UNC-CECL · mcflugen · Jan 3, 2020 · Jan 3, 2020 · Jan 3, 2020 · Jan 3, 2020
diff --git a/.github/workflows/conda-and-cmake.yml b/.github/workflows/conda-and-cmake.yml
@@ -0,0 +1,46 @@
+name: Build/Test CI
+
+on: [push, pull_request]
+
+jobs:
+  build-linux-and-macos:
+    runs-on: ${{ matrix.os }}
+
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: ["3.8"]
+        build-type: [Release]
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+          channels: conda-forge
+          channel-priority: true
+
+      - name: Show conda installation info
+        run: conda info
+
+      - name: Install build tools and dependencies into env
+        run: |
+          conda install --file=requirements.txt
+          conda list
+
+      - name: Make cmake build directory
+        run: cmake -E make_directory build
+
+      - name: Configure cmake
+        working-directory: ${{ github.workspace }}/build
+        run: cmake $GITHUB_WORKSPACE -DCMAKE_BUILD_TYPE=${{ matrix.build-type }}
+
+      - name: Build
+        working-directory: ${{ github.workspace }}/build
+        run: cmake --build . --config ${{ matrix.build-type }}
diff --git a/README.md b/README.md
@@ -1,2 +1,69 @@
-# CDM_v2.48
+# Coastal Dune Model
+
 Coastal Dune Model that includes updated vegetation and wrack dynamics.
+
+
+## Install
+
+### Prerequisites
+
+To install the Coastal Dune Model from source, you will need to install some
+prerequisite packages.
+* A C++ compiler
+* CMake
+* FFTW
+
+If you are using Anaconda, these can be installed through the *conda* command.
+
+    $ conda create -n cdm --file=requirements.txt
+    $ conda activate cdm
+
+This creates a new conda environment, *cdm*, with all of the prequisite packages
+installed.
+
+### Compile
+
+To build and install cmake, run
+
+    $ mkdir _build && cd _build
+    $ cmake ../src -DCMAKE_INSTALL_PREFIX=<path-to-installation>
+    $ make -j4
+    $ make install
+
+where `<path-to-installation>` is the base directory in which the Coastal Dune
+Model will be installed (`/usr/local` is the default).
+
+## Use
+
+With the Coastal Dune Model installed following the above instructions, you
+can run it with the *coastal-dune-model* executable that was installed in
+`<path-to-installation>/bin`. If this folder is in your *PATH*,
+
+    $ coastal-dune-model params.par
+
+## References
+
+Biel, R. G., Moore, L. J., and Goldstein, E. B. (submitted). Influence of wrack on dune forma-
+tion.Journal of Geophysical Research: Biogeosciences.
+
+Biel, R. G., Moore, L. J., Zinnert, J., and Brown, J. (in prep.). Inhibition or facilitation of
+dune development on barriers: The influence of back-beach vegetation on barrier island sta-
+ble states.Journal of Geophysical Research: Biogeosciences.
+
+Duran, O. and Moore, L. J. (2013). Vegetation controls on the maximum size of coastal dunes.
+Proceedings of the National Academy of Sciences, 110(43):17217–17222.
+
+Duran, O., Parteli, E. J., and Herrmann, H. J. (2010). A continuous model for sand dunes:
+Review, new developments and application to barchan dunes and barchan dune fields.Earth
+Surface Processes and Landforms, 35(13):1591–1600.
+
+Duran Vinent, O. and Moore, L. J. (2015). Barrier island bistability induced by biophysical
+interactions.Nature Clim. Change, 5(2):158–162.
+
+Moore, L. J., Vinent, O. D., and Ruggiero, P. (2016). Vegetation control allows autocyclic
+formation of multiple dunes on prograding coasts.Geology, 44(7):559–562.
+
+Weng, W. S., Hunt, J. C. R., Carruthers, D. J., Warren, A., Wiggs, G. F. S., Livingstone, I.,
+and Castro, I. (1991). Air flow and sand transport over sand-dunes. In Barndorff-Nielsen,
+O. E. and Willetts, B. B., editors,Aeolian Grain Transport, pages 1–22, Vienna. Springer
+Vienna.
diff --git a/requirements.txt b/requirements.txt
@@ -0,0 +1,4 @@
+cmake
+cxx-compiler
+fftw
+pkg-config
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -0,0 +1,46 @@
+cmake_minimum_required(VERSION 3.0)
+
+project (cdm CXX)
+
+set (CDM_VERSION 3.0)
+
+find_package(PkgConfig REQUIRED)
+pkg_check_modules(FFTW3 REQUIRED IMPORTED_TARGET fftw3)
+include_directories(${FFTW3_INCLUDE_DIRS})
+link_directories(${FFTW3_LIBRARY_DIRS})
+
+set(
+  CDM_SRCS
+    PTG_Func2dScalar.cc
+    PTG_Func2dVec.cc
+    analyze_new.cc
+    avalanche.cc
+    dune_evolution.cc
+    evolution.cc
+    flux_stationary.cc
+    func.cc
+    globals.cc
+    influx.cc
+    initsurf.cc
+    initsurfalea.cc
+    initsurfbeach.cc
+    iter_aval_new.cc
+    rfftw12d.cc
+    rotatematrix.cc
+    save.cc
+    sepbubble.cc
+    shear.cc
+    shear_hlr.cc
+    shore.cc
+    storm.cc
+    vegetation.cc
+    wind.cc
+)
+
+add_executable(coastal-dune-model main.cc ${CDM_SRCS})
+target_link_libraries(coastal-dune-model fftw3)
+
+install(
+  TARGETS coastal-dune-model
+  RUNTIME DESTINATION bin
+)
diff --git a/PTG_FileNames.h → src/PTG_FileNames.h b/PTG_FileNames.h → src/PTG_FileNames.h
diff --git a/PTG_Func.h → src/PTG_Func.h b/PTG_Func.h → src/PTG_Func.h
diff --git a/PTG_Func2d.h → src/PTG_Func2d.h b/PTG_Func2d.h → src/PTG_Func2d.h
diff --git a/PTG_Func2dScalar.cc → src/PTG_Func2dScalar.cc b/PTG_Func2dScalar.cc → src/PTG_Func2dScalar.cc
diff --git a/PTG_Func2dScalar.h → src/PTG_Func2dScalar.h b/PTG_Func2dScalar.h → src/PTG_Func2dScalar.h
diff --git a/PTG_Func2dVec.cc → src/PTG_Func2dVec.cc b/PTG_Func2dVec.cc → src/PTG_Func2dVec.cc
diff --git a/PTG_Func2dVec.h → src/PTG_Func2dVec.h b/PTG_Func2dVec.h → src/PTG_Func2dVec.h
diff --git a/analyze_new.cc → src/analyze_new.cc b/analyze_new.cc → src/analyze_new.cc
diff --git a/analyze_new.h → src/analyze_new.h b/analyze_new.h → src/analyze_new.h
diff --git a/avalanche.cc → src/avalanche.cc b/avalanche.cc → src/avalanche.cc
diff --git a/avalanche.h → src/avalanche.h b/avalanche.h → src/avalanche.h
diff --git a/dune_evolution.cc → src/dune_evolution.cc b/dune_evolution.cc → src/dune_evolution.cc
diff --git a/dune_evolution.h → src/dune_evolution.h b/dune_evolution.h → src/dune_evolution.h
diff --git a/evolution.cc → src/evolution.cc b/evolution.cc → src/evolution.cc
diff --git a/evolution.h → src/evolution.h b/evolution.h → src/evolution.h
diff --git a/flux_stationary.cc → src/flux_stationary.cc b/flux_stationary.cc → src/flux_stationary.cc
diff --git a/flux_stationary.h → src/flux_stationary.h b/flux_stationary.h → src/flux_stationary.h
diff --git a/func.cc → src/func.cc b/func.cc → src/func.cc
diff --git a/func.h → src/func.h b/func.h → src/func.h
diff --git a/globals.cc → src/globals.cc b/globals.cc → src/globals.cc
diff --git a/globals.h → src/globals.h b/globals.h → src/globals.h
diff --git a/influx.cc → src/influx.cc b/influx.cc → src/influx.cc
diff --git a/influx.h → src/influx.h b/influx.h → src/influx.h
diff --git a/initsurf.cc → src/initsurf.cc b/initsurf.cc → src/initsurf.cc
diff --git a/initsurf.h → src/initsurf.h b/initsurf.h → src/initsurf.h
diff --git a/initsurfalea.cc → src/initsurfalea.cc b/initsurfalea.cc → src/initsurfalea.cc
diff --git a/initsurfalea.h → src/initsurfalea.h b/initsurfalea.h → src/initsurfalea.h
diff --git a/initsurfbeach.cc → src/initsurfbeach.cc b/initsurfbeach.cc → src/initsurfbeach.cc
diff --git a/initsurfbeach.h → src/initsurfbeach.h b/initsurfbeach.h → src/initsurfbeach.h
diff --git a/iter_aval_new.cc → src/iter_aval_new.cc b/iter_aval_new.cc → src/iter_aval_new.cc
diff --git a/iter_aval_new.h → src/iter_aval_new.h b/iter_aval_new.h → src/iter_aval_new.h
diff --git a/main.cc → src/main.cc b/main.cc → src/main.cc
diff --git a/physics_const.h → src/physics_const.h b/physics_const.h → src/physics_const.h
diff --git a/rfftw12d.cc → src/rfftw12d.cc b/rfftw12d.cc → src/rfftw12d.cc
diff --git a/rfftw12d.h → src/rfftw12d.h b/rfftw12d.h → src/rfftw12d.h
diff --git a/rotatematrix.cc → src/rotatematrix.cc b/rotatematrix.cc → src/rotatematrix.cc
diff --git a/rotatematrix.h → src/rotatematrix.h b/rotatematrix.h → src/rotatematrix.h
diff --git a/save.cc → src/save.cc b/save.cc → src/save.cc
diff --git a/save.h → src/save.h b/save.h → src/save.h
diff --git a/sepbubble.cc → src/sepbubble.cc b/sepbubble.cc → src/sepbubble.cc
diff --git a/sepbubble.h → src/sepbubble.h b/sepbubble.h → src/sepbubble.h
diff --git a/shear.cc → src/shear.cc b/shear.cc → src/shear.cc
diff --git a/shear.h → src/shear.h b/shear.h → src/shear.h
diff --git a/shear_hlr.cc → src/shear_hlr.cc b/shear_hlr.cc → src/shear_hlr.cc
diff --git a/shear_hlr.h → src/shear_hlr.h b/shear_hlr.h → src/shear_hlr.h
diff --git a/shore.cc → src/shore.cc b/shore.cc → src/shore.cc
diff --git a/shore.h → src/shore.h b/shore.h → src/shore.h
diff --git a/storm.cc → src/storm.cc b/storm.cc → src/storm.cc
diff --git a/storm.h → src/storm.h b/storm.h → src/storm.h
diff --git a/vec.h → src/vec.h b/vec.h → src/vec.h
diff --git a/vegetation.cc → src/vegetation.cc b/vegetation.cc → src/vegetation.cc
diff --git a/vegetation.h → src/vegetation.h b/vegetation.h → src/vegetation.h
diff --git a/wind.cc → src/wind.cc b/wind.cc → src/wind.cc
diff --git a/wind.h → src/wind.h b/wind.h → src/wind.h