Fixed an issue with timeseries reports and the Birkhoff transcription. (

#1040)

* gitignore updates

* Add scripts used to build joss figures

* Added a duplicate method to phase.

* Fixed some issues with fix_initial and fix_final on states. Added duplicate to AnalyticPhase and SimulationPhase, but its not implemented in SimulationPhase yet

* docstring linting

* Fixed occasional extrapolation issue in the birkhoff cannonball case.

* Removed phase duplication from Birkhoff cannonball example until it is more well behaved.

* Made phase options all members of the component options so that they're saved in the Case recorders.

* Bokeh timeseries report handles _system_options with case numbers.

* Remove superfluous system_class option from Trajectory

* traj_results_report.html is created in the cwd if reports directory does not exist.

* Phase duplicate no longer assigns to the read-only `state_options` property in Phase.

* Removed old unused method SimulationPhase.initialize_from_phase

.gitignore

@@ -81,10 +81,15 @@ fort.6
 # mkdocs
 /mkdocs/site
 
-# Examples
-dymos/examples/*/*/_output/
-docs/examples/*/*.db
-docs/dymos_book/examples/*/coloring_files/
+# Docs
+docs/dymos_book/_build
+docs/dymos_book/_srcdocs
+
+# Dymos and OpenMDAO files
+**/*.db
+**/*.sql
+**/coloring_files
+**/reports
 
 # Misc files
 docs/faq/*/*.pkl

docs/dymos_book/api/phase_api.ipynb

@@ -248,6 +248,12 @@
     "        :noindex:\n",
     "```\n",
     "\n",
+    "## duplicate\n",
+    "```{eval-rst}\n",
+    "    .. automethod:: dymos.Phase.duplicate\n",
+    "        :noindex:\n",
+    "```\n",
+    "\n",
     "## set_refine_options\n",
     "```{eval-rst}\n",
     "    .. automethod:: dymos.Phase.set_refine_options\n",

docs/dymos_book/examples/multi_phase_cannonball/multi_phase_cannonball.ipynb

@@ -350,24 +350,16 @@
     "\n",
     "# Second Phase (descent)\n",
     "transcription = dm.GaussLobatto(num_segments=5, order=3, compressed=True)\n",
-    "descent = dm.Phase(ode_class=CannonballODE, transcription=transcription)\n",
+    "# descent = dm.Phase(ode_class=CannonballODE, transcription=transcription)\n",
+    "descent = ascent.duplicate(transcription=transcription)\n",
     "\n",
     "traj.add_phase('descent', descent)\n",
     "\n",
-    "# All initial states and time are free, since\n",
-    "#    they will be linked to the final states of ascent.\n",
-    "# Final altitude is fixed, because we will set\n",
-    "#    it to zero so that the phase ends at ground impact)\n",
-    "descent.set_time_options(initial_bounds=(.5, 100), duration_bounds=(.5, 100),\n",
-    "                         duration_ref=100, units='s')\n",
-    "descent.add_state('r')\n",
-    "descent.add_state('h', fix_initial=False, fix_final=True)\n",
-    "descent.add_state('gam', fix_initial=False, fix_final=False)\n",
-    "descent.add_state('v', fix_initial=False, fix_final=False)\n",
-    "\n",
-    "descent.add_parameter('S', units='m**2', static_target=True)\n",
-    "descent.add_parameter('m', units='kg', static_target=True)\n",
-    "\n",
+    "# Because we copied the descent phase\n",
+    "# - The 'fix_initial' option for time was set to False\n",
+    "# - All state 'fix_initial' and 'fix_final' options are set to False.\n",
+    "# - We only need to fix the final value of altitude so the descent phase ends at ground impact.\n",
+    "descent.set_state_options('h', fix_final=True)\n",
     "descent.add_objective('r', loc='final', scaler=-1.0)\n",
     "\n",
     "# Add internally-managed design parameters to the trajectory.\n",
@@ -554,7 +546,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.7"
+   "version": "3.11.4"
   }
  },
  "nbformat": 4,

dymos/examples/cannonball/test/test_two_phase_cannonball_birkhoff.py

@@ -96,7 +96,7 @@ def setup(self):
         rho_data = USatm1976Data.rho * om.unit_conversion('slug/ft**3', 'kg/m**3')[0]
         self.rho_interp = interp1d(np.array(alt_data, dtype=complex),
                                    np.array(rho_data, dtype=complex),
-                                   kind='linear')
+                                   kind='linear', bounds_error=False, fill_value='extrapolate')
 
     def compute(self, inputs, outputs):
 

dymos/phase/analytic_phase.py

@@ -1,3 +1,5 @@
+from copy import deepcopy
+
 import openmdao.api as om
 
 from .phase import Phase
@@ -472,3 +474,67 @@ def set_simulate_options(self, *args, **kwargs):
             Simulation cannot be performed on AnalyticPhase.
         """
         raise NotImplementedError('Method set_simulate_options is not available for AnalyticPhase.')
+
+    def duplicate(self, num_nodes=None, boundary_constraints=False, path_constraints=False, objectives=False,
+                  fix_initial_time=False):
+        """
+        Create a copy of this phase where most options and attributes are deep copies of those in the original.
+
+        By default, a deepcopy of the transcription in the original phase is used.
+        Boundary constraints, path constraints, and objectives are _NOT_ copied by default, but the user may opt to do so.
+        By default, initial time is not fixed, nor are the initial or final state values.
+        These also can be overridden with the appropriate arguments.
+
+        Parameters
+        ----------
+        num_nodes : int or None
+            The number of nodes to use in the new phase, or None if it should use the same
+            number as the phase being duplicated.
+        boundary_constraints : bool
+            If True, retain all boundary constraints from the phase to be copied.
+        path_constraints : bool
+            If True, retain all path constraints from the phase to be copied.
+        objectives : bool
+            If True, retain all objectives from the phase to be copied.
+        fix_initial_time : bool
+            If True, fix the initial time of the returned phase.
+
+        Returns
+        -------
+        AnalyticPhase
+            The new phase created by duplicating this one.
+        """
+        nn = num_nodes if num_nodes is not None else self.options['num_nodes']
+        ode_class = self.options['ode_class']
+        ode_init_kwargs = self.options['ode_init_kwargs']
+        auto_solvers = self.options['auto_solvers']
+
+        p = AnalyticPhase(num_nodes=nn, ode_class=ode_class, ode_init_kwargs=ode_init_kwargs,
+                          auto_solvers=auto_solvers)
+
+        p.time_options.update(deepcopy(self.time_options))
+        p.time_options['fix_initial'] = fix_initial_time
+
+        for state_name, state_options in self.state_options.items():
+            p.state_options[state_name] = deepcopy(state_options)
+
+        for param_name, param_options in self.parameter_options.items():
+            p.parameter_options[param_name] = deepcopy(param_options)
+
+        p._timeseries = deepcopy(self._timeseries)
+
+        p.refine_options = deepcopy(self.refine_options)
+        p.simulate_options = deepcopy(self.simulate_options)
+        p.timeseries_options = deepcopy(self.timeseries_options)
+
+        if boundary_constraints:
+            p._initial_boundary_constraints = deepcopy(self._initial_boundary_constraints)
+            p._final_boundary_constraints = deepcopy(self._final_boundary_constraints)
+
+        if path_constraints:
+            p._path_constraints = deepcopy(self._path_constraints)
+
+        if objectives:
+            p._objectives = deepcopy(self._objectives)
+
+        return p