1.3.1

This release contains bug fixes.

Full Changelog: v1.3.0...v1.3.1

Bug fixes

• #125 Add error for converting non-numeric strings to numbers. Author @rwsmith7531 in

• #129 Fix GEMC examples and prevent log volume moves. The diethylether and isobutane GEMC examples had an extra line after the maximum volume move parameter. This would trigger an error due to code that would look at this line as a flag to activate volume moves in log space. Since log space volume moves were implemented too long ago, and the
  code has changed since then, an error is thrown if the execution reaches
  tihs point. Most of the log volume move code looks good, but it has not been tested yet. Author @emarinri

• #135 Update CI. Author: @emarinri in

• #134 Fix CBMC dihedral selection. Previously, the CBMC Fragment_Placement subroutine would sometimes choose a dihedral trial with trial overlap despite its weight being zero. This was fixed by changing the "<=" operator to "<" and flagging cbmc_overlap if none of the trials are picked. Author @rwsmith7531

• #145 Upgrade gcc and gfortran versions used for Azure Pipelines CI runs. Author @rwsmith7531

• #90 Allow dashes in file names. Author @rwsmith7531

1.3.0

This release contains a number of bug fixes, documentation improvements and full support for Widom insertions.

Full Changelog: v1.2.6...v1.3.0

Documentation improvements

• #119 Clarify in the documentation that molecules must be input without broken bonds as initial configuration. Author: @emarinri

Bug fixes

• #121 lammpstrj converter script argument type fix Author: @rwsmith7531
• #124 Chargeless Widom insertion species with ewald fix. Author: @rwsmith7531
• #127 Fix denormalized floating-point exceptions. Author: @emarinri

New features

• #106 This PR completed the implementation of Widom insertions. It includes a Python script to read pre-generated LAMMPS trajectories of a liquid phase. These trajectories are used to perform Widom insertions in an embarrassingly parallel way. Additionally, a cell-list based method is included to improve efficiency of these insertions. Examples of this new feature included absorption of the R-32 refrigerant into an ionic liquid, as well as general documentation. Author: @rwsmith7531

1.2.6

This release contains a number of bug fixes, documentation improvements and initial support for Widom insertions.

Full Changelog: v1.2.5...v1.2.6

Documentation improvements

• #89 Better explanation of energy units as displayed in the property file. Extended discussion of extensive vs. intensive energies were added. List all the new properties available for output.
• #93 Initial RTD documentation for Widom insertions.
• #108 Replace int32 seeds with int64 seeds in examples and tests

Bug fixes

• #96 Fix a bug in Apply_PBC_Anint in the file minimum_image_separation.f90 regarding periodic boundary conditions for cubic boxes.
• #98 Utilize 64-bit integers for the number of steps in simulation, allowing for extended runs.
• #113 Increase the number of lines where to look for the keyword END and utilize the fractional to Cartesian conversion subroutines when applying PBC
• #116 Add a -s or --solid flag in the mcfgen.py script so that the CONECT PDB keyword is not utilized for solids when generating an MCF.

Testing/CI

• #102 Various improvements to CI

New features

• #64 Add initial Widom support, examples and documentation.

1.2.5

Hotfix to fix the mcfgen.py deprecation that was introduced in 1.2.2. See #84.

1.2.4

Hotfix patch (see #73).

1.2.3

Patch release with the following features:

• Adds force-shifted LJ potential (#54)
• Support up to 20 character atom names in custom mixing rules (#69)
• Extends maximum number of items per line (needed for large fragments) (#63)
• Ignore text after ! when parsing input file (#55)
• Clarify error message for invalid VDW type (#53)

and bug fixes:

• Fix ring fragment generation for ring fragments involving multiple different atom types (#67)
• Change restricted insertion deletion move acceptance criteria to use restricted volume (#66)
• Initialize identity switch (not yet implemented) counter to zero (#58)

1.2.2

Patch release with the following:

• Adds support for Python3 in auxiliary scripts
• Adds support for longer atom name (20 chars) and element name (6 chars)
• Checks that actual bond lengths match fixed bond lengths specified in MCF file
• Clarifies and extends available thermo property output options
• Adds python based test suite
• Adds ability to use a non-cubic box in NPT GEMC if the max volume move size is zero.