SOILWAT2

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An ecosystem water balance simulation model

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- - check_doc.yml
  - checks-macos.yaml
  - checks-ubuntu.yaml
  - checks-windows.yaml
  - clang-format-check.yml
  - clang-tidy-check.yml
  - code-coverage.yml
  - simulation-checks.yml
- pull_request_template.md
- - A_SOILWAT2_user_guide.md
  - code_contribution_guidelines.md
  - Description__SW2_netCDF_input_variables.md
  - Description__SW2_netCDF_output_variables.md
  - SOILWAT2_Inputs.md
  - SOILWAT2_Output_Variables.csv
  - SOILWAT2_Outputs.md
  - SOILWAT2_Parallelization.md
- - doxygen-awesome-darkmode-toggle.js
  - doxygen-awesome-fragment-copy-button.js
  - doxygen-awesome-interactive-toc.js
  - doxygen-awesome-paragraph-link.js
  - doxygen-awesome-sidebar-only-darkmode-toggle.css
  - doxygen-awesome-sidebar-only.css
  - doxygen-awesome-tabs.js
  - doxygen-awesome.css
  - LICENSE
  - README.md
- Changes_drs_dm_clk_rjm_v32.txt
- Doxyfile
- doxygen_exceptions.txt
- SOILWAT2.bib
- - R.h
  - Rmath.h
- .clang-format
- googletest
- pcg
- filefuncs.h
- generic.h
- myMemory.h
- rands.h
- SW_Carbon.h
- SW_Control.h
- SW_datastructs.h
- SW_Defines.h
- SW_DerivedMetrics.h
- SW_Domain.h
- SW_Files.h
- SW_Flow.h
- SW_Flow_lib.h
- SW_Flow_lib_PET.h
- SW_Main_lib.h
- SW_Markov.h
- SW_Model.h
- SW_MPI.h
- SW_netCDF_General.h
- SW_netCDF_Input.h
- SW_netCDF_Output.h
- SW_Output.h
- SW_Output_outarray.h
- SW_Output_outtext.h
- SW_Site.h
- SW_Sky.h
- SW_SoilWater.h
- SW_Times.h
- SW_VegEstab.h
- SW_VegProd.h
- SW_Weather.h
- Times.h
- filefuncs.c
- generic.c
- mymemory.c
- rands.c
- SW_Carbon.c
- SW_Control.c
- SW_datastructs.c
- SW_DerivedMetrics.c
- SW_Domain.c
- SW_Files.c
- SW_Flow.c
- SW_Flow_lib.c
- SW_Flow_lib_PET.c
- SW_Main.c
- SW_Main_lib.c
- SW_Markov.c
- SW_Model.c
- SW_MPI.c
- SW_netCDF_General.c
- SW_netCDF_Input.c
- SW_netCDF_Output.c
- SW_Output.c
- SW_Output_get_functions.c
- SW_Output_outarray.c
- SW_Output_outtext.c
- SW_Site.c
- SW_Sky.c
- SW_SoilWater.c
- SW_VegEstab.c
- SW_VegProd.c
- SW_Weather.c
- Times.c
- - collapseLogfiles.sh
  - metric_one.sh
  - ncSW2Standardize.sh
  - progressTally.sh
  - run-sw2_hpc.sh
  - run-sw2_local.sh
- README-PROJECT.md
- - files.in
  - README.md
- - sw_maintest.cc
  - sw_testhelpers.cc
  - sw_testhelpers.h
  - test_generic.cc
  - test_mymemory.cc
  - test_rands.cc
  - test_SW_Carbon.cc
  - test_SW_Defines.cc
  - test_SW_DerivedMetrics.cc
  - test_SW_Flow_Lib.cc
  - test_SW_Flow_Lib_PET.cc
  - test_SW_Flow_lib_temp.cc
  - test_SW_Main_lib.cc
  - test_SW_Markov.cc
  - test_SW_Site.cc
  - test_SW_SoilWater.cc
  - test_SW_SpinUp.cc
  - test_SW_VegEstab.cc
  - test_SW_VegProd.cc
  - test_SW_Weather.cc
  - test_Times.cc
  - test_WaterBalance.cc
- - .gitignore
- - Rscript__SW2_compareOutputNC.R
  - Rscript__SW2_output_txt_vs_r_vs_nc.R
  - Rscript__SW2_PET_Test__petfunc_by_temps.R
  - Rscript__SW2_SoilTemperature.R
  - Rscript__SW2_SolarPosition_Test__hourangles_by_lat_and_doy.R
  - Rscript__SW2_SolarPosition_Test__hourangles_by_lats.R
  - Rscript__SW2_SpinupEvaluation.R
- allCodeChecks.sh
- allOutputChecks.sh
- check_extras.sh
- check_functionality.sh
- check_ncTestRuns.sh
- check_outputModes.sh
- check_withCompilers.sh
- compile_flags.sh
- complianceChecker.sh
- doc_open.sh
- hasMPICC.sh
- run_bin.sh
- run_bin_leaks.sh
- run_bin_sanitizer.sh
- run_debug.sh
- run_debug_severe.sh
- run_doxygen.sh
- run_format.sh
- run_gcov.sh
- run_iwyu.sh
- run_test.sh
- run_test_leaks.sh
- run_test_sanitizer.sh
- run_test_severe.sh
- run_tidy.sh
.clang-format
.clang-tidy
.clang-tidy_mpi
.clang-tidy_swtest
.git-blame-ignore-revs
.gitignore
.gitmodules
.LSAN_suppr.txt
codecov.yml
LICENSE.md
makefile
NEWS.md
README.md

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[![ubuntu checks][1]][2]
[![macos checks][23]][24]
[![windows checks][25]][26]
[![codecov status][11]][12]
[![tidy][3]][13]
 
[![github release][5]][6]
[![DOI][7]][8]
[![license][9]][10]
 
[![doc status][4]][14]

[1]: https://github.com/DrylandEcology/SOILWAT2/actions/workflows/checks-ubuntu.yaml/badge.svg
[2]: https://github.com/DrylandEcology/SOILWAT2/actions/workflows/checks-ubuntu.yaml
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[13]: https://github.com/DrylandEcology/SOILWAT2/actions/workflows/clang-tidy-check.yml
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[14]: https://github.com/DrylandEcology/SOILWAT2/actions/workflows/check_doc.yml

[5]: https://img.shields.io/github/release/DrylandEcology/SOILWAT2.svg
[6]: https://github.com/DrylandEcology/SOILWAT2/releases
[7]: https://zenodo.org/badge/9551524.svg
[8]: https://zenodo.org/badge/latestdoi/9551524
[9]: https://img.shields.io/github/license/DrylandEcology/SOILWAT2.svg
[10]: https://www.gnu.org/licenses/gpl.html
[11]: https://codecov.io/gh/DrylandEcology/SOILWAT2/branch/master/graph/badge.svg
[12]: https://codecov.io/gh/DrylandEcology/SOILWAT2

[SOILWAT2]: https://github.com/DrylandEcology/SOILWAT2
[rSOILWAT2]: https://github.com/DrylandEcology/rSOILWAT2
[STEPWAT2]: https://github.com/DrylandEcology/STEPWAT2
[issues]: https://github.com/DrylandEcology/SOILWAT2/issues
[pull request]: https://github.com/DrylandEcology/SOILWAT2/pulls
[doxygen]: https://github.com/doxygen/doxygen
[netCDF]: https://downloads.unidata.ucar.edu/netcdf/
[udunits2]: https://downloads.unidata.ucar.edu/udunits/
[MPI]: https://www.open-mpi.org/

SOILWAT2 is an ecosystem water balance simulation model.

This repository of `SOILWAT2` contains the same code that is
used by [rSOILWAT2][] and [STEPWAT2][].

If you utilize this model, please cite the code (DOI 10.5281/zenodo.3352249),
appropriate references, and we would like to hear about your particular study
(especially a copy of any published paper).

Some references

* Bradford, J. B., D. R. Schlaepfer, and W. K. Lauenroth. 2014. Ecohydrology of
  adjacent sagebrush and lodgepole pine ecosystems: The consequences of climate
  change and disturbance. Ecosystems 17:590-605.
* Palmquist, K.A., Schlaepfer, D.R., Bradford, J.B., and Lauenroth, W.K. 2016.
  Mid-latitude shrub steppe plant communities: climate change consequences for
  soil water resources. Ecology 97:2342–2354.
* Schlaepfer, D. R., W. K. Lauenroth, and J. B. Bradford. 2012. Ecohydrological
  niche of sagebrush ecosystems. Ecohydrology 5:453-466.

## Table of contents

1. [How to get started](#get_started)
    1. [Compilation](#compile)
    2. [Documentation](#get_documentation)
2. [How to contribute](#contribute)

<a name="get_started"></a>
## How to get started

SOILWAT2 comes with a
[detailed manual](doc/additional_pages/A_SOILWAT2_user_guide.md)
and short overviews of
[inputs](doc/additional_pages/SOILWAT2_Inputs.md)
and [outputs](doc/additional_pages/SOILWAT2_Outputs.md).
A full code documentation may be built, see [here](#get_documentation).

<a name="compile"></a>
### Compilation
 * Requirements:
 - the `gcc` or `clang/llvm` toolchains compliant with `C99`
 - for unit tests (using `googletest`) and debugging
 - toolchains compliant with `C++17` (>= `gcc13`, >= `clang-15`)
 - `POSIX API`
 - GNU-compliant `make`
 - On Windows OS: an installation of `cygwin`
 - the `netCDF-C` library (if compiled with [netCDF][] support)
 - the `udunits2` library (if compiled with [udunits2][] support)
 - a `MPI` library (tested with OpenMPI) and a parallel `netCDF-C` library
 (if compiled with [MPI] support)

* Clone the repository
    (details can be found in the
    [manual](doc/additional_pages/A_SOILWAT2_user_guide.md)), for instance,
```{.sh}
        git clone --recursive https://github.com/DrylandEcology/SOILWAT2.git SOILWAT2
```

* Build with `make` (see `make help` to print information about all
 available targets). For instance,
```{.sh}
 make CPPFLAGS=-DSWTXT # text-based mode
 make CPPFLAGS=-DSWNC # netCDF-based mode with units
 make CPPFLAGS=-DSWMPI CC=mpicc # mpi-based mode with netCDFs and units
 # (here using the `mpicc` compiler)
```

<a name="get_documentation"></a>
### Documentation
 * Use [doxygen][] to generate help pages (locally) on the command-line with
 `make doc` (which basically runs `doxygen doc/Doxyfile`)

* View documentation in your browser with `make doc_open`

<a name="contribute"></a>
## How to contribute
You can help us in different ways

1. Reporting [issues][]
2. Contributing code and sending a [pull request][]

Thank you!

Please follow our code development and contribution guidelines
[here](doc/additional_pages/code_contribution_guidelines.md)

SOILWAT2

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