Nutils 6 Garak-Guksu

Nutils 6.0 was released on April 29th, 2020.

Nutils 6.1 was released on July 17th, 2020.

Nutils 6.2 was released on October 7th, 2020.

Nutils 6.3 was released on November 18th, 2021.

What's New?

These are the main additions and changes since Nutils 5 Farfalle.

Sparse module

The new nutils.sparse module 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.Matrix upon return. To prevent this conversion and receive the sparse objects instead use the new nutils.sample.Sample.integrate_sparse or nutils.sample.eval_integrals_sparse.

External dependency for parsing gmsh files

The nutils.mesh.gmsh method now depends on the external meshio module to parse .msh 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 nutils.function.vectorize.

Change from stickybar to bottombar

For nutils.cli.run to draw a status bar, it now requires the external bottombar module to be installed:

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

The 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, nutils.mesh.parsegmsh now takes file contents instead of a file name.

New command line option: gracefulexit

The new boolean command line option gracefulexit determines 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

The nutils.solver.newton method now sets the relative tolerance of the linear system to 1e-3 unless 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

The methods nutils.solver.newton, nutils.solver.minimize, nutils.solver.pseudotime, nutils.solver.solve_linear and nutils.solver.optimize now receive linear solver arguments as keyword arguments rather than via the solveargs dictionary, which is deprecated. To avoid name clashes with the remaining arguments, argument names must be prefixed by lin:

solver.solve_linear('lhs', res,
  solveargs=dict(solver='gmres')) # deprecated syntax

solver.solve_linear('lhs', res,
  linsolver='gmres') # new syntax

Iterative refinement

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 nutils.matrix.Matrix.solve via the atol resp. rtol arguments, 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

The nutils.function.Namespace has two new arguments: length_<indices> and fallback_length. The former can be used to assign fixed lengths to specific indices in expressions, say index i should 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>

Treelog update

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.log wrapper, 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

Unit type

The new nutils.types.unit allows for the creation of a unit system for easy specification of physical quantities. Used in conjunction 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!

Sample basis

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.

Repository location

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