Speed up functions for retrieving old/new positions from hybrid positions #1020
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ijpulidos
requested changes
May 31, 2022
perses/annihilation/relative.py
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| for idx in range(n_atoms_old): | ||
| old_positions[idx, :] = hybrid_positions[idx, :] | ||
| hybrid_indices = [self._old_to_hybrid_map[idx] for idx in range(n_atoms_old)] | ||
| old_positions = unit.Quantity(hybrid_positions[hybrid_indices, :], unit=unit.nanometer) |
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I think hybrid_positions at this point should already be of type Quantity (see lines 2156 and 2157), so there shouldn't be a need to cast them as such again. This might help with performance, but also in the case where we want to change the units without having to manually edit them in many places at the same time.
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Actually, I think this method expects the positions to be given in nanometers. We should change the docstring to reflect this.
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Thanks, just added changes to address these comments!
perses/annihilation/relative.py
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| for idx in range(n_atoms_new): | ||
| new_positions[idx, :] = hybrid_positions[self._new_to_hybrid_map[idx], :] | ||
| hybrid_indices = [self._new_to_hybrid_map[idx] for idx in range(n_atoms_new)] | ||
| new_positions = unit.Quantity(hybrid_positions[hybrid_indices, :], unit=unit.nanometer) |
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Same as previous comment.
zhang-ivy
added this to the 0.10.0 Enhanced CLI with more stable input/output formats milestone
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Description
Motivation and context
Resolves #1005
How has this been tested?
The existing test
test_relative.py::test_position_output()passes.I added a timer to this test and here are the times with the old approach vs new approach (this PR):
Change log