Once installation is complete, and any necessary adjustments are made to the user account, the user is now able to run Q-Chem. There are several ways to invoke Q-Chem:
IQmol offers a fully integrated graphical interface for the Q-Chem package and includes a sophisticated input generator with contextual help which is able to guide you through the many Q-Chem options available. It also provides a molecular builder, job submission and monitoring tools, and is able to visualize molecular orbitals, densities and vibrational frequencies. For the latest version and download/installation instructions, please see the IQmol homepage (www.iqmol.org).
qchem command line shell script. The simple format for command line execution is given below. The remainder of this manual covers the creation of input files in detail.
Via a third-party GUI. The two most popular ones are:
A general web-based interface for electronic structure software, WebMO
(www.webmo.net).
Wavefunction’s Spartan user interface on some platforms. Contact Wavefunction, Inc.
(www.wavefun.com) or Q-Chem for full details of current availability.
Using the Q-Chem command line shell script (qchem) is straightforward provided Q-Chem has been correctly installed on your machine and the necessary environment variables have been set in your .cshrc, .profile, or equivalent login file. If done correctly, the necessary changes will have been made to the $PATH variable automatically on login so that Q-Chem can be invoked from your working directory.
The qchem shell script can be used in either of the following ways:
qchem infile outfile qchem infile outfile savename qchem -save infile outfile savename
where infile is the name of a suitably formatted Q-Chem input file (detailed in Chapter 3, and the remainder of this manual), and the outfile is the name of the file to which Q-Chem will place the job output information.
Note: If the outfile already exists in the working directory, it will be overwritten.
The use of the savename command line variable allows the saving of a few key scratch files between runs, and is necessary when instructing Q-Chem to read information from previous jobs. If the savename argument is not given, Q-Chem deletes all temporary scratch files at the end of a run. The saved files are in $QCSCRATCH/savename/, and include files with the current molecular geometry, the current molecular orbitals and density matrix and the current force constants (if available). The –save option in conjunction with savename means that all temporary files are saved, rather than just the few essential files described above. Normally this is not required. When $QCLOCALSCR has been specified, the temporary files will be stored there and copied to $QCSCRATCH/savename/ at the end of normal termination.
The name of the input parameters infile, outfile and save can be chosen at the discretion of the user (usual UNIX file and directory name restrictions apply). It maybe helpful to use the same job name for infile and outfile, but with varying suffixes. For example:
localhost-1> qchem water.in water.out &
invokes Q-Chem where the input is taken from water.in and the output is placed into water.out. The & places the job into the background so that you may continue to work in the current shell.
localhost-2> qchem water.com water.log water &
invokes Q-Chem where the input is assumed to reside in water.com, the output is placed into water.log and the key scratch files are saved in a directory $QCSCRATCH/water/.
Note: A checkpoint file can be requested by setting GUI = 2 in the $rem section of the input. The checkpoint file name is determined by the $GUIFILE environment variable which by default is set to ${input}.fchk