Complete refactor (#46)

* Added some test meshes * reading nastran BC from bdf file * Big file reorganisation * Moving things around * Increase max file size limit * add meshio as dependency * rename nastranMeshReader file for consistency * Start on model class * Made a start on the model class * Started on a new element base class * array dimensions are confusing * A little progress on the model class * More element development * Starting to write down some theory * Testing more things * Finished example runscript * Modify model class to use baseclasses * Added some more TODO's * defining DOF and assembling K matrix * small updates * Add some assembly utility functions * Adding functionality to AssembleUtils * Alis work * create output mesh object - modifications * Some more element work * New element tests are passing * Ali + Jasmin's work * Some more of Jasmin's work * Started on base constitutive class * Jasmin work * Alis work * Alis work * Sajas work * Minor updates * Element residual computation done (maybe) * New changes * ISO stress functions * Strain sensitivities and test functions * Alis work * Make linAlg routines work with arbitrary size arrays * Fix error in routines for getting gauss integration points/weights * Lot's of fixes, residual computation is correctly returning zeros * Jasmin's work * Rejigged the residual computation * Jasmin's work * fix some bugs in the model class * Fix some more bugs in the model class * Jacobian product * Jasmin's work and Quad L Beam mesh * testing model * Trying to figure out Residual Jacobian computation * Fix faulty einsum in stress calculation * Stiffness matrix calculation seems to be working! * Removing old element and constitutive classes * add TODO * It runs, but I don't know if it's right * Trying to make BC application faster * Revert "Trying to make BC application faster" This reverts commit d07995f. * Fix some errors in BC, add tests for basic problem setup and solution * Add Residual Jacobian tests to element test * Got example runscript working * Remove some old files * Implemented 2D triangular element, closest point search not working properly, removed some old files * [pre-commit.ci lite] apply automatic fixes * remove python 3.7 support * Fix some testing issues * update code climate settings * SMall fix for IsoPlaneStrain Von Mises calculation * Fix bug in 2nd order Tri element node ordering * Fix tri element ascii art * Fix 9 node quad element node ordering * Add 3d lagrange polynomials * Fix 3rd order quad node ordering * Add test for element coordinate interpolation * un-comment getClosestPoints test * Comment out model tests that don't work yet * re-enable the get closest points test * Run example problem with Tri elements * Fix ordering of higher order tri element nodes, to match meshio * Rejig model test, rename testAssembly to testProblem * Jasmin's work, element/problem computeFunctions * [pre-commit.ci lite] apply automatic fixes * Jasmin's work - test for computeFunction * [pre-commit.ci lite] apply automatic fixes * Add constitutive model functions to solution file * Remove unneeded mesh processing stuff * Remove a bunch of stuff so that the docs build * Trying to fix docs build * more fixes * Add density to IsoPlaneStrain * Updating IPE figures * Jasmin's work - presentation live demo jupyter notebook * Jasmin's work - Presentation Live Demo jupyter notebook * More presentation figures * Some inconsequential changes * Adding more docstrings * Lets be very strict about docstrings * Fix interrogate settings in pre-commit * Ignore flake8 config file * Trying to address some code climate complaints * Cleaning up some docstrings * Switch back from code climate to codecov * covergae fix * Cleanup examples * Add CI jobs for benchmarks and examples * oops, numba doesn't like python 3.11 * typos * Fix non-editable install * Change example output * Add testflo dependency for benchmarks action * Add constitutive model unit tests * Getting some documentation working again * FOrmatting comments for the docs * Cleaning up some docstrings for documentation * Improved efficiency of boundary condition application * make problem solve method return timing data * Turn LinAlg benchmarks into separate cases * Add quad mesh benchmark case * Remove plotting imports from quad mesh benchmark * Import paramaterized for benchmarking github action * Would be great if I could spell * Print some nice output after benchmarking * Got 3D hex elements working! * add hex elements to docs * Remove hydrofoil example from repo * So much speeeeeeed! * More performance optimization * Jasmin's work - scaling study on new FEMpy * [pre-commit.ci lite] apply automatic fixes * Extremely important modification * More parallelisation * Jasmin's work - scaling study * [pre-commit.ci lite] apply automatic fixes * Jasmin's work - scaling study * [pre-commit.ci lite] apply automatic fixes * Updating theory figures used in NERS report * Add 3D constitutive model to unit tests * mesh convergence study for a cantilever beam * mesh convergence study minor edits * minor fix * removing matplotlib * removing niceplots * minor error fix in the code * Fix some docstrings * Update readme * Update docs homepage * Add von mises figure to readme * typo * Remove a bunch of stuff from the Benchmarks folder * Update quad mesh scaling plotting script * Readme tweak * Don't need requirements.txt files any more * Hopefully now we don't need requiremenets.txt * Switch to using numpy's default_rng for consistent random number generation in tests * Include cantilever benchmark in CI * Make validation separate step Co-authored-by: arshsaja <[email protected]> Co-authored-by: jasminlim-simba <[email protected]> Co-authored-by: pre-commit-ci-lite[bot] <117423508+pre-commit-ci-lite[bot]@users.noreply.github.com>
A-CGray · Dec 15, 2022 · e29ffd3 · e29ffd3
1 parent f0f4d4a
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diff --git a/.codeclimate.yml b/.codeclimate.yml
diff --git a/.codecov.yml b/.codecov.yml
@@ -0,0 +1,13 @@
+codecov:
+  disable_default_path_fixes: false
+
+coverage:
+  status:
+    project:
+      default:
+        threshold: 1%
+    patch:
+      default:
+        target: auto
+comment:
+  require_changes: true
diff --git a/.deepsource.toml b/.deepsource.toml
diff --git a/.github/workflows/Benchmarks.yml b/.github/workflows/Benchmarks.yml
@@ -0,0 +1,40 @@
+name: Run benchmarks
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        include:
+          - python-version: "3.8"
+          - python-version: "3.9"
+          - python-version: "3.10"
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+        cache: 'pip'
+        cache-dependency-path: setup.py
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install .[dev]
+
+    - name: Run performance benchmarks
+      run: |
+        cd Examples/Benchmarks
+        testflo -n 1 -v --benchmark .
+        python formatBenchmarkData.py
+        python CantileverValidation.py
+
+    - name: Run validation benchmarks
+      run: |
+        cd Examples/Benchmarks
+        python CantileverValidation.py
diff --git a/.github/workflows/Examples.yml b/.github/workflows/Examples.yml
@@ -0,0 +1,34 @@
+name: Run examples
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        include:
+          - python-version: "3.8"
+          - python-version: "3.9"
+          - python-version: "3.10"
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+        cache: 'pip'
+        cache-dependency-path: setup.py
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install .
+
+    - name: Run examples
+      run: |
+        set -e
+        cd Examples
+        for f in *.py; do python "$f"; done
diff --git a/.github/workflows/Tests.yml b/.github/workflows/Tests.yml
@@ -11,7 +11,6 @@ jobs:
     strategy:
       matrix:
         include:
-          - python-version: "3.7"
           - python-version: "3.8"
           - python-version: "3.9"
           - python-version: "3.10"
@@ -22,6 +21,7 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
         cache: 'pip'
+        cache-dependency-path: setup.py
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
@@ -36,12 +36,12 @@ jobs:
       run: |
         export NUMBA_DISABLE_JIT=1
         testflo -n 1 -v --coverage --coverpkg FEMpy .
+        coverage xml
 
-    - name: Upload coverage to Code Climate
+    - name: Upload coverage to Codecov
       if: ${{ matrix.python-version == 3.10}}
-      uses: paambaati/[email protected]
-      env:
-        CC_TEST_REPORTER_ID: ${{ secrets.CODECLIMATE_COVERAGE_ID }}
+      uses: codecov/codecov-action@v3
       with:
-        debug: true
-        coverageCommand: coverage xml
+        token: ${{ secrets.CODECOV_TOKEN }}
+        fail_ci_if_error: true
+        verbose: true
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -17,10 +17,10 @@ jobs:
         with:
           python-version: '3.9'
           cache: 'pip'
+          cache-dependency-path: setup.py
       - run: |
           python -m pip install --upgrade pip
-          python3 -m pip install -r ./requirements.txt
-          python3 -m pip install -e .
+          python3 -m pip install -e .[docs]
 
       - name: Build Docs
         run: mkdocs build -f docs/mkdocs.yml

diff --git a/.gitignore b/.gitignore
@@ -1,5 +1,21 @@
-# Gauss quadrature pkl files
-Gauss*.pkl
+# Ignore images, except those in the docs
+*.png
+*.pdf
+!docs/docs/Images/**.png
+!docs/docs/Images/**.pdf
+**.autosave.ipe
+
+# Ignore examples results files
+Examples/ExampleOutput
+*.vtk
+*.vtu
+*.dat
+
+# Ignore testflo benchmark data
+**benchmark_data.csv
+
+# Ignore flake 8 config
+.flake8
 
 # Profiling files
 *.prof

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -2,25 +2,28 @@ repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.4.0
     hooks:
+    -   id: check-added-large-files
+        args: ['--maxkb=5000']
     -   id: trailing-whitespace
     -   id: end-of-file-fixer
     -   id: check-yaml
     -   id: check-json
-    -   id: check-added-large-files
     -   id: mixed-line-ending
     -   id: check-merge-conflict
     -   id: debug-statements
 -   repo: https://github.com/psf/black
     rev: 22.10.0
     hooks:
       - id: black
-        # It is recommended to specify the latest version of Python
-        # supported by your project here, or alternatively use
-        # pre-commit's default_language_version, see
-        # https://pre-commit.com/#top_level-default_language_version
         language_version: python3
-        args: ["-l", "120", "--target-version", "py37", "--target-version", "py38", "--target-version", "py39", "--target-version", "py310"]
+        args: ["-l", "120", "--target-version", "py38", "--target-version", "py39", "--target-version", "py310"]
 -   repo: https://github.com/PyCQA/flake8
     rev: 6.0.0
     hooks:
     - id: flake8
+-   repo: https://github.com/econchick/interrogate
+    rev: 1.5.0
+    hooks:
+      - id: interrogate
+        args: ["-I", "--fail-under=100", "--ignore-nested-functions", "-vv"]
+        exclude: ^(docs|setup.py|tests|Examples|.*__init__.py)
diff --git a/Dockerfile b/Dockerfile
diff --git a/Examples/Benchmarks/CantileverValidation.py b/Examples/Benchmarks/CantileverValidation.py
@@ -0,0 +1,107 @@
+"""
+==============================================================================
+FEMpy cantilever beam validation case
+==============================================================================
+@Description : This file contains a simple 2D validation case where we compare
+FEMpy against the analytical solution for a cantilevel beam subject to a uniform
+load.
+"""
+
+# ==============================================================================
+# Standard Python modules
+# ==============================================================================
+
+from numba import njit
+
+# ==============================================================================
+# External Python modules
+# ==============================================================================
+import numpy as np
+import FEMpy as fp
+
+
+# ==============================================================================
+# Extension modules
+# ==============================================================================
+
+
+@njit(cache=True)
+def warpFunc(x, y):
+    return x, 0.02 * y
+
+
+# @njit( cache=True)
+def createGridMesh(nx, ny, warpFunc=None):
+    xNodes = np.tile(np.linspace(0.0, 1.0, nx + 1), ny + 1)
+    yNodes = np.repeat(np.linspace(0.0, 1.0, ny + 1), nx + 1)
+
+    # Warp the mesh
+    if warpFunc is not None:
+        xNodes, yNodes = warpFunc(xNodes, yNodes)
+
+    # Create Connectivity matrix
+    numEl = nx * ny
+    conn = np.zeros((numEl, 4), dtype=int)
+    conn[:, 0] = np.tile(np.arange(nx), ny) + np.repeat((nx + 1) * np.arange(ny), nx)  # Lower left
+    conn[:, 1] = conn[:, 0] + 1  # lower right
+    conn[:, 2] = conn[:, 1] + nx + 1  # upper right
+    conn[:, 3] = conn[:, 2] - 1  # upper left
+
+    return np.array([xNodes, yNodes]).T, conn
+
+
+if __name__ == "__main__":
+    refineVal = [1, 2, 4, 8, 16, 32, 64]
+    Error = []
+    numDOF = []
+    meshSize = []
+    for refine in refineVal:
+
+        # create constitutive model
+        con = fp.Constitutive.IsoPlaneStrain(E=70e9, nu=0.0, t=1.0, rho=2700.0)
+
+        # create mesh
+        nodeCoords, conn = createGridMesh(10 * refine, 1 * refine, warpFunc=warpFunc)
+        conn = {"quad": conn}
+
+        # create model
+        model = fp.FEMpyModel(con, nodeCoords=nodeCoords, connectivity=conn, options={"outputFormat": ".dat"})
+        prob = model.addProblem("Static")
+
+        # Find the right, left and top edges
+        rightEdgeNodeInds = np.argwhere(nodeCoords[:, 0] == 1.0).flatten()
+        topEdgeNodeInds = np.argwhere(nodeCoords[:, 1] == np.max(nodeCoords[:, 1])).flatten()
+        leftEdgeNodeInds = np.argwhere(nodeCoords[:, 0] == 0.0).flatten()
+
+        # apply BCs
+        prob.addFixedBCToNodes("Fixed", leftEdgeNodeInds, dof=[0, 1], value=0.0)
+        prob.addLoadToNodes("Load", topEdgeNodeInds, dof=[1], value=-(10**3), totalLoad=True)
+
+        # Calculate analytic displacement
+        momInertia = 1 / 12 * 0.02**3
+        dmax_analytic = 10**3 / (8 * 70e9 * momInertia)
+
+        # solve the problem
+        prob.solve()
+        prob.writeSolution(baseName="mesh%s.dat" % refine)
+
+        # average the vertical displacements along the tip of the beam and compute the error
+        averageDisplacement = np.average(prob.states[rightEdgeNodeInds, 1])
+        Error.append(np.abs(-averageDisplacement - dmax_analytic))
+        numDOF.append(prob.numDOF)
+        meshSize.append(1 / np.sqrt(numDOF[-1]))
+
+    # Print the results
+    Error = np.array(Error)
+    numDOF = np.array(numDOF)
+    meshSize = np.array(meshSize)
+    print("======================================")
+    print("Cantilever Beam Validation Results")
+    print("======================================")
+    print("|    num DOF     |        Error      |")
+    for i in range(len(Error)):
+        print(f"|{numDOF[i]:>10}      |   {Error[i]:11.6e}    |")
+    print("=====================================")
+
+    logFitCoeff = np.polyfit(np.log(meshSize[-3:]), np.log(Error[-3:]), 1)
+    print(f"Displacement error convergence Rate: {logFitCoeff[0]}")
diff --git a/Examples/Benchmarks/LinAlg.py b/Examples/Benchmarks/LinAlg.py