Make parameter assignment args const char* and reduce strcpy
[namd.git] / src / Molecule.C
2019-05-03 Jim PhillipsMake parameter assignment args const char* and reduce... 63/5163/1
2019-03-29 radakbOptimize alchemical scaling schedule for LJcorrection 61/4961/3
2018-12-19 radakbImprove energy conservation of vdwForceSwitching/LJcorr... 69/4869/4
2018-11-05 Jim PhillipsWarn that extraBonds angles are cosine-based and allow... 63/4763/3
2018-11-01 DavidFix uninitialized variable in QM 67/4767/1
2018-09-21 David HardyDocument solute scaling parameters in user guide 93/4593/2
2018-08-31 radakbPreliminary implementation of colinear lonepairs 22/4522/4
2018-07-31 radakbFix TIP4P water models when using AMBER inputs 24/4424/2
2018-07-17 radakbFix bug for Drude systems without lonepairs 64/4364/1
2018-05-14 radakbUpdate/fix incomplete behavior of nonbondedScaling 72/4172/1
2018-05-02 Wei JiangREST2 implementation in NAMD 88/3588/10
2018-01-29 radakbFix alchemical coupling + LJcorrection 85/3585/2
2017-11-09 David HardyAutomatic detection of lonepairs 29/3129/5
2017-10-03 DavidPerformance improvements for POWER 94/3094/1
2017-08-24 Brian RadakModification of LJcorrection for vdwForceSwitching 49/2949/2
2017-07-17 David HardyMerge "Oops, fix bad path for namdcph.tcl"
2017-07-17 David HardyMerge "Actual example for constant pH using a protein...
2017-07-17 David HardyMerge "Additional example for restarting constant pH"
2017-07-17 David HardyMerge "Initial commit for constant pH (namdcph)"
2017-07-14 melomcrCombined QM/MM updates. 80/2780/6
2017-05-25 Brian RadakFix counting of LJsites for LJCorrection 51/2551/3
2017-04-02 Jim PhillipsSpeed up dihedral parameter assignment when reading... origin
2016-11-14 Jim PhillipsFrom Marcelo Melo, changes to the execution of selected...
2016-09-30 Jim PhillipsInitialize QM/MM pointers to zero to avoid crash when...
2016-09-29 Jim PhillipsQM/MM interface from Marcelo Melo.
2016-09-16 Jim PhillipsFrom Brian Radak, small fix to LJcorrection calculation.
2016-09-07 Jim PhillipsFrom Brian Radak, alchemical cleanup and disable/re...
2016-02-07 Jim PhillipsAlchemical features from Brian Radak:
2015-12-07 Jim PhillipsExplicitly cast numAtoms to double in integer overflow...
2015-12-07 Jim PhillipsFix integer overflow bug in VDW tail correction (LJcorr...
2015-12-06 Peter FreddolinoFix an interger overflow bug that gave the wrong tail...
2015-12-03 Jim PhillipsMake CUDA full exclusion checksum work across multiple...
2015-11-19 Jim PhillipsFrom Brian Radak, revert vdwForceSwitching with LJcorre...
2015-11-02 Jim PhillipsChanges from Brian Radak:
2014-08-29 Jim PhillipsFix grid forces, etc. for memopt builds.
2013-11-20 Jim PhillipsNew Go GromacsPair implementation from Jonathan Lai.
2013-08-23 Jim PhillipsMore error checking for rigid water H-H distance determ...
2013-01-16 Jonathan LaiCommit version to update GromacsTopFile.C such that...
2012-12-31 Jim PhillipsEliminate variable-sized arrays.
2012-11-27 Jonathan Lai(JLai - 11/27/12)
2012-09-28 Jim PhillipsFix bug in fixedAtomListFile reader.
2012-08-21 Jim PhillipsAdd ignoreMass option, off by default, to not assume...
2012-08-21 Jim PhillipsFix implicit exclusions for Gromacs topology files.
2012-08-21 Jim PhillipsPrint number of implicit exclusions generated.
2012-08-07 Jim PhillipsEnable harmonic constraints for memory optimized builds...
2012-05-16 David HardyMolecule::assignLCPOType checks for Drude or LP and...
2012-05-15 David TannerLCPO types only calculated when LCPO is on
2012-03-17 Jim PhillipsProper fix to keep Go forces from breaking alchemical...
2012-03-14 David Tanneradding Amber structure support to LCPO
2012-03-08 Chris HarrisonBeginning initial integration of NAMD-OPENATOM QM/MM...
2012-02-23 David Tannermade LCPO a little faster and more robust
2012-02-22 Jim PhillipsEliminate variable-size array.
2012-02-21 Chao MeiFixed compilation errors regarding function assignLCPOT...
2012-02-21 David Tannerlinear combination of pairwise overlaps (LCPO) for...
2012-02-17 Jim PhillipsGo forces implementation from Jonathan Lai.
2012-01-28 Jim PhillipsUse fseeko instead of repeating fseek and add return...
2011-12-02 David WellsAdded Gridforce Lite feature, which uses a linear inter...
2011-08-02 David HardyFixed bug: create support arrays for Thole and aniso...
2011-06-16 Jim PhillipsModify extraBonds to allow sinusoidal dihedrals and...
2011-05-04 Jim PhillipsMake CUDA and memopt compatible.
2011-03-08 Jim PhillipsAdd printExclusions option to print exclusion lists...
2011-03-01 Jim PhillipsNot a bug, but support possibility of RIGID_NONE in...
2011-02-09 David WellsGridforce: Removed Charm++-based memory optimization...
2011-02-03 Chris HarrisonAdds output of atom indices to 'missing parameters...
2010-12-16 Jim PhillipsExclude from non-memopt build to not crash Mac PPC...
2010-12-14 David WellsInitial check-in of multi-resolution gridforce.
2010-11-13 Chao MeiA completely fresh implementation of Parallel IO implem...
2010-09-27 David HardyEnsure Drude and LP inherit modified 1-4 exclusion...
2010-09-23 David Hardymodified 1-4 interactions should not be treated as...
2010-09-20 David Hardyadded some comments regarding PSF format for Drude...
2010-08-05 Jim PhillipsKeep lame ancient MacOSX-PPC compiler from crashing.
2010-08-05 Jim PhillipsImprove warnings about ignored missing angle and dihedr...
2010-08-04 Jim PhillipsIgnore (but warn about) missing angle and dihedral...
2010-07-05 Jim PhillipsAdd warnings about LJcorrection and vdwForceSwitching...
2010-06-29 Jim PhillipsMake langevin dynamics work with parallel I/O.
2010-06-10 David Hardyfixed some latent bugs in build_inherited_excl() and...
2010-06-09 David HardyAllow use of lone pairs outside of Drude model.
2010-04-26 Jim PhillipsRemove useless NAMD_die for large exclusion check array...
2010-04-26 Jim Phillipsfix extra bonds
2010-04-24 Osman SaroodParallel IO index change
2010-04-24 Osman SaroodParallelIO correction for Index change
2010-04-23 Osman SaroodParallelIO Checkin
2010-03-30 David Hardyfixed compilation error for building memopt version
2010-03-29 David Hardymake sure that there are waters in a Drude or flucQ...
2010-03-24 David Hardyfixed bug in intializing constants for SWM4 rigid water
2010-03-19 Jim PhillipsUpdate molfile plugins.
2010-03-10 Jim PhillipsFix bugs.
2010-03-10 Chao MeiEncoded the atom's vdw_type (an index) into per-atom...
2010-03-04 Jim PhillipsDon't strip exclusions internal to hydrogen groups...
2010-02-17 Jim PhillipsOnly print lone pairs zero-mass warning on pe 0.
2010-02-10 David Hardyfix accidental breakage of tip4p
2010-02-05 Jim PhillipsFix compressed psf for migration groups. Only binary...
2010-02-04 Jim PhillipsUse migration groups based on lone pair hosts rather...
2010-02-03 Jim PhillipsEliminate global sorting with waters last and rename...
2010-01-24 David Hardyfor Drude model, don't count bonds to LPs as rigid...
2010-01-23 David HardyFixed a bug in counting rigid bonds (that I inadvertent...
2010-01-22 David HardyCan now set quartic restraints on Drude bonds to keep...
2010-01-20 David HardyPermit generalized lone pairs for Drude model
2010-01-19 David HardyFinished infrastructure for calculating anisotropic...
2010-01-19 David HardyInitialize numTholes and numCalcTholes to 0
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