Predominance diagrams

• 
  As-Fe-S-H2O predominance diagram, including adsorbed As, calculated with the 'grid' approach (101 x 101 grid).
• 
  The same as above but calculated with the 'hunt and track' approach.
• 
  U-C-H2O predominance diagram.

Speciation plots

• 
  Vanadium speciation vs pH (oxidising).
• 
  Aluminium solubility vs pH.

Reaction path calculations

• 
  An example of a redox ladder calculated using REACTION.

Fitting

• 
  Fitting data for As(V) sorbed by HFO according to the DLM.

Installation notes

Installing PhreePlot for the first time

Use the Download links from the PhreePlot homepage or one of the menus. There are two x64 versions of PhreePlot available for Windows: an 'admin' version and a 'noadmin' version. The 'admin' version is preferred if you have Administrator rights. The 'noadmin' version is necessary if you do not have administrator rights (privileges), or cannot use the UAC (User Account Control) to temporarily elevate your rights. You can check your rights by running

>net user <yourusername>

from a console and looking under 'Local Group Memberships'. The 'admin' version installs the executables to the protected 'Program Files' directory and will mean that they are available to all users of the machine. If you do not have administrator rights, it is best not to attempt to install the admin version as you will be requested with a UAC prompt for the credentials of a user with admin rights, and if accepted, the installation will by default go to their username rather than yours. Then you will not have access to it. So if you choose this option, you MUST use the Wizard to change the destination directory to a directory to which you have access. Otherwise install with the 'noadmin' version instead.

You will be asked to accept the License agreement (read here) and will not be able to go any further without doing so. PhreePlot is essentially free to use. After you accept the License Agreement, you will normally be asked for the Destination Location, i.e. where to store the settings, documentation and demo files. Rather than accepting the default, it is good to enter your own destination. For subsequent installations, you will not necessarily be asked for a new destination and the installer will automatically update your earlier installation. If you do not want this, delete the old version first, or use the 'noadmin' version which always asks for a Destination. A sub-directory, 'PhreePlot', will automatically be made for the installation when using the defaults but this can be overridden with the Destination Wizard although it makes sense to keep 'PhreePlot' as your lowest level directory. Do not make the Destination Location your 'Program Files' directory.

Three sub-directories will be created below your Destination folder: system, doc and demo. The 'noadmin' version makes a fourth \bin directory for the executables. C:\users\<username>\AppData\Roaming\PhreePlot is the default directory for the 'admin' option and ..\AppData\Local\PhreePlot for the 'noadmin' version. If the 'admin' option is run by a user without admin privileges, <username> will be the username of the user granting elevated privileges. The AppData directory may be hidden - if so, use the folder Properties to unhide it, or choose another directory as your destination. As mentioned above, it is probably best to choose a Destination folder that suits your own file structure. Admin privileges are not required to actually run PhreePlot just to install it.

Environment variables

PhreePlot locates its files via two environment variables, PHREEPLOT and PHREEPLOT_PATH, and these must be set. This is normally done automatically during installation. The PHREEPLOT environment variable must point to the application directory, i.e. the destination directory chosen during installation. The PHREEPLOT_PATH variable should point to the location of the executables. All these settings are deleted when you uninstall PhreePlot. The .ppi -> pp.exe file association should also be set during installation.

Checking the installation

It is essential to close and then reopen any console (cmd.exe) or file explorers after installation to ensure that the updated Environment (and registry) settings are inherited by these apps. If in doubt, re-logon or reboot after installation. To test the installation, either (i) Close down Windows File Explorer if open, then reopen it and navigate to the directory that you chose as your Destination directory. Double click on test.bat, or (ii) Open a new console (cmd.exe), navigate to the directory that you chose as your Destination directory. Then

>test.bat

These should produce a predominance diagram for Fe as a .ps file and as .pdf file if you have Ghostscript installed properly. A longer test is to run all the demo files by running demo.bat from the \demo folder. This may take up to 30 mins to complete. For more detailed checking, open a command window (cmd.exe) and run

>set ph

to inspect the settings. You should see PHREEPLOT and PHREEPLOT_PATH with valid values. If either of these has not been set properly, enter 'Edit the system environment variables' in the run box and then choose Advanced|Environment variables, and edit appropriately. Alternatively, use Control Panel and search for 'Edit environment variables'. Once set, re-log in or open a new console to apply. You can also check whether the PATH has been set with

>set PATH

which will show you the current PATH setting and should include the location of the PhreePlot executable.

>pp

should show the PhreePlot header. Other checks include:

>where pp

should show you where the pp.exe file has been installed, and

>dir %PHREEPLOT%

should show the contents of the PhreePlot directory.

PhreePlot does not have a GUI. It is run either from a console or from File Explorer or similar making use of the .ppi file association that should have been set up.

Installing a more up-to-date copy of PhreePlot

Repeat the installation above. The 'admin' version will default to the same user Application Data directory and version sub-directory as before and will overwrite all of the previously-installed files. If you want to change the installation directory or want to keep the installation directory 'clean', first delete the previous version of PhreePlot with the uninsxxx.exe uninstaller found in the original application directory. Then run the installer. This uninstallation will not delete any files that have been added or generated since the initial installation. The 'noadmin' version always gives you the opportunity of choosing a new directory.

If simply updating with no change in folders, there is no need to close and re-open other applications.

Installing Ghostscript and GSview

PhreePlot produces native Postscript (ps) files. Ghostscript enables PhreePlot to make conversions to other formats such as pdf, png, jpg and eps. As of 2018, PhreePlot comes with Ghostscript optionally pre-installed but you can install and use your own copy separately.

GSview (Ghostgum) is a separate viewer, also based on Ghostscript, that is useful. Follow the links on the PhreePlot homepage if you want to download this program.

If installed, it is useful to associate ps files with GSview or similar. If you are using the internal version of Ghostscript, GSview will initially report that it cannot find Ghostscript. So change the two paths required in GSview, e.g. : Options|Advanced Configure|Ghostscript DLL|C:\Program Files\PhreePlot\gsdll64.dll and the Ghostscript Include Path|C:\Program Files\PhreePlot\.

It is possible to use either Win32 or x64 versions of both Ghostscript and GSview with PhreePlot providing that the paths and settings have been set appropriately. The x64 version is recommended if you have a 64-bit PC. Starting with version 9.53.0, Ghostscript changed its version numbering system such that GSview will no longer work with this or later versions. If you want to use GSview, stay with earlier versions as given in the download links on the home page.

The pdfMaker setting in pp.set is used to locate the Ghostscript executable (gswinxxc.exe) and libraries (gsdllxx.dll) used in the conversions (xx = 32 or 64). If the path given by pdfMaker has not been set, then the internal version will be used if present. Currently, the pp.set file contains 'pdf TRUE' so a pdf file will always be produced when a plot is produced. If you would prefer the default image type to be png, say, set 'png TRUE' and 'pdf FALSE' in \system\pp.set.

Missing dll's

PhreePlot uses various libraries that are either incorporated into the pp.exe file, already available in your setup or have to be installed. These include some of the redistributable libraries from Microsoft Visual Studio and Intel's oneAPI compiler suite.

If your system reports missing dll's, download the missingdlls file. Extract the missing file(s) to the same directory as pp.exe and retry. If this does not work, please report.

Learning to use PHREEQC and PhreePlot

It is best to locate a demo example that is closest to your needs by browsing in the \demo folder and choosing one. Also learn how to use the PhreePlot pdf Guide. Once you have found a demo example of interest, copy the .ppi and associated files into a working directory and experiment with changes to see how it works. The Notepad++ editor is an excellent editor for editing these files and for viewing the text output. Look at the .log file for some details, and increase the debug setting to 1, 2 or 3 for more detailed output. Use the 'all t' setting to see the PHREEQC output. Investigate the PHREEQC output in detail to make sure that it is doing what you expect it to be doing. Use iPhreeqc to develop new models using the linked PHREEQC documentation where necessary. Thoroughly check the model by varying the sensitive parameters over the domain of interest to make sure that the model is well-behaved over the whole domain. Once that is all working smoothly, paste the code into a PhreePlot .ppi file and add the necessary tags to get the required looping, fitting and plotting. Needless to say, there is a lot to learn!

Uninstalling PhreePlot

You can either do this through the Apps Settings (Control Panel in older versions of Windows) or by going to the PhreePlot root directory and executing the uninstaller, uninsxxx.exe, where xxx is the version number. Even though administrator privileges are not required for the 'noadmin' installation, if you do install with administrator privileges, you will also have to run the uninstaller, uninsxxx.exe, with the same privileges. This will remove all the files and settings added during installation but will not remove any that have been added or generated after that. If you are not sure where the installation is located, try 'echo %PHREEPLOT%' in a console window.

Other operating systems

There are also binaries available for other operating systems, notably Linux and Mac (Darwin). See the separate installation notes for them.

Being kept informed of updates

Enable the checkForUpdate setting in pp.set. This will check the PhreePlot server for the latest version at user-defined intervals. See the Guide.

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