| Command name | Type | Description |
| alter_elements | action | Change an element parameter from the command file. |
| amplification_factors | action | Compute orbit amplification functions. |
| analyze_map | major action | Determine first-order matrix from tracking. |
| aperture_data | setup | Define aperture using an SDDS file. |
| bunched_beam | setup | Set up beam generation. |
| change_particle | action | Change the type of particle. Default is electron. |
| chromaticity | setup | Correct the chromaticity. |
| closed_orbit | setup | Compute the closed orbit. |
| correct | setup | Correct the orbit or trajectory. |
| correction_matrix_output | action/setup | Obtain orbit/trajectory correction matrix in a file. |
| correct_tunes | setup | Correct the tunes. |
| coupled_twiss_output | setup/action | Compute and output coupled twiss parameters. |
| divide_elements | setup | Specify division of elements into pieces. |
| error_element | setup | Define errors for a set of elements. |
| error_control | setup | Set up and control error generation process. |
| find_aperture | setup/major action | Determine the transverse (e.g., dynamic) aperture. |
| floor_coordinates | action | Compute and output floor coordinates. |
| frequency_map | major action | Compute and output frequency map. |
| global_settings | action | Change global settings. |
| insert_elements | action | Insert elements into the lattice at many places. |
| insert_sceffects | action | Insert space charge kick elements. |
| linear_chromatic_tracking_setup | setup | Set up for fast tracking with chromatic effects. |
| link_control | setup | Control linking of element parameters. |
| link_elements | setup | Define link between parameters of two elements. |
| load_parameters | setup/action | Load element parameters from SDDS file. |
| matrix_output | setup/action | Output transfer matrix along beamline. |
| modulate_elements | setup | Set up time-dependent modulation of elements. |
| moments_output | setup/action | Compute coupled beam moments, with radiation option. |
| momentum_aperture | major action | Determine s-dependent momentum aperture. |
| optimize | major action | Execute an optimization. |
| optimization_covariable | setup | Define a dependent parameter for optimization. |
| optimization_setup | setup | Perform initial optimization setup. |
| optimization_term | setup | Define a term of penalty function. |
| optimization_variable | setup | Define an optimization variable. |
| parallel_optimization_setup | setup | Perform initial parallel optimization setup. |
| print_dictionary | action | Print the element dictionary. |
| ramp_elements | setup | Set up turn-by-turn ramping of elements. |
| rpn_expression | action | Execute an expression in the rpn interpreter. |
| rpn_load | action | Load values from SDDS file into rpn interpreter. |
| run_control | setup | Set up simulation steps and passes. |
| run_setup | setup | Define global simulation parameters and output files. |
| sasefel | setup/action | Evaluate SASE FEL gain etc. |
| save_lattice | action | Save new lattice file. |
| sdds_beam | setup | Define loading of particles from SDDS file. |
| semaphores | setup | Define file semaphores for start/end of run. |
| slice_analysis | setup | Perform slice analysis along beamline. |
| subprocess | action | Execute a command in the shell. |
| steering_element | setup | Define element parameters as steering correctors. |
| transmute_elements | setup | Transmute elements from one type to another. |
| twiss_analysis | setup | Define subset of beamline for twiss parameter analysis. |
| twiss_output | setup/action | Set up twiss parameter and related computation. |
| track | major action | Execute tracking of particles and other operations. |
| tune_shift_with_amplitude | setup | Compute tune shifts with amplitude. |
| vary_element | setup | Vary element parameters in loops. |