Read Me First Schrödinger Applet

Read Me First
Schrödinger Applet

June 1, 1998 (Updated July, 2000)

If you want to skip the readme, you can start here.

This Applet was developed with Java 1.1 when Netscape 4 and IE 4 were the newest browsers. Since then, the process of doing input, output and printing has improved, so we expect that most of the discussion about printing problems below will be irrelevant to you, but you might come back and read them if you have problems or if you are using an old browser. As far as we know, everything else will work on any Java-active browsers (Netscape 2.0 and later and Internet Explorer 3.0 and later) on all common architectures (Unix, Windows, Apple).

For the curious or the expert, we describe below how we made the Applet and how to rebuild it (in case you want to add your own changes). If you don't care about that now and do not mind if clicking the "print", "read" and "write" buttons produces nothing, then skip directly to the Applet. It has self contained documentation. Bookmark that link to bypass this "readme".
You can always come back for the information once you decide you wish you could print or save your work.

Finally, we suggest that you print the documentation out and keep it next to you the first time you go through that Applet. The Applet is self-documented, so click on the PDF or PostScript version to make hardcopy.

For the studious, read on below. For the adventurous, go to the Applet and enjoy.

IO Operations
For full functionality of all IO operations the Applet requires Netscape 4.05 or later.
Navigator is available at Netscape's usual download site.
Currently, Internet Explorer 4.0 or later is the next best option if you do not have access to Navigator 4.05 or later. With IE 4.0, the Applet printing button may not work for you, but the work around below will allow you to get a printed picture of the Applet with your results graphed.

This Applet has not been tested on IE-5, so we would be happy to hear from you to know if Microsoft has fixed their Java implementation.
Security Issues
The Applet requires permissions to save and print results.

Internet Explorer 4.0 will pop up a screen when the Applet is first loaded asking if you want to allow the applet full access to your computer. You must answer yes to this if you want to read and write files. Alternatively, you can rename the Schroedinger/classes/Seqn.cab file. The Applet will no longer require permission to run, but will not be able to read/write files.
Netscape 4.05 (AWT 1.1.5) will pop up a dialog that requests permission to print, read, or write files the first time each of these operations is attempted. You should grant the privilege if you want to allow the Applet to do this. Please realize that granting these permissions at most makes the Applet have the same capabilities as any other executable that you would run from your own account on the computer.

Functionality on other systems and browsers
The Applet has been tested on a number of different operating systems and browsers. Here are the results of our tests on various browsers. We have tested it on Linux, SunOS, HP-UX, IRIX, and Windows NT.
- Netscape 4.05 (AWT 1.1.5) full functionality
- Netscape 4.04 with JDK1.1 patch no write/read
- Netscape 4.04 or 4.05 standard versions no print/write/read
- Netscape 3.0 no print/write/read
- Netscape 2.0, no print/write/read
- Internet Explorer 4.0 no print
- Internet Explorer 3.0 untested, but likely no print/write/read (This is a guess)
- Other Browsers: If they support Java at all, everything but print/write/read. If they support Java 1.1, then print/write/read will work if allowed by the Browser security.
Running as an application rather than an applet
If you prefer, the Schrödinger solver can be run as a Java application rather than an applet. This circumvents all Browsers problems including the security issues, since all applications always have full permissions. To use it this way, you need to have a Java Run Time Environment (JRE) or Java Development Kit (JDK) installed. See the JDK references below. If you are running a Sun or Sun derived version of Java, then you can run the applet by typing
java Seq2Window
at a command prompt while in the directory Schroedinger/classes.
Browser problem work arounds for Printing and File Read/write
If the Browser doesn't support Java 1.1, there is no way to read or write files. Printing A screen image of the Applet can be made fairly easily and printed. Pop up a separate applet window, and then use the usual method to print a screen dump of the window.
- On systems running X, this consists of running xwd and clicking on the window, and then converting the X-window dump to a printable file. One way is to use the portable pixmap package to convert to postscript, the following works for us:
  xwd | xwdtopnm | pnmtops -noturn > temp.ps
  and then print the temp.ps postscript file.
- On Microsoft Windows NT you can press ALT-PrintScreen to copy the image to the clipboard, and then paste this image into an application that understands images such as WordPad. Then print the document.
How to get a copy of the Applet
Normally, if you are reading this, you already have the applet. If you want to tell someone else how to get it the simplest way is to download the tar file. You can then use
tar -xovf S.tar
or the equivalent for your operating system to unpack the tar file. You can also download the smaller gzipped tar file S.tar.gz. It may get renamed to something funny by your browser.
Free versions of gzip and tar are available. See the GNU project web page and its links.
The authors will maintain a copy of the applet with current (May,1998) and subsequent updates for an undetermined length of time. Send mail to the authors for the download site information.
Building the Applet from Scratch
Once you have a copy of the Applet, you are free to change it and redistribute it in accordance with the Gnu Public License.
To build the applet from source you need a Java Development Kit from Sun Microsystems at http://java.sun.com/, or Linux users may prefer the most recent from the Java-Linux porting project at http://www.blackdown.org or you may find other related development kits.
We have used both JDK1.1.3 and JDK1.1.5. You will also need JavaCC (Java Compiler compiler) from http://www.sun.com/forte/ffj/resources/javacc.html to build our parser generator written using JJtree. JJtree is part of the JavaCC distribution. Note we used JavaCC version 0.7 which is compatible with JDK1.0 so that older browsers would be functional. It is simplest, but not absolutely necessary, to have a copy of Netscape 4.x so that you can add the Netscape java40.jar file to the classpath when compiling the Java code. A makefile that works in Unix/Linux is distributed in the javasrc directory. You will have to modify the first few lines to point to the various directories on your system. If you are compiling under a different operating system, the Makefile should still indicate the operations needed to build the system. Under Unix/Linux typing make will build all the java class files.
To build the documentation, you will need Latex2e, the makeidx, graphicx packages (these normally come with the tetex distribution all available at the Comprehensive Tex Archive Network sites, see for example ftp://ftp.freesoftware.com/pub/tex/ctan/CTAN.sites. You will also need the latex2html translator and the associated html package from http://cbl.leeds.ac.uk/nikos/tex2html/doc/latex2html/latex2html.html. If you want to make an Adobe PDF file you will need a copy of Adobe Acrobat. PDF files look best with PostScript Type 1 fonts available at ftp://ftp.ams.org. There is a makefile in the docsrc directory that will go through all the steps necessary to build the pdf, postscript, and html files.
Under Unix/Linux, typing make in the Schroedinger directory (once the Makefile in javasrc has been modified as mentioned above) will produce the entire distribution. Typing make clean will get rid of multiple copies of some files, and typing make veryclean will keep only those files necessary to rebuild the distribution from scratch.
Additional documentation on the source code is available in javadoc format.

Last updated: July 3, 2000