Bug fixes

.github/workflows/test_pvade.yaml

@@ -32,6 +32,9 @@ jobs:
       - name: Run pytest
         shell: bash -l {0}
         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)

input/3d_cyld.yaml

@@ -11,26 +11,26 @@ domain:
   y_max: 0.41
   z_min: 0.0
   z_max: 0.41
-  l_char: 2.0 #.02
-pv_array:
-  stream_rows: 1 # not used
-  elevation: 1.5 # not used
-  stream_spacing: 7.0 # not used
-  panel_chord: 2.0 # not used
-  panel_span: 7.0 # not used
-  panel_thickness: 0.1 # not used
-  tracker_angle: 30.0 # not used
+  l_char: 5.0 #.02
+# pv_array:
+#   stream_rows: 1 # not used
+#   elevation: 1.5 # not used
+#   stream_spacing: 7.0 # not used
+#   panel_chord: 2.0 # not used
+#   panel_span: 7.0 # not used
+#   panel_thickness: 0.1 # not used
+#   tracker_angle: 30.0 # not used
 solver:
-  dt: 0.025
-  t_final: 0.1
-  solver1_ksp: cg
+  dt: 0.001
+  t_final: 0.01
+  solver1_ksp: gmres
   solver2_ksp: cg
   solver3_ksp: cg
   solver1_pc: jacobi
   solver2_pc: jacobi
   solver3_pc: jacobi
-  save_text_interval: 0.1
-  save_xdmf_interval: 0.1
+  save_text_interval: 0.001
+  save_xdmf_interval: 0.001
 fluid:
   velocity_profile_type: parabolic
   inflow_coeff: 16 # only necessary/used when applying a parabolic vel profile

input/heated_panels2d.yaml

@@ -14,6 +14,7 @@ domain:
   l_char: 0.1
 pv_array:
   stream_rows: 8
+  span_rows: 1
   elevation: 1.5
   stream_spacing: 5.0
   panel_chord: 2.0

input/inflow_input.yaml

@@ -24,7 +24,7 @@ solver:
   solver1_ksp: gmres
   solver2_ksp: gmres
   solver3_ksp: gmres
-  solver4_ksp: gmres
+  # solver4_ksp: gmres
   solver1_pc: hypre
   solver2_pc: hypre
   solver3_pc: hypre

input/panels2d.yaml

@@ -9,9 +9,10 @@ domain:
   x_max: 50
   y_min: 0
   y_max: 20
-  l_char: 0.9
+  l_char: 0.5
 pv_array:
   stream_rows: 1
+  span_rows: 1
   elevation: 1.5
   stream_spacing: 7.0
   panel_chord: 2.0

input/panels3d.yaml

@@ -56,4 +56,4 @@ structure:
   body_force_y: 0
   body_force_z: -1 #100
   bc_list: [left ]
-  tube_connection: False
+  tube_connection: False

input/single_heliostat.yaml

@@ -11,7 +11,7 @@ domain:
   y_max: 20 # 20+39 39 is panel to panel 
   z_min: 0
   z_max: 40
-  l_char: 1.25 # 1.0
+  l_char: 4 #1.25 # 1.0
 pv_array:
   stream_rows: 1
   elevation: 5.5
@@ -38,7 +38,7 @@ solver:
   save_text_interval: .02 #0.01
   save_xdmf_interval: .02 #0.01
 fluid:
-  time_varying_inflow_bc: false # true
+  # time_varying_inflow_bc: false # true
   u_ref: 2.0
   rho: 1.0
   nu: 1.8e-05

pvade/IO/DataStream.py

@@ -1,9 +1,14 @@
-from dolfinx.io import XDMFFile
-
-# import logging
+import dolfinx
+import ufl
 import sys
+
+import numpy as np
+
 from datetime import datetime
 
+# from dolfinx.fem import create_nonmatching_meshes_interpolation_data
+# import logging
+
 
 def start_print_and_log(rank, logfile_name):
 
@@ -74,7 +79,7 @@ class DataStream:
 
     """
 
-    def __init__(self, domain, flow, structure, params):
+    def __init__(self, domain, flow, structure=None, params=None):
         """Initialize the DataStream object
 
         This initializes an object that manages the I/O for all of PVade.
@@ -98,7 +103,9 @@ def __init__(self, domain, flow, structure, params):
                 f"{params.general.output_dir_sol}/solution_fluid.xdmf"
             )
 
-            with XDMFFile(self.comm, self.results_filename_fluid, "w") as xdmf_file:
+            with dolfinx.io.XDMFFile(
+                self.comm, self.results_filename_fluid, "w"
+            ) as xdmf_file:
                 tt = 0.0
                 xdmf_file.write_mesh(domain.fluid.msh)
                 xdmf_file.write_function(flow.u_k, 0.0)
@@ -115,13 +122,31 @@ def __init__(self, domain, flow, structure, params):
                 f"{params.general.output_dir_sol}/solution_structure.xdmf"
             )
 
-            with XDMFFile(self.comm, self.results_filename_structure, "w") as xdmf_file:
+            # Since this is the first call, build solvers that project forms on an as-saved basis
+            # Set up the linear problem used for the projection, cg solver and jacobi pc
+            petsc_options = {"ksp_type": "cg", "pc_type": "jacobi"}
+            self.prob_k_nominal = dolfinx.fem.petsc.LinearProblem(
+                ufl.lhs(structure.elasticity.k_nominal_proj),
+                ufl.rhs(structure.elasticity.k_nominal_proj),
+                bcs=[],
+                petsc_options=petsc_options,
+            )
+
+            # Solve for the stress tensor
+            sol_k_nominal = self.prob_k_nominal.solve()
+            structure.elasticity.internal_stress.x.array[:] = sol_k_nominal.x.array[:]
+            structure.elasticity.internal_stress.x.scatter_forward()
+
+            with dolfinx.io.XDMFFile(
+                self.comm, self.results_filename_structure, "w"
+            ) as xdmf_file:
                 tt = 0.0
                 xdmf_file.write_mesh(domain.structure.msh)
                 xdmf_file.write_function(structure.elasticity.u, 0.0)
-                xdmf_file.write_function(structure.elasticity.stress, 0.0)
                 xdmf_file.write_function(structure.elasticity.v_old, 0.0)
-                xdmf_file.write_function(structure.elasticity.sigma_vm_h, 0.0)
+                xdmf_file.write_function(structure.elasticity.a_old, 0.0)
+                xdmf_file.write_function(structure.elasticity.stress, 0.0)
+                xdmf_file.write_function(structure.elasticity.internal_stress, 0.0)
 
         if self.comm.rank == 0 and self.comm.size > 1 and params.general.test:
             self.log_filename_structure = f"{params.general.output_dir_sol}/log_str.txt"
@@ -188,7 +213,9 @@ def save_XDMF_files(self, fsi_object, domain, tt):
         """
 
         if fsi_object.name == "fluid":
-            with XDMFFile(self.comm, self.results_filename_fluid, "a") as xdmf_file:
+            with dolfinx.io.XDMFFile(
+                self.comm, self.results_filename_fluid, "a"
+            ) as xdmf_file:
                 xdmf_file.write_function(fsi_object.u_k, tt)
                 xdmf_file.write_function(fsi_object.p_k, tt)
                 xdmf_file.write_function(fsi_object.panel_stress, tt)
@@ -197,11 +224,19 @@ def save_XDMF_files(self, fsi_object, domain, tt):
                     xdmf_file.write_function(fsi_object.theta_k, tt)
 
         elif fsi_object.name == "structure":
-            with XDMFFile(self.comm, self.results_filename_structure, "a") as xdmf_file:
+            # Solve for the stress tensor
+            sol_k_nominal = self.prob_k_nominal.solve()
+            fsi_object.elasticity.internal_stress.x.array[:] = sol_k_nominal.x.array[:]
+            fsi_object.elasticity.internal_stress.x.scatter_forward()
+
+            with dolfinx.io.XDMFFile(
+                self.comm, self.results_filename_structure, "a"
+            ) as xdmf_file:
                 xdmf_file.write_function(fsi_object.elasticity.u, tt)
-                xdmf_file.write_function(fsi_object.elasticity.stress, tt)
                 xdmf_file.write_function(fsi_object.elasticity.v_old, tt)
-                xdmf_file.write_function(fsi_object.elasticity.sigma_vm_h, tt)
+                xdmf_file.write_function(fsi_object.elasticity.a_old, tt)
+                xdmf_file.write_function(fsi_object.elasticity.stress, tt)
+                xdmf_file.write_function(fsi_object.elasticity.internal_stress, tt)
 
         else:
             raise ValueError(

pvade/IO/Utilities.py

@@ -23,7 +23,7 @@ def get_input_file():
     return input_file_path
 
 
-def write_metrics(flow, elasticity, prof_filename="profiling.txt"):
+def write_metrics(flow, prof_filename="profiling.txt"):
     with open(prof_filename, "r") as output_file:
         if flow.fluid_analysis == True:
             # solver_line = [line for line in output_file if "(solve)" in line]