how to use vmd to make a movie

Now you have one trajectory.xyz file from your MD simulations. And you want to make a nice movie using VMD.
1. open your VMD menu, extension/visulization/movie maker.
2. Click Format, choose MPEG-1.
3. Click Render, choose Tachyon (other selection could cause something weird).
4. Click Movie Setting, choose TRAJECTORY.
5. Make sure you choose the directory for your movie.
6. Choose frame interval (Trajectory step size) so that you do not have a too long movie.
7. MAKE SURE YOU KNOCK THE ENTER KEY for EVERY NUMBER INPUT. Otherwise you will have some weird mistakes.

Now wait for your movie.

some basic concepts about OPV

open circuit voltage:  where the electron current density is zero.

JSC: The photo current is referred to as the short circuit (SC) photocurrent.

A cathode: obtain electrons.
Anode: lose electrons.
Positive electrode: High voltage.
Negative electrond: low voltage.

,
PCE: PCE= Poutput/P(solar energy)= FF*Voc*Jsc/P(solar energy)







Except for the beyond equations, we also need learn:
Exciton binding energy: = E(affinity)-E(ionization)-E(optical gap) (HOMO and LUMO are not necessarily to be ionization and affinity energy.)

E(optical gap):  the threshold for photons to be absorbed.
In almost all inorganic semiconductors, such as silicon, gallium arsenide, etc., there is very little interaction between electrons and holes (very small exciton binding energy), and therefore the optical and electronic bandgap are essentially identical, and the distinction between them is ignored. However, in some systems, including organic solar cells, the distinction may be significant.


generalized Shockley equation:

Onsager model: 

How to systematically to master CPMD program?

Like leaning some real skills or having real ability, you have to make a plan first and then finish it.

For me, I have following plans.

First step, you need to learn how to use it. Download it, compile it, test it, and run it (such as a wave function optimization, geometry optimization, CPMD/BOMD for isolated or PBC systems, etc.).

Second step, learn the results of CPMD output, fully understand the meaning.

Third step, learn to change and optimize the CPMD input parameters, and get the meaningful, useful and correct outputs.

Fourth step, learn the code of CPMD, read the related references carefully, if possible, write a module to implement your own program in CPMD, for example, C-DFT in CPMD.

Fifth, if possible, try to combine CPMD and other programs such as GROMACS to run QM/MM simulations.

what is a binary tree?

A binary tree is a data structure where a node has the degree of 0 or 1 or at most 2. This may be due to the binary system (only 0 and 1 are recognized) in computer.

It is pretty easy to find desired data using this data structure.

learning method

curiosity is your instinct. So
First learning method is to ask your own questions. The simplest will be 'what is the meaning of XXX?' Do not think about its stupidity.

Second, you have to find your way to learn something. For our human, we need one standing point, i.e. origin. Namely, you have to copy something from your parents, your teachers, your observation, etc. Then try to use the knowledge you have to know other unknown things. Therefore, analog is important.

Third, we have to understand something based on your origin (the basic concepts). You can not just copy others' thoughts. We have to find our own ways to understand the new concept, new method, new principles, new knowledge. Your own way to understand new things or concepts are extremely important because it only works for you. Other peoples' methods may totally do not work for you. Or even they work for you, you may not find the best way for yourself, therefore you waste your time and lose your identity.

questions about yourself

1. How to be a good PI?
2. Where is your limitation?
3. How to test your limitation?
4. Why you care about outside if you even can not control yourself?

fortran learning note 6- some easily made mistakes

1. 3n should be 3*n (forget the multiplication)
2. The array index is out of range.
3. Forget to stop reading a file when it ends.
4. When counting the number of lines of a file, do not forget to use "read (unit,'(a120)')" to include the blank line too.
5. Recognize different types of variables and DO NOT use them with mistakes.