Read dump files with line segment info.
The ldump tool reads one or more LAMMPS dump files, and stores their contents as a series of snapshots with 2d arrays of atom attributes. It is assumed that each atom contains line segment info from a 2d LAMMPS simulation using atom_style line. Other tools use ldump objects to extract line segment info for visualization, like the dump tool via its extra() method.
The constructor method is passed a string containing one or more dump filenames. They can be listed in any order since snapshots are sorted by timestep after they are read and duplicate snapshots (with the same time stamp) are deleted. If a 2nd argument is specified, the files are not immediately read, but snapshots can be read one-at-a-time by the next() method.
The map() method assigns names to columns of atom attributes. The id,type,end1x,end1y,end2x,end2y names must be assigned in order for line segment info to be extracted.
The viz() method is called by Pizza.py tools that visualize snapshots of atoms (e.g. gl, raster, svg tools).
Normally, LAMMPS creates the dump files read in by this tool. If you want to create them yourself, the format of LAMMPS dump files is simple. Each snapshot is formatted as follows:
ITEM: TIMESTEP 100 ITEM: NUMBER OF ATOMS 32 ITEM: BOX BOUNDS 0 3.35919 0 3.35919 0 7.50 ITEM: ATOMS 1 1 0 0 0 2 1 0.25 0.25 0 3 1 0.25 0 0.25 ... N 3 0.7 0.5 0.6
The box bounds are listed as xlo xhi on the 1st line, ylo yhi on the next line, zlo zhi on the last. There are N lines following "ITEM: ATOMS" where N is the number of atoms. Atoms do not have to be listed in any particular order. There can be a different number of atoms in each snapshot. Each line must contain the atom ID, type, and the end points of the associated line segment, as specified by the map() command.
l = ldump("dump.one") read in one or more dump files l = ldump("dump.1 dump.2.gz") can be gzipped l = ldump("dump.*") wildcard expands to multiple files l = ldump("dump.*",0) two args = store filenames, but don't read
incomplete and duplicate snapshots are deleted no column name assignment is performed
time = l.next() read next snapshot from dump files
used with 2-argument constructor to allow reading snapshots one-at-a-time snapshot will be skipped only if another snapshot has same time stamp return time stamp of snapshot read return -1 if no snapshots left or last snapshot is incomplete no column name assignment is performed
l.map(1,"id",3,"x") assign names to atom columns (1-N)
must assign id,type,end1x,end1y,end2x,end2y
time,box,atoms,bonds,tris,lines = l.viz(index) return list of viz objects
viz() returns line info for specified timestep index can also call as viz(time,1) and will find index of preceding snapshot time = timestep value box = \[xlo,ylo,zlo,xhi,yhi,zhi\] atoms = NULL bonds = NULL tris = NULL lines = id,type,x1,y1,z1,x2,y2,z2 for each line as 2d array id,type are from associated atom
l.owrap(...) wrap lines to same image as their atoms
owrap() is called by dump tool's owrap() useful for wrapping all molecule's atoms/lines the same so it is contiguous
dump, gl, raster, svg
Numeric or NumPy Python packages. Gunzip command (if you want to read gzipped files).