Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Update main #6

Merged
merged 98 commits into from
Jan 30, 2023
Merged

Update main #6

merged 98 commits into from
Jan 30, 2023

Conversation

dominicrufa
Copy link
Owner

sync with main

Ruibin-Liu and others added 30 commits July 11, 2022 15:20
@Ruibin-Liu
Improve error message of checking box_size type
fba0c01 
It's also consistent with 
```
  raise ValueError(('Box must be either: a scalar, a vector, or a matrix. '
                    f'Found {box}.'))
```
in `space.py`
@sschoenholz
Changed signature of kinetic energy and temperature functions.
748ec10
@sschoenholz
Merge pull request jax-md#203 from Ruibin-Liu/patch-1
e6c461e 
Improve error message of checking `box_size` type
@sschoenholz
Fixed two bugs in rigid body code.
a19faab
@sschoenholz
Add reduce import.
9c9a48d
@sschoenholz
Switch to box_velocity in iL2.
cc07990
@sschoenholz
Once more...
c15dc72
@sschoenholz
Bump version.
b1d9d80
@sschoenholz
Add a lammps npt comparison.
36708f7
@sschoenholz
Fixed test case.
7c69588
@sschoenholz
Merge pull request jax-md#214 from google/npt_fix_3ls
e23102b 
Fix to regression in NPT from velocity -> momentum change.
@cagrikymk
Merge pull request #1 from google/main
4c67ec5 
Update from original
@sschoenholz @xiyudu
@ellamichelleking @mc2engel @rkruegs123
Refactoring of simulation environments to be more aligned with Suzuki…
0f0b9b0 
… Trotter decomposition.

Co-authored-by: Chrisy Xiyu Du <xiyudu@g.harvard.edu>
Co-authored-by: Ella M. King <ellamichelleking@gmail.com>
Co-authored-by: Megan C. Engel <mcengel@ualberta.ca>
Co-authored-by: Ryan Krueger <ryan_krueger@g.harvard.edu>
@sschoenholz
Removew UpdateFn from rigidbody.py.
d2e1996
@sschoenholz @Sohl-Dickstein
Add first version of TPU molecular dynamics code. (jax-md#216)
d9bc14b 
* TPU MD code

* animated gif

* Move gif to raw html.

* Update TPU_MD.ipynb

Co-authored-by: Jascha Sohl-dickstein <jaschasd@google.com>
Co-authored-by: Jascha Sohl-Dickstein <jascha.sohldickstein@gmail.com>
@sschoenholz
Bump version number.
6a4e6ae
@sschoenholz
Change notebook backend to TPU.
165c487
@sschoenholz
Merge pull request jax-md#215 from google/velocity_verlet_refactor
8708b55 
Refactor simulation environments to be aligned with Suzuki Trotter decomposition
@sschoenholz
Change import of jax_md.tpu in tpu_test.
ee14953
@sschoenholz
Change jax_md.tpu import.
63387ac
@sschoenholz @Sohl-Dickstein
Bring TPU code up to date.
064c5c1 
Co-authored-by: Jascha Sohl-Dickstein <jascha.sohldickstein@gmail.com>
@sschoenholz
Bump version number.
e6a5b03
@sschoenholz
Bring TPU test up to date.
2744466
@sschoenholz
Delete .partition_test.py.~undo-tree~
08f0351
@sschoenholz
jax_md.experimental.tpu -> jax_md.tpu
9c8c53f
@sschoenholz
Remove "raise" error mode for jax shape promotion.
d97eb79
@sschoenholz
Shrink 3d TPU tests.
52dbb04
@cagrikymk
Merge branch 'google:main' into main
e87d2a0
@cagrikymk
Fix the typo in canonicalize_force
1887ee8
@cpgoodri
improved documentation for pair_correlation(_neighbor_list) and add a…
d2a805c 
…n average utility fn
sschoenholz and others added 28 commits November 26, 2022 19:37
@sschoenholz
First pass at chapter 1.
dac1c61
@sschoenholz
Increase TPU test tolerance.
199f199
@sschoenholz
Merge branch 'main' of https://github.com/google/jax-md
796dcc9
@sschoenholz
Remove errant print statement.
78b2831
@sschoenholz
Shrink nequip tests some more.
8213c85
@sschoenholz
Bump version number.
acfbefc
@sschoenholz
Remove warning.
2d053f3
@sschoenholz
Disable a few nequip tests.
9d58103
@sschoenholz
Merge branch 'main' of https://github.com/google/jax-md
86b22ee
@sschoenholz
Remove testing parallelism.
2c98bcf
@amilmerchant
Add to main branch.
73892bc
@amilmerchant
Add data for chapter 3 of the tutorial
4dc3490
@amilmerchant
Updating jax_md in installation
63cbeeb
@sschoenholz
Merge pull request jax-md#236 from amilmerchant/chapter_3_tutorial
2985af6 
Add to chapter 3 of tutorial to main branch.
@cpgoodri
minor updates
fc0ef11
@sschoenholz
Merge pull request jax-md#235 from google/ci_testing
7d6bca3 
Remove testing parallelism.
@sschoenholz
Merge pull request jax-md#237 from cpgoodri/tutorial
64823c0 
minor updates
@ellamichelleking
Add files via upload (jax-md#238)
ffd4e02
@amilmerchant
Created using Colaboratory (jax-md#240)
8296ba0
@cpgoodri
Tutorial (jax-md#239)
a3864f2 
* Created using Colaboratory

* Created using Colaboratory
@amilmerchant
Created using Colaboratory (jax-md#241)
b1b02c5
@sschoenholz
Fix link to nequip in energy.
8072d89
@sschoenholz
Remove redundent copies of nequip code.
b8402e3
@sschoenholz
Delete .#nequip.py
7ced26d
@cpgoodri
quick fix to volume fraction (jax-md#243)
ddfc58d 
* import jax.scipy

* import gammaln
@sschoenholz
Remove an f32 from quantity.py
320e113
@sschoenholz
Remove quantity reference.
024a629
@dominicrufa
Merge branch 'main' into update_main
e6c03a3
@dominicrufa
Copy link
Owner Author

minimal conflicts; check the dispatch_by_state decorator

@dominicrufa dominicrufa merged commit 6bbea3b into main Jan 30, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
7 participants
@dominicrufa @Ruibin-Liu @sschoenholz @cagrikymk @cpgoodri @amilmerchant @ellamichelleking