Set up¶

Mouse¶

A three-button mouse is also very convenient for using the ADF-GUI, and on a Mac you can use a Magic mouse for this purpose. To get three buttons (instead of the standard one or two), download and install one of the free utilities BetterTouchTool or MagicPrefs, and configure it to add a middle click.

Running Remotely¶

To use ADFjobs with remote machines, you need to set up ssh first. You should take care to configure things such that you do not need to type a password when you access your remote machine. To do this you need to:

• create keys,
• run an ssh agent,
• add your public key to the authorized_keys file on the remote machine.
• set up a ssh config file, if needed. This allows you to automatically set options, like the user name to use on the remote machine.

Thus, users (and ADFjobs) should be able to use ssh to log in to the remote machine without ever needing to enter a password.

If you are using OpenSSH (typically on Linux machine or MacOSX) you can make the communication with the remote machine much more efficient by setting the SCM_SSH_MULTIPLEXING environment variable to yes (in the GUI Preferences module).

ADFjobs does not store passwords, it always uses the ssh command to communicate with remote systems.

OpenGL3.2+, fallback mode¶

The GUI needs OpenGL 3.2 or later. Using it results in a much better performance, especially for bigger systems. Also some new graphical features depend on it. That OpenGL version may not be available when you are running on old hardware or OS, or when you are running remotely via X11 with GLX or some remote desktop solutions.

When the GUI detects a problem with the OpenGL version it will automatically activate a fallback option. That will normally just run, but it will be significantly slower, and of course the features depending on OpenGl 3.2 will be missing. We advise that you try to update your system to solve this issue. For remote use of a linux machine a solution could be the use of VirtualGL.

For more details please see the Installation manual.

Font issues¶

The GUI used unicode characters in many places. For example, the proper characters for Angstrom, degrees Celcius, and many more. You can see examples by starting ADFinput, selecting a Geometry Optimization, and then going to the details page (by clicking the ... button). There you should see a couple of Angstrom symbols if everything is working as intended.

On most machines this will just work out of the box. If not, the issue might be that the default font on the machine does not support such characters. Try installing a font line DejaVU Sans and Monospace DejaVu. On Centos you can do this (as root) with the command::

yum install dejavu-sans-fonts dejavu-sans-mono-fonts dejavu-serif-fonts


Defining proper queues in ADFjobs will making the GUI much easier. For example, you can run as easily on a remote compute cluster that you have access to as on your local desktop. ADFjobs will handle all the details like transferring input and output files, and you can even monitor the progress of running jobs as if they were running on your local machine.

So you should take some time to set up the queues correctly. It is possible that there are predefined queues on your remote machine. Then you can configure ADFjobs to automatically use those queues.You can find a description of the ADFjobs queues and how to set them up later in this manual.

MOPAC¶

MOPAC (Molecular Orbital PACkage) is a semi-empirical quantum chemistry program based on Dewar and Thiel’s NDDO approximation. It is available from OpenMOPAC. The documentation for MOPAC is also available on that site.

If you wish to use a MOPAC version different from the one included with the ADF distribution, you can do this by setting the SCM_MOPAC environment variable, either in your shell startup script or via the SCM → Preferences command:

• do not set SCM_MOPAC when you want to run the MOPAC included with the ADF package, in most situations this is the easiest solution

• set SCM_MOPAC to the complete path to the Mopac executable

• set SCM_MOPAC it to some command if want to run MOPAC on a different machine, the command must pass the arguments and standard input, and should start the mopac.scm script on the other machine (located in $ADFHOME/bin) For example: to run the MOPAC included with the ADF distribution on the machine called mopac.domain.com, use the command: export SCM_MOPAC="ssh mopac.domain.com adfhome/bin/mopac.scm"  Quantum ESPRESSO¶ Quantum ESPRESSO is an open source package that can perform plane wave SCF calculations, among other things. See www.quantum-espresso.org for details. Quantum ESPRESSO is not included in the ADF distribution. The GUI works with the standard Quantum ESPRESSO distribution (version 6.2), no changes have been made. The easiest way to install it is just to open ADFinput and go to the Quantum ESPRESSO section. Then it will be installed in $ADFBIN and $ADFHOME/atomicdata for the pseudo potentials, or in "$HOME/Library/Application Support/SCM" (on a mac). The binaries will be in a folder qe6.0, and the pseudo potentials will be in a folder upf_files.

To force installation of Quantum ESPRESSO (for example to re-install it to make sure you have a clean version), use the Help → (Re)Install Quantum ESPRESSO command as available in most of the GUI modules. Another way is to run the $ADFBIN/get_QuantumEspresso.sh shell script. Alternatively, the precompiled Quantum ESPRESSO binaries are available from the SCM web site. The search path for Quantum ESPRESSO by the GUI and by the run scripts made by the GUI is: 1. $QEBIN (and $PSEUDO_DIR for the pseudo potentials) 2. "$HOME/Libaray/Applicaton Support/SCM"
3. $ADFBIN (and $ADFHOME/atomicdata for the pseudo potentials)
4. "/Libaray/Applicaton Support/SCM"

On a mac you can make the Quantum ESPRESSO installation available to all users by moving it from the \$HOME/Library/Application Support/SCM folder to the global /Library/Application Support/SCM folder. Obviously all users need proper permissions to access these files.