Nutils is being actively developed and the API is continuously evolving. The following overview lists user facing changes as well as newly added features in inverse chronological order.
Changes since version 5.0¶
nutils.sparsemodule introduces a data type and a suite of manipulation methods for arbitrary dimensional sparse data. The existing integrate and integral methods now create data of this type under the hood, and then convert it to a scalar, Numpy array or
nutils.matrix.Matrixupon return. In order to receive the sparse objects instead use the new
External dependency for parsing gmsh files
$ python3 -m pip install --user --upgrade meshio
Change dof order in basis.vector
When creating a vector basis using
topo.basis(..).vector(nd), the order of the degrees of freedom changed from grouping by vector components to grouping by scalar basis functions:
[b0, 0] [b0, 0] [b1, 0] [ 0, b0] [.., ..] old [b1, 0] [bn, 0] ------> [ 0, b1] [ 0, b0] new [.., ..] [.., ..] [bn, 0] [ 0, bn] [ 0, bn]
This should not affect applications unless the solution vector is manipulated directly, such as might happen in unit tests. If required for legacy purposes the old vector can be retrieved using
old = new.reshape(-1,nd).T.ravel(). Note that the change does not extend to
Change from stickybar to bottombar
$ python3 -m pip install --user bottombar
This replaces stickybar, which is no longer used. In addition to the log uri and runtime the status bar will now show the current memory usage, if that information is available. On Windows this requires psutil to be installed; on Linux and OSX it should work by default.
Support for gmsh ‘msh4’ file format
nutils.mesh.gmsh()method now supports input in the ‘msh4’ file format, in addition to the ‘msh2’ format which remains supported for backward compatibility. Internally, the function
nutils.mesh.parsegmsh()now takes file contents instead of a file name.
New command line option: gracefulexit.
The new boolean command line option
gracefulexitdetermines what happens when an exception reaches
nutils.cli.run(). If true (default) then the exception is handled as before and a system exit is initiated with an exit code of 2. If false then the exception is reraised as-is. This is useful in particular when combined with an external debugging tool.
Log tracebacks at debug level.
The way exceptions are handled by
nutils.cli.run()is changed from logging the entire exception and traceback as a single error message, to logging the exceptions as errors and tracebacks as debug messages. Additionally, the order of exceptions and traceback is fully reversed, such that the most relevant message is the first thing shown and context follows.
Solve leniently to relative tolerance in Newton systems.
nutils.solver.newtonmethod now sets the relative tolerance of the linear system to
1e-3unless otherwise specified via
linrtol. This is mainly useful for iterative solvers which can save computational effort by having their stopping criterion follow the current Newton residual, but it may also help with direct solvers to warn of ill conditioning issues. Iterations furthermore use
nutils.matrix.Matrix.solve_leniently(), thus proceeding after warning that tolerances have not been met in the hope that Newton convergence might be attained regardless.
Linear solver arguments.
nutils.solver.optimize()now receive linear solver arguments as keyword arguments rather than via the
solveargsdictionary, which is deprecated. To avoid name clashes with the remaining arguments, argument names must be prefixed by
# deprecated syntax >>> solver.solve_linear('lhs', res, solveargs=dict(solver='gmres')) # new syntax >>> solver.solve_linear('lhs', res, linsolver='gmres')
Direct solvers enter an iterative refinement loop in case the first pass did not meet the configured tolerance. In machine precision mode (atol=0, rtol=0) this refinement continues until the residual stagnates.
Matrix solver tolerances.
The absolute and/or relative tolerance for solutions of a linear system can now be specified in
rtolarguments, regardless of backend and solver. If the backend returns a solution that violates both tolerances then an exception is raised of type
nutils.matrix.ToleranceNotReached, from which the solution can still be obtained via the .best attribute. Alternatively the new method
nutils.matrix.Matrix.solve_leniently()always returns a solution while logging a warning if tolerances are not met. In case both tolerances are left at their default value or zero then solvers are instructed to produce a solution to machine precision, with subsequent checks disabled.
Use stringly for command line parsing.
Nutils now depends on stringly (version 1.0b1) for parsing of command line arguments. The new implementation of
nutils.cli.run()is fully backwards compatible, but the preferred method of annotating function arguments is now as demonstrated in all of the examples.
For new Nutils installations Stringly will be installed automatically as a dependency. For existing setups it can be installed manually as follows:
$ python3 -m pip install --user --upgrade stringly
Fixed and fallback lengths in (namespace) expressions
nutils.function.Namespacehas two new arguments:
fallback_length. The former can be used to assign fixed lengths to specific indices in expressions, say index
ishould have length 2, which is used for verification and resolving undefined lengths. The latter is used to resolve remaining undefined lengths:
>>> ns = nutils.function.Namespace(length_i=2, fallback_length=3) >>> ns.eval_ij('δ_ij') # using length_i Array<2,2> >>> ns.eval_jk('δ_jk') # using fallback_length Array<3,3>
Nutils now depends on treelog version 1.0b5, which brings improved iterators along with other enhancements. For transitional convenience the backwards incompatible changes have been backported in the
nutils.logwrapper, which now emits a warning in case the deprecated methods are used. This wrapper is scheduled for deletion prior to the release of version 6.0. To update treelog to the most recent version use:
python -m pip install -U treelog
nutils.types.unitallows for the creation of a unit system for easy specification of physical quantities. Used in conjuction with
nutils.cli.run()this facilitates specifying units from the command line, as well as providing a warning mechanism against incompatible units:
>>> U = types.unit.create(m=1, s=1, g=1e-3, N='kg*m/s2', Pa='N/m2') >>> def main(length=U('2m'), F=U('5kN')): ... topo, geom = mesh.rectilinear([numpy.linspace(0,length,10)]) # python myscript.py length=25cm # OK # python myscript.py F=10Pa # error!
Samples now provide a
nutils.sample.Sample.basis(): an array that for any point in the sample evaluates to the unit vector corresponding to its index. This new underpinning of
nutils.sample.Sample.asfunction()opens the way for sampled arguments, as demonstrated in the last example below:
>>> H1 = mysample.asfunction(mydata) # mysample.eval(H1) == mydata >>> H2 = mysample.basis().dot(mydata) # mysample.eval(H2) == mydata >>> ns.Hbasis = mysample.basis() >>> H3 = 'Hbasis_n ?d_n' @ ns # mysample.eval(H3, d=mydata) == mydata
Higher order gmsh geometries
Gmsh element support has been extended to include cubic and quartic meshes in 2D and quadratic meshes in 3D, and parsing the msh file is now a cacheable operation. Additionally, tetrahedra now define bezier points at any order.
The Nutils repository has moved to https://github.com/evalf/nutils.git. For the time being the old address is maintained by Github as an alias, but in the long term you are advised to update your remote as follows:
git remote set-url origin https://github.com/evalf/nutils.git