| Tags | Date | Developer | Last 200 Commit Logs |
|---|
| | 2008-06-20 | johns | Added some notes to the current Spaceball code documenting things
that need adjustment.
* src/Spaceball.C 1.49 (changed +28 -1)
Capped the maximum allowable Spaceball trajectory animation stride to 25
by default. This needs to be a user-defined parameter.
* src/VMDApp.C 1.409 (changed +3 -7)
* src/Spaceball.h 1.27 (changed +13 -3)
* src/Spaceball.C 1.50 (changed +6 -15)
Changed Spaceball behavior when the display projection is in orthographic
mode, so that rather than translating in Z, we scale the molecule.
This seems to match user preference for most people. We'll make this
a user-selectable mode toggle eventually.
* src/VMDApp.h 1.196 (changed +4 -1)
* src/VMDApp.C 1.410 (changed +8 -1)
* src/Spaceball.C 1.52 (changed +9 -2)
* src/DisplayDevice.h 1.125 (changed +5 -5)
Fix compiler warning.
* src/MeasureSymmetry.C 1.25 (changed +2 -2)
Further improvements for animate mode with regard to varying rendering load.
Still needs a timer to normalize the input by frame rendering time.
* src/Spaceball.C 1.51 (changed +11 -7)
Updated comments in the Spaceball code.
* src/Spaceball.C 1.53 (changed +3 -3)
|
| | 2008-06-17 | johns | Added "TDCONNEXION" configure option used to enable support for the
3DConnexion MacOS X device API.
* configure 1.1024 (changed +19 -1)
Added support for 3DConnexion SpaceNavigator on MacOS X
* src/Spaceball.C 1.47 (changed +161 -1)
Enabled the 3DConnexion SpaceNavigator API in the MacOS X builds by default.
* Makefile 1.65 (changed +2 -2)
Notes on MacOS X single-threaded event handling issues for the SpaceNavigator
* src/Spaceball.C 1.48 (changed +10 -2)
|
| | 2008-06-12 | saam | Added comparison of bond orientation for each atom. This can distinguish for example if the
orientation of a double bond in the transformed image atom is different than in the original
position. It cures the falsepositive detection of additional symmetry elements for instance in
some antiaromatic systems.
Also fixed a bug introduced when I got rid of the gridsearch that would in somme cases lead to
wrong idealized coordinates.
* src/MeasureSymmetry.h 1.15 (changed +13 -3)
* src/MeasureSymmetry.C 1.24 (changed +300 -175)
|
| | 2008-06-11 | saam | Made execution 2-10 times faster (depending on molecule) by eliminating gridsearch.
Improved robustness by comparing atom types instead of just chemical elements.
Added more comments
* src/TclMeasure.C 1.112 (changed +3 -2)
* src/MeasureSymmetry.h 1.14 (changed +18 -10)
* src/MeasureSymmetry.C 1.23 (changed +292 -287)
|
| | 2008-06-11 | johns | Fix builtin help
* src/cmd_spaceball.C 1.5 (changed +2 -2)
Reverted an unintentional change to the "VMDSPACEBALLPORT" environment
variable tests that occured during a global search/replace in the source code.
* src/Spaceball.C 1.46 (changed +6 -6)
|
| | 2008-06-09 | saam | Add RMSD between original and idealized coordinates to the TCL return
string.
More comments
* src/TclMeasure.C 1.111 (changed +2 -1)
* src/MeasureSymmetry.h 1.13 (changed +39 -14)
* src/MeasureSymmetry.C 1.22 (changed +59 -26)
Enhance robustness of search
Handle rotary reflections properly in all cases.
Cleanup
* src/TclMeasure.C 1.110 (changed +2 -2)
* src/MeasureSymmetry.h 1.12 (changed +5 -1)
* src/MeasureSymmetry.C 1.21 (changed +211 -52)
|
| | 2008-06-09 | johns | Added a new 'spaceball animate' command and matching input control
mode to allow the spaceball to be used as a jog/shuttle controller
for playing VMD trajectories
* src/cmd_spaceball.C 1.3 (changed +3 -2)
* src/Spaceball.h 1.23 (changed +3 -2)
* src/Spaceball.C 1.41 (changed +36 -2)
Added new "spaceball nullregion" command
* src/cmd_spaceball.C 1.2 (changed +16 -2)
* src/VMDApp.h 1.193 (changed +4 -1)
* src/VMDApp.C 1.406 (changed +12 -1)
* src/Spaceball.h 1.22 (changed +6 -1)
* src/Spaceball.C 1.39 (changed +58 -11)
Added new 'spaceball sensitivity' command
* src/VMDApp.h 1.191 (changed +4 -1)
* src/VMDApp.C 1.404 (changed +12 -1)
* src/Spaceball.h 1.20 (changed +5 -1)
* src/Spaceball.C 1.37 (changed +50 -32)
* src/OpenGLDisplayDevice.C 1.165 (changed +7 -7)
Added new Spaceball "user" mode that reports events via TextEvent callbacks.
* src/TextInterp.h 1.26 (changed +4 -2)
* src/TextEvent.h 1.44 (changed +37 -15)
* src/TclTextInterp.h 1.37 (changed +4 -2)
* src/TclTextInterp.C 1.97 (changed +14 -1)
* src/Spaceball.h 1.18 (changed +2 -2)
* src/Spaceball.C 1.35 (changed +23 -12)
Added new SpaceballButtons class for use with the console spaceball device.
* src/SpaceballButtons.h 1.1 (added +41 -0)
* src/SpaceballButtons.C 1.1 (added +56 -0)
Added new code to allow the console Spaceball device to be used as
a VMD tracker device, for use with the UIVR tools akin to how
the haptic devices are used. The console Spaceball code now
has a new "tracker" mode, which just stores incoming spaceball events
for reading by the SpaceballTracker and SpaceballButtons classes.
The .vmdsensors config lines for the local Spaceball device are:
device SpaceballTracker sballtracker://local/vmdlocal
device SpaceballButtons sballbuttons://local/vmdlocal
* src/cmd_spaceball.C 1.4 (changed +3 -2)
* src/VMDApp.h 1.195 (changed +7 -1)
* src/VMDApp.C 1.408 (changed +15 -2)
* src/SpaceballTracker.h 1.13 (changed +10 -7)
* src/SpaceballTracker.C 1.14 (changed +88 -35)
* src/Spaceball.h 1.26 (changed +16 -2)
* src/Spaceball.C 1.45 (changed +43 -7)
* src/P_UIVR.C 1.130 (changed +5 -4)
* src/P_PrintTool.C 1.9 (changed +1 -3)
* configure 1.1022 (changed +6 -4)
Added spaceball command source file
* src/cmd_spaceball.C 1.1 (added +88 -0)
Better defaults for Spaceball rotation/translation speeds and
null region values.
* src/Spaceball.C 1.40 (changed +6 -6)
Cranked version
* configure 1.1023 (changed +1 -1)
Eliminate compiler warning
* src/DispCmds.C 1.84 (changed +4 -4)
Eliminated compiler warnings
* src/P_TugTool.C 1.50 (changed +3 -3)
* src/P_GrabTool.C 1.30 (changed +5 -5)
Fix missing revision ID tag
* src/cmd_mouse.C 1.25 (changed +8 -0)
Implemented new "spaceball" command, to accept spaceball mode changes,
sensitivity adjustments, input modes, and so on.
* src/tcl_commands.h 1.19 (changed +2 -1)
* src/tcl_commands.C 1.29 (changed +4 -1)
* src/VMDApp.h 1.190 (changed +4 -1)
* src/VMDApp.C 1.403 (changed +14 -1)
* src/Spaceball.h 1.19 (changed +22 -1)
* src/Spaceball.C 1.36 (changed +26 -1)
* src/Mouse.h 1.65 (changed +5 -5)
* src/Command.h 1.159 (changed +2 -1)
More Spaceball cleanup
* src/Spaceball.h 1.25 (changed +1 -2)
* src/Spaceball.C 1.44 (changed +23 -28)
Redesigned the Spaceball animation velocity scaling to make use of
the animation playback speed control in addition to the step size.
The control now seems very usable all the way from very slow playback rates
all the way up to very fast ones.
* src/Spaceball.C 1.42 (changed +22 -12)
Renamed the old "SPACEBALL" configure option and corresponding
"VMDSPACEBALL" conditional compilation macros to "LIBSBALL" and
"VMDLIBSBALL" respectively, in order to differentiate the old
direct I/O LibSBall spaceball functionality from the new implementations
based on windowing system events, XInput, and other input libraries that
also support Spaceball devices.
* src/VMDApp.h 1.192 (changed +3 -3)
* src/VMDApp.C 1.405 (changed +7 -7)
* src/SpaceballTracker.h 1.12 (changed +2 -2)
* src/SpaceballTracker.C 1.13 (changed +2 -2)
* src/Spaceball.h 1.21 (changed +4 -4)
* src/Spaceball.C 1.38 (changed +15 -15)
* src/P_UIVR.C 1.129 (changed +3 -3)
* doc/pg_configure.dox 1.6 (changed +2 -2)
* doc/Doxyfile 1.12 (changed +1 -1)
* configure 1.1021 (changed +16 -15)
* Makefile 1.64 (changed +21 -21)
The Spaceball UIVR object is now compiled-in in all cases since we have
code that's "always on" in the windowing system drivers now. As a result
the space ball source files are now built into all builds and so a number
of places in the code needed cleanup and portability improvements which
are now taken care of.
* src/VMDApp.h 1.194 (changed +1 -5)
* src/VMDApp.C 1.407 (changed +1 -16)
* src/Spaceball.h 1.24 (changed +1 -6)
* src/Spaceball.C 1.43 (changed +29 -41)
The SpaceballTracker and SpaceballButtons devices are now always
compiled in.
* src/P_UIVR.C 1.131 (changed +1 -4)
|
| | 2008-06-08 | johns | Abbreviated the X-windows ClientMessage device detection message.
* src/OpenGLDisplayDevice.C 1.164 (changed +2 -2)
Cranked version
* configure 1.1020 (changed +1 -1)
Initialize stack variable
* src/MeasureSymmetry.C 1.20 (changed +2 -2)
Made the XInput startup code less chatty, it only announces when devices
are found, rather than when they aren't found.
* src/OpenGLDisplayDevice.C 1.163 (changed +2 -2)
|
| | 2008-06-07 | saam | Pretty up things.
* src/MeasureSymmetry.h 1.11 (changed +47 -37)
* src/MeasureSymmetry.C 1.19 (changed +87 -42)
|
| | 2008-06-07 | johns | Updated Spaceball event handling loop so that we accumulate inputs
for all of the queued spaceball events since the last redraw, rather
than throwing away all but the most recent input. This change makes
the input behavior much smoother with wildly varying scene complexity
and results in an approximate constant angular rate of rotation or
linear rate of translation for a given user-applied Spaceball
torque/deflection. We could do even better by adding timers to the code,
and scaling rates by the time since the last input event,
but this seems to be sufficient at the present moment.
* src/OpenGLDisplayDevice.C 1.162 (changed +31 -21)
|
| | 2008-06-06 | saam | Added comments.
* src/TclMeasure.C 1.109 (changed +24 -1)
* src/MeasureSymmetry.C 1.15 (changed +18 -2)
More function moving into logical order.
* src/MeasureSymmetry.C 1.18 (changed +162 -162)
Pretty
* src/MeasureSymmetry.h 1.10 (changed +7 -3)
* src/MeasureSymmetry.C 1.16 (changed +76 -42)
Pretty up more (Changed order of functions in the file).
* src/MeasureSymmetry.C 1.17 (changed +375 -373)
|
| | 2008-06-05 | saam | This is a fairly big change but it could not be cut into smaller ones:
Previously the symmetry guess was based on a elements that were
found in a single pass. The biggest problem with this is to decide which
symmetry elements to keep and which to discard, based on their score.
While the point group guess, relying only on certain key features, was
generally good, the number of found elements was often wrong. In case
additional elements were found this could totally screw up the
idealized coordinates.
Now we are passing through the element guess in a loop in which we only
keep the elements with a really good score and idealize them. The
subsequent generation of ideal coordinates will definitely yield "more
symmetric" coordinate set than the original one. In the next pass
we use these improved coordinates for guessing the elements and we will
probably find a few more this time. This is repeated until the number of
found symmetry elements converges.
The tcl command now also returns a summary string of the found elements
along with a string with elements that are missing wrt the ideal number
for the guessed point group and with a string containing additional
elements that would not be expected. This can provide good hints that
something might be wrong with the guess.
* src/TclMeasure.C 1.108 (changed +4 -1)
* src/MeasureSymmetry.h 1.9 (changed +43 -12)
* src/MeasureSymmetry.C 1.14 (changed +708 -309)
|
| | 2008-06-04 | johns | Change spaceball device axis mapping to assume a direct mapping.
Added code to skip over the "evdev brain" XInput devices found on
Xorg servers since they aren't usable devices for our purposes.
Prettied up the device enumeration messages and formatting.
* src/OpenGLDisplayDevice.C 1.161 (changed +19 -6)
Completed an initial implementation of XInput support for
Spaceball 6DOF devices. With minor tweaks, the same logic will work
for dial boxes, tablets, and other input devices that are supported
by the XInput extension.
* src/VMDApp.h 1.189 (changed +3 -3)
* src/VMDApp.C 1.402 (changed +5 -5)
* src/Spaceball.h 1.17 (changed +2 -2)
* src/Spaceball.C 1.33 (changed +9 -6)
* src/OpenGLDisplayDevice.C 1.160 (changed +134 -33)
Silence debugging info in spaceball event handler
* src/Spaceball.C 1.34 (changed +1 -1)
The Spaceball.C source file is now always compiled in, since we now
support various native windowing system-based 6DOF input device
mechanisms like XInput, ClientMessage, and other schemes that don't
require any device-specific serial I/O code to be compiled in.
At present all of these devices get mapped to the VMD Spaceball
input mechanism, but we may want to generalize this somewhat to
allow support for multiple devices simultaneously, etc.
* configure 1.1019 (changed +4 -4)
|
| | 2008-06-03 | johns | Added MacOS X 32-bit Intel text only build target
* Makefile 1.62 (changed +3 -0)
Added XINPUT option to all of the normal x86 linux builds.
* Makefile 1.63 (changed +5 -5)
Added code to merge direct spaceball and windowed spaceball events if
we happen to have two devices attached using different interfaces.
* src/Spaceball.C 1.31 (changed +24 -5)
Added comments to X-Windows Spaceball driver event decoder
* src/OpenGLDisplayDevice.C 1.155 (changed +22 -18)
Added new XINPUT compile time configuration option to enable/disable
support for the X-Windows XInput Extensions mechanism for advanced
input devices such as Spaceballs, Dial/Button boxes, Tablets, etc.
* configure 1.1018 (changed +22 -4)
Added skeletal XInput based 6DOF device I/O code with similar structure
to the X-Windows event-based Spaceball interface.
* src/OpenGLDisplayDevice.C 1.156 (changed +44 -1)
Additional tweak to SpaceballTracker messages
* src/SpaceballTracker.C 1.12 (changed +2 -2)
Apply mouse/keyboard focus state to the processing of
Spaceball/Magellan/SpaceNavigator events from the windowing system.
* src/OpenGLDisplayDevice.h 1.47 (changed +7 -11)
* src/OpenGLDisplayDevice.C 1.152 (changed +25 -8)
Built up the XInput device handling implementation significantly
* src/OpenGLDisplayDevice.h 1.48 (changed +16 -14)
* src/OpenGLDisplayDevice.C 1.159 (changed +113 -32)
Eliminated redundant code
* src/OpenGLDisplayDevice.C 1.153 (changed +1 -3)
Improved XInput device list code
* src/OpenGLDisplayDevice.C 1.157 (changed +10 -5)
Let the X-Windows Spaceball driver do window focus processing for us, except
when the user sets the environment variable VMDSPACEBALLXDRVGLOBALFOCUS
which will allow VMD to keep Spaceball focus all the time regardless of
the X11 keyboard/mouse focus.
* src/OpenGLDisplayDevice.C 1.154 (changed +15 -3)
Made XInput device attach more robust
* src/OpenGLDisplayDevice.C 1.158 (changed +7 -5)
Move CUDA device enumeration earlier in the startup process
immediately after the CPU and memory enumeration code.
* src/VMDApp.C 1.401 (changed +5 -5)
Pretty up CUDA device enumeration
* src/CUDAAccel.C 1.11 (changed +2 -2)
Updated Spaceball device open messages to better indicate which driver
interface/method is being used to talk to the device.
* src/SpaceballTracker.C 1.11 (changed +2 -2)
* src/Spaceball.C 1.32 (changed +3 -3)
|
| | 2008-06-02 | saam | Cleanup
* src/MeasureSymmetry.h 1.8 (changed +5 -5)
* src/MeasureSymmetry.C 1.13 (changed +107 -262)
|
| | 2008-06-02 | johns | Added MacOS X 64-bit build configurations and configure script logic.
Currently, 64-bit MacOS X builds are limited to X11 or text mode only
due to the lack of a 64-bit ABI version of Apple's Carbon framework, or
a version of Tcl/Tk that uses Cocoa rather than Carbon.
* configure 1.1016 (changed +23 -13)
* Makefile 1.60 (changed +6 -0)
Added X-Windows support for 3DConnexion SpaceNavigator, as well as all
of the older Magellan, and Spaceball devices using the Magellan style
X-Windows driver using client messages.
* src/OpenGLDisplayDevice.h 1.46 (changed +33 -1)
* src/OpenGLDisplayDevice.C 1.150 (changed +157 -3)
Added a bit more safety checking for initialization of the
spaceball X-Windows driver. Added an environment variable override
to disable it if necessary.
* src/OpenGLDisplayDevice.C 1.151 (changed +7 -3)
Added support for 64-bit builds on MacOS X. At present, MacOS X
doesn't include a version of Carbon for their 64-bit ABI, so 64-bit
VMD builds have to be done either for text-mode only, or they must be
classical X11 based builds rather than using the native Aqua windowing
system interfaces. When building for X11, matching X11 versions of
FLTK and Tcl/Tk must be linked against. Until Apple releases a
64-bit ABI version of Carbon, or the Tcl/Tk maintainers port Tk to
use 64-bit-capable Cocoa instead of Carbon, there's no other option.
* src/vmd.C 1.70 (changed +3 -3)
* src/utilities.C 1.111 (changed +2 -2)
* src/macosxvmdstart.C 1.16 (changed +5 -4)
* src/VMDApp.C 1.400 (changed +2 -2)
* src/Stride.C 1.32 (changed +2 -2)
* src/SpatialSearch.C 1.6 (changed +3 -3)
* src/OpenGLRenderer.C 1.386 (changed +8 -8)
* src/OpenGLExtensions.h 1.39 (changed +4 -4)
* src/OpenGLExtensions.C 1.54 (changed +3 -3)
* src/MainFltkMenu.C 1.133 (changed +2 -2)
* src/FltkOpenGLDisplayDevice.C 1.42 (changed +7 -4)
* src/AtomParser.C 1.16 (changed +2 -2)
Added workaround for a bug in the MacOS X linker when compiling for
X11+OpenGL rather than using the native Aqua windowing system.
* configure 1.1017 (changed +6 -0)
Applied AK's fix for the histogram build for 'measure gofr'
* src/Measure.C 1.110 (changed +5 -5)
Fixed 64-bit MacOS X ifdefs. Disabled the use of OpenGL extensions
for 64-bit MacOS X builds until more details are ironed out.
* src/OpenGLExtensions.h 1.40 (changed +2 -2)
* src/OpenGLExtensions.C 1.55 (changed +3 -1)
Raised optimization level for 64-bit Solaris x86 builds
* configure 1.1015 (changed +4 -4)
Updated build config for 64-bit MacOS X target using X11/OpenGL
* Makefile 1.61 (changed +1 -1)
Updated the main Spaceball event handling code to deal with events
from both the host windowing system as well as from the direct I/O
libsball driver. Ideally we'd beef this up even more to deal with
multiple simultaneous devices in a nice way, but even the windowing
system drivers are currently pretty weak in that regard.
* src/Spaceball.C 1.30 (changed +12 -10)
|
| | 2008-06-01 | saam | Made idealization more robust and efficient.
* src/MeasureSymmetry.h 1.7 (changed +12 -6)
* src/MeasureSymmetry.C 1.12 (changed +451 -343)
|
| | 2008-06-01 | johns | Added new VMDApp methods used by the Molecule class to inform the main
event loop when background I/O is going on so that the CPU throttling
code remains inactive until the background I/O is complete for all
molecules. With this change one can use VMD interactively
and achieve background trajectory I/O rates that approach the
performance achieved with the blocking "waitfor all" loading parameter.
Using "waitfor all" is still the best way to achieve peak I/O rates,
but this eliminates one potential performance bottleneck when people
are doing interactive analysis jobs and the like.
* src/VMDApp.h 1.188 (changed +13 -1)
* src/VMDApp.C 1.399 (changed +9 -3)
* src/Molecule.C 1.83 (changed +6 -1)
Cranked version
* configure 1.1014 (changed +1 -1)
Fix a bug in the CUDA device enumeration code that skips emulation devices
* src/CUDAUtil.cu 1.8 (changed +4 -3)
Fixed the main event loop logic so that the anti-CPU-hog code allows
background I/O to progress at full speed when display update is off.
An improved approach would consider background I/O independently
of the display update mode.
* src/VMDApp.C 1.398 (changed +5 -3)
|
| | 2008-05-30 | saam | Fixed bug pointed out by Peter where VMD would crash if measure bond
was called with an empty list instead of an atom index.
* src/TclMeasure.C 1.107 (changed +16 -1)
|
| | 2008-05-30 | johns | Added performance instrumentation code for coordinate I/O routines
* src/CoorPluginData.h 1.10 (changed +4 -5)
* src/CoorPluginData.C 1.18 (changed +43 -3)
Pretty
* src/utilities.h 1.85 (changed +2 -2)
|
| | 2008-05-23 | johns | Updated Solaris x86 compilation flags to eliminate compiler chatter
* configure 1.1013 (changed +2 -2)
|
| | 2008-05-22 | saam | Added missing documentation for a couple of arguments to the volmap ligand command.
* doc/ug_text_ui.tex 1.191 (changed +82 -54)
|
| | 2008-05-22 | johns | Cranked version
* configure 1.1012 (changed +1 -1)
|
| | 2008-05-21 | saam | Added inversion center to the returned TCL list.
Fixed a bug that in some case would return an axis with length zero.
* src/TclMeasure.C 1.106 (changed +10 -1)
* src/MeasureSymmetry.h 1.6 (changed +7 -1)
* src/MeasureSymmetry.C 1.11 (changed +37 -3)
Eliminated dead code.
* src/MeasureSymmetry.C 1.9 (changed +1 -57)
Fixed minor bug.
Reduced output.
* src/MeasureSymmetry.C 1.8 (changed +11 -5)
Improved generation of idealized coordinates.
Fixed a bug in the idealization of symmetry elements.
* src/MeasureSymmetry.C 1.10 (changed +48 -27)
Switched on and improved idealizing s of symmetry elements.
* src/MeasureSymmetry.C 1.7 (changed +310 -106)
|
| | 2008-05-19 | saam | Return rotary reflection to the user.
Cleanup
* src/TclMeasure.C 1.105 (changed +15 -1)
* src/MeasureSymmetry.h 1.5 (changed +9 -4)
* src/MeasureSymmetry.C 1.6 (changed +51 -31)
|
| | 2008-05-19 | johns | Applied Simon's patch which reverses the colour scale and
also fixes a bug in the calculation of the puckering parameters.
* src/DrawRingsUtils.C 1.10 (changed +16 -15)
|
| | 2008-05-16 | saam | Returns idealized coordinates now. The coordinated are generated by taking the
average if each coordinate and its transformed image for each symmetry element
(currently only planes, will add axes soon).
* src/TclMeasure.C 1.104 (changed +13 -1)
* src/MeasureSymmetry.h 1.4 (changed +11 -2)
* src/MeasureSymmetry.C 1.5 (changed +272 -49)
|
| | 2008-05-16 | johns | AK's patch to workaround GCC 4.x issues with pointer aliasing
* src/imd.C 1.14 (changed +3 -2)
Added VMD's "residue" index (internally determined unique residue ID) to
the atom pick output.
* src/PickList.C 1.42 (changed +2 -1)
|
| | 2008-05-15 | saam | * Fixed memory leak
* Added comments
* Renamed a variable for clarity
* src/VolMapCreate.h 1.32 (changed +4 -4)
* src/VolMapCreate.C 1.78 (changed +100 -97)
* src/TclVolMap.C 1.49 (changed +6 -1)
* Reorganized some parts of the code
* improved prediction
* better output
* store weight and overlap score with the found planes and axes
* src/MeasureSymmetry.h 1.3 (changed +24 -11)
* src/MeasureSymmetry.C 1.4 (changed +199 -102)
Added comment.
* src/VolMapCreate.h 1.33 (changed +6 -3)
Added security check to make sure no stale atomselection is used.
* src/TclVolMap.C 1.51 (changed +6 -1)
Eliminated warnings:
"TclVolMap.C", line XXX: Warning: String literal converted to char* in formal
argument str in call to Tcl_SetResult(Tcl_Interp*, char*, extern "C" void(*)(char*)).
by properly casting string literal to (char*).
* src/TclVolMap.C 1.50 (changed +3 -3)
Fixed a bug eliminating these annoying warnings:
"TclVolMap.C", line XXX: Warning: String literal converted to char* in assignment.
* src/TclVolMap.C 1.48 (changed +42 -12)
Fixed bug that would crash VMD when volmap ligand is accidentally run with a molecule
that contains no frames.
* src/VolMapCreate.C 1.80 (changed +4 -1)
Fixed memory leak.
* src/VolMap.C 1.18 (changed +2 -1)
Removed dependency from futile gridsize variable in VolMap.
* src/VolMapCreate.C 1.79 (changed +17 -14)
|
| | 2008-05-13 | johns | Added MeasureSymmetry source files
* msvc/winvmd/winvmd.dsp 1.115 (changed +4 -0)
Changed call to non-portable random() to vmd_random().
* src/MeasureSymmetry.C 1.3 (changed +3 -3)
Elminated non-portable fmin() call.
* src/DrawRingsUtils.C 1.9 (changed +2 -2)
|
| | 2008-05-12 | saam | * Added RCS header and comments.
* Limited the number of atoms on which finding planes and axes is based to
a given value (default=100). Now you can also feed large structures into
the algorithm without locking the machine.
* Doxygenized some comments
* src/MeasureSymmetry.h 1.2 (changed +84 -34)
* src/MeasureSymmetry.C 1.2 (changed +43 -3)
Added "measure symmetry" command which guesses the pointgroup of a selection and
returns the according symmetry elements (mirror planes rotary axes, rotary reflection
axes). The algorithm is is fairly forgiving about molecules where atoms are perturbed
from the ideal position and tries its best to guess the correct point group anyway.
The 'forgivingness' can be controlled with the -sigma parameter which is the average
allowed deviation from the ideal position.
Works nice on my 30 non-patholocical test cases. what pathological means in this
context will be explained in the docs when I add them. If you feed the algorithm with
the ribosome it's going to compute for 400,000 years I guess, but for the biggest
symmetrical things in my test set (C60/C70 fullerenes) it takes 3s. Smaller molecules
often take only a few milliseconds. But these times can probably be still reduced.
Added command 'measure transoverlap' which computes a score value for the structural
overlap of a selection and it's image that was transformed according to the given
transformation matrix. This is the underlying command for checking symmetry elements.
* src/TclMeasure.C 1.103 (changed +145 -1)
* src/MeasureSymmetry.h 1.1 (added +147 -0)
* src/MeasureSymmetry.C 1.1 (added +1550 -0)
Added MeasureSymmetry.[Ch] to the list.
* configure 1.1011 (changed +2 -0)
|
| | 2008-05-09 | saam | Added safety checcks into vmd_gridsearch3, so that it is not run with empty atom
selections.
* src/SpatialSearch.C 1.5 (changed +8 -1)
Added safety checks to measure inertia and measure pbcneighbors to prevent running
with stale atomselections, i.e ones that refer to a deleted molecule.
* src/TclMeasure.C 1.102 (changed +12 -1)
|
| | 2008-05-08 | johns | Simon Cross and James Gain's patch to use cold to hot color ramp for
pucker coloring of carbohydrate structures.
* src/DrawRingsUtils.C 1.8 (changed +21 -4)
|
| | 2008-05-07 | johns | Correct function signature ambiguity for fmod()
* src/DrawRingsUtils.C 1.7 (changed +2 -2)
|
| | 2008-05-06 | johns | Added tests and reporting of overlapped I/O during CUDA device enumeration
* src/CUDAUtil.cu 1.7 (changed +4 -2)
* src/CUDAKernels.h 1.10 (changed +2 -2)
* src/CUDAAccel.h 1.6 (changed +3 -1)
* src/CUDAAccel.C 1.9 (changed +16 -4)
General cleanup, conversion of arithmetic to single precision for
use of VMD vector routines.
* src/DrawRingsUtils.h 1.7 (changed +6 -15)
* src/DrawRingsUtils.C 1.6 (changed +265 -134)
Pretty up CUDA device enumeration a bit more
* src/CUDAAccel.C 1.10 (changed +3 -3)
Ring coloring based on Michelle's new coloring scheme.
The current implementation calculates the Hill-Reilly puckering
parameters and then maps x, the absolute value of their sum
(divided by a suitable guess at the range of sums), onto
RGB(x) = x, 0.5, 1-x. This gives nice blue and orange colours for
the 18 ring glucose chain.
* src/DrawMolItemRings.C 1.12 (changed +4 -58)
Updated the CUDA device enumeration routines for CUDA 2.0,
improved the display of device attributes, etc.
* src/CUDAUtil.cu 1.6 (changed +10 -3)
* src/CUDAKernels.h 1.9 (changed +3 -2)
* src/CUDAAccel.h 1.5 (changed +3 -1)
* src/CUDAAccel.C 1.8 (changed +23 -11)
|
| | 2008-05-02 | saam | * Added measure inertia command that returns the principle axes of inertia.
* Introduced a few newlines in the Usage message to make it more readable.
* src/TclMeasure.C 1.100 (changed +120 -9)
* src/Measure.h 1.52 (changed +7 -1)
* src/Measure.C 1.109 (changed +151 -1)
Added comments.
Aligned some lines of code (just whitespace)
* src/VolMapCreate.C 1.77 (changed +53 -27)
* src/TclVolMap.C 1.47 (changed +10 -8)
Replaced ?arg? with [arg] for optional arguments in some of the Usage messages to make them
appear uniform.
* src/TclMeasure.C 1.101 (changed +11 -11)
|
| | 2008-05-02 | johns | AK's bugfix when calculating the r values for measure gofr
* src/TclMeasure.C 1.99 (changed +2 -2)
AK's patch to enable compilation with Python 2.4.x
* src/py_vmd.C 1.4 (changed +6 -1)
Eliminated more redundant Pi constants and degree-to-radian macros
* src/VolumeTexture.C 1.8 (changed +5 -7)
* src/MeasureSurface.C 1.4 (changed +5 -5)
* src/Measure.h 1.51 (changed +2 -4)
* src/Measure.C 1.108 (changed +4 -4)
Make gofr code use VMD_PI constant
* src/Measure.C 1.107 (changed +3 -3)
Updated documentation for display commands
* doc/ug_text_ui.tex 1.190 (changed +86 -63)
|
| | 2008-04-30 | kvandivo | For
Creation of window for 'XXscript' failed
error message, changed it to:
Creation of window for 'XXscript' failed (Invalid args to blah blah)
where it gives the error message from the tcl interpreter back
* src/VMDTkMenu.C 1.14 (changed +3 -3)
|
| | 2008-04-30 | johns | Added a routine to return basis direction unit vectors
* src/VolumetricData.h 1.22 (changed +4 -1)
* src/VolumetricData.C 1.25 (changed +22 -1)
Corrected projection of surface normals into world coordinates,
for isosurfaces of density maps with non-axis aligned basis vectors,
and/or opposite handedness coordinate systems.
* src/Isosurface.h 1.19 (changed +1 -0)
* src/Isosurface.C 1.33 (changed +37 -9)
Cranked version
* configure 1.1010 (changed +1 -1)
Eliminate compiler warning on Solaris
* src/TachyonDisplayDevice.C 1.75 (changed +4 -4)
Eliminated compiler warnings about "volmap" parameters hiding class member
variables, and a problematic literal string conversion.
* src/VolMapCreate.C 1.76 (changed +22 -26)
Eliminated compiler warnings about gradient parameter hiding class member
* src/VolumetricData.C 1.26 (changed +10 -10)
Eliminated unnecessary display command objects
* src/DrawMolItemRings.C 1.11 (changed +1 -6)
More updates to feature/bug fix lists
* README 1.345 (changed +17 -4)
|
| | 2008-04-29 | johns | Added another variant of vec_scale() that accepts double precision values
* src/utilities.h 1.84 (changed +8 -1)
|
| | 2008-04-28 | johns | Correct floating point constant declaration to avoid compiler warning
* src/BaseMolecule.C 1.209 (changed +3 -3)
Corrected floating point precision consistency
* src/GeometryFltkMenu.C 1.46 (changed +2 -2)
* src/CUDAAccel.C 1.7 (changed +2 -2)
Eliminate MSVC compiler warnings
* src/Matrix4.C 1.47 (changed +3 -3)
Eliminate MSVC warnings
* src/OpenGLRenderer.C 1.385 (changed +3 -3)
* src/MoleculeGraphics.C 1.55 (changed +2 -2)
Fix floating point consistency for the PBC measure commands
* src/MeasurePBC.C 1.7 (changed +10 -10)
Fixed inconsistent floating point precision in the dipole and
bond/angle/dihed/imprp energy measure commands.
* src/Measure.C 1.106 (changed +31 -33)
Made Gelato and RenderMan output classes use self-consistent floating
point precision.
* src/RenderManDisplayDevice.C 1.39 (changed +3 -3)
* src/GelatoDisplayDevice.C 1.20 (changed +11 -11)
Reduce memory usage for ring finding routines by combining the
intree_flag and intree_parents arrays by using sentinel values for
atom indices.
* src/BaseMolecule.h 1.116 (changed +2 -2)
* src/BaseMolecule.C 1.207 (changed +7 -11)
Replace hard-coded constants in the ring finding code with locally
defined macros
* src/BaseMolecule.C 1.208 (changed +8 -5)
|
| | 2008-04-24 | johns | Cranked version
* configure 1.1009 (changed +1 -1)
Eliminate a massive proliferation of various forms of PI constants, e.g.
M_PI, M_1_PI, QUAT_PI, MYPI, and many others, in favor of
VMD_PI, VMD_TWOPI, and VMD_1_PI, now defined in utilities.h
Also eliminated a similar proliferation of macros conversion between
degrees and radians, and so on.
* src/utilities.h 1.83 (changed +9 -8)
* src/VrmlDisplayDevice.C 1.34 (changed +3 -3)
* src/VolumeTexture.C 1.7 (changed +3 -3)
* src/VolMapCreate.C 1.75 (changed +4 -4)
* src/VMDTitle.C 1.51 (changed +1 -3)
* src/VMDQuat.C 1.9 (changed +5 -10)
* src/Timestep.C 1.56 (changed +5 -9)
* src/TclVec.C 1.39 (changed +4 -7)
* src/RenderManDisplayDevice.C 1.38 (changed +8 -11)
* src/PSDisplayDevice.C 1.101 (changed +3 -3)
* src/OpenGLRenderer.C 1.384 (changed +4 -4)
* src/Measure.C 1.105 (changed +3 -3)
* src/Matrix4.h 1.36 (changed +2 -11)
* src/Matrix4.C 1.46 (changed +3 -3)
* src/LibGelatoDisplayDevice.C 1.8 (changed +2 -9)
* src/GelatoDisplayDevice.C 1.19 (changed +6 -13)
* src/FreeVRDisplayDevice.C 1.27 (changed +2 -2)
* src/FileRenderer.C 1.120 (changed +3 -3)
* src/DrawRingsUtils.h 1.6 (changed +1 -6)
* src/DrawRingsUtils.C 1.5 (changed +9 -8)
* src/DrawMolItemRings.C 1.10 (changed +2 -2)
* src/DrawMolItemRibbons.C 1.134 (changed +2 -2)
* src/DispCmds.C 1.83 (changed +3 -3)
* src/CaveDisplayDevice.C 1.45 (changed +2 -2)
Eliminate warning on MacOS X
* src/BaseMolecule.C 1.206 (changed +2 -2)
Fix duplicate definition of M_PI on some platforms.
* src/TclVec.C 1.38 (changed +4 -2)
Re-enable VRPN for the MacOS X builds after compiling the client library
for MacOS X 10.4.x on Intel.
* Makefile 1.59 (changed +6 -6)
|
| | 2008-04-23 | saam | * Added more documentation
* Pretty up
* src/VolMapCreate.h 1.31 (changed +2 -2)
* src/VolMapCreate.C 1.74 (changed +35 -23)
* src/TclVolMap.C 1.45 (changed +17 -17)
Pretty up the code by replacing multiple object casts by a cast pointer.
* src/VolMapCreate.h 1.30 (changed +13 -20)
* src/TclVolMap.C 1.44 (changed +55 -44)
Replaced the MYPRINTF by msgInfo stream.
* src/VolMapCreate.C 1.73 (changed +86 -72)
|
| | 2008-04-23 | johns | Added safety checks to cap the maximum number of rings that we'll search
for in the ring finding code. It was previously possible to crash the
the program during ring finding when analyzing large silicon nanodevice
structures with high connectivity.
* src/BaseMolecule.C 1.204 (changed +17 -4)
Create new variable declaration scopes in switch statement cases
for correct compilation on Win32 with MSVC6.
* src/TclVolMap.C 1.46 (changed +5 -1)
Eliminated bogus include of iostream from ring linkage header
* src/SmallRingLinkages.h 1.5 (changed +1 -2)
Prevent a problem with ambiguous overloading with bleeding edge C++ compilers
* src/BaseMolecule.C 1.205 (changed +2 -2)
|
| | 2008-04-22 | saam | * Replaced MYPRINTF hack with msgInfo outputting in a few places.
* Made file_writing independent of the VolMap class. There is a virtual
write_map() method in the base class now that calls the write_dx_dile()
(which will eventually be replaced by using molefile plugin). For the
FastEnergy derived class there is another write_map definition that adds
temperature and weight info to the dataset name string.
* When the dataset name string is set now all double quotes are
replaced by single quotes because double quotes delimit the name string
itself.
* Added more comments.
* src/VolMapCreate.h 1.29 (changed +26 -24)
* src/VolMapCreate.C 1.72 (changed +83 -36)
* src/VolMap.h 1.11 (changed +2 -2)
* src/VolMap.C 1.17 (changed +23 -12)
* src/TclVolMap.C 1.43 (changed +3 -3)
Added a function rotate_axis() to the Matrix4 class that rotates around
a given vector. It also corresponds to the TCL command transabout
which is currently defined in vectors.tcl. I created a TCL interface to
the C++ version such that the TCL script version can go away.
* src/TclVec.C 1.37 (changed +69 -1)
* src/Matrix4.h 1.35 (changed +6 -3)
* src/Matrix4.C 1.45 (changed +11 -2)
Remove transabout procedure since there's a C++ version now.
* scripts/vmd/vectors.tcl 1.14 (changed +1 -11)
|
| | 2008-04-22 | johns | Enable carbohydrate representations by default now that the ring finding
code is run on-the-fly rather than at start.
* configure 1.1008 (changed +1 -2)
More feature list updates
* README 1.344 (changed +5 -0)
|
| | 2008-04-21 | johns | More new features
* README 1.343 (changed +11 -2)
Updated README with more of the new features we've added
* README 1.342 (changed +30 -2)
|
| | 2008-04-20 | johns | Carbohydrate default ring search size patch from Simon Cross.
Simple patch to reduce the default maximum ring size from 20 to 10.
This just reduces the possibility of really pathalogical molecules
files causing problems by having huge numbers of rings. Perhaps less
necessary now because the BaseMolecule clean-ups also mean that the
ring finding code isn't called by default (Twister or PaperChain
already recalculate the results if the maximum ring size or path
length differ from the current settings).
* src/GraphicsFltkReps.h 1.68 (changed +3 -3)
* src/AtomRep.C 1.106 (changed +3 -3)
Carbohydrate structure analysis patch from Simon Cross.
* Removal of call to find_small_rings_and_linkages so that ring
finding code is only run on demand.
* Fix missing bracket in comment.
* Fix small but bad bug in back edge finding code (parent in the
spanning tree was being stored very late, resulting in some back edges
being missed).
* find_small_rings_from_partial(...) modified to excluded barred rings
(i.e. ones which are crossed by a single edge). This speeds up ring
finding quite a bit since a lot of cases can be quickly discarded. It
also reduces the number of rings found in highly linked molecules.
* Change ring orientating code to look for "C1" or "C1'" after the
oxygen atom, rather than trying to guess the first carbon by looking
for links to carbons outside the ring. I'm still not 100% sure that
this is a good part of the patch. The old system failed to orientate
rings quite often (for example, if the ring was bonded to another ring
via something other than a carbon) but the new system relies on the
carbons being labelled nicely in the files. A fair number of the test
files I have don't. However, at least the new method is predictable
and gives the user some more control over the orientation (i.e. they
can orientate the rings themselves by changing the labels on the
carbons next to the oxygen).
* Ring linkage finding code modified to ignore atoms which belong to
multiple rings. The ring finding code implicitly assumed that atoms
belonged to at most one ring and produced some spurious links between
rings which shared atoms as a result.
* src/BaseMolecule.h 1.115 (changed +2 -2)
* src/BaseMolecule.C 1.203 (changed +103 -74)
Carbohydrate structure representation update from Simon Cross.
The Twister code for rendering the ends of the ribbons when the "start
from ring centroid" option is selected has basically been completely
re-written. The new implementation actually starts the ribbon at a
point X which is lies on the plane formed by the ring centroid and the
ring normal. X is chosen to be as close to the point midway between
the centroid and the last atom on the path as possible. This is
cheating a bit, but it does bring the final sections of all ribbons
arriving at a single ring into a common plane so that they line-up
nicely. Any possible gaps where the ribbons meet are filled in by
rendering a small circular disk (actually it's a regular dodecagon).
* src/DrawMolItemRings.C 1.9 (changed +279 -24)
* src/DrawMolItem.h 1.151 (changed +10 -1)
Compact Tcl interface code
* src/TclVolMap.C 1.42 (changed +5 -6)
Cranked version
* configure 1.1007 (changed +1 -1)
Fix missing timer destroy call
* src/VolMapCreate.C 1.71 (changed +3 -1)
|
| | 2008-04-19 | saam | Added additional comments.
Added a timer for ILS so that I can tune it for speed later
* src/VolMapCreate.C 1.68 (changed +37 -8)
Deleted further functions from the VolMap class.
It is almost ready now to get replaced by VolumetricData.
* src/VolMapCreate.h 1.28 (changed +6 -2)
* src/VolMapCreate.C 1.69 (changed +76 -3)
* src/VolMap.h 1.9 (changed +5 -11)
* src/VolMap.C 1.15 (changed +2 -71)
* src/TclVolMap.C 1.41 (changed +8 -4)
Removed the update_internal (a misnomer anyway) from VolMap.
All that's left now should in some way correspond to stuff that is in
VolumetricData.
* src/VolMapCreate.C 1.70 (changed +12 -6)
* src/VolMap.h 1.10 (changed +2 -4)
* src/VolMap.C 1.16 (changed +1 -10)
|
| | 2008-04-18 | saam | Eliminated dead code.
* src/VolMap.h 1.8 (changed +3 -16)
* src/VolMap.C 1.14 (changed +5 -75)
|
| | 2008-04-18 | johns | Fix timestep memory leak introduced with the recent reorganization of the
Animation class, timestep storage, etc. Timesteps were not getting
deleted properly when their parent molecules were being deleted.
* src/DrawMolecule.C 1.131 (changed +11 -2)
|
| | 2008-04-14 | johns | Started update process for README
* README 1.341 (changed +6 -171)
|
| | 2008-04-06 | johns | Improved readability of the ribbon/cartoon spline computation loops,
reduced int/float conversions, and explicitly replaced a few divides
in favor of multiplies.
* src/DrawMolItemRibbons.C 1.132 (changed +20 -26)
Moved the material change command immediately prior to the
ribbon rendering commands. Coalescing rendering operations
into compact groupings makes addition of mutex locks
for multithreading much easier.
* src/DrawMolItemRibbons.C 1.133 (changed +4 -4)
|
| | 2008-04-05 | johns | Added code to precalculate control point lists used by ribbon/cartoon
reps, to help improve interactive trajectory display performance.
This will ultimately eliminate all of the on-the-fly traversal of
the atoms in residues presently being done to identify control points.
It will also allow VMD to use more robust control point selection
criteria that would otherwise be too costly to perform at redraw time.
* src/BaseMolecule.h 1.114 (changed +7 -1)
* src/BaseMolecule.C 1.200 (changed +101 -5)
Added performance measurement instrumentation for the ribbon
extrusion code.
* src/DrawMolItemRibbons.C 1.131 (changed +39 -2)
* src/BaseMolecule.C 1.202 (changed +2 -1)
More work on control point precalc code.
* src/BaseMolecule.C 1.201 (changed +24 -10)
Update comments on fragment finding code
* src/BaseMolecule.h 1.113 (changed +3 -5)
|
| | 2008-04-04 | johns | Fixed some out of date comments about the color index ranges, and updated
examples to query color ranges rather than hard coding them.
* doc/ug_text_ui.tex 1.189 (changed +4 -4)
* doc/ug_molecule_info.tex 1.29 (changed +5 -3)
* doc/ug_mol_colors.tex 1.22 (changed +9 -7)
Start preparing for precalculated control point storage
* src/BaseMolecule.h 1.112 (changed +15 -1)
* src/BaseMolecule.C 1.199 (changed +22 -1)
|
| | 2008-04-03 | johns | Cranked version
* configure 1.1006 (changed +1 -1)
|
| | 2008-04-01 | kvandivo | Corrected text
Sorry, this version of VMD was compiled with Python support disabled
(The 'of' was missing)
* src/UIText.C 1.185 (changed +2 -2)
|
| | 2008-04-01 | johns | Adjust benchmark grid size and thread block size to get
more accurate performance measurements for next-gen GPUs with
differing numbers of SMs.
* src/CUDABench.cu 1.7 (changed +4 -4)
Fix missing linefeeds in the built-in help for the "measure energy" and
"measure surface" commands.
* src/TclMeasure.C 1.98 (changed +3 -3)
|
| | 2008-03-31 | johns | Eliminated holdover code from old residue bond logic.
* src/Residue.h 1.32 (changed +1 -40)
* src/BaseMolecule.C 1.198 (changed +1 -101)
|
| | 2008-03-27 | johns | Cranked version
* configure 1.1005 (changed +1 -1)
Fix uninitialized curframe member variable.
* src/DrawMolecule.C 1.129 (changed +2 -1)
MacOS X 10.5.x changes the behavior of putenv() such that it no longer
makes copies of strings added to the environment. Changed the environment
initialization code to use setenv() instead, since it copies parameters and
provides a cleaner interface to work with.
* src/macosxvmdstart.C 1.14 (changed +16 -24)
Starting with MacOS X 10.4 we can use dlopen(), dlsym(), dlclose() natively,
so there's no need to emulate these anymore. We'll leave the code in place,
but for all current builds we're targeting 10.4 or later anyway.
* src/vmddlopen.c 1.14 (changed +6 -3)
Updated copyright headers
* src/PeriodicTable.h 1.3 (changed +2 -2)
* src/CUDAVolCPotential.cu 1.26 (changed +2 -2)
* src/CUDAUtil.cu 1.5 (changed +2 -2)
* src/CUDABench.cu 1.6 (changed +2 -2)
Updated copyright headers.
* src/win32vmdstart.h 1.7 (changed +2 -2)
* src/win32vmdstart.c 1.37 (changed +2 -2)
* src/vmdsock.h 1.12 (changed +2 -2)
* src/vmdsock.c 1.19 (changed +2 -2)
* src/vmdmain.C 1.4 (changed +2 -2)
* src/vmddlopen.h 1.7 (changed +2 -2)
* src/vmddlopen.c 1.15 (changed +2 -2)
* src/vmdconsole.h 1.3 (changed +2 -2)
* src/vmdconsole.c 1.4 (changed +2 -2)
* src/vmd.h 1.4 (changed +2 -2)
* src/vmd.C 1.69 (changed +2 -2)
* src/utilities.h 1.82 (changed +2 -2)
* src/utilities.C 1.110 (changed +2 -2)
* src/tcl_commands.h 1.18 (changed +2 -2)
* src/tcl_commands.C 1.28 (changed +2 -2)
* src/py_trans.C 1.13 (changed +2 -2)
* src/py_render.C 1.11 (changed +2 -2)
* src/py_numeric.C 1.17 (changed +2 -2)
* src/py_mouse.C 1.4 (changed +1 -1)
* src/py_molrep.C 1.21 (changed +2 -2)
* src/py_molecule.C 1.63 (changed +2 -2)
* src/py_menu.C 1.8 (changed +1 -1)
* src/py_material.C 1.15 (changed +2 -2)
* src/py_label.C 1.19 (changed +2 -2)
* src/py_imd.C 1.13 (changed +2 -2)
* src/py_graphics.C 1.21 (changed +2 -2)
* src/py_display.C 1.29 (changed +2 -2)
* src/py_commands.h 1.37 (changed +2 -2)
* src/py_commands.C 1.11 (changed +2 -2)
* src/py_color.C 1.16 (changed +2 -2)
* src/py_axes.C 1.9 (changed +2 -2)
* src/py_atomselection.C 1.46 (changed +2 -2)
* src/py_atomsel.C 1.14 (changed +2 -2)
* src/py_animate.C 1.15 (changed +2 -2)
* src/macosxvmdstart.C 1.15 (changed +2 -2)
* src/intstack.h 1.4 (changed +2 -2)
* src/intstack.c 1.5 (changed +2 -2)
* src/inthash.h 1.4 (changed +2 -2)
* src/inthash.c 1.4 (changed +2 -2)
* src/imd.h 1.18 (changed +2 -2)
* src/imd.C 1.13 (changed +2 -2)
* src/hash.h 1.10 (changed +2 -2)
* src/hash.c 1.12 (changed +2 -2)
* src/frame_selector.h 1.8 (changed +2 -2)
* src/frame_selector.C 1.18 (changed +2 -2)
* src/cmd_vmdbench.C 1.9 (changed +2 -2)
* src/cmd_util.C 1.32 (changed +2 -2)
* src/cmd_user.C 1.22 (changed +2 -2)
* src/cmd_trans.C 1.20 (changed +1 -1)
* src/cmd_tool.C 1.30 (changed +2 -2)
* src/cmd_render.C 1.33 (changed +1 -1)
* src/cmd_plugin.C 1.20 (changed +1 -1)
* src/cmd_mouse.C 1.24 (changed +1 -1)
* src/cmd_mol.C 1.99 (changed +1 -1)
* src/cmd_menu.C 1.33 (changed +1 -1)
* src/cmd_material.C 1.24 (changed +2 -2)
* src/cmd_label.C 1.38 (changed +1 -1)
* src/cmd_imd.C 1.21 (changed +2 -2)
* src/cmd_display.C 1.61 (changed +2 -2)
* src/cmd_color.C 1.27 (changed +2 -2)
* src/cmd_collab.C 1.4 (changed +2 -2)
* src/cmd_animate.C 1.44 (changed +2 -2)
* src/Win32ftp.h 1.8 (changed +2 -2)
* src/Win32ftp.C 1.10 (changed +2 -2)
* src/Win32OpenGLDisplayDevice.C 1.98 (changed +2 -2)
* src/Win32Joystick.h 1.14 (changed +2 -2)
* src/Win32Joystick.C 1.22 (changed +2 -2)
* src/WavefrontDisplayDevice.h 1.5 (changed +2 -2)
* src/WavefrontDisplayDevice.C 1.7 (changed +2 -2)
* src/VrmlDisplayDevice.h 1.22 (changed +2 -2)
* src/VrmlDisplayDevice.C 1.33 (changed +2 -2)
* src/Vrml2DisplayDevice.h 1.15 (changed +2 -2)
* src/Vrml2DisplayDevice.C 1.16 (changed +2 -2)
* src/VolumetricData.h 1.21 (changed +2 -2)
* src/VolumetricData.C 1.24 (changed +2 -2)
* src/VolumeTexture.h 1.3 (changed +2 -2)
* src/VolumeTexture.C 1.6 (changed +2 -2)
* src/VolMapCreate.h 1.27 (changed +3 -3)
* src/VolMapCreate.C 1.67 (changed +3 -3)
* src/VolMap.h 1.7 (changed +3 -3)
* src/VolMap.C 1.13 (changed +3 -3)
* src/VolCPotential.h 1.3 (changed +2 -2)
* src/VolCPotential.C 1.18 (changed +2 -2)
* src/VMDTkinterMenu.h 1.6 (changed +1 -1)
* src/VMDTkMenu.h 1.9 (changed +2 -2)
* src/VMDTkMenu.C 1.13 (changed +2 -2)
* src/VMDTitle.h 1.29 (changed +2 -2)
* src/VMDTitle.C 1.50 (changed +2 -2)
* src/VMDThreads.h 1.18 (changed +2 -2)
* src/VMDThreads.C 1.31 (changed +2 -2)
* src/VMDQuat.h 1.8 (changed +2 -2)
* src/VMDQuat.C 1.8 (changed +2 -2)
* src/VMDMenu.h 1.12 (changed +2 -2)
* src/VMDMenu.C 1.7 (changed +2 -2)
* src/VMDFltkMenu.h 1.13 (changed +2 -2)
* src/VMDFltkMenu.C 1.17 (changed +2 -2)
* src/VMDDisplayList.h 1.35 (changed +2 -2)
* src/VMDDisplayList.C 1.33 (changed +2 -2)
* src/VMDDir.h 1.10 (changed +2 -2)
* src/VMDDir.C 1.12 (changed +2 -2)
* src/VMDCollab.h 1.3 (changed +2 -2)
* src/VMDCollab.C 1.3 (changed +2 -2)
* src/VMDApp.h 1.187 (changed +3 -3)
* src/VMDApp.C 1.397 (changed +3 -3)
* src/UIText.h 1.72 (changed +2 -2)
* src/UIText.C 1.184 (changed +2 -2)
* src/UIObject.h 1.36 (changed +2 -2)
* src/UIObject.C 1.39 (changed +2 -2)
* src/ToolFltkMenu.h 1.12 (changed +2 -2)
* src/ToolFltkMenu.C 1.23 (changed +2 -2)
* src/Timestep.h 1.42 (changed +2 -2)
* src/Timestep.C 1.55 (changed +2 -2)
* src/TextInterp.h 1.25 (changed +3 -3)
* src/TextEvent.h 1.43 (changed +1 -1)
* src/TclVolMap.C 1.40 (changed +2 -2)
* src/TclVec.C 1.36 (changed +3 -3)
* src/TclTextInterp.h 1.36 (changed +3 -3)
* src/TclTextInterp.C 1.96 (changed +3 -3)
* src/TclMolInfo.C 1.45 (changed +2 -2)
* src/TclMeasure.C 1.97 (changed +3 -3)
* src/TclGraphics.C 1.42 (changed +2 -2)
* src/TclCommands.h 1.46 (changed +2 -2)
* src/TclCommands.C 1.148 (changed +2 -2)
* src/TachyonDisplayDevice.h 1.32 (changed +2 -2)
* src/TachyonDisplayDevice.C 1.74 (changed +2 -2)
* src/SymbolTable.h 1.57 (changed +2 -2)
* src/SymbolTable.C 1.58 (changed +2 -2)
* src/Surf.h 1.20 (changed +2 -2)
* src/Surf.C 1.44 (changed +2 -2)
* src/Stride.h 1.8 (changed +2 -2)
* src/Stride.C 1.31 (changed +2 -2)
* src/Stage.h 1.32 (changed +2 -2)
* src/Stage.C 1.44 (changed +2 -2)
* src/Stack.h 1.24 (changed +2 -2)
* src/SpringTool.h 1.13 (changed +1 -1)
* src/SpringTool.C 1.20 (changed +1 -1)
* src/SpatialSearch.h 1.3 (changed +2 -2)
* src/SpatialSearch.C 1.4 (changed +2 -2)
* src/SpaceballTracker.h 1.11 (changed +2 -2)
* src/SpaceballTracker.C 1.10 (changed +2 -2)
* src/Spaceball.h 1.16 (changed +2 -2)
* src/Spaceball.C 1.29 (changed +2 -2)
* src/SortableArray.h 1.22 (changed +2 -2)
* src/SnapshotDisplayDevice.h 1.22 (changed +2 -2)
* src/SnapshotDisplayDevice.C 1.40 (changed +2 -2)
* src/SmallRingLinkages.h 1.4 (changed +2 -2)
* src/SmallRing.h 1.7 (changed +2 -2)
* src/SelectionBuilder.h 1.11 (changed +2 -2)
* src/SelectionBuilder.C 1.23 (changed +2 -2)
* src/Scene.h 1.57 (changed +3 -3)
* src/Scene.C 1.81 (changed +2 -2)
* src/SaveTrajectoryFltkMenu.h 1.12 (changed +2 -2)
* src/SaveTrajectoryFltkMenu.C 1.27 (changed +2 -2)
* src/STLDisplayDevice.h 1.21 (changed +2 -2)
* src/STLDisplayDevice.C 1.34 (changed +2 -2)
* src/SDLOpenGLDisplayDevice.C 1.25 (changed +2 -2)
* src/ResizeArray.h 1.41 (changed +2 -2)
* src/Residue.h 1.31 (changed +2 -2)
* src/RenderManDisplayDevice.h 1.18 (changed +2 -2)
* src/RenderManDisplayDevice.C 1.37 (changed +2 -2)
* src/RenderFltkMenu.h 1.9 (changed +1 -1)
* src/RenderFltkMenu.C 1.10 (changed +1 -1)
* src/RayShadeDisplayDevice.h 1.23 (changed +2 -2)
* src/RayShadeDisplayDevice.C 1.39 (changed +2 -2)
* src/RadianceDisplayDevice.h 1.27 (changed +2 -2)
* src/RadianceDisplayDevice.C 1.39 (changed +2 -2)
* src/R3dDisplayDevice.h 1.31 (changed +2 -2)
* src/R3dDisplayDevice.C 1.75 (changed +2 -2)
* src/PythonTextInterp.h 1.24 (changed +3 -3)
* src/PythonTextInterp.C 1.62 (changed +3 -3)
* src/PluginMgr.h 1.12 (changed +2 -2)
* src/PluginMgr.C 1.31 (changed +2 -2)
* src/PlainTextInterp.h 1.8 (changed +2 -2)
* src/PlainTextInterp.C 1.9 (changed +2 -2)
* src/Pickable.h 1.30 (changed +2 -2)
* src/PickModeUser.h 1.3 (changed +1 -1)
* src/PickModeUser.C 1.4 (changed +3 -3)
* src/PickModeMove.h 1.12 (changed +2 -2)
* src/PickModeMove.C 1.19 (changed +2 -2)
* src/PickModeMolLabel.h 1.24 (changed +2 -2)
* src/PickModeMolLabel.C 1.41 (changed +2 -2)
* src/PickModeList.h 1.9 (changed +3 -3)
* src/PickModeList.C 1.13 (changed +2 -2)
* src/PickModeForce.h 1.12 (changed +2 -2)
* src/PickModeForce.C 1.12 (changed +2 -2)
* src/PickModeCenter.h 1.17 (changed +2 -2)
* src/PickModeCenter.C 1.28 (changed +2 -2)
* src/PickModeAddBond.h 1.9 (changed +1 -1)
* src/PickModeAddBond.C 1.14 (changed +2 -2)
* src/PickMode.h 1.21 (changed +2 -2)
* src/PickList.h 1.32 (changed +2 -2)
* src/PickList.C 1.41 (changed +2 -2)
* src/ParseTree.h 1.37 (changed +2 -2)
* src/ParseTree.C 1.118 (changed +2 -2)
* src/P_VRPNTracker.h 1.22 (changed +2 -2)
* src/P_VRPNTracker.C 1.24 (changed +2 -2)
* src/P_VRPNFeedback.h 1.24 (changed +2 -2)
* src/P_VRPNFeedback.C 1.31 (changed +2 -2)
* src/P_VRPNButtons.h 1.23 (changed +2 -2)
* src/P_VRPNButtons.C 1.24 (changed +2 -2)
* src/P_UIVR.h 1.70 (changed +2 -2)
* src/P_UIVR.C 1.128 (changed +2 -2)
* src/P_TugTool.h 1.37 (changed +2 -2)
* src/P_TugTool.C 1.49 (changed +2 -2)
* src/P_Tracker.h 1.26 (changed +2 -2)
* src/P_Tracker.C 1.20 (changed +2 -2)
* src/P_Tool.h 1.63 (changed +2 -2)
* src/P_Tool.C 1.77 (changed +2 -2)
* src/P_SensorConfig.h 1.24 (changed +2 -2)
* src/P_SensorConfig.C 1.34 (changed +2 -2)
* src/P_RotateTool.h 1.31 (changed +2 -2)
* src/P_RotateTool.C 1.41 (changed +2 -2)
* src/P_PrintTool.h 1.8 (changed +2 -2)
* src/P_PrintTool.C 1.8 (changed +2 -2)
* src/P_PinchTool.h 1.15 (changed +1 -1)
* src/P_PinchTool.C 1.18 (changed +1 -1)
* src/P_JoystickTool.h 1.28 (changed +2 -2)
* src/P_JoystickTool.C 1.36 (changed +2 -2)
* src/P_JoystickButtons.h 1.15 (changed +2 -2)
* src/P_JoystickButtons.C 1.14 (changed +2 -2)
* src/P_GrabTool.h 1.22 (changed +2 -2)
* src/P_GrabTool.C 1.29 (changed +2 -2)
* src/P_FreeVRTracker.h 1.13 (changed +2 -2)
* src/P_FreeVRTracker.C 1.13 (changed +2 -2)
* src/P_FreeVRButtons.h 1.13 (changed +2 -2)
* src/P_FreeVRButtons.C 1.11 (changed +2 -2)
* src/P_Feedback.h 1.24 (changed +2 -2)
* src/P_CmdTool.h 1.33 (changed +2 -2)
* src/P_CmdTool.C 1.45 (changed +2 -2)
* src/P_CaveTracker.h 1.16 (changed +2 -2)
* src/P_CaveTracker.C 1.15 (changed +2 -2)
* src/P_CaveButtons.h 1.18 (changed +2 -2)
* src/P_CaveButtons.C 1.16 (changed +2 -2)
* src/P_Buttons.h 1.21 (changed +2 -2)
* src/P_Buttons.C 1.15 (changed +2 -2)
* src/PSDisplayDevice.h 1.36 (changed +2 -2)
* src/PSDisplayDevice.C 1.100 (changed +2 -2)
* src/POV3DisplayDevice.h 1.38 (changed +2 -2)
* src/POV3DisplayDevice.C 1.99 (changed +2 -2)
* src/OpenGLStipples.h 1.7 (changed +2 -2)
* src/OpenGLShader.h 1.10 (changed +2 -2)
* src/OpenGLShader.C 1.20 (changed +2 -2)
* src/OpenGLRenderer.h 1.127 (changed +2 -2)
* src/OpenGLRenderer.C 1.383 (changed +2 -2)
* src/OpenGLExtensions.h 1.38 (changed +2 -2)
* src/OpenGLExtensions.C 1.53 (changed +2 -2)
* src/OpenGLDisplayDevice.h 1.45 (changed +2 -2)
* src/OpenGLDisplayDevice.C 1.149 (changed +2 -2)
* src/OpenGLCache.h 1.6 (changed +2 -2)
* src/OpenGLCache.C 1.6 (changed +2 -2)
* src/NameList.h 1.43 (changed +2 -2)
* src/Mouse.h 1.64 (changed +3 -3)
* src/Mouse.C 1.139 (changed +2 -2)
* src/MoleculeList.h 1.67 (changed +2 -2)
* src/MoleculeList.C 1.115 (changed +2 -2)
* src/MoleculeGraphics.h 1.44 (changed +2 -2)
* src/MoleculeGraphics.C 1.54 (changed +2 -2)
* src/Molecule.h 1.58 (changed +2 -2)
* src/Molecule.C 1.82 (changed +2 -2)
* src/MolFilePlugin.h 1.30 (changed +2 -2)
* src/MolFilePlugin.C 1.79 (changed +2 -2)
* src/MolBrowser.h 1.11 (changed +1 -1)
* src/MolBrowser.C 1.31 (changed +2 -2)
* src/MeasureSurface.C 1.3 (changed +2 -2)
* src/MeasurePBC.C 1.6 (changed +3 -3)
* src/Measure.h 1.50 (changed +3 -3)
* src/Measure.C 1.104 (changed +2 -2)
* src/Matrix4.h 1.34 (changed +3 -3)
* src/Matrix4.C 1.44 (changed +3 -3)
* src/MaterialList.h 1.21 (changed +2 -2)
* src/MaterialList.C 1.29 (changed +2 -2)
* src/MaterialFltkMenu.h 1.10 (changed +2 -2)
* src/MaterialFltkMenu.C 1.16 (changed +2 -2)
* src/MainFltkMenu.h 1.39 (changed +1 -1)
* src/MainFltkMenu.C 1.132 (changed +1 -1)
* src/MSMSInterface.h 1.23 (changed +2 -2)
* src/MSMSInterface.C 1.48 (changed +2 -2)
* src/LibTachyonDisplayDevice.h 1.20 (changed +2 -2)
* src/LibTachyonDisplayDevice.C 1.37 (changed +2 -2)
* src/LibGelatoDisplayDevice.h 1.3 (changed +2 -2)
* src/LibGelatoDisplayDevice.C 1.7 (changed +2 -2)
* src/JString.h 1.18 (changed +2 -2)
* src/JString.C 1.17 (changed +2 -2)
* src/JRegex.h 1.11 (changed +2 -2)
* src/JRegex.C 1.10 (changed +2 -2)
* src/Isosurface.h 1.18 (changed +1 -1)
* src/Isosurface.C 1.32 (changed +1 -1)
* src/Isocontour.h 1.3 (changed +1 -1)
* src/Isocontour.C 1.3 (changed +1 -1)
* src/Inform.h 1.24 (changed +2 -2)
* src/Inform.C 1.32 (changed +2 -2)
* src/ImageIO.h 1.9 (changed +2 -2)
* src/ImageIO.C 1.9 (changed +2 -2)
* src/IMDSimThread.h 1.10 (changed +2 -2)
* src/IMDSimThread.C 1.11 (changed +2 -2)
* src/IMDSimBlocking.h 1.11 (changed +2 -2)
* src/IMDSimBlocking.C 1.13 (changed +2 -2)
* src/IMDSim.h 1.21 (changed +2 -2)
* src/IMDSim.C 1.28 (changed +2 -2)
* src/IMDMgr.h 1.21 (changed +2 -2)
* src/IMDMgr.C 1.35 (changed +2 -2)
* src/GraphicsFltkReps.h 1.67 (changed +2 -2)
* src/GraphicsFltkMenu.h 1.27 (changed +2 -2)
* src/GraphicsFltkMenu.C 1.110 (changed +2 -2)
* src/GeometrySpring.h 1.11 (changed +2 -2)
* src/GeometrySpring.C 1.15 (changed +2 -2)
* src/GeometryMol.h 1.29 (changed +2 -2)
* src/GeometryMol.C 1.45 (changed +2 -2)
* src/GeometryList.h 1.38 (changed +2 -2)
* src/GeometryList.C 1.61 (changed +2 -2)
* src/GeometryFltkMenu.h 1.18 (changed +1 -1)
* src/GeometryFltkMenu.C 1.45 (changed +1 -1)
* src/GeometryDihedral.h 1.21 (changed +2 -2)
* src/GeometryDihedral.C 1.27 (changed +2 -2)
* src/GeometryBond.h 1.21 (changed +2 -2)
* src/GeometryBond.C 1.24 (changed +2 -2)
* src/GeometryAtom.h 1.21 (changed +2 -2)
* src/GeometryAtom.C 1.25 (changed +2 -2)
* src/GeometryAngle.h 1.21 (changed +2 -2)
* src/GeometryAngle.C 1.25 (changed +2 -2)
* src/GelatoDisplayDevice.h 1.8 (changed +2 -2)
* src/GelatoDisplayDevice.C 1.18 (changed +2 -2)
* src/FreeVRScene.h 1.25 (changed +2 -2)
* src/FreeVRScene.C 1.34 (changed +2 -2)
* src/FreeVRRoutines.h 1.9 (changed +2 -2)
* src/FreeVRRoutines.C 1.17 (changed +2 -2)
* src/FreeVRDisplayDevice.h 1.16 (changed +2 -2)
* src/FreeVRDisplayDevice.C 1.26 (changed +2 -2)
* src/Fragment.h 1.16 (changed +2 -2)
* src/FltkOpenGLDisplayDevice.h 1.16 (changed +2 -2)
* src/FltkOpenGLDisplayDevice.C 1.41 (changed +2 -2)
* src/FileRenderer.h 1.86 (changed +2 -2)
* src/FileRenderer.C 1.119 (changed +2 -2)
* src/FileRenderList.h 1.20 (changed +2 -2)
* src/FileRenderList.C 1.60 (changed +2 -2)
* src/FileChooserFltkMenu.h 1.14 (changed +2 -2)
* src/FileChooserFltkMenu.C 1.45 (changed +2 -2)
* src/FPS.h 1.13 (changed +1 -1)
* src/FPS.C 1.14 (changed +1 -1)
* src/DrawRingsUtils.h 1.5 (changed +2 -2)
* src/DrawRingsUtils.C 1.4 (changed +2 -2)
* src/DrawMolecule.h 1.74 (changed +2 -2)
* src/DrawMolecule.C 1.130 (changed +2 -2)
* src/DrawMolItemVolume.C 1.141 (changed +2 -2)
* src/DrawMolItemSurface.C 1.37 (changed +2 -2)
* src/DrawMolItemRings.C 1.8 (changed +2 -2)
* src/DrawMolItemRibbons.C 1.130 (changed +2 -2)
* src/DrawMolItemMSMS.C 1.43 (changed +2 -2)
* src/DrawMolItem2.C 1.30 (changed +2 -2)
* src/DrawMolItem.h 1.150 (changed +2 -2)
* src/DrawMolItem.C 1.302 (changed +2 -2)
* src/DrawForce.h 1.22 (changed +2 -2)
* src/DrawForce.C 1.49 (changed +2 -2)
* src/Displayable.h 1.84 (changed +2 -2)
* src/Displayable.C 1.109 (changed +2 -2)
* src/DisplayRocker.h 1.5 (changed +2 -2)
* src/DisplayRocker.C 1.5 (changed +2 -2)
* src/DisplayFltkMenu.h 1.9 (changed +2 -2)
* src/DisplayFltkMenu.C 1.16 (changed +2 -2)
* src/DisplayDevice.h 1.124 (changed +2 -2)
* src/DisplayDevice.C 1.121 (changed +2 -2)
* src/DispCmds.h 1.88 (changed +2 -2)
* src/DispCmds.C 1.82 (changed +2 -2)
* src/DepthSortObj.h 1.12 (changed +2 -2)
* src/CoorPluginData.h 1.9 (changed +2 -2)
* src/CoorPluginData.C 1.17 (changed +2 -2)
* src/CoorData.h 1.7 (changed +2 -2)
* src/CommandQueue.h 1.38 (changed +2 -2)
* src/CommandQueue.C 1.51 (changed +2 -2)
* src/Command.h 1.158 (changed +2 -2)
* src/ColorInfo.C 1.31 (changed +2 -2)
* src/ColorFltkMenu.h 1.14 (changed +1 -1)
* src/ColorFltkMenu.C 1.20 (changed +1 -1)
* src/CmdTrans.h 1.29 (changed +2 -2)
* src/CmdTrans.C 1.39 (changed +2 -2)
* src/CmdRender.h 1.25 (changed +2 -2)
* src/CmdRender.C 1.35 (changed +2 -2)
* src/CmdPlugin.h 1.9 ( |
