Crystal Lattice Structures: Reference Date:  1 Jan 2001
Last Modified: 21 Oct 2004

Frequently Asked Questions

(a.k.a. ``The FAQ'')



Contents:

Legal Stuff:

  1. Is your data reliable?
  2. Can I use your pictures/web pages?

Questions about content:

  1. What's the Structure of AxByCz?
  2. Why don't you add XyZw to your page?
  3. Can you tell me the lattice constants for QuMvRxy?
  4. What do you mean by ``Creation Date,'' ``Reference Date,'' and ``Revision Date,''" anyway?
  5. Do you ever answer your email?
  6. OK, can I do something to improve your response time?
  7. What's happened to the Valid XHTML 1.0! ?

Getting things to look right:

  1. My browser won't display the pictures!
  2. When I click on ``examine the structure'' nothing happens.
  3. I click where it says ``visualize the structure,'' but nothing (or not much) happens.
  4. The applet says ``The colors in this representation are arbitrary.'' Can I make them less arbitrary?
  5. Well, instead of using the applet, I clicked on ``examine the structure'' and looked at the picture. How can I use this in my own work?
  6. By the way, I can't seem to get the ``examine the structure'' feature to work with rasmol using newer versions of Netscape or Mozilla.

Graphics, HTML and XHTML:

  1. How do you produce your pictures?
  2. Why do I see α, β, and the like?
  3. How did you get the our favicon into my Location bar?
  4. How does the pop-up window trick work?

Final Queries:


  1. Is your data reliable?

    While we try to make everything as accurate as possible, honesty and our employer require us to say that

    This software and any accompanying documentation are released ``as is.'' The U.S. Government makes no warranty of any kind, expressed or implied, concerning this software and any accompanying documentation, including without limitation, any warranties of merchantability or fitness for a particular purpose. In no event will the U.S. Government be liable for any damages, including any lost profits, lost savings, or other incidental or consequential damages arising out of the use, or inability of use, of this software or any accompanying documentation, even if informed in advance of the possibility of such damages.

    For purposes of this statement, everything starting with the address http://cst-www.nrl.navy.mil/lattice/ is considered ``software'' (You are reading this on a computer, aren't you?) and/or documentation.

    If you happen to find a mistake, mail us (Privacy Advisory) and we'll try to correct it.

  2. Can I use your pictures/web pages?

    This page is in the public domain. You may therefore use any pictures, text, equations, etc. on the Crystal Lattice Structure (http://cst-www.nrl.navy.mil/lattice/) pages. Please realize that these pages are provided with absolutely no warranty, as noted above. That is, if you use one of our pictures/whatever, and it's wrong, it's your problem, not ours.

    If you do use our pages, please consider making an acknowledgment using one of the two following forms:

    For text publications:
    Pictures (and/or text) taken from the Crystal Lattice Structures Web page, http://cst-www.nrl.navy.mil/lattice/, provided by the Center for Computational Materials Science of the United States Naval Research Laboratory.
    For Web pages:
    Add the following code fragment to your page:

    <p>Pictures (and/or text) taken from the <a href="http://cst-www.nrl.navy.mil/lattice/">Crystal Lattice Structures web page</a>, provided by the <a href="http://cst-www.nrl.navy.mil/">Center for Computational Materials Science</a> of the <a href="http://www.nrl.navy.mil">United States Naval Research Laboratory.</a></p>

    You can, of course, modify the phrase ``Pictures (and/or text)'' to reflect the actual content you are using in your document.

Questions about content:

  1. What's the Structure of AxByCz?

    Wish we knew. However, if it is not on these pages, you are just as qualified to find the answer as we are. Check our list of references. If you find the structure, put the structural information into the proper form, send it to us, and we'll put it up on the page.

  2. Why don't you add XyZw to your page?

    Mainly it's a matter of time. We do have some helpful suggestions for those who would like to see something new on this page.

  3. Can you tell me the lattice constants for QuMvRxy?

    Unless they are hidden in one of our coordinate files (click on ``download the coordinates of the atoms in these pictures''), no. Structural parameters are taken from one of the sources in the references. Few of these books sit in our office, but they are all available from a good science library. The American Mineralogist Crystal Structure Database has structural parameters for a large number of minerals.

  4. What do you mean by ``Creation Date,'' ``Reference Date,'' and ``Revision Date,''" anyway?

    We are trying to keep better track of when these pages were created and revised. ``Creation Date'' is the first day a page appeared on the web site. Unfortunately, in the early days good records of this were not kept. If we don't know the creation date, we list a ``Reference Date,'' which is the earliest time a page was known to be on this web site. The first pages appeared in the summer of 1995, so the earliest revision date you will see is 1 Sep 1995.

    ``Revision Date'' is the date the latest revision of this page appeared on the site. (If we make changes in the HTML code which do not affect the appearance of the page, the revision date may not change to reflect the new code.)

    ``Last Modified'' is the date of the last visible modification to the page.

  5. Do you ever answer your email?

    Depends. There are various reasons for us not answering mail:

    1. Your email said something like ``my teacher said I should learn everything about the C3Cu15Rh7+2 molecule, by tomorrow, and I saw your web page, can you please help me?'' These questions are assumed to be rhetorical.
    2. Your email arrived while we were out of town, and it was buried under a lot of other email.
    3. Your email arrived during review season. This is, roughly, January-December. We'll get to it after the current review, unless we need to work on the next one first.
    4. Your email was buried under a pile of arriving SPAM. This happens infrequently, most often on Monday, Tuesday, Wednesday, Thursday, or Friday, except during review season, when it can happen any day of the week.

    If we don't answer your email after a decent interval (something longer than 24 hours, OK?) then please try again. If your question was of type ``a'', please elaborate a little more this time. We'll still consider it rhetorical, but we enjoy seeing rewrites.

  6. OK, can I do something to improve your response time?

    Error reports get the quickest attention. Other than that, if you show evidence that you've read this FAQ we are more likely to respond quickly.

  7. What's happened to the Valid XHTML 1.0! ?

    Our server now adds a disclaimer to the bottom of every web page. The way in which this is done invalidates the page for the World Wide Web Consortium (W3C)'s validation test (http://validator.w3.org/). As a result, we've removed the XHTML validation icon. However, we still validate the pre-disclaimer source with Dave Raggett's HTML Tidy (an invaluable tool for doing for checking the validity of HTML and XHTML documents, and for converting from HTML to XHTML).

Getting things to look right:

  1. My browser won't display the pictures!

    Most likely, your browser has difficulty displaying Portable Network Graphics (PNG) files. We use these files to avoid conflicts with Unisys' (perfectly legal) patent of the LZW compression algorithm used in the GIF format. For more information about GIFs, LZW, and Unisys, see this article (http://graphicssoft.about.com/compute/graphicssoft/library/weekly/aa083099.htm) and links therein. (The opinions in those articles are not necessarily ours.)

    Visit the Browser Test for PNG page to see if your browser is PNG compatible. If it doesn't show PNGs all that well, see the Applications with PNG Support page.

  2. When I click on ``examine the structure'' nothing happens.

    This is a link to an XYZ format molecule file, suitable for viewing with a molecular viewing program. The one we use is Rasmol 2.7, a freeware molecule viewer which has the advantage of running on most every type of computer. There are also various RasMol derivatives available. Many of these require you to either run Windows or have a Mac. A whole list of more-or-less free molecular viewers is available here.

    We export XYZ files as MIME type "chemical/x-xyz". See MIME types for Chemistry for more information about setting your browser to detect MIME types.

  3. I click where it says ``visualize the structure,'' but nothing (or not much) happens.

    This link launches a jmol applet, provided by the jmol project. It should launch a new window. Inside the window will be a graphical representation of the crystal, which you can rotate, enlarge, etc., using the keyboard and the mouse. You will need to have both javascript and java enabled to use the applet.

    If

    • No window pops up when you click on visualize the structure, you must enable javascript.
    • If the window comes up, but you don't see a molecule, you must install and/or enable java.
    • New: (17 May 2003): With a few hints on constructing java popup functions and putting them in script files, we have now achieved a state of Graceful Degradation. Which means, that if you don't have javascript turned on, clicking on the ``visualize the structure'' link will bring up the applet page in your regular browser window. From there you can rotate the crystal structure, provided your browser knows about java.

    See the documentation for your browser to find out how to enable javascript and java.

    Over the years, many people suggested that we provide an applet to view the crystal structures rather than using the helper application route. Jay Sullivan was the one who wrote the javascript to make the applet work. Thanks, Jay.

  4. The applet says ``The colors in this representation are arbitrary.'' Can I make them less arbitrary?

    jmol renders the colors of atoms, atomic radii, and bonding distances according to the information provided in a file called AtomTypes. Under versions of the Unix X-Windows system, this is located in your ~/.jmol directory. If you don't like the colors in your version of jmol uses, you can change it by editing this file. (You can also edit this file to add elements that jmol forgot.)

    For the curious, here is our current version of AtomTypes. This is subject to instantaneous and arbitrary change. Note that the columns are separated by tabs.

  5. Well, instead of using the applet, I clicked on ``examine the structure'' and looked at the picture. How can I use this in my own work?

    You need to get the ASCII "XYZ" format file which is read by your molecule viewer. While it is hidden in the cache of your computer, the easiest way to get it is to click on the link ``download the coordinates of the atoms in these pictures'', which is on the next line after ``examine the structure''. You can save this file from your browser, using the "Save As" feature.

  6. By the way, I can't seem to get the ``examine the structure'' feature to work with rasmol using newer versions of Netscape or Mozilla.

    We have the same problem. To get rasmol to load up an XYZ format file you must call call rasmol using rasmol -xyz file.xyz. Netscape and Mozilla, at least, don't seem to pass extensions anymore. If you know of a work-around, contact lattice@dave.nrl.navy.mil (Privacy Advisory).

Graphics, HTML and XHTML:

  1. How do you produce your pictures?

    The older large graphics seen when you click a link labeled ``examine the structure'' were produced using XMol (version 1.3.1, Minnesota Supercomputer Center, Inc., Minneapolis MN, 1993) from an atomic position file written in XYZ format. The XMol picture is captured from the screen by display, an image viewer/manipulator in the ImageMagick(TM) package, and then saved in Portable Network Graphics (PNG) format.

    The thumbnail graphics were produced in the same manner, but, of course, with smaller images.

    Currently, we use jmol, a Java-based GPL viewer which duplicates many (but not all) of the features of Xmol. Pictures are saved in Portable Pixmap (PPM) format, and then transformed to PNG format with John Cristy's convert program, also found in the ImageMagick(TM) package. jmol requires a Java runtime environment. We use Blackdown Java-Linux.

    Since jmol has yet to implement Xmol's ``split-view,'' we use a LaTeX template, convert that to Portable Document Format (PDF), and use convert to change that to a PNG graphic.

    The thumbnail graphics are produced using convert to resize the figure. Depending on the size of the figure, the thumbnail may be in either PNG or JPEG format.

  2. Why do I see &alpha;, &beta;, and the like?

    Because you have an old web browser. We did too, (Netscape 4.something), and finally upgraded. HTML 4 and XHTML use character entities, which are basically extensions of the old ISO 8859-1 (Latin-1) character set to include Greek letters and mathematical symbols. If you have a modern web browser the next line will contain the first letter of the Greek alphabet:

    α

    Otherwise, you just saw another &alpha;.

    We set things up this way because

    1. Greek letters are essential to mathematics,
    2. the difference between seeing &alpha; and alpha is minimal, and
    3. in a few years every browser will support character entities.

    Galeon, Netscape 7+, Mozilla 1.0, Opera and Amaya support character entities, as does Internet Explorer. We'll test other browsers as we get to them.

  3. How did you get the our favicon into my Location bar?

    We got this trick from http://www.thesitewizard.com/archive/favicon.shtml

Final Queries:

  1. The term ``Crystal Lattice'' is a misnomer.

    But it's such a catchy name. We're aware of this, but we were trained using Ashcroft and Mermin, so we don't worry about it too much. In reality, a lattice is a set of periodically repeated points, and nothing else. (This is what Ashcroft and Mermin call a Bravais lattice.) Except for a few simple cases, all of the structures here are a ``lattice plus basis,'' loosely referred to as a structure. If you like, think of this as the ``Crystal Structure'' page.


Go back to Crystal Lattice Structure page.

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This page was created at the
Naval Research Laboratory
Center for Computational Materials Science


Send comments and corrections to lattice@dave.nrl.navy.mil (Privacy Advisory)