Release candidate0.1 (#7)

rrsettgast · web-flow · commit b247c15c68b0 · 2025-06-25T22:57:01.000-07:00
* added ACKNOWLEDGEMENTS and LICENSE files

* add header to all source files
diff --git a/ACKNOWLEDGEMENTS b/ACKNOWLEDGEMENTS
@@ -0,0 +1,3 @@
+ACKNOWLEDGEMENTS
+----------------
+HPCReact is originally developed at	Lawrence Livermore National Laboratory operated by Lawrence Livermore National Security, LLC for the United States Department of Energy under Contract DE-AC52-07NA27344
diff --git a/LICENSE b/LICENSE
@@ -0,0 +1,12 @@
+Copyright (c) 2025 Lawrence Livermore National Security LLC
+All rights reserved
+
+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
@@ -1,2 +1,21 @@
-# hpcReact
-Package for modeling of chemical reactions on High Performance Computing Systems
+HPCReact
+-----------------------------
+HPCReact is a collection of inline, device-callable functions for modeling pointwise chemical reactions.
+It is designed to provide building blocks for constructing computational kernels that update chemical states in simulations involving reactive chemistry.
+
+
+Documentation
+-------------
+To be added...
+
+
+
+
+Release
+-------
+
+For release details and restrictions, please read the [LICENSE](./LICENSE) file.
+
+For acknowledgements, please read the [ACKNOWLEDGEMENTS](./ACKNOWLEDGEMENTS ) file.
+
+`LLNL-CODE-2006543`
diff --git a/src/common/CArrayWrapper.hpp b/src/common/CArrayWrapper.hpp
@@ -1,3 +1,14 @@
+/*
+ * ------------------------------------------------------------------------------------------------------------
+ * SPDX-License-Identifier: (BSD-3-Clause)
+ *
+ * Copyright (c) 2025- Lawrence Livermore National Security LLC
+ * All rights reserved
+ *
+ * See top level LICENSE files for details.
+ * ------------------------------------------------------------------------------------------------------------
+ */
+
 #pragma once
 #include "macros.hpp"
 #include <initializer_list>
diff --git a/src/common/DirectSystemSolve.hpp b/src/common/DirectSystemSolve.hpp
@@ -1,3 +1,14 @@
+/*
+ * ------------------------------------------------------------------------------------------------------------
+ * SPDX-License-Identifier: (BSD-3-Clause)
+ *
+ * Copyright (c) 2025- Lawrence Livermore National Security LLC
+ * All rights reserved
+ *
+ * See top level LICENSE files for details.
+ * ------------------------------------------------------------------------------------------------------------
+ */
+
 #pragma once
 
 #include "macros.hpp"
diff --git a/src/common/constants.hpp b/src/common/constants.hpp
@@ -1,3 +1,14 @@
+/*
+ * ------------------------------------------------------------------------------------------------------------
+ * SPDX-License-Identifier: (BSD-3-Clause)
+ *
+ * Copyright (c) 2025- Lawrence Livermore National Security LLC
+ * All rights reserved
+ *
+ * See top level LICENSE files for details.
+ * ------------------------------------------------------------------------------------------------------------
+ */
+
 #pragma once
 
 namespace hpcReact
diff --git a/src/common/macros.hpp b/src/common/macros.hpp
@@ -1,3 +1,14 @@
+/*
+ * ------------------------------------------------------------------------------------------------------------
+ * SPDX-License-Identifier: (BSD-3-Clause)
+ *
+ * Copyright (c) 2025- Lawrence Livermore National Security LLC
+ * All rights reserved
+ *
+ * See top level LICENSE files for details.
+ * ------------------------------------------------------------------------------------------------------------
+ */
+
 #pragma once
 
 
diff --git a/src/common/macrosCleanup.hpp b/src/common/macrosCleanup.hpp
@@ -1,3 +1,14 @@
+/*
+ * ------------------------------------------------------------------------------------------------------------
+ * SPDX-License-Identifier: (BSD-3-Clause)
+ *
+ * Copyright (c) 2025- Lawrence Livermore National Security LLC
+ * All rights reserved
+ *
+ * See top level LICENSE files for details.
+ * ------------------------------------------------------------------------------------------------------------
+ */
+
 // #undef HPCREACT_USE_DEVICE
 // #undef HPCREACT_HOST_DEVICE
 // #undef HPCREACT_GLOBAL
diff --git a/src/common/nonlinearSolvers.hpp b/src/common/nonlinearSolvers.hpp
@@ -1,3 +1,14 @@
+/*
+ * ------------------------------------------------------------------------------------------------------------
+ * SPDX-License-Identifier: (BSD-3-Clause)
+ *
+ * Copyright (c) 2025- Lawrence Livermore National Security LLC
+ * All rights reserved
+ *
+ * See top level LICENSE files for details.
+ * ------------------------------------------------------------------------------------------------------------
+ */
+
 #pragma once
 
 #include "macros.hpp"
diff --git a/src/common/pmpl.hpp b/src/common/pmpl.hpp
@@ -1,3 +1,14 @@
+/*
+ * ------------------------------------------------------------------------------------------------------------
+ * SPDX-License-Identifier: (BSD-3-Clause)
+ *
+ * Copyright (c) 2025- Lawrence Livermore National Security LLC
+ * All rights reserved
+ *
+ * See top level LICENSE files for details.
+ * ------------------------------------------------------------------------------------------------------------
+ */
+
 #pragma once
 
 #include "common/macros.hpp"
diff --git a/src/common/printers.hpp b/src/common/printers.hpp
@@ -1,3 +1,14 @@
+/*
+ * ------------------------------------------------------------------------------------------------------------
+ * SPDX-License-Identifier: (BSD-3-Clause)
+ *
+ * Copyright (c) 2025- Lawrence Livermore National Security LLC
+ * All rights reserved
+ *
+ * See top level LICENSE files for details.
+ * ------------------------------------------------------------------------------------------------------------
+ */
+
 #pragma once
 
 #include <stdio.h>
diff --git a/src/common/symmetricMatrix.hpp b/src/common/symmetricMatrix.hpp
@@ -1,3 +1,14 @@
+/*
+ * ------------------------------------------------------------------------------------------------------------
+ * SPDX-License-Identifier: (BSD-3-Clause)
+ *
+ * Copyright (c) 2025- Lawrence Livermore National Security LLC
+ * All rights reserved
+ *
+ * See top level LICENSE files for details.
+ * ------------------------------------------------------------------------------------------------------------
+ */
+
 #pragma once
 
 /**
diff --git a/src/common/unitTests/testDirectSystemSolve.cpp b/src/common/unitTests/testDirectSystemSolve.cpp
@@ -1,3 +1,14 @@
+/*
+ * ------------------------------------------------------------------------------------------------------------
+ * SPDX-License-Identifier: (BSD-3-Clause)
+ *
+ * Copyright (c) 2025- Lawrence Livermore National Security LLC
+ * All rights reserved
+ *
+ * See top level LICENSE files for details.
+ * ------------------------------------------------------------------------------------------------------------
+ */
+
 
 #include "../DirectSystemSolve.hpp"
 #include "common/pmpl.hpp"
diff --git a/src/reactions/exampleSystems/BulkGeneric.hpp b/src/reactions/exampleSystems/BulkGeneric.hpp
@@ -1,3 +1,14 @@
+/*
+ * ------------------------------------------------------------------------------------------------------------
+ * SPDX-License-Identifier: (BSD-3-Clause)
+ *
+ * Copyright (c) 2025- Lawrence Livermore National Security LLC
+ * All rights reserved
+ *
+ * See top level LICENSE files for details.
+ * ------------------------------------------------------------------------------------------------------------
+ */
+
 #pragma once
 
 #include "../reactionsSystems/Parameters.hpp"
diff --git a/src/reactions/exampleSystems/MoMasBenchmark.hpp b/src/reactions/exampleSystems/MoMasBenchmark.hpp
@@ -1,3 +1,14 @@
+/*
+ * ------------------------------------------------------------------------------------------------------------
+ * SPDX-License-Identifier: (BSD-3-Clause)
+ *
+ * Copyright (c) 2025- Lawrence Livermore National Security LLC
+ * All rights reserved
+ *
+ * See top level LICENSE files for details.
+ * ------------------------------------------------------------------------------------------------------------
+ */
+
 #pragma once
 
 #include "../reactionsSystems/Parameters.hpp"
diff --git a/src/reactions/exampleSystems/unitTests/testEquilibriumReactions.cpp b/src/reactions/exampleSystems/unitTests/testEquilibriumReactions.cpp
@@ -1,3 +1,14 @@
+/*
+ * ------------------------------------------------------------------------------------------------------------
+ * SPDX-License-Identifier: (BSD-3-Clause)
+ *
+ * Copyright (c) 2025- Lawrence Livermore National Security LLC
+ * All rights reserved
+ *
+ * See top level LICENSE files for details.
+ * ------------------------------------------------------------------------------------------------------------
+ */
+
 
 #include "reactions/unitTestUtilities/equilibriumReactionsTestUtilities.hpp"
 #include "../BulkGeneric.hpp"
diff --git a/src/reactions/exampleSystems/unitTests/testKineticReactions.cpp b/src/reactions/exampleSystems/unitTests/testKineticReactions.cpp
@@ -1,3 +1,14 @@
+/*
+ * ------------------------------------------------------------------------------------------------------------
+ * SPDX-License-Identifier: (BSD-3-Clause)
+ *
+ * Copyright (c) 2025- Lawrence Livermore National Security LLC
+ * All rights reserved
+ *
+ * See top level LICENSE files for details.
+ * ------------------------------------------------------------------------------------------------------------
+ */
+
 
 #include "reactions/unitTestUtilities/kineticReactionsTestUtilities.hpp"
 #include "../BulkGeneric.hpp"
diff --git a/src/reactions/geochemistry/Carbonate.hpp b/src/reactions/geochemistry/Carbonate.hpp
@@ -1,3 +1,14 @@
+/*
+ * ------------------------------------------------------------------------------------------------------------
+ * SPDX-License-Identifier: (BSD-3-Clause)
+ *
+ * Copyright (c) 2025- Lawrence Livermore National Security LLC
+ * All rights reserved
+ *
+ * See top level LICENSE files for details.
+ * ------------------------------------------------------------------------------------------------------------
+ */
+
 #pragma once
 
 #include "../reactionsSystems/Parameters.hpp"
diff --git a/src/reactions/geochemistry/Forge.hpp b/src/reactions/geochemistry/Forge.hpp
@@ -1,3 +1,14 @@
+/*
+ * ------------------------------------------------------------------------------------------------------------
+ * SPDX-License-Identifier: (BSD-3-Clause)
+ *
+ * Copyright (c) 2025- Lawrence Livermore National Security LLC
+ * All rights reserved
+ *
+ * See top level LICENSE files for details.
+ * ------------------------------------------------------------------------------------------------------------
+ */
+
 #pragma once
 
 #include "../reactionsSystems/Parameters.hpp"
diff --git a/src/reactions/geochemistry/GeochemicalSystems.hpp b/src/reactions/geochemistry/GeochemicalSystems.hpp
@@ -1,3 +1,14 @@
+/*
+ * ------------------------------------------------------------------------------------------------------------
+ * SPDX-License-Identifier: (BSD-3-Clause)
+ *
+ * Copyright (c) 2025- Lawrence Livermore National Security LLC
+ * All rights reserved
+ *
+ * See top level LICENSE files for details.
+ * ------------------------------------------------------------------------------------------------------------
+ */
+
 #pragma once
 
 #include "Carbonate.hpp"
diff --git a/src/reactions/geochemistry/Ultramafics.hpp b/src/reactions/geochemistry/Ultramafics.hpp
@@ -1,3 +1,14 @@
+/*
+ * ------------------------------------------------------------------------------------------------------------
+ * SPDX-License-Identifier: (BSD-3-Clause)
+ *
+ * Copyright (c) 2025- Lawrence Livermore National Security LLC
+ * All rights reserved
+ *
+ * See top level LICENSE files for details.
+ * ------------------------------------------------------------------------------------------------------------
+ */
+
 #pragma once
 
 #include "../reactionsSystems/Parameters.hpp"
diff --git a/src/reactions/geochemistry/unitTests/testGeochemicalEquilibriumReactions.cpp b/src/reactions/geochemistry/unitTests/testGeochemicalEquilibriumReactions.cpp
@@ -1,3 +1,14 @@
+/*
+ * ------------------------------------------------------------------------------------------------------------
+ * SPDX-License-Identifier: (BSD-3-Clause)
+ *
+ * Copyright (c) 2025- Lawrence Livermore National Security LLC
+ * All rights reserved
+ *
+ * See top level LICENSE files for details.
+ * ------------------------------------------------------------------------------------------------------------
+ */
+
 
 #include "reactions/unitTestUtilities/equilibriumReactionsTestUtilities.hpp"
 #include "../GeochemicalSystems.hpp"
diff --git a/src/reactions/geochemistry/unitTests/testGeochemicalKineticReactions.cpp b/src/reactions/geochemistry/unitTests/testGeochemicalKineticReactions.cpp
@@ -1,3 +1,14 @@
+/*
+ * ------------------------------------------------------------------------------------------------------------
+ * SPDX-License-Identifier: (BSD-3-Clause)
+ *
+ * Copyright (c) 2025- Lawrence Livermore National Security LLC
+ * All rights reserved
+ *
+ * See top level LICENSE files for details.
+ * ------------------------------------------------------------------------------------------------------------
+ */
+
 
 #include "reactions/unitTestUtilities/kineticReactionsTestUtilities.hpp"
 #include "../GeochemicalSystems.hpp"
diff --git a/src/reactions/geochemistry/unitTests/testGeochemicalMixedReactions.cpp b/src/reactions/geochemistry/unitTests/testGeochemicalMixedReactions.cpp
@@ -1,3 +1,14 @@
+/*
+ * ------------------------------------------------------------------------------------------------------------
+ * SPDX-License-Identifier: (BSD-3-Clause)
+ *
+ * Copyright (c) 2025- Lawrence Livermore National Security LLC
+ * All rights reserved
+ *
+ * See top level LICENSE files for details.
+ * ------------------------------------------------------------------------------------------------------------
+ */
+
 #include "reactions/unitTestUtilities/mixedReactionsTestUtilities.hpp"
 #include "../GeochemicalSystems.hpp"
 
diff --git a/src/reactions/massActions/MassActions.hpp b/src/reactions/massActions/MassActions.hpp
@@ -1,3 +1,14 @@
+/*
+ * ------------------------------------------------------------------------------------------------------------
+ * SPDX-License-Identifier: (BSD-3-Clause)
+ *
+ * Copyright (c) 2025- Lawrence Livermore National Security LLC
+ * All rights reserved
+ *
+ * See top level LICENSE files for details.
+ * ------------------------------------------------------------------------------------------------------------
+ */
+
 #pragma once
 
 #include "common/macros.hpp"
diff --git a/src/reactions/massActions/unitTests/testMassActions.cpp b/src/reactions/massActions/unitTests/testMassActions.cpp
@@ -1,3 +1,14 @@
+/*
+ * ------------------------------------------------------------------------------------------------------------
+ * SPDX-License-Identifier: (BSD-3-Clause)
+ *
+ * Copyright (c) 2025- Lawrence Livermore National Security LLC
+ * All rights reserved
+ *
+ * See top level LICENSE files for details.
+ * ------------------------------------------------------------------------------------------------------------
+ */
+
 #include "../MassActions.hpp"
 #include "reactions/geochemistry/GeochemicalSystems.hpp"
 #include "common/printers.hpp"
diff --git a/src/reactions/reactionsSystems/EquilibriumReactions.hpp b/src/reactions/reactionsSystems/EquilibriumReactions.hpp
diff --git a/src/reactions/reactionsSystems/EquilibriumReactionsAggregatePrimaryConcentration_impl.hpp b/src/reactions/reactionsSystems/EquilibriumReactionsAggregatePrimaryConcentration_impl.hpp
diff --git a/src/reactions/reactionsSystems/EquilibriumReactionsReactionExtents_impl.hpp b/src/reactions/reactionsSystems/EquilibriumReactionsReactionExtents_impl.hpp
diff --git a/src/reactions/reactionsSystems/KineticReactions.hpp b/src/reactions/reactionsSystems/KineticReactions.hpp
diff --git a/src/reactions/reactionsSystems/KineticReactions_impl.hpp b/src/reactions/reactionsSystems/KineticReactions_impl.hpp
diff --git a/src/reactions/reactionsSystems/MixedEquilibriumKineticReactions.hpp b/src/reactions/reactionsSystems/MixedEquilibriumKineticReactions.hpp
diff --git a/src/reactions/reactionsSystems/MixedEquilibriumKineticReactions_impl.hpp b/src/reactions/reactionsSystems/MixedEquilibriumKineticReactions_impl.hpp
diff --git a/src/reactions/reactionsSystems/Parameters.hpp b/src/reactions/reactionsSystems/Parameters.hpp
diff --git a/src/reactions/unitTestUtilities/equilibriumReactionsTestUtilities.hpp b/src/reactions/unitTestUtilities/equilibriumReactionsTestUtilities.hpp
diff --git a/src/reactions/unitTestUtilities/kineticReactionsTestUtilities.hpp b/src/reactions/unitTestUtilities/kineticReactionsTestUtilities.hpp
diff --git a/src/reactions/unitTestUtilities/mixedReactionsTestUtilities.hpp b/src/reactions/unitTestUtilities/mixedReactionsTestUtilities.hpp

Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,3 @@`
	`1`	`+ACKNOWLEDGEMENTS`
	`2`	`+----------------`
	`3`	`+HPCReact is originally developed at Lawrence Livermore National Laboratory operated by Lawrence Livermore National Security, LLC for the United States Department of Energy under Contract DE-AC52-07NA27344`