Refactor (#3)

* Refactoring updates

* test workflow updates

* bugfix

* bufix on workflow

* add timing to env creation and

* directing testing import opensg since pytest is being difficult

* add conda list to diagnose env

* debug

* try another approach to conda environment

* debug

* fix bug

* another attempt

* now using pytest again

* add an actual test

* add extra package isntallation via apt

* fix syntax in env file

* removing python version requirement, perhaps it conflicts with the setting for the action

* try another version

* another attempt

* one more try

* try old version of workflow

* try basic setup

* try to fix versions

* fix fenics-ufl version

* clean up test.yml

* fix variable name

* misc comments

* add basic test assertion

Author: kbonney

.github/workflows/test.yml

@@ -4,23 +4,28 @@ on: [push, pull_request, workflow_dispatch]
 
 jobs:
   test:
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        os: [windows-latest, macOS-13, ubuntu-latest]
-        python-version: ['3.8', '3.9', '3.10']
-      fail-fast: false
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -el {0}
+
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install pynumad
-      run: |
-        python -m pip install --upgrade pip
-        pip install -e .
-    - name: Test with pytest
-      run: |
-        pip install --upgrade pytest coverage
-        coverage run --source=pynumad --omit="*/tests/*" -m pytest
+      # Step 1: Checkout your code
+      - name: Checkout Code
+        uses: actions/checkout@v3
+
+      - name: Set up environment
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          environment-file: environment.yml
+          # python-version: "3.9" # setup-miniconda seems to ignore this setting.
+          auto-activate-base: false
+      - name: Check environmnet
+        run: |
+          conda info
+          conda list
+      - name: Run tests
+        run: |
+          python -c "import opensg"
+          pip install pytest
+          pytest opensg/tests/

environment.yml

@@ -2,20 +2,24 @@ name: opensg_env
 channels:
   - conda-forge
 dependencies:
-  - python=3.10
+  - python=3.12
   - numpy
   - scipy
   - mpi4py
   - meshio
-  - petsc4py
+  - petsc4py=3.21.5
   - yaml
   - contextlib2  # For compatibility
   - pathlib
   - typing-extensions
-  - fenics-dolfinx 
-  - fenics-basix 
-  - fenics-ufl
+  - fenics-dolfinx=0.8.0
+  - fenics-basix=0.8.0
+  - fenics-ufl=2024.1.0
+  - fenics-ffcx=0.8.0
   - mpich 
   - pyvista
   - pyyaml
-  # - gmsh # I have to install this through pip for it to work.
+  - pip
+  - pip:
+    - -e .
+    - gmsh

examples/compute_eb_blade.py

@@ -3,6 +3,7 @@
 # import pynumad
 import opensg
 import numpy as np
+import time
 
 # load blade.yml into pynumad
 # blade_path = join("data", "blade.yaml")
@@ -24,53 +25,68 @@
 mesh_data = opensg.load_yaml(mesh_yaml)
 
 blade_mesh = opensg.BladeMesh(mesh_data)
-section_mesh = blade_mesh.generate_segment_mesh(segment_index=1, filename="section.msh")
-
-section_layups = section_mesh._generate_layup_data()
-
-frame = section_mesh.generate_local_orientations()
-
-section_mesh.extract_boundaries()
-
-section_mesh.generate_boundary_ABD()
-
-
-
-pause
-
-
-## Extract the mesh for the section
-nodes = mesh_data['nodes']
-numNds = len(nodes)
-elements = mesh_data['elements']
-numEls = len(elements)
-
-ndNewLabs = -1*np.ones(numNds,dtype=int)
-elNewLabs = -1*np.ones(numEls,dtype=int)
-elLayID = -1*np.ones(numEls,dtype=int)
-
-# iterate through blade
-
-segment_matrices = []
-
-for i in range(len(blade.ispan)):
-    # select ith blade segment
-    blade_segment_mesh = opensg.blade.select_segment(blade_mesh_info)
-    # analysis options
-    #   solid vs shell
-    #   whole segment vs boundary
-    # analyses:
-    # stresses/stiffness/buckling
-    # stresses after beamdyn
-    data = opensg.compute_eb_segment(blade_segment_mesh)
-    # data = opensg.compute_eb_boundaries(blade_segment_mesh)
-    # data = opensg.compute_timo_segment(blade_segment_mesh) # ***** high priority
-    # data = opensg.compute_eb_buckling(blade_segment_mesh)
-    # data = opensg.compute_timo_buckling(blade_segment_mesh) # **** top priority
-    # data = opensg.compute_timo_boundaries(blade_segment_mesh)
+stiffness_matrices = []
+compute_times = []
+for i in range(1, 2):
+    start_time = time.time()
+    print(time.time()-start_time)
+ 
+    segment_mesh = blade_mesh.generate_segment_mesh(segment_index=i, filename="section.msh")
+    print(time.time()-start_time)
+
+    ABD = segment_mesh.compute_ABD()
+    print(time.time()-start_time)
+
+    stiffness_matrix = segment_mesh.compute_stiffness_EB(ABD)
+    print(time.time()-start_time)
+    
+    stiffness_matrices.append(stiffness_matrix)
+    end_time = time.time()
+    compute_times.append(end_time - start_time)
+    
+print("Average compute time for a single segment: ", sum(compute_times)/len(compute_times))
+print("Maximum compute time for a single segment: ", max(compute_times))
+
+# combine matrices into a global 
+combined_stiffness_matrices = np.concat(stiffness_matrices)
+
+np.savetxt('stiffness_m.txt', combined_stiffness_matrices, fmt='%d')
+
+# pause
+
+
+# ## Extract the mesh for the section
+# nodes = mesh_data['nodes']
+# numNds = len(nodes)
+# elements = mesh_data['elements']
+# numEls = len(elements)
+
+# ndNewLabs = -1*np.ones(numNds,dtype=int)
+# elNewLabs = -1*np.ones(numEls,dtype=int)
+# elLayID = -1*np.ones(numEls,dtype=int)
+
+# # iterate through blade
+
+# segment_matrices = []
+
+# for i in range(len(blade.ispan)):
+#     # select ith blade segment
+#     blade_segment_mesh = opensg.blade.select_segment(blade_mesh_info)
+#     # analysis options
+#     #   solid vs shell
+#     #   whole segment vs boundary
+#     # analyses:
+#     # stresses/stiffness/buckling
+#     # stresses after beamdyn
+#     data = opensg.compute_eb_segment(blade_segment_mesh)
+#     # data = opensg.compute_eb_boundaries(blade_segment_mesh)
+#     # data = opensg.compute_timo_segment(blade_segment_mesh) # ***** high priority
+#     # data = opensg.compute_eb_buckling(blade_segment_mesh)
+#     # data = opensg.compute_timo_buckling(blade_segment_mesh) # **** top priority
+#     # data = opensg.compute_timo_boundaries(blade_segment_mesh)
 
-    segment_matrices.append(data)
+#     segment_matrices.append(data)
 
 
-# ideally, we could also have a step to run beamdyn
-opensg.beamdyn.run_analysis(blade_mesh_info, segment_matrices)
+# # ideally, we could also have a step to run beamdyn
+# opensg.beamdyn.run_analysis(blade_mesh_info, segment_matrices)

opensg/__init__.py

@@ -1,7 +1,10 @@
-from opensg.solve import ksp_solve, ABD_mat, nullspace
-from opensg.timo import local_frame_1D, directional_derivative, local_grad, ddot
+from opensg.solve import compute_ABD_matrix, compute_timo_boun, compute_stiffness_EB_blade_segment
+# from kirklocal.timo import local_frame_1D, directional_derivative, local_grad, ddot
 from opensg.io import load_yaml, write_yaml
 from opensg.mesh import BladeMesh
-from opensg import util
+from opensg.compute_utils import solve_ksp, solve_boun, compute_nullspace, \
+    create_gamma_e, R_sig, Dee, sigma, eps, local_boun, local_frame_1D, \
+    local_frame, local_frame_1D_manual, local_grad, deri, ddot, gamma_d, \
+    construct_gamma_e, gamma_h, gamma_l, A_mat, initialize_array, dof_mapping_quad, generate_boundary_markers
 
 __version__ = "0.0.1"