31c91a8928
fix typo
2020-08-28 21:22:06 -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
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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
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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
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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
9c84fe8830
Add missing lammps_extract_compute.argtypes
2020-08-27 17:47:49 -04:00
d7e2be1c81
Start Python interface tests for numpy extensions
2020-08-27 17:47:49 -04:00
0b8136a38b
Add extract_compute, extract_fix, and extract_variable to lammps.numpy
2020-08-27 17:47:49 -04:00
a216d3f5f5
Fix typo
2020-08-27 17:47:49 -04:00
26d09ea648
Use datatype constants instead of magic numbers
2020-08-27 17:47:49 -04:00
b1fae04751
use consistent style when referencing packages
2020-08-27 17:44:49 -04:00
7b4891a9a3
document the behavior of the gauss pair style to ignore special bond factors
2020-08-27 17:41:43 -04:00
fa13e23f7a
add atomic test for gauss pair style
2020-08-27 17:41:25 -04:00
fdb726629f
revert "fix" for pair style beck/gpu and correct beck and beck/omp instead
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we should consistently apply factor_lj for both, force and energy, or not
2020-08-27 17:14:05 -04:00
a4f1be8fe3
Merge branch 'master' into gpu-bugfix
2020-08-27 17:05:26 -04:00
a54f99f774
Merge pull request #2315 from lammps/peri-doc-page
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fix two typos on pair peri doc page
2020-08-27 17:00:06 -04:00
de4bf77757
two typos on pair peri doc page
2020-08-27 13:32:27 -06:00
32aede7769
minor doc clarification
2020-08-27 14:53:09 -04:00
ab90493e5b
bond/react: RMSD, remove debugging statements
2020-08-27 14:45:42 -04:00
0d8baff7a9
Rename LAMMPS_DBLE2D to LAMMPS_DOUBLE2D
2020-08-27 14:03:17 -04:00
5c0edeb679
namespace clarify
2020-08-27 12:43:28 -04:00
977a89e537
add separators
2020-08-27 12:33:03 -04:00
