| 88 |
|
uri = {<Go to ISI>://000232532000064}, |
| 89 |
|
} |
| 90 |
|
|
| 91 |
– |
@BOOK{Alexander1987, |
| 92 |
– |
title = {A Pattern Language: Towns, Buildings, Construction}, |
| 93 |
– |
publisher = {Oxford University Press}, |
| 94 |
– |
year = {1987}, |
| 95 |
– |
author = {C. Alexander}, |
| 96 |
– |
address = {New York}, |
| 97 |
– |
} |
| 98 |
– |
|
| 99 |
– |
@BOOK{Allen1987, |
| 100 |
– |
title = {Computer Simulations of Liquids}, |
| 101 |
– |
publisher = {Oxford University Press}, |
| 102 |
– |
year = {1987}, |
| 103 |
– |
author = {M.~P. Allen and D.~J. Tildesley}, |
| 104 |
– |
address = {New York}, |
| 105 |
– |
} |
| 106 |
– |
|
| 91 |
|
@ARTICLE{Allison1991, |
| 92 |
|
author = {S. A. Allison}, |
| 93 |
|
title = {A Brownian Dynamics Algorithm for Arbitrary Rigid Bodies - Application |
| 231 |
|
uri = {<Go to ISI>://000221146400009}, |
| 232 |
|
} |
| 233 |
|
|
| 250 |
– |
@ARTICLE{Barojas1973, |
| 251 |
– |
author = {J. Barojas and D. Levesque}, |
| 252 |
– |
title = {Simulation of Diatomic Homonuclear Liquids}, |
| 253 |
– |
journal = {Phys. Rev. A}, |
| 254 |
– |
year = {1973}, |
| 255 |
– |
volume = {7}, |
| 256 |
– |
pages = {1092-1105}, |
| 257 |
– |
} |
| 258 |
– |
|
| 234 |
|
@ARTICLE{Barth1998, |
| 235 |
|
author = {E. Barth and T. Schlick}, |
| 236 |
|
title = {Overcoming stability limitations in biomolecular dynamics. I. Combining |
| 405 |
|
|
| 406 |
|
@ARTICLE{Berkov2005, |
| 407 |
|
author = {D. V. Berkov and N. L. Gorn}, |
| 408 |
+ |
title = {Stochastic dynamic simulations of fast remagnetization processes: |
| 409 |
+ |
recent advances and applications}, |
| 410 |
+ |
journal = {Journal of Magnetism and Magnetic Materials}, |
| 411 |
+ |
year = {2005}, |
| 412 |
+ |
volume = {290}, |
| 413 |
+ |
pages = {442-448}, |
| 414 |
+ |
month = {Apr}, |
| 415 |
+ |
abstract = {Numerical simulations of fast remagnetization processes using stochastic |
| 416 |
+ |
dynamics are widely used to study various magnetic systems. In this |
| 417 |
+ |
paper, we first address several crucial methodological problems |
| 418 |
+ |
of such simulations: (i) the influence of finite-element discretization |
| 419 |
+ |
on simulated dynamics, (ii) choice between Ito and Stratonovich |
| 420 |
+ |
stochastic calculi by the solution of micromagnetic stochastic equations |
| 421 |
+ |
of motion and (iii) non-trivial correlation properties of the random |
| 422 |
+ |
(thermal) field. Next, we discuss several examples to demonstrate |
| 423 |
+ |
the great potential of the Langevin dynamics for studying fast remagnetization |
| 424 |
+ |
processes in technically relevant applications: we present numerical |
| 425 |
+ |
analysis of equilibrium magnon spectra in patterned structures, |
| 426 |
+ |
study thermal noise effects on the magnetization dynamics of nanoelements |
| 427 |
+ |
in pulsed fields and show some results for a remagnetization dynamics |
| 428 |
+ |
induced by a spin-polarized current. (c) 2004 Elsevier B.V. All |
| 429 |
+ |
rights reserved.}, |
| 430 |
+ |
annote = {Part 1 Sp. Iss. SI 922KU Times Cited:2 Cited References Count:25}, |
| 431 |
+ |
issn = {0304-8853}, |
| 432 |
+ |
uri = {<Go to ISI>://000228837600109}, |
| 433 |
+ |
} |
| 434 |
+ |
|
| 435 |
+ |
@ARTICLE{Berkov2005a, |
| 436 |
+ |
author = {D. V. Berkov and N. L. Gorn}, |
| 437 |
|
title = {Magnetization precession due to a spin-polarized current in a thin |
| 438 |
|
nanoelement: Numerical simulation study}, |
| 439 |
|
journal = {Physical Review B}, |
| 464 |
|
uri = {<Go to ISI>://000232228500058}, |
| 465 |
|
} |
| 466 |
|
|
| 463 |
– |
@ARTICLE{Berkov2005a, |
| 464 |
– |
author = {D. V. Berkov and N. L. Gorn}, |
| 465 |
– |
title = {Stochastic dynamic simulations of fast remagnetization processes: |
| 466 |
– |
recent advances and applications}, |
| 467 |
– |
journal = {Journal of Magnetism and Magnetic Materials}, |
| 468 |
– |
year = {2005}, |
| 469 |
– |
volume = {290}, |
| 470 |
– |
pages = {442-448}, |
| 471 |
– |
month = {Apr}, |
| 472 |
– |
abstract = {Numerical simulations of fast remagnetization processes using stochastic |
| 473 |
– |
dynamics are widely used to study various magnetic systems. In this |
| 474 |
– |
paper, we first address several crucial methodological problems |
| 475 |
– |
of such simulations: (i) the influence of finite-element discretization |
| 476 |
– |
on simulated dynamics, (ii) choice between Ito and Stratonovich |
| 477 |
– |
stochastic calculi by the solution of micromagnetic stochastic equations |
| 478 |
– |
of motion and (iii) non-trivial correlation properties of the random |
| 479 |
– |
(thermal) field. Next, we discuss several examples to demonstrate |
| 480 |
– |
the great potential of the Langevin dynamics for studying fast remagnetization |
| 481 |
– |
processes in technically relevant applications: we present numerical |
| 482 |
– |
analysis of equilibrium magnon spectra in patterned structures, |
| 483 |
– |
study thermal noise effects on the magnetization dynamics of nanoelements |
| 484 |
– |
in pulsed fields and show some results for a remagnetization dynamics |
| 485 |
– |
induced by a spin-polarized current. (c) 2004 Elsevier B.V. All |
| 486 |
– |
rights reserved.}, |
| 487 |
– |
annote = {Part 1 Sp. Iss. SI 922KU Times Cited:2 Cited References Count:25}, |
| 488 |
– |
issn = {0304-8853}, |
| 489 |
– |
uri = {<Go to ISI>://000228837600109}, |
| 490 |
– |
} |
| 491 |
– |
|
| 467 |
|
@ARTICLE{Berkov2002, |
| 468 |
|
author = {D. V. Berkov and N. L. Gorn and P. Gornert}, |
| 469 |
|
title = {Magnetization dynamics in nanoparticle systems: Numerical simulation |
| 945 |
|
annote = {Ya587 Times Cited:35 Cited References Count:32}, |
| 946 |
|
issn = {0021-9606}, |
| 947 |
|
uri = {<Go to ISI>://A1997YA58700024}, |
| 973 |
– |
} |
| 974 |
– |
|
| 975 |
– |
@BOOK{Gamma1994, |
| 976 |
– |
title = {Design Patterns: Elements of Reusable Object-Oriented Software}, |
| 977 |
– |
publisher = {Perason Education}, |
| 978 |
– |
year = {1994}, |
| 979 |
– |
author = {E. Gamma, R. Helm, R. Johnson and J. Vlissides}, |
| 980 |
– |
address = {London}, |
| 981 |
– |
chapter = {7}, |
| 948 |
|
} |
| 949 |
|
|
| 950 |
|
@ARTICLE{Edwards2005, |
| 1075 |
|
annote = {633AD Times Cited:2 Cited References Count:43}, |
| 1076 |
|
issn = {0006-3495}, |
| 1077 |
|
uri = {<Go to ISI>://000180256300012}, |
| 1112 |
– |
} |
| 1113 |
– |
|
| 1114 |
– |
@BOOK{Frenkel1996, |
| 1115 |
– |
title = {Understanding Molecular Simulation : From Algorithms to Applications}, |
| 1116 |
– |
publisher = {Academic Press}, |
| 1117 |
– |
year = {1996}, |
| 1118 |
– |
author = {D. Frenkel and B. Smit}, |
| 1119 |
– |
address = {New York}, |
| 1078 |
|
} |
| 1079 |
|
|
| 1080 |
|
@ARTICLE{Gay1981, |
| 1121 |
|
annote = {257MM Times Cited:2 Cited References Count:82}, |
| 1122 |
|
issn = {1022-1344}, |
| 1123 |
|
uri = {<Go to ISI>://000083785700002}, |
| 1166 |
– |
} |
| 1167 |
– |
|
| 1168 |
– |
@BOOK{Goldstein2001, |
| 1169 |
– |
title = {Classical Mechanics}, |
| 1170 |
– |
publisher = {Addison Wesley}, |
| 1171 |
– |
year = {2001}, |
| 1172 |
– |
author = {H. Goldstein and C. Poole and J. Safko}, |
| 1173 |
– |
address = {San Francisco}, |
| 1174 |
– |
edition = {3rd}, |
| 1124 |
|
} |
| 1125 |
|
|
| 1126 |
|
@ARTICLE{Gray2003, |
| 1357 |
|
annote = {Ju251 Times Cited:55 Cited References Count:44}, |
| 1358 |
|
issn = {0006-3495}, |
| 1359 |
|
uri = {<Go to ISI>://A1992JU25100002}, |
| 1411 |
– |
} |
| 1412 |
– |
|
| 1413 |
– |
@BOOK{Hockney1981, |
| 1414 |
– |
title = {Computer Simulation Using Particles}, |
| 1415 |
– |
publisher = {McGraw-Hill}, |
| 1416 |
– |
year = {1981}, |
| 1417 |
– |
author = {R.W. Hockney and J.W. Eastwood}, |
| 1418 |
– |
address = {New York}, |
| 1360 |
|
} |
| 1361 |
|
|
| 1362 |
|
@ARTICLE{Hoover1985, |
| 1395 |
|
annote = {870FJ Times Cited:0 Cited References Count:63}, |
| 1396 |
|
issn = {0021-9606}, |
| 1397 |
|
uri = {<Go to ISI>://000225042700059}, |
| 1398 |
+ |
} |
| 1399 |
+ |
|
| 1400 |
+ |
@ARTICLE{Humphrey1996, |
| 1401 |
+ |
author = {W. Humphrey and A. Dalke and K. Schulten}, |
| 1402 |
+ |
title = {VMD: Visual molecular dynamics}, |
| 1403 |
+ |
journal = {Journal of Molecular Graphics}, |
| 1404 |
+ |
year = {1996}, |
| 1405 |
+ |
volume = {14}, |
| 1406 |
+ |
pages = {33-\&}, |
| 1407 |
+ |
number = {1}, |
| 1408 |
+ |
month = {Feb}, |
| 1409 |
+ |
abstract = {VMD is a molecular graphics program designed for the display and analysis |
| 1410 |
+ |
of molecular assemblies, in particular biopolymers such as proteins |
| 1411 |
+ |
and nucleic acids. VMD can simultaneously display any number of |
| 1412 |
+ |
structures using a wide variety of rendering styles and coloring |
| 1413 |
+ |
methods. Molecules are displayed as one or more ''representations,'' |
| 1414 |
+ |
in which each representation embodies a particular rendering method |
| 1415 |
+ |
and coloring scheme for a selected subset of atoms. The atoms displayed |
| 1416 |
+ |
in each representation are chosen using an extensive atom selection |
| 1417 |
+ |
syntax, which includes Boolean operators and regular expressions. |
| 1418 |
+ |
VMD provides a complete graphical user interface for program control, |
| 1419 |
+ |
as well as a text interface using the Tcl embeddable parser to allow |
| 1420 |
+ |
for complex scripts with variable substitution, control loops, and |
| 1421 |
+ |
function calls. Full session logging is supported, which produces |
| 1422 |
+ |
a VMD command script for later playback. High-resolution raster |
| 1423 |
+ |
images of displayed molecules may be produced by generating input |
| 1424 |
+ |
scripts for use by a number of photorealistic image-rendering applications. |
| 1425 |
+ |
VMD has also been expressly designed with the ability to animate |
| 1426 |
+ |
molecular dynamics (MD) simulation trajectories, imported either |
| 1427 |
+ |
from files or from a direct connection to a running MD simulation. |
| 1428 |
+ |
VMD is the visualization component of MDScope, a set of tools for |
| 1429 |
+ |
interactive problem solving in structural biology, which also includes |
| 1430 |
+ |
the parallel MD program NAMD, and the MDCOMM software used to connect |
| 1431 |
+ |
the visualization and simulation programs. VMD is written in C++, |
| 1432 |
+ |
using an object-oriented design; the program, including source code |
| 1433 |
+ |
and extensive documentation, is freely available via anonymous ftp |
| 1434 |
+ |
and through the World Wide Web.}, |
| 1435 |
+ |
annote = {Uh515 Times Cited:1418 Cited References Count:19}, |
| 1436 |
+ |
issn = {0263-7855}, |
| 1437 |
+ |
uri = {<Go to ISI>://A1996UH51500005}, |
| 1438 |
|
} |
| 1439 |
|
|
| 1440 |
|
@ARTICLE{Izaguirre2001, |
| 1478 |
|
uri = {<Go to ISI>://000166676100020}, |
| 1479 |
|
} |
| 1480 |
|
|
| 1500 |
– |
@ARTICLE{Torre1977, |
| 1501 |
– |
author = {Jose Garcia De La Torre, V.A. Bloomfield}, |
| 1502 |
– |
title = {Hydrodynamic properties of macromolecular complexes. I. Translation}, |
| 1503 |
– |
journal = {Biopolymers}, |
| 1504 |
– |
year = {1977}, |
| 1505 |
– |
volume = {16}, |
| 1506 |
– |
pages = {1747-1763}, |
| 1507 |
– |
} |
| 1508 |
– |
|
| 1481 |
|
@ARTICLE{Kane2000, |
| 1482 |
|
author = {C. Kane and J. E. Marsden and M. Ortiz and M. West}, |
| 1483 |
|
title = {Variational integrators and the Newmark algorithm for conservative |
| 1631 |
|
annote = {Part 1 646CM Times Cited:15 Cited References Count:38}, |
| 1632 |
|
issn = {1063-651X}, |
| 1633 |
|
uri = {<Go to ISI>://000181017300042}, |
| 1662 |
– |
} |
| 1663 |
– |
|
| 1664 |
– |
@BOOK{Leach2001, |
| 1665 |
– |
title = {Molecular Modeling: Principles and Applications}, |
| 1666 |
– |
publisher = {Pearson Educated Limited}, |
| 1667 |
– |
year = {2001}, |
| 1668 |
– |
author = {A. Leach}, |
| 1669 |
– |
address = {Harlow, England}, |
| 1670 |
– |
edition = {2nd}, |
| 1634 |
|
} |
| 1635 |
|
|
| 1636 |
|
@ARTICLE{Leimkuhler1999, |
| 1661 |
|
uri = {<Go to ISI>://000080466800007}, |
| 1662 |
|
} |
| 1663 |
|
|
| 1701 |
– |
@BOOK{Leimkuhler2004, |
| 1702 |
– |
title = {Simulating Hamiltonian Dynamics}, |
| 1703 |
– |
publisher = {Cambridge University Press}, |
| 1704 |
– |
year = {2004}, |
| 1705 |
– |
author = {B. Leimkuhler and S. Reich}, |
| 1706 |
– |
address = {Cambridge}, |
| 1707 |
– |
} |
| 1708 |
– |
|
| 1664 |
|
@ARTICLE{Levelut1981, |
| 1665 |
|
author = {A. M. Levelut and R. J. Tarento and F. Hardouin and M. F. Achard |
| 1666 |
|
and G. Sigaud}, |
| 1751 |
|
uri = {<Go to ISI>://A1994QF46400002}, |
| 1752 |
|
} |
| 1753 |
|
|
| 1799 |
– |
@BOOK{Marion1990, |
| 1800 |
– |
title = {Classical Dynamics of Particles and Systems}, |
| 1801 |
– |
publisher = {Academic Press}, |
| 1802 |
– |
year = {1990}, |
| 1803 |
– |
author = {J.~B. Marion}, |
| 1804 |
– |
address = {New York}, |
| 1805 |
– |
edition = {2rd}, |
| 1806 |
– |
} |
| 1807 |
– |
|
| 1754 |
|
@ARTICLE{Marrink1994, |
| 1755 |
|
author = {S. J. Marrink and H. J. C. Berendsen}, |
| 1756 |
|
title = {Simulation of Water Transport through a Lipid-Membrane}, |
| 1824 |
|
uri = {<Go to ISI>://000077902200006}, |
| 1825 |
|
} |
| 1826 |
|
|
| 1827 |
< |
@ARTICLE{McLachlan1993, |
| 1828 |
< |
author = {R.~I McLachlan}, |
| 1829 |
< |
title = {Explicit Lie-Poisson integration and the Euler equations}, |
| 1830 |
< |
journal = {prl}, |
| 1831 |
< |
year = {1993}, |
| 1832 |
< |
volume = {71}, |
| 1833 |
< |
pages = {3043-3046}, |
| 1827 |
> |
@ARTICLE{Matthey2004, |
| 1828 |
> |
author = {T. Matthey and T. Cickovski and S. Hampton and A. Ko and Q. Ma and |
| 1829 |
> |
M. Nyerges and T. Raeder and T. Slabach and J. A. Izaguirre}, |
| 1830 |
> |
title = {ProtoMol, an object-oriented framework for prototyping novel algorithms |
| 1831 |
> |
for molecular dynamics}, |
| 1832 |
> |
journal = {Acm Transactions on Mathematical Software}, |
| 1833 |
> |
year = {2004}, |
| 1834 |
> |
volume = {30}, |
| 1835 |
> |
pages = {237-265}, |
| 1836 |
> |
number = {3}, |
| 1837 |
> |
month = {Sep}, |
| 1838 |
> |
abstract = {PROTOMOL is a high-performance framework in C++ for rapid prototyping |
| 1839 |
> |
of novel algorithms for molecular dynamics and related applications. |
| 1840 |
> |
Its flexibility is achieved primarily through the use of inheritance |
| 1841 |
> |
and design patterns (object-oriented programming): Performance is |
| 1842 |
> |
obtained by using templates that enable generation of efficient |
| 1843 |
> |
code for sections critical to performance (generic programming). |
| 1844 |
> |
The framework encapsulates important optimizations that can be used |
| 1845 |
> |
by developers, such as parallelism in the force computation. Its |
| 1846 |
> |
design is based on domain analysis of numerical integrators for |
| 1847 |
> |
molecular dynamics (MD) and of fast solvers for the force computation, |
| 1848 |
> |
particularly due to electrostatic interactions. Several new and |
| 1849 |
> |
efficient algorithms are implemented in PROTOMOL. Finally, it is |
| 1850 |
> |
shown that PROTOMOL'S sequential performance is excellent when compared |
| 1851 |
> |
to a leading MD program, and that it scales well for moderate number |
| 1852 |
> |
of processors. Binaries and source codes for Windows, Linux, Solaris, |
| 1853 |
> |
IRIX, HP-UX, and AIX platforms are available under open source license |
| 1854 |
> |
at http://protomol.sourceforge.net.}, |
| 1855 |
> |
annote = {860EP Times Cited:2 Cited References Count:52}, |
| 1856 |
> |
issn = {0098-3500}, |
| 1857 |
> |
uri = {<Go to ISI>://000224325600001}, |
| 1858 |
|
} |
| 1859 |
|
|
| 1860 |
|
@ARTICLE{McLachlan1998, |
| 1926 |
|
annote = {911NS Times Cited:0 Cited References Count:14}, |
| 1927 |
|
issn = {1615-3375}, |
| 1928 |
|
uri = {<Go to ISI>://000228011900003}, |
| 1929 |
+ |
} |
| 1930 |
+ |
|
| 1931 |
+ |
@ARTICLE{Meineke2005, |
| 1932 |
+ |
author = {M. A. Meineke and C. F. Vardeman and T. Lin and C. J. Fennell and |
| 1933 |
+ |
J. D. Gezelter}, |
| 1934 |
+ |
title = {OOPSE: An object-oriented parallel simulation engine for molecular |
| 1935 |
+ |
dynamics}, |
| 1936 |
+ |
journal = {Journal of Computational Chemistry}, |
| 1937 |
+ |
year = {2005}, |
| 1938 |
+ |
volume = {26}, |
| 1939 |
+ |
pages = {252-271}, |
| 1940 |
+ |
number = {3}, |
| 1941 |
+ |
month = {Feb}, |
| 1942 |
+ |
abstract = {OOPSE is a new molecular dynamics simulation program that is capable |
| 1943 |
+ |
of efficiently integrating equations of motion for atom types with |
| 1944 |
+ |
orientational degrees of freedom (e.g. #sticky# atoms and point |
| 1945 |
+ |
dipoles). Transition metals can also be simulated using the embedded |
| 1946 |
+ |
atom method (EAM) potential included in the code. Parallel simulations |
| 1947 |
+ |
are carried out using the force-based decomposition method. Simulations |
| 1948 |
+ |
are specified using a very simple C-based meta-data language. A |
| 1949 |
+ |
number of advanced integrators are included, and the basic integrator |
| 1950 |
+ |
for orientational dynamics provides substantial improvements over |
| 1951 |
+ |
older quaternion-based schemes. (C) 2004 Wiley Periodicals, Inc.}, |
| 1952 |
+ |
annote = {891CF Times Cited:1 Cited References Count:56}, |
| 1953 |
+ |
issn = {0192-8651}, |
| 1954 |
+ |
uri = {<Go to ISI>://000226558200006}, |
| 1955 |
|
} |
| 1956 |
|
|
| 1957 |
|
@ARTICLE{Melchionna1993, |
| 2014 |
|
uri = {<Go to ISI>://000174410500001}, |
| 2015 |
|
} |
| 2016 |
|
|
| 2021 |
– |
@ARTICLE{Metropolis1949, |
| 2022 |
– |
author = {N. Metropolis and S. Ulam}, |
| 2023 |
– |
title = {The $\mbox{Monte Carlo}$ Method}, |
| 2024 |
– |
journal = {J. Am. Stat. Ass.}, |
| 2025 |
– |
year = {1949}, |
| 2026 |
– |
volume = {44}, |
| 2027 |
– |
pages = {335-341}, |
| 2028 |
– |
} |
| 2029 |
– |
|
| 2017 |
|
@ARTICLE{Mielke2004, |
| 2018 |
|
author = {S. P. Mielke and W. H. Fink and V. V. Krishnan and N. Gronbech-Jensen |
| 2019 |
|
and C. J. Benham}, |
| 2155 |
|
annote = {491UW Times Cited:48 Cited References Count:25}, |
| 2156 |
|
issn = {0021-9606}, |
| 2157 |
|
uri = {<Go to ISI>://000172129300049}, |
| 2171 |
– |
} |
| 2172 |
– |
|
| 2173 |
– |
@BOOK{Olver1986, |
| 2174 |
– |
title = {Applications of Lie groups to differential equatitons}, |
| 2175 |
– |
publisher = {Springer}, |
| 2176 |
– |
year = {1986}, |
| 2177 |
– |
author = {P.J. Olver}, |
| 2178 |
– |
address = {New York}, |
| 2158 |
|
} |
| 2159 |
|
|
| 2160 |
|
@ARTICLE{Omelyan1998, |
| 2304 |
|
uri = {<Go to ISI>://000077460000052}, |
| 2305 |
|
} |
| 2306 |
|
|
| 2307 |
+ |
@ARTICLE{Parr1995, |
| 2308 |
+ |
author = {T. J. Parr and R. W. Quong}, |
| 2309 |
+ |
title = {Antlr - a Predicated-Ll(K) Parser Generator}, |
| 2310 |
+ |
journal = {Software-Practice \& Experience}, |
| 2311 |
+ |
year = {1995}, |
| 2312 |
+ |
volume = {25}, |
| 2313 |
+ |
pages = {789-810}, |
| 2314 |
+ |
number = {7}, |
| 2315 |
+ |
month = {Jul}, |
| 2316 |
+ |
abstract = {Despite the parsing power of LR/LALR algorithms, e.g. YACC, programmers |
| 2317 |
+ |
often choose to write recursive-descent parsers by hand to obtain |
| 2318 |
+ |
increased flexibility, better error handling, and ease of debugging. |
| 2319 |
+ |
We introduce ANTLR, a public-domain parser generator that combines |
| 2320 |
+ |
the flexibility of hand-coded parsing with the convenience of a |
| 2321 |
+ |
parser generator, which is a component of PCCTS. ANTLR has many |
| 2322 |
+ |
features that make it easier to use than other language tools. Most |
| 2323 |
+ |
important, ANTLR provides predicates which let the programmer systematically |
| 2324 |
+ |
direct the parse via arbitrary expressions using semantic and syntactic |
| 2325 |
+ |
context; in practice, the use of predicates eliminates the need |
| 2326 |
+ |
to hand-tweak the ANTLR output, even for difficult parsing problems. |
| 2327 |
+ |
ANTLR also integrates the description of lexical and syntactic analysis, |
| 2328 |
+ |
accepts LL(k) grammars for k > 1 with extended BNF notation, and |
| 2329 |
+ |
can automatically generate abstract syntax trees. ANTLR is widely |
| 2330 |
+ |
used, with over 1000 registered industrial and academic users in |
| 2331 |
+ |
37 countries. It has been ported to many popular systems such as |
| 2332 |
+ |
the PC, Macintosh, and a variety of UNIX platforms; a commercial |
| 2333 |
+ |
C++ front-end has been developed as a result of one of our industrial |
| 2334 |
+ |
collaborations.}, |
| 2335 |
+ |
annote = {Rk104 Times Cited:19 Cited References Count:10}, |
| 2336 |
+ |
issn = {0038-0644}, |
| 2337 |
+ |
uri = {<Go to ISI>://A1995RK10400004}, |
| 2338 |
+ |
} |
| 2339 |
+ |
|
| 2340 |
|
@ARTICLE{Pastor1988, |
| 2341 |
|
author = {R. W. Pastor and B. R. Brooks and A. Szabo}, |
| 2342 |
|
title = {An Analysis of the Accuracy of Langevin and Molecular-Dynamics Algorithms}, |
| 2379 |
|
uri = {<Go to ISI>://A1985AKB9300008}, |
| 2380 |
|
} |
| 2381 |
|
|
| 2370 |
– |
@ARTICLE{Rotne1969, |
| 2371 |
– |
author = {F. Perrin}, |
| 2372 |
– |
title = {Variational treatment of hydrodynamic interaction in polymers}, |
| 2373 |
– |
journal = {J. Chem. Phys.}, |
| 2374 |
– |
year = {1969}, |
| 2375 |
– |
volume = {50}, |
| 2376 |
– |
pages = {4831¨C4837}, |
| 2377 |
– |
} |
| 2378 |
– |
|
| 2379 |
– |
@ARTICLE{Perrin1936, |
| 2380 |
– |
author = {F. Perrin}, |
| 2381 |
– |
title = {Mouvement brownien d'un ellipsoid(II). Rotation libre et depolarisation |
| 2382 |
– |
des fluorescences. Translation et diffusion de moleculese ellipsoidales}, |
| 2383 |
– |
journal = {J. Phys. Radium}, |
| 2384 |
– |
year = {1936}, |
| 2385 |
– |
volume = {7}, |
| 2386 |
– |
pages = {1-11}, |
| 2387 |
– |
} |
| 2388 |
– |
|
| 2389 |
– |
@ARTICLE{Perrin1934, |
| 2390 |
– |
author = {F. Perrin}, |
| 2391 |
– |
title = {Mouvement brownien d'un ellipsoid(I). Dispersion dielectrique pour |
| 2392 |
– |
des molecules ellipsoidales}, |
| 2393 |
– |
journal = {J. Phys. Radium}, |
| 2394 |
– |
year = {1934}, |
| 2395 |
– |
volume = {5}, |
| 2396 |
– |
pages = {497-511}, |
| 2397 |
– |
} |
| 2398 |
– |
|
| 2382 |
|
@ARTICLE{Petrache1998, |
| 2383 |
|
author = {H. I. Petrache and S. Tristram-Nagle and J. F. Nagle}, |
| 2384 |
|
title = {Fluid phase structure of EPC and DMPC bilayers}, |
| 2408 |
|
annote = {130AT Times Cited:98 Cited References Count:39}, |
| 2409 |
|
issn = {0009-3084}, |
| 2410 |
|
uri = {<Go to ISI>://000076497600007}, |
| 2428 |
– |
} |
| 2429 |
– |
|
| 2430 |
– |
@ARTICLE{Powles1973, |
| 2431 |
– |
author = {J.~G. Powles}, |
| 2432 |
– |
title = {A general ellipsoid can not always serve as a modle for the rotational |
| 2433 |
– |
diffusion properties of arbitrary shaped rigid molecules}, |
| 2434 |
– |
journal = {Advan. Phys.}, |
| 2435 |
– |
year = {1973}, |
| 2436 |
– |
volume = {22}, |
| 2437 |
– |
pages = {1-56}, |
| 2411 |
|
} |
| 2412 |
|
|
| 2413 |
|
@ARTICLE{Recio2004, |
| 2725 |
|
annote = {Uq975 Times Cited:32 Cited References Count:33}, |
| 2726 |
|
issn = {0009-2614}, |
| 2727 |
|
uri = {<Go to ISI>://A1996UQ97500017}, |
| 2728 |
+ |
} |
| 2729 |
+ |
|
| 2730 |
+ |
@ARTICLE{Schaps1999, |
| 2731 |
+ |
author = {G. L. Schaps}, |
| 2732 |
+ |
title = {Compiler construction with ANTLR and Java - Tools for building tools}, |
| 2733 |
+ |
journal = {Dr Dobbs Journal}, |
| 2734 |
+ |
year = {1999}, |
| 2735 |
+ |
volume = {24}, |
| 2736 |
+ |
pages = {84-+}, |
| 2737 |
+ |
number = {3}, |
| 2738 |
+ |
month = {Mar}, |
| 2739 |
+ |
annote = {163EC Times Cited:0 Cited References Count:0}, |
| 2740 |
+ |
issn = {1044-789X}, |
| 2741 |
+ |
uri = {<Go to ISI>://000078389200023}, |
| 2742 |
|
} |
| 2743 |
|
|
| 2744 |
|
@ARTICLE{Shen2002, |
| 2909 |
|
uri = {<Go to ISI>://000230332400077}, |
| 2910 |
|
} |
| 2911 |
|
|
| 2925 |
– |
@BOOK{Tolman1979, |
| 2926 |
– |
title = {The Principles of Statistical Mechanics}, |
| 2927 |
– |
publisher = {Dover Publications, Inc.}, |
| 2928 |
– |
year = {1979}, |
| 2929 |
– |
author = {R.~C. Tolman}, |
| 2930 |
– |
address = {New York}, |
| 2931 |
– |
chapter = {2}, |
| 2932 |
– |
pages = {19-22}, |
| 2933 |
– |
} |
| 2934 |
– |
|
| 2912 |
|
@ARTICLE{Tu1995, |
| 2913 |
|
author = {K. Tu and D. J. Tobias and M. L. Klein}, |
| 2914 |
|
title = {Constant pressure and temperature molecular dynamics simulation of |
| 2968 |
|
annote = {Je891 Times Cited:680 Cited References Count:19}, |
| 2969 |
|
issn = {0021-9606}, |
| 2970 |
|
uri = {<Go to ISI>://A1992JE89100044}, |
| 2994 |
– |
} |
| 2995 |
– |
|
| 2996 |
– |
@BOOK{Varadarajan1974, |
| 2997 |
– |
title = {Lie groups, Lie algebras, and their representations}, |
| 2998 |
– |
publisher = {Prentice-Hall}, |
| 2999 |
– |
year = {1974}, |
| 3000 |
– |
author = {V.S. Varadarajan}, |
| 3001 |
– |
address = {New York}, |
| 2971 |
|
} |
| 2972 |
|
|
| 3004 |
– |
@ARTICLE{Wegener1979, |
| 3005 |
– |
author = {W.~A. Wegener, V.~J. Koester and R.~M. Dowben}, |
| 3006 |
– |
title = {A general ellipsoid can not always serve as a modle for the rotational |
| 3007 |
– |
diffusion properties of arbitrary shaped rigid molecules}, |
| 3008 |
– |
journal = {Proc. Natl. Acad. Sci.}, |
| 3009 |
– |
year = {1979}, |
| 3010 |
– |
volume = {76}, |
| 3011 |
– |
pages = {6356-6360}, |
| 3012 |
– |
number = {12}, |
| 3013 |
– |
} |
| 3014 |
– |
|
| 3015 |
– |
@ARTICLE{Wilson2006, |
| 3016 |
– |
author = {G.~V. Wilson }, |
| 3017 |
– |
title = {Where's the Real Bottleneck in Scientific Computing?}, |
| 3018 |
– |
journal = {American Scientist}, |
| 3019 |
– |
year = {2006}, |
| 3020 |
– |
volume = {94}, |
| 3021 |
– |
} |
| 3022 |
– |
|
| 2973 |
|
@ARTICLE{Withers2003, |
| 2974 |
|
author = {I. M. Withers}, |
| 2975 |
|
title = {Effects of longitudinal quadrupoles on the phase behavior of a Gay-Berne |