| Tags | Date | Developer | Last 200 Commit Logs |
|---|
| | 2009-11-20 | saam | Eliminated obsolete symbolic constants RUNTYPE_TOTAL and SCFTYPE_TOTAL.
Added comments.
* src/QMData.h 1.76 (changed +7 -6)
* src/QMData.C 1.88 (changed +4 -4)
* src/MolFilePlugin.C 1.161 (changed +1 -4)
Replace MOLFILE_QMCHARGE_* by QMCHARGE_* and translate the symbolic
constants in MolFilePlugin.C.
Finally this allowed to eliminate references to molfile_plugin.h in
files other than MolFilePlugin.C.
* src/QMTimestep.C 1.63 (changed +5 -6)
* src/QMData.h 1.78 (changed +13 -5)
* src/QMData.C 1.90 (changed +1 -2)
* src/Orbital.C 1.115 (changed +1 -2)
* src/MolFilePlugin.C 1.163 (changed +25 -3)
Replace MOLFILE_WAVE_* by WAVE_*.
* src/QMTimestep.C 1.62 (changed +9 -9)
* src/QMData.C 1.89 (changed +10 -10)
Translate MOLFILE_WAVE_* macros.
* src/QMData.h 1.77 (changed +38 -1)
* src/MolFilePlugin.C 1.162 (changed +38 -4)
|
| | 2009-11-19 | saam | Add translation switch block for qm convergence status.
* src/QMData.h 1.75 (changed +10 -1)
* src/QMData.C 1.87 (changed +6 -5)
* src/MolFilePlugin.C 1.160 (changed +17 -2)
Translate between MOLFILE_SCFTYPE_* macros from molfile_plugin.h to
SCFTYPE_* enum defined in QMData.h. This will make it unnecessary to in
clude molfile_plugin.h anywhere else in VMD but MolFilePlugin.h. As a
result VMD will be more indedendent from the plugins.
* src/QMTimestep.C 1.61 (changed +4 -8)
* src/QMData.h 1.73 (changed +25 -5)
* src/QMData.C 1.85 (changed +3 -3)
* src/MolFilePlugin.C 1.158 (changed +33 -1)
Translate between RUNTYPE_* macros from molfile_plugin.h and QMData.h.
Replace hard-wired Lookup table for descriptive strings for runtype and
scftype by switch blocks so we don't have to keep the translation table
in sync with the macro definitions.
* src/QMData.h 1.74 (changed +13 -12)
* src/QMData.C 1.86 (changed +23 -20)
* src/MolFilePlugin.C 1.159 (changed +34 -3)
|
| | 2009-11-17 | saam | Use SCF type macros from molfile_plugin.
* src/QMTimestep.C 1.60 (changed +5 -5)
* src/QMData.h 1.72 (changed +1 -5)
* src/QMData.C 1.84 (changed +4 -2)
|
| | 2009-11-17 | johns | Set Python molecule load behavior to wait for all frames to load by default
as per JG's suggestion. Corrected comments in the header file.
* src/py_molecule.C 1.67 (changed +2 -1)
* src/VMDApp.h 1.209 (changed +2 -2)
Updated for Apple's OpenCL implementation
* src/OpenCLVolCPotential.C 1.26 (changed +5 -1)
Updated orbital kernel to compile on MacOS
* src/OpenCLOrbital.C 1.23 (changed +5 -1)
|
| | 2009-11-12 | johns | Fixed a bug in the calculation of partial distance components in the
CPU SSE code branch.
* src/Orbital.C 1.113 (changed +3 -3)
Found a typo in the SSE angular momenta for F_SHELL
* src/Orbital.C 1.114 (changed +2 -2)
|
| | 2009-11-11 | saam | Safety check for get_basis().
* src/TclMolInfo.C 1.87 (changed +3 -2)
* src/QMData.C 1.83 (changed +5 -1)
|
| | 2009-11-11 | johns | Added a code path to allow testing of the vec4 DCS kernel
* src/OpenCLVolCPotential.C 1.19 (changed +7 -1)
Added tunings for IBM Cell/Power kernel
* src/OpenCLVolCPotential.C 1.22 (changed +15 -6)
Corrected a typo in the OpenCL required work group size
kernel attributes which was causing a problem with the IBM OpenCL
implementation for Cell.
* src/OpenCLVolCPotential.C 1.18 (changed +3 -3)
* src/OpenCLOrbital.C 1.21 (changed +4 -4)
Corrected last remaining issues with the vec4 version of the orbital kernel
* src/OpenCLOrbital.C 1.22 (changed +4 -4)
Fix cut/paste typo in vec4 potential kernel
* src/OpenCLVolCPotential.C 1.20 (changed +2 -2)
Fixed dx lattice coordinate arithmetic for 2-times unrolled 4-way
vectorized DCS potential kernel
* src/OpenCLVolCPotential.C 1.24 (changed +2 -2)
Make non-CUDA builds (e.g. OpenCL-only) workable.
* src/DrawMolecule.C 1.136 (changed +2 -2)
Set block size (OpenCL workgroup size) for vec4 potential kernel
to give good performance on NVIDIA and AMD hardware. Need more tuning
to find the global optimal settings.
* src/OpenCLVolCPotential.C 1.21 (changed +3 -3)
Unrolled 4-way vectorized kernel for higher efficiency
* src/OpenCLVolCPotential.C 1.23 (changed +15 -2)
Use single-precision floating point constant to please some
of the weaker OpenCL compiler implementations.
* src/OpenCLVolCPotential.C 1.25 (changed +2 -2)
|
| | 2009-11-10 | johns | Added workarounds for bugs in the IBM Power/Cell OpenCL preview implementation
* src/OpenCLOrbital.C 1.20 (changed +32 -1)
Corrected OpenCL work unit X lattice index calculation
* src/OpenCLVolCPotential.C 1.17 (changed +3 -3)
Fixed typo in OpenCL potential kernel parameter setup
* src/OpenCLVolCPotential.C 1.16 (changed +2 -2)
Minor bug fixes and updates to both coulomb summation kernels
* src/OpenCLVolCPotential.C 1.14 (changed +68 -25)
Prevent pbwithin selections with a cutoff <= 0.0 from crashing.
* src/ParseTree.C 1.129 (changed +11 -1)
Updated padding logic to add support for 4-way vectorized potential kernel
* src/OpenCLVolCPotential.C 1.15 (changed +25 -10)
|
| | 2009-11-06 | johns | Corrected global dimensions to take into account the loop unrolling
within each work item.
* src/OpenCLVolCPotential.C 1.11 (changed +5 -6)
Eliminated lots of workarounds and ifdef blocks in the OpenCL kernel since
the latest NVIDIA OpenCL libs seem to have fixed all of the problems that
the workarounds were written for.
* src/OpenCLOrbital.C 1.19 (changed +2 -20)
Force OpenCL potential kernel to be single-threaded for now, started
culling some of the debugging code and unnecessary status messages.
Still need to pull kernel compilation the rest of the way out of the
compute loops.
* src/OpenCLVolCPotential.C 1.13 (changed +4 -28)
Started migrating OpenCL kernel compilation out of the compute loops
* src/OpenCLVolCPotential.C 1.12 (changed +26 -23)
|
| | 2009-11-05 | johns | Added typecast to please the mac CUDA compilers
* src/CUDAUtil.cu 1.32 (changed +2 -2)
Converted VMD to use the timers provided by the workforce library, making
it easier to use VMD components in standalone code, or to develop things
initially as standalone modules before adding them to VMD.
* src/utilities.h 1.95 (changed +1 -25)
* src/utilities.C 1.122 (changed +1 -133)
* src/VolMapCreateILS.C 1.163 (changed +35 -34)
* src/VolMapCreate.C 1.108 (changed +7 -6)
* src/VolCPotential.C 1.27 (changed +28 -27)
* src/SpatialSearch.C 1.13 (changed +5 -4)
* src/Orbital.C 1.112 (changed +17 -16)
* src/OpenCLVolCPotential.C 1.10 (changed +16 -15)
* src/MeasureSymmetry.C 1.51 (changed +7 -7)
* src/Measure.C 1.126 (changed +8 -7)
* src/DrawMolItemVolume.C 1.145 (changed +5 -4)
* src/DrawMolItemRibbons.C 1.138 (changed +21 -20)
* src/DrawMolItemOrbital.C 1.42 (changed +11 -10)
* src/CoorPluginData.h 1.13 (changed +3 -2)
* src/CoorPluginData.C 1.23 (changed +6 -5)
* src/CUDAVolMapCreateILS.cu 1.47 (changed +15 -14)
* src/CUDAVolCPotential.cu 1.40 (changed +16 -15)
* src/CUDABench.cu 1.29 (changed +53 -53)
* src/BondSearch.C 1.63 (changed +5 -4)
* src/Benchmark.C 1.5 (changed +30 -30)
* src/BaseMolecule.C 1.241 (changed +7 -6)
Cranked version
* configure 1.1111 (changed +1 -1)
Fixed polygon winding order for two-radii cones in the default
FileRenderer::cone() method used by renderers that don't provide
their own cone primitive.
* src/FileRenderer.C 1.128 (changed +3 -3)
OpenCL orbital kernel is now wired up for basic testing. The runtime
compilation of the kernel is done in a hackish way at present, but we
need a robust dynamic kernel compilation infrastructure the provides
thread-safety and the ability to create/destroy kernels dynamically in
order to really solve this problem properly. The current OpenCL kernel
is limited to single-threaded execution due to the fact that OpenCL
itself is not completely thread-safe.
* src/Orbital.C 1.111 (changed +66 -3)
|
| | 2009-11-04 | johns | Added the OpenCL orbital code to the configure script
* configure 1.1110 (changed +1 -0)
Corrected X index calculation to incorporate the correct loop unrolling
constants.
* src/OpenCLVolCPotential.C 1.9 (changed +3 -3)
|
| | 2009-11-03 | johns | Use an explicit single precision floating point constant when initializing
tmpshell, so CUDA and OpenCL kernels match
* src/CUDAOrbital.cu 1.97 (changed +3 -3)
|
| | 2009-11-02 | johns | Added draft 4-way vectorized orbital kernel
* src/OpenCLOrbital.C 1.14 (changed +208 -26)
Beginning cleanup of OpenCL orbital kernel compilation stages in prep for
moving them out to the VMD global application startup-phase.
* src/OpenCLOrbital.C 1.16 (changed +42 -27)
Further progress pulling OpenCL state initialization out of the orbital
computation routines themselves.
* src/OpenCLOrbital.C 1.17 (changed +115 -92)
Make OpenCL orbital kernels use native_exp2() for
(hopefully) better performance
* src/OpenCLOrbital.C 1.15 (changed +4 -4)
Migrated majority of OpenCL context setup code completely out of the orbital
routines.
* src/OpenCLOrbital.C 1.18 (changed +25 -47)
* src/OpenCLKernels.h 1.3 (changed +26 -1)
Renamed 4-way vectorized potential kernel
* src/OpenCLVolCPotential.C 1.8 (changed +2 -2)
|
| | 2009-10-30 | johns | Added a float4-based OpenCL kernel intended to be better suited to CPUs.
* src/OpenCLVolCPotential.C 1.7 (changed +34 -2)
Added code for setting up and running the tiled shared orbital kernel
in OpenCL. At present the kernel is disabled due to bugs in both of
the existing beta OpenCL toolkits, but hopefully it'll be runnable soon.
* src/OpenCLOrbital.C 1.12 (changed +26 -19)
Added more cleanup handling to the end of the potential kernel for now
until this gets pulled out into higher level routines.
* src/OpenCLVolCPotential.C 1.5 (changed +9 -3)
Eliminated unnecessary __constant address space qualifiers for non-pointer
kernel parameters.
* src/OpenCLOrbital.C 1.11 (changed +11 -11)
Eliminated unnecessary __constant address space qualifiers for the
non-pointer OpenCL potential kernel arguments
* src/OpenCLVolCPotential.C 1.6 (changed +2 -2)
Fixed incorrect copy length for initialization of the
const_num_shells_per_atom array
* src/OpenCLOrbital.C 1.13 (changed +2 -2)
Fixed missing type specifier
* src/OpenCLOrbital.C 1.10 (changed +5 -5)
Implemented an OpenCL version of the tiled shared memory orbital kernel
* src/OpenCLOrbital.C 1.9 (changed +237 -240)
|
| | 2009-10-29 | johns | Added OpenCL orbital kernel
* src/OpenCLKernels.h 1.2 (changed +18 -3)
Completed kernel launch code for constant memory version of the orbital kernel
* src/OpenCLOrbital.C 1.3 (changed +18 -11)
Converted constant memory buffers to OpenCL dynamic allocations.
* src/OpenCLOrbital.C 1.2 (changed +40 -12)
Corrected global work dimension for kernel launch
* src/OpenCLVolCPotential.C 1.4 (changed +3 -3)
Corrected logic that releases memory objects after the orbital kernel
completes, and fixed the memory object allocation code that will be used
by the tiled kernel.
* src/OpenCLOrbital.C 1.5 (changed +19 -17)
Mostly functioning OpenCL version of the constant memory orbital kernel
* src/OpenCLOrbital.C 1.4 (changed +21 -15)
Prettied up the constant memory orbital kernel
* src/OpenCLOrbital.C 1.6 (changed +22 -18)
Release the command queue when done
* src/OpenCLOrbital.C 1.7 (changed +2 -1)
Set fixed workgroup size for the constant memory orbital kernel
* src/OpenCLOrbital.C 1.8 (changed +3 -2)
|
| | 2009-10-28 | johns | Added explicit include of math.h so that OpenCL and CUDA codes are as close
to identical as possible.
* src/CUDAOrbital.cu 1.96 (changed +2 -1)
Crude first draft of OpenCL version of the existing CUDA orbital kernels.
At present, only the constant memory kernel is ported, and the constant
memory arrays need to be reorganized since OpenCL handles those a bit
differently.
* src/OpenCLOrbital.C 1.1 (added +837 -0)
Eliminated unused constant buffer leftover from CUDA version
* src/OpenCLVolCPotential.C 1.3 (changed +1 -2)
Pretty
* src/CUDAOrbital.cu 1.94 (changed +1 -2)
Pulled unrolling macros out of orbital kernel since we're not actually using
them at present.
* src/CUDAOrbital.cu 1.95 (changed +7 -13)
Updated and revised the standalone test harness so we can begin doing a
bringup of an OpenCL version of the orbital code.
* src/CUDAOrbital.cu 1.93 (changed +2 -2)
|
| | 2009-10-27 | johns | Corrected the CUDA init code for non-CUDA builds and init the class
pointers to NULL in all cases.
* src/VMDApp.C 1.448 (changed +4 -1)
Eliminated unnecessary printing from OpenCL platform selector routine
* src/OpenCLUtils.C 1.3 (changed +1 -12)
Eliminated unused code and added device count to platform info routines
* src/OpenCLUtils.h 1.2 (changed +2 -4)
* src/OpenCLUtils.C 1.4 (changed +16 -13)
Improved OpenCL platform info display
* src/OpenCLUtils.C 1.2 (changed +5 -4)
Limit OpenCL runs to a single host thread until we make our own thread-safe
kernel compilation infrastructure.
* src/OpenCLVolCPotential.C 1.2 (changed +3 -3)
|
| | 2009-10-26 | johns | Added workforce timer routines to the build, replacing the vmd versions based
on the Tachyon code.
* src/WKFUtils.h 1.1 (added +82 -0)
* src/WKFUtils.C 1.1 (added +217 -0)
Cranked version
* configure 1.1109 (changed +1 -1)
|
| | 2009-10-23 | johns | Fixed behavior of withinbonds selection when used as part of a compound
selection expression.
* src/ParseTree.C 1.128 (changed +14 -6)
Increase default resolution of representations. This will cost performance
for very large structures, but since the majority of the user community are
working on small items, it's a better default for modern GPUs. People working
on large structures are generally more skilled and will know how to change
their personal defaults using the "mol default" commands.
* src/AtomRep.C 1.117 (changed +3 -3)
|
| | 2009-10-12 | johns | Added basic OpenCL support to configure script
* configure 1.1108 (changed +24 -0)
Added crude first draft of OpenCL infrastructure.
* src/VolCPotential.C 1.26 (changed +12 -1)
* src/VMDApp.C 1.447 (changed +8 -1)
* src/OpenCLVolCPotential.C 1.1 (added +484 -0)
* src/OpenCLUtils.h 1.1 (added +43 -0)
* src/OpenCLUtils.C 1.1 (added +183 -0)
* src/OpenCLKernels.h 1.1 (added +29 -0)
|
| | 2009-10-09 | johns | Correct placement of comment
* src/UIText.C 1.189 (changed +3 -2)
Made the constant buffer update routine static for file-scope linkage.
* src/CUDAVolCPotential.cu 1.39 (changed +2 -2)
Pretty
* src/CommandQueue.C 1.54 (changed +2 -2)
|
| | 2009-09-24 | johns | Corrected missing device memory allocation when not building
using pinned memory buffers.
* src/CUDAOrbital.cu 1.92 (changed +4 -4)
Do a quick 1-byte memory allocation/deallocation during GPU device pool
initialization to cause all of the contexts to go live during the earliest
startup phase for the purposes of accurate init timings.
* src/CUDAUtil.cu 1.31 (changed +13 -7)
|
| | 2009-09-23 | johns | Added a prototype zero-copy variation of the orbital kernels.
Since we can't presently guarantee that the incoming grid is appropriately
padded in X and Y, we still have a de-striding copy loop to perform
to the final output buffer, but we have eliminated the need for calls
to cudaMemcpy() following kernel execution since the output array is
write-only. To do better, we need to eliminate the de-striding copies
and ideally use a "portable" mapped host allocation so that all GPUs
target the same output buufer automatically.
* src/CUDAOrbital.cu 1.90 (changed +56 -26)
Added timer calls to return absolute wall clock times for start/stop
times to enable detailed execution trace comparisons
* src/utilities.h 1.94 (changed +3 -1)
* src/utilities.C 1.121 (changed +32 -1)
Cranked version
* configure 1.1107 (changed +1 -1)
Don't call free CUDA device memory arrays unless we used them.
* src/CUDAOrbital.cu 1.88 (changed +11 -8)
Enable CUDA mapped host memory by default when initializing hardware
that's capable of using zero copy
* src/CUDAUtil.cu 1.30 (changed +13 -1)
Enabled zero-copy orbital kernel by default
* src/CUDAOrbital.cu 1.91 (changed +2 -2)
Fix typo
* src/CUDAOrbital.cu 1.89 (changed +3 -3)
Fixed incorrect orbital grid allocation size presumably caused by
conversion from malloc/free to new/delete syntax.
* src/Orbital.C 1.110 (changed +2 -2)
Made the mutexes on work distribution data structures use spin locks only,
this will prevent kernel-based queued waiting and the associated context
switches back and forth.
* src/WKFThreads.C 1.3 (changed +3 -3)
|
| | 2009-09-22 | saam | Comments.
* src/QMData.h 1.71 (changed +12 -5)
* src/QMData.C 1.82 (changed +17 -3)
|
| | 2009-09-21 | saam | Cleanup the wavefunction setup process a bit.
* src/QMTimestep.h 1.34 (changed +3 -2)
* src/QMTimestep.C 1.59 (changed +20 -3)
* src/QMData.C 1.81 (changed +3 -1)
* src/MolFilePlugin.C 1.157 (changed +9 -22)
Comtinue replacing shell_symmtry by shell_type.
* src/TclMolInfo.C 1.86 (changed +3 -3)
* src/Orbital.h 1.33 (changed +5 -5)
* src/Orbital.C 1.109 (changed +42 -42)
* src/CUDAOrbital.cu 1.87 (changed +16 -16)
* src/CUDAKernels.h 1.35 (changed +2 -2)
Explain the concept behind the QMTimestep and wavefunction classes.
* src/QMTimestep.h 1.33 (changed +45 -6)
* src/QMTimestep.C 1.58 (changed +37 -14)
Finish renaming shell_symmetry.
* src/MolFilePlugin.C 1.156 (changed +5 -5)
Remove unused class members.
* src/QMData.h 1.69 (changed +1 -7)
Rename shell_symmetry in QMData to shell_type which is more appropriate.
Improve comments.
* src/QMTimestep.C 1.57 (changed +3 -3)
* src/QMData.h 1.70 (changed +21 -12)
* src/QMData.C 1.80 (changed +60 -37)
* src/Orbital.h 1.32 (changed +5 -10)
* src/Orbital.C 1.108 (changed +7 -7)
* src/CUDAVolMapCreateILS.cu 1.46 (changed +6 -2)
|
| | 2009-09-20 | johns | Cranked version
* configure 1.1106 (changed +1 -1)
|
| | 2009-09-18 | akohlmey | Add "molinfo $mol get numvolumedata" to query the number of volumetric
data sets of a given VMD molecule.
* src/TclMolInfo.C 1.84 (changed +5 -2)
Revert last change as per john's request.
* src/TclMolInfo.C 1.85 (changed +0 -3)
|
| | 2009-09-16 | johns | Added code to test empty CUDA kernel launch latency. The code now skips
reporting data from the first "warmup" pass.
* src/cmd_vmdbench.C 1.21 (changed +16 -6)
* src/CUDAKernels.h 1.34 (changed +2 -1)
* src/CUDABench.cu 1.28 (changed +20 -1)
Added spin lock and try lock primitives for use in cases where we are
not willing to allow the OS to put the calling thread to sleep in a
wait queue due to detrimental effects on latency.
* src/WKFThreads.h 1.2 (changed +7 -1)
* src/WKFThreads.C 1.2 (changed +35 -1)
Eliminated vmd_msleep() call to keep CPU cores spun up during benchmark
* src/cmd_vmdbench.C 1.20 (changed +1 -2)
|
| | 2009-09-15 | johns | Added a device pool latency benchmark that includes a simple
no-op GPU kernel
* src/cmd_vmdbench.C 1.18 (changed +12 -12)
* src/CUDAKernels.h 1.33 (changed +3 -2)
* src/CUDABench.cu 1.25 (changed +48 -5)
Added a new benchmark test to measure the latency of a complete
device threadpool wake / run / barrier collect / sleep cycle doing
a no-op other than requesting work units as fast as possible.
* src/cmd_vmdbench.C 1.15 (changed +39 -6)
* src/Orbital.C 1.107 (changed +3 -3)
* src/CUDAKernels.h 1.31 (changed +4 -1)
* src/CUDABench.cu 1.23 (changed +45 -1)
Added device pool benchmarks for raw barrier syncs, and for a no-op
worker procedure.
* src/cmd_vmdbench.C 1.17 (changed +15 -6)
* src/CUDAKernels.h 1.32 (changed +4 -2)
* src/CUDABench.cu 1.24 (changed +30 -7)
Added multi-run averaging into CUDA device pool latency benchmarks
* src/cmd_vmdbench.C 1.19 (changed +2 -2)
* src/CUDABench.cu 1.27 (changed +32 -18)
CUDA device pools are used now even for single-threaded builds
* src/CUDAOrbital.cu 1.85 (changed +6 -3)
* src/CUDAAccel.C 1.35 (changed +3 -3)
Changed comments to ifdef
* src/CUDAUtil.cu 1.29 (changed +6 -3)
Eliminate unused variable
* src/cmd_vmdbench.C 1.16 (changed +1 -2)
Eliminated the old thread spawning code from the CUDA Orbital code, since
we can use the device pool APIs even for single-threaded runs now.
* src/CUDAOrbital.cu 1.86 (changed +4 -44)
Force wait on completion of GPU kernels before exiting worker
* src/CUDABench.cu 1.26 (changed +4 -1)
Re-enabled use of CUDA pinned memory for the multi-GPU orbital kernels since
the CUDA 2.3 drivers seem to have fixed the bugs that existed before.
* src/CUDAOrbital.cu 1.84 (changed +6 -3)
|
| | 2009-09-09 | johns | Removed code for detection of various archaic SGI and Sun graphics accelerators
along with code that provided workarounds for bugs in the graphics
hardware and/or drivers.
* src/OpenGLRenderer.C 1.402 (changed +2 -4)
* src/OpenGLExtensions.h 1.45 (changed +2 -3)
* src/OpenGLExtensions.C 1.60 (changed +3 -18)
Removed old comments related to bugs in the fog implementation on the
original SGI RealityEngine and hardware of the same era.
* src/OpenGLRenderer.C 1.403 (changed +1 -10)
Removed old machine-specific GLX visual acquisition comments
* src/OpenGLDisplayDevice.C 1.176 (changed +2 -6)
Removed queries and enumerations related to the old
Sun OpenGL mesh array extension, which is not used in VMD currently.
* src/OpenGLExtensions.h 1.46 (changed +1 -2)
* src/OpenGLExtensions.C 1.61 (changed +1 -12)
Removed the archaic SGI-specific multisample antialiasing code since the
ARB multisample feature has been available now for many years.
* src/OpenGLRenderer.C 1.401 (changed +1 -29)
* src/OpenGLDisplayDevice.C 1.175 (changed +4 -45)
* src/OpenGLDisplayDevice.C 1.174 (changed +1 -6)
|
| | 2009-09-04 | johns | Cranked version
* configure 1.1105 (changed +1 -1)
|
| | 2009-09-02 | akohlmey | Make vmdcon compile with the new WKF threads.
* src/vmdconsole.c 1.10 (changed +2 -2)
|
| | 2009-08-26 | johns | Updated MSVC6 build setting for new threading components
* msvc/winvmd/winvmd.dsp 1.127 (changed +5 -1)
Updated VS2005 build settings for new threading components
* msvc/vs2005/winvmd.vcproj 1.19 (changed +13 -1)
|
| | 2009-08-22 | johns | Added CUDA host-device memory copy latency benchmark tests
* src/cmd_vmdbench.C 1.14 (changed +19 -5)
* src/CUDAKernels.h 1.30 (changed +5 -3)
* src/CUDABench.cu 1.21 (changed +94 -22)
Fixed parameter ordering
* src/CUDABench.cu 1.22 (changed +2 -2)
|
| | 2009-08-21 | johns | Added CUDA global memory bandwidth benchmark test
* src/cmd_vmdbench.C 1.13 (changed +67 -1)
* src/CUDAKernels.h 1.29 (changed +4 -1)
* src/CUDABench.cu 1.19 (changed +239 -2)
CUDA memory bandwidth tests run faster with one thread per data element
rather than looping, and the code is much prettier.
* src/CUDABench.cu 1.20 (changed +13 -80)
Prettied up benchmark routines, eliminated an inadvertent use of
double precision constants in the multiply-add kernel.
* src/CUDABench.cu 1.18 (changed +8 -10)
|
| | 2009-08-18 | johns | Added first revision of WorkForce threads to VMD, to replace the old
VMDThreads code with something more program-agnostic. We'll keep the
truly VMD-specific threads routines in the old VMDThreads code, but
migrate the rest of the code to use the new API.
* src/WKFThreads.h 1.1 (added +404 -0)
* src/WKFThreads.C 1.1 (added +1331 -0)
Converted VMD to use the new WorkForce threading routines (also Tachyon-derived)
* src/vmdconsole.c 1.9 (changed +21 -21)
* src/vmd.C 1.78 (changed +3 -3)
* src/tcl_commands.C 1.31 (changed +4 -4)
* src/cmd_vmdbench.C 1.12 (changed +2 -2)
* src/VolCPotential.C 1.25 (changed +12 -12)
* src/VMDThreads.h 1.53 (changed +4 -292)
* src/VMDThreads.C 1.85 (changed +4 -785)
* src/VMDCollab.C 1.7 (changed +4 -4)
* src/VMDApp.C 1.446 (changed +2 -2)
* src/SpatialSearch.C 1.12 (changed +6 -6)
* src/Orbital.C 1.106 (changed +9 -9)
* src/Measure.C 1.125 (changed +8 -8)
* src/IMDSimThread.h 1.14 (changed +5 -5)
* src/IMDSimThread.C 1.14 (changed +25 -25)
* src/DrawMolecule.h 1.79 (changed +3 -3)
* src/DrawMolecule.C 1.135 (changed +2 -2)
* src/CUDAVolMapCreateILS.cu 1.45 (changed +3 -3)
* src/CUDAVolCPotential.cu 1.38 (changed +9 -9)
* src/CUDAUtil.cu 1.28 (changed +6 -6)
* src/CUDAOrbital.cu 1.83 (changed +15 -15)
* src/CUDAKernels.h 1.28 (changed +3 -3)
* src/CUDAClearDevice.cu 1.8 (changed +3 -3)
* src/CUDABench.cu 1.17 (changed +10 -10)
* src/CUDAAccel.h 1.16 (changed +4 -4)
* src/CUDAAccel.C 1.34 (changed +11 -11)
* src/BondSearch.C 1.62 (changed +14 -14)
Enable build of the WorkForce threads code.
* configure 1.1104 (changed +2 -1)
|
| | 2009-08-13 | saam | Allow disabling the automatic alignment code by setting the environment
variable VMDILSALIGNMAPS.
Pass alignment matrix and transformed grid origin and grid basis vectors
to the kernels.
* src/VolMapCreateILS.C 1.161 (changed +58 -16)
Fixed a stack corruption bug.
* src/VolMapCreateILS.C 1.162 (changed +10 -16)
|
| | 2009-08-08 | johns | Updated NVCC compiler flags for CUDA 2.3, including support for
cross-compilation mode on 64-bit hosts.
* configure 1.1103 (changed +5 -6)
|
vmd-1-8-7
| 2009-08-07 | saam | Improved error messages.
* src/TclVolMap.C 1.112 (changed +9 -3)
|
vmd-1-8-7
| 2009-08-07 | johns | Updated CUDA notes
* README 1.354 (changed +6 -4)
|
| | 2009-08-06 | johns | Changed win32 startup to look for VMD 1.8.8 registry key
* src/win32vmdstart.c 1.39 (changed +3 -3)
Cranked version to 1.8.8a1
* configure 1.1102 (changed +1 -1)
Updated equipment list
* doc/pg_devtools.dox 1.7 (changed +14 -14)
|
| | 2009-08-03 | johns | Correct release date
* doc/pg_cvsget.dox 1.20 (changed +2 -2)
Updates to README for completeness
* README 1.353 (changed +7 -2)
|
| | 2009-08-01 | johns | Added disabled code to tag the highest occupied MO in the GUI chooser.
This can't be enabled yet as there are a number of cases that arise
that a simple single-timestep lookup mechanism can't handle properly.
Leaving this disabled for release, and we'll enable it later.
* src/GraphicsFltkReps.h 1.107 (changed +27 -1)
Corrections to QMTimestep code fixing "animate dup" and related functionality,
and correcting the code that reports the highest occupied molecular orbital.
* src/QMTimestep.C 1.56 (changed +25 -19)
Cranked readme date
* README 1.352 (changed +2 -2)
Finalized win32 vs2005 project
* msvc/vs2005/winvmd.vcproj 1.18 (changed +1 -0)
ILS computations will use CUDA except when expressly disabled.
* src/VolMapCreateILS.C 1.160 (changed +3 -3)
Updated win32 installer
* msvc/inst/VMD/VMD.ipr 1.102 (changed +23 -23)
* msvc/inst/VMD/Text Substitutions/Setup.tsb 1.101 (changed +25 -25)
* msvc/inst/VMD/Text Substitutions/Build.tsb 1.101 (changed +15 -15)
* msvc/inst/VMD/String Tables/Default.shl 1.101 (changed +17 -17)
* msvc/inst/VMD/String Tables/0009-English/value.shl 1.103 (changed +7 -7)
* msvc/inst/VMD/File Groups/Default.fdf 1.101 (changed +4 -4)
|
| | 2009-07-31 | johns | Added docs for VMDNOCUDA environment variable
* doc/ug_exec_env.tex 1.54 (changed +10 -1)
Added new chapter to user's guide that discusses a little bit about
how VMD uses multi-core CPUs, and GPU acceleration of analysis tasks, etc.
* doc/ug_hardware.tex 1.1 (added +67 -0)
* doc/ug_chapters.tex 1.16 (changed +4 -2)
Added user guide docs for the FieldLines, Polyhedra, PaperChain, Twister,
and Orbital representations.
* doc/ug_mol_reps.tex 1.37 (changed +91 -21)
Enable CUDA-accelerated ILS calculation by default rather than only when
an environment variable is set.
* src/VolMapCreateILS.C 1.159 (changed +2 -2)
Force Orbital GUI choosers to default to existing wavefunction types
and spins when a rep is first created. When the code that loops testing
available types and spins runs, we record the first available type and
spin, and use it when initializing the chooser.
* src/GraphicsFltkReps.h 1.105 (changed +16 -1)
Force regen of wavefunction types, spins, excitations, and orbitals when
the user hits the default button.
* src/GraphicsFltkReps.h 1.106 (changed +5 -1)
Updated copyright dates for VMD, Tachyon
* doc/vmd_ref.tex 1.65 (changed +4 -4)
Updated programmer's guide docs to list the VMD 1.8.7 CVS tag
* doc/pg_cvsget.dox 1.19 (changed +5 -4)
|
| | 2009-07-29 | johns | Changed orbidx parameter to orbid for clarity in reading the code
* src/DrawMolItemOrbital.C 1.41 (changed +9 -9)
Renamed DrawMolItem::orbid to DrawMolItem::gridorbid to clarify that it's
associated with the computed grid.
* src/DrawMolItemOrbital.C 1.40 (changed +8 -15)
* src/DrawMolItem.h 1.159 (changed +2 -2)
* src/DrawMolItem.C 1.313 (changed +4 -4)
|
| | 2009-07-28 | saam | Correct size of copied memory in memcpy (float->double).
* src/QMTimestep.C 1.52 (changed +2 -2)
Fixed range check for get_orbital_index_from_id()
* src/QMTimestep.C 1.55 (changed +3 -3)
Proper handling of charges.
Eliminated per-molecule charges (ESP) even though some of them are
per-molecule in GAMESS. Instead we have a number of charge sets with
an type associated type per timestep. These can either be empty or
populated.
Actually we will need at some point another level in our data
structures:
each timstep can have N electronic configurations. Each configuration
can have an optional wavefunction associated and other
optional properties like charge sets.
* src/TclMolInfo.C 1.83 (changed +22 -2)
* src/QMTimestep.h 1.32 (changed +21 -5)
* src/QMTimestep.C 1.53 (changed +68 -11)
* src/QMData.h 1.68 (changed +1 -4)
* src/QMData.C 1.78 (changed +6 -10)
* src/MolFilePlugin.C 1.155 (changed +21 -9)
Use orbital ID consistently instead of orbital label.
* src/QMData.C 1.79 (changed +7 -7)
* src/DrawMolItemOrbital.C 1.39 (changed +2 -2)
|
| | 2009-07-28 | johns | Added comments about Orbital GUI update logic, and fixed the behavior
of the orbital GUI when the "apply changes automatically" control is
unchecked.
* src/GraphicsFltkMenu.C 1.144 (changed +11 -4)
Added lots of comments to the excitation and orbital chooser regeneration
routines, since they contain lots of indexing and mapping calculations
that convert between 1-based QM data and 0-based GUI elements in many places.
* src/GraphicsFltkReps.h 1.102 (changed +14 -9)
Call get_orbital_index_from_id() to convert from monotonically increasing
1-based orbital IDs to the internal orbital indices used in a given timestep.
* src/DrawMolItemOrbital.C 1.37 (changed +6 -17)
Don't accept orbital ID of zero
* src/DrawMolItemOrbital.C 1.38 (changed +3 -3)
Enabled new orbital list subset control, so that complex electronic structures
with hundreds of orbitals don't overwhelm the GUI choosers. The user can
change the orbital index range of interest and select from the list of
+-10 orbitals from the "list center".
* src/GraphicsFltkReps.h 1.101 (changed +72 -32)
* src/GraphicsFltkMenu.C 1.143 (changed +4 -1)
Fixed handling of 1-based orbital ID parameter
* src/QMTimestep.C 1.54 (changed +3 -3)
Removed old orbital GUI selector code
* src/GraphicsFltkMenu.C 1.145 (changed +2 -32)
Repositioned orbital rep controls based on user feedback (AK)
* src/GraphicsFltkReps.h 1.103 (changed +5 -6)
Updates to orbital indexing logic
* src/GraphicsFltkReps.h 1.104 (changed +9 -9)
|
| | 2009-07-27 | saam | Silence ILS debugging output for the release.
* src/VolMapCreateILS.C 1.158 (changed +3 -3)
* src/CUDAVolMapCreateILS.cu 1.44 (changed +26 -2)
|
| | 2009-07-25 | saam | Cleanup.
* src/MeasureSymmetry.h 1.30 (changed +11 -2)
* src/MeasureSymmetry.C 1.50 (changed +88 -88)
Extended documentation for measure symmetry.
* doc/ug_text_ui.tex 1.218 (changed +32 -5)
|
| | 2009-07-25 | akohlmey | Protect csh version of the vmd launch script to look for rlwrap
on any other platform than LINUX and LINUXAMD64, as others,
particularly AIX seem to have issues...
* bin/vmd.csh 1.90 (changed +11 -10)
|
| | 2009-07-24 | saam | Added code to handle the case where we have a Cn pointgroup but no
central atom ad no unique axes of inertia.
* src/MeasureSymmetry.h 1.29 (changed +6 -5)
* src/MeasureSymmetry.C 1.49 (changed +246 -19)
|
| | 2009-07-23 | saam | Added options to impose given symmetry elements on the structure.
It will wrap the atoms around these elements and average the coordinates
of the atoms and its images.
Added option -idealsel that allows to specify a second selection. The
symmetry search will be performed on the regular selection but then the
found symmetry elements will be imposed on the second selection an the
search is repeated with that second selection. This allows for example
to perform the symmetry guess on a selection without hydrogens which
point in random directions for rotable groups but still get the ideal
coordinates and unique atoms for the entire structure (in this case
the idealsel selection). idealsel must be a superset of sel.
* src/TclMeasure.C 1.136 (changed +276 -53)
* src/MeasureSymmetry.h 1.28 (changed +12 -2)
* src/MeasureSymmetry.C 1.47 (changed +118 -19)
Improve some comments.
* src/MeasureSymmetry.C 1.48 (changed +7 -3)
|
| | 2009-07-23 | johns | Align horizontal position of the orbital chooser with the excitation chooser
* src/GraphicsFltkReps.h 1.98 (changed +2 -2)
Set IsoSurface rep text command parameter types for easier interpretation
of saved state files
* src/GraphicsFltkReps.h 1.100 (changed +5 -5)
Set Orbital rep output precision and types for easier interpretation
* src/GraphicsFltkReps.h 1.99 (changed +5 -5)
Set default orbital isovalue to 0.05
* src/GraphicsFltkReps.h 1.97 (changed +2 -1)
|
| | 2009-07-22 | saam | Added function to query if a certain orbital ID exists in any frame in
the given wavefunction.
* src/QMData.h 1.67 (changed +5 -1)
* src/QMData.C 1.77 (changed +14 -1)
|
| | 2009-07-22 | johns | Don't used pinned memory for atom position/charge data in the multi-GPU
Coulomb kernel until future drivers have completely cured race conditions
with cudaMallocHost()/cudaFreeHost() in multi-GPU codes.
* src/CUDAVolCPotential.cu 1.37 (changed +2 -2)
Dynamically regenerate the list of excitations when the user
selects a different wavefunction type
* src/GraphicsFltkReps.h 1.94 (changed +56 -4)
* src/GraphicsFltkMenu.C 1.142 (changed +5 -1)
Make orbital indices active/inactive in the GUI depending on whether they
exist in any loaded frame for the selected wavefunction type, spin, and
excitation.
* src/GraphicsFltkReps.h 1.96 (changed +12 -2)
Reactivate orbitallist control in all cases
* src/GraphicsFltkReps.h 1.95 (changed +2 -1)
|
| | 2009-07-21 | saam | Improve code docs.
* src/MeasureSymmetry.h 1.24 (changed +3 -6)
* src/MeasureSymmetry.C 1.43 (changed +30 -7)
Improved code documentation for measure symmetry.
* src/TclMeasure.C 1.134 (changed +84 -31)
More docs.
* src/MeasureSymmetry.h 1.26 (changed +8 -6)
* src/MeasureSymmetry.C 1.45 (changed +12 -8)
Moved two #defines back into MeasureSymmetry.h. (Oops)
Updated Usage message for measure symmetry.
* src/TclMeasure.C 1.135 (changed +3 -6)
* src/MeasureSymmetry.h 1.25 (changed +9 -1)
* src/MeasureSymmetry.C 1.44 (changed +1 -10)
Tons of documentation.
* src/MeasureSymmetry.h 1.27 (changed +4 -3)
* src/MeasureSymmetry.C 1.46 (changed +58 -27)
Update/add documentation for
measure inertia and measure symmetry.
* doc/ug_text_ui.tex 1.216 (changed +126 -29)
|
| | 2009-07-21 | johns | Added new "imd copyunitcell" command to cause the IMD code to copy the
previous timestep's unit cell information rather than leaving it
uninitialized. This is helpful for demos that want to show the
periodic cell, until such time as we update the IMD protocol to actually
send/receive unit cell information.
* src/cmd_imd.C 1.23 (changed +16 -6)
* src/IMDMgr.h 1.23 (changed +5 -1)
* src/IMDMgr.C 1.39 (changed +24 -14)
* src/Command.h 1.165 (changed +2 -2)
* src/CmdIMD.h 1.24 (changed +15 -2)
* src/CmdIMD.C 1.29 (changed +9 -1)
Applied Simon's patch that adds C2, C2' and C_2 to the list of
names that are considered for the first atom after the oxygen.
* src/BaseMolecule.C 1.240 (changed +11 -3)
|
| | 2009-07-21 | akohlmey | Add documentation for the "imd copyunitcell" hack.
* doc/ug_text_ui.tex 1.217 (changed +12 -1)
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