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23339 Commits

Author SHA1 Message Date
Axel Kohlmeyer dc89f0879c
update specific pull request templates as they are available through the github cli now 2020-09-18 06:54:31 -04:00
Axel Kohlmeyer 90abe12a3e
update LAMMPS version reference 2020-09-17 21:04:43 -04:00
Axel Kohlmeyer 445e57923f
add one-time deprecation warning to lammps_open() and lammps_open_no_mpi() 2020-09-17 21:01:38 -04:00
Axel Kohlmeyer 6e22229424
Merge remote-tracking branch 'github/master' into collected-small-changes 2020-09-17 20:27:55 -04:00
Axel Kohlmeyer 94ad6821f7
Merge pull request #2373 from stanmoore1/kk_wkar 
Add workaround for performance regression in Kokkos Package
 2020-09-17 20:24:39 -04:00
Stan Moore d8b6ebdfc8 Add workaround for performance regression 2020-09-17 16:33:48 -06:00
Axel Kohlmeyer 6729a42cfa
Merge branch 'master' into collected-small-changes 2020-09-17 17:01:44 -04:00
Axel Kohlmeyer 3b96375888
Merge pull request #2371 from arghdos/kokkos_hip_porting 
Additional Kokkos/HIP porting work
 2020-09-17 16:58:46 -04:00
Giacomo Fiorin 3275419872 Allow Colvars to include headers from the LAMMPS source directory 2020-09-17 14:37:26 -04:00
Axel Kohlmeyer 4c5aedeaa0
fix typo 2020-09-17 12:50:53 -04:00
Axel Kohlmeyer 91eaaba1be
improve portability of docs makefile 
- 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
Nick Curtis 7bf177a1c7 Fast forward porting work to master 
Change-Id: Ieb428e4a001efadf880dbe2c64c2a685cebdd4ae
 2020-09-17 10:45:04 -05:00
Axel Kohlmeyer 0522e3d7b6
a few more unittest tweaks 2020-09-17 11:11:44 -04:00
Axel Kohlmeyer 00641f9f24
relax epsilon a little for passing cross-platform tests 2020-09-17 11:01:59 -04:00
Axel Kohlmeyer 62a63d0cd8
silence compiler warnings 2020-09-17 10:27:06 -04:00
Axel Kohlmeyer e2fc70da62
Merge branch 'master' into collected-small-changes 2020-09-17 06:51:21 -04:00
Axel Kohlmeyer e924fc6d6e
Merge pull request #2347 from jewettaij/math_eigen 
Replace eigensolver code in LAMMPS with math_eigen.h and updated docs
 2020-09-17 00:28:12 -04:00
Axel Kohlmeyer e839fe0d30
Merge branch 'master' into collected-small-changes 2020-09-16 23:53:29 -04:00
Axel Kohlmeyer b96512171c
set -DCOLVARS_LAMMPS when compiling colvars library 2020-09-16 23:52:06 -04:00
Axel Kohlmeyer 4e304177a1
Merge pull request #2356 from giacomofiorin/colvars-update 
Update Colvars to version 2020-07-07
 2020-09-16 23:37:02 -04:00
Axel Kohlmeyer b9919b72d7
make MSM test w/o PBC run faster 2020-09-16 23:36:17 -04:00
Axel Kohlmeyer 429cc0cacf
add missing updates for symbolic constants in Atom class 2020-09-16 23:19:10 -04:00
Axel Kohlmeyer 6e9a39cf22
remove trailing whitespace 2020-09-16 22:57:49 -04:00
Axel Kohlmeyer c14fd3131a
Merge pull request #2367 from ndtrung81/rigid-langevin 
Fixed a bug in computing the langevin torques applied to rigid bodies
 2020-09-16 22:36:04 -04:00
Axel Kohlmeyer b176cdf28c
remove trailing whitespace 2020-09-16 18:18:53 -04:00
Axel Kohlmeyer a8a9fb6eb8
adapt unit test for Jacobi class 2020-09-16 18:17:23 -04:00
Axel Kohlmeyer 96f4178d92
add URLs to upstream projects for eigensolvers 2020-09-16 17:53:27 -04:00
Axel Kohlmeyer 942ed3afeb
update copyright headers to match LAMMPS' conventions 2020-09-16 17:35:58 -04:00
Giacomo Fiorin 85d36ad6c4 Condense export of debug macro 2020-09-16 17:28:28 -04:00
Trung Nguyen dfcdb61d87 Used existing helper functions to make codes more consise 2020-09-16 15:40:04 -05:00
Axel Kohlmeyer bd542efa52
include math_eigen.h, remove it from .gitignore 2020-09-16 14:12:14 -04:00
Axel Kohlmeyer 0931cdd109
relax epsilon for rigid body integrators 2020-09-16 14:07:28 -04:00
Axel Kohlmeyer fd9e39bf1a
update docs 2020-09-16 14:07:06 -04:00
Axel Kohlmeyer 10991ee638
separate the MathEigen implementation into its own header file 2020-09-16 14:06:58 -04:00
Axel Kohlmeyer f7a939dec2
update atom_style tester for new jacobi implementation 2020-09-16 10:25:03 -04:00
Axel Kohlmeyer 981d60f1bd
update rigid tests for new eigensolver 2020-09-15 22:47:52 -04:00
Axel Kohlmeyer 48ad860889
only do Zstd tests if it is enabled/found. 2020-09-15 22:47:10 -04:00
Axel Kohlmeyer f5998692d0
Merge branch 'master' into math_eigen 2020-09-15 21:37:05 -04:00
Axel Kohlmeyer d611b85d7d
Merge pull request #2360 from akohlmey/symbolic-atom-constants 
Replace numeric with symbolic constants in Atom and AtomVec classes
 2020-09-15 21:27:47 -04:00
Axel Kohlmeyer cf7d2109a3
Merge branch 'library-progguide' into symbolic-atom-constants 2020-09-15 19:50:18 -04:00
Axel Kohlmeyer 4b25eb1a34
small tweaks 2020-09-15 19:08:40 -04:00
Axel Kohlmeyer 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
Axel Kohlmeyer a3765eb75b
Merge branch 'master' into library-progguide 2020-09-15 18:58:29 -04:00
Axel Kohlmeyer 0f6a34775c
Merge branch 'master' into symbolic-atom-constants 2020-09-15 17:44:31 -04:00
Axel Kohlmeyer cebf6d33ba
Merge pull request #2358 from eagunn/iss2345 
Replace instances of NULL with nullptr
 2020-09-15 17:41:24 -04:00
Trung Nguyen ae68becf4a Fixed a bug in computing the langevin torques applied to rigid bodies 2020-09-15 15:27:24 -05:00
Axel Kohlmeyer f481a403bc
Merge pull request #2366 from akohlmey/msm-fix 
Apply alternate bugfix to KSpace style MSM that avoids grid level overflow
 2020-09-15 16:22:19 -04:00
Axel Kohlmeyer 618b08dcfc
Merge branch 'master' into symbolic-atom-constants 2020-09-15 14:58:13 -04:00
Axel Kohlmeyer 3dd3c6a2a5
redo fix for class member shadowing while avoiding overflowing levels 2020-09-15 14:48:55 -04:00
Axel Kohlmeyer 16749566f8
Revert "fix issue with local variable shadowing a global variable" 
This reverts commit 3368eb79d8.
 2020-09-15 14:42:00 -04:00