Section 5.2.2.2. Loop packets and context within lists

Where multiple data names are declared in a loop header, STAR does however enforce the notion of a `loop packet'. The loop packet is the data structure including all individual data values at a particular iteration through the loop. Hence, in the simple example above, 5.2 and STAR File utilities comprise the tuple of values in a single loop packet. For the single level of loop considered so far, the loop packet plays the role of a table row.

For nested loops, the situation is more complex. Consider Fig. 5.2.2.1, which is an example of quantum chemistry basis sets for hydrogen and lithium. (The examples in this chapter are derived from various test applications, and do not represent specific adopted exchange protocols in the selected subject areas.) For each element, a list of basis sets is presented, each containing a set of parameters and a table of functional values. At the outermost level of looping in this example, a loop packet comprises all the data associated with an individual atom type, for example hydrogen. At the next inner level of looping, a loop packet corresponds to an individual basis set (including its embedded table of coefficients). At the innermost loop level, a loop packet is simply a row within a table of exponents and coefficients of the basis set function.

Figure 5.2.2.1 | top | pdf | Example quantum chemistry basis set functions in STAR File format.

If one were to treat this example file as a database of indeterminate structure and query the values associated with one of the data names, for example, _basis_set_function_exponent, one would retrieve a series of strings 1.3324838E+01, 2.0152720E-01 etc. However, the value strings in themselves are insufficient to allow the reconstitution of any data structure in the file. One also needs an expression of the levels within the nested loop structure at which the values were located, and an indication that they were associated with different packets of information at those various levels. This additional information about the context of each value is sufficient to determine its position within the data structure without any other a priori information regarding the data model. The context is most easily expressed by listing the output values in STAR File format.

Fig. 5.2.2.2 is an output listing of the requested values for this example, where the context is expressed as the innermost of three nested loop levels and distinct packets at this level are indicated. It will be seen also that by tracing the disposition of stop_ words the embedding within higher-level loop packets can also be inferred.

Figure 5.2.2.2 | top | pdf | Retrieval from the example file in Fig. 5.2.2.1 of the value of _basis_set_function_exponent with associated context.