Add support for Lennard-Jones PME to 'energy' command. #666
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added 29 commits
February 7, 2019 15:19
…en LJ Ewald parameter is negative.
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The PR of the beast! |
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added 8 commits
February 15, 2019 09:34
… performance by putting common energy kernels in include files.
…mproves the speed of the direct space calc for cases where e.g. the lj pme part is not needed.
…t it when debug info is on.
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This PR adds support for calculating LJ energy via PME - as with electrostatic PME the reciprocal part of the energy is handled by the HelPME library from Andy Simmonett (@andysim). Adds the following keywords to
energy:ljpme: Activates Lennard-Jones PME with default Ewald coefficient (0.4) - this is separate from the coefficient used for electrostatics.
ewcoefflj : Activates Lennard-Jones PME with given Ewald coefficient.
ljswidth : If specified, Lennard-Jones (PME or non-PME) will be determined using a switching function with given width.
The energy is properly corrected for Lorentz-Berthelot combining rules. Tested against the LJ PME energies output by CHARMM (implemented by Andy). The code could use some cleaning and optimization but it works.
This also implements a new command,
catcrd, which can be used to concatenate COORDS data sets:This command proved very useful when testing the LJ PME implementation.
Also fixes bug where box was not being updated for COORDS data sets after using
boxcommand.Adds tests for LJ PME and
catcrd.