Merge pull request #483 from ACCESS-NRI/esm1.5-patch-cice-history-nml

Enable seperate ice_history.nml & cice_in.nml settings

payu/models/cice.py

@@ -45,6 +45,8 @@ def __init__(self, expt, name, config):
 
         self.ice_nml_fname = 'cice_in.nml'
 
+        self.history_nml_fname = 'ice_history.nml'  # only used by payu
+
         self.set_timestep = self.set_local_timestep
 
         self.copy_inputs = False
@@ -156,6 +158,14 @@ def get_access_ptr_restart_dir(self):
     def setup(self):
         super(Cice, self).setup()
 
+        # If there is a seperate ice_history.nml,
+        # update the cice namelist with its contents
+        history_nml_fpath = os.path.join(self.control_path,
+                                         self.history_nml_fname)
+        if os.path.isfile(history_nml_fpath):
+            history_nml = f90nml.read(history_nml_fpath)
+            self.ice_in.patch(history_nml)
+
         setup_nml = self.ice_in['setup_nml']
         init_date = datetime.date(year=setup_nml['year_init'], month=1, day=1)
 
@@ -244,9 +254,6 @@ def setup(self):
         assert(total_runtime % setup_nml['dt'] == 0)
         setup_nml['istep0'] = int(total_runtime / setup_nml['dt'])
 
-        # Force creation of a dump (restart) file at end of run
-        setup_nml['dump_last'] = True
-
         nml_path = os.path.join(self.work_path, self.ice_nml_fname)
         self.ice_in.write(nml_path, force=True)
 

payu/models/cice5.py

@@ -53,6 +53,9 @@ def set_local_timestep(self, t_step):
         self.ice_in.write(ice_in_path, force=True)
 
     def setup(self):
+       # Force creation of a dump (restart) file at end of run
+        self.ice_in['setup_nml']['dump_last'] = True
+
         super(Cice5, self).setup()
 
         # Make log dir

test/models/test_cice.py

@@ -0,0 +1,144 @@
+import os
+import shutil
+
+import pytest
+import f90nml
+
+import payu
+
+from test.common import cd
+from test.common import tmpdir, ctrldir, labdir, expt_workdir, ctrldir_basename
+from test.common import write_config, write_metadata
+from test.common import make_inputs, make_exe
+
+verbose = True
+
+DEFAULT_CICE_NML = {
+    "setup_nml": {
+        "history_dir": "./HISTORY/",
+        "restart_dir": "./RESTART/",
+        "year_init": 9999,
+        "days_per_year": 360,
+        "ice_ic": "default",
+        "restart": ".false.",
+        "pointer_file": "./RESTART/ice.restart_file",
+        "runtype": "initial",
+        "npt": 99999,
+        "dt": 1,
+    },
+    "grid_nml": {"grid_file": "./INPUT/grid.nc", "kmt_file": "./INPUT/kmt.nc"},
+    "icefields_nml": {"f_icy": "x"},
+}
+CICE_NML_NAME = "cice_in.nml"
+HIST_NML_NAME = "ice_history.nml"
+
+
+def setup_module(module):
+    """
+    Put any test-wide setup code in here, e.g. creating test files
+    """
+    if verbose:
+        print("setup_module      module:%s" % module.__name__)
+
+    # Should be taken care of by teardown, in case remnants lying around
+    try:
+        shutil.rmtree(tmpdir)
+    except FileNotFoundError:
+        pass
+
+    try:
+        tmpdir.mkdir()
+        labdir.mkdir()
+        ctrldir.mkdir()
+        expt_workdir.mkdir(parents=True)
+        make_inputs()
+        make_exe()
+        write_metadata()
+    except Exception as e:
+        print(e)
+
+    config = {
+        "laboratory": "lab",
+        "jobname": "testrun",
+        "model": "cice",
+        "exe": "test.exe",
+        "experiment": ctrldir_basename,
+        "metadata": {"enable": False},
+    }
+    write_config(config)
+
+
+def teardown_module(module):
+    """
+    Put any test-wide teardown code in here, e.g. removing test outputs
+    """
+    if verbose:
+        print("teardown_module   module:%s" % module.__name__)
+
+    try:
+        shutil.rmtree(tmpdir)
+        print("removing tmp")
+    except Exception as e:
+        print(e)
+
+
+# Confirm that 1: payu overwrites cice_in with ice_history
+# 2: payu works without ice_history.nml
+# 3: payu overwrites cice_in and allows additional fields
+# In all cases confirm dump_last is not added to model_type='cice'
+@pytest.mark.parametrize(
+    "ice_history",
+    [
+        {"icefields_nml": { "f_icy": "m" }},
+        False,
+        {"icefields_nml": {"f_icy": "m", "f_new": "y"}},
+    ],
+)
+def test_setup(ice_history):
+    cice_nml = DEFAULT_CICE_NML
+
+    # create the files parsed by setup:
+    # 1. a restart pointer file
+    with cd(expt_workdir):
+        os.mkdir(cice_nml["setup_nml"]["restart_dir"])
+        with open(cice_nml["setup_nml"]["pointer_file"], "w") as f:
+            f.write("./RESTART/ice.r")
+            f.close()
+
+    with cd(ctrldir):
+        # 2. Create config.nml
+        f90nml.write(cice_nml, CICE_NML_NAME)
+        if ice_history:
+            f90nml.write(ice_history, HIST_NML_NAME)
+
+        lab = payu.laboratory.Laboratory(lab_path=str(labdir))
+        expt = payu.experiment.Experiment(lab, reproduce=False)
+        model = expt.models[0]
+
+        # Function to test
+        model.setup()
+
+    # Check config files are moved to model's work path
+    work_path_files = os.listdir(model.work_path)
+    assert CICE_NML_NAME in work_path_files
+
+    # Check cice_in was patched with ice_history
+    work_input_fpath = os.path.join(model.work_path, CICE_NML_NAME)
+    input_nml = f90nml.read(work_input_fpath)
+    if ice_history:
+        assert input_nml["icefields_nml"] == ice_history["icefields_nml"]
+    else:
+        assert input_nml["icefields_nml"] == DEFAULT_CICE_NML["icefields_nml"]
+
+    # Check dump_last doesn't exist
+    with pytest.raises(KeyError, match="dump_last"):
+        input_nml["setup_nml"]["dump_last"]
+
+    # cleanup
+    with cd(expt_workdir):
+        os.remove(cice_nml["setup_nml"]["pointer_file"])
+        os.rmdir(cice_nml["setup_nml"]["restart_dir"])
+    with cd(ctrldir):
+        os.remove(CICE_NML_NAME)
+        if ice_history:
+            os.remove(HIST_NML_NAME)