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Add unit class to FlowerMD and allow using real units in Simulation runs #137

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Add unit class to FlowerMD and allow using real units in Simulation runs #137

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d38aba8
calculate real T from kT
marjanalbooyeh Mar 15, 2024
05d594e
unit test for real_temperature
marjanalbooyeh Mar 15, 2024
0c47ee3
precommit reformat
marjanalbooyeh Mar 15, 2024
d2bad99
allow temperature to be passed to run methods instead of kT
marjanalbooyeh Mar 15, 2024
ee71094
test temperature for nvt runs
marjanalbooyeh Mar 15, 2024
27a2d74
add time_length parameter to run methods
marjanalbooyeh Mar 15, 2024
17b6043
fix None conditions
marjanalbooyeh Mar 18, 2024
822861f
add tests for time length
marjanalbooyeh Mar 20, 2024
b422a11
update docstrings
marjanalbooyeh Mar 20, 2024
4f44b55
Merge branch 'cmelab:main' into main
marjanalbooyeh Mar 21, 2024
e83b3c4
save reference values to pickle
marjanalbooyeh Mar 21, 2024
e4ce1c6
tests for save ref values
marjanalbooyeh Mar 21, 2024
4d91a49
added more unit tests for temperature and time length
marjanalbooyeh Mar 21, 2024
26af373
real temperature without energy unit
marjanalbooyeh Mar 21, 2024
68777e1
Merge branch 'cmelab:main' into main
marjanalbooyeh May 1, 2024
b70dd70
add units class
marjanalbooyeh May 1, 2024
f17dc4b
add temperature and duration parameters
marjanalbooyeh May 1, 2024
1cbfb07
Add an example to NVT docstring with real units for temperature and d…
marjanalbooyeh May 1, 2024
45ee688
update docstrings
marjanalbooyeh May 1, 2024
5521716
move units class to internal dir
marjanalbooyeh May 2, 2024
73c7b97
use validate_unit function to validate units
marjanalbooyeh May 2, 2024
b33279d
Add a utils function to validate units.
marjanalbooyeh May 2, 2024
2e4ea71
update system unit tests according to new changes in units
marjanalbooyeh May 2, 2024
68c6d78
add new units
marjanalbooyeh May 2, 2024
eee22fd
update unit error messages
marjanalbooyeh May 2, 2024
75cd5f4
update simulation unit tests according to units
marjanalbooyeh May 2, 2024
6f9f04d
fix unit test bugs
marjanalbooyeh May 2, 2024
6a9be73
remove validate_ref_value
marjanalbooyeh May 2, 2024
419f2d1
use flowermd units instead of unyt and fix tests
marjanalbooyeh May 2, 2024
faa114f
update utils tests
marjanalbooyeh May 2, 2024
8e72bec
add tests for validate_unit
marjanalbooyeh May 2, 2024
0eda3d4
update Units docstrings.
marjanalbooyeh May 2, 2024
b5c24f2
add femtosecond
marjanalbooyeh May 6, 2024
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2 changes: 1 addition & 1 deletion .pre-commit-config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@ repos:
name: isort (python)
args:
[ --profile=black, --line-length=80 ]
exclude: 'flowermd/tests/assets/.* '
exclude: 'flowermd/tests/assets/.* | */__init__.py'

- repo: https://github.com/pycqa/flake8
rev: 7.0.0
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1 change: 1 addition & 0 deletions flowermd/__init__.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
"""flowerMD package."""

from .internal.units import Units
from .base import (
CoPolymer,
Lattice,
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