def test_firefly(self):
"""
Tests (pychemia.searcher.firefly) with LJ Clusters :
"""
if not has_connection():
return
pcm_log.debug('FireFly')
popu = LJCluster('test',
composition='Xe13',
refine=True,
direct_evaluation=True)
popu.pcdb.clean()
searcher = FireFly(popu, generation_size=8, stabilization_limit=3)
searcher.run()
popu.pcdb.clean()
searcher = FireFly(popu, {
'delta': 0.1,
'gamma': 0.1,
'beta0': 0.8,
'alpha0': 0,
'multi_move': True
},
generation_size=8,
stabilization_limit=3)
searcher.run()
popu.pcdb.clean()
def test_firefly(self):
"""
Tests (pychemia.searcher.firefly) :
"""
pcm_log.debug('FireFly')
mini = Sphere().minimum(3)
popu = RealFunction(Sphere.function,
3, [-1, 1],
local_minimization=False)
searcher = FireFly(popu, generation_size=16, stabilization_limit=5)
searcher.run()
popu = RealFunction(Sphere.function,
3, [-1, 1],
local_minimization=True)
searcher = FireFly(popu, {
'delta': 0.1,
'gamma': 0.1,
'beta0': 0.8,
'alpha0': 0,
'multi_move': True
},
generation_size=16,
stabilization_limit=5)
searcher.run()
assert np.linalg.norm(
np.array(searcher.population.db[searcher.population.best_candidate]
['x']) - mini) < 0.2
def search(db_settings, search_settings, abipath):
pcdb = get_database(db_settings)
print("[%s] Path for abinit.in: %s" % (pcdb.name, abipath))
popu = OrbitalDFTU(pcdb, abipath + os.sep + 'abinit.in')
if 'generation_size' in search_settings:
generation_size = search_settings.pop('generation_size')
else:
generation_size = 32
if 'stabilization_limit' in search_settings:
stabilization_limit = search_settings.pop('stabilization_limit')
else:
stabilization_limit = 10
fire = FireFly(popu, params=search_settings, generation_size=generation_size,
stabilization_limit=stabilization_limit)
fire.run()
def search(db_settings, search_settings, abipath):
pcdb = get_database(db_settings)
print("[%s] Path for abinit.in: %s" % (pcdb.name, abipath))
popu = OrbitalDFTU(pcdb, abipath + os.sep + 'abinit.in')
if 'generation_size' in search_settings:
generation_size = search_settings.pop('generation_size')
else:
generation_size = 32
if 'stabilization_limit' in search_settings:
stabilization_limit = search_settings.pop('stabilization_limit')
else:
stabilization_limit = 10
fire = FireFly(popu,
params=search_settings,
generation_size=generation_size,
stabilization_limit=stabilization_limit)
fire.run()
def test_firefly(self):
"""
Test (pychemia.searcher.firefly) with NonCollinearMagMoms :
"""
logging.basicConfig(level=logging.DEBUG)
if not HAS_PYMONGO:
print('Could not load pymongo, leaving now')
return
else:
if not has_local_mongo():
return
pcm_log.debug('HarmonySearch')
source = 'tests/data/vasp_02'
assert os.path.isfile(source + os.sep + 'INCAR')
assert os.path.isfile(source + os.sep + 'POSCAR')
popu = NonCollinearMagMoms('test', source, debug=True)
popu.pcdb.clean()
searcher = FireFly(popu, generation_size=16, stabilization_limit=5)
searcher.run()
popu.pcdb.clean()
def test_firefly(self):
"""
Tests (pychemia.searcher.firefly) with NonCollinearMagMoms :
"""
logging.basicConfig(level=logging.DEBUG)
if not HAS_PYMONGO:
print('Could not load pymongo, leaving now')
return
else:
if not has_local_mongo():
return
pcm_log.debug('HarmonySearch')
source = 'pychemia/test/data/vasp_02'
assert os.path.isfile(source + os.sep + 'INCAR')
assert os.path.isfile(source + os.sep + 'POSCAR')
popu = NonCollinearMagMoms('test', source, debug=True)
popu.pcdb.clean()
searcher = FireFly(popu, generation_size=16, stabilization_limit=5)
searcher.run()
popu.pcdb.clean()
def test_firefly(self):
"""
Tests (pychemia.searcher.firefly) :
"""
pcm_log.debug('FireFly')
mini = Sphere().minimum(3)
popu = RealFunction(Sphere.function, 3, [-1, 1], local_minimization=False)
searcher = FireFly(popu, generation_size=16, stabilization_limit=5)
searcher.run()
popu = RealFunction(Sphere.function, 3, [-1, 1], local_minimization=True)
searcher = FireFly(popu, {'delta': 0.1, 'gamma': 0.1, 'beta0': 0.8, 'alpha0': 0, 'multi_move': True},
generation_size=16, stabilization_limit=5)
searcher.run()
assert np.linalg.norm(np.array(searcher.population.db[searcher.population.best_candidate]['x']) - mini) < 0.2
def test_firefly(self):
"""
Tests (pychemia.searcher.firefly) with LJ Clusters :
"""
pcm_log.debug('FireFly')
popu = LJCluster('test', composition='Xe13', refine=True, direct_evaluation=True)
popu.pcdb.clean()
searcher = FireFly(popu, generation_size=8, stabilization_limit=3)
searcher.run()
popu.pcdb.clean()
searcher = FireFly(popu, {'delta': 0.1, 'gamma': 0.1, 'beta0': 0.8, 'alpha0': 0, 'multi_move': True},
generation_size=8, stabilization_limit=3)
searcher.run()
popu.pcdb.clean()