diff --git a/Inst_eddies/Tests/long_tests.json b/Inst_eddies/Tests/long_tests.json
index 3dcee46aaeb8694463d6098c950e07e589391c04..4ff37cec549989b5b791695c147eaae5ce5c7541 100644
--- a/Inst_eddies/Tests/long_tests.json
+++ b/Inst_eddies/Tests/long_tests.json
@@ -6,15 +6,14 @@
"mkdir", "-p", "SHPC/Slice_0/Cyclones",
"SHPC/Slice_0/Anticyclones"
],
- "$build_dir/Inst_eddies/Tests/test_set_all_outerm"
+ [
+ "$build_dir/Inst_eddies/Tests/test_set_all_outerm",
+ "$src_dir/Inst_eddies/Tests/Input/h_region_3.nc",
+ "$src_dir/Inst_eddies/Tests/Input/uv_region_3.nc"
+ ]
],
"title": "Set_all_outerm",
- "create_file": ["config_nml.txt", "&config_nml min_radius = 20./\n"],
- "symlink":
- [
- ["$src_dir/Inst_eddies/Tests/Input/h_region_3.nc", "h.nc"],
- ["$src_dir/Inst_eddies/Tests/Input/uv_region_3.nc", "uv.nc"]
- ]
+ "create_file": ["config_nml.txt", "&config_nml min_radius = 20./\n"]
},
{
"commands":
@@ -23,14 +22,13 @@
"mkdir", "-p", "SHPC/Slice_0/Cyclones",
"SHPC/Slice_0/Anticyclones"
],
- "$build_dir/Inst_eddies/inst_eddies"
+ [
+ "$build_dir/Inst_eddies/inst_eddies",
+ "$src_dir/Inst_eddies/Tests/Input/h_region_3.nc",
+ "$src_dir/Inst_eddies/Tests/Input/uv_region_3.nc"
+ ]
],
"title": "Extraction_eddies_region_3",
- "symlink":
- [
- ["$src_dir/Inst_eddies/Tests/Input/h_region_3.nc", "h.nc"],
- ["$src_dir/Inst_eddies/Tests/Input/uv_region_3.nc", "uv.nc"]
- ],
"create_file": ["config_nml.txt", "&config_nml min_amp = 0./\n"],
"input": "&dates_nml date = 20454/\n",
"description": "Larger region, 120 x 120. Includes degenerate extrema."
@@ -42,14 +40,13 @@
"mkdir", "-p", "SHPC/Slice_0/Cyclones",
"SHPC/Slice_0/Anticyclones"
],
- "$build_dir/Inst_eddies/inst_eddies"
+ [
+ "$build_dir/Inst_eddies/inst_eddies",
+ "$src_dir/Inst_eddies/Tests/Input/h_region_3.nc",
+ "$src_dir/Inst_eddies/Tests/Input/uv_region_3.nc"
+ ]
],
"title": "Extraction_eddies_region_3_min",
- "symlink":
- [
- ["$src_dir/Inst_eddies/Tests/Input/h_region_3.nc", "h.nc"],
- ["$src_dir/Inst_eddies/Tests/Input/uv_region_3.nc", "uv.nc"]
- ],
"create_file": ["config_nml.txt", "&config_nml /\n"],
"input": "&dates_nml date = 20454/\n",
"description":
@@ -62,14 +59,13 @@
"mkdir", "-p", "SHPC/Slice_0/Cyclones",
"SHPC/Slice_0/Anticyclones"
],
- "$build_dir/Inst_eddies/inst_eddies"
+ [
+ "$build_dir/Inst_eddies/inst_eddies",
+ "$src_dir/Inst_eddies/Tests/Input/h_region_5.nc",
+ "$src_dir/Inst_eddies/Tests/Input/uv_region_5.nc"
+ ]
],
"title": "Extraction_eddies_region_5",
- "symlink":
- [
- ["$src_dir/Inst_eddies/Tests/Input/h_region_5.nc", "h.nc"],
- ["$src_dir/Inst_eddies/Tests/Input/uv_region_5.nc", "uv.nc"]
- ],
"create_file": ["config_nml.txt", "&config_nml /\n"],
"input": "&dates_nml date = 20454/\n",
"description": "Same as Extraction_eddies_region_4 with larger domain.",
diff --git a/Inst_eddies/Tests/short_tests.json b/Inst_eddies/Tests/short_tests.json
index 7e60c76ab13091840735981997b1f6490c3e97c0..324c7d54f291a5f0eba1be7b687e5816eba51144 100644
--- a/Inst_eddies/Tests/short_tests.json
+++ b/Inst_eddies/Tests/short_tests.json
@@ -5,14 +5,6 @@
"title": "Get_1_outerm",
"symlink":
[
- [
- "$src_dir/Inst_eddies/Tests/Input/Region_1/huv_region_1_2006_01_01.nc",
- "h.nc"
- ],
- [
- "$src_dir/Inst_eddies/Tests/Input/Region_1/huv_region_1_2006_01_01.nc",
- "uv.nc"
- ],
[
"$src_dir/Inst_eddies/Tests/Input/Region_1/outside_points_get_1_outerm.csv",
"outside_points.csv"
@@ -21,7 +13,11 @@
"commands":
[
["mkdir", "-p", "SHPC/Slice_0/Cyclones"],
- "$build_dir/Inst_eddies/Tests/test_get_1_outerm"
+ [
+ "$build_dir/Inst_eddies/Tests/test_get_1_outerm",
+ "$src_dir/Inst_eddies/Tests/Input/Region_1/huv_region_1_2006_01_01.nc",
+ "$src_dir/Inst_eddies/Tests/Input/Region_1/huv_region_1_2006_01_01.nc"
+ ]
]
},
{
@@ -31,21 +27,15 @@
"create_file": ["config_nml.txt", "&config_nml /\n"],
"title": "Get_1_outerm_noise_2_8",
"symlink":
- [
- [
- "$src_dir/Inst_eddies/Tests/Input/Region_1/huv_region_1_2006_01_01.nc",
- "h.nc"
- ],
- [
- "$src_dir/Inst_eddies/Tests/Input/Region_1/huv_region_1_2006_01_01.nc",
- "uv.nc"
- ],
- "$src_dir/Inst_eddies/Tests/Input/Region_1/outside_points.csv"
- ],
+ ["$src_dir/Inst_eddies/Tests/Input/Region_1/outside_points.csv"],
"commands":
[
["mkdir", "-p", "SHPC/Slice_0/Cyclones"],
- "$build_dir/Inst_eddies/Tests/test_get_1_outerm"
+ [
+ "$build_dir/Inst_eddies/Tests/test_get_1_outerm",
+ "$src_dir/Inst_eddies/Tests/Input/Region_1/huv_region_1_2006_01_01.nc",
+ "$src_dir/Inst_eddies/Tests/Input/Region_1/huv_region_1_2006_01_01.nc"
+ ]
]
},
{
@@ -55,14 +45,6 @@
"title": "Get_1_outerm_noise_2",
"symlink":
[
- [
- "$src_dir/Inst_eddies/Tests/Input/Region_1/huv_region_1_2006_01_01.nc",
- "h.nc"
- ],
- [
- "$src_dir/Inst_eddies/Tests/Input/Region_1/huv_region_1_2006_01_01.nc",
- "uv.nc"
- ],
[
"$src_dir/Inst_eddies/Tests/Input/Region_1/outside_points_get_1_outerm_noise_2.csv",
"outside_points.csv"
@@ -71,7 +53,11 @@
"commands":
[
["mkdir", "-p", "SHPC/Slice_0/Cyclones"],
- "$build_dir/Inst_eddies/Tests/test_get_1_outerm"
+ [
+ "$build_dir/Inst_eddies/Tests/test_get_1_outerm",
+ "$src_dir/Inst_eddies/Tests/Input/Region_1/huv_region_1_2006_01_01.nc",
+ "$src_dir/Inst_eddies/Tests/Input/Region_1/huv_region_1_2006_01_01.nc"
+ ]
]
},
{
@@ -252,14 +238,6 @@
"create_file": ["config_nml.txt", "&config_nml /\n"],
"symlink":
[
- [
- "$src_dir/Inst_eddies/Tests/Input/h_outermost.nc",
- "h.nc"
- ],
- [
- "$src_dir/Inst_eddies/Tests/Input/uv_outermost.nc",
- "uv.nc"
- ],
[
"$src_dir/Inst_eddies/Tests/Input/empty_outside_points.csv",
"outside_points.csv"
@@ -271,6 +249,8 @@
["mkdir", "-p", "SHPC/Slice_0/Cyclones"],
[
"$build_dir/Inst_eddies/Tests/test_set_max_speed",
+ "$src_dir/Inst_eddies/Tests/Input/h_outermost.nc",
+ "$src_dir/Inst_eddies/Tests/Input/uv_outermost.nc",
"$PWD/Get_1_outerm/SHPC"
]
],
@@ -279,23 +259,15 @@
{
"create_file": ["config_nml.txt", "&config_nml /\n"],
"symlink":
- [
- [
- "$src_dir/Inst_eddies/Tests/Input/Region_1/huv_region_1_2006_01_01.nc",
- "h.nc"
- ],
- [
- "$src_dir/Inst_eddies/Tests/Input/Region_1/huv_region_1_2006_01_01.nc",
- "uv.nc"
- ],
- "$src_dir/Inst_eddies/Tests/Input/Region_1/outside_points.csv"
- ],
+ ["$src_dir/Inst_eddies/Tests/Input/Region_1/outside_points.csv"],
"title": "Set_max_speed_noise",
"commands":
[
["mkdir", "-p", "SHPC/Slice_0/Cyclones"],
[
"$build_dir/Inst_eddies/Tests/test_set_max_speed",
+ "$src_dir/Inst_eddies/Tests/Input/Region_1/huv_region_1_2006_01_01.nc",
+ "$src_dir/Inst_eddies/Tests/Input/Region_1/huv_region_1_2006_01_01.nc",
"$PWD/Get_1_outerm_noise_2_8/SHPC"
]
],
@@ -305,8 +277,6 @@
"create_file": ["config_nml.txt", "&config_nml /\n"],
"symlink":
[
- ["$src_dir/Inst_eddies/Tests/Input/degenerated_SSH.nc", "h.nc"],
- ["$src_dir/Inst_eddies/Tests/Input/degenerated_SSH.nc", "uv.nc"],
[
"$src_dir/Inst_eddies/Tests/Input/empty_outside_points.csv",
"outside_points.csv"
@@ -319,6 +289,8 @@
["mkdir", "-p", "SHPC/Slice_0/Anticyclones"],
[
"$build_dir/Inst_eddies/Tests/test_set_max_speed",
+ "$src_dir/Inst_eddies/Tests/Input/degenerated_SSH.nc",
+ "$src_dir/Inst_eddies/Tests/Input/degenerated_SSH.nc",
"$src_dir/Inst_eddies/Tests/Input/SHPC_degenerate"
]
],
@@ -327,23 +299,17 @@
{
"create_file": ["config_nml.txt", "&config_nml min_amp = 0./\n"],
"input": "&dates_nml date = 20454/\n",
- "symlink": [
- [
- "$src_dir/Inst_eddies/Tests/Input/Region_1/huv_region_1_2006_01_01.nc",
- "h.nc"
- ],
- [
- "$src_dir/Inst_eddies/Tests/Input/Region_1/huv_region_1_2006_01_01.nc",
- "uv.nc"
- ]
- ],
"title": "Extraction_eddies_region_1",
"commands": [
[
"mkdir", "-p", "SHPC/Slice_0/Cyclones",
"SHPC/Slice_0/Anticyclones"
],
- "$build_dir/Inst_eddies/inst_eddies"
+ [
+ "$build_dir/Inst_eddies/inst_eddies",
+ "$src_dir/Inst_eddies/Tests/Input/Region_1/huv_region_1_2006_01_01.nc",
+ "$src_dir/Inst_eddies/Tests/Input/Region_1/huv_region_1_2006_01_01.nc"
+ ]
]
},
{
@@ -351,40 +317,33 @@
"Same as Extraction_eddies_region_1 but with non-zero minimal amplitude.",
"create_file": ["config_nml.txt", "&config_nml /\n"],
"input": "&dates_nml date = 20454/\n",
- "symlink":
- [
- [
- "$src_dir/Inst_eddies/Tests/Input/Region_1/huv_region_1_2006_01_01.nc",
- "h.nc"
- ],
- [
- "$src_dir/Inst_eddies/Tests/Input/Region_1/huv_region_1_2006_01_01.nc",
- "uv.nc"
- ]
- ],
"title": "Extraction_eddies_region_1_noise",
"commands": [
[
"mkdir", "-p", "SHPC/Slice_0/Cyclones",
"SHPC/Slice_0/Anticyclones"
],
- "$build_dir/Inst_eddies/inst_eddies"
+ [
+ "$build_dir/Inst_eddies/inst_eddies",
+ "$src_dir/Inst_eddies/Tests/Input/Region_1/huv_region_1_2006_01_01.nc",
+ "$src_dir/Inst_eddies/Tests/Input/Region_1/huv_region_1_2006_01_01.nc"
+ ]
]
},
{
"create_file": ["config_nml.txt", "&config_nml min_amp = 0./\n"],
"input": "&dates_nml date = 20454/\n",
- "symlink": [
- ["$src_dir/Inst_eddies/Tests/Input/h_region_2.nc", "h.nc"],
- ["$src_dir/Inst_eddies/Tests/Input/uv_region_2.nc", "uv.nc"]
- ],
"title": "Extraction_eddies_region_2",
"commands": [
[
"mkdir", "-p", "SHPC/Slice_0/Cyclones",
"SHPC/Slice_0/Anticyclones"
],
- "$build_dir/Inst_eddies/inst_eddies"
+ [
+ "$build_dir/Inst_eddies/inst_eddies",
+ "$src_dir/Inst_eddies/Tests/Input/h_region_2.nc",
+ "$src_dir/Inst_eddies/Tests/Input/uv_region_2.nc"
+ ]
]
},
{
@@ -449,16 +408,12 @@
"mkdir", "-p", "SHPC/Slice_0/Cyclones",
"SHPC/Slice_0/Anticyclones"
],
- "$build_dir/Inst_eddies/Tests/test_set_all_outerm"
- ],
- "symlink":
- [
- ["$src_dir/Inst_eddies/Tests/Input/h_2006_01_01_coarse.nc", "h.nc"],
[
- "$src_dir/Inst_eddies/Tests/Input/uv_2006_01_01_coarse.nc",
- "uv.nc"
+ "$build_dir/Inst_eddies/Tests/test_set_all_outerm",
+ "$src_dir/Inst_eddies/Tests/Input/h_2006_01_01_coarse.nc",
+ "$src_dir/Inst_eddies/Tests/Input/uv_2006_01_01_coarse.nc"
]
- ]
+ ]
},
{
"description": "Periodic domain.",
@@ -468,23 +423,17 @@
"&config_nml min_amp = 0., MAX_RADIUS_deg = 80., 72./\n"
],
"input": "&dates_nml date = 20454/\n",
- "symlink": [
- [
- "$src_dir/Inst_eddies/Tests/Input/h_2006_01_01_coarse.nc",
- "h.nc"
- ],
- [
- "$src_dir/Inst_eddies/Tests/Input/uv_2006_01_01_coarse.nc",
- "uv.nc"
- ]
- ],
"title": "Extraction_eddies_periodic",
"commands": [
[
"mkdir", "-p", "SHPC/Slice_0/Cyclones",
"SHPC/Slice_0/Anticyclones"
],
- "$build_dir/Inst_eddies/inst_eddies"
+ [
+ "$build_dir/Inst_eddies/inst_eddies",
+ "$src_dir/Inst_eddies/Tests/Input/h_2006_01_01_coarse.nc",
+ "$src_dir/Inst_eddies/Tests/Input/uv_2006_01_01_coarse.nc"
+ ]
]
},
{
@@ -494,14 +443,6 @@
"title": "Extr_proj",
"symlink":
[
- [
- "$src_dir/Inst_eddies/Tests/Input/Region_1/huv_region_1_2006_01_01.nc",
- "h.nc"
- ],
- [
- "$src_dir/Inst_eddies/Tests/Input/Region_1/huv_region_1_2006_01_01.nc",
- "uv.nc"
- ],
[
"$src_dir/Inst_eddies/Tests/Input/Region_1/outside_points_get_1_outerm.csv",
"outside_points.csv"
@@ -510,7 +451,11 @@
"commands":
[
["mkdir", "-p", "SHPC/Slice_0/Cyclones"],
- "$build_dir/Inst_eddies/Tests/test_get_1_outerm"
+ [
+ "$build_dir/Inst_eddies/Tests/test_get_1_outerm",
+ "$src_dir/Inst_eddies/Tests/Input/Region_1/huv_region_1_2006_01_01.nc",
+ "$src_dir/Inst_eddies/Tests/Input/Region_1/huv_region_1_2006_01_01.nc"
+ ]
]
},
{
diff --git a/Inst_eddies/Tests/test_set_max_speed.f90 b/Inst_eddies/Tests/test_set_max_speed.f90
index 1bdc7527d182ac5eef8a247b5c1d19a21f905691..68d5cf54684f9c4fde340468b62d33fcb9e0b3bd 100644
--- a/Inst_eddies/Tests/test_set_max_speed.f90
+++ b/Inst_eddies/Tests/test_set_max_speed.f90
@@ -30,12 +30,12 @@ program test_set_max_speed
!----------------------------------------------------------------
- call get_command_arg_dyn(1, shpc_dir, "Required argument: SHPC-directory")
print *, "test_set_max_speed: cyclone = ? "
read *, cyclone
call config
call input_ssh(corner, step, nlon, nlat, periodic, ssh, u, v)
print *, "test_set_max_speed: Reading from shapefiles..."
+ call get_command_arg_dyn(3, shpc_dir, "Required 3rd argument: SHPC-directory")
call shpc_open(hshp, shpc_dir, cyclone, slice = 0, pszaccess = "rb")
call read_eddy(e, d, i, hshp, ishape = 0)
CALL shpc_close(hshp)
diff --git a/Inst_eddies/input_ssh.f90 b/Inst_eddies/input_ssh.f90
index 9726cef49fe953ebb592816779cb3659e0c6d9db..e6f8d5b89394cfc3da9bfe69ca68616a21f059e5 100644
--- a/Inst_eddies/input_ssh.f90
+++ b/Inst_eddies/input_ssh.f90
@@ -13,7 +13,7 @@ contains
use, intrinsic:: ieee_arithmetic, only: ieee_value, IEEE_QUIET_NAN
! Libraries:
- use jumble, only: new_unit, assert, deg_to_rad, twopi
+ use jumble, only: new_unit, assert, deg_to_rad, twopi, get_command_arg_dyn
use netcdf95, only: nf95_open, nf95_find_coord, nf95_inquire_dimension, &
nf95_get_var, nf95_close, nf95_nowrite
@@ -53,13 +53,14 @@ contains
real corner_deg_new(2), step_deg_new(2)
real lon_max, lat_max ! longitude and latitude, in degrees
integer copy
-
+ character(len = :), allocatable:: fname ! file name
namelist /grid_nml/ corner_deg, step_deg, nlon, nlat
!----------------------------------------------------------------------
inquire(file = "SHPC/grid_nml.txt", exist = exist)
- call nf95_open("h.nc", nf95_nowrite, ncid)
+ call get_command_arg_dyn(1, fname, "Required arguments: h-file uv-file")
+ call nf95_open(fname, nf95_nowrite, ncid)
call nf95_find_coord(ncid, dimid = dimid, varid = varid, &
std_name = "longitude")
call new_unit(unit)
@@ -139,7 +140,8 @@ contains
! works with an upper limit for valid values.)
call nf95_close(ncid)
- call nf95_open("uv.nc", nf95_nowrite, ncid)
+ call get_command_arg_dyn(2, fname, "Required arguments: h-file uv-file")
+ call nf95_open(fname, nf95_nowrite, ncid)
call get_var(periodic, max_radius(1), u, ncid, nlon, name = "ugos", &
new_fill_value = ieee_value(0., IEEE_QUIET_NAN))
call get_var(periodic, max_radius(1), v, ncid, nlon, name = "vgos", &
diff --git a/Inst_eddies/inst_eddies.py.in b/Inst_eddies/inst_eddies.py.in
index 695104ff7386efa8bc40278692e43d97a16b29ef..5b837cd13373f86b781c1b1618ca73fc5c127cf6 100644
--- a/Inst_eddies/inst_eddies.py.in
+++ b/Inst_eddies/inst_eddies.py.in
@@ -75,15 +75,12 @@ def loop_inst_eddies(files, bbox, d, my_slice):
nco_instance.ncpdq(nc_file, output = "unpacked.nc",
options = ["--unpack"])
- os.symlink("unpacked.nc", "h.nc")
- os.symlink("unpacked.nc", "uv.nc")
elapsed_NCO = time.perf_counter() - my_pc
my_pc = time.perf_counter()
- subprocess.run(inst_eddies_exe, check = True, input = "&dates_nml "
- f"date = {d}, slice = {my_slice}/\n", text = True)
+ subprocess.run([inst_eddies_exe, "unpacked.nc", "unpacked.nc"],
+ check = True, input = f"&dates_nml date = {d}, "
+ f"slice = {my_slice}/\n", text = True)
elapsed_Fortran = time.perf_counter() - my_pc
- os.remove("h.nc")
- os.remove("uv.nc")
writer.writerow([d, elapsed_NCO, elapsed_Fortran])
else:
print("inst_eddies.loop_inst_eddies: Missing file:", nc_file)