Installation and Quick Start
__________________________________
Authors:
P.R. Watson, M.A. Van Hove, and K. Hermann
Consultants:
G.A. Somorjai and J.B. Pendry
April 2004
U.S. Department of Commerce
________________________
The National Institute of Standards and Technology (NIST) uses its best efforts to deliver a high quality copy of the database and to verify that the data contained therein have been selected on the basis of sound scientific judgment. However, NIST makes no warranties to that effect, and neither NIST nor Microsoft shall be held liable for any damage that may result from errors or omissions in the database.
________________________
For a literature citation, the database should be viewed as a book published by NIST; thus, the citation is:
© 1993, 1996, 1999, 2001, 2004 copyright by the U.S. Secretary of Commerce on behalf of the United States of America. All rights reserved.
No part of this database may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording, or otherwise, without the prior written permission of the distributor.
LICENSE AGREEMENT
This software uses the Microsoft Visual Basic C © and Compaq Visual Fortran Runtime libraries software that are owned by Microsoft. You agree to look solely to NIST and the developers of the Surface Structure Database for any support you may require.
Certain trade names and company products are mentioned in the text to specify adequately the computer products and equipment needed to use this software. In no case does such identification imply endorsement by the National Institute of Standards and Technology of these computer products and equipment, not does it imply that the products are necessarily the best available for the purpose.
Microsoft is a registered trademark of Microsoft Corporation.
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Visual Basic is a registered trademark of Microsoft Corporation.
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PREFACE
The PC-based NIST Surface Structure Database (SSD) is aimed at scientists and students in physics, chemistry and materials sciences who wish to know and compare the detailed atomic-scale structures of surfaces obtained from experiment.
Version 5.0 of SSD is an improved 32-bit version of the software for use under Windows NT/2000/XP. Improvements have been made in the database manipulation and in the graphical visualization and analysis. Version 5.0 expands the database to nearly 1400 structure determinations and attempts to cover all known surface structures since the inception of surface crystallography in the early 1970s through the end of 2002.
The complete documentation for running SSD is available as on-line help within
the program. This printed documentation provides information about hardware
and software requirements and about software installation, as well as a guide
to a quick start and easy use of the software. In addition, it provides illustrations
of the 17 2-D space groups used to define surface structure symmetries.
The NIST Surface Structure Database can be obtained from NIST directly at the following address:
U.S. Department of Commerce
Standard Reference Data Program
National Institute of Standards and Technology
Building 820, Room 113
Gaithersburg, MD 20899
ACKNOWLEDGMENTS
We are grateful to the National Institute of Standards and Technology, particularly to the Standard Reference Data Program, for undertaking the support of SSD, as well as for providing professional advice and help in setting up and distributing this database. We are also much indebted to our consultants, Prof. J.B. Pendry and Prof. G.A. Somorjai, for helpful advice. We also thank the many authors who contributed their data through the SSDIN input program.
The work in Berkeley was supported in part by the Director, Office of Energy Research, Office of Basic Energy Sciences, Materials Sciences Division of the U.S. Department of Energy under Contract No. DE-ACO3-76SF00098.
Signed: P. R. Watson, Corvallis, Oregon
M. A. Van Hove, Berkeley, California
K. Hermann, Berlin, Germany
April 2004
Hardware and Software Requirments
Starting SSD
Browse Mode
Search Mode
Data Windows
Graphics Window
Changing views
Changing the presentation of the atoms
Analysis
Compare Mode
Termination of SSD
The Surface Structure Database is designed to run on personal computers with the following hardware configuration:
Intel® Pentium processor;
64 megabytes or more of memory;
(S)VGA graphics with at least 256 colors and color monitor with 800x600 pixels or higher resolution;
20 Mb of free hard disk space (40 Mb for installation);
Microsoft Windows-compatible mouse;
Printer (optional; required for print output of listings, PostScript type for printing graphics).
The database has been tested on a variety of Intel® Pentium and similar systems from a number of manufacturers, but there is always the possibility of an incompatibility with some particular combination of hardware. If difficulties in installing or running SSD are encountered, please refer to the troubleshooting section or one of the authors, see Appendix C.
The software is contained on a single CD-ROM as a single self-extracting INSTALL.EXE file. Before installation, check for the presence of a README.1ST file for any last-minute changes or additions that are not in this document.
When installing to a Windows system that allows users with different levels
of rights, you will need to have administrator rights, or need to change your
authorization and log on as administrator before you will be able to successfully
install SSD 5.0.
Start the installation by either double-clicking on the file INSTALL.EXE on the CD via the Windows Explorer or My Computer, or by clicking on the Start button, selecting Run and entering the appropriate location for the installation file e.g. D:/INSTALL.EXE (if the CD-ROM drive is assigned the letter D:).
The installation process will prompt you several times to allow a choice of e.g. a particular directory for SSD 4.0 to reside, or whether to keep back-up copies of changed files. Many files necessary to the operation of Microsoft® Visual Basic as well as the database itself will be copied to your computer. Depending upon the configuration of your particular computer and operating system, one or more restarts may be necessary.
The installation process also installs an Uninstall option which allows you to remove SSD 4.0 from your system including many of the system files that had been installed.
2. You receive the error message “SAO\DAO360 DLL could not be opened. Access denied.” Please check that your disk is not full and that you have access to the destination directory. Access denied.”
This error occurs when installing to a Windows 2000 or NT4 system when logged on as a user that no administrator rights. The solution is to change your authorization and log on as administrator and reinstall the program.
If you have other installation problems, please contact one of the authors listed in Appendix C.
The purpose of this section is to provide a quick way to obtain useful information from SSD. To that end, a simple generic session with SSD is presented, which you can follow step by step.
With this quick approach, access to all of the database information is gained, a graphical image of a structure of interest will be produced, and methods will be introduced to analyze the structure. Additional options will be found by simply opening the menus and trying the different options.
Further details are provided in the on-line help. This is accessible at any time through the menu item Help or by pointing inside the appropriate window/entry field and pressing the F1 key.
NOTE: Clicking on the left and right mouse buttons will here be called L-clicking and R-clicking, respectively. D-clicking (double clicking) means quickly L-clicking twice in succession.
SSD is started like any other application under MS Windows 95 or later, e.g.:
- D-click on the SSD icon located on the desktop or in a program group on the desktop;
- or L-click on Start (on the bottom bar of Windows), then on Programs, and then on the SSD program name;
- or D-click on the file name ssd4.exe in the appropriate folder under Windows Explorer or under My Computer.
Initially, the SSD's title screen is displayed for a few seconds, followed by the default layout of SSD windows. SSD is now in its default “Browse Mode”, and already displays data and a graph for the first structure in the database (by virtue of the alphabetical order of its "common name” shown in the top left box).
In this Browse Mode, all structures in the database can be accessed directly by scanning down the Structure List shown in the bottom right window. To select a different structure from the Structure List, first use the vertical scroll bar at its right to find it. This is done by dragging the scroll button, L-clicking above or below it, or L-clicking on the arrows at top and bottom of that scroll bar. Alternatively you can type in the chemical symbol of the substrate and the cursor will jump to the first occurrence of that element. Then D-click on the small gray box to the left of the desired structure. This causes new data to be shown in the left “Summary” window and a new graph to be plotted in the graphics window at top right.
Suppose we wish to select the Rh(111)+c(4x2)-C2H3+CO structure (consisting of ethylidyne and carbon monoxide molecules coadsorbed on the Rh(111) surface). Browsing is not an efficient method to find it in the long Structure List. It is more effective to use the SSD's “Search Mode". To enter the Search Mode, L-click on the Search button on the button bar near the bottom of the screen, or select the menu item Mode, then option Search (if you don't see the item Mode, you are looking at the "Graphics menu": switch to the "Data menu" by L-clicking in a non-graphical window).>
This opens a powerful Search Criteria window, with which we can find structures through a variety of keywords or combinations of keywords. A brief description of the different options is shown in the window to the right of the Search Criteria window. We must now enter such search criteria into one or more boxes. The safest way to enter a criterion into a box is to open a “pick list” of available entries: L-click on the downward arrow at the right end of the box, scroll down to the desired entry and L-click on that entry. It is also possible to directly type in keywords (including partial words).
Now enter ‘Rh’ into the Substrate box and ‘CO’ into the Adsorbate box (without the quotation marks). Then L-click on the Search button at bottom left of the Search Criteria window. This causes the search to gather all applicable structures from the database into a “hit list”. L-click on Accept to make these available in the Structure List window at the bottom right of the screen. (Note that SSD is not case-sensitive: it does not distinguish between CO and Co.)
We could have been more selective, for example by also specifying a criterion for the Pattern (i.e. the particular LEED pattern of the structure), or some other aspect of the structure.
Whether we used the Browse Mode or the Search Mode, we should now select the desired Rh(111)+c(4x2)-C2H3+CO structure from the Structure List, by applying the procedure given above (scrolling as needed and then L-clicking on the gray box to the left of the desired structure).
We now discuss the variety of information that can be obtained about the last selected structure.
The left half of the screen is now occupied by the Summary window for the newly selected structure, and gives general information about this structure. The Help button within this window provides further information out the type of data contained in this window. For example, if the meaning or purpose of some data box is unclear, an explanation is available using Help. (This same information is also available at any time through menu item Help or by pressing F1 with the mouse pointing at the data box.)
Additional data about this structure are available in other windows that can be reached by pressing one of the buttons at bottom left (or by selecting menu item Windows, then an item from the List option): Expt/Th, 2D cells, Coords, or Bonds. Let’s select the button Expt/Th or the menu item Experiment/Theory: a new window appears, showing a variety of details concerning the experimental and theoretical procedures that were used to obtain the data for this particular surface structure.
Explore the other data windows in the same way to view the 2-dimensional unit cells present in the structure, the coordinates of the different atoms, as well as selected bond lengths and angles.
The structural image in the top right window can be used to view the currently-selected structure in a variety of ways. By L-clicking on its title bar, a new “graphics menu” appears at top left (above the data windows): this menu controls the graphics. (To return to the original “data menu”, click on any data window or the Structure List.)
Note that you can move or resize the graphics window. To move a window, drag its title bar (i.e. point at its title bar, press and keep pressed the left mouse button, move the mouse pointer where desired and then let go the left mouse button). To resize a window, drag one of its borders or corners. You can also let it fill the screen by L-clicking on the middle button at top right (the “Maximize” button). To restore the graphics window to its default position and size, reverse these steps (menu item Windows - Reset will not do it for this window).
The graphics window shows a piece of a surface (or interface) bounded by a rectangular box. By default you look down at an angle onto the surface, which is presented with perspective effect. Colors indicate chemical elements, as labeled at top right.
The easiest change of the graphics is the view orientation: drag the mouse pointer to see the bounding box rotate around its vertical axis (azimuthal rotation about the surface normal) and around a horizontal axis (polar rotation). This is the default action of dragging the mouse, also achieved by dragging the mouse while keeping the Alt key pressed on the keyboard.
The size of the image can be changed by dragging the mouse pointer up or down the window while keeping the Ctrl key pressed on the keyboard.
The image can be shifted laterally and up or down by dragging the mouse pointer in the desired direction while keeping the Shift key pressed on the keyboard.
The degree of perspective effect can likewise be changed by dragging the mouse pointer up or down while keeping both the Ctrl and Shift keys pressed on the keyboard. Moving the mouse pointer all the way down gives parallel perspective. The parallel perspective and the default perspective can also be easily chosen through menu item View, then option Parallel Perspective or option Default Perspective.
The image can be rotated around the line of sight by dragging the mouse pointer up or down while keeping both the Ctrl and Alt keys pressed on the keyboard.
The default (drag = 3-dimensional rotation) can be changed via the menu item Drag: click on a different n other choice to modify the default action of dragging the mouse.
Other convenient actions include (see further below for procedures involved in some of these):
- set the view direction to be parallel to the x, y or z axes through menu item View, then View -> x, etc.
- set the “view focus” (that part of the surface which is positioned at the center of the screen) through menu item View, option Set View Focus.
Some of the above actions require you to select specific atoms by pointing them out with the mouse. The line at the bottom of the graphics window tells you what to do, in shorthand form. The first step is to L-click on the desired atom: it is sufficient to move the mouse pointer to any position on the visible part of that atom and then to L-click. Depending on the action that follows, you may have to select a second atom in the same manner, or R-click to start the requested action, or fill in a dialogue box.
Several other changes of the graphical presentation are possible. These can be used for purposes of better viewing, for showing bonding relationships, or for embellishing the view. The latter is particularly useful in order to prepare and export a publication-quality plot (see the on-line documentation for details). All these changes are found as different options accessed through menu item Settings.
First, let’s change the type of ball that represents an atom. First make sure that the graphics menu is displayed above the data windows (if not, L-click on the graphics window to activate it and its menu). Then select menu item Settings, option Atom Design. Now choose the type of atom display desired, e.g. brilliant balls. Note that plotting these “brilliant balls” takes more time than the original “plain balls (one color)”. So one would normally first plot with a plainer design to adjust the many variables that go into a pleasing figure, before doing the final plotting, especially when the plot involves many atoms.
Other options include:
- change the drawn atomic radii collectively either by scaling (“relative” change) or one element at a time in Angstrom (“absolute” change), through menu item Settings, option Atom Radii.
- hide and revive atoms, i.e. make them temporarily invisible, through menu item Settings, option Atom Hide/Revive.
- change drawn bonds, through menu item Settings, option Atom Bonds.
- change the bounding box dimensions to allow more or fewer atoms to be seen, through menu item Settings, option Surface section.
Explore the Settings menu item to find other ways to change the plot.\
Another powerful set of options are provided to “analyze” the structure: they allow you to measure a variety of quantities in the current structure, such as bond lengths (in Angstroms), bond angles (in degrees), and interlayer distances (in Angstrom). See the menu item Analysis for the various options that are available.
As an example, let us find the bond length between two atoms. Again, make sure that the graphics menu is displayed above the data windows (if not, L-click on the graphics window to activate it and its menu). Choose menu item Analysis, then option Atom Distances/Vectors. At the bottom of the graphics window now appears the instruction
“Atom distance/vector AB: L-click 2 diff. atoms A,B; R-click evaluates”.
This tells you to first L-click on the two atoms in question (if they are invisible, you may have to exit the analysis (R-click) and rotate the view). See the last section on how to L-click on an atom. After each atom has been selected, you will see its identity, coordinates and radius displayed. After selecting the second atom, R-click. This results in a display of the interatomic distance (and, for comparison, the sum of the current atomic radii), followed by the vector pointing from the first to the second atom, all in Angstrom.Note that you cannot select (point at) an invisible atom. On the other hand, you may on purpose make atoms invisible so as to reveal deeper-lying atoms and analyze these.
It is often desirable to visually compare different structures, or to visually compare the same structure as determined in different studies. This is possible by switching SSD to its “Compare Mode”. In that mode 2 or 3 structures can be drawn in separate windows and individually displayed for optimum comparison.
Let’s compare some structures of O on Ni(100). To narrow down the list from which to select, we first do a Search, by specifying ‘Ni’ for the Substrate, ‘100’ for the Substrate Face, and ‘O’ for the Adsorbate. L-click Search, then Accept, resulting in a shorter hit list being displayed in the Structure List.
Next we must choose one structure from the Structure List, e.g. the first Ni(100)+c(2x2)-O that occurs.
Now L-click the Compare button on the button bar near the bottom of the screen. A “Compare Structures” window is opened, that allows you to select 1 or 2 other structures for comparison.
We can select a second structure from the same hit list by leaving the “Select from Search” option active. Let’s select the last Ni(100)+c(2x2)-O in the list, by D-clicking on the gray box in front of its name, or by highlighting the entry and clicking on the Select button. (It is also possible to select structures from the complete database by setting “Select from Database”.)
This results in a second graphics window being opened, displaying the second structure. Also, this second structure is listed as “Comparison 1” in the Compare Structures window.
To select a third structure for comparison, first activate the button to the right of the “Comparison 2” line in the Compare Structures window. Then select another structure from the Structure List.
Remember that you can move and resize the windows to obtain the most effective display. And within each window, you can adjust all graphical features as discussed above.
You can close any graphics window by L-clicking on its X button (at top right of each window), or by selecting its menu item File, option Exit.
You can also replace any of the comparison structures by activating the button to its right in the Compare Structures window and selecting another structure.
L-Click on Cancel to quit the comparisons. And close any excess graphical windows.
SSD is terminated by any of the standard MS Windows 95 methods, such as:
- select menu item File, option Exit.
- or L-click on the X button in the top right corner of the screen.
THE 17 TWO-DIMENSIONAL SPACE GROUPS
This Appendix illustrates the 17 two-dimensional space groups that exist for surfaces and interfaces in strictly two dimensions. SSD characterizes both the ideal substrate terminations and the actual surfaces by their respective space groups.
Additional space groups are possible if one allows symmetry operations across the interface, e.g., mirror symmetry about the interface, as may happen in twinning of two crystals. Then 80 space groups exist; they have been tabulated by Wood (1964). However, situations where any of these additional space groups might be useful are rare in surface science. The 17 two-dimensional space groups always remain applicable, even if they do not convey all the useful information in those rare cases.
The following diagrams show, for each of the 17 two-dimensional space groups:
one unit cell outlined in heavy lines (where not overdrawn by thin symmetry lines);
all applicable symmetry elements: 2-, 3-, 4- and 6-fold rotation axes (perpendicular to the surface), drawn as black ovals, triangles, squares and hexagons, respectively; mirror lines (planes perpendicular to the surface) drawn as thin lines, glide lines (planes perpendicular to the surface) as dashed lines;
a general point in the unit cell, symbolized by a yin-and-yang figure, together with all other points equivalent to it by symmetry; the left-handed and right-handed yin-and-yang symbols show how orientations are mirrored and rotated into each other.The 17 two-dimensional space groups
The 17 two-dimensional space groups - continued
The 17 two-dimensional space groups - continued
EXAMPLES OF SUPERLATTICE CELLS
This Appendix illustrates two-dimensional unit cells and their notations.
Superlattices on square substrate lattices
Superlattices on hexagonal substrate lattices
CONTACTS
If you have questions or comments about the database, the Standard Reference Data Program would like to hear from you. Please contact:
If you have technical questions relating to the data, contact:
M.A. Van Hove
MS 2R0100
Materials Sciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720, USA
e-mail: MAVanHove@lbl.gov
K. Hermann
Abteilung Theorie
Fritz-Haber-Institut
Faradayweg 4-6
D-14195 Berlin
Germany
e-mail: hermann@FHI-Berlin.MPG.DE
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