Organic Inorganic Physical Biological Editors: Charles L. Brooks Iii • Gernot

نویسندگان

  • FRENKING
  • SHIGEYOSHI SAKAKI
  • ANDRES JARAMILLO-BOTERO
  • JULIUS SU
  • AN QI
  • WILLIAM A. GODDARD
چکیده

We describe the first principle-based electron force field (eFF) methodology for modeling the simultaneous dynamics of electrons and nuclei (eMD) evolving nonadiabatically under transient extreme conditions. We introduce the parallel implementation of eFF (pEFF) that makes it practical to perform simulations of the nonadiabatic dynamics of materials in extreme environments involving millions of nuclei and electrons, over multi-picoseconds time scales, and demonstrate its application to: (i) accurately determine density and predict percent ionization of hydrogen at high pressure (∼61GPa) and temperatures up to 15,300K and (ii) determine, the single shock Hugoniot for lithium metal directly from the shock wave kinematics, i.e., mass velocities (Up) and shock wave velocities (Us), and shock density data. For (i), the density and ionization fractions of hydrogen atoms were calculated using the isobaric–isothermal ensemble at an isotropic pressure of 61.4GPa and for temperatures between 300K and 15,300K. The results at 15,300K describe a molecular fluid with density ρ = 0.36 g/cm3, in close agreement with existing experiments and theory, and∼0.5% ionization. This result provides no indication of the existence of a critical plasma phase-transition point at this particular temperature and pressure, as previously predicted by others. For (ii), the relationship betweenUp andUs was characterized to be linear and plastic in the range 1–20 km/s, and the single shock Hugoniot was determined in close agreement with published results for experimentally reported Ups. In addition to this, we provide a description of the materials’ behavior for large Ups in terms of the appearance of a weak metallic plasma phase byUp = 10 km/s, with 8% ionization, gradually transitioning to a denser plasmawith an estimated 35% ionization byUp = 15 km/s. Last but not least, we confirm the computational efficiency and scalability of pEFF by comparing its single processor performance against the fastest existing serial code, which results in a linear speedup ∼10× faster for every 16,000 particles in favor of pEFF, and by evaluating its parallel performance in terms of its strong and weak scaling capabilities. Our results, on Los Alamos’s Lobo supercomputer (a 38TFLOPSs Linux HPC with Quad-core AMD Opteron nodes interconnected with an Infiniband), show strong scaling with near ideal speedups for loads>62 particles per processor. Weak scaling is shown to be close to linear under the same per-processor load range. As an absolute reference, an NVT run with 2 million particle lithium bulk system (0.5M nuclei and 1.5M electrons) on Lobo takes ∼0.44 s/timestep on 1024 processors (∼1 day/ps using an integration timestep of 0.005 fs). © 2010 Wiley Periodicals, Inc. J Comput Chem 32: 497–512, 2011

برای دانلود رایگان متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Text S1. Supporting information to: “A universal trend among proteomes indicates an oily last common ancestor”

Ranjan V. Mannige, Charles L. Brooks III and Eugene I. Shakhnovich Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA Departments of Chemistry and Biophysics,University of Michigan, Ann Arbor, MI, USA Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA Center for Theoretical Biological Physics, UC San Diego, La Jolla, CA, USA To w...

متن کامل

Collective Variable Approaches for Single Molecule Flexible Fitting and Enhanced Sampling

and Enhanced Sampling Harish Vashisth,† Georgios Skiniotis,‡ and Charles Lee Brooks, III* †Department of Chemical Engineering, University of New Hampshire, Durham, New Hampshire 03824, United States ‡Life Sciences Institute, Department of Biological Chemistry, and Biophysics Program, and Department of Chemistry and Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United St...

متن کامل

Changes in organic carbon stable isotope ratios across the K/T boundary: global or local control?

Meyers, P.A., 1992. Changes in organic carbon stable isotope ratios across the K/T boundary: global or local control? In: S.A. Macko and M.H. Engel (Guest-Editors), Isotope Fractionations in Organic Matter: Biosynthetic and Diagenetic Processes. Chem. Geol. (Isot. Geosci. Sect. ), l 01: 283-29 I. A global shift in carbonate carbon j~3C-values from heavier values in the Maastrichtian to lighter ...

متن کامل

Effect of Urban Waste Compost Leachate on the Soil Physical, Hydraulic, Moisture Characteristics and Corn Yield

Compost leachate is a liquid resulting from physical, chemical and biological decomposition of organic materials. The main objective of this study was to evaluate the influence of leachate compost on the physical, hydraulic and soil moisture characteristic curves. Also, the effect of leachate on the aerial organ fresh weight of corn was investigated. Leachate was added to clay loam and sandy cl...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

عنوان ژورنال:

دوره   شماره 

صفحات  -

تاریخ انتشار 2010