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 .