1b07a4edee
Fix memory leak in pair python
2017-12-10 17:14:08 -05:00
0edad83b25
Update atom_vec_smd.cpp
2017-12-08 11:29:12 +11:00
81a1c007ed
correct file name for doc file
2017-12-07 16:39:41 -05:00
0b51e9b2ff
add documentation for fix move/python
2017-12-07 16:36:36 -05:00
4b1bcaa1ae
fix speelink in documentation files
2017-12-07 16:01:02 -05:00
ed8680d695
suspend support for sphinxcontrib.images
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the sphinxcontrib.image extension was broken with sphinx 16.x.
however, sphinx 15.x breaks with newer version of the multiprocessor module.
so we suspend the thumbnail processing and lift the lock to sphinx 15.x
also, the number of parallel sphinx tasks is can be overridden with SPHINXEXTRA="-j #'.
default is to try use all local CPU cores.
2017-12-07 15:38:15 -05:00
29df5a536f
Merge branch 'master' of https://github.com/lammps/lammps into USER-DPD_es_RNG
2017-12-07 10:57:01 -07:00
d029cb9002
Merge pull request #743 from stanmoore1/kk_yukawa_fix
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Fix compile error in pair_yukawa_kokkos
2017-12-07 10:31:04 -07:00
3e99d1a83a
Add pair yukawa/kk to Section_commands
2017-12-07 09:06:33 -07:00
c4e83be533
Fix compile error in pair_yukawa_kokkos
2017-12-07 08:42:17 -07:00
d7e5d60f90
Merge pull request #738 from rbberger/pylammps_thermo_style_fix
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PyLammps bugfix to support custom thermo output with vector element addressing
2017-12-07 08:25:01 -07:00
5179efd2bb
Merge pull request #741 from stanmoore1/kk_compile
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Reduce Kokkos compile dependencies
2017-12-07 08:24:22 -07:00
abb2fe5be7
Merge pull request #740 from stanmoore1/improve_reax
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Improve ReaxFF
2017-12-07 08:23:47 -07:00
bae45e2493
Merge pull request #737 from akohlmey/collected-bugfixes
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Collected bugfixes and small updates for next patch
2017-12-07 08:23:06 -07:00
73d509f339
Merge pull request #735 from jaapkroe/extep
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Add ExTeP pair style
2017-12-07 08:22:34 -07:00
fa0c28b717
Merge pull request #731 from Pakketeretet2/pair-yukawa-kk
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Added a KOKKOS-enabled Yukawa pair style.
2017-12-07 08:21:20 -07:00
bc3a84b480
Merge pull request #727 from lammps/fix-gcmc-examples
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new example scripts for fix gcmc
2017-12-07 08:19:56 -07:00
4d915dba08
Rename fix python/move to move/python
2017-12-05 23:42:57 -05:00
f64544a5fe
Move instantiation of MemoryKokkos class
2017-12-05 08:34:24 -07:00
fc742eb2ef
Remove outdated elastic constants
2017-12-05 16:23:20 +01:00
1baecc689e
Merge pull request #3 from stanmoore1/kk_yukawa
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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
d916416cc5
Add pair_yukawa_kokkos to Install.sh and minor cleanup
2017-12-04 12:02:32 -07:00
2813923f15
Add multiple inheritance to pair_multi_lucy_rx_kokkos
2017-12-04 10:43:41 -07:00
4a3a6b4455
no need to include library.o in the LAMMPS executable
2017-12-03 19:37:42 -05:00
f8891a4451
Rename fix python/integrate to python/move
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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
51688b2504
Improve performance of Python integrator (NVE_Opt version)
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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
93be2d264e
Detect correct integer type in lammps python interface
2017-12-02 00:39:15 -05:00
b9fd1156b2
Completed first version of fix python/integrate
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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
bbfe16782b
Adjust .gitignore
2017-12-02 00:37:14 -05:00
1931d2088a
Started FixPythonIntegrate
2017-12-02 00:37:14 -05:00
5d9a6c1fe2
Add checks to Kokkos Install.sh so that files aren't unnecessarily recompiled
2017-12-01 16:06:50 -07:00
e7f97728c3
disable disruptive debug output
2017-12-01 17:14:11 -05:00
58ed92d905
one more file that doesn't require to include accelerator_kokkos.h
2017-12-01 16:45:22 -05:00
14aa036f36
add missing header files to USER-INTEL package
2017-12-01 15:53:02 -05:00
42e03da70c
Remove redundant #include in input.cpp
2017-12-01 13:16:35 -07:00
5d2e097b27
Need dynamic cast for multiple inheritance
2017-12-01 12:53:40 -07:00
da51a8a0bb
Add missing header files to GPU package
2017-12-01 12:13:14 -07:00
80dffb27e2
Add missing header files
2017-12-01 11:33:42 -07:00
5b33f153f4
Add newline to memory_kokkos.h
2017-12-01 10:33:47 -07:00
31eb12920c
Use multiple inheritance to remove accelerator_kokkos.h out of region.h and kspace.h
2017-12-01 10:18:22 -07:00
31f2ca1e4c
Use multiple inheritance to remove accelerator_kokkos.h out of pair.h
2017-12-01 09:51:40 -07:00
15a3364c2c
Make memory_kokkos its own class
2017-12-01 09:13:31 -07:00
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
8c2d38c7e9
Remove non-existent function in reaxc_forces_omp
2017-11-30 09:13:03 -07:00
e3b961b622
Improve performance of PairReaxCKokkos
2017-11-30 09:10:39 -07:00
319508bd29
fix scoping ambiguity issue that confuses nvcc
2017-11-30 10:56:58 -05:00
6f7bd78ea2
Fixes issue #701
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PyLammps now supports thermo_style entries such as c_msd[4]
2017-11-29 01:06:44 -05:00
5647522906
various small cosmetic adjustments to increase conformance with LAMMPS programming conventions
2017-11-28 12:34:23 -05:00
e4b14213b4
delete old log files. new log files are approved by @athomps
2017-11-28 11:35:49 -05:00
fa6fc947f2
fix issues in FixNeighHistory and FixNeighHistoryOMP reported in https://sourceforge.net/p/lammps/mailman/message/36138319/
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This supersedes and closes PR #734
2017-11-28 11:28:15 -05:00
