Getting LAMMPS running with

AtomEye

Sachin Shanbhag
488 DSL, sshanbhag@fsu.edu

pic:http://roylez.wordpress.com
 Download
● Get the program from
http://lammps.sandia.gov/download.html
● Select C++, and hit download now
● This gets you lammps.tar.gz
● Untar-zip it using the command in an appropriate
directory
tar -zxvf lammps.tar.gz
● mv lammps-xxx to lammps, for simplicity.
 Building the Executable
● Detailed instructions available at:
http://lammps.sandia.gov/doc/Section_sta
rt.html#2_2
● Right now, lets do a simple compilation:
– single processor, no MPI
– no FFT (useful for long range Coulomb forces)
● cd lammps/src/STUBS/
– make (builds libmpi.a)
● cd lammps/src/MAKE/
– comment out LINKFORT, FORTLIB, and SYSLIB in Makefile.serial
 Building the Executable
● CC = g++
CCFLAGS = -O -DFFT_NONE -I../STUBS $(PKGINC)
DEPFLAGS = -M
LINK = g++
#LINKFORT =-L/opt/intel/fc/10.1.018/lib
LINKFLAGS =-O -L../STUBS $(PKGPATH) $(LINKFORT)
USRLIB = -lmpi $(PKGLIB)
#FORTLIB = -lifcore -lsvml -lompstub -limf
#SYSLIB = $(FORTLIB)

● cd lammps/src/
– make serial
● You should have an executable called lmp_serial
– I renamed this file as lmp_exe
 A sample input file
sachins% cat in.lj
# 3d Lennard-Jones melt
units lj
atom_style atomic
dimension 3

lattice fcc 0.8442

region box block 0 5 0 5 0 5
create_box 1 box
create_atoms 1 box
mass 1 1.0
velocity all create 0.728 87287 loop geom

pair_style lj/cut 2.5

pair_coeff 1 1 1.0 1.0 2.5
 A sample input file
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no

fix 1 all nve

thermo 25
thermo_style custom pe ke etotal temp
dump mydump all atom 100 dump.file
timestep 0.001
run_style verlet
run 500
 Run the program
sachins% lmp_exe < in.lj
LAMMPS (7 Jul 2009)
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
1 by 1 by 1 processor grid
Created 500 atoms
Setting up run ...
Memory usage per processor = 1.50018 Mbytes
PotEng KinEng TotEng Temp
-6.7733681 1.089816 -5.6835521 0.728
-6.729132 1.045577 -5.683555 0.69844822
-6.5781112 0.8959221 -5.6821891 0.59847836
-6.3237083 0.64218604 -5.6815223 0.42898199
-6.1193067 0.43545135 -5.6838553 0.29088267
 Convert to CFG format
● Goto lammps/tools/lmp2cfg
– This takes in a “dump” file produced by LAMMPS
– Converts it to CFG format which can be read by atomeye
● Compile lmp2cfg.f
f77 lmp2cfg.f -o lmp2cfg_exe

cat in.atomeye
500
1
'dump.file'
1
6
1
26.98
'ao'
 Download atomeye
● http://mt.seas.upenn.edu/Archive/Graphics/A/
 Download it!
● the binary i686 Linux version
– rename the file as atomeye
● get the test cfg file as well
– test whether you can see it alright
 Now have all three elements
● LAMMPS
– the molecular dynamics program
● lmp2cfg
– to convert dump files to cfg format
● atomeye
– to view cfg formats
 Previous Example
● lmp2cfg_exe < in.atomeye
● atomeye 00001.cfg
● Delete and Insert move you back and forth