Introduction
I.1 Welcome
Welcome to the lab component of the Chemistry 575 Advanced Electronic
Structure Theory. The lecture component of this course deals
with the theories behind much of the computational work
applied today to chemical problems that explicitly treats electrons.
The focus of the lab course is quite different. In the lab,
we will experience what it is like to run actual calculations
while dealing with problems of chemical interest. You will hopefully
gain some idea of what can be done with electronic structure
calculations and how you might go about doing it.
I.2 What You Should Know Already
The calculations required for this lab will be carried out
on a computer running the Linux operating system. It is not necessary
to know anything about Linux to be able to complete these labs nor
will you need to learn anything about Linux in the course of the
labs. It is assumed that you are familiar with common desktop
environments that utilize windows, menus, buttons and web browsers.
The kind of thing that you have in a computer running the Windows or
Macintosh operating systems.
Very little in the way of mathematical analysis will be required for
the course. Arithmatic and being able to calculate ex are about
as far as it will go. You should know what derivatives and integrals
are and how they relate to slopes, curvatures and volumes but you will
not be asked to perform any calculations with differentiation
or integration.
You are expected to know some chemistry. Many of the mini-projects
that will form part of the course will look at theoretical
approaches to chemical problems. As far as theoretical chemistry goes,
you should know a little bit about atomic and molecular orbitals
and about electron configurations and how you can determine the
symmetry of a state given its electron configuration.
I.3 The Lab
This lab will be quite different to your standard chemistry lab. Firstly,
it won't take place in a chemistry lab at all but in a computer lab.
No safety glasses required. Leave the lab coat at home. Have
your hair unbound if you want. Wear whatever shoes feel comfortable.
You should be able to do everything required for the lab on a computer.
The lab work will involve running a computational chemistry
program and interpreting the output of that program.
The actual hard work of the electronic structure calculations
will not be done by the computers in the lab or your own computer but by a big
computer cluster called Terminus that is located at the University of Calgary.
You cannot sit in front of Terminus itself so you will use another
computer as a terminal
connecting to Terminus to send the details of the calculations that you want to
run and to receive
the results of your work.
I.3.1 Connecting to Terminus
This process depends on what kind of computer you are using to connect to Terminus. You first
need to open a window with a command line in it called an xterminal. How this is achieved varies.
Once you have an xterminal the process proceeds pretty similarly irrespective of what kind of computer you are
sitting in front of.
In the computer lab we have computers running Windows XP. In order to connect to the Linux operated Terminus you need to open the Cygwin/X Server by doubleclicking the icon with the same name located on your Desktop. If you don't have this icon on the Desktop, press Start --> Programs --> Cygwin/X and look for the Cygwin/X Server line somewhere on the bottom of the Cygwin/X menu.
To connect to Terminus type
ssh -X terminus.ucalgary.ca -l username
but replace "username" with whatever username you have on Terminus. After pressing
return you will be asked to give your password. Upon entering that, you will be
on Terminus.
I.3.2 Connecting to Terminus from Off-Campus
Terminus is not behind the chemistry firewall and can be contacted directly from off-campus. You can connect to it using the command written above, as long as you have a computer with a xterminal.
These days, the majority of research described as "theoretical/quantum/computational chemistry"
makes use of a computer program to perform the mathematical manipulations
required to produce the desired numbers. Many such programs exist. In this
course we will make use of the Amsterdam Density Functional Theory (ADF) program (http://www.scm.com).
Although we will consider only ADF directly, most of what will be learnt
can be applied to other major programs.
ADF is actually a suite of programs. The ADF program itself is the main workhorse
that solves all the equations and does all the computational gruntwork. It can
perform many different types of calculations and will carry out most
of the tasks that we are interested in. Other programs in the suite
do other tasks. For example, the program BAND is used for studying periodic
systems like surfaces and solids.
We will not consider these other programs here.
The programs that we will actually be working with directly are not
ADF itself but a set of graphical user interface (GUI) programs. The
ADF program gets its input from a text file. These text files require quite
a bit of knowledge to work with directly and are usually the
province of experienced users. The GUIs,
on the other hand, will seem very familiar to anyone who has used
a computer operating in a windows-type environment. The GUIs
should be reasonably intuitive and easy to use.
The GUIs do not do the actual calculations
but they can be used to set up calculations, send the calculations to
the ADF program and then analyze the results. The GUIs are all linked
together via menus. Starting and getting familiar with the GUIs
will be the subject of the first lab.
I.3.4 Running ADFINPUT
ADFINPUT is the main GUI that you will be working with.
Once you have logged onto Terminus you must first set up your environment
so that the computer and programs know the location and details of several important
files.
To do this type
source /home/seth/ADF/profile_2006.sh
and press the return key. It should be assumed that you press return after all
commands that need to be typed into the command line.
We are now ready to run ADFINPUT. To start ADFINPUT type
$ADFBIN/adfinput &
It's possible that at this point you will get a funny error message and ADFINPUT
will not start. There are many reasons why you might get a funny error message
but the most common is that you need to type "-Y" in place of "-X" in the
ssh command to get a good connection. "-X" sometimes works and "-Y" sometimes works.
I.3.5 Supporting Documentation
In general, this lab manual will give only very short descriptions
of many of the software options to be invoked in the course of setting up
and running a particular calculation. Extensive documentation of the ADF program
can be found at the ADF website (http://www.scm.com/Doc/Doc2006.01/ADF/Welcome.html).
You are invited consult this website for further information concerning
any of the commands or methods used. Of course, your lecture notes will
cover the important points of methodology.
I.3.6 Saving the Results of Your Calculations
ADFINPUT will make sure that the outputs of you calculations are saved.
All of these files will be saved on Terminus. It is fine to leave them there. Your
lab demonstrator has access to them.
You should ensure that when prompted to give a calculation a name,
that each calculation is called something that makes it clear what it is.
The name of the calculation should include the
lab number and the exercise or project number.
I.3.7 Your Lab Writeup
A large part of your writeup will be given by the output files of your calculations. Pictures and
figures saved directly from the GUI should also be named with the lab number and exercise number or
project number. You will often be required to write some text, report some numbers
from the output or do some simple calculations. This information should be placed in a text
file by whatever method you prefer (wordpad, emacs, vi, pico etc) and sent by email to
the lab supervisor before the lab is due. The answers to exercises should be labelled
by the exercise number. The answers to exercises will usually be pretty short.
Full sentences are preferred.
Project write-ups should be more
extensive and should be in the form of a short report. That is, you should
briefly state what you are going to do, how you did it and what the
results and conclusions were. It should be possible for
somebody else to repeat what you did from simply reading your report
and looking at your outputs. Tables should be included in the text writeup.
Nothing fancy is required as long as the table is clear and clearly marked with the required
annotations.
Write-ups should be sent by email to Hristina at hzhekova@ucalgary.ca. To receive full credit for
the lab, the email should be sent before midnight on the Tuesday following the
lab.
A few graphs will need to be created in the course of this lab.
If possible, graphs should be saved in the jpg format and
left on Terminus or sent with the lab writeup as email.
I.4 Conventions
A few conventions are followed in the course of the lab.
Text in CAPITALS indicates the name of a program.
Text in
verbatim form
indicates something to be typed into a command line.
Text in italics indicates a menu option. If there
is more than one item: separated by : colons then
the item to the left of the colon is a menu, and the item
to the right of the colon is an item on that menu.
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