CVS analysis' parameters 
Project module namevmd
CVS root used/home/cvs/vmd/cvsroot
Range analysisMain Branch (HEAD)
Date analysis2019-07-17 02:33 (Built in 104s)
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 877 
Lines of code currently in repository (on non binary files only) 410035 
Activity indicatorsFrom startThis monthToday
Number of developers 2610
Number of commits3600530
Number of commits by status 1276 to add new file
34330 to change existing file
399 to remove file 
3 to change existing file
 
 
Different files commited 125420
Lines added / modified / removed (on non binary files only) +605752 / 272240 / -195717+14 / 12 / -2+0 / 0 / -0
Last commit 2019-07-102019-07-10 

 
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 
johns226001211344795 / 161408 / 9846115.2 / 7.1 / 4.32019-07-10 15:14 
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 
ryanmcgreevy268907 / 202 / 57934.8 / 7.7 / 22.22019-05-01 20:06 
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 
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
 2019-07-10johnsAdded comments about the lack of recursion safety checks for shadow
feeler rays associating with lighting calculations. Since we don't
take this level of recursion into account in the renderer's internal
recursion tracking, we must ask OptiX to allow for one extra level of
recursion beyond the depth we're internally tracking to ensure that
there's enough stack space available.
* src/OptiXShaders.cu 1.171 (changed +8 -2)
Improved both shading code and comments about the enforcement of
the maximum ray recursion depth since the interaction between the
renderer and the OptiX >= 6.x runtime system's memory allocation
for the recursion stack critically depends on absolute agreement
between what the renderer asks for and what it does during a run.
The way we had tracked the recursion depth previously was really
only tracking recursion of the last surface hit for shading and
it wasn't taking into account shadow feeler rays or the like, whereas
the OptiX runtime has to accurately compute the stack space for
any recursive rtTrace() call.
The recursion tracking logic in the renderer used zero-based counting
and also had an incorrect comparison test so the original code had
allowed one more recursion than requested in practice, which while
harmless in older OptiX APIs that used an application-provided
recursion stack memory request sizes, is intolerable with the new
implementation since it computes the necessary stack size directly
from the maximum recursion depth. The revised code now asks OptiX
for a maximum recursion depth one greater than the surface hit depth
to allow lighting calculations to complete, and the internal max recursion
counter tracking has been corrected for its use of zero-based indexing.
Further comments should probably be added to the lighting code about
the necessity for this extra level of recursion beyond what the shader
is tracking internally.
* src/OptiXShaders.cu 1.170 (changed +4 -6)
* src/OptiXRenderer.C 1.357 (changed +14 -6)
 2019-06-29johnsModified the RTX accelerated ray tracing path to be extra conservative
about its maximum recursion depth and associated stack size requirements,
and added a VMDOPTIXMAXSTACKSIZE environment variable that causes VMD
to set the RTX runtime for maximum supported recursion depth and associated
stack size allocation.
* src/OptiXRenderer.C 1.356 (changed +19 -3)
 2019-06-28johnsCranked version
* configure 1.1475 (changed +1 -1)
Misc cleanup. Time to revisit whether it would be wise to pull the
bond data structures out of the atom class to permit them to be dynamically
resized for better average-case memory efficiency while still permitting
loading of unusual molecular structures or models with huge per-particle
bond counts.
* src/Atom.h 1.71 (changed +6 -8)
Revert default compilation to 12-bonds-per-atom maximums for now.
* src/Atom.h 1.73 (changed +2 -2)
Temporarily increase per-atom bond storage to 256 for a special user-requested
build. While doing this, I've gone ahead and added comments about
rearchitecting the code to eliminate this limitation with dynamic
allocation outside of MolAtom in the containing molecule class,
resulting in a likely-acceptable performance trade-off given the
propensity for an improved (reduced) average case memory use for bond
storage and traversal.
* src/Atom.h 1.72 (changed +13 -2)
Updated format specifier for 64-bit Python APIs that return longs.
* src/py_molecule.C 1.81 (changed +2 -2)
 2019-06-24johnsUse calloc() rather than malloc() so we don't have to make an additional
subsequent memset() call to zero out the coordinate arrays.
* src/Timestep.C 1.72 (changed +5 -4)
 2019-06-21johnsCranked version
* configure 1.1474 (changed +1 -1)
 2019-06-06johnsAdded further URL references about Python 3 module initialization
practices that improve portability on recent compilers, particularly those
that support C++11.
* src/py_atomsel.C 1.46 (changed +7 -1)
Changed the atom selection module initialization approach to address
problems that arise with Clang++ 8.x, which gets upset about
the use of PyObject_HEAD_INIT() and suggests adding braces etc.
This is discussed in significant detail as part of PEP 1323:
https://www.python.org/dev/peps/pep-3123/
The discussion of PEP 1323 suggests the use of PyVarObject_HEAD_INIT()
instead of PyObject_HEAD_INIT().
* src/py_atomsel.C 1.45 (changed +9 -3)
Eliminate duplicated extern "C" linkage type qualifier used to ensure that
name mangling is disabled.
* src/PythonTextInterp.C 1.74 (changed +5 -1)
Eliminated warnings from clang++ related to potentially uninitialized
local variable state when the error handling branches are taken, by
improving locality of variable scoping for PyObject pointers so they
don't cross the boundary between normal execution and error condition cases.
* src/py_atomsel.C 1.41 (changed +3 -4)
Further variable initialization changes to avoid compiler diagnostics
from Clang++
* src/py_atomsel.C 1.43 (changed +2 -2)
Misc cleanup
* src/py_atomsel.C 1.44 (changed +72 -71)
Perform allocation/initialization of the result Python list early enough
that it isn't undefined if subsequent errors occur, but we're already past
basic initialization phases for the method in question. This is required
to please Clang++ in its analysis of code initialization and exception handling.
* src/py_atomsel.C 1.42 (changed +6 -2)
vmd-first-python3
2019-06-05johnsConst correctness fix for Python 3.x
* src/VMDTkinterMenu.C 1.4 (changed +1 -1)
Elimiante trailing whitespace
* python/testdisplay.py 1.5 (changed +2 -2)
Many more const correctness fixes for Python 3.x APIs, particularly
as fallout from the use of PyUnicode_AsUTF8().
* src/py_graphics.C 1.35 (changed +3 -3)
* src/py_commands.h 1.49 (changed +2 -2)
* src/py_commands.C 1.22 (changed +4 -3)
* src/py_color.C 1.34 (changed +5 -5)
* src/py_atomsel.C 1.40 (changed +8 -8)
Merged Robin Betz's Python API changes to support both Python 2.x and 3.x,
changes to Python module initialization, and module naming.
* python/testMolecule.py 1.17 (changed +2 -2)
* python/startvmd.py 1.5 (changed +2 -2)
* python/hotkeys.py 1.2 (changed +2 -2)
* python/VMD.py 1.16 (changed +24 -41)
* python/Tkinter.py 1.5 (changed +78 -72)
* python/Molecule.py 1.31 (changed +12 -12)
* python/Material.py 1.5 (changed +2 -2)
* python/Label.py 1.5 (changed +7 -7)
* python/AtomSel.py 1.23 (changed +4 -4)
Merged Robin Betz's Python API changes:
All functions take keyword arguments.
Clearer keyword arguments for some functions, but backwards-compatible, too.
All functions and modules have docstrings.
More comprehensive error checking of invalid input.
Careful reference counting of all Python objects to avoid memory leaks.
Test cases for all Python modulesĀ + bug fixes I found while writing
test cases in python/test.
Tested builds with address sanitizer and caught several memory leaks.
Compiled and tested with Python 2.7 and 3.6.
Greatly improved atomsel attribute access: instead of atomsel().get("x")
you can just say atomsel().x, etc.
Renamed atomsel module to selection to clarify difference between it and
atomsel type.
Python module initialization functions appear only in one spot
(py_commands.h), making it easier to add new modules.
* src/py_vmd.C 1.16 (changed +88 -72)
* src/py_selection.C 1.1 (added +226 -0)
* src/py_commands.h 1.47 (changed +1 -9)
* src/py_commands.C 1.21 (changed +1 -7)
* src/py_atomsel.C 1.36 (changed +1623 -957)
* src/PythonTextInterp.C 1.72 (changed +121 -68)
Merged Robin Betz's changes for keyword-based Python parameter parsing,
improved doc strings, and Python 3.x initialization.
* configure 1.1473 (changed +1 -1)
Misc cleanup.
Merged Robin Betz's Python API changes to support both Python 2.x and 3.x,
changes to Python module initialization, and module naming hierarchy.
* src/py_molecule.C 1.80 (changed +1096 -570)
Modify the VMDApp pointer checks to unify with the other implementations.
* src/py_selection.C 1.2 (changed +19 -14)
Re-merged the Python atom selection interface to make use of
firstsel/lastsel to improve atom selection traversal performance.
The Python 3.x changes led to a loss of this optimization, so this
revision puts it back in place.
* src/py_atomsel.C 1.37 (changed +6 -6)
Removed the py_atomselection.C source file that contained the original
(Oct 2000) VMD python bindings for performing atom selections.
The original atomselection interface has been deprecated since 2007, so
at this point we can safely remove it altogether as part of modernization
for Python 3.x. The newer implementations have now been further
improved and this reduces the code we're maintaining going forward.
* src/py_atomselection.C 1.60 (removed +0 -942)
Rewrote the build_set_values() helper in the Python atom selection
implementation to eliminate redundant passing of atom counts and
selection flag arrays in favor of passing a const pointer to the
atom selection itself, which allows the internal loops within
build_set_values() to make use of atom selection accelerator loop bounds.
* src/py_atomsel.C 1.39 (changed +12 -18)
Set numvalues prior to the first error handling branch to prevent
compiler errors related to jumping past the initialization of numvalues,
even though we're not really using it within the error handling block.
* src/py_measure.C 1.11 (changed +3 -3)
Updated Python 2.x/3.x initialization and fixes to prevent C++ name mangling.
* src/py_vmd.C 1.17 (changed +24 -7)
* src/py_commands.h 1.48 (changed +8 -6)
* src/PythonTextInterp.C 1.73 (changed +3 -2)
We need to revise the build_set_values() helper before we can exploit
atom selection accelerators.
* src/py_atomsel.C 1.38 (changed +7 -2)
 2019-06-04johnsContinued cleanup of the Python bindings.
Merged the last parts of Robin Betz's Python 3 initialization changes
along with improved error handling and improved Python type checking for
atom selections in particular. A few of the changes have to be held back
via conditional compilation until the matching changes have been completed,
e.g., in the atom selection code.
* src/py_commands.h 1.46 (changed +28 -2)
* src/py_commands.C 1.20 (changed +171 -90)
 2019-05-31johnsMisc cleanup and improvements.
Merged Robin Betz's changes for keyword-based Python parameter parsing,
improved doc strings, and Python 3.x initialization.
* src/py_trans.C 1.24 (changed +432 -187)
* src/py_topo.C 1.10 (changed +841 -345)
* src/py_molrep.C 1.32 (changed +493 -245)
* src/py_graphics.C 1.33 (changed +447 -243)
* src/py_color.C 1.33 (changed +377 -197)
Re-eliminated duplicated registration of the _sphere method accidentally
reintroduced when merging in Robin Betz's changes which were based on
an older version of the code. Eliminated the "graphics_" prefix in favor
of just "py_" leading to shorter function names and improved code
readability.
* src/py_graphics.C 1.34 (changed +16 -23)
Updated to latest colvars source with the STL algorithm fix
permanently implemented.
* src/colvars_version.h 1.12 (changed +1 -1)
* src/colvarcomp_protein.C 1.11 (changed +2 -1)
* src/colvarcomp.C 1.16 (changed +3 -1)
 2019-05-30johnsConsistency among Python module init routines
* src/py_axes.C 1.21 (changed +4 -5)
Merged Robin Betz's changes for keyword-based Python parameter parsing,
improved doc strings, and Python 3.x initialization.
* src/py_render.C 1.23 (changed +52 -13)
* src/py_mouse.C 1.14 (changed +53 -9)
* src/py_axes.C 1.20 (changed +57 -21)
Merged Robin Betz's changes for keyword-based Python parameter parsing,
improved doc strings, and Python 3.x initialization.
Continued cleanup.
* src/py_menu.C 1.19 (changed +98 -35)
Misc cleanup and comment improvements
* src/py_material.C 1.36 (changed +20 -15)
Misc cleanup and improvements.
Merged Robin Betz's changes for keyword-based Python parameter parsing,
improved doc strings, and Python 3.x initialization.
* src/py_numeric.C 1.27 (changed +133 -62)
* src/py_measure.C 1.10 (changed +102 -50)
* src/py_material.C 1.37 (changed +194 -88)
* src/py_label.C 1.31 (changed +390 -208)
* src/py_imd.C 1.29 (changed +119 -56)
* src/py_animate.C 1.30 (changed +122 -71)
Misc cleanup and improvements.
Merged Robin Betz's changes for keyword-based Python parameter parsing,
improved doc strings, and Python 3.x initialization.
A noteworthy deficiency in our Python interface parsing implementations
arises in cases (as in py_display) when we need to match parsed keywords
against a long list of potential candidates, triggering the correct
assignments, type conversions, and subsequent VMD actions to be taken.
At present, the parsing code performs what boils down to a variant of
linear search through the series of candidate keywords, either by looping
and/or branching with string compares. This makes the code ugly and
slower than it should be. We should instead create persistent hash tables
(that live for the life of the Python module, interpreter, or application)
that contain all of the keywords, and associate them with enumerations or
function pointers to directly trigger the right actions. That would
eliminate the linear search behavior (both variants), and if properly
generalized, this pattern could be used in many other parts of the VMD
Tcl/Python bindings where we have to parse keywords from large lists of
candidates.
* src/py_display.C 1.42 (changed +279 -122)
Renamed keyword arguments parameter from "keywds" to "kwargs" for clarity
and consistency with the rest of the python bindings that do keyword handling.
* src/py_material.C 1.35 (changed +12 -12)
Renamed registered Python method fctns, adding py_ prefix for clarity
* src/py_trans.C 1.23 (changed +33 -33)
* src/py_topo.C 1.9 (changed +33 -33)
* src/py_numeric.C 1.26 (changed +8 -8)
* src/py_molrep.C 1.31 (changed +43 -43)
* src/py_molecule.C 1.79 (changed +74 -69)
* src/py_measure.C 1.9 (changed +7 -7)
* src/py_material.C 1.34 (changed +15 -15)
* src/py_label.C 1.30 (changed +19 -21)
* src/py_graphics.C 1.32 (changed +31 -32)
* src/py_display.C 1.41 (changed +15 -15)
* src/py_axes.C 1.19 (changed +5 -5)
* src/py_atomsel.C 1.35 (changed +17 -17)
* src/py_atomselection.C 1.59 (changed +23 -23)
Revised all of the VMD Python initialization routines to match the
function signature needed for tabulated module initialization per
Robin Betz's patch to support Python 3.x.
* src/py_trans.C 1.22 (changed +4 -3)
* src/py_topo.C 1.8 (changed +4 -3)
* src/py_render.C 1.22 (changed +4 -3)
* src/py_numeric.C 1.25 (changed +5 -4)
* src/py_mouse.C 1.13 (changed +2 -1)
* src/py_molrep.C 1.30 (changed +4 -3)
* src/py_molecule.C 1.78 (changed +4 -3)
* src/py_menu.C 1.18 (changed +3 -2)
* src/py_measure.C 1.8 (changed +4 -3)
* src/py_material.C 1.33 (changed +4 -3)
* src/py_label.C 1.29 (changed +3 -2)
* src/py_imd.C 1.28 (changed +4 -3)
* src/py_graphics.C 1.31 (changed +4 -3)
* src/py_display.C 1.40 (changed +5 -2)
* src/py_commands.h 1.45 (changed +21 -20)
* src/py_color.C 1.32 (changed +4 -3)
* src/py_axes.C 1.18 (changed +8 -2)
* src/py_atomsel.C 1.34 (changed +7 -7)
* src/py_animate.C 1.29 (changed +4 -3)
* src/PythonTextInterp.C 1.71 (changed +5 -2)
* src/py_atomselection.C 1.58 (changed +4 -3)
 2019-05-29johnsAdded safety checks for VMDApp pointers
* src/py_topo.C 1.6 (changed +54 -18)
* src/py_molecule.C 1.77 (changed +147 -34)
* src/py_atomsel.C 1.33 (changed +24 -6)
* src/py_atomselection.C 1.57 (changed +62 -14)
Added safety checks for VMDApp pointers.
* src/py_trans.C 1.21 (changed +66 -17)
* src/py_numeric.C 1.24 (changed +18 -4)
* src/py_molrep.C 1.29 (changed +91 -21)
* src/py_material.C 1.31 (changed +34 -8)
* src/py_label.C 1.28 (changed +35 -9)
* src/py_imd.C 1.23 (changed +37 -9)
* src/py_graphics.C 1.30 (changed +14 -4)
* src/py_display.C 1.39 (changed +31 -8)
Applied several doc string and src comment improvements from Robin Betz.
* src/py_measure.C 1.7 (changed +87 -25)
Const correctness improvements for modern Python APIs.
* src/py_trans.C 1.20 (changed +35 -35)
* src/py_topo.C 1.4 (changed +30 -17)
* src/py_render.C 1.21 (changed +3 -3)
* src/py_numeric.C 1.23 (changed +10 -12)
* src/py_mouse.C 1.12 (changed +2 -2)
* src/py_molrep.C 1.28 (changed +72 -76)
* src/py_molecule.C 1.76 (changed +90 -103)
* src/py_material.C 1.30 (changed +43 -43)
* src/py_label.C 1.27 (changed +31 -31)
* src/py_imd.C 1.27 (changed +2 -2)
* src/py_imd.C 1.22 (changed +15 -22)
* src/py_graphics.C 1.29 (changed +28 -40)
* src/py_display.C 1.38 (changed +12 -12)
* src/py_commands.C 1.19 (changed +9 -9)
* src/py_color.C 1.31 (changed +2 -2)
* src/py_atomsel.C 1.32 (changed +62 -72)
* src/py_animate.C 1.28 (changed +2 -2)
* src/py_atomselection.C 1.56 (changed +30 -34)
Eliminated tabs in the source and misc other cleanup.
* src/py_topo.C 1.5 (changed +597 -489)
Eliminated unnecessary calls to PyArg_ParseTuple() for Python methods
that don't need to accept any arguments, and changed their registration
to METH_NOARGS.
* src/py_material.C 1.32 (changed +2 -5)
* src/py_imd.C 1.25 (changed +5 -18)
Misc cleanup
* src/py_topo.C 1.7 (changed +2 -2)
Renamed registered Python method fctns, adding py_ prefix for clarity
* src/py_imd.C 1.24 (changed +17 -18)
Revised Python doc strings per Robin Betz's suggestions.
* src/py_imd.C 1.26 (changed +47 -24)
 2019-05-28johnsAdded missing revision control header
* src/py_measure.C 1.4 (changed +20 -0)
Added new/improved Python doc strings from Robin Betz
* src/py_render.C 1.20 (changed +21 -8)
Added safety checks for VMDApp pointers
Renamed registered Python method fctns, adding py_ prefix for clarity
* src/py_menu.C 1.16 (changed +24 -8)
Added safety checks for VMDApp pointers.
* src/py_color.C 1.26 (changed +41 -9)
Added safety checks for VMDApp pointers.
Added new/improved Python doc strings from Robin Betz
* src/py_mouse.C 1.11 (changed +12 -4)
Added safety checks for VMDApp pointers.
Const correctness improvements for modern Python APIs.
Added new/improved Python doc strings from Robin Betz.
* src/py_vmd.C 1.15 (changed +40 -12)
Added safety checks for VMDApp pointers.
Eliminated unnecessary calls to PyArg_ParseTuple() for Python methods
that don't need to accept any arguments, and changed their registration
to METH_NOARGS.
* src/py_color.C 1.28 (changed +20 -31)
Began applying Robin Betz's Python doc string improvements and
improved error checking.
* src/py_animate.C 1.26 (changed +38 -14)
Began de-tabbing src code
* src/py_measure.C 1.5 (changed +93 -80)
Const correctness improvements for modern Python APIs.
* src/py_menu.C 1.15 (changed +10 -10)
* src/py_color.C 1.29 (changed +16 -20)
Const correctness improvements for modern Python APIs.
Improved Python doc strings from Robin Betz.
* src/py_animate.C 1.27 (changed +22 -6)
Misc cleanup
* src/py_color.C 1.30 (changed +4 -5)
More de-tabbing
* src/py_measure.C 1.6 (changed +46 -47)
Renamed registered Python method fctns, adding py_ prefix for clarity
* src/py_color.C 1.27 (changed +30 -27)
Revised Python doc strings per Robin Betz's suggestions.
* src/py_menu.C 1.17 (changed +34 -8)
 2019-05-24johnsAdded VMDApp pointer safety checks.
* src/py_axes.C 1.17 (changed +8 -2)
Added safety checks for VMDApp pointers, per Robin Betz's patch.
Const correctness improvements for modern Python APIs.
* src/py_animate.C 1.24 (changed +70 -28)
Applied Robin Betz's patch to eliminate stray cr/lf pairs from the end
of atom selection macros using strcspn().
* src/vmd.C 1.105 (changed +5 -1)
Applied part of Robin Betz's patch adding new wrapper functions for
Python/C++ intrinsic type conversions that abstract key API differences
between Python 2.x and Python 3.x
* src/py_commands.C 1.18 (changed +62 -1)
Applied part of Robin Betz's patch adding new wrapper functions for
Python/C++ intrinsic type conversions that abstract key API differences
between Python 2.x and Python 3.x.
* src/py_commands.h 1.44 (changed +11 -1)
* src/py_commands.C 1.17 (changed +109 -1)
Const correctness for doc strings. Revised doc strings per Robin Betz's
suggestions.
* src/py_animate.C 1.23 (changed +15 -15)
Eliminated ancient const correctness workarounds for old versions of Python
* src/py_topo.C 1.3 (changed +16 -16)
* src/py_render.C 1.18 (changed +2 -4)
* src/py_display.C 1.37 (changed +12 -16)
* src/py_axes.C 1.16 (changed +11 -11)
Eliminated unnecessary calls to PyArg_ParseTuple() for Python methods that don't
need to accept any arguments, and changed their registration to METH_NOARGS.
* src/py_animate.C 1.25 (changed +10 -40)
Modernized all of the Python bindings. Since the Python APIs have been
const-correct for quite a few years now, there's no longer a reason to
hold onto old typecasts that were only needed by very old Python revs.
* src/py_trans.C 1.19 (changed +17 -17)
* src/py_topo.C 1.2 (changed +16 -16)
* src/py_render.C 1.17 (changed +3 -3)
* src/py_mouse.C 1.10 (changed +2 -2)
* src/py_molrep.C 1.27 (changed +22 -22)
* src/py_molecule.C 1.75 (changed +38 -38)
* src/py_menu.C 1.14 (changed +7 -7)
* src/py_measure.C 1.3 (changed +3 -3)
* src/py_material.C 1.29 (changed +8 -8)
* src/py_label.C 1.26 (changed +9 -9)
* src/py_imd.C 1.21 (changed +17 -17)
* src/py_graphics.C 1.28 (changed +17 -17)
* src/py_display.C 1.36 (changed +8 -8)
* src/py_color.C 1.25 (changed +14 -14)
* src/py_axes.C 1.15 (changed +3 -3)
* src/py_animate.C 1.21 (changed +15 -15)
* src/py_atomselection.C 1.55 (changed +14 -14)
Rename method fctns for clarity, adding py_ prefix to functions we're
registering.
* src/py_render.C 1.19 (changed +5 -7)
Renamed registered Python method fctns, adding py_ prefix for clarity
* src/py_atomsel.C 1.31 (changed +15 -16)
* src/py_animate.C 1.22 (changed +29 -29)
Rewrote VMD Python bindings to use the standard PyCFunction function pointer
typedef rather than our own vmdPyMethod function pointer typedef.
Python itself now provides what we need, so there's no longer any reason
to maintain our own type. The function pointer typedef originally made it
easier for us to use static file scope linkage to avoid namespace collisions.
Since the Python provided typedef is identical to ours, there should be no
impact from this change other than improved standardization/style.
* src/py_trans.C 1.18 (changed +17 -17)
* src/py_render.C 1.16 (changed +2 -2)
* src/py_mouse.C 1.9 (changed +1 -1)
* src/py_molrep.C 1.26 (changed +20 -20)
* src/py_molecule.C 1.74 (changed +22 -22)
* src/py_menu.C 1.13 (changed +4 -4)
* src/py_material.C 1.28 (changed +7 -7)
* src/py_label.C 1.25 (changed +9 -9)
* src/py_imd.C 1.20 (changed +5 -5)
* src/py_graphics.C 1.27 (changed +11 -11)
* src/py_display.C 1.35 (changed +7 -7)
* src/py_commands.h 1.43 (changed +1 -9)
* src/py_color.C 1.24 (changed +13 -13)
* src/py_axes.C 1.14 (changed +3 -3)
* src/py_atomsel.C 1.30 (changed +2 -2)
* src/py_animate.C 1.20 (changed +15 -15)
* src/PythonTextInterp.C 1.70 (changed +3 -3)
* src/py_atomselection.C 1.54 (changed +13 -13)
vmd-last-python2
2019-05-22johnsAdded API to query menu index from its string name, needed for Python 3 APIs
* src/VMDApp.h 1.252 (changed +3 -2)
* src/VMDApp.C 1.562 (changed +8 -2)
Added access to the NVML CPU affinity mask setting routine given a
specific caller-supplied GPU index. It is noted that the NVML docs
currently state that the back-end implementation is limited to 64 CPUs,
so I have contacted NVIDIA engineering to ask about this vis-a-vis
systems like the DGX-2 and the ORNL Summit compute nodes.
* src/CUDAWrapNVML.h 1.2 (changed +7 -0)
* src/CUDAWrapNVML.cu 1.2 (changed +25 -0)
Added missing include of the STL algorithm header
* src/colvarcomp_protein.C 1.10 (changed +1 -0)
* src/colvarcomp.C 1.15 (changed +1 -1)
Added the colvars dashboard plugin to the extension menus
* scripts/vmd/loadplugins.tcl 1.54 (changed +2 -1)
Comment out hooks for as-yet-unimplemented features in the video streaming
client implementation.
* src/OptiXRenderer.C 1.355 (changed +4 -4)
Corrected internal debug reporting of P2P GPU link states/features.
* src/CUDAUtil.cu 1.51 (changed +5 -5)
Corrected plugin list ordering
* scripts/vmd/loadplugins.tcl 1.55 (changed +2 -2)
Cranked version
* configure 1.1472 (changed +1 -1)
Eliminated unused resname string.
* src/Stride.C 1.43 (changed +2 -2)
Eliminated unused variables from the video streaming interactive RT client.
* src/OptiXRenderer.C 1.354 (changed +2 -6)
Ensure we get all of the fctn pointers we need for NVML
* src/CUDAWrapNVML.cu 1.3 (changed +2 -1)
Misc cleanup to eliminate compiler warnings about unreachable code
due to return statements in each of several different OS/platform-specific
ifdef blocks.
* src/vmdfsinfo.c 1.2 (changed +9 -10)
Protect new GPU device query APIs and P2P GPU topology routines with
conditional compilation.
* src/CUDAAccel.C 1.65 (changed +4 -2)
Pulled in Robin Betz's change to more gracefully handle mismatched
atom counts in the topolgy vs. the coordinate file buffers. Needs testing.
* src/VMDApp.C 1.563 (changed +15 -1)
* src/CoorPluginData.h 1.19 (changed +6 -1)
Updated colvars docs
* doc/ug_colvars.tex 1.18 (changed +217 -58)
* doc/ug_colvars.bib 1.6 (changed +11 -0)
Updated colvars to the latest git trunk.
* src/colvarvalue.h 1.10 (changed +9 -9)
* src/colvarvalue.C 1.11 (changed +4 -4)
* src/colvartypes.h 1.10 (changed +39 -36)
* src/colvartypes.C 1.9 (changed +50 -36)
* src/colvarscript.h 1.11 (changed +3 -2)
* src/colvarscript.C 1.22 (changed +49 -0)
* src/colvars_version.h 1.11 (changed +1 -1)
* src/colvars_files.pl 1.3 (changed +1 -0)
* src/colvarproxy_vmd_version.h 1.9 (changed +1 -1)
* src/colvarproxy_vmd.h 1.14 (changed +0 -2)
* src/colvarproxy_vmd.C 1.18 (changed +10 -9)
* src/colvarproxy.h 1.18 (changed +21 -2)
* src/colvarproxy.C 1.8 (changed +9 -6)
* src/colvarparse.h 1.10 (changed +120 -53)
* src/colvarparse.C 1.13 (changed +228 -195)
* src/colvarmodule.h 1.27 (changed +217 -68)
* src/colvarmodule.C 1.25 (changed +213 -16)
* src/colvargrid.h 1.18 (changed +37 -37)
* src/colvargrid.C 1.9 (changed +1 -1)
* src/colvardeps.h 1.10 (changed +48 -16)
* src/colvardeps.C 1.14 (changed +36 -310)
* src/colvarcomp_rotations.C 1.10 (changed +76 -33)
* src/colvarcomp_protein.C 1.9 (changed +89 -10)
* src/colvarcomp_distances.C 1.19 (changed +75 -19)
* src/colvarcomp_coordnums.C 1.11 (changed +6 -12)
* src/colvarcomp_angles.C 1.10 (changed +28 -33)
* src/colvarcomp.h 1.13 (changed +63 -15)
* src/colvarcomp.C 1.14 (changed +164 -7)
* src/colvarbias_restraint.h 1.10 (changed +2 -3)
* src/colvarbias_restraint.C 1.16 (changed +60 -66)
* src/colvarbias_meta.h 1.11 (changed +17 -15)
* src/colvarbias_meta.C 1.17 (changed +17 -15)
* src/colvarbias_histogram.h 1.5 (changed +1 -1)
* src/colvarbias_abf.h 1.8 (changed +25 -9)
* src/colvarbias_abf.C 1.20 (changed +7 -7)
* src/colvarbias.h 1.13 (changed +5 -2)
* src/colvarbias.C 1.17 (changed +80 -9)
* src/colvaratoms.h 1.12 (changed +41 -11)
* src/colvaratoms.C 1.20 (changed +108 -35)
* src/colvar_UIestimator.h 1.6 (changed +47 -46)
* src/colvar.h 1.15 (changed +22 -13)
* src/colvar.C 1.26 (changed +282 -153)
Updated device enumeration comments to prepare for incorporation of
user-specified GPU device masks along with P2P PCIe/NVLink topology info.
* src/CUDAAccel.C 1.64 (changed +5 -2)
Updated for Python 3.x APIs.
* src/VMDTkinterMenu.C 1.3 (changed +4 -0)
 2019-05-16johnsAdded CUDAWrapNVML to the build.
* configure 1.1471 (changed +1 -0)
Added code (John's BSD-licensed src) to access the NVML shared library
at runtime using a simple set of wrapper functions that ensure safety.
The NVML shared library provides access to important host platform GPU
hardware details such as the best CPU affinity mask associated with each
GPU, taking into account the NUMA node, PCIe topology, and NVLink
topology that exist on the system.
* src/CUDAWrapNVML.h 1.1 (added +137 -0)
* src/CUDAWrapNVML.cu 1.1 (added +316 -0)
Added commentary about where host-GPU management thread affinity
assignment should be done.
* src/CUDAUtil.cu 1.50 (changed +31 -1)
Added first phase of NVML open/query to make use of CPU-GPU affinity mask
information at the top level.
* src/CUDAAccel.h 1.27 (changed +14 -10)
* src/CUDAAccel.C 1.62 (changed +23 -2)
Updated src comments and eliminated a redundant safety check that's now
handled much earlier in the GPU initialization code.
* src/CUDAAccel.C 1.63 (changed +5 -5)
 2019-05-14johnsCorrected a few bits of logic in the console output deduplication code for
GPU device enumeration during startup.
* src/CUDAAccel.C 1.61 (changed +8 -5)
Corrected logic for runtime determination of DSSP / XDSSP location.
* src/Stride.C 1.42 (changed +9 -10)
Imported thread affinity reporting/analysis code from ongoing work on Summit
to make VMD play nice with batch systems like IBM's 'jsrun' tool that
lock-down CPU thread affinity prior to launching the child process.
The new VMD CPU affinity code tries to detect the situation where the
OS or batch system are externally enforcing CPU-thread affinity and
"do the right thing" during startup. This implies that we must accept
the external CPU thread affinity assignment and put all of the brains for
CPU-GPU thread/context affinity in the CUDA startup code since we won't
be able to influence which CPU core or socket the host threads run on.
* src/VMDApp.C 1.561 (changed +23 -27)
 2019-05-03johnsTrack number of physical GPU devices as well as the number that are
available, for use in detailed formatting of console status output.
Draft implementation of condensed GPU console output inspired by the
approach taken by Solaris 'dmesg' to reduce repetitive syslog output.
* src/CUDAAccel.h 1.26 (changed +4 -3)
* src/CUDAAccel.C 1.60 (changed +119 -34)
 2019-05-02johnsAdded further comments for GPU P2P topology analysis and reporting routines
in preparation for adding abstractions to fully support the combination of
user-defined GPU device selection masks in combination with P2P kernels that
need to be able to access P2P topology info to enable and exploit P2P transfers,
direct GPU P2P memory access, etc.
* src/CUDAAccel.C 1.58 (changed +14 -1)
Revised description of the CUDAAccel class to make it clearer to the
uninitiated why it needs to exist and why all of the CUDA code in VMD
needs to use the various device query routines it provides rather than
making direct use of the underlying CUDA runtime or driver APIs themselves.
* src/CUDAAccel.h 1.25 (changed +12 -3)
* src/CUDAAccel.C 1.59 (changed +12 -3)
Revised the VMD CUDA startup code to enable analysis of the PCIe/NVLink
peer-to-peer communication topology, along with determination and reporting
of the total number of GPU P2P links and islands.
* src/CUDAUtil.cu 1.49 (changed +43 -8)
* src/CUDAKernels.h 1.60 (changed +2 -1)
* src/CUDAAccel.C 1.57 (changed +15 -7)
 2019-05-01ryanmcgreevyUpdated documentation for voltool to include new mask, write, hist, and info commands.
* doc/ug_text_ui.tex 1.238 (changed +19 -2)
 2019-05-01johnsAdded VMD info message when kernel-bypass I/O is disabled when operating
on files located on a remote filesystem.
* src/VMDApp.C 1.560 (changed +6 -1)
Added thin cross-platform wrappers to help VMD determine whether a given
file is located on a local or remote filesystem, to help determine whether
or not to engage kernel-bypass direct-I/O when reading gigabytes or terabytes
of trajectory data. This is particularly helpful on very large
RAID-0 SSD-cached filesystems such as the NFS cache mechanism on the
NVIDIA DGX-2.
* src/vmdfsinfo.h 1.1 (added +58 -0)
* src/vmdfsinfo.c 1.1 (added +169 -0)
Added vmdfsinfo sources to the build.
* configure 1.1470 (changed +2 -1)
Determine whether a given file on a local or remote filesystem.
We don't engage kernel-bypass direct-I/O when reading from
remote filesystems, as it turns out that filesystem caching
mechanisms like the Linux 'cachefilesd' daemon interpret
Unix direct-I/O (e.g. O_DIRECT) calls to be NFS-cache-bypassing
I/O operations, which is not what we want in that particular case.
We want local NFS caches to be utilized rather than hitting the
network, so in the case of remote filesystems we now revert to
normal I/O. We only engage kernel-bypass I/O when the file of
interest resides on a local filesystem where there are no
surprising side effects from direct-I/O. This is particularly
beneficial on the NVIDIA DGX-2 which incorporates a large 30+TB
RAID-0 NFS cache, as an example.
The implementation modifies the behavior the block-sized memory alignment
queries to cause the desired behavior on the side of the molfile plugins.
If we don't query the page alignment size, the associated molfile plugin
will have to assume that we can't support kernel-bypassing
block-based direct-I/O, and will revert to using normal I/O.
* src/VMDApp.C 1.559 (changed +23 -2)
Doxygenized filesystem locality APIs
* src/vmdfsinfo.h 1.2 (changed +11 -11)
Revised internal APIs for query of CUDA peer-to-peer NVLink connectivity
and GPU peer-to-peer link capabilities (performance, native atomic support, etc).
* src/CUDAUtil.cu 1.48 (changed +36 -24)
* src/CUDAKernels.h 1.59 (changed +8 -2)
* src/CUDAAccel.C 1.56 (changed +18 -2)
 2019-04-26johnsAdded comment about driver version check calls and their startup perf cost
* src/CUDAUtil.cu 1.46 (changed +2 -1)
Benchmarked VMD startup time on the NVIDIA DGX-2 and annotated the source
code with comments about the costs associated with each startup phase.
The overall CUDA-associated startup time is roughly 9.7 seconds on
the DGX-2 w/ 16 GPUs.
* src/CUDAUtil.cu 1.47 (changed +5 -1)
* src/CUDAAccel.C 1.55 (changed +15 -1)
Replace a missing conditional macro definition test needed to maintain
support for OptiX 4.x on ORNL Titan and NCSA Blue Waters, for the time being.
* src/OptiXRenderer.h 1.120 (changed +18 -1)
 2019-04-25johnsBegan adaptation of the VMD startup code to add a bunch of new hardware
queries about GPU-Host memory coherency, page table access, and wrote
an early draft query for determining the system-wide NVLink connectivity
and observed topological features such as the number of connected NVLink
islands, etc.
* src/CUDAUtil.cu 1.45 (changed +116 -6)
* src/CUDAKernels.h 1.58 (changed +16 -8)
* src/CUDAAccel.h 1.24 (changed +5 -1)
* src/CUDAAccel.C 1.54 (changed +51 -4)
 2019-04-14johnsSignificantly revised the CUDA startup device query code to eliminate
ancient #ifdef blocks for CUDA versions 4.0 and below. Added device
properties query for single-precision to double-precision perf ratio,
which can be useful to know for selection of particular arithmetic
strategies at runtime.
* src/CUDAUtil.cu 1.44 (changed +12 -35)
* src/CUDAKernels.h 1.57 (changed +3 -2)
* src/CUDAAccel.h 1.23 (changed +3 -1)
* src/CUDAAccel.C 1.53 (changed +21 -8)
 2019-04-12johnsAdded support for computing secondary structure using DSSP, either the
old original code or the newer descendant "xdssp" tools produced by
different authors.
* src/Stride.h 1.14 (changed +2 -1)
* src/Stride.C 1.41 (changed +179 -1)
* src/DrawMolecule.C 1.146 (changed +15 -1)
 2019-03-29ryanmcgreevyChanged the histogram code to use longs to avoid integer overflow issues on large density maps
* src/Voltool.h 1.9 (changed +3 -3)
* src/Voltool.C 1.8 (changed +5 -5)
* src/TclVoltool.C 1.6 (changed +2 -2)
 2019-03-28johnsGeneralized the naming and description of the secondary structure input
generator for Stride since the same approach also works for DSSP.
* src/Stride.h 1.13 (changed +5 -1)
* src/Stride.C 1.40 (changed +8 -7)
Misc cleanup of some ancient and hideous code in the STRIDE interface,
so that it doesn't provide a poor example for implementing DSSP and other
interfaces.
* src/Stride.C 1.39 (changed +44 -39)
OptiX 6.x build by default
* configure 1.1469 (changed +3 -3)
raytracinggems2019
2019-03-12johnsRemoved the pedagogical variants of the dome master camera projection implementations
that were really intended just for the Ray Tracing Gems book chapter. They were
included in VMD only to ensure that there were no significant problems in the
decomposed and simplified implementations that were included inline within the
book chapter. Now that the book has been finalized, there is no longer a
reason to maintain these alternative pedagogical implementations within the
VMD source code itself, and we can revert to the fully inlined and more mathematically
streamlined implementations that have been in use for the CADENS project up to now.
* src/OptiXShaders.cu 1.168 (changed +16 -229)
Replaced the original dome master implementation that was used for the
CADENS dome show renderings with the more optimal formulation that
resulted from the more thorough math checking that was done for the
Ray Tracing Gems book chapter. This version uses the same variable name
nomenclature found in the RTG chapter, and it eliminates a few normalization
operations that are avoidable due to the details of the underlying projection
arithmetic. For the final CADENS production renderings it was more important
to ensure 100% consistency of the image content despite multiple years of
development time and revisions to VMD intervening between the earlist
test shots and final rendering. Now that the "Birth of Planet Earth" dome
masters are finalized, there's no longer a reason to maintain the verbatim
original code. Any future CADENS dome renderings will now be done with the
latest RTG-descendant code instead.
* src/OptiXShaders.cu 1.169 (changed +1 -128)
Revised comments pertaining to global context-wide RTX initialization for
final OptiX 6.0.0 API behavior.
* src/OptiXRenderer.C 1.352 (changed +9 -7)
The rtContext[GS]etStackSize() APIs are not supported when
using the RTX execution strategy. Although they don't (yet)
return errors in that case, we protect against calling them
except when running in a non-RTX mode.
Presumably these APIs will be deprecated in future OptiX releases.
* src/OptiXRenderer.C 1.351 (changed +6 -1)
Updated and added details after re-testing the RTX-specific hardware
triangle instance list destruction code path with OptiX 6.0 and
the 418.30 drivers.
* src/OptiXRenderer.C 1.350 (changed +7 -3)
Updated the Ray Tracing Gems book references in the OptiX code to point
to the Apress web site, and add the final chapter and page numbers.
* src/OptiXShaders.h 1.39 (changed +5 -3)
* src/OptiXShaders.cu 1.167 (changed +19 -1)
* src/OptiXRenderer.h 1.119 (changed +5 -3)
* src/OptiXRenderer.C 1.353 (changed +5 -3)
* src/OptiXDisplayDevice.h 1.26 (changed +5 -3)
* src/OptiXDisplayDevice.C 1.77 (changed +5 -3)
Updated the VMD OptiX renderer to make use of the new OptiX 6.0.0 APIs
required for runtime calculation of stack size required for a given
max ray tracing recursion depth. Revised the internal shader state
recursion depth and transmission ray depth counter variables
to use unsigned types so they are consistent with the new OptiX APIs
and new the context-wide recursion limit state. The change from
signed to unsigned types for the shader-internal counters comes with
slight complexity in handling of transmission ray surface crossing counting
since we can no longer blindly decrement the surface crossing counter
and compare using less than or equal to 1, since we can now have integer
wrarparound. Using the expression (new.transcnt = max(1, old.transcnt) - 1)
resolves the basic problem albeit with extra complexity. It may be desirable
to reformulate the transmission ray surface crossing implementation to count
up rather than down, which deviates from the original Tachyon CPU
implementation, but is probably the right thing to do in light of the
new OptiX 6.0 APIs favoring unsigned types for recursion counts and the like.
* src/OptiXShaders.cu 1.166 (changed +11 -10)
* src/OptiXRenderer.h 1.118 (changed +4 -1)
* src/OptiXRenderer.C 1.349 (changed +61 -52)
 2019-03-08johnsImported the more streamlined dome master camera version as provided
for the book chapter.
* src/OptiXShaders.cu 1.165 (changed +115 -2)
 2019-02-27ryanmcgreevyCreated new method for writing volumetric data to files using molfile plugin interface instead of the hacky code in Volmap. The method is now used by all the voltool commands when the output option is used. The write_file method parses the output file name to determine the extension and load the correct molfile plugin. However, currently only the dx plugin is capable of writing. As writing capability is added to other volumetric data molfile plugins, the existing voltool code should work correctly as is.
* src/Voltool.h 1.8 (changed +3 -3)
* src/Voltool.C 1.7 (changed +5 -4)
* src/TclVoltool.C 1.5 (changed +231 -27)
 2019-02-26johnsCranked version
* configure 1.1467 (changed +3 -3)
Make another set of OptiX 5.1.0 builds for people with old drivers.
* configure 1.1468 (changed +2 -2)
 2019-02-22johnsOptiX 6.0 has dropped support for the VCA remote device APIs, so they
are now only conditionally compiled into VMD based on the OptiX version number
in use.
* src/OptiXShaders.h 1.38 (changed +2 -2)
* src/OptiXRenderer.h 1.117 (changed +3 -3)
* src/OptiXRenderer.C 1.347 (changed +3 -3)
Updated all of the VMD OptiX API calls for the final OptiX 6.0.0 API.
* src/OptiXRenderer.C 1.348 (changed +33 -27)
VMD versions built with OptiX 6.0.0 and greater no longer support
remote cluster-based rendering since the cluster rendering APIs are
deprecated as of OptiX 6.
* src/FileRenderList.C 1.97 (changed +3 -3)
 2019-02-21johnsAdded special shader modifications used for the final dome master renderings
for the NSF CADENS "Birth of Planet Earth" fulldome movie.
* src/OptiXShaders.cu 1.164 (changed +43 -1)
 2019-02-20johnsChanged conditional compilation to require OptiX version 6.0.0 or later
for RTX rather than prior versions, since we still have developmental
builds with old APIs hanging around on other platforms like ppc64le.
* src/OptiXShaders.h 1.37 (changed +2 -2)
* src/OptiXRenderer.h 1.116 (changed +2 -2)
 2019-02-08johnsCranked version
* configure 1.1466 (changed +1 -1)
* configure 1.1465 (changed +1 -1)
 2019-02-07johnsApplied patch from Robin Betz to correct mismatched calloc()/delete []
with a corrected call to free().
* src/ParseTree.C 1.150 (changed +2 -2)
Don't attempt to free the setids list if it's not allocated.
* src/VMDApp.h 1.251 (changed +3 -2)
Patch from Robin Betz prevents leak of per-node hardware stat/info
records during call to vmd_mpi_nodescan(),
* src/VMDMPI.C 1.23 (changed +2 -1)
 2019-01-30ryanmcgreevyUpdated sim to load density to new molecule and make output to file optional
* src/TclMDFF.C 1.30 (changed +8 -8)
 2019-01-29johnsAdded compilation rules for NVTX V3 profiling APIs in CUDA >= 10
* configure 1.1464 (changed +4 -2)
Began updating VMD profiling infrastructure for NVTX V3 APIs in CUDA 10
and later.
* src/ProfileHooks.h 1.18 (changed +3 -2)
 2019-01-25ryanmcgreevyAdded new mask command in Voltool, which masks a map around an atom selection. This command combines the previous two-step process between volmap and volutil into a single command that is executed entirely in memory and foregoes file i/o.
* src/TclVoltool.C 1.4 (changed +147 -1)
 2019-01-24johnsUpdated the UIVR tool methods to improve atom selection traversal with
the use of firstsel/lastsel
* src/P_Tool.C 1.84 (changed +9 -8)
 2019-01-23johnsAccelerate atom selection traversal using sel->firstsel and sel->lastsel
to split traversal loops into three separate stages, eliminating
all conditional assignments and branching from the the beginning and end loops.
* src/TclMeasure.C 1.171 (changed +24 -8)
Applied Giacomo Fiorin's patch to correct the behavior of the
volmap commands that accept weights, when processing MD trajectories.
Previously, the code worked correctly only by coincidence, as there
were no safety checks to determine if the number of weights could vary
due to selections having dependencies on time-varying properties.
Discussing with Giacomo, the most logical approach was to develop a new
scheme for handling this case rather than maintaining the old approach
that used the tc_get_weights() routine in an unsafe manner.
* src/VolMapCreate.h 1.93 (changed +11 -3)
* src/VolMapCreate.C 1.124 (changed +28 -12)
* src/TclVolMap.C 1.122 (changed +38 -10)
* src/TclMeasure.C 1.170 (changed +68 -1)
* src/TclCommands.h 1.56 (changed +16 -1)
Revised color lookup update routine to exploit firstsel/lastsel to
improve atom selection traversal performance.
* src/DrawMolItem.C 1.367 (changed +2 -2)
Updated the Python atom selection interface to make use of
firstsel/lastsel to improve atom selection traversal performance.
* src/py_atomsel.C 1.29 (changed +6 -6)
* src/py_atomselection.C 1.53 (changed +3 -3)
 2019-01-17johnsCranked version
* configure 1.1463 (changed +1 -1)
Updated colvars docs
* doc/ug_colvars.tex 1.17 (changed +2359 -2211)
Updated copyright headers
* src/win32vmdstart.h 1.11 (changed +2 -2)
* src/win32vmdstart.c 1.46 (changed +2 -2)
* src/vmdsock.h 1.17 (changed +2 -2)
* src/vmdsock.c 1.29 (changed +2 -2)
* src/vmdmain.C 1.18 (changed +2 -2)
* src/vmddlopen.h 1.12 (changed +2 -2)
* src/vmddlopen.c 1.21 (changed +2 -2)
* src/vmdconsole.h 1.10 (changed +2 -2)
* src/vmdconsole.c 1.13 (changed +2 -2)
* src/vmd.h 1.12 (changed +2 -2)
* src/vmd.C 1.104 (changed +2 -2)
* src/utilities.h 1.111 (changed +2 -2)
* src/utilities.C 1.173 (changed +3 -3)
* src/util_simd.C 1.13 (changed +2 -2)
* src/tcl_commands.h 1.29 (changed +2 -2)
* src/tcl_commands.C 1.56 (changed +2 -2)
* src/py_trans.C 1.17 (changed +2 -2)
* src/py_render.C 1.15 (changed +2 -2)
* src/py_numeric.C 1.22 (changed +2 -2)
* src/py_mouse.C 1.8 (changed +1 -1)
* src/py_molrep.C 1.25 (changed +2 -2)
* src/py_molecule.C 1.73 (changed +2 -2)
* src/py_menu.C 1.12 (changed +1 -1)
* src/py_material.C 1.27 (changed +2 -2)
* src/py_label.C 1.24 (changed +2 -2)
* src/py_imd.C 1.19 (changed +2 -2)
* src/py_graphics.C 1.26 (changed +2 -2)
* src/py_display.C 1.34 (changed +2 -2)
* src/py_commands.h 1.42 (changed +2 -2)
* src/py_commands.C 1.16 (changed +2 -2)
* src/py_color.C 1.23 (changed +2 -2)
* src/py_axes.C 1.13 (changed +2 -2)
* src/py_atomsel.C 1.28 (changed +2 -2)
* src/py_animate.C 1.19 (changed +2 -2)
* src/ptrstack.h 1.3 (changed +2 -2)
* src/ptrstack.c 1.3 (changed +2 -2)
* src/macosxvmdstart.C 1.26 (changed +2 -2)
* src/intstack.h 1.9 (changed +2 -2)
* src/intstack.c 1.10 (changed +2 -2)
* src/inthash.h 1.10 (changed +2 -2)
* src/inthash.c 1.9 (changed +2 -2)
* src/imd.h 1.23 (changed +2 -2)
* src/imd.C 1.20 (changed +2 -2)
* src/hash.h 1.17 (changed +2 -2)
* src/hash.c 1.17 (changed +2 -2)
* src/frame_selector.h 1.12 (changed +2 -2)
* src/frame_selector.C 1.22 (changed +2 -2)
* src/cmd_vmdbench.C 1.26 (changed +2 -2)
* src/cmd_videostream.C 1.9 (changed +2 -2)
* src/cmd_util.C 1.36 (changed +2 -2)
* src/cmd_user.C 1.28 (changed +2 -2)
* src/cmd_trans.C 1.26 (changed +2 -2)
* src/cmd_tool.C 1.36 (changed +2 -2)
* src/cmd_spaceball.C 1.10 (changed +2 -2)
* src/cmd_render.C 1.47 (changed +2 -2)
* src/cmd_profile.C 1.5 (changed +2 -2)
* src/cmd_plugin.C 1.25 (changed +2 -2)
* src/cmd_parallel.C 1.34 (changed +2 -2)
* src/cmd_mouse.C 1.30 (changed +2 -2)
* src/cmd_mol.C 1.133 (changed +2 -2)
* src/cmd_mobile.C 1.10 (changed +3 -3)
* src/cmd_menu.C 1.38 (changed +2 -2)
* src/cmd_material.C 1.31 (changed +2 -2)
* src/cmd_label.C 1.49 (changed +2 -2)
* src/cmd_imd.C 1.27 (changed +2 -2)
* src/cmd_display.C 1.78 (changed +2 -2)
* src/cmd_color.C 1.40 (changed +2 -2)
* src/cmd_collab.C 1.10 (changed +2 -2)
* src/cmd_animate.C 1.52 (changed +2 -2)
* src/androidvmdstart.h 1.3 (changed +3 -3)
* src/androidvmdstart.C 1.8 (changed +2 -2)
* src/X3DDisplayDevice.h 1.14 (changed +2 -2)
* src/X3DDisplayDevice.C 1.47 (changed +2 -2)
* src/Win32ftp.h 1.12 (changed +2 -2)
* src/Win32ftp.C 1.14 (changed +2 -2)
* src/Win32OpenGLDisplayDevice.C 1.124 (changed +2 -2)
* src/Win32Joystick.h 1.18 (changed +2 -2)
* src/Win32Joystick.C 1.27 (changed +2 -2)
* src/WavefrontDisplayDevice.h 1.16 (changed +2 -2)
* src/WavefrontDisplayDevice.C 1.30 (changed +2 -2)
* src/Watershed.h 1.17 (changed +3 -3)
* src/Watershed.C 1.36 (changed +3 -3)
* src/VrmlDisplayDevice.h 1.28 (changed +2 -2)
* src/VrmlDisplayDevice.C 1.40 (changed +2 -2)
* src/Vrml2DisplayDevice.h 1.29 (changed +2 -2)
* src/Vrml2DisplayDevice.C 1.45 (changed +2 -2)
* src/VolumetricData.h 1.47 (changed +2 -2)
* src/VolumetricData.C 1.60 (changed +3 -3)
* src/VolumeTexture.h 1.9 (changed +2 -2)
* src/VolumeTexture.C 1.23 (changed +2 -2)
* src/VolMapCreateILS.C 1.169 (changed +2 -2)
* src/VolMapCreate.h 1.92 (changed +2 -2)
* src/VolMapCreate.C 1.123 (changed +2 -2)
* src/VolCPotential.h 1.7 (changed +2 -2)
* src/VolCPotential.C 1.30 (changed +2 -2)
* src/VideoStream.h 1.21 (changed +2 -2)
* src/VideoStream.C 1.34 (changed +2 -2)
* src/VRJugglerTracker.h 1.4 (changed +2 -2)
* src/VRJugglerTracker.C 1.4 (changed +2 -2)
* src/VRJugglerSharedData.h 1.4 (changed +2 -2)
* src/VRJugglerSharedData.C 1.4 (changed +2 -2)
* src/VRJugglerScene.h 1.4 (changed +2 -2)
* src/VRJugglerScene.C 1.5 (changed +2 -2)
* src/VRJugglerRoutines.h 1.4 (changed +2 -2)
* src/VRJugglerRoutines.C 1.4 (changed +2 -2)
* src/VRJugglerDisplayDevice.h 1.4 (changed +2 -2)
* src/VRJugglerDisplayDevice.C 1.4 (changed +2 -2)
* src/VRJugglerButtons.h 1.4 (changed +2 -2)
* src/VRJugglerButtons.C 1.4 (changed +2 -2)
* src/VRJugglerApp.h 1.4 (changed +2 -2)
* src/VRJugglerApp.C 1.4 (changed +2 -2)
* src/VMDTkinterMenu.h 1.10 (changed +1 -1)
* src/VMDTkMenu.h 1.13 (changed +2 -2)
* src/VMDTkMenu.C 1.20 (changed +2 -2)
* src/VMDTitle.h 1.33 (changed +2 -2)
* src/VMDTitle.C 1.60 (changed +2 -2)
* src/VMDThreads.h 1.56 (changed +2 -2)
* src/VMDThreads.C 1.91 (changed +2 -2)
* src/VMDQuat.h 1.12 (changed +2 -2)
* src/VMDQuat.C 1.13 (changed +2 -2)
* src/VMDMenu.h 1.16 (changed +2 -2)
* src/VMDMenu.C 1.11 (changed +2 -2)
* src/VMDMPI.h 1.8 (changed +2 -2)
* src/VMDMPI.C 1.22 (changed +2 -2)
* src/VMDFltkMenu.h 1.36 (changed +2 -2)
* src/VMDFltkMenu.C 1.29 (changed +2 -2)
* src/VMDDisplayList.h 1.44 (changed +2 -2)
* src/VMDDisplayList.C 1.40 (changed +2 -2)
* src/VMDDir.h 1.14 (changed +2 -2)
* src/VMDDir.C 1.16 (changed +2 -2)
* src/VMDCollab.h 1.8 (changed +2 -2)
* src/VMDCollab.C 1.11 (changed +2 -2)
* src/VMDApp.h 1.250 (changed +2 -2)
* src/VMDApp.C 1.558 (changed +2 -2)
* src/UIText.h 1.79 (changed +2 -2)
* src/UIText.C 1.198 (changed +2 -2)
* src/UIObject.h 1.40 (changed +2 -2)
* src/UIObject.C 1.43 (changed +2 -2)
* src/ToolFltkMenu.h 1.16 (changed +2 -2)
* src/ToolFltkMenu.C 1.35 (changed +2 -2)
* src/Timestep.h 1.53 (changed +2 -2)
* src/Timestep.C 1.71 (changed +2 -2)
* src/TextInterp.h 1.33 (changed +3 -3)
* src/TextEvent.h 1.53 (changed +1 -1)
* src/TclVolMap.C 1.121 (changed +2 -2)
* src/TclVec.C 1.44 (changed +2 -2)
* src/TclTextInterp.h 1.46 (changed +2 -2)
* src/TclTextInterp.C 1.118 (changed +2 -2)
* src/TclMolInfo.C 1.97 (changed +2 -2)
* src/TclMeasure.C 1.169 (changed +2 -2)
* src/TclGraphics.C 1.49 (changed +2 -2)
* src/TclFastPBC.C 1.3 (changed +2 -2)
* src/TclCommands.h 1.55 (changed +2 -2)
* src/TclCommands.C 1.169 (changed +2 -2)
* src/TachyonDisplayDevice.h 1.47 (changed +2 -2)
* src/TachyonDisplayDevice.C 1.128 (changed +2 -2)
* src/SymbolTable.h 1.61 (changed +2 -2)
* src/SymbolTable.C 1.62 (changed +2 -2)
* src/Surf.h 1.24 (changed +2 -2)
* src/Surf.C 1.51 (changed +2 -2)
* src/Stride.h 1.12 (changed +2 -2)
* src/Stride.C 1.38 (changed +2 -2)
* src/Stage.h 1.41 (changed +2 -2)
* src/Stage.C 1.53 (changed +2 -2)
* src/Stack.h 1.28 (changed +2 -2)
* src/SpringTool.h 1.17 (changed +1 -1)
* src/SpringTool.C 1.26 (changed +1 -1)
* src/SpatialSearch.h 1.7 (changed +2 -2)
* src/SpatialSearch.C 1.24 (changed +2 -2)
* src/SpaceballTracker.h 1.17 (changed +2 -2)
* src/SpaceballTracker.C 1.18 (changed +2 -2)
* src/SpaceballButtons.h 1.5 (changed +2 -2)
* src/SpaceballButtons.C 1.5 (changed +2 -2)
* src/Spaceball.h 1.31 (changed +2 -2)
* src/Spaceball.C 1.63 (changed +2 -2)
* src/SortableArray.h 1.26 (changed +2 -2)
* src/SnapshotDisplayDevice.h 1.26 (changed +2 -2)
* src/SnapshotDisplayDevice.C 1.48 (changed +2 -2)
* src/SmallRingLinkages.h 1.9 (changed +2 -2)
* src/SmallRing.h 1.11 (changed +2 -2)
* src/SelectionBuilder.h 1.15 (changed +2 -2)
* src/SelectionBuilder.C 1.30 (changed +2 -2)
* src/Segmentation.h 1.6 (changed +2 -2)
* src/Segmentation.C 1.28 (changed +3 -3)
* src/Scene.h 1.64 (changed +2 -2)
* src/Scene.C 1.91 (changed +2 -2)
* src/ScaleSpaceFilter.h 1.9 (changed +2 -2)
* src/ScaleSpaceFilter.C 1.21 (changed +2 -2)
* src/SaveTrajectoryFltkMenu.h 1.17 (changed +2 -2)
* src/SaveTrajectoryFltkMenu.C 1.41 (changed +2 -2)
* src/STLDisplayDevice.h 1.25 (changed +2 -2)
* src/STLDisplayDevice.C 1.40 (changed +2 -2)
* src/SDLOpenGLDisplayDevice.C 1.40 (changed +2 -2)
* src/ResizeArray.h 1.53 (changed +2 -2)
* src/Residue.h 1.36 (changed +2 -2)
* src/RenderManDisplayDevice.h 1.30 (changed +2 -2)
* src/RenderManDisplayDevice.C 1.60 (changed +2 -2)
* src/RenderFltkMenu.h 1.13 (changed +1 -1)
* src/RenderFltkMenu.C 1.22 (changed +1 -1)
* src/RayShadeDisplayDevice.h 1.30 (changed +2 -2)
* src/RayShadeDisplayDevice.C 1.47 (changed +2 -2)
* src/RadianceDisplayDevice.h 1.33 (changed +2 -2)
* src/RadianceDisplayDevice.C 1.48 (changed +2 -2)
* src/R3dDisplayDevice.h 1.37 (changed +2 -2)
* src/R3dDisplayDevice.C 1.88 (changed +2 -2)
* src/QuickSurf.h 1.21 (changed +2 -2)
* src/QuickSurf.C 1.122 (changed +2 -2)
* src/QMTimestep.h 1.41 (changed +2 -2)
* src/QMTimestep.C 1.71 (changed +2 -2)
* src/QMData.h 1.87 (changed +2 -2)
* src/QMData.C 1.104 (changed +2 -2)
* src/PythonTextInterp.h 1.28 (changed +2 -2)
* src/PythonTextInterp.C 1.69 (changed +2 -2)
* src/ProfileHooks.h 1.17 (changed +2 -2)
* src/PluginMgr.h 1.17 (changed +2 -2)
* src/PluginMgr.C 1.38 (changed +2 -2)
* src/PlainTextInterp.h 1.12 (changed +2 -2)
* src/PlainTextInterp.C 1.13 (changed +2 -2)
* src/Pickable.h 1.34 (changed +2 -2)
* src/PickModeUser.h 1.7 (changed +1 -1)
* src/PickModeUser.C 1.8 (changed +2 -2)
* src/PickModeMove.h 1.16 (changed +2 -2)
* src/PickModeMove.C 1.24 (changed +2 -2)
* src/PickModeMolLabel.h 1.28 (changed +2 -2)
* src/PickModeMolLabel.C 1.46 (changed +2 -2)
* src/PickModeList.h 1.13 (changed +2 -2)
* src/PickModeList.C 1.18 (changed +2 -2)
* src/PickModeForce.h 1.16 (changed +2 -2)
* src/PickModeForce.C 1.16 (changed +2 -2)
* src/PickModeCenter.h 1.21 (changed +2 -2)
* src/PickModeCenter.C 1.33 (changed +2 -2)
* src/PickModeAddBond.h 1.13 (changed +1 -1)
* src/PickModeAddBond.C 1.19 (changed +2 -2)
* src/PickMode.h 1.26 (changed +2 -2)
* src/PickList.h 1.36 (changed +2 -2)
* src/PickList.C 1.49 (changed +2 -2)
* src/PhoneTracker.h 1.5 (changed +2 -2)
* src/PhoneTracker.C 1.6 (changed +2 -2)
* src/PhoneButtons.h 1.4 (changed +2 -2)
* src/PhoneButtons.C 1.5 (changed +2 -2)
* src/ParseTree.h 1.45 (changed +2 -2)
* src/ParseTree.C 1.149 (changed +2 -2)
* src/P_VRPNTracker.h 1.26 (changed +2 -2)
* src/P_VRPNTracker.C 1.29 (changed +2 -2)
* src/P_VRPNFeedback.h 1.28 (changed +2 -2)
* src/P_VRPNFeedback.C 1.35 (changed +2 -2)
* src/P_VRPNButtons.h 1.27 (changed +2 -2)
* src/P_VRPNButtons.C 1.28 (changed +2 -2)
* src/P_UIVR.h 1.74 (changed +2 -2)
* src/P_UIVR.C 1.138 (changed +2 -2)
* src/P_TugTool.h 1.42 (changed +2 -2)
* src/P_TugTool.C 1.54 (changed +2 -2)
* src/P_Tracker.h 1.30 (changed +2 -2)
* src/P_Tracker.C 1.24 (changed +2 -2)
* src/P_Tool.h 1.67 (changed +2 -2)
* src/P_Tool.C 1.83 (changed +2 -2)
* src/P_SensorConfig.h 1.28 (changed +2 -2)
* src/P_SensorConfig.C 1.41 (changed +2 -2)
* src/P_RotateTool.h 1.35 (changed +2 -2)
* src/P_RotateTool.C 1.46 (changed +2 -2)
* src/P_PrintTool.h 1.12 (changed +2 -2)
* src/P_PrintTool.C 1.13 (changed +2 -2)
* src/P_PinchTool.h 1.19 (changed +1 -1)
* src/P_PinchTool.C 1.22 (changed +1 -1)
* src/P_JoystickTool.h 1.32 (changed +2 -2)
* src/P_JoystickTool.C 1.40 (changed +2 -2)
* src/P_JoystickButtons.h 1.19 (changed +2 -2)
* src/P_JoystickButtons.C 1.18 (changed +2 -2)
* src/P_GrabTool.h 1.26 (changed +2 -2)
* src/P_GrabTool.C 1.34 (changed +2 -2)
* src/P_FreeVRTracker.h 1.18 (changed +2 -2)
* src/P_FreeVRTracker.C 1.18 (changed +2 -2)
* src/P_FreeVRButtons.h 1.18 (changed +2 -2)
* src/P_FreeVRButtons.C 1.20 (changed +2 -2)
* src/P_Feedback.h 1.28 (changed +2 -2)
* src/P_CmdTool.h 1.37 (changed +2 -2)
* src/P_CmdTool.C 1.49 (changed +2 -2)
* src/P_CaveTracker.h 1.20 (changed +2 -2)
* src/P_CaveTracker.C 1.19 (changed +2 -2)
* src/P_CaveButtons.h 1.22 (changed +2 -2)
* src/P_CaveButtons.C 1.20 (changed +2 -2)
* src/P_Buttons.h 1.25 (changed +2 -2)
* src/P_Buttons.C 1.20 (changed +2 -2)
* src/PSDisplayDevice.h 1.42 (changed +2 -2)
* src/PSDisplayDevice.C 1.115 (changed +2 -2)
* src/POV3DisplayDevice.h 1.48 (changed +2 -2)
* src/POV3DisplayDevice.C 1.127 (changed +2 -2)
* src/Orbital.h 1.43 (changed +2 -2)
* src/Orbital.C 1.150 (changed +2 -2)
* src/OptiXShaders.cu 1.162 (changed +244 -55)
* src/OptiXRenderer.h 1.115 (changed +2 -2)
* src/OptiXDisplayDevice.h 1.25 (changed +2 -2)
* src/OpenGLStipples.h 1.11 (changed +2 -2)
* src/OpenGLShader.h 1.14 (changed +2 -2)
* src/OpenGLShader.C 1.29 (changed +2 -2)
* src/OpenGLRenderer.h 1.150 (changed +2 -2)
* src/OpenGLRenderer.C 1.467 (changed +2 -2)
* src/OpenGLPbufferDisplayDevice.h 1.11 (changed +2 -2)
* src/OpenGLPbufferDisplayDevice.C 1.27 (changed +2 -2)
* src/OpenGLExtensions.h 1.55 (changed +2 -2)
* src/OpenGLExtensions.C 1.81 (changed +2 -2)
* src/OpenGLDisplayDevice.h 1.57 (changed +2 -2)
* src/OpenGLDisplayDevice.C 1.210 (changed +2 -2)
* src/OpenGLCache.h 1.10 (changed +2 -2)
* src/OpenGLCache.C 1.10 (changed +2 -2)
* src/OpenCLKernels.h 1.8 (changed +2 -2)
* src/OSPRayRenderer.h 1.24 (changed +2 -2)
* src/OSPRayDisplayDevice.h 1.13 (changed +2 -2)
* src/NanoShaperInterface.h 1.7 (changed +2 -2)
* src/NanoShaperInterface.C 1.13 (changed +2 -2)
* src/NameList.h 1.49 (changed +2 -2)
* src/NVENCMgr.h 1.3 (changed +2 -2)
* src/NVENCMgr.C 1.5 (changed +2 -2)
* src/Mouse.h 1.69 (changed +2 -2)
* src/Mouse.C 1.150 (changed +2 -2)
* src/MoleculeList.h 1.71 (changed +2 -2)
* src/MoleculeList.C 1.120 (changed +2 -2)
* src/MoleculeGraphics.h 1.49 (changed +2 -2)
* src/MoleculeGraphics.C 1.76 (changed +2 -2)
* src/Molecule.h 1.64 (changed +2 -2)
* src/Molecule.C 1.92 (changed +2 -2)
* src/MolFilePlugin.h 1.45 (changed +2 -2)
* src/MolFilePlugin.C 1.196 (changed +2 -2)
* src/MolBrowser.h 1.16 (changed +1 -1)
* src/MolBrowser.C 1.43 (changed +2 -2)
* src/MobileTracker.h 1.3 (changed +2 -2)
* src/MobileTracker.C 1.4 (changed +2 -2)
* src/MobileInterface.h 1.17 (changed +2 -2)
* src/MobileInterface.C 1.49 (changed +2 -2)
* src/MobileButtons.h 1.3 (changed +2 -2)
* src/MobileButtons.C 1.3 (changed +2 -2)
* src/MeasureSymmetry.h 1.33 (changed +2 -2)
* src/MeasureSymmetry.C 1.65 (changed +2 -2)
* src/MeasureSurface.C 1.10 (changed +2 -2)
* src/MeasureRDF.C 1.17 (changed +2 -2)
* src/MeasureQCP.C 1.27 (changed +2 -2)
* src/MeasurePBC.C 1.18 (changed +2 -2)
* src/MeasureCluster.C 1.19 (changed +2 -2)
* src/Measure.h 1.73 (changed +2 -2)
* src/Measure.C 1.149 (changed +2 -2)
* src/MayaDisplayDevice.h 1.5 (changed +2 -2)
* src/MayaDisplayDevice.C 1.9 (changed +2 -2)
* src/Matrix4.h 1.42 (changed +2 -2)
* src/Matrix4.C 1.56 (changed +2 -2)
* src/MaterialList.h 1.28 (changed +2 -2)
* src/MaterialList.C 1.36 (changed +2 -2)
* src/MaterialFltkMenu.h 1.17 (changed +2 -2)
* src/MaterialFltkMenu.C 1.30 (changed +2 -2)
* src/MainFltkMenu.h 1.45 (changed +1 -1)
* src/MainFltkMenu.C 1.151 (changed +1 -1)
* src/MSMSInterface.h 1.28 (changed +2 -2)
* src/MSMSInterface.C 1.55 (changed +2 -2)
* src/LibTachyonDisplayDevice.h 1.35 (changed +2 -2)
* src/LibTachyonDisplayDevice.C 1.96 (changed +2 -2)
* src/LibGelatoDisplayDevice.h 1.8 (changed +2 -2)
* src/LibGelatoDisplayDevice.C 1.17 (changed +2 -2)
* src/JString.h 1.22 (changed +2 -2)
* src/JString.C 1.21 (changed +2 -2)
* src/JRegex.h 1.15 (changed +2 -2)
* src/JRegex.C 1.14 (changed +2 -2)
* src/Isosurface.h 1.31 (changed +1 -1)
* src/Isosurface.C 1.50 (changed +1 -1)
* src/Isocontour.h 1.7 (changed +1 -1)
* src/Isocontour.C 1.8 (changed +1 -1)
* src/Inform.h 1.32 (changed +2 -2)
* src/Inform.C 1.43 (changed +2 -2)
* src/ImageIO.h 1.17 (changed +2 -2)
* src/ImageIO.C 1.25 (changed +2 -2)
* src/IMDSimThread.h 1.17 (changed +2 -2)
* src/IMDSimThread.C 1.18 (changed +2 -2)
* src/IMDSimBlocking.h 1.15 (changed +2 -2)
* src/IMDSimBlocking.C 1.18 (changed +2 -2)
* src/IMDSim.h 1.25 (changed +2 -2)
* src/IMDSim.C 1.32 (changed +2 -2)
* src/IMDMgr.h 1.26 (changed +2 -2)
* src/IMDMgr.C 1.43 (changed +2 -2)
* src/HMDMgr.h 1.5 (changed +2 -2)
* src/HMDMgr.C 1.8 (changed +2 -2)
* src/GraphicsFltkReps.h 1.138 (changed +2 -2)
* src/GraphicsFltkMenu.h 1.34 (changed +2 -2)
* src/GraphicsFltkMenu.C 1.163 (changed +2 -2)
* src/GeometrySpring.h 1.15 (changed +2 -2)
* src/GeometrySpring.C 1.19 (changed +2 -2)
* src/GeometryMol.h 1.34 (changed +2 -2)
* src/GeometryMol.C 1.56 (changed +2 -2)
* src/GeometryList.h 1.43 (changed +2 -2)
* src/GeometryList.C 1.66 (changed +2 -2)
* src/GeometryFltkMenu.h 1.24 (changed +1 -1)
* src/GeometryFltkMenu.C 1.62 (changed +1 -1)
* src/GeometryDihedral.h 1.25 (changed +2 -2)
* src/GeometryDihedral.C 1.31 (changed +2 -2)
* src/GeometryBond.h 1.25 (changed +2 -2)
* src/GeometryBond.C 1.28 (changed +2 -2)
* src/GeometryAtom.h 1.25 (changed +2 -2)
* src/GeometryAtom.C 1.29 (changed +2 -2)
* src/GeometryAngle.h 1.25 (changed +2 -2)
* src/GeometryAngle.C 1.29 (changed +2 -2)
* src/GelatoDisplayDevice.h 1.16 (changed +2 -2)
* src/GelatoDisplayDevice.C 1.34 (changed +2 -2)
* src/GaussianBlur.h 1.9 (changed +3 -3)
* src/GaussianBlur.C 1.25 (changed +2 -2)
* src/FreeVRScene.h 1.30 (changed +2 -2)
* src/FreeVRScene.C 1.41 (changed +2 -2)
* src/FreeVRRoutines.h 1.15 (changed +2 -2)
* src/FreeVRRoutines.C 1.24 (changed +2 -2)
* src/FreeVRDisplayDevice.h 1.20 (changed +2 -2)
* src/FreeVRDisplayDevice.C 1.33 (changed +2 -2)
* src/Fragment.h 1.20 (changed +2 -2)
* src/FltkOpenGLDisplayDevice.h 1.23 (changed +2 -2)
* src/FltkOpenGLDisplayDevice.C 1.69 (changed +2 -2)
* src/FileRenderer.h 1.127 (changed +2 -2)
* src/FileRenderer.C 1.181 (changed +2 -2)
* src/FileRenderList.h 1.29 (changed +2 -2)
* src/FileRenderList.C 1.96 (changed +2 -2)
* src/FileChooserFltkMenu.h 1.18 (changed +2 -2)
* src/FileChooserFltkMenu.C 1.56 (changed +2 -2)
* src/FastPBC.h 1.2 (changed +3 -3)
* src/FastPBC.C 1.2 (changed +3 -3)
* src/FPS.h 1.17 (changed +1 -1)
* src/FPS.C 1.19 (changed +1 -1)
* src/DrawRingsUtils.h 1.14 (changed +2 -2)
* src/DrawRingsUtils.C 1.40 (changed +2 -2)
* src/DrawMolecule.h 1.87 (changed +2 -2)
* src/DrawMolecule.C 1.145 (changed +2 -2)
* src/DrawMolItemVolume.C 1.166 (changed +2 -2)
* src/DrawMolItemSurface.C 1.45 (changed +2 -2)
* src/DrawMolItemRings.C 1.27 (changed +2 -2)
* src/DrawMolItemRibbons.C 1.149 (changed +2 -2)
* src/DrawMolItemQuickSurf.C 1.25 (changed +2 -2)
* src/DrawMolItemOrbital.C 1.51 (changed +2 -2)
* src/DrawMolItemNanoShaper.C 1.7 (changed +2 -2)
* src/DrawMolItemMSMS.C 1.51 (changed +2 -2)
* src/DrawMolItem2.C 1.38 (changed +2 -2)
* src/DrawMolItem.h 1.184 (changed +2 -2)
* src/DrawMolItem.C 1.366 (changed +2 -2)
* src/DrawForce.h 1.26 (changed +2 -2)
* src/DrawForce.C 1.57 (changed +2 -2)
* src/Displayable.h 1.88 (changed +2 -2)
* src/Displayable.C 1.117 (changed +2 -2)
* src/DisplayRocker.h 1.9 (changed +2 -2)
* src/DisplayRocker.C 1.9 (changed +2 -2)
* src/DisplayFltkMenu.h 1.15 (changed +2 -2)
* src/DisplayFltkMenu.C 1.26 (changed +2 -2)
* src/DisplayDevice.h 1.143 (changed +2 -2)
* src/DisplayDevice.C 1.147 (changed +2 -2)
* src/DispCmds.h 1.112 (changed +2 -2)
* src/DispCmds.C 1.113 (changed +2 -2)
* src/DepthSortObj.h 1.17 (changed +2 -2)
* src/CoorPluginData.h 1.18 (changed +2 -2)
* src/CoorPluginData.C 1.33 (changed +2 -2)
* src/CoorData.h 1.12 (changed +2 -2)
* src/CommandQueue.h 1.42 (changed +2 -2)
* src/CommandQueue.C 1.57 (changed +2 -2)
* src/Command.h 1.172 (changed +2 -2)
* src/ColorInfo.C 1.36 (changed +2 -2)
* src/ColorFltkMenu.h 1.18 (changed +1 -1)
* src/ColorFltkMenu.C 1.34 (changed +1 -1)
* src/CmdTrans.h 1.33 (changed +2 -2)
* src/CmdTrans.C 1.43 (changed +2 -2)
* src/CmdRender.h 1.29 (changed +2 -2)
* src/CmdRender.C 1.39 (changed +2 -2)
* src/CmdPlugin.h 1.13 (changed +1 -1)
* src/CmdMol.h 1.75 (changed +2 -2)
* src/CmdMol.C 1.153 (changed +2 -2)
* src/CmdMenu.h 1.33 (changed +2 -2)
* src/CmdMenu.C 1.34 (changed +2 -2)
* src/CmdMaterial.h 1.22 (changed +2 -2)
* src/CmdMaterial.C 1.32 (changed +2 -2)
* src/CmdLabel.h 1.41 (changed +2 -2)
* src/CmdLabel.C 1.70 (changed +2 -2)
* src/CmdIMD.h 1.27 (changed +2 -2)
* src/CmdIMD.C 1.32 (changed +2 -2)
* src/CmdDisplay.h 1.68 (changed +2 -2)
* src/CmdDisplay.C 1.84 (changed +2 -2)
* src/CmdColor.h 1.33 (changed +2 -2)
* src/CmdColor.C 1.46 (changed +2 -2)
* src/CmdAnimate.h 1.39 (changed +2 -2)
* src/CmdAnimate.C 1.53 (changed +2 -2)
* src/CaveScene.h 1.50 (changed +2 -2)
* src/CaveScene.C 1.53 (changed +2 -2)
* src/CaveRoutines.h 1.26 (changed +2 -2)
* src/CaveRoutines.C 1.38 (changed +2 -2)
* src/CaveDisplayDevice.h 1.37 (changed +2 -2)
* src/CaveDisplayDevice.C 1.49 (changed +2 -2)
* src/CUDAWatershed.h 1.9 (changed +3 -3)
* src/CUDAWatershed.cu 1.33 (changed +3 -3)
* src/CUDAUtil.cu 1.43 (changed +2 -2)
* src/CUDASort.h 1.5 (changed +2 -2)
* src/CUDASort.cu 1.5 (changed +2 -2)
* src/CUDASegmentation.h 1.8 (changed +2 -2)
* src/CUDASegmentation.cu 1.28 (changed +3 -3)
* src/CUDAQuickSurf.h 1.7 (changed +2 -2)
* src/CUDAParPrefixOps.h 1.7 (changed +2 -2)
* src/CUDAParPrefixOps.cu 1.10 (changed +3 -3)
* src/CUDAOrbital.h 1.3 (changed +2 -2)
* src/CUDAMarchingCubes.cu 1.35 (changed +2 -2)
* src/CUDAKernels.h 1.56 (changed +2 -2)
* src/CUDAGaussianBlur.h 1.5 (changed +3 -3)
* src/CUDAGaussianBlur.cu 1.16 (changed +3 -3)
* src/CUDAFastPBC.cu 1.2 (changed +3 -3)
* src/CUDADispCmds.cu 1.9 (changed +2 -2)
* src/CUDAAccel.h 1.22 (changed +2 -2)
* src/CUDAAccel.C 1.52 (changed +2 -2)
* src/BondSearch.h 1.27 (changed +2 -2)
* src/BondSearch.C 1.76 (changed +2 -2)
* src/Benchmark.h 1.6 (changed +2 -2)
* src/Benchmark.C 1.9 (changed +2 -2)
* src/BaseMolecule.h 1.148 (changed +2 -2)
* src/BaseMolecule.C 1.272 (changed +2 -2)
* src/Axes.h 1.41 (changed +2 -2)
* src/Axes.C 1.72 (changed +2 -2)
* src/py_atomselection.C 1.52 (changed +2 -2)
* src/AtomSel.h 1.56 (changed +2 -2)
* src/AtomSel.C 1.175 (changed +2 -2)
* src/AtomRep.h 1.74 (changed +2 -2)
* src/AtomRep.C 1.134 (changed +2 -2)
* src/AtomParser.y 1.51 (changed +2 -2)
* src/AtomParser.h 1.30 (changed +2 -2)
* src/AtomParser.C 1.28 (changed +2 -2)
* src/AtomLexer.l 1.54 (changed +2 -2)
* src/AtomLexer.C 1.22 (changed +3 -3)
* src/AtomColor.h 1.48 (changed +2 -2)
* src/AtomColor.C 1.105 (changed +2 -2)
* src/Atom.h 1.70 (changed +2 -2)
* src/ArtDisplayDevice.h 1.27 (changed +2 -2)
* src/ArtDisplayDevice.C 1.37 (changed +2 -2)
* src/Animation.h 1.44 (changed +2 -2)
* src/Animation.C 1.57 (changed +2 -2)
Updated copyright headers for self-consistency
* src/Voltool.h 1.7 (changed +2 -2)
* src/Voltool.C 1.6 (changed +2 -2)
* src/TclSegmentation.C 1.14 (changed +3 -3)
* src/TclMDFF.h 1.2 (changed +3 -3)
* src/TclMDFF.C 1.29 (changed +2 -2)
* src/OrbitalJIT.h 1.2 (changed +3 -3)
* src/OrbitalJIT.C 1.5 (changed +2 -2)
* src/OptiXShaders.h 1.36 (changed +2 -2)
* src/OptiXShaders.cu 1.163 (changed +2 -2)
* src/OptiXRenderer.C 1.346 (changed +2 -2)
* src/OptiXDisplayDevice.C 1.76 (changed +2 -2)
* src/OpenCLVolCPotential.C 1.32 (changed +2 -2)
* src/OpenCLUtils.h 1.4 (changed +2 -2)
* src/OpenCLUtils.C 1.14 (changed +2 -2)
* src/OpenCLOrbital.C 1.32 (changed +2 -2)
* src/OSPRayRenderer.C 1.71 (changed +2 -2)
* src/MeasureVolInterior.h 1.3 (changed +2 -2)
* src/MeasureVolInterior.C 1.11 (changed +2 -2)
* src/MDFF.h 1.2 (changed +3 -3)
* src/MDFF.C 1.15 (changed +2 -2)
* src/CUDAVolMapCreateILS.cu 1.52 (changed +2 -2)
* src/CUDAVolCPotential.cu 1.44 (changed +2 -2)
* src/CUDASpatialSearch.h 1.2 (changed +3 -3)
* src/CUDASpatialSearch.cu 1.8 (changed +2 -2)
* src/CUDAQuickSurf.cu 1.86 (changed +2 -2)
* src/CUDAOrbital.cu 1.116 (changed +2 -2)
* src/CUDAMeasureRDF.cu 1.27 (changed +2 -2)
* src/CUDAMeasureQCP.cu 1.7 (changed +2 -2)
* src/CUDAMDFF.h 1.4 (changed +2 -2)
* src/CUDAMDFF.cu 1.79 (changed +2 -2)
* src/CUDAClearDevice.cu 1.15 (changed +2 -2)
* src/CUDABench.cu 1.35 (changed +2 -2)
 2019-01-10ryanmcgreevyRemoved old Voltool code (unary ops) that was moved into VolumetricData and properly integrated. The old Voltool code was no longer in use anywhere.
* src/Voltool.h 1.6 (changed +1 -43)
* src/Voltool.C 1.5 (changed +1 -518)
 2019-01-09ryanmcgreevyAdded new hist and info commands to Voltool. hist calculates a histogram of the density map and returns a list of bin midpoint and count pairs. info returns the specified information about the density map (gridsizes, origin, minmax).
* src/Voltool.h 1.5 (changed +8 -2)
* src/Voltool.C 1.4 (changed +23 -1)
* src/TclVoltool.C 1.3 (changed +255 -2)
 2018-12-20johnsMinor perf tweak for dome primary ray gen
* src/OptiXShaders.cu 1.161 (changed +6 -2)
 2018-12-08johnsThe OptiXRenderer::render_to_videostream() method always gets compiled,
so that headless VMD builds for server hardware can do video streaming
w/ interactive ray tracing.
* src/OptiXRenderer.C 1.345 (changed +1547 -1547)
 2018-12-07johnsContinued cleanup
* src/TclMeasure.C 1.166 (changed +19 -22)
Continued cleanup of new measure routines
* src/TclMeasure.C 1.168 (changed +113 -139)
Continuing cleanup of Tcl bindings for "measure" commands
* src/TclMeasure.C 1.167 (changed +66 -78)
Did some overdue cleanup on various "measure" routines.
* src/TclMeasure.C 1.165 (changed +73 -70)
Eliminated a local variable declaration that inhibited the
proper handling of server socket management. Misc cleanup.
* src/VMDCollab.h 1.7 (changed +2 -3)
* src/VMDCollab.C 1.10 (changed +15 -5)
More updates
* README 1.409 (changed +53 -21)
Pulled in the latest colvars implementation.
* src/colvarvalue.h 1.9 (changed +38 -5)
* src/colvarvalue.C 1.10 (changed +34 -0)
* src/colvarscript.C 1.21 (changed +4 -0)
* src/colvars_version.h 1.10 (changed +1 -1)
* src/colvarproxy_vmd.C 1.17 (changed +6 -0)
* src/colvarmodule.h 1.26 (changed +3 -3)
* src/colvarmodule.C 1.24 (changed +36 -7)
* src/colvardeps.C 1.13 (changed +3 -0)
* src/colvarcomp_coordnums.C 1.10 (changed +20 -8)
* src/colvarbias_restraint.C 1.15 (changed +5 -2)
* src/colvarbias_abf.h 1.7 (changed +3 -3)
* src/colvarbias_abf.C 1.19 (changed +18 -40)
* src/colvarbias.h 1.12 (changed +3 -0)
* src/colvarbias.C 1.16 (changed +6 -0)
* src/colvar.h 1.14 (changed +11 -7)
* src/colvar.C 1.25 (changed +145 -98)
Start updating ascii docs/release notes
* Announcement 1.69 (changed +4 -4)
Started updates to text docs
* README 1.408 (changed +5 -4)
 2018-12-06ryanmcgreevyUpdated voxel_coord routine to use member variables instead of passed in VolumetricData
* src/VolumetricData.h 1.46 (changed +12 -16)
* src/Voltool.C 1.3 (changed +8 -13)
 2018-12-06johnsAdded an #ifdef and workaround for broken Clang SSE intrinsics on MacOS X
* src/util_simd.C 1.12 (changed +5 -1)
Commented out cmdQueue until it gets used by text commands that
need to be queued and logged, etc.
* src/cmd_videostream.C 1.8 (changed +3 -1)
Don't store return code presently since we don't have a well-defined
scenario where it's every going to be non-zero.
* src/MolFilePlugin.C 1.195 (changed +2 -2)
Eliminate unused parameter to please Solaris compilers.
* src/ProfileHooks.h 1.16 (changed +2 -2)
Eliminated extra local cmdSphere object.
* src/DrawMolItemVolume.C 1.165 (changed +1 -2)
Eliminated non-portable C++ code using runtime-sized stack-allocated arrays.
* src/GaussianBlur.C 1.23 (changed +5 -3)
Overcome template instantiation limitations associated with
macro on older C++ compilers.
* src/Watershed.h 1.16 (changed +4 -3)
Prefer truncation rather than case-specific rounding until we get past
old C++ compiler limitations with templates.
* src/GaussianBlur.C 1.24 (changed +11 -2)
Revised the camera implementation for the dome master projection to
eliminate unnecessary normalization operations, improve the DoF
circle of confusion disk basis vector calculation, and rename all of the
variables to follow the new naming conventions I established for the
Ray Tracing Gems book chapter.
* src/OptiXShaders.cu 1.157 (changed +24 -18)
Tiny readability tweak, and added VR developer gems reference
* src/OptiXShaders.cu 1.159 (changed +7 -2)
Updated all of the OptiX renderer src files to refer to the new
Ray Tracing Gems chapters that describe various of the implementation
details herein.
* src/OptiXShaders.h 1.34 (changed +12 -1)
* src/OptiXShaders.cu 1.158 (changed +12 -1)
* src/OptiXRenderer.h 1.113 (changed +12 -1)
* src/OptiXRenderer.C 1.343 (changed +12 -1)
* src/OptiXDisplayDevice.h 1.23 (changed +12 -1)
* src/OptiXDisplayDevice.C 1.74 (changed +12 -1)
Updated list of published refs to include the VR Developer Gems chapter
* src/OptiXShaders.h 1.35 (changed +6 -1)
* src/OptiXRenderer.h 1.114 (changed +6 -1)
* src/OptiXRenderer.C 1.344 (changed +6 -1)
* src/OptiXDisplayDevice.h 1.24 (changed +6 -1)
* src/OptiXDisplayDevice.C 1.75 (changed +6 -1)
Updated the dome master camera to allow elevation modulated stereo eye
separation akin to what I implemented previously in the omnidirection
stereoscopic projection camera.
* src/OptiXShaders.cu 1.160 (changed +13 -2)
 2018-12-02johnsAdded Siggraph/SC'18 demo code for alternative window titles when RTX is on.
* src/OptiXRenderer.C 1.342 (changed +14 -2)
Cranked versions
* configure 1.1462 (changed +2 -2)
 2018-11-11johnsAdded ref to DECH2018 in NanoShaper text.
* doc/ug_mol_reps.tex 1.47 (changed +4 -3)
* doc/ug.bib 1.12 (changed +2 -2)
Corrected an internal state change in the code to allow RTX mode to be
disabled when the OptiX context is created.
* src/OptiXRenderer.C 1.341 (changed +2 -2)
 2018-11-09johnsAdded DECH2018 reference so we can refer to it in the Nanoshaper docs
* doc/ug.bib 1.11 (changed +16 -1)
Updated copyright dates, NIH grant number formatting, and added
Ryan McGreevy to the list of authors.
* doc/vmd_title.tex 1.21 (changed +2 -2)
* doc/vmd_ref.tex 1.76 (changed +4 -4)
 2018-11-06johnsAdded handling of on-the-fly reconfiguration of video streaming codec
parameters on both client and server side.
* src/VideoStream.h 1.19 (changed +17 -1)
* src/VideoStream.C 1.32 (changed +32 -4)
Added videostream text commands to set the target "bitrate" and "framerate".
* src/cmd_videostream.C 1.7 (changed +16 -1)
* src/VideoStream.h 1.20 (changed +2 -2)
Changed CUDA builds to use CUDA 9.0 so that they support NGC containers.
* configure 1.1461 (changed +5 -5)
Changed the video streaming implementation to push OpenGL frames out at
GLX/EGL front/back buffer swap time rather than pulling them in at an
unspecified future time during event loop processing.
* src/VMDApp.C 1.557 (changed +2 -2)
* src/OpenGLPbufferDisplayDevice.C 1.26 (changed +19 -1)
* src/OpenGLDisplayDevice.C 1.209 (changed +22 -2)
Clear video frame pending flag by default so we don't pull a zero-sized
frame when running in pure-text mode with no attached GLX/EGL framebuffer.
* src/VideoStream.C 1.33 (changed +2 -1)
Improved remote streaming console startup messages
* src/VideoStream.C 1.29 (changed +7 -5)
Revised the video streaming constructor to explicitly clear internal
"pending frame" state variables, added several new safety checks
in the video encoder chain to ensure that any bogus inputs can't make
it to back-end encoders, since their default behavior is sometimes
implemented such that they terminate the entire process by calling exit()
rather than cleaning up error state.
Added first first round of code to set last_xxx timer values during
setup to prevent spurious console warnings about heartbeat timeouts,
still need to update the connection setup code to do the same.
* src/VideoStream.C 1.30 (changed +50 -9)
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