Ncrystal

* Add missing _hklobjects.py file which was left out by mistake. Thus
making the newly introduced info.hklObjects() function actually work.
* Fix debug compilation of MMC messages.

* This release brings both general improvements and new features, as well
as a slew of maintenance updates and bug fixes. The first few items below
will discuss the main highlights.
* General speedup in a lot of the code. In particular the Fast Fourier
Transform code, used when expanding phonon density of states to full
scattering kernels for inelastic modelling, was improved by as much as
40%. This will make a noticeable difference when initialising many
materials, and is an improvement independent from the multi-threading
option mentioned in the previous item.
* If requested, NCrystal can now initialise materials even faster, by
performing the initialisation calculations in multiple threads. This can
for instance be enabled by setting the environment variable
NCRYSTAL_FACTORY_THREADS to the number of threads you wish to use (e.g. 8
if you have 8 CPU cores available, or 9999 to have NCrystal pick a number
suitable for your machine). Alternatively, you can call functions in the
Python, C, or C++ APIs to enable this:
NC.enableFactoryThreads() Python
NC::FactoryThreadPool::enable(); //C++
ncrystal_enable_factory_threadpool(9999); //C
export NCRYSTAL_FACTORY_THREADS=9999 BASH
* NCrystal now includes the first iteration of a "Mini Monte Carlo"
framework (for lack of a better word), which makes it possible to insert
an NCrystal material into a simple geometric "sample" shape, subject it
to a source of neutrons, and obtain a spectrum or pattern of the outgoing
neutrons. Thus, one can easily produce a simplistic diffraction pattern,
including effects of multiple scattering and both elastic and inelastic
physics. For now, the focus has been on developing the framework itself,
rather than preparing a library of interesting shapes, sources, and
tallies. Thus, the only readily available setup in this release is that
of a monochromatic pencil beam impinging on a sphere, tallying the
outgoing angle of the neutrons as they leave that sphere. Nonetheless,
the results provides a very convenient view of how NCrystal modelling
translates into a particular pattern -- without the need for an
additional software package like McStas, Geant4, or OpenMC. The `nctool`
command will now by default show such scattering pattern, or they can be
explicitly requested, as shown in this example where 1.8Aa neutrons
impinge on an aluminium sphere with a diameter of 2cm:
$> nctool --mc 1.8Aa 2cm Al_sg225.ncmat
The scope of this "Mini Monte Carlo" framework is of course not to try to
rival existing applications in terms of ability to simulate complicated
geometries or beamlines, but rather to provide another convenient way to
quickly investigate NCrystal materials, as well as potentially serve as a
way for NCrystal to be used in a regression-loop while analysing actual
neutron scattering data. For that reason, speed has been a major concern,
and both multithreading and vectorisation has been utilised to bring the
time it takes to go from defined NCMAT data to having a high-statistics
diffraction pattern available, down to the sub-second scale.
* Internally NCrystal code no longer uses raw `std::cout` or `printf`
statements. Rather, all messages are now emitted via a centralised
infrastructure. This most importantly fixes an issue where output from
the Python and C++ layers could occasionally be emitted in incorrect
order - now, when using the NCrystal Python API, all output will be
emitted through Python's own print buffer. Secondly, several NCrystal
objects now gets a `.dump_str()` method, meaning for instance that
material dumps can be captured in strings rather than emitted on
std-output. Finally, this new feature could in principle be used for
various output redirection purposes (e.g. a GUI application might wish to
show all output from NCrystal in some dedicated text box).
* NCrystal has been updated to work with latest versions of Numpy, Clang,
GCC, Python, Gemmi, and Spglib. Additionally work has started to support
Intel OneAPI compilers and Microsoft VisualStudio, although more work is
needed to finalise this. As part of these efforts, the ABI had to be
broken in some places, since for instance Microsoft VisualStudio did not
support all the data structures used previously (for instance,
VisualStudio `std::vector` does not accept move-only objects like
`std::unique_ptr`).
* This concludes the highlights in this changelog entry - refer to the
following items for more detailed information about specific changes.
* Several speedups of the phonon convolution calculation code was
implemented, resulting in noticable speed increases (20-40%): the FFT
phase factor calculation by a factor of two, swap indices were cached,
and an integer division was rewritten as a bit shift.
* Reduce luxury in some VDOS integrations slightly for a more reasonable
amount of calculations, speeding up Info material creation.
* Add internal utilities to allow usage of multiple threads for material
loading, allowing for sizeable speedups. This required many changes to
ensure good behaviour (i.e. using a fixed number of threads only), and no
dead-locks of various kinds even though the multi-threading can take
place at various levels during the loading. For now, the number of
available threads can be controlled with the NCRYSTAL_FACTORY_THREADS
environment variable, the NCrystal::FactoryThreadPool::enable() C++
function, the NCrystal.enableFactoryThreads Python function, or the
ncrystal_enable_factory_threadpool C function.
* Build NCrystal library with -fno-math-errno (github issue 169).
* Several non-trivial fixes were implemented to prepare for MS VisualStudio
and Intel oneapi compilation support. This breaks ABI.
* Apply -fp-model=precise for intel oneapi compiler.
* Change C++ DynamicInfoList type from
std::vector<std::unique_ptr<DynamicInfo>> to typedef
SmallVector<std::unique_ptr<DynamicInfo>,4>, since VisualStudio
apparently does not support std::vector's with move-only objects. This in
principle breaks the ABI and API, but is deemed necessary. A few other
types in internal non-API headers were changed as well for the same
reason.
* Fix build error due to ODR violation in the TopLvlVar type.
* Removed noexcept from C++ functions where it should not have been added
(e.g. those used for streaming to std::ostream).
* Fix cfg-string bug (github issue 182). This only affected multiphase
cfg-strings in which the first phase contained either a density or
phasechoice setting, so is not believed to have affected many users.
* ProcComposition::consumeAndCombine(..) fct is now better at removing null
components.
* Adding the infrastructure for better control of NCrystal output, through
usage of a new setMessageHandler(..) function (related to github issues
53 and 122).
* Rewrote the NCrystal::dump C++ function (which provides printouts/"dumps"
of material Info objects) to stop using printf entirely and now only use
C++ output streams, but notably while preserving existing output
exactly. This makes it possible to capture the dumps into strings and
streams, rather than printing them out. Along with the general message
handling changes, this should prevent Python output buffering causing
incorrect output ordering (seen in e.g. Jupyter notebooks).
* Python objects with .dump(..) methods gets new .dump_str() methods as
well, which simply returns the information as a string instead of
printing it directly.
* Update cifutils to follow changes in upstream Gemmi project.
* Updates to reflect upstream API changes in spglib.
* Stop using numpy.asfarray which was removed in numpy 2.0.0 (github issue
185).
* More helpful error message when loading huge DFT-generated unit cells
(thousands of atoms, no symmetries) without raising dcutoff (github issue
160).
* DI_VDOSDebye Python objects now also get an analyseVDOS() method, for
consistency (github issue 174).
* Update NCMAT documentation to clarify the ordering of sab entries (github
issue 170).
* Add convenience .xsect(..) and .macroscopic_xsect(..) methods to
LoadedMaterial instances in the Python API.
* Add experimental material loading benchmark utility to nctool. This
feature is for now kept out of the documentation, but can be tested with:
"nctool --bench --help".
* Updated year in copyright notice in all files.
* Info objects gets a new .hklObjects() method which returns HKL list
information in a more object oriented and convenient format than the
existing .hklList(). See issue 164 for more details.

* Add importlib_metadata as python build dependency for Python < 3.8.
* CMake code no longer strictly disallows mixing of NCRYSTAL_NAMESPACE and
NCRYSTAL_GEANT4 options.

* Fix rare FPE in lcbragg code (github issue 171).
* Remove a few faulty noexcept modifiers in (found by cppcheck).
* Fix NCMatCfg::textData which technically returned a reference to a
temporary (although this is not believed to have actually caused any
issues, since the "temporary" came from a longer-lived shared_ptr). This
was also found with cppcheck.

* Completely obsolete the ncrystal_inspectfile command in favour of the
nctool command. Trying to invoke ncrystal_inspectfile now results in an
error message with a reminder to use nctool instead.
* The default value of the CMake cfg option -DNCRYSTAL_ENABLE_SETUPSH is
changed from "ON" to "OFF". Additionally, if setting
-DNCRYSTAL_ENABLE_SETUPSH=ON, the oly files installed are now named
<PREFIX>/ncrystal_setup.sh and <PREFIX>/ncrystal_unsetup.sh, whereas in
the past they were named <PREFIX>/setup.sh and <PREFIX>/unsetup.sh. Note
that in releases v3.7.0 and v3.7.1 both versions of the files were
available. Consequently, users who were manually compiling NCrystal and relying on
e.g. <PREFIX>/setup.sh files files will now need
to explicitly set -DNCRYSTAL_ENABLE_SETUPSH=ON and instead use the
<PREFIX>/ncrystal_setup.sh file. (github issue 126).
* NCrystal components and instrument examples for McStas (mcstas.org) are
no longer shipped with NCrystal, since all NCrystal components and
instrument examples are now shipped with McStas itself.
* Add a new NCRYSTAL_NAMESPACE option, which can be used when there is a
need to be able to use NCrystal header files and libraries from multiple
NCrystal installations into the same environment. Eventually, it is the
plan to enable such namespace protection in NCrystal conda-forge and PyPI
packages, to prevent hard-to-catch errors in case a user ends up having
both packages installed in the same environment (which can happen when
people mix "conda install .." and "pip install .."). CMake-based
downstream projects should not be affected by this, but if you are
maintaining downstream custom builds which hardcode linker flags like
"-L/path/to/ncrystal/lib -lNCrystal" you are encouraged to based your
flags instead on $(ncrystal-config --show libpath). That way you will be
future-proof and ready to also work with NCrystal installations where a
namespace has been enabled. See the README file for more details.
* As a result of the namespace support, all function names in the C-api are
now actually macros.
* Adding VERSION and SOVERSION to libNCrystal.so/dylib. For now, the
VERSION number is simply the full NCrystal release version number, while
the SOVERSION is the major release number (i.e. "3" for release
3.8.0). This feature can be disabled with -DNCRYSTAL_ENABLE_SOVERSION=OFF.
* CMake find_package(NCrystal ...) calls no longer sets NCrystal_DIR to the
installation prefix, since that could disrupt the usage of multiple
find_package calls. The prefix directory previously available as the
CMake variable NCrystal_DIR is thus instead made available under the name
NCrystal_PREFIX.
* Update Avogadro's constant to NIST/CODATA2018 value, changing it from
6.022140857e23/mol to 6.02214076e23/mol (a change of ~0.016ppm).
* The CMake code now also adds $CONDA_PREFIX/lib to rpath when appropriate.
* Explicitly forbid and $ chars in cfg-strings (github issue 153).
* Fix misleading values in ncrystal-config in some rare cases.
* Fix for a few (incorrect) compiler warnings.
* Fix for cmake test in python3 -mNCrystal.test cmake.
* Warnings emitted from python layer now has right stacklevel.
* Fix tests for Python 3.12 (a few tests depended on the now
deprecated distutils modules, cf. PEP-632).

* Update documentation to reflect availability on PyPI.
* Set version-based policies in NCrystalConfig.cmake to make
find_package(NCrystal) work when CMake is new enough, but the downstream
CMake project nevertheless specifies a very old version in their
cmake_minimum_required statement (cf. github issue/discussion 137).
* Add NCrystal_LIBRARIES variables for downstream CMake-based projects with
legacy 2.x-style CMake code. If the GEANT4BINDINGS component is enabled,
also set G4NCrystal_LIBDIR, G4NCrystal_INCDIR, G4NCrystal_LIBNAME and
G4NCrystal_LIBRARIES variables, likewise intended for such legacy
projects. Note of course, that usage of such legacy CMake 2.x-style code
is discouraged.
* Include type_traits in NCDefs.hh, to potentially fix some compilation
errors seen in 137.
* Fix several minor bugs in NCrystal Python code which were discovered via
the ruff static code analysis tool.
* Change signature of all 0-argument functions in C-API in ncrystal.h from
f() to f(void), since the first form is apparently deprecated since 30
years and gives issues in clang 14
(cf. https://github.com/madler/zlib/issues/633 and
https://github.com/mctools/dgcode/issues/34).
* For NCrystal builds, change max version in cmake_minimum_required to
3.27.