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Bessel

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[×ÊÔ´] LAMMPSʹÓóõÌåÑ飬Debian 6.0

ÎÒÊÇÔÚDebian 6.0ϱàÒë°²×°µÄ£¬ Ò²ÔÚUbuntu 10.04ϱàÒëͨ¹ý¡£Ê×ÏȽéÉÜһϲ¢ÐбàÒëµÄ¹ý³Ì£¬È»ºóÒÔL-JÏ໥×÷ÓÃÊÆµÄÒºÌåΪÀý£¬¸ø³öÁËinÎļþµÄд·¨¡£»¶Ó­´ó¼Ò²¹³ä¡£

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¡¶1¡·Ê×ÏȰ²×°ËùÓÐÒÀÀµµÄ°ü£º
sudo aptitude install mpich-bin libmpich1.0gf  libmpich1.0-dev fftw2 fftw-dev libjpeg62 libjpeg62-dev libblas-dev liblapack-dev  gfortran gcc make build-essential autoconf automake1.9 cvs subversion libsdl-dev libgl1-mesa-dev fakeroot libnss3-dev gdb libglib2.0-0 libglib-perl dh-make cdbs debhelper kernel-package lsb-release module-assistant

¡¶2¡·È¡ÏûSSHµÄÃÜÂë²½Öè
$ ssh-keygen -t dsa #ÖмäÌáʾÊäÈëÃÜÂ룬ֱ½Ó»Ø³µ£¬»áÔÚÉú³ÉÎļþ~/.ssh/id_dsa.pub
$ cat id_dsa.pub >> authorized_keys
ÕâÑùÔÚÔËÐÐmpirunµÄʱºò¾Í²»»áÓÐÃÜÂëÊäÈëÌáʾÁË

¡¶3¡·ÏÂÔØlammps×îÐµİ²×°°ü http://lammps.sandia.gov/

¡¶4¡·¿ªÊ¼±àÒë°²×°
(1)
go to ~/lammps/src:
ÔËÐÐÈçÏÂÃüÁ
make yes-all

make no-gpu

make no-user-atc

(2)

go to ~/lammps/lib/meam
ÔËÐÐÈçÏÂÃüÁ
make -f  Makefile.gfortran

(3)

go to ~/lammps/lib/poems
ÔËÐÐÈçÏÂÃüÁ
make -f Makefile.g++

(4)
go to  ~/lammps/lib/reax

make -f  Makefile.gfortran

(5)

go to ~/lammps/lib/awpmd

<5.1> go to ~/lammps/lib/awpmd/ivutils/include

ÔÚ logexc.hÎļþ¿ªÍ·²¹ÉÏ  #include

<5.2> go to the ~/lammps/lib/awpmd

ÐÞ¸Ä Makefile.openmpiÎļþ, °Ñmpic++¸ÄΪg++£¬ÐÞ¸ÄÍêµÄÑù×ÓÓ¦¸ÃÊÇ:

# include any MPI settings needed for the ATC library to build with
# the same MPI library that LAMMPS is built with

CC =            g++

......

ÐÞ¸ÄÍêÖ®ºó£¬ÔËÐÐ

make -f Makefile.openmpi

(6) go to ~/lammps/src/MAKE
ÐÞ¸ÄMakefile.g++Îļþ£¬ÏÂÃæÊÇÐÞ¸ÄÖ®ºóµÄÎļþ:


# g++ = RedHat Linux box, g++4, gfortran, MPICH2, FFTW

SHELL = /bin/sh

# ---------------------------------------------------------------------
# compiler/linker settings
# specify flags and libraries needed for your compiler

CC =                g++
CCFLAGS =        -g -O
DEPFLAGS =        -M
LINK =                g++
LINKFLAGS =        -g -O
LIB =           
ARCHIVE =        ar
ARFLAGS =        -rc
SIZE =                size

# ---------------------------------------------------------------------
# LAMMPS-specific settings
# specify settings for LAMMPS features you will use

# LAMMPS ifdef options, see doc/Section_start.html

LMP_INC =        -DLAMMPS_GZIP -DLAMMPS_JPEG

# MPI library, can be src/STUBS dummy lib
# INC = path for mpi.h, MPI compiler settings
# PATH = path for MPI library
# LIB = name of MPI library

MPI_INC =   -I/usr/lib/mpich/include
MPI_PATH =  -I/usr/lib/mpich/lib
MPI_LIB =   /usr/lib/mpich/lib/libmpich.a

# FFT library, can be -DFFT_NONE if not using PPPM from KSPACE package
# INC = -DFFT_FFTW, -DFFT_INTEL, -DFFT_NONE, etc, FFT compiler settings
# PATH = path for FFT library
# LIB = name of FFT library

FFT_INC =   -I/usr/include    -DFFT_FFTW
FFT_PATH =  -I/usr/lib
FFT_LIB =   /usr/lib/libfftw.a

# JPEG library, only needed if -DLAMMPS_JPEG listed with LMP_INC
# INC = path for jpeglib.h
# PATH = path for JPEG library
# LIB = name of JPEG library

JPG_INC =       -I/usr/include
JPG_PATH =         -I/usr/lib
JPG_LIB =        /usr/lib/libjpeg.a

# additional system settings needed by LAMMPS package libraries
# these settings are IGNORED if the corresponding LAMMPS package
#   (e.g. gpu, meam) is NOT included in the LAMMPS build
# SYSINC = settings to compile with
# SYSLIB = libraries to link with
# SYSPATH = paths to libraries

gpu_SYSINC =
meam_SYSINC =
reax_SYSINC =
user-atc_SYSINC =
user-awpmd_SYSINC =

gpu_SYSLIB =       -lcudart -lcuda
meam_SYSLIB =      -lgfortran
reax_SYSLIB =      -lgfortran
user-atc_SYSLIB =  -lblas -llapack
user-awpmd_SYSLIB =  -lblas -llapack

gpu_SYSPATH =      -L/usr/local/cuda/lib64
meam_SYSPATH =
reax_SYSPATH =
user-atc_SYSPATH =
user-awpmd_SYSPATH =

# ---------------------------------------------------------------------
# build rules and dependencies
# no need to edit this section

include        Makefile.package

EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) (PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)

# Link target

$(EXE):        $(OBJ)
        $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) (LIB) -o $(EXE)
        $(SIZE) $(EXE)

# Library target

lib:        $(OBJ)
        $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)

# Compilation rules

%.o:%.cpp
        $(CC) $(CCFLAGS) $(EXTRA_INC) -c $<

%.d:%.cpp
        $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@

# Individual dependencies

DEPENDS = $(OBJ:.o=.d)
include $(DEPENDS)

(7) go to src
ÔËÐÐÃüÁ

make g++

×îºóÔÚsrcÎļþ¼ÐÏÂÕÒµ½lmp_g++¿ÉÖ´ÐÐÎļþ£¬±à¼­¾ÍËãÊǽáÊøÁË¡£¿ÉÒÔ°Ñlmp_g++·Åµ½/usr/local/binÎļþ¼ÐÏ£¬ÒÔºóÓÃ×Å·½±ã¡£

£¨8£©L-JÒºÌåµÄinÎļþ in.lj, ¾ßÌåÃüÁîµÄ½éÉÜ¿ÉÒԲο¼lammps manual


# LJ system with NVE ensemble

units                lj
atom_style      atomic
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 3.0 825577 dist gaussian
pair_style      lj/cut 2.5
pair_coeff      * * 1.0 1.0 2.5
neighbor        0.3 bin
neigh_modify    every 20 delay 0 check no
fix             1 all nve
timestep        0.005
thermo          1000
run 10000

clear

(9)×îºóÔËÐÐmpirun ¨Cnp 2 /usr/local/bin/lmp_g++
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