It’s very easy to start molecular dynamics (MD) on Mac.
Molecular dynamics (MD) is a computer simulation method for studying the physical movements of atoms and molecules.Wikipedia
We can simulate the energy or motion of atoms by molecular dynamics (MD). An atom is too small to see it directly. However, we can observe an atom, its motion, reaction and so on, via MD. Recently, we can use MD very easily.
LAMMPS is a molecular dynamics software and is free. We can use Lammps.
Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a molecular dynamics program from Sandia National Laboratories. LAMMPS makes use of Message Passing Interface (MPI) for parallel communication and is free and open-source software, distributed under the terms of the GNU General Public License.Wikipedia
Install LAMMPS on Mac
For Mac, installation of LAMMPS is very easy.
(If you have not installed Homebrew, install Homebrew first.
Homebrew is a free and open-source software package management system.
Paste the following code in a macOS Terminal prompt.
/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
Now Homebrew is installed. Very easy!
Lammps can be installed using homebrew with the following code.
brew install lammps
Now LAMMPS is installed in you computer.
You can find the examples in “/usr/local/opt/lammps/share/lammps/examples/”. Here, we try to run “crack”. Go to “crack” directory.
Modify “in.crack” file as follwing. (Delete “#” on line 69 to 71)
# 2d LJ crack simulation dimension 2 boundary s s p atom_style atomic neighbor 0.3 bin neigh_modify delay 5 # create geometry lattice hex 0.93 region box block 0 100 0 40 -0.25 0.25 create_box 5 box create_atoms 1 box mass 1 1.0 mass 2 1.0 mass 3 1.0 mass 4 1.0 mass 5 1.0 # LJ potentials pair_style lj/cut 2.5 pair_coeff * * 1.0 1.0 2.5 # define groups region 1 block INF INF INF 1.25 INF INF group lower region 1 region 2 block INF INF 38.75 INF INF INF group upper region 2 group boundary union lower upper group mobile subtract all boundary region leftupper block INF 20 20 INF INF INF region leftlower block INF 20 INF 20 INF INF group leftupper region leftupper group leftlower region leftlower set group leftupper type 2 set group leftlower type 3 set group lower type 4 set group upper type 5 # initial velocities compute new mobile temp velocity mobile create 0.01 887723 temp new velocity upper set 0.0 0.3 0.0 velocity mobile ramp vy 0.0 0.3 y 1.25 38.75 sum yes # fixes fix 1 all nve fix 2 boundary setforce NULL 0.0 0.0 # run timestep 0.003 thermo 200 thermo_modify temp new neigh_modify exclude type 2 3 #dump 1 all atom 500 dump.crack dump 2 all image 250 image.*.jpg type type & zoom 1.6 adiam 1.5 dump_modify 2 pad 4 #dump 3 all movie 250 movie.mpg type type & # zoom 1.6 adiam 1.5 #dump_modify 3 pad 4 run 5000
After modification, run lammps with the following code.
lmp_serial -in in.crack
After the short calculation, you can find the jpeg files.
Congratulations! You can success to run MD with LAMMPS.