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LAMMPS 的安装与配置

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分子模拟开坑，我只是路过

先基于腾讯云尝试一下。

doc​

先看文档 2.2.1. Read this first — LAMMPS documentation

If you want to avoid building LAMMPS yourself, read the preceding section about options available for downloading and installing executables. Details are discussed on the download page.

Add Yum Repository​

先看 Configuring the LAMMPS-ICMS Snapshot Repository装一下源

Command Line Setup for Fedora, CentOS/RHEL with Yum

  • Enabling the repository for Fedora 19, 20, and 21:
    su -c 'yum localinstall --nogpgcheck http://git.icms.temple.edu/rpm/fedora/lammps-fedora-repo-1-2.noarch.rpm'
  • Enabling the repository for CentOS or RedHat Enterprise Linux 6.6 and later:
    su -c 'yum localinstall --nogpgcheck http://git.icms.temple.edu/rpm/centos/lammps-centos-rhel-repo-1-2.noarch.rpm'

LAMMPS-ICMS RPM Repository​

The LAMMPS distribution is split into multiple sub-packages and you only need to install the ones that you need.

到这里LAMMPS-ICMS RPM Repository 挑选需要的sub-packages

我装了这几个：

  • lammps
  • lammps-python
  • lammps-common
yum install lammps lammps-python lammps-common

剩余的 lammps-doc 是PDF格式的没必要装在服务器上，lammps-openmpi和lammps-mpich 是并行化用的，目前只是试一试，暂时用不上。

Hello world

ref:

AL​

  1. 下载Al99.eam.alloy
  2. 新建文件vim calc_fcc.in 
    # Find minimum energy fcc configuration
    # Mark Tschopp, 2010

    # ---------- Initialize Simulation --------------------- 
    clear 
    units metal 
    dimension 3 
    boundary p p p 
    atom_style atomic 
    atom_modify map array

    # ---------- Create Atoms --------------------- 
    lattice 	fcc 4
    region	box block 0 1 0 1 0 1 units lattice
    create_box	1 box

    lattice	fcc 4 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1  
    create_atoms 1 box
    replicate 1 1 1

    # ---------- Define Interatomic Potential --------------------- 
    pair_style eam/alloy 
    pair_coeff * * Al99.eam.alloy Al
    neighbor 2.0 bin 
    neigh_modify delay 10 check yes 
     
    # ---------- Define Settings --------------------- 
    compute eng all pe/atom 
    compute eatoms all reduce sum c_eng 

    # ---------- Run Minimization --------------------- 
    reset_timestep 0 
    fix 1 all box/relax iso 0.0 vmax 0.001
    thermo 10 
    thermo_style custom step pe lx ly lz press pxx pyy pzz c_eatoms 
    min_style cg 
    minimize 1e-25 1e-25 5000 10000 

    variable natoms equal "count(all)" 
    variable teng equal "c_eatoms"
    variable length equal "lx"
    variable ecoh equal "v_teng/v_natoms"

    print "Total energy (eV) = ${teng};"
    print "Number of atoms = ${natoms};"
    print "Lattice constant (Angstoms) = ${length};"
    print "Cohesive energy (eV) = ${ecoh};"

    print "All done!"
  3. 跑起来 lmp_g++ < calc_fcc.in
  4. 输出 
    Total energy (eV) = -13.4399999527351;
    Number of atoms = 4;
    Lattice constant (Angstoms) = 4.05000466178543;
    Cohesive energy (eV) = -3.35999998818377;
    All done!
    Total wall time: 0:00:00

FIN