vscht.cz).
See also the The ResearcherID:
Jiří Kolafa
Co je to počítačový experiment
Jiří Kolafa
Struktura a neobvyklé vlastnosti vody
Populární přednáška o anomáliích vody a jejich vysvětlení pomocí struktury
vodíkových vazeb.
Materiály:
Jiří Kolafa
Molekulární simulace iontových kapalin
23. Letní škola, 2009-08-25
Materiály:
Magda Francová, Jiří Kolafa, Pavel Morávek, Stanislav Labík, Anatol Malijevský
Fluids of hard nonspherical molecules. I. Higher virial coefficients
Virial coefficients of hard prolate spherocylinders and hard homonuclear diatomics are calculated up to the ninth for a number of molecule elongations. The results are fitted to an analytical formula as a function of the elongation.
Pavel Morávek, Jiří Kolafa, Magda Francová
Fluids of hard nonspherical molecules. II. Monte Carlo data and equation of state
New accurate data on the compressibility factor of the hard homonuclear diatomics with full range of elongations and the hard prolate spherocylinders with length-to-breadth ratio as high as 9 are presented. The data were obtained by Monte Carlo NpT simulations with finite-size corrections in the range of reduced pressures βp*=0.5 to 7.0. New equations of state based on simultaneous correlation of the data with the virial coefficients up to the ninth are presented.
supplementary material for both papers
Jiri Kolafa, Stanislav Labik
Density expansion of the radial distribution and bridge functions of the hard sphere fluid
preprint
The bridge function and the background correlation function (and consequently the radial distribution function) of the pure hard sphere fluid are expanded up to the sixth power in density. The calculations are based on the Ree--Hoover representation of the diagrams and Monte Carlo integration. The coefficients as functions of the particle-particle separation are fitted to splines taking into account discontinuities in higher derivatives up to the term of the order of (r–const)5.
Jiri Kolafa
Gear formalism of the always stable predictor-corrector method
for molecular dynamics of polarizable molecules
J. Chem. Phys. 122, 164105 (2005)
The recently proposed always stable predictor-corrector method for molecular dynamics of polarizable molecules [J. Kolafa, J. Comput. Chem. 25, 335 2004] is rewritten in the Gear formalism. This equivalent form simplifies an implementation if the Newton equations of motion are integrated by the Gear method and also enables a variable integration step. Algorithms are presented for both the original and new versions and tested on a pair of polarizable ions exhibiting anharmonic vibrations.
Supplementary material: tables of Gear ASPC coefficients
A reprint (PDF) is available upon request
(jiri.kolafavscht.cz).
Stanislav Labik, Jiri Kolafa, Anatol Malijevsky
Virial coefficients of hard spheres and hard disks up to the ninth
Phys. Rev. E 71, 021105 (2005)
A technique for topological analysis of the Ree-Hoover diagrams is developed with the aim to calculate the Ree-Hoover weights up to the ninth order with moderate demands on computer storage and CPU time. The ninth virial coefficients of hard spheres and disks are calculated, and the lower virial coefficients are accurately recalculated. The calculations require several spanning diagrams; the most important spanning chains are generated by reptation, other spanning diagrams by the standard Metropolis Monte Carlo algorithm. The tenth and eleventh virial coefficients for hard spheres are estimated.
Supplementary material: tables of virial coefficients
A reprint (PDF) is available upon request
(jiri.kolafavscht.cz).
Jiri Kolafa, Stanislav Labik, Anatol Malijevsky
Radial distribution function of the hard sphere fluid
Poster presented at the 18th IUPAC International Conference on Chemical Thermodynamics, August 17-21, Beijing, China
New accutate results of the radial distribution function of the hard sphere fluid in the range of reduced densities up to deeply metastable 1.02 are presented. The fuctions are fitted to a formula in variables density and interparticle separation taking into account both the low-density limit and the tail at large separations.
Poster resized to one page, gzipped PostScript --- the data and simulation software
Jiri Kolafa, Stanislav Labik, Anatol Malijevsky
Accurate equation of state of the hard sphere fluid in stable and metastable regions
Phys. Chem. Chem. Phys. 6, 2335-2340 (2004)
New accurate data on the compressibility factor of the hard sphere fluid are obtained by highly optimized molecular dynamics calculations in the range of reduced densities 0.20--1.03. The relative inaccuracy at the 95 % confidence level is better than 0.00004 for all densities but the last deeply metastable point. This accuracy requires careful examination of finite size effects and other possible sources of errors and applying corrections. The data are fitted to a power series in y/(1-y), where y is the packing fraction; the coefficients are determined so that virial coefficients B2--B6 are reproduced. To do this, values of B5 and B6 are accurately recalculated. Virial coefficients up to B11 are then estimated from the equation of state.
Supplementary material: source code and data.
A reprint (PDF) is available upon request
(jiri.kolafavscht.cz).
Jiri Kolafa, Stanislav Labik, Anatol Malijevsky
The bridge function of hard spheres
by direct inversion of computer simulation data
Molec. Phys. 100, 2629-2640 (2002)
The bridge function of the hard sphere fluid has been calculated from our new highly accurate Monte Carlo and molecular dynamics simulation data on the radial distribution function using the (inverted) Ornstein-Zernike equation. Both the systematic errors (finite size, grid size, tail) and statistical errors are analyzed in detail and ways to suppress them are proposed. Uncertainties in the resulting values of B(r) are about 0.001. In contrast with previous findings the bridge function is both positive and negative.
J. Kolafa and I. Nezbeda:
Effect of short- and long-range forces on the structure of water.
II. Orientational ordering and the dielectric constant
Mol. Phys. 98, 1505 (2000)
3D structure, supplementary material and data
Yi-Chia Lee, Jiri Kolafa, Larry A. Curtiss, Mark A. Ratner, and Duward F. Shriver
Movies etc.