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[r25390] by bugman

Created the lib.periodic_table.process_symbol() function.

This will take an atomic symbol and return a copy of it with an uppercase first letter and lowercase
second letter. This is used by the Periodic_table methods atomic_mass() and atomic_weight() to
allow for non-standard symbol input, for example if the element name comes directly from the all
uppercase PDB file format without translation.

2014-08-28 14:46:23 Tree
[r25389] by bugman

Tiny fix for the Diffusion_tensor.test_create_diff_tensor_pdb_ellipsoid system test.

The switch to using the lib.periodic_table module for atomic masses has caused the centre of mass of
the ellipsoid to shift just enough that one ATOM coordinate in the PDB file has changed its last
significant digit.

2014-08-28 14:37:16 Tree
[r25388] by bugman

Fix for the Periodic_table.lookup_symbol() method.

The __init__() method of the Periodic_table has been reintroduced to initialise a fast atomic symbol
lookup table. The _add() method then updates this table. And the lookup_symbol() method now uses
this lookup table to correctly return the symbol.

2014-08-28 14:33:37 Tree
[r25387] by bugman

Fix for the MolContainer.fill_object_from_gaussian() method.

This is in the lib.structure.internal.molecules module. The Periodic_table.lookup_z_to_symbol()
method in the lib.periodic_table module has been renamed to lookup_symbol().

2014-08-28 14:29:09 Tree
[r25386] by bugman

Deletion of the lib.physical_constants.return_atomic_mass() function and all relative atomic masses.

These were inaccurate and only included a tiny subset of all standard atomic weight and isotope
masses. The functionality has been replaced by the complete and 100% accurate complete
Periodic_table object in the lib.periodic_table module.

2014-08-28 14:21:39 Tree
[r25385] by bugman

Changed the operation of the lib.structure.mass.centre_of_mass() function.

Instead of using the lib.physical_constants.return_atomic_mass() function, the centre_of_mass()
function instead uses the lib.periodic_table.periodic_table.atomic_mass() method. This is a huge
improvement in that the exact mass of absolutely all elements are taken into account.

2014-08-28 14:19:12 Tree
[r25384] by bugman

Implemented the lib.periodic_table module Periodic_table.atomic_mass() method.

This method will return either the atomic mass of an isotope or the standard atomic weight.

2014-08-28 13:57:42 Tree
[r25383] by bugman

Fix for the Test_periodic_table.test_get_atomic_mass unit test - the method calls were incorrect.

2014-08-28 13:42:34 Tree
[r25382] by bugman

Changed the method call in the new Test_periodic_table.test_get_atomic_mass unit test.

2014-08-28 13:34:20 Tree
[r25381] by bugman

Created a unit test for the Periodic_table.atomic_mass() method.

This method is not implemented yet.

2014-08-28 13:24:39 Tree
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