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118 lines
3.8 KiB
Plaintext
118 lines
3.8 KiB
Plaintext
"Pizza.py WWW Site"_pws - "Pizza.py Documentation"_pd - "Pizza.py Tools"_pc :c
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:link(pws,http://www.cs.sandia.gov/~sjplimp/pizza.html)
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:link(pd,Manual.html)
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:link(pc,Section_tools.html)
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:line
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tdump tool :h3
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[Purpose:]
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Read dump files with triangle info.
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[Description:]
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The tdump tool reads one or more LAMMPS dump files, and stores their
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contents as a series of snapshots with 2d arrays of atom attributes.
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It is assumed that each atom contains triangle segment info from a
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LAMMPS simulation using atom_style tri. Other tools use tdump objects
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to extract triangle info for visualization, like the dump tool via its
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extra() method.
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The constructor method is passed a string containing one or more dump
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filenames. They can be listed in any order since snapshots are sorted
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by timestep after they are read and duplicate snapshots (with the same
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time stamp) are deleted. If a 2nd argument is specified, the files
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are not immediately read, but snapshots can be read one-at-a-time by
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the next() method.
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The map() method assigns names to columns of atom attributes. The
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id,type, corner1x,corner1y,corner1z, corner2x,corner2y,corner2z,
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corner3x,corner3y,corner3z names must be assigned in order for line
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segment info to be extracted.
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The viz() method is called by Pizza.py tools that visualize snapshots
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of atoms (e.g. gl, raster, svg tools).
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:line
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Normally, "LAMMPS"_http://lammps.sandia.gov creates the dump files
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read in by this tool. If you want to create them yourself, the format
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of LAMMPS dump files is simple. Each snapshot is formatted as
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follows:
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ITEM: TIMESTEP
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100
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ITEM: NUMBER OF ATOMS
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32
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ITEM: BOX BOUNDS
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0 3.35919
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0 3.35919
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0 7.50
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ITEM: ATOMS
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1 1 0 0 0
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2 1 0.25 0.25 0
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3 1 0.25 0 0.25
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...
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N 3 0.7 0.5 0.6 :pre
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The box bounds are listed as xlo xhi on the 1st line, ylo yhi on the
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next line, zlo zhi on the last. There are N lines following "ITEM:
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ATOMS" where N is the number of atoms. Atoms do not have to be listed
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in any particular order. There can be a different number of atoms in
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each snapshot. Each line must contain the atom ID, type, and the end
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points of the associated line segment, as specified by the map()
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command.
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:line
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[Usage:]
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t = tdump("dump.one") read in one or more dump files
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t = tdump("dump.1 dump.2.gz") can be gzipped
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t = tdump("dump.*") wildcard expands to multiple files
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t = tdump("dump.*",0) two args = store filenames, but don't read :pre
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incomplete and duplicate snapshots are deleted
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no column name assignment is performed :pre
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time = t.next() read next snapshot from dump files :pre
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used with 2-argument constructor to allow reading snapshots one-at-a-time
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snapshot will be skipped only if another snapshot has same time stamp
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return time stamp of snapshot read
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return -1 if no snapshots left or last snapshot is incomplete
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no column name assignment is performed :pre
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t.map(1,"id",3,"x") assign names to atom columns (1-N) :pre
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must assign id,type,corner1x,corner1y,corner1z,corner2x,corner2y,corner2z,corner3x,corner3y,corner3z :pre
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time,box,atoms,bonds,tris,lines = t.viz(index) return list of viz objects :pre
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viz() returns line info for specified timestep index
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can also call as viz(time,1) and will find index of preceding snapshot
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time = timestep value
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box = \\[xlo,ylo,zlo,xhi,yhi,zhi\\]
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atoms = NULL
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bonds = NULL
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tris = id,type,x1,y1,z1,x2,y2,z2,x3,y3,z3 for each tri as 2d array
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id,type are from associated atom
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lines = NULL :pre
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t.owrap(...) wrap tris to same image as their atoms :pre
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owrap() is called by dump tool's owrap()
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useful for wrapping all molecule's atoms/tris the same so it is contiguous :pre
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[Related tools:]
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"dump"_dump.html, "gl"_gl.html, "raster"_raster.html, "svg"_svg.html
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[Prerequisites:]
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Numeric or NumPy Python packages. Gunzip command (if you want to read
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gzipped files).
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