diff --git a/src/components/shell_variable_manifest.md b/src/components/shell_variable_manifest.md index fe61b91d..537ae019 100644 --- a/src/components/shell_variable_manifest.md +++ b/src/components/shell_variable_manifest.md @@ -21,8 +21,8 @@ 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/template_component/template.sh'] | ['src/components/template_component/template.sh'] | ['setup_template'] | ['setup_template'] | -| CondaEnv | ['config.yml', 'run_imi.sh', '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'] | [] | [] | | condaEnv | ['src/write_BCs/config_boundary_conditions.yml', 'src/write_BCs/run_boundary_conditions.sh'] | ['src/write_BCs/config_boundary_conditions.yml'] | [] | [] | +| CondaEnv | ['config.yml', 'run_imi.sh', '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'] | [] | [] | | CondaFile | ['config.yml', 'run_imi.sh'] | ['config.yml'] | [] | [] | | config_path | ['src/components/statevector_component/statevector.sh', 'src/components/inversion_component/inversion.sh', 'src/components/preview_component/preview.sh'] | ['src/components/statevector_component/statevector.sh', 'src/components/inversion_component/inversion.sh', 'src/components/preview_component/preview.sh'] | ['create_statevector', 'reduce_dimension', 'run_notebooks', 'run_preview'] | ['create_statevector', 'reduce_dimension', 'setup_inversion', 'run_inversion', 'run_notebooks', 'run_preview'] | | configFile | ['src/inversion_scripts/run_inversion.sh'] | ['src/inversion_scripts/run_inversion.sh'] | [] | ['send_error'] | @@ -51,8 +51,8 @@ Note: This does not include variables defined in python scripts. | DynamicKFClustering | ['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/kalman_component/kalman.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml'] | [] | ['reduce_dimension', 'run_period'] | | element | ['src/components/jacobian_component/jacobian.sh'] | ['src/components/jacobian_component/jacobian.sh'] | ['generate_BC_perturb_values'] | ['setup_jacobian', 'run_jacobian', 'generate_BC_perturb_values'] | | end_time | ['run_imi.sh'] | ['run_imi.sh'] | [] | [] | -| EndDate | ['config.yml', 'run_imi.sh', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'src/components/posterior_component/posterior.sh', 'src/components/spinup_component/spinup.sh', 'src/components/jacobian_component/jacobian.sh', 'src/components/kalman_component/kalman.sh', 'src/components/setup_component/setup.sh', 'src/components/preview_component/preview.sh', 'src/components/template_component/template.sh', 'src/inversion_scripts/run_inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml'] | [] | ['run_posterior', 'setup_spinup', 'run_jacobian', 'setup_kf', 'setup_imi', 'run_preview', 'setup_template'] | | endDate | ['src/write_BCs/config_boundary_conditions.yml', 'src/write_BCs/run_boundary_conditions.sh'] | ['src/write_BCs/config_boundary_conditions.yml'] | [] | [] | +| EndDate | ['config.yml', 'run_imi.sh', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'src/components/posterior_component/posterior.sh', 'src/components/spinup_component/spinup.sh', 'src/components/jacobian_component/jacobian.sh', 'src/components/kalman_component/kalman.sh', 'src/components/setup_component/setup.sh', 'src/components/preview_component/preview.sh', 'src/components/template_component/template.sh', 'src/inversion_scripts/run_inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml'] | [] | ['run_posterior', 'setup_spinup', 'run_jacobian', 'setup_kf', 'setup_imi', 'run_preview', 'setup_template'] | | EndDate_i | ['src/components/posterior_component/posterior.sh', 'src/components/inversion_component/inversion.sh', 'src/components/kalman_component/kalman.sh'] | ['src/components/posterior_component/posterior.sh', 'src/components/kalman_component/kalman.sh'] | ['run_posterior', 'run_period'] | ['setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'generate_optimized_OH_value', 'run_inversion', 'setup_kf', 'run_kf', 'run_period'] | | EndMonth | ['src/utilities/crop_met.sh'] | ['src/utilities/crop_met.sh'] | [] | [] | | ErrorBCs | ['src/inversion_scripts/run_inversion.sh'] | ['src/inversion_scripts/run_inversion.sh'] | [] | ['send_error'] | @@ -209,9 +209,9 @@ Note: This does not include variables defined in python scripts. | retVal | ['src/geoschem_run_scripts/run_jacobian_simulations.sh', 'src/geoschem_run_scripts/run_prior_simulation.sh'] | ['src/geoschem_run_scripts/run_jacobian_simulations.sh', 'src/geoschem_run_scripts/run_prior_simulation.sh'] | [] | [] | | rm_command | ['src/utilities/cleanup_script.sh'] | ['src/utilities/cleanup_script.sh'] | [] | [] | | ROOT | ['src/components/template_component/template.sh'] | [] | [] | ['setup_template'] | +| 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_jacobian_simulations.sh', 'src/geoschem_run_scripts/run_prior_simulation.sh'] | [] | [] | | runDir | ['src/components/posterior_component/posterior.sh', 'src/components/spinup_component/spinup.sh', 'src/components/jacobian_component/jacobian.sh', 'src/components/setup_component/setup.sh', 'src/components/preview_component/preview.sh', 'src/components/template_component/template.sh', 'src/write_BCs/run_boundary_conditions.sh'] | ['src/components/posterior_component/posterior.sh', 'src/components/spinup_component/spinup.sh', 'src/components/jacobian_component/jacobian.sh', 'src/components/setup_component/setup.sh', 'src/components/preview_component/preview.sh', 'src/write_BCs/run_boundary_conditions.sh'] | ['setup_posterior', 'setup_spinup', 'setup_jacobian', 'setup_imi', 'run_preview'] | ['setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'generate_optimized_OH_value', 'setup_spinup', 'run_spinup', 'setup_jacobian', 'run_jacobian', 'generate_BC_perturb_values', 'setup_imi', 'activate_observations', 'run_preview', 'setup_template'] | -| RunDir | ['src/utilities/cleanup_script.sh'] | ['src/utilities/cleanup_script.sh'] | [] | [] | | RunDirs | ['run_imi.sh', 'src/components/posterior_component/posterior.sh', 'src/components/spinup_component/spinup.sh', 'src/components/jacobian_component/jacobian.sh', 'src/components/statevector_component/statevector.sh', 'src/components/inversion_component/inversion.sh', 'src/components/kalman_component/kalman.sh', 'src/components/setup_component/setup.sh', 'src/components/preview_component/preview.sh', 'src/components/template_component/template.sh'] | ['run_imi.sh', 'src/components/setup_component/setup.sh'] | ['setup_imi'] | ['setup_posterior', 'run_posterior', 'setup_spinup', 'run_spinup', 'setup_jacobian', 'run_jacobian', 'create_statevector', 'reduce_dimension', 'setup_inversion', 'run_inversion', 'run_notebooks', 'setup_kf', 'run_kf', 'run_period', 'setup_imi', 'activate_observations', 'run_preview', 'setup_template'] | | RunFilesPath | ['src/components/setup_component/setup.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['setup_imi', 'activate_observations'] | | RunName | ['config.yml', 'run_imi.sh', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'src/components/posterior_component/posterior.sh', 'src/components/spinup_component/spinup.sh', 'src/components/jacobian_component/jacobian.sh', 'src/components/inversion_component/inversion.sh', 'src/components/kalman_component/kalman.sh', 'src/components/setup_component/setup.sh', 'src/components/preview_component/preview.sh', 'src/utilities/cleanup_script.sh', 'src/utilities/common.sh', 'src/inversion_scripts/run_inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'src/utilities/cleanup_script.sh'] | [] | ['setup_posterior', 'run_posterior', 'setup_spinup', 'run_spinup', 'setup_jacobian', 'run_jacobian', 'setup_inversion', 'run_kf', 'run_period', 'setup_imi', 'run_preview', 'imi_failed'] | @@ -247,8 +247,8 @@ Note: This does not include variables defined in python scripts. | SpinupStart | ['src/components/spinup_component/spinup.sh', 'src/components/setup_component/setup.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['setup_spinup', 'setup_imi', 'activate_observations'] | | START | ['src/components/setup_component/setup.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['setup_imi', 'activate_observations'] | | start_time | ['run_imi.sh'] | ['run_imi.sh'] | [] | [] | -| StartDate | ['config.yml', 'run_imi.sh', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'src/components/posterior_component/posterior.sh', 'src/components/spinup_component/spinup.sh', 'src/components/jacobian_component/jacobian.sh', 'src/components/kalman_component/kalman.sh', 'src/components/setup_component/setup.sh', 'src/components/preview_component/preview.sh', 'src/components/template_component/template.sh', 'src/inversion_scripts/run_inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml'] | [] | ['setup_posterior', 'run_posterior', 'setup_spinup', 'setup_jacobian', 'setup_kf', 'setup_imi', 'run_preview', 'setup_template'] | | startDate | ['src/write_BCs/config_boundary_conditions.yml', 'src/write_BCs/run_boundary_conditions.sh'] | ['src/write_BCs/config_boundary_conditions.yml'] | [] | [] | +| StartDate | ['config.yml', 'run_imi.sh', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'src/components/posterior_component/posterior.sh', 'src/components/spinup_component/spinup.sh', 'src/components/jacobian_component/jacobian.sh', 'src/components/kalman_component/kalman.sh', 'src/components/setup_component/setup.sh', 'src/components/preview_component/preview.sh', 'src/components/template_component/template.sh', 'src/inversion_scripts/run_inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml'] | [] | ['setup_posterior', 'run_posterior', 'setup_spinup', 'setup_jacobian', 'setup_kf', 'setup_imi', 'run_preview', 'setup_template'] | | StartDate_i | ['src/components/posterior_component/posterior.sh', 'src/components/inversion_component/inversion.sh', 'src/components/kalman_component/kalman.sh'] | ['src/components/posterior_component/posterior.sh', 'src/components/kalman_component/kalman.sh'] | ['run_posterior', 'run_period'] | ['setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'generate_optimized_OH_value', 'run_inversion', 'setup_kf', 'run_kf', 'run_period'] | | 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'] |