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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
<HTML>
<HEAD>
<TITLE>WebAtoms Help</TITLE>
<!-- Created by: Bruce Ravel, 12-Oct-1999 -->
<!-- Changed by: Bruce Ravel, 03-Feb-2006 -->
</HEAD>
<!--<LINK REL="stylesheet" TYPE="text/css" HREF="bruce.css">-->
<BODY bgcolor="white">
<H1 align=center>WebAtoms Help</H1>
<P>
This page provides quick, on-line help for using
Web<small>ATOMS</small>. For complete documentation of
<small>ATOMS</small> and its algorithms, please check out the <a
href="http://cars9.uchicago.edu/~ravel/software/doc/Atoms/Welcome.html">ATOMS
documentation page</a>.
</P>
<P>
This page is basically just a big long list of the keywords in
<small>ATOMS</small> with a few words of explanation. Just
enough to get you going.
</P>
<hr>
<UL>
<LI> <A HREF="#overview">Overview</A> </LI>
<LI> <A HREF="#abc">A, B, and C</A> </LI>
<LI> <A HREF="#alpha">Alpha</A> </LI>
<LI> <A HREF="#beta">Beta</A> </LI>
<LI> <A HREF="#central">Central Atom</A> </LI>
<LI> <A HREF="#edge">Edge</A> </LI>
<LI> <A HREF="#element">Element</A> </LI>
<LI> <A HREF="#gamma">Gamma</A> </LI>
<LI> <A HREF="#output">Output Types</A> </LI>
<LI> <A HREF="#rmax">Rmax</A> </LI>
<LI> <A HREF="#shift">Shift</A> </LI>
<LI> <A HREF="#space_group">Space Groups</A> </LI>
<LI> <A HREF="#tag">Site Tag</A> </LI>
<LI> <A HREF="#title">Titles</A> </LI>
<LI> <A HREF="#xyz">X, Y, and Z coordinates</A> </LI>
</UL>
<hr>
<H3> <A NAME="overview"><STRONG>Overview</STRONG></A> </H3>
<DL>
<DT> <STRONG>Run Atoms button</STRONG></DT>
<DD>
<P>
Click this button to submit your crystallographic data.
</P>
</DD>
<DT> <STRONG>Clear button</STRONG> </DT>
<DD>
<P>
Click this button to start over with a fresh page.
</P>
</DD>
<DT> <STRONG>Reset button</STRONG> </DT>
<DD>
<P>
Click this button to reset everything to its starting
values. This is most useful when modifying an input file
read in from the Atoms Database.
</P>
</DD>
<DT> <STRONG>Adding more atom positions</STRONG> </DT>
<DD>
<P>
At the bottom of the form is a space to indicate how many
atom positions you need. Simply fill in the number and
press the button marked "Do it!".
</P>
</DD>
<!--
<DT> <STRONG>Entering element symbols</STRONG> </DT>
<DD>
<P>
Normally element
symbols are chosen off a list. If you prefer to type them in
by hand or if the list does not work on your browser, click
the button labeled "Do it!".
<P>
</DD>
-->
</DL>
<HR>
<DL>
<DT> <A NAME="abc"><STRONG>A, B, and C</STRONG></A> </DT>
<DD>
<P>
Fill in these text fields with the lengths of the unit cell
axes. These should be numbers in Ångstroms. For many
space groups, it is ok to leave some of these blank. For
example, for the cubic groups, you only need to specify A.
For hexagonal and trigonal groups, you need to specify A and
C, but you can leave B blank. For low symmetry groups, you
will, of course, need to specify all three.
</P>
</DD>
<DT> <A NAME="alpha"><STRONG>Alpha</STRONG></A> </DT>
<DD>
<P>
Use this text field to specify the angle between the B and C
axes. This is needed for rhombohedral groups in the
rhombohedral setting, triclinic groups, and some settings of
some monoclinic groups.
</P>
</DD>
<DT> <A NAME="beta"><STRONG>Beta</STRONG></A> </DT>
<DD>
<P>
Use this text field to specify the angle between the A and C
axes. This is needed for triclinic groups, and the standard
settings of monoclinic groups.
</P>
</DD>
<DT> <A NAME="central"><STRONG>Central Atom</STRONG></A> </DT>
<DD>
<P>
Choose a site from the list of unique sites to be the central
atom of your cluster by selecting the radio button in the row
containing that site.
</P>
</DD>
<DT> <A NAME="edge"><STRONG>Edge</STRONG></A> </DT>
<DD>
<P>
Select a symbol from the popup menu. This is the symbol of
the absorption edge to use when <span
class=program>ATOMS</small> writes a <span
class=program>FEFF</small> input file. If you leave the
popup widget blank, then <small>ATOMS</small>
will choose an edge for you. If your central atom is
lighter than Cerium (Ce, number 58), the K edge will be
used. Otherwise the L3 edge is used.
</P>
</DD>
<DT> <A NAME="element"><STRONG>Element</STRONG></A> </DT>
<DD>
<P>
Specify the atomic species occupying a site by entering its
one- or two letter symbol in this column.
</P>
</DD>
<DT> <A NAME="gamma"><STRONG>Gamma</STRONG></A> </DT>
<DD>
<P>
Use this text field to specify the angle between the A and B
axes. This is needed for triclinic groups, and the certain
settings of some monoclinic groups. For hexagonal,
trigonal, and rhombohedral groups in the trigonal setting,
<small>ATOMS</small> will set this to 120 for
you.
</P>
</DD>
<DT> <A NAME="output"><STRONG>Output Types</STRONG></A> </DT>
<DD>
<P>
Use this popup menu to select the type of calculation you
would like <small>ATOMS</small> to make. You
choices include input files for <span
class=program>FEFF</small>6 and <span
class=program>FEFF</small>8, a couple of common file formats
for ball-and-stick viewers (alchemy and xyz), a list of the
entire contents of of the unit cell (p1.inp), a
non-stoichiometric description of the unit cell (unit.dat),
some calculations involving tables of absorption
coefficients (absorption), and two input formats for the
<small>GNXAS</small>' CRYMOL program.
</P>
</DD>
<DT> <A NAME="rmax"><STRONG>Rmax</STRONG></A> </DT>
<DD>
<P>
This defines the size of the cluster to be calculated by
<small>ATOMS</small>. It should be a positive
number in Ångstroms. It can also be left blank in
which case <small>ATOMS</small> will choose a
sensible default.
</P>
</DD>
<DT> <A NAME="shift"><STRONG>Shift</STRONG></A> </DT>
<DD>
<P>
Some space groups are commonly referenced to a choice of
symmetry positions. If your source of crystal data
references the structure to a symmetry position other than
the one that <small>ATOMS</small> uses, you will
need to specify the vector by which all the unique sites ill
need to be shifted so that the calculation will be made
correctly. In most situations it will be clear that you
will need to use a shift vector because the atom list in the
<small>FEFF</small> input file will be wrong and
Web<small>ATOMS</small> will print a little note
to you browser.
</P>
</DD>
<DT> <A NAME="tag"><STRONG>Site Tag</STRONG></A> </DT>
<DD>
<P>
Specify a unique label for a site in this column. These can
be up to 10 characters long. These tags are used to
differentiate between different sites which contain the same
atomic species.
</P>
</DD>
<DT> <A NAME="space_group"><STRONG>Space Group</STRONG></A> </DT>
<DD>
<P>
Use this text field to enter the symbol for the space group
of your crystal. <small>ATOMS</small> is
capable of interpreting lots of different things as a space
group symbols, including Hermann-Maguin symbols, Schoenflies
symbols, numeric indeces from the International Tables, and
some special words like "fcc" and "diamond". You have a lot
of latitude as to how you write the symbols. With only a
few obscure exceptions, spaces can be used in writing the
space group group symbols or they can be omited. "pm3m"
means the same thing as "P m 3 m".
</P>
</DD>
<DT> <A NAME="title"><STRONG>Titles</STRONG></A> </DT>
<DD>
<P>
Use this text field to enter any user-defined title lines
that you would like to have printed in the output of the
<small>ATOMS</small> calculation.
</P>
</DD>
<DT> <A NAME="xyz"><STRONG>X, Y, and Z coordinates</STRONG></A> </DT>
<DD>
<P>
Specify the fractional coordinate of a site in one of the cell
axis directions. You may use simple fractions such as
"1/2".
</P>
</DD>
</DL>
<HR>
<A NAME="features"><H3 align=center>Features of ATOMS</H3></A>
<P>
Although Web<small>ATOMS</small> is pretty handy at
generating input files for <small>FEFF</small> and
other interesting kinds of files, there are many features of <A
HREF="http://cars9.uchicago.edu/~ravel/software/aboutatoms/">
<small>ATOMS</small> </A> which are only available
in the version that you download and run on your own computer.
Here is an incomplete list of features. Perhaps this will
entice you to try it out!
</P>
<OL>
<LI>
<P>
Fine grained control over the appearence and content of the
output files and the ability to make entirely new kinds of
output files.
</P>
</LI>
<LI>
<P> Dopants can be used. </P>
</LI>
<LI>
<P>
Other functionality, such as calculations using tables of
absorption coefficients, DAFS simulations, powder
diffraction simulations (coming soon), and conversion of
molecule files into <small>FEFF</small> input
files.
</P>
</LI>
<LI>
<P>
The ability to have <small>ATOMS</small>
communicate with you in languages other than English.
Currently supported are French, Spanish, and German.
</P>
</LI>
<LI>
<P>
Object oriented perl libraries which you can use in your own
programs.
</P>
</LI>
</OL>
<HR>
<ADDRESS>
<A NAME="Signature"
HREF="http://cars9.uchicago.edu/~ravel/">Bruce Ravel</A>
</ADDRESS>
<EM>Modified: 3-Feb-2006</EM>
</BODY>
</HTML>
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