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LAMMPS使用初体验，Debian 6.0
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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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2楼2011-07-07 22:06:55
3楼2012-01-18 15:14:26
