LAMMPS, FLASH and MESA

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Robyn Armstrong
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1 , and 22 June 2017 Westgrid Summer School, and

2 What is? is a classical molecular dynamics simulator. Serial or parallel. GPU or CPU Not just classical: PIMD, Lattice Boltzmann Fluid,... Adapted from and

3 Classical MD in a nutshell What is molecular dynamics?, and

4 ? Large-scale Atomic/Molecular Massively Parallel Simulator Classical MD code Open source, portable C++ 3-legged stool: soft matter, solids, mesoscale Particle simulator at varying length and time scales electrons atomistic coarse-grained continuum Spatial-decomposition of simulation domain for parallelism MD, non-equilibrium MD, energy minimization GPU and OpenMP enhanced Can be coupled to other scales: QM, kmc, FE, CFD,..., and

5 Why? Versatile: bio, materials, mesoscale; atomistic, coarse-grained, continuum; use with other codes, e.g. multiscale models Good parallel performance Easy to extend Well documented: extensive web site, 1300 page manual, and

6 Getting Started Download the source code from Download VMD from Development/Download/download.cgi?PackageName=VMD Install ffmpeg if you don t have it already from and

7 Compiling Unpack the TARball: tar xfz lammps-stable.tar.gz Go to the source directory cd lammps-31mar17/src Compile: make serial, and

8 Your First Simulation comes with many example simulations in the examples directory. Let s first look at the one called obstacle. Copy it to a fresh direcory: cp -rp obstacle my obstacle Go to the new directory and run../../src/lmp serial < in.obstacle What new files are there?, and

9 Visualising with VMD Open VMD. Select File and New Molecule Click Load and choose Trajectory for the format. Choose dump.obstacle Click on Graphics and Representation and choose Drawing Method VDW Select Extensions, Visualization, Movie Maker Choose FFMPEG., and

10 Make a Movie with FFMPEG Let s change the input file so that an image is saved at each step. Uncomment at the following lines #dump 2 all image 500 image.*.jpg type type & # zoom 1.6 adiam 1.5 #dump_modify 2 pad 5 And change jpg to pnm. Run it again. Run: ffmpeg -framerate 24 -pattern-type glob -i *.pnm out.mpg, and

11 The Input File 1. Units and atom style 2. Create simulation box and atoms region, create box, create atoms, region commands lattice command vs box units read data command data file is a text file look at examples/micelle/data.micelle see read data doc page for full syntax 3. Define groups 4. Attributes of atoms: mass, velocity 5. Pair style for atom interactions 6. Fixes for time integration and constraints 7. Computes for diagnostics 8. Output: thermo, dump, restart 9. Run or minimize, and

12 The Log File Contains what your input file does. Contains thermodynamic information. Let s plot something (using ctioga2) sourceforge.net Pressure Time ctioga2 --name pressure log.lammps@1:6 -x Time -y Pressure, and

13 The Obstacle Input File First Section - setup box and create atoms # 2d LJ obstacle flow dimension 2 boundary p s p atom_style atomic neighbor 0.3 bin neigh_modify delay 5 # create geometry lattice hex 0.7 region box block create_box 3 box create_atoms 1 box, and

14 The Obstacle Input File Second Section - define potential and groups # LJ potentials pair style lj/cut pair coeff * * # define groups region 1 block INF INF INF 1.25 INF INF group lower region 1 region 2 block INF INF 8.75 INF INF INF group upper region 2 group boundary union lower upper group flow subtract all boundary set group lower type 2 set group upper type 3, and

15 The Obstacle Input File Third Section - set velocities and fixes # initial velocities mass * 1.0 compute mobile flow temp velocity flow create temp mobile fix 1 all nve fix 2 flow temp/rescale fix_modify 2 temp mobile # Poiseuille flow velocity boundary set fix 3 lower setforce fix 4 upper setforce 0.0 NULL 0.0 fix 5 upper aveforce fix 6 flow addforce , and

16 The Obstacle Input File Fourth Section - the voids # 2 obstacles region void1 sphere delete atoms region void1 region void2 sphere delete atoms region void2 fix 7 flow indent 100 sphere fix 8 flow indent 100 sphere fix 9 all enforce2d, and

17 The Obstacle Input File Fifth Section - do it # run timestep thermo 1000 thermo_modify temp mobile #dump 1 all atom 100 dump.obstacle dump 1 all image 500 image.*.jpg type type & zoom 1.6 adiam 1.5 dump_modify 1 pad 5 run 25000, and

18 A Third Obstacle Add a third obstacle region void3 sphere delete atoms region void3 fix 8a flow indent 100 sphere , and

19 Hands-on Time Work in groups of two or three Pick one or two examples from the examples directory or from the internet. Work through the example and try changing parameters. Ask questions. Make some movies using FFMPEG or VMD. What did you learn? Present your work in a 2-3 minute presentation., and

20 It s not just for astrophysics. Hydrodynamics Magnetohydrodynamics Equation of State: Ideal gas; Degenerate Ionized Plasma; Multimaterial Radiation Transfer: Multigroup Flux-limited Diffusion Diffusion and Conduction: Implicit with AMR Laser Energy Deposition: Geometric Optics with Inverse Brensstrahlung Opacity: Constant; Multimaterial Tabular Particles: Tracer; Massive; Sink; Charged Gravity: Constant; PointMass; Planar; Self Gravity Magnetic Resistivity, Conductivity, and

21 Infrastructure Driver: Split; Unsplit Grid: Uniform Grid; AMR (PARAMESH); AMR (Chombo) GridParticles: Lagrangian Framework GridSolvers: Multigrid; Multipole; Barnes-Hut Tree; PFFT; Direct Solvers for Uniform Grid IO: HDF5 ; PnetCDF Multispecies, and

22 Flames, and

23 Supersonic Flow around an Obstacle and

24 Combustion and

25 simulates stars. What it is in for you if you re not into stars? Large nuclear reaction network Neutrinos Numeric algorithms Equations of state Opacities All documented in the code with citations., and

26 , and

27 Numerical Treasure Chest The real treasure if you are not an astrophysicist is in the file mesa-r9793/num/public/num lib.f. Safe root finding Explicit ODEs solvers (non-stiff) Implicit ODEs solvers (stiff) Linear algebra Newton-Raphson Solver Minimization with and without constraints Random number generators Quicksort, binary search Everything documented, referenced and with tips for using them., and

LAMMPS for Molecular Dynamics Simulation

Gwangju Institute of Science and Technology (GIST) Super Computing & Collaboration Environment Technology Center (SCENT) LAMMPS for Molecular Dynamics Simulation Taekhee Ryu Molecular Modeling Laboratory