Update default behavior and documentation for Drude
[namd.git] / src / Sequencer.C
2019-03-29 radakbUpdate default behavior and documentation for Drude 43/5043/2
2018-05-02 Wei JiangREST2 implementation in NAMD 88/3588/10
2018-04-24 radakbFinalize stochastic velocity rescaling implementation 49/4049/4
2018-04-20 radakbImplementation of a stochastic velocity rescaling therm... 35/4035/6
2018-02-21 Jim PhillipsClean up Projections tracing for CUDA offload 53/3753/1
2017-11-28 DavidRevert "Find upper bound available for integration... 31/3331/1
2017-11-21 David HardyFind upper bound available for integration speedup 15/3315/4
2017-11-16 David HardyComments for SOA, array interface to Random 10/3310/1
2017-11-14 David HardyAdded comments outlining AOS to SOA copying 08/3308/1
2017-11-04 DavidProfiling CUDA 9 with NVTX 93/3193/3
2017-10-06 DavidCollapsed routines for HomePatch integration loops 12/3112/1
2017-10-03 DavidPerformance improvements for POWER 94/3094/1
2016-08-26 Jim PhillipsIntegrator cleanup from Brian Radak.
2016-03-02 Jim PhillipsFrom Antti-Pekka Hynninen, multigrator pressure/tempera...
2015-03-03 Jim PhillipsImplement asynchronous replica-shared named checkpoints...
2015-02-27 Jim PhillipsTweak Drude minimization.
2015-02-27 Jim PhillipsImprove rigid bond minimization.
2015-01-30 Jim PhillipsImproved minimization for Drude.
2015-01-30 Jim PhillipsImprove and re-enable rigid bond minimization for non...
2015-01-30 Jim PhillipsDisable rigid bonds during minimization for non-Drude.
2015-01-30 Jim PhillipsTweaks to Drude minimization.
2015-01-30 Jim PhillipsEnforce rigid bonds and waters during minimization.
2015-01-30 Jim PhillipsEnforce drudeHardWall constraints during minimization.
2014-01-22 Jim PhillipsShift MIC pairlist generation to PME steps (same as...
2013-11-13 Jim PhillipsImplement atom exchange via replicaAtomSend, replicaAto...
2013-11-08 Jim PhillipsFix initial temperature and reinitvels command with...
2013-11-07 Jim PhillipsEliminate duplicate accelMD reductions in force calcula...
2013-10-30 Jim PhillipsAdd "run norepeat" command option to avoid repeating...
2013-10-11 Jim PhillipsFix TclForces and colvars with minimzer by recording...
2013-10-08 Jim PhillipsImprove minimizer stability by limiting line search...
2013-09-17 Jim PhillipsFix for hard wall constraints on Drude oscillators...
2012-11-27 Jonathan Lai(JLai - 11/27/12)
2012-06-29 Charles MatthewsBAOAB integrator added by CMatthews
2012-06-29 David HardyIncorporated Langevin BAOAB integrator from Charles...
2012-06-12 Jim PhillipsFix load measurement of patch/sequencer when broadcasts...
2012-06-05 David HardyHard wall constraints on Drude oscillators implemented...
2012-05-18 Gengbin Zhengchanges from many people:
2012-02-21 David Tannerlinear combination of pairwise overlaps (LCPO) for...
2012-02-18 Jim PhillipsAdd debugging info to "Atoms moving too fast" messages.
2011-12-22 Jim PhillipsUse priorities with Sequencer thread resumes.
2011-12-22 Jim PhillipsAllow firstTimestep to not be a multiple of stepsPerCyc...
2011-12-22 David Tannerfixing gbisPhase
2011-12-11 Johan Strumpfermodified adaptive tempering to take initial temperature...
2011-12-06 David Tanneradding CUDA support for GBIS
2011-05-21 Chao MeiAdded trace note regarding the patch id and step info...
2011-05-10 Johan StrumpferAdded adaptive tempering code
2011-03-18 Chao MeiAdded a functionality to measure namd flops using PAPI...
2011-03-17 Yi WangaMD laststep zero test
2011-03-17 Chris HarrisonRemove accelMDskip command. Add accelMDFirstStep and...
2011-03-16 Jim PhillipsImplement force trajectory output and force options...
2011-03-09 Jim PhillipsNew scalable implementation of atom map for memopt...
2011-03-09 Chris HarrisonInitial import of accelerated MD method
2010-12-05 Chris HarrisonSpelling fixes.
2010-11-30 David TannerAdding GBIS (Generalized Born Implicit Solvent) by...
2010-10-24 Chao MeiReplaced the old projection trace scheme (which is...
2010-09-15 Jim PhillipsUse block flags as group-group pairlists in CUDA kernel.
2010-06-29 Jim PhillipsMake langevin dynamics work with parallel I/O.
2010-06-09 David HardyAllow use of lone pairs outside of Drude model.
2010-03-23 Jim PhillipsPopulate atom map for drude lone pairs at start of...
2010-02-25 David WellsInitial check-in for Lowe-Andersen thermostat code...
2010-02-18 Jim PhillipsFix pressure calculation for Drude. Also moved calls...
2010-02-11 Jim PhillipsTweaks to minimizer to slowly move more atoms further...
2010-02-10 Jim PhillipsLess clever loop construct that doesn't run off the...
2010-02-10 Jim PhillipsIn early minimization, if a hydrogen group parent ...
2009-12-17 Jim PhillipsRemove extra reposition_all_lonepairs() call since...
2009-12-17 Jim PhillipsInitialize AtomMap and call reposition_all_lonepairs.
2009-12-16 David HardyCalculation routines for general lone pair sites used...
2009-08-27 Jim Phillipsadditional diagnostics
2009-03-25 Jim PhillipsMinimizer should not slowly move *fixed* atoms downhill.
2009-02-13 Jim PhillipsStart minimization by moving atoms with bad contacts...
2008-11-12 Jim PhillipsCUDA support
2008-10-21 Abhinav Bhatelechanges (ifdefed) to use performance counters on BG/P
2008-10-01 David HardyCalculate number of degrees of freedom and related...
2008-09-28 Peter FreddolinoAllow TIP4P water to get proper parameters when used...
2008-09-26 David HardyDrude water model support enabled
2008-09-18 Chris HarrisonInitial add of colvar module (Following files added...
2008-08-28 Jim Phillipsremoved lots of extra copies in reduction system
2008-08-20 Abhinav BhateleCMK_VERSION_BLUEGENE flag is being changed to CMK_BLUEG...
2008-08-20 Peter FreddolinoFix behavior of TIP4 with multiple timestepping
2008-08-04 Abhinav Bhateleadded capability for barrier every step
2008-06-05 Abhinav Bhateleadded a SimParameter lastLdbStep to stop load balancing...
2008-02-25 Peter FreddolinoAdd initial implementation of TIP4P water.
2007-03-27 Jim PhillipsChanged maxmum velocity from 10/dt to cutoff/dt since...
2006-11-14 Sameer KumarSeveral commits into NAMD for Blue Gene
2006-11-06 Sameer KumarOptimized integrate code for BGL. Replaced the outer...
2006-08-21 Jim PhillipsAdd zeroMomentum config option; enables correction...
2006-07-17 Jim PhillipsZero out velocities in files written during minimization.
2006-06-07 Jim PhillipsJustin's new pressure profile patch.
2005-10-14 Gengbin Zhengminor change to work around a compiler bug with gcc...
2005-06-24 Jim PhillipsDo reasonable things with pressure when doing pair...
2005-06-16 Jim PhillipsInclude constraint forces in total force accessed by...
2005-03-24 Jim PhillipsIntegrator optimizations.
2004-08-06 Jim PhillipsAdded lesReduceTemp and lesReduceMass options to alter...
2004-07-26 Jim PhillipsAdded updateCharges Tcl command.
2003-07-29 Justin GullingsrudFixed stupid bug in kinetic pressure profile introduced...
2003-07-28 Justin GullingsrudOops, forgot to added constant pressure support to...
2003-07-07 Justin GullingsrudUse new PPROFILE reduction in place of USER1.
2003-07-01 Jim Phillipspairlistdist adjustment, multiple pairlist regeneration...
2003-06-28 Fangqiang ZhuImplemented the "loadtotalforces" TCL command.
2003-05-30 Jim PhillipsNew order: damping, normal forces, rigid bonds, noise...
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