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126 Commits

Author SHA1 Message Date
Richard Berger a4c8c9b1f9 Strip IPython notebooks of output 2016-09-21 11:35:00 -04:00
Richard Berger f1183cb97c Remove old copies of IPython notebooks 2016-09-21 11:28:15 -04:00
Richard Berger 04eadb6341 Merge remote-tracking branch 'akohlmey/integration' into library_interface_abort 2016-09-20 16:41:36 -04:00
Richard Berger f4263e3849 Simplify MPI abort code path, make C++ exceptions optional 2016-09-20 16:16:36 -04:00
Axel Kohlmeyer aa9fe38c5c consolidate ignoring python bytecompiled cache files 2016-09-17 09:50:49 -04:00
Richard Berger 8db7ef4364 Merge remote-tracking branch 'akohlmey/integration' into library_interface_abort 2016-09-16 18:46:43 -04:00
Richard Berger 76d876f861 Allow detection of MPI_Abort condition in library call 
The return value of `lammps_get_last_error_message` now encodes if the last
error was recoverable or should cause an `MPI_Abort`. The driving code is
responsible of reacting to the error and calling `MPI_Abort` on the
communicator it passed to the LAMMPS instance.
 2016-09-15 22:11:58 -04:00
Richard Berger 5cdc48dd0c Update ipython example to show interface usage 2016-09-14 16:26:19 -04:00
Richard Berger 0ec8fa02e0 Make thermo output accessable through PyLammps 
Thermo data of the last run is now accessable through the `last_run.thermo`
property. This is a dictionary containing the data columns of thermo output.
All run data is kept as list and can be found in the `runs` property.
See issue #144
 2016-09-14 16:14:41 -04:00
Richard Berger 6e3705f380 Allow writing input script from Python session 
This implements the requested feature in issue #145. The `write_script`
method now gives you a way of dumping out all used commands into a
LAMMPS input script file.

Note: this also dumps all commands which are indirectly issued by PyLammps
 2016-09-14 14:24:19 -04:00
sjplimp 1c3302d1db Merge pull request #15 from rbberger/pylammps-improvements 
PyLammps improvements
 2016-08-31 16:34:59 -06:00
Richard Berger 6cbdad7a97 Add utility function to IPyLammps for embedding videos 2016-08-30 11:34:16 -04:00
Richard Berger a08cf7a4b6 Add verbose option in PyLammps methods 
This option allows forcing LAMMPS output to be printed to the console.
 2016-08-30 11:34:16 -04:00
Richard Berger 691de01b33 Allow setting the position of atoms 2016-08-30 11:34:16 -04:00
Richard Berger 33a87a470a Return 2D vectors in 2D cases 2016-08-30 11:34:15 -04:00
Richard Berger 59dc83eadb Fix resource leak 2016-08-30 11:34:15 -04:00
Richard Berger e5c37bc7cb Implemented optional C++ exceptions in Error class 
These can be activated using the -DLAMMPS_EXCEPTIONS compiler flag.
It has no effect for regular execution. However, while using
it as a library, any issued command will capture the exception
and save its error message. This can be queried using the
lammps_has_error() and lammps_get_last_error_message() methods.

The Python wrapper checks these in order to rethrow these errors
as Python exceptions. See issue #146.

(cherry picked from commit 6c154bb0b67a13d38968bc42d31013b97f87db75)
 2016-08-24 15:31:30 -04:00
sjplimp 7dc6873c51 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15360 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-07-22 22:59:39 +00:00
sjplimp 952a0d1fb7 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15359 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-07-22 22:58:42 +00:00
sjplimp 778f4d338c git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15358 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-07-22 22:57:54 +00:00
sjplimp 80fce623ec git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15326 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-07-15 22:59:07 +00:00
sjplimp 194a512168 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15087 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-05-31 16:45:20 +00:00
sjplimp c3a95c782b git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15039 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-05-12 13:53:40 +00:00
sjplimp a70623ee43 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14592 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-02-15 15:30:15 +00:00
sjplimp 87a47d8b99 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14330 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2015-12-09 21:33:03 +00:00
sjplimp 900a3aaf9d git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14328 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2015-12-09 21:10:06 +00:00
sjplimp 6eed163c7b git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14327 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2015-12-09 21:09:58 +00:00
sjplimp e000e4a04f git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14326 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2015-12-09 21:09:50 +00:00
sjplimp b10ae0abaf git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14270 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2015-11-21 00:35:23 +00:00
sjplimp ae980d6fd1 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13986 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2015-09-02 20:41:38 +00:00
sjplimp 79e142b2ca git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13511 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2015-07-02 19:09:11 +00:00
sjplimp fb2a894e03 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13236 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2015-03-17 16:02:06 +00:00
sjplimp 6f706543fe git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13233 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2015-03-13 22:06:20 +00:00
sjplimp 3b9563910e git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12173 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2014-07-07 19:19:55 +00:00
sjplimp 87d0ff963b git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12098 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2014-06-06 23:44:49 +00:00
sjplimp d5a5342355 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12097 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2014-06-06 23:41:42 +00:00
sjplimp f4a776d4c3 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11247 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2014-01-17 16:11:02 +00:00
sjplimp 44917aeac7 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10064 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2013-06-10 15:01:35 +00:00
sjplimp d91cbdf923 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10063 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2013-06-10 15:01:13 +00:00
sjplimp 3ba07ca1e6 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9641 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2013-03-11 21:37:15 +00:00
sjplimp ed53c9d2d5 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9036 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2012-11-07 15:59:05 +00:00
sjplimp 8663c92293 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9012 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2012-10-25 16:36:45 +00:00
sjplimp 13dd457ae7 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9001 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2012-10-25 15:23:26 +00:00
sjplimp e2283d1609 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9000 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2012-10-25 15:21:37 +00:00
sjplimp f865058700 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8999 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2012-10-25 15:21:33 +00:00
sjplimp d4215d8844 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8675 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2012-08-16 21:16:03 +00:00
sjplimp 2e7bd3367f git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8672 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2012-08-15 19:49:01 +00:00
sjplimp 4486372868 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8670 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2012-08-15 14:34:23 +00:00
sjplimp 6139908a11 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8664 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2012-08-14 23:08:53 +00:00
sjplimp 7487754a4d git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8659 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2012-08-14 20:20:39 +00:00
sjplimp 7f5e8cb896 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8656 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2012-08-14 20:13:20 +00:00
sjplimp 1512b14f98 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8649 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2012-08-14 15:40:43 +00:00
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sjplimp 6f4f134d4d git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8630 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2012-08-13 22:13:06 +00:00
sjplimp 0ea3d01f09 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8616 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2012-08-13 16:12:54 +00:00
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sjplimp c6878811f0 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8602 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2012-08-10 23:13:26 +00:00
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