User Profile: WebMO
WebMO approaches the process of creating and running a calculation as a series of five steps:
Figure 1 illustrates the WebMO molecule building interface. It shows a Netscape browser window with a web page entitled "Build Molecule" being displayed within it. When we click on the Open Editor button on the bottom of the molecule window on the web page (the window in back in the illustration), a Java applet starts, which is where molecule building and modification takes place. This applet appears in the top window in the illustration, where we are building a simple organic compound. Figure 1. Building a Molecule with WebMO The WebMO builder is intuitive to use, yet powerful enough to accomplish the tasks that students would need to build the sorts of molecules they encounter in typical undergraduate courses. One of the most helpful features for beginners is its multiple levels of Undo commands. The various steps in completing a calculation are summarized in the toolbar along the bottom of each WebMO screen (as in Figure 1), and the various buttons can be used to move between different WebMO facilities. We will skip the second step in the process, choosing the computational engine, and move to the calculation setup phase, illustrated in Figure 2 (we've focused the illustration on the WebMO display and controls, omitting the browser window in which they appear). My one quibble with the package concerns the builder module. The current builder cannot import structures from external files. However, there is a work-around; what you must do is import a Gaussian input file via the calculation setup module (described below).. Thus, if you want to import a structure, you must create a Gaussian input file in order to do so (which is usually easy to accomplish), and then you can modify the molecule contained in it in WebMO's builder.
Figure 2. Setting up a Gaussian Calculation with WebMO
This panel allows us to specify the calculation type, level of theory and basis set from simple pull down menus. We can also specify the output detail level (corresponding to #, #T or #P) as well as any additional keywords we need. In this case, we set up an optimization plus frequency calculation, using the HF/6-31G(d) model chemistry. We also decide to view the generated input file in an editing window before submitting the job.
Figure 3. The WebMO Job Manager
Figure 3 illustrates the WebMO job management facility. The Available Jobs list displays summary information for recent calculations, in this case, one completed single point energy job and a running optimization job. You can terminate running jobs from this interface via the Kill button. Once a job completes, you have three options: Delete the job and all associated files from the server, Download the job files from the server to your local computer, or View the results of the job graphically. The Job Manager is also the location where you can import Gaussian input files into the WebMO facility, via the Import Job button. Figure 4 illustrates the WebMO results visualization facility as it appears for a frequency calculation. The structure appears in the upper window, and results from the calculation appear in the Calculated Quantities box below it, including the final energy, dipole moment, atomic charges and vibrational modes. The latter can also be displayed by clicking on the desired mode's View button; arrows then appear on the various atoms within the molecule indicating its motion for that normal mode. In our example, we are viewing the carbonyl stretch mode for formaldehyde.
Figure 4. Visualizing Frequency Output with WebMO
|Administering a WebMO Server|
Installing and configuring WebMO is as intuitive and straightforward as using it. We got a test server up and running in about 10 minutes (and some of that time included figuring out which directory Apache was hosting on that computer system). WebMo requires a UNIX-based computer system (Linux is supported) running a web server capable of executing CGI scripts written in Perl (Perl 5.0 or higher is needed). The package takes up about 1MB of disk space. If you want to use the WebMO facility for sending email to a user whenever one of his jobs completes, then sendmail must also be running on the system. Finally, Gaussian and any other desired computational engines must be installed on the server (which will obviously need to have adequate CPU power, memory and disk space for whatever jobs will be run on it). Computers which will be used to access the WebMO server have no hardware or software requirements other than a compatible browser. Recent versions of Netscape (4.07 or higher) and Internet Explorer (4.0 or higher) are supported, as well as HotJava. 3.0 (and higher). Client computers can be PCs (running either Windows or UNIX) or Macintoshes. Note that no software needs to be installed on the clients. The interface includes an administration module, also accessed via a web browser, illustrated in Figure 5. This illustration is a composite of three screens from the administration facility. The upper box is the main administration window, the middle box is the main display provided by the User Manager, designed to create user accounts within the WebMO system. These accounts are strictly limited to WebMO and thus totally separate from the user accounts native to the computer system hosting WebMO; accordingly, they grant their owners no rights on the computer itself.
Figure 5. WebMO Administration and User Management Facilities
The bottom box in Figure 5 shows the dialog used to define a new user account. The account settings consists of a username and password, and email address and check box indicating whether email notification of job completion is desired for this user, and two time limits specifying the amount of time the user may be connected to the WebMO facility and the maximum job CPU limits, respectively (both in seconds). In this case, we are adding the user rchavez, who will be limited to jobs taking less than 5 minutes of CPU time.
|The WebMO Website|
WebMO is available free of charge from www.chem.hope.edu/webmo which also includes a wealth of useful information about the package. This excellent website also includes an interactive tour of the WebMO package, a working demo site and 8 example student exercises ranging from simple molecule building to electrophilic aromatic substitution and ozone depletion cycles. For further information, visit this website or contact Prof. Polik with specific questions.
All in all, our experience with WebMO have been extremely positive. It is a well-thought designed and implemented package which makes running Gaussian calculations on a central server straightforward and simple, and we highly recommend it to anyone-educators and researchers alike-looking for a means of providing Gaussian access in such a manner.
|About the Authors|