HC-MD-QM-CS

From HP-SEE Wiki

Revision as of 07:55, 6 July 2011

General Information

• Applization's name : Hybrid Classical/Quantum Molecular Dynamics – Quantum Mechanical Computer Simulation of Condensed Phases
• Virtual Research Communities  : Computational Chemistry Applications
• Scientific contact  : Ljupco Pejov, ljupcop@iunona.pmf.ukim.edu.mk
• Technical contact : Ljupco Pejov, ljupcop@iunona.pmf.ukim.edu.mk
• Developers  : Ljupco Pejov, UKIM, Institute of Chemistry, Faculty of Natural Science and Mathematics, FYROM
• Web site  :

Application and Short Description

To study the properties of condensed phases, liquids (such as e.g. solutions of ions and various molecular systems in molecular liquids), solids (including small molecular systems adsorbed on surfaces), computer simulations, which will use parallel numerical algorithms will be carried out. Quantum molecular dynamics methods will be based either on the BOMD (Born-Oppenheimer MD) or ADMP (Atom-centered density matrix propagation) approaches. Subsequently, high-level quantum mechanical calculations will be carried out for selected configurations from MD runs, in which various systems’ properties will be computed and analyzed. This will include anharmonic vivrational frequencies, electronic transitions etc. In the QM calculations, usually first of even first+second solvation shells will be explicitly included in the “wavefunction-based” region, while the bulk liquid or solid contributions will be included either via charge field perturbation (i.e. charge embedding) or continuum solvation models.

Achieving good parallel efficiency for calculations of such type is far from a trivial task without the use of high-performance low-latency MPI interconnect. Often, the overall CPU time which is required is very high, and is unfortunately not available to us at present. Often, the overall CPU time which is required is very high, and is unfortunately not available to us at present.

Problems Solved

The overall objective of the work will be to develop a novel general computational methodology for modeling of complex in-liquid properties of the system, with potential applicability biomedical sciences, material science and engineering, catalysis, etc.

Scientific and Social Impact

The described studies are of high fundamental significance, concerning the properties of condensed phases and influence thereof on various molecular species, but is also of high relevance to biomedical and materials science.

Benefits for the industry, especially catalysis and nanoelectronics.

Collaborations and Beneficiaries

University of Uppsala, Sweden

Technical features and HP-SEE implementation

• Primary programming language : FORTRAN
• Parallel programming paradigm : SMP and MPI
• Main parallel code : In-house development
• Pre/post processing code : In-house development
• Full-scale number of logical CPUs : 64-128
• Minimum RAM/core required : 2-4GB
• Storage space during a single run : 100GB
• Long-term data storage : 2TB

Usage Example

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Publications and Presentations

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