--- vmd /src ---


Filename: ANARIRenderer.C
Revision 1.12johns 2020/11/16 07:40:51+5 -1
Added include of windows.h for interactive RT compilation on Windows platforms.
Show difference between Revision 1.11 and 1.12

Filename: AtomSel.C
Revision 1.179johns 2020/10/28 06:52:02+2 -2
Eliminate warning for ptrdiff_t to double conversion with explicit cast.
Show difference between Revision 1.178 and 1.179

Filename: BaseMolecule.C
Revision 1.277johns 2020/10/21 19:11:08+62 -22
Minor rewrite of default_mass() method for improved performance on
large structures, and to address JC Gumbart's patch to improve default
mass assignments for iron, fluorine, iodine, bromine, potassium, and calcium.
Show difference between Revision 1.276 and 1.277

Filename: BaseMolecule.h
Revision 1.151johns 2020/10/28 15:09:56+7 -7
Added explicit type conversions from ptrdiff_t sizes to int to greatly
reduce MSVS compiler conversion warnings.
Show difference between Revision 1.150 and 1.151

Filename: CUDAFastPBC.cu
Revision 1.4johns 2020/10/29 02:57:22+1 -22
Eliminated timer code leftover from standalone PBC implementation
Show difference between Revision 1.3 and 1.4

Filename: CmdColor.C
Revision 1.48johns 2020/12/24 04:21:51+4 -3
Revised color scale internals and the Color window GUI to implement
posterization of color scales down to a user-specified number of
individual color bands.
Show difference between Revision 1.47 and 1.48
Revision 1.47johns 2020/12/23 16:41:12+3 -3
Revised the color scale internals to facilitate ooptional color scale order
reversal for both built-in divergent midpoint/offset color scales as
well as tabulated color scales.
Show difference between Revision 1.46 and 1.47

Filename: CmdColor.h
Revision 1.35johns 2020/12/24 04:21:51+3 -3
Revised color scale internals and the Color window GUI to implement
posterization of color scales down to a user-specified number of
individual color bands.
Show difference between Revision 1.34 and 1.35
Revision 1.34johns 2020/12/23 16:41:12+4 -2
Revised the color scale internals to facilitate ooptional color scale order
reversal for both built-in divergent midpoint/offset color scales as
well as tabulated color scales.
Show difference between Revision 1.33 and 1.34

Filename: ColorFltkMenu.C
Revision 1.44johns 2020/12/24 04:21:51+37 -5
Revised color scale internals and the Color window GUI to implement
posterization of color scales down to a user-specified number of
individual color bands.
Show difference between Revision 1.43 and 1.44
Revision 1.43johns 2020/12/23 16:41:12+26 -15
Revised the color scale internals to facilitate ooptional color scale order
reversal for both built-in divergent midpoint/offset color scales as
well as tabulated color scales.
Show difference between Revision 1.42 and 1.43
Revision 1.42johns 2020/12/23 08:01:52+14 -7
Added a live color swatch box to the redesigned color menu.
Continued adjustment of widget sizes and placement.
Show difference between Revision 1.41 and 1.42
Revision 1.41johns 2020/12/21 15:22:52+1 -1
Shifted the L* 100 ligthness marker down 10 pixels to match Fl_Chart layout
slightly better.
Show difference between Revision 1.40 and 1.41
Revision 1.40johns 2020/12/21 15:18:16+7 -4
Improved color scale plot title to "CIELAB L* perceptual lightness"
which is more informative and technically correct.
Completed the remaining math for RGB to CIELAB color conversion.
Show difference between Revision 1.39 and 1.40
Revision 1.39johns 2020/12/21 07:40:29+228 -35
Significantly redesigned the Color window layout, resizing
the color definitions and color scale tabs to occupy the full
window, and migrating the entirety of the color definition browsers
into the color definitions tab. This change to the window layout
better separates controls that are relevant for color definition from
those used for color scale selection and editing. The larger space
made available within the color scale tab enables the addition of
a plot of color scale CIELAB L* luminance just below the color scale
test grating image.
Show difference between Revision 1.38 and 1.39
Revision 1.38johns 2020/12/21 05:12:51+110 -31
First steps in a major revision to the VMD color scale infrastructure.
The existing implementation has been extended with support for tabulated
color scales, new internal data structures and APIs to facilitate correct
GUI interaction for non-editable tabulated color scales.
Due to the significant increase in the total number of color scales
now available, the GUI has been revised to support forward
and reverse mapping of color scale menu names that include both scale
type categories and leaf node color scale names.
Redesigned the Color window layout to support a much larger color scale
test image, and added a high spatial frequency test grating image
based on the color scale test images developed by Peter Kovesi.
Show difference between Revision 1.37 and 1.38
Revision 1.37johns 2020/12/21 04:02:17+1 -1
Corrected width of color category name itembrowser widget.
Show difference between Revision 1.36 and 1.37
Revision 1.36johns 2020/12/19 07:12:19+92 -14
Major revision of the VMD color menu to optionally make use of the
FLTK-provided Fl_Color_Chooser instead of the classic VMD color sliders.
By default, when compiling with FLTK versions >= 1.1.10 VMD will use
Fl_Color_Chooser, and will revert to the classic sliders otherwise.
The window size is significantly increased, to match the width of the
VMD main window, and with additional height to provide an easy-to-use
widget size for the FLTK color selector and associated controls.
The FLTK color control supports floating point RGB, Hex, integer,
and HSV color value ranges, with mouse-based color component scrolling,
so all of the original features have been preserved while adding
significant convenience.
Show difference between Revision 1.35 and 1.36

Filename: ColorFltkMenu.h
Revision 1.25johns 2020/12/24 04:21:51+2 -0
Revised color scale internals and the Color window GUI to implement
posterization of color scales down to a user-specified number of
individual color bands.
Show difference between Revision 1.24 and 1.25
Revision 1.24johns 2020/12/23 16:41:12+2 -0
Revised the color scale internals to facilitate ooptional color scale order
reversal for both built-in divergent midpoint/offset color scales as
well as tabulated color scales.
Show difference between Revision 1.23 and 1.24
Revision 1.23johns 2020/12/23 08:01:52+2 -0
Added a live color swatch box to the redesigned color menu.
Continued adjustment of widget sizes and placement.
Show difference between Revision 1.22 and 1.23
Revision 1.22johns 2020/12/21 16:31:56+1 -1
Changed the conditional compilation tests for safe use of the
FLTK Fl_Color_Chooser class in place of the classic VMD color sliders.
Show difference between Revision 1.21 and 1.22
Revision 1.21johns 2020/12/21 07:40:29+2 -0
Significantly redesigned the Color window layout, resizing
the color definitions and color scale tabs to occupy the full
window, and migrating the entirety of the color definition browsers
into the color definitions tab. This change to the window layout
better separates controls that are relevant for color definition from
those used for color scale selection and editing. The larger space
made available within the color scale tab enables the addition of
a plot of color scale CIELAB L* luminance just below the color scale
test grating image.
Show difference between Revision 1.20 and 1.21
Revision 1.20johns 2020/12/21 05:12:51+21 -19
First steps in a major revision to the VMD color scale infrastructure.
The existing implementation has been extended with support for tabulated
color scales, new internal data structures and APIs to facilitate correct
GUI interaction for non-editable tabulated color scales.
Due to the significant increase in the total number of color scales
now available, the GUI has been revised to support forward
and reverse mapping of color scale menu names that include both scale
type categories and leaf node color scale names.
Redesigned the Color window layout to support a much larger color scale
test image, and added a high spatial frequency test grating image
based on the color scale test images developed by Peter Kovesi.
Show difference between Revision 1.19 and 1.20
Revision 1.19johns 2020/12/19 07:12:19+25 -2
Major revision of the VMD color menu to optionally make use of the
FLTK-provided Fl_Color_Chooser instead of the classic VMD color sliders.
By default, when compiling with FLTK versions >= 1.1.10 VMD will use
Fl_Color_Chooser, and will revert to the classic sliders otherwise.
The window size is significantly increased, to match the width of the
VMD main window, and with additional height to provide an easy-to-use
widget size for the FLTK color selector and associated controls.
The FLTK color control supports floating point RGB, Hex, integer,
and HSV color value ranges, with mouse-based color component scrolling,
so all of the original features have been preserved while adding
significant convenience.
Show difference between Revision 1.18 and 1.19

Filename: ColorInfo.C
Revision 1.38johns 2020/12/24 04:21:51+7 -3
Revised color scale internals and the Color window GUI to implement
posterization of color scales down to a user-specified number of
individual color bands.
Show difference between Revision 1.37 and 1.38
Revision 1.37johns 2020/12/23 16:41:12+7 -2
Revised the color scale internals to facilitate ooptional color scale order
reversal for both built-in divergent midpoint/offset color scales as
well as tabulated color scales.
Show difference between Revision 1.36 and 1.37

Filename: ColorScaleTables.h
Revision 1.2johns 2020/12/21 08:25:50+265 -3
Added an implementation of the "cividis" color scale which improves
upon the popular "viridis" color scale for viewers that have
color vision deficiencies.
Show difference between Revision 1.1 and 1.2
Revision 1.1johns 2020/12/21 04:19:03None
Freely licensed perceptually uniform color scales in tabulated form with
256 color entries per table. These are adapted from four of the popular
sequential color scales in Matplotlib, and a large selection of the
linear, cyclic, isoluminance, and rainbow color scales from the set of
CET perceptually uniform color scales published by Peter Kovesi.

Filename: Command.h

Filename: DispCmds.C
Revision 1.120johns 2020/10/31 06:47:50+3 -2
Updated the cone display command API to take const vertex buffer
parameters.
Show difference between Revision 1.119 and 1.120
Revision 1.119johns 2020/10/22 03:43:23+15 -15
Updated all of the volumetric data representations and associated data
structures, replacing the use of long types with ptrdiff_t and size_t to get
correct behavior on LLP64 platforms such as Windows x64 64-bit builds.
Show difference between Revision 1.118 and 1.119

Filename: DispCmds.h
Revision 1.119johns 2020/10/31 06:47:50+3 -2
Updated the cone display command API to take const vertex buffer
parameters.
Show difference between Revision 1.118 and 1.119

Filename: Displayable.h
Revision 1.91johns 2020/12/12 22:54:24+44 -1
Revised the low level VMDDisplayList clipping plane methods and
higher-level Displayable clipping plane methods to eliminate
Displayable methods from triggering _needUpdate scene regen/redraw
updates unless: the clipping plane is being changed; or
one of the the clipping plane plane properties is changed and the
active clipping plane mode is currently active (non-zero).
Show difference between Revision 1.90 and 1.91

Filename: DrawMolItemVolume.C
Revision 1.181johns 2020/10/22 03:43:23+14 -14
Updated all of the volumetric data representations and associated data
structures, replacing the use of long types with ptrdiff_t and size_t to get
correct behavior on LLP64 platforms such as Windows x64 64-bit builds.
Show difference between Revision 1.180 and 1.181

Filename: DrawMolecule.h
Revision 1.88johns 2020/10/28 15:09:56+4 -4
Added explicit type conversions from ptrdiff_t sizes to int to greatly
reduce MSVS compiler conversion warnings.
Show difference between Revision 1.87 and 1.88

Filename: FileRenderList.C
Revision 1.108johns 2020/11/17 20:39:43+3 -4
Eliminate direct calls to OptiXRenderer class, to limit the scope of
associated low-level OptiX header inclusion, which has particularly
detailed ordering and macro definition requirements for Windows builds.
Show difference between Revision 1.107 and 1.108

Filename: Fragment.h
Revision 1.21johns 2020/10/28 15:09:56+2 -2
Added explicit type conversions from ptrdiff_t sizes to int to greatly
reduce MSVS compiler conversion warnings.
Show difference between Revision 1.20 and 1.21

Filename: GaussianBlur.C
Revision 1.27johns 2020/10/29 03:16:18+6 -3
Eliminated non-portable variable sized stack allocated memory buffer.
Show difference between Revision 1.26 and 1.27

Filename: GraphicsFltkReps.h
Revision 1.141johns 2020/10/28 17:42:35+3 -3
Added explicit type conversions from ptrdiff_t sizes to int to greatly
reduce MSVS compiler conversion warnings.
Show difference between Revision 1.140 and 1.141

Filename: Inform.C
Revision 1.46johns 2020/10/22 03:40:41+19 -1
Added conditional compilation for _WIN64 (and any other LLP64 platforms)
to add support for size_t and ptrdiff_t Inform output, but avoid duplication
of long types on LP64 platforms (Unix/Linux) where ptrdiff_t and size_t are
defined as long types.
Show difference between Revision 1.45 and 1.46

Filename: Inform.h
Revision 1.34johns 2020/10/22 03:40:41+11 -1
Added conditional compilation for _WIN64 (and any other LLP64 platforms)
to add support for size_t and ptrdiff_t Inform output, but avoid duplication
of long types on LP64 platforms (Unix/Linux) where ptrdiff_t and size_t are
defined as long types.
Show difference between Revision 1.33 and 1.34

Filename: MeasureSymmetry.h
Revision 1.34johns 2020/10/28 17:42:35+4 -4
Added explicit type conversions from ptrdiff_t sizes to int to greatly
reduce MSVS compiler conversion warnings.
Show difference between Revision 1.33 and 1.34

Filename: MeasureVolInterior.C
Revision 1.17johns 2020/12/13 07:41:55+3 -3
Added conditional compilation tests for ARM64 MacOS X builds
checking for the compile-time macro ARCH_MACOSXARM64.
Show difference between Revision 1.16 and 1.17

Filename: MolFilePlugin.C
Revision 1.198johns 2020/10/22 03:43:23+9 -8
Updated all of the volumetric data representations and associated data
structures, replacing the use of long types with ptrdiff_t and size_t to get
correct behavior on LLP64 platforms such as Windows x64 64-bit builds.
Show difference between Revision 1.197 and 1.198

Filename: Molecule.h
Revision 1.67johns 2020/10/28 17:26:39+3 -3
Added explicit type conversions from ptrdiff_t sizes to int to greatly
reduce MSVS compiler conversion warnings.
Show difference between Revision 1.66 and 1.67

Filename: MoleculeGraphics.C
Revision 1.88johns 2020/11/06 07:19:59+46 -56
Changed implementation of spheretube color handling for inheritance
of bulk "draw color colorID" type coloring mode. The implementation
of colorID arrays needs rewriting so it will properly track updates
to color tables ex-post-facto, and that will also impact the
single-color color inheritance mode.
Show difference between Revision 1.87 and 1.88
Revision 1.87johns 2020/11/06 06:03:24+13 -7
Corrected handling of single-radius spheretube combinations
Show difference between Revision 1.86 and 1.87
Revision 1.86johns 2020/11/04 20:58:19+14 -4
Updated the "spheretubes" draw command to accept a list of colorIDs
rather than only fully-specified RGB colors. This makes it a more
directly usable replacement for existing sphere-at-a-time scripts
that follow a pattern of calling "draw color", then "draw sphere",
"draw cone", etc.
Show difference between Revision 1.85 and 1.86
Revision 1.85johns 2020/11/02 00:51:32+53 -3
Added support for the graphics "info" subcommands for spheretube primitives
and eliminated various debugging console messages.
Show difference between Revision 1.84 and 1.85
Revision 1.84johns 2020/11/01 21:34:30+19 -6
Near-complete implementation of "spheretube" drawing primitive.
Still needs to handle color-per-sphere mode in conjunction with
drawtubes being enabled, and command logging is as-yet unimplemented.
The new code does significantly more paraemter checking now.
Show difference between Revision 1.83 and 1.84
Revision 1.83johns 2020/11/01 19:53:37+55 -37
Renamed "tube" drawing primitive to "spheretube" and added new flags
and parameters to allow the use of per-sphere user-specified RGB colors,
flag control over tube drawing, and either constant radius or
radius-per-sphere drawing.
Show difference between Revision 1.82 and 1.83
Revision 1.82johns 2020/11/01 05:09:51+2 -2
Renamed MoleculeGraphics::find_sizes() to MoleculeGraphics::find_bounds()
which is a more accurate and meaningful method name.
Show difference between Revision 1.81 and 1.82
Revision 1.81johns 2020/11/01 05:06:45+12 -4
Implemented MoleculeGraphics::find_sizes() for the new "tube" command.
Show difference between Revision 1.80 and 1.81
Revision 1.80johns 2020/10/31 07:11:09+93 -1
Revised MoleculeGraphics to allow shapes to have an "extradata" field to
permit the implementation new graphics "draw" commands that accept
arbitrarily large vertex arrays, thereby making most efficient use
of the underlying array-oriented DispCmd primitives, which minimizes
the number of VMDDisplayList linked list nodes, and similarly reduces
the total count of API calls all of the way through the rendering system
to the lowest level rendering layers. The "extradata" field enables
the most efficient storage and management of complex geometry, completely
eliminating internal fragmentation of memory that normally occurs with
the original primitive-at-a-time drawing approach.
Added tracking of the active graphics drawing colorID so that batched
geometry DispCmd calls that require rgb floating point buffers can
be used more easily.
Show difference between Revision 1.79 and 1.80

Filename: MoleculeGraphics.h
Revision 1.57johns 2020/11/06 07:19:59+2 -2
Changed implementation of spheretube color handling for inheritance
of bulk "draw color colorID" type coloring mode. The implementation
of colorID arrays needs rewriting so it will properly track updates
to color tables ex-post-facto, and that will also impact the
single-color color inheritance mode.
Show difference between Revision 1.56 and 1.57
Revision 1.56johns 2020/11/04 20:58:19+3 -2
Updated the "spheretubes" draw command to accept a list of colorIDs
rather than only fully-specified RGB colors. This makes it a more
directly usable replacement for existing sphere-at-a-time scripts
that follow a pattern of calling "draw color", then "draw sphere",
"draw cone", etc.
Show difference between Revision 1.55 and 1.56
Revision 1.55johns 2020/11/02 00:51:32+18 -14
Added support for the graphics "info" subcommands for spheretube primitives
and eliminated various debugging console messages.
Show difference between Revision 1.54 and 1.55
Revision 1.54johns 2020/11/01 19:53:37+6 -4
Renamed "tube" drawing primitive to "spheretube" and added new flags
and parameters to allow the use of per-sphere user-specified RGB colors,
flag control over tube drawing, and either constant radius or
radius-per-sphere drawing.
Show difference between Revision 1.53 and 1.54
Revision 1.53johns 2020/11/01 05:09:51+4 -4
Renamed MoleculeGraphics::find_sizes() to MoleculeGraphics::find_bounds()
which is a more accurate and meaningful method name.
Show difference between Revision 1.52 and 1.53
Revision 1.52johns 2020/10/31 07:11:09+18 -6
Revised MoleculeGraphics to allow shapes to have an "extradata" field to
permit the implementation new graphics "draw" commands that accept
arbitrarily large vertex arrays, thereby making most efficient use
of the underlying array-oriented DispCmd primitives, which minimizes
the number of VMDDisplayList linked list nodes, and similarly reduces
the total count of API calls all of the way through the rendering system
to the lowest level rendering layers. The "extradata" field enables
the most efficient storage and management of complex geometry, completely
eliminating internal fragmentation of memory that normally occurs with
the original primitive-at-a-time drawing approach.
Added tracking of the active graphics drawing colorID so that batched
geometry DispCmd calls that require rgb floating point buffers can
be used more easily.
Show difference between Revision 1.51 and 1.52
Revision 1.51johns 2020/10/30 17:01:05+5 -3
Updated comments about the behavior of MoleculeGraphics::info_id()
Show difference between Revision 1.50 and 1.51
Revision 1.50johns 2020/10/28 17:42:35+2 -2
Added explicit type conversions from ptrdiff_t sizes to int to greatly
reduce MSVS compiler conversion warnings.
Show difference between Revision 1.49 and 1.50

Filename: MoleculeList.h
Revision 1.72johns 2020/10/28 17:26:39+2 -2
Added explicit type conversions from ptrdiff_t sizes to int to greatly
reduce MSVS compiler conversion warnings.
Show difference between Revision 1.71 and 1.72

Filename: OSPRay2DisplayDevice.C
Revision 1.3johns 2020/12/09 06:20:18+63 -1
Added placeholder clipping group implementation.
Show difference between Revision 1.2 and 1.3

Filename: OSPRay2DisplayDevice.h
Revision 1.3johns 2020/12/09 06:20:18+23 -6
Added placeholder clipping group implementation.
Show difference between Revision 1.2 and 1.3

Filename: OSPRay2Renderer.C
Revision 1.29johns 2020/11/16 07:40:51+5 -1
Added include of windows.h for interactive RT compilation on Windows platforms.
Show difference between Revision 1.28 and 1.29

Filename: OSPRayDisplayDevice.C
Revision 1.17johns 2020/12/09 06:20:18+64 -1
Added placeholder clipping group implementation.
Show difference between Revision 1.16 and 1.17

Filename: OSPRayDisplayDevice.h
Revision 1.18johns 2020/12/09 06:20:18+22 -5
Added placeholder clipping group implementation.
Show difference between Revision 1.17 and 1.18

Filename: OSPRayRenderer.C
Revision 1.88johns 2020/11/16 07:20:18+6 -2
Corrected added missing include of windows.h when compiling OSPRayRenderer
on windows platforms.
Show difference between Revision 1.87 and 1.88
Revision 1.87johns 2020/11/16 05:42:12+2 -2
use VMD_PI rather than M_PI to please MSVC.
Show difference between Revision 1.86 and 1.87

Filename: OptiXDisplayDevice.C
Revision 1.84johns 2020/11/17 21:03:47+7 -3
Changed order of header inclusion to ensure that low-level OptiX
headers are included prior to system-provided headers, as the OptiX
headers incorporate special handling, e.g., of min/max macros and
related functions on the Windows platform, which is very sensitive to
header ordering.
Show difference between Revision 1.83 and 1.84
Revision 1.83johns 2020/11/17 20:34:02+8 -1
Added a wrapper for OptiXRenderer::device_count() to limit overly
broad inclusion of low level OptiX API headers by classes that needed to
make calls into OptiXRenderer. On the Windows platform in particular, there
are some thorny header file ordering and macro definition issues that
must be satisfied, and while that is easy to do in OptiXRenderer and
OptiXDisplayDevice, this rapidly gets out of hand if other classes
start including those headers as well.
Show difference between Revision 1.82 and 1.83
Revision 1.82johns 2020/11/04 17:29:17+59 -1
Changed the intermediary OptiXDisplayDevice class to accumulate
individual spheres from FileRenderer::sphere() calls into local
buffers the same way that it already did for cylinders and particular
triangle geometry. When the primitive count exceeds a threshold,
the spheres are sent to OptiXRenderer as a sphere_array_color()
primitive, which greatly reduces overheads. By overriding the
FileRenderer::sphere() method, we eliminate sphere triangulation for
scenes that include handfuls of user-drawn spheres, and for spheres
drawn by plugins or the like, leading to higher quality and faster rendering.
Show difference between Revision 1.81 and 1.82

Filename: OptiXDisplayDevice.h
Revision 1.33johns 2020/11/17 20:34:02+5 -1
Added a wrapper for OptiXRenderer::device_count() to limit overly
broad inclusion of low level OptiX API headers by classes that needed to
make calls into OptiXRenderer. On the Windows platform in particular, there
are some thorny header file ordering and macro definition issues that
must be satisfied, and while that is easy to do in OptiXRenderer and
OptiXDisplayDevice, this rapidly gets out of hand if other classes
start including those headers as well.
Show difference between Revision 1.32 and 1.33
Revision 1.32johns 2020/11/04 17:29:17+27 -2
Changed the intermediary OptiXDisplayDevice class to accumulate
individual spheres from FileRenderer::sphere() calls into local
buffers the same way that it already did for cylinders and particular
triangle geometry. When the primitive count exceeds a threshold,
the spheres are sent to OptiXRenderer as a sphere_array_color()
primitive, which greatly reduces overheads. By overriding the
FileRenderer::sphere() method, we eliminate sphere triangulation for
scenes that include handfuls of user-drawn spheres, and for spheres
drawn by plugins or the like, leading to higher quality and faster rendering.
Show difference between Revision 1.31 and 1.32

Filename: OptiXRenderer.C
Revision 1.378johns 2020/12/13 05:40:45+12 -9
Updated OptiX renderer to add support for ray statistics reporting for
interactive display runs.
Show difference between Revision 1.377 and 1.378
Revision 1.377johns 2020/12/12 21:37:40+8 -2
Increased the default threshold for forcing VMD to perform
OptiX renderings in multiple accumulation buffer passes by a factor
of 4x, and permit user override of the default threshold and behavior.
The new code also uses the total number of primary aa samples
and AO shadow feeler rays rather than only the number of primary ray
aa samples, to provide better performance scaling on RTX
hardware-accelerated GPUs going forward. Increasing the number of
rays per launch significantly improves VMD's utilization of the RT cores on
the latest hardware. With too small of the ray batch size per pass, VMD
can't exploit the full hardware performance on the latest RTX cards.
Show difference between Revision 1.376 and 1.377
Revision 1.376johns 2020/12/12 18:03:43+14 -12
Changed the OptiX renderer's ray statistics buffer allocation code to specify
RT_BUFFER_OUTPUT instead of RT_BUFFER_INPUT_OUTPUT | RT_BUFFER_GPU_LOCAL,
since we never write to these buffers on the host side.
Show difference between Revision 1.375 and 1.376
Revision 1.375johns 2020/11/17 21:03:47+7 -3
Changed order of header inclusion to ensure that low-level OptiX
headers are included prior to system-provided headers, as the OptiX
headers incorporate special handling, e.g., of min/max macros and
related functions on the Windows platform, which is very sensitive to
header ordering.
Show difference between Revision 1.374 and 1.375
Revision 1.374johns 2020/11/17 20:40:58+7 -7
Use VMD_PI macro to simplify Windows builds.
Show difference between Revision 1.373 and 1.374
Revision 1.373johns 2020/11/16 07:40:51+5 -1
Added include of windows.h for interactive RT compilation on Windows platforms.
Show difference between Revision 1.372 and 1.373
Revision 1.372johns 2020/11/06 04:16:41+4 -1
Explicitly include CUDA runtime header with OptiX versions greater than 5.2,
since differences in CUDA runtime headers among versions lead to
cudaGetDeviceCount() being unprototyped in some cases but not others.
This ensures it will always be properly prototyped.
Show difference between Revision 1.371 and 1.372

Filename: OptiXRenderer.h
Revision 1.126johns 2020/11/18 07:07:47+8 -3
Added conditional definition of NOMINMAX macro when compiling the
OptiXRenderer code on Windows platform, as required by OptiX-internal headers.
Show difference between Revision 1.125 and 1.126

Filename: OptiXShaders.cu
Revision 1.175johns 2020/12/12 17:59:04+22 -22
Implemented slight optimizations for OptiX ray statistics gathering among
the various primary ray generation and shading kernels.
Show difference between Revision 1.174 and 1.175

Filename: Orbital.C
Revision 1.158johns 2020/10/28 07:51:25+7 -2
Updates for the SSE molecular orbital kernels to please current versions
of MSVS, which fail to define SSE macros at compile time, and that
no longer support some of the oldest MMX intrinsics and _m64 types
when compiling in 64-bit mode.
Show difference between Revision 1.157 and 1.158
Revision 1.157johns 2020/10/28 03:27:43+3 -1
Protect CPU capability data structure w/ conditional compilation tests
for runtime CPU dispatch.
Show difference between Revision 1.156 and 1.157
Revision 1.156johns 2020/10/27 04:05:35+30 -29
Greatly simplified conditional compilation macros, include files,
and ifdefs for runtime CPU dispatch and statically-launched SIMD kernels.
Show difference between Revision 1.155 and 1.156
Revision 1.155johns 2020/10/26 19:06:37+10 -509
Removed the previous static-launch code paths for AVX-512F and AVX-512ER
molecular orbital kernels.
Show difference between Revision 1.154 and 1.155

Filename: Orbital_AVX512.C
Revision 1.4johns 2020/10/27 04:18:28+6 -5
Simplified conditional compilation macros for runtime CPU dispatch
kernel source files.
Show difference between Revision 1.3 and 1.4

Filename: Orbital_AVX512ER.C
Revision 1.3johns 2020/10/27 04:18:28+6 -5
Simplified conditional compilation macros for runtime CPU dispatch
kernel source files.
Show difference between Revision 1.2 and 1.3

Filename: P_UIVR.h
Revision 1.75johns 2020/10/28 17:42:35+2 -2
Added explicit type conversions from ptrdiff_t sizes to int to greatly
reduce MSVS compiler conversion warnings.
Show difference between Revision 1.74 and 1.75

Filename: PickList.h
Revision 1.38johns 2020/10/28 17:42:35+2 -2
Added explicit type conversions from ptrdiff_t sizes to int to greatly
reduce MSVS compiler conversion warnings.
Show difference between Revision 1.37 and 1.38

Filename: PythonTextInterp.C
Revision 1.76johns 2020/10/21 20:33:20+15 -2
Rewrote command line argument passing for Python 3.x, since it requires
explicit translation to wide characters. The new code processes
incoming argc/argv by converting each argument to null terminated
wchar_t strings using Py_DecodeLocale() and passing them into PySys_SetArgv().
Also added placeholder call to Py_SetProgramName(), however it is disabled
since it doesn't appear to be particularly beneficial or needed at this time.
Show difference between Revision 1.75 and 1.76

Filename: QuickSurf.C
Revision 1.131johns 2020/12/13 07:41:55+2 -2
Added conditional compilation tests for ARM64 MacOS X builds
checking for the compile-time macro ARCH_MACOSXARM64.
Show difference between Revision 1.130 and 1.131
Revision 1.130johns 2020/10/29 06:31:57+9 -1
Protect x86-only runtime dispatch paths with appropriate
compile-time ifdefs
Show difference between Revision 1.129 and 1.130
Revision 1.129johns 2020/10/28 14:17:17+2 -2
Use __align() variable declaration attribute for portability to MSVS
Show difference between Revision 1.128 and 1.129
Revision 1.128johns 2020/10/28 14:12:47+10 -232
Migrated the AVX-512 specific loops to a new runtime dispatch version of
the QuickSurf kernels and removed them from the statically-launched
code path.
Show difference between Revision 1.127 and 1.128
Revision 1.127johns 2020/10/26 19:14:30+5 -270
Eliminated statically-launched QuickSurf AVX2 kernels in favor of
runtime CPU dispatch.
Show difference between Revision 1.126 and 1.127
Revision 1.126johns 2020/10/22 06:13:10+21 -21
Replaced the use of long types in CPU QuickSurf algorithm with ptrdiff_t
and size_t for x64 64-bit Windows builds.
Updated SIMD routines conditional compilation macros and tests
for use with MSVS 2017.
Show difference between Revision 1.125 and 1.126

Filename: QuickSurf_AVX2.C
Revision 1.6johns 2020/10/22 06:13:10+6 -6
Replaced the use of long types in CPU QuickSurf algorithm with ptrdiff_t
and size_t for x64 64-bit Windows builds.
Updated SIMD routines conditional compilation macros and tests
for use with MSVS 2017.
Show difference between Revision 1.5 and 1.6

Filename: ResizeArray.h
Revision 1.57johns 2020/10/22 03:42:04+24 -23
Replaced the use of long types with ptrdiff_t and size_t to get
correct behavior on LLP64 platforms such as Windows x64 64-bit builds.
Show difference between Revision 1.56 and 1.57

Filename: Scene.C
Revision 1.97johns 2020/12/24 04:21:51+17 -6
Revised color scale internals and the Color window GUI to implement
posterization of color scales down to a user-specified number of
individual color bands.
Show difference between Revision 1.96 and 1.97
Revision 1.96johns 2020/12/23 16:41:12+7 -3
Revised the color scale internals to facilitate ooptional color scale order
reversal for both built-in divergent midpoint/offset color scales as
well as tabulated color scales.
Show difference between Revision 1.95 and 1.96
Revision 1.95johns 2020/12/21 08:25:50+5 -2
Added an implementation of the "cividis" color scale which improves
upon the popular "viridis" color scale for viewers that have
color vision deficiencies.
Show difference between Revision 1.94 and 1.95
Revision 1.94johns 2020/12/21 05:12:51+191 -11
First steps in a major revision to the VMD color scale infrastructure.
The existing implementation has been extended with support for tabulated
color scales, new internal data structures and APIs to facilitate correct
GUI interaction for non-editable tabulated color scales.
Due to the significant increase in the total number of color scales
now available, the GUI has been revised to support forward
and reverse mapping of color scale menu names that include both scale
type categories and leaf node color scale names.
Redesigned the Color window layout to support a much larger color scale
test image, and added a high spatial frequency test grating image
based on the color scale test images developed by Peter Kovesi.
Show difference between Revision 1.93 and 1.94
Revision 1.93johns 2020/12/21 04:10:00+4 -4
Changed default colorscale "Offset" from 0.10 to 0.06 after comparisons
with high spatial frequency test grating images for both original
parameter and the new value. The built-in VMD divergent color scales
while still much better than the old Matlab "rainbow" scale,
leave much to be desired, both in terms of their ability to show
high frequency fine spatial details, luminance linearity, and other factors.
Show difference between Revision 1.92 and 1.93

Filename: Scene.h
Revision 1.69johns 2020/12/24 04:21:51+7 -3
Revised color scale internals and the Color window GUI to implement
posterization of color scales down to a user-specified number of
individual color bands.
Show difference between Revision 1.68 and 1.69
Revision 1.68johns 2020/12/23 16:41:12+7 -3
Revised the color scale internals to facilitate ooptional color scale order
reversal for both built-in divergent midpoint/offset color scales as
well as tabulated color scales.
Show difference between Revision 1.67 and 1.68
Revision 1.67johns 2020/12/21 05:12:51+37 -26
First steps in a major revision to the VMD color scale infrastructure.
The existing implementation has been extended with support for tabulated
color scales, new internal data structures and APIs to facilitate correct
GUI interaction for non-editable tabulated color scales.
Due to the significant increase in the total number of color scales
now available, the GUI has been revised to support forward
and reverse mapping of color scale menu names that include both scale
type categories and leaf node color scale names.
Redesigned the Color window layout to support a much larger color scale
test image, and added a high spatial frequency test grating image
based on the color scale test images developed by Peter Kovesi.
Show difference between Revision 1.66 and 1.67
Revision 1.66johns 2020/10/28 17:26:39+2 -2
Added explicit type conversions from ptrdiff_t sizes to int to greatly
reduce MSVS compiler conversion warnings.
Show difference between Revision 1.65 and 1.66

Filename: SmallRing.h
Revision 1.12johns 2020/10/28 15:09:57+3 -3
Added explicit type conversions from ptrdiff_t sizes to int to greatly
reduce MSVS compiler conversion warnings.
Show difference between Revision 1.11 and 1.12

Filename: SmallRingLinkages.h
Revision 1.10johns 2020/10/28 15:09:57+4 -4
Added explicit type conversions from ptrdiff_t sizes to int to greatly
reduce MSVS compiler conversion warnings.
Show difference between Revision 1.9 and 1.10

Filename: Spaceball.C
Revision 1.64johns 2020/12/13 07:41:55+3 -1
Added conditional compilation tests for ARM64 MacOS X builds
checking for the compile-time macro ARCH_MACOSXARM64.
Show difference between Revision 1.63 and 1.64

Filename: Stride.C
Revision 1.48johns 2020/12/13 07:41:55+2 -2
Added conditional compilation tests for ARM64 MacOS X builds
checking for the compile-time macro ARCH_MACOSXARM64.
Show difference between Revision 1.47 and 1.48
Revision 1.47johns 2020/11/02 07:43:20+2 -1
Added additional DSSP src URLs
Show difference between Revision 1.46 and 1.47
Revision 1.46johns 2020/11/02 06:04:44+16 -1
Added updated STRIDE, DSSP/xDSSP/HSSP URLs
Show difference between Revision 1.45 and 1.46

Filename: TclCommands.h
Revision 1.59johns 2020/11/04 20:57:00+4 -1
Added tcl_get_intarray() to pull in a tcl list as a 1-D flat array of ints
Show difference between Revision 1.58 and 1.59
Revision 1.58johns 2020/10/31 06:49:30+7 -1
Added new tcl_get_array() and tcl_get_vecarray() commands to ease
parsing of large vertex arrays and arrays of per-primitive scalars
for use in implementing new graphics primitives.
Show difference between Revision 1.57 and 1.58

Filename: TclGraphics.C
Revision 1.60johns 2020/11/30 07:09:12+6 -7
Corrected behavior of 'radius' flag per Barry's testing.
Show difference between Revision 1.59 and 1.60
Revision 1.59johns 2020/11/06 07:20:00+10 -8
Changed implementation of spheretube color handling for inheritance
of bulk "draw color colorID" type coloring mode. The implementation
of colorID arrays needs rewriting so it will properly track updates
to color tables ex-post-facto, and that will also impact the
single-color color inheritance mode.
Show difference between Revision 1.58 and 1.59
Revision 1.58johns 2020/11/06 06:03:24+2 -1
Corrected handling of single-radius spheretube combinations
Show difference between Revision 1.57 and 1.58
Revision 1.57johns 2020/11/04 20:58:19+46 -3
Updated the "spheretubes" draw command to accept a list of colorIDs
rather than only fully-specified RGB colors. This makes it a more
directly usable replacement for existing sphere-at-a-time scripts
that follow a pattern of calling "draw color", then "draw sphere",
"draw cone", etc.
Show difference between Revision 1.56 and 1.57
Revision 1.56johns 2020/11/02 00:51:32+3 -1
Added support for the graphics "info" subcommands for spheretube primitives
and eliminated various debugging console messages.
Show difference between Revision 1.55 and 1.56
Revision 1.55johns 2020/11/01 21:34:31+28 -3
Near-complete implementation of "spheretube" drawing primitive.
Still needs to handle color-per-sphere mode in conjunction with
drawtubes being enabled, and command logging is as-yet unimplemented.
The new code does significantly more paraemter checking now.
Show difference between Revision 1.54 and 1.55
Revision 1.54johns 2020/11/01 20:10:20+5 -5
Updated graphics command to "spheretube" due to its new capabilities
Show difference between Revision 1.53 and 1.54
Revision 1.53johns 2020/11/01 20:05:19+11 -16
Improved spheretube parameter checking
Show difference between Revision 1.52 and 1.53
Revision 1.52johns 2020/11/01 19:53:38+104 -5
Renamed "tube" drawing primitive to "spheretube" and added new flags
and parameters to allow the use of per-sphere user-specified RGB colors,
flag control over tube drawing, and either constant radius or
radius-per-sphere drawing.
Show difference between Revision 1.51 and 1.52
Revision 1.51johns 2020/10/31 07:13:02+34 -2
Added support for new "tube" graphics drawing primitive that renders a
series of spheres connected by cones, with arbitrary numbers of vertices,
per-vertex radii, and user specified polygonal representation resolution.
Still an early prototypical implementation.
Show difference between Revision 1.50 and 1.51

Filename: TclVec.C
Revision 1.46johns 2020/11/04 20:57:00+26 -1
Added tcl_get_intarray() to pull in a tcl list as a 1-D flat array of ints
Show difference between Revision 1.45 and 1.46
Revision 1.45johns 2020/10/31 06:49:30+56 -5
Added new tcl_get_array() and tcl_get_vecarray() commands to ease
parsing of large vertex arrays and arrays of per-primitive scalars
for use in implementing new graphics primitives.
Show difference between Revision 1.44 and 1.45

Filename: Timestep.C
Revision 1.74johns 2020/10/21 05:43:54+6 -8
Updated the unsigned integer pointer type conversion macro for 64-bit
Windows builds.
Show difference between Revision 1.73 and 1.74

Filename: VMDApp.C
Revision 1.580johns 2020/12/30 07:17:50+7 -2
Added runtime startup message to clearly indicate builds that have
runtime CPU dispatch enabled vs. those that do not.
Show difference between Revision 1.579 and 1.580
Revision 1.579johns 2020/12/24 04:21:51+8 -6
Revised color scale internals and the Color window GUI to implement
posterization of color scales down to a user-specified number of
individual color bands.
Show difference between Revision 1.578 and 1.579
Revision 1.578johns 2020/12/23 16:41:13+6 -6
Revised the color scale internals to facilitate ooptional color scale order
reversal for both built-in divergent midpoint/offset color scales as
well as tabulated color scales.
Show difference between Revision 1.577 and 1.578
Revision 1.577johns 2020/12/21 05:12:51+5 -1
First steps in a major revision to the VMD color scale infrastructure.
The existing implementation has been extended with support for tabulated
color scales, new internal data structures and APIs to facilitate correct
GUI interaction for non-editable tabulated color scales.
Due to the significant increase in the total number of color scales
now available, the GUI has been revised to support forward
and reverse mapping of color scale menu names that include both scale
type categories and leaf node color scale names.
Redesigned the Color window layout to support a much larger color scale
test image, and added a high spatial frequency test grating image
based on the color scale test images developed by Peter Kovesi.
Show difference between Revision 1.576 and 1.577
Revision 1.576johns 2020/12/13 07:41:55+3 -3
Added conditional compilation tests for ARM64 MacOS X builds
checking for the compile-time macro ARCH_MACOSXARM64.
Show difference between Revision 1.575 and 1.576
Revision 1.575johns 2020/11/17 19:45:50+1 -4
Eliminated inclusion of OptiXRenderer definition since hardware
enumeration is now done as part of FileRenderList and support for
VCA rendering clusters has been removed previously.
Show difference between Revision 1.574 and 1.575
Revision 1.574johns 2020/10/27 21:51:42+6 -6
Moved CPU hypervisor detection and reporting into x86 block since we don't
yet have the equivalent capability on ARM hardware.
Show difference between Revision 1.573 and 1.574
Revision 1.573johns 2020/10/27 21:35:18+10 -1
Added runtime dispatch reporting of ARM64 SVE hardware vector lengths
for 32-bit and 64-bit types.
Show difference between Revision 1.572 and 1.573
Revision 1.572johns 2020/10/27 15:30:49+28 -3
Updated CPU feature detection reporting code for ARM64 platforms, and pulled
in latest updates from Tachyon.
Show difference between Revision 1.571 and 1.572
Revision 1.571johns 2020/10/27 07:55:51+11 -1
Added first ARM64 CPU feature detection console diagnostics to indicate
the availability of Neon and SVE vector instructions, among others.
Show difference between Revision 1.570 and 1.571

Filename: VMDApp.h
Revision 1.257johns 2020/12/24 04:21:51+5 -3
Revised color scale internals and the Color window GUI to implement
posterization of color scales down to a user-specified number of
individual color bands.
Show difference between Revision 1.256 and 1.257
Revision 1.256johns 2020/12/23 16:41:13+11 -8
Revised the color scale internals to facilitate ooptional color scale order
reversal for both built-in divergent midpoint/offset color scales as
well as tabulated color scales.
Show difference between Revision 1.255 and 1.256
Revision 1.255johns 2020/12/21 05:12:51+2 -1
First steps in a major revision to the VMD color scale infrastructure.
The existing implementation has been extended with support for tabulated
color scales, new internal data structures and APIs to facilitate correct
GUI interaction for non-editable tabulated color scales.
Due to the significant increase in the total number of color scales
now available, the GUI has been revised to support forward
and reverse mapping of color scale menu names that include both scale
type categories and leaf node color scale names.
Redesigned the Color window layout to support a much larger color scale
test image, and added a high spatial frequency test grating image
based on the color scale test images developed by Peter Kovesi.
Show difference between Revision 1.254 and 1.255

Filename: VMDDisplayList.C
Revision 1.42johns 2020/12/12 22:54:24+6 -1
Revised the low level VMDDisplayList clipping plane methods and
higher-level Displayable clipping plane methods to eliminate
Displayable methods from triggering _needUpdate scene regen/redraw
updates unless: the clipping plane is being changed; or
one of the the clipping plane plane properties is changed and the
active clipping plane mode is currently active (non-zero).
Show difference between Revision 1.41 and 1.42

Filename: VMDDisplayList.h
Revision 1.46johns 2020/12/12 22:54:24+3 -2
Revised the low level VMDDisplayList clipping plane methods and
higher-level Displayable clipping plane methods to eliminate
Displayable methods from triggering _needUpdate scene regen/redraw
updates unless: the clipping plane is being changed; or
one of the the clipping plane plane properties is changed and the
active clipping plane mode is currently active (non-zero).
Show difference between Revision 1.45 and 1.46

Filename: VolumeTexture.C
Revision 1.29johns 2020/10/22 03:43:24+27 -27
Updated all of the volumetric data representations and associated data
structures, replacing the use of long types with ptrdiff_t and size_t to get
correct behavior on LLP64 platforms such as Windows x64 64-bit builds.
Show difference between Revision 1.28 and 1.29

Filename: VolumeTexture.h
Revision 1.10johns 2020/10/22 03:43:24+5 -3
Updated all of the volumetric data representations and associated data
structures, replacing the use of long types with ptrdiff_t and size_t to get
correct behavior on LLP64 platforms such as Windows x64 64-bit builds.
Show difference between Revision 1.9 and 1.10

Filename: VolumetricData.C
Revision 1.70johns 2020/10/22 03:43:24+63 -63
Updated all of the volumetric data representations and associated data
structures, replacing the use of long types with ptrdiff_t and size_t to get
correct behavior on LLP64 platforms such as Windows x64 64-bit builds.
Show difference between Revision 1.69 and 1.70

Filename: VolumetricData.h
Revision 1.57johns 2020/10/22 03:43:24+12 -10
Updated all of the volumetric data representations and associated data
structures, replacing the use of long types with ptrdiff_t and size_t to get
correct behavior on LLP64 platforms such as Windows x64 64-bit builds.
Show difference between Revision 1.56 and 1.57

Filename: WKFThreads.C
Revision 1.34johns 2021/01/05 16:00:44+3 -2
Added another cpuid project reference
Show difference between Revision 1.33 and 1.34
Revision 1.33johns 2020/12/27 08:18:18+5 -2
Added conditional compilation check for CPU info bailout.
Show difference between Revision 1.32 and 1.33
Revision 1.32johns 2020/11/02 07:44:44+7 -2
Added notes about AVX/AVX-512 clock rate reductions and high vector
registers causing false dependencies except when specifically cleared,
e.g., by calls to _mm256_zeroupper().
Show difference between Revision 1.31 and 1.32
Revision 1.31johns 2020/11/02 06:15:11+5 -2
Synced up cpuid() refs from Tachyon
Show difference between Revision 1.30 and 1.31
Revision 1.30johns 2020/10/28 14:44:31+5 -2
Pulled in Tachyon update to correct detection of FMA3 via x86 CPUID
instruction tests.
Show difference between Revision 1.29 and 1.30
Revision 1.29johns 2020/10/27 15:30:49+16 -3
Updated CPU feature detection reporting code for ARM64 platforms, and pulled
in latest updates from Tachyon.
Show difference between Revision 1.28 and 1.29
Revision 1.28johns 2020/10/27 07:53:18+6 -5
Pulled in corrections for ARM64 CPU feature detection from Tachyon.
Show difference between Revision 1.27 and 1.28
Revision 1.27johns 2020/10/27 07:12:18+21 -2
Added initial platform- and OS-specific conditional compilation macros
for runtime CPU feature detection on ARM64 hardware targets.
The initial ARM64 implementation makes use of the Linux getauxval() API.
Show difference between Revision 1.26 and 1.27
Revision 1.26johns 2020/10/22 04:52:38+9 -5
Pulled in CPU feature detection updates from Tachyon.
Show difference between Revision 1.25 and 1.26

Filename: WKFThreads.h
Revision 1.19johns 2020/10/27 15:30:49+16 -12
Updated CPU feature detection reporting code for ARM64 platforms, and pulled
in latest updates from Tachyon.
Show difference between Revision 1.18 and 1.19
Revision 1.18johns 2020/10/27 07:12:18+30 -16
Added initial platform- and OS-specific conditional compilation macros
for runtime CPU feature detection on ARM64 hardware targets.
The initial ARM64 implementation makes use of the Linux getauxval() API.
Show difference between Revision 1.17 and 1.18

Filename: cmd_color.C
Revision 1.43johns 2020/12/24 04:21:51+14 -4
Revised color scale internals and the Color window GUI to implement
posterization of color scales down to a user-specified number of
individual color bands.
Show difference between Revision 1.42 and 1.43
Revision 1.42johns 2020/12/23 16:41:13+5 -3
Revised the color scale internals to facilitate ooptional color scale order
reversal for both built-in divergent midpoint/offset color scales as
well as tabulated color scales.
Show difference between Revision 1.41 and 1.42

Filename: colvar.C
Revision 1.29johns 2020/12/21 20:48:04+6 -1
Pulled in latest colvars module from the git master.
Show difference between Revision 1.28 and 1.29
Revision 1.28johns 2020/11/01 06:55:40+30 -10
Updated the collective variables module to the latest git version, which
also bears the tag "vmd-1.9.4a49".
Show difference between Revision 1.27 and 1.28

Filename: colvar.h
Revision 1.18johns 2020/12/21 20:48:04+3 -0
Pulled in latest colvars module from the git master.
Show difference between Revision 1.17 and 1.18
Revision 1.17johns 2020/11/01 06:55:40+26 -0
Updated the collective variables module to the latest git version, which
also bears the tag "vmd-1.9.4a49".
Show difference between Revision 1.16 and 1.17

Filename: colvar_arithmeticpath.h
Revision 1.2johns 2020/11/01 06:55:40+13 -1
Updated the collective variables module to the latest git version, which
also bears the tag "vmd-1.9.4a49".
Show difference between Revision 1.1 and 1.2

Filename: colvaratoms.C
Revision 1.23johns 2020/12/21 20:48:04+2 -6
Pulled in latest colvars module from the git master.
Show difference between Revision 1.22 and 1.23
Revision 1.22johns 2020/11/01 06:55:40+3 -0
Updated the collective variables module to the latest git version, which
also bears the tag "vmd-1.9.4a49".
Show difference between Revision 1.21 and 1.22

Filename: colvarbias.C
Revision 1.19johns 2020/11/01 06:55:40+11 -0
Updated the collective variables module to the latest git version, which
also bears the tag "vmd-1.9.4a49".
Show difference between Revision 1.18 and 1.19

Filename: colvarbias.h
Revision 1.15johns 2020/11/01 06:55:40+4 -0
Updated the collective variables module to the latest git version, which
also bears the tag "vmd-1.9.4a49".
Show difference between Revision 1.14 and 1.15

Filename: colvarbias_abf.C
Revision 1.22johns 2020/11/01 06:55:40+22 -22
Updated the collective variables module to the latest git version, which
also bears the tag "vmd-1.9.4a49".
Show difference between Revision 1.21 and 1.22

Filename: colvarbias_abf.h
Revision 1.10johns 2020/11/01 06:55:40+6 -4
Updated the collective variables module to the latest git version, which
also bears the tag "vmd-1.9.4a49".
Show difference between Revision 1.9 and 1.10

Filename: colvarbias_histogram.C
Revision 1.12johns 2020/11/01 06:55:40+3 -3
Updated the collective variables module to the latest git version, which
also bears the tag "vmd-1.9.4a49".
Show difference between Revision 1.11 and 1.12

Filename: colvarbias_histogram.h
Revision 1.7johns 2020/11/01 06:55:40+0 -1
Updated the collective variables module to the latest git version, which
also bears the tag "vmd-1.9.4a49".
Show difference between Revision 1.6 and 1.7

Filename: colvarbias_meta.C
Revision 1.19johns 2020/11/01 06:55:40+7 -5
Updated the collective variables module to the latest git version, which
also bears the tag "vmd-1.9.4a49".
Show difference between Revision 1.18 and 1.19

Filename: colvarcomp.C
Revision 1.18johns 2020/11/01 06:55:40+2 -2
Updated the collective variables module to the latest git version, which
also bears the tag "vmd-1.9.4a49".
Show difference between Revision 1.17 and 1.18

Filename: colvarcomp.h
Revision 1.16johns 2020/12/21 20:48:04+65 -0
Pulled in latest colvars module from the git master.
Show difference between Revision 1.15 and 1.16
Revision 1.15johns 2020/11/01 06:55:40+13 -8
Updated the collective variables module to the latest git version, which
also bears the tag "vmd-1.9.4a49".
Show difference between Revision 1.14 and 1.15

Filename: colvarcomp_apath.C
Revision 1.2johns 2020/11/01 06:55:40+22 -20
Updated the collective variables module to the latest git version, which
also bears the tag "vmd-1.9.4a49".
Show difference between Revision 1.1 and 1.2

Filename: colvarcomp_distances.C
Revision 1.21johns 2020/11/01 06:55:40+4 -4
Updated the collective variables module to the latest git version, which
also bears the tag "vmd-1.9.4a49".
Show difference between Revision 1.20 and 1.21

Filename: colvarcomp_gpath.C
Revision 1.2johns 2020/11/01 06:55:40+2 -37
Updated the collective variables module to the latest git version, which
also bears the tag "vmd-1.9.4a49".
Show difference between Revision 1.1 and 1.2

Filename: colvarcomp_rotations.C
Revision 1.12johns 2020/12/21 20:48:04+332 -0
Pulled in latest colvars module from the git master.
Show difference between Revision 1.11 and 1.12

Filename: colvarcomp_volmaps.C
Revision 1.2johns 2020/11/01 06:55:40+87 -6
Updated the collective variables module to the latest git version, which
also bears the tag "vmd-1.9.4a49".
Show difference between Revision 1.1 and 1.2

Filename: colvardeps.C
Revision 1.16johns 2020/11/01 06:55:40+18 -16
Updated the collective variables module to the latest git version, which
also bears the tag "vmd-1.9.4a49".
Show difference between Revision 1.15 and 1.16

Filename: colvargrid.C
Revision 1.11johns 2020/11/01 06:55:40+11 -5
Updated the collective variables module to the latest git version, which
also bears the tag "vmd-1.9.4a49".
Show difference between Revision 1.10 and 1.11

Filename: colvargrid.h
Revision 1.20johns 2020/11/01 06:55:40+8 -7
Updated the collective variables module to the latest git version, which
also bears the tag "vmd-1.9.4a49".
Show difference between Revision 1.19 and 1.20

Filename: colvarmodule.C
Revision 1.27johns 2020/11/01 06:55:40+53 -23
Updated the collective variables module to the latest git version, which
also bears the tag "vmd-1.9.4a49".
Show difference between Revision 1.26 and 1.27

Filename: colvarmodule.h
Revision 1.29johns 2020/11/01 06:55:40+3 -0
Updated the collective variables module to the latest git version, which
also bears the tag "vmd-1.9.4a49".
Show difference between Revision 1.28 and 1.29

Filename: colvarproxy.C
Revision 1.10johns 2020/11/01 06:55:40+6 -0
Updated the collective variables module to the latest git version, which
also bears the tag "vmd-1.9.4a49".
Show difference between Revision 1.9 and 1.10

Filename: colvarproxy.h
Revision 1.20johns 2020/11/01 06:55:40+19 -0
Updated the collective variables module to the latest git version, which
also bears the tag "vmd-1.9.4a49".
Show difference between Revision 1.19 and 1.20

Filename: colvarproxy_vmd.C
Revision 1.21johns 2020/12/21 20:48:04+1 -1
Pulled in latest colvars module from the git master.
Show difference between Revision 1.20 and 1.21
Revision 1.20johns 2020/11/01 06:55:40+154 -4
Updated the collective variables module to the latest git version, which
also bears the tag "vmd-1.9.4a49".
Show difference between Revision 1.19 and 1.20

Filename: colvarproxy_vmd.h
Revision 1.16johns 2020/11/01 06:55:40+24 -5
Updated the collective variables module to the latest git version, which
also bears the tag "vmd-1.9.4a49".
Show difference between Revision 1.15 and 1.16

Filename: colvarproxy_vmd_version.h
Revision 1.11johns 2020/11/01 06:55:40+1 -1
Updated the collective variables module to the latest git version, which
also bears the tag "vmd-1.9.4a49".
Show difference between Revision 1.10 and 1.11

Filename: colvarproxy_volmaps.C
Revision 1.2johns 2020/11/01 06:55:40+44 -9
Updated the collective variables module to the latest git version, which
also bears the tag "vmd-1.9.4a49".
Show difference between Revision 1.1 and 1.2

Filename: colvarproxy_volmaps.h
Revision 1.2johns 2020/11/01 06:55:40+43 -3
Updated the collective variables module to the latest git version, which
also bears the tag "vmd-1.9.4a49".
Show difference between Revision 1.1 and 1.2

Filename: colvars_files.pl
Revision 1.5johns 2020/11/01 06:55:40+4 -2
Updated the collective variables module to the latest git version, which
also bears the tag "vmd-1.9.4a49".
Show difference between Revision 1.4 and 1.5

Filename: colvars_version.h
Revision 1.15johns 2020/12/21 20:48:04+1 -1
Pulled in latest colvars module from the git master.
Show difference between Revision 1.14 and 1.15
Revision 1.14johns 2020/11/01 06:55:40+1 -1
Updated the collective variables module to the latest git version, which
also bears the tag "vmd-1.9.4a49".
Show difference between Revision 1.13 and 1.14

Filename: colvarscript.C
Revision 1.24johns 2020/12/21 20:48:04+25 -4
Pulled in latest colvars module from the git master.
Show difference between Revision 1.23 and 1.24

Filename: colvarscript_commands.h
Revision 1.2johns 2020/11/01 06:55:40+14 -0
Updated the collective variables module to the latest git version, which
also bears the tag "vmd-1.9.4a49".
Show difference between Revision 1.1 and 1.2

Filename: colvarscript_commands_colvar.h
Revision 1.2johns 2020/11/01 06:55:40+15 -0
Updated the collective variables module to the latest git version, which
also bears the tag "vmd-1.9.4a49".
Show difference between Revision 1.1 and 1.2

Filename: colvartypes.C
Revision 1.11johns 2020/11/01 06:55:40+109 -157
Updated the collective variables module to the latest git version, which
also bears the tag "vmd-1.9.4a49".
Show difference between Revision 1.10 and 1.11

Filename: colvartypes.h
Revision 1.12johns 2020/11/01 06:55:40+6 -23
Updated the collective variables module to the latest git version, which
also bears the tag "vmd-1.9.4a49".
Show difference between Revision 1.11 and 1.12

Filename: colvarvalue.C
Revision 1.13johns 2020/11/01 06:55:40+2 -1
Updated the collective variables module to the latest git version, which
also bears the tag "vmd-1.9.4a49".
Show difference between Revision 1.12 and 1.13

Filename: colvarvalue.h
Revision 1.12johns 2020/11/01 06:55:40+3 -3
Updated the collective variables module to the latest git version, which
also bears the tag "vmd-1.9.4a49".
Show difference between Revision 1.11 and 1.12

Filename: glwin.c
Revision 1.32johns 2020/12/15 05:51:45+28 -15
Prevent glwin window destruction from killing the parent app
in Win32/Win64 builds.
Show difference between Revision 1.31 and 1.32
Revision 1.31johns 2020/11/25 16:49:35+10 -2
Windows platforms return raw key state without processing key modifiers,
so in order to provide the same behavior as X11, we process key modifiers
ourselves w/ toupper()/tolower() calls, etc.
Show difference between Revision 1.30 and 1.31
Revision 1.30johns 2020/11/16 07:35:50+17 -9
Imported Tachyon glwin updates to permit compilation on win32/win64
Show difference between Revision 1.29 and 1.30

Filename: macosxvmdstart.C
Revision 1.29johns 2020/12/13 07:41:55+13 -7
Added conditional compilation tests for ARM64 MacOS X builds
checking for the compile-time macro ARCH_MACOSXARM64.
Show difference between Revision 1.28 and 1.29

Filename: msmpot_setup.c
Revision 1.7johns 2020/10/21 20:35:05+2 -2
Corrected a C++ism that got into the MSM code while eliminating
visual studio warnings.
Show difference between Revision 1.6 and 1.7

Filename: nr_jacobi.C
Revision 1.1johns 2020/11/01 06:55:40None
Updated the collective variables module to the latest git version, which
also bears the tag "vmd-1.9.4a49".

Filename: nr_jacobi.h
Revision 1.1johns 2020/11/01 06:55:40None
Updated the collective variables module to the latest git version, which
also bears the tag "vmd-1.9.4a49".

Filename: pcre.c

Filename: py_color.C
Revision 1.38johns 2020/12/24 05:34:15+39 -1
Added Python bindings to permit querying and setting color scale reversal
and posterization parameters.
Show difference between Revision 1.37 and 1.38
Revision 1.37johns 2020/12/24 04:21:51+16 -13
Revised color scale internals and the Color window GUI to implement
posterization of color scales down to a user-specified number of
individual color bands.
Show difference between Revision 1.36 and 1.37
Revision 1.36johns 2020/12/23 16:41:13+14 -13
Revised the color scale internals to facilitate ooptional color scale order
reversal for both built-in divergent midpoint/offset color scales as
well as tabulated color scales.
Show difference between Revision 1.35 and 1.36

Filename: util_simd.C
Revision 1.30johns 2020/12/27 08:02:15+2 -2
Corrected conditional compilation checks for non-x86 CPU runtime dispatch
Show difference between Revision 1.29 and 1.30
Revision 1.29johns 2020/12/21 04:41:27+3 -2
Changed _mm_set_pd1() to _mm_set1_pd() which seems more portable
Show difference between Revision 1.28 and 1.29
Revision 1.28johns 2020/11/01 08:08:41+6 -2
Updated conditional compilation tests and logic for runtime CPU dispatched
atom selection analysis code to ensure proper compilation on both
x86 and ARM64 platforms, since VMD now supports runtime dispatch on both.
Show difference between Revision 1.27 and 1.28
Revision 1.27johns 2020/11/01 05:48:11+3 -70
Chopped out conditional compilation of alternative AVX-specific SIMD
loops now that runtime CPU dispatch is beginning to be more extensively
implemented.
Show difference between Revision 1.26 and 1.27
Revision 1.26johns 2020/11/01 05:22:13+14 -4
Added runtime CPU dispatch for analyze_selection_aligned_avx2()
Show difference between Revision 1.25 and 1.26
Revision 1.25johns 2020/10/28 08:11:37+10 -1
Updates for the SSE atom selection and statistics kernels to please current
versions of MSVS, which fail to define SSE macros at compile time.
Show difference between Revision 1.24 and 1.25
Revision 1.24johns 2020/10/28 08:09:06+7 -7
Added explicit call to _mm_castsi128_ps(mask) to please MSVS compilers.
Show difference between Revision 1.23 and 1.24
Revision 1.23johns 2020/10/22 05:50:28+28 -27
Updated SIMD routines conditional compilation macros and tests
for use with MSVS 2017, and replaced the use of long types with
ptrdiff_t and size_t for x64 64-bit Windows builds.
Show difference between Revision 1.22 and 1.23

Filename: util_simd_AVX.C
Revision 1.8johns 2020/11/01 05:40:57+1 -32
Eliminated remnants of AVX2-specific code which is now in its own source file.
Show difference between Revision 1.7 and 1.8
Revision 1.7johns 2020/11/01 04:53:05+43 -7
Changed the AVX atom selection loops to use the prior strategy for
finding vector-aligned starting/ending indices due to bugs that showed
up in testing with CPU dispatch enabled. Will revisit later.
Show difference between Revision 1.6 and 1.7
Revision 1.6johns 2020/10/22 05:50:28+18 -13
Updated SIMD routines conditional compilation macros and tests
for use with MSVS 2017, and replaced the use of long types with
ptrdiff_t and size_t for x64 64-bit Windows builds.
Show difference between Revision 1.5 and 1.6

Filename: util_simd_AVX2.C
Revision 1.1johns 2020/11/01 05:00:11None
Added AVX2 atom selection analysis loop

Filename: util_simd_SVE.C
Revision 1.5johns 2020/10/29 06:31:27+2 -1
Added include of stddef.h for ptrdiff_t
Show difference between Revision 1.4 and 1.5
Revision 1.4johns 2020/10/28 06:34:00+5 -1
Added more SVE doc references.
Show difference between Revision 1.3 and 1.4
Revision 1.3johns 2020/10/28 05:39:23+6 -1
Added links to current ARM ACLE SVE documentation used to develop
the first variable vector length SVE kernels.
Show difference between Revision 1.2 and 1.3
Revision 1.2johns 2020/10/28 05:01:25+93 -2
Begain implementing ARM64 SVE vectorized loops for high performance
analytical routines.
Show difference between Revision 1.1 and 1.2
Revision 1.1johns 2020/10/27 21:30:00None
Added ARM SVE general vectorized kernels and helper routines to the build.

Filename: utilities.C

Filename: utilities.h
Revision 1.120johns 2020/10/27 21:31:27+9 -1
Added prototypes for ARM SVE runtime dispatch SVE vector lengh query
helper routines.
Show difference between Revision 1.119 and 1.120
Revision 1.119johns 2020/10/27 05:30:05+2 -1
Added include of stddef.h for definition of ptrdiff_t
Show difference between Revision 1.118 and 1.119
Revision 1.118johns 2020/10/22 05:50:28+7 -6
Updated SIMD routines conditional compilation macros and tests
for use with MSVS 2017, and replaced the use of long types with
ptrdiff_t and size_t for x64 64-bit Windows builds.
Show difference between Revision 1.117 and 1.118

Filename: vmdsock.c
Revision 1.31johns 2020/12/13 07:41:55+2 -2
Added conditional compilation tests for ARM64 MacOS X builds
checking for the compile-time macro ARCH_MACOSXARM64.
Show difference between Revision 1.30 and 1.31

Filename: win32vmdstart.c
Revision 1.52johns 2020/12/14 20:26:02+2 -2
eliminated startup test messages for WIN64 builds
Show difference between Revision 1.51 and 1.52
Revision 1.51johns 2020/12/14 20:24:27+5 -13
Updated WIN32 and WIN64 registry query code and software keys to add
support for 64-bit builds.
Show difference between Revision 1.50 and 1.51


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