My blog - Literature summary

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Updated time: 11/06 2024.

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2024

November

• 2024.11.06

  加了六层FCC/HCP的弹性模量

  构建了surface energy的工作流

  完善了 finprim.py/check_direction() ，新添了对 a0 对齐于 x 方向，右手坐标系，a3 方向朝上。并添加判断条件，防止除以 0.

Octorber

• 2024.10.31

  计算了 bulk 平衡晶格常数对应的 gamma line，并加在了图中

  阅读了 zqk 发的关于金 ISF 和温度关系的 Acta

  对两个超算系统都进行了脚本部署，并且用本地 git 的方式实现了多平台的同步。在本地平台，git pullall, git pushall. 在超算系统，pei_git_univ_push_all

• 2024.10.30

  计算了 2.7/2.8/2.9 密排面晶格常数 FCC/HCP 的 gamma line

  创建了 my_plot.py ,可以熟练迅速的用 python 画图

  向赵庆坤请教了现在的课题进展以及接下来的研究方向

  写了 gsfe_full_relax.sh, hcp_gsfe, gsfe_preliminary.

• 2024.10.23

  完成作业工程管理/智能制造前沿导论

• 2024.10.22

  配置了A8分区的环境，部署了尹老师的脚本

  创建了自己的脚本，resubmit_isym_0, clean_outcar

  计算了18/24层的FCC/HCP金片

  创建了计算gamma line 的文件，熟悉了脚本，但是还没有计算

  安装了赵老师发的vaspkit pro版

• 2024.10.16

  用MD复现了tilted-cell method，计算层错能，但是面积部分并没有处理好，所以只是定性上是对的。

  安装了尹老师版本的VASP

  和刘韬请教了怎么计算层错能，讨论以后的工作方向

• 2024.10.13

  中期答辩PPT

  简单调研了FCC到HCP的相变机制

  和尹老师讨论了一次

  部署了hetbuilder在超算上

• 2024.10.05

  调研了贝恩相变及其在FCC/BCC/HCP中的用途

• 2024.10.04

  完成了Fe薄膜的调研，主要是集中于磁性的研究

• 2024.10.03

  完成了大应变下能量的计算

  写完了张通的Response letter关于我做的这部分

  写了我对当前相变机制的大概理解，和预期方向

• 2024.10.01

  复现了 Theoretical prediction of a phase transition in gold 中关于 HCP 和 FCC 在高压附近相变的结果

  和尹老师讨论了关于生长这部分 厚度/应变/界面 带来的影响该如何一步步算下去

September

• 2024.09.30

  提交了大应变时 FCC/HCP 12 层的计算任务

  完成了文献总结一篇

• 2024.09.21

  Engineering management assignment

  Move test.

  generate the final heterostructure, and at the begining of the structure optimization. Wish me luck.

• 2024.09.20

  Add the docstring on the Mymetal/build/film/strtch.py

  Move test along with z-direction.

• 2024.09.19

  generate the amorphous SiO2 using ReaxFF on Lammps.

  create a perfect pristine slab.

  try to relax pristine slab in DFT level, but failed because of the dangling bond.

  create python code to slice and passivate the surface according to the coordination number.

  After saturating the dangling bond, success to relax the hydroxylated slab in DFT level using less precise convergent criterion.

  Install the heater sample stage in Cypher AFM.

• 2024.09.02

  generate the amorphous SiO2 using Tersoff potential function. (too many unexpected defects)

  check the mismatch < 5%

• 2024.09.03

  group meeting.

  try to get a perfect slab, but there still has some unexpected defect, like Si-Si bond.

  have the dinner with roommates.

• 2024.09.04

  try to get the ReaxFF potential function using by literature 《Dynamics of ultrathin gold layers on vitreous silica
  probed by density functional theory》.

  Online return registration on CSC / ZJU website.

  get the haircut.

  send the email to the author of the original ReaxFFSiO force field.

• 2024.09.05

  get the updated force field SiOH.ff based on the original one.

  sort the favorite on the lammps page.

• 2024.09.06

  留服认证

  报到，学生证盖章

• 2024.09.07

  Find English APP

  make a timetable about my doctor student’s plan

  go to the gym

• 2024.09.08

  Find the appropriate Lammps package - lammps/intel18/20Sep2021

  sbatch the job

August

• study the driver license.

July

• Finish the diploma in the MAI and return to china.

June

• 2024.06.24

  update hexo/tools-summary.

  update endnote literatures.

• 2024.06.21

  fix error about my blog the main page.

  read literature 《Computational Approach for Epitaxial Polymorph Stabilization through Substrate Selection》

  read literature 《Zur algorithm, Lattice match: An application to heteroepitaxy》

  read literature 《High-throughput ab initio design of atomic interfaces using InterMatch》

• 2024.06.19

  write the SI-MD/DFT for ZT’s essay

• 2024.06.10

  delete the GSFE- it’s wrong.

  try to calculate the confusion matrix

  try to train all the classification model

• 2024.06.05

  calculate the MD of 8-layer gold flake nanoindentation.

  draw the figure about GSFE / nanoindentation

  start the job of ML

  analysis the dislocation under nanoindentation.

May

• 2024.05.23

  Try to install mymetal/hetbuilder package in supercomputer, but failed

• 2024.05.21

  Install the HDF5 support (zlib, szip, hdf5) for VASP 6.3.2 on Debian 12.5 and Supercomputer, for using py4vasp package.

• 2024.05.17

  install the p4vasp using apt-get.

• 2024.05.16

  The cubic heterostructure (123 atoms) has too more mismatch (>6%)

  And I select the non-cubic heterostructure (420 atoms) and lower mismatch (<5%)

  And then submit the job.

  Although it doesn’t convergent, more stable than cubic one.

  Fix error about filtering the result according to mismatch/strain.

• 2024.05.02

  find a cubic heterostructure not big mismatch and not large system.

  read the chapter 2 and 3 of DFT practical.

  reading the chapter 4.

April

• 2024.04.29

  MD of GSFE calculation

  introduce a mechanics parameters to evaluate the max stretch of thin film.

  storing the Endnote library

  install the VASP 6.3.2, LAMMPS 2023, VASPKIT, ATOMKIT on Debian 12.5.

  Deal with all WeiXin messages.

  Talk with ZhangTong (Tencent meeting)

• 2024.04.07
  Pyenv hetbuilder
  git, cmake, …

• 2024.04.08
  vs code
  ovito
  .bashrc file
  add git alias
  git PJ_advanced_reasearch

• 2024.04.09
  create a new env for mymetal contained myalloy, hetbuilder, py4vasp
  create a environment about requirement.txt

• 2024.04.10
  understand the workflow of hetbuilder
  add the find_hetero, construct_hetero
  test_weight for hetbuilder

• 2024.04.21

  have genegrated many hetero-structure

  update the baidu cloud, github

  construct the mymetal package (update calmismatch, add the rst file)

  back up my endnote library. (It’s important to back up files for researchers.)

• 2024.04.23

  create and check the function to calculate the strain matrix and filter the results. (Now, it’s only calculated the film strain, maybe next time, I’ll correct it.)

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