584943fc92
Merge pull request #2458 from akohlmey/next_lammps_version
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Step version string for next LAMMPS release
2020-10-28 19:53:36 -04:00
00ef63049a
Merge pull request #2456 from akohlmey/final-changes-for-stable
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Final changes for stable release
2020-10-28 18:46:51 -04:00
f55c24ff96
Merge pull request #2455 from stanmoore1/relax_NaN
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Add non-numeric pressure check to fix box/relax
2020-10-28 17:37:42 -04:00
4f9ec11311
Merge pull request #2448 from akohlmey/fix-read-dump-issues
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Fix a couple issues related to read dump
2020-10-28 17:15:26 -04:00
bf87c0dc56
add (incomplete) unit test for atom style template
2020-10-28 15:43:36 -04:00
9f1526c66d
cannot currently use replicate command with atom style template
2020-10-28 15:42:50 -04:00
c25ef8edb0
fix segfault: must not count bonds on atoms that are not in a molecule
2020-10-28 15:11:19 -04:00
72f4650b52
Merge pull request #2460 from stanmoore1/kk_bugfix
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Kokkos bugfix for pair forward comm
2020-10-28 12:46:46 -04:00
99c99e86e0
Kokkos bugfix for pair forward comm
2020-10-28 09:15:49 -06:00
94462bfb48
do not add langevin thermostat forces and torques if disabled, e.g. in 2d system.
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Note that fix rigid/small does not support the force or torque options and thus
the zeroing has to be done directly when computing the langevin data.
2020-10-28 10:41:20 -04:00
d2c6c89ccc
step version string for next LAMMPS release
2020-10-28 08:09:23 -04:00
94f57d8849
rephrase paragraph about availability of the manual and add note about browser compatibility
2020-10-28 04:49:09 -04:00
9a3f935c9b
do not include polyfill.js anymore
2020-10-27 20:17:59 -04:00
5dc09ae3c0
increase timeout, properly handle timeouts, and fix symbol lookup in exception handling
2020-10-27 17:16:47 -04:00
6f66f5b23b
Add non-numeric pressure check to fix box/relax
2020-10-27 13:55:50 -06:00
e38dcb9302
Merge branch 'master' into fix-read-dump-issues
2020-10-27 13:06:52 -04:00
5872b05e2f
Merge pull request #2447 from akohlmey/atom-style-template-fixes
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Fix bugs and update implementation of atom style template
2020-10-27 13:03:05 -04:00
b8e84d0070
Merge pull request #2442 from ProfessorMiller/master
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Create logic in parsing KIM Simulator Models to treat periodic vs. aperiodic simulations differently
2020-10-27 11:44:20 -04:00
3b267430ac
Merge pull request #2452 from jrgissing/bond_react-small-docs-updates
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Bond/react: docs clarifications
2020-10-27 11:03:46 -04:00
86f8b566f0
eliminate TABs
2020-10-27 00:39:52 -04:00
8976cf0230
Update data.spce
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The masses were assigned wrongly in the data file (although they eventually get overwritten in the in.gcmc.h2o script)
2020-10-27 00:35:51 -04:00
a3c887accb
update examples and include restart example, too.
2020-10-27 00:31:25 -04:00
6af2da7603
Correct path for icons and .desktop file
2020-10-26 23:56:55 -04:00
4a853cd838
Merge branch 'master' into atom-style-template-fixes
2020-10-26 23:56:48 -04:00
af483ca34f
small documentation update
2020-10-26 23:15:43 -04:00
d64bbb99bf
add examples for demonstrating the use of atom style template
2020-10-26 23:10:45 -04:00
955da06aca
avoid segfaults with non-template atoms when reading data files
2020-10-26 23:02:24 -04:00
8975c7e316
relax checks to avoid segfaults and accept non-template atoms
2020-10-26 23:01:58 -04:00
efd31fbb60
fix up placement of polyfill loader layout.html and load it only for internet explorer
2020-10-26 21:03:05 -04:00
731072cfb8
handle case of molecule template atoms not included in shake
2020-10-26 18:49:59 -04:00
f70775bd52
cannot determine communication without a box
2020-10-26 18:49:30 -04:00
656b7eac8b
correctly report number of constrained bonds and angles
2020-10-26 18:49:09 -04:00
4475a095ce
Merge pull request #2453 from rbberger/cmake_gitversion_fix
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Enable gathering of git info with git v1.8.3.1
2020-10-26 18:45:52 -04:00
f7d9cf813f
Enable gathering of git info with git v1.8.3.1
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The -C flag wasn't supported back then. The workaround is to change the
working directory via CMake. This issue was detected while building on
CentOS 7.
2020-10-26 17:26:46 -04:00
d84bb54019
do not enforce atom types in molecule files for atom style template.
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types are only needed when creating atoms and presence is tested then.
2020-10-26 17:26:18 -04:00
ba97141d45
restore and correct read_data docs for atom style template
2020-10-26 17:25:16 -04:00
6554547b41
Merge pull request #2444 from stanmoore1/kk_global_dof
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Add support for extra global DOFs to Kokkos minimize
2020-10-26 17:07:27 -04:00
65e93cbaab
decrement/increment molindex and atomindex to have 1-based indices in files and 0-based internally
2020-10-26 17:06:27 -04:00
d9646472c3
Revert "support choosing the molecule index from the set of molecules in a template"
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This reverts commit 186359caa9
2020-10-26 15:46:58 -04:00
f9b45faa76
Merge pull request #2445 from akohlmey/lammps-shell-desktop
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Add desktop integration for LAMMPS shell
2020-10-26 15:41:25 -04:00
406d6e27ce
bond/react: clarify how reactions are searched for
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thanks to Ben Jensen (NASA Langley)
2020-10-26 11:22:35 -04:00
b67950e130
update email
2020-10-24 13:54:27 -04:00
c2a852ddef
clarify exactly what is used to identify reaction site
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thanks to Øystein Gullbrekken for the suggestion
2020-10-24 13:46:28 -04:00
9c129d3a34
update output of read_restart to make read_data and signify if atom style template is used
2020-10-24 01:05:11 -04:00
186359caa9
support choosing the molecule index from the set of molecules in a template
2020-10-24 00:45:41 -04:00
13450606c6
update read_data docs with actual format for atom style template
2020-10-24 00:45:06 -04:00
4a6517fd51
for atom style template only write out the number of types
2020-10-23 21:51:55 -04:00
00e4e23456
only check for type overflows if a box has been created.
2020-10-23 21:51:10 -04:00
9e0062a9ef
we have a new map style when using atom style template
2020-10-23 21:50:38 -04:00
23e2a4af00
use symbolic constant
2020-10-23 21:50:18 -04:00
3bf081745d
add missing velocity comm ids
2020-10-23 21:50:04 -04:00
c62ddaa4a2
remove pre-box check so that atom style template can work
2020-10-23 21:10:41 -04:00
b4f1779b62
reformat with clang-format
2020-10-23 21:04:45 -04:00
1382559dbe
adapt behavior of lammps-shell when passing filename without -in/-i flag
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To better handle the case of file association. We now split the path into
a directory and basename string and change the current working directory
to that directory and read the file with the basename.
This simplifies the .desktop file and makes the LAMMPS shell behave as
expected on Windows, too.
2020-10-23 20:42:24 -04:00
b931501711
add utils::path_dirname() to complement utils::path_basename()
2020-10-23 20:40:18 -04:00
c51d2a286a
call resource compiler to include icon files into LAMMPS shell on Windows
2020-10-23 20:06:21 -04:00
5c98eeec1b
remove strtok dependency
2020-10-23 11:25:35 -04:00
ceaaf149eb
Whitespace cleanup
2020-10-23 08:53:53 -06:00
9543ff02c6
Fix memory issue
2020-10-23 08:49:53 -06:00
30c050fda7
Add missing global DOF calls
2020-10-23 08:36:48 -06:00
e3ecb6ccc4
must nullify "readers" array, so there is no crash when deleting it later
2020-10-23 04:21:15 -04:00
114f039a68
must not check for compatible dump frequency when using write_dump
2020-10-23 04:20:40 -04:00
39da827a2d
correct formatting style for keywords block
2020-10-23 02:24:11 -04:00
aa15f221d4
add missing "boff" keyword
2020-10-23 02:21:58 -04:00
3242cd5d31
mention desktop file and icons in README
2020-10-23 00:29:48 -04:00
8854e7b8de
Add desktop integration for LAMMPS shell
2020-10-23 00:20:15 -04:00
c29474c533
Merge pull request #2443 from akohlmey/next_lammps_version
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Step version strings for next release
2020-10-22 18:11:33 -04:00
ef048cad55
Add extra global DOFs for Kokkos minimize
2020-10-22 16:03:42 -06:00
c7a10050c2
Merge pull request #2439 from akohlmey/collected-small-changes
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Collected small changes for the next release
2020-10-22 17:23:49 -04:00
9bc3ccd49a
fix misplaced "#endif"
2020-10-22 15:45:24 -04:00
5ff0dbb431
step version strings for next patch release (and stable release candidate)
2020-10-22 15:36:58 -04:00
fcd442d751
simplify code. print warnings only on MPI rank 0. update parameter names
2020-10-22 15:35:45 -04:00
cfbeaad112
updates to kim_interactions to generalize interpretor for smspec.edn (logic to allow variants for aperiodic vs periodic simulations
2020-10-22 15:05:07 -04:00
68b533d1b8
correct order of functions
2020-10-22 14:59:55 -04:00
b64585c631
Merge branch 'collected-small-changes' of github.com:akohlmey/lammps into collected-small-changes
2020-10-22 12:11:58 -04:00
bcf5abccb5
reorder functions in library.h and library.cpp to match order in manual
2020-10-22 12:11:42 -04:00
bc43865f45
need to look for Java Development components, not just JNI parts
2020-10-22 01:55:42 -04:00
a14b38ce21
avoid bell
2020-10-21 22:23:45 -04:00
bb32cbc223
add a few more tests for the lammps-shell
2020-10-21 22:07:38 -04:00
ac6f85f8be
make expansion of internal command unambiguous
2020-10-21 21:14:53 -04:00
0ab8803d19
Merge pull request #2437 from akohlmey/correct-urls
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Make references to LAMMPS and other websites consistent
2020-10-21 20:34:14 -04:00
e79e53c540
Merge pull request #2438 from akohlmey/swig-support-fixes
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Small updates to SWIG tool for increased portability and correctness
2020-10-21 19:57:23 -04:00
386bea76cb
describe more clearly what is provided
2020-10-21 17:25:42 -04:00
6b2a98b537
ad few more manual updates of outdated, mistyped or no longer available URLs
2020-10-21 17:19:33 -04:00
f8bf4989f4
update URLs from http:// to https://
2020-10-21 17:04:23 -04:00
a914a3aac2
update outdated URLs
2020-10-21 17:03:46 -04:00
f23d831a90
update cslib homepage URLs to use https://
2020-10-21 16:53:30 -04:00
adf74b3a22
use https://lammps.sandia.gov based URLs consistently
2020-10-21 16:45:30 -04:00
9cdf6f1e8b
more portability changes
2020-10-21 14:22:06 -04:00
d7a0971578
make python support more portable, require python3
2020-10-21 14:14:46 -04:00
53028b24d6
improve portability for building SWIG Tcl wrappers
2020-10-21 14:06:25 -04:00
1753c9f361
Merge pull request #2434 from akohlmey/swig-wrappers
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Provide an interface file for creating script wrappers for LAMMPS with SWIG
2020-10-21 12:56:11 -04:00
2ed11f55d6
fix URLs to documentation files
2020-10-21 11:12:13 -04:00
0a30398d1f
get rid of obsolete README note. We have long ago fixed the aliasing issue in Coulomb tabulation
2020-10-21 11:10:26 -04:00
de8149154a
fix broken internal links in the manual
2020-10-21 10:56:52 -04:00
cc90596183
fix link to documentation
2020-10-21 10:49:01 -04:00
de40b3e637
remove trailing whitespace
2020-10-20 21:24:02 -04:00
7549edd844
Merge branch 'master' into swig-wrappers
2020-10-20 21:22:53 -04:00
a8c0142621
update docs for building SWIG Tcl wrapper
2020-10-20 21:22:39 -04:00
4b447fb3d8
Merge pull request #2429 from rbberger/python_docs
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Minor updates to the Python docs
2020-10-20 21:12:44 -04:00
955c7c1efb
Merge pull request #2433 from athomps/eamfs-doc
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Clarified order of rho_alpha_beta density functions
2020-10-20 20:13:35 -04:00
ad50db1feb
use a different/cleaner approach to build an extended Tcl shell
2020-10-20 18:53:29 -04:00
1b358603c2
simplify
2020-10-20 18:52:53 -04:00
0547425482
a few more small fixes
2020-10-20 18:30:32 -04:00
6259b277df
replace explicit clean-all target with added properties
2020-10-20 18:30:19 -04:00
fe7628f954
add check that that extension module is compiled before running example scripts
2020-10-20 18:29:43 -04:00
7db669df40
add support to also build an extended tcl shell as opposed to dynamically loading the extension
2020-10-20 18:29:16 -04:00
515f1d9ead
make module search path commands consistent
2020-10-20 17:38:03 -04:00
faf67662d5
fix typo
2020-10-20 16:47:56 -04:00
b9a57899a6
whitespace fix
2020-10-20 16:46:21 -04:00
eeaff55df7
SWIG support documentation update
2020-10-20 16:37:30 -04:00
bc1d325930
dmonstrate data access functions
2020-10-20 15:57:02 -04:00
75ac1857ab
Clarified order of rho_alpha_beta density functions
2020-10-20 11:47:41 -06:00
3ad397dd60
implement some more data access functions and handle passing string buffers
2020-10-20 11:43:03 -04:00
6c826823fe
update SWIG support readme
2020-10-20 11:42:23 -04:00
7297ed3115
apply stack-protector fix required by newer versions of MinGW, e.g. on Fedora 33
2020-10-19 21:59:27 -04:00
cd444eefe2
Merge branch 'master' into swig-wrappers
2020-10-19 21:58:23 -04:00
7af95dd396
Merge pull request #2432 from akohlmey/collected-small-changes
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Collected small changes for the stable release
2020-10-19 19:43:39 -04:00
5ac910a748
remove redundant file
2020-10-19 15:46:49 -04:00
56cecf2c3a
small tweaks: avoid overflow and add missing newline
2020-10-19 15:46:33 -04:00
4b2fd65585
fix issue where a variable was used before it was assigned.
2020-10-19 15:46:03 -04:00
2c54b7e505
update USER-SMD examples: rename files, shorten runs and add logfiles
2020-10-19 15:45:26 -04:00
ef9920bd37
Merge branch 'correct_user_smd_examples' of github.com:dboemer/lammps into collected-small-changes
2020-10-19 13:52:18 -04:00
4795e01d54
Support being called from a graphical shell through filename association.
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This adds a hack to the LAMMPS shell that hides the first argument from
the LAMMPS class, if it does not start with a '-' and instead tries to
open it as an input file.
2020-10-19 11:40:28 -04:00
f67d9bb523
Correct USER smd examples and remove tabs
2020-10-19 14:56:40 +02:00
c891b9dca6
add simple main function for building a static Tcl shell executable
2020-10-19 01:01:27 -04:00
8c5ac3d49c
add README file to SWIG tool
2020-10-19 01:01:06 -04:00
5a70ee8a40
make names of custom data functions consistent
2020-10-19 01:00:50 -04:00
f74203fb33
start adding documentation about SWIG wrapping to the manual
2020-10-19 01:00:02 -04:00
97767d0a3c
add some support functions to cast pointers and get values from pointers
2020-10-18 12:40:17 -04:00
eab5d68a09
move SWIG support to tools/swig folder
2020-10-18 08:19:20 -04:00
0f71c02059
suppress developer warnings
2020-10-18 08:12:29 -04:00
0685df3e64
add "clean-all" target to remove all content generated by build or example run scripts
2020-10-18 08:12:08 -04:00
1595c7ed48
copy example run scripts to the swig folder in the build tree
2020-10-18 08:11:20 -04:00
c6690eed6c
add ruby to the fold
2020-10-18 02:16:06 -04:00
23cfdaac11
simplify
2020-10-18 01:56:18 -04:00
c376b8ffa5
add java interface
2020-10-18 01:49:19 -04:00
42116fc444
expand examples to include some LAMMPS commands
2020-10-18 01:06:34 -04:00
e1b00a67f8
include enumerator constants into swig interface file
2020-10-18 01:06:17 -04:00
1ed735e311
add some minimal usage examples
2020-10-18 00:45:21 -04:00
58ceab93ec
include enumerators
2020-10-18 00:45:04 -04:00
fcbbc51a33
add minimally tested swig wrapper for Lua, Perl5, Python, and Tcl
2020-10-17 23:51:36 -04:00
722b9c8cf3
small tweak
2020-10-16 22:46:33 -04:00
a04c8c8a3b
fix typo
2020-10-16 22:46:20 -04:00
cd605d46bc
Add missing code-block language
2020-10-16 18:22:29 -04:00
b3b650acf2
Update Python_execute.rst
2020-10-16 18:22:29 -04:00
91a1e9abb4
Correct table in Python_examples.rst
2020-10-16 18:22:28 -04:00
4534e78df1
Add extra space in Python_run.rst
2020-10-16 17:20:38 -04:00
853b5ea576
Remove redundant links and wording
2020-10-16 17:13:31 -04:00
7420b7018a
Merge pull request #2427 from akohlmey/lammps-shell-tweaks
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A few more tweaks for the LAMMPS Shell
2020-10-16 16:43:42 -04:00
4d31ae7279
Beter system folder detection, add URL to "help" commmand. avoid buffer overflow.
2020-10-16 15:17:57 -04:00
eaa75417f2
Merge pull request #2425 from akohlmey/more-doc-updates
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More updates/reorganization of the programmer part of the manual
2020-10-16 15:02:21 -04:00
4335f3d2ab
Add LAMMPS icon in docs
2020-10-16 12:18:25 -04:00
f547cb4262
clarify tasks for single() for Bond and Angle classes
2020-10-16 10:48:00 -04:00
f2ba37e35d
try swithing the current working directory when dropped into a Windows system folder.
2020-10-16 10:47:23 -04:00
f5c457334a
make headers more compact
2020-10-16 02:43:20 -04:00
dd7a3a3a54
move the entries about using the Python module into its own (sub) toctree
2020-10-15 20:29:24 -04:00
08d892d0d9
whitespace
2020-10-15 19:56:31 -04:00
5d3f10611a
Adjust Python deprecation notice
2020-10-15 18:25:58 -04:00
99f9a16a25
Update Python docs
2020-10-15 18:19:57 -04:00
4a946f5388
rename sections to User Guide and Programmer Guide
2020-10-15 12:00:36 -04:00
f15dc4a0a8
add more details and derived class to the class diagram and use a different layout engine
2020-10-15 12:00:10 -04:00
bc16709150
tweak
2020-10-14 23:59:06 -04:00
dc8e6bc5ab
mention example using the new Fortran module in examples/COUPLE/simple
2020-10-14 23:29:03 -04:00
88644caaec
update header texts
2020-10-14 23:28:28 -04:00
937f8b3f61
reorder sections in developer guide
2020-10-14 22:57:41 -04:00
d41cce7660
update LAMMPS class diagram
2020-10-14 22:57:21 -04:00
a7a4ea76a2
update LAMMPS logo with raytraced version
2020-10-14 22:57:02 -04:00
89842fc7c4
Merge pull request #2418 from akohlmey/collected-small-changes
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Collected small changes and bugfixes for the stable release
2020-10-14 17:45:10 -04:00
28641bcbc7
Merge pull request #2402 from ndtrung81/gpu-dpd
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Allowed dpd/tstat/gpu and dpd/gpu to work together in pair style hybrid
2020-10-14 17:18:02 -04:00
61c33e5622
update documentation conventions for recent changes to the manual.
2020-10-14 17:01:58 -04:00
3926cbe5f0
Merge branch 'patch-3' of github.com:evoyiatzis/lammps into collected-small-changes
2020-10-14 15:18:03 -04:00
865b159d16
update singularity definitions for readline 6/7 to have a pkg-config file
2020-10-14 15:06:57 -04:00
234f27514f
avoid CMake failure when reporting packages without any of them enabled
2020-10-14 14:59:24 -04:00
65eb4b5527
explicitly enable C++11 and use pkg-config to get readline flags
2020-10-14 14:33:12 -04:00
d322e29f64
mention that C++11 also needs to be enabled with Ubuntu 16.04
2020-10-14 14:30:03 -04:00
45939602a5
Update fix_widom.rst
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the shake keyword is not applicable to widom insertions
2020-10-14 20:17:35 +02:00
18091f15e0
Merge branch 'master' into collected-small-changes
2020-10-14 13:11:30 -04:00
7f804512b7
rename to be consistent with example log files
2020-10-14 13:11:13 -04:00
d27c7cd2fc
Merge pull request #2421 from akohlmey/remove-obsolete-files
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Remove outdated or obsolete files
2020-10-14 13:09:52 -04:00
60ff1380d7
update log files for bench/POTENTIALS
2020-10-14 11:04:51 -04:00
50986d5f27
Merge pull request #2416 from akohlmey/lammps-shell-improvements
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Bug fixes and improvements for the LAMMPS Shell tool
2020-10-14 10:42:30 -04:00
1e2c8ce2e6
correct data file for USER-EFF
2020-10-14 08:15:59 -04:00
3894212712
correctly use REBO potential
2020-10-14 08:04:57 -04:00
bb6cfbeec1
mention AMD GPUs
2020-10-14 08:04:37 -04:00
a002194e26
remove outdated "bench/KEPLER" folder
2020-10-14 07:57:32 -04:00
07387d5e6c
remove outdated "examples/accelerate" folder
2020-10-14 07:56:58 -04:00
587be7a21a
Remove makefiles for obsolete machines and configurations or that are redundant
2020-10-14 07:54:07 -04:00
89d60afb91
make certain alpha_final is initialized
2020-10-14 04:51:51 -04:00
00e1edfae9
add a preset for selecting gcc compilers (for cases where they are not the default)
2020-10-14 04:51:34 -04:00
2026636f72
overview description for the unit test folders
2020-10-13 22:00:10 -04:00
acbb54d35f
tweak testing and add at test run for history expansion
2020-10-13 21:32:48 -04:00
f003a6c536
implement a test prototype for the LAMMPS shell
2020-10-13 20:36:24 -04:00
290763a844
add a test_mode where the isatty() check is bypassed and history not read
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this is enabled when the LAMMPS_SHELL_TESTING environment variable is set
2020-10-13 17:09:11 -04:00
114dd48779
change behavior with respect to OpenMP versus the regular LAMMPS executable
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since the shell is not meant to be run with MPI we can use all threads by default.
2020-10-13 17:08:23 -04:00
8ab5f3c71a
adjust recently added/expanded tests so they skip tests when packages are missing
2020-10-13 15:42:21 -04:00
d0ac698a41
must not assume that size_one == nfield in DumpCustom since DumpVTK changes it
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this changes all loops over format strings and output types to using nfield
2020-10-13 15:28:02 -04:00
e23774ed56
include "pointers.h" to avoid include file name conflicts when compiling with USER-VTK enabled
2020-10-13 15:26:38 -04:00
8920830909
utils.h is not needed (globally included via pointer.h)
2020-10-13 15:25:46 -04:00
338b05d9dd
set only build type specific compiler flags, so using -DCMAKE_CXX_FLAGS will work as expected
2020-10-13 12:00:03 -04:00
60a296fea8
small tweaks
2020-10-12 23:51:00 -04:00
49afab09a5
Building LAMMPS for Windows with the MinGW cross compiler is supported with CMake only
2020-10-12 23:49:40 -04:00
61381ad821
Use User's Guide and Programmer's Guide. Normalize header level formatting
2020-10-12 23:31:03 -04:00
ed885847a3
expose document and test more atom style property flags
2020-10-12 20:24:21 -04:00
a684f896de
rearrange doxygen docs for lammps_extract_settings() and lammps_extract_global()
...
this replaces two large tables whith multiple small tables that group
parameters by similar context
2020-10-12 18:59:35 -04:00
9bdae2b5c0
move installed packages summary to a different location further down in the output
2020-10-12 18:04:19 -04:00
1d7fa39bc2
don't print a message for each generated style/package header file
2020-10-12 17:10:38 -04:00
a97e632bb0
make enabled packages report more compact
2020-10-12 17:10:04 -04:00
ec4eab5061
CMake change requested by @junghans
2020-10-12 15:21:08 -04:00
24cec51e85
add tests for using python invoke and python style variables
2020-10-12 06:17:16 -04:00
8c5da70823
handle the case where the variable type is invalid and thus a null pointer is returned
2020-10-12 06:16:28 -04:00
6cda1e16ae
add test program template for testing the PYTHON package
2020-10-12 02:40:02 -04:00
c01ff34785
we must initialize the number of types with any "extra" values
...
so far, the "extra" value will only be applied if the "types" line is
present in the header. if not, the "extra" value is ignored. now will
first apply this and then lets it be overwritten in case a "types" line
is present in the header.
2020-10-11 23:26:35 -04:00
a6df6cf84c
fix format
2020-10-11 23:18:03 -04:00
a82c0a58af
improve error message
2020-10-11 23:17:46 -04:00
bdb4334210
add tip about using history as starting point for a new input
2020-10-11 16:13:13 -04:00
ee98ecc7bb
document save_history command and a few more small tweaks
2020-10-11 15:47:38 -04:00
556d48f1dc
implement a "save_history" command into the LAMMPS shell
2020-10-11 15:30:56 -04:00
f6683fefea
avoid segfault on the last word of the command history
2020-10-11 14:05:37 -04:00
9950f0d259
small LAMMPS shell updates
...
- implement a "source" command (same as "include")
- synchronize documentation in manual and README
- updates to readline customizations
2020-10-11 13:53:15 -04:00
44549ba81d
replace doc page with page or other appropriate text
2020-10-11 12:19:38 -04:00
4908a53612
correct example to include '=on' for package selection with CMake
2020-10-11 12:19:21 -04:00
3396897438
document both, CMake and traditional procedure to enable MPIIO
2020-10-11 12:18:26 -04:00
f63ff4cdc9
LAMMPS shell customization info and some usage tips
2020-10-11 12:00:16 -04:00
c0f58243cb
use correct header levels for LAMMPS shell docs
2020-10-10 23:40:34 -04:00
b3d9f648ef
Merge pull request #2414 from akohlmey/next_lammps_version
...
Update version strings for next patch release
2020-10-09 20:12:56 -04:00
0460dc3dfb
Merge pull request #2413 from akohlmey/progguide-updates
...
More Programmer Guide and Library Interface updates for next release
2020-10-09 19:30:37 -04:00
51489c1509
dedup anchor
2020-10-09 17:29:31 -04:00
97964604c6
no point in trying a static link of executables
2020-10-09 13:29:13 -04:00
362fe700a5
remove static libraries for cross-compiler. not used with .dll version.
2020-10-09 13:26:52 -04:00
43f2c14c8b
print warning when reading data files with non-zero image flags for non-periodic boundaries
2020-10-09 13:24:53 -04:00
57e0e64ffe
No MPI communicaton after MPI_Finalize() and no MPI_Finalize() unless we are initialized.
2020-10-09 12:47:13 -04:00
078f931393
add comment to explain using the LAMMPS_LIB_MPI define in example
2020-10-09 11:50:53 -04:00
84c9fcf6e9
add legacy warning to F77 style Fortran wrapper
2020-10-09 11:15:15 -04:00
74e1d0f8cf
move Tools compilation script code from CMakeLists.txt to separate Tools.cmake file
2020-10-09 11:15:00 -04:00
5457accb3d
make the legacy fortran wrapper work (again)
2020-10-09 07:52:36 -04:00
ca3d10fa39
need to define LAMMPS_LIB_MPI
2020-10-09 07:37:25 -04:00
bafba4235c
include versionadded tags
2020-10-09 07:26:01 -04:00
188e1c3828
correct versionadded dates
2020-10-09 07:22:16 -04:00
38bf231361
silence sphinx warning
2020-10-09 07:19:02 -04:00
471acb2ef8
add unit tests for added APIs
2020-10-09 07:16:34 -04:00
7a9b4ef0d4
include FFTW in MinGW cross-compiler libraries. Make static/dynamic explicit
2020-10-09 02:27:31 -04:00
eb3992a69a
enable static linkage for executables when cross-compiling with MinGW
2020-10-09 02:26:46 -04:00
bfcb78d5d7
fix bug with string passing
2020-10-09 01:42:48 -04:00
5a207247b6
update version strings for next patch release
2020-10-09 01:12:41 -04:00
6d67fa004c
tweak formulation
2020-10-08 23:35:49 -04:00
90d511bc86
add wrappers for new library functions
2020-10-08 22:32:33 -04:00
49ebc5ac40
update versionadded date
2020-10-08 22:32:08 -04:00
5c6bfa6ab5
Merge branch 'master' into progguide-axel
2020-10-08 21:51:22 -04:00
a581b4b85e
Merge pull request #2412 from lammps/progguide-updates
...
Updates to the Programmer Guide part of the Manual
2020-10-08 21:50:37 -04:00
4f4bc427ae
implement LAMMPS_LIB_NO_MPI to LAMMPS_LIB_MPI change
2020-10-08 21:50:15 -04:00
9f0002550e
Merge pull request #2404 from akohlmey/fortran-portable-string
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Make f2c_string utility function of the new Fortran module portable across Fortran compilers
2020-10-08 20:58:51 -04:00
4995ab3264
Merge pull request #2403 from akohlmey/fortran2-updates
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Update of fortran2 interface for recent changes in the C-library interface
2020-10-08 20:23:44 -04:00
4a856148ad
Merge pull request #2389 from kateryna-goloviznina/coul_tt
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Pair style for charge-dipole damping with Tang-Toennies function
2020-10-08 19:47:36 -04:00
677e8afdc5
update section headlines
2020-10-08 10:32:02 -04:00
a89741f7f6
more 'doc page' to 'page' changes
2020-10-08 08:32:15 -04:00
fdbcd202fa
Consolidate the redundant instructions for building the manual into one location.
2020-10-08 08:31:58 -04:00
60864f021f
replace "doc page" with "page" or equivalent
2020-10-07 22:29:26 -04:00
e683585bba
reformat reax/c control file parameter descriptions
2020-10-07 22:28:34 -04:00
353158f7e7
improve errors vs. exception not
2020-10-07 21:56:14 -04:00
20e1697dba
add ":class: note" to admonitions where it was missing for consistent formatting
2020-10-07 20:24:56 -04:00
08f8e7ed28
update titles as suggested by steve and move a few entries around
2020-10-07 20:07:30 -04:00
d48b0ebd7b
print OS/Compiler info when starting LAMMPS shell
2020-10-07 18:37:27 -04:00
0891a8ce7d
better MPI version detection.
2020-10-07 18:37:09 -04:00
ac6e99ae81
implement "mem" command into LAMMPS shell to print current and max memory use
2020-10-07 18:36:43 -04:00
50bfb9142d
add library API to print OS/Compiler info (for use with LAMMPS shell)
2020-10-07 18:35:59 -04:00
57cc8d6290
fix incorrectly formatted "notes"
2020-10-07 18:35:05 -04:00
1098ca8749
add some more explanation about exceptions from the library interface perspective
2020-10-07 13:08:49 -04:00
e637c150ba
add versionadded tags
2020-10-07 13:08:25 -04:00
395906b387
whitespace
2020-10-07 13:07:57 -04:00
5fa1cd7e86
small corrections
2020-10-07 05:33:55 -04:00
9ea38c545d
update global properties tests
2020-10-06 22:43:42 -04:00
355c68f304
Merge branch 'master' into progguide-axel
2020-10-06 21:40:43 -04:00
bf4773c3f7
Merge pull request #2407 from akohlmey/collected-small-fixes
...
Collected small changes and bugfixes for the next patch release
2020-10-06 20:17:45 -04:00
f0f933a711
allow forward slash in strings for if statements
2020-10-06 18:44:26 -04:00
15f9987c32
add custom commands "cd" and "pwd" to the LAMMPS shell
2020-10-06 18:39:22 -04:00
fb1dab6098
Merge branch 'master' into collected-small-fixes
2020-10-06 18:00:33 -04:00
1ee9e4eabd
Merge branch 'master' into progguide-axel
2020-10-06 17:11:47 -04:00
9274912a81
add note about no longer supporting PyPar and remove instructions related to it.
2020-10-06 16:19:43 -04:00
2f857176c8
stay compatible with cmake older than version 3.14
2020-10-06 13:45:46 -04:00
f442d811be
Merge commit 'dbf51af7d1565c62902eef22a7aa6f6eb552432b' of github.com:rbberger/lammps into collected-small-fixes
2020-10-06 12:29:36 -04:00
1afd9b1c83
update Python installation docs
2020-10-06 12:15:56 -04:00
887603d856
Merge pull request #2411 from rbberger/fix_wall_gran_region
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Corrections for fix wall/gran and wall/gran/region
2020-10-06 11:51:58 -04:00
7dd244a828
Correct fix wall/gran and wall/gran/region docs
2020-10-06 10:45:23 -04:00
18023ad9dc
Update fix_wall_gran_region.cpp
...
Don't store atom tag, just if there is a contact.
Fixes #2306
2020-10-06 10:39:14 -04:00
5d08f629ab
fix typo
2020-10-06 05:30:09 -04:00
b5db29bae4
revise python in LAMMPS docs
2020-10-05 22:48:57 -04:00
f2ba00ea9c
update label in graph
2020-10-05 21:50:54 -04:00
549e4df506
Merge branch 'progguide-richard' into progguide-axel
2020-10-05 21:04:29 -04:00
80a054471d
Merge branch 'progguide-updates' into progguide-richard
2020-10-05 19:31:03 -04:00
5244f49234
Fix broken page
2020-10-05 18:04:30 -04:00
caf434811a
Add example to Python_config.rst
2020-10-05 17:54:48 -04:00
b8c66b099d
Fix typo
2020-10-05 17:42:43 -04:00
93ed9b4266
Add PyLammps parts
2020-10-05 17:34:50 -04:00
22cca93603
Add tests for neighbor list API
2020-10-05 17:34:08 -04:00
02b10380bc
Create ctypes only neighbor list API variant
...
This moves the lammps.get_neighlist() method to lammps.numpy.get_neighlist().
lammps.get_neighlist() now returns a NeighList object, while the NumPy variants
returns a NumPyNeighList object. The main difference between the two is that while
the ctypes variant returns neighlist elements as
atom idx (int), numneighs (int), neighbors (POINTER(c_int))
the NumPy variant returns
atom idx (int), neighbors (numpy.array)
2020-10-05 16:21:37 -04:00
68147306e7
Add Python_neighbor.rst
2020-10-05 16:15:40 -04:00
c06348c507
Update Python docs
2020-10-05 15:07:57 -04:00
0fb91ec755
Merge pull request #2408 from akohlmey/lammps-shell
...
Add a LAMMPS shell tool as alternative to the LAMMPS executable for interactive use
2020-10-05 14:42:23 -04:00
d9f7ddfd6d
Merge pull request #2409 from mrcdr/math_eigen_impl
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PR to relate "math_eigen_impl.h" with an author
2020-10-05 14:07:09 -04:00
8f808a5e6e
Update Python_usage.rst and Python_module.rst
2020-10-05 14:06:09 -04:00
ed17eabe17
Add missing code highlights
2020-10-05 14:04:44 -04:00
884295eb5f
Add example showing Python exception handling
2020-10-05 14:04:14 -04:00
6672568fca
Change links
2020-10-05 14:03:50 -04:00
4f1ed775e9
Add missing docstrings
2020-10-05 14:03:19 -04:00
6933233c56
add tests for the new library APIs
2020-10-05 13:43:11 -04:00
113db3ac73
fold group specific query functions into the more generic ID query functions
2020-10-05 13:41:12 -04:00
68cca6d31a
make warning about lack of exception handling more specific
2020-10-05 12:51:42 -04:00
bd206dca10
simplify based on suggestions from @junghans
2020-10-05 11:44:19 -04:00
b6d333535c
correct variable name
2020-10-05 11:43:43 -04:00
47e08f63ac
Merge pull request #2406 from jrgissing/bond/react-rmsd_constraint_bugfix
...
bond/react: rmsd constraint bugfix
2020-10-05 10:43:21 -04:00
e08d905504
make a small change to math_eigen_impl.h
2020-10-05 22:32:15 +09:00
3e74e03bbb
update all_on/all_off presets to really include all packages
2020-10-04 16:46:29 -04:00
d500ffa784
implement handler for CTRL-C on windows.
2020-10-04 16:42:29 -04:00
f3b33ea0c6
address spelling issues
2020-10-04 14:10:35 -04:00
d1e76068e8
add new APIs to library docs
2020-10-04 14:10:18 -04:00
ffcd905bf1
complete LAMMPS shell docs interation. Warn if exceptions are missing but don't fail
2020-10-04 14:03:34 -04:00
e360219a8a
add readme and makefile for LAMMPS shell
2020-10-04 12:28:01 -04:00
e71806196f
ignore LAMMPS shell history files
2020-10-04 12:27:40 -04:00
cc14bae240
add LAMMPS shell to README
2020-10-04 12:22:37 -04:00
f6a7cbd2e8
fix typo
2020-10-04 11:31:15 -04:00
2f67f299e5
correct error messages and make use of utils and fmtlib
2020-10-04 11:26:22 -04:00
ecb5078ba7
add signal handler to smoothly interrupt ongoing runs. non-windows only.
2020-10-04 11:25:37 -04:00
f1ed6a9782
change word break characters to make direct variable expansion completion work
2020-10-04 11:25:05 -04:00
9353004e3e
add APIs to determine of LAMMPS is running and to interrupt a run cleanly
2020-10-04 11:23:49 -04:00
2eb07f7427
add expansions of IDs and references to IDs
2020-10-04 06:02:14 -04:00
9dfb715296
add support for variable names to id introspection in library interface
2020-10-04 06:01:26 -04:00
b1cc9949e4
include added introspection into docs
2020-10-03 23:38:22 -04:00
1988e4c24c
add introspection for various kinds of IDs
2020-10-03 23:38:02 -04:00
c08089c1a7
add missing pkg-config file for readline
2020-10-03 22:35:58 -04:00
4520eef1b0
include readline support to be ready for LAMMPS-Shell
2020-10-03 22:05:52 -04:00
7f3db6f8e3
improve wording
2020-10-03 22:04:54 -04:00
c5514c0a36
windows portability fix
2020-10-03 22:02:13 -04:00
4e8feff52c
add support for building the LAMMPS shell in CMake
2020-10-03 22:01:57 -04:00
acf53ff55e
add a few more context aware matcher functions
2020-10-03 12:26:40 -04:00
a2f7aae6db
add API to query group names
2020-10-03 12:26:17 -04:00
01c85a3032
correct embedded docs
2020-10-03 12:25:56 -04:00
b231fa8a16
add completion for force style names
2020-10-03 11:32:56 -04:00
4cf30ceda1
silence compiler warnings
2020-10-03 09:52:00 -04:00
af8f8d3c11
avoid segfault
2020-10-03 09:51:42 -04:00
024c9238f9
fix issue spotted by compiler warning
2020-10-03 09:51:28 -04:00
22cbac0b01
initial version of LAMMPS shell. without build system support (yet).
2020-10-03 09:49:35 -04:00
946a49662f
bond/react: rmsd constraint bugfix
...
previously, eligible reactions could have been temporarily prevented, at the edge of the box, in serial
2020-10-02 18:43:35 -04:00
fb1bd3e962
Correct links
2020-10-02 18:01:52 -04:00
d91d8de76d
Refactor LammpsNumpyWrapper to numpy_wrapper
...
LammpsNumpyWrapper was a class that was defined inside of the
lammps.numpy property when it was first accessed. This made it hard
to document the methods of this class.
This commit extracts this utility class into the lammps module and
renames it to 'numpy_wrapper'.
2020-10-02 17:28:25 -04:00
0089a35d95
Remove dead code
2020-10-02 17:27:08 -04:00
7355977819
Add missing exception handling for functions that could cause errors
2020-10-02 17:26:14 -04:00
d9cbb354d2
Move lammps exception code into its own property
2020-10-02 17:22:01 -04:00
0475397229
Update Python_usage.rst
2020-10-02 17:19:51 -04:00
60891fe6f9
Add Python_config.rst
2020-10-02 17:19:04 -04:00
b57c8f6b77
Add tests for LAMMPS exceptions in Python
2020-10-02 16:53:41 -04:00
52c6353f86
Fix typo
2020-10-02 15:09:29 -04:00
a0d0f96e52
make f2c_string utility function portable across fortran compilers
2020-10-02 10:36:17 -04:00
1f417f8eb4
mention Fortran interface in examples/COUPLE/fortran2 now that it is up-to-date again
2020-10-02 00:28:13 -04:00
086a71ba46
incorporate LAMMPS fortran2 interface updates and apply a few corrections
2020-10-02 00:07:01 -04:00
2c7a686220
update fortran2 module
2020-10-01 23:20:52 -04:00
51d55aa036
Merge pull request #2400 from akohlmey/code-analysis-fixes
...
A few more static code analysis fixes
2020-10-01 18:32:50 -04:00
2ea61b21f8
fix small memory leaks
2020-10-01 18:11:19 -04:00
48c45767f9
remove dead code
2020-10-01 18:11:08 -04:00
c5fc3f2c78
Update Python_usage.rst
2020-10-01 18:01:07 -04:00
533c453a08
Update Python docs
2020-10-01 15:00:08 -04:00
243a81e9d8
must initialize eflag_atom and vflag_atom to zero in constructor
2020-10-01 14:49:23 -04:00
9dc42262ec
one more edit
2020-10-01 11:34:27 -06:00
343b24dd5e
more edits to C library chapter
2020-10-01 10:50:33 -06:00
b94df09570
Merge pull request #2398 from lammps/progguide-updates
...
Documentation updates plus a few small bugfixes
2020-10-01 11:11:28 -04:00
774ac8b2d9
avoid overflow of per-local-atom computation
2020-10-01 09:49:28 -04:00
4a40a70870
avoid overflow of timestep related computations
2020-10-01 09:48:54 -04:00
8c56f60939
use bigint instead of int for timestep related variable functions to avoid overflows
2020-10-01 09:35:45 -04:00
ea3af3c2bc
resolve delete/free() mismatch
2020-10-01 09:34:38 -04:00
9efcaf2d61
update documentation for Windows installer
2020-10-01 00:57:53 -04:00
fb33a71720
look for liblammps.dll in windows binary dir only if that directory exists
2020-10-01 00:34:03 -04:00
507c2cb2a8
Update and reorganize Python docs
2020-09-30 22:20:01 -04:00
a79a7b2704
fix typo reported on lammps-users
2020-09-30 21:24:55 -04:00
77fb2ee311
add list of documented functions at the top of the C-Library doc pages
2020-09-30 21:16:48 -04:00
dc13a61b40
fix spelling
2020-09-30 20:00:53 -04:00
a9b27caf17
Merge branch 'master' into progguide-axel
2020-09-30 19:57:20 -04:00
38d954e038
Update the text to mention returning the handle instead of passing it as an argument.
2020-09-30 19:54:07 -04:00
0d9a2808b4
Merge branch 'progguide-updates' of github.com:lammps/lammps into progguide-axel
2020-09-30 19:50:00 -04:00
6928e79883
Merge pull request #2395 from rbberger/collected-small-fixes
...
Fixes issues found via Static Code Analysis and from bug reports
2020-09-30 19:23:52 -04:00
4b71e1cbda
initial library doc page edits
2020-09-30 15:37:11 -06:00
cbc529881c
support hybrid atom styles in in fix propel/self
2020-09-30 14:07:46 -04:00
23279836c9
Invalidate pointer after deallocation
2020-09-30 09:10:40 -04:00
d84300a3ac
do not fail when looking for gzip or ffmpeg executables when cross compiling to windows
2020-09-30 00:05:15 -04:00
555fba1e4b
add special case for windows installer package where the .dll file is in the bin folder
2020-09-29 18:46:32 -04:00
e4cfb91169
discuss that USER-MESONT package potentials are not bundled and provide URL
2020-09-29 16:57:19 -04:00
0ed935ab76
silence compiler warning on windows
2020-09-29 11:19:12 -04:00
54c4b95c4d
small format tweak
2020-09-28 14:09:03 -04:00
b1f6a6799c
Merge remote-tracking branch 'github/master' into coul_tt
2020-09-28 13:56:00 -04:00
3b1d07225d
corret strmatch() semantics and restore strcmp() in extract function
2020-09-28 13:49:38 -04:00
c217c8df24
shorten example and do not print CPU time output to avoid false positives when comparing
2020-09-28 13:49:08 -04:00
8bc67f17cc
fully integrate pair style coul/tt into manual
2020-09-28 13:46:53 -04:00
e0e4e516fc
Merge pull request #2396 from akohlmey/openmp-compat-auto
...
Autodetect OpenMP compatibility setting for known compiler signatures
2020-09-28 13:14:13 -04:00
25bda86ad0
fix typo
2020-09-28 12:52:32 -04:00
67803fe17f
Minor cleanup for dpd/tstat in the GPU library
2020-09-28 11:41:39 -05:00
d8b55ecd65
Merge pull request #2397 from akohlmey/remove-cilk-array-notation
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Remove specializations using cilk array notation from USER-INTEL
2020-09-28 11:56:02 -04:00
405c1b98c5
remove inactive code and documentation for dump image persp option
2020-09-28 08:19:26 -04:00
d868271b01
remove unneeded escapes from input examples
2020-09-28 07:52:38 -04:00
407f445753
remove specializations using cilk array notation
2020-09-28 07:32:11 -04:00
c626208c80
avoid failure with Intel compilers
2020-09-27 19:05:58 -04:00
9d39587d37
expand c-library properties example
2020-09-27 19:05:40 -04:00
fdbdd26585
include intel fortran compiler into intel cmake preset
2020-09-26 22:30:21 -04:00
b11b420b08
small doc update for singularity
2020-09-26 22:30:05 -04:00
d23f7d14c9
typo
2020-09-25 22:20:31 -04:00
7e68746ebe
use safe reader function
2020-09-25 22:16:19 -04:00
adef7d4e18
need to check for nthreads < 1 only if OpenMP is enabled
2020-09-25 22:14:21 -04:00
909960514a
avoid unneeded division
2020-09-25 22:10:51 -04:00
6967522a4f
fix logic error
2020-09-25 22:08:28 -04:00
172bb6050a
use safe read function
2020-09-25 22:08:22 -04:00
a963e85846
remove dead code
2020-09-25 21:50:53 -04:00
66c4627775
Merge branch 'collected-small-fixes' of github.com:rbberger/lammps into collected-small-changes
2020-09-25 18:14:50 -04:00
2ffa50f2f8
fix memory leak
2020-09-25 18:13:52 -04:00
ab08a27731
correct data layout for creating integrate style
2020-09-25 18:00:47 -04:00
bd60174fd3
fix argument dimensions
2020-09-25 18:00:19 -04:00
c0384eb264
update code owners
2020-09-25 17:52:51 -04:00
c496b18a9d
avoid memory leak
2020-09-25 17:50:02 -04:00
d1321a0860
fix argument dimensions
2020-09-25 17:49:52 -04:00
e378532003
avoid 32-bit integer overflow
2020-09-25 17:31:49 -04:00
5e110fe707
update docs for autodetected OpenMP compatibility
2020-09-25 16:45:39 -04:00
5489c64aef
remove trailing whitespace
2020-09-25 16:32:54 -04:00
2e67aa6b47
autodetect OpenMP 4.0 semantic compatibility if not explicitly set
2020-09-25 16:31:45 -04:00
cc5ef652e4
move Using Python with LAMMPS to programmer guide and integrate python module docs
2020-09-25 15:13:05 -04:00
0ffb2ce09c
move Tutorials to bottom of Howto section
2020-09-25 15:12:31 -04:00
5e6d222d29
fix up a few internal references
2020-09-25 14:04:44 -04:00
495438105f
mass renaming of programmer guide files
2020-09-25 13:59:29 -04:00
9a523fef65
add bibliography
2020-09-25 13:48:22 -04:00
089e55cc37
fix typo
2020-09-25 13:48:05 -04:00
26ad664079
Avoid string duplication and remove memory leak
2020-09-25 13:44:28 -04:00
e1b00e96ed
bug fixed
2020-09-25 17:10:54 +02:00
064f735272
source files updated, examples changes
2020-09-25 16:08:20 +02:00
7a35f786fb
tweak button size setting for active state, too.
2020-09-24 16:56:05 -04:00
28812b1ea7
Merge pull request #2381 from akohlmey/collected-small-changes
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Collected small changes
2020-09-24 16:17:28 -04:00
08270c3498
update container descriptions
2020-09-24 02:17:26 -04:00
02c1480546
update README in examples/COUPLE/simple
2020-09-24 02:17:11 -04:00
ac78f8f1e1
update examples/COUPLE/simple sources to work with the current version of LAMMPS
2020-09-24 01:30:34 -04:00
b350dce573
improve error messages for variables and python commands
2020-09-23 19:02:55 -04:00
2f8a5ddd1f
xindy doesn't seem to be required (and is not available on CentOS 8)
2020-09-23 17:13:09 -04:00
85fe94a6dd
Merge pull request #2388 from jrgissing/molecule_fragments_check
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molecule: findfragments correction
2020-09-23 15:54:37 -04:00
790f636523
rephrase
2020-09-23 15:45:29 -04:00
b6d98707ec
molecule: revert overzealous error checking
2020-09-23 11:23:10 -04:00
2b30661b07
molecule: correctly update docs
2020-09-23 10:46:23 -04:00
1be766c8cd
molecule fragment: let's add more checks
2020-09-23 10:37:33 -04:00
ed3975054a
fix typo
2020-09-23 10:30:19 -04:00
e29f838121
also add error checks
2020-09-23 10:28:48 -04:00
88b8461e0f
the right molecule fragment fix
2020-09-23 10:19:38 -04:00
343932f220
document -DLAMMPS_TRAP_FPE
2020-09-23 09:38:07 -04:00
ab4dc9c343
Merge pull request #2378 from junghans/cmake_install_fix
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cmake: do not install mpi.h without library
2020-09-22 21:37:57 -04:00
20027cc7ec
Merge pull request #2390 from Vsevak/hip_pppm_fix
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Fix atomicAdd in PPPM/GPU for the HIP backend
2020-09-22 18:04:12 -04:00
9df1bb4db0
remove obsolete makefiles. Makefile.xk7 is on death watch but Blue Waters still has such nodes
2020-09-22 17:47:14 -04:00
459d51bbea
Do not disable atomics for HIP
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atomics are disabled for NVIDIA 1.0 cards, which should not affect ROCm HIP
2020-09-22 22:34:24 +03:00
7b4304577a
add -std=c++11 flag to compilation of all .cpp files on Linux
2020-09-22 10:58:54 -04:00
2d7b6a9008
remove dead code
2020-09-22 10:12:59 -04:00
b878403aee
update a few more singularity container definitions for doc build requirements
2020-09-22 06:01:34 -04:00
1eebdcbd03
fix obvious bugs
2020-09-22 05:34:29 -04:00
b876f451f8
make compiler choice overridable
2020-09-22 05:34:12 -04:00
f186eb7005
be more selective about which elements not to display
...
we only want to skip the redundant User-Documentation and Programmer-Documentation captions
2020-09-21 22:41:19 -04:00
54aacc47ea
add section about citing LAMMPS
2020-09-21 22:40:36 -04:00
cc8b042abf
cmake: export LAMMPS_LIB_NO_MPI for serial version
2020-09-21 12:54:56 -06:00
fbcb888ec0
cmake: do not install install mpi.h
2020-09-21 12:41:34 -06:00
51b900b043
Merge remote-tracking branch 'origin/master' into cmake_install_fix
2020-09-21 12:39:51 -06:00
36fdba32e7
Merge pull request #2382 from junghans/cmake_install_fix_2
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cmake: install missing utils.h
2020-09-21 13:29:29 -04:00
19bc3d3643
Docs updated
2020-09-21 18:05:57 +02:00
7eab154786
one-line bug when checking for molecule fragments
2020-09-21 11:01:04 -04:00
8099e2a5d9
Docs updated
2020-09-21 16:16:38 +02:00
2206de7c68
Examples added, bug fixed
2020-09-21 16:14:33 +02:00
a1407de09d
have make yes/no package terminate with error status for non-existing packages
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this closes #2387
2020-09-21 07:09:13 -04:00
c7c7d2f474
Merge pull request #2377 from akohlmey/move-version-to-lammps
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Move the members `version` and `num_ver` form Universe class to LAMMPS class
2020-09-21 02:10:08 -04:00
29a7d598ac
update formatting style to be more consistent
2020-09-21 02:04:58 -04:00
0a11cc5eb9
make code valgrind clean
2020-09-21 01:55:07 -04:00
486131f4c5
fix segmentation fault bug in USER-PTM. closes #2386
2020-09-21 01:54:36 -04:00
0951fea738
Merge branch 'collected-small-changes' of github.com:akohlmey/lammps into collected-small-changes
2020-09-20 19:20:42 -04:00
acb5fd2ebf
Simplify GenerateBinaryHeader utility
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The function implementation was incomplete for handling the case
of multiple files. It would generate wrong C code in case more than
one files were specified. Since we don't have this use case, it's
safe to only leave the single input file implementation.
Closes issue #2294
2020-09-20 18:24:43 -04:00
7d07d04989
Use correct library for unit test if LAMMPS_MACHINE_NAME is set
2020-09-20 17:52:24 -04:00
54b9e60dd0
reformat
2020-09-20 14:06:40 -04:00
4cbf821af3
modernize example
2020-09-20 14:03:13 -04:00
774bffe623
relax result precision requirement somewhat
2020-09-20 13:57:04 -04:00
f2bb835e23
cmake: install missing utils.h
2020-09-20 10:44:54 -06:00
dfd447f570
Add missing tools for PDF index build to containers
2020-09-19 23:07:24 -04:00
61ce73273b
Add missing -u flag for unbuffered PyLammps tests
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Addresses issue #2380
2020-09-19 23:07:13 -04:00
92f8398bed
check more thoroughly for prerequisites to translate the PDF manual. update doc/README
2020-09-19 18:16:52 -04:00
705a9a0a8b
cmake: do not install mpi.h without library
2020-09-19 15:12:36 -06:00
f72fb7290b
fix links
2020-09-19 16:28:20 -04:00
67aeb7a5e5
Merge branch 'move-version-to-lammps' into collected-small-changes
2020-09-19 16:17:01 -04:00
6b0346c299
try use unencrypted download or using wget if normal download of polyfill.js fails
2020-09-19 16:14:08 -04:00
c91ee210e4
simplify variable lookup in set command
2020-09-19 16:04:09 -04:00
9c0808e95a
update unit tests for move of version string location
2020-09-19 15:00:03 -04:00
4c51a8ae57
move version and num_ver from Universe to LAMMPS and make num_ver an int
2020-09-19 11:37:08 -04:00
89506efd23
document Pointers class and LAMMPS_NS namespace
2020-09-19 11:16:44 -04:00
73c65d43e1
update list of main folders and descriptions
2020-09-19 02:53:36 -04:00
9030c987e6
tweak formatting and style setting to have the desired structure and layout
2020-09-19 00:54:54 -04:00
6dda562501
skip over uninitialized and internal variables. correctly identify all kinds of boolean values
2020-09-18 23:40:31 -04:00
9cdde97863
correct test logic
2020-09-18 22:37:54 -04:00
5ce6259632
correct reference to function
2020-09-18 22:35:56 -04:00
56d9222156
Merge pull request #2374 from akohlmey/next_patch_version
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Step version strings for the next patch release
2020-09-18 21:45:34 -04:00
897a7d0ed4
only try to broadcast if we have a proper communicator
2020-09-18 21:17:31 -04:00
f5fda95da6
Merge branch 'master' into next_patch_version
2020-09-18 21:15:12 -04:00
094a1bea91
Merge pull request #2369 from akohlmey/collected-small-changes
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Collected small changes and fixes for the next patch release
2020-09-18 20:20:41 -04:00
51957a6219
fix merge conflict
2020-09-18 19:49:36 -04:00
a0afb9b554
Merge branch 'master' into collected-small-changes
2020-09-18 18:38:47 -04:00
7580176020
Merge pull request #2376 from giacomofiorin/colvars-update
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Update Colvars to version 2020-09-17
2020-09-18 18:38:17 -04:00
b520a6287b
Revert parts of "Restore PDF index"
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We need to update the container image(s) for building the
pdf documentation on ci.lammps.org by adding `latexmk`
and `xindy` before we can re-enable this change to the makefile.
This partially reverts commit 3c3b76a781
2020-09-18 18:37:26 -04:00
494498df03
update docs on building the PDF version of the manual
2020-09-18 18:27:23 -04:00
906e000e4c
Merge pull request #2368 from jrgissing/bond/react-update_all_charges_default
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Bond/react update all charges by default
2020-09-18 18:17:54 -04:00
33a2857b33
Fix whitespace
2020-09-18 17:56:12 -04:00
3c3b76a781
Restore PDF index
2020-09-18 17:51:51 -04:00
07c9298558
Fix some broken internal hyperlinks in Colvars PDF
2020-09-18 17:24:12 -04:00
d4cd67ce74
tweak format some more and refactor manual sectioning to be logically correct
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now if only there was a way to make the titles of the parts show in the
navigation sidebar.
2020-09-18 17:15:42 -04:00
7deb773440
Update Colvars to version 2020-09-17
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Small changes
Implement global map of components (@HanatoK)
https://github.com/Colvars/colvars/pull/363
Format code examples with colored background (@giacomofiorin)
https://github.com/Colvars/colvars/pull/361
replaced jacobi() with an open-source version (@jewettaij)
https://github.com/Colvars/colvars/pull/360
2020-09-18 17:09:18 -04:00
e1397b9a88
Merge branch 'master' into collected-small-changes
2020-09-18 16:11:47 -04:00
34ba8ec83c
Merge pull request #2359 from rbberger/python_interface_guide
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Library interface updates and Python documentation
2020-09-18 16:11:08 -04:00
635b7c04a5
Update docs and docstrings
2020-09-18 14:49:25 -04:00
de811db221
address spelling issues
2020-09-18 14:13:35 -04:00
ae9abf0f7d
correctly update docs
2020-09-18 14:10:32 -04:00
9a6dfbc0ee
add some cross referencing
2020-09-18 13:45:33 -04:00
449513703b
Merge remote-tracking branch 'origin/master' into python_interface_guide
2020-09-18 12:35:17 -04:00
e0b22a51da
Doc updates
2020-09-18 12:35:07 -04:00
1afb355d09
Limit int types to LAMMPS_INT and LAMMPS_INT64
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Keep LAMMPS_TAGINT and LAMMPS_BIGINT internal to LAMMPS.
An external caller now only needs to distinguish between 32 and 64bit
integers, doubles and C strings.
2020-09-18 12:05:37 -04:00
edbfdde372
document ubuf union in developer guide
2020-09-18 11:55:06 -04:00
2c17652ad6
Created another static instance for dpd/tstat in the GPU library
2020-09-18 10:28:52 -05:00
1264184e7b
tweak some website layout and style settings
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- make previous/next buttoms smaller and show on top and bottom of page
- make tab header items smaller and more rounded
- reduce padding on a few selected items to make pages more compact
remove obsolete lammps.css file variant
2020-09-18 10:55:50 -04:00
df4ab6c39e
Merge pull request #2375 from akohlmey/fmtlib-update
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Update bundled fmtlib to version 7.0.3
2020-09-18 10:30:18 -04:00
dc89f0879c
update specific pull request templates as they are available through the github cli now
2020-09-18 06:54:31 -04:00
3a2457bb3d
update bundled fmtlib to version 7.0.3
2020-09-18 06:14:46 -04:00
2b1e249483
add comments to mark LAMMPS specific customizations
2020-09-18 06:12:42 -04:00
1ef36fd20a
step version strings for next patch release
2020-09-17 22:16:42 -04:00
0e81803c8b
some embedded documentation tweaks
2020-09-17 22:00:58 -04:00
90abe12a3e
update LAMMPS version reference
2020-09-17 21:04:43 -04:00
445e57923f
add one-time deprecation warning to lammps_open() and lammps_open_no_mpi()
2020-09-17 21:01:38 -04:00
6e22229424
Merge remote-tracking branch 'github/master' into collected-small-changes
2020-09-17 20:27:55 -04:00
94ad6821f7
Merge pull request #2373 from stanmoore1/kk_wkar
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Add workaround for performance regression in Kokkos Package
2020-09-17 20:24:39 -04:00
d8b6ebdfc8
Add workaround for performance regression
2020-09-17 16:33:48 -06:00
42aca25a58
Update docs, fix typos
2020-09-17 18:10:08 -04:00
b4a1c9c24c
Update examples
2020-09-17 17:08:13 -04:00
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
...
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
f8f2a94f60
coul/tt pair style added to USER-DRUDE
2020-09-17 15:14:27 +02:00
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
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
...
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
16749566f8
Revert "fix issue with local variable shadowing a global variable"
...
This reverts commit 3368eb79d8
2020-09-15 14:42:00 -04:00
2165f6ed38
Merge pull request #2363 from akohlmey/consistent-memory-usage
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Make memory usage reporting consistent
2020-09-15 14:21:07 -04:00
baa49984c2
update comments
2020-09-15 14:19:40 -04:00
326d9f398c
Merge branch 'master' into iss2345
2020-09-15 14:06:16 -04:00
5cbb54b844
Merge branch 'iss2345' of github.com:eagunn/lammps into iss2345
2020-09-15 14:04:16 -04:00
b5832191d8
Merge pull request #2364 from akohlmey/force-test-bugfix
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Force style unit test template bugfix
2020-09-15 13:40:13 -04:00
5da50d64c9
reformulate
2020-09-15 12:32:43 -04:00
2f3c916a57
add unit test for lammps_memory_usage()
2020-09-15 12:29:03 -04:00
3576464268
Merge branch 'master' into consistent-memory-usage
2020-09-15 12:25:16 -04:00
9490370eb0
Use consistent naming in PyLAMMPS classes
2020-09-15 12:22:36 -04:00
2c30de65d2
Fix typos in docstring
2020-09-15 12:16:47 -04:00
165444004e
Merge pull request #2362 from akohlmey/library-progguide
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Updates to C-Library interface progammer guide and reference
2020-09-15 11:51:02 -04:00
db59abf1b9
fix bug in lammps_has_style()
2020-09-15 11:34:24 -04:00
4a48ce76b8
Merge remote-tracking branch 'origin/master' into python_interface_guide
2020-09-15 11:34:16 -04:00
c6bc21febf
Merge pull request #2361 from akohlmey/collected-small-changes
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Collected small changes for the next patch release
2020-09-15 11:28:25 -04:00
2f3c73217b
detect if dt has been changed from default and print warning if reset by units command
2020-09-15 10:50:44 -04:00
b20b234ebe
Merge remote-tracking branch 'origin/master' into python_interface_guide
2020-09-15 10:45:28 -04:00
e30864431f
add test for missing quartic bond style
2020-09-15 10:12:18 -04:00
2794108837
don't update per-atom pair data if not available
2020-09-15 10:12:07 -04:00
238730b13d
update epsilon
2020-09-15 09:55:58 -04:00
c6b6369d2d
fix bug in input script templates that would have the timestep setting overwritten by a units command
2020-09-15 09:46:57 -04:00
bc31486fd1
start tests for lammps_extract_global()
2020-09-15 09:27:07 -04:00
bb76215ef0
add library interface to retrieve memory usage info
2020-09-15 01:59:58 -04:00
4b64be77e0
consolidate memory allocation information into a single function (in Info)
2020-09-15 01:59:58 -04:00
0183e999c9
consistently return "memory_usage" as double.
2020-09-15 01:59:58 -04:00
39681acfa4
add cross reference
2020-09-14 21:03:39 -04:00
d27d4912af
test lammps_extract_settings()
2020-09-14 20:53:19 -04:00
1e54a9fcf1
complete tests for extracting and resetting the box
2020-09-14 20:27:29 -04:00
5c7f67201b
make naming more consistent
2020-09-14 20:27:10 -04:00
93bd851ab0
fix typo
2020-09-14 17:39:31 -04:00
df9f0e244b
add false positive
2020-09-14 17:18:14 -04:00
5634dd4394
correct formatting of examples
2020-09-14 17:15:53 -04:00
b1e0990c46
update lammps config settings calls example
2020-09-14 17:11:27 -04:00
f70717710e
fix for zstd support. add styles to list at top and document .zst extension requirement
2020-09-14 17:07:09 -04:00
a1b2f82107
test for exceptions add example
2020-09-14 17:01:28 -04:00
4185608e92
complete testing for LAMMPS configuration queries
2020-09-14 14:56:56 -04:00
b455812434
more tests for properties and configuration
2020-09-14 14:25:17 -04:00
f5e9804557
cosmetic
2020-09-14 14:24:34 -04:00
6315b277c8
Revert commit 14dfd3876a which walked-back
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the NULL->nullptr changes for lib/awpmd.
Then, hand-applied a minor cleanup to comments, ala Axel's changes to the
rest of the codebase.
2020-09-14 12:05:46 -06:00
430d151660
Revert commit 05d41cd50d which walked-back
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the NULL->nullptr changes for lib/poems.
Then, hand-applied a minor cleanup to comments, ala Axel's changes to the
rest of the codebase.
2020-09-14 12:05:46 -06:00
58a17532bf
fix up some comments
2020-09-14 12:05:45 -06:00
ec1fe4e445
update molfile plugin headers with latest versions from VMD
2020-09-14 12:05:45 -06:00
a57a5c76a5
T2345: After examining comments changed by batch conversion of NULL
...
to nullptr, I've corrected a small number where it seemed clear
that the previous NULL should have been either "NULL" (where the
code is looking for a string with that value), or null char / null byte
(where the comment is talking about the char/byte that terminates
a c-style string).
Also changed 6 places where the batch change had changed 'NULL ptr'
to 'nullptr ptr'. Now they simply say 'nullptr'.
2020-09-14 12:05:45 -06:00
96f0e7e0d0
T2345: Walking back nullptr changes in #defines in STUBS/mpi.h
2020-09-14 12:05:45 -06:00
96b01f2383
T2345: Walking back nullptr changes to lib/awpmd
2020-09-14 12:05:45 -06:00
ed57554e18
T2345: Replace instances of NULL with nullptr
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revert lib/poems to remove nullptr changes.
Walking back changes to lib as needed.
2020-09-14 12:05:44 -06:00
f524fa758d
T2345: Replace instances of NULL with nullptr
...
Per guidance from Axel, revert lib/kokkos and lib/colvars
to remove nullptr changes.
2020-09-14 12:05:44 -06:00
9a5d8fd18b
Manually resolve two rebase conflicts.
2020-09-14 12:04:51 -06:00
50b80e078d
Merge pull request #2354 from stanmoore1/qeq_refactor
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small fix qeq/reax refactoring for base and accelerated variants
2020-09-14 12:18:32 -04:00
ac040dc85f
update prototype to allow constant strings
2020-09-14 12:17:49 -04:00
f4601235c9
add tests for lammps configuration introspection via library interface
2020-09-14 12:17:24 -04:00
155e7de859
fix bug in lammps_has_style()
2020-09-14 12:16:53 -04:00
a5740d75cf
add missing option
2020-09-14 09:27:49 -04:00
3655919c7c
tweak minimize summary output format
2020-09-14 09:09:22 -04:00
cc86214fe2
take back too eager change
2020-09-13 17:20:29 -04:00
2438f38afc
skip test if atom style is missing
2020-09-13 17:12:21 -04:00
96a5585d65
use more const char pointers
2020-09-13 17:12:11 -04:00
a2fc33b419
update c-library tests
2020-09-13 17:02:32 -04:00
de49325c0f
add properties example
2020-09-13 17:00:08 -04:00
fcb38354dc
import adapted example input deck
2020-09-13 16:47:29 -04:00
39255da6ae
use common main function that allows handling of common command line flags.
2020-09-13 16:46:59 -04:00
5a0623595b
make char * argument of lammps_get_thermo() const
2020-09-13 16:46:13 -04:00
b702298e83
fix typo
2020-09-12 19:06:58 -04:00
da0cdb0de4
update formatting of keyword summary
2020-09-12 19:06:30 -04:00
eda04dac98
update conventions and guidelines about C++ standard and requirements
2020-09-12 15:13:23 -04:00
93a0d4c096
fix up some comments
2020-09-12 14:26:34 -04:00
bc850bcd97
update molfile plugin headers with latest versions from VMD
2020-09-12 14:04:23 -04:00
1597cd5dcb
T2345: After examining comments changed by batch conversion of NULL
...
to nullptr, I've corrected a small number where it seemed clear
that the previous NULL should have been either "NULL" (where the
code is looking for a string with that value), or null char / null byte
(where the comment is talking about the char/byte that terminates
a c-style string).
Also changed 6 places where the batch change had changed 'NULL ptr'
to 'nullptr ptr'. Now they simply say 'nullptr'.
2020-09-12 09:34:39 -06:00
9f0354f816
T2345: Walking back nullptr changes in #defines in STUBS/mpi.h
2020-09-12 09:34:39 -06:00
14dfd3876a
T2345: Walking back nullptr changes to lib/awpmd
2020-09-12 09:34:39 -06:00
05d41cd50d
T2345: Replace instances of NULL with nullptr
...
revert lib/poems to remove nullptr changes.
Walking back changes to lib as needed.
2020-09-12 09:34:39 -06:00
13be8085e5
T2345: Replace instances of NULL with nullptr
...
Per guidance from Axel, revert lib/kokkos and lib/colvars
to remove nullptr changes.
2020-09-12 09:34:39 -06:00
f1ef7d85a8
T2345: Replace instances of NULL with nullptr
...
The following changes have been applied to src and lib folders:
regex replace: ([^"_])NULL ⇒ \1nullptr (8968 chgs in src, 1153 in lib)
Manually find/change: (void \*) nullptr ⇒ nullptr (1 case)
regex find: ".*?nullptr.*?"
Manually ~14 cases back to "NULL" in src, ~2 in lib
regex finds a few false positive where nullptr appears between two
strings in a function call
2020-09-12 09:34:38 -06:00
69962b4de5
add test for MSM kspace without periodic boundaries
2020-09-12 11:10:38 -04:00
3368eb79d8
fix issue with local variable shadowing a global variable
2020-09-12 11:10:12 -04:00
d7500c3e5a
MSM output format tweaks
2020-09-12 11:09:33 -04:00
16d2fef5ad
add check that shrinkwrap boundaries are not use when reading a data file while a MSM kspace style is defined
2020-09-12 11:06:20 -04:00
4a8d6016e4
Update docs
2020-09-11 22:49:44 -06:00
828ce84df5
add check for number of local atom indices overflowing neighbor lists for molecular systems
2020-09-11 22:09:09 -04:00
bc1b876a3d
make fix widom errors and test output consistent with the fix name capitalization
2020-09-11 19:29:17 -04:00
47b3039b28
update unit tests, too
2020-09-11 19:24:32 -04:00
9d0c3bc665
replace some numeric constants in Atom and AtomVec classes with enumerators
2020-09-11 19:07:55 -04:00
612f1d7ce3
fix typo
2020-09-11 17:49:06 -04:00
7b869e8ee8
Start with more detailed description of PyLammps
2020-09-11 17:09:38 -04:00
77d475d121
Add more tests
2020-09-11 15:48:23 -04:00
58833ce11e
Add API tests
2020-09-11 15:21:36 -04:00
cb253b2b1a
Add HTML report option for Python
2020-09-11 14:03:13 -04:00
1855f92694
Use include and omit
2020-09-11 12:44:41 -04:00
377163d940
Add target to generate Python coverage XML
2020-09-11 11:36:22 -04:00
101d39142e
Merge pull request #2357 from akohlmey/lib-get-mpi-comm
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Add ability to retrieve the MPI communicator from LAMMPS instance via library/python interface
2020-09-11 11:20:12 -04:00
97000fa016
Merge remote-tracking branch 'origin/master' into python_interface_guide
2020-09-11 09:48:28 -04:00
ded57ba749
move test to avoid issues with indentation from having tabs follow directly a list-table
2020-09-10 16:16:58 -04:00
4452109b60
address spelling issue
2020-09-10 16:15:03 -04:00
0d5f68bc30
make "new in" and "changed in" leads boldface
2020-09-10 16:14:53 -04:00
3d37fd05f4
disable caching - for now - to avoid bad side effects from sphinx-tabs
2020-09-10 16:14:18 -04:00
e813e2d30a
add minimal unit test for lammps_get_mpi_comm() API
2020-09-09 22:12:47 -04:00
bd72ef7996
add API to library/python interface to extract the MPI communicator
2020-09-09 22:03:11 -04:00
b99e005ca1
Update example output files
2020-09-09 18:26:34 -04:00
d43cb34c70
Support debugging flag for Colvars via CMake
2020-09-09 18:19:29 -04:00
85c394453c
Update Colvars to version 2020-07-07
...
This update contains several fixes and small new features or usability
improvements. Descriptions and authorship information can be accessed from
the pull requests listed below.
Skip the zero-step also when multiple run commands are executed in sequence (@giacomofiorin)
https://github.com/Colvars/colvars/pull/357
Do not accumulate data at step 0 (@giacomofiorin)
https://github.com/Colvars/colvars/pull/345
Support for symmetry permutations of atoms in RMSD (@jhenin)
https://github.com/Colvars/colvars/pull/344
Detect new grid parameters (@jhenin)
https://github.com/Colvars/colvars/pull/341
Only access the output streams in non-threaded regions (@giacomofiorin)
https://github.com/Colvars/colvars/pull/338
Fix incomplete setting of default colvarsRestartFrequency (@giacomofiorin)
https://github.com/Colvars/colvars/pull/334
Fix typo (@e-kwsm)
https://github.com/Colvars/colvars/pull/333
Convert the input keyword to lowercase in read_state_data_key (@HanatoK)
https://github.com/Colvars/colvars/pull/332
Implement reflecting b.c. for ext Lagrangian (@jhenin)
https://github.com/Colvars/colvars/pull/329
2020-09-09 18:19:21 -04:00
ed14793c69
moved eigensolver documentation into pg_dev_utils.rst
2020-09-09 14:59:00 -07:00
3bacf97468
Merge branch 'master' into math_eigen
2020-09-09 14:56:28 -07:00
2ab0878c9e
remreduced compile time by removing unnecessary instantiations from math_eigen.cpp
2020-09-09 14:43:28 -07:00
cdd9d693ad
Merge pull request #2349 from akohlmey/more-progguide-updates
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More Programmer docs updates and related code refactoring
2020-09-09 14:34:41 -04:00
e238201be5
add a couple more versionadded directives
2020-09-09 13:21:19 -04:00
790b2693ba
Merge pull request #2353 from junghans/cmake_clean_up
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cmake: consistent usage of find variable
2020-09-09 11:04:13 -04:00
a51bebc9e4
Merge pull request #2340 from rbberger/container_update
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Singularity Container definitions update
2020-09-09 09:53:48 -04:00
f4c4c62349
adjust test to updated API
2020-09-09 09:27:34 -04:00
03d43bda3c
make "New in" and "Changed in" statements boldface to stand out more
2020-09-09 09:25:58 -04:00
2b854ec64f
reformulate
2020-09-09 09:25:34 -04:00
a1cf6c087c
no need to use a deprecated argument in a newly added API
2020-09-09 09:06:28 -04:00
2a42fe66ad
discuss change to get LAMMPS handle as return value instead of argument
2020-09-09 09:06:00 -04:00
56b1300fd3
reverted the default behavior of "jacobi3()". By default it now sorts the eigenvalues again.
2020-09-08 21:58:54 -07:00
dad749b62b
make vget()/vgot() inline functions again for optimal performance.
2020-09-08 20:52:51 -04:00
6ade5dd740
changed the default sorting options in "jacobi3()" to be more similar to the original "jacobi()" function from "math_extra.h". This should not have any effect on LAMMPS behavior
2020-09-08 17:05:08 -07:00
c818a00523
remove unwanted docs
2020-09-08 16:53:26 -04:00
ea0a9f00e8
swap order of classes in toctree
2020-09-08 16:45:16 -04:00
ca1b5ed936
fix minor issues
2020-09-08 16:43:10 -04:00
daf8a2313a
split developer guide into multiple files
2020-09-08 16:38:06 -04:00
ee25ed3897
update/correct documentation for memory pool classes
2020-09-08 16:36:48 -04:00
9f4a991fc5
move over doxygen comments for a few LAMMPS classes
2020-09-08 16:36:29 -04:00
1273179d03
Fix compile error
2020-09-08 13:42:25 -06:00
9e47452382
recover compilation for platforms using malloc() instead of posix_memalign()
2020-09-08 15:36:21 -04:00
7a9d31328e
remove obsolete comment
2020-09-08 15:29:42 -04:00
4f8e627479
QEq refactor
2020-09-08 13:16:45 -06:00
9f7e309f07
small updates to MyPage and convert MyPoolChunk similar to MyPage
2020-09-08 15:13:16 -04:00
a3cc7581b1
rename test for memory pools
2020-09-08 15:12:08 -04:00
f72e5b6d13
Typo
2020-09-08 12:52:32 -06:00
b008ba5ecb
Merge remote-tracking branch 'origin/master' into cmake_clean_up
2020-09-08 12:51:49 -06:00
9f8b8529b1
Merge pull request #2348 from akohlmey/use-tabs-with-html
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Enable sphinx-tabs extension with the html version of the documentation
2020-09-08 12:02:43 -04:00
22fac9affc
more doc update
2020-09-08 09:49:07 -06:00
8fb13f4fd1
cmake: make doc more consistent
2020-09-08 09:43:21 -06:00
5df3deb8e6
update/refactor a few more build documentation files for using tabs
2020-09-08 11:40:21 -04:00
09b8b117fc
cmake: consistent usage of find variable
2020-09-08 09:35:45 -06:00
88cc673f78
more use of tabs in Build_extras.rst
2020-09-08 10:11:37 -04:00
dd20776915
fix spelling issues
2020-09-07 21:17:56 -04:00
9b01d5bf95
revise and add tabs to some sections
2020-09-07 21:08:47 -04:00
9afba50d01
update for zstd support
2020-09-07 21:00:45 -04:00
f02db43f63
add discussion and minimal code example for MyPage class.
2020-09-07 16:10:48 -04:00
0ee7c5f434
add more MyPage test variants
2020-09-07 15:27:13 -04:00
ab5c81f7d6
refactor some more to reduce redundant code.
2020-09-07 08:57:37 -04:00
bbb81a8dd0
add unit tester for MyPage class
2020-09-07 08:33:05 -04:00
3089205a54
tweak MyPage docs
2020-09-07 08:32:34 -04:00
0447616aaf
address spelling issues
2020-09-07 08:03:41 -04:00
f8ebcc90fb
define OneCoeff struct in my_page.h as HyperOneCoeff to resolve compilation issues
2020-09-07 07:57:23 -04:00
f329d56495
updated pg_developer.rst
2020-09-06 20:12:38 -07:00
a57a1404f3
bug fix fix unit tests, improve doc readability, and to prevent accidentally allocating memory on the heap. (Note: All of these changes are related to "jacobi3()". That function instantiates Jacobi without allocating memory on the heap, and this created some headaches. The original code at https://github/jewettaij/jacobi_pd does not have this feature, and the unit tests there do not test for these kinds of errors. Hopefully this commit fixes everything.)
2020-09-06 20:05:47 -07:00
2270d86519
whitespace cleanup and try to recover legacy build
2020-09-06 22:51:58 -04:00
4ca36d9526
add doxygen docs and convert MyPage template class from header only to header plus implementation
2020-09-06 22:26:17 -04:00
485a169ef2
move merge sort to utils namespace
2020-09-06 17:38:53 -04:00
19ce59ba38
use tabs for CMake vs. GNU make in LAMMPS library linking page
2020-09-06 16:50:28 -04:00
d77f08d5fb
tweak formatting to look better in the PDF file
2020-09-06 16:49:58 -04:00
fabf762fa8
reverting to previous version of util.h and util.cpp
2020-09-06 11:09:36 -07:00
eb6f7f9740
Merge branch 'master' into math_eigen
2020-09-06 10:59:20 -07:00
d97e8d8cbf
fixed linker problems in "utils.h" and "utils.cpp"
2020-09-06 10:12:07 -07:00
b29522273a
changed the "trim_and_count_words()" function declaration in "utils.h" to make sphinx happy. Fixed some new spelling mistakes.
2020-09-06 09:40:28 -07:00
9f24f056ff
reformat system sizes information and make explanations more concise
2020-09-06 07:12:43 -04:00
77e22c90ac
complete using tab/tabs directives in Build_settings
2020-09-06 06:11:12 -04:00
5536c1e6ee
make more compact
2020-09-06 06:10:39 -04:00
2ee2009356
removed assert() statements from "superpose3d.h"
2020-09-06 02:30:20 -07:00
c16321e9d3
purged greek characters from "pd_developer.rst"
...
I replaced the 'Σ' character that was causing problems with PDF generation with the word "sum". Hopefully PDF documentation generation works now.
2020-09-05 21:44:32 -07:00
77789f9ed8
small tweaks
2020-09-06 00:07:53 -04:00
7b6d07a812
load sphinx extension for content in tabs with html and for transforming them to admonitions for non-html builders
2020-09-05 23:54:10 -04:00
4ad6d99ca0
updated documentation files: "pg_developer.rst", "math_eigen.h", and "false_positives.txt"
2020-09-05 20:08:45 -07:00
7cb774e6bc
some corrections before rewriting the doxygen comments to comply with LAMMPS doxygen style.
2020-09-05 16:37:15 -07:00
4b66414bdf
fixed a type error in math_eigen.h
2020-09-05 10:38:14 -07:00
58fa72ddc5
replaced all numerical recipes jacobi() code with code from "math_eigen.h". moved "math_eigen.h" into the main "src" directory.
2020-09-05 10:19:19 -07:00
57f82abae3
updated all code in LAMMPS to use the open-source "math_eigen.h" instead of "math_extra.h". Code in "lib" now uses its own abbreviated local version of the "math_eigen.h" file (which is named "jacobi_pd.h"), since it is not clear how code from "lib/" can access the code in "src/"
2020-09-05 01:39:27 -07:00
d995ed0d87
Merge pull request #2344 from akohlmey/use-improved-sphinx-fortran
...
Use modernized version of sphinx-fortran
2020-09-04 18:46:34 -04:00
75a119d534
divert installation of sphinx-fortran to github branch with parallel read capable version
2020-09-04 17:40:26 -04:00
64728678f1
Merge branch 'python_interface_guide' of github.com:rbberger/lammps into python_interface_guide
2020-09-04 17:15:58 -04:00
96db122377
Add Python coverage collection if enabled
2020-09-04 17:15:51 -04:00
176f7c064d
Merge branch 'master' into python_interface_guide
2020-09-04 15:51:56 -04:00
e6592d2324
Merge pull request #2336 from akohlmey/collected-small-changes
...
Collected small changes for the next patch release
2020-09-04 15:22:31 -04:00
6a40eba2ae
Add Ubuntu 20.04 Intel OpenCL container
2020-09-04 15:03:53 -04:00
da0e60c173
Apply changes to remaining containers
2020-09-04 14:43:03 -04:00
f6abdf97c4
Remove -j in distribution container files
2020-09-04 14:28:03 -04:00
41a1c96e06
Update other GPU containers
2020-09-04 14:19:41 -04:00
3bdfbdcf09
Update Ubuntu 18.04 GPU container and add Ubuntu 20.04
2020-09-04 14:06:38 -04:00
ceed9284c1
Merge branch 'master' into collected-small-changes
2020-09-04 13:32:47 -04:00
de777ce994
Merge pull request #2341 from akohlmey/doc-updates
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Revised links and related descriptions in the manual
2020-09-04 13:29:58 -04:00
41a3e7c712
update a few links in the programmer guide
2020-09-04 11:59:04 -04:00
60d25c2eea
Update Ubuntu 20.04 container
2020-09-04 11:54:08 -04:00
5c22d1197e
Merge branch 'master' into doc-updates
2020-09-04 11:50:28 -04:00
d0d3cee28d
a few more cosmetic changes
2020-09-04 11:50:02 -04:00
598819229b
Fix missing OpenKIM models for testing due to KIM-API packaging
2020-09-04 11:47:38 -04:00
64d3be27a6
Add zstd to containers
2020-09-04 11:46:40 -04:00
90c13b1b14
update build files for plumed 2.6.1 release
2020-09-04 11:44:39 -04:00
7ea4177626
Set Plumed version to 2.6.1
2020-09-04 11:41:44 -04:00
2b1e4749dd
first chunk of revised updates to the manual addressing link issues.
2020-09-04 11:39:38 -04:00
c8327e66b3
Merge pull request #2338 from akohlmey/include-cleanup
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Update list of included headers for latest updates of the convention
2020-09-04 10:14:12 -04:00
f19ce32bf5
a few more small tweaks
2020-09-04 09:42:11 -04:00
255bf2f8fd
update iwyu custom mapping file
2020-09-04 09:41:57 -04:00
f541647d44
some more IWYU tweaks
2020-09-04 09:23:20 -04:00
d6ba95bed6
minor tweaks
2020-09-04 08:05:59 -04:00
2d802411e9
remove pointless stringstream abuse
2020-09-04 08:03:53 -04:00
91a87b745f
final second round IWYU cleanup
2020-09-04 08:01:11 -04:00
63e5ca53ef
add iwyu mappings for gtest and gmock
2020-09-04 08:00:38 -04:00
bb7447363c
more include cleanup and IWYU tweaks
2020-09-04 07:22:39 -04:00
7f6fc8a003
updated math_eigen.h and moved it into the main "src" directory
2020-09-04 04:10:47 -07:00
fc3d9fee5e
more USER-OMP updates
2020-09-04 01:32:52 -04:00
d0691d0a5d
add mapping for Eigen3 includes
2020-09-04 01:32:15 -04:00
2e0af2fdce
some more second pass cleanup
2020-09-04 00:46:23 -04:00
508b49c976
add missing comma
2020-09-04 00:45:41 -04:00
87dfdb8723
add comments/warnings to docs of fix property/atom and fix store/state about restarting
2020-09-04 00:14:01 -04:00
cb618e19d1
small tweak to address formal issues
2020-09-03 18:30:35 -04:00
18cea11100
Merge pull request #66 from junghans/include-cleanup
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cmake: use static iwyu-extra-map.imp
2020-09-03 18:27:00 -04:00
5a7189e95f
update note for write_data command on missing coefficient data.
2020-09-03 18:24:12 -04:00
ce78be864a
move date2num() convernience function from Universe class to utils namespace
2020-09-03 17:47:45 -04:00
390c6ba106
rechecking some corefiles with IWYU after the many updates
2020-09-03 15:28:07 -04:00
93d0358ebc
cmake: use static iwyu-extra-map.imp
2020-09-03 11:36:02 -06:00
05c7cfe59f
more include updates for USER-OMP
2020-09-03 11:16:32 -04:00
f67bd8eb5d
more KOKKOS, USER-OMP, and USER-INTEL include file cleanup
2020-09-03 10:54:06 -04:00
27203304d6
USER-INTEL include handling cleanup
2020-09-03 09:47:48 -04:00
88ddfa4eb0
more IWYU cleanup in packages
2020-09-03 05:20:02 -04:00
55704368d0
include updates for commonly used packages
2020-09-03 01:45:05 -04:00
c7c4297cfc
update include handling for commands
2020-09-03 00:51:58 -04:00
c2cf19bdd4
fixes for file readers
2020-09-03 00:32:57 -04:00
baa79bd1c4
add another iwyu-mapping entry
2020-09-03 00:22:28 -04:00
9925122cea
more IWYU updates
2020-09-03 00:22:09 -04:00
a4a1f7e848
more IWYU cleanup
2020-09-02 23:49:17 -04:00
047c14d17c
tweak iwyu target. generate file with custom mappings
2020-09-02 23:41:16 -04:00
45f80f4f06
more include file updates found by iwyu
2020-09-02 22:52:22 -04:00
7b8fe97a88
remove trailing whitespace
2020-09-02 22:51:42 -04:00
71d111ccd9
get rid of 'using namespace std;'
2020-09-02 22:51:30 -04:00
203e42073a
fix compilation error
2020-09-02 22:51:14 -04:00
f88f4cd60e
more include file updates
2020-09-02 21:44:04 -04:00
4ba6a4f958
have clang-style output for easier parsing in compilation mode in emacs
2020-09-02 21:43:20 -04:00
79584c842d
add false positive
2020-09-02 18:44:12 -04:00
b741a07a34
document IWYU analysis custom build target
2020-09-02 18:43:03 -04:00
5e429b8212
update include conventions and refer to the new CMake build target
2020-09-02 18:42:41 -04:00
4a10111ced
add iwyu target to CMake configuration
2020-09-02 18:42:19 -04:00
d5027c125c
rename fmt() macro to logfmt() to avoid clashes with fmtlib
2020-09-02 17:58:22 -04:00
1421817276
remove redundant includes
2020-09-02 17:54:29 -04:00
6113169a47
IWYU based include statement cleanup
2020-09-02 17:39:34 -04:00
a38873f3f6
Add venv example to pg_python.rst
2020-09-02 17:34:14 -04:00
2cd0e9edc4
Merge pull request #2335 from rbberger/doc_updates
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Update documentation pages headings and update style check tool to detect missing index entries.
2020-09-02 15:46:10 -04:00
a72ebb2ab2
update link and formatting of install via git page in manual.
2020-09-02 15:41:17 -04:00
862bc99772
add links to references of the two parts of the manual
2020-09-02 15:28:27 -04:00
8def5844c8
Skip old styles in check-styles
2020-09-02 14:06:35 -04:00
ac7129b3a9
Revert "Add missing index entries"
...
These are intentionally left out from docs
2020-09-02 14:02:53 -04:00
0f9c46235c
Add missing index entries
2020-09-02 13:56:17 -04:00
515746063f
Fix copy&paste error
2020-09-02 13:55:27 -04:00
e519919cae
Fix typo
2020-09-02 13:48:11 -04:00
28c90a6dea
Update index for kspace_style commands
2020-09-02 13:40:24 -04:00
12aa689e97
fix typo in cfg/zstd tester tool
2020-09-02 13:38:18 -04:00
c812bf7a91
Update headers in improper_*.rst files
2020-09-02 13:03:03 -04:00
a0c9c213fd
Update headers in dihedral_*.rst files
2020-09-02 12:57:44 -04:00
d01c985feb
Update headers in compute_*.rst files
2020-09-02 12:56:24 -04:00
f4d2523ce0
Update headers in bond_*.rst files
2020-09-02 12:55:18 -04:00
4e27c47f96
Undo lost headers
2020-09-02 12:54:08 -04:00
88e09fe648
Update headers in angle_*.rst files
2020-09-02 12:43:48 -04:00
286d3866e3
Add style index check in check-styles.py
2020-09-02 12:42:18 -04:00
549bdd080c
Add kspace_style to fixup_headers.py
2020-09-02 12:37:48 -04:00
84e922eff6
Add other styles to fixup_header.py
2020-09-02 11:55:53 -04:00
8468f4ab2e
fix missing comparison and thus reduce memory use in serial case
2020-09-02 11:12:15 -04:00
a4380a548d
make more readable
2020-09-02 11:11:48 -04:00
0c88074525
Apply header fix to all remaining fix styles docs
2020-09-02 11:05:33 -04:00
98808fb5ff
Skip doc files that don't have common file structure
2020-09-02 11:04:08 -04:00
8d1a117b75
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
09bc686f71
Avoid extra newline
2020-09-02 10:55:04 -04:00
cc594c0613
include fmt/format.h into pointers.h
2020-09-02 10:52:10 -04:00
e5e2abe446
update include file policy file and policy for pointers.h special case
2020-09-02 10:51:55 -04:00
e479033109
Avoid breaking already fixed headers
2020-09-02 10:51:47 -04:00
3c60a9e08e
Update fix_nh.rst
2020-09-02 10:31:21 -04:00
49a6bf5e30
Update pair_class2.rst
2020-09-02 10:30:31 -04:00
3a22f26e87
Update pair_cs.rst
2020-09-02 10:29:46 -04:00
4d6be195ec
Add utility to fixup doc headers
2020-09-02 10:29:29 -04:00
e5f1f58aab
Update pair_born.rst
2020-09-02 10:26:37 -04:00
a6a49d80b2
Update pair_sdk.rst
2020-09-02 10:19:20 -04:00
7ae98ffae1
Update fix_rigid.rst
2020-09-02 09:50:16 -04:00
dce7a39021
Update pair_buck.rst
2020-09-02 09:47:32 -04:00
77f803b366
Update pair_charmm.rst
2020-09-02 09:14:20 -04:00
a9cf25db4c
Update pair_eam.rst
2020-09-02 09:13:59 -04:00
7e733913d7
Update pair_fep_soft.rst
2020-09-02 09:03:00 -04:00
45100528ad
Update pair_coul.rst
2020-09-02 08:54:53 -04:00
c50a82af78
apply consistent naming scheme for tester source files and executables
2020-09-01 20:16:39 -04:00
2ffb5ddd5a
add kspace dependency to coul/streitz/long test
2020-09-01 17:34:08 -04:00
80519cd109
Merge pull request #2331 from rbberger/zstd_support
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Update COMPRESS package
2020-09-01 15:01:04 -04:00
e7dcb79ac5
Merge pull request #1472 from tomswinburne/master
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Add fix pafi
2020-09-01 14:36:46 -04:00
35cb41147a
update date
2020-09-01 14:16:06 -04:00
60b98f6b91
Require libzstd>=1.4 for Zstd dump styles
2020-09-01 13:52:56 -04:00
45c9478f5a
Merge pull request #2333 from akohlmey/iss1109
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Fix memory leaks and out-of-range memory access in USER-BOCS package
2020-09-01 13:37:56 -04:00
31bd76efa5
Merge remote-tracking branch 'origin/master' into zstd_support
2020-09-01 12:58:41 -04:00
40ea03234f
Update force->inumeric to utils::inumeric
2020-09-01 12:58:27 -04:00
9d3e3526a0
Add false positives and fix spelling in docs
2020-09-01 12:30:35 -04:00
f899a0f484
Reorder init to supress warnings
2020-09-01 12:25:38 -04:00
a2b5c379f2
Update docs for COMPRESS styles
2020-09-01 12:17:08 -04:00
3db1a6d690
Use PkgConfig to find Zstd
2020-09-01 11:14:36 -04:00
ae3a7d8901
minor changes to example
2020-09-01 17:02:24 +02:00
8e0c4d764e
Change include for fmt
2020-09-01 10:58:13 -04:00
75b3bbd657
modernize
2020-09-01 10:09:34 -04:00
95aab99c2a
remove redundant entries
2020-09-01 09:57:44 -04:00
2802db4493
correct application of the BEGIN_CAPTURE macro
2020-09-01 09:41:26 -04:00
3b765956d2
Manually resolve merge conflict
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Merge branch 'iss1109' of https://github.com/eagunn/lammps into iss1109
2020-09-01 06:31:35 -06:00
4f03acc560
Fix merge conflicts caused by code's do-si-do around Axel's additions
...
to the utils namespace.
2020-09-01 06:30:12 -06:00
2536f28e1a
Per comments from Axel, continued the evolution of the output messages.
...
- Converted Compute message with imputed value to fmt::format style.
- Condensed most error-> output messages to oneliners where fmt::format
is called within the call to the error method. For a couple, the
formatting string/value list were complex enough that I continued using
a temporary string variable to make the code easier to read.
2020-09-01 05:49:29 -06:00
52748f57da
Delete extraneous, unused file/folder that should never have gotten
...
into the repo.
2020-09-01 05:49:29 -06:00
9ef725ea52
Move destruction of splines data structure to FixBocs destructor
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from ComputePressure destructor.
2020-09-01 05:49:29 -06:00
e11a3c4799
Remove "test" example files.
2020-09-01 05:49:29 -06:00
4dca927693
Switch dynamically created arrays/matrices to use memory->create and
...
->destroy, LAMMPS-standard for dynamic memory management.
2020-09-01 05:49:29 -06:00
fe89edc828
Remove c_str() calls from message strings. Message class now accepts
...
actual strings.
2020-09-01 05:49:29 -06:00
0aa66319fe
Change the build_xxx_splines methods to accept a const reference parameter
...
to the data vector rather than a vector parameter. Vectors are, as all
types are, passed by value in C++. Using a vector directly as a parameter
causes the data to be copied. Using a reference to the vector neatly
avoids that problem.
Also tucked fmt/format.h into its rightful place in the include list
since Axel says there's no absolute rule about it being an exception.
2020-09-01 05:49:29 -06:00
076c834734
Manually reconciled conflict from:
...
Corrected two issues in code identified by valgrind:
1) memory leaks (the subject of the original #1109 ) and
2) an invalid memory access (reading from beyond the end of an array).
Also:
- replaced several dynamically-allocated (calloc and free) local arrays with std::vector.
- reorganized include statements per new conventions, and
- updated messages to use strings and fmt.
Added folders and files used in manual testing and verification to examples folder.
No changes in analysis results are expected or intended. This is pure refactoring except for a bit of error message cleanup.
2020-09-01 05:48:49 -06:00
aa12f4f78a
Per request from Axel, Revert revert one commit too far:
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"Per suggestion from Axel, reformat code to what I believe to be"
This reverts commit b72c1c0eda
2020-09-01 05:10:44 -06:00
fbffcf3321
spelling
2020-09-01 11:34:11 +02:00
c18eccad39
force -> utils::
2020-09-01 11:25:25 +02:00
2f182b4606
force-> -> utils::
2020-09-01 11:24:06 +02:00
c6de769696
Merge branch 'master' of github.com:tomswinburne/lammps
2020-09-01 11:12:29 +02:00
ac080228dc
whitespace style fix
2020-09-01 11:12:05 +02:00
0541996919
Merge branch 'master' into master
2020-09-01 10:59:03 +02:00
d601acd0ca
merge
2020-09-01 10:57:43 +02:00
2eb6a8a8a4
update python interface
2020-09-01 10:55:45 +02:00
db9de111be
updated python interface
2020-09-01 10:54:18 +02:00
fe833e6c87
Add missing #ifdef
2020-08-31 19:49:17 -04:00
0925fc822d
Make Zstd support optional
2020-08-31 18:21:58 -04:00
3865de8705
Add lost line
2020-08-31 16:43:06 -04:00
2effd2f707
Merge remote-tracking branch 'origin/master' into zstd_support
2020-08-31 15:38:56 -04:00
c5a2e50bf5
Add Zstd variants of dump local and xyz
2020-08-31 15:38:20 -04:00
a0f82a4b18
Add compression_level parameter to dump xyz/gz and local/gz
2020-08-31 15:00:57 -04:00
443a817152
Add tests for dump local/gz and xyz/gz
2020-08-31 14:54:10 -04:00
24f5807623
Merge pull request #2319 from akohlmey/move-convenience-functions
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Move some more convenience functions to utils namespace
2020-08-31 14:29:42 -04:00
99b83333c9
Add dump cfg/zstd
2020-08-31 14:20:52 -04:00
a922355e19
Add compression_level parameter to dump cfg/gz
2020-08-31 14:20:36 -04:00
54ed23448b
instantiate bounds() also with long long to make windows happy.
2020-08-31 14:14:51 -04:00
5faca3aef0
Add tests for dump cfg/gz
2020-08-31 13:36:42 -04:00
675cf20e93
Merge remote-tracking branch 'github/master' into move-convenience-functions
2020-08-31 12:58:21 -04:00
22ccde1d13
modernize utils::bounds() implementation and remove duplicate definition.
2020-08-31 12:58:00 -04:00
9a4ec23c7f
Merge pull request #2327 from akohlmey/remove-doxygen-tool
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Remove doxygen tool folder and references to it in the manual
2020-08-31 12:49:24 -04:00
7fca3b7a65
revert accidental change
2020-08-31 12:46:22 -04:00
1ff34d4b13
avoid doxygen lookup ambiguity
2020-08-31 12:46:05 -04:00
67a5db03c7
Merge pull request #2326 from ndtrung81/gpu-update-makefiles
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update makefiles in lib/gpu for more recent architectures
2020-08-31 12:30:28 -04:00
0c7b9a7c63
update utils tester for API change in bound()/boundsbig()
2020-08-31 11:43:25 -04:00
dd03c7232a
Merge remote-tracking branch 'github/master' into move-convenience-functions
2020-08-31 11:41:18 -04:00
a4d3b21a43
Merge pull request #2322 from Vsevak/cmake_cuda
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Fix CMake building for CUDA 11
2020-08-31 11:33:52 -04:00
cf11945e21
get rid of utils::boundsbig() by making it a template function with two specializations
2020-08-31 11:25:43 -04:00
8034a83ee8
Merge pull request #2325 from akohlmey/fortran-interface
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New Fortran interface to LAMMPS
2020-08-31 10:27:10 -04:00
3c71d300e5
Merge pull request #2320 from akohlmey/programmer-guide
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Add programmer guide part 2
2020-08-31 10:06:04 -04:00
b72c1c0eda
Per suggestion from Axel, reformat code to what I believe to be
...
LAMMPS standards. I used the .clang-format file from the unit-test
folder but changed all spacing settings to 2 from 4.
2020-08-31 06:31:48 -06:00
0c067700e6
Per comments from Axel, continued the evolution of the output messages.
...
- Converted Compute message with imputed value to fmt::format style.
- Condensed most error-> output messages to oneliners where fmt::format
is called within the call to the error method. For a couple, the
formatting string/value list were complex enough that I continued using
a temporary string variable to make the code easier to read.
2020-08-31 06:31:48 -06:00
f0b304efcb
Delete extraneous, unused file/folder that should never have gotten
...
into the repo.
2020-08-31 06:31:48 -06:00
69b42ea9ae
Move destruction of splines data structure to FixBocs destructor
...
from ComputePressure destructor.
2020-08-31 06:31:48 -06:00
a4790fdf00
Remove "test" example files.
2020-08-31 06:31:47 -06:00
c75c3451f6
Switch dynamically created arrays/matrices to use memory->create and
...
->destroy, LAMMPS-standard for dynamic memory management.
2020-08-31 06:31:47 -06:00
e8306a2535
Remove c_str() calls from message strings. Message class now accepts
...
actual strings.
2020-08-31 06:31:47 -06:00
3760ccd672
Change the build_xxx_splines methods to accept a const reference parameter
...
to the data vector rather than a vector parameter. Vectors are, as all
types are, passed by value in C++. Using a vector directly as a parameter
causes the data to be copied. Using a reference to the vector neatly
avoids that problem.
Also tucked fmt/format.h into its rightful place in the include list
since Axel says there's no absolute rule about it being an exception.
2020-08-31 06:31:47 -06:00
b241294e84
Corrected two issues in code identified by valgrind:
...
1) memory leaks (the subject of the original #1109 ) and
2) an invalid memory access (reading from beyond the end of an array).
Also:
- replaced several dynamically-allocated (calloc and free) local arrays with std::vector.
- reorganized include statements per new conventions, and
- updated messages to use strings and fmt.
Added folders and files used in manual testing and verification to examples folder.
No changes in analysis results are expected or intended. This is pure refactoring except for a bit of error message cleanup.
2020-08-31 06:31:47 -06:00
c7360fb808
include example use of PotentialFileReader class
2020-08-31 07:45:52 -04:00
c84033677c
add documentation for potential file reader
2020-08-31 07:31:28 -04:00
33f2cbc713
add docs for TextFileReader class to developer guide
2020-08-31 06:57:16 -04:00
39a9974f3d
add ValueTokenizer example and use captions with code-blocks
2020-08-30 23:57:02 -04:00
569b6f95a3
no need to use ValueTokenizer. Make code more compact.
2020-08-30 23:32:17 -04:00
e8e57b0628
remove doxygen tool folder and references to it in the input as it is no longer compatible and needed
2020-08-30 19:59:52 -04:00
ecb1f266b5
More updates
2020-08-30 15:10:29 -05:00
7a5f193c02
Updated several Makefile's in lib/gpu for newer compute capabilities
2020-08-30 15:06:44 -05:00
4484699ab6
fix spelling
2020-08-30 15:52:42 -04:00
65d2ee7464
add work-in-progress marker to fortran library wrapper
2020-08-30 15:23:02 -04:00
199cfeba78
more tweaks. doxygen translation has no more warnings now.
2020-08-30 14:32:53 -04:00
cd0cdf0b74
silence compiler warning
2020-08-30 14:28:29 -04:00
f3ed1dea4d
minor tweaks
2020-08-30 14:28:19 -04:00
8d45b724a6
fix bug in conventional build makefile preventing the correct Install.py in the lib folder to be run
2020-08-30 14:12:53 -04:00
4b0999e167
complete documentation of tokenizer classes
2020-08-30 14:12:21 -04:00
5623009962
arch 3.0 is dropped in CUDA 11
2020-08-30 13:12:42 +03:00
96ee132e85
start documenting tokenizer classes
2020-08-30 01:50:37 -04:00
8d2c16ad66
remove trailing whitespace
2020-08-30 00:31:04 -04:00
f123246189
minor doc updates
2020-08-30 00:25:01 -04:00
ceeaf1e988
update and correct documentation for utils functions
2020-08-29 23:51:46 -04:00
9c404e02fd
update include file conventions
2020-08-29 22:56:37 -04:00
83a9e5e724
handle spelling issues with new doc text
2020-08-29 22:55:05 -04:00
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
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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
2f629db3d4
Refactor Zstd dump styles
2020-08-27 13:43:36 -04:00
5c0edeb679
namespace clarify
2020-08-27 12:43:28 -04:00
977a89e537
add separators
2020-08-27 12:33:03 -04:00
794e74e064
return of the lost enum
2020-08-27 12:22:48 -04:00
91554d6287
move RMSD files to new reaction package
2020-08-27 12:13:07 -04:00
ce2b128cf9
Merge branch 'lammps-master' into bond/react-RMSD_constraint
2020-08-27 12:04:09 -04:00
583a09c808
Merge branch 'master' of https://github.com/lammps/lammps into lammps-master
2020-08-27 12:02:08 -04:00
bc49e854ba
bond/react RMSD constraint: manual rebase
2020-08-27 11:53:19 -04:00
e4e15157f8
Fixed bugs in the GPU kernels of pair styles beck/gpu and gauss/gpu involving factor_lj
2020-08-26 23:41:00 -05:00
f314b7e54f
update format from enumerate to itemize and start next subsection
2020-08-26 23:05:59 -04:00
6a68743e54
transfer a chunk of text from Developer.tex to the manual.
2020-08-26 22:46:55 -04:00
ced78a72eb
Add dump custom/zstd and tests
2020-08-26 19:59:28 -04:00
e9fd8b3ec6
Migrate changes to dump custom/gz and add tests
2020-08-26 19:44:55 -04:00
096cef40a8
remove redundant use of \brief
2020-08-26 19:44:23 -04:00
55829752c9
Merge branch 'master' into library-refactor
2020-08-26 19:08:09 -04:00
2f1086dfe4
Merge branch 'python-refactor' into library-refactor
2020-08-26 19:07:44 -04:00
85764b3774
replace a few more c++-style comments with old-fashion c-style comments
2020-08-26 19:07:29 -04:00
1ad82d7cdb
add separator comment lines
2020-08-26 19:07:08 -04:00
dbf51af7d1
Fixes segfault due to uninitialized pointers
2020-08-26 18:41:32 -04:00
78a1b92503
Add dump atom zstd tests
2020-08-26 16:35:35 -04:00
007a43a5b2
Add more atom/gz tests
2020-08-26 16:20:02 -04:00
32aa35009b
Start tests for compressed dump styles
2020-08-26 16:04:19 -04:00
046fd3d14b
Verify valid compression level ranges
2020-08-26 16:03:18 -04:00
d00807ee9a
Merge pull request #2311 from stanmoore1/kk_update_3.2
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Update Kokkos library in LAMMPS to v3.2
2020-08-26 15:35:25 -04:00
aeb3e20385
Merge pull request #2307 from Vsevak/zbl_reduce_declaration
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Fix NaN in GPU-accelerated Tersoff styles with OpenCL backend
2020-08-26 13:56:49 -04:00
629ead6348
Merge pull request #2309 from lammps/doxygen-integration
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Add doxygen and graphviz processing into the documentation build
2020-08-26 13:05:00 -04:00
50b8b1bf60
Fix Kokkos HIP compile error
2020-08-26 11:45:24 -05:00
94db627ba5
fix formatting issue
2020-08-26 12:09:43 -04:00
b4403de026
add false positive
2020-08-26 12:09:35 -04:00
d40b658644
cmake: update kokkos version/checksum
2020-08-26 10:05:14 -06:00
8137ada848
Merge branch 'collected-small-changes' into doxygen-integration
2020-08-26 11:51:45 -04:00
bdc952ac88
Merge branch 'master' into collected-small-changes
2020-08-26 11:51:05 -04:00
f89a0f9fe3
must not try to delete computes if they have not been created and their ids not yet set
2020-08-26 11:50:20 -04:00
c8af729701
Merge branch 'master' into collected-small-changes
2020-08-26 11:49:29 -04:00
4ad68c98a0
Merge pull request #2196 from jibril-b-coulibaly/mindlin_rescale
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Implement force history in Mindlin granular pair styles
2020-08-26 11:42:06 -04:00
e2fd95d8ed
Merge pull request #2240 from jrgissing/bond/react-reset_mol_ids
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support molecule ID resets in fix bond/react
2020-08-26 10:56:21 -04:00
ed63edc9da
lammps_has_error() and lammps_get_last_error_message() are always available but dummies without exceptions enabled
2020-08-26 09:10:59 -04:00
48d2a48a1f
import updated python module from progguide branch
2020-08-26 09:01:59 -04:00
7ab6def2ca
update list of Kokkos GPU archs in manual as well
2020-08-26 03:49:59 -04:00
abbbb0ab06
remove trailing whitespace
2020-08-26 03:42:50 -04:00
aa6dec84ed
update list of Kokkos supported architectures
2020-08-26 03:42:42 -04:00
e0439ac94f
Add compression_level parameter to dump atom gz
2020-08-26 00:14:32 -04:00
5cb8e73655
Add checksum and compression_level as dump atom/zstd options
2020-08-25 23:59:17 -04:00
0d8454ac25
First version of Zstd dump atom
2020-08-25 23:27:42 -04:00
b8f59fd37c
Update from master
2020-08-25 20:29:03 -06:00
4d90c2b74b
Update Kokkos library in LAMMPS to v3.2
2020-08-25 20:21:48 -06:00
1c10aa6a4d
GIFs are only supported in HTML
2020-08-25 17:15:34 -04:00
c256f2331f
JPG folder is no longer needed in HTML output
2020-08-25 16:59:39 -04:00
ae5c0bd8d1
Remove targets to JPG images
2020-08-25 16:44:50 -04:00
3a638440a4
Add missing PDF folder
2020-08-25 16:12:09 -04:00
80e07c69f0
add part of developer guide as to showcase the integration of the programmer guide
2020-08-25 15:07:09 -04:00
df8fb26272
Refactor changes to documentation build
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- Added CMake variables for readability
- Moved Mathjax files to _static to avoid special copy logic
- Moved JPG/lammps-logo.png to _static to avoid special copy logic
- Removed dead CMake code
2020-08-25 13:41:31 -04:00
14b66d1f84
tweak test tolerance of reax/c tests for running on ubuntu 18.04
2020-08-25 12:15:19 -04:00
f965786e74
refactor C library interface and add doxygen decorations
2020-08-25 11:45:07 -04:00
69cffb2d04
import test infrastructure for c, c++ and python library usage
2020-08-25 11:03:31 -04:00
024e4c5f21
make formatting and doxygen decorations for utils functions consistent
2020-08-24 20:55:13 -04:00
3f685c346f
add doxygen integration with conventional and cmake doc build
2020-08-24 17:58:37 -04:00
dc241abb85
Merge pull request #2305 from akohlmey/next_patch_version
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Update version strings for updated patch release
2020-08-24 13:46:50 -04:00
8cbc3e421f
clean up
2020-08-24 17:49:38 +02:00
93e4ed9770
Merge pull request #2304 from akohlmey/collected-small-changes
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Collected small changes for the next patch release
2020-08-24 11:43:42 -04:00
090ef2d1e8
merge error fix
2020-08-24 17:10:33 +02:00
9bdb7b5b98
gatherscatter
2020-08-24 17:09:16 +02:00
28d59ce594
final steps
2020-08-24 17:04:35 +02:00
2ee6e9077a
Merge remote-tracking branch 'upstream/master' into 2020
2020-08-24 17:02:53 +02:00
e8fb7c7ece
big update
2020-08-24 16:54:16 +02:00
7e1a3bd4d5
Merge pull request #2302 from akohlmey/consistent-doc-headers
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Consistent subsection headers for commands
2020-08-24 10:52:09 -04:00
47a44732e7
add test for fix restrain
2020-08-23 15:29:58 -04:00
8f5e8300ea
fix typos in fix restrain docs
2020-08-23 15:29:49 -04:00
0842911cd8
Rename local buffers 'red_acc' in lal_tersoff*
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Rename __local red_acc in lal_tersoff
2020-08-23 22:22:28 +03:00
10080079e3
ISO compliance
2020-08-23 11:44:48 -04:00
63abb2dff9
fix broken reset_mol_ids command
2020-08-23 11:32:54 -04:00
01dd80f35e
bond/react: actually make reset_mol_ids the default
2020-08-23 11:21:43 -04:00
fb634658de
add tests for a few more force manipulation fixes
2020-08-23 07:01:38 -04:00
c503bba008
add custom pair style tests for reax/c and edip/multi
2020-08-23 06:44:33 -04:00
0fb8f6e779
add test for pair style momb
2020-08-22 23:15:20 -04:00
66b17fd2ce
dispersion only tests for buckingham
2020-08-22 23:03:20 -04:00
3def826dbe
add more tests for variants using long-range dispersion pair styles
2020-08-22 22:55:15 -04:00
f18d0507b3
fix issues with lj/long pair styles when not using long-range for dispersion
2020-08-22 22:54:38 -04:00
c8f2634b44
add tests for tabulated msm coulomb
2020-08-22 22:08:08 -04:00
e78100bdba
add (partial) tests for pair styles dpd and dpd/tstat
2020-08-22 22:00:13 -04:00
2907a10937
update version strings for new attempt for a patch release
2020-08-22 16:42:39 -04:00
1879106cc3
Merge pull request #2299 from rbberger/doc_file_size
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Avoids HTML doc pages from becoming too large
2020-08-22 15:45:06 -04:00
9152a8e98f
avoid division by zero in imaging code
2020-08-22 15:32:04 -04:00
2fd654f4fd
silence compiler warnings about unused variables
2020-08-22 15:06:00 -04:00
86153a0f77
avoid division by zero in MathExtra normalize functions
2020-08-22 15:03:27 -04:00
9136f9b9c9
Merge pull request #2303 from rbberger/binary2txt_bug
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Fixes a bug in binary2txt
2020-08-22 14:46:29 -04:00
f82b19e21f
Fix off-by-one mistake, Fixes #2300
2020-08-22 12:03:24 -04:00
b776e1ee3c
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
66438539f2
Avoids HTML doc pages from becoming too large
2020-08-21 19:47:46 -04:00
450fd12d31
Changes needed for Kokkos v3.2
2020-08-21 14:45:12 -05:00
6fc2ab07ef
reset_mol_ids: unique created computes
2020-08-21 14:52:39 -04:00
2a6546d6f0
Merge pull request #2296 from akohlmey/next_patch_version
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Update version strings for next patch release
2020-08-21 14:43:56 -04:00
921b6d8135
relative threshold for contact frame update based on tangential critical force
2020-08-21 13:20:53 -05:00
cffc667259
Merge pull request #2298 from stanmoore1/mv2_var
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Fix MVAPICH2 env variable for CUDA/aware
2020-08-21 14:04:57 -04:00
e0c74a30bc
Fix MV2 env variable
2020-08-21 11:08:49 -06:00
7f87ccccc8
Merge branch 'collected-small-changes' into next_patch_version
2020-08-21 11:18:10 -04:00
3c7d59401c
Merge pull request #2107 from junghans/offline_gtest
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cmake: allow to overwrite GTest URL for offline machines
2020-08-21 10:57:08 -04:00
19c1fa8c94
need to re-initialize lattice variable after new lattice command
2020-08-21 01:01:12 -04:00
ee6ef98b9b
remove trailing whitespace
2020-08-21 00:43:40 -04:00
e742ae7475
fix RST syntax and spelling issues in granular pair style docs
2020-08-21 00:31:55 -04:00
900830a4a1
Merge branch 'master' into mindlin_rescale
2020-08-21 00:24:07 -04:00
c9773fc288
Merge branch 'master' into bond/react-reset_mol_ids
2020-08-21 00:19:52 -04:00
4c46119a48
Merge pull request #2280 from lammps/gridcomm-tiled
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Support for tiled decompositions in PPPM
2020-08-21 00:16:20 -04:00
42018d3b35
add dispersion only kspace style tests
2020-08-20 23:42:23 -04:00
3183af9b85
fix a few more initialization issues in pppm/disp and pppm/disp/intel
2020-08-20 23:42:00 -04:00
2855f04363
tweak output format
2020-08-20 23:41:32 -04:00
deb24626d1
fix gc vs. gc6 issues in fix pppm/disp
2020-08-20 22:45:37 -04:00
0440b13a6d
fix memory leaks
2020-08-20 22:27:15 -04:00
17a9612126
fix pppm/disp initialization issues
2020-08-20 22:17:32 -04:00
0a042be6b8
fix another pppm/disp bug for dispersion-only runs
2020-08-20 22:11:06 -04:00
e7639d4951
Merge pull request #2297 from akohlmey/more-fix-tests
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Add a few more unit tests for fixes and fix some issues related to it
2020-08-20 20:18:09 -04:00
287112761c
tweak load balancing output format
2020-08-20 18:51:28 -04:00
a742db2369
add a couple of kspace tests using tiled communication
2020-08-20 18:08:10 -04:00
398e929400
Merge branch 'master' into gridcomm-tiled
2020-08-20 17:58:35 -04:00
4fde9022a3
remove tabs
2020-08-20 17:54:26 -04:00
a70a5be2d8
Merge pull request #2289 from akohlmey/reduce-kokkos-compiler-warnings
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Reduce compiler warnings in KOKKOS package
2020-08-20 17:52:07 -04:00
203ab71b62
Merge branch 'master' into gridcomm-tiled
2020-08-20 17:00:55 -04:00
c513b60f97
Merge branch 'reduce-kokkos-compiler-warnings' of github.com:akohlmey/lammps into reduce-kokkos-compiler-warnings
2020-08-20 16:59:46 -04:00
f3b0bf8a33
Merge branch 'master' into reduce-kokkos-compiler-warnings
2020-08-20 16:59:31 -04:00
cd7ba1d007
Merge branch 'master' into more-fix-tests
2020-08-20 16:41:29 -04:00
f0335fabb1
Merge pull request #2295 from akohlmey/add-fix-momentum-chunk
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Add fix momentum/chunk
2020-08-20 16:40:51 -04:00
d6b19b80d0
Make all Kokkos functors structs
2020-08-20 13:52:53 -06:00
17b998edb3
fix whitespace issue
2020-08-20 15:51:41 -04:00
5306b39251
add tests for a few more wall fixes
2020-08-20 15:42:00 -04:00
56d00e115d
add more tests for fixes
2020-08-20 15:32:47 -04:00
92622d9079
add restart support to fix temp/rescale, fix spring/chunk, and fix spring/rg
2020-08-20 15:32:10 -04:00
ff2242385b
Tweak format
2020-08-20 12:56:56 -06:00
6862d70759
Merge branch 'master' of github.com:lammps/lammps into reduce-kokkos-compiler-warnings
2020-08-20 11:24:30 -06:00
6efc51d863
Update comment
2020-08-20 11:19:34 -06:00
394b2da585
Port changes to Kokkos
2020-08-20 11:09:21 -06:00
fc9f0dbcbc
correct fix npt/cauchy docs
2020-08-20 11:29:30 -04:00
ba00626764
more force adding fix tests
2020-08-20 10:59:39 -04:00
e72ea35c40
add tests for a bunch of rigid fixes
2020-08-20 10:10:25 -04:00
0f11532162
remove class member that was incorrectly shadowing a base class member
2020-08-20 10:10:03 -04:00
ca7fa2aeef
make names of fix-timestep inputs consistent with the rest
2020-08-20 09:25:40 -04:00
6bda49e8d8
step version strings for next patch release
2020-08-20 07:46:01 -04:00
ed26d8ef8f
revert change to fft3d.cpp that breaks all PPPM styles
2020-08-19 20:24:03 -04:00
2ed18bb841
tweak output format
2020-08-19 20:15:00 -04:00
2feccc2837
fix dispersion gridcomm buffer bug
2020-08-19 20:12:43 -04:00
729b3d2717
major whitespace cleanup
2020-08-19 18:46:35 -04:00
503d3826bb
Merge branch 'master' into gridcomm-tiled
2020-08-19 18:36:49 -04:00
fdb1e69768
silence compiler warnings
2020-08-19 18:36:28 -04:00
284cdceae8
silence compiler warnings
2020-08-19 18:19:28 -04:00
ba06a7bf0c
final gridcomm comments and flip FFT forward/reverse
2020-08-19 16:05:30 -06:00
8f156bfee6
Fix typo in pppm_gpu.cpp
2020-08-19 14:25:06 -06:00
6f37da4eb2
Whitespace cleanup
2020-08-19 14:10:35 -06:00
5ea7ca94f4
Revert accidental change
2020-08-19 13:54:06 -06:00
073c7ee138
Fix warnings related to virtual function override
2020-08-19 13:29:11 -06:00
33cc932d03
Eigen3 is now hosted at GitLab. The bitbucket repo is gone. Update URLs and MD5s
2020-08-19 15:21:43 -04:00
af50d90b55
add author to README
2020-08-19 15:15:28 -04:00
20c24b1f3b
add tests for momentum fixes and nve/limit
2020-08-19 15:08:46 -04:00
b1fbee9bd0
skip testing fix nve/limit for r-RESPA as it is not compatible by design
2020-08-19 15:08:32 -04:00
a0aca4cee4
improve error message
2020-08-19 15:08:04 -04:00
b4ce4a0979
must delete internal computes if they already exist (e.g. after a restart)
2020-08-19 15:07:56 -04:00
cc0d294478
Fix segfault
2020-08-19 13:05:23 -06:00
acd0a62de7
add new fix style momentum/chunk
2020-08-19 14:44:18 -04:00
3a8b2aef17
Small tweaks
2020-08-19 09:45:19 -06:00
e9de1c1a9a
Merge pull request #2293 from akohlmey/collected-small-changes
...
Collected small changes and fixes
2020-08-19 11:11:43 -04:00
fcec5c35ea
Remove error check in pppm_kokkos
2020-08-19 08:57:46 -06:00
f7c6e8e6b1
Eigen3 is now hosted at GitLab. The bitbucket repo is gone. Update URLs and MD5s
2020-08-19 10:50:54 -04:00
1413e61553
tweak test presision so it passes with more compilers
2020-08-19 00:59:50 -04:00
7e4e756b23
remove dead code
2020-08-18 22:46:34 -04:00
174a282e0c
fix signed vs. unsiged warning
2020-08-18 22:46:26 -04:00
8e74d5ad02
Eigen3 is now hosted at GitLab. The bitbucket repo is gone. Update URLs and MD5s
2020-08-18 21:29:43 -04:00
e4ab49c2e5
bond/react: bond-type-checking docs
2020-08-18 18:12:01 -04:00
4d31afce2d
Port changes to PPPMKokkos
2020-08-18 16:06:43 -06:00
df497e4853
bond/react: clarify bond-type-checking error
2020-08-18 17:53:07 -04:00
43f6fa4b29
Merge pull request #2136 from rbberger/refactor-reading
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Refactor value parsing code segments and add dump tests
2020-08-18 16:18:33 -04:00
a53ee5664e
silence compiler warnings about signed vs. unsigned ints
2020-08-18 15:51:06 -04:00
f6ac4a26c4
reorder initialization in constructor to silence compiler warnings
2020-08-18 15:47:03 -04:00
e2923d2d8c
Merge branch 'master' of ssh://github.com/lammps/lammps into gridcomm-tiled
2020-08-18 13:43:33 -06:00
02f66f1e9f
protect pragmas with ifdefs
2020-08-18 15:39:44 -04:00
b38bf6c06a
silence some more unused parameter/variable warnings
2020-08-18 15:28:23 -04:00
07c47fbd4a
silence some more signedness warnings
2020-08-18 15:28:02 -04:00
63575829da
reorder initialization
2020-08-18 15:26:37 -04:00
e185537255
avoid uninitialized access
2020-08-18 14:33:14 -04:00
78d5714247
silence signed vs. unsigned integer warnings
2020-08-18 14:33:02 -04:00
a537ffabf9
correct illegal and uninitialized data access issue
2020-08-18 14:19:57 -04:00
2fea8f888a
Merge branch 'master' into collected-small-changes
2020-08-18 14:15:06 -04:00
18b12e8979
Merge branch 'master' into reduce-kokkos-compiler-warnings
2020-08-18 13:50:35 -04:00
d63f3d87eb
Merge pull request #2292 from akohlmey/warning-no-mixing-data-file
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Print warning when writing PairCoeff section in data file may not sufficiently reproduce all pair coefficients
2020-08-18 13:45:44 -04:00
c7f8a6d154
Add format line test to dump atom
2020-08-18 13:15:28 -04:00
72f3c3803e
Fix warning with #pragma unroll
2020-08-18 11:13:50 -06:00
216a016a08
Add simple tests for dump cfg
2020-08-18 12:37:16 -04:00
0d38a1418e
Merge branch 'master' into warning-no-mixing-data-file
2020-08-18 12:24:01 -04:00
6b024d4697
Merge branch 'master' of github.com:lammps/lammps into reduce-kokkos-compiler-warnings
2020-08-18 10:15:55 -06:00
dae2cb2668
Merge pull request #2286 from weinbe2/fea-snap-ui-optim
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Kokkos SNAP optimizations – Pre-computing Cayley-Klein parameters, symmetrized data layouts for host and device backends, reducing number of atomics
2020-08-18 11:55:46 -04:00
9c769fe90e
Complete refactor of dump custom tests
2020-08-18 11:53:10 -04:00
6dfe2f3351
Minor code cleanup
2020-08-18 09:21:28 -06:00
d6ea2e9e9b
More refactoring
2020-08-17 17:56:33 -04:00
e75ba02701
Merge remote-tracking branch 'origin/master' into refactor-reading
2020-08-17 17:36:01 -04:00
fa0aa7f8d2
Merge pull request #2291 from ThFriedrich/master
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fix typos and indentations
2020-08-17 12:11:38 -04:00
23be41a1d3
fix typos and indentations
2020-08-16 04:43:07 +02:00
f0e36c74a8
silence more signedness comparison warnings
2020-08-15 18:10:13 -04:00
365d8f57f1
Refactor dump atom tests
2020-08-14 15:41:24 -04:00
b95cb37f62
correct indentation and silence warning about singed/unsigned comparison
2020-08-14 12:02:23 -04:00
71e0646063
Merge branch 'gridcomm-tiled' of github.com:lammps/lammps into gridcomm-tiled
2020-08-14 09:41:37 -06:00
eb78f8842f
another change to pppm/stagger
2020-08-14 09:41:30 -06:00
3aee1b75b1
update README
2020-08-14 11:21:51 -04:00
08a5a05ece
reduce compiler warnings in KOKKOS version of USER-DPD code
2020-08-13 20:54:06 -04:00
1939a9e665
silence a few more compiler warnings and remove dead code
2020-08-13 20:13:51 -04:00
4227c5e9e1
silence more compiler warnings about unused parameters and variables
2020-08-13 18:19:35 -04:00
1b60f876e0
Some refactoring of tests
2020-08-13 18:04:34 -04:00
dbcf66cf97
Increase coverage of dump custom
2020-08-13 17:41:06 -04:00
eab8652d3a
Fix triclinic binary header in dump custom
2020-08-13 17:40:44 -04:00
2ba4778640
Add missing cleanup
2020-08-13 17:39:57 -04:00
f1afa45b92
Merge branch 'gridcomm-tiled' of ssh://github.com/lammps/lammps into gridcomm-tiled
2020-08-13 14:52:31 -06:00
40e55af8d7
Port GridComm changes to Kokkos
2020-08-13 14:51:58 -06:00
abc3e17619
fix loop control bug in qeq/reax/kk
2020-08-13 16:30:12 -04:00
6778489247
silence a whole bunch more compiler warnings
2020-08-13 16:26:50 -04:00
0d2a280397
silence compiler warnings
2020-08-13 15:46:00 -04:00
fbcc97586f
Update binary format of dump custom
2020-08-13 14:45:22 -04:00
6225a7d45c
Merge branch 'gridcomm-tiled' of github.com:lammps/lammps into gridcomm-tiled
2020-08-13 12:03:42 -06:00
a1ca4ecbe8
add GridComm API changes to msm/cg/omp
2020-08-13 12:03:32 -06:00
71ec14087d
Reduce code duplication in tests
2020-08-13 13:00:37 -04:00
1fb7ba9e4b
Add tests for dump_custom
2020-08-13 12:35:47 -04:00
27e8ee7bd8
Fix typo
2020-08-13 12:34:16 -04:00
87a356a211
Add write_dump tests for dump atom
2020-08-13 12:04:54 -04:00
f9697bd9f5
Add optional TIME to binary dump atom format
2020-08-13 11:48:29 -04:00
6d725c9b1c
Merge pull request #2287 from akohlmey/lattice-region-tester
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Add unittest tool for lattice and region (/w create_box/create_atoms)
2020-08-13 11:47:08 -04:00
6d80435b51
Refactoring dump_atom.cpp
2020-08-13 11:35:05 -04:00
836ba01d51
Rename test_dump.cpp to test_dump_atom.cpp
2020-08-13 11:14:30 -04:00
4157ab3bd3
silence compiler warnings about unused parameters
2020-08-13 11:11:28 -04:00
7b0bfed01d
Add failure tests to dump atom
2020-08-13 11:01:16 -04:00
6d825dcb6b
Add UNITS information to dump atom binary format
2020-08-13 10:49:03 -04:00
1c2747739a
Merge pull request #2284 from akohlmey/fix-tester
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Add unit test tool for fixes that do time integration, thermostatting, force manipulations and similar
2020-08-13 10:23:29 -04:00
b27d63059c
Add tests for units in dump atom
2020-08-13 10:22:46 -04:00
dc484f06c8
do not mix class and struct for functors: use class consistently
2020-08-13 10:17:14 -04:00
bd7917919b
update list of pointer variables to be initialized to NULL in the msm constructor
2020-08-13 09:34:02 -04:00
ba793f2e56
add region tests and a few more death tests for lattice commands
2020-08-12 22:16:50 -04:00
6eb6ab308b
more tests for lattice command failures
2020-08-12 22:16:50 -04:00
f8c7c13168
complete lattice testers and start with regions+lattice+create_atoms
2020-08-12 22:16:50 -04:00
33118491a9
update custom lattice example for better syntax highlighting and remove unused lines
2020-08-12 22:16:50 -04:00
1cd2dfee3f
add more lattices
2020-08-12 22:16:50 -04:00
5c5774c8a4
add check for compatible lattice command when calling create_atoms
...
without this check it is possibly to use the dimension keyword after
using lattice and then create atoms with an unsuitable lattice setting
2020-08-12 22:16:49 -04:00
7e558e4628
add tester tool for lattice and region commands
2020-08-12 22:16:49 -04:00
e2cedebd29
more enumerator to class definition in header, so it can be accessed by tester
2020-08-12 22:16:49 -04:00
3a1b88c57f
enable MSM to work withe new GridComm class
2020-08-12 17:41:31 -06:00
e00544c8bf
Merge branch 'gridcomm-tiled' of github.com:lammps/lammps into gridcomm-tiled
2020-08-12 14:28:25 -06:00
ecec36cc15
remove trial versions of PPPM2 and GridComm2
2020-08-12 14:26:15 -06:00
eae7312680
changes to more PPPM variants for tiled support
2020-08-12 14:25:28 -06:00
a5d27763e5
Added support for symmetrized memory layouts for ui/duidrj for the CPU- and GPU-path SNAP Kokkos implementation, various perf optimizations for ComputeUi/ComputeFusedDeidrj
2020-08-12 16:15:06 -04:00
adf8d638e8
add missing word
2020-08-11 21:23:47 -04:00
5050538d59
add tests for addforce and aveforce fixes
2020-08-11 21:00:16 -04:00
99604a6155
Merge branch 'collected-small-fixes' into fix-tester
2020-08-11 20:26:46 -04:00
68d94f9b59
fix memory leaks in pair style meam/spline
2020-08-11 20:25:35 -04:00
dff8a50a46
fix memory leak in pair style edip
2020-08-11 20:14:39 -04:00
4cfc920d65
remove unused variable
2020-08-11 19:58:51 -04:00
90acace136
fix restart issues in pair style lennard/mdf
2020-08-11 19:57:32 -04:00
3dda6b5752
Increase test coverage of dump atom
2020-08-11 19:00:32 -04:00
ef13372d13
Remove debug message
2020-08-11 18:32:58 -04:00
873b8b0104
Add dump atom tests with image=yes
2020-08-11 18:12:53 -04:00
560c29a0e1
Extends header of new binary format of dump atom
2020-08-11 17:37:46 -04:00
9d486d734b
update bond/react for reset_mol_ids->create_computes
2020-08-11 17:29:27 -04:00
3c69ebc669
reset_mold_ids: add create_computes
2020-08-11 17:12:36 -04:00
1238ad5d83
Fix binary2txt output for triclinic
2020-08-11 16:20:05 -04:00
b08751d65a
Add triclinic tests for dump atom
2020-08-11 16:17:36 -04:00
51a7038dbf
Merge branch 'master' into fix-tester
2020-08-11 16:14:27 -04:00
ac43f8f685
Merge pull request #1865 from danicholson/bond-style-special
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Add bond style special
2020-08-11 16:06:26 -04:00
11af732aab
tweak precision for edip test
2020-08-11 15:43:03 -04:00
3593d371eb
Merge pull request #2285 from twhitehead/comm-for-fix-destructors
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Move comm destruction to after modify to leave available for fixes
2020-08-11 15:21:36 -04:00
83f81c42b9
Fix typo
2020-08-11 15:08:58 -04:00
15cd007d7b
Merge pull request #2283 from abhiShandy/soft-test
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Add unit tests for /soft pair styles
2020-08-11 15:04:54 -04:00
3cae295f5b
make test for unsupported pair styles more restrictive and improve docs about that
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EAM styles have a single function but are not compatible, so we test for
single_enable == 0 and manybody_flag != 0.
Improve explanation in the documentation about which pair styles are not supported.
2020-08-11 15:04:14 -04:00
f6d91b3b2c
move domain/comm commands
2020-08-11 15:02:37 -04:00
2ad9e06bac
Sync DumpAtom and binary2txt to generate the same
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Modifies the binary dump atom format to include columns information.
binary2txt showcases how to detect the new format by checking for
negative ntimestep values. It increases the binary file size
16 bytes per timestep.
2020-08-11 14:59:01 -04:00
265b7cf11c
use new dependency resolver in pip for the documentation build virtual environment
2020-08-11 14:11:44 -04:00
03ca86ee84
Merge branch 'master' into bond-style-special
2020-08-11 13:55:24 -04:00
e3a1fd7c02
Add tests for dumps
2020-08-11 12:55:39 -04:00
46021a57a6
addressed incompatibility with long range coulombics
2020-08-11 12:22:07 -04:00
65d9eef707
add test for pair style extep
2020-08-11 09:57:32 -04:00
6b84cd1c48
add test for pair style morse/smooth/linear
2020-08-11 09:57:23 -04:00
f685a7cc93
fix incorrect sign bug
2020-08-11 09:56:19 -04:00
8fb356d901
fix initialization after restart bug
2020-08-11 09:56:07 -04:00
5c0ec78cd2
add test for pair style e3b
2020-08-11 08:57:40 -04:00
0cb3163bd6
may test for atom types only after system is initialized
2020-08-11 08:57:27 -04:00
172435b662
add tests for lj/expand/coul/long
2020-08-11 08:38:42 -04:00
7ff5a7fccd
fix bugs with single and r-RESPA
2020-08-11 08:37:03 -04:00
f77b80180c
simplify
2020-08-11 08:36:39 -04:00
175a6c26a7
Add Info::get_mpi_vendor() function
2020-08-10 19:02:39 -04:00
5ee4346700
fixed test for tip4p_long_soft, and mentioned the required coefficients for coul/*/soft sub-styles
2020-08-10 17:16:07 -04:00
b9ce53e096
update tests for r-RESPA testing of fixes
2020-08-10 17:03:19 -04:00
70f37d6613
update for handling r-RESPA properly
2020-08-10 17:02:56 -04:00
33c97618be
using hybrid/overaly to add soft repulsion to purely coulombic pair-styles
2020-08-10 16:52:32 -04:00
a7fee0a96f
replace strstr with utils::strmatch
2020-08-10 16:28:42 -04:00
5ebac27fd5
safety for division by zero in scaling of the projection
2020-08-10 15:15:47 -05:00
a83147ce20
fixed bug in respa neighbor list
2020-08-10 16:01:28 -04:00
7d8dcb0fb0
Remove strtok from reader_native.cpp
2020-08-10 15:56:06 -04:00
2de98999c1
bug fix formula for frame of reference rotation for granular tangential history
2020-08-10 14:51:00 -05:00
1370090586
Move comm destruction to after modify to leave available for fixes
...
Needed in some cases to cleanup asynchronous inter-step transfers.
2020-08-10 15:49:52 -04:00
3993f53946
must skip DeathTests if no data file loaded
2020-08-10 15:46:28 -04:00
67af8c000e
fix r-RESPA bug in storing global total force data
2020-08-10 15:46:00 -04:00
b12f9d5150
Remove strtok in thermo.cpp
2020-08-10 13:53:59 -04:00
079cc123e5
Remove unused function
2020-08-10 12:27:08 -04:00
e2b113b5e1
Merge branch 'master' into refactor-reading
2020-08-10 12:25:16 -04:00
6f1055a9b1
Merge pull request #2281 from jtclemm/patch_fix_store
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Patch fix store to encode the size of per-atom data consistently with other related fixes for restarting.
2020-08-10 12:09:08 -04:00
bf724332d4
implement tangential force history in mindlin/force and mindlin_rescale/force
2020-08-10 10:53:30 -05:00
e3beec8b95
revert permission change and replace 'b/c' with 'because'
2020-08-10 11:37:52 -04:00
0025140902
flag which table - identified by keyword - has a warning
2020-08-10 11:09:10 -04:00
869b09a78f
fix typo
2020-08-10 11:08:30 -04:00
b92eda8ab8
enable testing with r-RESPA for real
2020-08-09 17:36:15 -04:00
c3903efb46
add test for berendsen barostat
2020-08-09 16:45:21 -04:00
4b7356f5af
add support for testing virial contributions from fixes (as an option)
2020-08-09 16:39:31 -04:00
f1da1ed180
document restart capability of fix temp/csld and fix temp/csvr
2020-08-09 15:29:12 -04:00
e51bec10a8
one more test variant for fix setforce
2020-08-09 15:18:28 -04:00
4708cd7e1f
always call MPI_Finalize() before exiting tester program
2020-08-09 15:17:53 -04:00
b223ca1436
cleanup and bugfix
2020-08-09 15:12:38 -04:00
2fcd7b79ab
make certain that internal data in RanMars is initialized to avoid false positive with valgrind
2020-08-09 15:12:10 -04:00
f1da2b2f5f
add tests for fix/csvr and fix/csld
2020-08-09 14:56:43 -04:00
bbcae3b20c
added restart capability to fix temp/csld and fix temp/csvr
2020-08-09 14:56:27 -04:00
383bb7f905
added restart capability to RanMars
2020-08-09 14:56:00 -04:00
897ae681d3
remove dead code
2020-08-09 14:55:35 -04:00
548e108695
simplify
2020-08-09 14:55:11 -04:00
6e9bf8709e
add tests for fix rattle
2020-08-09 13:58:10 -04:00
d8cd12b285
print warning only on MPI rank 0
2020-08-09 13:57:04 -04:00
3ebd194090
update documentation for unit testing to include timestepping fix tests
2020-08-09 08:18:35 -04:00
cabb166041
add tests for fix shake
2020-08-09 07:40:24 -04:00
a4eea29d90
add fix setforce test with variables
2020-08-09 07:32:46 -04:00
a6cc775241
add example for wall fix
2020-08-09 07:25:27 -04:00
1989279442
no need to list all dependencies. if atom style full is available, the rest is, too.
2020-08-09 07:25:15 -04:00
2053776118
increase code coverage
2020-08-09 07:13:26 -04:00
d7c1162e9d
make plain and omp test consistent
2020-08-09 07:12:56 -04:00
a27a03bc1a
now also test for global scalars and vectors and t_target for thermostats
2020-08-09 01:48:12 -04:00
b1e9b6d3fc
set variable for checking thermostat target temperature
2020-08-09 01:33:37 -04:00
88f89c8f14
correctly read entire vector
2020-08-09 01:27:56 -04:00
62a501ebda
store cumulative energy change in restart file
2020-08-09 01:27:14 -04:00
e94d1c5537
add function to query whether ErrorStats class has data
2020-08-09 01:01:35 -04:00
2edad432ce
add support for storing a global scalar and global vector
2020-08-09 00:03:43 -04:00
4b5bc8f63b
some more fix tests
2020-08-08 23:14:16 -04:00
6276e72509
also check fix styles. properly detect upper case.
2020-08-08 23:13:57 -04:00
511944d9bd
add a first set of tests for timestepping fixes
2020-08-08 22:54:58 -04:00
faac18ffd2
add tester tool for timestep related fixes: integrators, thermostats, force manipulations, constraints
2020-08-08 22:54:17 -04:00
0ce43efc34
reorder folders, so that the fast tests are run first
2020-08-08 22:52:41 -04:00
6cea5a9aef
added missing restart_settings() in morse/soft
2020-08-08 17:11:25 -04:00
9bbd6099af
unit tests for /soft pair styles
2020-08-08 16:30:27 -04:00
f69dd734b2
update format
2020-08-08 14:48:11 -04:00
d0720794a6
Replaced mistakenly dropped line
2020-08-08 09:24:37 -06:00
41904f7946
Added cautionary comments
2020-08-08 09:15:56 -06:00
2775b93789
Merge pull request #2282 from akohlmey/more-unit-tests
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Add more unit tests for pair and kspace styles
2020-08-07 19:06:44 -04:00
54b933164f
tweak epsilon
2020-08-07 18:34:39 -04:00
7aae5ba5d1
set molecule ids for testing interlayer potentials
2020-08-07 18:34:25 -04:00
17b7476217
avoid sqrt computation on cutoffs. make single functions consistent with compute
2020-08-07 18:34:10 -04:00
9f469623c0
add test for lj/smooth/linear and gaus/cut
2020-08-07 18:13:58 -04:00
e169a5c785
add tests for pair style coul/streitz
2020-08-07 18:06:57 -04:00
a17633bd20
use open_potential in pair style coul/streitz
2020-08-07 18:06:43 -04:00
c5cd108113
add tests for coul/shield, coul/slater/cut and coul/slater/long
2020-08-07 16:59:21 -04:00
2ffa7430ab
fix restart bug in pair style coul/shield
2020-08-07 16:58:56 -04:00
7d26fbc6e2
add test for pair style coul/diel
2020-08-07 16:51:23 -04:00
e217635e9a
fix bug in reading binary restarts for pair style coul/diel
2020-08-07 16:51:12 -04:00
0537cc721e
add test for pair style edip/multi
2020-08-07 16:32:53 -04:00
ec0c3d60a8
add test for pair style edip
2020-08-07 16:30:12 -04:00
4542a39f21
fix indexing bug in pair style edip/omp
2020-08-07 16:29:53 -04:00
8e0dccee2c
add test for pair style meam/sw/spline
2020-08-07 16:08:28 -04:00
51decfcf85
add test for pair style meam/spline
2020-08-07 14:53:11 -04:00
04cc5df27b
atom type to element mapping is not done correctly. for now require exactly one atom type per element
2020-08-07 14:52:51 -04:00
1c33bff557
add test for pair style yukawa/colloid
2020-08-07 12:04:23 -04:00
efa8b3486f
update colloid test template so it can handle different atom styles
2020-08-07 12:04:06 -04:00
15e969ca5b
add triclinic support to ewald/omp
2020-08-07 11:11:52 -04:00
094f52c378
make space style msm an explicit dependency
2020-08-07 00:07:36 -04:00
7d9f6b0dc5
add tests for pair styles from USER-SDK
2020-08-07 00:07:18 -04:00
a42365bf90
add support enforce writing a data file with pair ij as required by sdk styles
2020-08-07 00:05:34 -04:00
1d539ea787
make single function consistent with compute
2020-08-07 00:04:59 -04:00
c6d5715ea1
add tests for meam/c
2020-08-06 23:12:16 -04:00
d2a66cc9ee
Merge branch 'master' into gridcomm-tiled
2020-08-06 22:27:35 -04:00
aa393f35db
Merge pull request #2279 from akohlmey/collected-small-changes
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Collected small changes and fixes
2020-08-06 22:26:20 -04:00
3c21642bf1
Merge branch 'collected-small-changes' into gridcomm-tiled
2020-08-06 21:53:46 -04:00
522a76694f
test pppm with triclinic cell
2020-08-06 21:52:37 -04:00
b91419397d
update (some) kspace tests to run faster
2020-08-06 21:49:03 -04:00
6dd903cfff
Merge branch 'collected-small-changes' into gridcomm-tiled
2020-08-06 18:47:38 -04:00
8327613192
Merge branch 'master' into gridcomm-tiled
2020-08-06 18:35:33 -04:00
cd31006006
add test for pair style python
2020-08-06 17:53:11 -04:00
ec0b3ae8d2
add test for pair style tip4p/cut
2020-08-06 16:54:39 -04:00
e1219399b4
add tests for buck/long/coul/long
2020-08-06 16:26:37 -04:00
fefed73cb9
fix bug in single function of buck/long/coul/long
2020-08-06 16:26:26 -04:00
ad71475e91
more tests
2020-08-06 16:09:47 -04:00
dae97e1151
add tabulation for long-range coulomb
2020-08-06 16:09:36 -04:00
8826ea91e2
inherited single function doesn't match, we need to set single_enable to 0
2020-08-06 16:09:21 -04:00
0d677321d8
more tests for coreshell
2020-08-06 15:50:31 -04:00
ad9483343c
reformat pair_coeff section
2020-08-06 15:49:31 -04:00
e93e49a777
restore printing alphabetically sorted lists of missing styles
2020-08-06 15:30:52 -04:00
e777454888
add unittest for pppm/tip4p with kspace_modify diff ad and fix related bug in pppm/tip4p/omp
2020-08-06 14:42:15 -04:00
89694d3f8e
small tweak
2020-08-06 11:45:00 -04:00
5caeb2c2ee
generalize to allow GridComm to be called from Fixes or Computes
2020-08-06 08:36:59 -06:00
15db052c80
Merge branch 'master' into collected-small-changes
2020-08-05 22:10:10 -04:00
c3075250ee
Merge pull request #2273 from abhiShandy/pair-tests-aug4
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Bunch of units tests for pair-style, angle-style, bond-style
2020-08-05 22:09:28 -04:00
787d7d28d0
Merge pull request #1296 from Adrian-Diaz/multi-comm-tiled
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updated comm tiled to have multi style ghost communication
2020-08-05 21:27:33 -04:00
6b1191b1c0
Forgot to update saving buffer size
2020-08-05 18:59:33 -06:00
ae3df83ed8
Merge pull request #2275 from stanmoore1/kk_hip
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First set of changes for Kokkos HIP
2020-08-05 19:52:35 -04:00
458243604b
change atom style tests expand covered code paths: tiled vs. brick comm, orthogonal vs. triclinic. relax floating point check precision
2020-08-05 19:27:59 -04:00
27fe315db7
Matching style of other fixes
2020-08-05 17:25:58 -06:00
5f83edd127
remove references to non-existent MPI_Statuses
2020-08-05 17:24:09 -06:00
1871175871
Patched fix/store
2020-08-05 17:20:13 -06:00
ac08bcadf7
use bbox keyword on some replicate commands to increase code coverage
2020-08-05 18:49:05 -04:00
8b76e47d6b
support for tiled decompositions in PPPM
2020-08-05 16:44:56 -06:00
0e7c5a014d
Merge pull request #2276 from rbberger/fmtlib-upgrade
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Upgrades the fmt library to version 7.0.2
2020-08-05 18:34:34 -04:00
65574be178
whitespace fixes
2020-08-05 17:52:16 -04:00
304d6876f4
a few bug fixes for support for multi and triclinic in CommTiled
2020-08-05 15:44:02 -06:00
8f84b6cbe6
Merge branch 'fix_typo_doc_dpd' of github.com:pdebuyl/lammps into collected-small-changes
2020-08-04 19:42:32 -04:00
d53fc62fb0
change fmtlib internal namespace from v7 to v7_lmp to avoid clashes when linking with other fmtlib variants
2020-08-04 19:18:44 -04:00
8558e9bd45
fix bug when applying floating point output formatting to integers
2020-08-04 19:10:19 -04:00
67a9856e0c
silence compiler warning when converting MAXBIGINT to a double
2020-08-04 19:07:53 -04:00
ae765f9d6e
Add missing KOKKOS_INLINE_FUNCTION
2020-08-04 17:03:54 -05:00
1a642d36ae
fix typo in the math of pair style dpd doc
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- missing closing backticks for math
- V fixed to v for relative velocity
2020-08-04 22:50:26 +02:00
0b6c7ba502
Add missing KOKKOS_INLINE_FUNCTION
2020-08-04 13:07:35 -05:00
7294936322
Add missing fmt license
2020-08-04 13:39:18 -04:00
c6f5640d48
Simplify #ifdef
2020-08-04 11:25:42 -06:00
2fe7be0d37
Reapply fmt patches for Intel compiler issues
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- work around issue of the Intel compiler disguising as clang on MacOS
- {fmt}: don't use [[gnu::fallthrough]] on intel compilers
2020-08-04 13:18:54 -04:00
63cbbf9605
Upgrade embedded fmt library to v7.0.2
2020-08-04 13:17:57 -04:00
ed566bf6af
First set of changes for Kokkos HIP
2020-08-04 12:16:26 -05:00
18bc389339
print warning, when mixed pair coeffs were set explicitly but are not written in data file
2020-08-04 07:18:48 -04:00
e860779fa0
formatting update
2020-08-04 07:17:28 -04:00
357716ec4c
correctly check of mu and torque flags as those data structures are always accessed.
2020-08-04 07:17:12 -04:00
f9539f9ca6
remove unused code
2020-08-04 07:08:55 -04:00
f895904d2c
Merge branch 'pair-tests-aug4' of github.com:abhiShandy/lammps into pair-tests-aug4
2020-08-04 02:18:06 -04:00
5592bac69c
Merge branch 'bond-styles-Aug4' into pair-tests-aug4
2020-08-04 02:17:06 -04:00
59c5a62a00
Merge branch 'angle-tests-Aug4' into pair-tests-aug4
2020-08-04 02:16:57 -04:00
feadfaf9be
unit tests for angle-class2/p6, angle-cross and angle-mm3
2020-08-04 02:15:11 -04:00
eed7113506
tests for fene, fene/expand
2020-08-04 01:57:23 -04:00
f407db6198
add test for lj/cut/tip4p/cut
2020-08-04 00:11:14 -04:00
b217375744
add tests with AD instead of IK
2020-08-03 23:45:46 -04:00
83519290e7
add kspace tests with slab correction and pppm/stagger
2020-08-03 23:31:32 -04:00
ef8b619840
fix missing support for nozforce in ewald/omp
2020-08-03 23:21:54 -04:00
4e46c0aef4
add missing born/coul/long variant using tabulation
2020-08-03 23:02:29 -04:00
c2ed040529
simplify
2020-08-03 22:49:21 -04:00
89d85436f1
update reference data for triclinic case
2020-08-03 22:42:18 -04:00
f4aede49dc
Merge branch 'master' into multi-comm-tiled
2020-08-03 22:37:23 -04:00
ea900b3482
add test input template for tiled with triclinic and multi-cutoff
2020-08-03 22:17:04 -04:00
d89a047461
Simplify write data code
2020-08-03 22:08:06 -04:00
6bc65dc14c
reference typos in doc
2020-08-03 20:49:02 -04:00
a921c44a4f
fix bug in writing data
2020-08-03 20:48:37 -04:00
de828fceaf
test for cosine/squared
2020-08-03 20:48:11 -04:00
0db1c66b03
triclinic compatibility
2020-08-03 20:16:20 -04:00
33aa96b1bf
test for buck/mdf, fixed bug in broadcasting inner cutoff, typos in doc
2020-08-03 20:07:24 -04:00
6576c4cbf3
Merge pull request #2260 from akohlmey/collected-small-changes
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Collected small changes
2020-08-03 18:02:17 -04:00
ca7039aa96
Merge pull request #2271 from abhiShandy/pair-tests-Aug3
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Unit tests for born/coul, ufm, yukawa, soft
2020-08-03 17:23:22 -04:00
9cd0a52c44
Remove old comment
2020-08-03 16:58:56 -04:00
4126ba24c1
Move timespec2seconds to utils
2020-08-03 16:54:53 -04:00
436951fb34
Merge pull request #2270 from akohlmey/check-test-coverage
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Add utility to check for missing force style tests
2020-08-03 16:47:49 -04:00
851a22802e
add tests for pair style colloid in variants in several neighbor list and comm variants
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this does 3 tests:
- regular neighborlist binning with single cutoff communication
- comm style brick with multi-cutoff neighborlists and communication
- comm style tiled with multi-cutoff neighborlists and communication
2020-08-03 16:16:56 -04:00
6dcd962718
fix indentation and whitespace
2020-08-03 16:09:11 -04:00
a6b3ee7a07
fix bugs in comm style tiled with multi-cutoff
2020-08-03 16:08:13 -04:00
7ed748118e
add exception for single test for colloid pair style
2020-08-03 16:07:32 -04:00
8d406403bb
fix typo in manual
2020-08-03 16:07:06 -04:00
d0be219419
Refactor check-styles.py
2020-08-03 14:26:55 -04:00
9db3004d0c
Merge branch 'master' into multi-comm-tiled
2020-08-03 14:08:53 -04:00
f9d1a914fb
Update check-packages.py
2020-08-03 13:49:37 -04:00
4549493145
Refactor check-packages.py
2020-08-03 13:47:40 -04:00
944ac44b44
Update pair coul streitz
2020-08-03 13:13:47 -04:00
2ffb29f65e
Merge remote-tracking branch 'origin/master' into refactor-reading
2020-08-03 11:50:23 -04:00
23a8b3438d
Merge pull request #2267 from abhiShandy/force-tests
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unit tests for beck, morse, few LJ derivatives, few buck/coul and born/coul
2020-08-03 11:41:16 -04:00
d09d40af9d
make check for alternate linke more restrictive: also check for linker binary.
2020-08-03 11:36:02 -04:00
865e853a41
Refactor check_tests.py
2020-08-03 10:37:45 -04:00
9bc1da64fb
pair style gauss does not apply special_bonds
2020-08-03 08:42:36 -04:00
7e5e741ea1
update code for ufm/gpu to match changes in base class where uf4 is removed
2020-08-03 08:12:09 -04:00
d271ee65e8
Merge branch 'pair-tests-Aug3' of github.com:abhiShandy/lammps into pair-tests-Aug3
2020-08-03 08:03:01 -04:00
f3d7f0be2d
update test reference data for pair style ufm
2020-08-03 08:01:37 -04:00
69688bbc1a
must initialize scale array entries when using mixed parameters
2020-08-03 08:01:13 -04:00
c171b2ceda
fix incomplete restart bug in pair style ufm
2020-08-03 08:00:54 -04:00
ad6b37d688
bug in forcelj of gauss_omp
2020-08-03 08:00:41 -04:00
d241b17c8e
remove unused setting and array
2020-08-03 07:44:32 -04:00
86c6efc04c
sort list of missing styles alphabetically
2020-08-03 07:30:15 -04:00
bb183345bb
remove obsolete function
2020-08-03 07:29:53 -04:00
10c0b8d90e
passing test for soft
2020-08-03 06:23:23 -04:00
80ceff55d5
failing test for UFM, with cosmetic change in its CPP, and doc correction
2020-08-03 06:01:59 -04:00
8eb84229bd
passing tests for born-coul, gauss and yukawa
2020-08-03 05:59:44 -04:00
90028a3c71
properly handle hybrid styles when checking for missing tests
2020-08-03 00:43:41 -04:00
896a08883b
add a custom python script to check the completeness of tests inputs
2020-08-03 00:12:51 -04:00
bbb4c39692
Merge branch 'wip-tests' into force-tests
2020-08-01 14:53:10 -04:00
eb91c6feb6
correct data file output format for ZBL style. update reference output.
2020-08-01 14:43:14 -04:00
cc87557fa7
tweak parameters for lj/expand to stabilize test run
2020-08-01 14:24:50 -04:00
6827eb80a8
fix missing initialization bug in lj/cut/coul/wolf and update reference data
2020-08-01 14:18:40 -04:00
a4db52c30f
tweak potential parameters for better stability of test run
2020-08-01 14:05:27 -04:00
4c3dc9566c
need to explicitly clamp the forces and energy in single function to zero at (implicit) pairwise cutoff
2020-08-01 14:05:04 -04:00
891be9313a
fix parameters initialization bug in pair style lj/cubic
2020-08-01 13:37:07 -04:00
7158f47157
bugfix for pair style buck/coul/cut
2020-08-01 11:15:07 -04:00
34279840fc
unit tests for few buck/coul and born/coul; remove mixing from buck
2020-08-01 08:52:07 -04:00
d15db7b5a7
fix the atomic numbers in ZBL test
2020-08-01 07:49:06 -04:00
86c53cb211
unit tests for few LJ derivatives and ZBL
2020-08-01 07:39:33 -04:00
2a487f5f47
unit tests for beck, morse, and few LJ derivatives
2020-08-01 07:27:39 -04:00
729cc81f31
make more use of utils::logmesg()
2020-07-31 22:16:06 -04:00
74f50ed1bd
Merge branch 'master' into collected-small-changes
2020-07-31 21:51:10 -04:00
75dcd9ae29
Merge pull request #2266 from Vsevak/fix_opencl
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Fix handling of CL_DEVICE_TYPE flags
2020-07-31 21:50:33 -04:00
59b5c7c154
Merge pull request #2264 from akohlmey/fix_ttm_parser_update
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Refactor parsing of input files in fix ttm and fix ttm/mod
2020-07-31 18:14:54 -04:00
b6b5d369b4
Merge pull request #2265 from abhiShandy/easy-pairs
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Unit tests for born, buck, lj96 and mie cut
2020-07-31 15:45:14 -04:00
db47eeb2a9
Fix handling of CL_DEVICE_TYPE flags
2020-07-31 19:21:32 +03:00
067540fef1
diversify exponents in mie/cut test
2020-07-31 12:11:24 -04:00
1017b76c71
reformat pair_coeff section in buck test for better readability
2020-07-31 12:08:00 -04:00
12924346ac
unit tests for born, buck, lj96 and mie cut
2020-07-31 11:46:51 -04:00
1f1263645e
Document warning about short communication cutoff vs. bond length based estimate
2020-07-31 11:03:26 -04:00
adde2439a6
Merge pull request #2263 from junghans/gitattributes
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Add .gitattributes
2020-07-31 00:18:02 -04:00
8cb63194aa
optimize utils::strmatch() by using const string reference
2020-07-30 23:42:03 -04:00
814e2e9aaf
turn off optimization for Clang compilers when compiling atom style tester
2020-07-30 23:41:24 -04:00
1cf7a12a5f
trim whitespace before parsing numbers
2020-07-30 23:40:34 -04:00
c3db11a807
fix argument index bug carried over from syncing with fix ttm
2020-07-30 23:40:09 -04:00
4b91ab0d23
add utils::trim() function to remove leading and trailing whitespace from string
2020-07-30 23:39:37 -04:00
3370d2f8de
Add .gitattributes
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This will help to strip out some developer-only files from the
GitHub generated tarballs.
2020-07-30 10:51:21 -06:00
45af603c04
Make patch informational too
2020-07-30 12:26:55 -04:00
09e0ad19f5
Merge branch 'collected-small-changes' of github.com:akohlmey/lammps into collected-small-changes
2020-07-30 12:21:46 -04:00
763fa426cf
Enable patch status
2020-07-30 12:21:40 -04:00
6812649a65
Merge branch 'collected-small-changes' of github.com:akohlmey/lammps into collected-small-changes
2020-07-30 12:08:43 -04:00
1ae785132c
Add codecov.yml
2020-07-30 12:08:15 -04:00
f0e6651780
Merge branch 'first-test' of github.com:abhiShandy/lammps into collected-small-changes
2020-07-30 11:46:06 -04:00
facb2f3c27
fix error in determining A/B parameters. outputs now match lj/mdf as expected.
2020-07-30 11:44:37 -04:00
4a28a708b9
T_initial_set array is only required during reading of the mesh
2020-07-30 10:36:03 -04:00
36f4e6789a
simple test for pair-born
2020-07-30 03:30:57 -04:00
6a90a2affe
consistently check for presence of all input mesh data
2020-07-29 23:43:45 -04:00
7d46aa6185
Merge pull request #2256 from akohlmey/cmake-use-alternate-linker
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Use alternate/faster linker if available
2020-07-29 21:40:17 -04:00
2c3f9b111a
whitespace cleanup: replace tabs and remove trailing blanks
2020-07-29 21:36:24 -04:00
8c30b320fd
Merge branch 'master' into collected-small-changes
2020-07-29 21:32:16 -04:00
c355348ff9
remove local copy of "me"
2020-07-29 21:31:51 -04:00
df3d04662d
Merge pull request #2259 from lammps/rcb-tiled-tri
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enable comm_style tiled and load-balancing to work for triclinic boxes
2020-07-29 21:23:20 -04:00
dd001e80d2
Merge branch 'master' into rcb-tiled-tri
2020-07-29 20:37:28 -04:00
b00bfc82c8
Merge pull request #1426 from Adrian-Diaz/comm_tiled_sendself_fix
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Add bugfix for comm_tiled_sendself
2020-07-29 20:35:33 -04:00
b402b00882
Merge branch 'master' into comm_tiled_sendself_fix
2020-07-29 18:23:51 -04:00
2fa642d95e
document custom linker choice
2020-07-29 18:01:17 -04:00
d0b6ce8284
displace target link options (if supported by CMake version)
2020-07-29 17:46:24 -04:00
1f1767f5af
convert linker choice to (advanced) choice. only for Clang and GNU at the moment
2020-07-29 17:36:34 -04:00
2923dcbbd6
Merge pull request #2258 from akohlmey/phana-update
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Update phana tool for USER-PHONON from GitHub repo
2020-07-29 16:52:47 -04:00
8c849c0104
add test file for pair style lennard/mdf
2020-07-29 16:41:11 -04:00
6707e64d14
change class name and add write_data support with pair style lennard/mdf
2020-07-29 16:39:44 -04:00
d3b5e50da3
fix bugs in lennard/mdf pair style
2020-07-29 16:39:07 -04:00
59ff6b7abc
Add comment explaining the change
2020-07-29 16:33:54 -04:00
cb98fa00da
enable CommStyle tiled and load-balancing to work for triclinic
2020-07-29 14:30:49 -06:00
4d9781f9b6
fix typo an reorder
2020-07-29 11:10:14 -04:00
7df8a63045
update phana tool for USER-PHONON from github
2020-07-29 10:48:04 -04:00
1677b76b6c
try using faster alternatives to GNU ld when building (many) test executables
2020-07-28 20:56:32 -04:00
cc0cf3b94f
consolidate USER-REAXC init error message handling. avoid snprintf and buffer
2020-07-28 20:40:57 -04:00
29c50671da
Merge pull request #2254 from Vsevak/fix_opencl
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Fix corrupted character in GPU package
2020-07-27 20:08:18 -04:00
ae329acd3b
Merge pull request #2255 from akohlmey/charset-cleanup
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Charset cleanup in (most) source files
2020-07-27 19:41:36 -04:00
9db34bc18e
cosmetic changes to CommTiled for comm multi style
2020-07-27 16:15:41 -06:00
477b97f257
remove some more extended ASCII characters
2020-07-27 17:33:35 -04:00
2bb5c53a47
remove/replace extended ASCII characters from comments
2020-07-27 17:15:29 -04:00
634f274a04
whitespace cleanup: replace tabs and remove trailing whitespace
2020-07-27 17:14:53 -04:00
41535d8de3
Merge pull request #2253 from stanmoore1/kk_snap_bug
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Fix issue in pair_snap_kokkos
2020-07-27 14:09:43 -04:00
93f14e9bba
Fix broken ASCII symbol in GPU package
2020-07-27 20:16:55 +03:00
6dc52dff73
Fix bug in pair_snap_kokkos
2020-07-27 10:30:04 -06:00
884355b335
Merge pull request #2252 from akohlmey/collected-small-changes
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Collected small changes and bugfixes
2020-07-27 12:01:18 -04:00
780fb5b376
add test function to validate updated topology data after reset_atom_ids
2020-07-27 10:43:37 -04:00
1fb1a5f461
fix incorrect ubuf decoding bug in reset_atom_ids
2020-07-27 09:48:13 -04:00
94c9cdbc05
print messages about reading potential files only on MPI rank 0
2020-07-27 06:19:35 -04:00
5452f72bd9
convert fix ttm and fix ttm/mod to use tokenizer class for parsing files
2020-07-25 18:03:18 -04:00
cf83ce6745
reset_mol_ids->reset() version
2020-07-25 00:52:39 -06:00
79984e31db
small i/o tweaks
2020-07-24 14:10:30 -04:00
783b28906e
Merge pull request #2250 from rbberger/doc-remove-small-images
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Remove unnecessary thumbnails
2020-07-23 11:50:07 -04:00
5528d4d18c
trim excessive white from images
2020-07-23 00:36:15 -04:00
f60c13c845
fix incorrect link
2020-07-23 00:36:02 -04:00
c21ce0b289
make horizontally aligned image formatting consistent and display "click on" message only with html output
2020-07-23 00:35:49 -04:00
9ceb0fd6a0
update output formatting and send all to screen and log
2020-07-22 22:51:47 -04:00
11e3adc91b
make sure per-atom data is initialized to zero
2020-07-22 22:51:16 -04:00
545f50f9ec
limit precision
2020-07-22 22:50:57 -04:00
b97f2e5b6b
Update compute_saed.rst
2020-07-22 16:48:21 -04:00
bf848c0515
Update compute_xrd.rst
2020-07-22 16:45:56 -04:00
1123add481
Update create_atoms.rst
2020-07-22 16:44:04 -04:00
7f66099732
Update dump_image.rst
2020-07-22 16:41:59 -04:00
b664050e28
Update src/neb.rst
2020-07-22 16:39:18 -04:00
22a1e452ce
Update fix_wall_gran_region.rst
2020-07-22 16:35:45 -04:00
e82367b530
Update balance.rst and fix_balance.rst
2020-07-22 16:31:31 -04:00
e6f7a99ae2
Update Python_examples.rst
2020-07-22 16:27:04 -04:00
6f58ed1c83
Merge pull request #2248 from rbberger/docs-include-accel-text
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Remove duplicated accelerator text passage in docs
2020-07-22 14:14:57 -04:00
89c42d081f
Merge pull request #2247 from rbberger/wsl-docs-update
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Update Windows Subsystem for Linux Tutorial
2020-07-22 13:47:15 -04:00
73eccefeb3
Merge pull request #2246 from rbberger/docs-theme-update
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Update lammps_theme (based on latest sphinx_rtd_theme)
2020-07-22 12:55:27 -04:00
feebdf9149
print complete read_data and special output to both screen and logfile
2020-07-22 07:23:33 -04:00
f9e7b7dd19
Remove outdated or differently formatted common text blocks
2020-07-21 17:54:33 -04:00
177a93d22d
Replace common text block with include
2020-07-21 17:38:56 -04:00
6acc4bc849
Update Windows Subsystem for Linux Tutorial
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Fixes #1953
2020-07-21 14:39:08 -04:00
437ff2742d
Update lammps_theme (based on latest sphinx_rtd_theme)
2020-07-21 12:44:10 -04:00
938175d2bc
Merge pull request #2242 from akohlmey/next_lammps_version
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Update version strings for next patch release
2020-07-20 22:33:37 -04:00
472de2e85a
Merge pull request #2238 from yafshar/kim_fix
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KIM package corrections and refactoring
2020-07-20 21:22:59 -04:00
cbdf1d3a64
consolidate mpi4py link
2020-07-20 20:59:47 -04:00
68df62b869
support verbose option
2020-07-20 20:40:20 -04:00
cac4c5d930
fix merge artifact
2020-07-20 20:40:02 -04:00
5b4275002c
Merge branch 'master' into kim_fix
2020-07-20 20:27:41 -04:00
39cefc4eb3
Merge pull request #2241 from yafshar/cmake
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Update the deprecated property and fix the empty value on macOS
2020-07-20 12:23:20 -04:00
6d70c393e1
Merge pull request #2239 from akohlmey/collected-small-changes
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Collected small changes and fixes for the next patch release
2020-07-20 11:35:11 -04:00
1f819ca333
update the kim_param command test
2020-07-19 18:35:20 -05:00
3390e1d4c5
starting of the kim_property command test
2020-07-19 18:10:00 -05:00
02ff2068cd
cosmetic changes
2020-07-19 15:19:53 -04:00
78cfd3ff79
refactor fix tune/kspace
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- make use of std::string to simplify code
- skip over trying MSM, if no suitable pair style present
2020-07-19 12:15:07 -04:00
b162cefc5f
for ewald we also have evflag_atom that needs to be initialized
2020-07-19 12:12:50 -04:00
0008c0eca3
need to setup bins again if binning style has be reset
2020-07-19 12:12:20 -04:00
674514f822
update the kim_param command test
2020-07-19 10:35:00 -05:00
419404a9b5
Update the KIM error messages
2020-07-19 09:24:01 -05:00
c215278ad1
Update the KIM error messages
2020-07-19 08:41:52 -05:00
c73f8a5500
Update the KIM error messages
2020-07-19 08:13:03 -05:00
c844de03ef
Update the KIM error messages
2020-07-19 08:08:30 -05:00
5fec11a0db
Update the KIM error messages
2020-07-19 08:04:13 -05:00
262ce37eed
silence compiler warning
2020-07-19 07:19:44 -04:00
295d75f230
guess should reset_mol_IDs *after* updating bonds
2020-07-18 21:14:36 -06:00
845b918501
probably better reset_mol_id doc version
2020-07-18 20:59:17 -06:00
edd3fb7108
reset_mol_ids: documented verbose option
2020-07-18 20:51:14 -06:00
65bf187a39
update version string for patch release
2020-07-18 21:51:01 -04:00
0246feb1c2
Merge branch 'kim_fix' of github.com:yafshar/lammps into kim_fix
2020-07-18 20:47:28 -05:00
bba7e3554c
simplify building aligned mutable parameter trable using fmtlib
2020-07-18 21:42:33 -04:00
82f5bbf859
update the kim_interactions command test
2020-07-18 20:31:36 -05:00
894a7e4bce
update test
2020-07-18 21:10:22 -04:00
c1a650d50d
Update the error messages
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Update the error messages and removing an extra Error word at the
start of each message.
2020-07-18 20:00:11 -05:00
610fea20dd
clean up the code
2020-07-18 19:14:00 -05:00
40a053000d
update output formatting of info command
2020-07-18 18:54:03 -04:00
bc47ec5027
update the kim_init command test
2020-07-18 17:23:24 -05:00
fe6efe8861
need header file!
2020-07-18 14:29:39 -06:00
9ec5708f2f
Update reset_mol_ids.cpp
2020-07-18 14:21:10 -06:00
05c0b5d5ce
Update the deprecated property and fix the empty value on macOS
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The `IMPORTED_LINK_INTERFACE_LIBRARIES` is deprecated and is
updated to `INTERFACE_LINK_LIBRARIES` instead.
On macOS `CMAKE_THREAD_LIBS_INIT` is empty since empty the thread
functions are provided by the system libraries. To avoid getting
`set_target_properties called with incorrect number of arguments` error
message, we put it inside double quotes.
2020-07-18 15:12:31 -05:00
e00b0e96f6
bond/react: prevent reset_mol_ids printing
2020-07-18 14:00:46 -06:00
a2547701e6
fix verbose reset_mol_ids
2020-07-18 13:59:30 -06:00
6272b7d2bf
add (undocumented) verbosity option to reset_mol_ids
2020-07-18 13:52:13 -06:00
da91f81d40
bond/react:doc clarification
2020-07-18 13:42:47 -06:00
371a5c5b61
bond/react: reset_mol_ids docs
2020-07-18 12:44:34 -06:00
57f639c0e5
bond/react:reset_mol_ids keyword
2020-07-18 12:42:47 -06:00
859da19869
consistently skip death tests at runtime when using OpenMPI without exceptions
2020-07-18 13:09:17 -04:00
e0200cf3d7
consistently skip death tests at runtime when using OpenMPI without exceptions
2020-07-18 13:02:38 -04:00
211beaee48
Merge pull request #2230 from evoyiatzis/widom
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Implementation of Widom insertions through a new fix widom command
2020-07-18 11:40:04 -04:00
c9dc5d90d2
Merge remote-tracking branch 'origin/master' into refactor-reading
2020-07-17 23:08:26 -04:00
55c3d139c1
add Widom spc/e example
2020-07-17 21:42:00 -04:00
bf5c1dbc9e
accept const std::string as argument in Group::find()
2020-07-17 21:29:16 -04:00
eff159baf4
work around issue of the Intel compiler disguising as clang on macos
2020-07-17 21:28:35 -04:00
4d4ae93ef8
add missing group names in fix widom. refactor group definition in fix widom and gcmc
2020-07-17 21:27:58 -04:00
93ed07f445
accept const std::string as argument in Group::find()
2020-07-17 21:26:53 -04:00
0e6531e2b6
whitespace cleanup
2020-07-17 15:02:53 -04:00
117499e847
avoid floating point exception (log(0))
2020-07-17 15:02:47 -04:00
c9342aec31
add lj example for fix widom
2020-07-17 15:02:11 -04:00
c5698ac994
Merge branch 'collected-small-fixes' of github.com:rbberger/lammps into collected-small-changes
2020-07-17 14:03:17 -04:00
95c215d5d3
silence compiler warnings
2020-07-17 14:02:18 -04:00
65f9c1abf5
bugfix: reorder instructions
2020-07-17 14:00:16 -04:00
0748b12472
when processing quoted strings, the quotes need to be removed
2020-07-17 13:58:15 -04:00
b3bd36947d
add convenience function to allow variable->set() command with a single string argument
2020-07-17 13:57:54 -04:00
5c191e1e6e
fix the return call status
2020-07-17 11:21:25 -05:00
cdbcacffce
when processing quoted strings, the quotes need to be removed
2020-07-17 10:23:07 -04:00
a0bfe932b5
quote argument that needs to be kept intact
2020-07-17 10:08:26 -04:00
5fe83755b8
start tester tool for KIM commands
2020-07-17 02:23:48 -04:00
2fb6a61f2a
refactor code to make better use of std::string and simplify using changes to Variable class API
2020-07-17 01:23:17 -04:00
63bebf58fd
add convenience function to allow variable->set() command with a single string argument
2020-07-17 00:46:31 -04:00
dd7bc1d34e
use const char * instead of char * so we don't need a cast for string constants
2020-07-17 00:45:58 -04:00
e2efabc6c4
Revert "simplify"
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This reverts commit 2be20f424f
2020-07-17 00:35:13 -04:00
0af7fbe98e
use const char * instead of char * so we don't need a cast for string constants
2020-07-17 00:34:23 -04:00
abc9cfe30f
silence compiler warnings
2020-07-17 00:30:13 -04:00
4743bf4ea0
silence compiler warning
2020-07-17 00:27:03 -04:00
b61276b59d
Merge branch 'master' into kim_fix
2020-07-17 00:10:02 -04:00
74c9c15589
simplify and get rid of strtok()
2020-07-17 00:08:07 -04:00
5df8be2ca4
Replace macro with std::to_string
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Following the C++ Core Guidelines, Macros must go.
2020-07-16 20:21:12 -05:00
1b0f35c241
Replace macro with std::to_string
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Following the C++ Core Guidelines, Macros must go.
2020-07-16 20:19:51 -05:00
168fe438a5
Replace macro with std::to_string
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Following the C++ Core Guidelines, Macros must go.
2020-07-16 20:17:59 -05:00
2ba7abe57e
silence compiler warnings
2020-07-16 21:14:31 -04:00
fb7923df06
dead code removal
2020-07-16 21:14:22 -04:00
2be20f424f
simplify
2020-07-16 21:13:47 -04:00
78ddce5de1
Replace macro with std::to_string
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Following the C++ Core Guidelines, Macros must go.
2020-07-16 20:13:40 -05:00
08dd79b1ce
Clean up the code
2020-07-16 20:09:17 -05:00
dbbc60b4b8
Clean up the code
2020-07-16 20:04:55 -05:00
dff117fe53
Clean up the code
2020-07-16 20:02:26 -05:00
f163477d3a
Clean up the code
2020-07-16 20:00:09 -05:00
54b47212a1
Clean up the code & replace tabs with white spaces
2020-07-16 19:56:22 -05:00
81f8590df1
Clean up the code
2020-07-16 19:49:22 -05:00
96615ea97e
Clean up the code
2020-07-16 19:47:31 -05:00
91f97fa74c
Remove the previously created KIM log file.
2020-07-16 19:23:51 -05:00
585ed5e1dc
Merge pull request #2228 from athomps/compute-mliap
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Compute mliap updates
2020-07-16 20:20:45 -04:00
882210613e
Fix the write_log_cite interface.
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Fix the interface by correcting the data type. The `model_name`
variable is a `char *` and not a `string`.
2020-07-16 19:20:30 -05:00
e98056c0e8
whitespace fixes
2020-07-16 19:03:30 -04:00
31cfc99ad9
add missing empty line
2020-07-16 18:37:16 -04:00
52715cc804
Merge branch 'master' into compute-mliap
2020-07-16 18:35:49 -04:00
ad02d7a5e0
Merge pull request #2219 from lammps/write-bonus-data
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Enable write_data for atom styles with bonus data. Add tester code for that and many related cleanups and bugfixes.
2020-07-16 18:21:15 -04:00
34fdfb6b81
allow fix nvt/body npt/body and nph/body to be used for groups other than "all"
2020-07-16 17:56:56 -04:00
92f194ac93
make sure output buffer is initialized
2020-07-16 17:32:17 -04:00
f344629a29
simplify
2020-07-16 17:31:54 -04:00
209d3ff3ff
fix typo
2020-07-16 17:31:46 -04:00
35b030015d
Merge branch 'master' into write-bonus-data
2020-07-16 12:15:59 -04:00
9a13ad5230
Merge pull request #2206 from ohenrich/mc-fix-bond-create-angle
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New fix_bond_create_angle class
2020-07-16 11:54:04 -04:00
ee10b200e0
Merge branch 'master' into write-bonus-data
2020-07-15 22:10:38 -04:00
25a836b729
reformat and rephrase text about availability of fix bond/create/angle only keyword
2020-07-15 21:32:22 -04:00
52b30b11ec
add fix bond/create/angle to list in Fix command page
2020-07-15 21:31:22 -04:00
d7ef1b007d
Merge branch 'master' into mc-fix-bond-create-angle
2020-07-15 21:21:35 -04:00
29e2c82d71
fix broken line wrap.
2020-07-15 21:00:43 -04:00
4dc61f7f2a
make frenkel book anchors globally unique
2020-07-15 20:56:50 -04:00
300beb819b
change from DOS/Windows CR/LF to LF
2020-07-15 20:54:58 -04:00
3287f1cddc
fully integrate fix widom into manual. fix some style issues and reindent
2020-07-15 20:54:17 -04:00
94464f5390
Merge branch 'master' into widom
2020-07-15 20:46:39 -04:00
581d47a10a
move fix widom from USER-MISC to MC package
2020-07-15 20:46:31 -04:00
438346a936
Merge pull request #2237 from yafshar/memory
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Fix the system-dependent function call to `malloc_usable_size`.
2020-07-15 20:42:49 -04:00
dff2e93e2a
Merge pull request #2236 from stanmoore1/kk_qeq_nevery
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Fix issues in Kokkos fix qeq/reax
2020-07-15 20:41:00 -04:00
508a38a7fa
Fix the system-dependent function call to malloc_usable_size.
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Fix the system-dependent function call to get the size of the
block of memory allocated from the heap.
2020-07-15 17:49:49 -05:00
71344aaa28
Merge branch 'master' of https://github.com/lammps/lammps into kk_qeq_nevery
2020-07-15 16:18:56 -06:00
181b7cf34f
Merge branch 'master' into write-bonus-data
2020-07-15 18:14:49 -04:00
0105d1caa5
Merge pull request #2212 from akohlmey/compute-chunk-scalar
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Get number of chunks from compute chunk/atom
2020-07-15 18:13:48 -04:00
1021f5753b
Merge pull request #2218 from lammps/reset-molecules
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new reset_mol_ids command
2020-07-15 18:09:02 -04:00
dee38c26b3
Changed paragraph as per request
2020-07-15 22:51:51 +01:00
a392f212ee
Fix issues in Kokkos fix qeq/reax
2020-07-15 15:49:26 -06:00
73a076daf3
don't set CMAKE_TUNE_FLAGS to anything by default
2020-07-15 16:19:48 -04:00
8949b2f165
add recently added names to false positives list
2020-07-15 15:31:12 -04:00
bf37e6aae1
Merge branch 'master' into write-bonus-data
2020-07-15 15:20:34 -04:00
7a312ca8d8
Merge pull request #2231 from stanmoore1/reax_hybrid
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Fix issue with Kokkos ReaxFF and pair hybrid
2020-07-15 14:35:35 -04:00
28ee835103
Update fix_widom.rst
2020-07-15 20:35:15 +02:00
1a738f80e2
Update false_positives.txt
2020-07-15 20:14:17 +02:00
4cbe095444
Merge pull request #2234 from akohlmey/collected-small-fixes
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Collected small fixes and unittest updates
2020-07-15 14:13:21 -04:00
41a7557cc9
first attempt of a documentation file
2020-07-15 18:53:04 +02:00
74aa1d482a
Add missing sync
2020-07-15 10:48:39 -06:00
b37b45c817
use fmtlib to remove BIGINT_FORMAT
2020-07-15 11:55:08 -04:00
aa82608142
print warning for unknown/unsupported CUDA versions
2020-07-15 11:28:33 -04:00
a082895b90
update CMake script for GPU package to include handling of Arch 8.0 and CUDA 11
2020-07-15 11:08:06 -04:00
8108063f47
small bug fix for gather()
2020-07-15 12:21:03 +02:00
6c5d928358
small bug fix for gather()
2020-07-15 11:45:23 +02:00
2580ca78f4
guard better against 32-bit overflows for reax/c lists
2020-07-15 00:13:33 -04:00
e3818f031b
don't use error class if pointer variable has not been initialized
2020-07-15 00:12:31 -04:00
2fb0f95324
check against BODY package for body styles
2020-07-14 18:41:52 -04:00
ad818717cc
complete tester module for atom style body/nparticle
2020-07-14 18:36:50 -04:00
a7a63ee3fb
Merge branch 'write-bonus-data' of github.com:lammps/lammps into write-bonus-data
2020-07-14 16:48:01 -04:00
d37bb0fd6f
update intel compiler requirements and document alignment issues
2020-07-14 16:24:17 -04:00
449d7be8f8
updated rules for rounded body particles
2020-07-14 13:25:17 -06:00
1ddd8aa97c
Merge branch 'master' into collected-small-fixes
2020-07-14 14:00:24 -04:00
d3392dba45
update tester some more
2020-07-14 13:59:55 -04:00
fd2b5b1cd8
switch completed section from EXPECT to ASSERT
2020-07-14 12:45:54 -04:00
bc3860b462
must advance buffer while package bonus items, but only when a buffer is given
2020-07-14 12:45:22 -04:00
b33974cd19
add code to check for duplicate atom IDs in Bodies section
2020-07-14 12:44:50 -04:00
be440c7125
revert incorrect zeroing of non-existing inertia array elements
2020-07-14 12:44:24 -04:00
dcbdc7452b
Don't need virtual keyword
2020-07-14 09:57:04 -06:00
d6e6b840e9
update body/nparticle tester
2020-07-14 11:06:06 -04:00
548629958e
zero all six moments of inertia if small.
2020-07-14 11:05:44 -04:00
001dcb6bb1
Fix issue with Kokkos ReaxFF and pair hybrid
2020-07-14 09:02:57 -06:00
9068d17afc
Merge pull request #2229 from ellio167/pair_kim_before_box
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Update pair_kim.cpp so settings() may come before box is defined
2020-07-14 10:24:05 -04:00
113825f8fc
silence compiler warning
2020-07-14 08:12:51 -04:00
20824203ab
Merge branch 'write-bonus-data' of github.com:lammps/lammps into write-bonus-data
2020-07-14 08:11:29 -04:00
18928c6602
start writing tester for body/nparticle
2020-07-14 08:11:18 -04:00
4b9c2ab1f1
start writing tester for body/nparticle
2020-07-14 07:21:25 -04:00
a88237df99
source code for fix widom
2020-07-14 13:17:20 +02:00
ea1d447703
fix bug in tester for atom style tri
2020-07-13 21:49:18 -04:00
5a73b1de98
fix typo, reformat paragraph
2020-07-13 21:48:15 -04:00
e5d532c2c1
simplify and make more readable using utils:: functions
2020-07-13 18:59:21 -04:00
40e3fcd750
tweak output format
2020-07-13 18:58:43 -04:00
46675361a6
remove unused class members
2020-07-13 18:58:35 -04:00
315c829bd2
tweak box output format to include decimal point
2020-07-13 15:59:47 -04:00
c589dd5894
consistent initialization and setting of _nthreads and comm->nthreads
2020-07-13 15:59:29 -04:00
6c28adcf3b
make sure _need_tag is initialized
2020-07-13 15:59:05 -04:00
da66516dec
use references when creating styles
2020-07-13 09:40:58 -04:00
3847a3000c
paranoia
2020-07-12 21:40:30 -04:00
f8ad39e7d1
simplify fix generation for package commands
2020-07-12 21:40:22 -04:00
1c5c2d8f22
Merge branch 'master' into reset-molecules
2020-07-12 20:36:34 -04:00
db289ba0b3
update all force style reference results after refactoring of test codes
2020-07-12 20:36:10 -04:00
24b5cd7dec
rename test programs to be consistent with the other programs in the unittest tree
2020-07-12 19:22:14 -04:00
9cbb2e9df5
refactor force-style tester programs to get rid of stringstream and local buffers
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this uses now fmtlib and also outputs forces sorted by atom id
similarly, for all tests it is make certain that the local tag variable is updated
2020-07-12 19:17:51 -04:00
38011f6ac4
add test for pair style kim
2020-07-12 17:21:35 -04:00
b65f6b3b61
Merge branch 'pair_kim_before_box' of github.com:ellio167/lammps into collected-small-fixes
2020-07-12 16:36:00 -04:00
ed1bdb8ed4
update output formatting
2020-07-12 16:33:47 -04:00
00413ae956
add test for atom style tri
2020-07-12 16:32:59 -04:00
8f95b4a5d9
add tests for deleted bonds and angles to bond/angle tests suites
2020-07-12 15:48:21 -04:00
60f078a8f9
fix buffer size and format bugs in atom_vec_tri.cpp
2020-07-12 15:46:56 -04:00
66274e7863
Update pair_kim.cpp so settings() may come before box is defined
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Addresses #2215
2020-07-12 14:23:47 -05:00
116c2a56ca
Removed old files
2020-07-11 21:00:41 -06:00
031cae8e49
Fixed spelling errors
2020-07-11 20:31:38 -06:00
38d9c0bedf
tweak output formatting
2020-07-11 21:44:31 -04:00
9e1d560fda
refactor using fmtlib and utils::
2020-07-11 21:44:13 -04:00
095c6a9850
Finished cleaning up and testing. MLIAPData class is now fully integrated with ComputeMLIAP and PairMLIAP
2020-07-11 19:01:16 -06:00
5f14d5c87f
must not override flag for negative angles and bonds
2020-07-11 18:36:19 -04:00
25e54bd68e
Merge branch 'master' into write-bonus-data
2020-07-11 18:31:44 -04:00
284b1618f9
Merge pull request #2227 from akohlmey/collected-small-fixes
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Collected small updates and bugfixes
2020-07-11 18:30:27 -04:00
83291fdd67
may not use pair_style kim before box is defined
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NOTE: this will not happen when the kim_init and kim_interactions commands are used.
2020-07-11 18:07:25 -04:00
f969d9ab72
add space for terminating NULL byte in MPIIO dump styles.
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closes #2225
2020-07-11 13:19:08 -04:00
f307d7f5f9
count total number of styles including aliases, suffixes, and undocumented
2020-07-11 13:18:44 -04:00
cd0b034cab
adjust regex for removed styles to correctly handle command styles
2020-07-11 13:18:33 -04:00
b3060bc48e
add suppressions for googletest
2020-07-11 13:18:14 -04:00
e42342ff51
zero out additionally allocated struct Param storage
2020-07-11 13:18:04 -04:00
8359a4384a
more OpenMPI suppressions
2020-07-11 13:17:51 -04:00
c6dc8b5414
fix initialition issue
2020-07-11 13:17:39 -04:00
9fe0b1cb5e
ewald_order needs to be saved in restart
2020-07-11 13:17:24 -04:00
4778887243
fix memory leak in pair style sw/intel for good
2020-07-11 13:17:10 -04:00
510d5277c1
fix typo
2020-07-11 13:16:58 -04:00
b49f0a6a09
avoid memory leak in pair style sw/intel
2020-07-11 13:16:36 -04:00
4b2c1f5edd
some more OpenMPI suppressions
2020-07-11 13:16:25 -04:00
d4da99562f
use fmtlib for writing data file coefficients. use mixed coefficients for PairIJCoeffs
2020-07-11 13:16:01 -04:00
26e21852ff
several fixes to address issues detected by valgrind
...
- make sure g_ewald_6 is not accessed uninitialized
- fix memory leak
- do not override g_ewald_6 if it is explicitly set
2020-07-11 13:15:37 -04:00
8eb7791342
avoid googletest stalling on exit tests when using OpenMPI
2020-07-11 13:15:16 -04:00
207232c1a3
avoid illegal free()
2020-07-11 13:12:50 -04:00
ed452c3624
synchronize exception based and non-exception based code paths
2020-07-11 13:12:34 -04:00
e6a8f3c8c0
use parenthesis to correct precedence
2020-07-11 13:10:37 -04:00
17d59a4342
small tweak
2020-07-11 13:06:58 -04:00
6f775f6592
fix typo
2020-07-11 13:06:43 -04:00
d0c544224f
avoid exception when having a command fail due to an empty string
2020-07-11 13:06:31 -04:00
40e59b27a7
add prototypes for exception handling functions
2020-07-11 13:06:05 -04:00
f8321d77d8
add missing symlink
2020-07-11 13:05:41 -04:00
d32000239b
refactor tester
2020-07-11 13:05:03 -04:00
e2e4305fe9
Merge pull request #2226 from akohlmey/ubuntu-stable
...
Update documentation to recommend lammps-stable packages for Ubuntu
2020-07-11 13:02:00 -04:00
8396ade280
update information about the ubuntu binaries to recommend the new stable packages
2020-07-10 22:50:47 -04:00
6c6c47ce9c
Converted pair mliap to use mliap class
2020-07-10 17:19:02 -06:00
6c08503dff
Created MLIAP class for data, passes all tests
2020-07-10 16:25:28 -06:00
64dad33c12
whitespace fixes
2020-07-10 18:22:11 -04:00
a5a1706f82
Merge branch 'write-bonus-data' of github.com:lammps/lammps into write-bonus-data
2020-07-10 16:17:22 -06:00
92d225a68c
write_data support for body style rounded/polyhedron
2020-07-10 16:17:07 -06:00
07e05300c9
Created MLIAP class for data
2020-07-10 16:08:19 -06:00
f360cca1a3
Created MLIAP class for data
2020-07-10 16:04:04 -06:00
a28db101cc
add checks for atom style bond with newton off. add basic test for atom style angle
2020-07-10 17:44:05 -04:00
0825e71a5a
whitespace fixes
2020-07-10 13:21:22 -04:00
9b3ffa5487
enables body style rounded/polygon to write to data files
2020-07-10 10:42:36 -06:00
a402de41b7
finalize atom style tester changes
2020-07-10 10:47:30 -04:00
772d75a63a
update tester for renaming reset_ids to reset_atom_ids
2020-07-10 10:29:55 -04:00
df63d4147d
Merge branch 'reset-molecules' into write-bonus-data
2020-07-10 10:25:08 -04:00
8102045fdb
add initial implementation for atom style bond tester
2020-07-10 10:24:54 -04:00
9be30dcf61
add space for terminating NULL byte in MPIIO dump styles.
...
closes #2225
2020-07-10 09:22:44 -04:00
0c89b517a5
avoid segfaults if fewer than 10 atoms or bounding box length is zero
2020-07-10 08:25:37 -04:00
ab683a03ad
start tester for atom style hybrid full ellipsoid
2020-07-10 00:12:57 -04:00
f0af7c686a
more death tests to reach 100% coverage
2020-07-09 21:39:55 -04:00
e38f970676
Extended to handle gradgradflag 0/1 options
2020-07-09 19:23:57 -06:00
0d570f5577
Removed a lot of LAMMPS dependence from Descriptor and Model classes
2020-07-09 19:22:41 -06:00
d15264a668
update and expand tester code for reset_mol_ids changes
2020-07-09 21:18:58 -04:00
bade009b6c
remove debug code
2020-07-09 20:58:39 -04:00
49780480a8
count total number of styles including aliases, suffixes, and undocumented
2020-07-09 20:52:57 -04:00
9ec77585ea
make compress yes the default
2020-07-09 20:46:45 -04:00
9c97ca11fe
adjust regex for removed styles to correctly handle command styles
2020-07-09 20:46:31 -04:00
e0e24799c2
simplify formulations a little bit. update example command lines
2020-07-09 19:52:49 -04:00
4a1acffde9
whitespace fixes
2020-07-09 19:36:58 -04:00
9e83279887
minor adjustments to new reset_mol_ids command
2020-07-09 15:40:24 -06:00
f71513f483
update for atom style ellipsoid tester
2020-07-09 11:56:07 -04:00
cc9df9a76d
add test module for atom style line
2020-07-09 11:55:52 -04:00
71f13cee9d
add missing aspherical particle info to restart files
2020-07-09 11:21:59 -04:00
d7efa8d523
don't do zero byte allocations
2020-07-09 09:26:25 -04:00
0679c01c4b
add suppressions for googletest
2020-07-09 09:26:07 -04:00
2b1ca89b57
zero out additionally allocated struct Param storage
2020-07-09 00:31:08 -04:00
ea5015c630
more OpenMPI suppressions
2020-07-09 00:05:18 -04:00
d0cfb0ccae
fix initialition issue
2020-07-08 23:49:18 -04:00
e18a11d6bd
ewald_order needs to be saved in restart
2020-07-08 23:48:58 -04:00
bebd10712a
fix memory leak in pair style sw/intel for good
2020-07-08 22:04:55 -04:00
909bc5a801
fix typo
2020-07-08 21:35:54 -04:00
7ee73e44ad
will need ellipsoid field in restart file
2020-07-08 21:18:09 -04:00
4da8ec39de
complete testing ellipsoids short of having restart support.
2020-07-08 21:13:28 -04:00
ecc5d3e353
must copy/multiply the numbers of ellipsoids,lines,tris,bodies
2020-07-08 21:12:29 -04:00
7071cff481
avoid memory leak in pair style sw/intel
2020-07-08 20:11:17 -04:00
240c33b503
some more OpenMPI suppressions
2020-07-08 20:10:52 -04:00
f59e391713
avoid leaking empty allocations
2020-07-08 20:10:40 -04:00
2016333cf0
use fmtlib for writing data file coefficients. use mixed coefficients for PairIJCoeffs
2020-07-08 20:09:23 -04:00
7591343702
several fixes to address issues detected by valgrind
...
- make sure g_ewald_6 is not accessed uninitialized
- fix memory leak
- do not override g_ewald_6 if it is explicitly set
2020-07-08 20:07:54 -04:00
5918d9e6c7
avoid googletest stalling on exit tests when using OpenMPI
2020-07-08 16:31:36 -04:00
bda245339e
avoid illegal free()
2020-07-08 16:29:40 -04:00
6cd2c8d117
synchronize exception based and non-exception based code paths
2020-07-08 10:18:01 -04:00
d6665aba99
refactor tester
2020-07-08 10:08:00 -04:00
a98d21f002
Added gradgradflag option to compute mliap
2020-07-07 20:43:40 -06:00
a7369e76cd
Added gradgradflag option to compute mliap
2020-07-07 20:42:03 -06:00
06a199f7d0
Added gradgradflag option to compute mliap
2020-07-07 20:28:18 -06:00
a43428fd1b
use auto to simplify
2020-07-07 22:19:07 -04:00
cd739c2782
silence compiler warnings
2020-07-07 22:18:52 -04:00
1898fae3f6
simplify
2020-07-07 22:18:37 -04:00
5cef86d7b7
add missing MPI call
2020-07-07 21:37:33 -04:00
8fbc8a7148
make more use of fmtlib and replace fprintf with fputs where possible
2020-07-07 21:34:34 -04:00
c0f1472385
use parenthesis to correct precedence
2020-07-07 21:21:32 -04:00
6e3e13f2a8
remove unused variable
2020-07-07 20:53:50 -04:00
9a268da7de
remove unneeded typecasts and use fmt::print() instead of fprintf()
2020-07-07 20:53:42 -04:00
4c67822e6b
remove unneeded typecasts
2020-07-07 20:27:01 -04:00
e459ee8a58
whitespace fixes
2020-07-07 20:25:59 -04:00
61e3b41908
Merge pull request #2220 from lammps/doc-radians
...
clarify units for energy terms with angles
2020-07-07 20:13:56 -04:00
6239a579e8
clarify units for energy terms with angles
2020-07-07 15:19:17 -06:00
416467a154
update reset_mol_ids tests for the latest changes
2020-07-07 17:14:54 -04:00
fd95fc98c5
add support for auto offset and singlezero option
2020-07-07 17:14:29 -04:00
d3853af4be
add singlezero keyword to compute fragment/atom to give all single non-bonded atoms an ID of 0
2020-07-07 17:13:43 -04:00
12f62583f9
whitespace cleanup
2020-07-07 13:56:50 -04:00
5c59f6af87
Merge branch 'reset-molecules' of github.com:lammps/lammps into reset-molecules
2020-07-07 13:48:25 -04:00
88fc9360c0
resolve conflicts
2020-07-07 11:46:05 -06:00
37d56a6bf6
small cleanup in "deprecated" styles
2020-07-07 13:40:15 -04:00
955bff7c4e
add body support, change bonus buf to 1d so can be variable length
2020-07-07 11:34:30 -06:00
94e9b3bc82
rename reset_ids command to reset_atom_ids
2020-07-07 13:32:00 -04:00
7e140399db
add (initial) testing for ellipsoid atom style
2020-07-07 12:36:17 -04:00
f16c6f40a7
shape is converted from diameter to radius, so we have to scale back on writing
2020-07-07 12:24:04 -04:00
94d98b6aea
no typecasts needed when outputting ubuf integers with fmtlib auto format
2020-07-07 11:40:01 -04:00
bdac1ae3e7
add missing return statements
2020-07-07 11:14:52 -04:00
0944eda391
final details for offset keyword added to reset_mol_ids
2020-07-07 09:07:48 -06:00
7870a89133
added note to doc page
2020-07-07 08:48:24 -06:00
d6ebf3cd46
Merge branch 'reset-molecules' of github.com:lammps/lammps into reset-molecules
2020-07-07 08:38:03 -06:00
fcc6ed3a58
add offset option to reset_mol_ids command
2020-07-07 08:37:48 -06:00
169206790a
small tweak
2020-07-07 10:29:43 -04:00
de7f02e48b
fix typo
2020-07-07 09:54:16 -04:00
bb9ab025c1
avoid exception when having a command fail due to an empty string
2020-07-07 09:51:39 -04:00
0b1443ed23
add prototypes for exception handling functions
2020-07-07 09:51:02 -04:00
53d20c9ebc
add missing symlink
2020-07-06 21:44:39 -04:00
960addcc2c
simplify code string/fmtlib code some more
2020-07-06 21:26:49 -04:00
2351f99bef
add (incomplete) tester for reset_mol_ids (with a little use of reset_ids, too)
2020-07-06 21:26:11 -04:00
89f0116eab
fix communication data conversion bug corrupting bond list
2020-07-06 21:12:55 -04:00
7918919d30
enable write_data for atom styles with bonus data
2020-07-06 17:30:45 -06:00
91a8df1903
Modified files according to request
2020-07-06 20:20:28 +01:00
d37e943e8d
refactor tester
2020-07-06 14:12:50 -04:00
836570ec26
update docs
2020-07-06 14:12:37 -04:00
58cd6a160c
Merge branch 'master' into reset-molecules
2020-07-06 14:07:48 -04:00
6bf329098e
Merge pull request #2216 from ndtrung81/tersoff-gpu
...
Cleanup and bugfixes for some 3-body pair styles in the GPU package
2020-07-06 13:35:12 -04:00
a1011b606e
new reset_mol_ids command
2020-07-06 10:50:34 -06:00
9e96b71703
Merge pull request #2214 from akohlmey/kspace-tests
...
Add unit tests for some kspace styles and more pair styles
2020-07-06 12:48:09 -04:00
2977a8aa15
Merge pull request #2211 from athomps/compute-mliap
...
Add compute style mliap to MLIAP package
2020-07-06 12:47:41 -04:00
d1b5b0a168
Merge pull request #2210 from ohenrich/user-cgdna
...
Update of example input and log files
2020-07-06 12:47:09 -04:00
d768069cfe
Merge pull request #2205 from akohlmey/collected-small-changes
...
Collected small changes for the next patch release
2020-07-06 12:46:16 -04:00
5d0800beef
Merge pull request #2204 from rbberger/doc-changes
...
Documentation Changes: split pair_lj.rst
2020-07-06 12:19:06 -04:00
47d77530e2
updated as requested by @sjplimp
2020-07-06 11:45:16 -04:00
022252dde0
add a paragraph to the output howto explaining how ambiguity is resolved
2020-07-06 11:13:23 -04:00
9ec72d1406
add tests for unknown commands, quit, and reset_timestep
2020-07-06 10:26:04 -04:00
f1abfe2411
avoid segfault when calling the log command without arguments
2020-07-06 10:25:37 -04:00
461633e6f6
add unit tests for the suffix, thermo, and timestep commands
2020-07-06 00:11:13 -04:00
83d58ba57d
we may not use "suffix on" before a suffix is defined. switching back to a non-hybrid suffix must set suffix2 to NULL
2020-07-06 00:10:43 -04:00
1df59c4b95
change lammps2pdb.pl to only ignore the first line of a data file. whitespace fixes
2020-07-05 23:36:00 -04:00
fe12ea2734
simplify compute creation
2020-07-05 22:46:48 -04:00
134a2e8dd6
use fmtlib and utils::logmesg() in fix msst
2020-07-05 22:37:59 -04:00
759797733d
Generalized the variable and function names
2020-07-05 18:58:32 -06:00
a0157f8063
use fmtlib consistently when writing data files
2020-07-05 17:16:58 -04:00
443cc4445e
have compute property/atom output shape parameters as diameters not radii consistent with the manual
2020-07-05 16:44:44 -04:00
e2a07acb71
add test for units command
2020-07-05 13:20:23 -04:00
ca24cd5006
simplify tests for failures with a varyadic macro
2020-07-05 12:48:52 -04:00
ebfe7f68af
More cleanup
2020-07-05 00:20:28 -05:00
c488e6208d
Similar bug fixes to vashishta/gpu
2020-07-04 23:52:32 -05:00
69052fa337
add test for lj/mdf
2020-07-05 00:28:02 -04:00
4dee43cc2d
adjust accepted relative error for compiler optimization, make pppm/disp inputs 3x faster
2020-07-05 00:10:47 -04:00
84ded03e24
add tests for some core-shell package pair styles
2020-07-04 23:43:15 -04:00
8f6e454522
single functions for CORESHELL styles are not implemented
2020-07-04 23:40:28 -04:00
585466929f
add tests for pppm/disp/tip4p and lj/long/tip4p/long
2020-07-04 23:21:57 -04:00
a314b40aa0
skip testing broken pppm/disp/intel style
2020-07-04 23:07:50 -04:00
6e580bbdb5
add tests for long-range dispersion styles
2020-07-04 22:55:59 -04:00
3f068f7671
partial reformat, fix bug in single function
2020-07-04 22:55:38 -04:00
adacc7f2a4
Similar bug fixes for tersoff/mod/gpu and tersoff/zbl/gpu; some cleanup for sw/gpu
2020-07-04 19:08:55 -05:00
11099bb3f7
silence compiler warnings
2020-07-04 19:23:06 -04:00
2eec6c7f65
exclude MSM tests when compiling with single precision
2020-07-04 18:26:00 -04:00
0461599d0a
reduce base precision as required when running tests with pppm and FFT_SINGLE
2020-07-04 18:13:55 -04:00
37b2da637d
fix KOKKOS bug for FFT_KISSFFT and FFT_SINGLE
2020-07-04 17:39:07 -04:00
df40ffddf3
add some more tests for pair styles
2020-07-04 17:24:28 -04:00
ffe8e1c0e9
add tests for kspace styles using the pair style tester tool
2020-07-04 17:22:27 -04:00
fcec94579c
skip tests for single and extract when testing kspace styles (and pair styles are disabled)
2020-07-04 17:21:51 -04:00
75977367a1
fix memory leak
2020-07-04 17:21:19 -04:00
34cfe07f97
fix energy computation bug in pair style nm/cut/omp
2020-07-04 17:20:47 -04:00
37b2778d4b
Remove debug output
2020-07-04 13:34:35 -04:00
cfaa3be898
reduce screen output precision
2020-07-04 08:26:00 -04:00
6f8b8c2f71
more application of fmtlib and utils::logmesg()
2020-07-04 08:25:24 -04:00
9de3077b19
change misleading source code formatting
2020-07-04 05:12:35 -04:00
de815ed6ba
must not pass NULL pointer now that we use const std::string references
2020-07-04 04:48:16 -04:00
fac3c70d02
update style
2020-07-04 04:47:38 -04:00
9f733fb305
Removed unused variables
2020-07-04 00:23:34 -05:00
6de020805f
Fixed a bug with tersoff/gpu with building the short neighbor list
2020-07-03 23:55:26 -05:00
c37b5e50b1
flag error when trying to compute an average of an empty vector
2020-07-03 22:35:53 -04:00
53415592d2
compute gyration/shape/chunk did not update the number of local array rows
2020-07-03 22:20:28 -04:00
14321d1fa0
add option to compute chunk/atom to access the number of chunks as a global scalar
2020-07-03 22:19:44 -04:00
c3f8644613
Merge branch 'master' into compute-mliap
2020-07-03 14:26:38 -06:00
7fe2df423f
Added a package README
2020-07-03 14:22:43 -06:00
8dae5d5fc7
Added special_bonds command to input files
2020-07-03 21:03:24 +01:00
feec9673d8
Fixed html and spelling warnings
2020-07-03 14:03:00 -06:00
9d0aee7426
Added doc page for compute mliap and updated examples
2020-07-03 13:43:51 -06:00
def0cf8a7b
Corrected typo
2020-07-03 17:54:31 +01:00
59aa8a5e12
Modified files according to PR
2020-07-03 17:48:49 +01:00
fadfb1b482
Allow changing CMAKE_CXX_EXTENSIONS option to resolve #2079
2020-07-03 12:41:49 -04:00
543371374a
typo fix
2020-07-03 11:42:31 -04:00
ab785e8a89
Add Coulomb sections in TIP4P page
2020-07-03 11:37:11 -04:00
52b92e743e
Add missing reference
2020-07-03 11:33:51 -04:00
1815ab610e
remove hard dependency and configure spelling extension only if it can load enchant properly
2020-07-03 11:26:43 -04:00
735f9ad592
address logic error with check for KOKKOS version of hybrid styles
2020-07-03 09:01:59 -04:00
f9dc2b7ca8
Added fix_bond_create_angle files
2020-07-03 13:42:16 +01:00
089c4ed5d9
Added fix/bond/create/angle class and docu
2020-07-03 09:21:00 +01:00
17e419e251
Merge branch 'master' into user-cgdna
2020-07-03 08:19:48 +01:00
2c64809cd8
enlarge buffer for guessed file name
2020-07-02 23:35:25 -04:00
7e16a17f31
use consistently the name of the (unaccelerated) pair style in the potential file reader error messages
2020-07-02 23:23:25 -04:00
0b298c7193
add tests for supported and unsupported unit conversion when opening potentials
2020-07-02 23:07:01 -04:00
d331e75a14
tweak test name
2020-07-02 22:39:08 -04:00
28bbb6afbc
Doc page for compute mliap
2020-07-02 17:09:10 -06:00
07afe1c66d
Added basic element map
2020-07-02 16:14:15 -06:00
40088f558c
Revert "Added fix bond/create/angle code and docu"
...
This reverts commit 16eab647d4
2020-07-02 23:11:50 +01:00
db43aadf09
Got compute working for quadratic model
2020-07-02 15:05:14 -06:00
cae9788d42
Changed the compute examples to expose effect of different list orderings
2020-07-02 14:43:48 -06:00
307f54611f
use doubles to avoid multiple integer overflows in slope() function
2020-07-02 16:43:00 -04:00
f598ae7ebf
update/add error message for using hybrid pair styles with KOKKOS
2020-07-02 16:40:47 -04:00
bf8043fdb8
Correctly reproduced examples/in.snap.compute, not yet for quadratic case
2020-07-02 14:34:11 -06:00
bc36511767
Correctly reproduced examples/in.snap.compute, not yet for quadratic case
2020-07-02 14:32:47 -06:00
3a014a5430
add unit tests for some file operations
2020-07-02 14:50:56 -04:00
4660c043d8
fix typo
2020-07-02 13:31:02 -04:00
a524eaf424
add a few more tests
2020-07-02 10:27:35 -04:00
8929ba42cd
enable exceptions by default when testing is enabled, so we can test for failures
2020-07-02 09:50:15 -04:00
c3fe0e77c2
expose guesspath function and add unit test
2020-07-02 09:13:57 -04:00
2a4e51fa38
Fixed a few problems, still not quite matching compute snap
2020-07-01 17:11:02 -06:00
84ee52a6e5
add false positive
2020-07-01 19:09:11 -04:00
7350dd61d5
Tweaked input to match snap/in.snap.compute
2020-07-01 17:06:55 -06:00
70d3d56944
add minimal doc page for compute smd/ulsph/effm
2020-07-01 18:44:24 -04:00
ed56878271
remove specific dump styles from overview page
2020-07-01 18:43:53 -04:00
791bb9f6d5
Update mentions of soft variants
2020-07-01 17:14:30 -04:00
c57564252c
Added descriptor file for compute mliap
2020-07-01 15:07:37 -06:00
aee3d9f2cd
Generated working example, not quite correct
2020-07-01 15:03:45 -06:00
7671d12ef8
added some more detail to the bond special doc page
2020-07-01 14:55:48 -06:00
0a18c52414
Split pair_lj.rst into three files
2020-07-01 14:27:06 -04:00
c7a31aea97
force environment variable
2020-07-01 09:39:47 -04:00
8d12581f16
silence compiler warnings
2020-07-01 09:39:37 -04:00
558d2eb84f
Merge pull request #2203 from akohlmey/collected-small-changes
...
Various small fixes and cleanups. Bugfixes for atom style hybrid
2020-07-01 06:24:28 -04:00
0a9dd81288
silence compiler warnings
2020-07-01 05:53:46 -04:00
0363fe9b17
revive (some) dead code and add missing force computation/addition
2020-07-01 05:42:53 -04:00
9c7005a91c
It compiles, but not yet working
2020-06-30 19:14:01 -06:00
971ca4fe44
add missing lines for atom_vec comm bugfix
2020-06-30 19:20:34 -04:00
503a1f2246
still more dead code
2020-06-30 18:44:00 -04:00
8fd46095ae
remove more dead code
2020-06-30 18:41:09 -04:00
9279431593
bugfix for hybrid atom styles from @sjplimp fixing bug reported by @ohenrich
2020-06-30 18:34:46 -04:00
4492d61625
dead code removal
2020-06-30 18:14:47 -04:00
778d431d4c
reduce compiler warnings about unused parameters
2020-06-30 18:08:25 -04:00
10dcb08760
remove unused variable
2020-06-30 18:08:06 -04:00
6af407d01e
remove trailing whitespace
2020-06-30 17:48:18 -04:00
1035dcd4cc
fix possible bug in compute sna
2020-06-30 16:33:57 -04:00
19ee89fa10
use a hard error instead of changing settings without updating the underlying data structures controlled by it
2020-06-30 16:33:32 -04:00
ad38b5d306
whitespace fixes
2020-06-30 16:32:41 -04:00
edfb4076ff
remove dead code and unused variables
2020-06-30 16:32:30 -04:00
eafcc06670
secs -> seconds
2020-06-30 13:56:35 -04:00
d4c7455197
reduce output precision
2020-06-30 13:49:50 -04:00
b34b58c713
must not delete atom substyles twice
2020-06-30 13:27:27 -04:00
cccd04f46b
Merge branch 'collected-small-changes' of github.com:akohlmey/lammps into collected-small-changes
2020-06-30 12:36:06 -04:00
7488f22981
reduce excess precision in some output data
2020-06-30 10:11:52 -04:00
0f094c2501
Add PyYAML to Fedora 32 container
2020-06-30 10:05:14 -04:00
af2e1bf7c6
Update Ubuntu 18.04 GPU container
2020-06-30 09:38:28 -04:00
2a2219d049
reduce excess precision in some output data
2020-06-30 00:37:32 -04:00
911b95fdc9
std::string.find_last_of() wants a string not a character as argument
2020-06-29 23:26:01 -04:00
f958cacbb4
temporarily add atom style full to list of dependencies for Pair::single() test
2020-06-29 19:36:06 -04:00
ce4ca0e640
tweak epsilon to make test pass with optimization
2020-06-29 19:35:02 -04:00
a6cd4a935e
Replace accumulated displacement by accumulated force for tangential force in styles mindlin and mindlin_rescale. Change documentation accordingly
2020-06-27 01:17:46 -05:00
b75d9b8224
bond/react: RMSD constraint docs
2020-06-26 23:43:08 -06:00
6a68715d7b
bond/react:RMSD constraint
2020-06-26 23:33:40 -06:00
fa17ba7a8f
Merge pull request #86 from lammps/master
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rebase
2020-06-26 22:26:40 -06:00
cfa12bc1cf
Merge remote-tracking branch 'origin' into compute-mliap
2020-06-25 16:33:51 -06:00
6ec3aac3f0
extra return value
2020-06-25 13:32:13 +02:00
73ed317254
Added compute_mliap.cpp/h to MLIAP package
2020-06-22 11:38:02 -06:00
f0a3256151
Merge branch 'master' into user-cgdna
2020-06-15 08:41:42 +01:00
c2b557233e
Update value parsing in Molecule
2020-06-09 12:12:52 -04:00
c1f6c004ca
Add contains method to ValueTokenizer
2020-06-09 12:11:53 -04:00
65b4d87f99
Merge branch 'master' into user-cgdna
2020-06-02 19:04:33 +01:00
711f875001
Added fix bond/create/angle code and docu
2020-06-01 15:45:40 +01:00
16eab647d4
Added fix bond/create/angle code and docu
2020-06-01 15:42:45 +01:00
042cfc521b
cmake: allow to overwrite GTest URL for offline machines
2020-05-24 19:38:19 -06:00
36bac80978
up-to-date
2020-05-01 18:42:00 +02:00
215ad7e0b9
allreaduce
2020-05-01 17:52:31 +02:00
b96058eac3
gather/scatter custom
2020-05-01 16:53:07 +02:00
a64f70f0b5
removed broken soft link
2020-05-01 16:24:42 +02:00
2571e187d0
updated README, removed broken soft link to potential
2020-05-01 16:23:51 +02:00
64fdaaec3c
citation update
2020-05-01 16:19:03 +02:00
2ff463cc6e
fixed typo and checked make html
2020-05-01 16:11:25 +02:00
012c344622
updated documentation
2020-05-01 16:10:45 +02:00
6eb9923c68
added documentation
2020-05-01 15:58:32 +02:00
4e0c835e9e
fixed dimension in error message
2020-05-01 15:57:16 +02:00
95e81c7e47
allowed 0/1 or no/yes
2020-05-01 14:52:48 +02:00
7c620f7514
removed redundant region check, made com/overdamped "yes" or "no" instead of 0/1
2020-05-01 14:36:06 +02:00
bad3becac3
set com and overdamped flags as keywords with defaults 1,0
2020-05-01 14:28:36 +02:00
79f074eb6a
updated potential path in example
2020-05-01 14:27:33 +02:00
feb6e10734
error messages
2020-05-01 13:53:24 +02:00
e708479782
error messages for fix pafi
2020-05-01 13:28:36 +02:00
910d91bc93
some more tweaks to the example
2020-04-29 17:15:46 -04:00
6cd1b45a49
recover compilation with -DLAMMPS_BIGBIG
2020-04-29 17:12:58 -04:00
1ad85980fb
fix up include files
2020-04-29 17:12:43 -04:00
d3b88ab3e1
fix documentation translation issues
2020-04-29 17:12:30 -04:00
42d36e360e
cosmetic change
2020-04-29 17:02:18 -04:00
db631c941d
fix minor memory leak
2020-04-29 16:51:43 -04:00
cc6b55515b
add integration into manual and add dummy documentation
2020-04-29 16:51:30 -04:00
46739329c4
update PAFI example: remove unused data, replace potential with existing one, update logs
2020-04-29 16:41:08 -04:00
595bb30e14
Merge branch 'master' into user-pafi
2020-04-29 15:35:29 -04:00
3ab797984b
verified cmake compatibility
2020-04-27 18:21:42 +02:00
97ac67840b
corrections to headers
2020-04-27 17:40:09 +02:00
2fb71cfb62
Merge pull request #80 from jrgissing/master
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import Andrew's PR into create_atoms branch
2020-04-22 22:36:20 -06:00
08b4159c6b
Merge pull request #79 from lammps/master
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rebase
2020-04-22 22:32:01 -06:00
251517127d
Merge pull request #78 from lammps/master
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rebase
2020-04-22 22:13:33 -06:00
f63893bd7d
citation fix
2020-04-21 17:19:48 +02:00
1c1ff9623f
check for compute at fix_init()
2020-04-21 15:07:15 +02:00
1670196bc1
c++ style headers
2020-04-21 15:00:00 +02:00
cbe6e0dcb2
small updates
2020-04-21 14:32:52 +02:00
1cd5db683f
typo..
2020-04-20 19:59:26 +02:00
0f8669c51d
updated_extract_atom
2020-04-20 19:55:29 +02:00
4da1ba749f
removed changes to atom.cpp
2020-04-20 19:42:04 +02:00
1709bc3f83
cleaned makefile
2020-04-20 19:12:37 +02:00
b1bd0251a9
better example file
2020-04-20 18:32:44 +02:00
8fa2092580
example folder
2020-04-20 10:20:53 +02:00
946cb27267
ignore
2020-04-20 10:20:17 +02:00
0ea2eabbb2
start of clean up
2020-04-17 18:11:59 +02:00
6904e1e6ef
Merge pull request #2 from tomswinburne/newfix
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update
2020-04-17 16:39:28 +02:00
bddcc3519c
update
2020-04-17 14:55:24 +02:00
5b31077cef
Merge pull request #1 from tomswinburne/newfix
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Newfix
2020-04-17 14:49:57 +02:00
b8d6de2bdc
binary example
2020-04-14 21:21:22 +02:00
6cbd61d929
working with library interface
2020-04-14 21:11:32 +02:00
276608738c
working new version
2020-04-14 15:11:09 +02:00
430f2ae6aa
getting there
2020-04-13 19:28:43 +02:00
39799c62fc
update fork
2020-04-13 10:48:20 +02:00
581f65bacd
makefile
2020-04-13 10:39:54 +02:00
789a697d69
Merge pull request #77 from mrcdr/math_eigen_lanczos
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modified the "math_eigen.h" file
2020-04-04 20:59:24 -06:00
94e5e8de76
modified the "math_eigen.h" file to track the commit 9cdfcac069
2020-04-03 01:23:30 +09:00
9cdfcac069
Merge pull request #76 from jewettaij/bond-react_create_atoms
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libraries for matrix algebra and point cloud registration
2020-03-28 23:33:44 -06:00
8d0cb2a70a
removed the "superpose3d" namespace, and renamed "namespace math_eigen" to "namespace MathEigen" (to imitate the style used in "math_extra.h").
2020-03-23 14:19:04 -07:00
e795d9ff6a
added the "math_eigen.h" and "superpose3d.h" files
2020-03-12 17:33:50 -07:00
0fb341f7eb
Merge pull request #73 from lammps/master
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rebase
2020-03-05 22:46:07 -07:00
b3425afef5
Merge pull request #72 from lammps/master
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rebase
2020-03-03 23:12:46 -07:00
4b11e43660
Merge pull request #68 from lammps/master
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rebase
2020-02-17 21:07:30 -07:00
e982f418d3
remove whitespace issues
2020-02-05 13:54:56 -05:00
b35c271a12
spelling error
2020-01-31 16:31:42 -05:00
aefaab5769
readme for user-misc
2020-01-31 16:00:16 -05:00
14dfe53837
doc edit
2020-01-31 15:54:01 -05:00
035fba10e5
fixed special_bonds requirements
2020-01-31 15:33:59 -05:00
923ccaaff9
fixed error handling
2020-01-31 12:56:02 -05:00
6bb30a3312
revised doc for bond_style special
2020-01-31 12:26:00 -05:00
9b3a93d222
add bond_style special to the list
2020-01-31 11:30:41 -05:00
58a03f12eb
draft doc page for bond_style special
2020-01-30 15:25:55 -05:00
ddfdabf189
added bond style special
2020-01-30 14:16:59 -05:00
453649453e
Merge pull request #65 from jrgissing/master
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rebase
2020-01-24 21:25:59 -07:00
c262d08e84
remove comments
2019-12-04 12:32:04 -05:00
06964c58de
Merge branch 'master' into multi-comm-tiled
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Conflicts resolved:
src/comm_tiled.cpp
2019-11-27 12:12:03 -05:00
49d9089a63
USER-PAFI examples
2019-05-22 13:50:07 +02:00
646d833027
USER-PAFI
2019-05-22 10:29:29 +02:00
a76ba95f5b
comm_tiled_sendself_fix
2019-04-11 12:51:46 -06:00
0f88513f65
updated comm tiled to have multi
2019-01-21 12:29:31 -05:00
9a3f90294c
updated comm tiled to have multi
2019-01-21 11:50:10 -05:00
