CHANGELOG.md

Change Log

1.31.0

Added

• add external/CoMPullingForce to apply constant force to the center of mass of the specific particles

Changed

• enable to specify force strength and direction of PullingForce separately

1.30.0

Added

• add external/PullingForce to apply constant force to a specific particle
• add method to update delta_t to integrators

Changed

• reorganize 3SPN2 interaction and simplify input file

1.29.0

Added

• enable to restrain χ value in the multiple basin forcefield

1.28.1

Fixed

• Fix instability of the G-JF Integrator introduced in v1.28.0

1.28.0

Added

• add lambda-dynamics
• add dynamic_variables to System. They have virtual mass, velocity and force and are integrated over time.

Changed

• speedup by skipping virial calculation if virial is not needed
• enable EnergyCalculation to output pressure

1.27.0

Added

• Hybrid Forcefield

Changed

• refactoring: separate combination rule from global potentials

1.26.0

Added

• NPT Langevin
  • except external forcefield
• Add an option to tabulate pair parameter (not using a combination rule) for WCA and L-J Attractive

Changed

• update toml11 to v3.7.0

Fixed

• fix dcd file format to correctly save the interval
• fix force calculation in multi-unit multiple basin
• add missing .gitignore in G-JF Integration test (@bondrewd )
• update Boost URL (@bondrewd )
• add missing tests for OpenMP 3SPN.2

1.25.0

Added

• add LennardJonesAttractive to global potential
• output pressure if PBC is enabled

Fixed

• make warning message in EnergyCalculation mode informative
• consider the difference of sed command on BSD in CMakeLists

1.24.0

Changed

• update toml11 to v3.6.1
• update GitHub Actions setting

Fixed

• activate loggers in some tests (@yutakashi634)

1.23.0

Added

• a short example input file to the document

Changed

• enable margin-related functions to return a bool value (@yutakasi634 )
• reduce log output while loading msgpack to simplify and shorten the log file

1.22.0

Added

• support OpenMP in G-J&F Langevin
• add WormLikeChainOffsetPotential (@yutakasi634 )

Changed

• make boundary condition support optional in CMake

Fixed

• fix several tiny mistakes in the reference documents

1.21.0

Added

• RTree as a spatial partitioning
• G-JF Langevin Integrator

Fixed

• Fix formula of worm like chain (@yutakasi634 )

1.20.0

Added

• WCA potential
• iSoLF potential
• (SINGLE|DOUBLE)_PRECISION_SUPPORT=(ON|OFF) to CMake options

Changed

• speedup NeighborList construction

Fixed

• Allow negative offset value in global interaction
• Fix link in documentation (@yutakasi634 )

1.19.0

Added

• support OpenMP + g-BAOAB
• output version and compiler information in log

Changed

• make boundary condition more customizable

1.18.0

Added

• allow list of indices in offset (@yutakasi634)
• enable to load random number generator state from checkpoint file

Changed

• update toml11 to v3.6.0

Fixed

• avoid error in an edge case in PeriodicCellList
• stabilize FLP angle potential calculation in an edge case

1.17.0

Changed

• update toml11 to v3.5.0
• speedup EnergyCalculation simulator

Fixed

• read boundary information correctly in EnergyCalculation simulator

Misc

• refactor energy format methods

1.16.0

Added

• documents in English

Changed

• use Hugo instead of gitbook to host documents
• make MultipleBasin faster

1.15.1

Fixed

• enable to include a file in an array of tables
• avoid infinit recursive file inclusion

1.15.0

Added

• g-BAOABIntegrator (@yutakasi634)
• generalized MultipleBasinModel

Changed

• check initial condition is in the boundary
• make systems.boundary_shape omittable if there is no boundary

Fixed

• fix CMakeList for the case when only C++ implementation of OpenMP is found

1.14.0

Added

• RectangularBoxInteraction
  • with LennardJonesWallPotential and ExcludedVolumeWallPotential

Changed

• rename integrator.parameter to integrator.gamma in an input file

1.13.1

Fixed

• read env correctly while reading BAOABLangevin (@yutakasi634).
• add document about restarting via msgpack

1.13.0

Added

• enable to use offset and env in [simulator] table (@yutakasi634)
• check parameter duplication in [simulator] table (@yutakasi634)
• enable to include toml files in a input file

The included files will be expanded only once. Recursive inclusion does not work.

include = "some_table.toml"
[another_table]
include = ["parameter1.toml", "parameter2.toml"]

1.12.0

Added

• enable to use index offset in the [[forcefields]]
• enable to remove net translation/rotation while time integration

Changed

• update toml11 to v3.4.0

Misc

• move interaction and potential codes to forcefield/ directory

1.11.0

Added

• enable to save the last snapshot to msgpack and load it as the initial snapshot

Changed

• simplify OpenMP implementation
• make dihedral calculation slightly efficient

Refactoring

• move Topology from System to Forcefield

1.10.0

Added

• Add Inverse power potential (@yutakasi634 )
• Add AFMFlexibleFitting

Changed

• check energy values are finite when outputting a snapshot
• estimate the remaining time in the progress bar
• upgrade toml11 to v3.3.0

1.9.0

Added

• Add RepulsiveGoContact and AttractiveGoContact
• Add WormLikeChainPotential (@yutakasi634)

Changed

• Update toml11 to v3.2.1
• Warn if splitted input file has several top-level tables
• Notice ignore.particles_within status
• Write system attribute status (e.g. reference temperature) to .ene file

Misc

• Add API to re-scale neighbor-list margin
• Move FlexibleLocalPotential from general potential directory to forcefield/FLP

1.8.0

Added

• add EnergyCalculationSimulator

Changed

• warn if undefined group is found in [[forcefield.global]]
• warn if invalid key appears in [[forcefield.global]]

Misc

• enable to clone forcefield
• add initialize() to local potentials (@yutakasi634)
• refactor input funstions

1.7.1

Fixed

• fails to run simulation when non-uniform boundary is applied
• add missing line feed in the error message about dihedral potentials
• fix typo in the name of SI unit (@yutakashi)

Changed

• speedup initialization of FlexibleLocalDihedral potential

1.7.0

Added

• PDNS interaction
• PWMcos interaction
• DirectionalContactInteraction (@yutakashi634)

Changed

• update toml11 from v3.0.1 to v3.1.0
• internal architectural changes around neighboring list

1.6.3

Fixed

• fix default periodic cell list
  • Global potentials that are applied to all the particles, such as an excluded volume, are not affected

Added

• add the -static-intel flag to the optimization flags when intel compiler is used
• notice if simulation runs on single core.

1.6.2

Fixed

• bug in openmp implementation of CellLists
  • Do NOT use OpenMP and CellList if a potential is not applied to all the particles
  • Global potentials that are applied to all the particles, such as an excluded volume, are not affected

1.6.1

Fixed

• concurrency bug while generating velocity
  • Do NOT use OpenMP stuff in 1.6.0
• add missing docs about potential combination in Dihedral

Misc

• refactoring

1.6.0

Added

• add 3SPN2C potential for DNA
• add HardCoreExcludedVolumePotential (@yutakashi634)
• enable to generate initial velocity
• allow boundary.type = "Periodic"

Changed

• change 3SPN2 input format

Fixed

• suppress incorrect warnings

1.5.2

Fixed

• cutoff length of gaussian contact
  • Do not use Contact interaction with Gaussian potential in the earlier releases
• fix some typographical errors in the documentation

Changed

• change compile flags for test codes

1.5.1

Fixed

• add a workaround for intel compiler linker errors
• add a missing newline in an error message

Added

• warn if unknown keys appear in a toml file

1.5.0

Added

• support SwitchingForceFieldSimulator
• enable to change cut off ratio of global potentials

Changed

• optimize efficiency of BondLength and Contact
• add warning messages while reading input file
• upgrade toml11 to v3.0.1

Misc

• refactoring

1.4.1

Changed

• consider energy at cutoff in DebyeHuckel
• add SpatialPartitionBase to reduce compilation time
• replace constant values by constexpr functions

1.4.0

Added

• add 3SPN2 forcefield support
• enable to disable inter- and intra-group interactinos
• enalbe to compile files separately to reduce compilation time

Misc

• refactoring

1.3.2

Fixed

• ignore.molecule = "Others" option
  • Do not use this option in the earlier releases
• suppress warnings

Added

• Improve tests for ExclusionList

1.3.1

Fixed

• total count of molecules in Topology class
• avoid numerical error for edge cases in FlexibleLocalAngle

Added

• Improve tests for Topology class

1.3.0

Added

• add BAOABLangevinIntegrator
• add CosinePotential for DihedralAngleInteraction
• enable to define variables in input files

Changed

• upgrade toml11 to 2.4.0
• disallow to use some of non-periodic potential with DihedralAngle
• make special log message colorful
• check isatty before printing a progress bar

1.2.2

Fixed

• VelocityVerletIntegrator for OpenMP implementation (PR #115)
  • Do not use VelocityVerlet with OpenMP in v1.2.0 and v1.2.1
• output path of log files when files.output.path does not have the last '/'

Misc

• refactoring

1.2.1

Fixed

• incorrect include file in a test code

1.2.0

Added

• parallelism with OpenMP
• documentation (ja)
• Interaction
  • local/ContactInteraction
  • local/DummyInteraction

Changed

• upgrade toml11 to 2.3.0
• improve efficiency of Global Interactions

Misc

• refactoring
  • suppress linter's warnings
  • fix some typographic errors
  • simplify CMakeLists.txt
• improve unit tests
  • add another tests for LocalInteractions

1.1.0

Added

• Interaction
  • external/PositionRestraintInteraction
• Potential
  • external/HarmonicRestraintInteraction
• Observer
  • .trr file format
  • .dcd file format

Changed

• upgrade Boost to 1.69.0
• upgrade toml11 to 2.2.2

Misc

• refactoring
  • suppress compiler's warnings
  • unify the coding style
• improve unit tests
  • refactor test codes for input readers
  • add some missing tests

1.0.0

Added

• Simulator
  • MolecularDynamics
  • SimulatedAnnealing
  • SteepestDescent
• Integrator
  • VelocityVerlet
  • UnderdampedLangevin
• Interaction
  • BondLength
  • BondAngle
  • DihedralAngle
  • GlobalPair
  • ExternalDistance
• Potential
  • Harmonic
  • Gaussian
  • GoContact
  • FlexibleLocal
  • LennardJones
  • ExcludedVolume
  • DebyeHuckel