-
Notifications
You must be signed in to change notification settings - Fork 0
/
coagulatio.pyx
108 lines (102 loc) · 3.55 KB
/
coagulatio.pyx
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
#cython: np_pythran=False
#cython: language_level=3
#
# Copyright 2019 Benjamin Santos
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
cimport cython
cimport numpy as np
import numpy as np
cimport openmp
from cython.parallel cimport prange
from cython.parallel cimport parallel
@cython.boundscheck(False)
@cython.wraparound(False)
def deathlist_toarrays(list death_list,
short[:] larr, short[:] qarr,
short[:] marr, short[:] parr,
double[:] death_array):
cdef unsigned int N = len(death_list)
cdef unsigned int i
for i in range(N):
larr[i] = death_list[i][1]
qarr[i] = death_list[i][2]
marr[i] = death_list[i][3]
parr[i] = death_list[i][4]
death_array[i] = death_list[i][5]
@cython.boundscheck(False)
@cython.wraparound(False)
def birthlist_toarrays(list birth_list,
short[:] larr, short[:] qarr,
short[:] marr, short[:] parr,
short[:] narr, short[:] rarr,
double[:] birth_array):
cdef unsigned int N = len(birth_list)
cdef unsigned int i
for i in range(N):
larr[i] = birth_list[i][1]
qarr[i] = birth_list[i][2]
marr[i] = birth_list[i][3]
parr[i] = birth_list[i][4]
narr[i] = birth_list[i][5]
rarr[i] = birth_list[i][6]
birth_array[i] = birth_list[i][7]
@cython.boundscheck(False)
@cython.wraparound(False)
def serial_death(short[:] l, short[:] q,
short[:] m, short[:] p,
double[:] eta,
double[:, :] dens,
double[:, :] res):
cdef unsigned int N = eta.shape[0]
cdef unsigned int i
for i in range(N):
res[l[i], q[i]] += eta[i]*dens[m[i], p[i]]
@cython.boundscheck(False)
@cython.wraparound(False)
def parallel_death(short[:] l, short[:] q,
short[:] m, short[:] p,
double[:] eta,
double[:, :] dens,
double[:, :] res):
cdef unsigned int N = eta.shape[0]
cdef unsigned int i
with nogil:
for i in prange(N, schedule='static'):
res[l[i], q[i]] += eta[i]*dens[m[i], p[i]]
@cython.boundscheck(False)
@cython.wraparound(False)
def serial_birth(short[:] l, short[:] q,
short[:] m, short[:] p,
short[:] n, short[:] r,
double[:] eta,
double[:, :] dens,
double[:, :] res):
cdef unsigned int N = eta.shape[0]
cdef unsigned int i
for i in range(N):
res[l[i], q[i]] += eta[i]*dens[m[i], p[i]]*dens[n[i], r[i]]
@cython.boundscheck(False)
@cython.wraparound(False)
def parallel_birth(short[:] l, short[:] q,
short[:] m, short[:] p,
short[:] n, short[:] r,
double[:] eta,
double[:, :] dens,
double[:, :] res):
cdef unsigned int N = eta.shape[0]
cdef unsigned int i
with nogil:
for i in prange(N, schedule='static'):
res[l[i], q[i]] += eta[i]*dens[m[i], p[i]]*dens[n[i], r[i]]