Merge 2D magnetostatics branch into serac

.clang-tidy

@@ -26,10 +26,12 @@ Checks: 'clang-diagnostic*,
          -cppcoreguidelines-pro-type-union-access,
          -cppcoreguidelines-pro-type-vararg,
          -modernize-avoid-c-arrays,
+         -modernize-use-default-member-init,
          -modernize-use-nodiscard,
          -modernize-use-trailing-return-type,
          -readability-avoid-const-params-in-decls,
          -readability-else-after-return,
+         -readability-identifier-length,
          -readability-magic-numbers'
 
 CheckOptions:

.github/workflows/format.yml

@@ -12,7 +12,6 @@ jobs:
     steps:
     - uses: actions/checkout@v2
     - name: Run clang-format style check for C/C++ programs.
-      uses: jidicula/clang-format-action@v4.0.0
+      uses: jidicula/clang-format-action@v4.8.0
       with:
-        clang-format-version: '12'
         check-path: ${{ matrix.path }}

.github/workflows/tests.yml

@@ -45,6 +45,10 @@ jobs:
           }
 
     steps:
+    - name: Set up Homebrew
+      id: set-up-homebrew
+      uses: Homebrew/actions/setup-homebrew@master
+
     - name: Download Ninja
       id: cmake_and_ninja
       shell: cmake -P {0}

.github/workflows/tidy.yml

@@ -26,6 +26,10 @@ jobs:
             buildflags: "-fno-openmp",
           }
     steps:
+    - name: Set up Homebrew
+      id: set-up-homebrew
+      uses: Homebrew/actions/setup-homebrew@master
+
     - name: Clone Mach
       uses: actions/checkout@v2
       with:

CMakeLists.txt

@@ -71,7 +71,9 @@ endif (MFEM_USE_PUMI)
 # find the MPI compilers
 find_package(MPI REQUIRED)
 
-cmake_policy(SET CMP0077 NEW)
+if (POLICY CMP0077)
+   cmake_policy(SET CMP0077 NEW)
+endif (POLICY CMP0077)
 set(TINYSPLINE_ENABLE_CXX ON)
 set(TINYSPLINE_INSTALL ON)
 include(FetchContent)
@@ -169,8 +171,8 @@ option(MACH_USE_CLANG_TIDY
 if (MACH_USE_CLANG_TIDY)
    set_target_properties(mach
       PROPERTIES
-         CXX_CLANG_TIDY "clang-tidy;--format-style=file;--extra-arg=--std=c++17"
-         # CXX_CLANG_TIDY "clang-tidy;--fix;--fix-errors;--format-style=file;--extra-arg=--std=c++11"
+         CXX_CLANG_TIDY "clang-tidy;--fix;--format-style=file;--extra-arg=--std=c++17"
+         # CXX_CLANG_TIDY "clang-tidy;--fix;--fix-errors;--format-style=file;--extra-arg=--std=c++17;"
    )
 endif (MACH_USE_CLANG_TIDY)
 
@@ -281,10 +283,13 @@ if (BUILD_PYTHON_WRAPPER)
 
    include(FetchContent)
 
-   cmake_policy(SET CMP0127 NEW)
+   if (POLICY CMP0127)
+      cmake_policy(SET CMP0127 NEW)
+   endif (POLICY CMP0127)
    FetchContent_Declare(pybind11
       GIT_REPOSITORY "https://github.com/pybind/pybind11"
-      GIT_TAG v2.7.1
+      #GIT_TAG v2.7.1
+      GIT_TAG v2.10.0
    )
 
    FetchContent_MakeAvailable(pybind11)
@@ -305,7 +310,7 @@ if (BUILD_PYTHON_WRAPPER)
    if (MACH_USE_CLANG_TIDY)
       set_target_properties(pyMach
          PROPERTIES
-            CXX_CLANG_TIDY "clang-tidy;--format-style=file;--extra-arg=--std=c++17"
+            CXX_CLANG_TIDY "clang-tidy;--fix;--format-style=file;--extra-arg=--std=c++17"
             # CXX_CLANG_TIDY "clang-tidy;--fix;--fix-errors;--format-style=file;--extra-arg=--std=c++11"
       )
    endif (MACH_USE_CLANG_TIDY)

mach/mach_output.py

@@ -46,9 +46,11 @@ def setup(self):
                     self.vectors["state"] = np.empty(0)
 
                 elif input == "mesh_coords":
+                    mesh_size = solver.getFieldSize(input)
                     self.add_input("mesh_coords",
-                                   distributed=True,
-                                   shape_by_conn=True,
+                                #    distributed=True,
+                                   shape=mesh_size,
+                                #    shape_by_conn=True,
                                    desc="volume mesh node coordinates",
                                    tags=["mphys_coordinates"])
                     self.vectors["mesh_coords"] = np.empty(0)
@@ -112,6 +114,7 @@ def compute(self, inputs, outputs):
     def compute_jacvec_product(self, inputs, d_inputs, d_outputs, mode):
         solver = self.options["solver"]
         func = self.options["func"]
+        # print(f"Calling compute_jacvec_product for func {func} with inputs: {inputs}, d_inputs: {d_inputs}, d_outputs: {d_outputs}, and mode: {mode}")
 
         # Copy vector inputs into internal contiguous data buffers
         for input in inputs:
@@ -123,12 +126,28 @@ def compute_jacvec_product(self, inputs, d_inputs, d_outputs, mode):
         input_dict = dict(zip(inputs.keys(), inputs.values()))
         input_dict.update(self.vectors)  
 
+        # for input in inputs:
+            # print(f"inputs[{input}] stride: {inputs[input].strides}")
+
+        # for input in inputs:
+        #     if input in d_inputs:
+                # print(f"d_inputs[{input}]: {d_inputs[input]}")
+                # print(f"d_inputs[{input}] stride: {d_inputs[input].strides}")
+
+        # print(f"d_outputs[{func}] stride: {d_outputs[func].strides}")
+
         try:
             if mode == 'fwd':
                 if func in d_outputs:
+                    # print(f"func {func} is in d_outputs")
                     for input in inputs:
                         if input in d_inputs:
+                            # print(f"input {input} is in d_inputs")
+                            # print(f"")
                             func_dot = np.zeros_like(d_outputs[func])
+                            func_dot = np.zeros_like(d_outputs[func])
+
+                            # print(f"wrt_dot for input {input}: {d_inputs[input]} for fun {func}")
                             solver.outputJacobianVectorProduct(of=func,
                                                               inputs=input_dict,
                                                               wrt_dot=d_inputs[input],
@@ -145,6 +164,7 @@ def compute_jacvec_product(self, inputs, d_inputs, d_outputs, mode):
                                 # Recommended to make sure your code can run without MPI too, for testing.
                                 d_outputs[func] += func_dot
 
+                            # print(f"out_dot for func {func}: {d_outputs[func]}")
             elif mode == 'rev':
                 if func in d_outputs:
                     for input in inputs:
@@ -163,10 +183,22 @@ def compute_jacvec_product(self, inputs, d_inputs, d_outputs, mode):
                                                                out_bar=func_bar,
                                                                wrt=input,
                                                                wrt_bar=d_inputs[input])
-        except NotImplementedError as err:
-            if self.options["check_partials"]:
-                pass
+        except Exception as err:
+            if isinstance(err, NotImplementedError):
+                if self.options["check_partials"]:
+                    print(f"\n\nNot implemented error passed!!!\n\n")
+                    pass
+                else:
+                    print(f"\n\nNot implemented error raised!!!\n\n")
+                    raise err
             else:
+                print("\n\ngeneric exception!!!\n\n")
                 raise err
 
+        # except NotImplementedError as err:
+        #     if self.options["check_partials"]:
+        #         pass
+        #     else:
+        #         raise err
+