pwtools.parse.LammpsDcdMDOutputFile

class pwtools.parse.LammpsDcdMDOutputFile(*args, **kwds)[source]

Bases: DcdOutputFile, LammpsTextMDOutputFile

Parse Lammps DCD binary output + log.lammps text output.

Hardcodes files:
dcdfilename = basedir/lmp.out.dcd

Notes

  • cell: The DCD file format stores only cryst_const (see unitcell in dcd.f90). Trajectory.cell calculated from Trajectory.cryst_const is aligned in the same way as LammpsTextMDOutputFile.cell. That’s why the cell and cryst_const obtained from read_lammps_md_dcd() and read_lammps_md_txt() must be identical up to numerical noise (about 1e-6 for default lammps text printing precision).

__init__(*args, **kwds)[source]

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_nstep()

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