io_extended - read/write configurational filesΒΆ

This Python module allows one to read and write configurational files. One can choose folded or unfolded coordinates and write down velocities or not. It is similar to lammps read and write, but it writes down only: 1) number of particles + types 2) number of bonds (number of pairs) + types 3) number of angles (number of triples) + types 4) number of dihedrals (number of quadruples) + types 5) system size (Lx,Ly,Lz) 6) p_id, p_type, p_positions 7) velocities (if true) 8) bonds (if exist) 9) angles (if exist) 10)dihedrals (if exist)

read returns: Lx, Ly, Lz, p_ids, p_types, poss, vels, bonds, angles, dihedrals if something does not exist then it will return the empty list bonds, angles, dihedrals - will return list [type, (x,x,x,x)], where type is the type of bond, angle or dihedral (x,x,x,x) is (pid1,pid2) for bonds,

(pid1,pid2,pid3) for angles

(pid1,pid2,pid3,pid4) for dihedrals