Mesh for anisotropic particles by mayukh33 · Pull Request #52 · mphowardlab/flyft

mayukh33 · 2025-04-04T19:12:33Z

No description provided.

…r dimensions

mphoward · 2025-04-16T02:25:48Z

include/flyft/mesh.h

         BoundaryType upper_bc);

-    std::shared_ptr<Mesh> slice(int start, int end) const;
+    std::shared_ptr<Mesh> slice(std::vector<int> start, std::vector<int> end) const;


Make sure to pass all these vectors by const reference to avoid copies

Suggested change

std::shared_ptr<Mesh> slice(std::vector<int> start, std::vector<int> end) const;

std::shared_ptr<Mesh> slice(const std::vector<int>& start, const std::vector<int>& end) const;

mphoward · 2025-04-16T02:26:05Z

include/flyft/mesh.h


    //! Get position on the mesh, defined as center of bin
-    double center(int i) const;
+    std::vector<double> center(std::vector<int> i) const;


Suggested change

std::vector<double> center(std::vector<int> i) const;

std::vector<double> center(const std::vector<int>& i) const;

mphoward · 2025-04-16T02:26:17Z

include/flyft/mesh.h


    //! Get lower bound of bin
-    double lower_bound(int i) const;
+    std::vector<double> lower_bound(std::vector<int> i) const;


Suggested change

std::vector<double> lower_bound(std::vector<int> i) const;

std::vector<double> lower_bound(const std::vector<int>& i) const;

mphoward · 2025-04-16T02:26:28Z

include/flyft/mesh.h


    //! Get upper bound of bin
-    double upper_bound(int i) const;
+    std::vector<double> upper_bound(std::vector<int> i) const;


Suggested change

std::vector<double> upper_bound(std::vector<int> i) const;

std::vector<double> upper_bound(const std::vector<int>& i) const;

mphoward · 2025-04-16T02:26:54Z

include/flyft/mesh.h

    BoundaryType upper_boundary_condition() const;

-    int asShape(double dx) const;
+    std::vector<int> asShape(std::vector<double> dx) const;


Suggested change

std::vector<int> asShape(std::vector<double> dx) const;

std::vector<int> asShape(const std::vector<double>& dx) const;

mphoward · 2025-04-16T02:28:00Z

include/flyft/mesh.h

+    double integrateSurface(std::vector<int> idx, double j_lo, double j_hi) const;
+    double integrateSurface(std::vector<int> idx, const DataView<double>& j) const;
+    double integrateSurface(std::vector<int> idx, const DataView<const double>& j) const;


We need to be careful here. Isn't j now going to need to be a vector? Or 1 vector per face of the mesh site?

mphoward · 2025-04-16T02:29:08Z

include/flyft/mesh.h

+    double integrateVolume(std::vector<int> idx, double f) const;
+    double integrateVolume(std::vector<int> idx, const DataView<double>& f) const;
+    double integrateVolume(std::vector<int> idx, const DataView<const double>& f) const;


Suggested change

double integrateVolume(std::vector<int> idx, double f) const;

double integrateVolume(std::vector<int> idx, const DataView<double>& f) const;

double integrateVolume(std::vector<int> idx, const DataView<const double>& f) const;

double integrateVolume(const std::vector<int>& idx, double f) const;

double integrateVolume(const std::vector<int>& idx, const DataView<double>& f) const;

double integrateVolume(const std::vector<int>& idx, const DataView<const double>& f) const;

mphoward · 2025-04-16T02:29:38Z

include/flyft/mesh.h

+    virtual double gradient(std::vector<int> idx, double f_lo, double f_hi) const = 0;
+    double gradient(std::vector<int> idx, const DataView<const double>& f) const;
+    double gradient(std::vector<int> idx, const DataView<double>& f) const;


Similarly here, won't the gradient now return a vector?

mphoward · 2025-04-16T02:30:57Z

include/flyft/mesh.h


 template<typename T>
-typename std::remove_const<T>::type Mesh::interpolate(double x, const DataView<T>& f) const
+typename std::remove_const<T>::type Mesh::interpolate(std::vector<double> x,


Is this implementation right? Don't we need to do multidimensional interpolation?

Based on our discussion, this interpolation method probably needs to be updated so that it is operating only on one coordinate, with the rest fixed to a specific bin.

mphoward · 2025-04-16T02:31:33Z

src/mesh.cc

    : lower_(lower_bound), shape_(shape), lower_bc_(lower_bc), upper_bc_(upper_bc), start_(0)
    {
-    step_ = (upper_bound - lower_bound) / shape_;
+    std::vector<double> step_;


Step is already a member variable

Suggested change

std::vector<double> step_;

mphoward · 2025-04-18T18:31:29Z

include/flyft/mesh.h

+     * \param i Multidimensional bin index
+     * \return Upper bound of the multidimensional bin
+     */
    virtual double area(int i) const = 0;


For this method, what area is this going to return? Should it return the areas of all lower faces in some defined order? Or, should it take both an index to a bin and an index to a dimension and return the area of that lower face?

Or perhaps, it needs three arguments: bin, face, and +/- direction?

mphoward · 2025-04-18T19:59:16Z

include/flyft/mesh.h

+     * \param x Coordinate position of the bin
+     * \return Bin index
+     */
+    std::vector<int> bin(double x) const;


This is going to need to take a vector, right?

mphoward · 2025-04-18T19:59:34Z

include/flyft/mesh.h

+     * \param i Multidimensional bin index
+     * \return Volume of the bin
+     */
    virtual double volume(int i) const = 0;


This needs to be a vector

mphoward · 2025-04-18T20:00:48Z

include/flyft/mesh.h


 template<typename T>
-typename std::remove_const<T>::type Mesh::interpolate(double x, const DataView<T>& f) const
+typename std::remove_const<T>::type Mesh::interpolate(std::vector<double> x,


Based on our discussion, this interpolation method probably needs to be updated so that it is operating only on one coordinate, with the rest fixed to a specific bin.

mphoward · 2025-04-18T20:01:30Z

include/flyft/mesh.h

+    //! Get the integral of the surface over the mesh
+    /*!
+     * \param shape Shape of the mesh
+     * \return Length of the mesh
+     */
+    double integrateSurface(const std::vector<int>& idx, double j_lo, double j_hi) const;
+    double integrateSurface(const std::vector<int>& idx, const DataView<double>& j) const;
+    double integrateSurface(const std::vector<int>& idx, const DataView<const double>& j) const;


Did you think about how these are going to work in the new code? Is it going to integrate over a specific face, or all of them? And what will it integrate?

mphoward · 2025-06-05T14:33:53Z

@mayukh33 can this be merged into refactor-aniso before I work on it? It's OK if it isn't perfect so long as it isn't totally broken, since I will likely be making quite a few changes anyway.

mayukh33 · 2025-06-05T16:32:37Z

Hi! I think it can be merged into refactor-aniso. I also wanted to make a note that I had to change the black-pre-commit-mirror.yaml's black-pre-commit-mirror requirement from 24.10.0 to 24.8.0. Otherwise, it gave an error that it could not find the 24.10.0 among the list of supported distributions.

mphoward · 2025-06-05T16:43:18Z

Please revert that change, and I'll have a look at it locally

mayukh33 added 2 commits April 4, 2025 14:11

Extend center, lower_bound, upper_bound, shape, step and bin to highe…

58fa042

…r dimensions

Fix multi-dimensional indexing

e3dabd9

mphoward reviewed Apr 16, 2025

View reviewed changes

mayukh33 added 2 commits April 16, 2025 16:17

Apply fix and add documentation

f374be9

Minor fix

1ece6ab

mayukh33 requested a review from mphoward April 18, 2025 03:44

mphoward reviewed Apr 18, 2025

View reviewed changes

Apply review suggestions and minor fixes

fc8090e

Revert .pre-commit-config.yaml

361bd9c

mayukh33 requested a review from mphoward June 11, 2025 14:24

mphoward merged commit 009f2d3 into refactor-aniso Jun 12, 2025
1 check passed

mphoward deleted the feature/mesh-aniso branch June 12, 2025 14:45

	std::shared_ptr<Mesh> slice(std::vector<int> start, std::vector<int> end) const;
	std::shared_ptr<Mesh> slice(const std::vector<int>& start, const std::vector<int>& end) const;

	std::vector<double> center(std::vector<int> i) const;
	std::vector<double> center(const std::vector<int>& i) const;

	std::vector<double> lower_bound(std::vector<int> i) const;
	std::vector<double> lower_bound(const std::vector<int>& i) const;

	std::vector<double> upper_bound(std::vector<int> i) const;
	std::vector<double> upper_bound(const std::vector<int>& i) const;

	std::vector<int> asShape(std::vector<double> dx) const;
	std::vector<int> asShape(const std::vector<double>& dx) const;

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mayukh33 commented Apr 4, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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mphoward commented Jun 5, 2025

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mayukh33 commented Jun 5, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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mphoward commented Jun 5, 2025

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mayukh33 commented Apr 4, 2025 •

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mayukh33 commented Jun 5, 2025 •

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