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Sparsify and simplify #12

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b4e0d8f
Revise default training loss
ericyuan00000 Nov 17, 2023
91ff5f8
Change data parsing modes
ericyuan00000 Nov 17, 2023
dc7584d
Simplify generic parsing function
ericyuan00000 Nov 18, 2023
976cbd7
Debug setting keys defaults
ericyuan00000 Nov 18, 2023
d64f094
Merge remote-tracking branch 'origin/main' into Simplification
ericyuan00000 Nov 18, 2023
2a3acbf
Simplify neighbor masks of extensive environments
ericyuan00000 Nov 18, 2023
db187a3
Simplify dataloader
ericyuan00000 Nov 18, 2023
cf0f76a
Update dataloader as generators
ericyuan00000 Nov 19, 2023
fdfadbe
Implement random seed
ericyuan00000 Nov 19, 2023
1820217
Update dataset implementation in ASE interface
ericyuan00000 Nov 19, 2023
8bd4ca5
Migrate from float64 to float32
ericyuan00000 Nov 19, 2023
dc65b10
Change input format from dictionary to explicit
ericyuan00000 Nov 20, 2023
d6e45b2
Update compatibility with TorchScript
ericyuan00000 Nov 25, 2023
6344835
Simplify neighbor collection
ericyuan00000 Nov 29, 2023
6877035
Rename variables and simplify layers
ericyuan00000 Dec 1, 2023
32a41ca
Modularize training script
ericyuan00000 Dec 1, 2023
b3addfb
Modularize loss functions
ericyuan00000 Dec 2, 2023
5a51a4a
Update gradient flow visualization
ericyuan00000 Dec 2, 2023
85ed1fb
Update gradient flow visualization
ericyuan00000 Dec 2, 2023
fe09a28
Update flexible data properties
ericyuan00000 Dec 3, 2023
be536f3
Update data normalizer
ericyuan00000 Dec 3, 2023
e4911b3
Update initialization and node embedding
ericyuan00000 Dec 4, 2023
97662b1
Change loss default to normalized objective
ericyuan00000 Dec 4, 2023
094c78c
Sparsify distance matrices
ericyuan00000 Dec 4, 2023
0e1ea33
Partially impletment periodic boundary conditions
ericyuan00000 Dec 4, 2023
318f9f9
Refactor neighbor handling into shell
ericyuan00000 Dec 5, 2023
98ce561
Modularize output networks and rename variables
ericyuan00000 Dec 6, 2023
54d2070
Update resume training option
ericyuan00000 Dec 6, 2023
185735f
Update model precision option
ericyuan00000 Dec 6, 2023
71c1fb4
Modularize normalizer
ericyuan00000 Dec 8, 2023
3b67c76
Reimplement Hessian calculation
ericyuan00000 Dec 8, 2023
b29d980
Update ASE calculator
ericyuan00000 Dec 8, 2023
f369de2
Update TorchScript consistency
ericyuan00000 Dec 11, 2023
2d87d56
Update forward shape hint
ericyuan00000 Dec 12, 2023
ee95752
Revoke TorchScript consistency
ericyuan00000 Dec 14, 2023
c552fd7
Rename files
ericyuan00000 Dec 14, 2023
daa7e1e
Update model argument in trainer
ericyuan00000 Dec 14, 2023
0216915
Update file names
ericyuan00000 Dec 14, 2023
1a40056
Update trainer packages
ericyuan00000 Dec 14, 2023
bf1a035
Update version
ericyuan00000 Dec 14, 2023
de04b5b
Update representation function comment
ericyuan00000 Dec 14, 2023
12a4d9d
Update SwiGLU nonlinearity
ericyuan00000 Jan 9, 2024
4476cb8
Update AdamW optimizer
ericyuan00000 Jan 9, 2024
f351654
Update setup file
ericyuan00000 Jan 16, 2024
e286388
Update model device
ericyuan00000 Jan 17, 2024
05334fa
Update dependencies
ericyuan00000 Jul 11, 2024
db52a6f
Create PyG RadiusGraph
ericyuan00000 Jul 11, 2024
3972ab2
Update PyG Dataset
ericyuan00000 Jul 12, 2024
5927ac1
Update data split
ericyuan00000 Jul 12, 2024
f606a0c
Update data split
ericyuan00000 Jul 12, 2024
5ee9d30
Update atomic number report
ericyuan00000 Jul 12, 2024
b6f3ffb
Update atomic energy calculation
ericyuan00000 Jul 12, 2024
9353ca9
Update scale-shift layer
ericyuan00000 Jul 12, 2024
602732c
Update scale-shift layer
ericyuan00000 Jul 12, 2024
74a2c08
Update training script for PyG datasets
ericyuan00000 Jul 12, 2024
b81fcfd
Update stats calculation
ericyuan00000 Jul 13, 2024
a9d43bd
Update scaler construction
ericyuan00000 Jul 13, 2024
7b4bcf1
Update embeddings
ericyuan00000 Jul 14, 2024
daed7e8
Update edge index direction
ericyuan00000 Jul 14, 2024
26441ca
Update interaction layer
ericyuan00000 Jul 14, 2024
c821383
Update output layers
ericyuan00000 Jul 14, 2024
2077f24
Debug
ericyuan00000 Jul 15, 2024
5ce59f2
Update losses
ericyuan00000 Jul 16, 2024
cea7ee9
Update ASE calculator
ericyuan00000 Jul 17, 2024
334dc90
Debug boundary condition
ericyuan00000 Jul 17, 2024
4ff77cb
Add wandb logging
ericyuan00000 Jul 17, 2024
b162a27
Update parser
ericyuan00000 Jul 21, 2024
ecd3375
Fix solver in parser
ericyuan00000 Jul 21, 2024
21aa313
Fix trainer
ericyuan00000 Jul 24, 2024
8d207fc
Revise architecture
ericyuan00000 Jul 25, 2024
9f50a60
Fix layers
ericyuan00000 Aug 7, 2024
faf5735
Fix layers
ericyuan00000 Aug 7, 2024
2abf740
Fix force output
ericyuan00000 Aug 7, 2024
d0d5913
Return full model
ericyuan00000 Aug 7, 2024
55cf44c
Fix speed
ericyuan00000 Aug 7, 2024
f97e540
Return full model
ericyuan00000 Aug 7, 2024
d4a53ba
Speed up ASE calculator
ericyuan00000 Aug 8, 2024
0a50c5f
Edge index calculation in ASE calculator
ericyuan00000 Aug 8, 2024
0e566a8
Revise output formats
ericyuan00000 Aug 9, 2024
0a8a697
Revise precision
ericyuan00000 Aug 9, 2024
3bbb943
Revise radius graph transform
ericyuan00000 Aug 9, 2024
f7d40b1
Revise scalers
ericyuan00000 Aug 9, 2024
796274e
Revise representations
ericyuan00000 Aug 9, 2024
e3290dd
Revise representations
ericyuan00000 Aug 9, 2024
50c414c
Revise model
ericyuan00000 Aug 9, 2024
fc1edf0
Revise output
ericyuan00000 Aug 9, 2024
99b32d4
Revise loss
ericyuan00000 Aug 9, 2024
19e4208
Revise optimizer
ericyuan00000 Aug 9, 2024
01894c8
Revise training log
ericyuan00000 Aug 9, 2024
0df31e9
Revise training log
ericyuan00000 Aug 10, 2024
0f66ebb
Revise scheduler
ericyuan00000 Aug 10, 2024
61004b9
Revise training log
ericyuan00000 Aug 10, 2024
d752e54
Revise resume training procedure
ericyuan00000 Aug 10, 2024
cccc3e8
Revise scalers
ericyuan00000 Aug 11, 2024
9bcdf48
Revise checkpoints
ericyuan00000 Aug 11, 2024
0ac0807
Update model and scaler
ericyuan00000 Aug 11, 2024
14980b3
Revise early stopping
ericyuan00000 Aug 12, 2024
fc3d968
Reset scaler initial scaling
ericyuan00000 Aug 12, 2024
5b94cd6
Update model input as distance vectors
ericyuan00000 Aug 13, 2024
17b42c5
Update calculator
ericyuan00000 Aug 13, 2024
ed2180e
Merge pull request #2 from ericyuan00000/distance
ericyuan00000 Aug 13, 2024
db124ce
Modify statistics
ericyuan00000 Aug 14, 2024
c236a54
Revise model layer norm option
ericyuan00000 Aug 14, 2024
d18b392
Revise logging
ericyuan00000 Aug 15, 2024
369ee99
Revise stats parsing
ericyuan00000 Aug 15, 2024
1e09804
Revise early stopping
ericyuan00000 Aug 15, 2024
a18e122
Update trainer keys
ericyuan00000 Aug 16, 2024
e17e65c
Revise dataloader shuffle option
ericyuan00000 Aug 16, 2024
a08b2a5
Move data pre_transform to transform
ericyuan00000 Aug 17, 2024
ef79d5d
Change transform order
ericyuan00000 Aug 17, 2024
82a906e
Simplify trainer
ericyuan00000 Aug 18, 2024
04c7986
Modify wandb init order
ericyuan00000 Aug 18, 2024
12dc52b
Revise trainer logging key
ericyuan00000 Aug 18, 2024
731b7de
Clean up
ericyuan00000 Aug 19, 2024
5ba7174
Revise direct force output
ericyuan00000 Aug 19, 2024
e427c85
Clean up and update version
ericyuan00000 Aug 20, 2024
9c36097
Simplification (#3)
ericyuan00000 Sep 9, 2024
364859f
Remove debug output (#4)
ericyuan00000 Sep 10, 2024
7c9ae46
Fix force output (#5)
ericyuan00000 Sep 10, 2024
ff8e8e6
Add Hessian output (#6)
ericyuan00000 Oct 16, 2024
b32e6e8
Resume (#7)
ericyuan00000 Nov 14, 2024
413968f
Add support for stress calculation under periodic boundary condition …
ericyuan00000 Dec 4, 2024
c101bad
Units (#9)
ericyuan00000 Dec 5, 2024
cb54f70
Graph (#10)
ericyuan00000 Dec 5, 2024
c203c06
Graph (#11)
ericyuan00000 Dec 5, 2024
3e1250a
Merge branch 'main' into main
ericyuan00000 Dec 13, 2024
697c16b
Batched calc (#12)
ericyuan00000 Dec 17, 2024
7577963
Hessian in ASE calculator (#13)
ericyuan00000 Dec 17, 2024
4b115d2
Fix cell counts (#14)
ericyuan00000 Jan 18, 2025
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208 changes: 0 additions & 208 deletions cli/newtonnet_train

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29 changes: 0 additions & 29 deletions example/predict/run_ase.py

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66 changes: 0 additions & 66 deletions example/predict/train_h2/config.yml

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