Z1 code

This site presents addon material for
K. Foteinopoulou, N.C. Karayiannis, M. Laso, M. Kroger, M.L. Mansfield, Phys Rev Lett 101 (2008) 265702.
P. S. Stephanou, C. Baig, G. Tsolou, V.G. Mavrantzas, M. Kröger, Macromolecules (2008) submitted.
R. Hoy, K. Foteinopoulou, M. Kroger, Phys Rev E (2009) submitted.

Z1 - online version for 3D linear polymeric systems

Z1 is an updated version of the Z code [M. Kroger, Comput. Phys. Commun. 168 (2005) 209 »»].
Z1 has been compared with alternate approaches in [S. Shanbhag, M. Kroger, Macromolecules 40 (2007) 2897-2903 »»].
Quickly converging estimators for Ne have been proposed in [R. Hoy, K. Foteinopoulou, M. Kroger, PRE (2009) submitted »»]
Please cite these references when making use of Z1 results in your publication.


output should contain information about bead numbers at nodes?

Required format suitable for upload

 M 
 box_x box_y box_z 	
 N1 N2 N3 .. NM
 x1,1 y1,1 z1,1
 x1,2 y1,2 z1,2
 ...
 x1,N1 y1,N1 z1,N1
 x2,1 y2,1 z2,1
 ..
 x2,N2 y2,N2 z2,N2
 x3,1 y3,1 z3,1
 ..
 xM,NM yM,NM zM,NM
where M denotes the total number of chains
box_x the box size in x-direction
Ni the number of beads in chain #i
xi,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, 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).

21 November 2009 mk   usage