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

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

Open
wants to merge 54 commits into
base: main
Choose a base branch
from
Open

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

Show file tree
Hide file tree
Changes from 32 commits
Commits
Show all changes
54 commits
Select commit Hold shift + click to select a range
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
d7e3f2d
merge changes from upstream.
marjanalbooyeh Nov 23, 2024
2e7a4f8
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Nov 23, 2024
a4fccd4
Add functionalitiy to handle real pressure units. Add properties for …
marjanalbooyeh Nov 28, 2024
dc13ebb
Add density and pressure units.
marjanalbooyeh Nov 28, 2024
2ff5d79
Check for flowermd Units instance in unit validation.
marjanalbooyeh Nov 28, 2024
455b2ec
Merge branch 'main' of github.com:marjanalbooyeh/flowerMD
marjanalbooyeh Nov 28, 2024
7156c79
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Nov 28, 2024
5d70e13
Simplify functions.
marjanalbooyeh Nov 28, 2024
e8c70cb
Add reduced temperature and reduced pressure propoerties to sim.
marjanalbooyeh Nov 28, 2024
a194244
Merge branch 'main' of github.com:cmelab/flowerMD
marjanalbooyeh Nov 28, 2024
ae0d07d
updated pre-commit.
marjanalbooyeh Nov 28, 2024
0199a8d
merge with main
marjanalbooyeh Nov 28, 2024
0c93dc2
Test real units in simulations.
marjanalbooyeh Nov 28, 2024
15a2e8e
Add number density units.
marjanalbooyeh Nov 28, 2024
49e3657
Use flowermd Units class.
marjanalbooyeh Nov 28, 2024
1035eb5
Use and explain new variable names (duration, temperature, etc) in tu…
marjanalbooyeh Nov 29, 2024
06b35fb
Use correct unit import.
marjanalbooyeh Nov 29, 2024
652fcc8
Use duration and temperature variable names in recipes and tests.
marjanalbooyeh Nov 29, 2024
5f0def9
Fix variable names.
marjanalbooyeh Nov 29, 2024
b71ab0d
Temporary check for temperature Ramp.
marjanalbooyeh Nov 29, 2024
628acec
Fix tutorials bugs.
marjanalbooyeh Nov 29, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion .pre-commit-config.yaml
View file
Open in desktop
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
Expand Down
1 change: 1 addition & 0 deletions flowermd/__init__.py
View file
Open in desktop
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,
Expand Down
Loading
Loading