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commit b373a4f1c495f2783d1e832a8a1cd4deffedf1b3 Merge: ce75457 526a2cc Author: Paul Fuchs <[email protected]> Date: Tue Feb 10 13:57:59 2026 +0100 Merge branch 'compose' into 'main' Use MACE foundational models in chemtrain See merge request mfm/science/chemtrain!8 commit 526a2cccfdb239c572b9a1271800a3a5ae1378ac Author: Paul Fuchs <[email protected]> Date: Tue Feb 10 13:57:58 2026 +0100 Use MACE foundational models in chemtrain commit ce754576555d5df55c0855b2fa4ac3160d69f27c Merge: 7c44e50 20e06ef Author: Paul Fuchs <[email protected]> Date: Wed Jan 7 09:41:22 2026 +0100 Merge branch 'jax-version' into 'main' Updates See merge request mfm/science/chemtrain!5 commit 20e06ef6edbdd25a887d3ea97806d3fdc12ee640 Author: Paul Fuchs <[email protected]> Date: Wed Jan 7 09:41:21 2026 +0100 Updates commit 7c44e50a097a9c57e82dc34d3c87fae370ac5bbc Merge: 3695ef4 a97ca2d Author: Paul <[email protected]> Date: Thu Jun 12 16:55:29 2025 +0200 Merge remote-tracking branch 'public/main' commit 3695ef4c493e1a8f53ed8e698a59b819239ddb6b Author: Paul <[email protected]> Date: Wed Jun 4 17:47:57 2025 +0200 Revert "Remove electrostatics" This reverts commit ac24898a6f4e105eda2f76d7f94c334d4e992287. commit ac24898a6f4e105eda2f76d7f94c334d4e992287 Author: Paul <[email protected]> Date: Wed Jun 4 17:47:06 2025 +0200 Remove electrostatics commit a8f1db832156f220dab835f732e4b7ff3dccdb4a Merge: 8918322 6881c21 Author: Paul Fuchs <[email protected]> Date: Wed Jun 4 16:51:08 2025 +0200 Merge branch 'LAMMPS' into 'main' Lammps See merge request mfm/science/chemtrain!4 commit 6881c2191f3bf88d0257e58ba5438d7de6d2e048 Author: Paul Fuchs <[email protected]> Date: Wed Jun 4 16:51:07 2025 +0200 Lammps commit 89183224d8587e6d079bd065846335140ac919a0 Merge: a0b797d 07cf0fd Author: Paul Fuchs <[email protected]> Date: Fri May 30 10:21:12 2025 +0200 Merge branch 'LAMMPS' into 'main' Lammps See merge request mfm/science/chemtrain!3 commit 07cf0fdef0e1649032edfeb40401275860df1425 Author: Paul Fuchs <[email protected]> Date: Fri May 30 10:21:11 2025 +0200 Adds LAMMPS support for chemtrain-deploy commit a0b797d10184b5eccb44214058dc9d373f5e9768 Author: Paul <[email protected]> Date: Fri May 30 09:30:26 2025 +0200 Updated version commit 5eef9bc0a300a61b918c820df385c4a6b2d15223 Merge: 1c8da36 e378736 Author: Paul <[email protected]> Date: Fri May 30 09:29:59 2025 +0200 Merge remote-tracking branch 'public/main' # Conflicts: # chemtrain/version.py commit 1c8da36e6263cfb12c15cda9d2524fdc9d4b681b Author: Paul <[email protected]> Date: Fri Apr 25 16:55:29 2025 +0200 Cleaned up examples commit dba913bba00ad912439e6555f293945bfb505747 Merge: ecea4bc 351ec80 Author: Paul <[email protected]> Date: Fri Apr 25 16:49:36 2025 +0200 Merge remote-tracking branch 'github/main' # Conflicts: # .readthedocs.yml commit ecea4bc08a68c5bb3a54708656a05586b8106565 Merge: a2f95d8 64b3d52 Author: Paul <[email protected]> Date: Fri Apr 25 16:49:23 2025 +0200 Merge remote-tracking branch 'origin/main' # Conflicts: # jax_md_mod/custom_electrostatics.py commit a2f95d827b8ee572d163d58e4d45d7b39e6661ca Author: Paul <[email protected]> Date: Fri Apr 25 16:45:58 2025 +0200 Corrected licenses commit 64b3d526a8e560db9984a2714a69265c50945bea Merge: e3fec0b e3355f0 Author: Paul Fuchs <[email protected]> Date: Wed Apr 9 16:33:07 2025 +0200 Merge branch 'celli_example' into 'main' Celli example See merge request mfm/science/chemtrain!2 commit e3355f0741adecf03f79a89e3795ccfbf4bb2ba2 Author: Paul Fuchs <[email protected]> Date: Wed Apr 9 16:33:06 2025 +0200 Celli example commit e3fec0baeae7f39945a129baaf927212642316e4 Author: Paul <[email protected]> Date: Thu Mar 20 15:43:00 2025 +0100 Fixed checkpoint generation commit bacd08b1f00a3f12af6318e79cff31526cbc82ff Author: Paul <[email protected]> Date: Fri Feb 21 14:11:29 2025 +0100 Fixed rng key size commit 2dc1d0fdcbeea0ca4b21b69c462125ddb4fc12df Author: Paul <[email protected]> Date: Fri Feb 21 12:31:24 2025 +0100 Updated documentation commit c29072517db6c1616176b82011c11af8c79b64f8 Author: Paul <[email protected]> Date: Fri Feb 21 12:29:29 2025 +0100 Added rngkey to data loader commit 6fa32dfa791fab2e20dfb3ba17ba6eb216004c27 Author: Paul <[email protected]> Date: Fri Feb 21 11:24:14 2025 +0100 Updated jax dependency and small corrections commit 6b2b3efe502faf40df68993e7a4320e32c85eeaa Author: Paul <[email protected]> Date: Mon Feb 3 15:14:11 2025 +0100 Improved lint score commit db24905006bd6cb15cab8f3eb84bbfba4155941c Author: Paul <[email protected]> Date: Mon Feb 3 14:48:56 2025 +0100 Fixed step size adaption commit 6d063ca696ea5f4d53186cdbf2ba67d29d424bab Merge: b293d07 2ff6a5b Author: Paul <[email protected]> Date: Mon Feb 3 12:32:49 2025 +0100 Merge branch 'supramol' commit 2ff6a5bb332919585b1579997cb838a66862eb24 Author: Paul <[email protected]> Date: Mon Feb 3 12:32:40 2025 +0100 Removed unnecessary code commit 2f6f1832ecb6877d6772cfa0348536a22cfbb8e9 Author: Paul <[email protected]> Date: Mon Feb 3 12:19:08 2025 +0100 Added comments to DiffTreParallel commit b293d07a6d11a475ab341a8c1561a6f5bca1c08c Author: Paul <[email protected]> Date: Mon Feb 3 11:55:54 2025 +0100 Fixed error for force matching error function commit 4fcd51b6542cd8fc0774a820993da4d59bb00071 Author: Paul <[email protected]> Date: Mon Feb 3 11:43:23 2025 +0100 Documented changes commit a5b9a9a04ad0f8723d0325a47a83530e02605be2 Author: Paul <[email protected]> Date: Fri Jan 24 15:59:53 2025 +0100 WIP ML-CG commit 335feeeea5313a00abc67417e9ff79ba8f9cc0db Author: Paul <[email protected]> Date: Fri Jan 24 15:40:25 2025 +0100 WIP ML-CG commit 4a63dba48278805cec7853f034a24c7aea244a62 Author: Paul <[email protected]> Date: Fri Jan 24 15:31:35 2025 +0100 WIP ML-CG commit cc6ef131a15fa30d5c2a739d7981c68ec035d8c5 Author: Paul <[email protected]> Date: Fri Jan 24 15:21:10 2025 +0100 WIP Rigid body alignment commit f4356461231812d46810617941791c2273569cd6 Author: Paul <[email protected]> Date: Fri Jan 24 15:20:59 2025 +0100 WIP Multilevel CG method commit 656f38aa19a93e626cd059d09a63f55d9ed4d6b8 Author: Paul <[email protected]> Date: Wed Jan 15 18:18:18 2025 +0100 Added option to specify coulomb onset commit e2538b4fe5d30f7f4aa866d412219fd919b23fb4 Author: Paul <[email protected]> Date: Tue Jan 14 18:43:35 2025 +0100 Added possibility to predict charges simultaneously commit 14f015ee885b4d46fb6af3d9dea31f2c62074fd8 Author: Paul <[email protected]> Date: Tue Jan 14 18:26:42 2025 +0100 Adapted training for DimeNetPP commit 85e65d5b9b3245e1c4c17eef7d58c52c17acecd7 Author: Paul <[email protected]> Date: Mon Jan 13 16:33:47 2025 +0100 Drafted implementation for MACE commit e94e3a8c62d42c9b1d170cd4306bfc6fa286a249 Author: Paul <[email protected]> Date: Mon Dec 30 18:04:58 2024 +0100 WIP Reduced size of linear system commit 89756dbb8136e3acb27f63bae34f660e1b1dc6ea Author: Paul <[email protected]> Date: Tue Dec 24 09:20:48 2024 +0100 WIP Including validation splits commit 46849f2aa3ed92d2194a2d7e983d3c9c1893bd47 Author: Paul <[email protected]> Date: Mon Dec 23 07:10:45 2024 +0100 Added different polynomial schedule commit 03601b73b8382b59950dbba1aa5f3ed520298789 Author: Paul <[email protected]> Date: Wed Dec 18 18:20:13 2024 +0100 Trained competitive NaCl model commit 1e05928077934e318b3268a3fff3a52bd176766e Author: Paul <[email protected]> Date: Wed Dec 18 11:10:29 2024 +0100 Added more hyperparameters commit af1db34f3ea3820f07e04f0f7a5f6f5e8fc47eb6 Author: Paul <[email protected]> Date: Tue Dec 17 18:43:31 2024 +0100 Improved model commit 94d7e0b6ded346bd5b49448fa07517e4fa2968df Author: Paul <[email protected]> Date: Tue Dec 17 14:41:19 2024 +0100 (Final) model commit 4d852cd7ed0a5abe493e0995328c5d28d477e1ef Author: Paul <[email protected]> Date: Fri Dec 13 12:46:26 2024 +0100 Improved model commit cd87226b729e3bdc09abb1d576918a2d0f909b77 Author: Paul <[email protected]> Date: Thu Dec 12 20:33:21 2024 +0100 WIP Fix radius of charge commit e0167f764e0177244c5f0a7ab7e14e1cf65508b7 Author: Paul <[email protected]> Date: Wed Dec 11 16:26:55 2024 +0100 WIP Fix radius of charge commit ee7dd660a90bff1b92685b638f7f7b046a7483e4 Author: Paul <[email protected]> Date: Wed Dec 11 11:47:26 2024 +0100 WIP Corrected electrostatics and improved model commit 50b6e1b3ccd7722f8873eb58a9e6c1a632f8c291 Author: Paul <[email protected]> Date: Mon Dec 9 10:17:01 2024 +0100 Adjusted screening charge self-interaction correction commit 337fdef792cc1311fc55f9e6f7d21e2b9c6b34ca Author: Paul <[email protected]> Date: Fri Dec 6 19:41:41 2024 +0100 Adjusted screening charge self-interaction correction commit 26edb5f5a29539206d8397417eacbd7c7286af22 Author: Paul <[email protected]> Date: Fri Dec 6 19:12:40 2024 +0100 Adjusted screening charge self-interaction correction commit bec3320821767b6be25659bc1175950f7ac55289 Author: Paul <[email protected]> Date: Fri Dec 6 18:08:29 2024 +0100 Updated model commit 091350a5eb2202c7e8fc8475c67ddb85b7dd9a80 Author: Paul <[email protected]> Date: Fri Dec 6 13:46:30 2024 +0100 WIP commit 17f1a6db85787d84bc594d8e30cc102c5598881f Author: Paul <[email protected]> Date: Fri Dec 6 10:26:02 2024 +0100 Added energy shift and scale commit 971e780dd48554e115975429f0264063d29e9630 Author: Paul <[email protected]> Date: Thu Dec 5 15:41:09 2024 +0100 WIP Periodic commit 6efa9e8b6660f87c169acd88b58b507f52bf2259 Author: Paul <[email protected]> Date: Wed Dec 4 16:54:21 2024 +0100 Added option to train with PME commit 0c58e73a74d2f4a0dcea0a013b11d58c43c02afc Author: Paul <[email protected]> Date: Mon Dec 2 09:42:18 2024 +0100 Corrected model and training commit eed6b134645c6766a058078b60586b3ce516f04f Author: Paul <[email protected]> Date: Fri Nov 29 19:14:37 2024 +0100 Corrected model and training commit e546ea6e749d139119f247384b8af20968cd7652 Author: Paul <[email protected]> Date: Thu Nov 28 08:50:07 2024 +0100 Unified Allegro and Qeq commit 76a8c217d4c2c54b5993f80f3528b999f57ddf58 Author: Paul <[email protected]> Date: Tue Nov 26 09:37:24 2024 +0100 Training of Behler Carbonchain dataset commit 943207a67e810ed9be9706f58972369c5832ba63 Author: Paul <[email protected]> Date: Fri Nov 22 13:02:44 2024 +0100 Corrections in export commit c92c12eee77115e3a42559b8c4e57145a75a0a94 Author: Paul <[email protected]> Date: Fri Nov 22 10:59:45 2024 +0100 Cleaned up model commit 7b08b6c9647cc3aa9704ae0455240e69dd897dd2 Author: Paul <[email protected]> Date: Thu Nov 21 17:05:33 2024 +0100 Corrections in export commit 619a6df3d7a84a132ea59f74d7f3ae714c432270 Author: Paul <[email protected]> Date: Thu Nov 21 14:58:54 2024 +0100 Simplified parallelization commit 1f32267070599ff00b204779b3b3e7481150f9e0 Author: Paul <[email protected]> Date: Thu Nov 21 14:07:32 2024 +0100 Implemented graph pruning commit 78d391230cffa0e7ca515e4bfe4c8d56e7f41330 Author: Paul <[email protected]> Date: Wed Nov 20 11:29:52 2024 +0100 Qeq seems to work commit 7d6b156f169a355036b015a724266d50ba84d985 Author: Paul <[email protected]> Date: Fri Nov 15 13:27:45 2024 +0100 Fixed missing constant_kwargs in force matching commit 50769ac2280ec5e33a3d27c0bcd236cce0b637a4 Author: Paul <[email protected]> Date: Wed Nov 13 11:07:38 2024 +0100 Drafted parallelizable version of DiffTRe commit 3731f9e2a4ad4f1116957552513c626b811ace05 Author: Paul <[email protected]> Date: Mon Nov 11 13:22:29 2024 +0100 Usability adjustments commit 89b42fcecb9e9a68cdaddb44a31771e8bcbd68be Author: Paul <[email protected]> Date: Fri Nov 8 16:05:29 2024 +0100 Extended neighborlist generation routines commit 14eb5d85f8dbc1e050e40fb35fd838d39631cc4b Author: Paul <[email protected]> Date: Fri Nov 8 16:04:49 2024 +0100 Added option to automatic delayed initialization of trajectory commit bb3ebad26dc33631ed9995d2cbd698b42a1e5bb4 Author: Paul <[email protected]> Date: Fri Nov 8 16:04:12 2024 +0100 Updated step size adaption to simplify application to multiple (many) statepoints commit 1560682055117e6dedad07ad93d0244e28c17607 Author: Paul <[email protected]> Date: Fri Nov 8 16:02:49 2024 +0100 Standardized quantity name commit 34c27577cb488277b71172009b897e251f35ef6c Author: Paul <[email protected]> Date: Fri Nov 8 15:58:31 2024 +0100 Improved support for dynamic specification of statepoint commit cbd94e1cc15c22f8807432f0cbe60de657de5e28 Author: Paul <[email protected]> Date: Fri Nov 8 15:55:26 2024 +0100 Extended utilities to investigate the neighbor list commit 67ce55a16d615f21391690fd4ebc44b4679b31ec Author: Paul <[email protected]> Date: Fri Nov 8 15:52:37 2024 +0100 Added mask argument to temperature quantity commit c1101162480a0734bb853b1c85275960dd961a1f Author: Paul <[email protected]> Date: Fri Nov 8 15:51:56 2024 +0100 Added Langevin-Diffusion similar to GROMACS implementation commit 6a45379b13d26181f97fcafd401c4517da57327b Author: Paul <[email protected]> Date: Wed Nov 6 14:11:54 2024 +0100 Avoid removal of gamma values from config dict commit 95a6f7561d4fa518fc450e5f5293754bada971a8 Author: Paul <[email protected]> Date: Wed Nov 6 13:24:50 2024 +0100 Added dynamic statepoint definition to DiffTRe commit 5f519e2a42c4d755b524bcb8c15d29632209d7f5 Author: Paul <[email protected]> Date: Thu Oct 31 10:50:01 2024 +0100 Added TODO commit 6e7fcbb6f36830e9e351326082690d2e5665ee69 Author: Paul <[email protected]> Date: Wed Oct 30 17:52:39 2024 +0100 Added pages to docs commit e0ba9649b13c95e0de809c007e4f3dd07bbc8aa1 Author: Paul Fuchs <[email protected]> Date: Wed Oct 30 16:10:05 2024 +0100 Update .gitlab-ci.yml file commit f21b0898ab8228723a8c1179374bb0bb379b4e5b Merge: 54e85a5 79f935d Author: Paul <[email protected]> Date: Wed Oct 30 16:00:06 2024 +0100 Merge remote-tracking branch 'origin/nn_prior' into nn_prior commit 54e85a5ead4d8dfd0d8cb0cea8922039cc6a61e2 Author: Paul <[email protected]> Date: Wed Oct 30 15:03:28 2024 +0100 Log stdout to file commit 79f935d97118233062f18bfa204bd612a4660aec Author: Paul Fuchs <[email protected]> Date: Tue Oct 29 17:18:03 2024 +0100 Update .gitlab-ci.yml file commit b0366c77980341ae0cd02f9f04f9aca53364cdb7 Author: Paul Fuchs <[email protected]> Date: Tue Oct 29 15:55:13 2024 +0100 Update .gitlab-ci.yml file commit ca93cabcb2c921e7a752c04c770bd772539a9f92 Author: Paul Fuchs <[email protected]> Date: Tue Oct 29 15:38:12 2024 +0100 Update .gitlab-ci.yml file commit 90bf0272408aef12d1b85c9d986fb6227bf11d39 Author: Paul <[email protected]> Date: Tue Oct 29 11:54:33 2024 +0100 Updated docs build commit 6b160b3f23e360cc3d5eb0d5c51676d9119e46dc Author: Paul <[email protected]> Date: Tue Oct 29 11:39:10 2024 +0100 Updated docs build commit f7d46a2560db7fa7ecf30cd03f968bc8dc4990ea Merge: 58f5f24 6906a7c Author: Paul <[email protected]> Date: Tue Oct 29 11:35:59 2024 +0100 Merge remote-tracking branch 'origin/nn_prior' into nn_prior commit 58f5f24d1642e21c5543da819d19f21f3a49ac8a Author: Paul <[email protected]> Date: Tue Oct 29 11:35:52 2024 +0100 Added simple usage example for the LAMMPS plugin commit 6906a7ccd3f14604e3629ff0420671d20cf1694c Author: Paul Fuchs <[email protected]> Date: Tue Oct 29 10:49:55 2024 +0100 Update .gitlab-ci.yml file commit 2e360bb12dadf0692bf926e2e2da619206d94396 Author: Paul Fuchs <[email protected]> Date: Tue Oct 29 10:35:32 2024 +0100 Update .gitlab-ci.yml file commit d6ef498d321ab5e40d972057f4103ba39882d4df Author: Paul Fuchs <[email protected]> Date: Tue Oct 29 10:31:19 2024 +0100 Update .gitlab-ci.yml file commit 4ddead0ad4a68c94f8844a9fb5015bf73bc73616 Author: Paul Fuchs <[email protected]> Date: Tue Oct 29 10:28:26 2024 +0100 Update .gitlab-ci.yml file commit cef8c18628469d82be5ef652852f7c78fd7c7637 Author: Paul Fuchs <[email protected]> Date: Tue Oct 29 10:27:23 2024 +0100 Add new file commit 01a945bc6aa79d35c641ac331d2e129ebdcb700f Author: Paul <[email protected]> Date: Tue Oct 29 10:04:37 2024 +0100 Corrected dealing with ghost atoms commit 13c33143ea7680b1aaddf0656f88e5a6b5203ade Author: Paul <[email protected]> Date: Mon Oct 28 18:06:19 2024 +0100 WIP Writing docstrings commit 956081e73d21ca3fdbc48cd78bfdc5062bf8b28e Author: Paul <[email protected]> Date: Mon Oct 28 16:50:34 2024 +0100 Added alignment utility commit 463f59d27939be30d45d47f445bccfacfdfeaca9 Author: Paul <[email protected]> Date: Mon Oct 28 15:37:40 2024 +0100 Added loglevels to reduce output to std::cout commit e9b2073fd9b0657a281cef917c38faaea0c32a1d Author: Paul <[email protected]> Date: Mon Oct 28 11:43:40 2024 +0100 Train with adjusted hyperparameters commit b89172b6cabe7b1d64a4873f8b82fa3fd5744447 Author: Paul <[email protected]> Date: Sat Oct 26 10:59:46 2024 +0200 Add additional mask commit 900bc1826591f4fff4cb29197d829aeffe22026a Author: Paul <[email protected]> Date: Sat Oct 26 10:59:20 2024 +0200 Fixes and print data for debugging commit e89184a06ce777f0f452d8db9c8e95aae0e186d9 Author: Paul <[email protected]> Date: Thu Oct 24 18:58:00 2024 +0200 Return average number of neighbors commit a74d8b1c1265efc2d6e83da8572b529e4e00cafd Author: Paul <[email protected]> Date: Tue Oct 22 20:03:59 2024 +0200 Prepared execution via LAMMPS plugin commit 36019b24f2bf733e753b4f24e040778d449c1c77 Merge: 58b8dd0 1d6d33d Author: Paul <[email protected]> Date: Tue Oct 22 16:46:35 2024 +0200 Merge remote-tracking branch 'origin/parallelization' into nn_prior commit 1d6d33d72b03698af611a6a8d9bc72e6ab1c5c21 Author: Paul <[email protected]> Date: Tue Oct 22 16:46:18 2024 +0200 Added current protobuf format commit 58b8dd0f1364f20edbc36ec721c9a903dc16499b Merge: cf7939d 58cae76 Author: Paul <[email protected]> Date: Tue Oct 22 16:45:11 2024 +0200 Merge remote-tracking branch 'origin/parallelization' into nn_prior commit 58cae76877cb15b6d4d9cd41d03b1820d4b276d5 Author: Paul <[email protected]> Date: Tue Oct 22 16:44:37 2024 +0200 Updated build.py commit cf7939d77597f5e5f3d29fc943131f6889d881b8 Author: Paul <[email protected]> Date: Tue Oct 22 16:36:25 2024 +0200 Deleted chemutils commit a5c45fa4545dc6625b81f153a4fe759c194163a8 Merge: 9ddb3e2 fa91026 Author: Paul <[email protected]> Date: Tue Oct 22 15:58:22 2024 +0200 Merge remote-tracking branch 'origin/parallelization' into nn_prior # Conflicts: # chemtrain/trainers/base.py commit 9ddb3e2a90bda435ff26b5a23cb66c7133753719 Author: Paul <[email protected]> Date: Tue Oct 22 12:39:02 2024 +0200 Added option to compute validation loss more regularly by limiting number of updates per epoch commit bf7a8e2c843bffb789b05d89d03ed19a228989a6 Author: Paul <[email protected]> Date: Mon Oct 21 17:51:45 2024 +0200 Corrected masked neighbor list implementation commit 944fffdf74353020b55825370e8e2229bdc2ad79 Author: Paul <[email protected]> Date: Mon Oct 21 14:33:53 2024 +0200 Added utility to create optimally sized neighbor list for dataset commit 54e284f8d9f709df69ae2d361b054952ed510f7a Author: Paul <[email protected]> Date: Fri Oct 18 21:40:25 2024 +0200 Added option to return auxiliary output in force computation commit e772c4c7d707cdaa92b0de43775a3d2c2a62f264 Author: Paul <[email protected]> Date: Fri Oct 18 17:44:58 2024 +0200 Extended property prediction functionality to read out additional properties from energy function commit 7bcd6a2a81ad14270c6efd06d3e14ad97a6bd0f8 Author: Paul <[email protected]> Date: Fri Oct 18 17:39:13 2024 +0200 Corrected usage of weights in scalar loss function commit d50735143f3168f2a696e1daedf640057abd72a4 Author: Paul <[email protected]> Date: Fri Oct 18 17:38:52 2024 +0200 Added direct coulomb interaction with differentiable charges commit 01c0952eeda4df9ce663e4c4f2f4ea803eb2619b Author: Paul <[email protected]> Date: Wed Oct 9 17:11:16 2024 +0200 Export learned model commit 2609244954c5204249bca437b2d7a8d34c52c2eb Author: Paul <[email protected]> Date: Wed Oct 9 17:10:59 2024 +0200 Added option to specify preallocation fraction commit 9e46877e97721538fb4d0fb2aceed0d907ab3cb2 Author: Paul <[email protected]> Date: Wed Oct 9 13:28:54 2024 +0200 Train and run Allegro on silver dataset commit 80ca64a19666c1c1d85de61a5c1f0e5ba88986e1 Author: Paul <[email protected]> Date: Wed Oct 9 13:28:27 2024 +0200 Set GPUs to local MPI node number commit fa910265e770960ef0d6231d469257362560ae02 Author: Paul <[email protected]> Date: Tue Oct 8 18:23:10 2024 +0200 Train MACE and Allegro on Ag commit 8b88c0c92cf7af7c2699ef140c65c3218187eee0 Author: Paul <[email protected]> Date: Tue Oct 8 16:59:40 2024 +0200 Added documentation stubs commit c3fc60fdcc3efac50542f952890c7cbbe6908000 Merge: 45d578e 7098212 Author: Paul <[email protected]> Date: Tue Oct 8 16:46:36 2024 +0200 Merge remote-tracking branch 'gitlab/parallelization' into parallelization commit 70982124c692714a96046ebe2e278b51c3254d19 Author: Paul <[email protected]> Date: Tue Oct 8 16:43:32 2024 +0200 Cleaned up files commit 99b4e3dbc44104d4a6d3ec7646c8c5e3d8fc9308 Author: Paul <[email protected]> Date: Tue Oct 8 16:38:22 2024 +0200 Moved modules to the correct location commit cbd47d1ee87d12260e7180c9dd2611e620626acb Merge: c477b15 9ea4ab3 Author: Paul <[email protected]> Date: Tue Oct 8 16:35:12 2024 +0200 Merged connector commit 45d578e4cd4fcd596bf277cd7da105ad998520e8 Author: Paul <[email protected]> Date: Tue Oct 8 16:06:56 2024 +0200 Improved serialization commit 9ea4ab39e08231659233995d22893d9f795a4ce1 Author: Paul <[email protected]> Date: Tue Oct 8 16:04:59 2024 +0200 Improved serialization of model commit 5c48c9bd9e46ae62b44668ff595e4fab4abc0c35 Author: Paul <[email protected]> Date: Sun Oct 6 13:24:47 2024 +0200 Added compiler optimization to build options commit 17b571384396063b1bd608ad8d5fb977a3fd8e39 Author: Paul <[email protected]> Date: Sat Oct 5 12:42:51 2024 +0200 Drafted neighborlist computation on device commit f95326e0da5e137cfeff3e0e2c28e1c9f99332bc Author: Paul <[email protected]> Date: Fri Oct 4 18:18:25 2024 +0200 Drafted C++ interface for DeviceNeighborList class commit 969e8425be7832412546b86ebf4e06ae32f126bb Author: Paul <[email protected]> Date: Fri Oct 4 16:54:49 2024 +0200 Prepared addition of new neighbor list types commit c477b15e63ecc5df83bc5e803bd176be052bc642 Author: Paul <[email protected]> Date: Fri Oct 4 16:17:32 2024 +0200 Added neighbor list build on device commit 0732fb5574803b967d580d3b386f5b2b6932cf9e Author: Paul <[email protected]> Date: Fri Oct 4 11:18:34 2024 +0200 Added RNG keys to dataloader commit a931629e1d9ff952d36cea2070b9e6f1d0d8469d Author: Paul <[email protected]> Date: Fri Oct 4 11:18:14 2024 +0200 Moved dataset and models into new repository commit 83be59515cb26822b7e1a3cff563e38e7c9b4bbd Author: Paul <[email protected]> Date: Wed Oct 2 15:57:03 2024 +0200 Added MACE as trainable model commit 5b9a6e3f3c9c2f70ccb9c02cee88047420cd083b Author: Paul <[email protected]> Date: Wed Oct 2 11:59:59 2024 +0200 Added custom implementation of cell list commit 9197a88db7a27c66c7c28dd4f762fb2252cc6dd4 Author: Paul <[email protected]> Date: Tue Oct 1 11:05:45 2024 +0200 Only re-create neighbor list buffer when necessary commit e7796e6e13729394e08ea250f3b8aff0a611d4b3 Author: Paul <[email protected]> Date: Mon Sep 30 19:53:04 2024 +0200 Drafted documentation commit 60c0617b8cce455dbba9772deae02f192c9021ea Author: Paul <[email protected]> Date: Mon Sep 30 17:52:28 2024 +0200 Fixed memory leak error commit 19b6ef84eacef24b77a1e577ecf638a2b93266a4 Author: Paul <[email protected]> Date: Mon Sep 30 17:11:48 2024 +0200 Copy neighbor list only when necessary commit f4a52572d02a06edd0e872f04e4a0121c19e4647 Author: Paul <[email protected]> Date: Mon Sep 30 16:35:41 2024 +0200 Moved allocation of position array into separate file commit 85947651f01ddcd13690abe2cb9a7e6f65631c29 Author: Paul <[email protected]> Date: Mon Sep 30 14:29:55 2024 +0200 Reuse allocated literals commit 8279661024b93aa050d24bdf1db2cc13f28a9b2e Author: Paul <[email protected]> Date: Mon Sep 30 13:58:01 2024 +0200 Restructured directory commit d6f2c508522ec510d7f68e2041a4a6659fcb8511 Author: Paul <[email protected]> Date: Mon Sep 30 11:12:53 2024 +0200 Correction commit 713ce60381baa579c6dfa92b682b4823176ae6de Author: Paul <[email protected]> Date: Mon Sep 30 10:55:59 2024 +0200 WIP improving build commit eaa875138760dd9942a697af9351c7f7ddef4b3f Author: Paul <[email protected]> Date: Fri Sep 27 21:32:24 2024 +0200 LJ Fluid runs commit 8914fdfb3f2651fbecfa059ca1d1150e9cb6b2c1 Author: Paul <[email protected]> Date: Thu Sep 26 17:10:27 2024 +0200 Drafted new connector to XLA commit ea869ed192adc36ec8592e0ffd2a23f8c44455c3 Author: Paul <[email protected]> Date: Wed Sep 25 17:51:11 2024 +0200 Changes to the training commit a564f081c5c484a5f9935788807e60593bbe34f2 Author: Paul <[email protected]> Date: Tue Sep 24 19:49:17 2024 +0200 Drafted MLIR module compiler and neighborlist builder commit e7afc6340f8f76241222fa18ce7c7a84870f12f5 Author: Paul <[email protected]> Date: Tue Sep 24 11:41:38 2024 +0200 Added testing script to compile allegro model commit f5d6bf324a29d209548df8089354434da7f5d502 Author: Paul <[email protected]> Date: Tue Sep 24 08:31:00 2024 +0200 Added additional Allegro hyperparameters to the config dict commit 24a57db7f44da3b954c6c7dcf0e053c8fa2e868d Author: Paul <[email protected]> Date: Mon Sep 23 18:42:37 2024 +0200 Drafted module exporter commit f9742a8aea78d03d1be27ab55bba45e5d2c553f4 Author: Paul <[email protected]> Date: Mon Sep 23 18:42:22 2024 +0200 Train titanium with allegro model commit 611095e6ed92313d19bd2a85cef0a458d315320a Author: Paul <[email protected]> Date: Fri Sep 20 18:38:24 2024 +0200 Added more utilities commit aeba6d9a8e049b5af3eb3b11f844d761fa96a3d8 Merge: 36fe59b 20dc838 Author: Paul Fuchs <[email protected]> Date: Fri Sep 20 15:00:01 2024 +0200 Merge branch 'main-github' into 'main' Merge Code for Publication (#1) See merge request mfm/science/chemtrain!1 commit c058f2e592059da4338655ec6e4bed1409d10dfc Author: Paul <[email protected]> Date: Fri Sep 20 10:38:11 2024 +0200 Added command line args to the script commit 088e39981d9cf73c1333cce04799d6f503f7df94 Author: Paul <[email protected]> Date: Thu Sep 19 19:44:20 2024 +0200 Created script to train models with smaller cutoff and determine size of graph commit 6c4ba78d553763af7321869d8fbf6670deafec3a Author: Paul <[email protected]> Date: Tue Sep 17 15:57:19 2024 +0200 Use XlaCallModule to refine shapes of jax exported module commit 5f7156dceb01ebe80f7b89fe8473e6028955d48f Author: Paul <[email protected]> Date: Mon Sep 16 19:22:31 2024 +0200 WIP Not all passes run commit 625fe863b8020f3f7609de5fc8567c08a26a60f1 Author: Paul <[email protected]> Date: Mon Sep 16 18:45:23 2024 +0200 Run the model with fixed shapes requiring full recompilation commit 0b8a513f516cdec1c2d5ddb7a522575a506e308a Author: Paul <[email protected]> Date: Mon Sep 16 17:12:58 2024 +0200 WIP Dynamic shapes commit 20dc8387e24fdbd9cb5e4638289c0309425ace8d Merge: 0cdb814 cc91702 Author: Paul <[email protected]> Date: Sat Sep 14 10:37:50 2024 +0200 Merge branch 'main' into chemtrain-dev commit d2203a234d667c61a9d54dc07c48f042dc8b9163 Author: Paul <[email protected]> Date: Fri Sep 13 18:28:39 2024 +0200 Automatically compile the energy function commit 63a8bee21ee4797aee66b7758eea515fe33c5f5d Author: Paul <[email protected]> Date: Fri Sep 13 09:09:17 2024 +0200 Added pybind11 dependency commit e30ff848496e605ba549ebcc6f3a500ef20f4919 Author: Paul <[email protected]> Date: Thu Sep 12 16:27:51 2024 +0200 Added GPU support commit 65c7e3213ebb255e8c2d445154a73bfbbca1bc99 Author: Paul <[email protected]> Date: Wed Sep 11 17:57:44 2024 +0200 Removed calls to stdout commit f043a0a06c8f149a3b2d5809989211273a9001e1 Author: Paul <[email protected]> Date: Wed Sep 11 16:28:52 2024 +0200 Corrected initialization and added species to the network commit aea137b0c14adcb968cf0402993f581986eb0d7e Author: Paul <[email protected]> Date: Wed Sep 11 13:25:34 2024 +0200 Added executable HLO file commit 801eebd12592d64a23d6272ab3781b0f1503025c Author: Paul <[email protected]> Date: Wed Sep 11 13:24:29 2024 +0200 Switched from loading HLO.txt to HLO.pb to get correct force predictions commit 8deb0f8f16fb10608f95ff32237243bf727244c3 Author: Paul <[email protected]> Date: Tue Sep 10 19:54:56 2024 +0200 Runs (correctly?) with fractional coordinates commit 8803737e6336fbf2e0284297cfaf0287e11f5938 Author: Paul <[email protected]> Date: Tue Sep 10 19:34:04 2024 +0200 Force evaluation works but gets nan values commit 86a8c7bff216852b70a094eb06f541a90712d2e4 Author: Paul <[email protected]> Date: Tue Sep 10 18:36:55 2024 +0200 Initialization of plugin works commit 76bf18b3273d1a069241783c7b1dea514e5a053d Author: Paul <[email protected]> Date: Tue Sep 10 15:51:03 2024 +0200 Fixed configuration, can execute HLO instruction within LAMMPS commit a250e5d2da18db1fad32dde1a6429182f0b490fd Author: Paul <[email protected]> Date: Mon Sep 9 19:27:48 2024 +0200 Hide implementation commit 1eee6e153986a655ed0a87d78ae8d007c9baf4e8 Author: Paul <[email protected]> Date: Mon Sep 9 18:44:59 2024 +0200 WIP: Error with computation of class size commit fa3465e5982630846d6284b8a3dd27f070f3fdc4 Author: Paul <[email protected]> Date: Mon Sep 9 16:56:50 2024 +0200 Added simple class to link to model commit 04ab0ecf7ea1ee30a9cdad603e1eeecdc9039977 Author: Paul <[email protected]> Date: Mon Sep 9 14:27:04 2024 +0200 Add lammps application example commit e9b09bd0a2c4da4901a6f0c106f198af07187537 Author: Paul <[email protected]> Date: Mon Sep 9 14:25:04 2024 +0200 Added lammps source commit 16f3f017720fe4ceec8f553d5be030be344d4129 Author: Paul <[email protected]> Date: Mon Sep 9 14:25:01 2024 +0200 Added lammps source commit ebc37978423d43c7fdf217e66db2c0cd731f598d Author: Paul <[email protected]> Date: Mon Sep 9 14:11:42 2024 +0200 No gpu support commit 73e7f2f0c0471dc29f5f19c75fc18c99abc4f3c2 Author: Paul <[email protected]> Date: Mon Sep 9 11:33:50 2024 +0200 Compile in container with gpu support commit f1f0ba9aa734e43b6a4546468218e0bb8b12ded9 Author: paul <[email protected]> Date: Sun Sep 8 20:39:28 2024 +0200 Build shared library commit 4aeb168aa30782d22c802fd6dd378aa4b41466f1 Author: paul <[email protected]> Date: Sun Sep 8 16:11:26 2024 +0200 Build SO commit 68e5c3ffc1c2ac4256f8d3063c20a5aac61ee2f2 Author: paul <[email protected]> Date: Sun Sep 8 15:25:05 2024 +0200 Added example template files for lammps plugin commit 404d522ac6ed3795eac3d92204c4f8861439d74a Author: paul <[email protected]> Date: Sun Sep 8 15:24:26 2024 +0200 First test to execute DimeNet in C++ commit 0cdb8147255c7a53417d6a35ba254044ff168757 Merge: 7248d25 e7aed0e Author: Paul <[email protected]> Date: Thu Aug 29 08:41:19 2024 +0200 Merge branch 'main' into chemtrain-dev # Conflicts: # README.md # docs/conf.py # docs/requirements.txt commit 351ec800a52279defdb6febbec7da8cb6c1d350b Author: Paul Fuchs <[email protected]> Date: Wed Aug 28 17:59:12 2024 +0200 Merge public chemtrain repository (#26) * Initial commit * Added readthedocs --------- Co-authored-by: Stephan <[email protected]> commit 7248d2590ad2ddfa675ae16ee18d8abf7101086e Merge: a6d0172 42eec3b Author: Paul <[email protected]> Date: Wed Aug 28 17:44:50 2024 +0200 Merged commit a6d0172ed23110a183b67fcf6dde0f46a6545292 Author: Paul Fuchs <[email protected]> Date: Wed Aug 28 14:33:17 2024 +0200 Update README.md commit 5c5e5167aeb531350dbb88b55743351f24037cfa Author: Paul Fuchs <[email protected]> Date: Wed Aug 28 14:29:24 2024 +0200 Adds examples (#24) * Added dynamic definition of statepoint * Added possibility to provide observables and loss functions separately from the target values * Added utility function to split old target dict into new format * Added statepoint dict as TypedDict * Small corrections in the unit of the heat capacity * Simplified data loading * Extended scale fractional coordinates function * Fixed fractional coordinate scaling * Support parallel vectors in angle computation via masking * Adds option to save the best training params. * Fixes batch size not divisible by the device count. * Cleaned up * Added masking to validation/testing loss evaluation * Fixed sim_batch_size=-1 for DiffTRe * Fixed transpose of box * Re-executed AD example * Improved computation of potential, forces, and virial * Added per-sample mask * Added option to define per-sample weights * Corrected docs * Simplified documentation hierarchy * Added fused TI example * Removed not required workflows * Fixed some typos * Added licenses to all files --------- Co-authored-by: Sebastien Röcken <[email protected]> commit 87c568c1deea39c7baa0fc6a4637025bf65b0c84 Author: Paul Fuchs <[email protected]> Date: Thu Aug 22 13:04:53 2024 +0200 Update gitlab.yml commit f27bca968bea4612ac570835a42c8ef1987c140b Author: Paul Fuchs <[email protected]> Date: Thu Aug 22 13:03:49 2024 +0200 Update gitlab.yml commit 12e0a68ea3812f2d448bbff5e71c50e4527f5566 Author: Paul Fuchs <[email protected]> Date: Thu Aug 22 13:02:31 2024 +0200 Update gitlab.yml commit 27cdeeba690929ace73c1e6914b8db7da006652f Author: Paul Fuchs <[email protected]> Date: Thu Aug 22 13:01:34 2024 +0200 Update gitlab.yml commit 0f24d05c16502672d68e64bcef3358d0a62872b6 Author: Paul Fuchs <[email protected]> Date: Thu Aug 22 12:57:04 2024 +0200 Update gitlab.yml commit 65c9010e9be7ebde701ef23e8db5d9c295148e48 Author: Paul Fuchs <[email protected]> Date: Thu Aug 22 12:00:57 2024 +0200 Cleanup (#25) * Cleanup unused files * Added file to run algorithms * Moved data and executed simple examples * Adapted difftre example * Fixed deprecated jnp.trapz * Updated documentation landing page * Updated README.md * Bumped version to 0.1.0 * Update workflow with lfs flag commit 36fe59bbe03d33f550eddda2207acf84ea4ad1b5 Author: Paul Fuchs <[email protected]> Date: Mon Aug 5 13:59:55 2024 +0200 Extend alanine dipeptide example (#22) * Extended alanine dipeptide example * Patched jax_md to soften restriction of jax version * Added data access function not relying on host callbacks * Added non-shmap version of update function * Setup run of FM+RM * Adapted sum to mean in shmap_loss_fn * Set new hyperparameters * Dynamic batch per device * Fixed swapped batch_size and batch_cache parameters * Fixed out-of-bounds indexing when resampling simstates * Added option to run parts of example * Fixed failing test * Try to improve picklability by transforming trainer state to dict * Executed complete notebook * Corrected force-matching docstring * Removed unnecessary code commit 52a77f09bd84cf6c51868a667e06667629ac7c67 Author: Paul Fuchs <[email protected]> Date: Wed Jul 17 18:05:39 2024 +0200 Flexible force matching (#21) * Split property prediction into learning and application part * Added possibility to compute features for all snapshot compute functions * Adapted documentation to changes * Split sampling from an ensemble and evaluation of samples * Adapted force_matching to changes * Added additional targets to force matching * Small fixes * Log more detailed statistics * W&B Logging * WIP New force-matching interface * Simplified DataParallel trainer and added possibility for new DataLoaders * Corrected typo * Added custom neighbor list which accepts a mask argument * Small fixes and improvements commit e8b68ec951e2a2f2f4f695e3e37e3552c18075fe Author: Paul Fuchs <[email protected]> Date: Wed Jul 17 17:58:46 2024 +0200 Flexibilize difftre loss (#20) * Improved flexibility of default difftre loss * Check for nans in simulation earlier * Changed SingleTarget typed dict * Restructured target initializers * Changed documentation of constants commit 7106e43b228ccfe7a759a732943fc633abd06399 Author: Paul Fuchs <[email protected]> Date: Mon Jun 24 08:39:01 2024 +0200 Moved jax_md_mod out of chemtrain (#18) * Moved jax_md_mod out of chemtrain * Moved the potential submodule to jax_md_mod commit b8ad24c9a0ef4173efa9ffb2e79b0cf394e00082 Author: Stephan <[email protected]> Date: Thu Jun 20 17:43:44 2024 +0200 Small fixes for docs (#16) Co-authored-by: Stephan <[email protected]> commit 35da1596d9d8577cb70bed3d52e9ae18588bd81f Author: Paul Fuchs <[email protected]> Date: Thu Jun 20 17:43:01 2024 +0200 Documentation and Tests (#10) * Updated version and copyright in the documentation * Changed documentation theme * Improved readability of API documentation * Documented difftre module * Improved documentation of flexible MLETrainerTemplate * Deleted MonotonicInterpolatedSpline (not own implementation) * Fixed docstrings * Removed IBI * Added autosummaries * Shortened headers * Updated potentdial documentation * Updated learn documentation * Canonicalized custom quantity arguments and improved documentation of TargetBuilder * Improved documentation of trainers * Updated documentation for the reweighting subpackage * Fixed removing replica_kbt kwarg * Drafted real difftre example * Prepared DiffTRe example * Corretions in documentation * Executed DiffTRe example * Hide some cells in the example * Small improvements in the documentation commit cabccef283888e4666114e625c4f9741401300ee Author: Paul Fuchs <[email protected]> Date: Wed Jun 12 12:45:19 2024 +0200 Flexible Statepoint (#12) * Extended quantities to accept additional information * Extended ADF to multi-species systems * Extended RDF to multi-species systems * Added custom_partition.py to simplify neighborlist evaluation * Improved flexibility of trajectory generator * Improved flexibility of quantity_traj * Adapted Difftre and Relative_entropy trainers commit d5047848b3eb912aae71d89e199d5eb7cd0cca08 Author: Paul Fuchs <[email protected]> Date: Mon Jun 10 17:20:57 2024 +0200 Flexible training tasks (#14) * Flexible training tasks * Adapted convergence checking function * Renamed valid trigger array * W&B logging commit 8ff2abaecfb06bc505d825cc649eaa782bc1e32f Author: Stephan <[email protected]> Date: Mon Jun 10 11:18:57 2024 -0400 Docs stephan (#15) * Deleted custom simulator * Added docs for property prediction * Deleted active learning * Deleted NUTS trainer and added usage for EnsembleOfModels * Added docs for probabilistic.py --------- Co-authored-by: Stephan <[email protected]> Co-authored-by: Paul <[email protected]> commit e64ccaa4ce3cc6f209e508618faba2a4fc1213c4 Author: Paul Fuchs <[email protected]> Date: Mon Apr 29 11:20:12 2024 +0200 Relative entropy (#11) * Moved core of relative entropy minimization into module `chemtrain.learn.difftre` * Refactored computation of relative entropy gradient to align better with difftre implementation * Added quickstart example for relative entropy * Added real example for relative entropy and force matching commit 64cb5bbdd98c5fbac6bc8033c1151d501bbe7cd1 Author: Paul Fuchs <[email protected]> Date: Thu Apr 25 08:52:13 2024 +0200 Increased version number commit d90dd51ba8d8f4b12c111013d02d4e1015ddba4a Merge: 0759b24 e76615d Author: Paul <[email protected]> Date: Fri Apr 19 07:47:46 2024 +0200 Merge remote-tracking branch 'github/main' commit 0759b249c264ee9db1df9bfe4011a5928a72f054 Author: Paul <[email protected]> Date: Fri Apr 19 07:47:21 2024 +0200 Fixed bug of neighbor list error not printable commit e76615d8e68a532630fb754a596fbaf707cd3313 Author: Paul Fuchs <[email protected]> Date: Thu Apr 18 17:06:56 2024 +0200 Update .gitlab-ci.yml commit 59fd4b0bc7539cc292689df3549ae7d6b16b58ef Author: Paul Fuchs <[email protected]> Date: Thu Apr 18 17:00:43 2024 +0200 Changes (#9) * Improved documentation of traj_util.py * Rearranged trainers into concrete and abstract module *Improved documentation of trainers via autosummary * Updated subpackage initializations * Added getting started examples for the prior model and force matching * Improved getting started page commit 12bbb4b16ceb2e6a29f13f281cb21ffcc4e31b3c Author: Paul Fuchs <[email protected]> Date: Tue Apr 9 11:13:31 2024 +0200 Changes (#8) * Restructured chemtrain in multiple submodules * Adapted documentation to new structure and created documentation stubs * Added testing workflow * Updated chemtrain requirements and python version * Fixed bugs commit 2dbdb665ee14b9c6af78b88723eee3b781e3ddc4 Author: Paul Fuchs <[email protected]> Date: Tue Apr 9 10:20:58 2024 +0200 Update gitlab.yml commit c79e43ba672806c40865b3783e25b159a724632a Merge: abd0a23 bcaf566 Author: Paul Fuchs <[email protected]> Date: Tue Apr 9 10:14:18 2024 +0200 Merge pull request #7 from tummfm/workflows Added workflows to test chemtrain commit bcaf56632a23c0b167f508e04f6d8f8f91687cc0 Author: Paul <[email protected]> Date: Tue Apr 9 10:08:25 2024 +0200 Restricted scipy version commit 873afc46139b3812a138f6cdde79aa0991dfe3ec Author: Paul <[email protected]> Date: Tue Apr 9 10:02:32 2024 +0200 Restricted scipy version commit 15e445d66e5de34d59f0d462a97e2c372e8552e3 Author: Paul <[email protected]> Date: Tue Apr 9 09:43:35 2024 +0200 Increased mdtraj version commit 0b023cbcdafe134dfb58763be44f504ba806ff73 Author: Paul <[email protected]> Date: Tue Apr 9 09:34:21 2024 +0200 Increased python version commit 8bb53e47156b1a014412c9c553c6e0d4740ad684 Author: Paul <[email protected]> Date: Tue Apr 9 09:31:34 2024 +0200 Increased python version commit 61d29a2a311c645c605fee827638d09f6b7c5a72 Author: Paul <[email protected]> Date: Tue Apr 9 09:27:53 2024 +0200 Fixed installation requirement commit 6a45e30fabaec36ae10b1e4343c3eefce43e6a84 Author: Paul <[email protected]> Date: Tue Apr 9 09:18:16 2024 +0200 Fixed installation requirement commit abd0a23c1a2c75af829c845bad122ae8be30a519 Author: Paul <[email protected]> Date: Tue Apr 9 09:15:29 2024 +0200 Added test action commit e6354a2f38b79bb180c28db7fbdaf738f186e45e Author: Paul <[email protected]> Date: Fri Mar 22 09:21:30 2024 +0100 Merged prior potential improvements commit d009389e909dec757c09d35e8f48a771626babf0 Author: Paul Fuchs <[email protected]> Date: Thu Mar 21 10:09:53 2024 +0100 Create .gitlab-ci.yml commit 107d859d6ea098e0a706d7dca38706044c18dc63 Author: Paul Fuchs <[email protected]> Date: Thu Mar 21 10:01:23 2024 +0100 Create gitlab.yml commit ba93db516f032cd2b53477702e1f646d1578fa2f Author: Paul Fuchs <[email protected]> Date: Thu Mar 21 10:00:08 2024 +0100 Create gitlab.yml commit 84be145403ea8be60635cca721c2c21f62c1b974 Author: Paul <[email protected]> Date: Wed Mar 20 13:31:10 2024 +0100 Finished splitting commit 4cccdddfba547dfdfcaff6807493de5f328a96af Author: Paul <[email protected]> Date: Wed Mar 20 11:54:06 2024 +0100 WIP Splitting commit 4993dfb06718d1d29875f420f1ee53a345964e92 Author: Paul <[email protected]> Date: Wed Mar 20 11:12:48 2024 +0100 Added multiple dihedral terms to prior commit 691790a7ae1abc70bc8c333b8146c17adb674721 Author: Paul <[email protected]> Date: Tue Mar 19 16:31:01 2024 +0100 Added more dihedral terms commit d9f9b94c96150f1af325d64f17a86ad252a95673 Author: Paul <[email protected]> Date: Mon Mar 18 15:05:58 2024 +0100 Fixed constraining function commit e9a64f0867ba8fc3c4e2231cf2180dc350332e69 Author: Paul <[email protected]> Date: Mon Mar 18 10:33:41 2024 +0100 Added atom renaming utility commit 69c026214d3c6c0c7e8627854e6e30466d47be2a Author: Paul <[email protected]> Date: Mon Mar 18 10:19:26 2024 +0100 Added atom renaming utility commit 25f95a01dccdefc7f11385e6beedc66c47121f27 Author: Paul <[email protected]> Date: Mon Mar 18 10:10:59 2024 +0100 Added atom renaming utility commit e5b9b715d2169527425877e67df5597c1fdbd6eb Author: Paul <[email protected]> Date: Mon Mar 18 09:54:35 2024 +0100 Added atom renaming utility commit fea1b8b42cfc9cc6750c923c80ac3284acf10365 Author: Paul <[email protected]> Date: Thu Mar 14 17:19:29 2024 +0100 Implemented classical force field commit df03168f54213ab2e7ba7fb4c91626abb83d5797 Author: Paul <[email protected]> Date: Wed Mar 13 16:48:10 2024 +0100 WIP Flexible prior potential commit b7298b70d324206bbff74354e81d6f7790497057 Author: Paul <[email protected]> Date: Tue Mar 12 18:10:25 2024 +0100 WIP Flexible prior potential commit 390980e2e1fe0efcc34e656f0358a32ea01e03cd Author: Paul <[email protected]> Date: Thu Mar 7 18:15:19 2024 +0100 WIP Flexible prior potential commit 5eead3ca5406d2c0af892bfccaecaf636b525dfc Merge: 6935ac9 9a2e3e0 Author: Paul Fuchs <[email protected]> Date: Fri Feb 16 13:34:02 2024 +0100 Merge branch 'difftre_additions' into 'main' Additions to chemtrain See merge request mfm/science/myjaxmd!5 commit 9a2e3e03c8aab3f3e6569efca40738285d99279f Author: Paul Fuchs <[email protected]> Date: Fri Feb 16 13:34:02 2024 +0100 Additions to chemtrain commit 6935ac9ccecdbaaa9b5e954ea66cd5536c2fa24f Author: stephan <[email protected]> Date: Thu Jun 29 11:50:28 2023 +0200 Merged SGMCMC code and feature augmentations commit eb906c4c90ebe20eb3106e0bd33e350c049ac6c5 Author: stephan <[email protected]> Date: Mon Jun 19 09:09:01 2023 +0200 Circumvented bug in JAX commit 290e70b98251416c9b40dc42301d2e6ef710965d Author: stephan <[email protected]> Date: Tue Feb 21 21:09:22 2023 +0100 Fixed depreciated tree_utils commit 14791a3bfd685274a8903e3c1a59662b1e37d16b Author: stephan <[email protected]> Date: Tue Feb 21 21:03:20 2023 +0100 Deleted coax due to constant version issues commit e18e8404171b96888896840470754edad8e6afc1 Author: stephan <[email protected]> Date: Tue Feb 21 21:00:20 2023 +0100 Update temperature computation compatibility with newer jax_md commit 9bfd0abc0f2bbd75e92a3dda97790850fd269f94 Author: stephan <[email protected]> Date: Wed Aug 31 16:42:38 2022 +0200 # Conflicts: # examples/mof_al/active_property_prediction.py # examples/mof_al/plot_learning_curve.py commit 891a0d1d26585cd13a60179e97e0c1fe5fd7d255 Author: stephan <[email protected]> Date: Thu Aug 4 11:33:53 2022 +0200 Fixed incorrect NUTS data by using stateless full_data_mapper commit d8970dc13d8bd56e2f1e11811977a5bfafb4f305 Author: Stephan <[email protected]> Date: Mon Jul 4 18:24:36 2022 +0200 Fixed bug in neighbor update of trajectory generator and avoid pre-allocation in active learning to avoid OOM over time commit 61a7e6796444aaa0f6189cdac100bcc41209caa1 Author: Stephan <[email protected]> Date: Fri Jul 1 17:24:43 2022 +0200 Fixed versions of supplementary packages to avoid installation errors commit 5655a0bc27674c5310c764fd3de34f4ddcd531d4 Author: stephan <[email protected]> Date: Tue Jun 14 20:58:26 2022 +0200 Enabled training on multiple samples per al training commit 0d8acd5e1e376d590cacb8b5adb4ff3bfae330cf Author: stephan <[email protected]> Date: Fri Jun 10 14:47:52 2022 +0200 Generalized computation of per-box per species errors commit f19106ede7e2c095f10f7f34abb0e40e981672d0 Author: stephan <[email protected]> Date: Fri Jun 10 10:15:56 2022 +0200 Refactored best params selction in trainer such that correct selection without val loader also works when only calling self.best_params commit 8cd85e7175d21c9f768c26654a342212063b2055 Author: stephan <[email protected]> Date: Thu Jun 9 18:10:10 2022 +0200 Enabled shuffling in train_test_split commit cfa5fc1a2aee73cbef5bb0852d7e341d78ccd8c2 Author: stephan <[email protected]> Date: Tue Jun 7 20:16:25 2022 +0200 Updated Active property prediction commit 2e3b97b7dc0701aa00863e3840aafef6df592ce1 Author: stephan <[email protected]> Date: Fri Jun 3 17:06:07 2022 +0200 Incorporated improved dataloaders with parallel validation loss evaluation and without mapper state. Still picklable and clearing cache avoids data leaks. commit 5f0bc6a695c4ceeb8153b96ba2b75d94d8f3496c Author: stephan <[email protected]> Date: Wed Jun 1 11:03:14 2022 +0200 Enabled pmapped computation for dropout UQ commit 60ec22d6600aa5404b0d768463b7d8bf6e4fcc72 Author: stephan <[email protected]> Date: Fri May 27 15:14:53 2022 +0200 Reduce memory load in dataloaders, avoiding unnecessary copies commit 324c7e18237d0d08f8cf651ac7b001ef09043905 Author: stephan <[email protected]> Date: Thu May 26 15:53:48 2022 +0200 Bugfixes in relation to setting testloader commit 417f3901fee9f91907df1b603acd0be5da49284c Author: stephan <[email protected]> Date: Wed May 25 19:12:56 2022 +0200 Testloader can be set from outside trainer commit 6b3d147ddf6da437044874071c11dde4ad936117 Author: stephan <[email protected]> Date: Fri May 20 16:39:40 2022 +0200 Added training on single samples commit 297169f3148e1a5ccb31b048cae2707786a8f4d0 Author: stephan <[email protected]> Date: Fri May 20 14:05:41 2022 +0200 Trainers now work without validation set commit 2713448e8c386ca72cd5a8776b737abc451d627d Author: stephan <[email protected]> Date: Wed May 25 10:07:03 2022 +0200 Clearing cache to avoid memory leaks commit a3d2ed83c0075430f4d83a5423ad1ac3e259d3f0 Author: stephan <[email protected]> Date: Tue May 17 17:26:32 2022 +0200 First shot at active learning commit 4a1f849cb18f04e49a66a4a7e166106d656e69e2 Author: stephan <[email protected]> Date: Tue May 17 17:25:37 2022 +0200 Fixed batchsize if loaded trainer has other number of GPUs commit 8c79fe5b05242e4b2b4550c7339b7820a2184b24 Author: stephan <[email protected]> Date: Mon May 16 17:43:01 2022 +0200 Make validation error computation robust to small validation data sets commit fee46107159d725d9af991aaa62e40cae03831d7 Author: stephan <[email protected]> Date: Mon May 16 15:01:14 2022 +0200 Extended datasplit to allow 0 validation or test sets commit 39b6fdc5d6a483f68fb5a08fbd21c8f83fa9fdea Author: stephan <[email protected]> Date: Fri May 13 11:43:56 2022 +0200 Generalized per-species function to allow non-existing species-types and vectorization commit 639536e41d64ef935b20fdf219c9f6a66d04f6d9 Author: stephan <[email protected]> Date: Thu May 12 16:22:26 2022 +0200 Implemented per-species postprocessing commit 94e4ce286d2efcb71bcc4e79681895c669e8ce07 Author: stephan <[email protected]> Date: Thu May 12 09:52:03 2022 +0200 Implemented UQ calibration commit 8c588cbe15a360d2127d3cc7eeee934a91944bea Author: stephan <[email protected]> Date: Wed May 11 17:48:02 2022 +0200 Moved computation of uncertainty values into probabilistic.py commit 8b671f6e6693908a6f6a969e985618d207d220aa Author: stephan <[email protected]> Date: Wed May 11 15:50:17 2022 +0200 Saving matched model in trainer and making trainloader public for convenience commit 16de2ad1ffce6e764ad7513a085fd57f63bf2013 Author: stephan <[email protected]> Date: Tue May 10 11:57:19 2022 +0200 Adjusted property prediction to new trainer interface, now species mask is evaluated correctly in loss commit aabcc42835ce1b3f2385cd96db4a2fa70cd81cc4 Author: stephan <[email protected]> Date: Tue May 10 11:44:32 2022 +0200 Using best obtained params for test set, using batch_per_device for validation loop and fixed error in initialization of best params commit cda0b0b33f9636303600030f4e7c8bfd19382514 Author: stephan <[email protected]> Date: Mon May 9 16:04:30 2022 +0200 Unified validation evaluation with force matching loss commit 85d4ac64edb4206170acb07a5d971ed5d354108c Author: stephan <[email protected]> Date: Mon May 9 15:35:07 2022 +0200 Fixed SGMCMC bugs with refactor commit 35d835d571c1395f2229da498c27fed559ef0092 Author: stephan <[email protected]> Date: Tue May 3 13:35:04 2022 +0200 Fixed bug in new validation loss function, but does not yet work with pmap and data state still necessary commit bc88dd5c5d78b0b1df44ad703a817c6e5d760ee2 Author: stephan <[email protected]> Date: Tue May 3 12:07:09 2022 +0200 Updated dataloaders to new jax-sgmc API, fixing bug in dataloading sequence commit 44f888112ce301885aa88e808272e6d072a6d516 Author: stephan <[email protected]> Date: Mon May 2 16:50:35 2022 +0200 Drawing samples in epochs for data loaders commit 3617aecae5c7804220170309283367b8ae431370 Author: stephan <[email protected]> Date: Wed Apr 27 19:37:27 2022 +0200 Fixed bugs in DiffTRe with dropout and sim_keys commit 788feb1172b5ed1f37d3360fcd42717dcf36a26e Author: stephan <[email protected]> Date: Fri Apr 8 17:45:15 2022 +0200 In principle implemented mapping without masks and proper mean computation over dataset, but still bug in reshape of predictions commit 9bdf829e096296b166aa2bda5211619b6258f377 Author: stephan <[email protected]> Date: Fri Apr 8 12:10:52 2022 +0200 Small documentation improvements commit 28b875c0ce897a6e2a4503efbdf2254b5f8fdef4 Author: stephan <[email protected]> Date: Fri Apr 8 10:11:21 2022 +0200 Fixed on-the-fly checking if dropout is used, which slows down learning commit 9826b55dff950f49b036efa218be9c0d89b8e914 Merge: 29225c3 6c9934a Author: stephan <[email protected]> Date: Thu Apr 7 17:53:35 2022 +0200 Merge branch 'main' into mof_al commit 29225c38daf6063290199ea0339dd3e32c1188cd Author: stephan <[email protected]> Date: Thu Apr 7 17:35:25 2022 +0200 Trying to re-factor loss for padded species commit d5e1fe67b43742279ef09d763e40cd0d85f062c8 Author: stephan <[email protected]> Date: Thu Apr 7 16:33:22 2022 +0200 Deleted self._n_devices for better re-use after loading commit 6c9934a75eebd23bd1279d8731ea4e2ee88fed7a Author: stephan <[email protected]> Date: Thu Apr 7 14:20:10 2022 +0200 Bugfix: Took single tree of gradient twice which caused slowdown commit f3074c97b8810fd29474f9f8347e2b92f2d7fd30 Author: stephan <[email protected]> Date: Wed Apr 6 10:47:43 2022 +0200 Uncertainty prediction works so far commit 98f8906d4717ba5fd873b9ec2e23391809ced67f Author: stephan <[email protected]> Date: Tue Apr 5 19:15:23 2022 +0200 Fix dropout naming commit c281255bc1ab9b4a702ece8043485b782d7559cb Author: stephan <[email protected]> Date: Tue Apr 5 12:50:34 2022 +0200 Mapping uq over testdata works commit febb96f30769723738ff1bf8977957a218405aee Author: stephan <[email protected]> Date: Tue Apr 5 10:56:49 2022 +0200 Set defaults of n_species to 100 for safety commit d4ffa6a71e5370a07293172b1a48a4412df902a6 Author: stephan <[email protected]> Date: Tue Apr 5 10:40:18 2022 +0200 Initialize best_params to init_params commit d872b0340a3449e9cf88f127694e7384ab0e95f8 Author: stephan <[email protected]> Date: Mon Apr 4 10:14:56 2022 +0200 Using Dropout for property prediction commit 419bbe631753353e75f51d3844b22b0691e09b5d Author: stephan <[email protected]> Date: Fri Apr 1 21:09:00 2022 +0200 Refactored Dropout interface for better re-usability commit a212349d200db785835753df16c982d82d0a58db Merge: 3b7340b ab98c1f Author: stephan <[email protected]> Date: Fri Apr 1 12:09:24 2022 +0200 Merged Dropout commit ab98c1f388cf9d3f1ec69627bebee3ba03e690e2 Author: stephan <[email protected]> Date: Fri Apr 1 10:59:51 2022 +0200 Proper merging Dropout commit 3cdafa2c0b2913ea4e3d2d4d60e54490ce533593 Merge: 2de07c3 3b7340b Author: stephan <[email protected]> Date: Thu Mar 31 16:12:15 2022 +0200 Merge branch 'mof_al' into Dropout_remerge_from_active_learning # Conflicts: # chemtrain/active_learning.py # chemtrain/difftre.py # chemtrain/jax_md_mod/custom_energy.py # chemtrain/jax_md_mod/custom_nn.py # chemtrain/util.py # examples/DiffTRe_run.py # examples/simulation.py # util/Initialization.py # util/Postprocessing.py commit 3b7340ba3a1f5f71c7667310bc03d14d5926e983 Author: stephan <[email protected]> Date: Thu Mar 31 13:00:45 2022 +0200 Update docs commit 8616872e22538fa883ef130a19091b13e8ef218a Author: stephan <[email protected]> Date: Tue Mar 29 18:08:58 2022 +0200 Added molecular property predictor for carved-out dimenet and extended documentation commit 3d6bdf92f8104814135566d84ff6ab8aa698d9cf Author: stephan <[email protected]> Date: Fri Mar 25 17:42:32 2022 +0100 LJ simulation runs commit 2ef37314950e36dedf9f3fc59ac4ff5d45eba755 Author: stephan <[email protected]> Date: Thu Mar 24 17:41:57 2022 +0100 Fixed error that pad_per_atom_quantities only returned integers, irrespective of data type commit e180afb90dfa3201ee1b56bd3c222d62a591d7b9 Author: stephan <[email protected]> Date: Thu Mar 24 16:24:16 2022 +0100 Initial MOF Training runs through and extended property prediction trainer commit 71649108b5e0e07e9f906ff9c907dbb4ff620ae9 Author: stephan <[email protected]> Date: Thu Mar 24 11:02:58 2022 +0100 Don't move dataset to device at train_test_split to avoid memory overflow for datasets bigger than device memory commit 21e81f8e8c68293dac4c7fb38b5620faf94714e3 Author: stephan <[email protected]> Date: Thu Mar 24 09:31:44 2022 +0100 Preprocessed MOF data into DimeNet graphs commit 7327abc35f82c2f70276a8358970229c931fddb5 Author: stephan <[email protected]> Date: Tue Mar 15 17:09:59 2022 +0100 Added documentation for dimenet files commit 8c26576a006c2f5c10a9c724eb5fd0cf51e2bad0 Author: stephan <[email protected]> Date: Fri Mar 11 11:56:15 2022 +0100 Moved canonicalice species to sparse graph commit 7b240449cd1f7750f0e8f2d624c944e2be90e876 Author: stephan <[email protected]> Date: Thu Feb 24 17:16:13 2022 +0100 Unified MAE with parallel validation evaluation commit 6808ae172787d7ae3ca7b6d5ea806d90e1e8c46b Author: stephan <[email protected]> Date: Thu Feb 24 16:09:57 2022 +0100 Added MAE Force-matching error again commit 02d078306aafa3a3442837440fe3ec1f8f9867a3 Author: stephan <[email protected]> Date: Thu Feb 24 14:11:11 2022 +0100 Implemented parallel evaluation of validation loss commit 17b594cfa6da09825583eb073efc5b0904f85c0d Author: stephan <[email protected]> Date: Wed Feb 23 15:12:46 2022 +0100 Refactored Force-matching to be compatible with more general prediction of arbitrary quantities commit eb74cd68b7709667c7405a4dc3e9aa73805cd8f1 Author: stephan <[email protected]> Date: Tue Feb 22 18:31:27 2022 +0100 Moved data preprocessing into dedicated module commit 195dfca3c7d97bc25a532d7c84b0b394ebf2fd05 Author: stephan <[email protected]> Date: Tue Feb 22 16:04:40 2022 +0100 Abstract params unnecessary in MLETrainerTemplate commit d85184e889807b2476e94c8f79de6bfb92bff574 Author: stephan <[email protected]> Date: Tue Feb 22 15:34:29 2022 +0100 Moved fitting-related stuff into max_likelihood commit 500e9ce8daa9ac4e1d77305c54e3f89d68815ba6 Author: stephan <[email protected]> Date: Tue Feb 22 14:57:45 2022 +0100 Adjusted mae loss masking to match mse commit eed20c79af68221582196409a474105270b3afaf Author: stephan <[email protected]> Date: Tue Feb 22 11:50:23 2022 +0100 Enabled constructing sparse graph from dict for easy dealing with batched data commit 86a7143dd4d69fa567201d31c14bfa9c0321f190 Author: stephan <[email protected]> Date: Tue Feb 22 10:52:24 2022 +0100 Split pmapped update from pmapped loss function for better re-usability for validation commit 69927026a909d6fc7c1590e3e5c442e53cb9beb9 Author: stephan <[email protected]> Date: Tue Feb 22 10:25:58 2022 +0100 Carved out pmap parallelization from force loss function commit 7f58223ef7e79b9b7d3cb38e4bd8931a784fa6f1 Author: stephan <[email protected]> Date: Mon Feb 21 20:30:26 2022 +0100 Implemented morph from SparseGraph to dict for NumpyDataLoaders commit 5d9f7450e100214ffbd5860ee4d2d89b46a05d28 Author: stephan <[email protected]> Date: Mon Feb 21 20:22:44 2022 +0100 Included test-split in train-test-val split commit d953c482686dd59eb8ab5cde22dee6c3d7e0a579 Author: stephan <[email protected]> Date: Mon Feb 21 17:06:04 2022 +0100 Generalized test-train split to arbitrary pytree datasets commit 04ddd7d3a1c6821aad08e603f9e3f0d06fbc6abb Author: stephan <[email protected]> Date: Mon Feb 21 13:50:26 2022 +0100 Moved species padding into graph generation function commit 8c10ae8e4b085d47addd72dabf898a228d8c51e6 Author: stephan <[email protected]> Date: Fri Feb 18 18:33:29 2022 +0100 Predicting the partial charge structure works commit e21e02eaf15337759702eeff480d624806ed43e5 Author: stephan <[email protected]> Date: Fri Feb 18 18:03:33 2022 +0100 Saving dict of sparse graph for transparency. Can be used easily to construct Graph commit 2fbbf37762d6008e9837700595b663dc6e59b796 Author: stephan <[email protected]> Date: Fri Feb 18 16:12:24 2022 +0100 Added padded species and moved species into sparse graph commit 4247f3e1100298a6f10ad3b345ee07c1f7e11ac0 Author: stephan <[email protected]> Date: Fri Feb 18 10:54:01 2022 +0100 Only handinh kwargs through to dimenet to avoid repeating params and docstrings commit 550259d7bb56d399380798fd7c7c7d8b137caf97 Author: stephan <[email protected]> Date: Thu Feb 17 15:43:44 2022 +0100 Implemented test-train split commit 3bff330be2114f4e33ba8930c2b22e8f1db5177d Author: stephan <[email protected]> Date: Wed Feb 16 13:36:28 2022 +0100 Added function to compute sparse graph for whole dataset commit ca2bc3a9f7f24358b46452680d2c469ad8058d69 Author: stephan <[email protected]> Date: Wed Feb 16 13:24:05 2022 +0100 Improved documentation commit 704619c1feb09226e8b5ed0179c96c8862dde9a9 Author: stephan <[email protected]> Date: Tue Feb 15 14:01:41 2022 +0100 Re-formated custom_space.py commit 93401bfff286fd31ddaa9653e52730c8cba9871c Author: stephan <[email protected]> Date: Tue Feb 15 13:20:54 2022 +0100 Move sparse graph in dedicated dataclass for easier usage commit 7d7f72b1a28a80bd65bb7b50823555b40c08f391 Author: stephan <[email protected]> Date: Tue Feb 15 10:32:09 2022 +0100 Moved neighborlist preprocessing into sparse graph since sparse graph is hard-depending to neighborlist anyway commit c1e769f4ad51eee83c977ea2ff265027b5a0017b Author: stephan <[email protected]> Date: Mon Feb 14 15:45:40 2022 +0100 Fixed NUTS solver commit 09559693a445af541461e359bc1d6e6f7fbfa558 Author: stephan <[email protected]> Date: Mon Feb 14 15:05:11 2022 +0100 Redistributed forwardUQ functions commit cfd7d886b7fa7721cc91bb747cbe879df3b2a6d8 Merge: 003d35f 709179d Author: stephan <[email protected]> Date: Mon Feb 14 13:33:46 2022 +0100 Merged updated interface for probabilistic force matching commit 709179d1c3310245de2e944d5ca18b67d67ddd94 Author: Gregor Döhner <[email protected]> Date: Mon Feb 14 10:01:50 2022 +0100 Standardized parameters returned by trainer class commit 2d12bc6830dcc308c7db41844361479d098e70f7 Author: Gregor Döhner <[email protected]> Date: Fri Feb 11 19:24:46 2022 +0100 convert_to_ist and tree_slice works commit 003d35f4058d5e891bcc891aae846edac497832c Author: stephan <[email protected]> Date: Thu Feb 10 17:41:52 2022 +0100 First shot at property prediction network commit e22de7d556a84e5a1f5d7609770…
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