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22864 Commits

Author SHA1 Message Date
Axel Kohlmeyer f123246189
minor doc updates 2020-08-30 00:25:01 -04:00
Axel Kohlmeyer ceeaf1e988
update and correct documentation for utils functions 2020-08-29 23:51:46 -04:00
Axel Kohlmeyer 9c404e02fd
update include file conventions 2020-08-29 22:56:37 -04:00
Axel Kohlmeyer 83a9e5e724
handle spelling issues with new doc text 2020-08-29 22:55:05 -04:00
Axel Kohlmeyer e51a5ad8f4
import doxygen docs for new utils functions 2020-08-29 22:46:25 -04:00
Axel Kohlmeyer 4396dbd9a3
move Force::open_potential() to utils::open_potential() 2020-08-29 22:37:14 -04:00
Axel Kohlmeyer 798226967f
Merge branch 'move-convenience-functions' of github.com:akohlmey/lammps into move-convenience-functions 2020-08-29 22:22:45 -04:00
Axel Kohlmeyer 6b7f4c500f
document changes to LAMMPS_POTENTIALS environment variable 2020-08-29 22:22:27 -04:00
Axel Kohlmeyer 5a22f4d7f2
support that LAMMPS_POTENTIALS is a real path variable with multiple entries, not just a single folder 2020-08-29 22:22:03 -04:00
Axel Kohlmeyer b06ba74d18
support that LAMMPS_POTENTIALS is a real path variable with multiple entries, not just a single folder 2020-08-29 22:09:07 -04:00
Axel Kohlmeyer 05ff352021
add utils::open_potential() function to utils namespace 2020-08-29 22:08:16 -04:00
Axel Kohlmeyer 7413dc783e
add tokenizer tests for splitting path environment variables 2020-08-29 22:07:22 -04:00
Axel Kohlmeyer 8601e608ca
add unit tests for utils::bounds() and utils::boundsbig() 2020-08-29 22:00:07 -04:00
Axel Kohlmeyer 96d8d12a88
replace calls to force->*numeric() with the corresponding utils::*numeric() 
this also removes the now obsolete functions from Force
 2020-08-29 20:31:02 -04:00
Axel Kohlmeyer 27b4e93bf5
silence compiler warnings 2020-08-29 18:32:21 -04:00
Axel Kohlmeyer 741a1d1fc9
move Input::expand_args() to utils::expand_args() 2020-08-29 18:32:10 -04:00
Axel Kohlmeyer fcd0b9f78f
move Force::bounds() and Force::boundsbig() to utils. 2020-08-29 18:23:03 -04:00
Axel Kohlmeyer 3be064748d
Merge pull request #2318 from akohlmey/programmer-guide 
Programmer guide part 1
 2020-08-28 20:14:32 -04:00
Axel Kohlmeyer 02ea7af1f7
let dummy tests pass 2020-08-28 18:49:39 -04:00
Axel Kohlmeyer 52f7f3629d
Merge branch 'master' into programmer-guide 2020-08-28 18:49:15 -04:00
Axel Kohlmeyer 876c53a275
Merge pull request #2310 from lammps/library-refactor 
LAMMPS C library interface and python module refactor
 2020-08-28 18:40:16 -04:00
Axel Kohlmeyer 2a365c17e0
update utils namespace documentation including doxygen parts 2020-08-28 18:21:18 -04:00
Richard Berger cb09844182
Add placeholders for future tests 2020-08-28 17:52:15 -04:00
Axel Kohlmeyer e64a977ae9
include documentation of utility functions in utils:: to developer guide 2020-08-28 17:14:49 -04:00
Axel Kohlmeyer a1bf772df2
move modifying and extending LAMMPS section to programmer guide 2020-08-28 17:14:29 -04:00
Axel Kohlmeyer 8fcd72405a
port over more of the framework of the programmer guide and remove programming details from user guide 2020-08-28 16:32:23 -04:00
Axel Kohlmeyer 2e2763d0f1
update .gitignore for recent additions 2020-08-28 15:34:53 -04:00
Richard Berger 17ec3a4fe8
Fix typo 2020-08-28 15:15:01 -04:00
Richard Berger 9412d6f6fc
Add missing argtypes declarations in lammps.py 2020-08-28 15:12:36 -04:00
Axel Kohlmeyer ded657120d
Merge pull request #2312 from akohlmey/developer-guide 
Integrate text from developer.tex file to the manual
 2020-08-28 15:01:27 -04:00
Richard Berger 6bcc263b41
Ensure LAMMPS pointer is of type c_void_p 
Fixes segfaults caused by API change. The API change in
lammps_open and lammps_open_no_mpi makes them return the LAMMPS pointer
via their return value. However due to how ctypes operates, even
if restype is specified to be c_void_p, the function returns an integer.

Without the proper type of the pointer, calling functions without arglists would default
to using 32bit integers to pass an argument, which cuts away parts of the 64bit pointer.
Subsequently, resolving the truncated pointer in the library causes segfaults.

This commit fixes the root cause. But it also highlights the need of specifying
the arglists of all library functions.
 2020-08-28 14:21:03 -04:00
Richard Berger caeb0af0d1
Add missing argtypes for lammps_extract_global 2020-08-28 13:54:06 -04:00
Richard Berger 167f12a4a4
Add python test for extract_compute of peratom vector 2020-08-28 13:53:36 -04:00
Axel Kohlmeyer e8cfa185ac
update src/.gitignore for new files 2020-08-28 12:31:43 -04:00
Axel Kohlmeyer 899144c0f8
Merge pull request #2314 from jrgissing/bond/react-RMSD_constraint 
Bond/react: add RMSD constraint
 2020-08-28 12:29:11 -04:00
Axel Kohlmeyer 9f2eba981a
a few more tweaks and spellcheck to make this ready for merging 2020-08-28 11:44:31 -04:00
Jacob Gissinger ef50a67169 bond/react: make rmsd constraint lowercase 2020-08-28 11:06:27 -04:00
Axel Kohlmeyer f8495975d3
transfer the rest of the Developer guide and remove the .tex versions and references to it 2020-08-28 10:52:45 -04:00
Jacob Gissinger 2686df3760 Update math_eigen.h 
whitespace cleanup
 2020-08-28 10:46:22 -04:00
Axel Kohlmeyer f0788bfe86
transfer of developer.tex almost complete 2020-08-28 09:54:01 -04:00
Axel Kohlmeyer e777badfa8
Merge pull request #2317 from evoyiatzis/patch-1 
removal of a few duplicated lines in the drude polarizer tool
 2020-08-28 09:25:01 -04:00
Evangelos Voyiatzis d361f26ca2
removal of a few duplicated lines 
The "Velocities" sections is searched for in the input file twice - the second time being redundant.
 2020-08-28 11:28:47 +02:00
Axel Kohlmeyer b16746e46e
Merge pull request #2313 from ndtrung81/gpu-bugfix 
Fixed bugs in the CPU kernel for beck, beck/omp and the GPU kernel of gauss/gpu
 2020-08-27 19:56:50 -04:00
Richard Berger 992b981cee
Fixes segfault due to uninitialized pointers 2020-08-27 19:02:02 -04:00
Axel Kohlmeyer b1cca2cf74
update reference data for molecular test with pair style beck 2020-08-27 19:00:20 -04:00
Axel Kohlmeyer 463774319e
add missing parenthesis 2020-08-27 17:57:44 -04:00
Richard Berger 9c84fe8830
Add missing lammps_extract_compute.argtypes 2020-08-27 17:47:49 -04:00
Richard Berger d7e2be1c81
Start Python interface tests for numpy extensions 2020-08-27 17:47:49 -04:00
Richard Berger 0b8136a38b
Add extract_compute, extract_fix, and extract_variable to lammps.numpy 2020-08-27 17:47:49 -04:00
Richard Berger a216d3f5f5
Fix typo 2020-08-27 17:47:49 -04:00