diff --git a/src/components/shell_variable_manifest.md b/src/components/shell_variable_manifest.md index b45ec6eb..2afc9853 100644 --- a/src/components/shell_variable_manifest.md +++ b/src/components/shell_variable_manifest.md @@ -26,13 +26,13 @@ Note: This does not include variables defined in python scripts. | channels | ['envs/Harvard-Cannon/imi_env.yml'] | ['envs/Harvard-Cannon/imi_env.yml'] | [] | [] | | ClusteringMethod | ['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'] | [] | [] | | cmd | ['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'] | -| condaEnv | ['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'] | [] | [] | | CondaEnv | ['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'] | [] | [] | -| 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'] | [] | [] | +| condaEnv | ['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'] | [] | [] | +| 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'] | [] | [] | | 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/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 | ['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_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'] | @@ -168,8 +168,8 @@ Note: This does not include variables defined in python scripts. | MET | ['src/utilities/find_corrupt_files.sh'] | ['src/utilities/find_corrupt_files.sh'] | [] | ['download_aws_files', 'report'] | | 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'] | | mm | ['src/utilities/crop_met.sh'] | ['src/utilities/crop_met.sh'] | [] | [] | +| MM | ['src/components/template_component/template.sh'] | [] | [] | ['setup_template'] | | Month | ['src/utilities/crop_met.sh'] | [] | [] | [] | | n_elems | ['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'] | | name | ['envs/Harvard-Cannon/imi_env.yml', 'src/components/jacobian_component/jacobian.sh'] | ['envs/Harvard-Cannon/imi_env.yml', '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'] | @@ -251,8 +251,8 @@ 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 | ['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'] | +| 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'] | | 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'] | [] | [] | [] | @@ -266,9 +266,9 @@ Note: This does not include variables defined in python scripts. | rm_command | ['src/utilities/cleanup_script.sh'] | ['src/utilities/cleanup_script.sh'] | [] | [] | | ROOT | ['src/components/template_component/template.sh'] | [] | [] | ['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/utilities/cleanup_script.sh'] | ['src/utilities/cleanup_script.sh'] | [] | [] | -| 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 | ['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 | ['src/utilities/cleanup_script.sh'] | ['src/utilities/cleanup_script.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'] | | RunFilesPath | ['src/components/setup_component/setup.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['setup_imi', 'activate_observations'] | @@ -316,8 +316,8 @@ 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'] |