-
Notifications
You must be signed in to change notification settings - Fork 34
/
clim2bry.py
370 lines (305 loc) · 15.7 KB
/
clim2bry.py
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
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
"""
This is CLM2BRY
"""
from datetime import datetime
import numpy as np
from netCDF4 import Dataset, num2date
import IOBry
__author__ = 'Trond Kristiansen'
__email__ = '[email protected]'
__created__ = datetime(2009, 3, 2)
__modified__ = datetime(2019, 3, 12)
__version__ = "1.5"
__status__ = "Development"
def myhelp():
"""
This script generates boundary (BRY) files from the climatology (CLIM) files. The
climatology files are created using createForcing option in main.py of soda2roms package.
Since the variables have different lengths in eta and xi directions, the
clips of data along the East, WEst, and North and South transects will differ in size. The correct
sizes are defined below, where No is the number of vertical levels (length of s_rho):
Define the sizes of the clips along xi :
North and South = salt(No,Lpo),
temp(No,Lpo),
v(No,Lpo),
vbar(1,Lpo),
zeta(1,Lpo),
u(No,Lp)
ubar(1,Lp)
Define the sizes of the clips along eta :
East and West = salt(No,Mpo),
temp(No,Mpo),
v(No,Mp),
vbar(1,Mp),
zeta(1,Mpo),
u(No,Mpo)
ubar(1,Mpo)"""
def writebry(confM2R):
# See myhelp function for definition of these variables:
grdROMS = confM2R.grdROMS
Lpo = grdROMS.Lp
Mpo = grdROMS.Mp
Lp = grdROMS.Lp - 1
Mp = grdROMS.Mp - 1
# Open the CLIM file
clim = Dataset(confM2R.clim_name, 'r')
# Generate the BRY netcdf4 file that we will use to fill in data
IOBry.createBryFile(confM2R)
# Now open the file we created
f = Dataset(confM2R.bry_name, mode='a', format=confM2R.output_format, zlib=confM2R.use_zlib)
# Get the time from the clim file
climtime = np.array(clim.variables["ocean_time"][:])
ntimes = len(climtime)
# For each time in CLIM file, save clips of boundary data to BRY file
for itime in range(ntimes):
temp = np.array(clim.variables["temp"][itime, :, :, :])
salt = np.array(clim.variables["salt"][itime, :, :, :])
ssh = np.array(clim.variables["zeta"][itime, :, :])
u = np.array(clim.variables["u"][itime, :, :, :])
v = np.array(clim.variables["v"][itime, :, :, :])
ubar = np.array(clim.variables["ubar"][itime, :, :])
vbar = np.array(clim.variables["vbar"][itime, :, :])
if confM2R.write_bcg:
O3_c = np.array(clim.variables["O3_c"][itime, :, :, :])
O3_TA = np.array(clim.variables["O3_TA"][itime, :, :, :])
N1_p = np.array(clim.variables["N1_p"][itime, :, :, :])
N3_n = np.array(clim.variables["N3_n"][itime, :, :, :])
N5_s = np.array(clim.variables["N5_s"][itime, :, :, :])
O2_o = np.array(clim.variables["O2_o"][itime, :, :, :])
# Cut the boundary sections along Lpo, and Mpo to create the
# North, South, West, and East boundary clips. Write each clip
# to file for each time step
# NOTE: For East and West only V current (v,vbar) have size Mp, others have size Mpo
temp_west = np.squeeze(temp[:, :, 0])
salt_west = np.squeeze(salt[:, :, 0])
ssh_west = np.squeeze(ssh[:, 0])
u_west = np.squeeze(u[:, :, 0])
v_west = np.squeeze(v[:, :, 0])
ubar_west = np.squeeze(ubar[:, 0])
vbar_west = np.squeeze(vbar[:, 0])
if confM2R.write_bcg:
O3_c_west = np.squeeze(O3_c[:, :, 0])
O3_ta_west = np.squeeze(O3_TA[:, :, 0])
N1_p_west = np.squeeze(N1_p[:, :, 0])
N3_n_west = np.squeeze(N3_n[:, :, 0])
N5_s_west = np.squeeze(N5_s[:, :, 0])
O2_o_west = np.squeeze(O2_o[:, :, 0])
temp_east = np.squeeze(temp[:, :, Lp])
salt_east = np.squeeze(salt[:, :, Lp])
ssh_east = np.squeeze(ssh[:, Lp])
u_east = np.squeeze(u[:, :, Lp - 1])
v_east = np.squeeze(v[:, :, Lp])
ubar_east = np.squeeze(ubar[:, Lp - 1])
vbar_east = np.squeeze(vbar[:, Lp])
if confM2R.write_bcg:
O3_c_east = np.squeeze(O3_c[:, :, Lp])
O3_ta_east = np.squeeze(O3_TA[:, :, Lp])
N1_p_east = np.squeeze(N1_p[:, :, Lp])
N3_n_east = np.squeeze(N3_n[:, :, Lp])
N5_s_east = np.squeeze(N5_s[:, :, Lp])
O2_o_east = np.squeeze(O2_o[:, :, Lp])
# NOTE: For South and North only U current (u,ubar) have size Lp, others have size Lpo
temp_south = np.squeeze(temp[:, 0, :])
salt_south = np.squeeze(salt[:, 0, :])
ssh_south = np.squeeze(ssh[0, :])
u_south = np.squeeze(u[:, 0, :])
v_south = np.squeeze(v[:, 0, :])
ubar_south = np.squeeze(ubar[0, :])
vbar_south = np.squeeze(vbar[0, :])
if confM2R.write_bcg:
O3_c_south = np.squeeze(O3_c[:, 0, :])
O3_ta_south = np.squeeze(O3_TA[:, 0, :])
N1_p_south = np.squeeze(N1_p[:, 0, :])
N3_n_south = np.squeeze(N3_n[:, 0, :])
N5_s_south = np.squeeze(N5_s[:, 0, :])
O2_o_south = np.squeeze(O2_o[:, 0, :])
temp_north = np.squeeze(temp[:, Mp, :])
salt_north = np.squeeze(salt[:, Mp, :])
ssh_north = np.squeeze(ssh[Mp, :])
u_north = np.squeeze(u[:, Mp, :])
v_north = np.squeeze(v[:, Mp - 1, :])
ubar_north = np.squeeze(ubar[Mp, :])
vbar_north = np.squeeze(vbar[Mp - 1, :])
if confM2R.write_bcg:
O3_c_north = np.squeeze(O3_c[:, Mp, :])
O3_ta_north = np.squeeze(O3_TA[:, Mp, :])
N1_p_north = np.squeeze(N1_p[:, Mp, :])
N3_n_north = np.squeeze(N3_n[:, Mp, :])
N5_s_north = np.squeeze(N5_s[:, Mp, :])
O2_o_north = np.squeeze(O2_o[:, Mp, :])
if confM2R.write_ice:
ageice = np.array(clim.variables["ageice"][itime, :, :])
uice = np.array(clim.variables["uice"][itime, :, :])
vice = np.array(clim.variables["vice"][itime, :, :])
aice = np.array(clim.variables["aice"][itime, :, :])
hice = np.array(clim.variables["hice"][itime, :, :])
snow_thick = np.array(clim.variables["snow_thick"][itime, :, :])
ti = np.array(clim.variables["ti"][itime, :, :])
sfwat = np.array(clim.variables["sfwat"][itime, :, :])
tisrf = np.array(clim.variables["tisrf"][itime, :, :])
sig11 = np.array(clim.variables["sig11"][itime, :, :])
sig12 = np.array(clim.variables["sig12"][itime, :, :])
sig22 = np.array(clim.variables["sig22"][itime, :, :])
ageice_west = np.squeeze(ageice[:, 0])
ageice_east = np.squeeze(ageice[:, Lp])
ageice_south = np.squeeze(ageice[0, :])
ageice_north = np.squeeze(ageice[Mp, :])
uice_west = np.squeeze(uice[:, 0])
uice_east = np.squeeze(uice[:, Lp - 1])
uice_south = np.squeeze(uice[0, :])
uice_north = np.squeeze(uice[Mp, :])
vice_west = np.squeeze(vice[:, 0])
vice_east = np.squeeze(vice[:, Lp])
vice_south = np.squeeze(vice[0, :])
vice_north = np.squeeze(vice[Mp - 1, :])
aice_west = np.squeeze(aice[:, 0])
aice_east = np.squeeze(aice[:, Lp])
aice_south = np.squeeze(aice[0, :])
aice_north = np.squeeze(aice[Mp, :])
hice_west = np.squeeze(hice[:, 0])
hice_east = np.squeeze(hice[:, Lp])
hice_south = np.squeeze(hice[0, :])
hice_north = np.squeeze(hice[Mp, :])
snow_thick_west = np.squeeze(snow_thick[:, 0])
snow_thick_east = np.squeeze(snow_thick[:, Lp])
snow_thick_south = np.squeeze(snow_thick[0, :])
snow_thick_north = np.squeeze(snow_thick[Mp, :])
ti_west = np.squeeze(ti[:, 0])
ti_east = np.squeeze(ti[:, Lp])
ti_south = np.squeeze(ti[0, :])
ti_north = np.squeeze(ti[Mp, :])
sfwat_west = np.squeeze(sfwat[:, 0])
sfwat_east = np.squeeze(sfwat[:, Lp])
sfwat_south = np.squeeze(sfwat[0, :])
sfwat_north = np.squeeze(sfwat[Mp, :])
tisrf_west = np.squeeze(tisrf[:, 0])
tisrf_east = np.squeeze(tisrf[:, Lp])
tisrf_south = np.squeeze(tisrf[0, :])
tisrf_north = np.squeeze(tisrf[Mp, :])
sig11_west = np.squeeze(sig11[:, 0])
sig11_east = np.squeeze(sig11[:, Lp])
sig11_south = np.squeeze(sig11[0, :])
sig11_north = np.squeeze(sig11[Mp, :])
sig12_west = np.squeeze(sig12[:, 0])
sig12_east = np.squeeze(sig12[:, Lp])
sig12_south = np.squeeze(sig12[0, :])
sig12_north = np.squeeze(sig12[Mp, :])
sig22_west = np.squeeze(sig22[:, 0])
sig22_east = np.squeeze(sig22[:, Lp])
sig22_south = np.squeeze(sig22[0, :])
sig22_north = np.squeeze(sig22[Mp, :])
# ------- Write time to file -------------------------------
d = num2date(climtime[itime], units=clim.variables['ocean_time'].long_name,
calendar=clim.variables['ocean_time'].calendar)
print('clim2bry.py => Appending data to file %s for time %s' % (confM2R.bry_name, d))
f.variables['ocean_time'][itime] = climtime[itime]
# ------- Write out western boundary variables ------------
f.variables['temp_west'][itime, :, :] = temp_west
f.variables['salt_west'][itime, :, :] = salt_west
f.variables['zeta_west'][itime, :] = ssh_west
f.variables['u_west'][itime, :, :] = u_west
f.variables['v_west'][itime, :, :] = v_west
f.variables['ubar_west'][itime, :] = ubar_west
f.variables['vbar_west'][itime, :] = vbar_west
if confM2R.write_bcg:
f.variables['O3_c_west'][itime, :, :] = O3_c_west
f.variables['O3_TA_west'][itime, :, :] = O3_ta_west
f.variables['N1_p_west'][itime, :, :] = N1_p_west
f.variables['N3_n_west'][itime, :, :] = N3_n_west
f.variables['N5_s_west'][itime, :, :] = N5_s_west
f.variables['O2_o_west'][itime, :, :] = O2_o_west
# ------- Write out eastern boundary variables ------------
f.variables['temp_east'][itime, :, :] = temp_east
f.variables['salt_east'][itime, :, :] = salt_east
f.variables['zeta_east'][itime, :] = ssh_east
f.variables['u_east'][itime, :, :] = u_east
f.variables['v_east'][itime, :, :] = v_east
f.variables['ubar_east'][itime, :] = ubar_east
f.variables['vbar_east'][itime, :] = vbar_east
if confM2R.write_bcg:
f.variables['O3_c_east'][itime, :, :] = O3_c_east
f.variables['O3_TA_east'][itime, :, :] = O3_ta_east
f.variables['N1_p_east'][itime, :, :] = N1_p_east
f.variables['N3_n_east'][itime, :, :] = N3_n_east
f.variables['N5_s_east'][itime, :, :] = N5_s_east
f.variables['O2_o_east'][itime, :, :] = O2_o_east
# ------- Write out southern boundary variables ------------
f.variables['temp_south'][itime, :, :] = temp_south
f.variables['salt_south'][itime, :, :] = salt_south
f.variables['zeta_south'][itime, :] = ssh_south
f.variables['u_south'][itime, :, :] = u_south
f.variables['v_south'][itime, :, :] = v_south
f.variables['ubar_south'][itime, :] = ubar_south
f.variables['vbar_south'][itime, :] = vbar_south
if confM2R.write_bcg:
f.variables['O3_c_south'][itime, :, :] = O3_c_south
f.variables['O3_TA_south'][itime, :, :] = O3_ta_south
f.variables['N1_p_south'][itime, :, :] = N1_p_south
f.variables['N3_n_south'][itime, :, :] = N3_n_south
f.variables['N5_s_south'][itime, :, :] = N5_s_south
f.variables['O2_o_south'][itime, :, :] = O2_o_south
# ------- Write out northern boundary variables ------------
f.variables['temp_north'][itime, :, :] = temp_north
f.variables['salt_north'][itime, :, :] = salt_north
f.variables['zeta_north'][itime, :] = ssh_north
f.variables['u_north'][itime, :, :] = u_north
f.variables['v_north'][itime, :, :] = v_north
f.variables['ubar_north'][itime, :] = ubar_north
f.variables['vbar_north'][itime, :] = vbar_north
if confM2R.write_bcg:
f.variables['O3_c_north'][itime, :, :] = O3_c_north
f.variables['O3_TA_north'][itime, :, :] = O3_ta_north
f.variables['N1_p_north'][itime, :, :] = N1_p_north
f.variables['N3_n_north'][itime, :, :] = N3_n_north
f.variables['N5_s_north'][itime, :, :] = N5_s_north
f.variables['O2_o_north'][itime, :, :] = O2_o_north
if confM2R.write_ice:
f.variables['ageice_west'][itime, :] = ageice_west
f.variables['ageice_east'][itime, :] = ageice_east
f.variables['ageice_south'][itime, :] = ageice_south
f.variables['ageice_north'][itime, :] = ageice_north
f.variables['uice_west'][itime, :] = uice_west
f.variables['uice_east'][itime, :] = uice_east
f.variables['uice_south'][itime, :] = uice_south
f.variables['uice_north'][itime, :] = uice_north
f.variables['vice_west'][itime, :] = vice_west
f.variables['vice_east'][itime, :] = vice_east
f.variables['vice_south'][itime, :] = vice_south
f.variables['vice_north'][itime, :] = vice_north
f.variables['aice_west'][itime, :] = aice_west
f.variables['aice_east'][itime, :] = aice_east
f.variables['aice_south'][itime, :] = aice_south
f.variables['aice_north'][itime, :] = aice_north
f.variables['hice_west'][itime, :] = hice_west
f.variables['hice_east'][itime, :] = hice_east
f.variables['hice_south'][itime, :] = hice_south
f.variables['hice_north'][itime, :] = hice_north
f.variables['snow_thick_west'][itime, :] = snow_thick_west
f.variables['snow_thick_east'][itime, :] = snow_thick_east
f.variables['snow_thick_south'][itime, :] = snow_thick_south
f.variables['snow_thick_north'][itime, :] = snow_thick_north
f.variables['ti_west'][itime, :] = ti_west
f.variables['ti_east'][itime, :] = ti_east
f.variables['ti_south'][itime, :] = ti_south
f.variables['ti_north'][itime, :] = ti_north
f.variables['sfwat_west'][itime, :] = sfwat_west
f.variables['sfwat_east'][itime, :] = sfwat_east
f.variables['sfwat_south'][itime, :] = sfwat_south
f.variables['sfwat_north'][itime, :] = sfwat_north
f.variables['tisrf_west'][itime, :] = tisrf_west
f.variables['tisrf_east'][itime, :] = tisrf_east
f.variables['tisrf_south'][itime, :] = tisrf_south
f.variables['tisrf_north'][itime, :] = tisrf_north
f.variables['sig11_west'][itime, :] = sig11_west
f.variables['sig11_east'][itime, :] = sig11_east
f.variables['sig11_south'][itime, :] = sig11_south
f.variables['sig11_north'][itime, :] = sig11_north
f.variables['sig12_west'][itime, :] = sig12_west
f.variables['sig12_east'][itime, :] = sig12_east
f.variables['sig12_south'][itime, :] = sig12_south
f.variables['sig12_north'][itime, :] = sig12_north
f.variables['sig22_west'][itime, :] = sig22_west
f.variables['sig22_east'][itime, :] = sig22_east
f.variables['sig22_south'][itime, :] = sig22_south
f.variables['sig22_north'][itime, :] = sig22_north
f.close()