|Quantum 1 Modules|
The Quantum 1 module includes:
Quantum chemistry applications
This section includes:
Both techniques can be used to perform the same range of basic tasks, including:
Molecular mechanics simulations use the laws of classical physics to predict the structures and properties of molecules. Many different molecular mechanics methods exist, each characterized by a forcefield. Please see Forcefield-Based Simulations for details about molecular mechanics forcefields, theory, and methods.
Quantum mechanical simulations are based on the laws of quantum mechanics rather than classical physics. Quantum mechanics states that the energy and other related properties of a molecule can be obtained by solving the Schrödinger equation:
H = E
For any but the smallest symmetric systems, however, exact solutions to the Schrödinger equation cannot be obtained in practice. Quantum mechanical methods are characterized by their various mathematical approximations to its solution. Several major classes of quantum mechanical methods exist:
Advantages and disadvantages
Semi-empirical and ab initio methods differ in the trade-off made between accuracy and computational cost. Semi-empirical calculations are relatively inexpensive and provide reasonable qualitative descriptions of molecular systems and fairly accurate quantitative predictions of energies and structures for systems where good parameter sets exist.
This section introduces the individual interfaces that are included in the Quantum 1 module and provides an overview of some of the features and terminology common to them.
Overview of Quantum 1 module
Quantum programs in the Cerius2·Quantum 2 module are documented separately.|
ADF has been developed by the Vrije Universiteit Amsterdam and can be used in studies of molecular spectroscopy, organic and inorganic chemistry, crystallography, and pharmacochemistry. It is based on the Kohn-Sham approach to the density functional theory and, in principle, yields exact properties such as the electron density and related properties and the total energy.
DMol3 is a first-principles (ab initio) quantum chemistry software package that performs accurate theoretical calculations on a wide range of compounds, including metal clusters, biological compounds, organometallics, and organic compounds.
Gaussian 92 and Gaussian 94 are full-featured computational chemistry packages from Gaussian Inc. that provide a wide variety of powerful semi-empirical and ab initio molecular orbital methods. However, because input and output are in the form of ASCII text files, setting up and analyzing the results of Gaussian jobs in the absence of a graphical interface can prove time-consuming and difficult.
MOPAC is a general-purpose semi-empirical molecular orbital package that implements the MNDO, MINDO/3, AM1, and PM3 Hamiltonian approximation methods. Several versions are available in the public domain, and MOPAC6 executables are supplied with Cerius2.
Zindo is a comprehensive semi-empirical package developed by M. C. Zerner (University of Florida) and co-workers. Zindo calculates electronic and structural properties of molecular systems. It's advantage over other semi-empirical packages lies in its ability to calculate UV/visible spectra and its ability to treat systems including transition metal atoms. Zindo executables are provided with Cerius2.
The menus, control panels, and other elements that make up the ADF, DMol3, Gaussian, MOPAC, and Zindo interfaces in Cerius2 have been designed to provide an integrated, consistent look and feel throughout the Quantum 1 module.
Quantum mechanics applications are extremely powerful tools. However, these tools are generally very complex, offering many options and parameters for specifying and fine-tuning a job. Although an experienced user may be familiar with them, the number of options may be daunting to a novice whose requirements are somewhat less demanding.
You can specify all the options necessary for a basic job from the Run control panel--the interface automatically sets reasonable default values for all necessary ancillary parameters. To enable you to set up a more complex job and set the values of the ancillary parameters yourself, some pushbuttons on the Run control panels provide access to control panels that allow you to set options and parameters related to each area of functionality.
When the job ends successfully, the results of the run are written in output files with the same prefix as the input file. The Quantum 1 analysis tools allow you to select any such output file and, from the numeric description of the model's wavefunction, obtain more readily usable information.
Job execution and control
Interface to executables
Several issues help you understand how the Quantum 1 applications work:
The sophisticated job control facilities provided by the Quantum 1 module allow you to take full advantage of heterogeneous network environments. You can readily specify how and where your jobs should run, monitor their progress, and transfer input and output files to and from remote systems.
Interactive run mode
Quantum 1 jobs initiated in interactive mode run in much the same way as do other Cerius2 tasks (that is, the job runs as though Cerius2 were processing the job itself). Cerius2 waits, so you cannot perform other Cerius2 tasks until the job ends.
Background run mode
Jobs initiated in background mode run as a background process on the specified local or remote host. Once the job has been successfully initiated, Cerius2 is free to perform other tasks. If the job is run remotely, input files are transferred automatically to that host for execution; output files may need to be manually recovered from the remote host after the job is finished.
NQS run mode
Jobs initiated in NQS mode are submitted to queues on the specified local or remote host, provided that the Network Queueing System software has been installed on that host. Once the job has been successfully queued, Cerius2 is free to perform other tasks. If the job is run remotely, input files are transferred automatically to that host for execution; output files may need to be manually recovered from the remote host after the job is finished.
Jobs initiated in background mode or via the NQS mechanism can run for long periods of time and, when complete, terminate silently (although you can request that email be sent to you when an NQS job ends). For this reason, the Quantum 1 applications include a complete set of job control tools that allow you to monitor job status, stop jobs by killing the associated process, and manually recover output files from remote systems.
This section describes the procedures necessary for configuring three of the standalone quantum applications for use in the Cerius2 environment. You should have your system administrator perform the necessary configuration steps if this has not already been done.
Configuring Quantum 1 applications
Each of the products can be run on hosts other than those licensed for Cerius2. To support this functionality, rjrd (the MSI Remote Job Run Daemon), an application that controls Cerius2-initiated jobs on remote machines, must be available on potential hosts for any Quantum 1 application.|
ADF must be installed according to the standard installation instructions. As part of this procedure, you (or the system administrator) need to define an
A record in the applcomm.db file for each machine that ADF is installed on for each of these items:
ADFBIN--Where the ADF executable is located.
For each machine on which standalone DMol3 is installed, you need a dmol3exe entry in the applcomm.db file which points to the location of the DMol3 standalone executable.
In a standard installation, the dmol3exe entry in the applcomm.db file points to the DMol3 standalone executable provided with Cerius2.
Gaussian must be installed according to the standard installation instructions. As part of this procedure, you must set the environment variable
g92root(for Gaussian 92) or
g94root(for Gaussian 94) to point to the directory in which the program is installed. To run jobs using the Gaussian interface,
g94root) must be set (via applcomm.db) for all the hosts on which you want to run Gaussian.
Optional environment variables
The Gaussian software uses scratch files for temporary storage during calculations, and these can become very large. Gaussian allows the default location of the directory in which these files are held (that is, the working directory) to be changed via the environment variable GAUSS_SCRDIR. You can change the value of GAUSS_SCRDIR by setting the variables
g94scratch in applcomm.db. They are then used to set GAUSS_SCRDIR. If
g94scratch for Gaussian 94) is not set in applcomm.db, the current working directory is used.
g94newzmat, can also be set in the applcomm.db file to specify nonstandard locations for the main g92 executable and for the formchk and newzmat programs, respectively. You should need to use these only if you have a customized Gaussian 92 installation.
g94newzmat can be set if you have a customized Gaussian 94 installation.
Three different versions of the basic program exist:
In a standard installation, the directory c2_install_dir/mopac contains several files necessary to support MOPAC. These include a run script for each supported version of MOPAC (mopac6.sh, mopac7.sh, and mopac93.sh), a MOPAC6 executable (mopac6.exe), and a binary conversion utility (mopacconv.f).
The script files are used by the MOPAC interface to run the three supported versions of MOPAC, each calling the executable defined by the corresponding applcomm.db entry (see mopac6exe, mopac7exe, and mopac93exe).
mopacdir entry points to the directory that contains the three run scripts. These scripts must always be together in the same directory. In the supplied version of applcomm.db, this is set to c2_install_dir/mopac. If you want to use a customized version of any of these scripts, you should put the customized script(s) and other standard scripts together in another directory and change the mopacdir entry in applcomm.db to point to this location.
mopac6exe entry points to the MOPAC6 executable. In the supplied version of applcomm.db this is set to c2_install_dir/mopac/mopac6.exe.
mopac7exe entry points to the name of the MOPAC7 executable. Because MSI cannot distribute this version of the program, mopac7exe is not set in the supplied version of the applcomm.db file.
mopac93exe entry points to the name of the MOPAC93 executable. Because MSI cannot distribute this version of the program, mopac93exe is not set in the supplied version of the applcomm.db file.
mopacconv entry points to the name of the executable version of the binary conversion program, if required. If this entry is set, then binary graphics files (.gpt) are converted into formatted files (.fgpt). This entry is not set in the supplied version of the applcomm.db file.
Zindo must be installed according to the standard installation instructions.
zindoexe entry in the applcomm.db file which points to the location of the Zindo standalone executable
zindoexe entry in applcomm.db points to the Zindo standalone executable provided with Cerius2.
Example applcomm.db file entries
The following applcomm.db extract contains example entries for quantum applications.
# These lines specify the locations of the ADF
# files. You may need to alter the specifications
# if you want to run ADF on a machine on which you do
# not have Cerius2 licensed.
A SGI adf c2_install_dir/exec/adf.exe
A SGI ADFBIN c2_install_dir/adf/bin
A SGI ADFUTILITIES c2_install_dir/adf/bin
A SGI ADFRESOURCES c2_install_dir/Cerius2-Resources/ADF/atomicdata
# The following line specifies the location of the main
# Gaussian 92 directories. Replace the path name with that
# for your own installation. If you don't have Gaussian
# 92, omit this line.
A SGI g92root /usr/mydir/gaussian92
# The following line specifies the location of the main
# Gaussian 94 directories. Replace the path name with that
# for your own installation. If you don't have Gaussian
# 94, omit this line.
A SGI g94root /usr/mydir/gaussian94
# The following lines specify an alternative location for the
# Gaussian 92 and Gaussian 94 scratch directories. If this
# line is omitted, the current working directory is used.
A SGI g92scratch /usr/disk2/gaussian.scratch
A SGI g94scratch /usr/disk2/gaussian.scratch
# The following two lines are standard. Only change them
# if you have a non-standard installation, or if you
# want to run mopac on a machine on which you do not
# have Cerius2 installed.
A SGI mopacdir c2_install_dir/mopac
A SGI mopac6exe c2_install_dir/mopac/mopac6.exe
# The following line specifies the location of the MOPAC7
# executable. If you don't have MOPAC7, omit this line.
A SGI mopac7exe /usr/mydir/mopac7/mopac7_sgrw/mopac.exe
# The following line specifies the location of the MOPAC93
# executable. Replace the path name with that of your own
# installation. If you don't have MOPAC93, omit this line.
A SGI mopac93exe /usr/mydir/mopac93/m93_src/mopac93.exe
# The following line specifies the location of the
# DMol3 executable. Only change it if you have a
# non-standard installation, or if you want to run DMol3
# on a machine on which you do not have Cerius2 installed.
A SGI dmol3exe c2_install_dir/exec/dmol3