Stick Filter

Stick filter draws connections between particles. Use them with data of molecular dynamics.


Type / Width / Radius

Select line or cylinder. Line is faster but its width is pixel-based. (Would not be magnified even if the camera approaches.)
Cylinder displays the stick with polygons (slower than line).

Widths and Radius is parametres of them respectively.

Load File

Informations of particle connection can be loaded from file or be calculated in Zindaiji3.
The format of connection file is as following. (Note: following formats are tentative one. Would be changed in future.)

Ascii data

In ascii format, write information of single pair in one line.

0 1 0 1.000
0 2 0 1.000
0 3 0 0.500
1 2 0 1.000
1 3 0 1.000
...and so on...
First column and second column are particle indices.
With this sample, sticks would be drawn between particle pairs 0-1, 0-2, 0-3, 1-2, 1-3, and so on.

Third column is preserved for boundary condition information. (like bonding to the virtual particles beyond periodic boundary).

Fourth column is transparency (alpha). You can represent degree of bond continuosly. For example, for 30% or 60% bond, set alpha parameter to be 0.3 or 0.6.

Binary data

In binary format, the size of header part is fixed to be 13 byte.
The first 5 byte of the file must be "bond\0". And next 4 byte is preserved. The 4byte integer (particle number) follows.
When reading, Zindaiji 3 checks first 5 bytes for judging binary or ascii format.

After the header, binary data follows.

index0(integer)
index1(integer)
...Repeating particle number times.
Total file size must be 8 * particle_number + 13 bytes.
(Note: this format is tentative one. Boundary condition info and alpha are ignored.)

Sequential data

If printf-like format "%0nd" is included in the filename, Zindiji 3 would read file according to its global time index.
i.e., if path is set to data%03d.txt, when time index is 0, it reads data000.txt, and when time index is 10, it reads data010.txt, and so on.
Thus, you can make make animations of dynamic molecular dynamics.

Calculate

Zindaiji 3 calculates bonding according to the distance of every particle pairs.
Currently, the algoritm is not smart and it costs O(N^2) (all pair is directly calculated).

Calculate Type

Step

Particle pair with its distance smaller than critical value A is evaluated as bond (alpha = 1).

Ramp

Particle pair with its distance smaller than critical value A is evaluated as bond, and larger than value B is evaluated as "NOT" bond.
Between them, alpha value is calculated linearly.

Step Between A and B

Particle pair with its distance between value A and B is evaluated as bond.

Particle Type

Not implemented yet.

return
inserted by FC2 system