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Dino

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  1. Dino

    REACT error

    I tried to rerun the simulation after deleting the .gtp file...no soap. However, I just tried your suggestion of running an earlier simulation. That worked without error, but there were just as many minerals in the earlier one as in the troublesome one. I then set the graph for pH and reran the troublesome simulation and was able to get the graph without error. Thanks. Denis
  2. I have a simulation of glass dissolving in water with xaffin set to SiO2(am). The SiO2 is kinetic - has a rate equation associated with it. The simulation runs fine until Q/K approaches 1. It then slows dramatically and the slow down appears to be related to changes in Q/K. After letting the simulation run over night, I aborted it and looked at the values of Q/K. These were changing by less than 1 part in 10^7 (see the table below where the first col is the days of reaction, the second is the dissolution rate of the glass and the third is the Q/K. d - 4174.975215 R - 1.33E-17 Q/K - 0.999999219 4199.950368 1.22E-17 0.999999283 4224.926398 1.12E-17 0.999999342 I then picked up the 'system' from this simulation and started a new simulation at 4000 d. Again the simulation slowed at about 4200 d. I then increased theta to 0.6 and ran into the problem outlined in my other recent post. With theta set to 0.6, the simulation ran to its end at 5000 d, but I was unable to look at the output so I can't say how the results looked. Is this the best approach for these simulations that appear to be hung with Q/K changing very slowly (larger theta, pickup system, start where the simulation left off)?
  3. I just ran a long simulation. When I tried to graph the results, I got an error that there were too many minerals to plot. I tried many ways to get around this error, including deleting the two gtplot default files, to no avail. When both gtplot files are absent, I get the message that they do not exist and do I care to choose another file. Answering 'yes' gets me a graph of some previous simulation, but clicking the 'plot results' button gives the same result. I'm caught in a do loop. Additionally, clicking the 'view results' button gives me nothing...no file comes up. I've tried 'cntl-shift-L' and other menu options to no avail. I need someway out of this predicament.
  4. here they are. I use a modified (phases added and TRIS) version of the LLNL data base. it is too big to attach. you'll have to change the P0798 rate file since the link would not allow me to upload that type of file (even with the 'txt' extension). BTW, how do you generate a '.bas' file? I've done it in the past, but probably by accident... Denis P0798wSiO2add.9.rea amorphsilica.txt copy P0798 Rate.txt
  5. I have a file with a custom rate law for the dissolution of glass. in separate files, i have custom rate laws for the precipitation of alteration products. I recently added a rate law for the precipitation of amorphous silica and i get a react errro "bad rate law type". However, this rate law is nearly exactly the same as the others that work fine. The only difference is that the glass rate is connected to the amorphous silica through xaffin. Is that the problem? How would i get around that problem? Perhaps use chalcedony as the precipitating phase but with the same thermo properties as SiO2(am)? I can provide the appropriate files if needed. Thanks for your help.
  6. I see that this question was asked back in 2012, but I did not find a response with an answer. So... I tried launching React from GSS. After running the simulation and trying to look at the results with 'view results', I get the following error "Usage react [-i input_script] [-d thermos_dat] [-s surface_data] [-cd] [-nocd]" Displaying graphs is not a problem. This is a simulation in which the temperature of a solution is increased from 25 to 90, equilibrated with CO2, and the resulting solution decrease to 25. I get the error at any stage when trying to 'view results'. Figuring that there was some disconnect between GSS and React, I saved the file after running several simulations to get the answer I needed. I then opened the saved file with WordPad and copied and pasted the steps into the Command tab. Everything loaded and the simulations worked as before, however, requesting a 'view results' gave the same error. Where is the error and how to fix it? Thanks, Dino
  7. I have written a script file for a reaction rate equation. I wrote it in Wordpad, but it gets saved as a '.txt' file. How do you change this to a '.bas' file? I have used the '.txt' file with success, but REACT forgets that I used that file after saving the REACT simulation (on reopening, it reverts to the built-in rate equation). I've searched both the manuals and the user forum to no avail.
  8. This post covers two topics: charge balance and slide. Charge balance: I have tried a very simple solution pH 9, SiO2(aq) 1 mmol, precip on, suppress all, unsuppress SiO2(am) [i'm using the LLNL database]. When i run the solution in REACT or SPECI8, I get the message that the charge balance can not be determined because Cl is not in the input solution despite the solution being anion rich. Putting Cl in with it as charge balance gives the expected overload. Putting Na in gives me the same error but with Na as the problem. I have tried sneaking up on the solution by using no charge balance and determining the amount of cation (Na in this case) needed to get close to charge balance. With that amount of Na with charge balance gives me the same error. So, there is something I'm overlooking...but what? Slide: Ive tried to slide SiO2(aq) in the above and similar solutions only to be greeted with the error message "Exit: React stop: passem: bad basloc call" What is would like to do is to be able to slide SiO2(aq) from 1 umol to SiO2(am) saturation at constant pH (stabilized with a buffer e.g. TRIS) while calculating the initial reaction rate at each step for a silicate glass. I don't seem to be able to get beyond this error message even with a simple solution and no glass reacting just the simple solution from above. Thanks for your help.
  9. Has anyone successfully added the TRIS buffer [(CH2OH)3CNH2] to the LLNL data base? I have a vague idea as to how to do it, but if someone has done this and checked it out, I would be happy to save the time...an grateful for the info. What is unclear is if I have to add a new basis species, either TRIS or TRISH+, and a new solution species. Or do I just add two new solution species. Thanks for your help. Dino
  10. Tom, You are correct. So, the problem that I'm trying to simulate is that after glass has dissolved for quite a long time, we see in some cases analcime precipitate. When analcime precipitates, the glass reaction rate increases dramatically. We have always interpreted this as analcime consuming the rate controlling species orthosilicic acid. I also interpreted this to mean that analcime had to precipitate faster than the glass dissolved. What you are saying suggests that analcime has to precipitate slower than the glass, but still consume silicic acid. Is that correct? Denis
  11. Tom, I'm not sure how that helps. Unless Q/K > 1, the analcime will not ppt. Once Q/K = 1, analcime will stop dissolving and start ppt'ng as Q/K gets greater than 1. Since I only put in 0.01 ng, it doesn't take long for the analcime to be completely gone. The glass continues to dissolve until analcime is saturated. If you look at the output, with the current formulation, analcime does ppt and mass steadily accumulates. However, the code has a really hard time converging unless I relax epsilon. I'm just unsure how relaxing epsilon affects the results. If there is no problem with relaxing epsilon, I should be OK. Denis
  12. Tom, To continue the dialogue on the modeling of two kinetic minerals, I have been successful in modeling glass dissolving and a mineral phase precipitating. This is not totally satisfactory as I am unable to prevent dissolution even of a ng of mineral until saturation. However, for the time being, I am willing to live with that. However, as the glass dissolves and saturation of the second mineral is approached, the code begins to decrease the step size until it can converge. Another several small steps (5 or 6 at 0.00001 or so) are calculated before convergence is a problem again. This continues and, most of the time, the calculation completes. It often helps to relax the value of epsilon by 3 to 5 orders of magnetude, maybe as low as 10^7. Even with this, the calculation proceeds very slowly, often taking several hours to complete. In the output, I can often see spikes in the reaction rate and other output that suggests residual instability in the calculation. I am a bit concerned that the calculation is accurate. In an email, I'll send you the script and the database. When you get the time to take a squint at it, I'd appreciate your feed back, especially if you have a suggestion on how to make the code run better. Denis
  13. Tom, You are correct. When I use the built-in rate, the problem converges. However, to get some analcime to precipitate, I need to start with some present. If I start with a very small amount, say 1 ng, the problem still works. However, this amount must first dissolve. This means that the problem is not quite what I wanted, but it may be good enough. The reason for using the script was to make sure that no analcime dissolved. The script I sent you had Q/K < 1.03, but the same problem with convergence occurred when Q/K was constrained to be 1 or greater. As I think about it, the problem might lie in the case that there needs to be some analcime present before some can precipitate. Hence my observation that I needed some small amount present for the reaction to occur. Thnaks for your help. I think I am on the right track for now. Denis
  14. Tom, I have successfully gotten a glass to dissolve in solution with a known reaction rate law. I am trying to see if I can reproduce the observed effect of analcime precipitation on the dissolution rate of the glass. I have set up a script to read the information for the glass, analcime precipitation, and altered log K values. What seems to happen irrespective of what mineral I choose is that as the system gets close to the point at which the second mineral should begin to precipitate, the program cannot converge. It aborts when the step size gets too small. I've tried to decrease the step size, use 'log' instead of 'linear,' and some others. The same result at the same calculated time. Presumably what should happen is that the rate decreases as the silica from the glass increases (the glass has a cross affinity to chalcedony) and when the competing phase precipitates, the dissolution rate of the glass should increase. Any hints on how to proceed? I'll send you the files under a separate email. Denis
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