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The force array, used by each group except for the neighbor list update This array is used as read only data by the position update group and as accumulate data for the bonded and nonbonded force groups Because the position update group must follow the force computations (as determined using the Order Tasks pattern), we can put this array in the accumulate category for the force groups and in the read only category for the position update group The standard procedure for molecular dynamics simulations [MR95] begins by initializing the force array as a local array on each UE Contributions to elements of the force array are then computed by each UE, with the precise terms computed being unpredictable because of the way the molecule folds in space After all the forces have been computed, the local arrays are reduced into a single array, a copy of which is place on each UE (see the discussion of reduction in Sec 642 for more information)

When designing a system, the correct stream must be selected; when building a system, the type of stream used is not important, as a consistent interface is provided The end effect of the stream, not how it was constructed, is of interest Streams may be chained together, to provide an easier and more manageable interface If, for example, the data needed to be processed in a particular way, a second stream could connect to an existing stream, to provide for processing of the data For example, bytes might be converted from one form into another (such as a number), or a stream of bytes may be interpreted as sequences of characters, as shown in Figure 4-2 In Java, streams take a flexible, one-size-fits-all approach they are fairly interchangeable, and can be applied on top of another stream, or even several other streams Figure 4-2 Streams may be fitted together for additional functionality

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Interchangeability is an extremely important attribute of streams, as it simplifies programming considerably Streams are divided into two categories input streams that may be read from and output streams that may be written to Provided you don't try to read from an output stream, or write to an input stream, you can safely attach any "filter" stream (a stream that filters data in some fashion, such as processing it or converting it from bytes into a different form) to any lowlevel stream (such as a file or network stream) Readers should be aware that, although streams are usually one-way, multiple streams can be used together (eg, an input stream and an output stream) for two-way communication

The neighbor list, shared between the nonbonded force group and the neighbor list update group The neighbor list is essentially local data for the neighbor list update group and read only data for the nonbonded force computation The list can be managed in local storage on each UE

Each item returned from a single request is printed out in turnThe code for handling multiple pages is shown here:

At the heart of network programming is the transmission of data and the sending of sequences of bytes A stream-based approach to communication simplifies programming, as a standard interface for data transmission is offered regardless of the type of data being sent and received, or of the mechanism by which data is sent across the network Of course, streams are not limited to networking they can read from and be written to data structures, files, and other applications However, as will be seen in later chapters, there is more than one way to send data over a network, and I/O streams provide a consistent interface for working with network communication

Figure 35 Data sharing in molecular dynamics We distinguish between sharing for reads, read-writes, and accumulations

String select = "SELECT Rating, Make, Supplier" + " FROM products" + " WHERE Rating > '85'" + " AND ProductType = 'Cigar'" + " ORDER BY Rating DESC" + " LIMIT 2"; AmazonSimpleDB simpleDB = new AmazonSimpleDBClient(id, secret); SelectRequest request = new SelectRequest(); try { requestSelectExpression = select; SelectResult result = null; do { result = simpleDBSelect(request)SelectResult; printSelectResults(result); requestNextToken = resultNextToken; } while (resultIsSetNextToken()); } catch (AmazonSimpleDBException ex) { String code = exErrorCode; String message = exMessage; ConsoleWriteLine("select failed: {0}: {1}", code, message); }

As mentioned earlier, streams provide communication of data at the byte level, and are used for either reading or writing Streams for reading inherit from a common superclass, the javaioInputStream class, shown in Figure 4-3 Likewise, streams used for writing data inherit from the superclass javaio OutputStream, shown in Figure 4-4 These are abstract classes; they cannot be instantiated Instead, an appropriate subclass for the task at hand is created Several streams inherit directly from either InputStream or OutputStream, but most inherit from a filter stream Figure 4-3 Input streams inherit from InputStream, although not always directly

Problem Is the decomposition and dependency analysis so far good enough to move on to the next design space, or should the design be revisited Context At this point, the problem has been decomposed into tasks that can execute concurrently (using the Task Decomposition and Data Decomposition patterns) and the dependencies between them have been identified (using the Group Tasks, Order Tasks, and Data Sharing patterns) In particular, the original problem has been decomposed and analyzed to produce:

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