Levels structural parallelism

The exponential increase in computer power and the development of highly efficient algorithms has distinctly expanded the range of structures that can be treated on a first-principle level. Using parallel computers, AIMD simulations of systems with few hundred atoms can be performed nowadays. This range already starts to approach the one relevant in biochemistry. Indeed, some simulations of entire biomolecules in laboratory-realizable conditions (such as crystals or aqueous solutions) have been performed recently [25-28]. For most applications however, the systems are still too large to be treated fully at the AIMD level. By combining AIMD simulations with a classical MD force field in a mixed quantum mechanical/molecular mechanical fashion (Hybrid-AIMD) the effects of the protein environment can be explicitly taken into account and the system size can be extended. 

No Nested Parall el ism restriction Restricts the programmer from using nested explicitly parallel constructs, and disallows the compiler from implicitly inserting such constructs Can be specified in a Restrictions pragma to ensure tasklet DAGs remain one-level structures, to simplify analysis... 

Much effort has been invested to obtain a complete understanding of the detailed structure of Rydberg states of alkaline-earth atoms. In parallel to the experimental mapping of states went a successful parametrization of the observed spectra by the Multichannel Quantum Defect Theory (MQDT). The paper by Cooke presented at the last ICAP described the basic aspects of this approach. Specifically, the level structure was measured and analysed by MQDT for odd ... 

As noted above, one of the goals of NAMD 2 is to take advantage of clusters of symmetric multiprocessor workstations and other non-uniform memory access platforms. This can be achieved in the current design by allowing multiple compute objects to run concurrently on different processors via kernel-level threads. Because compute objects interact in a controlled manner with patches, access controls need only be applied to a small number of structures such as force and energy accumulators. A shared memory environment will therefore contribute almost no parallel overhead and generate communication equal to that of a single-processor node. 

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