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)
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
d.map(1,"id",3,"x") assign names to atom columns (1-N)
coeffs = d.get("Pair Coeffs") extract info from data file section
q = d.get("Atoms",4)
1 arg = all columns returned as 2d array of floats 2 args = Nth column returned as vector of floats
d.reorder("Atoms",1,3,2,4,5) reorder columns (1-N) in a data file section
1,3,2,4,5 = new order of previous columns, can delete columns this way
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
newxyz assumes id,x,y,z are defined in both data and dump files
also replaces ix,iy,iz if they are defined
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
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
d.write("data.new") write a LAMMPS data file
Related tools:
Prerequisites: none