cf1ae7afa6
Use wrapper lammps.extract_atom_datatype
2020-09-17 17:04:40 -04:00
6729a42cfa
Merge branch 'master' into collected-small-changes
2020-09-17 17:01:44 -04:00
3b96375888
Merge pull request #2371 from arghdos/kokkos_hip_porting
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Additional Kokkos/HIP porting work
2020-09-17 16:58:46 -04:00
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
3275419872
Allow Colvars to include headers from the LAMMPS source directory
2020-09-17 14:37:26 -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
4c5aedeaa0
fix typo
2020-09-17 12:50:53 -04:00
91eaaba1be
improve portability of docs makefile
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- detect if /bin/bash is not found and provide a suitable error message
- use $(MAKE) and $(MFLAGS) variables to handle cases where GNU make is not called "make"
2020-09-17 12:40:09 -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
7bf177a1c7
Fast forward porting work to master
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Change-Id: Ieb428e4a001efadf880dbe2c64c2a685cebdd4ae
2020-09-17 10:45:04 -05:00
0522e3d7b6
a few more unittest tweaks
2020-09-17 11:11:44 -04:00
00641f9f24
relax epsilon a little for passing cross-platform tests
2020-09-17 11:01:59 -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
62a63d0cd8
silence compiler warnings
2020-09-17 10:27:06 -04:00
e2fc70da62
Merge branch 'master' into collected-small-changes
2020-09-17 06:51:21 -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
e839fe0d30
Merge branch 'master' into collected-small-changes
2020-09-16 23:53:29 -04:00
b96512171c
set -DCOLVARS_LAMMPS when compiling colvars library
2020-09-16 23:52:06 -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
b9919b72d7
make MSM test w/o PBC run faster
2020-09-16 23:36:17 -04:00
429cc0cacf
add missing updates for symbolic constants in Atom class
2020-09-16 23:19:10 -04:00
6e9a39cf22
remove trailing whitespace
2020-09-16 22:57:49 -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
61b83901f5
bond/react: correct new custom_charges logic
2020-09-16 21:28:48 -04:00
55bc1baf97
bond/react: correct recent enum update
2020-09-16 20:33:45 -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
55a054a44a
bond/react: default charge update docs
2020-09-16 17:09:48 -04:00
6faf436850
bond/react: update all charges by default, even with edge atoms
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custom charges has new keyword, now done with molecule fragments (not backwards compatible)
2020-09-16 17:02:49 -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
