X2t and Xtplot - some inquiries

[maki]

Hi

 

I have four inquiries about X2t and Xtplot.

 

Inquiry #1: Script editor of microbial kinetics

When I posted the question about custom rate law script on July 24th, 2013, you answered me that the programmer was working on fixing the problem with the script editor of Custom rate law. Could you let me know about the current status of the maintenance? The problem seems to remain even in ver. 9.0.8. If the problem is fixed, it would be very helpful right now.

 

Inquiry #2: File name on title bar

In X2t, React, and other programs, the file name is not indicated on the title bar. Folder name of the upper directory is indicated. In the Xtplot file, the file name is indicated. Could you tell me how to indicate the file name on the title bar while opening X2t program?

 

Inquiry #3: Node number on Position tab

When I would like to select data of the specific Node with Time (several values at one node) for X axis, I can select them from Position tab (ex. Node 10, 1 (20m, 2m) there). I think it is based on the XY coordinates. On the other hand, I cannot select them by relying on the Node number. Can we make the Node number indicate on Position tab?

 

Inquiry #4: Overlap of objects

Even when all of appearances are reset on the X2t map view, the number with Coordinate Axes and the name of Variable partially lie on top of each other. How can we reset objects of Map View including the Coordinate Axes so as not to overlap them?

 

If you need further explanation, please let me know.

 

Best regards,

 

Maki

[Brian Farrell]

Hi Maki,

 

Sorry for the delay in responding to you. I was out of the office for the Thanksgiving holiday.

 

#1

It looked like everything was working with the custom rate laws, plotting, etc. Do rate law script files work for you? Or specifying rate law scripts from the command line? How about the error with variables not saving? I'll look into this some more.

 

#2

I think this is how the programs were designed to work. The plot file names (e.g. React_plot.gtp, React_plot_NewRun.gtp) are derived from the suffix you specify in the GWB programs (Config - Output - Suffix), not the name of the GWB script itself. So the GWB programs, like React, display the working directory (folder) where the plot files will be written, not the name of the React input script.

 

#3

Yes, it looks like Xtplot lists the x and y index, as well as the x and y position, of each node on the position tab. I'll talk to the developers about the possibility of including the node number itself as well.

 

#4

The default setting of Xtplot's Map view plot does not display the coordinate axes, so if you go to File - Reset Configuration everything will fit without overlapping. If you'd like to include coordinate axes, you can move any aspect of the plot (the Color Map, Map Scale, Coordinate Axes, etc.) to the desired location using your mouse or the X and Y position in the appropriate dialog box. Additionally, you can change the font, text size, scale size, etc. You can then save this custom configuration by going to File - Save As... in Xtplot. When you run a new model in X1t or X2t and open the results in Xtplot, just go to File - Open - Configuration (or drag the ...Xtplot_conf.dat file into Xtplot) to load your saved settings. Please let me know if you need additional explanation for this.

 

Hope this helps,

Brian

[maki]

Hi Brian,

 

Thank you for your reply.

 

#1

As we know, five means for setting rate law (Built in, Equation, Script file, Function, and Script) can be used in GWB software.

“Script file” works without any problem as you have advised me in the past posts.

However, ‘Script’ including same contents of the ‘Script file’ didn’t work, and error messages ‘Error: Don’t know keyword: ***’ were shown.

The form of pp. 66-67 of Reaction Modeling Guide was used and same contents of the ‘Script file’ that has worked were pasted to the input window as below.

Was it a mistake?

---------

aff = QoverK * exp(-ATP_number * ATP_energy / (8.3143 * TK))

aff = aff^order1

IF (aff > 1.0) THEN aff=1.0

. . .

return rprime * biomass *

---------

 

When line numbers were added to head of each line as below, it didn’t work either.

---------

10 aff = QoverK * exp(-ATP_number * ATP_energy / (8.3143 * TK))

20 aff = aff^order1

30 IF (aff > 1.0) THEN aff=1.0

. . .

440 return rprime * biomass *

---------

 

After the error messages were shown, only the first line (aff = QoverK * exp(-ATP_number * ATP_energy / (8.3143 * TK))) remained in both cases.

If there is any fundamental mistake throughout the setting, could you point out my mistake?

Or, should I input the other commands to deal with microbial kinetics using ‘Script’?

 

#2

I would like to display the name of GWB script file (Input file) on the title bar.

When I carry out several calculation derived from Input files of same folder at the same time, it would be helpful to distinguish their running files.

Is there any way that I can make it?

 

#3

Thank you for your consideration. Its improvement would be very convenient for extracting data.

 

#4

Thank you for your appropriate advice.

 

Best regards,

 

Maki

 

[Brian Farrell]

Hi Maki,

 

Regarding #1, can you try replacing all double quotes (") within your script with single quotes (')?

 

As for #2, the programs do not display the input file name. Instead, they show the working directory where the output files will be written. The suffix you specify within your script controls the output file name, not the name of the input file. For example, you might have a reactive transport model in which a pulse of some contaminant enters an aquifer. You might be interested in how the value chosen for the dispersivity affects the pulse's transport through the aquifer. You set the dispersivity, set a descriptive suffix for the output file (_1m), then run the model. You can repeat the procedure with different dispersivities and end up with a series of output files (x1t_plot_1m.xtp, x1t_plot_2m.xtp, x1t_plot_10m.xtp, ...) generated by adjusting the single base model. That's the way the programs are designed to work.

 

Hope this helps,

Brian

[maki]

Hi Brian,

 

 

#1

 

Thank you for your pointing out that.

 

After I tried replacing double quotes with single quotes, the program worked very well!

 

 

#2

 

Thank you for your explanation.

 

Of course, I also really think that the suffix function is very useful and helps me.

However, in my current case, I have needed to calculate many models at the same time and continuously, which were constructed based on various combinations of changed variables in Initial system, Reactants, Inlet fluid, Flow field, and Medium properties. In addition, the calculation of some models took a few days. So, I have needed to leave every original input file for checking their constraints and have wanted to specify which file were running, for preparing the subsequent one.

 

If there are several the same requests from users besides me and if the concerned maintenance would be easy to carry out for the developers, the maintenance would be grateful.

 

 

Best regards,

 

 

Maki