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798 Commits

Author SHA1 Message Date
Christoph Junghans 2f6be88c4a Merge remote-tracking branch 'origin/master' into exaalt 2017-09-08 07:04:12 -06:00
Richard Zamora 7b1542a0ba merging stable and exaalt branches into exaaltstable 2017-09-07 16:31:50 -06:00
Steve Plimpton 4161868bcf Merge pull request #640 from ohenrich/user-cgdna 
USER-CGDNA - sequence-dependent stacking and h-bonding strength
 2017-09-06 08:52:05 -06:00
Steve Plimpton b170606052 Merge pull request #620 from amilumas/master 
Temper_NPT
 2017-09-05 10:08:55 -06:00
Oliver Henrich 12fe614ddf Added sequence-dependent stacking and base-pairing strength 2017-09-05 10:48:38 +01:00
Axel Kohlmeyer 4d2ed30b35 add reference outputs to temper/npt example 2017-08-31 14:13:02 -04:00
Axel Kohlmeyer f3dda30f8e fully integrate temper/npt command into manual 2017-08-31 13:53:40 -04:00
Julien Devemy a5b65c1af4 Mods for extra/special/per/atom and add toluene 2017-08-31 15:03:04 +02:00
Amulya 6a4bbddb3b Add files via upload 
data file for example
 2017-08-28 14:56:37 -04:00
Amulya 2add18e013 Create in.temper_npt 
example for temper/npt
 2017-08-28 14:55:43 -04:00
Steve Plimpton f945d4567d new USER-MESO package 2017-08-18 17:33:42 -06:00
Axel Kohlmeyer 7d0d701eaf add reference outputs for QUIP/GAP example 2017-07-28 16:05:16 -04:00
Axel Kohlmeyer 85120842dd update QUIP examples to closer match typical LAMMPS examples 2017-07-28 15:20:33 -04:00
Axel Kohlmeyer da7a5f55d3 Merge branch 'kim-install' into install-and-docs-reviewed 2017-07-26 19:32:55 -04:00
sjplimp 1ddace4dba Merge pull request #595 from libAtoms/idces2quip 
Add a (contrived) molecular example for USER-QUIP
 2017-07-24 08:55:03 -06:00
Max Veit 1afab981b0 Clarified some points in in.molecular example 2017-07-22 14:40:33 +01:00
Axel Kohlmeyer 1af937e99d Update in.molecular 
- expand comments to provide more details on the choice of exclusion settings
- comment out dump file generation
 2017-07-21 22:00:29 -04:00
Max Veit 4e0a249e27 Add a (contrived) molecular example for USER-QUIP 
This example showcases the use of different 'special_bonds' settings for
different pair styles, so quip gets all the bonded neighbours but lj can
exclude them if it needs to.

The results have been checked against a pure quip implementation of the
potential; the expected lammps output is included.

DISCLAIMER: This example mixes parameters for methane and silane and is
NOT intended to be a realistic representation of either system.
 2017-07-22 01:33:15 +01:00
Axel Kohlmeyer b1b399d5c3 update readme for examples 2017-07-21 15:06:15 -04:00
Steve Plimpton 59db5f6a17 update of Fortran-DFTB interface to be compatible with fix msst 2017-07-20 14:40:35 -06:00
sjplimp 3cd597e948 Merge pull request #585 from akohlmey/make-py-manual-cleanup 
Make.py removal and manual cleanup
 2017-07-20 12:05:04 -06:00
Axel Kohlmeyer bdd2f3a6b2 remove references to Make.py and USER-CUDA 2017-07-20 12:25:42 -04:00
Axel Kohlmeyer 49b4cf9a77 remove references to Make.py and USER-CUDA 2017-07-18 13:24:32 -04:00
Axel Kohlmeyer d9186c8fde Revert "use neighbor list exclusions instead of a zero cutoff" 
This reverts commit bbb4d63db9.
 2017-07-18 01:17:34 -04:00
Steve Plimpton 296e572e69 better Install.py script for KIM from Ryan Elliott 2017-07-14 16:25:16 -06:00
Axel Kohlmeyer bbb4d63db9 use neighbor list exclusions instead of a zero cutoff 2017-07-14 14:52:08 -04:00
Axel Kohlmeyer 1c92eecea7 move updated gauss_flow example to the correct folder 2017-07-14 14:01:41 -04:00
Axel Kohlmeyer 14f1d646ad provide working examples for all four peridynamics models and reference outputs 2017-07-14 13:46:19 -04:00
Axel Kohlmeyer 4d4c03a1e4 restore gaussian flow example that was lost. tweak input to make it usable for comparing 2017-07-14 12:33:40 -04:00
sjplimp 9988030409 Merge pull request #563 from akohlmey/airebo-example 
Add AIREBO and AIREBO-M example input deck
 2017-07-13 13:12:30 -06:00
sjplimp a3a0c9b144 Merge pull request #570 from akohlmey/collected-small-changes 
Collected small changes
 2017-07-13 11:26:47 -06:00
sjplimp e58bcd8b4a Merge pull request #568 from akohlmey/fix_gcmc_parallel_workaround 
Workaround for data corruption when using fix gcmc in parallel with shake or fix rigid
 2017-07-13 11:23:49 -06:00
sjplimp d3a45f6d50 Merge pull request #560 from aershadinia/master 
EES wall potential
 2017-07-13 11:22:47 -06:00
Axel Kohlmeyer ddc9621325 remove absolutely last reference to xmovie 2017-07-11 18:30:41 -04:00
Axel Kohlmeyer 92395e9bb4 disallow MC moves with fix rigid and fix shake active. update examples and add shake example 2017-07-10 17:19:37 -04:00
Axel Kohlmeyer 7193fffe0d make example input / output conform with LAMMPS conventions (no dump files, no log command) and update reference outputs 2017-07-06 16:08:25 -04:00
Abdo 47649ff50f some edits to make examples more illustrative. 2017-07-06 15:35:06 +09:00
Axel Kohlmeyer fa469ae1d0 add polyethylene airebo example for future reference 2017-07-05 17:44:18 -04:00
Axel Kohlmeyer d451dbb1a0 adjust EES wall input example to print out some thermodynamic info that can be used for testing 2017-07-05 13:54:56 -04:00
Abdo 8e279d4ec8 Examples moved 2017-07-05 23:16:42 +09:00
Steve Plimpton f670dba3d0 3rd variant of Fortran wrapper for DFTB+ calling LAMMPS 2017-07-03 14:24:16 -06:00
sjplimp 6fc0a94e87 Merge pull request #524 from martok/package-meamc 
Package USER-MEAMC
 2017-07-03 12:30:01 -06:00
Axel Kohlmeyer db73eca29f correct example inputs for recent changes to create_bonds command 2017-07-03 11:43:55 -04:00
Axel Kohlmeyer 1fff30af90 update or create example outputs for meam and meam/c 2017-06-30 15:30:06 -04:00
Axel Kohlmeyer b0ddabbcde update examples for fix filter/corotate to comply with new CHARMM restrictions 2017-06-22 00:19:21 -04:00
Axel Kohlmeyer 72a1364d85 Merge branch 'master' into package-meamc 2017-06-20 13:21:46 -04:00
Steve Plimpton d2610d9e7c minor changes to NEB doc pages and examples 2017-06-20 08:19:23 -06:00
Emile Maras 8988b692a3 modified the documentation, first and last freeend can have different spring constants 2017-06-19 16:30:42 +02:00
Steve Plimpton 9b9f6d6fe2 USER-INTEL upgrade from M Brown 2017-06-16 16:56:28 -06:00
sjplimp 1a29048940 Merge pull request #531 from ohenrich/user-cgdna 
Affiliation Update for USER-CGDNA
 2017-06-15 08:54:52 -06:00
sjplimp 0a6b3f8790 Merge pull request #527 from dstelter92/master 
Added compute_scalar to fix_grem
 2017-06-15 08:54:22 -06:00
sjplimp a4bc233d86 Merge pull request #525 from akohlmey/user-tally-refactor 
Refactoring of USER-TALLY computes to handle sparse/hybrid system for many processors plus bugfixes
 2017-06-15 08:51:24 -06:00
sjplimp 9a7207e34c Merge pull request #511 from akohlmey/add-compute-cnp 
Integrate compute cnp/atom contributed by Paulo Branicio (USC)
 2017-06-15 08:38:05 -06:00
sjplimp 34cfc7bd51 Merge pull request #490 from EmileMaras/NEB-Change 
added several features to the NEB
 2017-06-15 08:23:04 -06:00
Oliver Henrich c98bb7fa5f Corrected minor bug in utility script 2017-06-15 12:57:44 +01:00
Oliver Henrich 77ca68a2b4 Changed affiliation 2017-06-15 12:52:19 +01:00
dstelter92 e7634a44f4 updated thermo_modify in example 2017-06-14 13:11:54 -04:00
dstelter92 3214d639aa removed unneeded .gitignore 2017-06-14 12:26:52 -04:00
dstelter92 0ad66ecb89 Added compute_scalar to fix_grem for easier output managment, updated example to show use 2017-06-14 12:18:22 -04:00
Axel Kohlmeyer 7a05d87f7c update USER-TALLY examples 2017-06-12 22:20:36 -04:00
Sebastian Hütter bab292b551 Create package USER-MEAMC 
Step 1: very literal translation of lib/meam
 2017-06-11 11:29:23 +02:00
Emile Maras e03cc99467 made the command options more lammps standard style 2017-06-02 23:42:16 +02:00
Axel Kohlmeyer 2b3c124e61 add example input for compute cnp/atom 2017-05-31 00:43:53 -04:00
Steve Plimpton 22fdb1fc14 SNAP changes by Aidan 2017-05-30 10:21:07 -06:00
Emile Maras c904cfb8bc removed a bug in fix_neb.cpp which prevented the freeend to work properly, plus added an example for the neb freeend 2017-05-29 15:49:04 +02:00
Emile Maras 32c87f3131 removed a bug in fix_neb.cpp which prevented the freeend to work properly, plus added an example for the neb freeend 2017-05-29 14:00:13 +02:00
Axel Kohlmeyer 8bc829c7f1 change example inputs to be backward compatible 2017-05-22 14:40:01 -04:00
Axel Kohlmeyer 654e09e999 correct input examples affected by the Pair::settings() bugfix 2017-05-18 18:34:27 -04:00
sjplimp 6ac9b7a1b0 Merge pull request #482 from akohlmey/add-pair-python 
Add python pair style for implementing simple pairwise additive potentials in python
 2017-05-18 11:15:58 -06:00
Axel Kohlmeyer 0208fe9996 update example outputs 2017-05-18 00:46:49 -04:00
Axel Kohlmeyer 8d46aa6056 add readme file to discuss various python pair style usage examples 2017-05-18 00:31:54 -04:00
Axel Kohlmeyer 09f3b687f7 new long-rance example with using hybrid/overlay and table only for lj part 2017-05-18 00:31:15 -04:00
Axel Kohlmeyer 436d3fd761 make hybrid example use half the atoms with python, half with lj/cut 2017-05-18 00:30:41 -04:00
Axel Kohlmeyer 9833f38499 change coulomb example to use cutoff coulomb 2017-05-18 00:30:19 -04:00
Axel Kohlmeyer 67962b15fc a bunch refactoring changes in the python pair style and the examples 
- make all python potential classes derived from LAMMPSPairPotential
  which contains shared functionality. We currently don't check
  for supported atom types. may want to add that again later.
- keep track of skipped atom types in the C++ code.
- add test against units setting. must set self.units='...' in constructor
- make compute_force method consistent with Pair::single() in LAMMPS and return force/r instead of force.
- rename potentials.py to py_pot.py
- update test runs. some small tweaks.
 2017-05-17 20:55:48 -04:00
Axel Kohlmeyer 1d48f287f0 add partial documentation for pair style python 2017-05-17 19:05:18 -04:00
Axel Kohlmeyer 43efe9e417 adding Pair::single() support to python pair style and examples 
with the single function, python pair styles can be massively
sped up and made compatible to accelerators, as one can translate
the analytic force and energy functions through LAMMPS into suitable
tables and then simply use the on-the-fly tables for production runs
 2017-05-17 17:20:56 -04:00
Axel Kohlmeyer a34c935e20 update log files in python pair style example 2017-05-17 08:00:21 -04:00
Axel Kohlmeyer 13e16dc3f1 update log files for pair style python examples 2017-05-17 07:52:13 -04:00
Axel Kohlmeyer 96f0a82aa5 simplify class names in pair style python examples. add SPC/E water example 2017-05-17 07:48:15 -04:00
Richard Berger 7caf6cf459 Change how a Python pair style is loaded 
Implements a class loader which takes a fully qualified Python class
name, loads the module and creates an object instance.

To add flexibility, the current working directory and the
directory specified by the LAMMPS_POTENTIALS environment variable are
added to the module search path.
 2017-05-16 23:29:48 -04:00
Axel Kohlmeyer 35e92733e9 import multi-element compatible pair style edip as edip/multi 2017-05-16 17:40:59 -04:00
Richard Berger 14f3deed6b Minor coefficient lookup improvement 2017-05-15 18:43:46 -04:00
Richard Berger 93cc6f4a5d Use in syntax for key lookup for Python 3 compatibility 2017-05-15 17:34:48 -04:00
Axel Kohlmeyer 6a1f7e61f2 provide reference output for python pair style inputs 2017-05-15 00:25:11 -04:00
Axel Kohlmeyer df55a90ef6 some example input file tweaks 2017-05-15 00:22:03 -04:00
Axel Kohlmeyer f484ab6dfb completed lj parameter set and compute functions for melt example 2017-05-15 00:14:36 -04:00
Axel Kohlmeyer 86283c6309 make melt input consistent with melt example again 2017-05-15 00:13:32 -04:00
Axel Kohlmeyer 34cc3946b8 first few pieces of pair style python 2017-05-14 18:29:06 -04:00
sjplimp 06c151421c Merge pull request #478 from akohlmey/add-python-source-cmd 
Add python support features
 2017-05-12 13:28:20 -06:00
Richard Berger c4d0f07093 Allow fix python to only execute every N steps 2017-05-12 00:29:58 -04:00
Richard Berger 110bb79b14 Implement fix python mentioned in issue #454 
Allows to call a python function at defined points in the integration loop
 2017-05-11 23:50:30 -04:00
Steve Plimpton 7c3b8e014c rename some USER/misc dirs 2017-05-11 10:15:28 -06:00
sjplimp d7f54464c6 Merge pull request #474 from rbberger/dump_vtk_fixes 
Various dump vtk fixes
 2017-05-11 09:25:42 -06:00
sjplimp deff6ffaac Merge pull request #466 from DallasTrinkle/meam-spline-multicomponent 
Meam spline multicomponent
 2017-05-11 09:22:25 -06:00
Richard Berger 4ecf876a64 Added two examples of using the VTK dump style 2017-05-10 19:52:00 -04:00
Axel Kohlmeyer d0da0639f0 add a couple of simple example single/multi-elment inputs for meam/spline pair styles 2017-05-09 15:51:59 -04:00
Richard Berger f8af7edf92 Merge remote-tracking branch 'upstream/master' into python_refactoring 2017-05-06 16:00:22 -04:00
Steve Plimpton addd87c0f7 new Section package and start doc pages and build scripts 2017-05-04 11:22:20 -06:00
Axel Kohlmeyer 949d61e01e rename examples folder for USER-CGSDK package 2017-04-26 19:26:27 -04:00
Steve Plimpton 2f32fb7f8b patch 13Apr17 2017-04-13 11:19:48 -06:00
Richard Berger 9a027a01da Add Python 3 compatibility to PYTHON package 2017-04-11 20:24:42 -04:00
Steve Plimpton 4da8c1c4e2 patch 11Apr17 2017-04-11 09:00:37 -06:00
sjplimp 9f6e126a2f Merge pull request #437 from ohenrich/user-cgdna 
User cgdna
 2017-03-28 12:52:26 -06:00
Steve Plimpton 111d350a22 fix gcmc units change for chemical potential 2017-03-28 12:34:46 -06:00
Oliver Henrich 604afebf6f Update to oxDNA2 2017-03-28 18:22:02 +01:00
Oliver Henrich 8afed61db1 Upgrade to oxDNA2 2017-03-28 18:16:36 +01:00
Steve Plimpton 394e9b42b0 new CHARMM pair styles with force swithing/shifting 2017-03-24 13:53:07 -06:00
sjplimp 277b93cb89 Merge pull request #417 from tonnamb/add-pair-zhou 
add new pair potential for metal-organic interactions - pair style momb
 2017-03-24 09:41:30 -06:00
Steve Plimpton 44841f6891 fix ave/chunk fixes, 2d disc option, fix_modify dynamic/dof 2017-03-23 15:31:27 -06:00
Axel Kohlmeyer 568b67eee9 include citation for reference paper into pair style momb 2017-03-23 12:00:53 -04:00
Axel Kohlmeyer 865b41e201 make pair style momb example follow LAMMPS conventions more closely 2017-03-23 11:50:10 -04:00
Tonnam Balankura 02e65900e6 add example log file generated from 17Nov16 version of lammps, make minimize and run short in system.in 2017-03-23 11:03:00 -04:00
Tonnam Balankura 1075be7eca rename zhou to momb in examples 2017-03-23 10:18:15 -04:00
Axel Kohlmeyer 43f27250b5 Merge branch 'add-pair-zhou' of https://github.com/tonnamb/lammps into pull-417 2017-03-22 14:05:16 -04:00
Oliver Henrich 7435084375 Verified oxDNA with modified nucleotide layout 2017-03-22 15:59:10 +00:00
dstelter92 5c39dfd740 re-ran example with fixed exchanges 2017-03-20 09:22:09 -04:00
Tonnam Balankura d04ea8653d add examples for pair_zhou 2017-03-18 21:21:25 -04:00
Axel Kohlmeyer bed288339e simplify and shorten examples for fix filter/corotate and combine into a single folder 2017-03-16 15:02:50 -04:00
Abdoreza Ershadinia 8f37285b05 UPLOAD examples 2017-03-16 21:12:10 +09:00
Abdoreza Ershadinia ef72145540 Readme for examples 2017-03-16 21:10:41 +09:00
Axel Kohlmeyer 0d8f74f0c5 Merge branch 'filter_corotate' of https://github.com/lukin17/lammps into pull-416 2017-03-15 18:54:41 -04:00
lukin17 c3ce3747e0 Added fix filter/corotate. 2017-03-15 11:34:01 +01:00
Oliver Henrich 7a75cd111c Minor updates in documentation and setup tool, merge before upgrade to oxDNA2 2017-03-14 11:39:09 +00:00
Oliver Henrich 23b8287933 Updated documentation and simple setup tool 2017-03-14 11:36:44 +00:00
sjplimp 920641bbff Merge pull request #399 from rbberger/docs_spelling_fixes 
Correct spelling errors in documentation
 2017-03-07 09:47:22 -07:00
sjplimp 4af6557568 Merge pull request #394 from jaapkroe/kolmogorov-crespi 
Added Kolmogorov-Crespi potential
 2017-03-07 09:46:08 -07:00
sjplimp 0798885bdb Merge pull request #389 from akohlmey/update-agni-potential 
update AGNI potential for Al, reference runs and output and citation
 2017-03-07 09:35:31 -07:00
Steve Plimpton efaa4c6710 new neigh_modify exclude option, other SNAP changes 2017-03-07 09:31:12 -07:00
Richard Berger d6800405a5 Fix more typos in examples 2017-03-07 00:57:23 -05:00
Richard Berger 17486a9319 Convert USER/lb/polymer files to UNIX line endings and remove trailing whitespace 2017-03-05 21:16:21 -05:00
Richard Berger 778a79b8ee Fix typos in examples folder 2017-03-05 21:10:33 -05:00
Christian Negre 48ed963fd2 latte in added 2017-03-01 12:05:00 -07:00
Christian Negre 1025c25548 latte.in added 2017-03-01 09:55:33 -07:00
Christian Negre 78a8f75a8f params added 2017-03-01 09:53:50 -07:00
Christian Negre 9736fb3be8 added sucrose latte min example 2017-02-28 10:40:46 -07:00
Jaap Kroes a1b40b902d Added Kolmogorov-Crespi potential 2017-02-28 14:59:13 +01:00
Axel Kohlmeyer 9999f363a1 remove outdated log files, too. 2017-02-24 15:34:59 -05:00
Axel Kohlmeyer a18b4ef4b0 update AGNI potential for Al, reference runs and output and citation 2017-02-24 15:33:13 -05:00
Christian Negre 2dcbc805ba min latte partially fixed 2017-02-23 18:20:02 -07:00
sjplimp 429264a12b Merge pull request #380 from hheenen/core_shell_documentation 
updated documentation and examples for coreshell
 2017-02-21 15:50:53 -07:00
Steve Plimpton 1cd4c48ccc new SNAP potential for W 2017-02-21 15:49:21 -07:00
Axel Kohlmeyer 48070011d9 update names in example, too 2017-02-14 07:42:36 -05:00
Hendrik Heenen 6b923476b9 updated documentation and examples for coreshell 2017-02-14 13:14:22 +01:00
Steve Plimpton 0068ef5616 added molecule option to compute group/group command 2017-02-10 09:25:32 -07:00
sjplimp 3af4b3c28c Merge pull request #337 from ohenrich/user-cgdna 
Added source code and documentation for USER-CGDNA
 2017-01-18 11:31:35 -07:00
sjplimp c52a26382f Merge pull request #339 from akohlmey/fixes-for-srp-example 
Fixes for srp example
 2017-01-17 09:36:28 -07:00
sjplimp 973bef4d45 Merge pull request #332 from akohlmey/coord-atom-orientorder-atom-enhancements 
Coord atom orientorder atom enhancements
 2017-01-17 09:11:45 -07:00
sjplimp 1b9e50c8cb Merge pull request #331 from timattox/USER-DPD_fix_example_typo 
USER-DPD: fix a typo in the DPD-H example input; update reference output.
 2017-01-17 09:08:14 -07:00
Steve Plimpton 5cd856c97f fix spring doc page update 2017-01-17 09:02:56 -07:00