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11773 Commits

Author SHA1 Message Date
Steve Plimpton 8756a1017d Kokkos updates by Stan 2016-11-17 08:58:22 -07:00
dstelter92 5c64934bc8 added documention, re-ran temper_grem example 2016-11-17 10:40:10 -05:00
Axel Kohlmeyer 4e62e58d29 Merge pull request #47 from dstelter92/grem-feature 
added internal tempering in grem with example
 2016-11-17 10:04:43 -05:00
dstelter92 5ac2d9532e Re-run example with debug off 2016-11-17 09:43:44 -05:00
dstelter92 19ac9d2959 turned off dev mode by default in temper_grem 2016-11-17 09:31:07 -05:00
dstelter92 9f313aac75 shorter example 2016-11-16 20:43:41 -05:00
dstelter92 0102c5dadc file cleanup 2016-11-16 20:38:53 -05:00
dstelter92 07e46b797a added internal tempering in grem with example 2016-11-16 20:27:14 -05:00
Axel Kohlmeyer b45d1e37ef integrate fix grem docs and update to match current conventions 2016-11-16 16:46:00 -05:00
Axel Kohlmeyer 2e7fd513d4 provide fix grem example input for nvt and npt 2016-11-16 16:42:01 -05:00
Axel Kohlmeyer 82364d10e3 Merge branch 'grem-feature' of https://github.com/dstelter92/lammps into grem-feature 
Resolved merge conflicts and adapted logic to most recent changes in feature branch

Closes #46
 2016-11-16 16:11:53 -05:00
dstelter92 16c8a307e5 removed leftover tex files 2016-11-16 15:39:02 -05:00
dstelter92 94f14ab051 spell check, minor typos 2016-11-16 15:34:32 -05:00
Axel Kohlmeyer 22d93fe8fb add restrict to CCFLAGS for makefiles intended for intel compilers 2016-11-16 14:31:10 -05:00
Axel Kohlmeyer 683f514fac simplify multi-replica run by passing per-replica parameters as variables on the command line 2016-11-16 14:22:20 -05:00
Axel Kohlmeyer f617993944 need to apply fix_modify already in fix grem constructor 2016-11-16 13:52:27 -05:00
dstelter92 4641c9e568 Added basic documentation for grem fix 2016-11-16 13:36:13 -05:00
Axel Kohlmeyer 705f66aaee remove superfluous code 2016-11-16 13:24:41 -05:00
Axel Kohlmeyer e57ae1ce3f compute scaled kinetic energy tensor without destroying the original data 2016-11-16 12:45:13 -05:00
dstelter92 950442b8b1 added check for nvt vs npt, enabled nvt simulation with fix_grem 2016-11-15 21:53:28 -05:00
Axel Kohlmeyer 1c68e42ecc fix_modify is not longer needed 2016-11-14 13:43:28 -05:00
Axel Kohlmeyer 5f94b31806 add multi-replica example for gREM 2016-11-14 10:12:48 -05:00
Axel Kohlmeyer fdf5d68f9f allow to extract properties in NH integrator only when they are active 2016-11-14 09:27:33 -05:00
Axel Kohlmeyer 0c25f3b1d6 whitespace cleanup 2016-11-13 23:20:09 -05:00
Axel Kohlmeyer 14c7cf4197 retrieve target temperature and pressure from fix npt. add sanity checks. 2016-11-13 23:18:59 -05:00
Axel Kohlmeyer 26870f223d add example for gREM 2016-11-13 23:18:14 -05:00
Axel Kohlmeyer 09544d0698 bugfix for compute pressure/grem: must make a copy of argument strings 2016-11-13 19:19:52 -05:00
Axel Kohlmeyer b5130a3b35 avoid NaN for variance from average output 2016-11-13 18:46:55 -05:00
Axel Kohlmeyer 20daf82463 initial import of adapted gREM code by David Stelter and Edyta Malolepsza 
The following changes were made:
- the modifications to compute pressure were transferred to a derived class compute pressure/grem
- fix scaleforce was renamed to fix grem
- identifying the grem fix was simplified as fix grem passes an additional argument to compute pressure/grem
- dead code was removed in both files
- checking of arguments was tightened
 2016-11-13 18:44:10 -05:00
Axel Kohlmeyer 57124b9b25 update documentation metadata files for recent changes 2016-11-12 09:18:21 -05:00
Axel Kohlmeyer 03b3834fe3 add documentation for pair style agni 2016-11-12 09:07:42 -05:00
Axel Kohlmeyer d0124eac95 optimized data access and using approximate exponential for USER-OMP version 2016-11-12 08:36:27 -05:00
Axel Kohlmeyer 5685131fe2 add USER-OMP version of pair style agni 2016-11-11 19:08:01 -05:00
Axel Kohlmeyer 22fc92f9d8 use special ev_tally() function suitable for this kind of force compute 2016-11-11 18:32:55 -05:00
Axel Kohlmeyer b9770766a8 add adatom and vacancy examples for AGNI pair style 2016-11-11 18:19:29 -05:00
Axel Kohlmeyer 9cc0c8badd error exit when requested element is not in potential file 2016-11-11 18:10:57 -05:00
Axel Kohlmeyer 6e1492a86c add potential file for pair style AGNI 2016-11-11 18:10:26 -05:00
Axel Kohlmeyer 9b0987d8c4 first complete implementation of AGNI pair style 2016-11-11 17:32:47 -05:00
Axel Kohlmeyer e453adaf81 implemented parser for 1 element potential files 2016-11-11 15:53:37 -05:00
Axel Kohlmeyer 8e0fd88697 add example demonstrating the use of fix addtorque 2016-11-11 10:52:50 -05:00
Axel Kohlmeyer fdcabd7d1d fix addtorque is compatible with dynamic groups 2016-11-11 09:01:18 -05:00
Axel Kohlmeyer c5c8c50e97 initialize 'nper' 2016-11-11 07:47:42 -05:00
Axel Kohlmeyer 72b0841b28 Merge branch 'doc-updates' of github.com:akohlmey/lammps into doc-updates 2016-11-11 07:44:44 -05:00
Axel Kohlmeyer 801111a7ab dummy framework implementation for AGNI pair style 2016-11-10 15:00:36 -05:00
Axel Kohlmeyer bfc478c320 simpler variant of the segfault workaround, that does not offend Clang c++. 2016-11-10 14:12:02 -05:00
Axel Kohlmeyer 2b75ee761d avoid segmentation fault, when creating a LAMMPS instance from the library interface. arg[] may be NULL. 2016-11-10 13:28:32 -05:00
Axel Kohlmeyer 352e177fcd Merge branch 'master' into small-fixes-and-updates 2016-11-10 13:26:00 -05:00
Anders Hafreager c20ee34c7b Initializing pointers in VORONOI 2016-11-10 09:30:07 +01:00
Anders Hafreager 95a7f7160e Initialize pointers in POEMS 2016-11-10 09:26:52 +01:00
Axel Kohlmeyer 1f38e1a771 Merge branch 'master' into doc-updates 2016-11-09 18:18:05 -05:00