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21335 Commits

Author SHA1 Message Date
Axel Kohlmeyer 661b0ee8b2
cannot compare Pair::compute() vs. Pair::single for styles with coul/dsf or coul/wolf due to missing self energy 2020-05-31 09:25:50 -04:00
Axel Kohlmeyer 64b684eec3
add tests for a whole bunch of CHARMM pair styles 2020-05-31 08:34:25 -04:00
Axel Kohlmeyer 1493ae5c87
correct force calculation in lj/charmm/coul/msm/omp 2020-05-31 08:33:26 -04:00
Axel Kohlmeyer a820b7d3fc
fix bug in r-RESPA neighborlist setup for lj/charmmfsw/coul/long 2020-05-31 08:33:05 -04:00
Axel Kohlmeyer f7a0f6671c
fix factor 0.5 bug in lj/charmm/coul/charmm/implicit/omp 2020-05-31 07:19:36 -04:00
Axel Kohlmeyer eb60b049fc
add endpoint gradients for two bond tables 2020-05-30 21:49:42 -04:00
Axel Kohlmeyer 91272e7654
output endpoint gradient for some angle tabulations 2020-05-30 21:36:47 -04:00
Axel Kohlmeyer bb8f6e94d3
Merge pull request #2113 from rbberger/tokenizer 
Refactoring to reduce strtok usage
 2020-05-30 21:13:12 -04:00
Axel Kohlmeyer 0f6e963058
add a whole bunch of angle style tests 2020-05-30 21:10:48 -04:00
Axel Kohlmeyer 69ba5ea9f0
use a smaller bond table 2020-05-30 21:05:03 -04:00
Axel Kohlmeyer 814082a23b
Merge pull request #2105 from ndtrung81/rigid-nve-norot 
Fixed an issue with fix rigid/nve for bodies with very small values of inertia moments
 2020-05-30 19:49:08 -04:00
Axel Kohlmeyer f33584cfb2
fix missing factor of 2 bug in single function 2020-05-30 18:37:54 -04:00
Axel Kohlmeyer f4431d0525
remove dead code 2020-05-30 18:00:23 -04:00
Axel Kohlmeyer bd4d4bc015
update bond/angle yaml files for changed equilibrium keyword syntax 2020-05-30 17:51:29 -04:00
Axel Kohlmeyer 1042e16423
change format for equilibrium values and update writer and reader code, so it will become compatible with class2 angles/dihedrals/impropers 2020-05-30 17:50:38 -04:00
Axel Kohlmeyer 07163a710a
correct bond table coefficients to find the table file 2020-05-30 17:22:33 -04:00
Axel Kohlmeyer e32409d32c
add tests for most bond styles except FENE type bonds 2020-05-30 10:44:40 -04:00
Axel Kohlmeyer 1452e6dfca
reduce displacements in single test for pair styles 2020-05-30 10:23:52 -04:00
Axel Kohlmeyer 4c0ce402c1
fix bug in bond style gromos/omp 2020-05-30 10:23:25 -04:00
ndtrung fac897587f Checked for zero inertia moments in a simpler way, similar to what is done in mq_to_omega() 2020-05-30 07:42:34 -05:00
Richard Berger 2b960d94ec
Fix pair_comb3 2020-05-30 08:01:39 -04:00
Axel Kohlmeyer 1ec179e80a
add a few more test inputs 2020-05-29 23:47:15 -04:00
Axel Kohlmeyer 43171052d5
fix multiple bugs in pair style tester for Pair::single() 2020-05-29 23:46:37 -04:00
Axel Kohlmeyer 8409e9d2be
Merge pull request #2118 from akohlmey/pair-hybrid-better-check 
Better argument parsing of pair style hybrid
 2020-05-29 22:54:34 -04:00
Axel Kohlmeyer 549ffda4d8
implement better pair style name detection in pair style hybrid arguments 2020-05-29 20:52:21 -04:00
Richard Berger 40cf106b8f
Fix segfault when running with MPI 2020-05-29 19:57:47 -04:00
Richard Berger 7a9590f007
More whitespace 2020-05-29 18:04:20 -04:00
Richard Berger 636a1bffe3
Fix whitespace 2020-05-29 17:25:41 -04:00
Richard Berger 447784212a
Remove d0 in float numbers in ffield.comb 2020-05-29 17:14:41 -04:00
Richard Berger e4d6970ac1
Fix whitespace 2020-05-29 16:32:17 -04:00
Richard Berger 8e1a6bc706
Update pair polymorphic 2020-05-29 16:12:19 -04:00
Axel Kohlmeyer d173ea4ad9
Merge pull request #2114 from akohlmey/more-unittest-changes 
More updates and corrections for unit tests
 2020-05-29 15:33:30 -04:00
Richard Berger 1375c154f9
Update pair eim 2020-05-29 14:58:04 -04:00
Richard Berger 10b0d60709
Fix typo 2020-05-29 14:56:10 -04:00
Axel Kohlmeyer c34501c137
Merge pull request #2116 from jdevemy/master 
Test to avoid bad delete and Seg Fault
 2020-05-29 11:34:14 -04:00
Julien Devemy 1984092135 Test to avoid bad delete and Seg Fault 2020-05-29 15:25:05 +02:00
Axel Kohlmeyer 2a4bd9ef53
small tweaks and documentation update to coverage cleaning targets 2020-05-29 08:33:34 -04:00
Axel Kohlmeyer 7bcf50b129
mention reset_coverage data 2020-05-29 08:26:26 -04:00
Axel Kohlmeyer c2ab177c3a
add some explanations and figures for code coverage 2020-05-29 08:24:05 -04:00
Axel Kohlmeyer 30020594df
add custom target to remove/reset collected coverage data 2020-05-29 08:23:25 -04:00
Richard Berger 0c503ab122
Move coverage html into folder 2020-05-29 08:23:08 -04:00
Axel Kohlmeyer 99c0c1ace1
simplify parsing of equilibrium data 2020-05-29 08:22:34 -04:00
Axel Kohlmeyer 7d62fd5106
remove debug code 2020-05-29 08:22:23 -04:00
Axel Kohlmeyer 797ba373c4
simplify reading key/value pairs from string 2020-05-28 22:38:23 -04:00
Axel Kohlmeyer 08ee1cb4fa
add single test to angle_style, add support for equilibrium data 2020-05-28 22:38:07 -04:00
Axel Kohlmeyer 47e4da4903
add support for writing/reading equilibrium bond/angle data 2020-05-28 22:20:43 -04:00
Axel Kohlmeyer 6ed4103365
synchronize flow of control and formatting between pair_style, bond_style and angle_style 2020-05-28 21:11:38 -04:00
Axel Kohlmeyer 9fc6abb2ef
add tests for pair style polymorphic 2020-05-28 20:43:26 -04:00
Richard Berger 5a4bbcc37a
Update pair vashishta 2020-05-28 16:17:15 -04:00
Richard Berger cadc374e0b
Update pair nb3b harmonic 2020-05-28 16:05:56 -04:00