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#31

Website issues, and Miscellaneous / Re: Installing Version 2.3.0

Last post by Paula - August 03, 2024, 05:57:29 PM

Version 2.3.1 has the corrected install script, plus updated version numbers and some bug fixes:

https://github.com/magmasource/alphaMELTS/releases/tag/v2.3.1

Paula

#32

Interactive operation / Re: Don't Open the melts-rhyol...

Last post by Paula - August 03, 2024, 03:14:02 PM

The early easyMelts versions were tested on El Capitan. This version should work on your machine:
 
https://magmasource.caltech.edu/gitlist/easyMelts.git/blob/92711c57cca31f2d143f3ffe62093d63c0c61ed4/easyMelts_0.2.4_beta-MacOS.zip

If you want to stick to the old GUI then I would experiment with a different version of Xquartz. Version 2.7.8 was the first to support El Capitan so you can't go older than that but 2.8.5 claims to support macOS 10.9+: https://www.xquartz.org/

I think you need at least 2.7.10 or later for the flat_namespace fix to work: https://www.xquartz.org/releases/XQuartz-2.7.10.html

Paula

#33

Interactive operation / Re: Can't open the melts-rhyol...

Last post by Pei fuping - August 02, 2024, 10:48:37 PM

Dear Paul,

Thanks for your reply. My apple computer is OS X EI Capitan, and Intel Iris Graphics 6100 1536 MB, as well as 2.9GHz Intel Core i5. I have installed Xquartz 2.7.8 and Melts-rhyolite-Mac-Os-10.8+. Since there is no new version of the computer, I still want to try again.

The operation condition is as follows:
rhyolite-MELTS (1.0.1) pMELTS (5.6.1) - (May 21 2015 - 18:06:14)
<><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>
---> Reading environment variables...
<><> There are three releases of rhyolite-MELTS and a version of pMELTS included in this package:
    (*) rhyolite-MELTS v. 1.0.2 (original version, with corrections) - old H2O model, no mixed fluids.
    (*) rhyolite-MELTS v, 1.1.0 (mixed fluid version that perserves the ternary minimum) - old H2O model.
    (*) rhyolite-MELTS v. 1.2.0 (mixed fluid version optimal for mafic and alkalic melts) - new H2O model.
    (*) pMELTS v. 5.6.1 (original version, with corrections) - - old H2O model, no mixed fluids.
<><> Visit the website melts.ofm-research.org for information on which version to use for your application.
---> Default calculation mode is rhyolite-MELTS (v. 1.0.2).  Change this? (y or n): n
---> ************************************************************
---> Calculation mode is rhyolite-MELTS (public release v 1.0.2).
---> ************************************************************
---> Initializing data structures using selected calculation mode...
---> Building interface...

Otherwise, I followed your instructions for a series of operations, and entered the command "export DYLD_LIBRARY_PATH=/opt/X10/lib/flat_namespace:$DYLD_LIBRARY_PATH", but the interface still does not appear.

Furthermore, the following lines occurred.

Last login: Sat Aug  3 13:59:10 on ttys000
appledeMacBook-Pro:~ apple$ source ~/.profile
-bash: /Users/apple/.profile: No such file or directory
appledeMacBook-Pro:~ apple$ source ~/.bash_profile
appledeMacBook-Pro:~ apple$ /rhyolite-MELTS-Mac-OS-10.8+/Melts-rhyolite-public
dyld: Library not loaded: /opt/X11/lib/libX11.6.dylib
  Referenced from: /opt/X11/lib/flat_namespace/libXt.6.dylib
  Reason: Incompatible library version: libXt.6.dylib requires version 11.0.0 or later, but libX11.6.dylib provides version 10.0.0
Trace/BPT trap: 5
appledeMacBook-Pro:~ apple$


Sincerely,

Pei
2024-8-1

#34

Interactive operation / Re: Don't Open the melts-rhyol...

Last post by Paula - July 31, 2024, 12:32:18 PM

My guess is that your Mac has an M2 or M3 chip, and that's why you're having trouble. Only XQuartz 2.8.X supports Apple Silicon natively. It certainly works on M1 chips, but even the latest beta release (https://www.xquartz.org/releases/XQuartz-2.8.6_beta2.html) predates M3 chip Macs and many M2 chips.

The Rhyolite-MELTS GUI is not really supported anymore. I recommend you try easyMelts instead. It has all the features of the GUI, plus working plots. There's more information here: https://magmasource.caltech.edu/alphamelts/links.php

At the moment you can download easyMelts from here: https://magmasource.caltech.edu/gitlist/easyMelts.git/

For now, you'd have to run it through Rosetta 2, but I am planning to make a native Apple Silicon version at some point. When that happens, the downloads will move to here: https://github.com/magmasource/MAGMA

If you want to try to get the Rhyolite-MELTS GUI working then try downloading the 10.08+ version. You will probably need to add the following to your .zshrc file:

Code Select Expand

export DYLD_LIBRARY_PATH=/opt/X11/lib/flat_namespace:$DYLD_LIBRARY_PATH
See here for a more detailed, but slightly out of date, explanation (substitute ".zshrc" for ".profile"):

https://magmasource.caltech.edu/forum/index.php/topic,821.msg1151.html#msg1151

#35

Interactive operation / Don't Open the melts-rhyolite-...

Last post by Pei fuping - July 31, 2024, 07:46:44 AM

When Melts-rhyolite-public is turned on, the system is always in the "Buiding interface..." There is no interface, no stand-alone version of the interface appears, what is going on?

Best wishes!

Pei

#36

General usage / Re: How to parse the output an...

Last post by Freewill - July 29, 2024, 11:14:03 PM

Hi Paula,

Thanks for your replying.

I did run alphaMELTS 1.9 (on Windows 10) by running the Perl script run_alphamelts.command (Perl was installed beforehand) and Phase_main_tbl.txt is one of the output.

I will try different ways of using alphaMELTS as you mentioned.

Best,
Qingwen

#37

General usage / Re: How to parse the output an...

Last post by Paula - July 29, 2024, 04:50:52 PM

Is this alphaMELTS 1.9 output? If so, you can use column_pick.command to select the table columns with the chemical formulas. There is lots of information about this in the documentation. But run_alphamelts.command needs to process the Phase_main_tbl.txt file first. That should happen automatically when you exit the alphaMELTS menu prompt, but what you've posted is not processed.

Assuming you have Perl installed (on Windows) or are on a Mac or Linux, which come with Perl, then the possible reasons for the failure include:

• You are running the alphamelts executable directly instead of through the run_alphamelts.command script
• You need to run install.command (once) to set up the software and links to the executables and scripts
• You are opening the file before exiting the alphamelts menu (this can cause the access errors, especially on Windows, so then run_alphamelts.command cannot process the file)

Depending what you are trying to do, alphaMELTS for MATLAB/Python, easyMelts or standalone alphaMELTS 2 may make processing the output in the way you need simpler:

• easyMelts produces Graphical User Interface (GUI) style output. You may be able to use that output with the Combine_tbl Excel workbook (see the alphaMELTS links page) though it has a tendency to break with updates to Excel and/or when Windows or Mac security settings change
• The GUI-style output also includes phase end member proportions
• The standalone alphaMELTS 2 app has a "Output: both" option that outputs alphaMELTS-style output and GUI-style output
• alphaMELTS for MALTAB/Python makes it fairly easy to get end member proportions from the regular output
• The alphaMELTS 2 version of column-pick.command is more powerful and easier to invoke than the alphaMELTS 1.9 one

[1. parse the chemical formula for the given P-T values, out of the output text file (Phase_main.tbl.txt), e.g., extract all the strings of the chemical formulas of each minerals (olivine, garnet, orthopyroxene, clinopyroxene, spinel, whitlockite), and neglect other information such as the oxide contents]

#38

General usage / How to parse the output and tr...

Last post by Freewill - July 29, 2024, 01:08:44 AM

Hi all,

I have trouble to deal with the raw output of alphaMelts (pMelts), which is tricky for me to be format and reorganize to an easy-to-use form such as a Excel datasheet.

To be specific, are there methods to

1. parse the chemical formula for the given P-T values, out of the output text file (Phase_main.tbl.txt), e.g., extract all the strings of the chemical formulas of each minerals (olivine, garnet, orthopyroxene, clinopyroxene, spinel, whitlockite), and neglect other information such as the oxide contents.

The raw data in Phase_main.tbl.txt is in the following form:
...
Pressure 10000.00 Temperature 1200.00 SiO2 TiO2 Al2O3 Fe2O3 Cr2O3 FeO MnO MgO NiO CaO Na2O K2O P2O5
olivine_0 57.805364 140.410297 -722473.178253 17.842285 72.833618 (Ca0.00Mg0.88Fe''0.11Mn0.00Co0.00Ni0.00)2SiO4 40.5462 0 0 0 0 10.6843 0.224893 47.8622 0.432486 0.249936 0 0 0
garnet_0 2.712072  6.516688 -36755.703009 0.769388 3.434173 (Ca0.00Fe''0.07Mg0.93)3Al2Si3O12 43.9718 0 24.8729 0 0 3.67999 0 27.3205 0 0.154776 0 0 0
orthopyroxene_0 24.655684 60.296146 -323061.983652 7.768338 32.002617 opx Na0.00Ca0.03Fe''0.14Mg1.79Fe'''0.01Ti0.01Al0.06Si1.96O6 57.2369 0.250956 1.4204 0.20259 0 4.99485 0 35.0577 0 0.804751 0.0318615 0 0
clinopyroxene_0 5.074600 11.991060 -65352.839099 1.585695 6.143241 cpx Na0.02Ca0.72Fe''0.11Mg1.08Fe'''0.01Ti0.01Al0.11Si1.94O6 53.857 0.406436 2.70987 0.328105 0 3.64023 0 20.0963 0 18.6616 0.300501 0 0
feldspar_0 7.885415 19.373262 -105822.290493 2.937619 9.700931 K0.01Na0.31Ca0.68Al1.68Si2.32O8 51.036 0 31.3326 0 0 0 0 0 0 13.9411 3.53818 0.15218 0
spinel_0 1.555376  3.359520 -13718.697509 0.365344 1.661910 Fe''0.37Mg0.67Fe'''0.07Al0.80Cr1.05Ti0.04O4 0 1.76806 22.3098 2.85461 43.7193 14.65 0 14.6981 0 0 0 0 0
whitlockite 0.030593  0.073791 -354.133757 0.009628 0.032521 Ca3(PO4)2
...

and the following is what I expect:
Pressure: 10000.00
Temperature: 1200.00
olivine_0: (Ca0.00Mg0.88Fe''0.11Mn0.00Co0.00Ni0.00)2SiO4
garnet_0: (Ca0.00Fe''0.07Mg0.93)3Al2Si3O12
orthopyroxene_0: Na0.00Ca0.03Fe''0.14Mg1.79Fe'''0.01Ti0.01Al0.06Si1.96O6
clinopyroxene_0: Na0.02Ca0.72Fe''0.11Mg1.08Fe'''0.01Ti0.01Al0.11Si1.94O6
feldspar_0: K0.01Na0.31Ca0.68Al1.68Si2.32O8
spinel_0: Fe''0.37Mg0.67Fe'''0.07Al0.80Cr1.05Ti0.04O4
whitlockite: Ca3(PO4)2


2. simplify the chemical formula of each mineral and transfer it into a form with combination of its end-member minerals
For example, for the chemical formula of olivine_0 above, the following is what the transition I want:
(Ca0.00Mg0.88Fe''0.11Mn0.00Co0.00Ni0.00)2SiO4 ==> 0.88 * Mg2SiO4 (Forsterite) + 0.11 * Fe2SiO4 (Fayalite)


Best regards,
Qingwen

#39

The MELTS family of algorithms, and scientific discussion / Re: Ni partitioning in cpx (ox...

Last post by asimow - July 25, 2024, 09:43:43 PM

Meanwhile, as for Co and Ni:
• These don't do anything as major element in pMELTS; they were left out of the calibration
• in MELTS and rhyoliteMELTS, CoO and NiO are handled by thermodynamic calculation, not as partition coefficients, at least for olivine-liquid partitioning, following the work of Hirschmann. Of course, you can also set partition coefficients for them and track them as trace elements in parallel with the thermodynamic modeling of them as oxide components of the system.
• Not sure what the previous post meant by "unstable". As major oxides, they may not be right, and they don't account for any solids other than olivine, but they shouldn't be unstable.

If you want to simulate major and trace elements together:
• It sounds like you are already doing that. That is what turning on trace elements in alphaMELTS 1.x does.

Windows:
• Most things now work the same on any operating system, once you get past installation. easyMELTS and alphaMELTS both run native on Windows now without emulators or Linux subsystem. To run alphaMELTS, you just have to have a perl installation. But it sounds like you are past those initial steps already. We don't have a lot of good teaching videos ... the conferences that have hosted our workshops recently have not allowed us to record them.

#40

The MELTS family of algorithms, and scientific discussion / Re: Ni partitioning in cpx (ox...

Last post by asimow - July 25, 2024, 09:08:41 PM

Hi Jimmy,

It should be possible to set a mineral/melt partition coefficient for Sc for each phase. The default Sc partition coefficients for many phases is 0 (the only defined values in the default file are: clinopyroxene 0.51, feldspar 0.02, garnet 2.27, olivine 0.16, orthopyroxene 0.33). So, let's say you want to change D_Sc_cpx/melt to 4 and, for good measure, D_Sc_ilm/melt to, say, 0.25.

You make a file with these values to override the defaults. Let's call it new_trace_data.txt:
Set D: clinopyroxene Sc 4
Set D: rhm-oxide Sc 0.25

Add as many lines as you like to activate partitioning of Sc into those phases.

Then in your setting file, such as alphamelts_default_env.txt, make sure you have these lines:
ALPHAMELTS_DO_TRACE true
ALPHAMELTS_TRACE_INPUT_FILE new_trace_data.txt

That last one is what tells the program to read in your new partition coefficients. Just editing default_trace_data.txt doesn't do this ... that file is for information purposes only, unless you tell alphaMELTS to read it using ALPHAMELTS_TRACE_INPUT_FILE

Then when you run, you should see values of bulk D above one when the solid assemblage is cox-rich.

Try it.

Meanwhile, as for Co and Ni: