NOTE: The information in this document is based on the Systre 1.2.0 release. Other versions of Systre may behave slightly differently.
The program SYSTRE is designed to analyze periodic nets as they arise in the study of extended crystal structures (as opposed to molecular crystals). The acronym stands for Symmetry, Structure and Refinement. SYSTRE uses a method called barycentric placement to determine the ideal (i.e., maximal embeddable) symmetry of a crystal net and to analyze its topological structure. It then generates a unique "fingerprint" for the topological type of the given net and uses that to look up the structure in its built-in database (see below). Users can also create their own databases.
SYSTRE also computes a refined embedding of the given net using a method based on simulated forces. The targeted embedding is one that minimizes the edge length variance (normalized to unit length) and maximizes the unit cell volume. The forces modeled are not physically realistic, but should in most cases result in viable input for molecular modeling software.
Currently, SYSTRE's built-in database contains all feasible nets from the RCSR online resource as of May 22, 2013.
The 13 RCSR nets that Systre currently does not recognize are bad, bae, bai, bbu, bcr, cys, fco, hyx, lcw, nbo-g, tep, uld and ulm.
SYSTRE is part of The Gavrog Project.
SYSTRE requires a Java runtime environment (JRE) of version 1.5 or higher. On some systems, Java will already be installed as a prerequisite for other programs. Otherwise, the most straightforward way to get a JRE is to download it from java.com and follow the installation instructions given there. Set all path variables correctly for your system as instructed (this should be done automatically in most cases), so that the java command can be recognized. If supported by your system, make sure that the file extension .jar is associated with the Java executable.
Installing SYSTRE itself is very easy. Just download the file Systre.jar and put it anywhere you like, for example on your desktop. A SYSTRE executable is also included in the main Gavrog distribution available from http://www.gavrog.org.
The Gavrog installer automatically installs SYSTRE along with 3dt and creates a batch file Systre or Systre.bat in the bin subdirectory of your chosen installation location. Please refer to your operating system documentation on how to execute such files. On Windows and some Unix machines, the installer can also create desktop icons for both 3dt and SYSTRE.
The simplest way to start SYSTRE is to double-click its icon. If that does not work, and you are sure that Java is correctly installed and all path variables set correctly, open a console window and type the command
java -jar Systre.jar
from the same folder that you put Systre.jar in. Alternatively, add the appropriate path. For example, if you downloaded Systre.jar to a folder named C:\Programs\Systre (on a Windows system), change the above to
java -jar C:\Programs\Systre\Systre.jar
To make things easier, you can create a batch file (a.k.a. shell script) containing the command. Please refer to your operating system manual on how to create and execute such files.
Using SYSTRE is very simple. Run SYSTRE, then use the [Open...] button to read in a file of net descriptions. SYSTRE will process the first net in the file and describe the results in an informal way. If there are more nets, use the [Next] button to step through them. When you are finished with a file, you can store the results in one of several formats using the [Save as...] button. The [Help] button displays this text and, finally, the [Options...] button lets you modify some of SYSTRE's internal workings.
SYSTRE uses three basic file types:
If you read or write a file from within SYSTRE, the extension will determine the format of the file and the extend of information in it. Typically, you would read a structure file and save the output in a protocol file. But you might also want to produce a .cgd file with the new symmetry group and node positions as determined by SYSTRE.
Here are some details on how to enter certain types of information in structure files:
Enter the space group symbol as it appears in the International Tables, except that "bar 3", "bar 4" etc. are written as -3, -4 and so on and subscripts are written as regular numbers. Examples: Fd-3m, I41/amd, P212121.
If you specify a crystal without explicit edges as in the first and fourth example below, SYSTRE needs to compute edges based on nearest neighbors. This does not only depend on the correct cell parameters, but also on the origin choice. For groups that have two conventional choices as according to the international tables, SYSTRE uses the second one by default. This can be changed in the 'Options' dialog.
Another way to make sure that the correct origin choice is used is to append :1 or :2, respectively, to the group name as in Example 4 below.
Hexagonal versus rhombohedral settings for rhombohedral groups are handled analogously to the above. In this case, append :H (the default) or :R, accordingly.
Below are some examples of legal input for SYSTRE. You can cut and paste any of the following examples (or all of them) into a .cgd file using your favorite text editor (e.g. Notepad on Windows) and open it from within SYSTRE.
The SYSTRE format allows comments, which start with a # character and continue until the end of the current line.
Example 1: Diamond, specified by space group, unit cell and positions. SYSTRE computes edges by finding nearest neighbors. Edge lengths have to be larger than 0.1. If any pair of nodes is closer than that, an error is reported. If this is the case for your data, you should try scaling the unit cell parameters accordingly. The keywords NODE and ATOM are equivalent, as are the keywords ID and NAME.
# The type of data to expect CRYSTAL # Structure id (optional; ID and NAME both work) ID diamond # The space group GROUP Fd-3m # Cell parameters: a b c alpha beta gamma CELL 2.3094 2.3094 2.3094 90.00000 90.00000 90.00000 # Atom specification: name coordination x y z # (decimal numbers or fractions can be used for coordinates) ATOM 1 4 5/8 5/8 5/8 # This ends the structure description END
Example 2: Diamond, specified as a periodic graph. Here, only translational symmetries are assumed, and no coordinates are needed. Edges are given explicitly in the form u v x y z, where u and v are node numbers and x y z specifies the "address" of the unit cell to connect to as an integer vector. For example, the line 1 1 0 1 0 defines an edge between node 1 and its copy shifted one unit along the y axis.
PERIODIC_GRAPH ID diamond EDGES 1 2 0 0 0 1 2 1 0 0 1 2 0 1 0 1 2 0 0 1 END
Example 3: For CRYSTAL input, edges can be given explicitly, as well. This is often preferable to letting SYSTRE compute them.
CRYSTAL NAME real CdSO4 GROUP Pmn21 CELL 6.558 4.698 4.719 90.0 90.0 90.0 # First kind of atom ATOM 1 4 0.0000 0.6657 0.7306 # Edges can be specified by giving the names of the endpoints EDGE 1 2 # or by giving a number for the first and coordinates for the second. EDGE 1 0.0000 0.1416 0.2500 # or by giving coordinates for both EDGE 0.0000 0.6657 0.7306 0.0000 1.1416 1.2500 # The Keyword EDGE may be missing on consecutive lines. 1 -0.5000 0.8584 0.7500 # Second kind of atom. ATOM 2 4 0.5000 0.8584 0.7500 # Second group of edge specifications. EDGE 2 0.0000 0.6657 0.7306 2 1.0000 0.6657 0.7306 2 0.5000 1.3343 0.2306 2 0.5000 0.3343 1.2306 END
Example 4: This example describes a more complicated graph and will take SYSTRE significantly longer to complete. It shows two situations in which quotes are required.
CRYSTAL ID LTN # Group Fd-3m with first origin choice instead of second # (likewise, use ":R" for rhombohedral setting, where applicable) GROUP "Fd-3m:1" CELL 35.622 35.622 35.622 90.000 90.000 90.000 ATOM # If the first field in a line starts with a letter, it is assumed # to be a keyword, so in this example, the atom names need to be quoted. "SI1" 4 0.3112 0.2500 0.3727 "SI2" 4 0.4345 0.2481 0.3721 "SI3" 4 0.3897 0.3285 0.4532 "SI4" 4 0.5396 0.3394 0.3996 END
If you are dealing with a large number of nets that SYSTRE does not know of, you might want to read and write your own archive files. These contain fingerprints of nets processed by SYSTRE. If you read in an archive file after starting SYSTRE, it will temporarily add those fingerprints to its list of "known" nets and thus recognize them. If you write an output file with the extension .arc, it will contain fingerprints of all the "new" nets so far encountered in the current input file. Each block of lines in which the first line starts with the word key and the last line reads end constitutes one fingerprint. You can use a standard text editor to cut and paste those blocks and thus maintain your own private archives of nets.
As of Version 1.1.8, Systre will look for a folder named .systre in your user home directory upon startup and load all archive files in that folder automatically.
If you encounter any problems, please check your input thoroughly. There are many opportunities for typos and SYSTRE is very sensitive to input errors, especially when edges are not given explicitly.
There are some quirks and limitations, though, that you should be aware of when using SYSTRE.
SYSTRE identifies nodes by their barycentric positions, which is the key to its efficient algorithms. If different nodes collide, i.e., if they have identical barycentric positions, this method fails. The present version of SYSTRE is not able to handle some nets with collisions and will produce an error message. This seems to be a fairly rare case, though, especially in nets that emerge from actual crystal structures.
Furthermore, SYSTRE currently only works for nets of dimensions 2 (plane nets) and 3.
With some versions of the Java runtime environment, occasional program crashes or miscalculations have been experienced. SYSTRE double-checks its computations very thoroughly, though, so that erroneous results are highly unlikely to go undetected. Much more likely, the program will terminate for no apparent reason or produce an "INTERNAL ERROR" message. In those cases, the best strategy is to restart SYSTRE or just to rerun the net that produced the problem.
For the moment, please report bugs to firstname.lastname@example.org. Make sure that your input is correct and that the problem is reproducible. Enclose your input file and any output that SYSTRE produced, or, if that is not possible, describe the problem and any messages that you may have seen as detailed as possible. Tell me which operating system and which version of Java you were using.
Version 2.0, January 2004
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Michael O'Keeffe made me aware of the problems that SYSTRE aims to solve and has supported and guided its development over many years. He also came up with the name.
Michael Treacy, Davide Proserpio, Martin Foster, Martijn Zwijnenburg, Stuart Ramsden, Vladislav Blatov, Stephen Hyde and others helped a lot by testing, criticizing and discussing SYSTRE.
My work on SYSTRE and its theoretical background was partially supported by grants from the Petroleum Research Foundation and the National Science Foundation.