how to systematically improve your paper writing

As a non-native English speaker and writer, I always have following concerns:
Will an American write like this?
Can other peoples understand what I want to say?
How do other peoples describe what I observed in the experiment or calculations?

Here I point out that I do not want to be regarded as a native English speaker when Americans read my papers. What I want is to avoid awkward sentences and bad usages of some words.

Before I present my opinions, one thing I want to emphasize is the criteria of good English writing.
All similar things can be distinguished as bad, good, super bad, super good, medium, etc. Now let's have some agreement about what is good English writing.

First thing, or the most important thing is nothing to do with English. You SHOULD KNOW what you want to say? That means you should know what you want to say and why you want to say. Only after that, it is about English writing.

So the rule 1:
A good English paper should have a strong purpose, or a center idea. All the words should serve for the idea.

Rule 2.
A good English writing should be compact. Simplicity and easiness to understanding or no misunderstanding should be remembered. Keep your sentences short. Long sentences are boring. Short sentences keep your readers interested. Short sentences promote clarity.

Rule 3.
A good scientific paper should be professional, which means that your audiences are your peers and you should use the professional words of physics, mathematics, chemistry, economy, etc, all the time in your paper.

Rule 4.
If possible, always use active verbs, not passive verbs. For instance, "we bought bread" is better than "Bread was bought".

Rule 5.
Abolish Index words such as this, that, these, etc.

Rule 6.
Rephrase your sentences if you do not feel right. Change the way you said and see if it is better.

Rule 7.
Avoiding clutter in the paper. If possible, consider to combine two sentences.

Rule 8.
Be careful about the usage of subordinate clauses. If possible, eliminate it.

Rule 9.
Avoid dead sentences, like 'it can be ' or 'it is well known'.

Rule 10.
Revision if possible. I know it is boring. But if you can revise for 5 times after finishing writing, you will have a much better version.

   

Find transition states using Gaussian software: some tips

Here, I would like to summarize my past month's work about transition state searching with Gaussian program package.

1. QST2, QST3, and OPT(TS) are three good ways to identify TS structure. I personally prefer the OPT(TS) because it can generate the imaginary frequency as a criteria, while QST method can not. But in general it is really hard to find the TS structure with human guess and TS could be very sensitive to DFT functional, basis sets, guess structures, step size, etc. Anything wrong could give a big headache. So QST3 or QST2 is very useful for initial TS structure guess. And of course, after QST method you need run OPT-TS again to get imaginary frequency.

2. I like B3LYP/6-31+G* method. HF is good for an initial guess and fast calculation. But HF or BLYP (pure functional) can be totally wrong for TS guess, or totally miss the TS.

3. Sometimes you get imaginary frequency from OPT-TS, but be careful that you need run IRC reverse and forward calculations to confirm that this is a real TS structure. It could be totally wrong.

4. Some people suggested after you get multiple imaginary frequencies you could add the coordinate matrix of corresponding largest imaginary frequency multiplied by some factor (0.1-0.5) with the initial TS coordinate matrix. The new coordinate can be used to eliminate the imaginary frequency.

5. Final check for TS: After you run IRC forward and backward calculations, make sure that your TS energy is always the highest, i.e. if you draw energy profile pictures for both calculations, the energy curves should always go down. Otherwise, it may be something wrong. At this time, you should choose the highest peak point as initial guess for TS again.

6. If the electron spin multiplicity is not consistent before and after reactions, you have to specify two multiplicity values for OPT(TS). Also do the IRC testing too. 

 

如何养成良好的习惯-转载

习惯的力量是惊人的，习惯能载着你走向成功，也能驮着你滑向失败。

一个人一天的行为中，大约只有5%是属于非习惯性的，而剩下的95%的行为都是习惯性的。即便是打破常规的创新，最终可以演变成为习惯性的创新。?

　　根据行为心理学的研究结果：3周以上的重复会形成习惯；3个月以上的重复会形成稳定的习惯，即同一个动作，重复3周就会变成习惯性动作，形成稳定的习惯。?

亚里士多德说：“人的行为总是一再重复。因此，卓越不是单一的举动，而是习惯。”

换句话说，失败者总是失败，成功者总是成功是有道理的。

“播下一个行动，收获一种习惯；播下一种习惯，收获一种性格；播下一种性格，收获一种命运。” 

一个人成功的欲望再强烈，也会被不利于成功的习惯所撕碎，而溶入平庸的日常生活中。所以说，思想决定行为，行为形成习惯，习惯决定性格，性格决定命运。你要想成功，就一定要养成高效率的工作习惯。

确定你的工作习惯是否有效率，是否有利于成功，我觉得可以用这个标准来检验：即在检省自己工作的时候，你是否为未完成工作而感到忧虑，即有焦灼感。如果你 应该做的事情而没有做，或做而未做完，并经常为此而感到焦灼，那就证明你需要改变工作习惯，找到并养成一种高效率的工作习惯。?

　　高效工作从办公室开始：?
　　1)了解你每天的精力充沛期。通常人们在早晨9点左右工作效率最高，可以把最困难的工作放到这时来完成。?
　　2)每天集中一、两个小时来处理手头紧急的工作，不接电话、不开会、不受打扰。这样可以事半功倍。?
　　3)立刻回复重要的邮件，将不重要的丢弃。若任它们积累成堆，反而更费时间。
　　4)做个任务清单，将所有的项目和约定记在效率手册中。手头一定要带着效率手册以帮助自己按计划行事。一个人一天的行为中，大约只有5%是属于非习惯性的，而剩下的95%的行为都是习惯性的。
　　5)学会高效地利用零碎时间，用来读点东西或是构思一个文件，不要发呆或做白日梦。?
　　6)减少回电话的时间。如果你需要传递的只是一个信息，不妨发个手机短信。?
　　7)对可能打来的电话做到心中有数，这样在你接到所期待的电话后便可迅速找到所需要的各种材料，不必当时乱翻乱找。
　　8)学习上网高效搜寻的技能，以节省上网查询的时间。把你经常要浏览的网站收集起来以便随时找到。?
　　9)用国际互联网简化商业旅行的安排。多数饭店和航线可以网上查询和预订。?
　　10)只要情况允许就可委派别人分担工作。事必躬亲会使自己疲惫不堪，而且永远也做不完。不妨请同事帮忙，或让助手更努力地投入。?
　　11)做灵活的日程安排，当你需要时便可以忙中偷闲。例如，在中午加班，然后早一小时离开办公室去健身，或是每天工作10个小时，然后用星期五来赴约会、看医生。?
　　12)在离开办公室之前开列次日工作的清单，这样第二天早晨一来便可以全力以赴。

中国有句老话：“吃不穷，喝不穷，没有计划（好习惯）就受穷。”尽量按照自己的目标，有计划地做事，这样可以提高工作效率，快速实现目标。

幽默的好习惯?
　　有人说，男人需要幽默，就像女人需要一个漂亮的脸蛋一样重要。?
　　男人需要幽默，就像女人需要一个漂亮的脸蛋一样重要。美国第16任总统林肯长相丑陋，但他从不忌讳这一点，相反，他常常诙谐地拿自己的长相开玩笑。在 竞选总统时，他的对手攻击他两面三刀，搞阴谋诡计。林肯听了指着自己的脸说：“让公众来评判吧。如果我还有另一张脸的话，我会用现在这一张吗？”还有一 次，一个反对林肯的议员走到林肯跟前挖苦地问：“听说总统您是一位成功的自我设计者？”“不错，先生。”林肯点点头说，“不过我不明白，一个成功的设计 者，怎么会把自己设计成这副模样？”林肯就是这种幽默的方法，多次成功地化解了可能出现的尴尬和难堪场面。?
　　没有幽默的男人不一定就差，但懂得幽默的男人一定是一个优秀的人，懂得幽默的女人更是珍稀动物。
 
 经常做一件事就会形成习惯，而习惯的力量是难以抗拒的。但是人类还有一种潜藏的缓冲能力，也不容小觑。既然人有可能养成一种习惯，那肯定他也有能力改掉这种习惯。

凡事变成习惯就好做了
养成了好的习惯又有什么用呢?这里实际上还隐藏着人类本能的秘诀，当你每天都重复这些话的时候，它们很快就会成为你心灵的一部分。而最重要的是，它们还会溜进你的心灵，变成奇妙的源泉，永无止歇，为你创造环境，并做出让你自己都难以相信的事情。
当话语被你的心完全吸收的时候，每天早上，你会带着一种从来没有过的活力从梦里醒来。你觉得自己精力旺盛。你的热情高涨，你迎接新世界的欲望将会让你克服一切恐惧，你会比你想象中过得更快乐。
随后，你发现自己有了应付一切的办法。你惊奇地发现，你能轻松自如地运用这些方法。因为，任何方法只要经过了练习，就是熟能生巧，难的也变成容易的了。
所以，一个好习惯就养成了，当一种习惯经常反复地练习而逐渐变得容易的时候，你就会喜欢去做。而你一旦喜欢去做，你就愿意经常去做。这是人的天性。当你经常去做时，这就是你的习惯了。你也就是习惯的奴仆了。

 

compile CPMD+PLUMED on a cray XT 5 machine

1. cd CPMD
2. export plumedir= your plumed directory
3. cp $plumedir/patches/cpmdpathcfile to current directory.
4. ./mkconfig.sh CRAY-XT4 > Makefile
5. ./cpmdpatch -patch
6. vi Makefile, and make following changes:
    change all XT4 to XT5.
    delete the -fno-exceptions in cflags.
7. make
after a long screen output, you should have cpmd.x executable file.

Note: Other MPI compiler wrappers such as mpicc, mpicxx, mpif77 and mpi90 may be not available in cray, not as in the intel/sun machine.
   

some knowledge about compilation on different architecture

Recently I am compiling some serial and parallel software packages.
Some often used abbreviations are listed below.

Before you compile the software, be sure that you know the architecture of the machine you will install. Is it IBM, CARY, or SUN? Generally speaking, the hardware could be very different, but the software OS is Unix/Linux.   

Now let's talk the compilers. The two most common languages are Fortran and C/C++ for scientific calculations. So you need know the compilers for both languages.

Several most often used Fortran compilers:
Intel: ifort
The Portland Group, Inc: pgf77, pgf90, pghpf
G95 project: g95
GNU (free software union) project: gfortran (forked off from g95)

Several most often used C/C++ compilers:
Intel: icc
The Portland Group, Inc: pgcc (for C), pgCC (for C++), 

GNU (free software union) project: gcc, gCC (cc and CC in fact are similar like gcc and gCC. However, cc or CC is a standard Unix compiler while gcc or gCC is produced by GNU.)


Often used mathematical library
MKL library from INTEL including Linear Algebra, Fast Fourier Transforms (FFT), Vector Math and Statistics. Cluster-based versions of LAPACK and FFT are also included to support MPI-based distributed memory computing.
 fftw from FFTW.org
 BLAS and LAPACK for linear algebra.
 
Parallel tools:
OPENMPI
MPICH

How to write a science paper?

I am deeply influenced by Chairman Mao, the former Chinese communist leader. He has mentioned the famous three paragraph writing: what is the definition of your research, why we do this research, and how we will do. I think it works for all the social, engineering, and science manuscript writing.

What is the definition of your research? Or what is the problem?
You need briefly introduce the background of your research, clearly narrow your research fields, give the conditions, and explain the limitation.
For example, if you study a kind of metal alloy, firstly, you should explain to your readers how the alloy is frequently used. You need specify the ratio of different metals, working conditions of this alloy, and general uses of the alloy.
And what is the problem of current alloy or related research.

Why we do this research?
You should briefly list two or three important points.
For example, for the alloy: Why the problem deserves further research? The challenges and future benefits if we make better alloy. And what can we do?

how we will do?
We can claim we improve some physical properties for this alloy by adding some elements. How we add elements? We can list the experimental procedures, conditions, device information, etc. How we test the new products? We can show how we measure the properties of the new alloy: Melting points, force constants, etc.

Finally, in the conclusion part, we can summarize the results, future influences of new alloy, and what we can do to improve it in the future.

Install JAVA plugin in Firefox in an Redhat Linux box

First, you need make sure you have JAVA installed.
For Redhat, you should use RPM based JAVA installation.

1. Open a terminal, type command "java -version" to make sure that you have the newest JAVA installed.
2. In general, the java should be installed here: /user/java
3. Use following command to make sure you enable JAVA in firefox.
    "ls ~/mozilla/plugins/"
    If it is empty, you need link java to this directory.
4. Use command "ln -s /usr/java/default/jre/lib/amd64/libnpjp2.so ~/.mozilla/plugins/".
5. Be careful if there are many versions of JAVA in /usr/java directory, please use default one. Otherwise you will have conflicts because the firefox can only load one JAVA version.
6. If you have old version in ~/.mozilla/plugins/ directory, you should delete it.
7. Go to JAVA test page: "http://www.java.com/en/download/testjava.jsp", now you should be able to see the JAVA runs now.