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CluE Oxide: 0.2.1

FIXED:

In the dependencies, updated the ndarray-linalg version to fix compilation errors on Windows.

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CluE Oxide: 0.2.0-alpha.2
2024-04-23

FIXED:

Bug fixed where find_exchange_groups() would give the wrong centroid value
for methyl groups.

CHANGED:

Particle indices in save files are now more consistent; bath particles start 
at 1, and increment by one for each atom regardless off whether the particle is 
active or not, or even has a spin.

The exchage_groups.csv now uses the same origin as the PDB, rather than
setting the detected electron to the origin.

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CluE Oxide: 0.2.0-alpha.1
2024-01-09

CHANGED:

The "filter" keyword has been deprecated and is replaced by "group".

If a particle falls under multiple groups (previously called filters),
CluE now errs rather than making an order dependent assignment.

Config arguments starting with "write_" now take bools rather than strings.

The config argument 
  temperature = T;
has been removed.  Use 
  cluster_density_matrix = thermal(T);
instead.

The config argument "neighbor_cutoff_dipole_dipole" has been renamed
"neighbor_cutoff_coupling".


ADDED:

The input modes "#[group()]", "#[structure_properties()]", and
"#[spin_properties()]" can now take either positional arguments or keyword
arguments.

Groups can be made specific to the primary unit cell by adding
  primary_cell;
within a #[group()] section, or to all cells other than the primary cell via
  extracells;
If neither is supplied, than the group applies to all cells.

Within a #[structure_properties(my_label)] section, the option
  cosubstitute = same_molecule;
is now available to enforce that atoms in the group my_label that are on the
same molecule are the same isotope.  Note that atoms not in the my_label group
are not affected regardless of which molecule they are on.

The option "void_probability" has been added.

The option "write_methyl_partitions" was added.

The option "write_sans_spin_signals" was added.

REMOVED:

The option "extracell_isotope_abundances" has been removed.

The option "extracell_void_probability" has been removed.

The option "cell_ids" has been removed.

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