pwtools.parse.LammpsTextMDOutputFile

class pwtools.parse.LammpsTextMDOutputFile(filename='log.lammps', order=None, **kwds)[source]

Bases: TrajectoryFileParser

Parse LAMMPS text output.

We parse the default log.lammps file (filename) with thermo output and, if present, a custom dump file lmp.out.dump created by something like dump 2 all custom 1 lmp.out.dump ... Tested with MD and structure optimization (minimize).

Currently hardcoded file names:
dumpfilename = basedir/lmp.out.dump
symbolsfilename = basedir/lmp.struct.symbols

where basedir is the dir where filename (i.e. log.lammps) lives.

default_units are for lammps metal units.

Examples

Example lammps input:

clear
units metal
boundary p p p
atom_style atomic

read_data lmp.struct

### interactions
pair_style tersoff
pair_coeff * * AlN.tersoff Al N

### IO
dump dump_txt all custom 1 lmp.out.dump id type xsu ysu zsu xu yu zu fx fy fz vx vy vz
dump dump_dcd all dcd 1 lmp.out.dcd
##dump dump_xyz all xyz 1 lmp.out.xyz
##dump_modify dump_xyz element Al N
dump_modify dump_txt sort id
dump_modify dump_dcd sort id unwrap yes
thermo_style custom step temp vol cella cellb cellc cellalpha cellbeta cellgamma &
                    ke pe etotal &
                    press pxx pyy pzz pxy pxz pyz cpu
thermo_modify flush yes
thermo 1

### init
velocity all create 300.0 123 rot yes dist gaussian

### run
fix fix_npt all npt temp 1000 1000 0.01 tri 0 0 0.3 tchain 4 pchain 4 &
    mtk yes scaleyz no scalexz no scalexy no flip no
timestep 2.5e-3
run 1000

Notes

  • columns in filename and dumpfilename: We automagically extract the “header” (e.g. “Step Temp Volume Cella …” in filename or “ITEM: ATOMS id type xsu ysu zsu fx fy fz vx vy vz” in dumpfilename) and map data to these symbols. See _thermo_dct and _dump_dct. Currently, “xsu ysu zsu” is parsed to get coords_frac. “xu yu zu” is parsed to get coords. Wrapped coordinates (e.g. “xs ys zs” and “x y z”) are ignored.

  • multiple runs from one input script (i.e. 2 or more run commands): it seems that the last step of the preceeding run is printed again by the new run by thermo_style, which results in more nstep in filename as there really are in dumpfilename. We parse all important stuff (coords, cell, velocity) from dumpfilename, but temperature and stress etc. is from filename. Watch out when plotting.

  • cell: We parse cell from “ITEM: BOX BOUNDS” in dumpfilename and the cell is always [[x,0,0],[xy,y,0],[xz,yz,z]], i.e. it is aligned in the same way in each timestep.

  • atom symbols: First we try to read symbolsfilename, which may have been written by pwtools.io.write_lammps(). If that is not found, we try to use the type column in dumpfilename together with a type number -> atom symbol mapping either from the order input keyword or a dump_modify ... element line in filename if found.

__init__(filename='log.lammps', order=None, **kwds)[source]
Parameters:

  • filename (str) – Text output file, where thermo_style [custom] output is written to. The lammps default is log.lammps.

  • order (dict, optional) – See pwtools.crys.Structure.get_order(). Mapping of atom symbols to type in lammps, i.e. {‘Al’: 1, ‘N’: 2}. If None then we try to use dump_modify ... element if present in filename, where lammps echos the input script. symbols is build from the type column in dumpfilename.

Methods

apply_units()

Like _apply_units_raw(), make sure that units are only applied once.

assert_attr(attr)

Raise AssertionError if self.<attr> is not set (is_set_attr() returns False.

assert_attr_lst(attr_lst)

assert_set_attr(attr)

Same as assert_attr(), but run try_set_attr() first.

assert_set_attr_lst(attr_lst)

check_set_attr(attr)

Run try_set_attr() and return the result of is_set_attr(), i.e. True or False.

check_set_attr_lst(attr_lst)

dump(dump_filename[, mkdir])

Write object to binary file using pickle.

get_cell()

get_cont([auto_calc])

Populate and return a Container object.

get_coords()

get_coords_frac()

get_cryst_const()

get_ekin()

get_etot()

Potetntial energy PotEng [eV].

get_forces()

get_natoms()

get_return_attr(attr_name)

Call try_set_attr() are return self.<attr_name> if set.

get_stress()

get_struct(**kwds)

get_symbols()

get_temperature()

get_timestep()

get_traj(**kwds)

get_velocity()

get_volume()

init_attr_lst([attr_lst])

Set each self.<attr> in attr_lst to None.

is_set_attr(attr)

Check if self has the attribute self.<attr> and if it is _not_ None.

is_set_attr_lst(attr_lst)

load(dump_filename)

Load pickled object.

parse()

raw_return(attr_name)

Call try_set_attr(_<attr_name>_raw) and return it if set, else None.

raw_slice_get(attr_name, sl, axis)

Shortcut method:

set_all([attr_lst])

Call getter for each attr name in attr_lst.

set_attr_lst(attr_lst)

Set self.attr_lst and init each attr to None.

try_set_attr(attr)

If self.<attr> does not exist or is None, then invoke an appropirately named getter as if this command would be executed.

try_set_attr_lst(attr_lst)

update_units(units)

Update self.units dict from units.

Attributes

default_units

timeaxis