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588 Commits

Author SHA1 Message Date
dstelter92 d58dd4f159 bugfix when parsing mpirun 2016-11-22 12:13:20 -05:00
dstelter92 ae70f1090f added readme for grem examples 2016-11-22 12:05:14 -05:00
sjplimp ff0441ac16 Merge pull request #286 from akohlmey/small-fixes-and-updates 
Collected small fixes and updates
 2016-11-22 08:49:46 -07:00
dstelter92 dab232c542 modified temper_grem name to fit conventions, re-ran example to match 2016-11-21 12:02:17 -05:00
Axel Kohlmeyer 2862c20815 Merge branch 'master' into grem-feature 2016-11-18 14:51:46 -05:00
Axel Kohlmeyer 78e018829f Merge branch 'grem-feature' of https://github.com/dstelter92/lammps into grem-feature 2016-11-18 14:48:47 -05:00
Axel Kohlmeyer 635f3ce128 synchronize USER-SMD examples with code 2016-11-18 08:09:24 -05:00
dstelter92 2a026c9ad8 revised temper_grem example, better file management 2016-11-17 12:53:25 -05:00
dstelter92 4a3091f844 modified temper_grem example with more exchanges 2016-11-17 11:24:29 -05:00
sjplimp 74c0e4dd5c Merge pull request #278 from akohlmey/pair-agni 
Implementation of the AGNI manybody potential
 2016-11-17 09:04:31 -07:00
sjplimp 073e8a0524 Merge pull request #276 from akohlmey/doc-updates 
Small bugfixes and updates
 2016-11-17 09:02:27 -07:00
sjplimp 2535e44991 Merge pull request #271 from akohlmey/tersoff-modc 
pair style tersoff/mod/c
 2016-11-17 09:00:52 -07:00
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 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
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 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 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 b9770766a8 add adatom and vacancy examples for AGNI pair style 2016-11-11 18:19:29 -05:00
Axel Kohlmeyer 8e0fd88697 add example demonstrating the use of fix addtorque 2016-11-11 10:52:50 -05:00
Steve Plimpton 9806da69f3 Stan bug fixes for fix reaxc/bonds/kk 2016-11-09 15:47:50 -07:00
Axel Kohlmeyer 71ee2ecaa1 integrate pair style tersoff/mod/c contributed by Ganga P Purja Pun (GMU) 
This includes docs, added testing and inclusion of USER-OMP support.
 2016-11-09 14:52:39 -05:00
arielzn 9de1a2a08f added input using born/coul/dsf/cs to examples/coreshell 2016-11-08 18:27:44 +01:00
Steve Plimpton f48b71f46b added examples/threebody, fix reaxc/speceies/kk 2016-11-04 10:56:04 -06:00
Steve Plimpton d9891abdf4 new library functions 2016-10-27 09:34:04 -06:00
Steve Plimpton 2106dce2b3 new fix halt command, other sundry small bug fixes 2016-10-18 13:11:40 -06:00
sjplimp 6f1162927a Merge pull request #207 from timattox/USER-DPD_new_VV_for_DPD 
USER-DPD: add support for using VV with DPD
 2016-10-11 13:39:25 -06:00
Steve Plimpton 04f5eadcf1 added LAST option to dump_modify thresh, more restart info printed out to screen 2016-10-11 12:39:52 -06:00
Tim Mattox 9789f047d7 USER-DPD: update the USER/dpd examples and their reference outputs 2016-10-07 15:55:35 -04:00
Tim Mattox e27ed6c94a USER-DPD: Added support to use VV integrator with USER-DPD if desired. 
Includes documentation and examples.
NOTE: VV requires very small timesteps under isoenergetic conditions.
Consider using fix_shardlow instead, since this VV support is
primarily for comparison purposes.
 2016-10-07 15:03:30 -04:00
sjplimp 54fc194e5b Merge pull request #199 from akohlmey/small-changes 
Collected small changes and bugfixes
 2016-10-06 15:49:24 -06:00
Steve Plimpton b3d2fb91bb new fix wall/gran/region command, REBO bug fix, new example log files 2016-10-06 15:47:41 -06:00
Steve Plimpton 493873fb93 clean up doc src 2016-10-06 13:00:46 -06:00
A Bartok-Partay fd16118cbb removed dump_modify command 2016-10-06 12:02:41 +01:00
Steve Plimpton 02bfa898ee adjustments to balancing weights and factors, also XOR op for formulas, if, dump_modify thresh 2016-10-05 15:46:20 -06:00
Steve Plimpton c46be7db62 changes to imbalance weight factors 2016-10-05 10:33:39 -06:00
sjplimp 91edee2530 Merge pull request #186 from akohlmey/small-bugfixes 
Collected small bugfixes and enhancements
 2016-09-30 09:20:25 -06:00
Steve Plimpton b9d0f96a19 change purge target in Makefile, also fixed one issue with Make.py 2016-09-30 09:17:55 -06:00
Axel Kohlmeyer 4337f2c240 include charmm22 and charmm36 cmap files and include date added signature 2016-09-30 07:39:12 -04:00
Steve Plimpton 446e7e7369 patch for allowing prd command to work with sorted atoms 2016-09-28 16:33:30 -06:00
Steve Plimpton 35705217f4 enable multi-processor NEB replicas 2016-09-27 15:34:08 -06:00
Steve Plimpton 9a2f738673 sync with SVN 2016-09-27 15:32:57 -06:00
Steve Plimpton f9677e6d7b released version of weighted balancing 2016-09-27 10:52:27 -06:00
Axel Kohlmeyer 47b52ed2dd Merge branch 'integration' into balance2 2016-09-26 15:19:48 -04:00
Steve Plimpton b97b9dd661 new fix cmap command 2016-09-26 08:40:53 -06:00
Steve Plimpton 08f0bf9025 new verion of balance weighting 2016-09-23 14:37:53 -06:00
Axel Kohlmeyer b27179bbef restore bugfixes and updates that were lost. flag time dependet. correct use of citeme. 2016-09-21 07:27:37 -04:00
Steve Plimpton b9b044e180 new fix ti/spring command, remove fix ti/rs 2016-09-20 10:44:12 -06:00
sjplimp a69e059be3 Merge pull request #27 from akohlmey/small-bugfixes 
Collected small changes and bugfixes
 2016-09-13 17:11:23 -06:00
Steve Plimpton fe2fca4e9b clean-up of example files 2016-09-13 14:58:02 -06:00
Steve Plimpton 944289b018 final version of pair vashishta/table 2016-09-13 14:45:53 -06:00
Axel Kohlmeyer 18cacb8e1d ignore *.mod generated by fortran compilers 2016-09-13 09:36:19 -04:00
Axel Kohlmeyer 7de5143050 update vashishta pair style example 2016-09-08 17:21:14 -04:00
Steve Plimpton 43b05a60c7 created vashishta/table variant 2016-09-07 11:56:38 -06:00
Axel Kohlmeyer ebce76c7f0 updated and slightly refactored tabulation for vashishta pair style 
- tables are now dimensioned by nelements instead of ntypes
- tables are only created if used
- correctly identify max size of table
- add test for illegal cutoff for tabulation
- allocated memory for tables is accounted for
- add example input using 16-bit tables
 2016-08-27 23:05:17 -04:00
Steve Plimpton c80dad0028 new fix flow/gauss command 2016-08-27 16:25:01 -06:00
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 3349f7e143 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15466 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-08-09 23:25:06 +00:00
athomps 1780c86b86 Fixed error in ave/time version 
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15449 f3b2605a-c512-4ea7-a41b-209d697bcdaa
 2016-08-05 17:53:52 +00:00
sjplimp 3fe162a42d git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15437 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-08-05 15:11:09 +00:00
sjplimp ee86bd2463 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15399 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-07-30 14:45:26 +00:00
sjplimp b3aeb43a93 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15300 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-07-13 21:35:51 +00:00
sjplimp cec2f2518f git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15225 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-06-28 13:23:54 +00:00
sjplimp ab7e896a76 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15150 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-06-07 18:18:53 +00:00
sjplimp 0129ff9696 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15149 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-06-07 18:17:05 +00:00
sjplimp b5abf9342b git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15148 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-06-07 18:16:44 +00:00
sjplimp f3d5260813 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15145 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-06-07 18:00:54 +00:00
sjplimp a5fef35ebd git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15144 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-06-07 18:00:49 +00:00
sjplimp b107958e80 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15143 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-06-07 17:57:47 +00:00
sjplimp 9c5655db7c git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15130 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-06-07 15:51:43 +00:00
sjplimp 5c19a0d788 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15094 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-06-01 15:07:48 +00:00
sjplimp 4c107f450c git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15085 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-05-31 16:39:57 +00:00
sjplimp ac14f5bc36 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15084 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-05-31 16:38:36 +00:00
sjplimp 87e06310cb git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15051 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-05-12 16:29:09 +00:00
sjplimp 62b95b6b34 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15050 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-05-12 16:28:22 +00:00
sjplimp b0eea89503 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15034 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-05-11 20:38:08 +00:00
sjplimp 1463cb2598 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15020 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-05-10 22:39:37 +00:00
athomps 00f3ccf3b0 Added Einstein version of Green-Kubo 
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14846 f3b2605a-c512-4ea7-a41b-209d697bcdaa
 2016-04-18 23:59:16 +00:00
athomps cf26690feb Corrected formula for case lx != ly 
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14820 f3b2605a-c512-4ea7-a41b-209d697bcdaa
 2016-04-12 14:56:22 +00:00
athomps 20f13bf13d Added a script to calculate elastic compliance tensor 
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14819 f3b2605a-c512-4ea7-a41b-209d697bcdaa
 2016-04-12 01:28:58 +00:00
sjplimp 7512821dd6 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14628 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-02-15 21:20:17 +00:00
sjplimp 507bde5b5a git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14627 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-02-15 21:19:55 +00:00
sjplimp ed9e162025 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14626 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-02-15 21:18:29 +00:00
sjplimp 2d43f007d1 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14617 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-02-15 18:32:58 +00:00
sjplimp 9ac8547feb git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14616 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-02-15 18:32:42 +00:00
sjplimp e7eced3711 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14615 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-02-15 18:16:07 +00:00
sjplimp 9fc1ec8d30 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14614 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-02-15 18:15:02 +00:00
sjplimp 2ed1861320 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14613 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-02-15 18:14:03 +00:00
sjplimp be035371f9 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14612 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-02-15 18:12:57 +00:00
sjplimp 701b4a00a1 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14611 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-02-15 18:11:41 +00:00
sjplimp bee7ffaee5 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14610 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-02-15 18:06:11 +00:00
sjplimp b1922ae7ca git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14609 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-02-15 18:04:59 +00:00
sjplimp c1aebdd391 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14544 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-02-03 21:39:32 +00:00