def test_generate_by_line2():
pm = ParameterHelper(verbose="DEBUG")
pm.define_group("specie", "O", ["O"])
pm.define_group("specie", "rest", ["C", "H"])
pm.define_group("twobody", "**", ["*", "*"])
pm.define_group("twobody", "OO", ["O", "O"])
pm.define_group("threebody", "***", ["*", "*", "*"])
pm.define_group("threebody", "Oall", ["O", "O", "O"])
pm.set_parameters("**", [1, 0.5])
pm.set_parameters("OO", [1, 0.5])
pm.set_parameters("Oall", [1, 0.5])
pm.set_parameters("***", [1, 0.5])
pm.set_parameters("cutoff_twobody", 5)
pm.set_parameters("cutoff_threebody", 4)
hm = pm.as_dict()
Parameters.check_instantiation(hm["hyps"], hm["cutoffs"], hm["kernels"], hm)
def test_generate_by_line2():
pm = ParameterHelper(verbose="DEBUG")
pm.define_group('specie', 'O', ['O'])
pm.define_group('specie', 'rest', ['C', 'H'])
pm.define_group('twobody', '**', ['*', '*'])
pm.define_group('twobody', 'OO', ['O', 'O'])
pm.define_group('threebody', '***', ['*', '*', '*'])
pm.define_group('threebody', 'Oall', ['O', 'O', 'O'])
pm.set_parameters('**', [1, 0.5])
pm.set_parameters('OO', [1, 0.5])
pm.set_parameters('Oall', [1, 0.5])
pm.set_parameters('***', [1, 0.5])
pm.set_parameters('cutoff_twobody', 5)
pm.set_parameters('cutoff_threebody', 4)
hm = pm.as_dict()
Parameters.check_instantiation(
hm['hyps'], hm['cutoffs'], hm['kernels'], hm)
def generate_hm(ntwobody,
nthreebody,
nmanybody=1,
constraint=False,
multihyps=True):
cutoff = 0.8
if multihyps is False:
kernels = []
parameters = {}
if ntwobody > 0:
kernels += ["twobody"]
parameters["cutoff_twobody"] = cutoff
if nthreebody > 0:
kernels += ["threebody"]
parameters["cutoff_threebody"] = cutoff
if nmanybody > 0:
kernels += ["manybody"]
parameters["cutoff_manybody"] = cutoff
pm = ParameterHelper(kernels=kernels,
random=True,
parameters=parameters)
hm = pm.as_dict()
hyps = hm["hyps"]
cut = hm["cutoffs"]
return hyps, hm, cut
pm = ParameterHelper(species=["H", "He"], parameters={"noise": 0.05})
if ntwobody > 0:
pm.define_group("twobody", "b1", ["*", "*"], parameters=random(2))
pm.set_parameters("cutoff_twobody", cutoff)
if nthreebody > 0:
pm.define_group("threebody",
"t1", ["*", "*", "*"],
parameters=random(2))
pm.set_parameters("cutoff_threebody", cutoff)
if nmanybody > 0:
pm.define_group("manybody",
"manybody1", ["*", "*"],
parameters=random(2))
pm.set_parameters("cutoff_manybody", cutoff)
if ntwobody > 1:
pm.define_group("twobody", "b2", ["H", "H"], parameters=random(2))
if nthreebody > 1:
pm.define_group("threebody",
"t2", ["H", "H", "H"],
parameters=random(2))
if constraint is False:
hm = pm.as_dict()
hyps = hm["hyps"]
cut = hm["cutoffs"]
return hyps, hm, cut
pm.set_constraints("b1", opt=[True, False])
pm.set_constraints("t1", opt=[False, True])
hm = pm.as_dict()
hyps = hm["hyps"]
cut = hm["cutoffs"]
return hyps, hm, cut
def generate_hm(ntwobody, nthreebody, nmanybody=1, constraint=False, multihyps=True):
cutoff = 0.8
if (multihyps is False):
kernels = []
parameters = {}
if (ntwobody > 0):
kernels += ['twobody']
parameters['cutoff_twobody'] = cutoff
if (nthreebody > 0):
kernels += ['threebody']
parameters['cutoff_threebody'] = cutoff
if (nmanybody > 0):
kernels += ['manybody']
parameters['cutoff_manybody'] = cutoff
pm = ParameterHelper(kernels=kernels, random=True,
parameters=parameters)
hm = pm.as_dict()
hyps = hm['hyps']
cut = hm['cutoffs']
return hyps, hm, cut
pm = ParameterHelper(species=['H', 'He'], parameters={'noise':0.05})
if (ntwobody > 0):
pm.define_group('twobody', 'b1', ['*', '*'], parameters=random(2))
pm.set_parameters('cutoff_twobody', cutoff)
if (nthreebody > 0):
pm.define_group('threebody', 't1', ['*', '*', '*'], parameters=random(2))
pm.set_parameters('cutoff_threebody', cutoff)
if (nmanybody > 0):
pm.define_group('manybody', 'manybody1', ['*', '*'], parameters=random(2))
pm.set_parameters('cutoff_manybody', cutoff)
if (ntwobody > 1):
pm.define_group('twobody', 'b2', ['H', 'H'], parameters=random(2))
if (nthreebody > 1):
pm.define_group('threebody', 't2', ['H', 'H', 'H'], parameters=random(2))
if (constraint is False):
hm = pm.as_dict()
hyps = hm['hyps']
cut = hm['cutoffs']
return hyps, hm, cut
pm.set_constraints('b1', opt=[True, False])
pm.set_constraints('t1', opt=[False, True])
hm = pm.as_dict()
hyps = hm['hyps']
cut = hm['cutoffs']
return hyps, hm, cut
def generate_diff_hm(kernels, diff_cutoff=False, constraint=False):
pm = ParameterHelper(species=["H", "He"], parameters={"noise": 0.05})
if "twobody" in kernels:
para1 = 2.5 + 0.1 * random(3)
para2 = 2.5 + 0.1 * random(3)
pm.set_parameters("cutoff_twobody", para1[-1])
pm.define_group("twobody", "twobody0", ["*", "*"])
pm.set_parameters("twobody0", para1[:-1], not constraint)
pm.define_group("twobody", "twobody1", ["H", "H"], para2[:-1])
if diff_cutoff:
pm.set_parameters("twobody0", para1, not constraint)
pm.set_parameters("twobody1", para2)
if "threebody" in kernels:
para1 = 1.2 + 0.1 * random(3)
para2 = 1.2 + 0.1 * random(3)
pm.set_parameters("cutoff_threebody", para1[-1])
pm.define_group("threebody", "threebody0", ["*", "*", "*"], para1[:-1])
pm.set_parameters("threebody0", para1[:-1], not constraint)
pm.define_group("threebody", "threebody1", ["H", "H", "H"], para2[:-1])
if diff_cutoff:
pm.define_group("cut3b", "c1", ["*", "*"], parameters=para1)
pm.define_group("cut3b", "c2", ["H", "H"], parameters=para2)
if "manybody" in kernels:
para1 = 1.2 + 0.1 * random(3)
para2 = 1.2 + 0.1 * random(3)
pm.set_parameters("cutoff_manybody", para1[-1])
pm.define_group("manybody", "manybody0", ["*", "*"])
pm.set_parameters("manybody0", para1[:-1], not constraint)
pm.define_group("manybody", "manybody1", ["H", "H"], para2[:-1])
if diff_cutoff:
pm.set_parameters("manybody0", para1, not constraint)
pm.set_parameters("manybody1", para2)
hm = pm.as_dict()
hyps = hm["hyps"]
cut = hm["cutoffs"]
return cut, hyps, hm
def generate_same_hm(kernels, multi_cutoff=False):
"""
generate hyperparameter and masks that are effectively the same
but with single or multi group expression
"""
pm1 = ParameterHelper(species=["H", "He"], parameters={"noise": 0.05})
pm2 = ParameterHelper(species=["H", "He"], parameters={"noise": 0.05})
if "twobody" in kernels:
para = 2.5 + 0.1 * random(3)
pm1.set_parameters("cutoff_twobody", para[-1])
pm1.define_group("twobody", "twobody0", ["*", "*"], para[:-1])
pm2.set_parameters("cutoff_twobody", para[-1])
pm2.define_group("twobody", "twobody0", ["*", "*"], para[:-1])
pm2.define_group("twobody", "twobody1", ["H", "H"], para[:-1])
if multi_cutoff:
pm2.set_parameters("twobody0", para)
pm2.set_parameters("twobody1", para)
if "threebody" in kernels:
para = 1.2 + 0.1 * random(3)
pm1.set_parameters("cutoff_threebody", para[-1])
pm1.define_group("threebody", "threebody0", ["*", "*", "*"], para[:-1])
pm2.set_parameters("cutoff_threebody", para[-1])
pm2.define_group("threebody", "threebody0", ["*", "*", "*"], para[:-1])
pm2.define_group("threebody", "threebody1", ["H", "H", "H"], para[:-1])
if multi_cutoff:
pm2.define_group("cut3b", "c1", ["*", "*"], parameters=para)
pm2.define_group("cut3b", "c2", ["H", "H"], parameters=para)
if "manybody" in kernels:
para = 1.2 + 0.1 * random(3)
pm1.set_parameters("cutoff_manybody", para[-1])
pm1.define_group("manybody", "manybody0", ["*", "*"], para[:-1])
pm2.set_parameters("cutoff_manybody", para[-1])
pm2.define_group("manybody", "manybody0", ["*", "*"], para[:-1])
pm2.define_group("manybody", "manybody1", ["H", "H"], para[:-1])
if multi_cutoff:
pm2.set_parameters("manybody0", para)
pm2.set_parameters("manybody1", para)
hm1 = pm1.as_dict()
hyps1 = hm1["hyps"]
cut = hm1["cutoffs"]
hm2 = pm2.as_dict()
hyps2 = hm2["hyps"]
cut = hm2["cutoffs"]
return cut, hyps1, hyps2, hm1, hm2
def test_generate_by_line():
pm = ParameterHelper(verbose="DEBUG")
pm.define_group('specie', 'O', ['O'])
pm.define_group('specie', 'C', ['C'])
pm.define_group('specie', 'H', ['H'])
pm.define_group('twobody', '**', ['C', 'H'])
pm.define_group('twobody', 'OO', ['O', 'O'], atomic_str=True)
pm.define_group('threebody', '***', ['O', 'O', 'C'])
pm.define_group('threebody', 'OOO', ['O', 'O', 'O'])
pm.define_group('manybody', '1.5', ['C', 'H'])
pm.define_group('manybody', '1.5', ['C', 'O'])
pm.define_group('manybody', '1.5', ['O', 'H'])
pm.define_group('manybody', '2', ['O', 'O'])
pm.define_group('manybody', '2', ['H', 'O'])
pm.define_group('manybody', '2.8', ['O', 'O'])
pm.set_parameters('**', [1, 0.5])
pm.set_parameters('OO', [1, 0.5])
pm.set_parameters('***', [1, 0.5])
pm.set_parameters('OOO', [1, 0.5])
pm.set_parameters('1.5', [1, 0.5, 1.5])
pm.set_parameters('2', [1, 0.5, 2])
pm.set_parameters('2.8', [1, 0.5, 2.8])
pm.set_constraints('2', [True, False])
pm.set_constraints('2.8', False)
pm.set_parameters('cutoff_twobody', 5)
pm.set_parameters('cutoff_threebody', 4)
pm.set_parameters('cutoff_manybody', 3)
hm = pm.as_dict()
Parameters.check_instantiation(
hm['hyps'], hm['cutoffs'], hm['kernels'], hm)
def test_generate_by_line():
pm = ParameterHelper(verbose="DEBUG")
pm.define_group("specie", "O", ["O"])
pm.define_group("specie", "C", ["C"])
pm.define_group("specie", "H", ["H"])
pm.define_group("twobody", "**", ["C", "H"])
pm.define_group("twobody", "OO", ["O", "O"], atomic_str=True)
pm.define_group("threebody", "***", ["O", "O", "C"])
pm.define_group("threebody", "OOO", ["O", "O", "O"])
pm.define_group("manybody", "1.5", ["C", "H"])
pm.define_group("manybody", "1.5", ["C", "O"])
pm.define_group("manybody", "1.5", ["O", "H"])
pm.define_group("manybody", "2", ["O", "O"])
pm.define_group("manybody", "2", ["H", "O"])
pm.define_group("manybody", "2.8", ["O", "O"])
pm.set_parameters("**", [1, 0.5])
pm.set_parameters("OO", [1, 0.5])
pm.set_parameters("***", [1, 0.5])
pm.set_parameters("OOO", [1, 0.5])
pm.set_parameters("1.5", [1, 0.5, 1.5])
pm.set_parameters("2", [1, 0.5, 2])
pm.set_parameters("2.8", [1, 0.5, 2.8])
pm.set_constraints("2", [True, False])
pm.set_constraints("2.8", False)
pm.set_parameters("cutoff_twobody", 5)
pm.set_parameters("cutoff_threebody", 4)
pm.set_parameters("cutoff_manybody", 3)
hm = pm.as_dict()
Parameters.check_instantiation(hm["hyps"], hm["cutoffs"], hm["kernels"], hm)
def generate_diff_hm(kernels, diff_cutoff=False, constraint=False):
pm = ParameterHelper(species=['H', 'He'], parameters={'noise': 0.05})
if ('twobody' in kernels):
para1 = 2.5 + 0.1 * random(3)
para2 = 2.5 + 0.1 * random(3)
pm.set_parameters('cutoff_twobody', para1[-1])
pm.define_group('twobody', 'twobody0', ['*', '*'])
pm.set_parameters('twobody0', para1[:-1], not constraint)
pm.define_group('twobody', 'twobody1', ['H', 'H'], para2[:-1])
if (diff_cutoff):
pm.set_parameters('twobody0', para1, not constraint)
pm.set_parameters('twobody1', para2)
if ('threebody' in kernels):
para1 = 1.2 + 0.1 * random(3)
para2 = 1.2 + 0.1 * random(3)
pm.set_parameters('cutoff_threebody', para1[-1])
pm.define_group('threebody', 'threebody0', ['*', '*', '*'], para1[:-1])
pm.set_parameters('threebody0', para1[:-1], not constraint)
pm.define_group('threebody', 'threebody1', ['H', 'H', 'H'], para2[:-1])
if (diff_cutoff):
pm.define_group('cut3b', 'c1', ['*', '*'], parameters=para1)
pm.define_group('cut3b', 'c2', ['H', 'H'], parameters=para2)
if ('manybody' in kernels):
para1 = 1.2 + 0.1 * random(3)
para2 = 1.2 + 0.1 * random(3)
pm.set_parameters('cutoff_manybody', para1[-1])
pm.define_group('manybody', 'manybody0', ['*', '*'])
pm.set_parameters('manybody0', para1[:-1], not constraint)
pm.define_group('manybody', 'manybody1', ['H', 'H'], para2[:-1])
if (diff_cutoff):
pm.set_parameters('manybody0', para1, not constraint)
pm.set_parameters('manybody1', para2)
hm = pm.as_dict()
hyps = hm['hyps']
cut = hm['cutoffs']
return cut, hyps, hm
def generate_same_hm(kernels, multi_cutoff=False):
"""
generate hyperparameter and masks that are effectively the same
but with single or multi group expression
"""
pm1 = ParameterHelper(species=['H', 'He'], parameters={'noise': 0.05})
pm2 = ParameterHelper(species=['H', 'He'], parameters={'noise': 0.05})
if ('twobody' in kernels):
para = 2.5 + 0.1 * random(3)
pm1.set_parameters('cutoff_twobody', para[-1])
pm1.define_group('twobody', 'twobody0', ['*', '*'], para[:-1])
pm2.set_parameters('cutoff_twobody', para[-1])
pm2.define_group('twobody', 'twobody0', ['*', '*'], para[:-1])
pm2.define_group('twobody', 'twobody1', ['H', 'H'], para[:-1])
if (multi_cutoff):
pm2.set_parameters('twobody0', para)
pm2.set_parameters('twobody1', para)
if ('threebody' in kernels):
para = 1.2 + 0.1 * random(3)
pm1.set_parameters('cutoff_threebody', para[-1])
pm1.define_group('threebody', 'threebody0', ['*', '*', '*'], para[:-1])
pm2.set_parameters('cutoff_threebody', para[-1])
pm2.define_group('threebody', 'threebody0', ['*', '*', '*'], para[:-1])
pm2.define_group('threebody', 'threebody1', ['H', 'H', 'H'], para[:-1])
if (multi_cutoff):
pm2.define_group('cut3b', 'c1', ['*', '*'], parameters=para)
pm2.define_group('cut3b', 'c2', ['H', 'H'], parameters=para)
if ('manybody' in kernels):
para = 1.2 + 0.1 * random(3)
pm1.set_parameters('cutoff_manybody', para[-1])
pm1.define_group('manybody', 'manybody0', ['*', '*'], para[:-1])
pm2.set_parameters('cutoff_manybody', para[-1])
pm2.define_group('manybody', 'manybody0', ['*', '*'], para[:-1])
pm2.define_group('manybody', 'manybody1', ['H', 'H'], para[:-1])
if (multi_cutoff):
pm2.set_parameters('manybody0', para)
pm2.set_parameters('manybody1', para)
hm1 = pm1.as_dict()
hyps1 = hm1['hyps']
cut = hm1['cutoffs']
hm2 = pm2.as_dict()
hyps2 = hm2['hyps']
cut = hm2['cutoffs']
return cut, hyps1, hyps2, hm1, hm2