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e3b1d27e0a
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whitespace
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2025-06-21 14:34:01 -04:00 |
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06d47f7279
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didn't count if atom-id was used
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2025-06-21 14:32:18 -04:00 |
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fc9efa1586
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update documentation for the recently added sections in JSON format molecule files
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2025-06-21 13:48:11 -04:00 |
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0310959053
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use consistent formatting of error messages and comments
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2025-06-21 12:59:40 -04:00 |
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9360038013
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implement the processing for special bonds in JSON
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2025-06-21 12:59:15 -04:00 |
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0caaca8a05
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honor atom-ids in Special Bonds section
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2025-06-21 12:36:31 -04:00 |
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9d38652033
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consistently quote JSON fields with double quotes
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2025-06-21 12:34:17 -04:00 |
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c08ee92801
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correctly honor atom-id in Special Bond Counts section
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2025-06-20 23:05:58 -04:00 |
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95fb6c75d2
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support special:counts section for JSON data, only special:bonds missing
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2025-06-20 23:05:38 -04:00 |
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67582ebf14
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some error hint updates based on recent discussions on MatSci.org
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2025-06-20 17:45:37 -04:00 |
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8dff25296b
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restore pylammps.py
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2025-06-20 14:42:52 -04:00 |
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b036c911e7
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fix copy-n-paste bug
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2025-06-20 14:23:22 -04:00 |
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6f72a56b4c
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stricter matching of header items and skip comments right away
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2025-06-20 14:12:25 -04:00 |
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fb088cdc57
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require .json extension for JSON format molecule files
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2025-06-20 14:12:00 -04:00 |
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c98ebb669e
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trigger warning on the correct fix style name
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2025-06-20 10:08:14 -04:00 |
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bb0bd289b7
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update unit tests
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2025-06-20 08:38:09 -04:00 |
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b909a782b6
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revert double adding of body info in create_atoms
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2025-06-20 08:07:17 -04:00 |
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6fff591c0d
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more checks
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2025-06-20 07:51:58 -04:00 |
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c6057f3780
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support creating body particles from molecule templates in create_atoms
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2025-06-20 07:31:58 -04:00 |
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765b3ad487
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need fewer checks with JSON data
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2025-06-20 07:30:59 -04:00 |
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9615cb466c
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support processing "bodies" sections from JSON data
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2025-06-20 07:30:43 -04:00 |
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500373d72b
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correct error message
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2025-06-20 07:24:35 -04:00 |
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25fecf7b7d
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update format
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2025-06-20 07:24:21 -04:00 |
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18455d07fe
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list possible pair styles with SPC Howto. Add comment about cutof vs. long-range coulomb
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2025-06-20 04:24:13 -04:00 |
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97d7e9e4a1
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correct cut-n-paste errors
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2025-06-18 10:16:19 -04:00 |
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8c0894fa84
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fix issues causing failed tests
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2025-06-18 07:49:15 -04:00 |
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004816a4ba
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update tests for changed argument names
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2025-06-18 07:09:03 -04:00 |
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6934932383
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document function
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2025-06-18 06:55:30 -04:00 |
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3f6dfa27bd
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apply pylint and refactor accordingly
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2025-06-18 06:51:17 -04:00 |
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40d88e9bda
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revert incorrect additions
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2025-06-18 03:35:28 -04:00 |
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210fdb8b98
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process "shake:atoms" and "shake:types" sections in JSON data
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2025-06-18 00:08:28 -04:00 |
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e01640c4f5
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fix out-of-bounds initialization for cvatom array
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2025-06-17 17:02:00 -04:00 |
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07c91f396e
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fix out-of-bounds access bug reported in issue #4632
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2025-06-17 16:43:07 -04:00 |
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ec2ef5b14c
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fix more issues with reading Shake sections in native file format
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2025-06-17 13:55:16 -04:00 |
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03a418809d
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implement general shake flags checking and partial JSON processing
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2025-06-17 10:32:36 -04:00 |
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2f088749ad
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add shake entries to schema
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2025-06-17 10:31:49 -04:00 |
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635719a2ec
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Correct implementation to actually follow the documentation.
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2025-06-17 10:31:17 -04:00 |
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632bc8f20d
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Removed line apparently copied from compute displace/atom
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2025-06-17 14:56:43 +02:00 |
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9a81c95104
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document unchanging group size restriction in compute msd
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2025-06-17 06:02:43 -04:00 |
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624c7a5ab8
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improve errors in compute msd
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2025-06-17 05:57:24 -04:00 |
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eeaca93974
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the number of atoms in the compute msd group must not change
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2025-06-17 05:51:03 -04:00 |
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515ccac51c
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avoid copies of C++ strings
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2025-06-16 20:19:53 -04:00 |
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53fec5563c
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Merge pull request #4543 from d-immel/apip
adaptive-precision interatomic potentials (APIP)
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2025-06-16 15:56:12 -04:00 |
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47fae6b786
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Merge pull request #4628 from akohlmey/collected-small-changes
Collected small changes and fixes
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2025-06-16 13:41:25 -04:00 |
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0538518dbd
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add missing entries to .gitignore
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2025-06-16 12:43:12 -04:00 |
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8f31b62e15
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make flow of control more obvious
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2025-06-15 17:39:06 -04:00 |
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d38f97e465
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remove dead code
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2025-06-15 05:40:39 -04:00 |
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bb1b854b47
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check for empty molecule to avoid division by zero
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2025-06-15 05:40:16 -04:00 |
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d95d97db28
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remove dead code, avoid uninitialized access
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2025-06-15 05:25:19 -04:00 |
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a6b30c35ac
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use more obvious flow of control that does not confuse static code analysis
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2025-06-15 05:24:37 -04:00 |
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