Line Plot Settings Dialog

This dialog is used to modify an existing line plot window.

Use this dialog to select the compartments and species to be included, to choose plot types and attributes, and to overlay externally generated data on the simulation results. Make your modifications according to the guidelines below, then click OK to apply your modifications to the results window. Click Cancel to close this dialog without modifying the results window.

The Data To Plot Page

Select Compartments

Use this list box to select one or more compartments whose data is to be included in the plot. A separate graph is created in the window for each compartment and for each plot type. A single reactor reaction scheme has only one compartment, and the compartment list is hidden in that case.

To select compartments whose data is to be included in the plots:
  • Click on a compartment's name using the left mouse button to select it.
  • To select multiple names, press the Ctrl key and click on each name you wish to include.
  • To select a range of compartments, click on a name at one end of the range, press the Shift key and then click on the name at the other end of the range.
  • Click None to unselect all compartments.
  • Click All to select all compartments in the list.
  • Click Previous to recall the compartment selection from the last time this dialog was used.

Select Species

Use this list box to select one or more species whose concentration or amount is to be included in the plot. All concentrations or amounts are plotted in a single graph for each compartment.

To select species whose data is to be included in the plots:
  • Click on a species name using the left mouse button to select it.
  • To select multiple names, press the Ctrl key and click on each name you wish to include.
  • To select a range of species, click on a name at one end of the range, press the Shift key and then click on the name at the other end of the range.
  • Click None to unselect all species.
  • Click All to select all species in the list.
  • Click Previous to recall the species selection from the last time this dialog was used.

Plot External Data

You may import external data from a regular text file to overlay on simulation results.

To overlay external data on a plot:

  1. Click the (Import external data) push button to select the file to be imported.

    When importing the text file:

    • Kinetiscope expects the text file to be a series of pairs of numeric values, one pair per line.
    • The first entry in each pair is taken to be a value of the first parameter (to be plotted on the horizontal axis), in the same units used in the reaction scheme. The second entry in each pair is the value of the second parameter (to be plotted on the vertical axis), again in units consistent with those in the reaction scheme.
    • Kinetiscope converts each line to numeric values as the file is read. If a line does not contain two valid numeric values as the first two words, then that line is not used. Therefore you may include non-numeric text such as column headings in the text file.

    Once a text file with valid data is loaded, the check box is given the name of that file.

  2. Choose the external data's type from the drop-down list box.
  3. Check the name of the external data file to overlay its data on the selected plot.

Here is an example of the contents of a valid external data file: 

Time Concentration
0	   0.00475			
300	0.1581			
600	0.2703			
900	0.35845			
1200	0.44741			
1500	0.52024

The column labels are optional.

The Plot Types Page

Using the left mouse button, click on the check boxes check the types of plots you wish to include in the line plot window. Plot types for which data are not available are disabled.

A separate graph is created in the window for each compartment and for each plot type.

The Plot Details Page

Plot Attributes

These controls allow you to modify the plot's appearance:

Show Points
Check this check box to display the individual data points on each graph. Both data points and connecting lines may be visible simultaneously.
Show Lines
Check this check box to display lines interconnecting individual data points on each graph. Both data points and connecting lines may be visible simultaneously.
Number of Columns
This modifies the layout of multiple plots on the window. Use the spin box to change the number of columns of individual plots.

Select Electrochemical Data to Plot

These controls are active only on three-dimensional reaction schemes that include electrochemical steps.

Kinetiscope tracks the movement of electrical charge during any simulation that includes electrochemical processes. In general, due to exchange current, charge will move both into and out of the Compartment.

Choose here which components of charge are to be shown. Forward current/charge will display charge flowing into the compartment, Reverse current/charge will display charge flowing out, and Total current/charge shows the sum of those two quantities. Click on the check boxes to select which components to include.

Under some circumstances the statistical noise inherent in stochastic simulations can lead to significant random noise in the calculated current. The drop-down list box in this group allows you to apply a smoothing algorithm to these data. You may select the strength of the smoothing here, or disable smoothing entirely (the initial default setting).

Number of Data Points

Indicate here the number of time points to be included in the new plot. You may use the up/down arrows to select the number or you may type it in directly. The default behavior is to plot no more than 1000 points. To include all available data points in the plot, Click All.