Disk space

Almost all chemical information systems work with tlicir own special type of connection table. They often use various formats distinguishing between internal and external connection tables. In most cases, the internal connection tables arc redundant, thus allowing maximum flexibility and increasing the speed of data processing. The external connection tables are usually non-redundant in order to save disk space. Although a connection table can be cprcsented in many different ways, the core remains the same the list of atoms and the list of bonds. Thus, the conversion of one connection table format into another is usually a fairly straightforward task. 

HypcrChcrn sup )orLs MP2 (second order Mollcr-Plessct) correlation cn crgy calculation s tisin g ah initio rn cth ods with an y ava liable basis set. In order lo save mam memory and disk space, the Hyper-Chern MP2 electron correlation calculation normally uses a so called frozen -core" appro.xiniatioii, i.e. the in n er sh ell (core) orbitals are om it ted,. A sett in g in CHKM. INI allows excitation s from the core orbitals lo be included if necessary (melted core). Only the single poin t calcii lation is available for this option. ... 

MP2 correlation energy calculations may increase the computational lime because a tw o-electron integral Iran sfonnalion from atomic orbitals (.40 s) to molecular orbitals (MO s) is ret]uired. HyperClicrn rnayalso need additional main memory arul/orcxtra disk space to store the two-eleetron integrals of the MO s. 

For fast access to the two-electron integrals, a fonr-dimensional array migh t be straigh t for ward. Th e four in times of the four diinen -sional array correspond to the four basis function indices, p, v, X, an d a. respectively. However, the four dimen sional array m ay lake a huge mam memtiry or computer disk space even for a mediiim-si/e molecule. Therefore, this may not be practical. 

Because ol Lhe use of Lwo double-precision words for each in tegral. IlyperCbem needs, for example, ahoiil 44 MByles of computer mam memory and/or disk space Lo store the elecLroii repulsion inlejrrals for benzene wilh a double-zeta 6-i lG basis set. 

With the current impressive CPU and main memory capacity of relatively in expen sive desktop PC s, non-direct SCFaft tnilto calculations involving 300-400 basis function scan be practical. However, to run til esc kin ds of calcti latiori, 20 GBytes of li ard disk space rn ight be needed. Such big disk space is unlikely to be available on desktop PCs.. A direct SCb calculation can elim inate th e n eed for large disk storage. 

The disadvantage of ah initio methods is that they are expensive. These methods often take enormous amounts of computer CPU time, memory, and disk space. The HF method scales as N, where N is the number of basis functions. This means that a calculation twice as big takes 16 times as long (2" ) to complete. Correlated calculations often scale much worse than this. In practice, extremely accurate solutions are only obtainable when the molecule contains a dozen electrons or less. However, results with an accuracy rivaling that of many experimental techniques can be obtained for moderate-size organic molecules. The minimally correlated methods, such as MP2 and GVB, are often used when correlation is important to the description of large molecules. 

Many computational chemistry techniques are extremely computer-intensive. Depending on the type of calculation desired, it could take anywhere from seconds to weeks to do a single calculation. There are many calculations, such as ah initio analysis of biomolecules, that cannot be done on the largest computers in existence. Likewise, calculations can take very large amounts of computer memory and hard disk space. In order to complete work in a reasonable amount of time, it is necessary to understand what factors contribute to the computer resource requirements. Ideally, the user should be able to predict in advance how much computing power will be needed. 

The program can use conventional, in-core, or direct integral evaluation. The default ah initio algorithm checks the disk space and memory available. It then uses an in-core method if sufficient memory is available. If memory is not available for in core evaluation, the program uses a conventional method if... 

Wave functions can be visualized as the total electron density, orbital densities, electrostatic potential, atomic densities, or the Laplacian of the electron density. The program computes the data from the basis functions and molecular orbital coefficients. Thus, it does not need a large amount of disk space to store data, but the computation can be time-consuming. Molden can also compute electrostatic charges from the wave function. Several visualization modes are available, including contour plots, three-dimensional isosurfaces, and data slices. 

Because of the use of two double-precision words for each integral, HyperChem needs, for example, about 44 MBytes of computer main memory and/or disk space to store the electron repulsion integrals for benzene with a double-zeta 6-3IG basis set. 

Sponsor Argonne National Lab, Environmental Assessment Division, Atmospheric Science Section, 9700 S. Cass Ave., Argonne, IL 60439. Developer University of Illinois, Dept, of Mechanical Engineering, 1206 W. Green, Urbana, IL 61801. Custodians D.F. Brown University of lUinois, Dept, of Mechanical Engineering, 1206 W. Green, Urbana IL 61801. Computer It runs on a 486, Pentium PC, or any workstation. The deterministic version runs (slowly) on a 386. The stochastic version of the code was originally written for a Sun Workstation. The PC version requires at least a 486, 33 MHz machine with a minimum of 10 MB of free hard disk space. Cost None ... 

Sponsor/Developing Organization LLNL. Developer. Steven G. Homann, LLNL L 380, P.O, Box 808, Livermore, CA 94551 Phone (501) 423-4962, Fax (501) 423-3090, E-mail shomann llnl.gov. Custodian Same. Hardware IBM PC compatible with a 80286 processor or greater, 512 kB of RAM, Microsoft DOS version 3.0 or later. Math coprocessor chip is desirable optional, hut highly recommended, 0.5 MB hard disk space. Software Pascal, tyjjical mn time several seconds. Cost No charge from LLNL. 

Minimum computer requirements to run THERdbASE are a 486 CPU, IBM or clone, at leasi 8 MB of RAM, at least 40 MB of disk space, color VGA monitor, a mouse, Microsoft Windows. v I To install THERdbASE, execute the File/Run option from within Windows and specify SETUP.F.XE found in the THERDCD directory. This program leads you through the installation. Updates foi THERdbASE can be obtained over the World Wide Web from the Harry Reid Center for Environmental Studies at the University of Nevada, Las Vegas (http //www.eeynre. -hrc, nevada.edu),... 

Selufien The basic strategy behind the direct SCF method is recomputing certain intermediate quantities within the calculation—specifically the two-electron integrals—as needed, rather than storing them on disk. This has the advantage of making it possible to study systems which would require more disk space than is available on the system. 

The disk space (or memory) requirement can be reduced dramatically by performing the SCF in a direct fashion. In the direct SCF method the integrals are calculated from scratch in each iteration. At first this would appear to involve a computational effort which is larger than a conventional FIF calculation by a factor close to the number of iterations. There are, however, a number of considerations which often make direct SCF methods computationally quite competitive or even advantageous. 

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