def test_fizzled_3(self):
# WF(Fizzled -> Completed(allow fizz parents)) == COMPLETED
one = fw.Firework([], state="FIZZLED", fw_id=1)
two = fw.Firework([],
state="COMPLETED",
fw_id=2,
spec={"_allow_fizzled_parents": True},
parents=one)
self.assertEqual(fw.Workflow([one, two]).state, "COMPLETED")
def test_fizzled_2(self):
# WF(Fizzled -> Ready(allow fizz parents)) == RUNNING
one = fw.Firework([], state="FIZZLED", fw_id=1)
two = fw.Firework([],
state="READY",
fw_id=2,
spec={"_allow_fizzled_parents": True},
parents=one)
self.assertEqual(fw.Workflow([one, two]).state, "RUNNING")
def test_fizzled_2(self):
# WF(Fizzled -> Ready(allow fizz parents)) == RUNNING
one = fw.Firework([], state='FIZZLED', fw_id=1)
two = fw.Firework([],
state='READY',
fw_id=2,
spec={'_allow_fizzled_parents': True},
parents=one)
self.assertEqual(fw.Workflow([one, two]).state, 'RUNNING')
def test_fizzled_4(self):
# one child doesn't allow fizzled parents
one = fw.Firework([], state="FIZZLED", fw_id=1)
two = fw.Firework([],
state="READY",
fw_id=2,
spec={"_allow_fizzled_parents": True},
parents=one)
three = fw.Firework([], state="WAITING", fw_id=3, parents=one)
self.assertEqual(fw.Workflow([one, two, three]).state, "FIZZLED")
def test_fizzled_4(self):
# one child doesn't allow fizzled parents
one = fw.Firework([], state='FIZZLED', fw_id=1)
two = fw.Firework([],
state='READY',
fw_id=2,
spec={'_allow_fizzled_parents': True},
parents=one)
three = fw.Firework([], state='WAITING', fw_id=3, parents=one)
self.assertEqual(fw.Workflow([one, two, three]).state, 'FIZZLED')
def test_fizzled_6(self):
# deep fizzled fireworks, but still RUNNING
one = fw.Firework([], state="FIZZLED", fw_id=1)
two = fw.Firework([],
state="FIZZLED",
fw_id=2,
spec={"_allow_fizzled_parents": True},
parents=one)
three = fw.Firework([],
state="READY",
fw_id=3,
spec={"_allow_fizzled_parents": True},
parents=two)
self.assertEqual(fw.Workflow([one, two, three]).state, "RUNNING")
def make_detour(nparallel, previous):
# make more simulations at higher pressures
temperature = max(r[0] for r in previous)
max_pressure = max(r[1] for r in previous)
new_pressures = [max_pressure * 2, max_pressure * 4, max_pressure * 8]
new_sims = []
new_pps = []
for P in new_presures:
new_sims = [
make_Simfireworks(parent_fw=None,
T=temperature,
P=P,
ncycles=None,
wfname='Capacity',
template=None,
workdir=None) for P in new_pressures
]
pp = make_PostProcess()
new_me = fw.Firework(
self.__class__(nparallel=nparallel, previous_results=previous),
parents=new_pps,
)
def Firstgen_PreGA_FW(template, pop, wf_name):
"""Variant of PreGA for the zeroth generation
Parameters
----------
template : str
path to the template for simulations
pop : tuple of tuples
description of the initial population
wf_name : str
unique key to refer to this workflow by
Returns
-------
firstgen_prega : fireworks.Firework
Firework for the setup of GA
"""
stuff = utils.slurp_directory(template)
return fw.Firework(
[
# creates template
InitTemplate(contents=stuff),
# creates candidates and population
InitPopulation(initial_population=pop),
],
spec={
'_category': wf_name,
},
name='Firstgen PreGA',
)
def PreGA_FW(parent, idx, bounds, wf_name):
"""Operations to set up candidates
Parameters
----------
parent : fw.Firework
ref to previous FW
idx : int
index of which generation of GA this is
bounds : tuple
tuple containing the minimum and maximum bounds for each parameter
eg `((1.0, 2.0), (10.0, 20.0))` clamps the first value between 1.0 and 2.0
wf_name : str
unique key to refer to this workflow by
Returns
-------
prega : fireworks.Firework
"""
settings = VaryCandidates.default_params.copy()
settings['bounds'] = bounds
return fw.Firework(
[
Tournament(),
VaryCandidates(**settings),
PassAlong(keys=['template', 'parents']),
],
spec={
'_category': wf_name,
},
parents=parent,
name='PreGA G={}'.format(idx),
)
def PostSim_FW(generation_id, candidate_id, parents, wf_name):
"""Collects Sims from different conditions in one candidate fitness
Parameters
----------
generation_id : int
id of the generation
candidate_id : int
id of this candidate
parents : list of fw.Firework
references to the preceeding Fireworks for this candidate
wf_name : str
unique key to refer to this workflow by
Returns
-------
postsim : fireworks.Firework
"""
return fw.Firework(
[
IsothermCreate(),
AssignFitness(candidate_id=candidate_id),
],
spec={
'_category': wf_name,
},
parents=parents,
name='PostSim G={} C={}'.format(generation_id, candidate_id),
)
def InitTempFW(sample_input):
firework = fw.Firework(gcwf.firetasks.InitTemplate(
contents=gcwf.utils.slurp_directory('template')),
spec={
"workdir": ".",
"name": "Template init test"
})
return firework
def Sim_FW(temperature, pressure, ref, generation_id, candidate_id, ff_updater,
parent, wf_name):
"""Generate a single simulation Firework
Parameters
----------
temperature : int
temperature
pressure : int
pressure
ref : float
desired result for this T & P
generation_id : int
id of the generation
candidate_id : int
which candidate this simulation refers to
ff_updater : function
function which does the manipulation of forcefield files
parent : fw.Firework
the preceeding Firework to this Firework
wf_name : str
unique key to refer to this workflow by
Returns
-------
sim : fireworks.Firework
"""
# convert python function to pickle form
ff_updater = utils.pickle_func(ff_updater)
return fw.Firework(
[
CopyTemplate(
temperature=temperature,
pressure=pressure,
fmt='raspa',
parallel_id=generation_id,
),
ManipulateForcefield(
candidate_id=candidate_id,
updater=ff_updater,
),
RunSimulation(fmt='raspa'),
EvaluateResult(
reference=ref,
fmt='raspa',
temperature=temperature,
pressure=pressure,
),
],
spec={
'_category': wf_name,
},
parents=parent,
name='Sim T={} P={} C={}'.format(temperature, pressure, candidate_id),
)
def analysis_task(successful_raspa, launchpad):
# run analysis on a successful raspa simulation
firework = fw.Firework(
[
gcwf.firetasks.AnalyseSimulation(fmt='raspa', parallel_id=1),
TellTale()
],
spec={'simtree': os.path.abspath(successful_raspa)},
)
launchpad(fw.Workflow([firework]))
yield successful_raspa
def _submit_task(self, task_spec: Dict[str, Any]) -> Tuple[Hashable, Any]:
import fireworks
kwargs = task_spec["spec"]["kwargs"]
kwargs["return_dict"] = True
fw = fireworks.Firework(fireworks.PyTask(
func=task_spec["spec"]["function"],
args=task_spec["spec"]["args"],
kwargs=kwargs,
stored_data_varname="fw_results"),
spec={"_launch_dir": "/tmp/"})
launches = self.client.add_wf(fw)
return list(launches.values())[0], task_spec["id"]
def copytemplate(sample_input, launchpad):
cp1 = fw.Firework(gcwf.firetasks.CopyTemplate(temperature=10,
pressure=20,
ncycles=1234,
parallel_id=1,
fmt='raspa'),
spec={
'template': os.path.join(sample_input,
'template'),
})
wf = fw.Workflow([cp1])
launchpad(wf)
print(os.listdir())
return glob.glob('sim_*')[0]
def analysis_task_with_previous(successful_raspa, launchpad):
# run analysis on a successful raspa simulation
firework = fw.Firework(
[
gcwf.firetasks.AnalyseSimulation(
fmt='raspa',
parallel_id=1,
previous_results='0,123\n673,456\n',
),
TellTale()
],
spec={'simtree': os.path.abspath(successful_raspa)},
)
launchpad(fw.Workflow([firework]))
yield successful_raspa
def bulk_relaxation(
self,
atoms,
parameters,
spec=None):
"""Run a relaxation of a given DB entry or atoms object. If a
database object is used, the calculation will automatically store
the keys and data for later retrieval.
The entries uuid will also be stored and `data.calculator_parameters`
will be used as the calculation parameters.
Parameters
----------
images : Atoms object
Initial atoms to perform workflow on.
parameters : dict
Calculation parameters to use.
workflow_name : str
Name of the fireworks calculation to be used.
spec : dict
Additional fireworks specifications to pass to the database.
"""
atoms.info['calculator_parameters'] = parameters
encoding = fwio.atoms_to_encode(atoms)
t0 = fireworks.PyTask(
func='catkit.flow.fwio.encode_to_atoms',
args=[encoding])
t1 = fireworks.PyTask(
func='catkit.flow.fwase.catflow_relaxation',
stored_data_varname='trajectory')
tasks = [t0, t1]
if spec is None:
spec = {}
firework = fireworks.Firework(tasks, spec=spec)
workflow = fireworks.Workflow([firework], name='bulk_relaxation')
workflow_id = self.launchpad.add_wf(workflow)[-1]
return workflow_id
def __new__(cls, command, **kwargs):
bsub_options_dict = {}
spec = None
name = None
for key in [
'queue', 'resources', 'walltime', 'est_wait_time', 'processors'
]:
if key in kwargs:
bsub_options_dict[key] = kwargs[key]
spec = {}
if len(bsub_options_dict.keys()) > 0:
spec['_queueadapter'] = bsub_options_dict
# spec['_dupefinder']={"_fw_name" : "DupeFinderScript"}
if 'name' in kwargs:
name = kwargs['name']
return fireworks.Firework(fireworks.ScriptTask.from_str(command),
name=name,
spec=spec)
def submit_tasks(self, tasks):
ret = []
for task in tasks:
tag = task["id"]
fw = fireworks.Firework(fireworks.PyTask(
func=task["spec"]["function"],
args=task["spec"]["args"],
kwargs=task["spec"]["kwargs"],
stored_data_varname="fw_results"),
spec={"_launch_dir": "/tmp/"})
launches = self.lpad.add_wf(fw)
self.queue[list(launches.values())[0]] = (tag, task["parser"],
task["hooks"])
ret.append(tag)
return ret
def test_already_existing(sample_input, launchpad, template_contents):
"""Check that CopyTemplate correctly overwrites an existing Simulation"""
T = 290.0
P = 100.0
gen = 1
pid = 2
# make something in the way
newdir = gcwf.utils.gen_sim_path(T, P, gen, pid)
os.makedirs(newdir)
with open(os.path.join(newdir, 'thing.txt'), 'w') as out:
out.write('hello!\n')
# make and run CopyTemplate
cp = fw.Firework(
[
gcwf.firetasks.CopyTemplate(
temperature=T,
pressure=P,
parallel_id=pid,
fmt='raspa',
workdir=os.path.abspath('.'),
)
],
spec={
'template': os.path.abspath('template'),
},
)
launchpad(cp)
newdir2 = gcwf.utils.gen_sim_path(T, P, gen + 1, pid)
assert os.path.exists(newdir)
assert os.path.exists(newdir2)
assert os.path.exists(os.path.join(newdir, 'thing.txt'))
for fn in template_contents:
assert os.path.exists(os.path.join(newdir2, fn))
def PostGA_FW(generation_id, parents, wf_name):
"""Operations to finish the GA generation
Parameters
----------
generation_id : int
id of the generation
parents : list of fw.Firework
references to PostSim Fireworks
wf_name : str
unique key to refer to this workflow by
Returns
-------
postga : fireworks.Firework
"""
return fw.Firework(
[Replacement(), PassAlong(keys=['template'])],
spec={
'_category': wf_name,
},
parents=parents,
name='PostGA G={}'.format(generation_id),
)
def test_archived(self):
one = fw.Firework([], state="ARCHIVED", fw_id=1)
two = fw.Firework([], state="ARCHIVED", fw_id=2)
self.assertEqual(fw.Workflow([one, two]).state, "ARCHIVED")
def submit_relaxation(
self,
image,
workflow_name,
parameters=None,
spec=None):
"""Run a relaxation of a given DB entry or atoms object. If a
database object is used, the calculation will automatically store
the keys and data for later retrieval.
The entries uuid will also be stored and `data.calculator_parameters`
will be used as the calculation parameters.
Parameters
----------
images : Atoms object | AtomsRow object
ASE database entry or atoms object to relax.
workflow_name : str
Name of the fireworks calculation to be used.
parameters : dict
Calculation parameters to use. Will be pulled from
a database entry `data.calculator_parameters`.
spec : dict
Additional fireworks specifications to pass to the database.
"""
keys, data = {}, {}
if isinstance(image, AtomsRow):
atoms = image.toatoms()
keys.update(image.key_value_pairs)
keys.update({'uuid': image.unique_id})
data.update(image.data)
else:
atoms = image
if parameters is None:
if data.get('calculator_parameters'):
parameters = data.get('calculator_parameters')
del data['calculator_parameters']
elif atoms.info.get('calculator_parameters'):
parameters = atoms.info.get('calculator_parameters')
else:
raise ValueError('Calculation parameters missing.')
calculator = parameters.pop('calculator_name', None)
if calculator is None:
raise ValueError("'calculator_name' missing from parameters.")
atoms.info['calculator_parameters'] = parameters
for k, v in data.items():
if isinstance(v, np.ndarray):
fwio.array_to_list(v)
data[k] = v
encoding = fwio.atoms_to_encode(atoms)
t0 = fireworks.PyTask(
func='catkit.flow.fwio.encode_to_atoms',
args=[encoding])
t1 = fireworks.PyTask(
func='catkit.flow.fwase.get_potential_energy',
args=[calculator],
stored_data_varname='trajectory')
tasks = [t0, t1]
if spec is None:
spec = {'keys': keys, 'data': data}
else:
spec.update({'keys': keys, 'data': data})
firework = fireworks.Firework(tasks, spec=spec)
workflow = fireworks.Workflow([firework], name=workflow_name)
self.launchpad.add_wf(workflow)
def run_raspa(short_raspa, launchpad):
job = fw.Firework([gcwf.firetasks.RunSimulation(fmt='raspa')],
spec={'simtree': short_raspa})
launchpad(fw.Workflow([job]))
def test_paused(self):
# any paused == paused
one = fw.Firework([], state="COMPLETED", fw_id=1)
two = fw.Firework([], state="PAUSED", fw_id=2)
self.assertEqual(fw.Workflow([one, two]).state, "PAUSED")
def test_fizzled_1(self):
# WF(Fizzled -> Waiting(no fizz parents)) == FIZZLED
one = fw.Firework([], state="FIZZLED", fw_id=1)
two = fw.Firework([], state="WAITING", fw_id=2, parents=one)
self.assertEqual(fw.Workflow([one, two]).state, "FIZZLED")
def test_completed(self):
# all leaves complete
one = fw.Firework([], state="COMPLETED", fw_id=1)
two = fw.Firework([], state="COMPLETED", fw_id=2)
self.assertEqual(fw.Workflow([one, two]).state, "COMPLETED")
def make_packing_workflow(spec, simple=True):
"""Create an entire Isotherm creation Workflow
Parameters
----------
spec : dict
has all the information for workflow
simple : bool, optional
use decorrelation analysis to determine if to run more sims
Returns
-------
workflow : fw.Workflow
Workflow object ready to submit to LaunchPad
"""
temperatures = spec['temperatures']
pressures = spec['pressures']
nparallel = spec['nparallel']
ncycles = spec['ncycles']
template = spec['template']
workdir = spec['workdir']
wfname = spec['name']
if not isinstance(template, dict):
dict_template = False
# Passed path to template
# if passed path to template, slurp it up
# old method of slurping up directory
stuff = utils.slurp_directory(template)
else:
dict_template = True
# Else passed dict of stuff
stuff = template
simfmt = utils.guess_format(stuff)
stuff = utils.escape_template(stuff)
if dict_template:
init = fw.Firework(firetasks.InitTemplate(contents=stuff,
workdir=workdir),
spec={'_category': wfname},
name='Template Init')
setup = [init]
else:
init = None
setup = []
simulations = [] # list of simulation fireworks
post_processing = [] # list of post processing fireworks
for T, P in itertools.product(temperatures, pressures):
this_condition = make_Simfireworks(
parent_fw=init,
T=T,
P=P,
ncycles=ncycles,
nparallel=nparallel,
simfmt=simfmt,
wfname=wfname,
template=template,
workdir=workdir,
)
this_condition_PP = make_PostProcess(
parent_fw=this_condition,
T=T,
P=P,
wfname=wfname,
simple=simple,
)
simulations.extend(this_condition)
post_processing.append(this_condition_PP)
flat_decide = fw.Firework(CapacityDecider(), )
iso_create = fw.Firework(firetasks.IsothermCreate(workdir=workdir),
parents=post_processing,
spec={'_category': wfname},
name='Isotherm create')
wf = fw.Workflow(
setup + simulations + post_processing + [iso_create],
name=wfname,
metadata={'GCMCWorkflow': True}, # tag as GCMCWorkflow workflow
)
return wf
def test_fizzled_5(self):
# leaf is fizzled, wf is fizzled
one = fw.Firework([], state="COMPLETED", fw_id=1)
two = fw.Firework([], state="FIZZLED", fw_id=2, parents=one)
self.assertEqual(fw.Workflow([one, two]).state, "FIZZLED")
def test_running_1(self):
one = fw.Firework([], state="COMPLETED", fw_id=1)
two = fw.Firework([], state="READY", fw_id=2, parents=one)
self.assertEqual(fw.Workflow([one, two]).state, "RUNNING")