Getting Lammps

Getting LAMMPS running with AtomEye

Sachin Shanbhag 488 DSL, [email protected] pic:http://roylez.wordpress.com

Download ●

Get the program from http://lammps.sandia.gov/download.html

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Select C++, and hit download now

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This gets you lammps.tar.gz

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Untar-zip it using the command in an appropriate directory tar -zxvf lammps.tar.gz

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mv lammps-xxx to lammps, for simplicity.

Building the Executable ●

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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

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no FFT (useful for long range Coulomb forces)

cd lammps/src/STUBS/ –

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make (builds libmpi.a)

cd lammps/src/MAKE/ –

comment out LINKFORT, FORTLIB, and SYSLIB in Makefile.serial

Building the Executable ●

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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/ –

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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 region create_box create_atoms mass velocity

fcc 0.8442 box block 0 5 0 5 0 5 1 box 1 box 1 1.0 all create 0.728 87287 loop geom

pair_style pair_coeff

lj/cut 2.5 1 1 1.0 1.0 2.5

A sample input file neighbor neigh_modify

0.3 bin delay 0 every 20 check no

fix thermo thermo_style dump timestep run_style run

1 all nve 25 custom pe ke etotal temp mydump all atom 100 dump.file 0.001 verlet 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 ●

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Goto lammps/tools/lmp2cfg –

This takes in a “dump” file produced by LAMMPS

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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 –

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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 –

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lmp2cfg –

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the molecular dynamics program

to convert dump files to cfg format

atomeye –

to view cfg formats

Previous Example ●

lmp2cfg_exe < in.atomeye

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atomeye 00001.cfg

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Delete and Insert move you back and forth