Skip to content

ZnH5MD v0.3 #93

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
Merged
merged 80 commits into from
Jul 16, 2024
Merged

ZnH5MD v0.3 #93

merged 80 commits into from
Jul 16, 2024

Conversation

PythonFZ
Copy link
Member

@PythonFZ PythonFZ commented Jun 20, 2024 •
edited
Loading

Benchmark against v0.2

main vs. v03

Single Shot write

5000 steps. x 5000 atoms
850 ms vs. 723 ms

Append

Add another 5000 steps. x 5000 atoms
2.94 s vs. 1.55 s

Single Shot read

5000 steps. x 5000 atoms
3.23 s vs. 3.6 s

PythonFZ and others added 30 commits June 20, 2024 10:58
@PythonFZ
znh5md v0.3 redesign draft
a2b8b9f
@PythonFZ
momenta
427a8fc
@PythonFZ
forces
4f60330
@PythonFZ
add inline TODOs
89ff900
@PythonFZ
support observables
aa8480f
@PythonFZ
first version of extend
f45d8f4
@PythonFZ
append / extend to existing dataset
fe5ce87
@PythonFZ
append testing
fe1ecb6
@PythonFZ
test more datasets
922da7e
@PythonFZ
bugfix arrays, info, calc shape
25785f3
@PythonFZ
support changes in pbc
bc27c6c
@PythonFZ
the simplest dataset
ec0094d
@PythonFZ
fix numpy pow and add mda tests
a4b760b
@PythonFZ
test against MDAnalysis
81a28d6
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
e202ceb 
for more information, see https://pre-commit.ci
@PythonFZ
update CI setup
a588bf8
@PythonFZ
Merge branch 'v03' of https://github.com/zincware/ZnH5MD into v03
1a7b88c
@PythonFZ
remove calc data
d1533dc
@PythonFZ
fix momenta / velocities confusion
ef4b7bc
@PythonFZ
a bit more testing
1559bea
@PythonFZ
bugfix energy shape
cb0f53d
@PythonFZ
add coverage to test deps
d10af0d
@PythonFZ
update Readme
edd7774
@PythonFZ
fix particle_group
4539ba6
@PythonFZ
add particle_group to README
e0002f5
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
2292fbc 
for more information, see https://pre-commit.ci
@PythonFZ
set lower bound to Python 3.10
984eba1
@PythonFZ
Merge branch 'v03' of https://github.com/zincware/ZnH5MD into v03
fa8c683
@PythonFZ
first pre-release
9f29a73
@PythonFZ
update README
3ecf24c
@github-actions GitHub Actions
Copy link

github-actions bot commented Jul 9, 2024 •
edited
Loading

Benchmark

Write: Varying number of images

Write: Varying number of atoms

Read: Varying number of images

Read: Varying number of atoms

PythonFZ and others added 19 commits July 9, 2024 11:38
@PythonFZ
create more data
a033c47
@PythonFZ
remove unused code
9532589
@PythonFZ
add TODOs
dd24ea3
@PythonFZ
add compression and benchmark it
b67a847
@PythonFZ
add compression_opts
4e6b2dc
@PythonFZ
better plotting
d3b977b
@PythonFZ
fix tests, improve cml report
641be62
@PythonFZ
depreciation update
ec76362
@PythonFZ
pre-release "0.3.0a2"
4b723c1
@PythonFZ
Support for IO(timestep: float) (#96)
ba34c75 
* support for time / step

* test time/step from ase

* support step / time
@PythonFZ
bump version
676019b
@PythonFZ
backwards compatibility fix
584cad4
@PythonFZ
step and time as native python types
5657dd6
@PythonFZ
support store with linear and time option (#97)
139beb0 
* test against fixed-time

* support linear datasets

* support linear and time store methods

* change default to `linear` and bugfix

* typo

* Update test_benchmark.py
@PythonFZ
draft for connectivity testing
1769dab
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
6dda1ba 
for more information, see https://pre-commit.ci
@PythonFZ
add and update networkx
65e96a2
@PythonFZ
lint
3a11e67
@PythonFZ
test "pbc_group" parameter
8b24da6
@PythonFZ PythonFZ marked this pull request as ready for review July 15, 2024 14:13
@PythonFZ PythonFZ merged commit e1cf321 into main Jul 16, 2024
6 checks passed
@PythonFZ PythonFZ deleted the v03 branch July 16, 2024 07:29
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
Development

Successfully merging this pull request may close these issues.

ase.io.iread and ase.io.write support get_magnetic_moments and get_initial_magnetic_moments Test non-cubic boxes
1 participant
@PythonFZ