Literate programming techniques

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. 

We briefly consider the use of literate programming techniques in enhancing collaborative virtual environments, which facilitate developed cooperation between geographically distributed sites. 

The use of literate programming techniques means that we can clearly indicate contravariant and covariant indices in the IAIj]]X fragment describing code for btas. 

By combining documentation, including the theoretical foundations of the model being employed, with the associated computer code, literate programming techniques offer, in order of importance, the follow benefits to the quantum chemistry community -... 

Unfortunately, it appears that literate programming techniques are today little used [5]. But, in recent work [3], we have emphasized their value as a means of placing quantum chemistry computer code in the public domain along side the associated theoretical apparatus. Such publication not only places the work in the body of scientific knowledge, where it can be [14]... 

Quantum chemistry is a field of research which depends heavily on computation. The potential of literate programming techniques to accelerate the development of computational quantum chemistry is evident. By placing quantum chemistry computer programs in the public domain in a form which can be easily read and comprehended by the human reader they are placed in the body of scientific knowledge where they can be openly criticized and used constructively. 

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. 

In a companion paper [34], we give an example of the a posteriori application of literate programming techniques to a quantum chemistry computer program - a program for MBPT electronic structure calculations. Such calculations have been a mainstay... 

We are examining those commonly used baits, the protein hydrolysates. Initial studies have used the corn gluten hydrolysate commonly known as PIB-7 or, now, as Nu-Lure Insect Bait (NLIB). This material was used in the recent successful Medfly eradication program in California. Since the fruit flies are probably attracted to the volatile emanations from the bait, we have used equipment and techniques previously developed by members of our group for flavor research. For example, a modified Likens-Nickerson simultaneous steam distillation-extraction head was developed by Flath and Forrey (67.). Also, there is a 90 liter... 

An analytical program must be established, capable of identifying and quantifying contaminants in a water source to be treated, in order to assess remedial technologies. MCLs (maximum contaminant levels) for volatile organic pollutants in micrograms per liter have been prescribed by the US EPA (US Environmental Protection Agency), based on continual improvements in detection techniques. 

The remaining, rather technical correctness criteria are specific to every SLDNF refutation procedure. These aspects are usually a simple manual task. They can also be handled by data-flow analysis or abstract interpretation techniques that reveal, for each directionality, a correct permutation of the program clauses, and a correct permutation of the literals in the body of each clause, and sometimes the addition or deletion of literals. Multi-directionality is usually difficult to achieve. The corresponding tool of the Folon environment is described by [De Boeck and Le Charlier 90]. 

Despite the fact that literally millions of peels are carried out annually in the United States, there is really no formal integration of peeling techniques in any established dermatologic or plastic surgery programs. The only way to learn how to perform peels is to watch someone do them... 

Chemisorbed molecules Literally hundreds of adsorbate-surface systems have been investigated in the circa 20 years over which HREELS measurements have been made. A selection of work will be presented that represents the major principles of HREELS and what can be learned from this technique. It is not comprehensive, and an electronic literature search program is recommended for up-to-the-minute references to the state of the art . Modes are often denoted by Greek letters, the most common are v for stretching modes, 8 for bending modes and p for wag, scissor or twisting modes. Aromatic molecules have several different labelling conventions. 

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