CVS analysis' parameters 
Project module namevmd
CVS root used/home/cvs/vmd/cvsroot
Range analysisMain Branch (HEAD)
Date analysis2022-01-20 02:31 (Built in 108s)
CVS report for module 'vmd' built by cvschangelogbuilder 2.3 (build 1.76) with option buildhtmlreport.
Summary   Lines of code   Developers activity   Days of week   Hours  Tags  Last commits  

 
SummaryTop 
Current status indicatorsValue  
Files currently in repository 950 
Lines of code currently in repository (on non binary files only) 472935 
Activity indicatorsFrom startThis monthToday
Number of developers 2610
Number of commits3753910
Number of commits by status 1351 to add new file
35787 to change existing file
401 to remove file 
1 to change existing file
 
 
Different files commited 132910
Lines added / modified / removed (on non binary files only) +673335 / 292108 / -200400+0 / 1 / -0+0 / 0 / -0
Last commit 2022-01-132022-01-13 

 
Lines of code*Top 
This chart represents the balance between number of lines added and removed in non binary files (source files).
 
 

 
Developers activity*Top 
DeveloperNumber of commitsDifferent files commitedLines*
(added, modified, removed)
Lines by commit*
(added, modified, removed)
Last commit 
johns241291286412321 / 181266 / 10310417 / 7.5 / 4.22022-01-13 23:31 
justin720868065345 / 38338 / 765679 / 5.3 / 10.62003-08-29 23:53 
billh164035871754 / 20025 / 365843.7 / 12.2 / 2.21996-04-10 04:57 
dalke135430657277 / 14001 / 521542.3 / 10.3 / 3.81998-09-11 15:17 
saam8544017267 / 14555 / 437120.2 / 17 / 5.12011-06-20 18:26 
pgrayson5141246934 / 2388 / 52513.4 / 4.6 / 12002-06-26 18:46 
jordi4691207001 / 3656 / 89514.9 / 7.7 / 1.92007-10-26 21:04 
sergei4563545952 / 6156 / 79913 / 13.5 / 1.71998-09-24 04:47 
danorris180495092 / 3518 / 173828.2 / 19.5 / 9.62001-11-30 18:24 
eamon133461011 / 1359 / 2697.6 / 10.2 / 22004-05-26 19:03 
ulrich98626225 / 393 / 5063.5 / 4 / 0.51997-05-15 06:06 
dhardy9385166 / 1350 / 210155.5 / 14.5 / 22.52010-06-10 22:36 
brendanbc172171095 / 1034 / 10515.2 / 14.3 / 1.42018-05-11 16:59 
kvandivo7216928 / 526 / 1212.8 / 7.3 / 0.12014-12-18 00:16 
khamer55172375 / 343 / 1243.1 / 6.2 / 0.21995-06-05 16:00 
leech52362540 / 750 / 1648.8 / 14.4 / 0.31996-11-22 02:54 
barryi44141869 / 1675 / 13042.4 / 38 / 2.92003-08-07 03:40 
akohlmey4426920 / 214 / 19420.9 / 4.8 / 4.42011-12-06 05:04 
ryanmcgreevy318964 / 214 / 61931 / 6.9 / 19.92019-07-22 19:27 
reeves1515801 / 461 / 1953.4 / 30.7 / 1.21996-12-20 08:02 
ltrabuco137206 / 114 / 115.8 / 8.7 / 02009-12-06 21:28 
bishop86299 / 26 / 037.3 / 3.2 / 01995-10-20 00:09 
johns22251 / 131 / 025.5 / 65.5 / 01998-05-30 00:59 
brunner111 / 3 / 01 / 3 / 02009-06-15 21:33 
johanstr110 / 3 / 00 / 3 / 02011-12-02 23:10 
petefred110 / 2 / 00 / 2 / 02006-09-26 23:17 

                   


 
Activity by days of weekTop 


 
Activity by hoursTop 


 
Last tags by dateTop 
DateFull dateTags 
2020-05-222020-05-22 05:54linenoise-char-at-a-time 
2020-05-212020-05-21 22:00linenoise-line-at-a-time 
2019-06-052019-06-05 05:32vmd-first-python3 
2019-05-222019-05-22 18:47vmd-last-python2 
2019-03-122019-03-12 20:06raytracinggems2019 
2018-08-282018-08-28 17:23siggraph2018 
2018-03-222018-03-22 03:52gtc2018-segprofile-final 
2018-03-072018-03-07 19:26gtc2018-seggigavoxels 
2018-03-022018-03-02 05:04gtc2018-segprofile 
2016-12-012016-12-01 05:40vmd-1-9-3 
2015-09-202015-09-20 20:56vr2016 
2014-12-302014-12-30 05:45vmd-1-9-2 
2014-11-082014-11-08 06:52quicksurf-globalization 
2014-11-072014-11-07 19:02sc2014-demos 
2013-10-112013-10-11 21:29ultravis2013 
2012-02-022012-02-02 04:15vmd-1-9-1 
2011-06-162011-06-16 15:40removeidxdispcmds 
2011-06-162011-06-16 02:25atomselrange 
2011-03-142011-03-14 17:54vmd-1-9-0 
2011-01-182011-01-18 15:32lastorbifdefs 
2009-11-052009-11-05 22:29msmpot-nonperiodic 
2009-08-072009-08-07 06:08vmd-1-8-7 
2009-04-292009-04-29 15:43hpg2009-submit 
2009-02-252009-02-25 01:28volmap-ils-estatics-orig 
2009-02-112009-02-11 00:44gpgpu-2009-final 
2008-12-032008-12-03 00:33qm-nosorting-1 
2007-05-142007-05-14 22:00cuda-0-8-0 
2007-04-052007-04-05 18:21vmd-1-8-6 
2006-08-262006-08-26 05:33vmd-1-8-5 
2006-04-172006-04-17 07:41vmd-1-8-4 
2005-02-162005-02-16 06:07vmd-1-8-3 
2003-12-052003-12-05 19:09vmd-1-8-2 
2003-06-152003-06-15 18:32vmd-1-8-1 
2002-12-092002-12-09 05:44vmd-1-8-0 

 
Last commit logsTop 
TagsDateDeveloperLast 200 Commit Logs
 2022-01-13johnsCorrected test and scoping for enabling the use of Address Sanitizer with
GCC and Clang based compilations
* configure 1.1535 (changed +1 -1)
 2021-12-22johnsSpecify color table constants as single-precision literals to eliminate
MSVS compiler warnings.
* src/ColorScaleTables.h 1.4 (changed +6145 -6145)
 2021-12-21johnsAdd explicit type conversions for SPHERETUBE primitives to eliminate
compiler warnings.
* src/MoleculeGraphics.C 1.89 (changed +17 -17)
Added explicit type conversion to eliminate compiler warnings.
* src/OptiXRenderer.C 1.391 (changed +7 -7)
* src/OSPRayRenderer.C 1.92 (changed +4 -4)
Added explicit typecast to eliminate compiler warning
* src/Win32OpenGLDisplayDevice.C 1.130 (changed +2 -2)
* src/TachyonDisplayDevice.C 1.134 (changed +2 -2)
* src/Scene.C 1.100 (changed +2 -2)
Added explicit typecast to eliminate compiler warnings
* src/OpenGLShader.C 1.33 (changed +3 -3)
* src/OpenGLRenderer.C 1.478 (changed +2 -2)
Added explicit typecast to silence compiler warnings.
* src/ColorFltkMenu.C 1.46 (changed +3 -1)
Added explicit typecasts to eliminate compiler warnings.
* src/CUDAMDFF.cu 1.84 (changed +15 -15)
Added placeholder set_window_title() method
* src/Win32OpenGLDisplayDevice.C 1.129 (changed +7 -1)
Corrected assignment of "maxDepth", to use ospSet1i().
Improve floating point consistency.
* src/OSPRayRenderer.C 1.91 (changed +10 -10)
Corrected window parameter typecasts
* src/glwin.c 1.34 (changed +2 -2)
* src/Win32OpenGLDisplayDevice.C 1.131 (changed +2 -2)
Eliminated a C++ism from type conversion
* src/glwin.c 1.35 (changed +2 -2)
Improve floating point consistency
* src/OptiXRenderer.C 1.390 (changed +4 -4)
* src/OptiXDisplayDevice.C 1.86 (changed +3 -3)
* src/OSPRay2Renderer.C 1.35 (changed +8 -8)
* src/FastPBC.C 1.4 (changed +8 -8)
* src/ColorFltkMenu.C 1.45 (changed +4 -4)
* src/CUDAQuickSurf.cu 1.97 (changed +2 -2)
* src/CUDAFastPBC.cu 1.8 (changed +5 -5)
Improved floating point consistency
* src/glwin.c 1.33 (changed +15 -15)
* src/OSPRayDisplayDevice.C 1.19 (changed +2 -2)
* src/FastPBC.C 1.5 (changed +3 -3)
 2021-12-20johnsAdd explicit type conversion to silence MSVS warning.
* src/CUDAMeasureQCP.cu 1.37 (changed +2 -2)
Corrected flawed condition syntax that yielded inconsistent intermediate
types. Improved floating point consistency.
* src/CUDAMDFF.cu 1.83 (changed +3 -3)
Improve floating point consistency
* src/CUDAOrbital.cu 1.119 (changed +2 -2)
 2021-12-18johnsRevised ANARI renderer implementation to more closely track the provisional
spec, but maintain the use of some extensions for particular renderers
for the purposes of rendering of high production value images for
the ANARI manuscript in the short term.
* src/ANARIRenderer.C 1.26 (changed +36 -19)
 2021-12-13johnsHardened the VMD FileRenderList startup and renderer registration
code for Intel OSPRay to ensure that any OSPRay initialization
failures don't crash VMD. This should handle both insufficient
CPU instruction set extensions as well as runtime errors that have
been observed with loading of the ISPC shared libs on Windows systems.
* src/OSPRayRenderer.h 1.36 (changed +2 -2)
* src/OSPRayRenderer.C 1.90 (changed +10 -4)
* src/OSPRayDisplayDevice.h 1.19 (changed +2 -2)
* src/OSPRayDisplayDevice.C 1.18 (changed +3 -3)
* src/OSPRay2Renderer.h 1.12 (changed +2 -2)
* src/OSPRay2Renderer.C 1.34 (changed +8 -3)
* src/OSPRay2DisplayDevice.h 1.5 (changed +2 -2)
* src/OSPRay2DisplayDevice.C 1.5 (changed +2 -2)
* src/FileRenderList.C 1.111 (changed +10 -5)
* src/FileRenderList.C 1.110 (changed +12 -8)
Updated OSPRay 2.x build rules to use OSPRay 2.8.0 by default
* configure 1.1534 (changed +2 -2)
 2021-12-12johnsUpdated default ANARI path for early public SDK structure.
* configure 1.1533 (changed +2 -2)
 2021-12-08johnsUpdated ANARI to default to the "example" device after renaming.
* src/ANARIRenderer.C 1.25 (changed +6 -6)
 2021-12-03johnsAdded QwikFold placeholder to the script that populates the extensions menu
during VMD startup
* scripts/vmd/loadplugins.tcl 1.57 (changed +2 -1)
Enable qwikfold for testing
* scripts/vmd/loadplugins.tcl 1.58 (changed +2 -2)
Sync w/ colvars git repo version 6d97a4339092d4f04f0dee0bf91c66cafc3bc406
* src/colvartypes.h 1.13 (changed +3 -0)
* src/colvartypes.C 1.12 (changed +11 -5)
* src/colvarscript_commands_colvar.C 1.2 (changed +4 -0)
* src/colvarscript_commands_bias.C 1.2 (changed +4 -0)
* src/colvarscript_commands.C 1.3 (changed +5 -0)
* src/colvars_version.h 1.18 (changed +1 -1)
* src/colvarproxy_volmaps.C 1.4 (changed +2 -2)
* src/colvarproxy_vmd_version.h 1.14 (changed +1 -1)
* src/colvarproxy_tcl.C 1.3 (changed +7 -0)
* src/colvarproxy.h 1.23 (changed +22 -5)
* src/colvarproxy.C 1.13 (changed +67 -9)
* src/colvarparams.C 1.2 (changed +1 -1)
* src/colvarmodule_refs.h 1.2 (changed +37 -35)
* src/colvargrid.h 1.23 (changed +6 -0)
* src/colvargrid.C 1.14 (changed +1 -0)
* src/colvardeps.h 1.14 (changed +1 -1)
* src/colvarcomp_volmaps.C 1.4 (changed +2 -2)
* src/colvarcomp_rotations.C 1.15 (changed +28 -37)
* src/colvarcomp_protein.C 1.13 (changed +4 -14)
* src/colvarcomp_gpath.C 1.4 (changed +7 -4)
* src/colvarcomp_distances.C 1.24 (changed +25 -23)
* src/colvarcomp_coordnums.C 1.14 (changed +5 -5)
* src/colvarcomp_apath.C 1.3 (changed +2 -2)
* src/colvarcomp_angles.C 1.12 (changed +18 -35)
* src/colvarcomp_alchlambda.C 1.2 (changed +56 -6)
* src/colvarcomp.h 1.18 (changed +33 -1)
* src/colvarcomp.C 1.21 (changed +31 -3)
* src/colvarbias_meta.C 1.21 (changed +2 -1)
* src/colvarbias_abf.C 1.24 (changed +3 -2)
* src/colvarbias.C 1.21 (changed +2 -2)
* src/colvaratoms.C 1.27 (changed +1 -1)
* src/colvar.h 1.20 (changed +1 -0)
* src/colvar.C 1.31 (changed +48 -51)
 2021-12-02johnsAdded two better designed fallback cases for VMD initialization on
Windows systems, to set the temporary directory if TMPDIR is unset
at startup.
* scripts/vmd/vmdinit.tcl 1.155 (changed +8 -2)
 2021-11-18johnsWrite atomic element and chain fields to the PDB input for Stride/DSSP
since the latest versions of DSSP require these to be present.
* src/Stride.C 1.51 (changed +25 -11)
 2021-11-12johnsAdded use of ptrdiff_t types for key voxel indexing arithmetic, to enable
QuickSurf density map generation for volumes containing more than 2 billion
voxels, such as the SARS-CoV-2 Delta Aerosol visualization..
* src/QuickSurf_NEON.C 1.2 (changed +4 -4)
* src/QuickSurf_AVX2.C 1.10 (changed +3 -3)
* src/QuickSurf.C 1.135 (changed +14 -9)
 2021-11-11johnsApplied Josh Vermaas' patch to ensure that VMD parses all possible
keywords for file writing operations passed by Molecule.py
* src/py_molecule.C 1.83 (changed +7 -6)
 2021-11-05johnsInhibit the "interactive" ANARI renderer from showing up as an option
when the USD back-end has been enabled.
* src/FileRenderList.C 1.109 (changed +2 -2)
Updated the ANARI renderer to allow the user to specify the behavior of
the USD back-end interface at runtime, including whether or not to
emit USD as local files or to make a network connection to an Omniverse
server, the root level USD path to use for exporting sessions, and
to select binary or ASCII USD formatting.
* src/ANARIRenderer.C 1.24 (changed +13 -8)
 2021-11-04johnsEnsure that DSSP emits verbose output if issues arise.
* src/Stride.C 1.50 (changed +2 -2)
Fixes for parsing issues with some versions of mkdssp.
* src/Stride.C 1.49 (changed +3 -3)
 2021-10-29johnsCleaned up unused local variables.
* src/TclFastPBC.C 1.5 (changed +5 -9)
Ensure spaces are preserved between compiler flags.
* configure 1.1532 (changed +2 -2)
Ensure zero-initialization of atomicnumfactor_4 regardless of state variables.
* src/QuickSurf.C 1.134 (changed +3 -3)
Replaced old Purify-based memory checking build rules with modern
Address Sanitizer based checking.
* configure 1.1531 (changed +8 -17)
Revised the ANARI FileRenderer subclass to ensure that VMD representations
lead to unified instance/group nodes containing all of the
surfaces, geometry, and materials that make up the representation.
* src/ANARIRenderer.h 1.14 (changed +7 -1)
* src/ANARIRenderer.C 1.23 (changed +121 -6)
Short-term workaround to prevent a crash that can occur at the
start of the vectorized texture map accumulation code, likely due
to memory alignment limitations.
* src/QuickSurf_AVX2.C 1.9 (changed +2 -2)
 2021-10-28johnsUpdated the per-representation comment DisplayList DCOMMENT token generation
code for complete coverage of reps, and the current rep names.
The comment token will be used to populate graphical interfaces that
show the structure of the molecular scene graph.
* src/DrawMolItemVolume.C 1.183 (changed +5 -1)
* src/DrawMolItemSurface.C 1.46 (changed +4 -1)
* src/DrawMolItemRibbons.C 1.157 (changed +6 -3)
* src/DrawMolItemOrbital.C 1.53 (changed +2 -2)
* src/DrawMolItemNanoShaper.C 1.8 (changed +6 -1)
* src/DrawMolItemMSMS.C 1.52 (changed +4 -1)
* src/DrawMolItem2.C 1.40 (changed +8 -1)
* src/DrawMolItem.C 1.374 (changed +6 -3)
 2021-10-25johnsEliminated completion side of Axes comment buffer output so that all
comment buffers are tagged at start only.
* src/Axes.C 1.76 (changed +2 -6)
Eliminated old sphere-specific workaround code path for the ANARI USD back-end.
The current code attempts to honor the provisional spec APIs, so the workaround
scheme is no longer needed, albeit there are still limitations on the
Omniverse side unrelated to VMD itself. Added USD naming for the top level
ANARI world object created by VMD, and began working on minimizing the
number of cases were USD would generate an empty session.
* src/ANARIRenderer.C 1.21 (changed +37 -73)
Made the comment buffer output for the reps considerably briefer for
better use within the ANARI USD namespace and other scene tree browser
displays that break down the scene components into groups of geometry,
instances, etc.
* src/DrawMolItemVolume.C 1.182 (changed +3 -5)
* src/DrawMolItemRings.C 1.29 (changed +3 -5)
* src/DrawMolItemRibbons.C 1.156 (changed +3 -5)
* src/DrawMolItemQuickSurf.C 1.26 (changed +2 -3)
* src/DrawMolItemOrbital.C 1.52 (changed +2 -3)
* src/DrawMolItem.C 1.373 (changed +14 -27)
Updated ANARI material handling code to more gracefully adapt to different
renderer subtypes and their associated limitations.
* src/ANARIRenderer.h 1.13 (changed +10 -3)
* src/ANARIRenderer.C 1.22 (changed +58 -68)
Updated the ANARI renderer implementation to use more narrowly defined
ANARI_ARRAY1D types for the geometry array API calls. Updated the geometry
subtype and parameter strings to bring them in sync with the ANARI
provisional spec.
* src/ANARIRenderer.h 1.12 (changed +0 -0)
* src/ANARIRenderer.C 1.20 (changed +21 -27)
 2021-10-24johnsContinued updates to bring VMD in sync with the ANARI provisional
specification and recent back-end renderer updates.
* src/ANARIRenderer.h 1.11 (changed +2 -1)
* src/ANARIRenderer.C 1.19 (changed +58 -16)
 2021-10-22johnsAdded support for new USD back-end, and updated framebuffer format
configuration to the current provisional spec.
* src/ANARIRenderer.C 1.18 (changed +44 -6)
 2021-10-20johnsEliminated Python startup warning reported by Josh Vermaas
* python/Molecule.py 1.32 (changed +3 -3)
Protect DSPHERE display list token RTRT processing code with a new scope
to prevent leaking of variables and state into the parent scope, and to
ensure successful compilation with the most recent revs of GCC which are less
permissive about skipped initialization scenarios.
* src/OptiXRenderer.C 1.389 (changed +3 -2)
 2021-10-19johnsCranked version
* configure 1.1530 (changed +1 -1)
 2021-10-08johnsAdded OpenGL background color state softcopy tracking to facilitate
correct state tracking when we enter/leave full-time RTX RTRT mode.
* src/OptiXDisplayDevice.C 1.85 (changed +8 -7)
* src/OpenGLRenderer.h 1.154 (changed +2 -1)
* src/OpenGLRenderer.C 1.477 (changed +62 -27)
Added support for lone DCYLINDER and DSPHERE display command tokens in the
full-time RTX RTRT display mode.
* src/OptiXRenderer.C 1.388 (changed +52 -1)
Roll OptiX PTX compute capability back to SM 5.0 for a while longer,
at lest for non-RTX RTRT builds.
* configure 1.1529 (changed +1 -1)
Updated to Colvars version 1f1c3c32dcd2cf9fba9457514ce63bf284271fa9.
* src/colvarmodule_refs.h 1.1 (added +539 -0)
* src/colvarcomp_alchlambda.C 1.1 (added +61 -0)
* src/colvarbias_histogram_reweight_amd.h 1.1 (added +109 -0)
* src/colvarbias_histogram_reweight_amd.C 1.1 (added +398 -0)
 2021-10-07johnsAdded support for modulation of the NewCartoon representation thickness
by user-specified per-atom fields, following the existing approach already
implemented for VDW and NewRibbons representations.
* src/DrawMolItemRibbons.C 1.155 (changed +51 -11)
Cranked version
* configure 1.1528 (changed +1 -1)
* configure 1.1527 (changed +1 -1)
Updated README
* README 1.413 (changed +3 -1)
Updated to Colvars version 1f1c3c32dcd2cf9fba9457514ce63bf284271fa9.
* src/colvarvalue.h 1.13 (changed +5 -17)
* src/colvarvalue.C 1.15 (changed +89 -62)
* src/colvarscript_commands.h 1.4 (changed +8 -0)
* src/colvarscript.h 1.14 (changed +0 -12)
* src/colvarscript.C 1.26 (changed +35 -4)
* src/colvars_version.h 1.17 (changed +1 -1)
* src/colvars_files.pl 1.7 (changed +4 -0)
* src/colvarproxy_vmd_version.h 1.13 (changed +1 -1)
* src/colvarproxy_vmd.C 1.23 (changed +12 -0)
* src/colvarproxy_tcl.h 1.3 (changed +6 -0)
* src/colvarproxy_tcl.C 1.2 (changed +2 -0)
* src/colvarproxy.h 1.22 (changed +40 -11)
* src/colvarproxy.C 1.12 (changed +173 -7)
* src/colvarparse.h 1.14 (changed +2 -2)
* src/colvarparse.C 1.17 (changed +6 -6)
* src/colvarmodule_utils.h 1.2 (changed +2 -0)
* src/colvarmodule.h 1.31 (changed +37 -5)
* src/colvarmodule.C 1.30 (changed +157 -18)
* src/colvargrid.h 1.22 (changed +69 -6)
* src/colvargrid.C 1.13 (changed +92 -1)
* src/colvardeps.h 1.13 (changed +4 -0)
* src/colvardeps.C 1.17 (changed +15 -15)
* src/colvarcomp_volmaps.C 1.3 (changed +5 -3)
* src/colvarcomp_rotations.C 1.14 (changed +1 -1)
* src/colvarcomp_coordnums.C 1.13 (changed +1 -0)
* src/colvarcomp.h 1.17 (changed +28 -8)
* src/colvarcomp.C 1.20 (changed +4 -1)
* src/colvarbias_restraint.C 1.18 (changed +8 -0)
* src/colvarbias_meta.h 1.13 (changed +7 -2)
* src/colvarbias_meta.C 1.20 (changed +134 -84)
* src/colvarbias_histogram.C 1.13 (changed +1 -0)
* src/colvarbias_alb.C 1.16 (changed +1 -0)
* src/colvarbias_abf.C 1.23 (changed +33 -19)
* src/colvarbias.C 1.20 (changed +5 -1)
* src/colvaratoms.h 1.16 (changed +3 -0)
* src/colvaratoms.C 1.26 (changed +18 -1)
* src/colvar_UIestimator.h 1.8 (changed +9 -7)
* src/colvar.h 1.19 (changed +2 -1)
* src/colvar.C 1.30 (changed +94 -23)
 2021-10-05johnsApplied Josh Vermaas' corrections to the built-in FastPBC implementation,
replacing the FastPBC unwrapping algorithm with a corrected displacement
method based on von Bulow's displacement algorithm.
* src/TclFastPBC.C 1.4 (changed +37 -67)
* src/FastPBC.C 1.3 (changed +26 -4)
* src/CUDAFastPBC.cu 1.7 (changed +129 -111)
Continued unification and optimization of the QuickSurf density/texture
kernels for multiple texture formats. Changed QuickSurf memory allocation
routines to track and incorporate the texture format in its calculations so
that it can be changed on-demand by the user's surface quality preference
at runtime.
* src/CUDAQuickSurf.h 1.10 (changed +2 -1)
* src/CUDAQuickSurf.cu 1.95 (changed +47 -25)
Tied runtime QuickSurf texture format selection to the user-specified
surface quality parameter assigned when the representation is computed.
* src/QuickSurf.C 1.133 (changed +17 -2)
* src/CUDAQuickSurf.h 1.11 (changed +3 -2)
* src/CUDAQuickSurf.cu 1.96 (changed +3 -3)
Updated ORNL Summit build configuration for CUDA 11.0.3, removed compilation
support for Kepler GPUs of compute capability 3.0 (now more than 10 years old),
and updated the OptiX ray tracing engine shader generation to use
compute capability 6.0 as the PTX targeting Pascal and later generation GPUs.
* configure 1.1526 (changed +7 -5)
 2021-09-24johnsUpdated the ANARI renderer to use the accumulation buffer, and run
multiple passes, since we don't standardize the meaning of sample count
parameters among renderers presently.
* src/ANARIRenderer.C 1.17 (changed +16 -41)
 2021-09-23johnsAdd explicit type conversion to please Clang.
* src/Measure.C 1.153 (changed +3 -3)
Added explicit type conversion to please Clang.
* src/TclMeasure.C 1.185 (changed +2 -2)
Added explicit type conversions to please Clang
* src/utilities.C 1.177 (changed +4 -4)
Corrected struct/class consistency
* src/HMDMgr.h 1.6 (changed +3 -3)
Corrected the behavior of Stack::clear() to ensure that the curr pointer
is reset correctly.
* src/Stack.h 1.30 (changed +2 -1)
Ensure that the colorscale posterization flag is initialized in the
constructor.
* src/Scene.C 1.99 (changed +2 -1)
Major revision of ANARI renderer subclass to sync up with the ANARI
provisional API and associated SDK updates. The updated implementation
isn't using the accumulation buffer yet and various other aspects of
object ownership and lifecycle still need cleanup. The current code isn't
handling the newly required interactions between the ANARIFrame object and
its required parameters in a graceful way. The code needs some refactoring
to better support the new object dependency graph associated with the
updated API.
* src/ANARIRenderer.h 1.10 (changed +18 -18)
* src/ANARIRenderer.C 1.16 (changed +395 -273)
VMD previously assumed that all python objects that can be read by
PyLong_FromLong pass the PyLong_Check test.
In Python 2, this was true, but in Python 3, numpy.int32 or numpy.int64
datatypes can be validly converted into python integers, but don't pass
PyLong_Checks.
Trying to do something relatively innocuous, setting resids for a
selection to a numpy array, was failing with the old Python 2 type approach:
values = np.cumsum(np.ones(len(sel)))
sel.resid = values
With the revised implementation, this now works correctly with Python 3.
* src/py_commands.C 1.23 (changed +12 -7)
 2021-09-21johnsBack-ported some CUDA kernel optimizations from the QuickSurf RGB4U
code path to the RGB3F code path. Ultimately these kernels should end
up being unified using templates.
* src/CUDAQuickSurf.cu 1.93 (changed +19 -19)
Fixed a bug in handling of user-specified isovalues for non-color-per-atom
mode (e.g. ColorID) in the CUDA QuickSurf code path.
* src/CUDAQuickSurf.cu 1.92 (changed +3 -3)
Simplified QuickSurf RGB3F kernel loops with some operator overloading.
* src/CUDAQuickSurf.cu 1.94 (changed +22 -15)
 2021-08-24johnsDisabled check/warning for the X11 Composite extension since all of the
newer distros have turned it on by default, and conventional planar
stereoscopic displays are all but gone from the face of the earth
at this point. Those rare sites that still have stereo displays will
know that they can't use one of the compositing window managers
and/or they will have system software that works correctly in such a case.
* src/OpenGLDisplayDevice.C 1.217 (changed +3 -1)
Eliminated check for the X11 composite extension when using off-screen Pbuffers.
* src/OpenGLPbufferDisplayDevice.C 1.29 (changed +1 -23)
 2021-06-18johnsCranked version
* configure 1.1525 (changed +1 -1)
 2021-05-14johnsAdded OptiX 6 based implementation of full-time RTRT rendering mode back end.
The new OptiX 7 version of Tachyon will end up being significantly more
efficient with caching and tracking of existing command list buffers
and other data in GPU-resident data structures, but this is a usable
placeholder implementation albeit the various holdovers from its
more offline-oriented original design. The new code adds methods to
aggregate materials, and command list buffers into a complete scene
description, and to efficiently render it.
* src/OptiXRenderer.h 1.133 (changed +18 -1)
* src/OptiXRenderer.C 1.387 (changed +269 -1)
Added code to generate molecular representations using cylinder array
primitives, especially for use in RTRT rendering modes.
* src/DrawMolItem.C 1.372 (changed +51 -3)
Added cylinder array display primitives which are far higher in performance
when using full-time RTRT display mode.
* src/DispCmds.h 1.121 (changed +36 -2)
* src/DispCmds.C 1.121 (changed +36 -1)
Added default handler for cylinder array primitive needed for better
full-time RTRT performance.
* src/FileRenderer.h 1.130 (changed +6 -2)
* src/FileRenderer.C 1.187 (changed +30 -1)
Added preliminary support code to permit full-time real-time ray tracing
as an alternative to OpenGL rasterization, but maintaining the use of OpenGL
to provide on-screen image presentation, double buffering, etc.
Added a new method to allow the main X11 OpenGL window title to be
modified at runtime, to more clearly indicate which renderer is active.
* src/OpenGLRenderer.h 1.153 (changed +17 -2)
* src/OpenGLRenderer.C 1.476 (changed +229 -2)
* src/OpenGLDisplayDevice.h 1.61 (changed +2 -1)
* src/OpenGLDisplayDevice.C 1.216 (changed +86 -1)
Ensure that anyhit traversals against opaque geometry end immediately.
* src/OptiXShaders.cu 1.176 (changed +5 -1)
Implemented many updates due to recent changes in the ANARI API design.
Still need to completely resolve changes related to having made the framebuffer
the object that collects camera and other global scene state that used
to be provided on render calls.
* src/ANARIRenderer.h 1.9 (changed +3 -2)
* src/ANARIRenderer.C 1.15 (changed +153 -126)
Minor tweak to improve context regen ordering
* src/ANARIDisplayDevice.C 1.3 (changed +3 -3)
 2021-04-04johnsMinor cleanup to GLSL shader compilation code while looking into
similarities with needs for loading OptiX 7.x compiled PTX.
* src/OpenGLShader.C 1.32 (changed +11 -3)
 2021-03-30johnsRemoved unnecessary "const" on radius scaling parameter.
* src/OptiXRenderer.h 1.132 (changed +2 -2)
Revised ANARI, OptiX, and OSPRay framebuffer methods to match recent
updates to the OptiX method names, and to incorporate corrections and
improvements already made in the OptiX framebuffer methods, in support
of fully interactive ray tracing pass-through to OpenGL DisplayDevice
subclasses..
* src/OptiXRenderer.C 1.386 (changed +6 -6)
* src/OSPRayRenderer.h 1.35 (changed +4 -4)
* src/OSPRayRenderer.C 1.89 (changed +19 -13)
* src/OSPRay2Renderer.h 1.11 (changed +4 -4)
* src/OSPRay2Renderer.C 1.33 (changed +19 -13)
* src/ANARIRenderer.h 1.8 (changed +4 -4)
* src/ANARIRenderer.C 1.14 (changed +20 -14)
 2021-03-29johnsAdded calc_matrix_scale_factor() method to compute a uniform scaling factor
for cone/cylinder/sphere primitives if/when flattening the scene graph
(by pre-transforming all geometry) for best interactive ray tracing
performance.
* src/OptiXRenderer.h 1.131 (changed +5 -1)
* src/OptiXRenderer.C 1.383 (changed +13 -1)
Added framebuffer map/unmap methods to permit OpenGL DisplayDevice
subclasses to implement full-time ray tracing pass-through.
* src/OptiXRenderer.h 1.130 (changed +3 -1)
* src/OptiXRenderer.C 1.382 (changed +11 -1)
Ensure that framebuffer_config() and framebuffer_resize() always set
internal width/height member variables so that framebuffer reads
and display are handled correctly for pass-through of full-time
ray tracing in OpenGL DisplayDevice subclasses.
* src/OptiXRenderer.C 1.384 (changed +7 -1)
Improved naming of framebuffer management methods prior to adding new
map/unmap calls required for full-time ray tracing pass-through from within
the OpenGLDisplayDevice hierarchy.
* src/OptiXRenderer.h 1.129 (changed +4 -4)
* src/OptiXRenderer.C 1.381 (changed +13 -13)
Minor optimizations for vmd_DrawConic()
* src/OpenGLRenderer.C 1.475 (changed +19 -10)
Print updated internal state variables when verbose output is enabled.
* src/OptiXRenderer.C 1.385 (changed +2 -2)
 2021-03-28johnsIndentation cleanup
* src/DispCmds.h 1.120 (changed +5 -4)
 2021-03-27johnsContinued revision of OptiX geometry methods to improve const correctness.
* src/OptiXRenderer.h 1.128 (changed +18 -15)
* src/OptiXRenderer.C 1.380 (changed +18 -17)
Improved const correctness of the materials and trimesh geometry methods.
* src/OptiXRenderer.h 1.127 (changed +39 -29)
* src/OptiXRenderer.C 1.379 (changed +38 -30)
 2021-03-22johnsAdded a clear() method to allow cleanup of loop-based clearing idioms found in the
DisplayDevice subclasses that manage matrix stacks.
* src/Stack.h 1.29 (changed +13 -1)
Replace stack clearing loop with call to new clear() method.
* src/FileRenderer.C 1.186 (changed +4 -7)
* src/DisplayDevice.C 1.151 (changed +3 -6)
 2021-03-17johnsApplied Josh's update to CUDAFastPBC to correct a race condition that
occured during tests with 2 million frame trajectories.
There was a rare race condition between memcpy and cudaMemcpyAsync.
The new CUDAFastPBC implementation has a cleaner memory copy
interface for the unwrapping portion of the code that no longer uses
the host-side memcpy, and has a distinct pinned buffer for every stream.
* src/CUDAFastPBC.cu 1.5 (changed +81 -84)
Eliminate duplicate declaration of blocks count.
* src/CUDAFastPBC.cu 1.6 (changed +1 -2)
 2021-03-12johnsA few cherry picked colvars module bug fixes and updates provided
by Jerome and Giacomo.
* src/colvarparse.h 1.13 (changed +4 -0)
* src/colvarparse.C 1.16 (changed +20 -0)
* src/colvarmodule.C 1.29 (changed +5 -0)
* src/colvarcomp_distances.C 1.23 (changed +2 -1)
* src/colvaratoms.h 1.15 (changed +2 -6)
* src/colvaratoms.C 1.25 (changed +3 -0)
 2021-03-10johnsSimplified conditional compilation tests and added further comments.
* src/OpenGLDisplayDevice.h 1.60 (changed +13 -12)
Simplified conditional compilation tests.
* src/OpenGLDisplayDevice.C 1.215 (changed +1 -5)
 2021-03-09johnsAdded the Google AI group's "Turbo" rainbow color scale.
Began adding infrastructure for conversion between sRGB colors (gamma 2.2)
and linear (gamma 1.0) RGB colors, since color scales, particularly those
that are tabulated, may not be in linear color spaces. This is complicated
by the fact that the VMD FLTK code presently displays the color scale
colors as-is, when they should actually be stored linear and rendered
in GL using linear colors, but drawn in sRGB in the FLTK GUI.
Further changes will be needed to ensure the correct color spaces are
always used for tabulated color scales.
* src/Scene.C 1.98 (changed +19 -3)
* src/ColorScaleTables.h 1.3 (changed +274 -1)
Corrected the behavior of the DisplayDevice base class implementation of
the cueing_on() and cueing_off() methods so that batch mode renderings
conducted with "-dispdev text" or "-dispdev none" don't force depth cueing on.
* src/DisplayDevice.h 1.144 (changed +18 -3)
* src/DisplayDevice.C 1.150 (changed +1 -6)
 2021-03-07johnsSynced up with devel versions
* configure 1.1524 (changed +2 -2)
 2021-03-06johnsAdded support for setting the AO maximum occlusion distance in the
CPU versions of Tachyon 0.99.2 and later.
* src/TachyonDisplayDevice.C 1.133 (changed +11 -1)
* src/LibTachyonDisplayDevice.C 1.99 (changed +14 -1)
Synced with current colvars git master.
* src/colvarvalue.C 1.14 (changed +1 -10)
* src/colvarscript_commands_colvar.h 1.3 (changed +40 -50)
* src/colvarscript_commands_bias.h 1.2 (changed +25 -15)
* src/colvarscript_commands.h 1.3 (changed +138 -17)
* src/colvarscript_commands.C 1.2 (changed +48 -0)
* src/colvarscript.h 1.13 (changed +99 -24)
* src/colvarscript.C 1.25 (changed +343 -34)
* src/colvars_version.h 1.16 (changed +1 -1)
* src/colvars_files.pl 1.6 (changed +1 -0)
* src/colvarproxy_volmaps.h 1.3 (changed +12 -0)
* src/colvarproxy_volmaps.C 1.3 (changed +19 -1)
* src/colvarproxy_vmd_version.h 1.12 (changed +1 -1)
* src/colvarproxy_vmd.h 1.17 (changed +0 -4)
* src/colvarproxy_vmd.C 1.22 (changed +0 -38)
* src/colvarproxy_tcl.h 1.2 (changed +1 -1)
* src/colvarproxy.h 1.21 (changed +119 -8)
* src/colvarproxy.C 1.11 (changed +63 -17)
* src/colvarparse.h 1.12 (changed +5 -1)
* src/colvarparse.C 1.15 (changed +4 -0)
* src/colvarmodule_utils.h 1.1 (added +83 -0)
* src/colvarmodule.h 1.30 (changed +6 -0)
* src/colvarmodule.C 1.28 (changed +3 -0)
* src/colvargrid.h 1.21 (changed +1 -1)
* src/colvargrid.C 1.12 (changed +12 -12)
* src/colvardeps.h 1.12 (changed +1 -0)
* src/colvarcomp_rotations.C 1.13 (changed +4 -4)
* src/colvarcomp_gpath.C 1.3 (changed +4 -4)
* src/colvarcomp_distances.C 1.22 (changed +12 -12)
* src/colvarcomp.C 1.19 (changed +4 -4)
* src/colvaratoms.h 1.14 (changed +7 -19)
* src/colvaratoms.C 1.24 (changed +41 -28)
 2021-02-24johnsEnable native cylinder rendering for ongoing testing of the new OSP_DISJOINT
curves API mode.
* src/OSPRay2DisplayDevice.h 1.4 (changed +3 -3)
* src/OSPRay2DisplayDevice.C 1.4 (changed +10 -6)
 2021-02-20johnsRevised the OSPRay 2.x renderer to use the new OSPRay 2.5.0
curve APIs with OSP_DISJOINT, for rendering cylinders and cones.
* src/OSPRay2Renderer.h 1.10 (changed +2 -4)
* src/OSPRay2Renderer.C 1.32 (changed +46 -43)
Updated OSPRay 2.x renderer to make use of the path tracer and add
experimental support for luminous materials.
* src/OSPRay2Renderer.C 1.31 (changed +65 -18)
 2021-02-19johnsCorrected missing ospRelease() calls on the futures returned from
asynchronous ospRenderFrame() calls.
* src/OSPRay2Renderer.C 1.30 (changed +3 -1)
Updated ANARIRenderer for recent API+spec revisions.
Eliminated ANARIGroup objects, and updated associated calls to
anariNewGeometricModel() and anariNewInstance() and their parameter set calls.
Added short-lived correction to leak of futures from asynchronous
anariRenderFrame() APIs. This will go away when the APIs are revised so
that the futures are implicit rather than explicit objects.
Updated all of the framebuffer creation/mapping and parameter assignment APIs.
* src/ANARIRenderer.C 1.13 (changed +55 -41)
Updated OSPRay 2.x paths for OSPRay 2.5.0
* configure 1.1523 (changed +2 -2)
 2021-02-16johnsAdded runtime dispatch for QuickSurf kernels on ARM64 CPUs with
NEON and FMA SIMD instructions.
* src/QuickSurf.C 1.132 (changed +24 -1)
Added the new ARM64 NEON+FMA QuickSurf kernels to the build.
* configure 1.1522 (changed +1 -0)
Completed AVX2 version of the molecular orbital kernels, based on
single-precision floating point AVX instructions, 32-bit integer
AVX2 instructions needed for the fast exponential approximation, and
single-precision fused-multiply add instructions used throughout.
At present, this kernel assumes availability of FMA, so it cannot be used
on CPUs that have AVX/AVX2 but lack FMA.
* src/Orbital_AVX2.C 1.1 (added +324 -0)
Implented complete molecular orbital kernel for ARM64 NEON SIMD instructions
on CPUs that support FMA instructions. A partial implementation exists for
machines lacking FMA, but more code is needed in the wavefunction loops
to make it complete. The ARM64 NEON exponential approximation uses a
different early-exit testing scheme from x86 SIMD variants, due to
the lack of equivalent instructions to gather high order bits from
multiple SIMD lanes into a single scalar, so this ARM64 NEON code
uses a horizontal maximum scheme to exploit the same early-exit opportunity
in a slightly different way.
* src/Orbital_NEON.C 1.1 (added +322 -0)
Misc cleanup of several leftover ifdef blocks and includes that aren't
needed for runtime CPU dispatch.
* src/QuickSurf_AVX2.C 1.7 (changed +8 -12)
Simplified and streamlined AVX2-specific QuickSurf kernel.
* src/QuickSurf_AVX2.C 1.8 (changed +8 -16)
Wrote a complete first implementation of QuickSuff for ARM64 NEON
SIMD instructions, on machines that have FMA.
Tested on a Mac "M1" processor thus far.
* src/QuickSurf_NEON.C 1.1 (added +457 -0)
 2021-02-11johnsAdded function prototype and runtime dispatch launch code for
NEON SIMD version of the molecular orbital kernel.
* src/Orbital.C 1.160 (changed +34 -1)
Enable compilation of the 16-byte-alignment check helper routine for ARM
for the time being. This should be replaced globally by the newer N-byte
alignment routines, but this is expedient for the moment.
* src/util_simd.C 1.31 (changed +2 -2)
 2021-02-01johnsAdded #ifdef protection for SVE vector length queries on ARM platforms
* src/VMDApp.C 1.581 (changed +2 -2)
Updated the build system to support runtime CPU dispatch for
ARM NEON with FMA instructions for the new Apple "M1" Mac hardware.
* configure 1.1521 (changed +34 -12)
 2021-01-27johnsAdded molecular orbital runtime dispatch logic for the new AVX2 kernel.
* src/Orbital.C 1.159 (changed +50 -12)
Added x86 runtime dispatch AVX2 molecular orbital kernel to the build.
* configure 1.1520 (changed +2 -1)
 2021-01-15johnsCranked version
* configure 1.1519 (changed +1 -1)
 2021-01-05johnsAdded another cpuid project reference
* src/WKFThreads.C 1.34 (changed +3 -2)
 2020-12-30johnsAdded runtime startup message to clearly indicate builds that have
runtime CPU dispatch enabled vs. those that do not.
* src/VMDApp.C 1.580 (changed +7 -2)
 2020-12-27johnsAdded conditional compilation check for CPU info bailout.
* src/WKFThreads.C 1.33 (changed +5 -2)
Corrected conditional compilation checks for non-x86 CPU runtime dispatch
* src/util_simd.C 1.30 (changed +2 -2)
 2020-12-24johnsAdded Python bindings to permit querying and setting color scale reversal
and posterization parameters.
* src/py_color.C 1.38 (changed +39 -1)
Cranked version
* configure 1.1518 (changed +1 -1)
Revised color scale internals and the Color window GUI to implement
posterization of color scales down to a user-specified number of
individual color bands.
* src/py_color.C 1.37 (changed +16 -13)
* src/cmd_color.C 1.43 (changed +14 -4)
* src/VMDApp.h 1.257 (changed +5 -3)
* src/VMDApp.C 1.579 (changed +8 -6)
* src/Scene.h 1.69 (changed +7 -3)
* src/Scene.C 1.97 (changed +17 -6)
* src/ColorInfo.C 1.38 (changed +7 -3)
* src/ColorFltkMenu.h 1.25 (changed +2 -0)
* src/ColorFltkMenu.C 1.44 (changed +37 -5)
* src/CmdColor.h 1.35 (changed +3 -3)
* src/CmdColor.C 1.48 (changed +4 -3)
 2020-12-23johnsAdded a live color swatch box to the redesigned color menu.
Continued adjustment of widget sizes and placement.
* src/ColorFltkMenu.h 1.23 (changed +2 -0)
* src/ColorFltkMenu.C 1.42 (changed +14 -7)
Revised the color scale internals to facilitate ooptional color scale order
reversal for both built-in divergent midpoint/offset color scales as
well as tabulated color scales.
* src/py_color.C 1.36 (changed +14 -13)
* src/cmd_color.C 1.42 (changed +5 -3)
* src/VMDApp.h 1.256 (changed +11 -8)
* src/VMDApp.C 1.578 (changed +6 -6)
* src/Scene.h 1.68 (changed +7 -3)
* src/Scene.C 1.96 (changed +7 -3)
* src/ColorInfo.C 1.37 (changed +7 -2)
* src/ColorFltkMenu.h 1.24 (changed +2 -0)
* src/ColorFltkMenu.C 1.43 (changed +26 -15)
* src/CmdColor.h 1.34 (changed +4 -2)
* src/CmdColor.C 1.47 (changed +3 -3)
 2020-12-21johnsAdded an implementation of the "cividis" color scale which improves
upon the popular "viridis" color scale for viewers that have
color vision deficiencies.
* src/Scene.C 1.95 (changed +5 -2)
* src/ColorScaleTables.h 1.2 (changed +265 -3)
Changed _mm_set_pd1() to _mm_set1_pd() which seems more portable
* src/util_simd.C 1.29 (changed +3 -2)
Changed default colorscale "Offset" from 0.10 to 0.06 after comparisons
with high spatial frequency test grating images for both original
parameter and the new value. The built-in VMD divergent color scales
while still much better than the old Matlab "rainbow" scale,
leave much to be desired, both in terms of their ability to show
high frequency fine spatial details, luminance linearity, and other factors.
* src/Scene.C 1.93 (changed +4 -4)
Changed the conditional compilation tests for safe use of the
FLTK Fl_Color_Chooser class in place of the classic VMD color sliders.
* src/ColorFltkMenu.h 1.22 (changed +1 -1)
Corrected width of color category name itembrowser widget.
* src/ColorFltkMenu.C 1.37 (changed +1 -1)
Cranked version
* configure 1.1517 (changed +1 -1)
First steps in a major revision to the VMD color scale infrastructure.
The existing implementation has been extended with support for tabulated
color scales, new internal data structures and APIs to facilitate correct
GUI interaction for non-editable tabulated color scales.
Due to the significant increase in the total number of color scales
now available, the GUI has been revised to support forward
and reverse mapping of color scale menu names that include both scale
type categories and leaf node color scale names.
Redesigned the Color window layout to support a much larger color scale
test image, and added a high spatial frequency test grating image
based on the color scale test images developed by Peter Kovesi.
* src/VMDApp.h 1.255 (changed +2 -1)
* src/VMDApp.C 1.577 (changed +5 -1)
* src/Scene.h 1.67 (changed +37 -26)
* src/Scene.C 1.94 (changed +191 -11)
* src/ColorFltkMenu.h 1.20 (changed +21 -19)
* src/ColorFltkMenu.C 1.38 (changed +110 -31)
Freely licensed perceptually uniform color scales in tabulated form with
256 color entries per table. These are adapted from four of the popular
sequential color scales in Matplotlib, and a large selection of the
linear, cyclic, isoluminance, and rainbow color scales from the set of
CET perceptually uniform color scales published by Peter Kovesi.
* src/ColorScaleTables.h 1.1 (added +5774 -0)
Improved color scale plot title to "CIELAB L* perceptual lightness"
which is more informative and technically correct.
Completed the remaining math for RGB to CIELAB color conversion.
* src/ColorFltkMenu.C 1.40 (changed +7 -4)
Mention color editing GUI revisions.
* README 1.412 (changed +1 -0)
Pulled in latest colvars module from the git master.
* src/colvarscript.C 1.24 (changed +25 -4)
* src/colvars_version.h 1.15 (changed +1 -1)
* src/colvarproxy_vmd.C 1.21 (changed +1 -1)
* src/colvarcomp_rotations.C 1.12 (changed +332 -0)
* src/colvarcomp.h 1.16 (changed +65 -0)
* src/colvaratoms.C 1.23 (changed +2 -6)
* src/colvar.h 1.18 (changed +3 -0)
* src/colvar.C 1.29 (changed +6 -1)
Shifted the L* 100 ligthness marker down 10 pixels to match Fl_Chart layout
slightly better.
* src/ColorFltkMenu.C 1.41 (changed +1 -1)
Significantly redesigned the Color window layout, resizing
the color definitions and color scale tabs to occupy the full
window, and migrating the entirety of the color definition browsers
into the color definitions tab. This change to the window layout
better separates controls that are relevant for color definition from
those used for color scale selection and editing. The larger space
made available within the color scale tab enables the addition of
a plot of color scale CIELAB L* luminance just below the color scale
test grating image.
* src/ColorFltkMenu.h 1.21 (changed +2 -0)
* src/ColorFltkMenu.C 1.39 (changed +228 -35)
Updated date
* README 1.411 (changed +1 -1)
 2020-12-19johnsMajor revision of the VMD color menu to optionally make use of the
FLTK-provided Fl_Color_Chooser instead of the classic VMD color sliders.
By default, when compiling with FLTK versions >= 1.1.10 VMD will use
Fl_Color_Chooser, and will revert to the classic sliders otherwise.
The window size is significantly increased, to match the width of the
VMD main window, and with additional height to provide an easy-to-use
widget size for the FLTK color selector and associated controls.
The FLTK color control supports floating point RGB, Hex, integer,
and HSV color value ranges, with mouse-based color component scrolling,
so all of the original features have been preserved while adding
significant convenience.
* src/ColorFltkMenu.h 1.19 (changed +25 -2)
* src/ColorFltkMenu.C 1.36 (changed +92 -14)
 2020-12-18johnsAdded VMD icon to VS2017 project, and Win64 builds.
* msvc/vs2017/vmd.vcxproj.filters 1.8 (changed +13 -0)
* msvc/vs2017/vmd.vcxproj 1.12 (changed +7 -0)
* msvc/vs2017/resource.h 1.1 (added +21 -0)
* msvc/vs2017/icon1.ico 1.1 (added binary)
* msvc/vs2017/Resource.rc 1.1 (added binary)
Added built-in OptiX and OSPRay ray tracing engines to the Win64 builds.
* msvc/vs2017/vmd.vcxproj.filters 1.7 (changed +22 -1)
* msvc/vs2017/vmd.vcxproj 1.11 (changed +20 -8)
Added x64 installation script based on V5 of VMD 1.9.4a50 installer build.
The installer scripts are re-generated using the "HM NIS Edit" 2.x,
followed by hand-patching the installer code to add/delete VMD registry
keys and deal with x64-specific installer steps and Administrative
privilege level setting. Ideally some of this would be done with macros
or some sort of script template, but these steps have to be inserted
deep into installer subsections making it an annoying manual editing
process at present. This script can be used as a point of reference to
recover the manual hand editing by carefully diffing a freshly generated
installer script with the previous version. It may eventually be possible
to automate this completely by writing an installer generation script or
by devising pathes that apply relative to subsection starting points
that the "patch" utility has a hope of recognizing automatically.
* msvc/inst-nsis/vmd-win64-nsis.nsi 1.1 (added +7655 -0)
 2020-12-15johnsPrevent glwin window destruction from killing the parent app
in Win32/Win64 builds.
* src/glwin.c 1.32 (changed +28 -15)
 2020-12-14johnsEliminated startup test messages for WIN64 builds
* src/win32vmdstart.c 1.52 (changed +2 -2)
MacOS 10.15 and 11.0 builds require Tcl/Tk 8.6 or later
* configure 1.1516 (changed +9 -5)
Updated WIN32 and WIN64 registry query code and software keys to add
support for 64-bit builds.
* src/win32vmdstart.c 1.51 (changed +5 -13)
Updated version dependency comments for FLTK builds for MacOS X
10.15 (Catalina) and 11.0 (Big Sur).
* configure 1.1515 (changed +6 -7)
 2020-12-13johnsAdded MacOS X ARM64 targets
* Makefile 1.127 (changed +11 -1)
Added build configuration for MACOSXARM64
* configure 1.1514 (changed +115 -9)
Added conditional compilation tests for ARM64 MacOS X builds
checking for the compile-time macro ARCH_MACOSXARM64.
* src/vmdsock.c 1.31 (changed +2 -2)
* src/macosxvmdstart.C 1.29 (changed +13 -7)
* src/VMDApp.C 1.576 (changed +3 -3)
* src/Stride.C 1.48 (changed +2 -2)
* src/Spaceball.C 1.64 (changed +3 -1)
* src/QuickSurf.C 1.131 (changed +2 -2)
* src/MeasureVolInterior.C 1.17 (changed +3 -3)
Updated OptiX renderer to add support for ray statistics reporting for
interactive display runs.
* src/OptiXRenderer.C 1.378 (changed +12 -9)
 2020-12-12johnsChanged the OptiX renderer's ray statistics buffer allocation code to specify
RT_BUFFER_OUTPUT instead of RT_BUFFER_INPUT_OUTPUT | RT_BUFFER_GPU_LOCAL,
since we never write to these buffers on the host side.
* src/OptiXRenderer.C 1.376 (changed +14 -12)
Implemented slight optimizations for OptiX ray statistics gathering among
the various primary ray generation and shading kernels.
* src/OptiXShaders.cu 1.175 (changed +22 -22)
Increased the default threshold for forcing VMD to perform
OptiX renderings in multiple accumulation buffer passes by a factor
of 4x, and permit user override of the default threshold and behavior.
The new code also uses the total number of primary aa samples
and AO shadow feeler rays rather than only the number of primary ray
aa samples, to provide better performance scaling on RTX
hardware-accelerated GPUs going forward. Increasing the number of
rays per launch significantly improves VMD's utilization of the RT cores on
the latest hardware. With too small of the ray batch size per pass, VMD
can't exploit the full hardware performance on the latest RTX cards.
* src/OptiXRenderer.C 1.377 (changed +8 -2)
Revised the low level VMDDisplayList clipping plane methods and
higher-level Displayable clipping plane methods to eliminate
Displayable methods from triggering _needUpdate scene regen/redraw
updates unless: the clipping plane is being changed; or
one of the the clipping plane plane properties is changed and the
active clipping plane mode is currently active (non-zero).
* src/VMDDisplayList.h 1.46 (changed +3 -2)
* src/VMDDisplayList.C 1.42 (changed +6 -1)
* src/Displayable.h 1.91 (changed +44 -1)
 2020-12-09johnsAdded placeholder clipping group implementation.
* src/OSPRayDisplayDevice.h 1.18 (changed +22 -5)
* src/OSPRayDisplayDevice.C 1.17 (changed +64 -1)
* src/OSPRay2DisplayDevice.h 1.3 (changed +23 -6)
* src/OSPRay2DisplayDevice.C 1.3 (changed +63 -1)
 2020-11-30johnsCorrected behavior of 'radius' flag per Barry's testing.
* src/TclGraphics.C 1.60 (changed +6 -7)
 2020-11-25johnsWindows platforms return raw key state without processing key modifiers,
so in order to provide the same behavior as X11, we process key modifiers
ourselves w/ toupper()/tolower() calls, etc.
* src/glwin.c 1.31 (changed +10 -2)
 2020-11-18johnsAdded conditional definition of NOMINMAX macro when compiling the
OptiXRenderer code on Windows platform, as required by OptiX-internal headers.
* src/OptiXRenderer.h 1.126 (changed +8 -3)
 2020-11-17johnsAdded a wrapper for OptiXRenderer::device_count() to limit overly
broad inclusion of low level OptiX API headers by classes that needed to
make calls into OptiXRenderer. On the Windows platform in particular, there
are some thorny header file ordering and macro definition issues that
must be satisfied, and while that is easy to do in OptiXRenderer and
OptiXDisplayDevice, this rapidly gets out of hand if other classes
start including those headers as well.
* src/OptiXDisplayDevice.h 1.33 (changed +5 -1)
* src/OptiXDisplayDevice.C 1.83 (changed +8 -1)
Changed order of header inclusion to ensure that low-level OptiX
headers are included prior to system-provided headers, as the OptiX
headers incorporate special handling, e.g., of min/max macros and
related functions on the Windows platform, which is very sensitive to
header ordering.
* src/OptiXRenderer.C 1.375 (changed +7 -3)
* src/OptiXDisplayDevice.C 1.84 (changed +7 -3)
Eliminate direct calls to OptiXRenderer class, to limit the scope of
associated low-level OptiX header inclusion, which has particularly
detailed ordering and macro definition requirements for Windows builds.
* src/FileRenderList.C 1.108 (changed +3 -4)
Eliminated inclusion of OptiXRenderer definition since hardware
enumeration is now done as part of FileRenderList and support for
VCA rendering clusters has been removed previously.
* src/VMDApp.C 1.575 (changed +1 -4)
Use VMD_PI macro to simplify Windows builds.
* src/OptiXRenderer.C 1.374 (changed +7 -7)
 2020-11-16johnsAdded include of windows.h for interactive RT compilation on Windows platforms.
* src/OptiXRenderer.C 1.373 (changed +5 -1)
* src/OSPRay2Renderer.C 1.29 (changed +5 -1)
* src/ANARIRenderer.C 1.12 (changed +5 -1)
Corrected added missing include of windows.h when compiling OSPRayRenderer
on windows platforms.
* src/OSPRayRenderer.C 1.88 (changed +6 -2)
Imported Tachyon glwin updates to permit compilation on win32/win64
* src/glwin.c 1.30 (changed +17 -9)
Use VMD_PI rather than M_PI to please MSVC.
* src/OSPRayRenderer.C 1.87 (changed +2 -2)
 2020-11-06johnsChanged implementation of spheretube color handling for inheritance
of bulk "draw color colorID" type coloring mode. The implementation
of colorID arrays needs rewriting so it will properly track updates
to color tables ex-post-facto, and that will also impact the
single-color color inheritance mode.
* src/TclGraphics.C 1.59 (changed +10 -8)
* src/MoleculeGraphics.h 1.57 (changed +2 -2)
* src/MoleculeGraphics.C 1.88 (changed +46 -56)
Changed rev to 50 skipping 49 so that special 49 builds don't get confused
with later revs.
* configure 1.1513 (changed +1 -1)
Corrected handling of single-radius spheretube combinations
* src/TclGraphics.C 1.58 (changed +2 -1)
* src/MoleculeGraphics.C 1.87 (changed +13 -7)
Cranked version
* configure 1.1512 (changed +1 -1)
Explicitly include CUDA runtime header with OptiX versions greater than 5.2,
since differences in CUDA runtime headers among versions lead to
cudaGetDeviceCount() being unprototyped in some cases but not others.
This ensures it will always be properly prototyped.
* src/OptiXRenderer.C 1.372 (changed +4 -1)
 2020-11-04johnsAdded tcl_get_intarray() to pull in a tcl list as a 1-D flat array of ints
* src/TclVec.C 1.46 (changed +26 -1)
* src/TclCommands.h 1.59 (changed +4 -1)
Changed the intermediary OptiXDisplayDevice class to accumulate
individual spheres from FileRenderer::sphere() calls into local
buffers the same way that it already did for cylinders and particular
triangle geometry. When the primitive count exceeds a threshold,
the spheres are sent to OptiXRenderer as a sphere_array_color()
primitive, which greatly reduces overheads. By overriding the
FileRenderer::sphere() method, we eliminate sphere triangulation for
scenes that include handfuls of user-drawn spheres, and for spheres
drawn by plugins or the like, leading to higher quality and faster rendering.
* src/OptiXDisplayDevice.h 1.32 (changed +27 -2)
* src/OptiXDisplayDevice.C 1.82 (changed +59 -1)
Updated the "spheretubes" draw command to accept a list of colorIDs
rather than only fully-specified RGB colors. This makes it a more
directly usable replacement for existing sphere-at-a-time scripts
that follow a pattern of calling "draw color", then "draw sphere",
"draw cone", etc.
* src/TclGraphics.C 1.57 (changed +46 -3)
* src/MoleculeGraphics.h 1.56 (changed +3 -2)
* src/MoleculeGraphics.C 1.86 (changed +14 -4)
 2020-11-02johnsAdded additional DSSP src URLs
* src/Stride.C 1.47 (changed +2 -1)
Added notes about AVX/AVX-512 clock rate reductions and high vector
registers causing false dependencies except when specifically cleared,
e.g., by calls to _mm256_zeroupper().
* src/WKFThreads.C 1.32 (changed +7 -2)
Added support for the graphics "info" subcommands for spheretube primitives
and eliminated various debugging console messages.
* src/TclGraphics.C 1.56 (changed +3 -1)
* src/MoleculeGraphics.h 1.55 (changed +18 -14)
* src/MoleculeGraphics.C 1.85 (changed +53 -3)
Added updated STRIDE, DSSP/xDSSP/HSSP URLs
* src/Stride.C 1.46 (changed +16 -1)
Synced up cpuid() refs from Tachyon
* src/WKFThreads.C 1.31 (changed +5 -2)
 2020-11-01johnsAdded AVX2 atom selection analysis loop
* src/util_simd_AVX2.C 1.1 (added +238 -0)
Added AVX2-specific atom selection analysis routine.
* configure 1.1511 (changed +1 -0)
Added runtime CPU dispatch for analyze_selection_aligned_avx2()
* src/util_simd.C 1.26 (changed +14 -4)
Changed the AVX atom selection loops to use the prior strategy for
finding vector-aligned starting/ending indices due to bugs that showed
up in testing with CPU dispatch enabled. Will revisit later.
* src/util_simd_AVX.C 1.7 (changed +43 -7)
Chopped out conditional compilation of alternative AVX-specific SIMD
loops now that runtime CPU dispatch is beginning to be more extensively
implemented.
* src/util_simd.C 1.27 (changed +3 -70)
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