Output files and directories ============================ This page describes the contents of various files and directories generated by the IMI in the course of an inversion. These files are created in ``{OutputPath}/{YourRunName}/``. When the IMI has completed successfully, you should see the following files and directories in your IMI output path: .. code-block:: console $ cd {OutputPath}/{YourRunName}/ # Replace with your path and run name $ ls archive_perturbation_sfs/ inversion/ satellite_data@ cleanup_script.sh jacobian_lowbg_ics_bcs/ spinup_run/ config_YourRunName.yml jacobian_runs/ StateVector.nc GEOSChem_build/ make_state_vector_file.py* template_run/ hemco_prior_emis/ posterior_run/ imi_output.log preview/ These directories and files are summarized below: .. list-table:: :widths: 30, 70 :class: tight-table * - ``archive_perturbation_sfs/`` - | Directory containing gridded perturbation scale factor files. If using the Kalman filter option, the period number will be included in the file name. * - ``cleanup_script.sh`` - | Bash script to cleanup the directories and files created by the IMI workflow. * - ``config_YourRunName.yml`` - | A copy of the configuration file used to run the IMI. * - ``GEOSChem_build/`` - | Contains the GEOS-Chem executable file and a summary of settings used to build GEOS-Chem. * - ``hemco_prior_emissions/`` - | HEMCO standalone run directory used to generate gridded prior emissions files for use in the IMI preview and in the Jacobian runs. * - ``imi_output.log`` - | Text file containing the output of print statements to a file. You can check the log files to see how your run has progressed and to check for any error messages. * - ``inversion/`` - | Directory containing inversion scripts, processed model output, and inversion results. The contents of this directory are described further in the next section. * - ``jacobian_lowbg_ics_bcs/`` - | Directory containing restart and boundary condition files with the species concentration to 1 mixing ratio unit for use in the Jacobian runs. * - ``jacobian_runs/`` - | Directory containing GEOS-Chem run directories for each state vector element. State vector elements may also be grouped into fewer GEOS-Chem simulations using the ``NumJacobianTracers`` setting in ``config.yml``. * - ``make_state_vector_file.py`` - | Python script used to generate the ``StateVector.nc``` file. * - ``posterior_run/`` - | GEOS-Chem run directory for running a simulation applying the scale factors generated by the inversion. * - ``preview/`` - | Directory containing images and textual output from the IMI preview. * - ``satellite_data`` - | Symbolic link to the satellite data used in the inversion. * - ``spinup_run/`` - | GEOS-Chem run directory for generating spun-up initial conditions for the Jacobian runs. * - ``StateVector.nc`` - | Gridded netCDF file containing the 2D elements to be optimized in the inversion. * - ``template_run/`` - | GEOS-Chem template run directory used to generate ``spinup_run``, ``jacobian_run``. and ``posterior_run``. Inversion directory ------------------- The ``inversion/`` directory is where the IMI computes the Jacobian, obtains the optimal estimate of emissions, and saves the results. In addition to a shell script and several Python scripts used in the inversion, you will find the following items in the inversion directory after completing an inversion: .. list-table:: :widths: 30, 70 :class: tight-table * - ``data_converted/`` - | Directory of Python pickle (``.pkl``) files containing - TROPOMI observations - virtual TROPOMI observations of the GEOS-Chem reference simulation - elements of the Jacobian matrix | for each TROPOMI orbit relevant to the inversion. | | All quantities have been converted to 1D fields indexed by latitude and longitude. * - ``data_converted_posterior/`` - | Directory of Python pickle (``.pkl``) files containing - TROPOMI observations - virtual TROPOMI observations of the GEOS-Chem posterior simulation | for each TROPOMI orbit relevant to the inversion. | | All quantities have been converted to 1D fields indexed by latitude and longitude. * - ``data_geoschem/`` - | Directory of netCDF (``.nc``) files containing daily GEOS-Chem ``SpeciesConc`` output from the reference simulation. | | These files are used to generate virtual TROPOMI observations for comparison with the true observations. * - ``data_geoschem_posterior/`` - | Directory of netCDF (``.nc``) files containing daily GEOS-Chem ``SpeciesConc`` output from the posterior simulation. | | These files are used to generate virtual TROPOMI observations for comparison with the true observations. * - ``data_sensitivities/`` - | Directory of netCDF (``.nc``) files containing daily 4-D GEOS-Chem sensitivities to perturbations in the state variables of the inversion (i.e., in the emission elements being optimized). | | The data have dimensions ``(element, lev, lat, lon)``, where ``element`` is the emission element id (state variable id) and ``lev`` is the vertical dimension. | | These files are used to compute the Jacobian matrix by application of the TROPOMI operator. * - ``inversion_result.nc`` - | NetCDF file containing the raw output of the inversion (``invert.py``) as vectors (posterior emission estimate) and matrices (posterior error covariance matrix, averaging kernel matrix ``A``). * - ``gridded_posterior.nc`` - | NetCDF file containing the posterior emission scale factors (``ScaleFactor``), diagonal elements of the posterior error covariance matrix (``S_post``), and diagonal elements of the averaging kernel matrix (``A``) projected onto the 2-D inversion grid. * - ``visualization_notebook.ipynb`` - | Jupyter notebook for quickly visualizing key results of the inversion. Plots generated by this notebook are also saved out to the `output/` directory as ``.png`` files. * - ``visualization_notebook.html`` - | For convenience, we run the Jupyter notebook as part of the IMI and output the resultant notebook to an html file, which can be viewed and rendered by your browser.