table files with Amoeba

[fmartina]

Hello,
I am trying to calculate the primary liquid composition from which a set of alkaline rocks were derived using the Amoeba routine but I am having problems with the -t table switch option. Despite using the file names (actually the path) as suggested by alphamelts immediately after entering the commands, when I call them in Amoeba they are not recognized (SILMIN input error). After that, the following message appear "Can't spawn "cmd.exe": No such file or directory at C:\Program Files\windows_alphamelts_1-8\run_alphamelts.command line 387". The same problem arises even when I use automatic mode. I am new to Alphamelt but I previously did the Amoeba exercise of the manual and it also works correctly when I enter each sample individually as a .txt file. The alphamelts is run on windows 10 and I am using the amoeba_env file provided by the tutorial. Any suggestions will be greatly appreciated.
Thank you in advance,
Fede

[Paula]

Hi Fede,

Which Amoeba exercise did you get to work (like which workshop or is it the old one from "MELTS camp exercises")? If it's the example I'm thinking of that's finding the parental melt for a single target composition. So, by using the table file, are you trying to repeat the same kind calculation for individual samples, or are you trying to fit a liquid line of descent (LLD)? Is the script generating the melts_file1, melts_file2 etc?

Automatic mode is useful if you want to make a batch file that inputs each melts_file1, melts_file2 in turn. You can modify the auto_batch.txt file to do lots of individual amoeba calculations instead. It is worth trying the first couple of calculations not in batch mode first to see exactly what needs to go in the modified auto_batch.txt file. Also make sure you rename auto_batch.txt when you use if for batch mode  ('-b batch_file'); otherwise you might overwrite it if you use automatic mode again.

If you are trying to fit the LLD, you need to replace the digits on the ends of the melts files that '-t table_file' makes with '?' wildcards. Can you copy and paste or take a screenshot of what you are actually typing and the SILMIN input error, please? (alphamelts.exe crashing just occurs because you are trying to do calculations where everything is zero.)

Paula

[fmartina]

Hi Paula.
Thanks for your prompt response. I did the exercises from the MELTS Camp webpage. I am looking for the parental magma that best fits my sample set through a LLD. In other words, I would like to revert the fractional crystallization until mantle composition is Mg # 72. Since my samples are quite differentiated I thought is was better to use Amoeba but I'm not sure if I did the right thing. As you pointed, the script generates the melts_file1, melts_file2 etc and I used them with the '?' wildcarde but they were not recognized as input files and I do not know where they are hosted (I only see one .txt_bak file). Below is what I see on the screen.
Cheers and many thanks again.
Fede

No command line switches specified! Please enter switches now
(or press return for default '-f C:\Users\usuario\Dropbox\Documents\Datos\Geoquimica\Calculos\Amoeba\LP\amoeba_env.txt').
-f C:\Users\usuario\Dropbox\Documents\Datos\Geoquimica\Calculos\Amoeba\LP\amoeba_env.txt -m C:\Users\usuario\Dropbox\Documents\Datos\Geoquimica\Calculos\Amoeba\LP\Dhyr_guess.txt -t "C:\Users\usuario\Dropbox\Documents\Datos\Geoquimica\Calculos\Amoeba\LP\Certified trachyte trend.csv" -p "C:\Users\usuario\Dropbox\Documents\Datos\Geoquimica\Calculos\Amoeba\LP\Pyroxenite\Certified trachyte trend"
ALPHAMELTS_VERSION MELTS
ALPHAMELTS_MAXP 30000
ALPHAMELTS_MINP 1
ALPHAMELTS_SAVE_ALL true
ALPHAMELTS_FRACTIONATE_SOLIDS true
ALPHAMELTS_FRACTIONATE_TARGET true
ALPHAMELTS_DELTAP 0
ALPHAMELTS_MAXT 2400
ALPHAMELTS_OLD_SPINEL true
ALPHAMELTS_MODE isobaric
ALPHAMELTS_MGNUMBER_TARGET 72
ALPHAMELTS_DELTAT -1

Please use melts files: C:\Users\usuario\Dropbox\Documents\Datos\Geoquimica\Calculos\Amoeba\LP\Dhyr_guess1.txt, C:\Users\usuario\Dropbox\Documents\Datos\Geoquimica\Calculos\Amoeba\LP\Dhyr_guess2.txt etc.

Checking for updates...


*** alphaMELTS 1.8 (Oct 13 2017 17:06:52) -- MELTS isobar w/ or w/o liquid ***

This front end is the work of Paul Asimow and Paula Antoshechkina
(nee Smith) and it uses the MELTS and pMELTS algorithms developed by
Mark Ghiorso & co-workers. You are welcome to use and distribute this
program, under the condition that you acknowledge all the contributors
by citing the appropriate references with any results:

Smith & Asimow (2005) -- front end
Ghiorso & Sack (1995) -- MELTS thermodynamic model
Asimow & Ghiorso (1998) -- subsolidus calculations (if used)

There may be others, depending on the exact calculation performed
and the source and / or partition coefficients (e.g. D(P,T,X)) used.
See Smith & Asimow (2005), documentation and the forum for details.

Unable to automatically check for updates; check for updates at
http://magmasource.caltech.edu/alphamelts/ and
http://magmasource.caltech.edu/forum/

Choose:
1. Read MELTS file to set composition of system
2. Twiddle starting or continuation parameters
3. Single (batch) calculation
4. Execute (follow path, mineral isograd or melt contour)
5. Set fO2 buffer or aFe
6. Set H2O (ppm) or aH2O
7. Impose initial entropy, enthalpy or volume
8. Adjust solid phase setting(s)
9. Turn liquid on / off
10. Turn phase diagram mode on / off
11. Update state using restart file
12. Update composition using MELTS file
13. Write out restart file
14. Write out MELTS file
15. Write thermodynamic output for all phases
16. Calculate integrated melt and output file(s)
17. Fit parental melt composition (amoeba)
18. Cumulate Invertor (not yet implemented)
-1. Turn off menu display for options 1-18
0. QUIT

Your choice: 1
MELTS filename: C:\Users\usuario\Dropbox\Documents\Datos\Geoquimica\Calculos\Amoeba\LP\Dhyr_guess.txt
input file open
Successfully read 'title: dyhr_ol_corrected '
Successfully read 'initial composition: sio2 45.9 '
Successfully read 'initial composition: tio2 1.26 '
Successfully read 'initial composition: al2o3 12.96 '
Successfully read 'initial composition: fe2o3 11.67 '
Successfully read 'initial composition: mno 0.17 '
Successfully read 'initial composition: mgo 15.88 '
Successfully read 'initial composition: cao 10.08 '
Successfully read 'initial composition: na2o 2.23 '
Successfully read 'initial composition: k2o 0.51'
Successfully read 'initial composition: p2o5 0.35 '
Successfully read 'initial composition: h2o 0.1 '
Successfully read 'initial temperature: 1300 '
Successfully read 'initial pressure: 600 '
Successfully read 'log fo2 path: nno '
Successfully read 'log fo2 delta: 1 '

Choose:
1. Read MELTS file to set composition of system
2. Twiddle starting or continuation parameters
3. Single (batch) calculation
4. Execute (follow path, mineral isograd or melt contour)
5. Set fO2 buffer or aFe
6. Set H2O (ppm) or aH2O
7. Impose initial entropy, enthalpy or volume
8. Adjust solid phase setting(s)
9. Turn liquid on / off
10. Turn phase diagram mode on / off
11. Update state using restart file
12. Update composition using MELTS file
13. Write out restart file
14. Write out MELTS file
15. Write thermodynamic output for all phases
16. Calculate integrated melt and output file(s)
17. Fit parental melt composition (amoeba)
18. Cumulate Invertor (not yet implemented)
-1. Turn off menu display for options 1-18
0. QUIT
Your choice: 17
Superliquidus (1) or subsolidus (0) initial guess ? 1
...Adding the solid phase olivine to the assemblage.
How many target liquid files (or 0 for adjusted initial solution)? 4
Target evolved liquid filenames (use '?' as wildcard): C:\Users\usuario\Dropbox\Documents\Datos\Geoquimica\Calculos\Amoeba\LP\Dhyr_guess?.txt
Error in SILMIN file input procedure. Cannot open file: C:\Users\usuario\Dropbox\Documents\Datos\Geoquimica\Calculos\Amoeba\LP\Dhyr_guess1.txt
Can't spawn "cmd.exe": No such file or directory at C:\Program Files\windows_alphamelts_1-8\run_alphamelts.command line 387.
RUN_ALPHAMELTS.COMMAND WARNING: alphamelts may have crashed!


RUN_ALPHAMELTS.COMMAND WARNING: Cannot find output file "Phase_main_tbl.txt" (No such file or directory)
Please check that alphamelts ran properly.
Run again (y or n)?

[Paula]

What does the table file look like? It appears that it is not matching any of the columns. run_alphamelts.command should really print a warning when there is no match, but it doesn't. I'll add a warning to the next version.

You might try renaming the .csv and output folder so that they don't have spaces in the names. run_alphamelts.command is supposed to cope with spaces etc. but it's possible that I missed something somewhere. Also, try not to nest folders so deeply - it makes the file names very long and, in alphaMELTS 1.X, that can lead to a buffer overflow if you are not careful.

Paula

[fmartina]

Paula.
I followed your suggestions and renamed the files and the output folder but the SILMIN input error is still there. I also tried changing the folder location to make it more accessible. The table I am using has a sample for each row and the major oxides are listed in the header of the columns.
Thanks!
Fede

[Paula]

Oh I meant perhaps you could show the table. It seems the problem is happening before alphamelts.exe starts. The .melts files are either not being generated or they are but are not ending up where we expect. I assume you've tried searching for them in Windows Explorer (or whatever it's called these days).

Actually one thing to check - on Windows you need to make sure that no other programs have either the table_file or the template .melts file open. I would have expected it to give a warning though.

Paula

[fmartina]

I run alphamelts with both the .csv and .melts files closed and it still does not work. Just in case, pasted below is a short version of my table.
Fede
PS I was not able to attach the table file  :(
Sample    SiO2    TiO2    Al2O3    Fe2O3    MnO    MgO    CaO    Na2O    K2O    P2O5    H2O
LP29    46.78    1.41    14.07    12.93    0.19    4.95    11.4    1.7    4.44    0.95    0.1
LP32    53.38    1.05    17.89    7.67    0.24    1.98    7.47    4.99    2.83    0.5    0.1
LP10    59.1    0.64    19.18    3.91    0.09    0.6    0.9    3.72    8.46    0.18    0.1
MDZA02    41.04    1.43    12.5    13.24    0.23    4.74    10.96    1.64    5.3    0.95    0.1

[fmartina]

Hi Paula.
I got Alphamelts to generate multiple .melts files from the FAZAR table.txt file hosted on the workshops webpage. So I think the problem is in the format of my table. I'll keep trying to solve it. Thank you for your assistance.
Fede

[Paula]

Hi Fede,

Interesting... I noticed that when the email notification of your previous forum post came through on my phone, there was some funny formatting in the table file bit. It looks fine when I browse on the computer, but there may be some hidden characters in there. I hope you manage to solve it.

Paula

P.S. You are right - I disabled attachments because they are a bit of a hassle, from this end.

[HaranHennig]

Hi Fede,
I think i had the same problem running multiple liquids.
the solution was in the files format.
try to name your files 1.tar.melts  2.tar.melts etc.
and then use the wildcard in the input line : ?.tar.melts

it worked for me with 4 liquid compositions.