New main update

.github/workflows/test_pvade.yaml

@@ -25,10 +25,16 @@ jobs:
       - name: Build Conda environment
         uses: conda-incubator/setup-miniconda@v3
         with:
+          # auto-update-conda: true
+          python-version: "3.10"
           environment-file: environment.yaml
+          activate-environment: pvade
       - name: Run pytest
         shell: bash -l {0}
-        run: pytest -sv pvade/tests/
+        run: PYTHONPATH=. pytest -sv pvade/tests/
+      - name: test all inputs
+        shell: bash -l {0}
+        run: pytest -sv  test_all_inputs.py 
 
   # Job 2 of 2 - enforce Black formatting
   formatting:

.gitignore

@@ -8,4 +8,5 @@
 *.h5
 
 docs/_build/
-results/
+results/input/
+input/

conftest.py

@@ -0,0 +1,29 @@
+from pathlib import Path
+
+
+def pytest_addoption(parser):
+    parser.addoption(
+        "--input-file",
+        action="store",
+        default=None,
+        help="Run test only for a specific input YAML file",
+    )
+
+
+def pytest_generate_tests(metafunc):
+    if "input_file" not in metafunc.fixturenames:
+        return
+
+    input_file_arg = metafunc.config.getoption("input_file")
+
+    if input_file_arg:
+        metafunc.parametrize("input_file", [Path(input_file_arg)])
+    else:
+        # 🔧 Always resolve input/ relative to location of conftest.py (PVade/)
+        this_dir = Path(__file__).resolve().parent  # PVade/
+        input_dir = this_dir / "input"
+
+        all_files = sorted(input_dir.glob("*.yaml"))
+        if not all_files:
+            raise RuntimeError(f"No input files found in {input_dir}")
+        metafunc.parametrize("input_file", all_files)

docs/how_to_guides/examples/Turbulent_Inflow_Panels_3D.rst

@@ -0,0 +1,94 @@
+PV Panels 3D with Turbulent Inflow
+===========
+This example demonstrates the use of PVade to simulate dynamic PV loading amidst a turbulent inflow velocity field. 
+
+Currently, this feature only works in 3D simulations.
+
+Geometry Definition
+-------------------
+
+
+This example consists of a turbulent atmospheric flow in which the fluid interacts with a single row of PV panels. The domain setup and geometry are described in the figure below.
+
+.. image:: pictures/turbinflow3d/duramat_dimensions.png
+  :alt: Alternative text
+
+where: 
+
+chord is the length of the solar panel, 
+span is the width of the solar panel, 
+elevation is the height of the mounting point, and
+tracker angle is the tilt angle of the solar panel.
+
+
+.. image:: pictures/turbinflow3d/turb_inflow_domain_setup.png
+  :alt: Alternative text
+
+L is the length of the domain and
+H is the height of the domain.
+
+
+For this example, the following values are used, as shown in the input file (``input/turbinflow_duramat_case_study.yaml``):
+
+.. container::
+   :name: tab:geometry
+
+   .. table:: Parameter settings
+
+      ==================================== =====
+      parameter [units]                    Value
+      ==================================== =====
+      L [m]                                80
+      H [m]                                20
+      chord [m]                            4.1
+      span [m]                             10.0
+      elevation [m]                        2.1
+      tracker angle [degrees]              0
+      ==================================== =====
+
+
+Synthetic Turbulence Generation
+-------------------------------
+
+The turbulent inflow velocity field is generated externally using `pyconturb` [1]_. This example uses unconstrained turbulence generated using the notebook here: ``examples/synthetic_turbulent_inflow/generate_turbulent_inflow_h5_file.ipynb``.
+
+The generated turbulent velocity field is written to an .h5 file (e.g. ``input/pct_turb_ny80_nz80_unconstrained_1.0s_dt0.01_uref20.h5``) so that it can be read in by `pvade`. This file contains velocity data of shape (nt, ny, nz) where nt = number of timesteps, ny = number of gridpoints in the spanwise direction, and nz = number of gridpoints in the vertical direction. At each timestep, `pvade` selects the y-z slice of turbulent inflow for that timestep and applies it as the boundary condition at the inlet.
+
+Currently, this functionality only works for 3D simulations.
+
+Running this example locally
+----------------------------
+
+This example is executed in parallel using::
+
+  mpirun -n 8 python pvade_main.py --input_file input/turbinflow_duramat_case_study.yaml
+
+For testing purposes, this example can be run for less time using::
+
+  mpirun -n 8 python pvade_main.py --input_file input/turbinflow_duramat_case_study.yaml --domain.l_char 2.5 --solver.t_final 0.2
+
+
+Running this example on HPC
+---------------------------
+
+This example is best run on a supercomputer using the included batch script as an example(``PVade/docs/how_to_guides/examples/runscripts/run.sh``). You will need to change the environment path and the paths to the files to your own.
+
+First, create a symbolic link to the ``input`` folder from where you are launching the simulation::
+
+    ln -s <path_to_PVade>/input input
+
+Then, edit and run the following script to launch the simulation::
+
+    sbatch run.sh
+
+For more details on running on HPC, please refer to :ref:`Running on HPC`.
+
+This example yields the following result:
+
+.. image:: pictures/turbinflow3d/turb_inflow_slices.gif
+  :alt: Alternative text
+
+
+References
+----------
+.. [1] J. M. Rinker, “PyConTurb: Constrained Stochastic Turbulence for Wind Energy Applications,” 2017, https://gitlab.windenergy.dtu.dk/pyconturb/pyconturb

docs/how_to_guides/examples/index.rst

@@ -5,6 +5,7 @@ Examples
    :maxdepth: 1
 
    Flag_2D
+   Turbulent_Inflow_Panels_3D
    Heliostat_3D
 ..   Cylinder_2D
 ..   Cylinder_3D

docs/how_to_guides/examples/runscripts/run.sh

@@ -2,11 +2,11 @@
 
 #SBATCH --ntasks-per-node=104
 #SBATCH --time=08:00:00
-#SBATCH --account=csphfm
-#SBATCH --job-name=heliostat_u2
+#SBATCH --account=pvopt
+#SBATCH --job-name=jobname
 #SBATCH --nodes=1
-#SBATCH --error=heliostat-0.err
-#SBATCH --output=heliostat-0.out
+#SBATCH --error=jobname.err
+#SBATCH --output=jobname.out
 #SBATCH --mem=0
 #SBATCH --exclusive
 
@@ -15,4 +15,4 @@ module load mamba
 mamba activate pvade
 export OMP_NUM_THREADS=1
 
-mpirun -np 104 python -u /home/bstanisl/pvade/PVade/ns_main.py --input_file /home/bstanisl/pvade/PVade/input/single_heliostat.yaml
+mpirun -np 104 python -u /home/bstanisl/pvade/PVade/pvade_main.py --input_file /home/bstanisl/pvade/PVade/input/<input_yaml_file>

docs/how_to_guides/pvade_input_file.rst

@@ -98,6 +98,8 @@ solver:
 fluid:
   The fluid Category sets the CFD parameters for the fluid simulation
 
+  - velocity_profile_type: General shape of inflow velocity profile
+  - initialize_with_inflow_bc: Boolean flag to set the velocity everywhere in the domain to match the inflow BC velocity.
   - u_ref: Reference velocity at the center of the panel  
   - nu: Dynamic viscosity 
   - turbulence_model:  can be set to smagorinsky or null for no turbulence  
@@ -114,7 +116,7 @@ structure:
 
   - dt : set the time step for the CSD simulation 
   - elasticity_modulus: set the Elasticity modulus for the structure 
-  - poissons_ratio: set poisson's ration for the structure
+  - poissons_ratio: set poisson's ratio for the structure
   - body_force_x: set the x component of the body force 
   - body_force_y: set the y component of the body force
   - body_force_z: set the z component of the body force

environment.yaml

@@ -1,12 +1,14 @@
-name: pvade
+name: pvade-test
 channels:
   - conda-forge  
-  - defaults
+  - nodefaults
 dependencies:
   # Dependencies should be kept as loosely pinned to version numbers as possible
+  - python >=3.10,<3.11
   - alive-progress
   - black
   - fenics-dolfinx=0.6
+  - h5py
   - jsonschema
   - jupyter
   - matplotlib
@@ -21,6 +23,7 @@ dependencies:
   - sphinx
   - tqdm
   - pip
+  - mpich >=4.0,<5.0
   - pip:
     - sphinx-rtd-theme
     - sphinxcontrib.datatemplates