pwtools.parse.Cp2kDcdMDOutputFile

class pwtools.parse.Cp2kDcdMDOutputFile(*args, **kwds)

Bases: DcdOutputFile, Cp2kMDOutputFile

Same as Cp2kMDOutputFile (all PROJECT* files are text), only that the coordinates file is a dcd format binary file PROJECT-pos-1.dcd.

__init__(*args, **kwds)

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()	[Ang]
get_cont([auto_calc])	Populate and return a Container object.
get_coords()	Cartesian [Ang]
get_cryst_const()
get_econst()	[Ha]
get_ekin()	[Ha]
get_etot()	[Ha]
get_forces()	[Ha/Bohr]
get_natoms()
get_nstep()
get_return_attr(attr_name)	Call try_set_attr() are return self.<attr_name> if set.
get_stress()	[bar]
get_struct(**kwds)
get_symbols()
get_temperature()	[K]
get_timestep()	[fs]
get_traj(**kwds)
get_velocity()	[Bohr/thart]
get_volume()	[Ang^3]
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