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13908 Commits

Author SHA1 Message Date
Richard Berger 2a131d1416 Merge remote-tracking branch 'upstream/master' into fix_python_move 2017-12-15 13:56:54 -05:00
Richard Berger bcc5f49d0b Rename fix python to fix python/invoke 2017-12-15 13:53:04 -05:00
Richard Berger 950bfb84a9 Clean up after renaming back to fix python/move 2017-12-15 13:27:27 -05:00
Richard Berger 4d725c3153 Revert "Rename fix python/move to move/python" 
This reverts commit 4d915dba08.
 2017-12-15 13:17:12 -05:00
Richard Berger 1b07a4edee Fix memory leak in pair python 2017-12-10 17:14:08 -05:00
Axel Kohlmeyer 81a1c007ed correct file name for doc file 2017-12-07 16:39:41 -05:00
Axel Kohlmeyer 0b51e9b2ff add documentation for fix move/python 2017-12-07 16:36:36 -05:00
Steve Plimpton d029cb9002
Merge pull request #743 from stanmoore1/kk_yukawa_fix 
Fix compile error in pair_yukawa_kokkos
 2017-12-07 10:31:04 -07:00
Stan Moore 3e99d1a83a Add pair yukawa/kk to Section_commands 2017-12-07 09:06:33 -07:00
Stan Moore c4e83be533 Fix compile error in pair_yukawa_kokkos 2017-12-07 08:42:17 -07:00
Steve Plimpton d7e5d60f90
Merge pull request #738 from rbberger/pylammps_thermo_style_fix 
PyLammps bugfix to support custom thermo output with vector element addressing
 2017-12-07 08:25:01 -07:00
Steve Plimpton 5179efd2bb
Merge pull request #741 from stanmoore1/kk_compile 
Reduce Kokkos compile dependencies
 2017-12-07 08:24:22 -07:00
Steve Plimpton abb2fe5be7
Merge pull request #740 from stanmoore1/improve_reax 
Improve ReaxFF
 2017-12-07 08:23:47 -07:00
Steve Plimpton bae45e2493
Merge pull request #737 from akohlmey/collected-bugfixes 
Collected bugfixes and small updates for next patch
 2017-12-07 08:23:06 -07:00
Steve Plimpton 73d509f339
Merge pull request #735 from jaapkroe/extep 
Add ExTeP pair style
 2017-12-07 08:22:34 -07:00
Steve Plimpton fa0c28b717
Merge pull request #731 from Pakketeretet2/pair-yukawa-kk 
Added a KOKKOS-enabled Yukawa pair style.
 2017-12-07 08:21:20 -07:00
Steve Plimpton bc3a84b480
Merge pull request #727 from lammps/fix-gcmc-examples 
new example scripts for fix gcmc
 2017-12-07 08:19:56 -07:00
Richard Berger 4d915dba08 Rename fix python/move to move/python 2017-12-05 23:42:57 -05:00
Stan Moore f64544a5fe Move instantiation of MemoryKokkos class 2017-12-05 08:34:24 -07:00
Jaap Kroes fc742eb2ef Remove outdated elastic constants 2017-12-05 16:23:20 +01:00
Stefan Paquay 1baecc689e
Merge pull request #3 from stanmoore1/kk_yukawa 
Add pair_yukawa_kokkos to Install.sh and minor cleanup.

These changes look fine. Sorry for the tabs, I must have forgotten about those.
 2017-12-04 14:16:53 -05:00
Stan Moore d916416cc5 Add pair_yukawa_kokkos to Install.sh and minor cleanup 2017-12-04 12:02:32 -07:00
Stan Moore 2813923f15 Add multiple inheritance to pair_multi_lucy_rx_kokkos 2017-12-04 10:43:41 -07:00
Axel Kohlmeyer 4a3a6b4455 no need to include library.o in the LAMMPS executable 2017-12-03 19:37:42 -05:00
Richard Berger f8891a4451 Rename fix python/integrate to python/move 
This is to avoid confusion to what LAMMPS considers to be an
integrator like Verlet and RESPA.
 2017-12-02 01:04:46 -05:00
Giacomo Fiorin 51688b2504 Improve performance of Python integrator (NVE_Opt version) 
Removing the loop over atoms by using NumPy array indexing allows to recover
performance close to that of plain fix nve.
 2017-12-02 00:40:21 -05:00
Richard Berger 93be2d264e Detect correct integer type in lammps python interface 2017-12-02 00:39:15 -05:00
Richard Berger b9fd1156b2 Completed first version of fix python/integrate 
This includes an example of how to implement fix NVE in Python.

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.
 2017-12-02 00:39:15 -05:00
Richard Berger bbfe16782b Adjust .gitignore 2017-12-02 00:37:14 -05:00
Richard Berger 1931d2088a Started FixPythonIntegrate 2017-12-02 00:37:14 -05:00
Stan Moore 5d9a6c1fe2 Add checks to Kokkos Install.sh so that files aren't unnecessarily recompiled 2017-12-01 16:06:50 -07:00
Axel Kohlmeyer e7f97728c3 disable disruptive debug output 2017-12-01 17:14:11 -05:00
Axel Kohlmeyer 58ed92d905 one more file that doesn't require to include accelerator_kokkos.h 2017-12-01 16:45:22 -05:00
Axel Kohlmeyer 14aa036f36 add missing header files to USER-INTEL package 2017-12-01 15:53:02 -05:00
Stan Moore 42e03da70c Remove redundant #include in input.cpp 2017-12-01 13:16:35 -07:00
Stan Moore 5d2e097b27 Need dynamic cast for multiple inheritance 2017-12-01 12:53:40 -07:00
Stan Moore da51a8a0bb Add missing header files to GPU package 2017-12-01 12:13:14 -07:00
Stan Moore 80dffb27e2 Add missing header files 2017-12-01 11:33:42 -07:00
Stan Moore 5b33f153f4 Add newline to memory_kokkos.h 2017-12-01 10:33:47 -07:00
Stan Moore 31eb12920c Use multiple inheritance to remove accelerator_kokkos.h out of region.h and kspace.h 2017-12-01 10:18:22 -07:00
Stan Moore 31f2ca1e4c Use multiple inheritance to remove accelerator_kokkos.h out of pair.h 2017-12-01 09:51:40 -07:00
Stan Moore 15a3364c2c Make memory_kokkos its own class 2017-12-01 09:13:31 -07:00
Stan Moore c3aa705d04 Improve performance of pair_reaxc, this change is safe because the non-bonded i-loop doesn't include ghost atoms; this optimization is already included in the USER-OMP version 2017-11-30 09:22:32 -07:00
Stan Moore 8c2d38c7e9 Remove non-existent function in reaxc_forces_omp 2017-11-30 09:13:03 -07:00
Stan Moore e3b961b622 Improve performance of PairReaxCKokkos 2017-11-30 09:10:39 -07:00
Axel Kohlmeyer 319508bd29 fix scoping ambiguity issue that confuses nvcc 2017-11-30 10:56:58 -05:00
Richard Berger 6f7bd78ea2 Fixes issue #701 
PyLammps now supports thermo_style entries such as c_msd[4]
 2017-11-29 01:06:44 -05:00
Axel Kohlmeyer 5647522906 various small cosmetic adjustments to increase conformance with LAMMPS programming conventions 2017-11-28 12:34:23 -05:00
Axel Kohlmeyer e4b14213b4 delete old log files. new log files are approved by @athomps 2017-11-28 11:35:49 -05:00
Axel Kohlmeyer fa6fc947f2 fix issues in FixNeighHistory and FixNeighHistoryOMP reported in https://sourceforge.net/p/lammps/mailman/message/36138319/ 
This supersedes and closes PR #734
 2017-11-28 11:28:15 -05:00