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data tool :h3

[Purpose:]

Read, write, manipulate LAMMPS data files.

[Description:]

The data tool reads and writes LAMMPS data files.  It also allows
their content to be accessed or modified.

The data constructor reads in the specified LAMMPS data file.  With no
argument, an empty data object is created which can have fields added
to it later, and then be written out.

The map() method assigns names to different atom attributes by their
column number (1-N).  The get() method extracts columns of information
from the specified section of the data file.

The title, headers, and sections variables can be set directly.  The
header values correspond to one-line definition that appear at the top
of the data file.  The box size values should be set to a Python
tuple, e.g.

d.headers\["xlo xhi"\] = (-30, 30) :pre

The section value should be a list of text lines, each of which
includes a newline at the end.

The delete() method deletes a header or entire section of the data
file.  The replace() method allows one column of a section to be
replaced with a vector of new values.  The newxyz() methods replaces
the xyz coords of the "Atoms" section of the data file with xyz values
from the Nth snapshot of a dump object containing snapshots.

The iterator() and viz() methods are called by Pizza.py tools that
visualize snapshots of atoms (e.g. raster, svg tools).  A data file
can be visualzed similarly to snapshots from a dump file.  In the case
of a data file, there is only a single snapshot with index 0.

The write() method outputs a LAMMPS data file.

[Usage:]

d = data("data.poly")            read a LAMMPS data file, can be gzipped
d = data()			 create an empty data file :pre

d.map(1,"id",3,"x")              assign names to atom columns (1-N) :pre

coeffs = d.get("Pair Coeffs")    extract info from data file section
q = d.get("Atoms",4) :pre

  1 arg = all columns returned as 2d array of floats
  2 args = Nth column returned as vector of floats :pre

d.reorder("Atoms",1,3,2,4,5)     reorder columns (1-N) in a data file section :pre

  1,3,2,4,5 = new order of previous columns, can delete columns this way :pre

d.title = "My LAMMPS data file"	 set title of the data file
d.headers\["atoms"\] = 1500        set a header value
d.sections\["Bonds"\] = lines      set a section to list of lines (with newlines)
d.delete("bonds")		 delete a keyword or section of data file
d.delete("Bonds")
d.replace("Atoms",5,vec)      	 replace Nth column of section with vector
d.newxyz(dmp,1000)		 replace xyz in Atoms with xyz of snapshot N :pre

  newxyz assumes id,x,y,z are defined in both data and dump files
    also replaces ix,iy,iz if they are defined :pre

index,time,flag = d.iterator(0/1)          loop over single data file snapshot
time,box,atoms,bonds,tris,lines = d.viz(index)   return list of viz objects :pre

  iterator() and viz() are compatible with equivalent dump calls
  iterator() called with arg = 0 first time, with arg = 1 on subsequent calls
    index = timestep index within dump object (only 0 for data file)
    time = timestep value (only 0 for data file)
    flag = -1 when iteration is done, 1 otherwise
  viz() returns info for specified timestep index (must be 0)
    time = 0
    box = \[xlo,ylo,zlo,xhi,yhi,zhi\]
    atoms = id,type,x,y,z for each atom as 2d array
    bonds = id,type,x1,y1,z1,x2,y2,z2,t1,t2 for each bond as 2d array
      NULL if bonds do not exist
    tris = NULL
    lines = NULL :pre

d.write("data.new")             write a LAMMPS data file :pre

[Related tools:]

"gl"_gl.html, "raster"_raster.html, "svg"_svg.html

[Prerequisites:] none
