11 May 07 Ab-Initio Molecular Dynamics Simulation: Theory and Implementation

by Dominic Marx et.al

Abstract:

The rapidly growing field of ab initio molecular dynamics is reviewed in the spirit of a series of lectures given at the Winterschool 2000 at the John von Neumann Institute for Computing, Juelich. Several such olecular dynamics schemes are compared which arise from following various approximations to the fully coupled Schroedinger equation for electrons and nuclei. Special focus is given to the Car-Parrinello method with discussion of both strengths and weaknesses in addition to its range of applicability. To shed light upon why the Car-Parrinello approach works several alternate perspectives of the underlying ideas are presented. The implementation of ab initio molecular dynamics within the framework of plane wave- pseudopotential density functional theory is given in detail, including diagonalization and minimization techniques as required for the Born-Oppenheimer variant. Efficient algorithms for the most important computational kernel routines are presented. The adaptation of these routines to distributed memory parallel computers is discussed using the implementation within the computer code CPMD as an example. Several advanced techniques from the field of molecular dynamics, (constant temperature dynamics, constant pressure dynamics) and electronic structure theory (free energy functional, excited states) are introduced. The combination of the path integral method with ab initio molecular dynamics is presented in detail, showing its limitations and possible extensions. Finally, a wide range of applications from materials science to biochemistry is listed, which shows the enormous potential of ab initio molecular dynamics for both explaining and predicting properties of molecules and materials on an atomic scale.

The paper could be download here (pdf-file)

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10 Mar 07 Algoritma Simulasi Dinamika Molekular (Molecular Dynamics Simulations (MDS))

Dissertasi F. Hedman, Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry, 2006 (pdf file)

Kata Kunci: Dinamika Molekular (DM), Dinamika Molekular ‘first principles’, Mekanikan Kuantum, liquid water, algoritma paralel, paralel data, MPI, Interkasi Coulomb, Summasi Ewald, nonuniform Fast Fourier transform, FFT, FFTW, NFFT, ENUF

Abstraksi

Methode untuk melakukan Simulasi Dinamika Molekular (SDM) paralel skala-besar di selidiki. Perspektif mengenai medan SDM paralel disajikan. Aspek-aspek hardware dan software dikarakteristikan dan peran keduan didiskusikan secara singkat.

Sebuah metode untuk melakukan DM ‘ab initio’ dideskripsikan; methode merupakan essensi utama dalam re-komputasi (recomputes) potensial interaksi pada setiap ‘time-step’. Metode telah diuji pada sebuah sistem ‘liquid water’ melalui pperbandingan hasil-hasil simulasi lainnya dan hasil-hasil eksperimen. Strategi-strategi yang berbeda dalam paralelisasi dieksploitasi. Di samping itu, metode paralel data bagi interaksi -interaksi jangkauan pendek (short-range) dan jangkauan panjang (long-range) pada platform paralel yang masif dideskripsikan dan dibandingkan.

Kemudian , sebuah metode untuk menghitung interaksi elektrostatis pada SDM di kembangkan. Metode ini mengkombinasikan teknik summasi Ewald dengan ‘nonuniform Fast Fourier transform’ (ENUF). Metode berskala N log N, dimana N adalah jumlah muatan dalam sistem. ENUF mempunyai perilaku sangat mirip dengan summasi Ewald dan dapat diimplentasikan dengan mudah dan efisiensi pada program-program simulasi yang sudah ada.

Akhirnya, sebuah pandangan disajikan dan beberapa arah untuk pengembangan-pengembangan lanjut diusulkan.