From b78d23c73c26571eb36def3a2f59f586585461ae Mon Sep 17 00:00:00 2001 From: lorenzo-rovigatti Date: Sat, 16 Nov 2024 11:14:04 +0100 Subject: [PATCH] Prepare the repo for the new release --- CHANGELOG | 47 ++++++++++++++++++++++++++++++++++++++++++++++- README.md | 2 +- 2 files changed, 47 insertions(+), 2 deletions(-) diff --git a/CHANGELOG b/CHANGELOG index 3e2ee39c..90bff441 100644 --- a/CHANGELOG +++ b/CHANGELOG @@ -1,4 +1,49 @@ -v. 3.6.1 +v. 3.7.0 + - Add two new options to manage the format of the numerical output of some observables [6d03f40] + - Deprecate many old plugins in the contrib/rovigatti folder [95bd2e0] + - Add compiler flags to support Ampere GPUs [21d7e48] + - Update generate-sa.py to support generation of dsDNA with sticky ends and add an example to show its functionalities [08dcc2c] + - Add an attraction plane that constrains particles to stay on one side of it while attracting them with a constant force (`type = attraction_plane`). Documentation is also included [f0e0c9d] + - Port the ANNaMo interaction to CUDA [3568256] + - Make it possible to print the kinetic and total energies with any precision [f42d61d] + - Make the NA interaction support custom bases (fix #129) [306a276] + - Make it possible to simulate arbitrary LJ binary mixtures [b191c3d] + - DPS: Add an optional Yukawa repulsion to the model [dbdc726] + - DPS: Add an input file key to disable three body interaction [2d62ba7] + - DPS: Fix a bug whereby species with 0 particles would not be handled correctly [2d33bcc] + - Fix a bug whereby the CUDA code would crash for particular initial configurations made by nucleotides aligned along z (#120) [2b69edf] + - Fix an example (#123) [f4853f9] + - Fix a bug whereby the code would hang if bases_file (used by HBEnergy) was not readable [a20df96] + - Fix a bug that made VMMC simulate the wrong model when used with the DNA2 interaction [6096fdb] + - Improve the docs (see *e.g.* #116) + oxpy: + - Fix #97 (FFS Simulation Type Fails to Log Correctly When Running Consecutive Processes) [2b93f63] + - Add a workaround documentation to a known oxpy bug [960a8c5] + - Fix #138: make oxpy's get_bool() to handle non-lowercase booleans [208049d] + - Improve the docs + oat: + - Duplex angle plotter now works with ANY nucleotide id in the duplex [eb17a42] + - Fixed bug where output_bonds would fail instead of exiting normally when no plot was requested [c287226] + - Fixed bug where duplexes were detected as longer than they should be if they became unpaired [e1580e6] + - Fixed bug where inboxing would always center the structure, center=False works now [b23bdb7] + - Fixed parser and data type errors in oxDNA_PDB [d951742] + - Fixed bug where strands would sometimes be backwards in converted PDBs and fixed bug where the box center was incorrect during inboxing [2f179ad] + - In oxview.py, now from_path supports multiple systems loading [0050492] + - Updated bond_analysis to be able to drop data files [27d2fbb] + - Added __len__ methods to System and Strand [ac5e632] + - Changed read_force_file to interpret particle IDs as ints rather than floats [e7f6818] + - Make oxDNA_PDB callable from scripting interface [a20207b] + - Improved consistency in oat cli calls [3d628eb] + - Updated oat superimpose to allow separate index files for each configuration [8a6ed9d] + - Removal of now removed 'center' keywords from align function call [1cb3b40] + - Fix error in input file parsing (#119) [bca41ab] + - Created forces/pairs to dot-bracket converters and a skeleton script for trajectory analysis [cce8009] + - Fixed bugs in pdb output file naming and improved RNA detection [e753007] + - Fix parsing error for strand circularity in oat's new topology reader [a168f8d] + - Faster linear version of decimate script [adbba3c] + - Added PDB -> oxDNA converter to oat [e0084bc] + +v. 3.6.1 [6854eec] - Fix some bugs and docs errors due to the DRH -> NA change (see #81) [79728d3 and 7cf4b94] - Add and document an option to control the DH cut-off (see #83) [95a9f0d] - Make the MPI VMMC backend runnable once again, after it had been broken for years (see #85) [8becd5f] diff --git a/README.md b/README.md index 44736d80..752c92a4 100644 --- a/README.md +++ b/README.md @@ -28,7 +28,7 @@ The `analysis/paper_examples` folder contains examples for `oxDNA_analysis_tools **Q: Can oxDNA be run on multiple CPU cores or GPUs?** -**A:** No, oxDNA can run simulations on single cores or single GPUs only. +**A:** No, oxDNA can run simulations on single cores or single GPUs only. However, the Python bindings (`oxpy`) can be used to implement parallel algorithms on top of `oxDNA`. See for instance `examples/METADYNAMICS` and `examples/OXPY_REMD`. **Q: How is the oxDNA force field defined?**