Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

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

Draft
wants to merge 33 commits into
base: main
Choose a base branch
from
Draft

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

wants to merge 33 commits into from

Conversation

marjanalbooyeh
Copy link
Collaborator

@marjanalbooyeh marjanalbooyeh commented May 2, 2024 •
edited
Loading

This PR introduces a new Unit class to FlowerMD, which contains commonly used units from unyt package.

With this change, all values with units in FlowerMD are formatted as value * flower.Units.<unit>. For example, a temperature in Kelvin is 300 * flowermd.Units.K.

This PR also makes the following changes to the interface of run functions in Simulation class:

  • The variable kT is now temperature , which can handle both kT values (unitless) and temperature values with units.
  • The n_steps variable is now called duration, which can be both a number (number of steps) or time length with units.

ToDo:

  • Make same changes for pressure and add pressure units

@marjanalbooyeh
calculate real T from kT
d38aba8
@marjanalbooyeh
unit test for real_temperature
05d594e
@marjanalbooyeh
precommit reformat
0c47ee3
@marjanalbooyeh
allow temperature to be passed to run methods instead of kT
d2bad99
@marjanalbooyeh
test temperature for nvt runs
ee71094
@marjanalbooyeh
add time_length parameter to run methods
27a2d74
@marjanalbooyeh
fix None conditions
17b6043
@marjanalbooyeh
add tests for time length
822861f
@marjanalbooyeh
update docstrings
b422a11
@marjanalbooyeh
Merge branch 'cmelab:main' into main
4f44b55
@marjanalbooyeh
save reference values to pickle
e83b3c4
@marjanalbooyeh
tests for save ref values
e4ce1c6
@marjanalbooyeh
added more unit tests for temperature and time length
4d91a49
@marjanalbooyeh
real temperature without energy unit
26af373
@marjanalbooyeh
Merge branch 'cmelab:main' into main
68777e1
@marjanalbooyeh
add units class
b70dd70
@marjanalbooyeh
add temperature and duration parameters
f17dc4b
@marjanalbooyeh
Add an example to NVT docstring with real units for temperature and d…
1cbfb07 
…uration.
@marjanalbooyeh
update docstrings
45ee688
@marjanalbooyeh
move units class to internal dir
5521716
@marjanalbooyeh
use validate_unit function to validate units
73c7b97
@marjanalbooyeh
Add a utils function to validate units.
b33279d
@marjanalbooyeh
update system unit tests according to new changes in units
2e4ea71
@marjanalbooyeh
add new units
68c6d78
@marjanalbooyeh
update unit error messages
eee22fd
@marjanalbooyeh
update simulation unit tests according to units
75cd5f4
@marjanalbooyeh
fix unit test bugs
6f9f04d
@marjanalbooyeh
remove validate_ref_value
6a9be73
@marjanalbooyeh
use flowermd units instead of unyt and fix tests
419f2d1
@marjanalbooyeh
update utils tests
faa114f
@marjanalbooyeh marjanalbooyeh linked an issue May 2, 2024 that may be closed by this pull request
Add units to FlowerMD #136
Open
chrisjonesBSU
chrisjonesBSU reviewed May 2, 2024
View reviewed changes
flowermd/internal/units.py
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Should we add some ready-to-go density units as well for the sake of convenience?

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@chrisjonesBSU chrisjonesBSU chrisjonesBSU left review comments

At least 1 approving review is required to merge this pull request.

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

Add units to FlowerMD
2 participants
@marjanalbooyeh @chrisjonesBSU