be72ce2534
Simplify Python examples to use numpy.extract_atom
2020-09-17 16:51:46 -04:00
ab6b69d6bd
Add documentation and better autodetect
2020-09-17 16:39:19 -04:00
c06d5f7fb7
Fix type cast
2020-09-17 16:37:25 -04:00
b81ad54baa
Simplify extract_atom and extract_global in Python interface
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Both extract methods now can auto-detect the datatype of both global
and per-atom properties. Callers can still enforce different types
if needed by specifying the now optional dtype argument.
The numpy wrapper now has a new extract_atom function method, which
replace the extract_atom_darray and extract_atom_iarray method and
autodetects both type and size. All parameters can still be forced
to use different values if needed.
2020-09-17 16:16:27 -04:00
d88810f13a
Add datatype introspection methods to library
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Adds lammps_extract_atom_datatype and lammps_extract_global_datatype functions
to allow extracting type information of properties.
2020-09-17 13:43:43 -04:00
706a898163
Merge remote-tracking branch 'origin/master' into python_interface_guide
2020-09-17 12:08:12 -04:00
9fa43b8b12
Skip Numpy tests if not installed
2020-09-17 12:03:36 -04:00
5dacfc47ca
Change return type of lammps.get_natoms to int
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Closes PR #2370
2020-09-17 10:57:49 -04:00
e924fc6d6e
Merge pull request #2347 from jewettaij/math_eigen
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Replace eigensolver code in LAMMPS with math_eigen.h and updated docs
2020-09-17 00:28:12 -04:00
4e304177a1
Merge pull request #2356 from giacomofiorin/colvars-update
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Update Colvars to version 2020-07-07
2020-09-16 23:37:02 -04:00
c14fd3131a
Merge pull request #2367 from ndtrung81/rigid-langevin
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Fixed a bug in computing the langevin torques applied to rigid bodies
2020-09-16 22:36:04 -04:00
b176cdf28c
remove trailing whitespace
2020-09-16 18:18:53 -04:00
a8a9fb6eb8
adapt unit test for Jacobi class
2020-09-16 18:17:23 -04:00
12582edfb7
Add numpy.extract_atom_darray test
2020-09-16 18:04:45 -04:00
96f4178d92
add URLs to upstream projects for eigensolvers
2020-09-16 17:53:27 -04:00
942ed3afeb
update copyright headers to match LAMMPS' conventions
2020-09-16 17:35:58 -04:00
85d36ad6c4
Condense export of debug macro
2020-09-16 17:28:28 -04:00
dfcdb61d87
Used existing helper functions to make codes more consise
2020-09-16 15:40:04 -05:00
e6703019bc
Update examples to use Python API constants
2020-09-16 16:10:43 -04:00
c82df186b5
Disable zstd tests if library is too old
2020-09-16 15:18:28 -04:00
ccc743e13e
Add test for thermo data
2020-09-16 15:14:05 -04:00
bd542efa52
include math_eigen.h, remove it from .gitignore
2020-09-16 14:12:14 -04:00
0931cdd109
relax epsilon for rigid body integrators
2020-09-16 14:07:28 -04:00
fd9e39bf1a
update docs
2020-09-16 14:07:06 -04:00
10991ee638
separate the MathEigen implementation into its own header file
2020-09-16 14:06:58 -04:00
8ccd3c03fa
Correct test name
2020-09-16 12:54:36 -04:00
2270d8f4ec
Add PyLammps.atoms test and fix bug with -echo screen/both
2020-09-16 12:48:20 -04:00
9cdd35e625
Make sure Python tests run unbuffered so PyLammps works
2020-09-16 11:28:38 -04:00
f7a939dec2
update atom_style tester for new jacobi implementation
2020-09-16 10:25:03 -04:00
ca24806f4c
Add tests
2020-09-16 10:11:00 -04:00
981d60f1bd
update rigid tests for new eigensolver
2020-09-15 22:47:52 -04:00
48ad860889
only do Zstd tests if it is enabled/found.
2020-09-15 22:47:10 -04:00
f5998692d0
Merge branch 'master' into math_eigen
2020-09-15 21:37:05 -04:00
d611b85d7d
Merge pull request #2360 from akohlmey/symbolic-atom-constants
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Replace numeric with symbolic constants in Atom and AtomVec classes
2020-09-15 21:27:47 -04:00
38f0a2e24c
Fix doc build errors
2020-09-15 19:50:28 -04:00
cf7d2109a3
Merge branch 'library-progguide' into symbolic-atom-constants
2020-09-15 19:50:18 -04:00
4b25eb1a34
small tweaks
2020-09-15 19:08:40 -04:00
88cee4ff09
the library interface is for calling from C, so switch nullptr in comments/docs back to NULL
2020-09-15 19:07:07 -04:00
a3765eb75b
Merge branch 'master' into library-progguide
2020-09-15 18:58:29 -04:00
7611efeea2
Update python docs
2020-09-15 18:03:26 -04:00
0f6a34775c
Merge branch 'master' into symbolic-atom-constants
2020-09-15 17:44:31 -04:00
cebf6d33ba
Merge pull request #2358 from eagunn/iss2345
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Replace instances of NULL with nullptr
2020-09-15 17:41:24 -04:00
ae68becf4a
Fixed a bug in computing the langevin torques applied to rigid bodies
2020-09-15 15:27:24 -05:00
60712e3f90
Add docstrings
2020-09-15 16:22:43 -04:00
f481a403bc
Merge pull request #2366 from akohlmey/msm-fix
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Apply alternate bugfix to KSpace style MSM that avoids grid level overflow
2020-09-15 16:22:19 -04:00
556dc67fdc
Correct filename of generated image
2020-09-15 15:20:38 -04:00
6cfad41be4
Add background_color argument to IPyLammps.image
2020-09-15 15:19:39 -04:00
e5e449795a
Add tests for has_style and available_styles
2020-09-15 15:16:19 -04:00
618b08dcfc
Merge branch 'master' into symbolic-atom-constants
2020-09-15 14:58:13 -04:00
3dd3c6a2a5
redo fix for class member shadowing while avoiding overflowing levels
2020-09-15 14:48:55 -04:00
