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Merge pull request #53 from NCAR/update_version
v0.5.0 Release
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,60 @@ | ||
| FROM ubuntu:22.04 | ||
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| RUN apt update \ | ||
| && apt -y install \ | ||
| cmake \ | ||
| cmake-curses-gui \ | ||
| curl \ | ||
| libcurl4-openssl-dev \ | ||
| libhdf5-dev \ | ||
| m4 \ | ||
| nlohmann-json3-dev \ | ||
| vim \ | ||
| zlib1g-dev \ | ||
| git \ | ||
| lcov \ | ||
| make \ | ||
| libnetcdff-dev \ | ||
| valgrind \ | ||
| gcc \ | ||
| gfortran \ | ||
| g++ \ | ||
| && apt clean | ||
|
|
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| # Set environment variables to install MUSICA using gcc | ||
| ENV FC=gfortran | ||
| ENV FFLAGS="-I/usr/include/" | ||
|
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| # Install json-fortran for gnu version | ||
| RUN curl -LO https://github.com/jacobwilliams/json-fortran/archive/8.2.0.tar.gz \ | ||
| && tar -zxvf 8.2.0.tar.gz \ | ||
| && cd json-fortran-8.2.0 \ | ||
| && mkdir build \ | ||
| && cd build \ | ||
| && cmake -D SKIP_DOC_GEN:BOOL=TRUE .. \ | ||
| && make install | ||
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| # Copy the musica code | ||
| COPY . musica | ||
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| # Set json-fortran variable to install MUSICA using gcc | ||
| ENV JSON_FORTRAN_HOME="/usr/local/jsonfortran-gnu-8.2.0" | ||
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| # Build and install MUSICA | ||
| RUN cd musica \ | ||
| && cmake -S . \ | ||
| -B build \ | ||
| -D ENABLE_TESTS=ON \ | ||
| -D ENABLE_TUVX=OFF \ | ||
| && cd build \ | ||
| && make install -j 8 | ||
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| RUN cd musica/musica-fortran/test \ | ||
| && mkdir build && cd build \ | ||
| && cmake .. \ | ||
| && make | ||
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| RUN cd musica/musica-fortran/test \ | ||
| && cp -r configs/chapman ./build/chapman | ||
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| WORKDIR musica/musica-fortran/test/build |
Submodule tuv-x
updated
39 files
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,4 @@ | ||
| module musica_micm | ||
| module micm_mod | ||
| use iso_c_binding | ||
| implicit none | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| { | ||
| "camp-files": [ | ||
| "species.json", | ||
| "reactions.json" | ||
| ] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,97 @@ | ||
| { | ||
| "camp-data": [ | ||
| { | ||
| "name": "Chapman", | ||
| "type": "MECHANISM", | ||
| "reactions": [ | ||
| { | ||
| "type": "PHOTOLYSIS", | ||
| "reactants": { | ||
| "O2": {} | ||
| }, | ||
| "products": { | ||
| "O": { | ||
| "yield": 2.0 | ||
| } | ||
| }, | ||
| "MUSICA name": "R1" | ||
| }, | ||
| { | ||
| "type": "ARRHENIUS", | ||
| "A": 8.018e-17, | ||
| "reactants": { | ||
| "O": {}, | ||
| "O2": {} | ||
| }, | ||
| "products": { | ||
| "O3": {} | ||
| }, | ||
| "MUSICA name": "R2" | ||
| }, | ||
| { | ||
| "type": "PHOTOLYSIS", | ||
| "reactants": { | ||
| "O3": {} | ||
| }, | ||
| "products": { | ||
| "O": {}, | ||
| "O2": {} | ||
| }, | ||
| "MUSICA name": "R3" | ||
| }, | ||
| { | ||
| "type": "ARRHENIUS", | ||
| "A": 1.576e-15, | ||
| "reactants": { | ||
| "O": {}, | ||
| "O3": {} | ||
| }, | ||
| "products": { | ||
| "O2": { | ||
| "yield": 2.0 | ||
| } | ||
| }, | ||
| "MUSICA name": "R4" | ||
| }, | ||
| { | ||
| "type": "PHOTOLYSIS", | ||
| "reactants": { | ||
| "O3": {} | ||
| }, | ||
| "products": { | ||
| "O1D": {}, | ||
| "O2": {} | ||
| }, | ||
| "MUSICA name": "R5" | ||
| }, | ||
| { | ||
| "type": "ARRHENIUS", | ||
| "A": 7.11e-11, | ||
| "reactants": { | ||
| "O1D": {}, | ||
| "M": {} | ||
| }, | ||
| "products": { | ||
| "O": {}, | ||
| "M": {} | ||
| }, | ||
| "MUSICA name": "R6" | ||
| }, | ||
| { | ||
| "type": "ARRHENIUS", | ||
| "A": 1.2e-10, | ||
| "reactants": { | ||
| "O1D": {}, | ||
| "O3": {} | ||
| }, | ||
| "products": { | ||
| "O2": { | ||
| "yield": 2.0 | ||
| } | ||
| }, | ||
| "MUSICA name": "R7" | ||
| } | ||
| ] | ||
| } | ||
| ] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,29 @@ | ||
| { | ||
| "camp-data": [ | ||
| { | ||
| "name": "M", | ||
| "type": "CHEM_SPEC", | ||
| "tracer type": "CONSTANT" | ||
| }, | ||
| { | ||
| "name": "O2", | ||
| "type": "CHEM_SPEC", | ||
| "tracer type": "CONSTANT" | ||
| }, | ||
| { | ||
| "name": "O", | ||
| "type": "CHEM_SPEC", | ||
| "absolute tolerance": 1e-12 | ||
| }, | ||
| { | ||
| "name": "O1D", | ||
| "type": "CHEM_SPEC", | ||
| "absolute tolerance": 1e-12 | ||
| }, | ||
| { | ||
| "name": "O3", | ||
| "type": "CHEM_SPEC", | ||
| "absolute tolerance": 1e-12 | ||
| } | ||
| ] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,38 +1,42 @@ | ||
| program test | ||
| use iso_c_binding | ||
| use musica_micm | ||
| use micm_mod | ||
| implicit none | ||
| type(micm_t) :: m | ||
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| real(c_double) :: temperature | ||
| real(c_double) :: pressure | ||
| real(c_double) :: time_step | ||
| real(c_double), dimension(10) :: concentrations | ||
| real(c_double), dimension(5) :: concentrations | ||
| integer(c_size_t) :: num_concentrations | ||
| integer :: errcode | ||
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| temperature = 10d0 | ||
| pressure = 20d0 | ||
| time_step = 1d0 | ||
| concentrations = (/ 1d0, 2d0, 3d0, 4d0, 5d0, 6d0, 7d0, 8d0, 9d0, 10d0 /) | ||
| num_concentrations = 10 | ||
| concentrations = (/ 0.75, 0.4, 0.8, 0.01, 0.02 /) | ||
| num_concentrations = 5 | ||
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| write(*,*) " * [Fortran] Creating MICM" | ||
| m = micm_t("micm_config") | ||
| m = micm_t("chapman") | ||
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| write(*,*) " * [Fortran] Creating solver" | ||
| write(*,*) " * [Fortran] Solver creating status indicates ", m%create_solver(), " (1 is success, else failure) " | ||
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| write(*,*) " * [Fortran] Initial temp", temperature | ||
| write(*,*) " * [Fortran] Initial pressure", pressure | ||
| write(*,*) " * [Fortran] Initial time_step", time_step | ||
| write(*,*) " * [Fortran] Initial concentrations", concentrations | ||
| write(*,*) " * [Fortran] Initial number of concentrations", num_concentrations | ||
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| write(*,*) " * [Fortran] Starting to solve" | ||
| call m%solve(temperature, pressure, time_step, concentrations, num_concentrations) | ||
| write(*,*) " * [Fortran] After solving, concentrations", concentrations | ||
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| write(*,*) " * [Fortran] Calling destructor for MICM" | ||
| call m%delete | ||
| errcode = m%create_solver() | ||
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| if (errcode == 1) then | ||
| write(*,*) " * [Fortran] Failed in creating solver" | ||
| stop 3 | ||
| else | ||
| write(*,*) " * [Fortran] Initial temp", temperature | ||
| write(*,*) " * [Fortran] Initial pressure", pressure | ||
| write(*,*) " * [Fortran] Initial time_step", time_step | ||
| write(*,*) " * [Fortran] Initial number of concentrations", num_concentrations | ||
| write(*,*) " * [Fortran] Initial concentrations", concentrations | ||
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| write(*,*) " * [Fortran] Solving starts..." | ||
| call m%solve(temperature, pressure, time_step, concentrations, num_concentrations) | ||
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| write(*,*) " * [Fortran] After solving, concentrations", concentrations | ||
| endif | ||
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| end program |
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