Patch Release 30 October 2019

Changes since patch release 19 September 2019:

  • new third_order command, a companion command to dynamical_matrix, that calculates the third order force constant tensor from finite differences, (Charles Sievers, UC Davis), PR #1690
  • add angle and Arrhenius constraints to fix bond/react, (Jake Gissinger, UC Boulder), PR #1697, PR #1713, PR #1734
  • support quasi-unique base pairing in USER-CGDNA (Oliver Henrich, U of Strathclyde), PR #1730
  • update to the Lepton library in the USER-COLVARS package, (Giacomo Fiorin, Temple U), PR #1724
  • updates to the gjf option in fix langevin to give access to either half-step or full-step velocities, (Charles Sievers, Niels Gronbech-Jensen, UC Davis), PR #1673, PR #1707, PR #1725
  • add missing option to add single impropers with the create_bonds command (Thomas Farmer, ISIS Neutron and Muon Source), PR #1706

  • add max_norm option to all minimizers and conjugate gradient and L-BFGS minimizers to the SPIN package. (Aleksei Ivanov, U of Iceland, Julien Tranchida, SNL), PR #1598
  • bugfix for pppm/tip4p when using non-orthogonal simulation cells, PR #1719
  • bugfix for restarting SPIN package runs and documentation clarification (Julien Tranchida, SNL), PR #1692
  • multiple bugfixes and documentation corrections for pair style granular (Jibril B. Coulibaly, Northwestern U), PR #1631
  • avoid correlations between multiple runs with random seeds incremented by 1 when using random placement of atoms (Jun-Chieh Wang (Applied Materials), PR #1569
  • fix a memory leak in the GPU package when doing multiple run commands in the same input, (Trung Nguyen, Northwestern U), PR #1735
  • Optimizations for using SNAP with KOKKOS (Stan Moore, SNL and Rahul Gayatri, NERSC), PR #1693
  • new examples folder “UNITS” with examples highlighting how to run inputs for the same system with different unit sets and convert output between different them (Steve Plimpton, SNL), PR #1709
  • capture return value of calls to fread by using a wrapper, utils::sfread() and thus enable error reporting on reading restarts, (Axel Kohlmeyer, Temple U/ICTP) PR #1731
  • A couple of singularity definition files to build container images for compiling/testing/debugging LAMMPS on different Linux variants, PR #1726, PR #1738
  • various small changes, updates, and bugfixes (multiple authors), PR #1701, PR #1699, PR #1716, PR #1714, PR #1727, PR #1728, PR #1733, PR #1732, PR #1746, PR #1750, PR #1744, PR #1751

Backward compatibility notice:

  • The gjf keyword for the fix langevin no longer supports yes as an option. Instead you have to use either vhalf or vfull.
  • due to changes in the random number generator initializations, results when using fix pour, fix deposit or fix evaporate and when using create_atoms random will not match with previous versions of LAMMPS. see PR #1569
  • Building the Colvars library with all features included now requires a C++11 compiler (see http://colvars.github.io/README-c++11.html).