HC-MD-QM-CS

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	== Publications and Presentations  ==		== Publications and Presentations  ==
-	''Tobefilledin''	+	* Lj. Pejov, D. Spångberg, Kersti Hermansson, Al3+, Ca2+, Mg2+, AND Li+ IN AQUEOUS SOLUTION: CALCULATED FIRST-SHELL ANHARMONIC OH VIBRATIONS AT 300K, J. Chem. Phys., 133, 174513 (2010).
		+	* J. Tomlinson-Phillips, J. Davis, D. Ben-Amotz, D. Spångberg, Lj. Pejov, K. Hermansson, STRUCTURE AND DYNAMICS OF WATER DANGLING OH BONDS IN HYDROPHOBIC HYDRATION SHELLS. COMPARISON OF SIMULATION AND EXPERIMENT, J. Phys. Chem. A, 115, 6177-6183 (2011).
		+	* K. Hermansson, P. A. Bopp, D. Spångberg, Lj. Pejov, I. Bakó, P. D. Mitev, THE VIBRATING HYDROXIDE ION IN WATER, Chem. Phys. Lett. (FRONTIER ARTICLE), in press.
		+	* P. Naumov, N. Ishizawa, J. Wang, Lj. Pejov, S. C. Lee, ON THE ORIGIN OF THE SOLID-STATE THERMOCHROMISM AND THERMAL FATIGUE OF POLYCYCLIC OVERCROWDED ENES, J. Phys. Chem. A, in press.
		+	* D. Sahpaski, Lj. Pejov, A. Misev, OPTIMIZATION OF INTERMOLECULAR INTERACTION POTENTIAL ENERGY PARAMETERS FOR MONTE-CARLO AND MOLECULAR DYNAMICS SIMULATIONS, Lecture Notes in Comp. Sci., in press.
		+	* A. Misev, D. Sahpaski, Lj. Pejov, IMPLEMENTATION OF HYBRID MONTE CARLO (MOLECULAR DYNAMICS) – QUANTUM MECHANICAL METHODOLOGY FOR MODELING OF CONDENSED PHASES ON HIGH PERFORMANCE COMPUTING ENVIRONMENT, submitted.

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Revision as of 05:32, 7 July 2011

Contents 1 General Information 2 Application and Short Description 3 Problems Solved 4 Scientific and Social Impact 5 Collaborations and Beneficiaries 6 Technical features and HP-SEE implementation 7 Usage Example 8 Publications and Presentations

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

Tobefilledin

Publications and Presentations

• Lj. Pejov, D. Spångberg, Kersti Hermansson, Al3+, Ca2+, Mg2+, AND Li+ IN AQUEOUS SOLUTION: CALCULATED FIRST-SHELL ANHARMONIC OH VIBRATIONS AT 300K, J. Chem. Phys., 133, 174513 (2010).
• J. Tomlinson-Phillips, J. Davis, D. Ben-Amotz, D. Spångberg, Lj. Pejov, K. Hermansson, STRUCTURE AND DYNAMICS OF WATER DANGLING OH BONDS IN HYDROPHOBIC HYDRATION SHELLS. COMPARISON OF SIMULATION AND EXPERIMENT, J. Phys. Chem. A, 115, 6177-6183 (2011).
• K. Hermansson, P. A. Bopp, D. Spångberg, Lj. Pejov, I. Bakó, P. D. Mitev, THE VIBRATING HYDROXIDE ION IN WATER, Chem. Phys. Lett. (FRONTIER ARTICLE), in press.
• P. Naumov, N. Ishizawa, J. Wang, Lj. Pejov, S. C. Lee, ON THE ORIGIN OF THE SOLID-STATE THERMOCHROMISM AND THERMAL FATIGUE OF POLYCYCLIC OVERCROWDED ENES, J. Phys. Chem. A, in press.
• D. Sahpaski, Lj. Pejov, A. Misev, OPTIMIZATION OF INTERMOLECULAR INTERACTION POTENTIAL ENERGY PARAMETERS FOR MONTE-CARLO AND MOLECULAR DYNAMICS SIMULATIONS, Lecture Notes in Comp. Sci., in press.
• A. Misev, D. Sahpaski, Lj. Pejov, IMPLEMENTATION OF HYBRID MONTE CARLO (MOLECULAR DYNAMICS) – QUANTUM MECHANICAL METHODOLOGY FOR MODELING OF CONDENSED PHASES ON HIGH PERFORMANCE COMPUTING ENVIRONMENT, submitted.