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Malthe Kjær Bisbo
GOFEE
Commits
5015902e
Commit
5015902e
authored
Dec 18, 2019
by
Malthe Kjær Bisbo
Browse files
slight changes to descriptors and prior
parent
dd3edadb
Changes
42
Hide whitespace changes
Inline
Side-by-side
surrogate/structures.traj
0 → 100644
View file @
5015902e
File added
surrogate/test_gpr.py
View file @
5015902e
...
...
@@ -2,6 +2,46 @@ import numpy as np
import
unittest
from
gpr
import
gpr
from
ase.io
import
read
# old gpr
from
gaussComparator
import
gaussComparator
from
featureCalculators_multi.angular_fingerprintFeature_cy
import
Angular_Fingerprint
from
delta_functions_multi.delta
import
delta
as
deltaFunc
from
GPR
import
GPR
def
initialize_old_gpr
(
atoms
):
### Set up feature ###
# Radial part
Rc1
=
6
binwidth1
=
0.2
sigma1
=
0.2
# Angular part
Rc2
=
4
Nbins2
=
30
sigma2
=
0.2
gamma
=
2
# Radial/angular weighting
eta
=
20
use_angular
=
True
# Initialize feature
featureCalculator
=
Angular_Fingerprint
(
atoms
,
Rc1
=
Rc1
,
Rc2
=
Rc2
,
binwidth1
=
binwidth1
,
Nbins2
=
Nbins2
,
sigma1
=
sigma1
,
sigma2
=
sigma2
,
gamma
=
gamma
,
eta
=
eta
,
use_angular
=
use_angular
)
kernel
=
C
(
10
,
(
1e1
,
1e6
))
*
(
C
(
1
,
(
1
,
1
))
*
RBF
(
10
,
(
1
,
1000
))
+
C
(
0.01
,
(
0.01
,
0.01
))
*
RBF
(
10
,
(
1
,
1000
))
+
WhiteKernel
(
1e-5
,
(
1e-6
,
1e-2
)))
delta
=
deltaFunc
(
atoms
=
a
,
rcut
=
6
)
gpr
=
GPR
(
kernel
=
kernel
,
featureCalculator
=
featureCalculator
,
delta_function
=
delta
,
bias_func
=
None
,
optimize
=
False
,
n_restarts_optimizer
=
1
)
return
gpr
class
test_kernel
(
unittest
.
TestCase
):
@
classmethod
...
...
@@ -15,30 +55,22 @@ class test_kernel(unittest.TestCase):
def
setUp
(
self
):
print
(
'setUp'
)
#self.kernel = gauss_kernel()
self
.
kernel
=
double_gauss_kernel
()
a
=
read
(
'structures.traj'
,
index
=
'0'
)
self
.
gpr_old
=
initialize_old_gpr
(
a
)
self
.
gpr
=
gpr
()
def
tearDown
(
self
):
print
(
'tearDown
\n
'
)
def
test_jac
(
self
):
x1
=
np
.
array
([
1.
,
2.
,
3.
])
x2
=
np
.
array
([
1.5
,
2.
,
1.
])
x3
=
np
.
array
([
3.
,
1.
,
1.
])
y
=
np
.
c_
[
x1
,
x2
,
x3
].
T
np
.
testing
.
assert_almost_equal
(
self
.
kernel
.
kernel_jacobian
(
x1
,
x2
),
self
.
kernel
.
numerical_jacobian
(
x1
,
x2
))
np
.
testing
.
assert_almost_equal
(
self
.
kernel
.
kernel_jacobian
(
x1
,
y
),
self
.
kernel
.
numerical_jacobian
(
x1
,
y
))
np
.
testing
.
assert_almost_equal
(
self
.
kernel
.
kernel_jacobian
(
x2
,
y
),
self
.
kernel
.
numerical_jacobian
(
x2
,
y
))
def
test_hyper_jac
(
self
):
x1
=
np
.
array
([
1.
,
2.
,
3.
])
x2
=
np
.
array
([
1.5
,
2.
,
1.
])
x3
=
np
.
array
([
3.
,
1.
,
1.
])
X
=
np
.
c_
[
x1
,
x2
,
x3
].
T
np
.
testing
.
assert_almost_equal
(
self
.
kernel
.
kernel_hyperparameter_gradient
(
X
),
self
.
kernel
.
numerical_hyperparameter_gradient
(
X
))
def
test_compare_with_old
(
self
):
traj
=
read
(
'structures.traj'
,
index
=
':50'
)
traj_train
=
traj
[:
40
]
traj_predict
=
traj
[
40
:]
self
.
gpr
.
def
test_forces
(
self
):
pass
if
__name__
==
'__main__'
:
unittest
.
main
()
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