ms2: A Molecular Simulation Tool for Thermodynamic Properties

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$Nanomechanical strength and fracture mechanisms of hierarchical ...$

Figure 5: Schematic of the molecule decomposition parallelization method by Plimpton [14]. The colored boxes signify the pair interactions that need to be determined in order to proceed the simulation. The black lines define the range of molecules each processor is assigned to calculate their interactions. 34
Figure 6: Runtime <strong>for</strong> the equimolar liquid mixture of methanol and ethanol at 298.15 K and 0.1 MPa in the NpT ensemble using different compilers and processors. The simulation was executed with 1372 molecules with MD <strong>for</strong> 200 NVT equilibration time steps, 500 NpT equilibration time steps and 4000 production time steps. For MC, 50NVT equilibration loops,200NpT equilibration loops and1000 production loops. 35
Page 1 and 2: ms2: A Molecular Simulation Tool fo
Page 3 and 4: 2. Introduction Due to the advances
Page 5 and 6: 3. Simulation programms2 The simula
Page 7 and 8: sense that the specified chemical p
Page 9 and 10: 3.3.3. Chemical potential The chemi
Page 11 and 12: 3.3.6. Transport properties In ms2,
Page 13 and 14: −0.5 < x, y, z < 0.5. The advanta
Page 15 and 16: Q = 2aq. The electrostatic interact
Page 17 and 18: Programming (OOP). It should be men
Page 19 and 20: motion, kinetic energy calculation,
Page 21 and 22: • PGI pgf95 4 with ”-r8 -fastss
Page 23 and 24: memory scales linearly with the num
Page 25 and 26: Applyingms2par is simple and should
Page 27 and 28: Table 1: Computational demand for t
Page 29 and 30: Table 3: NEC SX8R ”ftrace” prof
Page 31 and 32: i r ij ij Figure 2: Schematic of t
Page 33: Figure 4: UML class diagram of ms2,
Page 37 and 38: (a) (b) Figure 8: ms2 runtime of th
Page 39 and 40: Figure 10: Snapshot of ms2par gener
Page 41 and 42: Figure 12: Snapshot of a ternary mi
Page 43 and 44: [24] Eckl, B., Vrabec, J., and Hass
Page 45 and 46: Supplementary Material to ms2: A Mo
Page 47 and 48: The partial derivative of the resid
Page 49 and 50: 2. Details ofms2 This section provi
Page 51 and 52: where u µRF i is its contribution
Page 53 and 54: 3. Modular structure - example The
Page 55 and 56: Table 2 continued Parameter Option
Page 57 and 58: An example for a *.par file is give
Page 59 and 60: Table 4: Parameters and options spe
Page 61: References [1] Allen, M. and Tildes

ms2: A Molecular Simulation Tool for Thermodynamic Properties

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