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1
Windows / X410 version of rhyolite-MELTS display is tiny on high-resolution screen
« Last post by Paula on September 21, 2018, 02:50:51 pm »
X410 is pretty new software. The ability to run (older) apps scaled like this is amongst the feature requests. So it's possible that this workaround will not be needed with future versions of X410. Check out Running X410 on HiDPI Screens and other Howto entries on the Choung Networks site for more current details.

If you followed the instructions for enabling the WSL and installing the Rhyolite-MELTS GUI (new for 2018) on a laptop with a high-resolution screen, such as the Surface, you may find that the rhyoliteMELTS display looks tiny. There is a workaround for this behavior that should work for most X server software here.

However, if your X server is X410, then this 'bug' is actually a 'feature' ;) The idea is that Linux software that can deal with scaling for a high resolution screen should be allowed to do so (see Running X410 on HiDPI Screens). There is no way to make the rhyolite-MELTS GUI run in a high-resolution mode - the interface is too old - but there is a way to run rhyolite-MELTS with a user-defined scaling (actually it runs xterm, which is then used to open rhyolite-MELTS). This alternative workaround does not require admin access but only works for ubuntu 18.04 LTS... or at least it is difficult enough in ubuntu 16.04 LTS, that it is easier to install ubuntu 18.04 and 16.04 side by side than to attempt it!

This workaround does not require admin access (other than the one-off access you needed to set up the WSL in the first place) and uses the same formatting conventions as the WSL setup post i.e. things should type at the command line are in bold in quote boxes; names you should substitute are in italics and comments are preceded by ellipsis (...). Note that by 'command line', we mean the Ubuntu bash shell that opens when you click the 'ubuntu' program and not the Windows Command Prompt (cmd.exe). If it all seems like too much trouble, then there is always the option to use Windows' Ease of Access tools as a workaround; scroll down to the bottom for this alternative.

Use run_scaled to adjust the rhyolite-MELTS windows size

This solution uses Alexander Kauer's run_scaled script. If you didn't set up the 'bin' folder and path at the time then consult the "If you did not install alphaMELTS" section of the enabling the WSL etc. post for details on how to do this first. Otherwise, open ubuntu 18.04 LTS, which may be just called 'ubuntu' on your system:
Quote
cd bin
... if this gives an error, make sure the 'bin' folder and path are set up
wget raw.githubusercontent.com/kaueraal/run_scaled/master/run_scaled
... this downloads the run_scaled script as plain text because going through a Windows-based browser causes problems with line-endings etc.
cat run_scaled

We also need to install some libraries that are not included in the default ubuntu installation:
Quote
sudo apt install xterm xvfb xpra python-numpy python-opencv
... enter your Linux password when prompted and choose 'y' to install the necessary packages (there will be quite a lot of them)

Now navigate to where you want to start rhyolite-MELTS. Make sure X410 is running (else you will get an error like "Can't open display :0"). When you use run_scaled you will likely get several warnings, but most of them can be ignored.
Quote
run_scaled
... if you don't give any other input you will get the usage information for run_scaled
... note that the '--sleep' option can be used if you are getting 'InitException' errors on start up
run_scaled xterm
... or
run_scaled --sleep=5 xterm

If you are lucky, this will open a second terminal program; the text will look a little fuzzy because of the scaling. Increase the sleep value if needed (it's not that your machine is very slow, it's just that the WSL wasn't really intended for running windowed apps).
Quote
Melts-rhyolite
... or './Melts-rhyolite-public' if you didn't set up the path before
... answer the normal questions to select rhyolite-MELTS 1.0.2, 1.1.0, 1.2.0, or pMELTS

The default scaling factor is 2, which works well on my set up, but you can experiment with other values, including non-integer values, in the original terminal. Close the rhyolite-MELTS and xterm windows before typing 'run_scaled --scale=scale_factor' (with or w/o a sleep value).

Using Magnifier (does not require any additional setup)

Open Settings (click either the Start button in the bottom LH corner or the Notification icon bottom RH corner; then click the cog icon). Type 'Magnifier settings' in the search box. Reduce the Zoom level increments to 25%. You can experiment with the Magnification zoom level but something in the range 150 - 200% is likely to work. You probably want to leave the 'Start Magnifier...' boxes unchecked and put the Magnifier mode in 'Full Screen'. Turn the Magnifier on, scroll down and right-click the Magnifier icon and choose 'Pin to taskbar'. Now if you turn off the Magnifier (by clicking the 'X' in the top RH corner of the Magnifier popup), you can easily turn it on again by selecting it from the taskbar; the cog on the Magnifier popup is a shortcut to the Settings page.

Paula
2
VirtualBox / Re: Welcome to VM alphaMELTS 1.9
« Last post by Paula on September 20, 2018, 04:29:31 pm »
Note the link to Meltsout is missing in the links_folder in the currently posted VM alphaMELTS version. It will be in the next version. In the meantime, you can fix this by opening LXTerminal. Type:

Quote
cd bin
ln -sf ../MELTS/Meltsout-II/meltsout .

You need only do this once. 'ln' stands for 'link'; '-s' is for 'symbolic', so if you delete the link you do not delete the original file (much like Windows shortcuts); '-f' is for 'force', which makes no difference unless you move the 'Meltsout-II' location and need to remake the link.
3
VirtualBox / Notes for users of VM alphaMELTS 1.5 - 1.8
« Last post by Paula on September 20, 2018, 03:03:02 pm »
alphaMELTS 1.9 introduced a completely new version of the virtual machine, based on Lubuntu 16.04 instead of 14.04. (Ubuntu 16.04 is the last LTS release to properly support 32-bit systems, which is why we chose this over Lubuntu 18.04.) The desktop setup has been tweaked, adding a double-clickable launcher for alphaMELTS, as well as for rhyolite-MELTS. VM alphaMELTS 1.9 also contains a much updated preview of alphaMELTS 2 that is not generally available elsewhere, and a copy of the VMD program (the 32-bit version does not have the full VMD feature set but can be used for basic visualization).

As such, we strongly recommend that you update to the newer version. But if that is not possible for some reason then here is a quick summary of the old version for the bits that have changed:

Once you start the virtual machine you are logged in as the user 'melts' with a password that is the former name of alphaMELTS, as detailed here. You will need the password for this and some other system maintenance e.g. to check for Lubuntu security updates. To update VirtualBox Guest Additions:
  • Start the MELTS Lubuntu machine.
  • Select 'Devices'->'Insert Guest Additions CD image...' and click OK to open it in File Manager.
  • Open a Terminal and navigate to the CD location using 'cd'. You can use Right-click to Copy and Paste the location from the File Manager to the command line. Alternatively, you can type 'cd /media/melts/VBOX' (or 'cd /media/VBOX', if appropriate) and then press the tab key before return. It should autocomplete the location.
  • Type 'sudo ./VBoxLinuxAdditions.run' (or 'sudo ./VBoxLinux' and then the tab key) and press the return key.
  • Enter the password and then wait while it removes the old version and installs the new one.
The default desktop has icons for programs that will be useful for running alphaMELTS and rhyolite-MELTS placed next the start menu. From left to right, they are:
  • LXTerminal - needed to start rhyolite-MELTS and for running alphaMELTS in command line mode
  • Leafpad - a text editor with Windows-like short cuts (e.g. ctrl-C, ctrl-V for copy and paste respectively)
  • Gnumeric - a simple spreadsheet program that is nice as it opens space delimited text files automatically
  • File Manager - a file manager that opens in the melts user's home space
  • Web browser - Firefox
  • Customize tool - to change look and feel of the Desktop e.g. font sizes
  • File Manager - PCManFM that opens in the melts user's home space
There is a link on the Desktop to keep the Lubuntu operating system up to date. Also on the Desktop is a link to the Shared folder, which should point to a folder on the host operating system (see the VM alphaMELTS installation instructions for more details). If you open LXTerminal you can get to the Shared folder files by typing 'cd Desktop/Shared'.

There is a folder called alphaMELTS that contains links to the scripts that can be double-clicked, though getting this to work is finicky (the desktop launcher in VM alphaMELTS 1.9 is a little easier). There may be a Desktop icon for rhyolite-MELTS that you can double-click and it will open rhyolite-MELTS with the LXTerminal so that you can choose between rhyolite-MELTS 1.0.2, 1.1.0, 1.2.0, and pMELTS. If it can be double-clicked, it will have an icon with a stylized AFM plot with an 'M' in the middle. If it has a cog icon, then you should not double-click it; instead open LXTerminal and type 'Melts-rhyolite'.

As of November 30th, 2017, VM alphaMELTS also contains Jon Snow's Meltsout program.

Paula
4
Windows / Updated: enabling the WSL and installing the Rhyolite-MELTS GUI (new for 2018)
« Last post by Paula on September 19, 2018, 03:34:13 pm »
For 64-bit Windows 10 with the Fall Creators update (version 1709; released October 17th, 2017), it is possible to enable the 'Windows Subsystem for Linux' (WSL) and use the latest rhyolite-MELTS version linked on the alphaMELTS links page. This a more detailed version of the instructions on the alphaMELTS links page. Things that you should type at the command line are in bold in quote boxes; names you should substitute are in italics and comments are preceded by ellipsis (...). Note that by 'command line', we mean the Ubuntu bash shell that opens when you click the 'ubuntu' program and not the Windows Command Prompt (cmd.exe).

There are now two versions of Ubuntu available for the WSL. If you search for 'ubuntu' in the Microsoft Store you will see three versions: 'Ubuntu' and 'Ubuntu 18.04 LTS' are currently the same, though are offered as separate installations (click 'More' under the software description for a fuller explanation). 'Ubuntu 16.04 LTS' is older and was simply called 'ubuntu' when the WSL became available in 2017. For most purposes Ubuntu / Ubuntu 18.04 LTS should be fine. If you intend to use X410 as the X server on a high resolution screen you should definitely use 18.04 (see the section on choosing and installing an X server). If you are thinking of trying out MELTS for MATLAB while it is in the testing phase, then you might want to install Ubuntu 16.04 instead (contact me about trying out MELTS for MATLAB and we can discuss this). You can always install both 16.04 and 18.04 side-by-side if you have space - both of them together will still be much smaller than the VirtualBox VM alphaMELTS alternative.

Enable the WSL and install ubuntu
  • Open Settings (click either the Start button in the bottom LH corner or the Notification icon in the bottom RH corner; then click the cog icon). Type 'Windows features' in the search box and then select 'Turn Windows features on or off'. Scroll down and check the box beside 'Windows Subsystem for Linux'; click OK and reboot. If 'Windows Subsystem for Linux' has '(beta)' next to it then you do not have the Fall Creators update installed.
  • Open the Windows Store and search for 'ubuntu'. Choose 'Ubuntu', or another version, and select 'Get'. If you have any installation issues then consult this slightly out of date installation guide for troubleshooting (predates Fall Creators update).
  • Select 'Launch'. You will be prompted to enter a username and password for Linux. The username is case sensitive; it may, or may not, be the same as your Windows username but you should avoid spaces or special characters in it. The password should be different to your Windows password; you will need to enter it when installing or updating software at the Linux command line.
  • We recommend you select 'Pin to Start' and/or 'Pin to taskbar' for the ubuntu executable. If you want to do 'Pin to Start' at a later date, just open the Windows Store and search for 'ubuntu' again.
Set up the ubuntu command line
  • Open ubuntu, if it is not already open. Right-click on the ubuntu icon in the upper left-hand corner and choose Properties. Make sure that 'QuickEdit Mode' is checked. Now you can select text, including commands in these instructions (using control-c) and then paste them to the command line by right-clicking the mouse or trackpad in the ubuntu window.
  • Note that you can use ubuntu commands and Linux software to modify your regular files on Windows. Generally, you should not use Windows programs to modify the ubuntu files (by which we mean the ubuntu system files and the files in your ubuntu home space). So, it's a good idea to keep all your working files in your usual Windows folders and set up links so that you can access them from the command line:
    Quote
    ln -sf /mnt/c/Users/your_windows_username/Downloads .
    ... the space between 'Downloads' and '.' is required
    ... if you copy and paste the command then use the left arrow and delete to replace 'your_windows_username' with the actual name of the folder that your Windows files are stored in
    ... if the 'your_windows_username' folder has spaces in its name you need to put a '\' before each one e.g:
    ln -sf /mnt/c/Users/your\ windows\ username/Downloads .
    You can now switch to the folder by typing 'cd Downloads'. If you don't want the link to be called 'Downloads' then replace '.' with your choice of link name e.g. 'MyFiles'. 'ln' stands for 'link'; '-s' is for 'symbolic', so if you delete the link you do not delete the original file (much like Windows shortcuts); '-f' is for 'force', which makes no difference at this point but should you change your mind about where you want the 'MyFiles' link to point to, then is required to overwrite the original.
  • Substitute 'Downloads' and repeat the above for any other folders that you would like to be able to access from the command line while running rhyolite-MELTS, such as 'Documents' or 'Desktop'.
Install alphaMELTS (optional)

If you want to install alphaMELTS, then if you do that now it will do the next steps for you. Download the alphamelts_wsl_version.zip file. You should be able to unzip it on Windows. Put the extracted folder in 'Downloads' (or your choice of folder, as long as you have set up a link to it in ubuntu). Open ubuntu, if it is not already open. Navigate to the folder where alphamelts_wsl_version.zip is using 'cd' (which stands for 'change directory'). E.g:
Quote
cd Downloads
cd alphamelts_

... if you press the 'tab' key at this point it should complete the folder name
... depending how you extracted the files, you may to repeat the previous command to descend into the folder where the .command scripts are
./install.command
Choose the default settings offered by install.command (press 'enter' to each folder suggestion, and then 'y' when it asks whether to continue with the installation). This means it will make a 'bin' folder for you (to put links in), set the Path to include the 'bin' folder, and set up the DISPLAY variable that rhyolite-MELTS will need. Close ubuntu (type 'exit' or use the X in the top right hand corner) and open it again.

If you did not install alphaMELTS

This step make a 'bin' folder, which is short for 'binary' and is a folder where we will put a link (shortcut) to rhyolite-MELTS. It will set the Path to include the 'bin' folder,  so that you can run rhyolite-MELTS from anywhere on the system. It also sets up the DISPLAY variable that rhyolite-MELTS will need. Open ubuntu, if it is not already open:
Quote
cd
... this just ensures that you are in your ubuntu home directory
mkdir bin
... which means make a directory called 'bin' (where 'directory' is what is called 'folder' on Windows)
wget magmasource.caltech.edu/gitlist/alphaMELTS.git/raw/master/profile
... this downloads a settings file because going through a Windows-based browser causes problems with line-endings etc.
cat profile
This last command just prints the file we just downloaded, so we can check that it downloaded OK before using it. The output should look like this:
Quote
# ~/.profile: executed by the command interpreter for login shells.
# This file is not read by bash(1), if ~/.bash_profile or ~/.bash_login
# exists.

# set PATH so it includes user's private bin if it exists
if [ -d "$HOME/bin" ] ; then
    PATH="$HOME/bin:$PATH"
    export PATH
fi

# For the Rhyolite-MELTS graphical user interface on the Windows Subsystem for Linux with Xming
if [[ $(uname -r) =~ Microsoft ]] ; then
   export DISPLAY=:0
fi

# For the Rhyolite-MELTS graphical user interface on Macs, using the 10.8+ or 10.12+ executable:
# If you get "Segmentation fault: 11" (10.8+) or "Illegal instruction: 4" (10.12+)
# then include the following and try the 10.8+ executable.
if [[ $(uname) =~ Darwin ]] ; then
   export DYLD_LIBRARY_PATH=/opt/X11/lib/flat_namespace:$DYLD_LIBRARY_PATH
fi
If it does then type you can continue:
Quote
mv profile .profile
... where there is a space before the '.' but not after; a file beginning with with '.' is a hidden file in Linux
exit
... this closes ubuntu; when you next open it the settings file will be read and acted upon

Download and set up rhyolite-MELTS and some helper software
  • Download the 64-bit Ubuntu 16.04 LTS rhyolite-MELTS/pMELTS executable or the 64-bit Ubuntu 18.04 LTS rhyolite-MELTS/pMELTS executable, whichever matches your ubuntu installation, from the alphaMELTS links page. You should be able to unzip it on Windows. Put the extracted file in 'Downloads' (or your choice of folder, as long as you have set up a link to it in ubuntu). Open ubuntu, if it is not already open:
    Quote
    cd ~/bin
    ... '~' is shorthand for your home space on ubuntu
    ln -sf ../Downloads/Melts-rhyolite-public Melts-rhyolite
    ... see the 'Set up the ubuntu command line' section for an explanation of the 'ln' command; note that '..' means up one directory level
    Since we added the 'bin' folder to the Path you will be able to open rhyolite-MELTS from any folder by typing 'Melts-rhyolite'. (Without these settings you would need to navigate to the folder containing Melts-rhyolite-public and type './Melts-rhyolite-public', where '.' means the current directory.)
  • We need to install two libraries that are not included in the default ubuntu installation, as Microsoft intended the WSL to be command line only. Open ubuntu, if it is not already open:
    Quote
    sudo apt install libxft2 libxmu6
    ... enter your Linux password when prompted and choose 'y' to install the necessary packages
    'apt' is the ubuntu package manager; you will also use it for updating ubuntu when needed. If you get a message about updates being available then type the following:
    Quote
    sudo apt update
    ... enter your password
    sudo apt upgrade
    sudo apt full-upgrade

    ... choose 'y' as appropriate

Choose and install an X server

You will need to install an X server. We have tested Xming and X410, both of which are paid apps. There are free alternatives but we have not tried them out (and do not intend to). Xming requires a small donation and also admin access to allow apps to be installed from outside the Microsoft Store (although if your machine is set up to use campus-licensed software this may already have been done). X410 is installed via the Microsoft Store, so does not need administrator access, and works out of the box; at full price it is more expensive than Xming, though it is currently on sale. Xming set up and configuration is slightly more involved than X410, but still not complicated.
  • Note that if you have a high-resolution screen then you will likely have to do some extra configuration to get the rhyolite-MELTS display to render at a usable scale. The procedures for fixing "rhyolite-MELTS display is tiny on high-resolution screen" for Xming and for X410 are quite different and may influence your choice of which X server to install. So if you have a HiDPI screen, make sure to read those posts before continuing.
  • The Xming donation (approx. $15 US) is made via PayPal, but you do not need to have a PayPal account. You will receive a Donor Password via email, though bear in mind that the developer is located in the UK so there may be a few hours delay, due to the time difference. Once you have a Donor Password, go to Releases. Download and run the Xming-64 installer. Next download and install the Xming-fonts installer; make sure to install to the same location (should be 'C:\Program Files\Xming' by default).
  • To install X410 you will need a Microsoft account. There is a free trial option or you can buy it if you have a payment option set up. Open the Windows Store and search for 'X410'.
Start Xming or X410 by double-clicking. Test rhyolite-MELTS by typing 'Melts-rhyolite' at the command line and 'n' to select version 1.0.2. If the display is very small then follow the guidelines in this post for Xming or this post for X410. You will not need to repeat all these steps next time. Just open the ubuntu program, navigate to the folder where your input (.melts) files are, and type 'Melts-rhyolite'.

Any problems, please let me know,
Paula
5
General usage / Re: alphaMELTS 2 version of tutorial: 'Quick start using MELTS'
« Last post by Paula on September 18, 2018, 12:53:27 pm »
If you downloaded VM alphaMELTS 1.9 between August 30th and September 17th, 2018, you will probably find that this tutorial does not run properly. Corrected 64-bit and 32-bit virtual machines have been uploaded today (18th).

The problem is mainly due to a corrupted Morb.melts file. It can be fixed by copying the example from the alphaMELTS 1.9 installation:

Quote
cd MELTS/tutorial
cp ../linux_alphamelts_1-9/examples/Morb.melts .
... you only need to do this once ...
run-alphamelts.command
... and continue as described above ...

In addition, a minor bug - since fixed - means that the calculation overshoots the 1000 oC minimum temperature. If this is a problem and you do not want to download the whole virtual machine again, please contact me and I'll send you the updated executable.

Cheers,
Paula
6
General usage / [EX] alphaMELTS 2 version of tutorial: 'Quick start using MELTS'
« Last post by Paula on September 16, 2018, 05:48:21 pm »
This topic will show you how to work through one page of the MELTS tutorial, using the new version of the alphaMELTS program:

Testing MELTS installation using the sample input file - Try this first

The page is part of the 'Getting Started: Testing and Examples' section of the MELTS manual, written by Mark Ghiorso for the original graphical-user-interface (GUI) version. The idea of this topic is to show the similarities and differences between his GUI and our text-menu versions of MELTS and how to reproduce rhyolite-MELTS GUI MELTS calculations in alphaMELTS 2. It should be useful for newcomers to MELTS / alphaMELTS users, or for alphaMELTS users who want to use the rhyolite-MELTS and mixed H2O-CO2 fluid models, and for those who are familiar with the the rhyolite-MELTS GUI version. This post is for the version of alphaMELTS 2 (beta) included with VM alphaMELTS 1.9, but will be updated as alphaMELTS 2 approaches public release.

The alphaMELTS 2 beta is installed, alongside alphaMELTS 1.9 and the rhyolite-MELTS GUI, in the VM alphaMELTS software that can be downloaded from the alphaMELTS download site. The description in this particular example is for running within the virtual machine (i.e. on Linux) but should apply to other operating systems once alphaMELTS 2 is publicly available (the screen output here is actually from a run on Mac).

This example uses an input file that has been modified from the Morb.melts file used in the original tutorial. The modifications simply bring it up to date with the latest GUI versions of MELTS and do not affect software results. Early versions of the MELTS software used a 'Mode: Fractionation' line in the input file to select fractional crystallization, whereas in later versions this is replaced by 'Mode: Fractionate Solids'. Also some phases were suppressed in the original tutorial because the solid solution models were still being developed / tested. None of the phases are stable for the run conditions of the tutorial example, so suppressing these phases has no effect. However, the 'Suppress: ' lines can cause read errors as the names of some phases have changed slightly since (see here).

A version of the modified Morb.melts, with the correct line endings for Linux and Mac, is included in the VM alphaMELTS installation (in a folder called 'tutorial', within the 'MELTS' folder in the melts user's homespace). Note that the version of Morb.melts available on the MAGMA Source server is the same except that it has Windows line endings but the morb.melts version linked on the Mac OS X download site differs slightly in Cr2O3 content and in the P-T conditions.

In VM alphaMELTS there is a double-clickable alphaMELTS icon on the Desktop, but it is for alphaMELTS 1.9. Instead, click the LXTerminal icon that is located next to the start menu. Navigate to the tutorial folder by typing 'cd MELTS/tutorial'. alphaMELTS 2 is started by typing 'run-alphamelts.command' (note the dash, '-'; 'run_alphamelts.command' with an underscore, '_',  is for alphaMELTS 1.X). The script will ask whether you would like to add some command line switches. Unlike alphaMELTS 1.X, the settings_file is optional in alphaMELTS 2. For now we won't use one, so just press return for the default settings.

Quote
Mac:tutorial psmith$ run-alphamelts.command
No command line switches specified! Please enter switches now (or press return for defaults).

The alphamelts program will detect that there are no settings and print the same set of questions as the GUI for choosing the thermodynamic model. There is more explanation of the various MELTS versions in the MELTS decision tree. However, rhyolite-MELTS 1.0.2 should give identical results to the original MELTS model for the bulk composition used here. So, choose 'n' and press enter.

Quote
Checking for updates...

ALPHAMELTS_VERSION not set!

---> 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).

*** alphaMELTS 2.0 (beta Aug 27 2018 19:48:27) -- rhyolite-MELTS P-T path w/ or w/o liquid ***

... etc ...

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
 6. Set H2O (ppm) or aH2O
 7. Impose initial entropy, enthalpy or volume
-1. Turn off menu display for options 1-18
 0. QUIT

Several menu items are missing in the beta version of alphaMELTS 2. Some of these will be available soon; others will take a little longer. Choose option 1 to read in 'Morb.melts'. Note that you only need type the first letter(s) of Morb.melts, and then press the 'tab' button to complete the name:

Quote
Your choice: 1
MELTS filename: Morb.melts
Input file read. Waiting for command or user input.

In alphaMELTS 1.X, some lines of Morb.melts were ignored so only those lines that were used were echoed back. alphaMELTS 2 uses all lines in Morb.melts, so it does not print them unless there is a problem. Although the front-end program looks very different to the one in the original tutorial, the settings for the underlying MELTS algorithm are now exactly the same as described in the 'Four things have been accomplished:' list there. You can verify that the initial pressure and temperature are set correctly with option 2:

Quote
Your choice: 2
Starting Temp = 1200.000000 C
 Type new temperature (or 0 to keep old one): 0
Starting Pressure = 500.000000 bars
 Type new start pressure (or 0 to keep old one): 0

The phase diagram mode of alphaMELTS is not yet hooked up to the menu in alphaMELTS. However, a simple 'Find Liquidus' option has been built into the next step of the calculation. So go straight to option 3, the 'Single (batch) calculation' and choose the option to use the liquidus temperature:

Quote
Your choice: 3
Starting guess to use:
0. Norm-calculated subsolidus assemblage
1. Superliqidus starting guess at current temperature.
2. Superliqidus starting guess at liquidus temperature.
Choose: 2
<> Found the liquidus at T = 1220.31 (C).
...Checking saturation state of potential solids.
...Projecting equality constraints.
...Minimizing the thermodynamic potential.
...Checking saturation state of potential solids.
<> Stable liquid solid assemblage achieved.
Initial alphaMELTS calculation at: P 500.000000 (bars), T 1220.312500 (C)
liquid:    SiO2 TiO2 Al2O3 Fe2O3 Cr2O3  FeO  MnO  MgO  NiO  CoO   CaO Na2O  K2O P2O5  H2O
100.350 g 48.51 1.01 17.58  0.89  0.03 7.56 0.00 9.07 0.00 0.00 12.41 2.64 0.03 0.08 0.20
Activity of H2O = N/A  Melt fraction = 1

Note, this uses the 'Find Liquidus' algorithm from the GUI. It is only really reliable if used before any other phases are added to the assemblage, which is why is has been incorporated into the initial calculation step. This 'Find Liquidus' routine may give incorrect results if used later in the run, and is also unsuitable for water saturated systems. alphaMELTS has a phase diagram mode that can bracket F=1.0 (or another melt fraction contour) and includes a 'Find wet liquidus' option. This will be added to alphaMELTS 2 soon and will provide alternative ways to do the initial 'Find Liquidus' calculation.

Now choose option 4 to continue the calculation from the current conditions, incrementing the temperature by 3 oC until the temperature hits the Final Temperature (1000 oC). At each stage crystallized solids will be removed:

Quote
Your choice: 4
...Checking saturation state of potential solids.
...Projecting equality constraints.
...Minimizing the thermodynamic potential.
...Checking saturation state of potential solids.
<> Stable liquid solid assemblage achieved.
Initial alphaMELTS calculation at: P 500.000000 (bars), T 1220.312500 (C)
liquid:    SiO2 TiO2 Al2O3 Fe2O3 Cr2O3  FeO  MnO  MgO  NiO  CoO   CaO Na2O  K2O P2O5  H2O
100.350 g 48.51 1.01 17.58  0.89  0.03 7.56 0.00 9.07 0.00 0.00 12.41 2.64 0.03 0.08 0.20
Activity of H2O = N/A  Melt fraction = 1

... etc ...

...Checking saturation state of potential solids.
...Adding the solid phase apatite to the assemblage.
...Projecting equality constraints.
...Minimizing the thermodynamic potential.
...Checking saturation state of potential solids.
<> Stable liquid solid assemblage achieved.
alphaMELTS at: P 500.000000 (bars), T 1001.312500 (C)
liquid:    SiO2 TiO2 Al2O3 Fe2O3 Cr2O3   FeO  MnO  MgO  NiO  CoO  CaO Na2O  K2O P2O5  H2O
12.5185 g 58.75 0.53  8.91  1.50  0.00 14.11 0.00 0.72 0.00 0.00 5.08 7.98 0.20 0.62 1.60
Activity of H2O = N/A  Melt fraction = 0.981517
olivine: 0.059366 g, composition (Ca0.01Mg0.25Fe''0.75Mn0.00Co0.00Ni0.00)2SiO4
clinopyroxene: 0.025007 g, composition cpx Na0.03Ca0.81Fe''0.55Mg0.50Fe'''0.05Ti0.02Al0.16Si1.89O6
feldspar: 0.127634 g, composition K0.00Na0.59Ca0.41Al1.41Si2.59O8
spinel: 0.018452 g, composition Fe''1.57Mg0.10Fe'''0.55Al0.10Cr0.00Ti0.68O4
apatite: 0 g, composition Ca5(PO4)3OH
Minimum Temperature reached
Successful return from alphamelts...

Choose:

Once it has finished executing, choose option 0 to quit (as opposed to shutting the terminal window). You should find 7 new text files have been generated, which are described in the alphaMELTS 1.X documentation. Note that alphaMELTS 2 has another optional line for the melts_file that can take one of four values:

  • 'Output: txt' - alphaMELTS-style output (see the alphaMELTS documentation file)
  • 'Output: tbl' - GUI-style output, including melts.out and .tbl files that can be used with Excel-based tools for tabulation and plotting
  • 'Output: both' - alphaMELTS and GUI output
  • 'Output: none' - no text output

By default the output is alphaMELTS-style only. The output will differ from the original slightly from the as GUI Liquid table gives thermodynamic quantities, such as entropy, for the liquid whereas the main output table in alphaMELTS, 'System_main_tbl.txt', gives system values instead (including a small amount of solids prior to fractionation). For GUI-style output, there will also be slight discrepancies between the newly generated melts.out file and the original output file. The most striking differences are the addition of Mn, Co and Ni to the olivine solid solution model, though none of these components are in the Morb.melts bulk composition, and splitting of the pyroxene phase into separate clinopyroxene and orthopyroxene phases (see here). Either way, the phase compositions are essentially the same though and differences in the phase masses are a few hundredths of a gram, at most.

If there are any problems or feedback about this post then please let me know.

Cheers!
Paula
7
Copy and paste this into an editor that will use the correct line-endings. For example, on most systems you can type 'nano Morb.melts' in the Terminal program, and paste by right-clicking the mouse.

Title: Allan et al. 1989 (see Ghiorso 1997)
Initial Composition: SiO2 48.68
Initial Composition: TiO2 1.01
Initial Composition: Al2O3 17.64
Initial Composition: Fe2O3 0.89
Initial Composition: Cr2O3 0.03
Initial Composition: FeO 7.59
Initial Composition: MgO 9.10
Initial Composition: CaO 12.45
Initial Composition: Na2O 2.65
Initial Composition: K2O 0.03
Initial Composition: P2O5 0.08
Initial Composition: H2O 0.20
Initial Temperature: 1200.00
Final Temperature: 1000.00
Increment Temperature: 3.00
Initial Pressure: 500.00
Final Pressure: 500.00
Increment Pressure: 0.00
dp/dt: 0.00
log fo2 Path: None
Mode: Fractionate Solids

Make sure there are no blank lines before you save.
8
Great! You can expect my registration!
Cheers,
Sarah
9
Hi Sarah,

The workshop would be for researchers experienced in one or more MELTS interfaces and algorithms, as well as those new to all things MELTS. I should have made that more clear - will make sure to do so in the next circular, and I'll put up more details on a website sometime in the next few weeks.

For alphaMELTS, we will be concentrating on alphaMELTS 2, which includes rhyolite-MELTS and is more user friendly than older versions. There are other tools for calculation and visualization that may probably be new to you, and that will integrate well into a class situation.

Best wishes,
Paula
10
Hi Paula,

I have been an alphaMELTS (MELTS and pMELTS) user for a long time, but I'm interested in learning about other interfaces and algorithms (including rhyolite-MELTS).
I'm also thinking about integrating alphaMELTS in an advanced petrology class in my department and looking for tips and advice to do this.
Is this workshop adapted for this purpose or is it mostly dedicated for researchers with no experience with alphaMELTS?
Best,

Sarah

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