Uintah and Related C-SAFE Publications


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.

A. Violi, A.F. Sarofim, T.N. Truong. “Quantum mechanical study of molecular weight growth process by combination of aromatic molecules,” In Combustion and Flame, Vol. 126, No. 1-2, pp. 1506--1515. July, 2001.
DOI: 10.1016/S0010-2180(01)00268-1


Formation pathways for high-molecular-mass compound growth are presented, showing why reactions between aromatic moieties are needed to explain recent experimental findings. These reactions are then analyzed by using quantum mechanical density functional methods. A sequence of chemical reactions between aromatic compounds (e.g., phenyl) and compounds containing conjugated double bonds (e.g., acenaphthylene) was studied in detail. The sequence begins with the H-abstraction from acenaphthylene to produce the corresponding radical, which then furnishes higher aromatics through either a two-step radical-molecule reaction or a direct radical-radical addition to another aromatic radical. Iteration of this mechanism followed by rearrangement of the carbon framework ultimately leads to high-molecular-mass compounds. This sequence can be repeated for the formation of high-molecular-mass compounds. The distinguishing features of the proposed model lie in the chemical specificity of the routes considered. The aromatic radical attacks the double bond of five-membered-ring polycyclic aromatic hydrocarbons. This involves specific compounds that are exceptional soot precursors as they form resonantly stabilized radical intermediates, relieving part of the large strain in the five-membered rings by formation of linear aggregates.

S. Vyazovkin, J.S. Clawson, C.A. Wight. “Thermal Dissociation Kinetics of Solid and Liquid Ammonium Nitrate,” In Chemistry of Materials, Vol. 13, No. 3, pp. 960--966. February, 2001.
DOI: 10.1021/cm000708c


Thermogravimetry has been used to study the kinetics of the thermal dissociation of solid and liquid ammonium nitrate. Model-fitting and model-free kinetic methods have been applied to the sets of isothermal and nonisothermal measurements to derive kinetic characteristics of the processes. The application of the model-fitting method to the isothermal data has demonstrated that both solid- and liquid-phase kinetics are characterized by a single activation energy of ∼90 kJ mol-1 and by the model of a contracting cylinder. A model-free isoconversional method has also been applied to isothermal and nonisothermal data and has yielded an activation energy of ∼90 kJ mol-1, which is essentially independent of the extent of conversion. The obtained kinetic characteristics have been assigned to the process of dissociative sublimation/vaporization.

S. Zhang, T.N. Truong. “Branching Ratio and Pressure Dependent Rate Constants of Multi-Channel Unimolecular Decomposition of Gas-Phase a-HMX: An Ab Initio Dynamics Study,” In Journal of Physical Chemistry, A, Vol. 105, pp. 2427--2434. 2001.
DOI: 10.1021/jp0043064


The dynamics of the initial thermal decomposition step of gas-phase α-HMX is investigated using the master equation method. Both the NO2 fission and HONO elimination channels were considered. The structures, energies, and Hessian information along the minimum energy paths (MEP) of these two channels were calculated at the B3LYP/cc-pVDZ level of theory. Thermal rate constants at the high-pressure limit were calculated using the canonical variational transition state theory (CVT), microcanonical variational transition state theory (μVT). The pressure-dependent multichannel rate constants and the branching ratio were calculated using the master equation method. Quantum tunneling effects in the HONO elimination are included in the dynamical calculations and found to be important at low temperatures. At the high-pressure limit, the NO2 fission channel is found to be dominant in the temperature range (500-1500 K). Both channels exhibit strong pressure dependence at high temperatures. Both reach the high-pressure limits at low temperatures. We found that the HONO elimination channel can compete with the NO2 fission, one in the low-pressure and/or hightemperature regime.


D.H. Barich, A.M. Orendt, R.J. Pugmire, D.M. Grant. “Carbon-13 Chemical Shift Tensors in Polycyclic Aromatic Compounds. 9. Biphenylene,” In Journal of Physical Chemistry, A, Vol. 104, No. 35, pp. 8290--8295. August, 2000.
DOI: 10.1021/jp001911y


The principal values of the 13C chemical-shift tensors of natural abundance biphenylene were measured at room temperature with the FIREMAT experiment. Of 18 crystallographically distinct positions (three sets of six congruent carbons each), the three primary bands have been resolved into seven single peaks and four degenerate peaks (two double, one triple, and one quadruple). Hence, eleven different chemical-shift tensors are reported. An interpretation of the data is made by comparison to carbon chemical-shift tensors in other molecules with similar chemical environments. Experimental and theoretical values based on a model of the asymmetric unit of the crystal unit cell are in good agreement.

D. Bedrov, G. Smith, T.D. Sewell. “Thermal Conductivity of Liquid Octahydro-1,3,5,7-Tetranitro-1,3,5,7-Tetrazocine (HMX) From Molecular Dynamics Simulations,” In Chemical Physics Letters, Vol. 324, No. 1-3, pp. 64--68. June, 2000.
DOI: 10.1016/S0009-2614(00)00559-5


The thermal conductivity of liquid octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) has been determined from imposed heat flux non-equilibrium molecular dynamics (NEMD) simulations using a previously published quantum chemistry-based atomistic potential. The thermal conductivity was determined in the temperature domain 550⩽T⩽800 K, which corresponds approximately to the existence limits of the liquid phase of HMX at atmospheric pressure. The NEMD predictions, which comprise the first reported values for thermal conductivity of HMX liquid, were found to be consistent with measured values for crystalline HMX. The thermal conductivity of liquid HMX was found to exhibit a much weaker temperature dependence than the shear viscosity and self-diffusion coefficients.

D. Bedrov, G.D. Smith. “Thermal Conductivity of Molecular Fluids from Molecular Dynamics Simulations: Application of a New Imposed-Flux Method,” In Journal of Chemical Physics, Vol. 113, No. 18, pp. 8080--8084. 2000.
DOI: 10.1063/1.1312309


We have applied a new nonequilibrium molecular dynamics (NEMD) method [F. Müller-Plathe, J. Chem. Phys. 106, 6082 (1997)] previously applied to monatomic Lennard-Jones fluids in the determination of the thermal conductivity of molecular fluids. The method was modified in order to be applicable to systems with holonomic constraints. Because the method involves imposing a known heat flux it is particularly attractive for systems involving long-range and many-body interactions where calculation of the microscopic heat flux is difficult. The predicted thermal conductivities of liquid n-butane and water using the imposed-flux NEMD method were found to be in a good agreement with previous simulations and experiment.

D. Bedrov, G.D. Smith, T. Sewell. “Temperature-dependent shear viscosity coefficient of octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX): A molecular dynamics simulation study,” In Journal of Chemical Physics, Vol. 112, No. 16, pp. 7203--7208. 2000.
DOI: 10.1063/1.481285


Equilibrium molecular dynamics methods were used in conjunction with linear response theory and a recently published potential-energysurface [J. Phys. Chem. B 103, 3570 (1999)] to compute the liquid shear viscosity and self-diffusion coefficient of the high explosive HMX (octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine) over the temperature domain 550–800 K. Predicted values of the shear viscosity range from 0.0055 Pa *s at the highest temperature studied up to 0.45 Pa *s for temperatures near the melting point. The results, which represent the first publication of the shear viscosity of HMX, are found to be described by an Arrhenius rate law over the entire temperature domain studied. The apparent activation energy for the shear viscosity is found to scale with the heat of vaporization in a fashion consistent with those for a wide variety of simple nonmetallic liquids. The self-diffusion coefficient, which requires significantly shorter trajectories than the shear viscosity for accurate calculation, also exhibits an Arrhenius temperature dependence over the simulated temperature domain. This has potentially important implications for predictions of the shear viscosity at temperatures near the melting point.

O.G. Byutner, G.D. Smith. “Quantum Chemistry Based Force Field for Simulations of Poly(vinylidene fluoride),” In Macromolecules, Vol. 33, No. 11, pp. 4264--4270. May, 2000.
DOI: 10.1021/ma9918295


A classical potential function for simulations of poly(vinylidene fluoride) (PVDF) based upon quantum chemistry calculations on PVDF oligomers has been developed. Quantum chemistry analysis of the geometries and conformational energies of 1,1,1,3,3-pentafluorobutane (PFB), 1,1,1,3,3,5,5,5-octofluoropentane (OFP), 2,2,4,4-tetrafluoropentane (TFP), and 2,2,4,4,6,6-hexafluoroheptane (HFH) was undertaken. In addition, an ab initio investigation of the energies of CF4-CF4 and CH4-CF4 dimers was performed. The classical potential function accurately reproduces the molecular geometries and conformational energies of the PVDF oligomers as well as intermolecular interactions between CH4 and CF4. To validate the force field, molecular dynamics simulations of a PVDF melts have been carried out at several temperatures. Simulation results are in good agreement with extant experimental data for PVT properties for amorphous PVDF as well as for PVDF chain dimensions.

J.D. de St. Germain, J. McCorquodale, S.G. Parker, C.R. Johnson. “Uintah: A Massively Parallel Problem Solving Environment,” In Ninth IEEE International Symposium on High Performance and Distributed Computing, IEEE, Piscataway, NJ, pp. 33--41. Nov, 2000.

T.C. Henderson, P.A. McMurtry, P.J. Smith, G.A. Voth, C.A. Wight, D.W. Pershing. “Simulating Accidental Fires and Explosions,” In Computing in Science and Engineering, Vol. 2, No. 2, pp. 64--76. 2000.
DOI: 10.1109/5992.825750


The Center for the Simulation of Accidental Fires and Explosions (C‐SAFE) at the University of Utah is focused on providing state‐of‐the‐art, science‐based tools for the numerical simulation of accidental fires and explosions, especially within the context of handling and storage of highly flammable materials. The objective of the C‐SAFE effort is to provide a scalable, high‐performance system composed of a problem‐solving environment in which fundamental chemistry and engineering physics are fully coupled with non‐linear solvers, optimization, computational steering, visualization and experimental data verification. The availability of simulations using this system will help to better evaluate the risks and safety issues associated with fires and explosions. Our five‐year product, termed Uintah 5.0, will be validated and documented for practical application to accidents involving both hydrocarbon and energetic materials.