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Allow using real temperature and real time length in simulation #119

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Allow using real temperature and real time length in simulation #119

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marjanalbooyeh
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@marjanalbooyeh marjanalbooyeh commented Mar 15, 2024 •
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This PR allows user to specify the temperature (in real units) instead of kT and real time length (with units) instead of n_steps in the run methods of the simulation class.
This PR also adds new property to the simulation class that converts the kT (if specified) to real temperature units in kelvin.

I also added a function for saving the reference values into a pickle file, it might come handy.

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codecov bot commented Mar 15, 2024 •
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Codecov Report

Attention: Patch coverage is 94.80519% with 4 lines in your changes are missing coverage. Please review.

Project coverage is 95.10%. Comparing base (a600b73) to head (26af373).
Report is 4 commits behind head on main.

❗ Current head 26af373 differs from pull request most recent head 68777e1. Consider uploading reports for the commit 68777e1 to get more accurate results

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@@            Coverage Diff             @@
##             main     #119      +/-   ##
==========================================
+ Coverage   94.77%   95.10%   +0.33%     
==========================================
  Files          26       25       -1     
  Lines        1970     1899      -71     
==========================================
- Hits         1867     1806      -61     
+ Misses        103       93      -10
Files Coverage Δ
flowermd/base/system.py 92.14% <100.00%> (-0.25%) ⬇️
flowermd/base/simulation.py 94.08% <94.44%> (+2.06%) ⬆️

... and 8 files with indirect coverage changes

@marjanalbooyeh marjanalbooyeh changed the title Method for calculating temperature in kelvin Allow using real temperature and real time length in simulation Mar 15, 2024
@marjanalbooyeh marjanalbooyeh marked this pull request as draft March 15, 2024 21:02
@marjanalbooyeh marjanalbooyeh added the enhancement New feature or request label Mar 15, 2024
@marjanalbooyeh marjanalbooyeh marked this pull request as ready for review March 20, 2024 21:02
@chrisjonesBSU chrisjonesBSU linked an issue Mar 27, 2024 that may be closed by this pull request
Add method to save a simulation's reference values and units to file #97
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@chrisjonesBSU chrisjonesBSU added the API Change May require an API change label Mar 29, 2024
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Add method to save a simulation's reference values and units to file
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@marjanalbooyeh @chrisjonesBSU