Commits · 48eeb3dc79ac29c5d759186d646c2acb38763aff · OpenDAS / torchani

04 Jul, 2019 2 commits
- Scale by sqrt(natoms) instead of natoms (#259) · 48eeb3dc
  Gao, Xiang authored Jul 04, 2019
  
  48eeb3dc
- Simplify computation of strain (#260) · 74ea32b9
  Gao, Xiang authored Jul 04, 2019
```
* Update ase.py

* Update ase.py
```
  74ea32b9
03 Jul, 2019 1 commit
- Support 0 molecule subsets when loading dataset (#257) · 8b9c3d1a
  Gao, Xiang authored Jul 03, 2019
```
* Support 0 molecule subsets when loading dataset

* fix

* fix
```
  8b9c3d1a
20 Jun, 2019 1 commit
- import ignite and data separately (#256) · 909935a5
  Gao, Xiang authored Jun 19, 2019
  
  909935a5
17 Jun, 2019 1 commit
- compute atomic self energies for a given data set prior to training (#255) · e30b98a8
  Farhad Ramezanghorbani authored Jun 17, 2019
```
* using least-squares to compute atomic self energies from the dataset

* self atomic energy calculation in the example training file
```
  e30b98a8
14 Jun, 2019 1 commit
- Reformat the BuiltinModels and Builtins API to make them simpler and clearer (#252) · cecaf992
  Ignacio Pickering authored Jun 14, 2019
  
  cecaf992
13 Jun, 2019 1 commit
- Change unidiomatic type calls to isinstance and remove deprecated h5py operator (#250) · ae4cbe0a
  Ignacio Pickering authored Jun 13, 2019
```
* Change unidiomatic type calls to isinstance and remove deprecated h5py operator

* Add whitespace after , to make flake8 happy
```
  ae4cbe0a
10 Jun, 2019 1 commit
- Force coefficient is better to be 0.1 (#249) · 1c378970
  Gao, Xiang authored Jun 10, 2019
```
Being 1 does not work well
```
  1c378970
06 Jun, 2019 2 commits
- Updated nnp_training tutorial to be as close to NeuroChem as possible (#245) · e1c78efe
  Farhad Ramezanghorbani authored Jun 06, 2019
  
  e1c78efe
- Add @farhadrgh as a code owner for everything (#246) · dc8930ee
  Gao, Xiang authored Jun 05, 2019
```
@farhadrgh Please review and merge
```
  dc8930ee
04 Jun, 2019 1 commit
- Update activation list link (#244) · 45ee3a8a
  Gao, Xiang authored Jun 04, 2019
  
  45ee3a8a
03 Jun, 2019 1 commit
- Rename input->input_ to avoid name clash (#242) · abcb1217
  Gao, Xiang authored Jun 03, 2019
  
  abcb1217
26 May, 2019 1 commit
- Refactor BatchedANIDataset and create API for splittting datasets (#237) · 14a62dc4
  Gao, Xiang authored May 25, 2019
  
  14a62dc4
25 May, 2019 7 commits
- Reduce time for docs test in CI (#239) · 0ce36d82
  Gao, Xiang authored May 25, 2019
  
  0ce36d82
- Add @farhadrgh to code owner of /torchani/data (#235) · a8d93c54
  Gao, Xiang authored May 25, 2019
```
Hi @farhadrgh, I am adding you as a code owner of `/torchani/data` since you have experience on this. Later I will request your review if there are PR changing that part.
```
  a8d93c54
- Create graph for force in force training (#238) · bade1181
  Gao, Xiang authored May 25, 2019
  
  bade1181
- Add example for force training (#233) · c630982f
  Gao, Xiang authored May 25, 2019
  
  c630982f
- Move core function of BatchedANIDataset.__init__ outside (#236) · 7526da82
  Gao, Xiang authored May 25, 2019
  
  7526da82
- Refactor cache_aev and cache_sparse_aev (#232) · d9c0130f
  Gao, Xiang authored May 25, 2019
  
  d9c0130f
- Modify dataset API to allow atomic properties (#231) · 2ec2fb6d
  Gao, Xiang authored May 24, 2019
  
  2ec2fb6d
23 May, 2019 1 commit
- Support caching sparse representation of AEVs into disk (#230) · 4f63c32d
  Farhad Ramezanghorbani authored May 22, 2019
  
  4f63c32d
22 May, 2019 1 commit
- Delete duplicate line in cache_aev example (#229) · a86ea658
  Gao, Xiang authored May 22, 2019
  
  a86ea658
21 May, 2019 4 commits
- Add vibrational mode support (#228) · e88f6266
  Gao, Xiang authored May 21, 2019
  
  e88f6266
- Add warning for weight decay (#227) · 4452f68d
  Gao, Xiang authored May 21, 2019
  
  4452f68d
- Fix NeuroChem trainer pretraining criterion, MAE vs MaxAE (#225) · 245614f7
  Gao, Xiang authored May 20, 2019
  
  245614f7
- Use a seperate optimizer to pretrain, and pretrain more (#226) · 4dcd6ab0
  Gao, Xiang authored May 20, 2019
  
  4dcd6ab0
17 May, 2019 1 commit

Add AdamW optimizer, Add docs of nnp training to train a real ANI-1x model,... · 2ad4126f

Gao, Xiang authored May 16, 2019

Add AdamW optimizer, Add docs of nnp training to train a real ANI-1x model, remove h5py and ignite from dependencies, rename MAEMetric -> MaxAEMetric, use torch.utils.tensorboard to replace tensorboardX (#224)

2ad4126f

14 May, 2019 2 commits
- Fix benzene PBC MD test (#219) · 54ab56ee
  Gao, Xiang authored May 14, 2019
  
  54ab56ee
- Add support for weight decay (#223) · 71b9c75f
  Gao, Xiang authored May 14, 2019
  
  71b9c75f
10 May, 2019 2 commits
- Fix order of wrapping and strain (#221) · 4cec6442
  Gao, Xiang authored May 10, 2019
  
  4cec6442
- Add support for analytical hessian and vibrational analysis (#222) · 14d2ef70
  Gao, Xiang authored May 10, 2019
  
  14d2ef70
02 May, 2019 1 commit
- improve analytical stress (#220) · 0f006b3b
  Gao, Xiang authored May 02, 2019
  
  0f006b3b
30 Apr, 2019 1 commit
- Add support for analytical stress (#218) · 32e00bf3
  Gao, Xiang authored Apr 30, 2019
```
* implement stress

* fix

* more

* Add analytical stress support
```
  32e00bf3
24 Apr, 2019 3 commits
- Test AEV PBC by manual mirror (#217) · 19af71ea
  Gao, Xiang authored Apr 24, 2019
  
  19af71ea
- Test on benzene with PBC by repeating box (#216) · 65fb08d9
  Gao, Xiang authored Apr 23, 2019
  
  65fb08d9
- Add Benzene and Tripeptide MD trajectory to unit test (#213) · ba02a674
  Gao, Xiang authored Apr 23, 2019
  
  ba02a674
22 Apr, 2019 4 commits
- Write wrapped position to atoms (#215) · db36c1a0
  Gao, Xiang authored Apr 22, 2019
  
  db36c1a0
- Map atoms to central cell before computing energy (#214) · 3596f612
  Gao, Xiang authored Apr 22, 2019
  
  3596f612
- Fix ase interface on GPU (#212) · 95c3206b
  Gao, Xiang authored Apr 21, 2019
  
  95c3206b
- Change comp6 script a bit (#211) · cbfbab3f
  Gao, Xiang authored Apr 21, 2019
  
  cbfbab3f