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965 Commits

Author SHA1 Message Date
Axel Kohlmeyer 0aa64eaf14
portability improvement. replace POSIX-only functionality. 2021-04-24 07:14:29 -04:00
Axel Kohlmeyer e980d17882
reuse existing code. add tests for write_data 2021-04-24 07:14:04 -04:00
Axel Kohlmeyer 2c4017d3ac
add test for write_dump cfg 2021-04-24 07:13:26 -04:00
Axel Kohlmeyer 9e7d26351d
tweak epsilon for GPU package tests 2021-04-24 07:13:06 -04:00
Axel Kohlmeyer 6a9b441331
add tests for writing restart files 2021-04-24 01:22:23 -04:00
Axel Kohlmeyer cf81f72aad
more tests for tokenizer classes 2021-04-24 01:22:06 -04:00
Axel Kohlmeyer 8c50f56548
add unit test for TextFileReader class 2021-04-24 00:31:46 -04:00
Axel Kohlmeyer 9cdd926763
remove excess quotes 2021-04-23 19:19:41 -04:00
Axel Kohlmeyer a438c2bc7b
tweak unit test YAML epsilon values for GPU mixed precision tests to pass 2021-04-23 05:43:03 -04:00
Axel Kohlmeyer a49d783e16
check formatting and multiple arguments when using utils::logmesg() 2021-04-22 05:44:35 -04:00
Axel Kohlmeyer 7e2d40c5fa
Merge pull request #2642 from rbberger/balance_tests 
MPI balancing testing
 2021-04-21 16:00:01 -04:00
Richard Berger 1656661fc2
Disable rcb_min_size test 2021-04-21 11:17:32 -04:00
Axel Kohlmeyer 2e01bb8f62
Merge pull request #2713 from rbberger/collected_small_changes 
Collected small changes
 2021-04-20 20:40:49 -04:00
Richard Berger 7696d0f84c
Add ENVIRONMENT to RunLammps test 2021-04-20 15:40:59 -04:00
Richard Berger fcf17a709e
Don't store group if initial assignment failed 2021-04-20 14:24:07 -04:00
Richard Berger 8826e962de
Add info message when death test is skipped 2021-04-20 14:06:08 -04:00
Richard Berger a6efdf9b9f
Clean up molecule files creation 2021-04-19 15:14:01 -04:00
Richard Berger bc4b4147ef
Avoid filename collisions with AtomStyles test 2021-04-19 14:57:41 -04:00
Axel Kohlmeyer c46f1b5241
modify tests for hybrid pair styles to include some pair_coeff none settings 2021-04-19 08:51:53 -04:00
Axel Kohlmeyer f3eb577b3b
update hybrid tests, enable test for hybrid with CPU neigh list and no multiples of the same style 2021-04-19 01:14:25 -04:00
Axel Kohlmeyer 9469cba081
enable GPU unit test for pair style lj/charmm/coul/charmm 2021-04-19 00:34:22 -04:00
Axel Kohlmeyer f1680b0fdd
enable unit test runs on the GPU for tersoff and tersoff/zbl 2021-04-18 20:43:48 -04:00
Axel Kohlmeyer f07fa3d266
Merge pull request #2704 from rbberger/compress_package 
More refactoring of COMPRESS package
 2021-04-12 23:01:35 -04:00
Richard Berger dba3cce883
Make dump xyz/gz, xyz/zstd compatible to 'buffer no' option 2021-04-12 20:03:58 -04:00
Richard Berger 47814292a1
Make dump cfg/gz, cfg/zstd compatible to 'buffer no' option 2021-04-12 19:57:27 -04:00
Axel Kohlmeyer 0ca9f2e8a0
Merge pull request #2699 from yury-lysogorskiy/feature/user-pace 
USER-PACE pair_style integration into LAMMPS
 2021-04-12 17:05:40 -04:00
Axel Kohlmeyer d88cf587b2
add pair style coul/cut/global and fix restart/data bugs in coul/cut 2021-04-10 00:25:00 -04:00
Axel Kohlmeyer 0628bb89ce
Merge branch 'master' into pair-hybrid-scaled 2021-04-09 22:21:16 -04:00
Axel Kohlmeyer c16e4f241f
replace "leaky" call to putenv() with setenv() on non-windows platforms 2021-04-09 20:37:01 -04:00
Axel Kohlmeyer a69c5a5cae
fix bugs in shell putenv and getenv style variables. add more unit tests. 2021-04-09 20:19:04 -04:00
Richard Berger e5ee210f58
Make dump atom/gz, atom/zstd compatible to 'buffer no' option 2021-04-09 18:02:55 -04:00
Richard Berger 242881af55
Make dump custom/gz, custom/zstd compatible to 'buffer no' option 2021-04-09 17:46:59 -04:00
Richard Berger 511f64fde4
Update dump custom/gz 2021-04-09 16:36:30 -04:00
Richard Berger c17ee12989
Update dump xyz/gz 2021-04-09 15:57:17 -04:00
Richard Berger cf41ea6faf
Update dump local and local/gz 2021-04-09 15:42:28 -04:00
Richard Berger d19cd8fb11
Fix test 2021-04-09 14:49:45 -04:00
Richard Berger dc71d80306
Add dump local tests 2021-04-09 14:49:07 -04:00
Richard Berger 2682663df6
Use GzFileWriter in dump cfg/gz 2021-04-09 11:41:45 -04:00
Richard Berger 7b53ce572c
Merge branch 'master' into compress_package 2021-04-09 10:58:39 -04:00
Axel Kohlmeyer 08471cb88e
update path to updated log file 2021-04-09 10:29:36 -04:00
Axel Kohlmeyer 73a33abb44
add unit test for hybrid/scaled 2021-04-09 00:32:06 -04:00
Axel Kohlmeyer 492ddbbcfa
simplify 2021-04-08 09:32:24 -04:00
Axel Kohlmeyer 74a3796418
avoid ambiguous precedence through using parentheses. update unit test reference 2021-04-08 09:29:18 -04:00
Axel Kohlmeyer 8a233a5ec7
add unit test reference data for USER-PACE 2021-04-07 19:30:38 -04:00
Axel Kohlmeyer 6569c2e434
Merge pull request #2694 from akohlmey/neighlist-interface-updates 
Neighbor list library/python interface improvements
 2021-04-07 16:25:38 -04:00
Axel Kohlmeyer 5bdf032035
Merge pull request #2308 from akohlmey/gpu-unittest 
Add support for testing pair styles in the GPU package
 2021-04-07 15:03:03 -04:00
Axel Kohlmeyer 7b18bc1fec
correctly handle r-RESPA for lj/class2 and lj/class2/gpu 2021-04-07 14:26:27 -04:00
Axel Kohlmeyer 9af086916b
skip GPU tests for a couple more tabulated coulomb tests 2021-04-07 14:11:25 -04:00
Axel Kohlmeyer 6909bc234a
Merge pull request #2700 from rbberger/python_calls_refactor 
Python package refactor
 2021-04-07 13:35:53 -04:00
Axel Kohlmeyer 932ea80b25
update reference data for angle style cosine/periodic 2021-04-06 18:39:37 -04:00
Richard Berger b6776ca3de
Remove GCC optimization pragma for GCC < 4.9 due to compiler segfault 2021-04-06 16:48:18 -04:00
Richard Berger 5af294d49e
Update test_potential_file_reader.cpp 2021-04-06 16:47:06 -04:00
Axel Kohlmeyer 190a689354
Merge branch 'master' into gpu-unittest 
# Conflicts:
#	unittest/force-styles/test_pair_style.cpp
#	unittest/force-styles/tests/angle-cosine_periodic.yaml
#	unittest/force-styles/tests/mol-pair-born.yaml
#	unittest/force-styles/tests/mol-pair-born_coul_dsf.yaml
#	unittest/force-styles/tests/mol-pair-born_coul_long.yaml
#	unittest/force-styles/tests/mol-pair-born_coul_msm.yaml
#	unittest/force-styles/tests/mol-pair-born_coul_msm_table.yaml
#	unittest/force-styles/tests/mol-pair-born_coul_wolf.yaml
#	unittest/force-styles/tests/mol-pair-morse.yaml
#	unittest/force-styles/tests/mol-pair-morse_smooth_linear.yaml
 2021-04-06 14:45:06 -04:00
Axel Kohlmeyer 698b9b9519
relax epsilon some more 2021-04-06 13:36:27 -04:00
Axel Kohlmeyer db400c91ae
relax error a little bit to avoid failure on macos 2021-04-06 11:37:59 -04:00
Axel Kohlmeyer 7e57d6a334
add tests for "rerun" 2021-04-05 16:01:27 -04:00
Axel Kohlmeyer e00e2676fc
add tests for utils::open_potential() 2021-04-04 22:23:13 -04:00
Axel Kohlmeyer a858c07e8a
add unit tests for empty id, invalid timespecs, and merge sort 2021-04-04 21:51:48 -04:00
Axel Kohlmeyer 67d4302fc7
add tests for tokenizer skip() function and throwing an exception 2021-04-04 21:51:06 -04:00
Axel Kohlmeyer d1b6aaa3f3
plugins also have a .so suffix on MacOS (unlike shared libs) 2021-04-04 20:57:29 -04:00
Axel Kohlmeyer 7244ccf8b1
update format 2021-04-03 11:04:02 -04:00
Axel Kohlmeyer cfc39b5a73
complete porting python neighborlist test to c-library version 2021-04-03 10:44:07 -04:00
Axel Kohlmeyer 1a48667026
add minimal test for neighbor list functions 2021-04-03 10:25:14 -04:00
Axel Kohlmeyer cea4298946
silence LAMMPS output, if requested 2021-04-03 10:25:03 -04:00
Axel Kohlmeyer 5520d6edd7
confirm that no incompatible neighbor lists are found 2021-04-03 10:24:46 -04:00
Axel Kohlmeyer 432ccffb3e
find manybody potentials 2021-04-03 10:23:31 -04:00
Axel Kohlmeyer 50b789cc36
Merge branch 'master' into neighlist-interface-updates 2021-04-03 10:18:28 -04:00
Axel Kohlmeyer d3b2ccf9dd
numpy version of neighbor list tests 2021-04-02 21:41:26 -04:00
Axel Kohlmeyer 85a5698c1b
add find method to neighbor list wrapper classes 2021-04-02 21:41:08 -04:00
Axel Kohlmeyer c74bb9b56b
add more unit tests for neighbor list access 2021-04-02 21:00:26 -04:00
Axel Kohlmeyer 66e885b6e5
Merge branch 'master' into collected-small-changes 
# Conflicts:
#	src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp
#	src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp
 2021-04-02 17:57:54 -04:00
Axel Kohlmeyer b976c2d13c
Merge pull request #2679 from akohlmey/more-unittests 
Expand unit tests
 2021-04-02 17:51:29 -04:00
Axel Kohlmeyer 2c00136f22
used correct suffix when installing plugin binaries for testing 2021-04-02 17:49:15 -04:00
Axel Kohlmeyer c62b1b1050
Merge remote-tracking branch 'github/master' into collected-small-changes 2021-04-02 16:08:51 -04:00
Axel Kohlmeyer c4f59764d4
reformat pair_coeff section that got misformatted as string 2021-04-02 15:28:09 -04:00
Axel Kohlmeyer e613da98d6
Merge pull request #2650 from akohlmey/plugin-loader 
New PLUGIN package with a LAMMPS plugin loader command
 2021-04-02 15:08:44 -04:00
Axel Kohlmeyer 887eb40ad4
fix crash when requesting verbose output. 2021-04-02 12:07:59 -04:00
Axel Kohlmeyer 2dfafe4adb
add is_file() special variable function and unit tests for it 2021-04-02 12:07:43 -04:00
Axel Kohlmeyer c3eb52f46a
add force tests for USER-YAFF pair styles 2021-04-01 12:43:24 -04:00
Axel Kohlmeyer 3668ce1374
Merge branch 'master' into more-unittests 
# Conflicts:
#	unittest/testing/core.h
 2021-04-01 11:11:18 -04:00
Axel Kohlmeyer 0b60650c1b
Merge branch 'master' into collected-small-changes 2021-04-01 10:11:59 -04:00
Axel Kohlmeyer 21c934d2cd
Merge pull request #2682 from rbberger/python_unittests 
Python package unit tests
 2021-04-01 10:11:26 -04:00
Axel Kohlmeyer e0aec1b5d9
remove obsoleted comment 2021-04-01 09:39:17 -04:00
Axel Kohlmeyer eea2f45a95
force newton bond to be on since we don't support it to be off (yet) 2021-03-30 17:19:28 -04:00
Axel Kohlmeyer 20e6174e59
cannot use tokenizer for parse_args() as the search for commata must be away of parenthesis 2021-03-29 21:11:07 -04:00
Richard Berger 213fc06321
Add GzFileWriter implementation 2021-03-29 18:05:04 -04:00
Axel Kohlmeyer ddaeabf4d3
Merge branch 'more-unittests' of github.com:akohlmey/lammps into more-unittests 2021-03-29 16:18:38 -04:00
Axel Kohlmeyer ea808b8563
Merge branch 'master' into more-unittests 2021-03-29 15:27:26 -04:00
Richard Berger 6f986eee4e
Add missing changes 2021-03-29 15:01:29 -04:00
Richard Berger aaf9aa6d69
Refactoring of more tests 2021-03-29 14:27:42 -04:00
Axel Kohlmeyer 180d2895c4
Merge pull request #2678 from akohlmey/collected-small-changes 
Collected small changes and fixes
 2021-03-29 14:05:08 -04:00
Richard Berger 1752bd0276
Refactoring of some test files 2021-03-26 12:23:58 -04:00
Richard Berger 664335420a
Start refactoring tests 2021-03-26 11:50:58 -04:00
Richard Berger b1efdda75c
Merge remote-tracking branch 'origin/master' into more-unittests 2021-03-26 11:35:22 -04:00
Richard Berger 029db1413e
Add missing verbose after merge 2021-03-25 21:01:32 -04:00
Richard Berger 439bc4bb8e
Merge remote-tracking branch 'origin/master' into python_unittests 2021-03-25 20:58:28 -04:00
Richard Berger cb25e4aa39
Add nve respa testcase for python/move 2021-03-25 20:34:25 -04:00
Axel Kohlmeyer a193d9d429
fix several issues when using extract_global() from python exposed by tests 2021-03-25 20:34:25 -04:00
Axel Kohlmeyer b8f02d759a
add support for extracting respa levels and timestep values 2021-03-25 20:34:25 -04:00
Axel Kohlmeyer e0fdd2ad89
correct lammps.extract_global() method for returned arrays which are returned as list 2021-03-25 20:34:24 -04:00