02b10380bc
Create ctypes only neighbor list API variant
...
This moves the lammps.get_neighlist() method to lammps.numpy.get_neighlist().
lammps.get_neighlist() now returns a NeighList object, while the NumPy variants
returns a NumPyNeighList object. The main difference between the two is that while
the ctypes variant returns neighlist elements as
atom idx (int), numneighs (int), neighbors (POINTER(c_int))
the NumPy variant returns
atom idx (int), neighbors (numpy.array)
2020-10-05 16:21:37 -04:00
68147306e7
Add Python_neighbor.rst
2020-10-05 16:15:40 -04:00
c06348c507
Update Python docs
2020-10-05 15:07:57 -04:00
8f808a5e6e
Update Python_usage.rst and Python_module.rst
2020-10-05 14:06:09 -04:00
ed17eabe17
Add missing code highlights
2020-10-05 14:04:44 -04:00
884295eb5f
Add example showing Python exception handling
2020-10-05 14:04:14 -04:00
6672568fca
Change links
2020-10-05 14:03:50 -04:00
4f1ed775e9
Add missing docstrings
2020-10-05 14:03:19 -04:00
fb1bd3e962
Correct links
2020-10-02 18:01:52 -04:00
d91d8de76d
Refactor LammpsNumpyWrapper to numpy_wrapper
...
LammpsNumpyWrapper was a class that was defined inside of the
lammps.numpy property when it was first accessed. This made it hard
to document the methods of this class.
This commit extracts this utility class into the lammps module and
renames it to 'numpy_wrapper'.
2020-10-02 17:28:25 -04:00
0089a35d95
Remove dead code
2020-10-02 17:27:08 -04:00
7355977819
Add missing exception handling for functions that could cause errors
2020-10-02 17:26:14 -04:00
d9cbb354d2
Move lammps exception code into its own property
2020-10-02 17:22:01 -04:00
0475397229
Update Python_usage.rst
2020-10-02 17:19:51 -04:00
60891fe6f9
Add Python_config.rst
2020-10-02 17:19:04 -04:00
b57c8f6b77
Add tests for LAMMPS exceptions in Python
2020-10-02 16:53:41 -04:00
52c6353f86
Fix typo
2020-10-02 15:09:29 -04:00
c5fc3f2c78
Update Python_usage.rst
2020-10-01 18:01:07 -04:00
533c453a08
Update Python docs
2020-10-01 15:00:08 -04:00
507c2cb2a8
Update and reorganize Python docs
2020-09-30 22:20:01 -04:00
cc5ef652e4
move Using Python with LAMMPS to programmer guide and integrate python module docs
2020-09-25 15:13:05 -04:00
0ffb2ce09c
move Tutorials to bottom of Howto section
2020-09-25 15:12:31 -04:00
5e6d222d29
fix up a few internal references
2020-09-25 14:04:44 -04:00
495438105f
mass renaming of programmer guide files
2020-09-25 13:59:29 -04:00
9a523fef65
add bibliography
2020-09-25 13:48:22 -04:00
089e55cc37
fix typo
2020-09-25 13:48:05 -04:00
7a35f786fb
tweak button size setting for active state, too.
2020-09-24 16:56:05 -04:00
28812b1ea7
Merge pull request #2381 from akohlmey/collected-small-changes
...
Collected small changes
2020-09-24 16:17:28 -04:00
08270c3498
update container descriptions
2020-09-24 02:17:26 -04:00
02c1480546
update README in examples/COUPLE/simple
2020-09-24 02:17:11 -04:00
ac78f8f1e1
update examples/COUPLE/simple sources to work with the current version of LAMMPS
2020-09-24 01:30:34 -04:00
b350dce573
improve error messages for variables and python commands
2020-09-23 19:02:55 -04:00
2f8a5ddd1f
xindy doesn't seem to be required (and is not available on CentOS 8)
2020-09-23 17:13:09 -04:00
85fe94a6dd
Merge pull request #2388 from jrgissing/molecule_fragments_check
...
molecule: findfragments correction
2020-09-23 15:54:37 -04:00
790f636523
rephrase
2020-09-23 15:45:29 -04:00
b6d98707ec
molecule: revert overzealous error checking
2020-09-23 11:23:10 -04:00
2b30661b07
molecule: correctly update docs
2020-09-23 10:46:23 -04:00
1be766c8cd
molecule fragment: let's add more checks
2020-09-23 10:37:33 -04:00
ed3975054a
fix typo
2020-09-23 10:30:19 -04:00
e29f838121
also add error checks
2020-09-23 10:28:48 -04:00
88b8461e0f
the right molecule fragment fix
2020-09-23 10:19:38 -04:00
343932f220
document -DLAMMPS_TRAP_FPE
2020-09-23 09:38:07 -04:00
ab4dc9c343
Merge pull request #2378 from junghans/cmake_install_fix
...
cmake: do not install mpi.h without library
2020-09-22 21:37:57 -04:00
20027cc7ec
Merge pull request #2390 from Vsevak/hip_pppm_fix
...
Fix atomicAdd in PPPM/GPU for the HIP backend
2020-09-22 18:04:12 -04:00
9df1bb4db0
remove obsolete makefiles. Makefile.xk7 is on death watch but Blue Waters still has such nodes
2020-09-22 17:47:14 -04:00
459d51bbea
Do not disable atomics for HIP
...
atomics are disabled for NVIDIA 1.0 cards, which should not affect ROCm HIP
2020-09-22 22:34:24 +03:00
7b4304577a
add -std=c++11 flag to compilation of all .cpp files on Linux
2020-09-22 10:58:54 -04:00
2d7b6a9008
remove dead code
2020-09-22 10:12:59 -04:00
b878403aee
update a few more singularity container definitions for doc build requirements
2020-09-22 06:01:34 -04:00
1eebdcbd03
fix obvious bugs
2020-09-22 05:34:29 -04:00
