Commit 05fabfb7 authored by Malthe Kjær Bisbo's avatar Malthe Kjær Bisbo
Browse files

moved OperationConstraint to utils, wrote __init__ in surrogate folder and...

moved OperationConstraint to utils, wrote __init__ in surrogate folder and changed some class names to have capital letters, changed candidate_operations folder to candidates
parent 62fa4a29
from surrogate.gpr import GPR
from surrogate.descriptor.fingerprint import Fingerprint
from surrogate.prior.prior import RepulsivePrior
__all__ = ['GPR', 'Fingerprint', 'RepulsivePrior']
\ No newline at end of file
...@@ -2,9 +2,9 @@ import numpy as np ...@@ -2,9 +2,9 @@ import numpy as np
from scipy.linalg import cholesky, cho_solve, solve_triangular from scipy.linalg import cholesky, cho_solve, solve_triangular
from scipy.optimize import fmin_l_bfgs_b from scipy.optimize import fmin_l_bfgs_b
from surrogate.kernel import gauss_kernel, double_gauss_kernel from surrogate.kernel import GaussKernel, DoubleGaussKernel
from surrogate.descriptor.fingerprint import Fingerprint from surrogate import Fingerprint
from surrogate.prior.prior import repulsive_prior from surrogate import RepulsivePrior
from surrogate.gpr_calculator import gpr_calculator from surrogate.gpr_calculator import gpr_calculator
class gpr_memory(): class gpr_memory():
...@@ -89,14 +89,14 @@ class GPR(): ...@@ -89,14 +89,14 @@ class GPR():
Nsplit_eta = self.descriptor.Nelements_2body Nsplit_eta = self.descriptor.Nelements_2body
if kernel is 'single': if kernel is 'single':
self.kernel = gauss_kernel(Nsplit_eta=Nsplit_eta) self.kernel = GaussKernel(Nsplit_eta=Nsplit_eta)
elif kernel is 'double': elif kernel is 'double':
self.kernel = double_gauss_kernel(Nsplit_eta=Nsplit_eta) self.kernel = DoubleGaussKernel(Nsplit_eta=Nsplit_eta)
else: else:
self.kernel = kernel self.kernel = kernel
if prior is None: if prior is None:
self.prior = repulsive_prior() self.prior = RepulsivePrior()
else: else:
self.prior = prior self.prior = prior
......
...@@ -5,7 +5,7 @@ from scipy.spatial.distance import pdist, cdist, squareform ...@@ -5,7 +5,7 @@ from scipy.spatial.distance import pdist, cdist, squareform
from time import time from time import time
class kernel(ABC): class Kernel(ABC):
def __init__(self): def __init__(self):
self._theta = None self._theta = None
...@@ -79,7 +79,7 @@ class kernel(ABC): ...@@ -79,7 +79,7 @@ class kernel(ABC):
return dK_dTheta return dK_dTheta
class gauss_kernel(kernel): class GaussKernel(Kernel):
def __init__(self, amplitude=100.0, amplitude_bounds=(1e0, 1e5), def __init__(self, amplitude=100.0, amplitude_bounds=(1e0, 1e5),
length_scale=10.0, length_scale_bounds=(1e0, 1e3), length_scale=10.0, length_scale_bounds=(1e0, 1e3),
noise=1e-5, noise_bounds=None, noise=1e-5, noise_bounds=None,
...@@ -284,7 +284,7 @@ class gauss_kernel(kernel): ...@@ -284,7 +284,7 @@ class gauss_kernel(kernel):
class double_gauss_kernel(kernel): class DoubleGaussKernel(Kernel):
def __init__(self, amplitude=100., amplitude_bounds=(1e1,1e5), def __init__(self, amplitude=100., amplitude_bounds=(1e1,1e5),
length_scale1=10.0, length_scale1_bounds=(1e0, 1e3), length_scale1=10.0, length_scale1_bounds=(1e0, 1e3),
length_scale2=10.0, length_scale2_bounds=(1e0, 1e3), length_scale2=10.0, length_scale2_bounds=(1e0, 1e3),
......
...@@ -44,8 +44,7 @@ def convert_atom_types(num): ...@@ -44,8 +44,7 @@ def convert_atom_types(num):
num_converted[i] = j num_converted[i] = j
return num_converted return num_converted
class repulsive_prior(): class RepulsivePrior():
def __init__(self, rcut=6, ratio_of_covalent_radii=0.7): def __init__(self, rcut=6, ratio_of_covalent_radii=0.7):
self.rcut = rcut self.rcut = rcut
self.ratio_of_covalent_radii = ratio_of_covalent_radii self.ratio_of_covalent_radii = ratio_of_covalent_radii
......
...@@ -17,7 +17,6 @@ class test_gpr(unittest.TestCase): ...@@ -17,7 +17,6 @@ class test_gpr(unittest.TestCase):
def setUp(self): def setUp(self):
print('setUp') print('setUp')
#self.kernel = gauss_kernel()
a = read('structures.traj', index='0') a = read('structures.traj', index='0')
#self.gpr = gpr() #self.gpr = gpr()
#self.gpr = gpr(kernel='double', template_structure=a) #self.gpr = gpr(kernel='double', template_structure=a)
......
import numpy as np import numpy as np
import unittest import unittest
from kernel import gauss_kernel, double_gauss_kernel from kernel import GaussKernel, DoubleGaussKernel
class test_kernel(unittest.TestCase): class test_kernel(unittest.TestCase):
...@@ -14,11 +14,11 @@ class test_kernel(unittest.TestCase): ...@@ -14,11 +14,11 @@ class test_kernel(unittest.TestCase):
def setUp(self): def setUp(self):
print('setUp') print('setUp')
#self.kernel = gauss_kernel() #self.kernel = GaussKernel()
#self.kernel_old = C(10, (1e1, 1e6)) * RBF(10, (1,1000)) #self.kernel_old = C(10, (1e1, 1e6)) * RBF(10, (1,1000))
#self.kernel = double_gauss_kernel(Nsplit_eta=2, eta=10) #self.kernel = DoubleGaussKernel(Nsplit_eta=2, eta=10)
self.kernel = gauss_kernel(Nsplit_eta=2, eta=10) self.kernel = GaussKernel(Nsplit_eta=2, eta=10)
def tearDown(self): def tearDown(self):
print('tearDown\n') print('tearDown\n')
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment