Hi!
I am trying to create a nested domain with DOMAINcfg.
I want to use bathymetry field from my file 1_bathy_meter.nc
So I set nn_bathy = 1 in 1_namelist_cfg
But it seems that DOMAINcfg ignores 1_bathy_meter.nc and creates bathymetry field of it own. Even when 1_bathy_meter.nc is not in DOMAINcfg folder make_domain_cfg.exe
still runs successfully and creates 1_domain_cfg.nc
How can I use bathymetry field from 1_bathy_meter.nc in 1_domain_cfg.nc?
That’s weird. Have you checked what’s going on in your 1_ocean.output file ?
I attached my 1_ocean.output file.
There are no error messages. I checked that nn_bathy = 1
Also, I looked at bathy_metry field in 1_domain_cfg.nc
It seems that it is interpolated from bathy_meter.nc using nearest neighbor interpolation.
CNRS - NERC - Met OFFICE - MERCATOR-ocean - CMCC
NEMO team
Ocean General Circulation Model
NEMO version 4.0 (2019)
._ ._ ._ ._ ._
_.-._)`\_.-._)`\_.-._)`\_.-._)`\_.-._)`\_
o _, _,
o .' ( .-' /
o _/..._'. .' /
( o .-'` ` '-./ _.'
) ( o) ;= <_ (
( '-.,\\__ __.-;`\ '. )
) ) \) |`\ \) '. \ ( (
( ( \_/ '-._\ ) )
) ) jgs ` ( (
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Working precision = double-precision
AAAAAAAA
Namelist nammpp
jpni and jpnj will be calculated automatically
avoid use of mpi_allgather at the north fold ln_nnogather = T
halo width (applies to both rows and columns) nn_hls = 1
mpp_init:
~~~~~~~~
==> you use the best mpi decomposition
Number of mpi processes: 1
Number of ocean subdomains = 1
Number of suppressed land subdomains = 0
agrif_nemo_init : nesting
~~~~~~~
Namelist namagrif : set nesting parameters
ln_vert_remap = F
ln_remove_closedseas = T
npt_copy = 2
npt_connect = 2
AGRIF boundaries and ghost cells:
lk_west T
lk_east T
lk_south T
lk_north T
nbghostcells_y_s 4
nbghostcells_y_n 4
nbghostcells_x_w 4
nbghostcells_x_e 4
MPI Message Passing MPI - domain lay out over processors
defines mpp subdomains
jpni = 1
jpnj = 1
jpnij = 1
sum ijpi(i,1) = 634 jpiglo = 634
sum ijpj(1,j) = 313 jpjglo = 313
****************
* *
1 * 634 x313 *
* 0 *
* *
****************
1
resulting internal parameters :
nproc = 0
nowe = -1 noea = -1
nono = -1 noso = -1
nbondi = 2
nbondj = 2
npolj = 0
l_Iperio = F
l_Jperio = F
nimpp = 1
njmpp = 1
mpp init_ioipsl : iloc = 632 311
~~~~~~~~~~~~~~~ iabsf = 1 1
ihals = 0 0
ihale = 0 0
dom_cfg : set the ocean configuration
~~~~~~~
ocean model configuration used : cp_cfg =
my_cfg
jp_cfg = 2
global domain lateral boundaries
jperio= 0, closed
dom_init : domain initialization
~~~~~~~~
dom_glo : domain: global <<==>> local
~~~~~~~
global domain: jpiglo = 634 jpjglo = 313 jpkglo =
50
local domain: jpi = 634 jpj = 313 jpk =
50
dom_nam : domain initialization through namelist read
~~~~~~~
Namelist namrun
experiment name for output cn_exp =
my_exp
mask land points ln_mskland = F
additional CF standard metadata ln_cfmeta = F
overwrite an existing file ln_clobber = T
NetCDF chunksize (bytes) nn_chunksz = 0
Namelist namdom : space & time domain
flag read/compute bathymetry nn_bathy = 1
read bathymetry from file cn_topo = bathy_meter.nc
bathymetry name in file cn_bath = Bathymetry
read isf draft from file cn_fisfd = isf_draft_meter.nc
isf draft name in file cn_visfd = isf_draft
Depth (if =0 bathy=jpkm1) rn_bathy = 0.000000000000000E+000
min depth of the ocean (>0) or rn_hmin = -3.00000000000000
min number of ocean level (<0)
minimum thickness of partial rn_e3zps_min = 20.0000000000000
(m)
step level rn_e3zps_rat = 0.100000000000000
create mesh/mask file(s) nn_msh = 0
= 0 no file created
= 1 mesh_mask
= 2 mesh and mask
= 3 mesh_hgr, msh_zgr and mask
type of horizontal mesh jphgr_msh = 0
longitude of first raw and column T-point ppglam0 =
999999.000000000
latitude of first raw and column T-point ppgphi0 =
999999.000000000
zonal grid-spacing (degrees) ppe1_deg =
333333.000000000
meridional grid-spacing (degrees) ppe2_deg =
333333.000000000
zonal grid-spacing (degrees) ppe1_m =
333333.000000000
meridional grid-spacing (degrees) ppe2_m =
333333.000000000
ORCA r4, r2 and r05 coefficients ppsur =
999999.000000000
ppa0 =
999999.000000000
ppa1 =
999999.000000000
ppkth =
21.0000000000000
ppacr =
6.00000000000000
Minimum vertical spacing ppdzmin =
2.50000000000000
Maximum depth pphmax =
2200.00000000000
Use double tanf function for vertical coordinates ldbletanh = F
Double tanh function parameters ppa2 =
999999.000000000
ppkth2 =
999999.000000000
ppacr2 =
999999.000000000
dom_hgr : define the horizontal mesh from ithe following par_oce parameters
~~~~~~~ type of horizontal mesh jphgr_msh = 0
position of the first row and ppglam0 =
999999.000000000
column grid-point (degrees) ppgphi0 =
999999.000000000
zonal grid-spacing (degrees) ppe1_deg =
333333.000000000
meridional grid-spacing (degrees) ppe2_deg =
333333.000000000
zonal grid-spacing (meters) ppe1_m =
333333.000000000
meridional grid-spacing (meters) ppe2_m =
333333.000000000
longitude and e1 scale factors
------------------------------
1 0.00 0.00 0.00 32.08 0.0000000000 0.0000000000 0.0000000000 0.0000000000
11 0.00 0.00 0.00 32.20 0.0000000000 0.0000000000 0.0000000000 0.0000000000
21 0.00 0.00 0.00 32.32 0.0000000000 0.0000000000 0.0000000000 0.0000000000
31 0.00 0.00 0.00 32.44 0.0000000000 0.0000000000 0.0000000000 0.0000000000
41 0.00 0.00 0.00 32.57 0.0000000000 0.0000000000 0.0000000000 0.0000000000
51 0.00 0.00 0.00 32.69 0.0000000000 0.0000000000 0.0000000000 0.0000000000
61 0.00 0.00 0.00 32.81 0.0000000000 0.0000000000 0.0000000000 0.0000000000
71 0.00 0.00 0.00 32.94 0.0000000000 0.0000000000 0.0000000000 0.0000000000
81 0.00 0.00 0.00 33.06 0.0000000000 0.0000000000 0.0000000000 0.0000000000
91 0.00 0.00 0.00 33.19 0.0000000000 0.0000000000 0.0000000000 0.0000000000
101 0.00 0.00 0.00 33.31 0.0000000000 0.0000000000 0.0000000000 0.0000000000
111 0.00 0.00 0.00 33.43 0.0000000000 0.0000000000 0.0000000000 0.0000000000
121 0.00 0.00 0.00 33.56 0.0000000000 0.0000000000 0.0000000000 0.0000000000
131 0.00 0.00 0.00 33.68 0.0000000000 0.0000000000 0.0000000000 0.0000000000
141 0.00 0.00 0.00 33.80 0.0000000000 0.0000000000 0.0000000000 0.0000000000
151 0.00 0.00 0.00 33.93 0.0000000000 0.0000000000 0.0000000000 0.0000000000
161 0.00 0.00 0.00 34.05 0.0000000000 0.0000000000 0.0000000000 0.0000000000
171 0.00 0.00 0.00 34.17 0.0000000000 0.0000000000 0.0000000000 0.0000000000
181 0.00 0.00 0.00 34.30 0.0000000000 0.0000000000 0.0000000000 0.0000000000
191 0.00 0.00 0.00 34.42 0.0000000000 0.0000000000 0.0000000000 0.0000000000
201 0.00 0.00 0.00 34.55 0.0000000000 0.0000000000 0.0000000000 0.0000000000
211 0.00 0.00 0.00 34.67 0.0000000000 0.0000000000 0.0000000000 0.0000000000
221 0.00 0.00 0.00 34.79 0.0000000000 0.0000000000 0.0000000000 0.0000000000
231 0.00 0.00 0.00 34.92 0.0000000000 0.0000000000 0.0000000000 0.0000000000
241 0.00 0.00 0.00 35.04 0.0000000000 0.0000000000 0.0000000000 0.0000000000
251 0.00 0.00 0.00 35.16 0.0000000000 0.0000000000 0.0000000000 0.0000000000
261 0.00 0.00 0.00 35.29 0.0000000000 0.0000000000 0.0000000000 0.0000000000
271 0.00 0.00 0.00 35.41 0.0000000000 0.0000000000 0.0000000000 0.0000000000
281 0.00 0.00 0.00 35.54 0.0000000000 0.0000000000 0.0000000000 0.0000000000
291 0.00 0.00 0.00 35.66 0.0000000000 0.0000000000 0.0000000000 0.0000000000
301 0.00 0.00 0.00 35.78 0.0000000000 0.0000000000 0.0000000000 0.0000000000
311 0.00 0.00 0.00 35.91 0.0000000000 0.0000000000 0.0000000000 0.0000000000
321 0.00 0.00 0.00 36.03 0.0000000000 0.0000000000 0.0000000000 0.0000000000
331 0.00 0.00 0.00 36.15 0.0000000000 0.0000000000 0.0000000000 0.0000000000
341 0.00 0.00 0.00 36.28 0.0000000000 0.0000000000 0.0000000000 0.0000000000
351 0.00 0.00 0.00 36.40 0.0000000000 0.0000000000 0.0000000000 0.0000000000
361 0.00 0.00 0.00 36.53 0.0000000000 0.0000000000 0.0000000000 0.0000000000
371 0.00 0.00 0.00 36.65 0.0000000000 0.0000000000 0.0000000000 0.0000000000
381 0.00 0.00 0.00 36.77 0.0000000000 0.0000000000 0.0000000000 0.0000000000
391 0.00 0.00 0.00 36.90 0.0000000000 0.0000000000 0.0000000000 0.0000000000
401 0.00 0.00 0.00 37.02 0.0000000000 0.0000000000 0.0000000000 0.0000000000
411 0.00 0.00 0.00 37.14 0.0000000000 0.0000000000 0.0000000000 0.0000000000
421 0.00 0.00 0.00 37.27 0.0000000000 0.0000000000 0.0000000000 0.0000000000
431 0.00 0.00 0.00 37.39 0.0000000000 0.0000000000 0.0000000000 0.0000000000
441 0.00 0.00 0.00 37.51 0.0000000000 0.0000000000 0.0000000000 0.0000000000
451 0.00 0.00 0.00 37.64 0.0000000000 0.0000000000 0.0000000000 0.0000000000
461 0.00 0.00 0.00 37.76 0.0000000000 0.0000000000 0.0000000000 0.0000000000
471 0.00 0.00 0.00 37.88 0.0000000000 0.0000000000 0.0000000000 0.0000000000
481 0.00 0.00 0.00 38.01 0.0000000000 0.0000000000 0.0000000000 0.0000000000
491 0.00 0.00 0.00 38.13 0.0000000000 0.0000000000 0.0000000000 0.0000000000
501 0.00 0.00 0.00 38.26 0.0000000000 0.0000000000 0.0000000000 0.0000000000
511 0.00 0.00 0.00 38.38 0.0000000000 0.0000000000 0.0000000000 0.0000000000
521 0.00 0.00 0.00 38.50 0.0000000000 0.0000000000 0.0000000000 0.0000000000
531 0.00 0.00 0.00 38.63 0.0000000000 0.0000000000 0.0000000000 0.0000000000
541 0.00 0.00 0.00 38.75 0.0000000000 0.0000000000 0.0000000000 0.0000000000
551 0.00 0.00 0.00 38.87 0.0000000000 0.0000000000 0.0000000000 0.0000000000
561 0.00 0.00 0.00 39.00 0.0000000000 0.0000000000 0.0000000000 0.0000000000
571 0.00 0.00 0.00 39.12 0.0000000000 0.0000000000 0.0000000000 0.0000000000
581 0.00 0.00 0.00 39.24 0.0000000000 0.0000000000 0.0000000000 0.0000000000
591 0.00 0.00 0.00 39.37 0.0000000000 0.0000000000 0.0000000000 0.0000000000
601 0.00 0.00 0.00 39.49 0.0000000000 0.0000000000 0.0000000000 0.0000000000
611 0.00 0.00 0.00 39.61 0.0000000000 0.0000000000 0.0000000000 0.0000000000
621 0.00 0.00 0.00 39.74 0.0000000000 0.0000000000 0.0000000000 0.0000000000
631 0.00 0.00 0.00 39.86 0.0000000000 0.0000000000 0.0000000000 0.0000000000
latitude and e2 scale factors
-----------------------------
1 0.00 0.00 0.00 43.33 0.0000000000 0.0000000000 0.0000000000 0.0000000000
11 0.00 0.00 0.00 43.41 0.0000000000 0.0000000000 0.0000000000 0.0000000000
21 0.00 0.00 0.00 43.50 0.0000000000 0.0000000000 0.0000000000 0.0000000000
31 0.00 0.00 0.00 43.59 0.0000000000 0.0000000000 0.0000000000 0.0000000000
41 0.00 0.00 0.00 43.68 0.0000000000 0.0000000000 0.0000000000 0.0000000000
51 0.00 0.00 0.00 43.77 0.0000000000 0.0000000000 0.0000000000 0.0000000000
61 0.00 0.00 0.00 43.86 0.0000000000 0.0000000000 0.0000000000 0.0000000000
71 0.00 0.00 0.00 43.95 0.0000000000 0.0000000000 0.0000000000 0.0000000000
81 0.00 0.00 0.00 44.04 0.0000000000 0.0000000000 0.0000000000 0.0000000000
91 0.00 0.00 0.00 44.13 0.0000000000 0.0000000000 0.0000000000 0.0000000000
101 0.00 0.00 0.00 44.22 0.0000000000 0.0000000000 0.0000000000 0.0000000000
111 0.00 0.00 0.00 44.31 0.0000000000 0.0000000000 0.0000000000 0.0000000000
121 0.00 0.00 0.00 44.40 0.0000000000 0.0000000000 0.0000000000 0.0000000000
131 0.00 0.00 0.00 44.49 0.0000000000 0.0000000000 0.0000000000 0.0000000000
141 0.00 0.00 0.00 44.58 0.0000000000 0.0000000000 0.0000000000 0.0000000000
151 0.00 0.00 0.00 44.67 0.0000000000 0.0000000000 0.0000000000 0.0000000000
161 0.00 0.00 0.00 44.76 0.0000000000 0.0000000000 0.0000000000 0.0000000000
171 0.00 0.00 0.00 44.85 0.0000000000 0.0000000000 0.0000000000 0.0000000000
181 0.00 0.00 0.00 44.94 0.0000000000 0.0000000000 0.0000000000 0.0000000000
191 0.00 0.00 0.00 45.03 0.0000000000 0.0000000000 0.0000000000 0.0000000000
201 0.00 0.00 0.00 45.12 0.0000000000 0.0000000000 0.0000000000 0.0000000000
211 0.00 0.00 0.00 45.21 0.0000000000 0.0000000000 0.0000000000 0.0000000000
221 0.00 0.00 0.00 45.30 0.0000000000 0.0000000000 0.0000000000 0.0000000000
231 0.00 0.00 0.00 45.39 0.0000000000 0.0000000000 0.0000000000 0.0000000000
241 0.00 0.00 0.00 45.48 0.0000000000 0.0000000000 0.0000000000 0.0000000000
251 0.00 0.00 0.00 45.57 0.0000000000 0.0000000000 0.0000000000 0.0000000000
261 0.00 0.00 0.00 45.66 0.0000000000 0.0000000000 0.0000000000 0.0000000000
271 0.00 0.00 0.00 45.75 0.0000000000 0.0000000000 0.0000000000 0.0000000000
281 0.00 0.00 0.00 45.84 0.0000000000 0.0000000000 0.0000000000 0.0000000000
291 0.00 0.00 0.00 45.93 0.0000000000 0.0000000000 0.0000000000 0.0000000000
301 0.00 0.00 0.00 46.02 0.0000000000 0.0000000000 0.0000000000 0.0000000000
311 0.00 0.00 0.00 46.11 0.0000000000 0.0000000000 0.0000000000 0.0000000000
dom_zgr : vertical coordinate
~~~~~~~
Namelist namzgr : set vertical coordinate
z-coordinate - full steps ln_zco = F
z-coordinate - partial steps ln_zps = T
s- or hybrid z-s-coordinate ln_sco = F
ice shelf cavities ln_isfcav = F
zgr_z : Reference vertical z-coordinates
~~~~~~~
Value of coefficients for vertical mesh:
zsur = -607.288102966426
za0 = 38.3092924866436
za1 = 35.9005528597203
zkth = 21.0000000000000
zacr = 6.00000000000000
Reference z-coordinate depth and scale factors:
level gdept_1d gdepw_1d e3t_1d e3w_1d
1 1.25 0.00 2.52 2.51
2 3.79 2.52 2.56 2.54
3 6.38 5.08 2.62 2.59
4 9.04 7.70 2.70 2.66
5 11.79 10.40 2.82 2.76
6 14.68 13.22 2.98 2.89
7 17.76 16.19 3.20 3.08
8 21.11 19.40 3.51 3.34
9 24.81 22.91 3.94 3.71
10 29.02 26.84 4.52 4.21
11 33.91 31.36 5.32 4.89
12 39.74 36.69 6.41 5.83
13 46.83 43.10 7.88 7.09
14 55.61 50.98 9.81 8.78
15 66.60 60.79 12.33 10.99
16 80.45 73.12 15.54 13.85
17 97.87 88.66 19.49 17.42
18 119.61 108.15 24.19 21.75
19 146.41 132.34 29.54 26.79
20 178.80 161.88 35.33 32.39
21 217.11 197.21 41.29 38.31
22 261.33 238.49 47.08 44.22
23 311.16 285.58 52.43 49.83
24 366.03 338.01 57.13 54.87
25 425.23 395.14 61.08 59.20
26 488.00 456.22 64.28 62.77
27 553.63 520.50 66.81 65.62
28 621.47 587.31 68.74 67.84
29 691.00 656.05 70.21 69.53
30 761.79 726.26 71.29 70.79
31 833.51 797.55 72.10 71.73
32 905.93 869.65 72.68 72.41
33 978.84 942.33 73.11 72.91
34 1052.11 1015.44 73.42 73.28
35 1125.65 1088.85 73.64 73.54
36 1199.38 1162.50 73.80 73.73
37 1273.24 1236.30 73.92 73.86
38 1347.20 1310.21 74.00 73.96
39 1421.23 1384.21 74.06 74.03
40 1495.32 1458.27 74.10 74.08
41 1569.43 1532.37 74.13 74.12
42 1643.58 1606.50 74.15 74.14
43 1717.74 1680.66 74.17 74.16
44 1791.92 1754.83 74.18 74.18
45 1866.10 1829.01 74.19 74.19
46 1940.30 1903.20 74.20 74.19
47 2014.49 1977.39 74.20 74.20
48 2088.69 2051.59 74.20 74.20
49 2162.90 2125.80 74.20 74.20
50 2237.10 2200.00 74.20 74.21
zgr_bat : defines level and meter bathymetry
~~~~~~~
Minimum ocean depth: 7.69613904510015 minimum number of ocean levels :
3
zgr_zps : z-coordinate with partial steps
~~~~~~~
mbathy is recomputed : bathy_level file is NOT used
zgr_bat_ctl : check the bathymetry
~~~~~~~~~~~
suppress isolated ocean grid points
-----------------------------------
no isolated ocean grid points
mbathy set to 0 along east and west boundary: jperio = 0
zgr_bot_level : ocean bottom k-index of T-, U-, V- and W-levels
~~~~~~~~~~~~~
zgr_top_level : ocean top k-index of T-, U-, V- and W-levels
~~~~~~~~~~~~~
MIN val k_top 0 MAX 1
MIN val k_bot 1 MAX 49
MIN val depth t 0.547760927484126 w 0.000000000000000E+000
MIN val e3 t 0.270315649586287 f 0.270315649586287 u
0.270315649586287 u 0.270315649586287 uw 0.270315649586287
vw 0.270315649586287 w 0.270315649586287
MAX val depth t 2292.75592881161 w 2237.10278320312
MAX val e3 t 111.307229598818 f 111.307229598818 u
111.307229598818 u 111.307229598818 uw 111.307229598818
vw 111.307229598818 w 111.307229598818
dommsk : ocean mask
~~~~~~
Namelist namlbc
lateral momentum boundary cond. rn_shlat = 0.000000000000000E+000
consistency with analytical form ln_vorlat = F
==>>> ocean lateral free-slip
usr_def_fmask : NO alteration of fmask in specific straits
~~~~~~~~~~~~~
dom_nam : domain initialization through namelist read
~~~~~~~
Namelist namrun
experiment name for output cn_exp =
my_exp
mask land points ln_mskland = F
additional CF standard metadata ln_cfmeta = F
overwrite an existing file ln_clobber = T
NetCDF chunksize (bytes) nn_chunksz = 0
Namelist namdom : space & time domain
flag read/compute bathymetry nn_bathy = 1
read bathymetry from file cn_topo = bathy_meter.nc
bathymetry name in file cn_bath = Bathymetry
read isf draft from file cn_fisfd = isf_draft_meter.nc
isf draft name in file cn_visfd = isf_draft
Depth (if =0 bathy=jpkm1) rn_bathy = 0.000000000000000E+000
min depth of the ocean (>0) or rn_hmin = -3.00000000000000
min number of ocean level (<0)
minimum thickness of partial rn_e3zps_min = 20.0000000000000
(m)
step level rn_e3zps_rat = 0.100000000000000
create mesh/mask file(s) nn_msh = 0
= 0 no file created
= 1 mesh_mask
= 2 mesh and mask
= 3 mesh_hgr, msh_zgr and mask
type of horizontal mesh jphgr_msh = 0
longitude of first raw and column T-point ppglam0 =
999999.000000000
latitude of first raw and column T-point ppgphi0 =
999999.000000000
zonal grid-spacing (degrees) ppe1_deg =
333333.000000000
meridional grid-spacing (degrees) ppe2_deg =
333333.000000000
zonal grid-spacing (degrees) ppe1_m =
333333.000000000
meridional grid-spacing (degrees) ppe2_m =
333333.000000000
ORCA r4, r2 and r05 coefficients ppsur =
999999.000000000
ppa0 =
999999.000000000
ppa1 =
999999.000000000
ppkth =
21.0000000000000
ppacr =
6.00000000000000
Minimum vertical spacing ppdzmin =
2.50000000000000
Maximum depth pphmax =
2200.00000000000
Use double tanf function for vertical coordinates ldbletanh = F
Double tanh function parameters ppa2 =
999999.000000000
ppkth2 =
999999.000000000
ppacr2 =
999999.000000000
cfg_write : create the "domain_cfg.nc" file containing all required configurati
on information
~~~~~~~~~
iom_nf90_open ~~~ create new file: 1_domain_cfg.nc in WRITE
mode
---> 1_domain_cfg.nc OK