Documenti di Didattica
Documenti di Professioni
Documenti di Cultura
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
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