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Transfer","monthly_downloads":0,"total_dependent_repos":0,"total_dependent_packages":0,"readme":"# Juelich Rapid Spectral Simulation Code\n\nThe Juelich Rapid Spectral Simulation Code (JURASSIC) is a fast\ninfrared radiative transfer model for the analysis of atmospheric\nremote sensing measurements.\n\n![logo](https://github.com/slcs-jsc/jurassic/blob/HEAD/docs/logo/JURASSIC_320px.png)\n\n[![release (latest by date)](https://img.shields.io/github/v/release/slcs-jsc/jurassic)](https://github.com/slcs-jsc/jurassic/releases)\n[![commits since latest release (by SemVer)](https://img.shields.io/github/commits-since/slcs-jsc/jurassic/latest)](https://github.com/slcs-jsc/jurassic/commits/HEAD)\n[![last commit](https://img.shields.io/github/last-commit/slcs-jsc/jurassic.svg)](https://github.com/slcs-jsc/jurassic/commits/HEAD)\n[![top language](https://img.shields.io/github/languages/top/slcs-jsc/jurassic.svg)](https://github.com/slcs-jsc/jurassic/tree/HEAD/src)\n[![code size](https://img.shields.io/github/languages/code-size/slcs-jsc/jurassic.svg)](https://github.com/slcs-jsc/jurassic/tree/HEAD/src)\n[![repo size](https://img.shields.io/github/repo-size/slcs-jsc/jurassic.svg)](https://github.com/slcs-jsc/jurassic/tree/HEAD/src)\n[![codacy](https://api.codacy.com/project/badge/Grade/aaba414eaf9e4e6784f13458a285ec2f)](https://app.codacy.com/gh/slcs-jsc/jurassic?utm_source=github.com\u0026utm_medium=referral\u0026utm_content=slcs-jsc/jurassic\u0026utm_campaign=Badge_Grade_Settings)\n[![codecov](https://codecov.io/gh/slcs-jsc/jurassic/graph/badge.svg?token=TYGWEJMOLI)](https://codecov.io/gh/slcs-jsc/jurassic)\n[![tests](https://img.shields.io/github/actions/workflow/status/slcs-jsc/jurassic/tests.yml?label=tests)](https://github.com/slcs-jsc/jurassic/actions)\n[![docs](https://img.shields.io/github/actions/workflow/status/slcs-jsc/jurassic/docs.yml?label=docs)](https://slcs-jsc.github.io/jurassic)\n[![status](https://joss.theoj.org/papers/d4705c1b486fe332273aeeb0bfda3dd4/status.svg)](https://joss.theoj.org/papers/d4705c1b486fe332273aeeb0bfda3dd4)\n[![license](https://img.shields.io/github/license/slcs-jsc/jurassic.svg)](https://github.com/slcs-jsc/jurassic/blob/HEAD/COPYING)\n[![doi](https://zenodo.org/badge/DOI/10.5281/zenodo.4572889.svg)](https://doi.org/10.5281/zenodo.4572889)\n[![SWH](https://archive.softwareheritage.org/badge/origin/https://github.com/slcs-jsc/jurassic/)](https://archive.softwareheritage.org/browse/origin/?origin_url=https://github.com/slcs-jsc/jurassic)\n\n## Introduction\n\nThe Jülich Rapid Spectral Simulation Code (JURASSIC) is a radiative\ntransfer model for simulating infrared radiation in the Earth's\natmosphere. It combines radiative transfer approximations,\nspectroscopic lookup tables, and retrieval tools for atmospheric remote\nsensing applications.\n\n## Statement of need\n\nInfrared limb, nadir, and zenith observations are widely used to study\ntemperature, composition, and dynamical variability in the atmosphere.\nInterpreting these measurements requires radiative transfer calculations,\nbut full line-by-line models can be too computationally expensive for\nlarge satellite datasets, sensitivity studies, or iterative retrieval\nworkflows.\n\nJURASSIC addresses this use case by combining radiative transfer\napproximations with precomputed spectroscopic lookup tables. It is\nintended for users who need many infrared radiance or transmittance\ncalculations with configurable atmospheric states, instrument settings,\nand observation geometries.\n\nThe model has been used in studies of satellite remote sensing and\nmiddle-atmosphere dynamics, including temperature retrievals, trace-gas\nretrievals, and gravity-wave analyses. It complements line-by-line\nradiative transfer models by providing a faster modelling option for\nworkflows where lookup-table approximations are appropriate.\n\n## Features\n\nJURASSIC provides a comprehensive and efficient framework for infrared\nradiative transfer simulations, offering key capabilities to support\nresearch, operational, and development workflows:\n\n- **Efficient radiative transfer approximations**: JURASSIC implements\n    the Emissivity Growth Approximation (EGA) and the Curtis–Godson\n    Approximation (CGA) to model infrared radiative transfer. These\n    methods enable rapid yet accurate simulations of atmospheric\n    radiances and transmittances across a broad spectral range.\n\n- **Lookup-table spectroscopy**: Band\n    transmittances are derived from pre-calculated lookup tables based\n    on detailed line-by-line spectroscopy. This approach maintains\n    spectroscopic accuracy while largely reducing computational cost,\n    making the model suitable for large-scale and near-real-time\n    applications.\n\n- **Optimal estimation retrieval framework**: In addition to forward\n    modelling, JURASSIC includes an optimal estimation retrieval\n    module for inverse modelling of atmospheric state variables. This\n    enables the derivation of geophysical parameters such as\n    temperature or trace gas volume mixing ratios from observed\n    radiances, providing a complete forward–inverse modelling system\n    within the same framework.\n\n- **Flexible configuration and modular design**: The model supports\n    customizable spectral bands, instrument configurations, and\n    atmospheric input fields, allowing users to integrate JURASSIC\n    into diverse workflows and existing analysis pipelines.\n\n- **Comparison with reference models**: Published studies have\n    compared JURASSIC results with radiative transfer codes such as\n    KOPRA, RFM, and SARTA.\n\n- **Parallel execution for HPC environments**: JURASSIC supports\n    workflow-level parallelism, OpenMP acceleration across the tool\n    suite, and MPI-based task distribution for retrieval workloads.\n    This enables efficient execution on multicore CPUs and HPC\n    clusters for large datasets and campaign-style processing.\n\n- **Open source and community-oriented**: JURASSIC is distributed\n    under the GNU General Public License (GPL), fostering\n    transparency, collaboration, and community-driven development\n    within the atmospheric and remote sensing research community.\n\n## Getting started\n\n### Prerequisites\n\nThis documentation describes the installation of JURASSIC on a Linux\nsystem. A number of standard tools (gcc, git, make) and software\nlibraries are needed to install JURASSIC.\n\nMandatory build and runtime dependencies include:\n- GNU Scientific Library (GSL) for numerical calculations\n- netCDF-C and HDF5 libraries for file input/output\n- GNU C compiler with OpenMP support\n\nA complete list of mandatory and optional dependencies is provided in the\n[dependencies file](https://github.com/slcs-jsc/jurassic/blob/HEAD/DEPENDENCIES.md).\n\n### Installation\n\nTo install JURASSIC, follow these steps:\n\n**1. Download JURASSIC**\n\nGet the latest or a previous version from the\n[JURASSIC releases](https://github.com/slcs-jsc/jurassic/releases) page. After\ndownloading, extract the release file:\n\n    unzip jurassic-x.y.zip\n\nAlternatively, to get the latest development version, clone the GitHub repository:\n\n    git clone https://github.com/slcs-jsc/jurassic.git\n\n**2. Install dependencies**\n\nFor the default build, the JURASSIC git repository includes bundled\nthird-party libraries that can be compiled and installed using a build\nscript:\n\n    cd [jurassic_directory]/libs\n    ./build.sh\n\nThis builds the bundled third-party libraries into `libs/build/`.\n\nAlternatively, if you prefer to use existing system libraries, install\nthe required dependencies manually. Distribution-specific package\ninformation, optional tools, and version details are collected in the\n[dependencies file](https://github.com/slcs-jsc/jurassic/blob/HEAD/DEPENDENCIES.md).\n\n**3. Optional: adjust the Makefile for non-default setups**\n\nNavigate to the source directory and adjust the `Makefile` as needed:\n\n    cd [jurassic_directory]/src\n    edit Makefile\n\nPay special attention to the following settings:\n\n* Edit the `LIBDIR` and `INCDIR` paths to point to the directories\n  where the necessary libraries are located on your system.\n\n* By default, the JURASSIC binaries are linked dynamically. If you\n  used the bundled libs, ensure that your runtime environment can find\n  the shared libraries in `libs/build/lib`. The example scripts in\n  `projects/` set this automatically. If you installed system libraries\n  in standard paths, no additional setup is needed. If you prefer\n  static linking, you can enable it by setting the `STATIC` flag, which\n  allows you to copy and use the binaries on other machines. However,\n  in some cases, either static or dynamic linking may not be feasible\n  or could cause specific issues.\n\n**4. Compile JURASSIC**\n\nFor the default bundled-library build, no changes to the `Makefile` are\nusually required:\n\n    cd [jurassic_directory]/src\n    make [-j]\n\nRun the regression test suite to verify the installation:\n\n    make check\n\nThis uses the include and library paths prepared in `libs/build/`.\n\n### Run the examples\n\nJURASSIC includes a `projects` directory containing example setups\nthat demonstrate different observation geometries and typical model\nworkflows. This directory can also be used to store your own\nexperiments.\n\nRunning the examples provided in the `projects` directory is a convenient\nway to verify that the installation was successful. Example simulations\nare provided for three observation geometries. The example scripts set\nthe runtime library path for the bundled-library build automatically and\nuse `gnuplot` to generate diagnostic plots:\n\n    # Limb\n    cd [jurassic_directory]/projects/limb \u0026\u0026 ./run.sh\n    \n    # Nadir\n    cd [jurassic_directory]/projects/nadir \u0026\u0026 ./run.sh\n\n    # Zenith\n    cd [jurassic_directory]/projects/zenith \u0026\u0026 ./run.sh\n\nEach example performs a complete radiative transfer simulation. Inside\nthe corresponding example directory, the scripts generate an observation\ngeometry file,\n\n    cat obs.tab\n\na standard mid-latitude atmospheric profile,\n\n    cat atm.tab\n\nand simulated radiances for two or three detector channels:\n\n    cat rad.tab\n\nKernel functions (Jacobians) are calculated using a finite-difference\nmethod:\n\n    cat kernel.tab\n\nThe simulation output is automatically compared with reference data to\nverify the correctness of the results. Additionally, `gnuplot` is used\nto generate plots of the simulated radiances and kernel functions.\n\n\u003cp align=\"center\"\u003e\n  \u003cimg src=\"projects/limb/plot_rad.png\" alt=\"limb radiance data\" width=\"30%\"/\u003e\n  \u0026emsp;\n  \u003cimg src=\"projects/nadir/plot_rad.png\" alt=\"nadir radiance data\" width=\"30%\"/\u003e\n  \u0026emsp;\n  \u003cimg src=\"projects/zenith/plot_rad.png\" alt=\"zenith radiance data\" width=\"30%\"/\u003e\n\u003c/p\u003e\n\n\u003cp align=\"center\"\u003e\n  \u003cimg src=\"projects/limb/plot_kernel_temperature_792.png\" alt=\"limb temperature kernel function\" width=\"30%\"/\u003e\n  \u0026emsp;\n  \u003cimg src=\"projects/nadir/plot_kernel_temperature_668.5410.png\" alt=\"nadir temperature kernel function\" width=\"30%\"/\u003e\n  \u0026emsp;\n  \u003cimg src=\"projects/zenith/plot_kernel_temperature_792.0000.png\" alt=\"zenith temperature kernel function\" width=\"30%\"/\u003e\n\u003c/p\u003e\n\n### Lookup tables\n\nJURASSIC relies on precomputed spectroscopic lookup tables derived\nfrom high-resolution line-by-line calculations. These tables provide\nband transmittances used by the radiative transfer approximations\nimplemented in the model. Precomputed lookup tables for common\nconfigurations are available from the\n[JURASSIC data repository](https://datapub.fz-juelich.de/slcs/jurassic/).\n\nUsers may either download these datasets or generate custom lookup\ntables tailored to specific spectral bands or instrument configurations.\nCreating custom lookup tables requires access to a line-by-line\nradiative transfer model capable of calculating high-resolution\nabsorption spectra of a homogeneous gas cell. The lookup tables\ndistributed with JURASSIC were generated using the\n[Reference Forward Model (RFM) from the University of Oxford](https://eodg.atm.ox.ac.uk/RFM/).\nOther line-by-line models may be used if they provide the required\nhomogeneous-gas-cell absorption spectra.\n\n## Further information\n\nMore detailed information for new users and developers is available in\nthe [JURASSIC manual](https://slcs-jsc.github.io/jurassic/). The\n[GitHub wiki](https://github.com/slcs-jsc/jurassic/wiki) collects links\nto manuals, repository files, and related resources.\n\nThese are the main references for citing the JURASSIC model in\nscientific publications:\n\n* Baumeister, P. F. and Hoffmann, L.: Fast infrared radiative transfer\n  calculations using graphics processing units: JURASSIC-GPU v2.0,\n  Geosci. Model Dev., 15, 1855–1874,\n  \u003chttps://doi.org/10.5194/gmd-15-1855-2022\u003e, 2022.\n\n* Hoffmann, L., and M. J. Alexander, Retrieval of stratospheric\n  temperatures from Atmospheric Infrared Sounder radiance measurements\n  for gravity wave studies, J. Geophys. Res., 114, D07105,\n  \u003chttps://doi.org/10.1029/2008JD011241\u003e, 2009.\n\n* Hoffmann, L., Kaufmann, M., Spang, R., Müller, R., Remedios, J. J.,\n  Moore, D. P., Volk, C. M., von Clarmann, T., and Riese, M.: Envisat\n  MIPAS measurements of CFC-11: retrieval, validation, and\n  climatology, Atmos. Chem. Phys., 8, 3671-3688,\n  \u003chttps://doi.org/10.5194/acp-8-3671-2008\u003e, 2008.\n\n* You can cite the source code of JURASSIC by using the DOI\n  \u003chttps://doi.org/10.5281/zenodo.4572889\u003e. This DOI represents all\n  versions, and will always resolve to the latest one. Specific DOIs\n  for each release of JURASSIC can be found on the Zenodo website.\n\nPlease see the [citation file](https://github.com/slcs-jsc/jurassic/blob/HEAD/CITATION.cff)\nfor further information.\n\n## Contributing\n\nWe are interested in sharing JURASSIC for operational or research\napplications. Please do not hesitate to contact us if you have any\nfurther questions or need support. 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