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Online Simulations Via Nanohub: Nanoscale Thermal Transport Via MD

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Online Simulations Via Nanohub: Nanoscale Thermal Transport Via MD Online simulations via nanoHUB: Nanoscale thermal transport via MD In this tutorial: • Non-equilibrium MD simulations of thermal transport Keng-hua Lin and Ale Strachan [email protected] School of Materials Engineering & Birck Nanotechnology Center Purdue University West Lafayette, Indiana USA © Alejandro Strachan – Online simulaons: Geng Started 1 STEP 1: • From All Tools find: nanoMATERIALS nanoscale heat transport • Launch tool by clicking on: © Alejandro Strachan – Online simulaons: geng started 2 STEP 2: setup the atomistic simulation cell From the Input Model tab of the tool • Select prebuilt structures • Or create your own structure by checking the box We will create our own © Alejandro Strachan – Online simulaons: geng started 3 How the simulation cells are defined • Along the transport direc7on the simulaon contains: • 2 Heat baths (blue) • The middle bin defines the hot and cold regions • Interior material (red) • This can be defined to be a superlace • Periodic boundary condi7ons are applied along the transport direcon Material (5 bins) Heat bath (3 bins) Cold bin Hot bin F. Müller-Plathe, J. Chem. Phys. 106, 6082 (1997) Keng-Hua Lin and A. Strachan, Physical Review B, 87, 115302 (2013). © Alejandro Strachan – Online simulaons: geng started 3 STEP 2: setup the atomistic simulation cell • We would like to create a Si supercell by replicang the cubic Si unit cell • The tool allows users to build superlaces (laminates) so it is a bit convoluted Along the transport the system will be divided in bins Each bin is one unit cell long Cross-sec7onal area of the simulaon cell (5x5 unit cells) Lace parameter (5.43) Along the transport direc7on the “supercell” will have 5 Si bins (1 bin = 1 unit cell) and zero Ge (just Si) The number of Si bins will be varied to explore size effects The total simulaon length in this case is: (3+5) x 2 x 5.43A = 86.88A The effec7ve size for transport is the separaon between heat baths (1/2 of the simulaon cell length) Heat baths are 3 bins long The “supercell” will be repeated only once © Alejandro Strachan – Online simulaons: geng started 4 STEP 2: setup the atomistic simulation cell If you select to build your own structure In the Selecons for Material Shape tab Choose to simulate the material as a bulk (superlace thin film) or a superlace square nanowire 3-D periodic boundary condi7on for the simulaon cell Periodic boundary condi7on along the z direc7on and free boundary condi7on along the x and y direc7ons We will use 3D periodic boundary condi7ons © Alejandro Strachan – Online simulaons: geng started 7 STEP 3: setup the Simulation Details From the Driver Specifica1on tab of the tool Thermalize the system For 1000 MD steps (2 ps) This will equilibrate the system to the desired temperature before star7ng the thermal transport calculaon © Alejandro Strachan – Online simulaons: geng started 9 STEP 3: setup the Driver Specification From the Driver Specifica1on tab of the tool This sets up the non-equilibrium simulaon Timestep 2 fs MD steps 120,000 Swap atomic veloci7es every 100 MD steps Atomis7c snapshots for visualizaon Output temperature profile every this many steps for analysis Ignore the first 20,000 steps when compu7ng averages © Alejandro Strachan – Online simulaons: geng started 10 STEP 4: explore the results interactively Temperature profiles at different 7mes Average temperature profile Remember simulaon cell was ~86A © Alejandro Strachan – Online simulaons: geng started 13 STEP 4: explore the results interactively Analyze output: calculated thermal conduc7vity Material thermal conduc7vity computer from temperature gradient inside the material (away from contacts) Use this value © Alejandro Strachan – Online simulaons: geng started 13 .
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