Uintah and Related C-SAFE Publications


D. Bedrov, G.D. Smith. “Exploration of Conformational Phase Space in Polymer Melts: A Comparison of Parallel Tempering and Conventional Molecular Dynamics Simulations,” In Journal of Chemical Physics, Vol. 115, No. 3, pp. 1121--1124. 2001.
DOI: 10.1063/1.1386781


Parallel tempering molecular dynamics simulations have been performed for 1,4-polybutadiene polymer melts in the 323 K–473 K temperature domain at atmospheric pressure. The parallel tempering approach provides a vast improvement in the equilibration and sampling of conformational phase space for the atomistic melt chains in comparison with conventional molecular dynamics simulations even for molecular weights and temperatures considered to be routinely accessible via the latter technique.

O. Byutner, G.D. Smith. “Prediction of the Linear Viscoelastic Shera Modulus of an Entangled Polybutadiene Melt from Simulation and Theory,” In Macromolecules, Vol. 34, No. 1, pp. 134--139. 2001.

O. Byutner, G.D. Smith. “Temperature and Molecular Weight Dependence of the Zero Shear-Rate Viscosity of an Entangled Polymer Melt from Simulation and Theory,” In Journal of Polymer Science, B, Vol. 39, No. 23, pp. 3067--3071. December, 2001.
DOI: 10.1002/polb.10029


In a previous article, we described how the frequency-dependent complex shear modulus and the time-dependent shear stress relaxation modulus for a highly entangled polybutadiene (PBD) melt can be obtained from molecular dynamics (MD) simulations of an unentangled PBD melt.1 In that work, we obtained from simulations of an unentangled melt all properties required for the prediction of the dynamic shear modulus with three reptation theories for the dynamics of entangled melts of linear, monodisperse polymers.2–5 More recently, we showed how the high-frequency (glassy) behavior of PBD can be obtained directly from MD simulations.6 The calculated complex and stress relaxation shear moduli for a PBD melt with a molecular weight of 1.3 · 105 Da at 298 K were found to be in excellent agreement with experimental data.1, 6 In this work, we investigate the ability of MD simulations of the unentangled melt, in conjunction with reptation theory, to reproduce the molecular weight and temperature dependence of the viscoelastic properties of PBD. Here we concentrate on the low-frequency/long-time dynamics that determine the zero shear-rate viscosity, a property that has been extensively studied for PBD as a function of molecular weight and temperature.

A. D'Anna, A. Violi; A. D'Alessio, A.F. Sarofim. “A Reaction Pathway for Nanoparticle Formation in Rich Premixed Flames,” In Combustion and Flame, Vol. 127, No. 1-2, pp. 1995--2003. October, 2001.
DOI: 10.1016/S0010-2180(01)00303-0


Aromatics growth beyond 2-, 3-ring PAH is analyzed through a radical-molecule reaction mechanism which, in combination with a previously developed PAH model, is able to predict the size distribution of aromatic structures formed in rich premixed flames of ethylene at atmospheric pressure with C/O ratios across the soot threshold limit. Modeling results are in good agreement with experimental data and are used to interpret the ultraviolet absorption and the light scattering measured in flames before soot inception. The model shows that the total number concentration of high molecular mass aromatics and the different moments of the size distribution are functions of both the PAH and H-atom concentrations, two quantities which have different trends as functions of the residence time and the C/O ratio. Regimes of nearly stoichiometric or slightly rich premixed combustion are dominated by reactions between aromatics which lead to the formation of particles with sizes of the order of 3 to 4 nm. At higher C/O ratios the formation of nanoparticles is less efficient. Particles with sizes of the order of 2 nm are predicted in flames at the threshold of soot formation, whereas particles with sizes around 1 to 1.5 nm are predicted in fully sooting conditions.

J.C. Facelli, B.K. Nakagawa, A.M. Orendt, R.J. Pugmire. “Cluster Analysis of C-13 Chemical Shift Tensor Principal Values in Polycyclic Aromatic Hydrocarbons,” In Journal of Physical Chemistry, A, Vol. 105, pp. 7468--7472. 2001.


This paper presents a hierarchical cluster analysis of the principal values of the 13C chemical shift tensors encountered in polycyclic aromatic hydrocarbons (PAHs). Because of the limited set of experimental data presently available, the analysis was performed using chemical shifts tensors calculated using the DFT (B3PW91) GIAO method with a D95 basis set on optimized molecular geometries obtained using the CVFF force field and the DISCOVER routine in MSI's InsightII package. The good correlation observed between the calculated and the available experimental values supports the use of calculated values in the analysis. The hierarchical cluster analysis was performed for two data sets of increasing size and the classification was found independent of the size of the sample, leading to the conclusion that the results presented here are valid for the types of PAHs reported. The classification of the tensors using hierarchical cluster analysis produces classes of chemical shift principal values that can be associated with intuitive chemical types of carbons present in PAHs.

C.R. Johnson, D. Brederson, C.D. Hansen, M. Ikits, G. Kindlmann, Y. Livnat, S.G. Parker, D.M. Weinstein, R.T. Whitaker. “Computational Field Visualization,” In Computer Graphics, Vol. 35, No. 4, pp. 5--9. 2001.

C.R. Johnson, Y. Livnat, L. Zhukov, D. Hart, G. Kindlmann. “Computational Field Visualization,” In Mathematics Unlimited -- 2001 and Beyond, Vol. 2, Edited by B. Engquist and W. Schmid, Springer-Verlag, pp. 605--630. 2001.

J.M. Kniss, P. McCormick, A. McPherson, J. Ahrens, J. Painter, A. Keahey, C.D. Hansen. “T-Rex, Texture-based Volume Rendering for Extremely Large Datasets,” In IEEE Comp. Graph. & Applic., Vol. 21, No. 4, pp. 52--61. 2001.

J.P. Lewis, K.R. Glaesemann, G.A. Voth, J. Fritsch, A.A. Demkov, J. Ortega, O.F. Sankey. “Further Developments in the Local-orbital Density-functional Theory Tight-Binding Method,” In Physical Review, B, Vol. 64, No. 19, pp. 195103--195113. 2001.
DOI: 10.1103/PhysRevB.64.195103


Improvements to the Sankey-Niklewaki method [O. F. Sankey and D. J. Niklewski, Phys. Rev. B 40, 3979 (1989)] for computing total energies and forces, within an ab initio tight-binding formalism, are presented here. In particular, the improved method (called FIREBALL) uses the separable pseudopotential (Hamann or Troullier) and goes beyond the minimal sp2 basis set of the Sankey-Niklewski method, allowing for double numerical basis sets with the addition of polarization orbitals and d orbitals to the basis set. A major improvement includes the use of more complex exchange-correlation functionals, such as Becke exchange with the Lee-Yang-Parr correlation. Results for Cu and GaN band structures using d orbitals within the improved method are reported; the results for GaN are greatly improved compared to the minimal basis results. Finally, to demonstrate the flexibility of the method, results for the H2O dimer system and the energetics of a gas-phase octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine molecule are reported.

K. Ma, S.G. Parker. “Massively Parallel Software Rendering for Visualizing Large-Scale DataSets,” In IEEE Trans. Vis & Comp. Graph., pp. 72--83. July/August, 2001.

J. McCorquodale, J.D. de St. Germain, S.G. Parker, C.R. Johnson. “The Uintah Parallelism Infrastructure: A Performance Evaluation on the SGI Origin 2000,” In Proceedings of The 5th International Conference on High-Performance Computing, Seattle, Mar, 2001.

S. Mendez, J.G. Curro, M. Putz, D. Bedrov, G.D. Smith. “An Integral Equation Theory for Polymer Solutions: Explicit Inclusion of the Solvent Molecules,” In Journal of Chemical Physics, Vol. 115, No. 12, pp. 5669--5678. 2001.
DOI: 10.1063/1.1397333


Self-consistent Polymer Reference Interaction Site Model (PRISM) calculations and molecular dynamics (MD) simulations were performed on athermal solutions of linear polymers. Unlike most previous treatments of polymer solutions, we explicitly included the solvent molecules. The polymers were modeled as tangent site chains and the solvent molecules were taken to be spherical sites having the same intermolecular potential as the polymer sites. The PRISM theory was solved self-consistently for both the single chain structure and intermolecular correlations as a function of chain length and concentration. The rms end-to-end distance from PRISM theory was found to be in agreement with corresponding MD simulations, and exhibited molecular weight dependence in accordance with scaling predictions in the dilute and concentrated solution limits. The presence of explicit solvent molecules had a significant effect on the packing of the polymer by inducing additional structure in the intermolecular radial distribution function between polymer sites. Using the direct correlation functions from the athermal solution and the random phase approximation, we were able to estimate the spinodal curves for solutions when polymer and solvent attractions were turned on. We found significant deviations from Flory-Huggins theory that are likely due to compressibility and nonrandom mixing effects.

M. Pernice, M.D. Tocci. “A Multigrid-Preconditioned Newton-Krylov Method for the Incompressible Navier-Stokes Equations,” In SIAM Journal on Scientific Computing, Vol. 23, No. 2, pp. 398--418. 2001.
DOI: 10.1137/S1064827500372250


Globalized inexact Newton methods are well suited for solving large-scale systems of nonlinear equations. When combined with a Krylov iterative method, an explicit Jacobian is never needed, and the resulting matrix-free Newton--Krylov method greatly simplifies application of the method to complex problems. Despite asymptotically superlinear rates of convergence, the overall efficiency of a Newton--Krylov solver is determined by the preconditioner. High-quality preconditioners can be constructed from methods that incorporate problem-specific information, and for the incompressible Navier--Stokes equations, classical pressure-correction methods such as SIMPLE and SIMPLER fulfill this requirement. A preconditioner is constructed by using these pressure-correction methods as smoothers in a linear multigrid procedure. The effectiveness of the resulting Newton--Krylov-multigrid method is demonstrated on benchmark incompressible flow problems.

J.D. Peterson, S. Vyazovkin, C.A. Wight. “Kinetics of the Thermal and Thermooxidative Degradation of Polystyrene, Polyethylene and Poly(propylene),” In Macromolecular Chemistry and Physics, Vol. 202, No. 6, pp. 775--784. March, 2001.
DOI: 10.1002/1521-3935(20010301)202:63.0.CO;2-G


The thermal degradations of polystyrene (PS), polyethylene (PE), and poly(propylene) (PP) have been studied in both inert nitrogen and air atmospheres by using thermogravimetry and differential scanning calorimetry. The model-free isoconversional method has been employed to calculate activation energies as a function of the extent of degradation. The obtained dependencies are interpreted in terms of degradation mechanisms. Under nitrogen, the thermal degradation of polymers follows a random scission pathway that has an activation energy ≈200 kJ·mol–1 for PS and 240 and 250 kJ·mol–1 for PE and PP, respectively. Lower values (≈150 kJ·mol–1) are observed for the initial stages of the thermal degradation of PE and PS; this suggests that degradation is initiated at weak links. In air, the thermoxidative degradation occurs via a pathway that involves decomposition of polymer peroxide and exhibits an activation energy of 125 kJ·mol–1 for PS and 80 and 90 kJ·mol–1, for PE and PP respectively.

R. Rawat, S.G. Parker, P.J. Smith, C.R. Johnson. “Parallelization and Integration of Fire Simulations in the Uintah PSE,” In Proceedings of the Tenth SIAM Conference on Parallel Processing for Scientific Computing, Portsmouth, Virginia, March 12-14, 2001.

E. Reinhard, P. Shirley, C.D. Hansen. “Parallel point reprojection,” In Proceedings of the IEEE 2001 symposium on parallel and large-data visualization and graphics, pp. 29--35. 2001.
DOI: 10.1109/PVGS.2001.964400


Improvements in hardware have recently made interactive ray tracing practical for some applications. However, when the scene complexity or rendering algorithm cost is high, the frame rate is too low in practice. Researchers have attempted to solve this problem by caching results from ray tracing and using these results in multiple frames via reprojection. However, the reprojection can become too slow when the number of samples that are reused is high, so previous systems have been limited to small images or a sparse set of computed pixels. To overcome this problem we introduce techniques to perform this reprojection in a scalable fashion on multiple processors.

G.D. Smith, O. Borodin, D. Bedrov, W. Paul, M.D. Ediger. “13C NMR Spinlattice Relaxation and Conformational Dynamics in a 1,4-Polybutadiene Melt,” In Macromolecules, Vol. 34, No. 15, pp. 5192--5199. 2001.
DOI: 10.1021/ma002206q


We have performed molecular dynamics (MD) simulations of a melt of 1,4-polybutadiene (PBD, 1622 Da) over the temperature range 400-273 K. 13C NMR spin-lattice relaxation times (T1) and nuclear Overhauser enhancement (NOE) values have been measured from 357 to 272 K for 12 different resonances. The T1 and NOE values obtained from simulation C-H vector P2(t) orientational autocorrelation functions were in good agreement with experiment over the entire temperature range. Analysis of conformational dynamics from MD simulations revealed that T1 depends much less strongly on the local chain microstructure than does the mean conformational transition time. Spin−lattice relaxation for a given nucleus could not be associated with the dynamics of any particular dihedral; instead, spin−lattice relaxation occurs as the result of multiple conformational events. However, a much closer correspondence was found between torsional autocorrelation times and the C-H vector P2(t) autocorrelation times upon which T1 depends. Both processes exhibited stronger than exponential slowing with decreasing temperature. The non-Arrhenius temperature dependences of these relaxation times as well as the stretched-exponential character of the autocorrelation functions themselves were found to be consistent with increasing dynamic heterogeneity in conformational transition rates with decreasing temperature.

G.D. Smith, W. Paul, M. Monkenbusch, D. Richter. “On the Non-Gaussianity of Chain Motion in Unentangled Polymer Melts,” In Journal of Chemical Physics, Vol. 114, pp. 4285--4288. 2001.
DOI: 10.1063/1.1348032


We have investigated chain dynamics of an unentangled polybutadiene melt via molecular dynamics simulations and neutronspin echo experiments. Good short-time statistics allows for the first experimental confirmation of subdiffusive motion of polymer chains for times less than the Rouse time (TR) confirming behavior in this regime observed in simulations. Analysis of simulation trajectories obtained over several Rouse times reveals non-Gaussian segmental displacements for all time and length scales. These results, particularly non-Gaussian displacements on large time- and length scales, demonstrate the importance of intermolecular correlations on chain dynamics. Rouse-type analytical models fail to account for this non-Gaussianity leading to large deviations between the experimental dynamic structure factor and model predictions.

M.S. Solum, A.F. Sarofim, R.J. Pugmire, T.H. Fletcher, H. Zhang. “C-13 NMR Analysis of Soot Produced from Model Compounds and a Coal,” In Energy and Fuels, Vol. 15, pp. 961--971. 2001.
DOI: 10.1021/ef0100294


Soot samples, including the associated organics, produced from an Illinois No. 6 coal (five samples) and two model compounds, biphenyl (three samples) and pyrene (two samples), have been studied by 13C NMR methods. The coal soot data served as a guide to selection of the temperature range that would be most fruitful for investigation of the evolution of aerosols composed of soot and tars that are generated from model compounds. The evolution of the different materials in the gas phase followed different paths. The coal derived soots exhibited loss of aliphatic and oxygen functional groups prior to significant growth in average aromatic cluster size. Between 1410 and 1530 K, line broadening occurs in the aromatic band, which appears to have a Lorentzian component that is observable at the lower temperature and is quite pronounced at the higher temperature. The data indicate that the average aromatic cluster size (the number of carbon atoms in an aromatic ring system where the rings are connected through aromatic bridgehead carbon atoms) may be as large as 80-90 carbons/cluster. The data obtained for the biphenyl samples exhibit a different path for pyrolysis and soot growth. A significant amount of ring opening reactions occurs, followed by major structural rearrangements, after the initial ring opening and hydrogen transfer phase. The cluster size not only grows significantly, but the crosslinking structure also increases, indicating that soot growth in biphenyl soots consists not only of cluster size growth but also cluster cross-linking. The evolution of pyrene aerosol samples follows still another path. Little evidence is noted for ring opening reactions. Major ring growth has not occurred at 1410 K but cross-linking reactions are noted, indicating the formation of dimer/trimer structures. Although a significant amount of ring growth is noted, the data are inconclusive regarding the mechanism for ring growth in the pyrene aerosols between 1410 and 1460 K.

A. Violi, X. Chen, G. Lindstrom, E.G. Eddings, A.F. Sarofim. “The Validation Web Site: A Combustion Collaboratory over the Internet,” In Lecture Notes in Computer Science: Computational Science - ICCS 2001, Vol. 2074, pp. 485--493. 2001.


The Soot Model Development Web Site (SMDWS) is a project to develop collaborative technologies serving combustion researchers in DOE national laboratories, academia and research institutions throughout the world. The result is a shared forum for problem exploration in combustion research. Researchers collaborate over the Internet using SMDWS tools, which include a server for executing combustion models, web-accessible data storage for sharing experimental and modeling data, and graphical visualization of combustion effects. In this paper the authors describe the current status of the SMDWS project, as well as continuing goals for enhanced functionality, modes of collaboration, and community building.