Name
Title | ||
|---|---|---|
ProtoMol, an object-oriented framework for prototyping novel algorithms for molecular dynamics |
Abstract | ||
|---|---|---|
ProtoMol is a high-performance framework in C++ for rapid prototyping of novel algorithms for molecular dynamics and related applications. Its flexibility is achieved primarily through the use of inheritance and design patterns (object-oriented programming). Performance is obtained by using templates that enable generation of efficient code for sections critical to performance (generic programming). The framework encapsulates important optimizations that can be used by developers, such as parallelism in the force computation. Its design is based on domain analysis of numerical integrators for molecular dynamics (MD) and of fast solvers for the force computation, particularly due to electrostatic interactions. Several new and efficient algorithms are implemented in ProtoMol. Finally, it is shown that ProtoMol's sequential performance is excellent when compared to a leading MD program, and that it scales well for moderate number of processors. Binaries and source codes for Windows, Linux, Solaris, IRIX, HP-UX, and AIX platforms are available under open source license at http://protomol.sourceforge.net. |
Year | DOI | Venue |
|---|---|---|
2004 | 10.1145/1024074.1024075 | ACM Trans. Math. Softw. |
Keywords | Field | DocType |
generic programming,multigrid,sequential performance,object-oriented programming,force computation,leading md program,efficient algorithm,multiple time-stepping integration,design pattern,fast electrostatic methods,high-performance framework,molecular dynamic,incremental parallelism,prototyping novel algorithm,object-oriented framework,molecular dynamics,object-oriented framework.,efficient code,source code,domain analysis,numerical integration,object oriented programming | Domain analysis,Rapid prototyping,Object-oriented programming,Source code,Computer science,Parallel computing,Software design pattern,Algorithm,Theoretical computer science,Template,Generic programming,Computation | Journal |
Volume | Issue | ISSN |
30 | 3 | 0098-3500 |
Citations | PageRank | References |
24 | 2.11 | 10 |
Authors | ||
9 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Thierry Matthey | 1 | 43 | 4.16 |
| Trevor Cickovski | 2 | 92 | 13.78 |
| Scott Hampton | 3 | 24 | 2.11 |
| Alice Ko | 4 | 24 | 2.11 |
| Qun Ma | 5 | 28 | 5.08 |
| Matthew Nyerges | 6 | 24 | 2.11 |
| Troy Raeder | 7 | 297 | 15.57 |
| Thomas Slabach | 8 | 69 | 5.31 |
| Jesús A. Izaguirre | 9 | 129 | 15.40 |