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Object-oriented Programming Paradigms for Molecular Modeling
Abstract
This paper discusses the application of object-oriented programming (OOP) design concepts to the development of molecular simulation code. A number of new languages such as Fortran 90 (F90) have been developed over the last decade that support the OOP design philosophy. We briefly describe the salient features of F90 and some basic object-oriented design principles. As an illustration of the design concepts we implement a general interface in F90 for calculating pairwise interactions that can be extended easily to any number of different forcefield models. The ideas presented here are used in the development of a mu ltipurpose si mulation c ode, named Music. An example of the use of Music for grand canonical Monte Carlo (GCMC) simulations of flexible sorbate molecules in zeolites is given. The example illustrates how OOP allowed existing code for molecular dynamics and GCMC to be easily combined to perform hybrid GCMC simulations with minimal coding effort.
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Citations
Cites
Computer Simulation of Liquids
Allen, M. P., & Tildesley, D. J. (2017) · doi:10.1093/oso/9780198803195.001.0001 · Cited by 20,945
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Li, J.-R., Yu, J., Lu, W., Sun, L.-B., Sculley, J., Balbuena, P. B., & Zhou, H.-C. (2013) · Nature Communications · doi:10.1038/ncomms2552 · Cited by 631
On the inner workings of Monte Carlo codes
Dubbeldam, D., Torres-Knoop, A., & Walton, K. S. (2013) · Molecular Simulation · doi:10.1080/08927022.2013.819102 · Cited by 422
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Metadata
- Authors
- Gupta, A., Chempath, S., Sanborn, M. J., Clark, L. A., & Snurr, R. Q.
- Venue
- Molecular Simulation
- Publisher
- Informa UK Limited
- Published
- 2003-01
- Volume
- 29
- Issue
- 1
- Pages
- 29-46
- ISSN
- 0892-7022 (ISSN-L)
- 1029-0435
- OpenAlex
- W2093699236
- Cited by
- 378
- References
- 1
- FWCI
- 4.41
- Type
- journal article
- Language
- en
- Open access
- closed
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- Gupta, A., Chempath, S., Sanborn, M. J., Clark, L. A., & Snurr, R. Q. (2003). Object-oriented Programming Paradigms for Molecular Modeling. Molecular Simulation. https://doi.org/10.1080/0892702031000065719
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
