Refactoring and bug fixes for geometry and meshing (#455)

* Fix taper derivative and computation. Add comments for geometry transformations

* Optimize taper routines

* Add comments to chord and sweep transformation

* Comments to xshear and stretch:

* Add comments to ShearY and Dihedral

* Finish geometric transformation comments

* Add ref_axis_pos as input for geom transformations in utils. defaults to quarter chord as before

* Fixed and expanded the ability to bunch panels at both root and tip for rectangular meshes

* Reorganize all meshing tools into new meshing directory. Maintains backward compatibility with deprecation warnings

* revert accidental change to plot_wing

* Update test and docs to use new imports

* Updates for multi section mesh generator

* Added support for generation single section meshes using the surface dict itself in the standard geometry group

* Fixes to make the section mesh generator work properly  for standard geometry group

* Fixes for section mesh generator

* More fixes for section mesh generator

* Start mesh gen rework

* Fixes and rework of multi section mesh generator

* Last few mesh generator fixes

* Move multi section functions to utils. Merge ones unique to a class into the class. Update docs and examples

* Fix tests and correct issue with setting span

* Moved multisection tests to geometry to be more inline with how others are organized

* fix legacy imports and create a new test to make sure they work

* Replaced write_tecplot with working function

* black fixes

* more black fixes

* flake8 fixes

* Flake8 fixes

* Docs update and add back missing test

* Update setup.py

* Add taper=1 test

* Revised legacy imports and tests to use OM Deprecation warning instead of python one

* Add test for mesh generator

* Fix test for mesh

* Added test for regeneration of mesh points

* Fix black and flake8

Author: sabakhshi

openaerostruct/docs/advanced_features/geometry_manipulation.rst

@@ -129,7 +129,7 @@ Only two components need to have information from all lifting surfaces -- `Assem
 
 Utility Scripts
 ---------------
-A few useful scripts can be found in geometry/utils.py, such as
-:py:meth:`writing the mesh to a Tecplot file <openaerostruct.geometry.utils.writeMesh>`
+A few useful scripts can be found in geometry/utils.py and meshing/utils.py, such as
+:py:meth:`writing the mesh to a Tecplot file <openaerostruct.meshing.utils.write_tecplot>`
 and
-:py:meth:`mirroring half-meshes to obtain the full mesh <openaerostruct.geometry.utils.getFullMesh>`.
+:py:meth:`mirroring half-meshes to obtain the full mesh <openaerostruct.meshing.utils.getFullMesh>`.

openaerostruct/docs/advanced_features/scripts/basic_2_sec.py

@@ -6,8 +6,8 @@
 import openmdao.api as om
 from openaerostruct.geometry.geometry_group import MultiSecGeometry
 from openaerostruct.aerodynamics.aero_groups import AeroPoint
-from openaerostruct.geometry.geometry_group import build_sections
-from openaerostruct.geometry.geometry_unification import unify_mesh
+from openaerostruct.geometry.utils import build_section_dicts
+from openaerostruct.geometry.utils import unify_mesh
 import matplotlib.pyplot as plt
 
 
@@ -133,10 +133,10 @@
 prob.model.add_subsystem(surface["name"], multi_geom_group)
 
 
-# In this next part, we will setup the aerodynamics group. First we use a utility function called build_sections which takes our multi-section surface dictionary and outputs a
+# In this next part, we will setup the aerodynamics group. First we use a utility function called build_section_dicts which takes our multi-section surface dictionary and outputs a
 # surface dictionary for each individual section. We then inputs these dictionaries into the mesh unification function unify_mesh to produce a single mesh array for the the entire surface.
 # We then add this mesh to the multi-section surface dictionary
-section_surfaces = build_sections(surface)
+section_surfaces = build_section_dicts(surface)
 uniMesh = unify_mesh(section_surfaces)
 surface["mesh"] = uniMesh
 

openaerostruct/docs/advanced_features/scripts/basic_2_sec_construction.py

@@ -6,9 +6,7 @@
 import openmdao.api as om
 from openaerostruct.geometry.geometry_group import MultiSecGeometry
 from openaerostruct.aerodynamics.aero_groups import AeroPoint
-from openaerostruct.geometry.geometry_group import build_sections
-from openaerostruct.geometry.geometry_unification import unify_mesh
-from openaerostruct.geometry.multi_unified_bspline_utils import build_multi_spline, connect_multi_spline
+from openaerostruct.geometry.utils import build_section_dicts, unify_mesh, build_multi_spline, connect_multi_spline
 import matplotlib.pyplot as plt
 
 # docs checkpoint 1
@@ -57,7 +55,7 @@
     "S_ref_type": "wetted",  # how we compute the wing area, can be 'wetted' or 'projected'
     # Geometry Parameters
     "taper": [1.0, 1.0],  # Wing taper for each section. The list length must match the specified number of sections.
-    "span": [2.0, 2.0],  # Wing span for each section. The list length must match the specified number of sections.
+    "span": [1.0, 1.0],  # Span length of each section. The list length must match the specified number of sections.
     "sweep": [0.0, 0.0],  # Wing sweep for each section. The list length must match the specified number of sections.
     "chord_cp": sec_chord_cp,  # The chord B-spline parameterization for each section. The list length must match the specified number of sections.
     "twist_cp": [
@@ -112,9 +110,9 @@
 # In order to construct this global B-spline control vector we first need to generate the unified surface mesh.
 # The unified surface mesh is simply all the individual section surface meshes combine into a single unified OAS mesh array.
 
-# First we will call the utility function build_sections which takes the surface dictionary and outputs a list of surface dictionaries corresponding to
+# First we will call the utility function build_section_dicts which takes the surface dictionary and outputs a list of surface dictionaries corresponding to
 # each section.
-section_surfaces = build_sections(surface)
+section_surfaces = build_section_dicts(surface)
 
 # We can then call unify_mesh which outputs the unified mesh of all of the sections.
 uniMesh = unify_mesh(section_surfaces)

openaerostruct/docs/advanced_features/scripts/basic_2_sec_visc.py

@@ -8,9 +8,9 @@
 
 from openaerostruct.geometry.geometry_group import MultiSecGeometry
 from openaerostruct.aerodynamics.aero_groups import AeroPoint
-from openaerostruct.geometry.geometry_group import build_sections
-from openaerostruct.geometry.geometry_unification import unify_mesh
-from openaerostruct.geometry.multi_unified_bspline_utils import build_multi_spline, connect_multi_spline
+from openaerostruct.geometry.utils import build_section_dicts
+from openaerostruct.geometry.utils import unify_mesh
+from openaerostruct.geometry.utils import build_multi_spline, connect_multi_spline
 import matplotlib.pyplot as plt
 
 
@@ -86,7 +86,7 @@
 prob.model.add_subsystem("prob_vars", indep_var_comp, promotes=["*"])
 
 # Generate the sections and unified mesh here. It's needed to join the sections by construction.
-section_surfaces = build_sections(surface)
+section_surfaces = build_section_dicts(surface)
 uniMesh = unify_mesh(section_surfaces)
 surface["mesh"] = uniMesh
 

openaerostruct/docs/aero_walkthrough/generate_n2.py

@@ -2,7 +2,7 @@
 
 import openmdao.api as om
 
-from openaerostruct.geometry.utils import generate_mesh
+from openaerostruct.meshing.mesh_generator import generate_mesh
 from openaerostruct.geometry.geometry_group import Geometry
 from openaerostruct.aerodynamics.aero_groups import AeroPoint
 

openaerostruct/docs/aero_walkthrough/part_1.py

@@ -2,7 +2,7 @@
 
 import openmdao.api as om
 
-from openaerostruct.geometry.utils import generate_mesh
+from openaerostruct.meshing.mesh_generator import generate_mesh
 from openaerostruct.geometry.geometry_group import Geometry
 from openaerostruct.aerodynamics.aero_groups import AeroPoint
 

openaerostruct/docs/user_reference/mesh_surface_dict.rst

@@ -84,9 +84,9 @@ The surface dict will be provided to Groups, including ``Geometry``, ``AeroPoint
       - 
       - How we compute the wing reference area.
     * - mesh
-      - 3D ndarray
+      - 3D ndarray or "gen-mesh"
       - m
-      - ``x, y, z`` coordinates of the mesh vertices, can be created by ``generate_mesh``.
+      - ``x, y, z`` coordinates of the mesh vertices, can be created by ``generate_mesh``. Can also specify "gen-mesh" to generate a mesh based on taper, sweep, and span variables given in the surface dictionary.
     * - span
       - 10.0
       - m

openaerostruct/docs/wingbox_mpt_opt_example.py

@@ -2,7 +2,7 @@
 # docs checkpoint 0
 
 import numpy as np
-from openaerostruct.geometry.utils import generate_mesh
+from openaerostruct.meshing.mesh_generator import generate_mesh
 from openaerostruct.integration.aerostruct_groups import AerostructGeometry, AerostructPoint
 from openaerostruct.structures.wingbox_fuel_vol_delta import WingboxFuelVolDelta
 import openmdao.api as om

openaerostruct/examples/black_box_example.py

@@ -10,7 +10,7 @@
 
 import numpy as np
 
-from openaerostruct.geometry.utils import generate_mesh
+from openaerostruct.meshing.mesh_generator import generate_mesh
 
 from openaerostruct.integration.aerostruct_groups import AerostructGeometry, AerostructPoint
 

openaerostruct/examples/drag_polar.py

@@ -2,7 +2,7 @@
 import matplotlib.pylab as plt
 
 import openmdao.api as om
-from openaerostruct.geometry.utils import generate_mesh
+from openaerostruct.meshing.mesh_generator import generate_mesh
 from openaerostruct.geometry.geometry_group import Geometry
 from openaerostruct.aerodynamics.aero_groups import AeroPoint