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.

For more information, consult your ssh documentation or one of the many guides on the internet.

ADFjobs Queues

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.

MOPAC is included with the ADF distribution. However, it needs to be enabled in your license file. If it is not enabled, please contact SCM to get more information. Note that MOPAC is free for academic users. The MOPAC that is included with the ADF distribution is the standard MOPAC from OpenMOPAC, except it uses the license checking system by SCM. It is updated regularly.

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 6.0), 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.