Z1 code
18.119.130.231

Z1 - online version for 3D linear polymeric systems

Latest news: The successor, Z1+ is available for download and accompanied by a full paper at (Open Access) Comput. Phys. Commun. 283 (2023) 108567
Benchmark cofigurations, additional scripts for Z1+ users available at github.

Z1 is an updated version of the Z code [M. Kröger, Comput. Phys. Commun. 168 (2005) 209 »»].
Z1 has been compared with alternate approaches in [S. Shanbhag, M. Kröger, Macromolecules 40 (2007) 2897-2903 »»].
Quickly converging estimators for Ne have been proposed in [R. Hoy, K. Foteinopoulou, M. Kröger, Phys. Rev. E (2009) 031803 »»]
Implementation details of Z1 have been discussed in [N.C. Karayiannis, M. Kröger, Int. J. Mol. Sci. 10 (2009) 5054. »»]

Please cite these references when making use of Z1 results in your publication.

Two examples for the Z1 transformation from 'atomistic' to 'entanglement network' (click to watch movie)

Upload your 'atomistic' configuration


should Z1 wrap your coordinates to the central simulation cell?
output should contain information about bead numbers at nodes?
output should contain information about bead numbers at nodes and 'entanglement' points?

Required format suitable for upload (contact me, if you need a converter, see also comments below)

 c 
 box_x box_y box_z 	
 N1 N2 N3 .. Nc
 x(1,1)  y(1,1)  z(1,1)
 x(1,2)  y(1,2)  z(1,2)
 ...
 x(1,N1) y(1,N1) z(1,N1)
 x(2,1)  y(2,1)  z(2,1)
 ..
 x(2,N2) y(2,N2) z(2,N2)
 x(3,1)  y(3,1)  z(3,1)
 ..
 x(c,Nc) y(c,Nc) z(c,Nc)
where c denotes the total number of chains
box_x the box size in x-direction
Ni the (integer) number of beads in chain #i (if 50 chains have the same length 200, this line may be abbreviated as 50*200)
x(i,j) the x-component of the jth bead of chain i

Coordinates can be provided either in the unfolded or folded state, the program returns coordinates in the unfolded state, both the original, uploaded configuration (coords_before) and final configuration (coords_after). If you work with folded coordinates, the origin (0,0,0) should be centered in the simulation cell. The first coordinate of each chain should be located in the central simulation box. Output format: number of chains, box sizes followed by number of kinks and kink positions for each chain separately. Notice that a kink is not necessarly identical with an entanglement, as the latter quantity is not uniquely defined. The contour length of the shortest path, Lpp, for example, is uniquely defined. The online application cannot operate on 'large' files and folders containing trajectories (please contact me in case this is inconvenient). I may provide you with an executable that operates on the above format, or LAMMPS data or dump files (dump files with at least: id mol xu yu zu or id mol x y z).

19 May 2024 mk   usage

Please ignore the following information for insiders only:
types 00 0 1 2 3 [4] [5=2]
(A) uncrosslinked polymers move move move move move freeze move
(B) crosslinked polymers move move move move freeze move move
(C) crosslinkers ignore ignore freeze merge freeze merge merge
(N) nanoparticles ignore freeze freeze freeze freeze freeze freeze
YL_values.dat A+B A+B A+B A+B A B A,B