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553 Commits

Author SHA1 Message Date
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
sjplimp 7e67afad7b git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14511 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-01-28 21:19:43 +00:00
sjplimp d42ebe4e5e git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14510 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-01-28 21:17:32 +00:00
sjplimp 67d5513df1 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14483 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-01-23 00:59:04 +00:00
athomps 4da36d1c01 Added data output example 
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14468 f3b2605a-c512-4ea7-a41b-209d697bcdaa
 2016-01-22 02:49:52 +00:00
athomps 66a048bbb9 Added faces as local compute 
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14464 f3b2605a-c512-4ea7-a41b-209d697bcdaa
 2016-01-21 01:59:48 +00:00
athomps 81d55a7904 Changed behavior for non-periodic systems 
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14460 f3b2605a-c512-4ea7-a41b-209d697bcdaa
 2016-01-20 00:01:34 +00:00
athomps 7c810d6198 Added 2d example 
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14458 f3b2605a-c512-4ea7-a41b-209d697bcdaa
 2016-01-19 22:26:48 +00:00
sjplimp fb0230aed2 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14451 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-01-15 16:05:33 +00:00
sjplimp eb063200bf git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14411 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-01-11 17:59:15 +00:00
sjplimp e86cfe431a git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14410 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-01-11 17:58:37 +00:00
sjplimp 29b4d60141 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14398 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2015-12-23 17:04:56 +00:00
sjplimp 31f22919ab git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14369 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2015-12-15 16:03:53 +00:00
sjplimp 9f38620e13 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14368 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2015-12-15 16:01:54 +00:00
sjplimp 2cf6305dc1 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14351 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2015-12-10 17:40:52 +00:00
sjplimp 336aa4093e git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14181 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2015-10-23 00:06:46 +00:00
sjplimp f8d13ac853 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14174 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2015-10-22 23:36:53 +00:00
sjplimp ddfb996d8e git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14127 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2015-10-21 18:16:47 +00:00
athomps c7170a4296 Added Vashishta potential 
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14117 f3b2605a-c512-4ea7-a41b-209d697bcdaa
 2015-10-15 17:39:43 +00:00
athomps da1e4e4f25 Added elastic constant example at finite temperature 
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14105 f3b2605a-c512-4ea7-a41b-209d697bcdaa
 2015-10-05 21:02:38 +00:00
athomps 233eaea97d Added elastic constant example at finite temperature 
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14104 f3b2605a-c512-4ea7-a41b-209d697bcdaa
 2015-10-05 18:54:37 +00:00
athomps ae2a7e2ebd Made output prettier 
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14103 f3b2605a-c512-4ea7-a41b-209d697bcdaa
 2015-10-05 18:54:02 +00:00
athomps a1149efbfa Added elastic constant example at finite temperature 
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14102 f3b2605a-c512-4ea7-a41b-209d697bcdaa
 2015-10-05 18:52:13 +00:00
athomps 8a024fa64b Added elastic constant example at finite temperature 
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14101 f3b2605a-c512-4ea7-a41b-209d697bcdaa
 2015-10-05 18:49:23 +00:00
athomps db4d01260b Added elastic constant example at finite temperature 
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14100 f3b2605a-c512-4ea7-a41b-209d697bcdaa
 2015-10-05 18:41:56 +00:00
athomps 46545bb308 Added elastic constant example at finite temperature 
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14099 f3b2605a-c512-4ea7-a41b-209d697bcdaa
 2015-10-05 18:30:11 +00:00
athomps f343a9f4a0 Added elastic constant example at finite temperature 
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14097 f3b2605a-c512-4ea7-a41b-209d697bcdaa
 2015-10-05 18:22:14 +00:00
sjplimp 663551ee9f git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14073 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2015-09-24 22:48:45 +00:00
sjplimp d2a2124b56 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14072 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2015-09-24 22:48:28 +00:00
sjplimp 70128bfb92 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14054 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2015-09-24 20:01:39 +00:00
athomps 06bb2fb761 Modifed ZBL to accomodate mixing 
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14049 f3b2605a-c512-4ea7-a41b-209d697bcdaa
 2015-09-23 00:31:07 +00:00
athomps 40382cbda9 Added atom jiggle to initial structure 
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14000 f3b2605a-c512-4ea7-a41b-209d697bcdaa
 2015-09-04 23:23:47 +00:00
athomps 7b30c20b66 Addings xy, xz, and yz strains for axial strain 
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13999 f3b2605a-c512-4ea7-a41b-209d697bcdaa
 2015-09-04 23:17:02 +00:00
sjplimp c9188c0095 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13956 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2015-08-28 23:50:01 +00:00
sjplimp 7e1de6da04 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13834 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2015-08-04 20:57:54 +00:00
sjplimp 9ed741e904 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13738 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2015-07-27 18:12:18 +00:00