This section assumes that RMG is already installed according to the directions in Section Linux installation. Additionally, it is assumed that you have created a directory (either in your home directory or elsewhere) in which the initialization file condition.txt has been placed. In the example, we assume that we have created a directory /hexane_pyro, which contains the condition file hexane_pyro.txt.
Change the current working directory to the directory with the condition file:
$ cd /hexane_pyro/
Run the following Java command to launch the program (all one line):
$ java -Xmx500m -classpath $RMG/bin/RMG.jar RMG hexane_pyro.txt
When RMG is started, it creates several subdirectories: 2Dmolfiles, 3Dmolfiles, chemkin, fame, frankie, GATPFit, InChI, ODESolver, Pruning, QMfiles and Restart. By default these are in the directory from which you ran the command, but to configure them see Configuring paths using Environment Variables.
In this example, all of the output from RMG is piped to a file output.log. The > output part of the command is optional but recommended. The Java option -Xmx500m is hardware specific. In this example, we assume that we can allot five hundred megabytes of memory for Java Virtual Machine running RMG; please consult a guide to Java for more information. On unix systems we recommend allocating less than half of your available virtual memory, because of the way the Java Virtual Machine forks processes.
To see the content of the output file as it is being generated, use the command: $ tail -f output.log.
To run RMG in Windows: Open a DOS-prompt, change the current working directory to the directory with the condition file, and run the following Java command to launch the program. In this example, the condition file is located in a (new) folder named conditionFiles:
cd "%rmg%"\conditionFiles java -Xmx500m -jar "%rmg%"\bin\RMG.jar condition.txt
The name of the input file does not have to be condition.txt.
A log file containing the same information printed to the console, plus additional details, is automatically saved for you to RMG.log in the same directory as the condition file. Redirection of stdout to a file is no longer required.
As of version 3.2, several batch scripts have been provided to make running RMG on Windows more straightforward. These can be found along with the example condition files in the examples directory. There are currently three such scripts:
The easiest way to use them is:
You can edit the batch script file using a program like Notepad if you want to change thing like the filenames or memory allocation.
You can control where a lot of output and temporary files are stored by manipulating environment variables before running RMG. This can be useful for running on networked clusters of computers, eg. for running several jobs concurrently that can share the same quantum mechanics calculations results, or for saving your temporary scratch files on a local (fast) hard disk, and your final results on a shared network drive.
An example bash script provided in the 1,3-hexadiene example directory, demonstrates the variables and their default values:
The same approach should work for Windows.
You can also pass the variables when you call the program, eg:
$ RMG_QM_LIBRARY=$HOME/myQMlibrary java -Xmx500m -classpath $RMG/bin/RMG.jar RMG condition.txt