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_swarm(self):
"""
Test (pychemia.searcher.swarm) with LJ Clusters :
"""
if not has_connection():
return
pcm_log.debug('ParticleSwarm')
popu = LJCluster('test', composition='Xe13', refine=False, direct_evaluation=True)
popu.pcdb.clean()
searcher = ParticleSwarm(popu, generation_size=8, stabilization_limit=3)
searcher.run()
popu.pcdb.clean()
def notest_searcher():
"""
Test (pychemia.searcher) with LJ Clusters :
"""
if not has_connection():
return
p1 = multiprocessing.Process(target=lj_searcher)
p2 = multiprocessing.Process(target=evaluator)
p1.start()
time.sleep(10)
p2.start()
def notest_searcher():
"""
Testing HarmonySearch :
"""
if not has_connection():
return
p1 = multiprocessing.Process(target=searcher)
p2 = multiprocessing.Process(target=evaluator)
p1.start()
time.sleep(10)
p2.start()
def test_queue():
"""
Tests (pychemia.db.PyChemiaQueue) :
"""
if not has_connection():
return
print("Testing PyChemiaQueue")
source = 'pychemia/test/data/vasp_01'
destination = tempfile.mkdtemp()
print('Destination: %s' % destination)
st = pychemia.code.vasp.read_poscar(source + os.sep + 'POSCAR')
print('Structure: \n%s' % st)
vi = pychemia.code.vasp.read_incar(source + os.sep + 'INCAR')
print('VASP Input: \n%s' % vi)
pq = pychemia.db.PyChemiaQueue()
files = [source + os.sep + 'KPOINTS']
entry_id = pq.new_entry(structure=st,
variables=vi,
code='vasp',
files=files)
nfiles = pq.db.fs.files.count()
print('Number of files: ', nfiles)
pychemia.code.vasp.write_from_queue(pq, entry_id, destination)
for i in os.listdir(source):
assert hashfile(source + os.sep + i) == hashfile(destination + os.sep +
i)
print('Files in source and destination are identical')
print(
'Adding the same entry again and testing that the number of files is unchanged'
)
entry_id = pq.new_entry(structure=st,
variables=vi,
code='vasp',
files=files)
assert nfiles == pq.db.fs.files.count()
print('The number of files remains the same ', nfiles)
shutil.rmtree(destination)
def test_harmony(self):
"""
Tests (pychemia.searcher.harmony) with LJ Clusters :
"""
if not has_connection():
return
pcm_log.debug('HarmonySearch')
popu = LJCluster('test',
composition='Xe13',
refine=False,
direct_evaluation=True)
popu.pcdb.clean()
searcher = HarmonySearch(popu,
generation_size=8,
stabilization_limit=3)
searcher.run()
popu.pcdb.clean()
def test_queue():
"""
Tests (pychemia.db.PyChemiaQueue) :
"""
if not has_connection():
return
print("Testing PyChemiaQueue")
source = 'tests/data/vasp_01'
destination = tempfile.mkdtemp()
print('Destination: %s' % destination)
st = pychemia.code.vasp.read_poscar(source + os.sep + 'POSCAR')
print('Structure: \n%s' % st)
vi = pychemia.code.vasp.read_incar(source + os.sep + 'INCAR')
print('VASP Input: \n%s' % vi)
pq = pychemia.db.PyChemiaQueue()
files = [source + os.sep + 'KPOINTS']
entry_id = pq.new_entry(structure=st, variables=vi, code='vasp', files=files)
nfiles = pq.db.fs.files.count()
print('Number of files: ', nfiles)
pychemia.code.vasp.write_from_queue(pq, entry_id, destination)
for i in os.listdir(source):
assert hashfile(source + os.sep + i) == hashfile(destination + os.sep + i)
print('Files in source and destination are identical')
print('Adding the same entry again and testing that the number of files is unchanged')
entry_id = pq.new_entry(structure=st, variables=vi, code='vasp', files=files)
assert nfiles == pq.db.fs.files.count()
print('The number of files remains the same ', nfiles)
shutil.rmtree(destination)