a7bc3ed391
Add missing fences in comm_kokkos
2017-12-15 13:30:17 -07:00
68cf6941e1
Add Kokkos thread fences to pack/unpack routines
2017-12-15 13:01:38 -07:00
73c55ac4d1
Fix up docs after renaming
2017-12-15 14:06:16 -05:00
2a131d1416
Merge remote-tracking branch 'upstream/master' into fix_python_move
2017-12-15 13:56:54 -05:00
bcc5f49d0b
Rename fix python to fix python/invoke
2017-12-15 13:53:04 -05:00
950bfb84a9
Clean up after renaming back to fix python/move
2017-12-15 13:27:27 -05:00
4d725c3153
Revert "Rename fix python/move to move/python"
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This reverts commit 4d915dba08
2017-12-15 13:17:12 -05:00
10fa54b2fd
correct error messages. the atom style is called "smd" not "tlsph"
2017-12-13 18:44:31 -05:00
8a36cdc6bc
correct velocity output for write_data of atom style smd
2017-12-13 18:42:24 -05:00
e5cd068cd5
Merge branch 'patch-3' of https://github.com/abbatux/lammps into collected-bugfixes-and-updates
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This closes #745
2017-12-13 17:41:00 -05:00
cec22dda92
change pair style airebo/intel to compile with -DLAMMPS_BIGBIG
2017-12-13 16:20:49 -05:00
9a71efc5d5
fix neb bugfix from Emile Maras
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NEB was not working fine when using multiple proc
per replica and the keywords last/efirst or last/efirst/middle
I have corrected this in the enclosed fix_neb.cpp
I also slightly modified the nudging for this free end so that
it would be applied only when the target energy is larger than
the energy. Anyway if the target energy is lower than the energy,
the replica should relax toward the target energy without adding
any nudging.
I also modified the documentation according to this change.
2017-12-13 15:19:46 -05:00
2f857c6eda
correct fix neigh/history/omp to properly support -DLAMMPS_BIGBIG compilation
2017-12-13 15:12:14 -05:00
8a93f63de9
Update Kokkos docs
2017-12-13 10:05:53 -07:00
193252275f
A few more tweaks to charge history in fix_qeq_reax_kokkos
2017-12-12 09:54:28 -07:00
5968850306
Fix broken charge history in fix_qeq_reax_kokkos
2017-12-12 09:20:09 -07:00
3291a4fe96
Revert "no need to include library.o in the LAMMPS executable"
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This reverts commit 4a3a6b4455
2017-12-11 08:08:49 -05:00
1b07a4edee
Fix memory leak in pair python
2017-12-10 17:14:08 -05:00
16d6dfcab6
Bugfix for effective plastic strain rate calc
2017-12-08 11:40:44 +11:00
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
