faunus - Version 2.16.3

Conda build fix Full Changelog: https://github.com/mlund/faunus/compare/v2.16.2...v2.16.3

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Published by mlund over 1 year ago

faunus - Version 2.16.2

Stabilised build system for Conda

Full Changelog: https://github.com/mlund/faunus/compare/v2.16.1...v2.16.2

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Published by mlund over 1 year ago

What's Changed

Fix MPI build.
Fix dependency warnings with newer cmake versions.

Full Changelog: https://github.com/mlund/faunus/compare/v2.16.0...v2.16.1

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Published by mlund over 1 year ago

What's Changed

Partial migration from range-v3 to std::ranges by @mlund in https://github.com/mlund/faunus/pull/452
Tempering update by @mlund in https://github.com/mlund/faunus/pull/441
Tempering update by @IVinterbladh in https://github.com/mlund/faunus/pull/454
Use optional integer to store exchange partner by @mlund in https://github.com/mlund/faunus/pull/455
Update Voronota-LT, add alternative modes to Voronoi analysis. by @kliment-olechnovic in https://github.com/mlund/faunus/pull/456
Fix anglescan when the two molecules are different by @mlund in https://github.com/mlund/faunus/pull/458

New Contributors

@kliment-olechnovic made their first contribution in https://github.com/mlund/faunus/pull/456

Full Changelog: https://github.com/mlund/faunus/compare/v2.15.0...v2.16.0

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Published by mlund over 1 year ago

What's Changed

Make atomic displacement parameters optional by @mlund in https://github.com/mlund/faunus/pull/451

Full Changelog: https://github.com/mlund/faunus/compare/v2.14.0...v2.15.0

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Published by mlund almost 2 years ago

What's Changed

Add harmonic potential to constraint by @mlund in https://github.com/mlund/faunus/pull/445
Output inter-particle bond info by @mlund in https://github.com/mlund/faunus/pull/450
Clang tidy fixes by @mlund in https://github.com/mlund/faunus/pull/447
Apply clang format by @mlund in https://github.com/mlund/faunus/pull/449
Update list of contributers by @mlund in https://github.com/mlund/faunus/pull/446

Full Changelog: https://github.com/mlund/faunus/compare/v2.13.0...v2.14.0

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Published by mlund almost 2 years ago

What's Changed

Voronoi surface area analysis using Voronota-LT by @mlund in https://github.com/mlund/faunus/pull/444
Version bump of spdlog, pybind11, nlohmann_json.
Dangling reference fix (b0fee39)

Full Changelog: https://github.com/mlund/faunus/compare/v2.12.0...v2.13.0

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Published by mlund about 2 years ago

What's Changed

Write state file for minimum system energy by @mlund in https://github.com/mlund/faunus/pull/442
changed misspelled mininum to minimum in files by @IVinterbladh in https://github.com/mlund/faunus/pull/443
yason.py support script now requires the ruamel.yaml python package

Full Changelog: https://github.com/mlund/faunus/compare/v2.11.0...v2.12.0

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Published by mlund about 2 years ago

What's Changed

Add SASA analysis and test by @Smutekj in https://github.com/mlund/faunus/pull/399
Add save_min_conf to systemenergy analysis to save minimum energy configuration. By @mlund in https://github.com/mlund/faunus/pull/440
Use upstream ruamel.yaml instead of ruamel_yaml by @mbargull in https://github.com/mlund/faunus/pull/435
Update versions of external libraries
Fix readthedocs setup
Fix Github CI for C++20 by @mlund in https://github.com/mlund/faunus/pull/439

New Contributors

@mbargull made their first contribution in https://github.com/mlund/faunus/pull/435

Full Changelog: https://github.com/mlund/faunus/compare/v2.10.1...v2.11.0

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Published by mlund over 2 years ago

Changes

Fix install target for anglescan examples

Full Changelog: https://github.com/mlund/faunus/compare/v2.10.0...v2.10.1

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Published by mlund almost 3 years ago

What's Changed

Support for Gibbs ensemble for studying phase equilibria.
- Gibbs ensemble: volume exchange by @mlund in https://github.com/mlund/faunus/pull/430
- Gibbs ensemble: matter exchange by @mlund in https://github.com/mlund/faunus/pull/431
Updated documentation about multipole analysis by @IVinterbladh in https://github.com/mlund/faunus/pull/432
Add Random slump parameter for tempering by @IVinterbladh in https://github.com/mlund/faunus/pull/434. This should make it possible to use grand canonical schemes with parallel tempering.

Full Changelog: https://github.com/mlund/faunus/compare/v2.9.1...v2.10.0

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Published by mlund almost 3 years ago

Changes

Fix "progresstracker" compilation error on some systems, incl.

Full Changelog: https://github.com/mlund/faunus/compare/v2.9.0...v2.9.1

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Published by mlund about 3 years ago

What's Changed

Add a preface section to the user input which may contain a list of actions to be run prior to simulation. The discrete angle analysis below is an example of this.
Added --norun command line option to skip simulation.
Discrete angle integration by @mlund in https://github.com/mlund/faunus/pull/427 This allows for explicit angular integration of two rotating, rigid bodies. Energies and quaternions are streamed to disk and free energies and thermally averaged energies are reported.
Update minimum cmake version stated in manual by @SHervoe-Hansen in https://github.com/mlund/faunus/pull/424
Add VSC dev container config files by @mlund in https://github.com/mlund/faunus/pull/425
Enabled OpenMP by default

Full Changelog: https://github.com/mlund/faunus/compare/v2.8.0...v2.9.0

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Published by mlund about 3 years ago

What's Changed

Fix speciation moves for parallel tempering by @mlund in https://github.com/mlund/faunus/pull/419
Custom group to group pair-potential by @mlund in https://github.com/mlund/faunus/pull/421
Rename namespace and base classes by @mlund in https://github.com/mlund/faunus/pull/422
Upgrade nanobench from v3 to v4 by @mlund in https://github.com/mlund/faunus/pull/423
Table cleanup by @mlund in https://github.com/mlund/faunus/pull/420
Fix GCC warnings

Full Changelog: https://github.com/mlund/faunus/compare/v2.7.0...v2.8.0

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Published by mlund over 3 years ago

What's Changed

Add minimum distance option to groupmatrix analysis by @MarcoPolimeni in https://github.com/mlund/faunus/pull/418
Add scipy clustering example for groupmatrix analysis
Add optional particle-particle threshold to cluster move (com keyword)
Add PSC patchy particle unittest (964948e199d1f14fa6e2e22d5f7e6ab3c6094cb1)
Upgraded external libraries (0bf11d2352064aefc1378dd7fa9746a8b3cd4590)
Updated installation instructions (8bc5f8c706ed722f47114eed9e6caaecfb837bb4)
Updated TBB instructions for when using C++17 parallel algorithms and certain GCC installations.
Fixed a potentially dangling reference (7d168cbe3d247e399eec9750e2b6fa669c34b5e9)
OpenMP is now disabled by default (62036d3ac6101134744912c22532e1df3a3e0180)
Fixed GCC 12 warnings
Clarify positions keyword in manual (6da63c8d36625a6ce63c83a4d3fac134991ab612)
Fix plot pair-potential notebook

Full Changelog: https://github.com/mlund/faunus/compare/v2.6.1...v2.7.0

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Published by mlund over 3 years ago

What's Changed

Add policy to swap PSC patch information only by @mlund in https://github.com/mlund/faunus/pull/415
Group matrix analysis by @mlund in https://github.com/mlund/faunus/pull/416

Full Changelog: https://github.com/mlund/faunus/compare/v2.6.0...v2.6.1

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Published by mlund about 4 years ago

faunus - Version 2.6.0

Since the last release, 139 commits have been added. Full list of changes from v2.5.0 to v2.6.0.

New features

Generalised smart Monte Carlo move with support for regions (#405)
Quadratic charge move (#406)
Debye screening length can be deduced for complex salts
MPL is used for all MPI calls (#398)
Faster, internal SASA hamiltonian with support for periodic boundary conditions (#397)
Separate density analysis for atoms and groups
Reduce parallel summation memory requirement by a factor of two
Patchy sphero-cylinders (PSCs) are back! (#408)
- PSC trajectory format
- VMD visualiation
- Ancients tests are back
Enhanced translational displacement analysis for Dynamic MC (experimental)
Ability to save penalty function tables to disk during simulation

Compatibility

Compilation defaults to C++20 standard meaning that a pretty modern compiler is needed.
A scripts/Dockerfile is provided for creating containers with JupyterLab and Faunus preinstalled.

Partial list of fixes and enhancements

Refactoring of speciation move to allow for future expansion (#410)
Fix dirrot mass center error (bf088b45c77f97b71f882b86d3edb4d922f1f6dd)
Update manual for units on angles (dprot)
Fix potential harmonic bond breaking (#403)
Fix time stamp in output (#395)
Fix ion-ion Ewald energy (28f0c41b9ffd2ab7148fb6bf7faf8c07b4164f7d)
Enable C++20 mode compilation (a975438d8cd95a3b34b7f08f811f65cebbe58ab2)
Correctly handle inactive particles when using group output with xtc files (#402)
Fix 'constraint' energy when loading state (0d27a68f2c6ef60377a33c9d7a62c62823a5c513)
Safer xtc file handling

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Published by mlund about 4 years ago

Since 2.4.0 we have included more than 120 commits and closed 59 pull requests. While mostly invisible for users, we have made lots of internal refactoring and unit-testing to make Faunus more robust and maintainable.

Enhancements

Electric potential analysis (#379)
Constant interval moves (#381)
Force calculation and LD propagation of angular potentials (#368)
FASTA file loader
Improved structure file I/O (#376)
PCG Random number generator supprt (#369)
Add Langevin Dynamics that can be mixed with Monte Carlo moves (#298). It works with common pair-potentials and a subset of bonded interactions.
Add particle energy histogram to transrot move (#358)
Add shape anisotropy analysis to clustermove (#336)
Add copy_policy to conformation swap move (#354)
Support mapping of hexagonal cells to cuboids (#328)
Allow cuboids and hexagons in scattering analysis (#327)
Enable Intel Threading Building Blocks (#325)
Polymer shape analysis and tensor file output (#323, ea7c628)
Enable integer selection for inactive molecules (#317)
Introduced overwrite option to savestate (#309)
Allow Gzip compression a number of streaming outputs (#289, #308)
Add replay move (52e5364)
Optional to perform filename increment for savestate (#292)
Anisotropic volume perturbation (#291)
Optimize cluster search in ClusterMove (#285)
Relax Gouy-Chapman input (#248)
Add conformation id analysis (2e929b8)
Add python support module (555e8e7)
Add Apple M1 support (#355)
Store simulation duration in json output (#290)
Added example: bend for mixed MC/MD
Handle build dependencies using CPM (#380)

Bug Fixes and Optimisations

Fix empty error message from Hamiltonian (#360)
Use CPM.cmake for CMake dependency handling (#380)
Respect active particles in Langevin Dynamics (#324)
Refactor widom analysis (#310)
Splining of Yukawa fails bug (#301)
Fix speciation check for full or empty groups (#300)
Enable JSON output for nonbonded energy (#288)
Fix moltransrot if atomic group (#287)
Dipole mass center fix (#334)
Parallel Temper fix (#333)
VirtualVolumeAnalysis (Space is a reference) (#330)
AAM file reader (atoms begin at line 2) (#329)
Update crankshaft in schema.yml (#307)
Fix numeric overflow in energy (4f57102, 9b42049)
Fix possible infinite math in Release mode (b0859d9)
Clarify keyword inactive in manual (#316)
Optimisation: binary search in Bonded energy (#335)
Upgrade external libraries (#297)

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Published by mlund almost 5 years ago

faunus - Version 2.4.2

Changes

Bug fix

Fixes a bug (#300) where products or reactants could be wrongly (de)activated even if the groups are full/empty. This is a problem important only when simulating at extreme conditions where the groups are nearly empty or nearly full. The issue could appear as a non-zero net-charge upon restarting an equilibration run which would typically be initiated with all molecules in their active state. The issue would not appear with swap moves and only if multiple products or reactants were involved in the reaction.
Fixed broken Eigen library URL

Nothing else has changed since v2.4.1

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Published by mlund about 5 years ago

faunus - Version 2.4.1

In v2.4.0, the make install target is broken. This patches (#281) this problem, while the main Faunus code is unchanged.

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Published by mlund about 6 years ago

faunus - 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

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Published by mlund about 6 years ago

faunus - Version 2.3.0

New features
- all nonbonded interactions can be tabulated
- custom molecule-molecule thresholds and satellite groups for cluster move (f976cddb753b7ee6e0ddec696e6760390eadaee1)
- 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 (a2ee06fad1ae73e505ba07cd00476d37a9b66339)
- added customexternal potential for arbitrary external potentials
- GCMC works for molecular groups
- shell progress bar shows total runtime (b222d68717d5952d61e2464f96d975f1377dbbad)
- 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)

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Published by mlund over 6 years ago