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23843 Commits

Author SHA1 Message Date
Axel Kohlmeyer 1098ca8749
add some more explanation about exceptions from the library interface perspective 2020-10-07 13:08:49 -04:00
Axel Kohlmeyer e637c150ba
add versionadded tags 2020-10-07 13:08:25 -04:00
Axel Kohlmeyer 395906b387
whitespace 2020-10-07 13:07:57 -04:00
Axel Kohlmeyer 5fa1cd7e86
small corrections 2020-10-07 05:33:55 -04:00
Axel Kohlmeyer 9ea38c545d
update global properties tests 2020-10-06 22:43:42 -04:00
Axel Kohlmeyer 355c68f304
Merge branch 'master' into progguide-axel 2020-10-06 21:40:43 -04:00
Axel Kohlmeyer bf4773c3f7
Merge pull request #2407 from akohlmey/collected-small-fixes 
Collected small changes and bugfixes for the next patch release
 2020-10-06 20:17:45 -04:00
Axel Kohlmeyer f0f933a711
allow forward slash in strings for if statements 2020-10-06 18:44:26 -04:00
Axel Kohlmeyer 15f9987c32
add custom commands "cd" and "pwd" to the LAMMPS shell 2020-10-06 18:39:22 -04:00
Axel Kohlmeyer fb1dab6098
Merge branch 'master' into collected-small-fixes 2020-10-06 18:00:33 -04:00
Axel Kohlmeyer 1ee9e4eabd
Merge branch 'master' into progguide-axel 2020-10-06 17:11:47 -04:00
Axel Kohlmeyer 9274912a81
add note about no longer supporting PyPar and remove instructions related to it. 2020-10-06 16:19:43 -04:00
Axel Kohlmeyer 2f857176c8
stay compatible with cmake older than version 3.14 2020-10-06 13:45:46 -04:00
Axel Kohlmeyer f442d811be
Merge commit 'dbf51af7d1565c62902eef22a7aa6f6eb552432b' of github.com:rbberger/lammps into collected-small-fixes 2020-10-06 12:29:36 -04:00
Axel Kohlmeyer 1afd9b1c83
update Python installation docs 2020-10-06 12:15:56 -04:00
Axel Kohlmeyer 887603d856
Merge pull request #2411 from rbberger/fix_wall_gran_region 
Corrections for fix wall/gran and wall/gran/region
 2020-10-06 11:51:58 -04:00
Richard Berger 7dd244a828
Correct fix wall/gran and wall/gran/region docs 2020-10-06 10:45:23 -04:00
Richard Berger 18023ad9dc
Update fix_wall_gran_region.cpp 
Don't store atom tag, just if there is a contact.

Fixes #2306
 2020-10-06 10:39:14 -04:00
Axel Kohlmeyer 5d08f629ab
fix typo 2020-10-06 05:30:09 -04:00
Axel Kohlmeyer b5db29bae4
revise python in LAMMPS docs 2020-10-05 22:48:57 -04:00
Axel Kohlmeyer f2ba00ea9c
update label in graph 2020-10-05 21:50:54 -04:00
Axel Kohlmeyer 549e4df506
Merge branch 'progguide-richard' into progguide-axel 2020-10-05 21:04:29 -04:00
Axel Kohlmeyer 80a054471d
Merge branch 'progguide-updates' into progguide-richard 2020-10-05 19:31:03 -04:00
Richard Berger 5244f49234
Fix broken page 2020-10-05 18:04:30 -04:00
Richard Berger caf434811a
Add example to Python_config.rst 2020-10-05 17:54:48 -04:00
Richard Berger b8c66b099d
Fix typo 2020-10-05 17:42:43 -04:00
Richard Berger 93ed9b4266
Add PyLammps parts 2020-10-05 17:34:50 -04:00
Richard Berger 22cca93603
Add tests for neighbor list API 2020-10-05 17:34:08 -04:00
Richard Berger 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
Richard Berger 68147306e7
Add Python_neighbor.rst 2020-10-05 16:15:40 -04:00
Richard Berger c06348c507
Update Python docs 2020-10-05 15:07:57 -04:00
Axel Kohlmeyer 0fb91ec755
Merge pull request #2408 from akohlmey/lammps-shell 
Add a LAMMPS shell tool as alternative to the LAMMPS executable for interactive use
 2020-10-05 14:42:23 -04:00
Axel Kohlmeyer d9f7ddfd6d
Merge pull request #2409 from mrcdr/math_eigen_impl 
PR to relate "math_eigen_impl.h" with an author
 2020-10-05 14:07:09 -04:00
Richard Berger 8f808a5e6e
Update Python_usage.rst and Python_module.rst 2020-10-05 14:06:09 -04:00
Richard Berger ed17eabe17
Add missing code highlights 2020-10-05 14:04:44 -04:00
Richard Berger 884295eb5f
Add example showing Python exception handling 2020-10-05 14:04:14 -04:00
Richard Berger 6672568fca
Change links 2020-10-05 14:03:50 -04:00
Richard Berger 4f1ed775e9
Add missing docstrings 2020-10-05 14:03:19 -04:00
Axel Kohlmeyer 6933233c56
add tests for the new library APIs 2020-10-05 13:43:11 -04:00
Axel Kohlmeyer 113db3ac73
fold group specific query functions into the more generic ID query functions 2020-10-05 13:41:12 -04:00
Axel Kohlmeyer 68cca6d31a
make warning about lack of exception handling more specific 2020-10-05 12:51:42 -04:00
Axel Kohlmeyer bd206dca10
simplify based on suggestions from @junghans 2020-10-05 11:44:19 -04:00
Axel Kohlmeyer b6d333535c
correct variable name 2020-10-05 11:43:43 -04:00
Axel Kohlmeyer 47e08f63ac
Merge pull request #2406 from jrgissing/bond/react-rmsd_constraint_bugfix 
bond/react: rmsd constraint bugfix
 2020-10-05 10:43:21 -04:00
mrcdr e08d905504 make a small change to math_eigen_impl.h 2020-10-05 22:32:15 +09:00
Axel Kohlmeyer 3e74e03bbb
update all_on/all_off presets to really include all packages 2020-10-04 16:46:29 -04:00
Axel Kohlmeyer d500ffa784
implement handler for CTRL-C on windows. 2020-10-04 16:42:29 -04:00
Axel Kohlmeyer f3b33ea0c6
address spelling issues 2020-10-04 14:10:35 -04:00
Axel Kohlmeyer d1e76068e8
add new APIs to library docs 2020-10-04 14:10:18 -04:00
Axel Kohlmeyer ffcd905bf1
complete LAMMPS shell docs interation. Warn if exceptions are missing but don't fail 2020-10-04 14:03:34 -04:00