HSE Functional for Band Structures in VASP

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VASP the GUIDE: Hartree-Fock (HF) type and hybrid functional calculations
VASPwiki: Tutorial on hybrid functionals
Related discussion: How can I calculate the DOS by using HSE06 in vasp?

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Unix/Linux 及 vi 编辑器基本命令参考

Starting a Terminal. Continually updated…

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The Installation of Sci-hub Plugin

A lawsuit isn’t going to stop [Sci-Hub], nor is there any obvious technical means. Everyone should be thinking about the fact that this is here to stay.
Peter Suber, Harvard University

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VASP 计算问题小结

本文转载自博主一个人就是一个叠加态 ,有部分删减修改,文中对相关概念方法做了详细的总结,留坑待填…

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知识管理软件 Zotero 的使用

Zotero 简介

Zotero [zoh-TAIR-oh] is a free, easy-to-use tool to help you collect, organize, cite, and share your research sources.

Zotero是一个免费且易用的工具,可以帮助你收集、整理、引用和分享你的研究资讯。

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杭州-乌镇小记


  • 日期:2017/4/2 - 2017/4/4
  • 行程:芜湖/上海/池州 - 西湖 - 乌镇 - 嘉兴

大学计划多时的新马泰(大兴马集太和)三日游一直未果,时值清明公假,一来为放松心情,二来朋友许久未见甚是想念,便邀约杭州一聚,小辉和浩子已然参加工作,各种琐事绊扰,相聚着实不易。

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VASP 的 PDOS 计算及 P4vasp 的后处理


使用的软件:VASP, Origin, SshClient, p4vasp


The LDOS, or local density of states, is the the density of state at a particular site of a crystal with some asymetry. For example: A slab will have a different band structure on the surface than in the bulk region.
The PDOS is a projected density of states. In the context of VASP this means site-projected DOS, where the information about the different contributions of the different orbitals is computed. You then know which states (spd) contribute at which energy. You have to select the proper LORBIT tag in the INCAR file (e.g. LORBIT=11) to get the spd decomposed DOSCAR file output. The formatting is explained in the DOSCAR file link provided.

一 PDOS 计算

在完成结构优化和静态计算后,拷贝 scf 文件夹为 pdos

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cp -rf scf pdos

编辑 pdos 文件夹下 INCAR

INCAR

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SYSTEM=x
ISTART=1 # change
ICHARG=11 # add
LORBIT=11 # add
ENCUT=350
EDIFF=1E-5
IBRION=2
POTIM=0.25
NSW=0
EDIFFG=-1E-2
ISMEAR=0
SIGMA=0.05
PREC=ACCURATE
ISIF=2
NPAR=4
#LWAVE=FALSE
#LCHARG=FALSE
LREAL=Auto
#IALGO=48
ISYM=0

提交作业,计算完成后,使用 SshClient 将 vasprun.xml 导入本地电脑,使用可视化软件 p4vasp 处理。

二 P4vasp 的使用

1. 安装 Installation

从官方主页http://www.p4vasp.at) 下载 win 版本软件,解压后运行 p4v.exe, 图形界面如下

2. PDOS 处理

  1. 导入 vasprun.xml 文件,文件路径不能有中文字符。
  2. Electronic - Local Dos+bands control, 可选择原子和轨道进行可视化处理。
  3. Graph - Export, 若使用 origin 处理数据,导出添加后缀名.dat
  4. Origin 处理。
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Writing a Paper

By George M. Whitesides

1. What is a Scientific Paper ?

A paper is an organized description of hypotheses, date and conclusions, intended to instruct the reader. Papers are a central part of research . If you research does not generate papers, it might just as well not have been done. “Interesting and unpublished” is equivalent to “non-existent”.

Realize that your objective in research is to formulate and test hypotheses, to draw conclusions from these tests, and to teach these conclusions to others. Your objective is not to “collect data”.

A paper is not just an archival device for storing a completed program; it is also a structure for planning your research in progress. If you clearly unstand the purpose and form of a paper, it can be immensely useful to you in organizing and conducting ypur research. A good outline for the paper is also a good plan for the research program. You should write and rewrite these plans/outlines throughout the course of the research. At the beginning, you will have mostly plan; at the end, mostly outline. The continuous effort to understand, analyze, summarize, and reformulate hypotheses on paper will be immensely more efficient for you than a process in which you collect data and only start organize them when their collection is “complete”.

2. Outlines

2.1. The Reason for Outlines

I emphasize the central place of an outline in writing papers, preparing seminars, and planning research. I especially believe that for you, and for me, it is most efficient to write papers from outlines. An outline is a written plan of the organization of a paper, including the data which it rests. You should, in fact, think of an outline as a carefully organized and presented set of data, with attendent objectives, hypotheses, and conclusions, rather than an outline of text.

An outline itself contains little text. If you and I can agree on the details of the outline (that is on the data and organization), the supporting text canbe assembled fairly easily. If we do not agree on the outline, any text is useless. Much of the time in writing a paper goes into the text; most of the thought goes into the organization of the data and into the analysis. It can be relatively efficient in time to go through several (even many) cycles of an outline before beginning to write text; writing many versions of the full text of a paper is slow.

All writing that I do - papers, reports, proposals (and, of course, slides for seminars) - I do from outline. I urge you to learn how to use them as well.

2.2. How Should You Construt an Outline ?

The classical approach is to start with a blank piece of paper, and write down, in any order, all important ideas that occur to you concerning the paper. Ask yourself the obvious questions: “Why did I do this work ?”; “What does it mean ?”; “What hypotheses did I mean to test ?”; “What ones did i actually test ?”; “What were the result? Did the work yield a new method of compound? What?”; “What measurements did I make?”; “What compounds? How were they characterized?”. Sketch possible equations, figures, and schemes.It is essential to try to get the major ideas. If you strat research to test hypothesis, and decide, when you see what you have, that the data really seem to test some other hypothesis better, don’t worry. Write them done, and pick the best combinations of hypotheses, objectives, and data. Often the objectives of a paper when it is finished are different from those used to justify starting the work. Much of good science is opportunistic and revisionist.

1. Introduction

Why did I do this work? What were the central motivations and hypotheses?

2. Results and Discussion

What were the results? How were compounds made and characterized? What was measured?

3. Conclusions

What does it all mean? What hypotheses were proved or disproved? What did I learn? Why did it make a difference?

Next, take each of these sections, and organize it on yet finer scale. Concentrate on organizing the date. Construct figures, tables, and schemes to present the data as clearly and compactly as possible. This process can be slow - I may sketch a figure five to ten times in different ways trying to decide how it is most clear (and looks best aesthetically).

Finally, put everything - outline of sections, tables, sketches of figures, equationa - in good order.

When you are satisfied that you have included all the data (or that you know what additional data you intend to collect), and have a plausible organization, give the outline to me. Simply indicate where missing data will go, how you think (hypothesis) they will look, and how you will interpret them if you hypothesis is correct.
I will take this outline, add my opinions, suggest changes, and return it to you. It usually takes four to five iterations (often with additional experiments) to agree on an outline. When we have agreed, the data are usually in (or close to) final form (that is, the tables, figure, etc., in the outline will be best the tables, figures,… in the paper).

You can then start writing, with some assurance that much of your prose will be used.

The key to efficient use of your and my time is that we start exchanging outlines and proposals as early in a project as possible. Do not, at any cirumatances, wait until the collection of data is “complete” before starting to write an outline. No project is ever complete, and it saves enormous effort and much time to propose a plausible paper and outline as soon as you see the basic strucure of a project. Even if we decide to do significant additional work before seriously organizing to paper, the effort of writing an outline will have helped to guide the research.

2.3. The Outline

What an outline should contain:

1. Title

2. Authors

3. Abstract

Do not write an abstract. That can be done when paper is complete.

4. Introduction

The first paragraph or two should be written out completely. Pay particular attention to the opening sentence. Ideally, it should state concisely the objective of the work, and indicate why this objective is important.

In general, the Introduction should have these elements:

  • The objectives of the work
  • The justification for these objectives: Why is the work important?
  • Background: Who else has done what? How? What have we done previously?
  • Guidance to the reader: What should the reader watch for in the paper? What are the interesting high points? What strategy did we use?
  • Summary/conclusion: What should the reader expect as conclusion? In advanced versions of the outline, you should also include all the sections that will go in the Experimental section (at the level of paragraph subheadings) and indicate what information will go in the Micro-film section.

5. Results and Discussion

The results and discussion are usually combined. This section should be organized according to major topics. The separate parts should have subheadings in boldface to make this organization clear, and to help the reader scan through the final text to find the parts od interest. The following list includes examples of phrases that might plausibly serve as section headings:

  • Synthesis of Alkane Thiols
  • Characterization of Monolayers
  • Absolute Configuration of the Vicinal Diol Unit
  • Hysteresis Correlates with Roughness of the Surface
  • Dependence of the Rate Constant on Temperature
  • The Rate of Self-Exchange Decreases with the Polarity of the Solvent

Try to make these section headings as specific and information-rich as possible. For example, the phrase “The Rate of Self-Exchange Decreases with the Polarity of the Solvent” is obviously longer than “Measurement of Rates”, but much more usefulto the reader. In general, try to cover the major common points:

  • Synthrsis of starting materials
  • Characterization of products
  • Methods of characterization
  • Methods of measurement
  • Results (rate constants, contact angles,whatever)

In the outline, do not write any significant amount of text, but get all the data in their proper place: Any text should simply indicate what will go in that section.

  • Section Headings
  • Figures (with captions)
  • Schemes (with captions and footnotes)
  • Equations
  • Tables (correctly formatted)

Remember to think of a paper as a collection of experimental results, summarized as clearly and economically as possible in figures, tables, equations, and scheme. The text in the paper serves just to explain the data, and is secondary. The more information can be compressed into tables, equations, etc., the shorter and more readable the paper will be.

6. Conclusions

In the outline, summarize the conclusions of the paper as a list of short phrases or sentences. Do not repeat what is in the Results section, unless special emphasis is needed. The Conclusions section should be just that, and not a summary. It should add a new, higher level of analysis, and should indicate explicitly the significance of the work.

7. Experimental

Include, in the correct order to correspond to the order in the Results section, all of the paragraph subheadings of the Experimental section.

2.4. In Summary

  • Start writing possible outlines for papers early in a project. Do not wait until the “end”. The end may never come.
  • Organize the outline and the paper around easily assimilated data - tables, equations, figures, schemes - rather than around text.
  • Organize in order of importance, not in chronological order. An important detail in writing papers concerns the weight to be given to topics. Neophytes often organize a paper in terms of chronology: that is, they give a recitation of their experimental, starting with their cherished initial failures and leading up to a climactic syccessful finale. This approach is completely wrong. Start with the most important results, and put the secondary results later, if at all. The reader usually does not care how you arrived at your big results, only what they are. Shorter papers are easier to read than longer ones.

3. Some Points of Style

  • Do not use nouns as adjective:
    Not: ATP formation; reaction product
    But: formation of ATP; product of the reaction
  • The word “this” must always be followed by a noun, so that its reference is explicit.
    Not: This is a fast reaction; This lead us to conclude
    But: This reaction is fast; This observation leads us to conclude
  • Describe experimental results uniformly in the past tense.
    Not: Addition of water gives product.
    But: Addition of water gave product.
  • Use the active voice whenever possible.
    Not:It was observed that the solution turned red.
    But: The solution turned red. or We observed that the solution turned red.
  • Complete all comparisons.
    Not: The yield was higher using bromine.
    But: The yield was higher using bromine than chlorine.
  • Type all papers double-spaced (not single- or one-and-a-half-spaced), and leave two spaces after colons, and after periods at the end of sentences. leave generous margins.

Assume that we will write all papers using the style of the American Chemical Society. You can get a good idea of this style from three sources:

  • The journals. Simply look at articles in the journals and copy the organization you see there.
  • Previous papers from the group. By looking at previous papers, you can see exactly how a paper should “look”. If what you wrote looks different, it probably is not what we want.
  • The ACS Handbook for Authors. Useful, detailed, especially the section on references, pp. 173 - 229.

I also suggest you read Strunk and White, The Elements of Style (Macmillan: New York, 1979, 3rd ed.) to get a sense for usage. A number of other books on scientific writing are in the group library; these book all contain useful advice, but are not lively reading. There are also several excellent books on the design and figures.


1、何谓学术论文?

一篇论文是集假设、数据及结论为一体的系统性阐述,并以此引导读者。论文是研究的核心部分。如果你的一项研究没有产生任何论文,那便等于没有做过一样。“有意义但未发表”就如同“从未存在”一样。

研究的目的在于确切表述并验证假设,从不断的论证中得出结论,并将结论向读者展示。切记,你的研究目的不是简单地“收集数据”。

论文并非只是研究结果的资料储存器,而且也是进一步开展研究的有效框架。如果明确了论文的目的和写作形式,那将对你组织和开展进一步研究大有裨益。一份好的论文提纲对于研究项目具有良好的规划指引作用。在研究的整个过程中,你需要写下提纲并对其进行适应性修改。研究初始,应有主要计划;工作结束,应有充分总结。比起简单收集数据并在完成后才对其进行整理写作的方式,在进程中及时理解、分析、总结并修正显得更为高效。

2、论文提纲

2.1 为什么要写提纲?

在此,我必须强调提纲在论文写作、学术研讨及研究规划中的核心地位。我尤其相信,对于大家而言,以提纲为基础进行论文写作是最有效的方法。提纲是一份书面的行文计划,其中包括论文所依赖的数据。事实上,提纲不仅仅是列出各段的文字内容, 而是按照目的、 假说、 结论来精心组织和呈现数据。

提纲的文字以简练为宜。如果我们对提纲中的数据及结构这些细节达成一致意见,那么正文组织起来便相当容易。在提纲细节尚未敲定之时,进行正文写作是毫无意义的。论文写作时,大部分时间花费在正文写作上;而大部分思考是用在整理和分析数据上。动笔之前反复推敲并修改提纲,比起写完全文再反复全面修改,效率自然较高。

我所有的写作,包括论文、报告、项目申请书以及研讨会的幻灯片,都从提纲开始。我建议你们也学会如何使用提纲。

2.2 如何写好提纲?

最经典的方法就是拿出一张白纸,随意写下当时脑子里蹦出的与论文有关的任何点子。自问一些显而易见的问题:“我为什么要做这项工作?” “它的意义何在?” “我想要验证哪些假说?” “我实际验证了哪些假说?” “结果如何,是否产生了新的化合方法?” “我进行了哪些测试?” “有哪些化合物,它们是怎么表征的?” 并且勾勒出可能的反应式及图示。抓住这些主要想法非常重要。如果你的研究起初是为了证实一个假说,可是当你仔细审视手头的资料时却发现,这些数据似乎能更好地证实另外一个假说,也不要担心。将这些都写下来,从中选择一个假说、目标、数据相互匹配的最佳组合。时常,论文完成之时,其目的与最初的目的已经不一样了。要知道,很多优秀的科学往往是机会主义与修正主义的碰撞产物。

当你把这些都写在纸上后,拿出另一张纸,将这些思绪按照以下三个方面组织起来:

1 引言

为什么我要做这项工作?主要目的和假说是什么?

2 结果和讨论

结果是什么?化合物是怎样合成与表征的?测试了什么?

3 结论

所有这一切意味着什么?证实或否定了什么假说?我学到了什么?其意义何在?

接下来, 将以上各部分更好地组织起来。尤其着力于整理数据,尽可能用清晰简洁的图表来展示数据。这个过程可能比较慢,因为我可能5次甚至10次尝试以不同的方式去描绘一张图,以求达到最清晰最美观的程度。

最后,把所有这一切 - 内容提纲、表格、草图、方程式,安排好顺序。

当你已经掌握了所有需要的数据,或者明确知道自己还要收集哪些额外的数据,并且有了一个合理的构架,你对这些都感到满意时,请将提纲交给我。简要标注哪些地方还缺数据,你认为(或假设)这些数据大概是什么。如果你的假设是正确的,你将如何解释。我会仔细阅读你的提纲,提出我的观点和修改建议。通常情况下,我们需要四五个来回才能达成一致意见,期间经常还需要补做一些实验。我们的一致意见将确定所有的数据的最终形式或者接近最终形式,也就是说,提纲中的表格、图表等最终将成为论文中的表格、图表。

然后,你就可以开始动笔写,此时的你有信心在写作中用到大部分之前整理的数据。

高效利用你我时间的关键在于,项目开始时尽早彼此交换提纲和意见。千万不要等到数据都收集“完成”了才开始写提纲。研究永无“完成”之日,当研究项目初具雏形时,就应立即开始准备构思论文和提纲,这将节省很多的精力和时间。即使在正式组织成文前,我们突然决定补做重要的其他实验,提纲的写作对于研究仍有指导意义。

2.3 提纲的内容

提纲应当包括以下几个部分:

1 标题

2 作者

3 摘要

这部分先空出来,等到论文完成之后再撰写。

4 引言

第一段或者前两段应该详细写出来。开头尤其需要注意,最理想的状态是能够简洁明了地陈述研究工作的目的及意义。

总体上,引言由以下几个方面构成:

  • 研究目的
  • 研究的意义:为什么重要?
  • 研究背景:有谁做过同样的研究?是以什么样的方式?我们之前做过哪些研究?
  • 指引读者:读者能从中得到什么?哪些想法很独特且有意义?我们采取了哪些策略?
  • 总结:读者应期待怎样的结论?完善的提纲版本应该包括实验部分的所有环节(具体到段落小标题)。

5 结果与讨论

结果和讨论紧密联系。这一部分应该根据主题进行行文组织。不同章节应设有加粗小标题,使得结构清晰,同时便于读者迅速浏览全文,找到自己感兴趣的部分。以下列举一些可用作章节小标题的短语:

  • 烷基硫醇的合成
  • 单层膜的表征
  • 邻二醇结构的绝对构型
  • 滞后现象与表面粗糙度的关系
  • 温度对速率常数的影响
  • 自交换速率随溶剂极化度而降低

尽量使章节小标题具体化并且信息丰富。例如,“自交换速率随溶剂极化度而降低”虽然比“速率测试”字数多,但是对于读者来说更有价值。总的来说,尽量概括出段落主旨:

  • 初始材料的合成
  • 产物的表征
  • 表征方法
  • 测试方法
  • 结果(速率常数,接触角等)

提纲中,不要书写大量的文字,而是将数据安排在合适的位置:文字只是简明地提示每章的主要内容。

  • 章节标题
  • 图表(附说明)
  • 示意图(附说明和脚注)
  • 方程
  • 表格(格式正确)

记住,论文是实验结果的集成,运用图表、方程式和图示清晰简洁地呈现。论文中的文字是为解释数据服务的,因而它是次要的。其余的更多信息则可以通过表格、方程式等去展现,这样的文章短小精悍,通俗易读。

6 结论

应将论文的总结论概括成一系列短语或简短的句子。不要重复结果部分已陈述过的结论,除非有必要作特殊强调。结论不是简单的总结,而是更新更高层次的分析阐述,应该清晰地表现出研究工作的意义。

7 实验部分

包括所有实验部分的章节标题,顺序与结果部分一一对应。

2.4 要点总结

尽早写作论文提纲。切勿等到研究“结束”;研究永无“结束”之时。

提纲应通过表格、方程式、图表、图示等易于理解的方式组织数据,而不是纯文字内容。

按照数据重要程度进行排序,而不按时间顺序。论文写作一个重要细节在于各部分权重之分配。初学者往往采取时间顺序来组织行文:他们对实验项目进行详尽的叙述,从宝贵的初始失败经历写起,直至达到成功的巅峰。这是极其错误的方式。应该从最重要的结果开始叙述,如果还有次要的结果,再依次叙述。读者通常不会关心你是如何得出一个问答的结论,而是关注结果本身。短篇幅显然更加易读。

3、文体格式

  • 勿将名词用作形容词:
    错误用法:
    ATP formation;reaction product
    正确用法:
    formation of ATP (ATP的形成);product of the reaction(反应产物)
  • “this”后面必须接名词,以便明确指代对象。
    错误用法:
    This is a fast reaction;This leads us to conclude
    (这是一个快速反应;这使我们得出结论)
    正确用法:
    This reaction is fast;This observation leads us to conclude
    (这个反应是快速反应;这个观察结果使我们得出结论)
  • 描述实验结果一律要用过去时态。
    错误用法:
    Addition of water gives product.
    正确用法:
    Addition of water gave product. (加水后生成了产物)
  • 尽可能使用主动语态。
    错误用法:
    It was observed that the solution turned red.
    正确用法:
    The solution turned red. or
    We observed that the solution turned red. (溶液变成了红色)
  • 完整描述对比双方。
    错误用法:
    The yield was higher using bromine.
    正确用法:
    The yield was higher using bromine than chlorine. (用溴比用氯时产出率高。)
  • 使用两倍行距,冒号、逗号和句末的句号后空两个英文字符,留出足够的页边距。
    假设我们在写作中统一使用美国化学学会的文体模式。你可以在以下三类文献资源中获得启发。
    1)期刊。阅读期刊中的文章,模仿其行文结构。
    2)本组论文。阅读本组论文,你会清楚了解到论文的结构形式。如果你的论文看起来不太一样,或许就不符合我们的标准。
    3)ACS写作指南。该书非常有用、详细,尤其是173-229页有关参考文献的部分。

同时我推荐Strunk和White所著The Elements of Style(《文体要素》),阅读此书找找文体格式用法的感觉。也可以在化学学会的图书馆借阅很多其他有关学术写作的书籍,这些书中有很多有益的建议,只是不够生动有趣。那里也有一些非常不错的有关图表设计的书值得一读。

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VASP 的光学性质计算及 vaspkit 的安装与使用


使用的软件:VASP, Origin, SshClient, vaspkit


一 光学性质计算

在完成结构优化和静态计算后,拷贝 scf 文件夹为 optic

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cp -rf scf optic

编辑 optic 文件夹下 INCAR

INCAR

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SYSTEM=x
ISTART=0
ENCUT=350
EDIFF=1E-5
IBRION=-1 # change
POTIM=0.25
NSW=0 # change
EDIFFG=-1E-2
ISMEAR=0
SIGMA=0.05
PREC=ACCURATE
ISIF=2
NPAR=1 # change 4 to 1
#LWAVE=FALSE
#LCHARG=FALSE
LREAL=Auto
#IALGO=48
ISYM=0
NBANDS=x # add
LOPTICS=.TRUE. # add
  • 注:NBANDS=x x 为 OUTCAT 中 NBANDS*2, 可使用 grep 命令查询
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grep NBANDS OUTCAR

提交作业,计算完成后,可查看 OUTCAR 文件,有计算得出介电常数 (Dielectric constant) 的实部和虚部。

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frequency dependent IMAGINARY DIELECTRIC FUNCTION (independent particle, no local field effects)
E(ev) X Y Z XY YZ ZX

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frequency dependent REAL DIELECTRIC FUNCTION (independent particle, no local field effects)
E(ev) X Y Z XY YZ ZX

使用 vaspkit 程序对计算结果进行处理。

二 vaspkit 的安装与使用

安装 Installation

使用 SshClient 将已下载的 vaspkit 导入 linux 服务器,安装步骤:

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tar -zvxf vaspkit.*.tar.gz
cd vaspkit.*/src
modify the Makefile file based on your machine environment;
make
  • Note that the formats of POSCAR, CONCAR and CHGCAR files in VASP.5.x are slightly different from those in VASP.4.x. Please set the vasp5=.false. in the src/module.f90 file if you use VASP.4.x

设置环境变量

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vi ~/.bashrc
alias opt="~/software/vaspkit.0.51/examples/optic/optics.sh"
alias kit="~/software/vaspkit.0.51/src/vaspkit"
source ~/.bashrc
  • You need to preparethe REAL.IN and IMAG.IN files which include the real and imaginary parts of frequencydependent complex dielectric function. There is a bash script optics.sh as a reference in the vaspkit.*/examples/optic/ could help you to prepare the real.in and imag.in files.

光学数据处理

输入命令opt产生 REAL.INIMAG.IN 文件,依次输入命令kit51,屏幕显示如下

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+---------------------------------------------------+
| VASPKIT Version: 0.51 (10 Oct. 2016) |
| A Postprocessing Toolkit For VASP.5.x Code |
| Developed By Vei WANG (wangvei@icloud.com) |
+---------------------------------------------------+
=============== Structural Options ==================
2) Elastic Constant Calculator
3) Structure Converting 4) Supercell Building
5) EOS Fitting 6) Symmetry Toolkit
7) K-Mesh Generating
8) Band-Structure Path Generating (experimental)
=============== Electronic Options ==================
11) Total DOS 12) Projected DOS
13) l-m Decomposed DOS
21) Band-Structure 22) Projected Band-Structure
23) 3D Band-Structure for Two-Dimensional Materials
24) One Specific Band-Structure
======== Charge Density & Potential Options =========
31) CHG Density 32) Spin Density
33) Spin-Up & -Down Density
34) CHG Difference 35) Spin Density Difference
41) Planar-Average CHG 42) Planar-Average POT
=============== Optical Options =====================
51) Linear Optics
================ Misc Utilities =====================
91) Semiconductor Calculator
92) VASP2BoltzTraP
0) Quit
------------>>
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+---------------------------------------------------+
| Please prepared IMAG.in and REAL.in files |
| before runing optics |
|...................................................|
| Calculate absorb,refractive,energylossspectrum, |
| extinctionr and reflectivity (in eV). |
+---------------------------------------------------+
-->> (1) Reading IMAG.in and REAL.in Files...
-->> (2) Written Optical Files Succesfully!
+---------------------------------------------------+
| * DISCLAIMER * |
| CANNOT Guarantee Reliability of VASPKIT Code |
| CHECK Your Results for Consistency If Necessary |
| (^.^) GOOD LUCK (^.^) |
+---------------------------------------------------+

输出文件 ABSORB.dat,REFRACTIVE.dat,REFLECTIVITY.dat,EXTINCTION.dat 和 ENERGYLOSSSPECTRUM.dat,依次为 absorption coefficient, refractive coefficient, reflectivity coefficient, extinction coefficient and energy-loss function。导出使用 Origin 作图即可。


附:相关光学性质计算公式

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单层IVA主族硫化物/ORR 催化剂 [Presentation]

  1. 汇报的是一篇在 jmca 上发表的文章,基于第一性原理计算,第四主族硫族化合物可以作为潜在高效的氧化还原催化剂。
  2. 首先介绍一下研究背景,总所周知,燃料电池是一种环境友好的能源转化装置 ,具有较高的能量转换效率和低污染的特点,有规模化应用的前景,当前制约其发展的关键便是其阴极氧化还原反应的效率问题。
    1. 传统的电催化材料 Pt 及其合金,具有良好的催化性能,但 Pt 类材料也有明显的缺点,其中最主要的就是Pt益高昂的价格与电极循环过程中的不稳定性。
    2. 寻找替代 Pt 的电极催化材料是一个提高燃料电池工作效率的思路。在以往的研究中,科学家在寻找 ORR 电极反应催化材料以替代价格高昂的 Pt 己经取代了一些进展。诸如新型石墨烯杂原子催化剂,二维结构的黑磷,但都有或多或少的问题。
    3. GeS 及其衍生物具有类黑磷结构,且稳定性更优于黑磷,该文献便集中对 GeS 及其衍生物进行 ORR 理论研究,探索其是否具有成为高效电极催化剂的潜力
  3. 该研究使用的理论计算方法基于密度泛函理论,构建模型时采用导体屏蔽模型和标准氢电极模型,主要使用的软件包是 MS.
  4. 实验部分从以下五个方面逐步开展
    1. GeS 及其衍生物的结构和电性质,文章基于电荷理论计算及分析,表明该材料可能作为 ORR 催化剂。
    2. 该材料对于氧气分子的吸附解离,通过计算,得出氧气分子结合该材料的最优几何构型及其吸附能与解离能,可以看出其解离势能在降低,故氧气的吸附解离可正常进行。同时 SnS 由于其较低的结合能,发现在氧气环境下不稳定,故不适合作为催化剂。
    3. 该材料对于 ORR 中间体的吸附,图示为各个中间体与该材料的吸附构型以及其吸附能,可看出材料对于 CO 具有较低的吸附能,推测材料对于 CO 有更好的耐受性。同时文章通过模拟发现,GeS 在酸性介质中具有较高的稳定性,该催化反应可能为四电子路径。
    4. ORR 机制,图示为在酸性环境下,两种可能的催化机理,然后是通过两种机理所计算的反应自由能变化,可看到反应自由能一直在降低,该催化反应在热力学上可顺利进行,同时可通过对比发现,直接过程的第一步反应自由能降大于非直接过程,故该反应机理可能为直接过程。
    5. 超电势的影响,文章计算了在酸性环境下各个物质的超电势,可看出 GeS 的超电势略高于 Pt ,具有可以接受的超电势影响。
  5. 最后文章得出结论,二维的 GeS 成为高效催化剂的可能最大,由于其与氧气较大的结合能,较低的氧气解离势垒和可接受的超电势影响。同时文章在碱性环境下也做了类似的分析计算,发现它们在碱性环境下都可能作为催化剂。该文章对以后的相关实验设计提供了前瞻性参考。

附件:PPT Paper

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