1. 08 Dec, 2022 6 commits
  2. 06 Dec, 2022 8 commits
  3. 06 Dec, 2019 1 commit
    • Sandipan Mohanty's avatar
      Bug-fix: incorrect RMSD values for dynamic lhs · 9443330b
      Sandipan Mohanty authored
      When both comparison structures in RMSD come from the simulation,
      the RMSD value returned was incorrect, as it was still calculated
      on the assumption of fixedness of the first structure. Properties
      of the first structure such as radius of gyration, used in the
      RMSD calculation were calculated and stored at initialisation were
      used throughout, even when the first structure was not a fixed
      one from a PDB file.
  4. 25 Oct, 2019 1 commit
  5. 24 Oct, 2019 1 commit
    • Jan Meinke's avatar
      Fixed formatting of program description. · 57af4b61
      Jan Meinke authored
      The lines in the description of argparse are wrapped by default.
      Since we want to use the formatted doc string, we have to add
      `formatter_class=argparse.RawDescriptionHelpFormatter` as argument.
  6. 17 Oct, 2019 9 commits
    • Sandipan Mohanty's avatar
    • Sandipan Mohanty's avatar
      Make sure update_g can be called from tests · d2004cf5
      Sandipan Mohanty authored
      update_g, when called from ctest does not have an environment
      where other programs like "prf", "mc_stats" are in PATH. It
      therefore needs a special PATH set up for the subprocesses it
    • Sandipan Mohanty's avatar
    • Sandipan Mohanty's avatar
      Stop SimTempRun from generating a live gpars.out · c96536c5
      Sandipan Mohanty authored
      Live generation of gpars.out was broken, as pointed out by Stefan
      Wallin. The monte carlo statistics, such as visit counts to different
      temperatures are now calculated in bunches, and the counters are
      reset regularly. SimTempRun did not take that into account, and
      hence generated g_T = 0 for all T randomly in the middle of a
      run. The values in the file gpars.out were therefore completely
      wrong eversince the statistics collection method was changed.
      With this patch, we simply remove the live generation of gpars.out
      file, and move that action to a post processing step. The user
      is now supposed to run "prf simtemp update_g" after a simulated
      tempering run to generate a new g parameters file, and replace
      the gpars.in file consciously. There is more flexibility now,
      as we can choose how much of the previous run should be used to
      re-calculate the g-parameters after the run is finished and we
      have inspected the "rt" files. For instance, to use cycles
      starting from 200000 in the calculation of new g-parameters, we
      can now do this "prf simtemp update_g --starting_cycle 200000".
      See "prf simtemp update_g --help" for details.
    • Sandipan Mohanty's avatar
      prf_runinfo gets two new options wrt xml · 02fecf5f
      Sandipan Mohanty authored
      It is possible to request xml output with -xml. It is possible to
      pick a specific child node in the information tree with a -get
      option, similar to how prfxml handles that option.
    • Sandipan Mohanty's avatar
    • Sandipan Mohanty's avatar
      Update SimTemp with g-parameter I/O · 9881d599
      Sandipan Mohanty authored
      SimTemp will now write the g-parameters in the binary configuration
      files, so that the parameters used in the simulation will always
      be available for inspection along with the binary data. The
      values will be visible using the runinfo system : "prf runinfo -m"
    • Sandipan Mohanty's avatar
      Throw specific error when JTF istream fails to open · b94f678c
      Sandipan Mohanty authored
      If we try to open a normal file with JoinedTextFileIstream,
      it should emit an error, because all read operations will fail.
      For now, non-existent files are handled separately.
    • Sandipan Mohanty's avatar
      Scripts to manage simulated tempering · 299afada
      Sandipan Mohanty authored
      We expand the "prf" script interface to add a few scripts to
      manage simulated tempering runs. Eventually, there should be
      some setup scripts, and may be simulated tempering specific
      post-processing scripts here. For now, we have only the cover
      script "prf simtemp" and "prf simtemp update_g". The later
      calculates new g-parameters from input g-parameters and the
      visit counts to different temperatures collected from a run.
      This will now be the "official" way to update g-parameters.
      The parameters as generated during a run are no longer correct
      as they only take the visit counts in the latest "packet" in
      the monte carlo statistics. The live generation of gpars.out
      will be removed.
  7. 24 Sep, 2019 1 commit
    • Jan Meinke's avatar
      Moved documentation from source to reStructuredText files. · f55967df
      Jan Meinke authored
      The user documentation that was included in the source code of the
      corresponding classes was moved to reStructuredText files in the doc
      directory. It is now available again when documentation is build, but
      some cleanup is still needed.
  8. 19 Sep, 2019 4 commits
  9. 18 Sep, 2019 2 commits
    • Sandipan Mohanty's avatar
      Remove inaccurate ominous messages in AC · 77995ff5
      Sandipan Mohanty authored
      Some vestigial warning messages about the total number
      of moved atoms and apparent misplacement of atoms discovered
      during update_cells() were silenced.
    • Sandipan Mohanty's avatar
      Minor bug-fixes in regularize · 75830d37
      Sandipan Mohanty authored
      A typo broke the message about the atoms involved in a disulphide bond,
      writing out the id of the first atom twice. A logical operator, which
      should have been "and" was mistakenly written as "or".
  10. 16 Nov, 2018 7 commits