59de1a71c8
Merge branch 'history' of github.com:lammps/lammps into history
2017-10-16 14:37:30 -04:00
4c6779cb0d
USER-DPD Kokkos: propagate the new neigh_modify options from efaa4c67
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Propogate the efaa4c67
2017-10-16 13:37:27 -05:00
5fb5f70ec6
update USER-OMP code for shear history neighbor refactoring
2017-10-16 14:37:20 -04:00
b0bba1976b
USER-DPD: remove unused coord2bin() variants, and add ISFINITE checks
2017-10-16 13:36:44 -05:00
f8f13d929f
Merge pull request #693 from giacomofiorin/colvars-update
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Update Colvars to version 2017-10-11
2017-10-13 17:25:06 -06:00
3e89b270fd
Update Colvars to version 2017-10-11
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Notable features are the umbrella-integration based free energy estimator for
eABF, and the traditional thermodynamic integration estimator now available
for umbrella sampling, SMD, metadynamics. Also included are several small fixes.
Below is a list of relevant commits in the Colvars repository since the last update.
321d06a 2017-10-10 Add macros to manage colvarscript commands [Giacomo Fiorin]
26c3bec 2017-10-09 Document coming availability of Lepton in LAMMPS [Giacomo Fiorin]
cc8f249 2017-10-04 Clarify that SMP depends on code build [Giacomo Fiorin]
0b2ffac 2017-10-04 Summarize colvar definition options, clarify some details [Giacomo Fiorin]
28002e0 2017-10-01 Separate writing of restart file from other output (e.g. PMFs) [Giacomo Fiorin]
92f7c1d 2017-10-01 Deprecate colvarsTrajAppend [Giacomo Fiorin]
12a707f 2017-09-26 Accurate Jacobian calculation for RMSD variants [Jérôme Hénin]
fe389c9 2017-09-21 Allow subtractAppliedForce with extended-L again [Jérôme Hénin]
c050ce0 2017-09-18 Silence compiler warnings, remove Tabs [Giacomo Fiorin]
cb41905 2017-01-11 Add base class for TI estimator in other biases than ABF [Giacomo Fiorin]
a1bc676 2017-09-14 Avoid writing to unopened traj file [Jérôme Hénin]
b58d8cd 2017-09-08 Function to check for overlapping groups [Jérôme Hénin]
1e5efec 2017-09-07 Check for overlapping groups in coordNum [Jérôme Hénin]
03a61a4 2017-04-06 Add UI-based estimator [fhh2626]
ae43754 2017-08-17 Fix outputCenters parsing [Josh Vermaas]
1619e0e 2017-08-14 Delete static feature arrays in cvm destructor [Jérôme Hénin]
2017-10-13 13:45:10 -04:00
f6ddc8c7c9
Fix compile errors from neigh history refactor
2017-10-13 10:49:31 -06:00
a973c65d67
Merge pull request #691 from akohlmey/collected-fixes
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Collected small changes for next patch
2017-10-13 09:50:03 -06:00
1a200588bd
Merge pull request #689 from rbberger/pylammps_autocomplete_fix
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Limit IPython autocomplete to known commands and properties
2017-10-13 09:49:03 -06:00
18ca2292c2
Merge pull request #686 from giacomofiorin/lepton-library
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Add Lepton library within lib/colvars
2017-10-13 09:48:42 -06:00
d3ef4bd594
Merge pull request #685 from ellio167/kim-api-v1.9.2
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Update lib/kim for kim-api-v1.9.2
2017-10-13 09:48:16 -06:00
3df9caf435
drop const qualifier to allow bracketing of lookup index
2017-10-13 10:29:49 -04:00
fa2e5ac2d9
handle lookup exceptions consistently across energy and energy+force lookup in bond/angle style table
2017-10-13 10:13:34 -04:00
b7c7492608
handle invalid lookup for bond/angle tabulation
2017-10-13 09:50:56 -04:00
cee94da85e
bugfix. avoiding operating on uninitialize data. closes #690
2017-10-13 00:15:15 -04:00
45aa7de171
Limit IPython autocomplete to known commands and properties
2017-10-12 14:43:17 -04:00
53aa92cfaf
add support for neighbor list history refactoring in USER-OMP part 2
2017-10-11 10:30:29 -04:00
7e35042c42
add support for neighbor list history refactoring in USER-OMP part 1
2017-10-11 10:29:41 -04:00
01051e4cb1
refactoring of neighbor history
2017-10-10 16:53:51 -06:00
d90aad887e
Add Lepton library within lib/colvars
2017-10-09 15:25:43 -04:00
775a15b9da
Update lib/kim for kim-api-v1.9.2
2017-10-09 14:06:30 -05:00
93c9a92743
Merge pull request #684 from irisTa56/bugfix-in-domain.cpp
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Bugfix for checking image flags
2017-10-09 08:30:48 -06:00
14dc1c698c
Merge pull request #683 from wmbrownIntel/pppm_intel_fix
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Fixing bug in pppm/intel for AVX-512 with single precision and ik diff.
2017-10-09 08:29:52 -06:00
a1f5693fe0
Merge pull request #681 from lammps/dump-modify
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remove dependence of dump modify 'at' and 'append'
2017-10-09 08:29:12 -06:00
534b7adde4
Bugfix for checking image flags
2017-10-09 21:29:07 +09:00
02646100e9
correct handling of "at" keyword for netcdf dumps as suggested by @pastewka in PR #681 review
2017-10-09 07:49:29 -04:00
7e58f084d2
Fixing bug in pppm/intel for AVX-512 with single precision and ik diff.
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This commit simplifies the code by eliminating packing optimizations that were slower
under typical parameters and had some memory bugs.
2017-10-08 08:33:07 -07:00
0f5d7dcc0f
cmake: added USER-UEF
2017-10-07 12:38:41 -06:00
b6187173e6
Merge branch 'master' into HEAD
2017-10-07 12:35:51 -06:00
88a33edb50
Merge pull request #680 from lammps/map-yes
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add atom_modify map yes, also timers to create_atoms and replicate
2017-10-06 17:43:52 -06:00
6820db99e2
avoid merge conflict
2017-10-06 14:41:38 -04:00
58e1969de2
rename misleading "CPU time" into "Time spent"
2017-10-06 14:34:10 -04:00
e91e505fb3
remove dependence of dump modify 'at' and 'append'
2017-10-06 09:44:29 -06:00
f7cbdcf995
Merge pull request #673 from pastewka/17_dump_nc2
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Multi file support for NetCDF dump style
2017-10-06 09:14:12 -06:00
4cfa88b70f
Merge pull request #674 from wmbrownIntel/user-intel-update
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Mike Brown has added DPD to the USER-INTEL package with speedups over 3X for Xeon Phi and over 1.7X for some Xeon processors.
2017-10-06 09:12:39 -06:00
352a20fc1c
DOC: Updated doc to separate description of 'append' and 'at' keywords.
2017-10-06 16:38:15 +02:00
dc0e20947e
MAINT: Return error when 'at' keyword is used without 'append yes'.
2017-10-06 16:37:52 +02:00
05847a0e87
Merge branch 'master' into user-intel-update
2017-10-06 10:18:38 -04:00
439c2fd980
Merge pull request #677 from stanmoore1/kk_update
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Update to Kokkos r2.04.04 and add workaround for performance regression
2017-10-05 17:10:00 -06:00
15853a0e38
Merge pull request #676 from stanmoore1/kokkos_reverse_comm
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Add Kokkos threaded reverse communication
2017-10-05 17:08:49 -06:00
bd17ee5df7
Merge pull request #675 from wesbarnett/master
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cmake: Add -restrict for Intel compilers
2017-10-05 17:08:35 -06:00
a9b7ff1154
Merge pull request #679 from stanmoore1/kk_reax_comm
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ReaxC optimizations
2017-10-05 17:08:17 -06:00
0dd7ba26c0
Merge pull request #672 from akohlmey/phana-w-tricubic
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Streamline compilation of "phana" tool for fix phonon
2017-10-05 17:01:37 -06:00
7a90eef527
Merge pull request #668 from ovilab/modify_deallocation_fix
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Fixed proper deletion of fixes if fix is NULL
2017-10-05 17:00:10 -06:00
5d0626e50e
Merge pull request #665 from akohlmey/collected-small-fixes
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Collected small fixes
2017-10-05 16:58:49 -06:00
4b7ca0383a
Merge pull request #664 from timattox/kokkos_atom2bin
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Kokkos atom2bin
2017-10-05 16:58:16 -06:00
0ed987dc61
Merge pull request #663 from jdevemy/master
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Authorize hybrid/overlay for fix srp
2017-10-05 16:56:20 -06:00
55a3fdca80
Merge pull request #660 from junghans/latte_fix
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cmake: fix build with system latte
2017-10-05 16:55:22 -06:00
214c0cfb2b
add atom_modify map yes, also timers to create_atoms and replicate
2017-10-05 16:44:24 -06:00
e0efdd50fa
Switch to classic comm if ghost_velocity. The check_forward and check_reverse tests aren't necessary because the fix/pair/etc. comm is done in a separate routine.
2017-10-05 15:47:46 -06:00
Axel Kohlmeyer