Version 1.2.0

What's Changed

This is a first release after a long long time (8 years!). From now on, we plan to make more frequent releases so that users can more easily keep up with the new development.

Here are a few notable new features that have been added over the last few years:

• Implementation of alternative Surface Hopping algorithms that don't require analytical non-adiabatic couplings --- Landau-Zener approach (implemented by @suchanj and further developed by @JanosJiri) and Beack-An couplings (implemented by @JanosJiri).

• Many new interfaces to electronic structure code!

  • Interface to BAGEL electronic structure package by @JanosJiri, which allows a SH simulations at CASPT2 level of theory
  • Interface to xTB by @juraskov
  • Protocol buffer (TCPB) interface to TeraChem by @danielhollas
  • ChemShell interface for QM/MM simulations by @postulkj
  • and many more, see below for full list ⬇️

We hope you enjoy this release. 🫶 🤘

New features and enhancements 🧑‍🏭

Major new features ✨

• Landau Zener Surface Hopping by @suchanj in #24
• L-Z SH with TeraChem over MPI interface by @suchanj in #36
• Improvements of LZSH algorithm by @JanosJiri in #159
• Baeck-An couplings for SH by @JanosJiri in #186
• Python script for analyzing TSH trajectories from ABIN. by @JanosJiri in #206

New interfaces 🤝

• xTB interface by @juraskov in #138
• Protocol buffer (TCPB) interface to TeraChem by @danielhollas in #145
• Interface for Landau-Zener SH with MNDO program by @JanosJiri in #155
• BAGEL interface for XMS and MS-CASPT2 in FSSH and LZSH by @JanosJiri in #153
• OPENQP Landau-Zener interface by @JanosJiri in #225
• Interfaces to ChemShell by @postulkj in #208
• Fix wrong gradient state in ChemShell LZ by @postulkj in #217
• Bring back TeraChem file interface by @danielhollas in #165
• DFTB+ interface upgrade by @danielhollas in #179
• Enable classical MD with GLE thermostat by @danielhollas in #90

Minor features 🧪

• Use usleep to wait for TeraChem by @danielhollas in #164
• Support -V/--version command line options. by @danielhollas in #75
• Robust and reproducible PRNG initialization for REMD by @danielhollas in #110
• Rename &nhcopt input section to &thermostat (nhcopt still works as a fallback if thermostat is not present) by @JanosJiri in #213
• Rename r.abin to run.abin.sh by @danielhollas in #191
• Velocity and geometry units added to output files. by @JanosJiri in #200
• Add ignore_state in Launda-Zener hopping by @danielhollas in #185
• NaI analytic potential for FSSH by @JanosJiri in #178
• Add Schwenke's gas phase H2O analytical potential by @danielhollas in #166
• H2O CVRQD potential by @danielhollas in #171
• Implement numerical forces for Schwenke water potential by @mbarnfield63 in #174

Bug fixes 🐛

Critical bugs 😰

• Fix restart from old restart files by @danielhollas in #134
• FIX TC Surface Hopping interface, broken since #62 by @danielhollas in #80
• Harden TC-MPI connection (handle empty port case) by @danielhollas in #41
• FIX: Read velocities from file in r.terabin by @danielhollas in #124
• Use the correct decoherence correction by default by @danielhollas in #104
• LZ with TC fixes #142 by @suchanj in #150
• SH: Fix edge condition in try_hop_nacme_rescale() by @danielhollas in #136
• Fix MOLPRO-SH interface by @danielhollas in #131

Minor bugs 😅

• Langevin thermostats are incompatible with SHAKE by @danielhollas in #156
• Patch atom name comparison for velocity file reading by @suchanj in #43
• LZ zero division fix by @suchanj in #52
• SH: ignore_state for MOLPRO-SH by @danielhollas in #132
• Fix PIMD energy for internal water potentials by @danielhollas in #105
• Re-enable REMD with TC-MPI interface by @danielhollas in #68
• Fix -shiftdih option in analyze_movie by @danielhollas in #40
• Do not try to shutdown TC server if communication was not established by @danielhollas in #139
• Better shebang for tsh_traj_anal.py by @JanosJiri in #207
• Ignoring BA sigma for ignore_state by @JanosJiri in #197
• Correcting NaI conversion units for NAC by @JanosJiri in #194
• Make sure the last step is written when using dE_S0S1 by @danielhollas in #184

Dev changes 🛠️

Code refactor and improvements ⚙️

• Remove NAB by @danielhollas in #30
• Fix Makefile for Plumed by @danielhollas in #44
• Streamline Makefile by @danielhollas in #45
• Update Fortran MPI interface: "use mpi" instead of "include mpif.h" by @danielhollas in #46
• Clean compiler warnings and fix FFTW and Plumed compilation by @danielhollas in #37
• Remove on-the-fly histogramming by @danielhollas in #39
• Harden PLUMED restart by @danielhollas in #53
• Encapsulate FFTW, squash more compiler warnings by @danielhollas in #56
• Prettify everything! (add formatter) by @danielhollas in #64
• Refactor atom name normalization + test water.F90 by @danielhollas in #65
• Refactor r.abin and r.terabin by @danielhollas in #69
• Ensure implicit none via compiler option by @danielhollas in #77
• Remove stubs and comments for Ehrenfest method by @danielhollas in #87
• Refactor GLE module, re-enable PIGLET test by @danielhollas in #91
• SH: Remove inac==1 option, HST model by @danielhollas in #95
• Create MPI wrapper module by @danielhollas in #97
• Redirect stdout to /dev/null for my_rank>0 by @danielhollas in #100
• SH: Remove itrj index from all arrays by @danielhollas in #103
• Do not print file headers when restarting by @danielhollas in #106
• Mdstep refactor by @danielhollas in #108
• Refactor force_abin by @danielhollas in #109
• Prettify after refactor by @danielhollas in #117
• Fix intent in lz_restin by @danielhollas in #118
• convert all system() calls to execute_command_line() by @danielhollas in #119
• Refactor init by @danielhollas in #121
• Makefile in utils/ by @danielhollas in #127
• SH: Remove NSTMAX by @danielhollas in #125
• SH: Cleanup the main SH routine by @danielhollas in #126
• SH: Tests and minor refactor by @danielhollas in #133
• Mpich update by @danielhollas in #147
• Cleanup functions related to rotational velocity, improve sample input files by @danielhollas in #162
• Vendor fprettify autoformater and add to CI by @danielhollas in #167
• Cleanup create_trajectories.sh with shellcheck by @danielhollas in #177
• Disable spline potential by @danielhollas in #182
• Orca interface cleanup by @danielhollas in #181
• Fixes from Fortitude linter by @danielhollas in #190
• Update fortitude linter to v0.7 by @danielhollas in #201

Build, Testing and Continuous Integration (GitHub Actions)

• Continuous Integration via Github Actions by @danielhollas in #28
• Setup code coverage using Codecov.io by @danielhollas in #35
• Add pFUnit library for unit testing by @danielhollas in #42
• Add PLUMED to Github CI by @danielhollas in #47
• MAJOR fix to tests! by @danielhollas in #51
• Move source to src/ by @danielhollas in #50
• Surface floating-point operation errors in Github CI by @danielhollas in #49
• Fix test.sh by @danielhollas in #54
• Refactor cleaning test directories by @danielhollas in #55
• Tweaks and fixes for GA and Codecov configs by @danielhollas in #58
• Test TeraChem MPI interface by @danielhollas in #62
• Fix GitHub CI by @danielhollas in #67
• Fix compilation with ifort by @danielhollas in #70
• TC tests fixes by @danielhollas in #71
• Refactor error handling by @danielhollas in #72
• Pin pFUnit version by @danielhollas in #78
• Add a basic test for TC-MPI surface hopping interface by @danielhollas in #81
• Add test for Morse potential + refactor by @danielhollas in #84
• Reenable GLE and PIGLE tests by @danielhollas in #88
• Test Double-well potential + refactor by @danielhollas in #92
• Add MTS test by @danielhollas in #93
• Add SPLINE test by @danielhollas in #94
• Add test for global Nosé-Hoover thermostat + refactor by @danielhollas in #96
• Fix the code coverage for mpi error paths by @danielhollas in #101
• SH: test simple velocity rescaling by @danielhollas in #99
• GHA: support Plumed 2.8 by @danielhollas in #102
• Add test for Lennard-Jones / Coulomb potential + refactor by @danielhollas in #98
• Migrate Codecov from bash uploader by @danielhollas in #115
• Include ifort in test suite by @danielhollas in #111
• ERMD test by @suchanj in #120
• Fix intel test by @danielhollas in #169
• GHA: Use CODECOV_TOKEN to reduce failed uploads by @danielhollas in #170
• Add Dependabot config for GHA updates by @danielhollas in #173
• formatter: Add inline python requirements ala PEP 722 by @danielhollas in #180
• CI: Switch intel build to ifx by @danielhollas in #183
• CI: Add separate debug build with GCC 13 by @danielhollas in #187
• CI: Add fortitude linter check by @danielhollas in #202
• Update Ubuntu runners to fix CI by @danielhollas in #204
• Remove PyQT6 dependency in tsh_traj_anal.py by @danielhollas in #214
• Tweak Makefile to so that make test TEST="CMD PIGLE" works by @danielhollas in #218
• Fix GCC-9 build by @danielhollas in #226
• Update documentation for v1.2 release by @danielhollas in #228
• Preparation for v1.2 release by @danielhollas in #211

New Contributors

• @suchanj made their first contribution in #24
• @juraskov made their first contribution in #138
• @JanosJiri made their first contribution in #155
• @mbarnfield63 made their first contribution in #174
• @postulkj made their first contribution in #208

Full Changelog: v1.1-alpha...v1.2.0