Commits · 1a2b450477ce4f1f419ad0c8d6e8fdcb16e4d1e6 · OpenDAS / torchani

12 Nov, 2019 1 commit

Allow passing pbc and cell to sequential, and simplify ASE interface (#386) · 1a2b4504

Gao, Xiang authored Nov 12, 2019

* Allow passing pbc and cell to sequential

* revert

* Simplify ase interface

* fix

* fix

* fix

* flake8

* Update ase.py

* fix

1a2b4504

11 Nov, 2019 1 commit
- Fix tests for latest ASE (#381) · e784666f
  Gao, Xiang authored Nov 11, 2019
```
* Try latest ASE

Just to see if ASE fixes its bug

* fix
```
  e784666f
06 Nov, 2019 1 commit
- Remove AEV cacher (#361) · 86500df0
  Gao, Xiang authored Nov 05, 2019
```
* Remove AEV cacher

* more

* more

* more

* flake8

* further cleanup
```
  86500df0
05 Nov, 2019 1 commit
- Removing ignite (#354) · 123e4760
  Gao, Xiang authored Nov 05, 2019
```
* Remove ignite

* remove neurochem-test

* remove cache-aev
```
  123e4760
09 Oct, 2019 3 commits
- Add unit test for builtin models (#327) · 3132928c
  Gao, Xiang authored Oct 09, 2019
```
* Add unit test for builtin models

* flake8
```
  3132928c
- Add force to unittest of JIT (#326) · 273c9fd6
  Gao, Xiang authored Oct 09, 2019
  
  273c9fd6
- [JIT] Add TorchScript Compatibility for ANIModel and Ensemble (#307) · a1adceb0
  Farhad Ramezanghorbani authored Oct 09, 2019
```
* add test for scripted ensemble

* use torchani.nn.Sequential

* change OrderedDict to module list

* fix

* fix nn.py

* try more fix

* try

* more

* more

* fix more

* rename

* bring ensemble back

* make ANIModel iterable
```
  a1adceb0
23 Sep, 2019 1 commit

Reduce test latency (#319) · f9b074ce

Gao, Xiang authored Sep 23, 2019

* Move unittest check to GitHub Actions

Tests are parallelized

* Delete tests.yml

* Update setup.py

* Create test_requirements.txt

* Update unittest.yml

* Update unittest.yml

* Update README.md

* Delete install_dependencies.sh

* Delete install_dependencies_python2.sh

* Update unittest.yml

* split

* split

* fix

* fix

* -v

* more

* more

* fix

* fix

* flake8

* transform

* reduce testBenzeneMD

* version

* reduce number of epoches

* further reduce time

* Update docs.yml

f9b074ce

22 Sep, 2019 1 commit
- Use a modified Sequential class with type annotation (#308) · 465faa00
  Farhad Ramezanghorbani authored Sep 22, 2019
  
  465faa00
07 Sep, 2019 1 commit
- [JIT] Add TorchScript Compatibility for EnergyShifter (#306) · 379d2b33
  Farhad Ramezanghorbani authored Sep 07, 2019
```
* enable EnergyShifter scripting

* fix

* fix
```
  379d2b33
06 Sep, 2019 1 commit

[JIT] Add TorchScript compatibility for AEVComputer (#303) · f2170e24

Farhad Ramezanghorbani authored Sep 06, 2019

* make aev,model compatible with jit

* add type annotation to nn

* flake8 fix

* refactor AEVComputer

* fix doc

* an example with padding

* use Optional type instead of padding

* fix

* fix

* make pbc and cell keyword arguments in test_aev

* fix

* make pbc and cell keyword arguments in ase

* fix

* fix

* fix dtype

* fix

* aev_computer dtype to double

* change test files to have aev_computer with keyword argument

* fix JIT types

* add TestAEVJIT

* fix LGTM alerts

* fix TestAEVJIT

* Update aev.py

workaround for dtype in `torch.arange`

* More arange bugs

* Even more arange

* fix LGTM alert

f2170e24

25 Aug, 2019 1 commit

New Dataset API add other properties (#300) · 3957d19c

Richard Xue authored Aug 25, 2019

* cached

* typo and comments

* easy to read

* change some names

* fix unit test

* empty line

* fix

* fix

* add docs and add whether include_energies

* docs

* other properties for shuffled dataset

* docs

* dtype for benchmark

* add properties to test

* style

3957d19c

22 Aug, 2019 1 commit
- Add split to new dataset API (#299) · 9639d716
  Richard Xue authored Aug 21, 2019
```
* split

* clean

* docs

* docs

* Update new.py
```
  9639d716
20 Aug, 2019 1 commit
- New dataset API, cached dataset and shuffled dataset (#284) · b9e2c259
  Richard Xue authored Aug 20, 2019
  
  b9e2c259
15 Aug, 2019 1 commit
- Update test_data.py (#292) · 5bc96518
  Richard Xue authored Aug 15, 2019
  
  5bc96518
13 Aug, 2019 1 commit
- Remove all large files and stop using git-lfs (#289) · 560d37ac
  Gao, Xiang authored Aug 13, 2019
  
  560d37ac
12 Aug, 2019 1 commit
- small fix in methane, had a missing atom (#288) · 70eab38f
  Ignacio Pickering authored Aug 12, 2019
  
  70eab38f
11 Aug, 2019 1 commit
- Support len in ChemicalSymbolsToInts, len of it returns number of supported elements (#286) · 0b3e26ee
  Gao, Xiang authored Aug 11, 2019
```
* Support len in ChemicalSymbolsToInts

* fix

* flake8
```
  0b3e26ee
07 Aug, 2019 3 commits
- Remove the first layer's weight decay parameters of each atomic network (#279) · a2ba46e9
  Farhad Ramezanghorbani authored Aug 07, 2019
  
  a2ba46e9
- Adapt neurochem trainer to NC setup (#275) · 25dd28bb
  Farhad Ramezanghorbani authored Aug 07, 2019
  
  25dd28bb
- Add test for isolated atoms and large distances for 2 and 3 atoms (#274) · 347e845c
  Ignacio Pickering authored Aug 06, 2019
  
  347e845c
06 Aug, 2019 1 commit

Port to torch.bool data type where it should be (#278) · 6fe30cc9

Gao, Xiang authored Aug 06, 2019

* Port to torch.bool data type where it should be

* more

* more

* fix snoop

* hopefully fixed

* fix ignite

* remove snoop

* flake8

6fe30cc9

01 Aug, 2019 1 commit
- Replace BatchedANIDataset (#272) · a41cc8b7
  Ignacio Pickering authored Aug 01, 2019
  
  a41cc8b7
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
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 1 commit
- 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
21 May, 2019 1 commit
- Add vibrational mode support (#228) · e88f6266
  Gao, Xiang authored May 21, 2019
  
  e88f6266
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 1 commit
- Add support for analytical hessian and vibrational analysis (#222) · 14d2ef70
  Gao, Xiang authored May 10, 2019
  
  14d2ef70
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
09 Apr, 2019 1 commit
- reduce time on neurochem trainer on CI (#208) · a9df4b41
  Gao, Xiang authored Apr 09, 2019
  
  a9df4b41
08 Apr, 2019 1 commit
- Remove unnecessary molecule index (#206) · bacde2e7
  Gao, Xiang authored Apr 08, 2019
  
  bacde2e7
07 Apr, 2019 1 commit
- Added finite differences gradient check for aev_computer. (#200) · bc4ab994
  Kevin Ryan authored Apr 07, 2019
  
  bc4ab994
06 Apr, 2019 1 commit
- Completely rewrite AEVComputer (#197) · 35531421
  Gao, Xiang authored Apr 06, 2019
  
  35531421
24 Mar, 2019 1 commit
- Config flake8 and fix may linter errors (#198) · bc5f4312
  Gao, Xiang authored Mar 24, 2019
  
  bc5f4312