e51a5ad8f4
import doxygen docs for new utils functions
2020-08-29 22:46:25 -04:00
4396dbd9a3
move Force::open_potential() to utils::open_potential()
2020-08-29 22:37:14 -04:00
798226967f
Merge branch 'move-convenience-functions' of github.com:akohlmey/lammps into move-convenience-functions
2020-08-29 22:22:45 -04:00
6b7f4c500f
document changes to LAMMPS_POTENTIALS environment variable
2020-08-29 22:22:27 -04:00
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
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
05ff352021
add utils::open_potential() function to utils namespace
2020-08-29 22:08:16 -04:00
7413dc783e
add tokenizer tests for splitting path environment variables
2020-08-29 22:07:22 -04:00
8601e608ca
add unit tests for utils::bounds() and utils::boundsbig()
2020-08-29 22:00:07 -04:00
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
27b4e93bf5
silence compiler warnings
2020-08-29 18:32:21 -04:00
741a1d1fc9
move Input::expand_args() to utils::expand_args()
2020-08-29 18:32:10 -04:00
fcd0b9f78f
move Force::bounds() and Force::boundsbig() to utils.
2020-08-29 18:23:03 -04:00
60dfb6f77f
still need to disable variable tracking to silence unwanted warnings on ubuntu
2020-08-28 22:03:27 -04:00
31c91a8928
fix typo
2020-08-28 21:22:06 -04:00
cec18b6aef
add docs for the new fortran interface
2020-08-28 20:57:19 -04:00
e44707d5e1
add unittest support for the fortran interface to LAMMPS
2020-08-28 20:56:52 -04:00
3e92647abb
add new "official" fortran interface to LAMMPS in new folder "fortran"
2020-08-28 20:56:15 -04:00
2e1b4498bd
update false positives
2020-08-28 20:30:00 -04:00
7b6924329f
make doxygen docs and code consistent
2020-08-28 20:25:38 -04:00
cb1a2601e1
add more existing programmer guide docs
2020-08-28 20:25:09 -04:00
3be064748d
Merge pull request #2318 from akohlmey/programmer-guide
...
Programmer guide part 1
2020-08-28 20:14:32 -04:00
02ea7af1f7
let dummy tests pass
2020-08-28 18:49:39 -04:00
52f7f3629d
Merge branch 'master' into programmer-guide
2020-08-28 18:49:15 -04:00
876c53a275
Merge pull request #2310 from lammps/library-refactor
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LAMMPS C library interface and python module refactor
2020-08-28 18:40:16 -04:00
2a365c17e0
update utils namespace documentation including doxygen parts
2020-08-28 18:21:18 -04:00
cb09844182
Add placeholders for future tests
2020-08-28 17:52:15 -04:00
e64a977ae9
include documentation of utility functions in utils:: to developer guide
2020-08-28 17:14:49 -04:00
a1bf772df2
move modifying and extending LAMMPS section to programmer guide
2020-08-28 17:14:29 -04:00
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
2e2763d0f1
update .gitignore for recent additions
2020-08-28 15:34:53 -04:00
17ec3a4fe8
Fix typo
2020-08-28 15:15:01 -04:00
9412d6f6fc
Add missing argtypes declarations in lammps.py
2020-08-28 15:12:36 -04:00
ded657120d
Merge pull request #2312 from akohlmey/developer-guide
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Integrate text from developer.tex file to the manual
2020-08-28 15:01:27 -04:00
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
caeb0af0d1
Add missing argtypes for lammps_extract_global
2020-08-28 13:54:06 -04:00
167f12a4a4
Add python test for extract_compute of peratom vector
2020-08-28 13:53:36 -04:00
e8cfa185ac
update src/.gitignore for new files
2020-08-28 12:31:43 -04:00
899144c0f8
Merge pull request #2314 from jrgissing/bond/react-RMSD_constraint
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Bond/react: add RMSD constraint
2020-08-28 12:29:11 -04:00
9f2eba981a
a few more tweaks and spellcheck to make this ready for merging
2020-08-28 11:44:31 -04:00
ef50a67169
bond/react: make rmsd constraint lowercase
2020-08-28 11:06:27 -04:00
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
2686df3760
Update math_eigen.h
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whitespace cleanup
2020-08-28 10:46:22 -04:00
f0788bfe86
transfer of developer.tex almost complete
2020-08-28 09:54:01 -04:00
e777badfa8
Merge pull request #2317 from evoyiatzis/patch-1
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removal of a few duplicated lines in the drude polarizer tool
2020-08-28 09:25:01 -04:00
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
b16746e46e
Merge pull request #2313 from ndtrung81/gpu-bugfix
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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
992b981cee
Fixes segfault due to uninitialized pointers
2020-08-27 19:02:02 -04:00
b1cca2cf74
update reference data for molecular test with pair style beck
2020-08-27 19:00:20 -04:00
463774319e
add missing parenthesis
2020-08-27 17:57:44 -04:00
