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[资源] LAMMPS使用初体验，Debian 6.0

我是在Debian 6.0下编译安装的，也在Ubuntu 10.04下编译通过。首先介绍一下并行编译的过程，然后以L-J相互作用势的液体为例，给出了in文件的写法。欢迎大家补充。

第一部分，安装

《1》首先安装所有依赖的包：
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》取消SSH的密码步骤
$ ssh-keygen -t dsa #中间提示输入密码，直接回车，会在生成文件~/.ssh/id_dsa.pub
$ cat id_dsa.pub >> authorized_keys
这样在运行mpirun的时候就不会有密码输入提示了

《3》下载lammps最新的安装包 http://lammps.sandia.gov/

《4》开始编译安装
(1)
go to ~/lammps/src:
运行如下命令：
make yes-all

make no-gpu

make no-user-atc

(2)

go to ~/lammps/lib/meam
运行如下命令：
make -f  Makefile.gfortran

(3)

go to ~/lammps/lib/poems
运行如下命令：
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

在 logexc.h文件开头补上  #include

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

修改 Makefile.openmpi文件, 把mpic++改为g++，修改完的样子应该是:

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

CC =       g++

......

修改完之后，运行

make -f Makefile.openmpi

(6) go to ~/lammps/src/MAKE
修改Makefile.g++文件，下面是修改之后的文件:

# 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
运行命令：

make g++

最后在src文件夹下找到lmp_g++可执行文件，编辑就算是结束了。可以把lmp_g++放到/usr/local/bin文件夹下，以后用着方便。

（8）L-J液体的in文件 in.lj, 具体命令的介绍可以参考lammps 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)最后运行mpirun –np 2 /usr/local/bin/lmp_g++

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