adaptivemd.Trajectory

class adaptivemd.Trajectory(location, frame, length, engine=None)

Represents a trajectory File on the cluster

Variables:

• location (str or File) – the File location
• frame (Frame or File) – the initial frame used for the trajectory
• length (int) – the length of the trajectory in frames
• engine (Engine) – the engine used to create the trajectory

__init__(location, frame, length, engine=None)

x.__init__(…) initializes x; see help(type(x)) for signature

Methods

__init__(location, frame, length[, engine])	x.__init__(…) initializes x; see help(type(x)) for signature
args()	Return a list of args of the __init__ function of a class
base()	Return the most parent class actually derived from StorableMixin
clone()	create a cloned object with equal attributes
copy([target])	copy file to a target
create(scheduler)	Mark file as being existent on a specific scheduler.
descendants()	Return a list of all subclassed objects
extend(length)	Get a task to extend this trajectory if the engine is set
file(f)	Return a file location to a file inside the trajectory folder
from_dict(dct)	Reconstruct an object from a dictionary representation
get_file()	Return the file content it has been loaded
get_uuid()	Create a new unique ID :returns: the unique number for an object in the project :rtype: long
idx(store)	Return the index which is used for the object in the given store.
link([target])	link file to a target
load([scheduler])	Load a local file into memory
modified()	Mark a file as being altered and not existent anymore
move([target])	move file to a target
named(name)	Attach a .name property to an object
objects()	Returns a dictionary of all storable objects
outputs(outtype)	Get a location to the file containing the output by given name
pick()	Return a random frame from all possible full frames
remove()	remove file
run()	Return a task to run this engine
set_file(content)	Set the file content.
to_dict()	Convert object into a dictionary representation
touch()	touch file
transfer([target])	transfer file to a target

Attributes

ACTIVE_LONG
CREATION_COUNT
INSTANCE_UUID
allowed_drives
base_cls	Return the base class
base_cls_name	Return the name of the base class
basename	returns:the file basename
basename_short	returns:the basename without extension
cls	Return the class name as a string
created
default_drive
dirname	returns:the path of the directory, like os.path.dirname
drive	return the prefix name
engine
existing_frames	returns:a sorted list of frame indices with full coordinates that can be
exists	returns:True if the file exists, i.e. has a positive created timestamp
extension	returns:the filename extension or ‘’ of non exists
generator
has_file	returns:True if the file content is attached.
is_folder
is_temp	returns:True when the location is a temporary folder that might be
path	returns:the complete path without prefix
short	returns:a shortened form of the path
split	returns:
split_drive	returns: str – the drive (prefix with ://)
task
types	Return the OutputTypeDescriptions for this trajectory
url	returns:return the full form always with a prefix
use_absolute_local_paths

clone()

create a cloned object with equal attributes

Returns:the same type as this object Return type:Location

pick()

Return a random frame from all possible full frames

Returns:the frame you can restart from Return type:Frame

file(f)

Return a file location to a file inside the trajectory folder

Parameters:f (str or OutputTypeDescription) – the filename to be appended to the trajectories directory Returns:the object containing the location Return type:File

run()

Return a task to run this engine

Returns:the task object that can be submitted to the queue Return type:Task

extend(length)

Get a task to extend this trajectory if the engine is set

Parameters:length (int or list of int) – the length to extend by as a single int or a list of ints Returns:the task object to extend the trajectory Return type:Task

outputs(outtype)

Get a location to the file containing the output by given name

Parameters:outtype (str or OutputTypeDescription) – the name of the outputtype as str or the full description object Returns:a file location that points to the concrete file that contains the data for a particular output type Return type:File

types

Return the OutputTypeDescriptions for this trajectory

Returns:dict str – the output description dict of the engine Return type:OutputTypeDescription

existing_frames

Returns:a sorted list of frame indices with full coordinates that can be used for restart. relative to the engines timesteps Return type:list of int