README for AMPAC 9 with Graphical User Interface ------------------------------------------------ Copyright (c) 1996-2008 Semichem, Inc. All Rights Reserved. This README file describes how to get started using Ampac and Agui (AMPAC Graphic User Interface), the two primary applications of the AMPAC package. Further information about using Ampac and Agui can be found in their respective documentation sets, both of which are accessible from the Help menu of Agui or from the Ampac-9.1/ampacmanual and Ampac-9.1/agui/aguimanual directories. Throughout this document, the AMPAC package is assumed to be installed in the directory: ampac_parent_dir/Ampac-9.1 where ampac_parent_dir is system dependent and is typically one of the following: Windows: C:\Program Files\Semichem, Inc. Linux: /usr/local MacOSX: /Applications Other Unix: /usr/local Installing AMPAC - Windows -------------------------- On Windows systems, AMPAC is installed via a self-extracting executable file called something like Ampac-9_1_3-win32.exe. Simply run this application file by clicking on it and following the directions. Installing AMPAC - Linux ------------------------ On Linux systems, AMPAC is typically installed via a .rpm or .deb package called something like Ampac-9_1_3-Linux_x86.rpm or Ampac-9_1_3-Linux_x86.deb. This .rpm or .deb package can be installed either from a graphical package administration tool but can also be installed from a shell window using the command: rpm -i Ampac-9_1_3-Linux-x86.rpm or apt-get install Ampac-9_1_3-Linux-x86.deb Installing AMPAC - MacOSX and any Unix -------------------------------------- On other Unix-based systems, such as MacOSX and SGI Irix systems, AMPAC is installed via a "tar ball" called something like Ampac-9_1_3-MacOSX_Intel.tar or Ampac-9_1_3-SGI_Irix.tar. To install AMPAC from such a tar ball, run the following commands from a shell window: cd to the directory containing the tarball tar xvf Ampac-9_1_3-Linux.tar cd Ampac-9_1_3 ./INSTALL.csh and then follow the directions of the INSTALL.csh script. Setting up AMPAC ---------------- After installing the AMPAC package, there are a few steps that need to be performed before the Ampac and Agui applications can be used. These steps are outlined here but more detail can be found in the Package Administration section of the Ampac manual. These steps need to only be performed ONCE but may require administrator privileges. 1) A valid AMPAC key file MUST be installed before Ampac and Agui can be used. This key file must be obtained from Semichem's Customer Support (email support@semichem.com). Once the key file is obtained it must be copied to the Ampac-9.1 directory of the AMPAC installation and be given the name ampac.key. The ampac.key file must have read permissions for those users and groups who will be using Ampac or Agui. The ampac.key file is a TEXT file and MUST be transferred in ASCII mode if you are using ftp or sftp to copy it from your email system to the computer on which is AMPAC is installed. 2) Unix and MacOSX systems only. Set the proper file protections: Launch a shell window cd ampac_parent_dir/Ampac-9.1 chmod u+x Set_File_Protection.csh ./Set_File_Protection.csh 3) Unix and MacOSX systems only. Edit the setting of the AMPAC_DIR environment variable in the init_ampac.sh and init_ampac.csh initialization scripts located in the Ampac-9.1 directory. Make sure that the variable AMPAC_DIR near the top of the file is set to the correct full path of Ampac-9.1 directory. 4) Unix and MacOSX systems only. The Ampac initialization scripts appropriate to your preferred shell must be sourced before Ampac, Agui, or any of the AMPAC utilities can be used. If you are not sure of which shell you are using, issue the following command: echo $0 Users of the csh or tcsh shells should add the following to their .cshrc or .login files located in their $HOME directory: if ( -f ampac_parent_dir/init_ampac.csh ) then source ampac_parent_dir/init_ampac.csh endif Users of the sh, ksh or bash shells should add the following to their .profile or .bash_profile files located in their $HOME directory: if [ -f ampac_parent_dir/init_ampac.sh ] then . ampac_parent_dir/init_ampac.sh fi It is necessary to logout and login again before changes made to these these files will take effect. MacOSX users MUST edit their $HOME/.login file even if their preferred shell is bash. 5) Unix and MacOSX systems only. After performing steps 1-4 above, it is recommended that users run the check_env.csh script from a shell window to verify that everything has been set up properly: $AMPAC_DIR/bin/check_env.csh Output from the check_env.csh can be very helpful in diagnosing problems running Ampac or Agui. If you email support@semichem.com about problems running Ampac or Agui, please include the output from check_env.csh in your message. Running Agui ------------ Once the AMPAC package has been installed and setup on your system, launch the Agui application by clicking the Agui icon (located in the Ampac-9.1/agui directory, or via one of its shortcuts), or by entering the command "agui" (without the quotes) from a shell window. Once Agui is running, you can use it for a wide variety of purposes, including setting up and running Ampac calculations and visualizating Ampac results. Within Agui, consult the "Getting Started" section of the Agui Help dialog. Running Ampac Directly ---------------------- The Ampac application requires an Ampac input file in order to run. The Ampac application is typically run via Agui but can also be run directly by the user. To run the Ampac application directly on Windows systems you can simply click the Ampac icon (located in the Ampac-9.1 directory, or via one of its shortcuts) and then select an AMPAC input (*.dat) file using the "Open Ampac Data File(s)" dialog. On other systems, Ampac is best run from a shell window by issuing the command "ampac" (without the quotes") followed by the name of an Ampac input file. As an example, try the following: cd $HOME mkdir testampac cd testampac cp $AMPAC_DIR/agui/aguimanual/gettingstarted/2hydroxybenzaldehyde.dat . ampac 2hydroxybenzaldehyde After a few seconds, Ampac will finish and 3 Ampac result files will have been produced: 2hydroxybenzaldehyde.out, 2hydroxybenzaldehyde.arc and 2hydroxybenzaldehyde.vis. The first two are human-readable text files while the latter is a machine-dependent binary file. All of these result files can be opened in Agui. Semichem Customer Support ------------------------- If the instructions given above are not clear or if you are experiencing problems running Agui or Ampac, please visit our web support pages at: http://www.semichem.com/support.php If your questions are not answered on our website, please contact Semichem Customer Support at: E-Mail: support@semichem.com Phone: (913) 268-3271