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alphaMELTS 2.3 standalone & for MATLAB/Python is now open source and available on GitHub (https://github.com/magmasource/alphaMELTS).
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#91
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
#92
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.
#93
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:

#94
Website issues, and Miscellaneous / Re: Installing Version 2.3.0
Last post by asimow - July 25, 2024, 08:42:18 PM
There is a small typo in the install.command script. If you open it with any text editor, go to line 19 and change "install2.command" to "install.command". Save, then run it. That should fix the issue.
#95
Windows / Re: Melts for Excel: Server Er...
Last post by asimow - July 25, 2024, 08:40:08 PM
#96
Windows / Re: Melts for Excel: Server Er...
Last post by Susan DeBari - July 17, 2024, 07:31:50 PM
I just tried today too and had the same issue!
#97
Windows / Melts for Excel: Server Error ...
Last post by jtmitchell - July 17, 2024, 08:06:05 AM
Hi all,

I'm trying to do some panic modelling for a conference and I've been getting nothing but "server returned no results" errors today, both with updated and non-updated workbook links, and every flavour of Melts. I've been back through the troubleshooting guide and found the log file. It's giving me "invalid xml file received" and "requested URL is not found on the server" even on the default composition it downloads with. I've copied the log below. Has anyone else run into this issue? I'm used to the Excel version being a little wonky at times, but I've left it quite late to try and get this modelling done. Maybe I'm just missing something very obvious!


Thanks in advance!


MELTS model selected: rhyolite-MELTS_v1.0.x
------------------
Starting Equilibrate

Start: 7/17/2024 9:58:13 AM
------------------
Calculation number: 1
InputXML: dataXML=<MELTSinput><initialize><modelSelection>MELTS_v1.0.x</modelSelection><SiO2>70.934955066097</SiO2><TiO2>0.171639896651397</TiO2><Al2O3>12.9206699979246</Al2O3><Fe2O3>0.293263935644875</Fe2O3><Cr2O3>0</Cr2O3><FeO>0.97573935726614</FeO><MnO>0</MnO><MgO>0.476777490698326</MgO><NiO>0</NiO><CoO>0</CoO><CaO>1.36358362339721</CaO><Na2O>3.20394473749275</Na2O><K2O>4.85359485530896</K2O><P2O5>0</P2O5><H2O>4.80591710623913</H2O></initialize><calculationMode>equilibrate</calculationMode><title>MELTS Web Service called from Excel. [created 2014Apr23] (version 1.0.3)</title><sessionID></sessionID><constraints><setTP><initialT>1000</initialT><initialP>2000</initialP><fo2path>nno</fo2path><fo2Offset>0</fo2Offset></setTP></constraints><suppressPhase>amphibole</suppressPhase><suppressPhase>biotite</suppressPhase><suppressPhase>leucite</suppressPhase><fractionationMode>fractionateNone</fractionationMode></MELTSinput>
Request sent: 7/17/2024 9:58:13 AM
Current server state: 4
Request received: 7/17/2024 9:58:13 AM
Time to receive XML (s): 0.109375
Invalid XML received:<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
<title>404 Not Found</title>
<h1>Not Found</h1>
<p>The requested URL was not found on the server. If you entered the URL manually please check your spelling and try again.</p>

Time to load XML (s): 0
Calculation failed, trying again...
Request sent: 7/17/2024 9:58:13 AM
Current server state: 4
Request received: 7/17/2024 9:58:13 AM
Time to receive XML (s): 0.109375
Invalid XML received:<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
<title>404 Not Found</title>
<h1>Not Found</h1>
<p>The requested URL was not found on the server. If you entered the URL manually please check your spelling and try again.</p>

Time to load XML (s): 0
Two consecutive failures. Aborting...
#98
Website issues, and Miscellaneous / Installing Version 2.3.0
Last post by IsaiahSpring - June 20, 2024, 04:49:21 PM
Hi all,

I am having trouble installing the latest version of MELTS, 2.3.0. After downloading "alphamelts-app-2.3.0-macos-arm64.zip" from the Github and running the install.command I get this error:

Installation aborted or may be incomplete!
Use of uninitialized value $bin in concatenation (.) or string at ./install.command line 482.
Please log out and in and then and run the install script again.
Check the '' directory is in your path then choose 'n' to exit.
Press return to finish.

If anyone has any advice I would appreciate it!

Thanks
#99
Hi Paul,
The software you have developed is excellent and has greatly assisted me in understanding magmatic processes. However, I have encountered some issues during the operation that require your help.

I am a student who has recently been using alphaMELTS to simulate the mobility of the Sc (Scandium) element in layered mafic–ultramafic intrusions. That is, the process of Sc enrichment from a deep magma chamber (5kbar) to near the surface (1 kbar) and ultimately into different minerals (e.g., Cpx, Ilm, Amp).

I have already attempted simulation in the deep magma chamber under isobaric conditions, with an initial composition of Sc at 37.41 ppm. At the end of the simulation, only Cpx showed enrichment of Sc (26 ppm), and other minerals (e.g. Ilm, Amp) did not exhibit enrichment of Sc.

I also tried changing the partition coefficient of Sc in clinopyroxene (D=0.51 to 4), modifying it directly from the default_trace_data.txt file, but it did not work. The exported results show the partition coefficient fluctuating between 0.49xxxx and 0.51xxxx, which is not the value I set.

I would like to ask:
(1) Can the simulation of Sc enrichment in other minerals be performed? (e.g., Ilm, Amp) I saw a post on the forum mentioning that "the system cannot simulate Co and Ni because the partition coefficients of these elements in Ol/Cpx/Opx are unstable............" Is Sc subject to the same issue?
(2) If I want to simulate both major and trace elements, especially the enrichment trends of some key metallic elements, do you have any suggestions?
(3) There are some teaching videos on YouTube from a few years ago, which are basically for macOS and Linux OS. Since my computer operates on Windows, are there any teaching videos suitable for Windows users?


Best wishes,
Jimmy Young
#100
alphaMELTS for MATLAB/Python / v2.3.0 of alphaMELTS for MATLA...
Last post by Paula - June 02, 2024, 01:33:58 PM
alphaMELTS software has a new home on GitHub!

https://github.com/magmasource/alphaMELTS

v2.3.0 is now available for download. This release brings the suite of alphaMELTS software -- formerly alphaMELTS 2 (v2.2.1) and alphaMELTS for MATLAB/Python (v1.2.2) -- into one open-source repository. The same versioning is now applied to all interfaces, as the majority of edits are to the C library of MELTS functions that is common to all the software interfaces.

The binaries have been repackaged so that users need only download files for the platforms (MacOS, Windows, Linux) and alphaMELTS interface that they intend to use. This arrangement is transitional, while workflows are being developed to package the software for PyPI, Homebrew, CRAN, MATLAB File Exchange etc.

The Caltech-hosted GitList repository and the GitLab-hosted private repository are being preserved as placeholders for previous users of alphaMELTS for MATLAB/Python, but no new members will be added to the alphaMELTS group.