HC-MD-QM-CS

From HP-SEE Wiki

Revision as of 09:57, 20 February 2012

General Information

• Application's name: Hybrid Classical/Quantum Molecular Dynamics – Quantum Mechanical Computer Simulation of Condensed Phases
• Application's acronym: HC-MD-QM-CS
• Virtual Research Community: VRC "Computational Chemistry"
• Scientific contact: Ljupčo Pejov, Anastas Mišev, ljupcop[@]pmf.ukim.mk, anastas[@]finki.ukim.mk
• Technical contact: Anastas Mišev, Ljupčo Pejov, anastas[@]finki.ukim.mk, ljupcop[@]pmf.ukim.mk
• Developers: Prof. d-r Ljupčo Pejov, Institute of Chemistry, Faculty of Natural Sciences and Mathematics, UKIM, Skopje, Macedonia, Prof. d-r Anastas Mišev, Faculty of Computer Science and Engineering, UKIM, Skopje
• Web site  :

Short Description

HC-MD-QM-CS studies 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 use parallel numerical algorithms. Quantum molecular dynamics methods are based either on the BOMD (Born-Oppenheimer MD) or ADMP (Atom-centered density matrix propagation) approaches. Subsequently, high-level quantum mechanical calculations are carried out for selected configurations from MD runs, in which various systems’ properties are computed and analyzed. This include anharmonic vivrational frequencies, electronic transitions etc. In the QM calculations, usually first of even first+second solvation shells are explicitly included in the “wavefunction-based” region, while the bulk liquid or solid contributions are included either via charge field perturbation (i.e. charge embedding) or continuum solvation models. The overall objective of the work is to develop a novel general method for computation of complex in-liquid properties of the system, with potential applicability biomedical sciences, material science and engineering, catalysis, etc. 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 (such as, e.g. a supercomputer or HPC cluster).

Problems Solved

The application deals with simulation of condensed phases and properties thereof relevant to 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

University of Uppsala, Sweden

Beneficiaries

• Researchers in the field of biomedical sciences, material science and engineering, catalysis
• Manufacturers of catalysts and advanced materials

Number of users

5

Development plan

• Concept: The concept has been thoroughly planned before the official start of the project
• Start of alpha stage: M1-M6
• Start of beta stage: M7-M8
• Start of testing stage: M8-M9
• Start of deployment stage: M10-M11
• Start of production stage: M12-M24

Resource requirements

• Number of cores required for a single run: From 100 to up to 4000
• Minimum RAM/core required: 2-4 GB
• Storage space during a single run: 100 GB
• Long-term data storage: 2 TB
• Total core hours required: 10 000 000

Technical features and HP-SEE implementation

• Primary programming language: FORTRAN
• Parallel programming paradigm: MPI/OpenMP
• Main parallel code: MPI
• Pre/post processing code: Own developer
• Application tools and libraries: BLAS, LAPACK, SCALAPACK, FFT

Usage Example

Tobefilledin

Infrastructure usage

• Home system: HPCG
  • Applied for access on: 09.2010
  • Access granted on: 09.2010
  • Achieved scalability: 64 cores

Running on Several HP-SEE Centres

• Benchmarking activities and results: ‘’The computational methodology that we develop and use is a hybrid one, as explained elsewhere. It consists of several steps, each of which demands computational resources to a various extent, and scales rather differently with the number of processors/cores. As the procedure has not been fully automated yet, and due to the need to check certain results manually, it is possible that it could not be fully automated for a general case, it is best to judge on its overall scalability on the basis of scalability of its component phases. Such analysis, as explained below in this report, provides a good overview of the overall scalability of the method. The first phase of the complex methodology involves classical or quantum molecular dynamics or Monte-Carlo simulation of the system in question. In this report, we will focus on the scalability of some quantum molecular dynamics approaches. We will discuss first the scalability of the Car-Parrinello molecular dynamics (CPMD). Each CPMD simulation consists of two phases: wavefunction optimization and molecular dynamics simulation. As the optimization runs involve an iterative procedure that needs to converge, the number of iterations required to achieve final convergence being strongly dependent on the particular architecture, compilers and compilation parameters etc., this phase is strongly platform – dependent and not so suitable for benchmarking. Though in the future we aim to make careful comparisons of the optimization results as well, the main accent in the present report will be put on the molecular dynamics phase.
• Other issues: The methodology has been successfully applied to realistic problems; the results are rather encouraging and imply that the current method could become the method-of-choice for treatment of a vast variety of scientific/engineering problems.

Achieved Results

Besides the below-mentioned papers, results have also been obtained and analyzed to some extent for a number of other systems. In this context, we will just mention the following results that are being finalized and prepared for publication: • Solvation of pyrrole by carbon tetrachloride studied by hybrid classical or quantum molecular dynamics – quantum mechanical methods. • Solvation of fluoroform and fluoroform – acetone dimers in liquefied krypton and argon. • ND(H) vibrational frequency shifts in liquid ammonia. • Cyanide ion in water – insights from combined MC-QM studies. • Hydroxide ion in water by a hybrid MC-QM approach.

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.