跳转至

Notes on MD hands-on session of MSE6701H-CHN

约 2910 个字 180 行代码 18 张图片 预计阅读时间 12 分钟

Content: [TOC]

0.0 Notice

同学们好，今晚的课程为 MD 部分上机实操课：

  1. 请同学们尽量都准备好笔记本电脑并充保持充足的电量（充电器也可以带上），条件允许的同学可以把排插带上。

  2. 本次上机实操课将涉及远程服务器登录、任务提交与文件传输，Linux 操作系统与基本命令，Vim 文本编辑器，LAMMPS，结构建模，构型可视化及其分析等内容。

  3. 请同学们在今晚上课前按照该链接 https://notes.sjtu.edu.cn/s/ULArhqGqt 中的操作提前安装好 MobaXterm、OVITO、WinSCP 软件，并用自己的课程超算账号远程登录思源一号，熟悉远程登录与文件传输、Linux 基本命令、Vim 文本编辑器使用等基础操作。

  4. 在使用课程材料前，请先阅读该目录下的 README 文件内容来大致了解其使用说明、框架及功能，不要一开始就 " 盲目 " 进行操作（提交任务），以免出现不必要的错误。

  5. 使用课程材料过程中，请熟悉课程材料的目录及文件结构！课程材料及该 Notes 均测试正常。

0.1 Helpful things

可能有帮助的一些教程链接：

1. Preparation

1.1. Account lookup

  • For the hands-on session and for your homeworks, the Siyuan cluster of HPC, SJTU will be used. You have been offered a temporary account, please click & find it here!

Note: this account is used for the course related tasks only. Any abuse will lead to suspension of your previlige to use the superclusters.

1.2. SJTU HPC login

1.2.1 Windows Setup

  • If your computer system is Windows, to login the Siyuan cluster, you are advised to use MobaXterm free Xserver and tabbed SSH client for Windows. The free version is good enough. Please have it installed on your computer.

  • Besides MobaXterm, you can use other terminal emulators on Windows such as Windows Terminal, Tabby, Termius and so on.

  • For your first time to run MobaXterm, please open the "Session" tab:

image.png

  • which shall show you a window looks like, click on "SSH":

image.png

  • For "Remote host", input sylogin.hpc.sjtu.edu.cn . Check "Specify username" and input your username. Click on "Bookmark settings" and name your session as Siyuan-MMMS. Press "OK" to save:

image.png

  • Now you should have a bookmarked session "Siyuan-MMMS":

image.png

  • Click on "Siyuan-MMMS" to login to the remote Siyuan cluster, you will be asked for your password; and the program may ask if you would like to save your password, you can answer "yes" if you are the only person using this computer.

  • By providing the correct username and password, you should be logged into the supercluster by now:

image.png

Note: for the jobs in this course, use at most 4 cores for your jobs. i.e., #SBATCH --ntasks-per-node=4. In most cases, 1 is good enough.

1.2.2 macOS setup

# Note: -p 22 can be omitted

# login to Siyuan HPC
ssh -p 22 [email protected]

# Copy file from remote Siyuan to your local computer
scp -P 22 [email protected]:/dssg/home/acct-stu/stuXXX/* .

# Upload local file/folder to remote Siyuan HPC
scp -P 22 -r LocalFolderName [email protected]:/dssg/home/acct-stu/stuXXX/*

1.3. Retrieving of Course Materials

  • If you can't login Siyuan in class, you can visit MMMS Course Materials Gitee repo: https://gitee.com/sjtu_konglt/MSE6701H

  • Once login Siyuan, you can run the following commands on your shell, it will automatically git clone MMMS Course Materials MSE6701H to your home directory on Siyuan.

git clone https://gitee.com/sjtu_konglt/MSE6701H.git
  • If you have cloned the Course Materials, then just git pull to get latest commit.
cd ${HOME}/MSE6701H

current_branch=$(git branch --show-current)
git pull origin ${current_branch}
  • MMMS Course Materials directory structure:
    • 0-reference-solutions: provides two reference solutions to previous homeworks. You can check it for your reference.
    • 1-Linux: lists some necessary knowledge you should have in order to use a Linux system. You are advised to learn the commands by yourself.
    • 2-MolecularDynamics: contains the files needed for the hands-on session of the MD part of this course. We will start with this directory from now on.
.
├── 0-reference-solutions/
├── 1-Linux/
├── 2-MolecularDynamics/
├── 3-DFT/
├── Au_u3.eam
└── README.md

2. Step by step instructions on the MD examples

2.1. MD part Material directory structure

  • Get into the directory:
cd ~/MSE6701H/2-MolecularDynamics

tree -LF 1
  • The directory structure should look like:
├── 0-tools/
├── 1-Bulk-Energy-Cu/
├── 2-Slab-Relaxation/
├── 3-Cu-Heating-Cooling/
├── 4-Cu-Tm-two-phases/
├── 5-Cu-MSD/
├── 6-Dislocation-Motion/
├── 7-experiments/
└── 8-polymer/
  • We will run the examples one by one. Firstly, 1-Bulk-Energy-Cu.

2.2. Determination of equilibrium lattice constant of fcc Cu

This example illustrates the determination of the equibrium lattice constant of fcc Cu based on the adopted interatomic potential by calculating the total potential energy of the system at a series of volumes and fitting to the volume-energy data to an equation of state.

  • Get into the directory before running the example: 

    cd ~/MSE6701H/2-MolecularDynamics/1-Bulk-Energy-Cu
tree .

  • directory structure:

.
├── Cu_u6.eam
├── in.lmp
├── job.slurm
├── README
└── scan.sh

There should be 5 files in this directory. One can examine the in.lmp or scan.sh to understand the method.

  • To run the example:
sbatch job.slurm       # submitt job to Siyuan
squeue                 # monitor job queue
  • Your job is now submitted to Siyuan for calculation. It might be waiting for the computing resource to be available. Once completed, you should find 2 more files in your directory:
log.lammps
ev.dat
  • To check the content of ev.dat or log.lammps, one can use:
cat ev.dat

# or
more log.lammps

../0-tools/eos_fit ev.dat 2 3

image.png

According to the fitting results, the cohesive energy for fcc Cu is 3.54 eV/atom, and the lattice constant of fcc Cu based on the adopted potential is 3.615 Angstrom, agreeing perfectly with the experimental value.

2.3. Surface energy calculation

The second example illustrates the calculation of the surface energy of fcc Cu (001); the equilibrium bulk energy (3.54 eV/atom) and lattice constant 3.615 Angstrom from example (1) is used here.

  • To run this example:
cd ~/MSE6701H/2-MolecularDynamics/2-Slab-Relaxation

Please check the files and understand the method before submitting the job:

sbatch job.slurm
squeue
  • Once the job has been finished, one can find the results from the log.lammps file:
tail -n 7 log.lammps

Note: OVITO can be used to visualize the atomic configuration as in dump.lammpstrj. For instruction to use ovito with Siyuan, please refer to OVITO - 上海交大超算平台用户手册 Documentation.

  • Use interlayer_separations.py Python script to measure interlayer separations of the (001) surface of fcc Cu: \(\Delta d_{12}\) =-1.05%，\(\Delta d_{23}\) =-0.33%
# Retrieving interlayer_separations.py Python script
wget https://gitee.com/yangsl306/MMMS-MSE-SJTU/raw/main/scripts/interlayer_separations.py -O interlayer_separations.py

# Grants executable permissions
chmod +x interlayer_separations.py

# load miniconda3 on Siyuan HPC
module load miniconda3

# install necessary pacakges to run interlayer_separations.py
pip install ase
pip install pandas
pip install numpy


# Show help message
./interlayer_separations.py -h

# Measure interlayer separations
./interlayer_separations.py dump.lammpstrj

# Output
Inerlayer separations info:

       Layer_Distance_Final  Layer_Distance_Init  Inerlayer_Separations  Ratio(%)
16-17                 1.788                1.807                 -0.019     -1.05
15-16                 1.802                1.808                 -0.006     -0.33
14-15                 1.807                1.807                  0.000      0.00
13-14                 1.808                1.808                  0.000      0.00
12-13                 1.807                1.807                  0.000      0.00
11-12                 1.808                1.808                  0.000      0.00
10-11                 1.807                1.807                  0.000      0.00
9-10                  1.808                1.808                  0.000      0.00
8-9                   1.808                1.808                  0.000      0.00
7-8                   1.807                1.807                  0.000      0.00
6-7                   1.807                1.807                  0.000      0.00
5-6                   1.808                1.808                  0.000      0.00
4-5                   1.808                1.807                  0.001      0.06
3-4                   1.807                1.808                 -0.001     -0.06
2-3                   1.802                1.807                 -0.005     -0.28
1-2                   1.788                1.808                 -0.020     -1.11

2.4. Melting temperature estimation by heating-cooling

The 3rd example illustrates the estimation of the melting temperature of fcc Cu by heating and cooling. It also illustrates the usage of thermostat and barostat to monitor of the temperature and pressure of a system.

  • To run this example:
cd ~/MSE6701H/2-MolecularDynamics/3-Cu-Heating-Cooling

Please check the files and understand the method before submitting the job:

sbatch job.slurm
squeue
  • It might take some time for the simulation to be done. Once the job has been finished, one can analyze the variation of potential energy as a function of temperature during the heating and cooling cycle by running the script prepared:
./analyze_cooling_curve.sh

image.png

  • One can also analyze the variation of volume as a function of temperature during the heating/cooling cycle to estimate the melting temperature. The 1st order phase transformation should be observed from the curves.

Note: OVITO can be used to visualize the atomic configuration as in dump.lammpstrj. For instruction to use ovito with Siyuan, please refer to OVITO - 上海交大超算平台用户手册 Documentation.

2.5. Melting temperature evaluation by two-phase co-existence method

The 4th example illustrates the calculation of the melting temperature of fcc Cu by the two-phase co-existence method. It is a more or less accurate method to determine the melting temperature of a material.

  • To run this example:
cd ~/MSE6701H/2-MolecularDynamics/4-Cu-Tm-two-phases

Please check the files and understand the method before submitting the job:

sbatch job.slurm
squeue
  • It might take some time for the simulation to be done. Once the job has been finished, one can analyze the temperature profile by running the script prepared:
./show_temp_prof.sh

image.png

Note: OVITO can be used to visualize the atomic configuration as in dump.lammpstrj. For instruction to use ovito with Siyuan, please refer to OVITO - 上海交大超算平台用户手册 Documentation.

2.6. Self-diffusion coefficient calculation from MSD

The 5th example illustrates the calculation of the self-diffusion coefficient of fcc Cu at both 300 K and 1800 K. The computation of MSD is employed.

  • To run this example:
cd ~/MSE6701H/2-MolecularDynamics/5-Cu-MSD/1-300K
sbatch job.slurm

cd ../2-1800K/
sbatch job.slurm
squeue

Please check the files and understand the method adopted.

  • It might take some time for the simulation to be done. Once the job has been finished, one can analyze the MSD by running the script prepared in either 1-300K or 2-1800K directory:
./analyze_msd.sh

2.7. Dislocation energy and critical shear stress

The 6th example illustrates the calculation of dislocation energy and critical shear stress for dislocation motion.

  • Examples for both screw and edge dislocation are present.

  • Since the introduction of a single dislocation will enevitably lead to the existence of free surface in the atomic model, three separate runs are prepared for each dislocation:

    • The first one: shares a similar geometry as the second one, but without a dislocation. It servers as a reference in evaluating the dislocation energy.
    • The second one: introduces a dislocation and relax the geometry, and then find the dislocation energy by subtracing the reference energy and dividing the difference by the dislocation length.
    • The third example: applies a continuously increasing shear strain and measures the relaxed shear stress; the maximum stress along this process gives the critical shear stress required to trigue the dislocation motion under zero temperature.
1-screw/
├── 1-without-dislocation/
├── 2-dislocation-relax/
└── 3-dislocation-shear/

2-edge/
├── 1-without-dislocation/
├── 2-dislocation-relax/
└── 3-dislocation-shear/
  • To run the examples, one can follow the steps shown below:

2.7.1 For screw dislocation

2.7.1.1. Reference configuration without a dislocation
  • Get into the directory:
cd ~/MSE6701H/2-MolecularDynamics/6-Dislocation-Motion/1-screw/1-without-dislocation

tree -LF 1
  • You should find at least 5 files:
.
├── Cu_u6.eam
├── generate_model.sh
├── in.lmp
├── job.slurm
└── README

To run this calculation, you should generate the atomic model (name data.lmp) by using atomsk first:

./generate_model.sh

where generate_model.sh is a bash script I prepared for your to call atomsk and create the atomic model.

If you are running this example on your own computer, you should:

  1. install atomsk on your computer;

  2. modify generate_model.sh by redefining the variable ATOMSK. And then you can run the generate_model.sh.

  • And now you can run the LAMMPS calculation. If you are running on Siyuan cluster, you should use the commands:
sbatch job.slurm
squeue

But if you are running on your own computer, you can use the following command instead:

lmp -in in.lmp -sf opt

# or
mpirun -np 4 lmp -in in.lmp -sf opt
  • Once the calculation is done, you can check the log.lammps file for information:
more log.lammps
  • The energy (both total and average atomic energy) of the reference configuration can be obtained by:
grep '^^' log.lammps

2.7.1.2. Configuration with a dislocation

Now we can calculate the energy of the model with a screw dislocation:

cd ~/MSE6701H/2-MolecularDynamics/6-Dislocation-Motion/1-screw/2-dislocation-relax
  • Similarly, you should find at least 6 files:
.
├── compute_disl_energy.sh
├── Cu_u6.eam
├── generate_model.sh
├── in.lmp
├── job.slurm
└── README

To run this calculation, you should generate the atomic model (name data.lmp) by using atomsk first:

./generate_model.sh

where generate_model.sh is a bash script I prepared for your to call atomsk and create the atomic model.

If you are running this example on your own computer, you should:

  1. install atomsk on your computer;

  2. modify generate_model.sh by redefining the variable ATOMSK. And then you can run the generate_model.sh.

  • And now you can run the LAMMPS calculation. If you are running on Siyuan cluster, you should use the commands:
sbatch job.slurm
squeue

But if you are running on your own computer, you can use the following command instead:

lmp -in in.lmp -sf opt

# or
mpirun -np 4 lmp -in in.lmp -sf opt
  • Once the calculation is done, you can check the log.lammps file for information:
more log.lammps
  • The energy (both total and average atomic energy) of the relax configuration with a screw dislocation can be obtained by:
grep '^^' log.lammps

  • And the dislocation energy can be deduced by:
./compute_disl_energy.sh

Where compute_disl_energy.sh is another script I wrote for you to calculate the dislocation energy.

2.7.1.3. Critical shear stress measurement

To calculate the critical shear stress required for triguing the dislocation motion, one should move into the 3rd directory:

cd ~/MSE6701H/2-MolecularDynamics/6-Dislocation-Motion/1-screw/3-dislocation-shear
  • where you should find at least 6 files:
.
├── compute_critical_stress.sh
├── Cu_u6.eam
├── generate_model.sh
├── in.lmp
├── job.slurm
└── README

To run this calculation, you should generate the atomic model (name data.lmp) by using atomsk first:

./generate_model.sh

where generate_model.sh is a bash script I prepared for your to call atomsk and create the atomic model.

If you are running this example on your own computer, you should:

  1. install atomsk on your computer;

  2. modify generate_model.sh by redefining the variable ATOMSK. And then you can run the generate_model.sh.

  • And now you can run the LAMMPS calculation. If you are running on Siyuan cluster, you should use the commands:
sbatch job.slurm
squeue

But if you are running on your own computer, you can use the following command instead:

lmp -in in.lmp -sf opt

# or
mpirun -np 4 lmp -in in.lmp -sf opt
  • Once the calculation is done, you can check the Info.dat file for information:
cat Info.dat
  • The critical shear stress can be found by:
./compute_critical_stress.sh

Where compute_critical_stress.sh is another script I wrote for you to find the critical (minimum) shear stress for the screw dislocation to move under zero temperature.

2.7.2. Edge dislocation

For the edge dislocation, all the procedure should be the same as that for the screw dislocation, but one should move into the directory for the edge dislocation instead:

cd ~/MSE6701H/2-MolecularDynamics/6-Dislocation-Motion/2-edge

  • I will skip the details here.

  • The energy (both total and average atomic energy) of the reference configuration without edge dislocation:

  • The energy (both total and average atomic energy) of the relax configuration with a edge dislocation:

  • The dislocation energy:

  • The critical shear stress:

3. Surface Energy Calcucation Homework Content & Requirements

Based on the section 2.2 and 2.3 examples and codes, generate Au(100), Au(110), Au(111) slab models, run minimization at 0K.

a) Calculate their surface energies at 0K.

b) Measure the interlayer separations of the surface, and compare to data in Table1 of Solid State Communications 149(37–38): 1561-1564, 2009.

c) Write a report on your experiments.

The due is: Dec 11th, 2024.

Hint:

  • Append your LAMMPS script but not the lengthy outputs.

  • The possible potentials for Au could be found here: https://www.ctcms.nist.gov/potentials/system/Au/. You can adopt any potential you prefer, but please specify explicitly.

  • If you'd like to create surface configuration correctly, use atomsk tool or ASE build module (you can refer surface_generation_ase.py, surface_generation_atomsk.sh and in_slab_relaxation.lmp codes in https://gitee.com/yangsl306/MMMS-MSE-SJTU/tree/main/scripts:). Do not use LAMMPS internal command lattice with orient keyword (lattice command — LAMMPS documentation)!

  • You are advised to present the surface models (use "Common neighbor analysis" Modification in OVITO) and specific three axes in the report (You can use OVITO or VESTA to visualize configuration).

4. MD Course Project

This will be your first course project. The due is: Dec 25th, 2024.

  • The files needed to complete the MD course project are located in:
cd ~/MSE6701H/2-MolecularDynamics/7-experiments/
  • These are the experiments that you are expected to carry out. Please refer to the instructions above to accomplish your task and write a comprehensive epxerimental report for all the calculations.
.
├── 1-LatticeConstants
├── 2-SurfaceEnergy
├── 3-PointDefectFormationEnergy
└── 4-Dislocation-mobility

  • The first three are required for all students, while the last (4-Dislocation-mobility) is optional and for advanced learners only.

  • For the last task, the DXA tool within OVITO software is recommended to analyze the dislocation.