Python_functional_parameters

[CunchengZhu]

Description

Offload some complex parameter input to python by binding to std::function

Todos

Notable points that this PR has either accomplished or will accomplish.

• Prescribe protein density during simulation
• Return the center (now called notableVertex) as a surfacePoint a boolean Eigen vector with length of the number of vertices. Effectively constrain the type of notable element to be vertex only.
• Provide utility functions to pinpoint the notableVertex: 1) getVertexClosestToEmbeddedCoordinate() based on Euclidean distance, and 2) getVertexFurthestFromBoundary() based on geodesic distance.
• Save the notableVertex in trajectory both in .ply and .nc and read in the if simulation continuation with NetCDF.
• Use 1) time, 2) parameter form and 3) whether receive center in System initializer to decide wether prescribe in init(). Actually solely on whether receive center, if not receive center and no form, throw message and set default, when closed, set index = 0, when boundary, set center of boundary loop Geometry() takes in an explicit std::size_t argument to define the initial notableVertex, which defaults to the vertex with index 0. Expect user to use the utility functions described above to find the index of a special geometric vertex.
• rename point to notatioin element or center notableVertex
• write a update prescription function in System and store frequency of update (number of iteration) in parameter struct
• clean up Parameters.tension and Parameters.osmotic in conjugateGradient
• support multiple notable vertex and its corresponding geodesic distance

Status

• Ready to go

[ctlee]

Too big to review closely. Things look ok.