Hypercube

HyperCube, Inc., http //www.hyper.com/default.htm n. Product Summaries  

Hypercube specializes in molecular modeling software for researchers and students. Their principal product is HyperChem, which runs on Microsoft Windows and is available in two forms - Standard and Release 7.5. HyperChem Lite is a more affordable version and contains a product offering that is tailored to students. 

Computational Methods - HyperChem Lite integrates molecular mechanics and semi-empirical quantum mechanics (molecular orbital) calculations into a single package. A brief description of product features and capabilities follows. 

Pocket HyperChem 1.1 is the first chemistry software to run on Windows CE based devices. This product provides the basic molecular modeling and computational chemistry functionality of HyperChem on a portable Palmtop PC platform, allowing the user to work in environments beyond those possible with desktop PC s or notebook computers. 

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The HyperChem programs of Hypercube, Inc webpage http //www.hvper.com... 

Smith W 1991 Molecular dynamics on hypercube parallel computers Comput. Phys. Commun. 62 229-48... 

W. Smith, Molecular dynamics on hypercube parallel computers , Comp. Phys. Comm., Vol 62, no 2 3, 229-48, 1991. 

The HyperChem philosophy associated with back end computations is one which is in tended to in still eon fiden ce. as far as is possible. in the scientific results emanating from HyperChem. This ph ilosoph y is on e of open n ess — open n ess aboii t the prod net. the calculations being performed, the science embodied in the product, etc. Apart from protecting the proprietary code associated with a commercial product. Hypercube wushes to document and describe as fully as is possible tb e calculation s th at HypcrCb cm performs. There should be no mystery about the scientific results obtained with HyperChem. 

Price category student, individual, production, departmental Platforms PC (Windows), SGI, HP-UX, Win CE Contact information Hypercube, Inc. 

The HyperChem program from Hypercube Inc. and UniChem from Oxford Molecular can be used as graphic interfaces to Q-Chem. At the time we conducted our tests, it was not yet available on all the platforms listed as being supported. The current version is well designed for ground- and excited-state calculations on small or large organic molecules. 

The HyperChem MMh- code and program also differ from MM2(1977) by having parameters in text files separate from the code. These parameter files are available for your modification and additions. The parameters distributed with HyperChem include the public domain values, generally referred to as the MM2(1991) parameter set, that Dr. Allinger contributed to HyperCube, Inc. Parameters not obtained from Dr. Allinger are appropriately labeled in the distributed parameter files. 

Hypercube would like to thank the following authors for contributing significant portions of this text ... 

Hyper compressors Hypercube topology Hyperfiltration Hyperglycemia... 

A.C. Robinson, C.T. Vaughan, H.E. Fang, C.F. Diegert, and K. Cho, Hydrocode Development on the nCUBE and the Connection Machine Hypercubes, Proceedings of the 1991 APS Topical Conference on Shock Compression of Condensed Matter, Williamsburg, VA, 1991. 

Uncertainty - analyzes the uncertainty of a system, sequence, or end state using either the Monte Carlo or Latin Hypercube simulation technique. 

The Systems Module constructs and displays fault trees using EASYFLOW which aic read automatically to generate minimal cutsets that can be transferred, for solution, to SETS. CAFT A. or IRRAS and then transferred to RISKMAN for point estimates and uncertainty analysi,s using Monte Carlo simulations or Latin hypercube. Uncertainty analysis is performed on the systems lev el using a probability quantification model and using Monte Carlo simulations from unavailability distributions. 

Iman, R. L. and M. J. Shortencarrier, 1984, A FORTRAN 77 Program and User s Guide for the Generation of Latin Hypercube and Random Samples for Use with Computer Model, NUREG/CR-3624, March. 

Kauffman ([kauffSO], [kauffOOa]) has introduced a class of parametrizable fitness landscapes called NK-landscapes, that provide a formalism for studying the efficacy of GA evolution as a function of certain statistical properties of the landscape. Given N binary variables Xi = 1, so that x = (xi, X2, , Xjv) represents a vertex of an A -dimensional hypercube, an NK-landscape is defined by a fitness function, JF, of the form... 

One example of such a new approach is the hypercube architecture, in which many processors are linked together as a team to solve a single problem. A well-integrated team of cheap processing units can potentially outperform the most sophisticated single-processor machine. In addition, since each processor can have its own dedicated memory, the total system can have both more memory than current supercomputers and more memory in use at any given moment. 

Standard programs must be broken into smaller pieces to run on a hypercube. Each processor is assigned the responsibility for calculations for a specific piece of a problem. For example, in petroleum reservoir simulation, each processor might be assigned a different section of the reservoir to model. In modeling a complex chemical plant, each processor might be assigned a different piece of equipment. As each processor proceeds, it informs the other processors of its results, so that all the other processors can incorporate the information into their respective portions of the overall calculation. 

Hypercubes and other new computer architectures (e.g., systems based on simulations of neural networks) represent exciting new tools for chemical engineers. A wide variety of applications central to the concerns of chemical engineers (e.g., fluid dynamics and heat flow) have already been converted to run on these architectures. The new computer designs promise to move the field of chemical engineering substantially away from its dependence on simplified models toward computer simulations and calculations that more closely represent the incredible complexity of the real world. 

Hypercube Inc., 16 Blenheim Road, Cambridge, Ontario NIS 1E6 Canada. 

The simplest and fastest techniques for grouping molecules are partitioning methods. Every molecule is represented by a point in an n-dimensional space, the axes of which are defined by the n components of the descriptor vector. The range of values for each component is then subdivided into a set of subranges (or bins). As a result, the entire multidimensional space is partitioned into a number of hypercubes (or cells) of fixed size, and every molecule (represented as a point in this space) falls into one of these cells [57]. 

Input data mapping still corresponds to projection on a hypersphere however, ART uses vector direction to assess similarity rather than using a distance measure as shown in Fig. 15. This translates into the use of hypercone clusters in a unit hypercube. 

The third step is to select the number of iterations or calculations of dose that are to be performed as a part of each simulation. For the analysis here, a total of 10,000 iterations based on the selection of input variables from each defined distribution were performed as part of each simulation. The large number of iterations performed, as well as the Latin hypercube sampling (non-random sampling) technique employed by the Crystal Ball simulation program, ensured that the input distributions were well characterized, that all portions of the distribution (such as the tails) were included in the analysis, and that the resulting exposure distributions were stable. 

In the LB technique, the fluid to be simulated consists of a large set of fictitious particles. Essentially, the LB technique boils down to tracking a collection of these fictitious particles residing on a regular lattice. A typical lattice that is commonly used for the effective simulation of the NS equations (Somers, 1993) is a 3-D projection of a 4-D face-centred hypercube. This projected lattice has 18 velocity directions. Every time step, the particles move synchronously along these directions to neighboring lattice sites where they collide. The collisions at the lattice sites have to conserve mass and momentum and obey the so-called collision operator comprising a set of collision rules. The characteristic features of the LB technique are the distribution of particle densities over the various directions, the lattice velocities, and the collision rules. 

Local sensitivity analysis is of limited value when the chemical system is non-linear. In this case global methods, which vary the parameters over the range of their possible values, are preferable. Two global uncertainty methods have been used in this work, a screening method, the so-called Morris One-At-A-Time (MOAT) analysis and a Monte Carlo analysis with Latin Hypercube Sampling (Saltelli et al., 2000 Zador et al., submitted, 20041). The analyses were performed by varying rate parameters, branching ratios and constrained concentrations within their uncertainty interval,... 

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