adaptivemd package

Submodules

adaptivemd.brain module

class adaptivemd.brain.Brain(engine, analyzer)

Bases: adaptivemd.mongodb.base.StorableMixin

execute(project)

initial_tasks(project)

get_events(project)

adaptivemd.io module

adaptivemd.io.BINCOORwrite(coords, filename)

adaptivemd.io.BINCOORread(filename)

adaptivemd.model module

class adaptivemd.model.Model(data)

Bases: adaptivemd.mongodb.base.StorableMixin

A wrapper to hold model data

Examples

>>> m = Model({'msm' : [[0.9, 0.1], [0.1, 0.9]]})
>>> print m.msm
>>> print m['msm']

Variables:data (dict of str : anything) – the data of the model

adaptivemd.reducer module

class adaptivemd.reducer.ActionParser

Bases: object

A class that can interprete actions into scheduler understandable commands

parse(scheduler, action)

Parse a single action

Parameters:

• scheduler (Scheduler) – the used scheduler which knows about specifics in the parsing process, like, e.g., file paths
• action (Action or dict or list of str) – the actual action to be parsed

Returns:

Return type:

list of Action or dict or str

class adaptivemd.reducer.DictFilterParser

Bases: adaptivemd.reducer.ActionParser

parse(scheduler, action)

class adaptivemd.reducer.StrFilterParser

Bases: adaptivemd.reducer.ActionParser

parse(scheduler, action)

class adaptivemd.reducer.ChainedParser(parent, child)

Bases: adaptivemd.reducer.ActionParser

Parser that represents the chained application of two parser

class adaptivemd.reducer.StageInParser

Bases: adaptivemd.reducer.ActionParser

Special parser that can interpret actions into RP stage-in phase

parse(scheduler, action)

class adaptivemd.reducer.BashParser

Bases: adaptivemd.reducer.ActionParser

parse(scheduler, action)

class adaptivemd.reducer.StageParser

Bases: adaptivemd.reducer.ActionParser

Parse into possible RP Stage commands for ComputeUnits

parse(scheduler, action)

class adaptivemd.reducer.WorkerParser

Bases: adaptivemd.reducer.ActionParser

A parser that can interprete transactions from/to file:// for workers

This will write the files to the target location instead of a real transaction. It requires the file to be stored in the DB using load()

parse(scheduler, action)

class adaptivemd.reducer.PrefixParser

Bases: adaptivemd.reducer.ActionParser

Replace all adaptiveMD prefixes

Usually the last step to convert all file paths

parse(scheduler, action)

adaptivemd.util module

adaptivemd.util.get_function_source(func)

Determine the source file of a function

Parameters:func (function) – Returns:

• str – the module name
• list of str – a list of filenames necessary to be copied

class adaptivemd.util.DT(stamp)

Bases: object

Helper class to convert timestamps to human readable output

default_format = '%Y-%m-%d %H:%M:%S'

format(fmt=None)

date

time

length

ago