
+```
+monio::Monio::get().initialiseFile(grid, filePath); 
+```
+
+Where `grid` is a reference to the `atlas::CubedSphereGrid` used to setup the geometry of the `atlas::FieldSet`, `filePath` is a `std::string` defining a valid path to the file to be read. This particular function call returns an `int` that determines the variable naming convention used in the input file. However, it is necessary to capture and use that `int` here. 
+
+Following this, writing of an LFRic-compatible, time-independent, state file can be carried out with the following call:
 
 ```
 monio::Monio::get().writeState(localFieldSet, fieldMetadataVec, filePath, isLFRicNaming);
@@ -81,13 +97,13 @@ Where `localFieldSet` is the `atlas::FieldSet` containing the data to be written
 
 ### Writing A FieldSet
 
-For debugging, it may occasionally be useful to output a `FieldSet` from any arbitrary position in the code into a NetCDF so that it can be examined. For this reason, MONIO offers the following call:
+For debugging, it may occasionally be useful to output an `atlas::FieldSet` from any arbitrary position in the code into a NetCDF so that it can be examined. For this reason, MONIO offers the following call:
 
 ```
 monio::Monio::get().writeFieldSet(localFieldSet, filePath);
 ```
 
-Where `localFieldSet` is the `atlas::FieldSet` containing the data to be written to file, and `filePath` is a `std::string` defining a valid path to the intended output file.
+Where `localFieldSet` is the `atlas::FieldSet` containing the data to be written to file, and `filePath` is a `std::string` defining a valid path to the intended output file. It should be noted that this particular writing method requires no existing geometric data or metadata to be provided, and so requires no supporting function call to be executed beforehand. For this reason, data are written in their default, Atlas order.
 
 ## Issues
 

diff --git a/ci/CMakeLists.txt b/ci/CMakeLists.txt
@@ -1,10 +1,10 @@
 ###############################################################################
 # MONIO - Met Office NetCDF Input Output                                      #
 #                                                                             #
-# (C) Crown Copyright 2023, Met Office.                                       #
+# (C) Crown Copyright 2023, Met Office. All rights reserved.                  #
 #                                                                             #
-# This software is licensed under the terms of the Apache Licence Version 2.0 #
-# which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.        #
+# This software is licensed under the terms of the 3-Clause BSD License       #
+# which can be obtained from https://opensource.org/license/bsd-3-clause/.    #
 ###############################################################################
 
 cmake_minimum_required( VERSION 3.20 FATAL_ERROR )

diff --git a/ci/build-and-lint b/ci/build-and-lint
@@ -2,10 +2,10 @@
 ###############################################################################
 # MONIO - Met Office NetCDF Input Output                                      #
 #                                                                             #
-# (C) Crown Copyright 2023, Met Office.                                       #
+# (C) Crown Copyright 2023, Met Office. All rights reserved.                  #
 #                                                                             #
-# This software is licensed under the terms of the Apache Licence Version 2.0 #
-# which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.        #
+# This software is licensed under the terms of the 3-Clause BSD License       #
+# which can be obtained from https://opensource.org/license/bsd-3-clause/.    #
 ###############################################################################
 set -euo pipefail
 

diff --git a/ci/build-and-test b/ci/build-and-test
@@ -2,10 +2,10 @@
 ###############################################################################
 # MONIO - Met Office NetCDF Input Output                                      #
 #                                                                             #
-# (C) Crown Copyright 2023, Met Office.                                       #
+# (C) Crown Copyright 2023, Met Office. All rights reserved.                  #
 #                                                                             #
-# This software is licensed under the terms of the Apache Licence Version 2.0 #
-# which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.        #
+# This software is licensed under the terms of the 3-Clause BSD License       #
+# which can be obtained from https://opensource.org/license/bsd-3-clause/.    #
 ###############################################################################
 set -euxo pipefail
 

diff --git a/ci/get-ref-branch b/ci/get-ref-branch
@@ -2,10 +2,10 @@
 ###############################################################################
 # MONIO - Met Office NetCDF Input Output                                      #
 #                                                                             #
-# (C) Crown Copyright 2023, Met Office.                                       #
+# (C) Crown Copyright 2023, Met Office. All rights reserved.                  #
 #                                                                             #
-# This software is licensed under the terms of the Apache Licence Version 2.0 #
-# which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.        #
+# This software is licensed under the terms of the 3-Clause BSD License       #
+# which can be obtained from https://opensource.org/license/bsd-3-clause/.    #
 ###############################################################################
 set -euxo pipefail
 repo="$1"  # expect path to a repo clone

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -1,10 +1,10 @@
 ###############################################################################
 # MONIO - Met Office NetCDF Input Output                                      #
 #                                                                             #
-# (C) Crown Copyright 2023, Met Office.                                       #
+# (C) Crown Copyright 2023, Met Office. All rights reserved.                  #
 #                                                                             #
-# This software is licensed under the terms of the Apache Licence Version 2.0 #
-# which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.        #
+# This software is licensed under the terms of the 3-Clause BSD License       #
+# which can be obtained from https://opensource.org/license/bsd-3-clause/.    #
 ###############################################################################
 
 include_directories(${CMAKE_CURRENT_SOURCE_DIR})

diff --git a/src/monio/AtlasReader.cc b/src/monio/AtlasReader.cc
@@ -1,10 +1,10 @@
 /******************************************************************************
 * MONIO - Met Office NetCDF Input Output                                      *
 *                                                                             *
-* (C) Crown Copyright 2023 Met Office                                         *
+* (C) Crown Copyright 2023, Met Office. All rights reserved.                  *
 *                                                                             *
-* This software is licensed under the terms of the Apache Licence Version 2.0 *
-* which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.        *
+* This software is licensed under the terms of the 3-Clause BSD License       *
+* which can be obtained from https://opensource.org/license/bsd-3-clause/.    *
 ******************************************************************************/
 #include "AtlasReader.h"
 
@@ -41,25 +41,25 @@ void monio::AtlasReader::populateFieldWithDataContainer(atlas::Field& field,
   if (mpiCommunicator_.rank() == mpiRankOwner_) {
     int dataType = dataContainer.get()->getType();
     switch (dataType) {
-    case consts::eDataTypes::eDouble: {
-      const std::shared_ptr<DataContainerDouble> dataContainerDouble =
-          std::static_pointer_cast<DataContainerDouble>(dataContainer);
-          populateField(field, dataContainerDouble->getData(), lfricToAtlasMap, noFirstLevel);
-      break;
-    }
-    case consts::eDataTypes::eFloat: {
-      const std::shared_ptr<DataContainerFloat> dataContainerFloat =
-          std::static_pointer_cast<DataContainerFloat>(dataContainer);
-          populateField(field, dataContainerFloat->getData(), lfricToAtlasMap, noFirstLevel);
-      break;
-    }
-    case consts::eDataTypes::eInt: {
-      const std::shared_ptr<DataContainerInt> dataContainerInt =
-          std::static_pointer_cast<DataContainerInt>(dataContainer);
-          populateField(field, dataContainerInt->getData(), lfricToAtlasMap, noFirstLevel);
-      break;
-    }
-    default: {
+      case consts::eDataTypes::eDouble: {
+        const std::shared_ptr<DataContainerDouble> dataContainerDouble =
+            std::static_pointer_cast<DataContainerDouble>(dataContainer);
+            populateField(field, dataContainerDouble->getData(), lfricToAtlasMap, noFirstLevel);
+        break;
+      }
+      case consts::eDataTypes::eFloat: {
+        const std::shared_ptr<DataContainerFloat> dataContainerFloat =
+            std::static_pointer_cast<DataContainerFloat>(dataContainer);
+            populateField(field, dataContainerFloat->getData(), lfricToAtlasMap, noFirstLevel);
+        break;
+      }
+      case consts::eDataTypes::eInt: {
+        const std::shared_ptr<DataContainerInt> dataContainerInt =
+            std::static_pointer_cast<DataContainerInt>(dataContainer);
+            populateField(field, dataContainerInt->getData(), lfricToAtlasMap, noFirstLevel);
+        break;
+      }
+      default: {
         Monio::get().closeFiles();
         utils::throwException("AtlasReader::populateFieldWithDataContainer()> "
                                  "Data type not coded for...");
@@ -74,25 +74,25 @@ void monio::AtlasReader::populateFieldWithDataContainer(atlas::Field& field,
   if (mpiCommunicator_.rank() == mpiRankOwner_) {
     int dataType = dataContainer.get()->getType();
     switch (dataType) {
-    case consts::eDataTypes::eDouble: {
-      const std::shared_ptr<DataContainerDouble> dataContainerDouble =
-          std::static_pointer_cast<DataContainerDouble>(dataContainer);
-          populateField(field, dataContainerDouble->getData());
-      break;
-    }
-    case consts::eDataTypes::eFloat: {
-      const std::shared_ptr<DataContainerFloat> dataContainerFloat =
-          std::static_pointer_cast<DataContainerFloat>(dataContainer);
-          populateField(field, dataContainerFloat->getData());
-      break;
-    }
-    case consts::eDataTypes::eInt: {
-      const std::shared_ptr<DataContainerInt> dataContainerInt =
-          std::static_pointer_cast<DataContainerInt>(dataContainer);
-          populateField(field, dataContainerInt->getData());
-      break;
-    }
-    default: {
+      case consts::eDataTypes::eDouble: {
+        const std::shared_ptr<DataContainerDouble> dataContainerDouble =
+            std::static_pointer_cast<DataContainerDouble>(dataContainer);
+            populateField(field, dataContainerDouble->getData());
+        break;
+      }
+      case consts::eDataTypes::eFloat: {
+        const std::shared_ptr<DataContainerFloat> dataContainerFloat =
+            std::static_pointer_cast<DataContainerFloat>(dataContainer);
+            populateField(field, dataContainerFloat->getData());
+        break;
+      }
+      case consts::eDataTypes::eInt: {
+        const std::shared_ptr<DataContainerInt> dataContainerInt =
+            std::static_pointer_cast<DataContainerInt>(dataContainer);
+            populateField(field, dataContainerInt->getData());
+        break;
+      }
+      default: {
         Monio::get().closeFiles();
         utils::throwException("AtlasReader::populateFieldWithDataContainer()> "
                                  "Data type not coded for...");

diff --git a/src/monio/AtlasReader.h b/src/monio/AtlasReader.h
@@ -1,10 +1,10 @@
 /******************************************************************************
 * MONIO - Met Office NetCDF Input Output                                      *
 *                                                                             *
-* (C) Crown Copyright 2023 Met Office                                         *
+* (C) Crown Copyright 2023, Met Office. All rights reserved.                  *
 *                                                                             *
-* This software is licensed under the terms of the Apache Licence Version 2.0 *
-* which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.        *
+* This software is licensed under the terms of the 3-Clause BSD License       *
+* which can be obtained from https://opensource.org/license/bsd-3-clause/.    *
 ******************************************************************************/
 #pragma once