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1
Magma chamber processes / Re: Problem for changing environment settings file
« Last post by wzl123492 on August 18, 2021, 01:04:18 am »
I have ran the install.command, and checked these two problems to ensure they are OK. I think the problem is due to the system failure of my computer. I changed to use the computer of my colleague and the alphaMELTS runs smoothly.
Many thanks!

Zilong
2
Magma chamber processes / Re: Problem for changing environment settings file
« Last post by Paula on August 17, 2021, 12:59:35 pm »
The first one will fail unless there is an alphamelts_default_env.txt file where you are launching run_alphamelts.command from (e.g. the 'bin' folder if you are using the default double-click mode). The second one will fail because there is a space in the folder name. If you drag-and-drop the file onto the command line then the system should escape the space (probably by putting the whole path in quotes).

I would try going through the tutorial, either the regular 1.9 version or the double-click version and then see if you can get your example working:

https://magmasource.caltech.edu/forum/index.php/topic,131.0.html
https://magmasource.caltech.edu/forum/index.php/topic,752.0.html

Did you run install.command?

Paula
3
Magma chamber processes / Re: Problem for changing environment settings file
« Last post by wzl123492 on August 13, 2021, 10:00:17 pm »
Hello Paula,

Thanks for your reply! I have tried typing "-f alphamelts_default_env.txt" and "-f D:\Pictures\Saved Pictures\alphaMELTS_1-9\alphamelts_default_env.txt". Unfortunately, it is still not working, and the error message is the same as before.

Best regards,
Zilong
4
Magma chamber processes / Re: Problem for changing environment settings file
« Last post by Paula on August 13, 2021, 11:15:44 am »
Hi Zilong,

You need to type "-f pathtosettingsfile". Actually, you can type "-f " and then drag and drop the file from Windows Explorer.

I think there may be another problem because the error message is different to what I would have expected. But it depends a little on exactly how you start alphaMELTS. On a Mac from Terminal I get:

No command line switches specified! Please enter switches now
(or press return for default '-f alphamelts_default_env.txt').
-f
RUN_ALPHAMELTS.COMMAND ERROR: Cannot open settings_file "alphamelts_default_env.txt" (No such file or directory)
Run again (y or n)?

Anyway, trying adding the file name and let me know if it's still not working.

Thanks,
Paula
5
Magma chamber processes / Problem for changing environment settings file
« Last post by wzl123492 on August 11, 2021, 05:24:18 am »
Hi,

I am learning the online tutorials/manual and will use alphaMELTS to test the crystallization paths. I work on Windows 10 equipped with Strawberry Perl, and I have followed the install guidelines in the manual.
I opened the run_alphamelts.command through Perl, but when I then attempt to change the environment settings file using the -f command, I get the following error message:

No command line switches specified! Please enter switches now
(or press return for default '-f alphamelts_default_env.txt').
-f
ALPHAMELTS_DELTAT +10
ALPHAMELTS_MINT 0
ALPHAMELTS_MODE isentropic
ALPHAMELTS_MINP +1
ALPHAMELTS_MAXT +2000
ALPHAMELTS_VERSION pMELTS
ALPHAMELTS_MASSIN 0.001
ALPHAMELTS_MAXP +40000
ALPHAMELTS_DELTAP +1000
ALPHAMELTS_MINF 0.005

The system cannot find the file specified.
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)?


Could you please help me to make some guidances? I would appreciate it if you could do me the favour. Thanks!

Zilong
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We are pleased to announce that a training school, "Empirical and Ab Initio Thermodynamic Models of Minerals and Melts", will be held at the Agricultural University of Athens, Athens, Greece, from 1st - 5th November, 2021, and is sponsored by the European Geosciences Union.

The training school, aimed at early career scientists, is on thermodynamic modeling of natural silicate liquids and their equilibria with minerals and fluids, combining two quite different but complementary intellectual approaches — macroscopic and atomistic. The macroscopic approach will be based on the MELTS family of thermodynamic minimization algorithms, whereas the atomistic approach will use ab initio molecular dynamics based on the ABINIT density functional theory package.

Introductory sessions will include talks describing the models and software, with short demonstrations. Practical sessions will aim to give participants first-hand experience using a variety of software interfaces. Examples from the morning sessions will generally be expanded on in the afternoons, and some special calculations will highlight features that are only available (or only convenient) on particular platforms.
 
Registration form
Information can be accessed here (https://sites.google.com/view/2ndmeltsgr), and a link to the registration form here (https://forms.gle/6ehRgCyV8WCsCYFNA). Furthermore, please address any queries to the workshop organizer, Ioannis Baziotis (ibaziotis@aua.gr; ibaziotis@gmail.com).

Fees - Room and board
There is no registration fee, however, the participants will have to manage hotel accommodation for six nights - arrival on Sunday 31st Oct, 2021, and checking out on Saturday 6th Nov 2021. Participants will need to pay for the accommodation and then submit a claim to EGU. Upon the approval of the workshop, more details will be announced about the maximum amount to be reimbursed and the procedure for reimbursement by EGU.

Transportation
Attendees should make their own arrangements for travel to and from Athens. This will generally involve flying into Athens airport, transfer to the city center (~1 hour via "Metro" or "Proastiakos" train). Details for the transportation schedule can be found here (https://www.athensairporttaxi.com/metro/timetable-to-airport).

Contingencies
Agenda may be scaled back or cancelled in case of small enrollment (<20 participants). Our ability to hold the workshop in-person also depends on continued recovery from CoVID-19 in the European Union; a final decision will be made whether to move to a virtual format by October 1.

Field-trip
One-day post-conference optional tour of the Lavrion area is planned for the last day of the training school.

Subsistence
Refreshments will be provided during the workshop for all participants. Meals are not covered but there are plenty of inexpensive places to eat around workshop`s venue, so you should allow approximately 30 € per day for subsistence.
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On macOS Catalina and Big Sur, the first time you try to run alphaMELTS for MATLAB/Python it may fail due to new security settings. If you see the option like "Move to Trash" and "Cancel" then click Cancel. Go to System Preferences -> Security & Privacy->General tab and select "Allow anyway", and then try again. The second time you will be asked whether to Open or Move to Trash, so pick Open.

On Mac, if you have Xcode installed, and it is up to date, this will work for alphaMELTS for MATLAB. If you do not have Xcode you do not need to install it, and you probably don't want to as it is huge(~10 GB)! Instead install just the Command Line Tools, which are < 1 GB; you will get some warnings when you run alphaMELTS for MATLAB, but they are harmless and can be suppressed.
  • If you install Homebrew then the Command Line Tools will be installed automatically
  • Otherwise see: http://osxdaily.com/2014/02/12/install-command-line-tools-mac-os-x/
  • Copy and paste the following to Terminal to tell MATLAB that you agree to the Xcode license:
    Quote
    /usr/libexec/PlistBuddy -c 'Add :IDEXcodeVersionForAgreedToGMLicense string 10.0' ~/Library/Preferences/com.apple.dt.Xcode.plist
  • Finally when you open MATLAB type "mex -setup C" at the MATLAB command line (only needed once).
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alphaMELTS for MATLAB/Python / Notes for Mac users on Apple Silicon
« Last post by Paula on June 29, 2021, 01:19:04 am »
Apple Silicon running native M1 chip Python

If you install native arm64 Python via Miniforge or Homebrew then you will need to update to the latest alphaMELTS for MATLAB/Python (1.0.1 posted on June 29th, 2021) as that has a Universal libalphamelts.dylib file that should work on both native Apple Silicon and Intel. You need to install GSL with Homebrew.
  • Copy and paste the install command from: https://brew.sh
  • When it is done, copy and paste the commands that the install script tells you to
  • Type "brew install gsl"

Apple Silicon running Rosetta 2

If you are running another Python (Anaconda, miniconda, possibly others) or if you are running MATLAB then you will need to install the Intel version of Homebrew, as at the time of writing these still all run through Rosetta 2. This is what worked for me:
  • Type the following commands at the Terminal command line:
    Quote
    arch -x86_64 zsh
    cd /usr/local
    sudo mkdir Homebrew
    curl -L https://github.com/Homebrew/brew/tarball/master | sudo tar xz --strip 1 -C Homebrew
    sudo chown -R yourusername:wheel Homebrew
    sudo ln -sf Homebrew/opt opt
    Enter your normal user password if asked. Also, if you get a message that you need to change the ownership of the Homebrew directory at any point then just run the command it suggests.
  • Finally type "/usr/local/Homebrew/bin/brew install gsl"
See https://www.wisdomgeek.com/development/installing-intel-based-packages-using-homebrew-on-the-m1-mac/ for more information.
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As of June 27th, 2021 support for Apple Silicon has been added. The scripts have been updated to make installation smoother, add workarounds (e.g. for some university-administered systems), and new features added for processing and plotting output.

More details coming...
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    Work in progress

    Generic Mapping Tools



    It is primarily a mapping program but can also be used for x-y plots, histograms and much more. The nice thing about using GMT for plotting alphaMELTS output is is that there are standalone, MATLAB and Python versions, so you can easily generate exactly the same figures in all alphaMELTS versions with very few changes to the script. For that reason we are starting to include gmt scripts for plot generation in the alphaMELTS examples e.g. see the 'tutorial' folder included in alphaMELTS 2.1 for testing.

    • On Windows installing GMT also installs the MATLAB version (gmtmex).
    • On Mac/Linux the MATLAB version (gmtmex) must be installed separately, but the instructions on GitHub are a little out of date. What worked for me using a Homebrew installation of gmt was:
      Quote
      Run the gmt_prepmex.sh script which was located in /usr/local/Cellar/gmt/6.2.0/share/gmt/tools (obviously the version will change with time)
      Manually edit ~/.gmtversions ('~' means the user's home space, and '.' denotes a hidden file) so that it has one line /opt/gmt and another /usr/local/Cellar/gmt/6.2.0 (and no blank lines)
      Use gmtswitch to make the /opt/gmt version active
      Checkout the project with: git clone https://github.com/GenericMappingTools/gmtmex
      In the gmtmex directory, run autoconf then configure --enable-matlab
      Run make which builds the gmtmex.mexmaci64
      Copy gmtmex.mexmaci64 and gmt.m into the MELTS_Matlab/package folder
      [I missed out the bit about putting GMT_CUSTOM_LIBS=/opt/gmt/lib/gmt/plugins/supplements.so in gmt.conf as that directory was empty and it seems to work anyway...]
    • The Python version (pygmt) can be easily installed via conda or pip3

    I haven't explored the GMT community contributions yet to see if there are templates for common geochemical plots like TAS. The WebPlotDigitizer is useful for extracting coordinates for all sorts of plots and plotting software.

    MATLAB-based tools

    There are plenty of helpful packages that can be browsed on MathWork's File Exchange. Some that I have used either the current or predecessors of include:
    • A new ternary plot package - ternary_plots
    • A package for plotting TAS charts, which is quite old but simple enough that it works in newer MATLAB versions -plotTAS
    • Not geochemistry specific, but useful for producing publication-quality figures from MATLAB: export_fig

    Python-based tools

    The pyrolite package is a set of tools for making the most of geochemical data in Python. It is the work of Morgan Willliams and others. The pyrolite package actually has an Extension to work with alphaMELTS 1.X (url=https://pyrolite.readthedocs.io/en/master/ext/extensions.html?highlight=alphamelts#pyrolite-meltsutil]pyrolite-meltsutil[/url]), and the hope is to make it work directly with alphaMELTS for Python in future.

    Excel-based tools

    MELTS for Excel has a "Combine tbl" function on the Tools tab that can be used to import text files output by the Rhyolite-MELTS GUI, and automatically create tables and plots similar to those generated by full MELTS for Excel calculations. A pared-down version of MELTS_Excel contains only the 'Combine tbl' function, but can work on all versions of Excel, Windows or Mac is available on the alphaMELTS links page and is an excellent way to quickly browse the results of GUI calculations. easyMelts generates GUI-tyle output automatically, and alphaMELTS 2 and alphaMELTS for MATLAB/Python have options to generate GUI-style output files that can be imported with this tool.
    If you are using Excel then check out GeoPlotters (https://www.geoplotters.com/find-a-plot) for more information and downloadable Excel templates for many standard geochemical plots. It's an excellent resource.

    R-based tools

    alphaMELTS for Python can be run in R using the reticulate interface. The latest alphaMELTS for MATLAB/Python (v1.1) an R version of the 'tutorial' is included for testing, and we will gradually add R versions to the other examples. To run the tutorial example you will need to make sure you have the following (plus dependencies):
    Quote
    install.packages("reticulate")
    install.packages('ggplot2')
    install.packages('reshape')

    The GeoChemical Data ToolKIT, or in short GCDkit, is a system for handling and recalculation of whole-rock analyses from igneous rocks. It is written in R, and has been successfully used with alphaMELTS output (not by me personally yet). See Janoušek et al. 2006 for more details.[/list]
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