diff --git a/src/components/shell_variable_manifest.md b/src/components/shell_variable_manifest.md index 867445d3..9057ed4c 100644 --- a/src/components/shell_variable_manifest.md +++ b/src/components/shell_variable_manifest.md @@ -31,8 +31,8 @@ Note: This does not include variables defined in python scripts. | condaFile | ['src/write_BCs/run_boundary_conditions.sh', 'src/write_BCs/config_boundary_conditions.yml'] | ['src/write_BCs/run_boundary_conditions.sh', 'src/write_BCs/config_boundary_conditions.yml'] | [] | [] | | CondaFile | ['run_imi.sh', 'config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml'] | ['run_imi.sh', 'config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml'] | [] | [] | | config_path | ['src/components/preview_component/preview.sh'] | ['src/components/preview_component/preview.sh'] | ['run_preview'] | ['run_preview'] | -| configFile | ['src/inversion_scripts/run_inversion.sh'] | ['src/inversion_scripts/run_inversion.sh'] | [] | ['send_error'] | | ConfigFile | ['run_imi.sh', 'src/components/inversion_component/inversion.sh', 'src/components/preview_component/preview.sh', 'src/utilities/cleanup_script.sh'] | ['run_imi.sh', 'src/utilities/cleanup_script.sh'] | [] | ['setup_inversion', 'run_preview'] | +| configFile | ['src/inversion_scripts/run_inversion.sh'] | ['src/inversion_scripts/run_inversion.sh'] | [] | ['send_error'] | | ConfigPath | ['run_imi.sh', 'src/components/jacobian_component/jacobian.sh', 'src/components/statevector_component/statevector.sh', 'src/components/posterior_component/posterior.sh', 'src/components/preview_component/preview.sh', 'src/components/kalman_component/kalman.sh'] | ['run_imi.sh'] | [] | ['run_jacobian', 'create_statevector', 'reduce_dimension', 'run_posterior', 'run_preview', 'setup_kf', 'run_period'] | | constYr | ['src/components/statevector_component/statevector.sh', 'src/components/setup_component/setup.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['create_statevector', 'setup_imi', 'activate_observations'] | | copied_config | ['src/components/inversion_component/inversion.sh'] | ['src/components/inversion_component/inversion.sh'] | ['run_notebooks'] | ['setup_inversion', 'run_inversion', 'run_notebooks'] | @@ -73,8 +73,8 @@ Note: This does not include variables defined in python scripts. | ErrorBCs | ['src/inversion_scripts/run_inversion.sh'] | ['src/inversion_scripts/run_inversion.sh'] | [] | ['send_error'] | | ErrorOH | ['src/inversion_scripts/run_inversion.sh'] | ['src/inversion_scripts/run_inversion.sh'] | [] | ['send_error'] | | FetchTROPOMI | ['src/components/posterior_component/posterior.sh'] | ['src/components/posterior_component/posterior.sh'] | ['run_posterior'] | ['setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'generate_optimized_OH_value'] | -| file | ['src/inversion_scripts/run_inversion.sh', 'src/components/prior_component/prior.sh', 'src/utilities/find_corrupt_files.sh', 'src/utilities/crop_met.sh', 'src/utilities/common.sh'] | ['src/inversion_scripts/run_inversion.sh', 'src/utilities/common.sh'] | ['send_error', 'imi_failed'] | ['send_error', 'run_hemco_sa', 'print_stats', 'imi_failed', 'ncmax', 'ncmin', 'calculate_geoschem_domain'] | | FILE | ['src/geoschem_run_scripts/run_jacobian_simulations.sh', 'src/geoschem_run_scripts/run_prior_simulation.sh', 'src/geoschem_run_scripts/run_bkgd_simulation.sh'] | ['src/geoschem_run_scripts/run_jacobian_simulations.sh', 'src/geoschem_run_scripts/run_prior_simulation.sh', 'src/geoschem_run_scripts/run_bkgd_simulation.sh'] | [] | [] | +| file | ['src/inversion_scripts/run_inversion.sh', 'src/components/prior_component/prior.sh', 'src/utilities/find_corrupt_files.sh', 'src/utilities/crop_met.sh', 'src/utilities/common.sh'] | ['src/inversion_scripts/run_inversion.sh', 'src/utilities/common.sh'] | ['send_error', 'imi_failed'] | ['send_error', 'run_hemco_sa', 'print_stats', 'imi_failed', 'ncmax', 'ncmin', 'calculate_geoschem_domain'] | | FILE_LIST | ['src/utilities/find_corrupt_files.sh'] | ['src/utilities/find_corrupt_files.sh'] | [] | ['download_aws_files', 'report'] | | filename | ['src/components/kalman_component/kalman.sh'] | ['src/components/kalman_component/kalman.sh'] | ['run_period'] | ['setup_kf', 'run_kf', 'run_period', 'get_last_rundir_suffix'] | | FirstPeriod | ['src/components/kalman_component/kalman.sh'] | ['src/components/kalman_component/kalman.sh'] | ['run_kf'] | ['setup_kf', 'run_kf', 'run_period', 'get_last_rundir_suffix'] | @@ -93,8 +93,8 @@ Note: This does not include variables defined in python scripts. | GCVizDir | ['src/inversion_scripts/run_inversion.sh'] | ['src/inversion_scripts/run_inversion.sh'] | [] | ['send_error'] | | GEOSCHEM_VERSION | ['run_imi.sh', 'src/components/setup_component/setup.sh'] | ['run_imi.sh'] | [] | ['setup_imi'] | | geosChemDataPath | ['src/write_BCs/run_boundary_conditions.sh', 'src/write_BCs/config_boundary_conditions.yml'] | ['src/write_BCs/config_boundary_conditions.yml'] | [] | [] | -| GEOSChemEnv | ['run_imi.sh', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml'] | ['envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml'] | [] | [] | | geosChemEnv | ['src/write_BCs/run_boundary_conditions.sh', 'src/write_BCs/config_boundary_conditions.yml'] | ['src/write_BCs/config_boundary_conditions.yml'] | [] | [] | +| GEOSChemEnv | ['run_imi.sh', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml'] | ['envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml'] | [] | [] | | GlobalDir | ['src/utilities/crop_met.sh'] | ['src/utilities/crop_met.sh'] | [] | [] | | GOSAT | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'src/components/setup_component/setup.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml'] | [] | ['activate_observations'] | | gridded_posterior_filename | ['src/components/posterior_component/posterior.sh'] | ['src/components/posterior_component/posterior.sh'] | ['setup_posterior'] | ['setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'generate_optimized_OH_value'] | @@ -106,10 +106,12 @@ Note: This does not include variables defined in python scripts. | HcoNewLine2 | ['src/components/jacobian_component/jacobian.sh'] | ['src/components/jacobian_component/jacobian.sh'] | ['add_new_tracer'] | ['setup_jacobian', 'create_simulation_dir', 'add_new_tracer', 'run_jacobian', 'generate_BC_perturb_values', 'calculate_tracer_end', 'calculate_num_jacobian_runs', 'is_number'] | | HcoNewLine3 | ['src/components/jacobian_component/jacobian.sh'] | ['src/components/jacobian_component/jacobian.sh'] | ['add_new_tracer'] | ['setup_jacobian', 'create_simulation_dir', 'add_new_tracer', 'run_jacobian', 'generate_BC_perturb_values', 'calculate_tracer_end', 'calculate_num_jacobian_runs', 'is_number'] | | HcoNewLine4 | ['src/components/jacobian_component/jacobian.sh'] | ['src/components/jacobian_component/jacobian.sh'] | ['add_new_tracer'] | ['setup_jacobian', 'create_simulation_dir', 'add_new_tracer', 'run_jacobian', 'generate_BC_perturb_values', 'calculate_tracer_end', 'calculate_num_jacobian_runs', 'is_number'] | +| HcoNextLineMask | ['src/components/jacobian_component/jacobian.sh'] | ['src/components/jacobian_component/jacobian.sh'] | ['create_simulation_dir'] | ['setup_jacobian', 'create_simulation_dir', 'add_new_tracer', 'run_jacobian', 'generate_BC_perturb_values', 'calculate_tracer_end', 'calculate_num_jacobian_runs', 'is_number'] | | HcoPrevLine1 | ['src/components/jacobian_component/jacobian.sh'] | ['src/components/jacobian_component/jacobian.sh'] | ['create_simulation_dir', 'add_new_tracer'] | ['setup_jacobian', 'create_simulation_dir', 'add_new_tracer', 'run_jacobian', 'generate_BC_perturb_values', 'calculate_tracer_end', 'calculate_num_jacobian_runs', 'is_number'] | | HcoPrevLine2 | ['src/components/jacobian_component/jacobian.sh'] | ['src/components/jacobian_component/jacobian.sh'] | ['create_simulation_dir', 'add_new_tracer'] | ['setup_jacobian', 'create_simulation_dir', 'add_new_tracer', 'run_jacobian', 'generate_BC_perturb_values', 'calculate_tracer_end', 'calculate_num_jacobian_runs', 'is_number'] | | HcoPrevLine3 | ['src/components/jacobian_component/jacobian.sh'] | ['src/components/jacobian_component/jacobian.sh'] | ['create_simulation_dir', 'add_new_tracer'] | ['setup_jacobian', 'create_simulation_dir', 'add_new_tracer', 'run_jacobian', 'generate_BC_perturb_values', 'calculate_tracer_end', 'calculate_num_jacobian_runs', 'is_number'] | | HcoPrevLine4 | ['src/components/jacobian_component/jacobian.sh'] | ['src/components/jacobian_component/jacobian.sh'] | ['create_simulation_dir', 'add_new_tracer'] | ['setup_jacobian', 'create_simulation_dir', 'add_new_tracer', 'run_jacobian', 'generate_BC_perturb_values', 'calculate_tracer_end', 'calculate_num_jacobian_runs', 'is_number'] | +| HcoPrevLineMask | ['src/components/jacobian_component/jacobian.sh'] | ['src/components/jacobian_component/jacobian.sh'] | ['create_simulation_dir'] | ['setup_jacobian', 'create_simulation_dir', 'add_new_tracer', 'run_jacobian', 'generate_BC_perturb_values', 'calculate_tracer_end', 'calculate_num_jacobian_runs', 'is_number'] | | hemco_end | ['src/components/prior_component/prior.sh'] | ['src/components/prior_component/prior.sh'] | ['run_hemco_sa'] | ['run_prior', 'run_hemco_sa', 'exclude_soil_sink'] | | hemco_start | ['src/components/prior_component/prior.sh'] | ['src/components/prior_component/prior.sh'] | ['run_hemco_sa'] | ['run_prior', 'run_hemco_sa', 'exclude_soil_sink'] | | HEMCOconfig | ['src/components/prior_component/prior.sh'] | ['src/components/prior_component/prior.sh'] | ['run_prior'] | ['run_prior', 'run_hemco_sa', 'exclude_soil_sink'] | @@ -131,7 +133,7 @@ Note: This does not include variables defined in python scripts. | invPath | ['src/inversion_scripts/run_inversion.sh'] | ['src/inversion_scripts/run_inversion.sh'] | [] | ['send_error'] | | isAWS | ['run_imi.sh', 'config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'src/inversion_scripts/run_inversion.sh', 'src/components/statevector_component/statevector.sh', 'src/components/template_component/template.sh', 'src/components/setup_component/setup.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml'] | [] | ['create_statevector', 'setup_template', 'setup_imi'] | | isPost | ['src/inversion_scripts/run_inversion.sh', 'src/components/posterior_component/posterior.sh'] | ['src/inversion_scripts/run_inversion.sh', 'src/components/posterior_component/posterior.sh'] | ['run_posterior'] | ['send_error', 'setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'generate_optimized_OH_value'] | -| isRegional | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'src/components/statevector_component/statevector.sh', 'src/components/template_component/template.sh', 'src/components/setup_component/setup.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml'] | [] | ['create_statevector', 'setup_template', 'setup_imi'] | +| isRegional | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'src/inversion_scripts/run_inversion.sh', 'src/components/jacobian_component/jacobian.sh', 'src/components/statevector_component/statevector.sh', 'src/components/posterior_component/posterior.sh', 'src/components/template_component/template.sh', 'src/components/setup_component/setup.sh', 'src/components/kalman_component/kalman.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'src/components/jacobian_component/jacobian.sh'] | ['calculate_num_jacobian_runs'] | ['setup_jacobian', 'create_simulation_dir', 'add_new_tracer', 'run_jacobian', 'generate_BC_perturb_values', 'calculate_tracer_end', 'calculate_num_jacobian_runs', 'is_number', 'create_statevector', 'reduce_dimension', 'run_posterior', 'generate_optimized_BC_values', 'generate_optimized_OH_value', 'setup_template', 'setup_imi', 'setup_kf'] | | istr | ['src/components/jacobian_component/jacobian.sh'] | ['src/components/jacobian_component/jacobian.sh'] | ['add_new_tracer'] | ['setup_jacobian', 'create_simulation_dir', 'add_new_tracer', 'run_jacobian', 'generate_BC_perturb_values', 'calculate_tracer_end', 'calculate_num_jacobian_runs', 'is_number'] | | ithDates | ['src/components/kalman_component/kalman.sh'] | ['src/components/kalman_component/kalman.sh'] | ['run_period'] | ['setup_kf', 'run_kf', 'run_period', 'get_last_rundir_suffix'] | | ithLine | ['src/components/kalman_component/kalman.sh'] | ['src/components/kalman_component/kalman.sh'] | ['run_period'] | ['setup_kf', 'run_kf', 'run_period', 'get_last_rundir_suffix'] | @@ -164,8 +166,8 @@ Note: This does not include variables defined in python scripts. | Lons | ['src/components/template_component/template.sh'] | ['src/components/template_component/template.sh'] | ['setup_template'] | ['setup_template'] | | MakePeriodsCSV | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'src/components/setup_component/setup.sh', 'src/components/kalman_component/kalman.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml'] | [] | ['setup_imi', 'setup_kf'] | | MaxSimultaneousRuns | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'src/components/jacobian_component/jacobian.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml'] | [] | ['setup_jacobian'] | -| Met | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'src/components/statevector_component/statevector.sh', 'src/components/prior_component/prior.sh', 'src/components/template_component/template.sh', 'src/components/setup_component/setup.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml'] | [] | ['create_statevector', 'run_prior', 'setup_template', 'setup_imi'] | | MET | ['src/utilities/find_corrupt_files.sh'] | ['src/utilities/find_corrupt_files.sh'] | [] | ['download_aws_files', 'report'] | +| Met | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'src/components/statevector_component/statevector.sh', 'src/components/prior_component/prior.sh', 'src/components/template_component/template.sh', 'src/components/setup_component/setup.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml'] | [] | ['create_statevector', 'run_prior', 'setup_template', 'setup_imi'] | | metDir | ['src/components/statevector_component/statevector.sh', 'src/components/setup_component/setup.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['create_statevector', 'setup_imi', 'activate_observations'] | | metNum | ['src/components/prior_component/prior.sh', 'src/components/template_component/template.sh'] | ['src/components/prior_component/prior.sh', 'src/components/template_component/template.sh'] | ['run_prior', 'setup_template'] | ['run_prior', 'run_hemco_sa', 'exclude_soil_sink', 'setup_template'] | | MM | ['src/components/template_component/template.sh'] | [] | [] | ['setup_template'] | @@ -179,8 +181,8 @@ Note: This does not include variables defined in python scripts. | nElements | ['src/inversion_scripts/run_inversion.sh', 'src/components/inversion_component/inversion.sh', 'src/components/jacobian_component/jacobian.sh', 'src/components/statevector_component/statevector.sh', 'src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/components/kalman_component/kalman.sh'] | ['src/inversion_scripts/run_inversion.sh', 'src/components/jacobian_component/jacobian.sh', 'src/components/statevector_component/statevector.sh', 'src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/components/kalman_component/kalman.sh'] | ['calculate_num_jacobian_runs', 'reduce_dimension', 'run_posterior', 'setup_imi', 'setup_kf'] | ['send_error', 'setup_inversion', 'setup_jacobian', 'create_simulation_dir', 'add_new_tracer', 'run_jacobian', 'generate_BC_perturb_values', 'calculate_tracer_end', 'calculate_num_jacobian_runs', 'is_number', 'create_statevector', 'reduce_dimension', 'setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'generate_optimized_OH_value', 'setup_imi', 'activate_observations', 'setup_kf', 'run_kf', 'run_period', 'get_last_rundir_suffix'] | | NEW | ['src/components/template_component/template.sh', 'src/components/setup_component/setup.sh'] | ['src/components/template_component/template.sh', 'src/components/setup_component/setup.sh'] | ['setup_template', 'activate_observations'] | ['setup_template', 'setup_imi', 'activate_observations'] | | nPeriods | ['src/components/kalman_component/kalman.sh'] | ['src/components/kalman_component/kalman.sh'] | ['run_kf'] | ['setup_kf', 'run_kf', 'run_period', 'get_last_rundir_suffix'] | -| nRuns | ['src/components/jacobian_component/jacobian.sh'] | ['src/components/jacobian_component/jacobian.sh'] | ['setup_jacobian', 'calculate_num_jacobian_runs'] | ['setup_jacobian', 'create_simulation_dir', 'add_new_tracer', 'run_jacobian', 'generate_BC_perturb_values', 'calculate_tracer_end', 'calculate_num_jacobian_runs', 'is_number'] | | nruns | ['src/components/kalman_component/kalman.sh'] | ['src/components/kalman_component/kalman.sh'] | ['get_last_rundir_suffix'] | ['setup_kf', 'run_kf', 'run_period', 'get_last_rundir_suffix'] | +| nRuns | ['src/components/jacobian_component/jacobian.sh'] | ['src/components/jacobian_component/jacobian.sh'] | ['setup_jacobian', 'calculate_num_jacobian_runs'] | ['setup_jacobian', 'create_simulation_dir', 'add_new_tracer', 'run_jacobian', 'generate_BC_perturb_values', 'calculate_tracer_end', 'calculate_num_jacobian_runs', 'is_number'] | | nTracers | ['src/inversion_scripts/run_inversion.sh', 'src/components/jacobian_component/jacobian.sh'] | ['src/inversion_scripts/run_inversion.sh', 'src/components/jacobian_component/jacobian.sh'] | ['calculate_tracer_end', 'calculate_num_jacobian_runs'] | ['send_error', 'setup_jacobian', 'create_simulation_dir', 'add_new_tracer', 'run_jacobian', 'generate_BC_perturb_values', 'calculate_tracer_end', 'calculate_num_jacobian_runs', 'is_number'] | | NudgeFactor | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'src/components/kalman_component/kalman.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml'] | [] | ['run_period'] | | NumberOfElements | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml'] | [] | [] | @@ -189,7 +191,10 @@ Note: This does not include variables defined in python scripts. | ObsError | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'src/inversion_scripts/run_inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml'] | [] | [] | | OffshoreEmisThreshold | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml'] | [] | [] | | OH_elem | ['src/components/jacobian_component/jacobian.sh'] | ['src/components/jacobian_component/jacobian.sh'] | ['create_simulation_dir'] | ['setup_jacobian', 'create_simulation_dir', 'add_new_tracer', 'run_jacobian', 'generate_BC_perturb_values', 'calculate_tracer_end', 'calculate_num_jacobian_runs', 'is_number'] | +| oh_sfs | ['src/components/posterior_component/posterior.sh'] | ['src/components/posterior_component/posterior.sh'] | ['run_posterior'] | ['setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'generate_optimized_OH_value'] | | ohOptimized | ['src/components/jacobian_component/jacobian.sh'] | ['src/components/jacobian_component/jacobian.sh'] | ['calculate_num_jacobian_runs'] | ['setup_jacobian', 'create_simulation_dir', 'add_new_tracer', 'run_jacobian', 'generate_BC_perturb_values', 'calculate_tracer_end', 'calculate_num_jacobian_runs', 'is_number'] | +| OHPertNewLine | ['src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh'] | ['src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh'] | ['create_simulation_dir', 'run_posterior'] | ['setup_jacobian', 'create_simulation_dir', 'add_new_tracer', 'run_jacobian', 'generate_BC_perturb_values', 'calculate_tracer_end', 'calculate_num_jacobian_runs', 'is_number', 'setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'generate_optimized_OH_value'] | +| OHPertPrevLine | ['src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh'] | ['src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh'] | ['create_simulation_dir', 'run_posterior'] | ['setup_jacobian', 'create_simulation_dir', 'add_new_tracer', 'run_jacobian', 'generate_BC_perturb_values', 'calculate_tracer_end', 'calculate_num_jacobian_runs', 'is_number', 'setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'generate_optimized_OH_value'] | | ohThreshold | ['src/components/jacobian_component/jacobian.sh'] | ['src/components/jacobian_component/jacobian.sh'] | ['create_simulation_dir', 'calculate_tracer_end'] | ['setup_jacobian', 'create_simulation_dir', 'add_new_tracer', 'run_jacobian', 'generate_BC_perturb_values', 'calculate_tracer_end', 'calculate_num_jacobian_runs', 'is_number'] | | OLD | ['src/components/template_component/template.sh', 'src/components/setup_component/setup.sh'] | ['src/components/template_component/template.sh', 'src/components/setup_component/setup.sh'] | ['setup_template', 'activate_observations'] | ['setup_template', 'setup_imi', 'activate_observations'] | | OptimizeBCs | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'src/inversion_scripts/run_inversion.sh', 'src/components/jacobian_component/jacobian.sh', 'src/components/statevector_component/statevector.sh', 'src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/components/kalman_component/kalman.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml'] | [] | ['setup_jacobian', 'create_simulation_dir', 'reduce_dimension', 'run_posterior', 'setup_imi', 'setup_kf'] | @@ -251,8 +256,8 @@ Note: This does not include variables defined in python scripts. | RequestedCPUs | ['run_imi.sh', 'config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'src/components/inversion_component/inversion.sh', 'src/components/jacobian_component/jacobian.sh', 'src/components/spinup_component/spinup.sh', 'src/components/statevector_component/statevector.sh', 'src/components/posterior_component/posterior.sh', 'src/components/prior_component/prior.sh', 'src/components/preview_component/preview.sh', 'src/geoschem_run_scripts/submit_jacobian_simulations_array.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml'] | [] | ['run_inversion', 'run_jacobian', 'run_spinup', 'reduce_dimension', 'run_posterior', 'run_hemco_sa', 'run_preview'] | | RequestedMemory | ['run_imi.sh', 'config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'src/components/inversion_component/inversion.sh', 'src/components/jacobian_component/jacobian.sh', 'src/components/spinup_component/spinup.sh', 'src/components/statevector_component/statevector.sh', 'src/components/posterior_component/posterior.sh', 'src/components/prior_component/prior.sh', 'src/components/preview_component/preview.sh', 'src/geoschem_run_scripts/submit_jacobian_simulations_array.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml'] | [] | ['run_inversion', 'run_jacobian', 'run_spinup', 'reduce_dimension', 'run_posterior', 'run_hemco_sa', 'run_preview'] | | RequestedTime | ['run_imi.sh', 'config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'src/components/inversion_component/inversion.sh', 'src/components/jacobian_component/jacobian.sh', 'src/components/spinup_component/spinup.sh', 'src/components/statevector_component/statevector.sh', 'src/components/posterior_component/posterior.sh', 'src/components/prior_component/prior.sh', 'src/components/preview_component/preview.sh', 'src/geoschem_run_scripts/submit_jacobian_simulations_array.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml'] | [] | ['run_inversion', 'run_jacobian', 'run_spinup', 'reduce_dimension', 'run_posterior', 'run_hemco_sa', 'run_preview'] | -| RES | ['src/components/template_component/template.sh'] | [] | [] | ['setup_template'] | | Res | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'src/inversion_scripts/run_inversion.sh', 'src/components/inversion_component/inversion.sh', 'src/components/posterior_component/posterior.sh', 'src/components/prior_component/prior.sh', 'src/components/template_component/template.sh', 'src/components/setup_component/setup.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'src/inversion_scripts/run_inversion.sh'] | [] | ['send_error', 'setup_inversion', 'run_posterior', 'run_prior', 'setup_template', 'setup_imi'] | +| RES | ['src/components/template_component/template.sh'] | [] | [] | ['setup_template'] | | resnum | ['src/components/prior_component/prior.sh'] | ['src/components/prior_component/prior.sh'] | ['run_prior'] | ['run_prior', 'run_hemco_sa', 'exclude_soil_sink'] | | RESOLUTION | ['src/utilities/find_corrupt_files.sh'] | ['src/utilities/find_corrupt_files.sh'] | [] | ['download_aws_files', 'report'] | | response | ['src/utilities/cleanup_script.sh'] | [] | [] | [] | @@ -264,10 +269,10 @@ Note: This does not include variables defined in python scripts. | RestartFilePrefix | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'src/components/jacobian_component/jacobian.sh', 'src/components/spinup_component/spinup.sh', 'src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml'] | [] | ['create_simulation_dir', 'setup_spinup', 'setup_posterior', 'setup_imi'] | | retVal | ['src/components/prior_component/prior.sh', 'src/geoschem_run_scripts/run_jacobian_simulations.sh', 'src/geoschem_run_scripts/run_prior_simulation.sh', 'src/geoschem_run_scripts/run_bkgd_simulation.sh'] | ['src/components/prior_component/prior.sh', 'src/geoschem_run_scripts/run_jacobian_simulations.sh', 'src/geoschem_run_scripts/run_prior_simulation.sh', 'src/geoschem_run_scripts/run_bkgd_simulation.sh'] | ['run_prior'] | ['run_prior', 'run_hemco_sa', 'exclude_soil_sink'] | | rm_command | ['src/utilities/cleanup_script.sh'] | ['src/utilities/cleanup_script.sh'] | [] | [] | -| ROOT | ['src/components/template_component/template.sh'] | [] | [] | ['setup_template'] | +| ROOT | ['src/components/jacobian_component/jacobian.sh', 'src/components/template_component/template.sh'] | [] | [] | ['create_simulation_dir', 'setup_template'] | | run_dirs_pth | ['src/components/kalman_component/kalman.sh'] | ['src/components/kalman_component/kalman.sh'] | ['get_last_rundir_suffix'] | ['setup_kf', 'run_kf', 'run_period', 'get_last_rundir_suffix'] | -| runDir | ['src/components/jacobian_component/jacobian.sh', 'src/components/spinup_component/spinup.sh', 'src/components/posterior_component/posterior.sh', 'src/components/template_component/template.sh', 'src/components/setup_component/setup.sh', 'src/components/preview_component/preview.sh', 'src/write_BCs/run_boundary_conditions.sh'] | ['src/components/jacobian_component/jacobian.sh', 'src/components/spinup_component/spinup.sh', 'src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/components/preview_component/preview.sh', 'src/write_BCs/run_boundary_conditions.sh'] | ['create_simulation_dir', 'setup_spinup', 'setup_posterior', 'setup_imi', 'run_preview'] | ['setup_jacobian', 'create_simulation_dir', 'add_new_tracer', 'run_jacobian', 'generate_BC_perturb_values', 'calculate_tracer_end', 'calculate_num_jacobian_runs', 'is_number', 'setup_spinup', 'run_spinup', 'setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'generate_optimized_OH_value', 'setup_template', 'setup_imi', 'activate_observations', 'run_preview'] | | RunDir | ['src/utilities/cleanup_script.sh'] | ['src/utilities/cleanup_script.sh'] | [] | [] | +| runDir | ['src/components/jacobian_component/jacobian.sh', 'src/components/spinup_component/spinup.sh', 'src/components/posterior_component/posterior.sh', 'src/components/template_component/template.sh', 'src/components/setup_component/setup.sh', 'src/components/preview_component/preview.sh', 'src/write_BCs/run_boundary_conditions.sh'] | ['src/components/jacobian_component/jacobian.sh', 'src/components/spinup_component/spinup.sh', 'src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/components/preview_component/preview.sh', 'src/write_BCs/run_boundary_conditions.sh'] | ['create_simulation_dir', 'setup_spinup', 'setup_posterior', 'setup_imi', 'run_preview'] | ['setup_jacobian', 'create_simulation_dir', 'add_new_tracer', 'run_jacobian', 'generate_BC_perturb_values', 'calculate_tracer_end', 'calculate_num_jacobian_runs', 'is_number', 'setup_spinup', 'run_spinup', 'setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'generate_optimized_OH_value', 'setup_template', 'setup_imi', 'activate_observations', 'run_preview'] | | RUNDIR | ['src/geoschem_run_scripts/run_jacobian_simulations.sh', 'src/geoschem_run_scripts/run_prior_simulation.sh', 'src/geoschem_run_scripts/run_bkgd_simulation.sh'] | ['src/geoschem_run_scripts/run_jacobian_simulations.sh', 'src/geoschem_run_scripts/run_prior_simulation.sh', 'src/geoschem_run_scripts/run_bkgd_simulation.sh'] | [] | [] | | rundir_num | ['src/components/kalman_component/kalman.sh'] | ['src/components/kalman_component/kalman.sh'] | ['run_period'] | ['setup_kf', 'run_kf', 'run_period', 'get_last_rundir_suffix'] | | RunDirs | ['run_imi.sh', 'src/components/inversion_component/inversion.sh', 'src/components/jacobian_component/jacobian.sh', 'src/components/spinup_component/spinup.sh', 'src/components/statevector_component/statevector.sh', 'src/components/posterior_component/posterior.sh', 'src/components/prior_component/prior.sh', 'src/components/template_component/template.sh', 'src/components/setup_component/setup.sh', 'src/components/preview_component/preview.sh', 'src/components/kalman_component/kalman.sh'] | ['run_imi.sh', 'src/components/setup_component/setup.sh'] | ['setup_imi'] | ['setup_inversion', 'run_inversion', 'run_notebooks', 'setup_jacobian', 'create_simulation_dir', 'run_jacobian', 'setup_spinup', 'run_spinup', 'create_statevector', 'reduce_dimension', 'setup_posterior', 'run_posterior', 'run_prior', 'run_hemco_sa', 'setup_template', 'setup_imi', 'activate_observations', 'run_preview', 'setup_kf', 'run_kf', 'run_period'] | @@ -316,8 +321,8 @@ Note: This does not include variables defined in python scripts. | start_elem | ['src/components/jacobian_component/jacobian.sh'] | ['src/components/jacobian_component/jacobian.sh'] | ['calculate_tracer_end'] | ['setup_jacobian', 'create_simulation_dir', 'add_new_tracer', 'run_jacobian', 'generate_BC_perturb_values', 'calculate_tracer_end', 'calculate_num_jacobian_runs', 'is_number'] | | start_element | ['src/components/jacobian_component/jacobian.sh'] | ['src/components/jacobian_component/jacobian.sh'] | ['create_simulation_dir'] | ['setup_jacobian', 'create_simulation_dir', 'add_new_tracer', 'run_jacobian', 'generate_BC_perturb_values', 'calculate_tracer_end', 'calculate_num_jacobian_runs', 'is_number'] | | start_time | ['run_imi.sh'] | ['run_imi.sh'] | [] | [] | -| startDate | ['src/write_BCs/run_boundary_conditions.sh', 'src/write_BCs/config_boundary_conditions.yml'] | ['src/write_BCs/config_boundary_conditions.yml'] | [] | [] | | StartDate | ['run_imi.sh', 'config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'src/inversion_scripts/run_inversion.sh', 'src/components/jacobian_component/jacobian.sh', 'src/components/spinup_component/spinup.sh', 'src/components/posterior_component/posterior.sh', 'src/components/prior_component/prior.sh', 'src/components/template_component/template.sh', 'src/components/setup_component/setup.sh', 'src/components/kalman_component/kalman.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml'] | [] | ['setup_jacobian', 'create_simulation_dir', 'run_jacobian', 'setup_spinup', 'setup_posterior', 'run_posterior', 'run_prior', 'setup_template', 'setup_imi', 'setup_kf', 'run_period'] | +| startDate | ['src/write_BCs/run_boundary_conditions.sh', 'src/write_BCs/config_boundary_conditions.yml'] | ['src/write_BCs/config_boundary_conditions.yml'] | [] | [] | | StartDate_i | ['src/components/inversion_component/inversion.sh', 'src/components/posterior_component/posterior.sh', 'src/components/kalman_component/kalman.sh'] | ['src/components/posterior_component/posterior.sh', 'src/components/kalman_component/kalman.sh'] | ['run_posterior', 'run_period'] | ['run_inversion', 'setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'generate_optimized_OH_value', 'setup_kf', 'run_kf', 'run_period', 'get_last_rundir_suffix'] | | StartMonth | ['src/utilities/crop_met.sh'] | ['src/utilities/crop_met.sh'] | [] | [] | | state_vector_path | ['src/components/statevector_component/statevector.sh', 'src/components/preview_component/preview.sh'] | ['src/components/statevector_component/statevector.sh', 'src/components/preview_component/preview.sh'] | ['reduce_dimension', 'run_preview'] | ['create_statevector', 'reduce_dimension', 'run_preview'] | @@ -339,7 +344,7 @@ Note: This does not include variables defined in python scripts. | xhat | ['src/components/posterior_component/posterior.sh'] | ['src/components/posterior_component/posterior.sh'] | ['generate_optimized_BC_values', 'generate_optimized_OH_value'] | ['setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'generate_optimized_OH_value'] | | xstr | ['src/components/jacobian_component/jacobian.sh', 'src/geoschem_run_scripts/run_jacobian_simulations.sh', 'src/geoschem_run_scripts/run_prior_simulation.sh', 'src/geoschem_run_scripts/run_bkgd_simulation.sh'] | ['src/components/jacobian_component/jacobian.sh', 'src/geoschem_run_scripts/run_jacobian_simulations.sh', 'src/geoschem_run_scripts/run_prior_simulation.sh', 'src/geoschem_run_scripts/run_bkgd_simulation.sh'] | ['setup_jacobian'] | ['setup_jacobian', 'create_simulation_dir', 'add_new_tracer', 'run_jacobian', 'generate_BC_perturb_values', 'calculate_tracer_end', 'calculate_num_jacobian_runs', 'is_number'] | | xUSE | ['src/components/jacobian_component/jacobian.sh'] | ['src/components/jacobian_component/jacobian.sh'] | ['setup_jacobian'] | ['setup_jacobian', 'create_simulation_dir', 'add_new_tracer', 'run_jacobian', 'generate_BC_perturb_values', 'calculate_tracer_end', 'calculate_num_jacobian_runs', 'is_number'] | -| YEAR | ['src/utilities/find_corrupt_files.sh'] | ['src/utilities/find_corrupt_files.sh'] | [] | ['download_aws_files', 'report'] | | Year | ['src/utilities/crop_met.sh'] | ['src/utilities/crop_met.sh'] | [] | [] | +| YEAR | ['src/utilities/find_corrupt_files.sh'] | ['src/utilities/find_corrupt_files.sh'] | [] | ['download_aws_files', 'report'] | | YYYY | ['src/components/template_component/template.sh'] | [] | [] | ['setup_template'] | | yyyymmdd | ['src/geoschem_run_scripts/run_jacobian_simulations.sh'] | ['src/geoschem_run_scripts/run_jacobian_simulations.sh'] | [] | [] | \ No newline at end of file