Merge pull request #138 from NCAR/instructions

adding more instructions
NCAR · Aug 15, 2023 · 99d4e08 · 99d4e08
2 parents 4e6f30c + 295b6e9
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diff --git a/.gitmodules b/.gitmodules
@@ -1,6 +1,3 @@
-[submodule "libs/micm"]
-	path = libs/micm
-	url = https://github.com/NCAR/micm.git
 [submodule "libs/camp"]
 	path = libs/camp
 	url = https://github.com/open-atmos/camp.git
diff --git a/README.md b/README.md
@@ -9,6 +9,33 @@ MusicBox: A MUSICA model for boxes and columns.
 
 Copyright (C) 2020 National Center for Atmospheric Research
 
+# Install and run from local git clone
+
+```
+git clone https://github.com/NCAR/music-box
+cd music-box
+git submodule init
+git submodule update
+docker build -t music-box .
+docker run --rm -it music-box
+```
+
+Running those commands will put you in a docker container, at which point you can run
+
+```
+cd /music-box/build
+make test
+```
+
+and you will see tests run, and hopefully pass.
+
+There are a number of examples you can run and modify.
+
+```
+cd /music-box/examples/camp_examples/bright_chamber/use_case_7/
+/music-box/build/music_box use_case_7_config.json 
+```
+
 # Install and run (interactive version)
 
 The only requirement for running MusicBox is that you have [Docker Desktop](https://www.docker.com/get-started) installed and running. With Docker Desktop running, open a terminal window and run the following command: (The first time you run this command, the MusicBox code will be downloaded from Docker Hub, which may take a few minutes.)
@@ -37,16 +64,6 @@ You will need to have [Docker Desktop](https://www.docker.com/get-started) insta
 docker run -it --rm ncar/music-box bash
 ```
 
-## Running MusicBox with the MICM Solver
-MICM can be specified as the chemical solver by configuring the [model components](config_options.md#model-components) section of the configuration file. By default, MusicBox loads the Chapman chemistry mechanism for simulations using MICM. To run the model with this mechanism under one of the model configurations in the `examples/` folder:
-
-```
-cd /build
-cp examples/micm_examples/bright_chamber/use_case_4.json .
-cp examples/micm_examples/bright_chamber/use_case_4_initial.csv data/
-./music_box use_case_4.json
-```
-
 ## Running MusicBox with the CAMP Solver
 
 CAMP can be specified as the chemical solver by configuring the [model components](config_options.md#model-components) section of the configuration file. To run the model using the CAMP solver under one of the model configurations in the `examples/` folder:

diff --git a/config_options.md b/config_options.md
@@ -369,29 +369,6 @@ NetCDF files should have a dimension of <code>time</code>, and variables whose o
 </code></pre>
 <hr>
 <h3 class="code-line" data-line-start=321 data-line-end=322 ><a id="Model_Components_321"></a>Model Components</h3>
-<p class="has-line-data" data-line-start="322" data-line-end="323">The model components section of the MusicBox configuration specifies settings for the chemical solver. For most use cases of MusicBox, modifying the model components is not neccesary.</p>
-<h5 class="code-line" data-line-start=324 data-line-end=325 ><a id="Model_components_configuration_with_the_MICM_solver_324"></a>Model components configuration with the MICM solver:</h5>
-<h1 class="code-line" data-line-start=325 data-line-end=326 ><a id="_325"></a></h1>
-<pre><code class="has-line-data" data-line-start="327" data-line-end="347" class="language-json">{
-    "<span class="hljs-attribute">model components</span>" : <span class="hljs-value">[
-    {
-      "<span class="hljs-attribute">type</span>" : <span class="hljs-value"><span class="hljs-string">"MICM"</span></span>,
-      "<span class="hljs-attribute">solver</span>" : <span class="hljs-value">{
-        "<span class="hljs-attribute">type</span>" : <span class="hljs-value"><span class="hljs-string">"Rosenbrock"</span></span>,
-        "<span class="hljs-attribute">chemistry time step [min]</span>" : <span class="hljs-value"><span class="hljs-number">5.0</span></span>,
-        "<span class="hljs-attribute">absolute tolerance</span>" : <span class="hljs-value"><span class="hljs-number">1.0e-12</span></span>,
-        "<span class="hljs-attribute">relative tolerance</span>" : <span class="hljs-value"><span class="hljs-number">1.0e-4</span>
-      </span>}
-    </span>},
-    {
-      "<span class="hljs-attribute">type</span>" : <span class="hljs-value"><span class="hljs-string">"musica-emissions"</span>
-    </span>},
-    {
-      "<span class="hljs-attribute">type</span>" : <span class="hljs-value"><span class="hljs-string">"musica-loss"</span>
-    </span>}
-  ]
-</span>}
-</code></pre>
 <h5 class="code-line" data-line-start=348 data-line-end=349 ><a id="Configuring_the_CAMP_solver_348"></a>Configuring the CAMP solver:</h5>
 <p class="has-line-data" data-line-start="349" data-line-end="350"><strong>When using the CAMP solver, additional configuration files are required.</strong> By default, these are stored in a directory <code>camp_data</code>. Inside this folder:</p>
 <p class="has-line-data" data-line-start="351" data-line-end="354">|—<code>config.json</code> — Points to <code>specise.json</code> and <code>mechanism.json</code>.<br>

diff --git a/doc/Doxyfile b/doc/Doxyfile
@@ -765,7 +765,6 @@ WARN_LOGFILE           =
 
 INPUT                  = doxygen_files \
                          ../src \
-                         ../libs/micm/src \
                          ../libs/musica-core/src \
                          ../test
 

diff --git a/etc/casper/build_music_box_casper_gnu.sh b/etc/casper/build_music_box_casper_gnu.sh
@@ -113,7 +113,6 @@ mkdir -p build
 cd build
 cmake -D CMAKE_C_COMPILER=gcc \
       -D CMAKE_Fortran_COMPILER=gfortran \
-      -D ENABLE_MICM_TESTS=OFF \
       -D CMAKE_BUILD_TYPE=release \
       -D CMAKE_C_FLAGS="-std=c99 ${NCAR_LIBS_GSL}" \
       -D SUITE_SPARSE_AMD_LIB=$SUITE_SPARSE_HOME/lib/libamd.so \

diff --git a/etc/casper/build_music_box_casper_intel.sh b/etc/casper/build_music_box_casper_intel.sh
@@ -116,7 +116,6 @@ mkdir -p build
 cd build
 cmake -D CMAKE_C_COMPILER=icc \
       -D CMAKE_Fortran_COMPILER=ifort \
-      -D ENABLE_MICM_TESTS=OFF \
       -D CMAKE_BUILD_TYPE=release \
       -D CMAKE_C_FLAGS="-std=c99 ${NCAR_LIBS_GSL}" \
       -D SUITE_SPARSE_AMD_LIB=$SUITE_SPARSE_HOME/lib/libamd.so \

diff --git a/etc/change_mechanism.sh b/etc/change_mechanism.sh
diff --git a/etc/cheyenne/build_music_box_cheyenne_gnu.sh b/etc/cheyenne/build_music_box_cheyenne_gnu.sh
@@ -112,7 +112,6 @@ mkdir -p build
 cd build
 cmake -D CMAKE_C_COMPILER=gcc \
       -D CMAKE_Fortran_COMPILER=gfortran \
-      -D ENABLE_MICM_TESTS=OFF \
       -D CMAKE_BUILD_TYPE=release \
       -D CMAKE_C_FLAGS="-std=c99 ${NCAR_LIBS_GSL}" \
       -D SUITE_SPARSE_AMD_LIB=$SUITE_SPARSE_HOME/lib/libamd.so \

diff --git a/etc/cheyenne/build_music_box_cheyenne_intel.sh b/etc/cheyenne/build_music_box_cheyenne_intel.sh
@@ -114,7 +114,6 @@ mkdir -p build
 cd build
 cmake -D CMAKE_C_COMPILER=icc \
       -D CMAKE_Fortran_COMPILER=ifort \
-      -D ENABLE_MICM_TESTS=OFF \
       -D CMAKE_BUILD_TYPE=release \
       -D CMAKE_C_FLAGS="-std=c99 ${NCAR_LIBS_GSL}" \
       -D SUITE_SPARSE_AMD_LIB=$SUITE_SPARSE_HOME/lib/libamd.so \

diff --git a/etc/modeling2/build_music_box_modeling2_gnu.sh b/etc/modeling2/build_music_box_modeling2_gnu.sh
@@ -184,7 +184,6 @@ mkdir -p build
 cd build
 cmake3 -D CMAKE_C_COMPILER=gcc \
        -D CMAKE_Fortran_COMPILER=gfortran \
-       -D ENABLE_MICM_TESTS=OFF \
        -D CMAKE_BUILD_TYPE=release \
        -D CMAKE_C_FLAGS="-std=c99" \
        -D GSL_CBLAS_LIB=$GSL_HOME/lib/libgslcblas.so \