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Bug #2031

Bug with Parrinelo-Rahman and nstpcouple > 1

Added by Berk Hess over 3 years ago. Updated about 3 years ago.

Status:
Closed
Priority:
High
Assignee:
Category:
mdrun
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

When implementing multiple time-stepping for Parrinello-Rahman pressure coupling, we (I) forgot to increase the time step for the particle velocity scaling. Thus the coordinates were scaled correctly, but the velocities were scaled by to little by a factor 1/nstpcouple.


Related issues

Related to GROMACS - Bug #2749: Strange Fluctuations with NH+PR coupling in GROMACS 2018.3Closed

Associated revisions

Revision 971d66c1 (diff)
Added by Berk Hess over 3 years ago

Fix Parrinello-Rahman with nstpcouple>1

Fixes #2031.

Change-Id: I37cf18c40c6cf5e301d7981c9f10bbf963d8cda8

Revision 69470fc4 (diff)
Added by Berk Hess about 3 years ago

Restructure leap-frog integrators

There are now 2 template function for MD leap-frog integration
instead of 4 branches in multiple functions.
In addition to invmass, mdatoms now contains invMassPerDim.
invMassPerDim is set to zero for encode frozen dimensions, so LF
update functions no longer need to check the freeze groups.
Also removed the conditionals for vsites and shells in the LF update
functions. Their velocities are now set to zero at startup.
A template function for the most common leap-frog integrator setups
allows for full SIMD acceleration, at least for AVX with gcc5.
Changed dt from double to real in the update, since we need far less
than real precision.
Changed calculation of alpha for VV to real, as it is passed as real.

Fixed multiple time stepping with Parrinello-Rahman and Nose-Hoover.

Fixes #2031.
Fixes #2032.

Change-Id: Iae5e787f1338b99c2338c9d0c1f14e90393e9252

History

#1 Updated by Gerrit Code Review Bot over 3 years ago

Gerrit received a related patchset '1' for Issue #2031.
Uploader: Berk Hess ()
Change-Id: I37cf18c40c6cf5e301d7981c9f10bbf963d8cda8
Gerrit URL: https://gerrit.gromacs.org/6114

#2 Updated by Berk Hess over 3 years ago

  • Status changed from New to Fix uploaded

#3 Updated by Gerrit Code Review Bot over 3 years ago

Gerrit received a related patchset '8' for Issue #2031.
Uploader: Berk Hess ()
Change-Id: Iae5e787f1338b99c2338c9d0c1f14e90393e9252
Gerrit URL: https://gerrit.gromacs.org/6110

#4 Updated by Berk Hess over 3 years ago

  • Status changed from Fix uploaded to Resolved

#5 Updated by Mark Abraham about 3 years ago

  • Status changed from Resolved to Closed

#6 Updated by Berk Hess about 1 year ago

  • Related to Bug #2749: Strange Fluctuations with NH+PR coupling in GROMACS 2018.3 added

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