marjanalbooyeh commented 2 years ago

This PR saves the ParmEd structure built during system initialization to a file. After saving the ParmEd to the file, for any future initialization of the same system, ParmEd object is loaded from file instead of building it from scratch. This will save a significant amount of time, which makes running simulations with different parameters (density, temperature, ...) much faster.

Details:

This is an optional feature and it can be disabled by setting save_parmed=False in Initializer class.
Default directory for saving the files is pmd_structures, which can be changed by setting parmed_dir argument in Initializer class.
ParmEd object is stored using pickle. The reason I did not use ParmEd save function is because it loses all the connections (bonds, angles and dihedrals)

codecov[bot] commented 2 years ago

Codecov Report

Merging #95 (c01bb02) into master (ea09fde) will increase coverage by 0.15%. The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master      #95      +/-   ##
==========================================
+ Coverage   92.14%   92.29%   +0.15%     
==========================================
  Files           7        7              
  Lines         751      766      +15     
==========================================
+ Hits          692      707      +15     
  Misses         59       59

Impacted Files	Coverage Δ
polybinder/system.py	`95.67% <100.00%> (+0.16%)`	:arrow_up:

chrisjonesBSU commented 2 years ago

Thanks for the PR @marjanAlbouye! Looks good to me. I just made one small change to get the line lengths under 80.

cmelab / polybinder

Save ParmEd structures to file during system initialization #95

Codecov Report