Files
lammps/lib
Giacomo Fiorin 377c652a83 Update Colvars library to version 2023-05-01
This update consists exclusively of bugfixes or maintenance-related changes.

The following is a list of pull requests in the Colvars repository since the previous update to LAMMPS:

- 532 Add XYZ trajectory reading feature
  https://github.com/Colvars/colvars/pull/532 (@jhenin, @giacomofiorin)

- 531 Delete objects quietly, unless explicitly requested via script (including VMD)
  https://github.com/Colvars/colvars/pull/531 (@giacomofiorin)

- 530 Append newline to log and error messages if not already present
  https://github.com/Colvars/colvars/pull/530 (@giacomofiorin)

- 528 Forward-declare OpenMP lock
  https://github.com/Colvars/colvars/pull/528 (@giacomofiorin)

- 527 Remove unneeded STL container
  https://github.com/Colvars/colvars/pull/527 (@giacomofiorin)

- 526 Allow collecting configuration files and strings before setting up interface
  https://github.com/Colvars/colvars/pull/526 (@giacomofiorin, @jhenin)

- 523 Fallback to linearCombination when customFunction is missing in customColvar
  https://github.com/Colvars/colvars/pull/523 (@HanatoK, @giacomofiorin)

- 522 Use iostream::fail() to check for I/O error
  https://github.com/Colvars/colvars/pull/522 (@jhenin)

- 520 Fix ref count
  https://github.com/Colvars/colvars/pull/520 (@giacomofiorin)

- 513 Set target temperature through a common code path
  https://github.com/Colvars/colvars/pull/513 (@giacomofiorin, @jhenin)

- 509 Safer detection of Windows with recent Microsoft Visual Studio versions
  https://github.com/Colvars/colvars/pull/509 (@akohlmey)

- 508 Update LAMMPS patching method to reflect Lepton availability
  https://github.com/Colvars/colvars/pull/508 (@giacomofiorin)

- 497 Increase the precision of write_multicol
  https://github.com/Colvars/colvars/pull/497 (@HanatoK)

- 496 Only perform MTS automatic enable/disable for timeStepFactor > 1
  https://github.com/Colvars/colvars/pull/496 (@giacomofiorin)

- 493 Remove unused branch of quaternion input function
  https://github.com/Colvars/colvars/pull/493 (@giacomofiorin)

- 489 Ensure there are spaces between the fields in the header
  https://github.com/Colvars/colvars/pull/489 (@HanatoK)

- 487 Use map of output streams, and return references to its elements
  https://github.com/Colvars/colvars/pull/487 (@giacomofiorin, @jhenin)

- 486 Remember first step of moving restraint
  https://github.com/Colvars/colvars/pull/486 (@jhenin)

- 485 Add decoupling option for moving restraints
  https://github.com/Colvars/colvars/pull/485 (@jhenin)

- 483 Update Lepton via patching procedure
  https://github.com/Colvars/colvars/pull/483 (@giacomofiorin)

- 481 Make file-reading operations of input data abstractable
  https://github.com/Colvars/colvars/pull/481 (@giacomofiorin)

Authors: @akohlmey, @giacomofiorin, @HanatoK, @jhenin
2023-05-17 13:29:00 -04:00
..
2020-09-07 21:00:45 -04:00
2023-04-13 20:06:35 -04:00
2023-04-22 17:50:41 -04:00
2023-03-14 11:59:19 -04:00
2023-03-29 17:33:58 -04:00

This directory contains libraries that can be linked to when building
LAMMPS, if particular packages are included in the LAMMPS build.

Most of these directories contain code for the library; some contain
a Makefile.lammps file that points to where the library is installed
elsewhere on your system.

In either case, the library itself must be installed and/or built
first, so that the appropriate library files exist for LAMMPS to link
against.

Each library directory contains a README with additional info about
how to acquire and/or build the library.  This may require you to edit
one of the provided Makefiles to make it suitable for your machine.

The libraries in this directory are the following:

atc           atomistic-to-continuum methods, ATC package
                from Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia)
awpmd         antisymmetrized wave packet molecular dynamics, AWPMD package
                from Ilya Valuev (JIHT RAS)
colvars       collective variable module (Metadynamics, ABF and more)
                from Giacomo Fiorin and Jerome Henin (ICMS, Temple U)
compress      hook to system lib for performing I/O compression, COMPRESS pkg
                from Axel Kohlmeyer (Temple U)
gpu           general GPU routines, GPU package
                from Mike Brown (ORNL)
h5md          ch5md library for output of MD data in HDF5 format
                from Pierre de Buyl (KU Leuven)
hdnnp         hooks to n2p2, neural network potential package, used by ML-HDNNP
                from Andreas Singraber
kim           hooks to the KIM library, used by KIM package
                from Ryan Elliott and Ellad Tadmor (U Minn)
kokkos        Kokkos package for GPU and many-core acceleration
                from Kokkos development team (Sandia)
lepton        Lepton library for fast evaluation of mathematical
                expressions from a string. Imported from OpenMM.
linalg        set of BLAS and LAPACK routines needed by ATC package
                from Axel Kohlmeyer (Temple U)
mdi           hooks to the MDI library, used by MDI package
                from Taylor Barnes (MolSSI at Virginia Tech)
molfile       hooks to VMD molfile plugins, used by the MOLFILE package
                from Axel Kohlmeyer (Temple U) and the VMD development team
mscg          hooks to the MSCG library, used by fix_mscg command
                from Jacob Wagner and Greg Voth group (U Chicago)
netcdf        hooks to a NetCDF library installed on your system
                from Lars Pastewka (Karlsruhe Institute of Technology)
plugin        settings to load styles into LAMMPS from plugins
                from Axel Kohlmeyer (Temple U)
poems         POEMS rigid-body integration package, POEMS package
                from Rudranarayan Mukherjee (RPI)
python        hooks to the system Python library, used by the PYTHON package
                from the LAMMPS development team
qmmm          quantum mechanics/molecular mechanics coupling interface
                from Axel Kohlmeyer (Temple U)
quip          interface to QUIP/libAtoms framework, ML-QUIP package
                from Albert Bartok-Partay and Gabor Csanyi (U Cambridge)
machdyn       hooks to Eigen library, used by MACHDYN package
                from Georg Ganzenmueller (Ernst Mach Institute, Germany)
voronoi       hooks to the Voro++ library, used by compute voronoi/atom command
                from Daniel Schwen (LANL)
vtk           hooks to the VTK library, used by dump custom/vtk command
                from Richard Berger (JKU)