02b10380bc
Create ctypes only neighbor list API variant
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This moves the lammps.get_neighlist() method to lammps.numpy.get_neighlist().
lammps.get_neighlist() now returns a NeighList object, while the NumPy variants
returns a NumPyNeighList object. The main difference between the two is that while
the ctypes variant returns neighlist elements as
atom idx (int), numneighs (int), neighbors (POINTER(c_int))
the NumPy variant returns
atom idx (int), neighbors (numpy.array)
2020-10-05 16:21:37 -04:00
02c1480546
update README in examples/COUPLE/simple
2020-09-24 02:17:11 -04:00
ac78f8f1e1
update examples/COUPLE/simple sources to work with the current version of LAMMPS
2020-09-24 01:30:34 -04:00
4cbf821af3
modernize example
2020-09-20 14:03:13 -04:00
b4a1c9c24c
Update examples
2020-09-17 17:08:13 -04:00
be72ce2534
Simplify Python examples to use numpy.extract_atom
2020-09-17 16:51:46 -04:00
706a898163
Merge remote-tracking branch 'origin/master' into python_interface_guide
2020-09-17 12:08:12 -04:00
e6703019bc
Update examples to use Python API constants
2020-09-16 16:10:43 -04:00
b99e005ca1
Update example output files
2020-09-09 18:26:34 -04:00
ae3a7d8901
minor changes to example
2020-09-01 17:02:24 +02:00
2ee6e9077a
Merge remote-tracking branch 'upstream/master' into 2020
2020-08-24 17:02:53 +02:00
e8fb7c7ece
big update
2020-08-24 16:54:16 +02:00
211beaee48
Merge pull request #2230 from evoyiatzis/widom
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Implementation of Widom insertions through a new fix widom command
2020-07-18 11:40:04 -04:00
55c3d139c1
add Widom spc/e example
2020-07-17 21:42:00 -04:00
4d4ae93ef8
add missing group names in fix widom. refactor group definition in fix widom and gcmc
2020-07-17 21:27:58 -04:00
c9342aec31
add lj example for fix widom
2020-07-17 15:02:11 -04:00
52715cc804
Merge branch 'master' into compute-mliap
2020-07-16 18:35:49 -04:00
095c6a9850
Finished cleaning up and testing. MLIAPData class is now fully integrated with ComputeMLIAP and PairMLIAP
2020-07-11 19:01:16 -06:00
f8321d77d8
add missing symlink
2020-07-11 13:05:41 -04:00
e38f970676
Extended to handle gradgradflag 0/1 options
2020-07-09 19:23:57 -06:00
06a199f7d0
Added gradgradflag option to compute mliap
2020-07-07 20:28:18 -06:00
2977a8aa15
Merge pull request #2211 from athomps/compute-mliap
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Add compute style mliap to MLIAP package
2020-07-06 12:47:41 -04:00
d1b5b0a168
Merge pull request #2210 from ohenrich/user-cgdna
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Update of example input and log files
2020-07-06 12:47:09 -04:00
134a2e8dd6
use fmtlib and utils::logmesg() in fix msst
2020-07-05 22:37:59 -04:00
c3f8644613
Merge branch 'master' into compute-mliap
2020-07-03 14:26:38 -06:00
8dae5d5fc7
Added special_bonds command to input files
2020-07-03 21:03:24 +01:00
9d0aee7426
Added doc page for compute mliap and updated examples
2020-07-03 13:43:51 -06:00
db43aadf09
Got compute working for quadratic model
2020-07-02 15:05:14 -06:00
cae9788d42
Changed the compute examples to expose effect of different list orderings
2020-07-02 14:43:48 -06:00
bf8043fdb8
Correctly reproduced examples/in.snap.compute, not yet for quadratic case
2020-07-02 14:34:11 -06:00
7350dd61d5
Tweaked input to match snap/in.snap.compute
2020-07-01 17:06:55 -06:00
c57564252c
Added descriptor file for compute mliap
2020-07-01 15:07:37 -06:00
aee3d9f2cd
Generated working example, not quite correct
2020-07-01 15:03:45 -06:00
5911ad49ba
use symlink instead of copy of the potential file
2020-06-28 16:50:39 -04:00
bdb4cc561c
add update README files
2020-06-26 11:11:59 -04:00
284efadf9b
adjust USER-QTB examples to match more closely with LAMMPS' style. add log files.
2020-06-25 17:22:16 -04:00
a519ff2909
Fix broken QTB examples
2020-06-25 13:02:02 -06:00
f35d517a15
Merge pull request #2179 from charlessievers/fix_python_dynmat
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Update dynamical matrix examples
2020-06-23 21:09:27 -04:00
f812b94e40
Update relative paths to dynamic links
2020-06-23 14:23:41 -07:00
fefdd3dd9a
move MLIAP potential files to potentials folder and replace with symlinks
2020-06-23 09:34:34 -04:00
6fbcb84819
Update dynamical matrix examples
2020-06-22 15:26:04 -07:00
233b56105a
Merge branch 'master' into mliap
2020-06-22 11:24:49 -04:00
549c6343f3
Merged MLIAP package into latest LAMMPS created SNAP, quadratic SNAP, and ChemSNAP examples
2020-06-21 18:05:34 -06:00
564974b6a4
Merge remote-tracking branch 'origin/ml_chem_snap'
2020-06-21 16:07:03 -06:00
5148834d23
Merge pull request #2162 from akohlmey/collected-small-changes
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Collected small changes
2020-06-19 17:07:07 -04:00
b97cd78e80
change input and log files for new example to give consistent results in serial and parallel.
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the remaining files and logs are updated in PR #2162
2020-06-16 21:11:34 -04:00
1883788725
update SNAP package inputs and reference logs to give consistent results in serial and parallel
2020-06-16 20:59:58 -04:00
5e238b2cf4
Merge branch 'master' into chem_snap
2020-06-16 05:06:11 -04:00
3abbf57146
remove executable permissions on files that should not have them
2020-06-15 17:34:21 -04:00
ac87f1763c
Merge remote-tracking branch 'refs/remotes/origin/chem_snap' into chem_snap
2020-06-15 12:22:11 -07:00
