╨╧рб▒с>■  cb■   d                                                                                                                                                                                                                                                                                                                                                                                                                                                ■ рЕЯЄ∙OhлС+'│┘0иШа─╨ь° 0< X d p |ИРШафSet up a directory for MELet Edward B. Rastetterdwadwa Normal.dota Ed Rastettertet5 RMicrosoft Word 8.0@| ▐@╩ЦJ╗R╜@d╕└э░╛@Тo▓▒╛д) ■ ╒═╒Ь.УЧ+,∙оD╒═╒Ь.УЧ+,∙оt0 pxаи░╕└ ╚╨╪р ш фMarine Biological LaboratoryfvD~'j Set up a directory for MEL TitleШ 6> _PID_GUIDфAN{24F37C40-B540-11D2-91AE-00104B6C02Set up a directory for MEL on your hard drive. Place in that directory the 'melv110.exe', 'sample1.par', 'sample2.par', 'sample3.par', 'sample4.par', 'sample5.par', 'sample.drr' and 'sample.out' files. These contain the compiled code, sample parameter files, a sample driver file, and a sample output file, respectively. To run MEL: Double click the 'melv110.exe' icon in your file manager. A green form will appear on your screen. The first thing you must do to run the model is specify the number of species in your simulation. Enter a number between 1 and 5 (I suggest you start with just one species). Next, you must specify the files to be used for the parameters, drivers, and output. If these files exist, there are three ways these specifications can be made: First, you can type the path and names of the files in the edit boxes next to the respective labels. To get into the edit boxes, either single click on the appropriate box or type 'Alt-p', 'Alt-d', or 'Alt-u'. This way of doing things is hopelessly old fashion and not recommended for anyone under 60. In any case, to use this method you need to know the path and name of the files ahead of time. Second, you can select files by going through the 'Files' option on the main menu, then select the appropriate type of file, and the 'Choose...' option. This option will bring up a browse window from which you can navigate through your directory structures to find the file you want. Third, there is a shortcut for the second option described above. If you single click on the file label (i.e., the label in black letters to the left of the three edit boxes), you will be placed directly into the browse window. Do not worry if the parameter, driver, and output files do not exist. You can create them from within MEL. In fact this is the recommended way of creating new files; to create these files outside of MEL you would have to figure out the formats for each of the files. The easiest way to make new files is to make changes to an existing file FROM WITHIN MEL. Five sample parameter files are provided; they differ in the number of species represented and are numbered accordingly. We'll deal with the parameter files later. Let's deal with the other two types of file to get rid of the easy ones first. The output file is rewritten every time you run the model. The only thing you need to remember is to specify a path and name (MEL will not let you run until this specification is made). If you do not want to overwrite an earlier run, make sure to give the output file a new name. The driver file contains all the time-series data needed to run the model. To edit an existing or create a new driver file, select 'Edit' from the main menu and 'Drivers' from the pull-down menu or select 'drivers', 'Edit' from the pull-down menus under the main-menu 'Files'. An edit window will open (the edit window will behave much like the note-pad editor that came with your windows software). If a driver file was previously specified, its contents will be displayed in the edit window. If you did not previously specify a driver file, two lines of text will be displayed in the window. In the first line will be the name of the variables (i.e., time and the four drivers). In the second line will be the units for each of these variables. Below these lines, you will need to fill in data for time and all of the drivers, but you only need to specify these data for 1) the initial values of the drivers and 2) for time steps when the drivers change. For example, if you wanted to simulate an instantaneous change in year ten, but otherwise maintain everything constant then you only need to enter two lines of data. In the first would be a 1, for time one, followed by the initial values for all the drivers. In the second line would be a 10, for time ten, followed by the new values for ALL of the drivers, even if their individual values have not changed. MEL expects there to be at least one space between the drivers and for the drivers to be in the same order as they are listed at the top of the file. Otherwise the values can be placed anywhere on the line. You can have the drivers change as many times as you want during a run. You could even specify the drivers for each and every year of the simulation. You can also cause the drivers to ramp form one value to another over a specified time period. To create this ramp, specify the time and drivers for the beginning and end of the ramp as above, but put a minus sign (-) in front of the time at the end of the ramp. The model will interpolate linearly between these two end points (including within-year interpolation). The parameter file is also modified through the 'Edit' on the main menu. The parameter file contains both the parameters and the initial values for all the state variables. These two types of data are treated independently. Thus, on the pull-down menu under the main-menu 'Edit' there are choices for both parameters and state variables. By selecting 'State variables', a form will appear with three columns. In the first are the names of the state variables, in the second are the initial values for these variables, and in the third are their units. If a parameter file was not previously specified, the second column will have all zeros in it. Simply edit the second column to indicate the initial values you want to use (editing the first or third column has no effect on the model and is ignored when the file is saved). There are also check boxes to the left of the variable names. If you check one or more of these check boxes, the respective state variables will be held constant throughout the simulation (this can be handy during the parameterization phase). When you are finished, click on the 'OK' button and you will return to the main form. AT THIS POINT YOU HAVE NOT SAVED THE CHANGES TO THE PARAMETER FILE. To save your changes use the 'Save' or 'Save as' options on the pull-down menu under the main-menu 'Files' (a cntr-S will also save the parameter file). Remember that 'Save' or 'cntr-S' will overwrite the specified file, so if you want to retain the old file, use the 'Save as' option (the model will then automatically shift over to the 'Save as' file as its default). By selecting 'Parameters' from the pull-down menu under the main-menu 'Edit', a second form will appear and will terrify you with its complexity. See the accompanying Model Description for parameter definitions. The parameters are listed under the processes to which they pertain ('process' is used broadly here, e.g., leaf area is not truly a process). Because this version of MEL can have as many as five interacting species, all of the vegetation parameters have to be specified for each species individually. The form will look neater if you resize the window so that the 'GPP Sp' tabs for all your species are all on the left side of the window (the exact size of the window needed to accomplish this feat will depend on your monitor). If you then successively click on the 'GPP Sp' tabs and then successively on the 'Act Tiss' tabs, you will rearrange the tabs in a more obvious order. There is a separate tab for each process. On the sheet under each tab is a table with the parameter names, values, and units on it. At the top of the sheet, the current value of the process is given (usually the initial value). To update the process value after you change parameter values, click on the 'Update process' button at the bottom of the window. Some parameter changes will have a cascading effect on other processes in the model. Also, some processes do not have tabbed sheets associated with them because they have no parameters specifically linked to them. If you want to view all the processes to see what effect the parameter changes have had, click on the 'View all processes' button at the bottom of the window. You can leave the all processes window open while you edit the parameter values. When you click on 'update processes', the processes on the process window will also be updated. Once you have made all the changes you want to make, click on the 'OK' button. IF YOU WANT TO MAKE SURE YOUR CHANGES ARE SAVED, SAVE THE PARAMETER FILE NOW. You now have all the files specified. The next thing you need to do is specify the duration of the simulation. Click the edit box under the 'Stop Time' label and enter the number of years you want the simulation to run. After entering the stop time, the run button becomes active. You can run the model at this point. However, you might want to calibrate it first. An automated calibration routine is provided under the main-menu 'Calculate' option, which became active after entering the stop time. Three options are listed on the pull-down menu under the main-menu 'Calculate'; 'At time', 'Parameters', and 'State variables'. The 'State variables' option has not been implemented and has been disabled. The 'At time' option will allow you to specify which year in the driver file to use for calibration. By selecting 'Parameters', a window will open with a warning message and a yes/no option. By clicking the 'Yes' button, the software will recalculate values for the gN, gC, and qmin parameters for each species, the ( and (N parameters for the soil organic matter, and (Ne for the inorganic N loss. These parameters will be recalculated so that the system is at steady state with GPP for each species equal to NPP plus plant respiration, the optimum plant C:N ration (q) for each species equal to the actual C:N ratio (BC/BN), soil respiration equal to litter C inputs minus dissolved-organic-C leaching losses, net N mineralization equal to litter N inputs minus dissolved-organic-N leaching losses, and leaching losses of inorganic N equal to N deposition minus dissolved-organic-N leaching losses. OK, now run the model. You can view output from within the software using the main-menu 'View'. There are three options in the pull-down menu. The first ('time-step') allows you to specify the frequency at which the output data are reported. For example, you might want to run the model with a yearly time step, but to look at the output every ten years. The second output option allows you to view the output data as a data 'Table'. Selecting this option will open a window with a table containing all the output data. The third option allows you to open a 'Chart' where the output data can be plotted. When the window opens, there will be a blank graph at the top and a list of all the output data at the bottom. Select the variables to plot by clicking on them (they will then be highlighted). As many as five variables can be plotted at the same time. Once you have selected the variables you want to plot, simply click on the 'Update Chart' button. If you do not like the scale for the plot, you can change it by selecting the 'y-axis', 'scale' or 'x-axis', 'scale' choices on the pull-down menus under the main-menu 'Chart' option at the top of the window. OR.. you can place your pointer at the upper left corner of the portion of the graph you want to expand, hold the left button on your mouse down, and drag the pointer to the lower right corner of the portion of the graph you want to expand. By holding down the right mouse button, you can drag the field of view in any direction. By default, the independent variable on the plot is time. You can select any desired variable for your independent variable by selecting 'x-axis', 'define' from the pull-down menus under the main-menu 'Chart' option. You can also print the graph by selecting 'print' form the pull-down menu under the main-menu 'Form' option. To get out of the graph, click the 'Close Display' button. If you want to rerun the model, you can reset the state variables to the values stored on the parameter file by using the 'Reload' button at the lower right of the main window. With this button you can also reload the parameters saved on that file. Make sure to un-check the 'parameters' option if you do not want to overwrite the parameters currently being used by the model. Have fun! 99}рЕЯЄ∙OhлС+'│┘0иШа─╨ь° 0< X d p |ИРШафSet up a directory for MELet Edward B. 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