PVWIN Frequently Asked Questions and Answers

Japanese mode is here


Question: I downloaded the pvwin program for MD visualization but could not read the manuel file which seems to be in a special language format. Do you know where I can find a english verison for the manual?
Thank you for your time.

Answer: I am sorry I have not written the english manual.  Actually, Japanese manual is not completed.
I will try to upload the English manual. But, I am not sure when I will have time.
Please try to open sample *.pv files and see if it works.


Question: Your samples are well working but I can not read your samples. So I can not use them as basis to build a new .pv file. Could you send me one .pv file in the .txt or a very standard format?

Answer: *.pv files are binary files and you cannot edit. Let's try monoatomic sample directry.
You can find pos.dat files in the sample directry. These are ascii files with coordinates. And, mask.dat describes color of each molecules. In order to make a pv file, there is pvcom.exe.
If you run as
>pvcom.exe pos.dat mask.dat pos2.pv
you can make pos2.pv file which can be used as input file of pvwin.exe
pos.dat has some parameters in first 3 lines and x, y, z coordinates.
The coordinates of next time step just continue without any marks or blank
lines.
mask.dat has color numbers (0-15) of each molecules in the same order of x, y, z coordinates in pos.dat. The actual color shown is determined in ball.bmp palette.


Question: Thank you for your explanations. I opened a .dat file and found those first lines:
1 ?
84 I suppose those are the number of particles
1 ?
151 The number of time steps?
30.00000 ?
0.00000 ?
0.01000 ?
Are the parameters with (?) important?

Answer: Here are answers for your questions. The format of pos.dat files are slightly different in 3 examples.  I suppose the c file and exe file in each example directly for the conversion to binary files can be editted by the user. I mean read the c file like hpvc.c.
What you selected is the most complecated example, with bonds and two different kind of molecules.
1 ? : meaning monoatomic: don't change anyway
84 I suppose those are the number of particles : yes, but of carbon atoms
1 ? : number of metal atom (see the blue and large atom in side of fullerene)
151 The number of time steps? : yes
30.00000 ? : size of box (in this case cube, in other examples x, y, z sizes are described)
0.00000 ? : t0 (the time of the first scene)
0.01000 ? : delta t (time step of each scenes in ps)


Question: What is the definition of color of molecules?

Answer: You can define yourself.
The sample program argon.pv: color represent the potential of each molecule: Green shows lower potential and orange shows higher potentail.

The color can describled with mask.dat file. mask.dat has color numbers (0-15) of each molecules in the same order of x, y, z coordinates in pos.dat. The actual color shown is determined in ball.bmp palette as below.
If you want to change the color palette, use makeball program in makeball.zip


Question: Can we use polymer or chained molecules. The bond drawings do not work in pvutility.

Answer: Yes. Polymers can be recognized as just group of atoms. If you need many different atoms,
pvutility cannot handle. You need to make your own C program to convert. Refer to samples.zip .


Question: The bond drawings do not work in pvutility.
Answer: drawing bond with pvutility is not really general. This option is made for carbon and silicon clusters. You can use it for argon.dat, though.
Drag and Drop argon.dat to pvutility. Change NBond to say, 1000: enough number of bonds for each scene.
Then, put some number in Bond Length (2-2). Try 3.8. You will see red bond lines.

Then, try changing NMol1 = 108 and NMol2 = 0. Then, you need to give the bond length value for
Bond Length (1-1). Now, you will see yellow bond lines.
NOTICE: When you choose bondings, the definition of color of moleculs ignores mask.dat. The
color is
white: no bond
red: 1 bond
orange: 2 bonds
green: 3bonds
violet: 4 bonds

If you need to make more complecated bonding for complicated polymer, pvutility is not enough.
You need to make own C program to convert. Refer to samples.zip .


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Contact: maruyama [at] photon.t.u-tokyo.ac.jp