From c3e486600448c237f4a1fd7f292b06adee46e9cf Mon Sep 17 00:00:00 2001
From: Karsten Bolding <karsten@bolding-bruggeman.com>
Date: Tue, 28 Apr 2020 08:42:56 +0200
Subject: [PATCH 01/14] support for building the CVMix library and the CVMix
 driver using CMake

---
 CMakeLists.txt     | 102 +++++++++++++++++++++++++++++++++++++++++++++
 src/CMakeLists.txt |  40 ++++++++++++++++++
 2 files changed, 142 insertions(+)
 create mode 100644 CMakeLists.txt
 create mode 100644 src/CMakeLists.txt

diff --git a/CMakeLists.txt b/CMakeLists.txt
new file mode 100644
index 000000000..342ee1eba
--- /dev/null
+++ b/CMakeLists.txt
@@ -0,0 +1,102 @@
+cmake_minimum_required( VERSION 3.10 )
+
+project( cvmix VERSION 4.0.1 LANGUAGES Fortran )
+
+# Use solution folders in IDEs
+set_property(GLOBAL PROPERTY USE_FOLDERS ON)
+
+# Use standard GNU installation directories
+if ( NOT WIN32 )
+   include( GNUInstallDirs )
+endif()
+
+# Configuration options
+option( CVMIX_USE_NetCDF "Enable NetCDF format" OFF )
+option( CVMIX_BUILD_STATIC_LIBS "Build static library" ON )
+option( CVMIX_BUILD_SHARED_LIBS "Build shared library" ON )
+option( CVMIX_BUILD_DRIVER "Build CVMix example/test driver" OFF )
+
+# Check if shared or static builds are turned off
+if( NOT CVMIX_BUILD_STATIC_LIBS )
+   message( STATUS "Turning STATIC builds OFF" )
+endif()
+if( NOT CVMIX_BUILD_SHARED_LIBS )
+   message( STATUS "Turning SHARED builds OFF" )
+endif()
+
+# Set default build type to Release if not specified
+if( NOT CMAKE_CONFIGURATION_TYPES AND NOT CMAKE_BUILD_TYPE )
+   message( STATUS "Setting default build type to 'Release'.  Set CMAKE_BUILD_TYPE variable to change build types." )
+   set_property( CACHE CMAKE_BUILD_TYPE PROPERTY VALUE "Release" )
+endif()
+
+set( CMAKE_Fortran_MODULE_DIRECTORY ${CMAKE_BINARY_DIR}/modules )
+set( CMAKE_POSITION_INDEPENDENT_CODE ON )
+
+add_subdirectory( src )
+
+# Note - KB:
+# Building static and shared libs require an ugly construct to build on both
+# Windows and Linux. Windows will not create the libraries unless a Fortran
+# file is explicitly given - and Linux complains (I think due to a race 
+# condition) if it is. Therefor the construct below - a proper solution is 
+# most welcome.
+
+# Add static lib target
+if( CVMIX_BUILD_STATIC_LIBS )
+   if ( WIN32 )
+      add_library( cvmix_static STATIC ${CMAKE_BINARY_DIR}/src/cvmix_version.F90 $<TARGET_OBJECTS:cvmix_objects> )
+   else()
+      add_library( cvmix_static STATIC $<TARGET_OBJECTS:cvmix_objects> )
+   endif()
+   list( APPEND LIB_TARGETS cvmix_static )
+endif()
+
+# Add shared lib target
+if( CVMIX_BUILD_SHARED_LIBS )
+   if ( WIN32 )
+      add_library( cvmix_shared SHARED ${CMAKE_BINARY_DIR}/src/cvmix_version.F90 $<TARGET_OBJECTS:cvmix_objects> )
+   else()
+      add_library( cvmix_shared SHARED $<TARGET_OBJECTS:cvmix_objects> )
+   endif()
+   list( APPEND LIB_TARGETS cvmix_shared )
+endif()
+
+# Set common lib target properties
+foreach( _lib IN LISTS LIB_TARGETS )
+   target_compile_definitions( ${_lib} PUBLIC "${PUBLIC_FLAGS}" )
+   target_include_directories( ${_lib}
+      PUBLIC
+         $<INSTALL_INTERFACE:include/cvmix>
+      PRIVATE
+         $<BUILD_INTERFACE:${PROJECT_BINARY_DIR}/${INCLUDE_DIR}> )
+   set_target_properties( ${_lib} PROPERTIES OUTPUT_NAME cvmix)
+endforeach()
+
+if(CVMIX_BUILD_DRIVER)
+
+   if(CVMIX_USE_NetCDF)
+      find_package(NetCDF REQUIRED)
+   endif(CVMIX_USE_NetCDF)
+   add_executable( cvmix_driver . )
+   target_sources( cvmix_driver PRIVATE src/cvmix_driver.F90 )
+   set_property( TARGET cvmix_driver PROPERTY FOLDER driver )
+   target_include_directories( cvmix_driver PRIVATE ${CMAKE_BINARY_DIR}/modules )
+   target_link_libraries( cvmix_driver PRIVATE cvmix_drivers cvmix_static netcdf )
+
+endif()
+
+# Install
+if(CVMIX_BUILD_DRIVER)
+install( TARGETS cvmix_driver EXPORT cvmixConfig
+	 RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} )
+endif()
+install( TARGETS ${LIB_TARGETS} EXPORT cvmixConfig
+	 ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
+	 LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} )
+install( DIRECTORY ${CMAKE_BINARY_DIR}/modules/ EXPORT cvmixConfig
+	 DESTINATION  include/cvmix
+	 FILES_MATCHING
+	 PATTERN "*.mod" )
+install(EXPORT cvmixConfig DESTINATION cmake)
+
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
new file mode 100644
index 000000000..5333d0a2b
--- /dev/null
+++ b/src/CMakeLists.txt
@@ -0,0 +1,40 @@
+# CVMix library
+add_library(cvmix_objects OBJECT .)
+set_property( TARGET cvmix_objects PROPERTY FOLDER cvmixlib )
+target_sources( cvmix_objects PRIVATE
+   shared/cvmix_kinds_and_types.F90
+   shared/cvmix_background.F90
+   shared/cvmix_convection.F90
+   shared/cvmix_ddiff.F90
+   shared/cvmix_kpp.F90
+   shared/cvmix_math.F90
+   shared/cvmix_put_get.F90
+   shared/cvmix_shear.F90
+   shared/cvmix_tidal.F90
+   shared/cvmix_utils.F90
+)
+
+#configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cvmix_version.F90.in ${CMAKE_CURRENT_BINARY_DIR}/cvmix_version.F90)
+
+# CVMix driver dependencies
+if(CVMIX_BUILD_DRIVER)
+
+   add_library(cvmix_io STATIC .)
+   set_property( TARGET cvmix_io PROPERTY FOLDER drivers )
+   target_sources( cvmix_io PRIVATE
+      cvmix_io.F90
+   )
+   target_link_libraries(cvmix_io PRIVATE cvmix_static)
+
+   add_library(cvmix_drivers STATIC .)
+   set_property( TARGET cvmix_drivers PROPERTY FOLDER drivers )
+   target_sources( cvmix_drivers PRIVATE
+      drivers/cvmix_bgrnd_BL.F90
+      drivers/cvmix_ddiff_drv.F90
+      drivers/cvmix_kpp_drv.F90
+      drivers/cvmix_shear_drv.F90
+      drivers/cvmix_tidal_Simmons.F90
+   )
+   target_link_libraries( cvmix_drivers PRIVATE cvmix_io )
+
+endif()

From 29bf5b351016eccbdacdc9c062c3ff34f2bac268 Mon Sep 17 00:00:00 2001
From: Karsten Bolding <karsten@bolding-bruggeman.com>
Date: Tue, 28 Apr 2020 09:05:42 +0200
Subject: [PATCH 02/14] CMake build instructions added to README.md

---
 README.md | 39 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)

diff --git a/README.md b/README.md
index bb35506a8..75c816ff3 100644
--- a/README.md
+++ b/README.md
@@ -37,6 +37,12 @@ goes into details about how to contribute, but basically we ask three things:
 INSTALLATION NOTES
 ------------------
 
+CVMix can be installed using two different methods. The original using Make
+and a set of Makefiles. Or, using CMake using two CMakelists.txt files for
+configuration.
+
+### Building/installing using Make
+
 The src directory contains a Makefile and a simple 'make' should be sufficient
 to build the standalone driver. The first time you build, the 'cvmix_setup'
 utility will run and prompt you for compiler and netcdf information - it will
@@ -58,6 +64,39 @@ $ make FC=[compiler]                        \
 And then use -I$(INC_DIR) -L$(LIB_DIR) -lcvmix when you build software using
 the CVMix library.
 
+### Building/installing using CMake
+
+[CMake](https://cmake.org/) can be used in GUI mode. Further information can
+be found on the CMake web-page. Below is provided the command line commands
+to configure and compile CVMix. Note that CVMix has been build on Windows using
+VisualStudio and the Intel Fortran compiler.
+
+In this recipe CVMIX\_BASE s a convinience environmental variable pointing to 
+the CVMix source directory. It is possible to execute the following commands 
+providing the full path.
+
+
+1. mkdir ~/build/cvmix
+   * [CMake](https://cmake.org/) promotes out of source compilation
+2. cd ~/build/cvmix
+3. cmake $CVMIX\_BASE 
+   * The simplest configuration - using default Fortran compiler
+4. cmake $CVMIX\_BASE -DCMAKE\_Fortran\_COMPILER=ifort
+   * Specifying a Fortran compiler
+5. cmake $CVMIX\_BASE -DCVMIX\_BUILD\_DRIVER=on
+   * Build the CVMix driver program
+5. cmake $CVMIX\_BASE -DCMAKE\_INSTALL\_PREFIX=~/local
+   * Providing installation folder
+
+After configuration has been done compilation is as simple as:
+```
+make
+```
+
+and instllation by:
+```
+make install
+```
 
 DIRECTORY STRUCTURE
 -------------------

From 393ab26991412bf9b0105b0decb651fc508295a4 Mon Sep 17 00:00:00 2001
From: Karsten Bolding <karsten@bolding-bruggeman.com>
Date: Tue, 28 Apr 2020 09:16:24 +0200
Subject: [PATCH 03/14] update documentation

---
 README.md | 24 ++++++++++++++++++------
 1 file changed, 18 insertions(+), 6 deletions(-)

diff --git a/README.md b/README.md
index 75c816ff3..ea5f81202 100644
--- a/README.md
+++ b/README.md
@@ -37,11 +37,11 @@ goes into details about how to contribute, but basically we ask three things:
 INSTALLATION NOTES
 ------------------
 
-CVMix can be installed using two different methods. The original using Make
-and a set of Makefiles. Or, using CMake using two CMakelists.txt files for
-configuration.
+CVMix can be installed using two different methods. The original uses Make
+and a set of Makefiles. The new methos uses CMake and two CMakelists.txt 
+files.
 
-### Building/installing using Make
+#### Building/installing using Make
 
 The src directory contains a Makefile and a simple 'make' should be sufficient
 to build the standalone driver. The first time you build, the 'cvmix_setup'
@@ -64,7 +64,7 @@ $ make FC=[compiler]                        \
 And then use -I$(INC_DIR) -L$(LIB_DIR) -lcvmix when you build software using
 the CVMix library.
 
-### Building/installing using CMake
+#### Building/installing using CMake
 
 [CMake](https://cmake.org/) can be used in GUI mode. Further information can
 be found on the CMake web-page. Below is provided the command line commands
@@ -85,9 +85,14 @@ providing the full path.
    * Specifying a Fortran compiler
 5. cmake $CVMIX\_BASE -DCVMIX\_BUILD\_DRIVER=on
    * Build the CVMix driver program
-5. cmake $CVMIX\_BASE -DCMAKE\_INSTALL\_PREFIX=~/local
+6. cmake $CVMIX\_BASE -DCVMIX\_BUILD\_DRIVER=on CVMIX\_USE\_NetCDF=on
+   * Include support for NetCDF in the driver model
+   * Note that this requires proper configuration of the installed NetCDF library.
+7. cmake $CVMIX\_BASE -DCMAKE\_INSTALL\_PREFIX=~/local
    * Providing installation folder
 
+Combination of the above commands is possible.
+
 After configuration has been done compilation is as simple as:
 ```
 make
@@ -98,6 +103,13 @@ and instllation by:
 make install
 ```
 
+After installation the build directory can be removed.
+
+The support for CMake builds provides sufficient infrastructure for CVMix 
+being included in ocean models using the GIT submodule feature. This has
+been used in the [GOTM](https:/gotm.net) inclusion of the CVMix mixing
+models as a supplement to the original turbulence models in GOTM.
+
 DIRECTORY STRUCTURE
 -------------------
 

From 0f005b090513906b621a94eeccc4daf87f2ecde1 Mon Sep 17 00:00:00 2001
From: Karsten Bolding <karsten@bolding-bruggeman.com>
Date: Tue, 28 Apr 2020 12:54:21 +0200
Subject: [PATCH 04/14] improved support for NetCDF

---
 CMakeLists.txt     | 9 +++++----
 README.md          | 5 ++++-
 src/CMakeLists.txt | 7 ++++---
 3 files changed, 13 insertions(+), 8 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 342ee1eba..499e33901 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -12,6 +12,10 @@ endif()
 
 # Configuration options
 option( CVMIX_USE_NetCDF "Enable NetCDF format" OFF )
+if(CVMIX_USE_NetCDF)
+   add_compile_definitions(_NETCDF)
+   include_directories($ENV{NetCDF_INCLUDE})
+endif(CVMIX_USE_NetCDF)
 option( CVMIX_BUILD_STATIC_LIBS "Build static library" ON )
 option( CVMIX_BUILD_SHARED_LIBS "Build shared library" ON )
 option( CVMIX_BUILD_DRIVER "Build CVMix example/test driver" OFF )
@@ -75,14 +79,11 @@ endforeach()
 
 if(CVMIX_BUILD_DRIVER)
 
-   if(CVMIX_USE_NetCDF)
-      find_package(NetCDF REQUIRED)
-   endif(CVMIX_USE_NetCDF)
    add_executable( cvmix_driver . )
    target_sources( cvmix_driver PRIVATE src/cvmix_driver.F90 )
    set_property( TARGET cvmix_driver PROPERTY FOLDER driver )
    target_include_directories( cvmix_driver PRIVATE ${CMAKE_BINARY_DIR}/modules )
-   target_link_libraries( cvmix_driver PRIVATE cvmix_drivers cvmix_static netcdf )
+   target_link_libraries( cvmix_driver PRIVATE cvmix_drivers )
 
 endif()
 
diff --git a/README.md b/README.md
index ea5f81202..4f6502731 100644
--- a/README.md
+++ b/README.md
@@ -86,8 +86,9 @@ providing the full path.
 5. cmake $CVMIX\_BASE -DCVMIX\_BUILD\_DRIVER=on
    * Build the CVMix driver program
 6. cmake $CVMIX\_BASE -DCVMIX\_BUILD\_DRIVER=on CVMIX\_USE\_NetCDF=on
-   * Include support for NetCDF in the driver model
+   * Include support for NetCDF in the driver model(1)
    * Note that this requires proper configuration of the installed NetCDF library.
+   * Setting NetCDF\_INCLUDE and NetCDF\_LIBRARIES might help.
 7. cmake $CVMIX\_BASE -DCMAKE\_INSTALL\_PREFIX=~/local
    * Providing installation folder
 
@@ -110,6 +111,8 @@ being included in ocean models using the GIT submodule feature. This has
 been used in the [GOTM](https:/gotm.net) inclusion of the CVMix mixing
 models as a supplement to the original turbulence models in GOTM.
 
+1): There is unfortunately not an official NetCDF module finder in CMake.
+
 DIRECTORY STRUCTURE
 -------------------
 
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 5333d0a2b..b456cd394 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -20,14 +20,15 @@ target_sources( cvmix_objects PRIVATE
 if(CVMIX_BUILD_DRIVER)
 
    add_library(cvmix_io STATIC .)
-   set_property( TARGET cvmix_io PROPERTY FOLDER drivers )
+   set_property( TARGET cvmix_io PROPERTY FOLDER driver )
    target_sources( cvmix_io PRIVATE
       cvmix_io.F90
    )
-   target_link_libraries(cvmix_io PRIVATE cvmix_static)
+#   target_link_libraries(cvmix_io PRIVATE cvmix_static PUBLIC netcdff )
+   target_link_libraries(cvmix_io PRIVATE cvmix_static PUBLIC $ENV{NetCDF_LIBRARIES} )
 
    add_library(cvmix_drivers STATIC .)
-   set_property( TARGET cvmix_drivers PROPERTY FOLDER drivers )
+   set_property( TARGET cvmix_drivers PROPERTY FOLDER driver )
    target_sources( cvmix_drivers PRIVATE
       drivers/cvmix_bgrnd_BL.F90
       drivers/cvmix_ddiff_drv.F90

From 4dd8764ec56974752207567812607c556538a533 Mon Sep 17 00:00:00 2001
From: Karsten Bolding <karsten@bolding-bruggeman.com>
Date: Tue, 28 Apr 2020 13:08:30 +0200
Subject: [PATCH 05/14] fixed compilation with VisualStudio

---
 CMakeLists.txt | 4 ++--
 src/dummy.F90  | 5 +++++
 2 files changed, 7 insertions(+), 2 deletions(-)
 create mode 100644 src/dummy.F90

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 499e33901..983ec8336 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -49,7 +49,7 @@ add_subdirectory( src )
 # Add static lib target
 if( CVMIX_BUILD_STATIC_LIBS )
    if ( WIN32 )
-      add_library( cvmix_static STATIC ${CMAKE_BINARY_DIR}/src/cvmix_version.F90 $<TARGET_OBJECTS:cvmix_objects> )
+	   add_library( cvmix_static STATIC ${CMAKE_SOURCE_DIR}/src/dummy.F90 $<TARGET_OBJECTS:cvmix_objects> )
    else()
       add_library( cvmix_static STATIC $<TARGET_OBJECTS:cvmix_objects> )
    endif()
@@ -59,7 +59,7 @@ endif()
 # Add shared lib target
 if( CVMIX_BUILD_SHARED_LIBS )
    if ( WIN32 )
-      add_library( cvmix_shared SHARED ${CMAKE_BINARY_DIR}/src/cvmix_version.F90 $<TARGET_OBJECTS:cvmix_objects> )
+	   add_library( cvmix_shared SHARED ${CMAKE_SOURCE_DIR}/src/dummy.F90 $<TARGET_OBJECTS:cvmix_objects> )
    else()
       add_library( cvmix_shared SHARED $<TARGET_OBJECTS:cvmix_objects> )
    endif()
diff --git a/src/dummy.F90 b/src/dummy.F90
new file mode 100644
index 000000000..2bf5e0338
--- /dev/null
+++ b/src/dummy.F90
@@ -0,0 +1,5 @@
+! This file is needed to compile the driver program using VisualStudio.
+! This is a known issue when building static/dynamic libraries based on 
+! object library.
+! VisualStudio requires an explicit listed Fortran file to make the
+! libraries - even if it is empty.

From a323cef9b12755b25fe5d3c7a02e3efcbac3024e Mon Sep 17 00:00:00 2001
From: Karsten Bolding <karsten@bolding-bruggeman.com>
Date: Tue, 28 Apr 2020 13:10:22 +0200
Subject: [PATCH 06/14] updated README.md

---
 README.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 4f6502731..b1f8ef743 100644
--- a/README.md
+++ b/README.md
@@ -69,7 +69,8 @@ the CVMix library.
 [CMake](https://cmake.org/) can be used in GUI mode. Further information can
 be found on the CMake web-page. Below is provided the command line commands
 to configure and compile CVMix. Note that CVMix has been build on Windows using
-VisualStudio and the Intel Fortran compiler.
+VisualStudio and the Intel Fortran compiler but NetCDF support has not been
+tested.
 
 In this recipe CVMIX\_BASE s a convinience environmental variable pointing to 
 the CVMix source directory. It is possible to execute the following commands 

From f5818f55edaab5d50ec7056579f2ee2bfc1c4a48 Mon Sep 17 00:00:00 2001
From: Karsten Bolding <karsten@bolding-bruggeman.com>
Date: Tue, 28 Apr 2020 13:14:42 +0200
Subject: [PATCH 07/14] README.md - a few typos

---
 README.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index b1f8ef743..e6e2370cd 100644
--- a/README.md
+++ b/README.md
@@ -38,7 +38,7 @@ INSTALLATION NOTES
 ------------------
 
 CVMix can be installed using two different methods. The original uses Make
-and a set of Makefiles. The new methos uses CMake and two CMakelists.txt 
+and a set of Makefiles. The new method uses CMake and two CMakelists.txt 
 files.
 
 #### Building/installing using Make
@@ -85,13 +85,13 @@ providing the full path.
 4. cmake $CVMIX\_BASE -DCMAKE\_Fortran\_COMPILER=ifort
    * Specifying a Fortran compiler
 5. cmake $CVMIX\_BASE -DCVMIX\_BUILD\_DRIVER=on
-   * Build the CVMix driver program
+   * Build the CVMix driver program - off by default
 6. cmake $CVMIX\_BASE -DCVMIX\_BUILD\_DRIVER=on CVMIX\_USE\_NetCDF=on
    * Include support for NetCDF in the driver model(1)
    * Note that this requires proper configuration of the installed NetCDF library.
    * Setting NetCDF\_INCLUDE and NetCDF\_LIBRARIES might help.
 7. cmake $CVMIX\_BASE -DCMAKE\_INSTALL\_PREFIX=~/local
-   * Providing installation folder
+   * Providing an installation folder
 
 Combination of the above commands is possible.
 

From 6d7bb49124bb26ca0d05cbcdb0a7c9510b5756ef Mon Sep 17 00:00:00 2001
From: Karsten Bolding <karsten@bolding-bruggeman.com>
Date: Sat, 16 May 2020 13:57:56 +0200
Subject: [PATCH 08/14] removed trailing blank

---
 src/dummy.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/dummy.F90 b/src/dummy.F90
index 2bf5e0338..3ddf711b8 100644
--- a/src/dummy.F90
+++ b/src/dummy.F90
@@ -1,5 +1,5 @@
 ! This file is needed to compile the driver program using VisualStudio.
-! This is a known issue when building static/dynamic libraries based on 
+! This is a known issue when building static/dynamic libraries based on
 ! object library.
 ! VisualStudio requires an explicit listed Fortran file to make the
 ! libraries - even if it is empty.

From 1dbf89780f6ea078cd469cb84e9651198787b2e0 Mon Sep 17 00:00:00 2001
From: Michael Levy <mike.levy.work@gmail.com>
Date: Tue, 19 May 2020 21:33:00 -0600
Subject: [PATCH 09/14] Create directory for cmake build

---
 bld/cmake_bld/.gitignore | 2 ++
 1 file changed, 2 insertions(+)
 create mode 100644 bld/cmake_bld/.gitignore

diff --git a/bld/cmake_bld/.gitignore b/bld/cmake_bld/.gitignore
new file mode 100644
index 000000000..d6b7ef32c
--- /dev/null
+++ b/bld/cmake_bld/.gitignore
@@ -0,0 +1,2 @@
+*
+!.gitignore

From 1cb7ba2266f0ab1018170263a1df7b8608bd76c1 Mon Sep 17 00:00:00 2001
From: Michael Levy <mike.levy.work@gmail.com>
Date: Tue, 19 May 2020 21:52:13 -0600
Subject: [PATCH 10/14] Allow reg_tests to use cmake

At this point, it's pretty klunky -- no netcdf support, forces compiler to be
gfortran. But it should get cmake tested in travis, which is a good start.
---
 .travis.yml                      |  1 +
 reg_tests/common/build.sh        | 15 ++++++++++++---
 reg_tests/common/parse_inputs.sh |  3 +++
 reg_tests/common/run.sh          |  7 ++++++-
 4 files changed, 22 insertions(+), 4 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 60b929f48..cb8f49f7d 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -14,6 +14,7 @@ python:
 script:
   - cd bld; ./cvmix_setup gfortran $(dirname $(dirname $(which nc-config)))
   - cd ../CVMix_tools; ./run_test_suite.sh --already-ran-setup
+  - cd ../reg_tests/Bryan-Lewis/; ./Bryan-Lewis-test.sh --cmake
 
 branches:
   only:
diff --git a/reg_tests/common/build.sh b/reg_tests/common/build.sh
index 200be0e6d..1395a3a66 100644
--- a/reg_tests/common/build.sh
+++ b/reg_tests/common/build.sh
@@ -2,8 +2,17 @@
 
 build () {
   if [ -z ${NO_BUILD} ]; then
-    make -f $CVMix/src/Makefile CVMIX_ROOT=$CVMix ${USE_NETCDF}
-    if [ $? != 0 ]; then
+    if [ "${CMAKE_BUILD}" == "TRUE" ]; then
+      CWD=$PWD
+      cd $CVMix/bld/cmake_bld
+      cmake $CVMix -DCVMIX_BUILD_DRIVER=on -DCMAKE_Fortran_COMPILER=gfortran && make
+      STATUS=$?
+      cd $CWD
+    else
+      make -f $CVMix/src/Makefile CVMIX_ROOT=$CVMix ${USE_NETCDF}
+      STATUS=$?
+    fi
+    if [ $STATUS != 0 ]; then
       echo "Build error!"
       exit 2
     fi
@@ -12,7 +21,7 @@ build () {
       if [ "`cat ../../bld/.netcdf_info`" == "YES" ]; then
         USE_NETCDF=netcdf
       fi
-    fi  
+    fi
   fi
 
 }
diff --git a/reg_tests/common/parse_inputs.sh b/reg_tests/common/parse_inputs.sh
index c62a9f0a5..100a6e3d2 100644
--- a/reg_tests/common/parse_inputs.sh
+++ b/reg_tests/common/parse_inputs.sh
@@ -43,6 +43,9 @@ while [ $# -gt 0 ]; do
         bad_input $1
       fi
     ;;
+    -cm|--cmake)
+      CMAKE_BUILD=TRUE
+    ;;
     * )
       bad_input $1
     ;;
diff --git a/reg_tests/common/run.sh b/reg_tests/common/run.sh
index ed279dc29..4307868af 100644
--- a/reg_tests/common/run.sh
+++ b/reg_tests/common/run.sh
@@ -2,7 +2,12 @@
 
 run () {
 
-  $CVMix/bin/cvmix < $NAMELIST
+  if [ "${CMAKE_BUILD}" == "TRUE" ]; then
+    CVMIX_EXE=$CVMix/bld/cmake_bld/cvmix_driver
+  else
+    CVMIX_EXE=$CVMix/bin/cvmix
+  fi
+  ${CVMIX_EXE} < $NAMELIST
 
   if [ $? != 0 ]; then
     echo "Error in execution!"

From b583d7dfe59825246eb3efc53c5c02ad7ebbac26 Mon Sep 17 00:00:00 2001
From: Michael Levy <mike.levy.work@gmail.com>
Date: Tue, 19 May 2020 22:06:06 -0600
Subject: [PATCH 11/14] Lowering required version

Travis CI provides cmake 3.9.2 (we are using an old linux distribution so the
apt-get versions of gfortran and libnetcdf-dev play nicely together); hoping
there aren't actually features introduced in 3.10 in the system...
---
 CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 983ec8336..65d75055e 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,4 +1,4 @@
-cmake_minimum_required( VERSION 3.10 )
+cmake_minimum_required( VERSION 3.9 )
 
 project( cvmix VERSION 4.0.1 LANGUAGES Fortran )
 

From 4c6147632c8d08e4f6d7b1669a1102dd3a4d087e Mon Sep 17 00:00:00 2001
From: Michael Levy <mike.levy.work@gmail.com>
Date: Tue, 26 May 2020 11:28:44 -0600
Subject: [PATCH 12/14] Clean up install instructions in README

Also modified build.sh and run.sh to follow directions laid out in the README
(created cmake_bin/ for build target, build.sh calls "make install" and run.sh
runs from cmake_bin/bin/)
---
 README.md                 | 33 +++++++++++++++------------------
 cmake_bin/.gitignore      |  4 ++++
 reg_tests/common/build.sh |  5 ++++-
 reg_tests/common/run.sh   |  2 +-
 4 files changed, 24 insertions(+), 20 deletions(-)
 create mode 100644 cmake_bin/.gitignore

diff --git a/README.md b/README.md
index e6e2370cd..ba5fe1287 100644
--- a/README.md
+++ b/README.md
@@ -38,7 +38,7 @@ INSTALLATION NOTES
 ------------------
 
 CVMix can be installed using two different methods. The original uses Make
-and a set of Makefiles. The new method uses CMake and two CMakelists.txt 
+and a set of Makefiles. The new method uses CMake and two CMakelists.txt
 files.
 
 #### Building/installing using Make
@@ -72,42 +72,39 @@ to configure and compile CVMix. Note that CVMix has been build on Windows using
 VisualStudio and the Intel Fortran compiler but NetCDF support has not been
 tested.
 
-In this recipe CVMIX\_BASE s a convinience environmental variable pointing to 
-the CVMix source directory. It is possible to execute the following commands 
-providing the full path.
-
-
-1. mkdir ~/build/cvmix
-   * [CMake](https://cmake.org/) promotes out of source compilation
-2. cd ~/build/cvmix
-3. cmake $CVMIX\_BASE 
+1. cd $CVMix/bld/cmake_bld
+   * [CMake](https://cmake.org/) promotes out of source compilation,
+     any such directory will do.
+2. cmake $CVMix
    * The simplest configuration - using default Fortran compiler
-4. cmake $CVMIX\_BASE -DCMAKE\_Fortran\_COMPILER=ifort
+3. cmake $CVMix -DCMAKE\_Fortran\_COMPILER=ifort
    * Specifying a Fortran compiler
-5. cmake $CVMIX\_BASE -DCVMIX\_BUILD\_DRIVER=on
+4. cmake $CVMix -DCVMIX\_BUILD\_DRIVER=on
    * Build the CVMix driver program - off by default
-6. cmake $CVMIX\_BASE -DCVMIX\_BUILD\_DRIVER=on CVMIX\_USE\_NetCDF=on
+5. cmake $CVMix -DCVMIX\_BUILD\_DRIVER=on CVMIX\_USE\_NetCDF=on
    * Include support for NetCDF in the driver model(1)
    * Note that this requires proper configuration of the installed NetCDF library.
    * Setting NetCDF\_INCLUDE and NetCDF\_LIBRARIES might help.
-7. cmake $CVMIX\_BASE -DCMAKE\_INSTALL\_PREFIX=~/local
-   * Providing an installation folder
+6. cmake $CVMix -DCMAKE\_INSTALL\_PREFIX=$CVMix/bin
+   * Providing an installation folder (again, any such directory will do)
 
 Combination of the above commands is possible.
 
 After configuration has been done compilation is as simple as:
+
 ```
 make
 ```
 
 and instllation by:
+
 ```
 make install
 ```
 
 After installation the build directory can be removed.
 
-The support for CMake builds provides sufficient infrastructure for CVMix 
+The support for CMake builds provides sufficient infrastructure for CVMix
 being included in ocean models using the GIT submodule feature. This has
 been used in the [GOTM](https:/gotm.net) inclusion of the CVMix mixing
 models as a supplement to the original turbulence models in GOTM.
@@ -120,7 +117,7 @@ DIRECTORY STRUCTURE
 bin/ -- Default location for the cvmix executable.
 
 bld/ -- Contains auxiliary files needed by the build system. CompileFlags.mak
-        has default compile flags for 5 different compilers -- gfortran, 
+        has default compile flags for 5 different compilers -- gfortran,
         pgf90, ifort, xlf90, and nagfor, as well as ftn (the Cray wrapper for
         pgf90). At this time, no other compilers are supported on Cray systems.
         cvmix_setup is a python script that saves information about what
@@ -234,7 +231,7 @@ src/ -- Contains the source code, organized as follows. The top directory
 
   src/drivers/ -- Subroutines called by the driver (one per test).
 
-  src/shared/  -- Where all the modules that are needed to use CVMix with an 
+  src/shared/  -- Where all the modules that are needed to use CVMix with an
                   outside model are stored. Also contains the Makefile used to
                   build the libcvmix.a library.
 
diff --git a/cmake_bin/.gitignore b/cmake_bin/.gitignore
new file mode 100644
index 000000000..01319b51b
--- /dev/null
+++ b/cmake_bin/.gitignore
@@ -0,0 +1,4 @@
+bin
+include
+lib
+cmake
diff --git a/reg_tests/common/build.sh b/reg_tests/common/build.sh
index 1395a3a66..32e5896fb 100644
--- a/reg_tests/common/build.sh
+++ b/reg_tests/common/build.sh
@@ -5,7 +5,10 @@ build () {
     if [ "${CMAKE_BUILD}" == "TRUE" ]; then
       CWD=$PWD
       cd $CVMix/bld/cmake_bld
-      cmake $CVMix -DCVMIX_BUILD_DRIVER=on -DCMAKE_Fortran_COMPILER=gfortran && make
+      cmake $CVMix -DCVMIX_BUILD_DRIVER=on \
+                   -DCMAKE_Fortran_COMPILER=gfortran \
+                   -DCMAKE_INSTALL_PREFIX=$CVMix/cmake_bin \
+      && make && make install
       STATUS=$?
       cd $CWD
     else
diff --git a/reg_tests/common/run.sh b/reg_tests/common/run.sh
index 4307868af..db0e89ee5 100644
--- a/reg_tests/common/run.sh
+++ b/reg_tests/common/run.sh
@@ -3,7 +3,7 @@
 run () {
 
   if [ "${CMAKE_BUILD}" == "TRUE" ]; then
-    CVMIX_EXE=$CVMix/bld/cmake_bld/cvmix_driver
+    CVMIX_EXE=$CVMix/cmake_bin/bin/cvmix_driver
   else
     CVMIX_EXE=$CVMix/bin/cvmix
   fi

From 3019c4e75ae917cdbe89dffdae8634bb88bd286a Mon Sep 17 00:00:00 2001
From: Karsten Bolding <karsten@bolding-bruggeman.com>
Date: Wed, 27 May 2020 08:02:32 +0200
Subject: [PATCH 13/14] updated README

---
 README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index e6e2370cd..ccba66402 100644
--- a/README.md
+++ b/README.md
@@ -72,7 +72,7 @@ to configure and compile CVMix. Note that CVMix has been build on Windows using
 VisualStudio and the Intel Fortran compiler but NetCDF support has not been
 tested.
 
-In this recipe CVMIX\_BASE s a convinience environmental variable pointing to 
+In this recipe CVMIX\_BASE is a convinient environmental variable pointing to 
 the CVMix source directory. It is possible to execute the following commands 
 providing the full path.
 
@@ -100,7 +100,7 @@ After configuration has been done compilation is as simple as:
 make
 ```
 
-and instllation by:
+and installation by:
 ```
 make install
 ```

From 04cc49f10e08e1d8c6b2d8c8c69130c169a158ee Mon Sep 17 00:00:00 2001
From: Michael Levy <mike.levy.work@gmail.com>
Date: Fri, 19 Jun 2020 10:38:36 -0600
Subject: [PATCH 14/14] Clean up more trailing whitespace

---
 CMakeLists.txt | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 65d75055e..ee9a1e8a5 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -42,8 +42,8 @@ add_subdirectory( src )
 # Note - KB:
 # Building static and shared libs require an ugly construct to build on both
 # Windows and Linux. Windows will not create the libraries unless a Fortran
-# file is explicitly given - and Linux complains (I think due to a race 
-# condition) if it is. Therefor the construct below - a proper solution is 
+# file is explicitly given - and Linux complains (I think due to a race
+# condition) if it is. Therefor the construct below - a proper solution is
 # most welcome.
 
 # Add static lib target