UNC-CECL · mcflugen · Feb 26, 2021 · 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 +1,89 @@
+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 $GITHUB_WORKSPACE/src -DCMAKE_BUILD_TYPE=${{ matrix.build-type }}
+
+      - name: Build
+        working-directory: ${{ github.workspace }}/build
+        run: cmake --build . --config ${{ matrix.build-type }}
+
+  build-windows:
+    runs-on: windows-latest
+
+    env:
+      build-type: Release
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          python-version: 3.8
+          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, build, and test
+        shell: cmd /C CALL {0}
+        working-directory: ${{ github.workspace }}\build
+        run: |
+          call "C:\Program Files (x86)\Microsoft Visual Studio\2019\Enterprise\VC\Auxiliary\Build\vcvars64.bat" -vcvars_ver=14.16 10.0.19041.0
+
+          :: Configure
+          cmake ^
+            -LAH -G "NMake Makefiles" ^
+            -DPKG_CONFIG_EXECUTABLE:FILEPATH=C:/Miniconda/envs/test/Library/bin/pkg-config.exe ^
+            -DCMAKE_BUILD_TYPE=${{ env.build-type }} ^
+            ${{ github.workspace }}\src
+
+          :: Build and install
+          cmake --build . --target install --config ${{ env.build-type }}
diff --git a/README.md b/README.md
@@ -1,2 +1,93 @@
-# CDM_v2.48
+![Build/Test CI](https://github.com/mcflugen/CDM_v3.0/workflows/Build/Test%20CI/badge.svg)
+
+# 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
+
+#### Linux and Mac
+
+To build and install cmake, run
+
+    $ mkdir _build && cd _build
+    $ cmake ../src -DCMAKE_INSTALL_PREFIX=$CONDA_PREFIX
+    $ make -j4
+    $ make install
+
+This will install Coastal Dune Model into your current conda environment.
+
+#### Windows
+
+To build the *CDM* on Windows, you will need to install a C++ compiler. The
+following instructions assume *Microsoft Visual Studio 2017 or Microsoft Build
+Tools for Visual Studio 2017*.
+
+After you have activated the conda environment you created in the previous
+section, you need to set up your compiler by running *vcvarsall.bat*. This
+can be done from within the Anaconda Powershell Prompt by running the
+following,
+
+    $ & 'C:\Program Files (x86)\Microsoft Visual Studio\2017\Community\VC\Auxiliary\Build\vcvarsall.bat' x86
+
+You should now be able to run *cmake* and then compile the program in a
+way that is similar to with Linux and Mac,
+
+    $ mkdir _build
+    $ cd _build
+    $ cmake ../src -DCMAKE_INSTALL_PREFIX:PATH=$env:CONDA_PREFIX
+    $ cmake --build . --target install
+
+## 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 +1,66 @@
+cmake_minimum_required(VERSION 3.0)
+include(CheckIncludeFile)
+
+# project (cdm CXX)
+project (cdm)
+
+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})
+
+check_include_file(unistd.h WITH_UNISTD)
+check_include_file(sys/utsname.h WITH_UTSNAME)
+find_library(LIB_M m)
+
+if (WITH_UNISTD)
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DWITH_UNISTD")
+endif (WITH_UNISTD)
+if (WITH_UTSNAME)
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DWITH_UTSNAME")
+endif (WITH_UTSNAME)
+
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -D_USE_MATH_DEFINES")
+
+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})
+if (LIB_M)
+  target_link_libraries(coastal-dune-model fftw3 m)
+elseif (NOT LIB_M)
+  target_link_libraries(coastal-dune-model fftw3)
+endif (LIB_M)
+
+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
@@ -3,6 +3,7 @@
  ******************************************************************************/
 
 #include <iostream>
+
 #include <math.h>
 #include "globals.h"
 #include "PTG_Func2dScalar.h"
@@ -147,13 +148,13 @@ double PTG_Func2dScalar::CenterOfMassX() const
     for (int x=0; x < SizeX(); x++) {
         double linesum= 0.0;
         for (int y=0; y < SizeY(); y++)
-            if( finite((*this)(x, y)) )
+            if( isfinite((*this)(x, y)) )
                 linesum += (*this)(x,y);
         xsum += linesum * x;
         sum += linesum;
     }
     centerx= Delta()*xsum/sum;
-    if( finite(centerx) )
+    if( isfinite(centerx) )
         return centerx;
     else
         return Delta()*SizeX()/2.0;

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
@@ -5,7 +5,9 @@
 #include <stdio.h>
 #include <sys/types.h>
 #include <sys/stat.h>
-#include <unistd.h>
+#ifdef WITH_UNISTD
+  #include <unistd.h>
+#endif
 #include <errno.h>
 #include <math.h>
 
@@ -463,11 +465,13 @@ duneglobals::duneglobals( const dunepar& parameters )
         "'.  Data directory doesn't exist or permission denied.  Aborting.\n";
         exit(1);
     }
+#ifdef WITH_UNISTD
     if( !S_ISDIR(savedirstat.st_mode) ) {
         cerr << "duneglobals constructor:  Data directory `" << m_datadir <<
         "' is not a directory.  Aborting.\n";
         exit(1);
     }
+#endif
 }
 
 

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
@@ -3,9 +3,11 @@
 ******************************************************************************/
 
 #include <time.h>
-#include <sys/utsname.h>
+#ifdef WITH_UTSNAME
+  #include <sys/utsname.h>
+#endif
 #include <sys/types.h>
-#include <unistd.h>
+// #include <unistd.h>
 
 #include "globals.h"
 #include "dune_evolution.h"
@@ -39,12 +41,16 @@ parameter file version, a CPde object (for backward compatibility; version <
 CApp::CApp(int argc, char **argv) : m_evol(0)
 
 {
+#ifdef UTSNAME
   struct utsname u;
+#endif
   time_t t= time(NULL);
 
+#ifdef UTSNAME
   if( !uname(&u) )
     cout << "Running on " << u.nodename << ", machine type " << u.machine << ", with process id " << getpid() << "\n";
   cout << ctime( &t ) << "\n";
+#endif
 
   // find name for parameter file
   // Format for command line arguments: <token>=<value>, for instance 

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
@@ -178,7 +178,7 @@ double shearHLR::CalcPertTau(TFktScal& h, TFktVec& tau)
             ky2= ky*ky;
             ka= sqrt(kx2+ky2);
 
-        	if( (!finite(fft_h.freqre(x, y)) || !finite(fft_h.freqim(x, y))) && !naninfwarned ) {
+        	if( (!isfinite(fft_h.freqre(x, y)) || !isfinite(fft_h.freqim(x, y))) && !naninfwarned ) {
           		fprintf(stderr, "CShearHLR::CalcPertTau:  NAN or INF in fft_h after FT.\n");
           		naninfwarned= true;
         	}
@@ -226,7 +226,7 @@ double shearHLR::CalcPertTau(TFktScal& h, TFktVec& tau)
     }
     L = Int/(Int_x*m_dkx);
 
-    if( !finite(L) )	L= iNx;
+    if( !isfinite(L) )	L= iNx;
 
     return L;
 }

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
@@ -2,6 +2,7 @@
  $Id: wind.cc,v 1.5 2004/12/22 10:21:57 schatz Exp $
  ******************************************************************************/
 
+#include <random>
 #include <stdlib.h>
 #include <math.h>
 #include <time.h>
@@ -118,7 +119,8 @@ wind_flatrand::wind_flatrand(const dunepar& par)
     m_dir0= par.getdefault( "flatwind.avgdir", 0.0 ) / 360.0;
     m_ddir= par.getrequired<double>( "flatwind.ddir" ) / 360.0;
 
-    initstate( time(NULL), m_statearray, 256 );
+    // initstate( time(NULL), m_statearray, 256 );
+    srand(1973);
 }
 
 
@@ -130,17 +132,19 @@ void wind_flatrand::advance( double )
 {
     char *prevrngstate;
 
-    prevrngstate= setstate(m_statearray);
+    // prevrngstate = setstate(m_statearray);
+    srand(1973);
     if( m_ddir==0.0 )
         m_dir= m_dir0;
     else
-        m_dir= m_dir0 + m_ddir * 2.0 * ((double)random()/(double)RAND_MAX - 0.5);
+        m_dir= m_dir0 + m_ddir * 2.0 * ((double)rand()/(double)RAND_MAX - 0.5);
     if( m_dustar==0.0 )
         m_ustar= m_ustar0;
     else
         m_ustar= m_ustar0 +
-	    m_dustar * 2.0 * ((double)random()/(double)RAND_MAX - 0.5);
-    setstate(prevrngstate);
+	    m_dustar * 2.0 * ((double)rand()/(double)RAND_MAX - 0.5);
+    // setstate(prevrngstate);
+    srand(1973);
 }
 
 

diff --git a/wind.h → src/wind.h b/wind.h → src/wind.h