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 AMSjobs 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 AMSjobs) 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).

AMSjobs 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.


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 Celsius, and many more. You
can see examples by starting AMSinput, 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


AMSjobs Queues
==============

Defining proper queues in AMSjobs 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. AMSjobs 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 AMSjobs to automatically use those queues. You
can find a description of the AMSjobs queues and how to set them up
later in this manual.


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 main AMS distribution, but
can easily be installed through the AMSpackages package manager.

The easiest way to install it is just to open AMSinput and go to the
Quantum ESPRESSO section. This will use AMSpackages to check if QE has
already been installed, and if not it will install it using
AMSpackages. An environment variable "SCM_PKG_QE" will be set pointing
to the install location.

To force installation of Quantum ESPRESSO (for example to re-install
it to make sure you have a clean version), use the  **SCM → Packages**
command, and use the AMSpackages module to remove and reinstall
Quantum ESPRESSO.

From the command line (e.g. on a remote machine), you can install the
Quantum ESPRESSO package using the following command:

   "$AMSBIN"/amspackages install qe
