Invoke the program with its name and any of the optional command line parameters. If an input file is not given on the command line or in the initialisation file, you will be prompted for one during execution. The invocation names are ``stode'' (the stand-alone version) and ``stodeq'' (the GUI-enabled version).
On some platforms (well actually just Windows), the program does not take command line parameters. On platforms that do allow this, the command line parameters may be any of the following:
| -h | Prints a usage message. |
| -l | Prints the licence and terms of use. |
| -d level | Print debugging messages at level level or higher. Normally, you may omit this option (or, equivalently, choose runlevel 5). Running at level 4 causes some information on the state of the variables during execution to be shown, but at the cost of overall speed. |
| -f filename | Specify the name of the input file. |
| -o filename | Specify the name of the output file. |
| -F dirname | Specify the name of the input directory. |
| -O dirname | Specify the name of the output directory. |
| -S maxsteps | Specify the maximum number of simulation steps. |
| -T maxtime | Specify the maximum (simulation) time for which to run. |
| -i interval | Store results of every interval'th step. |
| -s conc_scale | Use concentrations of conc_scale molar. |
| -r rcfile | Specify the name of the run-control file. |
If the GUI version is being run, the following may additionally be specified:
| -b interval | Display results of every interval th step. |
| -B size | Display no more than size points on screen. |
| -c interval | Display results of every interval th step in the moving window. |
| -C size | Display no more than size points in the moving window. |
| -t timeout | Re-draw every timeout milliseconds. Using a low value here makes for a smoother display, but (slightly) slows down the program speed. Your choice. |
Each of these parameters may also be specified in the run control file. The command line parameters have a higher priority.
If you're running the GUI enabled version, you can change many of these parameters at run time.
After you hit the enter key, the program begins. Depending on the reactions being simulated and the chosen parameters, this could take a loooooong time. So if the program is being run in stand-alone mode, consider running it in the background (under Unix, place an ``SPMamp;'' at the end of the command line).
The GUI version allows several simulations to be run at once. Navigate from the main window File menu to Load predefined reaction sets or create a New window into which a reaction set specification may be entered. Each of these pops up a new simulation window. The keyboard short-cut CTRL_L will also popup the load files window, and there are similar short-cuts for most of the menus throughout the program.
In the GUI version, you'll need to start the simulation explicitly. From the Actions menu, you can choose to process the input before starting the simulation, run the simulation, pause or halt it, and reset the simulation. Some options may be grayed out if they are not available from the current state. While running, you can choose an option to see only the most recent results, or the whole buffer.
In each of the simulation windows, there are also menu items to save the edited specification files, choose the output file name, toggle the displayed variables, edit the run-time parameters, brew coffee, and much more. Explore.
A final note of caution: the output files can be very large. For a run which lasts several hours or days, make sure you have sufficient space on your hard drive, or choose a higher sampling interval to restrict the output size. Running the model in the GUI for a short while might give you an idea of how big the file might get, how much detail you want to include, etc.