namd.git
6 years agofixing even more PEBCK errors...renaming recvBGrid and recvQGrid to recvB and recvQ release-2-9-beta-1
Chris Harrison [Mon, 19 Mar 2012 16:47:18 +0000 (11:47 -0500)]
fixing even more PEBCK errors...renaming recvBGrid and recvQGrid to recvB and recvQ

6 years agofixing more PBECK errors for fixing msa/msa.h include
Chris Harrison [Mon, 19 Mar 2012 16:29:01 +0000 (11:29 -0500)]
fixing more PBECK errors for fixing msa/msa.h include

6 years agorestoring #include msa/msa.h b/c of PBECK and removing MSA PAGE SIZE define as it...
Chris Harrison [Mon, 19 Mar 2012 16:26:10 +0000 (11:26 -0500)]
restoring #include msa/msa.h b/c of PBECK and removing MSA PAGE SIZE define as it is now defined inside charm++ src

6 years agoremoving include of MoaMacros.h
Chris Harrison [Mon, 19 Mar 2012 16:23:29 +0000 (11:23 -0500)]
removing include of MoaMacros.h

6 years agofixing typo on recvB entry method
Chris Harrison [Mon, 19 Mar 2012 14:41:55 +0000 (09:41 -0500)]
fixing  typo on recvB entry method

6 years agoadding MSA_PAGE_SIZE def
Chris Harrison [Mon, 19 Mar 2012 14:40:49 +0000 (09:40 -0500)]
adding MSA_PAGE_SIZE def

6 years agoShould build without MSA now.
Jim Phillips [Mon, 19 Mar 2012 04:24:56 +0000 (23:24 -0500)]
Should build without MSA now.

6 years agoFix MOA build.
Jim Phillips [Mon, 19 Mar 2012 03:49:01 +0000 (22:49 -0500)]
Fix MOA build.

6 years agopushing in Moa files v0
Chris Harrison [Mon, 19 Mar 2012 02:57:32 +0000 (21:57 -0500)]
pushing in Moa files v0

6 years agoAdd J. Lai and D. Wells to authors.
Jim Phillips [Mon, 19 Mar 2012 02:36:37 +0000 (21:36 -0500)]
Add J. Lai and D. Wells to authors.

6 years agoUpdate for new replica exchange implementation.
Jim Phillips [Mon, 19 Mar 2012 02:34:20 +0000 (21:34 -0500)]
Update for new replica exchange implementation.

6 years agoUpdate CUDA docs.
Jim Phillips [Mon, 19 Mar 2012 01:42:42 +0000 (20:42 -0500)]
Update CUDA docs.

6 years agoProper fix to keep Go forces from breaking alchemical free energy calcs.
Jim Phillips [Sat, 17 Mar 2012 02:51:10 +0000 (21:51 -0500)]
Proper fix to keep Go forces from breaking alchemical free energy calcs.

6 years agoDon't break other features when Go is off.
Jim Phillips [Sat, 17 Mar 2012 02:24:09 +0000 (21:24 -0500)]
Don't break other features when Go is off.

6 years agoMove release date back.
Jim Phillips [Fri, 16 Mar 2012 22:50:07 +0000 (17:50 -0500)]
Move release date back.

6 years agoRemove -ftz=true option that was causing instability.
Jim Phillips [Fri, 16 Mar 2012 22:48:51 +0000 (17:48 -0500)]
Remove -ftz=true option that was causing instability.

6 years agoFixed bug in Gridforce wrapping code
David Wells [Fri, 16 Mar 2012 19:47:35 +0000 (14:47 -0500)]
Fixed bug in Gridforce wrapping code

6 years agoGenerating ptx code doesn't work with multiple device code generation.
Jim Phillips [Thu, 15 Mar 2012 20:12:08 +0000 (15:12 -0500)]
Generating ptx code doesn't work with multiple device code generation.

6 years agoGenerate code for both 1.1 and 2.0 devices.
Jim Phillips [Thu, 15 Mar 2012 20:11:15 +0000 (15:11 -0500)]
Generate code for both 1.1 and 2.0 devices.

6 years agoFix bug causing "PmePencilMap multiple pencils on a pe?" error.
Jim Phillips [Thu, 15 Mar 2012 16:46:26 +0000 (11:46 -0500)]
Fix bug causing "PmePencilMap multiple pencils on a pe?" error.

6 years agoAdd CUDA error checking in progress polling functions.
Jim Phillips [Thu, 15 Mar 2012 14:00:12 +0000 (09:00 -0500)]
Add CUDA error checking in progress polling functions.

6 years agoFix bug for multicore with one patch per pe.
Jim Phillips [Wed, 14 Mar 2012 23:06:38 +0000 (18:06 -0500)]
Fix bug for multicore with one patch per pe.

6 years agoRemove bogus "REDUCING NUMBER OF PATCHES" message.
Jim Phillips [Wed, 14 Mar 2012 22:28:04 +0000 (17:28 -0500)]
Remove bogus "REDUCING NUMBER OF PATCHES" message.

6 years agoTurn dual streams back on with timeout adding to polling functions.
Jim Phillips [Wed, 14 Mar 2012 17:56:57 +0000 (12:56 -0500)]
Turn dual streams back on with timeout adding to polling functions.

6 years agoadding Amber structure support to LCPO
David Tanner [Wed, 14 Mar 2012 15:44:14 +0000 (10:44 -0500)]
adding Amber structure support to LCPO

6 years agoUpdate docs/notes/announcement and bump version to 2.9b1.
Jim Phillips [Tue, 13 Mar 2012 17:02:52 +0000 (12:02 -0500)]
Update docs/notes/announcement and bump version to 2.9b1.

6 years agoUpdate dependencies.
Jim Phillips [Tue, 13 Mar 2012 15:08:15 +0000 (10:08 -0500)]
Update dependencies.

6 years agoDisable multiple streams because of unexplained hangs.
Jim Phillips [Tue, 13 Mar 2012 12:50:59 +0000 (07:50 -0500)]
Disable multiple streams because of unexplained hangs.

6 years agoCheck if local work is done immediately after processing remote work
Jim Phillips [Tue, 13 Mar 2012 06:22:28 +0000 (01:22 -0500)]
Check if local work is done immediately after processing remote work
rather than waiting for next polling period.

6 years agoDisable event timers, fix GBIS timing, clean up timing output.
Jim Phillips [Mon, 12 Mar 2012 01:17:38 +0000 (20:17 -0500)]
Disable event timers, fix GBIS timing, clean up timing output.

6 years agoAdd staticAtomAssignment parameter, which places equal numbers of atoms
Jim Phillips [Sun, 11 Mar 2012 23:40:49 +0000 (18:40 -0500)]
Add staticAtomAssignment parameter, which places equal numbers of atoms
in each patch and never migrates them, limiting the patch grid to 2
in each dimension, or 3 for dimensions with twoAway... enabled.  Never
enabled automatically since it can error on startup on missing bonds, etc.
Provides a benefit in CUDA-accelerated GBIS by balancing block runtime.

6 years agoMove all box opening to noWork to simplify code and fix GBIS with multiple
Jim Phillips [Sun, 11 Mar 2012 05:57:18 +0000 (23:57 -0600)]
Move all box opening to noWork to simplify code and fix GBIS with multiple
host threads.  Also fix nonbondedFreq > 1 with multiple host threads.

6 years agoSplit remote and local work into separate streams to allow overlap.
Jim Phillips [Sun, 11 Mar 2012 05:00:22 +0000 (23:00 -0600)]
Split remote and local work into separate streams to allow overlap.

6 years agoUncomment tabulated energies since implementation is fixed now.
Jim Phillips [Fri, 9 Mar 2012 07:37:04 +0000 (01:37 -0600)]
Uncomment tabulated energies since implementation is fixed now.

6 years agoFix and simplify tabulated energies.
Jim Phillips [Fri, 9 Mar 2012 07:35:02 +0000 (01:35 -0600)]
Fix and simplify tabulated energies.

6 years agoFix build with stub files includes.
Jim Phillips [Thu, 8 Mar 2012 22:55:46 +0000 (16:55 -0600)]
Fix build with stub files includes.

6 years agoBeginning initial integration of NAMD-OPENATOM QM/MM module
Chris Harrison [Thu, 8 Mar 2012 22:29:04 +0000 (16:29 -0600)]
Beginning initial integration of NAMD-OPENATOM QM/MM module

6 years agoBeginning initial integration of NAMD-OPENATOM QM/MM module
Chris Harrison [Thu, 8 Mar 2012 22:12:40 +0000 (16:12 -0600)]
Beginning initial integration of NAMD-OPENATOM QM/MM module

6 years agoComment out tabulated energies until implementation is fixed.
Jim Phillips [Thu, 8 Mar 2012 18:16:50 +0000 (12:16 -0600)]
Comment out tabulated energies until implementation is fixed.

6 years agoEliminate extra copy of CUDA atom data.
Jim Phillips [Wed, 7 Mar 2012 20:36:15 +0000 (14:36 -0600)]
Eliminate extra copy of CUDA atom data.

6 years agoMove formatting of position data for GPU to HomePatch to eliminate
Jim Phillips [Wed, 7 Mar 2012 07:07:05 +0000 (01:07 -0600)]
Move formatting of position data for GPU to HomePatch to eliminate
redundant work and serial bottleneck at cost of larger messages.

6 years agoPatch from Phil Miller for g++ 3.3 on ancient PPC Mac OS X cluster.
Jim Phillips [Tue, 6 Mar 2012 19:46:13 +0000 (13:46 -0600)]
Patch from Phil Miller for g++ 3.3 on ancient PPC Mac OS X cluster.

6 years agoMultiple CUDA devices use home patches rather than proxies for patches
Jim Phillips [Tue, 6 Mar 2012 06:22:57 +0000 (00:22 -0600)]
Multiple CUDA devices use home patches rather than proxies for patches
on the same node.  Should help single-node multi-GPU runs.

6 years agoreplicaRecv source required to avoid race condition when receiving multiple
Jim Phillips [Mon, 5 Mar 2012 17:56:44 +0000 (11:56 -0600)]
replicaRecv source required to avoid race condition when receiving multiple
messages. This could be avoided by adding tags to CmiReplica arguments to
distinguish size messages and including source in size message.

6 years agoChange < and > to $<$ and $>$.
Jim Phillips [Sat, 3 Mar 2012 23:48:49 +0000 (17:48 -0600)]
Change < and > to $<$ and $>$.

6 years agoremove extra \item tag.
Jim Phillips [Sat, 3 Mar 2012 23:40:27 +0000 (17:40 -0600)]
remove extra \item tag.

6 years agoDocument Go forces module.
Jim Phillips [Sat, 3 Mar 2012 23:38:22 +0000 (17:38 -0600)]
Document Go forces module.

6 years agoAdd braces around arguments to limit font changes.
Jim Phillips [Sat, 3 Mar 2012 23:38:04 +0000 (17:38 -0600)]
Add braces around arguments to limit font changes.

6 years agoMerge from VMD plugin tree. Handle long type names and large atom counts.
Jim Phillips [Fri, 2 Mar 2012 19:50:41 +0000 (13:50 -0600)]
Merge from VMD plugin tree.  Handle long type names and large atom counts.

6 years agoPull changes from VMD plugin tree. Tests _MSC_VER instead of WIN32,
Jim Phillips [Fri, 2 Mar 2012 19:33:30 +0000 (13:33 -0600)]
Pull changes from VMD plugin tree.  Tests _MSC_VER instead of WIN32,
prepends "psfgen)" to most messages on stdout, increases version to 1.6.

6 years agoInclude Charm++ patch to enable replica exchange in MPI builds.
Jim Phillips [Fri, 2 Mar 2012 07:13:19 +0000 (01:13 -0600)]
Include Charm++ patch to enable replica exchange in MPI builds.

6 years agoSwitch from storing a ComputeID and looking up the object in ComputeMap
Jim Phillips [Fri, 2 Mar 2012 07:00:05 +0000 (01:00 -0600)]
Switch from storing a ComputeID and looking up the object in ComputeMap
to do anything with it to storing the Compute* itself.

6 years agoUpdate to charm-6.4.0.
Jim Phillips [Thu, 1 Mar 2012 02:12:11 +0000 (20:12 -0600)]
Update to charm-6.4.0.

6 years agoMake multicore default charm arch.
Jim Phillips [Thu, 1 Mar 2012 01:58:56 +0000 (19:58 -0600)]
Make multicore default charm arch.

6 years agoFix Windows by using _ftelli64() instead of ftello(), etc.
Jim Phillips [Wed, 29 Feb 2012 23:22:23 +0000 (17:22 -0600)]
Fix Windows by using _ftelli64() instead of ftello(), etc.

6 years agoFix position_distance sign error to be consistent with code in NAMD.
Jim Phillips [Wed, 29 Feb 2012 21:57:04 +0000 (15:57 -0600)]
Fix position_distance sign error to be consistent with code in NAMD.

6 years agoFix printf format.
Jim Phillips [Wed, 29 Feb 2012 08:05:24 +0000 (02:05 -0600)]
Fix printf format.

6 years agoAdd internal consistency check for replica_neighbors proc.
Jim Phillips [Wed, 29 Feb 2012 07:59:01 +0000 (01:59 -0600)]
Add internal consistency check for replica_neighbors proc.

6 years agoTweak documentation.
Jim Phillips [Wed, 29 Feb 2012 07:15:34 +0000 (01:15 -0600)]
Tweak documentation.

6 years agoSkip first entry in colvars.traj file since it just repeats input state.
Jim Phillips [Wed, 29 Feb 2012 07:09:38 +0000 (01:09 -0600)]
Skip first entry in colvars.traj file since it just repeats input state.

6 years agoAdd final_step argument to trim trajectory back to restart point.
Jim Phillips [Wed, 29 Feb 2012 06:57:46 +0000 (00:57 -0600)]
Add final_step argument to trim trajectory back to restart point.

6 years agoRename colvars state file to save as part of restart files.
Jim Phillips [Wed, 29 Feb 2012 05:58:01 +0000 (23:58 -0600)]
Rename colvars state file to save as part of restart files.

6 years agoWrite colvars trajectory more often to test sortreplicas.
Jim Phillips [Wed, 29 Feb 2012 04:53:46 +0000 (22:53 -0600)]
Write colvars trajectory more often to test sortreplicas.

6 years agoMove Langevin params other than langevinTemperature to alanin_base.namd.
Jim Phillips [Wed, 29 Feb 2012 04:48:38 +0000 (22:48 -0600)]
Move Langevin params other than langevinTemperature to alanin_base.namd.

6 years agoFilter out repeated timesteps in colvar trajectory file.
Jim Phillips [Wed, 29 Feb 2012 04:36:32 +0000 (22:36 -0600)]
Filter out repeated timesteps in colvar trajectory file.

6 years agoProcess colvar trajectory files if they are present.
Jim Phillips [Wed, 29 Feb 2012 04:07:19 +0000 (22:07 -0600)]
Process colvar trajectory files if they are present.

6 years agoExpand to 64 replicas.
Jim Phillips [Tue, 28 Feb 2012 21:48:33 +0000 (15:48 -0600)]
Expand to 64 replicas.

6 years agoAdd script for creating multiple output directories.
Jim Phillips [Tue, 28 Feb 2012 21:48:05 +0000 (15:48 -0600)]
Add script for creating multiple output directories.

6 years agoImplement umbrella sampling using colvars in arbitrary dimensions.
Jim Phillips [Tue, 28 Feb 2012 18:42:10 +0000 (12:42 -0600)]
Implement umbrella sampling using colvars in arbitrary dimensions.

6 years agoMove "source ../replica.namd" from command line to jobX.conf files.
Jim Phillips [Tue, 28 Feb 2012 18:29:29 +0000 (12:29 -0600)]
Move "source ../replica.namd" from command line to jobX.conf files.

6 years agoMove "source ../replica.namd" from command line to jobX.conf files.
Jim Phillips [Tue, 28 Feb 2012 18:23:48 +0000 (12:23 -0600)]
Move "source ../replica.namd" from command line to jobX.conf files.

6 years agoFixed the bug in creating spanning tree for home patches in the case that
Chao Mei [Mon, 27 Feb 2012 17:11:57 +0000 (11:11 -0600)]
Fixed the bug in creating spanning tree for home patches in the case that
a node doesn't have any home patches.

6 years agocorrect LCPO pairlist update frequency
David Tanner [Mon, 27 Feb 2012 17:03:05 +0000 (11:03 -0600)]
correct LCPO pairlist update frequency

6 years agoAdd colvarbias Tcl command with changeconfig and energydiff sub-commands
Jim Phillips [Mon, 27 Feb 2012 04:03:03 +0000 (22:03 -0600)]
Add colvarbias Tcl command with changeconfig and energydiff sub-commands
to enable combining replica exchange with umbrella sampling.

6 years agoSwitch recursive bisection fallback from lowest-load node to space-filling curve.
Jim Phillips [Sat, 25 Feb 2012 02:33:37 +0000 (20:33 -0600)]
Switch recursive bisection fallback from lowest-load node to space-filling curve.

6 years agoOnly allocate as much memory as needed for X pencil. (Was safe before.)
Jim Phillips [Fri, 24 Feb 2012 22:19:36 +0000 (16:19 -0600)]
Only allocate as much memory as needed for X pencil.  (Was safe before.)

6 years agoDo not use GlobalMasterServer for IDM if IMDignore is on.
Jim Phillips [Fri, 24 Feb 2012 22:04:13 +0000 (16:04 -0600)]
Do not use GlobalMasterServer for IDM if IMDignore is on.

6 years agoReduce number of "Ignoring IMD forces due to IMDignore" messages.
Jim Phillips [Fri, 24 Feb 2012 22:01:57 +0000 (16:01 -0600)]
Reduce number of "Ignoring IMD forces due to IMDignore" messages.

6 years agoDon't die (but still warn) about low exclusion count if full electrostatics is off.
Jim Phillips [Fri, 24 Feb 2012 01:25:01 +0000 (19:25 -0600)]
Don't die (but still warn) about low exclusion count if full electrostatics is off.

6 years agoLCPO improved initial parameters
David Tanner [Thu, 23 Feb 2012 19:39:49 +0000 (13:39 -0600)]
LCPO improved initial parameters

6 years agoadding documentation for LCPO
David Tanner [Thu, 23 Feb 2012 19:26:01 +0000 (13:26 -0600)]
adding documentation for LCPO

6 years agomade LCPO a little faster and more robust
David Tanner [Thu, 23 Feb 2012 16:46:28 +0000 (10:46 -0600)]
made LCPO a little faster and more robust

6 years agoAdd -ugni arch suffix.
Jim Phillips [Thu, 23 Feb 2012 03:54:30 +0000 (21:54 -0600)]
Add -ugni arch suffix.

6 years agoTurn off "Num fixedAtom lookup" messages.
Jim Phillips [Thu, 23 Feb 2012 02:45:31 +0000 (20:45 -0600)]
Turn off "Num fixedAtom lookup" messages.

6 years agoFix uninitialized go energies when go not active.
Jim Phillips [Wed, 22 Feb 2012 21:56:25 +0000 (15:56 -0600)]
Fix uninitialized go energies when go not active.

6 years agoEliminate variable-size array.
Jim Phillips [Wed, 22 Feb 2012 21:15:24 +0000 (15:15 -0600)]
Eliminate variable-size array.

6 years agoMore information on bad exclusion count errors.
Jim Phillips [Wed, 22 Feb 2012 20:40:14 +0000 (14:40 -0600)]
More information on bad exclusion count errors.

6 years agoAdded note for PmePencil atomic blocks so that it is clear to know the meaning
Chao Mei [Wed, 22 Feb 2012 03:32:49 +0000 (21:32 -0600)]
Added note for PmePencil atomic blocks so that it is clear to know the meaning
of each atomic block in Projection

6 years agoDisable the debugging output for proxy lists of patches
Chao Mei [Tue, 21 Feb 2012 20:48:42 +0000 (14:48 -0600)]
Disable the debugging output for proxy lists of patches

6 years agoRebuild dependencies.
Jim Phillips [Tue, 21 Feb 2012 19:35:51 +0000 (13:35 -0600)]
Rebuild dependencies.

6 years agoAdd additional information to bad global atom count error.
Jim Phillips [Tue, 21 Feb 2012 18:51:05 +0000 (12:51 -0600)]
Add additional information to bad global atom count error.

6 years agoFix implementation of clear() plus other minor cleanups.
Jim Phillips [Tue, 21 Feb 2012 18:48:13 +0000 (12:48 -0600)]
Fix implementation of clear() plus other minor cleanups.

6 years agoAdd internal consistency check for combined migration message.
Jim Phillips [Tue, 21 Feb 2012 18:30:38 +0000 (12:30 -0600)]
Add internal consistency check for combined migration message.

6 years agoAdd internal consistency check.
Jim Phillips [Tue, 21 Feb 2012 18:29:35 +0000 (12:29 -0600)]
Add internal consistency check.

6 years agoset num LCPO patches to 8 instead of non c++ expression
David Tanner [Tue, 21 Feb 2012 17:48:21 +0000 (11:48 -0600)]
set num LCPO patches to 8 instead of non c++ expression

6 years agoFixed compilation errors regarding function assignLCPOTypes by allowing it
Chao Mei [Tue, 21 Feb 2012 17:14:36 +0000 (11:14 -0600)]
Fixed compilation errors regarding function assignLCPOTypes by allowing it
only in non-memopt version.

6 years agolinear combination of pairwise overlaps (LCPO) for solvent accessible surface area...
David Tanner [Tue, 21 Feb 2012 14:43:43 +0000 (08:43 -0600)]
linear combination of pairwise overlaps (LCPO) for solvent accessible surface area (SASA) calculation to accompany GBIS implicit solvent

6 years agoFix bug where if all home patches on a node start out empty they share the same atom...
Jim Phillips [Mon, 20 Feb 2012 23:00:41 +0000 (17:00 -0600)]
Fix bug where if all home patches on a node start out empty they share the same atom array.

6 years agoAvoid dynamically adjusting pairlist distance if patch is empty.
Jim Phillips [Sun, 19 Feb 2012 22:22:00 +0000 (16:22 -0600)]
Avoid dynamically adjusting pairlist distance if patch is empty.

6 years agoEliminate order-numPes loop to find messages in migration message array.
Jim Phillips [Sun, 19 Feb 2012 22:17:07 +0000 (16:17 -0600)]
Eliminate order-numPes loop to find messages in migration message array.