Resume of Simulation From Last Saved File

docs/getting_started/CHANGELOG.rst

@@ -1,6 +1,10 @@
 OpenCMP Changelog
 =================
 
+June 2, 2023 (v1.0.3)
+
+* Added ability for a simulation to resume from the last saved .sol file.
+
 August 11, 2022 (v1.0.2)
 
 * Implemented the DG version fo the multi-component INS code.

opencmp/config_functions/base_config_functions.py

@@ -28,7 +28,7 @@ class ConfigFunctions:
     """
 
     def __init__(self, config_rel_path: str, import_dir: str, mesh: Mesh, t_param: List[Parameter],
-                 new_variables: List[Dict[str, Union[float, CoefficientFunction, GridFunction]]] = None) -> None:
+                 new_variables: List[Dict[str, Union[float, CoefficientFunction, GridFunction]]] = [{}]) -> None:
         """
         Initializer
 
@@ -43,9 +43,6 @@ def __init__(self, config_rel_path: str, import_dir: str, mesh: Mesh, t_param: L
         # Set the run directory for the config functions.
         # Files could get accessed at run_dir + '/' + <path>. Make sure that if the config file is in the current
         # directory run_dir is specified such that this will still work.
-        if new_variables is None:
-            new_variables = [{}]
-
         if '/' in config_rel_path:
             idx = config_rel_path[::-1].index('/')
             self.run_dir = config_rel_path[:len(config_rel_path) - idx - 1]

opencmp/config_functions/boundary_conditions.py

@@ -27,13 +27,8 @@ class BCFunctions(ConfigFunctions):
     """
 
     def __init__(self, config_rel_path: str, import_dir: str, mesh: Mesh, bc_types: List[str],
-                 t_param: List[Parameter] = None,
-                 new_variables: List[Dict[str, Union[float, CoefficientFunction, GridFunction]]] = None) -> None:
-        if t_param is None:
-            t_param = [Parameter(0.0)]
-        if new_variables is None:
-            new_variables = [{}]
-
+                 t_param: List[Parameter] = [Parameter(0.0)],
+                 new_variables: List[Dict[str, Union[float, CoefficientFunction, GridFunction]]] = [{}]) -> None:
         bc_types = [type.upper() for type in bc_types]
         super().__init__(config_rel_path, import_dir, mesh, t_param)
 

opencmp/config_functions/controller_functions.py

@@ -11,9 +11,7 @@ class ControllerFunctions(ConfigFunctions):
     """
 
     def __init__(self, config_rel_path: str, import_dir: str, mesh: Mesh, t_param: List[Parameter],
-                 new_variables: List[Dict[str, Union[float, CoefficientFunction, GridFunction]]] = None) -> None:
-        if new_variables is None:
-            new_variables = [{}]
+                 new_variables: List[Dict[str, Union[float, CoefficientFunction, GridFunction]]] = [{}]) -> None:
         super().__init__(config_rel_path, import_dir, mesh, t_param, new_variables)
 
         tmp_vc_dict = _convert_dict_entries_to_list(self.config.get_one_level_dict('CONTROL_VARIABLES',

opencmp/config_functions/expanded_config_parser.py

@@ -58,7 +58,8 @@
               'component_names': [],
               'parameter_names': [],
               'velocity_fixed': False,
-              'run_dir': 'REQUIRED'},
+              'run_dir': 'REQUIRED',
+              'resume_from_previous': False},
     'VISUALIZATION': {'save_to_file': False,
                       'save_type': '.sol',
                       'save_frequency': ['1', 'numit'],
@@ -103,9 +104,9 @@ def __init__(self, config_file_path: str) -> None:
 
     def get_one_level_dict(self, config_section: str, import_dir: str, mesh: Mesh,
                            t_param: Optional[List[Parameter]] = None,
-                           new_variables: List[Dict[str,
-                                                    Union[int, str, float, CoefficientFunction, GridFunction, None]]]
-                           = None,
+                           new_variables: List[Dict[str, Union[int, str, float, CoefficientFunction, GridFunction,
+                                                               None]]]
+                           = [{}],
                            all_str: bool = False) -> Tuple[Dict, Dict]:
         """
         Function to load parameters from a config file into a single-level dictionary.
@@ -135,12 +136,10 @@ def get_one_level_dict(self, config_section: str, import_dir: str, mesh: Mesh,
                 - re_parse_dict: Dictionary containing only parameter values that may need to be re-parsed in the
                   future.
         """
-        if new_variables is None:
-            new_variables = [{}]
 
         dict_one: Dict[str, Union[str, float, CoefficientFunction, list]] = {}
         re_parse_dict: Dict[str, Union[str, Callable]] = {}
-        val_str_lst: Union[str, List]  # Just for type-hinting.
+        val_str_lst: Union[str, List] # Just for type-hinting.
         for key in self[config_section]:
             if all_str:
                 # If all_str option is passed none of the parameters should ever need to be re-parsed.
@@ -167,7 +166,7 @@ def get_two_level_dict(self, config_section: str, import_dir: str, mesh: Mesh,
                            t_param: Optional[List[Parameter]] = None,
                            new_variables: List[Dict[str, Union[int, str, float, CoefficientFunction, GridFunction,
                                                                None]]]
-                           = None) \
+                           = [{}]) \
             -> Tuple[Dict, Dict]:
         """
         Function to load parameters from a config file into a two-level dictionary.
@@ -195,8 +194,6 @@ def get_two_level_dict(self, config_section: str, import_dir: str, mesh: Mesh,
                 - re_parse_dict: Dictionary containing only parameter values that may need to be re-parsed in the
                   future.
         """
-        if new_variables is None:
-            new_variables = [{}]
 
         # Top level dictionaries.
         dict_one: Dict[str, Dict[str, Union[str, float, CoefficientFunction, list]]] = {}
@@ -214,9 +211,9 @@ def get_two_level_dict(self, config_section: str, import_dir: str, mesh: Mesh,
     def get_three_level_dict(self, import_dir: str, mesh: Mesh, t_param: Optional[List[Parameter]] = None,
                              new_variables: List[Dict[str, Union[int, str, float, CoefficientFunction, GridFunction,
                                                                  None]]]
-                             = None,
-                             white_list: List[str] = None,
-                             ignore: List[str] = None) -> Tuple[Dict, Dict]:
+                             = [{}],
+                             white_list: List[str] = [],
+                             ignore: List[str] = []) -> Tuple[Dict, Dict]:
         """
         Function to load parameters from a config file into a three-level dictionary.
 
@@ -249,12 +246,6 @@ def get_three_level_dict(self, import_dir: str, mesh: Mesh, t_param: Optional[Li
                 - re_parse_dict: Dictionary containing only parameter values that may need to be re-parsed in the
                   future.
         """
-        if new_variables is None:
-            new_variables = [{}]
-        if white_list is None:
-            white_list = []
-        if ignore is None:
-            ignore = []
 
         # Keys for the top level dictionaries
         keys_one = [item for item in self.sections() if item not in ignore]

opencmp/config_functions/initial_conditions.py

@@ -28,13 +28,8 @@ class ICFunctions(ConfigFunctions):
     Class to hold the initial condition functions.
     """
 
-    def __init__(self, config_rel_path: str, import_dir: str, mesh: Mesh, t_param: List[Parameter] = None,
-                 new_variables: List[Dict[str, Union[float, CoefficientFunction, GridFunction]]] = None) -> None:
-        if t_param is None:
-            t_param = [Parameter(0.0)]
-        if new_variables is None:
-            new_variables = [{}]
-
+    def __init__(self, config_rel_path: str, import_dir: str, mesh: Mesh, t_param: List[Parameter] = [Parameter(0.0)],
+                 new_variables: List[Dict[str, Union[float, CoefficientFunction, GridFunction]]] = [{}]) -> None:
         super().__init__(config_rel_path, import_dir, mesh, t_param)
 
         # Load the IC dict from the IC configfile.

opencmp/config_functions/load_config.py

@@ -21,8 +21,8 @@
 
 
 def parse_str(string: str, import_dir: str, t_param: Optional[List[Parameter]],
-              new_variables: List[Dict[str, Union[int, str, float, CoefficientFunction, GridFunction]]] = None,
-              filetypes: List[str] = None, mesh: Optional[Mesh] = None) \
+              new_variables: List[Dict[str, Union[int, str, float, CoefficientFunction, GridFunction]]] = [{}],
+              filetypes: List[str] = ['.vol', '.sol', '.vtk'], mesh: Optional[Mesh] = None) \
         -> Tuple[Union[str, float, CoefficientFunction, list], Union[str, bool, Callable]]:
     """
     Checks if a string appears to be a path to a file and if not parses the string into Python code.
@@ -45,10 +45,6 @@ def parse_str(string: str, import_dir: str, t_param: Optional[List[Parameter]],
             - variable_eval: Whether or not the expression contains any of the new model variables (would need to be
               re-parsed if their values change).
     """
-    if new_variables is None:
-        new_variables = [{}]
-    if filetypes is None:
-        filetypes = ['.vol', '.sol', '.vtk']
 
     if not isinstance(string, str):
         # Likely got a default value from config_defaults.
@@ -82,8 +78,8 @@ def parse_str(string: str, import_dir: str, t_param: Optional[List[Parameter]],
 
 
 def convert_str_to_dict(string: str, import_dir: str, t_param: Optional[List[Parameter]], mesh: Mesh,
-                        new_variables: List[Dict[str, Union[int, str, float, CoefficientFunction, GridFunction]]] = None,
-                        filetypes: List[str] = None, all_str: bool = False) -> Tuple[Dict, Dict]:
+                        new_variables: List[Dict[str, Union[int, str, float, CoefficientFunction, GridFunction]]] = [{}],
+                        filetypes: List[str] = ['.vol', '.sol', '.vtk'], all_str: bool = False) -> Tuple[Dict, Dict]:
     """
     Function to convert a string into a dict. The values of the dict may be parsed into Python
     code or left as strings.
@@ -105,10 +101,6 @@ def convert_str_to_dict(string: str, import_dir: str, t_param: Optional[List[Par
             - param_dict: Dictionary of the parameters from the string.
             - re_parse_dict: Dictionary containing only parameter values that may need to be re-parsed in the future.
     """
-    if new_variables is None:
-        new_variables = [{}]
-    if filetypes is None:
-        filetypes = ['.vol', '.sol', '.vtk']
 
     # Replace extraneous whitespace characters.
     param_tmp = string.replace('\t', '')

opencmp/config_functions/model_functions.py

@@ -26,14 +26,9 @@ class ModelFunctions(ConfigFunctions):
     Class to hold the model functions and parameters.
     """
 
-    def __init__(self, config_rel_path: str, import_dir: str, mesh: Mesh, t_param: List[Parameter] = None,
-                 new_variables: List[Dict[str, Union[int, str, float, CoefficientFunction, GridFunction, None]]] = None)\
+    def __init__(self, config_rel_path: str, import_dir: str, mesh: Mesh, t_param: List[Parameter] = [Parameter(0.0)],
+                 new_variables: List[Dict[str, Union[int, str, float, CoefficientFunction, GridFunction, None]]] = [{}])\
             -> None:
-        if t_param is None:
-            t_param = [Parameter(0.0)]
-        if new_variables is None:
-            new_variables = [{}]
-
         super().__init__(config_rel_path, import_dir, mesh, t_param)
 
         # Load the model functions/parameters/components dict from the main config file.

opencmp/config_functions/parse_arithmetic.py

@@ -306,7 +306,7 @@ def eval_item(string: str, import_dir: str, t_param: Optional[List[Parameter]],
         return val, variable_eval
 
 
-def eval_python(string: str, import_dir: str, mesh: Optional[Mesh] = None, new_variables: List[Dict[str, Any]] = None,
+def eval_python(string: str, import_dir: str, mesh: Optional[Mesh] = None, new_variables: List[Dict[str, Any]] = {},
                 t_param: Optional[List[Parameter]] = None, time_step: Optional[int] = None) \
         -> Tuple[Union[str, float, CoefficientFunction, bool, None], Union[str, bool, Callable]]:
     """
@@ -328,8 +328,6 @@ def eval_python(string: str, import_dir: str, mesh: Optional[Mesh] = None, new_v
               in its place. If the expression involved importing a Python function that Python function is returned in
               place of variable_eval.
     """
-    if new_variables is None:
-        new_variables = {}
 
     # Remove whitespace in case the string ends up being parsed manually.
     string = string.replace(' ', '')

opencmp/config_functions/reference_solutions.py

@@ -26,13 +26,8 @@ class RefSolFunctions(ConfigFunctions):
     Class to hold the reference solutions.
     """
 
-    def __init__(self, config_rel_path: str, import_dir: str, mesh: Mesh, t_param: List[Parameter] = None,
-                 new_variables: List[Dict[str, Union[float, CoefficientFunction, GridFunction]]] = None) -> None:
-        if t_param is None:
-            t_param = [Parameter(0.0)]
-        if new_variables is None:
-            new_variables = [{}]
-
+    def __init__(self, config_rel_path: str, import_dir: str, mesh: Mesh, t_param: List[Parameter] = [Parameter(0.0)],
+                 new_variables: List[Dict[str, Union[float, CoefficientFunction, GridFunction]]] = [{}]) -> None:
         super().__init__(config_rel_path, import_dir, mesh, t_param)
 
         # Load the reference solution dict from the reference solution configfile.

opencmp/diffuse_interface/interface.py

@@ -268,7 +268,7 @@ def nonconformal_subdomain_2d(boundary_lst: List, vertices: List, N: List[int],
 
 def split_nonconformal_subdomains_2d(boundary_lst: List, vertices: Dict, N: List[int], scale: List[float],
                                      offset: List[float], lmbda_overlap: Union[float, bool] = False,
-                                     remainder: bool = False, centroid: Dict = None) -> Dict[str, ndarray]:
+                                     remainder: bool = False, centroid: Dict = {}) -> Dict[str, ndarray]:
     """
     Function to generate all BC masks for a 2D diffuse interface simulation.
 
@@ -293,8 +293,6 @@ def split_nonconformal_subdomains_2d(boundary_lst: List, vertices: Dict, N: List
     Returns:
         Dictionary of numpy array masks.
     """
-    if centroid is None:
-        centroid = {}
 
     shape = (int(N[0] + 1), int(N[1] + 1))
 
@@ -416,7 +414,7 @@ def nonconformal_subdomain_3d(face_lst: ndarray, vertices: str, N: List[int], sc
 
 def split_nonconformal_subdomains_3d(face_lst: List, vertices: Dict[str, str], N: List[int], scale: List[float],
                                      offset: List[float], lmbda_overlap: Union[float, bool] = False,
-                                     remainder: bool = False, centroid: Dict = None) -> Dict[str, ndarray]:
+                                     remainder: bool = False, centroid: Dict = {}) -> Dict[str, ndarray]:
     """
     Function to generate all BC masks for a 3D diffuse interface simulation.
 
@@ -440,8 +438,6 @@ def split_nonconformal_subdomains_3d(face_lst: List, vertices: Dict[str, str], N
     Returns:
         Dictionary of numpy array masks.
     """
-    if centroid is None:
-        centroid = {}
 
     shape = (int(N[0] + 1), int(N[1] + 1), int(N[2] + 1))
 

opencmp/helpers/saving.py

@@ -41,15 +41,15 @@ def __init__(self, model: Model, quiet: bool = False) -> None:
             print('Can\'t output to file type {}.'.format(base_type))
 
         self.save_dir = model.config.get_item(['OTHER', 'run_dir'], str, quiet) + '/output/'
-        self.save_dir_sol = model.config.get_item(['OTHER', 'run_dir'], str, quiet) + '/output/' + model.name + '_sol/'
-        self.save_dir_vtu = model.config.get_item(['OTHER', 'run_dir'], str, quiet) + '/output/' + model.name + '_vtu/'
+        self.save_dir_sol = model.config.get_item(['OTHER', 'run_dir'], str, quiet) + '/output/' + model.name() + '_sol/'
+        self.save_dir_vtu = model.config.get_item(['OTHER', 'run_dir'], str, quiet) + '/output/' + model.name() + '_vtu/'
 
         # Specifically for diffuse interface rigid body motion.
         self.save_dir_phi = model.config.get_item(['OTHER', 'run_dir'], str, quiet) + '/output_phi/'
-        self.save_dir_phi_sol = model.config.get_item(['OTHER', 'run_dir'], str, quiet) + '/output_phi/' + model.name + '_sol/'
-        self.save_dir_phi_vtu = model.config.get_item(['OTHER', 'run_dir'], str, quiet) + '/output_phi/' + model.name + '_vtu/'
+        self.save_dir_phi_sol = model.config.get_item(['OTHER', 'run_dir'], str, quiet) + '/output_phi/' + model.name() + '_sol/'
+        self.save_dir_phi_vtu = model.config.get_item(['OTHER', 'run_dir'], str, quiet) + '/output_phi/' + model.name() + '_vtu/'
 
-        self.base_filename_sol = self.save_dir_sol + model.name + '_'
+        self.base_filename_sol = self.save_dir_sol + model.name() + '_'
         self.base_filename_phi_sol = self.save_dir_phi_sol + 'phi' + '_'
         self.base_subdivision = model.config.get_item(['VISUALIZATION', 'subdivision'], int, quiet)
 

opencmp/models/base_model.py

@@ -49,16 +49,7 @@ def __init__(self, config: ConfigParser, t_param: List[Parameter]) -> None:
             config: A configparser object loaded with config file.
             t_param: List of parameters representing the current and previous timestep times.
         """
-        # The name of the model (helper variable). It is the name of the class.
-        self.name = self.__class__.__name__.lower()
-
-        logging.info('Initializing model: ' + self.name)
-
-        # Remove the trailing "dim" from the model name if the Diffuse Interface Method version is used
-        # Lets us continue using "Poisson" or "INS" in config files without adding the DIM
-        if "dim" == self.name[-3:]:
-            self.name = self.name[:-3]
-
+        logging.info('Initializing model: ' + self.name())
         # Set config file.
         self.config = config
 
@@ -223,7 +214,7 @@ def __init__(self, config: ConfigParser, t_param: List[Parameter]) -> None:
 
         # Load initial condition.
         self.IC = self.construct_gfu_ic()
-        self.ic_functions.set_initial_conditions(self.IC, self.mesh, self.name, self.model_components_ic)
+        self.ic_functions.set_initial_conditions(self.IC, self.mesh, self.name(), self.model_components_ic)
 
         # 2/2: Create BCs
         # Now that we have the FES, we can load in the bc gridfunctions
@@ -631,7 +622,7 @@ def update_model_variables(self, updated_gfu: Union[GridFunction, List[ProxyFunc
             # Update the initial conditions.
             self.ic_functions.update_initial_conditions(self.t_param, self.update_variables, self.mesh)
             self.IC = self.construct_gfu_ic()
-            self.ic_functions.set_initial_conditions(self.IC, self.mesh, self.name, self.model_components)
+            self.ic_functions.set_initial_conditions(self.IC, self.mesh, self.name(), self.model_components)
 
         if ref_sol_update:
             # Update the reference solutions.
@@ -649,6 +640,23 @@ def update_timestep(self, gfu: GridFunction, gfu_0: GridFunction) -> None:
 
         gfu_0.vec.data = gfu.vec
 
+    @classmethod
+    def name(cls):
+        """
+        Helper function to generate a readable version of the class model name.
+
+        :return:
+            The formatted name of this model class.
+        """
+        name = cls.__name__.lower()
+
+        # Remove the trailing "dim" from the model name if the Diffuse Interface Method version is used
+        # Lets us continue using "Poisson" or "INS" in config files without adding the DIM
+        if "dim" == name[-3:]:
+            name = name[:-3]
+
+        return name
+
     @staticmethod
     @abstractmethod
     def allows_explicit_schemes() -> bool: