1. 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.
  2. 25 Oct, 2019 1 commit
  3. 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.
  4. 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.
  5. 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.
  6. 19 Sep, 2019 4 commits
  7. 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".
  8. 16 Nov, 2018 21 commits
    • Sandipan Mohanty's avatar
      Update extract_props expression usage · 4b99e0d5
      Sandipan Mohanty authored
    • Sandipan Mohanty's avatar
      Tests for LittleParser · 05eeded4
      Sandipan Mohanty authored
    • Sandipan Mohanty's avatar
      Some new tests for string utils · d5d3e3eb
      Sandipan Mohanty authored
    • Sandipan Mohanty's avatar
    • Sandipan Mohanty's avatar
      Bug-fix: return a value from post incr ops · 661be97b
      Sandipan Mohanty authored
      In prf::Wrap, because of copy-and-paste, post-increment and
      post-decrement operators were incorrectly returning references,
      leading to dangling references and SEGFAULTS.
    • Sandipan Mohanty's avatar
      Make most DOF_Index functions const · 09df88f8
      Sandipan Mohanty authored
    • Sandipan Mohanty's avatar
      Define GroupLibXML as a named wrapper · e30bd8cd
      Sandipan Mohanty authored
      GroupLibXML represents an XML node containing information about
      entities available for simulation, presumably provided by the
      force field class.
    • Sandipan Mohanty's avatar
      size member function for Catalogue · 35add889
      Sandipan Mohanty authored
    • Sandipan Mohanty's avatar
      Multiple small changes in LittleParser · f2a91f07
      Sandipan Mohanty authored
      LittleParser header needed an include guard. It is now possible to
      have a string with all the defined variables from the parser. It
      is possible to query if an expression is definitely false. An
      expression may be neither true or false, if information to determine
      its truth value is not available. For instance, if we want to evaluate
      "a < 10 and b > 0", and a = 2 and b is unknown, the expression is not
      true, but it is also not false. Under the same circumstances,
      "a < 10 or b > 0" will evaluate to true, because a<10 is sufficient
      to determine the truth value even if b is unknown.
    • Sandipan Mohanty's avatar
      Add stream IO for Vector3 and Point3D · d5f42588
      Sandipan Mohanty authored
    • Sandipan Mohanty's avatar
      Add has_key function to AttributeList · 6b9b165a
      Sandipan Mohanty authored
      It is now possible to just query whether an attribute list has
      an attribute of a given name.
    • Sandipan Mohanty's avatar
      New xml specification file for all AA · d72a5221
      Sandipan Mohanty authored
      Geometric information about all the amino acids is now in FF08.xml.
      We have a new way to specify geometry of entities to be used to
      construct molecules in ProFASi 2.0. The geometry is to be encoded
      in the XML file specifying all possible interacting entities in
      the model. So far, amino acids had very minimal information in the
      XML format, and their geometry was directly encoded in their own
      classes. Now, amino acid geometry is in a very easy extensible
      form, and we can begin the work of removing the individual
      amino acid classes.
    • Sandipan Mohanty's avatar
      Use pimpl in LittleParser implementation · a9c28f4b
      Sandipan Mohanty authored
      LittleParser is likely to be updated a lot in the comming weeks. This
      patch isolates the rest of ProFASi so that trivial changes in LittleParser
      do not trigger a big recompilation. From the outside, we only see a
      rudimentary interface: one can set variables to specific values, ask if
      an expression, represented by a string is true. Details about the tree
      structure of the expressions, how type information about variables is
      stored etc. can be kept under wraps in the implementation. They have
      currently no value to users of the LittleParser.
    • Sandipan Mohanty's avatar
      Integer comparison and equivalent tokens in parser · 4ecc79bc
      Sandipan Mohanty authored
      LittleParser now treats "&&" and "and" as interchangable signs for
      the logical AND operation, and similarly for logical OR. An explicit
      integer type was introduced to store values set as integers really
      as integers, so that equality comparisons between them can not be
      broken by rounding errors.
    • Sandipan Mohanty's avatar
      New asserts assert_true/false in macro_tests · fe4aab7f
      Sandipan Mohanty authored
      prf_assert_true does what prf_assert_throw also does, but the name
      is more intuitive. prf_assert_false throws UNLESS the condition provided
      is false.
    • Sandipan Mohanty's avatar
      Two new string_utils functions with any_of · d6a7a548
      Sandipan Mohanty authored
      find_any_of(i1, i2, j1, j2) takes an input range [i1, i2) and a token
      range [j1, j2), and tries to find a location in the input range which
      marks the start of any of the tokens found in [j1, j2). The token range
      can be, for instance, ["&&", "and", "AND"]. The idea is to treat the
      token range as equivalent, and find any entry in the range.
      split_by_any_of(string, string_container) accepts a token range as
      a string container and splits the input string by them, treating the
      entries in the token range as synonymous, even if they contain different
      number of characters.
    • Sandipan Mohanty's avatar
    • Sandipan Mohanty's avatar
      noexcept and alignment added to Matrix · 1250e369
      Sandipan Mohanty authored
      Most matrix functions can be noexcept, so they were labeled accordingly. For fixed size
      matrices, if they take more than 32 bytes they are aligned to 32 bytes, and if they are
      more than 64 bytes, they are aligned to 64 bytes.
    • Sandipan Mohanty's avatar
      Indexing operator for Catalogue · adb137a5
      Sandipan Mohanty authored
    • Sandipan Mohanty's avatar
      Update compiler specific CMake files · 8a7f381d
      Sandipan Mohanty authored
      Clang 7 moved experimental filesystem objects from libc++experimental to libc++fs,
      which requires that the choose_fslib had to be modified to adapt. GCC and Clang
      required versions in the compiler specific CMake files were updated to reflect
      what is stated in the installation.rst file. Options to enable aligned allocation
      from C++17 when available were added for both GCC and Clang.
    • Sandipan Mohanty's avatar
      Remove redundant functions from Vector3 · 11de862c
      Sandipan Mohanty authored