LAMMPS, FLASH and MESA

LAMMPSFLASHMESA

LAMMPS, FLASH and MESA

Jeremy Heyl

22 June 2017

Westgrid Summer School

Jeremy Heyl LAMMPS, FLASH and MESA

LAMMPSFLASHMESA

LAMMPS

I What is LAMMPS?

I LAMMPS is a classical molecular dynamics simulator.

I Serial or parallel.

I GPU or CPU

I Not just classical: PIMD, Lattice Boltzmann Fluid, . . .

I Adapted fromhttp://lammps.sandia.gov/tutorials.html


http://lammps.sandia.gov/tutorials.html

LAMMPSFLASHMESA

What is molecular dynamics?

Classical MD in a nutshell


LAMMPSFLASHMESA

LAMMPS?

Large-scale Atomic/Molecular Massively Parallel Simulatorhttp://lammps.sandia.gov

I Classical MD code

I Open source, portable C++

I 3-legged stool: soft matter, solids, mesoscale

I Particle simulator at varying length and time scales

I electrons atomistic coarse-grained continuum

I Spatial-decomposition of simulation domain for parallelism

I MD, non-equilibrium MD, energy minimization

I GPU and OpenMP enhanced

I Can be coupled to other scales: QM, kMC, FE, CFD, ...


http://lammps.sandia.gov

LAMMPSFLASHMESA

Why LAMMPS?

I Versatile: bio, materials, mesoscale; atomistic, coarse-grained,continuum; use with other codes, e.g. multiscale models

I Good parallel performance

I Easy to extend

I Well documented: extensive web site, 1300 page manual


LAMMPSFLASHMESA

Getting Started

I Download the LAMMPS source code fromhttp://lammps.sandia.gov/download.html.

I Download VMD from http://www.ks.uiuc.edu/

Development/Download/download.cgi?PackageName=VMD

I Install ffmpeg if you don’t have it already fromhttps://ffmpeg.org/download.html


http://lammps.sandia.gov/download.html

http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD

http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD

https://ffmpeg.org/download.html

LAMMPSFLASHMESA

Compiling LAMMPS

I Unpack the TARball: tar xfz lammps-stable.tar.gz

I Go to the source directory cd lammps-31Mar17/src

I Compile: make serial


LAMMPSFLASHMESA

Your First Simulation

I LAMMPS comes with many example simulations in theexamples directory.

I Let’s first look at the one called obstacle.

I Copy it to a fresh direcory: cp -rp obstacle my obstacle

I Go to the new directory and run ../../src/lmp serial <

in.obstacle

I What new files are there?


LAMMPSFLASHMESA

Visualising with VMD

I Open VMD.

I Select “File” and “New Molecule”

I Click “Load” and choose LAMMPS Trajectory for the format.

I Choose “dump.obstacle”

I Click on “Graphics” and “Representation” and choose“Drawing Method” “VDW”

I Select “Extensions”, “Visualization”, “Movie Maker”

I Choose FFMPEG.


LAMMPSFLASHMESA

Make a Movie with FFMPEG

I Let’s change the input file so that an image is saved at eachstep.

I 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

I And change jpg to pnm.

I Run it again.

I Run: ffmpeg -framerate 24 -pattern-type glob -i

’*.pnm’ out.mpg


LAMMPSFLASHMESA

The Input File

1. Units and atom style2. Create simulation box and atoms

I region, create box, create atoms, region commandsI lattice command vs box units

I read data commandI data file is a text fileI look at examples/micelle/data.micelleI 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


LAMMPSFLASHMESA

The Log File

I Contains what your inputfile does.

I Contains thermodynamicinformation.

I Let’s plot something (usingctioga2) http://ctioga2.

sourceforge.net

0.6

0.8

1.0

1.2

1.4

Pressure

0 5000 10000 15000 20000 25000

Time

ctioga2 --name pressure log.lammps@1:6 -x ’Time’ -y ’Pressure’


http://ctioga2.sourceforge.net

http://ctioga2.sourceforge.net

LAMMPSFLASHMESA

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 0 40 0 10 -0.25 0.25

create_box 3 box

create_atoms 1 box


LAMMPSFLASHMESA


Second Section - define potential and groups

# LJ potentials

pair style lj/cut 1.12246

pair coeff * * 1.0 1.0 1.12246

# 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


LAMMPSFLASHMESA


Third Section - set velocities and fixes

# initial velocities

mass * 1.0

compute mobile flow temp

velocity flow create 1.0 482748 temp mobile

fix 1 all nve

fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0

fix_modify 2 temp mobile

# Poiseuille flow

velocity boundary set 0.0 0.0 0.0

fix 3 lower setforce 0.0 0.0 0.0

fix 4 upper setforce 0.0 NULL 0.0

fix 5 upper aveforce 0.0 -0.5 0.0

fix 6 flow addforce 1.0 0.0 0.0


LAMMPSFLASHMESA


Fourth Section - the voids

# 2 obstacles

region void1 sphere 10 4 0 3

delete atoms region void1



fix 7 flow indent 100 sphere 10 4 0 4

fix 8 flow indent 100 sphere 20 7 0 4

fix 9 all enforce2d


LAMMPSFLASHMESA


Fifth Section - do it

# run

timestep 0.003

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


LAMMPSFLASHMESA

A Third Obstacle

Add a third obstacle



fix 8a flow indent 100 sphere 30 3 0 2


LAMMPSFLASHMESA

Hands-on Time

I Work in groups of two or three

I Pick one or two examples from the examples directory or fromthe internet.

I Work through the example and try changing parameters.

I Ask questions.

I Make some movies using FFMPEG or VMD.

I What did you learn?

I Present your work in a 2-3 minute presentation.


LAMMPSFLASHMESA

FLASH

It’s not just for astrophysics.

I Hydrodynamics

I Magnetohydrodynamics

I Equation of State: Ideal gas; Degenerate Ionized Plasma;Multimaterial

I Radiation Transfer: Multigroup Flux-limited Diffusion

I Diffusion and Conduction: Implicit with AMR

I Laser Energy Deposition: Geometric Optics with InverseBrensstrahlung

I Opacity: Constant; Multimaterial Tabular

I Particles: Tracer; Massive; Sink; Charged

I Gravity: Constant; PointMass; Planar; Self Gravity

I Magnetic Resistivity, Conductivity


LAMMPSFLASHMESA

FLASH Infrastructure

I Driver: Split; Unsplit

I Grid: Uniform Grid; AMR (PARAMESH); AMR (Chombo)

I GridParticles: Lagrangian Framework

I GridSolvers: Multigrid; Multipole; Barnes-Hut Tree; PFFT;Direct Solvers for Uniform Grid

I IO: HDF5 ; PnetCDF

I Multispecies


LAMMPSFLASHMESA

Flames


LAMMPSFLASHMESA

Supersonic Flow around an Obstacle

https://doi.org/10.1016/j.compfluid.2014.12.008



LAMMPSFLASHMESA

Combustion




LAMMPSFLASHMESA

MESA

MESA simulates stars. What it is in for you if you’re not intostars?

I Large nuclear reaction network

I Neutrinos

I Numeric algorithms

I Equations of state

I Opacities

I All documented in the code with citations.


LAMMPSFLASHMESA


LAMMPSFLASHMESA

Numerical Treasure Chest

I The real treasure if you are not an astrophysicist is in the filemesa-r9793/num/public/num lib.f.

I Safe root findingI Explicit ODEs solvers (non-stiff)I Implicit ODEs solvers (stiff)I Linear algebraI Newton-Raphson SolverI Minimization with and without constraintsI Random number generatorsI Quicksort, binary search

I Everything documented, referenced and with tips for usingthem.


Documents

LAMMPS, FLASH and MESA