Aplication already running

FelixDavis

I'm getting the following error. Also, I'm only running the application once. I also restarted the PC and made sure that there was only one application running. Please see the attached.

johnsoevans

If you've rebooted your computer my only thought is that it might be a license issue.
Has anything changed on your computer since ta last worked (change of topas directory, upgrade to windows 11, etc)?
You could check if tc.exe will run from a command prompt. In your topas directory type: "tc.exe filename.inp". I think you can run a single instance of tc.exe in addition to ta.exe, so this would check if ta.exe is really being blocked for the reason reported.

FelixDavis

Nothing has changed. We installed the program as per instructions. I rerun everything and this time I get this error message.

johnsoevans

Did you try the tc.exe check? My guess is that it's a licence issue, which will give different errors in different situations. If it's that you'll need to contact Alan.

FelixDavis

I ran the CMD from topas directory, however the Original-5-1-13_riet_01.inp file is located on the desktop. I ran the command "tc.exe Original-5-1-13_riet_01.inp" and I got the following error.

johnsoevans

So do what it says! You should also need to give the full path to the inp file or run one of the test inp files. For simple errors please just use txt so the server doesn’t fill with images.

Something like: .\tc.exe test_examples/zro2.inp

FelixDavis

followed your instructions, and still getting the same error message.

TOPAS-64 Version 7.25 (c) 1992-2020 Alan A. Coelho
Maximum number of threads 8
Cannot open file C:\Users\YourUsername\Desktop\Original-5-1-13_riet_01.inp

Abnormal program termination.
PS C:\Topas-7>

johnsoevans

You must read the error messages topas gives you carefully. They usually tell you where the problem is (the only unpredictable situation is when there is a licence error). The error you're getting now says that the input file can't be found. It's because you've put "YourUsername" in the path to the file, which is very unlikely to be correct.

Try the specific command I suggested: ".\tc.exe test_examples/zro2.inp" which should run one of the standard test examples? If this doesn't work it's probably a licence issue and you should contact Alan.

FelixDavis

The program's error message changes the folder name from "felix" to "YourUsername." The file location is definitely correct. Despite following every step in your Simple Refinement video tutorial, using only my XRD and CIF files, I still haven't been able to get it working properly. I suspect the issue is related to the license. I reached out to Alan yesterday but haven't received a response yet.

johnsoevans

That's strange,YourUsername doesn't get created in the error message for me. If you've tried running from the test_examples folder then it's probably the license. In general when using tc.exe (and ta.exe) I avoid using the Desktop if possible. Just because "desktop" can change location depending on your computer set up.

FelixDavis

Thanks for your response. I contacted Alan and he couldn't open my file either, and he asked me what XRD I was using, and I told him Rigaku, then he asked me to convert my file to xy file, which I did and now getting this error. This file is sitting on my OneDrive now not my desktop. Please see the error message below. If you have an email address, I can possibly send you the file so that you can try it.

TOPAS-64 Version 7.25 (c) 1992-2020 Alan A. Coelho
Maximum number of threads 8
Cannot open file C:\Users\User\OneDrive - Villanova University\research\1.5hours-5-1-15-M1057(Fridge-Plastic-container)-7days cured(2).5hours-5-1-15-M1057(Fridge-Plastic-container)-7days cured(2)\1_Theta_2-Theta_riet_01.inp

johnsoevans

Felix: I don't know how much coding you've done, so apologies if this is patronising.
You might have seen advice in some of the TOPAS instructions to avoid folders with spaces in their names if possible. This is because sometimes they will get interpreted as the end of a filename as they are passed between e.g. jEdit/topas-editor/the command line and TOPAS.
Things can be slightly unpredictable on different computers so I try to avoid directory names and INP names with any non-standard characters if possible. I nearly always stick to lowercase letters and use "_" instead of spaces. I also avoid "-" (which could be mistaken for minus), brackets, etc.
If possible it's also safest to work in a local directory rather than a cloud directory.
The jEdit and topas-editor things I have done try to sort these problems out, but they won't catch everything.
Your INP filename might work fine, but something simpler while you're trouble-shooting would be safer.

FelixDavis

Hi John, thanks for your help. I am now getting this error message. I searched the forum to see if anyone previously had a similar issue, but I couldn't find the solution to get this resolved. Could you please let me know why I am getting this error: "Cannot locate lam from riet_app_3 in data structures".

Thanks.

johnsoevans

Felix: have you managed to get one of the test INP files running to confirm your licence is ok?
If your license isn't working the error could just be because of that (remember that error messages related to licence issues are deliberately unhelpful).
If your licence is ok, then the error is saying "there's something incorrect in the INP file". The message itself is a bit cryptic but is to do with TOPAS not being able to find a wavelength (lam) to associate with part of the model. This could be due to a "scope" error in the INP file.
Scope is to do with the level of a keyword in the INP file. e.g. a site has to belong to a str which belongs to an xdd which has a lam associated with it. There are details in tech ref, but this basically means that you need a certain minimum set of information at different levels in the INP file. If there's an error with this, TOPAS can't run.
It's often difficult for TOPAS to report exactly where the error occurs in the INP file due to the flexibility of the syntax. For example, an error could be caused by a missing ; on line 15 of the file, but it's only on line 97 that what you've written becomes a definitively incorrect set of instructions.
If you can post your INP file somebody might be able to spot the error, but it's only worth doing this once we know your licence is working.

FelixDavis

Hi John,

I ran the ceo2.inp and I believe it did work. I am now trying to refine my XRD file. I have 4 different phases present in my sample. MOC (5phase), 3phase, MgO and Brucite. After loading my xrd file, I could only add CIF for 5phase and get a refinement. If I add for instance Brucite, I get this error message:" **Warning; Site H1 of phase Brucite has one of its equivalent positions at a distance of 0.0003142 Angstroms Recurring fractional atomic coordinates such as 0.3333 should be entered as x = 1/3;".

brucite.txt

2kB

mgo.txt

5kB

phase-3.txt

3kB

phase5.txt

7kB

I have attached all my CIF files and my xrd file (MOC). can you please run them to see if you get similar errors?

Cheers,
Felix

moc.txt

71kB

johnsoevans

Felix: I don't have time to do your refinements.
The message you're getting has been discussed many times on this forum. An atom at 0.3333 needs to be specified as =1/3; or it won't be precisely on the special position to TOPAS's internal precision (0.3333333333......)
If you use topas-editor in vs code this will get flagged for you automatically with a red underline and a pop-up message telling you what to do (see below)
This type of issue is covered in the various tutorials on line. You could also look at the youTube videos which go through some of the common refinement issues.

FelixDavis

I can read the error messages, but the issue is there many things that can go wrong with the software that you are not even sure if this is because of the issue that you are specifically dealing with, or the error is related to an entirely new issue. Like before, I have fixed the coordinates but now getting this error message. I also checked your forum and was not able to find anything helpful in regard to this error. If you take a look at my two messages before, you will see the same error which shows that I had done the right thing based on your forum. Now I'm getting the same error as before. I appreciate your help.

Loading C:\Topas-7\topas.inc
Time 0.01, INP file pre-processed
Cannot locate lam from riet_app_3 in data structures

johnsoevans

All you can do is go back to the earlier INP file that worked then try and build it up again to see where you created the error.
You might have a .out file in your directory which will have been created the last time TOPAS ran successfully. You can rename this as .inp and start from that.
If you use topas-editor you have an option to do ctrl-tx or right-click/topas-editor commands/topas-archive file and you get a date-stamped copy of the INP file saved. I do this periodically for complex files. topas-editor also makes a .bck backup file saved before each refinement, but that gets overwritten each time you do save/send.