Version 2.10

Version 2.10 (under development)

This page contains changes that will end up in 2.10

Version 2.10 will be a major upgrade of PLUMED, with a lot of new features and an extensive rewrite of the core of the code. In addition, we will stop supporting older compilers. For this reason, we will likely extend the support of version 2.9 longer than usual. Before switching to version 2.10, users are invited to carefully read the following text.

  • Changes relevant for users:
    • PLUMED 2.10 requires a C++17 compatible compiler.
    • The passing of data between actions has been made more flexible. Now, in addition to passing scalars between actions, you can also pass vectors, matrices and functions computed on grids between actions. The ways in which you can use these new functionalities are detailed at this link. The old input syntax for most actions should work the same as it did in previous versions of the code. However if you investigate the log you will see that these old functionalities are reproduced by using shortcut actions that generate more complicated plumed inputs.
    • A number of functionalities in the code have been carefully optimized. An incomplete list includes grids (with an impact on METAD, sum_hills, and other grid-based methods) and overhead associated to the simulation of small systems, where the overall performance should be significantly better than in previous versions.
    • The additional flexibility comes at the price of some decrease in performance. In most cases this decrease in performance should be negligible or largely mitigated by the other optimizations that we implemented. We are very interested in feedback on PLUMED performances in real applications. If you have a real application where you can see a measurable slowdown when upgrading from version 2.9 to version 2.10, please open an issue on GitHub and report it. Ideally, you could provide a simple input file for the benchmark which highlights the performance regression.
    • It is now possible to use an embedded Python interpreter to implement collective variables and functions in Python. This is largely based on a previous implementation by Toni Giorgino that is described in this paper and has been integrated in PLUMED by Daniele Rapetti. This feature is provided as a separate plugin that can be linked against the proper Python interpreter and loaded at runtime with LOAD. Documentation about how to install and use this feature can be found in directory plugins/pycv.
    • A prototype of the COORDINATION collective variable with limited functionalities is now included in a CUDA implementation which is orders of magnitude faster when using large groups. This implementation has been contributed by Daniele Rapetti and is provided as a separate plugin that can be linked against the proper CUDA libraries and loaded at runtime with LOAD. Documentation about how to install and use this feature can be found in directory plugins/cudaCoord.
    • New CLTool plotswitch for tabulating any switching function and its derivative.
    • A new @ndx selector can be used to read GROMACS index files (see Specifying Atoms) without the need to explicitly declare a GROUP.
    • The LOAD action has been improved (see this pull request).
      • It can be used in any position in the input file.
      • It is now working properly when multiple Plumed objects are present (e.g., in multithread applications or when creating multiple Plumed() objects in Python).
  • Changes leading to differences with previous versions:
    • GHOST now automatically makes molecules whole. In case you do not want it to do it, use the NOPBC flag.
    • In ANGLES you can no longer use the GROUP, GROUPA/GROUPB/GROUPC keywords. Explicitly list all the distances you want to compute using ATOMS1,ATOMS2,ATOMS3...
    • Action NBONDS no longer exists. The same effect can be achieved through a more transparent implementation that you can read about here: https://plumed-school.github.io/lessons/23/001/data/Steinhardt.html
    • Action CENTER_OF_MULTICOLVAR no longer exists. You now simply use CENTER with the PHASES option and a vector as input for the weights.
    • Dimensionality reduction methods and landmark selection actions have a new syntax. A good introduction that explains how to use these actions can be found in this tutorial
  • Places where we strongly recommend using the new sytax:
  • Modules that were built from code taken from the old crystllization and multicolvar modules.
    • symfunc contains code for computing symmetry functions much of which was taken from the old crystallization module
    • volumes contains code for determing whether atoms are within a particular part of the box or not. This is largely built from code that was formerly in the multicolvar module
    • clusters contains code for determining if atoms are clustered together or not. This is build from code that was formerly in the crystallization module
    • gridtools contains code for doing kernel density estimation and manipulating functions on grids
    • contour contains code for computing Willard-Chandler dividing surfaces.
    • refdist contains code for calculating distances between configuations.
    • fourier contains code for computing fourier transforms of functions on grids
  • New contributed modules:
    • A new crystdistrib module by Jake McKibben, Gareth Tribello and Erik Santiso for computing order parameters that can be used to study the formation of molecular crystals.
  • Changes relevant for developers:
    • Removed some shortcuts for ActionRegister.h (from the modules bias colvar function sasa and vatom) and CLToolRegister.h (from the module cltools), now the two headers can only be included with #include "core/ActionRegister.h" or #include "core/CLToolRegister.h".
    • plumed mklib can now process more than one cpp file. Files are combined in a single library.
    • When loading PLUMED at runtime using PLUMED_KERNEL, plumed is loaded with RTLD_LOCAL by default. This facilitates running multiple PLUMED versions, e.g. for benchmark.
    • On Linux, plumed-runtime executable can now find a working libplumedKernel.so by looking in the dlopen path (including LD_LIBRARY_PATH and stored RPATH). On MacOS, plumed-runtime executable can now find a working libplumedKernel.dylib by using a relative rpath. These changes should make this executable as functional as the normal plumed executable but with the advantage of loading symbols in a local namespace (see above).
    • A new benchmark tool has been added to time execution of sample input files and facilitate the comparison across multiple PLUMED versions.
    • You can now pass any scalars, vectors, matrices and functions (and forces on these objects) in and out of PLUMED using the functionality described here: https://plumed-school.github.io/lessons/23/001/data/MDInterfaceI.html
    • You can also pass vectors that are scattered across the domains by using the functionality detailed here: https://plumed-school.github.io/lessons/23/001/data/MDInterfaceII.html
    • You can use ActionShortcut to create complex inputs from a simpler initial input. The nest will then allow users to explore these more complex inputs.
    • You can use show_graph to create diagrams showing how values and forces are passed between the various actions in your input files.
    • Complete refactor of SwitchingFunction.cpp and SwitchingFunction.h, now adding new switching function is more straightforward and all the "book-keeping" can be done within a single class
    • Python (cython) wrappers now use nogil. This should facilitate integration with Python. See https://github.com/plumed/plumed2/pull/1129#issuecomment-2410867829 (thanks to Guillaume Fraux).