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@wehs7661 wehs7661 released this 01 May 19:21
· 457 commits to master since this release
0.6.0
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Learn about vigilant mode.

Several major changes have been made since the last release of version 0.5.0. Below we list all changes that would influence the way ensemble_md should be used, in the order of decreasing importance.

  • Deployed the package to PyPI: https://pypi.org/project/ensemble-md/0.6.0/
  • We have completely removed the use of gmxapi from the implementation of EEXE. This includes the following (see the PR #9 ):
    • Using subprocess.run to replace gmxapi.commandline_operation and gmxapi.mdrun.
    • Removing all functions and variables using gmxapi and their unit tests.
    • Updating setup.py and the installation instruction in the documentation.
    • Updating docs/conf.py and .circleci/config.yaml.
    • Updating the code for extending an EEXE simulation.
  • Modifications made to the weight-combining methods:
    • The methods mean and geo-mean have been disabled, which left only one method (g-diff)
    • The weight-combining method is now based on time-averaged weights, mainly enabled by get_averaged_weights.
    • The function combine_weights was modified so that simulation will end once the weights of all replicas get equilibrated.
  • The following bugs have been fixed:
    • The bug of using weights updated by get_swapping_pattern in update_MDP.
    • A minor bug in autocovert triggered by parsing an MDP file with the parameter pull-coord1-dim specified.
  • Modified ensemble_EXE.py so now the initial histogram counts for the next iteration can be specified.
  • Tweaked the available parameters in the input YAML file:
    • Added parameters grompp_args and gmx_executable.
    • Removed the parameter parallel.
    • Renamed the parameter w_scheme as w_combine.
  • Added the attribute n_empty_swappable to the class EnsembleEXE.
  • Developed get_time_metrics and analyze_EEXE_time
  • Eliminated the need to copy over gro and top files for the next iteration.
  • Developed unit tests for get_averaged_weights and removed unit tests for obsolete functions.
  • Updated the documentation.
    • Removed any description about gmxapi.
    • Added more description about the CLI run_EEXE
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