Add docstrings, and runtime checks to restart clone test, clean up

payu/models/cice.py

@@ -202,14 +202,32 @@ def setup(self):
             if setup_nml['restart']:
                 self.link_restart(setup_nml['pointer_file'])
 
-        self.calc_timestep_runtime(setup_nml)
+        self.calc_runtime(setup_nml)
 
         # Write any changes to the work directory copy of the cice
         # namelist
         nml_path = os.path.join(self.work_path, self.ice_nml_fname)
         self.ice_in.write(nml_path, force=True)
 
-    def calc_timestep_runtime(self, setup_nml):
+    def calc_runtime(self, setup_nml):
+        """
+        Calculate 1: the previous number of timesteps simulated, and 2:
+        the number of timesteps to simulate in the next run.
+
+        Note 1: This method is overridden in the cice5 driver, as cice5
+        in ACCESS OM2 does not require the calculated runtime information.
+        Instead it performs the calculations within the model using the
+        restart files and OM2 namelist.
+
+        Note 2: For ESM1.5, the actual model start date and run time are
+        controlled via the separate input_ice.nml namelist, with relevant
+        calculations in the access driver.
+
+        Parameters
+        ----------
+        setup_nml: Open 'setup_nml' section of the cice_in.nml namelist.
+        Modifies in place.
+        """
         init_date = datetime.date(year=setup_nml['year_init'], month=1, day=1)
         if setup_nml['days_per_year'] == 365:
             caltype = cal.NOLEAP
@@ -219,13 +237,18 @@ def calc_timestep_runtime(self, setup_nml):
         if self.prior_restart_path:
 
             prior_nml_path = os.path.join(self.prior_restart_path,
-                                        self.ice_nml_fname)
+                                          self.ice_nml_fname)
+
+            # TODO: Are there any models which leave cice_in.nml in
+            # the output rather than restart directory? If not we can remove
+            # this.
+
             # With later versions this file exists in the prior restart path,
             # but this was not always the case, so check, and if not there use
             # prior output path
             if not os.path.exists(prior_nml_path) and self.prior_output_path:
                 prior_nml_path = os.path.join(self.prior_output_path,
-                                                self.ice_nml_fname)
+                                              self.ice_nml_fname)
 
             # If we cannot find a prior namelist, then we cannot determine
             # the start time and must abort the run.
@@ -241,12 +264,13 @@ def calc_timestep_runtime(self, setup_nml):
             prior_runtime_seconds = prior_runtime * prior_setup_nml['dt']
 
         else:
-            # Initialise runtime
+            # If no prior restart directory exists, set the prior runtime to 0
             prior_runtime_seconds = 0
 
-        # Set runtime for this run.
+        # Calculate runtime for this run.
         if self.expt.runtime:
-            run_start_date = cal.date_plus_seconds(init_date, prior_runtime_seconds,
+            run_start_date = cal.date_plus_seconds(init_date,
+                                                   prior_runtime_seconds,
                                                    caltype)
             run_runtime = cal.runtime_from_date(
                 run_start_date,
@@ -258,18 +282,13 @@ def calc_timestep_runtime(self, setup_nml):
             )
         else:
             run_runtime = setup_nml['npt']*setup_nml['dt']
-        
+
         # Add the prior runtime and new runtime to the working copy of the
         # CICE namelist.
         setup_nml['npt'] = run_runtime / setup_nml['dt']
         assert (prior_runtime_seconds % setup_nml['dt'] == 0)
         setup_nml['istep0'] = int(prior_runtime_seconds / setup_nml['dt'])
 
-
-
-
-
-
     def set_local_timestep(self, t_step):
         dt = self.ice_in['setup_nml']['dt']
         npt = self.ice_in['setup_nml']['npt']

payu/models/cice5.py

@@ -53,7 +53,7 @@ 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
+        # Force creation of a dump (restart) file at end of run
         self.ice_in['setup_nml']['dump_last'] = True
 
         super(Cice5, self).setup()
@@ -73,4 +73,8 @@ def set_access_timestep(self, t_step):
         self.set_local_timestep(t_step)
 
     def calc_runtime(self, setup_nml):
+        """
+        Overrides the cice driver method, as CICE5 in OM2 does not use
+        the timing information in the cice_in.nml namelist.
+        """
         pass

test/models/test_cice.py

@@ -17,18 +17,20 @@
 
 verbose = True
 
+DEFAULT_YEAR_INIT = 101  # arbitrary value for tests
+DEFAULT_DT = 3600  # 1 hour
 DEFAULT_CICE_NML = {
     "setup_nml": {
         "history_dir": "./HISTORY/",
         "restart_dir": "./RESTART/",
-        "year_init": 9999,
-        "days_per_year": 360,
+        "year_init": DEFAULT_YEAR_INIT,
+        "days_per_year": 365,
         "ice_ic": "default",
         "restart": False,
         "pointer_file": "./RESTART/ice.restart_file",
         "runtype": "initial",
         "npt": 99999,
-        "dt": 1,
+        "dt": DEFAULT_DT,
     },
     "grid_nml": {"grid_file": "./INPUT/grid.nc", "kmt_file": "./INPUT/kmt.nc"},
     "icefields_nml": {"f_icy": "x"},
@@ -69,7 +71,7 @@ def setup_module(module):
         "model": "cice",
         "exe": "test.exe",
         "experiment": ctrldir_basename,
-        "metadata": {"enable": False},
+        "metadata": {"enable": False}
     }
     write_config(config)
 
@@ -95,7 +97,6 @@ def empty_workdir():
     a clean work directory
     """
     expt_workdir.mkdir(parents=True)
-    print(f"SPENCER {os.path.abspath('.')}")
 
     yield expt_workdir
     shutil.rmtree(expt_workdir)
@@ -191,20 +192,24 @@ class TestClone:
     """
     Test setting up the cice model in cloned control directories.
     """
+    PREVIOUS_ISTEP0 = 0
+    PREVIOUS_NPT = 8760  # 1 year of 1hr timesteps
 
     @pytest.fixture
     def prior_restart_dir_cice4(self, scope="class"):
         """
         Create fake prior restart files required by CICE4's setup.
+        This differs from CICE5, which doesn't require a cice_in.nml
+        file in the restart directory.
         """
         prior_restart_path = expt_archive_dir / "restartxyz"
         os.mkdir(prior_restart_path)
 
         # Previous cice_in namelist with time information
         restart_cice_in = {"setup_nml": {
-                "istep0": 100,
-                "npt": 10,
-                "dt": 123
+                "istep0": self.PREVIOUS_ISTEP0,
+                "npt": self.PREVIOUS_NPT,
+                "dt": DEFAULT_DT
             }}
         f90nml.write(restart_cice_in, prior_restart_path/CICE_NML_NAME)
 
@@ -294,7 +299,7 @@ def test_restart_clone(self, cice_config_files, ctrldir_repo,
         Test that seting up an experiment from a cloned control directory
         works when a restart directory is specified.
 
-        Use a restart directory mimicking the CICE4 restarts required by setup.
+        Use a restart directory mimicking the CICE4 files required by setup.
         """
         source_main = str(ctrldir_repo.active_branch)
 
@@ -313,9 +318,13 @@ def test_restart_clone(self, cice_config_files, ctrldir_repo,
 
         # Setup experiment
         with cd(cloned_repo_path):
-
             lab = payu.laboratory.Laboratory(lab_path=str(labdir))
             expt = payu.experiment.Experiment(lab, reproduce=False)
+
+            # Add a runtime to test calculated cice runtime values
+            expt.runtime = {"years": 0,
+                            "months": 0,
+                            "days": 2}
             model = expt.models[0]
 
             # Test that model setup runs without issue
@@ -324,6 +333,17 @@ def test_restart_clone(self, cice_config_files, ctrldir_repo,
         work_path_files = os.listdir(model.work_path)
         assert CICE_NML_NAME in work_path_files
 
+        # Check correct run time values written to work namelist
+        work_cice_nml = f90nml.read(
+            os.path.join(model.work_path, CICE_NML_NAME)
+            )
+        assert work_cice_nml["setup_nml"]["istep0"] == (
+            self.PREVIOUS_ISTEP0 + self.PREVIOUS_NPT
+        )
+        assert work_cice_nml["setup_nml"]["npt"] == (
+            48
+        )
+
         # Check restart files were copied to cloned experiment's
         # work directory.
         cice_work_restart_files = os.listdir(model.work_restart_path)

test/models/test_cice5.py

@@ -94,7 +94,6 @@ def empty_workdir():
     a clean work directory
     """
     expt_workdir.mkdir(parents=True)
-    print(f"SPENCER {expt_workdir}")
 
     yield expt_workdir
     shutil.rmtree(expt_workdir)
@@ -224,7 +223,7 @@ def prior_restart_dir_cice5(self, scope="class"):
         """
         Create fake prior restart files required by CICE5's setup.
         """
-        prior_restart_path = expt_archive_dir / "restartxyz"
+        prior_restart_path = expt_archive_dir / "restartXYZ"
         os.mkdir(prior_restart_path)
 
         # Restart files required by CICE5 setup