My blog - Literature summary

Life is a long relay race, sometimes leading, sometimes lagging behind, no matter how it ends, just enjoy the process!

人生是一场漫长的接力赛，有时领先，有时落后，不管结局怎样，享受过程就好！

Updated time: 11/20 2024.

Keep updating

• column about python - DFT calculation
• metal developing log
• research - Au film
• research - graphene/two-dimensional material/diamane
• literary
• theory book/website

11/20 2024.

• 计算薄膜表面的 gamma line
• 应变能密度与厚度相关的变化

11/13 2024.

• 自由能矫正
• COHP 计算
• 能量的分解
• 文章初稿

11/12 2024.

• 用 pymatgen 生成高对称 K 点，并结合到工作流中
• 用 pymatgen 生成高质量 DOS+BANDS 图，并结合在后处理工作流中

11/06 2024.

• 生成 python 包的完整 docstring.
• 修改 `my_read_vasp()` 输出 lattice scale factor
• 移除了 python 包对 ase, ovito 版本的依赖
• 张华文章中晶格取向的建模，形成能计算

11/04 2024.

• 排除数据结果是由于K网格密度差异导致的

10/31 2024.

• 薄膜体系可以计算吉布斯自由能嘛 G
• gamma line 再加两条 - 能量相等时的 gamma line
• 是否可以仿照尹老师的那篇 JMPS 用 MD 和 DFT 结合，计算一个面内应变对 gamma line 的影响
• 写一个计算 surface energy 的工作流

10/30 2024.

• 赵庆坤
  • Young's modulus 去掉 bulk, 再往右算
  • Surface energy 再往两边算一下，扩充一下数据
  • 补一个滑动示意图，如何相变，如何产生层错
  • 对于HCP晶格密排面方向看去的晶格间距，是否是均匀的，可以用GPA看，后续找张通要了数据，发给赵庆坤看一下
  • ISIF=6可以算Cij
  • 把2.7/2.8/2.9转换成对应的应变
  • 声子谱
  • 弹性模量是和电子结构紧密相关的，可以分析电荷密度，差分电荷分析键的强弱
  • 带基底的计算本质上还是不算个非晶
  • 表面最外一层层间距比较他他也观察到过
  • 算厚度比较大的表面能看是否会出现反转 表面能是个和厚度无关的量，我们的结果也已经收敛了
  • 发了三篇文献，关于电子结构分析高熵合金，还可以看一些博士论文
  • 搜吴渊 北科大，HEA, First calculation principles.
  • 拿体积比，晶格常数可能比较意义不够准确
• ybl
  • bulk 的电子结构
  • 平衡晶格常数对应的gamma line
  • E 的分解
  • 实验上尝试过的基底的晶格常数，有无单晶的
  • 把尹老师算的那两个点也加进来
• 读那篇 ISF 和正压力相关的 JMPS
• 表面能的晶格常数取的是slab 12层的a~0~，应该算到bulk的a~0~
• my_plot.py 中关于尺寸的 bug 调试

10/28 2024.

• 为什么HCP比FCC的面内弹性常数大？- 从电子结构角度分析
• 轴比图
• 层间距为什么最表面的一层离得比较远 - 有可能是最表面一层原子在面内方向最致密，导致离面方向反而更远，赵庆坤也观察到薄膜中的这个情况

10/22 2024.

• 写脚本 resubmit ISYM0
• 写脚本 clean_outcar, 结尾有大量的null
• 计算 16/20 层 FCC 金的弹性能密度
• 使用 python 绘制曲线
• 文章构图，文章框架构思

10/16 2024.

• 和老板讨论之后的工作方向

10/13 2024.

• 计算不同层数的能量差.
• 计算不同晶格常数下（2.7，2.8，2.9）的gamma-line.
• 安装尹老师版的 VASP，以及配套的vasp_utils.

10/09 2024.

• 对多个应变的HCP/FCC薄膜的表面能计算 - 8 % ， 10 %
• 生成相变的能垒模型
• 计算相变能垒

10/06 2024.

• 调研FCC->HCP，相变理论，相变驱动力
• 制定当前薄膜体系的相变研究框架
• 和尹老师讨论势垒的计算

10/05 2024.

• 判断FCC金是不是脆性的材料，以确定要不要以强韧化为研究方向

10/04 2024.

• 可不可以用过渡态搜索完成相变机制的诠释

10/03 2024.

• 把昨天和老板说的-关于现在这个体系怎么相变的机制/能量-应变双机制写出来，完整描述

09/30 2024.

• 计算尹老师得到的两种材料表面能
• 大应变下能量的比较
• 分析体系能量由哪几部分构成（表面能，体能，界面能） => 表面能、弹性能、体相能量
• 有无可能算出势垒，依据过渡态计算
• 比较bulk下，抛物线和opt-ccell方法比较
• 速读固体物理导论 / 固体与表面/原子物理学
• 分析VASP中应力张量怎么计算出的
• 阅读《若干金属纳米多层膜界面结构及力学性能研究》博士论文中关于厚度对金属薄膜面内弹性常数的影响的文献

09/26 2024.

• 调研纳米金属薄膜的相变-能量-电子结构分析机制/方法

09/25 2024.

• 测试/比较低精度的12层薄膜HCP/FCC Au能量

09/24 2024.

• 测试/复现尹老师的计算结果：抛物线和 opt-cell 方法比较
• 晶体衬底和薄膜的复合结构
• Amorphous 需要统计多次才能有意义
• 带饱和键基底的符合模型需要提高收敛判据和准确度
• 把上表面的赝氢换成金？

09/23 2024.

• Pristine substrate DFT

09/22 2024.

• VASP6 on the super computer. 工程师说跟核数有关。确实，尽量用十的倍数，大核数也可以算，但是得调试参数

09/21 2024.

• Move test of heterostructures.

09/19 2024.

• Response letter about the technical detail.
• Investigate how to generate the H2 plasma.
• AFM experiment: AFM + 加热。先用机械剥离的石墨烯，金刚石探针扫。

09/10 2024.

• make a technology summary ppt, including CVD generating graphene.
• 中期答辩PPT/个人小结/开题报告
• re-sbatch the structure optimization of the bulk amorphous SiO2
• literatures ppt about review of diamane

09/08 2024.

• Compile Lammps manualy in the supercomputer

09/04 2024.

MD-DFT

• Use ReaxFF potential field to generate the amorphous SiO2
• generate composed models / hetrostructures.
• structural optimization.

08/02 2024.

• 制定一个计划，什么时候考雅思，以及科研进展

07/23 2024.

MD-DFT

• Amorphous SiO2
• model with amorphous substrate

Experiment

• read the literature sending by GY and make a report using ppt, distinguish the difficulty, hard work, purpose.

• try to work on AC water mode

• investigating the simulating literature cited GY’s nature nanotechnology work.

06/25 2024.

• try to use interface-master to search after hetbuilder followed Zur algorithm from Material project.

06/24 2024.

• investigating the literature about the phase transition of Ultra-Fe film.
• try to schedule the timetable of my work.
• write the ML essay.
• check if it need to add H atoms - yes

06/21 2024.

• read the literature about 《interface-master》

06/20 2024.

• read the literature about 《material project - ref 16, 22》，《Fireworks》, 《[atommata2](https://materialsproject.github.io/atomate2/user/fireworks.html)》 from [description](http://www.cailiaoniu.com/68761.html)
• read the literature about 《Zur algorithm - ref 38 in |Computational Approach for Epitaxial Polymorph Stabilization through Substrate Selection|》

Gao

• redraw the picture 5B
• write some sentence about Zur algorithm on SI-MD
• investigating the literature about surface effect to explain that the ultra-film’s decreasing modulus

06/19 2024.

• try to use similar DFT parameters in material project

• read the literature about 《substrate selection》/《Computational Approach for Epitaxial Polymorph Stabilization through Substrate Selection》
• MLMD

06/11 2024.

• find the heterostructure in the material project
• try to connect the ASE with VASP / LAMMPS

06/10 2024.

• ML jobs - train the selected models
• ML jobs - post confusion matrix.
• read the < Introduction to dislocations> in 2-week.
• DFT jobs

06/05 2024.

• For MD, draw the figure for ZT paper
• analysis the dislocation type number using the ovito python module.

05/17 2024.

• For DFT result, find the force vector and change the initial model.
• write a script to submit the job that doesn’t change the before information.
• For MD, maybe we should use the minimum step around the big-deformation region.

05/16 2024.

• read the 《Introduction of dislocation》
• 《DFT practice》 the exercise
• Analyze the result of MD simulation
• The ML job - write the code to train model.

05/02 2024.

• change the add hydro-surf function to make the interface more stable.

04/29 2024.

• select the heterostructure and sbatch the DFT job.
• MD simulation of nanoindentation.

04/23 2024.

• create some functions on mymetal package to check the strain component tensor. => 100%
• change the structure now only calculate the film strain. It's not correct absolutely.

04/21 2024.

• construct the doc file of mymetal package => 10%
• check the lower mismatch of heterostructure and sbatch jobs (film, film-substrate). => 100%
• create a function to adjust the z-component of Atoms object according to $\nu=0.5$
• calculate the surface fault energy of HCP/FCC gold using EAM potential.

04/02 2024.

• add the Pymatgen package => 100%
• add the matlab code to Mymetal I have done
• read the future reading list

04/01 2024.

I‘ll keep read those books:

• 材料学的纳米尺度计算模拟
• 密度泛函理论 (Density Functional Theory A Practical Introduction)
• 固体与表面
• Quantum Chemistry/ Electronic Structure: Basic Theory and Practical Methods

And the best learning method is to doing some calculation about them.

Another job is to collect the 《The Feynman’s Lectures on Physics》

03/30 2024.

I’ll add the content below ASAP :

• My summary about some useful function website, Github, unit convert website, special website about some specified function to `My blog - My summary` => Done
• Note other blog is about my experience, but the below blog'll included all content like other people's summary blog
• Create a blog to add everything I am interested in `summary/other blog`
• The literary on WeiXin could be added the category Summary/Literary/skimming or intensive reading, and we need to create some literary tag => 0%
• Add some VASP theoretical like some classical literatures to `Software/VASP/theory` => Done

I’ll do some work about my scientific research:

• find a website/notebook that could execute the DFT calculation from the first step. => 0%
• sbatch some jobs of the structure optimization for the primitive cell of the bulk HCP/FCC gold. => 100%
• generate the heterostructures using my package => 100%

03/29 2024.

I’ll add the content below ASAP :

• some tools => Done
• some my zhihu text => 100%
• deal with Wechat text => 100%
• Theoretical website resource => Done
• Developing package mymetal => Done

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