Diffusion lammps (master) History

lammps/src
masterf3b15d6262e42883c2e26e7…

Sep 1 2015

add access to Universe::numver in info and variable
f3b15d6262e4
·Axel Kohlmeyer on Sep 1 2015, 00:03.
fix bugs in version string parser and output
42c0a76c6617
·Axel Kohlmeyer on Sep 1 2015, 00:03.

Aug 31 2015

add code to compute and provide a "comparable" numeric version id in Universe
b6c07bddc68c
·Axel Kohlmeyer on Aug 31 2015, 23:42.
remove isdef() function. will be replaced with a more generic solution
b15ee604a0ac
·Axel Kohlmeyer on Aug 31 2015, 23:42.
enforce that Universe::version is readonly
bf608bb71a9a
·Axel Kohlmeyer on Aug 31 2015, 22:10.
make sure that pointer are set NULL, if not used (compute fep).
7f432adc625b
·Axel Kohlmeyer on Aug 31 2015, 20:42.

Aug 29 2015

we cannot access comm after it has been deleted
ecd3cd9dcc39
·Axel Kohlmeyer on Aug 29 2015, 13:07.
fix stupid typo
70ad223e2a5a
·Axel Kohlmeyer on Aug 29 2015, 12:48.
Merge remote-tracking branch 'lammps-ro/master' into merge-upstream
d38957c1c0b5
·Axel Kohlmeyer on Aug 29 2015, 12:42.
fix typo
a6a64f3790f1
·Axel Kohlmeyer on Aug 29 2015, 12:23.
undo generic exception handler.
62ca7bdadd37
·Axel Kohlmeyer on Aug 29 2015, 12:22.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13964 f3b2605a-c512-4ea7…
d95acaced031
·sjplimp on Aug 29 2015, 02:19.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13958 f3b2605a-c512-4ea7…
272640d9dfc8
·sjplimp on Aug 29 2015, 01:51.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13957 f3b2605a-c512-4ea7…
546ccbe611a9
·sjplimp on Aug 29 2015, 01:51.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13952 f3b2605a-c512-4ea7…
6b854b397c17
·sjplimp on Aug 29 2015, 01:41.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13951 f3b2605a-c512-4ea7…
4e247c3b8cc1
·sjplimp on Aug 29 2015, 01:36.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13949 f3b2605a-c512-4ea7…
42968083e975
·sjplimp on Aug 29 2015, 01:35.

Aug 28 2015

avoid NULL pointer dereferences
a7aaefa836a5
·Axel Kohlmeyer on Aug 28 2015, 23:30.
be safe(r) from NULL pointer dereferences in case a processor hold no atoms
657b6896321c
·Axel Kohlmeyer on Aug 28 2015, 23:17.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13945 f3b2605a-c512-4ea7…
1fe96eb3d503
·sjplimp on Aug 28 2015, 22:45.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13940 f3b2605a-c512-4ea7…
cc7cb875847b
·sjplimp on Aug 28 2015, 22:06.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13937 f3b2605a-c512-4ea7…
ce59e32d1cf6
·sjplimp on Aug 28 2015, 22:00.
test more thoroughly for correct input on molecule file
2d37388dff08
·Axel Kohlmeyer on Aug 28 2015, 21:56.
assign color to "white" for a few 'cannot happen' cases
b06726c384a9
·Axel Kohlmeyer on Aug 28 2015, 21:27.
harden the code to not try balance a non-existing dimension
7eef1ddfeb1a
·Axel Kohlmeyer on Aug 28 2015, 21:18.
directory paths and install script were still broken for USER-H5MD
0391af765027
·Axel Kohlmeyer on Aug 28 2015, 21:06.

Aug 27 2015

Merge branch 'lammps-icms' of bitbucket.org:akohlmey/lammps-icms into lammps…
962e5442e142
·Axel Kohlmeyer on Aug 27 2015, 23:23.
be more paranoid with output file handling. stop, if there are i/o errors.
ac6de96dda48
·Axel Kohlmeyer on Aug 27 2015, 22:26.
fix permissions for source files
db891e156789
·Axel Kohlmeyer on Aug 27 2015, 16:56.
simplify variable lookup, avoid new/copy/delete sections, fix logic bug.
111eb143b96a
·Axel Kohlmeyer on Aug 27 2015, 16:33.
correct possible infinite loop
dee560327276
·Axel Kohlmeyer on Aug 27 2015, 15:46.
make checks for illegal run arguments safer and remove useless tests
361b2e0e35d4
·Axel Kohlmeyer on Aug 27 2015, 15:42.
remove pointless overflow test
c37f0a62f975
·Axel Kohlmeyer on Aug 27 2015, 15:35.
avoid division by zero and flag error on illegal range delta
bbb4b92a3661
·Axel Kohlmeyer on Aug 27 2015, 14:52.
remove useless test for overflow
eef3a36899b0
·Axel Kohlmeyer on Aug 27 2015, 14:26.
plug small memory leak
8102b35eb1fb
·Axel Kohlmeyer on Aug 27 2015, 05:38.
plug small memory leak
13b92a757700
·Axel Kohlmeyer on Aug 27 2015, 05:33.
initialize indexlo/indexhi
24d6caec2dba
·Axel Kohlmeyer on Aug 27 2015, 05:27.
delete useless tests for fp != NULL
ee7f72006e29
·Axel Kohlmeyer on Aug 27 2015, 05:22.
initialize periodicity to illegal value and handle short reads
941f4f001a5f
·Axel Kohlmeyer on Aug 27 2015, 05:13.
more read_restart paranoia
e4332c100cfe
·Axel Kohlmeyer on Aug 27 2015, 04:53.
flag case of negative buffer read request as error
76bbbfe537ec
·Axel Kohlmeyer on Aug 27 2015, 04:36.
make read_int/bigint/double() return -1/-1/0.0 on short reads
05570750a23f
·Axel Kohlmeyer on Aug 27 2015, 02:53.

Aug 26 2015

make sure string buffers are reset to empty before parsing or after read…
5576ecfcfe7f
·Axel Kohlmeyer on Aug 26 2015, 23:24.
make USER-TALLY package compatible with USER-OMP. add another safeguard against…
eb97abc636d5
·Axel Kohlmeyer on Aug 26 2015, 21:34.
undo bogus bugfix and add comments explaining the situation.
116ce148759e
·Axel Kohlmeyer on Aug 26 2015, 20:44.
add another array that needs to be copied in the comm copy constructor
b551971c6e8d
·Axel Kohlmeyer on Aug 26 2015, 17:51.
procgrid was not copied when initializing new comm style.
7e1e631f0d00
·Axel Kohlmeyer on Aug 26 2015, 14:03.
need to set pointers immediately to NULL to force segfault if used after delete
823c23787ee8
·Axel Kohlmeyer on Aug 26 2015, 13:30.
make sure unregister calls are not done during lammps class teardown
8a9e08c67ab0
·Axel Kohlmeyer on Aug 26 2015, 13:29.
make more destuctors virtual to ensure proper order of calls
d8ee06fb4a82
·Axel Kohlmeyer on Aug 26 2015, 13:17.
make sure cutneighmax is initialized early
b232161ff652
·Axel Kohlmeyer on Aug 26 2015, 12:27.
fix serious bug Comm class initialization
7b1f3f027f29
·Axel Kohlmeyer on Aug 26 2015, 12:27.
fix nasty USER-OMP bug for systems with few atoms
59ce36fa360d
·Axel Kohlmeyer on Aug 26 2015, 06:52.
remove obsolete, undocumented or unused styles
7746cf6aae01
·Axel Kohlmeyer on Aug 26 2015, 06:38.
remove unused flag from package omp command
ace1f1eb75b7
·Axel Kohlmeyer on Aug 26 2015, 06:25.
remove broken and unused pppm/tip4p/cg kspace style
5049cb79a295
·Axel Kohlmeyer on Aug 26 2015, 06:25.
fix bracketing bug. duh!
016c64ba1293
·Axel Kohlmeyer on Aug 26 2015, 04:19.
cutghostuser needs to be set to then MAX of the cutusermulti values
3748ec5d817e
·Axel Kohlmeyer on Aug 26 2015, 04:18.
provide additional info for communication including cutoffs
56ee125fc402
·Axel Kohlmeyer on Aug 26 2015, 03:28.
avoid a NULL pointer dereference
cf770da486b3
·Axel Kohlmeyer on Aug 26 2015, 02:03.
need to propagate error status so that Travis CI fails on crashing tests
5a04aee0de51
·Axel Kohlmeyer on Aug 26 2015, 02:03.
implemented a comm_modify cutoff/multi feature suggested by martin wagner
0989c9dabe86
·Axel Kohlmeyer on Aug 26 2015, 00:46.

Aug 25 2015

add proper tests and warning to USER-TALLY computes. fix index bug.
ac77971f8815
·Axel Kohlmeyer on Aug 25 2015, 23:38.
remove direct HDF5 API call from main code; redirect to wrapper library instead
06f8fa153c1f
·Axel Kohlmeyer on Aug 25 2015, 00:05.

Aug 24 2015

Merge branch 'master' of git://github.com/pdebuyl/lammps into h5md-fix
dd5d7ec3b1fb
·Axel Kohlmeyer on Aug 24 2015, 21:50.
do not throw an error if a thermostatted group has no DOFs. just do nothing.
9fe16d70f2d6
·Axel Kohlmeyer on Aug 24 2015, 16:31.

Aug 22 2015

Merge remote-tracking branch 'lammps-ro/master' into lammps-icms
4818ebab50e4
·Axel Kohlmeyer on Aug 22 2015, 12:25.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13933 f3b2605a-c512-4ea7…
01447fe9137a
·sjplimp on Aug 22 2015, 02:20.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13932 f3b2605a-c512-4ea7…
16d803e49eed
·sjplimp on Aug 22 2015, 02:18.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13931 f3b2605a-c512-4ea7…
3841dd58ca37
·sjplimp on Aug 22 2015, 00:55.

Aug 21 2015

fix initializing in the wrong constructor.
d1405527d857
·Axel Kohlmeyer on Aug 21 2015, 22:08.
safer handling of file pointers when reading/writing dumps and restarts
cba234e499e5
·Axel Kohlmeyer on Aug 21 2015, 19:51.
fix h5md library path
2da8a12e38f0
·Pierre de Buyl on Aug 21 2015, 14:42.
Merge remote-tracking branch 'lammps-ro/master' into lammps-icms
187e0b9ce49b
·Axel Kohlmeyer on Aug 21 2015, 12:48.
make the /tally computes a separate user-package.
3c62ef616bd6
·Axel Kohlmeyer on Aug 21 2015, 02:29.
get rid of obsolete and unmaintained support for MSVC++
e75f24fd429a
·Axel Kohlmeyer on Aug 21 2015, 02:04.
enforce initialization of pbc_flag to NULL.
3e3a14688a54
·Axel Kohlmeyer on Aug 21 2015, 00:47.

Aug 20 2015

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13928 f3b2605a-c512-4ea7…
717ecf0a095a
·sjplimp on Aug 20 2015, 23:38.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13927 f3b2605a-c512-4ea7…
01004c314aa2
·sjplimp on Aug 20 2015, 20:59.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13924 f3b2605a-c512-4ea7…
f842d1ba4151
·sjplimp on Aug 20 2015, 17:44.
Merge remote-tracking branch 'lammps-ro/master' into lammps-icms
e5f316ecf1f8
·Axel Kohlmeyer on Aug 20 2015, 13:42.
Adding optimizations to Kokkos EAM pair style
e4e52616dd89
·stamoor on Aug 20 2015, 00:50.

Aug 19 2015

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13918 f3b2605a-c512-4ea7…
8dae768dcf52
·sjplimp on Aug 19 2015, 18:15.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13910 f3b2605a-c512-4ea7…
cd861535f0d9
·sjplimp on Aug 19 2015, 17:32.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13909 f3b2605a-c512-4ea7…
56d0caefcb66
·sjplimp on Aug 19 2015, 17:23.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13905 f3b2605a-c512-4ea7…
c85a42ab6d62
·sjplimp on Aug 19 2015, 17:11.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13903 f3b2605a-c512-4ea7…
2f55b6da36a3
·sjplimp on Aug 19 2015, 16:55.
remove stray debug printf
2b71bee849ca
·Axel Kohlmeyer on Aug 19 2015, 13:15.
Merge remote-tracking branch 'lammps-ro/master' into lammps-icms
62b18db5921f
·Axel Kohlmeyer on Aug 19 2015, 13:15.
initialize return value
0c5f1d17b227
·Axel Kohlmeyer on Aug 19 2015, 04:55.
initialize pointer to pRNG.
ff62b51dea76
·Axel Kohlmeyer on Aug 19 2015, 04:53.
fix missing initialization
112568605fcd
·Axel Kohlmeyer on Aug 19 2015, 04:50.
better bugfix for OOB access in fix balance
5a93085e460d
·Axel Kohlmeyer on Aug 19 2015, 04:46.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13895 f3b2605a-c512-4ea7…
4d1904165b04
·sjplimp on Aug 19 2015, 01:22.
avoid segfault when evaporating by molecule id in a non-molecular system
1317dba8a07f
·Axel Kohlmeyer on Aug 19 2015, 01:10.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13892 f3b2605a-c512-4ea7…
dc2ebd0393b3
·sjplimp on Aug 19 2015, 00:59.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13891 f3b2605a-c512-4ea7…
6da9e4c21765
·sjplimp on Aug 19 2015, 00:54.
remove file pointer leak
efff543e9f5d
·Axel Kohlmeyer on Aug 19 2015, 00:20.

Aug 18 2015

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13890 f3b2605a-c512-4ea7…
adabfc38a6b8
·sjplimp on Aug 18 2015, 23:50.

lammps/srcmasterf3b15d6262e42883c2e26e7…

Sep 1 2015

Aug 31 2015

Aug 29 2015

Aug 28 2015

Aug 27 2015

Aug 26 2015

Aug 25 2015

Aug 24 2015

Aug 22 2015

Aug 21 2015

Aug 20 2015

Aug 19 2015

Aug 18 2015

lammps/src
masterf3b15d6262e42883c2e26e7…