def test_simulated(self):
exp_dataframe = pd.read_pickle(
os.path.join(CAMD_TEST_FILES, "mn-ni-o-sb.pickle"))
experiment = ATFSampler(exp_dataframe)
candidate_data = exp_dataframe.iloc[:, :-11]
# Set up agents and loop parameters
agent = AgentStabilityAdaBoost(
model=MLPRegressor(hidden_layer_sizes=(84, 50)),
n_query=2,
hull_distance=0.2,
exploit_fraction=1.0,
uncertainty=True,
alpha=0.5,
diversify=True,
n_estimators=20)
analyzer = StabilityAnalyzer(hull_distance=0.2)
# Reduce seed_data
icsd_data = load_dataframe("oqmd1.2_exp_based_entries_featurized_v2")
seed_data = filter_dataframe_by_composition(icsd_data, "MnNiOSb")
leftover = ~icsd_data.index.isin(seed_data.index)
# Add some random other data to test compositional flexibility
seed_data = seed_data.append(icsd_data.loc[leftover].sample(30))
del icsd_data
with ScratchDir('.'):
campaign = ProtoDFTCampaign(candidate_data=candidate_data,
agent=agent,
experiment=experiment,
analyzer=analyzer,
seed_data=seed_data,
heuristic_stopper=5)
campaign.autorun()
self.assertTrue(os.path.isfile('hull_finalized.png'))
def test_simple_dft(self):
with ScratchDir('.'):
campaign = ProtoDFTCampaign.from_chemsys("Si")
# Nerf agent a bit
agent = AgentStabilityML5(n_query=2)
campaign.agent = agent
campaign.autorun()
def run_campaign(self, **kwargs):
"""
Runs the campaign for a given chemsys
Args:
**kwargs: keyword-args for a given campaign,
specific to invocation method below i. e.
proto-dft/oqmd-atf require {'chemsys': CHEMSYS}
meta-agent requires {'name': NAME}
Returns:
None
"""
if self.campaign == "proto-dft-2":
campaign = ProtoDFTCampaign.from_chemsys(**kwargs)
elif self.campaign == "oqmd-atf":
# This is more or less just a test
campaign = CloudATFCampaign.from_chemsys(**kwargs)
elif self.campaign.startswith("meta-agent"):
# For meta-agent campaigns, submit with meta_agent/CAMPAIGN_NAME
campaign = MetaAgentCampaign.from_reserved_name(**kwargs)
else:
raise ValueError("Campaign {} is not valid".format(self.campaign))
campaign.autorun()
def main():
"""Utility function to run a reserved name campaign"""
args = docopt(__doc__)
campaign_type = args['CAMPAIGN_TYPE']
campaign_name = args['CAMPAIGN_NAME']
cwd = os.getcwd()
if args['--scratch']:
dirpath = tempfile.mkdtemp()
os.chdir(dirpath)
# Switch for different campaign types
if campaign_type.startswith("proto-dft"):
prefix = "{}/runs".format(campaign_type)
campaign = ProtoDFTCampaign.from_chemsys(campaign_name, prefix=prefix)
elif campaign_type == "meta_agent":
campaign = MetaAgentCampaign.from_reserved_name(campaign_name)
else:
raise ValueError(
"{} is not a supported campaign type".format(campaign_type))
campaign.autorun()
# Cleanup
if args['--scratch']:
os.chdir(cwd)
shutil.rmtree(dirpath)
def run_campaign(self, *args):
"""
Runs the campaign for a given chemsys
Args:
*args: args for a given campaign,
specific to invocation method below i. e.
proto-dft/oqmd-atf require CHEMSYS
meta-agent requires NAME
Returns:
None
"""
if self.campaign.startswith("proto-dft-high"):
campaign = ProtoDFTCampaign.from_chemsys_high_quality(*args)
elif self.campaign.startswith("proto-dft"):
campaign = ProtoDFTCampaign.from_chemsys(*args)
elif self.campaign.startswith("oqmd-atf"):
# This is more or less just a test
campaign = CloudATFCampaign.from_chemsys(*args)
elif self.campaign.startswith("meta-agent"):
# For meta-agent campaigns, submit with meta_agent/CAMPAIGN_NAME
campaign = MetaAgentCampaign.from_reserved_name(*args)
else:
raise ValueError("Campaign {} is not valid".format(self.campaign))
# Capture errors and store
if self.catch_errors:
try:
campaign.autorun()
except Exception as e:
error_msg = {
"error": "{}".format(e),
"traceback": traceback.format_exc()
}
campaign.logger.info("Error: {}".format(e))
campaign.logger.info("Traceback: {}".format(
traceback.format_exc()))
dumpfn(error_msg, "error.json")
dumpfn({"status": "error"}, "job_status.json")
campaign.s3_sync()
else:
campaign.autorun()
def test_simulated(self):
exp_dataframe = pd.read_pickle(
os.path.join(CAMD_TEST_FILES, "mn-ni-o-sb.pickle"))
experiment = ATFSampler(exp_dataframe)
candidate_data = exp_dataframe.iloc[:, :-11]
agent = RandomAgent(n_query=2)
analyzer = StabilityAnalyzer(hull_distance=0.2)
# Reduce seed_data
seed_data = load_dataframe("oqmd1.2_exp_based_entries_featurized_v2")
seed_data = filter_dataframe_by_composition(seed_data, "MnNiOSb")
with ScratchDir('.'):
campaign = ProtoDFTCampaign(candidate_data=candidate_data,
agent=agent,
experiment=experiment,
analyzer=analyzer,
seed_data=seed_data,
heuristic_stopper=5)
campaign.autorun()
def test_cached_campaign(self):
with ScratchDir('.'):
campaign = ProtoDFTCampaign.from_chemsys_high_quality("Si")
# Test seed data has other data
self.assertGreater(len(campaign.seed_data), 36581)