vscht.cz).
See also the The ResearcherID:
Jiří Kolafa
Molekulární simulace iontových kapalin
23. Letní škola, 2009-08-25
Osnova prezentace:
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 β p*=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
Nonanalytical equation of state of the hard sphere fluid
cond-mat/0506449
An equation of state of the hard sphere fluid which is not analytical at the freezing density is proposed and tested. The nonanalytical term is based on the the classical nucleation theory and is able to capture the observed "anomalous increase" of pressure at high densities. It is combined with the virial expansion at low densities.
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
Structure and unusual properties of water (in Czech)
Talk presented at the 18th Summer School for High School Teachers,
Institute of Chemical Technology, Prague, September 24-27, 2004
Anomalies of water are reviewed and explained using modern concepts on the structure of hydrogen bond network.
: PowerPoint presentation (3.3 MiB)
Movies (AVI/MPEG4): Water drop with H-bonds (4.0 MiB) --- H-bonds in frozen drop (3.4 MiB) --- Water-vapor equilibrium at 27 °C (26.2 MiB)
Jiri Kolafa
Nonanalytical equation of state of the hard sphere fluid
Poster presented at the 18th IUPAC International Conference on Chemical Thermodynamics, August 17-21, Beijing, China
An equation of state for the hard sphere fluid in stable and metastable regions is developed using the ideas of the classical nucleation theory. This equation of state is not analytical at the freezing point in accordance with the rigorously proven result for the Ising system [S.N. Isakov, Commun. Math. Phys. 95, 427 (1984)].
Poster resized to one page, gzipped PostScript
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
Molecular dynamics simulations of polarizable molecules
Gear-like formalism of the Always Stable Predictor-Corrector method
Poster presented at NATO Advanced Research Workshop
"Ionic Soft Matter: Novel trends in theory and applications"
April 14-17, 2004, Lviv, Ukraine
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).
Jan Bumba, Jiri Kolafa,
Global phase diagrams of the van der Waals-Dieterici and the BMCSL-Dieterici equations of state
Phys. Chem. Chem. Phys. 6, 2301-2306 (2004)
Global phase diagrams of a binary mixture of attractive hard spheres described by the van der Waals-Dieterici and Boublik-Mansoori-Carnahan-Starling-Leland-Dieterici equations of state (with a square root combining rule for cross attraction) are calculated in dependence on the ratio of the hard-sphere diameters and the attraction strength
A reprint (PDF) is available upon request
(jiri.kolafavscht.cz).
Jiri Kolafa
Time-Reversible Always Stable Predictor-Corrector Method
for Molecular Dynamics of Polarizable Molecules
J. Comput. Chem. 25, 335-342 (2004)
An improved method for classical molecular dynamics of polarizable molecules is proposed. The method uses a predictor, one evaluation of the electrostatic field per integration step, and relaxation (damping). The self-consistent solution is approximated with error of the second order (with respect to the timestep). The time reversibility (long time energy conservation) error is of the (2n-1)-th order, where n is the predictor length. The method is easy to implement, efficient, accurate, and suitable for any model of polarizability.
A reprint (PDF) is available upon request
(jiri.kolafavscht.cz).
Stanislav Labik, Hana Gabrielova, Jiri Kolafa, Anatol Malijevsky
Calculation of elementary diagrams using a Metropolis-like
simulation method
Mol. Phys. 101, 1139-1146 (2003)
A method for evaluation of higher-order elementary diagrams is proposed. The algorithm utilizes symbolic algebra programming and automatic code generation. The method is used to calculate elementary diagrams for hard spheres up to the fifth. The obtained values are fitted to suitable functions of interparticle distance. The resulting truncated density expansion is compared with recent values of the bridge function calculated directly from the simulated pair distribution function. The method can be straightforwardly extended to hard-body systems and their mixtures.
A reprint (PDF) is available upon request
(jiri.kolafavscht.cz).
Jiri Genzer, Jiri Kolafa
Molecular dynamics of potential models with polarizability:
comparison of methods
J. Mol. Liq. 109, 63-72 (2004)
Three methods for molecular dynamics of models with induced dipoles are optimized for accuracy and performance and compared: the predicted iteration method, the always stable predictor-corrector method, and the extended Lagrangian method (Car-Parrinello approach). The comparison criteria include thermodynamic quantities (energy, pressure, averaged induced dipoles), control quantities (total energy conservation, energy equipartition, errors in induced dipoles), and computer time. We recommend the always stable predictor-corrector method as a compromise between accuracy, speed, and simulation consistency.
A reprint (PDF) is available upon request
(jiri.kolafavscht.cz).
Martin Lisal, Jiri Kolafa, Ivo Nezbeda
An examination of the five-site potential (TIP5P) for water
J. Chem. Phys. 117, 8892-8897 (2002)
Parametrization of the TIP5P model of water [M. W. Mahoney and W. L. Jorgensen, J. Chem. Phys. 112, 8910 (2000)] has been examined by several computer simulation methods accounting properly for long-range forces. The structural and thermodynamic properties at a pressure of 1 atm over the temperature range (-25 °C,+75 °C3) and the vapor-liquid coexistence have been determined. It is shown that the simple spherical cutoff method used in the original simulations to find optimized parameters of this 5-site model is inaccurate and that its results differ from those obtained by both the Ewald summation and reaction field methods. Consequently, the pivot property to which the parameters were adjusted, the location of the density maximum at 1 atm, does not agree with experimental values. The equilibrium properties then show only a fair agreement with experimental data and are uniformly inferior to those of TIP4P water over the entire coexistence range.
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. Fulltext not available.
[ Older papers ] [Back to the department homepage] [Back to Kolafa homepage]