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.
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.)
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.
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.
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.
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).
Not implemented yet.