Feature/extensible bcs

.pre-commit-config.yaml

@@ -1,4 +1,15 @@
 repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+    -   id: check-yaml
+    -   id: end-of-file-fixer
+    -   id: trailing-whitespace
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 25.1.0
+    hooks:
+    - id: black
+      language_version: python3
   - repo: local
     hooks:
       - id: fprettify

CMakeLists.txt

@@ -1,28 +1,28 @@
-#  //////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// 
-# 
+#  ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
+#
 #  Maintainers : [email protected]
 #  Official Repository : https://github.com/FluidNumerics/self/
-# 
+#
 #  Copyright © 2024 Fluid Numerics LLC
-# 
+#
 #  Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
-# 
+#
 #  1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
-# 
+#
 #  2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in
 #     the documentation and/or other materials provided with the distribution.
-# 
+#
 #  3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from
 #     this software without specific prior written permission.
-# 
+#
 #  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
 #  LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
 #  HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
 #  LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
 #  THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
 #  THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-# 
-#  //////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// 
+#
+#  ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
 
 cmake_minimum_required(VERSION 3.21)
 cmake_policy(VERSION 3.21...3.27)
@@ -38,6 +38,7 @@ option(SELF_ENABLE_EXAMPLES "Option to enable build of examples. (Default On)"
 option(SELF_ENABLE_GPU "Option to enable GPU backend. Requires either CUDA or HIP. (Default Off)"  OFF)
 option(SELF_ENABLE_APU "Option to enable APU backend. Requires either CUDA or HIP. (Default Off)"  OFF)
 option(SELF_ENABLE_DOUBLE_PRECISION "Option to enable double precision for floating point arithmetic. (Default On)"  ON)
+option(SELF_ENABLE_INTERFACE "Option to enable Python interface. (Default Off)"  OFF)
 
 set(SELF_MPIEXEC_NUMPROCS "2" CACHE STRING "The number of MPI ranks to use to launch MPI tests. Only used when launching test programs via ctest.")
 set(SELF_MPIEXEC_OPTIONS "" CACHE STRING "Any additional options, such as binding options, to use for MPI tests.Only used when launching test programs via ctest. Defaults to nothing")
@@ -54,7 +55,7 @@ FortranCInterface_VERIFY()
 if(NOT FortranCInterface_VERIFIED_C)
 	message(FATAL_ERROR "Fortran compiler must support C Interface")
 endif(NOT FortranCInterface_VERIFIED_C)
-	
+
 if(NOT CMAKE_Fortran_COMPILER_SUPPORTS_F90)
     MESSAGE(FATAL_ERROR "Fortran compiler does not support F90")
 endif(NOT CMAKE_Fortran_COMPILER_SUPPORTS_F90)
@@ -131,11 +132,6 @@ find_package(MPI COMPONENTS Fortran C REQUIRED)
 # HDF5 : See https://cmake.org/cmake/help/latest/module/FindHDF5.html
 find_package(HDF5 REQUIRED Fortran)
 
-# # JSON-Fortran
-# find_library(JSONFORTRAN_LIBRARIES NAMES jsonfortran REQUIRED)
-# find_path(JSONFORTRAN_INCLUDE_DIRS json_module.mod)
-
-
 # FEQ-Parse
 find_library(FEQPARSE_LIBRARIES NAMES feqparse REQUIRED)
 find_path(FEQPARSE_INCLUDE_DIRS feqparse.mod)
@@ -225,19 +221,23 @@ endif()
 
 # Libraries
 add_subdirectory(${CMAKE_SOURCE_DIR}/src)
-# link_directories(${CMAKE_BINARY_DIR}/src)
+
+if(SELF_ENABLE_INTERFACE)
+    # JSON-Fortran
+    find_library(JSONFORTRAN_LIBRARIES NAMES jsonfortran REQUIRED)
+    find_path(JSONFORTRAN_INCLUDE_DIRS json_module.mod)
+    add_subdirectory(${CMAKE_SOURCE_DIR}/src/python)
+endif()
 
 if(SELF_ENABLE_TESTING)
     enable_testing()
     add_subdirectory(${CMAKE_SOURCE_DIR}/test)
-    if(SELF_ENABLE_EXAMPLES)
-        add_subdirectory(${CMAKE_SOURCE_DIR}/examples)
-    endif()
-else()
-    if(SELF_ENABLE_EXAMPLES)
-        enable_testing()
-        add_subdirectory(${CMAKE_SOURCE_DIR}/examples)
-    endif()
+endif()
+
+if(SELF_ENABLE_EXAMPLES)
+    add_subdirectory(${CMAKE_SOURCE_DIR}/examples)
 endif()
 
 
+# Share / etc resources
+install(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/share DESTINATION ${CMAKE_INSTALL_PREFIX})

docs/MeshGeneration/BoundaryConditions.md

@@ -0,0 +1,5 @@
+# Boundary Conditions
+
+In most mesh generation software, you are given the ability to align a name (string/character) and an integer id with each face, node, or edge that lies on a physical boundary. This information is often used in physical modeling software, like SELF, to implement the appropriate boundary conditions for your model. SELF provides a flexible framework for mapping boundary condition names and integer ids to procedures that you can implement for specific boundary conditions. This section of the documentation provides an overview of how you can register custom boundary conditions for a model built with SELF. Additionally we'll cover how you will want to register boundary conditions in a way that is consistent with the meshes that you create in other external software (e.g. HOHQMesh).
+
+## How boundary conditions are registered in SELF

examples/linear_shallow_water2d_kelvinwaves.py

@@ -0,0 +1,59 @@
+from pyself.interface import SelfModel
+from pyself.config import SelfModelConfig
+import os
+from datetime import datetime
+
+
+pwd = os.path.dirname(os.path.abspath(__file__))
+# Set the case directory to a new unique directory based in the time stamp
+# get current working directory
+
+case_directory = f"{os.getcwd()}/kelvinwaves-{datetime.now().strftime('%Y%m%d-%H%M%S')}"
+
+
+def configure_geometry(config):
+    # Configure geometry
+    config.set_parameter(
+        "geometry", "mesh_file", f"{pwd}/../share/mesh/Circle/Circle_mesh.h5"
+    )
+    config.set_parameter("geometry", "uniform_boundary_condition", "no_normal_flow")
+    config.set_parameter("geometry", "control_degree", 7)
+    config.set_parameter("geometry", "control_quadrature", "gauss")
+
+
+def configure_time_options(config):
+    # Configure time options
+    config.set_parameter("time_options", "integrator", "euler")
+    config.set_parameter("time_options", "dt", 0.0025)
+    config.set_parameter("time_options", "start_time", 0.0)
+    config.set_parameter("time_options", "duration", 1.0)
+    config.set_parameter("time_options", "io_interval", 0.05)
+    config.set_parameter("time_options", "update_interval", 50)
+
+
+def configure_shallow_water(config):
+    # Configure shallow water parameters
+    config.set_parameter("linear-shallow-water-2d", "g", 1.0)
+    config.set_parameter("linear-shallow-water-2d", "H", 1.0)
+    config.set_parameter("linear-shallow-water-2d", "Cd", 0.25)
+    config.set_parameter("linear-shallow-water-2d", "f0", 10.0)
+    config.set_parameter("linear-shallow-water-2d", "beta", 0.0)
+
+
+def main():
+
+    config = SelfModelConfig(case_directory=case_directory)
+    config.config["model_name"] = "linear-shallow-water-2d"
+
+    configure_geometry(config)
+    configure_time_options(config)
+    configure_shallow_water(config)
+
+    # Create the model
+    model = SelfModel(config=config)
+
+    x, y = model.get_coordinates()
+
+
+if __name__ == "__main__":
+    main()

pyself/__init__.py

@@ -4,6 +4,16 @@
 A python package for interfacing with the Spectral Element Library in Fortran (https://github.com/fluidnumerics/SELF).
 """
 
-__version__ = "0.1.0"
+from ._version import version
+
+__version__ = version
+__title__ = "pyself"
 __author__ = "Dr. Joe Schoonover"
 __credits__ = "Fluid Numerics LLC"
+
+
+from pyself.config import *
+from pyself.geometry import *
+from pyself.interface import *
+from pyself.lagrange import *
+from pyself.model import *

pyself/_utils/__init__.py

@@ -0,0 +1 @@
+from .library import *

pyself/_utils/library.py

@@ -0,0 +1,39 @@
+import ctypes.util
+import os
+
+
+def find_library_full_path(library_name):
+    """
+    Finds the full path of a library using ctypes.util.find_library.
+
+    Args:
+        library_name: The name of the library to find.
+
+    Returns:
+        The full path of the library, or None if not found.
+    """
+    library_path = ctypes.util.find_library(library_name)
+    print(f"Library path for {library_name}: {library_path}")
+    if library_path:
+        if os.path.isabs(library_path):
+            return library_path
+        else:
+            # On Linux, find_library often returns just the filename, so we search in common library paths
+            for path in ["/lib", "/usr/lib", "/usr/local/lib"]:
+                full_path = os.path.join(path, library_path)
+                if os.path.exists(full_path):
+                    return full_path
+            # If not found in standard paths, try searching in the directories in LD_LIBRARY_PATH
+            ld_library_path = os.environ.get("LD_LIBRARY_PATH")
+            print(f"LD_LIBRARY_PATH: {ld_library_path}")
+            if ld_library_path:
+                for path in ld_library_path.split(":"):
+                    full_path = os.path.join(path, library_path)
+                    print(
+                        f"Checking {full_path} for library {library_name} : {os.path.exists(full_path)}"
+                    )
+                    if os.path.exists(full_path):
+                        return full_path
+            # If still not found, return None
+            return None
+    return None

pyself/_version.py

@@ -0,0 +1 @@
+version = "v0.1.0"

pyself/config.py

@@ -0,0 +1,101 @@
+import json
+from typing import Optional, Dict, Any
+import os
+from ._version import version
+
+
+class SelfModelConfig:
+    def __init__(
+        self, config_file: Optional[str] = None, case_directory: Optional[str] = None
+    ):
+        """Initialize the SELF model configuration from a JSON file or defaults."""
+        self.config = self.default_config()
+
+        self.config_file = config_file
+
+        if config_file:
+            self.load_config(config_file)
+
+        if case_directory:
+            self.case_directory = case_directory
+            os.makedirs(self.case_directory, exist_ok=True)
+        else:
+            self.case_directory = os.getcwd()
+
+    @staticmethod
+    def default_config() -> Dict[str, Any]:
+        """Return default configuration based on the JSON schema."""
+        return {
+            "version": version,
+            "model_name": "linear-shallow-water-2d",
+            "geometry": {
+                "mesh_file": "",
+                "uniform_boundary_condition": "no_normal_flow",
+                "control_degree": 7,
+                "control_quadrature": "gauss",
+                "target_degree": 10,
+                "target_quadrature": "uniform",
+                "nX": 5,
+                "nY": 5,
+                "nZ": 5,
+                "nTx": 1,
+                "nTy": 1,
+                "nTz": 1,
+                "dx": 0.02,
+                "dy": 0.02,
+                "dz": 0.02,
+            },
+            "time_options": {
+                "integrator": "euler",
+                "dt": 0.001,
+                "cfl_max": 0.5,
+                "start_time": 0.0,
+                "duration": 1.0,
+                "io_interval": 0.1,
+                "update_interval": 50,
+            },
+            "units": {"time": "s", "length": "m", "mass": "kg"},
+            "linear-shallow-water-2d": {
+                "g": 1.0,
+                "H": 1.0,
+                "Cd": 0.01,
+                "f0": 0.0,
+                "beta": 0.0,
+                "initial_conditions": {
+                    "geostrophic_balance": False,
+                    "file": "",
+                    "u": 0.0,
+                    "v": 0.0,
+                    "eta": 0.0,
+                },
+                "boundary_conditions": {
+                    "time_dependent": False,
+                    "dt": 0.0,
+                    "from_initial_conditions": False,
+                    "u": 0.0,
+                    "v": 0.0,
+                    "eta": 0.0,
+                },
+            },
+        }
+
+    def load_config(self, file_path: str):
+        """Load configuration from a JSON file"""
+        with open(file_path, "r") as f:
+            self.config.update(json.load(f))
+
+    def save_config(self):
+        """Save configuration to a JSON file in the self.case_directory."""
+        with open(f"{self.case_directory}/model_input.json", "w") as f:
+            json.dump(self.config, f, indent=4)
+
+    def set_parameter(self, section: str, key: str, value: Any):
+        """Set a specific parameter within the configuration."""
+        if section in self.config and key in self.config[section]:
+            self.config[section][key] = value
+        else:
+            raise KeyError(f"Invalid section '{section}' or key '{key}'.")
+
+    def get_parameter(self, section: str, key: str) -> Any:
+        """Retrieve a specific parameter value."""
+        return self.config.get(section, {}).get(key, None)