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Merge pull request #98 from NCAR/main
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Merge to release 1.1.0
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@s-omas
s-omas committed Jun 3, 2021
2 parents da0e12a + 6e4d152 commit 66ac32d
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Showing 24 changed files with 122 additions and 9 deletions.
2 changes: 2 additions & 0 deletions .dockerignore
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Expand Up @@ -13,3 +13,5 @@

# exclude generated code
libs/micm-collection/configured_tags/*
!libs/micm-collection/configured_tags/chapman/
libs/micm-collection/configured_tags/chapman/output
13 changes: 8 additions & 5 deletions Dockerfile
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Expand Up @@ -28,7 +28,7 @@ RUN dnf -y update \
# python modules needed in scripts
RUN dnf -y install python3-pandas

RUN pip3 install requests numpy scipy matplotlib ipython jupyter nose Django pillow django-crispy-forms
RUN pip3 install requests numpy scipy matplotlib ipython jupyter nose Django pillow django-crispy-forms pyvis

# Build the SuiteSparse libraries for sparse matrix support
RUN curl -LO http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-5.1.0.tar.gz \
Expand Down Expand Up @@ -103,10 +103,13 @@ RUN if [ "$TAG_ID" = "false" ] ; then \
&& nohup bash -c "node combined.js &" && sleep 4 \
&& mkdir /data \
&& cd /music-box/libs/micm-collection \
&& python3 get_tag.py -tag_id $TAG_ID \
&& python3 preprocess_tag.py -mechanism_source_path configured_tags/$TAG_ID -preprocessor localhost:3000 \
&& python3 stage_tag.py -source_dir_kinetics configured_tags/$TAG_ID -target_dir_data /data \
&& cp /music-box/libs/micm-collection/configured_tags/${TAG_ID}/source_mechanism.json /build \
&& if [ "$TAG_ID" = "chapman" ] ; then \
python3 preprocess_tag.py -c configured_tags/$TAG_ID/config.json -p localhost:3000 \
&& python3 stage_tag.py -source_dir_kinetics configured_tags/$TAG_ID/output -target_dir_data /data \
; else \
echo "Only Chapman chemistry is currently available for MusicBox-MICM" \
&& exit 1 \
; fi \
; fi

# build the model
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6 changes: 6 additions & 0 deletions examples/micm_examples/bright_chamber/use_case_4.json
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Expand Up @@ -18,6 +18,12 @@
"model components" : [
{
"type" : "MICM",
"override species" : {
"M" : { "mixing ratio mol mol-1" : 1.0 }
},
"suppress output" : {
"M" : { }
},
"solver" : {
"type" : "Rosenbrock",
"chemistry time step [min]" : 5.0,
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6 changes: 6 additions & 0 deletions examples/micm_examples/bright_chamber/use_case_5.json
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Expand Up @@ -22,6 +22,12 @@
{
"type" : "MICM",
"solve" : false,
"override species" : {
"M" : { "mixing ratio mol mol-1" : 1.0 }
},
"suppress output" : {
"M" : { }
},
"solver" : {
"type" : "Rosenbrock",
"chemistry time step [min]" : 5.0,
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6 changes: 6 additions & 0 deletions examples/micm_examples/bright_chamber/use_case_6.json
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Expand Up @@ -36,6 +36,12 @@
{
"type" : "MICM",
"solve" : false,
"override species" : {
"M" : { "mixing ratio mol mol-1" : 1.0 }
},
"suppress output" : {
"M" : { }
},
"solver" : {
"type" : "Rosenbrock",
"chemistry time step [min]" : 5.0,
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6 changes: 6 additions & 0 deletions examples/micm_examples/bright_chamber/use_case_7.json
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Expand Up @@ -71,6 +71,12 @@
"model components" : [
{
"type" : "MICM",
"override species" : {
"M" : { "mixing ratio mol mol-1" : 1.0 }
},
"suppress output" : {
"M" : { }
},
"solver" : {
"type" : "Rosenbrock",
"chemistry time step [min]" : 5.0,
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6 changes: 6 additions & 0 deletions examples/micm_examples/bright_chamber/use_case_8.json
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Expand Up @@ -84,6 +84,12 @@
{
"type" : "MICM",
"solve" : false,
"override species" : {
"M" : { "mixing ratio mol mol-1" : 1.0 }
},
"suppress output" : {
"M" : { }
},
"solver" : {
"type" : "Rosenbrock",
"chemistry time step [min]" : 5.0,
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6 changes: 6 additions & 0 deletions examples/micm_examples/dark_chamber/use_case_1.json
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Expand Up @@ -20,6 +20,12 @@
{
"type" : "MICM",
"solve" : false,
"override species" : {
"M" : { "mixing ratio mol mol-1" : 1.0 }
},
"suppress output" : {
"M" : { }
},
"solver" : {
"type" : "Rosenbrock",
"chemistry time step [min]" : 5.0,
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6 changes: 6 additions & 0 deletions examples/micm_examples/dark_chamber/use_case_2.json
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Expand Up @@ -16,6 +16,12 @@
{
"type" : "MICM",
"solve" : false,
"override species" : {
"M" : { "mixing ratio mol mol-1" : 1.0 }
},
"suppress output" : {
"M" : { }
},
"solver" : {
"type" : "Rosenbrock",
"chemistry time step [min]" : 5.0,
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6 changes: 6 additions & 0 deletions examples/micm_examples/dark_chamber/use_case_3.json
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Expand Up @@ -14,6 +14,12 @@
{
"type" : "MICM",
"solve" : false,
"override species" : {
"M" : { "mixing ratio mol mol-1" : 1.0 }
},
"suppress output" : {
"M" : { }
},
"solver" : {
"type" : "Rosenbrock",
"chemistry time step [min]" : 5.0,
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2 changes: 1 addition & 1 deletion libs/micm
Submodule micm updated 16 files
+12 −3 src/CMakeLists.txt
+10 −0 src/constants.F90
+85 −10 src/core.F90
+3 −0 src/environment.F90
+3 −8 src/kinetics.F90
+0 −1 src/preprocessor_output/kinetics_utilities.F90
+40 −37 src/preprocessor_output/rate_constants_utility.F90
+38 −0 src/rate_constant.F90
+0 −338 src/rate_constant_functions.F90
+76 −0 src/rate_constants/arrhenius.F90
+63 −0 src/rate_constants/photolysis.F90
+87 −0 src/rate_constants/ternary_chemical_activation.F90
+87 −0 src/rate_constants/troe.F90
+99 −0 src/rate_constants/wennberg_alkoxy.F90
+99 −0 src/rate_constants/wennberg_nitrate.F90
+69 −0 src/rate_constants/wennberg_tunneling.F90
2 changes: 1 addition & 1 deletion libs/micm-collection
Submodule micm-collection updated from 1ea7a2 to 706fbb
2 changes: 1 addition & 1 deletion libs/micm-preprocessor
Submodule micm-preprocessor updated from 0cef97 to 393fa9
2 changes: 1 addition & 1 deletion libs/music-box-interactive
Submodule music-box-interactive updated from 232955 to 86ecff
6 changes: 6 additions & 0 deletions test/integration/input_use_cases/1/config.json
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Expand Up @@ -20,6 +20,12 @@
{
"type" : "MICM",
"solve" : false,
"override species" : {
"M" : { "mixing ratio mol mol-1" : 1.0 }
},
"suppress output" : {
"M" : { }
},
"solver" : {
"type" : "Rosenbrock",
"chemistry time step [min]" : 5.0,
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6 changes: 6 additions & 0 deletions test/integration/input_use_cases/2/config.json
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Expand Up @@ -16,6 +16,12 @@
{
"type" : "MICM",
"solve" : false,
"override species" : {
"M" : { "mixing ratio mol mol-1" : 1.0 }
},
"suppress output" : {
"M" : { }
},
"solver" : {
"type" : "Rosenbrock",
"chemistry time step [min]" : 5.0,
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6 changes: 6 additions & 0 deletions test/integration/input_use_cases/3/config.json
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Expand Up @@ -14,6 +14,12 @@
{
"type" : "MICM",
"solve" : false,
"override species" : {
"M" : { "mixing ratio mol mol-1" : 1.0 }
},
"suppress output" : {
"M" : { }
},
"solver" : {
"type" : "Rosenbrock",
"chemistry time step [min]" : 5.0,
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6 changes: 6 additions & 0 deletions test/integration/input_use_cases/4/config.json
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Expand Up @@ -18,6 +18,12 @@
"model components" : [
{
"type" : "MICM",
"override species" : {
"M" : { "mixing ratio mol mol-1" : 1.0 }
},
"suppress output" : {
"M" : { }
},
"solver" : {
"type" : "Rosenbrock",
"chemistry time step [min]" : 5.0,
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6 changes: 6 additions & 0 deletions test/integration/input_use_cases/4/config_b.json
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Expand Up @@ -13,6 +13,12 @@
"model components" : [
{
"type" : "MICM",
"override species" : {
"M" : { "mixing ratio mol mol-1" : 1.0 }
},
"suppress output" : {
"M" : { }
},
"solver" : {
"type" : "Rosenbrock",
"chemistry time step [min]" : 5.0,
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6 changes: 6 additions & 0 deletions test/integration/input_use_cases/5/config.json
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Expand Up @@ -22,6 +22,12 @@
{
"type" : "MICM",
"solve" : false,
"override species" : {
"M" : { "mixing ratio mol mol-1" : 1.0 }
},
"suppress output" : {
"M" : { }
},
"solver" : {
"type" : "Rosenbrock",
"chemistry time step [min]" : 5.0,
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6 changes: 6 additions & 0 deletions test/integration/input_use_cases/6/config.json
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Expand Up @@ -36,6 +36,12 @@
{
"type" : "MICM",
"solve" : false,
"override species" : {
"M" : { "mixing ratio mol mol-1" : 1.0 }
},
"suppress output" : {
"M" : { }
},
"solver" : {
"type" : "Rosenbrock",
"chemistry time step [min]" : 5.0,
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6 changes: 6 additions & 0 deletions test/integration/input_use_cases/7/config.json
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Expand Up @@ -71,6 +71,12 @@
"model components" : [
{
"type" : "MICM",
"override species" : {
"M" : { "mixing ratio mol mol-1" : 1.0 }
},
"suppress output" : {
"M" : { }
},
"solver" : {
"type" : "Rosenbrock",
"chemistry time step [min]" : 5.0,
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6 changes: 6 additions & 0 deletions test/integration/input_use_cases/8/config.json
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Expand Up @@ -84,6 +84,12 @@
{
"type" : "MICM",
"solve" : false,
"override species" : {
"M" : { "mixing ratio mol mol-1" : 1.0 }
},
"suppress output" : {
"M" : { }
},
"solver" : {
"type" : "Rosenbrock",
"chemistry time step [min]" : 5.0,
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6 changes: 6 additions & 0 deletions test/integration/input_use_cases/8/config_b.json
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Expand Up @@ -41,6 +41,12 @@
{
"type" : "MICM",
"solve" : false,
"override species" : {
"M" : { "mixing ratio mol mol-1" : 1.0 }
},
"suppress output" : {
"M" : { }
},
"solver" : {
"type" : "Rosenbrock",
"chemistry time step [min]" : 5.0,
Expand Down

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