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1
Hi,

It's Shaw 1972 (AJS November 1972 vol. 272 no. 9 870-893)
DOI: 10.2475/ajs.272.9.870

You're right it is not cited in Ghiorso and Sack 1995, though it has been included in the software for many years.

Paula
2
Hi,

I am currently using rhyolite-MELTS 1.2.0 and I noticed  that it can give the viscosity of the liquid phase in the result. However, I cannot find any information about what viscosity model it is based on in the papers about MELTS. Could you please tell me what the viscosity model is or where I can find it? Thanks a lot!
3
Version 1.8 of alphaMELTS was posted in November (originally November 15th, but the virtual machines were updated slightly on the 30th).

Version 1.8 fixes several minor bugs. It tweaks the output slightly, particularly for fO2, and offers a new option to buffer to an absolute fO2 value in log units. Accumulated melt compositions, calculated in "cubicquad2", can be now interpolated in F or Phi. The "Supplemental Calculator" type function (i.e. writing a "Thermodynamic output file" before equilibration) has been expanded and can now handle fO2 calculations. For more details about this and previous releases, please see the *README* link on the alphaMELTS download site.

Version 1.8 is the first version of to specifically target Windows 10's Windows Subsystem for Linux (WSL) and includes a package to easily enable tab-completion in alphaMELTS. It is possible to run the rhyolite-MELTS graphical user interface (GUI) this way too. VM (virtual machine) alphaMELTS is still based on Lubuntu 14.04 LTS (32-bit and 64-bit versions), but now include Jon Snow's Meltsout program pre-installed and a double-clickable version of the rhyolite-MELTS GUI; usually, double-clicking the GUI is not recommended.

In other news, the upgrade to the new server has been completed so that all binary movies now work, and no longer require installation of Flash. (The only exception is the spinel volume calculator, which is still being migrated to the newer PhP version.) The MAGMA and alphaMELTS links pages have been thoroughly updated, and tools for processing output from the rhyolite-MELTS GUI  newly posted. Several new forum posts should cover most of the frequently asked questions that we receive via email or Facebook.

Cheers,
Paula
4
Combine tbl

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. This "Combine tbl" function is available offline, and is an excellent way to quickly browse the results of GUI calculations (particularly those involving assimilation or fractionation, which cannot be modeled in MELTS_Excel). When alphaMELTS 2 is released properly, there will be an option to write GUI-style output files that can be imported with this tool.

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. You need to be logged into your forum account to see the link. After downloading, just double-click to extract the Excel file from the .zip archive. Minor differences between the original 'Combine tbl' and this one are documented in the file.

Thanks to Guil Gualda for allowing me to hack the MELTS_Excel Visual Basic code.

Meltsout

Another useful tool for parsing the 'melts.out' file from the rhyolite-MELTS GUI is the Meltsout program. A 64-bit Linux executable, built on Ubuntu 16.04 LTS, is included in the GitList repository. This executable can be used on the Windows Subsystem for Linux, which does not have gcc installed by default. On other Linux systems and MacOS, Meltsout can be simply built by copying and pasting the command given in the README.TXT file:
Quote
gcc *.c -o meltsout
Use the ZIP or TAR button to download all the files, including the executable. As of November 30th, 2017, the VirtualBox Linux installation available on the alphaMELTS download page comes with Meltsout pre-loaded.

Thanks to jesnow for providing the source code, README, and 32-bit Linux executable (built on Gentoo).

Paula
5
Note that this fix only works if you start the rhyolite-MELTS executable from the system's Terminal program (the one located in /Applications) and not if you open it from Xquartz's Terminal program (xterm). The /Applications/Terminal.app program is also convenient, as you can use command-c and command-v to copy and paste etc. However, you can set it up to work from xterm, if you prefer.

When it opens, xterm does not read the '~/.profile' file, but it does read '~/.bashrc' (if it exists). Traditionally '.profile' was used for environment settings, such as setting the user's PATH variable, and '.bashrc' is used for terminal settings, such as aliases. But there is nothing to stop you putting the required line in '.bashrc':
Quote
export DYLD_LIBRARY_PATH=/opt/X11/lib/flat_namespace:$DYLD_LIBRARY_PATH

Alternatively, you can type the following, after opening xterm, and before starting rhyolite-MELTS:
Quote
source ~/.profile

Paula
6
Windows / [FAQ] Troubleshooting MELTS_Excel e.g. 'Server returned no results, giving up!'
« Last post by Paula on December 01, 2017, 12:22:27 pm »
Caveat: I have not used MELTS for Excel very much, but Paul Asimow and I have demoed it at a couple of workshops and helped a few people to get it running at Caltech. I do not have access to the server (although I am somewhat familiar with the MELTS code it uses), and have only explored the Visual Basic code to the extent necessary to get the "Combine tbl" tool to work on MacOS. Any inaccuracies are mine. -Paula

We often get messages like this, either by email or via Facebook:
Quote
Excel gives the error "Server returned no results, giving up!"

The error message that MELTS for Excel gives is not very helpful, as it does not distinguish between a connectivity problem and the calculation failing for some reason. It would also be easier for us to debug if we were given a bit more information by the user e.g. have they successfully run MELTS_Excel previously, or has it never worked? What kind of calculation was he/she doing and on what kind of composition? Here are some ideas for troubleshooting MELTS_Excel, and for making it easier for us to help you if it still doesn't work.

First, make sure that you have the latest version of the MELTS_Excel file; April 5th, 2017 at the time of writing. This version does work in Excel 2016. It also implements the mixed H2O-CO2 fluid model (i.e. rhyolite-MELTS 1.0.2, 1.1.0 and 1.2.0 are available), as well as the pMELTS model. When you download the MELTS_Excel file make sure to keep a copy with the default composition and settings (Early Bishop Tuff, v1.0.2 etc.).

In Excel's default documents folder, probably 'Documents', there will be a file called MELTS_Excel.log. If you experience problems, check the contents of this file (if you double-click it should open in Notepad). If it is not obvious what the problem is then open the original Early Bishop Tuff version of MELTS_Excel and try "Find Wet Liquidus". If that fails, then go to the sections on Internet connection / Server problems. Note that it's a good idea to close MELTS_Excel.log between individual calculations.

Calculation problems

If the EBT calculation succeeds, but your own one doesn't, then it might help to work through the MELTS_Excel version of the Quick start using MELTS tutorial. The version of MELTS_Excel used there is older e.g. it is missing the "Find Wet Liquidus" and rhyolite-MELTS/pMELTS model choices. But none of these changes affect the simple tutorial example. Some things to think about in your own calculations:
  • If you use "Find Liquidus", "Find Wet Liquidus" or "Equilibrate" on the "Input" tab, the P-T conditions are not automatically transferred to the Sequences tab. You need to re-enter the starting conditions at the top. If you have used the rhyolite-MELTS graphical user interface (or alphaMELTS) and are used to starting where you just left off then it is pretty easy to accidentally ask MELTS_Excel to perform a huge jump in T or P, which will probably fail.
  • Make sure you are using the correct model, rhyolite-MELTS 1.0.2, 1.1.0 and 1.2.0, or pMELTS. You are given some guidance on the Model tab. Also bear in mind that the solidus and liquidus may be different for the same composition in different models. MELTS for Excel is not geared towards subsolidus calculations.
  • Many of the usual tricks for getting MELTS calculations to work apply to the Excel version. For example, you may try varying the T and/or P increments (Delta T and Delta P) if a Sequence seems to be failing.
  • The incorporation of some minor components in solid phases in MELTS is oversimplified. Cr2O3, which has a strong effect on spinel stability, is the most notable example. There can also be cases when it is better to set the mass of K2O, MnO, NiO or P2O5 to zero (and consider them as trace elements instead). Note also that, of the oxides mentioned here, only Cr2O3 and K2O are calibrated in the pMELTS model.
  • Depending on the composition and conditions, fO2-buffered calculations are sometimes problematic. So try repeating a calculation without the "fO2 Constrained" box checked. If fO2 is not constrained then you need to input the FeO and Fe2O3.
  • If you get "Run-time error '13': Type mismatch." and/or the temperature shoots up to > 5000 oC then you probably selected "Find Liquidus" for a water-saturated composition. In MELTS 'solids' is used to mean 'not silicate liquid', which includes any water or fluid phase. "Find Wet Liquidus" accounts for this and finds the temperature above which the system is liquid, plus vapour.
  • Calculations are relatively low temperatures, involving phases that have ordering (e.g. spinel, pyroxenes, felspathoids) can be slower and there is a possibility that the calculation will time out (see next section).
Server problems

The MELTS for Excel server is located in Seattle, WA, and administered by Mark Ghiorso. He and I are joint admins on the MELTS Facebook page.
  • If MELTS_Excel.log contains "502 Bad Gateway", "503 Service Unavailable" or another HTML error, then this is a server-end problem. More than likely, it is just very busy and if you try again in a few minutes it will be fine. If the problem persists you could try posting on the Facebook page to see if others are also having (unusual) problems and/or sending a message to Mark Ghiorso (either via the FB page, or by email), as the server may need rebooting.
  • If MELTS_Excel.log contains "Time limit reached" then Excel timed out before the server was able to return any results. That is probably an internet connectivity problem, though it may be down to the particular calculation (see previous section). If may also be down to server load, in which case trying again when the server is likely to be less busy may fix the issue.
  • When classes are in session, the MELTS for Excel server is likely to be busy during the daytime for US time zones (14:00 GMT - 24:00 GMT, say). To judge from the messages we get, there is also a spike in usage when a large conference is approaching, particularly the AGU Fall Meeting (as now!)
Connection problems

Obviously we're not able to offer support for internet connection problems, but one or more of these suggestions may help:
  • Slow wireless connections are probably the commonest causes of MELTS_Excel problems. If you can switch to a faster wireless, or wired connection then that should be better.
  • Depending on the network, if you can use a connection that does not require a USB or Thunderbolt ethernet adapter (e.g. try a desktop computer) then this may help...
  • ... although some university networks have a firewall that interferes with running MELTS_Excel, in which case try it elsewhere.
  • If you are able to set up your computer using a static IP, rather than DHCP, then that may make a difference.
  • If you know what you're doing, you may consider changing the DNS settings on your computer and/or router.
  • If MELTS_Excel usually works, but it timing out on a particular day then simply rebooting your computer and/or router may fix it.
If none of this works, note that 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. This "Combine tbl" function is available offline. So for classes or workshops, where connectivity on the day is critical, it may be worth having previously generated output from the GUI available as a backup.

If you experience errors other than "Server returned no results, giving up!" or "Run-time error '13': Type mismatch." do let us know. Also, if you have suggestions of your own for getting MELTS for Excel up and running please do add a comment below.

Thanks!
Paula
7
Melting processes / Re: Creating phase diagrams on rhyolite-MELTS
« Last post by Paula on December 01, 2017, 12:00:49 pm »
A link to a version of MELTS for Excel's 'Combine tbl' function that works in all versions of Excel on Windows and Mac (to my knowledge) is available on the alphaMELTS links page. You'll need to log in with your forum account to see the link, and double-click after downloading to extract the Excel file from the .zip archive.

Paula
8
Linux / How to install rhyolite-MELTS on Linux
« Last post by Paula on November 25, 2017, 10:25:38 am »
For Linux systems, the latest rhyolite-MELTS version is linked on the Linux Download site. Installation is very similar to what is described on the Mac OS X rhyolite-MELTS page, except that can skip the first few instructions as X11 is installed by default on Linux. Brief instructions are also given on the alphaMELTS links page and are expanded on a little here.

There are 32-bit and 64-bit files built on Ubuntu 14.04 and RHEL 6.7. They have been tested for forwards and backwards compatibility on multiple versions on Linux. In general you can use choose the one that most closely matches your operating system. Two exceptions are:
  • For older Ubuntu systems (pre-12.10), use the RedHat versions.
  • For Fedora systems, use the Ubuntu versions.
The software is packaged as .zip files, which can usually be decompressed by double-clicking; right-click and choose 'Properties', or similar, to check that the permissions are set to executable. Alternatively, open a terminal program and the use the 'unzip' and 'chmod' command line tools. First, navigate to the folder where you downloaded the software (usually ~/Downloads, where '~' is shorthand for your Linux home space). Type:
Quote
unzip rhyolite-MELTS-
... and then press the tab key, which should complete the file name, followed by return
chmod 755 Melts-rhyolite-public
... this makes sure the file is executable; if there is no output message then it has run correctly
./Melts-rhyolite-public
... this should start the program and give you a choice of rhyolite-MELTS version 1.0.2, 1.1.0 or 1.2.0, or pMELTS
... once you have chosen it should build the graphical user interface

You can move the executable to a more convenient place. You would then open the terminal program and navigate to the new location.

Note that it is generally not a good idea to double the click the executable, as described in the No choices given for rhyolite-MELTS / pMELTS graphical user interface for Linux (and the corresponding Where are my rhyolite-MELTS output files? for MacOS). An easy workaround that allows you to start rhyolite-MELTS from any file directory is described there.

Any problems, just let us know.

Thanks,
Paula
9
Windows / Rhyolite-MELTS (or other software) display is tiny on high-resolution screen
« Last post by Paula on November 25, 2017, 09:17:05 am »
If you followed the instructions for Enabling the Windows Subsystem for Linux and installing the Rhyolite-MELTS GUI on a laptop with a high-resolution screen, such as the Surface, you may find that the rhyoliteMELTS display looks tiny. This is due to Xming incorrectly reporting to Windows that it is able to deal with the high resolution. The problem is not restricted to Xming. Other software, such as Adobe Illustrator, Photoshop, CorelDraw and Dreamweaver have shown similar behavior.

A workaround involves adding a text file (the 'manifest') and telling Windows to handle the application scaling for the high resolution screen. The method outlined here borrows from write-ups by scrambler, Luis, and Dan Antonielli. This version uses the command line (cmd.exe) so that you can copy and paste the commands. The external manifest hack requires admin access. If you do not have admin access, or are not comfortable with editting the registry, you can use Windows' Ease of Access tools as a workaround; scroll down to the bottom for this alternative.

External Manifest file (requires admin access)

First we need to open cmd.exe as an Administrator. You can find 'Command Prompt' it in the Start Menu, under 'Windows System'. Right-click 'Command Prompt', then 'More', then 'Run as administrator'. Or right-click the Start button, then 'Run', then type 'cmd.exe'; then right-click the Command Prompt icon in the task bar, then right-click 'Command Prompt' and 'Run as administrator'. You may need to select 'Yes' and/or enter your Windows password.

The Command Prompt will open in the C:\Windows\system32 directory. First navigate to a folder in your home space, somewhere to put a backup file that you will be able to find. For example, 'cd C:\Users\your_username\folder_name'. Next right-click where is says 'Administrator: Command Prompt' at the top of the window and choose 'Properties'. Make sure 'Enable Ctrl key shortcuts' is checked. You can now copy (control-C) and paste (control-V) commands from here to the command line.

Quote
reg export HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\SideBySide sidebyside.reg /y

... this backs up the relevant Registry key
... in the unlikely event that something does not work just double-click the 'sidebyside.reg' file to restore the previous state

reg add HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\SideBySide /v PreferExternalManifest /t REG_DWORD /d 0x1

... this tells Windows to look in an external file (if available) to see whether a given application can handle the high-resolution screen

Download the manifest.txt file from Dan Antonielli's page. The next instructions assume that your browser saves files in 'Downloads' and that you installed Xming in the default location, but you can adjust accordingly:
Quote
cd C:\Users\your_username\Downloads
copy manifest.txt "C:\Program Files\Xming\Xming.exe.manifest"

You can use the same file trick for other software by replacing 'Program Files' with 'Programs Files (x86)', if appropriate, '\Xming\' with the installation folder, and 'Xming.exe.manifest' with the executable name+'.manifest'. For example:

Photoshopphotoshop.exe.manifest
Illustratorillustrator.exe.manifest
Dreamweaverdreamweaver.exe.manifest
CorelDrawdrawhome.exe.manifest

Using Magnifier (does not require admin access)

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
10
Linux / [FAQ] No choices given for rhyolite-MELTS / pMELTS graphical user interface
« Last post by Paula on November 25, 2017, 09:14:18 am »
We occasionally get messages that go something like this:
Quote
I want to use the mixed H2O-CO2 fluid model and the MELTS decision tree says I should use v1.20 ... or ... I want to select the pMELTS model. However, when I open the rhyolite-MELTS program that I downloaded it goes straight to v1.02.

The problem is probably that the user double-clicked the Melts-rhyolite-public executable (or a link to it) to start the program. On Mac, if the Melts-rhyolite-public file is double-clicked it will open in the Terminal program, and the graphical user interface is not started until the use chooses between rhyolite-MELTS 1.0.2, 1.1.0, 1.2.0, and pMELTS (though on Mac there may be other issues with double-clicking). On some combinations of Linux and desktop environment, even if the user select 'Open in Terminal', the terminal program closes without waiting for the user's input. So the GUI is started with the default model, i.e. rhyolite-MELTS 1.0.2. A better approach is to open the terminal program first. Navigate to the folder where the Melts-rhyolite-public is located, using 'cd path_to_MELTS' (cd = 'change directory'). Then type './Melts-rhyolite-public'.

Whilst it is an improvement on double-clicking the Melts-rhyolite-public executable, always running rhyolite-MELTS in the same place can also be problematic. You need to explicitly move all the .tbl files out of the folder between rhyolite-MELTS runs. Otherwise, if the phase assemblage differs between run 1 and run 2, melts.out and all the .tbl files for phases in run 2 will be overwritten but any other .tbl files from run 1 will still be hanging around. If you use the Combine tbl function from MELTS for Excel you will get a mixture of results from both runs.

Better is to make sure Melts-rhyolite-public, or a link to it, is in your Path. That way can make a new folder for the current run's output (e.g. melts_output_folder) and open rhyolite-MELTS in it the (empty) folder via Terminal. When you are finished the run, melts.out and all the .tbl files should be in melts_output_folder. On the VM alphaMELTS platform, we have already set this up for you. So you can simply type 'Melts-rhyolite' at the terminal command line (note there is no './' before 'Melts-rhyolite').

Otherwise, if you have installed alphaMELTS, and used the default settings then the '~bin' folder should be in your path. You can check by typing:
Quote
echo $PATH
You can either put the Melts-rhyolite-public executable in the 'bin' folder or you can put it elsewhere and make a link to it using 'ln' (type 'man ln' or check out the similar Mac-based post if you are unfamiliar with this command). If you have installed alphaMELTS, but you did not use the default location for the links_folder (i.e. '~/bin') then substitute links_folder for 'bin'.

Alternatively, you may have something like the following in your .profile file by default (type 'cat ~/.profile' to check):
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
If that is the case, then you can simply make a bin directory in your home space ('mkdir ~/bin'). Otherwise, you can edit .profile, .bash_profile, or .bashrc (or the appropriate file if bash is not your default shell). Set the path to point to your choice of directory and make a link there to Melts-rhyolite-public.

Alternative approach - make a desktop file that can be double-clicked

On the latest VM alphaMELTS virtual machines (downloaded November 20th, 2017 or later) we provide a 'Melts-rhyolite' icon that can be double-clicked. You can tell that 'Melts-rhyolite' can be double-clicked if its icon picture has an M in the middle of a stylized AFM plot (as opposed to a cog). Rhyolite-MELTS is opened in Lubuntu's terminal program, LXterminal, and the user is given the usual choice between rhyolite-MELTS 1.0.2, 1.1.0, 1.2.0, and pMELTS before the GUI starts.

The Melts-rhyolite.desktop file is a text file, that could easily be adapted to work on other systems:
Quote
[Desktop Entry]
Version=1.2.0
Name=Melts-rhyolite
Comment=Choose between rhyolite-MELTS 1.0.2, 1.1.0, 1.2.0, and pMELTS
Exec=lxterminal -e Melts-rhyolite
Icon=/home/melts/MELTS/rhyoliteMelts/meltsicon.png
Terminal=false
Type=Application
Categories=Utility;Application;
'Melts-rhyolite' is the link to the Melts-rhyolite-public executable and is in the user's Path in the VM alphaMELTS installation. 'Melts-rhyolite' could be replaced by the full path to the executable ('/home/melts/MELTS/rhyoliteMelts/Melts-rhyolite-public' in this case). Note, however, that if you use rhyolite-MELTS .desktop file like this, the program will always open in the melts your home space. So, as noted above, some care will be needed to make sure that results from different runs are not mixed together.

Hope this helps!
Paula


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