CVS analysis' parameters 
Project module nameplugins
CVS root used/home/cvs/vmd/cvsroot
Range analysisMain Branch (HEAD)
Date analysis2020-08-05 02:35 (Built in 182s)
CVS report for module 'plugins' built by cvschangelogbuilder 2.3 (build 1.76) with option buildhtmlreport.
Summary   Lines of code   Developers activity   Days of week   Hours  Tags  Last commits  

 
SummaryTop 
Current status indicatorsValue  
Files currently in repository 2291 
Lines of code currently in repository (on non binary files only) 1529797 
Activity indicatorsFrom startThis monthToday
Number of developers 2900
Number of commits1448100
Number of commits by status 2646 to add new file
11480 to change existing file
355 to remove file 
  
Different files commited 264300
Lines added / modified / removed (on non binary files only) +1702890 / 238838 / -173093+0 / 0 / -0+0 / 0 / -0
Last commit 2020-07-09  

 
Lines of code*Top 
This chart represents the balance between number of lines added and removed in non binary files (source files).
 
 

 
Developers activity*Top 
DeveloperNumber of commitsDifferent files commitedLines*
(added, modified, removed)
Lines by commit*
(added, modified, removed)
Last commit 
johns63631684732893 / 59037 / 67964115.1 / 9.2 / 10.62020-07-09 16:58 
kvandivo167767081069 / 31047 / 2054448.3 / 18.5 / 12.22015-06-11 14:31 
saam138020984737 / 33055 / 3729661.4 / 23.9 / 272011-06-28 02:19 
petefred83920638908 / 17012 / 2413846.3 / 20.2 / 28.72015-04-21 02:34 
jribeiro55219725124 / 28498 / 37045.5 / 51.6 / 0.62020-03-10 04:54 
akohlmey4231267894 / 5516 / 84018.6 / 13 / 1.92013-10-28 11:06 
justin37512397428 / 2134 / 5474259.8 / 5.6 / 14.52003-08-17 20:55 
eamon3627313510 / 5766 / 126637.3 / 15.9 / 3.42004-07-13 14:56 
jim358748226 / 1393 / 4122.9 / 3.8 / 0.12019-04-12 14:26 
jordi3578524196 / 4070 / 601967.7 / 11.4 / 16.82007-10-26 21:03 
ltrabuco30415335040 / 1663 / 632115.2 / 5.4 / 22011-05-17 10:07 
ryanmcgreevy26798253226 / 6669 / 1129948.4 / 24.9 / 4.22019-08-13 18:21 
mayne2623115848 / 12681 / 107160.4 / 48.4 / 42017-06-13 15:52 
dhardy200397320 / 795 / 7536.6 / 3.9 / 0.32020-05-05 07:43 
barryi1211215883 / 13437 / 741131.2 / 111 / 6.12015-06-19 16:26 
brunner118278211 / 3127 / 143369.5 / 26.5 / 12.12009-06-15 20:14 
mbach105123488 / 1610 / 39733.2 / 15.3 / 3.72007-02-28 22:38 
gumbart9454147177 / 2921 / 911565.7 / 31 / 0.92020-06-11 21:12 
johanstr92233875 / 1598 / 29742.1 / 17.3 / 3.22012-04-03 15:15 
markus8545515 / 3402 / 25664.8 / 40 / 32007-02-21 03:13 
anton45191463 / 1694 / 289732.5 / 37.6 / 64.32009-04-28 15:30 
pgrayson33151102 / 72 / 533.3 / 2.1 / 0.12002-07-12 15:07 
mjanuszy253626 / 1037 / 8125 / 41.4 / 3.22002-09-15 18:17 
ilya19986813 / 99 / 344569.1 / 5.2 / 1.72003-08-06 15:12 
dtwright82796 / 36 / 299.5 / 4.5 / 0.22005-07-29 21:06 
mariano882131 / 109 / 0266.3 / 13.6 / 02020-07-02 17:05 
brendanbc141359 / 395 / 089.7 / 98.7 / 02018-04-11 22:40 
yanchanky3328 / 9 / 09.3 / 3 / 02013-12-19 20:25 
eschrein214 / 10 / 02 / 5 / 02010-11-15 02:55 

                   


 
Activity by days of weekTop 


 
Activity by hoursTop 


 
Last tags by dateTop 
DateFull dateTags 
2018-12-132018-12-13 01:12fftk-1-2-0 
2018-07-312018-07-31 16:55siggraph2018 
2016-11-302016-11-30 06:23vmd-1-9-3 
2015-12-082015-12-08 22:39psfgen-stable-precharmm19-patch 
2015-12-082015-12-08 22:39namd-2-11 
2014-12-222014-12-22 17:25vmd-1-9-2 
2012-02-022012-02-02 21:37vmd-1-9-1 
2012-02-012012-02-01 17:13v1-0-01 
2012-01-252012-01-25 20:32v1-0 
2011-03-142011-03-14 16:08vmd-1-9-0 
2009-08-012009-08-01 05:20vmd-1-8-7 
2008-11-262008-11-26 23:16qm-nosorting-1 
2008-06-112008-06-11 09:28mgpot_cuda_lattice_cutoff_2 
2008-06-112008-06-11 00:36mgpot_cuda_lattice_cutoff_1 
2007-06-042007-06-04 22:14cuda-0-8-0 
2007-04-062007-04-06 18:26vmd-1-8-6 
2006-08-262006-08-26 02:02vmd-1-8-5 
2006-04-172006-04-17 07:07vmd-1-8-4 
2005-06-292005-06-29 03:50paratool-1_0 
2005-02-162005-02-16 03:16vmd-1-8-3 
2003-12-052003-12-05 18:58vmd-1-8-2 
2003-06-132003-06-13 21:18vmd-1-8-1 
2002-12-092002-12-09 05:01vmd-1-8-0 

 
Last commit logsTop 
TagsDateDeveloperLast 200 Commit Logs
 2020-07-09johnsUpdated binding free energy estimator plugin w/ new version from Chris Chipot
and collaborators.
* bfeestimator/bfee.tcl 1.2 (changed +482 -98)
* bfeestimator/Makefile 1.2 (changed +1 -1)
 2020-07-06johnsMerged Axel's latest topotools updates.
* topotools/topogromacs.tcl 1.16 (changed +2 -2)
* topotools/topocrossterms.tcl 1.5 (changed +2 -2)
* topotools/Makefile 1.17 (changed +6 -5)
Updated MRC/CCP4 plugin to emit extended header tags stored by some
commercial microscopy tools in the console messages to help with
identifying unusual proprietary file formats. Inhibit printing of
MRC symmetry records when the IMOD stamp has been identified.
* molfile_plugin/src/ccp4plugin.C 1.44 (changed +49 -22)
 2020-07-03johnsAllow jsplugin to be included into other source files with file scope
linkage for early testing of out-of-core APIs in multiple parts of VMD.
* molfile_plugin/src/jsplugin.c 1.88 (changed +4 -1)
 2020-07-02marianoAdded qcschema plugin for LINUXAMD64
* molfile_plugin/Makefile 1.133 (changed +24 -1)
Added qcschema plugin for LINUXAMD64.
Preliminary version uses json parser from
https://github.com/udp/json-parser
included as qcschema_json.c and .h files.
The plugin reads 'molecule' object
including geometry, symbols, charge and
multiplicity.
* molfile_plugin/src/qcschemaplugin.c 1.1 (added +750 -0)
* molfile_plugin/src/qcschema_json.h 1.1 (added +288 -0)
* molfile_plugin/src/qcschema_json.c 1.1 (added +1044 -0)
 2020-07-01johnsUpdated Josh Vermaas' current email and corrected spelling typos.
* topotools/topoutils.tcl 1.20 (changed +2 -2)
* topotools/topotools.tcl 1.34 (changed +3 -3)
 2020-06-29johnsCorrected missing check for verbose console output state.
* molfile_plugin/src/jsplugin.c 1.87 (changed +5 -3)
 2020-06-23marianoFixed 'pack' vs 'grid' problem. Requires MacOS testing
* qwikmd/qwikmd.tcl 1.84 (changed +5 -3)
 2020-06-12marianoModified GUI to remove 'pack' and replace it with 'grid'
Tested in linux, need to test in new macos with tcl8.6
* autopsf/autopsf.tcl 1.151 (changed +91 -90)
 2020-06-11gumbartFixed pattern matching for Gaussian 09.
* fftk/fftk_SharedFcns.tcl 1.17 (changed +2 -2)
 2020-05-29johnsRemoved old README in favor of Axel's markdown version
* topotools/README 1.18 (removed +0 -41)
Updated Makefile for markdown version README.md
* topotools/Makefile 1.16 (changed +1 -1)
Updated topotools plugin with Axel's latest v1.8 package.
* topotools/topovarxyz.tcl 1.6 (changed +2 -2)
* topotools/topoutils.tcl 1.19 (changed +1 -1)
* topotools/topotools.tcl 1.33 (changed +4 -4)
* topotools/topolammps.tcl 1.45 (changed +17 -29)
* topotools/topoimpropers.tcl 1.12 (changed +4 -4)
* topotools/topohelpers.tcl 1.11 (changed +1 -1)
* topotools/topogromacs.tcl 1.15 (changed +38 -4)
* topotools/topodihedrals.tcl 1.12 (changed +12 -10)
* topotools/topobonds.tcl 1.16 (changed +2 -2)
* topotools/topoatoms.tcl 1.17 (changed +2 -2)
* topotools/topoangles.tcl 1.13 (changed +2 -2)
* topotools/pkgIndex.tcl 1.11 (changed +1 -1)
* topotools/doc/index.html 1.23 (changed +2 -2)
* topotools/README.md 1.1 (added +66 -0)
* topotools/Makefile 1.15 (changed +1 -1)
* topotools/LICENSE 1.4 (changed +2 -2)
 2020-05-19johnsMinor stylistic cleanup revisions in preparation for Tcl 8.6 grid vs. pack
widget layout corrections.
* heatmapper/pkgIndex.tcl 1.3 (changed +1 -1)
* heatmapper/heatmapper.tcl 1.6 (changed +23 -97)
* heatmapper/Makefile 1.3 (changed +1 -1)
 2020-05-09johnsCranked version of clonerep plugin to 1.4 due to GUI fixes for Tk 8.6
to eliminate grid/pack conflicts.
* clonerep/pkgIndex.tcl 1.5 (changed +1 -1)
* clonerep/clonerep.tcl 1.15 (changed +2 -2)
* clonerep/Makefile 1.5 (changed +1 -1)
Revised chirality plugin GUI to eliminate grid/pack conflicts in Tk 8.6.
Cranked plugin version to 1.4. Further testing and GUI optimizations
should be done, but this version now runs on Tk 8.6 without errors thus far.
* torsionplot/torsionplot.tcl 1.6 (changed +21 -27)
* torsionplot/pkgIndex.tcl 1.4 (changed +1 -1)
* torsionplot/Makefile 1.4 (changed +1 -1)
* chirality/pkgIndex.tcl 1.5 (changed +2 -2)
* chirality/doc/index.html 1.5 (changed +1 -1)
* chirality/chirality_gui.tcl 1.8 (changed +13 -14)
* chirality/chirality.tcl 1.30 (changed +3 -1)
* chirality/Makefile 1.4 (changed +1 -1)
Revised cispeptide plugin GUI to eliminate grid/pack conflicts in Tk 8.6.
Cranked plugin version to 1.4. Further testing and GUI optimizations
should be done, but this version now runs on Tk 8.6 without errors thus far.
* cispeptide/pkgIndex.tcl 1.5 (changed +2 -2)
* cispeptide/doc/index.html 1.5 (changed +1 -1)
* cispeptide/cispeptide_gui.tcl 1.8 (changed +21 -21)
* cispeptide/cispeptide.tcl 1.22 (changed +2 -2)
* cispeptide/Makefile 1.4 (changed +1 -1)
Synced version number in docs.
* clonerep/doc/index.html 1.7 (changed +1 -1)
 2020-05-08johnsRevised the clonerep plugin to correct conflicting use of Tk pack/grid
layout managers on the same master container. It was never technically
legal to mix the use of grid and pack within the same master as they can
fight over layout control potentially leading to deadlock.
Tk 8.6.x and later versions now explicitly detect this type of
misuse of grid/pack and throw a runtime error. The problem can most
easily be rectified by ensuring that pack and grid are applied to
independent frame containers.
* clonerep/clonerep.tcl 1.14 (changed +7 -15)
 2020-05-07johnsUpdated membranemixer docs for the updated 'grid' based widget layout manager.
* membranemixer/doc/membranemixer_gui.png 1.2 (changed binary)
* membranemixer/doc/index.html 1.2 (changed +56 -35)
 2020-05-06johnsAdded membranemixer to the top level plugin docs page
* doc/index.html 1.107 (changed +1 -0)
Updated membranemixer plugin to address the problem with mixing the
"pack" and "grid" Tk widget managers by rewriting using only "grid".
* membranemixer/membranemixer.tcl 1.3 (changed +169 -122)
 2020-05-05johnsUpdated target console message
* build.csh 1.141 (changed +1 -1)
 2020-05-05dhardyFix hyperlinks for importing into NAMD User's Guide
* psfgen/doc/ug_psfgen.tex 1.23 (changed +3 -3)
* psfgen/doc/ug.tex 1.2 (changed +3 -0)
* psfgen/doc/ug.pdf 1.4 (changed binary)
 2020-05-01dhardyNeeded to remove the newline in PSFGENAUTHORS definition to build NAMD ug
* psfgen/doc/ug_macros.tex 1.16 (changed +1 -2)
 2020-04-23johnsAdded docs for membranemixer plugin
* membranemixer/doc/membranemixer_gui.png 1.1 (added binary)
* membranemixer/doc/index.html 1.1 (added +140 -0)
Added membranemixer build rules
* membranemixer/Makefile 1.1 (added +23 -0)
Added membranemixer to the build.
* Makefile 1.145 (changed +2 -1)
Added version tag to the membranemixer header.
* membranemixer/membranemixer.tcl 1.2 (changed +5 -3)
First rev of membranemixer plugin added to the tree.
* membranemixer/pkgIndex.tcl 1.1 (added +16 -0)
* membranemixer/membranemixer.tcl 1.1 (added +1914 -0)
 2020-04-19johnsAdded arrow_right.gif and arrow_down.gif icons to the build.
* qwikmd/Makefile 1.10 (changed +1 -1)
 2020-04-17johnsAdded further local build flags for other test systems
* build.csh 1.140 (changed +17 -0)
Updated plugin build script for local compilations on 'tijuana' test box.
* build.csh 1.139 (changed +21 -1)
Use framework linkage for 64-bit MacOS X builds
* Make-arch 1.93 (changed +1 -1)
 2020-04-13marianoAdded parsing of SCF energies
Based on gamess plugin
Required for new QMtool plugin
* molfile_plugin/src/orcaplugin.C 1.7 (changed +28 -6)
 2020-03-10jribeiroMove the PSFGENLOGFILE and VPBONDS to the psfgen_data data structure.
PSFGENLOGFILE and VPBONDS, like the counters of this data structure, are
only used and defined in the first position. This way, only one definition
is valid for all psfgen_context instances.
* psfgen/src/topo_mol_struct.h 1.26 (changed +5 -2)
* psfgen/src/topo_mol_pluginio.h 1.10 (changed +4 -4)
* psfgen/src/topo_mol_pluginio.c 1.61 (changed +63 -62)
* psfgen/src/topo_mol_output.h 1.7 (changed +8 -8)
* psfgen/src/topo_mol_output.c 1.46 (changed +40 -38)
* psfgen/src/topo_mol.h 1.15 (changed +3 -3)
* psfgen/src/topo_mol.c 1.69 (changed +30 -15)
* psfgen/src/topo_defs_struct.h 1.13 (changed +8 -2)
* psfgen/src/topo_defs.h 1.12 (changed +4 -4)
* psfgen/src/topo_defs.c 1.21 (changed +9 -6)
* psfgen/src/tcl_psfgen.c 1.91 (changed +131 -104)
* psfgen/src/tcl_main.c 1.10 (changed +16 -9)
* psfgen/src/psfgen.h 1.9 (changed +9 -6)
* psfgen/src/psf_file_extract.h 1.10 (changed +2 -2)
* psfgen/src/psf_file_extract.c 1.42 (changed +35 -35)
* psfgen/src/pdb_file_extract.h 1.5 (changed +4 -4)
* psfgen/src/pdb_file_extract.c 1.17 (changed +16 -16)
* psfgen/src/charmm_parse_topo_defs.h 1.4 (changed +4 -4)
* psfgen/src/charmm_parse_topo_defs.c 1.20 (changed +13 -13)
 2020-03-06jribeiroComment-out debugging print statement
* psfgen/src/topo_mol.c 1.68 (changed +1 -1)
 2020-03-05jribeiroComments typos fixes
* psfgen/src/topo_mol_output.c 1.45 (changed +2 -1)
* psfgen/src/tcl_psfgen.c 1.90 (changed +1 -1)
Fix the new psfgen code to allow multiple patches to the same residue.
This makes constant-ph running. A new test, test_constantPH.tcl,
was added to the automated suite to check these capabilities.
* psfgen/src/topo_mol.c 1.67 (changed +4 -4)
* psfgen/src/tcl_main.c 1.9 (changed +2 -1)
* psfgen/src/psf_file_extract.c 1.41 (changed +2 -0)
Silent compiler warning when compiling psfgen for NAMD
* psfgen/src/tcl_main.c 1.8 (changed +5 -2)
 2020-02-19jribeiroComments corrections
* psfgen/src/topo_mol_struct.h 1.25 (changed +9 -9)
* psfgen/src/topo_mol_pluginio.c 1.60 (changed +0 -0)
 2020-02-13johnsCorrected multiseq distribution version number to match the internal
versioning scheme which is also used for access to the web-based
versions.txt files that index all of the other datbases.
* multiseq/Makefile 1.3 (changed +1 -1)
 2020-02-11johnsCorrect flawed string handling in Orca plugin.
* molfile_plugin/src/orcaplugin.C 1.6 (changed +3 -3)
 2020-02-06jribeiroComments typos correction
* psfgen/src/topo_mol_struct.h 1.24 (changed +10 -10)
* psfgen/src/topo_defs_struct.h 1.12 (changed +3 -3)
Print the message "Info: generating structure..." in a new line
* psfgen/src/tcl_psfgen.c 1.89 (changed +3 -3)
Recognize the "PATCH" and "DRUDE" in the CHARMM topology command
"AUTOGENERATE ANGLES DIHEDRALS PATCH DRUDE" to avoid the printing of the
error during the topology parsing.
* psfgen/src/charmm_parse_topo_defs.c 1.19 (changed +3 -1)
 2020-02-05jribeiroRemoved the hyperlink to a personal webpage to prevent errors when the page
is moved when the contributor moves.
Added information regarding "null" results for the getstr command.
* cgenffcaller/doc/index.html 1.2 (changed +4 -2)
 2020-02-04jribeiroAdded the documentation page of the cgenffcaller plugin
* cgenffcaller/doc/index.html 1.1 (added +102 -0)
* cgenffcaller/doc/cgenffcaller_logo.png 1.1 (added binary)
Clean up the command-line interface, so the user doesn't need to deal
with namespaces.
The whole package has now 5 commands, and all start with "cgenffcaller":
cgenffcaller callcgenff <options> - to submit a job the cgenff server
cgenffcaller savemol <options> - export the current molecule and assign the
elements to the atoms' type to be
compatible with the server.
cgenffcaller numstr - number of stream files fetched
cgenffcaller getstr <index> - print the stream file strored in the index-th
position
cgenffcaller getsubcount - number of submissions to the server performed by
the username of the last callcgenff execution.
The "cgenffcaller getsubcount" only returns a valid number after the first
"cgenffcaller callcgenff" execution.
* cgenffcaller/cgenffcaller.tcl 1.2 (changed +164 -69)
Update to the new syntax of the cgenffcaller package
* molefacture/molefacture_internals.tcl 1.56 (changed +5 -5)
* molefacture/molefacture_gui.tcl 1.74 (changed +1 -2)
 2020-02-03jribeiroAdding the Makefile for the cgenffcaller plugin
* cgenffcaller/Makefile 1.1 (added +24 -0)
CGenFFCaller plugin automates the fetching of CHARMM topology and
parameters from the CGenFF server (https://cgenff.umaryland.edu/).
The plugin has a main proc "calllcgenff" and can be called as:
"callcgenff -molfile <List of Files> -username <CGenFF Server Username>
-method <Web Server Fetching Tool - default value = "auto"". The command
expects a MOL2 file compatible with the CGenFF server.
The communication between VMD and CGenFF webserver can be performed by 5
different mechanisms, depending on their availability in the machine
(in this order):
- curl (Linux and macOS)
- wget (Linux and macOS)
- PowerShell (on windows using curl command)
- python script (Linux and macOS)
- if all these mechanisms fail, using TCL HTTP and TLS packages. This is
not the default route since the availability of TLS package
is not guaranteed.
The JSON plugin parses the output returned by the CGenFF server.
To assist the user in creating webserver complaint mol2 files, CGenFFCaller
has a proc named saveMol, that receives an atomselect object, output
filename, and format. The output format can be mol2, XYZ, and PDB. This
proc ensures that the atom's type stores the atoms' elements to ensure
correct atoms' recognition by the CGenFF server, and also places the
comment "generated by VMD" at the end of the file as a comment. This proc
is used by molefacture to export molecules, either as mol2, XYZ, and PDB.
* cgenffcaller/pkgIndex.tcl 1.1 (added +16 -0)
* cgenffcaller/cgenffcaller.tcl 1.1 (added +420 -0)
Update the Molefacture to use cgenffcaller plugin without a password.
Molefacture still checks if the plugin exists. After some iterations of
alpha releases, or even beta, one can assume that the cgenffcaller will
always exist, and all the checks and fallbacks can be deleted.
* molefacture/molefacture_internals.tcl 1.55 (changed +7 -2)
* molefacture/molefacture_gui.tcl 1.73 (changed +9 -7)
* molefacture/molefacture.tcl 1.111 (changed +7 -2)
 2020-01-09johnsUpdated src comments about coording read/uncompress function.
* molfile_plugin/src/Gromacs.h 1.36 (changed +5 -2)
 2020-01-07jribeiroImprovements to the sort_to_writepdb procedure to support large systems. Avoid breaking the chain into one selection per residue if re-ordering is not needed.
* autopsf/autopsf.tcl 1.150 (changed +23 -6)
 2020-01-07johnsAdded links to EMBL "ahds" amira parsing tools in Python
* molfile_plugin/src/amiraplugin.C 1.4 (changed +4 -0)
 2020-01-06johnsAdded revision control version info into file header.
* molfile_plugin/src/raster3dplugin.C 1.19 (changed +9 -0)
Misc formatting cleanup
* molfile_plugin/src/raster3dplugin.C 1.20 (changed +6 -7)
 2019-12-02johnsCranked minor version for the fix for an AMBER cell angles string leak.
* molfile_plugin/src/netcdfplugin.c 1.31 (changed +2 -2)
Modified read_js_timestep_index_offsets() such that various parameters
are treated as optional since CPU-based and GPU-accelerated I/O cases
need different subsets of the parameters in practice.
* molfile_plugin/src/jsplugin.c 1.86 (changed +9 -5)
Netcdfplugin patch from Thomas Holder to prevent leaking the AMBER
cell angles units string, when present.
* molfile_plugin/src/netcdfplugin.c 1.30 (changed +4 -1)
 2019-11-26jribeiroInclude the option "-a" to output all the parameters when executing the local installation of cgenff
* molefacture/molefacture_internals.tcl 1.54 (changed +1 -1)
 2019-11-23johnsApplied Thomas Holder's patch for maeffplugin to support insertion codes
with CMS file import.
* molfile_plugin/src/maeffplugin.cxx 1.29 (changed +5 -1)
 2019-11-06johnsAdded an ARM64 build configuration based on the HPE Apollo 70 nodes and
v
* build.csh 1.138 (changed +13 -0)
* Make-arch 1.92 (changed +17 -0)
 2019-10-30jribeiroPrevent the user from using the "segname" to define QM Regions when preparing the simulation from a PDB and not from a previous simulation prepared with QwikMD. Autopsf changes the segname during the preparation phase.
* qwikmd/qwikmd_func.tcl 1.72 (changed +5 -0)
 2019-10-29jribeiroBugfix for the QM Orbitals Analysis and for the code to generate the mergefile.sh to merge the QM output files.
* qwikmd/qwikmd_func.tcl 1.71 (changed +12 -6)
* qwikmd/qwikmd.tcl 1.83 (changed +13 -11)
 2019-10-28johnsAdded test loops for GPU-Direct Storage into the JS plugin standalone
test framework.
* molfile_plugin/src/jsplugin.c 1.85 (changed +184 -11)
 2019-10-22johnsAdded double-buffering and asynchronous host-device DMAs for
the reference CUDA test case.
* molfile_plugin/src/jsplugin.c 1.84 (changed +31 -7)
Updated jsplugin standalone tests for CUDA
* molfile_plugin/src/jsplugin.c 1.83 (changed +26 -26)
Updated the standalone jsplugin test code to make correct use of
the new read_timestep_pagealign_size() entry point so that page-aligned
I/Os are used as expected.
* molfile_plugin/src/jsplugin.c 1.82 (changed +11 -2)
 2019-10-17johnsAdded draft experimental direct I/O plugin timestep read APIs for
high performance random access out-of-core trajectory I/O supporting
both OS kernel bypass and GPU-Direct I/O implementations.
* include/molfile_plugin.h 1.112 (changed +20 -1)
Eliminated C++isms that aren't tolerated by MSVC compilers.
* psfgen/src/topo_mol.c 1.66 (changed +6 -6)
 2019-10-11jribeiroDelete charmmprev unused variable that was causing some issues with the deletion of topology files.
* qwikmd/qwikmd_func.tcl 1.70 (changed +0 -1)
Delete legacy bond list updating call
* molefacture/molefacture_gui.tcl 1.72 (changed +3 -5)
Improvements to the hydrogen atoms deletion when the bond order is changed
* molefacture/molefacture_edit.tcl 1.17 (changed +21 -3)
Re-format and correction to some comments
* molefacture/molefacture_geometry.tcl 1.25 (changed +3 -2)
Re-wrote the text message in the info window when trying to select or modifying molecules anchor atoms.
* molefacture/molefacture_internals.tcl 1.53 (changed +1 -2)
 2019-10-08jribeiroBugfix for the creation of mutation/protonation state combobox selector to clean the array, and not unset the array.
* qwikmd/qwikmd_func.tcl 1.69 (changed +1 -1)
 2019-10-07jribeiroAdd giff images to be used as motion indicators (arrows to expand and collapse GUI' frames). These images should be used instead of the unicode characters to prevent missing characters.
Update QwikMD code to use the arrow giff images
* qwikmd/qwikmd_func.tcl 1.68 (changed +1 -1)
* qwikmd/qwikmd.tcl 1.82 (changed +46 -31)
* qwikmd/arrow_right.gif 1.1 (added binary)
* qwikmd/arrow_down.gif 1.1 (added binary)
Fix typo in the name of the lipid parameter file name.
* namdgui/namdgui.tcl 1.39 (changed +2 -2)
 2019-10-04jribeiroBugfix for the patches adding atoms to two residues and the atomArray resizing routine. The solution was to keep a record of the patch name applied to the residue. If the record is empty of the patch name is different from the record, then resize atoms array (if needed).
* psfgen/src/topo_mol_struct.h 1.23 (changed +2 -1)
* psfgen/src/topo_mol.c 1.64 (changed +34 -26)
Delete commented-out code and update the comments for the previous bugfix (adding atoms to two different residues)
* psfgen/src/topo_mol.c 1.65 (changed +4 -5)
 2019-10-01jribeiroBugfix for the calculation of the scaling factor used to place the colinear lone pairs.
* psfgen/src/topo_mol.c 1.63 (changed +10 -1)
 2019-09-17marianoFixed parsing of hess.log to correct for systems larger than 10 atoms.
Fixed output file name to be 'hess_job2_internal.hess'.
* fftk/fftk_QMORCA.tcl 1.2 (changed +10 -9)
 2019-09-17jribeiroAdded a comment about psfgen_static_init function called by namd during the start-up process
* psfgen/src/tcl_psfgen.c 1.88 (changed +4 -1)
 2019-09-17johnsUpdated psfplugin to correctly write out 10-character records for CHARMM
EXTended format, and corrected some C++isms that worked their way into
src comments, etc. The new code uses ternary expressions to select
the right fprintf() format specifier when the CHARMM EXTended output mode
is enabled.
* molfile_plugin/src/psfplugin.c 1.84 (changed +41 -28)
 2019-09-13jribeiroFix the writing of extended psf files to be compatible with CHARMM. The patch implements the 10 characters number in the "!N" header sections for the extended psf file format. Patch sent Joshua Vermaas.
* psfgen/src/topo_mol_output.c 1.44 (changed +16 -14)
 2019-09-05jribeiroUpdate the version number to 2.0
* molefacture/pkgIndex.tcl 1.9 (changed +1 -1)
* molefacture/molefacture.tcl 1.110 (changed +2 -2)
* molefacture/doc/index.html 1.21 (changed +1 -1)
* molefacture/Makefile 1.12 (changed +1 -1)
 2019-09-05johnsUpdated ffTK version numbers to 2.0.
* fftk/pkgIndex.tcl 1.4 (changed +1 -1)
* fftk/fftk.tcl 1.15 (changed +2 -2)
* fftk/doc/index.html 1.19 (changed +6 -6)
* fftk/Makefile 1.8 (changed +1 -1)
 2019-09-03johnsUpdated pre-built binary docs PDF.
* psfgen/doc/ug.pdf 1.3 (changed binary)
 2019-08-27johnsCorrected ffTK Makefile to add files to the distrib target.
* fftk/Makefile 1.7 (changed +1 -1)
Corrected hard-coded psfgen version dependency to 2.0
* solvate/solvate.tcl 1.65 (changed +2 -2)
Updated ffTK plugin that Mariano and Giuseppe have revised to add
abstractions that support multiple tools for quantum chemistry
calculations used in parameter development.
* fftk/fftk_guiProcs.tcl 1.48 (changed +23 -23)
* fftk/fftk_guiInterface.tcl 1.48 (changed +370 -188)
* fftk/fftk_distort.tcl 1.5 (changed +3 -2)
* fftk/fftk_SharedFcns.tcl 1.16 (changed +66 -1)
* fftk/fftk_QMORCA.tcl 1.1 (added +1689 -0)
* fftk/fftk_QMGaussian.tcl 1.1 (added +1457 -0)
* fftk/fftk_GeomOpt.tcl 1.10 (changed +25 -143)
* fftk/fftk_GenZMatrix.tcl 1.16 (changed +32 -547)
* fftk/fftk_GenDihScan.tcl 1.14 (changed +30 -153)
* fftk/fftk_GenBonded.tcl 1.20 (changed +16 -92)
* fftk/fftk_DihOpt.tcl 1.23 (changed +32 -108)
* fftk/fftk_Configuration.tcl 1.3 (changed +1 -1)
* fftk/fftk_ChargeOpt_ESP.tcl 1.2 (changed +154 -119)
* fftk/fftk_ChargeOpt.tcl 1.27 (changed +53 -146)
* fftk/fftk_BuildPar.tcl 1.19 (changed +1 -1)
* fftk/fftk_BondAngleOpt.tcl 1.21 (changed +37 -31)
* fftk/fftk.tcl 1.14 (changed +8 -4)
Updated hard-coded psfgen version dependency for psfgen 2.0
* networkview/networkView.tcl 1.11 (changed +2 -2)
* networkview/adjacencyMatrix.tcl 1.8 (changed +2 -2)
 2019-08-21jribeiroAdded the warning for setting the vpbonds to 0 when preparing simulations for NAMD 2.13 containing lone pairs and Drude particles.
* psfgen/doc/ug_psfgen.tex 1.22 (changed +1 -1)
 2019-08-13ryanmcgreevyChanged ReMDFF map generation to create initial unblurred map separately, avoiding issues with trying to apply a guassian with sigma 0
* mdff/mdff_gui.tcl 1.48 (changed +9 -4)
Changed ssrestraint balloon tooltip proc name to avoid conflicts with actual ssrestraint proc
* mdff/mdffgui_balloon.tcl 1.2 (changed +1 -1)
* mdff/mdff_gui.tcl 1.47 (changed +1 -1)
 2019-08-09jribeiroSet the psfgen version to 2.0
* psfgen/src/tcl_psfgen.c 1.87 (changed +3 -3)
* psfgen/src/pkgIndex.tcl 1.26 (changed +1 -1)
Update the psfgen version in the Makefile
* psfgen/Makefile 1.18 (changed +1 -1)
 2019-08-09johnsSwitched psfgen to use the new code paths by default.
* psfgen/Makefile 1.17 (changed +1 -1)
 2019-08-06jribeiroAdded Brian Radak to the authors' list
* psfgen/doc/ug_macros.tex 1.15 (changed +2 -2)
Deleted the declaration of topo_mol_lonepair_t *lonepairList in the topo_mol_segment_t structure since it was not being used.
* psfgen/src/topo_mol_struct.h 1.21 (changed +1 -17)
Implemented safety checks to prevent the use of the molfile plugin to write structures with lone pairs and drude particles until the plugins are updated. Also prevented the use of writenamdbin for structures containing drude particles. Since the lone pairs are treated as atoms at the pdb level, and there is no extra field to add to the file (alpha and thole), we can use this command to write structures with lone pairs.
* psfgen/src/topo_mol_struct.h 1.22 (changed +6 -1)
* psfgen/src/topo_mol_pluginio.c 1.59 (changed +13 -1)
* psfgen/src/topo_mol_output.c 1.43 (changed +16 -1)
* psfgen/src/topo_mol.c 1.62 (changed +12 -2)
* psfgen/src/psf_file_extract.c 1.40 (changed +5 -1)
 2019-08-02jribeiroThe first version of the updated documentation.
* psfgen/doc/ug_psfgen.tex 1.21 (changed +105 -1)
* psfgen/doc/ug_macros.tex 1.14 (changed +3 -2)
Update the plugin version on the webpage.
* psfgen/doc/index.html 1.13 (changed +1 -1)
 2019-08-02johnsAdded macro to permit compilation on Win32
* psfgen/src/pdb_file_extract.c 1.16 (changed +2 -1)
Eliminate warnings about potentially uninitialized vars.
* psfgen/src/topo_mol.c 1.61 (changed +2 -2)
Eliminated more uninitialized variable warnings
* psfgen/src/charmm_parse_topo_defs.c 1.18 (changed +9 -11)
Pretty
* psfgen/src/topo_defs.h 1.11 (changed +7 -7)
 2019-08-01jribeiroBug fix on the command delatom and fixed all the references to the dihedral atoms the during the writing process.
* psfgen/src/topo_mol_pluginio.c 1.57 (changed +10 -10)
* psfgen/src/topo_mol_output.c 1.41 (changed +13 -9)
* psfgen/src/topo_mol.c 1.59 (changed +22 -45)
Continuing to silence compiler warnings on the "new" psfgen version
* psfgen/src/topo_mol.c 1.60 (changed +8 -30)
* psfgen/src/tcl_psfgen.c 1.86 (changed +7 -9)
* psfgen/src/psf_file_extract.c 1.39 (changed +3 -3)
Deletion of the unused static_assert_int_is_32_bits variable
* psfgen/src/topo_mol_output.c 1.40 (changed +1 -2)
* psfgen/src/psf_file_extract.c 1.37 (changed +2 -3)
* psfgen/src/pdb_file_extract.c 1.15 (changed +3 -3)
Elimination of the compiler warnings from Hydrogen mass repartition code, and assume default values correctly. The command assumes now the form of "hmassrepart dowater 1/0 mass [float numer]". The arguments are optional, and the default values are 0 for dowater and 3.024 for (hydrogen target) mass. Elimination of the variable "i" as a flag for whether the mass value was defined in the command.
* psfgen/src/tcl_psfgen.c 1.85 (changed +57 -45)
Fix the compiler warning messages on psf_file_extract functions.
* psfgen/src/psf_file_extract.c 1.38 (changed +10 -8)
* psfgen/src/psf_file.h 1.9 (changed +10 -2)
Include prototype declaration of the topo_defs_anisotropy function in the topo_defs.h
* psfgen/src/topo_defs.h 1.10 (changed +7 -2)
Include prototype declaration of the topo_mol_set_drude_xyz function in the topo_mol.h
* psfgen/src/topo_mol.h 1.14 (changed +7 -1)
Silencing compiler warnings on the new psfgen version
* psfgen/src/topo_mol_pluginio.c 1.58 (changed +8 -8)
Use the proper definition of atomtype with drude in the case of charmm psf file format
* psfgen/src/topo_mol_output.c 1.42 (changed +9 -2)
 2019-07-30jribeiroAnisotropy section of the psf files is now being parsed and loaded in the readpsf command.
* psfgen/src/topo_mol_struct.h 1.20 (changed +5 -5)
* psfgen/src/topo_defs_struct.h 1.11 (changed +5 -5)
* psfgen/src/psf_file_extract.h 1.9 (changed +11 -0)
* psfgen/src/psf_file_extract.c 1.36 (changed +128 -8)
* psfgen/src/psf_file.c 1.16 (changed +49 -4)
Fix to the parsing and units conversion of the angles and dihedrals from the lone pair section. The distance, angles, and dihedrals are now float opposing to double, as this precision is enough for these quantities. The same change should be employed throughout the code in the areas where double is not necessary.
* psfgen/src/topo_mol_struct.h 1.19 (changed +5 -5)
* psfgen/src/topo_mol_output.c 1.39 (changed +4 -5)
* psfgen/src/psf_file_extract.h 1.8 (changed +7 -2)
* psfgen/src/psf_file_extract.c 1.35 (changed +18 -10)
Fixed some code formatting issues
* psfgen/src/topo_mol_pluginio.c 1.56 (changed +4 -4)
* psfgen/src/topo_mol.c 1.57 (changed +6 -4)
Set drude coordinates from the pdb when loading a psf and pdb containing drude particles. The coordinates from the drude are loaded from pdb either using the command coordpdb or the readpsf <> pdb <>. The other mechanisms to load structures are not yet up to date as molfile, psfgen, and NAMD binary files need to agree on how to store all this information. This is valid for reading and writing. Safety checks still need to be implemented to avoid segmentation fault if the user decides to use those mechanisms with drude.
* psfgen/src/topo_mol.c 1.58 (changed +27 -0)
* psfgen/src/pdb_file_extract.c 1.14 (changed +21 -1)
 2019-07-29jribeiroContinue to add read-in functionality for drude forcefield and lone pairs. The atoms are now filtered in the case of being lone pairs or drude particles. The bonds between these particles and their hosts may be present in the psf file. In this case, the bonds are not read from the psf, but they can be restored if the vpbonds option is set to 1 (default value) in the psfgen script.
* psfgen/src/topo_mol_struct.h 1.18 (changed +29 -16)
* psfgen/src/topo_mol_pluginio.c 1.55 (changed +2 -2)
* psfgen/src/topo_mol_output.c 1.38 (changed +23 -17)
* psfgen/src/topo_mol.c 1.56 (changed +27 -20)
* psfgen/src/tcl_psfgen.c 1.84 (changed +2 -2)
* psfgen/src/psf_file_extract.c 1.34 (changed +18 -4)
Fix the printout of the dihedrals and impropers when using the molfile plugin.
* psfgen/src/topo_mol_pluginio.c 1.54 (changed +20 -16)
Include the chain ID info extracted from the pdb when using the command readpsd <> pdb <> command.
Fix the out-of-bounds references when deleting dihedrals and impropers
Beginning of the implementation of the read of structures containing drude particles and lone pairs.
The compiler messages will be addressed after the read-in functionality is complete.
* psfgen/src/topo_mol_output.c 1.37 (changed +7 -11)
* psfgen/src/topo_mol.c 1.55 (changed +34 -15)
* psfgen/src/topo_defs.c 1.20 (changed +3 -2)
* psfgen/src/psf_file_extract.h 1.7 (changed +18 -6)
* psfgen/src/psf_file_extract.c 1.33 (changed +230 -23)
* psfgen/src/psf_file.c 1.15 (changed +43 -8)
 2019-07-29johnsChange plugin name for amira plugin as pointed out by Joao
* molfile_plugin/src/amiraplugin.C 1.3 (changed +1 -1)
 2019-07-25ryanmcgreevyRemoved old -allframes option from sim, a holdover from when this command used volmap. This functionality should be added back in the future.
* mdff/mdff_sim.tcl 1.4 (changed +2 -2)
 2019-07-24johnsAdded Makefile for the JSON package.
* json/Makefile 1.1 (added +23 -0)
Added TclLib pure-script JSON parser to the plugins tree to ease
implementation of particular web-based structure/forcefield query interfaces.
* json/pkgIndex.tcl 1.1 (added +12 -0)
* json/json_write.tcl 1.1 (added +190 -0)
* json/json.tcl 1.1 (added +325 -0)
* json/README 1.1 (added +6 -0)
* json/ChangeLog 1.1 (added +145 -0)
Added copyright and revision control headers to psfgen source files.
They should have been there all along, but they were missing. The headers
make it obvious what version was the basis for user-submitted patches
and the like, so they are helpful even aside from documentation/comments
that describe the source code purpose/structure etc.
* psfgen/src/topo_mol_struct.h 1.17 (changed +19 -0)
* psfgen/src/topo_mol_pluginio.h 1.9 (changed +19 -0)
* psfgen/src/topo_mol_pluginio.c 1.53 (changed +20 -0)
* psfgen/src/topo_mol_output.h 1.6 (changed +22 -2)
* psfgen/src/topo_mol_output.c 1.34 (changed +19 -0)
* psfgen/src/topo_mol.h 1.11 (changed +19 -0)
* psfgen/src/topo_mol.c 1.50 (changed +20 -0)
* psfgen/src/topo_defs_struct.h 1.10 (changed +19 -0)
* psfgen/src/topo_defs.h 1.9 (changed +19 -0)
* psfgen/src/topo_defs.c 1.18 (changed +19 -0)
* psfgen/src/tcl_psfgen.c 1.81 (changed +19 -0)
* psfgen/src/tcl_main.c 1.7 (changed +19 -0)
* psfgen/src/stringhash.h 1.3 (changed +19 -0)
* psfgen/src/stringhash.c 1.3 (changed +19 -0)
* psfgen/src/psfgen.h 1.8 (changed +26 -12)
* psfgen/src/psf_file_extract.h 1.6 (changed +19 -0)
* psfgen/src/psf_file_extract.c 1.32 (changed +20 -0)
* psfgen/src/psf_file.h 1.8 (changed +19 -0)
* psfgen/src/psf_file.c 1.14 (changed +20 -1)
* psfgen/src/pdb_file_extract.h 1.4 (changed +19 -0)
* psfgen/src/pdb_file_extract.c 1.12 (changed +20 -0)
* psfgen/src/pdb_file.h 1.3 (changed +14 -2)
* psfgen/src/pdb_file.c 1.6 (changed +15 -3)
* psfgen/src/memarena.h 1.3 (changed +19 -0)
* psfgen/src/memarena.c 1.4 (changed +19 -0)
* psfgen/src/hasharray.h 1.3 (changed +19 -0)
* psfgen/src/hasharray.c 1.5 (changed +19 -0)
* psfgen/src/extract_alias.h 1.2 (changed +19 -0)
* psfgen/src/extract_alias.c 1.2 (changed +19 -0)
* psfgen/src/charmm_parse_topo_defs.h 1.3 (changed +19 -0)
* psfgen/src/charmm_parse_topo_defs.c 1.17 (changed +19 -0)
* psfgen/src/charmm_file.h 1.4 (changed +19 -0)
* psfgen/src/charmm_file.c 1.4 (changed +19 -0)
Added the JSON package to the build.
* Makefile 1.144 (changed +2 -1)
Added the rest of the JSON package src files.
* json/json_write.test 1.1 (added +213 -0)
* json/json_write.pcx 1.1 (added +47 -0)
* json/json_write.man 1.1 (added +97 -0)
* json/json.test 1.1 (added +225 -0)
* json/json.pcx 1.1 (added +31 -0)
* json/json.man 1.1 (added +96 -0)
Commented problematic code in the hydrogen mass repartitioning command
processing (potentially uninitialized data) and eliminated
unused variables causing compiler warnings. Clearly more valgrind runs
are needed to find uninitialized data issues like these.
* psfgen/src/tcl_psfgen.c 1.83 (changed +13 -10)
Continued cleanup of compiler warnings, addressing missing includes for
required function prototypes, and so on.
* psfgen/src/topo_mol_output.c 1.36 (changed +9 -16)
* psfgen/src/topo_mol.c 1.53 (changed +35 -44)
Continued cleanup of compiler warnings, etc.
* psfgen/src/topo_mol.c 1.54 (changed +4 -7)
Corrected many portability, syntactic, and code style issues.
* psfgen/src/topo_mol.c 1.49 (changed +6 -8)
Corrected misspelled macro #ifdef check that led to bad function prototypes
* psfgen/src/topo_mol.h 1.12 (changed +3 -3)
Eliminated compiler warnings, misc cleanup.
* psfgen/src/topo_defs.c 1.19 (changed +6 -17)
Eliminated compiler warnings, unused variables, and unprototyped
functions due to lack of proper include files.
* psfgen/src/topo_mol.c 1.52 (changed +3 -10)
Elimination of compiler warnings
* psfgen/src/tcl_psfgen.c 1.82 (changed +4 -5)
Further corrections of the is_xxx() helper routine fctn prototypes.
* psfgen/src/topo_mol.h 1.13 (changed +4 -3)
Misc cleanup to eliminate compiler warnings
* psfgen/src/topo_mol.c 1.51 (changed +5 -5)
* psfgen/src/pdb_file_extract.c 1.13 (changed +3 -6)
Ongoing cleanup and elimination of compiler warnings
* psfgen/src/topo_mol_output.c 1.35 (changed +15 -24)
Replaced the old hash table implementation in psfgen with the current
one from VMD, which is also used by all of the plugins, for consistency.
The new version has better-doxygenized source comments (though still
in need of improvement), and is also updated with macros to handle the
namespace management needs of statically-linked plugins, e.g., the
molfile plugins so we don't encounter namespace collisions from multiple
plugins or other libs that contain the same hash table symbols.
* psfgen/src/hash.h 1.2 (changed +53 -21)
* psfgen/src/hash.c 1.2 (changed +67 -50)
 2019-07-23johnsContinuing cleanup of illegal and non-portable syntax.
* psfgen/src/topo_mol.c 1.44 (changed +19 -18)
Corrected C++ syntax that worked its way into code that should be
strict ANSI C.
* psfgen/src/topo_defs.c 1.16 (changed +6 -4)
* psfgen/src/charmm_parse_topo_defs.c 1.16 (changed +4 -6)
Corrected C++ syntax that worked its way into code that should be
strict ANSI C. Noted non-portable variable size local array allocation.
* psfgen/src/topo_mol.c 1.43 (changed +40 -49)
Corrected many portabilit, syntactic, and code style issues.
Commented on many locations where integer constants are used for
return codes without comments, these should all get replaced by
symbolic constants/enums/macros instead.
* psfgen/src/topo_mol.c 1.47 (changed +24 -21)
Corrected many portability, syntactic, and code style issues.
* psfgen/src/topo_defs.c 1.17 (changed +5 -0)
Ongoing correction of syntactic issues in psfgen.
* psfgen/src/topo_mol.c 1.46 (changed +62 -54)
Ongoing corrections to psfgen for ANSI C compliance
* psfgen/src/topo_mol.c 1.45 (changed +36 -24)
Orrected many portability, syntactic, and code style issues.
* psfgen/src/topo_mol_output.c 1.33 (changed +2 -1)
* psfgen/src/tcl_psfgen.c 1.80 (changed +31 -35)
Replaced non-portable/illegal dynamic array size construct with portable code.
* psfgen/src/topo_mol.c 1.48 (changed +3 -5)
 2019-07-23gumbartChanged readpsf / coordpdb lines to one line readpsf ___ pdb ___
original version fails to read coordinates when segnames
in pdb are truncated and do not match those in psf
* solvate/solvate.tcl 1.64 (changed +9 -7)
* autoionize/autoionize.tcl 1.28 (changed +4 -3)
 2019-07-18jribeiroSkip residues evaluation without topology to be submitted to the cgenff until the cgenffcaller plugin is available. This allows the user to export the topologies, psf, and pdb files without being prompted with the error that the cgenff (server or local copy) is not defined correctly.
* molefacture/molefacture_internals.tcl 1.52 (changed +10 -7)
 2019-07-17jribeiroInitialize atoms' lone pair and drude fields
* psfgen/src/topo_mol_pluginio.c 1.52 (changed +9 -0)
* psfgen/src/psf_file_extract.c 1.31 (changed +8 -7)
 2019-07-16jribeiroThe first psfgen version to pass the test suite; the hydrogen mass repartition (both in a small and half of a million atom structures) tests, and the build of the addictive charmm36 and drude force field with lone pairs and drude particles. As noticed before, there is still room for improvement in the data structure (avoiding the use of double and lone pair and drude information for all atoms); and also for speed up. Psfgen is now compiling with the molfile plugin and using it to generate js files (the other file formats can also be produced this way). The read-in of structures with lone pairs and drude particles will be developed next. Need to check if VMD still adds the space in the atoms' names with three characters when generating js files. This forces a while loop in the functions is_hydrogen and is_oxygen.
* psfgen/src/topo_mol_struct.h 1.16 (changed +5 -0)
* psfgen/src/topo_mol_pluginio.c 1.51 (changed +41 -44)
* psfgen/src/topo_mol_output.c 1.32 (changed +27 -20)
* psfgen/src/topo_mol.c 1.42 (changed +598 -152)
* psfgen/src/topo_defs.c 1.15 (changed +1 -1)
* psfgen/src/psf_file_extract.h 1.5 (changed +23 -0)
* psfgen/src/psf_file_extract.c 1.30 (changed +24 -7)
* psfgen/src/psf_file.h 1.7 (changed +10 -0)
* psfgen/src/psf_file.c 1.13 (changed +39 -2)
 2019-07-10jribeiroAdding missing molefacture_balloontext.tcl to the VMFILES list of the Makefile
* molefacture/Makefile 1.11 (changed +1 -1)
 2019-07-09jribeiroRemove the json parser package dependency from molefacture.
* molefacture/molefacture.tcl 1.109 (changed +1 -2)
 2019-07-02jribeiroAllow the import of topologies with halogens, but only if no lone pairs are detected. This ensures compatibility with the CHARMM36 pre-lone pairs in the halogens.
* molefacture/molefacture_internals.tcl 1.51 (changed +10 -3)
* molefacture/molefacture_gui.tcl 1.71 (changed +14 -2)
* molefacture/molefacture.tcl 1.108 (changed +9 -9)
 2019-07-01jribeiroCreate a new mechanism to store and retrieve the parameters read by the plugin. Now there is a global list that stores all the parameters fed by the user, and upon reading, there is handlerID that is returned. This handlerID points to the position of the topology in the global list. In this way, the program calling this plugin does not need to store the topologies but queries the readcharmmpar plugin for individual components of the topologies. The overhaul is not complete. Further modifications will need to happen, especially changing the arguments of the procs to accept the handlerID instead of the full digested parameters.
* readcharmmpar/readcharmmpar.tcl 1.21 (changed +51 -2)
Small changes and corrections to the documentation page
* molefacture/doc/index.html 1.20 (changed +24 -20)
Update plugin version
* readcharmmpar/readcharmmpar.tcl 1.22 (changed +2 -2)
* readcharmmpar/pkgIndex.tcl 1.8 (changed +1 -1)
* readcharmmpar/Makefile 1.10 (changed +1 -1)
 2019-06-28jribeiroAdd message of "*Terminal Patches not supported" in the patches entry label
* qwikmd/qwikmd.tcl 1.81 (changed +2 -2)
Fix bug in gui after detecting the presence of the cgenffcaller plugin
* molefacture/molefacture_gui.tcl 1.70 (changed +2 -2)
Fix hotkey definition for move fragments
* molefacture/molefacture_gui.tcl 1.69 (changed +1 -1)
Fix protein builder bug
* molefacture/molefacture_internals.tcl 1.50 (changed +1 -1)
* molefacture/molefacture_builder.tcl 1.41 (changed +1 -1)
Update the index.html of the Molefacture web page
* molefacture/doc/index.html 1.19 (changed +276 -59)
Update the plugin webpage according to the new version
* molefacture/doc/molefacture.png 1.5 (changed +316 -355)
* molefacture/doc/icons/translate.png 1.1 (added binary)
* molefacture/doc/icons/select_atom.png 1.1 (added binary)
* molefacture/doc/icons/rotate.png 1.1 (added binary)
* molefacture/doc/icons/move_frag.png 1.1 (added binary)
* molefacture/doc/icons/move_atom.png 1.1 (added binary)
* molefacture/doc/icons/duplicate_sel.png 1.1 (added binary)
* molefacture/doc/icons/del_bond.png 1.1 (added binary)
* molefacture/doc/icons/del_atom.png 1.1 (added binary)
* molefacture/doc/icons/bond_order.png 1.1 (added binary)
* molefacture/doc/icons/add_hydrogen.png 1.1 (added binary)
* molefacture/doc/icons/add_bond.png 1.1 (added binary)
* molefacture/doc/icons/add_atom.png 1.1 (added binary)
 2019-06-28johnsAdded rough draft initial placeholder data structures for
alchemical free energy information in trajectory files.
* include/molfile_plugin.h 1.111 (changed +48 -3)
 2019-06-26johnsEnable both plugin-based I/O and also the new psfgen internal implementation
path when building huge structures.
* psfgen/Makefile.pluginio 1.4 (changed +2 -1)
 2019-06-25jribeiroAdd the icons for the buttons of the new Molefacure interface. There are two versions of the same image, one for Linux and Windows, and the other "_mac.gif" for MacOS. This is necessary as tk 8.5 does not show the text of the radiobuttons when the "-indicatoron false" option is set. The Mac version of the icons has the text included in the image itself.
* molefacture/lib/icons/translate_selected_mac.gif 1.1 (added binary)
* molefacture/lib/icons/translate_selected.gif 1.1 (added binary)
* molefacture/lib/icons/translate_mac.gif 1.1 (added binary)
* molefacture/lib/icons/translate.gif 1.1 (added binary)
* molefacture/lib/icons/selectatom_sel_mac.gif 1.1 (added binary)
* molefacture/lib/icons/selectatom_sel.gif 1.1 (added binary)
* molefacture/lib/icons/selectatom_mac.gif 1.1 (added binary)
* molefacture/lib/icons/selectatom.gif 1.1 (added binary)
* molefacture/lib/icons/rotate_selected_mac.gif 1.1 (added binary)
* molefacture/lib/icons/rotate_selected.gif 1.1 (added binary)
* molefacture/lib/icons/rotate_mac.gif 1.1 (added binary)
* molefacture/lib/icons/rotate.gif 1.1 (added binary)
* molefacture/lib/icons/move_selected_mac.gif 1.1 (added binary)
* molefacture/lib/icons/move_selected.gif 1.1 (added binary)
* molefacture/lib/icons/move_mac.gif 1.1 (added binary)
* molefacture/lib/icons/move_frag_selected_mac.gif 1.1 (added binary)
* molefacture/lib/icons/move_frag_selected.gif 1.1 (added binary)
* molefacture/lib/icons/move_frag_mac.gif 1.1 (added binary)
* molefacture/lib/icons/move_frag.gif 1.1 (added binary)
* molefacture/lib/icons/move.gif 1.1 (added binary)
* molefacture/lib/icons/duplicate_mac.gif 1.1 (added binary)
* molefacture/lib/icons/duplicate.gif 1.1 (added binary)
* molefacture/lib/icons/delete_selected_mac.gif 1.1 (added binary)
* molefacture/lib/icons/delete_selected.gif 1.1 (added binary)
* molefacture/lib/icons/delete_mac.gif 1.1 (added binary)
* molefacture/lib/icons/delete_bond_mac.gif 1.1 (added binary)
* molefacture/lib/icons/delete_bond.gif 1.1 (added binary)
* molefacture/lib/icons/delete.gif 1.1 (added binary)
* molefacture/lib/icons/bond_order_mac.gif 1.1 (added binary)
* molefacture/lib/icons/bond_order.gif 1.1 (added binary)
* molefacture/lib/icons/arrow_right.gif 1.1 (added binary)
* molefacture/lib/icons/arrow_down.gif 1.1 (added binary)
* molefacture/lib/icons/add_hydrogen_mac.gif 1.1 (added binary)
* molefacture/lib/icons/add_hydrogen.gif 1.1 (added binary)
* molefacture/lib/icons/add_bond_mac.gif 1.1 (added binary)
* molefacture/lib/icons/add_bond.gif 1.1 (added binary)
* molefacture/lib/icons/add_atom_selected_mac.gif 1.1 (added binary)
* molefacture/lib/icons/add_atom_selected.gif 1.1 (added binary)
* molefacture/lib/icons/add_atom_mac.gif 1.1 (added binary)
* molefacture/lib/icons/add_atom.gif 1.1 (added binary)
Declare missing array ate the namespace level
* qwikmd/qwikmd.tcl 1.79 (changed +1 -0)
Molefacture redesign. The molefacture interface was completely redesigned to become more interactive and easy to use. Many features, like FEP and Nucleic Acid Builder, were hidden to reduce complexity while the new interface was being developed. These features will be re-implemented one at the time in the subsequent versions.
The new version is not based on xbgf files, as the molecule is designed in memory, and export to files only when necessary.
Instead of 3 different lists (atom, bonds, and angles), there is now only one table listing the atoms and its information (name, type, element, etc.). The bonds, angles, and dihedrals are detected automatically while the atoms are selected, and can be manipulated using the sliders in the respective GUI sections.
Molefacture can use Open Babel (obminimize command) or NAMD to minimize the structure being modeled. In the case of NAMD, CHARMM36 Force Field is used, and the user can submit the new molecule to the CGenFF server to fetch the topologies and parameters. TODO: The direct connection between VMD and CGenFF server (cgenffcaller plugin) is not yet distributed until the user authentication mechanism is defined. Once this is established, the plugin will be included in the VMD distribution, and the user will be able to submit to the server from directly within VMD. Until then, one has to this manually, or use the local version of CGenFF.
Many new functions were added, like adding independent fragments and bond them together; creating ring and chain "skeletons" made up of carbon atoms that can be decorated and modified for faster drafting of molecules, and an "Undo" button to go back to previous states in the modeling process.
This plugin will have more porpuses than just creating molecules, and the interface is planned to be modulated using the left panel (atom's table) by making this panel a notebook with tabs, in which each tab serves a different purpose. Example of one of these porpuses is the selection of the different partitions of a drug part of an alchemical transformation.
* molefacture/molefacture_state.tcl 1.22 (changed +266 -111)
* molefacture/molefacture_internals.tcl 1.49 (changed +2045 -1163)
* molefacture/molefacture_gui.tcl 1.68 (changed +3522 -1166)
* molefacture/molefacture_geometry.tcl 1.24 (changed +364 -288)
* molefacture/molefacture_edit.tcl 1.16 (changed +321 -118)
* molefacture/molefacture_builder.tcl 1.40 (changed +1222 -418)
* molefacture/molefacture_balloontext.tcl 1.1 (added +64 -0)
* molefacture/molefacture.tcl 1.106 (changed +1032 -82)
Update the definition of the amino acid fragments to ensure compatibility with the new Molefacture version.
* molefacture/lib/amino_acids/THR.mfrag 1.2 (changed +1 -1)
* molefacture/lib/amino_acids/PRO.mfrag 1.5 (changed +0 -3)
* molefacture/lib/amino_acids/GLY-end.mfrag 1.6 (changed +1 -3)
Update the definition of the fragments to ensure compatibility with the new Molefacture version.
* molefacture/lib/basemol/cyclooctane.mfrag 1.2 (changed +12 -36)
* molefacture/lib/basemol/cyclohexane.mfrag 1.2 (changed +8 -26)
* molefacture/lib/basemol/cycloheptane.mfrag 1.2 (changed +11 -32)
Update the definition of the fragments to ensure compatibility with the new Molefacture version. Add the carbonyl fragment
* molefacture/lib/fragments/frag.mdb 1.5 (changed +1 -1)
* molefacture/lib/fragments/cyclooctane.frag 1.2 (changed +11 -34)
* molefacture/lib/fragments/cycloheptane.frag 1.2 (changed +12 -32)
* molefacture/lib/fragments/carbonyl.mfrag 1.1 (added +11 -0)
Update version number.
* qwikmd/qwikmd.tcl 1.80 (changed +2 -2)
* qwikmd/pkgIndex.tcl 1.5 (changed +1 -1)
* qwikmd/Makefile 1.9 (changed +1 -1)
* paratool/pkgIndex.tcl 1.9 (changed +1 -1)
* paratool/paratool.tcl 1.111 (changed +2 -2)
* paratool/doc/index.html 1.9 (changed +1 -1)
* paratool/Makefile 1.15 (changed +1 -1)
* molefacture/pkgIndex.tcl 1.8 (changed +1 -1)
* molefacture/molefacture.tcl 1.107 (changed +2 -2)
* molefacture/Makefile 1.10 (changed +1 -1)
* idatm/pkgIndex.tcl 1.2 (changed +1 -1)
* idatm/idatm.tcl 1.19 (changed +2 -2)
* idatm/doc/index.html 1.3 (changed +1 -1)
* idatm/Makefile 1.4 (changed +1 -1)
* autopsf/pkgIndex.tcl 1.14 (changed +1 -1)
* autopsf/doc/tech.html 1.3 (changed +1 -1)
* autopsf/doc/index.html 1.14 (changed +1 -1)
* autopsf/autopsf.tcl 1.149 (changed +2 -2)
* autopsf/Makefile 1.22 (changed +1 -1)
 2019-06-25johnsRevised write_js_timestep() to ensure that it will always succeed,
regardless whether the caller provides page-aligned block-multiple-sized
memory buffers or not. Since write performance is generally far less
critical than read performance, two I/O calls (each) are used to
write out the Timestep coordinate and PBC unit cell blocks in
page-multiple-sized records on disk. We use a persistent zero-filled
buffer in the jshandle data structure to write the necessary padding bytes.
* molfile_plugin/src/jsplugin.c 1.81 (changed +32 -6)
 2019-06-24jribeiroFix typo: '#' missing from in the comment.
* autopsf/autopsf.tcl 1.148 (changed +2 -2)
Improvement of the ring detection using atomselection instead of moltoptools. moltoptools doesn't work for nanotubes.
make_bond now uses the bond list and bond order from the atomselection and not the one in memory. It is important to get the correct indexing when the atom's index is not consecutive.
As far as I am aware, only the new Molefacture uses this plugin.
* idatm/idatm.tcl 1.18 (changed +133 -42)
Prevent QwikMD from deleting molecules loaded before opening QwikMD. Update the Gui to use tktooltip and infobuttons plugin. Separate the GUI design from the declaration of long commands. Use a condensed atomselection in a single representation to represent the residues selected either on the "Manipulation Window" or in the OpenGL window, instead of creating individual representations per selected residue. Small Improvements and bug fix.
Add the interface between QwikMD and Molefacture. QwikMD can now export un-parameterized molecule to Molefacture. When Molefacture "apply to the parent," loads the information to the "Edit Atom" window of QwikMD. Although this works, one needs to make it more bulletproof.
* qwikmd/qwikmd_func.tcl 1.67 (changed +297 -71)
* qwikmd/qwikmd.tcl 1.78 (changed +1155 -1076)
Protect the filenames from spaces in the path. Enforce the detection of the first residue of the segment, so single residue segments are identified correctly.
* autopsf/autopsf.tcl 1.147 (changed +8 -8)
Reate a new mechanism to store and retrieve the topology read by the plugin. Now there is a global list that stores all the topologies fed by the user, and upon reading, there is handlerID that is returned. This handlerID points to the position of the topology in the global list. In this way, the program calling this plugin does not need to store the topologies but queries the readcharmmtop plugin for individual components of the topologies. The overhaul is not complete. Further modifications will need to happen, especially changing the arguments of the procs to accept the handlerID instead of the full digested topology.
* readcharmmtop/readcharmmtop.tcl 1.19 (changed +52 -4)
Update the plugin to use the new readcharmmtop plugin interface.
* qwikmd/qwikmd_func.tcl 1.66 (changed +3 -3)
* qwikmd/qwikmd.tcl 1.77 (changed +3 -2)
* paratool/paratool_topology.tcl 1.30 (changed +3 -2)
* paratool/paratool_readwrite.tcl 1.43 (changed +7 -4)
* paratool/paratool_components.tcl 1.35 (changed +5 -2)
* paratool/paratool.tcl 1.110 (changed +18 -8)
 2019-06-18johnsSync up psfgen plugin I/O Makefile with the Makefile for normal builds.
* psfgen/Makefile.pluginio 1.3 (changed +3 -1)
 2019-06-07ryanmcgreevyTooltips now use the new tktooltip plugin.
* mdff/mdff_gui.tcl 1.46 (changed +44 -66)
 2019-06-07johnsAdded cv_dashboard, infobutton, and tktooltip plugins to the build
* Makefile 1.143 (changed +4 -1)
Added info.gif to build
* infobutton/Makefile 1.2 (changed +1 -1)
Added initial infobutton Makefile
* infobutton/Makefile 1.1 (added +23 -0)
Added initial rev of infobutton plugin for use by QwikMD and MDFF plugins
* infobutton/pkgIndex.tcl 1.1 (added +16 -0)
* infobutton/infobutton.tcl 1.1 (added +148 -0)
* infobutton/info.gif 1.1 (added +10 -0)
Added initial tktooltip Makefile
* tktooltip/Makefile 1.1 (added +23 -0)
Added initial version of tktooltip plugin for use by QwikMD and MDFF plugins
* tktooltip/tktooltip.tcl 1.1 (added +47 -0)
* tktooltip/pkgIndex.tcl 1.1 (added +16 -0)
 2019-06-04ryanmcgreevyAdded tooltip text for labels of main tab of MDFF GUI, MDFF Setup, to aid users in understanding the purpose of each option.
* mdff/pkgIndex.tcl 1.7 (changed +1 -1)
* mdff/mdffgui_balloon.tcl 1.1 (added +162 -0)
* mdff/mdff_gui.tcl 1.45 (changed +70 -0)
* mdff/Makefile 1.7 (changed +2 -2)
 2019-05-31johnsUpdated cv_dashboard with a fix for the launch issue I previously reported.
* cv_dashboard/cv_dashboard_main.tcl 1.2 (changed +1 -1)
* cv_dashboard/cv_dashboard.tcl 1.2 (changed +6 -4)
 2019-05-22johnsAdded cv_dashboard templates to the plugin tree
* cv_dashboard/templates/moving_frame_of_reference.in 1.1 (added +25 -0)
* cv_dashboard/templates/components/tilt.in 1.1 (added +13 -0)
* cv_dashboard/templates/components/spinangle.in 1.1 (added +13 -0)
* cv_dashboard/templates/components/selfcoordnum.in 1.1 (added +11 -0)
* cv_dashboard/templates/components/rmsd.in 1.1 (added +12 -0)
* cv_dashboard/templates/components/orientation.in 1.1 (added +20 -0)
* cv_dashboard/templates/components/inertia.in 1.1 (added +11 -0)
* cv_dashboard/templates/components/hbond.in 1.1 (added +11 -0)
* cv_dashboard/templates/components/gyration.in 1.1 (added +11 -0)
* cv_dashboard/templates/components/groupcoord.in 1.1 (added +15 -0)
* cv_dashboard/templates/components/distancez.in 1.1 (added +16 -0)
* cv_dashboard/templates/components/distancexy.in 1.1 (added +16 -0)
* cv_dashboard/templates/components/distancevec.in 1.1 (added +14 -0)
* cv_dashboard/templates/components/distancepairs.in 1.1 (added +14 -0)
* cv_dashboard/templates/components/distanceinv.in 1.1 (added +15 -0)
* cv_dashboard/templates/components/distancedir.in 1.1 (added +13 -0)
* cv_dashboard/templates/components/distance.in 1.1 (added +13 -0)
* cv_dashboard/templates/components/dipolemagnitude.in 1.1 (added +10 -0)
* cv_dashboard/templates/components/dipoleangle.in 1.1 (added +16 -0)
* cv_dashboard/templates/components/dihedralPC.in 1.1 (added +12 -0)
* cv_dashboard/templates/components/dihedral.in 1.1 (added +19 -0)
* cv_dashboard/templates/components/coordnum.in 1.1 (added +20 -0)
* cv_dashboard/templates/components/angle.in 1.1 (added +17 -0)
* cv_dashboard/templates/colvar_extended.in 1.1 (added +36 -0)
* cv_dashboard/templates/colvar_analysis.in 1.1 (added +38 -0)
* cv_dashboard/templates/colvar.in 1.1 (added +37 -0)
Added new colvars cv_dashboard plugin to the plugin tree.
* cv_dashboard/pkgIndex.tcl 1.1 (added +16 -0)
* cv_dashboard/cv_dashboard_plots.tcl 1.1 (added +290 -0)
* cv_dashboard/cv_dashboard_main.tcl 1.1 (added +473 -0)
* cv_dashboard/cv_dashboard_editor.tcl 1.1 (added +395 -0)
* cv_dashboard/cv_dashboard.tcl 1.1 (added +286 -0)
* cv_dashboard/README.md 1.1 (added +52 -0)
* cv_dashboard/Makefile 1.1 (added +22 -0)
 2019-04-24jribeiroAs the drude particles are never stored as atoms in the atomArray, it is necessary to make a first pass through all atoms in the residue to update the atomid (additional increment for drude particles on the host) before starting printing any information to the psf file. This was not being done previously, and it is now fixed. The need to duplicate the atomid update before printing to any file (psf, pdb or namdbin) would be avoided if the write commands were somehow communicating and setting a global variable when the atomids were first assigned. Not implemented yet.
Fix the exclusion declaration as for every particle is necessary to have an entry, even for drude and lone pairs (0 as default).
* psfgen/src/topo_mol_output.c 1.31 (changed +74 -45)
 2019-04-22jribeiroFix lone pairs initialization
* psfgen/src/topo_mol.c 1.40 (changed +6 -2)
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