6aa756968d
Temper_NPT and example
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New function that allows for parallel tempering (replica exchange) in MD in LAMMPS in the isothermal-isobaric ensemble (NPT)
Similar to temper which works in the canonical (NVT) ensemble.
An example is included that uses temper_npt
2017-08-18 15:21:49 -04:00
d671a04274
whitespace cleanup
2017-08-18 14:24:09 -04:00
bf7cff73d4
allocate the temporary special array on the heap and not the stack (it may get too big quickly) and clear the array before use.
2017-08-18 14:23:48 -04:00
9e85b3178a
molecule maxspecial value corrected when specials autogenerated
2017-08-17 21:39:25 -06:00
b11fe2eddb
Merge pull request #573 from junghans/cmake
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Add secondary, cmake based build system
2017-08-17 16:06:19 -06:00
7ddcb6812b
patch 17Aug17
2017-08-17 16:02:20 -06:00
76cd61350d
Merge pull request #613 from akohlmey/collected-small-changes
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Collected small changes and bug fixes
2017-08-17 11:34:52 -06:00
fa3c0c61d6
Merge pull request #618 from lammps/intel
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USER-INTEL add-ons from Mike
2017-08-17 11:32:53 -06:00
c46d5ff422
Merge pull request #612 from giacomofiorin/colvars-update-2017-08-10
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Minor fixes to Colvars module
2017-08-17 11:32:38 -06:00
dd67989c76
Merge pull request #601 from stanmoore1/kokkos_update
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Update Kokkos library to v2.03.13
2017-08-17 11:32:18 -06:00
00aafef1a8
Merge pull request #597 from ndtrung81/three-body-short-nlist
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Implementing short neighbor lists for three-body gpu styles
2017-08-17 11:31:59 -06:00
7175abcc71
flag more pair styles as supporting USER-INTEL to match newly added code
2017-08-16 13:58:46 -04:00
e34b20405c
Fix a couple of typos in the docs
2017-08-15 21:10:05 -04:00
1d4d2155a2
USER-INTEL add-ons from Mike
2017-08-15 17:12:07 -06:00
cee87d7a54
update manual to point to packages.lammps.org instead of rpm.lammps.org
2017-08-15 16:19:09 -04:00
60e14f1490
add comment to msi2lmp README about symmetry limitations
2017-08-14 08:54:26 -04:00
81e7d4a942
fix incorrect preprocessor define for windows
2017-08-12 00:35:50 -04:00
13b804eeeb
Merge branch 'USER-DPD_kokkos' into USER-DPD_GBhacks as of patch 10Aug17
2017-08-11 14:53:44 -04:00
0b3f1b8a15
patch 11Aug17
2017-08-11 12:19:02 -06:00
4041db8d1a
Merge branch 'master' into USER-DPD_kokkos as of patch 10Aug17
2017-08-11 13:25:28 -04:00
b209a4e246
Merge pull request #614 from akohlmey/fixes-for-stable
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Fixes for stable
2017-08-11 08:35:20 -06:00
27553283c3
fix bug with pair_modify <style> compute not triggering the correct global change
2017-08-11 08:28:37 -04:00
df56b2d6a4
trigger relink after package library build through updating the time stamp on main.cpp
2017-08-11 08:16:20 -04:00
c6d923b6c8
make download function more resilient by also catching failed execution
2017-08-10 21:15:35 -04:00
6d24be8bb7
whitespace cleanup
2017-08-10 21:14:40 -04:00
52bec0f380
patch 10Aug17
2017-08-10 16:44:09 -06:00
8c16ea1bfc
add automatic triggering of review requests with a code owners file
2017-08-10 15:58:51 -04:00
c8741f3a01
remove special_bonds extra keyword and refer to read_data and create_box instead
2017-08-10 15:12:56 -04:00
2a7d2dee36
add more strict checking of data when parsing molecule files to detect format errors
2017-08-10 14:49:51 -04:00
378989e065
Merge pull request #27 from timattox/USER-DPD_kokkos_update
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Merge changes thru July 27, 2017 from master 6d0a228667a0183b7f9a331c
2017-08-10 13:21:53 -04:00
f68c6254d4
Merge pull request #611 from akohlmey/final-tweaks
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More tweaks for stable release
2017-08-10 08:02:55 -06:00
da01be7c18
More robust change from initial to target restraint centers in Colvars
2017-08-10 09:22:53 -04:00
146aa4cdbd
fall back to wget when curl is not available
2017-08-10 09:05:23 -04:00
2f3747eb6e
we need to override compiler flags in lib/voronoi/Install.py
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The default compiler flags in voro++'s config.mk file do not include
-fPIC, which makes it incompatible with building the shared object for
the python wrapper.
2017-08-10 08:34:46 -04:00
2bc6ad80d4
avoid writable string and deprecated implicit conversion warning
2017-08-10 07:45:21 -04:00
f9a515efd3
add some remarks about makefile settings on windows
2017-08-10 07:24:24 -04:00
5b55744209
fix a header line formatting issue
2017-08-10 07:21:39 -04:00
0dc3cbaa8a
Revert "remove -DLAMMPS_MEMALIGN from "make mpi" and "make serial" for increased portability"
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This reverts commit 4e97b57508
2017-08-10 06:51:57 -04:00
ce62c41252
when recomputing special bonds, make certain we do not shrink atom->maxspecial and add force->special_extra only once
2017-08-10 06:47:26 -04:00
4e97b57508
remove -DLAMMPS_MEMALIGN from "make mpi" and "make serial" for increased portability
2017-08-10 05:46:42 -04:00
7f437d7690
Merge pull request #609 from akohlmey/doc-changes-for-stable
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Final tweaks and doc changes for stable release
2017-08-09 17:37:35 -06:00
77a628e4ef
make the deprecation warning nicer looking
2017-08-09 19:13:40 -04:00
f01103dd08
correctly use the term CUDA (instead of Cuda) when not referring to the KOKKOS device flag (which is Cuda)
2017-08-09 19:08:23 -04:00
81f4d7ecb5
rework section 4 (Packages) in the manual to match Install.py scripts
2017-08-09 19:07:20 -04:00
210a77c5a0
add a deprecation warning to pair style meam and make the reax one consistent with it
2017-08-09 16:36:51 -04:00
e86b139817
Merge pull request #25 from timattox/USER-DPD_GBhacks_cudafix
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Fix CUDA runtime issues for USER-DPD Kokkos code.
2017-08-09 15:32:03 -04:00
3e9b41c6b7
Added references to GPU package citations
2017-08-09 10:09:40 -05:00
6780c73907
restore mpic++ makefile to resolve regression test failure
2017-08-09 07:10:08 -04:00
be25a7d9a4
updated comment for fix neb by steve
2017-08-08 20:37:20 -04:00
691d1b730d
Merge pull request #607 from akohlmey/final-changes-for-stable
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Final build system changes for stable release
2017-08-08 17:26:22 -06:00
