opencmp.helpers package
Submodules
opencmp.helpers.dg module
- opencmp.helpers.dg.avg(q)[source]
Returns the average of a scalar field.
- Parameters
q (
CoefficientFunction
) – The scalar field.- Return type
CoefficientFunction
- Returns
The average of q at every facet of the mesh.
- opencmp.helpers.dg.grad_avg(q)[source]
Returns the average of the gradient of a field.
- Parameters
q (
CoefficientFunction
) – The field.- Return type
CoefficientFunction
- Returns
The average of the gradient of q at every facet of the mesh.
opencmp.helpers.error module
- opencmp.helpers.error._divergence(sol, mesh)[source]
Function to calculate the divergence of a variable over the domain.
Use with velocity to confirm that conservation of mass is being satisfied.
- Parameters
sol (
GridFunction
) – The solution GridFunction.mesh (
Mesh
) – The mesh that was solved on.
- Return type
float
- Returns
The L2 norm of the divergence of the field.
- opencmp.helpers.error._facet_jumps(sol, mesh)[source]
Function to check how continuous the solution is across mesh facets.
This is mainly of interest when DG is used. Continuous Galerkin FEM solutions will always be perfectly continuous across facets.
- Parameters
sol (
GridFunction
) – The solution GridFunction.mesh (
Mesh
) – The mesh that was solved on.
- Return type
float
- Returns
The L2 norm of the facet jumps.
- opencmp.helpers.error._surface_traction(sol, model, marker)[source]
Function to calculate the surface traction on an object described by a given mesh surface.
- Parameters
sol (
GridFunction
) – The solution gridfunction.model (
None
) – The solved model to calculate the error for.marker (
Optional
[str
]) – The mesh marker for the surface of the object. If the diffuse interface method is being used this is not needed since the phase field will be used to locate the object.
- Return type
CoefficientFunction
- Returns
The surface traction on the object due to the flow field.
- opencmp.helpers.error.calc_error(config, model, sol)[source]
Function to calculate L2 error and other error metrics and print them.
- Parameters
config (
ConfigParser
) – Config file from which to grab.model (
None
) – The solved model to calculate the error for.sol (
GridFunction
) – Gridfunction that contains the current solution.
- Return type
List
- Returns
A list of all of the calculated error metrics ordered by the order of the model.ref_sol[‘metrics’] dictionary.
- opencmp.helpers.error.mean(gfu, mesh)[source]
Function to calculate the mean value of a gridfunction.
- Parameters
gfu (
Union
[GridFunction
,CoefficientFunction
]) – The gridfunction of interest.mesh (
Mesh
) – The mesh the gridfunction is defined on.
- Return type
float
- Returns
The mean value of the gridfunction.
- opencmp.helpers.error.mean_to_zero(gfu, fes, mesh)[source]
Function to bias a gridfunction so its mean is zero.
- Parameters
gfu (
GridFunction
) – The gridfunction to modify (or a component of a gridfunction).fes (
FESpace
) – The finite element space the gridfunction is defined on.mesh (
Mesh
) – The mesh the gridfunction is defined on.
- Return type
GridFunction
- Returns
The modified gridfunction.
- opencmp.helpers.error.norm(norm_type, sol, ref_sol, mesh, fes, average)[source]
Function to calculate some norm between a solution and an “exact” solution.
Uses NGSolve’s Integrate function. The “exact” solution can be a known exact solution or a reference solution previously loaded from file.
- Parameters
norm_type (
str
) – Which norm to calculate.sol (
GridFunction
) – The solution GridFunction.ref_sol (
Union
[GridFunction
,CoefficientFunction
]) – The “exact” solution to compare against.mesh (
Mesh
) – The mesh to compare the solutions on.fes (
FESpace
) – The finite element space that the solutions come from (or a component of it).average (
bool
) – If true offset each solution by its average (use for variables like pressure that are only solved up to a constant).
- Return type
float
- Returns
The calculated error using the specified norm.
opencmp.helpers.error_analysis module
- opencmp.helpers.error_analysis.h_convergence(config, solver, sol, var)[source]
Function to check h (mesh element size) convergence and print results.
- Parameters
config (
ConfigParser
) – Config file from which to grab.solver (
Solver
) – The solver used.sol (
GridFunction
) – Gridfunction that contains the current solution.var (
str
) – The variable of interest.
- Return type
None
- opencmp.helpers.error_analysis.p_convergence(config, solver, sol, var)[source]
Function to check p (interpolat polynomial order) convergence and print results.
- Parameters
config (
ConfigParser
) – Config file from which to grab.solver (
Solver
) – The solver used.sol (
GridFunction
) – Gridfunction that contains the current solution.var (
str
) – The variable of interest.
- Return type
None
opencmp.helpers.io module
- opencmp.helpers.io.create_and_load_gridfunction_from_file(filename, fes, current_dir=None)[source]
Function to create a gridfunction and load the contents of a file into it.
The gridfunction will be constructed from the same finite element space that the file data is assumed to come from. The file data must also fit the exact same dimensions and number of components as the given finite element space. NOTE: It is assumed that the gridfunction in the file is from the same FES and mesh as the one passed in, there is no way for the code to check. SECOND NOTE: If the FES and mesh are not the same, NGSolve will not necessarily crash, it will instead silently return garbage.
- Parameters
filename (
str
) – Path to the file to load.fes (
FESpace
) – The finite element space the file data was created for.current_dir (
Optional
[List
[str
]]) – The directory this command is being called from (ex: dim_dir if being called by DIM). Allows for file paths to be given relative to the specific config file’s directory instead of the main OpenCMP directory only.
- Return type
GridFunction
- Returns
A gridfunction containing the values from the file.
- opencmp.helpers.io.load_mesh(config)[source]
Loads an NGSolve mesh from a .sol file whose file path is specified in the given config file.
- Parameters
config (
ConfigParser
) – A ConfigParser object containing the information from the config file.- Return type
Mesh
- Returns
The NGSolve mesh pointed to in the config file.
- opencmp.helpers.io.update_gridfunction_from_files(gfu, file_dict)[source]
Function to take an existing gridfunction and load data into it from one or more files.
NOTE: It is assumed that the save data in the files is from the same FES and mesh as the existing grid function. There is no way to check this in code. SECOND NOTE: If the FES and mesh are not the same, NGSolve will not necessarily crash, it will instead silently return garbage.
- Parameters
file_dict (
Dict
[Optional
[int
],str
]) – Dict containing the paths to the filesgfu (
GridFunction
) – The gridfunction to load the values into
- Return type
None
opencmp.helpers.math module
- opencmp.helpers.math.H_s(t, w=0.1)[source]
Function to approximate the Heaviside function (step function) using a sigmoid.
- Parameters
t (
Union
[int
,float
,Parameter
,CoefficientFunction
]) – Parameter representing time (or another value)w (
float
) – Length of time over which to go from 0.0001 to 0.9999
- Return type
Union
[float
,CoefficientFunction
]- Returns
The evaluated value of the approximated Heaviside function
- opencmp.helpers.math.H_t(t, w=0.1)[source]
Function to approximate the Heaviside function (step function) using a hyperbolic tangent (tanh).
- Parameters
t (
Union
[int
,float
,Parameter
,CoefficientFunction
]) – Parameter reprenting time (or another value)w (
float
) – Length of time over which to go from 0.0001 to 0.9999
- Return type
Union
[float
,CoefficientFunction
]- Returns
The evaluated value of the approximated Heaviside function
- opencmp.helpers.math.ramp_cos(t, p1=0.0, p2=1.0, tr=1.0)[source]
Function to ramp from one specified value to another in a specified amount of time using the cosine function.
- Parameters
t (
Union
[int
,float
,Parameter
]) – Parameter representing time (or another value).p1 (
float
) – The value to start the ramp at.p2 (
float
) – The value to end the ramp at.tr (
float
) – How quickly to ramp.
- Return type
float
- Returns
The evaluated value of the ramp function.
- opencmp.helpers.math.sig(x)[source]
Function that implements the sigmoid function in a way that’s compatible with NGSolve Parameter and Coefficient objects.
- Parameters
x (
Union
[int
,float
,Parameter
,CoefficientFunction
]) – The value to evaluate the sigmoid at- Return type
Union
[float
,CoefficientFunction
]- Returns
sig(x)
- opencmp.helpers.math.tanh(x)[source]
Function that implements the hyperbolic tangent in a way that’s compatible with NGSolve Parameter and Coefficient objects.
- Parameters
x (
Union
[int
,float
,Parameter
,CoefficientFunction
]) – The value to evaluate tanh at.- Return type
Union
[float
,CoefficientFunction
]- Returns
tanh(x)
opencmp.helpers.mesh module
- opencmp.helpers.mesh.nondimensionalize_mesh_file(filename, char_length)[source]
Function to nondimensionalize a mesh file.
Given the path to a .vol or .msh file, a new file is created containing the exact same mesh but now nondimensionlized by the given characteristic length scale.
- Parameters
filename (
str
) – The path to the mesh file.char_length (
List
[float
]) – The characteristic length scale. Can be different for each dimension (ex: char_length = [x_scale, y_scale, z_scale]) or if a single value is given it is used for every dimension (ex: char_length = [scale] -> char_length = [scale, scale, scale]).
- Return type
None
- opencmp.helpers.mesh.nondimensionlize_loaded_mesh(mesh, char_length)[source]
Function to nondimensionalize an NGSolve mesh.
Given an NGSolve mesh, the mesh nodes are modified to nondimensionlize it by the given characteristic length scale.
- Parameters
mesh (
Mesh
) – The mesh to nondimensionalize.char_length (
List
[float
]) – The characteristic length scale. Can be different for each dimension (ex: char_length = [x_scale, y_scale, z_scale]) or if a single value is given it is used for every dimension (ex: char_length = [scale] -> char_length = [scale, scale, scale]).
- Return type
Mesh
- Returns
The original mesh now nondimensionalized.
opencmp.helpers.misc module
- opencmp.helpers.misc.can_import_module(module_name)[source]
This function checks if a module can be imported. From: https://docs.python.org/3/library/importlib.html#checking-if-a-module-can-be-imported
- Parameters
module_name (
str
) – The name of the module to be imported- Return type
bool
- Returns
True if the module can be imported, False otherwise
- opencmp.helpers.misc.merge_bc_dict(dict_add_to, dict_add_from)[source]
This function merges two boundary condition dictionaries recursively.
The value of each dictionary is either another dictionary or a list.
The merging will be done semi shallowly, so not
If dict_add_from contains a key which is not present in dict_add_to, dict_add_from[key] is copied, shallowly. If the key is present in both dictionary, then the type of value associated with it must be the same. I.e. type(dict_add_to[i]) == type(dict_add_from[i])
If it is a dictionary, the function is called recursively to merge the dictionaries and store them in dict_add_to.
If the entries are lists, then the entries will merged according to the following rules. Let: list_add_to come from dict_add_to and list_add_from come from dict_add_from. 1. list_add_from[i] is None: leave list_add_to[i] alone 2. Otherwise, override list_add_to[i] with list_add_from[i]
The two lists must be of the same length
- Parameters
dict_add_to (
Dict
) – The main dictionary into which things are addeddict_add_from (
Dict
) – The dictionary from which things are added
- Return type
Dict
- Returns
The dict_add_to dictionary with the new pieces added to it.
opencmp.helpers.ngsolve_ module
- opencmp.helpers.ngsolve_.construct_identity_mat(dim)[source]
Constructs an identity matrix of the given dimension.
This expects
- Parameters
dim (
int
) – The dimension of the matrix.- Return type
CoefficientFunction
- Returns
An identity matrix of the desired dimension.
- opencmp.helpers.ngsolve_.get_special_functions(mesh, nu)[source]
Generates a set of special functions needed for DG so they don’t need to be rewritten multiple times.
- Parameters
mesh (
Mesh
) – The mesh used for the simulation.nu (
float
) – The penalty parameter for interior penalty method DG.
- Returns
n: The unit normal for every facet of the mesh.
h: The “size” of every mesh element.
alpha: The penalty coefficient.
I_mat: An identity matrix that matches the mesh dimension.
- Return type
Tuple[CoefficientFunction, CoefficientFunction, CoefficientFunction, CoefficientFunction]
- opencmp.helpers.ngsolve_.gridfunction_rigid_body_motion(t, orig_gfu, gfu, inv_R, mesh, N, scale, offset)[source]
Construct a gridfunction following rigid body motion of an original field.
This function currently only handles rigid body rotation as the only application of the diffuse interface method to moving domains is currently simulation of impeller motion in a stirred-tank reactor.
- Parameters
t (
Parameter
) – Parameter containing the current time.orig_gfu (
GridFunction
) – Gridfunction containing the initial field.gfu (
GridFunction
) – The gridfunction whose values should be updated.inv_R (
Callable
) – The inverse of the rotation matrix.mesh (
Mesh
) – Structured quadrilateral/hexahedral NGSolve mesh.N (
List
[int
]) – Number of mesh elements in each direction (N+1 nodes).scale (
List
[float
]) – Extent of the meshed domain in each direction ([-2,2] square -> scale=[4,4]).offset (
List
[float
]) – Centers the meshed domain in each direction ([-2,2] square -> offset=[2,2]).
- Return type
GridFunction
- Returns
Gridfunction containing the field at the current time.
- opencmp.helpers.ngsolve_.inverse_rigid_body_motion(new_coords, inv_R, b, c)[source]
Based on future coordinates new_coords, find the previous coordinates if rigid body motion occurred.
- Parameters
new_coords (
ndarray
) – The coordinates at the future time.inv_R (
ndarray
) – The inverse of the rotation matrix.b (
ndarray
) – The vector to the center of rotation.c (
ndarray
) – The translation vector.
- Return type
ndarray
- Returns
The coordinates at the previous time.
- opencmp.helpers.ngsolve_.ngsolve_to_numpy(mesh, gfu, N, scale, offset, dim=2, binary=None)[source]
Assign the values in gfu to a numpy array whose elements correspond to the nodes of mesh while preserving spatial ordering.
The output array only contains node values, never the values of higher order dofs.
- Parameters
mesh (
Mesh
) – Structured quadrilateral/hexahedral NGSolve mesh.gfu (
GridFunction
) – NGSolve GridFunction containing the values to assign.N (
List
[int
]) – Number of mesh elements in each direction (N+1 nodes).scale (
List
[float
]) – Extent of the meshed domain in each direction ([-2,2] square -> scale=[4,4]).offset (
List
[float
]) – Centers the meshed domain in each direction ([-2,2] square -> offset=[2,2]).dim (
int
) – Dimension of the domain (must be 2 or 3).binary (
Optional
[ndarray
]) – If exists, arr is multiplied by binary to zero out any array elements outside of the approximated complex geometry.
- Return type
List
[ndarray
]- Returns
List of arrays containing the values in gfu. Since gfu may be vector-valued, the arrays in arr_vec correspond to the various components of gfu.
- opencmp.helpers.ngsolve_.numpy_to_ngsolve(mesh, interp_ord, arr, scale, offset, dim=2)[source]
Assign the values in arr to a NGSolve GridFunction defined over the given NGSolve mesh while preserving spatial ordering.
- Parameters
mesh (
Mesh
) – Mesh used by the problem the GridFunction will be needed to solve.interp_ord (
int
) – Interpolant order of the finite element space for the problem.arr (
ndarray
) – Array containing the values to assign.scale (
List
[float
]) – Extent of the meshed domain in each direction ([-2,2] square -> scale=[4,4]).offset (
List
[float
]) – Centers the meshed domain in each direction ([-2,2] square -> offset=[2,2]).dim (
int
) – Dimension of the domain (must be 2 or 3).
- Return type
GridFunction
- Returns
Gridfunction containing the values in arr.
opencmp.helpers.post_processing module
- class opencmp.helpers.post_processing.PhaseFieldModelMimic(model_to_copy)[source]
Bases:
object
Helper class that mimics the attributes of the Model class that are used during saving and post-processing in order to be able to post-process saved phase field .sol files to .vtu.
- opencmp.helpers.post_processing._sol_to_vtu(gfu, sol_path_str, output_dir_path, save_names, delete_sol_file, subdivision, mesh)[source]
Function that gets parallelized and does the actual sol-to-vtu conversion.
- Parameters
gfu (
GridFunction
) – The grid function into which to load the .sol filesol_path_str (
str
) – The path to the solve file to loadoutput_dir_path (
str
) – The path to the directory to save the .vtu intosave_names (
str
) – The names of the variables to savedelete_sol_file (
bool
) – Whether or not to delete the sol file aftersubdivision (
int
) – Number of subdivisions on each mesh elementmesh (
Mesh
) – The mesh on which the gfu was solved.
- Return type
str
- Returns
A string containing the entry for the .pvd file for this .vtu file.
- opencmp.helpers.post_processing.sol_to_vtu(config, output_dir_path, model=None, delete_sol_file=False, allow_all_threads=False)[source]
Function to take the output .sol files and convert them into .vtu for visualization.
- Parameters
config (
ConfigParser
) – The loaded config parser used by the modeloutput_dir_path (
str
) – The path to the folder in which the .sol files are, and where the .vtu files will be saved.model (
Union
[Model
,PhaseFieldModelMimic
,None
]) – The model that generated the .sol files.delete_sol_file (
bool
) – Bool to indicate if to delete the original .sol files after converting to .vtu, Default is False.allow_all_threads (
bool
) – Bool to indicate if to use all available threads (if there are enough files), Default is False.
- Return type
None
opencmp.helpers.saving module
- class opencmp.helpers.saving.SolutionFileSaver(model, quiet=False)[source]
Bases:
object
Class to handle the saving of GridFunctions and CoefficientFunctions to file
- save(gfu, timestep, DIM=False)[source]
Function to save the provided GridFunction or CoefficientFunction to file.
- Parameters
gfu (
Union
[GridFunction
,CoefficientFunction
]) – GridFunction or CoefficientFunction to savetimestep (
float
) – The current time step, used for naming the fileDIM – If True, a phase field is being saved so should be saved to the phi_sol directory.
- Return type
None