Merge pull request #211 from kejacobson/geometry_access

Add a geometry base class to the MPhys variable convention

Author: kejacobson

.flake8

@@ -0,0 +1,59 @@
+[flake8]
+max-line-length = 120
+
+extend-ignore =
+    # black
+    E203,
+    # too many leading '#' for block comment
+    E266,
+    # expected 2 blank lines, found 1
+    E302,
+    # do not use mutable data structures for argument defaults (too many false positives)
+    B006,
+    # ===== TODO: to be fixed:
+    # invalid escape sequence, necessary for sphinx directives in docstrings but should switch to raw string
+    W605,
+    # line length, exceeded by some docstrings
+    E501,
+    # Function definition does not bind loop variable, happens everywhere in our code
+    B023,
+    # pydocstyle
+    D
+
+# Only add patterns here that are not included by the defaults of flake8 or other plugins
+# extend-select =
+
+# flake8-docstrings
+docstring-convention = numpy
+
+# flake8-rst-docstrings
+rst-roles =
+    class,
+    func,
+    ref,
+    meth,
+
+rst-directives =
+    # Custom directives defined in the sphinx_mdolab_theme
+    embed-compare,
+    embed-bibtex,
+    embed-code,
+    embed-shell-cmd,
+    embed-n2,
+
+# mccabe complexity
+# max-complexity = 10
+
+# ignored files/directories
+# we use exclude here and extend-exclude in repo-specific config files
+# so that we can pass both to flake8 directly without needing to merge them first
+exclude =
+    # No need to traverse the git directory
+    .git,
+    # There's no value in checking cache directories
+    __pycache__,
+    # The conf file is mostly autogenerated, ignore it
+    doc/conf.py,
+    # No need for init and setup files
+    __init__.py,
+    setup.py,

.vscode/extensions.json

@@ -0,0 +1,16 @@
+{
+	// See https://go.microsoft.com/fwlink/?LinkId=827846 to learn about workspace recommendations.
+	// Extension identifier format: ${publisher}.${name}. Example: vscode.csharp
+
+	// List of extensions which should be recommended for users of this workspace.
+	"recommendations": [
+		"ms-python.python",
+		"ms-python.isort",
+		"ms-python.flake8",
+		"ms-python.black-formatter",
+	],
+	// List of extensions recommended by VS Code that should not be recommended for users of this workspace.
+	"unwantedRecommendations": [
+
+	]
+}

.vscode/settings.json

@@ -1,16 +1,10 @@
 {
-    "python.formatting.provider": "black",
-    "python.testing.unittestArgs": [
-        "-v",
-        "-s",
-        "./tests/unit_tests",
-        "-p",
-        "test*.py"
-    ],
-    "python.testing.pytestEnabled": false,
-    "python.testing.nosetestsEnabled": false,
-    "python.testing.unittestEnabled": true,
-    "python.analysis.useImportHeuristic": true,
-    "esbonio.server.enabled": true,
-    "esbonio.sphinx.confDir": "${workspaceFolder}/docs"
+    "[python]": {
+        "editor.defaultFormatter": "ms-python.black-formatter",
+        "editor.formatOnSave": true, // black on save
+        "editor.codeActionsOnSave": {
+            "source.organizeImports": "always" // isort on save
+        }
+    },
+    "flake8.args": ["--config", ".flake8"]
 }

examples/aerostructural/supersonic_panel/as_opt_parallel.py

@@ -8,12 +8,9 @@
 from structures_mphys import StructBuilder
 from xfer_mphys import XferBuilder
 
-from mphys import Multipoint, MultipointParallel
+from mphys import MPhysVariables, MultipointParallel
 from mphys.scenarios.aerostructural import ScenarioAeroStructural
 
-# True=check objective/constraint derivatives, False=run optimization
-check_totals = False
-
 # panel geometry
 panel_chord = 0.3
 panel_width = 0.01
@@ -23,7 +20,6 @@
 N_el_aero = 7
 
 
-# Mphys parallel multipoint scenarios
 class AerostructParallel(MultipointParallel):
     def initialize(self):
         self.options.declare("aero_builder")
@@ -108,8 +104,13 @@ def setup(self):
         )
 
         # geometry
-        builders = {"struct": struct_builder, "aero": aero_builder}
-        geometry_builder = GeometryBuilder(builders)
+        geometry_builder = GeometryBuilder()
+        geometry_builder.add_discipline(
+            struct_builder, MPhysVariables.Structures.Geometry
+        )
+        geometry_builder.add_discipline(
+            aero_builder, MPhysVariables.Aerodynamics.Surface.Geometry
+        )
 
         # add parallel multipoint group
         self.add_subsystem(
@@ -125,38 +126,34 @@ def setup(self):
 
         for i in range(len(self.scenario_names)):
 
-            # connect scalar inputs to the scenario
             for var in ["modulus", "yield_stress", "density", "dv_struct"]:
                 self.connect(var, "multipoint." + self.scenario_names[i] + "." + var)
 
-            # connect vector inputs
             for var in ["mach", "qdyn", "aoa"]:
                 self.connect(
                     var,
                     "multipoint." + self.scenario_names[i] + "." + var,
                     src_indices=[i],
                 )
 
-            # connect top-level geom parameter
             self.connect(
                 "geometry_morph_param",
                 "multipoint."
                 + self.scenario_names[i]
                 + ".geometry.geometry_morph_param",
             )
 
-        # add design vars
         self.add_design_var("geometry_morph_param", lower=0.1, upper=10.0)
         self.add_design_var("dv_struct", lower=1.0e-4, upper=1.0e-2, ref=1.0e-3)
         self.add_design_var("aoa", lower=-20.0, upper=20.0)
 
-        # add objective/constraints
         self.add_objective(f"multipoint.{self.scenario_names[0]}.mass", ref=0.01)
         self.add_constraint(
             f"multipoint.{self.scenario_names[0]}.func_struct",
             upper=1.0,
             parallel_deriv_color="struct_cons",
         )  # run func_struct derivatives in parallel
+
         self.add_constraint(
             f"multipoint.{self.scenario_names[1]}.func_struct",
             upper=1.0,
@@ -168,6 +165,7 @@ def setup(self):
             ref=0.1,
             parallel_deriv_color="lift_cons",
         )  # run C_L derivatives in parallel
+
         self.add_constraint(
             f"multipoint.{self.scenario_names[1]}.C_L",
             lower=0.45,
@@ -180,101 +178,92 @@ def get_model(scenario_names):
     return Model(scenario_names=scenario_names)
 
 
-# run model and check derivatives
-if __name__ == "__main__":
-
-    prob = om.Problem()
-    prob.model = Model()
-
-    if check_totals:
-        prob.setup(mode="rev")
-        om.n2(prob, show_browser=False, outfile="n2.html")
-        prob.run_model()
-        prob.check_totals(
-            step_calc="rel_avg",
-            compact_print=True,
-            directional=False,
-            show_progress=True,
-            out_stream=None if prob.model.comm.rank > 0 else _DEFAULT_OUT_STREAM,
-        )
-
-    else:
-
-        # setup optimization driver
-        prob.driver = om.ScipyOptimizeDriver(
-            debug_print=["nl_cons", "objs", "desvars", "totals"]
-        )
-        prob.driver.options["optimizer"] = "SLSQP"
-        prob.driver.options["tol"] = 1e-5
-        prob.driver.options["disp"] = True
-        prob.driver.options["maxiter"] = 300
-
-        # add optimization recorder
-        prob.driver.recording_options["record_objectives"] = True
-        prob.driver.recording_options["record_constraints"] = True
-        prob.driver.recording_options["record_desvars"] = True
-        prob.driver.recording_options["record_derivatives"] = True
-
-        recorder = om.SqliteRecorder("optimization_history.sql")
-        prob.driver.add_recorder(recorder)
-
-        # run the optimization
-        prob.setup(mode="rev")
-        prob.run_driver()
-        prob.cleanup()
-
-        if prob.model.comm.rank == 0:  # write out data
-            cr = om.CaseReader(f"{prob.get_outputs_dir()}/optimization_history.sql")
-            driver_cases = cr.list_cases("driver")
-
-            case = cr.get_case(0)
-            cons = case.get_constraints()
-            dvs = case.get_design_vars()
-            objs = case.get_objectives()
-
-            f = open("optimization_history.dat", "w+")
-
+def run_check_totals(prob: om.Problem):
+    prob.setup(mode="rev")
+    om.n2(prob, show_browser=False, outfile="n2.html")
+    prob.run_model()
+    prob.check_totals(
+        step_calc="rel_avg",
+        compact_print=True,
+        directional=False,
+        show_progress=True,
+        out_stream=None if prob.model.comm.rank > 0 else _DEFAULT_OUT_STREAM,
+    )
+
+
+def run_optimization(prob: om.Problem):
+    prob.driver = om.ScipyOptimizeDriver(
+        debug_print=["nl_cons", "objs", "desvars", "totals"]
+    )
+    prob.driver.options["optimizer"] = "SLSQP"
+    prob.driver.options["tol"] = 1e-5
+    prob.driver.options["disp"] = True
+    prob.driver.options["maxiter"] = 300
+
+    # add optimization recorder
+    prob.driver.recording_options["record_objectives"] = True
+    prob.driver.recording_options["record_constraints"] = True
+    prob.driver.recording_options["record_desvars"] = True
+    prob.driver.recording_options["record_derivatives"] = True
+
+    recorder = om.SqliteRecorder("optimization_history.sql")
+    prob.driver.add_recorder(recorder)
+
+    # run the optimization
+    prob.setup(mode="rev")
+    prob.run_driver()
+    prob.cleanup()
+
+    write_out_optimization_data(prob, "optimization_history.sql")
+
+
+def write_out_optimization_data(prob: om.Problem, sql_file: str):
+    if prob.model.comm.rank == 0:
+        cr = om.CaseReader(f"{prob.get_outputs_dir()}/{sql_file}")
+        driver_cases = cr.list_cases("driver")
+
+        case = cr.get_case(0)
+        cons = case.get_constraints()
+        dvs = case.get_design_vars()
+        objs = case.get_objectives()
+
+        with open("optimization_history.dat", "w+") as f:
             for i, k in enumerate(objs.keys()):
                 f.write("objective: " + k + "\n")
                 for j, case_id in enumerate(driver_cases):
                     f.write(
-                        str(j)
-                        + " "
-                        + str(cr.get_case(case_id).get_objectives(scaled=False)[k][0])
-                        + "\n"
+                        f"{j} {cr.get_case(case_id).get_objectives(scaled=False)[k][0]}\n"
                     )
-                f.write(" " + "\n")
+                f.write("\n")
 
             for i, k in enumerate(cons.keys()):
                 f.write("constraint: " + k + "\n")
                 for j, case_id in enumerate(driver_cases):
-                    f.write(
-                        str(j)
-                        + " "
-                        + " ".join(
-                            map(
-                                str,
-                                cr.get_case(case_id).get_constraints(scaled=False)[k],
-                            )
-                        )
-                        + "\n"
-                    )
-                f.write(" " + "\n")
+                    constraints = cr.get_case(case_id).get_constraints(scaled=False)[k]
+                    line = f"{j} {' '.join(map(str, constraints))}\n"
+                    f.write(line)
+                f.write("\n")
 
             for i, k in enumerate(dvs.keys()):
                 f.write("DV: " + k + "\n")
                 for j, case_id in enumerate(driver_cases):
-                    f.write(
-                        str(j)
-                        + " "
-                        + " ".join(
-                            map(
-                                str,
-                                cr.get_case(case_id).get_design_vars(scaled=False)[k],
-                            )
-                        )
-                        + "\n"
-                    )
-                f.write(" " + "\n")
+                    design_vars = cr.get_case(case_id).get_design_vars(scaled=False)[k]
+                    line = f"{j} {' '.join(map(str, design_vars))}\n"
+                    f.write(line)
+
+
+def main():
 
-            f.close()
+    check_totals = False
+
+    prob = om.Problem()
+    prob.model = Model()
+
+    if check_totals:
+        run_check_totals(prob)
+    else:
+        run_optimization(prob)
+
+
+if __name__ == "__main__":
+    main()