CHANGELOG.md

Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

Unreleased

Added

Changed

• Disabled hard assertion test that ensured that every edge in a topology.Mesh() object was connected to at most 2 faces (manifoldness preservation). Now we print out a warning since we are all consenting adults over here. The implications of this change is that area load calculations might be incorrect, but this needs to be more thoroughly tested at a later time.

Removed

[0.8.6] 2024-10-30

Added

• Wrapped two gradient-free optimizers from scipy: Nelder-Mead and Powell. They are available as jax_fdm.optimizers.NelderMead and jax_fdm.optimizers.Powell, respectively.
• Linked two evolutionary optimizers from scipy They are available as jax_fdm.optimizers.DualAnnealing and jax_fdm.optimizers.DifferentialEvolution.
• Added support for kwargs in LossPlotter.plot(). The kwargs control the parameters of the equilibrium model used to plot the loss history.
• Added VertexSupportParameter.index(). This change might appear redundant, but it was necessary to deal with the method resolution order of the parent classes of VertexSupportParameter.
• Added VertexGroupSupportParameter.index() for similar reasons as the listed above.

Changed

• Changed datastructure.print_stats() to report positive and negative forces separately.
• Turned off display in TruncatedNewton.
• Fixed bug in OptimizationRecorder. The recorder did not know how to record optimization history without an explictly initialized optimizer.
• Deprecated jax_fdm.optimization.optimizers.scipy in favor of jax_fdm.optimization.optimizers.gradient_based.
• Fixed bug. Return early in NetworkArtist.edge_width() if the artist edges list is empty.
• Fixed bug in EdgesForceEqualGoal.prediction(): the normalization mean of compressive edge forces was a negative number. This led to negative normalized variance values, which was plainly incorrect.
• VertexGroupSupportParameter inherits from VertexGroupParameter instead of NodeGroupParameter. This was a bug.

Removed

[0.8.5] 2024-09-15

Added

Changed

Removed

• Removed compas_singular from dependencies list. That package has been archived and it is not used in jax_fdm source code; only in a couple examples.

[0.8.4] 2024-05-09

Added

• Added NetworkSmoothGoal to smoothen the shape of a network based on the fairness energy of its nodes w.r.t. their immediate neighborhood.
• Implemented Graph.adjacency to access the connectivity among nodes/vertices to compute new goals.
• Added adjacency_matrix as numpy-only function to assemble Graph.adjacency. The function is largely inspired by compas.matrices.adjacency_matrix.

Changed

• Now we use time.perf_counter instead of time.time to measure logic execution time more accurately.

Removed

[0.8.3] 2024-04-18

Added

Goals

• Implemented EdgeLoadPathGoal.

Changed

Floating-point arithmetic

• Updated how to enable double floating precision (float64) to comply with changes of jax.config in jax==0.4.25.

Equilibrium

• Fixed duplicated fixed point iteration in EquilibriumModel.equilibrium_iterative. This led to unnecessarily long runtimes. This change also fixes the "mysterious" bug that made jaxopt implicit differentiation incompatible with sparse matrices.

Visualization

• LossPlotter exposes plot_legend to choose whether or not to show legend with curve labels.
• FDNetworkArtist takes absolute force density values to calculate viz colors in "fd" mode.
• Fixed bug in FDNetworkViewerArtist that threw error when inputing a custom list of edges to display. The problem was that the artist could not find the width of all the edges connected to a node because edge_width is only computed for the custom list of edges. The artist was expecting a dictionary with all the edge widths.
• Package compas-notebook became an optional dependency because it does not support compas<2.0 anymore.

Removed

[0.8.1] 2023-12-05

Added

Losses

• Implemented LogMaxError. The goal of this error function is to work as a barrier soft constraint for target maximum values. One good use example would be to restrict the height of a shell to a maximum height.

Changed

Removed

[0.8.0] 2023-11-23

Added

Models

• Added support for efficient reverse-mode AD of the calculation of equilibrium states in the presence of shape-dependent loads, via implicit differentiation. Forward-mode AD is pending.
• Added EquilibriumModel.equilibrium_iterative to compute equilibrium states that have shape-dependent edge and face loads using fixed point iteration.
• Added EquiibriumModel.edges_load and EquiibriumModel.faces_load to allow computation of edge and face loads.
• Implemented EquilibriumModelSparse.stiffness_matrix.
• Implemented EquilibriumModel.stiffness_matrix.
• Implemented EquilibriumModel.force_matrix.
• Implemented EquilibriumModel.force_fixed_matrix.
• Added linearsolve_fn, itersolve_fn, implicit_diff, and verbose as attributes of EquilibriumModel.
• Added Equilibrium.load_nodes_iter as attribute to include the node loads in LoadState.nodes when running EquilibriumModel.equilibrium_iterative(). Defaults to False.

Equilibrium

• Restored vectors field in EquilibriumState.
• Implemented equilibrium.states.LoadState.
• Implemented equilibrium.states.EquilibriumParametersState.

Solvers

• Implemented solver_anderson, to find fixed points of a function with jaxopt.AndersonAcceleration. The implicit differentiation operator of the solver provided by jaxopt is deactivated when using EquilibriumModelSparse because jaxopt does not support sparse matrices yet.
• Defined a jax.custom_vjp for fixed_point, an interface function that solves for fixed points of a function for different root-finding solver types: solver_fixedpoint, solver_forward, and solver_newton.
• Implemented solver_fixedpoint, a function that wraps jaxopt.FixedPointIterator to calculate static equilibrium iteratively.
• Implemented solver_forward, to find fixed points of a function using an equinox.while_loop.
• Implemented solver_netwon, to find fixed points of a function using Newton's method.

Loads

• Added equilibrium.loads module to enable support for edge and face-loads, which correspond to line and area loads, respectively. These two load types can be optionally become follower loads setting the is_local input flag to True. A follower load will update its direction iteratively, according to the local coordinate system of an edge or a face at an iteration. The two main functions that enable this feature are loads.nodes_load_from_faces and loads.nodes_load_from_edges. These functions are wrapped by EquilibriumModel under EquiibriumModel.edges_load and EquiibriumModel.faces_load.
• Implemented equilibrium.loads.nodes_.

Datastructures

• Report standard deviation in FDDatastructure.print_stats().
• Added constructor method FDNetwork.from_mesh.
• Added FDMesh.face_lcs to calculate the local coordinaty system of a mesh face.
• Added datastructures.FDDatastructure.edges_loads.
• Added datastructures.FDMesh.
• Added datastructures.Datastructure.
• Implemented structures.EquilibriumStructureMeshSparse.
• Implemented structures.EquilibriumStructureMesh.
• Implemented structures.Mesh.
• Implemented structures.MeshSparse.
• Implemented structures.Graph.
• Implemented structures.GraphSparse.
• Added FDNetwork.is_edge_fully_supported.
• Added EquilibriumMeshStructure.from_mesh with support for inhomogenous faces (i.e. faces with different number of vertices). The solution is to pad the rows of the faces 2D array with -1 to match max_num_vertices.

Goals

• Implemented NetworkXYZLaplacianGoal.
• Implemented base class MeshGoal.
• Implemented MeshXYZLaplacianGoal.
• Implemented MeshXYZFaceLaplacianGoal.
• Implemented MeshAreaGoal.
• Implemented MeshFacesAreaEqualizeGoal.

Optimization

• Added optimization.Optimizer.loads_static attribute to store edge and face loads during optimization.

Geometry

• Added polygon_lcs to compute the local coordinate system of a closed polygon.
• Added line_lcs to compute the local coordinate system of a line.
• Added nan gradient guardrail to normalize_vector calculations.

Parameters

• Added support for mesh vertex parameters.

Numerical

• Added explicit array integer types in __init__: DTYPE_INT_NP and DTYPE_INT_JAX

Sparse solver

• Set spsolve_gpu_ravel as the default sparse solver on GPUs (spsolve_gpu).
• Added spsolve_gpu_ravel to solve the FDM linear system all at once on GPUs.
• Implemented helper function sparse_blockdiag_matrix to spsolve_gpu_ravel.

Visualization

• Added plotters/VectorArtist to custom plot loads and reactions arrows.
• Implemented LossPlotter._print_error_stats to report loss breakdown of error terms.

Changed

Models

Equilibrium

• The functions fdm and constrained_fdm take iterative equilibrium parameters as function arguments.
• The functions fdm and constrained_fdm can take an FDMesh as input, in addition to FDNetwork.

Sparse solver

• Decoupled sparse_solver from any force density calculations. Now, it is a simpler solver that only takes as inputs the LHS matrix A and the RHS matrix b, and thus, it could be used to potentially solve any sparse linear system of equations. Its signature now is analogous to that of jax.numpy.linalg.solve.
• Condensed signature of sparse linear solver sparse_solve to take a structure EquilibriumStructure as input, instead of explicit attributes of a structure.
• Changed signature of sparse_solve_bwd to take two arguments, where the first is the "residual" values produced on the forward pass by fwd, and the second is the output cotangent with the same structure as the primal function output (sparse_solve).
• Condensed signature of helper functions sparse_solve_fwd to take matrices A and b as inputs, instead of explicit attributes of the FDM and of a EquilibriumStructure.
• Renamed previous verison of spsolve_gpu to spsolve_gpu_stack.

Geometry

• Added support for jnp.nan inputs in the calculations of geometry.normal_polygon.

Losses

• Changed signature of Regularizer.__call__ to take in parameters instead of equilibirum state.

Datastructures

• Overhauled EquilibriumStructure and EquilibriumStructureSparse. They are subclasses equinox.Module, and now they are meant to be immutable. They also have little idea of what an FDNetwork is.
• Modified face_matrix adjacency matrix creation function to skip -1 vertices. This is to add support for MeshStructures that have faces with different number of vertices.

Optimization

• Use jax.value_and_grad(loss_fn(x)) instead of using loss_fn(x) and jax.grad(loss_fn(x)) separately. This results in optimization speedup because we get both value and grad with a single VJP call.
• Optimizer.problem takes an FDNetwork as input.
• Optimizer.problem takes boolean jit_fn as arg to disable jitting if needed.
• Changed ParameterManager to require an FDNetwork as argument at initialization.
• Changed Parameter.value signature. Gets value from network directly, not from structure.network
• optimization.OptimizationRecorder has support to store, export and import named tuple parameters.

Visualization

• Fixed bug in viewers/network_artist.py that overshifted load arrows.
• Edge coloring considers force sign for force color scheme in artists/network_artist.py.
• Fixed bug with the coloring of reaction forces in viewers/network_artist.py.
• Fixed bug with the coloring of reaction forces in artists/network_artist.py.
• LossPlotter has support to plot named tuple parameters.

Removed

• Removed EquilibriumModel.from_network.
• Removed sparse.force_densities_to_A. Superseded by EquilibriumModelSparse.stiffness_matrix.
• Removed sparse.force_densities_to_b. Superseded by EquilibriumModel.force_matrix.
• Removed partial jitting from Loss.__call__.
• Removed partial jitting from Error.__call__.

[0.7.1] 2023-05-08

Added

Changed

• Fixed signature bug in constraint initialization in ConstrainedOptimizer.constraints.

Removed

• Removed implicit partial(jit) decorator on ConstrainedOptimizer.constraint. Jitting now takes place explicitly in ConstrainedOptimizer.constraints.

[0.7.0] 2023-05-08

Added

• Added EquilibriumStructure.init as a quick fix to warm start properties.

Changed

• Changed signature of equilibrium model to be EquilibriumModel(params, structure).
• The init function in goals, constraints and parameter takes (model, structure) as arguments.
• Removed connectivity related operations from EquilibriumModel and inserted them into EquilibriumStructure.
• Fixed bug in EquilibriumStructure.nodes that led to a recursive timeout error.
• Renamed example file butt.py to vault.py/
• Renamed file optimizers.py to scipy.py in jax_fdm.optimization.

Removed

• Removed structure attribute from EquilibriumModel en route to equinox modules.

[0.6.0] 2023-04-30

Added

Support for differentiable CPU sparse solver

• Added support for differentiable CPU and GPU sparse solvers to compute the XYZ coordinates of the free nodes with FDM. The solver is custom made and registered via a jax.custom_vjp. The forward and backward passes of the sparse solver were made possible thanks to the contributions of @denizokt. This solver lives in equilibrium.sparse.py.
• Added spsolve_gpu and spsolve_cpu. The sparse solver backend is different (the former uses CUDA and the latter scipy) and it gets selected automatically based on what the value of jax.default_device is at runtime with function register_sparse_solver.
• Implemented EquilibriumStructureSparse.
• Division of responsabilities: created a EquilibriumModelSparse that solves for static equilibrium using an EquilibriumStructureSparse and the sparse solver. EquilibriumModel implements the dense linear solver.

Changed

• LossPlotter instantiates a dense EquilibriumModel.

Removed

[0.5.2] 2023-03-15

Added

Changed

Removed

• Removed DTYPE from combine_parameters signature in jax_fdm.parameters due to clashes with JAX versions on windows.

[0.5.1] 2023-03-10

Added

Changed

• Added ParameterManager.indices_opt_sort to fix bug that mistmatch optimization values for unconsecutive parameter indices. This bug applied to individual parameters and to parameter groups.

Removed

[0.5.0] 2023-03-02

Added

• Implemented parameter groups!
• Added EdgesForceDensityParameter.
• Added NodesLoadXParameter, NodesLoadYParameter, NodesLoadZParameter.
• Added NodesSupportXParameter, NodesSupportYParameter, NodesSupportZParameter.
• Added EdgesForceEqualGoal to goals.
• Implemented area_polygon in jax_fdm.geometry.
• Added FDNetwork.number_of_supports() to count number of supported nodes in a network.
• Added network_validate to check the validity of a network before equilibrium calculations.

Changed

• Sped up EquilibriumModel.nodes_free_positions() computation after replacing jnp.diag(q) with vmap(jnp.dot)(q, *).
• Vectorized error computations in LossPlotter.plot() to expedite method.
• OptimizationRecorder.record() now stores history in a dictionary, not in a list.
• Fixed bug in FDNetworkViewerArtist that ocurred while plotting reaction forces on unconnected nodes.
• Turned TrustRegionConstrained into a first order optimizer.

Removed

• Removed LossPlotter.network attribute.
• Replaced NodeAnchorXParameter with NodeSupportXParameter.
• Replaced NodeAnchorYParameter with NodeSupportYParameter.
• Replaced NodeAnchorZParameter with NodeSupportZParameter.

[0.4.5] 2023-02-04

Added

• Added Goal.is_collectible flag to determine if a goal should form part of an optimization Collection.
• Implemented EdgesLengthEqualGoal.
• Added AbsoluteError term.
• Added MeanAbsoluteError terms.

Changed

• Fixed omission of gstate.weight when computing PredictionError.

Removed

[0.4.4] 2022-12-15

Added

• Implemented LBFGSBS to ensure compatibility of JAX gradients with scipy.

Changed

Removed

[0.4.3] 2022-12-14

Added

• Implemented NotebookViewer to visualize networks in jupyter notebooks.
• Added FDNetworkNotebookArtist to visualize networks in jupyter notebooks.
• Added noteboks.shapes.Arrow to display force vectors as meshed arrows.

Changed

Removed

[0.4.2] 2022-12-12

Added

• Implemented NodeTangentAngleGoal.
• Implemented NodeNormalAngleGoal.
• Implemented NodeTangentAngleConstraint.
• Implemented NodeNormalAngleConstraint.
• Added EquilibriumStructure.connectivity_faces to optimize for face-related quantities in an FDNetwork.

Changed

• Fixed bug in edgewidth sizing in NetworkArtist when all edges have the same force.
• Changed angle_vectors to return angle in radians by default.
• Shifted loads start point in plotters.NetworkArtist for them to be incident to the nodes.

Removed

[0.4.1] 2022-11-29

Added

Changed

• Changed generator unpacking *sarrays in parameters.split unsupported in Python 3.7.
• Changed tension-compression force color map gradient to a binary color map.

Removed

[0.4.0] 2022-11-22

Added

• Added goals.NodeZCoordinateGoal.
• Added goals.NodeYCoordinateGoal.
• Added goals.NodeXCoordinateGoal.
• Added constraints.NodeZCoordinateConstraint.
• Added constraints.NodeYCoordinateConstraint.
• Added constraints.NodeXCoordinateConstraint.
• Added IPOPT, a second-order, constrained optimizer that wraps cyipopt, to the repertoire of optimizers.

Changed

• Restructured optimization.optimizers into separate files.
• Renamed goals.edgegoal submodule to goals.edge.
• Renamed goals.nodegoal submodule to goals.node.
• Renamed goals.networkgoal submodule to goals.network.
• Enabled support for one-sided bounds in constraint.Constraints.
• NetworkLoadPathGoal uses jnp.multiply instead of multipication operator *.
• Broke down Optimizer.minimize() into .problem() and .solve().
• For efficiency, SecondOrderOptimizer calculates hessian as jax.jacfwd(jax.jacrev).
• Changed calculation of the scalar ouput of Loss using a compact loop.
• Changed calculation of the scalar ouput of Error using a compact loop.

Removed

[0.3.0] 2022-11-08

Added

• Implemented jax_fdm.parameters to choose optimization parameters a la carte!
• Created parameters.EdgeForceDensityParameter.
• Created parameters.NodeAnchorXParameter.
• Created parameters.NodeAnchorYParameter.
• Created parameters.NodeAnchorZParameter.
• Created parameters.NodeLoadXParameter.
• Created parameters.NodeLoadYParameter.
• Created parameters.NodeLoadZParameter.
• Implemented EquilibriumStructure.nodes.
• Implemented EquilibriumStructure.edges.
• Added EquilibriumStructure.anchor_index.
• Implemented ParameterManager.parameters_ordered to fix order mismatch between optimization parameters and their bounds.

Changed

• EquilibriumModel.__call__ tasks q, xyz_fixed and loads as arguments.
• FDNetwork.transform only modifies node coordinates.
• FDNetworkViewerArtist shifts a node load by the maximum edge width at the node.
• OptimizationRecorder.history stores q, xyz_fixed and loads.
• LossPlotter.plot supports q, xyz_fixed and loads to be compatible with OptimizationRecorder.history.

Removed

[0.2.4] 2022-10-27

Added

• Enabled the creation of animations with mesh representations of the elements of a FDNetwork!
• FDNetworkViewerArtist implements update_*() methods to update objects in the Viewer.
• FDNetworViewerArtist implements add_*() methods to add drawn objects to Viewer.
• FDNetworkArtist now stores network element collections as attributes.

Changed

Removed

• Removed FDNetworkPlotterArtist.draw_loads() as it is handled by parent artist class.
• Removed FDNetworkPlotterArtist.draw_reactions() as it is handled by parent artist class.

[0.2.3] 2022-10-25

Added

• Implemented SecondOrderOptimizer, which computes the hessian of a loss function.
• Added support for the NetwtonCG and LBFGSB scipy optimizers.
• Created NodeSegmentGoal
• Implemented closest_point_on_segment using lax.cond

Changed

• Pinned viewer dependency to compas_view2==0.7.0

Removed

• Removed Viewer.__init__()

[0.2.2] 2022-10-17

Added

• Added datastructures.FDNetwork.transformed()
• Created visualization.plotters.FDNetworkPlotterArtist
• Implemented visualization.plotters.Plotter

Changed

Removed

[0.2.1] 2022-10-17

Added

Changed

• Rolled back support for python 3.7.

Removed

[0.2.0] 2022-10-11

Added

• Implemented visualization.viewers.Viewer as a thin wrapper around compas_view2.App.
• Created visualization.plotters.LossPlotter.
• Implemented visualization.viewers.FDNetworkViewerArtist.
• Implemented visualization.artists.FDNetworkArtist.
• Created jax_fdm.visualization module.
• Implemented FDNetwork.print_stats().
• Implemented FDNetwork.node_reaction() to get the reaction force at a fixed node.
• Added FDNetwork.nodes_fixed() to query nodes with a support.

Changed

Removed

[0.1.2] 2022-09-30

Added

• Created beta release! 🎉 Since we were busy adding new features to JAX FDM, we forgot to log them. Sorry! We promise to do better from here on. Please check the git log (fairly granular) for details on the all the features.

Changed

Removed