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13530 Commits

Author SHA1 Message Date
Steve Plimpton 89a0bc947f small update to docs for new commands 2017-09-05 10:04:20 -06:00
Oliver Henrich c8967a335f Included hyperlink to package 2017-09-05 11:45:32 +01:00
Oliver Henrich 2105145f55 More minor changes 2017-09-05 11:40:36 +01:00
Oliver Henrich f7715ab6ce Added comment about optimised damping coefficient for BD 2017-09-05 11:35:26 +01:00
Oliver Henrich 12fe614ddf Added sequence-dependent stacking and base-pairing strength 2017-09-05 10:48:38 +01:00
Richard Berger 0b5a2e199d Add way of getting correct ctypes integer type for bigint, tagint, and imageint 2017-09-04 20:01:31 -04:00
Richard Berger 09bb687918 Correct indentation 2017-09-04 20:01:04 -04:00
Richard Berger bb3ee752e5 Added optional numpy access to atom data 
The library interface was extended to provide direct access to atom data using
numpy arrays. No data copies are made and numpy operations directly manipulate
memory of the native code.

To keep this numpy dependency optional, all functions are wrapped into the
lammps.numpy sub-object which is only loaded when accessed.
 2017-09-04 19:59:50 -04:00
Richard Berger 6b2d321d18 Add missing globals in library interface 2017-09-04 19:57:02 -04:00
Steve Plimpton 2b9646097c Merge branch 'master' of github.com:lammps/lammps 2017-09-01 09:16:11 -06:00
Steve Plimpton f58088ae61 patch 1Sep17 2017-09-01 09:15:37 -06:00
Axel Kohlmeyer 397bc225b2 add temper/npt to src/USER-MISC/README 2017-08-31 14:56:43 -04:00
Axel Kohlmeyer d9d9ba8244 update .gitignore 2017-08-31 14:52:56 -04:00
Axel Kohlmeyer eba4be18c2 adapt formatting and naming conventions to fully match LAMMPS style. allow rigid and accelerated integrators. 2017-08-31 14:48:30 -04:00
Axel Kohlmeyer 4d2ed30b35 add reference outputs to temper/npt example 2017-08-31 14:13:02 -04:00
Axel Kohlmeyer f3dda30f8e fully integrate temper/npt command into manual 2017-08-31 13:53:40 -04:00
Stan Moore d95a5f219e Remove all thread fences except one in verlet_kokkos 2017-08-31 10:38:36 -06:00
Julien Devemy a5b65c1af4 Mods for extra/special/per/atom and add toluene 2017-08-31 15:03:04 +02:00
Tim Mattox 3e6cdd1400 USER-DPD: finish renaming #ifdef DEBUG_PAIR_CT to DEBUG_SSA_PAIR_CT 2017-08-30 14:58:38 -05:00
Tim Mattox dc7f1281b8 USER-DPD: Kokkos version of Const Temperature DPD isn't implemented yet 
The Constant Energy DPD (DPDE) was our primary usage case, so only stubs
for the Constant Temperature case were included in Kokkos code so far.
The non-Kokkos version works fine for Constant Temperature DPD.
 2017-08-30 11:01:17 -05:00
Christoph Junghans 27c962dc3b link cuda in gpu only, remove duplicated incl. dir 2017-08-30 09:45:01 -06:00
Tim Mattox 2dd202cc76 USER-DPD: remove some out-of-date FIXME comments in fix_shardlow_kokkos.cpp 2017-08-30 10:34:09 -05:00
Tim Mattox f2d8c37f27 Rename SSA specific debug #ifdef to DEBUG_SSA_PAIR_CT 2017-08-30 10:24:29 -05:00
Stan Moore a4a45f1d9c Remove unnecessary check in npair_kokkos 2017-08-29 17:25:13 -06:00
Amulya f57d194920 Add files via upload 
documentation for temper/npt
 2017-08-29 10:40:37 -04:00
Richard Berger 34b3fc2157 Fix GPU CMake compilation 2017-08-29 01:20:34 -04:00
Christoph Junghans 098861375b SOVERSION not needed for STATIC libs 2017-08-28 16:18:58 -06:00
Christoph Junghans 19b77857dc fix Fortran flags for MEAM 2017-08-28 14:59:01 -06:00
Christoph Junghans bd9dc4886d cmake: README is markdown 2017-08-28 14:27:12 -06:00
Christoph Junghans 9207f6540e fix liblammps install 2017-08-28 14:11:21 -06:00
Tim Mattox 736e063971 Merge branch 'master' (21893539cb Aug 25) into USER-DPD_kokkos_merge 
Resolved conflicts in src/KOKKOS/npair_kokkos.cpp
 2017-08-28 14:46:50 -05:00
Christoph Junghans 62928a1637 make GPU flags local to libgpu 2017-08-28 13:24:41 -06:00
Christoph Junghans c8dfe0c3de drop BUILD_SHARED_PKG_LIBS and make all pkglibs static 2017-08-28 13:17:27 -06:00
Amulya 6a4bbddb3b Add files via upload 
data file for example
 2017-08-28 14:56:37 -04:00
Amulya 2add18e013 Create in.temper_npt 
example for temper/npt
 2017-08-28 14:55:43 -04:00
Amulya d0efd3a422 Add files via upload 
Updated command to temper/npt instead of temper_npt
 2017-08-28 14:48:00 -04:00
Christoph Junghans f47cc0aab5 simpilfy pkg lib build 2017-08-27 18:55:28 -06:00
Christoph Junghans 57872c8b60 drop INSTALL_LIB option 2017-08-27 18:42:32 -06:00
Christoph Junghans 4bff008777 enable PIC globally 2017-08-27 18:40:55 -06:00
Richard Berger 153c771a6d Use PIC in mpi_stubs when BUILD_SHARED_LIBS=on 2017-08-27 17:27:43 -04:00
Richard Berger 313b8bc2fa build lib/gpu as a library 2017-08-27 17:00:56 -04:00
Christoph Junghans 5308ee67fa fix shared build and mscg install 2017-08-27 13:45:48 -06:00
Christoph Junghans c196025ea9 make molfile less special 2017-08-27 12:23:30 -06:00
Christoph Junghans bc11868986 cmake: fixed a typo 2017-08-27 12:13:35 -06:00
Christoph Junghans e4415735f2 check for '-fno-second-underscore' 2017-08-27 12:10:46 -06:00
Christoph Junghans 98f27162ba make libmpi_stubs 2017-08-27 11:37:57 -06:00
Christoph Junghans bdc117bf10 cmake: convert mscg into a lib 2017-08-27 07:15:00 -06:00
Christoph Junghans b7ec720f91 link QUIP against LAPACK_LIB too 2017-08-27 07:13:55 -06:00
Christoph Junghans 47f16c0d70 cmake: move shared libs install warning in one place 2017-08-27 07:06:08 -06:00
Richard Berger 76926b7fcf Compile linalg as library and track link dependencies for correct link order 2017-08-27 03:54:40 -04:00