v3.7.0

This release contains both new features and bugfixes. Note that the bug fixed in 6096fdb, introduced in version 3.6.0, was particularly dire, and affected all simulations of the DNA2 model run with VMMC.

• 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]

Thanks to everybody who contributed (@lorenzo-rovigatti , @tgfrancesco , @mlsample , @ErikPoppleton , @zoombya , @Subhajit-Roy-Partho , @jinhzhou , @elija-feigl , @JeDeveloper , @eryykr)