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Update Website #428

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c832d19
Update app_files.md
danlwill Jan 22, 2025
892e815
Update app_files.md
danlwill Jan 26, 2025
f2d8b99
Update input_file.md
danlwill Jan 26, 2025
7366e26
Update installation.md
danlwill Jan 26, 2025
f8f262d
Update installation.md
danlwill Jan 26, 2025
ea4a0e1
Update running_apps.md
danlwill Jan 26, 2025
125a6fa
Delete doc/doxygen/user_manual/installation/install_prereqs.md
danlwill Jan 29, 2025
84f8985
Delete doc/doxygen/user_manual/installation/install_prismspf.md
danlwill Jan 29, 2025
7ef31e7
Delete doc/doxygen/user_manual/installation/install_vis.md
danlwill Jan 29, 2025
1a94063
Remove sub headings
danlwill Jan 29, 2025
4e83002
Added copyright heading to all .h and .cc files in applications.
danlwill Feb 3, 2025
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3 changes: 3 additions & 0 deletions applications/CHAC_anisotropy/ICs_and_BCs.cc
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

// ===========================================================================
// FUNCTION FOR INITIAL CONDITIONS
// ===========================================================================
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3 changes: 3 additions & 0 deletions applications/CHAC_anisotropy/customPDE.h
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

#include <core/matrixFreePDE.h>

using namespace dealii;
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3 changes: 3 additions & 0 deletions applications/CHAC_anisotropy/equations.cc
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

// =================================================================================
// Set the attributes of the primary field variables
// =================================================================================
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3 changes: 3 additions & 0 deletions applications/CHAC_anisotropy/postprocess.cc
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

// =============================================================================================
// loadPostProcessorVariableAttributes: Set the attributes of the postprocessing
// variables
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3 changes: 3 additions & 0 deletions applications/CHAC_anisotropyRegularized/ICs_and_BCs.cc
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

// ===========================================================================
// FUNCTION FOR INITIAL CONDITIONS
// ===========================================================================
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3 changes: 3 additions & 0 deletions applications/CHAC_anisotropyRegularized/customPDE.h
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

#include <core/matrixFreePDE.h>

using namespace dealii;
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3 changes: 3 additions & 0 deletions applications/CHAC_anisotropyRegularized/equations.cc
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

// =================================================================================
// Set the attributes of the primary field variables
// =================================================================================
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3 changes: 3 additions & 0 deletions applications/CHAC_anisotropyRegularized/postprocess.cc
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

// =============================================================================================
// loadPostProcessorVariableAttributes: Set the attributes of the postprocessing
// variables
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3 changes: 3 additions & 0 deletions applications/CHAC_performance_test/ICs_and_BCs.cc
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

// ===========================================================================
// FUNCTION FOR INITIAL CONDITIONS
// ===========================================================================
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3 changes: 3 additions & 0 deletions applications/CHAC_performance_test/customPDE.h
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

#include <core/matrixFreePDE.h>

using namespace dealii;
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3 changes: 3 additions & 0 deletions applications/CHAC_performance_test/equations.cc
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

// =================================================================================
// Set the attributes of the primary field variables
// =================================================================================
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3 changes: 3 additions & 0 deletions applications/CHAC_performance_test/postprocess.cc
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

// =================================================================================
// Set the attributes of the postprocessing variables
// =================================================================================
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3 changes: 3 additions & 0 deletions applications/CHiMaD_benchmarks/CHiMaD_benchmark1a/ICs_and_BCs.cc
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

// ===========================================================================
// FUNCTION FOR INITIAL CONDITIONS
// ===========================================================================
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3 changes: 3 additions & 0 deletions applications/CHiMaD_benchmarks/CHiMaD_benchmark1a/customPDE.h
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

#include <core/matrixFreePDE.h>

using namespace dealii;
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3 changes: 3 additions & 0 deletions applications/CHiMaD_benchmarks/CHiMaD_benchmark1a/equations.cc
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

// =================================================================================
// Set the attributes of the primary field variables
// =================================================================================
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3 changes: 3 additions & 0 deletions applications/CHiMaD_benchmarks/CHiMaD_benchmark1a/postprocess.cc
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

// =============================================================================================
// loadPostProcessorVariableAttributes: Set the attributes of the postprocessing
// variables
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3 changes: 3 additions & 0 deletions applications/CHiMaD_benchmarks/CHiMaD_benchmark1b/ICs_and_BCs.cc
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

// ===========================================================================
// FUNCTION FOR INITIAL CONDITIONS
// ===========================================================================
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3 changes: 3 additions & 0 deletions applications/CHiMaD_benchmarks/CHiMaD_benchmark1b/customPDE.h
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

#include <core/matrixFreePDE.h>

using namespace dealii;
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3 changes: 3 additions & 0 deletions applications/CHiMaD_benchmarks/CHiMaD_benchmark1b/equations.cc
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

// =================================================================================
// Set the attributes of the primary field variables
// =================================================================================
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3 changes: 3 additions & 0 deletions applications/CHiMaD_benchmarks/CHiMaD_benchmark1b/postprocess.cc
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

// =============================================================================================
// loadPostProcessorVariableAttributes: Set the attributes of the postprocessing
// variables
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3 changes: 3 additions & 0 deletions applications/CHiMaD_benchmarks/CHiMaD_benchmark1c/ICs_and_BCs.cc
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

// ===========================================================================
// FUNCTION FOR INITIAL CONDITIONS
// ===========================================================================
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5 changes: 4 additions & 1 deletion applications/CHiMaD_benchmarks/CHiMaD_benchmark1c/customPDE.h
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

#include <core/matrixFreePDE.h>

using namespace dealii;
Expand Down Expand Up @@ -181,4 +184,4 @@ customPDE<dim, degree>::create_triangulation(
}
}
}
}
}
3 changes: 3 additions & 0 deletions applications/CHiMaD_benchmarks/CHiMaD_benchmark1c/equations.cc
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

// =================================================================================
// Set the attributes of the primary field variables
// =================================================================================
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3 changes: 3 additions & 0 deletions applications/CHiMaD_benchmarks/CHiMaD_benchmark1c/postprocess.cc
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

// =============================================================================================
// loadPostProcessorVariableAttributes: Set the attributes of the postprocessing
// variables
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3 changes: 3 additions & 0 deletions applications/CHiMaD_benchmarks/CHiMaD_benchmark2a/ICs_and_BCs.cc
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

// ===========================================================================
// FUNCTION FOR INITIAL CONDITIONS
// ===========================================================================
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3 changes: 3 additions & 0 deletions applications/CHiMaD_benchmarks/CHiMaD_benchmark2a/customPDE.h
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

#include <core/matrixFreePDE.h>

using namespace dealii;
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3 changes: 3 additions & 0 deletions applications/CHiMaD_benchmarks/CHiMaD_benchmark2a/equations.cc
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

// =================================================================================
// Set the attributes of the primary field variables
// =================================================================================
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3 changes: 3 additions & 0 deletions applications/CHiMaD_benchmarks/CHiMaD_benchmark2a/postprocess.cc
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

// =============================================================================================
// loadPostProcessorVariableAttributes: Set the attributes of the postprocessing
// variables
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3 changes: 3 additions & 0 deletions applications/CHiMaD_benchmarks/CHiMaD_benchmark3a/ICs_and_BCs.cc
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

// ===========================================================================
// FUNCTION FOR INITIAL CONDITIONS
// ===========================================================================
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3 changes: 3 additions & 0 deletions applications/CHiMaD_benchmarks/CHiMaD_benchmark3a/customPDE.h
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

#include <core/matrixFreePDE.h>

using namespace dealii;
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3 changes: 3 additions & 0 deletions applications/CHiMaD_benchmarks/CHiMaD_benchmark3a/equations.cc
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

// =================================================================================
// Set the attributes of the primary field variables
// =================================================================================
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3 changes: 3 additions & 0 deletions applications/CHiMaD_benchmarks/CHiMaD_benchmark3a/postprocess.cc
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

// =============================================================================================
// loadPostProcessorVariableAttributes: Set the attributes of the postprocessing
// variables
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3 changes: 3 additions & 0 deletions applications/CHiMaD_benchmarks/CHiMaD_benchmark6a/ICs_and_BCs.cc
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

// ===========================================================================
// FUNCTION FOR INITIAL CONDITIONS
// ===========================================================================
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3 changes: 3 additions & 0 deletions applications/CHiMaD_benchmarks/CHiMaD_benchmark6a/customPDE.h
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

#include <core/matrixFreePDE.h>

using namespace dealii;
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3 changes: 3 additions & 0 deletions applications/CHiMaD_benchmarks/CHiMaD_benchmark6a/equations.cc
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

// =================================================================================
// Set the attributes of the primary field variables
// =================================================================================
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3 changes: 3 additions & 0 deletions applications/CHiMaD_benchmarks/CHiMaD_benchmark6a/postprocess.cc
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

// =============================================================================================
// loadPostProcessorVariableAttributes: Set the attributes of the postprocessing
// variables
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3 changes: 3 additions & 0 deletions applications/CHiMaD_benchmarks/CHiMaD_benchmark6b/ICs_and_BCs.cc
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

// ===========================================================================
// FUNCTION FOR INITIAL CONDITIONS
// ===========================================================================
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3 changes: 3 additions & 0 deletions applications/CHiMaD_benchmarks/CHiMaD_benchmark6b/customPDE.h
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

#include <deal.II/base/tensor.h>
#include <deal.II/grid/manifold.h>

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3 changes: 3 additions & 0 deletions applications/CHiMaD_benchmarks/CHiMaD_benchmark6b/equations.cc
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

// =================================================================================
// Set the attributes of the primary field variables
// =================================================================================
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3 changes: 3 additions & 0 deletions applications/CHiMaD_benchmarks/CHiMaD_benchmark6b/postprocess.cc
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

// =============================================================================================
// loadPostProcessorVariableAttributes: Set the attributes of the postprocessing
// variables
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3 changes: 3 additions & 0 deletions applications/CHiMaD_benchmarks/CHiMaD_benchmark7a/ICs_and_BCs.cc
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

// ===========================================================================
// FUNCTION FOR INITIAL CONDITIONS
// ===========================================================================
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3 changes: 3 additions & 0 deletions applications/CHiMaD_benchmarks/CHiMaD_benchmark7a/customPDE.h
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

#include <core/matrixFreePDE.h>

using namespace dealii;
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3 changes: 3 additions & 0 deletions applications/CHiMaD_benchmarks/CHiMaD_benchmark7a/equations.cc
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

// =================================================================================
// Set the attributes of the primary field variables
// =================================================================================
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3 changes: 3 additions & 0 deletions applications/CHiMaD_benchmarks/CHiMaD_benchmark7a/postprocess.cc
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

// =============================================================================================
// loadPostProcessorVariableAttributes: Set the attributes of the postprocessing
// variables
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3 changes: 3 additions & 0 deletions applications/MgNd_precipitate_single_Bppp/ICs_and_BCs.cc
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

// ===========================================================================
// FUNCTION FOR INITIAL CONDITIONS
// ===========================================================================
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3 changes: 3 additions & 0 deletions applications/MgNd_precipitate_single_Bppp/customPDE.h
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

#include <core/matrixFreePDE.h>

using namespace dealii;
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3 changes: 3 additions & 0 deletions applications/MgNd_precipitate_single_Bppp/equations.cc
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

// =================================================================================
// Set the attributes of the primary field variables
// =================================================================================
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3 changes: 3 additions & 0 deletions applications/MgNd_precipitate_single_Bppp/postprocess.cc
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

// =============================================================================================
// loadPostProcessorVariableAttributes: Set the attributes of the postprocessing
// variables
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3 changes: 3 additions & 0 deletions applications/allenCahn/ICs_and_BCs.cc
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

// ===========================================================================
// FUNCTION FOR INITIAL CONDITIONS
// ===========================================================================
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3 changes: 3 additions & 0 deletions applications/allenCahn/customPDE.h
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

#include <core/matrixFreePDE.h>

using namespace dealii;
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3 changes: 3 additions & 0 deletions applications/allenCahn/equations.cc
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

// =================================================================================
// Set the attributes of the primary field variables
// =================================================================================
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3 changes: 3 additions & 0 deletions applications/allenCahn/postprocess.cc
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

// =================================================================================
// Set the attributes of the postprocessing variables
// =================================================================================
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3 changes: 3 additions & 0 deletions applications/allenCahn_conserved/ICs_and_BCs.cc
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//SPDX-FileCopyrightText: © 2025 PRISMS Phase Field Laboratory at the University of Michigan <prisms-pf@umich.edu>
//SPDX-License-Identifier: GNU Lesser General Public Version 2.1

// ===========================================================================
// FUNCTION FOR INITIAL CONDITIONS
// ===========================================================================
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