| Tags | Date | Developer | Last 200 Commit Logs |
|---|
| | 2008-07-01 | kvandivo | Added docs for the bond/angle extraction
* cgtools/doc/select.jpg 1.4 (changed +132 -122)
* cgtools/doc/sbcg-baExtract.jpg 1.1 (added +139 -0)
* cgtools/doc/index.html 1.16 (changed +51 -0)
|
| | 2008-06-30 | kvandivo | Added a script that i've tweaked from anton that extracts values for
bond and angle parameters of a CG molecule from an all-atom simulation
of the same molecule.
* cgtools/pkgIndex.tcl 1.8 (changed +2 -2)
* cgtools/cgnetworking.tcl 1.16 (changed +418 -1)
* cgtools/cggui.tcl 1.31 (changed +171 -3)
|
| | 2008-06-30 | brunner | Fixed some problem in the addMaterial interface
* inorganicbuilder/inorganicbuilder.tcl 1.42 (changed +22 -7)
|
| | 2008-06-25 | johns | Fixed unprotected modification to the plugin ABI
* include/molfile_plugin.h 1.48 (changed +4 -2)
|
| | 2008-06-24 | kvandivo | Cleaned up some code that wasn't deleting selections. also code that
was unnecessarily creation atomselect macros.
* cgtools/cgtools.tcl 1.12 (changed +22 -14)
|
| | 2008-06-21 | saam | Added parameter scfiter to struct molfile_qm_timestep_t.
In a QM simulation for each trajectory point (i.e. optimization step)
a number of SCF iterations is performed until the energy converges for this
geometry. If we want to make use of the stored scfenergies for a given timestep we
also have to store the number of iteration for the timestep.
* include/molfile_plugin.h 1.47 (changed +2 -1)
|
| | 2008-06-20 | johns | Applied Olaf's bug fixes to correct for 'segid' rather than 'segment'.
* pbctools/pbcwrap.tcl 1.8 (changed +2 -1)
* pbctools/pbcunwrap.tcl 1.7 (changed +0 -0)
* pbctools/pbctools.tcl 1.7 (changed +0 -0)
* pbctools/pbcset.tcl 1.8 (changed +5 -4)
* pbctools/pbcjoin.tcl 1.6 (changed +6 -5)
* pbctools/pbcbox.tcl 1.8 (changed +0 -0)
* pbctools/doc/index.html 1.7 (changed +2 -2)
* pbctools/doc/ChangeLog 1.5 (changed +6 -0)
|
| | 2008-06-18 | brunner | Added a help button and text and image for docs
* mergestructs/mergestructs.tcl 1.4 (changed +3 -1)
* mergestructs/doc/mergewin.png 1.1 (added +122 -0)
* mergestructs/doc/index.html 1.3 (changed +8 -5)
Added docs and image files for docs
* inorganicbuilder/doc/index.html 1.5 (changed +80 -63)
* inorganicbuilder/doc/ib-surface.png 1.1 (added +175 -0)
* inorganicbuilder/doc/ib-start.png 1.1 (added +134 -0)
* inorganicbuilder/doc/ib-solvate.png 1.2 (changed +138 -162)
* inorganicbuilder/doc/ib-newmat.png 1.1 (added +140 -0)
* inorganicbuilder/doc/ib-build.png 1.2 (changed +226 -181)
* inorganicbuilder/doc/ib-bonds.png 1.1 (added +360 -0)
|
| | 2008-06-16 | saam | Fixed bug that would prevent proper reading of # of processors and memory for some versions of
GAMESS.
Added a debugging output function that makes it easy to compare what's in the file and
what was read.
The basis set info is now read by default, before it was only read for single point runs.
* molfile_plugin/src/gamessplugin.h 1.35 (changed +4 -2)
* molfile_plugin/src/gamessplugin.c 1.68 (changed +99 -7)
Making all functions static since they are not supposed to be used elsewhere.
* molfile_plugin/src/gamessplugin.h 1.36 (changed +7 -7)
* molfile_plugin/src/gamessplugin.c 1.69 (changed +20 -21)
|
| | 2008-06-15 | johns | Added a 64-bit build with Intel C/C++, CUDA, etc.
* cionize/Makefile.specialbuilds 1.21 (changed +18 -0)
Open the GPU device prior to starting timers, as there can be an
artificial delay during the first open call depending on whether
or not X-windows is running.
* cionize/mgpot_setup.c 1.12 (changed +2 -1)
* cionize/mgpot_defn.h 1.15 (changed +1 -0)
* cionize/mgpot.c 1.18 (changed +7 -1)
|
| | 2008-06-15 | dhardy | Added BENCH statements for profiling
* cionize/mgpot_shortrng.c 1.17 (changed +26 -0)
* cionize/mgpot_cubic.c 1.13 (changed +14 -0)
* cionize/mgpot.c 1.17 (changed +3 -0)
|
| | 2008-06-14 | johns | Eliminated Intel C/C++ libimf.so dependency
* cionize/Makefile.specialbuilds 1.20 (changed +9 -6)
Eliminated the Intel C/C++ libimf.so dependency
* cionize/Makefile.specialbuilds 1.19 (changed +1 -1)
|
| | 2008-06-13 | johns | Eliminated include of cutil.h so we can compile with MCUDA
* cionize/mgpot_cuda_shortrng.cu 1.12 (changed +0 -1)
* cionize/cudaenergythr.cu 1.11 (changed +1 -2)
|
| | 2008-06-13 | dhardy | *** empty log message ***
* cionize/mgpot_cubic.c 1.12 (changed +2 -1)
Added data for sequential short-range part, geometric hashing
* cionize/mgpot_defn.h 1.13 (changed +23 -1)
Added mgpot_cuda_binlarge.cu
removed -DMGPOT_GEOMHASH because it is now defined internally
* cionize/Makefile.specialbuilds 1.17 (changed +12 -4)
Added setup and cleanup routines for cuda short-range and long-range parts
* cionize/mgpot_cuda.h 1.8 (changed +23 -0)
* cionize/mgpot.c 1.16 (changed +24 -8)
Added setup and cleanup routines for cuda short-range and long-range parts,
factored large bin kernel into setup/cleanup and pre/post calls
* cionize/mgpot_cuda_setup.cu 1.9 (changed +256 -6)
Added small bin kernel
* cionize/mgpot_shortrng.c 1.16 (changed +24 -2)
* cionize/mgpot_defn.h 1.14 (changed +16 -8)
* cionize/mgpot_cutoff_cpu.c 1.1 (added +227 -0)
* cionize/mgpot_cuda_setup.cu 1.10 (changed +4 -2)
* cionize/mgpot_cuda_binsmall.cu 1.1 (added +621 -0)
* cionize/mgpot_cuda_binlarge.cu 1.2 (changed +0 -1)
* cionize/mgpot_cuda.h 1.9 (changed +10 -4)
* cionize/Makefile.specialbuilds 1.18 (changed +12 -1)
Factored setup/cleanup for geometric hashing from short-range routine
* cionize/mgpot_setup.c 1.11 (changed +63 -3)
Factored short-range part into a driver routine that calls either
some CUDA kernel or an optimized sequential version or a fallback version
* cionize/mgpot_shortrng.c 1.15 (changed +90 -114)
Fixed bug that fortunately never manifested itself
* cionize/mgpot_longrng.c 1.6 (changed +1 -1)
Mgpot_cuda_binlarge.cu is factored version of mgpot_cuda_shortrange.cu
* cionize/mgpot_cuda_binlarge.cu 1.1 (added +368 -0)
|
| | 2008-06-12 | johns | Added new 'linux-icc-cuda-thr' build target
* cionize/Makefile.specialbuilds 1.14 (changed +17 -0)
Updated Makefile.specialbuilds to use our CUDA 1.1 install by default.
* cionize/Makefile.specialbuilds 1.15 (changed +8 -8)
|
| | 2008-06-12 | dhardy | Modified clean and added veryclean targets
* cionize/Makefile.specialbuilds 1.16 (changed +8 -0)
Rearranged data structures and routines to prepare for short range cuda kernels
* cionize/mgpot_shortrng.c 1.14 (changed +10 -3)
* cionize/mgpot_setup.c 1.10 (changed +29 -11)
* cionize/mgpot_quintic1.c 1.4 (changed +1 -3)
* cionize/mgpot_longrng.c 1.5 (changed +17 -9)
* cionize/mgpot_defn.h 1.12 (changed +69 -22)
* cionize/mgpot_cuda_shortrng.cu 1.11 (changed +2 -2)
* cionize/mgpot_cuda.h 1.7 (changed +1 -1)
* cionize/mgpot_cubic.c 1.11 (changed +12 -7)
* cionize/mgpot.c 1.15 (changed +10 -39)
* cionize/cionize_userio.c 1.10 (changed +6 -6)
* cionize/cionize_enermethods.h 1.6 (changed +3 -3)
Some loop unrolling combined with shared memory copying to reduce global
memory copying gives significant performance improvements on both
the GT200 and Tesla even though the register count swells from 40 to 58.
* cionize/mgpot_cuda_latcut04.cu 1.2 (changed +163 -5)
|
mgpot_cuda_lattice_cutoff_2
mgpot_cuda_lattice_cutoff_1
| 2008-06-11 | dhardy | Attempted many optimizations in latcut03.
major optimizations:
SHMEMCOPY - Copy half the amount of subcubes from global memory on each
inner loop iteration and shift the shared memory storage.
This does not decrease time and it uses more registers.
SHIFT - Replace int multiplication by int powers of 2 by bit shifts.
This uses 3 fewer registers but slows down computation on
both Tesla and GT200 cards.
CPARM - Read srad and padding from constant memory rather than
passing them as parameters. This does not change the
register use and does not appear to change the time.
minor optimizations:
WTRAD - Pre-compute (8*srad) appearing in inner loop. Doesn't make
a difference to runtime or register use.
THRIDX - Change tx, ty, and tz to macro expansions of threadIdx.x,
etc., rather than variables. Doesn't make a difference.
built in:
- Calculate "tid = (tz*4 + ty)*4 + tx" as flat thread ID
outside of the main loops, rather than inside as "isrc",
since tx, ty, and tz don't change. Also reuse at end
of kernel for indexing global memory potential to write.
Doesn't seem to make a difference.
* cionize/mgpot_cuda_latcut03.cu 1.1 (added +296 -0)
* cionize/mgpot_cuda.h 1.5 (changed +4 -2)
* cionize/mgpot_cubic.c 1.9 (changed +8 -0)
* cionize/cionize_userio.c 1.8 (changed +5 -0)
* cionize/cionize_enermethods.h 1.4 (changed +1 -0)
* cionize/Makefile.specialbuilds 1.12 (changed +8 -0)
Changed text output title
* cionize/mgpot.c 1.14 (changed +1 -1)
Debugging code
* cionize/mgpot_cubic.c 1.6 (changed +126 -0)
Generate cubin output for cuda files
* cionize/Makefile.specialbuilds 1.11 (changed +48 -9)
Latcut02 is cleaned up copy of latcut01
* cionize/mgpot_cuda_latcut02.cu 1.1 (added +183 -0)
* cionize/Makefile.specialbuilds 1.10 (changed +4 -0)
Lattice cutoff computation on GPU works.
Requires padding around all edges with one layer of 0-charge subcubes.
For now, each thread block corresponds to a subcube; test for early
termination if subcube is padding.
* cionize/mgpot_cuda_setup.cu 1.5 (changed +30 -26)
* cionize/mgpot_cuda_latcut01.cu 1.4 (changed +36 -0)
Minor change to text output
* cionize/mgpot_cuda_setup.cu 1.8 (changed +3 -2)
Select mgpot cuda kernels from command line
* cionize/mgpot_setup.c 1.9 (changed +6 -5)
* cionize/mgpot_defn.h 1.10 (changed +3 -2)
* cionize/mgpot_cuda_setup.cu 1.6 (changed +8 -0)
* cionize/mgpot_cubic.c 1.7 (changed +9 -6)
* cionize/mgpot.h 1.2 (changed +2 -1)
* cionize/mgpot.c 1.13 (changed +12 -7)
* cionize/cionize_userio.h 1.3 (changed +1 -1)
* cionize/cionize_userio.c 1.7 (changed +85 -24)
* cionize/cionize_enermethods.h 1.3 (changed +32 -5)
* cionize/cionize.c 1.34 (changed +4 -3)
Thread blocks are no longer assigned to padding subcubes
* cionize/mgpot_defn.h 1.11 (changed +2 -0)
* cionize/mgpot_cuda_setup.cu 1.7 (changed +47 -27)
* cionize/mgpot_cuda_latcut01.cu 1.5 (changed +29 -19)
* cionize/mgpot_cuda.h 1.4 (changed +1 -0)
* cionize/mgpot_cubic.c 1.8 (changed +5 -0)
Use latcut04 to experiment with loop unrolling
* cionize/mgpot_cuda_latcut04.cu 1.1 (added +183 -0)
* cionize/mgpot_cuda.h 1.6 (changed +1 -0)
* cionize/mgpot_cubic.c 1.10 (changed +6 -0)
* cionize/cionize_userio.c 1.9 (changed +5 -0)
* cionize/cionize_enermethods.h 1.5 (changed +1 -0)
* cionize/Makefile.specialbuilds 1.13 (changed +8 -0)
|
| | 2008-06-10 | saam | Increased maximum number of bonds to 16.
* molfile_plugin/src/xbgfplugin.C 1.28 (changed +11 -10)
|
| | 2008-06-10 | dhardy | Build cuda in emulation mode
* cionize/Makefile.specialbuilds 1.9 (changed +14 -0)
Cosmetic
* cionize/mgpot_cubic.c 1.5 (changed +14 -14)
Debugging
* cionize/mgpot_cuda_setup.cu 1.4 (changed +16 -0)
Fixed bug with weight indexing
* cionize/mgpot_cuda_latcut01.cu 1.2 (changed +1 -1)
Fixed host to device memory copy, start index for weights, qgrid offset
* cionize/mgpot_cuda_latcut01.cu 1.3 (changed +92 -7)
Use cuda automatically
* cionize/mgpot_setup.c 1.8 (changed +1 -1)
|
| | 2008-06-09 | dhardy | Added data for lattice cutoff cuda kernel
* cionize/mgpot_defn.h 1.8 (changed +19 -0)
Clean also removes gpuionize
* cionize/Makefile.specialbuilds 1.6 (changed +2 -2)
Discovered race conditions in multi-threaded part
* cionize/mgpot.c 1.10 (changed +3 -0)
Got rid of warnings
* cionize/cionize_internals.c 1.8 (changed +5 -5)
* cionize/cionize.c 1.33 (changed +2 -2)
In progress
* cionize/mgpot_shortrng.c 1.13 (changed +1 -1)
* cionize/mgpot_setup.c 1.7 (changed +17 -2)
* cionize/mgpot_defn.h 1.9 (changed +1 -1)
* cionize/mgpot_cuda_shortrng.cu 1.10 (changed +1 -1)
* cionize/mgpot_cuda_setup.cu 1.3 (changed +23 -18)
* cionize/mgpot_cuda_latcut01.cu 1.1 (added +161 -0)
* cionize/mgpot_cuda.h 1.3 (changed +4 -2)
* cionize/mgpot_cubic.c 1.4 (changed +189 -86)
* cionize/mgpot.c 1.12 (changed +32 -9)
* cionize/Makefile.specialbuilds 1.8 (changed +7 -3)
Lattice cutoff cuda kernel setup/cleanup and condense/expand routines
* cionize/mgpot_cuda_setup.cu 1.2 (changed +221 -0)
* cionize/mgpot_cuda.h 1.2 (changed +10 -0)
Preparation for introducing additional cuda kernels
* cionize/mgpot_shortrng.c 1.12 (changed +17 -13)
* cionize/mgpot_defn.h 1.7 (changed +0 -5)
* cionize/mgpot_cuda_shortrng.cu 1.9 (changed +8 -3)
* cionize/mgpot_cuda_setup.cu 1.1 (added +32 -0)
* cionize/mgpot_cuda.h 1.1 (added +41 -0)
* cionize/mgpot.c 1.11 (changed +24 -0)
* cionize/Makefile.specialbuilds 1.7 (changed +5 -1)
|
| | 2008-06-09 | barryi | Fixed paste-typo bug.
* timeline/timeline.tcl 1.49 (changed +2 -4)
|
| | 2008-06-08 | johns | Added a build setting just for CUDA test compiles of 'cionize'
* build.csh 1.75 (changed +14 -1)
|
| | 2008-06-08 | dhardy | Added clean target
* cionize/Makefile.specialbuilds 1.5 (changed +8 -0)
Removed all calls to abort(). Now errors in MGPOT propagate back and
return an error value to the top level calling routine.
* cionize/mgpot_split.h 1.2 (changed +2 -2)
* cionize/mgpot_shortrng.c 1.11 (changed +15 -3)
* cionize/mgpot_setup.c 1.6 (changed +14 -20)
* cionize/mgpot_quintic1.c 1.3 (changed +2 -2)
* cionize/mgpot_longrng.c 1.4 (changed +11 -7)
* cionize/mgpot_lattice.h 1.3 (changed +5 -5)
* cionize/mgpot_error.h 1.2 (changed +1 -1)
* cionize/mgpot_defn.h 1.6 (changed +5 -5)
* cionize/mgpot_cuda_shortrng.cu 1.8 (changed +8 -5)
* cionize/mgpot_cubic.c 1.3 (changed +35 -22)
* cionize/mgpot.c 1.9 (changed +26 -10)
* cionize/binary_gridio.c 1.3 (changed +1 -1)
|
| | 2008-06-05 | johns | Updated URL for check sidechains plugin home page
* doc/index.html 1.71 (changed +1 -1)
|
| | 2008-06-05 | gumbart | Forgot to change back name used during testing (autoionize1 vs. autoionize)
* autoionize/autoionize.tcl 1.13 (changed +2 -2)
|
| | 2008-06-02 | johns | Added a 64-bit build target for MacOS X, so we can do text-only and X11-based
builds, despite the lack of a 64-bit Carbon framework that we'd otherwise
use for a native aqua version of Tcl/Tk. For now, all 64-bit MacOS X builds
have to use X11 or be text-only.
* vmdmovie/vmdmovie.tcl 1.101 (changed +3 -2)
* build.csh 1.74 (changed +5 -0)
* apbsrun/apbsrun.tcl 1.136 (changed +2 -1)
* Make-arch 1.63 (changed +18 -0)
|
| | 2008-06-02 | gumbart | Okay, I also learned to change the version number in this file at the same
time as changing it in the plugin itself...
* autoionize/pkgIndex.tcl 1.6 (changed +1 -1)
|
| | 2008-06-02 | barryi | All-residue user-defined function via entering function name (function must exist somewhere, can be in any name space)
Definable analysis frame range
Default user definable function set, exisits in global namespace. (May change this to very-unlikely name, but should keep as instructs user).
* timeline/timeline.tcl 1.48 (changed +153 -193)
|
| | 2008-06-01 | petefred | Change resolution of dihedral slider
* molefacture/molefacture_gui.tcl 1.41 (changed +1 -1)
Change tickmark size in dihedral slider
* molefacture/molefacture_gui.tcl 1.42 (changed +1 -1)
|
| | 2008-06-01 | johns | Added CVS id tag to makefile
* molfile_plugin/Makefile 1.89 (changed +1 -0)
Added the 'jsplugin' fast trajectory format to the default builds
* molfile_plugin/Makefile 1.90 (changed +14 -4)
|
| | 2008-05-30 | petefred | Fix protein cgc file to include glycine hydrogens in with the backbone bead
* cgtools/protein.cgc 1.3 (changed +2 -1)
|
| | 2008-05-29 | brunner | First draft of docs
* mergestructs/doc/index.html 1.2 (changed +24 -1)
Improved the text in several dialog boxes
* mergestructs/mergestructs.tcl 1.3 (changed +33 -7)
|
| | 2008-05-23 | johns | Updates for Solaris x86 builds
* build.csh 1.73 (changed +2 -2)
* Make-arch 1.62 (changed +0 -2)
|
| | 2008-05-22 | saam | Corrected a comment.
* utilities/utilities.tcl 1.3 (changed +1 -1)
Fixed small bug in the Gaussian file reader.
Added comments.
* qmtool/qmtool_readwrite.tcl 1.44 (changed +7 -7)
* qmtool/qmtool_aux.tcl 1.23 (changed +3 -1)
Improved a comment.
* moltoptools/moltoptools.tcl 1.2 (changed +2 -1)
|
| | 2008-05-22 | johns | Added casablanca to build script
* build.csh 1.72 (changed +1 -0)
|
| | 2008-05-21 | petefred | Allow user to keep charges if desired
* runante/runante.tcl 1.2 (changed +43 -5)
Modify opls typing to not overwrite current charges
* molefacture/molefacture_gui.tcl 1.40 (changed +1 -1)
|
| | 2008-05-12 | barryi | Update combining several checkins from (personally maintained) svn, much cleaner, but not such a major resturcture that greatly helped by multi-checkins to CVS.
features: "free selections" (arbitart selections, Hh-bonds provided as example), user-defined per-residue functions (e.g. measure contacts)
coding: generic per-res property and delta-per-res (e.g. done slightly sanely) ; switchable debug messages (via function edit)
Problems: Features slow and hard to use for users, but need to get some
feedback on borken things, so must checkin. Hope to get things presentable /
usable in next days .
Needed: Merge performance, interface for builtin/user-defined functions so one way to register functions. GUI / text UI to show which loaded / available at startup. Move user-defined per-residue to name-of-function via type in function, provide test option on tiny selection (provide adhjustable guess)
Debug silencing via proc in place
* timeline/timeline.tcl 1.47 (changed +777 -249)
|
| | 2008-05-08 | gumbart | Fixed painfully slow inner loop that selects waters to replace, speedup of at least a factor of 10
* autoionize/autoionize.tcl 1.12 (changed +26 -17)
|
| | 2008-05-07 | petefred | Fix bug reported by Jan with residue name lengths
* molefacture/molefacture_builder.tcl 1.27 (changed +1 -1)
|
| | 2008-05-05 | petefred | Add some extra aliasing for nucleotides suggested by leo
* autopsf/autopsf.tcl 1.108 (changed +3 -1)
|
| | 2008-05-02 | gumbart | *** empty log message ***
* hbonds/doc/index.html 1.2 (changed +47 -0)
* hbonds/doc/hbonds.png 1.1 (added +153 -0)
|
| | 2008-04-29 | kvandivo | Doc changes based on anton's suggestions/additions.
* cgtools/doc/index.html 1.15 (changed +120 -40)
|
| | 2008-04-28 | kvandivo | Added an option to ssign Lennard-Jones parameters for a shape based
coarse-grained structure based on the all-atom one from Anton.
Also added docs for said option, as well as docs for the mapping code
that I'd added a while back (but hadn't gotten the docs in for yet)
* cgtools/pkgIndex.tcl 1.7 (changed +2 -2)
* cgtools/doc/select.jpg 1.3 (changed +124 -58)
* cgtools/doc/sbcg-mapping.jpg 1.1 (added +68 -0)
* cgtools/doc/sbcg-ljPotential.jpg 1.1 (added +120 -0)
* cgtools/doc/index.html 1.14 (changed +108 -20)
* cgtools/doc/cgToAa.jpg 1.3 (changed +126 -460)
* cgtools/cgtools.tcl 1.11 (changed +149 -4)
* cgtools/cggui.tcl 1.30 (changed +250 -82)
|
| | 2008-04-20 | johns | Added notes file to docs subdirectory, with informal todo list, people
assignments for plugins, etc.
* doc/notes.txt 1.1 (added +331 -0)
|
| | 2008-04-19 | ltrabuco | Set menubutton width to avoid truncation in OS X.
* multimolanim/multimolanim.tcl 1.3 (changed +3 -0)
* molefacture/molefacture_gui.tcl 1.39 (changed +4 -2)
* irspecgui/irspecgui.tcl 1.9 (changed +4 -0)
* gofrgui/gofrgui.tcl 1.6 (changed +5 -0)
* dowser/dowser_gui.tcl 1.6 (changed +4 -0)
* dipwatch/dipwatch.tcl 1.3 (changed +3 -0)
* contactmap/contactmap.tcl 1.45 (changed +3 -1)
* colorscalebar/colorscalebar.tcl 1.19 (changed +3 -1)
* clonerep/clonerep.tcl 1.8 (changed +3 -0)
|
| | 2008-04-18 | saam | Corrected wrong comments:
* pbctools/pbcset.tcl 1.7 (changed +4 -5)
|
| | 2008-04-15 | kvandivo | Made the error message more descriptive when a login fails
* biocore/biocorelogin.tcl 1.25 (changed +8 -7)
|
| | 2008-04-11 | johns | Fixed documentation for exectool, which was still using the old namespace
* exectool/doc/index.html 1.7 (changed +2 -2)
|
| | 2008-04-03 | ltrabuco | Added a missing period.
* molfile_plugin/doc/xsfplugin.html 1.7 (changed +1 -1)
Added a missing space.
* molfile_plugin/doc/ccp4plugin.html 1.8 (changed +1 -1)
|
| | 2008-04-03 | johns | Updated pbctools makefile for the current version number
* pbctools/Makefile 1.4 (changed +1 -1)
Updated to pbctools version 2.2, based on the latest source and
documentation updates from Olaf Lenz.
* pbctools/pkgIndex.tcl 1.4 (changed +1 -1)
* pbctools/pbcwrap.tcl 1.7 (changed +3 -3)
* pbctools/pbcunwrap.tcl 1.6 (changed +1 -1)
* pbctools/pbctools.tcl 1.6 (changed +1 -1)
* pbctools/pbcset.tcl 1.6 (changed +1 -1)
* pbctools/pbcjoin.tcl 1.5 (changed +1 -1)
* pbctools/pbcbox.tcl 1.7 (changed +1 -1)
* pbctools/doc/index.html 1.6 (changed +6 -6)
* pbctools/doc/ChangeLog 1.4 (changed +9 -0)
|
| | 2008-04-01 | johns | Added new "plugin development best practices" document.
* doc/plg_mainpage.dox 1.8 (changed +2 -1)
* doc/plg_bestpractices.dox 1.1 (added +61 -0)
Doc tweaks
* doc/plg_mainpage.dox 1.9 (changed +2 -2)
* doc/plg_mainpage.dox 1.10 (changed +8 -1)
* doc/plg_bestpractices.dox 1.2 (changed +3 -3)
Doxygen doesn't correctly process list header HTML tags, so we'll
reformat things a bit.
* doc/plg_mainpage.dox 1.11 (changed +3 -4)
|
| | 2008-03-31 | johns | Added CVS ID tags to all of the plugin programmer's docs.
* doc/plg_tcltk.dox 1.6 (changed +3 -0)
* doc/plg_python.dox 1.3 (changed +2 -0)
* doc/plg_molfile_calling.dox 1.2 (changed +3 -0)
* doc/plg_molfile.dox 1.6 (changed +3 -0)
* doc/plg_mainpage.dox 1.6 (changed +4 -1)
* doc/plg_intro.dox 1.3 (changed +3 -0)
* doc/plg_filestruct.dox 1.3 (changed +4 -1)
* doc/plg_compiling.dox 1.7 (changed +4 -1)
Added basic info about the intracies of shared library handling on
Unix and Windows, with practical examples of why we do things the way
we do in the VMD plugin system.
* doc/plg_sharedlibs.dox 1.1 (added +95 -0)
Added shared libraries info
* doc/plg_mainpage.dox 1.7 (changed +2 -1)
|
| | 2008-03-28 | ltrabuco | Add rnaview docs.
* rnaview/doc/index.html 1.1 (added +18 -0)
Added rnaview plugin, which calls the external program RNAView and parses
its output, creating a bpseq file with base pair information (or an
extended bpseq file with a classification of the base pairs). This is
simply a helper plugin to be used by ssrestraints at the moment.
* rnaview/rnaview.tcl 1.1 (added +250 -0)
* rnaview/pkgIndex.tcl 1.1 (added +16 -0)
* rnaview/Makefile 1.1 (added +23 -0)
Added ssrestraints and rnaview to Makefile.
* Makefile 1.95 (changed +3 -1)
Added ssrestraints plugin, used to create an extraBonds file for NAMD to
restrain secondary structure of proteins or nucleic acids in a simulation.
* ssrestraints/ssrestraints.tcl 1.1 (added +801 -0)
* ssrestraints/pkgIndex.tcl 1.1 (added +16 -0)
* ssrestraints/doc/index.html 1.1 (added +56 -0)
* ssrestraints/Makefile 1.1 (added +23 -0)
|
| | 2008-03-25 | johns | Olaf's fixes to vtfplugin correcting linkage scope of the internal
plugin functions.
* molfile_plugin/src/vtfplugin.c 1.8 (changed +17 -24)
|
| | 2008-03-20 | petefred | Add option to type for opls
* molefacture/molefacture_gui.tcl 1.37 (changed +12 -0)
* molefacture/lib/ATOMTYPE_OPLS.DEF 1.1 (added +225 -0)
Fix the tert-butyl fragment, which had some incorrect bonds
* molefacture/lib/fragments/tbutyl.mfrag 1.2 (changed +12 -12)
Start using measure commands instead of labels where possible to speed things up
* molefacture/molefacture_internals.tcl 1.30 (changed +2 -7)
* molefacture/molefacture_gui.tcl 1.38 (changed +12 -9)
* molefacture/molefacture_geometry.tcl 1.18 (changed +2 -6)
* molefacture/molefacture_builder.tcl 1.26 (changed +6 -22)
|
| | 2008-03-15 | johns | New version of vtfplugin from Olaf Lenz.
* molfile_plugin/src/vtfplugin.c 1.7 (changed +25 -8)
|
| | 2008-03-11 | petefred | Add ability to turn off switching
* namdenergy/namdenergy.tcl 1.52 (changed +9 -2)
* namdenergy/doc/index.html 1.12 (changed +1 -1)
|
| | 2008-03-04 | kvandivo | Scripta -> script
* doc/plg_compiling.dox 1.6 (changed +1 -1)
|
| | 2008-02-29 | johns | Applied Axel Kohlmeyer's patch for the LAMMPS plugin to allow it to
correctly interpret both absolute and fractional atom coordinates.
* molfile_plugin/src/lammpsplugin.c 1.21 (changed +26 -8)
|
| | 2008-02-21 | kvandivo | Fixed a bug that anton found where the output status wasn't being put
into the box correctly (and was throwing an error instead)
* cgtools/cggui.tcl 1.29 (changed +3 -2)
|
| | 2008-02-20 | petefred | *** empty log message ***
* molfile_plugin/src/mol2plugin.C 1.30 (changed +10 -10)
* molfile_plugin/src/gamessplugin.c 1.66 (changed +5 -1)
Add FEP features to molefacture from Jonathan Degois
The implementation will likely be changed in the future to make
it more user friendly
* molefacture/molefacture_state.tcl 1.13 (changed +66 -0)
* molefacture/molefacture_internals.tcl 1.29 (changed +143 -1)
* molefacture/molefacture_gui.tcl 1.35 (changed +105 -0)
* molefacture/molefacture_edit.tcl 1.7 (changed +31 -0)
* molefacture/molefacture_builder.tcl 1.25 (changed +11 -1)
Add antechamber plugin
* runante/runante.tcl 1.1 (added +274 -0)
* runante/pkgIndex.tcl 1.1 (added +16 -0)
* runante/Makefile 1.1 (added +21 -0)
* Makefile 1.94 (changed +1 -0)
Add hooks to antechamber
* molefacture/molefacture_gui.tcl 1.36 (changed +20 -1)
* molefacture/molefacture.tcl 1.92 (changed +2 -1)
Fix bond order reading for 'ar' bonds
* molfile_plugin/src/mol2plugin.C 1.31 (changed +5 -30)
Fix the proline parent fragment
* molefacture/lib/amino_acids/PRO.mfrag 1.4 (changed +3 -0)
Roll back accidental change to gamessplugin.c
* molfile_plugin/src/gamessplugin.c 1.67 (changed +1 -5)
|
| | 2008-02-11 | kvandivo | Added in ability to map a previously generated shape based coarse grain
model onto an all atom model. This can then be called multiple times to
replicate CG models many times on a large all atom system.
Doc updates coming later to describe this in more detail.
* cgtools/cgtools.tcl 1.10 (changed +92 -0)
* cgtools/cggui.tcl 1.28 (changed +239 -42)
|
| | 2008-02-08 | petefred | Add recognition for 'ar' bond order output from antechamber
* molfile_plugin/src/mol2plugin.C 1.29 (changed +39 -8)
|
| | 2008-02-07 | petefred | Add a banner with the original idatm citation, and remove some unneccesary puts statements
* idatm/idatm.tcl 1.14 (changed +10 -3)
|
| | 2008-02-05 | petefred | Add the cyclopropane base fragment (it had been missing)
* molefacture/lib/basemol/cyclopropane.mfrag 1.1 (added +34 -0)
|
| | 2008-02-04 | ltrabuco | Fix help URL.
* dowser/dowser_gui.tcl 1.5 (changed +1 -2)
|
| | 2008-01-30 | johns | Counted FLOPS, global memory references, and conditional assignments
in the main fmtool CUDA kernel
* fmtool/time_steps_xy_to_r_cuda.cu 1.40 (changed +8 -1)
|
| | 2008-01-23 | petefred | Fix bug in writing topology files with newly added atoms
* molefacture/molefacture_state.tcl 1.12 (changed +2 -0)
|
| | 2008-01-18 | barryi | Mad less chaty on startup, marked debug messages as DEBUG, some others as Info)
* timeline/timeline.tcl 1.46 (changed +13 -15)
|
| | 2008-01-17 | brunner | Wrapped uses of psfgen in psfcontext commands, to preserve any psfgen state
the user may have created.
* inorganicbuilder/inorganicbuilder.tcl 1.41 (changed +110 -120)
|
| | 2008-01-16 | brunner | Added psfcontext commands to preserve any user psf context
* mergestructs/mergestructs.tcl 1.2 (changed +18 -16)
|
| | 2008-01-10 | kvandivo | Retrieving revision 1.14
diff -r1.14 cgnetworking.tcl
621c621
< if {$bondCutMethod == 0} {
---
> if {$bondCutMethod == 1} {
655c655
< set BBsel [atomselect top "backbone"]
---
> set BBsel [atomselect $inMolId "backbone"]
The bond determination checkbox was doing the opposite of what it
should have been. Changed the if to handle that.
Also revised an atom selection to use the molecule id being passed in
instead of always using top, per Anton.
* cgtools/cgnetworking.tcl 1.15 (changed +2 -2)
|
| | 2008-01-09 | johns | Corrected plugins that emitted diagnostic or error messages without
self-identification at the beginning of message strings.
* molfile_plugin/src/phiplugin.C 1.26 (changed +5 -5)
* molfile_plugin/src/mapplugin.C 1.12 (changed +5 -5)
* molfile_plugin/src/dxplugin.C 1.31 (changed +15 -15)
* molfile_plugin/src/avsplugin.C 1.19 (changed +28 -28)
Made diagnostic/error output conform to other plugins
* molfile_plugin/src/xsfplugin.C 1.17 (changed +6 -6)
* molfile_plugin/src/spiderplugin.C 1.14 (changed +2 -2)
* molfile_plugin/src/raster3dplugin.C 1.14 (changed +8 -8)
* molfile_plugin/src/pltplugin.C 1.12 (changed +4 -4)
* molfile_plugin/src/parmplugin.C 1.31 (changed +3 -3)
* molfile_plugin/src/parm7plugin.C 1.26 (changed +3 -3)
* molfile_plugin/src/mol2plugin.C 1.28 (changed +14 -16)
* molfile_plugin/src/mmcif.C 1.5 (changed +2 -2)
* molfile_plugin/src/mdfplugin.C 1.13 (changed +11 -11)
* molfile_plugin/src/mapplugin.C 1.13 (changed +2 -2)
* molfile_plugin/src/gromacsplugin.C 1.45 (changed +28 -27)
* molfile_plugin/src/gridplugin.C 1.13 (changed +6 -6)
* molfile_plugin/src/grdplugin.C 1.15 (changed +12 -12)
* molfile_plugin/src/fs4plugin.C 1.21 (changed +13 -13)
* molfile_plugin/src/edmplugin.C 1.30 (changed +12 -12)
* molfile_plugin/src/bgfplugin.C 1.23 (changed +3 -3)
* molfile_plugin/src/avsplugin.C 1.20 (changed +6 -6)
Made diagnostic/error output conform to the other plugins
* molfile_plugin/src/uhbdplugin.C 1.11 (changed +6 -6)
Made stlplugin error messages conform to the others
* molfile_plugin/src/stlplugin.C 1.13 (changed +11 -11)
|
| | 2008-01-04 | johns | Corrected PBCTools plugin version number
* pbctools/Makefile 1.3 (changed +1 -1)
|
| | 2008-01-03 | johns | Added Rob's mergestructs plugin
* mergestructs/pkgIndex.tcl 1.1 (added +16 -0)
* mergestructs/mergestructs.tcl 1.1 (added +970 -0)
* mergestructs/Makefile 1.1 (added +23 -0)
* Makefile 1.93 (changed +1 -0)
Added doc index
* mergestructs/doc/index.html 1.1 (added +12 -0)
|
| | 2007-12-24 | ltrabuco | Close log file before throwing an error.
* saltbr/saltbr.tcl 1.4 (changed +3 -0)
|
| | 2007-11-30 | brunner | Changed naming conventions for relabeling structures according to the number
of bonds to be "XX_#", for example SI_2. Also changed the parameter file
output to use .inp extension, even though both .par and .inp appear to
be used for parameters.
Added parameter files for sio2, asio2, and si3n4
* inorganicbuilder/materials/sio2.inp 1.1 (added +236 -0)
* inorganicbuilder/materials/si3n4.inp 1.1 (added +144 -0)
* inorganicbuilder/materials/asio2.inp 1.1 (added +236 -0)
* inorganicbuilder/inorganicbuilder.tcl 1.40 (changed +6 -7)
|
| | 2007-11-28 | brunner | I added a checkbox to the GUI so that renaming the atom types according to
the number of bonds is now optional.
* inorganicbuilder/inorganicbuilder.tcl 1.38 (changed +30 -14)
Material library now stores a parameter file name, which can be used to
copy a parameter file from the materials directory into the user's working
directory, to make it easier to set up a simulation. No files are currently
provided.
* inorganicbuilder/inorganicbuilder.tcl 1.39 (changed +62 -10)
|
| | 2007-11-27 | brunner | Added code and GUI to allow each axis to be specified as periodic or non-
periodic, for both specified bonds and boundary bonds.
* inorganicbuilder/inorganicbuilder.tcl 1.37 (changed +314 -192)
|
| | 2007-11-26 | brunner | Added options to retain file bonds, and updated the wrapped bond search
to implement VMD's heurstic 0.6*(r1+r2).
* inorganicbuilder/inorganicbuilder.tcl 1.36 (changed +118 -47)
Atom type selection for building bonds is now a menu derived from the names
in the currently-specified molecule, rather than just text fields.
* inorganicbuilder/inorganicbuilder.tcl 1.35 (changed +68 -6)
|
| | 2007-11-21 | barryi | Better menus. Threshold functions in menus.
(Up to SVN rev. 24)
* timeline/timeline.tcl 1.42 (changed +150 -26)
Decent packing
(up to SVN rev. 12)
* timeline/timeline.tcl 1.37 (changed +22 -10)
Improved appearance, more room for other controls.
(Up to SVN rev. 23. Note that prev CVS checkin was 'Up to SVN rev. 22')
* timeline/timeline.tcl 1.41 (changed +39 -21)
Many bugs gone.
button 2 scrub in progress
* timeline/timeline.tcl 1.35 (changed +55 -21)
NOTE: this is final transfer check in from Barry I. SVN directory
Working on startup errors seen on Mac (from Traced sliders)
Small edits to remove typo.
current changes entered. Likely were just to get running at good speed (commented out puts), some small corrections
Creates own font name, so is independent of other plugin (had been relying on Sequence Viewer/zoomseq to do this)
(Up to SVN rev. r34 -- final SVN checkin)
* timeline/timeline.tcl 1.44 (changed +46 -28)
Now it has okay packing. still much to do...
Another stage.
highlight looks good, toggleable
adding some demo files
(up to SVN rev. 15)
* timeline/timeline.tcl 1.38 (changed +350 -15)
Numframes + 2 gone. now to check out +1 cases
improvements, not quite working at this point
(to SVN r. 5)
* timeline/timeline.tcl 1.33 (changed +140 -126)
Ooops, THIS is actual final SVN checkin...
Some scale change,
(Now up to SVN rev 35.. really is final commit)
* timeline/timeline.tcl 1.45 (changed +2 -2)
Scrub label close
(to SVN rev. 11)
* timeline/timeline.tcl 1.36 (changed +53 -53)
Small change
struct is working
added thresholding, function only (no gui) may not yet work
some thresh graph
graphing of threshold looks ok, shows max and min
(up to rev. 21)
* timeline/timeline.tcl 1.39 (changed +113 -8)
Small changes (on laptop)
vaugely sane, many bugs gone.
(to SVN rev. 9)
* timeline/timeline.tcl 1.34 (changed +141 -107)
The next commits will be of changes to timline.tcl that took place
in Barry I.'s personal SVN directory. The 34 SVN revisions
are combined here to 13 major revisions, which will each be checked into
this CVS tree, along with the associated comments for each one
(excepting references to extraneous README and test files not included here).
These major revisions were made in March and April 2007.
Also: the SVN version will be noted for reference in case confusion comes
up.
Notes for this entry:
from VMD CVS tree 1.30, with some changes added not working as of this initial import. Plan to re-merge back to CVS tree after features added
removed an editor file
thresh seen, user data seen
(up to SVN rev. 3)
* timeline/timeline.tcl 1.32 (changed +66 -7)
Various changes and corrections
(Up to SVN rev. 25)
* timeline/timeline.tcl 1.43 (changed +29 -45)
Works on syndey (Mac), but outlines for bar and event (blue vox). The event box looks bad, since is made of many lines, not just outline.
* timeline/timeline.tcl 1.40 (changed +61 -22)
|
| | 2007-11-16 | brunner | - Removed commented out code that is no longer used now that the Specific
Bonds and Periodic Bonds commands have been merged
- Removed Merge Molecules code that is now in Merge Molecules plugin
- Added exact-charge adjustement to the charge correction code, so that,
after charge adjustments are distributed evenly across all atoms, any
remaining correction that is needed due to PSF rounding is applied to atom
zero
- Other bug fixes
* inorganicbuilder/inorganicbuilder.tcl 1.34 (changed +64 -911)
|
| | 2007-11-12 | brunner | Separated the angle and dihedral options when creating bonds
* inorganicbuilder/inorganicbuilder.tcl 1.33 (changed +31 -9)
|
| | 2007-11-08 | brunner | 1. Reformatted Start screen, made spacing nicer and added a button
2. Changed bond search method to use atom type instead of element
3. Combined PeriodicBonds and SpecifiedBonds GUIs into one window
* inorganicbuilder/inorganicbuilder.tcl 1.32 (changed +280 -76)
|
| | 2007-11-07 | johns | SGI IRIX builds are disabled until we have another build box available
* build.csh 1.71 (changed +2 -2)
|
| | 2007-11-05 | petefred | Get rid of hard-coded restriction on recursion depth for bond/angle/dihedral changes
* molefacture/molefacture_internals.tcl 1.28 (changed +9 -4)
* molefacture/molefacture_gui.tcl 1.34 (changed +14 -4)
* molefacture/molefacture_geometry.tcl 1.17 (changed +6 -3)
* molefacture/molefacture.tcl 1.91 (changed +2 -1)
|
| | 2007-11-05 | johns | Updated to Olaf's latest version. This update cures a problem on Windows,
and closes a small memory leak.
* molfile_plugin/src/vtfplugin.c 1.6 (changed +45 -23)
|
| | 2007-10-30 | brunner | New GUI for resolving segment name conflicts when merging two PSF files
* inorganicbuilder/inorganicbuilder.tcl 1.31 (changed +663 -4)
|
| | 2007-10-26 | jordi | By popular request, added a small GUI window to access the VMD ruler
* ruler/ruler.tcl 1.5 (changed +60 -1)
|
| | 2007-10-22 | brunner | Added parameter and GUI to force constructed devices to have an integer
charge, so that they can be easily neutralized by the addition of ions.
The current method of modifying the charge is to calculate the correction
and then add 1/n times the correction factor to every charge. Another
possible method is to scale all charges, but that may lead to larger
changes in the charge. I'll have to consult with Alek to find out what
method is correct.
* inorganicbuilder/inorganicbuilder.tcl 1.29 (changed +46 -7)
Fixed bug where the material state was not available when loading a saved
state... Also sorted material lists for uniform presentation in menus.
* inorganicbuilder/inorganicbuilder.tcl 1.30 (changed +10 -5)
Replaced charges in .top files with more useful values
* inorganicbuilder/materials/sio2.top 1.2 (changed +12 -12)
* inorganicbuilder/materials/si3n4.top 1.2 (changed +14 -14)
* inorganicbuilder/materials/asio2.top 1.2 (changed +12 -12)
Set the plugin to return to the Start screen whenever the plugin window is
opened/reopened.
* inorganicbuilder/inorganicbuilder.tcl 1.28 (changed +11 -1)
|
| | 2007-10-19 | brunner | - Added a Clear Device button, to erase any currently-defined structure
- Fixed a bug where an old device structure (Draw Box)
was not deleted when a new one was loaded
- Made the "Draw Box" function dynamic, so it occurs automatically whenever
the structure changes. This removes the need for the Draw Box button, so
that has also been removed.
* inorganicbuilder/inorganicbuilder.tcl 1.27 (changed +42 -14)
|
| | 2007-10-17 | saam | Exporting all commands so that they can be imported from other namespaces.
Added a couple new commands.
* utilities/utilities.tcl 1.2 (changed +46 -1)
* utilities/doc/index.html 1.2 (changed +17 -0)
Minor syntax bugfix.
* qmtool/qmtool_aux.tcl 1.22 (changed +2 -2)
|
| | 2007-10-17 | petefred | *** empty log message ***
* autopsf/autopsf.tcl 1.107 (changed +2 -2)
|
| | 2007-10-16 | saam | Added proper namespace to call of a procedure that has been moved to utilities.
* paratool/paratool_hessian.tcl 1.10 (changed +1 -1)
|
| | 2007-10-16 | brunner | Added a Start screen to start building a device
* inorganicbuilder/inorganicbuilder.tcl 1.25 (changed +44 -10)
Revised formatting on block input windows
* inorganicbuilder/inorganicbuilder.tcl 1.26 (changed +59 -56)
|
| | 2007-10-11 | brunner | Added File menu, with options to save and open a state file (for the plugin
state, not the complete VMD state)
* inorganicbuilder/inorganicbuilder.tcl 1.24 (changed +94 -34)
|
| | 2007-10-10 | brunner | Added menu options and GUI for viewing materials and adding new ones.
* inorganicbuilder/inorganicbuilder.tcl 1.23 (changed +438 -30)
|
| | 2007-10-05 | petefred | Add option to update selection every frame, so people don't have to do ugly hacks for this
* namdenergy/namdenergy.tcl 1.51 (changed +148 -52)
Fix issues with mixed solvent types
* solvate/solvate.tcl 1.30 (changed +11 -3)
* solvate/doc/index.html 1.10 (changed +1 -1)
|
| | 2007-10-04 | petefred | Fix atom ordering for input to bondedsel
* molefacture/molefacture_internals.tcl 1.27 (changed +9 -7)
* molefacture/molefacture_gui.tcl 1.33 (changed +8 -4)
* molefacture/molefacture_geometry.tcl 1.16 (changed +13 -4)
|
| | 2007-10-03 | johns | Updated default VdW radii assigned to elements to improve the default
behavior for commonly used ions by replacing the Bondi radii with
CHARMM27 Rmin/2 parameters for elements that are commonly ions in
simulated systems.
* molfile_plugin/src/periodic_table.h 1.11 (changed +7 -5)
|
| | 2007-10-02 | jordi | DX plugin: Use %g instead of %e for file output
* molfile_plugin/src/dxplugin.C 1.30 (changed +7 -7)
Situs plugin: Use %g instead of %e for Situs output. %e was a bit silly, %g
is more readable/debuggable and takes as little as 25% of the space
* molfile_plugin/src/situsplugin.C 1.11 (changed +4 -4)
|
| | 2007-09-28 | petefred | *** empty log message ***
* molefacture/lib/nucleic_acids/rna_backbone_added.mfrag 1.1 (added +70 -0)
* molefacture/lib/nucleic_acids/rna_backbone.mfrag 1.1 (added +74 -0)
* molefacture/lib/nucleic_acids/dna_dihedrals.gif 1.1 (added +33 -0)
* molefacture/lib/nucleic_acids/dna_backbone.mfrag 1.1 (added +68 -0)
* molefacture/lib/nucleic_acids/U.mfrag 1.1 (added +40 -0)
* molefacture/lib/nucleic_acids/T.mfrag 1.1 (added +49 -0)
* molefacture/lib/nucleic_acids/G.mfrag 1.1 (added +54 -0)
* molefacture/lib/nucleic_acids/C.mfrag 1.1 (added +43 -0)
* molefacture/lib/nucleic_acids/A.mfrag 1.1 (added +51 -0)
-Add a nucleic acid builder (still a work in progress, but needs to be committed)
-Fix up prolines in the protein builder to look better
* molefacture/molefacture_internals.tcl 1.26 (changed +11 -8)
* molefacture/molefacture_gui.tcl 1.32 (changed +114 -6)
* molefacture/molefacture_geometry.tcl 1.15 (changed +3 -3)
* molefacture/molefacture_builder.tcl 1.24 (changed +159 -7)
* molefacture/molefacture.tcl 1.90 (changed +12 -1)
* molefacture/lib/amino_acids/PRO.mfrag 1.3 (changed +44 -17)
|
| | 2007-09-28 | jordi | VolMap GUI:
* Added ability do create Coulomb potential maps through the GUI
* Added more options for the output molecule (including a "same as input"
option, now used as the default)
* volmapgui/volmapgui.tcl 1.19 (changed +35 -17)
|
| | 2007-09-27 | brunner | Added a min and max coordinate display in the build window
* inorganicbuilder/inorganicbuilder.tcl 1.22 (changed +103 -2)
|
| | 2007-09-26 | brunner | - Improved formatting of Create Box exclusion window
- Fixed bug where basis vector setting were getting reset in the Build
Specific Bonds window
- Reformatted the exclusion list so that all geometric exclusions are listed
first, followed by the VMD selection exclusions, to reflect how the exclusions
are actually applied to the structure
* inorganicbuilder/inorganicbuilder.tcl 1.21 (changed +41 -26)
|
| | 2007-09-25 | brunner | Revised GUI for other tasks, consolidated the molecule file dialogs into
one function, and fixed a couple of bugs in the solvate routine which occur
when the original box is rectangular
* inorganicbuilder/inorganicbuilder.tcl 1.20 (changed +69 -341)
* inorganicbuilder/doc/index.html 1.3 (changed +3 -0)
Revised layout of the Build Specified Bonds window
* inorganicbuilder/inorganicbuilder.tcl 1.18 (changed +123 -104)
Revised look of FindSurface window, consolidated more GUI code between
windows.
* inorganicbuilder/inorganicbuilder.tcl 1.19 (changed +179 -427)
Revised the layout of the Build Periodic Bonds screen
* inorganicbuilder/inorganicbuilder.tcl 1.17 (changed +88 -68)
Undo changes previously checked in
* inorganicbuilder/doc/index.html 1.4 (changed +0 -3)
|
| | 2007-09-24 | johns | Applied API changes creating timestep metadata structures and adding
support for velocities, for use in trajectory read/write plugins.
* include/vmdplugin.h 1.25 (changed +2 -2)
* include/molfile_plugin.h 1.46 (changed +17 -2)
Update main plugin doc index
* doc/index.html 1.70 (changed +1 -0)
|
| | 2007-09-24 | brunner | Added Basis Vector button to Specified Bonds and Find Surface atoms as well
* inorganicbuilder/inorganicbuilder.tcl 1.15 (changed +10 -0)
|
| Other commits are hidden... |
