Version 2.4.0

New features

• Support for JSON schema giving more robust input file checking (#240)
• Allow implicit molecules and finite reservoirs in reactive Monte Carlo (#259)
• Excluded neighbors in non-bonded interaction (#161)
• Draw from active molecular groups (#277)
• Add molarity keyword for insertmolecules (#263)
• Enhanced Gouy-Chapman support (#264)
• Non-electroneutrality compensation in Ewald summation (#255)
• OpenMP parallelisation for scattering analysis (#243)
• Virtual translation move for force calculation (#236)
• Enable muVT ensemble with cluster move (#230)
• Enable gzip compression for reactioncoordinate analysis (#280)
• Write analysis to disk every macro step (#227)
• PQR output respects inactive particles (#279)

Other improvements

• Fix: Group::contains for inactive groups fix (#267)
• Fix: pybind11 bug (#233)
• Fix: Speciation move gives segfault if all molecules are inactive (#249)
• Additional speciation tests (#252)
• Unittest for multipoledistribution analysis (#266)
• Better performance (#214)
• Warning for transrot move on the rigid molecule (#276)
• Provide debug output to the user (#160)
• Update auxiliary libraries and add C++17 requirement (#229)
• Refactoring of Ewald summation policies and Energy class (#247)
• Update manual for runtime steps (#275)

Checksums for tar.gz file

• sha256: 14b5628a6a05857a809d9ef56b97d0c67db9923e26683a69e65384fa7eaaa07a
• md5: 9e6d9440b1bde8a0b4e3cb66ac9077d1

Version 2.3.0

• New features

  • all nonbonded interactions can be tabulated
  • custom molecule-molecule thresholds and satellite groups for cluster move (f976cdd)
  • center of mass option in sliceddensity
  • periodic, hexagon prism container (#116)
  • isochoric moves for cylinder and hexagon
  • molecule selection for xtc trajectory output
  • added group/particle vector check to sanity analysis
  • cluster move analysis include size distribution (a2ee06f)
  • added customexternal potential for arbitrary external potentials
  • GCMC works for molecular groups
  • shell progress bar shows total runtime (b222d68)
  • stockmayer example and anisotropic particles are operational (#135)
  • readthedocs documentation (#148)
  • controlled info and log support via the spdlog library (#164, #160)
  • Hertz pair potential (#119)
  • Electrostatics through the CoulombGalore library.

• Internal changes and fixes

  • refactored pair potential self-energies (#138)
  • consistent control of mixing rules for LJ, WCA, hardsphere, Hertz, squarewell (#159)
  • fix for on-the-fly sasa calculation (#101)
  • Group::contains: optionally check also for inactive particles; unittests
  • fixed unit on Cv calculation in energy analysis
  • faster cluster move by skipping internal cluster energy
  • openmp optimizations
  • unknown atom given in custom LJ now force program abort
  • geometry refactoring
  • overall refactoring to reduce partial compile times
  • fixed stability of virtual volume move (#151)

Version 2.2.0

• New features

  • molecular titration added to rcmc move (beta status)
  • custom pair potential for mathematical expressions
  • analysis: added nskip keyword for skipping initial frames
  • chargefluctuations analysis for tracking charge states
  • wildcard, * for selecting atoms and molecules (in moves, analysis etc.)
  • new examples/tests: stripes, phosphate, sodiumphosphate
  • The yason.py conversion script accepts jinja2 replacements and links for external files
  • atomprofile analysis can calc. charge density
  • moleculelist: new keepcharges flag when loading from PQR/AAM
  • allow for molecules w. zero mass
  • mass center cutoff can be set for individual molecule combinations
  • constrain energy for limiting the system using reaction coordinates
  • end-to-end distance reaction coordinate

• Fixes and internal improvements:

  • relative drift produced NaN if initial energy == 0. While correct, we instead print absolute drift for this case.
  • documentation: fix broken PDF tables; updated install instructions to match conda-forge
  • fixed random position error for cylindrical geometry
  • stricter LennardJones/WCA input and checking
  • fix conformational swap move in non-cuboidal geometries (overlap check fix)
  • sanity check analysis w. more verbose output
  • catch too large molecules in pivot move and fixed a potential error when using pbc geometries
  • fix sign error on capacitance in multipole analysis
  • fix Average::stddev()
  • eliminated cppcheck warnings

Version 2.1.1

• Fixes and internal improvements:
  • Where available, CMake dependency downloading changed from ExternalProject to FetchContent.
  • cluster works with inactive molecules (still not dynamically updated, though)
  • improved memory efficiency for FunctorPotential
  • developer travis/osx build: mpich back to openmpi 1.6 due to abort trap 6 error (compiler mismatch)
  • cmake build compatible with conda-forge (circle/ci, travis)
  • fix compiler warning on GCC7
  • MPI destruction / MPI_Finalize() order fix for more stable MPI runs

Version 2.1.0

SHA256=26c807341502d1ec5f933d72273d89927113fbb8d0366b4b9207552104d10329 (faunus-2.1.0.tar.gz)

• New features

  • starting from this version, we aim to release using semantic versioning
  • tips are given in case of incorrect input. Disable from command line with --notips
  • added akesson mean field correction energy
  • added confid molecular reaction coordinate
  • added qrfile analysis and VMD script for visualising grand canonical ensembles
  • html manual install into share/faunus. Can be launched from shell with faunus-manual.
  • example/test for double-layer in slit geometry
  • example/test for weighted conformational swap moves
  • /usr/bin/env yason.py shebang added to example YAML files to
    automatically convert to JSON when executed. One can thus run
    simulations with ./minimal.yml | faunus

• Fixes and internal changes:

  • compilation passes with -Wall -Wextra -pedantic-errors
  • updated to latest versions of pybind11; nlohmann/json; Eigen
  • fixed random position generation in slit geometry
  • fixed penalty function error when loading from state file
  • bugfix: penalty function broken reference to space particles / molecules
  • anaconda osx: openmpi -> mpich
  • solved travis build timeout issue
  • added Equidistance2DTable for random-access, constant complexity lookup tables
  • added Space::activeParticles() for range-based for loops

Version 2.0.4

• overlap check with non-cuboidal simulation containers
• individual energy terms are timed
• moleculelist: FASTA sequence loader
• pivot: optimised energy evaluation
• bonded: optimisation of energy calculation
• nonbonded: control of OpenMP behaviour
• conda builds with OpenMP on Linux_x64 (not yet on osx)
• added chargemove
• added reactioncoordinate analysis
• added sanity analysis
• new reaction coordinates:
  • atom: charge
  • molecule: COM, number of atoms, net charge, dipole moment, angle, muangle
  • system: radius
• polymers example/test
• improved documentation
• fix translational moves on sphere/disc/line (needed for Dynamic MC)
• multiple minor fixes

Version 2.0.2

• Cluster move: rewritten mass-center routine
• Virtual volume move analysis: fix for numerical overflow error
• Geometries selectable from input (cuboid, slit, sphere, cylinder)
• Documentation update
• py36 and py37 targets in Anaconda (OSX and Linux)
• Multiple minor bugfixes

Version 2.0.1

v2.0.1

conda build name change

Version 2.0-beta.3

Bugfixes, more robust input handling, additional examples.

Version 2.0-beta.2

• many bugfixes
• manual improvements
• speciation examples