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10847 Commits

Author SHA1 Message Date
Steve Plimpton a0592d1b64 Merge branch 'gitignore-improvements' into integration 2016-08-26 13:54:29 -06:00
Axel Kohlmeyer 9be235d872 improved .gitignore files to show only changes in relevant folders and files 2016-08-26 14:34:42 -04:00
Steve Plimpton 2beecd1e73 removal of doc/html/_sources and minor sync with SVN 2016-08-26 11:34:37 -06:00
Richard Berger 95aabdf51a Add MacOS X instructions to doc generation README 2016-08-26 10:08:22 -04:00
Richard Berger ea368919f3 Remove sha1sum dependency for doc generation 
On MacOS X there is no sha1sum. So to simplify doc generation on those systems
use a Python script instead to generate a unique string from the repository
path.
 2016-08-26 00:01:34 -04:00
Axel Kohlmeyer 74516b571e port Make.py so it is compatible with python 2.7 *and* python 3.x 2016-08-25 06:30:53 -04:00
Anders Hafreager b06fa5670a find functions in atom.cpp checks for id/name being NULL 
(cherry picked from commit f7e741f344)
 2016-08-25 06:00:58 -04:00
Anders Hafreager a635c70a26 Fixed so we test for compute,fix and variable id's being NULL in find_ functions 
(cherry picked from commit 12e1857e30)
 2016-08-25 06:00:58 -04:00
Stefan Paquay b8e7f53017 Small update for USER-MANIFOLD docs. 
(cherry picked from commit d188bdbd86)
 2016-08-24 23:36:04 -04:00
Axel Kohlmeyer 849cec3400 fix memory leak in compute omega/chunk 
(cherry picked from commit e8d0342503)
 2016-08-24 23:15:08 -04:00
Axel Kohlmeyer a692398b6c fix bug in reserving sufficient space for special atoms 
assigning atom->maxspecial will not work, since it will be reset, e.g. when reading from a data file that doesn't have any special neighbors.
instead we need to set force->special_extra so this is going to be preserved.
 2016-08-24 23:08:03 -04:00
Axel Kohlmeyer ff541e9a84 fix typo in compute omega/chunk usage example 2016-08-24 23:04:27 -04:00
Anders Hafreager 7d43f349e6 Fixed initialization of arrays in computes 2016-08-24 17:26:04 -04:00
Anders Hafreager 5e811f16e8 Fixed initialization of arrays in computes 2016-08-24 17:26:03 -04:00
Anders Hafreager fcd54f02e6 Fixed initialization of arrays in computes 2016-08-24 17:26:03 -04:00
Anders Hafreager 1f3ef8e0ee Fixed initialization of arrays in computes 2016-08-24 17:26:03 -04:00
Anders Hafreager 3e793d6eb7 Fixed initialization of arrays in computes 2016-08-24 17:26:03 -04:00
Anders Hafreager 95dde5c041 Fixed initialization of arrays in computes 2016-08-24 17:26:02 -04:00
Anders Hafreager d09a85733b Fixed initialization of arrays in computes 2016-08-24 17:26:02 -04:00
Anders Hafreager 0e7ce194eb Fixed initialization of arrays in computes 2016-08-24 17:26:02 -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
Steve Plimpton e27196e91c doc files 2016-08-23 16:28:36 -06:00
Steve Plimpton 268fdab71b Merge branch 'small-bugfixes' into integration 2016-08-23 15:39:27 -06:00
Steve Plimpton 8750515cc4 changed dump.cpp back to the way it was 2016-08-23 15:38:38 -06:00
Steve Plimpton 270b07b035 Merge branch 'integration' into small-bugfixes 2016-08-23 15:35:31 -06:00
Steve Plimpton abc5a32c8a gpu lib sync 2016-08-23 15:30:01 -06:00
Steve Plimpton 0a3464eb30 test 2016-08-23 15:27:02 -06:00
Axel Kohlmeyer 1ab3891caf Merge branch 'merge-pull-153' into lammps-icms 
Submitted by Steven E. Strong via github
Contributing authors: Steven E. Strong and Joel D. Eaves   Joel.Eaves@Colorado.edu

This branch implements Gaussian dynamics (GD), which is a method to do
nonequilibrium molecular dynamics simulations of steady-state flow. See
http://dx.doi.org/10.1021/acs.jpclett.6b00748. It is simple to implement
and derives rigorously from Gauss's principle of least constraint.

(cherry picked from commit 75929ee01b)
 2016-08-23 15:33:16 -04:00
athomps 55fe1f6b29 fixed integer division problem in python code snippet 
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15486 f3b2605a-c512-4ea7-a41b-209d697bcdaa
 2016-08-22 22:35:23 +00:00
Axel Kohlmeyer 50a82bb345 address uninitialized variable issues pointed out by valgrind/coverity 2016-08-22 15:49:33 -04:00
Axel Kohlmeyer 5909bd5429 correct bug in tracking atom->nlocal vs. atom->nmax when allocating pbc enforcement buffers 
(cherry picked from commit 45a2dd36d0)
 2016-08-22 14:36:47 -04:00
Axel Kohlmeyer 1383684048 fix bug in recent dump changes for -DLAMMPS_BIGBIG 
(cherry picked from commit a507936878)
 2016-08-22 14:36:47 -04:00
Richard Berger 587bafdf2d Remove memory leak and unnecessary allocation 
(cherry picked from commit c998f7b81f)
 2016-08-22 14:36:46 -04:00
Richard Berger c8fe3799ed Add missing initialization 
(cherry picked from commit 054256cf0a)
 2016-08-22 14:36:46 -04:00
Axel Kohlmeyer 9babb7a4c2 fix indexing bugs in accessing compute and fix labels in fix ave/histo 
(cherry picked from commit 579c527718)
 2016-08-22 14:35:32 -04:00
Axel Kohlmeyer c88e9b46cf thread timing summare needs to be marked as preformatted 
(cherry picked from commit b745636a67)
 2016-08-22 14:35:11 -04:00
Axel Kohlmeyer 730e3cb4ac correct small (but harmless) logic error. 
(cherry picked from commit ac6f4f8a56)
 2016-08-22 14:34:43 -04:00
Axel Kohlmeyer 2a6561e52a add run 0 to USER-TALLY examples to enforce shake constraints on step 0 
(cherry picked from commit 433741564d)
 2016-08-22 14:32:47 -04:00
sjplimp 2fff78a78e git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15484 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-08-20 22:43:04 +00:00
sjplimp d4891754c8 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15483 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-08-20 22:42:24 +00:00
sjplimp ccf8cf20b3 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15482 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-08-20 22:42:17 +00:00
sjplimp 6ccf4b4525 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15481 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-08-20 22:41:29 +00:00
sjplimp bfba361f65 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15480 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-08-20 22:22:00 +00:00
sjplimp b1829c107c git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15479 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-08-13 15:03:16 +00:00
sjplimp 832f6a9f11 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15475 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-08-13 14:52:15 +00:00
sjplimp 6503590875 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15474 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-08-13 14:51:00 +00:00
sjplimp 2c9eef57d0 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15473 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-08-13 14:49:57 +00:00
sjplimp c03252f08d git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15471 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-08-12 14:34:16 +00:00
sjplimp ff933712b7 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15470 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-08-12 14:33:36 +00:00
sjplimp 112c98159b git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15469 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-08-12 13:49:50 +00:00