Literate programming methods

The use of literate programming methods leads naturally to structure and standardization in computer code. In turn, this structure leads to subroutine libraries and we describe the specification of a basic tensor algebra subroutine library, which we have recently developed, and which we expect to prove useful in a range of applications. 

In this paper, we advocate the use of literate programming methods, first introduced by Knuth [2], but now little used [3], as a means of placing computer code in the public domain along side the associate theoretical apparatus. Such publication not only places the work in the body of scientific knowledge but also serves to establish authorship. 

The adoption of literate programming methods should lead naturally to structure in a computer program. If we are to consider programs to be works of literature then, just as a book is divided into parts and chapters, and the chapters are further divided into sections and subsections, perhaps supplemented by appendices, the literate approach to programming leads to a modularity of the code. This modularity leads in turn to the concept of a library, a set of fundamental building blocks from which large codes can be synthesized. 

Knuth made these observations twenty years ago. Yet to date they have had surprising little impact in computational quantum chemistry or, indeed, computational chemistry in general. There is no mention of literate programming methods in, for example, the Encyclopedia of Computational Chemistry,28 a major reference work in the field published in 1998. (A notable exception is the... 

Cook describes the application a posteriori of literate programming methods to the last public release of the well known gaussian package, gaussian70, for molecular electronic structure calculations. 

Literate programming methods have been explored for a number of languages. We are not advocating a particular method here, but rather the concept of literate programming in practical quantum chemistry. 

We have demonstrated in this paper how literate programming methods can do much to facilitate the understanding of computer code by the reader and at the same time bring the coding details into the public domain where they can be critically evaluated and perhaps used as the basis for future studies. 

MULTICOMPONENT MANY-BODY PERTURBATION THEORY FOR THE SIMULTANEOUS DESCRIPTION OF ELECTRONIC AND NUCLEAR MOTION TOWARDS A PRACTICAL IMPLEMENTATION USING LITERATE PROGRAMMING METHODS... 

It is not our purpose to give a detailed description of literate programming and its application in quantum chemistry. We restrict our attention here to those details which are essential to our present purpose - the development of a literate quantum chemistry program for the simultaneous description of electronic and nuclear motion in molecules. For further details of literate programming methods we refer the reader to the original publication of Knuth [40]. For further details of applications of literate programming in quantum chemistry we refer the reader to our previous work [41 14] as well as our paper in the present volume [34],... 

Abstract. In this paper, we advocate the use of literate programming techniques in molecular physics and quantum chemistry. With a suitable choice of publication medium, literate programming allows both a theory and corresponding computer code to be placed in the public domain and subject to the usual open criticism and constructive use which form an essential ingredient of the scientific method. 

Thus literate programming appears ideally suited to the task of publication in computational molecular physics and quantum chemistry, and indeed, in other computational sciences and in engineering. This task must entail placing both the theoretical model and the associated computer code in the public domain, where they can be subjected to the open criticism and constructive use which forms an integral part of the scientific method. 

H. M. Quiney and S. Wilson, Literate programming for the molecular structure problem. I An Introduction to Computational Methods in Quantum Chemistry (in preparation). 

The practitioner of literate programming can be regarded as an essayist, whose main concern is with exposition and excellence of style. Such an author, with thesaurus in hand, chooses the names of variables carefully and explains what each variable means. He or she strives for a program that is comprehensible because its concepts have been introduced in an order that is best for human understanding, using a mixture of formal and informal methods that reinforce each other. ... 

The practical realization of multicomponent MBPT rests on the development of efficient algorithms and the associated computer code. In recent work, we have advocated the use literate programming techniques in the development and publication of computer code for molecular structure calculations. We briefly discuss the application of these methods to the multicomponent many-body perturbation expansion. 

With the advent of the stored-program digital computer a minor revolution occurred in quantum chemistry. The integrals appearing in the models being used for small molecules were actually evaluated and it became clear that molecules were enormously more complicated than had been anticipated. The oversimplified valence bond and molecular orbital methods often gave qualitatively ridiculous results when taken literally (11). 

Principles of Thermodynamics should be accessible to scientifically literate persons who are either learning the subject on their own or reviewing the material. At Emory University, this volume forms the basis of the first semester of a one-year sequence in physical chemistry. Problems and questions are included at the end of each chapter. Essentially, the questions test whether the students understand the material, and the problems test whether they can use the derived results. More difficult problems are indicated by an asterisk. Some problems, marked with an M, involve numerical calculations that are most easily performed with the use of a computer program such as Mathcad or Mathematica. A brief survey of some of these numerical methods is included in Appendix B, for cases in which the programs are unavailable or cumbersome to use. 

Time t, adiabatic rise of temperature T°K, and concentration of isocyanate C and C, were experimentally determined and recorded (Table II, columns 1,2, and 6). Other values were programmed by a regression method using a computer (Table II, columns 3,4,5,7, and 8). The initial concentration C of isocyanate for each of the five elastomers, expressed in equivalents per liter, as well as density values, were calculated and compiled in Table I. 

Since the time of this publication, literally thousands of datasets have been correlated the database of the equations generated by the Pomona group (BioLoom) contains more than six thousand equations. In addition, such studies led to the commercialization of products. Most recently, the European Community in its Registration, Evaluation, Authorisation and Restriction of Chemicals (REACH) program states that for each chemical circulating in the European territory, a complete dossier on physico-chemical, biological, and toxicological properties must be compiled. For this purpose, validated QSAR methods are accepted. ... 

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