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 fromTrajectory.cryst_const
is aligned in the same way asLammpsTextMDOutputFile.cell
. That’s why the cell and cryst_const obtained fromread_lammps_md_dcd()
andread_lammps_md_txt()
must be identical up to numerical noise (about 1e-6 for default lammps text printing precision).
Methods
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_ekin
()get_etot
()Potetntial energy PotEng [eV].
get_return_attr
(attr_name)Call try_set_attr() are return self.<attr_name> if set.
get_struct
(**kwds)get_traj
(**kwds)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