YammpScripter is a simple application to build scripts for computationally-intensive Yammp simulations. Currently, YammpScripter generates C-Shell scripts but the script is not dependent on the shell (the operating system if you like). Only two lines of the script use C-Shell syntax. It should be easy to modify these lines for other shells. The finished scripts should be submitted to a batch queue for processing. The YammpScripter user interface consists of a menu bar and a text window. Three of the menus generate Yammp commands for the script; these are grouped on the right of the menu bar after the "Vocabulary:" label. The menus can be torn off and placed anywhere on the screen. All four menus have been torn off and placed on top of the text window in the illustration below. The text window contains the script; selecting any item from the three menus on the right causes a command to be generated and added to the text window. Menu items are disabled and activated in stages so that you can only generate commands in the proper order. YammpScripter assumes that the sub-directory from which you started the program will be used as the working directory. You do not have to strictly observe this and the generated script is not dependent on the working directory. However, if you have your input files in the current directory and if you create output files in the same directory, you will find file navigation easier and it is easier to specify output file names. Before Yammp commands can be generated, the YammpScripter>Set... item must be selected (all the menu items after the Vocabulary: label are disabled at this point). This item is for you to specify settings for the shell and there is only one setting for now: you can redirect the standard output from Yammp to a file by entering a file name. If you do not wish to redirect the standard output, leave this entry blank and press the OK button or just Cancel the dialog. Up to this point, selecting YammpScripter>Quit... will cause the program to exit without any further ceremony. The YammpScripter>Set... item is now disabled and Start>Setup... is activated. In this dialog, you can set up the simulation by specifying the names of binary descriptor and archive files. Both files will be opened and verified so obviously they must exist and they must be the correct files for the simulation. If these are the wrong files, the program will terminate - this is a limitation of the yammp module. The three remaining items of the dialog are completely optional. The first optional item is the record number of the input archive that is to be used as a starting conformation for the simulation. To specify the last record enter 0. The program will exit if you enter a record number larger than the number of records in the input archive - another limitation of the yammp module. If this is not specified, it is assumed to be the last record of the input archive. The second optional item is the name of an output archive. If this is not specified, any archives written out during the simulation will be appended to the input archive. If the output archive is specified and the record number is not, the record number is assumed to be the first. A stub will be created for the output archive. When you run the finished script, the stub will be written over. The last optional item is the name of a file containing the CONTRA scoring function. This file must be created with the RPN compiler but this is no longer a supported feature. At this point, the Start>Setup... item is disabled and all the Modify items and all the Run items except one are activated. You can pick items from the Modify and Run menus in any order and as many times as you need. A common item of the Modify dialogs is the (print, archive or update) interval. In all cases, setting an interval of 0, turns off the corresponding action. Each Modify dialog will contain default settings or previously specified values. Change only the items that you need for your simulation and leave other settings alone. In particular, do not clear any entries because the dialog will not allow any null entries; you will then have to Cancel to exit the dialog. YammpScripter will generate commands to change only your settings. When you go back to the same Modify dialog, it will show updated settings. The Modify>Environment... dialog is a bit different from the other Modify dialogs. Some of the settings in this dialog are also updated by other commands. The rule about null items also do not apply to two items. The random number generator seed and the velocity adjustment items do not have preset values. Leave these items unspecified unless you want to reseed the random number generator or adjust the velocities. Note that unless you have read in velocities from the archive file, you must make new ones before you can carry out a Molecular Dynamics simulation. Note that some Yammp functions have return values. YammpScripter will assign these to variables and then discard them. Without the assignment, the return values will be printed on the standard output. You can of course make use of these variables. You can edit the generated commands in the text window but note that YammpScripter will always insert new commands to the end of the script, regardless of the position of the cursor. YammpScripter does not check your revisions and does not pass any changed values to the Modify dialogs. (This can be confusing.) However, YammpScripter will respect your revisions and will save them. For most simulations, you will have no need to review the generated script. If you need to script a complex simulation you can use this application to generate a script template. Shell commands at the beginning and again at the end of the script do not appear in the text window. These commands are added to the finished script when you save it to a file. You can use a text editor to modify the shell commands or the Yammp commands. To finish up, select YammpScripter>Quit... and you will be prompted to enter a file name. The script will be saved in the current directory but you can also save the file in another directory.